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Ingo
0

Bug when using min() with sparse matrices?

Asked by Ingo
on 8 Jan 2012
Hi,
I translated one of my Matlab routines to C and now I've encountered a really strange behaviour which seems to be a bug. M is a sparse matrix and I printed M, M', min(M, M') and min(full(M), full(M')), but all of them as full matrices to see the problem better:
The last matrix is what I want and what I'm supposed to already get by using min(M, M'), but for some reason min(M, M') shows some really weird behaviour. Any gueses what causes this?
Edit: Here's the mex file:
#include "mex.h"
void mexFunction(int nlhs, mxArray* plhs[], int nrhs, const mxArray *prhs[])
{
mxArray *tempArray, *outputDist[1], *inputDist[2], *outputSort[2];
double *tempVal, *pr, *sr, *sorted, *order;
mwSize n, nzmax;
mwIndex *irs, *jcs, i, j, k;
// distance function call
tempArray = mxCreateDoubleMatrix(1, 1, mxREAL);
tempVal = mxGetPr(tempArray);
inputDist[0] = prhs[0];
inputDist[1] = tempArray;
// read input matrix size
n = mxGetN(prhs[0]);
// read real part of input matrix
pr = mxGetPr(prhs[0]);
// read parameter for k
k = (mwIndex)*mxGetPr(prhs[1]);
// create output sparse matrix
nzmax = (mwSize)(n*k);
plhs[0] = mxCreateSparse(n, n, nzmax, mxREAL);
sr = mxGetPr(plhs[0]);
irs = mxGetIr(plhs[0]);
jcs = mxGetJc(plhs[0]);
// go through data points
for (i = 0; i < n; i++)
{
// calculate distance vector
tempVal[0] = (double)(i+1);
mexCallMATLAB(1, outputDist, 2, inputDist, "distEuclidean2");
// sort vector
mexCallMATLAB(2, outputSort, 1, &outputDist[0], "sort");
sorted = mxGetPr(outputSort[0]);
order = mxGetPr(outputSort[1]);
// assign values to sparse matrix
jcs[i] = i*k;
for (j = 0; j < k; j++)
{
irs[i*k+j] = (mwIndex)(order[j]-1);
sr[i*k+j] = sorted[j];
}
}
jcs[n] = n*k;
}
And here is the called distEuclidean2:
function [ d ] = distEuclidean2( M, ii )
d = sqrt(sum((repmat(M(:, ii), 1, size(M, 2)) - M) .^ 2, 1));
emd

  6 Comments

That might help - also the commands you used to create the mex files.
Suggest you edit the source in to your Question, as comments don't support formatting (or indentation even)
Ingo
on 9 Jan 2012
I added the mex source code now. The function is called with a d-by-n matrix of n data points and a number k as the second parameter. It then calculates the n-by-n distance matrix, but only keeps the k smallest distances, all other values are set to zero (thus making it sparse).
I added distEuclidean2.m as well. I compile the mex file with "mex filename.c -largeArrayDims" and I'm running a 64-bit Matlab. One can then run it with
A = (1:5);
M = whateveryoucalledit(A, 3);
for example.

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1 Answer

Answer by James Tursa
on 9 Jan 2012
 Accepted Answer

You might try using this to check the matrix:
href=""<http://www.mathworks.com/matlabcentral/fileexchange/20186-spok-checks-if-a-matlab-sparse-matrix-is-ok</a>>
Not sure if it works for 64-bit.

  1 Comment

Ingo
on 9 Jan 2012
Thanks. I could use it by modifying the installation to 64-bit. I knew about having explicit zero entries (didn't they they'd be a problem), but I also have row index problems. After using M = 1*M and M = M'' the min(M, M') command works. Now I know where the problem is!

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