From ab8b8a207767cf23e46f5d5d7b0a7b84d1954611 Mon Sep 17 00:00:00 2001 From: Mikhail Korobov Date: Tue, 2 Apr 2013 19:24:53 +0600 Subject: [PATCH 1/3] faster _hmmc._logsum --- sklearn/_hmmc.pyx | 102 ++++++++++++++++++++++++++-------------------- 1 file changed, 57 insertions(+), 45 deletions(-) diff --git a/sklearn/_hmmc.pyx b/sklearn/_hmmc.pyx index 5b054dbaddbc9..8d272df8dbbcd 100644 --- a/sklearn/_hmmc.pyx +++ b/sklearn/_hmmc.pyx @@ -7,23 +7,35 @@ np.import_array() ctypedef np.float64_t dtype_t +cdef dtype_t _NINF = -np.inf @cython.boundscheck(False) -def _logsum(int N, np.ndarray[dtype_t, ndim=1] X): - cdef int i - cdef double maxv, Xsum - Xsum = 0.0 - maxv = X.max() - for i in xrange(N): - Xsum += exp(X[i] - maxv) - return log(Xsum) + maxv +cdef dtype_t _max(dtype_t[:] values): + # find maximum value (builtin 'max' is unrolled for speed) + cdef dtype_t value + cdef dtype_t vmax = _NINF + for i in range(values.shape[0]): + value = values[i] + if value > vmax: + vmax = value + return vmax + +@cython.boundscheck(False) +cpdef dtype_t _logsum(dtype_t[:] X): + cdef dtype_t vmax = _max(X) + cdef dtype_t power_sum = 0 + + for i in range(X.shape[0]): + power_sum += exp(X[i]-vmax) + + return log(power_sum) + vmax @cython.boundscheck(False) -def _forward(int n_observations, int n_components, \ - np.ndarray[dtype_t, ndim=1] log_startprob, \ - np.ndarray[dtype_t, ndim=2] log_transmat, \ - np.ndarray[dtype_t, ndim=2] framelogprob, \ +def _forward(int n_observations, int n_components, + np.ndarray[dtype_t, ndim=1] log_startprob, + np.ndarray[dtype_t, ndim=2] log_transmat, + np.ndarray[dtype_t, ndim=2] framelogprob, np.ndarray[dtype_t, ndim=2] fwdlattice): cdef int t, i, j @@ -31,22 +43,21 @@ def _forward(int n_observations, int n_components, \ cdef np.ndarray[dtype_t, ndim = 1] work_buffer work_buffer = np.zeros(n_components) - for i in xrange(n_components): + for i in range(n_components): fwdlattice[0, i] = log_startprob[i] + framelogprob[0, i] - for t in xrange(1, n_observations): - for j in xrange(n_components): - for i in xrange(n_components): + for t in range(1, n_observations): + for j in range(n_components): + for i in range(n_components): work_buffer[i] = fwdlattice[t - 1, i] + log_transmat[i, j] - fwdlattice[t, j] = _logsum(n_components, work_buffer) \ - + framelogprob[t, j] + fwdlattice[t, j] = _logsum(work_buffer) + framelogprob[t, j] @cython.boundscheck(False) -def _backward(int n_observations, int n_components, \ - np.ndarray[dtype_t, ndim=1] log_startprob, \ - np.ndarray[dtype_t, ndim=2] log_transmat, \ - np.ndarray[dtype_t, ndim=2] framelogprob, \ +def _backward(int n_observations, int n_components, + np.ndarray[dtype_t, ndim=1] log_startprob, + np.ndarray[dtype_t, ndim=2] log_transmat, + np.ndarray[dtype_t, ndim=2] framelogprob, np.ndarray[dtype_t, ndim=2] bwdlattice): cdef int t, i, j @@ -54,38 +65,38 @@ def _backward(int n_observations, int n_components, \ cdef np.ndarray[dtype_t, ndim = 1] work_buffer work_buffer = np.zeros(n_components) - for i in xrange(n_components): + for i in range(n_components): bwdlattice[n_observations - 1, i] = 0.0 - for t in xrange(n_observations - 2, -1, -1): - for i in xrange(n_components): - for j in xrange(n_components): + for t in range(n_observations - 2, -1, -1): + for i in range(n_components): + for j in range(n_components): work_buffer[j] = log_transmat[i, j] + framelogprob[t + 1, j] \ + bwdlattice[t + 1, j] - bwdlattice[t, i] = _logsum(n_components, work_buffer) + bwdlattice[t, i] = _logsum(work_buffer) @cython.boundscheck(False) -def _compute_lneta(int n_observations, int n_components, \ - np.ndarray[dtype_t, ndim=2] fwdlattice, \ - np.ndarray[dtype_t, ndim=2] log_transmat, \ - np.ndarray[dtype_t, ndim=2] bwdlattice, \ - np.ndarray[dtype_t, ndim=2] framelogprob, \ - double logprob, \ +def _compute_lneta(int n_observations, int n_components, + np.ndarray[dtype_t, ndim=2] fwdlattice, + np.ndarray[dtype_t, ndim=2] log_transmat, + np.ndarray[dtype_t, ndim=2] bwdlattice, + np.ndarray[dtype_t, ndim=2] framelogprob, + double logprob, np.ndarray[dtype_t, ndim=3] lneta): cdef int i, j, t - for t in xrange(n_observations - 1): - for i in xrange(n_components): - for j in xrange(n_components): + for t in range(n_observations - 1): + for i in range(n_components): + for j in range(n_components): lneta[t, i, j] = fwdlattice[t, i] + log_transmat[i, j] \ + framelogprob[t + 1, j] + bwdlattice[t + 1, j] - logprob @cython.boundscheck(False) -def _viterbi(int n_observations, int n_components, \ - np.ndarray[dtype_t, ndim=1] log_startprob, \ - np.ndarray[dtype_t, ndim=2] log_transmat, \ +def _viterbi(int n_observations, int n_components, + np.ndarray[dtype_t, ndim=1] log_startprob, + np.ndarray[dtype_t, ndim=2] log_transmat, np.ndarray[dtype_t, ndim=2] framelogprob): cdef int i, j, t, max_pos @@ -100,23 +111,24 @@ def _viterbi(int n_observations, int n_components, \ viterbi_lattice = np.zeros((n_observations, n_components)) # viterbi_lattice[0,:] = log_startprob[:] + framelogprob[0,:] - for i in xrange(n_components): + for i in range(n_components): viterbi_lattice[0, i] = log_startprob[i] + framelogprob[0, i] # Induction - for t in xrange(1, n_observations): - for j in xrange(n_components): + for t in range(1, n_observations): + for j in range(n_components): work_buffer[:] = viterbi_lattice[t - 1, :] + log_transmat[:, j] - viterbi_lattice[t, j] = np.max(work_buffer[:]) + framelogprob[t, j] + viterbi_lattice[t, j] = np.max(work_buffer) + framelogprob[t, j] # observation traceback max_pos = np.argmax(viterbi_lattice[n_observations - 1, :]) state_sequence[n_observations - 1] = max_pos logprob = viterbi_lattice[n_observations - 1, max_pos] - - for t in xrange(n_observations - 2, -1, -1): + + for t in range(n_observations - 2, -1, -1): max_pos = np.argmax(viterbi_lattice[t, :] \ + log_transmat[:, state_sequence[t + 1]]) state_sequence[t] = max_pos return state_sequence, logprob + From 50814bfebefed8fd4a962339a3a4fbfbf170f4b9 Mon Sep 17 00:00:00 2001 From: Mikhail Korobov Date: Tue, 2 Apr 2013 21:47:59 +0600 Subject: [PATCH 2/3] _hmmc._viterbi speed improvements --- sklearn/_hmmc.pyx | 24 +++++++++--------------- 1 file changed, 9 insertions(+), 15 deletions(-) diff --git a/sklearn/_hmmc.pyx b/sklearn/_hmmc.pyx index 8d272df8dbbcd..4aacc0319c56c 100644 --- a/sklearn/_hmmc.pyx +++ b/sklearn/_hmmc.pyx @@ -99,28 +99,23 @@ def _viterbi(int n_observations, int n_components, np.ndarray[dtype_t, ndim=2] log_transmat, np.ndarray[dtype_t, ndim=2] framelogprob): - cdef int i, j, t, max_pos + cdef int t, max_pos cdef np.ndarray[dtype_t, ndim = 2] viterbi_lattice cdef np.ndarray[np.int_t, ndim = 1] state_sequence - cdef double logprob - cdef np.ndarray[dtype_t, ndim = 1] work_buffer + cdef dtype_t logprob + cdef np.ndarray[dtype_t, ndim = 2] work_buffer - # Initialize state_sequenceation - state_sequence = np.zeros(n_observations, dtype=np.int) - work_buffer = np.zeros(n_components) + # Initialization + state_sequence = np.empty(n_observations, dtype=np.int) viterbi_lattice = np.zeros((n_observations, n_components)) - - # viterbi_lattice[0,:] = log_startprob[:] + framelogprob[0,:] - for i in range(n_components): - viterbi_lattice[0, i] = log_startprob[i] + framelogprob[0, i] + viterbi_lattice[0] = log_startprob + framelogprob[0] # Induction for t in range(1, n_observations): - for j in range(n_components): - work_buffer[:] = viterbi_lattice[t - 1, :] + log_transmat[:, j] - viterbi_lattice[t, j] = np.max(work_buffer) + framelogprob[t, j] + work_buffer = viterbi_lattice[t-1] + log_transmat.T + viterbi_lattice[t] = np.max(work_buffer, axis=1) + framelogprob[t] - # observation traceback + # Observation traceback max_pos = np.argmax(viterbi_lattice[n_observations - 1, :]) state_sequence[n_observations - 1] = max_pos logprob = viterbi_lattice[n_observations - 1, max_pos] @@ -131,4 +126,3 @@ def _viterbi(int n_observations, int n_components, state_sequence[t] = max_pos return state_sequence, logprob - From 2c82feb82822658d0e5821dd8135b96d7305597d Mon Sep 17 00:00:00 2001 From: Mikhail Korobov Date: Tue, 2 Apr 2013 21:48:28 +0600 Subject: [PATCH 3/3] rebuild _hmmc.c --- sklearn/_hmmc.c | 15193 +++++++++++++++++++++++++++++++++++++++++----- 1 file changed, 13842 insertions(+), 1351 deletions(-) diff --git a/sklearn/_hmmc.c b/sklearn/_hmmc.c index b908b391553b4..738cea6e50186 100644 --- a/sklearn/_hmmc.c +++ b/sklearn/_hmmc.c @@ -1,4 +1,4 @@ -/* Generated by Cython 0.17.4 on Mon Jan 7 18:32:17 2013 */ +/* Generated by Cython 0.18 on Tue Apr 2 21:46:21 2013 */ #define PY_SSIZE_T_CLEAN #include "Python.h" @@ -252,10 +252,13 @@ #define __PYX_HAVE__sklearn___hmmc #define __PYX_HAVE_API__sklearn___hmmc #include "math.h" +#include "string.h" #include "stdio.h" #include "stdlib.h" #include "numpy/arrayobject.h" #include "numpy/ufuncobject.h" +#include "pythread.h" +#include "pystate.h" #ifdef _OPENMP #include #endif /* _OPENMP */ @@ -264,8 +267,6 @@ #define CYTHON_WITHOUT_ASSERTIONS #endif - -/* inline attribute */ #ifndef CYTHON_INLINE #if defined(__GNUC__) #define CYTHON_INLINE __inline__ @@ -277,8 +278,6 @@ #define CYTHON_INLINE #endif #endif - -/* unused attribute */ #ifndef CYTHON_UNUSED # if defined(__GNUC__) # if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) @@ -292,24 +291,17 @@ # define CYTHON_UNUSED # endif #endif - typedef struct {PyObject **p; char *s; const long n; const char* encoding; const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; /*proto*/ - -/* Type Conversion Predeclarations */ - #define __Pyx_PyBytes_FromUString(s) PyBytes_FromString((char*)s) #define __Pyx_PyBytes_AsUString(s) ((unsigned char*) PyBytes_AsString(s)) - #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); static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*); - #if CYTHON_COMPILING_IN_CPYTHON #define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) #else @@ -317,6 +309,7 @@ static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject*); #endif #define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) + #ifdef __GNUC__ /* Test for GCC > 2.95 */ #if __GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)) @@ -365,8 +358,18 @@ static const char *__pyx_filename; static const char *__pyx_f[] = { "_hmmc.pyx", "numpy.pxd", + "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) @@ -402,6 +405,54 @@ typedef struct { char is_valid_array; } __Pyx_BufFmt_Context; +#include +#ifndef CYTHON_ATOMICS + #define CYTHON_ATOMICS 1 +#endif +#define __pyx_atomic_int_type int +/* todo: Portland pgcc, maybe OS X's OSAtomicIncrement32, + libatomic + autotools-like distutils support? Such a pain... */ +#if CYTHON_ATOMICS && __GNUC__ >= 4 && (__GNUC_MINOR__ > 1 || \ + (__GNUC_MINOR__ == 1 && __GNUC_PATHLEVEL >= 2)) + #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 + /* "numpy.pxd":723 * # in Cython to enable them only on the right systems. @@ -597,7 +648,7 @@ typedef npy_longdouble __pyx_t_5numpy_longdouble_t; * * ctypedef np.float64_t dtype_t # <<<<<<<<<<<<<< * - * + * cdef dtype_t _NINF = -np.inf */ typedef __pyx_t_5numpy_float64_t __pyx_t_7sklearn_5_hmmc_dtype_t; #if CYTHON_CCOMPLEX @@ -622,6 +673,10 @@ typedef __pyx_t_5numpy_float64_t __pyx_t_7sklearn_5_hmmc_dtype_t; /*--- Type declarations ---*/ +struct __pyx_memoryview_obj; +struct __pyx_array_obj; +struct __pyx_memoryviewslice_obj; +struct __pyx_MemviewEnum_obj; /* "numpy.pxd":762 * ctypedef npy_longdouble longdouble_t @@ -658,6 +713,117 @@ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; * cdef inline object PyArray_MultiIterNew1(a): */ typedef npy_cdouble __pyx_t_5numpy_complex_t; + +/* "View.MemoryView":308 + * + * @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; + __pyx_atomic_int acquisition_count[2]; + __pyx_atomic_int *acquisition_count_aligned_p; + Py_buffer view; + int flags; + int dtype_is_object; + __Pyx_TypeInfo *typeinfo; +}; + + +/* "View.MemoryView":96 + * + * @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":927 + * + * @cname('__pyx_memoryviewslice') + * cdef class _memoryviewslice(memoryview): # <<<<<<<<<<<<<< + * "Internal class for passing memoryview slices to Python" + * + */ +struct __pyx_memoryviewslice_obj { + struct __pyx_memoryview_obj __pyx_base; + __Pyx_memviewslice from_slice; + PyObject *from_object; + PyObject *(*to_object_func)(char *); + int (*to_dtype_func)(char *, PyObject *); +}; + + +/* "View.MemoryView":275 + * + * @cname('__pyx_MemviewEnum') + * cdef class Enum(object): # <<<<<<<<<<<<<< + * cdef object name + * def __init__(self, name): + */ +struct __pyx_MemviewEnum_obj { + PyObject_HEAD + PyObject *name; +}; + + + +/* "View.MemoryView":308 + * + * @cname('__pyx_memoryview') + * cdef class memoryview(object): # <<<<<<<<<<<<<< + * + * cdef object obj + */ + +struct __pyx_vtabstruct_memoryview { + char *(*get_item_pointer)(struct __pyx_memoryview_obj *, PyObject *); + PyObject *(*is_slice)(struct __pyx_memoryview_obj *, PyObject *); + PyObject *(*setitem_slice_assignment)(struct __pyx_memoryview_obj *, PyObject *, PyObject *); + PyObject *(*setitem_slice_assign_scalar)(struct __pyx_memoryview_obj *, struct __pyx_memoryview_obj *, PyObject *); + PyObject *(*setitem_indexed)(struct __pyx_memoryview_obj *, PyObject *, PyObject *); + PyObject *(*convert_item_to_object)(struct __pyx_memoryview_obj *, char *); + PyObject *(*assign_item_from_object)(struct __pyx_memoryview_obj *, char *, PyObject *); +}; +static struct __pyx_vtabstruct_memoryview *__pyx_vtabptr_memoryview; + + +/* "View.MemoryView":927 + * + * @cname('__pyx_memoryviewslice') + * cdef class _memoryviewslice(memoryview): # <<<<<<<<<<<<<< + * "Internal class for passing memoryview slices to Python" + * + */ + +struct __pyx_vtabstruct__memoryviewslice { + struct __pyx_vtabstruct_memoryview __pyx_base; +}; +static struct __pyx_vtabstruct__memoryviewslice *__pyx_vtabptr__memoryviewslice; + #ifndef CYTHON_REFNANNY #define CYTHON_REFNANNY 0 #endif @@ -714,6 +880,48 @@ typedef npy_cdouble __pyx_t_5numpy_complex_t; static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name); /*proto*/ +static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname); + +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 int __pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b); + +#define __Pyx_BUF_MAX_NDIMS %(BUF_MAX_NDIMS)d +#define __Pyx_MEMVIEW_DIRECT 1 +#define __Pyx_MEMVIEW_PTR 2 +#define __Pyx_MEMVIEW_FULL 4 +#define __Pyx_MEMVIEW_CONTIG 8 +#define __Pyx_MEMVIEW_STRIDED 16 +#define __Pyx_MEMVIEW_FOLLOW 32 +#define __Pyx_IS_C_CONTIG 1 +#define __Pyx_IS_F_CONTIG 2 +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 int __Pyx_init_memviewslice( + struct __pyx_memoryview_obj *memview, + int ndim, + __Pyx_memviewslice *memviewslice, + int memview_is_new_reference); +static CYTHON_INLINE int __pyx_add_acquisition_count_locked(__pyx_atomic_int *acquisition_count, + PyThread_type_lock lock); +static CYTHON_INLINE int __pyx_sub_acquisition_count_locked(__pyx_atomic_int *acquisition_count, + PyThread_type_lock lock); +#define __pyx_get_slice_count_pointer(memview) (memview->acquisition_count_aligned_p) +#define __pyx_get_slice_count(memview) (*__pyx_get_slice_count_pointer(memview)) +#define __PYX_INC_MEMVIEW(slice, have_gil) __Pyx_INC_MEMVIEW(slice, have_gil, __LINE__) +#define __PYX_XDEC_MEMVIEW(slice, have_gil) __Pyx_XDEC_MEMVIEW(slice, have_gil, __LINE__) +static CYTHON_INLINE void __Pyx_INC_MEMVIEW(__Pyx_memviewslice *, int, int); +static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *, int, int); + 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*/ @@ -726,20 +934,146 @@ static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \ static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, const char *name, int exact); /*proto*/ -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 int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); /*proto*/ + +static void __Pyx_RaiseBufferFallbackError(void); /*proto*/ #define __Pyx_BufPtrStrided1d(type, buf, i0, s0) (type)((char*)buf + i0 * s0) +#define __Pyx_BufPtrStrided2d(type, buf, i0, s0, i1, s1) (type)((char*)buf + i0 * s0 + i1 * s1) 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*/ -static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); /*proto*/ +#define __Pyx_BufPtrStrided3d(type, buf, i0, s0, i1, s1, i2, s2) (type)((char*)buf + i0 * s0 + i1 * s1 + i2 * s2) +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; +} +#define __Pyx_GetItemInt_List(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \ + __Pyx_GetItemInt_List_Fast(o, i) : \ + __Pyx_GetItemInt_Generic(o, to_py_func(i))) +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) { +#if CYTHON_COMPILING_IN_CPYTHON + if (likely((0 <= i) & (i < PyList_GET_SIZE(o)))) { + PyObject *r = PyList_GET_ITEM(o, i); + Py_INCREF(r); + return r; + } + else if ((-PyList_GET_SIZE(o) <= i) & (i < 0)) { + PyObject *r = PyList_GET_ITEM(o, PyList_GET_SIZE(o) + i); + Py_INCREF(r); + return r; + } + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +#else + return PySequence_GetItem(o, i); +#endif +} +#define __Pyx_GetItemInt_Tuple(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \ + __Pyx_GetItemInt_Tuple_Fast(o, i) : \ + __Pyx_GetItemInt_Generic(o, to_py_func(i))) +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { +#if CYTHON_COMPILING_IN_CPYTHON + if (likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) { + PyObject *r = PyTuple_GET_ITEM(o, i); + Py_INCREF(r); + return r; + } + else if ((-PyTuple_GET_SIZE(o) <= i) & (i < 0)) { + PyObject *r = PyTuple_GET_ITEM(o, PyTuple_GET_SIZE(o) + i); + Py_INCREF(r); + return r; + } + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +#else + return PySequence_GetItem(o, i); +#endif +} +#define __Pyx_GetItemInt(o, i, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \ + __Pyx_GetItemInt_Fast(o, i) : \ + __Pyx_GetItemInt_Generic(o, to_py_func(i))) +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) { +#if CYTHON_COMPILING_IN_CPYTHON + if (PyList_CheckExact(o)) { + Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); + if (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 = (likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o); + if (likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) { + PyObject *r = PyTuple_GET_ITEM(o, n); + Py_INCREF(r); + return r; + } + } else { /* inlined PySequence_GetItem() */ + PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; + if (likely(m && m->sq_item)) { + if (unlikely(i < 0) && likely(m->sq_length)) { + Py_ssize_t l = m->sq_length(o); + if (unlikely(l < 0)) return NULL; + i += l; + } + return m->sq_item(o, i); + } + } +#else + if (PySequence_Check(o)) { + return PySequence_GetItem(o, i); + } +#endif + return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); +} -static void __Pyx_RaiseBufferFallbackError(void); /*proto*/ +#define __Pyx_SetItemInt(o, i, v, size, to_py_func) (((size) <= sizeof(Py_ssize_t)) ? \ + __Pyx_SetItemInt_Fast(o, i, v) : \ + __Pyx_SetItemInt_Generic(o, to_py_func(i), v)) +static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v) { + int r; + if (!j) return -1; + r = PyObject_SetItem(o, j, v); + Py_DECREF(j); + return r; +} +static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v) { +#if CYTHON_COMPILING_IN_CPYTHON + if (PyList_CheckExact(o)) { + Py_ssize_t n = (likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); + if (likely((n >= 0) & (n < PyList_GET_SIZE(o)))) { + PyObject* old = PyList_GET_ITEM(o, n); + Py_INCREF(v); + PyList_SET_ITEM(o, n, v); + Py_DECREF(old); + return 1; + } + } else { /* inlined PySequence_SetItem() */ + PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence; + if (likely(m && m->sq_ass_item)) { + if (unlikely(i < 0) && likely(m->sq_length)) { + Py_ssize_t l = m->sq_length(o); + if (unlikely(l < 0)) return -1; + i += l; + } + return m->sq_ass_item(o, i, v); + } + } +#else +#if CYTHON_COMPILING_IN_PYPY + if (PySequence_Check(o) && !PyDict_Check(o)) { +#else + if (PySequence_Check(o)) { +#endif + return PySequence_SetItem(o, i, v); + } +#endif + return __Pyx_SetItemInt_Generic(o, PyInt_FromSsize_t(i), v); +} -#define __Pyx_BufPtrStrided2d(type, buf, i0, s0, i1, s1) (type)((char*)buf + i0 * s0 + i1 * s1) -#define __Pyx_BufPtrStrided3d(type, buf, i0, s0, i1, s1, i2, s2) (type)((char*)buf + i0 * s0 + i1 * s1 + i2 * s2) static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); /*proto*/ static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); @@ -752,7 +1086,59 @@ static CYTHON_INLINE int __Pyx_IterFinish(void); /*proto*/ static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); /*proto*/ -typedef struct { +static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *, PyObject *, PyObject *); /*proto*/ + +static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t, Py_ssize_t); /* proto */ + +#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 CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals); /*proto*/ + +static PyObject *get_memview(PyObject *__pyx_v_self); /*proto*/ + 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)); + +#include + +static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ + +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_PyList_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_PyList_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*/ + #ifndef __PYX_FORCE_INIT_THREADS + #define __PYX_FORCE_INIT_THREADS 0 +#endif + +static CYTHON_INLINE long __Pyx_div_long(long, long); /* proto */ + +static PyObject *__pyx_memoryviewslice__get__base(PyObject *__pyx_v_self); /*proto*/ + typedef struct { Py_ssize_t shape, strides, suboffsets; } __Pyx_Buf_DimInfo; typedef struct { @@ -774,10 +1160,12 @@ typedef struct { #endif -static Py_ssize_t __Pyx_zeros[] = {0, 0, 0, 0, 0, 0, 0, 0}; + 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, long level); /*proto*/ +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); /*proto*/ + +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_nn___pyx_t_7sklearn_5_hmmc_dtype_t(PyObject *); static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_npy_long(npy_long); @@ -879,6 +1267,24 @@ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(do #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 void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); /*proto*/ +static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); /*proto*/ + static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject *); static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject *); @@ -911,8 +1317,13 @@ static CYTHON_INLINE signed long __Pyx_PyInt_AsSignedLong(PyObject *); static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject *); +static void __Pyx_WriteUnraisable(const char *name, int clineno, + int lineno, const char *filename); /*proto*/ + static int __Pyx_check_binary_version(void); +static int __Pyx_SetVtable(PyObject *dict, void *vtable); /*proto*/ + #if !defined(__Pyx_PyIdentifier_FromString) #if PY_MAJOR_VERSION < 3 #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s) @@ -951,6 +1362,8 @@ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /*proto*/ /* Module declarations from 'cpython.ref' */ +/* Module declarations from 'libc.string' */ + /* Module declarations from 'libc.stdio' */ /* Module declarations from 'cpython.object' */ @@ -972,43 +1385,153 @@ 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 'cython.view' */ + /* Module declarations from 'cython' */ /* Module declarations from 'sklearn._hmmc' */ +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 __pyx_t_7sklearn_5_hmmc_dtype_t __pyx_v_7sklearn_5_hmmc__NINF; +static PyObject *generic = 0; +static PyObject *strided = 0; +static PyObject *indirect = 0; +static PyObject *contiguous = 0; +static PyObject *indirect_contiguous = 0; +static __pyx_t_7sklearn_5_hmmc_dtype_t __pyx_f_7sklearn_5_hmmc__max(__Pyx_memviewslice); /*proto*/ +static __pyx_t_7sklearn_5_hmmc_dtype_t __pyx_f_7sklearn_5_hmmc__logsum(__Pyx_memviewslice, int __pyx_skip_dispatch); /*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 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, int); /*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_nn___pyx_t_7sklearn_5_hmmc_dtype_t = { "dtype_t", NULL, sizeof(__pyx_t_7sklearn_5_hmmc_dtype_t), { 0 }, 0, 'R', 0, 0 }; static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_int_t = { "int_t", NULL, sizeof(__pyx_t_5numpy_int_t), { 0 }, 0, IS_UNSIGNED(__pyx_t_5numpy_int_t) ? 'U' : 'I', IS_UNSIGNED(__pyx_t_5numpy_int_t), 0 }; #define __Pyx_MODULE_NAME "sklearn._hmmc" int __pyx_module_is_main_sklearn___hmmc = 0; /* Implementation of 'sklearn._hmmc' */ -static PyObject *__pyx_builtin_xrange; -static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_range; +static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_RuntimeError; -static PyObject *__pyx_pf_7sklearn_5_hmmc__logsum(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_v_N, PyArrayObject *__pyx_v_X); /* proto */ +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_5_hmmc__logsum(CYTHON_UNUSED PyObject *__pyx_self, __Pyx_memviewslice __pyx_v_X); /* proto */ static PyObject *__pyx_pf_7sklearn_5_hmmc_2_forward(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_v_n_observations, int __pyx_v_n_components, PyArrayObject *__pyx_v_log_startprob, PyArrayObject *__pyx_v_log_transmat, PyArrayObject *__pyx_v_framelogprob, PyArrayObject *__pyx_v_fwdlattice); /* proto */ static PyObject *__pyx_pf_7sklearn_5_hmmc_4_backward(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_v_n_observations, int __pyx_v_n_components, CYTHON_UNUSED PyArrayObject *__pyx_v_log_startprob, PyArrayObject *__pyx_v_log_transmat, PyArrayObject *__pyx_v_framelogprob, PyArrayObject *__pyx_v_bwdlattice); /* proto */ static PyObject *__pyx_pf_7sklearn_5_hmmc_6_compute_lneta(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_v_n_observations, int __pyx_v_n_components, PyArrayObject *__pyx_v_fwdlattice, PyArrayObject *__pyx_v_log_transmat, PyArrayObject *__pyx_v_bwdlattice, PyArrayObject *__pyx_v_framelogprob, double __pyx_v_logprob, PyArrayObject *__pyx_v_lneta); /* proto */ static PyObject *__pyx_pf_7sklearn_5_hmmc_8_viterbi(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_v_n_observations, int __pyx_v_n_components, PyArrayObject *__pyx_v_log_startprob, PyArrayObject *__pyx_v_log_transmat, PyArrayObject *__pyx_v_framelogprob); /* 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_6[] = "ndarray is not C contiguous"; -static char __pyx_k_8[] = "ndarray is not Fortran contiguous"; -static char __pyx_k_10[] = "Non-native byte order not supported"; -static char __pyx_k_12[] = "unknown dtype code in numpy.pxd (%d)"; -static char __pyx_k_13[] = "Format string allocated too short, see comment in numpy.pxd"; -static char __pyx_k_16[] = "Format string allocated too short."; -static char __pyx_k_20[] = "/scratch/apps/src/scikit-learn/sklearn/_hmmc.pyx"; -static char __pyx_k_21[] = "sklearn._hmmc"; +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 char __pyx_k_4[] = "ndarray is not C contiguous"; +static char __pyx_k_6[] = "ndarray is not Fortran contiguous"; +static char __pyx_k_8[] = "Non-native byte order not supported"; +static char __pyx_k_10[] = "unknown dtype code in numpy.pxd (%d)"; +static char __pyx_k_11[] = "Format string allocated too short, see comment in numpy.pxd"; +static char __pyx_k_14[] = "Format string allocated too short."; +static char __pyx_k_16[] = "Empty shape tuple for cython.array"; +static char __pyx_k_18[] = "itemsize <= 0 for cython.array"; +static char __pyx_k_21[] = "unable to allocate shape or strides."; +static char __pyx_k_23[] = "Invalid shape in axis %d: %d."; +static char __pyx_k_24[] = "Invalid mode, expected 'c' or 'fortran', got %s"; +static char __pyx_k_26[] = "unable to allocate array data."; +static char __pyx_k_28[] = "Can only create a buffer that is contiguous in memory."; +static char __pyx_k_30[] = "Unable to convert item to object"; +static char __pyx_k_32[] = "Buffer view does not expose strides"; +static char __pyx_k_34[] = ""; +static char __pyx_k_35[] = ""; +static char __pyx_k_38[] = "Cannot index with type '%s'"; +static char __pyx_k_40[] = "Indirect dimensions not supported"; +static char __pyx_k_42[] = "Index out of bounds (axis %d)"; +static char __pyx_k_43[] = "Step may not be zero (axis %d)"; +static char __pyx_k_44[] = "All dimensions preceding dimension %d must be indexed and not sliced"; +static char __pyx_k_45[] = "Out of bounds on buffer access (axis %d)"; +static char __pyx_k_46[] = "Cannot transpose memoryview with indirect dimensions"; +static char __pyx_k_47[] = "got differing extents in dimension %d (got %d and %d)"; +static char __pyx_k_48[] = "Dimension %d is not direct"; +static char __pyx_k_51[] = "/Users/kmike/svn/scikit-learn/sklearn/_hmmc.pyx"; +static char __pyx_k_52[] = "sklearn._hmmc"; +static char __pyx_k_59[] = "getbuffer(obj, view, flags)"; +static char __pyx_k_60[] = ""; +static char __pyx_k_62[] = ""; +static char __pyx_k_64[] = ""; +static char __pyx_k_66[] = ""; +static char __pyx_k_68[] = ""; static char __pyx_k__B[] = "B"; static char __pyx_k__H[] = "H"; static char __pyx_k__I[] = "I"; static char __pyx_k__L[] = "L"; -static char __pyx_k__N[] = "N"; static char __pyx_k__O[] = "O"; static char __pyx_k__Q[] = "Q"; -static char __pyx_k__X[] = "X"; +static char __pyx_k__T[] = "T"; 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"; @@ -1021,29 +1544,60 @@ static char __pyx_k__t[] = "t"; 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__inf[] = "inf"; static char __pyx_k__int[] = "int"; static char __pyx_k__max[] = "max"; -static char __pyx_k__Xsum[] = "Xsum"; -static char __pyx_k__maxv[] = "maxv"; +static char __pyx_k__obj[] = "obj"; +static char __pyx_k__axis[] = "axis"; +static char __pyx_k__base[] = "base"; +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__ASCII[] = "ASCII"; static char __pyx_k__dtype[] = "dtype"; +static char __pyx_k__empty[] = "empty"; +static char __pyx_k__error[] = "error"; +static char __pyx_k__flags[] = "flags"; static char __pyx_k__lneta[] = "lneta"; 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__zeros[] = "zeros"; static char __pyx_k__argmax[] = "argmax"; +static char __pyx_k__decode[] = "decode"; +static char __pyx_k__encode[] = "encode"; +static char __pyx_k__extend[] = "extend"; +static char __pyx_k__format[] = "format"; +static char __pyx_k__struct[] = "struct"; +static char __pyx_k__unpack[] = "unpack"; static char __pyx_k__xrange[] = "xrange"; -static char __pyx_k___logsum[] = "_logsum"; +static char __pyx_k__fortran[] = "fortran"; static char __pyx_k__logprob[] = "logprob"; static char __pyx_k__max_pos[] = "max_pos"; +static char __pyx_k__memview[] = "memview"; +static char __pyx_k__Ellipsis[] = "Ellipsis"; static char __pyx_k____main__[] = "__main__"; +static char __pyx_k____name__[] = "__name__"; static char __pyx_k____test__[] = "__test__"; static char __pyx_k___forward[] = "_forward"; static char __pyx_k___viterbi[] = "_viterbi"; +static char __pyx_k__itemsize[] = "itemsize"; +static char __pyx_k__TypeError[] = "TypeError"; +static char __pyx_k____class__[] = "__class__"; static char __pyx_k___backward[] = "_backward"; +static char __pyx_k__enumerate[] = "enumerate"; +static char __pyx_k__IndexError[] = "IndexError"; static char __pyx_k__ValueError[] = "ValueError"; static char __pyx_k__bwdlattice[] = "bwdlattice"; static char __pyx_k__fwdlattice[] = "fwdlattice"; +static char __pyx_k__MemoryError[] = "MemoryError"; static char __pyx_k__work_buffer[] = "work_buffer"; static char __pyx_k__RuntimeError[] = "RuntimeError"; static char __pyx_k__framelogprob[] = "framelogprob"; @@ -1053,34 +1607,83 @@ static char __pyx_k__log_startprob[] = "log_startprob"; static char __pyx_k___compute_lneta[] = "_compute_lneta"; static char __pyx_k__n_observations[] = "n_observations"; static char __pyx_k__state_sequence[] = "state_sequence"; +static char __pyx_k____pyx_getbuffer[] = "__pyx_getbuffer"; +static char __pyx_k__allocate_buffer[] = "allocate_buffer"; +static char __pyx_k__dtype_is_object[] = "dtype_is_object"; static char __pyx_k__viterbi_lattice[] = "viterbi_lattice"; static PyObject *__pyx_kp_u_10; -static PyObject *__pyx_kp_u_12; -static PyObject *__pyx_kp_u_13; -static PyObject *__pyx_kp_u_16; -static PyObject *__pyx_kp_s_20; -static PyObject *__pyx_n_s_21; +static PyObject *__pyx_kp_u_11; +static PyObject *__pyx_kp_u_14; +static PyObject *__pyx_kp_s_16; +static PyObject *__pyx_kp_s_18; +static PyObject *__pyx_kp_s_21; +static PyObject *__pyx_kp_s_23; +static 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*__pyx_n_s__TypeError; static PyObject *__pyx_n_s__ValueError; -static PyObject *__pyx_n_s__X; -static PyObject *__pyx_n_s__Xsum; +static PyObject *__pyx_n_s____class__; static PyObject *__pyx_n_s____main__; +static PyObject *__pyx_n_s____name__; +static PyObject *__pyx_n_s____pyx_getbuffer; static PyObject *__pyx_n_s____test__; static PyObject *__pyx_n_s___backward; static PyObject *__pyx_n_s___compute_lneta; static PyObject *__pyx_n_s___forward; -static PyObject *__pyx_n_s___logsum; static PyObject *__pyx_n_s___viterbi; +static PyObject *__pyx_n_s__allocate_buffer; static PyObject *__pyx_n_s__argmax; +static PyObject *__pyx_n_s__axis; +static PyObject *__pyx_n_s__base; static PyObject *__pyx_n_s__bwdlattice; +static PyObject *__pyx_n_b__c; +static PyObject *__pyx_n_s__c; +static PyObject *__pyx_n_u__c; +static PyObject *__pyx_n_s__decode; static PyObject *__pyx_n_s__dtype; +static PyObject *__pyx_n_s__dtype_is_object; +static PyObject *__pyx_n_s__empty; +static PyObject *__pyx_n_s__encode; +static PyObject *__pyx_n_s__enumerate; +static PyObject *__pyx_n_s__error; +static PyObject *__pyx_n_s__extend; +static PyObject *__pyx_n_s__flags; +static PyObject *__pyx_n_s__format; +static PyObject *__pyx_n_b__fortran; +static PyObject *__pyx_n_s__fortran; static PyObject *__pyx_n_s__framelogprob; static PyObject *__pyx_n_s__fwdlattice; static PyObject *__pyx_n_s__i; +static PyObject *__pyx_n_s__id; +static PyObject *__pyx_n_s__inf; static PyObject *__pyx_n_s__int; +static PyObject *__pyx_n_s__itemsize; static PyObject *__pyx_n_s__j; static PyObject *__pyx_n_s__lneta; static PyObject *__pyx_n_s__log_startprob; @@ -1088,216 +1691,290 @@ static PyObject *__pyx_n_s__log_transmat; static PyObject *__pyx_n_s__logprob; static PyObject *__pyx_n_s__max; static PyObject *__pyx_n_s__max_pos; -static PyObject *__pyx_n_s__maxv; +static PyObject *__pyx_n_s__memview; +static PyObject *__pyx_n_s__mode; static PyObject *__pyx_n_s__n_components; static PyObject *__pyx_n_s__n_observations; +static PyObject *__pyx_n_s__name; +static PyObject *__pyx_n_s__ndim; static PyObject *__pyx_n_s__np; static PyObject *__pyx_n_s__numpy; +static PyObject *__pyx_n_s__obj; +static PyObject *__pyx_n_s__pack; static PyObject *__pyx_n_s__range; +static PyObject *__pyx_n_s__shape; +static PyObject *__pyx_n_s__size; +static PyObject *__pyx_n_s__start; static PyObject *__pyx_n_s__state_sequence; +static PyObject *__pyx_n_s__step; +static PyObject *__pyx_n_s__stop; +static PyObject *__pyx_n_s__struct; static PyObject *__pyx_n_s__t; +static PyObject *__pyx_n_s__unpack; static PyObject *__pyx_n_s__viterbi_lattice; static PyObject *__pyx_n_s__work_buffer; static PyObject *__pyx_n_s__xrange; static PyObject *__pyx_n_s__zeros; +static PyObject *__pyx_int_0; +static PyObject *__pyx_int_1; +static PyObject *__pyx_int_neg_1; static PyObject *__pyx_int_15; static PyObject *__pyx_k_slice_1; static PyObject *__pyx_k_slice_2; static PyObject *__pyx_k_slice_3; -static PyObject *__pyx_k_slice_4; -static PyObject *__pyx_k_slice_5; +static PyObject *__pyx_k_tuple_5; static PyObject *__pyx_k_tuple_7; static PyObject *__pyx_k_tuple_9; -static PyObject *__pyx_k_tuple_11; -static PyObject *__pyx_k_tuple_14; +static PyObject *__pyx_k_tuple_12; +static PyObject *__pyx_k_tuple_13; static PyObject *__pyx_k_tuple_15; static PyObject *__pyx_k_tuple_17; -static PyObject *__pyx_k_tuple_18; +static PyObject *__pyx_k_tuple_19; +static PyObject *__pyx_k_tuple_20; static PyObject *__pyx_k_tuple_22; -static PyObject *__pyx_k_tuple_24; -static PyObject *__pyx_k_tuple_26; -static PyObject *__pyx_k_tuple_28; -static PyObject *__pyx_k_codeobj_19; -static PyObject *__pyx_k_codeobj_23; -static PyObject *__pyx_k_codeobj_25; -static PyObject *__pyx_k_codeobj_27; -static PyObject *__pyx_k_codeobj_29; +static PyObject *__pyx_k_tuple_25; +static PyObject *__pyx_k_tuple_27; +static PyObject *__pyx_k_tuple_29; +static PyObject *__pyx_k_tuple_31; +static PyObject *__pyx_k_tuple_33; +static PyObject *__pyx_k_tuple_36; +static PyObject *__pyx_k_tuple_37; +static PyObject *__pyx_k_tuple_39; +static PyObject *__pyx_k_tuple_41; +static PyObject *__pyx_k_tuple_49; +static PyObject *__pyx_k_tuple_53; +static PyObject *__pyx_k_tuple_55; +static PyObject *__pyx_k_tuple_57; +static PyObject *__pyx_k_tuple_61; +static PyObject *__pyx_k_tuple_63; +static PyObject *__pyx_k_tuple_65; +static PyObject *__pyx_k_tuple_67; +static PyObject *__pyx_k_tuple_69; +static PyObject *__pyx_k_codeobj_50; +static PyObject *__pyx_k_codeobj_54; +static PyObject *__pyx_k_codeobj_56; +static PyObject *__pyx_k_codeobj_58; + +/* "sklearn/_hmmc.pyx":13 + * + * @cython.boundscheck(False) + * cdef dtype_t _max(dtype_t[:] values): # <<<<<<<<<<<<<< + * # find maximum value (builtin 'max' is unrolled for speed) + * cdef dtype_t value + */ -/* Python wrapper */ -static PyObject *__pyx_pw_7sklearn_5_hmmc_1_logsum(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/ -static PyMethodDef 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__pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_n_components = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_n_components == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_log_startprob = ((PyArrayObject *)values[2]); __pyx_v_log_transmat = ((PyArrayObject *)values[3]); __pyx_v_framelogprob = ((PyArrayObject *)values[4]); @@ -1385,16 +2062,16 @@ static PyObject *__pyx_pw_7sklearn_5_hmmc_3_forward(PyObject *__pyx_self, PyObje } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("_forward", 1, 6, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_forward", 1, 6, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("sklearn._hmmc._forward", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_log_startprob), __pyx_ptype_5numpy_ndarray, 1, "log_startprob", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 24; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_log_transmat), __pyx_ptype_5numpy_ndarray, 1, "log_transmat", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 25; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_framelogprob), __pyx_ptype_5numpy_ndarray, 1, "framelogprob", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 26; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_fwdlattice), __pyx_ptype_5numpy_ndarray, 1, "fwdlattice", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 27; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_log_startprob), __pyx_ptype_5numpy_ndarray, 1, "log_startprob", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 36; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_log_transmat), __pyx_ptype_5numpy_ndarray, 1, "log_transmat", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 37; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_framelogprob), __pyx_ptype_5numpy_ndarray, 1, "framelogprob", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 38; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_fwdlattice), __pyx_ptype_5numpy_ndarray, 1, "fwdlattice", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 39; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_7sklearn_5_hmmc_2_forward(__pyx_self, __pyx_v_n_observations, __pyx_v_n_components, __pyx_v_log_startprob, __pyx_v_log_transmat, __pyx_v_framelogprob, __pyx_v_fwdlattice); goto __pyx_L0; __pyx_L1_error:; @@ -1404,12 +2081,12 @@ static PyObject *__pyx_pw_7sklearn_5_hmmc_3_forward(PyObject *__pyx_self, PyObje return __pyx_r; } -/* "sklearn/_hmmc.pyx":23 +/* "sklearn/_hmmc.pyx":35 * * @cython.boundscheck(False) - * def _forward(int n_observations, int n_components, \ # <<<<<<<<<<<<<< - * np.ndarray[dtype_t, ndim=1] log_startprob, \ - * np.ndarray[dtype_t, ndim=2] log_transmat, \ + * def _forward(int n_observations, int n_components, # <<<<<<<<<<<<<< + * np.ndarray[dtype_t, ndim=1] log_startprob, + * np.ndarray[dtype_t, ndim=2] log_transmat, */ static PyObject *__pyx_pf_7sklearn_5_hmmc_2_forward(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_v_n_observations, int __pyx_v_n_components, PyArrayObject *__pyx_v_log_startprob, PyArrayObject *__pyx_v_log_transmat, PyArrayObject *__pyx_v_framelogprob, PyArrayObject *__pyx_v_fwdlattice) { @@ -1452,7 +2129,7 @@ static PyObject *__pyx_pf_7sklearn_5_hmmc_2_forward(CYTHON_UNUSED PyObject *__py int __pyx_t_21; int __pyx_t_22; int __pyx_t_23; - __pyx_t_7sklearn_5_hmmc_dtype_t __pyx_t_24; + __Pyx_memviewslice __pyx_t_24 = { 0, 0, { 0 }, { 0 }, { 0 } }; int __pyx_t_25; int __pyx_t_26; int __pyx_lineno = 0; @@ -1481,49 +2158,49 @@ static PyObject *__pyx_pf_7sklearn_5_hmmc_2_forward(CYTHON_UNUSED PyObject *__py __pyx_pybuffernd_fwdlattice.rcbuffer = &__pyx_pybuffer_fwdlattice; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_log_startprob.rcbuffer->pybuffer, (PyObject*)__pyx_v_log_startprob, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_5_hmmc_dtype_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_log_startprob.rcbuffer->pybuffer, (PyObject*)__pyx_v_log_startprob, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_5_hmmc_dtype_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_log_startprob.diminfo[0].strides = __pyx_pybuffernd_log_startprob.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_log_startprob.diminfo[0].shape = __pyx_pybuffernd_log_startprob.rcbuffer->pybuffer.shape[0]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_log_transmat.rcbuffer->pybuffer, (PyObject*)__pyx_v_log_transmat, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_5_hmmc_dtype_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_log_transmat.rcbuffer->pybuffer, (PyObject*)__pyx_v_log_transmat, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_5_hmmc_dtype_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_log_transmat.diminfo[0].strides = __pyx_pybuffernd_log_transmat.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_log_transmat.diminfo[0].shape = __pyx_pybuffernd_log_transmat.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_log_transmat.diminfo[1].strides = __pyx_pybuffernd_log_transmat.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_log_transmat.diminfo[1].shape = __pyx_pybuffernd_log_transmat.rcbuffer->pybuffer.shape[1]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_framelogprob.rcbuffer->pybuffer, (PyObject*)__pyx_v_framelogprob, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_5_hmmc_dtype_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_framelogprob.rcbuffer->pybuffer, (PyObject*)__pyx_v_framelogprob, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_5_hmmc_dtype_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_framelogprob.diminfo[0].strides = __pyx_pybuffernd_framelogprob.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_framelogprob.diminfo[0].shape = __pyx_pybuffernd_framelogprob.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_framelogprob.diminfo[1].strides = __pyx_pybuffernd_framelogprob.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_framelogprob.diminfo[1].shape = __pyx_pybuffernd_framelogprob.rcbuffer->pybuffer.shape[1]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_fwdlattice.rcbuffer->pybuffer, (PyObject*)__pyx_v_fwdlattice, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_5_hmmc_dtype_t, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 23; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_fwdlattice.rcbuffer->pybuffer, (PyObject*)__pyx_v_fwdlattice, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_5_hmmc_dtype_t, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 35; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_fwdlattice.diminfo[0].strides = __pyx_pybuffernd_fwdlattice.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_fwdlattice.diminfo[0].shape = __pyx_pybuffernd_fwdlattice.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_fwdlattice.diminfo[1].strides = __pyx_pybuffernd_fwdlattice.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_fwdlattice.diminfo[1].shape = __pyx_pybuffernd_fwdlattice.rcbuffer->pybuffer.shape[1]; - /* "sklearn/_hmmc.pyx":32 + /* "sklearn/_hmmc.pyx":44 * cdef double logprob * cdef np.ndarray[dtype_t, ndim = 1] work_buffer * work_buffer = np.zeros(n_components) # <<<<<<<<<<<<<< * - * for i in xrange(n_components): + * for i in range(n_components): */ - __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__zeros); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_2 = PyObject_GetAttr(__pyx_t_1, __pyx_n_s__zeros); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_2); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_1 = PyInt_FromLong(__pyx_v_n_components); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyInt_FromLong(__pyx_v_n_components); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_3 = PyTuple_New(1); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); PyTuple_SET_ITEM(__pyx_t_3, 0, __pyx_t_1); __Pyx_GIVEREF(__pyx_t_1); __pyx_t_1 = 0; - __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyObject_Call(__pyx_t_2, ((PyObject *)__pyx_t_3), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __Pyx_DECREF(((PyObject *)__pyx_t_3)); __pyx_t_3 = 0; - if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_4 = ((PyArrayObject *)__pyx_t_1); { __Pyx_BufFmt_StackElem __pyx_stack[1]; @@ -1539,16 +2216,16 @@ static PyObject *__pyx_pf_7sklearn_5_hmmc_2_forward(CYTHON_UNUSED PyObject *__py } } __pyx_pybuffernd_work_buffer.diminfo[0].strides = __pyx_pybuffernd_work_buffer.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_work_buffer.diminfo[0].shape = __pyx_pybuffernd_work_buffer.rcbuffer->pybuffer.shape[0]; - if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 32; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 44; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_t_4 = 0; __pyx_v_work_buffer = ((PyArrayObject *)__pyx_t_1); __pyx_t_1 = 0; - /* "sklearn/_hmmc.pyx":34 + /* "sklearn/_hmmc.pyx":46 * work_buffer = np.zeros(n_components) * - * for i in xrange(n_components): # <<<<<<<<<<<<<< + * for i in range(n_components): # <<<<<<<<<<<<<< * fwdlattice[0, i] = log_startprob[i] + framelogprob[0, i] * */ @@ -1556,12 +2233,12 @@ static PyObject *__pyx_pf_7sklearn_5_hmmc_2_forward(CYTHON_UNUSED PyObject *__py for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_5; __pyx_t_9+=1) { __pyx_v_i = __pyx_t_9; - /* "sklearn/_hmmc.pyx":35 + /* "sklearn/_hmmc.pyx":47 * - * for i in xrange(n_components): + * for i in range(n_components): * fwdlattice[0, i] = log_startprob[i] + framelogprob[0, i] # <<<<<<<<<<<<<< * - * for t in xrange(1, n_observations): + * for t in range(1, n_observations): */ __pyx_t_10 = __pyx_v_i; if (__pyx_t_10 < 0) __pyx_t_10 += __pyx_pybuffernd_log_startprob.diminfo[0].shape; @@ -1576,45 +2253,45 @@ static PyObject *__pyx_pf_7sklearn_5_hmmc_2_forward(CYTHON_UNUSED PyObject *__py *__Pyx_BufPtrStrided2d(__pyx_t_7sklearn_5_hmmc_dtype_t *, __pyx_pybuffernd_fwdlattice.rcbuffer->pybuffer.buf, __pyx_t_13, __pyx_pybuffernd_fwdlattice.diminfo[0].strides, __pyx_t_14, __pyx_pybuffernd_fwdlattice.diminfo[1].strides) = ((*__Pyx_BufPtrStrided1d(__pyx_t_7sklearn_5_hmmc_dtype_t *, __pyx_pybuffernd_log_startprob.rcbuffer->pybuffer.buf, __pyx_t_10, __pyx_pybuffernd_log_startprob.diminfo[0].strides)) + (*__Pyx_BufPtrStrided2d(__pyx_t_7sklearn_5_hmmc_dtype_t *, 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__pyx_pybuffernd_log_transmat.diminfo[1].strides))); } - /* "sklearn/_hmmc.pyx":41 - * for i in xrange(n_components): - * work_buffer[i] = fwdlattice[t - 1, i] + log_transmat[i, j] - * fwdlattice[t, j] = _logsum(n_components, work_buffer) \ # <<<<<<<<<<<<<< - * + framelogprob[t, j] - * - */ - __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s___logsum); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); - __pyx_t_3 = PyInt_FromLong(__pyx_v_n_components); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_3); - __pyx_t_2 = PyTuple_New(2); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 41; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - PyTuple_SET_ITEM(__pyx_t_2, 0, __pyx_t_3); - __Pyx_GIVEREF(__pyx_t_3); - __Pyx_INCREF(((PyObject 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{__pyx_filename = __pyx_f[0]; __pyx_lineno = 53; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_17 = __pyx_v_t; __pyx_t_18 = __pyx_v_j; if (__pyx_t_17 < 0) __pyx_t_17 += __pyx_pybuffernd_framelogprob.diminfo[0].shape; if (__pyx_t_18 < 0) __pyx_t_18 += __pyx_pybuffernd_framelogprob.diminfo[1].shape; - __pyx_t_2 = PyFloat_FromDouble((*__Pyx_BufPtrStrided2d(__pyx_t_7sklearn_5_hmmc_dtype_t *, __pyx_pybuffernd_framelogprob.rcbuffer->pybuffer.buf, __pyx_t_17, __pyx_pybuffernd_framelogprob.diminfo[0].strides, __pyx_t_18, __pyx_pybuffernd_framelogprob.diminfo[1].strides))); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_2); - __pyx_t_1 = PyNumber_Add(__pyx_t_3, __pyx_t_2); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 42; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - __Pyx_GOTREF(__pyx_t_1); - __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __Pyx_DECREF(__pyx_t_2); 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*__Pyx_BufPtrStrided2d(__pyx_t_7sklearn_5_hmmc_dtype_t *, __pyx_pybuffernd_fwdlattice.rcbuffer->pybuffer.buf, __pyx_t_25, __pyx_pybuffernd_fwdlattice.diminfo[0].strides, __pyx_t_26, __pyx_pybuffernd_fwdlattice.diminfo[1].strides) = (__pyx_f_7sklearn_5_hmmc__logsum(__pyx_t_24, 0) + (*__Pyx_BufPtrStrided2d(__pyx_t_7sklearn_5_hmmc_dtype_t *, __pyx_pybuffernd_framelogprob.rcbuffer->pybuffer.buf, __pyx_t_17, __pyx_pybuffernd_framelogprob.diminfo[0].strides, __pyx_t_18, __pyx_pybuffernd_framelogprob.diminfo[1].strides))); + __PYX_XDEC_MEMVIEW(&__pyx_t_24, 1); } } @@ -1694,6 +2334,7 @@ static PyObject *__pyx_pf_7sklearn_5_hmmc_2_forward(CYTHON_UNUSED PyObject *__py __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); + __PYX_XDEC_MEMVIEW(&__pyx_t_24, 1); { PyObject *__pyx_type, *__pyx_value, *__pyx_tb; __Pyx_ErrFetch(&__pyx_type, &__pyx_value, &__pyx_tb); __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_framelogprob.rcbuffer->pybuffer); @@ -1755,31 +2396,31 @@ static PyObject *__pyx_pw_7sklearn_5_hmmc_5_backward(PyObject *__pyx_self, PyObj case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__n_components)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("_backward", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_backward", 1, 6, 6, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__log_startprob)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("_backward", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_backward", 1, 6, 6, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 3: if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__log_transmat)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("_backward", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_backward", 1, 6, 6, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 4: if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__framelogprob)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("_backward", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_backward", 1, 6, 6, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 5: if (likely((values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__bwdlattice)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("_backward", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_backward", 1, 6, 6, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_backward") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_backward") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 6) { goto __pyx_L5_argtuple_error; @@ -1791,8 +2432,8 @@ static PyObject *__pyx_pw_7sklearn_5_hmmc_5_backward(PyObject *__pyx_self, PyObj values[4] = PyTuple_GET_ITEM(__pyx_args, 4); values[5] = PyTuple_GET_ITEM(__pyx_args, 5); } - __pyx_v_n_observations = __Pyx_PyInt_AsInt(values[0]); if (unlikely((__pyx_v_n_observations == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_n_components = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_n_components == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_n_observations = __Pyx_PyInt_AsInt(values[0]); if (unlikely((__pyx_v_n_observations == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_n_components = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_n_components == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_log_startprob = ((PyArrayObject *)values[2]); __pyx_v_log_transmat = ((PyArrayObject *)values[3]); __pyx_v_framelogprob = ((PyArrayObject *)values[4]); @@ -1800,16 +2441,16 @@ static PyObject *__pyx_pw_7sklearn_5_hmmc_5_backward(PyObject *__pyx_self, PyObj } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("_backward", 1, 6, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_backward", 1, 6, 6, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("sklearn._hmmc._backward", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_log_startprob), __pyx_ptype_5numpy_ndarray, 1, "log_startprob", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 47; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_log_transmat), __pyx_ptype_5numpy_ndarray, 1, "log_transmat", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 48; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_framelogprob), __pyx_ptype_5numpy_ndarray, 1, "framelogprob", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 49; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_bwdlattice), __pyx_ptype_5numpy_ndarray, 1, "bwdlattice", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 50; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_log_startprob), __pyx_ptype_5numpy_ndarray, 1, "log_startprob", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 58; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_log_transmat), __pyx_ptype_5numpy_ndarray, 1, "log_transmat", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 59; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_framelogprob), __pyx_ptype_5numpy_ndarray, 1, "framelogprob", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 60; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_bwdlattice), __pyx_ptype_5numpy_ndarray, 1, "bwdlattice", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 61; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_7sklearn_5_hmmc_4_backward(__pyx_self, __pyx_v_n_observations, __pyx_v_n_components, __pyx_v_log_startprob, __pyx_v_log_transmat, __pyx_v_framelogprob, __pyx_v_bwdlattice); goto __pyx_L0; __pyx_L1_error:; @@ -1819,12 +2460,12 @@ static PyObject *__pyx_pw_7sklearn_5_hmmc_5_backward(PyObject *__pyx_self, PyObj return __pyx_r; } -/* "sklearn/_hmmc.pyx":46 +/* "sklearn/_hmmc.pyx":57 * * @cython.boundscheck(False) - * def _backward(int n_observations, int n_components, \ # <<<<<<<<<<<<<< - * np.ndarray[dtype_t, ndim=1] log_startprob, \ - * np.ndarray[dtype_t, ndim=2] log_transmat, \ + * def _backward(int n_observations, int n_components, # <<<<<<<<<<<<<< + * np.ndarray[dtype_t, ndim=1] log_startprob, + * np.ndarray[dtype_t, ndim=2] log_transmat, */ static PyObject *__pyx_pf_7sklearn_5_hmmc_4_backward(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_v_n_observations, int __pyx_v_n_components, CYTHON_UNUSED PyArrayObject *__pyx_v_log_startprob, PyArrayObject *__pyx_v_log_transmat, PyArrayObject *__pyx_v_framelogprob, PyArrayObject *__pyx_v_bwdlattice) { @@ -1865,7 +2506,7 @@ static PyObject *__pyx_pf_7sklearn_5_hmmc_4_backward(CYTHON_UNUSED PyObject *__p long __pyx_t_19; int __pyx_t_20; int __pyx_t_21; - __pyx_t_7sklearn_5_hmmc_dtype_t __pyx_t_22; + __Pyx_memviewslice __pyx_t_22 = { 0, 0, { 0 }, { 0 }, { 0 } }; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -1892,49 +2533,49 @@ static PyObject *__pyx_pf_7sklearn_5_hmmc_4_backward(CYTHON_UNUSED PyObject *__p __pyx_pybuffernd_bwdlattice.rcbuffer = &__pyx_pybuffer_bwdlattice; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_log_startprob.rcbuffer->pybuffer, (PyObject*)__pyx_v_log_startprob, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_5_hmmc_dtype_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_log_startprob.rcbuffer->pybuffer, (PyObject*)__pyx_v_log_startprob, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_5_hmmc_dtype_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_log_startprob.diminfo[0].strides = __pyx_pybuffernd_log_startprob.