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🎨 New EngineABC Design for Patches #635

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Merged
merged 153 commits into from
Oct 31, 2023
Merged

🎨 New EngineABC Design for Patches #635

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3eb4ab3
:recycle: Refactor base code from IOSegmentorConfig to IOConfigABC
shaneahmed Jun 8, 2023
c8d3458
:recycle: No need for a separate function
shaneahmed Jun 8, 2023
9623f86
:technologist: Enable git workflow on this PR
shaneahmed Jun 8, 2023
4c8f91f
:bug: Add missing variable
shaneahmed Jun 9, 2023
972d81d
:art: Move `to_baseline` code to ABC
shaneahmed Jun 9, 2023
5f81f9b
:art: Move `to_baseline` code to ABC
shaneahmed Jun 9, 2023
8270c4e
:bug: Fix incorrect calculations for output_resolutions
shaneahmed Jun 9, 2023
f3b6b96
:wrench: Update `PatchPredictor` to use `ModelIOConfigABC`
shaneahmed Jun 15, 2023
285d99a
:bricks: Define `ModelIOConfigABC` as a dataclass
shaneahmed Jun 16, 2023
ed638b7
Merge branch 'develop' into dev-define-ioconfig
shaneahmed Jun 16, 2023
b6c1a62
Merge branch 'dev-define-engines-abc' into dev-define-ioconfig
shaneahmed Jun 16, 2023
0d270bf
:boom: Remove kwargs
shaneahmed Jun 16, 2023
9e4266a
:sparkles: Add `IOInstanceSegmentorConfig`
shaneahmed Jun 16, 2023
d0ea031
:wrench: Update yaml for `IOInstanceSegmentorConfig`
shaneahmed Jun 16, 2023
fa70c40
:wrench: Update yaml for `IOInstanceSegmentorConfig`
shaneahmed Jun 16, 2023
70da57e
:wrench: Update `to_baseline` for `IOInstanceSegmentorConfig`
shaneahmed Jun 16, 2023
17e9a1f
:wrench: Update IOInstanceSegmentorConfig in test_nucleus_instance_s…
shaneahmed Jun 16, 2023
a976abe
:bug: Update cli for IOInstanceSegmentorConfig
shaneahmed Jun 16, 2023
4330e87
:fire: Remove unnecessary test after kwargs removal
shaneahmed Jun 16, 2023
1963923
:truck: Move ioconfigs to io_config.py
shaneahmed Jun 16, 2023
a8725a3
:bug: Fix circular import
shaneahmed Jun 16, 2023
b226202
:recycle: Refactor to reduce code in inheriting class
shaneahmed Jun 16, 2023
2fffb61
:bug: Fix deepsource errors
shaneahmed Jun 16, 2023
70da5d3
:recycle: Fix ioconfig import
shaneahmed Jun 16, 2023
cfc955f
:bug: Fix missing input arguments
shaneahmed Jun 17, 2023
b3ecadf
:goal_net: Improve error catching
shaneahmed Jun 17, 2023
09b8cc4
:goal_net: Default configuration is not correct
shaneahmed Jun 17, 2023
c2e7aae
:goal_net: Fix error check
shaneahmed Jun 17, 2023
e02fd47
:pencil2: Fix typo
shaneahmed Jun 17, 2023
ec6ff96
:bug: Fix unnecessary update
shaneahmed Jun 17, 2023
e24ca47
:recycle: Refactor code to improve behaviour
shaneahmed Jun 17, 2023
3fe5d13
:bug: Fix Consider decorating method with @staticmethod PYL-R0201
shaneahmed Jun 17, 2023
4d03533
:bug: Fix update config logic
shaneahmed Jun 17, 2023
45a1442
:bug: Fix update config logic
shaneahmed Jun 17, 2023
c6542a4
:memo: Update docstring
shaneahmed Jun 19, 2023
2d7f2d9
:white_check_mark: Add validation checks
shaneahmed Jun 19, 2023
2a5d38c
:white_check_mark: Add validation checks
