Jakub Kaczmarzyk

[TEST] ensure that wsinfer functions without openslide or without tiffslide

1

a test should be added that tests whether wsinfer still works if openslide is not installed or tiffslide is not installed. one of these must be installed, so the test...

[ENH] look into bioimage spec

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https://github.com/bioimage-io/spec-bioimage-io/blob/gh-pages/model_spec_latest.md Beware that this might not include microns resolution yet. what we should probably do is be able to convert our configuration to this bioimage spec.

add tests for the torch dataset child class `WholeSlideImagePatches`. https://github.com/SBU-BMI/wsinfer/blob/86294180757c70c8c7117020601663089043f7a3/wsinfer/modellib/data.py#L93-L172 you may want to create your own reference tiff image, as in https://github.com/SBU-BMI/wsinfer/blob/86294180757c70c8c7117020601663089043f7a3/tests/test_all.py#L27-L43

for tests that run model inference, use the different available devices. this includes cpu, gpu, and mps. on github actions, only cpu will be available. but locally run tests can...

this function reads a numpy array from an hdf5 file of coordinates. we do not have a test for it yet. to test it, one can create an hdf5 file...

See the functions in `wsinfer/wsi.py`

in email... Patch locations in prediction-* files are computed using the following coordinate computations: (df.minx + (df.width / 2)).round().astype(int) (df.miny + (df.height / 2)).round().astype(int) Patch locations in color-* files were...

garbled tiles from CAMELYON16 dataset using tiffslide but not openslide

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i have come across unexpected behavior when reading a tile from the CAMELYON16 dataset, slide `test_019.tif`. please see code to reproduce below. download image `test_019.tif` using: ``` # python -m...