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Fix for yx images in Cellpose task #789

Merged
merged 1 commit into from
Jul 16, 2024
Merged

Fix for yx images in Cellpose task #789

merged 1 commit into from
Jul 16, 2024

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jluethi
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@jluethi jluethi commented Jul 16, 2024

Closes #788

This PR contains a small special case handling to enable the Cellpose task to process yx images. Given the current generalizations we've already made, only the channel selection during dask image loading and the metadata updating needed minor adjustment.

With this PR, there are 2 additional checks for those 2 parts that then handle the yx case. It's working well in my local tests on yx data, but we don't currently have yx testing data available.

A cleaner implementation and better testing will come with the ngio work here, I'll already merge this now to unblock user workflows though.

Checklist before merging

  • I added an appropriate entry to CHANGELOG.md

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FileStatementsMissingCoverageCoverage
(new stmts)
Lines missing
  fractal_tasks_core/tasks
  cellpose_segmentation.py 320-322, 380
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@jluethi jluethi marked this pull request as ready for review July 16, 2024 12:34
@jluethi jluethi merged commit cd45cd3 into main Jul 16, 2024
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@jluethi jluethi deleted the 2d_yx_cellpose branch July 16, 2024 12:35
@tcompa tcompa mentioned this pull request Jul 22, 2024
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Support 2D yx data in Cellpose task
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