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Bug fixes, initial work to support OpenSlide 4.0.0, improve type checking #185

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merged 11 commits into from
Nov 10, 2023
Merged

Bug fixes, initial work to support OpenSlide 4.0.0, improve type checking #185

merged 11 commits into from
Nov 10, 2023

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jonasteuwen
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@jonasteuwen jonasteuwen commented Oct 22, 2023 •
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A few changes:

  • OpenSlide 4.0.0 adds ICC profiles (see Support OpenSlide 4.0 #184, OpenSlide attaches ICC profiles #182); this is now included in SlideImage with the OPENSLIDE backend.
  • openslide-python is updated
  • Fix mpp_x <-> mpp_y problem also addressed in mpp issues and requirements #183 (Closes mpp issues and requirements #183)
  • Change some **kwargs to parameters to enhance ability to type check
  • Revert to using OpenSlide as default backend in the SlideImage. This is because currently it might be difficult to link libvips to openslide 4.0.0, and therefore it's tricky to test the ICC profile for pyvips.
  • Fix a minor bug in OpenSlideSlide which crashed when no mpp value was found (now it will raise a UnsupportedSlideError)

To be able to solve #167 additional work needs to be performed in the dataset classes and in the SlideImage class

@jonasteuwen jonasteuwen self-assigned this Oct 22, 2023
@jonasteuwen jonasteuwen added this to the v0.4 milestone Oct 22, 2023
@jonasteuwen jonasteuwen marked this pull request as draft October 22, 2023 15:10
@jonasteuwen jonasteuwen mentioned this pull request Oct 22, 2023
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@jonasteuwen jonasteuwen marked this pull request as ready for review October 22, 2023 18:26
@jonasteuwen jonasteuwen changed the title Allow to pick the mpp level closest to an actual level in the pyramid Bug fixes, initial work to support OpenSlide 4.0.0, improve type checking Oct 25, 2023
@jonasteuwen jonasteuwen mentioned this pull request Nov 4, 2023
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@jonasteuwen jonasteuwen modified the milestones: v0.4, v0.3.32 Nov 4, 2023
sinberlin2
sinberlin2 approved these changes Nov 10, 2023
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The application of the ICC color profile works, and there are no errors using openslide 4.0 so far. The rest are minor changes where I did not see any problem!

@jonasteuwen jonasteuwen merged commit 975264b into main Nov 10, 2023
@jonasteuwen jonasteuwen deleted the feature/no-resample branch November 10, 2023 17:57
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@sinberlin2 sinberlin2 sinberlin2 approved these changes

@EricMarcus-ai EricMarcus-ai Awaiting requested review from EricMarcus-ai

@BPdeRooij BPdeRooij Awaiting requested review from BPdeRooij

@AjeyPaiK AjeyPaiK Awaiting requested review from AjeyPaiK

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