Vectorizing array indexing/subsetting in Matlab

Question

Suppose I have a long data vector y, plus some indices into it. I want to extract a short snippet or window around every index.

For example, suppose I want to construct a matrix containing 64 samples before and 64 samples after every value that is below three. This is trivial to do in a for-loop:

WIN_SIZE = 64; % Sample data with padding data = [nan(WIN_SIZE,1); randn(1e6,1); nan(WIN_SIZE,1)]; % Sample events, could be anything index = find(data < 3); snippets = nan(length(index), 2*WIN_SIZE + 1); for ii=1:length(index) snippets(ii,:) = data((index(ii)-WIN_SIZE):(index(ii)+WIN_SIZE)); end

However,this is not blazingly fast. Is there any way to vectorize (or otherwise speed up) this operation?

(In case this is unclear, the index could be anything and may not necessarily be a property of the data; I just wanted something simple to illustrate the idea.)

index is a (column) vector. You don't need a for-loop, you can vectorize it, see Get vector indices before-and-after (window +/- 1) given indices — smci
– smci, Commented Feb 21, 2018 at 14:52
Note that this question is 2+ years old and that doesn't work in anything older than 2016b. — Matt Krause
– Matt Krause, Commented Feb 21, 2018 at 19:00
Matt, ok then how should we handle this obsolete question and answer? I suggest we close-as-duplicate into Get vector indices before-and-after (window +/- 1) given indices — smci
– smci, Commented Feb 21, 2018 at 23:34
Possible duplicate of Get vector indices before-and-after (window +/- 1) given indices — smci
– smci, Commented Feb 21, 2018 at 23:35
@smci Who says the question/answer are obsolete? The answer still works, even though later MATLAB versions provide an additional way to handle it. — beaker
– beaker, Commented Feb 23, 2018 at 23:41

Divakar · Accepted Answer · 2016-01-25 20:03:17Z

7

Use bsxfun -

snippets = data(bsxfun(@plus,index(:),[-WIN_SIZE:WIN_SIZE]))

answered Jan 25, 2016 at 20:03

Divakar

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5 Comments

Matt Over a year ago

I just wanted to come up with a double repmat-answer. But this solution with bsxfun is better and slightly faster as well.

Divakar Over a year ago

@Matt That would follow the pattern of performance numbers seen in Comparing BSXFUN and REPMAT that shows 20-40% improvement with bsxfun(@plus over a repmat version.

Matt Over a year ago

You are perfectly right on this. Btw: That's a really nice comparison of bsxfunand repmat!

Divakar Over a year ago

@Matt Took me few days to compile and assemble those comparison results and seems like it's coming to some use huh! :)

Matt Krause Over a year ago

Thanks! For the record, this is about 10x faster than the naive for-loop!

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