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_log_startprob.diminfo[0].shape = __pyx_pybuffernd_log_startprob.rcbuffer->pybuffer.shape[0]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_log_transmat.rcbuffer->pybuffer, (PyObject*)__pyx_v_log_transmat, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_5_hmmc_dtype_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 46; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_log_transmat.rcbuffer->pybuffer, (PyObject*)__pyx_v_log_transmat, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_5_hmmc_dtype_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 57; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_log_transmat.diminfo[0].strides = __pyx_pybuffernd_log_transmat.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_log_transmat.diminfo[0].shape = __pyx_pybuffernd_log_transmat.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_log_transmat.diminfo[1].strides = 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__pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (!(likely(((__pyx_t_1) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_1, __pyx_ptype_5numpy_ndarray))))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_t_4 = ((PyArrayObject *)__pyx_t_1); { __Pyx_BufFmt_StackElem __pyx_stack[1]; @@ -1950,16 +2591,16 @@ static PyObject *__pyx_pf_7sklearn_5_hmmc_4_backward(CYTHON_UNUSED PyObject *__p } } __pyx_pybuffernd_work_buffer.diminfo[0].strides = __pyx_pybuffernd_work_buffer.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_work_buffer.diminfo[0].shape = __pyx_pybuffernd_work_buffer.rcbuffer->pybuffer.shape[0]; - if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 55; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__pyx_t_5 < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 66; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_t_4 = 0; __pyx_v_work_buffer = 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__pyx_pybuffernd_bwdlattice.diminfo[1].strides) = __pyx_t_22; + *__Pyx_BufPtrStrided2d(__pyx_t_7sklearn_5_hmmc_dtype_t *, __pyx_pybuffernd_bwdlattice.rcbuffer->pybuffer.buf, __pyx_t_13, __pyx_pybuffernd_bwdlattice.diminfo[0].strides, __pyx_t_14, __pyx_pybuffernd_bwdlattice.diminfo[1].strides) = __pyx_f_7sklearn_5_hmmc__logsum(__pyx_t_22, 0); + __PYX_XDEC_MEMVIEW(&__pyx_t_22, 1); } } @@ -2092,6 +2718,7 @@ static PyObject *__pyx_pf_7sklearn_5_hmmc_4_backward(CYTHON_UNUSED PyObject *__p __Pyx_XDECREF(__pyx_t_1); __Pyx_XDECREF(__pyx_t_2); __Pyx_XDECREF(__pyx_t_3); + __PYX_XDEC_MEMVIEW(&__pyx_t_22, 1); { PyObject *__pyx_type, *__pyx_value, *__pyx_tb; __Pyx_ErrFetch(&__pyx_type, &__pyx_value, &__pyx_tb); __Pyx_SafeReleaseBuffer(&__pyx_pybuffernd_bwdlattice.rcbuffer->pybuffer); @@ -2157,41 +2784,41 @@ static PyObject *__pyx_pw_7sklearn_5_hmmc_7_compute_lneta(PyObject *__pyx_self, case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__n_components)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("_compute_lneta", 1, 8, 8, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_compute_lneta", 1, 8, 8, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__fwdlattice)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("_compute_lneta", 1, 8, 8, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_compute_lneta", 1, 8, 8, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 3: if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__log_transmat)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("_compute_lneta", 1, 8, 8, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_compute_lneta", 1, 8, 8, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 4: if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__bwdlattice)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("_compute_lneta", 1, 8, 8, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_compute_lneta", 1, 8, 8, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 5: if (likely((values[5] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__framelogprob)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("_compute_lneta", 1, 8, 8, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_compute_lneta", 1, 8, 8, 5); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 6: if (likely((values[6] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__logprob)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("_compute_lneta", 1, 8, 8, 6); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_compute_lneta", 1, 8, 8, 6); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 7: if (likely((values[7] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__lneta)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("_compute_lneta", 1, 8, 8, 7); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_compute_lneta", 1, 8, 8, 7); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_compute_lneta") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_compute_lneta") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 8) { goto __pyx_L5_argtuple_error; @@ -2205,28 +2832,28 @@ static PyObject *__pyx_pw_7sklearn_5_hmmc_7_compute_lneta(PyObject *__pyx_self, values[6] = PyTuple_GET_ITEM(__pyx_args, 6); values[7] = PyTuple_GET_ITEM(__pyx_args, 7); } - __pyx_v_n_observations = __Pyx_PyInt_AsInt(values[0]); if (unlikely((__pyx_v_n_observations == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_n_components = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_n_components == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_n_observations = __Pyx_PyInt_AsInt(values[0]); if (unlikely((__pyx_v_n_observations == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_n_components = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_n_components == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_fwdlattice = ((PyArrayObject *)values[2]); __pyx_v_log_transmat = ((PyArrayObject *)values[3]); __pyx_v_bwdlattice = ((PyArrayObject *)values[4]); __pyx_v_framelogprob = ((PyArrayObject *)values[5]); - __pyx_v_logprob = __pyx_PyFloat_AsDouble(values[6]); if (unlikely((__pyx_v_logprob == (double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 74; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_logprob = __pyx_PyFloat_AsDouble(values[6]); if (unlikely((__pyx_v_logprob == (double)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 85; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_lneta = ((PyArrayObject *)values[7]); } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("_compute_lneta", 1, 8, 8, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_compute_lneta", 1, 8, 8, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("sklearn._hmmc._compute_lneta", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_fwdlattice), __pyx_ptype_5numpy_ndarray, 1, "fwdlattice", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 70; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_log_transmat), __pyx_ptype_5numpy_ndarray, 1, "log_transmat", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 71; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_bwdlattice), __pyx_ptype_5numpy_ndarray, 1, "bwdlattice", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 72; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_framelogprob), __pyx_ptype_5numpy_ndarray, 1, "framelogprob", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 73; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_lneta), __pyx_ptype_5numpy_ndarray, 1, "lneta", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 75; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_fwdlattice), __pyx_ptype_5numpy_ndarray, 1, "fwdlattice", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 81; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_log_transmat), __pyx_ptype_5numpy_ndarray, 1, "log_transmat", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 82; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_bwdlattice), __pyx_ptype_5numpy_ndarray, 1, "bwdlattice", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 83; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_framelogprob), __pyx_ptype_5numpy_ndarray, 1, "framelogprob", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_lneta), __pyx_ptype_5numpy_ndarray, 1, "lneta", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_7sklearn_5_hmmc_6_compute_lneta(__pyx_self, __pyx_v_n_observations, __pyx_v_n_components, __pyx_v_fwdlattice, __pyx_v_log_transmat, __pyx_v_bwdlattice, __pyx_v_framelogprob, __pyx_v_logprob, __pyx_v_lneta); goto __pyx_L0; __pyx_L1_error:; @@ -2236,12 +2863,12 @@ static PyObject *__pyx_pw_7sklearn_5_hmmc_7_compute_lneta(PyObject *__pyx_self, return __pyx_r; } -/* "sklearn/_hmmc.pyx":69 +/* "sklearn/_hmmc.pyx":80 * * @cython.boundscheck(False) - * def _compute_lneta(int n_observations, int n_components, \ # <<<<<<<<<<<<<< - * np.ndarray[dtype_t, ndim=2] fwdlattice, \ - * np.ndarray[dtype_t, ndim=2] log_transmat, \ + * def _compute_lneta(int n_observations, int n_components, # <<<<<<<<<<<<<< + * np.ndarray[dtype_t, ndim=2] fwdlattice, + * np.ndarray[dtype_t, ndim=2] log_transmat, */ static PyObject *__pyx_pf_7sklearn_5_hmmc_6_compute_lneta(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_v_n_observations, int __pyx_v_n_components, PyArrayObject *__pyx_v_fwdlattice, PyArrayObject *__pyx_v_log_transmat, PyArrayObject *__pyx_v_bwdlattice, PyArrayObject *__pyx_v_framelogprob, double __pyx_v_logprob, PyArrayObject *__pyx_v_lneta) { @@ -2303,56 +2930,56 @@ static PyObject *__pyx_pf_7sklearn_5_hmmc_6_compute_lneta(CYTHON_UNUSED PyObject __pyx_pybuffernd_lneta.rcbuffer = &__pyx_pybuffer_lneta; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_fwdlattice.rcbuffer->pybuffer, (PyObject*)__pyx_v_fwdlattice, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_5_hmmc_dtype_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_fwdlattice.rcbuffer->pybuffer, (PyObject*)__pyx_v_fwdlattice, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_5_hmmc_dtype_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_fwdlattice.diminfo[0].strides = __pyx_pybuffernd_fwdlattice.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_fwdlattice.diminfo[0].shape = __pyx_pybuffernd_fwdlattice.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_fwdlattice.diminfo[1].strides = __pyx_pybuffernd_fwdlattice.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_fwdlattice.diminfo[1].shape = __pyx_pybuffernd_fwdlattice.rcbuffer->pybuffer.shape[1]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_log_transmat.rcbuffer->pybuffer, (PyObject*)__pyx_v_log_transmat, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_5_hmmc_dtype_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_log_transmat.rcbuffer->pybuffer, (PyObject*)__pyx_v_log_transmat, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_5_hmmc_dtype_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_log_transmat.diminfo[0].strides = __pyx_pybuffernd_log_transmat.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_log_transmat.diminfo[0].shape = __pyx_pybuffernd_log_transmat.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_log_transmat.diminfo[1].strides = __pyx_pybuffernd_log_transmat.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_log_transmat.diminfo[1].shape = __pyx_pybuffernd_log_transmat.rcbuffer->pybuffer.shape[1]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_bwdlattice.rcbuffer->pybuffer, (PyObject*)__pyx_v_bwdlattice, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_5_hmmc_dtype_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_bwdlattice.rcbuffer->pybuffer, (PyObject*)__pyx_v_bwdlattice, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_5_hmmc_dtype_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_bwdlattice.diminfo[0].strides = __pyx_pybuffernd_bwdlattice.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_bwdlattice.diminfo[0].shape = __pyx_pybuffernd_bwdlattice.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_bwdlattice.diminfo[1].strides = __pyx_pybuffernd_bwdlattice.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_bwdlattice.diminfo[1].shape = __pyx_pybuffernd_bwdlattice.rcbuffer->pybuffer.shape[1]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_framelogprob.rcbuffer->pybuffer, (PyObject*)__pyx_v_framelogprob, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_5_hmmc_dtype_t, 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(unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_lneta.rcbuffer->pybuffer, (PyObject*)__pyx_v_lneta, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_5_hmmc_dtype_t, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 3, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 69; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_lneta.rcbuffer->pybuffer, (PyObject*)__pyx_v_lneta, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_5_hmmc_dtype_t, PyBUF_FORMAT| PyBUF_STRIDES| PyBUF_WRITABLE, 3, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 80; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_lneta.diminfo[0].strides = __pyx_pybuffernd_lneta.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_lneta.diminfo[0].shape = __pyx_pybuffernd_lneta.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_lneta.diminfo[1].strides = __pyx_pybuffernd_lneta.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_lneta.diminfo[1].shape = __pyx_pybuffernd_lneta.rcbuffer->pybuffer.shape[1]; __pyx_pybuffernd_lneta.diminfo[2].strides = __pyx_pybuffernd_lneta.rcbuffer->pybuffer.strides[2]; __pyx_pybuffernd_lneta.diminfo[2].shape = __pyx_pybuffernd_lneta.rcbuffer->pybuffer.shape[2]; - /* "sklearn/_hmmc.pyx":78 + /* "sklearn/_hmmc.pyx":89 * * cdef int i, j, t - * for t in xrange(n_observations - 1): # <<<<<<<<<<<<<< - * for i in xrange(n_components): - * for j in xrange(n_components): + * for t in range(n_observations - 1): # <<<<<<<<<<<<<< + * for i in range(n_components): + * for j in range(n_components): */ __pyx_t_1 = (__pyx_v_n_observations - 1); for (__pyx_t_2 = 0; __pyx_t_2 < __pyx_t_1; __pyx_t_2+=1) { __pyx_v_t = __pyx_t_2; - /* "sklearn/_hmmc.pyx":79 + /* "sklearn/_hmmc.pyx":90 * cdef int i, j, t - * for t in xrange(n_observations - 1): - * for i in xrange(n_components): # <<<<<<<<<<<<<< - * for j in xrange(n_components): + * for t in range(n_observations - 1): + * for i in range(n_components): # <<<<<<<<<<<<<< + * for j in range(n_components): * lneta[t, i, j] = fwdlattice[t, i] + log_transmat[i, j] \ */ __pyx_t_3 = __pyx_v_n_components; for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) { __pyx_v_i = __pyx_t_4; - /* "sklearn/_hmmc.pyx":80 - * for t in xrange(n_observations - 1): - * for i in xrange(n_components): - * for j in xrange(n_components): # <<<<<<<<<<<<<< + /* "sklearn/_hmmc.pyx":91 + * for t in range(n_observations - 1): + * for i in range(n_components): + * for j in range(n_components): # <<<<<<<<<<<<<< * lneta[t, i, j] = fwdlattice[t, i] + log_transmat[i, j] \ * + framelogprob[t + 1, j] + bwdlattice[t + 1, j] - logprob */ @@ -2360,9 +2987,9 @@ static PyObject *__pyx_pf_7sklearn_5_hmmc_6_compute_lneta(CYTHON_UNUSED PyObject for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { __pyx_v_j = __pyx_t_6; - /* "sklearn/_hmmc.pyx":81 - * for i in xrange(n_components): - * for j in xrange(n_components): + /* "sklearn/_hmmc.pyx":92 + * for i in range(n_components): + * for j in range(n_components): * lneta[t, i, j] = fwdlattice[t, i] + log_transmat[i, j] \ # <<<<<<<<<<<<<< * + framelogprob[t + 1, j] + bwdlattice[t + 1, j] - logprob * @@ -2376,8 +3003,8 @@ static PyObject *__pyx_pf_7sklearn_5_hmmc_6_compute_lneta(CYTHON_UNUSED PyObject if (__pyx_t_9 < 0) __pyx_t_9 += __pyx_pybuffernd_log_transmat.diminfo[0].shape; if (__pyx_t_10 < 0) __pyx_t_10 += __pyx_pybuffernd_log_transmat.diminfo[1].shape; - /* "sklearn/_hmmc.pyx":82 - * for j in xrange(n_components): + /* "sklearn/_hmmc.pyx":93 + * for j in range(n_components): * lneta[t, i, j] = fwdlattice[t, i] + log_transmat[i, j] \ * + framelogprob[t + 1, j] + bwdlattice[t + 1, j] - logprob # <<<<<<<<<<<<<< * @@ -2392,9 +3019,9 @@ static PyObject *__pyx_pf_7sklearn_5_hmmc_6_compute_lneta(CYTHON_UNUSED PyObject if (__pyx_t_13 < 0) __pyx_t_13 += __pyx_pybuffernd_bwdlattice.diminfo[0].shape; if (__pyx_t_14 < 0) __pyx_t_14 += __pyx_pybuffernd_bwdlattice.diminfo[1].shape; - /* "sklearn/_hmmc.pyx":81 - * for i in xrange(n_components): - * for j in xrange(n_components): + /* "sklearn/_hmmc.pyx":92 + * for i in range(n_components): + * for j in range(n_components): * lneta[t, i, j] = fwdlattice[t, i] + log_transmat[i, j] \ # <<<<<<<<<<<<<< * + framelogprob[t + 1, j] + bwdlattice[t + 1, j] - logprob * @@ -2471,26 +3098,26 @@ static PyObject *__pyx_pw_7sklearn_5_hmmc_9_viterbi(PyObject *__pyx_self, PyObje case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__n_components)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("_viterbi", 1, 5, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_viterbi", 1, 5, 5, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 137; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 2: if (likely((values[2] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__log_startprob)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("_viterbi", 