CODEWITHSUNDEEP
matlab
pseudoDust
pseudoDust

Reputation: 1386

Incrementing values in a sparse matrix takes very long

i'm running the following code, where M is a ~200,000 by ~200,000 sparse matrix and points is ~200,000 by 2 matrix

inds=sub2ind(size(M),points(:,1),points(:,2));
M(inds)=M(inds)+1;

the problem is that the second line takes very long to run (15-90 seconds). the operation takes longer depending on how many of the indices in inds are 'new' (i.e. that don't already have a value in the sparse matrix)

is there a more efficient way to do this?

Upvotes: 4

Views: 378

Answers (1)

Jacob
Jacob

Reputation: 34601

Here's an idea:

M = M + sparse(points(:,1),points(:,2),1,size(M,1),size(M,2),size(points,1));

Just so you know,

S = sparse(i,j,s,m,n,nzmax) uses vectors i, j, and s to generate an m-by-n sparse matrix such that S(i(k),j(k)) = s(k), with space allocated for nzmax nonzeros. Vectors i, j, and s are all the same length. Any elements of s that are zero are ignored, along with the corresponding values of i and j. Any elements of s that have duplicate values of i and j are added together.

For the curious:

M = sprand(200000,200000,1e-6);
points = [randperm(200000) ; randperm(200000)]'; %'//Initialization over
Mo = M;
tic; 
inds=sub2ind(size(Mo),points(:,1),points(:,2));
Mo(inds) = Mo(inds)+1;
toc
tic; 
M = M + sparse(points(:,1),points(:,2),1,size(M,1),size(M,2),size(points,1));
toc

Upvotes: 4

Related Questions