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Nov 8, 2023
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Cython: declare pointers one per line #544

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3 changes: 2 additions & 1 deletion nipy/algorithms/statistics/_quantile.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,8 @@ def _quantile(X, double ratio, int interp=False, int axis=0):
Y : array
Array of quantiles
"""
cdef double *x, *y
cdef double *x
cdef double *y
cdef long int size, stride
cdef np.flatiter itX, itY

Expand Down
19 changes: 14 additions & 5 deletions nipy/labs/bindings/array.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,8 @@ def array_get_block( A, size_t x0, size_t x1, size_t fX=1,
size_t z0=0, size_t z1=0, size_t fZ=1,
size_t t0=0, size_t t1=0, size_t fT=1 )
"""
cdef fff_array *a, *b
cdef fff_array *a
cdef fff_array *b
cdef fff_array asub
a = fff_array_fromPyArray(A)
asub = fff_array_get_block(a, x0, x1, fX, y0, y1, fY, z0, z1, fZ, t0, t1, fT)
Expand All @@ -57,7 +58,9 @@ def array_add(A, B):
"""
C = A + B
"""
cdef fff_array *a, *b, *c
cdef fff_array *a
cdef fff_array *b
cdef fff_array *c

a = fff_array_fromPyArray(A)
b = fff_array_fromPyArray(B)
Expand All @@ -74,7 +77,9 @@ def array_mul(A, B):
"""
C = A * B
"""
cdef fff_array *a, *b, *c
cdef fff_array *a
cdef fff_array *b
cdef fff_array *c

a = fff_array_fromPyArray(A)
b = fff_array_fromPyArray(B)
Expand All @@ -91,7 +96,9 @@ def array_sub(A, B):
"""
C = A - B
"""
cdef fff_array *a, *b, *c
cdef fff_array *a
cdef fff_array *b
cdef fff_array *c

a = fff_array_fromPyArray(A)
b = fff_array_fromPyArray(B)
Expand All @@ -108,7 +115,9 @@ def array_div(A, B):
"""
C = A / B
"""
cdef fff_array *a, *b, *c
cdef fff_array *a
cdef fff_array *b
cdef fff_array *c

a = fff_array_fromPyArray(A)
b = fff_array_fromPyArray(B)
Expand Down
72 changes: 53 additions & 19 deletions nipy/labs/bindings/linalg.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -105,7 +105,8 @@ def vector_set(X, size_t i, double a):
Set i-th element.
vector_set(x, i, a)
"""
cdef fff_vector *x, *y
cdef fff_vector *x
cdef fff_vector *y
x = fff_vector_fromPyArray(X)
y = fff_vector_new(x.size)
fff_vector_memcpy(y, x)
Expand All @@ -119,7 +120,8 @@ def vector_set_all(X, double a):
Set to a constant value.
vector_set_all(x, a)
"""
cdef fff_vector *x, *y
cdef fff_vector *x
cdef fff_vector *y
x = fff_vector_fromPyArray(X)
y = fff_vector_new(x.size)
fff_vector_memcpy(y, x)
Expand All @@ -133,7 +135,8 @@ def vector_scale(X, double a):
Multiply by a constant value.
y = vector_scale(x, a)
"""
cdef fff_vector *x, *y
cdef fff_vector *x
cdef fff_vector *y
x = fff_vector_fromPyArray(X)
y = fff_vector_new(x.size)
fff_vector_memcpy(y, x)
Expand All @@ -147,7 +150,8 @@ def vector_add_constant(X, double a):
Add a constant value.
y = vector_add_constant(x, a)
"""
cdef fff_vector *x, *y
cdef fff_vector *x
cdef fff_vector *y
x = fff_vector_fromPyArray(X)
y = fff_vector_new(x.size)
fff_vector_memcpy(y, x)
Expand All @@ -161,7 +165,9 @@ def vector_add(X, Y):
Add two vectors.
z = vector_add(x, y)
"""
cdef fff_vector *x, *y, *z
cdef fff_vector *x
cdef fff_vector *y
cdef fff_vector *z
x = fff_vector_fromPyArray(X)
y = fff_vector_fromPyArray(Y)
z = fff_vector_new(x.size)
Expand All @@ -177,7 +183,9 @@ def vector_sub(X, Y):
Substract two vectors: x - y
z = vector_sub(x, y)
"""
cdef fff_vector *x, *y, *z
cdef fff_vector *x
cdef fff_vector *y
cdef fff_vector *z
x = fff_vector_fromPyArray(X)
y = fff_vector_fromPyArray(Y)
z = fff_vector_new(x.size)
Expand All @@ -193,7 +201,9 @@ def vector_mul(X, Y):
Element-wise multiplication.
z = vector_mul(x, y)
"""
cdef fff_vector *x, *y, *z
cdef fff_vector *x
cdef fff_vector *y
cdef fff_vector *z
x = fff_vector_fromPyArray(X)
y = fff_vector_fromPyArray(Y)
z = fff_vector_new(x.size)
Expand All @@ -209,7 +219,9 @@ def vector_div(X, Y):
Element-wise division.
z = vector_div(x, y)
"""
cdef fff_vector *x, *y, *z
cdef fff_vector *x
cdef fff_vector *y
cdef fff_vector *z
x = fff_vector_fromPyArray(X)
y = fff_vector_fromPyArray(Y)
z = fff_vector_new(x.size)
Expand Down Expand Up @@ -300,7 +312,8 @@ def matrix_transpose(A):
Transpose a matrix.
B = matrix_transpose(A)
"""
cdef fff_matrix *a, *b
cdef fff_matrix *a
cdef fff_matrix *b
a = fff_matrix_fromPyArray(A)
b = fff_matrix_new(a.size2, a.size1)
fff_matrix_transpose(b, a)
Expand All @@ -312,7 +325,9 @@ def matrix_add(A, B):
"""
C = matrix_add(A, B)
"""
cdef fff_matrix *a, *b, *c
cdef fff_matrix *a
cdef fff_matrix *b
cdef fff_matrix *c
a = fff_matrix_fromPyArray(A)
b = fff_matrix_fromPyArray(B)
c = fff_matrix_new(a.size1, a.size2)
Expand Down Expand Up @@ -368,13 +383,16 @@ def blas_dasum(X):
return fff_blas_dasum(x)

