From fe09a077da0e6fcf6b92b0281523952d0d4874e0 Mon Sep 17 00:00:00 2001 From: Christopher Erick Moody Date: Wed, 14 Jan 2015 17:15:06 -0800 Subject: [PATCH 1/3] FEAT Barnes-Hut t-SNE Renamed example file & added comments FEAT Barnes-Hut t-SNE Vectorized the math calls -- 3x faster on neg grad Draft of n-dimensional barnes-hut; failing tests Tests pass, error being computed in cython Added error calculation to pos gradient Changed cases where points are very close to be clearer Clearer variable names --- doc/modules/manifold.rst | 91 +- examples/manifold/plot_tsne.py | 122 + examples/manifold/plot_tsne_faces.py | 148 + sklearn/manifold/_barnes_hut_tsne.c | 25636 ++++++++++++++++++++++++ sklearn/manifold/_barnes_hut_tsne.pyx | 829 + sklearn/manifold/_utils.c | 2868 +-- sklearn/manifold/_utils.pyx | 101 +- sklearn/manifold/setup.py | 12 + sklearn/manifold/t_sne.py | 531 +- sklearn/manifold/tests/test_t_sne.py | 309 +- 10 files changed, 29159 insertions(+), 1488 deletions(-) create mode 100644 examples/manifold/plot_tsne.py create mode 100644 examples/manifold/plot_tsne_faces.py create mode 100644 sklearn/manifold/_barnes_hut_tsne.c create mode 100644 sklearn/manifold/_barnes_hut_tsne.pyx diff --git a/doc/modules/manifold.rst b/doc/modules/manifold.rst index 0a7db76bb7461..09a3ba222ca6c 100644 --- a/doc/modules/manifold.rst +++ b/doc/modules/manifold.rst @@ -480,12 +480,37 @@ t-distributed Stochastic Neighbor Embedding (t-SNE) t-SNE (:class:`TSNE`) converts affinities of data points to probabilities. The affinities in the original space are represented by Gaussian joint probabilities and the affinities in the embedded space are represented by -Student's t-distributions. The Kullback-Leibler (KL) divergence of the joint +Student's t-distributions. This allows t-SNE to be particularly sensitive +to local structure and has a few other advantages over existing techniques: + +* Revealing the structure at many scales on a single map +* Revealing data that lie in multiple, different, manifolds or clusters +* Reducing the tendency to crowd points together at the center + +While Isomap, LLE and variants are best suited to unfold a single continuous +low dimensional manifold, t-SNE will focus on the local structure of the data +and will tend to extract clustered local groups of samples as highlighted on +the S-curve example. This ability to group samples based on the local structure +might be beneficial to visually disentangle a dataset that comprises several +manifolds at once as is the case in the digits dataset. + +The Kullback-Leibler (KL) divergence of the joint probabilities in the original space and the embedded space will be minimized by gradient descent. Note that the KL divergence is not convex, i.e. multiple restarts with different initializations will end up in local minima of the KL divergence. Hence, it is sometimes useful to try different seeds -and select the embedding with the lowest KL divergence. +and select the embedding with the lowest KL divergence. + +The disadvantages to using t-SNE are roughly: + +* t-SNE is computationally expensive, and can take several hours on million-sample + datasets where PCA will finish in seconds or minutes +* The Barnes-Hut t-SNE method is limited to two or three dimensional embeddings. +* The algorithm is stochastic and multiple restarts with different seeds can + yield different embeddings. However, it is perfectly legitimate to pick the the + embedding with the least error. +* Global structure is not explicitly preserved. This is problem is mitigated by + initializing points with PCA (using `init='pca'`). .. figure:: ../auto_examples/manifold/images/plot_lle_digits_013.png @@ -493,17 +518,27 @@ and select the embedding with the lowest KL divergence. :align: center :scale: 50 - +Optimizing t-SNE +---------------- The main purpose of t-SNE is visualization of high-dimensional data. Hence, it works best when the data will be embedded on two or three dimensions. Optimizing the KL divergence can be a little bit tricky sometimes. There are -three parameters that control the optimization of t-SNE: +five parameters that control the optimization of t-SNE and therefore possibly +the quality of the resulting embedding: +* perplexity * early exaggeration factor * learning rate * maximum number of iterations - +* angle (not used in the exact method) + +The perplexity is defined as :math:`k=2^(S)` where :math:`S` is the Shannon +entropy of the conditional probability distribution. The perplexity of a +:math:`k`-sided die is :math:`k`, so that :math:`k` is effectively the number of +nearest neighbors t-SNE considers when generating the conditional probabilities. +Larger perplexities lead to more nearest neighbors and less sensitive to small +structure. Larger datasets tend to require larger perplexities. The maximum number of iterations is usually high enough and does not need any tuning. The optimization consists of two phases: the early exaggeration phase and the final optimization. During early exaggeration the joint @@ -514,19 +549,37 @@ divergence could increase during this phase. Usually it does not have to be tuned. A critical parameter is the learning rate. If it is too low gradient descent will get stuck in a bad local minimum. If it is too high the KL divergence will increase during optimization. More tips can be found in -Laurens van der Maaten's FAQ (see references). +Laurens van der Maaten's FAQ (see references). The last parameter, angle, +is a tradeoff between performance and accuracy. Larger angles imply that we +can approximate larger regions by a single point,leading to better speed +but less accurate results. -Standard t-SNE that has been implemented here is usually much slower than -other manifold learning algorithms. The optimization is quite difficult -and the computation of the gradient is on :math:`O[d N^2]`, where :math:`d` -is the number of output dimensions and :math:`N` is the number of samples. +Barnes-Hut t-SNE +---------------- -While Isomap, LLE and variants are best suited to unfold a single continuous -low dimensional manifold, t-SNE will focus on the local structure of the data -and will tend to extract clustered local groups of samples as highlighted on -the S-curve example. This ability to group samples based on the local structure -might be beneficial to visually disentangle a dataset that comprises several -manifolds at once as is the case in the digits dataset. +The Barnes-Hut t-SNE that has been implemented here is usually much slower than +other manifold learning algorithms. The optimization is quite difficult +and the computation of the gradient is :math:`O[d N log(N)]`, where :math:`d` +is the number of output dimensions and :math:`N` is the number of samples. The +Barnes-Hut method improves on the exact method where t-SNE complexity is +:math:`O[d N^2]`, but has several other notable differences: + +* The Barnes-Hut implementation only works when the target dimensionality is 3 + or less. The 2D case is typical when building visualizations. +* Barnes-Hut only works with dense input data. Sparse data matrices can only be + embedded with the exact method or can be approximated by a dense low rank + projection for instance using :class:`sklearn.decomposition.TruncatedSVD` +* Barnes-Hut is an approximation of the exact method. The approximation is + parameterized with the angle parameter, therefore the angle parameter is + unused when method="exact" +* Barnes-Hut is significantly more scalable. Barnes-Hut can be used to embed + hundred of thousands of data points while the exact method can handle + thousands of samples before becoming computationally intractable + +For visualization purpose (which is the main use case of t-SNE), using the +Barnes-Hut method is strongly recommended. The exact t-SNE method is useful +for checking the theoretically properties of the embedding possibly in higher +dimensional space but limit to small datasets due to computational constraints. Also note that the digits labels roughly match the natural grouping found by t-SNE while the linear 2D projection of the PCA model yields a representation @@ -547,9 +600,13 @@ the internal structure of the data. (2008) * `"t-Distributed Stochastic Neighbor Embedding" - `_ + `_ van der Maaten, L.J.P. + * `"Accelerating t-SNE using Tree-Based Algorithms." + `_ + L.J.P. van der Maaten. Journal of Machine Learning Research 15(Oct):3221-3245, 2014. + Tips on practical use ===================== diff --git a/examples/manifold/plot_tsne.py b/examples/manifold/plot_tsne.py new file mode 100644 index 0000000000000..4b346fd2e1f92 --- /dev/null +++ b/examples/manifold/plot_tsne.py @@ -0,0 +1,122 @@ +# Authors: Christopher Erick Moody +# License: BSD 3 clause + +from sklearn.datasets import fetch_olivetti_faces +from sklearn import manifold +from time import time +import numpy as np +import matplotlib.pyplot as plt +from matplotlib import offsetbox +from sklearn.decomposition import RandomizedPCA + + +faces = fetch_olivetti_faces() + +verbose = 20 + +#---------------------------------------------------------------------- +# Scale and visualize the embedding vectors +def plot_embedding(dataset, X, title=None, ax=None): + x_min, x_max = np.min(X, 0), np.max(X, 0) + X = (X - x_min) / (x_max - x_min) + y = dataset.target + if ax is None: + ax = plt.subplot(111) + for i in range(X.shape[0]): + ax.text(X[i, 0], X[i, 1], str(dataset.target[i]), + color=plt.cm.Set1(y[i] / 10.), + fontdict={'weight': 'bold', 'size': 30}) + + if hasattr(offsetbox, 'AnnotationBbox'): + # only print thumbnails with matplotlib > 1.0 + shown_images = np.array([[1., 1.]]) # just something big + for i in range(dataset.data.shape[0]): + shown_images = np.r_[shown_images, [X[i]]] + r, g, b, a = plt.cm.Paired(i * 1.0 / dataset.data.shape[0]) + gray = dataset.images[i] + rgb_image = np.zeros((64, 64, 3)) + rgb_image[:, :, 0] = gray * r + rgb_image[:, :, 1] = gray * g + rgb_image[:, :, 2] = gray * b + imagebox = offsetbox.AnnotationBbox( + offsetbox.OffsetImage(rgb_image), + X[i], frameon=False) + ax.add_artist(imagebox) + ax.set_xticks([]), ax.set_yticks([]) + if title is not None: + ax.set_title(title, loc='left') + +f, axs = plt.subplots(2, 2, figsize=(30, 30)) + +#---------------------------------------------------------------------- +# Fit t-SNE on all 4096 dimensions with random initialization +tsne = manifold.TSNE(n_components=2, init='random', random_state=3, + n_iter=1000, verbose=verbose, early_exaggeration=50.0, + learning_rate=100, perplexity=50) +rpca = RandomizedPCA(n_components=50) +t0 = time() +reduced = rpca.fit_transform(faces.data) +embedded = tsne.fit_transform(reduced) +t1 = time() +dt = t1 - t0 + + +t = ("Barnes-Hut t-SNE Visualization of Olivetti Faces digits\n" + + "in %1.1f seconds & initialized embedding randomly") +t = t % dt +plot_embedding(faces, embedded, title=t, ax=axs[0, 0]) + + +#------------------------------------------------------------------------- +# Fit t-SNE on all 4096 dimensions, but use PCA to initialize the embedding +tsne = manifold.TSNE(n_components=2, init='pca', random_state=3, + n_iter=1000, verbose=verbose, early_exaggeration=50.0, + learning_rate=100, perplexity=50) +t0 = time() +embedded = tsne.fit_transform(faces.data) +t1 = time() +dt = t1 - t0 + + +t = ("Barnes-Hut t-SNE Visualization of Olivetti Faces digits\n" + + "in %1.1f seconds & initialized embedding with PCA ") +t = t % dt +plot_embedding(faces, embedded, title=t, ax=axs[0, 1]) + + +#---------------------------------------------------------------------- +# Fit t-SNE on PCA-reduced dataset from 4096 dimensions to 50 +tsne = manifold.TSNE(n_components=2, init='random', random_state=3, + n_iter=1000, verbose=verbose, early_exaggeration=50.0, + learning_rate=100, perplexity=50) +rpca = RandomizedPCA(n_components=50) +t0 = time() +reduced = rpca.fit_transform(faces.data) +embedded = tsne.fit_transform(reduced) +t1 = time() +dt = t1 - t0 + + +t = ("Barnes-Hut t-SNE Visualization of Olivetti Faces digits\n" + + "in %1.1f seconds & randomized PCA preprocessing") +t = t % dt +plot_embedding(faces, embedded, title=t, ax=axs[1, 0]) + + +#---------------------------------------------------------------------- +# Fit t-SNE using PCA and the exact method +tsne = manifold.TSNE(n_components=2, init='random', random_state=3, + method='exact', n_iter=10000, verbose=verbose, + learning_rate=100, perplexity=50) +t0 = time() +embedded = tsne.fit_transform(faces.data) +t1 = time() +dt = t1 - t0 + + +t = ("Barnes-Hut t-SNE Visualization of Olivetti Faces digits\n" + + "in %1.1f seconds with random initialization and exact method") +t = t % dt +plot_embedding(faces, embedded, title=t, ax=axs[1, 1]) + +plt.show() diff --git a/examples/manifold/plot_tsne_faces.py b/examples/manifold/plot_tsne_faces.py new file mode 100644 index 0000000000000..2f78e422c6fcf --- /dev/null +++ b/examples/manifold/plot_tsne_faces.py @@ -0,0 +1,148 @@ +""" +=================================== +Comparison of t-SNE methods and options +=================================== + +A comparison of t-SNE applied to the Olivetti faces data. The 'exact' and +'barnes-hut' methods are visualized, as well as init='pca' and init='random'. +In addition to varying method & init, the script also compares preprocessing +the input data by reducing the dimensionality via PCA and also varying the +perplexity. + +For a discussion and comparison of these algorithms, see the +:ref:`manifold module page ` + +""" +# Authors: Christopher Erick Moody +# License: BSD 3 clause + +from sklearn.datasets import fetch_olivetti_faces +from sklearn.decomposition import RandomizedPCA +from sklearn import manifold +from matplotlib import offsetbox +import matplotlib.pyplot as plt +import numpy as np +from time import time + + +faces = fetch_olivetti_faces() + +verbose = 5 + +#---------------------------------------------------------------------- +# Scale and visualize the embedding vectors +def plot_embedding(dataset, X, title=None, ax=None): + x_min, x_max = np.min(X, 0), np.max(X, 0) + X = (X - x_min) / (x_max - x_min) + y = dataset.target + if ax is None: + plt.figure(figsize=(18, 15)) + ax = plt.gca() + for i in range(X.shape[0]): + ax.text(X[i, 0], X[i, 1], str(dataset.target[i]), + color=plt.cm.Set1(y[i] / 10.), + fontdict={'weight': 'bold', 'size': 30}) + + if hasattr(offsetbox, 'AnnotationBbox'): + # only print thumbnails with matplotlib > 1.0 + shown_images = np.array([[1., 1.]]) # just something big + for i in range(dataset.data.shape[0]): + shown_images = np.r_[shown_images, [X[i]]] + r, g, b, a = plt.cm.Paired(i * 1.0 / dataset.data.shape[0]) + gray = dataset.images[i] + rgb_image = np.zeros((64, 64, 3)) + rgb_image[:, :, 0] = gray * r + rgb_image[:, :, 1] = gray * g + rgb_image[:, :, 2] = gray * b + imagebox = offsetbox.AnnotationBbox( + offsetbox.OffsetImage(rgb_image), + X[i], frameon=False) + ax.add_artist(imagebox) + ax.set_xticks([]), ax.set_yticks([]) + if title is not None: + ax.set_title(title, loc='left') + + +#---------------------------------------------------------------------- +# Fit t-SNE on 50 PCA-reduced dimensions with random initialization. +# We will frequently want to reduce the dimensionality when we have many +# dimensions since the t-SNE complexity grows linearly with the dimensionality. +tsne = manifold.TSNE(n_components=2, init='random', random_state=3, + n_iter=1000, verbose=verbose, early_exaggeration=50.0, + learning_rate=100, perplexity=50) +rpca = RandomizedPCA(n_components=50) +time_start = time() +reduced = rpca.fit_transform(faces.data) +embedded = tsne.fit_transform(reduced) +time_end = time() +dt = time_end - time_start + + +title = ("Barnes-Hut t-SNE Visualization of Olivetti Faces\n" + + "in %1.1f seconds on 50-dimensional PCA-reduced data ") +title = title % dt +plot_embedding(faces, embedded, title=title) + + +#------------------------------------------------------------------------- +# Fit t-SNE on all 4096 dimensions, but use PCA to initialize the embedding +# Initializing the embedding with PCA allows the final emebedding to preserve +# global structure leaving t-SNE to optimize the local structure +tsne = manifold.TSNE(n_components=2, init='pca', random_state=3, + n_iter=1000, verbose=verbose, early_exaggeration=50.0, + learning_rate=100, perplexity=5) +time_start = time() +embedded = tsne.fit_transform(faces.data) +time_end = time() +dt = time_end - time_start + + +title = ("Barnes-Hut t-SNE Visualization of Olivetti Faces\n" + + "in %1.1f seconds & initialized embedding with PCA ") +title = title % dt +plot_embedding(faces, embedded, title=title) + + +#---------------------------------------------------------------------- +# Fit t-SNE on 50 PCA-reduced dimensions with random initialization, but reduce +# the perplexity. Note that the increased perplexity roughly increases the +# number of neighbors, which effectively decreases the number of clusters. +# For the example here, theres about 5 images per person, which with a +# perplexity of 50 forces multiple face-clusters to come together +tsne = manifold.TSNE(n_components=2, init='random', random_state=3, + n_iter=1000, verbose=verbose, early_exaggeration=50.0, + learning_rate=100, perplexity=50) +rpca = RandomizedPCA(n_components=50) +time_start = time() +reduced = rpca.fit_transform(faces.data) +embedded = tsne.fit_transform(reduced) +time_end = time() +dt = time_end - time_start + + +title = ("Barnes-Hut t-SNE Visualization of Olivetti Faces\n" + + "in %1.1f seconds on 50-dimensional PCA-reduced data\n" + + "with perplexity increased from 5 to 50") +title = title % dt +plot_embedding(faces, embedded, title=title) + + +#---------------------------------------------------------------------- +# Fit t-SNE by random embedding and the exact method. The exact method +# is similar to Barnes-Hut, but this visualization reinforces the idea +# that the two methods yield similar results +tsne = manifold.TSNE(n_components=2, init='random', random_state=3, + method='exact', n_iter=10000, verbose=verbose, + learning_rate=100, perplexity=5) +time_start = time() +embedded = tsne.fit_transform(faces.data) +time_end = time() +dt = time_end - time_start + + +title = ("Exact t-SNE Visualization of Olivetti Faces\n" + + "in %1.1f seconds with random initialization") +title = title % dt +plot_embedding(faces, embedded, title=title) + +plt.show() diff --git a/sklearn/manifold/_barnes_hut_tsne.c b/sklearn/manifold/_barnes_hut_tsne.c new file mode 100644 index 0000000000000..9d741bd051a20 --- /dev/null +++ b/sklearn/manifold/_barnes_hut_tsne.c @@ -0,0 +1,25636 @@ +/* Generated by Cython 0.21 */ + +#define PY_SSIZE_T_CLEAN +#ifndef CYTHON_USE_PYLONG_INTERNALS +#ifdef PYLONG_BITS_IN_DIGIT +#define CYTHON_USE_PYLONG_INTERNALS 0 +#else +#include "pyconfig.h" +#ifdef PYLONG_BITS_IN_DIGIT +#define CYTHON_USE_PYLONG_INTERNALS 1 +#else +#define CYTHON_USE_PYLONG_INTERNALS 0 +#endif +#endif +#endif +#include "Python.h" +#ifndef Py_PYTHON_H + #error Python headers needed to compile C extensions, please install development version of Python. +#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000) + #error Cython requires Python 2.6+ or Python 3.2+. +#else +#define CYTHON_ABI "0_21" +#include +#ifndef offsetof +#define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) +#endif +#if !defined(WIN32) && !defined(MS_WINDOWS) + #ifndef __stdcall + #define __stdcall + #endif + #ifndef __cdecl + #define __cdecl + #endif + #ifndef __fastcall + #define __fastcall + #endif +#endif +#ifndef DL_IMPORT + #define DL_IMPORT(t) t +#endif +#ifndef DL_EXPORT + #define DL_EXPORT(t) t +#endif +#ifndef PY_LONG_LONG + #define PY_LONG_LONG LONG_LONG +#endif +#ifndef Py_HUGE_VAL + #define Py_HUGE_VAL HUGE_VAL +#endif +#ifdef PYPY_VERSION +#define CYTHON_COMPILING_IN_PYPY 1 +#define CYTHON_COMPILING_IN_CPYTHON 0 +#else +#define CYTHON_COMPILING_IN_PYPY 0 +#define CYTHON_COMPILING_IN_CPYTHON 1 +#endif +#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 +#define Py_OptimizeFlag 0 +#endif +#define __PYX_BUILD_PY_SSIZE_T "n" +#define CYTHON_FORMAT_SSIZE_T "z" +#if PY_MAJOR_VERSION < 3 + #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" + #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ + PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) + #define __Pyx_DefaultClassType PyClass_Type +#else + #define __Pyx_BUILTIN_MODULE_NAME "builtins" + #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ + PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) + #define __Pyx_DefaultClassType PyType_Type +#endif +#if PY_MAJOR_VERSION >= 3 + #define Py_TPFLAGS_CHECKTYPES 0 + #define Py_TPFLAGS_HAVE_INDEX 0 +#endif +#if PY_MAJOR_VERSION >= 3 + #define Py_TPFLAGS_HAVE_NEWBUFFER 0 +#endif +#if PY_VERSION_HEX < 0x030400a1 && !defined(Py_TPFLAGS_HAVE_FINALIZE) + #define Py_TPFLAGS_HAVE_FINALIZE 0 +#endif +#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) + #define CYTHON_PEP393_ENABLED 1 + #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \ + 0 : _PyUnicode_Ready((PyObject *)(op))) + #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) + #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) + #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u) + #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u) + #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) +#else + #define CYTHON_PEP393_ENABLED 0 + #define __Pyx_PyUnicode_READY(op) (0) + #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) + #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) + #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE)) + #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u)) + #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i])) +#endif +#if CYTHON_COMPILING_IN_PYPY + #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) + #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) +#else + #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) + #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ? \ + PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) +#endif +#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? 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If the first bit in the mantissa is 1, it is + a quiet NaN. */ + float value; + memset(&value, 0xFF, sizeof(value)); + return value; +} +#endif +#ifdef __cplusplus +template +void __Pyx_call_destructor(T* x) { + x->~T(); +} +#endif + + +#if PY_MAJOR_VERSION >= 3 + #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) + #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) +#else + #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y) + #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y) +#endif + +#ifndef __PYX_EXTERN_C + #ifdef __cplusplus + #define __PYX_EXTERN_C extern "C" + #else + #define __PYX_EXTERN_C extern + #endif +#endif + +#if defined(WIN32) || defined(MS_WINDOWS) +#define _USE_MATH_DEFINES +#endif +#include +#define __PYX_HAVE__sklearn__manifold___barnes_hut_tsne +#define __PYX_HAVE_API__sklearn__manifold___barnes_hut_tsne +#include "string.h" +#include "stdlib.h" +#include "stdio.h" +#include "math.h" +#include "numpy/arrayobject.h" +#include "numpy/ufuncobject.h" +#include "time.h" +#include "cblas.h" +#include "pythread.h" +#include "pystate.h" +#ifdef _OPENMP +#include +#endif /* _OPENMP */ + +#ifdef PYREX_WITHOUT_ASSERTIONS +#define CYTHON_WITHOUT_ASSERTIONS +#endif + +#ifndef CYTHON_UNUSED +# if defined(__GNUC__) +# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) +# else +# define CYTHON_UNUSED +# endif +# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) +# else +# define CYTHON_UNUSED +# endif +#endif +typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding; + const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; + +#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0 +#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0 +#define __PYX_DEFAULT_STRING_ENCODING "" +#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString +#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize +#define __Pyx_fits_Py_ssize_t(v, type, is_signed) ( \ + (sizeof(type) < sizeof(Py_ssize_t)) || \ + (sizeof(type) > sizeof(Py_ssize_t) && \ + likely(v < (type)PY_SSIZE_T_MAX || \ + v == (type)PY_SSIZE_T_MAX) && \ + (!is_signed || likely(v > (type)PY_SSIZE_T_MIN || \ + v == (type)PY_SSIZE_T_MIN))) || \ + (sizeof(type) == sizeof(Py_ssize_t) && \ + (is_signed || likely(v < (type)PY_SSIZE_T_MAX || \ + v == (type)PY_SSIZE_T_MAX))) ) +static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*); +static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length); +#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s)) +#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l) +#define __Pyx_PyBytes_FromString PyBytes_FromString +#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize +static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*); +#if PY_MAJOR_VERSION < 3 + #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString + #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize +#else + #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString + #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize +#endif +#define __Pyx_PyObject_AsSString(s) ((signed char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_AsUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s)) +#define __Pyx_PyObject_FromUString(s) __Pyx_PyObject_FromString((const char*)s) +#define __Pyx_PyBytes_FromUString(s) __Pyx_PyBytes_FromString((const char*)s) +#define __Pyx_PyByteArray_FromUString(s) __Pyx_PyByteArray_FromString((const char*)s) +#define __Pyx_PyStr_FromUString(s) __Pyx_PyStr_FromString((const char*)s) +#define __Pyx_PyUnicode_FromUString(s) __Pyx_PyUnicode_FromString((const char*)s) +#if PY_MAJOR_VERSION < 3 +static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) +{ + const Py_UNICODE *u_end = u; + while (*u_end++) ; + return (size_t)(u_end - u - 1); +} +#else +#define __Pyx_Py_UNICODE_strlen Py_UNICODE_strlen +#endif +#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u)) +#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode +#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode +#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None) +#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False)) +static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); +static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x); +static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); +static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); +#if CYTHON_COMPILING_IN_CPYTHON +#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) +#else +#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x) +#endif +#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) +#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII +static int __Pyx_sys_getdefaultencoding_not_ascii; +static int __Pyx_init_sys_getdefaultencoding_params(void) { + PyObject* sys; + PyObject* default_encoding = NULL; + PyObject* ascii_chars_u = NULL; + PyObject* ascii_chars_b = NULL; + const char* default_encoding_c; + sys = PyImport_ImportModule("sys"); + if (!sys) goto bad; + default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); + Py_DECREF(sys); + if (!default_encoding) goto bad; + default_encoding_c = PyBytes_AsString(default_encoding); + if (!default_encoding_c) goto bad; + if (strcmp(default_encoding_c, "ascii") == 0) { + __Pyx_sys_getdefaultencoding_not_ascii = 0; + } else { + char ascii_chars[128]; + int c; + for (c = 0; c < 128; c++) { + ascii_chars[c] = c; + } + __Pyx_sys_getdefaultencoding_not_ascii = 1; + ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL); + if (!ascii_chars_u) goto bad; + ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL); + if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) { + PyErr_Format( + PyExc_ValueError, + "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.", + default_encoding_c); + goto bad; + } + Py_DECREF(ascii_chars_u); + Py_DECREF(ascii_chars_b); + } + Py_DECREF(default_encoding); + return 0; +bad: + Py_XDECREF(default_encoding); + Py_XDECREF(ascii_chars_u); + Py_XDECREF(ascii_chars_b); + return -1; +} +#endif +#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3 +#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL) +#else +#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL) +#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT +static char* __PYX_DEFAULT_STRING_ENCODING; +static int __Pyx_init_sys_getdefaultencoding_params(void) { + PyObject* sys; + PyObject* default_encoding = NULL; + char* default_encoding_c; + sys = PyImport_ImportModule("sys"); + if (!sys) goto bad; + default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); + Py_DECREF(sys); + if (!default_encoding) goto bad; + default_encoding_c = PyBytes_AsString(default_encoding); + if (!default_encoding_c) goto bad; + __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c)); + if (!__PYX_DEFAULT_STRING_ENCODING) goto bad; + strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c); + Py_DECREF(default_encoding); + return 0; +bad: + Py_XDECREF(default_encoding); + return -1; +} +#endif +#endif + + +/* Test for GCC > 2.95 */ +#if defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))) + #define likely(x) __builtin_expect(!!(x), 1) + #define unlikely(x) __builtin_expect(!!(x), 0) +#else /* !__GNUC__ or GCC < 2.95 */ + #define likely(x) (x) + #define unlikely(x) (x) +#endif /* __GNUC__ */ + +static PyObject *__pyx_m; +static PyObject *__pyx_d; +static PyObject *__pyx_b; +static PyObject *__pyx_empty_tuple; +static PyObject *__pyx_empty_bytes; +static int __pyx_lineno; +static int __pyx_clineno = 0; +static const char * __pyx_cfilenm= __FILE__; +static const char *__pyx_filename; + +#if !defined(CYTHON_CCOMPLEX) + #if defined(__cplusplus) + #define CYTHON_CCOMPLEX 1 + #elif defined(_Complex_I) + #define CYTHON_CCOMPLEX 1 + #else + #define CYTHON_CCOMPLEX 0 + #endif +#endif +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + #include + #else + #include + #endif +#endif +#if CYTHON_CCOMPLEX && !defined(__cplusplus) && defined(__sun__) && defined(__GNUC__) + #undef _Complex_I + #define _Complex_I 1.0fj +#endif + + +static const char *__pyx_f[] = { + "sklearn/manifold/_barnes_hut_tsne.pyx", + "__init__.pxd", + "sklearn/manifold/stringsource", + "type.pxd", +}; +struct __pyx_memoryview_obj; +typedef struct { + struct __pyx_memoryview_obj *memview; + char *data; + Py_ssize_t shape[8]; + Py_ssize_t strides[8]; + Py_ssize_t suboffsets[8]; +} __Pyx_memviewslice; + +#define IS_UNSIGNED(type) (((type) -1) > 0) +struct __Pyx_StructField_; +#define __PYX_BUF_FLAGS_PACKED_STRUCT (1 << 0) +typedef struct { + const char* name; + struct __Pyx_StructField_* fields; + size_t size; + size_t arraysize[8]; + int ndim; + char typegroup; + char is_unsigned; + int flags; +} __Pyx_TypeInfo; +typedef struct __Pyx_StructField_ { + __Pyx_TypeInfo* type; + const char* name; + size_t offset; +} __Pyx_StructField; +typedef struct { + __Pyx_StructField* field; + size_t parent_offset; +} __Pyx_BufFmt_StackElem; +typedef struct { + __Pyx_StructField root; + __Pyx_BufFmt_StackElem* head; + size_t fmt_offset; + size_t new_count, enc_count; + size_t struct_alignment; + int is_complex; + char enc_type; + char new_packmode; + char enc_packmode; + char is_valid_array; +} __Pyx_BufFmt_Context; + +#include +#ifndef CYTHON_ATOMICS + #define CYTHON_ATOMICS 1 +#endif +#define __pyx_atomic_int_type int +#if CYTHON_ATOMICS && __GNUC__ >= 4 && (__GNUC_MINOR__ > 1 || \ + (__GNUC_MINOR__ == 1 && __GNUC_PATCHLEVEL >= 2)) && \ + !defined(__i386__) + #define __pyx_atomic_incr_aligned(value, lock) __sync_fetch_and_add(value, 1) + #define __pyx_atomic_decr_aligned(value, lock) __sync_fetch_and_sub(value, 1) + #ifdef __PYX_DEBUG_ATOMICS + #warning "Using GNU atomics" + #endif +#elif CYTHON_ATOMICS && MSC_VER + #include + #define __pyx_atomic_int_type LONG + #define __pyx_atomic_incr_aligned(value, lock) InterlockedIncrement(value) + #define __pyx_atomic_decr_aligned(value, lock) InterlockedDecrement(value) + #ifdef __PYX_DEBUG_ATOMICS + #warning "Using MSVC atomics" + #endif +#elif CYTHON_ATOMICS && (defined(__ICC) || defined(__INTEL_COMPILER)) && 0 + #define __pyx_atomic_incr_aligned(value, lock) _InterlockedIncrement(value) + #define __pyx_atomic_decr_aligned(value, lock) _InterlockedDecrement(value) + #ifdef __PYX_DEBUG_ATOMICS + #warning "Using Intel atomics" + #endif +#else + #undef CYTHON_ATOMICS + #define CYTHON_ATOMICS 0 + #ifdef __PYX_DEBUG_ATOMICS + #warning "Not using atomics" + #endif +#endif +typedef volatile __pyx_atomic_int_type __pyx_atomic_int; +#if CYTHON_ATOMICS + #define __pyx_add_acquisition_count(memview) \ + __pyx_atomic_incr_aligned(__pyx_get_slice_count_pointer(memview), memview->lock) + #define __pyx_sub_acquisition_count(memview) \ + __pyx_atomic_decr_aligned(__pyx_get_slice_count_pointer(memview), memview->lock) +#else + #define __pyx_add_acquisition_count(memview) \ + __pyx_add_acquisition_count_locked(__pyx_get_slice_count_pointer(memview), memview->lock) + #define __pyx_sub_acquisition_count(memview) \ + __pyx_sub_acquisition_count_locked(__pyx_get_slice_count_pointer(memview), memview->lock) +#endif + + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":723 + * # in Cython to enable them only on the right systems. + * + * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t + */ +typedef npy_int8 __pyx_t_5numpy_int8_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":724 + * + * ctypedef npy_int8 int8_t + * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< + * ctypedef npy_int32 int32_t + * ctypedef npy_int64 int64_t + */ +typedef npy_int16 __pyx_t_5numpy_int16_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":725 + * ctypedef npy_int8 int8_t + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< + * ctypedef npy_int64 int64_t + * #ctypedef npy_int96 int96_t + */ +typedef npy_int32 __pyx_t_5numpy_int32_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":726 + * ctypedef npy_int16 int16_t + * ctypedef npy_int32 int32_t + * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< + * #ctypedef npy_int96 int96_t + * #ctypedef npy_int128 int128_t + */ +typedef npy_int64 __pyx_t_5numpy_int64_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":730 + * #ctypedef npy_int128 int128_t + * + * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t + */ +typedef npy_uint8 __pyx_t_5numpy_uint8_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":731 + * + * ctypedef npy_uint8 uint8_t + * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< + * ctypedef npy_uint32 uint32_t + * ctypedef npy_uint64 uint64_t + */ +typedef npy_uint16 __pyx_t_5numpy_uint16_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":732 + * ctypedef npy_uint8 uint8_t + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< + * ctypedef npy_uint64 uint64_t + * #ctypedef npy_uint96 uint96_t + */ +typedef npy_uint32 __pyx_t_5numpy_uint32_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":733 + * ctypedef npy_uint16 uint16_t + * ctypedef npy_uint32 uint32_t + * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< + * #ctypedef npy_uint96 uint96_t + * #ctypedef npy_uint128 uint128_t + */ +typedef npy_uint64 __pyx_t_5numpy_uint64_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":737 + * #ctypedef npy_uint128 uint128_t + * + * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< + * ctypedef npy_float64 float64_t + * #ctypedef npy_float80 float80_t + */ +typedef npy_float32 __pyx_t_5numpy_float32_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":738 + * + * ctypedef npy_float32 float32_t + * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< + * #ctypedef npy_float80 float80_t + * #ctypedef npy_float128 float128_t + */ +typedef npy_float64 __pyx_t_5numpy_float64_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":747 + * # The int types are mapped a bit surprising -- + * # numpy.int corresponds to 'l' and numpy.long to 'q' + * ctypedef npy_long int_t # <<<<<<<<<<<<<< + * ctypedef npy_longlong long_t + * ctypedef npy_longlong longlong_t + */ +typedef npy_long __pyx_t_5numpy_int_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":748 + * # numpy.int corresponds to 'l' and numpy.long to 'q' + * ctypedef npy_long int_t + * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< + * ctypedef npy_longlong longlong_t + * + */ +typedef npy_longlong __pyx_t_5numpy_long_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":749 + * ctypedef npy_long int_t + * ctypedef npy_longlong long_t + * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< + * + * ctypedef npy_ulong uint_t + */ +typedef npy_longlong __pyx_t_5numpy_longlong_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":751 + * ctypedef npy_longlong longlong_t + * + * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< + * ctypedef npy_ulonglong ulong_t + * ctypedef npy_ulonglong ulonglong_t + */ +typedef npy_ulong __pyx_t_5numpy_uint_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":752 + * + * ctypedef npy_ulong uint_t + * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< + * ctypedef npy_ulonglong ulonglong_t + * + */ +typedef npy_ulonglong __pyx_t_5numpy_ulong_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":753 + * ctypedef npy_ulong uint_t + * ctypedef npy_ulonglong ulong_t + * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< + * + * ctypedef npy_intp intp_t + */ +typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":755 + * ctypedef npy_ulonglong ulonglong_t + * + * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< + * ctypedef npy_uintp uintp_t + * + */ +typedef npy_intp __pyx_t_5numpy_intp_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":756 + * + * ctypedef npy_intp intp_t + * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< + * + * ctypedef npy_double float_t + */ +typedef npy_uintp __pyx_t_5numpy_uintp_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":758 + * ctypedef npy_uintp uintp_t + * + * ctypedef npy_double float_t # <<<<<<<<<<<<<< + * ctypedef npy_double double_t + * ctypedef npy_longdouble longdouble_t + */ +typedef npy_double __pyx_t_5numpy_float_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":759 + * + * ctypedef npy_double float_t + * ctypedef npy_double double_t # <<<<<<<<<<<<<< + * ctypedef npy_longdouble longdouble_t + * + */ +typedef npy_double __pyx_t_5numpy_double_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":760 + * ctypedef npy_double float_t + * ctypedef npy_double double_t + * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< + * + * ctypedef npy_cfloat cfloat_t + */ +typedef npy_longdouble __pyx_t_5numpy_longdouble_t; +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + typedef ::std::complex< float > __pyx_t_float_complex; + #else + typedef float _Complex __pyx_t_float_complex; + #endif +#else + typedef struct { float real, imag; } __pyx_t_float_complex; +#endif + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + typedef ::std::complex< double > __pyx_t_double_complex; + #else + typedef double _Complex __pyx_t_double_complex; + #endif +#else + typedef struct { double real, imag; } __pyx_t_double_complex; +#endif + + +/*--- Type declarations ---*/ +struct __pyx_array_obj; +struct __pyx_MemviewEnum_obj; +struct __pyx_memoryview_obj; +struct __pyx_memoryviewslice_obj; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":762 + * ctypedef npy_longdouble longdouble_t + * + * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< + * ctypedef npy_cdouble cdouble_t + * ctypedef npy_clongdouble clongdouble_t + */ +typedef npy_cfloat __pyx_t_5numpy_cfloat_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":763 + * + * ctypedef npy_cfloat cfloat_t + * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< + * ctypedef npy_clongdouble clongdouble_t + * + */ +typedef npy_cdouble __pyx_t_5numpy_cdouble_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":764 + * ctypedef npy_cfloat cfloat_t + * ctypedef npy_cdouble cdouble_t + * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< + * + * ctypedef npy_cdouble complex_t + */ +typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; + +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":766 + * ctypedef npy_clongdouble clongdouble_t + * + * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< + * + * cdef inline object PyArray_MultiIterNew1(a): + */ +typedef npy_cdouble __pyx_t_5numpy_complex_t; +struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node; +struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree; + +/* "sklearn/manifold/_barnes_hut_tsne.pyx":28 + * # It allows us to write printf debugging lines + * # and remove them at compile time + * cdef enum: # <<<<<<<<<<<<<< + * DEBUGFLAG = 0 + * + */ +enum { + __pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG = 0 +}; + +/* "sklearn/manifold/_barnes_hut_tsne.pyx":42 + * + * + * cdef struct Node: # <<<<<<<<<<<<<< + * # Keep track of the center of mass + * float* barycenter + */ +struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node { + float *barycenter; + float *leaf_point_position; + long cumulative_size; + long size; + long point_index; + long level; + float *left_edge; + float *center; + float *width; + float max_width; + int is_leaf; + struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node **children; + struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *parent; + struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *tree; +}; + +/* "sklearn/manifold/_barnes_hut_tsne.pyx":78 + * Tree* tree + * + * cdef struct Tree: # <<<<<<<<<<<<<< + * # Holds a pointer to the root node + * Node* root_node + */ +struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree { + struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *root_node; + int n_dimensions; + long n_cells; + long n_points; + int verbose; + int n_cell_per_node; +}; + +/* "View.MemoryView":99 + * + * @cname("__pyx_array") + * cdef class array: # <<<<<<<<<<<<<< + * + * cdef: + */ +struct __pyx_array_obj { + PyObject_HEAD + char *data; + Py_ssize_t len; + char *format; + int ndim; + Py_ssize_t *_shape; + Py_ssize_t *_strides; + Py_ssize_t itemsize; + PyObject *mode; + PyObject *_format; + void (*callback_free_data)(void *); + int free_data; + int dtype_is_object; +}; + + +/* "View.MemoryView":269 + * + * @cname('__pyx_MemviewEnum') + * cdef class Enum(object): # <<<<<<<<<<<<<< + * cdef object name + * def __init__(self, name): + */ +struct __pyx_MemviewEnum_obj { + PyObject_HEAD + PyObject *name; +}; + + +/* "View.MemoryView":302 + * + * @cname('__pyx_memoryview') + * cdef class memoryview(object): # <<<<<<<<<<<<<< + * + * cdef object obj + */ +struct __pyx_memoryview_obj { + PyObject_HEAD + struct __pyx_vtabstruct_memoryview *__pyx_vtab; + PyObject *obj; + PyObject *_size; + PyObject *_array_interface; + PyThread_type_lock lock; 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r = NULL; __Pyx_DECREF(tmp);}} while(0) + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) { + PyTypeObject* tp = Py_TYPE(obj); + if (likely(tp->tp_getattro)) + return tp->tp_getattro(obj, attr_name); +#if PY_MAJOR_VERSION < 3 + if (likely(tp->tp_getattr)) + return tp->tp_getattr(obj, PyString_AS_STRING(attr_name)); +#endif + return PyObject_GetAttr(obj, attr_name); +} +#else +#define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n) +#endif + +static PyObject *__Pyx_GetBuiltinName(PyObject *name); + +static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name); + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw); +#else +#define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw) +#endif + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg); +#endif + +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg); + +static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, + Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); + +static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); + +static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \ + PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \ + const char* function_name); + +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); + +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); + +static CYTHON_INLINE int __Pyx_IterFinish(void); + +static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); + +static CYTHON_INLINE int __Pyx_GetBufferAndValidate(Py_buffer* buf, PyObject* obj, + __Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack); +static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info); 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/*proto*/ +static PyObject *get_memview(PyObject *__pyx_v_self); /*proto*/ +static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *, PyObject *); + +static CYTHON_INLINE PyObject* __Pyx_decode_c_string( + const char* cstring, Py_ssize_t start, Py_ssize_t stop, + const char* encoding, const char* errors, + PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)); + +static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); +static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); + +static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); + +static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); + +#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \ + __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) : \ + (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) : \ + __Pyx_GetItemInt_Generic(o, to_py_func(i)))) +#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \ + __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \ + (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL)) +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, + int wraparound, int boundscheck); +#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \ + __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \ + (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL)) +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, + int wraparound, int boundscheck); +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j); +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, + int is_list, int wraparound, int boundscheck); + +static CYTHON_UNUSED int __pyx_memoryview_getbuffer(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/ +static PyObject *__pyx_memoryview_transpose(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_memoryview__get__base(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_memoryview_get_shape(PyObject *__pyx_v_self); /*proto*/ +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) { + PyListObject* L = (PyListObject*) list; + Py_ssize_t len = Py_SIZE(list); + if (likely(L->allocated > len)) { + Py_INCREF(x); + PyList_SET_ITEM(list, len, x); + Py_SIZE(list) = len+1; + return 0; + } + return PyList_Append(list, x); +} +#else +#define __Pyx_ListComp_Append(L,x) PyList_Append(L,x) +#endif + +static PyObject *__pyx_memoryview_get_strides(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_memoryview_get_suboffsets(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_memoryview_get_ndim(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_memoryview_get_itemsize(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_memoryview_get_nbytes(PyObject *__pyx_v_self); /*proto*/ +static PyObject *__pyx_memoryview_get_size(PyObject *__pyx_v_self); /*proto*/ +static CYTHON_INLINE int __Pyx_PyList_Extend(PyObject* L, PyObject* v) { +#if CYTHON_COMPILING_IN_CPYTHON + PyObject* none = _PyList_Extend((PyListObject*)L, v); + if (unlikely(!none)) + return -1; + Py_DECREF(none); + return 0; +#else + return PyList_SetSlice(L, PY_SSIZE_T_MAX, PY_SSIZE_T_MAX, v); +#endif +} + +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { + PyListObject* L = (PyListObject*) list; + Py_ssize_t len = Py_SIZE(list); + if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) { + Py_INCREF(x); + PyList_SET_ITEM(list, len, x); + Py_SIZE(list) = len+1; + return 0; + } + return PyList_Append(list, x); +} +#else +#define __Pyx_PyList_Append(L,x) PyList_Append(L,x) +#endif + +static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname); + +static PyObject *__pyx_memoryviewslice__get__base(PyObject *__pyx_v_self); /*proto*/ +static void __Pyx_WriteUnraisable(const char *name, int clineno, + int lineno, const char *filename, + int full_traceback); + +static int __Pyx_SetVtable(PyObject *dict, void *vtable); + +typedef struct { + int code_line; + PyCodeObject* code_object; +} __Pyx_CodeObjectCacheEntry; +struct __Pyx_CodeObjectCache { + int count; + int max_count; + __Pyx_CodeObjectCacheEntry* entries; +}; +static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; +static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); +static PyCodeObject *__pyx_find_code_object(int code_line); +static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); + +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename); + +typedef struct { + Py_ssize_t shape, strides, suboffsets; +} __Pyx_Buf_DimInfo; +typedef struct { + size_t refcount; + Py_buffer pybuffer; +} __Pyx_Buffer; +typedef struct { + __Pyx_Buffer *rcbuffer; + char *data; + __Pyx_Buf_DimInfo diminfo[8]; +} __Pyx_LocalBuf_ND; + +#if PY_MAJOR_VERSION < 3 + static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags); + static void __Pyx_ReleaseBuffer(Py_buffer *view); +#else + #define __Pyx_GetBuffer PyObject_GetBuffer + #define __Pyx_ReleaseBuffer PyBuffer_Release +#endif + + +static Py_ssize_t __Pyx_zeros[] = {0, 0, 0, 0, 0, 0, 0, 0}; +static Py_ssize_t __Pyx_minusones[] = {-1, -1, -1, -1, -1, -1, -1, -1}; + +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); + +static int __pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b); + +static int __Pyx_ValidateAndInit_memviewslice( + int *axes_specs, + int c_or_f_flag, + int buf_flags, + int ndim, + __Pyx_TypeInfo *dtype, + __Pyx_BufFmt_StackElem stack[], + __Pyx_memviewslice *memviewslice, + PyObject *original_obj); + +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_float(PyObject *); + +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_long(PyObject *); + +static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); + +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); + +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_long(PyObject *); + +static CYTHON_INLINE long __Pyx_pow_long(long, long); /* proto */ + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_clock_t(clock_t value); + +static PyObject *__pyx_memview_get_float(const char *itemp); +static int __pyx_memview_set_float(const char *itemp, PyObject *obj); + +static PyObject *__pyx_memview_get_long(const char *itemp); +static int __pyx_memview_set_long(const char *itemp, PyObject *obj); + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + #define __Pyx_CREAL(z) ((z).real()) + #define __Pyx_CIMAG(z) ((z).imag()) + #else + #define __Pyx_CREAL(z) (__real__(z)) + #define __Pyx_CIMAG(z) (__imag__(z)) + #endif +#else + #define __Pyx_CREAL(z) ((z).real) + #define __Pyx_CIMAG(z) ((z).imag) +#endif +#if (defined(_WIN32) || defined(__clang__)) && defined(__cplusplus) && CYTHON_CCOMPLEX + #define __Pyx_SET_CREAL(z,x) ((z).real(x)) + #define __Pyx_SET_CIMAG(z,y) ((z).imag(y)) +#else + #define __Pyx_SET_CREAL(z,x) __Pyx_CREAL(z) = (x) + #define __Pyx_SET_CIMAG(z,y) __Pyx_CIMAG(z) = (y) +#endif + +static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float, float); + +#if CYTHON_CCOMPLEX + #define __Pyx_c_eqf(a, b) ((a)==(b)) + #define __Pyx_c_sumf(a, b) ((a)+(b)) + #define __Pyx_c_difff(a, b) ((a)-(b)) + #define __Pyx_c_prodf(a, b) ((a)*(b)) + #define __Pyx_c_quotf(a, b) ((a)/(b)) + #define __Pyx_c_negf(a) (-(a)) + #ifdef __cplusplus + #define __Pyx_c_is_zerof(z) ((z)==(float)0) + #define __Pyx_c_conjf(z) (::std::conj(z)) + #if 1 + #define __Pyx_c_absf(z) (::std::abs(z)) + #define __Pyx_c_powf(a, b) (::std::pow(a, b)) + #endif + #else + #define __Pyx_c_is_zerof(z) ((z)==0) + #define __Pyx_c_conjf(z) (conjf(z)) + #if 1 + #define __Pyx_c_absf(z) (cabsf(z)) + #define __Pyx_c_powf(a, b) (cpowf(a, b)) + #endif + #endif +#else + static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex); + static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex); + #if 1 + static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex, __pyx_t_float_complex); + #endif +#endif + +static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double, double); + +#if CYTHON_CCOMPLEX + #define __Pyx_c_eq(a, b) ((a)==(b)) + #define __Pyx_c_sum(a, b) ((a)+(b)) + #define __Pyx_c_diff(a, b) ((a)-(b)) + #define __Pyx_c_prod(a, b) ((a)*(b)) + #define __Pyx_c_quot(a, b) ((a)/(b)) + #define __Pyx_c_neg(a) (-(a)) + #ifdef __cplusplus + #define __Pyx_c_is_zero(z) ((z)==(double)0) + #define __Pyx_c_conj(z) (::std::conj(z)) + #if 1 + #define __Pyx_c_abs(z) (::std::abs(z)) + #define __Pyx_c_pow(a, b) (::std::pow(a, b)) + #endif + #else + #define __Pyx_c_is_zero(z) ((z)==0) + #define __Pyx_c_conj(z) (conj(z)) + #if 1 + #define __Pyx_c_abs(z) (cabs(z)) + #define __Pyx_c_pow(a, b) (cpow(a, b)) + #endif + #endif +#else + static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex); + static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex); + #if 1 + static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex, __pyx_t_double_complex); + #endif +#endif + +static int __pyx_memviewslice_is_contig(const __Pyx_memviewslice *mvs, + char order, int ndim); + +static int __pyx_slices_overlap(__Pyx_memviewslice *slice1, + __Pyx_memviewslice *slice2, + int ndim, size_t itemsize); + +static __Pyx_memviewslice +__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, + const char *mode, int ndim, + size_t sizeof_dtype, int contig_flag, + int dtype_is_object); + +static CYTHON_INLINE PyObject *__pyx_capsule_create(void *p, const char *sig); + +static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *); + +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_float(PyObject *); + +static int __Pyx_check_binary_version(void); + +#if !defined(__Pyx_PyIdentifier_FromString) +#if PY_MAJOR_VERSION < 3 + #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s) +#else + #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s) +#endif +#endif + +static PyObject *__Pyx_ImportModule(const char *name); + +static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); + +static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); + +static char *__pyx_memoryview_get_item_pointer(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index); /* proto*/ +static PyObject *__pyx_memoryview_is_slice(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj); /* proto*/ +static PyObject *__pyx_memoryview_setitem_slice_assignment(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_dst, PyObject *__pyx_v_src); /* proto*/ +static PyObject *__pyx_memoryview_setitem_slice_assign_scalar(struct __pyx_memoryview_obj *__pyx_v_self, struct __pyx_memoryview_obj *__pyx_v_dst, PyObject *__pyx_v_value); /* proto*/ +static PyObject *__pyx_memoryview_setitem_indexed(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto*/ +static PyObject *__pyx_memoryview_convert_item_to_object(struct __pyx_memoryview_obj *__pyx_v_self, char *__pyx_v_itemp); /* proto*/ +static PyObject *__pyx_memoryview_assign_item_from_object(struct __pyx_memoryview_obj *__pyx_v_self, char *__pyx_v_itemp, PyObject *__pyx_v_value); /* proto*/ +static PyObject *__pyx_memoryviewslice_convert_item_to_object(struct __pyx_memoryviewslice_obj *__pyx_v_self, char *__pyx_v_itemp); /* proto*/ +static PyObject *__pyx_memoryviewslice_assign_item_from_object(struct __pyx_memoryviewslice_obj *__pyx_v_self, char *__pyx_v_itemp, PyObject *__pyx_v_value); /* proto*/ + +/* Module declarations from 'libc.string' */ + +/* Module declarations from 'libc.stdlib' */ + +/* Module declarations from 'libc.stdio' */ + +/* Module declarations from 'libc.math' */ + +/* Module declarations from 'cpython.buffer' */ + +/* Module declarations from 'cpython.ref' */ + +/* Module declarations from 'cpython.object' */ + +/* Module declarations from '__builtin__' */ + +/* Module declarations from 'cpython.type' */ +static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0; + +/* Module declarations from 'numpy' */ + +/* Module declarations from 'numpy' */ +static PyTypeObject *__pyx_ptype_5numpy_dtype = 0; +static PyTypeObject *__pyx_ptype_5numpy_flatiter = 0; +static PyTypeObject *__pyx_ptype_5numpy_broadcast = 0; +static PyTypeObject *__pyx_ptype_5numpy_ndarray = 0; +static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0; +static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, char *, char *, int *); /*proto*/ + +/* Module declarations from 'sklearn.manifold._barnes_hut_tsne' */ +static PyTypeObject *__pyx_array_type = 0; +static PyTypeObject *__pyx_MemviewEnum_type = 0; +static PyTypeObject *__pyx_memoryview_type = 0; +static PyTypeObject *__pyx_memoryviewslice_type = 0; +static float __pyx_v_7sklearn_8manifold_16_barnes_hut_tsne_EPSILON; +static PyObject *generic = 0; +static PyObject *strided = 0; +static PyObject *indirect = 0; +static PyObject *contiguous = 0; +static PyObject *indirect_contiguous = 0; +static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *__pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_init_tree(__Pyx_memviewslice, __Pyx_memviewslice, int, int); /*proto*/ +static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_create_root(__Pyx_memviewslice, __Pyx_memviewslice, int); /*proto*/ +static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_create_child(struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *, int *); /*proto*/ +static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_select_child(struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *, float *, long); /*proto*/ +static CYTHON_INLINE void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_index2offset(int *, int, int); /*proto*/ +static CYTHON_INLINE int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_offset2index(int *, int); /*proto*/ +static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_subdivide(struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *); /*proto*/ +static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *, float *, long, long, long); /*proto*/ +static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert_many(struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *, __Pyx_memviewslice); /*proto*/ +static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_tree(struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *); /*proto*/ +static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_recursive(struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *, struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *, long *); /*proto*/ +static long __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_count_points(struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *, long); /*proto*/ +static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice, struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *, float, float, long, long); /*proto*/ +static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_positive(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice, float *, int, float, float, long, int); /*proto*/ +static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negative(__Pyx_memviewslice, __Pyx_memviewslice, float *, struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *, float *, float, float, long, long); /*proto*/ +static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_non_edge_forces(struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *, float, long, float *, float *, float *, long *, float *, long *); /*proto*/ +static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_error(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice, float, int, int); /*proto*/ +static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_helper_test_index2offset(int *, int, int); /*proto*/ +static struct __pyx_array_obj *__pyx_array_new(PyObject *, Py_ssize_t, char *, char *, char *); /*proto*/ +static void *__pyx_align_pointer(void *, size_t); /*proto*/ +static PyObject *__pyx_memoryview_new(PyObject *, int, int, __Pyx_TypeInfo *); /*proto*/ +static CYTHON_INLINE int __pyx_memoryview_check(PyObject *); /*proto*/ +static PyObject *_unellipsify(PyObject *, int); /*proto*/ +static PyObject *assert_direct_dimensions(Py_ssize_t *, int); /*proto*/ +static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_obj *, PyObject *); /*proto*/ +static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *, Py_ssize_t, Py_ssize_t, Py_ssize_t, int, int, int *, Py_ssize_t, Py_ssize_t, Py_ssize_t, int, int, int, int); /*proto*/ +static char *__pyx_pybuffer_index(Py_buffer *, char *, Py_ssize_t, Py_ssize_t); /*proto*/ +static int __pyx_memslice_transpose(__Pyx_memviewslice *); /*proto*/ +static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice, int, PyObject *(*)(char *), int (*)(char *, PyObject *), int); /*proto*/ +static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ +static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ +static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *); /*proto*/ +static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/ +static Py_ssize_t abs_py_ssize_t(Py_ssize_t); /*proto*/ +static char __pyx_get_best_slice_order(__Pyx_memviewslice *, int); /*proto*/ +static void _copy_strided_to_strided(char *, Py_ssize_t *, char *, Py_ssize_t *, Py_ssize_t *, Py_ssize_t *, int, size_t); /*proto*/ +static void copy_strided_to_strided(__Pyx_memviewslice *, __Pyx_memviewslice *, int, size_t); /*proto*/ +static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *, int); /*proto*/ +static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *, Py_ssize_t *, Py_ssize_t, int, char); /*proto*/ +static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *, __Pyx_memviewslice *, char, int); /*proto*/ +static int __pyx_memoryview_err_extents(int, Py_ssize_t, Py_ssize_t); /*proto*/ +static int __pyx_memoryview_err_dim(PyObject *, char *, int); /*proto*/ +static int __pyx_memoryview_err(PyObject *, char *); /*proto*/ +static int __pyx_memoryview_copy_contents(__Pyx_memviewslice, __Pyx_memviewslice, int, int, int); /*proto*/ +static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *, int, int); /*proto*/ +static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *, int, int, int); /*proto*/ +static void __pyx_memoryview_refcount_objects_in_slice_with_gil(char *, Py_ssize_t *, Py_ssize_t *, int, int); /*proto*/ +static void __pyx_memoryview_refcount_objects_in_slice(char *, Py_ssize_t *, Py_ssize_t *, int, int); /*proto*/ +static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *, int, size_t, void *, int); /*proto*/ +static void __pyx_memoryview__slice_assign_scalar(char *, Py_ssize_t *, Py_ssize_t *, int, size_t, void *); /*proto*/ +static __Pyx_TypeInfo __Pyx_TypeInfo_float = { "float", NULL, sizeof(float), { 0 }, 0, 'R', 0, 0 }; +static __Pyx_TypeInfo __Pyx_TypeInfo_long = { "long", NULL, sizeof(long), { 0 }, 0, IS_UNSIGNED(long) ? 'U' : 'I', IS_UNSIGNED(long), 0 }; +#define __Pyx_MODULE_NAME "sklearn.manifold._barnes_hut_tsne" +int __pyx_module_is_main_sklearn__manifold___barnes_hut_tsne = 0; + +/* Implementation of 'sklearn.manifold._barnes_hut_tsne' */ +static PyObject *__pyx_builtin_range; +static PyObject *__pyx_builtin_ValueError; +static PyObject *__pyx_builtin_RuntimeError; +static PyObject *__pyx_builtin_MemoryError; +static PyObject *__pyx_builtin_enumerate; +static PyObject *__pyx_builtin_Ellipsis; +static PyObject *__pyx_builtin_TypeError; +static PyObject *__pyx_builtin_xrange; +static PyObject *__pyx_builtin_id; +static PyObject *__pyx_builtin_IndexError; +static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_calculate_edge(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_pos_output); /* proto */ +static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_pij_input, __Pyx_memviewslice __pyx_v_pos_output, __Pyx_memviewslice __pyx_v_neighbors, __Pyx_memviewslice __pyx_v_forces, float __pyx_v_theta, int __pyx_v_n_dimensions, int __pyx_v_verbose, float __pyx_v_dof, long __pyx_v_skip_num_points); /* proto */ +static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_4check_quadtree(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_X, __Pyx_memviewslice __pyx_v_counts); /* proto */ +static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_6test_index2offset(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ +static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_8test_index_offset(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ +static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ +static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */ +static int __pyx_array_MemoryView_5array___cinit__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_shape, Py_ssize_t __pyx_v_itemsize, PyObject *__pyx_v_format, PyObject *__pyx_v_mode, int __pyx_v_allocate_buffer); /* proto */ +static int __pyx_array_getbuffer_MemoryView_5array_2__getbuffer__(struct __pyx_array_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ +static void __pyx_array_MemoryView_5array_4__dealloc__(struct __pyx_array_obj *__pyx_v_self); /* proto */ +static PyObject *get_memview_MemoryView_5array_7memview___get__(struct __pyx_array_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_array_MemoryView_5array_6__getattr__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_attr); /* proto */ +static PyObject *__pyx_array_MemoryView_5array_8__getitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item); /* proto */ +static int __pyx_array_MemoryView_5array_10__setitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item, PyObject *__pyx_v_value); /* proto */ +static int __pyx_MemviewEnum_MemoryView_4Enum___init__(struct __pyx_MemviewEnum_obj *__pyx_v_self, PyObject *__pyx_v_name); /* proto */ +static PyObject *__pyx_MemviewEnum_MemoryView_4Enum_2__repr__(struct __pyx_MemviewEnum_obj *__pyx_v_self); /* proto */ +static int __pyx_memoryview_MemoryView_10memoryview___cinit__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj, int __pyx_v_flags, int __pyx_v_dtype_is_object); /* proto */ +static void __pyx_memoryview_MemoryView_10memoryview_2__dealloc__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_MemoryView_10memoryview_4__getitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index); /* proto */ +static int __pyx_memoryview_MemoryView_10memoryview_6__setitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto */ +static int __pyx_memoryview_getbuffer_MemoryView_10memoryview_8__getbuffer__(struct __pyx_memoryview_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ +static PyObject *__pyx_memoryview_transpose_MemoryView_10memoryview_1T___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview__get__base_MemoryView_10memoryview_4base___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_get_shape_MemoryView_10memoryview_5shape___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_get_strides_MemoryView_10memoryview_7strides___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_get_suboffsets_MemoryView_10memoryview_10suboffsets___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_get_ndim_MemoryView_10memoryview_4ndim___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_get_itemsize_MemoryView_10memoryview_8itemsize___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_get_nbytes_MemoryView_10memoryview_6nbytes___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_get_size_MemoryView_10memoryview_4size___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static Py_ssize_t __pyx_memoryview_MemoryView_10memoryview_10__len__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_MemoryView_10memoryview_12__repr__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_MemoryView_10memoryview_14__str__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_MemoryView_10memoryview_16is_c_contig(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_MemoryView_10memoryview_18is_f_contig(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_MemoryView_10memoryview_20copy(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview_MemoryView_10memoryview_22copy_fortran(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static void __pyx_memoryviewslice_MemoryView_16_memoryviewslice___dealloc__(struct __pyx_memoryviewslice_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryviewslice__get__base_MemoryView_16_memoryviewslice_4base___get__(struct __pyx_memoryviewslice_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_tp_new_array(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_Enum(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_memoryview(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new__memoryviewslice(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static char __pyx_k_B[] = "B"; +static char __pyx_k_C[] = "C"; +static char __pyx_k_H[] = "H"; +static char __pyx_k_I[] = "I"; +static char __pyx_k_L[] = "L"; +static char __pyx_k_O[] = "O"; +static char __pyx_k_Q[] = "Q"; +static char __pyx_k_X[] = "X"; +static char __pyx_k_b[] = "b"; +static char __pyx_k_c[] = "c"; +static char __pyx_k_d[] = "d"; +static char __pyx_k_f[] = "f"; +static char __pyx_k_g[] = "g"; +static char __pyx_k_h[] = "h"; +static char __pyx_k_i[] = " %i"; +static char __pyx_k_k[] = "k"; +static char __pyx_k_l[] = "l"; +static char __pyx_k_m[] = "m"; +static char __pyx_k_n[] = "n"; +static char __pyx_k_q[] = "q"; +static char __pyx_k_Zd[] = "Zd"; +static char __pyx_k_Zf[] = "Zf"; +static char __pyx_k_Zg[] = "Zg"; +static char __pyx_k_id[] = "id"; +static char __pyx_k_np[] = "np"; +static char __pyx_k_qt[] = "qt"; +static char __pyx_k_dof[] = "dof"; +static char __pyx_k_err[] = "err"; +static char __pyx_k_i_2[] = "i"; +static char __pyx_k_idx[] = "idx"; +static char __pyx_k_max[] = "max"; +static char __pyx_k_min[] = "min"; +static char __pyx_k_obj[] = "obj"; +static char __pyx_k_ret[] = "ret"; +static char __pyx_k_axis[] = "axis"; +static char __pyx_k_base[] = "base"; +static char __pyx_k_main[] = "__main__"; +static char __pyx_k_mode[] = "mode"; +static char __pyx_k_name[] = "name"; +static char __pyx_k_ndim[] = "ndim"; +static char __pyx_k_pack[] = "pack"; +static char __pyx_k_size[] = "size"; +static char __pyx_k_step[] = "step"; +static char __pyx_k_stop[] = "stop"; +static char __pyx_k_test[] = "__test__"; +static char __pyx_k_tidx[] = "tidx"; +static char __pyx_k_class[] = "__class__"; +static char __pyx_k_count[] = "count"; +static char __pyx_k_error[] = "error"; +static char __pyx_k_flags[] = "flags"; +static char __pyx_k_numpy[] = "numpy"; +static char __pyx_k_range[] = "range"; +static char __pyx_k_shape[] = "shape"; +static char __pyx_k_start[] = "start"; +static char __pyx_k_sum_Q[] = "sum_Q"; +static char __pyx_k_theta[] = "theta"; +static char __pyx_k_width[] = "width"; +static char __pyx_k_astype[] = "astype"; +static char __pyx_k_center[] = "center"; +static char __pyx_k_counts[] = "counts"; +static char __pyx_k_forces[] = "forces"; +static char __pyx_k_format[] = "format"; +static char __pyx_k_import[] = "__import__"; +static char __pyx_k_name_2[] = "__name__"; +static char __pyx_k_offset[] = "offset"; +static char __pyx_k_struct[] = "struct"; +static char __pyx_k_unpack[] = "unpack"; +static char __pyx_k_xrange[] = "xrange"; +static char __pyx_k_float32[] = "float32"; +static char __pyx_k_fortran[] = "fortran"; +static char __pyx_k_maximum[] = "maximum"; +static char __pyx_k_memview[] = "memview"; +static char __pyx_k_verbose[] = "verbose"; +static char __pyx_k_Ellipsis[] = "Ellipsis"; +static char __pyx_k_gradient[] = "gradient"; +static char __pyx_k_itemsize[] = "itemsize"; +static char __pyx_k_subtract[] = "subtract"; +static char __pyx_k_TypeError[] = "TypeError"; +static char __pyx_k_enumerate[] = "enumerate"; +static char __pyx_k_left_edge[] = "left_edge"; +static char __pyx_k_neighbors[] = "neighbors"; +static char __pyx_k_pij_input[] = "pij_input"; +static char __pyx_k_IndexError[] = "IndexError"; +static char __pyx_k_ValueError[] = "ValueError"; +static char __pyx_k_pos_output[] = "pos_output"; +static char __pyx_k_pyx_vtable[] = "__pyx_vtable__"; +static char __pyx_k_right_edge[] = "right_edge"; +static char __pyx_k_MemoryError[] = "MemoryError"; +static char __pyx_k_error_check[] = "error_check"; +static char __pyx_k_t_SNE_ERROR[] = "[t-SNE] ERROR\n"; +static char __pyx_k_RuntimeError[] = "RuntimeError"; +static char __pyx_k_n_dimensions[] = "n_dimensions"; +static char __pyx_k_pyx_getbuffer[] = "__pyx_getbuffer"; +static char __pyx_k_calculate_edge[] = "calculate_edge"; +static char __pyx_k_check_quadtree[] = "check_quadtree"; +static char __pyx_k_n_dimensions_i[] = " n_dimensions %i\n"; +static char __pyx_k_allocate_buffer[] = "allocate_buffer"; +static char __pyx_k_dtype_is_object[] = "dtype_is_object"; +static char __pyx_k_skip_num_points[] = "skip_num_points"; +static char __pyx_k_test_index2offset[] = "test_index2offset"; +static char __pyx_k_test_index_offset[] = "test_index_offset"; +static char __pyx_k_strided_and_direct[] = ""; +static char __pyx_k_strided_and_indirect[] = ""; +static char __pyx_k_contiguous_and_direct[] = ""; +static char __pyx_k_MemoryView_of_r_object[] = ""; +static char __pyx_k_t_SNE_Child_has_size_d[] = "[t-SNE] Child has size %d\n"; +static char __pyx_k_t_SNE_Insertion_failed[] = "[t-SNE] Insertion failed"; +static char __pyx_k_MemoryView_of_r_at_0x_x[] = ""; +static char __pyx_k_contiguous_and_indirect[] = ""; +static char __pyx_k_Cannot_index_with_type_s[] = "Cannot index with type '%s'"; +static char __pyx_k_getbuffer_obj_view_flags[] = "getbuffer(obj, view, flags)"; +static char __pyx_k_o2i_index_i_dim_i_offset[] = "o2i index %i dim %i offset"; +static char __pyx_k_t_SNE_Computing_gradient[] = "[t-SNE] Computing gradient\n"; +static char __pyx_k_t_SNE_Inserting_i_points[] = "[t-SNE] Inserting %i points\n"; +static char __pyx_k_t_SNE_Tree_i_clock_ticks[] = "[t-SNE] Tree: %i clock ticks | "; +static char __pyx_k_t_SNE_i_points_in_node_p[] = "[t-SNE] %i points in node %p\n"; +static char __pyx_k_Dimension_d_is_not_direct[] = "Dimension %d is not direct"; +static char __pyx_k_Invalid_shape_in_axis_d_d[] = "Invalid shape in axis %d: %d."; +static char __pyx_k_t_SNE_Created_root_node_p[] = "[t-SNE] Created root node %p\n"; +static char __pyx_k_Index_out_of_bounds_axis_d[] = "Index out of bounds (axis %d)"; +static char __pyx_k_Step_may_not_be_zero_axis_d[] = "Step may not be zero (axis %d)"; +static char __pyx_k_itemsize_0_for_cython_array[] = "itemsize <= 0 for cython.array"; +static char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; +static char __pyx_k_t_SNE_i_points_in_this_node[] = "[t-SNE] %i points in this node\n"; +static char __pyx_k_t_SNE_inserting_point_i_f_f[] = "[t-SNE] inserting point %i: [%f, %f]\n"; +static char __pyx_k_i2o_index_i_k_i_rem_i_offset[] = "i2o index %i k %i rem %i offset"; +static char __pyx_k_t_SNE_Offset_i_i_with_LE_f_f[] = "[t-SNE] Offset [%i, %i] with LE [%f, %f]\n"; +static char __pyx_k_unable_to_allocate_array_data[] = "unable to allocate array data."; +static char __pyx_k_strided_and_direct_or_indirect[] = ""; +static char __pyx_k_t_SNE_Allocating_i_elements_in[] = "[t-SNE] Allocating %i elements in force arrays\n"; +static char __pyx_k_t_SNE_Computed_error_1_4f_in_1[] = "[t-SNE] Computed error=%1.4f in %1.1e ticks\n"; +static char __pyx_k_t_SNE_Tree_initialised_Width_1[] = "[t-SNE] Tree initialised. Width = (%1.9e, %1.9e, %1.9e)\n"; +static char __pyx_k_t_SNE_d_i_Node_p_leaf_i_Size_i[] = "[t-SNE] [d=%i] Node %p leaf = %i. Size %i\n"; +static char __pyx_k_t_SNE_d_i_Relocating_old_point[] = "[t-SNE] [d=%i] Relocating old point to node %p\n"; +static char __pyx_k_Force_computation_i_clock_ticks[] = "Force computation: %i clock ticks\n"; +static char __pyx_k_Users_chrismoody_code_scikit_le[] = "/Users/chrismoody/code/scikit-learn/sklearn/manifold/_barnes_hut_tsne.pyx"; +static char __pyx_k_t_SNE_Checking_tree_consistency[] = "[t-SNE] Checking tree consistency \n"; +static char __pyx_k_t_SNE_Child_is_not_a_leaf_Desce[] = "[t-SNE] Child is not a leaf. Descending\n"; +static char __pyx_k_t_SNE_Computing_negative_gradie[] = "[t-SNE] Computing negative gradient: %e ticks\n"; +static char __pyx_k_t_SNE_Computing_positive_gradie[] = "[t-SNE] Computing positive gradient: %e ticks\n"; +static char __pyx_k_t_SNE_Counting_nodes_at_root_no[] = "[t-SNE] Counting nodes at root node %p\n"; +static char __pyx_k_t_SNE_Counting_points_for_child[] = "[t-SNE] Counting points for child %p\n"; +static char __pyx_k_t_SNE_Error_point_1_9e_is_above[] = "[t-SNE] Error: point (%1.9e) is above right edge of node (%1.9e)\n"; +static char __pyx_k_t_SNE_Error_point_1_9e_is_below[] = "[t-SNE] Error: point (%1.9e) is below left edge of node (%1.9e)\n"; +static char __pyx_k_t_SNE_Initializing_tree_of_n_di[] = "[t-SNE] Initializing tree of n_dimensions %i\n"; +static char __pyx_k_t_SNE_Tree_initialised_Left_edg[] = "[t-SNE] Tree initialised. Left_edge = (%1.9e, %1.9e, %1.9e)\n"; +static char __pyx_k_t_SNE_Warning_d_i_Detected_iden[] = "[t-SNE] Warning: [d=%i] Detected identical points. Returning. Leaf now has size %i\n"; +static char __pyx_k_t_SNE_d_i_Inserting_f_f_into_bl[] = "[t-SNE] [d=%i] Inserting [%f, %f] into blank cell\n"; +static char __pyx_k_t_SNE_d_i_Inserting_pos_i_f_f_d[] = "[t-SNE] [d=%i] Inserting pos %i [%f, %f] duplicate_count=%i into child %p\n"; +static char __pyx_k_t_SNE_d_i_Node_p_is_occupied_or[] = "[t-SNE] [d=%i] Node %p is occupied or is a leaf.\n"; +static char __pyx_k_t_SNE_d_i_Selecting_node_for_ne[] = "[t-SNE] [d=%i] Selecting node for new point\n"; +static char __pyx_k_t_SNE_d_i_Subdividing_this_leaf[] = "[t-SNE] [d=%i] Subdividing this leaf node %p\n"; +static char __pyx_k_t_SNE_p_is_a_leaf_node_no_child[] = "[t-SNE] %p is a leaf node, no children\n"; +static char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)"; +static char __pyx_k_All_dimensions_preceding_dimensi[] = "All dimensions preceding dimension %d must be indexed and not sliced"; +static char __pyx_k_Buffer_view_does_not_expose_stri[] = "Buffer view does not expose strides"; +static char __pyx_k_Can_only_create_a_buffer_that_is[] = "Can only create a buffer that is contiguous in memory."; +static char __pyx_k_Cannot_transpose_memoryview_with[] = "Cannot transpose memoryview with indirect dimensions"; +static char __pyx_k_Empty_shape_tuple_for_cython_arr[] = "Empty shape tuple for cython.array"; +static char __pyx_k_Forces_array_and_pos_output_shap[] = "Forces array and pos_output shapes are incompatible"; +static char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd"; +static char __pyx_k_Indirect_dimensions_not_supporte[] = "Indirect dimensions not supported"; +static char __pyx_k_Invalid_mode_expected_c_or_fortr[] = "Invalid mode, expected 'c' or 'fortran', got %s"; +static char __pyx_k_Non_native_byte_order_not_suppor[] = "Non-native byte order not supported"; +static char __pyx_k_Number_of_neighbors_must_be_of_p[] = "Number of neighbors must be < # of points - 1"; +static char __pyx_k_Out_of_bounds_on_buffer_access_a[] = "Out of bounds on buffer access (axis %d)"; +static char __pyx_k_Pij_and_pos_output_shapes_are_in[] = "Pij and pos_output shapes are incompatible"; +static char __pyx_k_Tree_consistency_failed_unexpect[] = "Tree consistency failed: unexpected number of points=%i at root node=%i"; +static char __pyx_k_Unable_to_convert_item_to_object[] = "Unable to convert item to object"; +static char __pyx_k_got_differing_extents_in_dimensi[] = "got differing extents in dimension %d (got %d and %d)"; +static char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous"; +static char __pyx_k_neighbors_array_and_pos_output_s[] = "neighbors array and pos_output shapes are incompatible"; +static char __pyx_k_sklearn_manifold__barnes_hut_tsn[] = "sklearn.manifold._barnes_hut_tsne"; +static char __pyx_k_unable_to_allocate_shape_and_str[] = "unable to allocate shape and strides."; +static char __pyx_k_Format_string_allocated_too_shor_2[] = "Format string allocated too short."; +static char __pyx_k_Tree_consistency_failed_unexpect_2[] = "Tree consistency failed: unexpected number of points on the tree"; +static PyObject *__pyx_kp_s_Buffer_view_does_not_expose_stri; +static PyObject *__pyx_n_s_C; +static PyObject *__pyx_kp_s_Can_only_create_a_buffer_that_is; +static PyObject *__pyx_kp_s_Cannot_index_with_type_s; +static PyObject *__pyx_n_s_Ellipsis; +static PyObject *__pyx_kp_s_Empty_shape_tuple_for_cython_arr; +static PyObject *__pyx_kp_s_Forces_array_and_pos_output_shap; +static PyObject *__pyx_kp_u_Format_string_allocated_too_shor; +static PyObject *__pyx_kp_u_Format_string_allocated_too_shor_2; +static PyObject *__pyx_n_s_IndexError; +static PyObject *__pyx_kp_s_Indirect_dimensions_not_supporte; +static PyObject *__pyx_kp_s_Invalid_mode_expected_c_or_fortr; +static PyObject *__pyx_kp_s_Invalid_shape_in_axis_d_d; +static PyObject *__pyx_n_s_MemoryError; +static PyObject *__pyx_kp_s_MemoryView_of_r_at_0x_x; +static PyObject *__pyx_kp_s_MemoryView_of_r_object; +static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor; +static PyObject *__pyx_kp_s_Number_of_neighbors_must_be_of_p; +static PyObject *__pyx_n_b_O; +static PyObject *__pyx_kp_s_Out_of_bounds_on_buffer_access_a; +static PyObject *__pyx_kp_s_Pij_and_pos_output_shapes_are_in; +static PyObject *__pyx_n_s_RuntimeError; +static PyObject *__pyx_kp_s_Tree_consistency_failed_unexpect; +static PyObject *__pyx_kp_s_Tree_consistency_failed_unexpect_2; +static PyObject *__pyx_n_s_TypeError; +static PyObject *__pyx_kp_s_Unable_to_convert_item_to_object; +static PyObject *__pyx_kp_s_Users_chrismoody_code_scikit_le; +static PyObject *__pyx_n_s_ValueError; +static PyObject *__pyx_n_s_X; +static PyObject *__pyx_n_s_allocate_buffer; +static PyObject *__pyx_n_s_astype; +static PyObject *__pyx_n_s_axis; +static PyObject *__pyx_n_s_base; +static PyObject *__pyx_n_s_c; +static PyObject *__pyx_n_u_c; +static PyObject *__pyx_n_s_calculate_edge; +static PyObject *__pyx_n_s_center; +static PyObject *__pyx_n_s_check_quadtree; +static PyObject *__pyx_n_s_class; +static PyObject *__pyx_kp_s_contiguous_and_direct; +static PyObject *__pyx_kp_s_contiguous_and_indirect; +static PyObject *__pyx_n_s_count; +static PyObject *__pyx_n_s_counts; +static PyObject *__pyx_n_s_dof; +static PyObject *__pyx_n_s_dtype_is_object; +static PyObject *__pyx_n_s_enumerate; +static PyObject *__pyx_n_s_err; +static PyObject *__pyx_n_s_error; +static PyObject *__pyx_n_s_error_check; +static PyObject *__pyx_n_s_flags; +static PyObject *__pyx_n_s_float32; +static PyObject *__pyx_n_s_forces; +static PyObject *__pyx_n_s_format; +static PyObject *__pyx_n_s_fortran; +static PyObject *__pyx_n_u_fortran; +static PyObject *__pyx_kp_s_got_differing_extents_in_dimensi; +static PyObject *__pyx_n_s_gradient; +static PyObject *__pyx_n_s_id; +static PyObject *__pyx_n_s_idx; +static PyObject *__pyx_n_s_import; +static PyObject *__pyx_n_s_itemsize; +static PyObject *__pyx_kp_s_itemsize_0_for_cython_array; +static PyObject *__pyx_n_s_k; +static PyObject *__pyx_n_s_left_edge; +static PyObject *__pyx_n_s_m; +static PyObject *__pyx_n_s_main; +static PyObject *__pyx_n_s_max; +static PyObject *__pyx_n_s_maximum; +static PyObject *__pyx_n_s_memview; +static PyObject *__pyx_n_s_min; +static PyObject *__pyx_n_s_mode; +static PyObject *__pyx_n_s_n; +static PyObject *__pyx_n_s_n_dimensions; +static PyObject *__pyx_n_s_name; +static PyObject *__pyx_n_s_name_2; +static PyObject *__pyx_kp_u_ndarray_is_not_C_contiguous; +static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou; +static PyObject *__pyx_n_s_ndim; +static PyObject *__pyx_n_s_neighbors; +static PyObject *__pyx_kp_s_neighbors_array_and_pos_output_s; +static PyObject *__pyx_n_s_np; +static PyObject *__pyx_n_s_numpy; +static PyObject *__pyx_n_s_obj; +static PyObject *__pyx_n_s_offset; +static PyObject *__pyx_n_s_pack; +static PyObject *__pyx_n_s_pij_input; +static PyObject *__pyx_n_s_pos_output; +static PyObject *__pyx_n_s_pyx_getbuffer; +static PyObject *__pyx_n_s_pyx_vtable; +static PyObject *__pyx_n_s_qt; +static PyObject *__pyx_n_s_range; +static PyObject *__pyx_n_s_ret; +static PyObject *__pyx_n_s_right_edge; +static PyObject *__pyx_n_s_shape; +static PyObject *__pyx_n_s_size; +static PyObject *__pyx_n_s_skip_num_points; +static PyObject *__pyx_n_s_sklearn_manifold__barnes_hut_tsn; +static PyObject *__pyx_n_s_start; +static PyObject *__pyx_n_s_step; +static PyObject *__pyx_n_s_stop; +static PyObject *__pyx_kp_s_strided_and_direct; +static PyObject *__pyx_kp_s_strided_and_direct_or_indirect; +static PyObject *__pyx_kp_s_strided_and_indirect; +static PyObject *__pyx_n_s_struct; +static PyObject *__pyx_n_s_subtract; +static PyObject *__pyx_n_s_sum_Q; +static PyObject *__pyx_kp_s_t_SNE_Insertion_failed; +static PyObject *__pyx_n_s_test; +static PyObject *__pyx_n_s_test_index2offset; +static PyObject *__pyx_n_s_test_index_offset; +static PyObject *__pyx_n_s_theta; +static PyObject *__pyx_n_s_tidx; +static PyObject *__pyx_kp_s_unable_to_allocate_array_data; +static PyObject *__pyx_kp_s_unable_to_allocate_shape_and_str; +static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd; +static PyObject *__pyx_n_s_unpack; +static PyObject *__pyx_n_s_verbose; +static PyObject *__pyx_n_s_width; +static PyObject *__pyx_n_s_xrange; +static PyObject *__pyx_float_0_5; +static PyObject *__pyx_float_2_0; +static PyObject *__pyx_float_1_001; +static PyObject *__pyx_int_0; +static PyObject *__pyx_int_1; +static PyObject *__pyx_int_4; +static PyObject *__pyx_int_neg_1; +static PyObject *__pyx_tuple_; +static PyObject *__pyx_tuple__2; +static PyObject *__pyx_tuple__3; +static PyObject *__pyx_tuple__4; +static PyObject *__pyx_tuple__5; +static PyObject *__pyx_tuple__6; +static PyObject *__pyx_tuple__7; +static PyObject *__pyx_tuple__8; +static PyObject *__pyx_tuple__9; +static PyObject *__pyx_slice__14; +static PyObject *__pyx_slice__15; +static PyObject *__pyx_slice__16; +static PyObject *__pyx_tuple__10; +static PyObject *__pyx_tuple__11; +static PyObject *__pyx_tuple__12; +static PyObject *__pyx_tuple__13; +static PyObject *__pyx_tuple__17; +static PyObject *__pyx_tuple__18; +static PyObject *__pyx_tuple__20; +static PyObject *__pyx_tuple__22; +static PyObject *__pyx_tuple__24; +static PyObject *__pyx_tuple__26; +static PyObject *__pyx_tuple__28; +static PyObject *__pyx_tuple__29; +static PyObject *__pyx_tuple__30; +static PyObject *__pyx_tuple__31; +static PyObject *__pyx_tuple__32; +static PyObject *__pyx_codeobj__19; +static PyObject *__pyx_codeobj__21; +static PyObject *__pyx_codeobj__23; +static PyObject *__pyx_codeobj__25; +static PyObject *__pyx_codeobj__27; + +/* "sklearn/manifold/_barnes_hut_tsne.pyx":92 + * int n_cell_per_node + * + * cdef Tree* init_tree(float[:] left_edge, float[:] width, int n_dimensions, # <<<<<<<<<<<<<< + * int verbose) nogil: + * # tree is freed by free_tree + */ + +static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *__pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_init_tree(__Pyx_memviewslice __pyx_v_left_edge, __Pyx_memviewslice __pyx_v_width, int __pyx_v_n_dimensions, int __pyx_v_verbose) { + struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *__pyx_v_tree; + struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *__pyx_r; + Py_ssize_t __pyx_t_1; + Py_ssize_t __pyx_t_2; + Py_ssize_t __pyx_t_3; + Py_ssize_t __pyx_t_4; + Py_ssize_t __pyx_t_5; + Py_ssize_t __pyx_t_6; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":95 + * int verbose) nogil: + * # tree is freed by free_tree + * cdef Tree* tree = malloc(sizeof(Tree)) # <<<<<<<<<<<<<< + * tree.n_dimensions = n_dimensions + * tree.n_cells = 0 + */ + __pyx_v_tree = ((struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *)malloc((sizeof(struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree)))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":96 + * # tree is freed by free_tree + * cdef Tree* tree = malloc(sizeof(Tree)) + * tree.n_dimensions = n_dimensions # <<<<<<<<<<<<<< + * tree.n_cells = 0 + * tree.n_points = 0 + */ + __pyx_v_tree->n_dimensions = __pyx_v_n_dimensions; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":97 + * cdef Tree* tree = malloc(sizeof(Tree)) + * tree.n_dimensions = n_dimensions + * tree.n_cells = 0 # <<<<<<<<<<<<<< + * tree.n_points = 0 + * tree.verbose = verbose + */ + __pyx_v_tree->n_cells = 0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":98 + * tree.n_dimensions = n_dimensions + * tree.n_cells = 0 + * tree.n_points = 0 # <<<<<<<<<<<<<< + * tree.verbose = verbose + * tree.root_node = create_root(left_edge, width, n_dimensions) + */ + __pyx_v_tree->n_points = 0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":99 + * tree.n_cells = 0 + * tree.n_points = 0 + * tree.verbose = verbose # <<<<<<<<<<<<<< + * tree.root_node = create_root(left_edge, width, n_dimensions) + * tree.root_node.tree = tree + */ + __pyx_v_tree->verbose = __pyx_v_verbose; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":100 + * tree.n_points = 0 + * tree.verbose = verbose + * tree.root_node = create_root(left_edge, width, n_dimensions) # <<<<<<<<<<<<<< + * tree.root_node.tree = tree + * tree.n_cells += 1 + */ + __pyx_v_tree->root_node = __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_create_root(__pyx_v_left_edge, __pyx_v_width, __pyx_v_n_dimensions); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":101 + * tree.verbose = verbose + * tree.root_node = create_root(left_edge, width, n_dimensions) + * tree.root_node.tree = tree # <<<<<<<<<<<<<< + * tree.n_cells += 1 + * tree.n_cell_per_node = 2 ** n_dimensions + */ + __pyx_v_tree->root_node->tree = __pyx_v_tree; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":102 + * tree.root_node = create_root(left_edge, width, n_dimensions) + * tree.root_node.tree = tree + * tree.n_cells += 1 # <<<<<<<<<<<<<< + * tree.n_cell_per_node = 2 ** n_dimensions + * if DEBUGFLAG: + */ + __pyx_v_tree->n_cells = (__pyx_v_tree->n_cells + 1); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":103 + * tree.root_node.tree = tree + * tree.n_cells += 1 + * tree.n_cell_per_node = 2 ** n_dimensions # <<<<<<<<<<<<<< + * if DEBUGFLAG: + * printf("[t-SNE] Tree initialised. Left_edge = (%1.9e, %1.9e, %1.9e)\n", + */ + __pyx_v_tree->n_cell_per_node = __Pyx_pow_long(2, ((long)__pyx_v_n_dimensions)); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":104 + * tree.n_cells += 1 + * tree.n_cell_per_node = 2 ** n_dimensions + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] Tree initialised. Left_edge = (%1.9e, %1.9e, %1.9e)\n", + * left_edge[0], left_edge[1], left_edge[2]) + */ + if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":106 + * if DEBUGFLAG: + * printf("[t-SNE] Tree initialised. Left_edge = (%1.9e, %1.9e, %1.9e)\n", + * left_edge[0], left_edge[1], left_edge[2]) # <<<<<<<<<<<<<< + * printf("[t-SNE] Tree initialised. Width = (%1.9e, %1.9e, %1.9e)\n", + * width[0], width[1], width[2]) + */ + __pyx_t_1 = 0; + __pyx_t_2 = 1; + __pyx_t_3 = 2; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":105 + * tree.n_cell_per_node = 2 ** n_dimensions + * if DEBUGFLAG: + * printf("[t-SNE] Tree initialised. Left_edge = (%1.9e, %1.9e, %1.9e)\n", # <<<<<<<<<<<<<< + * left_edge[0], left_edge[1], left_edge[2]) + * printf("[t-SNE] Tree initialised. Width = (%1.9e, %1.9e, %1.9e)\n", + */ + printf(__pyx_k_t_SNE_Tree_initialised_Left_edg, (*((float *) ( /* dim=0 */ (__pyx_v_left_edge.data + __pyx_t_1 * __pyx_v_left_edge.strides[0]) ))), (*((float *) ( /* dim=0 */ (__pyx_v_left_edge.data + __pyx_t_2 * __pyx_v_left_edge.strides[0]) ))), (*((float *) ( /* dim=0 */ (__pyx_v_left_edge.data + __pyx_t_3 * __pyx_v_left_edge.strides[0]) )))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":108 + * left_edge[0], left_edge[1], left_edge[2]) + * printf("[t-SNE] Tree initialised. Width = (%1.9e, %1.9e, %1.9e)\n", + * width[0], width[1], width[2]) # <<<<<<<<<<<<<< + * return tree + * + */ + __pyx_t_4 = 0; + __pyx_t_5 = 1; + __pyx_t_6 = 2; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":107 + * printf("[t-SNE] Tree initialised. Left_edge = (%1.9e, %1.9e, %1.9e)\n", + * left_edge[0], left_edge[1], left_edge[2]) + * printf("[t-SNE] Tree initialised. Width = (%1.9e, %1.9e, %1.9e)\n", # <<<<<<<<<<<<<< + * width[0], width[1], width[2]) + * return tree + */ + printf(__pyx_k_t_SNE_Tree_initialised_Width_1, (*((float *) ( /* dim=0 */ (__pyx_v_width.data + __pyx_t_4 * __pyx_v_width.strides[0]) ))), (*((float *) ( /* dim=0 */ (__pyx_v_width.data + __pyx_t_5 * __pyx_v_width.strides[0]) ))), (*((float *) ( /* dim=0 */ (__pyx_v_width.data + __pyx_t_6 * __pyx_v_width.strides[0]) )))); + goto __pyx_L3; + } + __pyx_L3:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":109 + * printf("[t-SNE] Tree initialised. Width = (%1.9e, %1.9e, %1.9e)\n", + * width[0], width[1], width[2]) + * return tree # <<<<<<<<<<<<<< + * + * cdef Node* create_root(float[:] left_edge, float[:] width, int n_dimensions) nogil: + */ + __pyx_r = __pyx_v_tree; + goto __pyx_L0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":92 + * int n_cell_per_node + * + * cdef Tree* init_tree(float[:] left_edge, float[:] width, int n_dimensions, # <<<<<<<<<<<<<< + * int verbose) nogil: + * # tree is freed by free_tree + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "sklearn/manifold/_barnes_hut_tsne.pyx":111 + * return tree + * + * cdef Node* create_root(float[:] left_edge, float[:] width, int n_dimensions) nogil: # <<<<<<<<<<<<<< + * # Create a default root node + * cdef int ax + */ + +static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_create_root(__Pyx_memviewslice __pyx_v_left_edge, __Pyx_memviewslice __pyx_v_width, int __pyx_v_n_dimensions) { + int __pyx_v_ax; + CYTHON_UNUSED int __pyx_v_n_cell_per_node; + struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_v_root; + struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_r; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + int __pyx_t_4; + float __pyx_t_5; + float __pyx_t_6; + float __pyx_t_7; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":114 + * # Create a default root node + * cdef int ax + * cdef int n_cell_per_node = 2 ** n_dimensions # <<<<<<<<<<<<<< + * # root is freed by free_tree + * root = malloc(sizeof(Node)) + */ + __pyx_v_n_cell_per_node = __Pyx_pow_long(2, ((long)__pyx_v_n_dimensions)); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":116 + * cdef int n_cell_per_node = 2 ** n_dimensions + * # root is freed by free_tree + * root = malloc(sizeof(Node)) # <<<<<<<<<<<<<< + * root.is_leaf = 1 + * root.parent = NULL + */ + __pyx_v_root = ((struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *)malloc((sizeof(struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node)))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":117 + * # root is freed by free_tree + * root = malloc(sizeof(Node)) + * root.is_leaf = 1 # <<<<<<<<<<<<<< + * root.parent = NULL + * root.level = 0 + */ + __pyx_v_root->is_leaf = 1; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":118 + * root = malloc(sizeof(Node)) + * root.is_leaf = 1 + * root.parent = NULL # <<<<<<<<<<<<<< + * root.level = 0 + * root.cumulative_size = 0 + */ + __pyx_v_root->parent = NULL; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":119 + * root.is_leaf = 1 + * root.parent = NULL + * root.level = 0 # <<<<<<<<<<<<<< + * root.cumulative_size = 0 + * root.size = 0 + */ + __pyx_v_root->level = 0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":120 + * root.parent = NULL + * root.level = 0 + * root.cumulative_size = 0 # <<<<<<<<<<<<<< + * root.size = 0 + * root.point_index = -1 + */ + __pyx_v_root->cumulative_size = 0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":121 + * root.level = 0 + * root.cumulative_size = 0 + * root.size = 0 # <<<<<<<<<<<<<< + * root.point_index = -1 + * root.max_width = 0.0 + */ + __pyx_v_root->size = 0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":122 + * root.cumulative_size = 0 + * root.size = 0 + * root.point_index = -1 # <<<<<<<<<<<<<< + * root.max_width = 0.0 + * root.width = malloc(sizeof(float) * n_dimensions) + */ + __pyx_v_root->point_index = -1; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":123 + * root.size = 0 + * root.point_index = -1 + * root.max_width = 0.0 # <<<<<<<<<<<<<< + * root.width = malloc(sizeof(float) * n_dimensions) + * root.left_edge = malloc(sizeof(float) * n_dimensions) + */ + __pyx_v_root->max_width = 0.0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":124 + * root.point_index = -1 + * root.max_width = 0.0 + * root.width = malloc(sizeof(float) * n_dimensions) # <<<<<<<<<<<<<< + * root.left_edge = malloc(sizeof(float) * n_dimensions) + * root.center = malloc(sizeof(float) * n_dimensions) + */ + __pyx_v_root->width = ((float *)malloc(((sizeof(float)) * __pyx_v_n_dimensions))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":125 + * root.max_width = 0.0 + * root.width = malloc(sizeof(float) * n_dimensions) + * root.left_edge = malloc(sizeof(float) * n_dimensions) # <<<<<<<<<<<<<< + * root.center = malloc(sizeof(float) * n_dimensions) + * root.barycenter = malloc(sizeof(float) * n_dimensions) + */ + __pyx_v_root->left_edge = ((float *)malloc(((sizeof(float)) * __pyx_v_n_dimensions))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":126 + * root.width = malloc(sizeof(float) * n_dimensions) + * root.left_edge = malloc(sizeof(float) * n_dimensions) + * root.center = malloc(sizeof(float) * n_dimensions) # <<<<<<<<<<<<<< + * root.barycenter = malloc(sizeof(float) * n_dimensions) + * root.leaf_point_position= malloc(sizeof(float) * n_dimensions) + */ + __pyx_v_root->center = ((float *)malloc(((sizeof(float)) * __pyx_v_n_dimensions))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":127 + * root.left_edge = malloc(sizeof(float) * n_dimensions) + * root.center = malloc(sizeof(float) * n_dimensions) + * root.barycenter = malloc(sizeof(float) * n_dimensions) # <<<<<<<<<<<<<< + * root.leaf_point_position= malloc(sizeof(float) * n_dimensions) + * root.children = NULL + */ + __pyx_v_root->barycenter = ((float *)malloc(((sizeof(float)) * __pyx_v_n_dimensions))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":128 + * root.center = malloc(sizeof(float) * n_dimensions) + * root.barycenter = malloc(sizeof(float) * n_dimensions) + * root.leaf_point_position= malloc(sizeof(float) * n_dimensions) # <<<<<<<<<<<<<< + * root.children = NULL + * for ax in range(n_dimensions): + */ + __pyx_v_root->leaf_point_position = ((float *)malloc(((sizeof(float)) * __pyx_v_n_dimensions))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":129 + * root.barycenter = malloc(sizeof(float) * n_dimensions) + * root.leaf_point_position= malloc(sizeof(float) * n_dimensions) + * root.children = NULL # <<<<<<<<<<<<<< + * for ax in range(n_dimensions): + * root.width[ax] = width[ax] + */ + __pyx_v_root->children = NULL; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":130 + * root.leaf_point_position= malloc(sizeof(float) * n_dimensions) + * root.children = NULL + * for ax in range(n_dimensions): # <<<<<<<<<<<<<< + * root.width[ax] = width[ax] + * root.left_edge[ax] = left_edge[ax] + */ + __pyx_t_1 = __pyx_v_n_dimensions; + for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { + __pyx_v_ax = __pyx_t_2; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":131 + * root.children = NULL + * for ax in range(n_dimensions): + * root.width[ax] = width[ax] # <<<<<<<<<<<<<< + * root.left_edge[ax] = left_edge[ax] + * root.center[ax] = 0.0 + */ + __pyx_t_3 = __pyx_v_ax; + (__pyx_v_root->width[__pyx_v_ax]) = (*((float *) ( /* dim=0 */ (__pyx_v_width.data + __pyx_t_3 * __pyx_v_width.strides[0]) ))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":132 + * for ax in range(n_dimensions): + * root.width[ax] = width[ax] + * root.left_edge[ax] = left_edge[ax] # <<<<<<<<<<<<<< + * root.center[ax] = 0.0 + * root.barycenter[ax] = 0. + */ + __pyx_t_4 = __pyx_v_ax; + (__pyx_v_root->left_edge[__pyx_v_ax]) = (*((float *) ( /* dim=0 */ (__pyx_v_left_edge.data + __pyx_t_4 * __pyx_v_left_edge.strides[0]) ))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":133 + * root.width[ax] = width[ax] + * root.left_edge[ax] = left_edge[ax] + * root.center[ax] = 0.0 # <<<<<<<<<<<<<< + * root.barycenter[ax] = 0. + * root.leaf_point_position[ax] = -1 + */ + (__pyx_v_root->center[__pyx_v_ax]) = 0.0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":134 + * root.left_edge[ax] = left_edge[ax] + * root.center[ax] = 0.0 + * root.barycenter[ax] = 0. # <<<<<<<<<<<<<< + * root.leaf_point_position[ax] = -1 + * for ax in range(n_dimensions): + */ + (__pyx_v_root->barycenter[__pyx_v_ax]) = 0.; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":135 + * root.center[ax] = 0.0 + * root.barycenter[ax] = 0. + * root.leaf_point_position[ax] = -1 # <<<<<<<<<<<<<< + * for ax in range(n_dimensions): + * root.max_width = max(root.max_width, root.width[ax]) + */ + (__pyx_v_root->leaf_point_position[__pyx_v_ax]) = -1.0; + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":136 + * root.barycenter[ax] = 0. + * root.leaf_point_position[ax] = -1 + * for ax in range(n_dimensions): # <<<<<<<<<<<<<< + * root.max_width = max(root.max_width, root.width[ax]) + * if DEBUGFLAG: + */ + __pyx_t_1 = __pyx_v_n_dimensions; + for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { + __pyx_v_ax = __pyx_t_2; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":137 + * root.leaf_point_position[ax] = -1 + * for ax in range(n_dimensions): + * root.max_width = max(root.max_width, root.width[ax]) # <<<<<<<<<<<<<< + * if DEBUGFLAG: + * printf("[t-SNE] Created root node %p\n", root) + */ + __pyx_t_5 = (__pyx_v_root->width[__pyx_v_ax]); + __pyx_t_6 = __pyx_v_root->max_width; + if (((__pyx_t_5 > __pyx_t_6) != 0)) { + __pyx_t_7 = __pyx_t_5; + } else { + __pyx_t_7 = __pyx_t_6; + } + __pyx_v_root->max_width = __pyx_t_7; + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":138 + * for ax in range(n_dimensions): + * root.max_width = max(root.max_width, root.width[ax]) + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] Created root node %p\n", root) + * return root + */ + if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":139 + * root.max_width = max(root.max_width, root.width[ax]) + * if DEBUGFLAG: + * printf("[t-SNE] Created root node %p\n", root) # <<<<<<<<<<<<<< + * return root + * + */ + printf(__pyx_k_t_SNE_Created_root_node_p, __pyx_v_root); + goto __pyx_L7; + } + __pyx_L7:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":140 + * if DEBUGFLAG: + * printf("[t-SNE] Created root node %p\n", root) + * return root # <<<<<<<<<<<<<< + * + * cdef Node* create_child(Node *parent, int[3] offset) nogil: + */ + __pyx_r = __pyx_v_root; + goto __pyx_L0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":111 + * return tree + * + * cdef Node* create_root(float[:] left_edge, float[:] width, int n_dimensions) nogil: # <<<<<<<<<<<<<< + * # Create a default root node + * cdef int ax + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "sklearn/manifold/_barnes_hut_tsne.pyx":142 + * return root + * + * cdef Node* create_child(Node *parent, int[3] offset) nogil: # <<<<<<<<<<<<<< + * # Create a new child node with default parameters + * cdef int ax + */ + +static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_create_child(struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_v_parent, int *__pyx_v_offset) { + int __pyx_v_ax; + struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_v_child; + struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_r; + struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *__pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + float __pyx_t_4; + float __pyx_t_5; + float __pyx_t_6; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":146 + * cdef int ax + * # these children are freed by free_recursive + * child = malloc(sizeof(Node)) # <<<<<<<<<<<<<< + * child.is_leaf = 1 + * child.parent = parent + */ + __pyx_v_child = ((struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *)malloc((sizeof(struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node)))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":147 + * # these children are freed by free_recursive + * child = malloc(sizeof(Node)) + * child.is_leaf = 1 # <<<<<<<<<<<<<< + * child.parent = parent + * child.level = parent.level + 1 + */ + __pyx_v_child->is_leaf = 1; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":148 + * child = malloc(sizeof(Node)) + * child.is_leaf = 1 + * child.parent = parent # <<<<<<<<<<<<<< + * child.level = parent.level + 1 + * child.size = 0 + */ + __pyx_v_child->parent = __pyx_v_parent; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":149 + * child.is_leaf = 1 + * child.parent = parent + * child.level = parent.level + 1 # <<<<<<<<<<<<<< + * child.size = 0 + * child.cumulative_size = 0 + */ + __pyx_v_child->level = (__pyx_v_parent->level + 1); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":150 + * child.parent = parent + * child.level = parent.level + 1 + * child.size = 0 # <<<<<<<<<<<<<< + * child.cumulative_size = 0 + * child.point_index = -1 + */ + __pyx_v_child->size = 0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":151 + * child.level = parent.level + 1 + * child.size = 0 + * child.cumulative_size = 0 # <<<<<<<<<<<<<< + * child.point_index = -1 + * child.tree = parent.tree + */ + __pyx_v_child->cumulative_size = 0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":152 + * child.size = 0 + * child.cumulative_size = 0 + * child.point_index = -1 # <<<<<<<<<<<<<< + * child.tree = parent.tree + * child.max_width = 0.0 + */ + __pyx_v_child->point_index = -1; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":153 + * child.cumulative_size = 0 + * child.point_index = -1 + * child.tree = parent.tree # <<<<<<<<<<<<<< + * child.max_width = 0.0 + * child.width = malloc(sizeof(float) * parent.tree.n_dimensions) + */ + __pyx_t_1 = __pyx_v_parent->tree; + __pyx_v_child->tree = __pyx_t_1; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":154 + * child.point_index = -1 + * child.tree = parent.tree + * child.max_width = 0.0 # <<<<<<<<<<<<<< + * child.width = malloc(sizeof(float) * parent.tree.n_dimensions) + * child.left_edge = malloc(sizeof(float) * parent.tree.n_dimensions) + */ + __pyx_v_child->max_width = 0.0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":155 + * child.tree = parent.tree + * child.max_width = 0.0 + * child.width = malloc(sizeof(float) * parent.tree.n_dimensions) # <<<<<<<<<<<<<< + * child.left_edge = malloc(sizeof(float) * parent.tree.n_dimensions) + * child.center = malloc(sizeof(float) * parent.tree.n_dimensions) + */ + __pyx_v_child->width = ((float *)malloc(((sizeof(float)) * __pyx_v_parent->tree->n_dimensions))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":156 + * child.max_width = 0.0 + * child.width = malloc(sizeof(float) * parent.tree.n_dimensions) + * child.left_edge = malloc(sizeof(float) * parent.tree.n_dimensions) # <<<<<<<<<<<<<< + * child.center = malloc(sizeof(float) * parent.tree.n_dimensions) + * child.barycenter = malloc(sizeof(float) * parent.tree.n_dimensions) + */ + __pyx_v_child->left_edge = ((float *)malloc(((sizeof(float)) * __pyx_v_parent->tree->n_dimensions))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":157 + * child.width = malloc(sizeof(float) * parent.tree.n_dimensions) + * child.left_edge = malloc(sizeof(float) * parent.tree.n_dimensions) + * child.center = malloc(sizeof(float) * parent.tree.n_dimensions) # <<<<<<<<<<<<<< + * child.barycenter = malloc(sizeof(float) * parent.tree.n_dimensions) + * child.leaf_point_position = malloc(sizeof(float) * parent.tree.n_dimensions) + */ + __pyx_v_child->center = ((float *)malloc(((sizeof(float)) * __pyx_v_parent->tree->n_dimensions))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":158 + * child.left_edge = malloc(sizeof(float) * parent.tree.n_dimensions) + * child.center = malloc(sizeof(float) * parent.tree.n_dimensions) + * child.barycenter = malloc(sizeof(float) * parent.tree.n_dimensions) # <<<<<<<<<<<<<< + * child.leaf_point_position = malloc(sizeof(float) * parent.tree.n_dimensions) + * child.children = NULL + */ + __pyx_v_child->barycenter = ((float *)malloc(((sizeof(float)) * __pyx_v_parent->tree->n_dimensions))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":159 + * child.center = malloc(sizeof(float) * parent.tree.n_dimensions) + * child.barycenter = malloc(sizeof(float) * parent.tree.n_dimensions) + * child.leaf_point_position = malloc(sizeof(float) * parent.tree.n_dimensions) # <<<<<<<<<<<<<< + * child.children = NULL + * for ax in range(parent.tree.n_dimensions): + */ + __pyx_v_child->leaf_point_position = ((float *)malloc(((sizeof(float)) * __pyx_v_parent->tree->n_dimensions))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":160 + * child.barycenter = malloc(sizeof(float) * parent.tree.n_dimensions) + * child.leaf_point_position = malloc(sizeof(float) * parent.tree.n_dimensions) + * child.children = NULL # <<<<<<<<<<<<<< + * for ax in range(parent.tree.n_dimensions): + * child.width[ax] = parent.width[ax] / 2.0 + */ + __pyx_v_child->children = NULL; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":161 + * child.leaf_point_position = malloc(sizeof(float) * parent.tree.n_dimensions) + * child.children = NULL + * for ax in range(parent.tree.n_dimensions): # <<<<<<<<<<<<<< + * child.width[ax] = parent.width[ax] / 2.0 + * child.left_edge[ax] = parent.left_edge[ax] + offset[ax] * parent.width[ax] / 2.0 + */ + __pyx_t_2 = __pyx_v_parent->tree->n_dimensions; + for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { + __pyx_v_ax = __pyx_t_3; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":162 + * child.children = NULL + * for ax in range(parent.tree.n_dimensions): + * child.width[ax] = parent.width[ax] / 2.0 # <<<<<<<<<<<<<< + * child.left_edge[ax] = parent.left_edge[ax] + offset[ax] * parent.width[ax] / 2.0 + * child.center[ax] = child.left_edge[ax] + child.width[ax] / 2.0 + */ + (__pyx_v_child->width[__pyx_v_ax]) = ((__pyx_v_parent->width[__pyx_v_ax]) / 2.0); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":163 + * for ax in range(parent.tree.n_dimensions): + * child.width[ax] = parent.width[ax] / 2.0 + * child.left_edge[ax] = parent.left_edge[ax] + offset[ax] * parent.width[ax] / 2.0 # <<<<<<<<<<<<<< + * child.center[ax] = child.left_edge[ax] + child.width[ax] / 2.0 + * child.barycenter[ax] = 0. + */ + (__pyx_v_child->left_edge[__pyx_v_ax]) = ((__pyx_v_parent->left_edge[__pyx_v_ax]) + (((__pyx_v_offset[__pyx_v_ax]) * (__pyx_v_parent->width[__pyx_v_ax])) / 2.0)); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":164 + * child.width[ax] = parent.width[ax] / 2.0 + * child.left_edge[ax] = parent.left_edge[ax] + offset[ax] * parent.width[ax] / 2.0 + * child.center[ax] = child.left_edge[ax] + child.width[ax] / 2.0 # <<<<<<<<<<<<<< + * child.barycenter[ax] = 0. + * child.leaf_point_position[ax] = -1. + */ + (__pyx_v_child->center[__pyx_v_ax]) = ((__pyx_v_child->left_edge[__pyx_v_ax]) + ((__pyx_v_child->width[__pyx_v_ax]) / 2.0)); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":165 + * child.left_edge[ax] = parent.left_edge[ax] + offset[ax] * parent.width[ax] / 2.0 + * child.center[ax] = child.left_edge[ax] + child.width[ax] / 2.0 + * child.barycenter[ax] = 0. # <<<<<<<<<<<<<< + * child.leaf_point_position[ax] = -1. + * for ax in range(parent.tree.n_dimensions): + */ + (__pyx_v_child->barycenter[__pyx_v_ax]) = 0.; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":166 + * child.center[ax] = child.left_edge[ax] + child.width[ax] / 2.0 + * child.barycenter[ax] = 0. + * child.leaf_point_position[ax] = -1. # <<<<<<<<<<<<<< + * for ax in range(parent.tree.n_dimensions): + * child.max_width = max(child.max_width, child.width[ax]) + */ + (__pyx_v_child->leaf_point_position[__pyx_v_ax]) = -1.; + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":167 + * child.barycenter[ax] = 0. + * child.leaf_point_position[ax] = -1. + * for ax in range(parent.tree.n_dimensions): # <<<<<<<<<<<<<< + * child.max_width = max(child.max_width, child.width[ax]) + * child.tree.n_cells += 1 + */ + __pyx_t_2 = __pyx_v_parent->tree->n_dimensions; + for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { + __pyx_v_ax = __pyx_t_3; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":168 + * child.leaf_point_position[ax] = -1. + * for ax in range(parent.tree.n_dimensions): + * child.max_width = max(child.max_width, child.width[ax]) # <<<<<<<<<<<<<< + * child.tree.n_cells += 1 + * return child + */ + __pyx_t_4 = (__pyx_v_child->width[__pyx_v_ax]); + __pyx_t_5 = __pyx_v_child->max_width; + if (((__pyx_t_4 > __pyx_t_5) != 0)) { + __pyx_t_6 = __pyx_t_4; + } else { + __pyx_t_6 = __pyx_t_5; + } + __pyx_v_child->max_width = __pyx_t_6; + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":169 + * for ax in range(parent.tree.n_dimensions): + * child.max_width = max(child.max_width, child.width[ax]) + * child.tree.n_cells += 1 # <<<<<<<<<<<<<< + * return child + * + */ + __pyx_v_child->tree->n_cells = (__pyx_v_child->tree->n_cells + 1); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":170 + * child.max_width = max(child.max_width, child.width[ax]) + * child.tree.n_cells += 1 + * return child # <<<<<<<<<<<<<< + * + * cdef Node* select_child(Node *node, float[3] pos, long index) nogil: + */ + __pyx_r = __pyx_v_child; + goto __pyx_L0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":142 + * return root + * + * cdef Node* create_child(Node *parent, int[3] offset) nogil: # <<<<<<<<<<<<<< + * # Create a new child node with default parameters + * cdef int ax + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "sklearn/manifold/_barnes_hut_tsne.pyx":172 + * return child + * + * cdef Node* select_child(Node *node, float[3] pos, long index) nogil: # <<<<<<<<<<<<<< + * # Find which sub-node a position should go into + * # And return the appropriate node + */ + +static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_select_child(struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_v_node, float *__pyx_v_pos, CYTHON_UNUSED long __pyx_v_index) { + int *__pyx_v_offset; + int __pyx_v_ax; + int __pyx_v_idx; + struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_v_child; + struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_r; + int __pyx_t_1; + int __pyx_t_2; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":175 + * # Find which sub-node a position should go into + * # And return the appropriate node + * cdef int* offset = malloc(sizeof(int) * node.tree.n_dimensions) # <<<<<<<<<<<<<< + * cdef int ax, idx + * cdef Node* child + */ + __pyx_v_offset = ((int *)malloc(((sizeof(int)) * __pyx_v_node->tree->n_dimensions))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":179 + * cdef Node* child + * cdef int error + * for ax in range(node.tree.n_dimensions): # <<<<<<<<<<<<<< + * offset[ax] = (pos[ax] - (node.left_edge[ax] + node.width[ax] / 2.0)) > 0. + * idx = offset2index(offset, node.tree.n_dimensions) + */ + __pyx_t_1 = __pyx_v_node->tree->n_dimensions; + for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { + __pyx_v_ax = __pyx_t_2; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":180 + * cdef int error + * for ax in range(node.tree.n_dimensions): + * offset[ax] = (pos[ax] - (node.left_edge[ax] + node.width[ax] / 2.0)) > 0. # <<<<<<<<<<<<<< + * idx = offset2index(offset, node.tree.n_dimensions) + * child = node.children[idx] + */ + (__pyx_v_offset[__pyx_v_ax]) = (((__pyx_v_pos[__pyx_v_ax]) - ((__pyx_v_node->left_edge[__pyx_v_ax]) + ((__pyx_v_node->width[__pyx_v_ax]) / 2.0))) > 0.); + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":181 + * for ax in range(node.tree.n_dimensions): + * offset[ax] = (pos[ax] - (node.left_edge[ax] + node.width[ax] / 2.0)) > 0. + * idx = offset2index(offset, node.tree.n_dimensions) # <<<<<<<<<<<<<< + * child = node.children[idx] + * if DEBUGFLAG: + */ + __pyx_v_idx = __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_offset2index(__pyx_v_offset, __pyx_v_node->tree->n_dimensions); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":182 + * offset[ax] = (pos[ax] - (node.left_edge[ax] + node.width[ax] / 2.0)) > 0. + * idx = offset2index(offset, node.tree.n_dimensions) + * child = node.children[idx] # <<<<<<<<<<<<<< + * if DEBUGFLAG: + * printf("[t-SNE] Offset [%i, %i] with LE [%f, %f]\n", + */ + __pyx_v_child = (__pyx_v_node->children[__pyx_v_idx]); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":183 + * idx = offset2index(offset, node.tree.n_dimensions) + * child = node.children[idx] + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] Offset [%i, %i] with LE [%f, %f]\n", + * offset[0], offset[1], child.left_edge[0], child.left_edge[1]) + */ + if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":184 + * child = node.children[idx] + * if DEBUGFLAG: + * printf("[t-SNE] Offset [%i, %i] with LE [%f, %f]\n", # <<<<<<<<<<<<<< + * offset[0], offset[1], child.left_edge[0], child.left_edge[1]) + * free(offset) + */ + printf(__pyx_k_t_SNE_Offset_i_i_with_LE_f_f, (__pyx_v_offset[0]), (__pyx_v_offset[1]), (__pyx_v_child->left_edge[0]), (__pyx_v_child->left_edge[1])); + goto __pyx_L5; + } + __pyx_L5:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":186 + * printf("[t-SNE] Offset [%i, %i] with LE [%f, %f]\n", + * offset[0], offset[1], child.left_edge[0], child.left_edge[1]) + * free(offset) # <<<<<<<<<<<<<< + * return child + * + */ + free(__pyx_v_offset); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":187 + * offset[0], offset[1], child.left_edge[0], child.left_edge[1]) + * free(offset) + * return child # <<<<<<<<<<<<<< + * + * + */ + __pyx_r = __pyx_v_child; + goto __pyx_L0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":172 + * return child + * + * cdef Node* select_child(Node *node, float[3] pos, long index) nogil: # <<<<<<<<<<<<<< + * # Find which sub-node a position should go into + * # And return the appropriate node + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "sklearn/manifold/_barnes_hut_tsne.pyx":190 + * + * + * cdef inline void index2offset(int* offset, int index, int n_dimensions) nogil: # <<<<<<<<<<<<<< + * # Convert a 1D index into N-D index; useful for indexing + * # children of a quadtree, octree, N-tree + */ + +static CYTHON_INLINE void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_index2offset(int *__pyx_v_offset, int __pyx_v_index, int __pyx_v_n_dimensions) { + int __pyx_v_rem; + int __pyx_v_k; + int __pyx_v_shift; + int __pyx_v_j; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + int __pyx_t_4; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":199 + * # such that the least significat bit is on the right + * cdef int rem, k, shift + * for k in range(n_dimensions): # <<<<<<<<<<<<<< + * shift = n_dimensions -k -1 + * rem = ((index >> shift) << shift) + */ + __pyx_t_1 = __pyx_v_n_dimensions; + for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { + __pyx_v_k = __pyx_t_2; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":200 + * cdef int rem, k, shift + * for k in range(n_dimensions): + * shift = n_dimensions -k -1 # <<<<<<<<<<<<<< + * rem = ((index >> shift) << shift) + * offset[k] = rem > 0 + */ + __pyx_v_shift = ((__pyx_v_n_dimensions - __pyx_v_k) - 1); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":201 + * for k in range(n_dimensions): + * shift = n_dimensions -k -1 + * rem = ((index >> shift) << shift) # <<<<<<<<<<<<<< + * offset[k] = rem > 0 + * if DEBUGFLAG: + */ + __pyx_v_rem = ((__pyx_v_index >> __pyx_v_shift) << __pyx_v_shift); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":202 + * shift = n_dimensions -k -1 + * rem = ((index >> shift) << shift) + * offset[k] = rem > 0 # <<<<<<<<<<<<<< + * if DEBUGFLAG: + * printf("i2o index %i k %i rem %i offset", index, k, rem) + */ + (__pyx_v_offset[__pyx_v_k]) = (__pyx_v_rem > 0); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":203 + * rem = ((index >> shift) << shift) + * offset[k] = rem > 0 + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("i2o index %i k %i rem %i offset", index, k, rem) + * for j in range(n_dimensions): + */ + if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":204 + * offset[k] = rem > 0 + * if DEBUGFLAG: + * printf("i2o index %i k %i rem %i offset", index, k, rem) # <<<<<<<<<<<<<< + * for j in range(n_dimensions): + * printf(" %i", offset[j]) + */ + printf(__pyx_k_i2o_index_i_k_i_rem_i_offset, __pyx_v_index, __pyx_v_k, __pyx_v_rem); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":205 + * if DEBUGFLAG: + * printf("i2o index %i k %i rem %i offset", index, k, rem) + * for j in range(n_dimensions): # <<<<<<<<<<<<<< + * printf(" %i", offset[j]) + * printf(" n_dimensions %i\n", n_dimensions) + */ + __pyx_t_3 = __pyx_v_n_dimensions; + for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { + __pyx_v_j = __pyx_t_4; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":206 + * printf("i2o index %i k %i rem %i offset", index, k, rem) + * for j in range(n_dimensions): + * printf(" %i", offset[j]) # <<<<<<<<<<<<<< + * printf(" n_dimensions %i\n", n_dimensions) + * index -= rem + */ + printf(__pyx_k_i, (__pyx_v_offset[__pyx_v_j])); + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":207 + * for j in range(n_dimensions): + * printf(" %i", offset[j]) + * printf(" n_dimensions %i\n", n_dimensions) # <<<<<<<<<<<<<< + * index -= rem + * + */ + printf(__pyx_k_n_dimensions_i, __pyx_v_n_dimensions); + goto __pyx_L5; + } + __pyx_L5:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":208 + * printf(" %i", offset[j]) + * printf(" n_dimensions %i\n", n_dimensions) + * index -= rem # <<<<<<<<<<<<<< + * + * + */ + __pyx_v_index = (__pyx_v_index - __pyx_v_rem); + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":190 + * + * + * cdef inline void index2offset(int* offset, int index, int n_dimensions) nogil: # <<<<<<<<<<<<<< + * # Convert a 1D index into N-D index; useful for indexing + * # children of a quadtree, octree, N-tree + */ + + /* function exit code */ +} + +/* "sklearn/manifold/_barnes_hut_tsne.pyx":211 + * + * + * cdef inline int offset2index(int* offset, int n_dimensions) nogil: # <<<<<<<<<<<<<< + * # Calculate the 1:1 index for a given offset array + * # We read the the offset array right-to-left + */ + +static CYTHON_INLINE int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_offset2index(int *__pyx_v_offset, int __pyx_v_n_dimensions) { + int __pyx_v_dim; + int __pyx_v_index; + int __pyx_v_j; + int __pyx_r; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + int __pyx_t_4; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":216 + * # such that the least significat bit is on the right + * cdef int dim + * cdef int index = 0 # <<<<<<<<<<<<<< + * for dim in range(n_dimensions): + * index += (2 ** dim) * offset[n_dimensions - dim - 1] + */ + __pyx_v_index = 0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":217 + * cdef int dim + * cdef int index = 0 + * for dim in range(n_dimensions): # <<<<<<<<<<<<<< + * index += (2 ** dim) * offset[n_dimensions - dim - 1] + * if DEBUGFLAG: + */ + __pyx_t_1 = __pyx_v_n_dimensions; + for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { + __pyx_v_dim = __pyx_t_2; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":218 + * cdef int index = 0 + * for dim in range(n_dimensions): + * index += (2 ** dim) * offset[n_dimensions - dim - 1] # <<<<<<<<<<<<<< + * if DEBUGFLAG: + * printf("o2i index %i dim %i offset", index, dim) + */ + __pyx_v_index = (__pyx_v_index + (__Pyx_pow_long(2, ((long)__pyx_v_dim)) * (__pyx_v_offset[((__pyx_v_n_dimensions - __pyx_v_dim) - 1)]))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":219 + * for dim in range(n_dimensions): + * index += (2 ** dim) * offset[n_dimensions - dim - 1] + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("o2i index %i dim %i offset", index, dim) + * for j in range(n_dimensions): + */ + if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":220 + * index += (2 ** dim) * offset[n_dimensions - dim - 1] + * if DEBUGFLAG: + * printf("o2i index %i dim %i offset", index, dim) # <<<<<<<<<<<<<< + * for j in range(n_dimensions): + * printf(" %i", offset[j]) + */ + printf(__pyx_k_o2i_index_i_dim_i_offset, __pyx_v_index, __pyx_v_dim); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":221 + * if DEBUGFLAG: + * printf("o2i index %i dim %i offset", index, dim) + * for j in range(n_dimensions): # <<<<<<<<<<<<<< + * printf(" %i", offset[j]) + * printf(" n_dimensions %i\n", n_dimensions) + */ + __pyx_t_3 = __pyx_v_n_dimensions; + for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { + __pyx_v_j = __pyx_t_4; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":222 + * printf("o2i index %i dim %i offset", index, dim) + * for j in range(n_dimensions): + * printf(" %i", offset[j]) # <<<<<<<<<<<<<< + * printf(" n_dimensions %i\n", n_dimensions) + * return index + */ + printf(__pyx_k_i, (__pyx_v_offset[__pyx_v_j])); + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":223 + * for j in range(n_dimensions): + * printf(" %i", offset[j]) + * printf(" n_dimensions %i\n", n_dimensions) # <<<<<<<<<<<<<< + * return index + * + */ + printf(__pyx_k_n_dimensions_i, __pyx_v_n_dimensions); + goto __pyx_L5; + } + __pyx_L5:; + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":224 + * printf(" %i", offset[j]) + * printf(" n_dimensions %i\n", n_dimensions) + * return index # <<<<<<<<<<<<<< + * + * + */ + __pyx_r = __pyx_v_index; + goto __pyx_L0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":211 + * + * + * cdef inline int offset2index(int* offset, int n_dimensions) nogil: # <<<<<<<<<<<<<< + * # Calculate the 1:1 index for a given offset array + * # We read the the offset array right-to-left + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "sklearn/manifold/_barnes_hut_tsne.pyx":227 + * + * + * cdef void subdivide(Node* node) nogil: # <<<<<<<<<<<<<< + * # This instantiates 2**n_dimensions = n_cell_per_node nodes for the current node + * cdef int idx = 0 + */ + +static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_subdivide(struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_v_node) { + int __pyx_v_idx; + int *__pyx_v_offset; + int __pyx_t_1; + int __pyx_t_2; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":229 + * cdef void subdivide(Node* node) nogil: + * # This instantiates 2**n_dimensions = n_cell_per_node nodes for the current node + * cdef int idx = 0 # <<<<<<<<<<<<<< + * cdef int* offset = malloc(sizeof(int) * node.tree.n_dimensions) + * node.is_leaf = False + */ + __pyx_v_idx = 0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":230 + * # This instantiates 2**n_dimensions = n_cell_per_node nodes for the current node + * cdef int idx = 0 + * cdef int* offset = malloc(sizeof(int) * node.tree.n_dimensions) # <<<<<<<<<<<<<< + * node.is_leaf = False + * node.children = malloc(sizeof(Node*) * node.tree.n_cell_per_node) + */ + __pyx_v_offset = ((int *)malloc(((sizeof(int)) * __pyx_v_node->tree->n_dimensions))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":231 + * cdef int idx = 0 + * cdef int* offset = malloc(sizeof(int) * node.tree.n_dimensions) + * node.is_leaf = False # <<<<<<<<<<<<<< + * node.children = malloc(sizeof(Node*) * node.tree.n_cell_per_node) + * for idx in range(node.tree.n_cell_per_node): + */ + __pyx_v_node->is_leaf = 0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":232 + * cdef int* offset = malloc(sizeof(int) * node.tree.n_dimensions) + * node.is_leaf = False + * node.children = malloc(sizeof(Node*) * node.tree.n_cell_per_node) # <<<<<<<<<<<<<< + * for idx in range(node.tree.n_cell_per_node): + * index2offset(offset, idx, node.tree.n_dimensions) + */ + __pyx_v_node->children = ((struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node **)malloc(((sizeof(struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *)) * __pyx_v_node->tree->n_cell_per_node))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":233 + * node.is_leaf = False + * node.children = malloc(sizeof(Node*) * node.tree.n_cell_per_node) + * for idx in range(node.tree.n_cell_per_node): # <<<<<<<<<<<<<< + * index2offset(offset, idx, node.tree.n_dimensions) + * node.children[idx] = create_child(node, offset) + */ + __pyx_t_1 = __pyx_v_node->tree->n_cell_per_node; + for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { + __pyx_v_idx = __pyx_t_2; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":234 + * node.children = malloc(sizeof(Node*) * node.tree.n_cell_per_node) + * for idx in range(node.tree.n_cell_per_node): + * index2offset(offset, idx, node.tree.n_dimensions) # <<<<<<<<<<<<<< + * node.children[idx] = create_child(node, offset) + * free(offset) + */ + __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_index2offset(__pyx_v_offset, __pyx_v_idx, __pyx_v_node->tree->n_dimensions); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":235 + * for idx in range(node.tree.n_cell_per_node): + * index2offset(offset, idx, node.tree.n_dimensions) + * node.children[idx] = create_child(node, offset) # <<<<<<<<<<<<<< + * free(offset) + * + */ + (__pyx_v_node->children[__pyx_v_idx]) = __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_create_child(__pyx_v_node, __pyx_v_offset); + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":236 + * index2offset(offset, idx, node.tree.n_dimensions) + * node.children[idx] = create_child(node, offset) + * free(offset) # <<<<<<<<<<<<<< + * + * + */ + free(__pyx_v_offset); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":227 + * + * + * cdef void subdivide(Node* node) nogil: # <<<<<<<<<<<<<< + * # This instantiates 2**n_dimensions = n_cell_per_node nodes for the current node + * cdef int idx = 0 + */ + + /* function exit code */ +} + +/* "sklearn/manifold/_barnes_hut_tsne.pyx":239 + * + * + * cdef int insert(Node *root, float pos[3], long point_index, long depth, long # <<<<<<<<<<<<<< + * duplicate_count) nogil: + * # Introduce a new point into the tree + */ + +static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_v_root, float *__pyx_v_pos, long __pyx_v_point_index, long __pyx_v_depth, long __pyx_v_duplicate_count) { + struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_v_child; + int __pyx_v_ax; + int __pyx_v_not_identical; + int __pyx_v_n_dimensions; + double __pyx_v_frac_seen; + double __pyx_v_frac_new; + int __pyx_r; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + int __pyx_t_4; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":248 + * cdef long i + * cdef int ax + * cdef int not_identical = 1 # <<<<<<<<<<<<<< + * cdef int n_dimensions = root.tree.n_dimensions + * if DEBUGFLAG: + */ + __pyx_v_not_identical = 1; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":249 + * cdef int ax + * cdef int not_identical = 1 + * cdef int n_dimensions = root.tree.n_dimensions # <<<<<<<<<<<<<< + * if DEBUGFLAG: + * printf("[t-SNE] [d=%i] Inserting pos %i [%f, %f] duplicate_count=%i " + */ + __pyx_t_1 = __pyx_v_root->tree->n_dimensions; + __pyx_v_n_dimensions = __pyx_t_1; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":250 + * cdef int not_identical = 1 + * cdef int n_dimensions = root.tree.n_dimensions + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] [d=%i] Inserting pos %i [%f, %f] duplicate_count=%i " + * "into child %p\n", depth, point_index, pos[0], pos[1], + */ + if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":251 + * cdef int n_dimensions = root.tree.n_dimensions + * if DEBUGFLAG: + * printf("[t-SNE] [d=%i] Inserting pos %i [%f, %f] duplicate_count=%i " # <<<<<<<<<<<<<< + * "into child %p\n", depth, point_index, pos[0], pos[1], + * duplicate_count, root) + */ + printf(__pyx_k_t_SNE_d_i_Inserting_pos_i_f_f_d, __pyx_v_depth, __pyx_v_point_index, (__pyx_v_pos[0]), (__pyx_v_pos[1]), __pyx_v_duplicate_count, __pyx_v_root); + goto __pyx_L3; + } + __pyx_L3:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":256 + * # Increment the total number points including this + * # node and below it + * root.cumulative_size += duplicate_count # <<<<<<<<<<<<<< + * # Evaluate the new center of mass, weighting the previous + * # center of mass against the new point data + */ + __pyx_v_root->cumulative_size = (__pyx_v_root->cumulative_size + __pyx_v_duplicate_count); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":259 + * # Evaluate the new center of mass, weighting the previous + * # center of mass against the new point data + * cdef double frac_seen = (root.cumulative_size - 1) / ( # <<<<<<<<<<<<<< + * root.cumulative_size) + * cdef double frac_new = 1.0 / root.cumulative_size + */ + __pyx_v_frac_seen = (((double)(__pyx_v_root->cumulative_size - 1)) / ((double)__pyx_v_root->cumulative_size)); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":261 + * cdef double frac_seen = (root.cumulative_size - 1) / ( + * root.cumulative_size) + * cdef double frac_new = 1.0 / root.cumulative_size # <<<<<<<<<<<<<< + * # Assert that duplicate_count > 0 + * if duplicate_count < 1: + */ + __pyx_v_frac_new = (1.0 / ((double)__pyx_v_root->cumulative_size)); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":263 + * cdef double frac_new = 1.0 / root.cumulative_size + * # Assert that duplicate_count > 0 + * if duplicate_count < 1: # <<<<<<<<<<<<<< + * return -1 + * # Assert that the point is inside the left & right edges + */ + __pyx_t_2 = ((__pyx_v_duplicate_count < 1) != 0); + if (__pyx_t_2) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":264 + * # Assert that duplicate_count > 0 + * if duplicate_count < 1: + * return -1 # <<<<<<<<<<<<<< + * # Assert that the point is inside the left & right edges + * for ax in range(n_dimensions): + */ + __pyx_r = -1; + goto __pyx_L0; + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":266 + * return -1 + * # Assert that the point is inside the left & right edges + * for ax in range(n_dimensions): # <<<<<<<<<<<<<< + * root.barycenter[ax] *= frac_seen + * if (pos[ax] > (root.left_edge[ax] + root.width[ax] + EPSILON)): + */ + __pyx_t_1 = __pyx_v_n_dimensions; + for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_1; __pyx_t_3+=1) { + __pyx_v_ax = __pyx_t_3; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":267 + * # Assert that the point is inside the left & right edges + * for ax in range(n_dimensions): + * root.barycenter[ax] *= frac_seen # <<<<<<<<<<<<<< + * if (pos[ax] > (root.left_edge[ax] + root.width[ax] + EPSILON)): + * printf("[t-SNE] Error: point (%1.9e) is above right edge of node " + */ + __pyx_t_4 = __pyx_v_ax; + (__pyx_v_root->barycenter[__pyx_t_4]) = ((__pyx_v_root->barycenter[__pyx_t_4]) * __pyx_v_frac_seen); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":268 + * for ax in range(n_dimensions): + * root.barycenter[ax] *= frac_seen + * if (pos[ax] > (root.left_edge[ax] + root.width[ax] + EPSILON)): # <<<<<<<<<<<<<< + * printf("[t-SNE] Error: point (%1.9e) is above right edge of node " + * "(%1.9e)\n", pos[ax], root.left_edge[ax] + root.width[ax]) + */ + __pyx_t_2 = (((__pyx_v_pos[__pyx_v_ax]) > (((__pyx_v_root->left_edge[__pyx_v_ax]) + (__pyx_v_root->width[__pyx_v_ax])) + __pyx_v_7sklearn_8manifold_16_barnes_hut_tsne_EPSILON)) != 0); + if (__pyx_t_2) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":269 + * root.barycenter[ax] *= frac_seen + * if (pos[ax] > (root.left_edge[ax] + root.width[ax] + EPSILON)): + * printf("[t-SNE] Error: point (%1.9e) is above right edge of node " # <<<<<<<<<<<<<< + * "(%1.9e)\n", pos[ax], root.left_edge[ax] + root.width[ax]) + * return -1 + */ + printf(__pyx_k_t_SNE_Error_point_1_9e_is_above, (__pyx_v_pos[__pyx_v_ax]), ((__pyx_v_root->left_edge[__pyx_v_ax]) + (__pyx_v_root->width[__pyx_v_ax]))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":271 + * printf("[t-SNE] Error: point (%1.9e) is above right edge of node " + * "(%1.9e)\n", pos[ax], root.left_edge[ax] + root.width[ax]) + * return -1 # <<<<<<<<<<<<<< + * if (pos[ax] < root.left_edge[ax] - EPSILON): + * printf("[t-SNE] Error: point (%1.9e) is below left edge of node " + */ + __pyx_r = -1; + goto __pyx_L0; + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":272 + * "(%1.9e)\n", pos[ax], root.left_edge[ax] + root.width[ax]) + * return -1 + * if (pos[ax] < root.left_edge[ax] - EPSILON): # <<<<<<<<<<<<<< + * printf("[t-SNE] Error: point (%1.9e) is below left edge of node " + * "(%1.9e)\n", pos[ax], root.left_edge[ax]) + */ + __pyx_t_2 = (((__pyx_v_pos[__pyx_v_ax]) < ((__pyx_v_root->left_edge[__pyx_v_ax]) - __pyx_v_7sklearn_8manifold_16_barnes_hut_tsne_EPSILON)) != 0); + if (__pyx_t_2) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":273 + * return -1 + * if (pos[ax] < root.left_edge[ax] - EPSILON): + * printf("[t-SNE] Error: point (%1.9e) is below left edge of node " # <<<<<<<<<<<<<< + * "(%1.9e)\n", pos[ax], root.left_edge[ax]) + * return -1 + */ + printf(__pyx_k_t_SNE_Error_point_1_9e_is_below, (__pyx_v_pos[__pyx_v_ax]), (__pyx_v_root->left_edge[__pyx_v_ax])); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":275 + * printf("[t-SNE] Error: point (%1.9e) is below left edge of node " + * "(%1.9e)\n", pos[ax], root.left_edge[ax]) + * return -1 # <<<<<<<<<<<<<< + * for ax in range(n_dimensions): + * root.barycenter[ax] += pos[ax] * frac_new + */ + __pyx_r = -1; + goto __pyx_L0; + } + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":276 + * "(%1.9e)\n", pos[ax], root.left_edge[ax]) + * return -1 + * for ax in range(n_dimensions): # <<<<<<<<<<<<<< + * root.barycenter[ax] += pos[ax] * frac_new + * + */ + __pyx_t_1 = __pyx_v_n_dimensions; + for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_1; __pyx_t_3+=1) { + __pyx_v_ax = __pyx_t_3; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":277 + * return -1 + * for ax in range(n_dimensions): + * root.barycenter[ax] += pos[ax] * frac_new # <<<<<<<<<<<<<< + * + * # If this node is unoccupied, fill it. + */ + __pyx_t_4 = __pyx_v_ax; + (__pyx_v_root->barycenter[__pyx_t_4]) = ((__pyx_v_root->barycenter[__pyx_t_4]) + ((__pyx_v_pos[__pyx_v_ax]) * __pyx_v_frac_new)); + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":284 + * # 1) Insert into this node if it is a leaf and empty + * # 2) Subdivide this node if it is currently occupied + * if (root.size == 0) & root.is_leaf: # <<<<<<<<<<<<<< + * # Root node is empty and a leaf + * if DEBUGFLAG: + */ + __pyx_t_2 = (((__pyx_v_root->size == 0) & __pyx_v_root->is_leaf) != 0); + if (__pyx_t_2) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":286 + * if (root.size == 0) & root.is_leaf: + * # Root node is empty and a leaf + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] [d=%i] Inserting [%f, %f] into blank cell\n", depth, + * pos[0], pos[1]) + */ + if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":287 + * # Root node is empty and a leaf + * if DEBUGFLAG: + * printf("[t-SNE] [d=%i] Inserting [%f, %f] into blank cell\n", depth, # <<<<<<<<<<<<<< + * pos[0], pos[1]) + * for ax in range(n_dimensions): + */ + printf(__pyx_k_t_SNE_d_i_Inserting_f_f_into_bl, __pyx_v_depth, (__pyx_v_pos[0]), (__pyx_v_pos[1])); + goto __pyx_L12; + } + __pyx_L12:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":289 + * printf("[t-SNE] [d=%i] Inserting [%f, %f] into blank cell\n", depth, + * pos[0], pos[1]) + * for ax in range(n_dimensions): # <<<<<<<<<<<<<< + * root.leaf_point_position[ax] = pos[ax] + * root.point_index = point_index + */ + __pyx_t_1 = __pyx_v_n_dimensions; + for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_1; __pyx_t_3+=1) { + __pyx_v_ax = __pyx_t_3; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":290 + * pos[0], pos[1]) + * for ax in range(n_dimensions): + * root.leaf_point_position[ax] = pos[ax] # <<<<<<<<<<<<<< + * root.point_index = point_index + * root.size = duplicate_count + */ + (__pyx_v_root->leaf_point_position[__pyx_v_ax]) = (__pyx_v_pos[__pyx_v_ax]); + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":291 + * for ax in range(n_dimensions): + * root.leaf_point_position[ax] = pos[ax] + * root.point_index = point_index # <<<<<<<<<<<<<< + * root.size = duplicate_count + * return 0 + */ + __pyx_v_root->point_index = __pyx_v_point_index; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":292 + * root.leaf_point_position[ax] = pos[ax] + * root.point_index = point_index + * root.size = duplicate_count # <<<<<<<<<<<<<< + * return 0 + * else: + */ + __pyx_v_root->size = __pyx_v_duplicate_count; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":293 + * root.point_index = point_index + * root.size = duplicate_count + * return 0 # <<<<<<<<<<<<<< + * else: + * # Root node is occupied or not a leaf + */ + __pyx_r = 0; + goto __pyx_L0; + } + /*else*/ { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":296 + * else: + * # Root node is occupied or not a leaf + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] [d=%i] Node %p is occupied or is a leaf.\n", depth, + * root) + */ + if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":297 + * # Root node is occupied or not a leaf + * if DEBUGFLAG: + * printf("[t-SNE] [d=%i] Node %p is occupied or is a leaf.\n", depth, # <<<<<<<<<<<<<< + * root) + * printf("[t-SNE] [d=%i] Node %p leaf = %i. Size %i\n", depth, root, + */ + printf(__pyx_k_t_SNE_d_i_Node_p_is_occupied_or, __pyx_v_depth, __pyx_v_root); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":299 + * printf("[t-SNE] [d=%i] Node %p is occupied or is a leaf.