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⚡ Improve Engine Performance and Implementation #578

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  • Improve Engines performance and implementation

@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

Codecov Report

Attention: Patch coverage is 78.90071% with 119 lines in your changes are missing coverage. Please review.

Project coverage is 89.51%. Comparing base (3da5ca2) to head (06af594).

❗ Current head 06af594 differs from pull request most recent head 3dd2c7b. Consider uploading reports for the commit 3dd2c7b to get more accurate results

Files Patch % Lines
tiatoolbox/models/dataset/dataset_abc.py 70.76% 38 Missing ⚠️
tiatoolbox/models/engine/io_config.py 56.16% 32 Missing ⚠️
tiatoolbox/utils/misc.py 50.94% 26 Missing ⚠️
tiatoolbox/models/engine/semantic_segmentor.py 30.00% 14 Missing ⚠️
tiatoolbox/models/engine/patch_predictor.py 66.66% 6 Missing ⚠️
tiatoolbox/models/architecture/vanilla.py 50.00% 2 Missing ⚠️
tiatoolbox/cli/nucleus_instance_segment.py 0.00% 1 Missing ⚠️
Additional details and impacted files
@@             Coverage Diff              @@
##           develop     #578       +/-   ##
============================================
- Coverage    99.89%   89.51%   -10.39%     
============================================
  Files           69       71        +2     
  Lines         8588     8848      +260     
  Branches      1645     1701       +56     
============================================
- Hits          8579     7920      -659     
- Misses           1      913      +912     
- Partials         8       15        +7     

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- 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 Jan 12, 2024 that may be closed by this pull request
8 tasks
shaneahmed and others added 19 commits February 2, 2024 12:00
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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Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>
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