✨ Add WSI processing to `EngineABC` #737

AbishekRajVG · 2023-11-10T13:59:21Z

Implements cache mode for processing using EngineABC. Cache_mode saves intermediate results to zarr file which can be converted to AnnotationStore. Full WSI pipeline needs to be implemented for Engines inheriting the base class.

The output of models should be a dictionary according to the new Engine design.

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…geAnalytics/tiatoolbox into dev-update-engine-abc-wsi

…ImageAnalytics/tiatoolbox into dev-update-engine-abc-wsi

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…ImageAnalytics/tiatoolbox into dev-update-engine-abc-wsi

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…ImageAnalytics/tiatoolbox into dev-update-engine-abc-wsi

codecov · 2023-11-22T08:10:49Z

Codecov Report

Attention: Patch coverage is 86.29442% with 27 lines in your changes are missing coverage. Please review.

Project coverage is 89.49%. Comparing base (d84ab45) to head (16332b1).
Report is 227 commits behind head on dev-define-engines-abc.

❗ Current head 16332b1 differs from pull request most recent head 0af9a32. Consider uploading reports for the commit 0af9a32 to get more accurate results

Files	Patch %	Lines
tiatoolbox/utils/misc.py	50.94%	26 Missing ⚠️
tiatoolbox/models/architecture/vanilla.py	50.00%	1 Missing ⚠️

Additional details and impacted files

@@                     Coverage Diff                     @@
##           dev-define-engines-abc     #737       +/-   ##
===========================================================
- Coverage                   99.77%   89.49%   -10.29%     
===========================================================
  Files                          63       71        +8     
  Lines                        6784     8834     +2050     
  Branches                     1352     1697      +345     
===========================================================
+ Hits                         6769     7906     +1137     
- Misses                          7      913      +906     
- Partials                        8       15        +7

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…ImageAnalytics/tiatoolbox into dev-update-engine-abc-wsi

tests/engines/test_engine_abc.py

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tiatoolbox/models/engine/engine_abc.py

measty

Loos good so far, just added a few comments.

It will be easier to give feedback and see any issues that might need to be addressed once we start trying to implement the other engines we have using this ABC.

tiatoolbox/models/engine/engine_abc.py

tiatoolbox/utils/misc.py

tiatoolbox/models/engine/engine_abc.py

tiatoolbox/utils/misc.py

Signed-off-by: Shan E Ahmed Raza <[email protected]>

…dev-update-engine-abc-wsi

Signed-off-by: Shan E Ahmed Raza <[email protected]>

tiatoolbox/models/engine/engine_abc.py

Signed-off-by: Shan E Ahmed Raza <[email protected]>

tiatoolbox/utils/misc.py

Abdol · 2024-03-22T16:45:55Z

Thanks @shaneahmed. Only minor comments from my side.

tiatoolbox/models/engine/engine_abc.py

mostafajahanifar

All looks good to me 💯

Well done on this PR 👍

AbishekRajVG added 2 commits November 10, 2023 13:44

Updating engine_abc to support WSI

ccac220

ruff basic checks addressed

ed4193c

AbishekRajVG added the dev tools Changes/Updates in Development tools label Nov 10, 2023

AbishekRajVG self-assigned this Nov 10, 2023

[pre-commit.ci] auto fixes from pre-commit.com hooks

bb99b58

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AbishekRajVG added enhancement New feature or request and removed dev tools Changes/Updates in Development tools labels Nov 10, 2023

shaneahmed changed the title ~~Updating Engine ABC for Whole Slide Images~~ ✨ Add WSI processing to EngineABC Nov 10, 2023

shaneahmed added this to the Release v2.0.0 milestone Nov 10, 2023

shaneahmed and others added 12 commits November 16, 2023 09:31

Merge branch 'dev-define-engines-abc' into dev-update-engine-abc-wsi

02c041a

Merge branch 'dev-define-engines-abc' of https://github.com/TissueIma…

e06c29f

…geAnalytics/tiatoolbox into dev-update-engine-abc-wsi

EngineABC updated with WSI mode

b354ed9

Merge branch 'dev-update-engine-abc-wsi' of https://github.com/Tissue…

45b7916

…ImageAnalytics/tiatoolbox into dev-update-engine-abc-wsi

[pre-commit.ci] auto fixes from pre-commit.com hooks

3df8776

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Updating final file_dict logic for WSI mode in EngineABC

