Thread Subject: how to pass cell of 3D matrices to C mex

Hi
I have a 1x30 cell. Each element in it consists of a MxNx3 matrix(image).
How can I send it into C mex file in similar format, but not read only.(duplicate will not work).
Basically it contains video frames.


Thanking you very much,

with regards,
ramana

"oruganti murthy" <omurthy@yahoo.com> wrote in message <h6tl9j$a0p$1@fred.mathworks.com>...
>
> I have a 1x30 cell. Each element in it consists of a MxNx3 matrix(image).
> How can I send it into C mex file in similar format, but not read only.(duplicate will not work).

Pass it in like any other variable. Then prhs[0] will be the cell array. If you want to modify it, use mxDuplicateArray to create a deep copy. Then use mxGetCell followed by mxGetPr to get at the cells and the arrays contained in the cells respectively. Why did you write that "duplicate will not work"?

James Tursa

 
> Pass it in like any other variable. Then prhs[0] will be the cell array. If you want to modify it, use mxDuplicateArray to create a deep copy. Then use mxGetCell followed by mxGetPr to get at the cells and the arrays contained in the cells respectively. Why did you write that "duplicate will not work"?
>
> James Tursa

Hi James,
I thought that duplicating will not allow the matrix to change. After your comment, I have verified it and I am taking my statement back.
As per your guidance, I wrote the following. and got the following output.
Can you please comment?

with regards,
ramana
************
#include "mex.h"
void
        mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]) {
    mxArray *cell_array_ptr, *cell_element_ptr;
    mwIndex i, j, index;
    mwSize m, n, total_num_of_cells, total_num_of_elements;
    double **carray;
    double *data;
    
    (void)plhs; /* unused parameter */
    
    /* Create a nrhs x 1 cell mxArray. */
    cell_array_ptr = mxCreateCellMatrix((mwSize)nrhs, 1);
    
    /* Fill cell matrix with input arguments */
    for( i=0; i<(mwIndex)nrhs; i++){
        mxSetCell(cell_array_ptr, i, mxDuplicateArray(prhs[i]));
    }
    total_num_of_cells = mxGetNumberOfElements(cell_array_ptr);
    
    for (index=0; index<total_num_of_cells; index++) {
        cell_element_ptr = mxGetCell(cell_array_ptr, index);
        data = mxGetPr(cell_element_ptr);
        m = mxGetM(cell_element_ptr);
        n = mxGetN(cell_element_ptr);
        carray = mxCalloc(n, sizeof(double*));
        for (j=0; j<n; j++)
            carray[j] = data+m*j;
        for (i=0;i<m;i++)
            for(j = 0;j<n;j++)
                mexPrintf("data(%i,%i) = %f \n", i+1, j+1, carray[i][j]);
    }
}
*********************************
clear all
clc
img = imread('cameraman.tif');
for i=1:3
    img1 = im2double(imresize(img,0.01*i));
    sources{i} = img1(:,:,1)';
end
struct1(sources)
**************
data(1,1) = 0.000000
data(1,2) = 0.000000
data(1,3) = 0.000000
>>

"oruganti murthy" <omurthy@yahoo.com> wrote in message <h72u3f$5qi$1@fred.mathworks.com>...
>

Try this:

#include "mex.h"
#define DATA(i,j) data[i+j*m]
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
    mxArray *cell_array_ptr, *cell_element_ptr;
    mwIndex i, j, index;
    mwSize m, n;
    double *data;
    
    (void)plhs; /* unused parameter */
    
    /* Create a nrhs x 1 cell mxArray. */
    cell_array_ptr = mxCreateCellMatrix(nrhs, 1);
    
