RF: refactor import_array as documented

matthew-brett · matthew-brett · commit cd595cf9b42a · 2015-08-28T23:13:31.000+01:00
Instead of calling `import_array()` in every C function, use the method of sharing the numpy API pointer table documented here: http://docs.scipy.org/doc/numpy/reference/c-api.array.html#importing-the-api Also, deal with different return types from `import_array()` in Python 3 and Python 2 - see http://mail.scipy.org/pipermail/numpy-discussion/2010-December/054345.html
diff --git a/lib/fff_python_wrapper/fffpy.c b/lib/fff_python_wrapper/fffpy.c
@@ -9,12 +9,14 @@
    because PyArray_API is defined static, in order not to share that symbol
    within the dso. (import_array() asks the pointer value to the python process)
 */
-void fffpy_import_array(void) { 
-  import_array(); 
-  return;
+/*
+ * deal with differences in macro return result between Python 2 and 3
+ * http://mail.scipy.org/pipermail/numpy-discussion/2010-December/054350.html
+ */
+IMP_OUT fffpy_import_array(void) {
+  import_array();
 }
 
-
 /* Static functions */
 static npy_intp _PyArray_main_axis(const PyArrayObject* x, int* ok); 
 static fff_vector* _fff_vector_new_from_buffer(const char* data, npy_intp dim, npy_intp stride, int type, int itemsize);
diff --git a/lib/fff_python_wrapper/fffpy.h b/lib/fff_python_wrapper/fffpy.h
@@ -31,8 +31,17 @@
    static, in order not to share that symbol within the
    dso. (import_array() asks the pointer value to the python process)
 */
-extern void fffpy_import_array(void);
+/*
+ * deal with differences in macro return result between Python 2 and 3
+ * http://mail.scipy.org/pipermail/numpy-discussion/2010-December/054350.html
+ */
+#if PY_MAJOR_VERSION >= 3
+typedef int IMP_OUT;
+#else
+typedef void IMP_OUT;
+#endif
 
+extern IMP_OUT fffpy_import_array(void);
 
 /*!
   \brief Convert \c PyArrayObject to \c fff_vector 
diff --git a/nipy/algorithms/registration/_registration.h b/nipy/algorithms/registration/_registration.h
@@ -0,0 +1 @@
+#define PY_ARRAY_UNIQUE_SYMBOL _registration_ARRAY_API
diff --git a/nipy/algorithms/registration/_registration.pyx b/nipy/algorithms/registration/_registration.pyx
@@ -8,23 +8,24 @@ transformations.
 
 __version__ = '0.3'
 
+# Set symbol for array_import; must come before cimport numpy
+cdef extern from "_registration.h":
+    int PY_ARRAY_UNIQUE_SYMBOL
+
 
 # Includes
 from numpy cimport (import_array, ndarray, flatiter, broadcast, 
                     PyArray_MultiIterNew, PyArray_MultiIter_DATA, 
                     PyArray_MultiIter_NEXT)
 
 
-# Externals
 cdef extern from "joint_histogram.h":
-    void joint_histogram_import_array()
     int joint_histogram(ndarray H, unsigned int clampI, unsigned int clampJ,  
                         flatiter iterI, ndarray imJ_padded, 
                         ndarray Tvox, int interp)
     int L1_moments(double* n, double* median, double* dev, ndarray H)
 
 cdef extern from "cubic_spline.h":
-    void cubic_spline_import_array()
     void cubic_spline_transform(ndarray res, ndarray src)
     double cubic_spline_sample1d(double x, ndarray coef, 
                                  int mode) 
@@ -39,14 +40,10 @@ cdef extern from "cubic_spline.h":
                                  int mode_x, int mode_y, int mode_z)
 
 cdef extern from "polyaffine.h": 
-    void polyaffine_import_array()
     void apply_polyaffine(ndarray XYZ, ndarray Centers, ndarray Affines, ndarray Sigma)
 
 
 # Initialize numpy
-joint_histogram_import_array()
-cubic_spline_import_array()
-polyaffine_import_array()
 import_array()
 import numpy as np
 
diff --git a/nipy/algorithms/registration/cubic_spline.c b/nipy/algorithms/registration/cubic_spline.c
@@ -54,13 +54,6 @@ static inline void _apply_affine_transform(double* Tx, double* Ty, double* Tz,
 					   size_t x, size_t y, size_t z); 
 
 
-/* Numpy import */
-void cubic_spline_import_array(void) { 
-  import_array(); 
-  return;
-}
-
-
 /* Returns the value of the cubic B-spline function at x */
 double cubic_spline_basis (double x)
 {
diff --git a/nipy/algorithms/registration/cubic_spline.h b/nipy/algorithms/registration/cubic_spline.h
@@ -25,10 +25,14 @@ extern "C" {
 #endif
 