\n", depth, + * root) + * printf("[t-SNE] [d=%i] Node %p leaf = %i. Size %i\n", depth, root, # <<<<<<<<<<<<<< + * root.is_leaf, root.size) + * if root.is_leaf & (root.size > 0): + */ + printf(__pyx_k_t_SNE_d_i_Node_p_leaf_i_Size_i, __pyx_v_depth, __pyx_v_root, __pyx_v_root->is_leaf, __pyx_v_root->size); + goto __pyx_L15; + } + __pyx_L15:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":301 + * printf("[t-SNE] [d=%i] Node %p leaf = %i. Size %i\n", depth, root, + * root.is_leaf, root.size) + * if root.is_leaf & (root.size > 0): # <<<<<<<<<<<<<< + * # is a leaf node and is occupied + * for ax in range(n_dimensions): + */ + __pyx_t_2 = ((__pyx_v_root->is_leaf & (__pyx_v_root->size > 0)) != 0); + if (__pyx_t_2) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":303 + * if root.is_leaf & (root.size > 0): + * # is a leaf node and is occupied + * for ax in range(n_dimensions): # <<<<<<<<<<<<<< + * not_identical &= (fabsf(pos[ax] - root.leaf_point_position[ax]) < EPSILON) + * not_identical &= (root.point_index != point_index) + */ + __pyx_t_1 = __pyx_v_n_dimensions; + for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_1; __pyx_t_3+=1) { + __pyx_v_ax = __pyx_t_3; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":304 + * # is a leaf node and is occupied + * for ax in range(n_dimensions): + * not_identical &= (fabsf(pos[ax] - root.leaf_point_position[ax]) < EPSILON) # <<<<<<<<<<<<<< + * not_identical &= (root.point_index != point_index) + * if not_identical == 1: + */ + __pyx_v_not_identical = (__pyx_v_not_identical & (fabsf(((__pyx_v_pos[__pyx_v_ax]) - (__pyx_v_root->leaf_point_position[__pyx_v_ax]))) < __pyx_v_7sklearn_8manifold_16_barnes_hut_tsne_EPSILON)); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":305 + * for ax in range(n_dimensions): + * not_identical &= (fabsf(pos[ax] - root.leaf_point_position[ax]) < EPSILON) + * not_identical &= (root.point_index != point_index) # <<<<<<<<<<<<<< + * if not_identical == 1: + * root.size += duplicate_count + */ + __pyx_v_not_identical = (__pyx_v_not_identical & (__pyx_v_root->point_index != __pyx_v_point_index)); + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":306 + * not_identical &= (fabsf(pos[ax] - root.leaf_point_position[ax]) < EPSILON) + * not_identical &= (root.point_index != point_index) + * if not_identical == 1: # <<<<<<<<<<<<<< + * root.size += duplicate_count + * if DEBUGFLAG: + */ + __pyx_t_2 = ((__pyx_v_not_identical == 1) != 0); + if (__pyx_t_2) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":307 + * not_identical &= (root.point_index != point_index) + * if not_identical == 1: + * root.size += duplicate_count # <<<<<<<<<<<<<< + * if DEBUGFLAG: + * printf("[t-SNE] Warning: [d=%i] Detected identical " + */ + __pyx_v_root->size = (__pyx_v_root->size + __pyx_v_duplicate_count); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":308 + * if not_identical == 1: + * root.size += duplicate_count + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] Warning: [d=%i] Detected identical " + * "points. Returning. Leaf now has size %i\n", + */ + if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":309 + * root.size += duplicate_count + * if DEBUGFLAG: + * printf("[t-SNE] Warning: [d=%i] Detected identical " # <<<<<<<<<<<<<< + * "points. Returning. Leaf now has size %i\n", + * depth, root.size) + */ + printf(__pyx_k_t_SNE_Warning_d_i_Detected_iden, __pyx_v_depth, __pyx_v_root->size); + goto __pyx_L20; + } + __pyx_L20:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":312 + * "points. Returning. Leaf now has size %i\n", + * depth, root.size) + * return 0 # <<<<<<<<<<<<<< + * # If necessary, subdivide this node before + * # descending + */ + __pyx_r = 0; + goto __pyx_L0; + } + goto __pyx_L16; + } + __pyx_L16:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":315 + * # If necessary, subdivide this node before + * # descending + * if root.is_leaf: # <<<<<<<<<<<<<< + * if DEBUGFLAG: + * printf("[t-SNE] [d=%i] Subdividing this leaf node %p\n", depth, + */ + __pyx_t_2 = (__pyx_v_root->is_leaf != 0); + if (__pyx_t_2) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":316 + * # descending + * if root.is_leaf: + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] [d=%i] Subdividing this leaf node %p\n", depth, + * root) + */ + if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":317 + * if root.is_leaf: + * if DEBUGFLAG: + * printf("[t-SNE] [d=%i] Subdividing this leaf node %p\n", depth, # <<<<<<<<<<<<<< + * root) + * subdivide(root) + */ + printf(__pyx_k_t_SNE_d_i_Subdividing_this_leaf, __pyx_v_depth, __pyx_v_root); + goto __pyx_L22; + } + __pyx_L22:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":319 + * printf("[t-SNE] [d=%i] Subdividing this leaf node %p\n", depth, + * root) + * subdivide(root) # <<<<<<<<<<<<<< + * # We have two points to relocate: the one previously + * # at this node, and the new one we're attempting + */ + __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_subdivide(__pyx_v_root); + goto __pyx_L21; + } + __pyx_L21:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":323 + * # at this node, and the new one we're attempting + * # to insert + * if root.size > 0: # <<<<<<<<<<<<<< + * child = select_child(root, root.leaf_point_position, root.point_index) + * if DEBUGFLAG: + */ + __pyx_t_2 = ((__pyx_v_root->size > 0) != 0); + if (__pyx_t_2) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":324 + * # to insert + * if root.size > 0: + * child = select_child(root, root.leaf_point_position, root.point_index) # <<<<<<<<<<<<<< + * if DEBUGFLAG: + * printf("[t-SNE] [d=%i] Relocating old point to node %p\n", + */ + __pyx_v_child = __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_select_child(__pyx_v_root, __pyx_v_root->leaf_point_position, __pyx_v_root->point_index); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":325 + * if root.size > 0: + * child = select_child(root, root.leaf_point_position, root.point_index) + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] [d=%i] Relocating old point to node %p\n", + * depth, child) + */ + if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":326 + * child = select_child(root, root.leaf_point_position, root.point_index) + * if DEBUGFLAG: + * printf("[t-SNE] [d=%i] Relocating old point to node %p\n", # <<<<<<<<<<<<<< + * depth, child) + * insert(child, root.leaf_point_position, root.point_index, depth + 1, root.size) + */ + printf(__pyx_k_t_SNE_d_i_Relocating_old_point, __pyx_v_depth, __pyx_v_child); + goto __pyx_L24; + } + __pyx_L24:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":328 + * printf("[t-SNE] [d=%i] Relocating old point to node %p\n", + * depth, child) + * insert(child, root.leaf_point_position, root.point_index, depth + 1, root.size) # <<<<<<<<<<<<<< + * # Insert the new point + * if DEBUGFLAG: + */ + __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(__pyx_v_child, __pyx_v_root->leaf_point_position, __pyx_v_root->point_index, (__pyx_v_depth + 1), __pyx_v_root->size); + goto __pyx_L23; + } + __pyx_L23:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":330 + * insert(child, root.leaf_point_position, root.point_index, depth + 1, root.size) + * # Insert the new point + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] [d=%i] Selecting node for new point\n", depth) + * child = select_child(root, pos, point_index) + */ + if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":331 + * # Insert the new point + * if DEBUGFLAG: + * printf("[t-SNE] [d=%i] Selecting node for new point\n", depth) # <<<<<<<<<<<<<< + * child = select_child(root, pos, point_index) + * if root.size > 0: + */ + printf(__pyx_k_t_SNE_d_i_Selecting_node_for_ne, __pyx_v_depth); + goto __pyx_L25; + } + __pyx_L25:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":332 + * if DEBUGFLAG: + * printf("[t-SNE] [d=%i] Selecting node for new point\n", depth) + * child = select_child(root, pos, point_index) # <<<<<<<<<<<<<< + * if root.size > 0: + * # Remove the point from this node + */ + __pyx_v_child = __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_select_child(__pyx_v_root, __pyx_v_pos, __pyx_v_point_index); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":333 + * printf("[t-SNE] [d=%i] Selecting node for new point\n", depth) + * child = select_child(root, pos, point_index) + * if root.size > 0: # <<<<<<<<<<<<<< + * # Remove the point from this node + * for ax in range(n_dimensions): + */ + __pyx_t_2 = ((__pyx_v_root->size > 0) != 0); + if (__pyx_t_2) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":335 + * if root.size > 0: + * # Remove the point from this node + * for ax in range(n_dimensions): # <<<<<<<<<<<<<< + * root.leaf_point_position[ax] = -1 + * root.size = 0 + */ + __pyx_t_1 = __pyx_v_n_dimensions; + for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_1; __pyx_t_3+=1) { + __pyx_v_ax = __pyx_t_3; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":336 + * # Remove the point from this node + * for ax in range(n_dimensions): + * root.leaf_point_position[ax] = -1 # <<<<<<<<<<<<<< + * root.size = 0 + * root.point_index = -1 + */ + (__pyx_v_root->leaf_point_position[__pyx_v_ax]) = -1.0; + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":337 + * for ax in range(n_dimensions): + * root.leaf_point_position[ax] = -1 + * root.size = 0 # <<<<<<<<<<<<<< + * root.point_index = -1 + * return insert(child, pos, point_index, depth + 1, 1) + */ + __pyx_v_root->size = 0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":338 + * root.leaf_point_position[ax] = -1 + * root.size = 0 + * root.point_index = -1 # <<<<<<<<<<<<<< + * return insert(child, pos, point_index, depth + 1, 1) + * + */ + __pyx_v_root->point_index = -1; + goto __pyx_L26; + } + __pyx_L26:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":339 + * root.size = 0 + * root.point_index = -1 + * return insert(child, pos, point_index, depth + 1, 1) # <<<<<<<<<<<<<< + * + * cdef int insert_many(Tree* tree, float[:,:] pos_array) nogil: + */ + __pyx_r = __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(__pyx_v_child, __pyx_v_pos, __pyx_v_point_index, (__pyx_v_depth + 1), 1); + goto __pyx_L0; + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":239 + * + * + * cdef int insert(Node *root, float pos[3], long point_index, long depth, long # <<<<<<<<<<<<<< + * duplicate_count) nogil: + * # Introduce a new point into the tree + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "sklearn/manifold/_barnes_hut_tsne.pyx":341 + * return insert(child, pos, point_index, depth + 1, 1) + * + * cdef int insert_many(Tree* tree, float[:,:] pos_array) nogil: # <<<<<<<<<<<<<< + * # Insert each data point into the tree one at a time + * cdef long nrows = pos_array.shape[0] + */ + +static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert_many(struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *__pyx_v_tree, __Pyx_memviewslice __pyx_v_pos_array) { + long __pyx_v_nrows; + long __pyx_v_i; + int __pyx_v_ax; + float __pyx_v_row[3]; + long __pyx_v_err; + int __pyx_r; + long __pyx_t_1; + long __pyx_t_2; + int __pyx_t_3; + int __pyx_t_4; + long __pyx_t_5; + int __pyx_t_6; + int __pyx_t_7; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":343 + * cdef int insert_many(Tree* tree, float[:,:] pos_array) nogil: + * # Insert each data point into the tree one at a time + * cdef long nrows = pos_array.shape[0] # <<<<<<<<<<<<<< + * cdef long i + * cdef int ax + */ + __pyx_v_nrows = (__pyx_v_pos_array.shape[0]); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":347 + * cdef int ax + * cdef float row[3] + * cdef long err = 0 # <<<<<<<<<<<<<< + * for i in range(nrows): + * for ax in range(tree.n_dimensions): + */ + __pyx_v_err = 0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":348 + * cdef float row[3] + * cdef long err = 0 + * for i in range(nrows): # <<<<<<<<<<<<<< + * for ax in range(tree.n_dimensions): + * row[ax] = pos_array[i, ax] + */ + __pyx_t_1 = __pyx_v_nrows; + for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { + __pyx_v_i = __pyx_t_2; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":349 + * cdef long err = 0 + * for i in range(nrows): + * for ax in range(tree.n_dimensions): # <<<<<<<<<<<<<< + * row[ax] = pos_array[i, ax] + * if DEBUGFLAG: + */ + __pyx_t_3 = __pyx_v_tree->n_dimensions; + for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { + __pyx_v_ax = __pyx_t_4; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":350 + * for i in range(nrows): + * for ax in range(tree.n_dimensions): + * row[ax] = pos_array[i, ax] # <<<<<<<<<<<<<< + * if DEBUGFLAG: + * printf("[t-SNE] inserting point %i: [%f, %f]\n", i, row[0], row[1]) + */ + __pyx_t_5 = __pyx_v_i; + __pyx_t_6 = __pyx_v_ax; + (__pyx_v_row[__pyx_v_ax]) = (*((float *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_pos_array.data + __pyx_t_5 * __pyx_v_pos_array.strides[0]) ) + __pyx_t_6 * __pyx_v_pos_array.strides[1]) ))); + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":351 + * for ax in range(tree.n_dimensions): + * row[ax] = pos_array[i, ax] + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] inserting point %i: [%f, %f]\n", i, row[0], row[1]) + * err = insert(tree.root_node, row, i, 0, 1) + */ + if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":352 + * row[ax] = pos_array[i, ax] + * if DEBUGFLAG: + * printf("[t-SNE] inserting point %i: [%f, %f]\n", i, row[0], row[1]) # <<<<<<<<<<<<<< + * err = insert(tree.root_node, row, i, 0, 1) + * if err != 0: + */ + printf(__pyx_k_t_SNE_inserting_point_i_f_f, __pyx_v_i, (__pyx_v_row[0]), (__pyx_v_row[1])); + goto __pyx_L7; + } + __pyx_L7:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":353 + * if DEBUGFLAG: + * printf("[t-SNE] inserting point %i: [%f, %f]\n", i, row[0], row[1]) + * err = insert(tree.root_node, row, i, 0, 1) # <<<<<<<<<<<<<< + * if err != 0: + * printf("[t-SNE] ERROR\n") + */ + __pyx_v_err = __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(__pyx_v_tree->root_node, __pyx_v_row, __pyx_v_i, 0, 1); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":354 + * printf("[t-SNE] inserting point %i: [%f, %f]\n", i, row[0], row[1]) + * err = insert(tree.root_node, row, i, 0, 1) + * if err != 0: # <<<<<<<<<<<<<< + * printf("[t-SNE] ERROR\n") + * return err + */ + __pyx_t_7 = ((__pyx_v_err != 0) != 0); + if (__pyx_t_7) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":355 + * err = insert(tree.root_node, row, i, 0, 1) + * if err != 0: + * printf("[t-SNE] ERROR\n") # <<<<<<<<<<<<<< + * return err + * tree.n_points += 1 + */ + printf(__pyx_k_t_SNE_ERROR); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":356 + * if err != 0: + * printf("[t-SNE] ERROR\n") + * return err # <<<<<<<<<<<<<< + * tree.n_points += 1 + * return err + */ + __pyx_r = __pyx_v_err; + goto __pyx_L0; + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":357 + * printf("[t-SNE] ERROR\n") + * return err + * tree.n_points += 1 # <<<<<<<<<<<<<< + * return err + * + */ + __pyx_v_tree->n_points = (__pyx_v_tree->n_points + 1); + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":358 + * return err + * tree.n_points += 1 + * return err # <<<<<<<<<<<<<< + * + * cdef int free_tree(Tree* tree) nogil: + */ + __pyx_r = __pyx_v_err; + goto __pyx_L0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":341 + * return insert(child, pos, point_index, depth + 1, 1) + * + * cdef int insert_many(Tree* tree, float[:,:] pos_array) nogil: # <<<<<<<<<<<<<< + * # Insert each data point into the tree one at a time + * cdef long nrows = pos_array.shape[0] + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "sklearn/manifold/_barnes_hut_tsne.pyx":360 + * return err + * + * cdef int free_tree(Tree* tree) nogil: # <<<<<<<<<<<<<< + * cdef int check + * cdef long* cnt = malloc(sizeof(long) * 3) + */ + +static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_tree(struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *__pyx_v_tree) { + int __pyx_v_check; + long *__pyx_v_cnt; + long __pyx_v_i; + int __pyx_r; + long __pyx_t_1; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":362 + * cdef int free_tree(Tree* tree) nogil: + * cdef int check + * cdef long* cnt = malloc(sizeof(long) * 3) # <<<<<<<<<<<<<< + * for i in range(3): + * cnt[i] = 0 + */ + __pyx_v_cnt = ((long *)malloc(((sizeof(long)) * 3))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":363 + * cdef int check + * cdef long* cnt = malloc(sizeof(long) * 3) + * for i in range(3): # <<<<<<<<<<<<<< + * cnt[i] = 0 + * free_recursive(tree, tree.root_node, cnt) + */ + for (__pyx_t_1 = 0; __pyx_t_1 < 3; __pyx_t_1+=1) { + __pyx_v_i = __pyx_t_1; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":364 + * cdef long* cnt = malloc(sizeof(long) * 3) + * for i in range(3): + * cnt[i] = 0 # <<<<<<<<<<<<<< + * free_recursive(tree, tree.root_node, cnt) + * free(tree.root_node) + */ + (__pyx_v_cnt[__pyx_v_i]) = 0; + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":365 + * for i in range(3): + * cnt[i] = 0 + * free_recursive(tree, tree.root_node, cnt) # <<<<<<<<<<<<<< + * free(tree.root_node) + * free(tree) + */ + __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_recursive(__pyx_v_tree, __pyx_v_tree->root_node, __pyx_v_cnt); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":366 + * cnt[i] = 0 + * free_recursive(tree, tree.root_node, cnt) + * free(tree.root_node) # <<<<<<<<<<<<<< + * free(tree) + * check = cnt[0] == tree.n_cells + */ + free(__pyx_v_tree->root_node); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":367 + * free_recursive(tree, tree.root_node, cnt) + * free(tree.root_node) + * free(tree) # <<<<<<<<<<<<<< + * check = cnt[0] == tree.n_cells + * check &= cnt[2] == tree.n_points + */ + free(__pyx_v_tree); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":368 + * free(tree.root_node) + * free(tree) + * check = cnt[0] == tree.n_cells # <<<<<<<<<<<<<< + * check &= cnt[2] == tree.n_points + * free(cnt) + */ + __pyx_v_check = ((__pyx_v_cnt[0]) == __pyx_v_tree->n_cells); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":369 + * free(tree) + * check = cnt[0] == tree.n_cells + * check &= cnt[2] == tree.n_points # <<<<<<<<<<<<<< + * free(cnt) + * return check + */ + __pyx_v_check = (__pyx_v_check & ((__pyx_v_cnt[2]) == __pyx_v_tree->n_points)); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":370 + * check = cnt[0] == tree.n_cells + * check &= cnt[2] == tree.n_points + * free(cnt) # <<<<<<<<<<<<<< + * return check + * + */ + free(__pyx_v_cnt); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":371 + * check &= cnt[2] == tree.n_points + * free(cnt) + * return check # <<<<<<<<<<<<<< + * + * cdef void free_recursive(Tree* tree, Node *root, long* counts) nogil: + */ + __pyx_r = __pyx_v_check; + goto __pyx_L0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":360 + * return err + * + * cdef int free_tree(Tree* tree) nogil: # <<<<<<<<<<<<<< + * cdef int check + * cdef long* cnt = malloc(sizeof(long) * 3) + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "sklearn/manifold/_barnes_hut_tsne.pyx":373 + * return check + * + * cdef void free_recursive(Tree* tree, Node *root, long* counts) nogil: # <<<<<<<<<<<<<< + * # Free up all of the tree nodes recursively + * # while counting the number of nodes visited + */ + +static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_recursive(struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *__pyx_v_tree, struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_v_root, long *__pyx_v_counts) { + int __pyx_v_idx; + struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_v_child; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + long __pyx_t_4; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":379 + * cdef int idx + * cdef Node* child + * if not root.is_leaf: # <<<<<<<<<<<<<< + * for idx in range(tree.n_cell_per_node): + * child = root.children[idx] + */ + __pyx_t_1 = ((!(__pyx_v_root->is_leaf != 0)) != 0); + if (__pyx_t_1) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":380 + * cdef Node* child + * if not root.is_leaf: + * for idx in range(tree.n_cell_per_node): # <<<<<<<<<<<<<< + * child = root.children[idx] + * free_recursive(tree, child, counts) + */ + __pyx_t_2 = __pyx_v_tree->n_cell_per_node; + for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { + __pyx_v_idx = __pyx_t_3; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":381 + * if not root.is_leaf: + * for idx in range(tree.n_cell_per_node): + * child = root.children[idx] # <<<<<<<<<<<<<< + * free_recursive(tree, child, counts) + * counts[0] += 1 + */ + __pyx_v_child = (__pyx_v_root->children[__pyx_v_idx]); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":382 + * for idx in range(tree.n_cell_per_node): + * child = root.children[idx] + * free_recursive(tree, child, counts) # <<<<<<<<<<<<<< + * counts[0] += 1 + * if child.is_leaf: + */ + __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_recursive(__pyx_v_tree, __pyx_v_child, __pyx_v_counts); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":383 + * child = root.children[idx] + * free_recursive(tree, child, counts) + * counts[0] += 1 # <<<<<<<<<<<<<< + * if child.is_leaf: + * counts[1] += 1 + */ + __pyx_t_4 = 0; + (__pyx_v_counts[__pyx_t_4]) = ((__pyx_v_counts[__pyx_t_4]) + 1); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":384 + * free_recursive(tree, child, counts) + * counts[0] += 1 + * if child.is_leaf: # <<<<<<<<<<<<<< + * counts[1] += 1 + * if child.size > 0: + */ + __pyx_t_1 = (__pyx_v_child->is_leaf != 0); + if (__pyx_t_1) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":385 + * counts[0] += 1 + * if child.is_leaf: + * counts[1] += 1 # <<<<<<<<<<<<<< + * if child.size > 0: + * counts[2] +=1 + */ + __pyx_t_4 = 1; + (__pyx_v_counts[__pyx_t_4]) = ((__pyx_v_counts[__pyx_t_4]) + 1); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":386 + * if child.is_leaf: + * counts[1] += 1 + * if child.size > 0: # <<<<<<<<<<<<<< + * counts[2] +=1 + * else: + */ + __pyx_t_1 = ((__pyx_v_child->size > 0) != 0); + if (__pyx_t_1) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":387 + * counts[1] += 1 + * if child.size > 0: + * counts[2] +=1 # <<<<<<<<<<<<<< + * else: + * free(child.children) + */ + __pyx_t_4 = 2; + (__pyx_v_counts[__pyx_t_4]) = ((__pyx_v_counts[__pyx_t_4]) + 1); + goto __pyx_L7; + } + __pyx_L7:; + goto __pyx_L6; + } + /*else*/ { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":389 + * counts[2] +=1 + * else: + * free(child.children) # <<<<<<<<<<<<<< + * free(child.width) + * free(child.left_edge) + */ + free(__pyx_v_child->children); + } + __pyx_L6:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":390 + * else: + * free(child.children) + * free(child.width) # <<<<<<<<<<<<<< + * free(child.left_edge) + * free(child.center) + */ + free(__pyx_v_child->width); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":391 + * free(child.children) + * free(child.width) + * free(child.left_edge) # <<<<<<<<<<<<<< + * free(child.center) + * free(child.barycenter) + */ + free(__pyx_v_child->left_edge); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":392 + * free(child.width) + * free(child.left_edge) + * free(child.center) # <<<<<<<<<<<<<< + * free(child.barycenter) + * free(child.leaf_point_position) + */ + free(__pyx_v_child->center); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":393 + * free(child.left_edge) + * free(child.center) + * free(child.barycenter) # <<<<<<<<<<<<<< + * free(child.leaf_point_position) + * free(child) + */ + free(__pyx_v_child->barycenter); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":394 + * free(child.center) + * free(child.barycenter) + * free(child.leaf_point_position) # <<<<<<<<<<<<<< + * free(child) + * + */ + free(__pyx_v_child->leaf_point_position); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":395 + * free(child.barycenter) + * free(child.leaf_point_position) + * free(child) # <<<<<<<<<<<<<< + * + * + */ + free(__pyx_v_child); + } + goto __pyx_L3; + } + __pyx_L3:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":373 + * return check + * + * cdef void free_recursive(Tree* tree, Node *root, long* counts) nogil: # <<<<<<<<<<<<<< + * # Free up all of the tree nodes recursively + * # while counting the number of nodes visited + */ + + /* function exit code */ +} + +/* "sklearn/manifold/_barnes_hut_tsne.pyx":398 + * + * + * cdef long count_points(Node* root, long count) nogil: # <<<<<<<<<<<<<< + * # Walk through the whole tree and count the number + * # of points at the leaf nodes + */ + +static long __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_count_points(struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_v_root, long __pyx_v_count) { + struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_v_child; + int __pyx_v_idx; + long __pyx_r; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + int __pyx_t_4; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":401 + * # Walk through the whole tree and count the number + * # of points at the leaf nodes + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] Counting nodes at root node %p\n", root) + * cdef Node* child + */ + if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":402 + * # of points at the leaf nodes + * if DEBUGFLAG: + * printf("[t-SNE] Counting nodes at root node %p\n", root) # <<<<<<<<<<<<<< + * cdef Node* child + * cdef int idx + */ + printf(__pyx_k_t_SNE_Counting_nodes_at_root_no, __pyx_v_root); + goto __pyx_L3; + } + __pyx_L3:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":405 + * cdef Node* child + * cdef int idx + * if root.is_leaf: # <<<<<<<<<<<<<< + * count += root.size + * if DEBUGFLAG : + */ + __pyx_t_1 = (__pyx_v_root->is_leaf != 0); + if (__pyx_t_1) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":406 + * cdef int idx + * if root.is_leaf: + * count += root.size # <<<<<<<<<<<<<< + * if DEBUGFLAG : + * printf("[t-SNE] %p is a leaf node, no children\n", root) + */ + __pyx_v_count = (__pyx_v_count + __pyx_v_root->size); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":407 + * if root.is_leaf: + * count += root.size + * if DEBUGFLAG : # <<<<<<<<<<<<<< + * printf("[t-SNE] %p is a leaf node, no children\n", root) + * printf("[t-SNE] %i points in node %p\n", count, root) + */ + if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":408 + * count += root.size + * if DEBUGFLAG : + * printf("[t-SNE] %p is a leaf node, no children\n", root) # <<<<<<<<<<<<<< + * printf("[t-SNE] %i points in node %p\n", count, root) + * return count + */ + printf(__pyx_k_t_SNE_p_is_a_leaf_node_no_child, __pyx_v_root); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":409 + * if DEBUGFLAG : + * printf("[t-SNE] %p is a leaf node, no children\n", root) + * printf("[t-SNE] %i points in node %p\n", count, root) # <<<<<<<<<<<<<< + * return count + * # Otherwise, get the children + */ + printf(__pyx_k_t_SNE_i_points_in_node_p, __pyx_v_count, __pyx_v_root); + goto __pyx_L5; + } + __pyx_L5:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":410 + * printf("[t-SNE] %p is a leaf node, no children\n", root) + * printf("[t-SNE] %i points in node %p\n", count, root) + * return count # <<<<<<<<<<<<<< + * # Otherwise, get the children + * for idx in range(root.tree.n_cell_per_node): + */ + __pyx_r = __pyx_v_count; + goto __pyx_L0; + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":412 + * return count + * # Otherwise, get the children + * for idx in range(root.tree.n_cell_per_node): # <<<<<<<<<<<<<< + * child = root.children[idx] + * if DEBUGFLAG: + */ + __pyx_t_2 = __pyx_v_root->tree->n_cell_per_node; + for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { + __pyx_v_idx = __pyx_t_3; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":413 + * # Otherwise, get the children + * for idx in range(root.tree.n_cell_per_node): + * child = root.children[idx] # <<<<<<<<<<<<<< + * if DEBUGFLAG: + * printf("[t-SNE] Counting points for child %p\n", child) + */ + __pyx_v_child = (__pyx_v_root->children[__pyx_v_idx]); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":414 + * for idx in range(root.tree.n_cell_per_node): + * child = root.children[idx] + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] Counting points for child %p\n", child) + * if child.is_leaf and child.size > 0: + */ + if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":415 + * child = root.children[idx] + * if DEBUGFLAG: + * printf("[t-SNE] Counting points for child %p\n", child) # <<<<<<<<<<<<<< + * if child.is_leaf and child.size > 0: + * if DEBUGFLAG: + */ + printf(__pyx_k_t_SNE_Counting_points_for_child, __pyx_v_child); + goto __pyx_L8; + } + __pyx_L8:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":416 + * if DEBUGFLAG: + * printf("[t-SNE] Counting points for child %p\n", child) + * if child.is_leaf and child.size > 0: # <<<<<<<<<<<<<< + * if DEBUGFLAG: + * printf("[t-SNE] Child has size %d\n", child.size) + */ + __pyx_t_4 = (__pyx_v_child->is_leaf != 0); + if (__pyx_t_4) { + goto __pyx_L11_next_and; + } else { + __pyx_t_1 = __pyx_t_4; + goto __pyx_L10_bool_binop_done; + } + __pyx_L11_next_and:; + __pyx_t_4 = ((__pyx_v_child->size > 0) != 0); + __pyx_t_1 = __pyx_t_4; + __pyx_L10_bool_binop_done:; + if (__pyx_t_1) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":417 + * printf("[t-SNE] Counting points for child %p\n", child) + * if child.is_leaf and child.size > 0: + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] Child has size %d\n", child.size) + * count += child.size + */ + if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":418 + * if child.is_leaf and child.size > 0: + * if DEBUGFLAG: + * printf("[t-SNE] Child has size %d\n", child.size) # <<<<<<<<<<<<<< + * count += child.size + * elif not child.is_leaf: + */ + printf(__pyx_k_t_SNE_Child_has_size_d, __pyx_v_child->size); + goto __pyx_L12; + } + __pyx_L12:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":419 + * if DEBUGFLAG: + * printf("[t-SNE] Child has size %d\n", child.size) + * count += child.size # <<<<<<<<<<<<<< + * elif not child.is_leaf: + * if DEBUGFLAG: + */ + __pyx_v_count = (__pyx_v_count + __pyx_v_child->size); + goto __pyx_L9; + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":420 + * printf("[t-SNE] Child has size %d\n", child.size) + * count += child.size + * elif not child.is_leaf: # <<<<<<<<<<<<<< + * if DEBUGFLAG: + * printf("[t-SNE] Child is not a leaf. Descending\n") + */ + __pyx_t_1 = ((!(__pyx_v_child->is_leaf != 0)) != 0); + if (__pyx_t_1) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":421 + * count += child.size + * elif not child.is_leaf: + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] Child is not a leaf. Descending\n") + * count = count_points(child, count) + */ + if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":422 + * elif not child.is_leaf: + * if DEBUGFLAG: + * printf("[t-SNE] Child is not a leaf. Descending\n") # <<<<<<<<<<<<<< + * count = count_points(child, count) + * # else case is we have an empty leaf node + */ + printf(__pyx_k_t_SNE_Child_is_not_a_leaf_Desce); + goto __pyx_L13; + } + __pyx_L13:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":423 + * if DEBUGFLAG: + * printf("[t-SNE] Child is not a leaf. Descending\n") + * count = count_points(child, count) # <<<<<<<<<<<<<< + * # else case is we have an empty leaf node + * # which happens when we create a quadtree for + */ + __pyx_v_count = __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_count_points(__pyx_v_child, __pyx_v_count); + goto __pyx_L9; + } + __pyx_L9:; + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":428 + * # one point, and then the other neighboring cells + * # don't get filled in + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] %i points in this node\n", count) + * return count + */ + if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":429 + * # don't get filled in + * if DEBUGFLAG: + * printf("[t-SNE] %i points in this node\n", count) # <<<<<<<<<<<<<< + * return count + * + */ + printf(__pyx_k_t_SNE_i_points_in_this_node, __pyx_v_count); + goto __pyx_L14; + } + __pyx_L14:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":430 + * if DEBUGFLAG: + * printf("[t-SNE] %i points in this node\n", count) + * return count # <<<<<<<<<<<<<< + * + * + */ + __pyx_r = __pyx_v_count; + goto __pyx_L0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":398 + * + * + * cdef long count_points(Node* root, long count) nogil: # <<<<<<<<<<<<<< + * # Walk through the whole tree and count the number + * # of points at the leaf nodes + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "sklearn/manifold/_barnes_hut_tsne.pyx":433 + * + * + * cdef float compute_gradient(float[:,:] val_P, # <<<<<<<<<<<<<< + * float[:,:] pos_reference, + * long[:,:] neighbors, + */ + +static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Pyx_memviewslice __pyx_v_val_P, __Pyx_memviewslice __pyx_v_pos_reference, __Pyx_memviewslice __pyx_v_neighbors, __Pyx_memviewslice __pyx_v_tot_force, struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_v_root_node, float __pyx_v_theta, float __pyx_v_dof, long __pyx_v_start, long __pyx_v_stop) { + long __pyx_v_i; + long __pyx_v_coord; + int __pyx_v_ax; + long __pyx_v_n; + int __pyx_v_n_dimensions; + float *__pyx_v_sum_Q; + float *__pyx_v_neg_f; + float *__pyx_v_neg_f_fast; + float *__pyx_v_pos_f; + clock_t __pyx_v_t1; + clock_t __pyx_v_t2; + float __pyx_v_sQ; + CYTHON_UNUSED float __pyx_v_error; + float __pyx_r; + int __pyx_t_1; + int __pyx_t_2; + long __pyx_t_3; + long __pyx_t_4; + int __pyx_t_5; + long __pyx_t_6; + int __pyx_t_7; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":446 + * cdef long i, coord + * cdef int ax + * cdef long n = pos_reference.shape[0] # <<<<<<<<<<<<<< + * cdef int n_dimensions = root_node.tree.n_dimensions + * if root_node.tree.verbose > 11: + */ + __pyx_v_n = (__pyx_v_pos_reference.shape[0]); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":447 + * cdef int ax + * cdef long n = pos_reference.shape[0] + * cdef int n_dimensions = root_node.tree.n_dimensions # <<<<<<<<<<<<<< + * if root_node.tree.verbose > 11: + * printf("[t-SNE] Allocating %i elements in force arrays\n", + */ + __pyx_t_1 = __pyx_v_root_node->tree->n_dimensions; + __pyx_v_n_dimensions = __pyx_t_1; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":448 + * cdef long n = pos_reference.shape[0] + * cdef int n_dimensions = root_node.tree.n_dimensions + * if root_node.tree.verbose > 11: # <<<<<<<<<<<<<< + * printf("[t-SNE] Allocating %i elements in force arrays\n", + * n * n_dimensions * 2) + */ + __pyx_t_2 = ((__pyx_v_root_node->tree->verbose > 11) != 0); + if (__pyx_t_2) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":449 + * cdef int n_dimensions = root_node.tree.n_dimensions + * if root_node.tree.verbose > 11: + * printf("[t-SNE] Allocating %i elements in force arrays\n", # <<<<<<<<<<<<<< + * n * n_dimensions * 2) + * cdef float* sum_Q = malloc(sizeof(float)) + */ + printf(__pyx_k_t_SNE_Allocating_i_elements_in, ((__pyx_v_n * __pyx_v_n_dimensions) * 2)); + goto __pyx_L3; + } + __pyx_L3:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":451 + * printf("[t-SNE] Allocating %i elements in force arrays\n", + * n * n_dimensions * 2) + * cdef float* sum_Q = malloc(sizeof(float)) # <<<<<<<<<<<<<< + * cdef float* neg_f = malloc(sizeof(float) * n * n_dimensions) + * cdef float* neg_f_fast = malloc(sizeof(float) * n * n_dimensions) + */ + __pyx_v_sum_Q = ((float *)malloc((sizeof(float)))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":452 + * n * n_dimensions * 2) + * cdef float* sum_Q = malloc(sizeof(float)) + * cdef float* neg_f = malloc(sizeof(float) * n * n_dimensions) # <<<<<<<<<<<<<< + * cdef float* neg_f_fast = malloc(sizeof(float) * n * n_dimensions) + * cdef float* pos_f = malloc(sizeof(float) * n * n_dimensions) + */ + __pyx_v_neg_f = ((float *)malloc((((sizeof(float)) * __pyx_v_n) * __pyx_v_n_dimensions))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":453 + * cdef float* sum_Q = malloc(sizeof(float)) + * cdef float* neg_f = malloc(sizeof(float) * n * n_dimensions) + * cdef float* neg_f_fast = malloc(sizeof(float) * n * n_dimensions) # <<<<<<<<<<<<<< + * cdef float* pos_f = malloc(sizeof(float) * n * n_dimensions) + * cdef clock_t t1, t2 + */ + __pyx_v_neg_f_fast = ((float *)malloc((((sizeof(float)) * __pyx_v_n) * __pyx_v_n_dimensions))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":454 + * cdef float* neg_f = malloc(sizeof(float) * n * n_dimensions) + * cdef float* neg_f_fast = malloc(sizeof(float) * n * n_dimensions) + * cdef float* pos_f = malloc(sizeof(float) * n * n_dimensions) # <<<<<<<<<<<<<< + * cdef clock_t t1, t2 + * cdef float sQ, error + */ + __pyx_v_pos_f = ((float *)malloc((((sizeof(float)) * __pyx_v_n) * __pyx_v_n_dimensions))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":458 + * cdef float sQ, error + * + * sum_Q[0] = 0.0 # <<<<<<<<<<<<<< + * t1 = clock() + * compute_gradient_negative(val_P, pos_reference, neg_f, root_node, sum_Q, + */ + (__pyx_v_sum_Q[0]) = 0.0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":459 + * + * sum_Q[0] = 0.0 + * t1 = clock() # <<<<<<<<<<<<<< + * compute_gradient_negative(val_P, pos_reference, neg_f, root_node, sum_Q, + * dof, theta, start, stop) + */ + __pyx_v_t1 = clock(); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":460 + * sum_Q[0] = 0.0 + * t1 = clock() + * compute_gradient_negative(val_P, pos_reference, neg_f, root_node, sum_Q, # <<<<<<<<<<<<<< + * dof, theta, start, stop) + * t2 = clock() + */ + __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negative(__pyx_v_val_P, __pyx_v_pos_reference, __pyx_v_neg_f, __pyx_v_root_node, __pyx_v_sum_Q, __pyx_v_dof, __pyx_v_theta, __pyx_v_start, __pyx_v_stop); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":462 + * compute_gradient_negative(val_P, pos_reference, neg_f, root_node, sum_Q, + * dof, theta, start, stop) + * t2 = clock() # <<<<<<<<<<<<<< + * if root_node.tree.verbose > 15: + * printf("[t-SNE] Computing negative gradient: %e ticks\n", ((float) (t2 - t1))) + */ + __pyx_v_t2 = clock(); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":463 + * dof, theta, start, stop) + * t2 = clock() + * if root_node.tree.verbose > 15: # <<<<<<<<<<<<<< + * printf("[t-SNE] Computing negative gradient: %e ticks\n", ((float) (t2 - t1))) + * sQ = sum_Q[0] + */ + __pyx_t_2 = ((__pyx_v_root_node->tree->verbose > 15) != 0); + if (__pyx_t_2) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":464 + * t2 = clock() + * if root_node.tree.verbose > 15: + * printf("[t-SNE] Computing negative gradient: %e ticks\n", ((float) (t2 - t1))) # <<<<<<<<<<<<<< + * sQ = sum_Q[0] + * t1 = clock() + */ + printf(__pyx_k_t_SNE_Computing_negative_gradie, ((double)(__pyx_v_t2 - __pyx_v_t1))); + goto __pyx_L4; + } + __pyx_L4:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":465 + * if root_node.tree.verbose > 15: + * printf("[t-SNE] Computing negative gradient: %e ticks\n", ((float) (t2 - t1))) + * sQ = sum_Q[0] # <<<<<<<<<<<<<< + * t1 = clock() + * error = compute_gradient_positive(val_P, pos_reference, neighbors, pos_f, + */ + __pyx_v_sQ = (__pyx_v_sum_Q[0]); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":466 + * printf("[t-SNE] Computing negative gradient: %e ticks\n", ((float) (t2 - t1))) + * sQ = sum_Q[0] + * t1 = clock() # <<<<<<<<<<<<<< + * error = compute_gradient_positive(val_P, pos_reference, neighbors, pos_f, + * n_dimensions, dof, sQ, start, root_node.tree.verbose) + */ + __pyx_v_t1 = clock(); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":467 + * sQ = sum_Q[0] + * t1 = clock() + * error = compute_gradient_positive(val_P, pos_reference, neighbors, pos_f, # <<<<<<<<<<<<<< + * n_dimensions, dof, sQ, start, root_node.tree.verbose) + * t2 = clock() + */ + __pyx_v_error = __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_positive(__pyx_v_val_P, __pyx_v_pos_reference, __pyx_v_neighbors, __pyx_v_pos_f, __pyx_v_n_dimensions, __pyx_v_dof, __pyx_v_sQ, __pyx_v_start, __pyx_v_root_node->tree->verbose); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":469 + * error = compute_gradient_positive(val_P, pos_reference, neighbors, pos_f, + * n_dimensions, dof, sQ, start, root_node.tree.verbose) + * t2 = clock() # <<<<<<<<<<<<<< + * if root_node.tree.verbose > 15: + * printf("[t-SNE] Computing positive gradient: %e ticks\n", ((float) (t2 - t1))) + */ + __pyx_v_t2 = clock(); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":470 + * n_dimensions, dof, sQ, start, root_node.tree.verbose) + * t2 = clock() + * if root_node.tree.verbose > 15: # <<<<<<<<<<<<<< + * printf("[t-SNE] Computing positive gradient: %e ticks\n", ((float) (t2 - t1))) + * for i in range(start, n): + */ + __pyx_t_2 = ((__pyx_v_root_node->tree->verbose > 15) != 0); + if (__pyx_t_2) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":471 + * t2 = clock() + * if root_node.tree.verbose > 15: + * printf("[t-SNE] Computing positive gradient: %e ticks\n", ((float) (t2 - t1))) # <<<<<<<<<<<<<< + * for i in range(start, n): + * for ax in range(n_dimensions): + */ + printf(__pyx_k_t_SNE_Computing_positive_gradie, ((double)(__pyx_v_t2 - __pyx_v_t1))); + goto __pyx_L5; + } + __pyx_L5:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":472 + * if root_node.tree.verbose > 15: + * printf("[t-SNE] Computing positive gradient: %e ticks\n", ((float) (t2 - t1))) + * for i in range(start, n): # <<<<<<<<<<<<<< + * for ax in range(n_dimensions): + * coord = i * n_dimensions + ax + */ + __pyx_t_3 = __pyx_v_n; + for (__pyx_t_4 = __pyx_v_start; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { + __pyx_v_i = __pyx_t_4; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":473 + * printf("[t-SNE] Computing positive gradient: %e ticks\n", ((float) (t2 - t1))) + * for i in range(start, n): + * for ax in range(n_dimensions): # <<<<<<<<<<<<<< + * coord = i * n_dimensions + ax + * tot_force[i, ax] = pos_f[coord] - (neg_f[coord] / sum_Q[0]) + */ + __pyx_t_1 = __pyx_v_n_dimensions; + for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_1; __pyx_t_5+=1) { + __pyx_v_ax = __pyx_t_5; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":474 + * for i in range(start, n): + * for ax in range(n_dimensions): + * coord = i * n_dimensions + ax # <<<<<<<<<<<<<< + * tot_force[i, ax] = pos_f[coord] - (neg_f[coord] / sum_Q[0]) + * free(sum_Q) + */ + __pyx_v_coord = ((__pyx_v_i * __pyx_v_n_dimensions) + __pyx_v_ax); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":475 + * for ax in range(n_dimensions): + * coord = i * n_dimensions + ax + * tot_force[i, ax] = pos_f[coord] - (neg_f[coord] / sum_Q[0]) # <<<<<<<<<<<<<< + * free(sum_Q) + * free(neg_f) + */ + __pyx_t_6 = __pyx_v_i; + __pyx_t_7 = __pyx_v_ax; + *((float *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_tot_force.data + __pyx_t_6 * __pyx_v_tot_force.strides[0]) ) + __pyx_t_7 * __pyx_v_tot_force.strides[1]) )) = ((__pyx_v_pos_f[__pyx_v_coord]) - ((__pyx_v_neg_f[__pyx_v_coord]) / (__pyx_v_sum_Q[0]))); + } + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":476 + * coord = i * n_dimensions + ax + * tot_force[i, ax] = pos_f[coord] - (neg_f[coord] / sum_Q[0]) + * free(sum_Q) # <<<<<<<<<<<<<< + * free(neg_f) + * free(neg_f_fast) + */ + free(__pyx_v_sum_Q); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":477 + * tot_force[i, ax] = pos_f[coord] - (neg_f[coord] / sum_Q[0]) + * free(sum_Q) + * free(neg_f) # <<<<<<<<<<<<<< + * free(neg_f_fast) + * free(pos_f) + */ + free(__pyx_v_neg_f); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":478 + * free(sum_Q) + * free(neg_f) + * free(neg_f_fast) # <<<<<<<<<<<<<< + * free(pos_f) + * return sQ + */ + free(__pyx_v_neg_f_fast); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":479 + * free(neg_f) + * free(neg_f_fast) + * free(pos_f) # <<<<<<<<<<<<<< + * return sQ + * + */ + free(__pyx_v_pos_f); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":480 + * free(neg_f_fast) + * free(pos_f) + * return sQ # <<<<<<<<<<<<<< + * + * + */ + __pyx_r = __pyx_v_sQ; + goto __pyx_L0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":433 + * + * + * cdef float compute_gradient(float[:,:] val_P, # <<<<<<<<<<<<<< + * float[:,:] pos_reference, + * long[:,:] neighbors, + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "sklearn/manifold/_barnes_hut_tsne.pyx":483 + * + * + * cdef float compute_gradient_positive(float[:,:] val_P, # <<<<<<<<<<<<<< + * float[:,:] pos_reference, + * long[:,:] neighbors, + */ + +static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_positive(__Pyx_memviewslice __pyx_v_val_P, __Pyx_memviewslice __pyx_v_pos_reference, __Pyx_memviewslice __pyx_v_neighbors, float *__pyx_v_pos_f, int __pyx_v_n_dimensions, float __pyx_v_dof, float __pyx_v_sum_Q, long __pyx_v_start, int __pyx_v_verbose) { + int __pyx_v_ax; + long __pyx_v_i; + long __pyx_v_j; + long __pyx_v_k; + long __pyx_v_K; + long __pyx_v_n; + float __pyx_v_buff[3]; + float __pyx_v_D; + float __pyx_v_Q; + float __pyx_v_pij; + float __pyx_v_C; + float __pyx_v_exponent; + clock_t __pyx_v_t1; + clock_t __pyx_v_t2; + double __pyx_v_dt; + float __pyx_r; + long __pyx_t_1; + long __pyx_t_2; + int __pyx_t_3; + int __pyx_t_4; + long __pyx_t_5; + long __pyx_t_6; + long __pyx_t_7; + long __pyx_t_8; + long __pyx_t_9; + long __pyx_t_10; + long __pyx_t_11; + int __pyx_t_12; + long __pyx_t_13; + int __pyx_t_14; + long __pyx_t_15; + int __pyx_t_16; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":500 + * int ax + * long i, j, k + * long K = neighbors.shape[1] # <<<<<<<<<<<<<< + * long n = val_P.shape[0] + * float[3] buff + */ + __pyx_v_K = (__pyx_v_neighbors.shape[1]); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":501 + * long i, j, k + * long K = neighbors.shape[1] + * long n = val_P.shape[0] # <<<<<<<<<<<<<< + * float[3] buff + * float D, Q, pij + */ + __pyx_v_n = (__pyx_v_val_P.shape[0]); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":504 + * float[3] buff + * float D, Q, pij + * float C = 0.0 # <<<<<<<<<<<<<< + * float exponent = (dof + 1.0) / -2.0 + * cdef clock_t t1, t2 + */ + __pyx_v_C = 0.0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":505 + * float D, Q, pij + * float C = 0.0 + * float exponent = (dof + 1.0) / -2.0 # <<<<<<<<<<<<<< + * cdef clock_t t1, t2 + * t1 = clock() + */ + __pyx_v_exponent = ((__pyx_v_dof + 1.0) / -2.0); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":507 + * float exponent = (dof + 1.0) / -2.0 + * cdef clock_t t1, t2 + * t1 = clock() # <<<<<<<<<<<<<< + * for i in range(start, n): + * for ax in range(n_dimensions): + */ + __pyx_v_t1 = clock(); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":508 + * cdef clock_t t1, t2 + * t1 = clock() + * for i in range(start, n): # <<<<<<<<<<<<<< + * for ax in range(n_dimensions): + * pos_f[i * n_dimensions + ax] = 0.0 + */ + __pyx_t_1 = __pyx_v_n; + for (__pyx_t_2 = __pyx_v_start; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { + __pyx_v_i = __pyx_t_2; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":509 + * t1 = clock() + * for i in range(start, n): + * for ax in range(n_dimensions): # <<<<<<<<<<<<<< + * pos_f[i * n_dimensions + ax] = 0.0 + * for k in range(K): + */ + __pyx_t_3 = __pyx_v_n_dimensions; + for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { + __pyx_v_ax = __pyx_t_4; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":510 + * for i in range(start, n): + * for ax in range(n_dimensions): + * pos_f[i * n_dimensions + ax] = 0.0 # <<<<<<<<<<<<<< + * for k in range(K): + * j = neighbors[i, k] + */ + (__pyx_v_pos_f[((__pyx_v_i * __pyx_v_n_dimensions) + __pyx_v_ax)]) = 0.0; + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":511 + * for ax in range(n_dimensions): + * pos_f[i * n_dimensions + ax] = 0.0 + * for k in range(K): # <<<<<<<<<<<<<< + * j = neighbors[i, k] + * # we don't need to exclude the i==j case since we've + */ + __pyx_t_5 = __pyx_v_K; + for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { + __pyx_v_k = __pyx_t_6; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":512 + * pos_f[i * n_dimensions + ax] = 0.0 + * for k in range(K): + * j = neighbors[i, k] # <<<<<<<<<<<<<< + * # we don't need to exclude the i==j case since we've + * # already thrown it out from the list of neighbors + */ + __pyx_t_7 = __pyx_v_i; + __pyx_t_8 = __pyx_v_k; + __pyx_v_j = (*((long *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_neighbors.data + __pyx_t_7 * __pyx_v_neighbors.strides[0]) ) + __pyx_t_8 * __pyx_v_neighbors.strides[1]) ))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":515 + * # we don't need to exclude the i==j case since we've + * # already thrown it out from the list of neighbors + * D = 0.0 # <<<<<<<<<<<<<< + * Q = 0.0 + * pij = val_P[i, j] + */ + __pyx_v_D = 0.0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":516 + * # already thrown it out from the list of neighbors + * D = 0.0 + * Q = 0.0 # <<<<<<<<<<<<<< + * pij = val_P[i, j] + * for ax in range(n_dimensions): + */ + __pyx_v_Q = 0.0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":517 + * D = 0.0 + * Q = 0.0 + * pij = val_P[i, j] # <<<<<<<<<<<<<< + * for ax in range(n_dimensions): + * buff[ax] = pos_reference[i, ax] - pos_reference[j, ax] + */ + __pyx_t_9 = __pyx_v_i; + __pyx_t_10 = __pyx_v_j; + __pyx_v_pij = (*((float *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_val_P.data + __pyx_t_9 * __pyx_v_val_P.strides[0]) ) + __pyx_t_10 * __pyx_v_val_P.strides[1]) ))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":518 + * Q = 0.0 + * pij = val_P[i, j] + * for ax in range(n_dimensions): # <<<<<<<<<<<<<< + * buff[ax] = pos_reference[i, ax] - pos_reference[j, ax] + * D += buff[ax] ** 2.0 + */ + __pyx_t_3 = __pyx_v_n_dimensions; + for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { + __pyx_v_ax = __pyx_t_4; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":519 + * pij = val_P[i, j] + * for ax in range(n_dimensions): + * buff[ax] = pos_reference[i, ax] - pos_reference[j, ax] # <<<<<<<<<<<<<< + * D += buff[ax] ** 2.0 + * Q = (((1.0 + D) / dof) ** exponent) + */ + __pyx_t_11 = __pyx_v_i; + __pyx_t_12 = __pyx_v_ax; + __pyx_t_13 = __pyx_v_j; + __pyx_t_14 = __pyx_v_ax; + (__pyx_v_buff[__pyx_v_ax]) = ((*((float *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_pos_reference.data + __pyx_t_11 * __pyx_v_pos_reference.strides[0]) ) + __pyx_t_12 * __pyx_v_pos_reference.strides[1]) ))) - (*((float *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_pos_reference.data + __pyx_t_13 * __pyx_v_pos_reference.strides[0]) ) + __pyx_t_14 * __pyx_v_pos_reference.strides[1]) )))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":520 + * for ax in range(n_dimensions): + * buff[ax] = pos_reference[i, ax] - pos_reference[j, ax] + * D += buff[ax] ** 2.0 # <<<<<<<<<<<<<< + * Q = (((1.0 + D) / dof) ** exponent) + * D = pij * Q + */ + __pyx_v_D = (__pyx_v_D + pow(((double)(__pyx_v_buff[__pyx_v_ax])), 2.0)); + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":521 + * buff[ax] = pos_reference[i, ax] - pos_reference[j, ax] + * D += buff[ax] ** 2.0 + * Q = (((1.0 + D) / dof) ** exponent) # <<<<<<<<<<<<<< + * D = pij * Q + * Q /= sum_Q + */ + __pyx_v_Q = pow(((1.0 + __pyx_v_D) / __pyx_v_dof), ((double)__pyx_v_exponent)); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":522 + * D += buff[ax] ** 2.0 + * Q = (((1.0 + D) / dof) ** exponent) + * D = pij * Q # <<<<<<<<<<<<<< + * Q /= sum_Q + * C += pij * log((pij + EPSILON) / (Q + EPSILON)) + */ + __pyx_v_D = (__pyx_v_pij * __pyx_v_Q); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":523 + * Q = (((1.0 + D) / dof) ** exponent) + * D = pij * Q + * Q /= sum_Q # <<<<<<<<<<<<<< + * C += pij * log((pij + EPSILON) / (Q + EPSILON)) + * for ax in range(n_dimensions): + */ + __pyx_v_Q = (__pyx_v_Q / __pyx_v_sum_Q); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":524 + * D = pij * Q + * Q /= sum_Q + * C += pij * log((pij + EPSILON) / (Q + EPSILON)) # <<<<<<<<<<<<<< + * for ax in range(n_dimensions): + * pos_f[i * n_dimensions + ax] += D * buff[ax] + */ + __pyx_v_C = (__pyx_v_C + (__pyx_v_pij * log(((__pyx_v_pij + __pyx_v_7sklearn_8manifold_16_barnes_hut_tsne_EPSILON) / (__pyx_v_Q + __pyx_v_7sklearn_8manifold_16_barnes_hut_tsne_EPSILON))))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":525 + * Q /= sum_Q + * C += pij * log((pij + EPSILON) / (Q + EPSILON)) + * for ax in range(n_dimensions): # <<<<<<<<<<<<<< + * pos_f[i * n_dimensions + ax] += D * buff[ax] + * t2 = clock() + */ + __pyx_t_3 = __pyx_v_n_dimensions; + for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { + __pyx_v_ax = __pyx_t_4; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":526 + * C += pij * log((pij + EPSILON) / (Q + EPSILON)) + * for ax in range(n_dimensions): + * pos_f[i * n_dimensions + ax] += D * buff[ax] # <<<<<<<<<<<<<< + * t2 = clock() + * dt = ((float) (t2 - t1)) + */ + __pyx_t_15 = ((__pyx_v_i * __pyx_v_n_dimensions) + __pyx_v_ax); + (__pyx_v_pos_f[__pyx_t_15]) = ((__pyx_v_pos_f[__pyx_t_15]) + (__pyx_v_D * (__pyx_v_buff[__pyx_v_ax]))); + } + } + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":527 + * for ax in range(n_dimensions): + * pos_f[i * n_dimensions + ax] += D * buff[ax] + * t2 = clock() # <<<<<<<<<<<<<< + * dt = ((float) (t2 - t1)) + * if verbose > 10: + */ + __pyx_v_t2 = clock(); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":528 + * pos_f[i * n_dimensions + ax] += D * buff[ax] + * t2 = clock() + * dt = ((float) (t2 - t1)) # <<<<<<<<<<<<<< + * if verbose > 10: + * printf("[t-SNE] Computed error=%1.4f in %1.1e ticks\n", C, dt) + */ + __pyx_v_dt = ((double)(__pyx_v_t2 - __pyx_v_t1)); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":529 + * t2 = clock() + * dt = ((float) (t2 - t1)) + * if verbose > 10: # <<<<<<<<<<<<<< + * printf("[t-SNE] Computed error=%1.4f in %1.1e ticks\n", C, dt) + * return C + */ + __pyx_t_16 = ((__pyx_v_verbose > 10) != 0); + if (__pyx_t_16) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":530 + * dt = ((float) (t2 - t1)) + * if verbose > 10: + * printf("[t-SNE] Computed error=%1.4f in %1.1e ticks\n", C, dt) # <<<<<<<<<<<<<< + * return C + * + */ + printf(__pyx_k_t_SNE_Computed_error_1_4f_in_1, __pyx_v_C, __pyx_v_dt); + goto __pyx_L13; + } + __pyx_L13:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":531 + * if verbose > 10: + * printf("[t-SNE] Computed error=%1.4f in %1.1e ticks\n", C, dt) + * return C # <<<<<<<<<<<<<< + * + * + */ + __pyx_r = __pyx_v_C; + goto __pyx_L0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":483 + * + * + * cdef float compute_gradient_positive(float[:,:] val_P, # <<<<<<<<<<<<<< + * float[:,:] pos_reference, + * long[:,:] neighbors, + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "sklearn/manifold/_barnes_hut_tsne.pyx":535 + * + * + * cdef void compute_gradient_negative(float[:,:] val_P, # <<<<<<<<<<<<<< + * float[:,:] pos_reference, + * float* neg_f, + */ + +static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negative(CYTHON_UNUSED __Pyx_memviewslice __pyx_v_val_P, __Pyx_memviewslice __pyx_v_pos_reference, float *__pyx_v_neg_f, struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_v_root_node, float *__pyx_v_sum_Q, float __pyx_v_dof, float __pyx_v_theta, long __pyx_v_start, long __pyx_v_stop) { + int __pyx_v_ax; + long __pyx_v_i; + long __pyx_v_j; + long __pyx_v_n; + float *__pyx_v_force; + float *__pyx_v_iQ; + float *__pyx_v_pos; + float *__pyx_v_dist2s; + long *__pyx_v_sizes; + float *__pyx_v_deltas; + long *__pyx_v_l; + int __pyx_v_n_dimensions; + float __pyx_v_qijZ; + float __pyx_v_mult; + long __pyx_v_idx; + long __pyx_v_dta; + long __pyx_v_dtb; + clock_t __pyx_v_t1; + clock_t __pyx_v_t2; + clock_t __pyx_v_t3; + float *__pyx_v_neg_force; + double __pyx_v_exponent; + int __pyx_t_1; + int __pyx_t_2; + long __pyx_t_3; + long __pyx_t_4; + int __pyx_t_5; + long __pyx_t_6; + int __pyx_t_7; + long __pyx_t_8; + long __pyx_t_9; + long __pyx_t_10; + int __pyx_t_11; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":544 + * long start, + * long stop) nogil: + * if stop == -1: # <<<<<<<<<<<<<< + * stop = pos_reference.shape[0] + * cdef: + */ + __pyx_t_1 = ((__pyx_v_stop == -1) != 0); + if (__pyx_t_1) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":545 + * long stop) nogil: + * if stop == -1: + * stop = pos_reference.shape[0] # <<<<<<<<<<<<<< + * cdef: + * int ax + */ + __pyx_v_stop = (__pyx_v_pos_reference.shape[0]); + goto __pyx_L3; + } + __pyx_L3:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":549 + * int ax + * long i, j + * long n = stop - start # <<<<<<<<<<<<<< + * float* force + * float* iQ + */ + __pyx_v_n = (__pyx_v_stop - __pyx_v_start); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":557 + * float* deltas + * long* l + * int n_dimensions = root_node.tree.n_dimensions # <<<<<<<<<<<<<< + * float qijZ, mult + * long idx, + */ + __pyx_t_2 = __pyx_v_root_node->tree->n_dimensions; + __pyx_v_n_dimensions = __pyx_t_2; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":560 + * float qijZ, mult + * long idx, + * long dta = 0 # <<<<<<<<<<<<<< + * long dtb = 0 + * clock_t t1, t2, t3 + */ + __pyx_v_dta = 0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":561 + * long idx, + * long dta = 0 + * long dtb = 0 # <<<<<<<<<<<<<< + * clock_t t1, t2, t3 + * float* neg_force + */ + __pyx_v_dtb = 0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":565 + * float* neg_force + * + * iQ = malloc(sizeof(float)) # <<<<<<<<<<<<<< + * force = malloc(sizeof(float) * n_dimensions) + * pos = malloc(sizeof(float) * n_dimensions) + */ + __pyx_v_iQ = ((float *)malloc((sizeof(float)))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":566 + * + * iQ = malloc(sizeof(float)) + * force = malloc(sizeof(float) * n_dimensions) # <<<<<<<<<<<<<< + * pos = malloc(sizeof(float) * n_dimensions) + * dist2s = malloc(sizeof(float) * n) + */ + __pyx_v_force = ((float *)malloc(((sizeof(float)) * __pyx_v_n_dimensions))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":567 + * iQ = malloc(sizeof(float)) + * force = malloc(sizeof(float) * n_dimensions) + * pos = malloc(sizeof(float) * n_dimensions) # <<<<<<<<<<<<<< + * dist2s = malloc(sizeof(float) * n) + * sizes = malloc(sizeof(long) * n) + */ + __pyx_v_pos = ((float *)malloc(((sizeof(float)) * __pyx_v_n_dimensions))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":568 + * force = malloc(sizeof(float) * n_dimensions) + * pos = malloc(sizeof(float) * n_dimensions) + * dist2s = malloc(sizeof(float) * n) # <<<<<<<<<<<<<< + * sizes = malloc(sizeof(long) * n) + * deltas = malloc(sizeof(float) * n * n_dimensions) + */ + __pyx_v_dist2s = ((float *)malloc(((sizeof(float)) * __pyx_v_n))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":569 + * pos = malloc(sizeof(float) * n_dimensions) + * dist2s = malloc(sizeof(float) * n) + * sizes = malloc(sizeof(long) * n) # <<<<<<<<<<<<<< + * deltas = malloc(sizeof(float) * n * n_dimensions) + * l = malloc(sizeof(long)) + */ + __pyx_v_sizes = ((long *)malloc(((sizeof(long)) * __pyx_v_n))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":570 + * dist2s = malloc(sizeof(float) * n) + * sizes = malloc(sizeof(long) * n) + * deltas = malloc(sizeof(float) * n * n_dimensions) # <<<<<<<<<<<<<< + * l = malloc(sizeof(long)) + * neg_force= malloc(sizeof(float) * n_dimensions) + */ + __pyx_v_deltas = ((float *)malloc((((sizeof(float)) * __pyx_v_n) * __pyx_v_n_dimensions))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":571 + * sizes = malloc(sizeof(long) * n) + * deltas = malloc(sizeof(float) * n * n_dimensions) + * l = malloc(sizeof(long)) # <<<<<<<<<<<<<< + * neg_force= malloc(sizeof(float) * n_dimensions) + * + */ + __pyx_v_l = ((long *)malloc((sizeof(long)))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":572 + * deltas = malloc(sizeof(float) * n * n_dimensions) + * l = malloc(sizeof(long)) + * neg_force= malloc(sizeof(float) * n_dimensions) # <<<<<<<<<<<<<< + * + * for i in range(start, stop): + */ + __pyx_v_neg_force = ((float *)malloc(((sizeof(float)) * __pyx_v_n_dimensions))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":574 + * neg_force= malloc(sizeof(float) * n_dimensions) + * + * for i in range(start, stop): # <<<<<<<<<<<<<< + * # Clear the arrays + * for ax in range(n_dimensions): + */ + __pyx_t_3 = __pyx_v_stop; + for (__pyx_t_4 = __pyx_v_start; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { + __pyx_v_i = __pyx_t_4; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":576 + * for i in range(start, stop): + * # Clear the arrays + * for ax in range(n_dimensions): # <<<<<<<<<<<<<< + * force[ax] = 0.0 + * neg_force[ax] = 0.0 + */ + __pyx_t_2 = __pyx_v_n_dimensions; + for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_2; __pyx_t_5+=1) { + __pyx_v_ax = __pyx_t_5; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":577 + * # Clear the arrays + * for ax in range(n_dimensions): + * force[ax] = 0.0 # <<<<<<<<<<<<<< + * neg_force[ax] = 0.0 + * pos[ax] = pos_reference[i, ax] + */ + (__pyx_v_force[__pyx_v_ax]) = 0.0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":578 + * for ax in range(n_dimensions): + * force[ax] = 0.0 + * neg_force[ax] = 0.0 # <<<<<<<<<<<<<< + * pos[ax] = pos_reference[i, ax] + * iQ[0] = 0.0 + */ + (__pyx_v_neg_force[__pyx_v_ax]) = 0.0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":579 + * force[ax] = 0.0 + * neg_force[ax] = 0.0 + * pos[ax] = pos_reference[i, ax] # <<<<<<<<<<<<<< + * iQ[0] = 0.0 + * l[0] = 0 + */ + __pyx_t_6 = __pyx_v_i; + __pyx_t_7 = __pyx_v_ax; + (__pyx_v_pos[__pyx_v_ax]) = (*((float *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_pos_reference.data + __pyx_t_6 * __pyx_v_pos_reference.strides[0]) ) + __pyx_t_7 * __pyx_v_pos_reference.strides[1]) ))); + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":580 + * neg_force[ax] = 0.0 + * pos[ax] = pos_reference[i, ax] + * iQ[0] = 0.0 # <<<<<<<<<<<<<< + * l[0] = 0 + * # Find which nodes are summarizing and collect their centers of mass + */ + (__pyx_v_iQ[0]) = 0.0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":581 + * pos[ax] = pos_reference[i, ax] + * iQ[0] = 0.0 + * l[0] = 0 # <<<<<<<<<<<<<< + * # Find which nodes are summarizing and collect their centers of mass + * # deltas, and sizes, into vectorized arrays + */ + (__pyx_v_l[0]) = 0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":584 + * # Find which nodes are summarizing and collect their centers of mass + * # deltas, and sizes, into vectorized arrays + * t1 = clock() # <<<<<<<<<<<<<< + * compute_non_edge_forces(root_node, theta, i, pos, force, dist2s, + * sizes, deltas, l) + */ + __pyx_v_t1 = clock(); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":585 + * # deltas, and sizes, into vectorized arrays + * t1 = clock() + * compute_non_edge_forces(root_node, theta, i, pos, force, dist2s, # <<<<<<<<<<<<<< + * sizes, deltas, l) + * t2 = clock() + */ + __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_non_edge_forces(__pyx_v_root_node, __pyx_v_theta, __pyx_v_i, __pyx_v_pos, __pyx_v_force, __pyx_v_dist2s, __pyx_v_sizes, __pyx_v_deltas, __pyx_v_l); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":587 + * compute_non_edge_forces(root_node, theta, i, pos, force, dist2s, + * sizes, deltas, l) + * t2 = clock() # <<<<<<<<<<<<<< + * # Compute the t-SNE negative force + * # for the digits dataset, walking the tree + */ + __pyx_v_t2 = clock(); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":592 + * # is about 10-15x more expensive than the + * # following for loop + * exponent = (dof + 1.0) / -2.0 # <<<<<<<<<<<<<< + * for j in range(l[0]): + * qijZ = ((1.0 + dist2s[j]) / dof) ** exponent + */ + __pyx_v_exponent = ((__pyx_v_dof + 1.0) / -2.0); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":593 + * # following for loop + * exponent = (dof + 1.0) / -2.0 + * for j in range(l[0]): # <<<<<<<<<<<<<< + * qijZ = ((1.0 + dist2s[j]) / dof) ** exponent + * sum_Q[0] += sizes[j] * qijZ + */ + __pyx_t_8 = (__pyx_v_l[0]); + for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) { + __pyx_v_j = __pyx_t_9; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":594 + * exponent = (dof + 1.0) / -2.0 + * for j in range(l[0]): + * qijZ = ((1.0 + dist2s[j]) / dof) ** exponent # <<<<<<<<<<<<<< + * sum_Q[0] += sizes[j] * qijZ + * mult = sizes[j] * qijZ * qijZ + */ + __pyx_v_qijZ = pow(((1.0 + (__pyx_v_dist2s[__pyx_v_j])) / __pyx_v_dof), __pyx_v_exponent); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":595 + * for j in range(l[0]): + * qijZ = ((1.0 + dist2s[j]) / dof) ** exponent + * sum_Q[0] += sizes[j] * qijZ # <<<<<<<<<<<<<< + * mult = sizes[j] * qijZ * qijZ + * for ax in range(n_dimensions): + */ + __pyx_t_10 = 0; + (__pyx_v_sum_Q[__pyx_t_10]) = ((__pyx_v_sum_Q[__pyx_t_10]) + ((__pyx_v_sizes[__pyx_v_j]) * __pyx_v_qijZ)); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":596 + * qijZ = ((1.0 + dist2s[j]) / dof) ** exponent + * sum_Q[0] += sizes[j] * qijZ + * mult = sizes[j] * qijZ * qijZ # <<<<<<<<<<<<<< + * for ax in range(n_dimensions): + * idx = j * n_dimensions + ax + */ + __pyx_v_mult = (((__pyx_v_sizes[__pyx_v_j]) * __pyx_v_qijZ) * __pyx_v_qijZ); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":597 + * sum_Q[0] += sizes[j] * qijZ + * mult = sizes[j] * qijZ * qijZ + * for ax in range(n_dimensions): # <<<<<<<<<<<<<< + * idx = j * n_dimensions + ax + * neg_force[ax] += mult * deltas[idx] + */ + __pyx_t_2 = __pyx_v_n_dimensions; + for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_2; __pyx_t_5+=1) { + __pyx_v_ax = __pyx_t_5; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":598 + * mult = sizes[j] * qijZ * qijZ + * for ax in range(n_dimensions): + * idx = j * n_dimensions + ax # <<<<<<<<<<<<<< + * neg_force[ax] += mult * deltas[idx] + * t3 = clock() + */ + __pyx_v_idx = ((__pyx_v_j * __pyx_v_n_dimensions) + __pyx_v_ax); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":599 + * for ax in range(n_dimensions): + * idx = j * n_dimensions + ax + * neg_force[ax] += mult * deltas[idx] # <<<<<<<<<<<<<< + * t3 = clock() + * for ax in range(n_dimensions): + */ + __pyx_t_11 = __pyx_v_ax; + (__pyx_v_neg_force[__pyx_t_11]) = ((__pyx_v_neg_force[__pyx_t_11]) + (__pyx_v_mult * (__pyx_v_deltas[__pyx_v_idx]))); + } + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":600 + * idx = j * n_dimensions + ax + * neg_force[ax] += mult * deltas[idx] + * t3 = clock() # <<<<<<<<<<<<<< + * for ax in range(n_dimensions): + * neg_f[i * n_dimensions + ax] = neg_force[ax] + */ + __pyx_v_t3 = clock(); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":601 + * neg_force[ax] += mult * deltas[idx] + * t3 = clock() + * for ax in range(n_dimensions): # <<<<<<<<<<<<<< + * neg_f[i * n_dimensions + ax] = neg_force[ax] + * dta += t2 - t1 + */ + __pyx_t_2 = __pyx_v_n_dimensions; + for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_2; __pyx_t_5+=1) { + __pyx_v_ax = __pyx_t_5; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":602 + * t3 = clock() + * for ax in range(n_dimensions): + * neg_f[i * n_dimensions + ax] = neg_force[ax] # <<<<<<<<<<<<<< + * dta += t2 - t1 + * dtb += t3 - t2 + */ + (__pyx_v_neg_f[((__pyx_v_i * __pyx_v_n_dimensions) + __pyx_v_ax)]) = (__pyx_v_neg_force[__pyx_v_ax]); + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":603 + * for ax in range(n_dimensions): + * neg_f[i * n_dimensions + ax] = neg_force[ax] + * dta += t2 - t1 # <<<<<<<<<<<<<< + * dtb += t3 - t2 + * if root_node.tree.verbose > 20: + */ + __pyx_v_dta = (__pyx_v_dta + (__pyx_v_t2 - __pyx_v_t1)); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":604 + * neg_f[i * n_dimensions + ax] = neg_force[ax] + * dta += t2 - t1 + * dtb += t3 - t2 # <<<<<<<<<<<<<< + * if root_node.tree.verbose > 20: + * printf("[t-SNE] Tree: %i clock ticks | ", dta) + */ + __pyx_v_dtb = (__pyx_v_dtb + (__pyx_v_t3 - __pyx_v_t2)); + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":605 + * dta += t2 - t1 + * dtb += t3 - t2 + * if root_node.tree.verbose > 20: # <<<<<<<<<<<<<< + * printf("[t-SNE] Tree: %i clock ticks | ", dta) + * printf("Force computation: %i clock ticks\n", dtb) + */ + __pyx_t_1 = ((__pyx_v_root_node->tree->verbose > 20) != 0); + if (__pyx_t_1) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":606 + * dtb += t3 - t2 + * if root_node.tree.verbose > 20: + * printf("[t-SNE] Tree: %i clock ticks | ", dta) # <<<<<<<<<<<<<< + * printf("Force computation: %i clock ticks\n", dtb) + * free(iQ) + */ + printf(__pyx_k_t_SNE_Tree_i_clock_ticks, __pyx_v_dta); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":607 + * if root_node.tree.verbose > 20: + * printf("[t-SNE] Tree: %i clock ticks | ", dta) + * printf("Force computation: %i clock ticks\n", dtb) # <<<<<<<<<<<<<< + * free(iQ) + * free(force) + */ + printf(__pyx_k_Force_computation_i_clock_ticks, __pyx_v_dtb); + goto __pyx_L14; + } + __pyx_L14:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":608 + * printf("[t-SNE] Tree: %i clock ticks | ", dta) + * printf("Force computation: %i clock ticks\n", dtb) + * free(iQ) # <<<<<<<<<<<<<< + * free(force) + * free(pos) + */ + free(__pyx_v_iQ); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":609 + * printf("Force computation: %i clock ticks\n", dtb) + * free(iQ) + * free(force) # <<<<<<<<<<<<<< + * free(pos) + * free(dist2s) + */ + free(__pyx_v_force); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":610 + * free(iQ) + * free(force) + * free(pos) # <<<<<<<<<<<<<< + * free(dist2s) + * free(sizes) + */ + free(__pyx_v_pos); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":611 + * free(force) + * free(pos) + * free(dist2s) # <<<<<<<<<<<<<< + * free(sizes) + * free(deltas) + */ + free(__pyx_v_dist2s); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":612 + * free(pos) + * free(dist2s) + * free(sizes) # <<<<<<<<<<<<<< + * free(deltas) + * free(l) + */ + free(__pyx_v_sizes); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":613 + * free(dist2s) + * free(sizes) + * free(deltas) # <<<<<<<<<<<<<< + * free(l) + * free(neg_force) + */ + free(__pyx_v_deltas); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":614 + * free(sizes) + * free(deltas) + * free(l) # <<<<<<<<<<<<<< + * free(neg_force) + * + */ + free(__pyx_v_l); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":615 + * free(deltas) + * free(l) + * free(neg_force) # <<<<<<<<<<<<<< + * + * + */ + free(__pyx_v_neg_force); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":535 + * + * + * cdef void compute_gradient_negative(float[:,:] val_P, # <<<<<<<<<<<<<< + * float[:,:] pos_reference, + * float* neg_f, + */ + + /* function exit code */ +} + +/* "sklearn/manifold/_barnes_hut_tsne.pyx":618 + * + * + * cdef void compute_non_edge_forces(Node* node, # <<<<<<<<<<<<<< + * float theta, + * long point_index, + */ + +static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_non_edge_forces(struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_v_node, float __pyx_v_theta, long __pyx_v_point_index, float *__pyx_v_pos, float *__pyx_v_force, float *__pyx_v_dist2s, long *__pyx_v_sizes, float *__pyx_v_deltas, long *__pyx_v_l) { + struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_v_child; + int __pyx_v_i; + int __pyx_v_n_dimensions; + long __pyx_v_idx; + long __pyx_v_idx1; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + int __pyx_t_4; + int __pyx_t_5; + long __pyx_t_6; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":631 + * Node* child + * int i, j + * int n_dimensions = node.tree.n_dimensions # <<<<<<<<<<<<<< + * long idx, idx1 + * float dist_check + */ + __pyx_t_1 = __pyx_v_node->tree->n_dimensions; + __pyx_v_n_dimensions = __pyx_t_1; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":638 + * # so do not bother to calculate any force contributions + * # Also do not compute self-interactions + * if node.cumulative_size > 0 and not (node.is_leaf and (node.point_index == # <<<<<<<<<<<<<< + * point_index)): + * # Compute distance between node center of mass and the reference point + */ + __pyx_t_3 = ((__pyx_v_node->cumulative_size > 0) != 0); + if (__pyx_t_3) { + goto __pyx_L5_next_and; + } else { + __pyx_t_2 = __pyx_t_3; + goto __pyx_L4_bool_binop_done; + } + __pyx_L5_next_and:; + __pyx_t_4 = (__pyx_v_node->is_leaf != 0); + if (__pyx_t_4) { + goto __pyx_L7_next_and; + } else { + __pyx_t_3 = __pyx_t_4; + goto __pyx_L6_bool_binop_done; + } + __pyx_L7_next_and:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":639 + * # Also do not compute self-interactions + * if node.cumulative_size > 0 and not (node.is_leaf and (node.point_index == + * point_index)): # <<<<<<<<<<<<<< + * # Compute distance between node center of mass and the reference point + * # I've tried rewriting this in terms of BLAS functions, but it's about + */ + __pyx_t_4 = ((__pyx_v_node->point_index == __pyx_v_point_index) != 0); + __pyx_t_3 = __pyx_t_4; + __pyx_L6_bool_binop_done:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":638 + * # so do not bother to calculate any force contributions + * # Also do not compute self-interactions + * if node.cumulative_size > 0 and not (node.is_leaf and (node.point_index == # <<<<<<<<<<<<<< + * point_index)): + * # Compute distance between node center of mass and the reference point + */ + __pyx_t_4 = ((!__pyx_t_3) != 0); + __pyx_t_2 = __pyx_t_4; + __pyx_L4_bool_binop_done:; + if (__pyx_t_2) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":643 + * # I've tried rewriting this in terms of BLAS functions, but it's about + * # 1.5x worse when we do so, probbaly because the vectors are small + * idx1 = l[0] * n_dimensions # <<<<<<<<<<<<<< + * deltas[idx1] = pos[0] - node.barycenter[0] + * idx = idx1 + */ + __pyx_v_idx1 = ((__pyx_v_l[0]) * __pyx_v_n_dimensions); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":644 + * # 1.5x worse when we do so, probbaly because the vectors are small + * idx1 = l[0] * n_dimensions + * deltas[idx1] = pos[0] - node.barycenter[0] # <<<<<<<<<<<<<< + * idx = idx1 + * for i in range(1, n_dimensions): + */ + (__pyx_v_deltas[__pyx_v_idx1]) = ((__pyx_v_pos[0]) - (__pyx_v_node->barycenter[0])); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":645 + * idx1 = l[0] * n_dimensions + * deltas[idx1] = pos[0] - node.barycenter[0] + * idx = idx1 # <<<<<<<<<<<<<< + * for i in range(1, n_dimensions): + * idx += 1 + */ + __pyx_v_idx = __pyx_v_idx1; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":646 + * deltas[idx1] = pos[0] - node.barycenter[0] + * idx = idx1 + * for i in range(1, n_dimensions): # <<<<<<<<<<<<<< + * idx += 1 + * deltas[idx] = pos[i] - node.barycenter[i] + */ + __pyx_t_1 = __pyx_v_n_dimensions; + for (__pyx_t_5 = 1; __pyx_t_5 < __pyx_t_1; __pyx_t_5+=1) { + __pyx_v_i = __pyx_t_5; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":647 + * idx = idx1 + * for i in range(1, n_dimensions): + * idx += 1 # <<<<<<<<<<<<<< + * deltas[idx] = pos[i] - node.barycenter[i] + * # do np.sqrt(np.sum(deltas**2.0)) + */ + __pyx_v_idx = (__pyx_v_idx + 1); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":648 + * for i in range(1, n_dimensions): + * idx += 1 + * deltas[idx] = pos[i] - node.barycenter[i] # <<<<<<<<<<<<<< + * # do np.sqrt(np.sum(deltas**2.0)) + * dist2s[l[0]] = snrm2(n_dimensions, &deltas[idx1], 1) + */ + (__pyx_v_deltas[__pyx_v_idx]) = ((__pyx_v_pos[__pyx_v_i]) - (__pyx_v_node->barycenter[__pyx_v_i])); + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":650 + * deltas[idx] = pos[i] - node.barycenter[i] + * # do np.sqrt(np.sum(deltas**2.0)) + * dist2s[l[0]] = snrm2(n_dimensions, &deltas[idx1], 1) # <<<<<<<<<<<<<< + * # Check whether we can use this node as a summary + * # It's a summary node if the angular size as measured from the point + */ + (__pyx_v_dist2s[(__pyx_v_l[0])]) = cblas_snrm2(__pyx_v_n_dimensions, (&(__pyx_v_deltas[__pyx_v_idx1])), 1); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":656 + * # If it can be summarized, we use the cell center of mass + * # Otherwise, we go a higher level of resolution and into the leaves. + * if node.is_leaf or ((node.max_width / dist2s[l[0]]) < theta): # <<<<<<<<<<<<<< + * # Compute the t-SNE force between the reference point and the + * # current node + */ + __pyx_t_4 = (__pyx_v_node->is_leaf != 0); + if (!__pyx_t_4) { + goto __pyx_L12_next_or; + } else { + __pyx_t_2 = __pyx_t_4; + goto __pyx_L11_bool_binop_done; + } + __pyx_L12_next_or:; + __pyx_t_4 = (((__pyx_v_node->max_width / (__pyx_v_dist2s[(__pyx_v_l[0])])) < __pyx_v_theta) != 0); + __pyx_t_2 = __pyx_t_4; + __pyx_L11_bool_binop_done:; + if (__pyx_t_2) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":659 + * # Compute the t-SNE force between the reference point and the + * # current node + * sizes[l[0]] = node.cumulative_size # <<<<<<<<<<<<<< + * dist2s[l[0]] = dist2s[l[0]] * dist2s[l[0]] + * l[0] += 1 + */ + __pyx_t_6 = __pyx_v_node->cumulative_size; + (__pyx_v_sizes[(__pyx_v_l[0])]) = __pyx_t_6; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":660 + * # current node + * sizes[l[0]] = node.cumulative_size + * dist2s[l[0]] = dist2s[l[0]] * dist2s[l[0]] # <<<<<<<<<<<<<< + * l[0] += 1 + * else: + */ + (__pyx_v_dist2s[(__pyx_v_l[0])]) = ((__pyx_v_dist2s[(__pyx_v_l[0])]) * (__pyx_v_dist2s[(__pyx_v_l[0])])); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":661 + * sizes[l[0]] = node.cumulative_size + * dist2s[l[0]] = dist2s[l[0]] * dist2s[l[0]] + * l[0] += 1 # <<<<<<<<<<<<<< + * else: + * # Recursively apply Barnes-Hut to child nodes + */ + __pyx_t_6 = 0; + (__pyx_v_l[__pyx_t_6]) = ((__pyx_v_l[__pyx_t_6]) + 1); + goto __pyx_L10; + } + /*else*/ { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":664 + * else: + * # Recursively apply Barnes-Hut to child nodes + * for idx in range(node.tree.n_cell_per_node): # <<<<<<<<<<<<<< + * child = node.children[idx] + * if child.cumulative_size == 0: + */ + __pyx_t_1 = __pyx_v_node->tree->n_cell_per_node; + for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_1; __pyx_t_6+=1) { + __pyx_v_idx = __pyx_t_6; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":665 + * # Recursively apply Barnes-Hut to child nodes + * for idx in range(node.tree.n_cell_per_node): + * child = node.children[idx] # <<<<<<<<<<<<<< + * if child.cumulative_size == 0: + * continue + */ + __pyx_v_child = (__pyx_v_node->children[__pyx_v_idx]); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":666 + * for idx in range(node.tree.n_cell_per_node): + * child = node.children[idx] + * if child.cumulative_size == 0: # <<<<<<<<<<<<<< + * continue + * compute_non_edge_forces(child, theta, + */ + __pyx_t_2 = ((__pyx_v_child->cumulative_size == 0) != 0); + if (__pyx_t_2) { + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":667 + * child = node.children[idx] + * if child.cumulative_size == 0: + * continue # <<<<<<<<<<<<<< + * compute_non_edge_forces(child, theta, + * point_index, pos, force, dist2s, sizes, deltas, + */ + goto __pyx_L13_continue; + } + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":668 + * if child.cumulative_size == 0: + * continue + * compute_non_edge_forces(child, theta, # <<<<<<<<<<<<<< + * point_index, pos, force, dist2s, sizes, deltas, + * l) + */ + __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_non_edge_forces(__pyx_v_child, __pyx_v_theta, __pyx_v_point_index, __pyx_v_pos, __pyx_v_force, __pyx_v_dist2s, __pyx_v_sizes, __pyx_v_deltas, __pyx_v_l); + __pyx_L13_continue:; + } + } + __pyx_L10:; + goto __pyx_L3; + } + __pyx_L3:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":618 + * + * + * cdef void compute_non_edge_forces(Node* node, # <<<<<<<<<<<<<< + * float theta, + * long point_index, + */ + + /* function exit code */ +} + +/* "sklearn/manifold/_barnes_hut_tsne.pyx":673 + * + * + * cdef float compute_error(float[:, :] val_P, # <<<<<<<<<<<<<< + * float[:, :] pos_reference, + * long[:,:] neighbors, + */ + +static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_error(__Pyx_memviewslice __pyx_v_val_P, __Pyx_memviewslice __pyx_v_pos_reference, __Pyx_memviewslice __pyx_v_neighbors, float __pyx_v_sum_Q, int __pyx_v_n_dimensions, int __pyx_v_verbose) { + int __pyx_v_i; + int __pyx_v_j; + int __pyx_v_ax; + int __pyx_v_I; + int __pyx_v_K; + float __pyx_v_pij; + float __pyx_v_Q; + float __pyx_v_C; + clock_t __pyx_v_t1; + clock_t __pyx_v_t2; + float __pyx_v_dt; + float __pyx_v_delta; + int __pyx_v_k; + float __pyx_r; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + int __pyx_t_4; + int __pyx_t_5; + int __pyx_t_6; + int __pyx_t_7; + int __pyx_t_8; + int __pyx_t_9; + int __pyx_t_10; + int __pyx_t_11; + int __pyx_t_12; + int __pyx_t_13; + int __pyx_t_14; + int __pyx_t_15; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":680 + * int verbose) nogil: + * cdef int i, j, ax + * cdef int I = neighbors.shape[0] # <<<<<<<<<<<<<< + * cdef int K = neighbors.shape[1] + * cdef float pij, Q + */ + __pyx_v_I = (__pyx_v_neighbors.shape[0]); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":681 + * cdef int i, j, ax + * cdef int I = neighbors.shape[0] + * cdef int K = neighbors.shape[1] # <<<<<<<<<<<<<< + * cdef float pij, Q + * cdef float C = 0.0 + */ + __pyx_v_K = (__pyx_v_neighbors.shape[1]); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":683 + * cdef int K = neighbors.shape[1] + * cdef float pij, Q + * cdef float C = 0.0 # <<<<<<<<<<<<<< + * cdef clock_t t1, t2 + * cdef float dt, delta + */ + __pyx_v_C = 0.0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":686 + * cdef clock_t t1, t2 + * cdef float dt, delta + * t1 = clock() # <<<<<<<<<<<<<< + * for i in range(I): + * for k in range(K): + */ + __pyx_v_t1 = clock(); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":687 + * cdef float dt, delta + * t1 = clock() + * for i in range(I): # <<<<<<<<<<<<<< + * for k in range(K): + * j = neighbors[i, k] + */ + __pyx_t_1 = __pyx_v_I; + for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { + __pyx_v_i = __pyx_t_2; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":688 + * t1 = clock() + * for i in range(I): + * for k in range(K): # <<<<<<<<<<<<<< + * j = neighbors[i, k] + * pij = val_P[i, j] + */ + __pyx_t_3 = __pyx_v_K; + for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { + __pyx_v_k = __pyx_t_4; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":689 + * for i in range(I): + * for k in range(K): + * j = neighbors[i, k] # <<<<<<<<<<<<<< + * pij = val_P[i, j] + * Q = 0.0 + */ + __pyx_t_5 = __pyx_v_i; + __pyx_t_6 = __pyx_v_k; + __pyx_v_j = (*((long *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_neighbors.data + __pyx_t_5 * __pyx_v_neighbors.strides[0]) ) + __pyx_t_6 * __pyx_v_neighbors.strides[1]) ))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":690 + * for k in range(K): + * j = neighbors[i, k] + * pij = val_P[i, j] # <<<<<<<<<<<<<< + * Q = 0.0 + * for ax in range(n_dimensions): + */ + __pyx_t_7 = __pyx_v_i; + __pyx_t_8 = __pyx_v_j; + __pyx_v_pij = (*((float *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_val_P.data + __pyx_t_7 * __pyx_v_val_P.strides[0]) ) + __pyx_t_8 * __pyx_v_val_P.strides[1]) ))); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":691 + * j = neighbors[i, k] + * pij = val_P[i, j] + * Q = 0.0 # <<<<<<<<<<<<<< + * for ax in range(n_dimensions): + * delta = (pos_reference[i, ax] - pos_reference[j, ax]) + */ + __pyx_v_Q = 0.0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":692 + * pij = val_P[i, j] + * Q = 0.0 + * for ax in range(n_dimensions): # <<<<<<<<<<<<<< + * delta = (pos_reference[i, ax] - pos_reference[j, ax]) + * Q += delta * delta + */ + __pyx_t_9 = __pyx_v_n_dimensions; + for (__pyx_t_10 = 0; __pyx_t_10 < __pyx_t_9; __pyx_t_10+=1) { + __pyx_v_ax = __pyx_t_10; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":693 + * Q = 0.0 + * for ax in range(n_dimensions): + * delta = (pos_reference[i, ax] - pos_reference[j, ax]) # <<<<<<<<<<<<<< + * Q += delta * delta + * Q = (1.0 / (sum_Q + Q * sum_Q)) + */ + __pyx_t_11 = __pyx_v_i; 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suboffset_dim = -1, dim + * cdef bint negative_step + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_9); + __Pyx_AddTraceback("View.MemoryView.memview_slice", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XDECREF((PyObject *)__pyx_v_memviewsliceobj); + __Pyx_XDECREF(__pyx_v_index); + __Pyx_XGIVEREF((PyObject *)__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "View.MemoryView":764 + * + * @cname('__pyx_memoryview_slice_memviewslice') + * cdef int slice_memviewslice( # <<<<<<<<<<<<<< + * __Pyx_memviewslice *dst, + * Py_ssize_t shape, Py_ssize_t stride, Py_ssize_t suboffset, + */ + +static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, Py_ssize_t __pyx_v_shape, Py_ssize_t __pyx_v_stride, Py_ssize_t __pyx_v_suboffset, int __pyx_v_dim, int __pyx_v_new_ndim, int *__pyx_v_suboffset_dim, Py_ssize_t __pyx_v_start, Py_ssize_t __pyx_v_stop, Py_ssize_t __pyx_v_step, int __pyx_v_have_start, int __pyx_v_have_stop, int __pyx_v_have_step, int __pyx_v_is_slice) { + Py_ssize_t __pyx_v_new_shape; + int __pyx_v_negative_step; + int __pyx_r; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + + /* "View.MemoryView":784 + * cdef bint negative_step + * + * if not is_slice: # <<<<<<<<<<<<<< + * + * if start < 0: + */ + __pyx_t_1 = ((!(__pyx_v_is_slice != 0)) != 0); + if (__pyx_t_1) { + + /* "View.MemoryView":786 + * if not is_slice: + * + * if start < 0: # <<<<<<<<<<<<<< + * start += shape + * if not 0 <= start < shape: + */ + __pyx_t_1 = ((__pyx_v_start < 0) != 0); + if (__pyx_t_1) { + + /* "View.MemoryView":787 + * + * if start < 0: + * start += shape # <<<<<<<<<<<<<< + * if not 0 <= start < shape: + * _err_dim(IndexError, "Index out of bounds (axis %d)", dim) + */ + __pyx_v_start = (__pyx_v_start + __pyx_v_shape); + goto __pyx_L4; + } + __pyx_L4:; + + /* "View.MemoryView":788 + * if start < 0: + * start += shape + * if not 0 <= start < shape: # <<<<<<<<<<<<<< + * _err_dim(IndexError, "Index out of bounds (axis %d)", dim) + * else: + */ + __pyx_t_1 = (0 <= __pyx_v_start); + if (__pyx_t_1) { + __pyx_t_1 = (__pyx_v_start < __pyx_v_shape); + } + __pyx_t_2 = ((!(__pyx_t_1 != 0)) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":789 + * start += shape + * if not 0 <= start < shape: + * _err_dim(IndexError, "Index out of bounds (axis %d)", dim) # <<<<<<<<<<<<<< + * else: + * + */ + __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_IndexError, __pyx_k_Index_out_of_bounds_axis_d, __pyx_v_dim); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + goto __pyx_L5; + } + __pyx_L5:; + goto __pyx_L3; + } + /*else*/ { + + /* "View.MemoryView":792 + * else: + * + * negative_step = have_step != 0 and step < 0 # <<<<<<<<<<<<<< + * + * if have_step and step == 0: + */ + __pyx_t_1 = ((__pyx_v_have_step != 0) != 0); + if (__pyx_t_1) { + goto __pyx_L7_next_and; + } else { + __pyx_t_2 = __pyx_t_1; + goto __pyx_L6_bool_binop_done; + } + __pyx_L7_next_and:; + __pyx_t_1 = ((__pyx_v_step < 0) != 0); + __pyx_t_2 = __pyx_t_1; + __pyx_L6_bool_binop_done:; + __pyx_v_negative_step = __pyx_t_2; + + /* "View.MemoryView":794 + * negative_step = have_step != 0 and step < 0 + * + * if have_step and step == 0: # <<<<<<<<<<<<<< + * _err_dim(ValueError, "Step may not be zero (axis %d)", dim) + * + */ + __pyx_t_1 = (__pyx_v_have_step != 0); + if (__pyx_t_1) { + goto __pyx_L10_next_and; + } else { + __pyx_t_2 = __pyx_t_1; + goto __pyx_L9_bool_binop_done; + } + __pyx_L10_next_and:; + __pyx_t_1 = ((__pyx_v_step == 0) != 0); + __pyx_t_2 = __pyx_t_1; + __pyx_L9_bool_binop_done:; + if (__pyx_t_2) { + + /* "View.MemoryView":795 + * + * if have_step and step == 0: + * _err_dim(ValueError, "Step may not be zero (axis %d)", dim) # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, __pyx_k_Step_may_not_be_zero_axis_d, __pyx_v_dim); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + goto __pyx_L8; + } + __pyx_L8:; + + /* "View.MemoryView":798 + * + * + * if have_start: # <<<<<<<<<<<<<< + * if start < 0: + * start += shape + */ + __pyx_t_2 = (__pyx_v_have_start != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":799 + * + * if have_start: + * if start < 0: # <<<<<<<<<<<<<< + * start += shape + * if start < 0: + */ + __pyx_t_2 = ((__pyx_v_start < 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":800 + * if have_start: + * if start < 0: + * start += shape # <<<<<<<<<<<<<< + * if start < 0: + * start = 0 + */ + __pyx_v_start = (__pyx_v_start + __pyx_v_shape); + + /* "View.MemoryView":801 + * if start < 0: + * start += shape + * if start < 0: # <<<<<<<<<<<<<< + * start = 0 + * elif start >= shape: + */ + __pyx_t_2 = ((__pyx_v_start < 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":802 + * start += shape + * if start < 0: + * start = 0 # <<<<<<<<<<<<<< + * elif start >= shape: + * if negative_step: + */ + __pyx_v_start = 0; + goto __pyx_L13; + } + __pyx_L13:; + goto __pyx_L12; + } + + /* "View.MemoryView":803 + * if start < 0: + * start = 0 + * elif start >= shape: # <<<<<<<<<<<<<< + * if negative_step: + * start = shape - 1 + */ + __pyx_t_2 = ((__pyx_v_start >= __pyx_v_shape) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":804 + * start = 0 + * elif start >= shape: + * if negative_step: # <<<<<<<<<<<<<< + * start = shape - 1 + * else: + */ + __pyx_t_2 = (__pyx_v_negative_step != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":805 + * elif start >= shape: + * if negative_step: + * start = shape - 1 # <<<<<<<<<<<<<< + * else: + * start = shape + */ + __pyx_v_start = (__pyx_v_shape - 1); + goto __pyx_L14; + } + /*else*/ { + + /* "View.MemoryView":807 + * start = shape - 1 + * else: + * start = shape # <<<<<<<<<<<<<< + * else: + * if negative_step: + */ + __pyx_v_start = __pyx_v_shape; + } + __pyx_L14:; + goto __pyx_L12; + } + __pyx_L12:; + goto __pyx_L11; + } + /*else*/ { + + /* "View.MemoryView":809 + * start = shape + * else: + * if negative_step: # <<<<<<<<<<<<<< + * start = shape - 1 + * else: + */ + __pyx_t_2 = (__pyx_v_negative_step != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":810 + * else: + * if negative_step: + * start = shape - 1 # <<<<<<<<<<<<<< + * else: + * start = 0 + */ + __pyx_v_start = (__pyx_v_shape - 1); + goto __pyx_L15; + } + /*else*/ { + + /* "View.MemoryView":812 + * start = shape - 1 + * else: + * start = 0 # <<<<<<<<<<<<<< + * + * if have_stop: + */ + __pyx_v_start = 0; + } + __pyx_L15:; + } + __pyx_L11:; + + /* "View.MemoryView":814 + * start = 0 + * + * if have_stop: # <<<<<<<<<<<<<< + * if stop < 0: + * stop += shape + */ + __pyx_t_2 = (__pyx_v_have_stop != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":815 + * + * if have_stop: + * if stop < 0: # <<<<<<<<<<<<<< + * stop += shape + * if stop < 0: + */ + __pyx_t_2 = ((__pyx_v_stop < 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":816 + * if have_stop: + * if stop < 0: + * stop += shape # <<<<<<<<<<<<<< + * if stop < 0: + * stop = 0 + */ + __pyx_v_stop = (__pyx_v_stop + __pyx_v_shape); + + /* "View.MemoryView":817 + * if stop < 0: + * stop += shape + * if stop < 0: # <<<<<<<<<<<<<< + * stop = 0 + * elif stop > shape: + */ + __pyx_t_2 = ((__pyx_v_stop < 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":818 + * stop += shape + * if stop < 0: + * stop = 0 # <<<<<<<<<<<<<< + * elif stop > shape: + * stop = shape + */ + __pyx_v_stop = 0; + goto __pyx_L18; + } + __pyx_L18:; + goto __pyx_L17; + } + + /* "View.MemoryView":819 + * if stop < 0: + * stop = 0 + * elif stop > shape: # <<<<<<<<<<<<<< + * stop = shape + * else: + */ + __pyx_t_2 = ((__pyx_v_stop > __pyx_v_shape) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":820 + * stop = 0 + * elif stop > shape: + * stop = shape # <<<<<<<<<<<<<< + * else: + * if negative_step: + */ + __pyx_v_stop = __pyx_v_shape; + goto __pyx_L17; + } + __pyx_L17:; + goto __pyx_L16; + } + /*else*/ { + + /* "View.MemoryView":822 + * stop = shape + * else: + * if negative_step: # <<<<<<<<<<<<<< + * stop = -1 + * else: + */ + __pyx_t_2 = (__pyx_v_negative_step != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":823 + * else: + * if negative_step: + * stop = -1 # <<<<<<<<<<<<<< + * else: + * stop = shape + */ + __pyx_v_stop = -1; + goto __pyx_L19; + } + /*else*/ { + + /* "View.MemoryView":825 + * stop = -1 + * else: + * stop = shape # <<<<<<<<<<<<<< + * + * if not have_step: + */ + __pyx_v_stop = __pyx_v_shape; + } + __pyx_L19:; + } + __pyx_L16:; + + /* "View.MemoryView":827 + * stop = shape + * + * if not have_step: # <<<<<<<<<<<<<< + * step = 1 + * + */ + __pyx_t_2 = ((!(__pyx_v_have_step != 0)) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":828 + * + * if not have_step: + * step = 1 # <<<<<<<<<<<<<< + * + * + */ + __pyx_v_step = 1; + goto __pyx_L20; + } + __pyx_L20:; + + /* "View.MemoryView":832 + * + * with cython.cdivision(True): + * new_shape = (stop - start) // step # <<<<<<<<<<<<<< + * + * if (stop - start) - step * new_shape: + */ + __pyx_v_new_shape = ((__pyx_v_stop - __pyx_v_start) / __pyx_v_step); + + /* "View.MemoryView":834 + * new_shape = (stop - start) // step + * + * if (stop - start) - step * new_shape: # <<<<<<<<<<<<<< + * new_shape += 1 + * + */ + __pyx_t_2 = (((__pyx_v_stop - __pyx_v_start) - (__pyx_v_step * __pyx_v_new_shape)) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":835 + * + * if (stop - start) - step * new_shape: + * new_shape += 1 # <<<<<<<<<<<<<< + * + * if new_shape < 0: + */ + __pyx_v_new_shape = (__pyx_v_new_shape + 1); + goto __pyx_L21; + } + __pyx_L21:; + + /* "View.MemoryView":837 + * new_shape += 1 + * + * if new_shape < 0: # <<<<<<<<<<<<<< + * new_shape = 0 + * + */ + __pyx_t_2 = ((__pyx_v_new_shape < 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":838 + * + * if new_shape < 0: + * new_shape = 0 # <<<<<<<<<<<<<< + * + * + */ + __pyx_v_new_shape = 0; + goto __pyx_L22; + } + __pyx_L22:; + + /* "View.MemoryView":841 + * + * + * dst.strides[new_ndim] = stride * step # <<<<<<<<<<<<<< + * dst.shape[new_ndim] = new_shape + * dst.suboffsets[new_ndim] = suboffset + */ + (__pyx_v_dst->strides[__pyx_v_new_ndim]) = (__pyx_v_stride * __pyx_v_step); + + /* "View.MemoryView":842 + * + * dst.strides[new_ndim] = stride * step + * dst.shape[new_ndim] = new_shape # <<<<<<<<<<<<<< + * dst.suboffsets[new_ndim] = suboffset + * + */ + (__pyx_v_dst->shape[__pyx_v_new_ndim]) = __pyx_v_new_shape; + + /* "View.MemoryView":843 + * dst.strides[new_ndim] = stride * step + * dst.shape[new_ndim] = new_shape + * dst.suboffsets[new_ndim] = suboffset # <<<<<<<<<<<<<< + * + * + */ + (__pyx_v_dst->suboffsets[__pyx_v_new_ndim]) = __pyx_v_suboffset; + } + __pyx_L3:; + + /* "View.MemoryView":846 + * + * + * if suboffset_dim[0] < 0: # <<<<<<<<<<<<<< + * dst.data += start * stride + * else: + */ + __pyx_t_2 = (((__pyx_v_suboffset_dim[0]) < 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":847 + * + * if suboffset_dim[0] < 0: + * dst.data += start * stride # <<<<<<<<<<<<<< + * else: + * dst.suboffsets[suboffset_dim[0]] += start * stride + */ + __pyx_v_dst->data = (__pyx_v_dst->data + (__pyx_v_start * __pyx_v_stride)); + goto __pyx_L23; + } + /*else*/ { + + /* "View.MemoryView":849 + * dst.data += start * stride + * else: + * dst.suboffsets[suboffset_dim[0]] += start * stride # <<<<<<<<<<<<<< + * + * if suboffset >= 0: + */ + __pyx_t_3 = (__pyx_v_suboffset_dim[0]); + (__pyx_v_dst->suboffsets[__pyx_t_3]) = ((__pyx_v_dst->suboffsets[__pyx_t_3]) + (__pyx_v_start * __pyx_v_stride)); + } + __pyx_L23:; + + /* "View.MemoryView":851 + * dst.suboffsets[suboffset_dim[0]] += start * stride + * + * if suboffset >= 0: # <<<<<<<<<<<<<< + * if not is_slice: + * if new_ndim == 0: + */ + __pyx_t_2 = ((__pyx_v_suboffset >= 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":852 + * + * if suboffset >= 0: + * if not is_slice: # <<<<<<<<<<<<<< + * if new_ndim == 0: + * dst.data = ( dst.data)[0] + suboffset + */ + __pyx_t_2 = ((!(__pyx_v_is_slice != 0)) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":853 + * if suboffset >= 0: + * if not is_slice: + * if new_ndim == 0: # <<<<<<<<<<<<<< + * dst.data = ( dst.data)[0] + suboffset + * else: + */ + __pyx_t_2 = ((__pyx_v_new_ndim == 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":854 + * if not is_slice: + * if new_ndim == 0: + * dst.data = ( dst.data)[0] + suboffset # <<<<<<<<<<<<<< + * else: + * _err_dim(IndexError, "All dimensions preceding dimension %d " + */ + __pyx_v_dst->data = ((((char **)__pyx_v_dst->data)[0]) + __pyx_v_suboffset); + goto __pyx_L26; + } + /*else*/ { + + /* "View.MemoryView":856 + * dst.data = ( dst.data)[0] + suboffset + * else: + * _err_dim(IndexError, "All dimensions preceding dimension %d " # <<<<<<<<<<<<<< + * "must be indexed and not sliced", dim) + * else: + */ + __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_IndexError, __pyx_k_All_dimensions_preceding_dimensi, __pyx_v_dim); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 856; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + __pyx_L26:; + goto __pyx_L25; + } + /*else*/ { + + /* "View.MemoryView":859 + * "must be indexed and not sliced", dim) + * else: + * suboffset_dim[0] = new_ndim # <<<<<<<<<<<<<< + * + * return 0 + */ + (__pyx_v_suboffset_dim[0]) = __pyx_v_new_ndim; + } + __pyx_L25:; + goto __pyx_L24; + } + __pyx_L24:; + + /* "View.MemoryView":861 + * suboffset_dim[0] = new_ndim + * + * return 0 # <<<<<<<<<<<<<< + * + * + */ + __pyx_r = 0; + goto __pyx_L0; + + /* "View.MemoryView":764 + * + * @cname('__pyx_memoryview_slice_memviewslice') + * cdef int slice_memviewslice( # <<<<<<<<<<<<<< + * __Pyx_memviewslice *dst, + * Py_ssize_t shape, Py_ssize_t stride, Py_ssize_t suboffset, + */ + + /* function exit code */ + __pyx_L1_error:; + { + #ifdef WITH_THREAD + PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); + #endif + __Pyx_AddTraceback("View.MemoryView.slice_memviewslice", __pyx_clineno, __pyx_lineno, __pyx_filename); + #ifdef WITH_THREAD + PyGILState_Release(__pyx_gilstate_save); + #endif + } + __pyx_r = -1; + __pyx_L0:; + return __pyx_r; +} + +/* "View.MemoryView":867 + * + * @cname('__pyx_pybuffer_index') + * cdef char *pybuffer_index(Py_buffer *view, char *bufp, Py_ssize_t index, # <<<<<<<<<<<<<< + * Py_ssize_t dim) except NULL: + * cdef Py_ssize_t shape, stride, suboffset = -1 + */ + +static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, Py_ssize_t __pyx_v_index, Py_ssize_t __pyx_v_dim) { + Py_ssize_t __pyx_v_shape; + Py_ssize_t __pyx_v_stride; + Py_ssize_t __pyx_v_suboffset; + Py_ssize_t __pyx_v_itemsize; + char *__pyx_v_resultp; + char *__pyx_r; + __Pyx_RefNannyDeclarations + Py_ssize_t __pyx_t_1; + int __pyx_t_2; + PyObject *__pyx_t_3 = NULL; + PyObject *__pyx_t_4 = NULL; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + __Pyx_RefNannySetupContext("pybuffer_index", 0); + + /* "View.MemoryView":869 + * cdef char *pybuffer_index(Py_buffer *view, char *bufp, Py_ssize_t index, + * Py_ssize_t dim) except NULL: + * cdef Py_ssize_t shape, stride, suboffset = -1 # <<<<<<<<<<<<<< + * cdef Py_ssize_t itemsize = view.itemsize + * cdef char *resultp + */ + __pyx_v_suboffset = -1; + + /* "View.MemoryView":870 + * Py_ssize_t dim) except NULL: + * cdef Py_ssize_t shape, stride, suboffset = -1 + * cdef Py_ssize_t itemsize = view.itemsize # <<<<<<<<<<<<<< + * cdef char *resultp + * + */ + __pyx_t_1 = __pyx_v_view->itemsize; + __pyx_v_itemsize = __pyx_t_1; + + /* "View.MemoryView":873 + * cdef char *resultp + * + * if view.ndim == 0: # <<<<<<<<<<<<<< + * shape = view.len / itemsize + * stride = itemsize + */ + __pyx_t_2 = ((__pyx_v_view->ndim == 0) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":874 + * + * if view.ndim == 0: + * shape = view.len / itemsize # <<<<<<<<<<<<<< + * stride = itemsize + * else: + */ + if (unlikely(__pyx_v_itemsize == 0)) { + #ifdef WITH_THREAD + PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); + #endif + PyErr_SetString(PyExc_ZeroDivisionError, "integer division or modulo by zero"); + #ifdef WITH_THREAD + PyGILState_Release(__pyx_gilstate_save); + #endif + {__pyx_filename = __pyx_f[2]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + else if (sizeof(Py_ssize_t) == sizeof(long) && unlikely(__pyx_v_itemsize == -1) && unlikely(UNARY_NEG_WOULD_OVERFLOW(__pyx_v_view->len))) { + #ifdef WITH_THREAD + PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); + #endif + PyErr_SetString(PyExc_OverflowError, "value too large to perform division"); + #ifdef WITH_THREAD + PyGILState_Release(__pyx_gilstate_save); + #endif + {__pyx_filename = __pyx_f[2]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + __pyx_v_shape = (__pyx_v_view->len / __pyx_v_itemsize); + + /* "View.MemoryView":875 + * if view.ndim == 0: + * shape = view.len / itemsize + * stride = itemsize # <<<<<<<<<<<<<< + * else: + * shape = view.shape[dim] + */ + __pyx_v_stride = __pyx_v_itemsize; + goto __pyx_L3; + } + /*else*/ { + + /* "View.MemoryView":877 + * stride = itemsize + * else: + * shape = view.shape[dim] # <<<<<<<<<<<<<< + * stride = view.strides[dim] + * if view.suboffsets != NULL: + */ + __pyx_v_shape = (__pyx_v_view->shape[__pyx_v_dim]); + + /* "View.MemoryView":878 + * else: + * shape = view.shape[dim] + * stride = view.strides[dim] # <<<<<<<<<<<<<< + * if view.suboffsets != NULL: + * suboffset = view.suboffsets[dim] + */ + __pyx_v_stride = (__pyx_v_view->strides[__pyx_v_dim]); + + /* "View.MemoryView":879 + * shape = view.shape[dim] + * stride = view.strides[dim] + * if view.suboffsets != NULL: # <<<<<<<<<<<<<< + * suboffset = view.suboffsets[dim] + * + */ + __pyx_t_2 = ((__pyx_v_view->suboffsets != NULL) != 0); + if (__pyx_t_2) { + + /* 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memview).to_dtype_func + * else: + */ + __pyx_t_3 = ((struct __pyx_memoryviewslice_obj *)__pyx_v_memview)->to_object_func; + __pyx_v_to_object_func = __pyx_t_3; + + /* "View.MemoryView":1049 + * if isinstance(memview, _memoryviewslice): + * to_object_func = (<_memoryviewslice> memview).to_object_func + * to_dtype_func = (<_memoryviewslice> memview).to_dtype_func # <<<<<<<<<<<<<< + * else: + * to_object_func = NULL + */ + __pyx_t_4 = ((struct __pyx_memoryviewslice_obj *)__pyx_v_memview)->to_dtype_func; + __pyx_v_to_dtype_func = __pyx_t_4; + goto __pyx_L3; + } + /*else*/ { + + /* "View.MemoryView":1051 + * to_dtype_func = (<_memoryviewslice> memview).to_dtype_func + * else: + * to_object_func = NULL # <<<<<<<<<<<<<< + * to_dtype_func = NULL + * + */ + __pyx_v_to_object_func = NULL; + + /* "View.MemoryView":1052 + * else: + * to_object_func = NULL + * to_dtype_func = NULL # <<<<<<<<<<<<<< + * + * return memoryview_fromslice(memviewslice[0], memview.view.ndim, + */ + __pyx_v_to_dtype_func = NULL; + } + __pyx_L3:; + + /* "View.MemoryView":1054 + * to_dtype_func = NULL + * + * return memoryview_fromslice(memviewslice[0], memview.view.ndim, # <<<<<<<<<<<<<< + * to_object_func, to_dtype_func, + * memview.dtype_is_object) + */ + __Pyx_XDECREF(__pyx_r); + + /* "View.MemoryView":1056 + * return memoryview_fromslice(memviewslice[0], memview.view.ndim, + * to_object_func, to_dtype_func, + * memview.dtype_is_object) # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_5 = __pyx_memoryview_fromslice((__pyx_v_memviewslice[0]), __pyx_v_memview->view.ndim, __pyx_v_to_object_func, __pyx_v_to_dtype_func, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1054; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_5); + __pyx_r = __pyx_t_5; + __pyx_t_5 = 0; + goto __pyx_L0; + + /* "View.MemoryView":1040 + * + * @cname('__pyx_memoryview_copy_object_from_slice') + * cdef memoryview_copy_from_slice(memoryview memview, __Pyx_memviewslice *memviewslice): # <<<<<<<<<<<<<< + * """ + * Create a new memoryview object from a given memoryview object and slice. + */ + + /* function exit code */ + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_5); + __Pyx_AddTraceback("View.MemoryView.memoryview_copy_from_slice", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = 0; + __pyx_L0:; + __Pyx_XGIVEREF(__pyx_r); + __Pyx_RefNannyFinishContext(); + return __pyx_r; +} + +/* "View.MemoryView":1062 + * + * + * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: # <<<<<<<<<<<<<< + * if arg < 0: + * return -arg + */ + +static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { + Py_ssize_t __pyx_r; + int __pyx_t_1; + + /* "View.MemoryView":1063 + * + * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: + * if arg < 0: # <<<<<<<<<<<<<< + * return -arg + * else: + */ + __pyx_t_1 = ((__pyx_v_arg < 0) != 0); + if (__pyx_t_1) { + + /* "View.MemoryView":1064 + * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: + * if arg < 0: + * return -arg # <<<<<<<<<<<<<< + * else: + * return arg + */ + __pyx_r = (-__pyx_v_arg); + goto __pyx_L0; + } + /*else*/ { + + /* "View.MemoryView":1066 + * return -arg + * else: + * return arg # <<<<<<<<<<<<<< + * + * @cname('__pyx_get_best_slice_order') + */ + __pyx_r = __pyx_v_arg; + goto __pyx_L0; + } + + /* "View.MemoryView":1062 + * + * + * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: # <<<<<<<<<<<<<< + * if arg < 0: + * return -arg + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "View.MemoryView":1069 + * + * @cname('__pyx_get_best_slice_order') + * cdef char get_best_order(__Pyx_memviewslice *mslice, int ndim) nogil: # <<<<<<<<<<<<<< + * """ + * Figure out the best memory access order for a given slice. + */ + +static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int __pyx_v_ndim) { + int __pyx_v_i; + Py_ssize_t __pyx_v_c_stride; + Py_ssize_t __pyx_v_f_stride; + char __pyx_r; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + + /* "View.MemoryView":1074 + * """ + * cdef int i + * cdef Py_ssize_t c_stride = 0 # <<<<<<<<<<<<<< + * cdef Py_ssize_t f_stride = 0 + * + */ + __pyx_v_c_stride = 0; + + /* "View.MemoryView":1075 + * cdef int i + * cdef Py_ssize_t c_stride = 0 + * cdef Py_ssize_t f_stride = 0 # <<<<<<<<<<<<<< + * + * for i in range(ndim - 1, -1, -1): + */ + __pyx_v_f_stride = 0; + + /* "View.MemoryView":1077 + * cdef Py_ssize_t f_stride = 0 + * + * for i in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< + * if mslice.shape[i] > 1: + * c_stride = mslice.strides[i] + */ + for (__pyx_t_1 = (__pyx_v_ndim - 1); __pyx_t_1 > -1; __pyx_t_1-=1) { + __pyx_v_i = __pyx_t_1; + + /* "View.MemoryView":1078 + * + * for i in range(ndim - 1, -1, -1): + * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< + * c_stride = mslice.strides[i] + * break + */ + __pyx_t_2 = (((__pyx_v_mslice->shape[__pyx_v_i]) > 1) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1079 + * for i in range(ndim - 1, -1, -1): + * if mslice.shape[i] > 1: + * c_stride = mslice.strides[i] # <<<<<<<<<<<<<< + * break + * + */ + __pyx_v_c_stride = (__pyx_v_mslice->strides[__pyx_v_i]); + + /* "View.MemoryView":1080 + * if mslice.shape[i] > 1: + * c_stride = mslice.strides[i] + * break # <<<<<<<<<<<<<< + * + * for i in range(ndim): + */ + goto __pyx_L4_break; + } + } + __pyx_L4_break:; + + /* "View.MemoryView":1082 + * break + * + * for i in range(ndim): # <<<<<<<<<<<<<< + * if mslice.shape[i] > 1: + * f_stride = mslice.strides[i] + */ + __pyx_t_1 = __pyx_v_ndim; + for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_1; __pyx_t_3+=1) { + __pyx_v_i = __pyx_t_3; + + /* "View.MemoryView":1083 + * + * for i in range(ndim): + * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< + * f_stride = mslice.strides[i] + * break + */ + __pyx_t_2 = (((__pyx_v_mslice->shape[__pyx_v_i]) > 1) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1084 + * for i in range(ndim): + * if mslice.shape[i] > 1: + * f_stride = mslice.strides[i] # <<<<<<<<<<<<<< + * break + * + */ + __pyx_v_f_stride = (__pyx_v_mslice->strides[__pyx_v_i]); + + /* "View.MemoryView":1085 + * if mslice.shape[i] > 1: + * f_stride = mslice.strides[i] + * break # <<<<<<<<<<<<<< + * + * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): + */ + goto __pyx_L7_break; + } + } + __pyx_L7_break:; + + /* "View.MemoryView":1087 + * break + * + * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): # <<<<<<<<<<<<<< + * return 'C' + * else: + */ + __pyx_t_2 = ((abs_py_ssize_t(__pyx_v_c_stride) <= abs_py_ssize_t(__pyx_v_f_stride)) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1088 + * + * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): + * return 'C' # <<<<<<<<<<<<<< + * else: + * return 'F' + */ + __pyx_r = 'C'; + goto __pyx_L0; + } + /*else*/ { + + /* "View.MemoryView":1090 + * return 'C' + * else: + * return 'F' # <<<<<<<<<<<<<< + * + * @cython.cdivision(True) + */ + __pyx_r = 'F'; + goto __pyx_L0; + } + + /* "View.MemoryView":1069 + * + * @cname('__pyx_get_best_slice_order') + * cdef char get_best_order(__Pyx_memviewslice *mslice, int ndim) nogil: # <<<<<<<<<<<<<< + * """ + * Figure out the best memory access order for a given slice. + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "View.MemoryView":1093 + * + * @cython.cdivision(True) + * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< + * char *dst_data, Py_ssize_t *dst_strides, + * Py_ssize_t *src_shape, Py_ssize_t *dst_shape, + */ + +static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v_src_strides, char *__pyx_v_dst_data, Py_ssize_t *__pyx_v_dst_strides, Py_ssize_t *__pyx_v_src_shape, Py_ssize_t *__pyx_v_dst_shape, int __pyx_v_ndim, size_t __pyx_v_itemsize) { + CYTHON_UNUSED Py_ssize_t __pyx_v_i; + CYTHON_UNUSED Py_ssize_t __pyx_v_src_extent; + Py_ssize_t __pyx_v_dst_extent; + Py_ssize_t __pyx_v_src_stride; + Py_ssize_t __pyx_v_dst_stride; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + Py_ssize_t __pyx_t_4; + Py_ssize_t __pyx_t_5; + + /* "View.MemoryView":1100 + * + * cdef Py_ssize_t i + * cdef Py_ssize_t src_extent = src_shape[0] # <<<<<<<<<<<<<< + * cdef Py_ssize_t dst_extent = dst_shape[0] + * cdef Py_ssize_t src_stride = src_strides[0] + */ + __pyx_v_src_extent = (__pyx_v_src_shape[0]); + + /* "View.MemoryView":1101 + * cdef Py_ssize_t i + * cdef Py_ssize_t src_extent = src_shape[0] + * cdef Py_ssize_t dst_extent = dst_shape[0] # <<<<<<<<<<<<<< + * cdef Py_ssize_t src_stride = src_strides[0] + * cdef Py_ssize_t dst_stride = dst_strides[0] + */ + __pyx_v_dst_extent = (__pyx_v_dst_shape[0]); + + /* "View.MemoryView":1102 + * cdef Py_ssize_t src_extent = src_shape[0] + * cdef Py_ssize_t dst_extent = dst_shape[0] + * cdef Py_ssize_t src_stride = src_strides[0] # <<<<<<<<<<<<<< + * cdef Py_ssize_t dst_stride = dst_strides[0] + * + */ + __pyx_v_src_stride = (__pyx_v_src_strides[0]); + + /* "View.MemoryView":1103 + * cdef Py_ssize_t dst_extent = dst_shape[0] + * cdef Py_ssize_t src_stride = src_strides[0] + * cdef Py_ssize_t dst_stride = dst_strides[0] # <<<<<<<<<<<<<< + * + * if ndim == 1: + */ + __pyx_v_dst_stride = (__pyx_v_dst_strides[0]); + + /* "View.MemoryView":1105 + * cdef Py_ssize_t dst_stride = dst_strides[0] + * + * if ndim == 1: # <<<<<<<<<<<<<< + * if (src_stride > 0 and dst_stride > 0 and + * src_stride == itemsize == dst_stride): + */ + __pyx_t_1 = ((__pyx_v_ndim == 1) != 0); + if (__pyx_t_1) { + + /* "View.MemoryView":1106 + * + * if ndim == 1: + * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< + * src_stride == itemsize == dst_stride): + * memcpy(dst_data, src_data, itemsize * dst_extent) + */ + __pyx_t_2 = ((__pyx_v_src_stride > 0) != 0); + if (__pyx_t_2) { + goto __pyx_L6_next_and; + } else { + __pyx_t_1 = __pyx_t_2; + goto __pyx_L5_bool_binop_done; + } + __pyx_L6_next_and:; + __pyx_t_2 = ((__pyx_v_dst_stride > 0) != 0); + if (__pyx_t_2) { + goto __pyx_L7_next_and; + } else { + __pyx_t_1 = __pyx_t_2; + goto __pyx_L5_bool_binop_done; + } + __pyx_L7_next_and:; + + /* "View.MemoryView":1107 + * if ndim == 1: + * if (src_stride > 0 and dst_stride > 0 and + * src_stride == itemsize == dst_stride): # <<<<<<<<<<<<<< + * memcpy(dst_data, src_data, itemsize * dst_extent) + * else: + */ + __pyx_t_2 = (((size_t)__pyx_v_src_stride) == __pyx_v_itemsize); + if (__pyx_t_2) { + __pyx_t_2 = (__pyx_v_itemsize == ((size_t)__pyx_v_dst_stride)); + } + __pyx_t_3 = (__pyx_t_2 != 0); + __pyx_t_1 = __pyx_t_3; + __pyx_L5_bool_binop_done:; + if (__pyx_t_1) { + + /* "View.MemoryView":1108 + * if (src_stride > 0 and dst_stride > 0 and + * src_stride == itemsize == dst_stride): + * memcpy(dst_data, src_data, itemsize * dst_extent) # <<<<<<<<<<<<<< + * else: + * for i in range(dst_extent): + */ + memcpy(__pyx_v_dst_data, __pyx_v_src_data, (__pyx_v_itemsize * __pyx_v_dst_extent)); + goto __pyx_L4; + } + /*else*/ { + + /* "View.MemoryView":1110 + * memcpy(dst_data, src_data, itemsize * dst_extent) + * else: + * for i in range(dst_extent): # <<<<<<<<<<<<<< + * memcpy(dst_data, src_data, itemsize) + * src_data += src_stride + */ + __pyx_t_4 = __pyx_v_dst_extent; + for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { + __pyx_v_i = __pyx_t_5; + + /* "View.MemoryView":1111 + * else: + * for i in range(dst_extent): + * memcpy(dst_data, src_data, itemsize) # <<<<<<<<<<<<<< + * src_data += src_stride + * dst_data += dst_stride + */ + memcpy(__pyx_v_dst_data, __pyx_v_src_data, __pyx_v_itemsize); + + /* "View.MemoryView":1112 + * for i in range(dst_extent): + * memcpy(dst_data, src_data, itemsize) + * src_data += src_stride # <<<<<<<<<<<<<< + * dst_data += dst_stride + * else: + */ + __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); + + /* "View.MemoryView":1113 + * memcpy(dst_data, src_data, itemsize) + * src_data += src_stride + * dst_data += dst_stride # <<<<<<<<<<<<<< + * else: + * for i in range(dst_extent): + */ + __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); + } + } + __pyx_L4:; + goto __pyx_L3; + } + /*else*/ { + + /* "View.MemoryView":1115 + * dst_data += dst_stride + * else: + * for i in range(dst_extent): # <<<<<<<<<<<<<< + * _copy_strided_to_strided(src_data, src_strides + 1, + * dst_data, dst_strides + 1, + */ + __pyx_t_4 = __pyx_v_dst_extent; + for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { + __pyx_v_i = __pyx_t_5; + + /* "View.MemoryView":1116 + * else: + * for i in range(dst_extent): + * _copy_strided_to_strided(src_data, src_strides + 1, # <<<<<<<<<<<<<< + * dst_data, dst_strides + 1, + * src_shape + 1, dst_shape + 1, + */ + _copy_strided_to_strided(__pyx_v_src_data, (__pyx_v_src_strides + 1), __pyx_v_dst_data, (__pyx_v_dst_strides + 1), (__pyx_v_src_shape + 1), (__pyx_v_dst_shape + 1), (__pyx_v_ndim - 1), __pyx_v_itemsize); + + /* "View.MemoryView":1120 + * src_shape + 1, dst_shape + 1, + * ndim - 1, itemsize) + * src_data += src_stride # <<<<<<<<<<<<<< + * dst_data += dst_stride + * + */ + __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); + + /* "View.MemoryView":1121 + * ndim - 1, itemsize) + * src_data += src_stride + * dst_data += dst_stride # <<<<<<<<<<<<<< + * + * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, + */ + __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride); + } + } + __pyx_L3:; + + /* "View.MemoryView":1093 + * + * @cython.cdivision(True) + * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< + * char *dst_data, Py_ssize_t *dst_strides, + * Py_ssize_t *src_shape, Py_ssize_t *dst_shape, + */ + + /* function exit code */ +} + +/* "View.MemoryView":1123 + * dst_data += dst_stride + * + * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< + * __Pyx_memviewslice *dst, + * int ndim, size_t itemsize) nogil: + */ + +static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memviewslice *__pyx_v_dst, int __pyx_v_ndim, size_t __pyx_v_itemsize) { + + /* "View.MemoryView":1126 + * __Pyx_memviewslice *dst, + * int ndim, size_t itemsize) nogil: + * _copy_strided_to_strided(src.data, src.strides, dst.data, dst.strides, # <<<<<<<<<<<<<< + * src.shape, dst.shape, ndim, itemsize) + * + */ + _copy_strided_to_strided(__pyx_v_src->data, __pyx_v_src->strides, __pyx_v_dst->data, __pyx_v_dst->strides, __pyx_v_src->shape, __pyx_v_dst->shape, __pyx_v_ndim, __pyx_v_itemsize); + + /* "View.MemoryView":1123 + * dst_data += dst_stride + * + * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< + * __Pyx_memviewslice *dst, + * int ndim, size_t itemsize) nogil: + */ + + /* function exit code */ +} + +/* "View.MemoryView":1130 + * + * @cname('__pyx_memoryview_slice_get_size') + * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< + * "Return the size of the memory occupied by the slice in number of bytes" + * cdef int i + */ + +static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_src, int __pyx_v_ndim) { + int __pyx_v_i; + Py_ssize_t __pyx_v_size; + Py_ssize_t __pyx_r; + Py_ssize_t __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + + /* "View.MemoryView":1133 + * "Return the size of the memory occupied by the slice in number of bytes" + * cdef int i + * cdef Py_ssize_t size = src.memview.view.itemsize # <<<<<<<<<<<<<< + * + * for i in range(ndim): + */ + __pyx_t_1 = __pyx_v_src->memview->view.itemsize; + __pyx_v_size = __pyx_t_1; + + /* "View.MemoryView":1135 + * cdef Py_ssize_t size = src.memview.view.itemsize + * + * for i in range(ndim): # <<<<<<<<<<<<<< + * size *= src.shape[i] + * + */ + __pyx_t_2 = __pyx_v_ndim; + for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { + __pyx_v_i = __pyx_t_3; + + /* "View.MemoryView":1136 + * + * for i in range(ndim): + * size *= src.shape[i] # <<<<<<<<<<<<<< + * + * return size + */ + __pyx_v_size = (__pyx_v_size * (__pyx_v_src->shape[__pyx_v_i])); + } + + /* "View.MemoryView":1138 + * size *= src.shape[i] + * + * return size # <<<<<<<<<<<<<< + * + * @cname('__pyx_fill_contig_strides_array') + */ + __pyx_r = __pyx_v_size; + goto __pyx_L0; + + /* "View.MemoryView":1130 + * + * @cname('__pyx_memoryview_slice_get_size') + * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< + * "Return the size of the memory occupied by the slice in number of bytes" + * cdef int i + */ + + /* function exit code */ + __pyx_L0:; + return __pyx_r; +} + +/* "View.MemoryView":1141 + * + * @cname('__pyx_fill_contig_strides_array') + * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<< + * Py_ssize_t *shape, Py_ssize_t *strides, Py_ssize_t stride, + * int ndim, char order) nogil: + */ + +static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ssize_t *__pyx_v_strides, Py_ssize_t __pyx_v_stride, int __pyx_v_ndim, char __pyx_v_order) { + int __pyx_v_idx; + Py_ssize_t __pyx_r; + int __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + + /* "View.MemoryView":1150 + * cdef int idx + * + * if order == 'F': # <<<<<<<<<<<<<< + * for idx in range(ndim): + * strides[idx] = stride + */ + __pyx_t_1 = ((__pyx_v_order == 'F') != 0); + if (__pyx_t_1) { + + /* "View.MemoryView":1151 + * + * if order == 'F': + * for idx in range(ndim): # <<<<<<<<<<<<<< + * strides[idx] = stride + * stride = stride * shape[idx] + */ + __pyx_t_2 = __pyx_v_ndim; + for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { + __pyx_v_idx = __pyx_t_3; + + /* "View.MemoryView":1152 + * if order == 'F': + * for idx in range(ndim): + * strides[idx] = stride # <<<<<<<<<<<<<< + * stride = stride * shape[idx] + * else: + */ + (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride; + + /* "View.MemoryView":1153 + * for idx in range(ndim): + * strides[idx] = stride + * stride = stride * shape[idx] # <<<<<<<<<<<<<< + * else: + * for idx in range(ndim - 1, -1, -1): + */ + __pyx_v_stride = (__pyx_v_stride * (__pyx_v_shape[__pyx_v_idx])); + 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__pyx_memoryview_copy_data_to_temp((&__pyx_v_src), (&__pyx_v_tmp), __pyx_v_order, __pyx_v_ndim); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1261; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_v_tmpdata = __pyx_t_6; + + /* "View.MemoryView":1262 + * + * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) + * src = tmp # <<<<<<<<<<<<<< + * + * if not broadcasting: + */ + __pyx_v_src = __pyx_v_tmp; + goto __pyx_L9; + } + __pyx_L9:; + + /* "View.MemoryView":1264 + * src = tmp + * + * if not broadcasting: # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_2 = ((!(__pyx_v_broadcasting != 0)) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1267 + * + * + * if slice_is_contig(&src, 'C', ndim): # <<<<<<<<<<<<<< + * direct_copy = slice_is_contig(&dst, 'C', ndim) + * elif slice_is_contig(&src, 'F', ndim): + */ + __pyx_t_2 = (__pyx_memviewslice_is_contig((&__pyx_v_src), 'C', __pyx_v_ndim) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1268 + * + * if slice_is_contig(&src, 'C', ndim): + * direct_copy = slice_is_contig(&dst, 'C', ndim) # <<<<<<<<<<<<<< + * elif slice_is_contig(&src, 'F', ndim): + * direct_copy = slice_is_contig(&dst, 'F', ndim) + */ + __pyx_v_direct_copy = __pyx_memviewslice_is_contig((&__pyx_v_dst), 'C', __pyx_v_ndim); + goto __pyx_L12; + } + + /* "View.MemoryView":1269 + * if slice_is_contig(&src, 'C', ndim): + * direct_copy = slice_is_contig(&dst, 'C', ndim) + * elif slice_is_contig(&src, 'F', ndim): # <<<<<<<<<<<<<< + * direct_copy = slice_is_contig(&dst, 'F', ndim) + * + */ + __pyx_t_2 = (__pyx_memviewslice_is_contig((&__pyx_v_src), 'F', __pyx_v_ndim) != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1270 + * direct_copy = slice_is_contig(&dst, 'C', ndim) + * elif slice_is_contig(&src, 'F', ndim): + * direct_copy = slice_is_contig(&dst, 'F', ndim) # <<<<<<<<<<<<<< + * + * if direct_copy: + */ + __pyx_v_direct_copy = __pyx_memviewslice_is_contig((&__pyx_v_dst), 'F', __pyx_v_ndim); + goto __pyx_L12; + } + __pyx_L12:; + + /* "View.MemoryView":1272 + * direct_copy = slice_is_contig(&dst, 'F', ndim) + * + * if direct_copy: # <<<<<<<<<<<<<< + * + * refcount_copying(&dst, dtype_is_object, ndim, False) + */ + __pyx_t_2 = (__pyx_v_direct_copy != 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1274 + * if direct_copy: + * + * refcount_copying(&dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< + * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) + * refcount_copying(&dst, dtype_is_object, ndim, True) + */ + __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 0); + + /* "View.MemoryView":1275 + * + * refcount_copying(&dst, dtype_is_object, ndim, False) + * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) # <<<<<<<<<<<<<< + * refcount_copying(&dst, dtype_is_object, ndim, True) + * free(tmpdata) + */ + memcpy(__pyx_v_dst.data, __pyx_v_src.data, __pyx_memoryview_slice_get_size((&__pyx_v_src), __pyx_v_ndim)); + + /* "View.MemoryView":1276 + * refcount_copying(&dst, dtype_is_object, ndim, False) + * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) + * refcount_copying(&dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< + * free(tmpdata) + * return 0 + */ + __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 1); + + /* "View.MemoryView":1277 + * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) + * refcount_copying(&dst, dtype_is_object, ndim, True) + * free(tmpdata) # <<<<<<<<<<<<<< + * return 0 + * + */ + free(__pyx_v_tmpdata); + + /* "View.MemoryView":1278 + * refcount_copying(&dst, dtype_is_object, ndim, True) + * free(tmpdata) + * return 0 # <<<<<<<<<<<<<< + * + * if order == 'F' == get_best_order(&dst, ndim): + */ + __pyx_r = 0; + goto __pyx_L0; + } + goto __pyx_L11; + } + __pyx_L11:; + + /* "View.MemoryView":1280 + * return 0 + * + * if order == 'F' == get_best_order(&dst, ndim): # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_2 = (__pyx_v_order == 'F'); + if (__pyx_t_2) { + __pyx_t_2 = ('F' == __pyx_get_best_slice_order((&__pyx_v_dst), __pyx_v_ndim)); + } + __pyx_t_7 = (__pyx_t_2 != 0); + if (__pyx_t_7) { + + /* "View.MemoryView":1283 + * + * + * transpose_memslice(&src) # <<<<<<<<<<<<<< + * transpose_memslice(&dst) + * + */ + __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_src)); if (unlikely(__pyx_t_5 == 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "View.MemoryView":1284 + * + * transpose_memslice(&src) + * transpose_memslice(&dst) # <<<<<<<<<<<<<< + * + * refcount_copying(&dst, dtype_is_object, ndim, False) + */ + __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_dst)); if (unlikely(__pyx_t_5 == 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1284; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + goto __pyx_L14; + } + __pyx_L14:; + + /* "View.MemoryView":1286 + * transpose_memslice(&dst) + * + * refcount_copying(&dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< + * copy_strided_to_strided(&src, &dst, ndim, itemsize) + * refcount_copying(&dst, dtype_is_object, ndim, True) + */ + __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 0); + + /* "View.MemoryView":1287 + * + * refcount_copying(&dst, dtype_is_object, ndim, False) + * copy_strided_to_strided(&src, &dst, ndim, itemsize) # <<<<<<<<<<<<<< + * refcount_copying(&dst, dtype_is_object, ndim, True) + * + */ + copy_strided_to_strided((&__pyx_v_src), (&__pyx_v_dst), __pyx_v_ndim, __pyx_v_itemsize); + + /* "View.MemoryView":1288 + * refcount_copying(&dst, dtype_is_object, ndim, False) + * copy_strided_to_strided(&src, &dst, ndim, itemsize) + * refcount_copying(&dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< + * + * free(tmpdata) + */ + __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 1); + + /* "View.MemoryView":1290 + * refcount_copying(&dst, dtype_is_object, ndim, True) + * + * free(tmpdata) # <<<<<<<<<<<<<< + * return 0 + * + */ + free(__pyx_v_tmpdata); + + /* "View.MemoryView":1291 + * + * free(tmpdata) + * return 0 # <<<<<<<<<<<<<< + * + * @cname('__pyx_memoryview_broadcast_leading') + */ + __pyx_r = 0; + goto __pyx_L0; + + /* "View.MemoryView":1222 + * + * @cname('__pyx_memoryview_copy_contents') + * cdef int memoryview_copy_contents(__Pyx_memviewslice src, # <<<<<<<<<<<<<< + * __Pyx_memviewslice dst, + * int src_ndim, int dst_ndim, + */ + + /* function exit code */ + __pyx_L1_error:; + { + #ifdef WITH_THREAD + PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); + #endif + __Pyx_AddTraceback("View.MemoryView.memoryview_copy_contents", __pyx_clineno, __pyx_lineno, __pyx_filename); + #ifdef WITH_THREAD + PyGILState_Release(__pyx_gilstate_save); + #endif + } + __pyx_r = -1; + __pyx_L0:; + return __pyx_r; +} + +/* "View.MemoryView":1294 + * + * @cname('__pyx_memoryview_broadcast_leading') + * cdef void broadcast_leading(__Pyx_memviewslice *slice, # <<<<<<<<<<<<<< + * int ndim, + * int ndim_other) nogil: + */ + +static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_slice, int __pyx_v_ndim, int __pyx_v_ndim_other) { + int __pyx_v_i; + int __pyx_v_offset; + int __pyx_t_1; + int __pyx_t_2; + + /* "View.MemoryView":1298 + * int ndim_other) nogil: + * cdef int i + * cdef int offset = ndim_other - ndim # <<<<<<<<<<<<<< + * + * for i in range(ndim - 1, -1, -1): + */ + __pyx_v_offset = (__pyx_v_ndim_other - __pyx_v_ndim); + + /* "View.MemoryView":1300 + * cdef int offset = ndim_other - ndim + * + * for i in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< + * slice.shape[i + offset] = slice.shape[i] + * slice.strides[i + offset] = slice.strides[i] + */ + for (__pyx_t_1 = (__pyx_v_ndim - 1); __pyx_t_1 > -1; __pyx_t_1-=1) { + __pyx_v_i = __pyx_t_1; + + /* "View.MemoryView":1301 + * + * for i in range(ndim - 1, -1, -1): + * slice.shape[i + offset] = slice.shape[i] # <<<<<<<<<<<<<< + * slice.strides[i + offset] = slice.strides[i] + * slice.suboffsets[i + offset] = slice.suboffsets[i] + */ + (__pyx_v_slice->shape[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_slice->shape[__pyx_v_i]); + + /* "View.MemoryView":1302 + * for i in range(ndim - 1, -1, -1): + * slice.shape[i + offset] = slice.shape[i] + * slice.strides[i + offset] = slice.strides[i] # <<<<<<<<<<<<<< + * slice.suboffsets[i + offset] = slice.suboffsets[i] + * + */ + (__pyx_v_slice->strides[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_slice->strides[__pyx_v_i]); + + /* "View.MemoryView":1303 + * slice.shape[i + offset] = slice.shape[i] + * slice.strides[i + offset] = slice.strides[i] + * slice.suboffsets[i + offset] = slice.suboffsets[i] # <<<<<<<<<<<<<< + * + * for i in range(offset): + */ + (__pyx_v_slice->suboffsets[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_slice->suboffsets[__pyx_v_i]); + } + + /* "View.MemoryView":1305 + * slice.suboffsets[i + offset] = slice.suboffsets[i] + * + * for i in range(offset): # <<<<<<<<<<<<<< + * slice.shape[i] = 1 + * slice.strides[i] = slice.strides[0] + */ + __pyx_t_1 = __pyx_v_offset; + for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { + __pyx_v_i = __pyx_t_2; + + /* "View.MemoryView":1306 + * + * for i in range(offset): + * slice.shape[i] = 1 # <<<<<<<<<<<<<< + * slice.strides[i] = slice.strides[0] + * slice.suboffsets[i] = -1 + */ + (__pyx_v_slice->shape[__pyx_v_i]) = 1; + + /* "View.MemoryView":1307 + * for i in range(offset): + * slice.shape[i] = 1 + * slice.strides[i] = slice.strides[0] # <<<<<<<<<<<<<< + * slice.suboffsets[i] = -1 + * + */ + (__pyx_v_slice->strides[__pyx_v_i]) = (__pyx_v_slice->strides[0]); + + /* "View.MemoryView":1308 + * slice.shape[i] = 1 + * slice.strides[i] = slice.strides[0] + * slice.suboffsets[i] = -1 # <<<<<<<<<<<<<< + * + * + */ + (__pyx_v_slice->suboffsets[__pyx_v_i]) = -1; + } + + /* "View.MemoryView":1294 + * + * @cname('__pyx_memoryview_broadcast_leading') + * cdef void broadcast_leading(__Pyx_memviewslice *slice, # <<<<<<<<<<<<<< + * int ndim, + * int ndim_other) nogil: + */ + + /* function 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*__pyx_v_strides, int __pyx_v_ndim, int __pyx_v_inc) { + CYTHON_UNUSED Py_ssize_t __pyx_v_i; + __Pyx_RefNannyDeclarations + Py_ssize_t __pyx_t_1; + Py_ssize_t __pyx_t_2; + int __pyx_t_3; + __Pyx_RefNannySetupContext("refcount_objects_in_slice", 0); + + /* "View.MemoryView":1335 + * cdef Py_ssize_t i + * + * for i in range(shape[0]): # <<<<<<<<<<<<<< + * if ndim == 1: + * if inc: + */ + __pyx_t_1 = (__pyx_v_shape[0]); + for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { + __pyx_v_i = __pyx_t_2; + + /* "View.MemoryView":1336 + * + * for i in range(shape[0]): + * if ndim == 1: # <<<<<<<<<<<<<< + * if inc: + * Py_INCREF(( data)[0]) + */ + __pyx_t_3 = ((__pyx_v_ndim == 1) != 0); + if (__pyx_t_3) { + + /* "View.MemoryView":1337 + * for i in range(shape[0]): + * if ndim == 1: + * if inc: # <<<<<<<<<<<<<< + * Py_INCREF(( data)[0]) + * else: + */ + __pyx_t_3 = (__pyx_v_inc != 0); + if (__pyx_t_3) { + + /* "View.MemoryView":1338 + * if ndim == 1: + * if inc: + * Py_INCREF(( data)[0]) # 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/* "View.MemoryView":1355 + * bint dtype_is_object) nogil: + * refcount_copying(dst, dtype_is_object, ndim, False) + * _slice_assign_scalar(dst.data, dst.shape, dst.strides, ndim, # <<<<<<<<<<<<<< + * itemsize, item) + * refcount_copying(dst, dtype_is_object, ndim, True) + */ + __pyx_memoryview__slice_assign_scalar(__pyx_v_dst->data, __pyx_v_dst->shape, __pyx_v_dst->strides, __pyx_v_ndim, __pyx_v_itemsize, __pyx_v_item); + + /* "View.MemoryView":1357 + * _slice_assign_scalar(dst.data, dst.shape, dst.strides, ndim, + * itemsize, item) + * refcount_copying(dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< + * + * + */ + __pyx_memoryview_refcount_copying(__pyx_v_dst, __pyx_v_dtype_is_object, __pyx_v_ndim, 1); + + /* "View.MemoryView":1351 + * + * @cname('__pyx_memoryview_slice_assign_scalar') + * cdef void slice_assign_scalar(__Pyx_memviewslice *dst, int ndim, # <<<<<<<<<<<<<< + * size_t itemsize, void *item, + * bint dtype_is_object) nogil: + */ + + /* function exit code */ +} + +/* 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__pyx_getprop___pyx_memoryview_size, 0, 0, 0}, + {0, 0, 0, 0, 0} +}; + +static PySequenceMethods __pyx_tp_as_sequence_memoryview = { + __pyx_memoryview___len__, /*sq_length*/ + 0, /*sq_concat*/ + 0, /*sq_repeat*/ + __pyx_sq_item_memoryview, /*sq_item*/ + 0, /*sq_slice*/ + 0, /*sq_ass_item*/ + 0, /*sq_ass_slice*/ + 0, /*sq_contains*/ + 0, /*sq_inplace_concat*/ + 0, /*sq_inplace_repeat*/ +}; + +static PyMappingMethods __pyx_tp_as_mapping_memoryview = { + __pyx_memoryview___len__, /*mp_length*/ + __pyx_memoryview___getitem__, /*mp_subscript*/ + __pyx_mp_ass_subscript_memoryview, /*mp_ass_subscript*/ +}; + +static PyBufferProcs __pyx_tp_as_buffer_memoryview = { + #if PY_MAJOR_VERSION < 3 + 0, /*bf_getreadbuffer*/ + #endif + #if PY_MAJOR_VERSION < 3 + 0, /*bf_getwritebuffer*/ + #endif + #if PY_MAJOR_VERSION < 3 + 0, /*bf_getsegcount*/ + #endif + #if PY_MAJOR_VERSION < 3 + 0, /*bf_getcharbuffer*/ + #endif + __pyx_memoryview_getbuffer, /*bf_getbuffer*/ + 0, /*bf_releasebuffer*/ +}; + +static PyTypeObject __pyx_type___pyx_memoryview = { + PyVarObject_HEAD_INIT(0, 0) + "sklearn.manifold._barnes_hut_tsne.memoryview", /*tp_name*/ + sizeof(struct __pyx_memoryview_obj), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_memoryview, /*tp_dealloc*/ + 0, /*tp_print*/ + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ + #if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ + #else + 0, /*reserved*/ + #endif + __pyx_memoryview___repr__, /*tp_repr*/ + 0, /*tp_as_number*/ + &__pyx_tp_as_sequence_memoryview, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_memoryview, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + __pyx_memoryview___str__, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + &__pyx_tp_as_buffer_memoryview, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + 0, /*tp_doc*/ + __pyx_tp_traverse_memoryview, /*tp_traverse*/ + __pyx_tp_clear_memoryview, /*tp_clear*/ + 0, 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__pyx_vtabstruct_memoryview*)__pyx_vtabptr__memoryviewslice; + p->from_object = Py_None; Py_INCREF(Py_None); + p->from_slice.memview = NULL; + return o; +} + +static void __pyx_tp_dealloc__memoryviewslice(PyObject *o) { + struct __pyx_memoryviewslice_obj *p = (struct __pyx_memoryviewslice_obj *)o; + #if PY_VERSION_HEX >= 0x030400a1 + if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { + if (PyObject_CallFinalizerFromDealloc(o)) return; + } + #endif + PyObject_GC_UnTrack(o); + { + PyObject *etype, *eval, *etb; + PyErr_Fetch(&etype, &eval, &etb); + ++Py_REFCNT(o); + __pyx_memoryviewslice___dealloc__(o); + --Py_REFCNT(o); + PyErr_Restore(etype, eval, etb); + } + Py_CLEAR(p->from_object); + PyObject_GC_Track(o); + __pyx_tp_dealloc_memoryview(o); +} + +static int __pyx_tp_traverse__memoryviewslice(PyObject *o, visitproc v, void *a) { + int e; + struct __pyx_memoryviewslice_obj *p = (struct __pyx_memoryviewslice_obj *)o; + e = __pyx_tp_traverse_memoryview(o, v, a); if (e) return e; + if (p->from_object) { + e = (*v)(p->from_object, a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear__memoryviewslice(PyObject *o) { + PyObject* tmp; + struct __pyx_memoryviewslice_obj *p = (struct __pyx_memoryviewslice_obj *)o; + __pyx_tp_clear_memoryview(o); + tmp = ((PyObject*)p->from_object); + p->from_object = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + __PYX_XDEC_MEMVIEW(&p->from_slice, 1); + return 0; +} + +static PyObject *__pyx_getprop___pyx_memoryviewslice_base(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_memoryviewslice__get__base(o); +} + +static PyMethodDef __pyx_methods__memoryviewslice[] = { + {0, 0, 0, 0} +}; + +static struct PyGetSetDef __pyx_getsets__memoryviewslice[] = { + {(char *)"base", __pyx_getprop___pyx_memoryviewslice_base, 0, 0, 0}, + {0, 0, 0, 0, 0} +}; + +static PyTypeObject __pyx_type___pyx_memoryviewslice = { + PyVarObject_HEAD_INIT(0, 0) + "sklearn.manifold._barnes_hut_tsne._memoryviewslice", /*tp_name*/ + 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self = PyCFunction_GET_SELF(func); + if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) + return NULL; + result = cfunc(self, arg); + Py_LeaveRecursiveCall(); + if (unlikely(!result) && unlikely(!PyErr_Occurred())) { + PyErr_SetString( + PyExc_SystemError, + "NULL result without error in PyObject_Call"); + } + return result; +} +#endif + +#if CYTHON_COMPILING_IN_CPYTHON +static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) { + PyObject *result; + PyObject *args = PyTuple_New(1); + if (unlikely(!args)) return NULL; + Py_INCREF(arg); + PyTuple_SET_ITEM(args, 0, arg); + result = __Pyx_PyObject_Call(func, args, NULL); + Py_DECREF(args); + return result; +} +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { +#ifdef __Pyx_CyFunction_USED + if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) { +#else + if (likely(PyCFunction_Check(func))) { +#endif + if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { + return __Pyx_PyObject_CallMethO(func, arg); + } + } + return __Pyx__PyObject_CallOneArg(func, arg); +} +#else +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { + PyObject* args = PyTuple_Pack(1, arg); + return (likely(args)) ? __Pyx_PyObject_Call(func, args, NULL) : NULL; +} +#endif + +static void __Pyx_RaiseArgtupleInvalid( + const char* func_name, + int exact, + Py_ssize_t num_min, + Py_ssize_t num_max, + Py_ssize_t num_found) +{ + Py_ssize_t num_expected; + const char *more_or_less; + if (num_found < num_min) { + num_expected = num_min; + more_or_less = "at least"; + } else { + num_expected = num_max; + more_or_less = "at most"; + } + if (exact) { + more_or_less = "exactly"; + } + PyErr_Format(PyExc_TypeError, + "%.200s() takes %.8s %" CYTHON_FORMAT_SSIZE_T "d positional argument%.1s (%" CYTHON_FORMAT_SSIZE_T "d given)", + func_name, more_or_less, num_expected, + (num_expected == 1) ? "" : "s", num_found); +} + +static void __Pyx_RaiseDoubleKeywordsError( + const char* func_name, + PyObject* kw_name) +{ + PyErr_Format(PyExc_TypeError, + #if PY_MAJOR_VERSION >= 3 + "%s() got multiple values for keyword argument '%U'", func_name, kw_name); + #else + "%s() got multiple values for keyword argument '%s'", func_name, + PyString_AsString(kw_name)); + #endif +} + +static int __Pyx_ParseOptionalKeywords( + PyObject *kwds, + PyObject **argnames[], + PyObject *kwds2, + PyObject *values[], + Py_ssize_t num_pos_args, + const char* function_name) +{ + PyObject *key = 0, *value = 0; + Py_ssize_t pos = 0; + PyObject*** name; + PyObject*** first_kw_arg = argnames + num_pos_args; + while (PyDict_Next(kwds, &pos, &key, &value)) { + name = first_kw_arg; + while (*name && (**name != key)) name++; + if (*name) { + values[name-argnames] = value; + continue; + } + name = first_kw_arg; + #if PY_MAJOR_VERSION < 3 + if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) { + while (*name) { + if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key)) + && _PyString_Eq(**name, key)) { + values[name-argnames] = value; + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + if ((**argname == key) || ( + (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key)) + && _PyString_Eq(**argname, key))) { + goto arg_passed_twice; + } + argname++; + } + } + } else + #endif + if (likely(PyUnicode_Check(key))) { + while (*name) { + int cmp = (**name == key) ? 0 : + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : + #endif + PyUnicode_Compare(**name, key); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) { + values[name-argnames] = value; + break; + } + name++; + } + if (*name) continue; + else { + PyObject*** argname = argnames; + while (argname != first_kw_arg) { + int cmp = (**argname == key) ? 0 : + #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3 + (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 : + #endif + PyUnicode_Compare(**argname, key); + if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad; + if (cmp == 0) goto arg_passed_twice; + argname++; + } + } + } else + goto invalid_keyword_type; + if (kwds2) { + if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad; + } else { + goto invalid_keyword; + } + } + return 0; +arg_passed_twice: + __Pyx_RaiseDoubleKeywordsError(function_name, key); + goto bad; +invalid_keyword_type: + PyErr_Format(PyExc_TypeError, + "%.200s() keywords must be strings", function_name); + goto bad; +invalid_keyword: + PyErr_Format(PyExc_TypeError, + #if PY_MAJOR_VERSION < 3 + "%.200s() got an unexpected keyword argument '%.200s'", + function_name, PyString_AsString(key)); + #else + "%s() got an unexpected keyword argument '%U'", + function_name, key); + #endif +bad: + return -1; +} + +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { + PyErr_Format(PyExc_ValueError, + "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); +} + +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { + PyErr_Format(PyExc_ValueError, + "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", + index, (index == 1) ? "" : "s"); +} + +static CYTHON_INLINE int __Pyx_IterFinish(void) { +#if CYTHON_COMPILING_IN_CPYTHON + PyThreadState *tstate = PyThreadState_GET(); + PyObject* exc_type = tstate->curexc_type; + if (unlikely(exc_type)) { + if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) { + PyObject *exc_value, *exc_tb; + exc_value = tstate->curexc_value; + exc_tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; + Py_DECREF(exc_type); + Py_XDECREF(exc_value); + Py_XDECREF(exc_tb); + return 0; + } else { + return -1; + } + } + return 0; +#else + if (unlikely(PyErr_Occurred())) { + if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) { + PyErr_Clear(); + return 0; + } else { + return -1; + } + } + return 0; +#endif +} + +static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { + if (unlikely(retval)) { + Py_DECREF(retval); + __Pyx_RaiseTooManyValuesError(expected); + return -1; + } else { + return __Pyx_IterFinish(); + } + return 0; +} + +static CYTHON_INLINE int __Pyx_IsLittleEndian(void) { + unsigned int n = 1; + return *(unsigned char*)(&n) != 0; +} +static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx, + __Pyx_BufFmt_StackElem* stack, + __Pyx_TypeInfo* type) { + stack[0].field = &ctx->root; + stack[0].parent_offset = 0; + ctx->root.type = type; + ctx->root.name = "buffer dtype"; + ctx->root.offset = 0; + ctx->head = stack; + ctx->head->field = &ctx->root; + ctx->fmt_offset = 0; + ctx->head->parent_offset = 0; + ctx->new_packmode = '@'; + ctx->enc_packmode = '@'; + ctx->new_count = 1; + ctx->enc_count = 0; + ctx->enc_type = 0; + ctx->is_complex = 0; + ctx->is_valid_array = 0; + ctx->struct_alignment = 0; + while (type->typegroup == 'S') { + ++ctx->head; + ctx->head->field = type->fields; + ctx->head->parent_offset = 0; + type = type->fields->type; + } +} +static int __Pyx_BufFmt_ParseNumber(const char** ts) { + int count; + const char* t = *ts; + if (*t < '0' || *t > '9') { + return -1; + } else { + count = *t++ - '0'; + while (*t >= '0' && *t < '9') { + count *= 10; + count += *t++ - '0'; + } + } + *ts = t; + return count; +} +static int __Pyx_BufFmt_ExpectNumber(const char **ts) { + int number = __Pyx_BufFmt_ParseNumber(ts); + if (number == -1) + PyErr_Format(PyExc_ValueError,\ + "Does not understand character buffer dtype format string ('%c')", **ts); + return number; +} +static void __Pyx_BufFmt_RaiseUnexpectedChar(char ch) { + PyErr_Format(PyExc_ValueError, + "Unexpected format string character: '%c'", ch); +} +static const char* __Pyx_BufFmt_DescribeTypeChar(char ch, int is_complex) { + switch (ch) { + case 'c': return "'char'"; + case 'b': return "'signed char'"; + case 'B': return "'unsigned char'"; + case 'h': return "'short'"; + case 'H': return "'unsigned short'"; + case 'i': return "'int'"; + case 'I': return "'unsigned int'"; + case 'l': return "'long'"; + case 'L': return "'unsigned long'"; + case 'q': return "'long long'"; + case 'Q': return "'unsigned long long'"; + case 'f': return (is_complex ? "'complex float'" : "'float'"); + case 'd': return (is_complex ? "'complex double'" : "'double'"); + case 'g': return (is_complex ? "'complex long double'" : "'long double'"); + case 'T': return "a struct"; + case 'O': return "Python object"; + case 'P': return "a pointer"; + case 's': case 'p': return "a string"; + case 0: return "end"; + default: return "unparseable format string"; + } +} +static size_t __Pyx_BufFmt_TypeCharToStandardSize(char ch, int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return 2; + case 'i': case 'I': case 'l': case 'L': return 4; + case 'q': case 'Q': return 8; + case 'f': return (is_complex ? 8 : 4); + case 'd': return (is_complex ? 16 : 8); + case 'g': { + PyErr_SetString(PyExc_ValueError, "Python does not define a standard format string size for long double ('g').."); + return 0; + } + case 'O': case 'P': return sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +static size_t __Pyx_BufFmt_TypeCharToNativeSize(char ch, int is_complex) { + switch (ch) { + case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(short); + case 'i': case 'I': return sizeof(int); + case 'l': case 'L': return sizeof(long); + #ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(PY_LONG_LONG); + #endif + case 'f': return sizeof(float) * (is_complex ? 2 : 1); + case 'd': return sizeof(double) * (is_complex ? 2 : 1); + case 'g': return sizeof(long double) * (is_complex ? 2 : 1); + case 'O': case 'P': return sizeof(void*); + default: { + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } + } +} +typedef struct { char c; short x; } __Pyx_st_short; +typedef struct { char c; int x; } __Pyx_st_int; +typedef struct { char c; long x; } __Pyx_st_long; +typedef struct { char c; float x; } __Pyx_st_float; +typedef struct { char c; double x; } __Pyx_st_double; +typedef struct { char c; long double x; } __Pyx_st_longdouble; +typedef struct { char c; void *x; } __Pyx_st_void_p; +#ifdef HAVE_LONG_LONG +typedef struct { char c; PY_LONG_LONG x; } __Pyx_st_longlong; +#endif +static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short); + case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int); + case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long); +#ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG); +#endif + case 'f': return sizeof(__Pyx_st_float) - sizeof(float); + case 'd': return sizeof(__Pyx_st_double) - sizeof(double); + case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double); + case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +/* These are for computing the padding at the end of the struct to align + on the first member of the struct. This will probably the same as above, + but we don't have any guarantees. + */ +typedef struct { short x; char c; } __Pyx_pad_short; +typedef struct { int x; char c; } __Pyx_pad_int; +typedef struct { long x; char c; } __Pyx_pad_long; +typedef struct { float x; char c; } __Pyx_pad_float; +typedef struct { double x; char c; } __Pyx_pad_double; +typedef struct { long double x; char c; } __Pyx_pad_longdouble; +typedef struct { void *x; char c; } __Pyx_pad_void_p; +#ifdef HAVE_LONG_LONG +typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong; +#endif +static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) { + switch (ch) { + case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1; + case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short); + case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int); + case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long); +#ifdef HAVE_LONG_LONG + case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG); +#endif + case 'f': return sizeof(__Pyx_pad_float) - sizeof(float); + case 'd': return sizeof(__Pyx_pad_double) - sizeof(double); + case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double); + case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*); + default: + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } +} +static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) { + switch (ch) { + case 'c': + return 'H'; + case 'b': case 'h': case 'i': + case 'l': case 'q': case 's': case 'p': + return 'I'; + case 'B': case 'H': case 'I': case 'L': case 'Q': + return 'U'; + case 'f': case 'd': case 'g': + return (is_complex ? 'C' : 'R'); + case 'O': + return 'O'; + case 'P': + return 'P'; + default: { + __Pyx_BufFmt_RaiseUnexpectedChar(ch); + return 0; + } + } +} +static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) { + if (ctx->head == NULL || ctx->head->field == &ctx->root) { + const char* expected; + const char* quote; + if (ctx->head == NULL) { + expected = "end"; + quote = ""; + } else { + expected = ctx->head->field->type->name; + quote = "'"; + } + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch, expected %s%s%s but got %s", + quote, expected, quote, + __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex)); + } else { + __Pyx_StructField* field = ctx->head->field; + __Pyx_StructField* parent = (ctx->head - 1)->field; + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'", + field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex), + parent->type->name, field->name); + } +} +static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { + char group; + size_t size, offset, arraysize = 1; + if (ctx->enc_type == 0) return 0; + if (ctx->head->field->type->arraysize[0]) { + int i, ndim = 0; + if (ctx->enc_type == 's' || ctx->enc_type == 'p') { + ctx->is_valid_array = ctx->head->field->type->ndim == 1; + ndim = 1; + if (ctx->enc_count != ctx->head->field->type->arraysize[0]) { + PyErr_Format(PyExc_ValueError, + "Expected a dimension of size %zu, got %zu", + ctx->head->field->type->arraysize[0], ctx->enc_count); + return -1; + } + } + if (!ctx->is_valid_array) { + PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d", + ctx->head->field->type->ndim, ndim); + return -1; + } + for (i = 0; i < ctx->head->field->type->ndim; i++) { + arraysize *= ctx->head->field->type->arraysize[i]; + } + ctx->is_valid_array = 0; + ctx->enc_count = 1; + } + group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex); + do { + __Pyx_StructField* field = ctx->head->field; + __Pyx_TypeInfo* type = field->type; + if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') { + size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex); + } else { + size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex); + } + if (ctx->enc_packmode == '@') { + size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex); + size_t align_mod_offset; + if (align_at == 0) return -1; + align_mod_offset = ctx->fmt_offset % align_at; + if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset; + if (ctx->struct_alignment == 0) + ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type, + ctx->is_complex); + } + if (type->size != size || type->typegroup != group) { + if (type->typegroup == 'C' && type->fields != NULL) { + size_t parent_offset = ctx->head->parent_offset + field->offset; + ++ctx->head; + ctx->head->field = type->fields; + ctx->head->parent_offset = parent_offset; + continue; + } + if ((type->typegroup == 'H' || group == 'H') && type->size == size) { + } else { + __Pyx_BufFmt_RaiseExpected(ctx); + return -1; + } + } + offset = ctx->head->parent_offset + field->offset; + if (ctx->fmt_offset != offset) { + PyErr_Format(PyExc_ValueError, + "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected", + (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset); + return -1; + } + ctx->fmt_offset += size; + if (arraysize) + ctx->fmt_offset += (arraysize - 1) * size; + --ctx->enc_count; + while (1) { + if (field == &ctx->root) { + ctx->head = NULL; + if (ctx->enc_count != 0) { + __Pyx_BufFmt_RaiseExpected(ctx); + return -1; + } + break; + } + ctx->head->field = ++field; + if (field->type == NULL) { + --ctx->head; + field = ctx->head->field; + continue; + } else if (field->type->typegroup == 'S') { + size_t parent_offset = ctx->head->parent_offset + field->offset; + if (field->type->fields->type == NULL) continue; + field = field->type->fields; + ++ctx->head; + ctx->head->field = field; + ctx->head->parent_offset = parent_offset; + break; + } else { + break; + } + } + } while (ctx->enc_count); + ctx->enc_type = 0; + ctx->is_complex = 0; + return 0; +} +static CYTHON_INLINE PyObject * +__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) +{ + const char *ts = *tsp; + int i = 0, number; + int ndim = ctx->head->field->type->ndim; +; + ++ts; + if (ctx->new_count != 1) { + PyErr_SetString(PyExc_ValueError, + "Cannot handle repeated arrays in format string"); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + while (*ts && *ts != ')') { + switch (*ts) { + case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue; + default: break; + } + number = __Pyx_BufFmt_ExpectNumber(&ts); + if (number == -1) return NULL; + if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i]) + return PyErr_Format(PyExc_ValueError, + "Expected a dimension of size %zu, got %d", + ctx->head->field->type->arraysize[i], number); + if (*ts != ',' && *ts != ')') + return PyErr_Format(PyExc_ValueError, + "Expected a comma in format string, got '%c'", *ts); + if (*ts == ',') ts++; + i++; + } + if (i != ndim) + return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d", + ctx->head->field->type->ndim, i); + if (!*ts) { + PyErr_SetString(PyExc_ValueError, + "Unexpected end of format string, expected ')'"); + return NULL; + } + ctx->is_valid_array = 1; + ctx->new_count = 1; + *tsp = ++ts; + return Py_None; +} +static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) { + int got_Z = 0; + while (1) { + switch(*ts) { + case 0: + if (ctx->enc_type != 0 && ctx->head == NULL) { + __Pyx_BufFmt_RaiseExpected(ctx); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + if (ctx->head != NULL) { + __Pyx_BufFmt_RaiseExpected(ctx); + return NULL; + } + return ts; + case ' ': + case '\r': + case '\n': + ++ts; + break; + case '<': + if (!