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POArray of pointers from C++ to NumPy through Cython
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  1. POArray of pointers from C++ to NumPy through Cython
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    copied!<p>I have a library in c++ and I'm trying to wrap it for python using Cython. One function returns an array of 3D vectors (float (*x)[3]) and I want to access that data from python. I was able to do so by doing something like</p> <pre><code>res = [ (self.thisptr.x[j][0],self.thisptr.x[j][1],self.thisptr.x[j][2]) for j in xrange(self.natoms) ] </code></pre> <p>but I would like to access this as a numpy array, so I tried numpy.array on that and it was much slower. I also tried</p> <pre><code> cdef np.ndarray res = np.zeros([self.thisptr.natoms,3], dtype=np.float) cdef int i for i in range(self.natoms): res[i][0] = self.thisptr.x[i][0] res[i][1] = self.thisptr.x[i][1] res[i][2] = self.thisptr.x[i][2] </code></pre> <p>But is about three times slower than the list version. </p> <p>Any suggestions on how to convert the list of vectors to an numpy array faster?</p> <p>The complete code is </p> <pre><code>cimport cython import numpy as np cimport numpy as np ctypedef np.float_t ftype_t cdef extern from "ccxtc.h" namespace "ccxtc": cdef cppclass xtc: xtc(char []) except + int next() int natoms float (*x)[3] float time cdef class pyxtc: cdef xtc *thisptr def __cinit__(self, char fname[]): self.thisptr = new xtc(fname) def __dealloc__(self): del self.thisptr property natoms: def __get__(self): return self.thisptr.natoms property x: def __get__(self): cdef np.ndarray res = np.zeros([self.thisptr.natoms,3], dtype=np.float) cdef int i for i in range(self.natoms): res[i][0] = self.thisptr.x[i][0] res[i][1] = self.thisptr.x[i][1] res[i][2] = self.thisptr.x[i][2] return res #return [ (self.thisptr.x[j][0],self.thisptr.x[j][1],self.thisptr.x[j][2]) for j in xrange(self.natoms)] @cython.boundscheck(False) def next(self): return self.thisptr.next() </code></pre>
 

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