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Updates to ROI loader #7

Merged
merged 10 commits into from
May 23, 2024
Merged

Updates to ROI loader #7

merged 10 commits into from
May 23, 2024

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jluethi
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@jluethi jluethi commented May 20, 2024

TODO:

  • Add option to load as numpy array, not as dask array (what should the default be? How should it be exposed to the user?)

Tests:

  • Add tests for new functions in OMEZarrImage: get_omero_metadata
  • also add unit test for read_table in OMEZarrImage
  • Add tests for ROILoader Widget

@jluethi jluethi marked this pull request as ready for review May 20, 2024 20:37
@jluethi jluethi changed the title [WIP] Updates to ROI loader Updates to ROI loader May 20, 2024
@jluethi
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jluethi commented May 20, 2024

@fdsteffen I have a prototype ready for the ROI loader for our meeting on Thursday. Still some cleanup needed, but it now has the core functionality of loading intensity images, labels & ROIs.

I will want to:

  1. Expose option to force layers to be loaded as numpy arrays (non-lazily)
  2. Add a thread worker for the run function in case loading is slow (or some other method to not freeze the main thread)

And we should then discuss on Thursday how the 2 parts come together! :)

@fdsteffen
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Sounds great, looking forward!

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Codecov Report

Attention: Patch coverage is 19.75309% with 65 lines in your changes are missing coverage. Please review.

Please upload report for BASE (main@b1b5f69). Learn more about missing BASE report.

Files Patch % Lines
src/napari_ome_zarr_navigator/roi_loader.py 9.52% 57 Missing ⚠️
src/napari_ome_zarr_navigator/ome_zarr_image.py 55.55% 8 Missing ⚠️

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Additional details and impacted files
@@           Coverage Diff           @@
##             main       #7   +/-   ##
=======================================
  Coverage        ?   44.33%           
=======================================
  Files           ?       14           
  Lines           ?      785           
  Branches        ?        0           
=======================================
  Hits            ?      348           
  Misses          ?      437           
  Partials        ?        0           

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@jluethi jluethi merged commit 0093ea3 into main May 23, 2024
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@jluethi jluethi deleted the 2_roi_loader branch May 23, 2024 14:19
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3 participants