C Function in Python: Return an Array and Variables

Question

I just got transited into Python from Matlab and I know that calling C function is different than Matlab mex. With lacks of proper documentation, I have scourge the web for days now and couldn't find the solution to my simple problem.

Basically I want to call a C-Function in Python, input 2 integers and an 2D array, do some calculations, and return a 2D Array. I would also like to output some other variables too (this might require the use of structure). I know this are very basic stuffs but if someone can help me, I will greatly appreciated.

So what I am hoping for is the equivalent of this in matlab! Thx!!!

[Nxy,outArray] = Function(Nx,Ny,inArray)

Code for setup.py

from distutils.core import setup, Extension
import numpy.distutils.misc_util

setup(
    ext_modules=[Extension("myfunc", ["myfunc.c"])],
    include_dirs=numpy.distutils.misc_util.get_numpy_include_dirs(),
)

Code for myfunc.c

static char module_docstring[] =
    "This function does some calculations...";
static char Run_docstring[] =
    "Run what ever algorithm there is!";

static PyObject *Run(PyObject *self, PyObject *args)
{
    int i, j, Nx, Ny;
    PyObject *Data;

    /* Parse the input tuple */
    if (!PyArg_ParseTuple(args, "iiO", &Nx, &Ny, &Data))   // Data is a 2D array  
        return NULL;

    PyObject *array = PyArray_FROM_OTF(Data, NPY_DOUBLE, NPY_IN_ARRAY); // Interpret as numpy array
    double *newData = (double*)PyArray_DATA(array); // Pointers to the data as C-types

    double outData[Ny][Nx]; // Creating output 2D Array
    int outCount;

    // Calculations
    outCount = Nx*Ny;

    for (i=0; i<Nx; i++){
        for (j=0; i<Ny; j++){
           outData[j][i] = sqrt(Data[j][i]) + sqrt(outCount);
        }
    }

    // Free memory used in PyObject
    Py_DECREF(array);

    // Return output Data
    PyObject *ret = Py_BuildValue("i", outCount);
    return ret, PyArray_Return(outData);   

}

static PyMethodDef module_methods[] = {
    {"Run", Run, METH_VARARGS, Run_docstring},
    {NULL, NULL, 0, NULL}
};

PyMODINIT_FUNC initmyfunc(void)
{
    PyObject *m = Py_InitModule3("myfunc", module_methods, module_docstring);
    if (m == NULL)
        return;
    import_array();
}

What behavior does this code give you? How do you want it to behave instead? — Kevin
– Kevin, Commented Mar 3, 2015 at 14:09
If your intention is to use Numpy as an matlab replacement, please have look at swig with numpy. It makes interfacing python with C functions (e.g. even with openmp) for fast computation easy. — Bort
– Bort, Commented Mar 3, 2015 at 15:26
well this code doesn't work because you can't return two variables. — user4627923
– user4627923, Commented Mar 11, 2015 at 18:09

rth · Accepted Answer · 2015-03-04 21:56:10Z

1

It is possible to call optimised C functions from Python using Cython.

In this particular case, we can for instance create a myfunc.pyx file,

import numpy as np
cimport numpy as np
from libc.math cimport sqrt

cpdef tuple myfunc(int Nx, int Ny, double[:,::1] inArray):

        cdef double [:,::1] outData = np.zeros((Nx, Ny))
        cdef int i,j, res

        with nogil:
            for i in range(Nx):
                for j in range(Ny):
                    outData[i, j] = sqrt(inArray[i,j]) + sqrt(<double> Nx*Ny)
        res = 0 # not sure how res is computed

        return res, outData.base

that can be compiled with the following setup.py,

from distutils.core import setup, Extension
import numpy as np
from Cython.Distutils import build_ext

setup(
    ext_modules=[Extension("myfunc", ["myfunc.pyx"])],
    cmdclass = {'build_ext': build_ext},
    include_dirs=[np.get_include()])

using

$ python setup.py build_ext --inplace

This generates and compiles the myfunc.c. The resulting Python module can be then used as follows,

from myfunc import myfunc
import numpy as np
Nx, Ny = 2, 2
inArray =  np.ones((Nx,Ny))
res, outArray = myfunc(Ny,Ny, inArray)
print(outArray)
# which would return
[[ 3.  3.]
[ 3.  3.]]

Note, that it in this case it is not necessary to pass the array dimensions Nx, Ny to the function as they can be accessed through inArray.shape in Cython.

Please refer to the Cython documentation regarding Numpy for further optimisation details.

edited Mar 4, 2015 at 21:56

answered Mar 3, 2015 at 17:48

rth

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9 Comments

user4627923 Over a year ago

I try not to use Cython. but I will check what you have done here thx :-)

user4627923 Over a year ago

Ok i got a liste of errors while compiling the above code. I am using Python 2.7 - 64 bits.

rth Over a year ago

@user4627923 python 2.7, numpy 0.19, cython 0.22 I don't get any errors. What are the error messages you get? Btw, everything after print(outArray) is the output of the script and is not to be used.

rth Over a year ago

@ user4627923 Well actually, no, those are not errors, just warnings (in functions that are named SomethingError which is confusing), and the compiled module is produced. Those warnings do not happens on linux and I'm not sure why they happen with Anaconda on Windows (I do get the same ones). Still it seems to be mostly due to some issues in string formatting elsewhere, and is thus not related to the problem at hand . Importing myfunc and running the example above should work )

rth Over a year ago

@user4627923 That's not really critical here, but the with nogil releases the Python's global interpret lock (GIL), which allows in particular parallel OpenMP calculations with Cython

|

user4627923 · Accepted Answer · 2015-03-14 01:27:04Z

0

I followed what rth suggested and I got this error message during compilation!

Running Anaconda 2.7, 64 bits, win7x64

Thanks and Cheers,

enter image description here

answered Mar 14, 2015 at 1:27

user4627923

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