__Pyx_IsLittleEndian()) { + PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler"); + return NULL; + } + ctx->new_packmode = '='; + ++ts; + break; + case '>': + case '!': + if (__Pyx_IsLittleEndian()) { + PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler"); + return NULL; + } + ctx->new_packmode = '='; + ++ts; + break; + case '=': + case '@': + case '^': + ctx->new_packmode = *ts++; + break; + case 'T': + { + const char* ts_after_sub; + size_t i, struct_count = ctx->new_count; + size_t struct_alignment = ctx->struct_alignment; + ctx->new_count = 1; + ++ts; + if (*ts != '{') { + PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'"); + return NULL; + } + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_type = 0; + ctx->enc_count = 0; + ctx->struct_alignment = 0; + ++ts; + ts_after_sub = ts; + for (i = 0; i != struct_count; ++i) { + ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts); + if (!ts_after_sub) return NULL; + } + ts = ts_after_sub; + if (struct_alignment) ctx->struct_alignment = struct_alignment; + } + break; + case '}': + { + size_t alignment = ctx->struct_alignment; + ++ts; + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_type = 0; + if (alignment && ctx->fmt_offset % alignment) { + ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment); + } + } + return ts; + case 'x': + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->fmt_offset += ctx->new_count; + ctx->new_count = 1; + ctx->enc_count = 0; + ctx->enc_type = 0; + ctx->enc_packmode = ctx->new_packmode; + ++ts; + break; + case 'Z': + got_Z = 1; + ++ts; + if (*ts != 'f' && *ts != 'd' && *ts != 'g') { + __Pyx_BufFmt_RaiseUnexpectedChar('Z'); + return NULL; + } + case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': + case 'l': case 'L': case 'q': case 'Q': + case 'f': case 'd': case 'g': + case 'O': case 'p': + if (ctx->enc_type == *ts && got_Z == ctx->is_complex && + ctx->enc_packmode == ctx->new_packmode) { + ctx->enc_count += ctx->new_count; + ctx->new_count = 1; + got_Z = 0; + ++ts; + break; + } + case 's': + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_count = ctx->new_count; + ctx->enc_packmode = ctx->new_packmode; + ctx->enc_type = *ts; + ctx->is_complex = got_Z; + ++ts; + ctx->new_count = 1; + got_Z = 0; + break; + case ':': + ++ts; + while(*ts != ':') ++ts; + ++ts; + break; + case '(': + if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL; + break; + default: + { + int number = __Pyx_BufFmt_ExpectNumber(&ts); + if (number == -1) return NULL; + ctx->new_count = (size_t)number; + } + } + } +} +static CYTHON_INLINE void __Pyx_ZeroBuffer(Py_buffer* buf) { + buf->buf = NULL; + buf->obj = NULL; + buf->strides = __Pyx_zeros; + buf->shape = __Pyx_zeros; + buf->suboffsets = __Pyx_minusones; +} +static CYTHON_INLINE int __Pyx_GetBufferAndValidate( + Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, + int nd, int cast, __Pyx_BufFmt_StackElem* stack) +{ + if (obj == Py_None || obj == NULL) { + __Pyx_ZeroBuffer(buf); + return 0; + } + buf->buf = NULL; + if (__Pyx_GetBuffer(obj, buf, flags) == -1) goto fail; + if (buf->ndim != nd) { + PyErr_Format(PyExc_ValueError, + "Buffer has wrong number of dimensions (expected %d, got %d)", + nd, buf->ndim); + goto fail; + } + if (!cast) { + __Pyx_BufFmt_Context ctx; + __Pyx_BufFmt_Init(&ctx, stack, dtype); + if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; + } + if ((unsigned)buf->itemsize != dtype->size) { + PyErr_Format(PyExc_ValueError, + "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "d byte%s) does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "d byte%s)", + buf->itemsize, (buf->itemsize > 1) ? "s" : "", + dtype->name, (Py_ssize_t)dtype->size, (dtype->size > 1) ? "s" : ""); + goto fail; + } + if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones; + return 0; +fail:; + __Pyx_ZeroBuffer(buf); + return -1; +} +static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) { + if (info->buf == NULL) return; + if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL; + __Pyx_ReleaseBuffer(info); +} + +static int +__Pyx_init_memviewslice(struct __pyx_memoryview_obj *memview, + int ndim, + __Pyx_memviewslice *memviewslice, + int memview_is_new_reference) +{ + __Pyx_RefNannyDeclarations + int i, retval=-1; + Py_buffer *buf = &memview->view; + __Pyx_RefNannySetupContext("init_memviewslice", 0); + if (!buf) { + PyErr_SetString(PyExc_ValueError, + "buf is NULL."); + goto fail; + } else if (memviewslice->memview || memviewslice->data) { + PyErr_SetString(PyExc_ValueError, + "memviewslice is already initialized!"); + goto fail; + } + if (buf->strides) { + for (i = 0; i < ndim; i++) { + memviewslice->strides[i] = buf->strides[i]; + } + } else { + Py_ssize_t stride = buf->itemsize; + for (i = ndim - 1; i >= 0; i--) { + memviewslice->strides[i] = stride; + stride *= buf->shape[i]; + } + } + for (i = 0; i < ndim; i++) { + memviewslice->shape[i] = buf->shape[i]; + if (buf->suboffsets) { + memviewslice->suboffsets[i] = buf->suboffsets[i]; + } else { + memviewslice->suboffsets[i] = -1; + } + } + memviewslice->memview = memview; + memviewslice->data = (char *)buf->buf; + if (__pyx_add_acquisition_count(memview) == 0 && !memview_is_new_reference) { + Py_INCREF(memview); + } + retval = 0; + goto no_fail; +fail: + memviewslice->memview = 0; + memviewslice->data = 0; + retval = -1; +no_fail: + __Pyx_RefNannyFinishContext(); + return retval; +} +static CYTHON_INLINE void __pyx_fatalerror(const char *fmt, ...) { + va_list vargs; + char msg[200]; + va_start(vargs, fmt); +#ifdef HAVE_STDARG_PROTOTYPES + va_start(vargs, fmt); +#else + va_start(vargs); +#endif + vsnprintf(msg, 200, fmt, vargs); + Py_FatalError(msg); + va_end(vargs); +} +static CYTHON_INLINE int +__pyx_add_acquisition_count_locked(__pyx_atomic_int *acquisition_count, + PyThread_type_lock lock) +{ + int result; + PyThread_acquire_lock(lock, 1); + result = (*acquisition_count)++; + PyThread_release_lock(lock); + return result; +} +static CYTHON_INLINE int +__pyx_sub_acquisition_count_locked(__pyx_atomic_int *acquisition_count, + PyThread_type_lock lock) +{ + int result; + PyThread_acquire_lock(lock, 1); + result = (*acquisition_count)--; + PyThread_release_lock(lock); + return result; +} +static CYTHON_INLINE void +__Pyx_INC_MEMVIEW(__Pyx_memviewslice *memslice, int have_gil, int lineno) +{ + int first_time; + struct __pyx_memoryview_obj *memview = memslice->memview; + if (!memview || (PyObject *) memview == Py_None) + return; + if (__pyx_get_slice_count(memview) < 0) + __pyx_fatalerror("Acquisition count is %d (line %d)", + __pyx_get_slice_count(memview), lineno); + first_time = __pyx_add_acquisition_count(memview) == 0; + if (first_time) { + if (have_gil) { + Py_INCREF((PyObject *) memview); + } else { + PyGILState_STATE _gilstate = PyGILState_Ensure(); + Py_INCREF((PyObject *) memview); + PyGILState_Release(_gilstate); + } + } +} +static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *memslice, + int have_gil, int lineno) { + int last_time; + struct __pyx_memoryview_obj *memview = memslice->memview; + if (!memview ) { + return; + } else if ((PyObject *) memview == Py_None) { + memslice->memview = NULL; + return; + } + if (__pyx_get_slice_count(memview) <= 0) + __pyx_fatalerror("Acquisition count is %d (line %d)", + __pyx_get_slice_count(memview), lineno); + last_time = __pyx_sub_acquisition_count(memview) == 1; + memslice->data = NULL; + if (last_time) { + if (have_gil) { + Py_CLEAR(memslice->memview); + } else { + PyGILState_STATE _gilstate = PyGILState_Ensure(); + Py_CLEAR(memslice->memview); + PyGILState_Release(_gilstate); + } + } else { + memslice->memview = NULL; + } +} + +static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyThreadState *tstate = PyThreadState_GET(); + tmp_type = tstate->curexc_type; + tmp_value = tstate->curexc_value; + tmp_tb = tstate->curexc_traceback; + tstate->curexc_type = type; + tstate->curexc_value = value; + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +#else + PyErr_Restore(type, value, tb); +#endif +} +static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyThreadState *tstate = PyThreadState_GET(); + *type = tstate->curexc_type; + *value = tstate->curexc_value; + *tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; +#else + PyErr_Fetch(type, value, tb); +#endif +} + +#if PY_MAJOR_VERSION < 3 +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, + CYTHON_UNUSED PyObject *cause) { + Py_XINCREF(type); + if (!value || value == Py_None) + value = NULL; + else + Py_INCREF(value); + if (!tb || tb == Py_None) + tb = NULL; + else { + Py_INCREF(tb); + if (!PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto raise_error; + } + } + if (PyType_Check(type)) { +#if CYTHON_COMPILING_IN_PYPY + if (!value) { + Py_INCREF(Py_None); + value = Py_None; + } +#endif + PyErr_NormalizeException(&type, &value, &tb); + } else { + if (value) { + PyErr_SetString(PyExc_TypeError, + "instance exception may not have a separate value"); + goto raise_error; + } + value = type; + type = (PyObject*) Py_TYPE(type); + Py_INCREF(type); + if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { + PyErr_SetString(PyExc_TypeError, + "raise: exception class must be a subclass of BaseException"); + goto raise_error; + } + } + __Pyx_ErrRestore(type, value, tb); + return; +raise_error: + Py_XDECREF(value); + Py_XDECREF(type); + Py_XDECREF(tb); + return; +} +#else +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { + PyObject* owned_instance = NULL; + if (tb == Py_None) { + tb = 0; + } else if (tb && !PyTraceBack_Check(tb)) { + PyErr_SetString(PyExc_TypeError, + "raise: arg 3 must be a traceback or None"); + goto bad; + } + if (value == Py_None) + value = 0; + if (PyExceptionInstance_Check(type)) { + if (value) { + PyErr_SetString(PyExc_TypeError, + "instance exception may not have a separate value"); + goto bad; + } + value = type; + type = (PyObject*) Py_TYPE(value); + } else if (PyExceptionClass_Check(type)) { + PyObject *instance_class = NULL; + if (value && PyExceptionInstance_Check(value)) { + instance_class = (PyObject*) Py_TYPE(value); + if (instance_class != type) { + if (PyObject_IsSubclass(instance_class, type)) { + type = instance_class; + } else { + instance_class = NULL; + } + } + } + if (!instance_class) { + PyObject *args; + if (!value) + args = PyTuple_New(0); + else if (PyTuple_Check(value)) { + Py_INCREF(value); + args = value; + } else + args = PyTuple_Pack(1, value); + if (!args) + goto bad; + owned_instance = PyObject_Call(type, args, NULL); + Py_DECREF(args); + if (!owned_instance) + goto bad; + value = owned_instance; + if (!PyExceptionInstance_Check(value)) { + PyErr_Format(PyExc_TypeError, + "calling %R should have returned an instance of " + "BaseException, not %R", + type, Py_TYPE(value)); + goto bad; + } + } + } else { + PyErr_SetString(PyExc_TypeError, + "raise: exception class must be a subclass of BaseException"); + goto bad; + } +#if PY_VERSION_HEX >= 0x03030000 + if (cause) { +#else + if (cause && cause != Py_None) { +#endif + PyObject *fixed_cause; + if (cause == Py_None) { + fixed_cause = NULL; + } else if (PyExceptionClass_Check(cause)) { + fixed_cause = PyObject_CallObject(cause, NULL); + if (fixed_cause == NULL) + goto bad; + } else if (PyExceptionInstance_Check(cause)) { + fixed_cause = cause; + Py_INCREF(fixed_cause); + } else { + PyErr_SetString(PyExc_TypeError, + "exception causes must derive from " + "BaseException"); + goto bad; + } + PyException_SetCause(value, fixed_cause); + } + PyErr_SetObject(type, value); + if (tb) { + PyThreadState *tstate = PyThreadState_GET(); + PyObject* tmp_tb = tstate->curexc_traceback; + if (tb != tmp_tb) { + Py_INCREF(tb); + tstate->curexc_traceback = tb; + Py_XDECREF(tmp_tb); + } + } +bad: + Py_XDECREF(owned_instance); + return; +} +#endif + +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { + PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); +} + +static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { + if (unlikely(!type)) { + PyErr_SetString(PyExc_SystemError, "Missing type object"); + return 0; + } + if (likely(PyObject_TypeCheck(obj, type))) + return 1; + PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", + Py_TYPE(obj)->tp_name, type->tp_name); + return 0; +} + +static void __Pyx_RaiseArgumentTypeInvalid(const char* name, PyObject *obj, PyTypeObject *type) { + PyErr_Format(PyExc_TypeError, + "Argument '%.200s' has incorrect type (expected %.200s, got %.200s)", + name, type->tp_name, Py_TYPE(obj)->tp_name); +} +static CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, + const char *name, int exact) +{ + if (unlikely(!type)) { + PyErr_SetString(PyExc_SystemError, "Missing type object"); + return 0; + } + if (none_allowed && obj == Py_None) return 1; + else if (exact) { + if (likely(Py_TYPE(obj) == type)) return 1; + #if PY_MAJOR_VERSION == 2 + else if ((type == &PyBaseString_Type) && likely(__Pyx_PyBaseString_CheckExact(obj))) return 1; + #endif + } + else { + if (likely(PyObject_TypeCheck(obj, type))) return 1; + } + __Pyx_RaiseArgumentTypeInvalid(name, obj, type); + return 0; +} + +static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) { +#if CYTHON_COMPILING_IN_PYPY + return PyObject_RichCompareBool(s1, s2, equals); +#else + if (s1 == s2) { + return (equals == Py_EQ); + } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) { + const char *ps1, *ps2; + Py_ssize_t length = PyBytes_GET_SIZE(s1); + if (length != PyBytes_GET_SIZE(s2)) + return (equals == Py_NE); + ps1 = PyBytes_AS_STRING(s1); + ps2 = PyBytes_AS_STRING(s2); + if (ps1[0] != ps2[0]) { + return (equals == Py_NE); + } else if (length == 1) { + return (equals == Py_EQ); + } else { + int result = memcmp(ps1, ps2, (size_t)length); + return (equals == Py_EQ) ? (result == 0) : (result != 0); + } + } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) { + return (equals == Py_NE); + } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) { + return (equals == Py_NE); + } else { + int result; + PyObject* py_result = PyObject_RichCompare(s1, s2, equals); + if (!py_result) + return -1; + result = __Pyx_PyObject_IsTrue(py_result); + Py_DECREF(py_result); + return result; + } +#endif +} + +static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) { +#if CYTHON_COMPILING_IN_PYPY + return PyObject_RichCompareBool(s1, s2, equals); +#else +#if PY_MAJOR_VERSION < 3 + PyObject* owned_ref = NULL; +#endif + int s1_is_unicode, s2_is_unicode; + if (s1 == s2) { + goto return_eq; + } + s1_is_unicode = PyUnicode_CheckExact(s1); + s2_is_unicode = PyUnicode_CheckExact(s2); +#if PY_MAJOR_VERSION < 3 + if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) { + owned_ref = PyUnicode_FromObject(s2); + if (unlikely(!owned_ref)) + return -1; + s2 = owned_ref; + s2_is_unicode = 1; + } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) { + owned_ref = PyUnicode_FromObject(s1); + if (unlikely(!owned_ref)) + return -1; + s1 = owned_ref; + s1_is_unicode = 1; + } else if (((!s2_is_unicode) & (!s1_is_unicode))) { + return __Pyx_PyBytes_Equals(s1, s2, equals); + } +#endif + if (s1_is_unicode & s2_is_unicode) { + Py_ssize_t length; + int kind; + void *data1, *data2; + if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0)) + return -1; + length = __Pyx_PyUnicode_GET_LENGTH(s1); + if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) { + goto return_ne; + } + kind = __Pyx_PyUnicode_KIND(s1); + if (kind != __Pyx_PyUnicode_KIND(s2)) { + goto return_ne; + } + data1 = __Pyx_PyUnicode_DATA(s1); + data2 = __Pyx_PyUnicode_DATA(s2); + if (__Pyx_PyUnicode_READ(kind, data1, 0) != __Pyx_PyUnicode_READ(kind, data2, 0)) { + goto return_ne; + } else if (length == 1) { + goto return_eq; + } else { + int result = memcmp(data1, data2, (size_t)(length * kind)); + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(owned_ref); + #endif + return (equals == Py_EQ) ? (result == 0) : (result != 0); + } + } else if ((s1 == Py_None) & s2_is_unicode) { + goto return_ne; + } else if ((s2 == Py_None) & s1_is_unicode) { + goto return_ne; + } else { + int result; + PyObject* py_result = PyObject_RichCompare(s1, s2, equals); + if (!py_result) + return -1; + result = __Pyx_PyObject_IsTrue(py_result); + Py_DECREF(py_result); + return result; + } +return_eq: + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(owned_ref); + #endif + return (equals == Py_EQ); +return_ne: + #if PY_MAJOR_VERSION < 3 + Py_XDECREF(owned_ref); + #endif + return (equals == Py_NE); +#endif +} + +static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *o, PyObject *n) { +#if CYTHON_COMPILING_IN_CPYTHON +#if PY_MAJOR_VERSION >= 3 + if (likely(PyUnicode_Check(n))) +#else + if (likely(PyString_Check(n))) +#endif + return __Pyx_PyObject_GetAttrStr(o, n); +#endif + return PyObject_GetAttr(o, n); +} + +static CYTHON_INLINE PyObject* __Pyx_decode_c_string( + const char* cstring, Py_ssize_t start, Py_ssize_t stop, + const char* encoding, const char* errors, + PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) { + Py_ssize_t length; + if (unlikely((start < 0) | (stop < 0))) { + length = strlen(cstring); + if (start < 0) { + start += length; + if (start < 0) + start = 0; + } + if (stop < 0) + stop += length; + } + length = stop - start; + if (unlikely(length <= 0)) + return PyUnicode_FromUnicode(NULL, 0); + cstring += start; + if (decode_func) { + return decode_func(cstring, length, errors); + } else { + return PyUnicode_Decode(cstring, length, encoding, errors); + } +} + +static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyThreadState *tstate = PyThreadState_GET(); + *type = tstate->exc_type; + *value = tstate->exc_value; + *tb = tstate->exc_traceback; + Py_XINCREF(*type); + Py_XINCREF(*value); + Py_XINCREF(*tb); +#else + PyErr_GetExcInfo(type, value, tb); +#endif +} +static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyThreadState *tstate = PyThreadState_GET(); + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = type; + tstate->exc_value = value; + tstate->exc_traceback = tb; + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +#else + PyErr_SetExcInfo(type, value, tb); +#endif +} + +static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) { + PyObject *local_type, *local_value, *local_tb; +#if CYTHON_COMPILING_IN_CPYTHON + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyThreadState *tstate = PyThreadState_GET(); + local_type = tstate->curexc_type; + local_value = tstate->curexc_value; + local_tb = tstate->curexc_traceback; + tstate->curexc_type = 0; + tstate->curexc_value = 0; + tstate->curexc_traceback = 0; +#else + PyErr_Fetch(&local_type, &local_value, &local_tb); +#endif + PyErr_NormalizeException(&local_type, &local_value, &local_tb); +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(tstate->curexc_type)) +#else + if (unlikely(PyErr_Occurred())) +#endif + goto bad; + #if PY_MAJOR_VERSION >= 3 + if (local_tb) { + if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) + goto bad; + } + #endif + Py_XINCREF(local_tb); + Py_XINCREF(local_type); + Py_XINCREF(local_value); + *type = local_type; + *value = local_value; + *tb = local_tb; +#if CYTHON_COMPILING_IN_CPYTHON + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = local_type; + tstate->exc_value = local_value; + tstate->exc_traceback = local_tb; + Py_XDECREF(tmp_type); + Py_XDECREF(tmp_value); + Py_XDECREF(tmp_tb); +#else + PyErr_SetExcInfo(local_type, local_value, local_tb); +#endif + return 0; +bad: + *type = 0; + *value = 0; + *tb = 0; + Py_XDECREF(local_type); + Py_XDECREF(local_value); + Py_XDECREF(local_tb); + return -1; +} + +static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) { + PyObject *tmp_type, *tmp_value, *tmp_tb; +#if CYTHON_COMPILING_IN_CPYTHON + PyThreadState *tstate = PyThreadState_GET(); + tmp_type = tstate->exc_type; + tmp_value = tstate->exc_value; + tmp_tb = tstate->exc_traceback; + tstate->exc_type = *type; + tstate->exc_value = *value; + tstate->exc_traceback = *tb; +#else + PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb); + PyErr_SetExcInfo(*type, *value, *tb); +#endif + *type = tmp_type; + *value = tmp_value; + *tb = tmp_tb; +} + +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { + PyObject *r; + if (!j) return NULL; + r = PyObject_GetItem(o, j); + Py_DECREF(j); + return r; +} +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, + int wraparound, int boundscheck) { +#if CYTHON_COMPILING_IN_CPYTHON + if (wraparound & unlikely(i < 0)) i += PyList_GET_SIZE(o); + if ((!boundscheck) || likely((0 <= i) & (i < PyList_GET_SIZE(o)))) { + PyObject *r = PyList_GET_ITEM(o, i); + Py_INCREF(r); + return r; + } + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +#else + return PySequence_GetItem(o, i); +#endif +} +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, + int wraparound, int boundscheck) { +#if CYTHON_COMPILING_IN_CPYTHON + if (wraparound & unlikely(i < 0)) i += PyTuple_GET_SIZE(o); + if ((!boundscheck) || likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) { + PyObject *r = PyTuple_GET_ITEM(o, i); + Py_INCREF(r); + return r; + } + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +#else + return PySequence_GetItem(o, i); +#endif +} +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, + int is_list, int wraparound, int boundscheck) { +#if CYTHON_COMPILING_IN_CPYTHON + if (is_list || PyList_CheckExact(o)) { + Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); + if ((!boundscheck) || (likely((n >= 0) & (n < PyList_GET_SIZE(o))))) { + PyObject *r = PyList_GET_ITEM(o, n); + Py_INCREF(r); + return r; + } + } + else if (PyTuple_CheckExact(o)) { + Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o); + if ((!boundscheck) || likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) { + PyObject *r = PyTuple_GET_ITEM(o, n); + Py_INCREF(r); + return r; + } + } else { + PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; + if (likely(m && m->sq_item)) { + if (wraparound && unlikely(i < 0) && likely(m->sq_length)) { + Py_ssize_t l = m->sq_length(o); + if (likely(l >= 0)) { + i += l; + } else { + if (PyErr_ExceptionMatches(PyExc_OverflowError)) + PyErr_Clear(); + else + return NULL; + } + } + return m->sq_item(o, i); + } + } +#else + if (is_list || PySequence_Check(o)) { + return PySequence_GetItem(o, i); + } +#endif + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +} + +static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { + PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); +} + +static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno, + CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename, + int full_traceback) { + PyObject *old_exc, *old_val, *old_tb; + PyObject *ctx; + __Pyx_ErrFetch(&old_exc, &old_val, &old_tb); + if (full_traceback) { + Py_XINCREF(old_exc); + Py_XINCREF(old_val); + Py_XINCREF(old_tb); + __Pyx_ErrRestore(old_exc, old_val, old_tb); + PyErr_PrintEx(1); + } + #if PY_MAJOR_VERSION < 3 + ctx = PyString_FromString(name); + #else + ctx = PyUnicode_FromString(name); + #endif + __Pyx_ErrRestore(old_exc, old_val, old_tb); + if (!ctx) { + PyErr_WriteUnraisable(Py_None); + } else { + PyErr_WriteUnraisable(ctx); + Py_DECREF(ctx); + } +} + +static int __Pyx_SetVtable(PyObject *dict, void *vtable) { +#if PY_VERSION_HEX >= 0x02070000 + PyObject *ob = PyCapsule_New(vtable, 0, 0); +#else + PyObject *ob = PyCObject_FromVoidPtr(vtable, 0); +#endif + if (!ob) + goto bad; + if (PyDict_SetItem(dict, __pyx_n_s_pyx_vtable, ob) < 0) + goto bad; + Py_DECREF(ob); + return 0; +bad: + Py_XDECREF(ob); + return -1; +} + +static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { + int start = 0, mid = 0, end = count - 1; + if (end >= 0 && code_line > entries[end].code_line) { + return count; + } + while (start < end) { + mid = (start + end) / 2; + if (code_line < entries[mid].code_line) { + end = mid; + } else if (code_line > entries[mid].code_line) { + start = mid + 1; + } else { + return mid; + } + } + if (code_line <= entries[mid].code_line) { + return mid; + } else { + return mid + 1; + } +} +static PyCodeObject *__pyx_find_code_object(int code_line) { + PyCodeObject* code_object; + int pos; + if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { + return NULL; + } + pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); + if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { + return NULL; + } + code_object = __pyx_code_cache.entries[pos].code_object; + Py_INCREF(code_object); + return code_object; +} +static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { + int pos, i; + __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; + if (unlikely(!code_line)) { + return; + } + if (unlikely(!entries)) { + entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); + if (likely(entries)) { + __pyx_code_cache.entries = entries; + __pyx_code_cache.max_count = 64; + __pyx_code_cache.count = 1; + entries[0].code_line = code_line; + entries[0].code_object = code_object; + Py_INCREF(code_object); + } + return; + } + pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); + if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { + PyCodeObject* tmp = entries[pos].code_object; + entries[pos].code_object = code_object; + Py_DECREF(tmp); + return; + } + if (__pyx_code_cache.count == __pyx_code_cache.max_count) { + int new_max = __pyx_code_cache.max_count + 64; + entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( + __pyx_code_cache.entries, (size_t)new_max*sizeof(__Pyx_CodeObjectCacheEntry)); + if (unlikely(!entries)) { + return; + } + __pyx_code_cache.entries = entries; + __pyx_code_cache.max_count = new_max; + } + for (i=__pyx_code_cache.count; i>pos; i--) { + entries[i] = entries[i-1]; + } + entries[pos].code_line = code_line; + entries[pos].code_object = code_object; + __pyx_code_cache.count++; + Py_INCREF(code_object); +} + +#include "compile.h" +#include "frameobject.h" +#include "traceback.h" +static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( + const char *funcname, int c_line, + int py_line, const char *filename) { + PyCodeObject *py_code = 0; + PyObject *py_srcfile = 0; + PyObject *py_funcname = 0; + #if PY_MAJOR_VERSION < 3 + py_srcfile = PyString_FromString(filename); + #else + py_srcfile = PyUnicode_FromString(filename); + #endif + if (!py_srcfile) goto bad; + if (c_line) { + #if PY_MAJOR_VERSION < 3 + py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); + #else + py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); + #endif + } + else { + #if PY_MAJOR_VERSION < 3 + py_funcname = PyString_FromString(funcname); + #else + py_funcname = PyUnicode_FromString(funcname); + #endif + } + if (!py_funcname) goto bad; + py_code = __Pyx_PyCode_New( + 0, + 0, + 0, + 0, + 0, + __pyx_empty_bytes, /*PyObject *code,*/ + __pyx_empty_tuple, /*PyObject *consts,*/ + __pyx_empty_tuple, /*PyObject *names,*/ + __pyx_empty_tuple, /*PyObject *varnames,*/ + __pyx_empty_tuple, /*PyObject *freevars,*/ + __pyx_empty_tuple, /*PyObject *cellvars,*/ + py_srcfile, /*PyObject *filename,*/ + py_funcname, /*PyObject *name,*/ + py_line, + __pyx_empty_bytes /*PyObject *lnotab*/ + ); + Py_DECREF(py_srcfile); + Py_DECREF(py_funcname); + return py_code; +bad: + Py_XDECREF(py_srcfile); + Py_XDECREF(py_funcname); + return NULL; +} +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename) { + PyCodeObject *py_code = 0; + PyFrameObject *py_frame = 0; + py_code = __pyx_find_code_object(c_line ? c_line : py_line); + if (!py_code) { + py_code = __Pyx_CreateCodeObjectForTraceback( + funcname, c_line, py_line, filename); + if (!py_code) goto bad; + __pyx_insert_code_object(c_line ? c_line : py_line, py_code); + } + py_frame = PyFrame_New( + PyThreadState_GET(), /*PyThreadState *tstate,*/ + py_code, /*PyCodeObject *code,*/ + __pyx_d, /*PyObject *globals,*/ + 0 /*PyObject *locals*/ + ); + if (!py_frame) goto bad; + py_frame->f_lineno = py_line; + PyTraceBack_Here(py_frame); +bad: + Py_XDECREF(py_code); + Py_XDECREF(py_frame); +} + +#if PY_MAJOR_VERSION < 3 +static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { + if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); + if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags); + if (PyObject_TypeCheck(obj, __pyx_array_type)) return __pyx_array_getbuffer(obj, view, flags); + if (PyObject_TypeCheck(obj, __pyx_memoryview_type)) return __pyx_memoryview_getbuffer(obj, view, flags); + PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); + return -1; +} +static void __Pyx_ReleaseBuffer(Py_buffer *view) { + PyObject *obj = view->obj; + if (!obj) return; + if (PyObject_CheckBuffer(obj)) { + PyBuffer_Release(view); + return; + } + if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; } + Py_DECREF(obj); + view->obj = NULL; +} +#endif + + + static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { + PyObject *empty_list = 0; + PyObject *module = 0; + PyObject *global_dict = 0; + PyObject *empty_dict = 0; + PyObject *list; + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_import; + py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); + if (!py_import) + goto bad; + #endif + if (from_list) + list = from_list; + else { + empty_list = PyList_New(0); + if (!empty_list) + goto bad; + list = empty_list; + } + global_dict = PyModule_GetDict(__pyx_m); + if (!global_dict) + goto bad; + empty_dict = PyDict_New(); + if (!empty_dict) + goto bad; + { + #if PY_MAJOR_VERSION >= 3 + if (level == -1) { + if (strchr(__Pyx_MODULE_NAME, '.')) { + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_level = PyInt_FromLong(1); + if (!py_level) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, global_dict, empty_dict, list, py_level, NULL); + Py_DECREF(py_level); + #else + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, 1); + #endif + if (!module) { + if (!PyErr_ExceptionMatches(PyExc_ImportError)) + goto bad; + PyErr_Clear(); + } + } + level = 0; + } + #endif + if (!module) { + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_level = PyInt_FromLong(level); + if (!py_level) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, global_dict, empty_dict, list, py_level, NULL); + Py_DECREF(py_level); + #else + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, level); + #endif + } + } +bad: + #if PY_VERSION_HEX < 0x03030000 + Py_XDECREF(py_import); + #endif + Py_XDECREF(empty_list); + Py_XDECREF(empty_dict); + return module; +} + +static int +__pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b) +{ + int i; + if (!a || !b) + return 0; + if (a == b) + return 1; + if (a->size != b->size || a->typegroup != b->typegroup || + a->is_unsigned != b->is_unsigned || a->ndim != b->ndim) { + if (a->typegroup == 'H' || b->typegroup == 'H') { + return a->size == b->size; + } else { + return 0; + } + } + if (a->ndim) { + for (i = 0; i < a->ndim; i++) + if (a->arraysize[i] != b->arraysize[i]) + return 0; + } + if (a->typegroup == 'S') { + if (a->flags != b->flags) + return 0; + if (a->fields || b->fields) { + if (!(a->fields && b->fields)) + return 0; + for (i = 0; a->fields[i].type && b->fields[i].type; i++) { + __Pyx_StructField *field_a = a->fields + i; + __Pyx_StructField *field_b = b->fields + i; + if (field_a->offset != field_b->offset || + !__pyx_typeinfo_cmp(field_a->type, field_b->type)) + return 0; + } + return !a->fields[i].type && !b->fields[i].type; + } + } + return 1; +} + +static int +__pyx_check_strides(Py_buffer *buf, int dim, int ndim, int spec) +{ + if (buf->shape[dim] <= 1) + return 1; + if (buf->strides) { + if (spec & __Pyx_MEMVIEW_CONTIG) { + if (spec & (__Pyx_MEMVIEW_PTR|__Pyx_MEMVIEW_FULL)) { + if (buf->strides[dim] != sizeof(void *)) { + PyErr_Format(PyExc_ValueError, + "Buffer is not indirectly contiguous " + "in dimension %d.", dim); + goto fail; + } + } else if (buf->strides[dim] != buf->itemsize) { + PyErr_SetString(PyExc_ValueError, + "Buffer and memoryview are not contiguous " + "in the same dimension."); + goto fail; + } + } + if (spec & __Pyx_MEMVIEW_FOLLOW) { + Py_ssize_t stride = buf->strides[dim]; + if (stride < 0) + stride = -stride; + if (stride < buf->itemsize) { + PyErr_SetString(PyExc_ValueError, + "Buffer and memoryview are not contiguous " + "in the same dimension."); + goto fail; + } + } + } else { + if (spec & __Pyx_MEMVIEW_CONTIG && dim != ndim - 1) { + PyErr_Format(PyExc_ValueError, + "C-contiguous buffer is not contiguous in " + "dimension %d", dim); + goto fail; + } else if (spec & (__Pyx_MEMVIEW_PTR)) { + PyErr_Format(PyExc_ValueError, + "C-contiguous buffer is not indirect in " + "dimension %d", dim); + goto fail; + } else if (buf->suboffsets) { + PyErr_SetString(PyExc_ValueError, + "Buffer exposes suboffsets but no strides"); + goto fail; + } + } + return 1; +fail: + return 0; +} +static int +__pyx_check_suboffsets(Py_buffer *buf, int dim, CYTHON_UNUSED int ndim, int spec) +{ + if (spec & __Pyx_MEMVIEW_DIRECT) { + if (buf->suboffsets && buf->suboffsets[dim] >= 0) { + PyErr_Format(PyExc_ValueError, + "Buffer not compatible with direct access " + "in dimension %d.", dim); + goto fail; + } + } + if (spec & __Pyx_MEMVIEW_PTR) { + if (!buf->suboffsets || (buf->suboffsets && buf->suboffsets[dim] < 0)) { + PyErr_Format(PyExc_ValueError, + "Buffer is not indirectly accessible " + "in dimension %d.", dim); + goto fail; + } + } + return 1; +fail: + return 0; +} +static int +__pyx_verify_contig(Py_buffer *buf, int ndim, int c_or_f_flag) +{ + int i; + if (c_or_f_flag & __Pyx_IS_F_CONTIG) { + Py_ssize_t stride = 1; + for (i = 0; i < ndim; i++) { + if (stride * buf->itemsize != buf->strides[i] && + buf->shape[i] > 1) + { + PyErr_SetString(PyExc_ValueError, + "Buffer not fortran contiguous."); + goto fail; + } + stride = stride * buf->shape[i]; + } + } else if (c_or_f_flag & __Pyx_IS_C_CONTIG) { + Py_ssize_t stride = 1; + for (i = ndim - 1; i >- 1; i--) { + if (stride * buf->itemsize != buf->strides[i] && + buf->shape[i] > 1) { + PyErr_SetString(PyExc_ValueError, + "Buffer not C contiguous."); + goto fail; + } + stride = stride * buf->shape[i]; + } + } + return 1; +fail: + return 0; +} +static int __Pyx_ValidateAndInit_memviewslice( + int *axes_specs, + int c_or_f_flag, + int buf_flags, + int ndim, + __Pyx_TypeInfo *dtype, + __Pyx_BufFmt_StackElem stack[], + __Pyx_memviewslice *memviewslice, + PyObject *original_obj) +{ + struct __pyx_memoryview_obj *memview, *new_memview; + __Pyx_RefNannyDeclarations + Py_buffer *buf; + int i, spec = 0, retval = -1; + __Pyx_BufFmt_Context ctx; + int from_memoryview = __pyx_memoryview_check(original_obj); + __Pyx_RefNannySetupContext("ValidateAndInit_memviewslice", 0); + if (from_memoryview && __pyx_typeinfo_cmp(dtype, ((struct __pyx_memoryview_obj *) + original_obj)->typeinfo)) { + memview = (struct __pyx_memoryview_obj *) original_obj; + new_memview = NULL; + } else { + memview = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( + original_obj, buf_flags, 0, dtype); + new_memview = memview; + if (unlikely(!memview)) + goto fail; + } + buf = &memview->view; + if (buf->ndim != ndim) { + PyErr_Format(PyExc_ValueError, + "Buffer has wrong number of dimensions (expected %d, got %d)", + ndim, buf->ndim); + goto fail; + } + if (new_memview) { + __Pyx_BufFmt_Init(&ctx, stack, dtype); + if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail; + } + if ((unsigned) buf->itemsize != dtype->size) { + PyErr_Format(PyExc_ValueError, + "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "u byte%s) " + "does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "u byte%s)", + buf->itemsize, + (buf->itemsize > 1) ? "s" : "", + dtype->name, + dtype->size, + (dtype->size > 1) ? "s" : ""); + goto fail; + } + for (i = 0; i < ndim; i++) { + spec = axes_specs[i]; + if (!__pyx_check_strides(buf, i, ndim, spec)) + goto fail; + if (!__pyx_check_suboffsets(buf, i, ndim, spec)) + goto fail; + } + if (buf->strides && !__pyx_verify_contig(buf, ndim, c_or_f_flag)) + goto fail; + if (unlikely(__Pyx_init_memviewslice(memview, ndim, memviewslice, + new_memview != NULL) == -1)) { + goto fail; + } + retval = 0; + goto no_fail; +fail: + Py_XDECREF(new_memview); + retval = -1; +no_fail: + __Pyx_RefNannyFinishContext(); + return retval; +} + +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_float(PyObject *obj) { + __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; + __Pyx_BufFmt_StackElem stack[1]; + int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; + int retcode; + if (obj == Py_None) { + result.memview = (struct __pyx_memoryview_obj *) Py_None; + return result; + } + retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, + PyBUF_RECORDS, 2, + &__Pyx_TypeInfo_float, stack, + &result, obj); + if (unlikely(retcode == -1)) + goto __pyx_fail; + return result; +__pyx_fail: + result.memview = NULL; + result.data = NULL; + return result; +} + +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_long(PyObject *obj) { + __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; + __Pyx_BufFmt_StackElem stack[1]; + int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; + int retcode; + if (obj == Py_None) { + result.memview = (struct __pyx_memoryview_obj *) Py_None; + return result; + } + retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, + PyBUF_RECORDS, 2, + &__Pyx_TypeInfo_long, stack, + &result, obj); + if (unlikely(retcode == -1)) + goto __pyx_fail; + return result; +__pyx_fail: + result.memview = NULL; + result.data = NULL; + return result; +} + +#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value) \ + { \ + func_type value = func_value; \ + if (sizeof(target_type) < sizeof(func_type)) { \ + if (unlikely(value != (func_type) (target_type) value)) { \ + func_type zero = 0; \ + if (is_unsigned && unlikely(value < zero)) \ + goto raise_neg_overflow; \ + else \ + goto raise_overflow; \ + } \ + } \ + return (target_type) value; \ + } + +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + #include "longintrepr.h" + #endif +#endif + +static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { + const int neg_one = (int) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(int) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (int) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(int, digit, ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } + if (sizeof(int) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(int) <= sizeof(unsigned long long)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long long, PyLong_AsUnsignedLongLong(x)) + } + } else { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(int, digit, +(((PyLongObject*)x)->ob_digit[0])); + case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (sizeof(int) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT(int, long, PyLong_AsLong(x)) + } else if (sizeof(int) <= sizeof(long long)) { + __PYX_VERIFY_RETURN_INT(int, long long, PyLong_AsLongLong(x)) + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + int val; + PyObject *v = __Pyx_PyNumber_Int(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (int) -1; + } + } else { + int val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (int) -1; + val = __Pyx_PyInt_As_int(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to int"); + return (int) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to int"); + return (int) -1; +} + +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { + const long neg_one = (long) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(long) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (long) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(long, digit, ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } + if (sizeof(long) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(long) <= sizeof(unsigned long long)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long long, PyLong_AsUnsignedLongLong(x)) + } + } else { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(long, digit, +(((PyLongObject*)x)->ob_digit[0])); + case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (sizeof(long) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT(long, long, PyLong_AsLong(x)) + } else if (sizeof(long) <= sizeof(long long)) { + __PYX_VERIFY_RETURN_INT(long, long long, PyLong_AsLongLong(x)) + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + long val; + PyObject *v = __Pyx_PyNumber_Int(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (long) -1; + } + } else { + long val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (long) -1; + val = __Pyx_PyInt_As_long(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to long"); + return (long) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to long"); + return (long) -1; +} + +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_long(PyObject *obj) { + __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; + __Pyx_BufFmt_StackElem stack[1]; + int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; + int retcode; + if (obj == Py_None) { + result.memview = (struct __pyx_memoryview_obj *) Py_None; + return result; + } + retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, + PyBUF_RECORDS, 1, + &__Pyx_TypeInfo_long, stack, + &result, obj); + if (unlikely(retcode == -1)) + goto __pyx_fail; + return result; +__pyx_fail: + result.memview = NULL; + result.data = NULL; + return result; +} + +static CYTHON_INLINE long __Pyx_pow_long(long b, long e) { + long t = b; + switch (e) { + case 3: + t *= b; + case 2: + t *= b; + case 1: + return t; + case 0: + return 1; + } + #if 1 + if (unlikely(e<0)) return 0; + #endif + t = 1; + while (likely(e)) { + t *= (b * (e&1)) | ((~e)&1); /* 1 or b */ + b *= b; + e >>= 1; + } + return t; +} + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { + const int neg_one = (int) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(int) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(int) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(int) <= sizeof(unsigned long long)) { + return PyLong_FromUnsignedLongLong((unsigned long long) value); + } + } else { + if (sizeof(int) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(int) <= sizeof(long long)) { + return PyLong_FromLongLong((long long) value); + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(int), + little, !is_unsigned); + } +} + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { + const long neg_one = (long) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(long) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(long) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(long) <= sizeof(unsigned long long)) { + return PyLong_FromUnsignedLongLong((unsigned long long) value); + } + } else { + if (sizeof(long) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(long) <= sizeof(long long)) { + return PyLong_FromLongLong((long long) value); + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(long), + little, !is_unsigned); + } +} + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_clock_t(clock_t value) { + const clock_t neg_one = (clock_t) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(clock_t) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(clock_t) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(clock_t) <= sizeof(unsigned long long)) { + return PyLong_FromUnsignedLongLong((unsigned long long) value); + } + } else { + if (sizeof(clock_t) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(clock_t) <= sizeof(long long)) { + return PyLong_FromLongLong((long long) value); + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(clock_t), + little, !is_unsigned); + } +} + +static PyObject *__pyx_memview_get_float(const char *itemp) { + return (PyObject *) PyFloat_FromDouble(*(float *) itemp); +} +static int __pyx_memview_set_float(const char *itemp, PyObject *obj) { + float value = __pyx_PyFloat_AsFloat(obj); + if ((value == (float)-1) && PyErr_Occurred()) + return 0; + *(float *) itemp = value; + return 1; +} + +static PyObject *__pyx_memview_get_long(const char *itemp) { + return (PyObject *) __Pyx_PyInt_From_long(*(long *) itemp); +} +static int __pyx_memview_set_long(const char *itemp, PyObject *obj) { + long value = __Pyx_PyInt_As_long(obj); + if ((value == (long)-1) && PyErr_Occurred()) + return 0; + *(long *) itemp = value; + return 1; +} + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return ::std::complex< float >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + return x + y*(__pyx_t_float_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { + __pyx_t_float_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +#if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + float denom = b.real * b.real + b.imag * b.imag; + z.real = (a.real * b.real + a.imag * b.imag) / denom; + z.imag = (a.imag * b.real - a.real * b.imag) / denom; + return z; + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) { + __pyx_t_float_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrtf(z.real*z.real + z.imag*z.imag); + #else + return hypotf(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + float r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + float denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(a, a); + case 3: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(z, a); + case 4: + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } + r = a.real; + theta = 0; + } else { + r = __Pyx_c_absf(a); + theta = atan2f(a.imag, a.real); + } + lnr = logf(r); + z_r = expf(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cosf(z_theta); + z.imag = z_r * sinf(z_theta); + return z; + } + #endif +#endif + +#if CYTHON_CCOMPLEX + #ifdef __cplusplus + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return ::std::complex< double >(x, y); + } + #else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + return x + y*(__pyx_t_double_complex)_Complex_I; + } + #endif +#else + static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { + __pyx_t_double_complex z; + z.real = x; + z.imag = y; + return z; + } +#endif + +#if CYTHON_CCOMPLEX +#else + static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) { + return (a.real == b.real) && (a.imag == b.imag); + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real + b.real; + z.imag = a.imag + b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real - b.real; + z.imag = a.imag - b.imag; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + z.real = a.real * b.real - a.imag * b.imag; + z.imag = a.real * b.imag + a.imag * b.real; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + double denom = b.real * b.real + b.imag * b.imag; + z.real = (a.real * b.real + a.imag * b.imag) / denom; + z.imag = (a.imag * b.real - a.real * b.imag) / denom; + return z; + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = -a.real; + z.imag = -a.imag; + return z; + } + static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) { + return (a.real == 0) && (a.imag == 0); + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) { + __pyx_t_double_complex z; + z.real = a.real; + z.imag = -a.imag; + return z; + } + #if 1 + static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex z) { + #if !defined(HAVE_HYPOT) || defined(_MSC_VER) + return sqrt(z.real*z.real + z.imag*z.imag); + #else + return hypot(z.real, z.imag); + #endif + } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + double r, lnr, theta, z_r, z_theta; + if (b.imag == 0 && b.real == (int)b.real) { + if (b.real < 0) { + double denom = a.real * a.real + a.imag * a.imag; + a.real = a.real / denom; + a.imag = -a.imag / denom; + b.real = -b.real; + } + switch ((int)b.real) { + case 0: + z.real = 1; + z.imag = 0; + return z; + case 1: + return a; + case 2: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(a, a); + case 3: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(z, a); + case 4: + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(z, z); + } + } + if (a.imag == 0) { + if (a.real == 0) { + return a; + } + r = a.real; + theta = 0; + } else { + r = __Pyx_c_abs(a); + theta = atan2(a.imag, a.real); + } + lnr = log(r); + z_r = exp(lnr * b.real - theta * b.imag); + z_theta = theta * b.real + lnr * b.imag; + z.real = z_r * cos(z_theta); + z.imag = z_r * sin(z_theta); + return z; + } + #endif +#endif + +static int +__pyx_memviewslice_is_contig(const __Pyx_memviewslice *mvs, + char order, int ndim) +{ + int i, index, step, start; + Py_ssize_t itemsize = mvs->memview->view.itemsize; + if (order == 'F') { + step = 1; + start = 0; + } else { + step = -1; + start = ndim - 1; + } + for (i = 0; i < ndim; i++) { + index = start + step * i; + if (mvs->suboffsets[index] >= 0 || mvs->strides[index] != itemsize) + return 0; + itemsize *= mvs->shape[index]; + } + return 1; +} + +static void +__pyx_get_array_memory_extents(__Pyx_memviewslice *slice, + void **out_start, void **out_end, + int ndim, size_t itemsize) +{ + char *start, *end; + int i; + start = end = slice->data; + for (i = 0; i < ndim; i++) { + Py_ssize_t stride = slice->strides[i]; + Py_ssize_t extent = slice->shape[i]; + if (extent == 0) { + *out_start = *out_end = start; + return; + } else { + if (stride > 0) + end += stride * (extent - 1); + else + start += stride * (extent - 1); + } + } + *out_start = start; + *out_end = end + itemsize; +} +static int +__pyx_slices_overlap(__Pyx_memviewslice *slice1, + __Pyx_memviewslice *slice2, + int ndim, size_t itemsize) +{ + void *start1, *end1, *start2, *end2; + __pyx_get_array_memory_extents(slice1, &start1, &end1, ndim, itemsize); + __pyx_get_array_memory_extents(slice2, &start2, &end2, ndim, itemsize); + return (start1 < end2) && (start2 < end1); +} + +static __Pyx_memviewslice +__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs, + const char *mode, int ndim, + size_t sizeof_dtype, int contig_flag, + int dtype_is_object) +{ + __Pyx_RefNannyDeclarations + int i; + __Pyx_memviewslice new_mvs = { 0, 0, { 0 }, { 0 }, { 0 } }; + struct __pyx_memoryview_obj *from_memview = from_mvs->memview; + Py_buffer *buf = &from_memview->view; + PyObject *shape_tuple = NULL; + PyObject *temp_int = NULL; + struct __pyx_array_obj *array_obj = NULL; + struct __pyx_memoryview_obj *memview_obj = NULL; + __Pyx_RefNannySetupContext("__pyx_memoryview_copy_new_contig", 0); + for (i = 0; i < ndim; i++) { + if (from_mvs->suboffsets[i] >= 0) { + PyErr_Format(PyExc_ValueError, "Cannot copy memoryview slice with " + "indirect dimensions (axis %d)", i); + goto fail; + } + } + shape_tuple = PyTuple_New(ndim); + if (unlikely(!shape_tuple)) { + goto fail; + } + __Pyx_GOTREF(shape_tuple); + for(i = 0; i < ndim; i++) { + temp_int = PyInt_FromSsize_t(from_mvs->shape[i]); + if(unlikely(!temp_int)) { + goto fail; + } else { + PyTuple_SET_ITEM(shape_tuple, i, temp_int); + temp_int = NULL; + } + } + array_obj = __pyx_array_new(shape_tuple, sizeof_dtype, buf->format, (char *) mode, NULL); + if (unlikely(!array_obj)) { + goto fail; + } + __Pyx_GOTREF(array_obj); + memview_obj = (struct __pyx_memoryview_obj *) __pyx_memoryview_new( + (PyObject *) array_obj, contig_flag, + dtype_is_object, + from_mvs->memview->typeinfo); + if (unlikely(!memview_obj)) + goto fail; + if (unlikely(__Pyx_init_memviewslice(memview_obj, ndim, &new_mvs, 1) < 0)) + goto fail; + if (unlikely(__pyx_memoryview_copy_contents(*from_mvs, new_mvs, ndim, ndim, + dtype_is_object) < 0)) + goto fail; + goto no_fail; +fail: + __Pyx_XDECREF(new_mvs.memview); + new_mvs.memview = NULL; + new_mvs.data = NULL; +no_fail: + __Pyx_XDECREF(shape_tuple); + __Pyx_XDECREF(temp_int); + __Pyx_XDECREF(array_obj); + __Pyx_RefNannyFinishContext(); + return new_mvs; +} + +static CYTHON_INLINE PyObject * +__pyx_capsule_create(void *p, CYTHON_UNUSED const char *sig) +{ + PyObject *cobj; +#if PY_VERSION_HEX >= 0x02070000 + cobj = PyCapsule_New(p, sig, NULL); +#else + cobj = PyCObject_FromVoidPtr(p, NULL); +#endif + return cobj; +} + +static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { + const char neg_one = (char) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(char) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(char, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (char) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(char, digit, ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } + if (sizeof(char) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(char) <= sizeof(unsigned long long)) { + __PYX_VERIFY_RETURN_INT(char, unsigned long long, PyLong_AsUnsignedLongLong(x)) + } + } else { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(char, digit, +(((PyLongObject*)x)->ob_digit[0])); + case -1: __PYX_VERIFY_RETURN_INT(char, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (sizeof(char) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT(char, long, PyLong_AsLong(x)) + } else if (sizeof(char) <= sizeof(long long)) { + __PYX_VERIFY_RETURN_INT(char, long long, PyLong_AsLongLong(x)) + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + char val; + PyObject *v = __Pyx_PyNumber_Int(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (char) -1; + } + } else { + char val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (char) -1; + val = __Pyx_PyInt_As_char(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to char"); + return (char) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to char"); + return (char) -1; +} + +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_float(PyObject *obj) { + __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; + __Pyx_BufFmt_StackElem stack[1]; + int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; + int retcode; + if (obj == Py_None) { + result.memview = (struct __pyx_memoryview_obj *) Py_None; + return result; + } + retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, + PyBUF_RECORDS, 1, + &__Pyx_TypeInfo_float, stack, + &result, obj); + if (unlikely(retcode == -1)) + goto __pyx_fail; + return result; +__pyx_fail: + result.memview = NULL; + result.data = NULL; + return result; +} + +static int __Pyx_check_binary_version(void) { + char ctversion[4], rtversion[4]; + PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); + PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); + if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) { + char message[200]; + PyOS_snprintf(message, sizeof(message), + "compiletime version %s of module '%.100s' " + "does not match runtime version %s", + ctversion, __Pyx_MODULE_NAME, rtversion); + return PyErr_WarnEx(NULL, message, 1); + } + return 0; +} + +#ifndef __PYX_HAVE_RT_ImportModule +#define __PYX_HAVE_RT_ImportModule +static PyObject *__Pyx_ImportModule(const char *name) { + PyObject *py_name = 0; + PyObject *py_module = 0; + py_name = __Pyx_PyIdentifier_FromString(name); + if (!py_name) + goto bad; + py_module = PyImport_Import(py_name); + Py_DECREF(py_name); + return py_module; +bad: + Py_XDECREF(py_name); + return 0; +} +#endif + +#ifndef __PYX_HAVE_RT_ImportType +#define __PYX_HAVE_RT_ImportType +static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, + size_t size, int strict) +{ + PyObject *py_module = 0; + PyObject *result = 0; + PyObject *py_name = 0; + char warning[200]; + Py_ssize_t basicsize; +#ifdef Py_LIMITED_API + PyObject *py_basicsize; +#endif + py_module = __Pyx_ImportModule(module_name); + if (!py_module) + goto bad; + py_name = __Pyx_PyIdentifier_FromString(class_name); + if (!py_name) + goto bad; + result = PyObject_GetAttr(py_module, py_name); + Py_DECREF(py_name); + py_name = 0; + Py_DECREF(py_module); + py_module = 0; + if (!result) + goto bad; + if (!PyType_Check(result)) { + PyErr_Format(PyExc_TypeError, + "%.200s.%.200s is not a type object", + module_name, class_name); + goto bad; + } +#ifndef Py_LIMITED_API + basicsize = ((PyTypeObject *)result)->tp_basicsize; +#else + py_basicsize = PyObject_GetAttrString(result, "__basicsize__"); + if (!py_basicsize) + goto bad; + basicsize = PyLong_AsSsize_t(py_basicsize); + Py_DECREF(py_basicsize); + py_basicsize = 0; + if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred()) + goto bad; +#endif + if (!strict && (size_t)basicsize > size) { + PyOS_snprintf(warning, sizeof(warning), + "%s.%s size changed, may indicate binary incompatibility", + module_name, class_name); + if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; + } + else if ((size_t)basicsize != size) { + PyErr_Format(PyExc_ValueError, + "%.200s.%.200s has the wrong size, try recompiling", + module_name, class_name); + goto bad; + } + return (PyTypeObject *)result; +bad: + Py_XDECREF(py_module); + Py_XDECREF(result); + return NULL; +} +#endif + +static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { + while (t->p) { + #if PY_MAJOR_VERSION < 3 + if (t->is_unicode) { + *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL); + } else if (t->intern) { + *t->p = PyString_InternFromString(t->s); + } else { + *t->p = PyString_FromStringAndSize(t->s, t->n - 1); + } + #else + if (t->is_unicode | t->is_str) { + if (t->intern) { + *t->p = PyUnicode_InternFromString(t->s); + } else if (t->encoding) { + *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL); + } else { + *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1); + } + } else { + *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1); + } + #endif + if (!*t->p) + return -1; + ++t; + } + return 0; +} + +static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { + return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str)); +} +static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) { + Py_ssize_t ignore; + return __Pyx_PyObject_AsStringAndSize(o, &ignore); +} +static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT + if ( +#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + __Pyx_sys_getdefaultencoding_not_ascii && +#endif + PyUnicode_Check(o)) { +#if PY_VERSION_HEX < 0x03030000 + char* defenc_c; + PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL); + if (!defenc) return NULL; + defenc_c = PyBytes_AS_STRING(defenc); +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + { + char* end = defenc_c + PyBytes_GET_SIZE(defenc); + char* c; + for (c = defenc_c; c < end; c++) { + if ((unsigned char) (*c) >= 128) { + PyUnicode_AsASCIIString(o); + return NULL; + } + } + } +#endif + *length = PyBytes_GET_SIZE(defenc); + return defenc_c; +#else + if (__Pyx_PyUnicode_READY(o) == -1) return NULL; +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII + if (PyUnicode_IS_ASCII(o)) { + *length = PyUnicode_GET_LENGTH(o); + return PyUnicode_AsUTF8(o); + } else { + PyUnicode_AsASCIIString(o); + return NULL; + } +#else + return PyUnicode_AsUTF8AndSize(o, length); +#endif +#endif + } else +#endif +#if !CYTHON_COMPILING_IN_PYPY + if (PyByteArray_Check(o)) { + *length = PyByteArray_GET_SIZE(o); + return PyByteArray_AS_STRING(o); + } else +#endif + { + char* result; + int r = PyBytes_AsStringAndSize(o, &result, length); + if (unlikely(r < 0)) { + return NULL; + } else { + return result; + } + } +} +static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { + int is_true = x == Py_True; + if (is_true | (x == Py_False) | (x == Py_None)) return is_true; + else return PyObject_IsTrue(x); +} +static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) { + PyNumberMethods *m; + const char *name = NULL; + PyObject *res = NULL; +#if PY_MAJOR_VERSION < 3 + if (PyInt_Check(x) || PyLong_Check(x)) +#else + if (PyLong_Check(x)) +#endif + return Py_INCREF(x), x; + m = Py_TYPE(x)->tp_as_number; +#if PY_MAJOR_VERSION < 3 + if (m && m->nb_int) { + name = "int"; + res = PyNumber_Int(x); + } + else if (m && m->nb_long) { + name = "long"; + res = PyNumber_Long(x); + } +#else + if (m && m->nb_int) { + name = "int"; + res = PyNumber_Long(x); + } +#endif + if (res) { +#if PY_MAJOR_VERSION < 3 + if (!PyInt_Check(res) && !PyLong_Check(res)) { +#else + if (!PyLong_Check(res)) { +#endif + PyErr_Format(PyExc_TypeError, + "__%.4s__ returned non-%.4s (type %.200s)", + name, name, Py_TYPE(res)->tp_name); + Py_DECREF(res); + return NULL; + } + } + else if (!PyErr_Occurred()) { + PyErr_SetString(PyExc_TypeError, + "an integer is required"); + } + return res; +} +static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { + Py_ssize_t ival; + PyObject *x; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_CheckExact(b))) + return PyInt_AS_LONG(b); +#endif + if (likely(PyLong_CheckExact(b))) { + #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(b)) { + case -1: return -(sdigit)((PyLongObject*)b)->ob_digit[0]; + case 0: return 0; + case 1: return ((PyLongObject*)b)->ob_digit[0]; + } + #endif + #endif + return PyLong_AsSsize_t(b); + } + x = PyNumber_Index(b); + if (!x) return -1; + ival = PyInt_AsSsize_t(x); + Py_DECREF(x); + return ival; +} +static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { + return PyInt_FromSize_t(ival); +} + + +#endif /* Py_PYTHON_H */ diff --git a/sklearn/manifold/_barnes_hut_tsne.pyx b/sklearn/manifold/_barnes_hut_tsne.pyx new file mode 100644 index 0000000000000..a5579b55e1256 --- /dev/null +++ b/sklearn/manifold/_barnes_hut_tsne.pyx @@ -0,0 +1,829 @@ +# cython: boundscheck=False +# cython: wraparound=False +# cython: cdivision=True +# Author: Christopher Moody +# Author: Nick Travers +# Implementation by Chris Moody & Nick Travers +# See http://homepage.tudelft.nl/19j49/t-SNE.html for reference +# implementations and papers describing the technique + + +from libc.stdlib cimport malloc, free +from libc.stdio cimport printf +from libc.math cimport sqrt, log +cimport numpy as np +import numpy as np + +cdef extern from "math.h": + float fabsf(float x) nogil + +# Round points differing by less than this amount +# effectively ignoring differences near the 32bit +# floating point precision +cdef float EPSILON = 1e-6 + +# This is effectively an ifdef statement in Cython +# It allows us to write printf debugging lines +# and remove them at compile time +cdef enum: + DEBUGFLAG = 0 + +cdef extern from "time.h": + # Declare only what is necessary from `tm` structure. + ctypedef long clock_t + clock_t clock() nogil + double CLOCKS_PER_SEC + + +cdef extern from "cblas.h": + float snrm2 "cblas_snrm2"(int N, float *X, int incX) nogil + + +cdef struct Node: + # Keep track of the center of mass + float* barycenter + # If this is a leaf, the position of the point within this leaf + float* leaf_point_position + # The number of points including all + # nodes below this one + long cumulative_size + # Number of points at this node + long size + # Index of the point at this node + # Only defined for non-empty leaf nodes + long point_index + # level = 0 is the root node + # And each subdivision adds 1 to the level + long level + # Left edge of this node + float* left_edge + # The center of this node, equal to le + w/2.0 + float* center + # The width of this node -- used to calculate the opening + # angle. Equal to width = re - le + float* width + # The value of the maximum width w + float max_width + + # Does this node have children? + # Default to leaf until we add points + int is_leaf + # Array of pointers to pointers of children + Node **children + # Keep a pointer to the parent + Node *parent + # Pointer to the tree this node belongs too + Tree* tree + +cdef struct Tree: + # Holds a pointer to the root node + Node* root_node + # Number of dimensions in the ouput + int n_dimensions + # Total number of cells + long n_cells + # Total number of points + long n_points + # Spit out diagnostic information? + int verbose + # How many cells per node? Should go as 2 ** n_dimensionss + int n_cell_per_node + +cdef Tree* init_tree(float[:] left_edge, float[:] width, int n_dimensions, + int verbose) nogil: + # tree is freed by free_tree + cdef Tree* tree = malloc(sizeof(Tree)) + tree.n_dimensions = n_dimensions + tree.n_cells = 0 + tree.n_points = 0 + tree.verbose = verbose + tree.root_node = create_root(left_edge, width, n_dimensions) + tree.root_node.tree = tree + tree.n_cells += 1 + tree.n_cell_per_node = 2 ** n_dimensions + if DEBUGFLAG: + printf("[t-SNE] Tree initialised. Left_edge = (%1.9e, %1.9e, %1.9e)\n", + left_edge[0], left_edge[1], left_edge[2]) + printf("[t-SNE] Tree initialised. Width = (%1.9e, %1.9e, %1.9e)\n", + width[0], width[1], width[2]) + return tree + +cdef Node* create_root(float[:] left_edge, float[:] width, int n_dimensions) nogil: + # Create a default root node + cdef int ax + cdef int n_cell_per_node = 2 ** n_dimensions + # root is freed by free_tree + root = malloc(sizeof(Node)) + root.is_leaf = 1 + root.parent = NULL + root.level = 0 + root.cumulative_size = 0 + root.size = 0 + root.point_index = -1 + root.max_width = 0.0 + root.width = malloc(sizeof(float) * n_dimensions) + root.left_edge = malloc(sizeof(float) * n_dimensions) + root.center = malloc(sizeof(float) * n_dimensions) + root.barycenter = malloc(sizeof(float) * n_dimensions) + root.leaf_point_position= malloc(sizeof(float) * n_dimensions) + root.children = NULL + for ax in range(n_dimensions): + root.width[ax] = width[ax] + root.left_edge[ax] = left_edge[ax] + root.center[ax] = 0.0 + root.barycenter[ax] = 0. + root.leaf_point_position[ax] = -1 + for ax in range(n_dimensions): + root.max_width = max(root.max_width, root.width[ax]) + if DEBUGFLAG: + printf("[t-SNE] Created root node %p\n", root) + return root + +cdef Node* create_child(Node *parent, int[3] offset) nogil: + # Create a new child node with default parameters + cdef int ax + # these children are freed by free_recursive + child = malloc(sizeof(Node)) + child.is_leaf = 1 + child.parent = parent + child.level = parent.level + 1 + child.size = 0 + child.cumulative_size = 0 + child.point_index = -1 + child.tree = parent.tree + child.max_width = 0.0 + child.width = malloc(sizeof(float) * parent.tree.n_dimensions) + child.left_edge = malloc(sizeof(float) * parent.tree.n_dimensions) + child.center = malloc(sizeof(float) * parent.tree.n_dimensions) + child.barycenter = malloc(sizeof(float) * parent.tree.n_dimensions) + child.leaf_point_position = malloc(sizeof(float) * parent.tree.n_dimensions) + child.children = NULL + for ax in range(parent.tree.n_dimensions): + child.width[ax] = parent.width[ax] / 2.0 + child.left_edge[ax] = parent.left_edge[ax] + offset[ax] * parent.width[ax] / 2.0 + child.center[ax] = child.left_edge[ax] + child.width[ax] / 2.0 + child.barycenter[ax] = 0. + child.leaf_point_position[ax] = -1. + for ax in range(parent.tree.n_dimensions): + child.max_width = max(child.max_width, child.width[ax]) + child.tree.n_cells += 1 + return child + +cdef Node* select_child(Node *node, float[3] pos, long index) nogil: + # Find which sub-node a position should go into + # And return the appropriate node + cdef int* offset = malloc(sizeof(int) * node.tree.n_dimensions) + cdef int ax, idx + cdef Node* child + cdef int error + for ax in range(node.tree.n_dimensions): + offset[ax] = (pos[ax] - (node.left_edge[ax] + node.width[ax] / 2.0)) > 0. + idx = offset2index(offset, node.tree.n_dimensions) + child = node.children[idx] + if DEBUGFLAG: + printf("[t-SNE] Offset [%i, %i] with LE [%f, %f]\n", + offset[0], offset[1], child.left_edge[0], child.left_edge[1]) + free(offset) + return child + + +cdef inline void index2offset(int* offset, int index, int n_dimensions) nogil: + # Convert a 1D index into N-D index; useful for indexing + # children of a quadtree, octree, N-tree + # Quite likely there's a fancy bitshift way of doing this + # since the offset is equivalent to the binary representation + # of the integer index + # We read the the offset array left-to-right + # such that the least significat bit is on the right + cdef int rem, k, shift + for k in range(n_dimensions): + shift = n_dimensions -k -1 + rem = ((index >> shift) << shift) + offset[k] = rem > 0 + if DEBUGFLAG: + printf("i2o index %i k %i rem %i offset", index, k, rem) + for j in range(n_dimensions): + printf(" %i", offset[j]) + printf(" n_dimensions %i\n", n_dimensions) + index -= rem + + +cdef inline int offset2index(int* offset, int n_dimensions) nogil: + # Calculate the 1:1 index for a given offset array + # We read the the offset array right-to-left + # such that the least significat bit is on the right + cdef int dim + cdef int index = 0 + for dim in range(n_dimensions): + index += (2 ** dim) * offset[n_dimensions - dim - 1] + if DEBUGFLAG: + printf("o2i index %i dim %i offset", index, dim) + for j in range(n_dimensions): + printf(" %i", offset[j]) + printf(" n_dimensions %i\n", n_dimensions) + return index + + +cdef void subdivide(Node* node) nogil: + # This instantiates 2**n_dimensions = n_cell_per_node nodes for the current node + cdef int idx = 0 + cdef int* offset = malloc(sizeof(int) * node.tree.n_dimensions) + node.is_leaf = False + node.children = malloc(sizeof(Node*) * node.tree.n_cell_per_node) + for idx in range(node.tree.n_cell_per_node): + index2offset(offset, idx, node.tree.n_dimensions) + node.children[idx] = create_child(node, offset) + free(offset) + + +cdef int insert(Node *root, float pos[3], long point_index, long depth, long + duplicate_count) nogil: + # Introduce a new point into the tree + # by recursively inserting it and subdividng as necessary + # Carefully treat the case of identical points at the same node + # by increasing the root.size and tracking duplicate_count + cdef Node *child + cdef long i + cdef int ax + cdef int not_identical = 1 + cdef int n_dimensions = root.tree.n_dimensions + if DEBUGFLAG: + printf("[t-SNE] [d=%i] Inserting pos %i [%f, %f] duplicate_count=%i " + "into child %p\n", depth, point_index, pos[0], pos[1], + duplicate_count, root) + # Increment the total number points including this + # node and below it + root.cumulative_size += duplicate_count + # Evaluate the new center of mass, weighting the previous + # center of mass against the new point data + cdef double frac_seen = (root.cumulative_size - 1) / ( + root.cumulative_size) + cdef double frac_new = 1.0 / root.cumulative_size + # Assert that duplicate_count > 0 + if duplicate_count < 1: + return -1 + # Assert that the point is inside the left & right edges + for ax in range(n_dimensions): + root.barycenter[ax] *= frac_seen + if (pos[ax] > (root.left_edge[ax] + root.width[ax] + EPSILON)): + printf("[t-SNE] Error: point (%1.9e) is above right edge of node " + "(%1.9e)\n", pos[ax], root.left_edge[ax] + root.width[ax]) + return -1 + if (pos[ax] < root.left_edge[ax] - EPSILON): + printf("[t-SNE] Error: point (%1.9e) is below left edge of node " + "(%1.9e)\n", pos[ax], root.left_edge[ax]) + return -1 + for ax in range(n_dimensions): + root.barycenter[ax] += pos[ax] * frac_new + + # If this node is unoccupied, fill it. + # Otherwise, we need to insert recursively. + # Two insertion scenarios: + # 1) Insert into this node if it is a leaf and empty + # 2) Subdivide this node if it is currently occupied + if (root.size == 0) & root.is_leaf: + # Root node is empty and a leaf + if DEBUGFLAG: + printf("[t-SNE] [d=%i] Inserting [%f, %f] into blank cell\n", depth, + pos[0], pos[1]) + for ax in range(n_dimensions): + root.leaf_point_position[ax] = pos[ax] + root.point_index = point_index + root.size = duplicate_count + return 0 + else: + # Root node is occupied or not a leaf + if DEBUGFLAG: + printf("[t-SNE] [d=%i] Node %p is occupied or is a leaf.\n", depth, + root) + printf("[t-SNE] [d=%i] Node %p leaf = %i. Size %i\n", depth, root, + root.is_leaf, root.size) + if root.is_leaf & (root.size > 0): + # is a leaf node and is occupied + for ax in range(n_dimensions): + not_identical &= (fabsf(pos[ax] - root.leaf_point_position[ax]) < EPSILON) + not_identical &= (root.point_index != point_index) + if not_identical == 1: + root.size += duplicate_count + if DEBUGFLAG: + printf("[t-SNE] Warning: [d=%i] Detected identical " + "points. Returning. Leaf now has size %i\n", + depth, root.size) + return 0 + # If necessary, subdivide this node before + # descending + if root.is_leaf: + if DEBUGFLAG: + printf("[t-SNE] [d=%i] Subdividing this leaf node %p\n", depth, + root) + subdivide(root) + # We have two points to relocate: the one previously + # at this node, and the new one we're attempting + # to insert + if root.size > 0: + child = select_child(root, root.leaf_point_position, root.point_index) + if DEBUGFLAG: + printf("[t-SNE] [d=%i] Relocating old point to node %p\n", + depth, child) + insert(child, root.leaf_point_position, root.point_index, depth + 1, root.size) + # Insert the new point + if DEBUGFLAG: + printf("[t-SNE] [d=%i] Selecting node for new point\n", depth) + child = select_child(root, pos, point_index) + if root.size > 0: + # Remove the point from this node + for ax in range(n_dimensions): + root.leaf_point_position[ax] = -1 + root.size = 0 + root.point_index = -1 + return insert(child, pos, point_index, depth + 1, 1) + +cdef int insert_many(Tree* tree, float[:,:] pos_array) nogil: + # Insert each data point into the tree one at a time + cdef long nrows = pos_array.shape[0] + cdef long i + cdef int ax + cdef float row[3] + cdef long err = 0 + for i in range(nrows): + for ax in range(tree.n_dimensions): + row[ax] = pos_array[i, ax] + if DEBUGFLAG: + printf("[t-SNE] inserting point %i: [%f, %f]\n", i, row[0], row[1]) + err = insert(tree.root_node, row, i, 0, 1) + if err != 0: + printf("[t-SNE] ERROR\n") + return err + tree.n_points += 1 + return err + +cdef int free_tree(Tree* tree) nogil: + cdef int check + cdef long* cnt = malloc(sizeof(long) * 3) + for i in range(3): + cnt[i] = 0 + free_recursive(tree, tree.root_node, cnt) + free(tree.root_node) + free(tree) + check = cnt[0] == tree.n_cells + check &= cnt[2] == tree.n_points + free(cnt) + return check + +cdef void free_recursive(Tree* tree, Node *root, long* counts) nogil: + # Free up all of the tree nodes recursively + # while counting the number of nodes visited + # and total number of data points removed + cdef int idx + cdef Node* child + if not root.is_leaf: + for idx in range(tree.n_cell_per_node): + child = root.children[idx] + free_recursive(tree, child, counts) + counts[0] += 1 + if child.is_leaf: + counts[1] += 1 + if child.size > 0: + counts[2] +=1 + else: + free(child.children) + free(child.width) + free(child.left_edge) + free(child.center) + free(child.barycenter) + free(child.leaf_point_position) + free(child) + + +cdef long count_points(Node* root, long count) nogil: + # Walk through the whole tree and count the number + # of points at the leaf nodes + if DEBUGFLAG: + printf("[t-SNE] Counting nodes at root node %p\n", root) + cdef Node* child + cdef int idx + if root.is_leaf: + count += root.size + if DEBUGFLAG : + printf("[t-SNE] %p is a leaf node, no children\n", root) + printf("[t-SNE] %i points in node %p\n", count, root) + return count + # Otherwise, get the children + for idx in range(root.tree.n_cell_per_node): + child = root.children[idx] + if DEBUGFLAG: + printf("[t-SNE] Counting points for child %p\n", child) + if child.is_leaf and child.size > 0: + if DEBUGFLAG: + printf("[t-SNE] Child has size %d\n", child.size) + count += child.size + elif not child.is_leaf: + if DEBUGFLAG: + printf("[t-SNE] Child is not a leaf. Descending\n") + count = count_points(child, count) + # else case is we have an empty leaf node + # which happens when we create a quadtree for + # one point, and then the other neighboring cells + # don't get filled in + if DEBUGFLAG: + printf("[t-SNE] %i points in this node\n", count) + return count + + +cdef float compute_gradient(float[:,:] val_P, + float[:,:] pos_reference, + long[:,:] neighbors, + float[:,:] tot_force, + Node* root_node, + float theta, + float dof, + long start, + long stop) nogil: + # Having created the tree, calculate the gradient + # in two components, the positive and negative forces + cdef long i, coord + cdef int ax + cdef long n = pos_reference.shape[0] + cdef int n_dimensions = root_node.tree.n_dimensions + if root_node.tree.verbose > 11: + printf("[t-SNE] Allocating %i elements in force arrays\n", + n * n_dimensions * 2) + cdef float* sum_Q = malloc(sizeof(float)) + cdef float* neg_f = malloc(sizeof(float) * n * n_dimensions) + cdef float* neg_f_fast = malloc(sizeof(float) * n * n_dimensions) + cdef float* pos_f = malloc(sizeof(float) * n * n_dimensions) + cdef clock_t t1, t2 + cdef float sQ, error + + sum_Q[0] = 0.0 + t1 = clock() + compute_gradient_negative(val_P, pos_reference, neg_f, root_node, sum_Q, + dof, theta, start, stop) + t2 = clock() + if root_node.tree.verbose > 15: + printf("[t-SNE] Computing negative gradient: %e ticks\n", ((float) (t2 - t1))) + sQ = sum_Q[0] + t1 = clock() + error = compute_gradient_positive(val_P, pos_reference, neighbors, pos_f, + n_dimensions, dof, sQ, start, root_node.tree.verbose) + t2 = clock() + if root_node.tree.verbose > 15: + printf("[t-SNE] Computing positive gradient: %e ticks\n", ((float) (t2 - t1))) + for i in range(start, n): + for ax in range(n_dimensions): + coord = i * n_dimensions + ax + tot_force[i, ax] = pos_f[coord] - (neg_f[coord] / sum_Q[0]) + free(sum_Q) + free(neg_f) + free(neg_f_fast) + free(pos_f) + return sQ + + +cdef float compute_gradient_positive(float[:,:] val_P, + float[:,:] pos_reference, + long[:,:] neighbors, + float* pos_f, + int n_dimensions, + float dof, + float sum_Q, + long start, + int verbose) nogil: + # Sum over the following expression for i not equal to j + # grad_i = p_ij (1 + ||y_i - y_j||^2)^-1 (y_i - y_j) + # This is equivalent to compute_edge_forces in the authors' code + # It just goes over the nearest neighbors instead of all the data points + # (unlike the non-nearest neighbors version of `compute_gradient_positive') + cdef: + int ax + long i, j, k + long K = neighbors.shape[1] + long n = val_P.shape[0] + float[3] buff + float D, Q, pij + float C = 0.0 + float exponent = (dof + 1.0) / -2.0 + cdef clock_t t1, t2 + t1 = clock() + for i in range(start, n): + for ax in range(n_dimensions): + pos_f[i * n_dimensions + ax] = 0.0 + for k in range(K): + j = neighbors[i, k] + # we don't need to exclude the i==j case since we've + # already thrown it out from the list of neighbors + D = 0.0 + Q = 0.0 + pij = val_P[i, j] + for ax in range(n_dimensions): + buff[ax] = pos_reference[i, ax] - pos_reference[j, ax] + D += buff[ax] ** 2.0 + Q = (((1.0 + D) / dof) ** exponent) + D = pij * Q + Q /= sum_Q + C += pij * log((pij + EPSILON) / (Q + EPSILON)) + for ax in range(n_dimensions): + pos_f[i * n_dimensions + ax] += D * buff[ax] + t2 = clock() + dt = ((float) (t2 - t1)) + if verbose > 10: + printf("[t-SNE] Computed error=%1.4f in %1.1e ticks\n", C, dt) + return C + + + +cdef void compute_gradient_negative(float[:,:] val_P, + float[:,:] pos_reference, + float* neg_f, + Node *root_node, + float* sum_Q, + float dof, + float theta, + long start, + long stop) nogil: + if stop == -1: + stop = pos_reference.shape[0] + cdef: + int ax + long i, j + long n = stop - start + float* force + float* iQ + float* pos + float* dist2s + long* sizes + float* deltas + long* l + int n_dimensions = root_node.tree.n_dimensions + float qijZ, mult + long idx, + long dta = 0 + long dtb = 0 + clock_t t1, t2, t3 + float* neg_force + + iQ = malloc(sizeof(float)) + force = malloc(sizeof(float) * n_dimensions) + pos = malloc(sizeof(float) * n_dimensions) + dist2s = malloc(sizeof(float) * n) + sizes = malloc(sizeof(long) * n) + deltas = malloc(sizeof(float) * n * n_dimensions) + l = malloc(sizeof(long)) + neg_force= malloc(sizeof(float) * n_dimensions) + + for i in range(start, stop): + # Clear the arrays + for ax in range(n_dimensions): + force[ax] = 0.0 + neg_force[ax] = 0.0 + pos[ax] = pos_reference[i, ax] + iQ[0] = 0.0 + l[0] = 0 + # Find which nodes are summarizing and collect their centers of mass + # deltas, and sizes, into vectorized arrays + t1 = clock() + compute_non_edge_forces(root_node, theta, i, pos, force, dist2s, + sizes, deltas, l) + t2 = clock() + # Compute the t-SNE negative force + # for the digits dataset, walking the tree + # is about 10-15x more expensive than the + # following for loop + exponent = (dof + 1.0) / -2.0 + for j in range(l[0]): + qijZ = ((1.0 + dist2s[j]) / dof) ** exponent + sum_Q[0] += sizes[j] * qijZ + mult = sizes[j] * qijZ * qijZ + for ax in range(n_dimensions): + idx = j * n_dimensions + ax + neg_force[ax] += mult * deltas[idx] + t3 = clock() + for ax in range(n_dimensions): + neg_f[i * n_dimensions + ax] = neg_force[ax] + dta += t2 - t1 + dtb += t3 - t2 + if root_node.tree.verbose > 20: + printf("[t-SNE] Tree: %i clock ticks | ", dta) + printf("Force computation: %i clock ticks\n", dtb) + free(iQ) + free(force) + free(pos) + free(dist2s) + free(sizes) + free(deltas) + free(l) + free(neg_force) + + +cdef void compute_non_edge_forces(Node* node, + float theta, + long point_index, + float* pos, + float* force, + float* dist2s, + long* sizes, + float* deltas, + long* l) nogil: + # Compute the t-SNE force on the point in pos given by point_index + cdef: + Node* child + int i, j + int n_dimensions = node.tree.n_dimensions + long idx, idx1 + float dist_check + + # There are no points below this node if cumulative_size == 0 + # so do not bother to calculate any force contributions + # Also do not compute self-interactions + if node.cumulative_size > 0 and not (node.is_leaf and (node.point_index == + point_index)): + # Compute distance between node center of mass and the reference point + # I've tried rewriting this in terms of BLAS functions, but it's about + # 1.5x worse when we do so, probbaly because the vectors are small + idx1 = l[0] * n_dimensions + deltas[idx1] = pos[0] - node.barycenter[0] + idx = idx1 + for i in range(1, n_dimensions): + idx += 1 + deltas[idx] = pos[i] - node.barycenter[i] + # do np.sqrt(np.sum(deltas**2.0)) + dist2s[l[0]] = snrm2(n_dimensions, &deltas[idx1], 1) + # Check whether we can use this node as a summary + # It's a summary node if the angular size as measured from the point + # is relatively small (w.r.t. to theta) or if it is a leaf node. + # If it can be summarized, we use the cell center of mass + # Otherwise, we go a higher level of resolution and into the leaves. + if node.is_leaf or ((node.max_width / dist2s[l[0]]) < theta): + # Compute the t-SNE force between the reference point and the + # current node + sizes[l[0]] = node.cumulative_size + dist2s[l[0]] = dist2s[l[0]] * dist2s[l[0]] + l[0] += 1 + else: + # Recursively apply Barnes-Hut to child nodes + for idx in range(node.tree.n_cell_per_node): + child = node.children[idx] + if child.cumulative_size == 0: + continue + compute_non_edge_forces(child, theta, + point_index, pos, force, dist2s, sizes, deltas, + l) + + +cdef float compute_error(float[:, :] val_P, + float[:, :] pos_reference, + long[:,:] neighbors, + float sum_Q, + int n_dimensions, + int verbose) nogil: + cdef int i, j, ax + cdef int I = neighbors.shape[0] + cdef int K = neighbors.shape[1] + cdef float pij, Q + cdef float C = 0.0 + cdef clock_t t1, t2 + cdef float dt, delta + t1 = clock() + for i in range(I): + for k in range(K): + j = neighbors[i, k] + pij = val_P[i, j] + Q = 0.0 + for ax in range(n_dimensions): + delta = (pos_reference[i, ax] - pos_reference[j, ax]) + Q += delta * delta + Q = (1.0 / (sum_Q + Q * sum_Q)) + C += pij * log((pij + EPSILON) / (Q + EPSILON)) + t2 = clock() + dt = ((float) (t2 - t1)) + if verbose > 10: + printf("[t-SNE] Computed error=%1.4f in %1.1e ticks\n", C, dt) + return C + + +def calculate_edge(pos_output): + # Make the boundaries slightly outside of the data + # to avoid floating point error near the edge + left_edge = np.min(pos_output, axis=0) + right_edge = np.max(pos_output, axis=0) + center = (right_edge + left_edge) * 0.5 + width = np.maximum(np.subtract(right_edge, left_edge), EPSILON) + # Exagerate width to avoid boundary edge + width = width.astype(np.float32) * 1.001 + left_edge = center - width / 2.0 + right_edge = center + width / 2.0 + return left_edge, right_edge, width + +def gradient(float[:,:] pij_input, + float[:,:] pos_output, + long[:,:] neighbors, + float[:,:] forces, + float theta, + int n_dimensions, + int verbose, + float dof = 1.0, + long skip_num_points=0): + # This function is designed to be called from external Python + # it passes the 'forces' array by reference and fills thats array + # up in-place + cdef float C + n = pos_output.shape[0] + left_edge, right_edge, width = calculate_edge(pos_output) + assert width.itemsize == 4 + assert pij_input.itemsize == 4 + assert pos_output.itemsize == 4 + assert forces.itemsize == 4 + m = "Number of neighbors must be < # of points - 1" + assert n - 1 >= neighbors.shape[1], m + m = "neighbors array and pos_output shapes are incompatible" + assert n == neighbors.shape[0], m + m = "Forces array and pos_output shapes are incompatible" + assert n == forces.shape[0], m + m = "Pij and pos_output shapes are incompatible" + assert n == pij_input.shape[0], m + m = "Pij and pos_output shapes are incompatible" + assert n == pij_input.shape[1], m + if verbose > 10: + printf("[t-SNE] Initializing tree of n_dimensions %i\n", n_dimensions) + cdef Tree* qt = init_tree(left_edge, width, n_dimensions, verbose) + if verbose > 10: + printf("[t-SNE] Inserting %i points\n", pos_output.shape[0]) + err = insert_many(qt, pos_output) + assert err == 0, "[t-SNE] Insertion failed" + if verbose > 10: + printf("[t-SNE] Computing gradient\n") + sum_Q = compute_gradient(pij_input, pos_output, neighbors, forces, + qt.root_node, theta, dof, skip_num_points, -1) + C = compute_error(pij_input, pos_output, neighbors, sum_Q, n_dimensions, + verbose) + if verbose > 10: + printf("[t-SNE] Checking tree consistency \n") + cdef long count = count_points(qt.root_node, 0) + m = ("Tree consistency failed: unexpected number of points=%i " + "at root node=%i" % (count, qt.root_node.cumulative_size)) + assert count == qt.root_node.cumulative_size, m + m = "Tree consistency failed: unexpected number of points on the tree" + assert count == qt.n_points, m + free_tree(qt) + return C + + +# Helper functions +def check_quadtree(X, long[:] counts): + """ + Helper function to access quadtree functions for testing + """ + + X = X.astype(np.float32) + left_edge, right_edge, width = calculate_edge(X) + # Initialise a tree + qt = init_tree(left_edge, width, 2, 2) + # Insert data into the tree + insert_many(qt, X) + + cdef long count = count_points(qt.root_node, 0) + counts[0] = count + counts[1] = qt.root_node.cumulative_size + counts[2] = qt.n_points + free_tree(qt) + return counts + + +cdef int helper_test_index2offset(int* check, int index, int n_dimensions): + cdef int* offset = malloc(sizeof(int) * n_dimensions) + cdef int error_check = 1 + for i in range(n_dimensions): + offset[i] = 0 + index2offset(offset, index, n_dimensions) + for i in range(n_dimensions): + error_check &= offset[i] == check[i] + free(offset) + return error_check + + +def test_index2offset(): + ret = 1 + ret &= helper_test_index2offset([1, 0, 1], 5, 3) == 1 + ret &= helper_test_index2offset([0, 0, 0], 0, 3) == 1 + ret &= helper_test_index2offset([0, 0, 1], 1, 3) == 1 + ret &= helper_test_index2offset([0, 1, 0], 2, 3) == 1 + ret &= helper_test_index2offset([0, 1, 1], 3, 3) == 1 + ret &= helper_test_index2offset([1, 0, 0], 4, 3) == 1 + return ret + + +def test_index_offset(): + cdef int n_dimensions, idx, tidx, k + cdef int error_check = 1 + cdef int* offset + for n_dimensions in range(2, 10): + offset = malloc(sizeof(int) * n_dimensions) + for k in range(n_dimensions): + offset[k] = 0 + for idx in range(2 ** n_dimensions): + index2offset(offset, idx, n_dimensions) + tidx = offset2index(offset, n_dimensions) + error_check &= tidx == idx + assert error_check == 1 + free(offset) + return error_check diff --git a/sklearn/manifold/_utils.c b/sklearn/manifold/_utils.c index 237896982ef20..120edb6c37f32 100644 --- a/sklearn/manifold/_utils.c +++ b/sklearn/manifold/_utils.c @@ -1,4 +1,4 @@ -/* Generated by Cython 0.20.1 on Thu Jun 5 16:28:05 2014 */ +/* Generated by Cython 0.21.1 */ #define PY_SSIZE_T_CLEAN #ifndef CYTHON_USE_PYLONG_INTERNALS @@ -16,11 +16,11 @@ #include "Python.h" #ifndef Py_PYTHON_H #error Python headers needed to compile C extensions, please install development version of Python. -#elif PY_VERSION_HEX < 0x02040000 - #error Cython requires Python 2.4+. +#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000) + #error Cython requires Python 2.6+ or Python 3.2+. #else -#define CYTHON_ABI "0_20_1" -#include /* For offsetof */ +#define CYTHON_ABI "0_21_1" +#include #ifndef offsetof #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) #endif @@ -54,65 +54,11 @@ #define CYTHON_COMPILING_IN_PYPY 0 #define CYTHON_COMPILING_IN_CPYTHON 1 #endif -#if CYTHON_COMPILING_IN_PYPY +#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 #define Py_OptimizeFlag 0 #endif -#if PY_VERSION_HEX < 0x02050000 - typedef int Py_ssize_t; - #define PY_SSIZE_T_MAX INT_MAX - #define PY_SSIZE_T_MIN INT_MIN - #define PY_FORMAT_SIZE_T "" - #define CYTHON_FORMAT_SSIZE_T "" - #define PyInt_FromSsize_t(z) PyInt_FromLong(z) - #define PyInt_AsSsize_t(o) __Pyx_PyInt_As_int(o) - #define PyNumber_Index(o) ((PyNumber_Check(o) && !PyFloat_Check(o)) ? PyNumber_Int(o) : \ - (PyErr_Format(PyExc_TypeError, \ - "expected index value, got %.200s", Py_TYPE(o)->tp_name), \ - (PyObject*)0)) - #define __Pyx_PyIndex_Check(o) (PyNumber_Check(o) && !PyFloat_Check(o) && \ - !PyComplex_Check(o)) - #define PyIndex_Check __Pyx_PyIndex_Check - #define PyErr_WarnEx(category, message, stacklevel) PyErr_Warn(category, message) - #define __PYX_BUILD_PY_SSIZE_T "i" -#else - #define __PYX_BUILD_PY_SSIZE_T "n" - #define CYTHON_FORMAT_SSIZE_T "z" - #define __Pyx_PyIndex_Check PyIndex_Check -#endif -#if PY_VERSION_HEX < 0x02060000 - #define Py_REFCNT(ob) (((PyObject*)(ob))->ob_refcnt) - #define Py_TYPE(ob) (((PyObject*)(ob))->ob_type) - #define Py_SIZE(ob) (((PyVarObject*)(ob))->ob_size) - #define PyVarObject_HEAD_INIT(type, size) \ - PyObject_HEAD_INIT(type) size, - #define PyType_Modified(t) - typedef struct { - void *buf; - PyObject *obj; - Py_ssize_t len; - Py_ssize_t itemsize; - int readonly; - int ndim; - char *format; - Py_ssize_t *shape; - Py_ssize_t *strides; - Py_ssize_t *suboffsets; - void *internal; - } Py_buffer; - #define PyBUF_SIMPLE 0 - #define PyBUF_WRITABLE 0x0001 - #define PyBUF_FORMAT 0x0004 - #define PyBUF_ND 0x0008 - #define PyBUF_STRIDES (0x0010 | PyBUF_ND) - #define PyBUF_C_CONTIGUOUS (0x0020 | PyBUF_STRIDES) - #define PyBUF_F_CONTIGUOUS (0x0040 | PyBUF_STRIDES) - #define PyBUF_ANY_CONTIGUOUS (0x0080 | PyBUF_STRIDES) - #define PyBUF_INDIRECT (0x0100 | PyBUF_STRIDES) - #define PyBUF_RECORDS (PyBUF_STRIDES | PyBUF_FORMAT | PyBUF_WRITABLE) - #define PyBUF_FULL (PyBUF_INDIRECT | PyBUF_FORMAT | PyBUF_WRITABLE) - typedef int (*getbufferproc)(PyObject *, Py_buffer *, int); - typedef void (*releasebufferproc)(PyObject *, Py_buffer *); -#endif +#define __PYX_BUILD_PY_SSIZE_T "n" +#define CYTHON_FORMAT_SSIZE_T "z" #if PY_MAJOR_VERSION < 3 #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ @@ -124,22 +70,11 @@ PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #define __Pyx_DefaultClassType PyType_Type #endif -#if PY_VERSION_HEX < 0x02060000 - #define PyUnicode_FromString(s) PyUnicode_Decode(s, strlen(s), "UTF-8", "strict") -#endif #if PY_MAJOR_VERSION >= 3 #define Py_TPFLAGS_CHECKTYPES 0 #define Py_TPFLAGS_HAVE_INDEX 0 -#endif -#if (PY_VERSION_HEX < 0x02060000) || (PY_MAJOR_VERSION >= 3) #define Py_TPFLAGS_HAVE_NEWBUFFER 0 #endif -#if PY_VERSION_HEX < 0x02060000 - #define Py_TPFLAGS_HAVE_VERSION_TAG 0 -#endif -#if PY_VERSION_HEX < 0x02060000 && !defined(Py_TPFLAGS_IS_ABSTRACT) - #define Py_TPFLAGS_IS_ABSTRACT 0 -#endif #if PY_VERSION_HEX < 0x030400a1 && !defined(Py_TPFLAGS_HAVE_FINALIZE) #define Py_TPFLAGS_HAVE_FINALIZE 0 #endif @@ -164,12 +99,14 @@ #if CYTHON_COMPILING_IN_PYPY #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) + #define __Pyx_PyFrozenSet_Size(s) PyObject_Size(s) #else #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ? \ PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) + #define __Pyx_PyFrozenSet_Size(s) PySet_Size(s) #endif -#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b)) +#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b)) #define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b)) #if PY_MAJOR_VERSION >= 3 #define __Pyx_PyString_Format(a, b) PyUnicode_Format(a, b) @@ -183,36 +120,13 @@ #define PyString_Check PyUnicode_Check #define PyString_CheckExact PyUnicode_CheckExact #endif -#if PY_VERSION_HEX < 0x02060000 - #define PyBytesObject PyStringObject - #define PyBytes_Type PyString_Type - #define PyBytes_Check PyString_Check - #define PyBytes_CheckExact PyString_CheckExact - #define PyBytes_FromString PyString_FromString - #define PyBytes_FromStringAndSize PyString_FromStringAndSize - #define PyBytes_FromFormat PyString_FromFormat - #define PyBytes_DecodeEscape PyString_DecodeEscape - #define PyBytes_AsString PyString_AsString - #define PyBytes_AsStringAndSize PyString_AsStringAndSize - #define PyBytes_Size PyString_Size - #define PyBytes_AS_STRING PyString_AS_STRING - #define PyBytes_GET_SIZE PyString_GET_SIZE - #define PyBytes_Repr PyString_Repr - #define PyBytes_Concat PyString_Concat - #define PyBytes_ConcatAndDel PyString_ConcatAndDel -#endif #if PY_MAJOR_VERSION >= 3 #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj) #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj) #else - #define __Pyx_PyBaseString_Check(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj) || \ - PyString_Check(obj) || PyUnicode_Check(obj)) + #define __Pyx_PyBaseString_Check(obj) (PyString_Check(obj) || PyUnicode_Check(obj)) #define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj)) #endif -#if PY_VERSION_HEX < 0x02060000 - #define PySet_Check(obj) PyObject_TypeCheck(obj, &PySet_Type) - #define PyFrozenSet_Check(obj) PyObject_TypeCheck(obj, &PyFrozenSet_Type) -#endif #ifndef PySet_CheckExact #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type) #endif @@ -237,6 +151,11 @@ #if PY_MAJOR_VERSION >= 3 #define PyBoolObject PyLongObject #endif +#if PY_MAJOR_VERSION >= 3 && CYTHON_COMPILING_IN_PYPY + #ifndef PyUnicode_InternFromString + #define PyUnicode_InternFromString(s) PyUnicode_FromString(s) + #endif +#endif #if PY_VERSION_HEX < 0x030200A4 typedef long Py_hash_t; #define __Pyx_PyInt_FromHash_t PyInt_FromLong @@ -245,42 +164,10 @@ #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t #endif -#if (PY_MAJOR_VERSION < 3) || (PY_VERSION_HEX >= 0x03010300) - #define __Pyx_PySequence_GetSlice(obj, a, b) PySequence_GetSlice(obj, a, b) - #define __Pyx_PySequence_SetSlice(obj, a, b, value) PySequence_SetSlice(obj, a, b, value) - #define __Pyx_PySequence_DelSlice(obj, a, b) PySequence_DelSlice(obj, a, b) -#else - #define __Pyx_PySequence_GetSlice(obj, a, b) (unlikely(!(obj)) ? \ - (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), (PyObject*)0) : \ - (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_GetSlice(obj, a, b)) : \ - (PyErr_Format(PyExc_TypeError, "'%.200s' object is unsliceable", (obj)->ob_type->tp_name), (PyObject*)0))) - #define __Pyx_PySequence_SetSlice(obj, a, b, value) (unlikely(!(obj)) ? \ - (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \ - (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_SetSlice(obj, a, b, value)) : \ - (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice assignment", (obj)->ob_type->tp_name), -1))) - #define __Pyx_PySequence_DelSlice(obj, a, b) (unlikely(!(obj)) ? \ - (PyErr_SetString(PyExc_SystemError, "null argument to internal routine"), -1) : \ - (likely((obj)->ob_type->tp_as_mapping) ? (PySequence_DelSlice(obj, a, b)) : \ - (PyErr_Format(PyExc_TypeError, "'%.200s' object doesn't support slice deletion", (obj)->ob_type->tp_name), -1))) -#endif #if PY_MAJOR_VERSION >= 3 - #define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func)) -#endif -#if PY_VERSION_HEX < 0x02050000 - #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),((char *)(n))) - #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),((char *)(n)),(a)) - #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),((char *)(n))) + #define __Pyx_PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func)) #else - #define __Pyx_GetAttrString(o,n) PyObject_GetAttrString((o),(n)) - #define __Pyx_SetAttrString(o,n,a) PyObject_SetAttrString((o),(n),(a)) - #define __Pyx_DelAttrString(o,n) PyObject_DelAttrString((o),(n)) -#endif -#if PY_VERSION_HEX < 0x02050000 - #define __Pyx_NAMESTR(n) ((char *)(n)) - #define __Pyx_DOCSTR(n) ((char *)(n)) -#else - #define __Pyx_NAMESTR(n) (n) - #define __Pyx_DOCSTR(n) (n) + #define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass) #endif #ifndef CYTHON_INLINE #if defined(__GNUC__) @@ -316,6 +203,12 @@ static CYTHON_INLINE float __PYX_NAN() { return value; } #endif +#ifdef __cplusplus +template +void __Pyx_call_destructor(T* x) { + x->~T(); +} +#endif #if PY_MAJOR_VERSION >= 3 @@ -369,7 +262,7 @@ static CYTHON_INLINE float __PYX_NAN() { # endif #endif typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding; - const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/ + const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; #define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0 #define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0 @@ -392,7 +285,7 @@ static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* #define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l) #define __Pyx_PyBytes_FromString PyBytes_FromString #define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize -static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(char*); +static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*); #if PY_MAJOR_VERSION < 3 #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize @@ -402,17 +295,17 @@ static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(char*); #endif #define __Pyx_PyObject_AsSString(s) ((signed char*) __Pyx_PyObject_AsString(s)) #define __Pyx_PyObject_AsUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_FromUString(s) __Pyx_PyObject_FromString((char*)s) -#define __Pyx_PyBytes_FromUString(s) __Pyx_PyBytes_FromString((char*)s) -#define __Pyx_PyByteArray_FromUString(s) __Pyx_PyByteArray_FromString((char*)s) -#define __Pyx_PyStr_FromUString(s) __Pyx_PyStr_FromString((char*)s) -#define __Pyx_PyUnicode_FromUString(s) __Pyx_PyUnicode_FromString((char*)s) +#define __Pyx_PyObject_FromUString(s) __Pyx_PyObject_FromString((const char*)s) +#define __Pyx_PyBytes_FromUString(s) __Pyx_PyBytes_FromString((const char*)s) +#define __Pyx_PyByteArray_FromUString(s) __Pyx_PyByteArray_FromString((const char*)s) +#define __Pyx_PyStr_FromUString(s) __Pyx_PyStr_FromString((const char*)s) +#define __Pyx_PyUnicode_FromUString(s) __Pyx_PyUnicode_FromString((const char*)s) #if PY_MAJOR_VERSION < 3 static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) { const Py_UNICODE *u_end = u; while (*u_end++) ; - return u_end - u - 1; + return (size_t)(u_end - u - 1); } #else #define __Pyx_Py_UNICODE_strlen Py_UNICODE_strlen @@ -435,18 +328,21 @@ static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); #if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII static int __Pyx_sys_getdefaultencoding_not_ascii; static int __Pyx_init_sys_getdefaultencoding_params(void) { - PyObject* sys = NULL; + PyObject* sys; PyObject* default_encoding = NULL; PyObject* ascii_chars_u = NULL; PyObject* ascii_chars_b = NULL; + const char* default_encoding_c; sys = PyImport_ImportModule("sys"); - if (sys == NULL) goto bad; + if (!sys) goto bad; default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); - if (default_encoding == NULL) goto bad; - if (strcmp(PyBytes_AsString(default_encoding), "ascii") == 0) { + Py_DECREF(sys); + if (!default_encoding) goto bad; + default_encoding_c = PyBytes_AsString(default_encoding); + if (!default_encoding_c) goto bad; + if (strcmp(default_encoding_c, "ascii") == 0) { __Pyx_sys_getdefaultencoding_not_ascii = 0; } else { - const char* default_encoding_c = PyBytes_AS_STRING(default_encoding); char ascii_chars[128]; int c; for (c = 0; c < 128; c++) { @@ -454,23 +350,21 @@ static int __Pyx_init_sys_getdefaultencoding_params(void) { } __Pyx_sys_getdefaultencoding_not_ascii = 1; ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL); - if (ascii_chars_u == NULL) goto bad; + if (!ascii_chars_u) goto bad; ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL); - if (ascii_chars_b == NULL || strncmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) { + if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) { PyErr_Format( PyExc_ValueError, "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.", default_encoding_c); goto bad; } + Py_DECREF(ascii_chars_u); + Py_DECREF(ascii_chars_b); } - Py_XDECREF(sys); - Py_XDECREF(default_encoding); - Py_XDECREF(ascii_chars_u); - Py_XDECREF(ascii_chars_b); + Py_DECREF(default_encoding); return 0; bad: - Py_XDECREF(sys); Py_XDECREF(default_encoding); Py_XDECREF(ascii_chars_u); Py_XDECREF(ascii_chars_b); @@ -484,21 +378,22 @@ static int __Pyx_init_sys_getdefaultencoding_params(void) { #if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT static char* __PYX_DEFAULT_STRING_ENCODING; static int __Pyx_init_sys_getdefaultencoding_params(void) { - PyObject* sys = NULL; + PyObject* sys; PyObject* default_encoding = NULL; char* default_encoding_c; sys = PyImport_ImportModule("sys"); - if (sys == NULL) goto bad; + if (!sys) goto bad; default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); - if (default_encoding == NULL) goto bad; - default_encoding_c = PyBytes_AS_STRING(default_encoding); + Py_DECREF(sys); + if (!default_encoding) goto bad; + default_encoding_c = PyBytes_AsString(default_encoding); + if (!default_encoding_c) goto bad; __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c)); + if (!__PYX_DEFAULT_STRING_ENCODING) goto bad; strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c); - Py_DECREF(sys); Py_DECREF(default_encoding); return 0; bad: - Py_XDECREF(sys); Py_XDECREF(default_encoding); return -1; } @@ -506,16 +401,11 @@ static int __Pyx_init_sys_getdefaultencoding_params(void) { #endif -#ifdef __GNUC__ - /* Test for GCC > 2.95 */ - #if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)) - #define likely(x) __builtin_expect(!!(x), 1) - #define unlikely(x) __builtin_expect(!!(x), 0) - #else /* __GNUC__ > 2 ... */ - #define likely(x) (x) - #define unlikely(x) (x) - #endif /* __GNUC__ > 2 ... */ -#else /* __GNUC__ */ +/* Test for GCC > 2.95 */ +#if defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95))) + #define likely(x) __builtin_expect(!!(x), 1) + #define unlikely(x) __builtin_expect(!!(x), 0) +#else /* !__GNUC__ or GCC < 2.95 */ #define likely(x) (x) #define unlikely(x) (x) #endif /* __GNUC__ */ @@ -553,7 +443,7 @@ static const char *__pyx_filename; static const char *__pyx_f[] = { - "_utils.pyx", + "sklearn/manifold/_utils.pyx", "__init__.pxd", "type.pxd", }; @@ -561,12 +451,12 @@ static const char *__pyx_f[] = { struct __Pyx_StructField_; #define __PYX_BUF_FLAGS_PACKED_STRUCT (1 << 0) typedef struct { - const char* name; /* for error messages only */ + const char* name; struct __Pyx_StructField_* fields; - size_t size; /* sizeof(type) */ - size_t arraysize[8]; /* length of array in each dimension */ + size_t size; + size_t arraysize[8]; int ndim; - char typegroup; /* _R_eal, _C_omplex, Signed _I_nt, _U_nsigned int, _S_truct, _P_ointer, _O_bject, c_H_ar */ + char typegroup; char is_unsigned; int flags; } __Pyx_TypeInfo; @@ -593,7 +483,7 @@ typedef struct { } __Pyx_BufFmt_Context; -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":723 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":723 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< @@ -602,7 +492,7 @@ typedef struct { */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":724 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":724 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< @@ -611,7 +501,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":725 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":725 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< @@ -620,7 +510,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t; */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":726 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":726 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< @@ -629,7 +519,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t; */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":730 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":730 * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< @@ -638,7 +528,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t; */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":731 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":731 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< @@ -647,7 +537,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":732 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":732 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< @@ -656,7 +546,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t; */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":733 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":733 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< @@ -665,7 +555,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t; */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":737 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":737 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< @@ -674,7 +564,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t; */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":738 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":738 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< @@ -683,7 +573,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":747 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":747 * # The int types are mapped a bit surprising -- * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t # <<<<<<<<<<<<<< @@ -692,7 +582,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t; */ typedef npy_long __pyx_t_5numpy_int_t; -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":748 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":748 * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< @@ -701,7 +591,7 @@ typedef npy_long __pyx_t_5numpy_int_t; */ typedef npy_longlong __pyx_t_5numpy_long_t; -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":749 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":749 * ctypedef npy_long int_t * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< @@ -710,7 +600,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t; */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":751 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":751 * ctypedef npy_longlong longlong_t * * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< @@ -719,7 +609,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t; */ typedef npy_ulong __pyx_t_5numpy_uint_t; -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":752 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":752 * * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< @@ -728,7 +618,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":753 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":753 * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< @@ -737,7 +627,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":755 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":755 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< @@ -746,7 +636,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":756 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":756 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< @@ -755,7 +645,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t; */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":758 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":758 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< @@ -764,7 +654,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t; */ typedef npy_double __pyx_t_5numpy_float_t; -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":759 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":759 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< @@ -773,7 +663,7 @@ typedef npy_double __pyx_t_5numpy_float_t; */ typedef npy_double __pyx_t_5numpy_double_t; -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":760 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":760 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< @@ -804,7 +694,7 @@ typedef npy_longdouble __pyx_t_5numpy_longdouble_t; /*--- Type declarations ---*/ -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":762 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":762 * ctypedef npy_longdouble longdouble_t * * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< @@ -813,7 +703,7 @@ typedef npy_longdouble __pyx_t_5numpy_longdouble_t; */ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":763 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":763 * * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< @@ -822,7 +712,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; */ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":764 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":764 * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< @@ -831,7 +721,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; */ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":766 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":766 * ctypedef npy_clongdouble clongdouble_t * * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< @@ -852,7 +742,7 @@ typedef npy_cdouble __pyx_t_5numpy_complex_t; void (*FinishContext)(void**); } __Pyx_RefNannyAPIStruct; static __Pyx_RefNannyAPIStruct *__Pyx_RefNanny = NULL; - static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname); /*proto*/ + static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname); #define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL; #ifdef WITH_THREAD #define __Pyx_RefNannySetupContext(name, acquire_gil) \ @@ -889,7 +779,7 @@ typedef npy_cdouble __pyx_t_5numpy_complex_t; #define __Pyx_XDECREF(r) Py_XDECREF(r) #define __Pyx_XGOTREF(r) #define __Pyx_XGIVEREF(r) -#endif /* CYTHON_REFNANNY */ +#endif #define __Pyx_XDECREF_SET(r, v) do { \ PyObject *tmp = (PyObject *) r; \ r = v; __Pyx_XDECREF(tmp); \ @@ -916,20 +806,22 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject #define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n) #endif -static PyObject *__Pyx_GetBuiltinName(PyObject *name); /*proto*/ +static PyObject *__Pyx_GetBuiltinName(PyObject *name); static CYTHON_INLINE int __Pyx_GetBufferAndValidate(Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack); static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info); -static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name); /*proto*/ +static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name); #if CYTHON_COMPILING_IN_CPYTHON -static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw); /*proto*/ +static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw); #else #define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw) #endif +static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); + #define __Pyx_BufPtrStrided2d(type, buf, i0, s0, i1, s1) (type)((char*)buf + i0 * s0 + i1 * s1) static CYTHON_INLINE long __Pyx_mod_long(long, long); /* proto */ @@ -937,22 +829,28 @@ static CYTHON_INLINE long __Pyx_mod_long(long, long); /* proto */ #define __PYX_FORCE_INIT_THREADS 0 #endif -static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); /*proto*/ -static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg); +#endif + +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg); + +static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); +static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, - Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); /*proto*/ + Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); -static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); /*proto*/ +static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \ PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \ - const char* function_name); /*proto*/ + const char* function_name); static CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, - const char *name, int exact); /*proto*/ + const char *name, int exact); -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); /*proto*/ +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); @@ -960,7 +858,22 @@ static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); -static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); /*proto*/ +typedef struct { + int code_line; + PyCodeObject* code_object; +} __Pyx_CodeObjectCacheEntry; +struct __Pyx_CodeObjectCache { + int count; + int max_count; + __Pyx_CodeObjectCacheEntry* entries; +}; +static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; +static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); +static PyCodeObject *__pyx_find_code_object(int code_line); +static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); + +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename); typedef struct { Py_ssize_t shape, strides, suboffsets; @@ -987,21 +900,23 @@ typedef struct { static Py_ssize_t __Pyx_zeros[] = {0, 0, 0, 0, 0, 0, 0, 0}; static Py_ssize_t __Pyx_minusones[] = {-1, -1, -1, -1, -1, -1, -1, -1}; -static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); /*proto*/ +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); -static int __Pyx_Print(PyObject*, PyObject *, int); /*proto*/ +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); + +static int __Pyx_Print(PyObject*, PyObject *, int); #if CYTHON_COMPILING_IN_PYPY || PY_MAJOR_VERSION >= 3 static PyObject* __pyx_print = 0; static PyObject* __pyx_print_kwargs = 0; #endif -static int __Pyx_PrintOne(PyObject* stream, PyObject *o); /*proto*/ +static int __Pyx_PrintOne(PyObject* stream, PyObject *o); #if CYTHON_CCOMPLEX #ifdef __cplusplus @@ -1101,8 +1016,6 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do #endif #endif -static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); - static int __Pyx_check_binary_version(void); #if !defined(__Pyx_PyIdentifier_FromString) @@ -1113,28 +1026,11 @@ static int __Pyx_check_binary_version(void); #endif #endif -static PyObject *__Pyx_ImportModule(const char *name); /*proto*/ - -static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); /*proto*/ - -typedef struct { - int code_line; - PyCodeObject* code_object; -} __Pyx_CodeObjectCacheEntry; -struct __Pyx_CodeObjectCache { - int count; - int max_count; - __Pyx_CodeObjectCacheEntry* entries; -}; -static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL}; -static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line); -static PyCodeObject *__pyx_find_code_object(int code_line); -static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); +static PyObject *__Pyx_ImportModule(const char *name); -static void __Pyx_AddTraceback(const char *funcname, int c_line, - int py_line, const char *filename); /*proto*/ +static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); -static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/ +static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /* Module declarations from 'libc.string' */ @@ -1171,10 +1067,12 @@ static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0; static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, char *, char *, int *); /*proto*/ /* Module declarations from 'sklearn.manifold._utils' */ -static double __pyx_v_7sklearn_8manifold_6_utils_EPSILON_DBL; -static double __pyx_v_7sklearn_8manifold_6_utils_PERPLEXITY_TOLERANCE; -static PyArrayObject *__pyx_f_7sklearn_8manifold_6_utils__binary_search_perplexity(PyArrayObject *, double, int, int __pyx_skip_dispatch); /*proto*/ -static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_float_t = { "float_t", NULL, sizeof(__pyx_t_5numpy_float_t), { 0 }, 0, 'R', 0, 0 }; +static float __pyx_v_7sklearn_8manifold_6_utils_EPSILON_DBL; +static float __pyx_v_7sklearn_8manifold_6_utils_PERPLEXITY_TOLERANCE; +static PyArrayObject *__pyx_f_7sklearn_8manifold_6_utils__binary_search_perplexity(PyArrayObject *, PyArrayObject *, float, int, int __pyx_skip_dispatch); /*proto*/ +static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t = { "float32_t", NULL, sizeof(__pyx_t_5numpy_float32_t), { 0 }, 0, 'R', 0, 0 }; +static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_int64_t = { "int64_t", NULL, sizeof(__pyx_t_5numpy_int64_t), { 0 }, 0, IS_UNSIGNED(__pyx_t_5numpy_int64_t) ? 'U' : 'I', IS_UNSIGNED(__pyx_t_5numpy_int64_t), 0 }; +static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_float64_t = { "float64_t", NULL, sizeof(__pyx_t_5numpy_float64_t), { 0 }, 0, 'R', 0, 0 }; #define __Pyx_MODULE_NAME "sklearn.manifold._utils" int __pyx_module_is_main_sklearn__manifold___utils = 0; @@ -1182,7 +1080,7 @@ int __pyx_module_is_main_sklearn__manifold___utils = 0; static PyObject *__pyx_builtin_range; static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_RuntimeError; -static PyObject *__pyx_pf_7sklearn_8manifold_6_utils__binary_search_perplexity(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_affinities, double __pyx_v_desired_perplexity, int __pyx_v_verbose); /* proto */ +static PyObject *__pyx_pf_7sklearn_8manifold_6_utils__binary_search_perplexity(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_affinities, PyArrayObject *__pyx_v_neighbors, float __pyx_v_desired_perplexity, int __pyx_v_verbose); /* proto */ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */ static char __pyx_k_B[] = "B"; @@ -1212,14 +1110,14 @@ static char __pyx_k_dtype[] = "dtype"; static char __pyx_k_numpy[] = "numpy"; static char __pyx_k_print[] = "print"; static char __pyx_k_range[] = "range"; -static char __pyx_k_double[] = "double"; +static char __pyx_k_zeros[] = "zeros"; static char __pyx_k_import[] = "__import__"; +static char __pyx_k_float64[] = "float64"; static char __pyx_k_verbose[] = "verbose"; +static char __pyx_k_neighbors[] = "neighbors"; static char __pyx_k_ValueError[] = "ValueError"; static char __pyx_k_affinities[] = "affinities"; static char __pyx_k_RuntimeError[] = "RuntimeError"; -static char __pyx_k_pyx_getbuffer[] = "__pyx_getbuffer"; -static char __pyx_k_pyx_releasebuffer[] = "__pyx_releasebuffer"; static char __pyx_k_desired_perplexity[] = "desired_perplexity"; static char __pyx_k_t_SNE_Mean_sigma_f[] = "[t-SNE] Mean sigma: %f"; static char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; @@ -1236,26 +1134,26 @@ static PyObject *__pyx_n_s_RuntimeError; static PyObject *__pyx_n_s_ValueError; static PyObject *__pyx_n_s_affinities; static PyObject *__pyx_n_s_desired_perplexity; -static PyObject *__pyx_n_s_double; static PyObject *__pyx_n_s_dtype; static PyObject *__pyx_n_s_end; static PyObject *__pyx_n_s_file; +static PyObject *__pyx_n_s_float64; static PyObject *__pyx_n_s_import; static PyObject *__pyx_n_s_main; static PyObject *__pyx_n_s_mean; static PyObject *__pyx_kp_u_ndarray_is_not_C_contiguous; static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou; +static PyObject *__pyx_n_s_neighbors; static PyObject *__pyx_n_s_np; static PyObject *__pyx_n_s_numpy; static PyObject *__pyx_n_s_print; -static PyObject *__pyx_n_s_pyx_getbuffer; -static PyObject *__pyx_n_s_pyx_releasebuffer; static PyObject *__pyx_n_s_range; static PyObject *__pyx_kp_s_t_SNE_Computed_conditional_prob; static PyObject *__pyx_kp_s_t_SNE_Mean_sigma_f; static PyObject *__pyx_n_s_test; static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd; static PyObject *__pyx_n_s_verbose; +static PyObject *__pyx_n_s_zeros; static PyObject *__pyx_tuple_; static PyObject *__pyx_tuple__2; static PyObject *__pyx_tuple__3; @@ -1266,61 +1164,85 @@ static PyObject *__pyx_tuple__6; /* "sklearn/manifold/_utils.pyx":14 * * @cython.boundscheck(False) - * cpdef np.ndarray[np.float_t, ndim=2] _binary_search_perplexity( # <<<<<<<<<<<<<< - * np.ndarray[np.float_t, ndim=2] affinities, double desired_perplexity, - * int verbose): + * cpdef np.ndarray[np.float32_t, ndim=2] _binary_search_perplexity( # <<<<<<<<<<<<<< + * np.ndarray[np.float32_t, ndim=2] affinities, + * np.ndarray[np.int64_t, ndim=2] neighbors, */ static PyObject *__pyx_pw_7sklearn_8manifold_6_utils_1_binary_search_perplexity(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyArrayObject *__pyx_f_7sklearn_8manifold_6_utils__binary_search_perplexity(PyArrayObject *__pyx_v_affinities, double __pyx_v_desired_perplexity, int __pyx_v_verbose, CYTHON_UNUSED int __pyx_skip_dispatch) { - int __pyx_v_n_steps; - int __pyx_v_n_samples; +static PyArrayObject *__pyx_f_7sklearn_8manifold_6_utils__binary_search_perplexity(PyArrayObject *__pyx_v_affinities, PyArrayObject *__pyx_v_neighbors, float __pyx_v_desired_perplexity, int __pyx_v_verbose, CYTHON_UNUSED int __pyx_skip_dispatch) { + long __pyx_v_n_steps; + long __pyx_v_n_samples; PyArrayObject *__pyx_v_P = 0; - double __pyx_v_beta; - double __pyx_v_beta_min; - double __pyx_v_beta_max; - double __pyx_v_beta_sum; - double __pyx_v_desired_entropy; - double __pyx_v_entropy_diff; - double __pyx_v_entropy; - double __pyx_v_sum_Pi; - double __pyx_v_sum_disti_Pi; - int __pyx_v_i; - int __pyx_v_j; - CYTHON_UNUSED int __pyx_v__; + float __pyx_v_beta; + float __pyx_v_beta_min; + float __pyx_v_beta_max; + float __pyx_v_beta_sum; + float __pyx_v_desired_entropy; + float __pyx_v_entropy_diff; + float __pyx_v_entropy; + float __pyx_v_sum_Pi; + float __pyx_v_sum_disti_Pi; + long __pyx_v_i; + long __pyx_v_j; + long __pyx_v_k; + CYTHON_UNUSED long __pyx_v_l; + long __pyx_v_K; + int __pyx_v_using_neighbors; __Pyx_LocalBuf_ND __pyx_pybuffernd_P; __Pyx_Buffer __pyx_pybuffer_P; __Pyx_LocalBuf_ND __pyx_pybuffernd_affinities; __Pyx_Buffer __pyx_pybuffer_affinities; + __Pyx_LocalBuf_ND __pyx_pybuffernd_neighbors; + __Pyx_Buffer __pyx_pybuffer_neighbors; PyArrayObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; PyObject *__pyx_t_2 = NULL; PyObject *__pyx_t_3 = NULL; PyObject *__pyx_t_4 = NULL; - int __pyx_t_5; - int __pyx_t_6; + PyObject *__pyx_t_5 = NULL; + PyArrayObject *__pyx_t_6 = NULL; int __pyx_t_7; - int __pyx_t_8; - int __pyx_t_9; - int __pyx_t_10; - int __pyx_t_11; - int __pyx_t_12; - int __pyx_t_13; - int __pyx_t_14; - int __pyx_t_15; - int __pyx_t_16; - int __pyx_t_17; - int __pyx_t_18; - int __pyx_t_19; - int __pyx_t_20; - int __pyx_t_21; - int __pyx_t_22; - int __pyx_t_23; - int __pyx_t_24; - int __pyx_t_25; - int __pyx_t_26; - int __pyx_t_27; + long __pyx_t_8; + long __pyx_t_9; + long __pyx_t_10; + long __pyx_t_11; + long __pyx_t_12; + long __pyx_t_13; + long __pyx_t_14; + long __pyx_t_15; + long __pyx_t_16; + long __pyx_t_17; + long __pyx_t_18; + long __pyx_t_19; + long __pyx_t_20; + long __pyx_t_21; + long __pyx_t_22; + long __pyx_t_23; + long __pyx_t_24; + long __pyx_t_25; + long __pyx_t_26; + long __pyx_t_27; + long __pyx_t_28; + long __pyx_t_29; + long __pyx_t_30; + long __pyx_t_31; + long __pyx_t_32; + long __pyx_t_33; + long __pyx_t_34; + long __pyx_t_35; + long __pyx_t_36; + long __pyx_t_37; + long __pyx_t_38; + long __pyx_t_39; + long __pyx_t_40; + long __pyx_t_41; + long __pyx_t_42; + long __pyx_t_43; + long __pyx_t_44; + long __pyx_t_45; + int __pyx_t_46; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -1333,124 +1255,192 @@ static PyArrayObject *__pyx_f_7sklearn_8manifold_6_utils__binary_search_perplexi __pyx_pybuffer_affinities.refcount = 0; __pyx_pybuffernd_affinities.data = NULL; __pyx_pybuffernd_affinities.rcbuffer = &__pyx_pybuffer_affinities; + __pyx_pybuffer_neighbors.pybuffer.buf = NULL; + __pyx_pybuffer_neighbors.refcount = 0; + __pyx_pybuffernd_neighbors.data = NULL; + __pyx_pybuffernd_neighbors.rcbuffer = &__pyx_pybuffer_neighbors; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_affinities.rcbuffer->pybuffer, (PyObject*)__pyx_v_affinities, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_affinities.rcbuffer->pybuffer, (PyObject*)__pyx_v_affinities, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_affinities.diminfo[0].strides = __pyx_pybuffernd_affinities.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_affinities.diminfo[0].shape = __pyx_pybuffernd_affinities.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_affinities.diminfo[1].strides = __pyx_pybuffernd_affinities.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_affinities.diminfo[1].shape = __pyx_pybuffernd_affinities.rcbuffer->pybuffer.shape[1]; + { + __Pyx_BufFmt_StackElem __pyx_stack[1]; + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_neighbors.rcbuffer->pybuffer, (PyObject*)__pyx_v_neighbors, &__Pyx_TypeInfo_nn___pyx_t_5numpy_int64_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + __pyx_pybuffernd_neighbors.diminfo[0].strides = __pyx_pybuffernd_neighbors.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_neighbors.diminfo[0].shape = __pyx_pybuffernd_neighbors.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_neighbors.diminfo[1].strides = __pyx_pybuffernd_neighbors.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_neighbors.diminfo[1].shape = __pyx_pybuffernd_neighbors.rcbuffer->pybuffer.shape[1]; - /* "sklearn/manifold/_utils.pyx":43 + /* "sklearn/manifold/_utils.pyx":46 * """ * # Maximum number of binary search steps - * cdef int n_steps = 100 # <<<<<<<<<<<<<< + * cdef long n_steps = 100 # <<<<<<<<<<<<<< * - * cdef int n_samples = affinities.shape[0] + * cdef long n_samples = affinities.shape[0] */ __pyx_v_n_steps = 100; - /* "sklearn/manifold/_utils.pyx":45 - * cdef int n_steps = 100 + /* "sklearn/manifold/_utils.pyx":48 + * cdef long n_steps = 100 * - * cdef int n_samples = affinities.shape[0] # <<<<<<<<<<<<<< - * cdef np.ndarray[np.float_t, ndim=2] P = np.ndarray((n_samples, n_samples), - * dtype=np.double) + * cdef long n_samples = affinities.shape[0] # <<<<<<<<<<<<<< + * # This array is later used as a 32bit array. It has multiple intermediate + * # floating point additions that benefit from the extra precision */ __pyx_v_n_samples = (__pyx_v_affinities->dimensions[0]); - /* "sklearn/manifold/_utils.pyx":46 - * - * cdef int n_samples = affinities.shape[0] - * cdef np.ndarray[np.float_t, ndim=2] P = np.ndarray((n_samples, n_samples), # <<<<<<<<<<<<<< - * dtype=np.double) + /* "sklearn/manifold/_utils.pyx":51 + * # This array is later used as a 32bit array. It has multiple intermediate + * # floating point additions that benefit from the extra precision + * cdef np.ndarray[np.float64_t, ndim=2] P = np.zeros((n_samples, n_samples), # <<<<<<<<<<<<<< + * dtype=np.float64) * # Precisions of conditional Gaussian distrubutions */ - __pyx_t_1 = __Pyx_PyInt_From_int(__pyx_v_n_samples); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 51; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = __Pyx_PyInt_From_int(__pyx_v_n_samples); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_zeros); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 51; __pyx_clineno = __LINE__; 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+ *__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_P.rcbuffer->pybuffer.buf, __pyx_t_22, __pyx_pybuffernd_P.diminfo[0].strides, __pyx_t_23, __pyx_pybuffernd_P.diminfo[1].strides) = exp(((-(*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_affinities.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_affinities.diminfo[0].strides, __pyx_t_21, __pyx_pybuffernd_affinities.diminfo[1].strides))) * __pyx_v_beta)); + } } + __pyx_L8:; - /* "sklearn/manifold/_utils.pyx":73 - * for j in range(n_samples): - * P[i, j] = math.exp(-affinities[i, j] * beta) + /* "sklearn/manifold/_utils.pyx":89 + * for j in range(K): + * P[i, j] = math.exp(-affinities[i, j] * beta) * P[i, i] = 0.0 # <<<<<<<<<<<<<< * sum_Pi = 0.0 - * for j in range(n_samples): + * if using_neighbors: */ - __pyx_t_9 = __pyx_v_i; - __pyx_t_10 = __pyx_v_i; - if (__pyx_t_9 < 0) __pyx_t_9 += __pyx_pybuffernd_P.diminfo[0].shape; - if (__pyx_t_10 < 0) __pyx_t_10 += __pyx_pybuffernd_P.diminfo[1].shape; - *__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float_t *, __pyx_pybuffernd_P.rcbuffer->pybuffer.buf, __pyx_t_9, __pyx_pybuffernd_P.diminfo[0].strides, __pyx_t_10, __pyx_pybuffernd_P.diminfo[1].strides) = 0.0; + __pyx_t_12 = __pyx_v_i; + __pyx_t_13 = __pyx_v_i; + if (__pyx_t_12 < 0) __pyx_t_12 += __pyx_pybuffernd_P.diminfo[0].shape; + if (__pyx_t_13 < 0) __pyx_t_13 += __pyx_pybuffernd_P.diminfo[1].shape; + *__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_P.rcbuffer->pybuffer.buf, __pyx_t_12, __pyx_pybuffernd_P.diminfo[0].strides, __pyx_t_13, __pyx_pybuffernd_P.diminfo[1].strides) = 0.0; - /* "sklearn/manifold/_utils.pyx":74 - * P[i, j] = math.exp(-affinities[i, j] * beta) + /* "sklearn/manifold/_utils.pyx":90 + * P[i, j] = math.exp(-affinities[i, j] * beta) * P[i, i] = 0.0 * sum_Pi = 0.0 # <<<<<<<<<<<<<< - * for j in range(n_samples): - * sum_Pi += P[i, j] + * if using_neighbors: + * for k in range(K): */ __pyx_v_sum_Pi = 0.0; - /* "sklearn/manifold/_utils.pyx":75 + /* "sklearn/manifold/_utils.pyx":91 * P[i, i] = 0.0 * sum_Pi = 0.0 - * for j in range(n_samples): # <<<<<<<<<<<<<< - * sum_Pi += P[i, j] - * if sum_Pi == 0.0: + * if using_neighbors: # <<<<<<<<<<<<<< + * for k in range(K): + * j = neighbors[i, k] */ - __pyx_t_15 = __pyx_v_n_samples; - for (__pyx_t_16 = 0; __pyx_t_16 < __pyx_t_15; __pyx_t_16+=1) { - __pyx_v_j = __pyx_t_16; + __pyx_t_7 = (__pyx_v_using_neighbors != 0); + if (__pyx_t_7) { - /* "sklearn/manifold/_utils.pyx":76 + /* "sklearn/manifold/_utils.pyx":92 * sum_Pi = 0.0 - * for j in range(n_samples): - * sum_Pi += P[i, j] # <<<<<<<<<<<<<< + * if using_neighbors: + * for k in range(K): # <<<<<<<<<<<<<< + * j = neighbors[i, k] + * sum_Pi += P[i, j] + */ + __pyx_t_24 = __pyx_v_K; + for (__pyx_t_25 = 0; __pyx_t_25 < __pyx_t_24; __pyx_t_25+=1) { + __pyx_v_k = __pyx_t_25; + + /* "sklearn/manifold/_utils.pyx":93 + * if using_neighbors: + * for k in range(K): + * j = neighbors[i, k] # <<<<<<<<<<<<<< + * sum_Pi += P[i, j] + * else: + */ + __pyx_t_26 = __pyx_v_i; + __pyx_t_27 = __pyx_v_k; + if (__pyx_t_26 < 0) __pyx_t_26 += __pyx_pybuffernd_neighbors.diminfo[0].shape; + if (__pyx_t_27 < 0) __pyx_t_27 += __pyx_pybuffernd_neighbors.diminfo[1].shape; + __pyx_v_j = (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_int64_t *, __pyx_pybuffernd_neighbors.rcbuffer->pybuffer.buf, __pyx_t_26, __pyx_pybuffernd_neighbors.diminfo[0].strides, __pyx_t_27, __pyx_pybuffernd_neighbors.diminfo[1].strides)); + + /* "sklearn/manifold/_utils.pyx":94 + * for k in range(K): + * j = neighbors[i, k] + * sum_Pi += P[i, j] # <<<<<<<<<<<<<< + * else: + * for j in range(K): + */ + __pyx_t_28 = __pyx_v_i; + __pyx_t_29 = __pyx_v_j; + if (__pyx_t_28 < 0) __pyx_t_28 += __pyx_pybuffernd_P.diminfo[0].shape; + if (__pyx_t_29 < 0) __pyx_t_29 += __pyx_pybuffernd_P.diminfo[1].shape; + __pyx_v_sum_Pi = (__pyx_v_sum_Pi + (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_P.rcbuffer->pybuffer.buf, __pyx_t_28, __pyx_pybuffernd_P.diminfo[0].strides, __pyx_t_29, __pyx_pybuffernd_P.diminfo[1].strides))); + } + goto __pyx_L13; + } + /*else*/ { + + /* "sklearn/manifold/_utils.pyx":96 + * sum_Pi += P[i, j] + * else: + * for j in range(K): # <<<<<<<<<<<<<< + * sum_Pi += P[i, j] + * if sum_Pi == 0.0: + */ + __pyx_t_24 = __pyx_v_K; + for (__pyx_t_25 = 0; __pyx_t_25 < __pyx_t_24; __pyx_t_25+=1) { + __pyx_v_j = __pyx_t_25; + + /* "sklearn/manifold/_utils.pyx":97 + * else: + * for j in range(K): + * sum_Pi += P[i, j] # <<<<<<<<<<<<<< * if sum_Pi == 0.0: * sum_Pi = EPSILON_DBL */ - __pyx_t_17 = __pyx_v_i; - __pyx_t_18 = __pyx_v_j; - if (__pyx_t_17 < 0) __pyx_t_17 += __pyx_pybuffernd_P.diminfo[0].shape; - if (__pyx_t_18 < 0) __pyx_t_18 += __pyx_pybuffernd_P.diminfo[1].shape; - __pyx_v_sum_Pi = (__pyx_v_sum_Pi + (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float_t *, __pyx_pybuffernd_P.rcbuffer->pybuffer.buf, __pyx_t_17, __pyx_pybuffernd_P.diminfo[0].strides, __pyx_t_18, __pyx_pybuffernd_P.diminfo[1].strides))); + __pyx_t_30 = __pyx_v_i; + __pyx_t_31 = __pyx_v_j; + if (__pyx_t_30 < 0) __pyx_t_30 += __pyx_pybuffernd_P.diminfo[0].shape; + if (__pyx_t_31 < 0) __pyx_t_31 += __pyx_pybuffernd_P.diminfo[1].shape; + __pyx_v_sum_Pi = (__pyx_v_sum_Pi + (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_P.rcbuffer->pybuffer.buf, __pyx_t_30, __pyx_pybuffernd_P.diminfo[0].strides, __pyx_t_31, __pyx_pybuffernd_P.diminfo[1].strides))); + } } + __pyx_L13:; - /* "sklearn/manifold/_utils.pyx":77 - * for j in range(n_samples): - * sum_Pi += P[i, j] + /* "sklearn/manifold/_utils.pyx":98 + * for j in range(K): + * sum_Pi += P[i, j] * if sum_Pi == 0.0: # <<<<<<<<<<<<<< * sum_Pi = EPSILON_DBL * sum_disti_Pi = 0.0 */ - __pyx_t_19 = ((__pyx_v_sum_Pi == 0.0) != 0); - if (__pyx_t_19) { + __pyx_t_7 = ((__pyx_v_sum_Pi == 0.0) != 0); + if (__pyx_t_7) { - /* "sklearn/manifold/_utils.pyx":78 - * sum_Pi += P[i, j] + /* "sklearn/manifold/_utils.pyx":99 + * sum_Pi += P[i, j] * if sum_Pi == 0.0: * sum_Pi = EPSILON_DBL # <<<<<<<<<<<<<< * sum_disti_Pi = 0.0 - * for j in range(n_samples): + * if using_neighbors: */ __pyx_v_sum_Pi = __pyx_v_7sklearn_8manifold_6_utils_EPSILON_DBL; - goto __pyx_L11; + goto __pyx_L18; } - __pyx_L11:; + __pyx_L18:; - /* "sklearn/manifold/_utils.pyx":79 + /* "sklearn/manifold/_utils.pyx":100 * if sum_Pi == 0.0: * sum_Pi = EPSILON_DBL * sum_disti_Pi = 0.0 # <<<<<<<<<<<<<< - * for j in range(n_samples): - * P[i, j] /= sum_Pi + * if using_neighbors: + * for k in range(K): */ __pyx_v_sum_disti_Pi = 0.0; - /* "sklearn/manifold/_utils.pyx":80 + /* "sklearn/manifold/_utils.pyx":101 * sum_Pi = EPSILON_DBL * sum_disti_Pi = 0.0 - * for j in range(n_samples): # <<<<<<<<<<<<<< - * P[i, j] /= sum_Pi - * sum_disti_Pi += affinities[i, j] * P[i, j] + * if using_neighbors: # <<<<<<<<<<<<<< + * for k in range(K): + * j = neighbors[i, k] */ - __pyx_t_15 = __pyx_v_n_samples; - for (__pyx_t_16 = 0; __pyx_t_16 < __pyx_t_15; __pyx_t_16+=1) { - __pyx_v_j = __pyx_t_16; + __pyx_t_7 = (__pyx_v_using_neighbors != 0); + if (__pyx_t_7) { - /* "sklearn/manifold/_utils.pyx":81 + /* "sklearn/manifold/_utils.pyx":102 * sum_disti_Pi = 0.0 - * for j in range(n_samples): - * P[i, j] /= sum_Pi # <<<<<<<<<<<<<< - * sum_disti_Pi += affinities[i, j] * P[i, j] + * if using_neighbors: + * for k in range(K): # <<<<<<<<<<<<<< + * j = neighbors[i, k] + * P[i, j] /= sum_Pi + */ + __pyx_t_24 = __pyx_v_K; + for (__pyx_t_25 = 0; __pyx_t_25 < __pyx_t_24; __pyx_t_25+=1) { + __pyx_v_k = __pyx_t_25; + + /* "sklearn/manifold/_utils.pyx":103 + * if using_neighbors: + * for k in range(K): + * j = neighbors[i, k] # <<<<<<<<<<<<<< + * P[i, j] /= sum_Pi + * sum_disti_Pi += affinities[i, j] * P[i, j] + */ + __pyx_t_32 = __pyx_v_i; + __pyx_t_33 = __pyx_v_k; + if (__pyx_t_32 < 0) __pyx_t_32 += __pyx_pybuffernd_neighbors.diminfo[0].shape; + if (__pyx_t_33 < 0) __pyx_t_33 += __pyx_pybuffernd_neighbors.diminfo[1].shape; + __pyx_v_j = (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_int64_t *, __pyx_pybuffernd_neighbors.rcbuffer->pybuffer.buf, __pyx_t_32, __pyx_pybuffernd_neighbors.diminfo[0].strides, __pyx_t_33, __pyx_pybuffernd_neighbors.diminfo[1].strides)); + + /* "sklearn/manifold/_utils.pyx":104 + * for k in range(K): + * j = neighbors[i, k] + * P[i, j] /= sum_Pi # <<<<<<<<<<<<<< + * sum_disti_Pi += affinities[i, j] * P[i, j] + * else: + */ + __pyx_t_34 = __pyx_v_i; + __pyx_t_35 = __pyx_v_j; + if (__pyx_t_34 < 0) __pyx_t_34 += __pyx_pybuffernd_P.diminfo[0].shape; + if (__pyx_t_35 < 0) __pyx_t_35 += __pyx_pybuffernd_P.diminfo[1].shape; + *__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_P.rcbuffer->pybuffer.buf, __pyx_t_34, __pyx_pybuffernd_P.diminfo[0].strides, __pyx_t_35, __pyx_pybuffernd_P.diminfo[1].strides) /= __pyx_v_sum_Pi; + + /* "sklearn/manifold/_utils.pyx":105 + * j = neighbors[i, k] + * P[i, j] /= sum_Pi + * sum_disti_Pi += affinities[i, j] * P[i, j] # <<<<<<<<<<<<<< + * else: + * for j in range(K): + */ + __pyx_t_36 = __pyx_v_i; + __pyx_t_37 = __pyx_v_j; + if (__pyx_t_36 < 0) __pyx_t_36 += __pyx_pybuffernd_affinities.diminfo[0].shape; + if (__pyx_t_37 < 0) __pyx_t_37 += __pyx_pybuffernd_affinities.diminfo[1].shape; + __pyx_t_38 = __pyx_v_i; + __pyx_t_39 = __pyx_v_j; + if (__pyx_t_38 < 0) __pyx_t_38 += __pyx_pybuffernd_P.diminfo[0].shape; + if (__pyx_t_39 < 0) __pyx_t_39 += __pyx_pybuffernd_P.diminfo[1].shape; + __pyx_v_sum_disti_Pi = (__pyx_v_sum_disti_Pi + ((*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_affinities.rcbuffer->pybuffer.buf, __pyx_t_36, __pyx_pybuffernd_affinities.diminfo[0].strides, __pyx_t_37, __pyx_pybuffernd_affinities.diminfo[1].strides)) * (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_P.rcbuffer->pybuffer.buf, __pyx_t_38, __pyx_pybuffernd_P.diminfo[0].strides, __pyx_t_39, __pyx_pybuffernd_P.diminfo[1].strides)))); + } + goto __pyx_L19; + } + /*else*/ { + + /* "sklearn/manifold/_utils.pyx":107 + * sum_disti_Pi += affinities[i, j] * P[i, j] + * else: + * for j in range(K): # <<<<<<<<<<<<<< + * P[i, j] /= sum_Pi + * sum_disti_Pi += affinities[i, j] * P[i, j] + */ + __pyx_t_24 = __pyx_v_K; + for (__pyx_t_25 = 0; __pyx_t_25 < __pyx_t_24; __pyx_t_25+=1) { + __pyx_v_j = __pyx_t_25; + + /* "sklearn/manifold/_utils.pyx":108 + * else: + * for j in range(K): + * P[i, j] /= sum_Pi # <<<<<<<<<<<<<< + * sum_disti_Pi += affinities[i, j] * P[i, j] * entropy = math.log(sum_Pi) + beta * sum_disti_Pi */ - __pyx_t_20 = __pyx_v_i; - __pyx_t_21 = __pyx_v_j; - if (__pyx_t_20 < 0) __pyx_t_20 += __pyx_pybuffernd_P.diminfo[0].shape; - if (__pyx_t_21 < 0) __pyx_t_21 += __pyx_pybuffernd_P.diminfo[1].shape; - *__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float_t *, __pyx_pybuffernd_P.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_P.diminfo[0].strides, __pyx_t_21, __pyx_pybuffernd_P.diminfo[1].strides) /= __pyx_v_sum_Pi; + __pyx_t_40 = __pyx_v_i; + __pyx_t_41 = __pyx_v_j; + if (__pyx_t_40 < 0) __pyx_t_40 += __pyx_pybuffernd_P.diminfo[0].shape; + if (__pyx_t_41 < 0) __pyx_t_41 += __pyx_pybuffernd_P.diminfo[1].shape; + *__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_P.rcbuffer->pybuffer.buf, __pyx_t_40, __pyx_pybuffernd_P.diminfo[0].strides, __pyx_t_41, __pyx_pybuffernd_P.diminfo[1].strides) /= __pyx_v_sum_Pi; - /* "sklearn/manifold/_utils.pyx":82 - * for j in range(n_samples): - * P[i, j] /= sum_Pi - * sum_disti_Pi += affinities[i, j] * P[i, j] # <<<<<<<<<<<<<< + /* "sklearn/manifold/_utils.pyx":109 + * for j in range(K): + * P[i, j] /= sum_Pi + * sum_disti_Pi += affinities[i, j] * P[i, j] # <<<<<<<<<<<<<< * entropy = math.log(sum_Pi) + beta * sum_disti_Pi * entropy_diff = entropy - desired_entropy */ - __pyx_t_22 = __pyx_v_i; - __pyx_t_23 = __pyx_v_j; - if (__pyx_t_22 < 0) __pyx_t_22 += __pyx_pybuffernd_affinities.diminfo[0].shape; - if (__pyx_t_23 < 0) __pyx_t_23 += __pyx_pybuffernd_affinities.diminfo[1].shape; - __pyx_t_24 = __pyx_v_i; - __pyx_t_25 = __pyx_v_j; - if (__pyx_t_24 < 0) __pyx_t_24 += __pyx_pybuffernd_P.diminfo[0].shape; - if (__pyx_t_25 < 0) __pyx_t_25 += __pyx_pybuffernd_P.diminfo[1].shape; - __pyx_v_sum_disti_Pi = (__pyx_v_sum_disti_Pi + ((*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float_t *, __pyx_pybuffernd_affinities.rcbuffer->pybuffer.buf, __pyx_t_22, __pyx_pybuffernd_affinities.diminfo[0].strides, __pyx_t_23, __pyx_pybuffernd_affinities.diminfo[1].strides)) * (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float_t *, __pyx_pybuffernd_P.rcbuffer->pybuffer.buf, __pyx_t_24, __pyx_pybuffernd_P.diminfo[0].strides, __pyx_t_25, __pyx_pybuffernd_P.diminfo[1].strides)))); + __pyx_t_42 = __pyx_v_i; + __pyx_t_43 = __pyx_v_j; + if (__pyx_t_42 < 0) __pyx_t_42 += __pyx_pybuffernd_affinities.diminfo[0].shape; + if (__pyx_t_43 < 0) __pyx_t_43 += __pyx_pybuffernd_affinities.diminfo[1].shape; + __pyx_t_44 = __pyx_v_i; + __pyx_t_45 = __pyx_v_j; + if (__pyx_t_44 < 0) __pyx_t_44 += __pyx_pybuffernd_P.diminfo[0].shape; + if (__pyx_t_45 < 0) __pyx_t_45 += __pyx_pybuffernd_P.diminfo[1].shape; + __pyx_v_sum_disti_Pi = (__pyx_v_sum_disti_Pi + ((*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float32_t *, __pyx_pybuffernd_affinities.rcbuffer->pybuffer.buf, __pyx_t_42, __pyx_pybuffernd_affinities.diminfo[0].strides, __pyx_t_43, __pyx_pybuffernd_affinities.diminfo[1].strides)) * (*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_float64_t *, __pyx_pybuffernd_P.rcbuffer->pybuffer.buf, __pyx_t_44, __pyx_pybuffernd_P.diminfo[0].strides, __pyx_t_45, __pyx_pybuffernd_P.diminfo[1].strides)))); + } } + __pyx_L19:; - /* "sklearn/manifold/_utils.pyx":83 - * P[i, j] /= sum_Pi - * sum_disti_Pi += affinities[i, j] * P[i, j] + /* "sklearn/manifold/_utils.pyx":110 + * P[i, j] /= sum_Pi + * sum_disti_Pi += affinities[i, j] * P[i, j] * entropy = math.log(sum_Pi) + beta * sum_disti_Pi # <<<<<<<<<<<<<< * entropy_diff = entropy - desired_entropy * */ __pyx_v_entropy = (log(__pyx_v_sum_Pi) + (__pyx_v_beta * __pyx_v_sum_disti_Pi)); - /* "sklearn/manifold/_utils.pyx":84 - * sum_disti_Pi += affinities[i, j] * P[i, j] + /* "sklearn/manifold/_utils.pyx":111 + * sum_disti_Pi += affinities[i, j] * P[i, j] * entropy = math.log(sum_Pi) + beta * sum_disti_Pi * entropy_diff = entropy - desired_entropy # <<<<<<<<<<<<<< * @@ -1655,37 +1825,37 @@ static PyArrayObject *__pyx_f_7sklearn_8manifold_6_utils__binary_search_perplexi */ __pyx_v_entropy_diff = (__pyx_v_entropy - __pyx_v_desired_entropy); - /* "sklearn/manifold/_utils.pyx":86 + /* "sklearn/manifold/_utils.pyx":113 * entropy_diff = entropy - desired_entropy * * if math.fabs(entropy_diff) <= PERPLEXITY_TOLERANCE: # <<<<<<<<<<<<<< * break * */ - __pyx_t_19 = ((fabs(__pyx_v_entropy_diff) <= __pyx_v_7sklearn_8manifold_6_utils_PERPLEXITY_TOLERANCE) != 0); - if (__pyx_t_19) { + __pyx_t_7 = ((fabs(__pyx_v_entropy_diff) <= __pyx_v_7sklearn_8manifold_6_utils_PERPLEXITY_TOLERANCE) != 0); + if (__pyx_t_7) { - /* "sklearn/manifold/_utils.pyx":87 + /* "sklearn/manifold/_utils.pyx":114 * * if math.fabs(entropy_diff) <= PERPLEXITY_TOLERANCE: * break # <<<<<<<<<<<<<< * * if entropy_diff > 0.0: */ - goto __pyx_L6_break; + goto __pyx_L7_break; } - /* "sklearn/manifold/_utils.pyx":89 + /* "sklearn/manifold/_utils.pyx":116 * break * * if entropy_diff > 0.0: # <<<<<<<<<<<<<< * beta_min = beta * if beta_max == NPY_INFINITY: */ - __pyx_t_19 = ((__pyx_v_entropy_diff > 0.0) != 0); - if (__pyx_t_19) { + __pyx_t_7 = ((__pyx_v_entropy_diff > 0.0) != 0); + if (__pyx_t_7) { - /* "sklearn/manifold/_utils.pyx":90 + /* "sklearn/manifold/_utils.pyx":117 * * if entropy_diff > 0.0: * beta_min = beta # <<<<<<<<<<<<<< @@ -1694,17 +1864,17 @@ static PyArrayObject *__pyx_f_7sklearn_8manifold_6_utils__binary_search_perplexi */ __pyx_v_beta_min = __pyx_v_beta; - /* "sklearn/manifold/_utils.pyx":91 + /* "sklearn/manifold/_utils.pyx":118 * if entropy_diff > 0.0: * beta_min = beta * if beta_max == NPY_INFINITY: # <<<<<<<<<<<<<< * beta *= 2.0 * else: */ - __pyx_t_19 = ((__pyx_v_beta_max == NPY_INFINITY) != 0); - if (__pyx_t_19) { + __pyx_t_7 = ((__pyx_v_beta_max == NPY_INFINITY) != 0); + if (__pyx_t_7) { - /* "sklearn/manifold/_utils.pyx":92 + /* "sklearn/manifold/_utils.pyx":119 * beta_min = beta * if beta_max == NPY_INFINITY: * beta *= 2.0 # <<<<<<<<<<<<<< @@ -1712,11 +1882,11 @@ static PyArrayObject *__pyx_f_7sklearn_8manifold_6_utils__binary_search_perplexi * beta = (beta + beta_max) / 2.0 */ __pyx_v_beta = (__pyx_v_beta * 2.0); - goto __pyx_L16; + goto __pyx_L26; } /*else*/ { - /* "sklearn/manifold/_utils.pyx":94 + /* "sklearn/manifold/_utils.pyx":121 * beta *= 2.0 * else: * beta = (beta + beta_max) / 2.0 # <<<<<<<<<<<<<< @@ -1725,12 +1895,12 @@ static PyArrayObject *__pyx_f_7sklearn_8manifold_6_utils__binary_search_perplexi */ __pyx_v_beta = ((__pyx_v_beta + __pyx_v_beta_max) / 2.0); } - __pyx_L16:; - goto __pyx_L15; + __pyx_L26:; + goto __pyx_L25; } /*else*/ { - /* "sklearn/manifold/_utils.pyx":96 + /* "sklearn/manifold/_utils.pyx":123 * beta = (beta + beta_max) / 2.0 * else: * beta_max = beta # <<<<<<<<<<<<<< @@ -1739,17 +1909,17 @@ static PyArrayObject *__pyx_f_7sklearn_8manifold_6_utils__binary_search_perplexi */ __pyx_v_beta_max = __pyx_v_beta; - /* "sklearn/manifold/_utils.pyx":97 + /* "sklearn/manifold/_utils.pyx":124 * else: * beta_max = beta * if beta_min == -NPY_INFINITY: # <<<<<<<<<<<<<< * beta /= 2.0 * else: */ - __pyx_t_19 = ((__pyx_v_beta_min == (-NPY_INFINITY)) != 0); - if (__pyx_t_19) { + __pyx_t_7 = ((__pyx_v_beta_min == (-NPY_INFINITY)) != 0); 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__Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - goto __pyx_L19; + if (__Pyx_PrintOne(0, __pyx_t_5) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 136; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; + goto __pyx_L32; } - __pyx_L19:; + __pyx_L32:; - /* "sklearn/manifold/_utils.pyx":111 + /* "sklearn/manifold/_utils.pyx":138 * print("[t-SNE] Mean sigma: %f" * % np.mean(math.sqrt(n_samples / beta_sum))) * return P # <<<<<<<<<<<<<< @@ -1899,9 +2089,9 @@ static PyArrayObject *__pyx_f_7sklearn_8manifold_6_utils__binary_search_perplexi /* "sklearn/manifold/_utils.pyx":14 * * @cython.boundscheck(False) - * cpdef np.ndarray[np.float_t, ndim=2] _binary_search_perplexity( # <<<<<<<<<<<<<< - * np.ndarray[np.float_t, ndim=2] affinities, double desired_perplexity, - * int verbose): + * cpdef np.ndarray[np.float32_t, ndim=2] _binary_search_perplexity( # <<<<<<<<<<<<<< + * np.ndarray[np.float32_t, ndim=2] affinities, + * np.ndarray[np.int64_t, ndim=2] neighbors, */ /* function exit code */ @@ -1910,10 +2100,12 @@ static PyArrayObject *__pyx_f_7sklearn_8manifold_6_utils__binary_search_perplexi __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); __Pyx_XDECREF(__pyx_t_4); + __Pyx_XDECREF(__pyx_t_5); { PyObject *__pyx_type, *__pyx_value, *__pyx_tb; __Pyx_ErrFetch(&__pyx_type, &__pyx_value, &__pyx_tb); __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_P.rcbuffer->pybuffer); __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_affinities.rcbuffer->pybuffer); + __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_neighbors.rcbuffer->pybuffer); __Pyx_ErrRestore(__pyx_type, __pyx_value, __pyx_tb);} __Pyx_AddTraceback("sklearn.manifold._utils._binary_search_perplexity", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = 0; @@ -1921,6 +2113,7 @@ static PyArrayObject *__pyx_f_7sklearn_8manifold_6_utils__binary_search_perplexi __pyx_L0:; __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_P.rcbuffer->pybuffer); __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_affinities.rcbuffer->pybuffer); + __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_neighbors.rcbuffer->pybuffer); __pyx_L2:; __Pyx_XDECREF((PyObject *)__pyx_v_P); __Pyx_XGIVEREF((PyObject *)__pyx_r); @@ -1930,10 +2123,11 @@ static PyArrayObject *__pyx_f_7sklearn_8manifold_6_utils__binary_search_perplexi /* Python wrapper */ static PyObject *__pyx_pw_7sklearn_8manifold_6_utils_1_binary_search_perplexity(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static char __pyx_doc_7sklearn_8manifold_6_utils__binary_search_perplexity[] = "Binary search for sigmas of conditional Gaussians.\n\n We are looking for sigma = sqrt(1/beta) so that the perplexity\n of the conditional distribution p_i|j matches approximately the\n desired value. p_i|j are Gaussian distributed.\n\n The idea has been proposed in \"Stochastic Neighbor Embedding\"\n Geoffrey Hinton and Sam Roweis, 2003.\n\n Parameters\n ----------\n affinities : array-like, shape (n_samples, n_samples)\n Distances between training samples.\n\n desired_perplexity : double\n Desired perplexity (2^entropy) of the conditional Gaussians.\n\n verbose : int\n Verbosity level.\n\n Returns\n -------\n P : array, shape (n_samples, n_samples)\n Probabilities of conditional Gaussian distributions p_i|j.\n "; +static char __pyx_doc_7sklearn_8manifold_6_utils__binary_search_perplexity[] = "Binary search for sigmas of conditional Gaussians. \n \n This approximation reduces the computational complexity from O(N^2) to\n O(uN). See the exact method '_binary_search_perplexity' for more details.