memcpy function calling inside mex

Question

I have an interesting problem. Namely like that; I am trying to use std::memcpy function inside by mex function and calling that mex function inside MATLAB like that;

I2 = b_filter(I);

When I copy the whole image, it works well;

plhs[0] =  mxCreateDoubleMatrix(mxGetM(plhs[0]), mxGetN(plhs[0]), mxREAL);          
memcpy(mxGetPr(plhs[0]), mxGetPr(prhs[0]), sizeof(double) *mxGetM(plhs[0]) * mxGetN(plhs[0]));

But when I try to copy some part of image

plhs[0] =  mxCreateDoubleMatrix(100, 100, mxREAL);              
memcpy(mxGetPr(plhs[0]), mxGetPr(prhs[0]), sizeof(double) * 100 * 100);

it doesn't give right image part but gives unmeaningful pixel values.

So what is going on here?

Answer 1

Ha Ha! You've been caught by one of the nastiest of mex file nuances! It's got me before too. Arrays in mex functions are stored in column order not row order, so you:

You still use column-first indexing like in Matlab, though

Blog URL

Try this page too for a nice picture of the ordering.

Finally I would recommend reading this thread to get a better idea behind the difference of C and MATLAB matrix memory being column-ordered.

Answer 2

As explained by @macduff, MATLAB uses a column-major order to store arrays, while C arrays are row-major.

Here is a sample implementation showing how to copy part of a matrix.

matrix_slice_mex.c

#include "mex.h"
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
    double *in, *out;
    mwIndex i,j;
    mwSize numRows;

    /* input checks */
    if (nrhs != 1 || nlhs > 1) {
        mexErrMsgIdAndTxt("MATLAB:nargchk", "Wrong number of arguments.");
    }
    if (mxGetNumberOfDimensions(prhs[0])>2 || !mxIsDouble(prhs[0])) {
        mexErrMsgIdAndTxt("MATLAB:wrongDims", "Expecting 2D double matrix.");
    }
    if (mxGetM(prhs[0])<100 || mxGetN(prhs[0])<100) {
        mexErrMsgIdAndTxt("MATLAB:wrongDims", "Matrix size must be >= 100x100.");
    }

    /* extract sub-matrix */
    plhs[0] = mxCreateDoubleMatrix(100, 100, mxREAL);
    out = mxGetPr(plhs[0]);
    in = mxGetPr(prhs[0]);
    numRows = mxGetM(prhs[0]);
    for(j=0; j<100; j++) {
        for(i=0; i<100; i++) {
            *out++ = in[i + numRows*j];
        }
    }
}

And to test this:

x = rand(1000);
y = x(1:100,1:100);
yy = matrix_slice_mex(x);
isequal(y,yy)

You could have also used memcpy to copy each of the columns (one for-loop instead)