1, 5, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_viterbi", 1, 5, 5, 2); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 137; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 3: if (likely((values[3] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__log_transmat)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("_viterbi", 1, 5, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_viterbi", 1, 5, 5, 3); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 137; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } case 4: if (likely((values[4] = PyDict_GetItem(__pyx_kwds, __pyx_n_s__framelogprob)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("_viterbi", 1, 5, 5, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_viterbi", 1, 5, 5, 4); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 137; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_viterbi") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "_viterbi") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 137; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 5) { goto __pyx_L5_argtuple_error; @@ -2501,23 +3128,23 @@ static PyObject *__pyx_pw_7sklearn_5_hmmc_9_viterbi(PyObject *__pyx_self, PyObje values[3] = PyTuple_GET_ITEM(__pyx_args, 3); values[4] = PyTuple_GET_ITEM(__pyx_args, 4); } - __pyx_v_n_observations = __Pyx_PyInt_AsInt(values[0]); if (unlikely((__pyx_v_n_observations == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L3_error;} - __pyx_v_n_components = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_n_components == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_n_observations = __Pyx_PyInt_AsInt(values[0]); if (unlikely((__pyx_v_n_observations == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 137; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __pyx_v_n_components = __Pyx_PyInt_AsInt(values[1]); if (unlikely((__pyx_v_n_components == (int)-1) && PyErr_Occurred())) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 137; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_v_log_startprob = ((PyArrayObject *)values[2]); __pyx_v_log_transmat = ((PyArrayObject *)values[3]); __pyx_v_framelogprob = ((PyArrayObject *)values[4]); } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("_viterbi", 1, 5, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L3_error;} + __Pyx_RaiseArgtupleInvalid("_viterbi", 1, 5, 5, PyTuple_GET_SIZE(__pyx_args)); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 137; __pyx_clineno = __LINE__; goto __pyx_L3_error;} __pyx_L3_error:; __Pyx_AddTraceback("sklearn._hmmc._viterbi", __pyx_clineno, __pyx_lineno, __pyx_filename); __Pyx_RefNannyFinishContext(); return NULL; __pyx_L4_argument_unpacking_done:; - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_log_startprob), __pyx_ptype_5numpy_ndarray, 1, "log_startprob", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 87; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_log_transmat), __pyx_ptype_5numpy_ndarray, 1, "log_transmat", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} - if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_framelogprob), __pyx_ptype_5numpy_ndarray, 1, "framelogprob", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 89; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_log_startprob), __pyx_ptype_5numpy_ndarray, 1, "log_startprob", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 138; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_log_transmat), __pyx_ptype_5numpy_ndarray, 1, "log_transmat", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 139; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(!__Pyx_ArgTypeTest(((PyObject *)__pyx_v_framelogprob), __pyx_ptype_5numpy_ndarray, 1, "framelogprob", 0))) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 140; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __pyx_r = __pyx_pf_7sklearn_5_hmmc_8_viterbi(__pyx_self, __pyx_v_n_observations, __pyx_v_n_components, __pyx_v_log_startprob, __pyx_v_log_transmat, __pyx_v_framelogprob); goto __pyx_L0; __pyx_L1_error:; @@ -2527,22 +3154,20 @@ static PyObject *__pyx_pw_7sklearn_5_hmmc_9_viterbi(PyObject *__pyx_self, PyObje return __pyx_r; } -/* "sklearn/_hmmc.pyx":86 +/* "sklearn/_hmmc.pyx":137 * * @cython.boundscheck(False) - * def _viterbi(int n_observations, int n_components, \ # <<<<<<<<<<<<<< - * np.ndarray[dtype_t, ndim=1] log_startprob, \ - * np.ndarray[dtype_t, ndim=2] log_transmat, \ + * def _viterbi(int n_observations, int n_components, # <<<<<<<<<<<<<< + * np.ndarray[dtype_t, ndim=1] log_startprob, + * np.ndarray[dtype_t, ndim=2] log_transmat, */ static PyObject *__pyx_pf_7sklearn_5_hmmc_8_viterbi(CYTHON_UNUSED PyObject *__pyx_self, int __pyx_v_n_observations, int __pyx_v_n_components, PyArrayObject *__pyx_v_log_startprob, PyArrayObject *__pyx_v_log_transmat, PyArrayObject *__pyx_v_framelogprob) { - int __pyx_v_i; - int __pyx_v_j; int __pyx_v_t; int __pyx_v_max_pos; PyArrayObject *__pyx_v_viterbi_lattice = 0; PyArrayObject *__pyx_v_state_sequence = 0; - double __pyx_v_logprob; + __pyx_t_7sklearn_5_hmmc_dtype_t __pyx_v_logprob; PyArrayObject *__pyx_v_work_buffer = 0; __Pyx_LocalBuf_ND __pyx_pybuffernd_framelogprob; __Pyx_Buffer __pyx_pybuffer_framelogprob; @@ -2569,23 +3194,12 @@ static PyObject *__pyx_pf_7sklearn_5_hmmc_8_viterbi(CYTHON_UNUSED PyObject *__py PyObject *__pyx_t_9 = NULL; PyObject *__pyx_t_10 = NULL; PyArrayObject *__pyx_t_11 = NULL; - PyArrayObject *__pyx_t_12 = NULL; - int __pyx_t_13; - int __pyx_t_14; - long __pyx_t_15; - int __pyx_t_16; + int __pyx_t_12; + long __pyx_t_13; + PyArrayObject *__pyx_t_14 = NULL; + int __pyx_t_15; + long __pyx_t_16; long __pyx_t_17; - int __pyx_t_18; - int __pyx_t_19; - int __pyx_t_20; - int __pyx_t_21; - int __pyx_t_22; - __pyx_t_7sklearn_5_hmmc_dtype_t __pyx_t_23; - int __pyx_t_24; - int __pyx_t_25; - long __pyx_t_26; - long __pyx_t_27; - long __pyx_t_28; int __pyx_lineno = 0; const char *__pyx_filename = NULL; int __pyx_clineno = 0; @@ -2616,54 +3230,54 @@ static PyObject *__pyx_pf_7sklearn_5_hmmc_8_viterbi(CYTHON_UNUSED PyObject *__py __pyx_pybuffernd_framelogprob.rcbuffer = &__pyx_pybuffer_framelogprob; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_log_startprob.rcbuffer->pybuffer, (PyObject*)__pyx_v_log_startprob, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_5_hmmc_dtype_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_log_startprob.rcbuffer->pybuffer, (PyObject*)__pyx_v_log_startprob, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_5_hmmc_dtype_t, PyBUF_FORMAT| PyBUF_STRIDES, 1, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 137; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_log_startprob.diminfo[0].strides = __pyx_pybuffernd_log_startprob.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_log_startprob.diminfo[0].shape = __pyx_pybuffernd_log_startprob.rcbuffer->pybuffer.shape[0]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_log_transmat.rcbuffer->pybuffer, (PyObject*)__pyx_v_log_transmat, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_5_hmmc_dtype_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_log_transmat.rcbuffer->pybuffer, (PyObject*)__pyx_v_log_transmat, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_5_hmmc_dtype_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 137; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_log_transmat.diminfo[0].strides = __pyx_pybuffernd_log_transmat.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_log_transmat.diminfo[0].shape = __pyx_pybuffernd_log_transmat.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_log_transmat.diminfo[1].strides = __pyx_pybuffernd_log_transmat.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_log_transmat.diminfo[1].shape = __pyx_pybuffernd_log_transmat.rcbuffer->pybuffer.shape[1]; { __Pyx_BufFmt_StackElem __pyx_stack[1]; - if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_framelogprob.rcbuffer->pybuffer, (PyObject*)__pyx_v_framelogprob, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_5_hmmc_dtype_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (unlikely(__Pyx_GetBufferAndValidate(&__pyx_pybuffernd_framelogprob.rcbuffer->pybuffer, (PyObject*)__pyx_v_framelogprob, &__Pyx_TypeInfo_nn___pyx_t_7sklearn_5_hmmc_dtype_t, PyBUF_FORMAT| PyBUF_STRIDES, 2, 0, __pyx_stack) == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 137; __pyx_clineno = __LINE__; goto __pyx_L1_error;} } __pyx_pybuffernd_framelogprob.diminfo[0].strides = __pyx_pybuffernd_framelogprob.rcbuffer->pybuffer.strides[0]; __pyx_pybuffernd_framelogprob.diminfo[0].shape = __pyx_pybuffernd_framelogprob.rcbuffer->pybuffer.shape[0]; __pyx_pybuffernd_framelogprob.diminfo[1].strides = __pyx_pybuffernd_framelogprob.rcbuffer->pybuffer.strides[1]; __pyx_pybuffernd_framelogprob.diminfo[1].shape = __pyx_pybuffernd_framelogprob.rcbuffer->pybuffer.shape[1]; - /* "sklearn/_hmmc.pyx":98 + /* "sklearn/_hmmc.pyx":149 * - * # Initialize state_sequenceation - * state_sequence = np.zeros(n_observations, dtype=np.int) # <<<<<<<<<<<<<< - * work_buffer = np.zeros(n_components) + * # Initialization + * state_sequence = np.empty(n_observations, dtype=np.int) # <<<<<<<<<<<<<< * viterbi_lattice = np.zeros((n_observations, n_components)) + * viterbi_lattice[0] = log_startprob + framelogprob[0] */ - __pyx_t_1 = __Pyx_GetName(__pyx_m, __pyx_n_s__np); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 98; 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goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_5); + if (!(likely(((__pyx_t_5) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_5, __pyx_memoryview_type))))) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 744; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_r = ((struct __pyx_memoryview_obj *)__pyx_t_5); + __pyx_t_5 = 0; + goto __pyx_L0; + } + __pyx_L7:; + + __pyx_r = ((struct __pyx_memoryview_obj *)Py_None); __Pyx_INCREF(Py_None); + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_5); + __Pyx_XDECREF(__pyx_t_8); + __Pyx_XDECREF(__pyx_t_11); + __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":769 + * + * @cname('__pyx_memoryview_slice_memviewslice') + * cdef int slice_memviewslice( # <<<<<<<<<<<<<< + * 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__pyx_v_dim); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 794; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + goto __pyx_L5; + } + __pyx_L5:; + goto __pyx_L3; + } + /*else*/ { + + /* "View.MemoryView":797 + * else: + * + * negative_step = have_step != 0 and step < 0 # <<<<<<<<<<<<<< + * + * if have_step and step == 0: + */ + __pyx_t_2 = (__pyx_v_have_step != 0); + if (__pyx_t_2) { + __pyx_t_1 = (__pyx_v_step < 0); + __pyx_t_4 = __pyx_t_1; + } else { + __pyx_t_4 = __pyx_t_2; + } + __pyx_v_negative_step = __pyx_t_4; + + /* "View.MemoryView":799 + * 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) + * + */ + if (__pyx_v_have_step) { + __pyx_t_4 = (__pyx_v_step == 0); + __pyx_t_2 = __pyx_t_4; + } else { + __pyx_t_2 = __pyx_v_have_step; + } + if (__pyx_t_2) { + + /* "View.MemoryView":800 + * + * 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_43, __pyx_v_dim); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 800; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + goto __pyx_L6; + } + __pyx_L6:; + + /* "View.MemoryView":803 + * + * + * if have_start: # <<<<<<<<<<<<<< + * if start < 0: + * start += shape + */ + if (__pyx_v_have_start) { + + /* "View.MemoryView":804 + * + * if have_start: + * if start < 0: # <<<<<<<<<<<<<< + * start += shape + * if start < 0: + */ + __pyx_t_2 = (__pyx_v_start < 0); + if (__pyx_t_2) { + + /* "View.MemoryView":805 + * if have_start: + * if start < 0: + * start += shape # <<<<<<<<<<<<<< + * if start < 0: + * start = 0 + */ + __pyx_v_start = (__pyx_v_start + __pyx_v_shape); + + /* "View.MemoryView":806 + * if start < 0: + * start += shape + * if start < 0: # <<<<<<<<<<<<<< + * start = 0 + * elif start >= shape: + */ + __pyx_t_2 = (__pyx_v_start < 0); + if (__pyx_t_2) { + + /* "View.MemoryView":807 + * start += shape + * if start < 0: + * start = 0 # <<<<<<<<<<<<<< + * elif start >= shape: + * if negative_step: + */ + __pyx_v_start = 0; + goto __pyx_L9; + } + __pyx_L9:; + goto __pyx_L8; + } + + /* "View.MemoryView":808 + * if start < 0: + * start = 0 + * elif start >= shape: # <<<<<<<<<<<<<< + * if negative_step: + * start = shape - 1 + */ + __pyx_t_2 = (__pyx_v_start >= __pyx_v_shape); + if (__pyx_t_2) { + + /* "View.MemoryView":809 + * start = 0 + * elif start >= shape: + * if negative_step: # <<<<<<<<<<<<<< + * start = shape - 1 + * else: + */ + if (__pyx_v_negative_step) { + + /* "View.MemoryView":810 + * elif start >= shape: + * if negative_step: + * start = shape - 1 # <<<<<<<<<<<<<< + * else: + * start = shape + */ + __pyx_v_start = (__pyx_v_shape - 1); + goto __pyx_L10; + } + /*else*/ { + + /* "View.MemoryView":812 + * start = shape - 1 + * else: + * start = shape # <<<<<<<<<<<<<< + * else: + * if negative_step: + */ + __pyx_v_start = __pyx_v_shape; + } + __pyx_L10:; + goto __pyx_L8; + } + __pyx_L8:; + goto __pyx_L7; + } + /*else*/ { + + /* "View.MemoryView":814 + * start = shape + * else: + * if negative_step: # <<<<<<<<<<<<<< + * start = shape - 1 + * else: + */ + if (__pyx_v_negative_step) { + + /* "View.MemoryView":815 + * else: + * if negative_step: + * start = shape - 1 # <<<<<<<<<<<<<< + * else: + * start = 0 + */ + __pyx_v_start = (__pyx_v_shape - 1); + goto __pyx_L11; + } + /*else*/ { + + /* "View.MemoryView":817 + * start = shape - 1 + * else: + * start = 0 # <<<<<<<<<<<<<< + * + * if have_stop: + */ + __pyx_v_start = 0; + } + __pyx_L11:; + } + __pyx_L7:; + + /* "View.MemoryView":819 + * start = 0 + * + * if have_stop: # <<<<<<<<<<<<<< + * if stop < 0: + * stop += shape + */ + if (__pyx_v_have_stop) { + + /* "View.MemoryView":820 + * + * if have_stop: + * if stop < 0: # <<<<<<<<<<<<<< + * stop += shape + * if stop < 0: + */ + __pyx_t_2 = (__pyx_v_stop < 0); + if (__pyx_t_2) { + + /* "View.MemoryView":821 + * if have_stop: + * if stop < 0: + * stop += shape # <<<<<<<<<<<<<< + * if stop < 0: + * stop = 0 + */ + __pyx_v_stop = (__pyx_v_stop + __pyx_v_shape); + + /* "View.MemoryView":822 + * if stop < 0: + * stop += shape + * if stop < 0: # <<<<<<<<<<<<<< + * stop = 0 + * elif stop > shape: + */ + __pyx_t_2 = (__pyx_v_stop < 0); + if (__pyx_t_2) { + + /* "View.MemoryView":823 + * stop += shape + * if stop < 0: + * stop = 0 # <<<<<<<<<<<<<< + * elif stop > shape: + * stop = shape + */ + __pyx_v_stop = 0; + goto __pyx_L14; + } + __pyx_L14:; + goto __pyx_L13; + } + + /* "View.MemoryView":824 + * if stop < 0: + * stop = 0 + * elif stop > shape: # <<<<<<<<<<<<<< + * stop = shape + * else: + */ + __pyx_t_2 = (__pyx_v_stop > __pyx_v_shape); + if (__pyx_t_2) { + + /* "View.MemoryView":825 + * stop = 0 + * elif stop > shape: + * stop = shape # <<<<<<<<<<<<<< + * else: + * if negative_step: + */ + __pyx_v_stop = __pyx_v_shape; + goto __pyx_L13; + } + __pyx_L13:; + goto __pyx_L12; + } + /*else*/ { + + /* "View.MemoryView":827 + * stop = shape + * else: + * if negative_step: # <<<<<<<<<<<<<< + * stop = -1 + * else: + */ + if (__pyx_v_negative_step) { + + /* "View.MemoryView":828 + * else: + * if negative_step: + * stop = -1 # <<<<<<<<<<<<<< + * else: + * stop = shape + */ + __pyx_v_stop = -1; + goto __pyx_L15; + } + /*else*/ { + + /* "View.MemoryView":830 + * stop = -1 + * else: + * stop = shape # <<<<<<<<<<<<<< + * + * if not have_step: + */ + __pyx_v_stop = __pyx_v_shape; + } + __pyx_L15:; + } + __pyx_L12:; + + /* "View.MemoryView":832 + * stop = shape + * + * if not have_step: # <<<<<<<<<<<<<< + * step = 1 + * + */ + __pyx_t_2 = (!__pyx_v_have_step); + if (__pyx_t_2) { + + /* "View.MemoryView":833 + * + * if not have_step: + * step = 1 # <<<<<<<<<<<<<< + * + * + */ + __pyx_v_step = 1; + goto __pyx_L16; + } + __pyx_L16:; + + /* "View.MemoryView":837 + * + * 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":839 + * new_shape = (stop - start) // step + * + * if (stop - start) - step * new_shape: # <<<<<<<<<<<<<< + * new_shape += 1 + * + */ + __pyx_t_5 = ((__pyx_v_stop - __pyx_v_start) - (__pyx_v_step * __pyx_v_new_shape)); + if (__pyx_t_5) { + + /* "View.MemoryView":840 + * + * if (stop - start) - step * new_shape: + * new_shape += 1 # <<<<<<<<<<<<<< + * + * if new_shape < 0: + */ + __pyx_v_new_shape = (__pyx_v_new_shape + 1); + goto __pyx_L17; + } + __pyx_L17:; + + /* "View.MemoryView":842 + * new_shape += 1 + * + * if new_shape < 0: # <<<<<<<<<<<<<< + * new_shape = 0 + * + */ + __pyx_t_2 = (__pyx_v_new_shape < 0); + if (__pyx_t_2) { + + /* "View.MemoryView":843 + * + * if new_shape < 0: + * new_shape = 0 # <<<<<<<<<<<<<< + * + * + */ + __pyx_v_new_shape = 0; + goto __pyx_L18; + } + __pyx_L18:; + + /* "View.MemoryView":846 + * + * + * 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":847 + * + * 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":848 + * 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":851 + * + * + * if suboffset_dim[0] < 0: # <<<<<<<<<<<<<< + * dst.data += start * stride + * else: + */ + __pyx_t_2 = ((__pyx_v_suboffset_dim[0]) < 0); + if (__pyx_t_2) { + + /* "View.MemoryView":852 + * + * 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_L19; + } + /*else*/ { + + /* "View.MemoryView":854 + * 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_L19:; + + /* "View.MemoryView":856 + * 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); + if (__pyx_t_2) { + + /* "View.MemoryView":857 + * + * if suboffset >= 0: + * if not is_slice: # <<<<<<<<<<<<<< + * if new_ndim == 0: + * dst.data = ( dst.data)[0] + suboffset + */ + __pyx_t_2 = (!