CODEWITHSUNDEEP
pythonctypedefcython
eaponte
eaponte

Reputation: 439

Using typedef'd struct in cython

I have the following definition in the header file dcm.h:

typedef struct
{    
    double alpha;
    double gamma;
    double tau;
} ThetaDCM;

I want to import it in cython, so I have:

cdef extern from "dcm.h":

    ctypedef struct ThetaDCM:

        np.float64_t alpha
        np.float64_t gamma
        np.float64_t tau

Now I want to allocate memory to an array of ThetaDCM's. I have the following:

cdef ThetaDCM *c_theta = <ThetaDCM *> malloc(nt * nb * sizeof(ThetaDCM))

free(c_theta)

This did not compile and reported the following error:

error: ‘ThetaDCM’ undeclared (first use in this function)
   __pyx_v_c_theta = ((ThetaDCM *)malloc(((__pyx_v_nt * __pyx_v_nb) * (sizeof(ThetaDCM)))));

There where other errors related to this one. If I define ThetaDCM outside the extern block, the code compiles without problem. Therefore, if I import Theta, cython cannot see my declaration. Is there any standard way to solve this?

Edit:

The header of my file was a bit more complicated than what I posted. It was

# ifdef __CUDACC__
# ifndef DDM_HEADER
# define DDM_HEADER

#include "math.h"
#include "curand_kernel.h"
#include "curand.h"
#include <stdio.h>
...
# endif 

# ifdef __CUDACC__
# define BDDM_EXTERN extern "C"
# else
# define BDDM_DEVICE
# endif

BDDM_EXTERN
int llh_m0t( double *x, double *y, double *u,
    double *theta, double *ptheta, int ny, int nt, double *llh);
...
typedef struct
{    
    double alpha;
    double gamma;
    double tau;
} ThetaDCM;

# endif

The directive on top is used to check if the compiler is nvcc, a compiler for cuda code. Now I realize that there was an error and that I should have had:

# ifndef DDM_HEADER
# define DDM_HEADER
# ifdef __CUDACC__

#include "math.h"
#include "curand_kernel.h"
#include "curand.h"
#include <stdio.h>
...
# endif

BDDM_EXTERN
int llh_m0t( double *x, double *y, double *u,
    double *theta, double *ptheta, int ny, int nt, double *llh);
...

typedef struct
{    
    double alpha;
    double gamma;
    double tau;
} ThetaDCM;
# endif

What confused me is that the cython code compiled despite of the # ifdef CUDACC. I used cython to wrap c functions defined inside the first #ifdef statement (like llh_m0t), so the confusing thing is that cython could see those function definitions.

Upvotes: 2

Views: 4985

Answers (2)

Sylvain Leroux
Sylvain Leroux

Reputation: 51990

Cython does not provide support to #define macro for conditional compilation as required by your header:

dcm.h

# ifdef __CUDACC__

typedef struct
{    
    double alpha;
    double gamma;
    double tau;
} ThetaDCM;

# endif

A quick workaround:

dcm.pyh

#define __CUDACC__
#include "dcm.h"


dcm.pyx

[...]

cdef extern from "dcm.pyh":
#                     ^^^
    [...]

Upvotes: 1

Sylvain Leroux
Sylvain Leroux

Reputation: 51990

Probably an issue with an old (or too ... beta ?) version of cython.

I agree this is not really an answer -- mostly a very long comment... but this works for me using cython 0.20.0:

dcm.h

typedef struct
{    
    double alpha;
    double gamma;
    double tau;
} ThetaDCM;


dcm.pyx

cimport numpy as np
from libc.stdlib cimport malloc, free

nt = 1
nb = 1

cdef extern from "dcm.h":

    ctypedef struct ThetaDCM:

        np.float64_t alpha
        np.float64_t gamma
        np.float64_t tau

cdef ThetaDCM *c_theta = <ThetaDCM *> malloc(nt * nb * sizeof(ThetaDCM))

print(hex(<long>c_theta))

free(c_theta)

sh$ cython dcm.pyx
sh$ gcc -shared -pthread -fPIC -fwrapv -O2 -Wall -fno-strict-aliasing -I../include/python3.4m/ -L../lib/python3.4/ dcm.c -o dcm.so
sh$ python3Python 3.4.1 (default, Aug 20 2014, 14:47:11) 
[GCC 4.7.2] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import dcm
0x23e44f0

Upvotes: 2

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