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✨ Add WSI processing to EngineABC #737

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merged 123 commits into from
Apr 26, 2024
Merged

✨ Add WSI processing to EngineABC #737

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ccac220
Updating engine_abc to support WSI
AbishekRajVG Nov 10, 2023
ed4193c
ruff basic checks addressed
AbishekRajVG Nov 10, 2023
bb99b58
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 10, 2023
02c041a
Merge branch 'dev-define-engines-abc' into dev-update-engine-abc-wsi
shaneahmed Nov 16, 2023
e06c29f
Merge branch 'dev-define-engines-abc' of https://github.com/TissueIma…
AbishekRajVG Nov 16, 2023
b354ed9
EngineABC updated with WSI mode
AbishekRajVG Nov 17, 2023
45b7916
Merge branch 'dev-update-engine-abc-wsi' of https://github.com/Tissue…
AbishekRajVG Nov 17, 2023
3df8776
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 17, 2023
7eb36ee
Updating final file_dict logic for WSI mode in EngineABC
AbishekRajVG Nov 17, 2023
cb48a53
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 17, 2023
6a10e46
Preprocess images unified as the set_dataloader() method
AbishekRajVG Nov 21, 2023
007742b
Merge branch 'dev-update-engine-abc-wsi' of https://github.com/Tissue…
AbishekRajVG Nov 21, 2023
9073a03
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 21, 2023
2e2e666
Fix lint errors
AbishekRajVG Nov 22, 2023
f74bed7
Merge branch 'dev-update-engine-abc-wsi' of https://github.com/Tissue…
AbishekRajVG Nov 22, 2023
a93ca54
Merge branch 'dev-define-engines-abc' into dev-update-engine-abc-wsi
shaneahmed Nov 22, 2023
055e9fc
Merge branch 'dev-define-engines-abc' into dev-update-engine-abc-wsi
shaneahmed Nov 22, 2023
24fcff9
Improving Unit test coverage: Merge Predictions
AbishekRajVG Nov 23, 2023
626ca66
Merge branch 'dev-update-engine-abc-wsi' of https://github.com/Tissue…
AbishekRajVG Nov 23, 2023
69d79f1
Improving unit test cases: ioconfig
AbishekRajVG Nov 24, 2023
c551097
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 24, 2023
5327066
Improving unit test coverage: wsi_predictor_merge_predictions
AbishekRajVG Nov 24, 2023
5eb553d
Merge branch 'dev-update-engine-abc-wsi' of https://github.com/Tissue…
AbishekRajVG Nov 24, 2023
456fb60
Improve EngineABC's post_process_wsi to support Annotation Store
AbishekRajVG Nov 27, 2023
b316c16
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 27, 2023
6fcce1c
Reverting classes_predicted and updating class_dict in tiatoolbox.uti…
AbishekRajVG Nov 27, 2023
20b91e8
Merge Remote dev-update-engine-abc-wsi branch to local
AbishekRajVG Nov 27, 2023
a5a44e6
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 27, 2023
18e510f
Merge branch 'dev-define-engines-abc' into dev-update-engine-abc-wsi
shaneahmed Nov 30, 2023
f6604f4
Update mypy-type-check.yml
shaneahmed Nov 30, 2023
d8e7cc2
Improving Zarr and Annotation Store tests in test_engine_abc
AbishekRajVG Dec 1, 2023
1096c31
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 1, 2023
cadad70
Fix lint error
AbishekRajVG Dec 1, 2023
89587a2
Merge branch 'dev-update-engine-abc-wsi' of https://github.com/Tissue…
AbishekRajVG Dec 1, 2023
2173c46
Adding patch_mode argument to the engine_abc.get_dataloader() method
AbishekRajVG Dec 1, 2023
dc5cdee
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 1, 2023
5968b98
Reducing complexity in EngineABC as per review comments
AbishekRajVG Dec 15, 2023
d2ed5e2
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 15, 2023
3528f7c
Merge branch 'dev-define-engines-abc' into dev-update-engine-abc-wsi