 #include <Python.h>
-#include <numpy/arrayobject.h>
 
-  /* Numpy import */
-  extern void cubic_spline_import_array(void);
+/*
+ * Use extension numpy symbol table
+ */
+#define NO_IMPORT_ARRAY
+#include "_registration.h"
+
+#include <numpy/arrayobject.h>
 
   /*! 
     \brief Cubic spline basis function
diff --git a/nipy/algorithms/registration/joint_histogram.c b/nipy/algorithms/registration/joint_histogram.c
@@ -34,14 +34,6 @@ static inline void _rand_interpolation(unsigned int i,
 				       int nn, 
 				       void* params); 
 
-
-/* Numpy import */
-void joint_histogram_import_array(void) {
-  import_array(); 
-  return;
-}
-
-
 /* 
    
 JOINT HISTOGRAM COMPUTATION. 
diff --git a/nipy/algorithms/registration/joint_histogram.h b/nipy/algorithms/registration/joint_histogram.h
@@ -17,12 +17,14 @@ extern "C" {
 #endif
 
 #include <Python.h>
-#include <numpy/arrayobject.h>
-
 
-  /* Numpy import */
-  extern void joint_histogram_import_array(void);
+/*
+ * Use extension numpy symbol table
+ */
+#define NO_IMPORT_ARRAY
+#include "_registration.h"
 
+#include <numpy/arrayobject.h>
 
   /* 
      Update a pre-allocated joint histogram. Important notice: in all
diff --git a/nipy/algorithms/registration/polyaffine.c b/nipy/algorithms/registration/polyaffine.c
@@ -6,13 +6,6 @@
 #define TINY 1e-200
 
 
-/* Numpy import */
-void polyaffine_import_array(void) { 
-  import_array(); 
-  return;
-}
-
-
 static double _gaussian(double* xyz, double* center, double* sigma)
 {
   double aux, d2 = 0.0; 
diff --git a/nipy/algorithms/registration/polyaffine.h b/nipy/algorithms/registration/polyaffine.h
@@ -6,9 +6,14 @@ extern "C" {
 #endif
 
 #include <Python.h>
-#include <numpy/arrayobject.h>
 
-  extern void polyaffine_import_array(void);
+/*
+ * Use extension numpy symbol table
+ */
+#define NO_IMPORT_ARRAY
+#include "_registration.h"
+
+#include <numpy/arrayobject.h>
 
   extern void apply_polyaffine(PyArrayObject* XYZ, 
 			       const PyArrayObject* Centers, 
diff --git a/nipy/algorithms/segmentation/_segmentation.h b/nipy/algorithms/segmentation/_segmentation.h
@@ -0,0 +1 @@
+#define PY_ARRAY_UNIQUE_SYMBOL _segmentation_ARRAY_API
diff --git a/nipy/algorithms/segmentation/_segmentation.pyx b/nipy/algorithms/segmentation/_segmentation.pyx
@@ -8,12 +8,15 @@ Author: Alexis Roche, 2010.
 
 __version__ = '0.2'
 
+# Set symbol for array_import; must come before cimport numpy
+cdef extern from "_segmentation.h":
+    int PY_ARRAY_UNIQUE_SYMBOL
+
 # Includes
 from numpy cimport import_array, ndarray
 
 # Externals
 cdef extern from "mrf.h":
-    void mrf_import_array()
     void ve_step(ndarray ppm, 
                  ndarray ref,
                  ndarray XYZ, 
@@ -30,7 +33,6 @@ cdef extern from "mrf.h":
 
 
 # Initialize numpy
-mrf_import_array()
 import_array()
 import numpy as np
 
diff --git a/nipy/algorithms/segmentation/mrf.c b/nipy/algorithms/segmentation/mrf.c
@@ -8,12 +8,6 @@
 #endif
 
 
-/* Numpy import */
-void mrf_import_array(void) { 
-  import_array(); 
-  return;
-}
-
 /* Encode neighborhood systems using static arrays */
 int ngb6 [] = {1,0,0,
 	       -1,0,0,
diff --git a/nipy/algorithms/segmentation/mrf.h b/nipy/algorithms/segmentation/mrf.h
@@ -6,9 +6,15 @@ extern "C" {
 #endif
 
 #include <Python.h>
+
+/*
+ * Use extension numpy symbol table
+ */
+#define NO_IMPORT_ARRAY
+#include "_segmentation.h"
+
 #include <numpy/arrayobject.h>
 
-  extern void mrf_import_array(void);
 
   extern void ve_step(PyArrayObject* ppm, 
 		      const PyArrayObject* ref,

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1 @@`
	`1`	`+#define PY_ARRAY_UNIQUE_SYMBOL _registration_ARRAY_API`
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1 @@`
	`1`	`+#define PY_ARRAY_UNIQUE_SYMBOL _segmentation_ARRAY_API`