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dredge fixes - #4889

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cwindolf merged 19 commits into
SpikeInterface:mainfrom
cwindolf:dredge-ap-chunked-updates
Oct 23, 2026
Merged

dredge fixes#4889
cwindolf merged 19 commits into
SpikeInterface:mainfrom
cwindolf:dredge-ap-chunked-updates

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@cwindolf

@cwindolf cwindolf commented Oct 21, 2026

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Would close #4829

This has two groups of changes:

  • Fixes related to the online algorithm: most importantly, a time horizon issue which meant that the current algorithm was processing chunks across boundaries strangely. The first few commits here break these changes up into logical groups.
  • Other dredge fixes: biggest one here is adding a log transform to the histogram. Meant to do that a long time ago. Also affects full-mode users, but it is helpful! Should have done this before the benchmark papers @_@

@cwindolf cwindolf mentioned this pull request Oct 21, 2026
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@cwindolf cwindolf added motion correction Questions related to motion correction chronic labels Oct 21, 2026
@alejoe91

alejoe91 commented Oct 22, 2026 •
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Thanks @cwindolf

This seems to close the gap with the differences we saw between the IBL and SI results:

IBL internal results

image

SI: main

image

SI: this PR

image

SI: this PR + YASS denoising from #4706

image

So it seems that the main effect is due to the updated dredge implementation, with minimal changes due to denoising!

@cwindolf

cwindolf commented Oct 22, 2026

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@alejoe91 thanks for talking! added a couple of commits based on that (and some other fixes). should be ready to go!

alejoe91
alejoe91 approved these changes Oct 23, 2026
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LGTM! @chrishalcrow want to take a fina look?

chrishalcrow
chrishalcrow reviewed Oct 23, 2026
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Comment thread src/spikeinterface/preprocessing/motion.py
chrishalcrow
chrishalcrow reviewed Oct 23, 2026
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Comment thread src/spikeinterface/sortingcomponents/motion/dredge.py Outdated
chrishalcrow
chrishalcrow reviewed Oct 23, 2026
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Comment thread src/spikeinterface/sortingcomponents/motion/dredge.py Outdated
chrishalcrow
chrishalcrow reviewed Oct 23, 2026
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Comment thread src/spikeinterface/sortingcomponents/motion/motion_utils.py
@cwindolf

cwindolf commented Oct 23, 2026

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Thanks @chrishalcrow @alejoe91! Added a couple of commits, should I merge?

@cwindolf
cwindolf merged commit d00edb7 into SpikeInterface:main Oct 23, 2026
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@alejoe91 alejoe91 mentioned this pull request Oct 27, 2026
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@alejoe91 alejoe91 alejoe91 approved these changes
@chrishalcrow chrishalcrow chrishalcrow approved these changes

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chronic motion correction Questions related to motion correction

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DREDge differences (parameters, online mode, math)

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