Importing C function with cython, how to pass a pointer to a python function

Question

I'm trying to make a function which is defined in a C library callable from python. I'm begginer with cython n C

Sooo in short I ended up having the following problem:

#.pyx file
cdef extern from "lsd.h":
    double *lsd_scale(int *n_out, double *img, int X, int Y, double scale)

def detector(int n_out, double  img, int  X, int  Y, double scale):
    return lsd_scale(n_out, img, X, Y, scale)

The definition from library.h file

    @param n_out       Pointer to an int where LSD will store the number of
                       line segments detected.

    @param img         Pointer to input image data. It must be an array of
                       doubles of size X x Y, and the pixel at coordinates
                       (x,y) is obtained by img[x+y*X].

    @param X           X size of the image: the number of columns.

    @param Y           Y size of the image: the number of rows.

    @return            A double array of size 7 x n_out, containing the list
                       of line segments detected. The array contains first
                       7 values of line segment number 1, then the 7 values
                       of line segment number 2, and so on, and it finish
                       by the 7 values of line segment number n_out.
                       The seven values are:
                       - x1,y1,x2,y2,width,p,-log10(NFA)
                       .
                       for a line segment from coordinates (x1,y1) to (x2,y2),
                       a width 'width', an angle precision of p in (0,1) given
                       by angle_tolerance/180 degree, and NFA value 'NFA'.
                       If 'out' is the returned pointer, the 7 values of
                       line segment number 'n+1' are obtained with
                       'out[7*n+0]' to 'out[7*n+6]'.

Soo in short the question is how to indicate in the python function that n_out is a pointer to an integer and img is a pointer to an array. I tried the following

ctypedef int*p_int
ctypedef double*p_double

cdef extern from "lsd.h":
    double *lsd_scale(int *n_out, double *img, int X, int Y, double scale)

def detector(p_int n_out, p_double  img, int  X, int  Y, double scale):
    return lsd_scale(n_out, img, X, Y, scale)

But throws same error

Error compiling Cython file:
------------------------------------------------------------
...

cdef extern from "lsd.h":
    double *lsd_scale(int *n_out, double *img, int X, int Y, double scale)

def detector(int n_out, double  img, int  X, int  Y, double scale):
    return lsd_scale(n_out, img, X, Y, scale)
                    ^
------------------------------------------------------------

detector.pyx:6:21: Cannot assign type 'int' to 'int *'

Error compiling Cython file:
------------------------------------------------------------
...

cdef extern from "lsd.h":
    double *lsd_scale(int *n_out, double *img, int X, int Y, double scale)

def detector(int n_out, double  img, int  X, int  Y, double scale):
    return lsd_scale(n_out, img, X, Y, scale)
                           ^
------------------------------------------------------------

detector.pyx:6:28: Cannot assign type 'double' to 'double *'

Error compiling Cython file:
------------------------------------------------------------
...

cdef extern from "lsd.h":
    double *lsd_scale(int *n_out, double *img, int X, int Y, double scale)

def detector(int n_out, double  img, int  X, int  Y, double scale):
    return lsd_scale(n_out, img, X, Y, scale)
                   ^
------------------------------------------------------------

Thanks for helping

DavidW · Accepted Answer · 2020-05-27 16:51:38Z

The idea should be to create a useful Python interface, not directly reproduce the C interface. Some of these arguments are pointless to the Python interface because they're already stored in (say) a Numpy array.

double *img, int X, int Y all describe the input array. Essentially the requirement is "2D, contiguous block of memory". In Cython this can be expressed using a typed memoryview:

def detector(..., double[:,::1] img, ...):
    ... = lsd_scale(..., &img[0,0], # address of first element
                         img.shape[0], img.shape[1], # (it's possible these are the wrong way round, test!)
                         ...)

The return value and n_out combine to describe the output array, which is (7xn_out). You could get Numpy to take ownership of this data, or you could copy the data. I recommend the latter. Therefore, you don't actually want n_out to be an input from Python. Instead:

def detector(...):
    cdef double[:,::1] result_memview # useful for later

    cdef int n_out
    cdef double* result = lsd_scale(&n_out, ...)
    try:
        # copy the data to an output array.
        # The following is an untested outline. Making it work is an exercise for you

        result_memview = <double[:7,:n_out:1]>result # make a temporary memoryview of the data
        return np.array(result_memview) # should make a copy, I think
    finally:
        free(result) # cimported.

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