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examples/cython/openGJK_cython.pxd

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+# Declare C function and data types
+cdef extern from "openGJK.h":
+	struct bd:
+		int numpoints
+		double s[3]
+		double ** coord
+
+	struct simplex:
+		int nvrtx
+		double vrtx[4][3]
+		int wids[4]
+		double lambdas[4]
+
+	double gjk(bd bd1, bd bd2, simplex *s)

examples/cython/openGJK_cython.pyx

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+#!python
+# cython: language_level=3
+# distutils: sources = src/openGJK.c
+# distutils: include_dirs = include/openGJK
+
+cimport openGJK_cython
+
+import numpy as np
+from libc.stdlib cimport free, malloc
+from cpython.mem  cimport PyMem_Malloc, PyMem_Free
+
+# Create Python function
+def pygjk(bod1, bod2):
+
+	# Declare data types
+	cdef: 
+		simplex s
+		bd bd1
+		bd bd2
+		double dist2
+
+	# Convert 1D array to 2D, if any
+	if bod1.ndim < 2:
+		bod1 = np.append([bod1], [[1.,1.,1.]], axis = 0)
+		bd1.numpoints = np.size(bod1,0) - 1
+	else:
+		bd1.numpoints = np.size(bod1,0)
+
+
+	if bod2.ndim < 2:
+		bod2 = np.append([bod2], [[1.,1.,1.]], axis = 0)
+		bd2.numpoints = np.size(bod2,0) - 1
+	else:
+		bd2.numpoints = np.size(bod2,0)
+
+	
+	# Allocate memory for bodies
+	bd1.coord = <double **> malloc(bd1.numpoints * sizeof(double *))
+	if not bd1.coord:
+		raise NameError('Not enough memory for bd1.coord')
+	for i in range(0, bd1.numpoints):
+		bd1.coord[i] = <double *> malloc(3 * sizeof(double))
+		if not bd1.coord[i]:
+			raise NameError('Not enough memory for bd1.coord[]')
+
+	bd2.coord = <double **> malloc(bd2.numpoints * sizeof(double *))
+	if not bd2.coord:
+		raise NameError('Not enough memory for bd2.coord')
+	for j in range(0, bd2.numpoints):
+		bd2.coord[j] = <double *> malloc(3 * sizeof(double))
+		if not bd2.coord[j]:
+			raise NameError('Not enough memory for bd2.coord[]')
+
+	# Create numpy-array MemoryView
+	cdef:	
+		double [:,:] narr1 = bod1 	
+		double [:,:] narr2 = bod2
+
+	# Assign coordinate values
+	for i in range(0, bd1.numpoints):
+		for j in range(0,3):
+			bd1.coord[i][j] = narr1[i,j]
+	
+	for i in range(0, bd2.numpoints):
+		for j in range(0,3):
+			bd2.coord[i][j] = narr2[i,j]
+
+	# Call C function
+	dist2 = gjk(bd1, bd2, &s)
+
+	# Free the memory
+	for ii in range(0, bd1.numpoints):
+		free(bd1.coord[ii])
+	free(bd1.coord)
+
+	for jj in range(0, bd2.numpoints):
+		free(bd2.coord[jj])
+	free(bd2.coord)
+
+	return dist2
+

examples/cython/pygjk_trial.py

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+import numpy as np
+import openGJK_cython as opengjk
+a = np.array([[1.,1.,1.],[1.,1.,1.]])
+b = np.array([[11.,1.,1.],[1.,1.,1.]])
+d = opengjk.pygjk(a,b)
+print(d)

examples/cython/setup.py

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+from setuptools import Extension, setup
+from Cython.Build import cythonize
+
+exts = Extension(
+	"openGJK_cython",
+	sources = ["openGJK_cython.pyx"],
+	extra_compile_args=['-Iinclude/','-fopenmp'],
+	extra_link_args=['-fopenmp'],
+)
+
+setup(
+	name='openGJK-cython-version',
+	ext_modules = cythonize( [exts] )
+)