Hi everyone, I have been using NumPy for a couple of month now, as part of my research project at the university. But now, I have to use a big C library I wrote myself in a python project. So I choose to use SWIG for the interface between both my python script and my C library. To make things more comprehensible, I wrote a small C methods that illustrate my problem: /* matrix.c */ #include <stdlib.h> #include <stdio.h> /* Compute the sum of a vector of reals */ double vecSum(int* vec,int m){ int i; double sum =0.0; for(i=0;i<m;i++){ sum += vec[i]; } return sum; } /***/ /* matrix.h */ double vecSum(int* vec,int m); /***/ /* matrix.i */ %module matrix %{ #define SWIG_FILE_WITH_INIT #include "matrix.h" %} extern double vecSum(int* vec, int m); %include "numpy.i" %init %{ import_array(); %} %apply (int* IN_ARRAY1, int DIM1) {(int* vec, int m)}; %include "matrix.h" /***/ I'm using a python script to compile my swig interface and my C files (running Mac OS X 10.5) /* matrixSetup.py */ from distutils.core import setup, Extension import numpy setup(name='matrix', version='1.0', ext_modules =[Extension('_matrix', ['matrix.c','matrix.i'], include_dirs = [numpy.get_include(),'.'])]) /***/ Everything seems to work fine ! But when I test my wrapped module in python with an small NumPy array, here what I get :
import matrix from numpy import * a = arange(10) matrix.vecSum(a,a.shape[0]) Traceback (most recent call last): File "<stdin>", line 1, in <module> TypeError: in method 'vecSum', argument 1 of type 'int *'
How can I tell SWIG that my Integer NumPy array should represent a int* array in C ? Thank you very much, Kevin
Kevin, You need to declare vecSum() *after* you %include "numpy.i" and use the %apply directive. Based on what you have, I think you can just get rid of the "extern double vecSum(...)". I don't see what purpose it serves. As is, it is telling swig to wrap vecSum() before you have set up your numpy typemaps. On Mar 24, 2009, at 10:33 AM, Kevin Françoisse wrote:
Hi everyone,
I have been using NumPy for a couple of month now, as part of my research project at the university. But now, I have to use a big C library I wrote myself in a python project. So I choose to use SWIG for the interface between both my python script and my C library. To make things more comprehensible, I wrote a small C methods that illustrate my problem:
/* matrix.c */
#include <stdlib.h> #include <stdio.h> /* Compute the sum of a vector of reals */ double vecSum(int* vec,int m){ int i; double sum =0.0;
for(i=0;i<m;i++){ sum += vec[i]; } return sum; }
/***/
/* matrix.h */
double vecSum(int* vec,int m);
/***/
/* matrix.i */
%module matrix %{ #define SWIG_FILE_WITH_INIT #include "matrix.h" %}
extern double vecSum(int* vec, int m);
%include "numpy.i"
%init %{ import_array(); %}
%apply (int* IN_ARRAY1, int DIM1) {(int* vec, int m)}; %include "matrix.h"
/***/
I'm using a python script to compile my swig interface and my C files (running Mac OS X 10.5)
/* matrixSetup.py */
from distutils.core import setup, Extension import numpy
setup(name='matrix', version='1.0', ext_modules =[Extension('_matrix', ['matrix.c','matrix.i'], include_dirs = [numpy.get_include(),'.'])])
/***/
Everything seems to work fine ! But when I test my wrapped module in python with an small NumPy array, here what I get :
import matrix from numpy import * a = arange(10) matrix.vecSum(a,a.shape[0]) Traceback (most recent call last): File "<stdin>", line 1, in <module> TypeError: in method 'vecSum', argument 1 of type 'int *'
How can I tell SWIG that my Integer NumPy array should represent a int* array in C ?
