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Extensions starts with a dot #1326

Merged
merged 1 commit into from
Apr 11, 2024
Merged

Extensions starts with a dot #1326

merged 1 commit into from
Apr 11, 2024

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marberi
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@marberi marberi commented Apr 8, 2024

When attempting to motioncorrect data in a zarr file, then:
MotionCorrect(fname)

claim the extension was not found. It should be ".zarr" and ".n5" with
dots at the beginning. Including this fix uncovers a different problem
later (zarr array does not have .keys()).

Type of change

Please delete options that are not relevant.

  • Bug fix (non-breaking change which fixes an issue)
  • New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would break back-compatibility)
  • Changes in documentation or new examples for demos and/or use cases.

Branching

  • All PRs should be made against the dev branch. The main branch is not often merged back to dev.
  • If you want to get your PR out to the world faster (urgent bugfix), poke pgunn to cut a release; this will get it onto github and into conda faster

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caimanmanager test

and

caimanmanager demotest

prior to submitting your pull request.

Please describe any additional tests that you ran to verify your changes. If they are fast you can also
include them in the folder 'caiman/tests/and name themtest_***.py` so they can be included in our lists of tests.

@pgunn
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pgunn commented Apr 11, 2024

I am likely to merge this today.

Regarding the further-downstream issues you found, I think locally I converted some of our test data to n5 and zarr and run the pipeline on them, but my process may not have been through enough; do you have handy the exact error messages you got? (if you have sample data and params that go with them that'd also be great).

@pgunn pgunn merged commit f5d5295 into flatironinstitute:dev Apr 11, 2024
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@marberi
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marberi commented Apr 21, 2024

I don't have it readily available. For getting some results I did some workaround...

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2 participants