⚡ Improve Engine Performance and Implementation
#578
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- Use `pyproject.toml` for `bdist_wheel` configuration
- Improve `Engines` performance and implementation
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## develop #578 +/- ##
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- Coverage 99.09% 91.19% -7.90%
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Files 71 73 +2
Lines 9161 9374 +213
Branches 1196 1230 +34
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- Hits 9078 8549 -529
- Misses 59 792 +733
- Partials 24 33 +9 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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- Refactor engines_abc.py
shaneahmed
changed the title
Engines Performance and ImplementationEngine Performance and Implementation
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…917) * ♻️ Use `input_resolutions` instead of resolution - Use `input_resolutions` instead of resolution to make engines outputs compatible with ioconfig. - Uses input resolution as a list of dictionaries on units and resolution. * ♻️ Use `input_resolutions` instead of resolution - Use `input_resolutions` instead of resolution to make engines outputs compatible with ioconfig. - Uses input resolution as a list of dictionaries on units and resolution. * ✅ Add test to cli.
# Conflicts: # tiatoolbox/models/engine/patch_predictor.py
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# Conflicts: # tiatoolbox/utils/misc.py
# Conflicts: # tests/models/test_feature_extractor.py # tiatoolbox/models/models_abc.py
# Conflicts: # tiatoolbox/cli/common.py # tiatoolbox/cli/nucleus_instance_segment.py # tiatoolbox/cli/patch_predictor.py # tiatoolbox/models/engine/semantic_segmentor.py
* ⚡ Make WSIPatchDataset Pickleable to Support Windows Multithreading (#947) This PR makes the WSIPatchDataset class picklable by delaying the creation of the reader object until the first call to `__getitem__`. This enables the use of multiple loader workers on Windows without errors and provides significant performance improvements. - Delays reader object instantiation to the first `__getitem__` call instead of during initialization - Extracts reader creation logic into a separate `_get_reader` method - Stores image path and mode as instance variables for lazy initialization Speedup for the WSI prediction cell of the patch_prediction example notebook: 2min 48 sec with 0 loader workers -> 1min 13 sec with 4 workers. Note: this PR doesn't have any effect for Linux as the multi-threading already works fine there because Linux multithreading doesn't require things to be pickleable * 🔀 Merge branch develop into dev-engine-abc * 🐛 Fix reader_info read --------- Co-authored-by: Mark Eastwood <[email protected]>
# Conflicts: # tiatoolbox/models/dataset/classification.py
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Enginesperformance and implementationmypyType Checks forcli/common.pyPatchPredictorEngine based onEngineABCreturn_probabilitiesoption to Paramsmerge_predictionsoption inPatchPredictorengine.post_process_cache_modewhich allows running the algorithm onWSIinfer_wsifor WSI inferencesave_wsi_outputas this is not required after post processing.merge_predictionsand fixes docstring in EngineABCRunParamscompile_modelis now moved to EngineABC init_calculate_scale_factorclass_dictdefinition._get_zarr_arrayis now a public functionget_zarr_arrayinmiscpatch_predictions_as_annotationsruns the loop onpatch_coordsinstead ofclass_probs