    /* Fill cell matrix with input arguments */
    for( i=0; i<nrhs; i++){
        mxSetCell(cell_array_ptr, i, mxDuplicateArray(prhs[i]));
    }
    for (index=0; index<nrhs; index++) {
        cell_element_ptr = mxGetCell(cell_array_ptr, index);
        data = mxGetPr(cell_element_ptr);
        m = mxGetM(cell_element_ptr);
        n = mxGetN(cell_element_ptr);
        mexPrintf("Cell array index %d\n",index);
        for (i=0; i<m; i++)
            for(j=0; j<n; j++)
                mexPrintf("data(%i,%i) = %g \n", i+1, j+1, DATA(i,j));
        // other code to use cell_element_ptr
    }
    // other code to use cell_array_ptr
    mxDestroyArray(cell_array_ptr); // so this if not returned in a plhs
}

James Tursa

Hi james,
I compiled your code. But I am getting some strange output

Cell array index 0
data(1,1) = 8.41049e-288
data(1,2) = 5.45389e-312
data(1,3) = -9.60206e+303


I was expecting to print the individual elements(of matrix) of each entry of cell.

with regards,
ramana

"Ramana murthy" <omurthy@yahoo.com> wrote in message <h74ttb$t3r$1@fred.mathworks.com>...
> Hi james,
> I compiled your code. But I am getting some strange output
>
> Cell array index 0
> data(1,1) = 8.41049e-288
> data(1,2) = 5.45389e-312
> data(1,3) = -9.60206e+303
>
>
> I was expecting to print the individual elements(of matrix) of each entry of cell.
>
> with regards,
> ramana

Your posted code had double * for the data type, so I assumed that was the data type being passed in. Your strange results are because the data type being passed in is not double. Just check what the data type is and then adjust the code accordingly. e.g., if the data type is int8, then change these lines:

    double *data;
                :
        data = mxGetPr(cell_element_ptr);
                        :
                mexPrintf("data(%i,%i) = %g \n", i+1, j+1, DATA(i,j));

to this:

    signed char *data;
                :
        data = mxGetData(cell_element_ptr);
                        :
                mexPrintf("data(%i,%i) = %d \n", i+1, j+1, DATA(i,j));

Or if the data is uint16, then change the lines to this:

    unsigned short *data;
                :
        data = mxGetData(cell_element_ptr);
                        :
                mexPrintf("data(%i,%i) = %d \n", i+1, j+1, DATA(i,j));

etc. etc.

James Tursa

Hi James,
As I have posted in my previous mail,
My matlab code calling this mex file is

*********************************
clear all
clc
img = imread('cameraman.tif');
for i=1:3
    img1 = im2double(imresize(img,0.01*i));
    sources{i} = img1(:,:,1)';
end
struct1(sources)
**************
Clearly, I'm passing a matrix of double values.
My problem is
1. I'm not getting output matrices
2. Very strange values
Any suggestions?


with regards,
ramana

"Ramana murthy" <omurthy@yahoo.com> wrote in message <h75fld$ort$1@fred.mathworks.com>...
> Hi James,
> As I have posted in my previous mail,
> My matlab code calling this mex file is
>
> *********************************
> clear all
> clc
> img = imread('cameraman.tif');
> for i=1:3
> img1 = im2double(imresize(img,0.01*i));
> sources{i} = img1(:,:,1)';
> end
> struct1(sources)
> **************
> Clearly, I'm passing a matrix of double values.

OK, please clear something up. Is your function called "struct1", and are you passing in your "sources" variable? If that is the case, then you are passing in a cell array, not a double. e.g., try out this code to verify what the mex file is actually getting:

#include "mex.h"
#define DATA(i,j) data[i+j*m]
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
    mxArray *cell_array_ptr, *cell_element_ptr;
    mwIndex i, j, index;
    mwSize m, n;
    double *data;
    
    (void)plhs; /* unused parameter */
    
    /* Create a nrhs x 1 cell mxArray. */
    cell_array_ptr = mxCreateCellMatrix(nrhs, 1);
    
