MATLAB Tensor Indexing in C++ - c++

Question

I am attempting to load in a .mat file containing a tensor of known dimensions in C++; 144x192x256.
I have adjusted the linear index for the read operation to be column major as in MATLAB. However I am still getting memory access issues.
void FeatureLoader::readMat(const std::string &fname, Image< std::vector<float> > *out) {
//Read MAT file.
const char mode = 'r';
MATFile *matFile = matOpen(fname.c_str(), &mode);
if (matFile == NULL) {
throw std::runtime_error("Cannot read MAT file.");
}
//Copy the data from column major to row major storage.
float *newData = newImage->GetData();
const mxArray *arr = matGetVariable(matFile, "map");
if (arr == NULL) {
throw std::runtime_error("Cannot read variable.");
}
double *arrData = (double*)mxGetPr(arr);
#pragma omp parallel for
for (int i = 0; i < 144; i++) {
#pragma omp parallel for
for (int j = 0; j < 192; j++) {
for (int k = 0; k < 256; k++) {
int rowMajIdx = (i * 192 + j) * 256 + k;
int colMajIdx = (j * 144 + i) * 256 + k;
newData[rowMajIdx] = static_cast<float>(arrData[colMajIdx]);
}
}
}
}
In the above snippet, am I right to be accessing the data linearly as with a flattened 3D array in C++? For example:-
idx_row_major = (x*WIDTH + y)*DEPTH + z
idx_col_major = (y*HEIGHT + x)*DEPTH + z
Is this the underlying representation that MATLAB uses?

Answer 1

You have some errors in the indexing of the row mayor and column mayor Idx. Additionally, naively accessing the data can lead to very slow times due to random memory access (memory latency is key! Read more here).
The best way to pass from MATLAB to C++ types (From 3D to 1D) is following the example below.
In this example we illustrate how to take a double real-type 3D matrix from MATLAB, and pass it to a C double* array.
The main objectives of this example are showing how to obtain data from MATLAB MEX arrays and to highlight some small details in matrix storage and handling.
matrixIn.cpp
#include "mex.h"
void mexFunction(int nlhs , mxArray *plhs[],
int nrhs, mxArray const *prhs[]){
// check amount of inputs
if (nrhs!=1) {
mexErrMsgIdAndTxt("matrixIn:InvalidInput", "Invalid number of inputs to MEX file.");
}
// check type of input
if( !mxIsDouble(prhs[0]) || mxIsComplex(prhs[0])){
mexErrMsgIdAndTxt("matrixIn:InvalidType", "Input matrix must be a double, non-complex array.");
}
// extract the data
double const * const matrixAux= static_cast<double const *>(mxGetData(prhs[0]));
// Get matrix size
const mwSize *sizeInputMatrix= mxGetDimensions(prhs[0]);
// allocate array in C. Note: its 1D array, not 3D even if our input is 3D
double* matrixInC= (double*)malloc(sizeInputMatrix[0] *sizeInputMatrix[1] *sizeInputMatrix[2]* sizeof(double));
// MATLAB is column major, not row major (as C). We need to reorder the numbers
// Basically permutes dimensions
// NOTE: the ordering of the loops is optimized for fastest memory access!
// This improves the speed in about 300%
const int size0 = sizeInputMatrix[0]; // Const makes compiler optimization kick in
const int size1 = sizeInputMatrix[1];
const int size2 = sizeInputMatrix[2];
for (int j = 0; j < size2; j++)
{
int jOffset = j*size0*size1; // this saves re-computation time
for (int k = 0; k < size0; k++)
{
int kOffset = k*size1; // this saves re-computation time
for (int i = 0; i < size1; i++)
{
int iOffset = i*size0;
matrixInC[i + jOffset + kOffset] = matrixAux[iOffset + jOffset + k];
}
}
}
// we are done!
// Use your C matrix here
// free memory
free(matrixInC);
return;
}
The relevant concepts to be aware of:
MATLAB matrices are all 1D in memory, no matter how many dimensions they have when used in MATLAB. This is also true for most (if not all) main matrix representation in C/C++ libraries, as allows optimization and faster execution.
You need to explicitly copy matrices from MATLAB to C in a loop.
MATLAB matrices are stored in column major order, as in Fortran, but C/C++ and most modern languages are row major. It is important to permute the input matrix , or else the data will look completely different.
The relevant function in this example are:
mxIsDouble checks if input is double type.
mxIsComplex checks if input is real or imaginary.
mxGetData returns a pointer to the real data in the input array. NULL if there is no real data.
mxGetDimensions returns an pointer to a mwSize array, with the size of the dimension in each index.