def blas_ddot(X, Y):
cdef fff_vector *x, *y
cdef fff_vector *x
cdef fff_vector *y
x = fff_vector_fromPyArray(X)
y = fff_vector_fromPyArray(Y)
return fff_blas_ddot(x, y)

def blas_daxpy(double alpha, X, Y):
cdef fff_vector *x, *y, *z
cdef fff_vector *x
cdef fff_vector *y
cdef fff_vector *z
x = fff_vector_fromPyArray(X)
y = fff_vector_fromPyArray(Y)
z = fff_vector_new(y.size)
Expand All @@ -384,7 +402,8 @@ def blas_daxpy(double alpha, X, Y):
return Z

def blas_dscal(double alpha, X):
cdef fff_vector *x, *y
cdef fff_vector *x
cdef fff_vector *y
x = fff_vector_fromPyArray(X)
y = fff_vector_new(x.size)
fff_vector_memcpy(y, x)
Expand All @@ -403,7 +422,10 @@ def blas_dgemm(int TransA, int TransB, double alpha, A, B, double beta, C):
beta C where op(A) = A, A^T, A^H for TransA = CblasNoTrans,
CblasTrans, CblasConjTrans and similarly for the parameter TransB.
"""
cdef fff_matrix *a, *b, *c, *d
cdef fff_matrix *a
cdef fff_matrix *b
cdef fff_matrix *c
cdef fff_matrix *d
a = fff_matrix_fromPyArray(A)
b = fff_matrix_fromPyArray(B)
c = fff_matrix_fromPyArray(C)
Expand All @@ -428,7 +450,10 @@ def blas_dsymm(int Side, int Uplo, double alpha, A, B, beta, C):
when Uplo is CblasLower then the lower triangle and diagonal of A
are used.
"""
cdef fff_matrix *a, *b, *c, *d
cdef fff_matrix *a
cdef fff_matrix *b
cdef fff_matrix *c
cdef fff_matrix *d
a = fff_matrix_fromPyArray(A)
b = fff_matrix_fromPyArray(B)
c = fff_matrix_fromPyArray(C)
Expand All @@ -455,7 +480,9 @@ def blas_dtrmm(int Side, int Uplo, int TransA, int Diag, double alpha, A, B):
diagonal elements of the matrix A are taken as unity and are not
referenced.
"""
cdef fff_matrix *a, *b, *c
cdef fff_matrix *a
cdef fff_matrix *b
cdef fff_matrix *c
a = fff_matrix_fromPyArray(A)
b = fff_matrix_fromPyArray(B)
c = fff_matrix_new(a.size1, a.size2)
Expand All @@ -482,7 +509,9 @@ def blas_dtrsm(int Side, int Uplo, int TransA, int Diag, double alpha, A, B):
CblasUnit then the diagonal elements of the matrix A are taken as
unity and are not referenced.
"""
cdef fff_matrix *a, *b, *c
cdef fff_matrix *a
cdef fff_matrix *b
cdef fff_matrix *c
a = fff_matrix_fromPyArray(A)
b = fff_matrix_fromPyArray(B)
c = fff_matrix_new(a.size1, a.size2)
Expand All @@ -507,7 +536,9 @@ def blas_dsyrk(int Uplo, int Trans, double alpha, A, double beta, C):
when Uplo is CblasLower then the lower triangle and diagonal of C
are used.
"""
cdef fff_matrix *a, *c, *d
cdef fff_matrix *a
cdef fff_matrix *c
cdef fff_matrix *d
a = fff_matrix_fromPyArray(A)
c = fff_matrix_fromPyArray(C)
d = fff_matrix_new(a.size1, a.size2)
Expand All @@ -529,7 +560,10 @@ def blas_dsyr2k(int Uplo, int Trans, double alpha, A, B, double beta, C):
and when Uplo is CblasLower then the lower triangle and diagonal of C
are used.
"""
cdef fff_matrix *a, *b, *c, *d
cdef fff_matrix *a
cdef fff_matrix *b
cdef fff_matrix *c
cdef fff_matrix *d
a = fff_matrix_fromPyArray(A)
b = fff_matrix_fromPyArray(B)
c = fff_matrix_fromPyArray(C)
Expand Down
19 changes: 13 additions & 6 deletions nipy/labs/bindings/wrapper.pyx
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Expand Up @@ -62,7 +62,8 @@ def pass_vector(ndarray X):
"""
Y = pass_vector(X)
"""
cdef fff_vector *x, *y
cdef fff_vector *x
cdef fff_vector *y
x = fff_vector_fromPyArray(X)
y = fff_vector_new(x.size)
fff_vector_memcpy(y, x)
Expand Down Expand Up @@ -105,7 +106,8 @@ def pass_matrix(ndarray X):
"""
Y = pass_matrix(X)
"""
cdef fff_matrix *x, *y
cdef fff_matrix *x
cdef fff_matrix *y
x = fff_matrix_fromPyArray(X)
y = fff_matrix_new(x.size1, x.size2)
fff_matrix_memcpy(y, x)
Expand All @@ -117,7 +119,8 @@ def pass_array(ndarray X):
"""
Y = pass_array(X)
"""
cdef fff_array *x, *y
cdef fff_array *x
cdef fff_array *y
x = fff_array_fromPyArray(X)
y = fff_array_new(x.datatype, x.dimX, x.dimY, x.dimZ, x.dimT)
fff_array_copy(y, x)
Expand All @@ -129,7 +132,9 @@ def pass_vector_via_iterator(ndarray X, int axis=0, int niters=0):
"""
Y = pass_vector_via_iterator(X, axis=0, niters=0)
"""
cdef fff_vector *x, *y, *z
cdef fff_vector *x
cdef fff_vector *y
cdef fff_vector *z
cdef fffpy_multi_iterator* multi

