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efficiency of structure.pairwise #42

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bmcfee opened this issue Apr 17, 2014 · 0 comments
Closed

efficiency of structure.pairwise #42

bmcfee opened this issue Apr 17, 2014 · 0 comments
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enhancement requirement
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0.0.1

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bmcfee commented Apr 17, 2014

structure.pairwise currently uses np.triu_indices to find all unique pairs of frames and evaluate their agreement. It turns out that this is woefully inefficient in memory, as np.triu_indices constructs an intermediate (int64) masking matrix.

This should be replaced with a more direct implementation with leaner memory requirements.
@bmcfee bmcfee added this to the 0.0.1 milestone Apr 17, 2014
@bmcfee bmcfee self-assigned this Apr 17, 2014
@bmcfee bmcfee closed this as completed in a490a1e Apr 17, 2014
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