7eb36ee

[pre-commit.ci] auto fixes from pre-commit.com hooks

cb48a53

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Preprocess images unified as the set_dataloader() method

6a10e46

Merge branch 'dev-update-engine-abc-wsi' of https://github.com/Tissue…

007742b

…ImageAnalytics/tiatoolbox into dev-update-engine-abc-wsi

[pre-commit.ci] auto fixes from pre-commit.com hooks

9073a03

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Fix lint errors

2e2e666

Merge branch 'dev-update-engine-abc-wsi' of https://github.com/Tissue…

f74bed7

…ImageAnalytics/tiatoolbox into dev-update-engine-abc-wsi

shaneahmed and others added 4 commits November 22, 2023 10:02

Merge branch 'dev-define-engines-abc' into dev-update-engine-abc-wsi

a93ca54

Merge branch 'dev-define-engines-abc' into dev-update-engine-abc-wsi

055e9fc

Improving Unit test coverage: Merge Predictions

24fcff9

Merge branch 'dev-update-engine-abc-wsi' of https://github.com/Tissue…

626ca66

…ImageAnalytics/tiatoolbox into dev-update-engine-abc-wsi

shaneahmed reviewed Nov 24, 2023

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AbishekRajVG and others added 3 commits November 24, 2023 17:03

Improving unit test cases: ioconfig

69d79f1

[pre-commit.ci] auto fixes from pre-commit.com hooks

c551097

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Improving unit test coverage: wsi_predictor_merge_predictions

5327066

shaneahmed added 2 commits March 21, 2024 13:27

📝 Update docstrings for infer_wsi

8608494

📝 Update docstrings for save_predictions

84ba4e7

Abdol reviewed Mar 22, 2024

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shaneahmed reviewed Mar 22, 2024

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shaneahmed added 6 commits March 22, 2024 14:41

♻️ Refactor save_output to save_wsi_output

f32ebcb

📝 Fix docstring for TIAToolbox output format.

f204c99

Signed-off-by: Shan E Ahmed Raza <[email protected]>

♻️ Use a dictionary to update_model_output

81df7b4

Merge remote-tracking branch 'origin/dev-update-engine-abc-wsi' into …

788a112

…dev-update-engine-abc-wsi

🐛 Reset raw_predictions in cache_mode

af641e3

Signed-off-by: Shan E Ahmed Raza <[email protected]>

📝 Address minor changes from comments.

af39813

Signed-off-by: Shan E Ahmed Raza <[email protected]>

Abdol reviewed Mar 22, 2024

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💥 Return dictionary as model output.

16332b1

Signed-off-by: Shan E Ahmed Raza <[email protected]>

Abdol reviewed Mar 22, 2024

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shaneahmed added 4 commits April 8, 2024 21:21

Merge branch 'dev-define-engines-abc' into dev-update-engine-abc-wsi

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Merge branch 'dev-define-engines-abc' into dev-update-engine-abc-wsi

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Merge branch 'dev-define-engines-abc' into dev-update-engine-abc-wsi

0af9a32

📝 Address review comments.

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adamshephard reviewed Apr 26, 2024

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mostafajahanifar approved these changes Apr 26, 2024

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shaneahmed merged commit 466d005 into dev-define-engines-abc Apr 26, 2024
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shaneahmed deleted the dev-update-engine-abc-wsi branch April 26, 2024 13:12

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✨ Add WSI processing to `EngineABC` #737

✨ Add WSI processing to `EngineABC` #737

AbishekRajVG commented Nov 10, 2023 •

edited by shaneahmed

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codecov bot commented Nov 22, 2023 •

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measty left a comment

Abdol commented Mar 22, 2024

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✨ Add WSI processing to EngineABC #737

✨ Add WSI processing to EngineABC #737

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AbishekRajVG commented Nov 10, 2023 • edited by shaneahmed Loading

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✨ Add WSI processing to `EngineABC` #737

✨ Add WSI processing to `EngineABC` #737

AbishekRajVG commented Nov 10, 2023 •

edited by shaneahmed

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codecov bot commented Nov 22, 2023 •

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