Cython Example

gistfile1.pyx

cdef DTYPE_t getEpsilon(int xi, DTYPE_t[:,:] RMSD, DTYPE_t[:] epsilonList, DTYPE_t[:] derivativeEpsilonList, int N):
	cdef DTYPE_t e,k
	cdef int i,j,x,y,neighborsLength
	cdef DTYPE_t[:,:] eigenValues=np.zeros((len(derivativeEpsilonList),N), dtype=DTYPE)
	cdef DTYPE_t[:,:] neighborsMatrix
	cdef DTYPE_t[:] A

	for i,e in enumerate(derivativeEpsilonList):
		neighbors=[]
		for j in range(N):
			if(RMSD[xi,j]<=e+.01):
				neighbors.append(j)

		neighborsLength=len(neighbors)

		if neighborsLength>1:
			neighborsMatrix=np.zeros((neighborsLength,neighborsLength), dtype=DTYPE)
			
			for x in range(neighborsLength):
				for y in range(neighborsLength):
					neighborsMatrix[x][y]=RMSD[x,neighbors[y]]

			A=np.linalg.svd(neighborsMatrix, compute_uv=False)
			for j,k in enumerate(A):
				eigenValues[i][j]=k*k
		else:
			print "maxEpsilon too small! Try again with a larger maxEpsilon value."
			return derivativeEpsilonList[i+3]

	eps= getIntrinsicScaleAndDim(xi,eigenValues, epsilonList, derivativeEpsilonList)
	return eps