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⚡ Improve Engine Performance and Implementation #578

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@shaneahmed shaneahmed commented Mar 31, 2023 •
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  • Improve Engines performance and implementation
  • Redesigns PatchPredictor engine using the new EngineABC base class.
  • The WSIs are now processed using the same code as for the processing the patches using WSI based dataloader.
  • The intermediate output is saved as zarr for the WSIs to resolve memory issues.
  • The output of model architectures should now be a dictionary.
  • The output can be specified as AnnotationStore for visualisation using TIAViz.

@shaneahmed shaneahmed self-assigned this Mar 31, 2023
@shaneahmed shaneahmed added the enhancement New feature or request label Mar 31, 2023
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codecov bot commented Mar 31, 2023 •
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Codecov Report

Attention: Patch coverage is 81.67939% with 120 lines in your changes missing coverage. Please review.

Project coverage is 91.30%. Comparing base (12d435e) to head (02aa0e5).

Files with missing lines Patch % Lines
tiatoolbox/models/dataset/dataset_abc.py 70.99% 38 Missing ⚠️
tiatoolbox/models/engine/io_config.py 56.16% 32 Missing ⚠️
tiatoolbox/utils/misc.py 52.38% 28 Missing and 2 partials ⚠️
tiatoolbox/models/engine/semantic_segmentor.py 30.00% 14 Missing ⚠️
tiatoolbox/models/architecture/vanilla.py 50.00% 2 Missing ⚠️
tiatoolbox/cli/common.py 91.66% 0 Missing and 1 partial ⚠️
tiatoolbox/cli/nucleus_instance_segment.py 0.00% 1 Missing ⚠️
tiatoolbox/models/engine/engine_abc.py 99.65% 0 Missing and 1 partial ⚠️
tiatoolbox/models/engine/patch_predictor.py 93.75% 1 Missing ⚠️
Additional details and impacted files 
@@             Coverage Diff             @@
##           develop     #578      +/-   ##
===========================================
- Coverage    99.88%   91.30%   -8.59%     
===========================================
  Files           69       71       +2     
  Lines         8664     8840     +176     
  Branches      1148     1179      +31     
===========================================
- Hits          8654     8071     -583     
- Misses           4      750     +746     
- Partials         6       19      +13

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@shaneahmed shaneahmed added this to the Release v2.0.0 milestone Apr 10, 2023
@shaneahmed shaneahmed mentioned this pull request Apr 19, 2023
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@shaneahmed
♻️ Refactor engines_abc.py
fac1000 
- Refactor engines_abc.py
@shaneahmed shaneahmed changed the title ⚡ Improve Engines Performance and Implementation ⚡ Improve Engine Performance and Implementation Apr 28, 2023
@shaneahmed shaneahmed linked an issue Jul 14, 2023 that may be closed by this pull request
Shifted patches when merging patch predictions! #634
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@shaneahmed shaneahmed mentioned this pull request Jul 14, 2023
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shaneahmed and others added 14 commits June 3, 2024 14:23
@shaneahmed
Merge branch 'develop' into dev-define-engines-abc
7af1ac4
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Merge branch 'develop' into dev-define-engines-abc
468aeb8
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Merge branch 'develop' into dev-define-engines-abc
47a81f1
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Merge branch 'develop' into dev-define-engines-abc
01e2262
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Merge branch 'develop' into dev-define-engines-abc
557bda5
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Merge branch 'develop' into dev-define-engines-abc
6495099
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Merge branch 'develop' into dev-define-engines-abc
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Merge branch 'develop' into dev-define-engines-abc
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Merge branch 'develop' into dev-define-engines-abc
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Merge branch 'develop' into dev-define-engines-abc
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Merge branch 'develop' into dev-define-engines-abc
ca294dd
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
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for more information, see https://pre-commit.ci
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Merge branch 'develop' into dev-define-engines-abc
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Merge branch 'develop' into dev-define-engines-abc
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@shaneahmed shaneahmed mentioned this pull request Aug 16, 2024
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@shaneahmed shaneahmed mentioned this pull request Sep 3, 2024
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shaneahmed and others added 9 commits September 18, 2024 12:43
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Merge branch 'develop' into dev-define-engines-abc
ca355aa
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Merge branch 'develop' into dev-define-engines-abc
05b1b1d
@shaneahmed @AbishekRajVG @pre-commit-ci
🧑‍💻 Define PatchPredictor (#783)
81e575d 
- Redesigns PatchPredictor engine using the new EngineABC base class.
- The WSIs are now processed using the same code as for the processing the patches using WSI based dataloader.
- The intermediate output is saved as zarr for the WSIs to resolve memory issues.
- The output of model architectures should now be a dictionary.
- The output can be specified as AnnotationStore for visualisation using TIAViz.

---------

Co-authored-by: abishekrajvg <abishekraj6797@gmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
@shaneahmed
Merge branch 'develop' into dev-define-engines-abc
bc73c5b
@shaneahmed
🐛 Fix mypy Type Checks for cli/common.py (#864)
8c2f50b 
- Fix `mypy` Type Checks for `cli/common.py`
@shaneahmed
Merge branch 'develop' into dev-define-engines-abc
e80b77b
@shaneahmed
Merge branch 'develop' into dev-define-engines-abc
843f1a6
@shaneahmed
Merge branch 'develop' into dev-define-engines-abc
d93fd94
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Merge branch 'develop' into dev-define-engines-abc
02aa0e5
This was referenced Nov 15, 2024
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