shaneahmed Dec 18, 2023
5a293b1
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 18, 2023
9344c06
Replacing tolist() with Zarr groups
AbishekRajVG Dec 31, 2023
82ecb35
Merge branch 'dev-update-engine-abc-wsi' of https://github.com/Tissue…
AbishekRajVG Dec 31, 2023
6a8f070
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 31, 2023
07b8d3a
:test_tube: Remove failing test temporarily.
shaneahmed Jan 12, 2024
57162d2
Merge branch 'dev-define-engines-abc' into dev-update-engine-abc-wsi
shaneahmed Jan 12, 2024
f9839db
Merge branch 'dev-define-engines-abc' into dev-update-engine-abc-wsi
shaneahmed Jan 19, 2024
c043032
Merge branch 'dev-define-engines-abc' into dev-update-engine-abc-wsi
shaneahmed Jan 26, 2024
702c558
Merge branch 'dev-define-engines-abc' into dev-update-engine-abc-wsi
shaneahmed Feb 2, 2024
6a360ad
Merge branch 'dev-define-engines-abc' into dev-update-engine-abc-wsi
shaneahmed Feb 2, 2024
030d84f
:pencil2: Address minor comments
shaneahmed Feb 9, 2024
2c0a5b8
:hammer: Use `model.to`
shaneahmed Feb 9, 2024
1cd34af
Merge branch 'dev-define-engines-abc' into dev-update-engine-abc-wsi
shaneahmed Feb 12, 2024
bd7a103
:memo: Add todos from discussion.
shaneahmed Feb 15, 2024
1a01b28
:technologist: Address comments
shaneahmed Feb 16, 2024
4c55aca
Merge remote-tracking branch 'origin/dev-update-engine-abc-wsi' into …
shaneahmed Feb 16, 2024
7d6169e
Merge branch 'dev-define-engines-abc' into dev-update-engine-abc-wsi
shaneahmed Feb 16, 2024
9859ffb
:bug: Fix SIM401 errors
shaneahmed Feb 16, 2024
9a00d10
:technologist: Default is None for `kwargs.get()`
shaneahmed Feb 16, 2024
dbdf797
:bug: Fix patch processing.
shaneahmed Feb 16, 2024
b703eef
:white_check_mark: Add tests
shaneahmed Feb 16, 2024
17cad00
Merge branch 'dev-define-engines-abc' into dev-update-engine-abc-wsi
shaneahmed Feb 20, 2024
561e995
:bug: Fix testing abstract class
shaneahmed Feb 23, 2024
8097b74
:hammer: Set overwrite to False as per documentation.
shaneahmed Feb 23, 2024
d3cdf44
:memo: Improve documentation documentation.
shaneahmed Feb 23, 2024
080e7f3
:memo: Improve documentation documentation.
shaneahmed Feb 23, 2024
c22059a
:memo: Improve documentation documentation.
shaneahmed Feb 23, 2024
e9b89a6
:memo: Improve documentation documentation.
shaneahmed Feb 23, 2024
ac5b8bb
:memo: Improve documentation documentation.
shaneahmed Feb 23, 2024
68b021e
:memo: Improve documentation documentation.
shaneahmed Feb 23, 2024
510fd1b
:memo: Improve documentation.
shaneahmed Mar 1, 2024
bd23bd1
Merge branch 'dev-define-engines-abc' into dev-update-engine-abc-wsi
shaneahmed Mar 13, 2024
8b84e1e
:memo: Fix comments to fix ruff error.
shaneahmed Mar 13, 2024
faae676
:white_check_mark: Add tests for `eng.run()` in WSI mode.
shaneahmed Mar 15, 2024
f5d0385
:memo: Fix typos
shaneahmed Mar 15, 2024
3a0e40c
:memo: Add comments from discussion.
shaneahmed Mar 15, 2024
3735356
Merge branch 'dev-define-engines-abc' into dev-update-engine-abc-wsi
shaneahmed Mar 15, 2024
5633ce5
:memo: Fix comments.
shaneahmed Mar 15, 2024
ee1816f
Merge branch 'dev-define-engines-abc' into dev-update-engine-abc-wsi
shaneahmed Mar 19, 2024
6bb8f2e
:sparkles: Add `EngineABCRunParams` for engine run parameters.
shaneahmed Mar 19, 2024
a260993
:recycle: Add `_update_run_params` for engine run parameters.
shaneahmed Mar 19, 2024
8024c04
:recycle: Add `_update_run_params` for engine run parameters.
shaneahmed Mar 19, 2024
e7fca8f
:recycle: Separate out patch mode.
shaneahmed Mar 19, 2024
c97a258
:new: Add cache_mode and cache_size to the parameters.
shaneahmed Mar 19, 2024
