my code become busy for euclidean distance
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i write code for euclidean distance in nested for like this:
for rsize=1:tests
for k=1:ts
dis(k,1)= pdist2( testset(rsize,1:57),tmatrix(k,1:57),'euclidean');
end
end
its run time is very long 1-2 hours why? how can i correct this code?
4 Comments
Roger Stafford
on 9 Feb 2014
The point I am making, Fatemeh, is that if you actually need the output of 'pdist2' for each possible combination of values of 'rsize' and 'k', it should be possible to quickly extract it in an appropriate manner from that single "maximum" run, rather than having to go through 'pdist2' calls repeatedly. Doing it that way should save a lot of time if you do it right. That "maximum" run contains all the pairs that you will need.
In all this discussion I am assuming that the matrices 'testset' and 'tmatrix' remain unchanged for each computation of 'pdist2', except that different portions of each are used. Is that correct? Otherwise the code you have shown wouldn't make sense.
Answers (1)
Jan
on 9 Feb 2014
Did you pre-allocate the result?
dis = zeros(ts, 1)
By the way, you overwrite the result dis in each iteration over rsize.
pdist2 is vectorized, so try to omit the loops:
dis = pdist2(testset(:, 1:57), tmatrix(:,1:57), 'euclidean');
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