\n\n Parameters\n ----------\n affinities : array-like, shape (n_samples, n_samples)\n Distances between training samples.\n\n neighbors : array-like, shape (n_samples, K) or None\n Each row contains the indices to the K nearest neigbors. 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- PyObject* values[3] = {0,0,0}; + static PyObject **__pyx_pyargnames[] = {&__pyx_n_s_affinities,&__pyx_n_s_neighbors,&__pyx_n_s_desired_perplexity,&__pyx_n_s_verbose,0}; + PyObject* values[4] = {0,0,0,0}; if (unlikely(__pyx_kwds)) { Py_ssize_t kw_args; const Py_ssize_t pos_args = PyTuple_GET_SIZE(__pyx_args); switch (pos_args) { + case 4: values[3] = PyTuple_GET_ITEM(__pyx_args, 3); case 3: values[2] = PyTuple_GET_ITEM(__pyx_args, 2); case 2: values[1] = PyTuple_GET_ITEM(__pyx_args, 1); case 1: values[0] = PyTuple_GET_ITEM(__pyx_args, 0); @@ -1960,40 +2155,48 @@ static PyObject *__pyx_pw_7sklearn_8manifold_6_utils_1_binary_search_perplexity( if (likely((values[0] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_affinities)) != 0)) kw_args--; else goto __pyx_L5_argtuple_error; case 1: - if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_desired_perplexity)) != 0)) kw_args--; + if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_neighbors)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("_binary_search_perplexity", 1, 3, 3, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_binary_search_perplexity", 1, 4, 4, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: - if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_verbose)) != 0)) kw_args--; + if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_desired_perplexity)) != 0)) kw_args--; + else { + __Pyx_RaiseArgtupleInvalid("_binary_search_perplexity", 1, 4, 4, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + } + case 3: + if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_verbose)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("_binary_search_perplexity", 1, 3, 3, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_binary_search_perplexity", 1, 4, 4, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_binary_search_perplexity") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } - } else if (PyTuple_GET_SIZE(__pyx_args) != 3) { + } else if (PyTuple_GET_SIZE(__pyx_args) != 4) { goto __pyx_L5_argtuple_error; } else { values[0] = PyTuple_GET_ITEM(__pyx_args, 0); values[1] = PyTuple_GET_ITEM(__pyx_args, 1); values[2] = PyTuple_GET_ITEM(__pyx_args, 2); + values[3] = PyTuple_GET_ITEM(__pyx_args, 3); } __pyx_v_affinities = ((PyArrayObject *)values[0]); - __pyx_v_desired_perplexity = __pyx_PyFloat_AsDouble(values[1]); if (unlikely((__pyx_v_desired_perplexity == (double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_verbose = __Pyx_PyInt_As_int(values[2]); if (unlikely((__pyx_v_verbose == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 16; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_neighbors = ((PyArrayObject *)values[1]); + __pyx_v_desired_perplexity = __pyx_PyFloat_AsFloat(values[2]); if (unlikely((__pyx_v_desired_perplexity == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 17; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_verbose = __Pyx_PyInt_As_int(values[3]); if (unlikely((__pyx_v_verbose == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 18; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("_binary_search_perplexity", 1, 3, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_binary_search_perplexity", 1, 4, 4, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("sklearn.manifold._utils._binary_search_perplexity", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_affinities), __pyx_ptype_5numpy_ndarray, 1, "affinities", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_r = __pyx_pf_7sklearn_8manifold_6_utils__binary_search_perplexity(__pyx_self, __pyx_v_affinities, __pyx_v_desired_perplexity, __pyx_v_verbose); + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_neighbors), __pyx_ptype_5numpy_ndarray, 1, "neighbors", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 16; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_r = __pyx_pf_7sklearn_8manifold_6_utils__binary_search_perplexity(__pyx_self, __pyx_v_affinities, __pyx_v_neighbors, __pyx_v_desired_perplexity, __pyx_v_verbose); /* function exit code */ goto __pyx_L0; @@ -2004,9 +2207,11 @@ static PyObject *__pyx_pw_7sklearn_8manifold_6_utils_1_binary_search_perplexity( return __pyx_r; } -static PyObject *__pyx_pf_7sklearn_8manifold_6_utils__binary_search_perplexity(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_affinities, double __pyx_v_desired_perplexity, int __pyx_v_verbose) { +static PyObject *__pyx_pf_7sklearn_8manifold_6_utils__binary_search_perplexity(CYTHON_UNUSED PyObject *__pyx_self, PyArrayObject *__pyx_v_affinities, PyArrayObject *__pyx_v_neighbors, float __pyx_v_desired_perplexity, int __pyx_v_verbose) { __Pyx_LocalBuf_ND __pyx_pybuffernd_affinities; __Pyx_Buffer __pyx_pybuffer_affinities; + __Pyx_LocalBuf_ND __pyx_pybuffernd_neighbors; + __Pyx_Buffer __pyx_pybuffer_neighbors; PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations PyObject *__pyx_t_1 = NULL; @@ -2018,13 +2223,22 @@ static PyObject *__pyx_pf_7sklearn_8manifold_6_utils__binary_search_perplexity(C __pyx_pybuffer_affinities.refcount = 0; __pyx_pybuffernd_affinities.data = NULL; __pyx_pybuffernd_affinities.rcbuffer = &__pyx_pybuffer_affinities; + __pyx_pybuffer_neighbors.pybuffer.buf = NULL; + __pyx_pybuffer_neighbors.refcount = 0; + __pyx_pybuffernd_neighbors.data = NULL; + __pyx_pybuffernd_neighbors.rcbuffer = &__pyx_pybuffer_neighbors; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_affinities.rcbuffer->pybuffer, (PyObject*)__pyx_v_affinities, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_affinities.rcbuffer->pybuffer, (PyObject*)__pyx_v_affinities, &__Pyx_TypeInfo_nn___pyx_t_5numpy_float32_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 14; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_affinities.diminfo[0].strides = __pyx_pybuffernd_affinities.rcbuffer->pybuffer.strides[0]; 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- if (__pyx_t_3) { + __pyx_t_2 = (((__pyx_v_flags & PyBUF_F_CONTIGUOUS) == PyBUF_F_CONTIGUOUS) != 0); + if (__pyx_t_2) { + } else { + __pyx_t_1 = __pyx_t_2; + goto __pyx_L9_bool_binop_done; + } - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":218 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":218 * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): # <<<<<<<<<<<<<< * raise ValueError(u"ndarray is not Fortran contiguous") * */ - __pyx_t_1 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_F_CONTIGUOUS) != 0)) != 0); - __pyx_t_2 = __pyx_t_1; - } else { - __pyx_t_2 = __pyx_t_3; - } - if (__pyx_t_2) { + __pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_F_CONTIGUOUS) != 0)) != 0); + __pyx_t_1 = __pyx_t_2; + __pyx_L9_bool_binop_done:; + if (__pyx_t_1) { - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":219 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":219 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< * * info.buf = PyArray_DATA(self) */ - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__2, NULL); 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- /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":222 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":222 * * info.buf = PyArray_DATA(self) * info.ndim = ndim # <<<<<<<<<<<<<< @@ -2267,17 +2485,17 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->ndim = __pyx_v_ndim; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":223 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":223 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if copy_shape: # <<<<<<<<<<<<<< * # Allocate new buffer for strides and shape info. * # This is allocated as one block, strides first. */ - __pyx_t_2 = (__pyx_v_copy_shape != 0); - if (__pyx_t_2) { + __pyx_t_1 = (__pyx_v_copy_shape != 0); + if (__pyx_t_1) { - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":226 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":226 * # Allocate new buffer for strides and shape info. * # This is allocated as one block, strides first. * info.strides = stdlib.malloc(sizeof(Py_ssize_t) * ndim * 2) # <<<<<<<<<<<<<< @@ -2286,7 +2504,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->strides = ((Py_ssize_t *)malloc((((sizeof(Py_ssize_t)) * ((size_t)__pyx_v_ndim)) * 2))); 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__pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { - __pyx_v_i = __pyx_t_6; + __pyx_t_4 = __pyx_v_ndim; + for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { + __pyx_v_i = __pyx_t_5; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":229 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":229 * info.shape = info.strides + ndim * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] # <<<<<<<<<<<<<< @@ -2315,7 +2533,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->strides[__pyx_v_i]) = (PyArray_STRIDES(__pyx_v_self)[__pyx_v_i]); - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":230 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":230 * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] * info.shape[i] = PyArray_DIMS(self)[i] # <<<<<<<<<<<<<< @@ -2324,11 +2542,11 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->shape[__pyx_v_i]) = (PyArray_DIMS(__pyx_v_self)[__pyx_v_i]); 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if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_Raise(__pyx_t_3, 0, 0, 0); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":274 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":274 * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" * elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<< @@ -2530,7 +2753,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ switch (__pyx_v_t) { - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":258 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":258 * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" # <<<<<<<<<<<<<< @@ -2541,7 +2764,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_b; break; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":259 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":259 * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" # <<<<<<<<<<<<<< @@ -2552,7 +2775,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_B; break; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":260 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":260 * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" # <<<<<<<<<<<<<< @@ -2563,7 +2786,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_h; break; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":261 * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" # <<<<<<<<<<<<<< @@ -2574,7 +2797,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_H; break; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":262 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":262 * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" # <<<<<<<<<<<<<< @@ -2585,7 +2808,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_i; break; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":263 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":263 * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" # <<<<<<<<<<<<<< @@ -2596,7 +2819,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_I; break; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":264 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":264 * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" # <<<<<<<<<<<<<< @@ -2607,7 +2830,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_l; break; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":265 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":265 * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" # <<<<<<<<<<<<<< @@ -2618,7 +2841,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_L; break; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":266 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":266 * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" # <<<<<<<<<<<<<< @@ -2629,7 +2852,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_q; break; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":267 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":267 * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" # <<<<<<<<<<<<<< @@ -2640,7 +2863,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_Q; break; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":268 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":268 * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" # <<<<<<<<<<<<<< @@ -2651,7 +2874,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_f; break; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":269 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":269 * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" # <<<<<<<<<<<<<< @@ -2662,7 +2885,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_d; break; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":270 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":270 * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" # <<<<<<<<<<<<<< @@ -2673,7 +2896,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_g; 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break; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":274 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":274 * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" * elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<< @@ -2718,33 +2941,33 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; default: - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":276 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":276 * elif t == NPY_OBJECT: f = "O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< * info.format = f * return */ - __pyx_t_4 = __Pyx_PyInt_From_int(__pyx_v_t); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_4); - __pyx_t_8 = PyUnicode_Format(__pyx_kp_u_unknown_dtype_code_in_numpy_pxd, __pyx_t_4); 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__pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __pyx_t_6 = PyUnicode_Format(__pyx_kp_u_unknown_dtype_code_in_numpy_pxd, __pyx_t_3); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_6); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_6); + __Pyx_GIVEREF(__pyx_t_6); + __pyx_t_6 = 0; + __pyx_t_6 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_6)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_6); + __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; + __Pyx_Raise(__pyx_t_6, 0, 0, 0); + __Pyx_DECREF(__pyx_t_6); __pyx_t_6 = 0; + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + break; + } - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":277 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":277 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f # <<<<<<<<<<<<<< @@ -2753,7 +2976,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->format = __pyx_v_f; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":278 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":278 * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f * return # <<<<<<<<<<<<<< @@ -2765,7 +2988,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } /*else*/ { - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":280 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":280 * return * else: * info.format = stdlib.malloc(_buffer_format_string_len) # <<<<<<<<<<<<<< @@ -2774,7 +2997,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->format = ((char *)malloc(255)); - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":281 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":281 * else: * info.format = stdlib.malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment # <<<<<<<<<<<<<< @@ -2783,7 +3006,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->format[0]) = '^'; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":282 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":282 * info.format = stdlib.malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 # <<<<<<<<<<<<<< @@ -2792,17 +3015,17 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_offset = 0; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":283 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":283 * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 * f = _util_dtypestring(descr, info.format + 1, # <<<<<<<<<<<<<< * info.format + _buffer_format_string_len, * &offset) */ - __pyx_t_9 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 255), (&__pyx_v_offset)); if (unlikely(__pyx_t_9 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_v_f = __pyx_t_9; + __pyx_t_7 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 255), (&__pyx_v_offset)); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_v_f = __pyx_t_7; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":286 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":286 * info.format + _buffer_format_string_len, * &offset) * f[0] = c'\0' # Terminate format string # <<<<<<<<<<<<<< @@ -2812,7 +3035,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_f[0]) = '\x00'; } - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":194 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":194 * # experimental exception made for __getbuffer__ and __releasebuffer__ * # -- the details of this may change. * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< @@ -2824,8 +3047,8 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_r = 0; goto __pyx_L0; __pyx_L1_error:; - __Pyx_XDECREF(__pyx_t_4); - __Pyx_XDECREF(__pyx_t_8); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_XDECREF(__pyx_t_6); __Pyx_AddTraceback("numpy.ndarray.__getbuffer__", __pyx_clineno, __pyx_lineno, __pyx_filename); __pyx_r = -1; if (__pyx_v_info != NULL && __pyx_v_info->obj != NULL) { @@ -2844,7 +3067,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P return __pyx_r; } -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":288 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":288 * f[0] = c'\0' # Terminate format string * * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< @@ -2868,7 +3091,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s int __pyx_t_1; __Pyx_RefNannySetupContext("__releasebuffer__", 0); - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":289 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":289 * * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< @@ -2878,7 +3101,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __pyx_t_1 = (PyArray_HASFIELDS(__pyx_v_self) != 0); if (__pyx_t_1) { - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":290 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":290 * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): * stdlib.free(info.format) # <<<<<<<<<<<<<< @@ -2890,7 +3113,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s } __pyx_L3:; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":291 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":291 * if PyArray_HASFIELDS(self): * stdlib.free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -2900,7 +3123,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":292 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":292 * stdlib.free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): * stdlib.free(info.strides) # <<<<<<<<<<<<<< @@ -2912,7 +3135,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s } __pyx_L4:; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":288 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":288 * f[0] = c'\0' # Terminate format string * * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< @@ -2924,7 +3147,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __Pyx_RefNannyFinishContext(); } -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":768 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":768 * ctypedef npy_cdouble complex_t * * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< @@ -2941,7 +3164,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew1", 0); - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":769 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":769 * * cdef inline object PyArray_MultiIterNew1(a): * return PyArray_MultiIterNew(1, a) # <<<<<<<<<<<<<< @@ -2955,7 +3178,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":768 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":768 * ctypedef npy_cdouble complex_t * * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< @@ -2974,7 +3197,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ return __pyx_r; } -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":771 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":771 * return PyArray_MultiIterNew(1, a) * * cdef inline object PyArray_MultiIterNew2(a, b): # <<<<<<<<<<<<<< @@ -2991,7 +3214,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew2", 0); - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":772 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":772 * * cdef inline object PyArray_MultiIterNew2(a, b): * return PyArray_MultiIterNew(2, a, b) # <<<<<<<<<<<<<< @@ -3005,7 +3228,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":771 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":771 * return PyArray_MultiIterNew(1, a) * * cdef inline object PyArray_MultiIterNew2(a, b): # <<<<<<<<<<<<<< @@ -3024,7 +3247,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew2(PyObject *__ return __pyx_r; } -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":774 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":774 * return PyArray_MultiIterNew(2, a, b) * * cdef inline object PyArray_MultiIterNew3(a, b, c): # <<<<<<<<<<<<<< @@ -3041,7 +3264,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew3", 0); - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":775 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":775 * * cdef inline object PyArray_MultiIterNew3(a, b, c): * return PyArray_MultiIterNew(3, a, b, c) # <<<<<<<<<<<<<< @@ -3055,7 +3278,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":774 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":774 * return PyArray_MultiIterNew(2, a, b) * * cdef inline object PyArray_MultiIterNew3(a, b, c): # <<<<<<<<<<<<<< @@ -3074,7 +3297,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew3(PyObject *__ return __pyx_r; } -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":777 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":777 * return PyArray_MultiIterNew(3, a, b, c) * * cdef inline object PyArray_MultiIterNew4(a, b, c, d): # <<<<<<<<<<<<<< @@ -3091,7 +3314,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew4", 0); - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":778 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":778 * * cdef inline object PyArray_MultiIterNew4(a, b, c, d): * return PyArray_MultiIterNew(4, a, b, c, d) # <<<<<<<<<<<<<< @@ -3105,7 +3328,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":777 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":777 * return PyArray_MultiIterNew(3, a, b, c) * * cdef inline object PyArray_MultiIterNew4(a, b, c, d): # <<<<<<<<<<<<<< @@ -3124,7 +3347,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew4(PyObject *__ return __pyx_r; } -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":780 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":780 * return PyArray_MultiIterNew(4, a, b, c, d) * * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): # <<<<<<<<<<<<<< @@ -3141,7 +3364,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew5", 0); - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":781 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":781 * * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): * return PyArray_MultiIterNew(5, a, b, c, d, e) # <<<<<<<<<<<<<< @@ -3155,7 +3378,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__ __pyx_t_1 = 0; goto __pyx_L0; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":780 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":780 * return PyArray_MultiIterNew(4, a, b, c, d) * * cdef inline object PyArray_MultiIterNew5(a, b, c, d, e): # <<<<<<<<<<<<<< @@ -3174,7 +3397,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew5(PyObject *__ return __pyx_r; } -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":783 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":783 * return PyArray_MultiIterNew(5, a, b, c, d, e) * * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< @@ -3199,16 +3422,14 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx int __pyx_t_5; int __pyx_t_6; int __pyx_t_7; - int __pyx_t_8; - int __pyx_t_9; - long __pyx_t_10; - char *__pyx_t_11; + long __pyx_t_8; + char *__pyx_t_9; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; __Pyx_RefNannySetupContext("_util_dtypestring", 0); - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":790 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":790 * cdef int delta_offset * cdef tuple i * cdef int endian_detector = 1 # <<<<<<<<<<<<<< @@ -3217,7 +3438,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_endian_detector = 1; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":791 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":791 * cdef tuple i * cdef int endian_detector = 1 * cdef bint little_endian = ((&endian_detector)[0] != 0) # <<<<<<<<<<<<<< @@ -3226,7 +3447,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0); - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":794 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":794 * cdef tuple fields * * for childname in descr.names: # <<<<<<<<<<<<<< @@ -3248,7 +3469,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_childname, __pyx_t_3); __pyx_t_3 = 0; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":795 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":795 * * for childname in descr.names: * fields = descr.fields[childname] # <<<<<<<<<<<<<< @@ -3261,7 +3482,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_fields, ((PyObject*)__pyx_t_3)); __pyx_t_3 = 0; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":796 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":796 * for childname in descr.names: * fields = descr.fields[childname] * child, new_offset = fields # <<<<<<<<<<<<<< @@ -3300,7 +3521,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_new_offset, __pyx_t_4); __pyx_t_4 = 0; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":798 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":798 * child, new_offset = fields * * if (end - f) - (new_offset - offset[0]) < 15: # <<<<<<<<<<<<<< @@ -3317,7 +3538,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = ((((__pyx_v_end - __pyx_v_f) - ((int)__pyx_t_5)) < 15) != 0); if (__pyx_t_6) { - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":799 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":799 * * if (end - f) - (new_offset - offset[0]) < 15: * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<< @@ -3331,42 +3552,45 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":801 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":801 * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") * * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") */ - __pyx_t_6 = ((__pyx_v_child->byteorder == '>') != 0); - if (__pyx_t_6) { - __pyx_t_7 = (__pyx_v_little_endian != 0); + __pyx_t_7 = ((__pyx_v_child->byteorder == '>') != 0); + if (!__pyx_t_7) { + goto __pyx_L8_next_or; } else { - __pyx_t_7 = __pyx_t_6; } + __pyx_t_7 = (__pyx_v_little_endian != 0); if (!__pyx_t_7) { + } else { + __pyx_t_6 = __pyx_t_7; + goto __pyx_L7_bool_binop_done; + } + __pyx_L8_next_or:; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":802 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":802 * * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< * raise ValueError(u"Non-native byte order not supported") * # One could encode it in the format string and have Cython */ - __pyx_t_6 = ((__pyx_v_child->byteorder == '<') != 0); - if (__pyx_t_6) { - __pyx_t_8 = ((!(__pyx_v_little_endian != 0)) != 0); - __pyx_t_9 = __pyx_t_8; - } else { - __pyx_t_9 = __pyx_t_6; - } - __pyx_t_6 = __pyx_t_9; + __pyx_t_7 = ((__pyx_v_child->byteorder == '<') != 0); + if (__pyx_t_7) { } else { __pyx_t_6 = __pyx_t_7; + goto __pyx_L7_bool_binop_done; } + __pyx_t_7 = ((!(__pyx_v_little_endian != 0)) != 0); + __pyx_t_6 = __pyx_t_7; + __pyx_L7_bool_binop_done:; if (__pyx_t_6) { - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":803 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":803 * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -3380,7 +3604,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":813 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":813 * * # Output padding bytes * while offset[0] < new_offset: # <<<<<<<<<<<<<< @@ -3396,7 +3620,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (!__pyx_t_6) break; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":814 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":814 * # Output padding bytes * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte # <<<<<<<<<<<<<< @@ -3405,7 +3629,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ (__pyx_v_f[0]) = 120; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":815 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":815 * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte * f += 1 # <<<<<<<<<<<<<< @@ -3414,28 +3638,28 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":816 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":816 * f[0] = 120 # "x"; pad byte * f += 1 * offset[0] += 1 # <<<<<<<<<<<<<< * * offset[0] += child.itemsize */ - __pyx_t_10 = 0; - (__pyx_v_offset[__pyx_t_10]) = ((__pyx_v_offset[__pyx_t_10]) + 1); + __pyx_t_8 = 0; + (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + 1); } - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":818 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":818 * offset[0] += 1 * * offset[0] += child.itemsize # <<<<<<<<<<<<<< * * if not PyDataType_HASFIELDS(child): */ - __pyx_t_10 = 0; - (__pyx_v_offset[__pyx_t_10]) = ((__pyx_v_offset[__pyx_t_10]) + __pyx_v_child->elsize); + __pyx_t_8 = 0; + (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + __pyx_v_child->elsize); - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":820 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":820 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -3445,7 +3669,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = ((!(PyDataType_HASFIELDS(__pyx_v_child) != 0)) != 0); if (__pyx_t_6) { - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":821 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":821 * * if not PyDataType_HASFIELDS(child): * t = child.type_num # <<<<<<<<<<<<<< @@ -3457,7 +3681,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_4); __pyx_t_4 = 0; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":822 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":822 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -3467,7 +3691,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = (((__pyx_v_end - __pyx_v_f) < 5) != 0); if (__pyx_t_6) { - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":823 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":823 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< @@ -3481,7 +3705,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":826 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":826 * * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" # <<<<<<<<<<<<<< @@ -3496,10 +3720,10 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (__pyx_t_6) { (__pyx_v_f[0]) = 98; - goto __pyx_L11; + goto __pyx_L15; } - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":827 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":827 * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" # <<<<<<<<<<<<<< @@ -3514,10 +3738,10 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (__pyx_t_6) { (__pyx_v_f[0]) = 66; - goto __pyx_L11; + goto __pyx_L15; } - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":828 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":828 * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" # <<<<<<<<<<<<<< @@ -3532,10 +3756,10 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (__pyx_t_6) { (__pyx_v_f[0]) = 104; - goto __pyx_L11; + goto __pyx_L15; } - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":829 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":829 * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" # <<<<<<<<<<<<<< @@ -3550,10 +3774,10 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (__pyx_t_6) { (__pyx_v_f[0]) = 72; - goto __pyx_L11; + goto __pyx_L15; } - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":830 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":830 * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" # <<<<<<<<<<<<<< @@ -3568,10 +3792,10 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (__pyx_t_6) { (__pyx_v_f[0]) = 105; - goto __pyx_L11; + goto __pyx_L15; } - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":831 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":831 * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" # <<<<<<<<<<<<<< @@ -3586,10 +3810,10 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (__pyx_t_6) { (__pyx_v_f[0]) = 73; - goto __pyx_L11; + goto __pyx_L15; } - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":832 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":832 * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" # <<<<<<<<<<<<<< @@ -3604,10 +3828,10 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (__pyx_t_6) { (__pyx_v_f[0]) = 108; - goto __pyx_L11; + goto __pyx_L15; } - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":833 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":833 * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" # <<<<<<<<<<<<<< @@ -3622,10 +3846,10 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (__pyx_t_6) { (__pyx_v_f[0]) = 76; - goto __pyx_L11; + goto __pyx_L15; } - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":834 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":834 * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" # <<<<<<<<<<<<<< @@ -3640,10 +3864,10 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (__pyx_t_6) { (__pyx_v_f[0]) = 113; - goto __pyx_L11; + goto __pyx_L15; } - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":835 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":835 * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" # <<<<<<<<<<<<<< @@ -3658,10 +3882,10 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (__pyx_t_6) { (__pyx_v_f[0]) = 81; - goto __pyx_L11; + goto __pyx_L15; } - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":836 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":836 * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" # <<<<<<<<<<<<<< @@ -3676,10 +3900,10 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (__pyx_t_6) { (__pyx_v_f[0]) = 102; - goto __pyx_L11; + goto __pyx_L15; } - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":837 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":837 * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" # <<<<<<<<<<<<<< @@ -3694,10 +3918,10 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (__pyx_t_6) { (__pyx_v_f[0]) = 100; - goto __pyx_L11; + goto __pyx_L15; } - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":838 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":838 * elif t == NPY_FLOAT: f[0] = 102 #"f" * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" # <<<<<<<<<<<<<< @@ -3712,10 +3936,10 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (__pyx_t_6) { (__pyx_v_f[0]) = 103; - goto __pyx_L11; + goto __pyx_L15; } - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":839 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":839 * elif t == NPY_DOUBLE: f[0] = 100 #"d" * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf # <<<<<<<<<<<<<< @@ -3732,10 +3956,10 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx (__pyx_v_f[0]) = 90; (__pyx_v_f[1]) = 102; __pyx_v_f = (__pyx_v_f + 1); - goto __pyx_L11; + goto __pyx_L15; } - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":840 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":840 * elif t == NPY_LONGDOUBLE: f[0] = 103 #"g" * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd # <<<<<<<<<<<<<< @@ -3752,10 +3976,10 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx (__pyx_v_f[0]) = 90; (__pyx_v_f[1]) = 100; __pyx_v_f = (__pyx_v_f + 1); - goto __pyx_L11; + goto __pyx_L15; } - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":841 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":841 * elif t == NPY_CFLOAT: f[0] = 90; f[1] = 102; f += 1 # Zf * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg # <<<<<<<<<<<<<< @@ -3772,10 +3996,10 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx (__pyx_v_f[0]) = 90; (__pyx_v_f[1]) = 103; __pyx_v_f = (__pyx_v_f + 1); - goto __pyx_L11; + goto __pyx_L15; } - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":842 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":842 * elif t == NPY_CDOUBLE: f[0] = 90; f[1] = 100; f += 1 # Zd * elif t == NPY_CLONGDOUBLE: f[0] = 90; f[1] = 103; f += 1 # Zg * elif t == NPY_OBJECT: f[0] = 79 #"O" # <<<<<<<<<<<<<< @@ -3790,11 +4014,11 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (__pyx_t_6) { (__pyx_v_f[0]) = 79; - goto __pyx_L11; + goto __pyx_L15; } /*else*/ { - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":844 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":844 * elif t == NPY_OBJECT: f[0] = 79 #"O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< @@ -3815,9 +4039,9 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_3); 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goto __pyx_L0; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":783 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":783 * return PyArray_MultiIterNew(5, a, b, c, d, e) * * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< @@ -3878,7 +4110,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx return __pyx_r; } -/* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":966 +/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":966 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -3893,7 +4125,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a int __pyx_t_2; __Pyx_RefNannySetupContext("set_array_base", 0); - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":968 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":968 * cdef inline void set_array_base(ndarray arr, object base): * cdef PyObject* baseptr * if base is None: # <<<<<<<<<<<<<< @@ -3904,7 +4136,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":969 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":969 * cdef PyObject* baseptr * if base is None: * baseptr = NULL # <<<<<<<<<<<<<< @@ -3916,7 +4148,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a } /*else*/ { - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":971 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":971 * baseptr = NULL * else: * Py_INCREF(base) # important to do this before decref below! # <<<<<<<<<<<<<< @@ -3925,7 +4157,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ Py_INCREF(__pyx_v_base); - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":972 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":972 * else: * Py_INCREF(base) # important to do this before decref below! * baseptr = base # <<<<<<<<<<<<<< @@ -3936,7 +4168,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a } __pyx_L3:; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":973 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":973 * Py_INCREF(base) # important to do this before decref below! * baseptr = base * Py_XDECREF(arr.base) # <<<<<<<<<<<<<< @@ -3945,7 +4177,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ Py_XDECREF(__pyx_v_arr->base); - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":974 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":974 * baseptr = base * Py_XDECREF(arr.base) * arr.base = baseptr # <<<<<<<<<<<<<< @@ -3954,7 +4186,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a */ __pyx_v_arr->base = __pyx_v_baseptr; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":966 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":966 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -3966,7 +4198,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a __Pyx_RefNannyFinishContext(); 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static int __Pyx_InitCachedBuiltins(void) { - __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 63; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_builtin_RuntimeError = __Pyx_GetBuiltinName(__pyx_n_s_RuntimeError); if (!__pyx_builtin_RuntimeError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} return 0; @@ -4096,7 +4328,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0); - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":215 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":215 * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): * raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<< @@ -4107,7 +4339,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple_); __Pyx_GIVEREF(__pyx_tuple_); - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":219 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":219 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< @@ -4118,7 +4350,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__2); __Pyx_GIVEREF(__pyx_tuple__2); - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":257 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":257 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -4129,7 +4361,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__3); __Pyx_GIVEREF(__pyx_tuple__3); - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":799 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":799 * * if (end - f) - (new_offset - offset[0]) < 15: * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<< @@ -4140,7 +4372,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__4); __Pyx_GIVEREF(__pyx_tuple__4); - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":803 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":803 * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -4151,7 +4383,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__5); __Pyx_GIVEREF(__pyx_tuple__5); - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":823 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":823 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< @@ -4219,25 +4451,25 @@ PyMODINIT_FUNC PyInit__utils(void) #endif /*--- Module creation code ---*/ #if PY_MAJOR_VERSION < 3 - __pyx_m = Py_InitModule4(__Pyx_NAMESTR("_utils"), __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m); + __pyx_m = Py_InitModule4("_utils", __pyx_methods, 0, 0, PYTHON_API_VERSION); Py_XINCREF(__pyx_m); #else __pyx_m = PyModule_Create(&__pyx_moduledef); #endif if (unlikely(!__pyx_m)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_d = PyModule_GetDict(__pyx_m); if (unlikely(!__pyx_d)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} Py_INCREF(__pyx_d); - __pyx_b = PyImport_AddModule(__Pyx_NAMESTR(__Pyx_BUILTIN_MODULE_NAME)); if (unlikely(!__pyx_b)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_b = PyImport_AddModule(__Pyx_BUILTIN_MODULE_NAME); if (unlikely(!__pyx_b)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #if CYTHON_COMPILING_IN_PYPY Py_INCREF(__pyx_b); #endif - if (__Pyx_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + if (PyObject_SetAttrString(__pyx_m, "__builtins__", __pyx_b) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; /*--- Initialize various global constants etc. ---*/ if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #if PY_MAJOR_VERSION < 3 && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT) if (__Pyx_init_sys_getdefaultencoding_params() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif if (__pyx_module_is_main_sklearn__manifold___utils) { - if (__Pyx_SetAttrString(__pyx_m, "__name__", __pyx_n_s_main) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + if (PyObject_SetAttrString(__pyx_m, "__name__", __pyx_n_s_main) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; } #if PY_MAJOR_VERSION >= 3 { @@ -4277,28 +4509,28 @@ PyMODINIT_FUNC PyInit__utils(void) * cimport cython * import numpy as np # <<<<<<<<<<<<<< * cimport numpy as np - * cdef extern from "numpy/npy_math.h": + * from libc.stdio cimport printf */ __pyx_t_1 = __Pyx_Import(__pyx_n_s_numpy, 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyDict_SetItem(__pyx_d, __pyx_n_s_np, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 3; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "sklearn/manifold/_utils.pyx":9 + /* "sklearn/manifold/_utils.pyx":10 * * - * cdef double EPSILON_DBL = 1e-7 # <<<<<<<<<<<<<< - * cdef double PERPLEXITY_TOLERANCE = 1e-5 + * cdef float EPSILON_DBL = 1e-8 # <<<<<<<<<<<<<< + * cdef float PERPLEXITY_TOLERANCE = 1e-5 * */ - __pyx_v_7sklearn_8manifold_6_utils_EPSILON_DBL = 1e-7; + __pyx_v_7sklearn_8manifold_6_utils_EPSILON_DBL = 1e-8; - /* "sklearn/manifold/_utils.pyx":10 - * - * cdef double EPSILON_DBL = 1e-7 - * cdef double PERPLEXITY_TOLERANCE = 1e-5 # <<<<<<<<<<<<<< + /* "sklearn/manifold/_utils.pyx":11 * + * cdef float EPSILON_DBL = 1e-8 + * cdef float PERPLEXITY_TOLERANCE = 1e-5 # <<<<<<<<<<<<<< * + * @cython.boundscheck(False) */ __pyx_v_7sklearn_8manifold_6_utils_PERPLEXITY_TOLERANCE = 1e-5; @@ -4312,18 +4544,23 @@ PyMODINIT_FUNC PyInit__utils(void) if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "/volatile/ogrisel/envs/py34/lib/python3.4/site-packages/Cython/Includes/numpy/__init__.pxd":976 + /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":976 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< * if arr.base is NULL: * return None */ + + /*--- Wrapped vars code ---*/ + goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); if (__pyx_m) { - __Pyx_AddTraceback("init sklearn.manifold._utils", __pyx_clineno, __pyx_lineno, __pyx_filename); + if (__pyx_d) { + __Pyx_AddTraceback("init sklearn.manifold._utils", __pyx_clineno, __pyx_lineno, __pyx_filename); + } Py_DECREF(__pyx_m); __pyx_m = 0; } else if (!PyErr_Occurred()) { PyErr_SetString(PyExc_ImportError, "init sklearn.manifold._utils"); @@ -4352,7 +4589,7 @@ static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) { Py_XDECREF(m); return (__Pyx_RefNannyAPIStruct *)r; } -#endif /* CYTHON_REFNANNY */ +#endif static PyObject *__Pyx_GetBuiltinName(PyObject *name) { PyObject* result = __Pyx_PyObject_GetAttrStr(__pyx_b, name); @@ -4415,7 +4652,7 @@ static int __Pyx_BufFmt_ParseNumber(const char** ts) { } static int __Pyx_BufFmt_ExpectNumber(const char **ts) { int number = __Pyx_BufFmt_ParseNumber(ts); - if (number == -1) /* First char was not a digit */ + if (number == -1) PyErr_Format(PyExc_ValueError,\ "Does not understand character buffer dtype format string ('%c')", **ts); return number; @@ -4660,7 +4897,7 @@ static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { ctx->fmt_offset += size; if (arraysize) ctx->fmt_offset += (arraysize - 1) * size; - --ctx->enc_count; /* Consume from buffer string */ + --ctx->enc_count; while (1) { if (field == &ctx->root) { ctx->head = NULL; @@ -4668,7 +4905,7 @@ static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { __Pyx_BufFmt_RaiseExpected(ctx); return -1; } - break; /* breaks both loops as ctx->enc_count == 0 */ + break; } ctx->head->field = ++field; if (field->type == NULL) { @@ -4677,7 +4914,7 @@ static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) { continue; } else if (field->type->typegroup == 'S') { size_t parent_offset = ctx->head->parent_offset + field->offset; - if (field->type->fields->type == NULL) continue; /* empty struct */ + if (field->type->fields->type == NULL) continue; field = field->type->fields; ++ctx->head; ctx->head->field = field; @@ -4709,7 +4946,7 @@ __pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp) while (*ts && *ts != ')') { switch (*ts) { case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue; - default: break; /* not a 'break' in the loop */ + default: break; } number = __Pyx_BufFmt_ExpectNumber(&ts); if (number == -1) return NULL; @@ -4750,10 +4987,10 @@ static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const cha __Pyx_BufFmt_RaiseExpected(ctx); return NULL; } - return ts; + return ts; case ' ': - case 10: - case 13: + case '\r': + case '\n': ++ts; break; case '<': @@ -4778,7 +5015,7 @@ static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const cha case '^': ctx->new_packmode = *ts++; break; - case 'T': /* substruct */ + case 'T': { const char* ts_after_sub; size_t i, struct_count = ctx->new_count; @@ -4790,7 +5027,7 @@ static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const cha return NULL; } if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_type = 0; /* Erase processed last struct element */ + ctx->enc_type = 0; ctx->enc_count = 0; ctx->struct_alignment = 0; ++ts; @@ -4803,12 +5040,12 @@ static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const cha if (struct_alignment) ctx->struct_alignment = struct_alignment; } break; - case '}': /* end of substruct; either repeat or move on */ + case '}': { size_t alignment = ctx->struct_alignment; ++ts; if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_type = 0; /* Erase processed last struct element */ + ctx->enc_type = 0; if (alignment && ctx->fmt_offset % alignment) { ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment); } @@ -4829,21 +5066,25 @@ static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const cha if (*ts != 'f' && *ts != 'd' && *ts != 'g') { __Pyx_BufFmt_RaiseUnexpectedChar('Z'); return NULL; - } /* fall through */ + } case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I': case 'l': case 'L': case 'q': case 'Q': case 'f': case 'd': case 'g': - case 'O': case 's': case 'p': + case 'O': case 'p': if (ctx->enc_type == *ts && got_Z == ctx->is_complex && ctx->enc_packmode == ctx->new_packmode) { ctx->enc_count += ctx->new_count; - } else { - if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; - ctx->enc_count = ctx->new_count; - ctx->enc_packmode = ctx->new_packmode; - ctx->enc_type = *ts; - ctx->is_complex = got_Z; + ctx->new_count = 1; + got_Z = 0; + ++ts; + break; } + case 's': + if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL; + ctx->enc_count = ctx->new_count; + ctx->enc_packmode = ctx->new_packmode; + ctx->enc_type = *ts; + ctx->is_complex = got_Z; ++ts; ctx->new_count = 1; got_Z = 0; @@ -4916,7 +5157,7 @@ static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) { PyObject *result; #if CYTHON_COMPILING_IN_CPYTHON result = PyDict_GetItem(__pyx_d, name); - if (result) { + if (likely(result)) { Py_INCREF(result); } else { #else @@ -4935,14 +5176,10 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg ternaryfunc call = func->ob_type->tp_call; if (unlikely(!call)) return PyObject_Call(func, arg, kw); -#if PY_VERSION_HEX >= 0x02060000 if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) return NULL; -#endif result = (*call)(func, arg, kw); -#if PY_VERSION_HEX >= 0x02060000 Py_LeaveRecursiveCall(); -#endif if (unlikely(!result) && unlikely(!PyErr_Occurred())) { PyErr_SetString( PyExc_SystemError, @@ -4952,12 +5189,73 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg } #endif +static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { + if (unlikely(!type)) { + PyErr_SetString(PyExc_SystemError, "Missing type object"); + return 0; + } + if (likely(PyObject_TypeCheck(obj, type))) + return 1; + PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", + Py_TYPE(obj)->tp_name, type->tp_name); + return 0; +} + static CYTHON_INLINE long __Pyx_mod_long(long a, long b) { long r = a % b; r += ((r != 0) & ((r ^ b) < 0)) * b; return r; } +#if CYTHON_COMPILING_IN_CPYTHON +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) { + PyObject *self, *result; + PyCFunction cfunc; + cfunc = PyCFunction_GET_FUNCTION(func); + self = PyCFunction_GET_SELF(func); + if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object"))) + return NULL; + result = cfunc(self, arg); + Py_LeaveRecursiveCall(); + if (unlikely(!result) && unlikely(!PyErr_Occurred())) { + PyErr_SetString( + PyExc_SystemError, + "NULL result without error in PyObject_Call"); + } + return result; +} +#endif + +#if CYTHON_COMPILING_IN_CPYTHON +static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) { + PyObject *result; + PyObject *args = PyTuple_New(1); + if (unlikely(!args)) return NULL; + Py_INCREF(arg); + PyTuple_SET_ITEM(args, 0, arg); + result = __Pyx_PyObject_Call(func, args, NULL); + Py_DECREF(args); + return result; +} +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { +#ifdef __Pyx_CyFunction_USED + if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) { +#else + if (likely(PyCFunction_Check(func))) { +#endif + if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { + return __Pyx_PyObject_CallMethO(func, arg); + } + } + return __Pyx__PyObject_CallOneArg(func, arg); +} +#else +static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { + PyObject* args = PyTuple_Pack(1, arg); + return (likely(args)) ? __Pyx_PyObject_Call(func, args, NULL) : NULL; +} +#endif + static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { #if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; @@ -5172,11 +5470,7 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, goto raise_error; } } - #if PY_VERSION_HEX < 0x02050000 - if (PyClass_Check(type)) { - #else if (PyType_Check(type)) { - #endif #if CYTHON_COMPILING_IN_PYPY if (!value) { Py_INCREF(Py_None); @@ -5191,17 +5485,6 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, goto raise_error; } value = type; - #if PY_VERSION_HEX < 0x02050000 - if (PyInstance_Check(type)) { - type = (PyObject*) ((PyInstanceObject*)type)->in_class; - Py_INCREF(type); - } else { - type = 0; - PyErr_SetString(PyExc_TypeError, - "raise: exception must be an old-style class or instance"); - goto raise_error; - } - #else type = (PyObject*) Py_TYPE(type); Py_INCREF(type); if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) { @@ -5209,7 +5492,6 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, "raise: exception class must be a subclass of BaseException"); goto raise_error; } - #endif } __Pyx_ErrRestore(type, value, tb); return; @@ -5219,7 +5501,7 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, Py_XDECREF(tb); return; } -#else /* Python 3+ */ +#else static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) { PyObject* owned_instance = NULL; if (tb == Py_None) { @@ -5305,6 +5587,13 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject } PyErr_SetObject(type, value); if (tb) { +#if CYTHON_COMPILING_IN_PYPY + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyErr_Fetch(tmp_type, tmp_value, tmp_tb); + Py_INCREF(tb); + PyErr_Restore(tmp_type, tmp_value, tb); + Py_XDECREF(tmp_tb); +#else PyThreadState *tstate = PyThreadState_GET(); PyObject* tmp_tb = tstate->curexc_traceback; if (tb != tmp_tb) { @@ -5312,6 +5601,7 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject tstate->curexc_traceback = tb; Py_XDECREF(tmp_tb); } +#endif } bad: Py_XDECREF(owned_instance); @@ -5334,110 +5624,212 @@ static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); } -static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { - if (unlikely(!type)) { - PyErr_SetString(PyExc_SystemError, "Missing type object"); - return 0; +static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { + int start = 0, mid = 0, end = count - 1; + if (end >= 0 && code_line > entries[end].code_line) { + return count; } - if (likely(PyObject_TypeCheck(obj, type))) - return 1; - PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s", - Py_TYPE(obj)->tp_name, type->tp_name); - return 0; -} - -#if PY_MAJOR_VERSION < 3 -static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { - #if PY_VERSION_HEX >= 0x02060000 - if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); - #endif - if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags); - #if PY_VERSION_HEX < 0x02060000 - if (obj->ob_type->tp_dict) { - PyObject *getbuffer_cobj = PyObject_GetItem( - obj->ob_type->tp_dict, __pyx_n_s_pyx_getbuffer); - if (getbuffer_cobj) { - getbufferproc func = (getbufferproc) PyCObject_AsVoidPtr(getbuffer_cobj); - Py_DECREF(getbuffer_cobj); - if (!func) - goto fail; - return func(obj, view, flags); + while (start < end) { + mid = (start + end) / 2; + if (code_line < entries[mid].code_line) { + end = mid; + } else if (code_line > entries[mid].code_line) { + start = mid + 1; } else { - PyErr_Clear(); + return mid; } } - #endif - PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); -#if PY_VERSION_HEX < 0x02060000 -fail: -#endif - return -1; + if (code_line <= entries[mid].code_line) { + return mid; + } else { + return mid + 1; + } } -static void __Pyx_ReleaseBuffer(Py_buffer *view) { - PyObject *obj = view->obj; - if (!obj) return; - #if PY_VERSION_HEX >= 0x02060000 - if (PyObject_CheckBuffer(obj)) { - PyBuffer_Release(view); +static PyCodeObject *__pyx_find_code_object(int code_line) { + PyCodeObject* code_object; + int pos; + if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { + return NULL; + } + pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); + if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { + return NULL; + } + code_object = __pyx_code_cache.entries[pos].code_object; + Py_INCREF(code_object); + return code_object; +} +static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { + int pos, i; + __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; + if (unlikely(!code_line)) { return; } - #endif - if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; } - #if PY_VERSION_HEX < 0x02060000 - if (obj->ob_type->tp_dict) { - PyObject *releasebuffer_cobj = PyObject_GetItem( - obj->ob_type->tp_dict, __pyx_n_s_pyx_releasebuffer); - if (releasebuffer_cobj) { - releasebufferproc func = (releasebufferproc) PyCObject_AsVoidPtr(releasebuffer_cobj); - Py_DECREF(releasebuffer_cobj); - if (!func) - goto fail; - func(obj, view); + if (unlikely(!entries)) { + entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); + if (likely(entries)) { + __pyx_code_cache.entries = entries; + __pyx_code_cache.max_count = 64; + __pyx_code_cache.count = 1; + entries[0].code_line = code_line; + entries[0].code_object = code_object; + Py_INCREF(code_object); + } + return; + } + pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); + if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { + PyCodeObject* tmp = entries[pos].code_object; + entries[pos].code_object = code_object; + Py_DECREF(tmp); + return; + } + if (__pyx_code_cache.count == __pyx_code_cache.max_count) { + int new_max = __pyx_code_cache.max_count + 64; + entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( + __pyx_code_cache.entries, (size_t)new_max*sizeof(__Pyx_CodeObjectCacheEntry)); + if (unlikely(!entries)) { return; - } else { - PyErr_Clear(); } + __pyx_code_cache.entries = entries; + __pyx_code_cache.max_count = new_max; } - #endif - goto nofail; -#if PY_VERSION_HEX < 0x02060000 -fail: -#endif - PyErr_WriteUnraisable(obj); -nofail: - Py_DECREF(obj); - view->obj = NULL; + for (i=__pyx_code_cache.count; i>pos; i--) { + entries[i] = entries[i-1]; + } + entries[pos].code_line = code_line; + entries[pos].code_object = code_object; + __pyx_code_cache.count++; + Py_INCREF(code_object); } -#endif /* PY_MAJOR_VERSION < 3 */ - - static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { - PyObject *empty_list = 0; - PyObject *module = 0; - PyObject *global_dict = 0; - PyObject *empty_dict = 0; - PyObject *list; - #if PY_VERSION_HEX < 0x03030000 - PyObject *py_import; - py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); - if (!py_import) - goto bad; +#include "compile.h" +#include "frameobject.h" +#include "traceback.h" +static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( + const char *funcname, int c_line, + int py_line, const char *filename) { + PyCodeObject *py_code = 0; + PyObject *py_srcfile = 0; + PyObject *py_funcname = 0; + #if PY_MAJOR_VERSION < 3 + py_srcfile = PyString_FromString(filename); + #else + py_srcfile = PyUnicode_FromString(filename); #endif - if (from_list) - list = from_list; - else { - empty_list = PyList_New(0); - if (!empty_list) - goto bad; - list = empty_list; + if (!py_srcfile) goto bad; + if (c_line) { + #if PY_MAJOR_VERSION < 3 + py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); + #else + py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); + #endif } - global_dict = PyModule_GetDict(__pyx_m); - if (!global_dict) - goto bad; - empty_dict = PyDict_New(); + else { + #if PY_MAJOR_VERSION < 3 + py_funcname = PyString_FromString(funcname); + #else + py_funcname = PyUnicode_FromString(funcname); + #endif + } + if (!py_funcname) goto bad; + py_code = __Pyx_PyCode_New( + 0, + 0, + 0, + 0, + 0, + __pyx_empty_bytes, /*PyObject *code,*/ + __pyx_empty_tuple, /*PyObject *consts,*/ + __pyx_empty_tuple, /*PyObject *names,*/ + __pyx_empty_tuple, /*PyObject *varnames,*/ + __pyx_empty_tuple, /*PyObject *freevars,*/ + __pyx_empty_tuple, /*PyObject *cellvars,*/ + py_srcfile, /*PyObject *filename,*/ + py_funcname, /*PyObject *name,*/ + py_line, + __pyx_empty_bytes /*PyObject *lnotab*/ + ); + Py_DECREF(py_srcfile); + Py_DECREF(py_funcname); + return py_code; +bad: + Py_XDECREF(py_srcfile); + Py_XDECREF(py_funcname); + return NULL; +} +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename) { + PyCodeObject *py_code = 0; + PyFrameObject *py_frame = 0; + py_code = __pyx_find_code_object(c_line ? c_line : py_line); + if (!py_code) { + py_code = __Pyx_CreateCodeObjectForTraceback( + funcname, c_line, py_line, filename); + if (!py_code) goto bad; + __pyx_insert_code_object(c_line ? c_line : py_line, py_code); + } + py_frame = PyFrame_New( + PyThreadState_GET(), /*PyThreadState *tstate,*/ + py_code, /*PyCodeObject *code,*/ + __pyx_d, /*PyObject *globals,*/ + 0 /*PyObject *locals*/ + ); + if (!py_frame) goto bad; + py_frame->f_lineno = py_line; + PyTraceBack_Here(py_frame); +bad: + Py_XDECREF(py_code); + Py_XDECREF(py_frame); +} + +#if PY_MAJOR_VERSION < 3 +static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { + if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); + if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags); + PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); + return -1; +} +static void __Pyx_ReleaseBuffer(Py_buffer *view) { + PyObject *obj = view->obj; + if (!obj) return; + if (PyObject_CheckBuffer(obj)) { + PyBuffer_Release(view); + return; + } + if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; } + Py_DECREF(obj); + view->obj = NULL; +} +#endif + + + static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { + PyObject *empty_list = 0; + PyObject *module = 0; + PyObject *global_dict = 0; + PyObject *empty_dict = 0; + PyObject *list; + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_import; + py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); + if (!py_import) + goto bad; + #endif + if (from_list) + list = from_list; + else { + empty_list = PyList_New(0); + if (!empty_list) + goto bad; + list = empty_list; + } + global_dict = PyModule_GetDict(__pyx_m); + if (!global_dict) + goto bad; + empty_dict = PyDict_New(); if (!empty_dict) goto bad; - #if PY_VERSION_HEX >= 0x02050000 { #if PY_MAJOR_VERSION >= 3 if (level == -1) { @@ -5459,7 +5851,7 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { PyErr_Clear(); } } - level = 0; /* try absolute import on failure */ + level = 0; } #endif if (!module) { @@ -5476,14 +5868,6 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { #endif } } - #else - if (level>0) { - PyErr_SetString(PyExc_RuntimeError, "Relative import is not supported for Python <=2.4."); - goto bad; - } - module = PyObject_CallFunctionObjArgs(py_import, - name, global_dict, empty_dict, list, NULL); - #endif bad: #if PY_VERSION_HEX < 0x03030000 Py_XDECREF(py_import); @@ -5493,17 +5877,16 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { return module; } -#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func) \ +#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value) \ { \ - func_type value = func(x); \ + func_type value = func_value; \ if (sizeof(target_type) < sizeof(func_type)) { \ if (unlikely(value != (func_type) (target_type) value)) { \ func_type zero = 0; \ - PyErr_SetString(PyExc_OverflowError, \ - (is_unsigned && unlikely(value < zero)) ? \ - "can't convert negative value to " #target_type : \ - "value too large to convert to " #target_type); \ - return (target_type) -1; \ + if (is_unsigned && unlikely(value < zero)) \ + goto raise_neg_overflow; \ + else \ + goto raise_overflow; \ } \ } \ return (target_type) value; \ @@ -5514,19 +5897,18 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { #include "longintrepr.h" #endif #endif + static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { const int neg_one = (int) -1, const_zero = 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { if (sizeof(int) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG) + __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) } else { long val = PyInt_AS_LONG(x); if (is_unsigned && unlikely(val < 0)) { - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to int"); - return (int) -1; + goto raise_neg_overflow; } return (int) val; } @@ -5536,40 +5918,34 @@ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { if (is_unsigned) { #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS - if (sizeof(digit) <= sizeof(int)) { - switch (Py_SIZE(x)) { - case 0: return 0; - case 1: return (int) ((PyLongObject*)x)->ob_digit[0]; - } + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(int, digit, ((PyLongObject*)x)->ob_digit[0]); } #endif #endif if (unlikely(Py_SIZE(x) < 0)) { - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to int"); - return (int) -1; + goto raise_neg_overflow; } if (sizeof(int) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, PyLong_AsUnsignedLong) + __PYX_VERIFY_RETURN_INT(int, unsigned long, PyLong_AsUnsignedLong(x)) } else if (sizeof(int) <= sizeof(unsigned long long)) { - __PYX_VERIFY_RETURN_INT(int, unsigned long long, PyLong_AsUnsignedLongLong) + __PYX_VERIFY_RETURN_INT(int, unsigned long long, PyLong_AsUnsignedLongLong(x)) } } else { #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 #if CYTHON_USE_PYLONG_INTERNALS - if (sizeof(digit) <= sizeof(int)) { - switch (Py_SIZE(x)) { - case 0: return 0; - case 1: return +(int) ((PyLongObject*)x)->ob_digit[0]; - case -1: return -(int) ((PyLongObject*)x)->ob_digit[0]; - } + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(int, digit, +(((PyLongObject*)x)->ob_digit[0])); + case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]); } #endif #endif if (sizeof(int) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int, long, PyLong_AsLong) + __PYX_VERIFY_RETURN_INT(int, long, PyLong_AsLong(x)) } else if (sizeof(int) <= sizeof(long long)) { - __PYX_VERIFY_RETURN_INT(int, long long, PyLong_AsLongLong) + __PYX_VERIFY_RETURN_INT(int, long long, PyLong_AsLongLong(x)) } } { @@ -5607,56 +5983,159 @@ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { Py_DECREF(tmp); return val; } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to int"); + return (int) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to int"); + return (int) -1; } -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { - const int neg_one = (int) -1, const_zero = 0; +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { + const long neg_one = (long) -1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (is_unsigned) { - if (sizeof(int) < sizeof(long)) { + if (sizeof(long) < sizeof(long)) { return PyInt_FromLong((long) value); - } else if (sizeof(int) <= sizeof(unsigned long)) { + } else if (sizeof(long) <= sizeof(unsigned long)) { return PyLong_FromUnsignedLong((unsigned long) value); - } else if (sizeof(int) <= sizeof(unsigned long long)) { + } else if (sizeof(long) <= sizeof(unsigned long long)) { return PyLong_FromUnsignedLongLong((unsigned long long) value); } } else { - if (sizeof(int) <= sizeof(long)) { + if (sizeof(long) <= sizeof(long)) { return PyInt_FromLong((long) value); - } else if (sizeof(int) <= sizeof(long long)) { + } else if (sizeof(long) <= sizeof(long long)) { return PyLong_FromLongLong((long long) value); } } { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(int), + return _PyLong_FromByteArray(bytes, sizeof(long), little, !is_unsigned); } } -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { const long neg_one = (long) -1, const_zero = 0; const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { if (sizeof(long) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (long) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(long, digit, ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } + if (sizeof(long) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(long) <= sizeof(unsigned long long)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long long, PyLong_AsUnsignedLongLong(x)) + } + } else { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(long, digit, +(((PyLongObject*)x)->ob_digit[0])); + case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (sizeof(long) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT(long, long, PyLong_AsLong(x)) + } else if (sizeof(long) <= sizeof(long long)) { + __PYX_VERIFY_RETURN_INT(long, long long, PyLong_AsLongLong(x)) + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + long val; + PyObject *v = __Pyx_PyNumber_Int(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (long) -1; + } + } else { + long val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (long) -1; + val = __Pyx_PyInt_As_long(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to long"); + return (long) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to long"); + return (long) -1; +} + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { + const int neg_one = (int) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(int) < sizeof(long)) { return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(unsigned long)) { + } else if (sizeof(int) <= sizeof(unsigned long)) { return PyLong_FromUnsignedLong((unsigned long) value); - } else if (sizeof(long) <= sizeof(unsigned long long)) { + } else if (sizeof(int) <= sizeof(unsigned long long)) { return PyLong_FromUnsignedLongLong((unsigned long long) value); } } else { - if (sizeof(long) <= sizeof(long)) { + if (sizeof(int) <= sizeof(long)) { return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(long long)) { + } else if (sizeof(int) <= sizeof(long long)) { return PyLong_FromLongLong((long long) value); } } { int one = 1; int little = (int)*(unsigned char *)&one; unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(long), + return _PyLong_FromByteArray(bytes, sizeof(int), little, !is_unsigned); } } @@ -5710,7 +6189,7 @@ static int __Pyx_Print(PyObject* f, PyObject *arg_tuple, int newline) { Py_DECREF(f); return -1; } -#else /* Python 3 has a print function */ +#else static int __Pyx_Print(PyObject* stream, PyObject *arg_tuple, int newline) { PyObject* kwargs = 0; PyObject* result = 0; @@ -5790,7 +6269,7 @@ static int __Pyx_PrintOne(PyObject* f, PyObject *o) { * warnings about unused functions */ return __Pyx_Print(f, NULL, 0); } -#else /* Python 3 has a print function */ +#else static int __Pyx_PrintOne(PyObject* stream, PyObject *o) { int res; PyObject* arg_tuple = PyTuple_Pack(1, o); @@ -6042,106 +6521,6 @@ static int __Pyx_PrintOne(PyObject* stream, PyObject *o) { #endif #endif -#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 - #if CYTHON_USE_PYLONG_INTERNALS - #include "longintrepr.h" - #endif -#endif -static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { - const long neg_one = (long) -1, const_zero = 0; - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(long) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to long"); - return (long) -1; - } - return (long) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 - #if CYTHON_USE_PYLONG_INTERNALS - if (sizeof(digit) <= sizeof(long)) { - switch (Py_SIZE(x)) { - case 0: return 0; - case 1: return (long) ((PyLongObject*)x)->ob_digit[0]; - } - } - #endif -#endif - if (unlikely(Py_SIZE(x) < 0)) { - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to long"); - return (long) -1; - } - if (sizeof(long) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, PyLong_AsUnsignedLong) - } else if (sizeof(long) <= sizeof(unsigned long long)) { - __PYX_VERIFY_RETURN_INT(long, unsigned long long, PyLong_AsUnsignedLongLong) - } - } else { -#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 - #if CYTHON_USE_PYLONG_INTERNALS - if (sizeof(digit) <= sizeof(long)) { - switch (Py_SIZE(x)) { - case 0: return 0; - case 1: return +(long) ((PyLongObject*)x)->ob_digit[0]; - case -1: return -(long) ((PyLongObject*)x)->ob_digit[0]; - } - } - #endif -#endif - if (sizeof(long) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT(long, long, PyLong_AsLong) - } else if (sizeof(long) <= sizeof(long long)) { - __PYX_VERIFY_RETURN_INT(long, long long, PyLong_AsLongLong) - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - long val; - PyObject *v = __Pyx_PyNumber_Int(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (long) -1; - } - } else { - long val; - PyObject *tmp = __Pyx_PyNumber_Int(x); - if (!tmp) return (long) -1; - val = __Pyx_PyInt_As_long(tmp); - Py_DECREF(tmp); - return val; - } -} - static int __Pyx_check_binary_version(void) { char ctversion[4], rtversion[4]; PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); @@ -6152,11 +6531,7 @@ static int __Pyx_check_binary_version(void) { "compiletime version %s of module '%.100s' " "does not match runtime version %s", ctversion, __Pyx_MODULE_NAME, rtversion); - #if PY_VERSION_HEX < 0x02050000 - return PyErr_Warn(NULL, message); - #else return PyErr_WarnEx(NULL, message, 1); - #endif } return 0; } @@ -6226,11 +6601,7 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class PyOS_snprintf(warning, sizeof(warning), "%s.%s size changed, may indicate binary incompatibility", module_name, class_name); - #if PY_VERSION_HEX < 0x02050000 - if (PyErr_Warn(NULL, warning) < 0) goto bad; - #else if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; - #endif } else if ((size_t)basicsize != size) { PyErr_Format(PyExc_ValueError, @@ -6246,168 +6617,6 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class } #endif -static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { - int start = 0, mid = 0, end = count - 1; - if (end >= 0 && code_line > entries[end].code_line) { - return count; - } - while (start < end) { - mid = (start + end) / 2; - if (code_line < entries[mid].code_line) { - end = mid; - } else if (code_line > entries[mid].code_line) { - start = mid + 1; - } else { - return mid; - } - } - if (code_line <= entries[mid].code_line) { - return mid; - } else { - return mid + 1; - } -} -static PyCodeObject *__pyx_find_code_object(int code_line) { - PyCodeObject* code_object; - int pos; - if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) { - return NULL; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) { - return NULL; - } - code_object = __pyx_code_cache.entries[pos].code_object; - Py_INCREF(code_object); - return code_object; -} -static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { - int pos, i; - __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries; - if (unlikely(!code_line)) { - return; - } - if (unlikely(!entries)) { - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry)); - if (likely(entries)) { - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = 64; - __pyx_code_cache.count = 1; - entries[0].code_line = code_line; - entries[0].code_object = code_object; - Py_INCREF(code_object); - } - return; - } - pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line); - if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) { - PyCodeObject* tmp = entries[pos].code_object; - entries[pos].code_object = code_object; - Py_DECREF(tmp); - return; - } - if (__pyx_code_cache.count == __pyx_code_cache.max_count) { - int new_max = __pyx_code_cache.max_count + 64; - entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc( - __pyx_code_cache.entries, new_max*sizeof(__Pyx_CodeObjectCacheEntry)); - if (unlikely(!entries)) { - return; - } - __pyx_code_cache.entries = entries; - __pyx_code_cache.max_count = new_max; - } - for (i=__pyx_code_cache.count; i>pos; i--) { - entries[i] = entries[i-1]; - } - entries[pos].code_line = code_line; - entries[pos].code_object = code_object; - __pyx_code_cache.count++; - Py_INCREF(code_object); -} - -#include "compile.h" -#include "frameobject.h" -#include "traceback.h" -static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( - const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = 0; - PyObject *py_srcfile = 0; - PyObject *py_funcname = 0; - #if PY_MAJOR_VERSION < 3 - py_srcfile = PyString_FromString(filename); - #else - py_srcfile = PyUnicode_FromString(filename); - #endif - if (!py_srcfile) goto bad; - if (c_line) { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - #else - py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line); - #endif - } - else { - #if PY_MAJOR_VERSION < 3 - py_funcname = PyString_FromString(funcname); - #else - py_funcname = PyUnicode_FromString(funcname); - #endif - } - if (!py_funcname) goto bad; - py_code = __Pyx_PyCode_New( - 0, /*int argcount,*/ - 0, /*int kwonlyargcount,*/ - 0, /*int nlocals,*/ - 0, /*int stacksize,*/ - 0, /*int flags,*/ - __pyx_empty_bytes, /*PyObject *code,*/ - __pyx_empty_tuple, /*PyObject *consts,*/ - __pyx_empty_tuple, /*PyObject *names,*/ - __pyx_empty_tuple, /*PyObject *varnames,*/ - __pyx_empty_tuple, /*PyObject *freevars,*/ - __pyx_empty_tuple, /*PyObject *cellvars,*/ - py_srcfile, /*PyObject *filename,*/ - py_funcname, /*PyObject *name,*/ - py_line, /*int firstlineno,*/ - __pyx_empty_bytes /*PyObject *lnotab*/ - ); - Py_DECREF(py_srcfile); - Py_DECREF(py_funcname); - return py_code; -bad: - Py_XDECREF(py_srcfile); - Py_XDECREF(py_funcname); - return NULL; -} -static void __Pyx_AddTraceback(const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = 0; - PyObject *py_globals = 0; - PyFrameObject *py_frame = 0; - py_code = __pyx_find_code_object(c_line ? c_line : py_line); - if (!py_code) { - py_code = __Pyx_CreateCodeObjectForTraceback( - funcname, c_line, py_line, filename); - if (!py_code) goto bad; - __pyx_insert_code_object(c_line ? c_line : py_line, py_code); - } - py_globals = PyModule_GetDict(__pyx_m); - if (!py_globals) goto bad; - py_frame = PyFrame_New( - PyThreadState_GET(), /*PyThreadState *tstate,*/ - py_code, /*PyCodeObject *code,*/ - py_globals, /*PyObject *globals,*/ - 0 /*PyObject *locals*/ - ); - if (!py_frame) goto bad; - py_frame->f_lineno = py_line; - PyTraceBack_Here(py_frame); -bad: - Py_XDECREF(py_code); - Py_XDECREF(py_frame); -} - static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { while (t->p) { #if PY_MAJOR_VERSION < 3 @@ -6418,7 +6627,7 @@ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { } else { *t->p = PyString_FromStringAndSize(t->s, t->n - 1); } - #else /* Python 3+ has unicode identifiers */ + #else if (t->is_unicode | t->is_str) { if (t->intern) { *t->p = PyUnicode_InternFromString(t->s); @@ -6438,8 +6647,8 @@ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { return 0; } -static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(char* c_str) { - return __Pyx_PyUnicode_FromStringAndSize(c_str, strlen(c_str)); +static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) { + return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str)); } static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) { Py_ssize_t ignore; @@ -6468,32 +6677,30 @@ static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_ } } } -#endif /*__PYX_DEFAULT_STRING_ENCODING_IS_ASCII*/ +#endif *length = PyBytes_GET_SIZE(defenc); return defenc_c; -#else /* PY_VERSION_HEX < 0x03030000 */ - if (PyUnicode_READY(o) == -1) return NULL; +#else + if (__Pyx_PyUnicode_READY(o) == -1) return NULL; #if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII if (PyUnicode_IS_ASCII(o)) { - *length = PyUnicode_GET_DATA_SIZE(o); + *length = PyUnicode_GET_LENGTH(o); return PyUnicode_AsUTF8(o); } else { PyUnicode_AsASCIIString(o); return NULL; } -#else /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII */ +#else return PyUnicode_AsUTF8AndSize(o, length); -#endif /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII */ -#endif /* PY_VERSION_HEX < 0x03030000 */ +#endif +#endif } else -#endif /* __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT */ +#endif #if !CYTHON_COMPILING_IN_PYPY -#if PY_VERSION_HEX >= 0x02060000 if (PyByteArray_Check(o)) { *length = PyByteArray_GET_SIZE(o); return PyByteArray_AS_STRING(o); } else -#endif #endif { char* result; @@ -6555,11 +6762,6 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) { } return res; } -#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 - #if CYTHON_USE_PYLONG_INTERNALS - #include "longintrepr.h" - #endif -#endif static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { Py_ssize_t ival; PyObject *x; @@ -6577,11 +6779,7 @@ static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { } #endif #endif - #if PY_VERSION_HEX < 0x02060000 - return PyInt_AsSsize_t(b); - #else return PyLong_AsSsize_t(b); - #endif } x = PyNumber_Index(b); if (!x) return -1; @@ -6590,17 +6788,7 @@ static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { return ival; } static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { -#if PY_VERSION_HEX < 0x02050000 - if (ival <= LONG_MAX) - return PyInt_FromLong((long)ival); - else { - unsigned char *bytes = (unsigned char *) &ival; - int one = 1; int little = (int)*(unsigned char*)&one; - return _PyLong_FromByteArray(bytes, sizeof(size_t), little, 0); - } -#else - return PyInt_FromSize_t(ival); -#endif + return PyInt_FromSize_t(ival); } diff --git a/sklearn/manifold/_utils.pyx b/sklearn/manifold/_utils.pyx index def2715cde3fb..b85da09dbaefd 100644 --- a/sklearn/manifold/_utils.pyx +++ b/sklearn/manifold/_utils.pyx @@ -2,33 +2,36 @@ from libc cimport math cimport cython import numpy as np cimport numpy as np +from libc.stdio cimport printf cdef extern from "numpy/npy_math.h": float NPY_INFINITY -cdef double EPSILON_DBL = 1e-7 -cdef double PERPLEXITY_TOLERANCE = 1e-5 - +cdef float EPSILON_DBL = 1e-8 +cdef float PERPLEXITY_TOLERANCE = 1e-5 @cython.boundscheck(False) -cpdef np.ndarray[np.float_t, ndim=2] _binary_search_perplexity( - np.ndarray[np.float_t, ndim=2] affinities, double desired_perplexity, +cpdef np.ndarray[np.float32_t, ndim=2] _binary_search_perplexity( + np.ndarray[np.float32_t, ndim=2] affinities, + np.ndarray[np.int64_t, ndim=2] neighbors, + float desired_perplexity, int verbose): - """Binary search for sigmas of conditional Gaussians. - - We are looking for sigma = sqrt(1/beta) so that the perplexity - of the conditional distribution p_i|j matches approximately the - desired value. p_i|j are Gaussian distributed. - - The idea has been proposed in "Stochastic Neighbor Embedding" - Geoffrey Hinton and Sam Roweis, 2003. + """Binary search for sigmas of conditional Gaussians. + + This approximation reduces the computational complexity from O(N^2) to + O(uN). See the exact method '_binary_search_perplexity' for more details. Parameters ---------- affinities : array-like, shape (n_samples, n_samples) Distances between training samples. - desired_perplexity : double + neighbors : array-like, shape (n_samples, K) or None + Each row contains the indices to the K nearest neigbors. If this + array is None, then the perplexity is estimated over all data + not just the nearest neighbors. + + desired_perplexity : float Desired perplexity (2^entropy) of the conditional Gaussians. verbose : int @@ -40,25 +43,31 @@ cpdef np.ndarray[np.float_t, ndim=2] _binary_search_perplexity( Probabilities of conditional Gaussian distributions p_i|j. """ # Maximum number of binary search steps - cdef int n_steps = 100 + cdef long n_steps = 100 - cdef int n_samples = affinities.shape[0] - cdef np.ndarray[np.float_t, ndim=2] P = np.ndarray((n_samples, n_samples), - dtype=np.double) + cdef long n_samples = affinities.shape[0] + # This array is later used as a 32bit array. It has multiple intermediate + # floating point additions that benefit from the extra precision + cdef np.ndarray[np.float64_t, ndim=2] P = np.zeros((n_samples, n_samples), + dtype=np.float64) # Precisions of conditional Gaussian distrubutions - cdef double beta - cdef double beta_min - cdef double beta_max - cdef double beta_sum = 0.0 + cdef float beta + cdef float beta_min + cdef float beta_max + cdef float beta_sum = 0.0 # Now we go to log scale - cdef double desired_entropy = math.log(desired_perplexity) - cdef double entropy_diff + cdef float desired_entropy = math.log(desired_perplexity) + cdef float entropy_diff - cdef double entropy - cdef double sum_Pi - cdef double sum_disti_Pi - cdef int i - cdef int j + cdef float entropy + cdef float sum_Pi + cdef float sum_disti_Pi + cdef long i, j, k, l = 0 + cdef long K = n_samples + cdef int using_neighbors = neighbors is not None + + if using_neighbors: + K = neighbors.shape[1] for i in range(n_samples): beta_min = -NPY_INFINITY @@ -66,20 +75,38 @@ cpdef np.ndarray[np.float_t, ndim=2] _binary_search_perplexity( beta = 1.0 # Binary search of precision for i-th conditional distribution - for _ in range(n_steps): + for l in range(n_steps): # Compute current entropy and corresponding probabilities - for j in range(n_samples): - P[i, j] = math.exp(-affinities[i, j] * beta) + # computed just over the nearest neighbors or over all data + # if we're not using neighbors + if using_neighbors: + for k in range(K): + j = neighbors[i, k] + P[i, j] = math.exp(-affinities[i, j] * beta) + else: + for j in range(K): + P[i, j] = math.exp(-affinities[i, j] * beta) P[i, i] = 0.0 sum_Pi = 0.0 - for j in range(n_samples): - sum_Pi += P[i, j] + if using_neighbors: + for k in range(K): + j = neighbors[i, k] + sum_Pi += P[i, j] + else: + for j in range(K): + sum_Pi += P[i, j] if sum_Pi == 0.0: sum_Pi = EPSILON_DBL sum_disti_Pi = 0.0 - for j in range(n_samples): - P[i, j] /= sum_Pi - sum_disti_Pi += affinities[i, j] * P[i, j] + if using_neighbors: + for k in range(K): + j = neighbors[i, k] + P[i, j] /= sum_Pi + sum_disti_Pi += affinities[i, j] * P[i, j] + else: + for j in range(K): + P[i, j] /= sum_Pi + sum_disti_Pi += affinities[i, j] * P[i, j] entropy = math.log(sum_Pi) + beta * sum_disti_Pi entropy_diff = entropy - desired_entropy diff --git a/sklearn/manifold/setup.py b/sklearn/manifold/setup.py index c9fe4ddf9a324..54bbd0dd3e1e6 100644 --- a/sklearn/manifold/setup.py +++ b/sklearn/manifold/setup.py @@ -1,7 +1,9 @@ import os +from os.path import join import numpy from numpy.distutils.misc_util import Configuration +from sklearn._build_utils import get_blas_info def configuration(parent_package="", top_path=None): @@ -14,6 +16,16 @@ def configuration(parent_package="", top_path=None): include_dirs=[numpy.get_include()], libraries=libraries, extra_compile_args=["-O3"]) + cblas_libs, blas_info = get_blas_info() + eca = blas_info.pop('extra_compile_args', []) + eca.append("-O4") + config.add_extension("_barnes_hut_tsne", + libraries=cblas_libs, + sources=["_barnes_hut_tsne.c"], + include_dirs=[join('..', 'src', 'cblas'), + numpy.get_include(), + blas_info.pop('include_dirs', [])], + extra_compile_args=eca) return config diff --git a/sklearn/manifold/t_sne.py b/sklearn/manifold/t_sne.py index 22029f5cff7e1..9c4cf03462d6f 100644 --- a/sklearn/manifold/t_sne.py +++ b/sklearn/manifold/t_sne.py @@ -1,17 +1,20 @@ # Author: Alexander Fabisch -- +# Author: Christopher Moody +# Author: Nick Travers # License: BSD 3 clause (C) 2014 -# This is the standard t-SNE implementation. There are faster modifications of -# the algorithm: -# * Barnes-Hut-SNE: reduces the complexity of the gradient computation from -# N^2 to N log N (http://arxiv.org/abs/1301.3342) +# This is the exact and Barnes-Hut t-SNE implementation. There are other +# modifications of the algorithm: # * Fast Optimization for t-SNE: # http://cseweb.ucsd.edu/~lvdmaaten/workshops/nips2010/papers/vandermaaten.pdf import numpy as np from scipy import linalg +import scipy.sparse as sp +import warnings from scipy.spatial.distance import pdist from scipy.spatial.distance import squareform +from ..neighbors import BallTree from ..base import BaseEstimator from ..utils import check_array from ..utils import check_random_state @@ -19,6 +22,8 @@ from ..decomposition import RandomizedPCA from ..metrics.pairwise import pairwise_distances from . import _utils +from . import _barnes_hut_tsne +from ..utils.fixes import astype MACHINE_EPSILON = np.finfo(np.double).eps @@ -47,16 +52,60 @@ def _joint_probabilities(distances, desired_perplexity, verbose): """ # Compute conditional probabilities such that they approximately match # the desired perplexity + distances = astype(distances, np.float32, copy=False) conditional_P = _utils._binary_search_perplexity( - distances, desired_perplexity, verbose) + distances, None, desired_perplexity, verbose) P = conditional_P + conditional_P.T sum_P = np.maximum(np.sum(P), MACHINE_EPSILON) P = np.maximum(squareform(P) / sum_P, MACHINE_EPSILON) return P -def _kl_divergence(params, P, alpha, n_samples, n_components): - """t-SNE objective function: KL divergence of p_ijs and q_ijs. +def _joint_probabilities_nn(distances, neighbors, desired_perplexity, verbose): + """Compute joint probabilities p_ij from distances using just nearest + neighbors. + + This method is approximately equal to _joint_probabilities. The latter + is O(N), but limiting the joint probability to nearest neighbors improves + this substantially to O(uN). + + Parameters + ---------- + distances : array, shape (n_samples * (n_samples-1) / 2,) + Distances of samples are stored as condensed matrices, i.e. + we omit the diagonal and duplicate entries and store everything + in a one-dimensional array. + + desired_perplexity : float + Desired perplexity of the joint probability distributions. + + verbose : int + Verbosity level. + + Returns + ------- + P : array, shape (n_samples * (n_samples-1) / 2,) + Condensed joint probability matrix. + """ + # Compute conditional probabilities such that they approximately match + # the desired perplexity + distances = astype(distances, np.float32, copy=False) + neighbors = astype(neighbors, np.int64, copy=False) + conditional_P = _utils._binary_search_perplexity( + distances, neighbors, desired_perplexity, verbose) + m = "All probabilities should be finite" + assert np.all(np.isfinite(conditional_P)), m + P = conditional_P + conditional_P.T + sum_P = np.maximum(np.sum(P), MACHINE_EPSILON) + P = np.maximum(squareform(P) / sum_P, MACHINE_EPSILON) + assert np.all(np.abs(P) <= 1.0) + return P + + +def _kl_divergence(params, P, degrees_of_freedom, n_samples, n_components, + skip_num_points=0): + """t-SNE objective function: gradient of the KL divergence + of p_ijs and q_ijs and the absolute error. Parameters ---------- @@ -66,7 +115,7 @@ def _kl_divergence(params, P, alpha, n_samples, n_components): P : array, shape (n_samples * (n_samples-1) / 2,) Condensed joint probability matrix. - alpha : float + degrees_of_freedom : float Degrees of freedom of the Student's-t distribution. n_samples : int @@ -75,6 +124,11 @@ def _kl_divergence(params, P, alpha, n_samples, n_components): n_components : int Dimension of the embedded space. + skip_num_points : int (optional, default:0) + This does not compute the gradient for points with indices below + `skip_num_points`. This is useful when computing transforms of new + data where you'd like to keep the old data fixed. + Returns ------- kl_divergence : float @@ -89,8 +143,8 @@ def _kl_divergence(params, P, alpha, n_samples, n_components): # Q is a heavy-tailed distribution: Student's t-distribution n = pdist(X_embedded, "sqeuclidean") n += 1. - n /= alpha - n **= (alpha + 1.0) / -2.0 + n /= degrees_of_freedom + n **= (degrees_of_freedom + 1.0) / -2.0 Q = np.maximum(n / (2.0 * np.sum(n)), MACHINE_EPSILON) # Optimization trick below: np.dot(x, y) is faster than @@ -102,26 +156,159 @@ def _kl_divergence(params, P, alpha, n_samples, n_components): # Gradient: dC/dY grad = np.ndarray((n_samples, n_components)) PQd = squareform((P - Q) * n) - for i in range(n_samples): + for i in range(skip_num_points, n_samples): np.dot(_ravel(PQd[i]), X_embedded[i] - X_embedded, out=grad[i]) grad = grad.ravel() - c = 2.0 * (alpha + 1.0) / alpha + c = 2.0 * (degrees_of_freedom + 1.0) / degrees_of_freedom grad *= c return kl_divergence, grad -def _gradient_descent(objective, p0, it, n_iter, n_iter_without_progress=30, +def _kl_divergence_error(params, P, neighbors, degrees_of_freedom, n_samples, + n_components): + """t-SNE objective function: the absolute error of the + KL divergence of p_ijs and q_ijs. + + Parameters + ---------- + params : array, shape (n_params,) + Unraveled embedding. + + P : array, shape (n_samples * (n_samples-1) / 2,) + Condensed joint probability matrix. + + neighbors : array (n_samples, K) + The neighbors is not actually required to calculate the + divergence, but is here to match the signature of the + gradient function + + degrees_of_freedom : float + Degrees of freedom of the Student's-t distribution. + + n_samples : int + Number of samples. + + n_components : int + Dimension of the embedded space. + + Returns + ------- + kl_divergence : float + Kullback-Leibler divergence of p_ij and q_ij. + + grad : array, shape (n_params,) + Unraveled gradient of the Kullback-Leibler divergence with respect to + the embedding. + """ + X_embedded = params.reshape(n_samples, n_components) + + # Q is a heavy-tailed distribution: Student's t-distribution + n = pdist(X_embedded, "sqeuclidean") + n += 1. + n /= degrees_of_freedom + n **= (degrees_of_freedom + 1.0) / -2.0 + Q = np.maximum(n / (2.0 * np.sum(n)), MACHINE_EPSILON) + + # Optimization trick below: np.dot(x, y) is faster than + # np.sum(x * y) because it calls BLAS + + # Objective: C (Kullback-Leibler divergence of P and Q) + if len(P.shape) == 2: + P = squareform(P) + kl_divergence = 2.0 * np.dot(P, np.log(P / Q)) + + return kl_divergence + + +def _kl_divergence_bh(params, P, neighbors, degrees_of_freedom, n_samples, + n_components, angle=0.5, skip_num_points=0, + verbose=False): + """t-SNE objective function: KL divergence of p_ijs and q_ijs. + + Uses Barnes-Hut tree methods to calculate the gradient that + runs in O(NlogN) instead of O(N^2) + + Parameters + ---------- + params : array, shape (n_params,) + Unraveled embedding. + + P : array, shape (n_samples * (n_samples-1) / 2,) + Condensed joint probability matrix. + + neighbors: int64 array, shape (n_samples, K) + Array with element [i, j] giving the index for the jth + closest neighbor to point i. + + degrees_of_freedom : float + Degrees of freedom of the Student's-t distribution. + + n_samples : int + Number of samples. + + n_components : int + Dimension of the embedded space. + + angle : float (default: 0.5) + This is the trade-off between speed and accuracy for Barnes-Hut T-SNE. + 'angle' is the angular size (referred to as theta in [3]) of a distant + node as measured from a point. If this size is below 'angle' then it is + used as a summary node of all points contained within it. + This method is not very sensitive to changes in this parameter + in the range of 0.2 - 0.8. Angle less than 0.2 has quickly increasing + computation time and angle greater 0.8 has quickly increasing error. + + skip_num_points : int (optional, default:0) + This does not compute the gradient for points with indices below + `skip_num_points`. This is useful when computing transforms of new + data where you'd like to keep the old data fixed. + + verbose : int + Verbosity level. + + Returns + ------- + kl_divergence : float + Kullback-Leibler divergence of p_ij and q_ij. + + grad : array, shape (n_params,) + Unraveled gradient of the Kullback-Leibler divergence with respect to + the embedding. + """ + params = astype(params, np.float32, copy=False) + X_embedded = params.reshape(n_samples, n_components) + neighbors = astype(neighbors, np.int64, copy=False) + if len(P.shape) == 1: + sP = squareform(P).astype(np.float32) + else: + sP = P.astype(np.float32) + + grad = np.zeros(X_embedded.shape, dtype=np.float32) + error = _barnes_hut_tsne.gradient(sP, X_embedded, neighbors, + grad, angle, n_components, verbose, + dof=degrees_of_freedom) + c = 2.0 * (degrees_of_freedom + 1.0) / degrees_of_freedom + grad = grad.ravel() + grad *= c + + return error, grad + + +def _gradient_descent(objective, p0, it, n_iter, objective_error=None, + n_iter_check=1, n_iter_without_progress=50, momentum=0.5, learning_rate=1000.0, min_gain=0.01, min_grad_norm=1e-7, min_error_diff=1e-7, verbose=0, - args=None): + args=None, kwargs=None): """Batch gradient descent with momentum and individual gains. Parameters ---------- objective : function or callable Should return a tuple of cost and gradient for a given parameter - vector. + vector. When expensive to compute, the cost can optionally + be None and can be computed every n_iter_check steps using + the objective_error function. p0 : array-like, shape (n_params,) Initial parameter vector. @@ -133,6 +320,14 @@ def _gradient_descent(objective, p0, it, n_iter, n_iter_without_progress=30, n_iter : int Maximum number of gradient descent iterations. + n_iter_check : int + Number of iterations before evaluating the global error. If the error + is sufficiently low, we abort the optimization. + + objective_error : function or callable + Should return a tuple of cost and gradient for a given parameter + vector. + n_iter_without_progress : int, optional (default: 30) Maximum number of iterations without progress before we abort the optimization. @@ -162,6 +357,9 @@ def _gradient_descent(objective, p0, it, n_iter, n_iter_without_progress=30, args : sequence Arguments to pass to objective function. + kwargs : dict + Keyword arguments to pass to objective function. + Returns ------- p : array, shape (n_params,) @@ -184,31 +382,9 @@ def _gradient_descent(objective, p0, it, n_iter, n_iter_without_progress=30, best_iter = 0 for i in range(it, n_iter): - new_error, grad = objective(p, *args) - error_diff = np.abs(new_error - error) - error = new_error + new_error, grad = objective(p, *args, **kwargs) grad_norm = linalg.norm(grad) - if error < best_error: - best_error = error - best_iter = i - elif i - best_iter > n_iter_without_progress: - if verbose >= 2: - print("[t-SNE] Iteration %d: did not make any progress " - "during the last %d episodes. Finished." - % (i + 1, n_iter_without_progress)) - break - if min_grad_norm >= grad_norm: - if verbose >= 2: - print("[t-SNE] Iteration %d: gradient norm %f. Finished." - % (i + 1, grad_norm)) - break - if min_error_diff >= error_diff: - if verbose >= 2: - print("[t-SNE] Iteration %d: error difference %f. Finished." - % (i + 1, error_diff)) - break - inc = update * grad >= 0.0 dec = np.invert(inc) gains[inc] += 0.05 @@ -218,9 +394,38 @@ def _gradient_descent(objective, p0, it, n_iter, n_iter_without_progress=30, update = momentum * update - learning_rate * grad p += update - if verbose >= 2 and (i + 1) % 10 == 0: - print("[t-SNE] Iteration %d: error = %.7f, gradient norm = %.7f" - % (i + 1, error, grad_norm)) + if (i + 1) % n_iter_check == 0: + if new_error is None: + new_error = objective_error(p, *args) + error_diff = np.abs(new_error - error) + error = new_error + + if verbose >= 2: + m = "[t-SNE] Iteration %d: error = %.7f, gradient norm = %.7f" + print(m % (i + 1, error, grad_norm)) + + if error < best_error: + best_error = error + best_iter = i + elif i - best_iter > n_iter_without_progress: + if verbose >= 2: + print("[t-SNE] Iteration %d: did not make any progress " + "during the last %d episodes. Finished." + % (i + 1, n_iter_without_progress)) + break + if grad_norm <= min_grad_norm: + if verbose >= 2: + print("[t-SNE] Iteration %d: gradient norm %f. Finished." + % (i + 1, grad_norm)) + break + if error_diff <= min_error_diff: + if verbose >= 2: + m = "[t-SNE] Iteration %d: error difference %f. Finished." + print(m % (i + 1, error_diff)) + break + + if new_error is not None: + error = new_error return p, error, i @@ -371,6 +576,25 @@ class TSNE(BaseEstimator): numpy.random singleton. Note that different initializations might result in different local minima of the cost function. + method : string (default: 'barnes_hut') + By default the gradient calculation algorithm uses Barnes-Hut + approximation running in O(NlogN) time. method='exact' + will run on the slower, but exact, algorithm in O(N^2) time. The + exact algorithm should be used when nearest-neighbor errors need + to be better than 3%. However, the exact method cannot scale to + millions of examples. + + angle : float (default: 0.5) + Only used if method='barnes_hut' + This is the trade-off between speed and accuracy for Barnes-Hut T-SNE. + 'angle' is the angular size (referred to as theta in [3]) of a distant + node as measured from a point. If this size is below 'angle' then it is + used as a summary node of all points contained within it. + This method is not very sensitive to changes in this parameter + in the range of 0.2 - 0.8. Angle less than 0.2 has quickly increasing + computation time and angle greater 0.8 has quickly increasing error. + + Attributes ---------- embedding_ : array-like, shape (n_samples, n_components) @@ -387,10 +611,10 @@ class TSNE(BaseEstimator): >>> X = np.array([[0, 0, 0], [0, 1, 1], [1, 0, 1], [1, 1, 1]]) >>> model = TSNE(n_components=2, random_state=0) >>> model.fit_transform(X) # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE - array([[ 887.28..., 238.61...], - [ -714.79..., 3243.34...], - [ 957.30..., -2505.78...], - [-1130.28..., -974.78...]) + array([[ 1.75677320e-04, 4.08340798e-05], + [ 9.93642843e-05, 2.17790936e-04], + [ 1.85517575e-04, -9.32909822e-05], + [ 9.54209795e-05, -1.40144791e-05]]) References ---------- @@ -400,14 +624,20 @@ class TSNE(BaseEstimator): [2] van der Maaten, L.J.P. t-Distributed Stochastic Neighbor Embedding http://homepage.tudelft.nl/19j49/t-SNE.html + + [3] L.J.P. van der Maaten. Accelerating t-SNE using Tree-Based Algorithms. + Journal of Machine Learning Research 15(Oct):3221-3245, 2014. + http://lvdmaaten.github.io/publications/papers/JMLR_2014.pdf """ + def __init__(self, n_components=2, perplexity=30.0, early_exaggeration=4.0, learning_rate=1000.0, n_iter=1000, n_iter_without_progress=30, min_grad_norm=1e-7, metric="euclidean", init="random", verbose=0, - random_state=None): - if init not in ["pca", "random"]: - raise ValueError("'init' must be either 'pca' or 'random'") + random_state=None, method='barnes_hut', angle=0.5): + if init not in ["pca", "random"] or isinstance(init, np.ndarray): + msg = "'init' must be 'pca', 'random' or a NumPy array" + raise ValueError(msg) self.n_components = n_components self.perplexity = perplexity self.early_exaggeration = early_exaggeration @@ -419,17 +649,46 @@ def __init__(self, n_components=2, perplexity=30.0, self.init = init self.verbose = verbose self.random_state = random_state + self.method = method + self.angle = angle + self.embedding_ = None - def fit(self, X, y=None): + def _fit(self, X, skip_num_points=0): """Fit the model using X as training data. + Note that sparse arrays can only be handled by method='exact'. + It is recommended that you convert your sparse array to dense + (e.g. `X.toarray()`) if it fits in memory, or otherwise using a + dimensionality reduction technique (e.g. TrucnatedSVD). + Parameters ---------- X : array, shape (n_samples, n_features) or (n_samples, n_samples) If the metric is 'precomputed' X must be a square distance - matrix. Otherwise it contains a sample per row. + matrix. Otherwise it contains a sample per row. Note that this + when method='barnes_hut', X cannot be a sparse array and if need be + will be converted to a 32 bit float array. Method='exact' allows + sparse arrays and 64bit floating point inputs. + + skip_num_points : int (optional, default:0) + This does not compute the gradient for points with indices below + `skip_num_points`. This is useful when computing transforms of new + data where you'd like to keep the old data fixed. """ - X = check_array(X, accept_sparse=['csr', 'csc', 'coo'], dtype=np.float64) + if self.method not in ['barnes_hut', 'exact']: + raise ValueError("'method' must be 'barnes_hut' or 'exact'") + if self.angle < 0.0 or self.angle > 1.0: + raise ValueError("'angle' must be between 0.0 - 1.0") + if self.method == 'barnes_hut' and sp.issparse(X): + raise TypeError('A sparse matrix was passed, but dense ' + 'data is required for method="barnes_hut". Use ' + 'X.toarray() to convert to a dense numpy array if ' + 'the array is small enough for it to fit in ' + 'memory. Otherwise consider dimensionality ' + 'reduction techniques (e.g. TruncatedSVD)') + X = check_array(X, dtype=np.float32) + else: + X = check_array(X, accept_sparse=['csr', 'csc', 'coo'], dtype=np.float64) random_state = check_random_state(self.random_state) if self.early_exaggeration < 1.0: @@ -449,36 +708,74 @@ def fit(self, X, y=None): else: if self.verbose: print("[t-SNE] Computing pairwise distances...") - if self.metric == "euclidean": - distances = pairwise_distances(X, metric=self.metric, squared=True) + distances = pairwise_distances(X, metric=self.metric, + squared=True) else: distances = pairwise_distances(X, metric=self.metric) + if not np.all(distances >= 0): + raise ValueError("All distances should be positive, either " + "the metric or precomputed distances given " + "as X are not correct") + # Degrees of freedom of the Student's t-distribution. The suggestion - # alpha = n_components - 1 comes from "Learning a Parametric Embedding - # by Preserving Local Structure" Laurens van der Maaten, 2009. - alpha = max(self.n_components - 1.0, 1) + # degrees_of_freedom = n_components - 1 comes from + # "Learning a Parametric Embedding by Preserving Local Structure" + # Laurens van der Maaten, 2009. + degrees_of_freedom = max(self.n_components - 1.0, 1) n_samples = X.shape[0] self.training_data_ = X + # the number of nearest neighbors to find + k = min(n_samples - 1, int(3. * self.perplexity + 1)) + + neighbors_nn = None + if self.method == 'barnes_hut': + if self.verbose: + print("[t-SNE] Computing %i nearest neighbors..." % k) + if self.metric == 'precomputed': + # Use the precomputed distances to find + # the k nearest neighbors and their distances + neighbors_nn = np.argsort(distances, axis=1)[:, :k] + else: + # Find the nearest neighbors for every point + bt = BallTree(X) + # LvdM uses 3 * perplexity as the number of neighbors + # And we add one to not count the data point itself + # In the event that we have very small # of points + # set the neighbors to n - 1 + distances_nn, neighbors_nn = bt.query(X, k=k + 1) + neighbors_nn = neighbors_nn[:, 1:] + P = _joint_probabilities_nn(distances, neighbors_nn, + self.perplexity, self.verbose) + else: + P = _joint_probabilities(distances, self.perplexity, self.verbose) + assert np.all(np.isfinite(P)), "All probabilities should be finite" + assert np.all(P >= 0), "All probabilities should be zero or positive" + assert np.all(P <= 1), ("All probabilities should be less " + "or then equal to one") - P = _joint_probabilities(distances, self.perplexity, self.verbose) if self.init == 'pca': pca = RandomizedPCA(n_components=self.n_components, random_state=random_state) X_embedded = pca.fit_transform(X) + elif isinstance(self.init, np.ndarray): + X_embedded = self.init elif self.init == 'random': X_embedded = None else: raise ValueError("Unsupported initialization scheme: %s" % self.init) - self.embedding_ = self._tsne(P, alpha, n_samples, random_state, - X_embedded=X_embedded) + return self._tsne(P, degrees_of_freedom, n_samples, random_state, + X_embedded=X_embedded, + neighbors=neighbors_nn, + skip_num_points=skip_num_points) return self - def _tsne(self, P, alpha, n_samples, random_state, X_embedded=None): + def _tsne(self, P, degrees_of_freedom, n_samples, random_state, + X_embedded=None, neighbors=None, skip_num_points=0): """Runs t-SNE.""" # t-SNE minimizes the Kullback-Leiber divergence of the Gaussians P # and the Student's t-distributions Q. The optimization algorithm that @@ -495,31 +792,53 @@ def _tsne(self, P, alpha, n_samples, random_state, X_embedded=None): self.n_components) params = X_embedded.ravel() + opt_args = {} + opt_args = {"n_iter": 50, "momentum": 0.5, "it": 0, + "learning_rate": self.learning_rate, + "verbose": self.verbose, "n_iter_check": 25, + "kwargs": dict(skip_num_points=skip_num_points)} + if self.method == 'barnes_hut': + m = "Must provide an array of neighbors to use Barnes-Hut" + assert neighbors is not None, m + obj_func = _kl_divergence_bh + objective_error = _kl_divergence_error + sP = squareform(P).astype(np.float32) + neighbors = neighbors.astype(np.int64) + args = [sP, neighbors, degrees_of_freedom, n_samples, + self.n_components] + opt_args['args'] = args + opt_args['min_grad_norm'] = 1e-3 + opt_args['n_iter_without_progress'] = 30 + # Don't always calculate the cost since that calculation + # can be nearly as expensive as the gradient + opt_args['objective_error'] = objective_error + opt_args['kwargs']['angle'] = self.angle + opt_args['kwargs']['verbose'] = self.verbose + else: + obj_func = _kl_divergence + opt_args['args'] = [P, degrees_of_freedom, n_samples, + self.n_components] + opt_args['min_error_diff'] = 0.0 + opt_args['min_grad_norm'] = 0.0 + # Early exaggeration P *= self.early_exaggeration - params, error, it = _gradient_descent( - _kl_divergence, params, it=0, n_iter=50, momentum=0.5, - min_grad_norm=0.0, min_error_diff=0.0, - learning_rate=self.learning_rate, verbose=self.verbose, - args=[P, alpha, n_samples, self.n_components]) - params, error, it = _gradient_descent( - _kl_divergence, params, it=it + 1, n_iter=100, momentum=0.8, - min_grad_norm=0.0, min_error_diff=0.0, - learning_rate=self.learning_rate, verbose=self.verbose, - args=[P, alpha, n_samples, self.n_components]) + params, error, it = _gradient_descent(obj_func, params, **opt_args) + opt_args['n_iter'] = 100 + opt_args['momentum'] = 0.8 + opt_args['it'] = it + 1 + params, error, it = _gradient_descent(obj_func, params, **opt_args) if self.verbose: print("[t-SNE] Error after %d iterations with early " "exaggeration: %f" % (it + 1, error)) + # Save the final number of iterations + self.n_iter_final = it # Final optimization P /= self.early_exaggeration - params, error, it = _gradient_descent( - _kl_divergence, params, it=it + 1, n_iter=self.n_iter, - min_grad_norm=self.min_grad_norm, - n_iter_without_progress=self.n_iter_without_progress, - momentum=0.8, learning_rate=self.learning_rate, - verbose=self.verbose, args=[P, alpha, n_samples, - self.n_components]) + opt_args['n_iter'] = self.n_iter + opt_args['it'] = it + 1 + params, error, it = _gradient_descent(obj_func, params, **opt_args) if self.verbose: print("[t-SNE] Error after %d iterations: %f" % (it + 1, error)) @@ -528,7 +847,8 @@ def _tsne(self, P, alpha, n_samples, random_state, X_embedded=None): return X_embedded def fit_transform(self, X, y=None): - """Transform X to the embedded space. + """Fit X into an embedded space and return that transformed + output. Parameters ---------- @@ -541,5 +861,58 @@ def fit_transform(self, X, y=None): X_new : array, shape (n_samples, n_components) Embedding of the training data in low-dimensional space. """ - self.fit(X) + embedding = self._fit(X) + self.embedding_ = embedding return self.embedding_ + + def fit(self, X): + """Fit X into an embedded space. + + Parameters + ---------- + X : array, shape (n_samples, n_features) or (n_samples, n_samples) + If the metric is 'precomputed' X must be a square distance + matrix. Otherwise it contains a sample per row. If the method + is 'exact', X may be a sparse matrix of type 'csr', 'csc' + or 'coo'. + """ + self.fit_transform(X) + return self + + def _check_fitted(self): + if self.embedding_ is None: + raise ValueError("Cannot call `transform` unless `fit` has" + "already been called") + + def transform(self, X): + """Transform X to a previously fit embedded space. + + A previous training set must have already been fit. + The new gradient is calculated using contributions from + previously fit data, but only the new data is transformed. + This is not the equivalent of running fit_transform, + since calling fit(X) followed by transform(X) runs the + gradient calculation twice, once for just X and the second time + on the concatenated array [X, X]. + + Parameters + ---------- + X : array, shape (n_samples, n_features) or (n_samples, n_samples) + If the metric is 'precomputed' X must be a square distance + matrix. Otherwise it contains a sample per row. + + Returns + ------- + X_new : array, shape (n_samples, n_components) + Embedding of the training data in low-dimensional space. + """ + self._check_fitted() + if np.allclose(X, self.training_data_, rtol=1e-4): + warnings.warn("The transform input appears to be similar " + "to previously fit data. This can result in " + "duplicated data; consider using fit_transform") + + skip_num_points = self.embedding_.shape[0] + full_set = np.vstack((self.embedding_, X)) + Xt = self._fit(full_set, skip_num_points=skip_num_points) + return Xt diff --git a/sklearn/manifold/tests/test_t_sne.py b/sklearn/manifold/tests/test_t_sne.py index c990b55c35181..bb335f77e8533 100644 --- a/sklearn/manifold/tests/test_t_sne.py +++ b/sklearn/manifold/tests/test_t_sne.py @@ -1,21 +1,28 @@ import sys +import warnings from sklearn.externals.six.moves import cStringIO as StringIO import numpy as np import scipy.sparse as sp +from sklearn.neighbors import BallTree from sklearn.utils.testing import assert_equal from sklearn.utils.testing import assert_almost_equal +from sklearn.utils.testing import assert_array_almost_equal from sklearn.utils.testing import assert_less from sklearn.utils.testing import assert_raises_regexp from sklearn.utils import check_random_state from sklearn.manifold.t_sne import _joint_probabilities +from sklearn.manifold.t_sne import _joint_probabilities_nn from sklearn.manifold.t_sne import _kl_divergence +from sklearn.manifold.t_sne import _kl_divergence_bh from sklearn.manifold.t_sne import _gradient_descent from sklearn.manifold.t_sne import trustworthiness from sklearn.manifold.t_sne import TSNE +from sklearn.manifold import _barnes_hut_tsne from sklearn.manifold._utils import _binary_search_perplexity from scipy.optimize import check_grad from scipy.spatial.distance import pdist from scipy.spatial.distance import squareform +from sklearn.metrics.pairwise import pairwise_distances def test_gradient_descent_stops(): @@ -99,17 +106,78 @@ def flat_function(_): def test_binary_search(): # Test if the binary search finds Gaussians with desired perplexity. random_state = check_random_state(0) - distances = random_state.randn(50, 2) - distances = distances.dot(distances.T) + distances = random_state.randn(50, 2).astype(np.float32) + # Distances shouldn't be negative + distances = np.abs(distances.dot(distances.T)) np.fill_diagonal(distances, 0.0) desired_perplexity = 25.0 - P = _binary_search_perplexity(distances, desired_perplexity, verbose=0) + P = _binary_search_perplexity(distances, None, desired_perplexity, + verbose=0) P = np.maximum(P, np.finfo(np.double).eps) mean_perplexity = np.mean([np.exp(-np.sum(P[i] * np.log(P[i]))) for i in range(P.shape[0])]) assert_almost_equal(mean_perplexity, desired_perplexity, decimal=3) +def test_binary_search_neighbors(): + # Binary perplexity search approximation. + # Should be approximately equal to the slow method when we use + # all points as neighbors. + n_samples = 500 + desired_perplexity = 25.0 + random_state = check_random_state(0) + distances = random_state.randn(n_samples, 2).astype(np.float32) + # Distances shouldn't be negative + distances = np.abs(distances.dot(distances.T)) + np.fill_diagonal(distances, 0.0) + P1 = _binary_search_perplexity(distances, None, desired_perplexity, + verbose=0) + + # Test that when we use all the neighbors the results are identical + k = n_samples + neighbors_nn = np.argsort(distances, axis=1)[:, :k].astype(np.int64) + P2 = _binary_search_perplexity(distances, neighbors_nn, + desired_perplexity, verbose=0) + assert_array_almost_equal(P1, P2, decimal=4) + + # Test that the highest P_ij are the same when few neighbors are used + for k in np.linspace(80, n_samples, 10): + k = int(k) + topn = k * 10 # check the top 10 *k entries out of k * k entries + neighbors_nn = np.argsort(distances, axis=1)[:, :k] + P2k = _binary_search_perplexity(distances, neighbors_nn, + desired_perplexity, verbose=0) + idx = np.argsort(P1.ravel())[::-1] + P1top = P1.ravel()[idx][:topn] + P2top = P2k.ravel()[idx][:topn] + assert_array_almost_equal(P1top, P2top, decimal=2) + + +def test_binary_perplexity_stability(): + # Binary perplexity search should be stable. + # The binary_search_perplexity had a bug wherein the P array + # was uninitialized, leading to sporadically failing tests. + k = 10 + n_samples = 100 + random_state = check_random_state(0) + distances = random_state.randn(n_samples, 2).astype(np.float32) + # Distances shouldn't be negative + distances = np.abs(distances.dot(distances.T)) + np.fill_diagonal(distances, 0.0) + last_P = None + neighbors_nn = np.argsort(distances, axis=1)[:, :k] + for _ in range(100): + P = _binary_search_perplexity(distances.copy(), neighbors_nn.copy(), + 3, verbose=0) + P1 = _joint_probabilities_nn(distances, neighbors_nn, 3, verbose=0) + if last_P is None: + last_P = P + last_P1 = P1 + else: + assert_array_almost_equal(P, last_P, decimal=4) + assert_array_almost_equal(P1, last_P1, decimal=4) + + def test_gradient(): # Test gradient of Kullback-Leibler divergence. random_state = check_random_state(0) @@ -119,7 +187,7 @@ def test_gradient(): n_components = 2 alpha = 1.0 - distances = random_state.randn(n_samples, n_features) + distances = random_state.randn(n_samples, n_features).astype(np.float32) distances = distances.dot(distances.T) np.fill_diagonal(distances, 0.0) X_embedded = random_state.randn(n_samples, n_components) @@ -157,13 +225,21 @@ def test_trustworthiness(): def test_preserve_trustworthiness_approximately(): # Nearest neighbors should be preserved approximately. random_state = check_random_state(0) - X = random_state.randn(100, 2) + # The Barnes-Hut approximation uses a different method to estimate + # P_ij using only a a number of nearest neighbors instead of all + # points (so that k = 3 * perplexity). As a result we set the + # perplexity=5, so that the number of neighbors is 5%. + n_components = 2 + methods = ['exact', 'barnes_hut'] + X = random_state.randn(100, n_components).astype(np.float32) for init in ('random', 'pca'): - tsne = TSNE(n_components=2, perplexity=10, learning_rate=100.0, - init=init, random_state=0) - X_embedded = tsne.fit_transform(X) - assert_almost_equal(trustworthiness(X, X_embedded, n_neighbors=1), 1.0, - decimal=1) + for method in methods: + tsne = TSNE(n_components=n_components, perplexity=50, + learning_rate=100.0, init=init, random_state=0, + method=method) + X_embedded = tsne.fit_transform(X) + T = trustworthiness(X, X_embedded, n_neighbors=1) + assert_almost_equal(T, 1.0, decimal=1) def test_fit_csr_matrix(): @@ -173,7 +249,7 @@ def test_fit_csr_matrix(): X[(np.random.randint(0, 100, 50), np.random.randint(0, 2, 50))] = 0.0 X_csr = sp.csr_matrix(X) tsne = TSNE(n_components=2, perplexity=10, learning_rate=100.0, - random_state=0) + random_state=0, method='exact') X_embedded = tsne.fit_transform(X_csr) assert_almost_equal(trustworthiness(X_csr, X_embedded, n_neighbors=1), 1.0, decimal=1) @@ -184,8 +260,8 @@ def test_preserve_trustworthiness_approximately_with_precomputed_distances(): random_state = check_random_state(0) X = random_state.randn(100, 2) D = squareform(pdist(X), "sqeuclidean") - tsne = TSNE(n_components=2, perplexity=10, learning_rate=100.0, - metric="precomputed", random_state=0) + tsne = TSNE(n_components=2, perplexity=2, learning_rate=100.0, + metric="precomputed", random_state=0, verbose=0) X_embedded = tsne.fit_transform(D) assert_almost_equal(trustworthiness(D, X_embedded, n_neighbors=1, precomputed=True), 1.0, decimal=1) @@ -214,8 +290,8 @@ def test_non_square_precomputed_distances(): def test_init_not_available(): # 'init' must be 'pca' or 'random'. - assert_raises_regexp(ValueError, "'init' must be either 'pca' or 'random'", - TSNE, init="not available") + m = "'init' must be 'pca', 'random' or a NumPy array" + assert_raises_regexp(ValueError, m, TSNE, init="not available") def test_distance_not_available(): @@ -233,7 +309,86 @@ def test_pca_initialization_not_compatible_with_precomputed_kernel(): tsne.fit_transform, np.array([[0.0], [1.0]])) +def test_answer_gradient_two_points(): + # Test the tree with only a single set of children. + # + # These tests & answers have been checked against the reference + # implementation by LvdM. + pos_input = np.array([[1.0, 0.0], [0.0, 1.0]]) + pos_output = np.array([[-4.961291e-05, -1.072243e-04], + [9.259460e-05, 2.702024e-04]]) + neighbors = np.array([[1], + [0]]) + grad_output = np.array([[-2.37012478e-05, -6.29044398e-05], + [2.37012478e-05, 6.29044398e-05]]) + _run_answer_test(pos_input, pos_output, neighbors, grad_output) + + +def test_answer_gradient_four_points(): + # Four points tests the tree with multiple levels of children. + # + # These tests & answers have been checked against the reference + # implementation by LvdM. + pos_input = np.array([[1.0, 0.0], [0.0, 1.0], + [5.0, 2.0], [7.3, 2.2]]) + pos_output = np.array([[6.080564e-05, -7.120823e-05], + [-1.718945e-04, -4.000536e-05], + [-2.271720e-04, 8.663310e-05], + [-1.032577e-04, -3.582033e-05]]) + neighbors = np.array([[1, 2, 3], + [0, 2, 3], + [1, 0, 3], + [1, 2, 0]]) + grad_output = np.array([[5.81128448e-05, -7.78033454e-06], + [-5.81526851e-05, 7.80976444e-06], + [4.24275173e-08, -3.69569698e-08], + [-2.58720939e-09, 7.52706374e-09]]) + _run_answer_test(pos_input, pos_output, neighbors, grad_output) + + +def test_skip_num_points_gradient(): + # Test the kwargs option skip_num_points. + # + # Skip num points should make it such that the Barnes_hut gradient + # is not calculated for indices below skip_num_point. + # Aside from skip_num_points=2 and the first two gradient rows + # being set to zero, these data points are the same as in + # test_answer_gradient_four_points() + pos_input = np.array([[1.0, 0.0], [0.0, 1.0], + [5.0, 2.0], [7.3, 2.2]]) + pos_output = np.array([[6.080564e-05, -7.120823e-05], + [-1.718945e-04, -4.000536e-05], + [-2.271720e-04, 8.663310e-05], + [-1.032577e-04, -3.582033e-05]]) + neighbors = np.array([[1, 2, 3], + [0, 2, 3], + [1, 0, 3], + [1, 2, 0]]) + grad_output = np.array([[0.0, 0.0], + [0.0, 0.0], + [4.24275173e-08, -3.69569698e-08], + [-2.58720939e-09, 7.52706374e-09]]) + _run_answer_test(pos_input, pos_output, neighbors, grad_output, + False, 0.1, 2) + + +def _run_answer_test(pos_input, pos_output, neighbors, grad_output, + verbose=False, perplexity=0.1, skip_num_points=0): + distances = pairwise_distances(pos_input).astype(np.float32) + args = distances, perplexity, verbose + pos_output = pos_output.astype(np.float32) + neighbors = neighbors.astype(np.int64) + pij_input = _joint_probabilities(*args) + pij_input = squareform(pij_input).astype(np.float32) + grad_bh = np.zeros(pos_output.shape, dtype=np.float32) + + _barnes_hut_tsne.gradient(pij_input, pos_output, neighbors, + grad_bh, 0.5, 2, 1, skip_num_points=0) + assert_array_almost_equal(grad_bh, grad_output, decimal=4) + + def test_verbose(): + # Verbose options write to stdout. random_state = check_random_state(0) tsne = TSNE(verbose=2) X = random_state.randn(5, 2) @@ -271,3 +426,127 @@ def test_reduction_to_one_component(): X = random_state.randn(5, 2) X_embedded = tsne.fit(X).embedding_ assert(np.all(np.isfinite(X_embedded))) + + +def test_no_sparse_on_barnes_hut(): + # No sparse matrices allowed on Barnes-Hut. + random_state = check_random_state(0) + X = random_state.randn(100, 2) + X[(np.random.randint(0, 100, 50), np.random.randint(0, 2, 50))] = 0.0 + X_csr = sp.csr_matrix(X) + tsne = TSNE(n_iter=199, method='barnes_hut') + assert_raises_regexp(TypeError, "A sparse matrix was.*", + tsne.fit_transform, X_csr) + + +def test_64bit(): + # Ensure 64bit arrays are handled correctly. + random_state = check_random_state(0) + methods = ['barnes_hut', 'exact'] + for method in methods: + for dt in [np.float32, np.float64]: + X = random_state.randn(100, 2).astype(dt) + tsne = TSNE(n_components=2, perplexity=2, learning_rate=100.0, + random_state=0, method=method) + tsne.fit_transform(X) + + +def test_transform_before_fit(): + # transform() cannot be called before fit(). + random_state = check_random_state(0) + X = random_state.randn(100, 2) + tsne = TSNE(n_components=2, perplexity=2, learning_rate=100.0, + random_state=0, method='barnes_hut') + m = "Cannot call `transform` unless `fit` has" + assert_raises_regexp(ValueError, m, tsne.transform, X) + + +def test_transform_warning(): + # Raise a warning if fit and transform encountered the same data. + with warnings.catch_warnings(record=True) as w: + warnings.simplefilter("always") + random_state = check_random_state(0) + X = random_state.randn(100, 2) + tsne = TSNE(n_components=2, perplexity=2, learning_rate=100.0, + random_state=0, method='barnes_hut') + tsne.fit(X) + tsne.transform(X) + m = str(w[0].message) + assert "The transform input appears to be similar" in m + + +def test_barnes_hut_angle(): + # When Barnes-Hut's angle=0 this corresponds to the exact method. + angle = 0.0 + perplexity = 10 + n_samples = 100 + for n_components in [2, 3]: + n_features = 5 + degrees_of_freedom = float(n_components - 1.0) + + random_state = check_random_state(0) + distances = random_state.randn(n_samples, n_features) + distances = distances.astype(np.float32) + distances = distances.dot(distances.T) + np.fill_diagonal(distances, 0.0) + params = random_state.randn(n_samples, n_components) + P = _joint_probabilities(distances, perplexity, False) + kl, gradex = _kl_divergence(params, P, degrees_of_freedom, n_samples, + n_components) + + k = n_samples - 1 + bt = BallTree(distances) + distances_nn, neighbors_nn = bt.query(distances, k=k + 1) + neighbors_nn = neighbors_nn[:, 1:] + Pbh = _joint_probabilities_nn(distances, neighbors_nn, + perplexity, False) + kl, gradbh = _kl_divergence_bh(params, Pbh, neighbors_nn, + degrees_of_freedom, n_samples, + n_components, angle=angle, + skip_num_points=0, verbose=False) + assert_array_almost_equal(Pbh, P, decimal=5) + assert_array_almost_equal(gradex, gradbh, decimal=5) + + +def test_quadtree_similar_point(): + # Introduce a point into a quad tree where a similar point already exists. + # Test will hang if it doesn't complete. + Xs = [] + + # check the case where points are actually different + Xs.append(np.array([[1, 2], [3, 4]], dtype=np.float32)) + # check the case where points are the same on X axis + Xs.append(np.array([[1.0, 2.0], [1.0, 3.0]], dtype=np.float32)) + # check the case where points are arbitrarily close on X axis + Xs.append(np.array([[1.00001, 2.0], [1.00002, 3.0]], dtype=np.float32)) + # check the case where points are the same on Y axis + Xs.append(np.array([[1.0, 2.0], [3.0, 2.0]], dtype=np.float32)) + # check the case where points are arbitrarily close on Y axis + Xs.append(np.array([[1.0, 2.00001], [3.0, 2.00002]], dtype=np.float32)) + # check the case where points are arbitraryily close on both axes + Xs.append(np.array([[1.00001, 2.00001], [1.00002, 2.00002]], + dtype=np.float32)) + + # check the case where points are arbitraryily close on both axes + # close to machine epsilon - x axis + Xs.append(np.array([[1, 0.0003817754041], [2, 0.0003817753750]], + dtype=np.float32)) + + # check the case where points are arbitraryily close on both axes + # close to machine epsilon - y axis + Xs.append(np.array([[0.0003817754041, 1.0], [0.0003817753750, 2.0]], + dtype=np.float32)) + + for X in Xs: + counts = np.zeros(3, dtype='int64') + _barnes_hut_tsne.check_quadtree(X, counts) + m = "Tree consistency failed: unexpected number of points at root node" + assert_equal(counts[0], counts[1], m) + m = "Tree consistency failed: unexpected number of points on the tree" + assert_equal(counts[0], counts[2], m) + + +def test_index_offset(): + # Make sure translating between 1D and N-D indices are preserved + assert_equal(_barnes_hut_tsne.test_index2offset(), 1) + assert_equal(_barnes_hut_tsne.test_index_offset(), 1) From 1ce9ba36230c3575c0eb4d3d50fc929c0e38b045 Mon Sep 17 00:00:00 2001 From: Andreas Mueller Date: Thu, 12 Mar 2015 15:55:00 -0400 Subject: [PATCH 2/3] add necessary blas files. --- sklearn/manifold/setup.py | 2 +- sklearn/src/cblas/ATL_srefnrm2.c | 204 +++++++++++++++++++++++++++++++ sklearn/src/cblas/cblas_snrm2.c | 44 +++++++ 3 files changed, 249 insertions(+), 1 deletion(-) create mode 100644 sklearn/src/cblas/ATL_srefnrm2.c create mode 100644 sklearn/src/cblas/cblas_snrm2.c diff --git a/sklearn/manifold/setup.py b/sklearn/manifold/setup.py index 54bbd0dd3e1e6..18dee2d537742 100644 --- a/sklearn/manifold/setup.py +++ b/sklearn/manifold/setup.py @@ -25,7 +25,7 @@ def configuration(parent_package="", top_path=None): include_dirs=[join('..', 'src', 'cblas'), numpy.get_include(), blas_info.pop('include_dirs', [])], - extra_compile_args=eca) + extra_compile_args=eca, **blas_info) return config diff --git a/sklearn/src/cblas/ATL_srefnrm2.c b/sklearn/src/cblas/ATL_srefnrm2.c new file mode 100644 index 0000000000000..c4188fb7db1f4 --- /dev/null +++ b/sklearn/src/cblas/ATL_srefnrm2.c @@ -0,0 +1,204 @@ +/* --------------------------------------------------------------------- + * + * -- Automatically Tuned Linear Algebra Software (ATLAS) + * (C) Copyright 2000 All Rights Reserved + * + * -- ATLAS routine -- Version 3.9.24 -- December 25, 2000 + * + * Author : Antoine P. Petitet + * Originally developed at the University of Tennessee, + * Innovative Computing Laboratory, Knoxville TN, 37996-1301, USA. + * + * --------------------------------------------------------------------- + * + * -- Copyright notice and Licensing terms: + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions + * are met: + * + * 1. Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * 2. Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions, and the following disclaimer in + * the documentation and/or other materials provided with the distri- + * bution. + * 3. The name of the University, the ATLAS group, or the names of its + * contributors may not be used to endorse or promote products deri- + * ved from this software without specific written permission. + * + * -- Disclaimer: + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + * ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT + * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR + * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE UNIVERSITY + * OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPE- + * CIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED + * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, + * OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEO- + * RY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (IN- + * CLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF + * THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * + * --------------------------------------------------------------------- + */ +/* + * Include files + */ +#include "atlas_refmisc.h" +#include "atlas_reflevel1.h" + +float ATL_srefnrm2 +( + const int N, + const float * X, + const int INCX +) +{ +/* + * Purpose + * ======= + * + * ATL_srefnrm2 returns the 2-norm of an n-vector x. + * + * Arguments + * ========= + * + * N (input) const int + * On entry, N specifies the length of the vector x. N must be + * at least zero. Unchanged on exit. + * + * X (input) const float * + * On entry, X points to the first entry to be accessed of an + * incremented array of size equal to or greater than + * ( 1 + ( n - 1 ) * abs( INCX ) ) * sizeof( float ), + * that contains the vector x. Unchanged on exit. + * + * INCX (input) const int + * On entry, INCX specifies the increment for the elements of X. + * INCX must not be zero. Unchanged on exit. + * + * --------------------------------------------------------------------- + */ +/* + * .. Local Variables .. + */ + register float absxi, scale = ATL_sZERO, + ssq = ATL_sONE, temp, x0, x1, x2, x3, x4, + x5, x6, x7; + float * StX = (float *)(X) + N * INCX; + register int i; + int n = (int)(N), nu; + const int incX2 = 2 * INCX, incX3 = 3 * INCX, + incX4 = 4 * INCX, incX5 = 5 * INCX, + incX6 = 6 * INCX, incX7 = 7 * INCX, + incX8 = 8 * INCX; +/* .. + * .. Executable Statements .. + * + */ + if( ( N < 1 ) || ( INCX < 1 ) ) return( ATL_sZERO ); + else if( N == 1 ) return( Msabs( *X ) ); + + while( (X != StX) && ( *X == ATL_sZERO ) ) { X += INCX; n--; } + + if( X == StX ) return( ATL_sZERO ); + + if( ( nu = ( n >> 3 ) << 3 ) != 0 ) + { + StX = (float *)X + nu * INCX; + + do + { + x0 = (*X); x4 = X[incX4]; x1 = X[INCX ]; x5 = X[incX5]; + x2 = X[incX2]; x6 = X[incX6]; x3 = X[incX3]; x7 = X[incX7]; + + absxi = Msabs( x0 ); + if( scale < absxi ) + { + temp = scale / absxi; scale = absxi; + ssq = ATL_sONE + ssq * ( temp * temp ); + } + else { temp = absxi / scale; ssq += temp * temp; } + + absxi = Msabs( x4 ); + if( scale < absxi ) + { + temp = scale / absxi; scale = absxi; + ssq = ATL_sONE + ssq * ( temp * temp ); + } + else { temp = absxi / scale; ssq += temp * temp; } + + absxi = Msabs( x1 ); + if( scale < absxi ) + { + temp = scale / absxi; scale = absxi; + ssq = ATL_sONE + ssq * ( temp * temp ); + } + else { temp = absxi / scale; ssq += temp * temp; } + + absxi = Msabs( x5 ); + if( scale < absxi ) + { + temp = scale / absxi; scale = absxi; + ssq = ATL_sONE + ssq * ( temp * temp ); + } + else { temp = absxi / scale; ssq += temp * temp; } + + absxi = Msabs( x2 ); + if( scale < absxi ) + { + temp = scale / absxi; scale = absxi; + ssq = ATL_sONE + ssq * ( temp * temp ); + } + else { temp = absxi / scale; ssq += temp * temp; } + + absxi = Msabs( x6 ); + if( scale < absxi ) + { + temp = scale / absxi; scale = absxi; + ssq = ATL_sONE + ssq * ( temp * temp ); + } + else { temp = absxi / scale; ssq += temp * temp; } + + absxi = Msabs( x3 ); + if( scale < absxi ) + { + temp = scale / absxi; scale = absxi; + ssq = ATL_sONE + ssq * ( temp * temp ); + } + else { temp = absxi / scale; ssq += temp * temp; } + + absxi = Msabs( x7 ); + if( scale < absxi ) + { + temp = scale / absxi; scale = absxi; + ssq = ATL_sONE + ssq * ( temp * temp ); + } + else { temp = absxi / scale; ssq += temp * temp; } + + X += incX8; + + } while( X != StX ); + } + + for( i = n - nu; i != 0; i-- ) + { + x0 = (*X); + + absxi = Msabs( x0 ); + if( scale < absxi ) + { + temp = scale / absxi; scale = absxi; + ssq = ATL_sONE + ssq * ( temp * temp ); + } + else { temp = absxi / scale; ssq += temp * temp; } + + X += INCX; + } + return( scale * (float)(sqrt( (double)(ssq) )) ); +/* + * End of ATL_srefnrm2 + */ +} diff --git a/sklearn/src/cblas/cblas_snrm2.c b/sklearn/src/cblas/cblas_snrm2.c new file mode 100644 index 0000000000000..45e5668fafe38 --- /dev/null +++ b/sklearn/src/cblas/cblas_snrm2.c @@ -0,0 +1,44 @@ +/* + * Automatically Tuned Linear Algebra Software v3.10.0 + * (C) Copyright 1999 R. Clint Whaley + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions + * are met: + * 1. Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * 2. Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions, and the following disclaimer in the + * documentation and/or other materials provided with the distribution. + * 3. The name of the ATLAS group or the names of its contributers may + * not be used to endorse or promote products derived from this + * software without specific written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + * ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED + * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR + * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE ATLAS GROUP OR ITS CONTRIBUTORS + * BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR + * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF + * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS + * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN + * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) + * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE + * POSSIBILITY OF SUCH DAMAGE. + * + */ + +#define SREAL +#include "atlas_misc.h" +#ifdef ATL_USEPTHREADS + #include "atlas_ptalias1.h" +#endif +#include "atlas_level1.h" +#include "cblas.h" + +float cblas_snrm2(const int N, const float *X, const int incX) +{ + if (N > 0 && incX > 0) + return(ATL_snrm2(N, X, incX)); + return(0.0f); +} From fe49161fc7ee478dd035c2d0fc3a0a527e9d4ec0 Mon Sep 17 00:00:00 2001 From: Andreas Mueller Date: Fri, 11 Sep 2015 13:23:57 -0400 Subject: [PATCH 3/3] Minor fixes, remove transform for now. --- doc/whats_new.rst | 7 +- examples/manifold/plot_tsne.py | 122 - examples/manifold/plot_tsne_faces.py | 148 - sklearn/manifold/_barnes_hut_tsne.c | 8969 ++++++++++++++++--------- sklearn/manifold/_barnes_hut_tsne.pyx | 28 +- sklearn/manifold/_utils.c | 721 +- sklearn/manifold/t_sne.py | 53 +- sklearn/manifold/tests/test_t_sne.py | 25 - 8 files changed, 6094 insertions(+), 3979 deletions(-) delete mode 100644 examples/manifold/plot_tsne.py delete mode 100644 examples/manifold/plot_tsne_faces.py diff --git a/doc/whats_new.rst b/doc/whats_new.rst index bfc16d0d90db5..b4f621e00a1e8 100644 --- a/doc/whats_new.rst +++ b/doc/whats_new.rst @@ -54,6 +54,9 @@ New features Enhancements ............ + - :class:`manifold.TSNE` now supports approximate optimization via the + Barnes-Hut method, leading to much faster fitting. By Christopher Erick Moody. + (`#4025 `_) - :class:`cluster.mean_shift_.MeanShift` now supports parallel execution, as implemented in the ``mean_shift`` function. By `Martino Sorbaro`_. @@ -182,7 +185,9 @@ Enhancements , to set the seed of the pseudo random generator used in ``sag`` solver. By `Tom Dupre la Tour`_. - Added optional parameter ``warm_start`` in - :class:`linear_model.LogisticRegression`. If set to True, the solvers ``lbfgs``, ``newton-cg`` and ``sag`` will be initialized with the coefficients computed in the previous fit. By `Tom Dupre la Tour`_. + :class:`linear_model.LogisticRegression`. If set to True, the solvers + ``lbfgs``, ``newton-cg`` and ``sag`` will be initialized with the + coefficients computed in the previous fit. By `Tom Dupre la Tour`_. Bug fixes ......... diff --git a/examples/manifold/plot_tsne.py b/examples/manifold/plot_tsne.py deleted file mode 100644 index 4b346fd2e1f92..0000000000000 --- a/examples/manifold/plot_tsne.py +++ /dev/null @@ -1,122 +0,0 @@ -# Authors: Christopher Erick Moody -# License: BSD 3 clause - -from sklearn.datasets import fetch_olivetti_faces -from sklearn import manifold -from time import time -import numpy as np -import matplotlib.pyplot as plt -from matplotlib import offsetbox -from sklearn.decomposition import RandomizedPCA - - -faces = fetch_olivetti_faces() - -verbose = 20 - -#---------------------------------------------------------------------- -# Scale and visualize the embedding vectors -def plot_embedding(dataset, X, title=None, ax=None): - x_min, x_max = np.min(X, 0), np.max(X, 0) - X = (X - x_min) / (x_max - x_min) - y = dataset.target - if ax is None: - ax = plt.subplot(111) - for i in range(X.shape[0]): - ax.text(X[i, 0], X[i, 1], str(dataset.target[i]), - color=plt.cm.Set1(y[i] / 10.), - fontdict={'weight': 'bold', 'size': 30}) - - if hasattr(offsetbox, 'AnnotationBbox'): - # only print thumbnails with matplotlib > 1.0 - shown_images = np.array([[1., 1.]]) # just something big - for i in range(dataset.data.shape[0]): - shown_images = np.r_[shown_images, [X[i]]] - r, g, b, a = plt.cm.Paired(i * 1.0 / dataset.data.shape[0]) - gray = dataset.images[i] - rgb_image = np.zeros((64, 64, 3)) - rgb_image[:, :, 0] = gray * r - rgb_image[:, :, 1] = gray * g - rgb_image[:, :, 2] = gray * b - imagebox = offsetbox.AnnotationBbox( - offsetbox.OffsetImage(rgb_image), - X[i], frameon=False) - ax.add_artist(imagebox) - ax.set_xticks([]), ax.set_yticks([]) - if title is not None: - ax.set_title(title, loc='left') - -f, axs = plt.subplots(2, 2, figsize=(30, 30)) - -#---------------------------------------------------------------------- -# Fit t-SNE on all 4096 dimensions with random initialization -tsne = manifold.TSNE(n_components=2, init='random', random_state=3, - n_iter=1000, verbose=verbose, early_exaggeration=50.0, - learning_rate=100, perplexity=50) -rpca = RandomizedPCA(n_components=50) -t0 = time() -reduced = rpca.fit_transform(faces.data) -embedded = tsne.fit_transform(reduced) -t1 = time() -dt = t1 - t0 - - -t = ("Barnes-Hut t-SNE Visualization of Olivetti Faces digits\n" + - "in %1.1f seconds & initialized embedding randomly") -t = t % dt -plot_embedding(faces, embedded, title=t, ax=axs[0, 0]) - - -#------------------------------------------------------------------------- -# Fit t-SNE on all 4096 dimensions, but use PCA to initialize the embedding -tsne = manifold.TSNE(n_components=2, init='pca', random_state=3, - n_iter=1000, verbose=verbose, early_exaggeration=50.0, - learning_rate=100, perplexity=50) -t0 = time() -embedded = tsne.fit_transform(faces.data) -t1 = time() -dt = t1 - t0 - - -t = ("Barnes-Hut t-SNE Visualization of Olivetti Faces digits\n" + - "in %1.1f seconds & initialized embedding with PCA ") -t = t % dt -plot_embedding(faces, embedded, title=t, ax=axs[0, 1]) - - -#---------------------------------------------------------------------- -# Fit t-SNE on PCA-reduced dataset from 4096 dimensions to 50 -tsne = manifold.TSNE(n_components=2, init='random', random_state=3, - n_iter=1000, verbose=verbose, early_exaggeration=50.0, - learning_rate=100, perplexity=50) -rpca = RandomizedPCA(n_components=50) -t0 = time() -reduced = rpca.fit_transform(faces.data) -embedded = tsne.fit_transform(reduced) -t1 = time() -dt = t1 - t0 - - -t = ("Barnes-Hut t-SNE Visualization of Olivetti Faces digits\n" + - "in %1.1f seconds & randomized PCA preprocessing") -t = t % dt -plot_embedding(faces, embedded, title=t, ax=axs[1, 0]) - - -#---------------------------------------------------------------------- -# Fit t-SNE using PCA and the exact method -tsne = manifold.TSNE(n_components=2, init='random', random_state=3, - method='exact', n_iter=10000, verbose=verbose, - learning_rate=100, perplexity=50) -t0 = time() -embedded = tsne.fit_transform(faces.data) -t1 = time() -dt = t1 - t0 - - -t = ("Barnes-Hut t-SNE Visualization of Olivetti Faces digits\n" + - "in %1.1f seconds with random initialization and exact method") -t = t % dt -plot_embedding(faces, embedded, title=t, ax=axs[1, 1]) - -plt.show() diff --git a/examples/manifold/plot_tsne_faces.py b/examples/manifold/plot_tsne_faces.py deleted file mode 100644 index 2f78e422c6fcf..0000000000000 --- a/examples/manifold/plot_tsne_faces.py +++ /dev/null @@ -1,148 +0,0 @@ -""" -=================================== -Comparison of t-SNE methods and options -=================================== - -A comparison of t-SNE applied to the Olivetti faces data. The 'exact' and -'barnes-hut' methods are visualized, as well as init='pca' and init='random'. -In addition to varying method & init, the script also compares preprocessing -the input data by reducing the dimensionality via PCA and also varying the -perplexity. - -For a discussion and comparison of these algorithms, see the -:ref:`manifold module page ` - -""" -# Authors: Christopher Erick Moody -# License: BSD 3 clause - -from sklearn.datasets import fetch_olivetti_faces -from sklearn.decomposition import RandomizedPCA -from sklearn import manifold -from matplotlib import offsetbox -import matplotlib.pyplot as plt -import numpy as np -from time import time - - -faces = fetch_olivetti_faces() - -verbose = 5 - -#---------------------------------------------------------------------- -# Scale and visualize the embedding vectors -def plot_embedding(dataset, X, title=None, ax=None): - x_min, x_max = np.min(X, 0), np.max(X, 0) - X = (X - x_min) / (x_max - x_min) - y = dataset.target - if ax is None: - plt.figure(figsize=(18, 15)) - ax = plt.gca() - for i in range(X.shape[0]): - ax.text(X[i, 0], X[i, 1], str(dataset.target[i]), - color=plt.cm.Set1(y[i] / 10.), - fontdict={'weight': 'bold', 'size': 30}) - - if hasattr(offsetbox, 'AnnotationBbox'): - # only print thumbnails with matplotlib > 1.0 - shown_images = np.array([[1., 1.]]) # just something big - for i in range(dataset.data.shape[0]): - shown_images = np.r_[shown_images, [X[i]]] - r, g, b, a = plt.cm.Paired(i * 1.0 / dataset.data.shape[0]) - gray = dataset.images[i] - rgb_image = np.zeros((64, 64, 3)) - rgb_image[:, :, 0] = gray * r - rgb_image[:, :, 1] = gray * g - rgb_image[:, :, 2] = gray * b - imagebox = offsetbox.AnnotationBbox( - offsetbox.OffsetImage(rgb_image), - X[i], frameon=False) - ax.add_artist(imagebox) - ax.set_xticks([]), ax.set_yticks([]) - if title is not None: - ax.set_title(title, loc='left') - - -#---------------------------------------------------------------------- -# Fit t-SNE on 50 PCA-reduced dimensions with random initialization. -# We will frequently want to reduce the dimensionality when we have many -# dimensions since the t-SNE complexity grows linearly with the dimensionality. -tsne = manifold.TSNE(n_components=2, init='random', random_state=3, - n_iter=1000, verbose=verbose, early_exaggeration=50.0, - learning_rate=100, perplexity=50) -rpca = RandomizedPCA(n_components=50) -time_start = time() -reduced = rpca.fit_transform(faces.data) -embedded = tsne.fit_transform(reduced) -time_end = time() -dt = time_end - time_start - - -title = ("Barnes-Hut t-SNE Visualization of Olivetti Faces\n" + - "in %1.1f seconds on 50-dimensional PCA-reduced data ") -title = title % dt -plot_embedding(faces, embedded, title=title) - - -#------------------------------------------------------------------------- -# Fit t-SNE on all 4096 dimensions, but use PCA to initialize the embedding -# Initializing the embedding with PCA allows the final emebedding to preserve -# global structure leaving t-SNE to optimize the local structure -tsne = manifold.TSNE(n_components=2, init='pca', random_state=3, - n_iter=1000, verbose=verbose, early_exaggeration=50.0, - learning_rate=100, perplexity=5) -time_start = time() -embedded = tsne.fit_transform(faces.data) -time_end = time() -dt = time_end - time_start - - -title = ("Barnes-Hut t-SNE Visualization of Olivetti Faces\n" + - "in %1.1f seconds & initialized embedding with PCA ") -title = title % dt -plot_embedding(faces, embedded, title=title) - - -#---------------------------------------------------------------------- -# Fit t-SNE on 50 PCA-reduced dimensions with random initialization, but reduce -# the perplexity. Note that the increased perplexity roughly increases the -# number of neighbors, which effectively decreases the number of clusters. -# For the example here, theres about 5 images per person, which with a -# perplexity of 50 forces multiple face-clusters to come together -tsne = manifold.TSNE(n_components=2, init='random', random_state=3, - n_iter=1000, verbose=verbose, early_exaggeration=50.0, - learning_rate=100, perplexity=50) -rpca = RandomizedPCA(n_components=50) -time_start = time() -reduced = rpca.fit_transform(faces.data) -embedded = tsne.fit_transform(reduced) -time_end = time() -dt = time_end - time_start - - -title = ("Barnes-Hut t-SNE Visualization of Olivetti Faces\n" + - "in %1.1f seconds on 50-dimensional PCA-reduced data\n" + - "with perplexity increased from 5 to 50") -title = title % dt -plot_embedding(faces, embedded, title=title) - - -#---------------------------------------------------------------------- -# Fit t-SNE by random embedding and the exact method. The exact method -# is similar to Barnes-Hut, but this visualization reinforces the idea -# that the two methods yield similar results -tsne = manifold.TSNE(n_components=2, init='random', random_state=3, - method='exact', n_iter=10000, verbose=verbose, - learning_rate=100, perplexity=5) -time_start = time() -embedded = tsne.fit_transform(faces.data) -time_end = time() -dt = time_end - time_start - - -title = ("Exact t-SNE Visualization of Olivetti Faces\n" + - "in %1.1f seconds with random initialization") -title = title % dt -plot_embedding(faces, embedded, title=title) - -plt.show() diff --git a/sklearn/manifold/_barnes_hut_tsne.c b/sklearn/manifold/_barnes_hut_tsne.c index 9d741bd051a20..d606f2fc096b7 100644 --- a/sklearn/manifold/_barnes_hut_tsne.c +++ b/sklearn/manifold/_barnes_hut_tsne.c @@ -1,25 +1,13 @@ -/* Generated by Cython 0.21 */ +/* Generated by Cython 0.23.1 */ #define PY_SSIZE_T_CLEAN -#ifndef CYTHON_USE_PYLONG_INTERNALS -#ifdef PYLONG_BITS_IN_DIGIT -#define CYTHON_USE_PYLONG_INTERNALS 0 -#else -#include "pyconfig.h" -#ifdef PYLONG_BITS_IN_DIGIT -#define CYTHON_USE_PYLONG_INTERNALS 1 -#else -#define CYTHON_USE_PYLONG_INTERNALS 0 -#endif -#endif -#endif #include "Python.h" #ifndef Py_PYTHON_H #error Python headers needed to compile C extensions, please install development version of Python. #elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000) #error Cython requires Python 2.6+ or Python 3.2+. #else -#define CYTHON_ABI "0_21" +#define CYTHON_ABI "0_23_1" #include #ifndef offsetof #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) @@ -54,35 +42,40 @@ #define CYTHON_COMPILING_IN_PYPY 0 #define CYTHON_COMPILING_IN_CPYTHON 1 #endif -#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 +#if !defined(CYTHON_USE_PYLONG_INTERNALS) && CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x02070000 +#define CYTHON_USE_PYLONG_INTERNALS 1 +#endif +#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag) #define Py_OptimizeFlag 0 #endif #define __PYX_BUILD_PY_SSIZE_T "n" #define CYTHON_FORMAT_SSIZE_T "z" #if PY_MAJOR_VERSION < 3 #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ + #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #define __Pyx_DefaultClassType PyClass_Type #else #define __Pyx_BUILTIN_MODULE_NAME "builtins" - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ + #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #define __Pyx_DefaultClassType PyType_Type #endif -#if PY_MAJOR_VERSION >= 3 +#ifndef Py_TPFLAGS_CHECKTYPES #define Py_TPFLAGS_CHECKTYPES 0 +#endif +#ifndef Py_TPFLAGS_HAVE_INDEX #define Py_TPFLAGS_HAVE_INDEX 0 #endif -#if PY_MAJOR_VERSION >= 3 +#ifndef Py_TPFLAGS_HAVE_NEWBUFFER #define Py_TPFLAGS_HAVE_NEWBUFFER 0 #endif -#if PY_VERSION_HEX < 0x030400a1 && !defined(Py_TPFLAGS_HAVE_FINALIZE) +#ifndef Py_TPFLAGS_HAVE_FINALIZE #define Py_TPFLAGS_HAVE_FINALIZE 0 #endif #if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) #define CYTHON_PEP393_ENABLED 1 - #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \ + #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\ 0 : _PyUnicode_Ready((PyObject *)(op))) #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) @@ -103,9 +96,12 @@ #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) #else #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) - #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ? \ + #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\ PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) #endif +#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains) + #define PyUnicode_Contains(u, s) PySequence_Contains(u, s) +#endif #define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b)) #define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b)) #if PY_MAJOR_VERSION >= 3 @@ -151,6 +147,11 @@ #if PY_MAJOR_VERSION >= 3 #define PyBoolObject PyLongObject #endif +#if PY_MAJOR_VERSION >= 3 && CYTHON_COMPILING_IN_PYPY + #ifndef PyUnicode_InternFromString + #define PyUnicode_InternFromString(s) PyUnicode_FromString(s) + #endif +#endif #if PY_VERSION_HEX < 0x030200A4 typedef long Py_hash_t; #define __Pyx_PyInt_FromHash_t PyInt_FromLong @@ -160,18 +161,22 @@ #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t #endif #if PY_MAJOR_VERSION >= 3 - #define PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func)) + #define __Pyx_PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func)) +#else + #define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass) #endif -#ifndef CYTHON_INLINE - #if defined(__GNUC__) - #define CYTHON_INLINE __inline__ - #elif defined(_MSC_VER) - #define CYTHON_INLINE __inline - #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L - #define CYTHON_INLINE inline - #else - #define CYTHON_INLINE - #endif +#if PY_VERSION_HEX >= 0x030500B1 +#define __Pyx_PyAsyncMethodsStruct PyAsyncMethods +#define __Pyx_PyType_AsAsync(obj) (Py_TYPE(obj)->tp_as_async) +#elif CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 +typedef struct { + unaryfunc am_await; + unaryfunc am_aiter; + unaryfunc am_anext; +} __Pyx_PyAsyncMethodsStruct; +#define __Pyx_PyType_AsAsync(obj) ((__Pyx_PyAsyncMethodsStruct*) (Py_TYPE(obj)->tp_reserved)) +#else +#define __Pyx_PyType_AsAsync(obj) NULL #endif #ifndef CYTHON_RESTRICT #if defined(__GNUC__) @@ -184,24 +189,33 @@ #define CYTHON_RESTRICT #endif #endif +#define __Pyx_void_to_None(void_result) (void_result, Py_INCREF(Py_None), Py_None) + +#ifndef CYTHON_INLINE + #if defined(__GNUC__) + #define CYTHON_INLINE __inline__ + #elif defined(_MSC_VER) + #define CYTHON_INLINE __inline + #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define CYTHON_INLINE inline + #else + #define CYTHON_INLINE + #endif +#endif + +#if defined(WIN32) || defined(MS_WINDOWS) + #define _USE_MATH_DEFINES +#endif +#include #ifdef NAN #define __PYX_NAN() ((float) NAN) #else static CYTHON_INLINE float __PYX_NAN() { - /* Initialize NaN. The sign is irrelevant, an exponent with all bits 1 and - a nonzero mantissa means NaN. If the first bit in the mantissa is 1, it is - a quiet NaN. */ float value; memset(&value, 0xFF, sizeof(value)); return value; } #endif -#ifdef __cplusplus -template -void __Pyx_call_destructor(T* x) { - x->~T(); -} -#endif #if PY_MAJOR_VERSION >= 3 @@ -220,10 +234,6 @@ void __Pyx_call_destructor(T* x) { #endif #endif -#if defined(WIN32) || defined(MS_WINDOWS) -#define _USE_MATH_DEFINES -#endif -#include #define __PYX_HAVE__sklearn__manifold___barnes_hut_tsne #define __PYX_HAVE_API__sklearn__manifold___barnes_hut_tsne #include "string.h" @@ -257,6 +267,13 @@ void __Pyx_call_destructor(T* x) { # define CYTHON_UNUSED # endif #endif +#ifndef CYTHON_NCP_UNUSED +# if CYTHON_COMPILING_IN_CPYTHON +# define CYTHON_NCP_UNUSED +# else +# define CYTHON_NCP_UNUSED CYTHON_UNUSED +# endif +#endif typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding; const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; @@ -265,16 +282,34 @@ typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding; #define __PYX_DEFAULT_STRING_ENCODING "" #define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString #define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize -#define __Pyx_fits_Py_ssize_t(v, type, is_signed) ( \ - (sizeof(type) < sizeof(Py_ssize_t)) || \ - (sizeof(type) > sizeof(Py_ssize_t) && \ - likely(v < (type)PY_SSIZE_T_MAX || \ - v == (type)PY_SSIZE_T_MAX) && \ - (!is_signed || likely(v > (type)PY_SSIZE_T_MIN || \ - v == (type)PY_SSIZE_T_MIN))) || \ - (sizeof(type) == sizeof(Py_ssize_t) && \ - (is_signed || likely(v < (type)PY_SSIZE_T_MAX || \ +#define __Pyx_uchar_cast(c) ((unsigned char)c) +#define __Pyx_long_cast(x) ((long)x) +#define __Pyx_fits_Py_ssize_t(v, type, is_signed) (\ + (sizeof(type) < sizeof(Py_ssize_t)) ||\ + (sizeof(type) > sizeof(Py_ssize_t) &&\ + likely(v < (type)PY_SSIZE_T_MAX ||\ + v == (type)PY_SSIZE_T_MAX) &&\ + (!is_signed || likely(v > (type)PY_SSIZE_T_MIN ||\ + v == (type)PY_SSIZE_T_MIN))) ||\ + (sizeof(type) == sizeof(Py_ssize_t) &&\ + (is_signed || likely(v < (type)PY_SSIZE_T_MAX ||\ v == (type)PY_SSIZE_T_MAX))) ) +#if defined (__cplusplus) && __cplusplus >= 201103L + #include + #define __Pyx_sst_abs(value) std::abs(value) +#elif SIZEOF_INT >= SIZEOF_SIZE_T + #define __Pyx_sst_abs(value) abs(value) +#elif SIZEOF_LONG >= SIZEOF_SIZE_T + #define __Pyx_sst_abs(value) labs(value) +#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define __Pyx_sst_abs(value) llabs(value) +#elif defined (_MSC_VER) && defined (_M_X64) + #define __Pyx_sst_abs(value) _abs64(value) +#elif defined (__GNUC__) + #define __Pyx_sst_abs(value) __builtin_llabs(value) +#else + #define __Pyx_sst_abs(value) ((value<0) ? -value : value) +#endif static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*); static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length); #define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s)) @@ -291,11 +326,11 @@ static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*); #endif #define __Pyx_PyObject_AsSString(s) ((signed char*) __Pyx_PyObject_AsString(s)) #define __Pyx_PyObject_AsUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_FromUString(s) __Pyx_PyObject_FromString((const char*)s) -#define __Pyx_PyBytes_FromUString(s) __Pyx_PyBytes_FromString((const char*)s) -#define __Pyx_PyByteArray_FromUString(s) __Pyx_PyByteArray_FromString((const char*)s) -#define __Pyx_PyStr_FromUString(s) __Pyx_PyStr_FromString((const char*)s) -#define __Pyx_PyUnicode_FromUString(s) __Pyx_PyUnicode_FromString((const char*)s) +#define __Pyx_PyObject_FromCString(s) __Pyx_PyObject_FromString((const char*)s) +#define __Pyx_PyBytes_FromCString(s) __Pyx_PyBytes_FromString((const char*)s) +#define __Pyx_PyByteArray_FromCString(s) __Pyx_PyByteArray_FromString((const char*)s) +#define __Pyx_PyStr_FromCString(s) __Pyx_PyStr_FromString((const char*)s) +#define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s) #if PY_MAJOR_VERSION < 3 static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) { @@ -309,8 +344,9 @@ static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) #define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u)) #define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode #define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode -#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None) -#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False)) +#define __Pyx_NewRef(obj) (Py_INCREF(obj), obj) +#define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None) +#define __Pyx_PyBool_FromLong(b) ((b) ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False)) static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x); static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); @@ -331,7 +367,7 @@ static int __Pyx_init_sys_getdefaultencoding_params(void) { const char* default_encoding_c; sys = PyImport_ImportModule("sys"); if (!sys) goto bad; - default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); + default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL); Py_DECREF(sys); if (!default_encoding) goto bad; default_encoding_c = PyBytes_AsString(default_encoding); @@ -493,21 +529,22 @@ typedef struct { #define CYTHON_ATOMICS 1 #endif #define __pyx_atomic_int_type int -#if CYTHON_ATOMICS && __GNUC__ >= 4 && (__GNUC_MINOR__ > 1 || \ - (__GNUC_MINOR__ == 1 && __GNUC_PATCHLEVEL >= 2)) && \ +#if CYTHON_ATOMICS && __GNUC__ >= 4 && (__GNUC_MINOR__ > 1 ||\ + (__GNUC_MINOR__ == 1 && __GNUC_PATCHLEVEL >= 2)) &&\ !defined(__i386__) #define __pyx_atomic_incr_aligned(value, lock) __sync_fetch_and_add(value, 1) #define __pyx_atomic_decr_aligned(value, lock) __sync_fetch_and_sub(value, 1) #ifdef __PYX_DEBUG_ATOMICS #warning "Using GNU atomics" #endif -#elif CYTHON_ATOMICS && MSC_VER +#elif CYTHON_ATOMICS && defined(_MSC_VER) && 0 #include + #undef __pyx_atomic_int_type #define __pyx_atomic_int_type LONG #define __pyx_atomic_incr_aligned(value, lock) InterlockedIncrement(value) #define __pyx_atomic_decr_aligned(value, lock) InterlockedDecrement(value) #ifdef __PYX_DEBUG_ATOMICS - #warning "Using MSVC atomics" + #pragma message ("Using MSVC atomics") #endif #elif CYTHON_ATOMICS && (defined(__ICC) || defined(__INTEL_COMPILER)) && 0 #define __pyx_atomic_incr_aligned(value, lock) _InterlockedIncrement(value) @@ -524,19 +561,19 @@ typedef struct { #endif typedef volatile __pyx_atomic_int_type __pyx_atomic_int; #if CYTHON_ATOMICS - #define __pyx_add_acquisition_count(memview) \ + #define __pyx_add_acquisition_count(memview)\ __pyx_atomic_incr_aligned(__pyx_get_slice_count_pointer(memview), memview->lock) - #define __pyx_sub_acquisition_count(memview) \ + #define __pyx_sub_acquisition_count(memview)\ __pyx_atomic_decr_aligned(__pyx_get_slice_count_pointer(memview), memview->lock) #else - #define __pyx_add_acquisition_count(memview) \ + #define __pyx_add_acquisition_count(memview)\ __pyx_add_acquisition_count_locked(__pyx_get_slice_count_pointer(memview), memview->lock) - #define __pyx_sub_acquisition_count(memview) \ + #define __pyx_sub_acquisition_count(memview)\ __pyx_sub_acquisition_count_locked(__pyx_get_slice_count_pointer(memview), memview->lock) #endif -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":723 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":725 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< @@ -545,7 +582,7 @@ typedef volatile __pyx_atomic_int_type __pyx_atomic_int; */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":724 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":726 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< @@ -554,7 +591,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":725 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":727 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< @@ -563,7 +600,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t; */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":726 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":728 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< @@ -572,7 +609,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t; */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":730 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":732 * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< @@ -581,7 +618,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t; */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":731 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":733 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< @@ -590,7 +627,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":732 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":734 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< @@ -599,7 +636,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t; */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":733 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":735 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< @@ -608,7 +645,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t; */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":737 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":739 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< @@ -617,7 +654,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t; */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":738 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":740 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< @@ -626,7 +663,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":747 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":749 * # The int types are mapped a bit surprising -- * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t # <<<<<<<<<<<<<< @@ -635,7 +672,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t; */ typedef npy_long __pyx_t_5numpy_int_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":748 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":750 * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< @@ -644,7 +681,7 @@ typedef npy_long __pyx_t_5numpy_int_t; */ typedef npy_longlong __pyx_t_5numpy_long_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":749 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":751 * ctypedef npy_long int_t * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< @@ -653,7 +690,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t; */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":751 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":753 * ctypedef npy_longlong longlong_t * * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< @@ -662,7 +699,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t; */ typedef npy_ulong __pyx_t_5numpy_uint_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":752 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":754 * * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< @@ -671,7 +708,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":753 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":755 * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< @@ -680,7 +717,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":755 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":757 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< @@ -689,7 +726,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":756 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":758 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< @@ -698,7 +735,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t; */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":758 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":760 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< @@ -707,7 +744,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t; */ typedef npy_double __pyx_t_5numpy_float_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":759 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":761 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< @@ -716,7 +753,7 @@ typedef npy_double __pyx_t_5numpy_float_t; */ typedef npy_double __pyx_t_5numpy_double_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":760 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":762 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< @@ -751,7 +788,7 @@ struct __pyx_MemviewEnum_obj; struct __pyx_memoryview_obj; struct __pyx_memoryviewslice_obj; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":762 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":764 * ctypedef npy_longdouble longdouble_t * * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< @@ -760,7 +797,7 @@ struct __pyx_memoryviewslice_obj; */ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":763 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":765 * * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< @@ -769,7 +806,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; */ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":764 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":766 * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< @@ -778,7 +815,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; */ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":766 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":768 * ctypedef npy_clongdouble clongdouble_t * * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< @@ -789,7 +826,7 @@ typedef npy_cdouble __pyx_t_5numpy_complex_t; struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node; struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree; -/* "sklearn/manifold/_barnes_hut_tsne.pyx":28 +/* "sklearn/manifold/_barnes_hut_tsne.pyx":30 * # It allows us to write printf debugging lines * # and remove them at compile time * cdef enum: # <<<<<<<<<<<<<< @@ -800,7 +837,7 @@ enum { __pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG = 0 }; -/* "sklearn/manifold/_barnes_hut_tsne.pyx":42 +/* "sklearn/manifold/_barnes_hut_tsne.pyx":44 * * * cdef struct Node: # <<<<<<<<<<<<<< @@ -824,7 +861,7 @@ struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node { struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *tree; }; -/* "sklearn/manifold/_barnes_hut_tsne.pyx":78 +/* "sklearn/manifold/_barnes_hut_tsne.pyx":80 * Tree* tree * * cdef struct Tree: # <<<<<<<<<<<<<< @@ -840,7 +877,7 @@ struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree { int n_cell_per_node; }; -/* "View.MemoryView":99 +/* "View.MemoryView":101 * * @cname("__pyx_array") * cdef class array: # <<<<<<<<<<<<<< @@ -864,7 +901,7 @@ struct __pyx_array_obj { }; -/* "View.MemoryView":269 +/* "View.MemoryView":271 * * @cname('__pyx_MemviewEnum') * cdef class Enum(object): # <<<<<<<<<<<<<< @@ -877,7 +914,7 @@ struct __pyx_MemviewEnum_obj { }; -/* "View.MemoryView":302 +/* "View.MemoryView":304 * * @cname('__pyx_memoryview') * cdef class memoryview(object): # <<<<<<<<<<<<<< @@ -900,7 +937,7 @@ struct __pyx_memoryview_obj { }; -/* "View.MemoryView":922 +/* "View.MemoryView":923 * * @cname('__pyx_memoryviewslice') * cdef class _memoryviewslice(memoryview): # <<<<<<<<<<<<<< @@ -917,7 +954,7 @@ struct __pyx_memoryviewslice_obj { -/* "View.MemoryView":302 +/* "View.MemoryView":304 * * @cname('__pyx_memoryview') * cdef class memoryview(object): # <<<<<<<<<<<<<< @@ -937,7 +974,7 @@ struct __pyx_vtabstruct_memoryview { static struct __pyx_vtabstruct_memoryview *__pyx_vtabptr_memoryview; -/* "View.MemoryView":922 +/* "View.MemoryView":923 * * @cname('__pyx_memoryviewslice') * cdef class _memoryviewslice(memoryview): # <<<<<<<<<<<<<< @@ -949,6 +986,8 @@ struct __pyx_vtabstruct__memoryviewslice { struct __pyx_vtabstruct_memoryview __pyx_base; }; static struct __pyx_vtabstruct__memoryviewslice *__pyx_vtabptr__memoryviewslice; + +/* --- Runtime support code (head) --- */ #ifndef CYTHON_REFNANNY #define CYTHON_REFNANNY 0 #endif @@ -965,19 +1004,19 @@ static struct __pyx_vtabstruct__memoryviewslice *__pyx_vtabptr__memoryviewslice; static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname); #define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL; #ifdef WITH_THREAD - #define __Pyx_RefNannySetupContext(name, acquire_gil) \ - if (acquire_gil) { \ - PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); \ - __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__); \ - PyGILState_Release(__pyx_gilstate_save); \ - } else { \ - __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__); \ + #define __Pyx_RefNannySetupContext(name, acquire_gil)\ + if (acquire_gil) {\ + PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();\ + __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__);\ + PyGILState_Release(__pyx_gilstate_save);\ + } else {\ + __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__);\ } #else - #define __Pyx_RefNannySetupContext(name, acquire_gil) \ + #define __Pyx_RefNannySetupContext(name, acquire_gil)\ __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__) #endif - #define __Pyx_RefNannyFinishContext() \ + #define __Pyx_RefNannyFinishContext()\ __Pyx_RefNanny->FinishContext(&__pyx_refnanny) #define __Pyx_INCREF(r) __Pyx_RefNanny->INCREF(__pyx_refnanny, (PyObject *)(r), __LINE__) #define __Pyx_DECREF(r) __Pyx_RefNanny->DECREF(__pyx_refnanny, (PyObject *)(r), __LINE__) @@ -1000,13 +1039,13 @@ static struct __pyx_vtabstruct__memoryviewslice *__pyx_vtabptr__memoryviewslice; #define __Pyx_XGOTREF(r) #define __Pyx_XGIVEREF(r) #endif -#define __Pyx_XDECREF_SET(r, v) do { \ - PyObject *tmp = (PyObject *) r; \ - r = v; __Pyx_XDECREF(tmp); \ +#define __Pyx_XDECREF_SET(r, v) do {\ + PyObject *tmp = (PyObject *) r;\ + r = v; __Pyx_XDECREF(tmp);\ } while (0) -#define __Pyx_DECREF_SET(r, v) do { \ - PyObject *tmp = (PyObject *) r; \ - r = v; __Pyx_DECREF(tmp); \ +#define __Pyx_DECREF_SET(r, v) do {\ + PyObject *tmp = (PyObject *) r;\ + r = v; __Pyx_DECREF(tmp);\ } while (0) #define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0) #define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0) @@ -1042,13 +1081,20 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg); +#if CYTHON_COMPILING_IN_CPYTHON +static PyObject* __Pyx_PyFloat_DivideObjC(PyObject *op1, PyObject *op2, double floatval, int inplace); +#else +#define __Pyx_PyFloat_DivideObjC(op1, op2, floatval, inplace)\ + ((inplace ? __Pyx_PyNumber_InPlaceDivide(op1, op2) : __Pyx_PyNumber_Divide(op1, op2))) + #endif + static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); -static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \ - PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \ +static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[],\ + PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args,\ const char* function_name); static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); @@ -1059,6 +1105,20 @@ static CYTHON_INLINE int __Pyx_IterFinish(void); static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); +#if CYTHON_COMPILING_IN_CPYTHON +static PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, long intval, int inplace); +#else +#define __Pyx_PyInt_EqObjC(op1, op2, intval, inplace)\ + PyObject_RichCompare(op1, op2, Py_EQ) + #endif + +#if CYTHON_COMPILING_IN_CPYTHON +static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, long intval, int inplace); +#else +#define __Pyx_PyInt_SubtractObjC(op1, op2, intval, inplace)\ + (inplace ? PyNumber_InPlaceSubtract(op1, op2) : PyNumber_Subtract(op1, op2)) +#endif + static CYTHON_INLINE int __Pyx_GetBufferAndValidate(Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack); static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info); @@ -1093,6 +1153,26 @@ static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyOb static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); +#if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY +static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { + PyObject *value; + value = PyDict_GetItemWithError(d, key); + if (unlikely(!value)) { + if (!PyErr_Occurred()) { + PyObject* args = PyTuple_Pack(1, key); + if (likely(args)) + PyErr_SetObject(PyExc_KeyError, args); + Py_XDECREF(args); + } + return NULL; + } + Py_INCREF(value); + return value; +} +#else + #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key) +#endif + static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); @@ -1112,11 +1192,8 @@ static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int #define __Pyx_PyString_Equals __Pyx_PyBytes_Equals #endif -#ifndef __PYX_FORCE_INIT_THREADS - #define __PYX_FORCE_INIT_THREADS 0 -#endif - -#define UNARY_NEG_WOULD_OVERFLOW(x) (((x) < 0) & ((unsigned long)(x) == 0-(unsigned long)(x))) +#define UNARY_NEG_WOULD_OVERFLOW(x)\ + (((x) < 0) & ((unsigned long)(x) == 0-(unsigned long)(x))) static CYTHON_UNUSED int __pyx_array_getbuffer(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/ static PyObject *get_memview(PyObject *__pyx_v_self); /*proto*/ @@ -1134,20 +1211,22 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); -#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \ - __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) : \ - (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) : \ +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); + +#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ + __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) :\ + (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) :\ __Pyx_GetItemInt_Generic(o, to_py_func(i)))) -#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \ - __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \ +#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ + __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL)) static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, int wraparound, int boundscheck); -#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \ - __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \ +#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ + __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL)) static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, int wraparound, int boundscheck); @@ -1181,6 +1260,13 @@ static PyObject *__pyx_memoryview_get_ndim(PyObject *__pyx_v_self); /*proto*/ static PyObject *__pyx_memoryview_get_itemsize(PyObject *__pyx_v_self); /*proto*/ static PyObject *__pyx_memoryview_get_nbytes(PyObject *__pyx_v_self); /*proto*/ static PyObject *__pyx_memoryview_get_size(PyObject *__pyx_v_self); /*proto*/ +#if CYTHON_COMPILING_IN_CPYTHON +static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, long intval, int inplace); +#else +#define __Pyx_PyInt_AddObjC(op1, op2, intval, inplace)\ + (inplace ? PyNumber_InPlaceAdd(op1, op2) : PyNumber_Add(op1, op2)) +#endif + static CYTHON_INLINE int __Pyx_PyList_Extend(PyObject* L, PyObject* v) { #if CYTHON_COMPILING_IN_CPYTHON PyObject* none = _PyList_Extend((PyListObject*)L, v); @@ -1211,10 +1297,14 @@ static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname); +#ifndef __PYX_FORCE_INIT_THREADS + #define __PYX_FORCE_INIT_THREADS 0 +#endif + static PyObject *__pyx_memoryviewslice__get__base(PyObject *__pyx_v_self); /*proto*/ static void __Pyx_WriteUnraisable(const char *name, int clineno, int lineno, const char *filename, - int full_traceback); + int full_traceback, int nogil); static int __Pyx_SetVtable(PyObject *dict, void *vtable); @@ -1260,8 +1350,6 @@ typedef struct { static Py_ssize_t __Pyx_zeros[] = {0, 0, 0, 0, 0, 0, 0, 0}; static Py_ssize_t __Pyx_minusones[] = {-1, -1, -1, -1, -1, -1, -1, -1}; -static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); - static int __pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b); static int __Pyx_ValidateAndInit_memviewslice( @@ -1276,15 +1364,15 @@ static int __Pyx_ValidateAndInit_memviewslice( static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_float(PyObject *); -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_long(PyObject *); +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_nn___pyx_t_5numpy_int64_t(PyObject *); static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_long(PyObject *); +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_nn___pyx_t_5numpy_int64_t(PyObject *); -static CYTHON_INLINE long __Pyx_pow_long(long, long); /* proto */ +static CYTHON_INLINE long __Pyx_pow_long(long, long); static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); @@ -1292,11 +1380,15 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); static CYTHON_INLINE PyObject* __Pyx_PyInt_From_clock_t(clock_t value); +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_npy_int64(npy_int64 value); + static PyObject *__pyx_memview_get_float(const char *itemp); static int __pyx_memview_set_float(const char *itemp, PyObject *obj); -static PyObject *__pyx_memview_get_long(const char *itemp); -static int __pyx_memview_set_long(const char *itemp, PyObject *obj); +static CYTHON_INLINE npy_int64 __Pyx_PyInt_As_npy_int64(PyObject *); + +static PyObject *__pyx_memview_get_nn___pyx_t_5numpy_int64_t(const char *itemp); +static int __pyx_memview_set_nn___pyx_t_5numpy_int64_t(const char *itemp, PyObject *obj); #if CYTHON_CCOMPLEX #ifdef __cplusplus @@ -1396,6 +1488,8 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do #endif #endif +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value); + static int __pyx_memviewslice_is_contig(const __Pyx_memviewslice *mvs, char order, int ndim); @@ -1451,15 +1545,17 @@ static PyObject *__pyx_memoryviewslice_assign_item_from_object(struct __pyx_memo /* Module declarations from 'cpython.buffer' */ -/* Module declarations from 'cpython.ref' */ - -/* Module declarations from 'cpython.object' */ - /* Module declarations from '__builtin__' */ /* Module declarations from 'cpython.type' */ static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0; +/* Module declarations from 'cpython' */ + +/* Module declarations from 'cpython.object' */ + +/* Module declarations from 'cpython.ref' */ + /* Module declarations from 'numpy' */ /* Module declarations from 'numpy' */ @@ -1475,6 +1571,7 @@ static PyTypeObject *__pyx_array_type = 0; static PyTypeObject *__pyx_MemviewEnum_type = 0; static PyTypeObject *__pyx_memoryview_type = 0; static PyTypeObject *__pyx_memoryviewslice_type = 0; +static char *__pyx_v_7sklearn_8manifold_16_barnes_hut_tsne_EMPTY_STRING; static float __pyx_v_7sklearn_8manifold_16_barnes_hut_tsne_EPSILON; static PyObject *generic = 0; static PyObject *strided = 0; @@ -1494,7 +1591,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_tree(struct __pyx_ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_recursive(struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *, struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *, long *); /*proto*/ static long __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_count_points(struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *, long); /*proto*/ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice, struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *, float, float, long, long); /*proto*/ -static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_positive(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice, float *, int, float, float, long, int); /*proto*/ +static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_positive(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice, float *, int, float, float, __pyx_t_5numpy_int64_t, int); /*proto*/ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negative(__Pyx_memviewslice, __Pyx_memviewslice, float *, struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *, float *, float, float, long, long); /*proto*/ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_non_edge_forces(struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *, float, long, float *, float *, float *, long *, float *, long *); /*proto*/ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_error(__Pyx_memviewslice, __Pyx_memviewslice, __Pyx_memviewslice, float, int, int); /*proto*/ @@ -1532,7 +1629,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *, Py_ssize_t *, Py_ static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *, int, size_t, void *, int); /*proto*/ static void __pyx_memoryview__slice_assign_scalar(char *, Py_ssize_t *, Py_ssize_t *, int, size_t, void *); /*proto*/ static __Pyx_TypeInfo __Pyx_TypeInfo_float = { "float", NULL, sizeof(float), { 0 }, 0, 'R', 0, 0 }; -static __Pyx_TypeInfo __Pyx_TypeInfo_long = { "long", NULL, sizeof(long), { 0 }, 0, IS_UNSIGNED(long) ? 'U' : 'I', IS_UNSIGNED(long), 0 }; +static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_int64_t = { "int64_t", NULL, sizeof(__pyx_t_5numpy_int64_t), { 0 }, 0, IS_UNSIGNED(__pyx_t_5numpy_int64_t) ? 'U' : 'I', IS_UNSIGNED(__pyx_t_5numpy_int64_t), 0 }; #define __Pyx_MODULE_NAME "sklearn.manifold._barnes_hut_tsne" int __pyx_module_is_main_sklearn__manifold___barnes_hut_tsne = 0; @@ -1544,52 +1641,8 @@ static PyObject *__pyx_builtin_MemoryError; static PyObject *__pyx_builtin_enumerate; static PyObject *__pyx_builtin_Ellipsis; static PyObject *__pyx_builtin_TypeError; -static PyObject *__pyx_builtin_xrange; static PyObject *__pyx_builtin_id; static PyObject *__pyx_builtin_IndexError; -static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_calculate_edge(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_pos_output); /* proto */ -static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_pij_input, __Pyx_memviewslice __pyx_v_pos_output, __Pyx_memviewslice __pyx_v_neighbors, __Pyx_memviewslice __pyx_v_forces, float __pyx_v_theta, int __pyx_v_n_dimensions, int __pyx_v_verbose, float __pyx_v_dof, long __pyx_v_skip_num_points); /* proto */ -static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_4check_quadtree(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_X, __Pyx_memviewslice __pyx_v_counts); /* proto */ -static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_6test_index2offset(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ -static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_8test_index_offset(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ -static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ -static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */ -static int __pyx_array_MemoryView_5array___cinit__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_shape, Py_ssize_t __pyx_v_itemsize, PyObject *__pyx_v_format, PyObject *__pyx_v_mode, int __pyx_v_allocate_buffer); /* proto */ -static int __pyx_array_getbuffer_MemoryView_5array_2__getbuffer__(struct __pyx_array_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ -static void __pyx_array_MemoryView_5array_4__dealloc__(struct __pyx_array_obj *__pyx_v_self); /* proto */ -static PyObject *get_memview_MemoryView_5array_7memview___get__(struct __pyx_array_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_array_MemoryView_5array_6__getattr__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_attr); /* proto */ -static PyObject *__pyx_array_MemoryView_5array_8__getitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item); /* proto */ -static int __pyx_array_MemoryView_5array_10__setitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item, PyObject *__pyx_v_value); /* proto */ -static int __pyx_MemviewEnum_MemoryView_4Enum___init__(struct __pyx_MemviewEnum_obj *__pyx_v_self, PyObject *__pyx_v_name); /* proto */ -static PyObject *__pyx_MemviewEnum_MemoryView_4Enum_2__repr__(struct __pyx_MemviewEnum_obj *__pyx_v_self); /* proto */ -static int __pyx_memoryview_MemoryView_10memoryview___cinit__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj, int __pyx_v_flags, int __pyx_v_dtype_is_object); /* proto */ -static void __pyx_memoryview_MemoryView_10memoryview_2__dealloc__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview_MemoryView_10memoryview_4__getitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index); /* proto */ -static int __pyx_memoryview_MemoryView_10memoryview_6__setitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto */ -static int __pyx_memoryview_getbuffer_MemoryView_10memoryview_8__getbuffer__(struct __pyx_memoryview_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ -static PyObject *__pyx_memoryview_transpose_MemoryView_10memoryview_1T___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview__get__base_MemoryView_10memoryview_4base___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview_get_shape_MemoryView_10memoryview_5shape___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview_get_strides_MemoryView_10memoryview_7strides___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview_get_suboffsets_MemoryView_10memoryview_10suboffsets___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview_get_ndim_MemoryView_10memoryview_4ndim___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview_get_itemsize_MemoryView_10memoryview_8itemsize___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview_get_nbytes_MemoryView_10memoryview_6nbytes___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview_get_size_MemoryView_10memoryview_4size___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static Py_ssize_t __pyx_memoryview_MemoryView_10memoryview_10__len__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview_MemoryView_10memoryview_12__repr__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview_MemoryView_10memoryview_14__str__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview_MemoryView_10memoryview_16is_c_contig(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview_MemoryView_10memoryview_18is_f_contig(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview_MemoryView_10memoryview_20copy(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryview_MemoryView_10memoryview_22copy_fortran(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ -static void __pyx_memoryviewslice_MemoryView_16_memoryviewslice___dealloc__(struct __pyx_memoryviewslice_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_memoryviewslice__get__base_MemoryView_16_memoryviewslice_4base___get__(struct __pyx_memoryviewslice_obj *__pyx_v_self); /* proto */ -static PyObject *__pyx_tp_new_array(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ -static PyObject *__pyx_tp_new_Enum(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ -static PyObject *__pyx_tp_new_memoryview(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ -static PyObject *__pyx_tp_new__memoryviewslice(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static char __pyx_k_B[] = "B"; static char __pyx_k_C[] = "C"; static char __pyx_k_H[] = "H"; @@ -1616,6 +1669,7 @@ static char __pyx_k_Zg[] = "Zg"; static char __pyx_k_id[] = "id"; static char __pyx_k_np[] = "np"; static char __pyx_k_qt[] = "qt"; +static char __pyx_k__20[] = ""; static char __pyx_k_dof[] = "dof"; static char __pyx_k_err[] = "err"; static char __pyx_k_i_2[] = "i"; @@ -1636,6 +1690,7 @@ static char __pyx_k_step[] = "step"; static char __pyx_k_stop[] = "stop"; static char __pyx_k_test[] = "__test__"; static char __pyx_k_tidx[] = "tidx"; +static char __pyx_k_ASCII[] = "ASCII"; static char __pyx_k_class[] = "__class__"; static char __pyx_k_count[] = "count"; static char __pyx_k_error[] = "error"; @@ -1650,6 +1705,7 @@ static char __pyx_k_width[] = "width"; static char __pyx_k_astype[] = "astype"; static char __pyx_k_center[] = "center"; static char __pyx_k_counts[] = "counts"; +static char __pyx_k_encode[] = "encode"; static char __pyx_k_forces[] = "forces"; static char __pyx_k_format[] = "format"; static char __pyx_k_import[] = "__import__"; @@ -1657,7 +1713,6 @@ static char __pyx_k_name_2[] = "__name__"; static char __pyx_k_offset[] = "offset"; static char __pyx_k_struct[] = "struct"; static char __pyx_k_unpack[] = "unpack"; -static char __pyx_k_xrange[] = "xrange"; static char __pyx_k_float32[] = "float32"; static char __pyx_k_fortran[] = "fortran"; static char __pyx_k_maximum[] = "maximum"; @@ -1679,10 +1734,10 @@ static char __pyx_k_pyx_vtable[] = "__pyx_vtable__"; static char __pyx_k_right_edge[] = "right_edge"; static char __pyx_k_MemoryError[] = "MemoryError"; static char __pyx_k_error_check[] = "error_check"; -static char __pyx_k_t_SNE_ERROR[] = "[t-SNE] ERROR\n"; static char __pyx_k_RuntimeError[] = "RuntimeError"; static char __pyx_k_n_dimensions[] = "n_dimensions"; static char __pyx_k_pyx_getbuffer[] = "__pyx_getbuffer"; +static char __pyx_k_t_SNE_ERROR_s[] = "[t-SNE] ERROR\n%s"; static char __pyx_k_calculate_edge[] = "calculate_edge"; static char __pyx_k_check_quadtree[] = "check_quadtree"; static char __pyx_k_n_dimensions_i[] = " n_dimensions %i\n"; @@ -1702,7 +1757,6 @@ static char __pyx_k_contiguous_and_indirect[] = ""; static char __pyx_k_Cannot_index_with_type_s[] = "Cannot index with type '%s'"; static char __pyx_k_getbuffer_obj_view_flags[] = "getbuffer(obj, view, flags)"; static char __pyx_k_o2i_index_i_dim_i_offset[] = "o2i index %i dim %i offset"; -static char __pyx_k_t_SNE_Computing_gradient[] = "[t-SNE] Computing gradient\n"; static char __pyx_k_t_SNE_Inserting_i_points[] = "[t-SNE] Inserting %i points\n"; static char __pyx_k_t_SNE_Tree_i_clock_ticks[] = "[t-SNE] Tree: %i clock ticks | "; static char __pyx_k_t_SNE_i_points_in_node_p[] = "[t-SNE] %i points in node %p\n"; @@ -1710,6 +1764,7 @@ static char __pyx_k_Dimension_d_is_not_direct[] = "Dimension %d is not direct"; static char __pyx_k_Invalid_shape_in_axis_d_d[] = "Invalid shape in axis %d: %d."; static char __pyx_k_t_SNE_Created_root_node_p[] = "[t-SNE] Created root node %p\n"; static char __pyx_k_Index_out_of_bounds_axis_d[] = "Index out of bounds (axis %d)"; +static char __pyx_k_t_SNE_Computing_gradient_s[] = "[t-SNE] Computing gradient\n%s"; static char __pyx_k_Step_may_not_be_zero_axis_d[] = "Step may not be zero (axis %d)"; static char __pyx_k_itemsize_0_for_cython_array[] = "itemsize <= 0 for cython.array"; static char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; @@ -1725,9 +1780,9 @@ static char __pyx_k_t_SNE_Tree_initialised_Width_1[] = "[t-SNE] Tree initialised static char __pyx_k_t_SNE_d_i_Node_p_leaf_i_Size_i[] = "[t-SNE] [d=%i] Node %p leaf = %i. Size %i\n"; static char __pyx_k_t_SNE_d_i_Relocating_old_point[] = "[t-SNE] [d=%i] Relocating old point to node %p\n"; static char __pyx_k_Force_computation_i_clock_ticks[] = "Force computation: %i clock ticks\n"; -static char __pyx_k_Users_chrismoody_code_scikit_le[] = "/Users/chrismoody/code/scikit-learn/sklearn/manifold/_barnes_hut_tsne.pyx"; -static char __pyx_k_t_SNE_Checking_tree_consistency[] = "[t-SNE] Checking tree consistency \n"; -static char __pyx_k_t_SNE_Child_is_not_a_leaf_Desce[] = "[t-SNE] Child is not a leaf. Descending\n"; +static char __pyx_k_home_andy_checkout_scikit_learn[] = "/home/andy/checkout/scikit-learn/sklearn/manifold/_barnes_hut_tsne.pyx"; +static char __pyx_k_t_SNE_Checking_tree_consistency[] = "[t-SNE] Checking tree consistency\n%s"; +static char __pyx_k_t_SNE_Child_is_not_a_leaf_Desce[] = "[t-SNE] Child is not a leaf. Descending\n%s"; static char __pyx_k_t_SNE_Computing_negative_gradie[] = "[t-SNE] Computing negative gradient: %e ticks\n"; static char __pyx_k_t_SNE_Computing_positive_gradie[] = "[t-SNE] Computing positive gradient: %e ticks\n"; static char __pyx_k_t_SNE_Counting_nodes_at_root_no[] = "[t-SNE] Counting nodes at root node %p\n"; @@ -1766,6 +1821,7 @@ static char __pyx_k_sklearn_manifold__barnes_hut_tsn[] = "sklearn.manifold._barn static char __pyx_k_unable_to_allocate_shape_and_str[] = "unable to allocate shape and strides."; static char __pyx_k_Format_string_allocated_too_shor_2[] = "Format string allocated too short."; static char __pyx_k_Tree_consistency_failed_unexpect_2[] = "Tree consistency failed: unexpected number of points on the tree"; +static PyObject *__pyx_n_s_ASCII; static PyObject *__pyx_kp_s_Buffer_view_does_not_expose_stri; static PyObject *__pyx_n_s_C; static PyObject *__pyx_kp_s_Can_only_create_a_buffer_that_is; @@ -1792,7 +1848,6 @@ static PyObject *__pyx_kp_s_Tree_consistency_failed_unexpect; static PyObject *__pyx_kp_s_Tree_consistency_failed_unexpect_2; static PyObject *__pyx_n_s_TypeError; static PyObject *__pyx_kp_s_Unable_to_convert_item_to_object; -static PyObject *__pyx_kp_s_Users_chrismoody_code_scikit_le; static PyObject *__pyx_n_s_ValueError; static PyObject *__pyx_n_s_X; static PyObject *__pyx_n_s_allocate_buffer; @@ -1811,6 +1866,7 @@ static PyObject *__pyx_n_s_count; static PyObject *__pyx_n_s_counts; static PyObject *__pyx_n_s_dof; static PyObject *__pyx_n_s_dtype_is_object; +static PyObject *__pyx_n_s_encode; static PyObject *__pyx_n_s_enumerate; static PyObject *__pyx_n_s_err; static PyObject *__pyx_n_s_error; @@ -1823,6 +1879,7 @@ static PyObject *__pyx_n_s_fortran; static PyObject *__pyx_n_u_fortran; static PyObject *__pyx_kp_s_got_differing_extents_in_dimensi; static PyObject *__pyx_n_s_gradient; +static PyObject *__pyx_kp_s_home_andy_checkout_scikit_learn; static PyObject *__pyx_n_s_id; static PyObject *__pyx_n_s_idx; static PyObject *__pyx_n_s_import; @@ -1884,7 +1941,49 @@ static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd; static PyObject *__pyx_n_s_unpack; static PyObject *__pyx_n_s_verbose; static PyObject *__pyx_n_s_width; -static PyObject *__pyx_n_s_xrange; +static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_calculate_edge(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_pos_output); /* proto */ +static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_pij_input, __Pyx_memviewslice __pyx_v_pos_output, __Pyx_memviewslice __pyx_v_neighbors, __Pyx_memviewslice __pyx_v_forces, float __pyx_v_theta, int __pyx_v_n_dimensions, int __pyx_v_verbose, float __pyx_v_dof, long __pyx_v_skip_num_points); /* proto */ +static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_4check_quadtree(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_X, __Pyx_memviewslice __pyx_v_counts); /* proto */ +static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_6test_index2offset(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ +static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_8test_index_offset(CYTHON_UNUSED PyObject *__pyx_self); /* proto */ +static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ +static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */ +static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array___cinit__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_shape, Py_ssize_t __pyx_v_itemsize, PyObject *__pyx_v_format, PyObject *__pyx_v_mode, int __pyx_v_allocate_buffer); /* proto */ +static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_2__getbuffer__(struct __pyx_array_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ +static void __pyx_array___pyx_pf_15View_dot_MemoryView_5array_4__dealloc__(struct __pyx_array_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_5array_7memview___get__(struct __pyx_array_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_array___pyx_pf_15View_dot_MemoryView_5array_6__getattr__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_attr); /* proto */ +static PyObject *__pyx_array___pyx_pf_15View_dot_MemoryView_5array_8__getitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item); /* proto */ +static int __pyx_array___pyx_pf_15View_dot_MemoryView_5array_10__setitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item, PyObject *__pyx_v_value); /* proto */ +static int __pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum___init__(struct __pyx_MemviewEnum_obj *__pyx_v_self, PyObject *__pyx_v_name); /* proto */ +static PyObject *__pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum_2__repr__(struct __pyx_MemviewEnum_obj *__pyx_v_self); /* proto */ +static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview___cinit__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj, int __pyx_v_flags, int __pyx_v_dtype_is_object); /* proto */ +static void __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_2__dealloc__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_4__getitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index); /* proto */ +static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_6__setitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto */ +static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_8__getbuffer__(struct __pyx_memoryview_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_1T___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_4base___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_5shape___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_7strides___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_10suboffsets___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_4ndim___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_8itemsize___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_6nbytes___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_10memoryview_4size___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static Py_ssize_t __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_10__len__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_12__repr__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_14__str__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_16is_c_contig(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_18is_f_contig(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_20copy(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_22copy_fortran(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */ +static void __pyx_memoryviewslice___pyx_pf_15View_dot_MemoryView_16_memoryviewslice___dealloc__(struct __pyx_memoryviewslice_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_15View_dot_MemoryView_16_memoryviewslice_4base___get__(struct __pyx_memoryviewslice_obj *__pyx_v_self); /* proto */ +static PyObject *__pyx_tp_new_array(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_Enum(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_memoryview(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new__memoryviewslice(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static PyObject *__pyx_float_0_5; static PyObject *__pyx_float_2_0; static PyObject *__pyx_float_1_001; @@ -1901,31 +2000,33 @@ static PyObject *__pyx_tuple__6; static PyObject *__pyx_tuple__7; static PyObject *__pyx_tuple__8; static PyObject *__pyx_tuple__9; -static PyObject *__pyx_slice__14; -static PyObject *__pyx_slice__15; static PyObject *__pyx_slice__16; +static PyObject *__pyx_slice__17; +static PyObject *__pyx_slice__18; static PyObject *__pyx_tuple__10; static PyObject *__pyx_tuple__11; static PyObject *__pyx_tuple__12; static PyObject *__pyx_tuple__13; -static PyObject *__pyx_tuple__17; -static PyObject *__pyx_tuple__18; -static PyObject *__pyx_tuple__20; -static PyObject *__pyx_tuple__22; -static PyObject *__pyx_tuple__24; -static PyObject *__pyx_tuple__26; -static PyObject *__pyx_tuple__28; +static PyObject *__pyx_tuple__14; +static PyObject *__pyx_tuple__15; +static PyObject *__pyx_tuple__19; +static PyObject *__pyx_tuple__21; +static PyObject *__pyx_tuple__23; +static PyObject *__pyx_tuple__25; +static PyObject *__pyx_tuple__27; static PyObject *__pyx_tuple__29; -static PyObject *__pyx_tuple__30; static PyObject *__pyx_tuple__31; static PyObject *__pyx_tuple__32; -static PyObject *__pyx_codeobj__19; -static PyObject *__pyx_codeobj__21; -static PyObject *__pyx_codeobj__23; -static PyObject *__pyx_codeobj__25; -static PyObject *__pyx_codeobj__27; - -/* "sklearn/manifold/_barnes_hut_tsne.pyx":92 +static PyObject *__pyx_tuple__33; +static PyObject *__pyx_tuple__34; +static PyObject *__pyx_tuple__35; +static PyObject *__pyx_codeobj__22; +static PyObject *__pyx_codeobj__24; +static PyObject *__pyx_codeobj__26; +static PyObject *__pyx_codeobj__28; +static PyObject *__pyx_codeobj__30; + +/* "sklearn/manifold/_barnes_hut_tsne.pyx":94 * int n_cell_per_node * * cdef Tree* init_tree(float[:] left_edge, float[:] width, int n_dimensions, # <<<<<<<<<<<<<< @@ -1943,7 +2044,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *__pyx_f_7sklea Py_ssize_t __pyx_t_5; Py_ssize_t __pyx_t_6; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":95 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":97 * int verbose) nogil: * # tree is freed by free_tree * cdef Tree* tree = malloc(sizeof(Tree)) # <<<<<<<<<<<<<< @@ -1952,7 +2053,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *__pyx_f_7sklea */ __pyx_v_tree = ((struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *)malloc((sizeof(struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree)))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":96 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":98 * # tree is freed by free_tree * cdef Tree* tree = malloc(sizeof(Tree)) * tree.n_dimensions = n_dimensions # <<<<<<<<<<<<<< @@ -1961,7 +2062,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *__pyx_f_7sklea */ __pyx_v_tree->n_dimensions = __pyx_v_n_dimensions; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":97 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":99 * cdef Tree* tree = malloc(sizeof(Tree)) * tree.n_dimensions = n_dimensions * tree.n_cells = 0 # <<<<<<<<<<<<<< @@ -1970,7 +2071,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *__pyx_f_7sklea */ __pyx_v_tree->n_cells = 0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":98 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":100 * tree.n_dimensions = n_dimensions * tree.n_cells = 0 * tree.n_points = 0 # <<<<<<<<<<<<<< @@ -1979,7 +2080,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *__pyx_f_7sklea */ __pyx_v_tree->n_points = 0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":99 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":101 * tree.n_cells = 0 * tree.n_points = 0 * tree.verbose = verbose # <<<<<<<<<<<<<< @@ -1988,7 +2089,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *__pyx_f_7sklea */ __pyx_v_tree->verbose = __pyx_v_verbose; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":100 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":102 * tree.n_points = 0 * tree.verbose = verbose * tree.root_node = create_root(left_edge, width, n_dimensions) # <<<<<<<<<<<<<< @@ -1997,7 +2098,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *__pyx_f_7sklea */ __pyx_v_tree->root_node = __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_create_root(__pyx_v_left_edge, __pyx_v_width, __pyx_v_n_dimensions); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":101 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":103 * tree.verbose = verbose * tree.root_node = create_root(left_edge, width, n_dimensions) * tree.root_node.tree = tree # <<<<<<<<<<<<<< @@ -2006,7 +2107,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *__pyx_f_7sklea */ __pyx_v_tree->root_node->tree = __pyx_v_tree; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":102 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":104 * tree.root_node = create_root(left_edge, width, n_dimensions) * tree.root_node.tree = tree * tree.n_cells += 1 # <<<<<<<<<<<<<< @@ -2015,7 +2116,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *__pyx_f_7sklea */ __pyx_v_tree->n_cells = (__pyx_v_tree->n_cells + 1); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":103 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":105 * tree.root_node.tree = tree * tree.n_cells += 1 * tree.n_cell_per_node = 2 ** n_dimensions # <<<<<<<<<<<<<< @@ -2024,7 +2125,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *__pyx_f_7sklea */ __pyx_v_tree->n_cell_per_node = __Pyx_pow_long(2, ((long)__pyx_v_n_dimensions)); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":104 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":106 * tree.n_cells += 1 * tree.n_cell_per_node = 2 ** n_dimensions * if DEBUGFLAG: # <<<<<<<<<<<<<< @@ -2033,7 +2134,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *__pyx_f_7sklea */ if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":106 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":108 * if DEBUGFLAG: * printf("[t-SNE] Tree initialised. Left_edge = (%1.9e, %1.9e, %1.9e)\n", * left_edge[0], left_edge[1], left_edge[2]) # <<<<<<<<<<<<<< @@ -2044,7 +2145,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *__pyx_f_7sklea __pyx_t_2 = 1; __pyx_t_3 = 2; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":105 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":107 * tree.n_cell_per_node = 2 ** n_dimensions * if DEBUGFLAG: * printf("[t-SNE] Tree initialised. Left_edge = (%1.9e, %1.9e, %1.9e)\n", # <<<<<<<<<<<<<< @@ -2053,7 +2154,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *__pyx_f_7sklea */ printf(__pyx_k_t_SNE_Tree_initialised_Left_edg, (*((float *) ( /* dim=0 */ (__pyx_v_left_edge.data + __pyx_t_1 * __pyx_v_left_edge.strides[0]) ))), (*((float *) ( /* dim=0 */ (__pyx_v_left_edge.data + __pyx_t_2 * __pyx_v_left_edge.strides[0]) ))), (*((float *) ( /* dim=0 */ (__pyx_v_left_edge.data + __pyx_t_3 * __pyx_v_left_edge.strides[0]) )))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":108 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":110 * left_edge[0], left_edge[1], left_edge[2]) * printf("[t-SNE] Tree initialised. Width = (%1.9e, %1.9e, %1.9e)\n", * width[0], width[1], width[2]) # <<<<<<<<<<<<<< @@ -2064,7 +2165,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *__pyx_f_7sklea __pyx_t_5 = 1; __pyx_t_6 = 2; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":107 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":109 * printf("[t-SNE] Tree initialised. Left_edge = (%1.9e, %1.9e, %1.9e)\n", * left_edge[0], left_edge[1], left_edge[2]) * printf("[t-SNE] Tree initialised. Width = (%1.9e, %1.9e, %1.9e)\n", # <<<<<<<<<<<<<< @@ -2072,11 +2173,17 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *__pyx_f_7sklea * return tree */ printf(__pyx_k_t_SNE_Tree_initialised_Width_1, (*((float *) ( /* dim=0 */ (__pyx_v_width.data + __pyx_t_4 * __pyx_v_width.strides[0]) ))), (*((float *) ( /* dim=0 */ (__pyx_v_width.data + __pyx_t_5 * __pyx_v_width.strides[0]) ))), (*((float *) ( /* dim=0 */ (__pyx_v_width.data + __pyx_t_6 * __pyx_v_width.strides[0]) )))); - goto __pyx_L3; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":106 + * tree.n_cells += 1 + * tree.n_cell_per_node = 2 ** n_dimensions + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] Tree initialised. Left_edge = (%1.9e, %1.9e, %1.9e)\n", + * left_edge[0], left_edge[1], left_edge[2]) + */ } - __pyx_L3:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":109 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":111 * printf("[t-SNE] Tree initialised. Width = (%1.9e, %1.9e, %1.9e)\n", * width[0], width[1], width[2]) * return tree # <<<<<<<<<<<<<< @@ -2086,7 +2193,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *__pyx_f_7sklea __pyx_r = __pyx_v_tree; goto __pyx_L0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":92 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":94 * int n_cell_per_node * * cdef Tree* init_tree(float[:] left_edge, float[:] width, int n_dimensions, # <<<<<<<<<<<<<< @@ -2099,7 +2206,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Tree *__pyx_f_7sklea return __pyx_r; } -/* "sklearn/manifold/_barnes_hut_tsne.pyx":111 +/* "sklearn/manifold/_barnes_hut_tsne.pyx":113 * return tree * * cdef Node* create_root(float[:] left_edge, float[:] width, int n_dimensions) nogil: # <<<<<<<<<<<<<< @@ -2114,13 +2221,13 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_r; int __pyx_t_1; int __pyx_t_2; - int __pyx_t_3; - int __pyx_t_4; + Py_ssize_t __pyx_t_3; + Py_ssize_t __pyx_t_4; float __pyx_t_5; float __pyx_t_6; float __pyx_t_7; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":114 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":116 * # Create a default root node * cdef int ax * cdef int n_cell_per_node = 2 ** n_dimensions # <<<<<<<<<<<<<< @@ -2129,7 +2236,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_n_cell_per_node = __Pyx_pow_long(2, ((long)__pyx_v_n_dimensions)); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":116 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":118 * cdef int n_cell_per_node = 2 ** n_dimensions * # root is freed by free_tree * root = malloc(sizeof(Node)) # <<<<<<<<<<<<<< @@ -2138,7 +2245,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_root = ((struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *)malloc((sizeof(struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node)))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":117 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":119 * # root is freed by free_tree * root = malloc(sizeof(Node)) * root.is_leaf = 1 # <<<<<<<<<<<<<< @@ -2147,7 +2254,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_root->is_leaf = 1; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":118 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":120 * root = malloc(sizeof(Node)) * root.is_leaf = 1 * root.parent = NULL # <<<<<<<<<<<<<< @@ -2156,7 +2263,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_root->parent = NULL; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":119 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":121 * root.is_leaf = 1 * root.parent = NULL * root.level = 0 # <<<<<<<<<<<<<< @@ -2165,7 +2272,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_root->level = 0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":120 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":122 * root.parent = NULL * root.level = 0 * root.cumulative_size = 0 # <<<<<<<<<<<<<< @@ -2174,7 +2281,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_root->cumulative_size = 0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":121 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":123 * root.level = 0 * root.cumulative_size = 0 * root.size = 0 # <<<<<<<<<<<<<< @@ -2183,7 +2290,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_root->size = 0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":122 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":124 * root.cumulative_size = 0 * root.size = 0 * root.point_index = -1 # <<<<<<<<<<<<<< @@ -2192,7 +2299,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_root->point_index = -1; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":123 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":125 * root.size = 0 * root.point_index = -1 * root.max_width = 0.0 # <<<<<<<<<<<<<< @@ -2201,7 +2308,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_root->max_width = 0.0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":124 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":126 * root.point_index = -1 * root.max_width = 0.0 * root.width = malloc(sizeof(float) * n_dimensions) # <<<<<<<<<<<<<< @@ -2210,7 +2317,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_root->width = ((float *)malloc(((sizeof(float)) * __pyx_v_n_dimensions))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":125 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":127 * root.max_width = 0.0 * root.width = malloc(sizeof(float) * n_dimensions) * root.left_edge = malloc(sizeof(float) * n_dimensions) # <<<<<<<<<<<<<< @@ -2219,7 +2326,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_root->left_edge = ((float *)malloc(((sizeof(float)) * __pyx_v_n_dimensions))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":126 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":128 * root.width = malloc(sizeof(float) * n_dimensions) * root.left_edge = malloc(sizeof(float) * n_dimensions) * root.center = malloc(sizeof(float) * n_dimensions) # <<<<<<<<<<<<<< @@ -2228,7 +2335,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_root->center = ((float *)malloc(((sizeof(float)) * __pyx_v_n_dimensions))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":127 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":129 * root.left_edge = malloc(sizeof(float) * n_dimensions) * root.center = malloc(sizeof(float) * n_dimensions) * root.barycenter = malloc(sizeof(float) * n_dimensions) # <<<<<<<<<<<<<< @@ -2237,7 +2344,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_root->barycenter = ((float *)malloc(((sizeof(float)) * __pyx_v_n_dimensions))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":128 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":130 * root.center = malloc(sizeof(float) * n_dimensions) * root.barycenter = malloc(sizeof(float) * n_dimensions) * root.leaf_point_position= malloc(sizeof(float) * n_dimensions) # <<<<<<<<<<<<<< @@ -2246,7 +2353,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_root->leaf_point_position = ((float *)malloc(((sizeof(float)) * __pyx_v_n_dimensions))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":129 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":131 * root.barycenter = malloc(sizeof(float) * n_dimensions) * root.leaf_point_position= malloc(sizeof(float) * n_dimensions) * root.children = NULL # <<<<<<<<<<<<<< @@ -2255,7 +2362,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_root->children = NULL; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":130 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":132 * root.leaf_point_position= malloc(sizeof(float) * n_dimensions) * root.children = NULL * for ax in range(n_dimensions): # <<<<<<<<<<<<<< @@ -2266,7 +2373,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { __pyx_v_ax = __pyx_t_2; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":131 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":133 * root.children = NULL * for ax in range(n_dimensions): * root.width[ax] = width[ax] # <<<<<<<<<<<<<< @@ -2276,7 +2383,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea __pyx_t_3 = __pyx_v_ax; (__pyx_v_root->width[__pyx_v_ax]) = (*((float *) ( /* dim=0 */ (__pyx_v_width.data + __pyx_t_3 * __pyx_v_width.strides[0]) ))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":132 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":134 * for ax in range(n_dimensions): * root.width[ax] = width[ax] * root.left_edge[ax] = left_edge[ax] # <<<<<<<<<<<<<< @@ -2286,7 +2393,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea __pyx_t_4 = __pyx_v_ax; (__pyx_v_root->left_edge[__pyx_v_ax]) = (*((float *) ( /* dim=0 */ (__pyx_v_left_edge.data + __pyx_t_4 * __pyx_v_left_edge.strides[0]) ))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":133 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":135 * root.width[ax] = width[ax] * root.left_edge[ax] = left_edge[ax] * root.center[ax] = 0.0 # <<<<<<<<<<<<<< @@ -2295,7 +2402,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ (__pyx_v_root->center[__pyx_v_ax]) = 0.0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":134 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":136 * root.left_edge[ax] = left_edge[ax] * root.center[ax] = 0.0 * root.barycenter[ax] = 0. # <<<<<<<<<<<<<< @@ -2304,7 +2411,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ (__pyx_v_root->barycenter[__pyx_v_ax]) = 0.; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":135 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":137 * root.center[ax] = 0.0 * root.barycenter[ax] = 0. * root.leaf_point_position[ax] = -1 # <<<<<<<<<<<<<< @@ -2314,7 +2421,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea (__pyx_v_root->leaf_point_position[__pyx_v_ax]) = -1.0; } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":136 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":138 * root.barycenter[ax] = 0. * root.leaf_point_position[ax] = -1 * for ax in range(n_dimensions): # <<<<<<<<<<<<<< @@ -2325,7 +2432,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { __pyx_v_ax = __pyx_t_2; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":137 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":139 * root.leaf_point_position[ax] = -1 * for ax in range(n_dimensions): * root.max_width = max(root.max_width, root.width[ax]) # <<<<<<<<<<<<<< @@ -2342,7 +2449,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea __pyx_v_root->max_width = __pyx_t_7; } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":138 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":140 * for ax in range(n_dimensions): * root.max_width = max(root.max_width, root.width[ax]) * if DEBUGFLAG: # <<<<<<<<<<<<<< @@ -2351,7 +2458,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":139 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":141 * root.max_width = max(root.max_width, root.width[ax]) * if DEBUGFLAG: * printf("[t-SNE] Created root node %p\n", root) # <<<<<<<<<<<<<< @@ -2359,11 +2466,17 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea * */ printf(__pyx_k_t_SNE_Created_root_node_p, __pyx_v_root); - goto __pyx_L7; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":140 + * for ax in range(n_dimensions): + * root.max_width = max(root.max_width, root.width[ax]) + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] Created root node %p\n", root) + * return root + */ } - __pyx_L7:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":140 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":142 * if DEBUGFLAG: * printf("[t-SNE] Created root node %p\n", root) * return root # <<<<<<<<<<<<<< @@ -2373,7 +2486,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea __pyx_r = __pyx_v_root; goto __pyx_L0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":111 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":113 * return tree * * cdef Node* create_root(float[:] left_edge, float[:] width, int n_dimensions) nogil: # <<<<<<<<<<<<<< @@ -2386,7 +2499,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea return __pyx_r; } -/* "sklearn/manifold/_barnes_hut_tsne.pyx":142 +/* "sklearn/manifold/_barnes_hut_tsne.pyx":144 * return root * * cdef Node* create_child(Node *parent, int[3] offset) nogil: # <<<<<<<<<<<<<< @@ -2405,7 +2518,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea float __pyx_t_5; float __pyx_t_6; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":146 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":148 * cdef int ax * # these children are freed by free_recursive * child = malloc(sizeof(Node)) # <<<<<<<<<<<<<< @@ -2414,7 +2527,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_child = ((struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *)malloc((sizeof(struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node)))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":147 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":149 * # these children are freed by free_recursive * child = malloc(sizeof(Node)) * child.is_leaf = 1 # <<<<<<<<<<<<<< @@ -2423,7 +2536,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_child->is_leaf = 1; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":148 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":150 * child = malloc(sizeof(Node)) * child.is_leaf = 1 * child.parent = parent # <<<<<<<<<<<<<< @@ -2432,7 +2545,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_child->parent = __pyx_v_parent; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":149 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":151 * child.is_leaf = 1 * child.parent = parent * child.level = parent.level + 1 # <<<<<<<<<<<<<< @@ -2441,7 +2554,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_child->level = (__pyx_v_parent->level + 1); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":150 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":152 * child.parent = parent * child.level = parent.level + 1 * child.size = 0 # <<<<<<<<<<<<<< @@ -2450,7 +2563,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_child->size = 0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":151 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":153 * child.level = parent.level + 1 * child.size = 0 * child.cumulative_size = 0 # <<<<<<<<<<<<<< @@ -2459,7 +2572,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_child->cumulative_size = 0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":152 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":154 * child.size = 0 * child.cumulative_size = 0 * child.point_index = -1 # <<<<<<<<<<<<<< @@ -2468,7 +2581,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_child->point_index = -1; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":153 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":155 * child.cumulative_size = 0 * child.point_index = -1 * child.tree = parent.tree # <<<<<<<<<<<<<< @@ -2478,7 +2591,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea __pyx_t_1 = __pyx_v_parent->tree; __pyx_v_child->tree = __pyx_t_1; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":154 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":156 * child.point_index = -1 * child.tree = parent.tree * child.max_width = 0.0 # <<<<<<<<<<<<<< @@ -2487,7 +2600,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_child->max_width = 0.0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":155 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":157 * child.tree = parent.tree * child.max_width = 0.0 * child.width = malloc(sizeof(float) * parent.tree.n_dimensions) # <<<<<<<<<<<<<< @@ -2496,7 +2609,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_child->width = ((float *)malloc(((sizeof(float)) * __pyx_v_parent->tree->n_dimensions))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":156 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":158 * child.max_width = 0.0 * child.width = malloc(sizeof(float) * parent.tree.n_dimensions) * child.left_edge = malloc(sizeof(float) * parent.tree.n_dimensions) # <<<<<<<<<<<<<< @@ -2505,7 +2618,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_child->left_edge = ((float *)malloc(((sizeof(float)) * __pyx_v_parent->tree->n_dimensions))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":157 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":159 * child.width = malloc(sizeof(float) * parent.tree.n_dimensions) * child.left_edge = malloc(sizeof(float) * parent.tree.n_dimensions) * child.center = malloc(sizeof(float) * parent.tree.n_dimensions) # <<<<<<<<<<<<<< @@ -2514,7 +2627,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_child->center = ((float *)malloc(((sizeof(float)) * __pyx_v_parent->tree->n_dimensions))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":158 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":160 * child.left_edge = malloc(sizeof(float) * parent.tree.n_dimensions) * child.center = malloc(sizeof(float) * parent.tree.n_dimensions) * child.barycenter = malloc(sizeof(float) * parent.tree.n_dimensions) # <<<<<<<<<<<<<< @@ -2523,7 +2636,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_child->barycenter = ((float *)malloc(((sizeof(float)) * __pyx_v_parent->tree->n_dimensions))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":159 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":161 * child.center = malloc(sizeof(float) * parent.tree.n_dimensions) * child.barycenter = malloc(sizeof(float) * parent.tree.n_dimensions) * child.leaf_point_position = malloc(sizeof(float) * parent.tree.n_dimensions) # <<<<<<<<<<<<<< @@ -2532,7 +2645,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_child->leaf_point_position = ((float *)malloc(((sizeof(float)) * __pyx_v_parent->tree->n_dimensions))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":160 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":162 * child.barycenter = malloc(sizeof(float) * parent.tree.n_dimensions) * child.leaf_point_position = malloc(sizeof(float) * parent.tree.n_dimensions) * child.children = NULL # <<<<<<<<<<<<<< @@ -2541,7 +2654,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_child->children = NULL; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":161 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":163 * child.leaf_point_position = malloc(sizeof(float) * parent.tree.n_dimensions) * child.children = NULL * for ax in range(parent.tree.n_dimensions): # <<<<<<<<<<<<<< @@ -2552,7 +2665,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { __pyx_v_ax = __pyx_t_3; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":162 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":164 * child.children = NULL * for ax in range(parent.tree.n_dimensions): * child.width[ax] = parent.width[ax] / 2.0 # <<<<<<<<<<<<<< @@ -2561,7 +2674,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ (__pyx_v_child->width[__pyx_v_ax]) = ((__pyx_v_parent->width[__pyx_v_ax]) / 2.0); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":163 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":165 * for ax in range(parent.tree.n_dimensions): * child.width[ax] = parent.width[ax] / 2.0 * child.left_edge[ax] = parent.left_edge[ax] + offset[ax] * parent.width[ax] / 2.0 # <<<<<<<<<<<<<< @@ -2570,7 +2683,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ (__pyx_v_child->left_edge[__pyx_v_ax]) = ((__pyx_v_parent->left_edge[__pyx_v_ax]) + (((__pyx_v_offset[__pyx_v_ax]) * (__pyx_v_parent->width[__pyx_v_ax])) / 2.0)); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":164 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":166 * child.width[ax] = parent.width[ax] / 2.0 * child.left_edge[ax] = parent.left_edge[ax] + offset[ax] * parent.width[ax] / 2.0 * child.center[ax] = child.left_edge[ax] + child.width[ax] / 2.0 # <<<<<<<<<<<<<< @@ -2579,7 +2692,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ (__pyx_v_child->center[__pyx_v_ax]) = ((__pyx_v_child->left_edge[__pyx_v_ax]) + ((__pyx_v_child->width[__pyx_v_ax]) / 2.0)); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":165 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":167 * child.left_edge[ax] = parent.left_edge[ax] + offset[ax] * parent.width[ax] / 2.0 * child.center[ax] = child.left_edge[ax] + child.width[ax] / 2.0 * child.barycenter[ax] = 0. # <<<<<<<<<<<<<< @@ -2588,7 +2701,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ (__pyx_v_child->barycenter[__pyx_v_ax]) = 0.; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":166 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":168 * child.center[ax] = child.left_edge[ax] + child.width[ax] / 2.0 * child.barycenter[ax] = 0. * child.leaf_point_position[ax] = -1. # <<<<<<<<<<<<<< @@ -2598,7 +2711,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea (__pyx_v_child->leaf_point_position[__pyx_v_ax]) = -1.; } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":167 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":169 * child.barycenter[ax] = 0. * child.leaf_point_position[ax] = -1. * for ax in range(parent.tree.n_dimensions): # <<<<<<<<<<<<<< @@ -2609,7 +2722,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { __pyx_v_ax = __pyx_t_3; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":168 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":170 * child.leaf_point_position[ax] = -1. * for ax in range(parent.tree.n_dimensions): * child.max_width = max(child.max_width, child.width[ax]) # <<<<<<<<<<<<<< @@ -2626,7 +2739,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea __pyx_v_child->max_width = __pyx_t_6; } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":169 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":171 * for ax in range(parent.tree.n_dimensions): * child.max_width = max(child.max_width, child.width[ax]) * child.tree.n_cells += 1 # <<<<<<<<<<<<<< @@ -2635,7 +2748,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_child->tree->n_cells = (__pyx_v_child->tree->n_cells + 1); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":170 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":172 * child.max_width = max(child.max_width, child.width[ax]) * child.tree.n_cells += 1 * return child # <<<<<<<<<<<<<< @@ -2645,7 +2758,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea __pyx_r = __pyx_v_child; goto __pyx_L0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":142 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":144 * return root * * cdef Node* create_child(Node *parent, int[3] offset) nogil: # <<<<<<<<<<<<<< @@ -2658,7 +2771,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea return __pyx_r; } -/* "sklearn/manifold/_barnes_hut_tsne.pyx":172 +/* "sklearn/manifold/_barnes_hut_tsne.pyx":174 * return child * * cdef Node* select_child(Node *node, float[3] pos, long index) nogil: # <<<<<<<<<<<<<< @@ -2675,7 +2788,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea int __pyx_t_1; int __pyx_t_2; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":175 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":177 * # Find which sub-node a position should go into * # And return the appropriate node * cdef int* offset = malloc(sizeof(int) * node.tree.n_dimensions) # <<<<<<<<<<<<<< @@ -2684,7 +2797,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_offset = ((int *)malloc(((sizeof(int)) * __pyx_v_node->tree->n_dimensions))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":179 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":181 * cdef Node* child * cdef int error * for ax in range(node.tree.n_dimensions): # <<<<<<<<<<<<<< @@ -2695,7 +2808,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { __pyx_v_ax = __pyx_t_2; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":180 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":182 * cdef int error * for ax in range(node.tree.n_dimensions): * offset[ax] = (pos[ax] - (node.left_edge[ax] + node.width[ax] / 2.0)) > 0. # <<<<<<<<<<<<<< @@ -2705,7 +2818,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea (__pyx_v_offset[__pyx_v_ax]) = (((__pyx_v_pos[__pyx_v_ax]) - ((__pyx_v_node->left_edge[__pyx_v_ax]) + ((__pyx_v_node->width[__pyx_v_ax]) / 2.0))) > 0.); } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":181 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":183 * for ax in range(node.tree.n_dimensions): * offset[ax] = (pos[ax] - (node.left_edge[ax] + node.width[ax] / 2.0)) > 0. * idx = offset2index(offset, node.tree.n_dimensions) # <<<<<<<<<<<<<< @@ -2714,7 +2827,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_idx = __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_offset2index(__pyx_v_offset, __pyx_v_node->tree->n_dimensions); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":182 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":184 * offset[ax] = (pos[ax] - (node.left_edge[ax] + node.width[ax] / 2.0)) > 0. * idx = offset2index(offset, node.tree.n_dimensions) * child = node.children[idx] # <<<<<<<<<<<<<< @@ -2723,7 +2836,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ __pyx_v_child = (__pyx_v_node->children[__pyx_v_idx]); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":183 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":185 * idx = offset2index(offset, node.tree.n_dimensions) * child = node.children[idx] * if DEBUGFLAG: # <<<<<<<<<<<<<< @@ -2732,7 +2845,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":184 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":186 * child = node.children[idx] * if DEBUGFLAG: * printf("[t-SNE] Offset [%i, %i] with LE [%f, %f]\n", # <<<<<<<<<<<<<< @@ -2740,11 +2853,17 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea * free(offset) */ printf(__pyx_k_t_SNE_Offset_i_i_with_LE_f_f, (__pyx_v_offset[0]), (__pyx_v_offset[1]), (__pyx_v_child->left_edge[0]), (__pyx_v_child->left_edge[1])); - goto __pyx_L5; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":185 + * idx = offset2index(offset, node.tree.n_dimensions) + * child = node.children[idx] + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] Offset [%i, %i] with LE [%f, %f]\n", + * offset[0], offset[1], child.left_edge[0], child.left_edge[1]) + */ } - __pyx_L5:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":186 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":188 * printf("[t-SNE] Offset [%i, %i] with LE [%f, %f]\n", * offset[0], offset[1], child.left_edge[0], child.left_edge[1]) * free(offset) # <<<<<<<<<<<<<< @@ -2753,7 +2872,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea */ free(__pyx_v_offset); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":187 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":189 * offset[0], offset[1], child.left_edge[0], child.left_edge[1]) * free(offset) * return child # <<<<<<<<<<<<<< @@ -2763,7 +2882,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea __pyx_r = __pyx_v_child; goto __pyx_L0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":172 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":174 * return child * * cdef Node* select_child(Node *node, float[3] pos, long index) nogil: # <<<<<<<<<<<<<< @@ -2776,7 +2895,7 @@ static struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_f_7sklea return __pyx_r; } -/* "sklearn/manifold/_barnes_hut_tsne.pyx":190 +/* "sklearn/manifold/_barnes_hut_tsne.pyx":192 * * * cdef inline void index2offset(int* offset, int index, int n_dimensions) nogil: # <<<<<<<<<<<<<< @@ -2794,7 +2913,7 @@ static CYTHON_INLINE void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_index2of int __pyx_t_3; int __pyx_t_4; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":199 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":201 * # such that the least significat bit is on the right * cdef int rem, k, shift * for k in range(n_dimensions): # <<<<<<<<<<<<<< @@ -2805,7 +2924,7 @@ static CYTHON_INLINE void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_index2of for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { __pyx_v_k = __pyx_t_2; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":200 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":202 * cdef int rem, k, shift * for k in range(n_dimensions): * shift = n_dimensions -k -1 # <<<<<<<<<<<<<< @@ -2814,7 +2933,7 @@ static CYTHON_INLINE void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_index2of */ __pyx_v_shift = ((__pyx_v_n_dimensions - __pyx_v_k) - 1); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":201 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":203 * for k in range(n_dimensions): * shift = n_dimensions -k -1 * rem = ((index >> shift) << shift) # <<<<<<<<<<<<<< @@ -2823,7 +2942,7 @@ static CYTHON_INLINE void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_index2of */ __pyx_v_rem = ((__pyx_v_index >> __pyx_v_shift) << __pyx_v_shift); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":202 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":204 * shift = n_dimensions -k -1 * rem = ((index >> shift) << shift) * offset[k] = rem > 0 # <<<<<<<<<<<<<< @@ -2832,7 +2951,7 @@ static CYTHON_INLINE void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_index2of */ (__pyx_v_offset[__pyx_v_k]) = (__pyx_v_rem > 0); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":203 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":205 * rem = ((index >> shift) << shift) * offset[k] = rem > 0 * if DEBUGFLAG: # <<<<<<<<<<<<<< @@ -2841,7 +2960,7 @@ static CYTHON_INLINE void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_index2of */ if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":204 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":206 * offset[k] = rem > 0 * if DEBUGFLAG: * printf("i2o index %i k %i rem %i offset", index, k, rem) # <<<<<<<<<<<<<< @@ -2850,7 +2969,7 @@ static CYTHON_INLINE void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_index2of */ printf(__pyx_k_i2o_index_i_k_i_rem_i_offset, __pyx_v_index, __pyx_v_k, __pyx_v_rem); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":205 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":207 * if DEBUGFLAG: * printf("i2o index %i k %i rem %i offset", index, k, rem) * for j in range(n_dimensions): # <<<<<<<<<<<<<< @@ -2861,7 +2980,7 @@ static CYTHON_INLINE void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_index2of for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { __pyx_v_j = __pyx_t_4; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":206 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":208 * printf("i2o index %i k %i rem %i offset", index, k, rem) * for j in range(n_dimensions): * printf(" %i", offset[j]) # <<<<<<<<<<<<<< @@ -2871,7 +2990,7 @@ static CYTHON_INLINE void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_index2of printf(__pyx_k_i, (__pyx_v_offset[__pyx_v_j])); } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":207 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":209 * for j in range(n_dimensions): * printf(" %i", offset[j]) * printf(" n_dimensions %i\n", n_dimensions) # <<<<<<<<<<<<<< @@ -2879,11 +2998,17 @@ static CYTHON_INLINE void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_index2of * */ printf(__pyx_k_n_dimensions_i, __pyx_v_n_dimensions); - goto __pyx_L5; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":205 + * rem = ((index >> shift) << shift) + * offset[k] = rem > 0 + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("i2o index %i k %i rem %i offset", index, k, rem) + * for j in range(n_dimensions): + */ } - __pyx_L5:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":208 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":210 * printf(" %i", offset[j]) * printf(" n_dimensions %i\n", n_dimensions) * index -= rem # <<<<<<<<<<<<<< @@ -2893,7 +3018,7 @@ static CYTHON_INLINE void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_index2of __pyx_v_index = (__pyx_v_index - __pyx_v_rem); } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":190 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":192 * * * cdef inline void index2offset(int* offset, int index, int n_dimensions) nogil: # <<<<<<<<<<<<<< @@ -2904,7 +3029,7 @@ static CYTHON_INLINE void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_index2of /* function exit code */ } -/* "sklearn/manifold/_barnes_hut_tsne.pyx":211 +/* "sklearn/manifold/_barnes_hut_tsne.pyx":213 * * * cdef inline int offset2index(int* offset, int n_dimensions) nogil: # <<<<<<<<<<<<<< @@ -2922,7 +3047,7 @@ static CYTHON_INLINE int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_offset2in int __pyx_t_3; int __pyx_t_4; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":216 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":218 * # such that the least significat bit is on the right * cdef int dim * cdef int index = 0 # <<<<<<<<<<<<<< @@ -2931,7 +3056,7 @@ static CYTHON_INLINE int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_offset2in */ __pyx_v_index = 0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":217 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":219 * cdef int dim * cdef int index = 0 * for dim in range(n_dimensions): # <<<<<<<<<<<<<< @@ -2942,7 +3067,7 @@ static CYTHON_INLINE int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_offset2in for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { __pyx_v_dim = __pyx_t_2; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":218 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":220 * cdef int index = 0 * for dim in range(n_dimensions): * index += (2 ** dim) * offset[n_dimensions - dim - 1] # <<<<<<<<<<<<<< @@ -2951,7 +3076,7 @@ static CYTHON_INLINE int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_offset2in */ __pyx_v_index = (__pyx_v_index + (__Pyx_pow_long(2, ((long)__pyx_v_dim)) * (__pyx_v_offset[((__pyx_v_n_dimensions - __pyx_v_dim) - 1)]))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":219 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":221 * for dim in range(n_dimensions): * index += (2 ** dim) * offset[n_dimensions - dim - 1] * if DEBUGFLAG: # <<<<<<<<<<<<<< @@ -2960,7 +3085,7 @@ static CYTHON_INLINE int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_offset2in */ if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":220 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":222 * index += (2 ** dim) * offset[n_dimensions - dim - 1] * if DEBUGFLAG: * printf("o2i index %i dim %i offset", index, dim) # <<<<<<<<<<<<<< @@ -2969,7 +3094,7 @@ static CYTHON_INLINE int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_offset2in */ printf(__pyx_k_o2i_index_i_dim_i_offset, __pyx_v_index, __pyx_v_dim); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":221 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":223 * if DEBUGFLAG: * printf("o2i index %i dim %i offset", index, dim) * for j in range(n_dimensions): # <<<<<<<<<<<<<< @@ -2980,7 +3105,7 @@ static CYTHON_INLINE int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_offset2in for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { __pyx_v_j = __pyx_t_4; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":222 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":224 * printf("o2i index %i dim %i offset", index, dim) * for j in range(n_dimensions): * printf(" %i", offset[j]) # <<<<<<<<<<<<<< @@ -2990,7 +3115,7 @@ static CYTHON_INLINE int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_offset2in printf(__pyx_k_i, (__pyx_v_offset[__pyx_v_j])); } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":223 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":225 * for j in range(n_dimensions): * printf(" %i", offset[j]) * printf(" n_dimensions %i\n", n_dimensions) # <<<<<<<<<<<<<< @@ -2998,12 +3123,18 @@ static CYTHON_INLINE int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_offset2in * */ printf(__pyx_k_n_dimensions_i, __pyx_v_n_dimensions); - goto __pyx_L5; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":221 + * for dim in range(n_dimensions): + * index += (2 ** dim) * offset[n_dimensions - dim - 1] + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("o2i index %i dim %i offset", index, dim) + * for j in range(n_dimensions): + */ } - __pyx_L5:; } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":224 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":226 * printf(" %i", offset[j]) * printf(" n_dimensions %i\n", n_dimensions) * return index # <<<<<<<<<<<<<< @@ -3013,7 +3144,7 @@ static CYTHON_INLINE int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_offset2in __pyx_r = __pyx_v_index; goto __pyx_L0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":211 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":213 * * * cdef inline int offset2index(int* offset, int n_dimensions) nogil: # <<<<<<<<<<<<<< @@ -3026,7 +3157,7 @@ static CYTHON_INLINE int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_offset2in return __pyx_r; } -/* "sklearn/manifold/_barnes_hut_tsne.pyx":227 +/* "sklearn/manifold/_barnes_hut_tsne.pyx":229 * * * cdef void subdivide(Node* node) nogil: # <<<<<<<<<<<<<< @@ -3040,7 +3171,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_subdivide(struct __pyx int __pyx_t_1; int __pyx_t_2; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":229 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":231 * cdef void subdivide(Node* node) nogil: * # This instantiates 2**n_dimensions = n_cell_per_node nodes for the current node * cdef int idx = 0 # <<<<<<<<<<<<<< @@ -3049,7 +3180,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_subdivide(struct __pyx */ __pyx_v_idx = 0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":230 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":232 * # This instantiates 2**n_dimensions = n_cell_per_node nodes for the current node * cdef int idx = 0 * cdef int* offset = malloc(sizeof(int) * node.tree.n_dimensions) # <<<<<<<<<<<<<< @@ -3058,7 +3189,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_subdivide(struct __pyx */ __pyx_v_offset = ((int *)malloc(((sizeof(int)) * __pyx_v_node->tree->n_dimensions))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":231 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":233 * cdef int idx = 0 * cdef int* offset = malloc(sizeof(int) * node.tree.n_dimensions) * node.is_leaf = False # <<<<<<<<<<<<<< @@ -3067,7 +3198,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_subdivide(struct __pyx */ __pyx_v_node->is_leaf = 0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":232 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":234 * cdef int* offset = malloc(sizeof(int) * node.tree.n_dimensions) * node.is_leaf = False * node.children = malloc(sizeof(Node*) * node.tree.n_cell_per_node) # <<<<<<<<<<<<<< @@ -3076,7 +3207,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_subdivide(struct __pyx */ __pyx_v_node->children = ((struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node **)malloc(((sizeof(struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *)) * __pyx_v_node->tree->n_cell_per_node))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":233 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":235 * node.is_leaf = False * node.children = malloc(sizeof(Node*) * node.tree.n_cell_per_node) * for idx in range(node.tree.n_cell_per_node): # <<<<<<<<<<<<<< @@ -3087,7 +3218,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_subdivide(struct __pyx for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { __pyx_v_idx = __pyx_t_2; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":234 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":236 * node.children = malloc(sizeof(Node*) * node.tree.n_cell_per_node) * for idx in range(node.tree.n_cell_per_node): * index2offset(offset, idx, node.tree.n_dimensions) # <<<<<<<<<<<<<< @@ -3096,7 +3227,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_subdivide(struct __pyx */ __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_index2offset(__pyx_v_offset, __pyx_v_idx, __pyx_v_node->tree->n_dimensions); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":235 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":237 * for idx in range(node.tree.n_cell_per_node): * index2offset(offset, idx, node.tree.n_dimensions) * node.children[idx] = create_child(node, offset) # <<<<<<<<<<<<<< @@ -3106,7 +3237,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_subdivide(struct __pyx (__pyx_v_node->children[__pyx_v_idx]) = __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_create_child(__pyx_v_node, __pyx_v_offset); } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":236 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":238 * index2offset(offset, idx, node.tree.n_dimensions) * node.children[idx] = create_child(node, offset) * free(offset) # <<<<<<<<<<<<<< @@ -3115,7 +3246,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_subdivide(struct __pyx */ free(__pyx_v_offset); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":227 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":229 * * * cdef void subdivide(Node* node) nogil: # <<<<<<<<<<<<<< @@ -3126,7 +3257,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_subdivide(struct __pyx /* function exit code */ } -/* "sklearn/manifold/_barnes_hut_tsne.pyx":239 +/* "sklearn/manifold/_barnes_hut_tsne.pyx":241 * * * cdef int insert(Node *root, float pos[3], long point_index, long depth, long # <<<<<<<<<<<<<< @@ -3147,7 +3278,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 int __pyx_t_3; int __pyx_t_4; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":248 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":250 * cdef long i * cdef int ax * cdef int not_identical = 1 # <<<<<<<<<<<<<< @@ -3156,7 +3287,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 */ __pyx_v_not_identical = 1; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":249 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":251 * cdef int ax * cdef int not_identical = 1 * cdef int n_dimensions = root.tree.n_dimensions # <<<<<<<<<<<<<< @@ -3166,7 +3297,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 __pyx_t_1 = __pyx_v_root->tree->n_dimensions; __pyx_v_n_dimensions = __pyx_t_1; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":250 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":252 * cdef int not_identical = 1 * cdef int n_dimensions = root.tree.n_dimensions * if DEBUGFLAG: # <<<<<<<<<<<<<< @@ -3175,7 +3306,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 */ if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":251 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":253 * cdef int n_dimensions = root.tree.n_dimensions * if DEBUGFLAG: * printf("[t-SNE] [d=%i] Inserting pos %i [%f, %f] duplicate_count=%i " # <<<<<<<<<<<<<< @@ -3183,11 +3314,17 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 * duplicate_count, root) */ printf(__pyx_k_t_SNE_d_i_Inserting_pos_i_f_f_d, __pyx_v_depth, __pyx_v_point_index, (__pyx_v_pos[0]), (__pyx_v_pos[1]), __pyx_v_duplicate_count, __pyx_v_root); - goto __pyx_L3; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":252 + * cdef int not_identical = 1 + * cdef int n_dimensions = root.tree.n_dimensions + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] [d=%i] Inserting pos %i [%f, %f] duplicate_count=%i " + * "into child %p\n", depth, point_index, pos[0], pos[1], + */ } - __pyx_L3:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":256 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":258 * # Increment the total number points including this * # node and below it * root.cumulative_size += duplicate_count # <<<<<<<<<<<<<< @@ -3196,7 +3333,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 */ __pyx_v_root->cumulative_size = (__pyx_v_root->cumulative_size + __pyx_v_duplicate_count); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":259 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":261 * # Evaluate the new center of mass, weighting the previous * # center of mass against the new point data * cdef double frac_seen = (root.cumulative_size - 1) / ( # <<<<<<<<<<<<<< @@ -3205,7 +3342,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 */ __pyx_v_frac_seen = (((double)(__pyx_v_root->cumulative_size - 1)) / ((double)__pyx_v_root->cumulative_size)); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":261 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":263 * cdef double frac_seen = (root.cumulative_size - 1) / ( * root.cumulative_size) * cdef double frac_new = 1.0 / root.cumulative_size # <<<<<<<<<<<<<< @@ -3214,7 +3351,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 */ __pyx_v_frac_new = (1.0 / ((double)__pyx_v_root->cumulative_size)); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":263 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":265 * cdef double frac_new = 1.0 / root.cumulative_size * # Assert that duplicate_count > 0 * if duplicate_count < 1: # <<<<<<<<<<<<<< @@ -3224,7 +3361,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 __pyx_t_2 = ((__pyx_v_duplicate_count < 1) != 0); if (__pyx_t_2) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":264 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":266 * # Assert that duplicate_count > 0 * if duplicate_count < 1: * return -1 # <<<<<<<<<<<<<< @@ -3233,9 +3370,17 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 */ __pyx_r = -1; goto __pyx_L0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":265 + * cdef double frac_new = 1.0 / root.cumulative_size + * # Assert that duplicate_count > 0 + * if duplicate_count < 1: # <<<<<<<<<<<<<< + * return -1 + * # Assert that the point is inside the left & right edges + */ } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":266 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":268 * return -1 * # Assert that the point is inside the left & right edges * for ax in range(n_dimensions): # <<<<<<<<<<<<<< @@ -3246,7 +3391,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_1; __pyx_t_3+=1) { __pyx_v_ax = __pyx_t_3; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":267 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":269 * # Assert that the point is inside the left & right edges * for ax in range(n_dimensions): * root.barycenter[ax] *= frac_seen # <<<<<<<<<<<<<< @@ -3256,7 +3401,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 __pyx_t_4 = __pyx_v_ax; (__pyx_v_root->barycenter[__pyx_t_4]) = ((__pyx_v_root->barycenter[__pyx_t_4]) * __pyx_v_frac_seen); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":268 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":270 * for ax in range(n_dimensions): * root.barycenter[ax] *= frac_seen * if (pos[ax] > (root.left_edge[ax] + root.width[ax] + EPSILON)): # <<<<<<<<<<<<<< @@ -3266,7 +3411,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 __pyx_t_2 = (((__pyx_v_pos[__pyx_v_ax]) > (((__pyx_v_root->left_edge[__pyx_v_ax]) + (__pyx_v_root->width[__pyx_v_ax])) + __pyx_v_7sklearn_8manifold_16_barnes_hut_tsne_EPSILON)) != 0); if (__pyx_t_2) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":269 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":271 * root.barycenter[ax] *= frac_seen * if (pos[ax] > (root.left_edge[ax] + root.width[ax] + EPSILON)): * printf("[t-SNE] Error: point (%1.9e) is above right edge of node " # <<<<<<<<<<<<<< @@ -3275,7 +3420,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 */ printf(__pyx_k_t_SNE_Error_point_1_9e_is_above, (__pyx_v_pos[__pyx_v_ax]), ((__pyx_v_root->left_edge[__pyx_v_ax]) + (__pyx_v_root->width[__pyx_v_ax]))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":271 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":273 * printf("[t-SNE] Error: point (%1.9e) is above right edge of node " * "(%1.9e)\n", pos[ax], root.left_edge[ax] + root.width[ax]) * return -1 # <<<<<<<<<<<<<< @@ -3284,9 +3429,17 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 */ __pyx_r = -1; goto __pyx_L0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":270 + * for ax in range(n_dimensions): + * root.barycenter[ax] *= frac_seen + * if (pos[ax] > (root.left_edge[ax] + root.width[ax] + EPSILON)): # <<<<<<<<<<<<<< + * printf("[t-SNE] Error: point (%1.9e) is above right edge of node " + * "(%1.9e)\n", pos[ax], root.left_edge[ax] + root.width[ax]) + */ } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":272 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":274 * "(%1.9e)\n", pos[ax], root.left_edge[ax] + root.width[ax]) * return -1 * if (pos[ax] < root.left_edge[ax] - EPSILON): # <<<<<<<<<<<<<< @@ -3296,7 +3449,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 __pyx_t_2 = (((__pyx_v_pos[__pyx_v_ax]) < ((__pyx_v_root->left_edge[__pyx_v_ax]) - __pyx_v_7sklearn_8manifold_16_barnes_hut_tsne_EPSILON)) != 0); if (__pyx_t_2) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":273 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":275 * return -1 * if (pos[ax] < root.left_edge[ax] - EPSILON): * printf("[t-SNE] Error: point (%1.9e) is below left edge of node " # <<<<<<<<<<<<<< @@ -3305,7 +3458,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 */ printf(__pyx_k_t_SNE_Error_point_1_9e_is_below, (__pyx_v_pos[__pyx_v_ax]), (__pyx_v_root->left_edge[__pyx_v_ax])); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":275 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":277 * printf("[t-SNE] Error: point (%1.9e) is below left edge of node " * "(%1.9e)\n", pos[ax], root.left_edge[ax]) * return -1 # <<<<<<<<<<<<<< @@ -3314,10 +3467,18 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 */ __pyx_r = -1; goto __pyx_L0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":274 + * "(%1.9e)\n", pos[ax], root.left_edge[ax] + root.width[ax]) + * return -1 + * if (pos[ax] < root.left_edge[ax] - EPSILON): # <<<<<<<<<<<<<< + * printf("[t-SNE] Error: point (%1.9e) is below left edge of node " + * "(%1.9e)\n", pos[ax], root.left_edge[ax]) + */ } } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":276 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":278 * "(%1.9e)\n", pos[ax], root.left_edge[ax]) * return -1 * for ax in range(n_dimensions): # <<<<<<<<<<<<<< @@ -3328,7 +3489,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_1; __pyx_t_3+=1) { __pyx_v_ax = __pyx_t_3; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":277 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":279 * return -1 * for ax in range(n_dimensions): * root.barycenter[ax] += pos[ax] * frac_new # <<<<<<<<<<<<<< @@ -3339,7 +3500,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 (__pyx_v_root->barycenter[__pyx_t_4]) = ((__pyx_v_root->barycenter[__pyx_t_4]) + ((__pyx_v_pos[__pyx_v_ax]) * __pyx_v_frac_new)); } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":284 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":286 * # 1) Insert into this node if it is a leaf and empty * # 2) Subdivide this node if it is currently occupied * if (root.size == 0) & root.is_leaf: # <<<<<<<<<<<<<< @@ -3349,7 +3510,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 __pyx_t_2 = (((__pyx_v_root->size == 0) & __pyx_v_root->is_leaf) != 0); if (__pyx_t_2) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":286 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":288 * if (root.size == 0) & root.is_leaf: * # Root node is empty and a leaf * if DEBUGFLAG: # <<<<<<<<<<<<<< @@ -3358,7 +3519,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 */ if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":287 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":289 * # Root node is empty and a leaf * if DEBUGFLAG: * printf("[t-SNE] [d=%i] Inserting [%f, %f] into blank cell\n", depth, # <<<<<<<<<<<<<< @@ -3366,11 +3527,17 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 * for ax in range(n_dimensions): */ printf(__pyx_k_t_SNE_d_i_Inserting_f_f_into_bl, __pyx_v_depth, (__pyx_v_pos[0]), (__pyx_v_pos[1])); - goto __pyx_L12; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":288 + * if (root.size == 0) & root.is_leaf: + * # Root node is empty and a leaf + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] [d=%i] Inserting [%f, %f] into blank cell\n", depth, + * pos[0], pos[1]) + */ } - __pyx_L12:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":289 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":291 * printf("[t-SNE] [d=%i] Inserting [%f, %f] into blank cell\n", depth, * pos[0], pos[1]) * for ax in range(n_dimensions): # <<<<<<<<<<<<<< @@ -3381,7 +3548,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_1; __pyx_t_3+=1) { __pyx_v_ax = __pyx_t_3; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":290 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":292 * pos[0], pos[1]) * for ax in range(n_dimensions): * root.leaf_point_position[ax] = pos[ax] # <<<<<<<<<<<<<< @@ -3391,7 +3558,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 (__pyx_v_root->leaf_point_position[__pyx_v_ax]) = (__pyx_v_pos[__pyx_v_ax]); } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":291 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":293 * for ax in range(n_dimensions): * root.leaf_point_position[ax] = pos[ax] * root.point_index = point_index # <<<<<<<<<<<<<< @@ -3400,7 +3567,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 */ __pyx_v_root->point_index = __pyx_v_point_index; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":292 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":294 * root.leaf_point_position[ax] = pos[ax] * root.point_index = point_index * root.size = duplicate_count # <<<<<<<<<<<<<< @@ -3409,7 +3576,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 */ __pyx_v_root->size = __pyx_v_duplicate_count; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":293 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":295 * root.point_index = point_index * root.size = duplicate_count * return 0 # <<<<<<<<<<<<<< @@ -3418,19 +3585,27 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 */ __pyx_r = 0; goto __pyx_L0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":286 + * # 1) Insert into this node if it is a leaf and empty + * # 2) Subdivide this node if it is currently occupied + * if (root.size == 0) & root.is_leaf: # <<<<<<<<<<<<<< + * # Root node is empty and a leaf + * if DEBUGFLAG: + */ } - /*else*/ { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":296 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":298 * else: * # Root node is occupied or not a leaf * if DEBUGFLAG: # <<<<<<<<<<<<<< * printf("[t-SNE] [d=%i] Node %p is occupied or is a leaf.\n", depth, * root) */ + /*else*/ { if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":297 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":299 * # Root node is occupied or not a leaf * if DEBUGFLAG: * printf("[t-SNE] [d=%i] Node %p is occupied or is a leaf.\n", depth, # <<<<<<<<<<<<<< @@ -3439,7 +3614,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 */ printf(__pyx_k_t_SNE_d_i_Node_p_is_occupied_or, __pyx_v_depth, __pyx_v_root); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":299 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":301 * printf("[t-SNE] [d=%i] Node %p is occupied or is a leaf.\n", depth, * root) * printf("[t-SNE] [d=%i] Node %p leaf = %i. Size %i\n", depth, root, # <<<<<<<<<<<<<< @@ -3447,11 +3622,17 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 * if root.is_leaf & (root.size > 0): */ printf(__pyx_k_t_SNE_d_i_Node_p_leaf_i_Size_i, __pyx_v_depth, __pyx_v_root, __pyx_v_root->is_leaf, __pyx_v_root->size); - goto __pyx_L15; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":298 + * else: + * # Root node is occupied or not a leaf + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] [d=%i] Node %p is occupied or is a leaf.\n", depth, + * root) + */ } - __pyx_L15:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":301 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":303 * printf("[t-SNE] [d=%i] Node %p leaf = %i. Size %i\n", depth, root, * root.is_leaf, root.size) * if root.is_leaf & (root.size > 0): # <<<<<<<<<<<<<< @@ -3461,7 +3642,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 __pyx_t_2 = ((__pyx_v_root->is_leaf & (__pyx_v_root->size > 0)) != 0); if (__pyx_t_2) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":303 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":305 * if root.is_leaf & (root.size > 0): * # is a leaf node and is occupied * for ax in range(n_dimensions): # <<<<<<<<<<<<<< @@ -3472,7 +3653,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_1; __pyx_t_3+=1) { __pyx_v_ax = __pyx_t_3; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":304 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":306 * # is a leaf node and is occupied * for ax in range(n_dimensions): * not_identical &= (fabsf(pos[ax] - root.leaf_point_position[ax]) < EPSILON) # <<<<<<<<<<<<<< @@ -3481,7 +3662,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 */ __pyx_v_not_identical = (__pyx_v_not_identical & (fabsf(((__pyx_v_pos[__pyx_v_ax]) - (__pyx_v_root->leaf_point_position[__pyx_v_ax]))) < __pyx_v_7sklearn_8manifold_16_barnes_hut_tsne_EPSILON)); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":305 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":307 * for ax in range(n_dimensions): * not_identical &= (fabsf(pos[ax] - root.leaf_point_position[ax]) < EPSILON) * not_identical &= (root.point_index != point_index) # <<<<<<<<<<<<<< @@ -3491,7 +3672,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 __pyx_v_not_identical = (__pyx_v_not_identical & (__pyx_v_root->point_index != __pyx_v_point_index)); } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":306 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":308 * not_identical &= (fabsf(pos[ax] - root.leaf_point_position[ax]) < EPSILON) * not_identical &= (root.point_index != point_index) * if not_identical == 1: # <<<<<<<<<<<<<< @@ -3501,7 +3682,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 __pyx_t_2 = ((__pyx_v_not_identical == 1) != 0); if (__pyx_t_2) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":307 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":309 * not_identical &= (root.point_index != point_index) * if not_identical == 1: * root.size += duplicate_count # <<<<<<<<<<<<<< @@ -3510,7 +3691,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 */ __pyx_v_root->size = (__pyx_v_root->size + __pyx_v_duplicate_count); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":308 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":310 * if not_identical == 1: * root.size += duplicate_count * if DEBUGFLAG: # <<<<<<<<<<<<<< @@ -3519,7 +3700,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 */ if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":309 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":311 * root.size += duplicate_count * if DEBUGFLAG: * printf("[t-SNE] Warning: [d=%i] Detected identical " # <<<<<<<<<<<<<< @@ -3527,11 +3708,17 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 * depth, root.size) */ printf(__pyx_k_t_SNE_Warning_d_i_Detected_iden, __pyx_v_depth, __pyx_v_root->size); - goto __pyx_L20; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":310 + * if not_identical == 1: + * root.size += duplicate_count + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] Warning: [d=%i] Detected identical " + * "points. Returning. Leaf now has size %i\n", + */ } - __pyx_L20:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":312 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":314 * "points. Returning. Leaf now has size %i\n", * depth, root.size) * return 0 # <<<<<<<<<<<<<< @@ -3540,12 +3727,26 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 */ __pyx_r = 0; goto __pyx_L0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":308 + * not_identical &= (fabsf(pos[ax] - root.leaf_point_position[ax]) < EPSILON) + * not_identical &= (root.point_index != point_index) + * if not_identical == 1: # <<<<<<<<<<<<<< + * root.size += duplicate_count + * if DEBUGFLAG: + */ } - goto __pyx_L16; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":303 + * printf("[t-SNE] [d=%i] Node %p leaf = %i. Size %i\n", depth, root, + * root.is_leaf, root.size) + * if root.is_leaf & (root.size > 0): # <<<<<<<<<<<<<< + * # is a leaf node and is occupied + * for ax in range(n_dimensions): + */ } - __pyx_L16:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":315 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":317 * # If necessary, subdivide this node before * # descending * if root.is_leaf: # <<<<<<<<<<<<<< @@ -3555,7 +3756,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 __pyx_t_2 = (__pyx_v_root->is_leaf != 0); if (__pyx_t_2) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":316 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":318 * # descending * if root.is_leaf: * if DEBUGFLAG: # <<<<<<<<<<<<<< @@ -3564,7 +3765,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 */ if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":317 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":319 * if root.is_leaf: * if DEBUGFLAG: * printf("[t-SNE] [d=%i] Subdividing this leaf node %p\n", depth, # <<<<<<<<<<<<<< @@ -3572,11 +3773,17 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 * subdivide(root) */ printf(__pyx_k_t_SNE_d_i_Subdividing_this_leaf, __pyx_v_depth, __pyx_v_root); - goto __pyx_L22; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":318 + * # descending + * if root.is_leaf: + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] [d=%i] Subdividing this leaf node %p\n", depth, + * root) + */ } - __pyx_L22:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":319 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":321 * printf("[t-SNE] [d=%i] Subdividing this leaf node %p\n", depth, * root) * subdivide(root) # <<<<<<<<<<<<<< @@ -3584,11 +3791,17 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 * # at this node, and the new one we're attempting */ __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_subdivide(__pyx_v_root); - goto __pyx_L21; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":317 + * # If necessary, subdivide this node before + * # descending + * if root.is_leaf: # <<<<<<<<<<<<<< + * if DEBUGFLAG: + * printf("[t-SNE] [d=%i] Subdividing this leaf node %p\n", depth, + */ } - __pyx_L21:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":323 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":325 * # at this node, and the new one we're attempting * # to insert * if root.size > 0: # <<<<<<<<<<<<<< @@ -3598,7 +3811,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 __pyx_t_2 = ((__pyx_v_root->size > 0) != 0); if (__pyx_t_2) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":324 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":326 * # to insert * if root.size > 0: * child = select_child(root, root.leaf_point_position, root.point_index) # <<<<<<<<<<<<<< @@ -3607,7 +3820,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 */ __pyx_v_child = __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_select_child(__pyx_v_root, __pyx_v_root->leaf_point_position, __pyx_v_root->point_index); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":325 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":327 * if root.size > 0: * child = select_child(root, root.leaf_point_position, root.point_index) * if DEBUGFLAG: # <<<<<<<<<<<<<< @@ -3616,7 +3829,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 */ if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":326 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":328 * child = select_child(root, root.leaf_point_position, root.point_index) * if DEBUGFLAG: * printf("[t-SNE] [d=%i] Relocating old point to node %p\n", # <<<<<<<<<<<<<< @@ -3624,11 +3837,17 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 * insert(child, root.leaf_point_position, root.point_index, depth + 1, root.size) */ printf(__pyx_k_t_SNE_d_i_Relocating_old_point, __pyx_v_depth, __pyx_v_child); - goto __pyx_L24; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":327 + * if root.size > 0: + * child = select_child(root, root.leaf_point_position, root.point_index) + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] [d=%i] Relocating old point to node %p\n", + * depth, child) + */ } - __pyx_L24:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":328 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":330 * printf("[t-SNE] [d=%i] Relocating old point to node %p\n", * depth, child) * insert(child, root.leaf_point_position, root.point_index, depth + 1, root.size) # <<<<<<<<<<<<<< @@ -3636,11 +3855,17 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 * if DEBUGFLAG: */ __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(__pyx_v_child, __pyx_v_root->leaf_point_position, __pyx_v_root->point_index, (__pyx_v_depth + 1), __pyx_v_root->size); - goto __pyx_L23; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":325 + * # at this node, and the new one we're attempting + * # to insert + * if root.size > 0: # <<<<<<<<<<<<<< + * child = select_child(root, root.leaf_point_position, root.point_index) + * if DEBUGFLAG: + */ } - __pyx_L23:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":330 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":332 * insert(child, root.leaf_point_position, root.point_index, depth + 1, root.size) * # Insert the new point * if DEBUGFLAG: # <<<<<<<<<<<<<< @@ -3649,7 +3874,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 */ if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":331 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":333 * # Insert the new point * if DEBUGFLAG: * printf("[t-SNE] [d=%i] Selecting node for new point\n", depth) # <<<<<<<<<<<<<< @@ -3657,11 +3882,17 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 * if root.size > 0: */ printf(__pyx_k_t_SNE_d_i_Selecting_node_for_ne, __pyx_v_depth); - goto __pyx_L25; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":332 + * insert(child, root.leaf_point_position, root.point_index, depth + 1, root.size) + * # Insert the new point + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] [d=%i] Selecting node for new point\n", depth) + * child = select_child(root, pos, point_index) + */ } - __pyx_L25:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":332 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":334 * if DEBUGFLAG: * printf("[t-SNE] [d=%i] Selecting node for new point\n", depth) * child = select_child(root, pos, point_index) # <<<<<<<<<<<<<< @@ -3670,7 +3901,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 */ __pyx_v_child = __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_select_child(__pyx_v_root, __pyx_v_pos, __pyx_v_point_index); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":333 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":335 * printf("[t-SNE] [d=%i] Selecting node for new point\n", depth) * child = select_child(root, pos, point_index) * if root.size > 0: # <<<<<<<<<<<<<< @@ -3680,7 +3911,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 __pyx_t_2 = ((__pyx_v_root->size > 0) != 0); if (__pyx_t_2) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":335 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":337 * if root.size > 0: * # Remove the point from this node * for ax in range(n_dimensions): # <<<<<<<<<<<<<< @@ -3691,7 +3922,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_1; __pyx_t_3+=1) { __pyx_v_ax = __pyx_t_3; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":336 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":338 * # Remove the point from this node * for ax in range(n_dimensions): * root.leaf_point_position[ax] = -1 # <<<<<<<<<<<<<< @@ -3701,7 +3932,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 (__pyx_v_root->leaf_point_position[__pyx_v_ax]) = -1.0; } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":337 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":339 * for ax in range(n_dimensions): * root.leaf_point_position[ax] = -1 * root.size = 0 # <<<<<<<<<<<<<< @@ -3710,7 +3941,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 */ __pyx_v_root->size = 0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":338 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":340 * root.leaf_point_position[ax] = -1 * root.size = 0 * root.point_index = -1 # <<<<<<<<<<<<<< @@ -3718,11 +3949,17 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 * */ __pyx_v_root->point_index = -1; - goto __pyx_L26; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":335 + * printf("[t-SNE] [d=%i] Selecting node for new point\n", depth) + * child = select_child(root, pos, point_index) + * if root.size > 0: # <<<<<<<<<<<<<< + * # Remove the point from this node + * for ax in range(n_dimensions): + */ } - __pyx_L26:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":339 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":341 * root.size = 0 * root.point_index = -1 * return insert(child, pos, point_index, depth + 1, 1) # <<<<<<<<<<<<<< @@ -3733,7 +3970,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 goto __pyx_L0; } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":239 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":241 * * * cdef int insert(Node *root, float pos[3], long point_index, long depth, long # <<<<<<<<<<<<<< @@ -3746,7 +3983,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(struct __pyx_t_7 return __pyx_r; } -/* "sklearn/manifold/_barnes_hut_tsne.pyx":341 +/* "sklearn/manifold/_barnes_hut_tsne.pyx":343 * return insert(child, pos, point_index, depth + 1, 1) * * cdef int insert_many(Tree* tree, float[:,:] pos_array) nogil: # <<<<<<<<<<<<<< @@ -3765,11 +4002,11 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert_many(struct __py long __pyx_t_2; int __pyx_t_3; int __pyx_t_4; - long __pyx_t_5; - int __pyx_t_6; + Py_ssize_t __pyx_t_5; + Py_ssize_t __pyx_t_6; int __pyx_t_7; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":343 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":345 * cdef int insert_many(Tree* tree, float[:,:] pos_array) nogil: * # Insert each data point into the tree one at a time * cdef long nrows = pos_array.shape[0] # <<<<<<<<<<<<<< @@ -3778,7 +4015,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert_many(struct __py */ __pyx_v_nrows = (__pyx_v_pos_array.shape[0]); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":347 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":349 * cdef int ax * cdef float row[3] * cdef long err = 0 # <<<<<<<<<<<<<< @@ -3787,7 +4024,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert_many(struct __py */ __pyx_v_err = 0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":348 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":350 * cdef float row[3] * cdef long err = 0 * for i in range(nrows): # <<<<<<<<<<<<<< @@ -3798,7 +4035,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert_many(struct __py for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { __pyx_v_i = __pyx_t_2; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":349 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":351 * cdef long err = 0 * for i in range(nrows): * for ax in range(tree.n_dimensions): # <<<<<<<<<<<<<< @@ -3809,7 +4046,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert_many(struct __py for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { __pyx_v_ax = __pyx_t_4; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":350 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":352 * for i in range(nrows): * for ax in range(tree.n_dimensions): * row[ax] = pos_array[i, ax] # <<<<<<<<<<<<<< @@ -3821,7 +4058,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert_many(struct __py (__pyx_v_row[__pyx_v_ax]) = (*((float *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_pos_array.data + __pyx_t_5 * __pyx_v_pos_array.strides[0]) ) + __pyx_t_6 * __pyx_v_pos_array.strides[1]) ))); } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":351 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":353 * for ax in range(tree.n_dimensions): * row[ax] = pos_array[i, ax] * if DEBUGFLAG: # <<<<<<<<<<<<<< @@ -3830,7 +4067,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert_many(struct __py */ if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":352 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":354 * row[ax] = pos_array[i, ax] * if DEBUGFLAG: * printf("[t-SNE] inserting point %i: [%f, %f]\n", i, row[0], row[1]) # <<<<<<<<<<<<<< @@ -3838,51 +4075,65 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert_many(struct __py * if err != 0: */ printf(__pyx_k_t_SNE_inserting_point_i_f_f, __pyx_v_i, (__pyx_v_row[0]), (__pyx_v_row[1])); - goto __pyx_L7; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":353 + * for ax in range(tree.n_dimensions): + * row[ax] = pos_array[i, ax] + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] inserting point %i: [%f, %f]\n", i, row[0], row[1]) + * err = insert(tree.root_node, row, i, 0, 1) + */ } - __pyx_L7:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":353 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":355 * if DEBUGFLAG: * printf("[t-SNE] inserting point %i: [%f, %f]\n", i, row[0], row[1]) * err = insert(tree.root_node, row, i, 0, 1) # <<<<<<<<<<<<<< * if err != 0: - * printf("[t-SNE] ERROR\n") + * printf("[t-SNE] ERROR\n%s", EMPTY_STRING) */ __pyx_v_err = __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert(__pyx_v_tree->root_node, __pyx_v_row, __pyx_v_i, 0, 1); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":354 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":356 * printf("[t-SNE] inserting point %i: [%f, %f]\n", i, row[0], row[1]) * err = insert(tree.root_node, row, i, 0, 1) * if err != 0: # <<<<<<<<<<<<<< - * printf("[t-SNE] ERROR\n") + * printf("[t-SNE] ERROR\n%s", EMPTY_STRING) * return err */ __pyx_t_7 = ((__pyx_v_err != 0) != 0); if (__pyx_t_7) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":355 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":357 * err = insert(tree.root_node, row, i, 0, 1) * if err != 0: - * printf("[t-SNE] ERROR\n") # <<<<<<<<<<<<<< + * printf("[t-SNE] ERROR\n%s", EMPTY_STRING) # <<<<<<<<<<<<<< * return err * tree.n_points += 1 */ - printf(__pyx_k_t_SNE_ERROR); + printf(__pyx_k_t_SNE_ERROR_s, __pyx_v_7sklearn_8manifold_16_barnes_hut_tsne_EMPTY_STRING); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":356 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":358 * if err != 0: - * printf("[t-SNE] ERROR\n") + * printf("[t-SNE] ERROR\n%s", EMPTY_STRING) * return err # <<<<<<<<<<<<<< * tree.n_points += 1 * return err */ __pyx_r = __pyx_v_err; goto __pyx_L0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":356 + * printf("[t-SNE] inserting point %i: [%f, %f]\n", i, row[0], row[1]) + * err = insert(tree.root_node, row, i, 0, 1) + * if err != 0: # <<<<<<<<<<<<<< + * printf("[t-SNE] ERROR\n%s", EMPTY_STRING) + * return err + */ } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":357 - * printf("[t-SNE] ERROR\n") + /* "sklearn/manifold/_barnes_hut_tsne.pyx":359 + * printf("[t-SNE] ERROR\n%s", EMPTY_STRING) * return err * tree.n_points += 1 # <<<<<<<<<<<<<< * return err @@ -3891,7 +4142,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert_many(struct __py __pyx_v_tree->n_points = (__pyx_v_tree->n_points + 1); } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":358 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":360 * return err * tree.n_points += 1 * return err # <<<<<<<<<<<<<< @@ -3901,7 +4152,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert_many(struct __py __pyx_r = __pyx_v_err; goto __pyx_L0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":341 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":343 * return insert(child, pos, point_index, depth + 1, 1) * * cdef int insert_many(Tree* tree, float[:,:] pos_array) nogil: # <<<<<<<<<<<<<< @@ -3914,7 +4165,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert_many(struct __py return __pyx_r; } -/* "sklearn/manifold/_barnes_hut_tsne.pyx":360 +/* "sklearn/manifold/_barnes_hut_tsne.pyx":362 * return err * * cdef int free_tree(Tree* tree) nogil: # <<<<<<<<<<<<<< @@ -3929,7 +4180,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_tree(struct __pyx_ int __pyx_r; long __pyx_t_1; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":362 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":364 * cdef int free_tree(Tree* tree) nogil: * cdef int check * cdef long* cnt = malloc(sizeof(long) * 3) # <<<<<<<<<<<<<< @@ -3938,7 +4189,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_tree(struct __pyx_ */ __pyx_v_cnt = ((long *)malloc(((sizeof(long)) * 3))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":363 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":365 * cdef int check * cdef long* cnt = malloc(sizeof(long) * 3) * for i in range(3): # <<<<<<<<<<<<<< @@ -3948,7 +4199,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_tree(struct __pyx_ for (__pyx_t_1 = 0; __pyx_t_1 < 3; __pyx_t_1+=1) { __pyx_v_i = __pyx_t_1; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":364 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":366 * cdef long* cnt = malloc(sizeof(long) * 3) * for i in range(3): * cnt[i] = 0 # <<<<<<<<<<<<<< @@ -3958,7 +4209,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_tree(struct __pyx_ (__pyx_v_cnt[__pyx_v_i]) = 0; } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":365 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":367 * for i in range(3): * cnt[i] = 0 * free_recursive(tree, tree.root_node, cnt) # <<<<<<<<<<<<<< @@ -3967,7 +4218,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_tree(struct __pyx_ */ __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_recursive(__pyx_v_tree, __pyx_v_tree->root_node, __pyx_v_cnt); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":366 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":368 * cnt[i] = 0 * free_recursive(tree, tree.root_node, cnt) * free(tree.root_node) # <<<<<<<<<<<<<< @@ -3976,7 +4227,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_tree(struct __pyx_ */ free(__pyx_v_tree->root_node); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":367 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":369 * free_recursive(tree, tree.root_node, cnt) * free(tree.root_node) * free(tree) # <<<<<<<<<<<<<< @@ -3985,7 +4236,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_tree(struct __pyx_ */ free(__pyx_v_tree); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":368 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":370 * free(tree.root_node) * free(tree) * check = cnt[0] == tree.n_cells # <<<<<<<<<<<<<< @@ -3994,7 +4245,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_tree(struct __pyx_ */ __pyx_v_check = ((__pyx_v_cnt[0]) == __pyx_v_tree->n_cells); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":369 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":371 * free(tree) * check = cnt[0] == tree.n_cells * check &= cnt[2] == tree.n_points # <<<<<<<<<<<<<< @@ -4003,7 +4254,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_tree(struct __pyx_ */ __pyx_v_check = (__pyx_v_check & ((__pyx_v_cnt[2]) == __pyx_v_tree->n_points)); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":370 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":372 * check = cnt[0] == tree.n_cells * check &= cnt[2] == tree.n_points * free(cnt) # <<<<<<<<<<<<<< @@ -4012,7 +4263,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_tree(struct __pyx_ */ free(__pyx_v_cnt); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":371 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":373 * check &= cnt[2] == tree.n_points * free(cnt) * return check # <<<<<<<<<<<<<< @@ -4022,7 +4273,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_tree(struct __pyx_ __pyx_r = __pyx_v_check; goto __pyx_L0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":360 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":362 * return err * * cdef int free_tree(Tree* tree) nogil: # <<<<<<<<<<<<<< @@ -4035,7 +4286,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_tree(struct __pyx_ return __pyx_r; } -/* "sklearn/manifold/_barnes_hut_tsne.pyx":373 +/* "sklearn/manifold/_barnes_hut_tsne.pyx":375 * return check * * cdef void free_recursive(Tree* tree, Node *root, long* counts) nogil: # <<<<<<<<<<<<<< @@ -4051,7 +4302,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_recursive(struct int __pyx_t_3; long __pyx_t_4; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":379 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":381 * cdef int idx * cdef Node* child * if not root.is_leaf: # <<<<<<<<<<<<<< @@ -4061,7 +4312,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_recursive(struct __pyx_t_1 = ((!