How do I convert to Mex from Cpp using Xcode ver 10

Question

Stelios Fanourakis 2019-6-18

0
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此问题的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/467674-how-do-i-convert-to-mex-from-cpp-using-xcode-ver-10

评论： Walter Roberson 2019-6-23

采纳的回答： Walter Roberson

For Mac Users, I need that info. Thanks

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Stelios Fanourakis 2019-6-18

在 MATLAB Online 中打开

It's a cpp program that I need to run it in Matlab. I need to convert it to Mex. This is the code I need to run in Matlab.

#include "mex.h"
#include "string.h"
void mexFunction( int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
    if (nrhs!=5)
		mexErrMsgTxt("Wrong number of inputs");
	if (nlhs!=1)
		mexErrMsgTxt("Wrong number of outputs");
    
    //---------------------- inputs -----------------------//
    double *Bness;
    double F0,F1,Bth,JumpConst;
    
    const int *DimsBness;
    
    DimsBness = mxGetDimensions(prhs[0]);
	int bH = DimsBness[0];
	int bW = DimsBness[1];
    Bness = (double *)mxGetData(prhs[0]);
    double *pF0,*pF1,*pBth,*pJumpConst;
    pF0 = (double *)mxGetData(prhs[1]);
    pF1 = (double *)mxGetData(prhs[2]);
    pBth = (double *)mxGetData(prhs[3]);
    pJumpConst = (double *)mxGetData(prhs[4]);
    F0 = *pF0; F1 = *pF1; Bth = *pBth; JumpConst = *pJumpConst;
    
    //---------------------- outputs ----------------------//
    plhs[0] = mxCreateNumericArray(2,DimsBness,mxDOUBLE_CLASS,mxREAL);
	double *imSeg = (double *)mxGetData(plhs[0]);
	memset(imSeg, 0, bH*bW*sizeof(double));
    
    //===================================================================//
    double *CostF = (double *)mxCalloc(bH*bW, sizeof(double));
    for (int i=0; i<bH*bW; i++) CostF[i] = 1000;  // The total cost for each point
    
    double *mini = (double *)mxCalloc(bH*bW, sizeof(double));
    for (int i=0; i<bH*bW; i++) mini[i] = 1;  // The index of minimum cost path from each point
    
    double *diffF = (double *)mxCalloc(bH*bW, sizeof(double));
    for (int i=0; i<bH*bW; i++) diffF[i] = JumpConst;   //The slop of path at each point (for smoothness)
    
    // The last row is used as "no bone" pass.
    for (int i = 0; i<bW; i++) Bness[bH-1+bH*i] = Bth; //use a threshold for no bone
    
    double minCF;
    double Cdiff, Econt, Esmth, Etotal, CF, tmp;
    double Ecnct = -0.01;
    
    for (int ww = 1; ww<bW; ww++) {
        for (int hh = 0; hh<(bH-1); hh++) {
            
            if (Bness[hh+bH*ww]) {
                // Go through the CostF(i-1,:) and find min path from there to current state
                minCF = 100000;
                for (int k=0; k<(bH-1); k++) {
                    Cdiff = (k-hh)/(double)(bH);   // Current Difference (bH is just for normalization)
                    Econt = Cdiff*Cdiff + 1/(double)(bH*bH);  // Energy of Continuity
                    tmp = Cdiff-diffF[k+ bH*(ww-1)];
                    Esmth = tmp*tmp;   // Energy of Smoothness
                    Etotal = F0*Econt + F1*Esmth + Ecnct;
                    CF = CostF[k+ bH*(ww-1)] + Etotal;
                    if (CF<minCF) {
                        minCF = CF;
                        mini[hh+bH*ww] = k;
                    }
                }
                // From No Bone To Bone Find the cost for no bone (bH-1)
                // Smoothness is found differently
                // second term: a constant smoothness cost for being in no bone zone
				int kk = bH-1;
                Etotal = JumpConst; //(F0+F1) * (hh~=kk) * Bth;
                CF = CostF[kk+bH*(ww-1)] + Etotal;
                if (CF<minCF) {
                    minCF = CF;
                    mini[hh+bH*ww] = kk;
                    diffF[hh+bH*ww] = 0;
                } else
                    diffF[hh+bH*ww] = (mini[hh+bH*ww]-hh)/(double)(bH);
                
