Cython wrapper trial 3 seg-fault

Cython/openGJK.c

@@ -671,7 +671,6 @@ inline static void subalgorithm(struct simplex *s, double *v) {
   }
 }
 
-#define DEBUG
 
 double gjk(struct bd bd1, struct bd bd2, struct simplex *s) {
 

Cython/openGJK_cython.pyx

@@ -1,7 +1,9 @@
 #cython: language_level=3, boundscheck=False
-import numpy as np 
-from libc.stdlib cimport free
 
+import numpy as np
+from libc.stdlib cimport free, malloc
+
+# Declare C function and data 
 cdef extern from "openGJK.h":
 	struct bd: 
 		int numpoints
@@ -16,17 +18,27 @@ cdef extern from "openGJK.h":
 
 	double gjk(bd bd1, bd bd2, simplex *s)
 
+# Create Python function
 def pygjk(bod1, bod2):
-	"""Returns distance between two bodies, input: array of nodal coordinates for each body"""
 
-	print("Hello!!")
+	# Declare data types
 	cdef: 
-		simplex ss
+		simplex s
 		bd bd1
 		bd bd2
 		int i, j
 		double answer
 
+	print("Break 1")#--------------------------------------------------
+
+	# Allocate memory for pointers
+	bd1.coord = <double**> malloc(sizeof(double)*bod1.ndim)
+	bd1.coord[0] = <double*> malloc(sizeof(double)*3)
+	bd2.coord = <double**> malloc(sizeof(double)*bod2.ndim)
+	bd2.coord[0] = <double*> malloc(sizeof(double)*3)
+
+
+	# Convert 1D array to 2D, if any
 	if bod1.ndim < 2:
 		bod1 = np.append([bod1], [[1.,1.,1.]], axis = 0)
 	if bod2.ndim < 2:
@@ -35,26 +47,37 @@ def pygjk(bod1, bod2):
 	bd1.numpoints = np.size(bod1,0)
 	bd2.numpoints = np.size(bod2,0)
 
+
+	print("Break 2")#--------------------------------------------------
+	
+	# Create numpy-array MemoryView
 	cdef:	
-		double [:,:] narr1 = bod1 	# create numpy-array MemoryView
+		double [:,:] narr1 = bod1 	
 		double [:,:] narr2 = bod2
 
+	print("Break 3")#--------------------------------------------------
 
+	# Assign coordinate values (Segmentation Fault Here!!, )
 	for i in range(0, bd1.numpoints):
-		bd1.coord[i] = hex(id(bod1[i]))
+		bd1.coord[i][0] = narr1[i,0]
+		bd1.coord[i][1] = narr1[i,1]
+		bd1.coord[i][2] = narr1[i,2]
 
 	
 	for j in range(0, bd2.numpoints):
-		bd2.coord[i][0] = narr2[j,0]
-		bd2.coord[i][1] = narr2[j,1]
-		bd2.coord[i][2] = narr2[j,2]
+		bd2.coord[j][0] = narr2[j,0]
+		bd2.coord[j][1] = narr2[j,1]
+		bd2.coord[j][2] = narr2[j,2]
 
 
-	answer = gjk(bd1, bd2, &ss)
+	print("Break 4")#--------------------------------------------------
 
+	# Call C function
+	answer = gjk(bd1, bd2, &s)
+
+	# Free the memory
 	free(bd1.coord)
 	free(bd2.coord)
 
-
 	return answer
 

Cython/pygjk_trial.py

@@ -0,0 +1,5 @@
+import numpy as np
+import openGJKpy 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)