(__pyx_v_root->is_leaf != 0)) != 0); if (__pyx_t_1) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":380 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":382 * cdef Node* child * if not root.is_leaf: * for idx in range(tree.n_cell_per_node): # <<<<<<<<<<<<<< @@ -4072,7 +4323,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_recursive(struct for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { __pyx_v_idx = __pyx_t_3; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":381 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":383 * if not root.is_leaf: * for idx in range(tree.n_cell_per_node): * child = root.children[idx] # <<<<<<<<<<<<<< @@ -4081,7 +4332,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_recursive(struct */ __pyx_v_child = (__pyx_v_root->children[__pyx_v_idx]); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":382 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":384 * for idx in range(tree.n_cell_per_node): * child = root.children[idx] * free_recursive(tree, child, counts) # <<<<<<<<<<<<<< @@ -4090,7 +4341,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_recursive(struct */ __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_recursive(__pyx_v_tree, __pyx_v_child, __pyx_v_counts); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":383 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":385 * child = root.children[idx] * free_recursive(tree, child, counts) * counts[0] += 1 # <<<<<<<<<<<<<< @@ -4100,7 +4351,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_recursive(struct __pyx_t_4 = 0; (__pyx_v_counts[__pyx_t_4]) = ((__pyx_v_counts[__pyx_t_4]) + 1); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":384 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":386 * free_recursive(tree, child, counts) * counts[0] += 1 * if child.is_leaf: # <<<<<<<<<<<<<< @@ -4110,7 +4361,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_recursive(struct __pyx_t_1 = (__pyx_v_child->is_leaf != 0); if (__pyx_t_1) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":385 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":387 * counts[0] += 1 * if child.is_leaf: * counts[1] += 1 # <<<<<<<<<<<<<< @@ -4120,7 +4371,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_recursive(struct __pyx_t_4 = 1; (__pyx_v_counts[__pyx_t_4]) = ((__pyx_v_counts[__pyx_t_4]) + 1); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":386 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":388 * if child.is_leaf: * counts[1] += 1 * if child.size > 0: # <<<<<<<<<<<<<< @@ -4130,7 +4381,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_recursive(struct __pyx_t_1 = ((__pyx_v_child->size > 0) != 0); if (__pyx_t_1) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":387 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":389 * counts[1] += 1 * if child.size > 0: * counts[2] +=1 # <<<<<<<<<<<<<< @@ -4139,25 +4390,39 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_recursive(struct */ __pyx_t_4 = 2; (__pyx_v_counts[__pyx_t_4]) = ((__pyx_v_counts[__pyx_t_4]) + 1); - goto __pyx_L7; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":388 + * if child.is_leaf: + * counts[1] += 1 + * if child.size > 0: # <<<<<<<<<<<<<< + * counts[2] +=1 + * else: + */ } - __pyx_L7:; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":386 + * free_recursive(tree, child, counts) + * counts[0] += 1 + * if child.is_leaf: # <<<<<<<<<<<<<< + * counts[1] += 1 + * if child.size > 0: + */ goto __pyx_L6; } - /*else*/ { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":389 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":391 * counts[2] +=1 * else: * free(child.children) # <<<<<<<<<<<<<< * free(child.width) * free(child.left_edge) */ + /*else*/ { free(__pyx_v_child->children); } __pyx_L6:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":390 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":392 * else: * free(child.children) * free(child.width) # <<<<<<<<<<<<<< @@ -4166,7 +4431,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_recursive(struct */ free(__pyx_v_child->width); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":391 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":393 * free(child.children) * free(child.width) * free(child.left_edge) # <<<<<<<<<<<<<< @@ -4175,7 +4440,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_recursive(struct */ free(__pyx_v_child->left_edge); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":392 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":394 * free(child.width) * free(child.left_edge) * free(child.center) # <<<<<<<<<<<<<< @@ -4184,7 +4449,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_recursive(struct */ free(__pyx_v_child->center); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":393 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":395 * free(child.left_edge) * free(child.center) * free(child.barycenter) # <<<<<<<<<<<<<< @@ -4193,7 +4458,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_recursive(struct */ free(__pyx_v_child->barycenter); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":394 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":396 * free(child.center) * free(child.barycenter) * free(child.leaf_point_position) # <<<<<<<<<<<<<< @@ -4202,7 +4467,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_recursive(struct */ free(__pyx_v_child->leaf_point_position); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":395 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":397 * free(child.barycenter) * free(child.leaf_point_position) * free(child) # <<<<<<<<<<<<<< @@ -4211,11 +4476,17 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_recursive(struct */ free(__pyx_v_child); } - goto __pyx_L3; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":381 + * cdef int idx + * cdef Node* child + * if not root.is_leaf: # <<<<<<<<<<<<<< + * for idx in range(tree.n_cell_per_node): + * child = root.children[idx] + */ } - __pyx_L3:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":373 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":375 * return check * * cdef void free_recursive(Tree* tree, Node *root, long* counts) nogil: # <<<<<<<<<<<<<< @@ -4226,7 +4497,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_recursive(struct /* function exit code */ } -/* "sklearn/manifold/_barnes_hut_tsne.pyx":398 +/* "sklearn/manifold/_barnes_hut_tsne.pyx":400 * * * cdef long count_points(Node* root, long count) nogil: # <<<<<<<<<<<<<< @@ -4243,7 +4514,7 @@ static long __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_count_points(struct __ int __pyx_t_3; int __pyx_t_4; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":401 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":403 * # Walk through the whole tree and count the number * # of points at the leaf nodes * if DEBUGFLAG: # <<<<<<<<<<<<<< @@ -4252,7 +4523,7 @@ static long __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_count_points(struct __ */ if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":402 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":404 * # of points at the leaf nodes * if DEBUGFLAG: * printf("[t-SNE] Counting nodes at root node %p\n", root) # <<<<<<<<<<<<<< @@ -4260,11 +4531,17 @@ static long __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_count_points(struct __ * cdef int idx */ printf(__pyx_k_t_SNE_Counting_nodes_at_root_no, __pyx_v_root); - goto __pyx_L3; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":403 + * # Walk through the whole tree and count the number + * # of points at the leaf nodes + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] Counting nodes at root node %p\n", root) + * cdef Node* child + */ } - __pyx_L3:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":405 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":407 * cdef Node* child * cdef int idx * if root.is_leaf: # <<<<<<<<<<<<<< @@ -4274,7 +4551,7 @@ static long __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_count_points(struct __ __pyx_t_1 = (__pyx_v_root->is_leaf != 0); if (__pyx_t_1) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":406 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":408 * cdef int idx * if root.is_leaf: * count += root.size # <<<<<<<<<<<<<< @@ -4283,7 +4560,7 @@ static long __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_count_points(struct __ */ __pyx_v_count = (__pyx_v_count + __pyx_v_root->size); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":407 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":409 * if root.is_leaf: * count += root.size * if DEBUGFLAG : # <<<<<<<<<<<<<< @@ -4292,7 +4569,7 @@ static long __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_count_points(struct __ */ if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":408 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":410 * count += root.size * if DEBUGFLAG : * printf("[t-SNE] %p is a leaf node, no children\n", root) # <<<<<<<<<<<<<< @@ -4301,7 +4578,7 @@ static long __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_count_points(struct __ */ printf(__pyx_k_t_SNE_p_is_a_leaf_node_no_child, __pyx_v_root); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":409 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":411 * if DEBUGFLAG : * printf("[t-SNE] %p is a leaf node, no children\n", root) * printf("[t-SNE] %i points in node %p\n", count, root) # <<<<<<<<<<<<<< @@ -4309,11 +4586,17 @@ static long __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_count_points(struct __ * # Otherwise, get the children */ printf(__pyx_k_t_SNE_i_points_in_node_p, __pyx_v_count, __pyx_v_root); - goto __pyx_L5; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":409 + * if root.is_leaf: + * count += root.size + * if DEBUGFLAG : # <<<<<<<<<<<<<< + * printf("[t-SNE] %p is a leaf node, no children\n", root) + * printf("[t-SNE] %i points in node %p\n", count, root) + */ } - __pyx_L5:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":410 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":412 * printf("[t-SNE] %p is a leaf node, no children\n", root) * printf("[t-SNE] %i points in node %p\n", count, root) * return count # <<<<<<<<<<<<<< @@ -4322,9 +4605,17 @@ static long __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_count_points(struct __ */ __pyx_r = __pyx_v_count; goto __pyx_L0; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":407 + * cdef Node* child + * cdef int idx + * if root.is_leaf: # <<<<<<<<<<<<<< + * count += root.size + * if DEBUGFLAG : + */ } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":412 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":414 * return count * # Otherwise, get the children * for idx in range(root.tree.n_cell_per_node): # <<<<<<<<<<<<<< @@ -4335,7 +4626,7 @@ static long __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_count_points(struct __ for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { __pyx_v_idx = __pyx_t_3; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":413 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":415 * # Otherwise, get the children * for idx in range(root.tree.n_cell_per_node): * child = root.children[idx] # <<<<<<<<<<<<<< @@ -4344,7 +4635,7 @@ static long __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_count_points(struct __ */ __pyx_v_child = (__pyx_v_root->children[__pyx_v_idx]); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":414 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":416 * for idx in range(root.tree.n_cell_per_node): * child = root.children[idx] * if DEBUGFLAG: # <<<<<<<<<<<<<< @@ -4353,7 +4644,7 @@ static long __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_count_points(struct __ */ if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":415 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":417 * child = root.children[idx] * if DEBUGFLAG: * printf("[t-SNE] Counting points for child %p\n", child) # <<<<<<<<<<<<<< @@ -4361,11 +4652,17 @@ static long __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_count_points(struct __ * if DEBUGFLAG: */ printf(__pyx_k_t_SNE_Counting_points_for_child, __pyx_v_child); - goto __pyx_L8; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":416 + * for idx in range(root.tree.n_cell_per_node): + * child = root.children[idx] + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] Counting points for child %p\n", child) + * if child.is_leaf and child.size > 0: + */ } - __pyx_L8:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":416 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":418 * if DEBUGFLAG: * printf("[t-SNE] Counting points for child %p\n", child) * if child.is_leaf and child.size > 0: # <<<<<<<<<<<<<< @@ -4374,18 +4671,16 @@ static long __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_count_points(struct __ */ __pyx_t_4 = (__pyx_v_child->is_leaf != 0); if (__pyx_t_4) { - goto __pyx_L11_next_and; } else { __pyx_t_1 = __pyx_t_4; goto __pyx_L10_bool_binop_done; } - __pyx_L11_next_and:; __pyx_t_4 = ((__pyx_v_child->size > 0) != 0); __pyx_t_1 = __pyx_t_4; __pyx_L10_bool_binop_done:; if (__pyx_t_1) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":417 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":419 * printf("[t-SNE] Counting points for child %p\n", child) * if child.is_leaf and child.size > 0: * if DEBUGFLAG: # <<<<<<<<<<<<<< @@ -4394,7 +4689,7 @@ static long __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_count_points(struct __ */ if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":418 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":420 * if child.is_leaf and child.size > 0: * if DEBUGFLAG: * printf("[t-SNE] Child has size %d\n", child.size) # <<<<<<<<<<<<<< @@ -4402,11 +4697,17 @@ static long __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_count_points(struct __ * elif not child.is_leaf: */ printf(__pyx_k_t_SNE_Child_has_size_d, __pyx_v_child->size); - goto __pyx_L12; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":419 + * printf("[t-SNE] Counting points for child %p\n", child) + * if child.is_leaf and child.size > 0: + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] Child has size %d\n", child.size) + * count += child.size + */ } - __pyx_L12:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":419 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":421 * if DEBUGFLAG: * printf("[t-SNE] Child has size %d\n", child.size) * count += child.size # <<<<<<<<<<<<<< @@ -4414,54 +4715,75 @@ static long __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_count_points(struct __ * if DEBUGFLAG: */ __pyx_v_count = (__pyx_v_count + __pyx_v_child->size); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":418 + * if DEBUGFLAG: + * printf("[t-SNE] Counting points for child %p\n", child) + * if child.is_leaf and child.size > 0: # <<<<<<<<<<<<<< + * if DEBUGFLAG: + * printf("[t-SNE] Child has size %d\n", child.size) + */ goto __pyx_L9; } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":420 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":422 * printf("[t-SNE] Child has size %d\n", child.size) * count += child.size * elif not child.is_leaf: # <<<<<<<<<<<<<< * if DEBUGFLAG: - * printf("[t-SNE] Child is not a leaf. Descending\n") + * printf("[t-SNE] Child is not a leaf. Descending\n%s", EMPTY_STRING) */ __pyx_t_1 = ((!(__pyx_v_child->is_leaf != 0)) != 0); if (__pyx_t_1) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":421 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":423 * count += child.size * elif not child.is_leaf: * if DEBUGFLAG: # <<<<<<<<<<<<<< - * printf("[t-SNE] Child is not a leaf. Descending\n") + * printf("[t-SNE] Child is not a leaf. Descending\n%s", EMPTY_STRING) * count = count_points(child, count) */ if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":422 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":424 * elif not child.is_leaf: * if DEBUGFLAG: - * printf("[t-SNE] Child is not a leaf. Descending\n") # <<<<<<<<<<<<<< + * printf("[t-SNE] Child is not a leaf. Descending\n%s", EMPTY_STRING) # <<<<<<<<<<<<<< * count = count_points(child, count) * # else case is we have an empty leaf node */ - printf(__pyx_k_t_SNE_Child_is_not_a_leaf_Desce); - goto __pyx_L13; + printf(__pyx_k_t_SNE_Child_is_not_a_leaf_Desce, __pyx_v_7sklearn_8manifold_16_barnes_hut_tsne_EMPTY_STRING); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":423 + * count += child.size + * elif not child.is_leaf: + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] Child is not a leaf. Descending\n%s", EMPTY_STRING) + * count = count_points(child, count) + */ } - __pyx_L13:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":423 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":425 * if DEBUGFLAG: - * printf("[t-SNE] Child is not a leaf. Descending\n") + * printf("[t-SNE] Child is not a leaf. Descending\n%s", EMPTY_STRING) * count = count_points(child, count) # <<<<<<<<<<<<<< * # else case is we have an empty leaf node * # which happens when we create a quadtree for */ __pyx_v_count = __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_count_points(__pyx_v_child, __pyx_v_count); - goto __pyx_L9; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":422 + * printf("[t-SNE] Child has size %d\n", child.size) + * count += child.size + * elif not child.is_leaf: # <<<<<<<<<<<<<< + * if DEBUGFLAG: + * printf("[t-SNE] Child is not a leaf. Descending\n%s", EMPTY_STRING) + */ } __pyx_L9:; } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":428 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":430 * # one point, and then the other neighboring cells * # don't get filled in * if DEBUGFLAG: # <<<<<<<<<<<<<< @@ -4470,7 +4792,7 @@ static long __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_count_points(struct __ */ if (__pyx_e_7sklearn_8manifold_16_barnes_hut_tsne_DEBUGFLAG) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":429 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":431 * # don't get filled in * if DEBUGFLAG: * printf("[t-SNE] %i points in this node\n", count) # <<<<<<<<<<<<<< @@ -4478,11 +4800,17 @@ static long __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_count_points(struct __ * */ printf(__pyx_k_t_SNE_i_points_in_this_node, __pyx_v_count); - goto __pyx_L14; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":430 + * # one point, and then the other neighboring cells + * # don't get filled in + * if DEBUGFLAG: # <<<<<<<<<<<<<< + * printf("[t-SNE] %i points in this node\n", count) + * return count + */ } - __pyx_L14:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":430 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":432 * if DEBUGFLAG: * printf("[t-SNE] %i points in this node\n", count) * return count # <<<<<<<<<<<<<< @@ -4492,7 +4820,7 @@ static long __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_count_points(struct __ __pyx_r = __pyx_v_count; goto __pyx_L0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":398 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":400 * * * cdef long count_points(Node* root, long count) nogil: # <<<<<<<<<<<<<< @@ -4505,12 +4833,12 @@ static long __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_count_points(struct __ return __pyx_r; } -/* "sklearn/manifold/_barnes_hut_tsne.pyx":433 +/* "sklearn/manifold/_barnes_hut_tsne.pyx":435 * * * cdef float compute_gradient(float[:,:] val_P, # <<<<<<<<<<<<<< * float[:,:] pos_reference, - * long[:,:] neighbors, + * np.int64_t[:,:] neighbors, */ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Pyx_memviewslice __pyx_v_val_P, __Pyx_memviewslice __pyx_v_pos_reference, __Pyx_memviewslice __pyx_v_neighbors, __Pyx_memviewslice __pyx_v_tot_force, struct __pyx_t_7sklearn_8manifold_16_barnes_hut_tsne_Node *__pyx_v_root_node, float __pyx_v_theta, float __pyx_v_dof, long __pyx_v_start, long __pyx_v_stop) { @@ -4533,10 +4861,10 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py long __pyx_t_3; long __pyx_t_4; int __pyx_t_5; - long __pyx_t_6; - int __pyx_t_7; + Py_ssize_t __pyx_t_6; + Py_ssize_t __pyx_t_7; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":446 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":448 * cdef long i, coord * cdef int ax * cdef long n = pos_reference.shape[0] # <<<<<<<<<<<<<< @@ -4545,7 +4873,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py */ __pyx_v_n = (__pyx_v_pos_reference.shape[0]); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":447 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":449 * cdef int ax * cdef long n = pos_reference.shape[0] * cdef int n_dimensions = root_node.tree.n_dimensions # <<<<<<<<<<<<<< @@ -4555,7 +4883,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py __pyx_t_1 = __pyx_v_root_node->tree->n_dimensions; __pyx_v_n_dimensions = __pyx_t_1; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":448 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":450 * cdef long n = pos_reference.shape[0] * cdef int n_dimensions = root_node.tree.n_dimensions * if root_node.tree.verbose > 11: # <<<<<<<<<<<<<< @@ -4565,7 +4893,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py __pyx_t_2 = ((__pyx_v_root_node->tree->verbose > 11) != 0); if (__pyx_t_2) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":449 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":451 * cdef int n_dimensions = root_node.tree.n_dimensions * if root_node.tree.verbose > 11: * printf("[t-SNE] Allocating %i elements in force arrays\n", # <<<<<<<<<<<<<< @@ -4573,11 +4901,17 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py * cdef float* sum_Q = malloc(sizeof(float)) */ printf(__pyx_k_t_SNE_Allocating_i_elements_in, ((__pyx_v_n * __pyx_v_n_dimensions) * 2)); - goto __pyx_L3; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":450 + * cdef long n = pos_reference.shape[0] + * cdef int n_dimensions = root_node.tree.n_dimensions + * if root_node.tree.verbose > 11: # <<<<<<<<<<<<<< + * printf("[t-SNE] Allocating %i elements in force arrays\n", + * n * n_dimensions * 2) + */ } - __pyx_L3:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":451 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":453 * printf("[t-SNE] Allocating %i elements in force arrays\n", * n * n_dimensions * 2) * cdef float* sum_Q = malloc(sizeof(float)) # <<<<<<<<<<<<<< @@ -4586,7 +4920,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py */ __pyx_v_sum_Q = ((float *)malloc((sizeof(float)))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":452 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":454 * n * n_dimensions * 2) * cdef float* sum_Q = malloc(sizeof(float)) * cdef float* neg_f = malloc(sizeof(float) * n * n_dimensions) # <<<<<<<<<<<<<< @@ -4595,7 +4929,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py */ __pyx_v_neg_f = ((float *)malloc((((sizeof(float)) * __pyx_v_n) * __pyx_v_n_dimensions))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":453 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":455 * cdef float* sum_Q = malloc(sizeof(float)) * cdef float* neg_f = malloc(sizeof(float) * n * n_dimensions) * cdef float* neg_f_fast = malloc(sizeof(float) * n * n_dimensions) # <<<<<<<<<<<<<< @@ -4604,7 +4938,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py */ __pyx_v_neg_f_fast = ((float *)malloc((((sizeof(float)) * __pyx_v_n) * __pyx_v_n_dimensions))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":454 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":456 * cdef float* neg_f = malloc(sizeof(float) * n * n_dimensions) * cdef float* neg_f_fast = malloc(sizeof(float) * n * n_dimensions) * cdef float* pos_f = malloc(sizeof(float) * n * n_dimensions) # <<<<<<<<<<<<<< @@ -4613,7 +4947,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py */ __pyx_v_pos_f = ((float *)malloc((((sizeof(float)) * __pyx_v_n) * __pyx_v_n_dimensions))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":458 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":460 * cdef float sQ, error * * sum_Q[0] = 0.0 # <<<<<<<<<<<<<< @@ -4622,7 +4956,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py */ (__pyx_v_sum_Q[0]) = 0.0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":459 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":461 * * sum_Q[0] = 0.0 * t1 = clock() # <<<<<<<<<<<<<< @@ -4631,7 +4965,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py */ __pyx_v_t1 = clock(); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":460 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":462 * sum_Q[0] = 0.0 * t1 = clock() * compute_gradient_negative(val_P, pos_reference, neg_f, root_node, sum_Q, # <<<<<<<<<<<<<< @@ -4640,7 +4974,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py */ __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negative(__pyx_v_val_P, __pyx_v_pos_reference, __pyx_v_neg_f, __pyx_v_root_node, __pyx_v_sum_Q, __pyx_v_dof, __pyx_v_theta, __pyx_v_start, __pyx_v_stop); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":462 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":464 * compute_gradient_negative(val_P, pos_reference, neg_f, root_node, sum_Q, * dof, theta, start, stop) * t2 = clock() # <<<<<<<<<<<<<< @@ -4649,7 +4983,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py */ __pyx_v_t2 = clock(); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":463 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":465 * dof, theta, start, stop) * t2 = clock() * if root_node.tree.verbose > 15: # <<<<<<<<<<<<<< @@ -4659,7 +4993,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py __pyx_t_2 = ((__pyx_v_root_node->tree->verbose > 15) != 0); if (__pyx_t_2) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":464 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":466 * t2 = clock() * if root_node.tree.verbose > 15: * printf("[t-SNE] Computing negative gradient: %e ticks\n", ((float) (t2 - t1))) # <<<<<<<<<<<<<< @@ -4667,11 +5001,17 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py * t1 = clock() */ printf(__pyx_k_t_SNE_Computing_negative_gradie, ((double)(__pyx_v_t2 - __pyx_v_t1))); - goto __pyx_L4; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":465 + * dof, theta, start, stop) + * t2 = clock() + * if root_node.tree.verbose > 15: # <<<<<<<<<<<<<< + * printf("[t-SNE] Computing negative gradient: %e ticks\n", ((float) (t2 - t1))) + * sQ = sum_Q[0] + */ } - __pyx_L4:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":465 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":467 * if root_node.tree.verbose > 15: * printf("[t-SNE] Computing negative gradient: %e ticks\n", ((float) (t2 - t1))) * sQ = sum_Q[0] # <<<<<<<<<<<<<< @@ -4680,7 +5020,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py */ __pyx_v_sQ = (__pyx_v_sum_Q[0]); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":466 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":468 * printf("[t-SNE] Computing negative gradient: %e ticks\n", ((float) (t2 - t1))) * sQ = sum_Q[0] * t1 = clock() # <<<<<<<<<<<<<< @@ -4689,7 +5029,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py */ __pyx_v_t1 = clock(); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":467 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":469 * sQ = sum_Q[0] * t1 = clock() * error = compute_gradient_positive(val_P, pos_reference, neighbors, pos_f, # <<<<<<<<<<<<<< @@ -4698,7 +5038,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py */ __pyx_v_error = __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_positive(__pyx_v_val_P, __pyx_v_pos_reference, __pyx_v_neighbors, __pyx_v_pos_f, __pyx_v_n_dimensions, __pyx_v_dof, __pyx_v_sQ, __pyx_v_start, __pyx_v_root_node->tree->verbose); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":469 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":471 * error = compute_gradient_positive(val_P, pos_reference, neighbors, pos_f, * n_dimensions, dof, sQ, start, root_node.tree.verbose) * t2 = clock() # <<<<<<<<<<<<<< @@ -4707,7 +5047,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py */ __pyx_v_t2 = clock(); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":470 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":472 * n_dimensions, dof, sQ, start, root_node.tree.verbose) * t2 = clock() * if root_node.tree.verbose > 15: # <<<<<<<<<<<<<< @@ -4717,7 +5057,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py __pyx_t_2 = ((__pyx_v_root_node->tree->verbose > 15) != 0); if (__pyx_t_2) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":471 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":473 * t2 = clock() * if root_node.tree.verbose > 15: * printf("[t-SNE] Computing positive gradient: %e ticks\n", ((float) (t2 - t1))) # <<<<<<<<<<<<<< @@ -4725,11 +5065,17 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py * for ax in range(n_dimensions): */ printf(__pyx_k_t_SNE_Computing_positive_gradie, ((double)(__pyx_v_t2 - __pyx_v_t1))); - goto __pyx_L5; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":472 + * n_dimensions, dof, sQ, start, root_node.tree.verbose) + * t2 = clock() + * if root_node.tree.verbose > 15: # <<<<<<<<<<<<<< + * printf("[t-SNE] Computing positive gradient: %e ticks\n", ((float) (t2 - t1))) + * for i in range(start, n): + */ } - __pyx_L5:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":472 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":474 * if root_node.tree.verbose > 15: * printf("[t-SNE] Computing positive gradient: %e ticks\n", ((float) (t2 - t1))) * for i in range(start, n): # <<<<<<<<<<<<<< @@ -4740,7 +5086,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py for (__pyx_t_4 = __pyx_v_start; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { __pyx_v_i = __pyx_t_4; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":473 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":475 * printf("[t-SNE] Computing positive gradient: %e ticks\n", ((float) (t2 - t1))) * for i in range(start, n): * for ax in range(n_dimensions): # <<<<<<<<<<<<<< @@ -4751,7 +5097,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_1; __pyx_t_5+=1) { __pyx_v_ax = __pyx_t_5; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":474 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":476 * for i in range(start, n): * for ax in range(n_dimensions): * coord = i * n_dimensions + ax # <<<<<<<<<<<<<< @@ -4760,7 +5106,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py */ __pyx_v_coord = ((__pyx_v_i * __pyx_v_n_dimensions) + __pyx_v_ax); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":475 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":477 * for ax in range(n_dimensions): * coord = i * n_dimensions + ax * tot_force[i, ax] = pos_f[coord] - (neg_f[coord] / sum_Q[0]) # <<<<<<<<<<<<<< @@ -4773,7 +5119,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py } } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":476 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":478 * coord = i * n_dimensions + ax * tot_force[i, ax] = pos_f[coord] - (neg_f[coord] / sum_Q[0]) * free(sum_Q) # <<<<<<<<<<<<<< @@ -4782,7 +5128,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py */ free(__pyx_v_sum_Q); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":477 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":479 * tot_force[i, ax] = pos_f[coord] - (neg_f[coord] / sum_Q[0]) * free(sum_Q) * free(neg_f) # <<<<<<<<<<<<<< @@ -4791,7 +5137,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py */ free(__pyx_v_neg_f); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":478 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":480 * free(sum_Q) * free(neg_f) * free(neg_f_fast) # <<<<<<<<<<<<<< @@ -4800,7 +5146,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py */ free(__pyx_v_neg_f_fast); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":479 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":481 * free(neg_f) * free(neg_f_fast) * free(pos_f) # <<<<<<<<<<<<<< @@ -4809,7 +5155,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py */ free(__pyx_v_pos_f); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":480 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":482 * free(neg_f_fast) * free(pos_f) * return sQ # <<<<<<<<<<<<<< @@ -4819,12 +5165,12 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py __pyx_r = __pyx_v_sQ; goto __pyx_L0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":433 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":435 * * * cdef float compute_gradient(float[:,:] val_P, # <<<<<<<<<<<<<< * float[:,:] pos_reference, - * long[:,:] neighbors, + * np.int64_t[:,:] neighbors, */ /* function exit code */ @@ -4832,15 +5178,15 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__Py return __pyx_r; } -/* "sklearn/manifold/_barnes_hut_tsne.pyx":483 +/* "sklearn/manifold/_barnes_hut_tsne.pyx":485 * * * cdef float compute_gradient_positive(float[:,:] val_P, # <<<<<<<<<<<<<< * float[:,:] pos_reference, - * long[:,:] neighbors, + * np.int64_t[:,:] neighbors, */ -static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_positive(__Pyx_memviewslice __pyx_v_val_P, __Pyx_memviewslice __pyx_v_pos_reference, __Pyx_memviewslice __pyx_v_neighbors, float *__pyx_v_pos_f, int __pyx_v_n_dimensions, float __pyx_v_dof, float __pyx_v_sum_Q, long __pyx_v_start, int __pyx_v_verbose) { +static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_positive(__Pyx_memviewslice __pyx_v_val_P, __Pyx_memviewslice __pyx_v_pos_reference, __Pyx_memviewslice __pyx_v_neighbors, float *__pyx_v_pos_f, int __pyx_v_n_dimensions, float __pyx_v_dof, float __pyx_v_sum_Q, __pyx_t_5numpy_int64_t __pyx_v_start, int __pyx_v_verbose) { int __pyx_v_ax; long __pyx_v_i; long __pyx_v_j; @@ -4863,18 +5209,18 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_posi int __pyx_t_4; long __pyx_t_5; long __pyx_t_6; - long __pyx_t_7; - long __pyx_t_8; - long __pyx_t_9; - long __pyx_t_10; - long __pyx_t_11; - int __pyx_t_12; - long __pyx_t_13; - int __pyx_t_14; + Py_ssize_t __pyx_t_7; + Py_ssize_t __pyx_t_8; + Py_ssize_t __pyx_t_9; + Py_ssize_t __pyx_t_10; + Py_ssize_t __pyx_t_11; + Py_ssize_t __pyx_t_12; + Py_ssize_t __pyx_t_13; + Py_ssize_t __pyx_t_14; long __pyx_t_15; int __pyx_t_16; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":500 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":502 * int ax * long i, j, k * long K = neighbors.shape[1] # <<<<<<<<<<<<<< @@ -4883,7 +5229,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_posi */ __pyx_v_K = (__pyx_v_neighbors.shape[1]); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":501 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":503 * long i, j, k * long K = neighbors.shape[1] * long n = val_P.shape[0] # <<<<<<<<<<<<<< @@ -4892,7 +5238,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_posi */ __pyx_v_n = (__pyx_v_val_P.shape[0]); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":504 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":506 * float[3] buff * float D, Q, pij * float C = 0.0 # <<<<<<<<<<<<<< @@ -4901,7 +5247,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_posi */ __pyx_v_C = 0.0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":505 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":507 * float D, Q, pij * float C = 0.0 * float exponent = (dof + 1.0) / -2.0 # <<<<<<<<<<<<<< @@ -4910,7 +5256,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_posi */ __pyx_v_exponent = ((__pyx_v_dof + 1.0) / -2.0); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":507 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":509 * float exponent = (dof + 1.0) / -2.0 * cdef clock_t t1, t2 * t1 = clock() # <<<<<<<<<<<<<< @@ -4919,7 +5265,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_posi */ __pyx_v_t1 = clock(); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":508 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":510 * cdef clock_t t1, t2 * t1 = clock() * for i in range(start, n): # <<<<<<<<<<<<<< @@ -4930,7 +5276,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_posi for (__pyx_t_2 = __pyx_v_start; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { __pyx_v_i = __pyx_t_2; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":509 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":511 * t1 = clock() * for i in range(start, n): * for ax in range(n_dimensions): # <<<<<<<<<<<<<< @@ -4941,7 +5287,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_posi for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { __pyx_v_ax = __pyx_t_4; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":510 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":512 * for i in range(start, n): * for ax in range(n_dimensions): * pos_f[i * n_dimensions + ax] = 0.0 # <<<<<<<<<<<<<< @@ -4951,7 +5297,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_posi (__pyx_v_pos_f[((__pyx_v_i * __pyx_v_n_dimensions) + __pyx_v_ax)]) = 0.0; } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":511 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":513 * for ax in range(n_dimensions): * pos_f[i * n_dimensions + ax] = 0.0 * for k in range(K): # <<<<<<<<<<<<<< @@ -4962,7 +5308,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_posi for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { __pyx_v_k = __pyx_t_6; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":512 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":514 * pos_f[i * n_dimensions + ax] = 0.0 * for k in range(K): * j = neighbors[i, k] # <<<<<<<<<<<<<< @@ -4971,9 +5317,9 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_posi */ __pyx_t_7 = __pyx_v_i; __pyx_t_8 = __pyx_v_k; - __pyx_v_j = (*((long *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_neighbors.data + __pyx_t_7 * __pyx_v_neighbors.strides[0]) ) + __pyx_t_8 * __pyx_v_neighbors.strides[1]) ))); + __pyx_v_j = (*((__pyx_t_5numpy_int64_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_neighbors.data + __pyx_t_7 * __pyx_v_neighbors.strides[0]) ) + __pyx_t_8 * __pyx_v_neighbors.strides[1]) ))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":515 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":517 * # we don't need to exclude the i==j case since we've * # already thrown it out from the list of neighbors * D = 0.0 # <<<<<<<<<<<<<< @@ -4982,7 +5328,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_posi */ __pyx_v_D = 0.0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":516 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":518 * # already thrown it out from the list of neighbors * D = 0.0 * Q = 0.0 # <<<<<<<<<<<<<< @@ -4991,7 +5337,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_posi */ __pyx_v_Q = 0.0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":517 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":519 * D = 0.0 * Q = 0.0 * pij = val_P[i, j] # <<<<<<<<<<<<<< @@ -5002,7 +5348,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_posi __pyx_t_10 = __pyx_v_j; __pyx_v_pij = (*((float *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_val_P.data + __pyx_t_9 * __pyx_v_val_P.strides[0]) ) + __pyx_t_10 * __pyx_v_val_P.strides[1]) ))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":518 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":520 * Q = 0.0 * pij = val_P[i, j] * for ax in range(n_dimensions): # <<<<<<<<<<<<<< @@ -5013,7 +5359,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_posi for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { __pyx_v_ax = __pyx_t_4; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":519 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":521 * pij = val_P[i, j] * for ax in range(n_dimensions): * buff[ax] = pos_reference[i, ax] - pos_reference[j, ax] # <<<<<<<<<<<<<< @@ -5026,7 +5372,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_posi __pyx_t_14 = __pyx_v_ax; (__pyx_v_buff[__pyx_v_ax]) = ((*((float *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_pos_reference.data + __pyx_t_11 * __pyx_v_pos_reference.strides[0]) ) + __pyx_t_12 * __pyx_v_pos_reference.strides[1]) ))) - (*((float *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_pos_reference.data + __pyx_t_13 * __pyx_v_pos_reference.strides[0]) ) + __pyx_t_14 * __pyx_v_pos_reference.strides[1]) )))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":520 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":522 * for ax in range(n_dimensions): * buff[ax] = pos_reference[i, ax] - pos_reference[j, ax] * D += buff[ax] ** 2.0 # <<<<<<<<<<<<<< @@ -5036,7 +5382,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_posi __pyx_v_D = (__pyx_v_D + pow(((double)(__pyx_v_buff[__pyx_v_ax])), 2.0)); } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":521 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":523 * buff[ax] = pos_reference[i, ax] - pos_reference[j, ax] * D += buff[ax] ** 2.0 * Q = (((1.0 + D) / dof) ** exponent) # <<<<<<<<<<<<<< @@ -5045,7 +5391,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_posi */ __pyx_v_Q = pow(((1.0 + __pyx_v_D) / __pyx_v_dof), ((double)__pyx_v_exponent)); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":522 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":524 * D += buff[ax] ** 2.0 * Q = (((1.0 + D) / dof) ** exponent) * D = pij * Q # <<<<<<<<<<<<<< @@ -5054,7 +5400,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_posi */ __pyx_v_D = (__pyx_v_pij * __pyx_v_Q); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":523 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":525 * Q = (((1.0 + D) / dof) ** exponent) * D = pij * Q * Q /= sum_Q # <<<<<<<<<<<<<< @@ -5063,7 +5409,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_posi */ __pyx_v_Q = (__pyx_v_Q / __pyx_v_sum_Q); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":524 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":526 * D = pij * Q * Q /= sum_Q * C += pij * log((pij + EPSILON) / (Q + EPSILON)) # <<<<<<<<<<<<<< @@ -5072,7 +5418,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_posi */ __pyx_v_C = (__pyx_v_C + (__pyx_v_pij * log(((__pyx_v_pij + __pyx_v_7sklearn_8manifold_16_barnes_hut_tsne_EPSILON) / (__pyx_v_Q + __pyx_v_7sklearn_8manifold_16_barnes_hut_tsne_EPSILON))))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":525 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":527 * Q /= sum_Q * C += pij * log((pij + EPSILON) / (Q + EPSILON)) * for ax in range(n_dimensions): # <<<<<<<<<<<<<< @@ -5083,7 +5429,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_posi for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { __pyx_v_ax = __pyx_t_4; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":526 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":528 * C += pij * log((pij + EPSILON) / (Q + EPSILON)) * for ax in range(n_dimensions): * pos_f[i * n_dimensions + ax] += D * buff[ax] # <<<<<<<<<<<<<< @@ -5096,7 +5442,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_posi } } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":527 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":529 * for ax in range(n_dimensions): * pos_f[i * n_dimensions + ax] += D * buff[ax] * t2 = clock() # <<<<<<<<<<<<<< @@ -5105,7 +5451,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_posi */ __pyx_v_t2 = clock(); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":528 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":530 * pos_f[i * n_dimensions + ax] += D * buff[ax] * t2 = clock() * dt = ((float) (t2 - t1)) # <<<<<<<<<<<<<< @@ -5114,7 +5460,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_posi */ __pyx_v_dt = ((double)(__pyx_v_t2 - __pyx_v_t1)); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":529 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":531 * t2 = clock() * dt = ((float) (t2 - t1)) * if verbose > 10: # <<<<<<<<<<<<<< @@ -5124,7 +5470,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_posi __pyx_t_16 = ((__pyx_v_verbose > 10) != 0); if (__pyx_t_16) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":530 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":532 * dt = ((float) (t2 - t1)) * if verbose > 10: * printf("[t-SNE] Computed error=%1.4f in %1.1e ticks\n", C, dt) # <<<<<<<<<<<<<< @@ -5132,11 +5478,17 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_posi * */ printf(__pyx_k_t_SNE_Computed_error_1_4f_in_1, __pyx_v_C, __pyx_v_dt); - goto __pyx_L13; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":531 + * t2 = clock() + * dt = ((float) (t2 - t1)) + * if verbose > 10: # <<<<<<<<<<<<<< + * printf("[t-SNE] Computed error=%1.4f in %1.1e ticks\n", C, dt) + * return C + */ } - __pyx_L13:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":531 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":533 * if verbose > 10: * printf("[t-SNE] Computed error=%1.4f in %1.1e ticks\n", C, dt) * return C # <<<<<<<<<<<<<< @@ -5146,12 +5498,12 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_posi __pyx_r = __pyx_v_C; goto __pyx_L0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":483 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":485 * * * cdef float compute_gradient_positive(float[:,:] val_P, # <<<<<<<<<<<<<< * float[:,:] pos_reference, - * long[:,:] neighbors, + * np.int64_t[:,:] neighbors, */ /* function exit code */ @@ -5159,7 +5511,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_posi return __pyx_r; } -/* "sklearn/manifold/_barnes_hut_tsne.pyx":535 +/* "sklearn/manifold/_barnes_hut_tsne.pyx":537 * * * cdef void compute_gradient_negative(float[:,:] val_P, # <<<<<<<<<<<<<< @@ -5195,14 +5547,14 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat long __pyx_t_3; long __pyx_t_4; int __pyx_t_5; - long __pyx_t_6; - int __pyx_t_7; + Py_ssize_t __pyx_t_6; + Py_ssize_t __pyx_t_7; long __pyx_t_8; long __pyx_t_9; long __pyx_t_10; int __pyx_t_11; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":544 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":546 * long start, * long stop) nogil: * if stop == -1: # <<<<<<<<<<<<<< @@ -5212,7 +5564,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat __pyx_t_1 = ((__pyx_v_stop == -1) != 0); if (__pyx_t_1) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":545 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":547 * long stop) nogil: * if stop == -1: * stop = pos_reference.shape[0] # <<<<<<<<<<<<<< @@ -5220,11 +5572,17 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat * int ax */ __pyx_v_stop = (__pyx_v_pos_reference.shape[0]); - goto __pyx_L3; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":546 + * long start, + * long stop) nogil: + * if stop == -1: # <<<<<<<<<<<<<< + * stop = pos_reference.shape[0] + * cdef: + */ } - __pyx_L3:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":549 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":551 * int ax * long i, j * long n = stop - start # <<<<<<<<<<<<<< @@ -5233,7 +5591,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ __pyx_v_n = (__pyx_v_stop - __pyx_v_start); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":557 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":559 * float* deltas * long* l * int n_dimensions = root_node.tree.n_dimensions # <<<<<<<<<<<<<< @@ -5243,7 +5601,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat __pyx_t_2 = __pyx_v_root_node->tree->n_dimensions; __pyx_v_n_dimensions = __pyx_t_2; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":560 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":562 * float qijZ, mult * long idx, * long dta = 0 # <<<<<<<<<<<<<< @@ -5252,7 +5610,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ __pyx_v_dta = 0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":561 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":563 * long idx, * long dta = 0 * long dtb = 0 # <<<<<<<<<<<<<< @@ -5261,7 +5619,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ __pyx_v_dtb = 0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":565 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":567 * float* neg_force * * iQ = malloc(sizeof(float)) # <<<<<<<<<<<<<< @@ -5270,7 +5628,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ __pyx_v_iQ = ((float *)malloc((sizeof(float)))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":566 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":568 * * iQ = malloc(sizeof(float)) * force = malloc(sizeof(float) * n_dimensions) # <<<<<<<<<<<<<< @@ -5279,7 +5637,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ __pyx_v_force = ((float *)malloc(((sizeof(float)) * __pyx_v_n_dimensions))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":567 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":569 * iQ = malloc(sizeof(float)) * force = malloc(sizeof(float) * n_dimensions) * pos = malloc(sizeof(float) * n_dimensions) # <<<<<<<<<<<<<< @@ -5288,7 +5646,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ __pyx_v_pos = ((float *)malloc(((sizeof(float)) * __pyx_v_n_dimensions))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":568 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":570 * force = malloc(sizeof(float) * n_dimensions) * pos = malloc(sizeof(float) * n_dimensions) * dist2s = malloc(sizeof(float) * n) # <<<<<<<<<<<<<< @@ -5297,7 +5655,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ __pyx_v_dist2s = ((float *)malloc(((sizeof(float)) * __pyx_v_n))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":569 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":571 * pos = malloc(sizeof(float) * n_dimensions) * dist2s = malloc(sizeof(float) * n) * sizes = malloc(sizeof(long) * n) # <<<<<<<<<<<<<< @@ -5306,7 +5664,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ __pyx_v_sizes = ((long *)malloc(((sizeof(long)) * __pyx_v_n))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":570 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":572 * dist2s = malloc(sizeof(float) * n) * sizes = malloc(sizeof(long) * n) * deltas = malloc(sizeof(float) * n * n_dimensions) # <<<<<<<<<<<<<< @@ -5315,7 +5673,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ __pyx_v_deltas = ((float *)malloc((((sizeof(float)) * __pyx_v_n) * __pyx_v_n_dimensions))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":571 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":573 * sizes = malloc(sizeof(long) * n) * deltas = malloc(sizeof(float) * n * n_dimensions) * l = malloc(sizeof(long)) # <<<<<<<<<<<<<< @@ -5324,7 +5682,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ __pyx_v_l = ((long *)malloc((sizeof(long)))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":572 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":574 * deltas = malloc(sizeof(float) * n * n_dimensions) * l = malloc(sizeof(long)) * neg_force= malloc(sizeof(float) * n_dimensions) # <<<<<<<<<<<<<< @@ -5333,7 +5691,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ __pyx_v_neg_force = ((float *)malloc(((sizeof(float)) * __pyx_v_n_dimensions))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":574 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":576 * neg_force= malloc(sizeof(float) * n_dimensions) * * for i in range(start, stop): # <<<<<<<<<<<<<< @@ -5344,7 +5702,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat for (__pyx_t_4 = __pyx_v_start; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { __pyx_v_i = __pyx_t_4; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":576 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":578 * for i in range(start, stop): * # Clear the arrays * for ax in range(n_dimensions): # <<<<<<<<<<<<<< @@ -5355,7 +5713,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_2; __pyx_t_5+=1) { __pyx_v_ax = __pyx_t_5; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":577 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":579 * # Clear the arrays * for ax in range(n_dimensions): * force[ax] = 0.0 # <<<<<<<<<<<<<< @@ -5364,7 +5722,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ (__pyx_v_force[__pyx_v_ax]) = 0.0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":578 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":580 * for ax in range(n_dimensions): * force[ax] = 0.0 * neg_force[ax] = 0.0 # <<<<<<<<<<<<<< @@ -5373,7 +5731,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ (__pyx_v_neg_force[__pyx_v_ax]) = 0.0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":579 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":581 * force[ax] = 0.0 * neg_force[ax] = 0.0 * pos[ax] = pos_reference[i, ax] # <<<<<<<<<<<<<< @@ -5385,7 +5743,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat (__pyx_v_pos[__pyx_v_ax]) = (*((float *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_pos_reference.data + __pyx_t_6 * __pyx_v_pos_reference.strides[0]) ) + __pyx_t_7 * __pyx_v_pos_reference.strides[1]) ))); } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":580 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":582 * neg_force[ax] = 0.0 * pos[ax] = pos_reference[i, ax] * iQ[0] = 0.0 # <<<<<<<<<<<<<< @@ -5394,7 +5752,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ (__pyx_v_iQ[0]) = 0.0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":581 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":583 * pos[ax] = pos_reference[i, ax] * iQ[0] = 0.0 * l[0] = 0 # <<<<<<<<<<<<<< @@ -5403,7 +5761,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ (__pyx_v_l[0]) = 0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":584 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":586 * # Find which nodes are summarizing and collect their centers of mass * # deltas, and sizes, into vectorized arrays * t1 = clock() # <<<<<<<<<<<<<< @@ -5412,7 +5770,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ __pyx_v_t1 = clock(); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":585 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":587 * # deltas, and sizes, into vectorized arrays * t1 = clock() * compute_non_edge_forces(root_node, theta, i, pos, force, dist2s, # <<<<<<<<<<<<<< @@ -5421,7 +5779,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_non_edge_forces(__pyx_v_root_node, __pyx_v_theta, __pyx_v_i, __pyx_v_pos, __pyx_v_force, __pyx_v_dist2s, __pyx_v_sizes, __pyx_v_deltas, __pyx_v_l); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":587 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":589 * compute_non_edge_forces(root_node, theta, i, pos, force, dist2s, * sizes, deltas, l) * t2 = clock() # <<<<<<<<<<<<<< @@ -5430,7 +5788,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ __pyx_v_t2 = clock(); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":592 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":594 * # is about 10-15x more expensive than the * # following for loop * exponent = (dof + 1.0) / -2.0 # <<<<<<<<<<<<<< @@ -5439,7 +5797,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ __pyx_v_exponent = ((__pyx_v_dof + 1.0) / -2.0); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":593 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":595 * # following for loop * exponent = (dof + 1.0) / -2.0 * for j in range(l[0]): # <<<<<<<<<<<<<< @@ -5450,7 +5808,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) { __pyx_v_j = __pyx_t_9; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":594 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":596 * exponent = (dof + 1.0) / -2.0 * for j in range(l[0]): * qijZ = ((1.0 + dist2s[j]) / dof) ** exponent # <<<<<<<<<<<<<< @@ -5459,7 +5817,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ __pyx_v_qijZ = pow(((1.0 + (__pyx_v_dist2s[__pyx_v_j])) / __pyx_v_dof), __pyx_v_exponent); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":595 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":597 * for j in range(l[0]): * qijZ = ((1.0 + dist2s[j]) / dof) ** exponent * sum_Q[0] += sizes[j] * qijZ # <<<<<<<<<<<<<< @@ -5469,7 +5827,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat __pyx_t_10 = 0; (__pyx_v_sum_Q[__pyx_t_10]) = ((__pyx_v_sum_Q[__pyx_t_10]) + ((__pyx_v_sizes[__pyx_v_j]) * __pyx_v_qijZ)); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":596 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":598 * qijZ = ((1.0 + dist2s[j]) / dof) ** exponent * sum_Q[0] += sizes[j] * qijZ * mult = sizes[j] * qijZ * qijZ # <<<<<<<<<<<<<< @@ -5478,7 +5836,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ __pyx_v_mult = (((__pyx_v_sizes[__pyx_v_j]) * __pyx_v_qijZ) * __pyx_v_qijZ); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":597 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":599 * sum_Q[0] += sizes[j] * qijZ * mult = sizes[j] * qijZ * qijZ * for ax in range(n_dimensions): # <<<<<<<<<<<<<< @@ -5489,7 +5847,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_2; __pyx_t_5+=1) { __pyx_v_ax = __pyx_t_5; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":598 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":600 * mult = sizes[j] * qijZ * qijZ * for ax in range(n_dimensions): * idx = j * n_dimensions + ax # <<<<<<<<<<<<<< @@ -5498,7 +5856,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ __pyx_v_idx = ((__pyx_v_j * __pyx_v_n_dimensions) + __pyx_v_ax); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":599 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":601 * for ax in range(n_dimensions): * idx = j * n_dimensions + ax * neg_force[ax] += mult * deltas[idx] # <<<<<<<<<<<<<< @@ -5510,7 +5868,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat } } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":600 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":602 * idx = j * n_dimensions + ax * neg_force[ax] += mult * deltas[idx] * t3 = clock() # <<<<<<<<<<<<<< @@ -5519,7 +5877,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ __pyx_v_t3 = clock(); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":601 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":603 * neg_force[ax] += mult * deltas[idx] * t3 = clock() * for ax in range(n_dimensions): # <<<<<<<<<<<<<< @@ -5530,7 +5888,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_2; __pyx_t_5+=1) { __pyx_v_ax = __pyx_t_5; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":602 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":604 * t3 = clock() * for ax in range(n_dimensions): * neg_f[i * n_dimensions + ax] = neg_force[ax] # <<<<<<<<<<<<<< @@ -5540,7 +5898,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat (__pyx_v_neg_f[((__pyx_v_i * __pyx_v_n_dimensions) + __pyx_v_ax)]) = (__pyx_v_neg_force[__pyx_v_ax]); } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":603 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":605 * for ax in range(n_dimensions): * neg_f[i * n_dimensions + ax] = neg_force[ax] * dta += t2 - t1 # <<<<<<<<<<<<<< @@ -5549,7 +5907,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ __pyx_v_dta = (__pyx_v_dta + (__pyx_v_t2 - __pyx_v_t1)); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":604 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":606 * neg_f[i * n_dimensions + ax] = neg_force[ax] * dta += t2 - t1 * dtb += t3 - t2 # <<<<<<<<<<<<<< @@ -5559,7 +5917,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat __pyx_v_dtb = (__pyx_v_dtb + (__pyx_v_t3 - __pyx_v_t2)); } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":605 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":607 * dta += t2 - t1 * dtb += t3 - t2 * if root_node.tree.verbose > 20: # <<<<<<<<<<<<<< @@ -5569,7 +5927,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat __pyx_t_1 = ((__pyx_v_root_node->tree->verbose > 20) != 0); if (__pyx_t_1) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":606 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":608 * dtb += t3 - t2 * if root_node.tree.verbose > 20: * printf("[t-SNE] Tree: %i clock ticks | ", dta) # <<<<<<<<<<<<<< @@ -5578,7 +5936,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ printf(__pyx_k_t_SNE_Tree_i_clock_ticks, __pyx_v_dta); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":607 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":609 * if root_node.tree.verbose > 20: * printf("[t-SNE] Tree: %i clock ticks | ", dta) * printf("Force computation: %i clock ticks\n", dtb) # <<<<<<<<<<<<<< @@ -5586,11 +5944,17 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat * free(force) */ printf(__pyx_k_Force_computation_i_clock_ticks, __pyx_v_dtb); - goto __pyx_L14; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":607 + * dta += t2 - t1 + * dtb += t3 - t2 + * if root_node.tree.verbose > 20: # <<<<<<<<<<<<<< + * printf("[t-SNE] Tree: %i clock ticks | ", dta) + * printf("Force computation: %i clock ticks\n", dtb) + */ } - __pyx_L14:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":608 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":610 * printf("[t-SNE] Tree: %i clock ticks | ", dta) * printf("Force computation: %i clock ticks\n", dtb) * free(iQ) # <<<<<<<<<<<<<< @@ -5599,7 +5963,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ free(__pyx_v_iQ); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":609 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":611 * printf("Force computation: %i clock ticks\n", dtb) * free(iQ) * free(force) # <<<<<<<<<<<<<< @@ -5608,7 +5972,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ free(__pyx_v_force); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":610 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":612 * free(iQ) * free(force) * free(pos) # <<<<<<<<<<<<<< @@ -5617,7 +5981,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ free(__pyx_v_pos); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":611 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":613 * free(force) * free(pos) * free(dist2s) # <<<<<<<<<<<<<< @@ -5626,7 +5990,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ free(__pyx_v_dist2s); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":612 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":614 * free(pos) * free(dist2s) * free(sizes) # <<<<<<<<<<<<<< @@ -5635,7 +5999,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ free(__pyx_v_sizes); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":613 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":615 * free(dist2s) * free(sizes) * free(deltas) # <<<<<<<<<<<<<< @@ -5644,7 +6008,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ free(__pyx_v_deltas); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":614 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":616 * free(sizes) * free(deltas) * free(l) # <<<<<<<<<<<<<< @@ -5653,7 +6017,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ free(__pyx_v_l); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":615 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":617 * free(deltas) * free(l) * free(neg_force) # <<<<<<<<<<<<<< @@ -5662,7 +6026,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat */ free(__pyx_v_neg_force); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":535 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":537 * * * cdef void compute_gradient_negative(float[:,:] val_P, # <<<<<<<<<<<<<< @@ -5673,7 +6037,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient_negat /* function exit code */ } -/* "sklearn/manifold/_barnes_hut_tsne.pyx":618 +/* "sklearn/manifold/_barnes_hut_tsne.pyx":620 * * * cdef void compute_non_edge_forces(Node* node, # <<<<<<<<<<<<<< @@ -5694,7 +6058,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_non_edge_force int __pyx_t_5; long __pyx_t_6; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":631 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":633 * Node* child * int i, j * int n_dimensions = node.tree.n_dimensions # <<<<<<<<<<<<<< @@ -5704,7 +6068,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_non_edge_force __pyx_t_1 = __pyx_v_node->tree->n_dimensions; __pyx_v_n_dimensions = __pyx_t_1; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":638 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":640 * # so do not bother to calculate any force contributions * # Also do not compute self-interactions * if node.cumulative_size > 0 and not (node.is_leaf and (node.point_index == # <<<<<<<<<<<<<< @@ -5713,22 +6077,18 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_non_edge_force */ __pyx_t_3 = ((__pyx_v_node->cumulative_size > 0) != 0); if (__pyx_t_3) { - goto __pyx_L5_next_and; } else { __pyx_t_2 = __pyx_t_3; goto __pyx_L4_bool_binop_done; } - __pyx_L5_next_and:; __pyx_t_4 = (__pyx_v_node->is_leaf != 0); if (__pyx_t_4) { - goto __pyx_L7_next_and; } else { __pyx_t_3 = __pyx_t_4; goto __pyx_L6_bool_binop_done; } - __pyx_L7_next_and:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":639 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":641 * # Also do not compute self-interactions * if node.cumulative_size > 0 and not (node.is_leaf and (node.point_index == * point_index)): # <<<<<<<<<<<<<< @@ -5739,7 +6099,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_non_edge_force __pyx_t_3 = __pyx_t_4; __pyx_L6_bool_binop_done:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":638 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":640 * # so do not bother to calculate any force contributions * # Also do not compute self-interactions * if node.cumulative_size > 0 and not (node.is_leaf and (node.point_index == # <<<<<<<<<<<<<< @@ -5751,7 +6111,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_non_edge_force __pyx_L4_bool_binop_done:; if (__pyx_t_2) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":643 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":645 * # I've tried rewriting this in terms of BLAS functions, but it's about * # 1.5x worse when we do so, probbaly because the vectors are small * idx1 = l[0] * n_dimensions # <<<<<<<<<<<<<< @@ -5760,7 +6120,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_non_edge_force */ __pyx_v_idx1 = ((__pyx_v_l[0]) * __pyx_v_n_dimensions); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":644 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":646 * # 1.5x worse when we do so, probbaly because the vectors are small * idx1 = l[0] * n_dimensions * deltas[idx1] = pos[0] - node.barycenter[0] # <<<<<<<<<<<<<< @@ -5769,7 +6129,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_non_edge_force */ (__pyx_v_deltas[__pyx_v_idx1]) = ((__pyx_v_pos[0]) - (__pyx_v_node->barycenter[0])); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":645 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":647 * idx1 = l[0] * n_dimensions * deltas[idx1] = pos[0] - node.barycenter[0] * idx = idx1 # <<<<<<<<<<<<<< @@ -5778,7 +6138,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_non_edge_force */ __pyx_v_idx = __pyx_v_idx1; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":646 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":648 * deltas[idx1] = pos[0] - node.barycenter[0] * idx = idx1 * for i in range(1, n_dimensions): # <<<<<<<<<<<<<< @@ -5789,7 +6149,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_non_edge_force for (__pyx_t_5 = 1; __pyx_t_5 < __pyx_t_1; __pyx_t_5+=1) { __pyx_v_i = __pyx_t_5; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":647 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":649 * idx = idx1 * for i in range(1, n_dimensions): * idx += 1 # <<<<<<<<<<<<<< @@ -5798,7 +6158,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_non_edge_force */ __pyx_v_idx = (__pyx_v_idx + 1); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":648 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":650 * for i in range(1, n_dimensions): * idx += 1 * deltas[idx] = pos[i] - node.barycenter[i] # <<<<<<<<<<<<<< @@ -5808,7 +6168,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_non_edge_force (__pyx_v_deltas[__pyx_v_idx]) = ((__pyx_v_pos[__pyx_v_i]) - (__pyx_v_node->barycenter[__pyx_v_i])); } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":650 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":652 * deltas[idx] = pos[i] - node.barycenter[i] * # do np.sqrt(np.sum(deltas**2.0)) * dist2s[l[0]] = snrm2(n_dimensions, &deltas[idx1], 1) # <<<<<<<<<<<<<< @@ -5817,7 +6177,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_non_edge_force */ (__pyx_v_dist2s[(__pyx_v_l[0])]) = cblas_snrm2(__pyx_v_n_dimensions, (&(__pyx_v_deltas[__pyx_v_idx1])), 1); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":656 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":658 * # If it can be summarized, we use the cell center of mass * # Otherwise, we go a higher level of resolution and into the leaves. * if node.is_leaf or ((node.max_width / dist2s[l[0]]) < theta): # <<<<<<<<<<<<<< @@ -5826,18 +6186,16 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_non_edge_force */ __pyx_t_4 = (__pyx_v_node->is_leaf != 0); if (!__pyx_t_4) { - goto __pyx_L12_next_or; } else { __pyx_t_2 = __pyx_t_4; goto __pyx_L11_bool_binop_done; } - __pyx_L12_next_or:; __pyx_t_4 = (((__pyx_v_node->max_width / (__pyx_v_dist2s[(__pyx_v_l[0])])) < __pyx_v_theta) != 0); __pyx_t_2 = __pyx_t_4; __pyx_L11_bool_binop_done:; if (__pyx_t_2) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":659 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":661 * # Compute the t-SNE force between the reference point and the * # current node * sizes[l[0]] = node.cumulative_size # <<<<<<<<<<<<<< @@ -5847,7 +6205,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_non_edge_force __pyx_t_6 = __pyx_v_node->cumulative_size; (__pyx_v_sizes[(__pyx_v_l[0])]) = __pyx_t_6; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":660 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":662 * # current node * sizes[l[0]] = node.cumulative_size * dist2s[l[0]] = dist2s[l[0]] * dist2s[l[0]] # <<<<<<<<<<<<<< @@ -5856,7 +6214,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_non_edge_force */ (__pyx_v_dist2s[(__pyx_v_l[0])]) = ((__pyx_v_dist2s[(__pyx_v_l[0])]) * (__pyx_v_dist2s[(__pyx_v_l[0])])); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":661 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":663 * sizes[l[0]] = node.cumulative_size * dist2s[l[0]] = dist2s[l[0]] * dist2s[l[0]] * l[0] += 1 # <<<<<<<<<<<<<< @@ -5865,22 +6223,30 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_non_edge_force */ __pyx_t_6 = 0; (__pyx_v_l[__pyx_t_6]) = ((__pyx_v_l[__pyx_t_6]) + 1); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":658 + * # If it can be summarized, we use the cell center of mass + * # Otherwise, we go a higher level of resolution and into the leaves. + * if node.is_leaf or ((node.max_width / dist2s[l[0]]) < theta): # <<<<<<<<<<<<<< + * # Compute the t-SNE force between the reference point and the + * # current node + */ goto __pyx_L10; } - /*else*/ { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":664 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":666 * else: * # Recursively apply Barnes-Hut to child nodes * for idx in range(node.tree.n_cell_per_node): # <<<<<<<<<<<<<< * child = node.children[idx] * if child.cumulative_size == 0: */ + /*else*/ { __pyx_t_1 = __pyx_v_node->tree->n_cell_per_node; for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_1; __pyx_t_6+=1) { __pyx_v_idx = __pyx_t_6; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":665 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":667 * # Recursively apply Barnes-Hut to child nodes * for idx in range(node.tree.n_cell_per_node): * child = node.children[idx] # <<<<<<<<<<<<<< @@ -5889,7 +6255,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_non_edge_force */ __pyx_v_child = (__pyx_v_node->children[__pyx_v_idx]); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":666 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":668 * for idx in range(node.tree.n_cell_per_node): * child = node.children[idx] * if child.cumulative_size == 0: # <<<<<<<<<<<<<< @@ -5899,7 +6265,7 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_non_edge_force __pyx_t_2 = ((__pyx_v_child->cumulative_size == 0) != 0); if (__pyx_t_2) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":667 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":669 * child = node.children[idx] * if child.cumulative_size == 0: * continue # <<<<<<<<<<<<<< @@ -5907,9 +6273,17 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_non_edge_force * point_index, pos, force, dist2s, sizes, deltas, */ goto __pyx_L13_continue; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":668 + * for idx in range(node.tree.n_cell_per_node): + * child = node.children[idx] + * if child.cumulative_size == 0: # <<<<<<<<<<<<<< + * continue + * compute_non_edge_forces(child, theta, + */ } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":668 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":670 * if child.cumulative_size == 0: * continue * compute_non_edge_forces(child, theta, # <<<<<<<<<<<<<< @@ -5921,11 +6295,17 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_non_edge_force } } __pyx_L10:; - goto __pyx_L3; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":640 + * # so do not bother to calculate any force contributions + * # Also do not compute self-interactions + * if node.cumulative_size > 0 and not (node.is_leaf and (node.point_index == # <<<<<<<<<<<<<< + * point_index)): + * # Compute distance between node center of mass and the reference point + */ } - __pyx_L3:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":618 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":620 * * * cdef void compute_non_edge_forces(Node* node, # <<<<<<<<<<<<<< @@ -5936,12 +6316,12 @@ static void __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_non_edge_force /* function exit code */ } -/* "sklearn/manifold/_barnes_hut_tsne.pyx":673 +/* "sklearn/manifold/_barnes_hut_tsne.pyx":675 * * * cdef float compute_error(float[:, :] val_P, # <<<<<<<<<<<<<< * float[:, :] pos_reference, - * long[:,:] neighbors, + * np.int64_t[:,:] neighbors, */ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_error(__Pyx_memviewslice __pyx_v_val_P, __Pyx_memviewslice __pyx_v_pos_reference, __Pyx_memviewslice __pyx_v_neighbors, float __pyx_v_sum_Q, int __pyx_v_n_dimensions, int __pyx_v_verbose) { @@ -5963,19 +6343,19 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_error(__Pyx_m int __pyx_t_2; int __pyx_t_3; int __pyx_t_4; - int __pyx_t_5; - int __pyx_t_6; - int __pyx_t_7; - int __pyx_t_8; + Py_ssize_t __pyx_t_5; + Py_ssize_t __pyx_t_6; + Py_ssize_t __pyx_t_7; + Py_ssize_t __pyx_t_8; int __pyx_t_9; int __pyx_t_10; - int __pyx_t_11; - int __pyx_t_12; - int __pyx_t_13; - int __pyx_t_14; + Py_ssize_t __pyx_t_11; + Py_ssize_t __pyx_t_12; + Py_ssize_t __pyx_t_13; + Py_ssize_t __pyx_t_14; int __pyx_t_15; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":680 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":682 * int verbose) nogil: * cdef int i, j, ax * cdef int I = neighbors.shape[0] # <<<<<<<<<<<<<< @@ -5984,7 +6364,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_error(__Pyx_m */ __pyx_v_I = (__pyx_v_neighbors.shape[0]); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":681 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":683 * cdef int i, j, ax * cdef int I = neighbors.shape[0] * cdef int K = neighbors.shape[1] # <<<<<<<<<<<<<< @@ -5993,7 +6373,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_error(__Pyx_m */ __pyx_v_K = (__pyx_v_neighbors.shape[1]); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":683 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":685 * cdef int K = neighbors.shape[1] * cdef float pij, Q * cdef float C = 0.0 # <<<<<<<<<<<<<< @@ -6002,7 +6382,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_error(__Pyx_m */ __pyx_v_C = 0.0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":686 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":688 * cdef clock_t t1, t2 * cdef float dt, delta * t1 = clock() # <<<<<<<<<<<<<< @@ -6011,7 +6391,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_error(__Pyx_m */ __pyx_v_t1 = clock(); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":687 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":689 * cdef float dt, delta * t1 = clock() * for i in range(I): # <<<<<<<<<<<<<< @@ -6022,7 +6402,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_error(__Pyx_m for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { __pyx_v_i = __pyx_t_2; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":688 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":690 * t1 = clock() * for i in range(I): * for k in range(K): # <<<<<<<<<<<<<< @@ -6033,7 +6413,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_error(__Pyx_m for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { __pyx_v_k = __pyx_t_4; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":689 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":691 * for i in range(I): * for k in range(K): * j = neighbors[i, k] # <<<<<<<<<<<<<< @@ -6042,9 +6422,9 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_error(__Pyx_m */ __pyx_t_5 = __pyx_v_i; __pyx_t_6 = __pyx_v_k; - __pyx_v_j = (*((long *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_neighbors.data + __pyx_t_5 * __pyx_v_neighbors.strides[0]) ) + __pyx_t_6 * __pyx_v_neighbors.strides[1]) ))); + __pyx_v_j = (*((__pyx_t_5numpy_int64_t *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_neighbors.data + __pyx_t_5 * __pyx_v_neighbors.strides[0]) ) + __pyx_t_6 * __pyx_v_neighbors.strides[1]) ))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":690 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":692 * for k in range(K): * j = neighbors[i, k] * pij = val_P[i, j] # <<<<<<<<<<<<<< @@ -6055,7 +6435,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_error(__Pyx_m __pyx_t_8 = __pyx_v_j; __pyx_v_pij = (*((float *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_val_P.data + __pyx_t_7 * __pyx_v_val_P.strides[0]) ) + __pyx_t_8 * __pyx_v_val_P.strides[1]) ))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":691 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":693 * j = neighbors[i, k] * pij = val_P[i, j] * Q = 0.0 # <<<<<<<<<<<<<< @@ -6064,7 +6444,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_error(__Pyx_m */ __pyx_v_Q = 0.0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":692 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":694 * pij = val_P[i, j] * Q = 0.0 * for ax in range(n_dimensions): # <<<<<<<<<<<<<< @@ -6075,7 +6455,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_error(__Pyx_m for (__pyx_t_10 = 0; __pyx_t_10 < __pyx_t_9; __pyx_t_10+=1) { __pyx_v_ax = __pyx_t_10; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":693 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":695 * Q = 0.0 * for ax in range(n_dimensions): * delta = (pos_reference[i, ax] - pos_reference[j, ax]) # <<<<<<<<<<<<<< @@ -6088,7 +6468,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_error(__Pyx_m __pyx_t_14 = __pyx_v_ax; __pyx_v_delta = ((*((float *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_pos_reference.data + __pyx_t_11 * __pyx_v_pos_reference.strides[0]) ) + __pyx_t_12 * __pyx_v_pos_reference.strides[1]) ))) - (*((float *) ( /* dim=1 */ (( /* dim=0 */ (__pyx_v_pos_reference.data + __pyx_t_13 * __pyx_v_pos_reference.strides[0]) ) + __pyx_t_14 * __pyx_v_pos_reference.strides[1]) )))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":694 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":696 * for ax in range(n_dimensions): * delta = (pos_reference[i, ax] - pos_reference[j, ax]) * Q += delta * delta # <<<<<<<<<<<<<< @@ -6098,7 +6478,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_error(__Pyx_m __pyx_v_Q = (__pyx_v_Q + (__pyx_v_delta * __pyx_v_delta)); } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":695 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":697 * delta = (pos_reference[i, ax] - pos_reference[j, ax]) * Q += delta * delta * Q = (1.0 / (sum_Q + Q * sum_Q)) # <<<<<<<<<<<<<< @@ -6107,7 +6487,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_error(__Pyx_m */ __pyx_v_Q = (1.0 / (__pyx_v_sum_Q + (__pyx_v_Q * __pyx_v_sum_Q))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":696 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":698 * Q += delta * delta * Q = (1.0 / (sum_Q + Q * sum_Q)) * C += pij * log((pij + EPSILON) / (Q + EPSILON)) # <<<<<<<<<<<<<< @@ -6118,7 +6498,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_error(__Pyx_m } } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":697 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":699 * Q = (1.0 / (sum_Q + Q * sum_Q)) * C += pij * log((pij + EPSILON) / (Q + EPSILON)) * t2 = clock() # <<<<<<<<<<<<<< @@ -6127,7 +6507,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_error(__Pyx_m */ __pyx_v_t2 = clock(); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":698 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":700 * C += pij * log((pij + EPSILON) / (Q + EPSILON)) * t2 = clock() * dt = ((float) (t2 - t1)) # <<<<<<<<<<<<<< @@ -6136,7 +6516,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_error(__Pyx_m */ __pyx_v_dt = ((double)(__pyx_v_t2 - __pyx_v_t1)); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":699 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":701 * t2 = clock() * dt = ((float) (t2 - t1)) * if verbose > 10: # <<<<<<<<<<<<<< @@ -6146,7 +6526,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_error(__Pyx_m __pyx_t_15 = ((__pyx_v_verbose > 10) != 0); if (__pyx_t_15) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":700 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":702 * dt = ((float) (t2 - t1)) * if verbose > 10: * printf("[t-SNE] Computed error=%1.4f in %1.1e ticks\n", C, dt) # <<<<<<<<<<<<<< @@ -6154,11 +6534,17 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_error(__Pyx_m * */ printf(__pyx_k_t_SNE_Computed_error_1_4f_in_1, __pyx_v_C, __pyx_v_dt); - goto __pyx_L9; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":701 + * t2 = clock() + * dt = ((float) (t2 - t1)) + * if verbose > 10: # <<<<<<<<<<<<<< + * printf("[t-SNE] Computed error=%1.4f in %1.1e ticks\n", C, dt) + * return C + */ } - __pyx_L9:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":701 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":703 * if verbose > 10: * printf("[t-SNE] Computed error=%1.4f in %1.1e ticks\n", C, dt) * return C # <<<<<<<<<<<<<< @@ -6168,12 +6554,12 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_error(__Pyx_m __pyx_r = __pyx_v_C; goto __pyx_L0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":673 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":675 * * * cdef float compute_error(float[:, :] val_P, # <<<<<<<<<<<<<< * float[:, :] pos_reference, - * long[:,:] neighbors, + * np.int64_t[:,:] neighbors, */ /* function exit code */ @@ -6181,7 +6567,7 @@ static float __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_error(__Pyx_m return __pyx_r; } -/* "sklearn/manifold/_barnes_hut_tsne.pyx":704 +/* "sklearn/manifold/_barnes_hut_tsne.pyx":706 * * * def calculate_edge(pos_output): # <<<<<<<<<<<<<< @@ -6222,27 +6608,27 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_calculate_edge(C int __pyx_clineno = 0; __Pyx_RefNannySetupContext("calculate_edge", 0); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":707 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":709 * # Make the boundaries slightly outside of the data * # to avoid floating point error near the edge * left_edge = np.min(pos_output, axis=0) # <<<<<<<<<<<<<< * right_edge = np.max(pos_output, axis=0) * center = (right_edge + left_edge) * 0.5 */ - __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 707; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_min); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 707; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_t_1, __pyx_n_s_min); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 707; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyTuple_New(1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_INCREF(__pyx_v_pos_output); - PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_pos_output); __Pyx_GIVEREF(__pyx_v_pos_output); - __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 707; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_v_pos_output); + __pyx_t_3 = PyDict_New(); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_axis, __pyx_int_0) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 707; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_1, __pyx_t_3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 707; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_3, __pyx_n_s_axis, __pyx_int_0) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_1, __pyx_t_3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; @@ -6250,27 +6636,27 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_calculate_edge(C __pyx_v_left_edge = __pyx_t_4; __pyx_t_4 = 0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":708 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":710 * # to avoid floating point error near the edge * left_edge = np.min(pos_output, axis=0) * right_edge = np.max(pos_output, axis=0) # <<<<<<<<<<<<<< * center = (right_edge + left_edge) * 0.5 * width = np.maximum(np.subtract(right_edge, left_edge), EPSILON) */ - __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 710; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_max); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_GetAttrStr(__pyx_t_4, __pyx_n_s_max); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 710; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 710; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_INCREF(__pyx_v_pos_output); - PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_pos_output); __Pyx_GIVEREF(__pyx_v_pos_output); - __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_v_pos_output); + __pyx_t_1 = PyDict_New(); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 710; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_axis, __pyx_int_0) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_4, __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 708; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_t_1, __pyx_n_s_axis, __pyx_int_0) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 710; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_Call(__pyx_t_3, __pyx_t_4, __pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 710; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -6278,36 +6664,36 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_calculate_edge(C __pyx_v_right_edge = __pyx_t_2; __pyx_t_2 = 0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":709 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":711 * left_edge = np.min(pos_output, axis=0) * right_edge = np.max(pos_output, axis=0) * center = (right_edge + left_edge) * 0.5 # <<<<<<<<<<<<<< * width = np.maximum(np.subtract(right_edge, left_edge), EPSILON) * # Exagerate width to avoid boundary edge */ - __pyx_t_2 = PyNumber_Add(__pyx_v_right_edge, __pyx_v_left_edge); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyNumber_Add(__pyx_v_right_edge, __pyx_v_left_edge); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_1 = PyNumber_Multiply(__pyx_t_2, __pyx_float_0_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 709; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyNumber_Multiply(__pyx_t_2, __pyx_float_0_5); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 711; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_v_center = __pyx_t_1; __pyx_t_1 = 0; - 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__Pyx_RaiseArgtupleInvalid("gradient", 0, 7, 9, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 717; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("gradient", 0, 7, 9, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 6: if (likely((values[6] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_verbose)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("gradient", 0, 7, 9, 6); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 717; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("gradient", 0, 7, 9, 6); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 7: if (kw_args > 0) { @@ -6589,7 +6975,7 @@ static PyObject *__pyx_pw_7sklearn_8manifold_16_barnes_hut_tsne_3gradient(PyObje } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "gradient") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 717; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "gradient") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else { switch (PyTuple_GET_SIZE(__pyx_args)) { @@ -6606,27 +6992,27 @@ static PyObject *__pyx_pw_7sklearn_8manifold_16_barnes_hut_tsne_3gradient(PyObje default: goto __pyx_L5_argtuple_error; } } - 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__pyx_v_n_dimensions = __Pyx_PyInt_As_int(values[5]); if (unlikely((__pyx_v_n_dimensions == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 722; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_verbose = __Pyx_PyInt_As_int(values[6]); if (unlikely((__pyx_v_verbose == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 723; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_pij_input = __Pyx_PyObject_to_MemoryviewSlice_dsds_float(values[0]); if (unlikely(!__pyx_v_pij_input.memview)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_pos_output = __Pyx_PyObject_to_MemoryviewSlice_dsds_float(values[1]); if (unlikely(!__pyx_v_pos_output.memview)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 720; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_neighbors = __Pyx_PyObject_to_MemoryviewSlice_dsds_nn___pyx_t_5numpy_int64_t(values[2]); if (unlikely(!__pyx_v_neighbors.memview)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 721; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_forces = __Pyx_PyObject_to_MemoryviewSlice_dsds_float(values[3]); if (unlikely(!__pyx_v_forces.memview)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 722; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_theta = __pyx_PyFloat_AsFloat(values[4]); if (unlikely((__pyx_v_theta == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 723; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_n_dimensions = __Pyx_PyInt_As_int(values[5]); if (unlikely((__pyx_v_n_dimensions == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_verbose = __Pyx_PyInt_As_int(values[6]); if (unlikely((__pyx_v_verbose == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 725; __pyx_clineno = __LINE__; goto __pyx_L3_error;} if (values[7]) { - __pyx_v_dof = __pyx_PyFloat_AsFloat(values[7]); if (unlikely((__pyx_v_dof == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_dof = __pyx_PyFloat_AsFloat(values[7]); if (unlikely((__pyx_v_dof == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 726; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } else { __pyx_v_dof = ((float)1.0); } if (values[8]) { - __pyx_v_skip_num_points = __Pyx_PyInt_As_long(values[8]); if (unlikely((__pyx_v_skip_num_points == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 725; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_skip_num_points = __Pyx_PyInt_As_long(values[8]); if (unlikely((__pyx_v_skip_num_points == (long)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 727; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } else { __pyx_v_skip_num_points = ((long)0); } } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("gradient", 0, 7, 9, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 717; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("gradient", 0, 7, 9, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("sklearn.manifold._barnes_hut_tsne.gradient", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); @@ -6667,28 +7053,28 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON int __pyx_clineno = 0; __Pyx_RefNannySetupContext("gradient", 0); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":730 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":732 * # up in-place * cdef float C * n = pos_output.shape[0] # <<<<<<<<<<<<<< * left_edge, right_edge, width = calculate_edge(pos_output) * assert width.itemsize == 4 */ - __pyx_t_1 = PyInt_FromSsize_t((__pyx_v_pos_output.shape[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 730; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyInt_FromSsize_t((__pyx_v_pos_output.shape[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 732; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_v_n = __pyx_t_1; __pyx_t_1 = 0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":731 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":733 * cdef float C * n = pos_output.shape[0] * left_edge, right_edge, width = calculate_edge(pos_output) # <<<<<<<<<<<<<< * assert width.itemsize == 4 * assert pij_input.itemsize == 4 */ - __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_calculate_edge); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 731; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_calculate_edge); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_pos_output, 2, (PyObject *(*)(char *)) __pyx_memview_get_float, (int (*)(char *, PyObject *)) __pyx_memview_set_float, 0);; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 731; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_pos_output, 2, (PyObject *(*)(char *)) __pyx_memview_get_float, (int (*)(char *, PyObject *)) __pyx_memview_set_float, 0);; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = NULL; if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_2))) { @@ -6701,17 +7087,17 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON } } if (!__pyx_t_4) { - __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 731; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_GOTREF(__pyx_t_1); } else { - __pyx_t_5 = PyTuple_New(1+1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 731; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(1+1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_4); __Pyx_GIVEREF(__pyx_t_4); __pyx_t_4 = NULL; - PyTuple_SET_ITEM(__pyx_t_5, 0+1, __pyx_t_3); + __Pyx_GIVEREF(__pyx_t_4); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_4); __pyx_t_4 = NULL; __Pyx_GIVEREF(__pyx_t_3); + PyTuple_SET_ITEM(__pyx_t_5, 0+1, __pyx_t_3); __pyx_t_3 = 0; - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 731; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; } @@ -6726,7 +7112,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON if (unlikely(size != 3)) { if (size > 3) __Pyx_RaiseTooManyValuesError(3); else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 731; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { @@ -6742,17 +7128,17 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON __Pyx_INCREF(__pyx_t_5); __Pyx_INCREF(__pyx_t_3); #else - 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__pyx_t_4 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 731; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_6 = Py_TYPE(__pyx_t_4)->tp_iternext; @@ -6762,7 +7148,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON __Pyx_GOTREF(__pyx_t_5); index = 2; __pyx_t_3 = __pyx_t_6(__pyx_t_4); if (unlikely(!__pyx_t_3)) goto __pyx_L3_unpacking_failed; __Pyx_GOTREF(__pyx_t_3); - if (__Pyx_IternextUnpackEndCheck(__pyx_t_6(__pyx_t_4), 3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 731; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_IternextUnpackEndCheck(__pyx_t_6(__pyx_t_4), 3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_6 = NULL; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; goto __pyx_L4_unpacking_done; @@ -6770,7 +7156,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_t_6 = NULL; if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 731; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L4_unpacking_done:; } __pyx_v_left_edge = __pyx_t_2; @@ -6780,7 +7166,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON __pyx_v_width = __pyx_t_3; __pyx_t_3 = 0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":732 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":734 * n = pos_output.shape[0] * left_edge, right_edge, width = calculate_edge(pos_output) * assert width.itemsize == 4 # <<<<<<<<<<<<<< @@ -6789,20 +7175,21 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON */ #ifndef CYTHON_WITHOUT_ASSERTIONS if (unlikely(!Py_OptimizeFlag)) { - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_width, __pyx_n_s_itemsize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 732; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_width, __pyx_n_s_itemsize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 734; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_int_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 732; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_EqObjC(__pyx_t_1, __pyx_int_4, 4, 0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 734; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 732; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 734; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (unlikely(!__pyx_t_7)) { PyErr_SetNone(PyExc_AssertionError); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 732; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 734; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } } #endif - /* "sklearn/manifold/_barnes_hut_tsne.pyx":733 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":735 * left_edge, right_edge, width = calculate_edge(pos_output) * assert width.itemsize == 4 * assert pij_input.itemsize == 4 # <<<<<<<<<<<<<< @@ -6811,23 +7198,24 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON */ #ifndef CYTHON_WITHOUT_ASSERTIONS if (unlikely(!Py_OptimizeFlag)) { - __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_pij_input, 2, (PyObject *(*)(char *)) __pyx_memview_get_float, (int (*)(char *, PyObject *)) __pyx_memview_set_float, 0);; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_pij_input, 2, (PyObject *(*)(char *)) __pyx_memview_get_float, (int (*)(char *, PyObject *)) __pyx_memview_set_float, 0);; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_itemsize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_itemsize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_int_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_EqObjC(__pyx_t_1, __pyx_int_4, 4, 0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (unlikely(!__pyx_t_7)) { PyErr_SetNone(PyExc_AssertionError); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 733; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } } #endif - /* "sklearn/manifold/_barnes_hut_tsne.pyx":734 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":736 * assert width.itemsize == 4 * assert pij_input.itemsize == 4 * assert pos_output.itemsize == 4 # <<<<<<<<<<<<<< @@ -6836,23 +7224,24 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON */ #ifndef CYTHON_WITHOUT_ASSERTIONS if (unlikely(!Py_OptimizeFlag)) { - __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_pos_output, 2, (PyObject *(*)(char *)) __pyx_memview_get_float, (int (*)(char *, PyObject *)) __pyx_memview_set_float, 0);; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 734; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_pos_output, 2, (PyObject *(*)(char *)) __pyx_memview_get_float, (int (*)(char *, PyObject *)) __pyx_memview_set_float, 0);; if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_itemsize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 734; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_itemsize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_int_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 734; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_EqObjC(__pyx_t_1, __pyx_int_4, 4, 0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 734; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (unlikely(!__pyx_t_7)) { PyErr_SetNone(PyExc_AssertionError); - 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__pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_itemsize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_t_3, __pyx_n_s_itemsize); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = PyObject_RichCompare(__pyx_t_1, __pyx_int_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_EqObjC(__pyx_t_1, __pyx_int_4, 4, 0); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_3); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; if (unlikely(!__pyx_t_7)) { PyErr_SetNone(PyExc_AssertionError); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } } #endif - /* "sklearn/manifold/_barnes_hut_tsne.pyx":736 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":738 * assert pos_output.itemsize == 4 * assert forces.itemsize == 4 * m = "Number of neighbors must be < # of points - 1" # <<<<<<<<<<<<<< @@ -6887,7 +7277,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON __Pyx_INCREF(__pyx_kp_s_Number_of_neighbors_must_be_of_p); __pyx_v_m = __pyx_kp_s_Number_of_neighbors_must_be_of_p; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":737 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":739 * assert forces.itemsize == 4 * m = "Number of neighbors must be < # of points - 1" * assert n - 1 >= neighbors.shape[1], m # <<<<<<<<<<<<<< @@ -6896,26 +7286,26 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON */ #ifndef CYTHON_WITHOUT_ASSERTIONS if (unlikely(!Py_OptimizeFlag)) { - 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__pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; if (unlikely(!__pyx_t_7)) { - __pyx_t_5 = PyTuple_Pack(1, __pyx_v_m); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_Pack(1, __pyx_v_m); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); PyErr_SetObject(PyExc_AssertionError, __pyx_t_5); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } } #endif - /* "sklearn/manifold/_barnes_hut_tsne.pyx":738 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":740 * m = "Number of neighbors must be < # of points - 1" * assert n - 1 >= neighbors.shape[1], m * m = "neighbors array and pos_output shapes are incompatible" # <<<<<<<<<<<<<< @@ -6925,7 +7315,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON __Pyx_INCREF(__pyx_kp_s_neighbors_array_and_pos_output_s); __Pyx_DECREF_SET(__pyx_v_m, __pyx_kp_s_neighbors_array_and_pos_output_s); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":739 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":741 * assert n - 1 >= neighbors.shape[1], m * m = "neighbors array and pos_output shapes are incompatible" * assert n == neighbors.shape[0], m # <<<<<<<<<<<<<< @@ -6934,23 +7324,23 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON */ #ifndef CYTHON_WITHOUT_ASSERTIONS if (unlikely(!Py_OptimizeFlag)) { - __pyx_t_5 = PyInt_FromSsize_t((__pyx_v_neighbors.shape[0])); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyInt_FromSsize_t((__pyx_v_neighbors.shape[0])); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_1 = PyObject_RichCompare(__pyx_v_n, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_RichCompare(__pyx_v_n, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (unlikely(!__pyx_t_7)) { - __pyx_t_1 = PyTuple_Pack(1, __pyx_v_m); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyTuple_Pack(1, __pyx_v_m); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); PyErr_SetObject(PyExc_AssertionError, __pyx_t_1); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } } #endif - /* "sklearn/manifold/_barnes_hut_tsne.pyx":740 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":742 * m = "neighbors array and pos_output shapes are incompatible" * assert n == neighbors.shape[0], m * m = "Forces array and pos_output shapes are incompatible" # <<<<<<<<<<<<<< @@ -6960,7 +7350,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON __Pyx_INCREF(__pyx_kp_s_Forces_array_and_pos_output_shap); __Pyx_DECREF_SET(__pyx_v_m, __pyx_kp_s_Forces_array_and_pos_output_shap); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":741 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":743 * assert n == neighbors.shape[0], m * m = "Forces array and pos_output shapes are incompatible" * assert n == forces.shape[0], m # <<<<<<<<<<<<<< @@ -6969,23 +7359,23 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON */ #ifndef CYTHON_WITHOUT_ASSERTIONS if (unlikely(!Py_OptimizeFlag)) { - __pyx_t_1 = PyInt_FromSsize_t((__pyx_v_forces.shape[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyInt_FromSsize_t((__pyx_v_forces.shape[0])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_5 = PyObject_RichCompare(__pyx_v_n, __pyx_t_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyObject_RichCompare(__pyx_v_n, __pyx_t_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; if (unlikely(!__pyx_t_7)) { - __pyx_t_5 = PyTuple_Pack(1, __pyx_v_m); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_Pack(1, __pyx_v_m); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); PyErr_SetObject(PyExc_AssertionError, __pyx_t_5); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 741; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } } #endif - /* "sklearn/manifold/_barnes_hut_tsne.pyx":742 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":744 * m = "Forces array and pos_output shapes are incompatible" * assert n == forces.shape[0], m * m = "Pij and pos_output shapes are incompatible" # <<<<<<<<<<<<<< @@ -6995,7 +7385,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON __Pyx_INCREF(__pyx_kp_s_Pij_and_pos_output_shapes_are_in); __Pyx_DECREF_SET(__pyx_v_m, __pyx_kp_s_Pij_and_pos_output_shapes_are_in); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":743 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":745 * assert n == forces.shape[0], m * m = "Pij and pos_output shapes are incompatible" * assert n == pij_input.shape[0], m # <<<<<<<<<<<<<< @@ -7004,23 +7394,23 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON */ #ifndef CYTHON_WITHOUT_ASSERTIONS if (unlikely(!Py_OptimizeFlag)) { - __pyx_t_5 = PyInt_FromSsize_t((__pyx_v_pij_input.shape[0])); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyInt_FromSsize_t((__pyx_v_pij_input.shape[0])); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_1 = PyObject_RichCompare(__pyx_v_n, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_RichCompare(__pyx_v_n, __pyx_t_5, Py_EQ); __Pyx_XGOTREF(__pyx_t_1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_1); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; if (unlikely(!__pyx_t_7)) { - __pyx_t_1 = PyTuple_Pack(1, __pyx_v_m); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyTuple_Pack(1, __pyx_v_m); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); PyErr_SetObject(PyExc_AssertionError, __pyx_t_1); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 743; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } } #endif - /* "sklearn/manifold/_barnes_hut_tsne.pyx":744 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":746 * m = "Pij and pos_output shapes are incompatible" * assert n == pij_input.shape[0], m * m = "Pij and pos_output shapes are incompatible" # <<<<<<<<<<<<<< @@ -7030,7 +7420,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON __Pyx_INCREF(__pyx_kp_s_Pij_and_pos_output_shapes_are_in); __Pyx_DECREF_SET(__pyx_v_m, __pyx_kp_s_Pij_and_pos_output_shapes_are_in); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":745 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":747 * assert n == pij_input.shape[0], m * m = "Pij and pos_output shapes are incompatible" * assert n == pij_input.shape[1], m # <<<<<<<<<<<<<< @@ -7039,23 +7429,23 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON */ #ifndef CYTHON_WITHOUT_ASSERTIONS if (unlikely(!Py_OptimizeFlag)) { - __pyx_t_1 = PyInt_FromSsize_t((__pyx_v_pij_input.shape[1])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyInt_FromSsize_t((__pyx_v_pij_input.shape[1])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 747; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_5 = PyObject_RichCompare(__pyx_v_n, __pyx_t_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyObject_RichCompare(__pyx_v_n, __pyx_t_1, Py_EQ); __Pyx_XGOTREF(__pyx_t_5); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 747; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __Pyx_PyObject_IsTrue(__pyx_t_5); if (unlikely(__pyx_t_7 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 747; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; if (unlikely(!__pyx_t_7)) { - __pyx_t_5 = PyTuple_Pack(1, __pyx_v_m); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_Pack(1, __pyx_v_m); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 747; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); PyErr_SetObject(PyExc_AssertionError, __pyx_t_5); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 745; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 747; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } } #endif - /* "sklearn/manifold/_barnes_hut_tsne.pyx":746 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":748 * m = "Pij and pos_output shapes are incompatible" * assert n == pij_input.shape[1], m * if verbose > 10: # <<<<<<<<<<<<<< @@ -7065,7 +7455,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON __pyx_t_7 = ((__pyx_v_verbose > 10) != 0); if (__pyx_t_7) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":747 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":749 * assert n == pij_input.shape[1], m * if verbose > 10: * printf("[t-SNE] Initializing tree of n_dimensions %i\n", n_dimensions) # <<<<<<<<<<<<<< @@ -7073,11 +7463,17 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON * if verbose > 10: */ printf(__pyx_k_t_SNE_Initializing_tree_of_n_di, __pyx_v_n_dimensions); - goto __pyx_L5; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":748 + * m = "Pij and pos_output shapes are incompatible" + * assert n == pij_input.shape[1], m + * if verbose > 10: # <<<<<<<<<<<<<< + * printf("[t-SNE] Initializing tree of n_dimensions %i\n", n_dimensions) + * cdef Tree* qt = init_tree(left_edge, width, n_dimensions, verbose) + */ } - __pyx_L5:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":748 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":750 * if verbose > 10: * printf("[t-SNE] Initializing tree of n_dimensions %i\n", n_dimensions) * cdef Tree* qt = init_tree(left_edge, width, n_dimensions, verbose) # <<<<<<<<<<<<<< @@ -7085,14 +7481,14 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON * printf("[t-SNE] Inserting %i points\n", pos_output.shape[0]) */ __pyx_t_8 = __Pyx_PyObject_to_MemoryviewSlice_ds_float(__pyx_v_left_edge); - if (unlikely(!__pyx_t_8.memview)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 748; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__pyx_t_8.memview)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 750; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_9 = __Pyx_PyObject_to_MemoryviewSlice_ds_float(__pyx_v_width); - if (unlikely(!__pyx_t_9.memview)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 748; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__pyx_t_9.memview)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 750; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_qt = __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_init_tree(__pyx_t_8, __pyx_t_9, __pyx_v_n_dimensions, __pyx_v_verbose); __PYX_XDEC_MEMVIEW(&__pyx_t_8, 1); __PYX_XDEC_MEMVIEW(&__pyx_t_9, 1); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":749 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":751 * printf("[t-SNE] Initializing tree of n_dimensions %i\n", n_dimensions) * cdef Tree* qt = init_tree(left_edge, width, n_dimensions, verbose) * if verbose > 10: # <<<<<<<<<<<<<< @@ -7102,7 +7498,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON __pyx_t_7 = ((__pyx_v_verbose > 10) != 0); if (__pyx_t_7) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":750 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":752 * cdef Tree* qt = init_tree(left_edge, width, n_dimensions, verbose) * if verbose > 10: * printf("[t-SNE] Inserting %i points\n", pos_output.shape[0]) # <<<<<<<<<<<<<< @@ -7110,11 +7506,17 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON * assert err == 0, "[t-SNE] Insertion failed" */ printf(__pyx_k_t_SNE_Inserting_i_points, (__pyx_v_pos_output.shape[0])); - goto __pyx_L6; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":751 + * printf("[t-SNE] Initializing tree of n_dimensions %i\n", n_dimensions) + * cdef Tree* qt = init_tree(left_edge, width, n_dimensions, verbose) + * if verbose > 10: # <<<<<<<<<<<<<< + * printf("[t-SNE] Inserting %i points\n", pos_output.shape[0]) + * err = insert_many(qt, pos_output) + */ } - __pyx_L6:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":751 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":753 * if verbose > 10: * printf("[t-SNE] Inserting %i points\n", pos_output.shape[0]) * err = insert_many(qt, pos_output) # <<<<<<<<<<<<<< @@ -7123,131 +7525,143 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON */ __pyx_v_err = __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert_many(__pyx_v_qt, __pyx_v_pos_output); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":752 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":754 * printf("[t-SNE] Inserting %i points\n", pos_output.shape[0]) * err = insert_many(qt, pos_output) * assert err == 0, "[t-SNE] Insertion failed" # <<<<<<<<<<<<<< * if verbose > 10: - * printf("[t-SNE] Computing gradient\n") + * # XXX: format hack to workaround lack of `const char *` type */ #ifndef CYTHON_WITHOUT_ASSERTIONS if (unlikely(!Py_OptimizeFlag)) { if (unlikely(!((__pyx_v_err == 0) != 0))) { PyErr_SetObject(PyExc_AssertionError, __pyx_kp_s_t_SNE_Insertion_failed); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 752; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 754; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } } #endif - /* "sklearn/manifold/_barnes_hut_tsne.pyx":753 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":755 * err = insert_many(qt, pos_output) * assert err == 0, "[t-SNE] Insertion failed" * if verbose > 10: # <<<<<<<<<<<<<< - * printf("[t-SNE] Computing gradient\n") - * sum_Q = compute_gradient(pij_input, pos_output, neighbors, forces, + * # XXX: format hack to workaround lack of `const char *` type + * # in the generated C code that triggers error with gcc 4.9 */ __pyx_t_7 = ((__pyx_v_verbose > 10) != 0); if (__pyx_t_7) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":754 - * assert err == 0, "[t-SNE] Insertion failed" - * if verbose > 10: - * printf("[t-SNE] Computing gradient\n") # <<<<<<<<<<<<<< + /* "sklearn/manifold/_barnes_hut_tsne.pyx":759 + * # in the generated C code that triggers error with gcc 4.9 + * # and -Werror=format-security + * printf("[t-SNE] Computing gradient\n%s", EMPTY_STRING) # <<<<<<<<<<<<<< * sum_Q = compute_gradient(pij_input, pos_output, neighbors, forces, * qt.root_node, theta, dof, skip_num_points, -1) */ - printf(__pyx_k_t_SNE_Computing_gradient); - goto __pyx_L7; + printf(__pyx_k_t_SNE_Computing_gradient_s, __pyx_v_7sklearn_8manifold_16_barnes_hut_tsne_EMPTY_STRING); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":755 + * err = insert_many(qt, pos_output) + * assert err == 0, "[t-SNE] Insertion failed" + * if verbose > 10: # <<<<<<<<<<<<<< + * # XXX: format hack to workaround lack of `const char *` type + * # in the generated C code that triggers error with gcc 4.9 + */ } - __pyx_L7:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":755 - * if verbose > 10: - * printf("[t-SNE] Computing gradient\n") + /* "sklearn/manifold/_barnes_hut_tsne.pyx":760 + * # and -Werror=format-security + * printf("[t-SNE] Computing gradient\n%s", EMPTY_STRING) * sum_Q = compute_gradient(pij_input, pos_output, neighbors, forces, # <<<<<<<<<<<<<< * qt.root_node, theta, dof, skip_num_points, -1) * C = compute_error(pij_input, pos_output, neighbors, sum_Q, n_dimensions, */ - __pyx_t_5 = PyFloat_FromDouble(__pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__pyx_v_pij_input, __pyx_v_pos_output, __pyx_v_neighbors, __pyx_v_forces, __pyx_v_qt->root_node, __pyx_v_theta, __pyx_v_dof, __pyx_v_skip_num_points, -1)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 755; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyFloat_FromDouble(__pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_gradient(__pyx_v_pij_input, __pyx_v_pos_output, __pyx_v_neighbors, __pyx_v_forces, __pyx_v_qt->root_node, __pyx_v_theta, __pyx_v_dof, __pyx_v_skip_num_points, -1)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 760; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __pyx_v_sum_Q = __pyx_t_5; __pyx_t_5 = 0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":757 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":762 * sum_Q = compute_gradient(pij_input, pos_output, neighbors, forces, * qt.root_node, theta, dof, skip_num_points, -1) * C = compute_error(pij_input, pos_output, neighbors, sum_Q, n_dimensions, # <<<<<<<<<<<<<< * verbose) * if verbose > 10: */ - __pyx_t_10 = __pyx_PyFloat_AsFloat(__pyx_v_sum_Q); if (unlikely((__pyx_t_10 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 757; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_10 = __pyx_PyFloat_AsFloat(__pyx_v_sum_Q); if (unlikely((__pyx_t_10 == (float)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 762; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "sklearn/manifold/_barnes_hut_tsne.pyx":758 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":763 * qt.root_node, theta, dof, skip_num_points, -1) * C = compute_error(pij_input, pos_output, neighbors, sum_Q, n_dimensions, * verbose) # <<<<<<<<<<<<<< * if verbose > 10: - * printf("[t-SNE] Checking tree consistency \n") + * # XXX: format hack to workaround lack of `const char *` type */ __pyx_v_C = __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_compute_error(__pyx_v_pij_input, __pyx_v_pos_output, __pyx_v_neighbors, __pyx_t_10, __pyx_v_n_dimensions, __pyx_v_verbose); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":759 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":764 * C = compute_error(pij_input, pos_output, neighbors, sum_Q, n_dimensions, * verbose) * if verbose > 10: # <<<<<<<<<<<<<< - * printf("[t-SNE] Checking tree consistency \n") - * cdef long count = count_points(qt.root_node, 0) + * # XXX: format hack to workaround lack of `const char *` type + * # in the generated C code */ __pyx_t_7 = ((__pyx_v_verbose > 10) != 0); if (__pyx_t_7) { - /* "sklearn/manifold/_barnes_hut_tsne.pyx":760 - * verbose) - * if verbose > 10: - * printf("[t-SNE] Checking tree consistency \n") # <<<<<<<<<<<<<< + /* "sklearn/manifold/_barnes_hut_tsne.pyx":768 + * # in the generated C code + * # and -Werror=format-security + * printf("[t-SNE] Checking tree consistency\n%s", EMPTY_STRING) # <<<<<<<<<<<<<< * cdef long count = count_points(qt.root_node, 0) * m = ("Tree consistency failed: unexpected number of points=%i " */ - printf(__pyx_k_t_SNE_Checking_tree_consistency); - goto __pyx_L8; + printf(__pyx_k_t_SNE_Checking_tree_consistency, __pyx_v_7sklearn_8manifold_16_barnes_hut_tsne_EMPTY_STRING); + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":764 + * C = compute_error(pij_input, pos_output, neighbors, sum_Q, n_dimensions, + * verbose) + * if verbose > 10: # <<<<<<<<<<<<<< + * # XXX: format hack to workaround lack of `const char *` type + * # in the generated C code + */ } - __pyx_L8:; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":761 - * if verbose > 10: - * printf("[t-SNE] Checking tree consistency \n") + /* "sklearn/manifold/_barnes_hut_tsne.pyx":769 + * # and -Werror=format-security + * printf("[t-SNE] Checking tree consistency\n%s", EMPTY_STRING) * cdef long count = count_points(qt.root_node, 0) # <<<<<<<<<<<<<< * m = ("Tree consistency failed: unexpected number of points=%i " * "at root node=%i" % (count, qt.root_node.cumulative_size)) */ __pyx_v_count = __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_count_points(__pyx_v_qt->root_node, 0); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":763 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":771 * cdef long count = count_points(qt.root_node, 0) * m = ("Tree consistency failed: unexpected number of points=%i " * "at root node=%i" % (count, qt.root_node.cumulative_size)) # <<<<<<<<<<<<<< * assert count == qt.root_node.cumulative_size, m * m = "Tree consistency failed: unexpected number of points on the tree" */ - __pyx_t_5 = __Pyx_PyInt_From_long(__pyx_v_count); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyInt_From_long(__pyx_v_count); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - __pyx_t_1 = __Pyx_PyInt_From_long(__pyx_v_qt->root_node->cumulative_size); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyInt_From_long(__pyx_v_qt->root_node->cumulative_size); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); - PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_1); + PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_1); + PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_1); __pyx_t_5 = 0; __pyx_t_1 = 0; - __pyx_t_1 = __Pyx_PyString_Format(__pyx_kp_s_Tree_consistency_failed_unexpect, __pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 763; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyString_Format(__pyx_kp_s_Tree_consistency_failed_unexpect, __pyx_t_3); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 771; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF_SET(__pyx_v_m, __pyx_t_1); __pyx_t_1 = 0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":764 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":772 * m = ("Tree consistency failed: unexpected number of points=%i " * "at root node=%i" % (count, qt.root_node.cumulative_size)) * assert count == qt.root_node.cumulative_size, m # <<<<<<<<<<<<<< @@ -7257,16 +7671,16 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON #ifndef CYTHON_WITHOUT_ASSERTIONS if (unlikely(!Py_OptimizeFlag)) { if (unlikely(!((__pyx_v_count == __pyx_v_qt->root_node->cumulative_size) != 0))) { - __pyx_t_1 = PyTuple_Pack(1, __pyx_v_m); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 764; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyTuple_Pack(1, __pyx_v_m); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); PyErr_SetObject(PyExc_AssertionError, __pyx_t_1); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 764; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } } #endif - /* "sklearn/manifold/_barnes_hut_tsne.pyx":765 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":773 * "at root node=%i" % (count, qt.root_node.cumulative_size)) * assert count == qt.root_node.cumulative_size, m * m = "Tree consistency failed: unexpected number of points on the tree" # <<<<<<<<<<<<<< @@ -7276,7 +7690,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON __Pyx_INCREF(__pyx_kp_s_Tree_consistency_failed_unexpect_2); __Pyx_DECREF_SET(__pyx_v_m, __pyx_kp_s_Tree_consistency_failed_unexpect_2); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":766 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":774 * assert count == qt.root_node.cumulative_size, m * m = "Tree consistency failed: unexpected number of points on the tree" * assert count == qt.n_points, m # <<<<<<<<<<<<<< @@ -7286,16 +7700,16 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON #ifndef CYTHON_WITHOUT_ASSERTIONS if (unlikely(!Py_OptimizeFlag)) { if (unlikely(!((__pyx_v_count == __pyx_v_qt->n_points) != 0))) { - __pyx_t_1 = PyTuple_Pack(1, __pyx_v_m); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyTuple_Pack(1, __pyx_v_m); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 774; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); PyErr_SetObject(PyExc_AssertionError, __pyx_t_1); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 766; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 774; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } } #endif - /* "sklearn/manifold/_barnes_hut_tsne.pyx":767 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":775 * m = "Tree consistency failed: unexpected number of points on the tree" * assert count == qt.n_points, m * free_tree(qt) # <<<<<<<<<<<<<< @@ -7304,7 +7718,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON */ __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_tree(__pyx_v_qt); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":768 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":776 * assert count == qt.n_points, m * free_tree(qt) * return C # <<<<<<<<<<<<<< @@ -7312,18 +7726,18 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON * */ __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = PyFloat_FromDouble(__pyx_v_C); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 768; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyFloat_FromDouble(__pyx_v_C); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 776; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":717 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":719 * return left_edge, right_edge, width * * def gradient(float[:,:] pij_input, # <<<<<<<<<<<<<< * float[:,:] pos_output, - * long[:,:] neighbors, + * np.int64_t[:,:] neighbors, */ /* function exit code */ @@ -7353,10 +7767,10 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_2gradient(CYTHON return __pyx_r; } -/* "sklearn/manifold/_barnes_hut_tsne.pyx":772 +/* "sklearn/manifold/_barnes_hut_tsne.pyx":780 * * # Helper functions - * def check_quadtree(X, long[:] counts): # <<<<<<<<<<<<<< + * def check_quadtree(X, np.int64_t[:] counts): # <<<<<<<<<<<<<< * """ * Helper function to access quadtree functions for testing */ @@ -7394,11 +7808,11 @@ static PyObject *__pyx_pw_7sklearn_8manifold_16_barnes_hut_tsne_5check_quadtree( case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_counts)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("check_quadtree", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("check_quadtree", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "check_quadtree") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 772; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "check_quadtree") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 2) { goto __pyx_L5_argtuple_error; @@ -7407,11 +7821,11 @@ static PyObject *__pyx_pw_7sklearn_8manifold_16_barnes_hut_tsne_5check_quadtree( values[1] = PyTuple_GET_ITEM(__pyx_args, 1); } __pyx_v_X = values[0]; - 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/* "sklearn/manifold/_barnes_hut_tsne.pyx":777 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":785 * """ * * X = X.astype(np.float32) # <<<<<<<<<<<<<< * left_edge, right_edge, width = calculate_edge(X) * # Initialise a tree */ - __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_X, __pyx_n_s_astype); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyObject_GetAttrStr(__pyx_v_X, __pyx_n_s_astype); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_GetModuleGlobalName(__pyx_n_s_np); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - 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__pyx_t_5 = PyTuple_New(1+1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PyTuple_New(1+1); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); - PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); __pyx_t_3 = NULL; - PyTuple_SET_ITEM(__pyx_t_5, 0+1, __pyx_t_4); + __Pyx_GIVEREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_5, 0, __pyx_t_3); __pyx_t_3 = NULL; __Pyx_GIVEREF(__pyx_t_4); + PyTuple_SET_ITEM(__pyx_t_5, 0+1, __pyx_t_4); __pyx_t_4 = 0; - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 777; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 785; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; } @@ -7494,14 +7908,14 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_4check_quadtree( __Pyx_DECREF_SET(__pyx_v_X, __pyx_t_1); __pyx_t_1 = 0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":778 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":786 * * X = X.astype(np.float32) * left_edge, right_edge, width = calculate_edge(X) # <<<<<<<<<<<<<< * # Initialise a tree * qt = init_tree(left_edge, width, 2, 2) */ - __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_calculate_edge); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_GetModuleGlobalName(__pyx_n_s_calculate_edge); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 786; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __pyx_t_5 = NULL; if (CYTHON_COMPILING_IN_CPYTHON && unlikely(PyMethod_Check(__pyx_t_2))) { @@ -7514,16 +7928,16 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_4check_quadtree( } } if (!__pyx_t_5) { - __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_v_X); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_CallOneArg(__pyx_t_2, __pyx_v_X); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 786; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); } else { - __pyx_t_4 = PyTuple_New(1+1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyTuple_New(1+1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 786; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); __pyx_t_5 = NULL; + __Pyx_GIVEREF(__pyx_t_5); PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_5); __pyx_t_5 = NULL; __Pyx_INCREF(__pyx_v_X); - PyTuple_SET_ITEM(__pyx_t_4, 0+1, __pyx_v_X); __Pyx_GIVEREF(__pyx_v_X); - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_4, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyTuple_SET_ITEM(__pyx_t_4, 0+1, __pyx_v_X); + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_4, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 786; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; } @@ -7538,7 +7952,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_4check_quadtree( if (unlikely(size != 3)) { if (size > 3) __Pyx_RaiseTooManyValuesError(3); else if (size >= 0) __Pyx_RaiseNeedMoreValuesError(size); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 786; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if CYTHON_COMPILING_IN_CPYTHON if (likely(PyTuple_CheckExact(sequence))) { @@ -7554,17 +7968,17 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_4check_quadtree( __Pyx_INCREF(__pyx_t_4); __Pyx_INCREF(__pyx_t_5); #else - __pyx_t_2 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PySequence_ITEM(sequence, 0); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 786; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_4 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PySequence_ITEM(sequence, 1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 786; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_5 = PySequence_ITEM(sequence, 2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = PySequence_ITEM(sequence, 2); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 786; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); #endif __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; } else { Py_ssize_t index = -1; - __pyx_t_3 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyObject_GetIter(__pyx_t_1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 786; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; __pyx_t_6 = Py_TYPE(__pyx_t_3)->tp_iternext; @@ -7574,7 +7988,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_4check_quadtree( __Pyx_GOTREF(__pyx_t_4); index = 2; __pyx_t_5 = __pyx_t_6(__pyx_t_3); if (unlikely(!__pyx_t_5)) goto __pyx_L3_unpacking_failed; __Pyx_GOTREF(__pyx_t_5); - if (__Pyx_IternextUnpackEndCheck(__pyx_t_6(__pyx_t_3), 3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_IternextUnpackEndCheck(__pyx_t_6(__pyx_t_3), 3) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 786; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_6 = NULL; __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; goto __pyx_L4_unpacking_done; @@ -7582,7 +7996,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_4check_quadtree( __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __pyx_t_6 = NULL; if (__Pyx_IterFinish() == 0) __Pyx_RaiseNeedMoreValuesError(index); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 778; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 786; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_L4_unpacking_done:; } __pyx_v_left_edge = __pyx_t_2; @@ -7592,7 +8006,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_4check_quadtree( __pyx_v_width = __pyx_t_5; __pyx_t_5 = 0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":780 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":788 * left_edge, right_edge, width = calculate_edge(X) * # Initialise a tree * qt = init_tree(left_edge, width, 2, 2) # <<<<<<<<<<<<<< @@ -7600,14 +8014,14 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_4check_quadtree( * insert_many(qt, X) */ __pyx_t_7 = __Pyx_PyObject_to_MemoryviewSlice_ds_float(__pyx_v_left_edge); - if (unlikely(!__pyx_t_7.memview)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__pyx_t_7.memview)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 788; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_8 = __Pyx_PyObject_to_MemoryviewSlice_ds_float(__pyx_v_width); - if (unlikely(!__pyx_t_8.memview)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 780; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__pyx_t_8.memview)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 788; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_qt = __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_init_tree(__pyx_t_7, __pyx_t_8, 2, 2); __PYX_XDEC_MEMVIEW(&__pyx_t_7, 1); __PYX_XDEC_MEMVIEW(&__pyx_t_8, 1); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":782 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":790 * qt = init_tree(left_edge, width, 2, 2) * # Insert data into the tree * insert_many(qt, X) # <<<<<<<<<<<<<< @@ -7615,11 +8029,11 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_4check_quadtree( * cdef long count = count_points(qt.root_node, 0) */ __pyx_t_9 = __Pyx_PyObject_to_MemoryviewSlice_dsds_float(__pyx_v_X); - if (unlikely(!__pyx_t_9.memview)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 782; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__pyx_t_9.memview)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_insert_many(__pyx_v_qt, __pyx_t_9); __PYX_XDEC_MEMVIEW(&__pyx_t_9, 1); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":784 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":792 * insert_many(qt, X) * * cdef long count = count_points(qt.root_node, 0) # <<<<<<<<<<<<<< @@ -7628,7 +8042,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_4check_quadtree( */ __pyx_v_count = __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_count_points(__pyx_v_qt->root_node, 0); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":785 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":793 * * cdef long count = count_points(qt.root_node, 0) * counts[0] = count # <<<<<<<<<<<<<< @@ -7636,9 +8050,9 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_4check_quadtree( * counts[2] = qt.n_points */ __pyx_t_10 = 0; - *((long *) ( /* dim=0 */ (__pyx_v_counts.data + __pyx_t_10 * __pyx_v_counts.strides[0]) )) = __pyx_v_count; + *((__pyx_t_5numpy_int64_t *) ( /* dim=0 */ (__pyx_v_counts.data + __pyx_t_10 * __pyx_v_counts.strides[0]) )) = __pyx_v_count; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":786 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":794 * cdef long count = count_points(qt.root_node, 0) * counts[0] = count * counts[1] = qt.root_node.cumulative_size # <<<<<<<<<<<<<< @@ -7647,9 +8061,9 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_4check_quadtree( */ __pyx_t_11 = __pyx_v_qt->root_node->cumulative_size; __pyx_t_12 = 1; - *((long *) ( /* dim=0 */ (__pyx_v_counts.data + __pyx_t_12 * __pyx_v_counts.strides[0]) )) = __pyx_t_11; + *((__pyx_t_5numpy_int64_t *) ( /* dim=0 */ (__pyx_v_counts.data + __pyx_t_12 * __pyx_v_counts.strides[0]) )) = __pyx_t_11; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":787 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":795 * counts[0] = count * counts[1] = qt.root_node.cumulative_size * counts[2] = qt.n_points # <<<<<<<<<<<<<< @@ -7658,9 +8072,9 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_4check_quadtree( */ __pyx_t_11 = __pyx_v_qt->n_points; __pyx_t_13 = 2; - *((long *) ( /* dim=0 */ (__pyx_v_counts.data + __pyx_t_13 * __pyx_v_counts.strides[0]) )) = __pyx_t_11; + *((__pyx_t_5numpy_int64_t *) ( /* dim=0 */ (__pyx_v_counts.data + __pyx_t_13 * __pyx_v_counts.strides[0]) )) = __pyx_t_11; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":788 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":796 * counts[1] = qt.root_node.cumulative_size * counts[2] = qt.n_points * free_tree(qt) # <<<<<<<<<<<<<< @@ -7669,7 +8083,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_4check_quadtree( */ __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_free_tree(__pyx_v_qt); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":789 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":797 * counts[2] = qt.n_points * free_tree(qt) * return counts # <<<<<<<<<<<<<< @@ -7677,16 +8091,16 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_4check_quadtree( * */ __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = __pyx_memoryview_fromslice(__pyx_v_counts, 1, (PyObject *(*)(char *)) __pyx_memview_get_long, (int (*)(char *, PyObject *)) __pyx_memview_set_long, 0);; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __pyx_memoryview_fromslice(__pyx_v_counts, 1, (PyObject *(*)(char *)) __pyx_memview_get_nn___pyx_t_5numpy_int64_t, (int (*)(char *, PyObject *)) __pyx_memview_set_nn___pyx_t_5numpy_int64_t, 0);; if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 797; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":772 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":780 * * # Helper functions - * def check_quadtree(X, long[:] counts): # <<<<<<<<<<<<<< + * def check_quadtree(X, np.int64_t[:] counts): # <<<<<<<<<<<<<< * """ * Helper function to access quadtree functions for testing */ @@ -7714,7 +8128,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_4check_quadtree( return __pyx_r; } -/* "sklearn/manifold/_barnes_hut_tsne.pyx":792 +/* "sklearn/manifold/_barnes_hut_tsne.pyx":800 * * * cdef int helper_test_index2offset(int* check, int index, int n_dimensions): # <<<<<<<<<<<<<< @@ -7732,7 +8146,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_helper_test_index2offse int __pyx_t_2; __Pyx_RefNannySetupContext("helper_test_index2offset", 0); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":793 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":801 * * cdef int helper_test_index2offset(int* check, int index, int n_dimensions): * cdef int* offset = malloc(sizeof(int) * n_dimensions) # <<<<<<<<<<<<<< @@ -7741,7 +8155,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_helper_test_index2offse */ __pyx_v_offset = ((int *)malloc(((sizeof(int)) * __pyx_v_n_dimensions))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":794 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":802 * cdef int helper_test_index2offset(int* check, int index, int n_dimensions): * cdef int* offset = malloc(sizeof(int) * n_dimensions) * cdef int error_check = 1 # <<<<<<<<<<<<<< @@ -7750,7 +8164,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_helper_test_index2offse */ __pyx_v_error_check = 1; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":795 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":803 * cdef int* offset = malloc(sizeof(int) * n_dimensions) * cdef int error_check = 1 * for i in range(n_dimensions): # <<<<<<<<<<<<<< @@ -7761,7 +8175,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_helper_test_index2offse for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { __pyx_v_i = __pyx_t_2; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":796 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":804 * cdef int error_check = 1 * for i in range(n_dimensions): * offset[i] = 0 # <<<<<<<<<<<<<< @@ -7771,7 +8185,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_helper_test_index2offse (__pyx_v_offset[__pyx_v_i]) = 0; } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":797 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":805 * for i in range(n_dimensions): * offset[i] = 0 * index2offset(offset, index, n_dimensions) # <<<<<<<<<<<<<< @@ -7780,7 +8194,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_helper_test_index2offse */ __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_index2offset(__pyx_v_offset, __pyx_v_index, __pyx_v_n_dimensions); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":798 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":806 * offset[i] = 0 * index2offset(offset, index, n_dimensions) * for i in range(n_dimensions): # <<<<<<<<<<<<<< @@ -7791,7 +8205,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_helper_test_index2offse for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { __pyx_v_i = __pyx_t_2; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":799 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":807 * index2offset(offset, index, n_dimensions) * for i in range(n_dimensions): * error_check &= offset[i] == check[i] # <<<<<<<<<<<<<< @@ -7801,7 +8215,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_helper_test_index2offse __pyx_v_error_check = (__pyx_v_error_check & ((__pyx_v_offset[__pyx_v_i]) == (__pyx_v_check[__pyx_v_i]))); } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":800 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":808 * for i in range(n_dimensions): * error_check &= offset[i] == check[i] * free(offset) # <<<<<<<<<<<<<< @@ -7810,7 +8224,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_helper_test_index2offse */ free(__pyx_v_offset); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":801 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":809 * error_check &= offset[i] == check[i] * free(offset) * return error_check # <<<<<<<<<<<<<< @@ -7820,7 +8234,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_helper_test_index2offse __pyx_r = __pyx_v_error_check; goto __pyx_L0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":792 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":800 * * * cdef int helper_test_index2offset(int* check, int index, int n_dimensions): # <<<<<<<<<<<<<< @@ -7834,7 +8248,7 @@ static int __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_helper_test_index2offse return __pyx_r; } -/* "sklearn/manifold/_barnes_hut_tsne.pyx":804 +/* "sklearn/manifold/_barnes_hut_tsne.pyx":812 * * * def test_index2offset(): # <<<<<<<<<<<<<< @@ -7873,7 +8287,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_6test_index2offs int __pyx_clineno = 0; __Pyx_RefNannySetupContext("test_index2offset", 0); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":805 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":813 * * def test_index2offset(): * ret = 1 # <<<<<<<<<<<<<< @@ -7883,7 +8297,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_6test_index2offs __Pyx_INCREF(__pyx_int_1); __pyx_v_ret = __pyx_int_1; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":806 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":814 * def test_index2offset(): * ret = 1 * ret &= helper_test_index2offset([1, 0, 1], 5, 3) == 1 # <<<<<<<<<<<<<< @@ -7893,15 +8307,15 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_6test_index2offs __pyx_t_1[0] = 1; __pyx_t_1[1] = 0; __pyx_t_1[2] = 1; - __pyx_t_2 = __Pyx_PyBool_FromLong((__pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_helper_test_index2offset(__pyx_t_1, 5, 3) == 1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyBool_FromLong((__pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_helper_test_index2offset(__pyx_t_1, 5, 3) == 1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = PyNumber_InPlaceAnd(__pyx_v_ret, __pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyNumber_InPlaceAnd(__pyx_v_ret, __pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 814; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF_SET(__pyx_v_ret, __pyx_t_3); __pyx_t_3 = 0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":807 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":815 * ret = 1 * ret &= helper_test_index2offset([1, 0, 1], 5, 3) == 1 * ret &= helper_test_index2offset([0, 0, 0], 0, 3) == 1 # <<<<<<<<<<<<<< @@ -7911,15 +8325,15 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_6test_index2offs __pyx_t_4[0] = 0; __pyx_t_4[1] = 0; __pyx_t_4[2] = 0; - __pyx_t_3 = __Pyx_PyBool_FromLong((__pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_helper_test_index2offset(__pyx_t_4, 0, 3) == 1)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 807; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyBool_FromLong((__pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_helper_test_index2offset(__pyx_t_4, 0, 3) == 1)); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 815; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_2 = PyNumber_InPlaceAnd(__pyx_v_ret, __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 807; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyNumber_InPlaceAnd(__pyx_v_ret, __pyx_t_3); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 815; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_DECREF_SET(__pyx_v_ret, __pyx_t_2); __pyx_t_2 = 0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":808 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":816 * ret &= helper_test_index2offset([1, 0, 1], 5, 3) == 1 * ret &= helper_test_index2offset([0, 0, 0], 0, 3) == 1 * ret &= helper_test_index2offset([0, 0, 1], 1, 3) == 1 # <<<<<<<<<<<<<< @@ -7929,15 +8343,15 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_6test_index2offs __pyx_t_5[0] = 0; __pyx_t_5[1] = 0; __pyx_t_5[2] = 1; - __pyx_t_2 = __Pyx_PyBool_FromLong((__pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_helper_test_index2offset(__pyx_t_5, 1, 3) == 1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 808; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyBool_FromLong((__pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_helper_test_index2offset(__pyx_t_5, 1, 3) == 1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = PyNumber_InPlaceAnd(__pyx_v_ret, __pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 808; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyNumber_InPlaceAnd(__pyx_v_ret, __pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 816; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF_SET(__pyx_v_ret, __pyx_t_3); __pyx_t_3 = 0; - 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/* "sklearn/manifold/_barnes_hut_tsne.pyx":810 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":818 * ret &= helper_test_index2offset([0, 0, 1], 1, 3) == 1 * ret &= helper_test_index2offset([0, 1, 0], 2, 3) == 1 * ret &= helper_test_index2offset([0, 1, 1], 3, 3) == 1 # <<<<<<<<<<<<<< @@ -7965,15 +8379,15 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_6test_index2offs __pyx_t_7[0] = 0; __pyx_t_7[1] = 1; __pyx_t_7[2] = 1; - __pyx_t_2 = __Pyx_PyBool_FromLong((__pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_helper_test_index2offset(__pyx_t_7, 3, 3) == 1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyBool_FromLong((__pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_helper_test_index2offset(__pyx_t_7, 3, 3) == 1)); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 818; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); - __pyx_t_3 = PyNumber_InPlaceAnd(__pyx_v_ret, __pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 810; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyNumber_InPlaceAnd(__pyx_v_ret, __pyx_t_2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 818; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF_SET(__pyx_v_ret, __pyx_t_3); __pyx_t_3 = 0; - 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/* "sklearn/manifold/_barnes_hut_tsne.pyx":812 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":820 * ret &= helper_test_index2offset([0, 1, 1], 3, 3) == 1 * ret &= helper_test_index2offset([1, 0, 0], 4, 3) == 1 * return ret # <<<<<<<<<<<<<< @@ -8003,7 +8417,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_6test_index2offs __pyx_r = __pyx_v_ret; goto __pyx_L0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":804 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":812 * * * def test_index2offset(): # <<<<<<<<<<<<<< @@ -8024,7 +8438,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_6test_index2offs return __pyx_r; } -/* "sklearn/manifold/_barnes_hut_tsne.pyx":815 +/* "sklearn/manifold/_barnes_hut_tsne.pyx":823 * * * def test_index_offset(): # <<<<<<<<<<<<<< @@ -8065,7 +8479,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_8test_index_offs int __pyx_clineno = 0; __Pyx_RefNannySetupContext("test_index_offset", 0); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":817 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":825 * def test_index_offset(): * cdef int n_dimensions, idx, tidx, k * cdef int error_check = 1 # <<<<<<<<<<<<<< @@ -8074,7 +8488,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_8test_index_offs */ __pyx_v_error_check = 1; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":819 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":827 * cdef int error_check = 1 * cdef int* offset * for n_dimensions in range(2, 10): # <<<<<<<<<<<<<< @@ -8084,7 +8498,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_8test_index_offs for (__pyx_t_1 = 2; __pyx_t_1 < 10; __pyx_t_1+=1) { __pyx_v_n_dimensions = __pyx_t_1; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":820 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":828 * cdef int* offset * for n_dimensions in range(2, 10): * offset = malloc(sizeof(int) * n_dimensions) # <<<<<<<<<<<<<< @@ -8093,7 +8507,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_8test_index_offs */ __pyx_v_offset = ((int *)malloc(((sizeof(int)) * __pyx_v_n_dimensions))); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":821 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":829 * for n_dimensions in range(2, 10): * offset = malloc(sizeof(int) * n_dimensions) * for k in range(n_dimensions): # <<<<<<<<<<<<<< @@ -8104,7 +8518,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_8test_index_offs for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { __pyx_v_k = __pyx_t_3; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":822 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":830 * offset = malloc(sizeof(int) * n_dimensions) * for k in range(n_dimensions): * offset[k] = 0 # <<<<<<<<<<<<<< @@ -8114,7 +8528,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_8test_index_offs (__pyx_v_offset[__pyx_v_k]) = 0; } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":823 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":831 * for k in range(n_dimensions): * offset[k] = 0 * for idx in range(2 ** n_dimensions): # <<<<<<<<<<<<<< @@ -8125,7 +8539,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_8test_index_offs for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_4; __pyx_t_2+=1) { __pyx_v_idx = __pyx_t_2; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":824 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":832 * offset[k] = 0 * for idx in range(2 ** n_dimensions): * index2offset(offset, idx, n_dimensions) # <<<<<<<<<<<<<< @@ -8134,7 +8548,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_8test_index_offs */ __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_index2offset(__pyx_v_offset, __pyx_v_idx, __pyx_v_n_dimensions); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":825 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":833 * for idx in range(2 ** n_dimensions): * index2offset(offset, idx, n_dimensions) * tidx = offset2index(offset, n_dimensions) # <<<<<<<<<<<<<< @@ -8143,7 +8557,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_8test_index_offs */ __pyx_v_tidx = __pyx_f_7sklearn_8manifold_16_barnes_hut_tsne_offset2index(__pyx_v_offset, __pyx_v_n_dimensions); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":826 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":834 * index2offset(offset, idx, n_dimensions) * tidx = offset2index(offset, n_dimensions) * error_check &= tidx == idx # <<<<<<<<<<<<<< @@ -8152,7 +8566,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_8test_index_offs */ __pyx_v_error_check = (__pyx_v_error_check & (__pyx_v_tidx == __pyx_v_idx)); - /* "sklearn/manifold/_barnes_hut_tsne.pyx":827 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":835 * tidx = offset2index(offset, n_dimensions) * error_check &= tidx == idx * assert error_check == 1 # <<<<<<<<<<<<<< @@ -8163,13 +8577,13 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_8test_index_offs if (unlikely(!Py_OptimizeFlag)) { if (unlikely(!