:art: New `EngineABC` Design for `Patches` by shaneahmed · Pull Request #635 · TissueImageAnalytics/tiatoolbox

shaneahmed · 2023-07-06T12:54:51Z

New EngineABC design
Update PatchPredictor based on the new design
Move model_to from utils.misc to model_abc
Define load_torch_model in model_abc

- Refactor base code from IOSegmentorConfig to IOConfigABC

- No need for a separate function

- Enable git workflow on this PR

- Add missing variable

- Move `to_baseline` code to ABC

- Fix incorrect calculations for output_resolutions

- Update `PatchPredictor` to use `ModelIOConfigABC` Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

- Define `ModelIOConfigABC` as a dataclass Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

- Remove kwargs. - Define dataclass attributes. Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

- Add `IOInstanceSegmentorConfig` Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

- Update yaml for `IOInstanceSegmentorConfig` Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

- Update `to_baseline` for `IOInstanceSegmentorConfig` Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

- Update IOInstanceSegmentorConfig in test_nucleus_instance_segmentor.py Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

- Update cli for IOInstanceSegmentorConfig Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

- Remove unnecessary test after kwargs removal Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

- Move ioconfigs to io_config.py Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

- Fix circular import Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

- Refactor to reduce code in inheriting class Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

- Fix deepsource errors Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

- Fix ioconfig import to avoid circular imports Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

- Fix missing input arguments Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

- Improve error catching Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

- Default configuration is not correct Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

- Fix error check Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

- Fix typo Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

- Fix unnecessary update Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

…ueImageAnalytics/tiatoolbox into dev-redefine-patchpredictor

tiatoolbox/models/engine/engine_abc.py

AbishekRajVG · 2023-10-20T12:40:04Z

Review comments addressed and pushed. I've only made changes to engine_abc and test_engine_abc. The misc.py changes are moved to a separate branch dev-persist-patchpredictor-output and are tracked in PR #724

mostafajahanifar

Thanks, Shan and collaborators for working on this. Looks like to is in good shape. I only made a couple of suggestions to consider.

tiatoolbox/models/models_abc.py

tiatoolbox/models/engine/engine_abc.py

mostafajahanifar · 2023-10-20T12:55:03Z

tiatoolbox/models/engine/engine_abc.py

+        num_postproc_workers (int):
+            Number of workers to postprocess the results of the model. default = 0
+        verbose (bool):
+            Whether to output logging information.


Actually, it would be nice to give the user option set the path to save engine logs for a specific run.

Shan: let's do it in a separate PR.

Abishek: EngineABC's verbose option displays the progress bar. Should we really have an option to save this to a file?

________________________________________________________________ test_engine_run_with_verbose _________________________________________________________________ -------------------------------------------------------------------- Captured stderr call --------------------------------------------------------------------- 100%|#############################################| 2/2 [00:00<00:00, 5.37it/s]

progress_bar = None if self.verbose: progress_bar = tqdm.tqdm( total=int(len(data_loader)), leave=True, ncols=80, ascii=True, position=0, )

tiatoolbox/models/engine/engine_abc.py

…-redefine-patchpredictor # Conflicts: # tests/test_utils.py # tiatoolbox/utils/misc.py

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…ueImageAnalytics/tiatoolbox into dev-redefine-patchpredictor

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…ueImageAnalytics/tiatoolbox into dev-redefine-patchpredictor

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…ueImageAnalytics/tiatoolbox into dev-redefine-patchpredictor

shaneahmed

Thanks @AbishekRajVG Looks good!

shaneahmed added 30 commits June 8, 2023 18:10

♻️ Refactor base code from IOSegmentorConfig to IOConfigABC

3eb4ab3

- Refactor base code from IOSegmentorConfig to IOConfigABC

♻️ No need for a separate function

c8d3458

- No need for a separate function

🧑‍💻 Enable git workflow on this PR

9623f86

- Enable git workflow on this PR

🐛 Add missing variable

4c8f91f

- Add missing variable

🎨 Move to_baseline code to ABC

972d81d

- Move `to_baseline` code to ABC

🎨 Move to_baseline code to ABC

5f81f9b

- Move `to_baseline` code to ABC

🐛 Fix incorrect calculations for output_resolutions

8270c4e

- Fix incorrect calculations for output_resolutions

🔧 Update PatchPredictor to use ModelIOConfigABC

f3b6b96

- Update `PatchPredictor` to use `ModelIOConfigABC` Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

🧱 Define ModelIOConfigABC as a dataclass

285d99a

- Define `ModelIOConfigABC` as a dataclass Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

Merge branch 'develop' into dev-define-ioconfig

ed638b7

Merge branch 'dev-define-engines-abc' into dev-define-ioconfig

b6c1a62

💥 Remove kwargs

0d270bf

- Remove kwargs. - Define dataclass attributes. Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