shaneahmed Jun 19, 2023
cd4acbb
:technologist: Improve error message
shaneahmed Jun 19, 2023
caab9a9
:art: Improve code structure
shaneahmed Jun 19, 2023
7bebf9a
:fire: Remove invalid tests
shaneahmed Jun 19, 2023
37d826a
:art: New `EngineABC` design
shaneahmed Jul 6, 2023
d696aa4
Merge branch 'dev-define-engines-abc' into dev-redefine-patchpredictor
shaneahmed Jul 6, 2023
2df715f
:bug: Fix import
shaneahmed Jul 6, 2023
556c673
Merge remote-tracking branch 'origin/dev-redefine-patchpredictor' int…
shaneahmed Jul 6, 2023
027a6e5
:recycle: Rename `run_pipeline` to `run`
shaneahmed Jul 7, 2023
de48fce
:bug: Remove `abstractmethod` from `property`
shaneahmed Jul 7, 2023
2ed5c38
:bug: Remove `_ioconfig`
shaneahmed Jul 7, 2023
8bf0c2d
Merge branch 'dev-define-engines-abc' into dev-redefine-patchpredictor
shaneahmed Jul 12, 2023
683139f
Merge branch 'dev-define-engines-abc' into dev-redefine-patchpredictor
shaneahmed Jul 12, 2023
4b93f19
Merge branch 'dev-define-engines-abc' into dev-redefine-patchpredictor
shaneahmed Jul 14, 2023
3c963ca
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 14, 2023
87fcd7c
Merge branch 'dev-define-engines-abc' into dev-redefine-patchpredictor
shaneahmed Jul 21, 2023
fceb5b7
:twisted_rightwards_arrows: Merge dev-define-engines-abc into dev-red…
shaneahmed Aug 1, 2023
8938ea9
:rotating_light: Fix linter errors
shaneahmed Aug 2, 2023
47d7acb
Merge branch 'dev-define-engines-abc' into dev-redefine-patchpredictor
shaneahmed Aug 2, 2023
5f5eafd
Merge branch 'dev-define-engines-abc' into dev-redefine-patchpredictor
shaneahmed Aug 8, 2023
91cd2dd
Merge branch 'dev-define-engines-abc' into dev-redefine-patchpredictor
shaneahmed Aug 10, 2023
b4dceea
:recycle: Remove tests for engines and move them to tests/engine
shaneahmed Aug 10, 2023
08039de
:bug: Fix linter errors
shaneahmed Aug 10, 2023
3e8bcb4
:sparkles: Add basic structure for `run`
shaneahmed Aug 10, 2023
ee076cb
:memo: Add suggestions
shaneahmed Aug 11, 2023
1987a2d
:twisted_rightwards_arrows: Merge develop into dev-redefine-patch-pre…
shaneahmed Aug 11, 2023
295cdc0
Merge branch 'dev-define-engines-abc' into dev-redefine-patchpredictor
shaneahmed Aug 14, 2023
e8b0f90
:art: Remove extra input arguments for `run`. Use some variables as a…
shaneahmed Aug 14, 2023
04ef3a1
Merge remote-tracking branch 'origin/dev-define-engines-abc' into dev…
shaneahmed Aug 14, 2023
7bb62c1
:memo: Update documentation.
shaneahmed Aug 14, 2023
8866110
:bug: Remove _rm_dir
shaneahmed Aug 14, 2023
42341d3
Merge branch 'dev-define-engines-abc' into dev-redefine-patchpredictor
shaneahmed Aug 21, 2023
a406620
Merge branch 'dev-define-engines-abc' into dev-redefine-patchpredictor
shaneahmed Aug 23, 2023
1fc17fa
Merge branch 'dev-define-engines-abc' into dev-redefine-patchpredictor
shaneahmed Aug 24, 2023
b9c704b
:twisted_rightwards_arrows: Merge develop into dev-define-engines-abc
shaneahmed Aug 24, 2023
c6444e4
:rewind: Remove flake8-annotations check.
shaneahmed Aug 24, 2023
8faa23f
:white_check_mark: Add default model parameter checks.