Xdum = X.copy() ## at least two arrays needed for multi iterator
Expand All @@ -152,7 +157,8 @@ def copy_via_iterators(ndarray Y, int axis=0):
Copy array Y into Z via fff's PyArray_MultiIterAllButAxis C function.
Behavior should be equivalent to Z = Y.copy().
"""
cdef fff_vector *y, *z
cdef fff_vector *y
cdef fff_vector *z
cdef fffpy_multi_iterator* multi

# Allocate output array
Expand Down Expand Up @@ -184,7 +190,8 @@ def sum_via_iterators(ndarray Y, int axis=0):
Return the sum of input elements along the dimension specified by axis.
Behavior should be equivalent to Z = Y.sum(axis).
"""
cdef fff_vector *y, *z
cdef fff_vector *y
cdef fff_vector *z
cdef fffpy_multi_iterator* multi

# Allocate output array
Expand Down
10 changes: 8 additions & 2 deletions nipy/labs/glm/kalman.pyx
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Expand Up @@ -84,7 +84,9 @@ def ols(ndarray Y, ndarray X, int axis=0):

REFERENCE: Roche et al, ISBI 2004.
"""
cdef fff_vector *y, *b, *s2
cdef fff_vector *y
cdef fff_vector *b
cdef fff_vector *s2
cdef fff_matrix *x
cdef fff_glm_KF *kfilt
cdef size_t p
Expand Down Expand Up @@ -161,7 +163,11 @@ def ar1(ndarray Y, ndarray X, int niter=2, int axis=0):
REFERENCE:
Roche et al, MICCAI 2004.
"""
cdef fff_vector *y, *b, *vb, *s2, *a
cdef fff_vector *y
cdef fff_vector *b
cdef fff_vector *vb
cdef fff_vector *s2
cdef fff_vector *a
cdef fff_vector Vb_flat
cdef fff_matrix *x
cdef fff_glm_RKF *rkfilt
Expand Down
15 changes: 12 additions & 3 deletions nipy/labs/group/glm_twolevel.pyx
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Expand Up @@ -61,8 +61,12 @@ def em(ndarray Y, ndarray VY, ndarray X, ndarray C=None, int axis=0, int niter=D
Keller and Roche, ISBI 2008.
"""
cdef size_t n, p
cdef fff_vector *y, *vy, *b, *s2
cdef fff_matrix *x, *ppx
cdef fff_vector *y
cdef fff_vector *vy
cdef fff_vector *b
cdef fff_vector *s2
cdef fff_matrix *x
cdef fff_matrix *ppx
cdef fff_glm_twolevel_EM *em
cdef fffpy_multi_iterator* multi

Expand Down Expand Up @@ -131,7 +135,12 @@ def log_likelihood(Y, VY, X, B, S2, int axis=0):
REFERENCE:
Keller and Roche, ISBI 2008.
"""
cdef fff_vector *y, *vy, *b, *s2, *ll, *tmp
cdef fff_vector *y
cdef fff_vector *vy
cdef fff_vector *b
cdef fff_vector *s2
cdef fff_vector *ll
cdef fff_vector *tmp
cdef fff_matrix *x
cdef fffpy_multi_iterator* multi

Expand Down
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