    /* Fill cell matrix with input arguments */
    for( i=0; i<nrhs; i++){
        if( !mxIsDouble(prhs[i]) ) {
            mexPrintf("Input argument is not double, it is %s\n",mxGetClassName(prhs[i]));
            mxDestroyArray(cell_array_ptr);
            mexErrMsgTxt("Returning to MATLAB");
        }
        mxSetCell(cell_array_ptr, i, mxDuplicateArray(prhs[i]));
    }
    for (index=0; index<nrhs; index++) {
        cell_element_ptr = mxGetCell(cell_array_ptr, index);
        data = mxGetPr(cell_element_ptr);
        m = mxGetM(cell_element_ptr);
        n = mxGetN(cell_element_ptr);
        mexPrintf("Cell array index %d\n",index);
        for (i=0; i<m; i++)
            for(j=0; j<n; j++)
                mexPrintf("data(%i,%i) = %g \n", i+1, j+1, DATA(i,j));
        // other code to use cell_element_ptr
    }
    // other code to use cell_array_ptr
    mxDestroyArray(cell_array_ptr); // so this if not returned in a plhs
}

After doing that, please advise me what, exactly, you would like the mex file to do, as I have been under the apparently mistaken impression you wanted to copy some double inputs into a cell array for manipulation inside the mex routine.

James Tursa

> After doing that, please advise me what, exactly, you would like the mex file to do, as I have been under the apparently mistaken impression you wanted to copy some double inputs into a cell array for manipulation inside the mex routine.
>
> James Tursa


Hi James,
Sorry if I have confused you. My C mex file name is struct1.c
I wanted to pass all all the 2D matrices in a cell to Mex file. In the mex file I want to use each element of any matrix according to my requirements
In C file I want all the 2D matrices accessible seperately.

By running your new code I got...
*****************
Input argument is not double, it is cell
??? Error using ==> struct1
Returning to MATLAB

***********************

INput from Matlab file
A cell of size k, containing a MxN matrix entries
Desired variable in C MEx file
A 3D matrix data[i][j][k] where k is the kth cell entry
or equivalent representation so that I can access MxNth matrix elements

with regards,
ramana

"Ramana murthy" <omurthy@yahoo.com> wrote in message <h75tia$ov3$1@fred.mathworks.com>...
> INput from Matlab file
> A cell of size k, containing a MxN matrix entries
> Desired variable in C MEx file
> A 3D matrix data[i][j][k] where k is the kth cell entry
> or equivalent representation so that I can access MxNth matrix elements
>
> with regards,
> ramana

Try this:

#include "mex.h"
#define DOUBLEDATA(i,j) doubledata[i+j*m+k*m*n]
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
    mxArray *mxcell, *mxdouble;
    mwSize i, j, m, n, k, p, numel;
    mwSize ndim = 3;
    mwSize dims[3];
    double *celldata, *doubledata;
    
    (void)plhs; /* unused parameter */

    if( nrhs != 1 ) {
        mexErrMsgTxt("Need exactly one input");
    }
    if( nlhs != 0 ) {
        mexErrMsgTxt("Too many outputs");
    }
    if( !mxIsCell(prhs[0]) ) {
        mexPrintf("Input argument is not cell, it is %s\n",mxGetClassName(prhs[0]));
        mexErrMsgTxt("Returning to MATLAB");
    }
    
    p = mxGetNumberOfElements(prhs[0]);
    dims[2] = p;
    