shaneahmed Aug 24, 2023
7e1ed8a
:recycle: Remove test_feature_extractor.py
shaneahmed Aug 25, 2023
d44bddd
:sparkles: Add _initialize_model_ioconfig
shaneahmed Aug 25, 2023
105f32e
:recycle: Refactor `load_torch_model` and `model_to` to models_abc.py
shaneahmed Aug 25, 2023
7999944
:bug: Fix deepsource errors
shaneahmed Aug 25, 2023
cb5c986
:sparkles: Add `_load_ioconfig`
shaneahmed Aug 25, 2023
43b3239
:white_check_mark: Add test for ioconfig load error.
shaneahmed Aug 25, 2023
7a70ad8
:sparkles: Add `model_to` in EngineABC and initialize variables in __…
shaneahmed Aug 25, 2023
748e0eb
:sparkles: Add preprocessing logic to engine_abc.py
shaneahmed Aug 25, 2023
9b461c2
Merge branch 'dev-define-engines-abc' into dev-redefine-patchpredictor
shaneahmed Aug 29, 2023
8619719
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 29, 2023
e4e78c5
:bug: F811 Redefinition of unused `model_to`
shaneahmed Aug 30, 2023
ce02a58
Merge branch 'dev-define-engines-abc' into dev-redefine-patchpredictor
shaneahmed Aug 30, 2023
e6342bb
Merge branch 'dev-define-engines-abc' into dev-redefine-patchpredictor
shaneahmed Aug 30, 2023
b54f3a3
:recycle: Fix `_prepare_save_dir` logic
shaneahmed Aug 31, 2023
263b664
Merge remote-tracking branch 'origin/dev-redefine-patchpredictor' int…
shaneahmed Aug 31, 2023
ea47cca
Merge branch 'dev-define-engines-abc' into dev-redefine-patchpredictor
shaneahmed Aug 31, 2023
36ed0ed
:white_check_mark: Add tests for `_prepare_save_dir`
shaneahmed Aug 31, 2023
87ba44c
:white_check_mark: Add tests for EngineABC
shaneahmed Aug 31, 2023
382c265
:white_check_mark: Add tests for EngineABC.run()
shaneahmed Aug 31, 2023
f75babd
:bug: Fix Tests
shaneahmed Aug 31, 2023
a948826
:white_check_mark: Add Tests for `run()`
shaneahmed Aug 31, 2023
a9bf747
:white_check_mark: Add checks for length of images, labels, masks
shaneahmed Sep 1, 2023
b78d386
:bug: Fix tests
shaneahmed Sep 1, 2023
84f69a7
add patch store
measty Sep 5, 2023
11eb57f
add store conversion for patch pred
measty Sep 7, 2023
d598fa9
:recycle: Refactor code to include post_process_patches
shaneahmed Sep 8, 2023
409f128
:bug: test initialization was overwriting the function.
shaneahmed Sep 8, 2023
77bdef0
Merge branch 'dev-define-engines-abc' into dev-redefine-patchpredictor
shaneahmed Sep 13, 2023
d970f49
:recycle: Address comments from the previous discussion.
shaneahmed Sep 22, 2023
bd892fd
:bug: Fix breaking changes due to use of device instead of `on_gpu`.
shaneahmed Sep 22, 2023
4ca18be
:memo: Fix docstrings.
