Creating numpy array from c-pointer crashes ipython kernel [duplicate]

Question

With this code I am trying to create a numpy array from a malloc'ed c pointer, inspired by a blog post from Gaël Varoquaux.

The line that creates the array seems to lead to an invalid memory access as it crashes the kernel. What did I do wrong?

%%cython -f

from libc.stdlib cimport malloc
import numpy as np
cimport numpy as np

cdef array_from_pointer(double* ptr, int size):
    cdef np.npy_intp shape_c[1]
    shape_c[0] = <np.npy_intp> size
    ndarray = np.PyArray_SimpleNewFromData(1, shape_c, np.NPY_FLOAT64, ptr)
    return ndarray


cdef N = 12
cdef double* ptr = <double*> malloc(sizeof(double)*N)

array_from_pointer(ptr, N)

related: stackoverflow.com/a/25496494/2272172

cel
– cel

2020-03-11 18:08:29 +00:00
Commented Mar 11, 2020 at 18:08 — cel
– cel, Commented Mar 11, 2020 at 18:08

cel · Accepted Answer · 2020-03-11 18:08:14Z

0

Before using numpy's Array API, you need to call np.import_array():

%%cython -f

from libc.stdlib cimport malloc
import numpy as np
cimport numpy as np
np.import_array()

cdef array_from_pointer(double* ptr, int size):
    cdef np.npy_intp shape_c[1]
    shape_c[0] = <np.npy_intp> size
    ndarray = np.PyArray_SimpleNewFromData(1, shape_c, np.NPY_FLOAT64, ptr)
    return ndarray


cdef N = 12
cdef double* ptr = <double*> malloc(sizeof(double)*N)

array_from_pointer(ptr, N)

Failing to do so causes the segmentation fault that crashes the ipython kernel.

answered Mar 11, 2020 at 18:08

cel

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