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improve radial average speed with nimdage.mean() #63

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merged 2 commits into from
Nov 10, 2023
Merged

improve radial average speed with nimdage.mean() #63

merged 2 commits into from
Nov 10, 2023

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McHaillet
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One more update for version 0.3.2. I discovered online that the radial average calculation could be much faster using ndimage.mean().

Results completely overlap but the speed increase is massive:

whitening_filter

@McHaillet McHaillet marked this pull request as ready for review November 9, 2023 15:26
@McHaillet McHaillet requested a review from sroet November 9, 2023 15:26
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sroet approved these changes Nov 10, 2023
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1 small comment, feel free to ignore. LGTM otherwise.
Also, please document the "massive speed increase" are we talking about 2x, 10x 10000x?

src/pytom_tm/weights.py Outdated Show resolved Hide resolved
@McHaillet
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1 small comment, feel free to ignore. LGTM otherwise. Also, please document the "massive speed increase" are we talking about 2x, 10x 10000x?

This is for a large tomogram, dimensions 900x900x300.
Old version took ~425s, new version ~16s. So the speed up is roughly 25x

@McHaillet McHaillet merged commit 81b0d64 into SBC-Utrecht:main Nov 10, 2023
@McHaillet McHaillet deleted the patch-radial-average-speed branch November 10, 2023 13:07
@McHaillet McHaillet mentioned this pull request Nov 17, 2023
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@sroet sroet sroet approved these changes

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@McHaillet @sroet