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Fix coords assignment in CombineAdjustFeatures.run #1965

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merged 1 commit into from
Oct 20, 2021

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sgratiy
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@sgratiy sgratiy commented Oct 19, 2021

This PR fixes a bug in with the CombineAdjustFeatures.run that was flipping round and channel coordinates in the resulting DecodedIntensityTable compare to the input intensities.

The fix:
Use explicit parameter calls when building table coordinates
Correct shape definition for the IntensityTable docstring

This notebook shows demonstrates the intensity table coordinates before and after the fix.

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njmei commented Oct 20, 2021

@sgratiy FYI, there was a repo configuration setting that was not running the CI for external first-time contributors. I've been told that that issue is now fixed so if you do a force push or something like that it should now properly run the CI.

@sgratiy sgratiy force-pushed the bugfix/round-chanel-swap branch from ef6cc21 to c2cef14 Compare October 20, 2021 17:00
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sgratiy commented Oct 20, 2021

Hey @berl, @neuromusic could you please review this bugfix.

Use explicit parameter calls when building table coordinates
Fix shape definition for the IntensityTable docs
@sgratiy sgratiy force-pushed the bugfix/round-chanel-swap branch from c2cef14 to ddb6e39 Compare October 20, 2021 17:32
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looks good.

@berl berl merged commit 89baf83 into spacetx:master Oct 20, 2021
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berl commented Oct 20, 2021

@sgratiy sorry this needs more careful checking of downstream impacts. Can you verify that switching the dimensions in the DecodedIntensityTable doesn't impact anything? Even if there's no test coverage, this would likely introduce a breaking change in the output that we use later.

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sgratiy commented Oct 21, 2021

@berl I have added the notebook demonstrating the problem in the main description.

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berl commented Oct 21, 2021

thanks @sgratiy.
For the record, this was indeed a bug in how starfish/core/spots/DetectPixels/combine_adjacent_features.py created a DecodedIntensityTable. This was previously missed because users (and the starfish codebase) never did anything with the IntensityTable part of a DecodedIntensityTable created in this way. I'll revert the revert and we can pretend like this never happened.

berl added a commit that referenced this pull request Oct 21, 2021
berl added a commit that referenced this pull request Oct 21, 2021
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3 participants