Saving a numpy array in a C structure

Question

I am passing numpy arrays to C code using ctypes. I would like to keep that information in a C structure. I have the following code in C:

my_file.h

typedef struct container
{
    int nb_rows;
    int nb_cols;
    double ** data;
};
void save_d2_double(int nb_rows, int nb_cols, double *data[nb_cols]);
void print_container();

my_file.c

#include <stdio.h>
#include "my_file.h"    

struct container c;

void save_d2_double(int nb_rows, int nb_cols, double * data[nb_cols] ){
    c.nb_rows = nb_rows;
    c.nb_cols = nb_cols;
    c.data = data;
}

void print_container(){
   printf("\n");
   printf("%d\t%d", c.nb_rows, c.nb_cols);
   for(int i = 0; i < c.nb_rows; i++){
       for(int j = 0; j < c.nb_cols; j++){
           printf("%f\t", c.data[i][j]); \\ Error here
       }
       printf("\n");
   }
   printf("\n");
}

And the following in python:

my_file.py

import numpy as np
import numpy.ctypeslib as npct
import ctypes

LIBC = ctypes.CDLL("my_file.so")
array_2d_double = npct.ndpointer(dtype=np.double, ndim=2)
LIBC.save_d2_double.restype = None
LIBC.save_d2_double.argtypes = [ctypes.c_int, ctypes.c_int, array_2d_double]
LIBC.print_container.restype = None
LIBC.print_container.argtypes = []

# The shape of this array vary in the end application.
x_2d_d = np.array([[1.,2.,3.,10.],[4.,5.,6.,11.],[7.,8.,9.,12.]], dtype=np.float64)

shape = x_2d_d.shape
LIBC.save_d2_double(shape[0], shape[1], x_2d_d)
LIBC.print_container()

When I want to access c.data I get:

Segmentation fault (core dumped)

I suspect that the problem is in the declaration of double ** data; however, since C doesn't know in advance the dimensions of the numpy array, I don't know how to declare this filed.

Thanks in advance !

@ Joseph Sible-Reinstate Monica, You helped me out with questinos about ctypes before. Do you have suggestions for this one? — mm_
– mm_, Commented Nov 21, 2020 at 18:23

Joseph Sible-Reinstate Monica · Accepted Answer · 2020-11-21 18:54:34Z

1

First problem: double *data[nb_cols] is an array of pointers, or equivalently a double pointer, but that's not what Python is passing. Python is passing a 2D array, or equivalently a pointer to an array, so your function should take double (*data)[nb_cols] instead.

Second problem: C doesn't let you store a pointer to a VLA in a struct. You tried to use a double pointer instead, but a double pointer isn't compatible with a pointer to an array. However, there is a solution: since arrays are contiguous, you can instead treat the pointer as if it were just a pointer to the first element, and then cast it to a pointer to a VLA in the function where you use it (or manually convert the indices instead).

my_file.h:

struct container
{
    int nb_rows;
    int nb_cols;
    double *data;
};
void save_d2_double(int nb_rows, int nb_cols, double *data); /* or double (*data)[nb_cols] */
void print_container(void);

my_file.c:

#include <stdio.h>
#include "my_file.h"    

struct container c;

void save_d2_double(int nb_rows, int nb_cols, double *data) { /* or double (*data)[nb_cols] */
    c.nb_rows = nb_rows;
    c.nb_cols = nb_cols;
    c.data = data;
}

void print_container(void) {
   double (*data)[c.nb_cols] = (double (*)[c.nb_cols])c.data; /* optional; see below */
   printf("\n");
   printf("%d\t%d", c.nb_rows, c.nb_cols);
   for(int i = 0; i < c.nb_rows; i++) {
       for(int j = 0; j < c.nb_cols; j++) {
           printf("%f\t", data[i][j]); /* or c.data[i * c.nb_cols + j] */
       }
       printf("\n");
   }
   printf("\n");
}

answered Nov 21, 2020 at 18:54

Joseph Sible-Reinstate Monica

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6 Comments

mm_ Over a year ago

Dear @Joseph Sible, you are a life saver. What should I read to learn all these nuances?

Joseph Sible-Reinstate Monica Over a year ago

@mm_ I just picked this up over time and can't really point to a single source where I learned it.

mm_ Over a year ago

@ Joseph Sible, could you unpack double (*data)[c.nb_cols] = (double (*)[c.nb_cols])c.data; please? How would you do it for a 3 dim or 4 dim array?

Joseph Sible-Reinstate Monica Over a year ago

@mm_ There should be a separate [] for every dimension but the first. So something like double (*data)[c.nb_cols][c.nb_third_dimension_size][c.nb_fourth_dimension_size]

Joseph Sible-Reinstate Monica Over a year ago

@mm_ You should post a new question for that with all of your code and the exact problem details.

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