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Asked: 2026-06-13T08:59:27+00:00

I’m attempting to optimise a simple cython routine I’ve written that accepts a 1D

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I’m attempting to optimise a simple cython routine I’ve written that accepts a 1D numpy array as input and returns a 1D numpy array as output.

I have a naive version working, and am now attempting to do some standard optimisations to the numpy parts of the cython code.

However, as soon as I add cimport numpy to my cython source file, I am unable to run the extension module (though it compiles okay), throwing a ValueError: numpy.dtype does not appear to be the correct type object.

My numpy version is 1.6.0 and python version 2.6.5 (default, Ubuntu 10.04 apt-get installations)

Minimal example causing the problem:

test_ext.pyx

import numpy as np
cimport numpy as np #Commenting this line un-breaks the extension

def test_ext(refls, str mode, int nguard, int nblock):

    cdef int i
    cdef int _len = refls.shape[0]
    _out = np.zeros([_len])

    for i in range(_len):
        _out[i] = refls[i] + 1
    return _out

setup.py

from distutils.core import setup
from distutils.extension import Extension
from Cython.Distutils import build_ext

ext_modules = [Extension("test_ext", ["test_ext.pyx"])]

setup(
    name = 'test',
    cmdclass = {'build_ext': build_ext},
    ext_modules = ext_modules
)

run_ext.py

import numpy
from test_ext import test_ext

a = np.array([x for x in range(260)])
_res = test_ext.test_ext(a, 'avg', 2, 3)

build with:

python setup.py build_ext --inplace

My build output:

running build_ext
cythoning my_ext.pyx to my_ext.c
building 'my_ext' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/python2.6 -c my_ext.c -o build/temp.linux-x86_64-2.6/my_ext.o
/usr/include/python2.6/numpy/__multiarray_api.h:968: warning: ‘_import_array’ defined but not used
my_ext.c:732: warning: ‘__pyx_k_3’ defined but not used
my_ext.c:733: warning: ‘__pyx_k_4’ defined but not used
my_ext.c:753: warning: ‘__pyx_k_24’ defined but not used
my_ext.c:759: warning: ‘__pyx_k_26’ defined but not used
my_ext.c:760: warning: ‘__pyx_k_27’ defined but not used
my_ext.c:1118: warning: ‘__pyx_pf_5numpy_7ndarray___getbuffer__’ defined but not used
my_ext.c:1876: warning: ‘__pyx_pf_5numpy_7ndarray___releasebuffer__’ defined but not used
gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions build/temp.linux-x86_64-2.6/my_ext.o -o /home/path/to/my_ext.so

and run then run_ext.py.

With the cimport line uncommented, I get the error:

Traceback (most recent call last):
  File "run_ext.py", line 2, in <module>
    from test_ext import test_ext
  File "numpy.pxd", line 43, in test_ext (test_ext.c:2788)
ValueError: numpy.dtype does not appear to be the correct type object

What causes this and how can I fix it to continue optimising my extension? I have attempted to continue with the optimisations as per the link above, but however far along I get, nothing un-breaks this issue for me.

I’ve seen some other people with this problem that had version problems with python/numpy, but I don’t think that’s the case for me (though I’m open to suggestion there). Any suggestions appreciated.

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1 Answer

  1. Editorial Team

    Looks like my build file just needed to include the numpy include files. Changing setup.py to what is below fixed everything:

    setup.py

    from distutils.core import setup
from distutils.extension import Extension
from Cython.Distutils import build_ext
import numpy   # << New line

ext_modules = [Extension("test_ext", ["test_ext.pyx"])]

setup(
    name = 'test',
    cmdclass = {'build_ext': build_ext},
    include_dirs = [numpy.get_include()], # << New line
    ext_modules = ext_modules
)
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