((__pyx_v_error_check == 1) != 0))) { PyErr_SetNone(PyExc_AssertionError); - {__pyx_filename = __pyx_f[0]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[0]; __pyx_lineno = 835; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } } #endif } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":828 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":836 * error_check &= tidx == idx * assert error_check == 1 * free(offset) # <<<<<<<<<<<<<< @@ -8178,19 +8592,19 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_8test_index_offs free(__pyx_v_offset); } - /* "sklearn/manifold/_barnes_hut_tsne.pyx":829 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":837 * assert error_check == 1 * free(offset) * return error_check # <<<<<<<<<<<<<< */ __Pyx_XDECREF(__pyx_r); - __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_error_check); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __Pyx_PyInt_From_int(__pyx_v_error_check); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 837; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __pyx_r = __pyx_t_5; __pyx_t_5 = 0; goto __pyx_L0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":815 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":823 * * * def test_index_offset(): # <<<<<<<<<<<<<< @@ -8209,7 +8623,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_16_barnes_hut_tsne_8test_index_offs return __pyx_r; } -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":194 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":197 * # experimental exception made for __getbuffer__ and __releasebuffer__ * # -- the details of this may change. * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< @@ -8259,7 +8673,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_GIVEREF(__pyx_v_info->obj); } - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":200 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":203 * # of flags * * if info == NULL: return # <<<<<<<<<<<<<< @@ -8272,7 +8686,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L0; } - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":203 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":206 * * cdef int copy_shape, i, ndim * cdef int endian_detector = 1 # <<<<<<<<<<<<<< @@ -8281,7 +8695,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_endian_detector = 1; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":204 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":207 * cdef int copy_shape, i, ndim * cdef int endian_detector = 1 * cdef bint little_endian = ((&endian_detector)[0] != 0) # <<<<<<<<<<<<<< @@ -8290,7 +8704,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":206 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":209 * cdef bint little_endian = ((&endian_detector)[0] != 0) * * ndim = PyArray_NDIM(self) # <<<<<<<<<<<<<< @@ -8299,7 +8713,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_ndim = PyArray_NDIM(__pyx_v_self); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":208 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":211 * ndim = PyArray_NDIM(self) * * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -8309,7 +8723,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":209 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":212 * * if sizeof(npy_intp) != sizeof(Py_ssize_t): * copy_shape = 1 # <<<<<<<<<<<<<< @@ -8317,22 +8731,30 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P * copy_shape = 0 */ __pyx_v_copy_shape = 1; + + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":211 + * ndim = PyArray_NDIM(self) + * + * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< + * copy_shape = 1 + * else: + */ goto __pyx_L4; } - /*else*/ { - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":211 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":214 * copy_shape = 1 * else: * copy_shape = 0 # <<<<<<<<<<<<<< * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) */ + /*else*/ { __pyx_v_copy_shape = 0; } __pyx_L4:; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":213 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":216 * copy_shape = 0 * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -8341,14 +8763,12 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_t_2 = (((__pyx_v_flags & PyBUF_C_CONTIGUOUS) == PyBUF_C_CONTIGUOUS) != 0); if (__pyx_t_2) { - goto __pyx_L7_next_and; } else { __pyx_t_1 = __pyx_t_2; goto __pyx_L6_bool_binop_done; } - __pyx_L7_next_and:; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":214 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":217 * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): # <<<<<<<<<<<<<< @@ -8358,23 +8778,39 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_C_CONTIGUOUS) != 0)) != 0); __pyx_t_1 = __pyx_t_2; __pyx_L6_bool_binop_done:; + + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":216 + * copy_shape = 0 + * + * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< + * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): + * raise ValueError(u"ndarray is not C contiguous") + */ if (__pyx_t_1) { - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":215 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":218 * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): * raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<< * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) */ - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple_, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple_, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":216 + * copy_shape = 0 + * + * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< + * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): + * raise ValueError(u"ndarray is not C contiguous") + */ } - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":217 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":220 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -8383,14 +8819,12 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_t_2 = (((__pyx_v_flags & PyBUF_F_CONTIGUOUS) == PyBUF_F_CONTIGUOUS) != 0); if (__pyx_t_2) { - goto __pyx_L10_next_and; } else { __pyx_t_1 = __pyx_t_2; goto __pyx_L9_bool_binop_done; } - __pyx_L10_next_and:; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":218 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":221 * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): # <<<<<<<<<<<<<< @@ -8400,23 +8834,39 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_F_CONTIGUOUS) != 0)) != 0); __pyx_t_1 = __pyx_t_2; __pyx_L9_bool_binop_done:; + + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":220 + * raise ValueError(u"ndarray is not C contiguous") + * + * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< + * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): + * raise ValueError(u"ndarray is not Fortran contiguous") + */ if (__pyx_t_1) { - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":219 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":222 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< * * info.buf = PyArray_DATA(self) */ - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - {__pyx_filename = __pyx_f[1]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":220 + * raise ValueError(u"ndarray is not C contiguous") + * + * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< + * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): + * raise ValueError(u"ndarray is not Fortran contiguous") + */ } - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":221 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":224 * raise ValueError(u"ndarray is not Fortran contiguous") * * info.buf = PyArray_DATA(self) # <<<<<<<<<<<<<< @@ -8425,7 +8875,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->buf = PyArray_DATA(__pyx_v_self); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":222 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":225 * * info.buf = PyArray_DATA(self) * info.ndim = ndim # <<<<<<<<<<<<<< @@ -8434,7 +8884,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->ndim = __pyx_v_ndim; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":223 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":226 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if copy_shape: # <<<<<<<<<<<<<< @@ -8444,7 +8894,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = (__pyx_v_copy_shape != 0); if (__pyx_t_1) { - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":226 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":229 * # Allocate new buffer for strides and shape info. * # This is allocated as one block, strides first. * info.strides = stdlib.malloc(sizeof(Py_ssize_t) * ndim * 2) # <<<<<<<<<<<<<< @@ -8453,7 +8903,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->strides = ((Py_ssize_t *)malloc((((sizeof(Py_ssize_t)) * ((size_t)__pyx_v_ndim)) * 2))); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":227 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":230 * # This is allocated as one block, strides first. * info.strides = stdlib.malloc(sizeof(Py_ssize_t) * ndim * 2) * info.shape = info.strides + ndim # <<<<<<<<<<<<<< @@ -8462,7 +8912,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->shape = (__pyx_v_info->strides + __pyx_v_ndim); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":228 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":231 * info.strides = stdlib.malloc(sizeof(Py_ssize_t) * ndim * 2) * info.shape = info.strides + ndim * for i in range(ndim): # <<<<<<<<<<<<<< @@ -8473,7 +8923,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { __pyx_v_i = __pyx_t_5; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":229 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":232 * info.shape = info.strides + ndim * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] # <<<<<<<<<<<<<< @@ -8482,7 +8932,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->strides[__pyx_v_i]) = (PyArray_STRIDES(__pyx_v_self)[__pyx_v_i]); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":230 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":233 * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] * info.shape[i] = PyArray_DIMS(self)[i] # <<<<<<<<<<<<<< @@ -8491,20 +8941,28 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->shape[__pyx_v_i]) = (PyArray_DIMS(__pyx_v_self)[__pyx_v_i]); } + + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":226 + * info.buf = PyArray_DATA(self) + * info.ndim = ndim + * if copy_shape: # <<<<<<<<<<<<<< + * # Allocate new buffer for strides and shape info. + * # This is allocated as one block, strides first. + */ goto __pyx_L11; } - /*else*/ { - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":232 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":235 * info.shape[i] = PyArray_DIMS(self)[i] * else: * info.strides = PyArray_STRIDES(self) # <<<<<<<<<<<<<< * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL */ + /*else*/ { __pyx_v_info->strides = ((Py_ssize_t *)PyArray_STRIDES(__pyx_v_self)); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":233 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":236 * else: * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) # <<<<<<<<<<<<<< @@ -8515,7 +8973,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L11:; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":234 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":237 * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL # <<<<<<<<<<<<<< @@ -8524,7 +8982,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->suboffsets = NULL; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":235 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":238 * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) # <<<<<<<<<<<<<< @@ -8533,7 +8991,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->itemsize = PyArray_ITEMSIZE(__pyx_v_self); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":236 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":239 * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) * info.readonly = not PyArray_ISWRITEABLE(self) # <<<<<<<<<<<<<< @@ -8542,28 +9000,28 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->readonly = (!(PyArray_ISWRITEABLE(__pyx_v_self) != 0)); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":239 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":242 * * cdef int t * cdef char* f = NULL # <<<<<<<<<<<<<< * cdef dtype descr = self.descr - * cdef list stack + * cdef int offset */ __pyx_v_f = NULL; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":240 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":243 * cdef int t * cdef char* f = NULL * cdef dtype descr = self.descr # <<<<<<<<<<<<<< - * cdef list stack * cdef int offset + * */ __pyx_t_3 = ((PyObject *)__pyx_v_self->descr); __Pyx_INCREF(__pyx_t_3); __pyx_v_descr = ((PyArray_Descr *)__pyx_t_3); __pyx_t_3 = 0; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":244 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":246 * cdef int offset * * cdef bint hasfields = PyDataType_HASFIELDS(descr) # <<<<<<<<<<<<<< @@ -8572,7 +9030,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_hasfields = PyDataType_HASFIELDS(__pyx_v_descr); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":246 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":248 * cdef bint hasfields = PyDataType_HASFIELDS(descr) * * if not hasfields and not copy_shape: # <<<<<<<<<<<<<< @@ -8581,18 +9039,16 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_t_2 = ((!(__pyx_v_hasfields != 0)) != 0); if (__pyx_t_2) { - goto __pyx_L16_next_and; } else { __pyx_t_1 = __pyx_t_2; goto __pyx_L15_bool_binop_done; } - __pyx_L16_next_and:; __pyx_t_2 = ((!(__pyx_v_copy_shape != 0)) != 0); __pyx_t_1 = __pyx_t_2; __pyx_L15_bool_binop_done:; if (__pyx_t_1) { - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":248 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":250 * if not hasfields and not copy_shape: * # do not call releasebuffer * info.obj = None # <<<<<<<<<<<<<< @@ -8604,17 +9060,25 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_GOTREF(__pyx_v_info->obj); __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = Py_None; + + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":248 + * cdef bint hasfields = PyDataType_HASFIELDS(descr) + * + * if not hasfields and not copy_shape: # <<<<<<<<<<<<<< + * # do not call releasebuffer + * info.obj = None + */ goto __pyx_L14; } - /*else*/ { - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":251 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":253 * else: * # need to call releasebuffer * info.obj = self # <<<<<<<<<<<<<< * * if not hasfields: */ + /*else*/ { __Pyx_INCREF(((PyObject *)__pyx_v_self)); __Pyx_GIVEREF(((PyObject *)__pyx_v_self)); __Pyx_GOTREF(__pyx_v_info->obj); @@ -8623,7 +9087,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L14:; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":253 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":255 * info.obj = self * * if not hasfields: # <<<<<<<<<<<<<< @@ -8633,7 +9097,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = ((!(__pyx_v_hasfields != 0)) != 0); if (__pyx_t_1) { - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":254 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":256 * * if not hasfields: * t = descr.type_num # <<<<<<<<<<<<<< @@ -8643,7 +9107,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_4 = __pyx_v_descr->type_num; __pyx_v_t = __pyx_t_4; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":255 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":257 * if not hasfields: * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -8654,19 +9118,16 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P if (!__pyx_t_2) { goto __pyx_L20_next_or; } else { - goto __pyx_L21_next_and; } - __pyx_L21_next_and:; __pyx_t_2 = (__pyx_v_little_endian != 0); if (!__pyx_t_2) { - goto __pyx_L20_next_or; } else { __pyx_t_1 = __pyx_t_2; goto __pyx_L19_bool_binop_done; } __pyx_L20_next_or:; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":256 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":258 * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -8675,52 +9136,58 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_t_2 = ((__pyx_v_descr->byteorder == '<') != 0); if (__pyx_t_2) { - goto __pyx_L22_next_and; } else { __pyx_t_1 = __pyx_t_2; goto __pyx_L19_bool_binop_done; } - __pyx_L22_next_and:; __pyx_t_2 = ((!(__pyx_v_little_endian != 0)) != 0); __pyx_t_1 = __pyx_t_2; __pyx_L19_bool_binop_done:; + + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":257 + * if not hasfields: + * t = descr.type_num + * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< + * (descr.byteorder == c'<' and not little_endian)): + * raise ValueError(u"Non-native byte order not supported") + */ if (__pyx_t_1) { - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":257 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":259 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" */ - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__3, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__3, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 259; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - {__pyx_filename = __pyx_f[1]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - } + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 259; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":274 - * elif t == NPY_CDOUBLE: f = "Zd" - * elif t == NPY_CLONGDOUBLE: f = "Zg" - * elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<< - * else: - * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":257 + * if not hasfields: + * t = descr.type_num + * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< + * (descr.byteorder == c'<' and not little_endian)): + * raise ValueError(u"Non-native byte order not supported") */ - switch (__pyx_v_t) { + } - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":258 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":260 * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" # <<<<<<<<<<<<<< * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" */ + switch (__pyx_v_t) { case NPY_BYTE: __pyx_v_f = __pyx_k_b; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":259 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":261 * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" # <<<<<<<<<<<<<< @@ -8731,7 +9198,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_B; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":260 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":262 * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" # <<<<<<<<<<<<<< @@ -8742,7 +9209,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_h; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":263 * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" # <<<<<<<<<<<<<< @@ -8753,7 +9220,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_H; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":262 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":264 * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" # <<<<<<<<<<<<<< @@ -8764,7 +9231,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_i_2; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":263 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":265 * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" # <<<<<<<<<<<<<< @@ -8775,7 +9242,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_I; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":264 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":266 * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" # <<<<<<<<<<<<<< @@ -8786,7 +9253,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_l; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":265 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":267 * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" # <<<<<<<<<<<<<< @@ -8797,7 +9264,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_L; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":266 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":268 * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" # <<<<<<<<<<<<<< @@ -8808,7 +9275,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_q; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":267 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":269 * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" # <<<<<<<<<<<<<< @@ -8819,7 +9286,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_Q; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":268 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":270 * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" # <<<<<<<<<<<<<< @@ -8830,7 +9297,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_f; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":269 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":271 * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" # <<<<<<<<<<<<<< @@ -8841,7 +9308,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_d; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":270 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":272 * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" # <<<<<<<<<<<<<< @@ -8852,7 +9319,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_g; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":271 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":273 * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" # <<<<<<<<<<<<<< @@ -8863,7 +9330,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_Zf; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":272 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":274 * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" # <<<<<<<<<<<<<< @@ -8874,7 +9341,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_Zd; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":273 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":275 * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" # <<<<<<<<<<<<<< @@ -8885,7 +9352,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_Zg; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":274 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":276 * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" * elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<< @@ -8897,33 +9364,33 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P break; default: - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":276 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":278 * elif t == NPY_OBJECT: f = "O" * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) # <<<<<<<<<<<<<< * info.format = f * return */ - __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_t); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_From_int(__pyx_v_t); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 278; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - 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{__pyx_filename = __pyx_f[1]; __pyx_lineno = 276; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 278; __pyx_clineno = __LINE__; goto __pyx_L1_error;} break; } - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":277 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":279 * else: * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f # <<<<<<<<<<<<<< @@ -8932,7 +9399,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->format = __pyx_v_f; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":278 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":280 * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f * return # <<<<<<<<<<<<<< @@ -8941,19 +9408,27 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_r = 0; goto __pyx_L0; + + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":255 + * info.obj = self + * + * if not hasfields: # <<<<<<<<<<<<<< + * t = descr.type_num + * if ((descr.byteorder == c'>' and little_endian) or + */ } - 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/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":283 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":285 * info.format[0] = c'^' # Native data types, manual alignment * offset = 0 * f = _util_dtypestring(descr, info.format + 1, # <<<<<<<<<<<<<< * info.format + _buffer_format_string_len, * &offset) */ - __pyx_t_7 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 255), (&__pyx_v_offset)); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __pyx_f_5numpy__util_dtypestring(__pyx_v_descr, (__pyx_v_info->format + 1), (__pyx_v_info->format + 255), (&__pyx_v_offset)); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 285; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_f = __pyx_t_7; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":286 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":288 * info.format + _buffer_format_string_len, * &offset) * f[0] = c'\0' # Terminate format string # <<<<<<<<<<<<<< @@ -8991,7 +9466,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P (__pyx_v_f[0]) = '\x00'; } - 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/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":290 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":292 * def __releasebuffer__(ndarray self, Py_buffer* info): * if PyArray_HASFIELDS(self): * stdlib.free(info.format) # <<<<<<<<<<<<<< @@ -9065,11 +9540,17 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s * stdlib.free(info.strides) */ free(__pyx_v_info->format); - goto __pyx_L3; + + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":291 + * + * def __releasebuffer__(ndarray self, Py_buffer* info): + * if PyArray_HASFIELDS(self): # <<<<<<<<<<<<<< + * stdlib.free(info.format) + * if sizeof(npy_intp) != sizeof(Py_ssize_t): + */ } - __pyx_L3:; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":291 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":293 * if PyArray_HASFIELDS(self): * stdlib.free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -9079,7 +9560,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":292 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":294 * stdlib.free(info.format) * if sizeof(npy_intp) != sizeof(Py_ssize_t): * stdlib.free(info.strides) # <<<<<<<<<<<<<< @@ -9087,11 +9568,17 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s * */ free(__pyx_v_info->strides); - goto __pyx_L4; + + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":293 + * if PyArray_HASFIELDS(self): + * stdlib.free(info.format) + * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< + * stdlib.free(info.strides) + * # info.shape was stored after info.strides in the same block + */ } - __pyx_L4:; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":288 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":290 * f[0] = c'\0' # Terminate format string * * def __releasebuffer__(ndarray self, Py_buffer* info): # <<<<<<<<<<<<<< @@ -9103,7 +9590,7 @@ static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_s __Pyx_RefNannyFinishContext(); } -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":768 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":770 * ctypedef npy_cdouble complex_t * * cdef inline object PyArray_MultiIterNew1(a): # <<<<<<<<<<<<<< @@ -9120,7 +9607,7 @@ static CYTHON_INLINE PyObject *__pyx_f_5numpy_PyArray_MultiIterNew1(PyObject *__ int __pyx_clineno = 0; __Pyx_RefNannySetupContext("PyArray_MultiIterNew1", 0); - 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goto __pyx_L9_next_and; } - __pyx_L9_next_and:; __pyx_t_7 = (__pyx_v_little_endian != 0); if (!__pyx_t_7) { - goto __pyx_L8_next_or; } else { __pyx_t_6 = __pyx_t_7; goto __pyx_L7_bool_binop_done; } __pyx_L8_next_or:; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":802 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":802 * * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -9540,18 +10037,24 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_t_7 = ((__pyx_v_child->byteorder == '<') != 0); if (__pyx_t_7) { - goto __pyx_L10_next_and; } else { __pyx_t_6 = __pyx_t_7; goto __pyx_L7_bool_binop_done; } - __pyx_L10_next_and:; __pyx_t_7 = ((!(__pyx_v_little_endian != 0)) != 0); __pyx_t_6 = __pyx_t_7; __pyx_L7_bool_binop_done:; + + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":801 + * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") + * + * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< + * (child.byteorder == c'<' and not little_endian)): + * raise ValueError(u"Non-native byte order not supported") + */ if (__pyx_t_6) { - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":803 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":803 * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -9563,9 +10066,17 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":801 + * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") + * + * if ((child.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< + * (child.byteorder == c'<' and not little_endian)): + * raise ValueError(u"Non-native byte order not supported") + */ } - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":813 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":813 * * # Output padding bytes * while offset[0] < new_offset: # <<<<<<<<<<<<<< @@ -9581,7 +10092,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; if (!__pyx_t_6) break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":814 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":814 * # Output padding bytes * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte # <<<<<<<<<<<<<< @@ -9590,7 +10101,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ (__pyx_v_f[0]) = 120; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":815 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":815 * while offset[0] < new_offset: * f[0] = 120 # "x"; pad byte * f += 1 # <<<<<<<<<<<<<< @@ -9599,7 +10110,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx */ __pyx_v_f = (__pyx_v_f + 1); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":816 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":816 * f[0] = 120 # "x"; pad byte * f += 1 * offset[0] += 1 # <<<<<<<<<<<<<< @@ -9610,7 +10121,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + 1); } - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":818 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":818 * offset[0] += 1 * * offset[0] += child.itemsize # <<<<<<<<<<<<<< @@ -9620,7 +10131,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_8 = 0; (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + __pyx_v_child->elsize); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":820 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":820 * offset[0] += child.itemsize * * if not PyDataType_HASFIELDS(child): # <<<<<<<<<<<<<< @@ -9630,7 +10141,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = ((!(PyDataType_HASFIELDS(__pyx_v_child) != 0)) != 0); if (__pyx_t_6) { - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":821 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":821 * * if not PyDataType_HASFIELDS(child): * t = child.type_num # <<<<<<<<<<<<<< @@ -9642,7 +10153,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_XDECREF_SET(__pyx_v_t, __pyx_t_4); __pyx_t_4 = 0; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":822 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":822 * if not PyDataType_HASFIELDS(child): * t = child.type_num * if end - f < 5: # <<<<<<<<<<<<<< @@ -9652,7 +10163,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_t_6 = (((__pyx_v_end - __pyx_v_f) < 5) != 0); if (__pyx_t_6) { - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":823 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":823 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< @@ -9664,16 +10175,24 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __Pyx_Raise(__pyx_t_4, 0, 0, 0); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":822 + * if not PyDataType_HASFIELDS(child): + * t = child.type_num + * if end - f < 5: # <<<<<<<<<<<<<< + * raise RuntimeError(u"Format string allocated too short.") + * + */ } - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":826 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":826 * * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" # <<<<<<<<<<<<<< * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" */ - __pyx_t_4 = PyInt_FromLong(NPY_BYTE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_BYTE); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -9684,14 +10203,14 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":827 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":827 * # Until ticket #99 is fixed, use integers to avoid warnings * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" # <<<<<<<<<<<<<< * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" */ - __pyx_t_3 = PyInt_FromLong(NPY_UBYTE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_UBYTE); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 827; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; @@ -9702,14 +10221,14 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":828 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":828 * if t == NPY_BYTE: f[0] = 98 #"b" * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" # <<<<<<<<<<<<<< * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" */ - __pyx_t_4 = PyInt_FromLong(NPY_SHORT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_SHORT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 828; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -9720,14 +10239,14 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":829 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":829 * elif t == NPY_UBYTE: f[0] = 66 #"B" * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" # <<<<<<<<<<<<<< * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" */ - __pyx_t_3 = PyInt_FromLong(NPY_USHORT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_USHORT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 829; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; @@ -9738,14 +10257,14 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":830 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":830 * elif t == NPY_SHORT: f[0] = 104 #"h" * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" # <<<<<<<<<<<<<< * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" */ - __pyx_t_4 = PyInt_FromLong(NPY_INT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_INT); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 830; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -9756,14 +10275,14 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":831 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":831 * elif t == NPY_USHORT: f[0] = 72 #"H" * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" # <<<<<<<<<<<<<< * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" */ - __pyx_t_3 = PyInt_FromLong(NPY_UINT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_UINT); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = PyObject_RichCompare(__pyx_v_t, __pyx_t_3, Py_EQ); __Pyx_XGOTREF(__pyx_t_4); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 831; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; @@ -9774,14 +10293,14 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":832 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":832 * elif t == NPY_INT: f[0] = 105 #"i" * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" # <<<<<<<<<<<<<< * elif t == NPY_ULONG: f[0] = 76 #"L" * elif t == NPY_LONGLONG: f[0] = 113 #"q" */ - __pyx_t_4 = PyInt_FromLong(NPY_LONG); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyInt_From_enum__NPY_TYPES(NPY_LONG); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __pyx_t_3 = PyObject_RichCompare(__pyx_v_t, __pyx_t_4, Py_EQ); __Pyx_XGOTREF(__pyx_t_3); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 832; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -9792,14 +10311,14 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx goto __pyx_L15; } - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":833 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":833 * elif t == NPY_UINT: f[0] = 73 #"I" * elif t == NPY_LONG: f[0] = 108 #"l" * elif t == NPY_ULONG: f[0] = 76 #"L" # <<<<<<<<<<<<<< * elif t == NPY_LONGLONG: f[0] = 113 #"q" * elif t == NPY_ULONGLONG: f[0] = 81 #"Q" */ - 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/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":850 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":850 * # so don't output it * f = _util_dtypestring(child, f, end, offset) * return f # <<<<<<<<<<<<<< @@ -10046,7 +10573,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx __pyx_r = __pyx_v_f; goto __pyx_L0; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":783 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":785 * return PyArray_MultiIterNew(5, a, b, c, d, e) * * cdef inline char* _util_dtypestring(dtype descr, char* f, char* end, int* offset) except NULL: # <<<<<<<<<<<<<< @@ -10071,7 +10598,7 @@ static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *__pyx return __pyx_r; } -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":966 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":966 * * * cdef inline void set_array_base(ndarray arr, object base): # <<<<<<<<<<<<<< @@ -10086,7 +10613,7 @@ static CYTHON_INLINE void __pyx_f_5numpy_set_array_base(PyArrayObject *__pyx_v_a int __pyx_t_2; __Pyx_RefNannySetupContext("set_array_base", 0); - 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/* "View.MemoryView":186 + /* "View.MemoryView":188 * bufmode = PyBUF_F_CONTIGUOUS | PyBUF_ANY_CONTIGUOUS * if not (flags & bufmode): * raise ValueError("Can only create a buffer that is contiguous in memory.") # <<<<<<<<<<<<<< * info.buf = self.data * info.len = self.len */ - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__11, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 186; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__12, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - {__pyx_filename = __pyx_f[2]; __pyx_lineno = 186; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[2]; __pyx_lineno = 188; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "View.MemoryView":187 + * elif self.mode == u"fortran": + * bufmode = PyBUF_F_CONTIGUOUS | PyBUF_ANY_CONTIGUOUS + * if not (flags & bufmode): # <<<<<<<<<<<<<< + * raise ValueError("Can only create a buffer that is contiguous in memory.") + * info.buf = self.data + */ } - 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/* "View.MemoryView":190 + /* "View.MemoryView":192 * info.len = self.len * info.ndim = self.ndim * info.shape = self._shape # <<<<<<<<<<<<<< @@ -11052,7 +11680,7 @@ static int __pyx_array_getbuffer_MemoryView_5array_2__getbuffer__(struct __pyx_a __pyx_t_7 = __pyx_v_self->_shape; __pyx_v_info->shape = __pyx_t_7; - /* "View.MemoryView":191 + /* "View.MemoryView":193 * info.ndim = self.ndim * info.shape = self._shape * info.strides = self._strides # <<<<<<<<<<<<<< @@ -11062,7 +11690,7 @@ static int __pyx_array_getbuffer_MemoryView_5array_2__getbuffer__(struct __pyx_a __pyx_t_7 = __pyx_v_self->_strides; __pyx_v_info->strides = __pyx_t_7; - /* "View.MemoryView":192 + /* "View.MemoryView":194 * info.shape = self._shape * info.strides = self._strides * info.suboffsets = NULL # <<<<<<<<<<<<<< @@ -11071,7 +11699,7 @@ static int __pyx_array_getbuffer_MemoryView_5array_2__getbuffer__(struct __pyx_a */ __pyx_v_info->suboffsets = NULL; - /* "View.MemoryView":193 + /* "View.MemoryView":195 * info.strides = self._strides * info.suboffsets = NULL * info.itemsize = self.itemsize # <<<<<<<<<<<<<< @@ -11081,7 +11709,7 @@ static int __pyx_array_getbuffer_MemoryView_5array_2__getbuffer__(struct __pyx_a __pyx_t_5 = __pyx_v_self->itemsize; __pyx_v_info->itemsize = __pyx_t_5; - 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__Pyx_RaiseArgtupleInvalid("__init__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 271; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__init__", 1, 1, 1, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 273; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("View.MemoryView.Enum.__init__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return -1; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_MemviewEnum_MemoryView_4Enum___init__(((struct __pyx_MemviewEnum_obj *)__pyx_v_self), __pyx_v_name); + __pyx_r = __pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum___init__(((struct __pyx_MemviewEnum_obj *)__pyx_v_self), __pyx_v_name); /* function exit code */ __Pyx_RefNannyFinishContext(); return __pyx_r; } -static int __pyx_MemviewEnum_MemoryView_4Enum___init__(struct __pyx_MemviewEnum_obj *__pyx_v_self, PyObject *__pyx_v_name) { +static int __pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum___init__(struct __pyx_MemviewEnum_obj *__pyx_v_self, PyObject *__pyx_v_name) { int __pyx_r; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__init__", 0); - /* "View.MemoryView":272 + /* "View.MemoryView":274 * cdef object name * def __init__(self, name): * self.name = name # <<<<<<<<<<<<<< @@ -11813,7 +12478,7 @@ static int __pyx_MemviewEnum_MemoryView_4Enum___init__(struct __pyx_MemviewEnum_ __Pyx_DECREF(__pyx_v_self->name); __pyx_v_self->name = __pyx_v_name; - /* "View.MemoryView":271 + /* "View.MemoryView":273 * cdef class Enum(object): * cdef object name * def __init__(self, name): # <<<<<<<<<<<<<< @@ -11827,7 +12492,7 @@ static int __pyx_MemviewEnum_MemoryView_4Enum___init__(struct __pyx_MemviewEnum_ return __pyx_r; } -/* "View.MemoryView":273 +/* "View.MemoryView":275 * def __init__(self, name): * self.name = name * def __repr__(self): # <<<<<<<<<<<<<< @@ -11841,19 +12506,19 @@ static PyObject *__pyx_MemviewEnum___repr__(PyObject *__pyx_v_self) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__repr__ (wrapper)", 0); - __pyx_r = __pyx_MemviewEnum_MemoryView_4Enum_2__repr__(((struct __pyx_MemviewEnum_obj *)__pyx_v_self)); + __pyx_r = __pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum_2__repr__(((struct __pyx_MemviewEnum_obj *)__pyx_v_self)); /* function exit code */ __Pyx_RefNannyFinishContext(); return __pyx_r; } -static PyObject *__pyx_MemviewEnum_MemoryView_4Enum_2__repr__(struct __pyx_MemviewEnum_obj *__pyx_v_self) { +static PyObject *__pyx_MemviewEnum___pyx_pf_15View_dot_MemoryView_4Enum_2__repr__(struct __pyx_MemviewEnum_obj *__pyx_v_self) { PyObject *__pyx_r = NULL; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__repr__", 0); - /* "View.MemoryView":274 + /* "View.MemoryView":276 * self.name = name * def __repr__(self): * return self.name # <<<<<<<<<<<<<< @@ -11865,7 +12530,7 @@ static PyObject *__pyx_MemviewEnum_MemoryView_4Enum_2__repr__(struct __pyx_Memvi __pyx_r = __pyx_v_self->name; goto __pyx_L0; - /* "View.MemoryView":273 + /* "View.MemoryView":275 * def __init__(self, name): * self.name = name * def __repr__(self): # <<<<<<<<<<<<<< @@ -11880,7 +12545,7 @@ static PyObject *__pyx_MemviewEnum_MemoryView_4Enum_2__repr__(struct __pyx_Memvi return __pyx_r; } -/* "View.MemoryView":288 +/* "View.MemoryView":290 * * @cname('__pyx_align_pointer') * cdef void *align_pointer(void *memory, size_t alignment) nogil: # <<<<<<<<<<<<<< @@ -11894,7 +12559,7 @@ static void *__pyx_align_pointer(void *__pyx_v_memory, size_t __pyx_v_alignment) void *__pyx_r; int __pyx_t_1; - /* "View.MemoryView":290 + /* "View.MemoryView":292 * cdef void *align_pointer(void *memory, size_t alignment) nogil: * "Align pointer memory on a given boundary" * cdef Py_intptr_t aligned_p = memory # <<<<<<<<<<<<<< @@ -11903,7 +12568,7 @@ static void *__pyx_align_pointer(void *__pyx_v_memory, size_t __pyx_v_alignment) */ __pyx_v_aligned_p = ((Py_intptr_t)__pyx_v_memory); - /* "View.MemoryView":294 + /* "View.MemoryView":296 * * with cython.cdivision(True): * offset = aligned_p % alignment # <<<<<<<<<<<<<< @@ -11912,7 +12577,7 @@ static void *__pyx_align_pointer(void *__pyx_v_memory, size_t __pyx_v_alignment) */ __pyx_v_offset = (__pyx_v_aligned_p % __pyx_v_alignment); - /* "View.MemoryView":296 + /* "View.MemoryView":298 * offset = aligned_p % alignment * * if offset > 0: # <<<<<<<<<<<<<< @@ -11922,7 +12587,7 @@ static void *__pyx_align_pointer(void *__pyx_v_memory, size_t __pyx_v_alignment) __pyx_t_1 = ((__pyx_v_offset > 0) != 0); if (__pyx_t_1) { - /* "View.MemoryView":297 + /* "View.MemoryView":299 * * if offset > 0: * aligned_p += alignment - offset # <<<<<<<<<<<<<< @@ -11930,21 +12595,27 @@ static void *__pyx_align_pointer(void *__pyx_v_memory, size_t __pyx_v_alignment) * return aligned_p */ __pyx_v_aligned_p = (__pyx_v_aligned_p + (__pyx_v_alignment - __pyx_v_offset)); - goto __pyx_L3; - } - __pyx_L3:; - /* "View.MemoryView":299 + /* "View.MemoryView":298 + * offset = aligned_p % alignment + * + * if offset > 0: # <<<<<<<<<<<<<< * aligned_p += alignment - offset * - * return aligned_p # <<<<<<<<<<<<<< + */ + } + + /* "View.MemoryView":301 + * aligned_p += alignment - offset + * + * return aligned_p # <<<<<<<<<<<<<< * * @cname('__pyx_memoryview') */ __pyx_r = ((void *)__pyx_v_aligned_p); goto __pyx_L0; - /* "View.MemoryView":288 + /* "View.MemoryView":290 * * @cname('__pyx_align_pointer') * cdef void *align_pointer(void *memory, size_t alignment) nogil: # <<<<<<<<<<<<<< @@ -11957,7 +12628,7 @@ static void *__pyx_align_pointer(void *__pyx_v_memory, size_t __pyx_v_alignment) return __pyx_r; } -/* "View.MemoryView":317 +/* "View.MemoryView":319 * cdef __Pyx_TypeInfo *typeinfo * * def __cinit__(memoryview self, object obj, int flags, bint dtype_is_object=False): # <<<<<<<<<<<<<< @@ -11998,7 +12669,7 @@ static int __pyx_memoryview___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_ar case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_flags)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 2, 3, 1); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 2, 3, 1); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (kw_args > 0) { @@ -12007,7 +12678,7 @@ static int __pyx_memoryview___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_ar } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__cinit__") < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else { switch (PyTuple_GET_SIZE(__pyx_args)) { @@ -12019,29 +12690,29 @@ static int __pyx_memoryview___cinit__(PyObject *__pyx_v_self, PyObject *__pyx_ar } } __pyx_v_obj = values[0]; - __pyx_v_flags = __Pyx_PyInt_As_int(values[1]); if (unlikely((__pyx_v_flags == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_flags = __Pyx_PyInt_As_int(values[1]); if (unlikely((__pyx_v_flags == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L3_error;} if (values[2]) { - __pyx_v_dtype_is_object = __Pyx_PyObject_IsTrue(values[2]); if (unlikely((__pyx_v_dtype_is_object == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_dtype_is_object = __Pyx_PyObject_IsTrue(values[2]); if (unlikely((__pyx_v_dtype_is_object == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } else { __pyx_v_dtype_is_object = ((int)0); } } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 2, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 317; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("__cinit__", 0, 2, 3, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 319; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("View.MemoryView.memoryview.__cinit__", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return -1; __pyx_L4_argument_unpacking_done:; - __pyx_r = __pyx_memoryview_MemoryView_10memoryview___cinit__(((struct __pyx_memoryview_obj *)__pyx_v_self), __pyx_v_obj, __pyx_v_flags, __pyx_v_dtype_is_object); + __pyx_r = __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview___cinit__(((struct __pyx_memoryview_obj *)__pyx_v_self), __pyx_v_obj, __pyx_v_flags, __pyx_v_dtype_is_object); /* function exit code */ __Pyx_RefNannyFinishContext(); return __pyx_r; } -static int __pyx_memoryview_MemoryView_10memoryview___cinit__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj, int __pyx_v_flags, int __pyx_v_dtype_is_object) { +static int __pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview___cinit__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj, int __pyx_v_flags, int __pyx_v_dtype_is_object) { int __pyx_r; __Pyx_RefNannyDeclarations int __pyx_t_1; @@ -12055,7 +12726,7 @@ static int __pyx_memoryview_MemoryView_10memoryview___cinit__(struct __pyx_memor int __pyx_clineno = 0; __Pyx_RefNannySetupContext("__cinit__", 0); - /* "View.MemoryView":318 + /* "View.MemoryView":320 * * def __cinit__(memoryview self, object obj, int flags, bint dtype_is_object=False): * self.obj = obj # <<<<<<<<<<<<<< @@ -12068,7 +12739,7 @@ static int __pyx_memoryview_MemoryView_10memoryview___cinit__(struct __pyx_memor __Pyx_DECREF(__pyx_v_self->obj); __pyx_v_self->obj = __pyx_v_obj; - /* "View.MemoryView":319 + /* "View.MemoryView":321 * def __cinit__(memoryview self, object obj, int flags, bint dtype_is_object=False): * self.obj = obj * self.flags = flags # <<<<<<<<<<<<<< @@ -12077,38 +12748,36 @@ static int __pyx_memoryview_MemoryView_10memoryview___cinit__(struct __pyx_memor */ __pyx_v_self->flags = __pyx_v_flags; - /* "View.MemoryView":320 + /* "View.MemoryView":322 * self.obj = obj * self.flags = flags * if type(self) is memoryview or obj is not None: # <<<<<<<<<<<<<< * __Pyx_GetBuffer(obj, &self.view, flags) * if self.view.obj == NULL: */ - __pyx_t_2 = (((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))) == ((PyObject *)((PyObject *)__pyx_memoryview_type))); + __pyx_t_2 = (((PyObject *)Py_TYPE(((PyObject *)__pyx_v_self))) == ((PyObject *)__pyx_memoryview_type)); __pyx_t_3 = (__pyx_t_2 != 0); if (!__pyx_t_3) { - 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else {__pyx_filename = __pyx_f[2]; __pyx_lineno = 350; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + else {__pyx_filename = __pyx_f[2]; __pyx_lineno = 352; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } break; } @@ -12416,18 +13127,18 @@ static char *__pyx_memoryview_get_item_pointer(struct __pyx_memoryview_obj *__py __pyx_v_dim = __pyx_t_1; __pyx_t_1 = (__pyx_t_1 + 1); - /* "View.MemoryView":351 + /* "View.MemoryView":353 * * for dim, idx in enumerate(index): * itemp = pybuffer_index(&self.view, itemp, idx, dim) # <<<<<<<<<<<<<< * * return itemp */ - __pyx_t_6 = __Pyx_PyIndex_AsSsize_t(__pyx_v_idx); if (unlikely((__pyx_t_6 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 351; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_t_7 = __pyx_pybuffer_index((&__pyx_v_self->view), __pyx_v_itemp, __pyx_t_6, __pyx_v_dim); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 351; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __Pyx_PyIndex_AsSsize_t(__pyx_v_idx); if (unlikely((__pyx_t_6 == (Py_ssize_t)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 353; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = __pyx_pybuffer_index((&__pyx_v_self->view), __pyx_v_itemp, __pyx_t_6, __pyx_v_dim); if (unlikely(__pyx_t_7 == NULL)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 353; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_itemp = __pyx_t_7; - 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PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_obj); __Pyx_GIVEREF(__pyx_v_obj); - PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_6); + PyTuple_SET_ITEM(__pyx_t_8, 0, __pyx_v_obj); __Pyx_GIVEREF(__pyx_t_6); - PyTuple_SET_ITEM(__pyx_t_8, 2, __pyx_t_7); + PyTuple_SET_ITEM(__pyx_t_8, 1, __pyx_t_6); __Pyx_GIVEREF(__pyx_t_7); + PyTuple_SET_ITEM(__pyx_t_8, 2, __pyx_t_7); __pyx_t_6 = 0; __pyx_t_7 = 0; - __pyx_t_7 = __Pyx_PyObject_Call(((PyObject *)((PyObject *)__pyx_memoryview_type)), __pyx_t_8, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 384; __pyx_clineno = __LINE__; goto __pyx_L4_error;} + __pyx_t_7 = __Pyx_PyObject_Call(((PyObject *)__pyx_memoryview_type), __pyx_t_8, NULL); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L4_error;} __Pyx_GOTREF(__pyx_t_7); __Pyx_DECREF(__pyx_t_8); __pyx_t_8 = 0; __Pyx_DECREF_SET(__pyx_v_obj, __pyx_t_7); __pyx_t_7 = 0; + + /* "View.MemoryView":385 + * cdef is_slice(self, obj): + * if not isinstance(obj, memoryview): + * try: # <<<<<<<<<<<<<< + * obj = memoryview(obj, self.flags|PyBUF_ANY_CONTIGUOUS, + * self.dtype_is_object) + */ } __Pyx_XDECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_XDECREF(__pyx_t_4); __pyx_t_4 = 0; @@ -12932,7 +13683,7 @@ static PyObject *__pyx_memoryview_is_slice(struct __pyx_memoryview_obj *__pyx_v_ __Pyx_XDECREF(__pyx_t_8); __pyx_t_8 = 0; __Pyx_XDECREF(__pyx_t_7); __pyx_t_7 = 0; - /* "View.MemoryView":386 + /* "View.MemoryView":388 * obj = memoryview(obj, self.flags|PyBUF_ANY_CONTIGUOUS, * self.dtype_is_object) * except TypeError: # <<<<<<<<<<<<<< @@ -12942,12 +13693,12 @@ static PyObject *__pyx_memoryview_is_slice(struct __pyx_memoryview_obj *__pyx_v_ __pyx_t_9 = PyErr_ExceptionMatches(__pyx_builtin_TypeError); if (__pyx_t_9) { __Pyx_AddTraceback("View.MemoryView.memoryview.is_slice", __pyx_clineno, __pyx_lineno, __pyx_filename); - if (__Pyx_GetException(&__pyx_t_7, &__pyx_t_8, &__pyx_t_6) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;} + if (__Pyx_GetException(&__pyx_t_7, &__pyx_t_8, &__pyx_t_6) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 388; __pyx_clineno = __LINE__; goto __pyx_L6_except_error;} __Pyx_GOTREF(__pyx_t_7); __Pyx_GOTREF(__pyx_t_8); __Pyx_GOTREF(__pyx_t_6); - /* "View.MemoryView":387 + /* "View.MemoryView":389 * self.dtype_is_object) * except TypeError: * return None # <<<<<<<<<<<<<< @@ -12964,6 +13715,14 @@ static PyObject *__pyx_memoryview_is_slice(struct __pyx_memoryview_obj *__pyx_v_ } goto __pyx_L6_except_error; __pyx_L6_except_error:; + + /* "View.MemoryView":385 + * cdef is_slice(self, obj): + * if not isinstance(obj, memoryview): + * try: # <<<<<<<<<<<<<< + * obj = memoryview(obj, self.flags|PyBUF_ANY_CONTIGUOUS, + * self.dtype_is_object) + */ __Pyx_XGIVEREF(__pyx_t_3); __Pyx_XGIVEREF(__pyx_t_4); __Pyx_XGIVEREF(__pyx_t_5); @@ -12977,11 +13736,17 @@ static PyObject *__pyx_memoryview_is_slice(struct __pyx_memoryview_obj *__pyx_v_ goto __pyx_L0; __pyx_L11_try_end:; } - goto __pyx_L3; + + /* "View.MemoryView":384 + * + * cdef is_slice(self, obj): + * if not isinstance(obj, memoryview): # <<<<<<<<<<<<<< + * try: + * obj = memoryview(obj, self.flags|PyBUF_ANY_CONTIGUOUS, + */ } - __pyx_L3:; - /* "View.MemoryView":389 + /* "View.MemoryView":391 * return None * * return obj # <<<<<<<<<<<<<< @@ -12993,7 +13758,7 @@ static PyObject *__pyx_memoryview_is_slice(struct __pyx_memoryview_obj *__pyx_v_ __pyx_r = __pyx_v_obj; goto __pyx_L0; - /* "View.MemoryView":381 + /* "View.MemoryView":383 * self.setitem_indexed(index, value) * * cdef is_slice(self, obj): # <<<<<<<<<<<<<< @@ -13015,7 +13780,7 @@ static PyObject *__pyx_memoryview_is_slice(struct __pyx_memoryview_obj *__pyx_v_ return __pyx_r; } -/* "View.MemoryView":391 +/* "View.MemoryView":393 * return obj * * cdef setitem_slice_assignment(self, dst, src): # <<<<<<<<<<<<<< @@ -13037,50 +13802,50 @@ static PyObject *__pyx_memoryview_setitem_slice_assignment(struct __pyx_memoryvi int __pyx_clineno = 0; __Pyx_RefNannySetupContext("setitem_slice_assignment", 0); - /* "View.MemoryView":395 + /* "View.MemoryView":397 * cdef __Pyx_memviewslice src_slice * * memoryview_copy_contents(get_slice_from_memview(src, &src_slice)[0], # <<<<<<<<<<<<<< * get_slice_from_memview(dst, &dst_slice)[0], * src.ndim, dst.ndim, self.dtype_is_object) */ - if (!(likely(((__pyx_v_src) == Py_None) || likely(__Pyx_TypeTest(__pyx_v_src, __pyx_memoryview_type))))) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 395; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_v_src) == Py_None) || likely(__Pyx_TypeTest(__pyx_v_src, __pyx_memoryview_type))))) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "View.MemoryView":396 + /* "View.MemoryView":398 * * memoryview_copy_contents(get_slice_from_memview(src, &src_slice)[0], * get_slice_from_memview(dst, &dst_slice)[0], # <<<<<<<<<<<<<< * src.ndim, dst.ndim, self.dtype_is_object) * */ - if (!(likely(((__pyx_v_dst) == Py_None) || likely(__Pyx_TypeTest(__pyx_v_dst, __pyx_memoryview_type))))) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 396; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_v_dst) == Py_None) || likely(__Pyx_TypeTest(__pyx_v_dst, __pyx_memoryview_type))))) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 398; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "View.MemoryView":397 + /* "View.MemoryView":399 * memoryview_copy_contents(get_slice_from_memview(src, &src_slice)[0], * get_slice_from_memview(dst, &dst_slice)[0], * src.ndim, dst.ndim, self.dtype_is_object) # <<<<<<<<<<<<<< * * cdef setitem_slice_assign_scalar(self, memoryview dst, value): */ - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_src, __pyx_n_s_ndim); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_src, __pyx_n_s_ndim); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = __Pyx_PyInt_As_int(__pyx_t_1); if (unlikely((__pyx_t_2 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = __Pyx_PyInt_As_int(__pyx_t_1); if (unlikely((__pyx_t_2 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_dst, __pyx_n_s_ndim); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_PyObject_GetAttrStr(__pyx_v_dst, __pyx_n_s_ndim); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_3 = __Pyx_PyInt_As_int(__pyx_t_1); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyInt_As_int(__pyx_t_1); if (unlikely((__pyx_t_3 == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 399; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "View.MemoryView":395 + /* "View.MemoryView":397 * cdef __Pyx_memviewslice src_slice * * memoryview_copy_contents(get_slice_from_memview(src, &src_slice)[0], # <<<<<<<<<<<<<< * get_slice_from_memview(dst, &dst_slice)[0], * src.ndim, dst.ndim, self.dtype_is_object) */ - __pyx_t_4 = __pyx_memoryview_copy_contents((__pyx_memoryview_get_slice_from_memoryview(((struct __pyx_memoryview_obj *)__pyx_v_src), (&__pyx_v_src_slice))[0]), (__pyx_memoryview_get_slice_from_memoryview(((struct __pyx_memoryview_obj *)__pyx_v_dst), (&__pyx_v_dst_slice))[0]), __pyx_t_2, __pyx_t_3, __pyx_v_self->dtype_is_object); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 395; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __pyx_memoryview_copy_contents((__pyx_memoryview_get_slice_from_memoryview(((struct __pyx_memoryview_obj *)__pyx_v_src), (&__pyx_v_src_slice))[0]), (__pyx_memoryview_get_slice_from_memoryview(((struct __pyx_memoryview_obj *)__pyx_v_dst), (&__pyx_v_dst_slice))[0]), __pyx_t_2, __pyx_t_3, __pyx_v_self->dtype_is_object); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 397; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "View.MemoryView":391 + /* "View.MemoryView":393 * return obj * * cdef setitem_slice_assignment(self, dst, src): # <<<<<<<<<<<<<< @@ -13101,7 +13866,7 @@ static PyObject *__pyx_memoryview_setitem_slice_assignment(struct __pyx_memoryvi return __pyx_r; } -/* "View.MemoryView":399 +/* "View.MemoryView":401 * src.ndim, dst.ndim, self.dtype_is_object) * * cdef setitem_slice_assign_scalar(self, memoryview dst, value): # <<<<<<<<<<<<<< @@ -13133,7 +13898,7 @@ static PyObject *__pyx_memoryview_setitem_slice_assign_scalar(struct __pyx_memor int __pyx_clineno = 0; __Pyx_RefNannySetupContext("setitem_slice_assign_scalar", 0); - /* "View.MemoryView":401 + /* "View.MemoryView":403 * cdef setitem_slice_assign_scalar(self, memoryview dst, value): * cdef int array[128] * cdef void *tmp = NULL # <<<<<<<<<<<<<< @@ -13142,7 +13907,7 @@ static PyObject *__pyx_memoryview_setitem_slice_assign_scalar(struct __pyx_memor */ __pyx_v_tmp = NULL; - /* "View.MemoryView":406 + /* "View.MemoryView":408 * cdef __Pyx_memviewslice *dst_slice * cdef __Pyx_memviewslice tmp_slice * dst_slice = get_slice_from_memview(dst, &tmp_slice) # <<<<<<<<<<<<<< @@ -13151,7 +13916,7 @@ static PyObject *__pyx_memoryview_setitem_slice_assign_scalar(struct __pyx_memor */ __pyx_v_dst_slice = __pyx_memoryview_get_slice_from_memoryview(__pyx_v_dst, (&__pyx_v_tmp_slice)); - /* "View.MemoryView":408 + /* "View.MemoryView":410 * dst_slice = get_slice_from_memview(dst, &tmp_slice) * * if self.view.itemsize > sizeof(array): # <<<<<<<<<<<<<< @@ -13161,7 +13926,7 @@ static PyObject *__pyx_memoryview_setitem_slice_assign_scalar(struct __pyx_memor __pyx_t_1 = ((((size_t)__pyx_v_self->view.itemsize) > (sizeof(__pyx_v_array))) != 0); if (__pyx_t_1) { - /* "View.MemoryView":409 + /* "View.MemoryView":411 * * if self.view.itemsize > sizeof(array): * tmp = PyMem_Malloc(self.view.itemsize) # <<<<<<<<<<<<<< @@ -13170,7 +13935,7 @@ static PyObject *__pyx_memoryview_setitem_slice_assign_scalar(struct __pyx_memor */ __pyx_v_tmp = PyMem_Malloc(__pyx_v_self->view.itemsize); - /* "View.MemoryView":410 + /* "View.MemoryView":412 * if self.view.itemsize > sizeof(array): * tmp = PyMem_Malloc(self.view.itemsize) * if tmp == NULL: # <<<<<<<<<<<<<< @@ -13180,17 +13945,25 @@ static PyObject *__pyx_memoryview_setitem_slice_assign_scalar(struct __pyx_memor __pyx_t_1 = ((__pyx_v_tmp == NULL) != 0); if (__pyx_t_1) { - /* "View.MemoryView":411 + /* "View.MemoryView":413 * tmp = PyMem_Malloc(self.view.itemsize) * if tmp == NULL: * raise MemoryError # <<<<<<<<<<<<<< * item = tmp * else: */ - PyErr_NoMemory(); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 411; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + PyErr_NoMemory(); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 413; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "View.MemoryView":412 + * if self.view.itemsize > sizeof(array): + * tmp = PyMem_Malloc(self.view.itemsize) + * if tmp == NULL: # <<<<<<<<<<<<<< + * raise MemoryError + * item = tmp + */ } - /* "View.MemoryView":412 + /* "View.MemoryView":414 * if tmp == NULL: * raise MemoryError * item = tmp # <<<<<<<<<<<<<< @@ -13198,22 +13971,30 @@ static PyObject *__pyx_memoryview_setitem_slice_assign_scalar(struct __pyx_memor * item = array */ __pyx_v_item = __pyx_v_tmp; + + /* "View.MemoryView":410 + * dst_slice = get_slice_from_memview(dst, &tmp_slice) + * + * if self.view.itemsize > sizeof(array): # <<<<<<<<<<<<<< + * tmp = PyMem_Malloc(self.view.itemsize) + * if tmp == NULL: + */ goto __pyx_L3; } - /*else*/ { - /* "View.MemoryView":414 + /* "View.MemoryView":416 * item = tmp * else: * item = array # <<<<<<<<<<<<<< * * try: */ + /*else*/ { __pyx_v_item = ((void *)__pyx_v_array); } __pyx_L3:; - /* "View.MemoryView":416 + /* "View.MemoryView":418 * item = array * * try: # <<<<<<<<<<<<<< @@ -13222,7 +14003,7 @@ static PyObject *__pyx_memoryview_setitem_slice_assign_scalar(struct __pyx_memor */ /*try:*/ { - /* "View.MemoryView":417 + /* "View.MemoryView":419 * * try: * if self.dtype_is_object: # <<<<<<<<<<<<<< @@ -13232,7 +14013,7 @@ static PyObject *__pyx_memoryview_setitem_slice_assign_scalar(struct __pyx_memor __pyx_t_1 = (__pyx_v_self->dtype_is_object != 0); if (__pyx_t_1) { - /* "View.MemoryView":418 + /* "View.MemoryView":420 * try: * if self.dtype_is_object: * ( item)[0] = value # <<<<<<<<<<<<<< @@ -13240,24 +14021,32 @@ static PyObject *__pyx_memoryview_setitem_slice_assign_scalar(struct __pyx_memor * self.assign_item_from_object( item, value) */ (((PyObject **)__pyx_v_item)[0]) = ((PyObject *)__pyx_v_value); + + /* "View.MemoryView":419 + * + * try: + * if self.dtype_is_object: # <<<<<<<<<<<<<< + * ( item)[0] = value + * else: + */ goto __pyx_L8; } - /*else*/ { - /* "View.MemoryView":420 + /* "View.MemoryView":422 * ( item)[0] = value * else: * self.assign_item_from_object( item, value) # <<<<<<<<<<<<<< * * */ - __pyx_t_2 = ((struct __pyx_vtabstruct_memoryview *)__pyx_v_self->__pyx_vtab)->assign_item_from_object(__pyx_v_self, ((char *)__pyx_v_item), __pyx_v_value); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 420; __pyx_clineno = __LINE__; goto __pyx_L6_error;} + /*else*/ { + __pyx_t_2 = ((struct __pyx_vtabstruct_memoryview *)__pyx_v_self->__pyx_vtab)->assign_item_from_object(__pyx_v_self, ((char *)__pyx_v_item), __pyx_v_value); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 422; __pyx_clineno = __LINE__; goto __pyx_L6_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; } __pyx_L8:; - /* "View.MemoryView":424 + /* "View.MemoryView":426 * * * if self.view.suboffsets != NULL: # <<<<<<<<<<<<<< @@ -13267,21 +14056,27 @@ static PyObject *__pyx_memoryview_setitem_slice_assign_scalar(struct __pyx_memor __pyx_t_1 = ((__pyx_v_self->view.suboffsets != NULL) != 0); if (__pyx_t_1) { - /* "View.MemoryView":425 + /* "View.MemoryView":427 * * if self.view.suboffsets != NULL: * assert_direct_dimensions(self.view.suboffsets, self.view.ndim) # <<<<<<<<<<<<<< * slice_assign_scalar(dst_slice, dst.view.ndim, self.view.itemsize, * item, self.dtype_is_object) */ - __pyx_t_2 = assert_direct_dimensions(__pyx_v_self->view.suboffsets, __pyx_v_self->view.ndim); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 425; __pyx_clineno = __LINE__; goto __pyx_L6_error;} + __pyx_t_2 = assert_direct_dimensions(__pyx_v_self->view.suboffsets, __pyx_v_self->view.ndim); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 427; __pyx_clineno = __LINE__; goto __pyx_L6_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; - goto __pyx_L9; + + /* "View.MemoryView":426 + * + * + * if self.view.suboffsets != NULL: # <<<<<<<<<<<<<< + * assert_direct_dimensions(self.view.suboffsets, self.view.ndim) + * slice_assign_scalar(dst_slice, dst.view.ndim, self.view.itemsize, + */ } - __pyx_L9:; - /* "View.MemoryView":426 + /* "View.MemoryView":428 * if self.view.suboffsets != NULL: * assert_direct_dimensions(self.view.suboffsets, self.view.ndim) * slice_assign_scalar(dst_slice, dst.view.ndim, self.view.itemsize, # <<<<<<<<<<<<<< @@ -13291,7 +14086,7 @@ static PyObject *__pyx_memoryview_setitem_slice_assign_scalar(struct __pyx_memor __pyx_memoryview_slice_assign_scalar(__pyx_v_dst_slice, __pyx_v_dst->view.ndim, __pyx_v_self->view.itemsize, __pyx_v_item, __pyx_v_self->dtype_is_object); } - /* "View.MemoryView":429 + /* "View.MemoryView":431 * item, self.dtype_is_object) * finally: * PyMem_Free(tmp) # <<<<<<<<<<<<<< @@ -13336,7 +14131,7 @@ static PyObject *__pyx_memoryview_setitem_slice_assign_scalar(struct __pyx_memor __pyx_L7:; } - 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/* "View.MemoryView":683 + /* "View.MemoryView":684 * if isinstance(memview, _memoryviewslice): * memviewsliceobj = memview * p_src = &memviewsliceobj.from_slice # <<<<<<<<<<<<<< @@ -16265,20 +17155,28 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ * slice_copy(memview, &src) */ __pyx_v_p_src = (&__pyx_v_memviewsliceobj->from_slice); + + /* "View.MemoryView":682 + * assert memview.view.ndim > 0 + * + * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< + * memviewsliceobj = memview + * p_src = &memviewsliceobj.from_slice + */ goto __pyx_L3; } - /*else*/ { - /* "View.MemoryView":685 + /* "View.MemoryView":686 * p_src = &memviewsliceobj.from_slice * else: * slice_copy(memview, &src) # <<<<<<<<<<<<<< * p_src = &src * */ + /*else*/ { __pyx_memoryview_slice_copy(__pyx_v_memview, (&__pyx_v_src)); - /* "View.MemoryView":686 + /* "View.MemoryView":687 * else: * slice_copy(memview, &src) * p_src = &src # <<<<<<<<<<<<<< @@ -16289,7 +17187,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ } __pyx_L3:; - /* "View.MemoryView":692 + /* "View.MemoryView":693 * * * dst.memview = p_src.memview # <<<<<<<<<<<<<< @@ -16299,7 +17197,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ __pyx_t_4 = __pyx_v_p_src->memview; __pyx_v_dst.memview = __pyx_t_4; - /* "View.MemoryView":693 + /* "View.MemoryView":694 * * dst.memview = p_src.memview * dst.data = p_src.data # <<<<<<<<<<<<<< @@ -16309,7 +17207,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ __pyx_t_5 = __pyx_v_p_src->data; __pyx_v_dst.data = __pyx_t_5; - /* "View.MemoryView":698 + /* "View.MemoryView":699 * * * cdef __Pyx_memviewslice *p_dst = &dst # <<<<<<<<<<<<<< @@ -16318,7 +17216,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ */ __pyx_v_p_dst = (&__pyx_v_dst); - /* "View.MemoryView":699 + /* "View.MemoryView":700 * * cdef __Pyx_memviewslice *p_dst = &dst * cdef int *p_suboffset_dim = &suboffset_dim # <<<<<<<<<<<<<< @@ -16327,7 +17225,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ */ __pyx_v_p_suboffset_dim = (&__pyx_v_suboffset_dim); - /* "View.MemoryView":703 + /* "View.MemoryView":704 * cdef bint have_start, have_stop, have_step * * for dim, index in enumerate(indices): # <<<<<<<<<<<<<< @@ -16339,25 +17237,27 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ __pyx_t_3 = __pyx_v_indices; __Pyx_INCREF(__pyx_t_3); __pyx_t_7 = 0; __pyx_t_8 = NULL; } else { - __pyx_t_7 = -1; __pyx_t_3 = PyObject_GetIter(__pyx_v_indices); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 703; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_7 = -1; __pyx_t_3 = PyObject_GetIter(__pyx_v_indices); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - __pyx_t_8 = Py_TYPE(__pyx_t_3)->tp_iternext; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 703; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_8 = Py_TYPE(__pyx_t_3)->tp_iternext; if (unlikely(!__pyx_t_8)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } for (;;) { if (likely(!__pyx_t_8)) { if (likely(PyList_CheckExact(__pyx_t_3))) { if (__pyx_t_7 >= PyList_GET_SIZE(__pyx_t_3)) break; #if CYTHON_COMPILING_IN_CPYTHON - __pyx_t_9 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_7); __Pyx_INCREF(__pyx_t_9); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 703; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = PyList_GET_ITEM(__pyx_t_3, __pyx_t_7); __Pyx_INCREF(__pyx_t_9); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_9 = PySequence_ITEM(__pyx_t_3, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 703; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = PySequence_ITEM(__pyx_t_3, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); #endif } else { if (__pyx_t_7 >= PyTuple_GET_SIZE(__pyx_t_3)) break; #if CYTHON_COMPILING_IN_CPYTHON - __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_7); __Pyx_INCREF(__pyx_t_9); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 703; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = PyTuple_GET_ITEM(__pyx_t_3, __pyx_t_7); __Pyx_INCREF(__pyx_t_9); __pyx_t_7++; if (unlikely(0 < 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #else - __pyx_t_9 = PySequence_ITEM(__pyx_t_3, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 703; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = PySequence_ITEM(__pyx_t_3, __pyx_t_7); __pyx_t_7++; if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); #endif } } else { @@ -16366,7 +17266,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ PyObject* exc_type = PyErr_Occurred(); if (exc_type) { if (likely(exc_type == PyExc_StopIteration || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration))) PyErr_Clear(); - else {__pyx_filename = __pyx_f[2]; __pyx_lineno = 703; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + else {__pyx_filename = __pyx_f[2]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } break; } @@ -16377,7 +17277,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ __pyx_v_dim = __pyx_t_6; __pyx_t_6 = (__pyx_t_6 + 1); - 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/* "View.MemoryView":705 + /* "View.MemoryView":706 * for dim, index in enumerate(indices): * if PyIndex_Check(index): * slice_memviewslice( # <<<<<<<<<<<<<< * p_dst, p_src.shape[dim], p_src.strides[dim], p_src.suboffsets[dim], * dim, new_ndim, p_suboffset_dim, */ - __pyx_t_11 = __pyx_memoryview_slice_memviewslice(__pyx_v_p_dst, (__pyx_v_p_src->shape[__pyx_v_dim]), (__pyx_v_p_src->strides[__pyx_v_dim]), (__pyx_v_p_src->suboffsets[__pyx_v_dim]), __pyx_v_dim, __pyx_v_new_ndim, __pyx_v_p_suboffset_dim, __pyx_t_10, 0, 0, 0, 0, 0, 0); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 705; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_11 = __pyx_memoryview_slice_memviewslice(__pyx_v_p_dst, (__pyx_v_p_src->shape[__pyx_v_dim]), (__pyx_v_p_src->strides[__pyx_v_dim]), (__pyx_v_p_src->suboffsets[__pyx_v_dim]), __pyx_v_dim, __pyx_v_new_ndim, __pyx_v_p_suboffset_dim, __pyx_t_10, 0, 0, 0, 0, 0, 0); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 706; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "View.MemoryView":705 + * + * for dim, index in enumerate(indices): + * if PyIndex_Check(index): # <<<<<<<<<<<<<< + * slice_memviewslice( + * p_dst, p_src.shape[dim], p_src.strides[dim], p_src.suboffsets[dim], + */ goto __pyx_L6; } - 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/* "View.MemoryView":721 + /* "View.MemoryView":722 * step = index.step or 0 * * have_start = index.start is not None # <<<<<<<<<<<<<< * have_stop = index.stop is not None * have_step = index.step is not None */ - __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_start); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 721; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_start); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 722; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); __pyx_t_1 = (__pyx_t_9 != Py_None); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __pyx_v_have_start = __pyx_t_1; - /* "View.MemoryView":722 + /* "View.MemoryView":723 * * have_start = index.start is not None * have_stop = index.stop is not None # <<<<<<<<<<<<<< * have_step = index.step is not None * */ - __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_stop); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 722; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_stop); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 723; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); __pyx_t_1 = (__pyx_t_9 != Py_None); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __pyx_v_have_stop = __pyx_t_1; - /* "View.MemoryView":723 + /* "View.MemoryView":724 * have_start = index.start is not None * have_stop = index.stop is not None * have_step = index.step is not None # <<<<<<<<<<<<<< * * slice_memviewslice( */ - __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_step); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 723; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_9 = __Pyx_PyObject_GetAttrStr(__pyx_v_index, __pyx_n_s_step); if (unlikely(!__pyx_t_9)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 724; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_9); __pyx_t_1 = (__pyx_t_9 != Py_None); __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __pyx_v_have_step = __pyx_t_1; - /* "View.MemoryView":725 + /* "View.MemoryView":726 * have_step = index.step is not None * * slice_memviewslice( # <<<<<<<<<<<<<< * p_dst, p_src.shape[dim], p_src.strides[dim], p_src.suboffsets[dim], * dim, new_ndim, p_suboffset_dim, */ - __pyx_t_11 = __pyx_memoryview_slice_memviewslice(__pyx_v_p_dst, (__pyx_v_p_src->shape[__pyx_v_dim]), (__pyx_v_p_src->strides[__pyx_v_dim]), (__pyx_v_p_src->suboffsets[__pyx_v_dim]), __pyx_v_dim, __pyx_v_new_ndim, __pyx_v_p_suboffset_dim, __pyx_v_start, __pyx_v_stop, __pyx_v_step, __pyx_v_have_start, __pyx_v_have_stop, __pyx_v_have_step, 1); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 725; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_11 = __pyx_memoryview_slice_memviewslice(__pyx_v_p_dst, (__pyx_v_p_src->shape[__pyx_v_dim]), (__pyx_v_p_src->strides[__pyx_v_dim]), (__pyx_v_p_src->suboffsets[__pyx_v_dim]), __pyx_v_dim, __pyx_v_new_ndim, __pyx_v_p_suboffset_dim, __pyx_v_start, __pyx_v_stop, __pyx_v_step, __pyx_v_have_start, __pyx_v_have_stop, __pyx_v_have_step, 1); if (unlikely(__pyx_t_11 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 726; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "View.MemoryView":731 + /* "View.MemoryView":732 * have_start, have_stop, have_step, * True) * new_ndim += 1 # <<<<<<<<<<<<<< @@ -16588,7 +17498,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ } __pyx_L6:; - /* "View.MemoryView":703 + /* "View.MemoryView":704 * cdef bint have_start, have_stop, have_step * * for dim, index in enumerate(indices): # <<<<<<<<<<<<<< @@ -16598,18 +17508,18 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ } __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - /* "View.MemoryView":733 + /* "View.MemoryView":734 * new_ndim += 1 * * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< * return memoryview_fromslice(dst, new_ndim, * memviewsliceobj.to_object_func, */ - __pyx_t_1 = __Pyx_TypeCheck(((PyObject *)__pyx_v_memview), ((PyObject *)__pyx_memoryviewslice_type)); + __pyx_t_1 = __Pyx_TypeCheck(((PyObject *)__pyx_v_memview), __pyx_memoryviewslice_type); __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "View.MemoryView":734 + /* "View.MemoryView":735 * * if isinstance(memview, _memoryviewslice): * return memoryview_fromslice(dst, new_ndim, # <<<<<<<<<<<<<< @@ -16618,73 +17528,81 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ */ __Pyx_XDECREF(((PyObject *)__pyx_r)); - /* "View.MemoryView":735 + /* "View.MemoryView":736 * if isinstance(memview, _memoryviewslice): * return memoryview_fromslice(dst, new_ndim, * memviewsliceobj.to_object_func, # <<<<<<<<<<<<<< * memviewsliceobj.to_dtype_func, * memview.dtype_is_object) */ - if (unlikely(!__pyx_v_memviewsliceobj)) { __Pyx_RaiseUnboundLocalError("memviewsliceobj"); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } + if (unlikely(!__pyx_v_memviewsliceobj)) { __Pyx_RaiseUnboundLocalError("memviewsliceobj"); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - /* "View.MemoryView":736 + /* "View.MemoryView":737 * return memoryview_fromslice(dst, new_ndim, * memviewsliceobj.to_object_func, * memviewsliceobj.to_dtype_func, # <<<<<<<<<<<<<< * memview.dtype_is_object) * else: */ - if (unlikely(!__pyx_v_memviewsliceobj)) { __Pyx_RaiseUnboundLocalError("memviewsliceobj"); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } + if (unlikely(!__pyx_v_memviewsliceobj)) { __Pyx_RaiseUnboundLocalError("memviewsliceobj"); {__pyx_filename = __pyx_f[2]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - /* "View.MemoryView":734 + /* "View.MemoryView":735 * * if isinstance(memview, _memoryviewslice): * return memoryview_fromslice(dst, new_ndim, # <<<<<<<<<<<<<< * memviewsliceobj.to_object_func, * memviewsliceobj.to_dtype_func, */ - __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_dst, __pyx_v_new_ndim, __pyx_v_memviewsliceobj->to_object_func, __pyx_v_memviewsliceobj->to_dtype_func, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 734; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_dst, __pyx_v_new_ndim, __pyx_v_memviewsliceobj->to_object_func, __pyx_v_memviewsliceobj->to_dtype_func, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_memoryview_type))))) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 734; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_memoryview_type))))) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 735; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = ((struct __pyx_memoryview_obj *)__pyx_t_3); __pyx_t_3 = 0; goto __pyx_L0; + + /* "View.MemoryView":734 + * new_ndim += 1 + * + * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< + * return memoryview_fromslice(dst, new_ndim, + * memviewsliceobj.to_object_func, + */ } - /*else*/ { - /* "View.MemoryView":739 + /* "View.MemoryView":740 * memview.dtype_is_object) * else: * return memoryview_fromslice(dst, new_ndim, NULL, NULL, # <<<<<<<<<<<<<< * memview.dtype_is_object) * */ + /*else*/ { __Pyx_XDECREF(((PyObject *)__pyx_r)); - /* "View.MemoryView":740 + /* "View.MemoryView":741 * else: * return memoryview_fromslice(dst, new_ndim, NULL, NULL, * memview.dtype_is_object) # <<<<<<<<<<<<<< * * */ - __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_dst, __pyx_v_new_ndim, NULL, NULL, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __pyx_memoryview_fromslice(__pyx_v_dst, __pyx_v_new_ndim, NULL, NULL, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - /* "View.MemoryView":739 + /* "View.MemoryView":740 * memview.dtype_is_object) * else: * return memoryview_fromslice(dst, new_ndim, NULL, NULL, # <<<<<<<<<<<<<< * memview.dtype_is_object) * */ - if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_memoryview_type))))) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_memoryview_type))))) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = ((struct __pyx_memoryview_obj *)__pyx_t_3); __pyx_t_3 = 0; goto __pyx_L0; } - /* "View.MemoryView":667 + /* "View.MemoryView":668 * * @cname('__pyx_memview_slice') * cdef memoryview memview_slice(memoryview memview, object indices): # <<<<<<<<<<<<<< @@ -16706,7 +17624,7 @@ static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_ return __pyx_r; } -/* "View.MemoryView":764 +/* "View.MemoryView":765 * * @cname('__pyx_memoryview_slice_memviewslice') * cdef int slice_memviewslice( # <<<<<<<<<<<<<< @@ -16725,7 +17643,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, const char *__pyx_filename = NULL; int __pyx_clineno = 0; - /* "View.MemoryView":784 + /* "View.MemoryView":785 * cdef bint negative_step * * if not is_slice: # <<<<<<<<<<<<<< @@ -16735,7 +17653,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_1 = ((!(__pyx_v_is_slice != 0)) != 0); if (__pyx_t_1) { - /* "View.MemoryView":786 + /* "View.MemoryView":787 * if not is_slice: * * if start < 0: # <<<<<<<<<<<<<< @@ -16745,7 +17663,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_1 = ((__pyx_v_start < 0) != 0); if (__pyx_t_1) { - /* "View.MemoryView":787 + /* "View.MemoryView":788 * * if start < 0: * start += shape # <<<<<<<<<<<<<< @@ -16753,11 +17671,17 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, * _err_dim(IndexError, "Index out of bounds (axis %d)", dim) */ __pyx_v_start = (__pyx_v_start + __pyx_v_shape); - goto __pyx_L4; + + /* "View.MemoryView":787 + * if not is_slice: + * + * if start < 0: # <<<<<<<<<<<<<< + * start += shape + * if not 0 <= start < shape: + */ } - __pyx_L4:; - /* "View.MemoryView":788 + /* "View.MemoryView":789 * if start < 0: * start += shape * if not 0 <= start < shape: # <<<<<<<<<<<<<< @@ -16771,42 +17695,54 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((!(__pyx_t_1 != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":789 + /* "View.MemoryView":790 * start += shape * if not 0 <= start < shape: * _err_dim(IndexError, "Index out of bounds (axis %d)", dim) # <<<<<<<<<<<<<< * else: * */ - __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_IndexError, __pyx_k_Index_out_of_bounds_axis_d, __pyx_v_dim); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L5; + __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_IndexError, __pyx_k_Index_out_of_bounds_axis_d, __pyx_v_dim); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "View.MemoryView":789 + * if start < 0: + * start += shape + * if not 0 <= start < shape: # <<<<<<<<<<<<<< + * _err_dim(IndexError, "Index out of bounds (axis %d)", dim) + * else: + */ } - __pyx_L5:; + + /* "View.MemoryView":785 + * cdef bint negative_step + * + * if not is_slice: # <<<<<<<<<<<<<< + * + * if start < 0: + */ goto __pyx_L3; } - /*else*/ { - /* "View.MemoryView":792 + /* "View.MemoryView":793 * else: * * negative_step = have_step != 0 and step < 0 # <<<<<<<<<<<<<< * * if have_step and step == 0: */ + /*else*/ { __pyx_t_1 = ((__pyx_v_have_step != 0) != 0); if (__pyx_t_1) { - goto __pyx_L7_next_and; } else { __pyx_t_2 = __pyx_t_1; goto __pyx_L6_bool_binop_done; } - __pyx_L7_next_and:; __pyx_t_1 = ((__pyx_v_step < 0) != 0); __pyx_t_2 = __pyx_t_1; __pyx_L6_bool_binop_done:; __pyx_v_negative_step = __pyx_t_2; - /* "View.MemoryView":794 + /* "View.MemoryView":795 * negative_step = have_step != 0 and step < 0 * * if have_step and step == 0: # <<<<<<<<<<<<<< @@ -16815,30 +17751,34 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_t_1 = (__pyx_v_have_step != 0); if (__pyx_t_1) { - goto __pyx_L10_next_and; } else { __pyx_t_2 = __pyx_t_1; goto __pyx_L9_bool_binop_done; } - __pyx_L10_next_and:; __pyx_t_1 = ((__pyx_v_step == 0) != 0); __pyx_t_2 = __pyx_t_1; __pyx_L9_bool_binop_done:; if (__pyx_t_2) { - /* "View.MemoryView":795 + /* "View.MemoryView":796 * * if have_step and step == 0: * _err_dim(ValueError, "Step may not be zero (axis %d)", dim) # <<<<<<<<<<<<<< * * */ - __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, __pyx_k_Step_may_not_be_zero_axis_d, __pyx_v_dim); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L8; + __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, __pyx_k_Step_may_not_be_zero_axis_d, __pyx_v_dim); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 796; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "View.MemoryView":795 + * negative_step = have_step != 0 and step < 0 + * + * if have_step and step == 0: # <<<<<<<<<<<<<< + * _err_dim(ValueError, "Step may not be zero (axis %d)", dim) + * + */ } - __pyx_L8:; - /* "View.MemoryView":798 + /* "View.MemoryView":799 * * * if have_start: # <<<<<<<<<<<<<< @@ -16848,7 +17788,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (__pyx_v_have_start != 0); if (__pyx_t_2) { - /* "View.MemoryView":799 + /* "View.MemoryView":800 * * if have_start: * if start < 0: # <<<<<<<<<<<<<< @@ -16858,7 +17798,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_start < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":800 + /* "View.MemoryView":801 * if have_start: * if start < 0: * start += shape # <<<<<<<<<<<<<< @@ -16867,7 +17807,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_start = (__pyx_v_start + __pyx_v_shape); - /* "View.MemoryView":801 + /* "View.MemoryView":802 * if start < 0: * start += shape * if start < 0: # <<<<<<<<<<<<<< @@ -16877,7 +17817,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_start < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":802 + /* "View.MemoryView":803 * start += shape * if start < 0: * start = 0 # <<<<<<<<<<<<<< @@ -16885,13 +17825,27 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, * if negative_step: */ __pyx_v_start = 0; - goto __pyx_L13; + + /* "View.MemoryView":802 + * if start < 0: + * start += shape + * if start < 0: # <<<<<<<<<<<<<< + * start = 0 + * elif start >= shape: + */ } - __pyx_L13:; + + /* "View.MemoryView":800 + * + * if have_start: + * if start < 0: # <<<<<<<<<<<<<< + * start += shape + * if start < 0: + */ goto __pyx_L12; } - /* "View.MemoryView":803 + /* "View.MemoryView":804 * if start < 0: * start = 0 * elif start >= shape: # <<<<<<<<<<<<<< @@ -16901,7 +17855,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_start >= __pyx_v_shape) != 0); if (__pyx_t_2) { - /* "View.MemoryView":804 + /* "View.MemoryView":805 * start = 0 * elif start >= shape: * if negative_step: # <<<<<<<<<<<<<< @@ -16911,7 +17865,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (__pyx_v_negative_step != 0); if (__pyx_t_2) { - /* "View.MemoryView":805 + /* "View.MemoryView":806 * elif start >= shape: * if negative_step: * start = shape - 1 # <<<<<<<<<<<<<< @@ -16919,38 +17873,61 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, * start = shape */ __pyx_v_start = (__pyx_v_shape - 1); + + /* "View.MemoryView":805 + * start = 0 + * elif start >= shape: + * if negative_step: # <<<<<<<<<<<<<< + * start = shape - 1 + * else: + */ goto __pyx_L14; } - /*else*/ { - /* "View.MemoryView":807 + /* "View.MemoryView":808 * start = shape - 1 * else: * start = shape # <<<<<<<<<<<<<< * else: * if negative_step: */ + /*else*/ { __pyx_v_start = __pyx_v_shape; } __pyx_L14:; - goto __pyx_L12; + + /* "View.MemoryView":804 + * if start < 0: + * start = 0 + * elif start >= shape: # <<<<<<<<<<<<<< + * if negative_step: + * start = shape - 1 + */ } __pyx_L12:; + + /* "View.MemoryView":799 + * + * + * if have_start: # <<<<<<<<<<<<<< + * if start < 0: + * start += shape + */ goto __pyx_L11; } - /*else*/ { - /* "View.MemoryView":809 + /* "View.MemoryView":810 * start = shape * else: * if negative_step: # <<<<<<<<<<<<<< * start = shape - 1 * else: */ + /*else*/ { __pyx_t_2 = (__pyx_v_negative_step != 0); if (__pyx_t_2) { - /* "View.MemoryView":810 + /* "View.MemoryView":811 * else: * if negative_step: * start = shape - 1 # <<<<<<<<<<<<<< @@ -16958,24 +17935,32 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, * start = 0 */ __pyx_v_start = (__pyx_v_shape - 1); + + /* "View.MemoryView":810 + * start = shape + * else: + * if negative_step: # <<<<<<<<<<<<<< + * start = shape - 1 + * else: + */ goto __pyx_L15; } - /*else*/ { - /* "View.MemoryView":812 + /* "View.MemoryView":813 * start = shape - 1 * else: * start = 0 # <<<<<<<<<<<<<< * * if have_stop: */ + /*else*/ { __pyx_v_start = 0; } __pyx_L15:; } __pyx_L11:; - /* "View.MemoryView":814 + /* "View.MemoryView":815 * start = 0 * * if have_stop: # <<<<<<<<<<<<<< @@ -16985,7 +17970,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (__pyx_v_have_stop != 0); if (__pyx_t_2) { - /* "View.MemoryView":815 + /* "View.MemoryView":816 * * if have_stop: * if stop < 0: # <<<<<<<<<<<<<< @@ -16995,7 +17980,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_stop < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":816 + /* "View.MemoryView":817 * if have_stop: * if stop < 0: * stop += shape # <<<<<<<<<<<<<< @@ -17004,7 +17989,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_stop = (__pyx_v_stop + __pyx_v_shape); - /* "View.MemoryView":817 + /* "View.MemoryView":818 * if stop < 0: * stop += shape * if stop < 0: # <<<<<<<<<<<<<< @@ -17014,7 +17999,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_stop < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":818 + /* "View.MemoryView":819 * stop += shape * if stop < 0: * stop = 0 # <<<<<<<<<<<<<< @@ -17022,13 +18007,27 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, * stop = shape */ __pyx_v_stop = 0; - goto __pyx_L18; + + /* "View.MemoryView":818 + * if stop < 0: + * stop += shape + * if stop < 0: # <<<<<<<<<<<<<< + * stop = 0 + * elif stop > shape: + */ } - __pyx_L18:; + + /* "View.MemoryView":816 + * + * if have_stop: + * if stop < 0: # <<<<<<<<<<<<<< + * stop += shape + * if stop < 0: + */ goto __pyx_L17; } - /* "View.MemoryView":819 + /* "View.MemoryView":820 * if stop < 0: * stop = 0 * elif stop > shape: # <<<<<<<<<<<<<< @@ -17038,7 +18037,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_stop > __pyx_v_shape) != 0); if (__pyx_t_2) { - /* "View.MemoryView":820 + /* "View.MemoryView":821 * stop = 0 * elif stop > shape: * stop = shape # <<<<<<<<<<<<<< @@ -17046,24 +18045,39 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, * if negative_step: */ __pyx_v_stop = __pyx_v_shape; - goto __pyx_L17; + + /* "View.MemoryView":820 + * if stop < 0: + * stop = 0 + * elif stop > shape: # <<<<<<<<<<<<<< + * stop = shape + * else: + */ } __pyx_L17:; + + /* "View.MemoryView":815 + * start = 0 + * + * if have_stop: # <<<<<<<<<<<<<< + * if stop < 0: + * stop += shape + */ goto __pyx_L16; } - /*else*/ { - /* "View.MemoryView":822 + /* "View.MemoryView":823 * stop = shape * else: * if negative_step: # <<<<<<<<<<<<<< * stop = -1 * else: */ + /*else*/ { __pyx_t_2 = (__pyx_v_negative_step != 0); if (__pyx_t_2) { - /* "View.MemoryView":823 + /* "View.MemoryView":824 * else: * if negative_step: * stop = -1 # <<<<<<<<<<<<<< @@ -17071,24 +18085,32 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, * stop = shape */ __pyx_v_stop = -1; + + /* "View.MemoryView":823 + * stop = shape + * else: + * if negative_step: # <<<<<<<<<<<<<< + * stop = -1 + * else: + */ goto __pyx_L19; } - /*else*/ { - /* "View.MemoryView":825 + /* "View.MemoryView":826 * stop = -1 * else: * stop = shape # <<<<<<<<<<<<<< * * if not have_step: */ + /*else*/ { __pyx_v_stop = __pyx_v_shape; } __pyx_L19:; } __pyx_L16:; - /* "View.MemoryView":827 + /* "View.MemoryView":828 * stop = shape * * if not have_step: # <<<<<<<<<<<<<< @@ -17098,7 +18120,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((!(__pyx_v_have_step != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":828 + /* "View.MemoryView":829 * * if not have_step: * step = 1 # <<<<<<<<<<<<<< @@ -17106,11 +18128,17 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, * */ __pyx_v_step = 1; - goto __pyx_L20; + + /* "View.MemoryView":828 + * stop = shape + * + * if not have_step: # <<<<<<<<<<<<<< + * step = 1 + * + */ } - __pyx_L20:; - /* "View.MemoryView":832 + /* "View.MemoryView":833 * * with cython.cdivision(True): * new_shape = (stop - start) // step # <<<<<<<<<<<<<< @@ -17119,7 +18147,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ __pyx_v_new_shape = ((__pyx_v_stop - __pyx_v_start) / __pyx_v_step); - /* "View.MemoryView":834 + /* "View.MemoryView":835 * new_shape = (stop - start) // step * * if (stop - start) - step * new_shape: # <<<<<<<<<<<<<< @@ -17129,7 +18157,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (((__pyx_v_stop - __pyx_v_start) - (__pyx_v_step * __pyx_v_new_shape)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":835 + /* "View.MemoryView":836 * * if (stop - start) - step * new_shape: * new_shape += 1 # <<<<<<<<<<<<<< @@ -17137,11 +18165,17 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, * if new_shape < 0: */ __pyx_v_new_shape = (__pyx_v_new_shape + 1); - goto __pyx_L21; + + /* "View.MemoryView":835 + * new_shape = (stop - start) // step + * + * if (stop - start) - step * new_shape: # <<<<<<<<<<<<<< + * new_shape += 1 + * + */ } - __pyx_L21:; - /* "View.MemoryView":837 + /* "View.MemoryView":838 * new_shape += 1 * * if new_shape < 0: # <<<<<<<<<<<<<< @@ -17151,7 +18185,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_new_shape < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":838 + /* "View.MemoryView":839 * * if new_shape < 0: * new_shape = 0 # <<<<<<<<<<<<<< @@ -17159,11 +18193,17 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, * */ __pyx_v_new_shape = 0; - goto __pyx_L22; + + /* "View.MemoryView":838 + * new_shape += 1 + * + * if new_shape < 0: # <<<<<<<<<<<<<< + * new_shape = 0 + * + */ } - __pyx_L22:; - /* "View.MemoryView":841 + /* "View.MemoryView":842 * * * dst.strides[new_ndim] = stride * step # <<<<<<<<<<<<<< @@ -17172,7 +18212,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ (__pyx_v_dst->strides[__pyx_v_new_ndim]) = (__pyx_v_stride * __pyx_v_step); - /* "View.MemoryView":842 + /* "View.MemoryView":843 * * dst.strides[new_ndim] = stride * step * dst.shape[new_ndim] = new_shape # <<<<<<<<<<<<<< @@ -17181,7 +18221,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, */ (__pyx_v_dst->shape[__pyx_v_new_ndim]) = __pyx_v_new_shape; - /* "View.MemoryView":843 + /* "View.MemoryView":844 * dst.strides[new_ndim] = stride * step * dst.shape[new_ndim] = new_shape * dst.suboffsets[new_ndim] = suboffset # <<<<<<<<<<<<<< @@ -17192,7 +18232,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, } __pyx_L3:; - /* "View.MemoryView":846 + /* "View.MemoryView":847 * * * if suboffset_dim[0] < 0: # <<<<<<<<<<<<<< @@ -17202,7 +18242,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = (((__pyx_v_suboffset_dim[0]) < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":847 + /* "View.MemoryView":848 * * if suboffset_dim[0] < 0: * dst.data += start * stride # <<<<<<<<<<<<<< @@ -17210,23 +18250,31 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, * dst.suboffsets[suboffset_dim[0]] += start * stride */ __pyx_v_dst->data = (__pyx_v_dst->data + (__pyx_v_start * __pyx_v_stride)); + + /* "View.MemoryView":847 + * + * + * if suboffset_dim[0] < 0: # <<<<<<<<<<<<<< + * dst.data += start * stride + * else: + */ goto __pyx_L23; } - /*else*/ { - /* "View.MemoryView":849 + /* "View.MemoryView":850 * dst.data += start * stride * else: * dst.suboffsets[suboffset_dim[0]] += start * stride # <<<<<<<<<<<<<< * * if suboffset >= 0: */ + /*else*/ { __pyx_t_3 = (__pyx_v_suboffset_dim[0]); (__pyx_v_dst->suboffsets[__pyx_t_3]) = ((__pyx_v_dst->suboffsets[__pyx_t_3]) + (__pyx_v_start * __pyx_v_stride)); } __pyx_L23:; - /* "View.MemoryView":851 + /* "View.MemoryView":852 * dst.suboffsets[suboffset_dim[0]] += start * stride * * if suboffset >= 0: # <<<<<<<<<<<<<< @@ -17236,7 +18284,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_suboffset >= 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":852 + /* "View.MemoryView":853 * * if suboffset >= 0: * if not is_slice: # <<<<<<<<<<<<<< @@ -17246,7 +18294,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((!(__pyx_v_is_slice != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":853 + /* "View.MemoryView":854 * if suboffset >= 0: * if not is_slice: * if new_ndim == 0: # <<<<<<<<<<<<<< @@ -17256,7 +18304,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_t_2 = ((__pyx_v_new_ndim == 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":854 + /* "View.MemoryView":855 * if not is_slice: * if new_ndim == 0: * dst.data = ( dst.data)[0] + suboffset # <<<<<<<<<<<<<< @@ -17264,39 +18312,69 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, * _err_dim(IndexError, "All dimensions preceding dimension %d " */ __pyx_v_dst->data = ((((char **)__pyx_v_dst->data)[0]) + __pyx_v_suboffset); + + /* "View.MemoryView":854 + * if suboffset >= 0: + * if not is_slice: + * if new_ndim == 0: # <<<<<<<<<<<<<< + * dst.data = ( dst.data)[0] + suboffset + * else: + */ goto __pyx_L26; } + + /* "View.MemoryView":857 + * dst.data = ( dst.data)[0] + suboffset + * else: + * _err_dim(IndexError, "All dimensions preceding dimension %d " # <<<<<<<<<<<<<< + * "must be indexed and not sliced", dim) + * else: + */ /*else*/ { - /* "View.MemoryView":856 + /* "View.MemoryView":858 + * else: + * _err_dim(IndexError, "All dimensions preceding dimension %d " + * "must be indexed and not sliced", dim) # <<<<<<<<<<<<<< + * else: + * suboffset_dim[0] = new_ndim + */ + __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_IndexError, __pyx_k_All_dimensions_preceding_dimensi, __pyx_v_dim); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 857; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + __pyx_L26:; + + /* "View.MemoryView":853 + * + * if suboffset >= 0: + * if not is_slice: # <<<<<<<<<<<<<< + * if new_ndim == 0: * dst.data = ( dst.data)[0] + suboffset - * else: - * _err_dim(IndexError, "All dimensions preceding dimension %d " # <<<<<<<<<<<<<< - * "must be indexed and not sliced", dim) - * else: */ - __pyx_t_3 = __pyx_memoryview_err_dim(__pyx_builtin_IndexError, __pyx_k_All_dimensions_preceding_dimensi, __pyx_v_dim); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 856; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - } - __pyx_L26:; goto __pyx_L25; } - /*else*/ { - /* "View.MemoryView":859 + /* "View.MemoryView":860 * "must be indexed and not sliced", dim) * else: * suboffset_dim[0] = new_ndim # <<<<<<<<<<<<<< * * return 0 */ + /*else*/ { (__pyx_v_suboffset_dim[0]) = __pyx_v_new_ndim; } __pyx_L25:; - goto __pyx_L24; + + /* "View.MemoryView":852 + * dst.suboffsets[suboffset_dim[0]] += start * stride + * + * if suboffset >= 0: # <<<<<<<<<<<<<< + * if not is_slice: + * if new_ndim == 0: + */ } - __pyx_L24:; - /* "View.MemoryView":861 + /* "View.MemoryView":862 * suboffset_dim[0] = new_ndim * * return 0 # <<<<<<<<<<<<<< @@ -17306,7 +18384,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, __pyx_r = 0; goto __pyx_L0; - /* "View.MemoryView":764 + /* "View.MemoryView":765 * * @cname('__pyx_memoryview_slice_memviewslice') * cdef int slice_memviewslice( # <<<<<<<<<<<<<< @@ -17330,7 +18408,7 @@ static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, return __pyx_r; } -/* "View.MemoryView":867 +/* "View.MemoryView":868 * * @cname('__pyx_pybuffer_index') * cdef char *pybuffer_index(Py_buffer *view, char *bufp, Py_ssize_t index, # <<<<<<<<<<<<<< @@ -17355,7 +18433,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P int __pyx_clineno = 0; __Pyx_RefNannySetupContext("pybuffer_index", 0); - /* "View.MemoryView":869 + /* "View.MemoryView":870 * cdef char *pybuffer_index(Py_buffer *view, char *bufp, Py_ssize_t index, * Py_ssize_t dim) except NULL: * cdef Py_ssize_t shape, stride, suboffset = -1 # <<<<<<<<<<<<<< @@ -17364,7 +18442,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P */ __pyx_v_suboffset = -1; - /* "View.MemoryView":870 + /* "View.MemoryView":871 * Py_ssize_t dim) except NULL: * cdef Py_ssize_t shape, stride, suboffset = -1 * cdef Py_ssize_t itemsize = view.itemsize # <<<<<<<<<<<<<< @@ -17374,7 +18452,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P __pyx_t_1 = __pyx_v_view->itemsize; __pyx_v_itemsize = __pyx_t_1; - /* "View.MemoryView":873 + /* "View.MemoryView":874 * cdef char *resultp * * if view.ndim == 0: # <<<<<<<<<<<<<< @@ -17384,7 +18462,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P __pyx_t_2 = ((__pyx_v_view->ndim == 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":874 + /* "View.MemoryView":875 * * if view.ndim == 0: * shape = view.len / itemsize # <<<<<<<<<<<<<< @@ -17392,28 +18470,16 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P * else: */ if (unlikely(__pyx_v_itemsize == 0)) { - #ifdef WITH_THREAD - PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); - #endif PyErr_SetString(PyExc_ZeroDivisionError, "integer division or modulo by zero"); - #ifdef WITH_THREAD - PyGILState_Release(__pyx_gilstate_save); - #endif - {__pyx_filename = __pyx_f[2]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[2]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - else if (sizeof(Py_ssize_t) == sizeof(long) && unlikely(__pyx_v_itemsize == -1) && unlikely(UNARY_NEG_WOULD_OVERFLOW(__pyx_v_view->len))) { - #ifdef WITH_THREAD - PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); - #endif + else if (sizeof(Py_ssize_t) == sizeof(long) && (!(((Py_ssize_t)-1) > 0)) && unlikely(__pyx_v_itemsize == (Py_ssize_t)-1) && unlikely(UNARY_NEG_WOULD_OVERFLOW(__pyx_v_view->len))) { PyErr_SetString(PyExc_OverflowError, "value too large to perform division"); - #ifdef WITH_THREAD - PyGILState_Release(__pyx_gilstate_save); - #endif - {__pyx_filename = __pyx_f[2]; __pyx_lineno = 874; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[2]; __pyx_lineno = 875; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_v_shape = (__pyx_v_view->len / __pyx_v_itemsize); - /* "View.MemoryView":875 + /* "View.MemoryView":876 * if view.ndim == 0: * shape = view.len / itemsize * stride = itemsize # <<<<<<<<<<<<<< @@ -17421,20 +18487,28 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P * shape = view.shape[dim] */ __pyx_v_stride = __pyx_v_itemsize; + + /* "View.MemoryView":874 + * cdef char *resultp + * + * if view.ndim == 0: # <<<<<<<<<<<<<< + * shape = view.len / itemsize + * stride = itemsize + */ goto __pyx_L3; } - /*else*/ { - /* "View.MemoryView":877 + /* "View.MemoryView":878 * stride = itemsize * else: * shape = view.shape[dim] # <<<<<<<<<<<<<< * stride = view.strides[dim] * if view.suboffsets != NULL: */ + /*else*/ { __pyx_v_shape = (__pyx_v_view->shape[__pyx_v_dim]); - /* "View.MemoryView":878 + /* "View.MemoryView":879 * else: * shape = view.shape[dim] * stride = view.strides[dim] # <<<<<<<<<<<<<< @@ -17443,7 +18517,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P */ __pyx_v_stride = (__pyx_v_view->strides[__pyx_v_dim]); - /* "View.MemoryView":879 + /* "View.MemoryView":880 * shape = view.shape[dim] * stride = view.strides[dim] * if view.suboffsets != NULL: # <<<<<<<<<<<<<< @@ -17453,7 +18527,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P __pyx_t_2 = ((__pyx_v_view->suboffsets != NULL) != 0); if (__pyx_t_2) { - /* "View.MemoryView":880 + /* "View.MemoryView":881 * stride = view.strides[dim] * if view.suboffsets != NULL: * suboffset = view.suboffsets[dim] # <<<<<<<<<<<<<< @@ -17461,13 +18535,19 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P * if index < 0: */ __pyx_v_suboffset = (__pyx_v_view->suboffsets[__pyx_v_dim]); - goto __pyx_L4; + + /* "View.MemoryView":880 + * shape = view.shape[dim] + * stride = view.strides[dim] + * if view.suboffsets != NULL: # <<<<<<<<<<<<<< + * suboffset = view.suboffsets[dim] + * + */ } - __pyx_L4:; } __pyx_L3:; - /* "View.MemoryView":882 + /* "View.MemoryView":883 * suboffset = view.suboffsets[dim] * * if index < 0: # <<<<<<<<<<<<<< @@ -17477,7 +18557,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P __pyx_t_2 = ((__pyx_v_index < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":883 + /* "View.MemoryView":884 * * if index < 0: * index += view.shape[dim] # <<<<<<<<<<<<<< @@ -17486,7 +18566,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P */ __pyx_v_index = (__pyx_v_index + (__pyx_v_view->shape[__pyx_v_dim])); - /* "View.MemoryView":884 + /* "View.MemoryView":885 * if index < 0: * index += view.shape[dim] * if index < 0: # <<<<<<<<<<<<<< @@ -17496,35 +18576,49 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P __pyx_t_2 = ((__pyx_v_index < 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":885 + /* "View.MemoryView":886 * index += view.shape[dim] * if index < 0: * raise IndexError("Out of bounds on buffer access (axis %d)" % dim) # <<<<<<<<<<<<<< * * if index >= shape: */ - 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PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_4); __Pyx_GIVEREF(__pyx_t_4); + PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_IndexError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 885; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = __Pyx_PyObject_Call(__pyx_builtin_IndexError, __pyx_t_3, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 886; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; __Pyx_Raise(__pyx_t_4, 0, 0, 0); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - {__pyx_filename = __pyx_f[2]; __pyx_lineno = 885; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[2]; __pyx_lineno = 886; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "View.MemoryView":885 + * if index < 0: + * index += view.shape[dim] + * if index < 0: # <<<<<<<<<<<<<< + * raise IndexError("Out of bounds on buffer access (axis %d)" % dim) + * + */ } - goto __pyx_L5; + + /* "View.MemoryView":883 + * suboffset = view.suboffsets[dim] + * + * if index < 0: # <<<<<<<<<<<<<< + * index += view.shape[dim] + * if index < 0: + */ } - __pyx_L5:; - /* "View.MemoryView":887 + /* "View.MemoryView":888 * raise IndexError("Out of bounds on buffer access (axis %d)" % dim) * * if index >= shape: # <<<<<<<<<<<<<< @@ -17534,32 +18628,40 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P __pyx_t_2 = ((__pyx_v_index >= __pyx_v_shape) != 0); if (__pyx_t_2) { - /* "View.MemoryView":888 + /* "View.MemoryView":889 * * if index >= shape: * raise IndexError("Out of bounds on buffer access (axis %d)" % dim) # <<<<<<<<<<<<<< * * resultp = bufp + index * stride */ - __pyx_t_4 = PyInt_FromSsize_t(__pyx_v_dim); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyInt_FromSsize_t(__pyx_v_dim); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 889; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - __pyx_t_3 = __Pyx_PyString_Format(__pyx_kp_s_Out_of_bounds_on_buffer_access_a, __pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyString_Format(__pyx_kp_s_Out_of_bounds_on_buffer_access_a, __pyx_t_4); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 889; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; - __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_4 = PyTuple_New(1); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 889; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3); __Pyx_GIVEREF(__pyx_t_3); + PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_3); __pyx_t_3 = 0; - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_IndexError, __pyx_t_4, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_IndexError, __pyx_t_4, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 889; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - {__pyx_filename = __pyx_f[2]; __pyx_lineno = 888; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[2]; __pyx_lineno = 889; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "View.MemoryView":888 + * raise IndexError("Out of bounds on buffer access (axis %d)" % dim) + * + * if index >= shape: # <<<<<<<<<<<<<< + * raise IndexError("Out of bounds on buffer access (axis %d)" % dim) + * + */ } - /* "View.MemoryView":890 + /* "View.MemoryView":891 * raise IndexError("Out of bounds on buffer access (axis %d)" % dim) * * resultp = bufp + index * stride # <<<<<<<<<<<<<< @@ -17568,7 +18670,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P */ __pyx_v_resultp = (__pyx_v_bufp + (__pyx_v_index * __pyx_v_stride)); - /* "View.MemoryView":891 + /* "View.MemoryView":892 * * resultp = bufp + index * stride * if suboffset >= 0: # <<<<<<<<<<<<<< @@ -17578,7 +18680,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P __pyx_t_2 = ((__pyx_v_suboffset >= 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":892 + /* "View.MemoryView":893 * resultp = bufp + index * stride * if suboffset >= 0: * resultp = ( resultp)[0] + suboffset # <<<<<<<<<<<<<< @@ -17586,11 +18688,17 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P * return resultp */ __pyx_v_resultp = ((((char **)__pyx_v_resultp)[0]) + __pyx_v_suboffset); - goto __pyx_L8; + + /* "View.MemoryView":892 + * + * resultp = bufp + index * stride + * if suboffset >= 0: # <<<<<<<<<<<<<< + * resultp = ( resultp)[0] + suboffset + * + */ } - __pyx_L8:; - /* "View.MemoryView":894 + /* "View.MemoryView":895 * resultp = ( resultp)[0] + suboffset * * return resultp # <<<<<<<<<<<<<< @@ -17600,7 +18708,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P __pyx_r = __pyx_v_resultp; goto __pyx_L0; - /* "View.MemoryView":867 + /* "View.MemoryView":868 * * @cname('__pyx_pybuffer_index') * cdef char *pybuffer_index(Py_buffer *view, char *bufp, Py_ssize_t index, # <<<<<<<<<<<<<< @@ -17619,7 +18727,7 @@ static char *__pyx_pybuffer_index(Py_buffer *__pyx_v_view, char *__pyx_v_bufp, P return __pyx_r; } -/* "View.MemoryView":900 +/* "View.MemoryView":901 * * @cname('__pyx_memslice_transpose') * cdef int transpose_memslice(__Pyx_memviewslice *memslice) nogil except 0: # <<<<<<<<<<<<<< @@ -17646,7 +18754,7 @@ static int __pyx_memslice_transpose(__Pyx_memviewslice *__pyx_v_memslice) { const char *__pyx_filename = NULL; int __pyx_clineno = 0; - /* "View.MemoryView":901 + /* "View.MemoryView":902 * @cname('__pyx_memslice_transpose') * cdef int transpose_memslice(__Pyx_memviewslice *memslice) nogil except 0: * cdef int ndim = memslice.memview.view.ndim # <<<<<<<<<<<<<< @@ -17656,7 +18764,7 @@ static int __pyx_memslice_transpose(__Pyx_memviewslice *__pyx_v_memslice) { __pyx_t_1 = __pyx_v_memslice->memview->view.ndim; __pyx_v_ndim = __pyx_t_1; - /* "View.MemoryView":903 + /* "View.MemoryView":904 * cdef int ndim = memslice.memview.view.ndim * * cdef Py_ssize_t *shape = memslice.shape # <<<<<<<<<<<<<< @@ -17666,7 +18774,7 @@ static int __pyx_memslice_transpose(__Pyx_memviewslice *__pyx_v_memslice) { __pyx_t_2 = __pyx_v_memslice->shape; __pyx_v_shape = __pyx_t_2; - /* "View.MemoryView":904 + /* "View.MemoryView":905 * * cdef Py_ssize_t *shape = memslice.shape * cdef Py_ssize_t *strides = memslice.strides # <<<<<<<<<<<<<< @@ -17676,7 +18784,7 @@ static int __pyx_memslice_transpose(__Pyx_memviewslice *__pyx_v_memslice) { __pyx_t_2 = __pyx_v_memslice->strides; __pyx_v_strides = __pyx_t_2; - /* "View.MemoryView":908 + /* "View.MemoryView":909 * * cdef int i, j * for i in range(ndim / 2): # <<<<<<<<<<<<<< @@ -17687,7 +18795,7 @@ static int __pyx_memslice_transpose(__Pyx_memviewslice *__pyx_v_memslice) { for (__pyx_t_1 = 0; __pyx_t_1 < __pyx_t_3; __pyx_t_1+=1) { __pyx_v_i = __pyx_t_1; - /* "View.MemoryView":909 + /* "View.MemoryView":910 * cdef int i, j * for i in range(ndim / 2): * j = ndim - 1 - i # <<<<<<<<<<<<<< @@ -17696,7 +18804,7 @@ static int __pyx_memslice_transpose(__Pyx_memviewslice *__pyx_v_memslice) { */ __pyx_v_j = ((__pyx_v_ndim - 1) - __pyx_v_i); - /* "View.MemoryView":910 + /* "View.MemoryView":911 * for i in range(ndim / 2): * j = ndim - 1 - i * strides[i], strides[j] = strides[j], strides[i] # <<<<<<<<<<<<<< @@ -17708,7 +18816,7 @@ static int __pyx_memslice_transpose(__Pyx_memviewslice *__pyx_v_memslice) { (__pyx_v_strides[__pyx_v_i]) = __pyx_t_4; (__pyx_v_strides[__pyx_v_j]) = __pyx_t_5; - /* "View.MemoryView":911 + /* "View.MemoryView":912 * j = ndim - 1 - i * strides[i], strides[j] = strides[j], strides[i] * shape[i], shape[j] = shape[j], shape[i] # <<<<<<<<<<<<<< @@ -17720,7 +18828,7 @@ static int __pyx_memslice_transpose(__Pyx_memviewslice *__pyx_v_memslice) { (__pyx_v_shape[__pyx_v_i]) = __pyx_t_5; (__pyx_v_shape[__pyx_v_j]) = __pyx_t_4; - /* "View.MemoryView":913 + /* "View.MemoryView":914 * shape[i], shape[j] = shape[j], shape[i] * * if memslice.suboffsets[i] >= 0 or memslice.suboffsets[j] >= 0: # <<<<<<<<<<<<<< @@ -17729,31 +18837,35 @@ static int __pyx_memslice_transpose(__Pyx_memviewslice *__pyx_v_memslice) { */ __pyx_t_7 = (((__pyx_v_memslice->suboffsets[__pyx_v_i]) >= 0) != 0); if (!__pyx_t_7) { - goto __pyx_L7_next_or; } else { __pyx_t_6 = __pyx_t_7; goto __pyx_L6_bool_binop_done; } - __pyx_L7_next_or:; __pyx_t_7 = (((__pyx_v_memslice->suboffsets[__pyx_v_j]) >= 0) != 0); __pyx_t_6 = __pyx_t_7; __pyx_L6_bool_binop_done:; if (__pyx_t_6) { - /* "View.MemoryView":914 + /* "View.MemoryView":915 * * if memslice.suboffsets[i] >= 0 or memslice.suboffsets[j] >= 0: * _err(ValueError, "Cannot transpose memoryview with indirect dimensions") # <<<<<<<<<<<<<< * * return 1 */ - 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/* "View.MemoryView":997 + /* "View.MemoryView":1003 * * result.to_object_func = to_object_func * result.to_dtype_func = to_dtype_func # <<<<<<<<<<<<<< @@ -18286,7 +19486,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl */ __pyx_v_result->to_dtype_func = __pyx_v_to_dtype_func; - /* "View.MemoryView":999 + /* "View.MemoryView":1005 * result.to_dtype_func = to_dtype_func * * return result # <<<<<<<<<<<<<< @@ -18298,7 +19498,7 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl __pyx_r = ((PyObject *)__pyx_v_result); goto __pyx_L0; - /* "View.MemoryView":957 + /* "View.MemoryView":958 * * @cname('__pyx_memoryview_fromslice') * cdef memoryview_fromslice(__Pyx_memviewslice memviewslice, # <<<<<<<<<<<<<< @@ -18314,12 +19514,13 @@ static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice __pyx_v_memviewsl __pyx_r = 0; __pyx_L0:; __Pyx_XDECREF((PyObject *)__pyx_v_result); + __Pyx_XDECREF(__pyx_v_length); __Pyx_XGIVEREF(__pyx_r); __Pyx_RefNannyFinishContext(); return __pyx_r; } -/* "View.MemoryView":1002 +/* "View.MemoryView":1008 * * @cname('__pyx_memoryview_get_slice_from_memoryview') * cdef __Pyx_memviewslice *get_slice_from_memview(memoryview memview, # <<<<<<<<<<<<<< @@ -18339,31 +19540,31 @@ static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __p int __pyx_clineno = 0; __Pyx_RefNannySetupContext("get_slice_from_memview", 0); - /* "View.MemoryView":1005 + /* "View.MemoryView":1011 * __Pyx_memviewslice *mslice): * cdef _memoryviewslice obj * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< * obj = memview * return &obj.from_slice */ - __pyx_t_1 = __Pyx_TypeCheck(((PyObject *)__pyx_v_memview), ((PyObject *)__pyx_memoryviewslice_type)); + __pyx_t_1 = __Pyx_TypeCheck(((PyObject *)__pyx_v_memview), __pyx_memoryviewslice_type); __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "View.MemoryView":1006 + /* "View.MemoryView":1012 * cdef _memoryviewslice obj * if isinstance(memview, _memoryviewslice): * obj = memview # <<<<<<<<<<<<<< * return &obj.from_slice * else: */ - if (!(likely(((((PyObject *)__pyx_v_memview)) == Py_None) || likely(__Pyx_TypeTest(((PyObject *)__pyx_v_memview), __pyx_memoryviewslice_type))))) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1006; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((((PyObject *)__pyx_v_memview)) == Py_None) || likely(__Pyx_TypeTest(((PyObject *)__pyx_v_memview), __pyx_memoryviewslice_type))))) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1012; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_3 = ((PyObject *)__pyx_v_memview); __Pyx_INCREF(__pyx_t_3); __pyx_v_obj = ((struct __pyx_memoryviewslice_obj *)__pyx_t_3); __pyx_t_3 = 0; - /* "View.MemoryView":1007 + /* "View.MemoryView":1013 * if isinstance(memview, _memoryviewslice): * obj = memview * return &obj.from_slice # <<<<<<<<<<<<<< @@ -18372,19 +19573,27 @@ static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __p */ __pyx_r = (&__pyx_v_obj->from_slice); goto __pyx_L0; + + /* "View.MemoryView":1011 + * __Pyx_memviewslice *mslice): + * cdef _memoryviewslice obj + * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< + * obj = memview + * return &obj.from_slice + */ } - /*else*/ { - /* "View.MemoryView":1009 + /* "View.MemoryView":1015 * return &obj.from_slice * else: * slice_copy(memview, mslice) # <<<<<<<<<<<<<< * return mslice * */ + /*else*/ { __pyx_memoryview_slice_copy(__pyx_v_memview, __pyx_v_mslice); - /* "View.MemoryView":1010 + /* "View.MemoryView":1016 * else: * slice_copy(memview, mslice) * return mslice # <<<<<<<<<<<<<< @@ -18395,7 +19604,7 @@ static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __p goto __pyx_L0; } - /* "View.MemoryView":1002 + /* "View.MemoryView":1008 * * @cname('__pyx_memoryview_get_slice_from_memoryview') * cdef __Pyx_memviewslice *get_slice_from_memview(memoryview memview, # <<<<<<<<<<<<<< @@ -18406,7 +19615,7 @@ static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __p /* function exit code */ __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_3); - __Pyx_WriteUnraisable("View.MemoryView.get_slice_from_memview", __pyx_clineno, __pyx_lineno, __pyx_filename, 0); + __Pyx_WriteUnraisable("View.MemoryView.get_slice_from_memview", __pyx_clineno, __pyx_lineno, __pyx_filename, 0, 0); __pyx_r = 0; __pyx_L0:; __Pyx_XDECREF((PyObject *)__pyx_v_obj); @@ -18414,7 +19623,7 @@ static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __p return __pyx_r; } -/* "View.MemoryView":1013 +/* "View.MemoryView":1019 * * @cname('__pyx_memoryview_slice_copy') * cdef void slice_copy(memoryview memview, __Pyx_memviewslice *dst): # <<<<<<<<<<<<<< @@ -18431,10 +19640,10 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem Py_ssize_t *__pyx_t_1; int __pyx_t_2; int __pyx_t_3; - int __pyx_t_4; + Py_ssize_t __pyx_t_4; __Pyx_RefNannySetupContext("slice_copy", 0); - /* "View.MemoryView":1017 + /* "View.MemoryView":1023 * cdef (Py_ssize_t*) shape, strides, suboffsets * * shape = memview.view.shape # <<<<<<<<<<<<<< @@ -18444,7 +19653,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem __pyx_t_1 = __pyx_v_memview->view.shape; __pyx_v_shape = __pyx_t_1; - /* "View.MemoryView":1018 + /* "View.MemoryView":1024 * * shape = memview.view.shape * strides = memview.view.strides # <<<<<<<<<<<<<< @@ -18454,7 +19663,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem __pyx_t_1 = __pyx_v_memview->view.strides; __pyx_v_strides = __pyx_t_1; - /* "View.MemoryView":1019 + /* "View.MemoryView":1025 * shape = memview.view.shape * strides = memview.view.strides * suboffsets = memview.view.suboffsets # <<<<<<<<<<<<<< @@ -18464,7 +19673,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem __pyx_t_1 = __pyx_v_memview->view.suboffsets; __pyx_v_suboffsets = __pyx_t_1; - /* "View.MemoryView":1021 + /* "View.MemoryView":1027 * suboffsets = memview.view.suboffsets * * dst.memview = <__pyx_memoryview *> memview # <<<<<<<<<<<<<< @@ -18473,7 +19682,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem */ __pyx_v_dst->memview = ((struct __pyx_memoryview_obj *)__pyx_v_memview); - /* "View.MemoryView":1022 + /* "View.MemoryView":1028 * * dst.memview = <__pyx_memoryview *> memview * dst.data = memview.view.buf # <<<<<<<<<<<<<< @@ -18482,7 +19691,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem */ __pyx_v_dst->data = ((char *)__pyx_v_memview->view.buf); - /* "View.MemoryView":1024 + /* "View.MemoryView":1030 * dst.data = memview.view.buf * * for dim in range(memview.view.ndim): # <<<<<<<<<<<<<< @@ -18493,59 +19702,40 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { __pyx_v_dim = __pyx_t_3; - /* "View.MemoryView":1025 + /* "View.MemoryView":1031 * * for dim in range(memview.view.ndim): * dst.shape[dim] = shape[dim] # <<<<<<<<<<<<<< * dst.strides[dim] = strides[dim] - * if suboffsets == NULL: + * dst.suboffsets[dim] = suboffsets[dim] if suboffsets else -1 */ (__pyx_v_dst->shape[__pyx_v_dim]) = (__pyx_v_shape[__pyx_v_dim]); - /* "View.MemoryView":1026 + /* "View.MemoryView":1032 * for dim in range(memview.view.ndim): * dst.shape[dim] = shape[dim] * dst.strides[dim] = strides[dim] # <<<<<<<<<<<<<< - * if suboffsets == NULL: - * dst.suboffsets[dim] = -1 + * dst.suboffsets[dim] = suboffsets[dim] if suboffsets else -1 + * */ (__pyx_v_dst->strides[__pyx_v_dim]) = (__pyx_v_strides[__pyx_v_dim]); - /* "View.MemoryView":1027 + /* "View.MemoryView":1033 * dst.shape[dim] = shape[dim] * dst.strides[dim] = strides[dim] - * if suboffsets == NULL: # <<<<<<<<<<<<<< - * dst.suboffsets[dim] = -1 - * else: - */ - __pyx_t_4 = ((__pyx_v_suboffsets == NULL) != 0); - if (__pyx_t_4) { - - /* "View.MemoryView":1028 - * dst.strides[dim] = strides[dim] - * if suboffsets == NULL: - * dst.suboffsets[dim] = -1 # <<<<<<<<<<<<<< - * else: - * dst.suboffsets[dim] = suboffsets[dim] - */ - (__pyx_v_dst->suboffsets[__pyx_v_dim]) = -1; - goto __pyx_L5; - } - /*else*/ { - - /* "View.MemoryView":1030 - * dst.suboffsets[dim] = -1 - * else: - * dst.suboffsets[dim] = suboffsets[dim] # <<<<<<<<<<<<<< + * dst.suboffsets[dim] = suboffsets[dim] if suboffsets else -1 # <<<<<<<<<<<<<< * * @cname('__pyx_memoryview_copy_object') */ - (__pyx_v_dst->suboffsets[__pyx_v_dim]) = (__pyx_v_suboffsets[__pyx_v_dim]); + if ((__pyx_v_suboffsets != 0)) { + __pyx_t_4 = (__pyx_v_suboffsets[__pyx_v_dim]); + } else { + __pyx_t_4 = -1; } - __pyx_L5:; + (__pyx_v_dst->suboffsets[__pyx_v_dim]) = __pyx_t_4; } - /* "View.MemoryView":1013 + /* "View.MemoryView":1019 * * @cname('__pyx_memoryview_slice_copy') * cdef void slice_copy(memoryview memview, __Pyx_memviewslice *dst): # <<<<<<<<<<<<<< @@ -18557,7 +19747,7 @@ static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *__pyx_v_mem __Pyx_RefNannyFinishContext(); } -/* "View.MemoryView":1033 +/* "View.MemoryView":1036 * * @cname('__pyx_memoryview_copy_object') * cdef memoryview_copy(memoryview memview): # <<<<<<<<<<<<<< @@ -18575,7 +19765,7 @@ static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *__pyx int __pyx_clineno = 0; __Pyx_RefNannySetupContext("memoryview_copy", 0); - /* "View.MemoryView":1036 + /* "View.MemoryView":1039 * "Create a new memoryview object" * cdef __Pyx_memviewslice memviewslice * slice_copy(memview, &memviewslice) # <<<<<<<<<<<<<< @@ -18584,7 +19774,7 @@ static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *__pyx */ __pyx_memoryview_slice_copy(__pyx_v_memview, (&__pyx_v_memviewslice)); - /* "View.MemoryView":1037 + /* "View.MemoryView":1040 * cdef __Pyx_memviewslice memviewslice * slice_copy(memview, &memviewslice) * return memoryview_copy_from_slice(memview, &memviewslice) # <<<<<<<<<<<<<< @@ -18592,13 +19782,13 @@ static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *__pyx * @cname('__pyx_memoryview_copy_object_from_slice') */ __Pyx_XDECREF(__pyx_r); - __pyx_t_1 = __pyx_memoryview_copy_object_from_slice(__pyx_v_memview, (&__pyx_v_memviewslice)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1037; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __pyx_memoryview_copy_object_from_slice(__pyx_v_memview, (&__pyx_v_memviewslice)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1040; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __pyx_r = __pyx_t_1; __pyx_t_1 = 0; goto __pyx_L0; - /* "View.MemoryView":1033 + /* "View.MemoryView":1036 * * @cname('__pyx_memoryview_copy_object') * cdef memoryview_copy(memoryview memview): # <<<<<<<<<<<<<< @@ -18617,7 +19807,7 @@ static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *__pyx return __pyx_r; } -/* "View.MemoryView":1040 +/* "View.MemoryView":1043 * * @cname('__pyx_memoryview_copy_object_from_slice') * cdef memoryview_copy_from_slice(memoryview memview, __Pyx_memviewslice *memviewslice): # <<<<<<<<<<<<<< @@ -18640,18 +19830,18 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview int __pyx_clineno = 0; __Pyx_RefNannySetupContext("memoryview_copy_from_slice", 0); - /* "View.MemoryView":1047 + /* "View.MemoryView":1050 * cdef int (*to_dtype_func)(char *, object) except 0 * * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< * to_object_func = (<_memoryviewslice> memview).to_object_func * to_dtype_func = (<_memoryviewslice> memview).to_dtype_func */ - __pyx_t_1 = __Pyx_TypeCheck(((PyObject *)__pyx_v_memview), ((PyObject *)__pyx_memoryviewslice_type)); + __pyx_t_1 = __Pyx_TypeCheck(((PyObject *)__pyx_v_memview), __pyx_memoryviewslice_type); __pyx_t_2 = (__pyx_t_1 != 0); if (__pyx_t_2) { - /* "View.MemoryView":1048 + /* "View.MemoryView":1051 * * if isinstance(memview, _memoryviewslice): * to_object_func = (<_memoryviewslice> memview).to_object_func # <<<<<<<<<<<<<< @@ -18661,7 +19851,7 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview __pyx_t_3 = ((struct __pyx_memoryviewslice_obj *)__pyx_v_memview)->to_object_func; __pyx_v_to_object_func = __pyx_t_3; - /* "View.MemoryView":1049 + /* "View.MemoryView":1052 * if isinstance(memview, _memoryviewslice): * to_object_func = (<_memoryviewslice> memview).to_object_func * to_dtype_func = (<_memoryviewslice> memview).to_dtype_func # <<<<<<<<<<<<<< @@ -18670,20 +19860,28 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview */ __pyx_t_4 = ((struct __pyx_memoryviewslice_obj *)__pyx_v_memview)->to_dtype_func; __pyx_v_to_dtype_func = __pyx_t_4; + + /* "View.MemoryView":1050 + * cdef int (*to_dtype_func)(char *, object) except 0 + * + * if isinstance(memview, _memoryviewslice): # <<<<<<<<<<<<<< + * to_object_func = (<_memoryviewslice> memview).to_object_func + * to_dtype_func = (<_memoryviewslice> memview).to_dtype_func + */ goto __pyx_L3; } - /*else*/ { - /* "View.MemoryView":1051 + /* "View.MemoryView":1054 * to_dtype_func = (<_memoryviewslice> memview).to_dtype_func * else: * to_object_func = NULL # <<<<<<<<<<<<<< * to_dtype_func = NULL * */ + /*else*/ { __pyx_v_to_object_func = NULL; - /* "View.MemoryView":1052 + /* "View.MemoryView":1055 * else: * to_object_func = NULL * to_dtype_func = NULL # <<<<<<<<<<<<<< @@ -18694,7 +19892,7 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview } __pyx_L3:; - /* "View.MemoryView":1054 + /* "View.MemoryView":1057 * to_dtype_func = NULL * * return memoryview_fromslice(memviewslice[0], memview.view.ndim, # <<<<<<<<<<<<<< @@ -18703,20 +19901,20 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview */ __Pyx_XDECREF(__pyx_r); - /* "View.MemoryView":1056 + /* "View.MemoryView":1059 * return memoryview_fromslice(memviewslice[0], memview.view.ndim, * to_object_func, to_dtype_func, * memview.dtype_is_object) # <<<<<<<<<<<<<< * * */ - __pyx_t_5 = __pyx_memoryview_fromslice((__pyx_v_memviewslice[0]), __pyx_v_memview->view.ndim, __pyx_v_to_object_func, __pyx_v_to_dtype_func, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1054; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __pyx_memoryview_fromslice((__pyx_v_memviewslice[0]), __pyx_v_memview->view.ndim, __pyx_v_to_object_func, __pyx_v_to_dtype_func, __pyx_v_memview->dtype_is_object); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1057; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_5); __pyx_r = __pyx_t_5; __pyx_t_5 = 0; goto __pyx_L0; - /* "View.MemoryView":1040 + /* "View.MemoryView":1043 * * @cname('__pyx_memoryview_copy_object_from_slice') * cdef memoryview_copy_from_slice(memoryview memview, __Pyx_memviewslice *memviewslice): # <<<<<<<<<<<<<< @@ -18735,7 +19933,7 @@ static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview return __pyx_r; } -/* "View.MemoryView":1062 +/* "View.MemoryView":1065 * * * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: # <<<<<<<<<<<<<< @@ -18747,7 +19945,7 @@ static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { Py_ssize_t __pyx_r; int __pyx_t_1; - /* "View.MemoryView":1063 + /* "View.MemoryView":1066 * * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: * if arg < 0: # <<<<<<<<<<<<<< @@ -18757,7 +19955,7 @@ static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { __pyx_t_1 = ((__pyx_v_arg < 0) != 0); if (__pyx_t_1) { - /* "View.MemoryView":1064 + /* "View.MemoryView":1067 * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: * if arg < 0: * return -arg # <<<<<<<<<<<<<< @@ -18766,21 +19964,29 @@ static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { */ __pyx_r = (-__pyx_v_arg); goto __pyx_L0; - } - /*else*/ { /* "View.MemoryView":1066 + * + * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: + * if arg < 0: # <<<<<<<<<<<<<< + * return -arg + * else: + */ + } + + /* "View.MemoryView":1069 * return -arg * else: * return arg # <<<<<<<<<<<<<< * * @cname('__pyx_get_best_slice_order') */ + /*else*/ { __pyx_r = __pyx_v_arg; goto __pyx_L0; } - /* "View.MemoryView":1062 + /* "View.MemoryView":1065 * * * cdef Py_ssize_t abs_py_ssize_t(Py_ssize_t arg) nogil: # <<<<<<<<<<<<<< @@ -18793,7 +19999,7 @@ static Py_ssize_t abs_py_ssize_t(Py_ssize_t __pyx_v_arg) { return __pyx_r; } -/* "View.MemoryView":1069 +/* "View.MemoryView":1072 * * @cname('__pyx_get_best_slice_order') * cdef char get_best_order(__Pyx_memviewslice *mslice, int ndim) nogil: # <<<<<<<<<<<<<< @@ -18810,7 +20016,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ int __pyx_t_2; int __pyx_t_3; - /* "View.MemoryView":1074 + /* "View.MemoryView":1077 * """ * cdef int i * cdef Py_ssize_t c_stride = 0 # <<<<<<<<<<<<<< @@ -18819,7 +20025,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ __pyx_v_c_stride = 0; - /* "View.MemoryView":1075 + /* "View.MemoryView":1078 * cdef int i * cdef Py_ssize_t c_stride = 0 * cdef Py_ssize_t f_stride = 0 # <<<<<<<<<<<<<< @@ -18828,7 +20034,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ __pyx_v_f_stride = 0; - /* "View.MemoryView":1077 + /* "View.MemoryView":1080 * cdef Py_ssize_t f_stride = 0 * * for i in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< @@ -18838,7 +20044,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ for (__pyx_t_1 = (__pyx_v_ndim - 1); __pyx_t_1 > -1; __pyx_t_1-=1) { __pyx_v_i = __pyx_t_1; - /* "View.MemoryView":1078 + /* "View.MemoryView":1081 * * for i in range(ndim - 1, -1, -1): * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< @@ -18848,7 +20054,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ __pyx_t_2 = (((__pyx_v_mslice->shape[__pyx_v_i]) > 1) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1079 + /* "View.MemoryView":1082 * for i in range(ndim - 1, -1, -1): * if mslice.shape[i] > 1: * c_stride = mslice.strides[i] # <<<<<<<<<<<<<< @@ -18857,7 +20063,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ __pyx_v_c_stride = (__pyx_v_mslice->strides[__pyx_v_i]); - /* "View.MemoryView":1080 + /* "View.MemoryView":1083 * if mslice.shape[i] > 1: * c_stride = mslice.strides[i] * break # <<<<<<<<<<<<<< @@ -18865,11 +20071,19 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ * for i in range(ndim): */ goto __pyx_L4_break; + + /* "View.MemoryView":1081 + * + * for i in range(ndim - 1, -1, -1): + * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< + * c_stride = mslice.strides[i] + * break + */ } } __pyx_L4_break:; - /* "View.MemoryView":1082 + /* "View.MemoryView":1085 * break * * for i in range(ndim): # <<<<<<<<<<<<<< @@ -18880,7 +20094,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_1; __pyx_t_3+=1) { __pyx_v_i = __pyx_t_3; - /* "View.MemoryView":1083 + /* "View.MemoryView":1086 * * for i in range(ndim): * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< @@ -18890,7 +20104,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ __pyx_t_2 = (((__pyx_v_mslice->shape[__pyx_v_i]) > 1) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1084 + /* "View.MemoryView":1087 * for i in range(ndim): * if mslice.shape[i] > 1: * f_stride = mslice.strides[i] # <<<<<<<<<<<<<< @@ -18899,7 +20113,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ __pyx_v_f_stride = (__pyx_v_mslice->strides[__pyx_v_i]); - /* "View.MemoryView":1085 + /* "View.MemoryView":1088 * if mslice.shape[i] > 1: * f_stride = mslice.strides[i] * break # <<<<<<<<<<<<<< @@ -18907,11 +20121,19 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): */ goto __pyx_L7_break; + + /* "View.MemoryView":1086 + * + * for i in range(ndim): + * if mslice.shape[i] > 1: # <<<<<<<<<<<<<< + * f_stride = mslice.strides[i] + * break + */ } } __pyx_L7_break:; - /* "View.MemoryView":1087 + /* "View.MemoryView":1090 * break * * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): # <<<<<<<<<<<<<< @@ -18921,7 +20143,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ __pyx_t_2 = ((abs_py_ssize_t(__pyx_v_c_stride) <= abs_py_ssize_t(__pyx_v_f_stride)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1088 + /* "View.MemoryView":1091 * * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): * return 'C' # <<<<<<<<<<<<<< @@ -18930,21 +20152,29 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ */ __pyx_r = 'C'; goto __pyx_L0; - } - /*else*/ { /* "View.MemoryView":1090 + * break + * + * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): # <<<<<<<<<<<<<< + * return 'C' + * else: + */ + } + + /* "View.MemoryView":1093 * return 'C' * else: * return 'F' # <<<<<<<<<<<<<< * * @cython.cdivision(True) */ + /*else*/ { __pyx_r = 'F'; goto __pyx_L0; } - /* "View.MemoryView":1069 + /* "View.MemoryView":1072 * * @cname('__pyx_get_best_slice_order') * cdef char get_best_order(__Pyx_memviewslice *mslice, int ndim) nogil: # <<<<<<<<<<<<<< @@ -18957,7 +20187,7 @@ static char __pyx_get_best_slice_order(__Pyx_memviewslice *__pyx_v_mslice, int _ return __pyx_r; } -/* "View.MemoryView":1093 +/* "View.MemoryView":1096 * * @cython.cdivision(True) * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< @@ -18977,7 +20207,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v Py_ssize_t __pyx_t_4; Py_ssize_t __pyx_t_5; - /* "View.MemoryView":1100 + /* "View.MemoryView":1103 * * cdef Py_ssize_t i * cdef Py_ssize_t src_extent = src_shape[0] # <<<<<<<<<<<<<< @@ -18986,7 +20216,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_src_extent = (__pyx_v_src_shape[0]); - /* "View.MemoryView":1101 + /* "View.MemoryView":1104 * cdef Py_ssize_t i * cdef Py_ssize_t src_extent = src_shape[0] * cdef Py_ssize_t dst_extent = dst_shape[0] # <<<<<<<<<<<<<< @@ -18995,7 +20225,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_dst_extent = (__pyx_v_dst_shape[0]); - /* "View.MemoryView":1102 + /* "View.MemoryView":1105 * cdef Py_ssize_t src_extent = src_shape[0] * cdef Py_ssize_t dst_extent = dst_shape[0] * cdef Py_ssize_t src_stride = src_strides[0] # <<<<<<<<<<<<<< @@ -19004,7 +20234,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_src_stride = (__pyx_v_src_strides[0]); - /* "View.MemoryView":1103 + /* "View.MemoryView":1106 * cdef Py_ssize_t dst_extent = dst_shape[0] * cdef Py_ssize_t src_stride = src_strides[0] * cdef Py_ssize_t dst_stride = dst_strides[0] # <<<<<<<<<<<<<< @@ -19013,7 +20243,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_dst_stride = (__pyx_v_dst_strides[0]); - /* "View.MemoryView":1105 + /* "View.MemoryView":1108 * cdef Py_ssize_t dst_stride = dst_strides[0] * * if ndim == 1: # <<<<<<<<<<<<<< @@ -19023,7 +20253,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v __pyx_t_1 = ((__pyx_v_ndim == 1) != 0); if (__pyx_t_1) { - /* "View.MemoryView":1106 + /* "View.MemoryView":1109 * * if ndim == 1: * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< @@ -19032,22 +20262,18 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_t_2 = ((__pyx_v_src_stride > 0) != 0); if (__pyx_t_2) { - goto __pyx_L6_next_and; } else { __pyx_t_1 = __pyx_t_2; goto __pyx_L5_bool_binop_done; } - __pyx_L6_next_and:; __pyx_t_2 = ((__pyx_v_dst_stride > 0) != 0); if (__pyx_t_2) { - goto __pyx_L7_next_and; } else { __pyx_t_1 = __pyx_t_2; goto __pyx_L5_bool_binop_done; } - __pyx_L7_next_and:; - /* "View.MemoryView":1107 + /* "View.MemoryView":1110 * if ndim == 1: * if (src_stride > 0 and dst_stride > 0 and * src_stride == itemsize == dst_stride): # <<<<<<<<<<<<<< @@ -19061,9 +20287,17 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v __pyx_t_3 = (__pyx_t_2 != 0); __pyx_t_1 = __pyx_t_3; __pyx_L5_bool_binop_done:; + + /* "View.MemoryView":1109 + * + * if ndim == 1: + * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< + * src_stride == itemsize == dst_stride): + * memcpy(dst_data, src_data, itemsize * dst_extent) + */ if (__pyx_t_1) { - /* "View.MemoryView":1108 + /* "View.MemoryView":1111 * if (src_stride > 0 and dst_stride > 0 and * src_stride == itemsize == dst_stride): * memcpy(dst_data, src_data, itemsize * dst_extent) # <<<<<<<<<<<<<< @@ -19071,22 +20305,30 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v * for i in range(dst_extent): */ memcpy(__pyx_v_dst_data, __pyx_v_src_data, (__pyx_v_itemsize * __pyx_v_dst_extent)); + + /* "View.MemoryView":1109 + * + * if ndim == 1: + * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<< + * src_stride == itemsize == dst_stride): + * memcpy(dst_data, src_data, itemsize * dst_extent) + */ goto __pyx_L4; } - /*else*/ { - /* "View.MemoryView":1110 + /* "View.MemoryView":1113 * memcpy(dst_data, src_data, itemsize * dst_extent) * else: * for i in range(dst_extent): # <<<<<<<<<<<<<< * memcpy(dst_data, src_data, itemsize) * src_data += src_stride */ + /*else*/ { __pyx_t_4 = __pyx_v_dst_extent; for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { __pyx_v_i = __pyx_t_5; - /* "View.MemoryView":1111 + /* "View.MemoryView":1114 * else: * for i in range(dst_extent): * memcpy(dst_data, src_data, itemsize) # <<<<<<<<<<<<<< @@ -19095,7 +20337,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ memcpy(__pyx_v_dst_data, __pyx_v_src_data, __pyx_v_itemsize); - /* "View.MemoryView":1112 + /* "View.MemoryView":1115 * for i in range(dst_extent): * memcpy(dst_data, src_data, itemsize) * src_data += src_stride # <<<<<<<<<<<<<< @@ -19104,7 +20346,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); - /* "View.MemoryView":1113 + /* "View.MemoryView":1116 * memcpy(dst_data, src_data, itemsize) * src_data += src_stride * dst_data += dst_stride # <<<<<<<<<<<<<< @@ -19115,22 +20357,30 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v } } __pyx_L4:; + + /* "View.MemoryView":1108 + * cdef Py_ssize_t dst_stride = dst_strides[0] + * + * if ndim == 1: # <<<<<<<<<<<<<< + * if (src_stride > 0 and dst_stride > 0 and + * src_stride == itemsize == dst_stride): + */ goto __pyx_L3; } - /*else*/ { - /* "View.MemoryView":1115 + /* "View.MemoryView":1118 * dst_data += dst_stride * else: * for i in range(dst_extent): # <<<<<<<<<<<<<< * _copy_strided_to_strided(src_data, src_strides + 1, * dst_data, dst_strides + 1, */ + /*else*/ { __pyx_t_4 = __pyx_v_dst_extent; for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { __pyx_v_i = __pyx_t_5; - /* "View.MemoryView":1116 + /* "View.MemoryView":1119 * else: * for i in range(dst_extent): * _copy_strided_to_strided(src_data, src_strides + 1, # <<<<<<<<<<<<<< @@ -19139,7 +20389,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ _copy_strided_to_strided(__pyx_v_src_data, (__pyx_v_src_strides + 1), __pyx_v_dst_data, (__pyx_v_dst_strides + 1), (__pyx_v_src_shape + 1), (__pyx_v_dst_shape + 1), (__pyx_v_ndim - 1), __pyx_v_itemsize); - /* "View.MemoryView":1120 + /* "View.MemoryView":1123 * src_shape + 1, dst_shape + 1, * ndim - 1, itemsize) * src_data += src_stride # <<<<<<<<<<<<<< @@ -19148,7 +20398,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v */ __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride); - /* "View.MemoryView":1121 + /* "View.MemoryView":1124 * ndim - 1, itemsize) * src_data += src_stride * dst_data += dst_stride # <<<<<<<<<<<<<< @@ -19160,7 +20410,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v } __pyx_L3:; - /* "View.MemoryView":1093 + /* "View.MemoryView":1096 * * @cython.cdivision(True) * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<< @@ -19171,7 +20421,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v /* function exit code */ } -/* "View.MemoryView":1123 +/* "View.MemoryView":1126 * dst_data += dst_stride * * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< @@ -19181,7 +20431,7 @@ static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memviewslice *__pyx_v_dst, int __pyx_v_ndim, size_t __pyx_v_itemsize) { - /* "View.MemoryView":1126 + /* "View.MemoryView":1129 * __Pyx_memviewslice *dst, * int ndim, size_t itemsize) nogil: * _copy_strided_to_strided(src.data, src.strides, dst.data, dst.strides, # <<<<<<<<<<<<<< @@ -19190,7 +20440,7 @@ static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memvi */ _copy_strided_to_strided(__pyx_v_src->data, __pyx_v_src->strides, __pyx_v_dst->data, __pyx_v_dst->strides, __pyx_v_src->shape, __pyx_v_dst->shape, __pyx_v_ndim, __pyx_v_itemsize); - /* "View.MemoryView":1123 + /* "View.MemoryView":1126 * dst_data += dst_stride * * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< @@ -19201,7 +20451,7 @@ static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memvi /* function exit code */ } -/* "View.MemoryView":1130 +/* "View.MemoryView":1133 * * @cname('__pyx_memoryview_slice_get_size') * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< @@ -19217,7 +20467,7 @@ static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_sr int __pyx_t_2; int __pyx_t_3; - /* "View.MemoryView":1133 + /* "View.MemoryView":1136 * "Return the size of the memory occupied by the slice in number of bytes" * cdef int i * cdef Py_ssize_t size = src.memview.view.itemsize # <<<<<<<<<<<<<< @@ -19227,7 +20477,7 @@ static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_sr __pyx_t_1 = __pyx_v_src->memview->view.itemsize; __pyx_v_size = __pyx_t_1; - /* "View.MemoryView":1135 + /* "View.MemoryView":1138 * cdef Py_ssize_t size = src.memview.view.itemsize * * for i in range(ndim): # <<<<<<<<<<<<<< @@ -19238,7 +20488,7 @@ static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_sr for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { __pyx_v_i = __pyx_t_3; - /* "View.MemoryView":1136 + /* "View.MemoryView":1139 * * for i in range(ndim): * size *= src.shape[i] # <<<<<<<<<<<<<< @@ -19248,7 +20498,7 @@ static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_sr __pyx_v_size = (__pyx_v_size * (__pyx_v_src->shape[__pyx_v_i])); } - /* "View.MemoryView":1138 + /* "View.MemoryView":1141 * size *= src.shape[i] * * return size # <<<<<<<<<<<<<< @@ -19258,7 +20508,7 @@ static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_sr __pyx_r = __pyx_v_size; goto __pyx_L0; - /* "View.MemoryView":1130 + /* "View.MemoryView":1133 * * @cname('__pyx_memoryview_slice_get_size') * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<< @@ -19271,7 +20521,7 @@ static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_sr return __pyx_r; } -/* "View.MemoryView":1141 +/* "View.MemoryView":1144 * * @cname('__pyx_fill_contig_strides_array') * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<< @@ -19286,7 +20536,7 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ int __pyx_t_2; int __pyx_t_3; - /* "View.MemoryView":1150 + /* "View.MemoryView":1153 * cdef int idx * * if order == 'F': # <<<<<<<<<<<<<< @@ -19296,7 +20546,7 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ __pyx_t_1 = ((__pyx_v_order == 'F') != 0); if (__pyx_t_1) { - /* "View.MemoryView":1151 + /* "View.MemoryView":1154 * * if order == 'F': * for idx in range(ndim): # <<<<<<<<<<<<<< @@ -19307,7 +20557,7 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { __pyx_v_idx = __pyx_t_3; - /* "View.MemoryView":1152 + /* "View.MemoryView":1155 * if order == 'F': * for idx in range(ndim): * strides[idx] = stride # <<<<<<<<<<<<<< @@ -19316,7 +20566,7 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ */ (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride; - /* "View.MemoryView":1153 + /* "View.MemoryView":1156 * for idx in range(ndim): * strides[idx] = stride * stride = stride * shape[idx] # <<<<<<<<<<<<<< @@ -19325,21 +20575,29 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ */ __pyx_v_stride = (__pyx_v_stride * (__pyx_v_shape[__pyx_v_idx])); } + + /* "View.MemoryView":1153 + * cdef int idx + * + * if order == 'F': # <<<<<<<<<<<<<< + * for idx in range(ndim): + * strides[idx] = stride + */ goto __pyx_L3; } - /*else*/ { - /* "View.MemoryView":1155 + /* "View.MemoryView":1158 * stride = stride * shape[idx] * else: * for idx in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< * strides[idx] = stride * stride = stride * shape[idx] */ + /*else*/ { for (__pyx_t_2 = (__pyx_v_ndim - 1); __pyx_t_2 > -1; __pyx_t_2-=1) { __pyx_v_idx = __pyx_t_2; - /* "View.MemoryView":1156 + /* "View.MemoryView":1159 * else: * for idx in range(ndim - 1, -1, -1): * strides[idx] = stride # <<<<<<<<<<<<<< @@ -19348,7 +20606,7 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ */ (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride; - /* "View.MemoryView":1157 + /* "View.MemoryView":1160 * for idx in range(ndim - 1, -1, -1): * strides[idx] = stride * stride = stride * shape[idx] # <<<<<<<<<<<<<< @@ -19360,7 +20618,7 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ } __pyx_L3:; - /* "View.MemoryView":1159 + /* "View.MemoryView":1162 * stride = stride * shape[idx] * * return stride # <<<<<<<<<<<<<< @@ -19370,7 +20628,7 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ __pyx_r = __pyx_v_stride; goto __pyx_L0; - /* "View.MemoryView":1141 + /* "View.MemoryView":1144 * * @cname('__pyx_fill_contig_strides_array') * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<< @@ -19383,7 +20641,7 @@ static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ return __pyx_r; } -/* "View.MemoryView":1162 +/* "View.MemoryView":1165 * * @cname('__pyx_memoryview_copy_data_to_temp') * cdef void *copy_data_to_temp(__Pyx_memviewslice *src, # <<<<<<<<<<<<<< @@ -19406,7 +20664,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, const char *__pyx_filename = NULL; int __pyx_clineno = 0; - /* "View.MemoryView":1173 + /* "View.MemoryView":1176 * cdef void *result * * cdef size_t itemsize = src.memview.view.itemsize # <<<<<<<<<<<<<< @@ -19416,7 +20674,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, __pyx_t_1 = __pyx_v_src->memview->view.itemsize; __pyx_v_itemsize = __pyx_t_1; - /* "View.MemoryView":1174 + /* "View.MemoryView":1177 * * cdef size_t itemsize = src.memview.view.itemsize * cdef size_t size = slice_get_size(src, ndim) # <<<<<<<<<<<<<< @@ -19425,7 +20683,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, */ __pyx_v_size = __pyx_memoryview_slice_get_size(__pyx_v_src, __pyx_v_ndim); - /* "View.MemoryView":1176 + /* "View.MemoryView":1179 * cdef size_t size = slice_get_size(src, ndim) * * result = malloc(size) # <<<<<<<<<<<<<< @@ -19434,7 +20692,7 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, */ __pyx_v_result = malloc(__pyx_v_size); - /* "View.MemoryView":1177 + /* "View.MemoryView":1180 * * result = malloc(size) * if not result: # <<<<<<<<<<<<<< @@ -19444,19 +20702,25 @@ static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, __pyx_t_2 = ((!(__pyx_v_result != