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Extend HCS label parsing #189

Merged
merged 11 commits into from
Oct 31, 2023
Merged

Extend HCS label parsing #189

merged 11 commits into from
Oct 31, 2023

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ieivanov
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This PR extend HSC site label parsing with the format like 1-Pos000_000

@ieivanov ieivanov requested a review from ziw-liu September 25, 2023 18:21
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ziw-liu commented Sep 25, 2023

Can you modify the failing test case to reflect the expected behavior?

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Can I defer this to you? I think in the MM20_ome-tiffs collection there are datasets that use the 1-Pos000_000 name format.

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split three parts in the numerical labels
34cd2b0 
also strips leading zeros
so that the FOV names start with '0'
and is compatible with napari-ome-zarr
@ziw-liu ziw-liu requested a review from edyoshikun September 27, 2023 22:16
@ziw-liu ziw-liu added enhancement New feature or request μManager Micro-Manager files and metadata labels Sep 27, 2023
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ieivanov commented Oct 25, 2023 •
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The tests occasionally fail because test_converter_ometiff_hcs_numerical samples from MM20_ome-tiffs and enforces hcs format (hcs_plate=True) even though some datasets in that collection do not have more than one position - fixed.

ziw-liu
ziw-liu reviewed Oct 30, 2023
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@edyoshikun @ziw-liu let's try to merge this today, we'll likely need to use this branch to reconstruct the data from tomorrow's experiment. This branch will also fix the failing tests in the main branch.

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ziw-liu approved these changes Oct 31, 2023
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@edyoshikun can you take a look at the proposed behavior and confirm it does not break your workflow?

edyoshikun
edyoshikun approved these changes Oct 31, 2023
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This does not break my workflow since we still support the original '0/0/0' position. It can also adapt to this

@ieivanov ieivanov merged commit f5b2e72 into main Oct 31, 2023
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@ziw-liu ziw-liu deleted the extend_hcs_parsing branch November 1, 2023 04:45
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@ziw-liu ziw-liu ziw-liu approved these changes

@edyoshikun edyoshikun edyoshikun approved these changes

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enhancement New feature or request μManager Micro-Manager files and metadata
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@ieivanov @ziw-liu @edyoshikun