                CostF[hh+bH*ww] = (1-Bness[hh+bH*ww]) + minCF;
                
            } else {    // (!Bness[hh+bH*ww])
                mini[hh+bH*ww] = bH;   // go to no bone area
                CostF[hh+bH*ww] = 1000 + CostF[hh+bH*(ww-1)];  // very high cost
            }
        }
        ///////// From Bone To No Bone /////////
        int hhh = bH-1;
        minCF = 100000;
        for (int k=0; k<bH; k++) {
            // add jump cost if moving from bone to no bone and add average
            // smoothing factors if staying in no bone
            Etotal = JumpConst*(k!=hhh) + (F0+F1) * (k==hhh) /(double)(bH*bH);
            CF = CostF[k + bH*(ww-1)] + Etotal;
            if (CF<minCF) {
                minCF = CF;
                mini[hhh+bH*ww] = k;
            }
        }
        CostF[hhh+bH*ww] = (1-Bness[hhh+bH*ww]) + minCF;
        diffF[hhh+bH*ww] = 0;
        
    }
    ///////////////////////////////
   
	double *indSeg = (double *)mxCalloc(bW, sizeof(double)); //The slop of path at each point (for smoothness)
    memset(indSeg, 0, bW*sizeof(double));
    /*// find the minimum cost function for the last column
    double minCost = 100000;
    for (int i=0; i<bH; i++) {
        if (minCost>CostF[i+bH*(bW-1)]) {
            indSeg[bW-1] = i;
            minCost=CostF[i+bH*(bW-1)];
        }
    }*/
    indSeg[bW-1] = bH-1;
    
    
    // memoization
    for (int i=bW-2; i>=0; i--) {
        indSeg[i] = mini[ (int)(indSeg[i+1] + bH*(i+1)) ];
    }
    
    for (int i=0; i<bW; i++)  imSeg[ (int)(indSeg[i] + bH* i) ] = 1;
    
}

Stelios Fanourakis 2019-6-18

在 MATLAB Online 中打开

I use the line

mex SegmentBone.cpp

This should do the compiling from cpp to Mex. However, I get the error

mex SegmentBoneDP.cpp
Building with 'Xcode Clang++'.
Error using mex
/Users/steliosphanourakes/Desktop/Matlab/DesMoines/karadokei -
Copy/FANOURAKIS_STELIOS12/20190516144930/SegmentBoneDP.cpp:17:17: error: assigning to 'const int *' from
incompatible type 'const mwSize *' (aka 'const unsigned long *')
    DimsBness = mxGetDimensions(prhs[0]);
                ^~~~~~~~~~~~~~~~~~~~~~~~
/Applications/MATLAB_R2018b.app/extern/include/matrix.h:243:25: note: expanded from macro 'mxGetDimensions'
#define mxGetDimensions mxGetDimensions_730
                        ^
/Users/steliosphanourakes/Desktop/Matlab/DesMoines/karadokei -
Copy/FANOURAKIS_STELIOS12/20190516144930/SegmentBoneDP.cpp:30:15: error: no matching function for call to
'mxCreateNumericArray_730'
    plhs[0] = mxCreateNumericArray(2,DimsBness,mxDOUBLE_CLASS,mxREAL);
              ^~~~~~~~~~~~~~~~~~~~
/Applications/MATLAB_R2018b.app/extern/include/matrix.h:275:30: note: expanded from macro 'mxCreateNumericArray'
#define mxCreateNumericArray mxCreateNumericArray_730
                             ^~~~~~~~~~~~~~~~~~~~~~~~
/Applications/MATLAB_R2018b.app/extern/include/matrix.h:1247:1: note: candidate function not viable: no known
conversion from 'const int *' to 'const mwSize *' (aka 'const unsigned long *') for 2nd argument
mxCreateNumericArray(mwSize ndim, const mwSize *dims, mxClassID classid, mxComplexity flag);
^
/Applications/MATLAB_R2018b.app/extern/include/matrix.h:275:30: note: expanded from macro 'mxCreateNumericArray'
#define mxCreateNumericArray mxCreateNumericArray_730
                             ^
2 errors generated.