    /* Fill 3D matrix with input arguments */
    for( i=0; i<p; i++){
        mxcell = mxGetCell(prhs[0],i);
        if( !mxIsDouble(mxcell) ) {
            mexPrintf("Input cell is not double, it is %s\n",mxGetClassName(mxcell));
        }
        if( mxIsComplex(mxcell) ) {
            mexErrMsgTxt("Input cell cannot be complex");
        }
        if( mxGetNumberOfDimensions(mxcell) != 2 ) {
            mexErrMsgTxt("Input cell must be 2D");
        }
        if( i == 0 ) {
            m = mxGetM(mxcell);
            n = mxGetN(mxcell);
            dims[0] = m;
            dims[1] = n;
            mxdouble = mxCreateNumericArray(ndim, dims, mxDOUBLE_CLASS, mxREAL);
            numel = mxGetNumberOfElements(mxcell);
            doubledata = mxGetPr(mxdouble);
        }
        if( mxGetM(mxcell) != m || mxGetN(mxcell) != n ) {
            mexErrMsgTxt("Input cell dimensions must all be the same");
        }
        celldata = mxGetPr(mxcell);
        for( j=0; j<numel; j++ ) {
            *doubledata++ = *celldata++;
        }
    }
    doubledata = mxGetPr(mxdouble);
    for (k=0; k<p; k++) {
        for (j=0; j<n; j++) {
            for(i=0; i<m; i++) {
                mexPrintf("data(%d,%d,%d) = %g \n", i+1, j+1, k+1, DOUBLEDATA(i,j,k));
            }
        }
    }
    // other code to use mxdouble
    mxDestroyArray(mxdouble); // do this if not returned in a plhs
}

James Tursa

"Ramana murthy" <omurthy@yahoo.com> wrote in message <h75tia$ov3$1@fred.mathworks.com>...
> INput from Matlab file
> A cell of size k, containing a MxN matrix entries
> Desired variable in C MEx file
> A 3D matrix data[i][j][k] where k is the kth cell entry
> or equivalent representation so that I can access MxNth matrix elements
>

Follow-up question: Are you going to be *changing* the data inside your mex routine, or are you treating it as read-only? In the latter case, a much more efficient mex routine can be written than the one I just posted.

James Tursa

"James Tursa" <aclassyguy_with_a_k_not_a_c@hotmail.com> wrote in message <h7696t$i7u$1@fred.mathworks.com>...
>
> #define DOUBLEDATA(i,j) doubledata[i+j*m+k*m*n]

Typo. Should be:

#define DOUBLEDATA(i,j,k) doubledata[i+j*m+k*m*n]

James Tursa

Hi James,
Thank you very much. Now it is working fine.
Yes, I want to change the contents of the matrices in the mex file. I don't want it as Read only file.
Though not required for my present application, I wanted to know if the matrices can be of different sizes. Right now, I see in your code you have restricted to be same size.


with regards,
ramana

"Ramana murthy" <omurthy@yahoo.com> wrote in message <h77jke$cl2$1@fred.mathworks.com>...
> Hi James,
> Thank you very much. Now it is working fine.
> Yes, I want to change the contents of the matrices in the mex file. I don't want it as Read only file.
> Though not required for my present application, I wanted to know if the matrices can be of different sizes. Right now, I see in your code you have restricted to be same size.

Yes, this can be done with a technique often used in C. Basically, instead of allocating one contiguous block of memory to hold everything, you create an array of double *, each one pointing to a copy of one of your 2D matrices. You allocate the matrix memory on the fly depending on how large the matrix is. It does take a little more clean-up at the end to free all the memory piecemeal, however. e.g.,

#include "mex.h"
#define ARRAYDATA(i,j,k) array[k][i+j*arrayM[k]]
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
    mxArray *mxcell;
    mwSize i, j, m, n, k, p, numel;
    mwSize *arrayM, *arrayN;
    double *celldata, *arraydata;
    double **array;
    
    (void)plhs; /* unused parameter */

    if( nrhs != 1 ) {
        mexErrMsgTxt("Need exactly one input");
    }
    if( nlhs != 0 ) {
        mexErrMsgTxt("Too many outputs");
    }
    if( !mxIsCell(prhs[0]) ) {
        mexPrintf("Input argument is not cell, it is %s\n",mxGetClassName(prhs[0]));
        mexErrMsgTxt("Returning to MATLAB");
    }
    
    p = mxGetNumberOfElements(prhs[0]);
    array = mxMalloc(p * sizeof(*array));
    arrayM = mxMalloc(p * sizeof(*arrayM));
    arrayN = mxMalloc(p * sizeof(*arrayN));
    
