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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 •
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Codecov Report

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

Project coverage is 89.51%. Comparing base (73aa802) to head (06af594).
Report is 1 commits behind head on develop.

❗ Current head 06af594 differs from pull request most recent head 557bda5

Please upload reports for the commit 557bda5 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         8650     8848      +198     
  Branches      1653     1701       +48     
============================================
- Hits          8641     7920      -721     
- Misses           1      913      +912     
- Partials         8       15        +7

☔ View full report in Codecov by Sentry.
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@shaneahmed shaneahmed added this to the Release v2.0.0 milestone Apr 10, 2023
@shaneahmed shaneahmed mentioned this pull request Apr 19, 2023
Closed
@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
Open
@shaneahmed shaneahmed mentioned this pull request Jul 14, 2023
Open
@shaneahmed shaneahmed linked an issue Jan 12, 2024 that may be closed by this pull request
Models Inconsistency #566
Open
8 tasks
@shaneahmed shaneahmed linked an issue Feb 2, 2024 that may be closed by this pull request
NucleusInstanceSegmentor.predict() has no "patch" mode #780
Open
@shaneahmed shaneahmed mentioned this pull request Feb 2, 2024
Open
shaneahmed and others added 24 commits February 2, 2024 12:00
@shaneahmed
🔀 Merge develop into dev-define-engine-abc
c812932
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
aaff1f8 
for more information, see https://pre-commit.ci
@shaneahmed
Merge branch 'develop' into dev-define-engines-abc
af05d15
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
17581f5 
for more information, see https://pre-commit.ci
@shaneahmed
Merge branch 'develop' into dev-define-engines-abc
2ee5723
@shaneahmed
Merge branch 'develop' into dev-define-engines-abc
f883e81
@pre-commit-ci
[pre-commit.ci] auto fixes from pre-commit.com hooks
90f396c 
for more information, see https://pre-commit.ci
@shaneahmed
Merge branch 'develop' into dev-define-engines-abc
f60f69c
@shaneahmed
Merge branch 'develop' into dev-define-engines-abc
7d3b530
@shaneahmed
Merge branch 'develop' into dev-define-engines-abc
2e522be
@shaneahmed
Merge branch 'develop' into dev-define-engines-abc
3a0c884
@shaneahmed
Merge branch 'develop' into dev-define-engines-abc
fe3c697
@shaneahmed
Merge branch 'develop' into dev-define-engines-abc
5b24ba2
@shaneahmed
Merge branch 'develop' into dev-define-engines-abc
0bcf27d
@AbishekRajVG @pre-commit-ci @shaneahmed
✨ Add WSI processing to EngineABC (#737)
466d005 
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.

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Shan E Ahmed Raza <[email protected]>
@shaneahmed
Merge branch 'develop' into dev-define-engines-abc
8ba4bca
@shaneahmed
Merge branch 'develop' into dev-define-engines-abc
3252633
@shaneahmed
Merge branch 'develop' into dev-define-engines-abc
06af594
@shaneahmed
⏪ Restore test_patch_predictor.py
3dd2c7b
@shaneahmed
Merge branch 'develop' into dev-define-engines-abc
7af1ac4
@shaneahmed
Merge branch 'develop' into dev-define-engines-abc
468aeb8
@shaneahmed
Merge branch 'develop' into dev-define-engines-abc
47a81f1
@shaneahmed
Merge branch 'develop' into dev-define-engines-abc
01e2262
@shaneahmed
Merge branch 'develop' into dev-define-engines-abc
557bda5
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@shaneahmed @AbishekRajVG