shaneahmed Sep 22, 2023
e7a6d1e
:bug: Fix test_arch_nuclick.py
shaneahmed Sep 22, 2023
40846ff
:rewind: Revert back to pretrained_model
shaneahmed Sep 22, 2023
c513ddc
:bug: Fix issues with on_gpu
shaneahmed Sep 22, 2023
e829967
:bug: Fix issues with on_gpu
shaneahmed Sep 26, 2023
52c4415
:bug: Fix infer_batch() takes 2 positional arguments but 3 were given
shaneahmed Sep 26, 2023
eaf6b25
Merge branch 'dev-define-engines-abc' into dev-redefine-patchpredictor
shaneahmed Oct 6, 2023
b46e0bd
Merge branch 'dev-define-engines-abc' into dev-redefine-patchpredictor
shaneahmed Oct 10, 2023
263d869
:bug: Fix flake8-annotations
shaneahmed Oct 10, 2023
0358b99
:bug: Fix flake8-annotations for multi_task_segmentor.py
shaneahmed Oct 10, 2023
040cb7c
:bug: Fix flake8-annotations for nucleus_instance_segmentor.py
shaneahmed Oct 10, 2023
b993146
:bug: Fix flake8-annotations for semantic_segmentor.py
shaneahmed Oct 10, 2023
9c68cc3
:bug: Fix flake8-annotations for patch_predictor.py
shaneahmed Oct 10, 2023
b0d11fe
:bug: Fix flake8-annotations for models_abc.py
shaneahmed Oct 10, 2023
ae06e45
Added Zarr save to post_process_patches method in engine_abc
AbishekRajVG Oct 10, 2023
034720e
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 10, 2023
d1ce671
Fix linter errors changed os.path to pathlib.Path
AbishekRajVG Oct 11, 2023
a80c408
Merge branch 'dev-define-engines-abc' into dev-redefine-patchpredictor
shaneahmed Oct 13, 2023
c2419f1
Resolving review comments
AbishekRajVG Oct 18, 2023
9b805f8
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 18, 2023
bdcee00
Fix linter errors resolved
AbishekRajVG Oct 18, 2023
e001eef
merged pre-commit auto changes to local
AbishekRajVG Oct 18, 2023
4467e78
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 18, 2023
f8d8292
fix linter error resolved
AbishekRajVG Oct 18, 2023
ee6adaa
Merge branch 'dev-redefine-patchpredictor' of https://github.com/Tiss…
AbishekRajVG Oct 18, 2023
7f6941a
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 18, 2023
40117ff
fix linter error resolved
AbishekRajVG Oct 18, 2023
e10be6a
merge local updates with autofix updates
AbishekRajVG Oct 18, 2023
ec8fe97
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 18, 2023
cad3a4f
fix D205 1 blank line required between summary line and description
AbishekRajVG Oct 18, 2023
7beb238
merge local updates with autofix updates
AbishekRajVG Oct 18, 2023
5882be6
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 18, 2023
e7df499
docstring sytax error fixed
AbishekRajVG Oct 18, 2023
1f85c50
Merge branch 'dev-redefine-patchpredictor' of https://github.com/Tiss…
AbishekRajVG Oct 18, 2023
e86f440
Improving engine_abc based on review comments
AbishekRajVG Oct 20, 2023
122e114
added link to pretrained models
AbishekRajVG Oct 23, 2023
d86f668
Merge remote-tracking branch 'origin/dev-define-engines-abc' into dev…
shaneahmed Oct 26, 2023
b47cd35
Delete '
shaneahmed Oct 26, 2023
92bde5b
update method patch_pred method names in EngineABC
AbishekRajVG Oct 26, 2023
ac4fc45
fix pytest errors
AbishekRajVG Oct 26, 2023
53594fe
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 26, 2023
5c7f2fc
Added testcase for vrifying file overwrite with Path.mkdir() method
AbishekRajVG Oct 27, 2023
434bea9
Merge branch 'dev-redefine-patchpredictor' of https://github.com/Tiss…
AbishekRajVG Oct 27, 2023
0924e1c
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 27, 2023
b8ae18d
fix lint errors pytest
AbishekRajVG Oct 27, 2023
3f5347f
Merge branch 'dev-redefine-patchpredictor' of https://github.com/Tiss…
AbishekRajVG Oct 27, 2023
07837ae
improving test coverage for engine_abc
AbishekRajVG Oct 31, 2023
ed83480
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 31, 2023
b8d3c4e
improving test coverage for engine_abc
AbishekRajVG Oct 31, 2023
10cec39
Merge branch 'dev-redefine-patchpredictor' of https://github.com/Tiss…
AbishekRajVG Oct 31, 2023
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3 changes: 3 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -115,3 +115,6 @@ ENV/

# vim/vi generated
*.swp

# output zarr generated
*.zarr
99 changes: 0 additions & 99 deletions tests/engines/_test_feature_extractor.py
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