✨ Add IOInstanceSegmentorConfig

9e4266a

- Add `IOInstanceSegmentorConfig` Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

🔧 Update yaml for IOInstanceSegmentorConfig

d0ea031

- Update yaml for `IOInstanceSegmentorConfig` Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

🔧 Update yaml for IOInstanceSegmentorConfig

fa70c40

- Update yaml for `IOInstanceSegmentorConfig` Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

🔧 Update to_baseline for IOInstanceSegmentorConfig

70da57e

- Update `to_baseline` for `IOInstanceSegmentorConfig` Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

🔧 Update IOInstanceSegmentorConfig in test_nucleus_instance_segmentor.py

17e9a1f

- Update IOInstanceSegmentorConfig in test_nucleus_instance_segmentor.py Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

🐛 Update cli for IOInstanceSegmentorConfig

a976abe

- Update cli for IOInstanceSegmentorConfig Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

🔥 Remove unnecessary test after kwargs removal

4330e87

- Remove unnecessary test after kwargs removal Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

🚚 Move ioconfigs to io_config.py

1963923

- Move ioconfigs to io_config.py Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

🐛 Fix circular import

a8725a3

- Fix circular import Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

♻️ Refactor to reduce code in inheriting class

b226202

- Refactor to reduce code in inheriting class Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

🐛 Fix deepsource errors

2fffb61

- Fix deepsource errors Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

♻️ Fix ioconfig import

70da5d3

- Fix ioconfig import to avoid circular imports Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

🐛 Fix missing input arguments

cfc955f

- Fix missing input arguments Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

🥅 Improve error catching

b3ecadf

- Improve error catching Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

🥅 Default configuration is not correct

09b8cc4

- Default configuration is not correct Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

🥅 Fix error check

c2e7aae

- Fix error check Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

✏️ Fix typo

e02fd47

- Fix typo Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

🐛 Fix unnecessary update

ec6ff96

- Fix unnecessary update Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

Merge branch 'dev-redefine-patchpredictor' of https://github.com/Tiss…

1f85c50

…ueImageAnalytics/tiatoolbox into dev-redefine-patchpredictor

shaneahmed commented Oct 18, 2023

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adamshephard approved these changes Oct 20, 2023

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Improving engine_abc based on review comments

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mostafajahanifar requested changes Oct 20, 2023

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added link to pretrained models

122e114

shaneahmed force-pushed the dev-redefine-patchpredictor branch from 570615d to 122e114 Compare October 26, 2023 09:39

shaneahmed and others added 5 commits October 26, 2023 10:41

Merge remote-tracking branch 'origin/dev-define-engines-abc' into dev…

d86f668

…-redefine-patchpredictor # Conflicts: # tests/test_utils.py # tiatoolbox/utils/misc.py

Delete '

b47cd35

update method patch_pred method names in EngineABC

92bde5b

fix pytest errors

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AbishekRajVG mentioned this pull request Oct 26, 2023

Update model_to() and load_torch_model() methods in ModelABC #728

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AbishekRajVG and others added 6 commits October 27, 2023 11:42

Added testcase for vrifying file overwrite with Path.mkdir() method

5c7f2fc

Merge branch 'dev-redefine-patchpredictor' of https://github.com/Tiss…

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…ueImageAnalytics/tiatoolbox into dev-redefine-patchpredictor

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fix lint errors pytest

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Merge branch 'dev-redefine-patchpredictor' of https://github.com/Tiss…

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…ueImageAnalytics/tiatoolbox into dev-redefine-patchpredictor

improving test coverage for engine_abc

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AbishekRajVG requested a review from mostafajahanifar October 31, 2023 09:07

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

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improving test coverage for engine_abc

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shaneahmed commented Oct 31, 2023

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shaneahmed merged commit a6cd508 into dev-define-engines-abc Oct 31, 2023

shaneahmed deleted the dev-redefine-patchpredictor branch October 31, 2023 11:24

AbishekRajVG mentioned this pull request Nov 6, 2023

♻️ Update model_to() and load_torch_model() methods in ModelABC #733

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🎨 New `EngineABC` Design for `Patches`#635

🎨 New `EngineABC` Design for `Patches`#635
shaneahmed merged 153 commits intodev-define-engines-abcfrom
dev-redefine-patchpredictor

shaneahmed commented Jul 6, 2023 •

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AbishekRajVG commented Oct 20, 2023

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mostafajahanifar Oct 20, 2023 •

edited by AbishekRajVG

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mostafajahanifar Oct 20, 2023 • edited by AbishekRajVG Loading Uh oh! There was an error while loading. Please reload this page.

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shaneahmed commented Jul 6, 2023 •

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mostafajahanifar Oct 20, 2023 •

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