Read and access MAT file data in C

Hi everyone,

I'm new to the C programmation with the API library in Matlab and I'm trying to read and access a mat file data which is a 3d array. In my C code "p" is a pointer to the 3d array which values I'm trying to print, but when I compile (mex MyCode.c) I have a errors, here's my C code:

#include "mex.h"

#include "matrix.h"

#include "mat.h"

   void mexFunction( int nlhs, mxArray *plhs[],int nrhs, const mxArray *prhs[] )
  {
    MATFile *pmat;
    double x;
    mxArray *pa;
    int n;
    const char *name;
    const char **dir;
    int    ndir;
    int i,c;
    int num_of_dim, num_of_fields, rows, col, bands,r,cc,b;
   const int *dim_array;
   mxArray ***p;

    /*
     * Open file to get directory
     */
    pmat = matOpen("data3.mat", "r");
    if (pmat == NULL)
    {
      printf("Error creating file \n");
      printf("(Do you have write permission in this directory?)\n");
      return(EXIT_FAILURE);
    }

    /*
     * get directory of MAT-file
     */
    dir = (const char **)matGetDir(pmat, &ndir);
    if (dir == NULL) {
        printf("Error reading directory of file ");
      return(EXIT_FAILURE);
    } 

    mxFree(dir);

    if (matClose(pmat) != 0) 
    {
      printf("Error closing file \n");
      return(EXIT_FAILURE);
    }
    pmat = matOpen("data3.mat", "r");
    if (pmat == NULL) {
      printf("Error reopening file \n");
      return(EXIT_FAILURE);
    }

     /* Read in each array. */
    printf("\nReading in the actual array contents:\n");

    for (i=0; i<ndir; i++) 
    {
        pa = matGetNextVariable(pmat, name);
        if (pa == NULL) 
        {
      printf("Error reading in file \n");
      return(EXIT_FAILURE);
        }

    } 

     /* Get the number of dimensions in array */

      num_of_dim=mxGetNumberOfDimensions(pa);
      dim_array = mxGetDimensions(pa);
      printf("the number of dimensions are %d \n",num_of_dim);
      for (c=0; c<num_of_dim; c++)
      {
         mexPrintf("%d\n", *(dim_array+c)); 
      }

     rows = *(dim_array);
     col = *(dim_array+1);
     bands = *(dim_array+2);

      p=mxGetData(pmat);

      /* Display the values of the mat file */
     for (r=0;r<rows;r++,printf("\n"))
     {
         for(cc=0;cc<col;cc++,printf("\n"))
         {
             for(b=0;b,<bands;b++,printf("\n"))
             {
                mexPrintf("%d\n",*(p + col*bands*r + bands*cc + b));
             }
         }
     }

   }

I will be really grateful to know what's wrong with my C code.

Thanks.

-J

[Jan]

It would be useful, if you mention which error messages you see. Then we do not have to guess them ;-)

Answer 1

[James Tursa]

This:

const int *dim_array;

should probably be this

const mwSize *dim_array;

Also, this

mxArray ***p;

should probably be this, assuming the array is double class (you should check this in your code)

double *p;

And if the values really are double, then you should be using a format other than %d for printing, since that is for integer types. E.g., this

              mexPrintf("%d\n",*(p + col*bands*r + bands*cc + b));

should be something like this instead

              mexPrintf("%g\n",*(p + col*bands*r + bands*cc + b));

And this

    p=mxGetData(pmat);

should probably be this

    p = mxGetData(pa);

And you should have this at the end of your outer loop

    mxDestroyArray(pa);

This might not be totally correct either ... seems like you would need to free the name strings as well:

    mxFree(dir);

Finally, it is not clear to me which variable you are trying to display here. You read them all in a loop, and then display only the last one? Is that intended?

And then in the following call, I think "name" needs to have memory allocated behind it prior to the call ... I will have to check on this later.

    pa = matGetNextVariable(pmat, name);

EDIT:

I checked, and that last line should be this:

    pa = matGetNextVariable(pmat, &name);

[JM]

Thank you for your answer. I corrected my code and took into account your suggestions and I managed to display the content of my mat file like this :

 res=rows*col*bands;

for (r=0;r<res;r++)
{
    mexPrintf("%.4g \n",*p++);
}

but I couldn't display each matrix of my 3D array pointed to by "pa".

The goal of my C code is to speed up my matlab code where I used to compare small 3D parts of my main 3D array. I tried many things but it's still not clear to me how I can access each 2D matrix of my 3D array and then access each element of each 2D matrix. It's the handling of a pointer of type "mxArray*" that is still a mystery to me. I hope I made myself clear but don't hesitate to ask for further details if it's not the case.

Thank you.

-J

[James Tursa]

Can you write out, in m-code or pseudo-code, the equivalent of what you want the mex function to do?

[JM]

Basically my m-code consists of six nested loop and does this:

%the first three nested loops are for the extraction the first 3D cube
for f=idx_start:idx_end
  for i=idx_start:idx_end
    for j=idx_start:idx_end
      % the saving of the first 3D cube 
        tmp_1=image_3d(i-pace:i+pace,j-pace:j+pace,f-pace:f+pace)

           % the last three nested loop are for the extraction of the second 3D cube 
           idx1=formula();
           for ff=idx_start:idx_end
             for ii=idx_start:idx_end
               for jj=idx_start:idx_end
                 % the saving of the second 3D cube 
                  tmp_2=image_3d(ii-pace:ii+pace,jj-pace:jj+pace,ff-pace:ff+pace)

                  idx2=formula();
                  %computing the l2 norm between the two 3d cubes
                   res=sum(sum(sum((tmp_1-tmp_2).^2)));

                   %saving the data in a 1D arrays
                   tab(1,id1)=res;
                   tab_indices(1,id1)=idx2;
                end
              end
           end
        % saving the data in a sparse matrix
        weights(idx1,tab_indices)=tab;
    end
  end
end

I have many arrays and sparse matrices in my m-code, is it obligatory to work with pointers all the time when I'm using the API library in matlab ?

Thanks in advance,

-J

[JM]

I'm getting through mex programming little by little, I managed to display the content of my MAT-file like this:

    for(b=0;b<bands;b++,printf("\n"))
    {
        for (r=0;r<rows;r++,printf("\n"))
        {
            for(cc=0;cc<col;cc++)
            {

                printf("%.4g \t",p[b*rows*col+cc*rows+r]); 

            }
        }
    }

where "b*rows*col+cc*rows+r" is the conversion to 1D indexing from the coordinates (r,cc,b) with the fact that data are stored in column. Thank you for your comments and answers.