    /* Fill 3D array with input arguments, each a different size */
    for( i=0; i<p; i++){
        mxcell = mxGetCell(prhs[0],i);
        if( !mxIsDouble(mxcell) ) {
            mexPrintf("Input cell is not double, it is %s\n",mxGetClassName(mxcell));
        }
        if( mxIsComplex(mxcell) ) {
            mexErrMsgTxt("Input cell cannot be complex");
        }
        if( mxGetNumberOfDimensions(mxcell) != 2 ) {
            mexErrMsgTxt("Input cell must be 2D");
        }
        celldata = mxGetPr(mxcell);
        arrayM[i] = mxGetM(mxcell);
        arrayN[i] = mxGetN(mxcell);
        numel = mxGetNumberOfElements(mxcell);
        array[i] = mxMalloc(numel * sizeof(**array));
        for( j=0; j<numel; j++ ) {
            array[i][j] = celldata[j]; // copy the data linearly, not as 2D
        }
    }
    for (k=0; k<p; k++) {
        for (j=0; j<arrayN[k]; j++) {
            for(i=0; i<arrayM[k]; i++) {
                mexPrintf("array(%d,%d,%d) = %g \n", i+1, j+1, k+1, ARRAYDATA(i,j,k));
            }
        }
    }
    // other code to use array here
    // free up the allocated memory when done
    for( k=0; k<p; k++ ) {
        mxFree(array[k]);
    }
    mxFree(array);
    mxFree(arrayM);
    mxFree(arrayN);
}

James Tursa

Thank you very much Mr.James.

with regards,
Ramana

"James Tursa" <aclassyguy_with_a_k_not_a_c@hotmail.com> wrote in message <h77vh1$373$1@fred.mathworks.com>...
> "Ramana murthy" <omurthy@yahoo.com> wrote in message <h77jke$cl2$1@fred.mathworks.com>...
> > Hi James,
> > Thank you very much. Now it is working fine.
> > Yes, I want to change the contents of the matrices in the mex file. I don't want it as Read only file.
> > Though not required for my present application, I wanted to know if the matrices can be of different sizes. Right now, I see in your code you have restricted to be same size.
>
> Yes, this can be done with a technique often used in C. Basically, instead of allocating one contiguous block of memory to hold everything, you create an array of double *, each one pointing to a copy of one of your 2D matrices. You allocate the matrix memory on the fly depending on how large the matrix is. It does take a little more clean-up at the end to free all the memory piecemeal, however. e.g.,
>
> #include "mex.h"
> #define ARRAYDATA(i,j,k) array[k][i+j*arrayM[k]]
> void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
> {
> mxArray *mxcell;
> mwSize i, j, m, n, k, p, numel;
> mwSize *arrayM, *arrayN;
> double *celldata, *arraydata;
> double **array;
>
> (void)plhs; /* unused parameter */
>
> if( nrhs != 1 ) {
> mexErrMsgTxt("Need exactly one input");
> }
> if( nlhs != 0 ) {
> mexErrMsgTxt("Too many outputs");
> }
> if( !mxIsCell(prhs[0]) ) {
> mexPrintf("Input argument is not cell, it is %s\n",mxGetClassName(prhs[0]));
> mexErrMsgTxt("Returning to MATLAB");
> }
>
> p = mxGetNumberOfElements(prhs[0]);
> array = mxMalloc(p * sizeof(*array));
> arrayM = mxMalloc(p * sizeof(*arrayM));
> arrayN = mxMalloc(p * sizeof(*arrayN));
>
> /* Fill 3D array with input arguments, each a different size */
> for( i=0; i<p; i++){
> mxcell = mxGetCell(prhs[0],i);
> if( !mxIsDouble(mxcell) ) {
> mexPrintf("Input cell is not double, it is %s\n",mxGetClassName(mxcell));
> }
> if( mxIsComplex(mxcell) ) {
> mexErrMsgTxt("Input cell cannot be complex");
> }
> if( mxGetNumberOfDimensions(mxcell) != 2 ) {
> mexErrMsgTxt("Input cell must be 2D");
> }
> celldata = mxGetPr(mxcell);
> arrayM[i] = mxGetM(mxcell);
> arrayN[i] = mxGetN(mxcell);
> numel = mxGetNumberOfElements(mxcell);
> array[i] = mxMalloc(numel * sizeof(**array));
> for( j=0; j<numel; j++ ) {
> array[i][j] = celldata[j]; // copy the data linearly, not as 2D
> }
> }
> for (k=0; k<p; k++) {
> for (j=0; j<arrayN[k]; j++) {
> for(i=0; i<arrayM[k]; i++) {
> mexPrintf("array(%d,%d,%d) = %g \n", i+1, j+1, k+1, ARRAYDATA(i,j,k));
> }
> }
> }
> // other code to use array here
> // free up the allocated memory when done
> for( k=0; k<p; k++ ) {
> mxFree(array[k]);
> }
> mxFree(array);
> mxFree(arrayM);
> mxFree(arrayN);
> }
>
> James Tursa

