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Cleanup + add strided patches #218

Merged
merged 15 commits into from
Feb 22, 2024
Merged

Cleanup + add strided patches #218

merged 15 commits into from
Feb 22, 2024

Commits on Feb 22, 2024

  1. rm unused args, fix #185

    @kaczmarj
    kaczmarj committed Feb 22, 2024
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  2. account for empty hierarchy or patches 

    fix #195
    @kaczmarj
    kaczmarj committed Feb 22, 2024
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  3. please mypy

    @kaczmarj
    kaczmarj committed Feb 22, 2024
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  4. make error message more helpful if patch dir does not exist

    @kaczmarj
    kaczmarj committed Feb 22, 2024
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  5. rm unused args in wsi patches dataset 

    fixes #185
    @kaczmarj
    kaczmarj committed Feb 22, 2024
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  6. check that there are patches in the loaded file 

    fixes #195
    @kaczmarj
    kaczmarj committed Feb 22, 2024
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  7. ensure thumbnail is RGB 

    fixes #216
    @kaczmarj
    kaczmarj committed Feb 22, 2024
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  8. appease mypy

    @kaczmarj
    kaczmarj committed Feb 22, 2024
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  9. test that openslide and tiffslide pad regions 

    fixes #203
    @kaczmarj
    kaczmarj committed Feb 22, 2024
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  10. rm unused import

    @kaczmarj
    kaczmarj committed Feb 22, 2024
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  11. handle symlinked slides dirs 

    fixes #214
    @kaczmarj
    kaczmarj committed Feb 22, 2024
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  12. add strided patches 

    fixes #202

This adds a command line option '--patch-overlap-ratio' that controls
the level of overlap between adjacent patches. Negative values create
space between patches, and values closer to 1 makes patches overlap
more.
    @kaczmarj
    kaczmarj committed Feb 22, 2024
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  13. save jsons with geojson ext

    @kaczmarj
    kaczmarj committed Feb 22, 2024
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  14. print some logs

    @kaczmarj
    kaczmarj committed Feb 22, 2024
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  15. use geojson ext for purple.json

    @kaczmarj
    kaczmarj committed Feb 22, 2024
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