⚡ Improve Engine Performance and Implementation
#578
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- Use `pyproject.toml` for `bdist_wheel` configuration
- Improve `Engines` performance and implementation
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## develop #578 +/- ##
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- Coverage 99.90% 91.53% -8.38%
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Files 69 71 +2
Lines 8715 8930 +215
Branches 1149 1184 +35
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- Hits 8707 8174 -533
- Misses 3 742 +739
- Partials 5 14 +9 ☔ View full report in Codecov by Sentry. |
- Refactor engines_abc.py
shaneahmed
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Engines Performance and ImplementationEngine Performance and Implementation
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
- 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 <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
- Fix `mypy` Type Checks for `cli/common.py`
- Add `PatchPredictor` Engine based on `EngineABC` - Add `return_probabilities` option to Params - Removes `merge_predictions` option in `PatchPredictor` engine. - Defines `post_process_cache_mode` which allows running the algorithm on `WSI` - Add `infer_wsi` for WSI inference - Removes `save_wsi_output` as this is not required after post processing. - Removes `merge_predictions` and fixes docstring in EngineABCRunParams - `compile_model` is now moved to EngineABC init - Fixes bug with `_calculate_scale_factor` - Fixes a bug in `class_dict` definition. - `_get_zarr_array` is now a public function `get_zarr_array` in `misc` - `patch_predictions_as_annotations` runs the loop on `patch_coords` instead of `class_probs` --------- Co-authored-by: Mark Eastwood <[email protected]> Co-authored-by: Mostafa Jahanifar <[email protected]> Co-authored-by: Adam Shephard <[email protected]> Co-authored-by: Jiaqi-Lv <[email protected]>
shaneahmed
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Nov 21, 2024
- Add changes from New engine design #578. This will not only simplify the PR but also keep the main repo up to date. - Refactor `model_to` to `model_abc` - Instead of `on_gpu` use `device` as an input in line with `PyTorch`. - `infer_batch` uses `device` as an input instead of `on_gpu`
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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