09673b4
:new: Add cache_mode to save_predictions.
shaneahmed Mar 19, 2024
e9e3655
:new: Update batch size if cache mode and cache size > batch size.
shaneahmed Mar 19, 2024
37baee8
:new: Add how to infer in cache_mode.
shaneahmed Mar 19, 2024
afe6742
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 19, 2024
2e7db04
:bug: Fix `mypy` check
shaneahmed Mar 19, 2024
a3fb7b7
:bug: Fix tests
shaneahmed Mar 19, 2024
b9fdfac
:bug: Remove commented code.
shaneahmed Mar 20, 2024
5af1dad
:bug: Fix `test_io_config_delegation`
shaneahmed Mar 20, 2024
4858ddc
:bug: Remove wsi mode tests.
shaneahmed Mar 20, 2024
ce59474
:white_check_mark: Add tests for cache mode.
shaneahmed Mar 20, 2024
01bbd83
:white_check_mark: Add tests for get_dataloader.
shaneahmed Mar 20, 2024
e9a4ab7
:white_check_mark: Add tests for `save_output`.
shaneahmed Mar 20, 2024
222cce3
:white_check_mark: Add tests for `ioconfig delegation`.
shaneahmed Mar 20, 2024
914114d
:white_check_mark: Add tests for `NotImplementedError` with patch_mod…
shaneahmed Mar 20, 2024
7e21ca4
:white_check_mark: Add tests for `_update_ioconfig` with patch_mode F…
shaneahmed Mar 20, 2024
46679e5
:bug: Fix docs.
shaneahmed Mar 20, 2024
7850cdd
:white_check_mark: Add tests for coverage.
shaneahmed Mar 20, 2024
4152601
Merge branch 'dev-define-engines-abc' into dev-update-engine-abc-wsi
shaneahmed Mar 20, 2024
9d9a476
:fire: Remove `predictions` folder.
shaneahmed Mar 21, 2024
c5f7f6f
:recycle: Use `kwargs.get()` for compressor.
shaneahmed Mar 21, 2024
6f67048
:memo: Update docstrings for `prepare_engines_save_dir`.
shaneahmed Mar 21, 2024
35a0bfb
:memo: Update docstrings for `EngineABCRunParams`.
shaneahmed Mar 21, 2024
65b9881
:memo: Update docstrings for `EngineABCinit`.
shaneahmed Mar 21, 2024
395a353
:memo: Update docstrings for `get_dataloader` and `_initialize_model_…
shaneahmed Mar 21, 2024
b622bc0
:memo: Update docstrings for `infer_patches`
shaneahmed Mar 21, 2024
61a68e8
:memo: Update docstrings for `post_process_patches`
shaneahmed Mar 21, 2024
441c6cb
:memo: Update docstrings for `post_process_patches`
shaneahmed Mar 21, 2024
8608494
:memo: Update docstrings for `infer_wsi`
shaneahmed Mar 21, 2024
84ba4e7
:memo: Update docstrings for `save_predictions`
shaneahmed Mar 21, 2024
f32ebcb
:recycle: Refactor `save_output` to `save_wsi_output`
shaneahmed Mar 22, 2024
f204c99
:memo: Fix docstring for TIAToolbox output format.
shaneahmed Mar 22, 2024
81df7b4
:recycle: Use a dictionary to `update_model_output`
shaneahmed Mar 22, 2024
788a112
Merge remote-tracking branch 'origin/dev-update-engine-abc-wsi' into …
shaneahmed Mar 22, 2024
af641e3
:bug: Reset raw_predictions in cache_mode
shaneahmed Mar 22, 2024
af39813
:memo: Address minor changes from comments.
shaneahmed Mar 22, 2024
16332b1
:boom: Return dictionary as model output.
shaneahmed Mar 22, 2024
4be55be
Merge branch 'dev-define-engines-abc' into dev-update-engine-abc-wsi
shaneahmed Apr 8, 2024
0676da4
Merge branch 'dev-define-engines-abc' into dev-update-engine-abc-wsi
shaneahmed Apr 16, 2024
0af9a32
Merge branch 'dev-define-engines-abc' into dev-update-engine-abc-wsi
shaneahmed Apr 23, 2024
3774dcd
:memo: Address review comments.
shaneahmed Apr 26, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/mypy-type-check.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ on:
push:
branches: [ develop, pre-release, master, main ]
pull_request:
branches: [ develop, pre-release, master, main ]
branches: [ develop, pre-release, master, main, dev-define-engines-abc ]

jobs:

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