## Question

Asked By – Noob Saibot

I’m trying to speed up the answer here using Cython. I try to compile the code (after doing the `cygwinccompiler.py`

hack explained here), but get a `fatal error: numpy/arrayobject.h: No such file or directory...compilation terminated`

error. Can anyone tell me if it’s a problem with my code, or some esoteric subtlety with Cython?

Below is my code.

```
import numpy as np
import scipy as sp
cimport numpy as np
cimport cython
cdef inline np.ndarray[np.int, ndim=1] fbincount(np.ndarray[np.int_t, ndim=1] x):
cdef int m = np.amax(x)+1
cdef int n = x.size
cdef unsigned int i
cdef np.ndarray[np.int_t, ndim=1] c = np.zeros(m, dtype=np.int)
for i in xrange(n):
c[<unsigned int>x[i]] += 1
return c
cdef packed struct Point:
np.float64_t f0, f1
@cython.boundscheck(False)
def sparsemaker(np.ndarray[np.float_t, ndim=2] X not None,
np.ndarray[np.float_t, ndim=2] Y not None,
np.ndarray[np.float_t, ndim=2] Z not None):
cdef np.ndarray[np.float64_t, ndim=1] counts, factor
cdef np.ndarray[np.int_t, ndim=1] row, col, repeats
cdef np.ndarray[Point] indices
cdef int x_, y_
_, row = np.unique(X, return_inverse=True); x_ = _.size
_, col = np.unique(Y, return_inverse=True); y_ = _.size
indices = np.rec.fromarrays([row,col])
_, repeats = np.unique(indices, return_inverse=True)
counts = 1. / fbincount(repeats)
Z.flat *= counts.take(repeats)
return sp.sparse.csr_matrix((Z.flat,(row,col)), shape=(x_, y_)).toarray()
```

**Now we will see solution for issue: Cython: “fatal error: numpy/arrayobject.h: No such file or directory” **

## Answer

In your `setup.py`

, the `Extension`

should have the argument `include_dirs=[numpy.get_include()]`

.

Also, you are missing `np.import_array()`

in your code.

—

**Example setup.py:**

```
from distutils.core import setup, Extension
from Cython.Build import cythonize
import numpy
setup(
ext_modules=[
Extension("my_module", ["my_module.c"],
include_dirs=[numpy.get_include()]),
],
)
# Or, if you use cythonize() to make the ext_modules list,
# include_dirs can be passed to setup()
setup(
ext_modules=cythonize("my_module.pyx"),
include_dirs=[numpy.get_include()]
)
```

This question is answered By – Robert Kern

**This answer is collected from stackoverflow and reviewed by FixPython community admins, is licensed under cc by-sa 2.5 , cc by-sa 3.0 and cc by-sa 4.0 **