__pyx_v_is_slice); + if (__pyx_t_2) { + + /* "View.MemoryView":858 + * 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); + if (__pyx_t_2) { + + /* "View.MemoryView":859 + * 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_L22; + } + /*else*/ { + + /* "View.MemoryView":862 + * 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_44, __pyx_v_dim); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 861; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + __pyx_L22:; + goto __pyx_L21; + } + /*else*/ { + + /* "View.MemoryView":864 + * "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_L21:; + goto __pyx_L20; + } + __pyx_L20:; + + /* "View.MemoryView":866 + * suboffset_dim[0] = new_ndim + * + * return 0 # <<<<<<<<<<<<<< + * + * + */ + __pyx_r = 0; + goto __pyx_L0; + + __pyx_r = 0; + goto __pyx_L0; + __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":872 + * + * @cname('__pyx_pybuffer_index') + * cdef char *pybuffer_index(Py_buffer *view, char *bufp, Py_ssize_t index, # <<<<<<<<<<<<<< + * int 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, int __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":874 + * cdef char *pybuffer_index(Py_buffer *view, char *bufp, Py_ssize_t index, + * int 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":875 + * int 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":878 + * cdef char *resultp + * + * if view.ndim == 0: # <<<<<<<<<<<<<< + * shape = view.len / itemsize + * stride = itemsize + */ + __pyx_t_2 = (__pyx_v_view->ndim == 0); + if (__pyx_t_2) { + + /* "View.MemoryView":879 + * + * if view.ndim == 0: + * shape = view.len / itemsize # <<<<<<<<<<<<<< + * stride = itemsize + * else: + */ + if (unlikely(__pyx_v_itemsize == 0)) { + PyErr_Format(PyExc_ZeroDivisionError, "integer division or modulo by zero"); + {__pyx_filename = __pyx_f[2]; __pyx_lineno = 879; __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))) { + PyErr_Format(PyExc_OverflowError, "value too large to perform division"); + {__pyx_filename = __pyx_f[2]; __pyx_lineno = 879; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + __pyx_v_shape = __Pyx_div_Py_ssize_t(__pyx_v_view->len, __pyx_v_itemsize); + + /* "View.MemoryView":880 + * 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":882 + * 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":883 + * 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":884 + * shape = view.shape[dim] + * stride = view.strides[dim] + * if view.suboffsets != NULL: # <<<<<<<<<<<<<< + * suboffset = view.suboffsets[dim] + * + */ + __pyx_t_2 = (__pyx_v_view->suboffsets != NULL); + if (__pyx_t_2) { + + /* "View.MemoryView":885 + * stride = view.strides[dim] + * if view.suboffsets != NULL: + * suboffset = view.suboffsets[dim] # <<<<<<<<<<<<<< + * + * if index < 0: + */ + __pyx_v_suboffset = (__pyx_v_view->suboffsets[__pyx_v_dim]); + goto __pyx_L4; + } + __pyx_L4:; + } + __pyx_L3:; + + /* "View.MemoryView":887 + * suboffset = view.suboffsets[dim] + * + * if index < 0: # <<<<<<<<<<<<<< + * index += view.shape[dim] + * if index < 0: + */ + __pyx_t_2 = (__pyx_v_index < 0); + if (__pyx_t_2) { + + /* "View.MemoryView":888 + * + * if index < 0: + * index += view.shape[dim] # <<<<<<<<<<<<<< + * if index < 0: + * raise IndexError("Out of bounds on buffer access (axis %d)" % dim) + */ + __pyx_v_index = (__pyx_v_index + (__pyx_v_view->shape[__pyx_v_dim])); + + /* "View.MemoryView":889 + * if index < 0: + * index += view.shape[dim] 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to_dtype_func, + * memview.dtype_is_object) + */ + __Pyx_XDECREF(__pyx_r); + + /* "View.MemoryView":1061 + * return memoryview_fromslice(memviewslice[0], memview.view.ndim, + * to_object_func, to_dtype_func, + * memview.dtype_is_object) # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_4 = __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_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1059; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_4); + __pyx_r = __pyx_t_4; + __pyx_t_4 = 0; + goto __pyx_L0; + + __pyx_r = Py_None; __Pyx_INCREF(Py_None); + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_4); + __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":1067 + * + * + * 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":1068 + * + * 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); + if (__pyx_t_1) { + + /* "View.MemoryView":1069 + * 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; + goto __pyx_L3; + } + /*else*/ { + + /* "View.MemoryView":1071 + * return -arg + * else: + * return arg # <<<<<<<<<<<<<< + * + * @cname('__pyx_get_best_slice_order') + */ + __pyx_r = __pyx_v_arg; + goto __pyx_L0; + } + __pyx_L3:; + + __pyx_r = 0; + __pyx_L0:; + return __pyx_r; +} + +/* "View.MemoryView":1074 + * + * @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":1079 + * """ + * cdef int i + * cdef Py_ssize_t c_stride = 0 # <<<<<<<<<<<<<< + * cdef Py_ssize_t f_stride = 0 + * + */ + __pyx_v_c_stride = 0; + + /* "View.MemoryView":1080 + * 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":1082 + * 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":1083 + * + * 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); + if (__pyx_t_2) { + + /* "View.MemoryView":1084 + * 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":1085 + * if mslice.shape[i] > 1: + * c_stride = mslice.strides[i] + * break # <<<<<<<<<<<<<< + * + * for i in range(ndim): + */ + goto __pyx_L4_break; + goto __pyx_L5; + } + __pyx_L5:; + } + __pyx_L4_break:; + + /* "View.MemoryView":1087 + * 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":1088 + * + * 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); + if (__pyx_t_2) { + + /* "View.MemoryView":1089 + * 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":1090 + * 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; + goto __pyx_L8; + } + __pyx_L8:; + } + __pyx_L7_break:; + + /* "View.MemoryView":1092 + * 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)); + if (__pyx_t_2) { + + /* "View.MemoryView":1093 + * + * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): + * return 'C' # <<<<<<<<<<<<<< + * else: + * return 'F' + */ + __pyx_r = 'C'; + goto __pyx_L0; + goto __pyx_L9; + } + /*else*/ { + + /* "View.MemoryView":1095 + * return 'C' + * else: + * return 'F' # <<<<<<<<<<<<<< + * + * @cython.cdivision(True) + */ + __pyx_r = 'F'; + goto __pyx_L0; + } + __pyx_L9:; + + __pyx_r = 0; + __pyx_L0:; + return __pyx_r; +} + +/* "View.MemoryView":1098 + * + * @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; + int __pyx_t_4; + Py_ssize_t __pyx_t_5; + Py_ssize_t __pyx_t_6; + + /* "View.MemoryView":1105 + * + * 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":1106 + * 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":1107 + * 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":1108 + * 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":1110 + * 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); + if (__pyx_t_1) { + + /* "View.MemoryView":1111 + * + * 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_1 = (__pyx_v_src_stride > 0); + if (__pyx_t_1) { + __pyx_t_2 = (__pyx_v_dst_stride > 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1112 + * 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_3 = (((size_t)__pyx_v_src_stride) == __pyx_v_itemsize); + if (__pyx_t_3) { + __pyx_t_3 = (__pyx_v_itemsize == ((size_t)__pyx_v_dst_stride)); + } + __pyx_t_4 = __pyx_t_3; + } else { + __pyx_t_4 = __pyx_t_2; + } + __pyx_t_2 = __pyx_t_4; + } else { + __pyx_t_2 = __pyx_t_1; + } + if (__pyx_t_2) { + + /* "View.MemoryView":1113 + * 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":1115 + * 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_5 = __pyx_v_dst_extent; + for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { + __pyx_v_i = __pyx_t_6; + + /* "View.MemoryView":1116 + * 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":1117 + * 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":1118 + * 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":1120 + * 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_5 = __pyx_v_dst_extent; + for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { + __pyx_v_i = __pyx_t_6; + + /* "View.MemoryView":1124 + * dst_data, dst_strides + 1, + * src_shape + 1, dst_shape + 1, + * ndim - 1, itemsize) # <<<<<<<<<<<<<< + * src_data += src_stride + * dst_data += dst_stride + */ + _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":1125 + * 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":1126 + * 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":1128 + * 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":1132 + * int ndim, size_t itemsize) nogil: + * _copy_strided_to_strided(src.data, src.strides, dst.data, dst.strides, + * src.shape, dst.shape, ndim, itemsize) # <<<<<<<<<<<<<< + * + * @cname('__pyx_memoryview_slice_get_size') + */ + _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":1135 + * + * @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":1138 + * "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":1140 + * 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":1141 + * + * 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":1143 + * size *= src.shape[i] + * + * return size # <<<<<<<<<<<<<< + * + * @cname('__pyx_fill_contig_strides_array') + */ + __pyx_r = __pyx_v_size; + goto __pyx_L0; + + __pyx_r = 0; + __pyx_L0:; + return __pyx_r; +} + +/* "View.MemoryView":1146 + * + * @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 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@cname('__pyx_memoryview_copy_contents') + */ + __Pyx_Raise(__pyx_v_error, 0, 0, 0); + {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1224; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + __pyx_L3:; + + __pyx_r = 0; + goto __pyx_L0; + __pyx_L1_error:; + __Pyx_XDECREF(__pyx_t_2); + __Pyx_XDECREF(__pyx_t_3); + __Pyx_AddTraceback("View.MemoryView._err", __pyx_clineno, __pyx_lineno, __pyx_filename); + __pyx_r = -1; + __pyx_L0:; + __Pyx_XDECREF(__pyx_v_error); + __Pyx_RefNannyFinishContext(); + #ifdef WITH_THREAD + PyGILState_Release(__pyx_gilstate_save); + #endif + return __pyx_r; +} + +/* "View.MemoryView":1227 + * + * @cname('__pyx_memoryview_copy_contents') + * cdef int memoryview_copy_contents(__Pyx_memviewslice src, # <<<<<<<<<<<<<< + * __Pyx_memviewslice dst, + * int src_ndim, int dst_ndim, + */ + +static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_memviewslice __pyx_v_dst, int __pyx_v_src_ndim, int __pyx_v_dst_ndim, int __pyx_v_dtype_is_object) { + void *__pyx_v_tmpdata; + size_t __pyx_v_itemsize; + int __pyx_v_i; + char __pyx_v_order; + int __pyx_v_broadcasting; + int __pyx_v_direct_copy; + __Pyx_memviewslice __pyx_v_tmp; + int __pyx_v_ndim; + int __pyx_r; + Py_ssize_t __pyx_t_1; + int __pyx_t_2; + int __pyx_t_3; + int __pyx_t_4; + int __pyx_t_5; + void *__pyx_t_6; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; + + /* "View.MemoryView":1235 + * Check for overlapping memory and verify the shapes. + * """ + * cdef void *tmpdata = NULL # <<<<<<<<<<<<<< + * cdef size_t itemsize = src.memview.view.itemsize + * cdef int i + */ + __pyx_v_tmpdata = NULL; + + /* "View.MemoryView":1236 + * """ + * cdef void *tmpdata = NULL + * cdef size_t itemsize = src.memview.view.itemsize # <<<<<<<<<<<<<< + * cdef int i + * cdef char order = get_best_order(&src, src_ndim) + */ + __pyx_t_1 = __pyx_v_src.memview->view.itemsize; + __pyx_v_itemsize = __pyx_t_1; + + /* "View.MemoryView":1238 + * cdef size_t itemsize = src.memview.view.itemsize + * cdef int i + * cdef char order = get_best_order(&src, src_ndim) # <<<<<<<<<<<<<< + * cdef bint broadcasting = False + * cdef bint direct_copy = False + */ + __pyx_v_order = __pyx_get_best_slice_order((&__pyx_v_src), __pyx_v_src_ndim); + + /* "View.MemoryView":1239 + * cdef int i + * cdef char order = get_best_order(&src, src_ndim) + * cdef bint broadcasting = False # <<<<<<<<<<<<<< + * cdef bint direct_copy = False + * cdef __Pyx_memviewslice tmp + */ + __pyx_v_broadcasting = 0; + + /* "View.MemoryView":1240 + * cdef char order = get_best_order(&src, src_ndim) + * cdef bint broadcasting = False + * cdef bint direct_copy = False # <<<<<<<<<<<<<< + * cdef __Pyx_memviewslice tmp + * + */ + __pyx_v_direct_copy = 0; + + /* "View.MemoryView":1243 + * cdef __Pyx_memviewslice tmp + * + * if src_ndim < dst_ndim: # <<<<<<<<<<<<<< + * broadcast_leading(&src, src_ndim, dst_ndim) + * elif dst_ndim < src_ndim: + */ + __pyx_t_2 = (__pyx_v_src_ndim < __pyx_v_dst_ndim); + if (__pyx_t_2) { + + /* "View.MemoryView":1244 + * + * if src_ndim < dst_ndim: + * broadcast_leading(&src, src_ndim, dst_ndim) # <<<<<<<<<<<<<< + * elif dst_ndim < src_ndim: + * broadcast_leading(&dst, dst_ndim, src_ndim) + */ + __pyx_memoryview_broadcast_leading((&__pyx_v_src), __pyx_v_src_ndim, __pyx_v_dst_ndim); + goto __pyx_L3; + } + + /* "View.MemoryView":1245 + * if src_ndim < dst_ndim: + * broadcast_leading(&src, src_ndim, dst_ndim) + * elif dst_ndim < src_ndim: # <<<<<<<<<<<<<< + * broadcast_leading(&dst, dst_ndim, src_ndim) + * + */ + __pyx_t_2 = (__pyx_v_dst_ndim < __pyx_v_src_ndim); + if (__pyx_t_2) { + + /* "View.MemoryView":1246 + * broadcast_leading(&src, src_ndim, dst_ndim) + * elif dst_ndim < src_ndim: + * broadcast_leading(&dst, dst_ndim, src_ndim) # <<<<<<<<<<<<<< + * + * cdef int ndim = max(src_ndim, dst_ndim) + */ + __pyx_memoryview_broadcast_leading((&__pyx_v_dst), __pyx_v_dst_ndim, __pyx_v_src_ndim); + goto __pyx_L3; + } + __pyx_L3:; + + /* "View.MemoryView":1248 + * broadcast_leading(&dst, dst_ndim, src_ndim) + * + * cdef int ndim = max(src_ndim, dst_ndim) # <<<<<<<<<<<<<< + * + * for i in range(ndim): + */ + __pyx_t_3 = __pyx_v_dst_ndim; + __pyx_t_4 = __pyx_v_src_ndim; + if ((__pyx_t_3 > __pyx_t_4)) { + __pyx_t_5 = __pyx_t_3; + } else { + __pyx_t_5 = __pyx_t_4; + } + __pyx_v_ndim = __pyx_t_5; + + /* "View.MemoryView":1250 + * cdef int ndim = max(src_ndim, dst_ndim) + * + * for i in range(ndim): # <<<<<<<<<<<<<< + * if src.shape[i] != dst.shape[i]: + * if src.shape[i] == 1: + */ + __pyx_t_5 = __pyx_v_ndim; + for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_5; __pyx_t_3+=1) { + __pyx_v_i = __pyx_t_3; + + /* "View.MemoryView":1251 + * + * for i in range(ndim): + * if src.shape[i] != dst.shape[i]: # <<<<<<<<<<<<<< + * if src.shape[i] == 1: + * broadcasting = True + */ + __pyx_t_2 = ((__pyx_v_src.shape[__pyx_v_i]) != (__pyx_v_dst.shape[__pyx_v_i])); + if (__pyx_t_2) { + + /* "View.MemoryView":1252 + * for i in range(ndim): + * if src.shape[i] != dst.shape[i]: + * if src.shape[i] == 1: # <<<<<<<<<<<<<< + * broadcasting = True + * src.strides[i] = 0 + */ + __pyx_t_2 = ((__pyx_v_src.shape[__pyx_v_i]) == 1); + if (__pyx_t_2) { + + /* "View.MemoryView":1253 + * if src.shape[i] != dst.shape[i]: + * if src.shape[i] == 1: + * broadcasting = True # <<<<<<<<<<<<<< + * src.strides[i] = 0 + * else: + */ + __pyx_v_broadcasting = 1; + + /* "View.MemoryView":1254 + * if src.shape[i] == 1: + * broadcasting = True + * src.strides[i] = 0 # <<<<<<<<<<<<<< + * else: + * _err_extents(i, dst.shape[i], src.shape[i]) + */ + (__pyx_v_src.strides[__pyx_v_i]) = 0; + goto __pyx_L7; + } + /*else*/ { + + /* "View.MemoryView":1256 + * 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 = 1256; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } + __pyx_L7:; + goto __pyx_L6; + } + __pyx_L6:; + + /* "View.MemoryView":1258 + * _err_extents(i, dst.shape[i], src.shape[i]) + * + * if src.suboffsets[i] >= 0: # <<<<<<<<<<<<<< + * _err_dim(ValueError, "Dimension %d is not direct", i) + * + */ + __pyx_t_2 = ((__pyx_v_src.suboffsets[__pyx_v_i]) >= 0); + if (__pyx_t_2) { + + /* "View.MemoryView":1259 + * + * 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_48, __pyx_v_i); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 1259; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + goto __pyx_L8; + } + __pyx_L8:; + } + + /* "View.MemoryView":1261 + * _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_t_2 = __pyx_slices_overlap((&__pyx_v_src), (&__pyx_v_dst), __pyx_v_ndim, __pyx_v_itemsize); + if (__pyx_t_2) { + + /* "View.MemoryView":1263 + * if slices_overlap(&src, &dst, ndim, itemsize): + * + * if not slice_is_contig(&src, order, ndim): # <<<<<<<<<<<<<< + * order = get_best_order(&dst, ndim) + * + */ + __pyx_t_2 = (!__pyx_memviewslice_is_contig((&__pyx_v_src), __pyx_v_order, __pyx_v_ndim)); + if (__pyx_t_2) { + + /* "View.MemoryView":1264 + * + * if not slice_is_contig(&src, order, ndim): + * order = get_best_order(&dst, ndim) # <<<<<<<<<<<<<< + * + * 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; + } + __pyx_L10:; + + /* "View.MemoryView":1266 + * 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 = 1266; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_v_tmpdata = __pyx_t_6; + + /* "View.MemoryView":1267 + * + * 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":1269 + * src = tmp + * + * if not broadcasting: # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_2 = (!