Hello James,

I've tried to use your example but every time when a function uses "mxcell" as an input argument I have the following error: MATLAB: Unexpected Exception.

I debugged it with VS and every time at the line: if( !mxIsDouble(mxcell) ) I got this error. If I remove this line I will get at if( mxIsComplex(mxcell) ) and so on.

The compiler used for building the MEX was from Visual Studio 2008 and the command: mex -g test1.c.

Do you have any idea why I got this error.

Thanks,
Paul

"Paul " <paul_tutzu@yahoo.com> wrote in message <hildcr$n7e$1@fred.mathworks.com>...
>
> I've tried to use your example but every time when a function uses "mxcell" as an input argument I have the following error: MATLAB: Unexpected Exception.
>
> I debugged it with VS and every time at the line: if( !mxIsDouble(mxcell) ) I got this error. If I remove this line I will get at if( mxIsComplex(mxcell) ) and so on.
>
> The compiler used for building the MEX was from Visual Studio 2008 and the command: mex -g test1.c.
>
> Do you have any idea why I got this error.

Hmmm. The posted code works fine with MSVC8. I haven't tried it yet with VS 2008. If I get some time I will install VS 2008 and give it a try. I have no idea why mxcell would be causing a problem for you. Are you using the code exactly as posted or have you made some changes?

James Tursa

"James Tursa" <aclassyguy_with_a_k_not_a_c@hotmail.com> wrote in message <him8gq$3iu$1@fred.mathworks.com>...
> "Paul " <paul_tutzu@yahoo.com> wrote in message <hildcr$n7e$1@fred.mathworks.com>...
> >
> > I've tried to use your example but every time when a function uses "mxcell" as an input argument I have the following error: MATLAB: Unexpected Exception.
> >
> > I debugged it with VS and every time at the line: if( !mxIsDouble(mxcell) ) I got this error. If I remove this line I will get at if( mxIsComplex(mxcell) ) and so on.
> >
> > The compiler used for building the MEX was from Visual Studio 2008 and the command: mex -g test1.c.
> >
> > Do you have any idea why I got this error.
>
> Hmmm. The posted code works fine with MSVC8. I haven't tried it yet with VS 2008. If I get some time I will install VS 2008 and give it a try. I have no idea why mxcell would be causing a problem for you. Are you using the code exactly as posted or have you made some changes?

Just tried in with VS 2008 and it works fine for me. Don't know what your problem could be since I can't reproduce the error.

James Tursa