Passing Numpy arrays to a C function for input and output

Question

Oh my word I'm a fool. I was simply omitting the second and third arguments when calling the function. Like a fool. Because that's what I am. Original silly question follows:

This seems like it must be a very common thing to do, but I can't find a relevant tutorial, and I'm too ignorant about Numpy and ctypes to figure it out myself.

I have a C function in file ctest.c.

#include <stdio.h>

void cfun(const void * indatav, int rowcount, int colcount, void * outdatav) {
    //void cfun(const double * indata, int rowcount, int colcount, double * outdata) {
    const double * indata = (double *) indatav;
    double * outdata = (double *) outdatav;
    int i;
    puts("Here we go!");
    for (i = 0; i < rowcount * colcount; ++i) {
        outdata[i] = indata[i] * 2;
    }
    puts("Done!");
}

(As you may guess, I originally had the arguments as double * rather than void *, but couldn't figure out what to do on the Python side. I'd certainly love to change them back, but I'm not picky as long as it works.)

I make a shared library out of it. gcc -fPIC -shared -o ctest.so ctest.c

Then in Python, I have a couple numpy arrays, and I'd like to pass them to the C function, one as input and one as output.

indata = numpy.ones((5,6), dtype=numpy.double)
outdata = numpy.zeros((5,6), dtype=numpy.double)
lib = ctypes.cdll.LoadLibrary('./ctest.so')
fun = lib.cfun
# Here comes the fool part.
fun(ctypes.c_void_p(indata.ctypes.data), ctypes.c_void_p(outdata.ctypes.data))

print 'indata: %s' % indata
print 'outdata: %s' % outdata

This doesn't report any errors, but prints out

>>> Here we go!
Done!
indata: [[ 1.  1.  1.  1.  1.  1.]
 [ 1.  1.  1.  1.  1.  1.]
 [ 1.  1.  1.  1.  1.  1.]
 [ 1.  1.  1.  1.  1.  1.]
 [ 1.  1.  1.  1.  1.  1.]]
outdata: [[ 0.  0.  0.  0.  0.  0.]
 [ 0.  0.  0.  0.  0.  0.]
 [ 0.  0.  0.  0.  0.  0.]
 [ 0.  0.  0.  0.  0.  0.]
 [ 0.  0.  0.  0.  0.  0.]]

The outdata array is not modified. And in fact if I call the function again I get a segfault. Which doesn't surprise me -- I really don't know what I'm doing here. Can anyone point me in the right direction?

Sorry. It seems you are mixing C and python and I don't know how it works. The fact that the puts in C is called tells it is being called from python code. But I suspect what you are passing to the C function is causing the problems. — Mahesh
– Mahesh, Commented May 2, 2011 at 22:15

Guillaume Jacquenot · Accepted Answer · 2018-02-12 11:13:10Z

88

While not a direct answer to your original question, here's a much more convenient way to call your function. First, make the prototype of your C function exactly as you would do it in plain C. Since you don't need rowcount and colcount separately, I'll collapse them into a single size parameter:

void cfun(const double *indatav, size_t size, double *outdatav) 
{
    size_t i;
    for (i = 0; i < size; ++i)
        outdatav[i] = indatav[i] * 2.0;
}

Now define the ctypes prototype in the following way:

import ctypes
from numpy.ctypeslib import ndpointer
lib = ctypes.cdll.LoadLibrary("./ctest.so")
fun = lib.cfun
fun.restype = None
fun.argtypes = [ndpointer(ctypes.c_double, flags="C_CONTIGUOUS"),
                ctypes.c_size_t,
                ndpointer(ctypes.c_double, flags="C_CONTIGUOUS")]

Now, calls to your function will be really convenient:

indata = numpy.ones((5,6))
outdata = numpy.empty((5,6))
fun(indata, indata.size, outdata)

You could also define a wrapper to make this even more convenient:

def wrap_fun(indata, outdata):
    assert indata.size == outdata.size
    fun(indata, indata.size, outdata)

edited Feb 12, 2018 at 11:13

Guillaume Jacquenot

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answered May 3, 2011 at 10:16

Sven Marnach

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12 Comments

jfs Over a year ago

you might need numpy.ascontiguousarray() if the arrays are non-contiguous e.g., numpy.arange(1, 7)[::2].

Sven Marnach Over a year ago

@J.F.Sebastian: You can add flags="C_CONTIGUOUS" to the ndpointer() calls to dynamically check whether the array is C-contiguous. (Maybe I should add this to this answer.)

jfs Over a year ago

flags parameter leads to TypeError if input array is not contiguous.

Sven Marnach Over a year ago

@J.F.Sebastian: That's what I tried to imply by saying that it adds dynamic type checks.

jfs Over a year ago

Do you consider TypeError to be the correct answer?

|

stderr · Accepted Answer · 2011-05-02 23:21:17Z

22

Just pass all four arguments to the C function. Change your Python code from:

fun(ctypes.c_void_p(indata.ctypes.data), ctypes.c_void_p(outdata.ctypes.data))

To:

fun(ctypes.c_void_p(indata.ctypes.data), ctypes.c_int(5), ctypes.c_int(6),
    ctypes.c_void_p(outdata.ctypes.data))

answered May 2, 2011 at 23:21

stderr

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