__pyx_v_broadcasting); + if (__pyx_t_2) { + + /* "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): + */ + __pyx_t_2 = __pyx_memviewslice_is_contig((&__pyx_v_src), 'C', __pyx_v_ndim); + if (__pyx_t_2) { + + /* "View.MemoryView":1273 + * + * 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":1274 + * 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); + if (__pyx_t_2) { + + /* "View.MemoryView":1275 + * 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":1277 + * direct_copy = slice_is_contig(&dst, 'F', ndim) + * + * if direct_copy: # <<<<<<<<<<<<<< + * + * refcount_copying(&dst, dtype_is_object, ndim, False) + */ + if (__pyx_v_direct_copy) { + + /* "View.MemoryView":1279 + * 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":1280 + * + * 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) + * return 0 + */ + memcpy(__pyx_v_dst.data, __pyx_v_src.data, __pyx_memoryview_slice_get_size((&__pyx_v_src), __pyx_v_ndim)); + + /* "View.MemoryView":1281 + * 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) # <<<<<<<<<<<<<< + * return 0 + * + */ + __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 1); + + /* "View.MemoryView":1282 + * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) + * refcount_copying(&dst, dtype_is_object, ndim, True) + * return 0 # <<<<<<<<<<<<<< + * + * if order == 'F' == get_best_order(&dst, ndim): + */ + __pyx_r = 0; + goto __pyx_L0; + goto __pyx_L13; + } + __pyx_L13:; + goto __pyx_L11; + } + __pyx_L11:; + + /* "View.MemoryView":1284 + * 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)); + } + if (__pyx_t_2) { + + /* "View.MemoryView":1287 + * + * + * 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 = 1287; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + + /* "View.MemoryView":1288 + * + * 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 = 1288; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + goto __pyx_L14; + } + __pyx_L14:; + + /* "View.MemoryView":1290 + * 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":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) + * + */ + copy_strided_to_strided((&__pyx_v_src), (&__pyx_v_dst), __pyx_v_ndim, __pyx_v_itemsize); + + /* "View.MemoryView":1292 + * 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":1294 + * refcount_copying(&dst, dtype_is_object, ndim, True) + * + * free(tmpdata) # <<<<<<<<<<<<<< + * return 0 + * + */ + free(__pyx_v_tmpdata); + + /* "View.MemoryView":1295 + * + * free(tmpdata) + * return 0 # <<<<<<<<<<<<<< + * + * @cname('__pyx_memoryview_broadcast_leading') + */ + __pyx_r = 0; + goto __pyx_L0; + + __pyx_r = 0; + goto __pyx_L0; + __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":1298 + * + * @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":1302 + * 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":1304 + * cdef int offset = 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struct __pyx_MemviewEnum_obj *p = (struct __pyx_MemviewEnum_obj *)o; + if (p->name) { + e = (*v)(p->name, a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear_Enum(PyObject *o) { + struct __pyx_MemviewEnum_obj *p = (struct __pyx_MemviewEnum_obj *)o; + PyObject* tmp; + tmp = ((PyObject*)p->name); + p->name = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + return 0; +} + +static PyMethodDef __pyx_methods_Enum[] = { + {0, 0, 0, 0} +}; + +static PyNumberMethods __pyx_tp_as_number_Enum = { + 0, /*nb_add*/ + 0, /*nb_subtract*/ + 0, /*nb_multiply*/ + #if PY_MAJOR_VERSION < 3 + 0, /*nb_divide*/ + #endif + 0, /*nb_remainder*/ + 0, /*nb_divmod*/ + 0, /*nb_power*/ + 0, /*nb_negative*/ + 0, /*nb_positive*/ + 0, /*nb_absolute*/ + 0, /*nb_nonzero*/ + 0, /*nb_invert*/ + 0, /*nb_lshift*/ + 0, /*nb_rshift*/ + 0, /*nb_and*/ + 0, /*nb_xor*/ + 0, /*nb_or*/ + #if PY_MAJOR_VERSION < 3 + 0, /*nb_coerce*/ + #endif + 0, /*nb_int*/ + #if PY_MAJOR_VERSION < 3 + 0, /*nb_long*/ + #else + 0, /*reserved*/ + #endif + 0, /*nb_float*/ + #if PY_MAJOR_VERSION < 3 + 0, /*nb_oct*/ + #endif + #if PY_MAJOR_VERSION < 3 + 0, /*nb_hex*/ + #endif + 0, /*nb_inplace_add*/ + 0, /*nb_inplace_subtract*/ + 0, /*nb_inplace_multiply*/ + #if PY_MAJOR_VERSION < 3 + 0, /*nb_inplace_divide*/ + #endif + 0, /*nb_inplace_remainder*/ + 0, /*nb_inplace_power*/ + 0, /*nb_inplace_lshift*/ + 0, /*nb_inplace_rshift*/ + 0, /*nb_inplace_and*/ + 0, /*nb_inplace_xor*/ + 0, /*nb_inplace_or*/ + 0, /*nb_floor_divide*/ + 0, /*nb_true_divide*/ + 0, /*nb_inplace_floor_divide*/ + 0, /*nb_inplace_true_divide*/ + #if PY_VERSION_HEX >= 0x02050000 + 0, /*nb_index*/ + #endif +}; + +static PySequenceMethods __pyx_tp_as_sequence_Enum = { + 0, /*sq_length*/ + 0, /*sq_concat*/ + 0, /*sq_repeat*/ + 0, /*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_Enum = { + 0, /*mp_length*/ + 0, /*mp_subscript*/ + 0, /*mp_ass_subscript*/ +}; + +static PyBufferProcs __pyx_tp_as_buffer_Enum = { + #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 + #if PY_VERSION_HEX >= 0x02060000 + 0, /*bf_getbuffer*/ + #endif + #if PY_VERSION_HEX >= 0x02060000 + 0, /*bf_releasebuffer*/ + #endif +}; + +static PyTypeObject __pyx_type___pyx_MemviewEnum = { + PyVarObject_HEAD_INIT(0, 0) + __Pyx_NAMESTR("sklearn._hmmc.Enum"), /*tp_name*/ + sizeof(struct __pyx_MemviewEnum_obj), /*tp_basicsize*/ + 0, /*tp_itemsize*/ + __pyx_tp_dealloc_Enum, /*tp_dealloc*/ + 0, /*tp_print*/ + 0, /*tp_getattr*/ + 0, /*tp_setattr*/ + #if PY_MAJOR_VERSION < 3 + 0, /*tp_compare*/ + #else + 0, /*reserved*/ + #endif + __pyx_MemviewEnum___repr__, /*tp_repr*/ + &__pyx_tp_as_number_Enum, /*tp_as_number*/ + &__pyx_tp_as_sequence_Enum, /*tp_as_sequence*/ + &__pyx_tp_as_mapping_Enum, /*tp_as_mapping*/ + 0, /*tp_hash*/ + 0, /*tp_call*/ + 0, /*tp_str*/ + 0, /*tp_getattro*/ + 0, /*tp_setattro*/ + &__pyx_tp_as_buffer_Enum, /*tp_as_buffer*/ + Py_TPFLAGS_DEFAULT|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/ + 0, /*tp_doc*/ + __pyx_tp_traverse_Enum, /*tp_traverse*/ + __pyx_tp_clear_Enum, /*tp_clear*/ + 0, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_Enum, /*tp_methods*/ + 0, /*tp_members*/ + 0, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + __pyx_MemviewEnum___init__, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_Enum, /*tp_new*/ + 0, /*tp_free*/ + 0, /*tp_is_gc*/ + 0, /*tp_bases*/ + 0, /*tp_mro*/ + 0, /*tp_cache*/ + 0, /*tp_subclasses*/ + 0, /*tp_weaklist*/ + 0, /*tp_del*/ + #if PY_VERSION_HEX >= 0x02060000 + 0, /*tp_version_tag*/ + #endif +}; +static struct __pyx_vtabstruct_memoryview __pyx_vtable_memoryview; + +static PyObject *__pyx_tp_new_memoryview(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_memoryview_obj *p; + PyObject *o = (*t->tp_alloc)(t, 0); + if (!o) return 0; + p = ((struct __pyx_memoryview_obj *)o); + p->__pyx_vtab = __pyx_vtabptr_memoryview; + p->obj = Py_None; Py_INCREF(Py_None); + p->_size = Py_None; Py_INCREF(Py_None); + p->_array_interface = Py_None; Py_INCREF(Py_None); + p->view.obj = NULL; + if (__pyx_memoryview___cinit__(o, a, k) < 0) { + Py_DECREF(o); o = 0; + } + return o; +} + +static void __pyx_tp_dealloc_memoryview(PyObject *o) { + struct __pyx_memoryview_obj *p = (struct __pyx_memoryview_obj *)o; + PyObject_GC_UnTrack(o); + { + PyObject *etype, *eval, *etb; + PyErr_Fetch(&etype, &eval, &etb); + ++Py_REFCNT(o); + __pyx_memoryview___dealloc__(o); + if (PyErr_Occurred()) PyErr_WriteUnraisable(o); + --Py_REFCNT(o); + PyErr_Restore(etype, eval, etb); + } + Py_CLEAR(p->obj); + Py_CLEAR(p->_size); + Py_CLEAR(p->_array_interface); + PyObject_GC_Track(o); + (*Py_TYPE(o)->tp_free)(o); +} + +static int __pyx_tp_traverse_memoryview(PyObject *o, visitproc v, void *a) { + int e; + struct __pyx_memoryview_obj *p = (struct __pyx_memoryview_obj *)o; + if (p->obj) { + e = (*v)(p->obj, a); if (e) return e; + } + if (p->_size) { + e = (*v)(p->_size, a); if (e) return e; + } + if (p->_array_interface) { + e = (*v)(p->_array_interface, a); if (e) return e; + } + if (p->view.obj) { + e = (*v)(p->view.obj, a); if (e) return e; + } + return 0; +} + +static int __pyx_tp_clear_memoryview(PyObject *o) { + struct __pyx_memoryview_obj *p = (struct __pyx_memoryview_obj *)o; + PyObject* tmp; + tmp = ((PyObject*)p->obj); + p->obj = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->_size); + p->_size = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + tmp = ((PyObject*)p->_array_interface); + p->_array_interface = Py_None; Py_INCREF(Py_None); + Py_XDECREF(tmp); + Py_CLEAR(p->view.obj); + return 0; +} +static PyObject *__pyx_sq_item_memoryview(PyObject *o, Py_ssize_t i) { + PyObject *r; + PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0; + r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x); + Py_DECREF(x); + return r; +} + +static int __pyx_mp_ass_subscript_memoryview(PyObject *o, PyObject *i, PyObject *v) { + if (v) { + return __pyx_memoryview___setitem__(o, i, v); + } + else { + PyErr_Format(PyExc_NotImplementedError, + "Subscript deletion not supported by %s", Py_TYPE(o)->tp_name); + return -1; + } +} + +static PyObject *__pyx_getprop___pyx_memoryview_T(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_memoryview_transpose(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_base(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_memoryview__get__base(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_shape(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_memoryview_get_shape(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_strides(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_memoryview_get_strides(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_suboffsets(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_memoryview_get_suboffsets(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_ndim(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_memoryview_get_ndim(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_itemsize(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_memoryview_get_itemsize(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_nbytes(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_memoryview_get_nbytes(o); +} + +static PyObject *__pyx_getprop___pyx_memoryview_size(PyObject *o, CYTHON_UNUSED void *x) { + return __pyx_memoryview_get_size(o); +} + +static PyMethodDef __pyx_methods_memoryview[] = { + {__Pyx_NAMESTR("is_c_contig"), (PyCFunction)__pyx_memoryview_is_c_contig, METH_NOARGS, __Pyx_DOCSTR(0)}, + {__Pyx_NAMESTR("is_f_contig"), (PyCFunction)__pyx_memoryview_is_f_contig, METH_NOARGS, __Pyx_DOCSTR(0)}, + {__Pyx_NAMESTR("copy"), (PyCFunction)__pyx_memoryview_copy, METH_NOARGS, __Pyx_DOCSTR(0)}, + {__Pyx_NAMESTR("copy_fortran"), (PyCFunction)__pyx_memoryview_copy_fortran, METH_NOARGS, __Pyx_DOCSTR(0)}, + {0, 0, 0, 0} +}; + +static struct PyGetSetDef __pyx_getsets_memoryview[] = { + {(char *)"T", __pyx_getprop___pyx_memoryview_T, 0, 0, 0}, + {(char *)"base", __pyx_getprop___pyx_memoryview_base, 0, 0, 0}, + {(char *)"shape", __pyx_getprop___pyx_memoryview_shape, 0, 0, 0}, + {(char *)"strides", __pyx_getprop___pyx_memoryview_strides, 0, 0, 0}, + {(char *)"suboffsets", __pyx_getprop___pyx_memoryview_suboffsets, 0, 0, 0}, + {(char *)"ndim", __pyx_getprop___pyx_memoryview_ndim, 0, 0, 0}, + {(char *)"itemsize", __pyx_getprop___pyx_memoryview_itemsize, 0, 0, 0}, + {(char *)"nbytes", __pyx_getprop___pyx_memoryview_nbytes, 0, 0, 0}, + {(char *)"size", __pyx_getprop___pyx_memoryview_size, 0, 0, 0}, + {0, 0, 0, 0, 0} +}; + +static PyNumberMethods __pyx_tp_as_number_memoryview = { + 0, /*nb_add*/ + 0, /*nb_subtract*/ + 0, /*nb_multiply*/ + #if PY_MAJOR_VERSION < 3 + 0, /*nb_divide*/ + #endif + 0, /*nb_remainder*/ + 0, /*nb_divmod*/ + 0, /*nb_power*/ + 0, /*nb_negative*/ + 0, /*nb_positive*/ + 0, /*nb_absolute*/ + 0, /*nb_nonzero*/ + 0, /*nb_invert*/ + 0, /*nb_lshift*/ + 0, /*nb_rshift*/ + 0, /*nb_and*/ + 0, /*nb_xor*/ + 0, /*nb_or*/ + #if PY_MAJOR_VERSION < 3 + 0, /*nb_coerce*/ + #endif + 0, /*nb_int*/ + #if PY_MAJOR_VERSION < 3 + 0, /*nb_long*/ + #else + 0, /*reserved*/ + #endif + 0, /*nb_float*/ + #if PY_MAJOR_VERSION < 3 + 0, /*nb_oct*/ + #endif + #if PY_MAJOR_VERSION < 3 + 0, /*nb_hex*/ + #endif + 0, /*nb_inplace_add*/ + 0, /*nb_inplace_subtract*/ + 0, /*nb_inplace_multiply*/ + #if PY_MAJOR_VERSION < 3 + 0, /*nb_inplace_divide*/ + #endif + 0, /*nb_inplace_remainder*/ + 0, /*nb_inplace_power*/ + 0, /*nb_inplace_lshift*/ + 0, /*nb_inplace_rshift*/ + 0, /*nb_inplace_and*/ + 0, /*nb_inplace_xor*/ + 0, /*nb_inplace_or*/ + 0, /*nb_floor_divide*/ + 0, /*nb_true_divide*/ + 0, /*nb_inplace_floor_divide*/ + 0, /*nb_inplace_true_divide*/ + #if PY_VERSION_HEX >= 0x02050000 + 0, /*nb_index*/ + #endif +}; + +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 + #if PY_VERSION_HEX >= 0x02060000 + __pyx_memoryview_getbuffer, /*bf_getbuffer*/ + #endif + #if PY_VERSION_HEX >= 0x02060000 + 0, /*bf_releasebuffer*/ + #endif +}; + +static PyTypeObject __pyx_type___pyx_memoryview = { + PyVarObject_HEAD_INIT(0, 0) + __Pyx_NAMESTR("sklearn._hmmc.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*/ + &__pyx_tp_as_number_memoryview, /*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_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, /*tp_richcompare*/ + 0, /*tp_weaklistoffset*/ + 0, /*tp_iter*/ + 0, /*tp_iternext*/ + __pyx_methods_memoryview, /*tp_methods*/ + 0, /*tp_members*/ + __pyx_getsets_memoryview, /*tp_getset*/ + 0, /*tp_base*/ + 0, /*tp_dict*/ + 0, /*tp_descr_get*/ + 0, /*tp_descr_set*/ + 0, /*tp_dictoffset*/ + 0, /*tp_init*/ + 0, /*tp_alloc*/ + __pyx_tp_new_memoryview, /*tp_new*/ + 0, /*tp_free*/ + 0, /*tp_is_gc*/ + 0, /*tp_bases*/ + 0, /*tp_mro*/ + 0, /*tp_cache*/ + 0, /*tp_subclasses*/ + 0, /*tp_weaklist*/ + 0, /*tp_del*/ + #if PY_VERSION_HEX >= 0x02060000 + 0, /*tp_version_tag*/ + #endif +}; +static struct __pyx_vtabstruct__memoryviewslice __pyx_vtable__memoryviewslice; + +static PyObject *__pyx_tp_new__memoryviewslice(PyTypeObject *t, PyObject *a, PyObject *k) { + struct __pyx_memoryviewslice_obj *p; + PyObject *o = __pyx_tp_new_memoryview(t, a, k); + if (!o) return 0; + p = ((struct __pyx_memoryviewslice_obj *)o); + p->__pyx_base.__pyx_vtab = (struct __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; + PyObject_GC_UnTrack(o); + { + PyObject *etype, *eval, *etb; + PyErr_Fetch(&etype, &eval, &etb); + ++Py_REFCNT(o); + __pyx_memoryviewslice___dealloc__(o); + if (PyErr_Occurred()) PyErr_WriteUnraisable(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) { + struct __pyx_memoryviewslice_obj *p = (struct __pyx_memoryviewslice_obj *)o; + PyObject* tmp; + __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 PyNumberMethods __pyx_tp_as_number__memoryviewslice = { + 0, /*nb_add*/ + 0, /*nb_subtract*/ + 0, /*nb_multiply*/ + #if PY_MAJOR_VERSION < 3 + 0, /*nb_divide*/ + #endif + 0, /*nb_remainder*/ + 0, /*nb_divmod*/ + 0, /*nb_power*/ + 0, /*nb_negative*/ + 0, /*nb_positive*/ + 0, /*nb_absolute*/ + 0, /*nb_nonzero*/ + 0, /*nb_invert*/ + 0, /*nb_lshift*/ + 0, /*nb_rshift*/ + 0, /*nb_and*/ + 0, /*nb_xor*/ + 0, /*nb_or*/ + #if PY_MAJOR_VERSION < 3 + 0, /*nb_coerce*/ + #endif + 0, /*nb_int*/ + #if PY_MAJOR_VERSION < 3 + 0, /*nb_long*/ + #else + 0, /*reserved*/ + #endif + 0, /*nb_float*/ + #if PY_MAJOR_VERSION < 3 + 0, /*nb_oct*/ + #endif + #if PY_MAJOR_VERSION < 3 + 0, /*nb_hex*/ + #endif + 0, /*nb_inplace_add*/ + 0, /*nb_inplace_subtract*/ + 0, /*nb_inplace_multiply*/ + #if PY_MAJOR_VERSION < 3 + 0, /*nb_inplace_divide*/ + #endif + 0, /*nb_inplace_remainder*/ + 0, /*nb_inplace_power*/ + 0, /*nb_inplace_lshift*/ + 0, /*nb_inplace_rshift*/ + 0, /*nb_inplace_and*/ + 0, /*nb_inplace_xor*/ + 0, /*nb_inplace_or*/ + 0, /*nb_floor_divide*/ + 0, /*nb_true_divide*/ + 0, /*nb_inplace_floor_divide*/ + 0, /*nb_inplace_true_divide*/ + #if PY_VERSION_HEX >= 0x02050000 + 0, /*nb_index*/ + #endif +}; + +static PySequenceMethods __pyx_tp_as_sequence__memoryviewslice = { + #if CYTHON_COMPILING_IN_PYPY + __pyx_memoryview___len__, /*sq_length*/ + #else + 0, /*sq_length*/ + #endif + 0, /*sq_concat*/ + 0, /*sq_repeat*/ + 0, /*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__memoryviewslice = { + #if CYTHON_COMPILING_IN_PYPY + __pyx_memoryview___len__, /*mp_length*/ + #else + 0, /*mp_length*/ + #endif + #if CYTHON_COMPILING_IN_PYPY + __pyx_memoryview___getitem__, /*mp_subscript*/ + #else + 0, /*mp_subscript*/ + #endif + 0, /*mp_ass_subscript*/ +}; + +static PyBufferProcs __pyx_tp_as_buffer__memoryviewslice = { + #if PY_MAJOR_VERSION < 3 + 0, /*bf_getreadbuffer*/ + #endif + #if PY_MAJOR_VERSION < 3 + 0, 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{&__pyx_n_s__extend, __pyx_k__extend, sizeof(__pyx_k__extend), 0, 0, 1, 1}, + {&__pyx_n_s__flags, __pyx_k__flags, sizeof(__pyx_k__flags), 0, 0, 1, 1}, + {&__pyx_n_s__format, __pyx_k__format, sizeof(__pyx_k__format), 0, 0, 1, 1}, + {&__pyx_n_b__fortran, __pyx_k__fortran, sizeof(__pyx_k__fortran), 0, 0, 0, 1}, + {&__pyx_n_s__fortran, __pyx_k__fortran, sizeof(__pyx_k__fortran), 0, 0, 1, 1}, {&__pyx_n_s__framelogprob, __pyx_k__framelogprob, sizeof(__pyx_k__framelogprob), 0, 0, 1, 1}, {&__pyx_n_s__fwdlattice, __pyx_k__fwdlattice, sizeof(__pyx_k__fwdlattice), 0, 0, 1, 1}, {&__pyx_n_s__i, __pyx_k__i, sizeof(__pyx_k__i), 0, 0, 1, 1}, + {&__pyx_n_s__id, __pyx_k__id, sizeof(__pyx_k__id), 0, 0, 1, 1}, + {&__pyx_n_s__inf, __pyx_k__inf, sizeof(__pyx_k__inf), 0, 0, 1, 1}, {&__pyx_n_s__int, __pyx_k__int, sizeof(__pyx_k__int), 0, 0, 1, 1}, + {&__pyx_n_s__itemsize, __pyx_k__itemsize, sizeof(__pyx_k__itemsize), 0, 0, 1, 1}, {&__pyx_n_s__j, __pyx_k__j, sizeof(__pyx_k__j), 0, 0, 1, 1}, {&__pyx_n_s__lneta, 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0, 0, 1, 1}, {&__pyx_n_s__np, __pyx_k__np, sizeof(__pyx_k__np), 0, 0, 1, 1}, {&__pyx_n_s__numpy, __pyx_k__numpy, sizeof(__pyx_k__numpy), 0, 0, 1, 1}, + {&__pyx_n_s__obj, __pyx_k__obj, sizeof(__pyx_k__obj), 0, 0, 1, 1}, + {&__pyx_n_s__pack, __pyx_k__pack, sizeof(__pyx_k__pack), 0, 0, 1, 1}, {&__pyx_n_s__range, __pyx_k__range, sizeof(__pyx_k__range), 0, 0, 1, 1}, + {&__pyx_n_s__shape, __pyx_k__shape, sizeof(__pyx_k__shape), 0, 0, 1, 1}, + {&__pyx_n_s__size, __pyx_k__size, sizeof(__pyx_k__size), 0, 0, 1, 1}, + {&__pyx_n_s__start, __pyx_k__start, sizeof(__pyx_k__start), 0, 0, 1, 1}, {&__pyx_n_s__state_sequence, __pyx_k__state_sequence, sizeof(__pyx_k__state_sequence), 0, 0, 1, 1}, + {&__pyx_n_s__step, __pyx_k__step, sizeof(__pyx_k__step), 0, 0, 1, 1}, + {&__pyx_n_s__stop, __pyx_k__stop, sizeof(__pyx_k__stop), 0, 0, 1, 1}, + {&__pyx_n_s__struct, __pyx_k__struct, sizeof(__pyx_k__struct), 0, 0, 1, 1}, {&__pyx_n_s__t, __pyx_k__t, sizeof(__pyx_k__t), 0, 0, 1, 1}, + {&__pyx_n_s__unpack, 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__pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_MemoryError = __Pyx_GetName(__pyx_b, __pyx_n_s__MemoryError); if (!__pyx_builtin_MemoryError) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 141; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_enumerate = __Pyx_GetName(__pyx_b, __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_GetName(__pyx_b, __pyx_n_s__Ellipsis); if (!__pyx_builtin_Ellipsis) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 363; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_TypeError = __Pyx_GetName(__pyx_b, __pyx_n_s__TypeError); if (!