Thank you very much,
Kevin <ATT00002.txt>
** Bill Spotz ** ** Sandia National Laboratories Voice: (505)845-0170 ** ** P.O. Box 5800 Fax: (505)284-0154 ** ** Albuquerque, NM 87185-0370 Email: wfspotz@sandia.gov **
Thanks Bill, it helps me a lot ! My function works fine now. But I encounter an other problem. This time with a NumPy array of 2 dimensions. Here is the function I want to use : /****************/ double matSum(double** mat, int n, int m){ int i,j; double sum = 0.0; for (i=0;i<n;i++){ for (j=0;j<m;j++){ sum += mat[i][j]; } } return sum; } /****************/ I supposed that the typemaps to use is the following : %apply (double* IN_ARRAY2, int DIM1, int DIM2) {(double** mat, int n, int m)}; But it is not working. Of course, my typemaps assignement is not compatible with my function parameters. I tried several ways of using a two dimensional array but I'm not sure what is the best way to do it ? Thanks --- Kevin Françoisse Ph.D. at Machine Learning Group at UCL Belgium kevin.francoisse@uclouvain.be On Tue, Mar 24, 2009 at 6:13 PM, Bill Spotz <wfspotz@sandia.gov> wrote:
Kevin,
You need to declare vecSum() *after* you %include "numpy.i" and use the %apply directive. Based on what you have, I think you can just get rid of the "extern double vecSum(...)". I don't see what purpose it serves. As is, it is telling swig to wrap vecSum() before you have set up your numpy typemaps.
On Mar 24, 2009, at 10:33 AM, Kevin Françoisse wrote:
Hi everyone,
I have been using NumPy for a couple of month now, as part of my research project at the university. But now, I have to use a big C library I wrote myself in a python project. So I choose to use SWIG for the interface between both my python script and my C library. To make things more comprehensible, I wrote a small C methods that illustrate my problem:
/* matrix.c */
#include <stdlib.h> #include <stdio.h> /* Compute the sum of a vector of reals */ double vecSum(int* vec,int m){ int i; double sum =0.0;
for(i=0;i<m;i++){ sum += vec[i]; } return sum; }
/***/
/* matrix.h */
double vecSum(int* vec,int m);
/***/
/* matrix.i */
%module matrix %{ #define SWIG_FILE_WITH_INIT #include "matrix.h" %}
extern double vecSum(int* vec, int m);
%include "numpy.i"
%init %{ import_array(); %}
%apply (int* IN_ARRAY1, int DIM1) {(int* vec, int m)}; %include "matrix.h"
/***/
I'm using a python script to compile my swig interface and my C files (running Mac OS X 10.5)
/* matrixSetup.py */
from distutils.core import setup, Extension import numpy
setup(name='matrix', version='1.0', ext_modules =[Extension('_matrix', ['matrix.c','matrix.i'], include_dirs = [numpy.get_include(),'.'])])
/***/
Everything seems to work fine ! But when I test my wrapped module in python with an small NumPy array, here what I get :
import matrix from numpy import * a = arange(10) matrix.vecSum(a,a.shape[0]) Traceback (most recent call last): File "<stdin>", line 1, in <module> TypeError: in method 'vecSum', argument 1 of type 'int *'
How can I tell SWIG that my Integer NumPy array should represent a int* array in C ?
Thank you very much,
Kevin <ATT00002.txt>
** Bill Spotz ** ** Sandia National Laboratories Voice: (505)845-0170 ** ** P.O. Box 5800 Fax: (505)284-0154 ** ** Albuquerque, NM 87185-0370 Email: wfspotz@sandia.gov **
Kevin, In this instance, the best thing is to write a wrapper function that calls your matSum() function, and takes a double* rather than a double**. You can %ignore the original function and %rename the wrapper so that the python interface gets the name you want. On Mar 25, 2009, at 7:39 AM, Kevin Françoisse wrote:
Thanks Bill, it helps me a lot ! My function works fine now.
But I encounter an other problem. This time with a NumPy array of 2 dimensions.
