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ENH: Enable setting plot options in the containers config #441

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merged 57 commits into from
Jun 21, 2022

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kenza-bouzid
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@kenza-bouzid kenza-bouzid commented Jun 16, 2022

Main contributions:

  • Seperate top and bottom tiles selection and plotting
  • Create a DeepMILPlotsHandler to manage all plotting capabilities available in the pipeline
  • Enable activating certain plot options for validation and test separately
  • Set plot options in the containers configs
  • Get rid off of all boolean parameters to activate/desactivate certain plots
  • Improve WSI ploppts titles by adding true and predicted labels
  • Group slide figures in the same directory
  • Delete metrics_utils.py because all functions there were used for plotting and move these to viz_utils.py

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codecov bot commented Jun 16, 2022

Codecov Report

Merging #441 (56e884a) into main (f07d6f3) will increase coverage by 0.30%.
The diff coverage is 81.97%.

Impacted file tree graph

Flag Coverage Δ
hi-ml-histopathology 79.75% <81.97%> (+0.69%) ⬆️

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

Impacted Files Coverage Δ
...pathology/configs/classification/DeepSMILEPanda.py 78.94% <50.00%> (-2.75%) ⬇️
...pathology/src/histopathology/utils/output_utils.py 70.85% <62.50%> (+8.97%) ⬆️
...opathology/src/histopathology/utils/plots_utils.py 68.35% <68.35%> (ø)
...c/histopathology/configs/classification/BaseMIL.py 70.10% <75.00%> (-0.42%) ⬇️
...stopathology/src/histopathology/utils/viz_utils.py 86.23% <98.83%> (+37.96%) ⬆️
...istopathology/src/histopathology/models/deepmil.py 85.16% <100.00%> (ø)
...-histopathology/src/histopathology/utils/naming.py 98.68% <100.00%> (+0.09%) ⬆️
.../src/histopathology/utils/tiles_selection_utils.py 98.42% <100.00%> (ø)

@kenza-bouzid kenza-bouzid changed the title ENH: Enable setting plot options at config level ENH: Enable setting plot options at containers config level Jun 16, 2022
@kenza-bouzid kenza-bouzid marked this pull request as ready for review June 17, 2022 17:35
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@ant0nsc ant0nsc left a comment

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Looking good overall! left some minor comments.

@kenza-bouzid kenza-bouzid merged commit 85ba192 into main Jun 21, 2022
@kenza-bouzid kenza-bouzid deleted the kenzab/refactor_slides_thumb_and_att_plots branch June 21, 2022 10:07
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3 participants