__pyx_builtin_TypeError) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 392; __pyx_clineno = __LINE__; goto __pyx_L1_error;} #if PY_MAJOR_VERSION >= 3 - __pyx_builtin_xrange = __Pyx_GetName(__pyx_b, __pyx_n_s__range); if 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"sklearn/_hmmc.pyx":137 * * @cython.boundscheck(False) - * def _viterbi(int n_observations, int n_components, \ # <<<<<<<<<<<<<< - * np.ndarray[dtype_t, ndim=1] log_startprob, \ - * np.ndarray[dtype_t, ndim=2] log_transmat, \ + * def _viterbi(int n_observations, int n_components, # <<<<<<<<<<<<<< + * np.ndarray[dtype_t, ndim=1] log_startprob, + * np.ndarray[dtype_t, ndim=2] log_transmat, */ - __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_7sklearn_5_hmmc_9_viterbi, NULL, __pyx_n_s_21); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_t_1 = PyCFunction_NewEx(&__pyx_mdef_7sklearn_5_hmmc_9_viterbi, NULL, __pyx_n_s_52); 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); - if (PyObject_SetAttr(__pyx_m, __pyx_n_s___viterbi, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 86; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + if (PyObject_SetAttr(__pyx_m, __pyx_n_s___viterbi, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 137; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; /* "sklearn/_hmmc.pyx":1 @@ -5737,16 +17383,131 @@ PyMODINIT_FUNC PyInit__hmmc(void) if (PyObject_SetAttr(__pyx_m, __pyx_n_s____test__, ((PyObject *)__pyx_t_1)) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(((PyObject *)__pyx_t_1)); __pyx_t_1 = 0; - /* "numpy.pxd":975 - * arr.base = baseptr + /* "View.MemoryView":207 + * info.obj = self + * + * __pyx_getbuffer = capsule( &__pyx_array_getbuffer, "getbuffer(obj, view, flags)") # <<<<<<<<<<<<<< + * + * def __dealloc__(array self): + */ + __pyx_t_1 = __pyx_capsule_create(((void *)(&__pyx_array_getbuffer)), __pyx_k_59); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 207; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_array_type->tp_dict, __pyx_n_s____pyx_getbuffer, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 207; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + PyType_Modified(__pyx_array_type); + + /* "View.MemoryView":282 + * return self.name + * + * cdef generic = Enum("") # <<<<<<<<<<<<<< + * cdef strided = Enum("") # default + * cdef indirect = Enum("") + */ + __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject *)__pyx_MemviewEnum_type)), ((PyObject *)__pyx_k_tuple_61), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 282; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_XGOTREF(generic); + __Pyx_DECREF(generic); + __Pyx_GIVEREF(__pyx_t_1); + generic = __pyx_t_1; + __pyx_t_1 = 0; + + /* "View.MemoryView":283 + * + * cdef generic = Enum("") + * cdef strided = Enum("") # default # <<<<<<<<<<<<<< + * cdef indirect = Enum("") + * + */ + __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject *)__pyx_MemviewEnum_type)), ((PyObject *)__pyx_k_tuple_63), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 283; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_XGOTREF(strided); + __Pyx_DECREF(strided); + __Pyx_GIVEREF(__pyx_t_1); + strided = __pyx_t_1; + __pyx_t_1 = 0; + + /* "View.MemoryView":284 + * cdef generic = Enum("") + * cdef strided = Enum("") # default + * cdef indirect = Enum("") # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject *)__pyx_MemviewEnum_type)), ((PyObject *)__pyx_k_tuple_65), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_XGOTREF(indirect); + __Pyx_DECREF(indirect); + __Pyx_GIVEREF(__pyx_t_1); + indirect = __pyx_t_1; + __pyx_t_1 = 0; + + /* "View.MemoryView":287 + * + * + * cdef contiguous = Enum("") # <<<<<<<<<<<<<< + * cdef indirect_contiguous = Enum("") * - * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< - * if arr.base is NULL: - * return None + */ + __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject *)__pyx_MemviewEnum_type)), ((PyObject *)__pyx_k_tuple_67), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 287; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_XGOTREF(contiguous); + __Pyx_DECREF(contiguous); + __Pyx_GIVEREF(__pyx_t_1); + contiguous = __pyx_t_1; + __pyx_t_1 = 0; + + /* "View.MemoryView":288 + * + * cdef contiguous = Enum("") + * cdef indirect_contiguous = Enum("") # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_1 = PyObject_Call(((PyObject *)((PyObject *)__pyx_MemviewEnum_type)), ((PyObject *)__pyx_k_tuple_69), NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 288; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_XGOTREF(indirect_contiguous); + __Pyx_DECREF(indirect_contiguous); + __Pyx_GIVEREF(__pyx_t_1); + indirect_contiguous = __pyx_t_1; + __pyx_t_1 = 0; + + /* "View.MemoryView":503 + * info.obj = self + * + * __pyx_getbuffer = capsule( &__pyx_memoryview_getbuffer, "getbuffer(obj, view, flags)") # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_1 = __pyx_capsule_create(((void *)(&__pyx_memoryview_getbuffer)), __pyx_k_59); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 503; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_memoryview_type->tp_dict, __pyx_n_s____pyx_getbuffer, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 503; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + PyType_Modified(__pyx_memoryview_type); + + /* "View.MemoryView":958 + * return self.from_object + * + * __pyx_getbuffer = capsule( &__pyx_memoryview_getbuffer, "getbuffer(obj, view, flags)") # <<<<<<<<<<<<<< + * + * + */ + __pyx_t_1 = __pyx_capsule_create(((void *)(&__pyx_memoryview_getbuffer)), __pyx_k_59); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 958; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + if (PyDict_SetItem(__pyx_memoryviewslice_type->tp_dict, __pyx_n_s____pyx_getbuffer, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 958; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; + PyType_Modified(__pyx_memoryviewslice_type); + + /* "View.MemoryView":1365 + * + * @cname('__pyx_memoryview__slice_assign_scalar') + * cdef void _slice_assign_scalar(char *data, Py_ssize_t *shape, # <<<<<<<<<<<<<< + * Py_ssize_t *strides, int ndim, + * size_t itemsize, void *item) nogil: */ goto __pyx_L0; __pyx_L1_error:; __Pyx_XDECREF(__pyx_t_1); + __Pyx_XDECREF(__pyx_t_2); if (__pyx_m) { __Pyx_AddTraceback("init sklearn._hmmc", __pyx_clineno, __pyx_lineno, __pyx_filename); Py_DECREF(__pyx_m); __pyx_m = 0; @@ -5788,169 +17549,14 @@ static PyObject *__Pyx_GetName(PyObject *dict, PyObject *name) { result = PyObject_GetAttr(__pyx_b, name); } if (!result) { - PyErr_SetObject(PyExc_NameError, name); - } - } - return result; -} - -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, - "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" 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, - "%s() keywords must be strings", function_name); - goto bad; -invalid_keyword: - PyErr_Format(PyExc_TypeError, - #if PY_MAJOR_VERSION < 3 - "%s() got an unexpected keyword argument '%s'", - function_name, PyString_AsString(key)); - #else - "%s() got an unexpected keyword argument '%U'", - function_name, key); - #endif -bad: - return -1; -} - -static int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, - const char *name, int exact) -{ - if (!type) { - PyErr_Format(PyExc_SystemError, "Missing type object"); - return 0; - } - if (none_allowed && obj == Py_None) return 1; - else if (exact) { - if (Py_TYPE(obj) == type) return 1; - } - else { - if (PyObject_TypeCheck(obj, type)) return 1; - } - PyErr_Format(PyExc_TypeError, - "Argument '%s' has incorrect type (expected %s, got %s)", - name, type->tp_name, Py_TYPE(obj)->tp_name); - return 0; + PyErr_SetObject(PyExc_NameError, name); + } + } + return result; +} + +static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { + PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); } static CYTHON_INLINE int __Pyx_IsLittleEndian(void) { @@ -6447,53 +18053,550 @@ static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const cha 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 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_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_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 (buf->strides) { + if (spec & __Pyx_MEMVIEW_CONTIG) { + if (spec & (__Pyx_MEMVIEW_PTR|__Pyx_MEMVIEW_FULL)) { + if (buf->strides[i] != sizeof(void *)) { + PyErr_Format(PyExc_ValueError, + "Buffer is not indirectly contiguous in dimension %d.", i); + goto fail; + } + } else if (buf->strides[i] != 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[i]; + 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 && i != ndim - 1) { + PyErr_Format(PyExc_ValueError, + "C-contiguous buffer is not contiguous in " + "dimension %d", i); + goto fail; + } else if (spec & (__Pyx_MEMVIEW_PTR)) { + PyErr_Format(PyExc_ValueError, + "C-contiguous buffer is not indirect in " + "dimension %d", i); + goto fail; + } else if (buf->suboffsets) { + PyErr_SetString(PyExc_ValueError, + "Buffer exposes suboffsets but no strides"); + goto fail; + } + } + /* Todo: without PyBUF_INDIRECT we may not have suboffset information, i.e., the + ptr may not be set to NULL but may be uninitialized? */ + if (spec & __Pyx_MEMVIEW_DIRECT) { + if (buf->suboffsets && buf->suboffsets[i] >= 0) { + PyErr_Format(PyExc_ValueError, + "Buffer not compatible with direct access in dimension %d.", i); + goto fail; + } + } + if (spec & __Pyx_MEMVIEW_PTR) { + if (!buf->suboffsets || (buf->suboffsets && buf->suboffsets[i] < 0)) { + PyErr_Format(PyExc_ValueError, + "Buffer is not indirectly accessisble in dimension %d.", i); + goto fail; + } + } + } + if (buf->strides) { + if (c_or_f_flag & __Pyx_IS_F_CONTIG) { + Py_ssize_t stride = 1; + for (i=0; iitemsize != buf->strides[i]) { + 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]) { + PyErr_SetString(PyExc_ValueError, + "Buffer not C contiguous."); + goto fail; + } + stride = stride * buf->shape[i]; + } + } + } + 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 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; /* allow uninitialized memoryview assignment */ + 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 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, + "%s() takes %s %" CYTHON_FORMAT_SSIZE_T "d positional argument%s (%" 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, + "%s() keywords must be strings", function_name); + goto bad; +invalid_keyword: + PyErr_Format(PyExc_TypeError, + #if PY_MAJOR_VERSION < 3 + "%s() got an unexpected keyword argument '%s'", + function_name, PyString_AsString(key)); + #else + "%s() got an unexpected keyword argument '%U'", + function_name, key); + #endif +bad: + return -1; } -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 int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed, + const char *name, int exact) { - if (obj == Py_None || obj == NULL) { - __Pyx_ZeroBuffer(buf); + if (!type) { + PyErr_Format(PyExc_SystemError, "Missing type object"); + return 0; + } + if (none_allowed && obj == Py_None) return 1; + else if (exact) { + if (Py_TYPE(obj) == type) return 1; + } + else { + if (PyObject_TypeCheck(obj, type)) return 1; + } + PyErr_Format(PyExc_TypeError, + "Argument '%s' has incorrect type (expected %s, got %s)", + name, type->tp_name, Py_TYPE(obj)->tp_name); 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 CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { + if (unlikely(!type)) { + PyErr_Format(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_RaiseBufferFallbackError(void) { + PyErr_Format(PyExc_ValueError, + "Buffer acquisition failed on assignment; and then reacquiring the old buffer failed too!"); } static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { @@ -6527,23 +18630,6 @@ static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyOb #endif } -static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { - if (unlikely(!type)) { - PyErr_Format(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_RaiseBufferFallbackError(void) { - PyErr_Format(PyExc_ValueError, - "Buffer acquisition failed on assignment; and then reacquiring the old buffer failed too!"); -} - #if PY_MAJOR_VERSION < 3 static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, CYTHON_UNUSED PyObject *cause) { @@ -6754,6 +18840,163 @@ static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { return 0; } +static CYTHON_INLINE PyObject *__Pyx_GetAttr3(PyObject *o, PyObject *n, PyObject *d) { + PyObject *r = PyObject_GetAttr(o, n); + if (!r) { + if (!PyErr_ExceptionMatches(PyExc_AttributeError)) + goto bad; + PyErr_Clear(); + r = d; + Py_INCREF(d); + } + return r; +bad: + return NULL; +} + +static CYTHON_INLINE Py_ssize_t __Pyx_div_Py_ssize_t(Py_ssize_t a, Py_ssize_t b) { + Py_ssize_t q = a / b; + Py_ssize_t r = a - q*b; + q -= ((r != 0) & ((r ^ b) < 0)); + return q; +} + +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 (s1 == s2) { + return (equals == Py_EQ); + } else if (PyUnicode_CheckExact(s1) & PyUnicode_CheckExact(s2)) { + #if CYTHON_PEP393_ENABLED + if ((PyUnicode_READY(s1) < 0) || (PyUnicode_READY(s2) < 0)) + return -1; + if (PyUnicode_GET_LENGTH(s1) != PyUnicode_GET_LENGTH(s2)) { + return (equals == Py_NE); + } else if (PyUnicode_GET_LENGTH(s1) == 1) { + Py_UCS4 ch1 = PyUnicode_READ_CHAR(s1, 0); + Py_UCS4 ch2 = PyUnicode_READ_CHAR(s2, 0); + return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2); + #else + if (PyUnicode_GET_SIZE(s1) != PyUnicode_GET_SIZE(s2)) { + return (equals == Py_NE); + } else if (PyUnicode_GET_SIZE(s1) == 1) { + Py_UNICODE ch1 = PyUnicode_AS_UNICODE(s1)[0]; + Py_UNICODE ch2 = PyUnicode_AS_UNICODE(s2)[0]; + return (equals == Py_EQ) ? (ch1 == ch2) : (ch1 != ch2); + #endif + } else { + int result = PyUnicode_Compare(s1, s2); + if ((result == -1) && unlikely(PyErr_Occurred())) + return -1; + return (equals == Py_EQ) ? (result == 0) : (result != 0); + } + } else if ((s1 == Py_None) & PyUnicode_CheckExact(s2)) { + return (equals == Py_NE); + } else if ((s2 == Py_None) & PyUnicode_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 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 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 (unlikely(PyException_SetTraceback(local_value, local_tb) < 0)) + goto bad; + #endif + Py_INCREF(local_type); + Py_INCREF(local_value); + Py_INCREF(local_tb); + *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; + /* Make sure tstate is in a consistent state when we XDECREF + these objects (DECREF may run arbitrary code). */ + 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 long __Pyx_div_long(long a, long b) { + long q = a / b; + long r = a - q*b; + q -= ((r != 0) & ((r ^ b) < 0)); + return q; +} + #if PY_MAJOR_VERSION < 3 static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { CYTHON_UNUSED PyObject *getbuffer_cobj; @@ -6761,6 +19004,8 @@ static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) { 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 (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); #if PY_VERSION_HEX < 0x02060000 if (obj->ob_type->tp_dict && (getbuffer_cobj = PyMapping_GetItemString(obj->ob_type->tp_dict, @@ -6827,16 +19072,18 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { #endif /* PY_MAJOR_VERSION < 3 */ - static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, long level) { - PyObject *py_import = 0; + 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 = 0; py_import = __Pyx_GetAttrString(__pyx_b, "__import__"); if (!py_import) goto bad; + #endif if (from_list) list = from_list; else { @@ -6856,13 +19103,17 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { #if PY_MAJOR_VERSION >= 3 if (level == -1) { if (strchr(__Pyx_MODULE_NAME, '.')) { - /* try package relative import first */ + #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; @@ -6873,12 +19124,17 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { } #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 } } #else @@ -6890,12 +19146,36 @@ static void __Pyx_ReleaseBuffer(Py_buffer *view) { name, global_dict, empty_dict, list, NULL); #endif bad: - Py_XDECREF(empty_list); + #if PY_VERSION_HEX < 0x03030000 Py_XDECREF(py_import); + #endif + Py_XDECREF(empty_list); Py_XDECREF(empty_dict); return module; } +static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_nn___pyx_t_7sklearn_5_hmmc_dtype_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) }; + 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_nn___pyx_t_7sklearn_5_hmmc_dtype_t, 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 PyObject *__Pyx_PyInt_to_py_npy_long(npy_long val) { const npy_long neg_one = (npy_long)-1, const_zero = (npy_long)0; const int is_unsigned = const_zero < neg_one; @@ -7161,6 +19441,172 @@ static CYTHON_INLINE PyObject *__Pyx_PyInt_to_py_npy_long(npy_long val) { #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_FromLong(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, const char *sig) +{ + PyObject *cobj; +#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION == 3 && PY_MINOR_VERSION == 0) + cobj = PyCapsule_New(p, sig, NULL); +#else + cobj = PyCObject_FromVoidPtr(p, NULL); +#endif + return cobj; +} + +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 CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { const unsigned char neg_one = (unsigned char)-1, const_zero = 0; const int is_unsigned = neg_one > const_zero; @@ -7561,6 +20007,25 @@ static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* } } +static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno, + CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename) { + PyObject *old_exc, *old_val, *old_tb; + PyObject *ctx; + __Pyx_ErrFetch(&old_exc, &old_val, &old_tb); + #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_check_binary_version(void) { char ctversion[4], rtversion[4]; PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); @@ -7580,6 +20045,23 @@ static int __Pyx_check_binary_version(void) { return 0; } +static int __Pyx_SetVtable(PyObject *dict, void *vtable) { +#if PY_VERSION_HEX >= 0x02070000 && !(PY_MAJOR_VERSION==3&&PY_MINOR_VERSION==0) + PyObject *ob = PyCapsule_New(vtable, 0, 0); +#else + PyObject *ob = PyCObject_FromVoidPtr(vtable, 0); +#endif + if (!ob) + goto bad; + if (PyDict_SetItemString(dict, "__pyx_vtable__", ob) < 0) + goto bad; + Py_DECREF(ob); + return 0; +bad: + Py_XDECREF(ob); + return -1; +} + #ifndef __PYX_HAVE_RT_ImportModule #define __PYX_HAVE_RT_ImportModule static PyObject *__Pyx_ImportModule(const char *name) { @@ -7606,6 +20088,10 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class 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; @@ -7625,7 +20111,19 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class module_name, class_name); goto bad; } - if (!strict && (size_t)((PyTypeObject *)result)->tp_basicsize > size) { +#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); @@ -7635,7 +20133,7 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; #endif } - else if ((size_t)((PyTypeObject *)result)->tp_basicsize != size) { + else if ((size_t)basicsize != size) { PyErr_Format(PyExc_ValueError, "%s.%s has the wrong size, try recompiling", module_name, class_name); @@ -7841,15 +20339,11 @@ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { return 0; } - -/* Type Conversion Functions */ - 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; @@ -7895,7 +20389,6 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) { } return res; } - static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { Py_ssize_t ival; PyObject* x = PyNumber_Index(b); @@ -7904,7 +20397,6 @@ static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { Py_DECREF(x); return ival; } - static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { #if PY_VERSION_HEX < 0x02050000 if (ival <= LONG_MAX) @@ -7918,7 +20410,6 @@ static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { return PyInt_FromSize_t(ival); #endif } - static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { unsigned PY_LONG_LONG val = __Pyx_PyInt_AsUnsignedLongLong(x); if (unlikely(val == (unsigned PY_LONG_LONG)-1 && PyErr_Occurred())) {