Cython memoryviews: wrapping c function with array parameter to pass numpy array

Question

I am trying to use Cython to wrap c function with an array parameter (quick_sort()), so I can pass a numpy array to it. I've searched the documentation, SO and web for a working, minimal example but didn't find it. I've tried several possibilities but without any progress, so please help me to figure it out. Here are my files:

quicksort.c

#include <stdio.h>

void quick_sort (int* a, int n) {
    int i, j, p, t;
    if (n < 2)
        return;
    p = a[n / 2];
    for (i = 0, j = n - 1;; i++, j--) {
        while (a[i] < p)
            i++;
        while (p < a[j])
            j--;
        if (i >= j)
            break;
        t = a[i];
        a[i] = a[j];
        a[j] = t;
    }
    quick_sort(a, i);
    quick_sort(a + i, n - i);
}

quicksort.h

void quick_sort (int* a, int n);

quicksort.pxd

cdef extern from "quicksort.h":
    void quick_sort (int[:] a, int n)

cy_quicksort.pyx

cimport quicksort

def quicksort_c(int[:] a):
    quicksort.quick_sort(a, a.size)

setup.py

from distutils.core import setup
from Cython.Build import cythonize

setup(
    name='quicksort cython',
    ext_modules=cythonize("*.pyx"),
)

When I'm running python setup.py build_ext --inplace command, it returns the following error:

cy_quicksort.c:1362:14: error: passing '__Pyx_memviewslice' to parameter of
      incompatible type 'int *'
  quick_sort(__pyx_v_a, __pyx_t_3);
             ^~~~~~~~~
./quicksort.h:1:23: note: passing argument to parameter 'a' here
void quick_sort (int* a, int n);

What I want to achieve is to compile this and be able to run for example:

import numpy as np
from cy_quicksort import quicksort_c
a = np.array(range(9, 0, -1), dtype=np.int32)
quicksort_c(a)

Thanks in advance for Your time!

Edit:

After changes suggested by DavidW in quicksort.pxd, cy_quicksort.pyx and changing the setup.py file into the following form, it's working as intended.

setup.py

from distutils.core import setup
from Cython.Build import cythonize
from distutils.extension import Extension

sourcefiles = ['cy_quicksort.pyx', 'quicksort.c']

extensions = [Extension("cy_quicksort", sourcefiles)]

setup(
    ext_modules = cythonize(extensions)
)

DavidW · Accepted Answer · 2016-04-08 17:11:58Z

5

The problem is mainly in "quicksort.pxd" - the definition needs to match that in quicksort.h:

cdef extern from "quicksort.h":
    void quick_sort (int* a, int n)

([:] defines it as a memoryview instead, which is a Cythony invention and can't be cast directly to a pointer, as your error says).

You then need to get a pointer from the memoryview in "cy_quicksort.pyx"

def quicksort_c(int[::1] a):
    quicksort.quick_sort(&a[0], a.size) # get address of first element

I've changed the input parameter to [::1] to specify that the elements must be continuous in memory, which I think is what quicksort expects.

(Note - untested, but reasonably simple so should work!)

answered Apr 8, 2016 at 17:11

DavidW

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5 Comments

Tony Babarino Over a year ago

Thank You for Your answer. With Your fixes it compiles, however when I try to import cy_quicksort it returns

ImportError: dlopen(./cy_quicksort.so, 2): Symbol not found: _quick_sort Referenced from: ./cy_quicksort.so Expected in: flat namespace in ./cy_quicksort.so

. Do You know what can be the issue?

DavidW Over a year ago

You need to make sure quicksort.c is compiled and linked when the module is generated. Have a look at docs.cython.org/src/reference/… (the bottom example). I think you need to do sourcefiles = ['cy_quicksort.pyx', 'quicksort.c'] and then follow the rest of the example given in the link. link

Tony Babarino Over a year ago

Thank You very much, now it's working! I would spend hours trying to figure that out by myself... I've edited my question to add working setup.py for any potential reader.

rbaleksandar Over a year ago

Talking about complicated syntax... :D But it works. It took me quite a while to find this information. Thanks for the great answer and explanation.

DavidW Over a year ago

@Azerila you probably haven't told Cython about the C function you're trying to use (so it's assuming the function is a Python function that takes Python objects)

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