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BUG: Remove padding when loading slides #387

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merged 2 commits into from
May 30, 2022
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@fepegar fepegar commented May 27, 2022

Fixes #314.

Cucim adds black padding when loading slides using a bounding box that is not fully within the slide's field of view.
Some margin can be added to bounding boxes in LoadPandaROId, but that's not needed in this application.
This PR sets padding (margin) to 0 when creating the tiles dataset, therefore

I will also upload the new data set to Azure and modify the dataset name in our code.

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codecov bot commented May 27, 2022

Codecov Report

Merging #387 (66498d9) into main (b8eef6b) will decrease coverage by 0.36%.
The diff coverage is 100.00%.

Impacted file tree graph

Flag Coverage Δ
hi-ml-histopathology 74.67% <100.00%> (-0.79%) ⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
...hology/preprocessing/create_panda_tiles_dataset.py 33.73% <ø> (ø)
...ology/src/histopathology/datasets/default_paths.py 100.00% <100.00%> (ø)
...pathology/src/histopathology/utils/report_utils.py 65.97% <0.00%> (-8.72%) ⬇️
...istopathology/src/histopathology/models/deepmil.py 83.33% <0.00%> (-6.06%) ⬇️
...stopathology/src/histopathology/models/encoders.py 84.05% <0.00%> (-4.66%) ⬇️
...c/histopathology/configs/classification/BaseMIL.py 63.74% <0.00%> (-1.92%) ⬇️
...-histopathology/src/histopathology/utils/naming.py 98.57% <0.00%> (+0.13%) ⬆️

@fepegar fepegar requested review from dccastro and harshita-s May 30, 2022 10:15
@fepegar fepegar marked this pull request as ready for review May 30, 2022 10:15
@fepegar fepegar merged commit d320962 into main May 30, 2022
@fepegar fepegar deleted the 314-fix-tiles-padding branch May 30, 2022 11:12
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Default padding color is black when loading slides
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