Here is the function I want to use :
/****************/ double matSum(double** mat, int n, int m){ int i,j; double sum = 0.0; for (i=0;i<n;i++){ for (j=0;j<m;j++){ sum += mat[i][j]; } } return sum; } /****************/
I supposed that the typemaps to use is the following :
%apply (double* IN_ARRAY2, int DIM1, int DIM2) {(double** mat, int n, int m)};
But it is not working. Of course, my typemaps assignement is not compatible with my function parameters. I tried several ways of using a two dimensional array but I'm not sure what is the best way to do it ?
Thanks
--- Kevin Françoisse Ph.D. at Machine Learning Group at UCL Belgium kevin.francoisse@uclouvain.be
On Tue, Mar 24, 2009 at 6:13 PM, Bill Spotz <wfspotz@sandia.gov> wrote: Kevin,
You need to declare vecSum() *after* you %include "numpy.i" and use the %apply directive. Based on what you have, I think you can just get rid of the "extern double vecSum(...)". I don't see what purpose it serves. As is, it is telling swig to wrap vecSum() before you have set up your numpy typemaps.
On Mar 24, 2009, at 10:33 AM, Kevin Françoisse wrote:
Hi everyone,
I have been using NumPy for a couple of month now, as part of my research project at the university. But now, I have to use a big C library I wrote myself in a python project. So I choose to use SWIG for the interface between both my python script and my C library. To make things more comprehensible, I wrote a small C methods that illustrate my problem:
/* matrix.c */
#include <stdlib.h> #include <stdio.h> /* Compute the sum of a vector of reals */ double vecSum(int* vec,int m){ int i; double sum =0.0;
for(i=0;i<m;i++){ sum += vec[i]; } return sum; }
/***/
/* matrix.h */
double vecSum(int* vec,int m);
/***/
/* matrix.i */
%module matrix %{ #define SWIG_FILE_WITH_INIT #include "matrix.h" %}
extern double vecSum(int* vec, int m);
%include "numpy.i"
%init %{ import_array(); %}
%apply (int* IN_ARRAY1, int DIM1) {(int* vec, int m)}; %include "matrix.h"
/***/
I'm using a python script to compile my swig interface and my C files (running Mac OS X 10.5)
/* matrixSetup.py */
from distutils.core import setup, Extension import numpy
setup(name='matrix', version='1.0', ext_modules =[Extension('_matrix', ['matrix.c','matrix.i'], include_dirs = [numpy.get_include(),'.'])])
/***/
Everything seems to work fine ! But when I test my wrapped module in python with an small NumPy array, here what I get :
import matrix from numpy import * a = arange(10) matrix.vecSum(a,a.shape[0]) Traceback (most recent call last): File "<stdin>", line 1, in <module> TypeError: in method 'vecSum', argument 1 of type 'int *'
How can I tell SWIG that my Integer NumPy array should represent a int* array in C ?
Thank you very much,
Kevin <ATT00002.txt>
** Bill Spotz ** ** Sandia National Laboratories Voice: (505)845-0170 ** ** P.O. Box 5800 Fax: (505)284-0154 ** ** Albuquerque, NM 87185-0370 Email: wfspotz@sandia.gov **
** Bill Spotz ** ** Sandia National Laboratories Voice: (505)845-0170 ** ** P.O. Box 5800 Fax: (505)284-0154 ** ** Albuquerque, NM 87185-0370 Email: wfspotz@sandia.gov **
Hello Bill, Finaly, I just change my function header to take a double* rather than a double**. It's working fine now. Thank you for all your answer and your help! Swig and numpy.i are really cool when you now how to use it! I also use INPLACE array as a way output 2D arrays from my C function. Kevin On Wed, Mar 25, 2009 at 3:03 PM, Bill Spotz <wfspotz@sandia.gov> wrote:
Kevin,
In this instance, the best thing is to write a wrapper function that calls your matSum() function, and takes a double* rather than a double**. You can %ignore the original function and %rename the wrapper so that the python interface gets the name you want.