Anyone who can responsibly help me?

Thanks

Rik 2019-6-19

With example.mexmaci64 you can use example('input') from inside Matlab (assuming that your function takes such an input).

Stelios Fanourakis 2019-6-20

Yes. The point is that I don't know the number and type of inputs the function requires since I cannot open it to see it.

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Answer 1

Walter Roberson 2019-6-20

1
链接

此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/467674-how-do-i-convert-to-mex-from-cpp-using-xcode-ver-10#answer_380009

在 MATLAB Online 中打开

Your SegmentBoneDP.cpp file is the source code.

If you need something that converts C++ code into MATLAB code, then you are using the wrong product family. There is no known program that converts C++ code into MATLAB code.

"The point is that I don't know the number and type of inputs the function requires since I cannot open it to see it. "

You read them out of the C++ source code.

    Bness = (double *)mxGetData(prhs[0]);
    double *pF0,*pF1,*pBth,*pJumpConst;
    pF0 = (double *)mxGetData(prhs[1]);
    pF1 = (double *)mxGetData(prhs[2]);
    pBth = (double *)mxGetData(prhs[3]);
    pJumpConst = (double *)mxGetData(prhs[4]);

The first parameter is Bness, and is a 2D double array.

The second parameter is F0, and it is a double scalar. It appears to be used as a weight or smoothing factor

The third parameter is F1, and it is a double scalar. It appears to be used as a weight or smoothing factor

The fourth parameter is Bth, and it is a double scalar. It is a threshold between bone and no bone.

The fifth parameter is JumpConst, and it is a double scalar. It appears to be some kind of penalty for moving from bone to no bone.

The output is an array the same size as Bness, and it is a real double 2D array.

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Answer 2

Jan 2019-6-19

1
链接

此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/467674-how-do-i-convert-to-mex-from-cpp-using-xcode-ver-10#answer_379924

编辑：Jan 2019-6-19

在 MATLAB Online 中打开

Wow, what an inefficient communication.

As Walter has said already, the line

const int *DimsBness;

must be changed to

const mwSize *DimsBness;

This might matter other variables of the type int also.

C++ Mex files are compiled to mexmaci64 files. Of course you can neither edit these output files, not run it directly. This is the nature of compiled files. Simply put this file to a folder, which is included to your Matlab path and call it like any other function stored in an M-file:

result = BoneSegmentationDP(args)

where args are the 5 needed inputs.

"I was getting the error message that I needed to update my Xcode compiler in order to utilize the new API, that's why I used mex -compatibleArrayDims BoneSegmentationDP.cpp"

No. If you get the message, that the Xcode compiler needs an update, update the Xcode compiler. It is off-track to play around with the compatibleArrayDims flag.

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Walter Roberson 2019-6-23

mwSize is size_t which is unsigned long long for your system. It causes 8 bytes to be reserved for each variable that is to store an array size. That permits arrays larger than 2 gigabytes. Your existing use of int for the size is reserving only 4 bytes for array sizes.

Now you might be thinking that your particular use never involves arrays 2 gb or larger and you might be thinking that means that you do not need to use the larger variable. However 8 bytes is what matlab uses internally now and when matlab builds its internal description of the parameters to the call it is going to allocate memory based on the larger size. If your code were to try to use the sizes as if only 32 bits were allocated for the size then you would be looking for the second dimension size at the wrong place in memory.

Walter Roberson 2019-6-23

"Where do I replace them? In the C++ code?"

Yes. Edit the darn C++ code.

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How do I convert to Mex from Cpp using Xcode ver 10

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