MATLAB: How to pass an image to a 2D array using Matlab MEX

2d arraycmex

I want to read some image to run a C++ MEX function to process this image. The image is originally stored as a Matlab 3D matrix, and then converted to a 2D matrix and each slice of the image is stored as a 1D vector. Here is some example codes below.

The MEX function:

include "mex.h"
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]) {
unsigned int** ubuff;
size_t col_ubuff    = mxGetN(prhs[0]);
size_t row_ubuff    = mxGetM(prhs[0]);
ubuff               = (unsigned int **)mxCalloc(col_ubuff, row_ubuff);
for(int x = 0; x < col_ubuff; x++) {
    ubuff[x] = (unsigned int *) mxCalloc(row_ubuff, sizeof(unsigned int));
}
for (int col=0; col < col_ubuff; col++) {
    for (int row=0; row < row_ubuff; row++) {
        ubuff[col][row] = mxGetPr(prhs[0])[row+col*row_ubuff];
    }
}
unsigned int the_pixel_i_want = ubuff[16][2*32 + 2];
printf ("Debug: %d\n\n", the_pixel_i_want);
return;
}

2. The program can be compiled; however, the results of running the program is strange; for example, I have some test codes and test image with all pixels to be 188,

%%Test input image as 2D array clc; clf; clear all; close all;
volImage = 188.*ones(32,32,32); 
volImageVec = reshape(volImage, 32*32, 32)'; 
volImageVec = uint32(volImageVec);
TestInputImage(volImageVec');

But the output sometimes be 188 and sometimes be 0. Is there a memory leak somewhere in my code? Thanks very much for your help.

Best Answer

Thanks for editing. I found a way from other people. Just put it here for other people's interest.

1) The line

ubuff = (unsigned int **)mxCalloc(col_ubuff, row_ubuff);
should be
ubuff = (unsigned int **)mxCalloc(col_ubuff, sizeof(unsigned int *));
2) The line
   ubuff[col][row] = mxGetPr(prhs[0])[row+col*row_ubuff];
should be
   ubuff[col][row] = ((unsigned int *)mxGetData(prhs[0]))[row+col*row_ubuff];

Related Solutions

MATLAB: How to output a 2D integer array using Matlab mex

I got the answer with the help from someone. I put it here for others' reference.

    // Output the results 
    plhs[0]                     = mxCreateNumericMatrix(col_outputBuff, row_outputBuff, mxINT32_CLASS, mxREAL);
    int* outputMatrix         = (int *)mxGetData(plhs[0]);
    // Read in the data
    for (int col=0; col < col_outputBuff; col++) {
        for (int row=0; row < row_outputBuff; row++) {
            outputMatrix[row + col*row_outputBuff] = outputBuff[col][row];
        }
    }

MATLAB: With mxMalloc() and mxSetDoubles(), mex function crash matlab

You have memory leaks in your current code. E.g.,

    tmpResult = mxMalloc(numRows*numRows*sizeof(*tmpResult)); // this memory gets leaked by the very next line
    tmpResult = r8mat_expm1(numRows, inputMat); // leaks memory from the mxMalloc( ) call
    plhs[0] = mxCreateDoubleMatrix(numRows, numRows, mxREAL); // this memory gets leaked by the very next line
    mxSetDoubles(plhs[0], tmpResult); // leaks memory from the mxCreateDoubleMatrix( ) call

This leaked memory is bad but does not cause the crash.

It appears you attach native C/C++ allocated memory to an mxArray, and this will cause a crash. You can't mix native C/C++ allocated memory in an mxArray. All memory in an mxArray must come from MATLAB API memory allocation functions.

You really need to post some details about the r8mat_expm1( ) function for us to be sure about what the real problem is. But from your description it sounds like it allocates the memory for the result using native C/C++ routines (e.g., malloc or calloc) and then returns the pointer to that, which you then attach to an mxArray ... resulting in a crash. If this is true, then you will either need to change the function to use MATLAB API allocation functions, or copy the results. To copy the results you would do something like this:

#include <string.h> // for memcpy( )
#include <stdlib.h> // for free( )
    double *tmpResult;
    double *inputMat;
    double *pr;
    int numRows;
    numRows = mxGetM(prhs[0]);
    inputMat = mxGetDoubles(prhs[0]);
    tmpResult = r8mat_expm1(numRows, inputMat); // calculate matrix exponential
    plhs[0] = mxCreateDoubleMatrix(numRows, numRows, mxREAL);
    pr = mxGetDoubles(plhs[0]);
    memcpy(pr,tmpResult,numRows*numRows*sizeof(double));
    free(tmpResult); // use free( ) for native C/C++ allocated memory

To avoid the data copy and use MATLAB API allocation functions, you would need to alter the source code of r8mat_expm1( ) and pass in the pointer instead of allocating memory inside the function. Then your mexFunction( ) code would look like this instead of the above:

    double *inputMat;
    double *pr;
    int numRows;
    numRows = mxGetM(prhs[0]);
    inputMat = mxGetDoubles(prhs[0]);
    plhs[0] = mxCreateDoubleMatrix(numRows, numRows, mxREAL);
    pr = mxGetDoubles(plhs[0]);
    r8mat_expm1(numRows, inputMat, pr); // calculate matrix exponential

And the signature for the r8mat_expm1( ) function would change to this:

    void r8mat_expm1(int, double *, double *);

where the 3rd input argument is used inside r8mat_expm1( ) for the output, and no memory allocation is done inside this function.

Another way to do this is to change the malloc( ) and calloc( ) inside r8mat_expm1( ) to be mxMalloc( ) and mxCalloc( ) instead, and then attach that result to the mxArray. If you want I can post that code, but frankly it is more complicated than what I have posted above so I would see no practical reason to code it this way.

Best Answer

Related Solutions

MATLAB: How to output a 2D integer array using Matlab mex

MATLAB: With mxMalloc() and mxSetDoubles(), mex function crash matlab

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