Matlab: fast way to sum ones in binary numbers with Sparse structure?

Question

Most answers only address the already-answered question about Hamming weights but ignore the point about find and dealing with the sparsity. Apparently the

Answer 1

Mex it!

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Save this code as countTransBits.cpp:

#include "mex.h"

void mexFunction( int nout, mxArray* pout[], int nin, mxArray* pin[] ) {
mxAssert( nin == 1 && mxIsSparse(pin[0]) && mxGetN( pin[0] ) == 1,
            "expecting single sparse column vector input" );
    mxAssert( nout == 1, "expecting single output" );

    // set output, assuming 32 bits, set to 64 if needed
    pout[0] = mxCreateNumericMatrix( 32, 1, mxUINT32_CLASS, mxREAL );
    unsigned int* counter = (unsigned int*)mxGetData( pout[0] );
    for ( int i = 0; i < 32; i++ ) {
        counter[i] = 0;
    }

    // start working
    mwIndex *pIr = mxGetIr( pin[0] );
    mwIndex* pJc = mxGetJc( pin[0] );
    double*  pr = mxGetPr( pin[0] );
    for ( mwSize i = pJc[0]; i < pJc[1]; i++ ) {
        if ( pr[i] != 0 ) {// make sure entry is non-zero
            unsigned int entry = pIr[i] + 1; // cast to unsigned int and add 1 for 1-based indexing in Matlab
            int bit = 0;
            while ( entry != 0 && bit < 32 ) {
                counter[bit] += ( entry & 0x1 ); // count the lsb
                bit++;
                entry >>= 1; // shift right
            }
        }
    }
}

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Compile it in Matlab

>> mex -largeArrayDims -O countTransBits.cpp

Run the code

>> countTransBits( mlf )

Note that the output count in 32 bins lsb to msb.