How to read back (and use) a matrix from a matlab function called from a mex file?

I want to read back a matrix from a matlab function called from a mex file and I have been getting a segmentation violation when I try to run it. (At least my assumption is that it is related to how I am reading the matrix; I'm not exactly sure)

Here is an example representing what I am trying to do: (apologies if I include unnecessary detail, I am a novice mex user)

void mexFunction(int nlhs, mxArray *plhs[],int nrhs, const mxArray   *prhs[]){

    int ncols=210;
    int mrows=210;
    int i,j,
    double ** a;
    double ** b; // matrix to hold matlab output

    mxArray * histforce_ips[1];
    mxArray * histforce_ops[1];

    // allocate memory:
    a=(double**)malloc(mrows*sizeof(double *));
    b=(double**)malloc(mrows*sizeof(double *));

    for(i=0;i<mrows;i++){
        a[i]=(double*)calloc(ncols,sizeof(double));
        b[i]=(double*)calloc(ncols,sizeof(double));
    }

    // put something into a:
    // ...

    // pass a to matlab function
    for(i=0;i<ncols;i++){
      for(j=0;j<mrows;j++){        
             (mxGetPr(histforce_ips[0]))[i*mrows+j]=a[j][i];
            }
    }

     // call function:
     mexCallMATLAB(1,histforce_ops,1,histforce_ips,"calchistforce");

     // extract data
     for(i=0;i<ncols;i++){
          for(j=0;j<mrows;j++){        
                 b[j][i]=(mxGetPr(histforce_ops[0]))[i*mrows+j];
          }
     }

      // free  memory 
      for(i=0;i<mrows;i++){
        free(a[i]);  
        free(b[i]); 
      }
      free(a); free(b);

   }

Thank you for your help.

N

Answer 1

[James Tursa]

I don't see anywhere in your code where you create a variable in histforce_ips[0]. E.g.,

mxArray * histforce_ips[1];
    :
mexCallMATLAB(1,histforce_ops,1,histforce_ips,"calchistforce");

There is nothing inbetween these lines that sets histforce_ips[0] to anything, so when you call mexCallMATLAB you are passing an invalid pointer for the input argument. You need to do something like this instead:

mxArray * histforce_ips[1];
    :
histforce_ips[0] = mxCreateDoubleMatrix(mrows,ncols,mxREAL);
    :
// Then fill in the values of histforce_ips[0] via mxGetPr etc
    :
mexCallMATLAB(1,histforce_ops,1,histforce_ips,"calchistforce");
    :
mxDestroyArray(histforce_ips[0]);
mxDestroyArray(histforce_ops[0]);

Also, I don't know if this will eventually make a difference in your code at some point, but the way you allocate your "a" and "b" matrices piecemeal means that the memory for them is not guaranteed to be contiguous. Generally, if you want to preserve the a[j][i] syntax of indexing I would recommend allocating a single block of memory and work with that instead. E.g.,

// allocate memory:
  a=(double**)malloc(mrows*sizeof(double *));
  b=(double**)malloc(mrows*sizeof(double *));
  a[0] = (double *) malloc(mrows*ncols*sizeof(double));
  b[0] = (double *) malloc(mrows*ncols*sizeof(double));
  for(i=1;i<mrows;i++){
      a[i] = a[i-1] + ncols;
      b[i] = b[i-1] + ncols;
  }
  :
  free(a[0]); free(a);
  free(b[0]); free(b);

[Nora]

Thank you, I've added: histforce_ips[0] = mxCreateDoubleMatrix(mrows,ncols,mxREAL); to my code; however, I'm still getting a segmentation violation. Could you tell if I am reading histforce_ops in the correct way? Thanks again.

[James Tursa]

Please post your current code. It is critical where you create the variable. It needs to be done prior to accessing it in any way.

[Nora]

Thank you, I think what you suggested solved the problem. Now I am facing another problem, which is causing the segmentation error, but my posted minimal example isn't representative of this new issue (I haven't localized the issue yet). Thanks again, N