Build separate GSL/native Python modules.

igormis · Jan 10, 2011 · 27db9e4 · 27db9e4
1 parent 32e682c
commit 27db9e4
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Showing 4 changed files with 571 additions and 163 deletions.
diff --git a/Makefile b/Makefile
@@ -1,6 +1,6 @@
 CXXFLAGS                 = -Wall
 # OUTPUT_OPTION            = -o .obj/$@
-swig_flags               = -Wall -c++ -python
+swig_flags               = -Wall -c++ -python -outputtuple
 objects                  = assortativity.o \
                            betweenness_bin.o \
                            betweenness_wei.o \
@@ -90,9 +90,12 @@ libbct.a: $(objects)
 	$(AR) rcs libbct.a $(objects)
 
 swig: $(objects)
-	swig $(swig_flags) -o bct_wrap.cpp bct.i
-	$(CXX) $(CXXFLAGS) -c -I$(python_dir) bct_wrap.cpp
-	$(CXX) $(CXXFLAGS) -lgsl -lgslcblas $(swig_lib_flags) -o _bct.so $(objects) bct_wrap.o
+	swig $(swig_flags) -o bct_gsl_wrap.cpp bct_gsl.i
+	swig $(swig_flags) -o bct_py_wrap.cpp bct_py.i
+	$(CXX) $(CXXFLAGS) -c -I$(python_dir) bct_gsl_wrap.cpp
+	$(CXX) $(CXXFLAGS) -c -I$(python_dir) bct_py_wrap.cpp
+	$(CXX) $(CXXFLAGS) -lgsl -lgslcblas $(swig_lib_flags) -o _bct_gsl.so $(objects) bct_gsl_wrap.o
+	$(CXX) $(CXXFLAGS) -lgsl -lgslcblas $(swig_lib_flags) -o _bct_py.so $(objects) bct_py_wrap.o
 
 $(objects): matlab/matlab.h bct.h
 
@@ -115,4 +118,4 @@ uninstall:
 	-rm $(install_dir)/lib/libbct.a
 
 clean:
-	-rm _bct.so bct.py bct.pyc bct_swig.o bct_wrap.cpp bct_wrap.o libbct.a $(objects)
+	-rm _bct_gsl.so _bct_py.so bct_gsl.py bct_py.py bct_gsl.pyc bct_py.pyc bct_gsl_wrap.cpp bct_py_wrap.cpp bct_gsl_wrap.o bct_py_wrap.o libbct.a $(objects)
diff --git a/bct.i → bct_gsl.i b/bct.i → bct_gsl.i
@@ -1,8 +1,13 @@
-%module bct
+%module bct_gsl
 %include "std_string.i"
+%include "swig.i"
 %include "typemaps.i"
 %feature("autodoc", "1");
 
+%{
+	#include "bct.h"
+%}
+
 %apply int* OUTPUT { int* qstop, int* K };
 %apply double* OUTPUT { double* radius, double* diameter, double* eta, double* fs };
 
@@ -12,157 +17,6 @@
 %typemap(in, numinputs = 0) gsl_matrix** (gsl_matrix* temp) { $1 = &temp; }
 %typemap(argout) gsl_matrix** { %append_output(SWIG_NewPointerObj(*$1, $descriptor(gsl_matrix*), 0)); }
 