On Mar 25, 2009, at 7:39 AM, Kevin Françoisse wrote:
Thanks Bill, it helps me a lot ! My function works fine now.
But I encounter an other problem. This time with a NumPy array of 2 dimensions.
Here is the function I want to use :
/****************/ double matSum(double** mat, int n, int m){ int i,j; double sum = 0.0; for (i=0;i<n;i++){ for (j=0;j<m;j++){ sum += mat[i][j]; } } return sum; } /****************/
I supposed that the typemaps to use is the following :
%apply (double* IN_ARRAY2, int DIM1, int DIM2) {(double** mat, int n, int m)};
But it is not working. Of course, my typemaps assignement is not compatible with my function parameters. I tried several ways of using a two dimensional array but I'm not sure what is the best way to do it ?
Thanks
--- Kevin Françoisse Ph.D. at Machine Learning Group at UCL Belgium kevin.francoisse@uclouvain.be
On Tue, Mar 24, 2009 at 6:13 PM, Bill Spotz <wfspotz@sandia.gov> wrote: Kevin,
You need to declare vecSum() *after* you %include "numpy.i" and use the %apply directive. Based on what you have, I think you can just get rid of the "extern double vecSum(...)". I don't see what purpose it serves. As is, it is telling swig to wrap vecSum() before you have set up your numpy typemaps.
On Mar 24, 2009, at 10:33 AM, Kevin Françoisse wrote:
Hi everyone,
I have been using NumPy for a couple of month now, as part of my research project at the university. But now, I have to use a big C library I wrote myself in a python project. So I choose to use SWIG for the interface between both my python script and my C library. To make things more comprehensible, I wrote a small C methods that illustrate my problem:
/* matrix.c */
#include <stdlib.h> #include <stdio.h> /* Compute the sum of a vector of reals */ double vecSum(int* vec,int m){ int i; double sum =0.0;
for(i=0;i<m;i++){ sum += vec[i]; } return sum; }
/***/
/* matrix.h */
double vecSum(int* vec,int m);
/***/
/* matrix.i */
%module matrix %{ #define SWIG_FILE_WITH_INIT #include "matrix.h" %}
extern double vecSum(int* vec, int m);
%include "numpy.i"
%init %{ import_array(); %}
%apply (int* IN_ARRAY1, int DIM1) {(int* vec, int m)}; %include "matrix.h"
/***/
I'm using a python script to compile my swig interface and my C files (running Mac OS X 10.5)
/* matrixSetup.py */
from distutils.core import setup, Extension import numpy
setup(name='matrix', version='1.0', ext_modules =[Extension('_matrix', ['matrix.c','matrix.i'], include_dirs = [numpy.get_include(),'.'])])
/***/
Everything seems to work fine ! But when I test my wrapped module in python with an small NumPy array, here what I get :
import matrix from numpy import * a = arange(10) matrix.vecSum(a,a.shape[0]) Traceback (most recent call last): File "<stdin>", line 1, in <module> TypeError: in method 'vecSum', argument 1 of type 'int *'
How can I tell SWIG that my Integer NumPy array should represent a int* array in C ?
Thank you very much,
Kevin <ATT00002.txt>
** Bill Spotz ** ** Sandia National Laboratories Voice: (505)845-0170 ** ** P.O. Box 5800 Fax: (505)284-0154 ** ** Albuquerque, NM 87185-0370 Email: wfspotz@sandia.gov **
** Bill Spotz ** ** Sandia National Laboratories Voice: (505)845-0170 ** ** P.O. Box 5800 Fax: (505)284-0154 ** ** Albuquerque, NM 87185-0370 Email: wfspotz@sandia.gov **
participants (2)
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Bill Spotz -
Kevin Françoisse