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1178 + /* "View.MemoryView":1181 * result = malloc(size) * if not result: * _err(MemoryError, NULL) # <<<<<<<<<<<<<< * * */ - __pyx_t_3 = __pyx_memoryview_err(__pyx_builtin_MemoryError, NULL); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1178; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L3; + __pyx_t_3 = __pyx_memoryview_err(__pyx_builtin_MemoryError, NULL); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1181; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "View.MemoryView":1180 + * + * result = malloc(size) + * if not result: # <<<<<<<<<<<<<< + * _err(MemoryError, NULL) + * + */ } - 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/* "View.MemoryView":1248 + /* "View.MemoryView":1251 * if src.shape[i] != dst.shape[i]: * if src.shape[i] == 1: * broadcasting = True # <<<<<<<<<<<<<< @@ -20092,7 +21393,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_v_broadcasting = 1; - /* "View.MemoryView":1249 + /* "View.MemoryView":1252 * if src.shape[i] == 1: * broadcasting = True * src.strides[i] = 0 # <<<<<<<<<<<<<< @@ -20100,25 +21401,39 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ * _err_extents(i, dst.shape[i], src.shape[i]) */ (__pyx_v_src.strides[__pyx_v_i]) = 0; + + /* "View.MemoryView":1250 + * for i in range(ndim): + * if src.shape[i] != dst.shape[i]: + * if src.shape[i] == 1: # <<<<<<<<<<<<<< + * broadcasting = True + * src.strides[i] = 0 + */ goto __pyx_L7; } - /*else*/ { - /* "View.MemoryView":1251 + /* "View.MemoryView":1254 * src.strides[i] = 0 * else: * _err_extents(i, dst.shape[i], src.shape[i]) # <<<<<<<<<<<<<< * * if src.suboffsets[i] >= 0: */ - __pyx_t_4 = __pyx_memoryview_err_extents(__pyx_v_i, (__pyx_v_dst.shape[__pyx_v_i]), (__pyx_v_src.shape[__pyx_v_i])); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1251; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + /*else*/ { + __pyx_t_4 = __pyx_memoryview_err_extents(__pyx_v_i, (__pyx_v_dst.shape[__pyx_v_i]), (__pyx_v_src.shape[__pyx_v_i])); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1254; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_L7:; - goto __pyx_L6; + + /* "View.MemoryView":1249 + * + * for i in range(ndim): + * if src.shape[i] != dst.shape[i]: # <<<<<<<<<<<<<< + * if src.shape[i] == 1: + * broadcasting = True + */ } - __pyx_L6:; - /* "View.MemoryView":1253 + /* "View.MemoryView":1256 * _err_extents(i, dst.shape[i], src.shape[i]) * * if src.suboffsets[i] >= 0: # <<<<<<<<<<<<<< @@ -20128,20 +21443,26 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (((__pyx_v_src.suboffsets[__pyx_v_i]) >= 0) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1254 + /* "View.MemoryView":1257 * * if src.suboffsets[i] >= 0: * _err_dim(ValueError, "Dimension %d is not direct", i) # <<<<<<<<<<<<<< * * if slices_overlap(&src, &dst, ndim, itemsize): */ - __pyx_t_4 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, __pyx_k_Dimension_d_is_not_direct, __pyx_v_i); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1254; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L8; + __pyx_t_4 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, __pyx_k_Dimension_d_is_not_direct, __pyx_v_i); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1257; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "View.MemoryView":1256 + * _err_extents(i, dst.shape[i], src.shape[i]) + * + * if src.suboffsets[i] >= 0: # <<<<<<<<<<<<<< + * _err_dim(ValueError, "Dimension %d is not direct", i) + * + */ } - __pyx_L8:; } - /* "View.MemoryView":1256 + /* "View.MemoryView":1259 * _err_dim(ValueError, "Dimension %d is not direct", i) * * if slices_overlap(&src, &dst, ndim, itemsize): # <<<<<<<<<<<<<< @@ -20151,7 +21472,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (__pyx_slices_overlap((&__pyx_v_src), (&__pyx_v_dst), __pyx_v_ndim, __pyx_v_itemsize) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1258 + /* "View.MemoryView":1261 * if slices_overlap(&src, &dst, ndim, itemsize): * * if not slice_is_contig(&src, order, ndim): # <<<<<<<<<<<<<< @@ -20161,7 +21482,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = ((!(__pyx_memviewslice_is_contig((&__pyx_v_src), __pyx_v_order, __pyx_v_ndim) != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1259 + /* "View.MemoryView":1262 * * if not slice_is_contig(&src, order, ndim): * order = get_best_order(&dst, ndim) # <<<<<<<<<<<<<< @@ -20169,21 +21490,27 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) */ __pyx_v_order = __pyx_get_best_slice_order((&__pyx_v_dst), __pyx_v_ndim); - goto __pyx_L10; + + /* "View.MemoryView":1261 + * if slices_overlap(&src, &dst, ndim, itemsize): + * + * if not slice_is_contig(&src, order, ndim): # <<<<<<<<<<<<<< + * order = get_best_order(&dst, ndim) + * + */ } - __pyx_L10:; - /* "View.MemoryView":1261 + /* "View.MemoryView":1264 * order = get_best_order(&dst, ndim) * * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) # <<<<<<<<<<<<<< * src = tmp * */ - __pyx_t_6 = __pyx_memoryview_copy_data_to_temp((&__pyx_v_src), (&__pyx_v_tmp), __pyx_v_order, __pyx_v_ndim); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1261; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_6 = __pyx_memoryview_copy_data_to_temp((&__pyx_v_src), (&__pyx_v_tmp), __pyx_v_order, __pyx_v_ndim); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1264; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_v_tmpdata = __pyx_t_6; - /* "View.MemoryView":1262 + /* "View.MemoryView":1265 * * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) * src = tmp # <<<<<<<<<<<<<< @@ -20191,11 +21518,17 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ * if not broadcasting: */ __pyx_v_src = __pyx_v_tmp; - goto __pyx_L9; + + /* "View.MemoryView":1259 + * _err_dim(ValueError, "Dimension %d is not direct", i) + * + * if slices_overlap(&src, &dst, ndim, itemsize): # <<<<<<<<<<<<<< + * + * if not slice_is_contig(&src, order, ndim): + */ } - __pyx_L9:; - /* "View.MemoryView":1264 + /* "View.MemoryView":1267 * src = tmp * * if not broadcasting: # <<<<<<<<<<<<<< @@ -20205,7 +21538,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = ((!(__pyx_v_broadcasting != 0)) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1267 + /* "View.MemoryView":1270 * * * if slice_is_contig(&src, 'C', ndim): # <<<<<<<<<<<<<< @@ -20215,7 +21548,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (__pyx_memviewslice_is_contig((&__pyx_v_src), 'C', __pyx_v_ndim) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1268 + /* "View.MemoryView":1271 * * if slice_is_contig(&src, 'C', ndim): * direct_copy = slice_is_contig(&dst, 'C', ndim) # <<<<<<<<<<<<<< @@ -20223,10 +21556,18 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ * direct_copy = slice_is_contig(&dst, 'F', ndim) */ __pyx_v_direct_copy = __pyx_memviewslice_is_contig((&__pyx_v_dst), 'C', __pyx_v_ndim); + + /* "View.MemoryView":1270 + * + * + * if slice_is_contig(&src, 'C', ndim): # <<<<<<<<<<<<<< + * direct_copy = slice_is_contig(&dst, 'C', ndim) + * elif slice_is_contig(&src, 'F', ndim): + */ goto __pyx_L12; } - /* "View.MemoryView":1269 + /* "View.MemoryView":1272 * if slice_is_contig(&src, 'C', ndim): * direct_copy = slice_is_contig(&dst, 'C', ndim) * elif slice_is_contig(&src, 'F', ndim): # <<<<<<<<<<<<<< @@ -20236,19 +21577,26 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (__pyx_memviewslice_is_contig((&__pyx_v_src), 'F', __pyx_v_ndim) != 0); if (__pyx_t_2) { - /* "View.MemoryView":1270 + /* "View.MemoryView":1273 * direct_copy = slice_is_contig(&dst, 'C', ndim) * elif slice_is_contig(&src, 'F', ndim): * direct_copy = slice_is_contig(&dst, 'F', ndim) # <<<<<<<<<<<<<< * * if direct_copy: */ - __pyx_v_direct_copy = __pyx_memviewslice_is_contig((&__pyx_v_dst), 'F', __pyx_v_ndim); - goto __pyx_L12; + __pyx_v_direct_copy = __pyx_memviewslice_is_contig((&__pyx_v_dst), 'F', __pyx_v_ndim); + + /* "View.MemoryView":1272 + * if slice_is_contig(&src, 'C', ndim): + * direct_copy = slice_is_contig(&dst, 'C', ndim) + * elif slice_is_contig(&src, 'F', ndim): # <<<<<<<<<<<<<< + * direct_copy = slice_is_contig(&dst, 'F', ndim) + * + */ } __pyx_L12:; - /* "View.MemoryView":1272 + /* "View.MemoryView":1275 * direct_copy = slice_is_contig(&dst, 'F', ndim) * * if direct_copy: # <<<<<<<<<<<<<< @@ -20258,7 +21606,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_2 = (__pyx_v_direct_copy != 0); if (__pyx_t_2) { - /* "View.MemoryView":1274 + /* "View.MemoryView":1277 * if direct_copy: * * refcount_copying(&dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< @@ -20267,7 +21615,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 0); - /* "View.MemoryView":1275 + /* "View.MemoryView":1278 * * refcount_copying(&dst, dtype_is_object, ndim, False) * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) # <<<<<<<<<<<<<< @@ -20276,7 +21624,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ memcpy(__pyx_v_dst.data, __pyx_v_src.data, __pyx_memoryview_slice_get_size((&__pyx_v_src), __pyx_v_ndim)); - /* "View.MemoryView":1276 + /* "View.MemoryView":1279 * refcount_copying(&dst, dtype_is_object, ndim, False) * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) * refcount_copying(&dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< @@ -20285,7 +21633,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 1); - /* "View.MemoryView":1277 + /* "View.MemoryView":1280 * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) * refcount_copying(&dst, dtype_is_object, ndim, True) * free(tmpdata) # <<<<<<<<<<<<<< @@ -20294,7 +21642,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ free(__pyx_v_tmpdata); - /* "View.MemoryView":1278 + /* "View.MemoryView":1281 * refcount_copying(&dst, dtype_is_object, ndim, True) * free(tmpdata) * return 0 # <<<<<<<<<<<<<< @@ -20303,12 +21651,26 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_r = 0; goto __pyx_L0; + + /* "View.MemoryView":1275 + * direct_copy = slice_is_contig(&dst, 'F', ndim) + * + * if direct_copy: # <<<<<<<<<<<<<< + * + * refcount_copying(&dst, dtype_is_object, ndim, False) + */ } - goto __pyx_L11; + + /* "View.MemoryView":1267 + * src = tmp + * + * if not broadcasting: # <<<<<<<<<<<<<< + * + * + */ } - __pyx_L11:; - /* "View.MemoryView":1280 + /* "View.MemoryView":1283 * return 0 * * if order == 'F' == get_best_order(&dst, ndim): # <<<<<<<<<<<<<< @@ -20322,28 +21684,34 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_t_7 = (__pyx_t_2 != 0); if (__pyx_t_7) { - /* "View.MemoryView":1283 + /* "View.MemoryView":1286 * * * transpose_memslice(&src) # <<<<<<<<<<<<<< * transpose_memslice(&dst) * */ - __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_src)); if (unlikely(__pyx_t_5 == 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_src)); if (unlikely(__pyx_t_5 == 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1286; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - /* "View.MemoryView":1284 + /* "View.MemoryView":1287 * * transpose_memslice(&src) * transpose_memslice(&dst) # <<<<<<<<<<<<<< * * refcount_copying(&dst, dtype_is_object, ndim, False) */ - __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_dst)); if (unlikely(__pyx_t_5 == 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1284; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - goto __pyx_L14; + __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_dst)); if (unlikely(__pyx_t_5 == 0)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1287; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "View.MemoryView":1283 + * return 0 + * + * if order == 'F' == get_best_order(&dst, ndim): # <<<<<<<<<<<<<< + * + * + */ } - __pyx_L14:; - /* "View.MemoryView":1286 + /* "View.MemoryView":1289 * transpose_memslice(&dst) * * refcount_copying(&dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< @@ -20352,7 +21720,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 0); - /* "View.MemoryView":1287 + /* "View.MemoryView":1290 * * refcount_copying(&dst, dtype_is_object, ndim, False) * copy_strided_to_strided(&src, &dst, ndim, itemsize) # <<<<<<<<<<<<<< @@ -20361,7 +21729,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ copy_strided_to_strided((&__pyx_v_src), (&__pyx_v_dst), __pyx_v_ndim, __pyx_v_itemsize); - /* "View.MemoryView":1288 + /* "View.MemoryView":1291 * refcount_copying(&dst, dtype_is_object, ndim, False) * copy_strided_to_strided(&src, &dst, ndim, itemsize) * refcount_copying(&dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< @@ -20370,7 +21738,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 1); - /* "View.MemoryView":1290 + /* "View.MemoryView":1293 * refcount_copying(&dst, dtype_is_object, ndim, True) * * free(tmpdata) # <<<<<<<<<<<<<< @@ -20379,7 +21747,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ */ free(__pyx_v_tmpdata); - /* "View.MemoryView":1291 + /* "View.MemoryView":1294 * * free(tmpdata) * return 0 # <<<<<<<<<<<<<< @@ -20389,7 +21757,7 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ __pyx_r = 0; goto __pyx_L0; - /* "View.MemoryView":1222 + /* "View.MemoryView":1225 * * @cname('__pyx_memoryview_copy_contents') * cdef int memoryview_copy_contents(__Pyx_memviewslice src, # <<<<<<<<<<<<<< @@ -20413,21 +21781,21 @@ static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_ return __pyx_r; } -/* "View.MemoryView":1294 +/* "View.MemoryView":1297 * * @cname('__pyx_memoryview_broadcast_leading') - * cdef void broadcast_leading(__Pyx_memviewslice *slice, # <<<<<<<<<<<<<< + * cdef void broadcast_leading(__Pyx_memviewslice *mslice, # <<<<<<<<<<<<<< * int ndim, * int ndim_other) nogil: */ -static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_slice, int __pyx_v_ndim, int __pyx_v_ndim_other) { +static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_mslice, int __pyx_v_ndim, int __pyx_v_ndim_other) { int __pyx_v_i; int __pyx_v_offset; int __pyx_t_1; int __pyx_t_2; - /* "View.MemoryView":1298 + /* "View.MemoryView":1301 * int ndim_other) nogil: * cdef int i * cdef int offset = ndim_other - ndim # <<<<<<<<<<<<<< @@ -20436,87 +21804,87 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_slice */ __pyx_v_offset = (__pyx_v_ndim_other - __pyx_v_ndim); - /* "View.MemoryView":1300 + /* "View.MemoryView":1303 * cdef int offset = ndim_other - ndim * * for i in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<< - * slice.shape[i + offset] = slice.shape[i] - * slice.strides[i + offset] = slice.strides[i] + * mslice.shape[i + offset] = mslice.shape[i] + * mslice.strides[i + offset] = mslice.strides[i] */ for (__pyx_t_1 = (__pyx_v_ndim - 1); __pyx_t_1 > -1; __pyx_t_1-=1) { __pyx_v_i = __pyx_t_1; - /* "View.MemoryView":1301 + /* "View.MemoryView":1304 * * for i in range(ndim - 1, -1, -1): - * slice.shape[i + offset] = slice.shape[i] # <<<<<<<<<<<<<< - * slice.strides[i + offset] = slice.strides[i] - * slice.suboffsets[i + offset] = slice.suboffsets[i] + * mslice.shape[i + offset] = mslice.shape[i] # <<<<<<<<<<<<<< + * mslice.strides[i + offset] = mslice.strides[i] + * mslice.suboffsets[i + offset] = mslice.suboffsets[i] */ - (__pyx_v_slice->shape[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_slice->shape[__pyx_v_i]); + (__pyx_v_mslice->shape[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_mslice->shape[__pyx_v_i]); - /* "View.MemoryView":1302 + /* "View.MemoryView":1305 * for i in range(ndim - 1, -1, -1): - * slice.shape[i + offset] = slice.shape[i] - * slice.strides[i + offset] = slice.strides[i] # <<<<<<<<<<<<<< - * slice.suboffsets[i + offset] = slice.suboffsets[i] + * mslice.shape[i + offset] = mslice.shape[i] + * mslice.strides[i + offset] = mslice.strides[i] # <<<<<<<<<<<<<< + * mslice.suboffsets[i + offset] = mslice.suboffsets[i] * */ - (__pyx_v_slice->strides[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_slice->strides[__pyx_v_i]); + (__pyx_v_mslice->strides[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_mslice->strides[__pyx_v_i]); - /* "View.MemoryView":1303 - * slice.shape[i + offset] = slice.shape[i] - * slice.strides[i + offset] = slice.strides[i] - * slice.suboffsets[i + offset] = slice.suboffsets[i] # <<<<<<<<<<<<<< + /* "View.MemoryView":1306 + * mslice.shape[i + offset] = mslice.shape[i] + * mslice.strides[i + offset] = mslice.strides[i] + * mslice.suboffsets[i + offset] = mslice.suboffsets[i] # <<<<<<<<<<<<<< * * for i in range(offset): */ - (__pyx_v_slice->suboffsets[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_slice->suboffsets[__pyx_v_i]); + (__pyx_v_mslice->suboffsets[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_mslice->suboffsets[__pyx_v_i]); } - /* "View.MemoryView":1305 - * slice.suboffsets[i + offset] = slice.suboffsets[i] + /* "View.MemoryView":1308 + * mslice.suboffsets[i + offset] = mslice.suboffsets[i] * * for i in range(offset): # <<<<<<<<<<<<<< - * slice.shape[i] = 1 - * slice.strides[i] = slice.strides[0] + * mslice.shape[i] = 1 + * mslice.strides[i] = mslice.strides[0] */ __pyx_t_1 = __pyx_v_offset; for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { __pyx_v_i = __pyx_t_2; - /* "View.MemoryView":1306 + /* "View.MemoryView":1309 * * for i in range(offset): - * slice.shape[i] = 1 # <<<<<<<<<<<<<< - * slice.strides[i] = slice.strides[0] - * slice.suboffsets[i] = -1 + * mslice.shape[i] = 1 # <<<<<<<<<<<<<< + * mslice.strides[i] = mslice.strides[0] + * mslice.suboffsets[i] = -1 */ - (__pyx_v_slice->shape[__pyx_v_i]) = 1; + (__pyx_v_mslice->shape[__pyx_v_i]) = 1; - /* "View.MemoryView":1307 + /* "View.MemoryView":1310 * for i in range(offset): - * slice.shape[i] = 1 - * slice.strides[i] = slice.strides[0] # <<<<<<<<<<<<<< - * slice.suboffsets[i] = -1 + * mslice.shape[i] = 1 + * mslice.strides[i] = mslice.strides[0] # <<<<<<<<<<<<<< + * mslice.suboffsets[i] = -1 * */ - (__pyx_v_slice->strides[__pyx_v_i]) = (__pyx_v_slice->strides[0]); + (__pyx_v_mslice->strides[__pyx_v_i]) = (__pyx_v_mslice->strides[0]); - /* "View.MemoryView":1308 - * slice.shape[i] = 1 - * slice.strides[i] = slice.strides[0] - * slice.suboffsets[i] = -1 # <<<<<<<<<<<<<< + /* "View.MemoryView":1311 + * mslice.shape[i] = 1 + * mslice.strides[i] = mslice.strides[0] + * mslice.suboffsets[i] = -1 # <<<<<<<<<<<<<< * * */ - (__pyx_v_slice->suboffsets[__pyx_v_i]) = -1; + (__pyx_v_mslice->suboffsets[__pyx_v_i]) = -1; } - /* "View.MemoryView":1294 + /* "View.MemoryView":1297 * * @cname('__pyx_memoryview_broadcast_leading') - * cdef void broadcast_leading(__Pyx_memviewslice *slice, # <<<<<<<<<<<<<< + * cdef void broadcast_leading(__Pyx_memviewslice *mslice, # <<<<<<<<<<<<<< * int ndim, * int ndim_other) nogil: */ @@ -20524,7 +21892,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_slice /* function exit code */ } -/* "View.MemoryView":1316 +/* "View.MemoryView":1319 * * @cname('__pyx_memoryview_refcount_copying') * cdef void refcount_copying(__Pyx_memviewslice *dst, bint dtype_is_object, # <<<<<<<<<<<<<< @@ -20535,7 +21903,7 @@ static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_slice static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *__pyx_v_dst, int __pyx_v_dtype_is_object, int __pyx_v_ndim, int __pyx_v_inc) { int __pyx_t_1; - /* "View.MemoryView":1320 + /* "View.MemoryView":1323 * * * if dtype_is_object: # <<<<<<<<<<<<<< @@ -20545,7 +21913,7 @@ static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *__pyx_v_dst, i __pyx_t_1 = (__pyx_v_dtype_is_object != 0); if (__pyx_t_1) { - /* "View.MemoryView":1321 + /* "View.MemoryView":1324 * * if dtype_is_object: * refcount_objects_in_slice_with_gil(dst.data, dst.shape, # <<<<<<<<<<<<<< @@ -20553,11 +21921,17 @@ static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *__pyx_v_dst, i * */ __pyx_memoryview_refcount_objects_in_slice_with_gil(__pyx_v_dst->data, __pyx_v_dst->shape, __pyx_v_dst->strides, __pyx_v_ndim, __pyx_v_inc); - goto __pyx_L3; + + /* "View.MemoryView":1323 + * + * + * if dtype_is_object: # <<<<<<<<<<<<<< + * refcount_objects_in_slice_with_gil(dst.data, dst.shape, + * dst.strides, ndim, inc) + */ } - __pyx_L3:; - /* "View.MemoryView":1316 + /* "View.MemoryView":1319 * * @cname('__pyx_memoryview_refcount_copying') * cdef void refcount_copying(__Pyx_memviewslice *dst, bint dtype_is_object, # <<<<<<<<<<<<<< @@ -20568,7 +21942,7 @@ static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *__pyx_v_dst, i /* function exit code */ } -/* "View.MemoryView":1325 +/* "View.MemoryView":1328 * * @cname('__pyx_memoryview_refcount_objects_in_slice_with_gil') * cdef void refcount_objects_in_slice_with_gil(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -20583,7 +21957,7 @@ static void __pyx_memoryview_refcount_objects_in_slice_with_gil(char *__pyx_v_da #endif __Pyx_RefNannySetupContext("refcount_objects_in_slice_with_gil", 0); - /* "View.MemoryView":1328 + /* "View.MemoryView":1331 * Py_ssize_t *strides, int ndim, * bint inc) with gil: * refcount_objects_in_slice(data, shape, strides, ndim, inc) # <<<<<<<<<<<<<< @@ -20592,7 +21966,7 @@ static void __pyx_memoryview_refcount_objects_in_slice_with_gil(char *__pyx_v_da */ __pyx_memoryview_refcount_objects_in_slice(__pyx_v_data, __pyx_v_shape, __pyx_v_strides, __pyx_v_ndim, __pyx_v_inc); - /* "View.MemoryView":1325 + /* "View.MemoryView":1328 * * @cname('__pyx_memoryview_refcount_objects_in_slice_with_gil') * cdef void refcount_objects_in_slice_with_gil(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -20607,7 +21981,7 @@ static void __pyx_memoryview_refcount_objects_in_slice_with_gil(char *__pyx_v_da #endif } -/* "View.MemoryView":1331 +/* "View.MemoryView":1334 * * @cname('__pyx_memoryview_refcount_objects_in_slice') * cdef void refcount_objects_in_slice(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -20623,7 +21997,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss int __pyx_t_3; __Pyx_RefNannySetupContext("refcount_objects_in_slice", 0); - /* "View.MemoryView":1335 + /* "View.MemoryView":1338 * cdef Py_ssize_t i * * for i in range(shape[0]): # <<<<<<<<<<<<<< @@ -20634,7 +22008,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { __pyx_v_i = __pyx_t_2; - /* "View.MemoryView":1336 + /* "View.MemoryView":1339 * * for i in range(shape[0]): * if ndim == 1: # <<<<<<<<<<<<<< @@ -20644,7 +22018,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss __pyx_t_3 = ((__pyx_v_ndim == 1) != 0); if (__pyx_t_3) { - /* "View.MemoryView":1337 + /* "View.MemoryView":1340 * for i in range(shape[0]): * if ndim == 1: * if inc: # <<<<<<<<<<<<<< @@ -20654,7 +22028,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss __pyx_t_3 = (__pyx_v_inc != 0); if (__pyx_t_3) { - /* "View.MemoryView":1338 + /* "View.MemoryView":1341 * if ndim == 1: * if inc: * Py_INCREF(( data)[0]) # <<<<<<<<<<<<<< @@ -20662,36 +22036,60 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss * Py_DECREF(( data)[0]) */ Py_INCREF((((PyObject **)__pyx_v_data)[0])); + + /* "View.MemoryView":1340 + * for i in range(shape[0]): + * if ndim == 1: + * if inc: # <<<<<<<<<<<<<< + * Py_INCREF(( data)[0]) + * else: + */ goto __pyx_L6; } - /*else*/ { - /* "View.MemoryView":1340 + /* "View.MemoryView":1343 * Py_INCREF(( data)[0]) * else: * Py_DECREF(( data)[0]) # <<<<<<<<<<<<<< * else: * refcount_objects_in_slice(data, shape + 1, strides + 1, */ + /*else*/ { Py_DECREF((((PyObject **)__pyx_v_data)[0])); } __pyx_L6:; + + /* "View.MemoryView":1339 + * + * for i in range(shape[0]): + * if ndim == 1: # <<<<<<<<<<<<<< + * if inc: + * Py_INCREF(( data)[0]) + */ goto __pyx_L5; } - /*else*/ { - /* "View.MemoryView":1342 + /* "View.MemoryView":1345 * Py_DECREF(( data)[0]) * else: * refcount_objects_in_slice(data, shape + 1, strides + 1, # <<<<<<<<<<<<<< * ndim - 1, inc) * + */ + /*else*/ { + + /* "View.MemoryView":1346 + * else: + * refcount_objects_in_slice(data, shape + 1, strides + 1, + * ndim - 1, inc) # <<<<<<<<<<<<<< + * + * data += strides[0] */ __pyx_memoryview_refcount_objects_in_slice(__pyx_v_data, (__pyx_v_shape + 1), (__pyx_v_strides + 1), (__pyx_v_ndim - 1), __pyx_v_inc); } __pyx_L5:; - /* "View.MemoryView":1345 + /* "View.MemoryView":1348 * ndim - 1, inc) * * data += strides[0] # <<<<<<<<<<<<<< @@ -20701,7 +22099,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss __pyx_v_data = (__pyx_v_data + (__pyx_v_strides[0])); } - /* "View.MemoryView":1331 + /* "View.MemoryView":1334 * * @cname('__pyx_memoryview_refcount_objects_in_slice') * cdef void refcount_objects_in_slice(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -20713,7 +22111,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss __Pyx_RefNannyFinishContext(); } -/* "View.MemoryView":1351 +/* "View.MemoryView":1354 * * @cname('__pyx_memoryview_slice_assign_scalar') * cdef void slice_assign_scalar(__Pyx_memviewslice *dst, int ndim, # <<<<<<<<<<<<<< @@ -20723,7 +22121,7 @@ static void __pyx_memoryview_refcount_objects_in_slice(char *__pyx_v_data, Py_ss static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *__pyx_v_dst, int __pyx_v_ndim, size_t __pyx_v_itemsize, void *__pyx_v_item, int __pyx_v_dtype_is_object) { - /* "View.MemoryView":1354 + /* "View.MemoryView":1357 * size_t itemsize, void *item, * bint dtype_is_object) nogil: * refcount_copying(dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<< @@ -20732,7 +22130,7 @@ static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *__pyx_v_dst */ __pyx_memoryview_refcount_copying(__pyx_v_dst, __pyx_v_dtype_is_object, __pyx_v_ndim, 0); - /* "View.MemoryView":1355 + /* "View.MemoryView":1358 * bint dtype_is_object) nogil: * refcount_copying(dst, dtype_is_object, ndim, False) * _slice_assign_scalar(dst.data, dst.shape, dst.strides, ndim, # <<<<<<<<<<<<<< @@ -20741,7 +22139,7 @@ static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *__pyx_v_dst */ __pyx_memoryview__slice_assign_scalar(__pyx_v_dst->data, __pyx_v_dst->shape, __pyx_v_dst->strides, __pyx_v_ndim, __pyx_v_itemsize, __pyx_v_item); - /* "View.MemoryView":1357 + /* "View.MemoryView":1360 * _slice_assign_scalar(dst.data, dst.shape, dst.strides, ndim, * itemsize, item) * refcount_copying(dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<< @@ -20750,7 +22148,7 @@ static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *__pyx_v_dst */ __pyx_memoryview_refcount_copying(__pyx_v_dst, __pyx_v_dtype_is_object, __pyx_v_ndim, 1); - /* "View.MemoryView":1351 + /* "View.MemoryView":1354 * * @cname('__pyx_memoryview_slice_assign_scalar') * cdef void slice_assign_scalar(__Pyx_memviewslice *dst, int ndim, # <<<<<<<<<<<<<< @@ -20761,7 +22159,7 @@ static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *__pyx_v_dst /* function exit code */ } -/* "View.MemoryView":1361 +/* "View.MemoryView":1364 * * @cname('__pyx_memoryview__slice_assign_scalar') * cdef void _slice_assign_scalar(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -20777,7 +22175,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t Py_ssize_t __pyx_t_2; Py_ssize_t __pyx_t_3; - /* "View.MemoryView":1365 + /* "View.MemoryView":1368 * size_t itemsize, void *item) nogil: * cdef Py_ssize_t i * cdef Py_ssize_t stride = strides[0] # <<<<<<<<<<<<<< @@ -20786,7 +22184,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t */ __pyx_v_stride = (__pyx_v_strides[0]); - /* "View.MemoryView":1366 + /* "View.MemoryView":1369 * cdef Py_ssize_t i * cdef Py_ssize_t stride = strides[0] * cdef Py_ssize_t extent = shape[0] # <<<<<<<<<<<<<< @@ -20795,7 +22193,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t */ __pyx_v_extent = (__pyx_v_shape[0]); - /* "View.MemoryView":1368 + /* "View.MemoryView":1371 * cdef Py_ssize_t extent = shape[0] * * if ndim == 1: # <<<<<<<<<<<<<< @@ -20805,7 +22203,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t __pyx_t_1 = ((__pyx_v_ndim == 1) != 0); if (__pyx_t_1) { - /* "View.MemoryView":1369 + /* "View.MemoryView":1372 * * if ndim == 1: * for i in range(extent): # <<<<<<<<<<<<<< @@ -20816,7 +22214,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { __pyx_v_i = __pyx_t_3; - /* "View.MemoryView":1370 + /* "View.MemoryView":1373 * if ndim == 1: * for i in range(extent): * memcpy(data, item, itemsize) # <<<<<<<<<<<<<< @@ -20825,7 +22223,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t */ memcpy(__pyx_v_data, __pyx_v_item, __pyx_v_itemsize); - /* "View.MemoryView":1371 + /* "View.MemoryView":1374 * for i in range(extent): * memcpy(data, item, itemsize) * data += stride # <<<<<<<<<<<<<< @@ -20834,22 +22232,30 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t */ __pyx_v_data = (__pyx_v_data + __pyx_v_stride); } + + /* "View.MemoryView":1371 + * cdef Py_ssize_t extent = shape[0] + * + * if ndim == 1: # <<<<<<<<<<<<<< + * for i in range(extent): + * memcpy(data, item, itemsize) + */ goto __pyx_L3; } - /*else*/ { - /* "View.MemoryView":1373 + /* "View.MemoryView":1376 * data += stride * else: * for i in range(extent): # <<<<<<<<<<<<<< * _slice_assign_scalar(data, shape + 1, strides + 1, * ndim - 1, itemsize, item) */ + /*else*/ { __pyx_t_2 = __pyx_v_extent; for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) { __pyx_v_i = __pyx_t_3; - /* "View.MemoryView":1374 + /* "View.MemoryView":1377 * else: * for i in range(extent): * _slice_assign_scalar(data, shape + 1, strides + 1, # <<<<<<<<<<<<<< @@ -20858,7 +22264,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t */ __pyx_memoryview__slice_assign_scalar(__pyx_v_data, (__pyx_v_shape + 1), (__pyx_v_strides + 1), (__pyx_v_ndim - 1), __pyx_v_itemsize, __pyx_v_item); - /* "View.MemoryView":1376 + /* "View.MemoryView":1379 * _slice_assign_scalar(data, shape + 1, strides + 1, * ndim - 1, itemsize, item) * data += stride # <<<<<<<<<<<<<< @@ -20870,7 +22276,7 @@ static void __pyx_memoryview__slice_assign_scalar(char *__pyx_v_data, Py_ssize_t } __pyx_L3:; - /* "View.MemoryView":1361 + /* "View.MemoryView":1364 * * @cname('__pyx_memoryview__slice_assign_scalar') * cdef void _slice_assign_scalar(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< @@ -21007,8 +22413,9 @@ static PyTypeObject __pyx_type___pyx_array = { 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ - #else - 0, /*reserved*/ + #endif + #if PY_MAJOR_VERSION >= 3 + 0, /*tp_as_async*/ #endif 0, /*tp_repr*/ 0, /*tp_as_number*/ @@ -21112,8 +22519,9 @@ static PyTypeObject __pyx_type___pyx_MemviewEnum = { 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ - #else - 0, /*reserved*/ + #endif + #if PY_MAJOR_VERSION >= 3 + 0, /*tp_as_async*/ #endif __pyx_MemviewEnum___repr__, /*tp_repr*/ 0, /*tp_as_number*/ @@ -21358,8 +22766,9 @@ static PyTypeObject __pyx_type___pyx_memoryview = { 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ - #else - 0, /*reserved*/ + #endif + #if PY_MAJOR_VERSION >= 3 + 0, /*tp_as_async*/ #endif __pyx_memoryview___repr__, /*tp_repr*/ 0, /*tp_as_number*/ @@ -21482,8 +22891,9 @@ static PyTypeObject __pyx_type___pyx_memoryviewslice = { 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ - #else - 0, /*reserved*/ + #endif + #if PY_MAJOR_VERSION >= 3 + 0, /*tp_as_async*/ #endif #if CYTHON_COMPILING_IN_PYPY __pyx_memoryview___repr__, /*tp_repr*/ @@ -21559,6 +22969,7 @@ static struct PyModuleDef __pyx_moduledef = { #endif static __Pyx_StringTabEntry __pyx_string_tab[] = { + {&__pyx_n_s_ASCII, __pyx_k_ASCII, sizeof(__pyx_k_ASCII), 0, 0, 1, 1}, {&__pyx_kp_s_Buffer_view_does_not_expose_stri, __pyx_k_Buffer_view_does_not_expose_stri, sizeof(__pyx_k_Buffer_view_does_not_expose_stri), 0, 0, 1, 0}, {&__pyx_n_s_C, __pyx_k_C, sizeof(__pyx_k_C), 0, 0, 1, 1}, {&__pyx_kp_s_Can_only_create_a_buffer_that_is, __pyx_k_Can_only_create_a_buffer_that_is, sizeof(__pyx_k_Can_only_create_a_buffer_that_is), 0, 0, 1, 0}, @@ -21585,7 +22996,6 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_kp_s_Tree_consistency_failed_unexpect_2, __pyx_k_Tree_consistency_failed_unexpect_2, sizeof(__pyx_k_Tree_consistency_failed_unexpect_2), 0, 0, 1, 0}, {&__pyx_n_s_TypeError, __pyx_k_TypeError, sizeof(__pyx_k_TypeError), 0, 0, 1, 1}, {&__pyx_kp_s_Unable_to_convert_item_to_object, __pyx_k_Unable_to_convert_item_to_object, sizeof(__pyx_k_Unable_to_convert_item_to_object), 0, 0, 1, 0}, - {&__pyx_kp_s_Users_chrismoody_code_scikit_le, __pyx_k_Users_chrismoody_code_scikit_le, sizeof(__pyx_k_Users_chrismoody_code_scikit_le), 0, 0, 1, 0}, {&__pyx_n_s_ValueError, __pyx_k_ValueError, sizeof(__pyx_k_ValueError), 0, 0, 1, 1}, {&__pyx_n_s_X, __pyx_k_X, sizeof(__pyx_k_X), 0, 0, 1, 1}, {&__pyx_n_s_allocate_buffer, __pyx_k_allocate_buffer, sizeof(__pyx_k_allocate_buffer), 0, 0, 1, 1}, @@ -21604,6 +23014,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_counts, __pyx_k_counts, sizeof(__pyx_k_counts), 0, 0, 1, 1}, {&__pyx_n_s_dof, __pyx_k_dof, sizeof(__pyx_k_dof), 0, 0, 1, 1}, {&__pyx_n_s_dtype_is_object, __pyx_k_dtype_is_object, sizeof(__pyx_k_dtype_is_object), 0, 0, 1, 1}, + {&__pyx_n_s_encode, __pyx_k_encode, sizeof(__pyx_k_encode), 0, 0, 1, 1}, {&__pyx_n_s_enumerate, __pyx_k_enumerate, sizeof(__pyx_k_enumerate), 0, 0, 1, 1}, {&__pyx_n_s_err, __pyx_k_err, sizeof(__pyx_k_err), 0, 0, 1, 1}, {&__pyx_n_s_error, __pyx_k_error, sizeof(__pyx_k_error), 0, 0, 1, 1}, @@ -21616,6 +23027,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_u_fortran, __pyx_k_fortran, sizeof(__pyx_k_fortran), 0, 1, 0, 1}, {&__pyx_kp_s_got_differing_extents_in_dimensi, __pyx_k_got_differing_extents_in_dimensi, sizeof(__pyx_k_got_differing_extents_in_dimensi), 0, 0, 1, 0}, {&__pyx_n_s_gradient, __pyx_k_gradient, sizeof(__pyx_k_gradient), 0, 0, 1, 1}, + {&__pyx_kp_s_home_andy_checkout_scikit_learn, __pyx_k_home_andy_checkout_scikit_learn, sizeof(__pyx_k_home_andy_checkout_scikit_learn), 0, 0, 1, 0}, {&__pyx_n_s_id, __pyx_k_id, sizeof(__pyx_k_id), 0, 0, 1, 1}, {&__pyx_n_s_idx, __pyx_k_idx, sizeof(__pyx_k_idx), 0, 0, 1, 1}, {&__pyx_n_s_import, __pyx_k_import, sizeof(__pyx_k_import), 0, 0, 1, 1}, @@ -21677,24 +23089,18 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_unpack, __pyx_k_unpack, sizeof(__pyx_k_unpack), 0, 0, 1, 1}, {&__pyx_n_s_verbose, __pyx_k_verbose, sizeof(__pyx_k_verbose), 0, 0, 1, 1}, {&__pyx_n_s_width, __pyx_k_width, sizeof(__pyx_k_width), 0, 0, 1, 1}, - {&__pyx_n_s_xrange, __pyx_k_xrange, sizeof(__pyx_k_xrange), 0, 0, 1, 1}, {0, 0, 0, 0, 0, 0, 0} }; static int __Pyx_InitCachedBuiltins(void) { - __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 130; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 132; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_builtin_RuntimeError = __Pyx_GetBuiltinName(__pyx_n_s_RuntimeError); if (!__pyx_builtin_RuntimeError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_MemoryError = __Pyx_GetBuiltinName(__pyx_n_s_MemoryError); if (!__pyx_builtin_MemoryError) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_enumerate = __Pyx_GetBuiltinName(__pyx_n_s_enumerate); if (!__pyx_builtin_enumerate) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 145; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_Ellipsis = __Pyx_GetBuiltinName(__pyx_n_s_Ellipsis); if (!__pyx_builtin_Ellipsis) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 357; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_TypeError = __Pyx_GetBuiltinName(__pyx_n_s_TypeError); if (!__pyx_builtin_TypeError) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - #if PY_MAJOR_VERSION >= 3 - __pyx_builtin_xrange = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_xrange) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - #else - __pyx_builtin_xrange = __Pyx_GetBuiltinName(__pyx_n_s_xrange); if (!__pyx_builtin_xrange) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 514; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - #endif - __pyx_builtin_id = __Pyx_GetBuiltinName(__pyx_n_s_id); if (!__pyx_builtin_id) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 569; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_IndexError = __Pyx_GetBuiltinName(__pyx_n_s_IndexError); if (!__pyx_builtin_IndexError) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 789; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_MemoryError = __Pyx_GetBuiltinName(__pyx_n_s_MemoryError); if (!__pyx_builtin_MemoryError) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 144; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_enumerate = __Pyx_GetBuiltinName(__pyx_n_s_enumerate); if (!__pyx_builtin_enumerate) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 147; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_Ellipsis = __Pyx_GetBuiltinName(__pyx_n_s_Ellipsis); if (!__pyx_builtin_Ellipsis) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 359; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_TypeError = __Pyx_GetBuiltinName(__pyx_n_s_TypeError); if (!__pyx_builtin_TypeError) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 388; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_id = __Pyx_GetBuiltinName(__pyx_n_s_id); if (!__pyx_builtin_id) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 571; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_IndexError = __Pyx_GetBuiltinName(__pyx_n_s_IndexError); if (!__pyx_builtin_IndexError) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 790; __pyx_clineno = __LINE__; goto __pyx_L1_error;} return 0; __pyx_L1_error:; return -1; @@ -21704,40 +23110,40 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":215 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":218 * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): * raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<< * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) */ - __pyx_tuple_ = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_C_contiguous); if (unlikely(!__pyx_tuple_)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple_ = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_C_contiguous); if (unlikely(!__pyx_tuple_)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple_); __Pyx_GIVEREF(__pyx_tuple_); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":219 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":222 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< * * info.buf = PyArray_DATA(self) */ - __pyx_tuple__2 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_Fortran_contiguou); if (unlikely(!__pyx_tuple__2)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple__2 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_Fortran_contiguou); if (unlikely(!__pyx_tuple__2)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__2); __Pyx_GIVEREF(__pyx_tuple__2); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":257 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":259 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" */ - __pyx_tuple__3 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple__3 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 259; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__3); __Pyx_GIVEREF(__pyx_tuple__3); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":799 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":799 * * if (end - f) - (new_offset - offset[0]) < 15: * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<< @@ -21748,7 +23154,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__4); __Pyx_GIVEREF(__pyx_tuple__4); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":803 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":803 * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< @@ -21759,7 +23165,7 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__5); __Pyx_GIVEREF(__pyx_tuple__5); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":823 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":823 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< @@ -21770,241 +23176,266 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_GOTREF(__pyx_tuple__6); __Pyx_GIVEREF(__pyx_tuple__6); - /* "View.MemoryView":127 + /* "View.MemoryView":129 * * if not self.ndim: * raise ValueError("Empty shape tuple for cython.array") # <<<<<<<<<<<<<< * * if itemsize <= 0: */ - __pyx_tuple__7 = PyTuple_Pack(1, __pyx_kp_s_Empty_shape_tuple_for_cython_arr); if (unlikely(!__pyx_tuple__7)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 127; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple__7 = PyTuple_Pack(1, __pyx_kp_s_Empty_shape_tuple_for_cython_arr); if (unlikely(!__pyx_tuple__7)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 129; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__7); __Pyx_GIVEREF(__pyx_tuple__7); - /* "View.MemoryView":130 + /* "View.MemoryView":132 * * if itemsize <= 0: * raise ValueError("itemsize <= 0 for cython.array") # <<<<<<<<<<<<<< * - 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__pyx_tuple__9 = PyTuple_Pack(1, __pyx_kp_s_unable_to_allocate_shape_and_str); if (unlikely(!__pyx_tuple__9)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 142; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__9); - __Pyx_GIVEREF(__pyx_tuple__9); + __pyx_tuple__10 = PyTuple_Pack(1, __pyx_kp_s_unable_to_allocate_shape_and_str); if (unlikely(!__pyx_tuple__10)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 144; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_tuple__10); + __Pyx_GIVEREF(__pyx_tuple__10); - /* "View.MemoryView":170 + /* "View.MemoryView":172 * self.data = malloc(self.len) * if not self.data: * raise MemoryError("unable to allocate array data.") # <<<<<<<<<<<<<< * * if self.dtype_is_object: */ - __pyx_tuple__10 = PyTuple_Pack(1, __pyx_kp_s_unable_to_allocate_array_data); if (unlikely(!__pyx_tuple__10)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 170; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_tuple__10); - 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if (unlikely(__Pyx_InitGlobals() < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_InitGlobals() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #if PY_MAJOR_VERSION < 3 && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT) if (__Pyx_init_sys_getdefaultencoding_params() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #endif if (__pyx_module_is_main_sklearn__manifold___barnes_hut_tsne) { - if (PyObject_SetAttrString(__pyx_m, "__name__", __pyx_n_s_main) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; + if (PyObject_SetAttrString(__pyx_m, "__name__", __pyx_n_s_main) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } #if PY_MAJOR_VERSION >= 3 { @@ -22099,9 +23536,9 @@ PyMODINIT_FUNC PyInit__barnes_hut_tsne(void) } #endif /*--- Builtin init code ---*/ - 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if (PyType_Ready(&__pyx_type___pyx_MemviewEnum) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 269; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyType_Ready(&__pyx_type___pyx_MemviewEnum) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 271; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_type___pyx_MemviewEnum.tp_print = 0; __pyx_MemviewEnum_type = &__pyx_type___pyx_MemviewEnum; __pyx_vtabptr_memoryview = &__pyx_vtable_memoryview; @@ -22125,18 +23562,18 @@ PyMODINIT_FUNC PyInit__barnes_hut_tsne(void) __pyx_vtable_memoryview.setitem_indexed = (PyObject *(*)(struct __pyx_memoryview_obj *, PyObject *, PyObject *))__pyx_memoryview_setitem_indexed; __pyx_vtable_memoryview.convert_item_to_object = (PyObject *(*)(struct __pyx_memoryview_obj *, char *))__pyx_memoryview_convert_item_to_object; __pyx_vtable_memoryview.assign_item_from_object = (PyObject *(*)(struct __pyx_memoryview_obj *, char *, PyObject *))__pyx_memoryview_assign_item_from_object; - if (PyType_Ready(&__pyx_type___pyx_memoryview) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 302; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyType_Ready(&__pyx_type___pyx_memoryview) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_type___pyx_memoryview.tp_print = 0; - if (__Pyx_SetVtable(__pyx_type___pyx_memoryview.tp_dict, __pyx_vtabptr_memoryview) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 302; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetVtable(__pyx_type___pyx_memoryview.tp_dict, __pyx_vtabptr_memoryview) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_memoryview_type = &__pyx_type___pyx_memoryview; __pyx_vtabptr__memoryviewslice = &__pyx_vtable__memoryviewslice; __pyx_vtable__memoryviewslice.__pyx_base = *__pyx_vtabptr_memoryview; __pyx_vtable__memoryviewslice.__pyx_base.convert_item_to_object = (PyObject *(*)(struct __pyx_memoryview_obj *, char *))__pyx_memoryviewslice_convert_item_to_object; __pyx_vtable__memoryviewslice.__pyx_base.assign_item_from_object = (PyObject *(*)(struct __pyx_memoryview_obj *, char *, PyObject *))__pyx_memoryviewslice_assign_item_from_object; __pyx_type___pyx_memoryviewslice.tp_base = __pyx_memoryview_type; - if (PyType_Ready(&__pyx_type___pyx_memoryviewslice) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 922; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyType_Ready(&__pyx_type___pyx_memoryviewslice) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 923; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_type___pyx_memoryviewslice.tp_print = 0; - if (__Pyx_SetVtable(__pyx_type___pyx_memoryviewslice.tp_dict, __pyx_vtabptr__memoryviewslice) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 922; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (__Pyx_SetVtable(__pyx_type___pyx_memoryviewslice.tp_dict, __pyx_vtabptr__memoryviewslice) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 923; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_memoryviewslice_type = &__pyx_type___pyx_memoryviewslice; /*--- Type import code ---*/ __pyx_ptype_7cpython_4type_type = __Pyx_ImportType(__Pyx_BUILTIN_MODULE_NAME, "type", @@ -22147,27 +23584,39 @@ PyMODINIT_FUNC PyInit__barnes_hut_tsne(void) #endif 0); if (unlikely(!__pyx_ptype_7cpython_4type_type)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_5numpy_dtype = __Pyx_ImportType("numpy", "dtype", sizeof(PyArray_Descr), 0); if (unlikely(!__pyx_ptype_5numpy_dtype)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_5numpy_flatiter = __Pyx_ImportType("numpy", "flatiter", sizeof(PyArrayIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_flatiter)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_5numpy_broadcast = __Pyx_ImportType("numpy", "broadcast", sizeof(PyArrayMultiIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_broadcast)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 169; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_5numpy_ndarray = __Pyx_ImportType("numpy", "ndarray", sizeof(PyArrayObject), 0); if (unlikely(!__pyx_ptype_5numpy_ndarray)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 178; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_flatiter = __Pyx_ImportType("numpy", "flatiter", sizeof(PyArrayIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_flatiter)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_broadcast = __Pyx_ImportType("numpy", "broadcast", sizeof(PyArrayMultiIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_broadcast)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_ndarray = __Pyx_ImportType("numpy", "ndarray", sizeof(PyArrayObject), 0); if (unlikely(!__pyx_ptype_5numpy_ndarray)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_5numpy_ufunc = __Pyx_ImportType("numpy", "ufunc", sizeof(PyUFuncObject), 0); if (unlikely(!__pyx_ptype_5numpy_ufunc)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /*--- Variable import code ---*/ /*--- Function import code ---*/ /*--- Execution code ---*/ + #if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED) + if (__Pyx_patch_abc() < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + #endif /* "sklearn/manifold/_barnes_hut_tsne.pyx":15 * from libc.math cimport sqrt, log * cimport numpy as np * import numpy as np # <<<<<<<<<<<<<< * - * cdef extern from "math.h": + * cdef char* EMPTY_STRING = "" */ __pyx_t_1 = __Pyx_Import(__pyx_n_s_numpy, 0, -1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); if (PyDict_SetItem(__pyx_d, __pyx_n_s_np, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 15; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":23 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":17 + * import numpy as np + * + * cdef char* EMPTY_STRING = "" # <<<<<<<<<<<<<< + * + * cdef extern from "math.h": + */ + __pyx_v_7sklearn_8manifold_16_barnes_hut_tsne_EMPTY_STRING = __pyx_k__20; + + /* "sklearn/manifold/_barnes_hut_tsne.pyx":25 * # effectively ignoring differences near the 32bit * # floating point precision * cdef float EPSILON = 1e-6 # <<<<<<<<<<<<<< @@ -22176,64 +23625,64 @@ PyMODINIT_FUNC PyInit__barnes_hut_tsne(void) */ __pyx_v_7sklearn_8manifold_16_barnes_hut_tsne_EPSILON = 1e-6; - /* "sklearn/manifold/_barnes_hut_tsne.pyx":704 + /* "sklearn/manifold/_barnes_hut_tsne.pyx":706 * * * def calculate_edge(pos_output): # <<<<<<<<<<<<<< * # Make the boundaries slightly outside of the data * # to avoid floating point error near the edge */ - __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_7sklearn_8manifold_16_barnes_hut_tsne_1calculate_edge, NULL, __pyx_n_s_sklearn_manifold__barnes_hut_tsn); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_7sklearn_8manifold_16_barnes_hut_tsne_1calculate_edge, NULL, __pyx_n_s_sklearn_manifold__barnes_hut_tsn); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 706; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (PyDict_SetItem(__pyx_d, __pyx_n_s_calculate_edge, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 704; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyDict_SetItem(__pyx_d, __pyx_n_s_calculate_edge, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 706; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - 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return 0; -#endif + return 0; +#endif +} + +static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { + if (unlikely(retval)) { + Py_DECREF(retval); + __Pyx_RaiseTooManyValuesError(expected); + return -1; + } else { + return __Pyx_IterFinish(); + } + return 0; +} + +#if CYTHON_COMPILING_IN_CPYTHON +static PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, CYTHON_UNUSED int inplace) { + if (op1 == op2) { + Py_RETURN_TRUE; + } + #if PY_MAJOR_VERSION < 3 + if (likely(PyInt_CheckExact(op1))) { + const long b = intval; + long a = PyInt_AS_LONG(op1); + if (a == b) { + Py_RETURN_TRUE; + } else { + Py_RETURN_FALSE; + } + } + #endif + #if CYTHON_USE_PYLONG_INTERNALS && PY_MAJOR_VERSION >= 3 + if (likely(PyLong_CheckExact(op1))) { + const long b = intval; + long a; + const digit* digits = ((PyLongObject*)op1)->ob_digit; + const Py_ssize_t size = Py_SIZE(op1); + if (likely(__Pyx_sst_abs(size) <= 1)) { + a = likely(size) ? digits[0] : 0; + if (size == -1) a = -a; + } else { + switch (size) { + case -2: + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0])); + break; + } + case 2: + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0])); + break; + } + case -3: + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + break; + } + case 3: + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + break; + } + case -4: + if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + break; + } + case 4: + if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + break; + } + #if PyLong_SHIFT < 30 && PyLong_SHIFT != 15 + default: return PyLong_Type.tp_richcompare(op1, op2, Py_EQ); + #else + default: Py_RETURN_FALSE; + #endif + } + } + if (a == b) { + Py_RETURN_TRUE; + } else { + Py_RETURN_FALSE; + } + } + #endif + if (PyFloat_CheckExact(op1)) { + const long b = intval; + double a = PyFloat_AS_DOUBLE(op1); + if ((double)a == (double)b) { + Py_RETURN_TRUE; + } else { + Py_RETURN_FALSE; + } + } + return PyObject_RichCompare(op1, op2, Py_EQ); } +#endif -static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { - if (unlikely(retval)) { - Py_DECREF(retval); - __Pyx_RaiseTooManyValuesError(expected); - return -1; - } else { - return __Pyx_IterFinish(); +#if CYTHON_COMPILING_IN_CPYTHON +static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, CYTHON_UNUSED int inplace) { + #if PY_MAJOR_VERSION < 3 + if (likely(PyInt_CheckExact(op1))) { + const long b = intval; + long x; + long a = PyInt_AS_LONG(op1); + x = (long)((unsigned long)a - b); + if (likely((x^a) >= 0 || (x^~b) >= 0)) + return PyInt_FromLong(x); + return PyLong_Type.tp_as_number->nb_subtract(op1, op2); } - return 0; + #endif + #if CYTHON_USE_PYLONG_INTERNALS && PY_MAJOR_VERSION >= 3 + if (likely(PyLong_CheckExact(op1))) { + const long b = intval; + long a, x; + const PY_LONG_LONG llb = intval; + PY_LONG_LONG lla, llx; + const digit* digits = ((PyLongObject*)op1)->ob_digit; + const Py_ssize_t size = Py_SIZE(op1); + if (likely(__Pyx_sst_abs(size) <= 1)) { + a = likely(size) ? digits[0] : 0; + if (size == -1) a = -a; + } else { + switch (size) { + case -2: + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0])); + break; + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { + lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | digits[0])); + goto long_long; + } + case 2: + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0])); + break; + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { + lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | digits[0])); + goto long_long; + } + case -3: + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + break; + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { + lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + goto long_long; + } + case 3: + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + break; + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { + lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + goto long_long; + } + case -4: + if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + break; + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { + lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + goto long_long; + } + case 4: + if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + break; + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { + lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + goto long_long; + } + default: return PyLong_Type.tp_as_number->nb_subtract(op1, op2); + } + } + x = a - b; + return PyLong_FromLong(x); + long_long: + llx = lla - llb; + return PyLong_FromLongLong(llx); + } + #endif + if (PyFloat_CheckExact(op1)) { + const long b = intval; + double a = PyFloat_AS_DOUBLE(op1); + double result; + PyFPE_START_PROTECT("subtract", return NULL) + result = ((double)a) - (double)b; + PyFPE_END_PROTECT(result) + return PyFloat_FromDouble(result); + } + return (inplace ? PyNumber_InPlaceSubtract : PyNumber_Subtract)(op1, op2); } +#endif static CYTHON_INLINE int __Pyx_IsLittleEndian(void) { unsigned int n = 1; @@ -23301,7 +25001,6 @@ __Pyx_init_memviewslice(struct __pyx_memoryview_obj *memview, static CYTHON_INLINE void __pyx_fatalerror(const char *fmt, ...) { va_list vargs; char msg[200]; - va_start(vargs, fmt); #ifdef HAVE_STDARG_PROTOTYPES va_start(vargs, fmt); #else @@ -23485,10 +25184,13 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject if (value && PyExceptionInstance_Check(value)) { instance_class = (PyObject*) Py_TYPE(value); if (instance_class != type) { - if (PyObject_IsSubclass(instance_class, type)) { - type = instance_class; - } else { + int is_subclass = PyObject_IsSubclass(instance_class, type); + if (!is_subclass) { instance_class = NULL; + } else if (unlikely(is_subclass == -1)) { + goto bad; + } else { + type = instance_class; } } } @@ -23546,6 +25248,13 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject } PyErr_SetObject(type, value); if (tb) { +#if CYTHON_COMPILING_IN_PYPY + PyObject *tmp_type, *tmp_value, *tmp_tb; + PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb); + Py_INCREF(tb); + PyErr_Restore(tmp_type, tmp_value, tb); + Py_XDECREF(tmp_tb); +#else PyThreadState *tstate = PyThreadState_GET(); PyObject* tmp_tb = tstate->curexc_traceback; if (tb != tmp_tb) { @@ -23553,6 +25262,7 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject tstate->curexc_traceback = tb; Py_XDECREF(tmp_tb); } +#endif } bad: Py_XDECREF(owned_instance); @@ -23867,6 +25577,79 @@ static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, *tb = tmp_tb; } +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { + PyObject *empty_list = 0; + PyObject *module = 0; + PyObject *global_dict = 0; + PyObject *empty_dict = 0; + PyObject *list; + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_import; + py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); + if (!py_import) + goto bad; + #endif + if (from_list) + list = from_list; + else { + empty_list = PyList_New(0); + if (!empty_list) + goto bad; + list = empty_list; + } + global_dict = PyModule_GetDict(__pyx_m); + if (!global_dict) + goto bad; + empty_dict = PyDict_New(); + if (!empty_dict) + goto bad; + { + #if PY_MAJOR_VERSION >= 3 + if (level == -1) { + if (strchr(__Pyx_MODULE_NAME, '.')) { + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_level = PyInt_FromLong(1); + if (!py_level) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, global_dict, empty_dict, list, py_level, NULL); + Py_DECREF(py_level); + #else + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, 1); + #endif + if (!module) { + if (!PyErr_ExceptionMatches(PyExc_ImportError)) + goto bad; + PyErr_Clear(); + } + } + level = 0; + } + #endif + if (!module) { + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_level = PyInt_FromLong(level); + if (!py_level) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, global_dict, empty_dict, list, py_level, NULL); + Py_DECREF(py_level); + #else + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, level); + #endif + } + } +bad: + #if PY_VERSION_HEX < 0x03030000 + Py_XDECREF(py_import); + #endif + Py_XDECREF(empty_list); + Py_XDECREF(empty_dict); + return module; +} + static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { PyObject *r; if (!j) return NULL; @@ -23875,7 +25658,8 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j return r; } static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, - int wraparound, int boundscheck) { + CYTHON_NCP_UNUSED int wraparound, + CYTHON_NCP_UNUSED int boundscheck) { #if CYTHON_COMPILING_IN_CPYTHON if (wraparound & unlikely(i < 0)) i += PyList_GET_SIZE(o); if ((!boundscheck) || likely((0 <= i) & (i < PyList_GET_SIZE(o)))) { @@ -23889,7 +25673,8 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_ #endif } static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, - int wraparound, int boundscheck) { + CYTHON_NCP_UNUSED int wraparound, + CYTHON_NCP_UNUSED int boundscheck) { #if CYTHON_COMPILING_IN_CPYTHON if (wraparound & unlikely(i < 0)) i += PyTuple_GET_SIZE(o); if ((!boundscheck) || likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) { @@ -23902,8 +25687,9 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize return PySequence_GetItem(o, i); #endif } -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, - int is_list, int wraparound, int boundscheck) { +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list, + CYTHON_NCP_UNUSED int wraparound, + CYTHON_NCP_UNUSED int boundscheck) { #if CYTHON_COMPILING_IN_CPYTHON if (is_list || PyList_CheckExact(o)) { Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); @@ -23945,15 +25731,117 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); } +#if CYTHON_COMPILING_IN_CPYTHON +static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, CYTHON_UNUSED int inplace) { + #if PY_MAJOR_VERSION < 3 + if (likely(PyInt_CheckExact(op1))) { + const long b = intval; + long x; + long a = PyInt_AS_LONG(op1); + x = (long)((unsigned long)a + b); + if (likely((x^a) >= 0 || (x^b) >= 0)) + return PyInt_FromLong(x); + return PyLong_Type.tp_as_number->nb_add(op1, op2); + } + #endif + #if CYTHON_USE_PYLONG_INTERNALS && PY_MAJOR_VERSION >= 3 + if (likely(PyLong_CheckExact(op1))) { + const long b = intval; + long a, x; + const PY_LONG_LONG llb = intval; + PY_LONG_LONG lla, llx; + const digit* digits = ((PyLongObject*)op1)->ob_digit; + const Py_ssize_t size = Py_SIZE(op1); + if (likely(__Pyx_sst_abs(size) <= 1)) { + a = likely(size) ? digits[0] : 0; + if (size == -1) a = -a; + } else { + switch (size) { + case -2: + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0])); + break; + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { + lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | digits[0])); + goto long_long; + } + case 2: + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0])); + break; + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { + lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | digits[0])); + goto long_long; + } + case -3: + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + break; + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { + lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + goto long_long; + } + case 3: + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + break; + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { + lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + goto long_long; + } + case -4: + if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + break; + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { + lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + goto long_long; + } + case 4: + if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + break; + } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { + lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + goto long_long; + } + default: return PyLong_Type.tp_as_number->nb_add(op1, op2); + } + } + x = a + b; + return PyLong_FromLong(x); + long_long: + llx = lla + llb; + return PyLong_FromLongLong(llx); + } + #endif + if (PyFloat_CheckExact(op1)) { + const long b = intval; + double a = PyFloat_AS_DOUBLE(op1); + double result; + PyFPE_START_PROTECT("add", return NULL) + result = ((double)a) + (double)b; + PyFPE_END_PROTECT(result) + return PyFloat_FromDouble(result); + } + return (inplace ? PyNumber_InPlaceAdd : PyNumber_Add)(op1, op2); +} +#endif + static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); } static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno, CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename, - int full_traceback) { + int full_traceback, CYTHON_UNUSED int nogil) { PyObject *old_exc, *old_val, *old_tb; PyObject *ctx; +#ifdef WITH_THREAD + PyGILState_STATE state; + if (nogil) + state = PyGILState_Ensure(); +#endif __Pyx_ErrFetch(&old_exc, &old_val, &old_tb); if (full_traceback) { Py_XINCREF(old_exc); @@ -23974,6 +25862,10 @@ static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno, PyErr_WriteUnraisable(ctx); Py_DECREF(ctx); } +#ifdef WITH_THREAD + if (nogil) + PyGILState_Release(state); +#endif } static int __Pyx_SetVtable(PyObject *dict, void *vtable) { @@ -23999,7 +25891,7 @@ static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int co return count; } while (start < end) { - mid = (start + end) / 2; + mid = start + (end - start) / 2; if (code_line < entries[mid].code_line) { end = mid; } else if (code_line > entries[mid].code_line) { @@ -24123,132 +26015,59 @@ static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( Py_DECREF(py_funcname); return py_code; bad: - Py_XDECREF(py_srcfile); - Py_XDECREF(py_funcname); - return NULL; -} -static void __Pyx_AddTraceback(const char *funcname, int c_line, - int py_line, const char *filename) { - PyCodeObject *py_code = 0; - PyFrameObject *py_frame = 0; - py_code = __pyx_find_code_object(c_line ? c_line : py_line); - if (!py_code) { - py_code = __Pyx_CreateCodeObjectForTraceback( - funcname, c_line, py_line, filename); - if (!py_code) goto bad; - __pyx_insert_code_object(c_line ? c_line : py_line, py_code); - } - py_frame = PyFrame_New( - PyThreadState_GET(), /*PyThreadState *tstate,*/ - py_code, /*PyCodeObject *code,*/ - __pyx_d, /*PyObject *globals,*/ - 0 /*PyObject *locals*/ - ); - if (!py_frame) goto bad; - py_frame->f_lineno = py_line; - PyTraceBack_Here(py_frame); -bad: - Py_XDECREF(py_code); - Py_XDECREF(py_frame); -} - -#if PY_MAJOR_VERSION < 3 -static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { - if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); - if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags); - if (PyObject_TypeCheck(obj, __pyx_array_type)) return __pyx_array_getbuffer(obj, view, flags); - if (PyObject_TypeCheck(obj, __pyx_memoryview_type)) return __pyx_memoryview_getbuffer(obj, view, flags); - PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); - return -1; -} -static void __Pyx_ReleaseBuffer(Py_buffer *view) { - PyObject *obj = view->obj; - if (!obj) return; - if (PyObject_CheckBuffer(obj)) { - PyBuffer_Release(view); - return; - } - if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; } - Py_DECREF(obj); - view->obj = NULL; -} -#endif - - - static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { - PyObject *empty_list = 0; - PyObject *module = 0; - PyObject *global_dict = 0; - PyObject *empty_dict = 0; - PyObject *list; - #if PY_VERSION_HEX < 0x03030000 - PyObject *py_import; - py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); - if (!py_import) - goto bad; - #endif - if (from_list) - list = from_list; - else { - empty_list = PyList_New(0); - if (!empty_list) - goto bad; - list = empty_list; - } - global_dict = PyModule_GetDict(__pyx_m); - if (!global_dict) - goto bad; - empty_dict = PyDict_New(); - if (!empty_dict) - goto bad; - { - #if PY_MAJOR_VERSION >= 3 - if (level == -1) { - if (strchr(__Pyx_MODULE_NAME, '.')) { - #if PY_VERSION_HEX < 0x03030000 - PyObject *py_level = PyInt_FromLong(1); - if (!py_level) - goto bad; - module = PyObject_CallFunctionObjArgs(py_import, - name, global_dict, empty_dict, list, py_level, NULL); - Py_DECREF(py_level); - #else - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, 1); - #endif - if (!module) { - if (!PyErr_ExceptionMatches(PyExc_ImportError)) - goto bad; - PyErr_Clear(); - } - } - level = 0; - } - #endif - if (!module) { - #if PY_VERSION_HEX < 0x03030000 - PyObject *py_level = PyInt_FromLong(level); - if (!py_level) - goto bad; - module = PyObject_CallFunctionObjArgs(py_import, - name, global_dict, empty_dict, list, py_level, NULL); - Py_DECREF(py_level); - #else - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, level); - #endif - } + Py_XDECREF(py_srcfile); + Py_XDECREF(py_funcname); + return NULL; +} +static void __Pyx_AddTraceback(const char *funcname, int c_line, + int py_line, const char *filename) { + PyCodeObject *py_code = 0; + PyFrameObject *py_frame = 0; + py_code = __pyx_find_code_object(c_line ? c_line : py_line); + if (!py_code) { + py_code = __Pyx_CreateCodeObjectForTraceback( + funcname, c_line, py_line, filename); + if (!py_code) goto bad; + __pyx_insert_code_object(c_line ? c_line : py_line, py_code); } + py_frame = PyFrame_New( + PyThreadState_GET(), /*PyThreadState *tstate,*/ + py_code, /*PyCodeObject *code,*/ + __pyx_d, /*PyObject *globals,*/ + 0 /*PyObject *locals*/ + ); + if (!py_frame) goto bad; + py_frame->f_lineno = py_line; + PyTraceBack_Here(py_frame); bad: - #if PY_VERSION_HEX < 0x03030000 - Py_XDECREF(py_import); - #endif - Py_XDECREF(empty_list); - Py_XDECREF(empty_dict); - return module; + Py_XDECREF(py_code); + Py_XDECREF(py_frame); } -static int +#if PY_MAJOR_VERSION < 3 +static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { + if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags); + if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags); + if (PyObject_TypeCheck(obj, __pyx_array_type)) return __pyx_array_getbuffer(obj, view, flags); + if (PyObject_TypeCheck(obj, __pyx_memoryview_type)) return __pyx_memoryview_getbuffer(obj, view, flags); + PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name); + return -1; +} +static void __Pyx_ReleaseBuffer(Py_buffer *view) { + PyObject *obj = view->obj; + if (!obj) return; + if (PyObject_CheckBuffer(obj)) { + PyBuffer_Release(view); + return; + } + if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; } + Py_DECREF(obj); + view->obj = NULL; +} +#endif + + + static int __pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b) { int i; @@ -24491,7 +26310,7 @@ static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_f return result; } -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_long(PyObject *obj) { +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_nn___pyx_t_5numpy_int64_t(PyObject *obj) { __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; __Pyx_BufFmt_StackElem stack[1]; int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; @@ -24502,7 +26321,7 @@ static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_l } retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, PyBUF_RECORDS, 2, - &__Pyx_TypeInfo_long, stack, + &__Pyx_TypeInfo_nn___pyx_t_5numpy_int64_t, stack, &result, obj); if (unlikely(retcode == -1)) goto __pyx_fail; @@ -24513,29 +26332,29 @@ static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_l return result; } -#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value) \ - { \ - func_type value = func_value; \ - if (sizeof(target_type) < sizeof(func_type)) { \ - if (unlikely(value != (func_type) (target_type) value)) { \ - func_type zero = 0; \ - if (is_unsigned && unlikely(value < zero)) \ - goto raise_neg_overflow; \ - else \ - goto raise_overflow; \ - } \ - } \ - return (target_type) value; \ +#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ + __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) +#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ + __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) +#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ + {\ + func_type value = func_value;\ + if (sizeof(target_type) < sizeof(func_type)) {\ + if (unlikely(value != (func_type) (target_type) value)) {\ + func_type zero = 0;\ + if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ + return (target_type) -1;\ + if (is_unsigned && unlikely(value < zero))\ + goto raise_neg_overflow;\ + else\ + goto raise_overflow;\ + }\ + }\ + return (target_type) value;\ } -#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 - #if CYTHON_USE_PYLONG_INTERNALS - #include "longintrepr.h" - #endif -#endif - static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { - const int neg_one = (int) -1, const_zero = 0; + const int neg_one = (int) -1, const_zero = (int) 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { @@ -24552,36 +26371,125 @@ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { -#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 - #if CYTHON_USE_PYLONG_INTERNALS +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; switch (Py_SIZE(x)) { - case 0: return 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, ((PyLongObject*)x)->ob_digit[0]); + case 0: return (int) 0; + case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) + case 2: + if (8 * sizeof(int) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { + return (int) (((((int)digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case 3: + if (8 * sizeof(int) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { + return (int) (((((((int)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case 4: + if (8 * sizeof(int) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { + return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; } - #endif #endif +#if CYTHON_COMPILING_IN_CPYTHON if (unlikely(Py_SIZE(x) < 0)) { goto raise_neg_overflow; } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (int) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif if (sizeof(int) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, PyLong_AsUnsignedLong(x)) - } else if (sizeof(int) <= sizeof(unsigned long long)) { - __PYX_VERIFY_RETURN_INT(int, unsigned long long, PyLong_AsUnsignedLongLong(x)) + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) } } else { -#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 - #if CYTHON_USE_PYLONG_INTERNALS +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; switch (Py_SIZE(x)) { - case 0: return 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, +(((PyLongObject*)x)->ob_digit[0])); - case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]); + case 0: return (int) 0; + case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, -(sdigit) digits[0]) + case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) + case -2: + if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + return (int) -(((((int)digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case 2: + if (8 * sizeof(int) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + return (int) (((((int)digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case -3: + if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + return (int) -(((((((int)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case 3: + if (8 * sizeof(int) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + return (int) (((((((int)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case -4: + if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { + return (int) -(((((((((int)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case 4: + if (8 * sizeof(int) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { + return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; } - #endif #endif if (sizeof(int) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int, long, PyLong_AsLong(x)) - } else if (sizeof(int) <= sizeof(long long)) { - __PYX_VERIFY_RETURN_INT(int, long long, PyLong_AsLongLong(x)) + __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) + } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) } } { @@ -24630,7 +26538,7 @@ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { } static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { - const long neg_one = (long) -1, const_zero = 0; + const long neg_one = (long) -1, const_zero = (long) 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { @@ -24647,36 +26555,125 @@ static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { -#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 - #if CYTHON_USE_PYLONG_INTERNALS +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; switch (Py_SIZE(x)) { - case 0: return 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, ((PyLongObject*)x)->ob_digit[0]); + case 0: return (long) 0; + case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) + case 2: + if (8 * sizeof(long) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { + return (long) (((((long)digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case 3: + if (8 * sizeof(long) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { + return (long) (((((((long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case 4: + if (8 * sizeof(long) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { + return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; } - #endif #endif +#if CYTHON_COMPILING_IN_CPYTHON if (unlikely(Py_SIZE(x) < 0)) { goto raise_neg_overflow; } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (long) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif if (sizeof(long) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, PyLong_AsUnsignedLong(x)) - } else if (sizeof(long) <= sizeof(unsigned long long)) { - __PYX_VERIFY_RETURN_INT(long, unsigned long long, PyLong_AsUnsignedLongLong(x)) + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) } } else { -#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 - #if CYTHON_USE_PYLONG_INTERNALS +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; switch (Py_SIZE(x)) { - case 0: return 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, +(((PyLongObject*)x)->ob_digit[0])); - case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]); + case 0: return (long) 0; + case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, -(sdigit) digits[0]) + case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) + case -2: + if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + return (long) -(((((long)digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case 2: + if (8 * sizeof(long) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + return (long) (((((long)digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case -3: + if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + return (long) -(((((((long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case 3: + if (8 * sizeof(long) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + return (long) (((((((long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case -4: + if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + return (long) -(((((((((long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case 4: + if (8 * sizeof(long) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { + return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; } - #endif #endif if (sizeof(long) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT(long, long, PyLong_AsLong(x)) - } else if (sizeof(long) <= sizeof(long long)) { - __PYX_VERIFY_RETURN_INT(long, long long, PyLong_AsLongLong(x)) + __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) + } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) } } { @@ -24724,7 +26721,7 @@ static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { return (long) -1; } -static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_long(PyObject *obj) { +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_nn___pyx_t_5numpy_int64_t(PyObject *obj) { __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } }; __Pyx_BufFmt_StackElem stack[1]; int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) }; @@ -24735,7 +26732,7 @@ static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_lon } retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0, PyBUF_RECORDS, 1, - &__Pyx_TypeInfo_long, stack, + &__Pyx_TypeInfo_nn___pyx_t_5numpy_int64_t, stack, &result, obj); if (unlikely(retcode == -1)) goto __pyx_fail; @@ -24763,7 +26760,7 @@ static CYTHON_INLINE long __Pyx_pow_long(long b, long e) { #endif t = 1; while (likely(e)) { - t *= (b * (e&1)) | ((~e)&1); /* 1 or b */ + t *= (b * (e&1)) | ((~e)&1); b *= b; e >>= 1; } @@ -24771,21 +26768,21 @@ static CYTHON_INLINE long __Pyx_pow_long(long b, long e) { } static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { - const int neg_one = (int) -1, const_zero = 0; + const int neg_one = (int) -1, const_zero = (int) 0; const int is_unsigned = neg_one > const_zero; if (is_unsigned) { if (sizeof(int) < sizeof(long)) { return PyInt_FromLong((long) value); } else if (sizeof(int) <= sizeof(unsigned long)) { return PyLong_FromUnsignedLong((unsigned long) value); - } else if (sizeof(int) <= sizeof(unsigned long long)) { - return PyLong_FromUnsignedLongLong((unsigned long long) value); + } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); } } else { if (sizeof(int) <= sizeof(long)) { return PyInt_FromLong((long) value); - } else if (sizeof(int) <= sizeof(long long)) { - return PyLong_FromLongLong((long long) value); + } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); } } { @@ -24797,21 +26794,21 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { } static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { - const long neg_one = (long) -1, const_zero = 0; + const long neg_one = (long) -1, const_zero = (long) 0; const int is_unsigned = neg_one > const_zero; if (is_unsigned) { if (sizeof(long) < sizeof(long)) { return PyInt_FromLong((long) value); } else if (sizeof(long) <= sizeof(unsigned long)) { return PyLong_FromUnsignedLong((unsigned long) value); - } else if (sizeof(long) <= sizeof(unsigned long long)) { - return PyLong_FromUnsignedLongLong((unsigned long long) value); + } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); } } else { if (sizeof(long) <= sizeof(long)) { return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(long long)) { - return PyLong_FromLongLong((long long) value); + } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); } } { @@ -24823,21 +26820,21 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { } static CYTHON_INLINE PyObject* __Pyx_PyInt_From_clock_t(clock_t value) { - const clock_t neg_one = (clock_t) -1, const_zero = 0; + const clock_t neg_one = (clock_t) -1, const_zero = (clock_t) 0; const int is_unsigned = neg_one > const_zero; if (is_unsigned) { if (sizeof(clock_t) < sizeof(long)) { return PyInt_FromLong((long) value); } else if (sizeof(clock_t) <= sizeof(unsigned long)) { return PyLong_FromUnsignedLong((unsigned long) value); - } else if (sizeof(clock_t) <= sizeof(unsigned long long)) { - return PyLong_FromUnsignedLongLong((unsigned long long) value); + } else if (sizeof(clock_t) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); } } else { if (sizeof(clock_t) <= sizeof(long)) { return PyInt_FromLong((long) value); - } else if (sizeof(clock_t) <= sizeof(long long)) { - return PyLong_FromLongLong((long long) value); + } else if (sizeof(clock_t) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); } } { @@ -24848,6 +26845,32 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_clock_t(clock_t value) { } } +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_npy_int64(npy_int64 value) { + const npy_int64 neg_one = (npy_int64) -1, const_zero = (npy_int64) 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(npy_int64) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(npy_int64) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(npy_int64) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); + } + } else { + if (sizeof(npy_int64) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(npy_int64) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(npy_int64), + little, !is_unsigned); + } +} + static PyObject *__pyx_memview_get_float(const char *itemp) { return (PyObject *) PyFloat_FromDouble(*(float *) itemp); } @@ -24859,14 +26882,198 @@ static int __pyx_memview_set_float(const char *itemp, PyObject *obj) { return 1; } -static PyObject *__pyx_memview_get_long(const char *itemp) { - return (PyObject *) __Pyx_PyInt_From_long(*(long *) itemp); +static CYTHON_INLINE npy_int64 __Pyx_PyInt_As_npy_int64(PyObject *x) { + const npy_int64 neg_one = (npy_int64) -1, const_zero = (npy_int64) 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(npy_int64) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(npy_int64, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (npy_int64) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (npy_int64) 0; + case 1: __PYX_VERIFY_RETURN_INT(npy_int64, digit, digits[0]) + case 2: + if (8 * sizeof(npy_int64) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_int64, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(npy_int64) >= 2 * PyLong_SHIFT) { + return (npy_int64) (((((npy_int64)digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case 3: + if (8 * sizeof(npy_int64) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_int64, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(npy_int64) >= 3 * PyLong_SHIFT) { + return (npy_int64) (((((((npy_int64)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case 4: + if (8 * sizeof(npy_int64) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_int64, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(npy_int64) >= 4 * PyLong_SHIFT) { + return (npy_int64) (((((((((npy_int64)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + } +#endif +#if CYTHON_COMPILING_IN_CPYTHON + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (npy_int64) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif + if (sizeof(npy_int64) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT_EXC(npy_int64, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(npy_int64) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(npy_int64, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) + } + } else { +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; + switch (Py_SIZE(x)) { + case 0: return (npy_int64) 0; + case -1: __PYX_VERIFY_RETURN_INT(npy_int64, sdigit, -(sdigit) digits[0]) + case 1: __PYX_VERIFY_RETURN_INT(npy_int64, digit, +digits[0]) + case -2: + if (8 * sizeof(npy_int64) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_int64, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(npy_int64) - 1 > 2 * PyLong_SHIFT) { + return (npy_int64) -(((((npy_int64)digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case 2: + if (8 * sizeof(npy_int64) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_int64, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(npy_int64) - 1 > 2 * PyLong_SHIFT) { + return (npy_int64) (((((npy_int64)digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case -3: + if (8 * sizeof(npy_int64) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_int64, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(npy_int64) - 1 > 3 * PyLong_SHIFT) { + return (npy_int64) -(((((((npy_int64)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case 3: + if (8 * sizeof(npy_int64) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_int64, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(npy_int64) - 1 > 3 * PyLong_SHIFT) { + return (npy_int64) (((((((npy_int64)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case -4: + if (8 * sizeof(npy_int64) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_int64, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(npy_int64) - 1 > 4 * PyLong_SHIFT) { + return (npy_int64) -(((((((((npy_int64)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case 4: + if (8 * sizeof(npy_int64) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(npy_int64, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(npy_int64) - 1 > 4 * PyLong_SHIFT) { + return (npy_int64) (((((((((npy_int64)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + } +#endif + if (sizeof(npy_int64) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT_EXC(npy_int64, long, PyLong_AsLong(x)) + } else if (sizeof(npy_int64) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(npy_int64, PY_LONG_LONG, PyLong_AsLongLong(x)) + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + npy_int64 val; + PyObject *v = __Pyx_PyNumber_Int(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (npy_int64) -1; + } + } else { + npy_int64 val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (npy_int64) -1; + val = __Pyx_PyInt_As_npy_int64(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to npy_int64"); + return (npy_int64) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to npy_int64"); + return (npy_int64) -1; +} + +static PyObject *__pyx_memview_get_nn___pyx_t_5numpy_int64_t(const char *itemp) { + return (PyObject *) __Pyx_PyInt_From_npy_int64(*(__pyx_t_5numpy_int64_t *) itemp); } -static int __pyx_memview_set_long(const char *itemp, PyObject *obj) { - long value = __Pyx_PyInt_As_long(obj); - if ((value == (long)-1) && PyErr_Occurred()) +static int __pyx_memview_set_nn___pyx_t_5numpy_int64_t(const char *itemp, PyObject *obj) { + __pyx_t_5numpy_int64_t value = __Pyx_PyInt_As_npy_int64(obj); + if ((value == (npy_int64)-1) && PyErr_Occurred()) return 0; - *(long *) itemp = value; + *(__pyx_t_5numpy_int64_t *) itemp = value; return 1; } @@ -25110,6 +27317,32 @@ static int __pyx_memview_set_long(const char *itemp, PyObject *obj) { #endif #endif +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value) { + const enum NPY_TYPES neg_one = (enum NPY_TYPES) -1, const_zero = (enum NPY_TYPES) 0; + const int is_unsigned = neg_one > const_zero; + if (is_unsigned) { + if (sizeof(enum NPY_TYPES) < sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned long)) { + return PyLong_FromUnsignedLong((unsigned long) value); + } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); + } + } else { + if (sizeof(enum NPY_TYPES) <= sizeof(long)) { + return PyInt_FromLong((long) value); + } else if (sizeof(enum NPY_TYPES) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); + } + } + { + int one = 1; int little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&value; + return _PyLong_FromByteArray(bytes, sizeof(enum NPY_TYPES), + little, !is_unsigned); + } +} + static int __pyx_memviewslice_is_contig(const __Pyx_memviewslice *mvs, char order, int ndim) @@ -25246,7 +27479,7 @@ __pyx_capsule_create(void *p, CYTHON_UNUSED const char *sig) } static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { - const char neg_one = (char) -1, const_zero = 0; + const char neg_one = (char) -1, const_zero = (char) 0; const int is_unsigned = neg_one > const_zero; #if PY_MAJOR_VERSION < 3 if (likely(PyInt_Check(x))) { @@ -25263,36 +27496,125 @@ static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) { #endif if (likely(PyLong_Check(x))) { if (is_unsigned) { -#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 - #if CYTHON_USE_PYLONG_INTERNALS +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; switch (Py_SIZE(x)) { - case 0: return 0; - case 1: __PYX_VERIFY_RETURN_INT(char, digit, ((PyLongObject*)x)->ob_digit[0]); + case 0: return (char) 0; + case 1: __PYX_VERIFY_RETURN_INT(char, digit, digits[0]) + case 2: + if (8 * sizeof(char) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(char) >= 2 * PyLong_SHIFT) { + return (char) (((((char)digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case 3: + if (8 * sizeof(char) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(char) >= 3 * PyLong_SHIFT) { + return (char) (((((((char)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case 4: + if (8 * sizeof(char) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(char) >= 4 * PyLong_SHIFT) { + return (char) (((((((((char)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; } - #endif #endif +#if CYTHON_COMPILING_IN_CPYTHON if (unlikely(Py_SIZE(x) < 0)) { goto raise_neg_overflow; } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (char) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif if (sizeof(char) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT(char, unsigned long, PyLong_AsUnsignedLong(x)) - } else if (sizeof(char) <= sizeof(unsigned long long)) { - __PYX_VERIFY_RETURN_INT(char, unsigned long long, PyLong_AsUnsignedLongLong(x)) + __PYX_VERIFY_RETURN_INT_EXC(char, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(char) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(char, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) } } else { -#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 - #if CYTHON_USE_PYLONG_INTERNALS +#if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)x)->ob_digit; switch (Py_SIZE(x)) { - case 0: return 0; - case 1: __PYX_VERIFY_RETURN_INT(char, digit, +(((PyLongObject*)x)->ob_digit[0])); - case -1: __PYX_VERIFY_RETURN_INT(char, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]); + case 0: return (char) 0; + case -1: __PYX_VERIFY_RETURN_INT(char, sdigit, -(sdigit) digits[0]) + case 1: __PYX_VERIFY_RETURN_INT(char, digit, +digits[0]) + case -2: + if (8 * sizeof(char) - 1 > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { + return (char) -(((((char)digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case 2: + if (8 * sizeof(char) > 1 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { + return (char) (((((char)digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case -3: + if (8 * sizeof(char) - 1 > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { + return (char) -(((((((char)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case 3: + if (8 * sizeof(char) > 2 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { + return (char) (((((((char)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case -4: + if (8 * sizeof(char) - 1 > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { + return (char) -(((((((((char)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; + case 4: + if (8 * sizeof(char) > 3 * PyLong_SHIFT) { + if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { + __PYX_VERIFY_RETURN_INT(char, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0]))) + } else if (8 * sizeof(char) - 1 > 4 * PyLong_SHIFT) { + return (char) (((((((((char)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + } + break; } - #endif #endif if (sizeof(char) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT(char, long, PyLong_AsLong(x)) - } else if (sizeof(char) <= sizeof(long long)) { - __PYX_VERIFY_RETURN_INT(char, long long, PyLong_AsLongLong(x)) + __PYX_VERIFY_RETURN_INT_EXC(char, long, PyLong_AsLong(x)) + } else if (sizeof(char) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT_EXC(char, PY_LONG_LONG, PyLong_AsLongLong(x)) } } { @@ -25496,7 +27818,7 @@ static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) { return __Pyx_PyObject_AsStringAndSize(o, &ignore); } static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { -#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT +#if CYTHON_COMPILING_IN_CPYTHON && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT) if ( #if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII __Pyx_sys_getdefaultencoding_not_ascii && @@ -25537,7 +27859,7 @@ static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_ #endif } else #endif -#if !CYTHON_COMPILING_IN_PYPY +#if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE)) if (PyByteArray_Check(o)) { *length = PyByteArray_GET_SIZE(o); return PyByteArray_AS_STRING(o); @@ -25567,7 +27889,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) { #else if (PyLong_Check(x)) #endif - return Py_INCREF(x), x; + return __Pyx_NewRef(x); m = Py_TYPE(x)->tp_as_number; #if PY_MAJOR_VERSION < 3 if (m && m->nb_int) { @@ -25607,18 +27929,55 @@ static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { Py_ssize_t ival; PyObject *x; #if PY_MAJOR_VERSION < 3 - if (likely(PyInt_CheckExact(b))) - return PyInt_AS_LONG(b); + if (likely(PyInt_CheckExact(b))) { + if (sizeof(Py_ssize_t) >= sizeof(long)) + return PyInt_AS_LONG(b); + else + return PyInt_AsSsize_t(x); + } #endif if (likely(PyLong_CheckExact(b))) { - #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 - #if CYTHON_USE_PYLONG_INTERNALS - switch (Py_SIZE(b)) { - case -1: return -(sdigit)((PyLongObject*)b)->ob_digit[0]; - case 0: return 0; - case 1: return ((PyLongObject*)b)->ob_digit[0]; - } - #endif + #if CYTHON_USE_PYLONG_INTERNALS + const digit* digits = ((PyLongObject*)b)->ob_digit; + const Py_ssize_t size = Py_SIZE(b); + if (likely(__Pyx_sst_abs(size) <= 1)) { + ival = likely(size) ? digits[0] : 0; + if (size == -1) ival = -ival; + return ival; + } else { + switch (size) { + case 2: + if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { + return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | digits[0])); + } + break; + case -2: + if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { + return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | digits[0])); + } + break; + case 3: + if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { + return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + break; + case -3: + if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { + return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + break; + case 4: + if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { + return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + break; + case -4: + if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { + return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | digits[2]) << PyLong_SHIFT) | digits[1]) << PyLong_SHIFT) | digits[0])); + } + break; + } + } #endif return PyLong_AsSsize_t(b); } diff --git a/sklearn/manifold/_barnes_hut_tsne.pyx b/sklearn/manifold/_barnes_hut_tsne.pyx index a5579b55e1256..5aea39d90c48f 100644 --- a/sklearn/manifold/_barnes_hut_tsne.pyx +++ b/sklearn/manifold/_barnes_hut_tsne.pyx @@ -14,6 +14,8 @@ from libc.math cimport sqrt, log cimport numpy as np import numpy as np +cdef char* EMPTY_STRING = "" + cdef extern from "math.h": float fabsf(float x) nogil @@ -352,7 +354,7 @@ cdef int insert_many(Tree* tree, float[:,:] pos_array) nogil: printf("[t-SNE] inserting point %i: [%f, %f]\n", i, row[0], row[1]) err = insert(tree.root_node, row, i, 0, 1) if err != 0: - printf("[t-SNE] ERROR\n") + printf("[t-SNE] ERROR\n%s", EMPTY_STRING) return err tree.n_points += 1 return err @@ -419,7 +421,7 @@ cdef long count_points(Node* root, long count) nogil: count += child.size elif not child.is_leaf: if DEBUGFLAG: - printf("[t-SNE] Child is not a leaf. Descending\n") + printf("[t-SNE] Child is not a leaf. Descending\n%s", EMPTY_STRING) count = count_points(child, count) # else case is we have an empty leaf node # which happens when we create a quadtree for @@ -432,7 +434,7 @@ cdef long count_points(Node* root, long count) nogil: cdef float compute_gradient(float[:,:] val_P, float[:,:] pos_reference, - long[:,:] neighbors, + np.int64_t[:,:] neighbors, float[:,:] tot_force, Node* root_node, float theta, @@ -482,12 +484,12 @@ cdef float compute_gradient(float[:,:] val_P, cdef float compute_gradient_positive(float[:,:] val_P, float[:,:] pos_reference, - long[:,:] neighbors, + np.int64_t[:,:] neighbors, float* pos_f, int n_dimensions, float dof, float sum_Q, - long start, + np.int64_t start, int verbose) nogil: # Sum over the following expression for i not equal to j # grad_i = p_ij (1 + ||y_i - y_j||^2)^-1 (y_i - y_j) @@ -672,7 +674,7 @@ cdef void compute_non_edge_forces(Node* node, cdef float compute_error(float[:, :] val_P, float[:, :] pos_reference, - long[:,:] neighbors, + np.int64_t[:,:] neighbors, float sum_Q, int n_dimensions, int verbose) nogil: @@ -716,7 +718,7 @@ def calculate_edge(pos_output): def gradient(float[:,:] pij_input, float[:,:] pos_output, - long[:,:] neighbors, + np.int64_t[:,:] neighbors, float[:,:] forces, float theta, int n_dimensions, @@ -751,13 +753,19 @@ def gradient(float[:,:] pij_input, err = insert_many(qt, pos_output) assert err == 0, "[t-SNE] Insertion failed" if verbose > 10: - printf("[t-SNE] Computing gradient\n") + # XXX: format hack to workaround lack of `const char *` type + # in the generated C code that triggers error with gcc 4.9 + # and -Werror=format-security + printf("[t-SNE] Computing gradient\n%s", EMPTY_STRING) sum_Q = compute_gradient(pij_input, pos_output, neighbors, forces, qt.root_node, theta, dof, skip_num_points, -1) C = compute_error(pij_input, pos_output, neighbors, sum_Q, n_dimensions, verbose) if verbose > 10: - printf("[t-SNE] Checking tree consistency \n") + # XXX: format hack to workaround lack of `const char *` type + # in the generated C code + # and -Werror=format-security + printf("[t-SNE] Checking tree consistency\n%s", EMPTY_STRING) cdef long count = count_points(qt.root_node, 0) m = ("Tree consistency failed: unexpected number of points=%i " "at root node=%i" % (count, qt.root_node.cumulative_size)) @@ -769,7 +777,7 @@ def gradient(float[:,:] pij_input, # Helper functions -def check_quadtree(X, long[:] counts): +def check_quadtree(X, np.int64_t[:] counts): """ Helper function to access quadtree functions for testing """ diff --git a/sklearn/manifold/_utils.c b/sklearn/manifold/_utils.c index 120edb6c37f32..f8279c85b55ab 100644 --- a/sklearn/manifold/_utils.c +++ b/sklearn/manifold/_utils.c @@ -1,4 +1,4 @@ -/* Generated by Cython 0.21.1 */ +/* Generated by Cython 0.22.1 */ #define PY_SSIZE_T_CLEAN #ifndef CYTHON_USE_PYLONG_INTERNALS @@ -19,7 +19,7 @@ #elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000) #error Cython requires Python 2.6+ or Python 3.2+. #else -#define CYTHON_ABI "0_21_1" +#define CYTHON_ABI "0_22_1" #include #ifndef offsetof #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) @@ -54,7 +54,7 @@ #define CYTHON_COMPILING_IN_PYPY 0 #define CYTHON_COMPILING_IN_CPYTHON 1 #endif -#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 +#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag) #define Py_OptimizeFlag 0 #endif #define __PYX_BUILD_PY_SSIZE_T "n" @@ -70,12 +70,16 @@ PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #define __Pyx_DefaultClassType PyType_Type #endif -#if PY_MAJOR_VERSION >= 3 +#ifndef Py_TPFLAGS_CHECKTYPES #define Py_TPFLAGS_CHECKTYPES 0 +#endif +#ifndef Py_TPFLAGS_HAVE_INDEX #define Py_TPFLAGS_HAVE_INDEX 0 +#endif +#ifndef Py_TPFLAGS_HAVE_NEWBUFFER #define Py_TPFLAGS_HAVE_NEWBUFFER 0 #endif -#if PY_VERSION_HEX < 0x030400a1 && !defined(Py_TPFLAGS_HAVE_FINALIZE) +#ifndef Py_TPFLAGS_HAVE_FINALIZE #define Py_TPFLAGS_HAVE_FINALIZE 0 #endif #if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) @@ -106,6 +110,9 @@ PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) #define __Pyx_PyFrozenSet_Size(s) PySet_Size(s) #endif +#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains) + #define PyUnicode_Contains(u, s) PySequence_Contains(u, s) +#endif #define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b)) #define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b)) #if PY_MAJOR_VERSION >= 3 @@ -203,11 +210,22 @@ static CYTHON_INLINE float __PYX_NAN() { return value; } #endif +#define __Pyx_void_to_None(void_result) (void_result, Py_INCREF(Py_None), Py_None) #ifdef __cplusplus template void __Pyx_call_destructor(T* x) { x->~T(); } +template +class __Pyx_FakeReference { + public: + __Pyx_FakeReference() : ptr(NULL) { } + __Pyx_FakeReference(T& ref) : ptr(&ref) { } + T *operator->() { return ptr; } + operator T&() { return *ptr; } + private: + T *ptr; +}; #endif @@ -261,6 +279,13 @@ void __Pyx_call_destructor(T* x) { # define CYTHON_UNUSED # endif #endif +#ifndef CYTHON_NCP_UNUSED +# if CYTHON_COMPILING_IN_CPYTHON +# define CYTHON_NCP_UNUSED +# else +# define CYTHON_NCP_UNUSED CYTHON_UNUSED +# endif +#endif typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding; const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; @@ -295,11 +320,11 @@ static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*); #endif #define __Pyx_PyObject_AsSString(s) ((signed char*) __Pyx_PyObject_AsString(s)) #define __Pyx_PyObject_AsUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_FromUString(s) __Pyx_PyObject_FromString((const char*)s) -#define __Pyx_PyBytes_FromUString(s) __Pyx_PyBytes_FromString((const char*)s) -#define __Pyx_PyByteArray_FromUString(s) __Pyx_PyByteArray_FromString((const char*)s) -#define __Pyx_PyStr_FromUString(s) __Pyx_PyStr_FromString((const char*)s) -#define __Pyx_PyUnicode_FromUString(s) __Pyx_PyUnicode_FromString((const char*)s) +#define __Pyx_PyObject_FromCString(s) __Pyx_PyObject_FromString((const char*)s) +#define __Pyx_PyBytes_FromCString(s) __Pyx_PyBytes_FromString((const char*)s) +#define __Pyx_PyByteArray_FromCString(s) __Pyx_PyByteArray_FromString((const char*)s) +#define __Pyx_PyStr_FromCString(s) __Pyx_PyStr_FromString((const char*)s) +#define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s) #if PY_MAJOR_VERSION < 3 static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) { @@ -335,7 +360,7 @@ static int __Pyx_init_sys_getdefaultencoding_params(void) { const char* default_encoding_c; sys = PyImport_ImportModule("sys"); if (!sys) goto bad; - default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); + default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL); Py_DECREF(sys); if (!default_encoding) goto bad; default_encoding_c = PyBytes_AsString(default_encoding); @@ -483,7 +508,7 @@ typedef struct { } __Pyx_BufFmt_Context; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":723 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":726 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< @@ -492,7 +517,7 @@ typedef struct { */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":724 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":727 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< @@ -501,7 +526,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":725 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":728 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< @@ -510,7 +535,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t; */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":726 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":729 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< @@ -519,7 +544,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t; */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":730 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":733 * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< @@ -528,7 +553,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t; */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":731 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":734 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< @@ -537,7 +562,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":732 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":735 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< @@ -546,7 +571,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t; */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":733 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":736 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< @@ -555,7 +580,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t; */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":737 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":740 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< @@ -564,7 +589,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t; */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":738 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":741 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< @@ -573,7 +598,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":747 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":750 * # The int types are mapped a bit surprising -- * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t # <<<<<<<<<<<<<< @@ -582,7 +607,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t; */ typedef npy_long __pyx_t_5numpy_int_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":748 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":751 * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< @@ -591,7 +616,7 @@ typedef npy_long __pyx_t_5numpy_int_t; */ typedef npy_longlong __pyx_t_5numpy_long_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":749 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":752 * ctypedef npy_long int_t * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< @@ -600,7 +625,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t; */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":751 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":754 * ctypedef npy_longlong longlong_t * * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< @@ -609,7 +634,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t; */ typedef npy_ulong __pyx_t_5numpy_uint_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":752 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":755 * * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< @@ -618,7 +643,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":753 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":756 * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< @@ -627,7 +652,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":755 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":758 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< @@ -636,7 +661,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":756 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":759 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< @@ -645,7 +670,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t; */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":758 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":761 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< @@ -654,7 +679,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t; */ typedef npy_double __pyx_t_5numpy_float_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":759 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":762 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< @@ -663,7 +688,7 @@ typedef npy_double __pyx_t_5numpy_float_t; */ typedef npy_double __pyx_t_5numpy_double_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":760 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":763 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< @@ -694,7 +719,7 @@ typedef npy_longdouble __pyx_t_5numpy_longdouble_t; /*--- Type declarations ---*/ -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":762 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":765 * ctypedef npy_longdouble longdouble_t * * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< @@ -703,7 +728,7 @@ typedef npy_longdouble __pyx_t_5numpy_longdouble_t; */ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":763 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":766 * * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< @@ -712,7 +737,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; */ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":764 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":767 * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< @@ -721,7 +746,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; */ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":766 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":769 * ctypedef npy_clongdouble clongdouble_t * * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< @@ -729,6 +754,8 @@ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; * cdef inline object PyArray_MultiIterNew1(a): */ typedef npy_cdouble __pyx_t_5numpy_complex_t; + +/* --- Runtime support code (head) --- */ #ifndef CYTHON_REFNANNY #define CYTHON_REFNANNY 0 #endif @@ -852,6 +879,26 @@ static CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, in static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); +#if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY +static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { + PyObject *value; + value = PyDict_GetItemWithError(d, key); + if (unlikely(!value)) { + if (!PyErr_Occurred()) { + PyObject* args = PyTuple_Pack(1, key); + if (likely(args)) + PyErr_SetObject(PyExc_KeyError, args); + Py_XDECREF(args); + } + return NULL; + } + Py_INCREF(value); + return value; +} +#else + #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key) +#endif + static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); @@ -1306,16 +1353,16 @@ static PyArrayObject *__pyx_f_7sklearn_8manifold_6_utils__binary_search_perplexi __Pyx_GOTREF(__pyx_t_3); __pyx_t_4 = PyTuple_New(2); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 51; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); - PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_1); - PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_3); + PyTuple_SET_ITEM(__pyx_t_4, 0, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_3); + PyTuple_SET_ITEM(__pyx_t_4, 1, __pyx_t_3); __pyx_t_1 = 0; __pyx_t_3 = 0; __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 51; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_4); __Pyx_GIVEREF(__pyx_t_4); + PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_4); __pyx_t_4 = 0; __pyx_t_4 = PyDict_New(); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 51; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); @@ -1992,10 +2039,10 @@ static PyArrayObject *__pyx_f_7sklearn_8manifold_6_utils__binary_search_perplexi __Pyx_GOTREF(__pyx_t_4); __pyx_t_3 = PyTuple_New(2); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 133; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); - PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_5); - PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_4); + PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_5); __Pyx_GIVEREF(__pyx_t_4); + PyTuple_SET_ITEM(__pyx_t_3, 1, __pyx_t_4); __pyx_t_5 = 0; __pyx_t_4 = 0; __pyx_t_4 = __Pyx_PyString_Format(__pyx_kp_s_t_SNE_Computed_conditional_prob, __pyx_t_3); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 133; __pyx_clineno = __LINE__; goto __pyx_L1_error;} @@ -2058,9 +2105,9 @@ static PyArrayObject *__pyx_f_7sklearn_8manifold_6_utils__binary_search_perplexi } else { __pyx_t_1 = PyTuple_New(1+1); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 137; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_2); __Pyx_GIVEREF(__pyx_t_2); __pyx_t_2 = NULL; - PyTuple_SET_ITEM(__pyx_t_1, 0+1, __pyx_t_3); + __Pyx_GIVEREF(__pyx_t_2); PyTuple_SET_ITEM(__pyx_t_1, 0, __pyx_t_2); __pyx_t_2 = NULL; __Pyx_GIVEREF(__pyx_t_3); + PyTuple_SET_ITEM(__pyx_t_1, 0+1, __pyx_t_3); __pyx_t_3 = 0; __pyx_t_4 = __Pyx_PyObject_Call(__pyx_t_5, __pyx_t_1, NULL); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 137; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_4); @@ -2264,7 +2311,7 @@ static PyObject *__pyx_pf_7sklearn_8manifold_6_utils__binary_search_perplexity(C return __pyx_r; } -/* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":194 +/* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":197 * # experimental exception made for __getbuffer__ and __releasebuffer__ * # -- the details of this may change. * def __getbuffer__(ndarray self, Py_buffer* info, int flags): # <<<<<<<<<<<<<< @@ -2314,7 +2361,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_GIVEREF(__pyx_v_info->obj); } - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":200 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":203 * # of flags * * if info == NULL: return # <<<<<<<<<<<<<< @@ -2327,7 +2374,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L0; } - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":203 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":206 * * cdef int copy_shape, i, ndim * cdef int endian_detector = 1 # <<<<<<<<<<<<<< @@ -2336,7 +2383,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_endian_detector = 1; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":204 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":207 * cdef int copy_shape, i, ndim * cdef int endian_detector = 1 * cdef bint little_endian = ((&endian_detector)[0] != 0) # <<<<<<<<<<<<<< @@ -2345,7 +2392,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_little_endian = ((((char *)(&__pyx_v_endian_detector))[0]) != 0); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":206 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":209 * cdef bint little_endian = ((&endian_detector)[0] != 0) * * ndim = PyArray_NDIM(self) # <<<<<<<<<<<<<< @@ -2354,7 +2401,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_ndim = PyArray_NDIM(__pyx_v_self); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":208 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":211 * ndim = PyArray_NDIM(self) * * if sizeof(npy_intp) != sizeof(Py_ssize_t): # <<<<<<<<<<<<<< @@ -2364,7 +2411,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = (((sizeof(npy_intp)) != (sizeof(Py_ssize_t))) != 0); if (__pyx_t_1) { - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":209 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":212 * * if sizeof(npy_intp) != sizeof(Py_ssize_t): * copy_shape = 1 # <<<<<<<<<<<<<< @@ -2376,7 +2423,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } /*else*/ { - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":211 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":214 * copy_shape = 1 * else: * copy_shape = 0 # <<<<<<<<<<<<<< @@ -2387,7 +2434,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L4:; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":213 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":216 * copy_shape = 0 * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -2401,7 +2448,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L6_bool_binop_done; } - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":214 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":217 * * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): # <<<<<<<<<<<<<< @@ -2413,21 +2460,21 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_L6_bool_binop_done:; if (__pyx_t_1) { - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":215 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":218 * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): * raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<< * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) */ - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple_, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple_, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":217 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":220 * raise ValueError(u"ndarray is not C contiguous") * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) # <<<<<<<<<<<<<< @@ -2441,7 +2488,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P goto __pyx_L9_bool_binop_done; } - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":218 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":221 * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): # <<<<<<<<<<<<<< @@ -2453,21 +2500,21 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_L9_bool_binop_done:; if (__pyx_t_1) { - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":219 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":222 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< * * info.buf = PyArray_DATA(self) */ - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__2, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - {__pyx_filename = __pyx_f[1]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":221 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":224 * raise ValueError(u"ndarray is not Fortran contiguous") * * info.buf = PyArray_DATA(self) # <<<<<<<<<<<<<< @@ -2476,7 +2523,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->buf = PyArray_DATA(__pyx_v_self); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":222 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":225 * * info.buf = PyArray_DATA(self) * info.ndim = ndim # <<<<<<<<<<<<<< @@ -2485,7 +2532,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->ndim = __pyx_v_ndim; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":223 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":226 * info.buf = PyArray_DATA(self) * info.ndim = ndim * if copy_shape: # <<<<<<<<<<<<<< @@ -2495,7 +2542,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = (__pyx_v_copy_shape != 0); if (__pyx_t_1) { - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":226 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":229 * # Allocate new buffer for strides and shape info. * # This is allocated as one block, strides first. * info.strides = stdlib.malloc(sizeof(Py_ssize_t) * ndim * 2) # <<<<<<<<<<<<<< @@ -2504,7 +2551,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->strides = ((Py_ssize_t *)malloc((((sizeof(Py_ssize_t)) * ((size_t)__pyx_v_ndim)) * 2))); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":227 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":230 * # This is allocated as one block, strides first. * info.strides = stdlib.malloc(sizeof(Py_ssize_t) * ndim * 2) * info.shape = info.strides + ndim # <<<<<<<<<<<<<< @@ -2513,7 +2560,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->shape = (__pyx_v_info->strides + __pyx_v_ndim); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":228 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":231 * info.strides = stdlib.malloc(sizeof(Py_ssize_t) * ndim * 2) * info.shape = info.strides + ndim * for i in range(ndim): # <<<<<<<<<<<<<< @@ -2524,7 +2571,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { __pyx_v_i = __pyx_t_5; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":229 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":232 * info.shape = info.strides + ndim * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] # <<<<<<<<<<<<<< @@ -2533,7 +2580,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->strides[__pyx_v_i]) = (PyArray_STRIDES(__pyx_v_self)[__pyx_v_i]); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":230 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":233 * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] * info.shape[i] = PyArray_DIMS(self)[i] # <<<<<<<<<<<<<< @@ -2546,7 +2593,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } /*else*/ { - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":232 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":235 * info.shape[i] = PyArray_DIMS(self)[i] * else: * info.strides = PyArray_STRIDES(self) # <<<<<<<<<<<<<< @@ -2555,7 +2602,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->strides = ((Py_ssize_t *)PyArray_STRIDES(__pyx_v_self)); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":233 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":236 * else: * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) # <<<<<<<<<<<<<< @@ -2566,7 +2613,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L11:; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":234 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":237 * info.strides = PyArray_STRIDES(self) * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL # <<<<<<<<<<<<<< @@ -2575,7 +2622,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->suboffsets = NULL; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":235 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":238 * info.shape = PyArray_DIMS(self) * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) # <<<<<<<<<<<<<< @@ -2584,7 +2631,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->itemsize = PyArray_ITEMSIZE(__pyx_v_self); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":236 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":239 * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) * info.readonly = not PyArray_ISWRITEABLE(self) # <<<<<<<<<<<<<< @@ -2593,7 +2640,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->readonly = (!(PyArray_ISWRITEABLE(__pyx_v_self) != 0)); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":239 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":242 * * cdef int t * cdef char* f = NULL # <<<<<<<<<<<<<< @@ -2602,7 +2649,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_f = NULL; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":240 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":243 * cdef int t * cdef char* f = NULL * cdef dtype descr = self.descr # <<<<<<<<<<<<<< @@ -2614,7 +2661,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_descr = ((PyArray_Descr *)__pyx_t_3); __pyx_t_3 = 0; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":244 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":247 * cdef int offset * * cdef bint hasfields = PyDataType_HASFIELDS(descr) # <<<<<<<<<<<<<< @@ -2623,7 +2670,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_hasfields = PyDataType_HASFIELDS(__pyx_v_descr); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":246 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":249 * cdef bint hasfields = PyDataType_HASFIELDS(descr) * * if not hasfields and not copy_shape: # <<<<<<<<<<<<<< @@ -2641,7 +2688,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_L15_bool_binop_done:; if (__pyx_t_1) { - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":248 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":251 * if not hasfields and not copy_shape: * # do not call releasebuffer * info.obj = None # <<<<<<<<<<<<<< @@ -2657,7 +2704,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } /*else*/ { - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":251 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":254 * else: * # need to call releasebuffer * info.obj = self # <<<<<<<<<<<<<< @@ -2672,7 +2719,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L14:; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":253 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":256 * info.obj = self * * if not hasfields: # <<<<<<<<<<<<<< @@ -2682,7 +2729,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = ((!(__pyx_v_hasfields != 0)) != 0); if (__pyx_t_1) { - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":254 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":257 * * if not hasfields: * t = descr.type_num # <<<<<<<<<<<<<< @@ -2692,7 +2739,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_4 = __pyx_v_descr->type_num; __pyx_v_t = __pyx_t_4; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":255 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":258 * if not hasfields: * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -2712,7 +2759,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L20_next_or:; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":256 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":259 * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -2730,21 +2777,21 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_L19_bool_binop_done:; if (__pyx_t_1) { - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":257 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":260 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" */ - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__3, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__3, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - {__pyx_filename = __pyx_f[1]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":274 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":277 * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" * elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<< @@ -2753,7 +2800,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ switch (__pyx_v_t) { - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":258 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":261 * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" # <<<<<<<<<<<<<< @@ -2764,7 +2811,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_b; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":259 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":262 * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" # <<<<<<<<<<<<<< @@ -2775,7 +2822,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_B; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":260 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":263 * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" # <<<<<<<<<<<<<< @@ -2786,7 +2833,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_h; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":264 * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" # <<<<<<<<<<<<<< @@ -2797,7 +2844,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_H; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":262 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":265 * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" # <<<<<<<<<<<<<< @@ -2808,7 +2855,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_i; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":263 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":266 * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" # <<<<<<<<<<<<<< @@ -2819,7 +2866,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_I; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":264 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":267 * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" # <<<<<<<<<<<<<< @@ -2830,7 +2877,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_l; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":265 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":268 * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" # <<<<<<<<<<<<<< @@ -2841,7 +2888,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_L; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":266 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":269 * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" # <<<<<<<<<<<<<< @@ -2852,7 +2899,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_q; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":267 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":270 * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" # <<<<<<<<<<<<<< @@ -2863,7 +2910,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_Q; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":268 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":271 * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" # <<<<<<<<<<<<<< @@ -2874,7 +2921,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_f; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":269 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":272 * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" # <<<<<<<<<<<<<< @@ -2885,7 +2932,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_d; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":270 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":273 * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" # <<<<<<<<<<<<<< @@ -2896,7 +2943,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_g; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":271 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":274 * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" # <<<<<<<<<<<<<< @@ -2907,7 +2954,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_Zf; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":272 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":275 * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" # <<<<<<<<<<<<<< @@ -2918,7 +2965,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_Zd; break; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":273 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":276 * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" * elif t == NPY_CLONGDOUBLE: f = "Zg" # <<<<<<<<<<<<<< @@ -2929,7 +2976,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_v_f = __pyx_k_Zg; 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- /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":278 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":281 * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) * info.format = f * return # <<<<<<<<<<<<<< @@ -2988,7 +3035,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } /*else*/ { - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":280 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":283 * return * else: * info.format = stdlib.malloc(_buffer_format_string_len) # <<<<<<<<<<<<<< @@ -2997,7 +3044,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->format = ((char *)malloc(255)); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":281 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":284 * else: * info.format = stdlib.malloc(_buffer_format_string_len) * info.format[0] = c'^' # Native data types, manual alignment # <<<<<<<<<<<<<< @@ -3006,7 +3053,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->format[0]) = '^'; 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} - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":976 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":979 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -4317,8 +4369,8 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { }; static int __Pyx_InitCachedBuiltins(void) { __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_builtin_RuntimeError = __Pyx_GetBuiltinName(__pyx_n_s_RuntimeError); if (!__pyx_builtin_RuntimeError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_RuntimeError = __Pyx_GetBuiltinName(__pyx_n_s_RuntimeError); if (!__pyx_builtin_RuntimeError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;} return 0; __pyx_L1_error:; return -1; @@ -4328,69 +4380,69 @@ static int __Pyx_InitCachedConstants(void) { __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__Pyx_InitCachedConstants", 0); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":215 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":218 * if ((flags & pybuf.PyBUF_C_CONTIGUOUS == pybuf.PyBUF_C_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_C_CONTIGUOUS)): * raise ValueError(u"ndarray is not C contiguous") # <<<<<<<<<<<<<< * * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) */ - __pyx_tuple_ = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_C_contiguous); if (unlikely(!__pyx_tuple_)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 215; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple_ = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_C_contiguous); if (unlikely(!__pyx_tuple_)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 218; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple_); __Pyx_GIVEREF(__pyx_tuple_); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":219 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":222 * if ((flags & pybuf.PyBUF_F_CONTIGUOUS == pybuf.PyBUF_F_CONTIGUOUS) * and not PyArray_CHKFLAGS(self, NPY_F_CONTIGUOUS)): * raise ValueError(u"ndarray is not Fortran contiguous") # <<<<<<<<<<<<<< * * info.buf = PyArray_DATA(self) */ - __pyx_tuple__2 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_Fortran_contiguou); if (unlikely(!__pyx_tuple__2)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 219; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple__2 = PyTuple_Pack(1, __pyx_kp_u_ndarray_is_not_Fortran_contiguou); if (unlikely(!__pyx_tuple__2)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 222; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__2); __Pyx_GIVEREF(__pyx_tuple__2); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":257 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":260 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" */ - __pyx_tuple__3 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple__3 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 260; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__3); __Pyx_GIVEREF(__pyx_tuple__3); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":799 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":802 * * if (end - f) - (new_offset - offset[0]) < 15: * raise RuntimeError(u"Format string allocated too short, see comment in numpy.pxd") # <<<<<<<<<<<<<< * * if ((child.byteorder == c'>' and little_endian) or */ - __pyx_tuple__4 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor); if (unlikely(!__pyx_tuple__4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple__4 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor); if (unlikely(!__pyx_tuple__4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 802; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__4); __Pyx_GIVEREF(__pyx_tuple__4); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":803 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":806 * if ((child.byteorder == c'>' and little_endian) or * (child.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< * # One could encode it in the format string and have Cython * # complain instead, BUT: < and > in format strings also imply */ - __pyx_tuple__5 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 803; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple__5 = PyTuple_Pack(1, __pyx_kp_u_Non_native_byte_order_not_suppor); if (unlikely(!__pyx_tuple__5)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 806; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__5); __Pyx_GIVEREF(__pyx_tuple__5); - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":823 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":826 * t = child.type_num * if end - f < 5: * raise RuntimeError(u"Format string allocated too short.") # <<<<<<<<<<<<<< * * # Until ticket #99 is fixed, use integers to avoid warnings */ - __pyx_tuple__6 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor_2); if (unlikely(!__pyx_tuple__6)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_tuple__6 = PyTuple_Pack(1, __pyx_kp_u_Format_string_allocated_too_shor_2); if (unlikely(!__pyx_tuple__6)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__6); __Pyx_GIVEREF(__pyx_tuple__6); __Pyx_RefNannyFinishContext(); @@ -4496,10 +4548,10 @@ PyMODINIT_FUNC PyInit__utils(void) #endif 0); if (unlikely(!__pyx_ptype_7cpython_4type_type)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 9; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_ptype_5numpy_dtype = __Pyx_ImportType("numpy", "dtype", sizeof(PyArray_Descr), 0); if (unlikely(!__pyx_ptype_5numpy_dtype)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 155; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_5numpy_flatiter = __Pyx_ImportType("numpy", "flatiter", sizeof(PyArrayIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_flatiter)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 165; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_5numpy_broadcast = __Pyx_ImportType("numpy", "broadcast", sizeof(PyArrayMultiIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_broadcast)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 169; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_5numpy_ndarray = __Pyx_ImportType("numpy", "ndarray", sizeof(PyArrayObject), 0); if (unlikely(!__pyx_ptype_5numpy_ndarray)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 178; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __pyx_ptype_5numpy_ufunc = __Pyx_ImportType("numpy", "ufunc", sizeof(PyUFuncObject), 0); if (unlikely(!__pyx_ptype_5numpy_ufunc)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_flatiter = __Pyx_ImportType("numpy", "flatiter", sizeof(PyArrayIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_flatiter)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 168; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_broadcast = __Pyx_ImportType("numpy", "broadcast", sizeof(PyArrayMultiIterObject), 0); if (unlikely(!__pyx_ptype_5numpy_broadcast)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 172; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_ndarray = __Pyx_ImportType("numpy", "ndarray", sizeof(PyArrayObject), 0); if (unlikely(!__pyx_ptype_5numpy_ndarray)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 181; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_ptype_5numpy_ufunc = __Pyx_ImportType("numpy", "ufunc", sizeof(PyUFuncObject), 0); if (unlikely(!__pyx_ptype_5numpy_ufunc)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 864; __pyx_clineno = __LINE__; goto __pyx_L1_error;} /*--- Variable import code ---*/ /*--- Function import code ---*/ /*--- Execution code ---*/ @@ -4544,7 +4596,7 @@ PyMODINIT_FUNC PyInit__utils(void) if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "../../../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":976 + /* "../../../../.local/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":979 * arr.base = baseptr * * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< @@ -4574,7 +4626,7 @@ PyMODINIT_FUNC PyInit__utils(void) #endif } -/* Runtime support code */ +/* --- Runtime support code --- */ #if CYTHON_REFNANNY static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) { PyObject *m = NULL, *p = NULL; @@ -5526,10 +5578,13 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject if (value && PyExceptionInstance_Check(value)) { instance_class = (PyObject*) Py_TYPE(value); if (instance_class != type) { - if (PyObject_IsSubclass(instance_class, type)) { - type = instance_class; - } else { + int is_subclass = PyObject_IsSubclass(instance_class, type); + if (!is_subclass) { instance_class = NULL; + } else if (unlikely(is_subclass == -1)) { + goto bad; + } else { + type = instance_class; } } } @@ -5589,7 +5644,7 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject if (tb) { #if CYTHON_COMPILING_IN_PYPY PyObject *tmp_type, *tmp_value, *tmp_tb; - PyErr_Fetch(tmp_type, tmp_value, tmp_tb); + PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb); Py_INCREF(tb); PyErr_Restore(tmp_type, tmp_value, tb); Py_XDECREF(tmp_tb); @@ -5924,13 +5979,23 @@ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { } #endif #endif +#if CYTHON_COMPILING_IN_CPYTHON if (unlikely(Py_SIZE(x) < 0)) { goto raise_neg_overflow; } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (int) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif if (sizeof(int) <= sizeof(unsigned long)) { __PYX_VERIFY_RETURN_INT(int, unsigned long, PyLong_AsUnsignedLong(x)) - } else if (sizeof(int) <= sizeof(unsigned long long)) { - __PYX_VERIFY_RETURN_INT(int, unsigned long long, PyLong_AsUnsignedLongLong(x)) + } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) } } else { #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 @@ -5944,8 +6009,8 @@ static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { #endif if (sizeof(int) <= sizeof(long)) { __PYX_VERIFY_RETURN_INT(int, long, PyLong_AsLong(x)) - } else if (sizeof(int) <= sizeof(long long)) { - __PYX_VERIFY_RETURN_INT(int, long long, PyLong_AsLongLong(x)) + } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT(int, PY_LONG_LONG, PyLong_AsLongLong(x)) } } { @@ -6001,14 +6066,14 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { return PyInt_FromLong((long) value); } else if (sizeof(long) <= sizeof(unsigned long)) { return PyLong_FromUnsignedLong((unsigned long) value); - } else if (sizeof(long) <= sizeof(unsigned long long)) { - return PyLong_FromUnsignedLongLong((unsigned long long) value); + } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); } } else { if (sizeof(long) <= sizeof(long)) { return PyInt_FromLong((long) value); - } else if (sizeof(long) <= sizeof(long long)) { - return PyLong_FromLongLong((long long) value); + } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); } } { @@ -6045,13 +6110,23 @@ static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { } #endif #endif +#if CYTHON_COMPILING_IN_CPYTHON if (unlikely(Py_SIZE(x) < 0)) { goto raise_neg_overflow; } +#else + { + int result = PyObject_RichCompareBool(x, Py_False, Py_LT); + if (unlikely(result < 0)) + return (long) -1; + if (unlikely(result == 1)) + goto raise_neg_overflow; + } +#endif if (sizeof(long) <= sizeof(unsigned long)) { __PYX_VERIFY_RETURN_INT(long, unsigned long, PyLong_AsUnsignedLong(x)) - } else if (sizeof(long) <= sizeof(unsigned long long)) { - __PYX_VERIFY_RETURN_INT(long, unsigned long long, PyLong_AsUnsignedLongLong(x)) + } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) } } else { #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 @@ -6065,8 +6140,8 @@ static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { #endif if (sizeof(long) <= sizeof(long)) { __PYX_VERIFY_RETURN_INT(long, long, PyLong_AsLong(x)) - } else if (sizeof(long) <= sizeof(long long)) { - __PYX_VERIFY_RETURN_INT(long, long long, PyLong_AsLongLong(x)) + } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { + __PYX_VERIFY_RETURN_INT(long, PY_LONG_LONG, PyLong_AsLongLong(x)) } } { @@ -6122,14 +6197,14 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { return PyInt_FromLong((long) value); } else if (sizeof(int) <= sizeof(unsigned long)) { return PyLong_FromUnsignedLong((unsigned long) value); - } else if (sizeof(int) <= sizeof(unsigned long long)) { - return PyLong_FromUnsignedLongLong((unsigned long long) value); + } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { + return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); } } else { if (sizeof(int) <= sizeof(long)) { return PyInt_FromLong((long) value); - } else if (sizeof(int) <= sizeof(long long)) { - return PyLong_FromLongLong((long long) value); + } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { + return PyLong_FromLongLong((PY_LONG_LONG) value); } } { diff --git a/sklearn/manifold/t_sne.py b/sklearn/manifold/t_sne.py index 9c4cf03462d6f..2191cc5be2d45 100644 --- a/sklearn/manifold/t_sne.py +++ b/sklearn/manifold/t_sne.py @@ -11,7 +11,6 @@ import numpy as np from scipy import linalg import scipy.sparse as sp -import warnings from scipy.spatial.distance import pdist from scipy.spatial.distance import squareform from ..neighbors import BallTree @@ -373,6 +372,8 @@ def _gradient_descent(objective, p0, it, n_iter, objective_error=None, """ if args is None: args = [] + if kwargs is None: + kwargs = {} p = p0.copy().ravel() update = np.zeros_like(p) @@ -600,9 +601,6 @@ class TSNE(BaseEstimator): embedding_ : array-like, shape (n_samples, n_components) Stores the embedding vectors. - training_data_ : array-like, shape (n_samples, n_features) - Stores the training data. - Examples -------- @@ -610,11 +608,12 @@ class TSNE(BaseEstimator): >>> from sklearn.manifold import TSNE >>> X = np.array([[0, 0, 0], [0, 1, 1], [1, 0, 1], [1, 1, 1]]) >>> model = TSNE(n_components=2, random_state=0) + >>> np.set_printoptions(suppress=True) >>> model.fit_transform(X) # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE - array([[ 1.75677320e-04, 4.08340798e-05], - [ 9.93642843e-05, 2.17790936e-04], - [ 1.85517575e-04, -9.32909822e-05], - [ 9.54209795e-05, -1.40144791e-05]]) + array([[ 0.00017599, 0.00003993], + [ 0.00009891, 0.00021913], + [ 0.00018554, -0.00009357], + [ 0.00009528, -0.00001407]]) References ---------- @@ -725,7 +724,6 @@ def _fit(self, X, skip_num_points=0): # Laurens van der Maaten, 2009. degrees_of_freedom = max(self.n_components - 1.0, 1) n_samples = X.shape[0] - self.training_data_ = X # the number of nearest neighbors to find k = min(n_samples - 1, int(3. * self.perplexity + 1)) @@ -772,8 +770,6 @@ def _fit(self, X, skip_num_points=0): neighbors=neighbors_nn, skip_num_points=skip_num_points) - return self - def _tsne(self, P, degrees_of_freedom, n_samples, random_state, X_embedded=None, neighbors=None, skip_num_points=0): """Runs t-SNE.""" @@ -865,7 +861,7 @@ def fit_transform(self, X, y=None): self.embedding_ = embedding return self.embedding_ - def fit(self, X): + def fit(self, X, y=None): """Fit X into an embedded space. Parameters @@ -883,36 +879,3 @@ def _check_fitted(self): if self.embedding_ is None: raise ValueError("Cannot call `transform` unless `fit` has" "already been called") - - def transform(self, X): - """Transform X to a previously fit embedded space. - - A previous training set must have already been fit. - The new gradient is calculated using contributions from - previously fit data, but only the new data is transformed. - This is not the equivalent of running fit_transform, - since calling fit(X) followed by transform(X) runs the - gradient calculation twice, once for just X and the second time - on the concatenated array [X, X]. - - Parameters - ---------- - X : array, shape (n_samples, n_features) or (n_samples, n_samples) - If the metric is 'precomputed' X must be a square distance - matrix. Otherwise it contains a sample per row. - - Returns - ------- - X_new : array, shape (n_samples, n_components) - Embedding of the training data in low-dimensional space. - """ - self._check_fitted() - if np.allclose(X, self.training_data_, rtol=1e-4): - warnings.warn("The transform input appears to be similar " - "to previously fit data. This can result in " - "duplicated data; consider using fit_transform") - - skip_num_points = self.embedding_.shape[0] - full_set = np.vstack((self.embedding_, X)) - Xt = self._fit(full_set, skip_num_points=skip_num_points) - return Xt diff --git a/sklearn/manifold/tests/test_t_sne.py b/sklearn/manifold/tests/test_t_sne.py index bb335f77e8533..a4f056a7e14f2 100644 --- a/sklearn/manifold/tests/test_t_sne.py +++ b/sklearn/manifold/tests/test_t_sne.py @@ -1,5 +1,4 @@ import sys -import warnings from sklearn.externals.six.moves import cStringIO as StringIO import numpy as np import scipy.sparse as sp @@ -451,30 +450,6 @@ def test_64bit(): tsne.fit_transform(X) -def test_transform_before_fit(): - # transform() cannot be called before fit(). - random_state = check_random_state(0) - X = random_state.randn(100, 2) - tsne = TSNE(n_components=2, perplexity=2, learning_rate=100.0, - random_state=0, method='barnes_hut') - m = "Cannot call `transform` unless `fit` has" - assert_raises_regexp(ValueError, m, tsne.transform, X) - - -def test_transform_warning(): - # Raise a warning if fit and transform encountered the same data. - with warnings.catch_warnings(record=True) as w: - warnings.simplefilter("always") - random_state = check_random_state(0) - X = random_state.randn(100, 2) - tsne = TSNE(n_components=2, perplexity=2, learning_rate=100.0, - random_state=0, method='barnes_hut') - tsne.fit(X) - tsne.transform(X) - m = str(w[0].message) - assert "The transform input appears to be similar" in m - - def test_barnes_hut_angle(): # When Barnes-Hut's angle=0 this corresponds to the exact method. angle = 0.0