-%{
-	#include "bct.h"
-	#include <gsl/gsl_matrix.h>
-	#include <gsl/gsl_vector.h>
-	#include <Python.h>
-	#include <vector>
-
-	/*
-	 * Converts a gsl_vector* to a Python list.
-	 */
-	PyObject* from_gsl(const gsl_vector* v) {
-		PyObject* list = PyList_New(v->size);
-		for (int i = 0; i < (int)v->size; i++) {
-			PyObject* value = PyFloat_FromDouble(gsl_vector_get(v, i));
-			PyList_SetItem(list, i, value);
-		}
-		return list;
-	}
-
-	/*
-	 * Converts a gsl_matrix* to a Python list of lists.
-	 */
-	PyObject* from_gsl(const gsl_matrix* m) {
-		PyObject* list = PyList_New(m->size1);
-		for (int i = 0; i < (int)m->size1; i++) {
-			PyObject* sublist = PyList_New(m->size2);
-			PyList_SetItem(list, i, sublist);
-			for (int j = 0; j < (int)m->size2; j++) {
-				PyObject* value = PyFloat_FromDouble(gsl_matrix_get(m, i, j));
-				PyList_SetItem(sublist, j, value);
-			}
-		}
-		return list;
-	}
-
-	/*
-	 * Converts a std::vector<gsl_matrix*> to a Python list of lists of lists.
-	 */
-	PyObject* from_gsl(const std::vector<gsl_matrix*>& m) {
-		PyObject* list = PyList_New(m.size());
-		for (int i = 0; i < (int)m.size(); i++) {
-			if (m[i] == NULL) {
-				PyObject* sublist = PyList_New(0);
-				PyList_SetItem(list, i, sublist);
-			} else {
-				PyObject* sublist = PyList_New(m[i]->size1);
-				PyList_SetItem(list, i, sublist);
-				for (int j = 0; j < (int)m[i]->size1; j++) {
-					PyObject* subsublist = PyList_New(m[i]->size2);
-					PyList_SetItem(sublist, j, subsublist);
-					for (int k = 0; k < (int)m[i]->size2; k++) {
-						PyObject* value = PyFloat_FromDouble(gsl_matrix_get(m[i], j, k));
-						PyList_SetItem(subsublist, k, value);
-					}
-				}
-			}
-		}
-		return list;
-	}
-
-	/*
-	 * Converts a double* to a gsl_vector*.
-	 */
-	gsl_vector* to_gslv(const double* array, int size) {
-		gsl_vector* v = gsl_vector_alloc(size);
-		for (int i = 0; i < size; i++) {
-			gsl_vector_set(v, i, array[i]);
-		}
-		return v;
-	}
-
-	/*
-	 * Converts a double* to a gsl_matrix*.
-	 */
-	gsl_matrix* to_gslm(const double* array, int size1, int size2) {
-		gsl_matrix* m = gsl_matrix_alloc(size1, size2);
-		for (int i = 0; i < size1; i++) {
-			for (int j = 0; j < size2; j++) {
-				gsl_matrix_set(m, i, j, array[i * size2 + j]);
-			}
-		}
-		return m;
-	}
-
-	/*
-	 * Converts a Python list to a gsl_vector*.
-	 */
-	gsl_vector* to_gslv(PyObject* list) {
-		int n = PyList_Size(list);
-		gsl_vector* v = gsl_vector_alloc(n);
-		for (int i = 0; i < n; i++) {
-			double value = PyFloat_AsDouble(PyList_GetItem(list, i));
-			gsl_vector_set(v, i, value);
-		}
-		return v;
-	}
-
-	/*
-	 * Converts a Python list of lists to a gsl_matrix*.
-	 */
-	gsl_matrix* to_gslm(PyObject* list) {
-		int n_rows = PyList_Size(list);
-		int n_cols = PyList_Size(PyList_GetItem(list, 0));
-		gsl_matrix* m = gsl_matrix_alloc(n_rows, n_cols);
-		for (int i = 0; i < n_rows; i++) {
-			PyObject* sublist = PyList_GetItem(list, i);
-			for (int j = 0; j < n_cols; j++) {
-				double value = PyFloat_AsDouble(PyList_GetItem(sublist, j));
-				gsl_matrix_set(m, i, j, value);
-			}
-		}
-		return m;
-	}
-
-	/*
-	 * Converts a Python list of lists of lists to a std::vector<gsl_matrix*>.
-	 */
-	std::vector<gsl_matrix*> to_gsl3dm(PyObject* list) {
-		int n_matrices = PyList_Size(list);
-		std::vector<gsl_matrix*> m(n_matrices);
-		for (int i = 0; i < n_matrices; i++) {
-			PyObject* sublist = PyList_GetItem(list, i);
-			int n_rows = PyList_Size(sublist);
-			int n_cols = PyList_Size(PyList_GetItem(sublist, 0));
-			if (n_rows == 0 || n_cols == 0) {
-				m[i] = NULL;
-			} else {
-				gsl_matrix* subm = gsl_matrix_alloc(n_rows, n_cols);
-				m[i] = subm;
-				for (int j = 0; j < n_rows; j++) {
-					PyObject* subsublist = PyList_GetItem(sublist, j);
-					for (int k = 0; k < n_cols; k++) {
-						double value = PyFloat_AsDouble(PyList_GetItem(subsublist, k));
-						gsl_matrix_set(subm, j, k, value);
-					}
-				}
-			}
-		}
-		return m;
-	}
-%}
-
-PyObject* from_gsl(const gsl_vector* v);
-PyObject* from_gsl(const gsl_matrix* m);
-PyObject* from_gsl(const std::vector<gsl_matrix*>& m);
-gsl_vector* to_gslv(const double* array, int size);
-gsl_matrix* to_gslm(const double* array, int size1, int size2);
-gsl_vector* to_gslv(PyObject* list);
-gsl_matrix* to_gslm(PyObject* list);
-std::vector<gsl_matrix*> to_gsl3dm(PyObject* list);
-
 namespace bct {
 
 	// Density, degree, and assortativity
@@ -267,12 +121,12 @@ namespace bct {
 	gsl_matrix* randmio_und_connected(const gsl_matrix* R, int ITER);
 
 	// Data sets
-	extern const double cat_all[95 * 95];
-	extern const double cat_ctx[52 * 52];
-	extern const double fve30[30 * 30];
-	extern const double fve32[32 * 32];
-	extern const double macaque47[47 * 47];
-	extern const double macaque71[71 * 71];
+	gsl_matrix* get_cat_all();
+	gsl_matrix* get_cat_ctx();
+	gsl_matrix* get_fve30();
+	gsl_matrix* get_fve32();
+	gsl_matrix* get_macaque47();
+	gsl_matrix* get_macaque71();
 
 	// Matrix status checking
 	enum status {
@@ -522,3 +376,10 @@ namespace matlab {
 	gsl_matrix* permute_columns(const gsl_permutation* p, const gsl_matrix* m);
 	gsl_matrix* permute_rows(const gsl_permutation* p, const gsl_matrix* m);
 }
+
+PyObject* from_gsl(const gsl_vector* v);
+PyObject* from_gsl(const gsl_matrix* m);
+PyObject* from_gsl(const std::vector<gsl_matrix*>& m);
+gsl_vector* to_gslv(PyObject* list);
+gsl_matrix* to_gslm(PyObject* list);
+std::vector<gsl_matrix*> to_gsl3dm(PyObject* list);