⚡ Improve Engine Performance and Implementation
#578
+4,779
−5,023
Commits on Mar 24, 2023
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🔧 Use
pyproject.tomlforbdist_wheelconfiguration- Use `pyproject.toml` for `bdist_wheel` configuration
Commits on Mar 31, 2023
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⚡ Improve
Enginesperformance and implementation- Improve `Engines` performance and implementation
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♻️ Refactor base code from
IOSegmentorConfigtoModelIOConfigABC(#……618) - Moved all ioconfigs to a single file. - Used dataclass to define ioconfig. - Refactor base code from `IOSegmentorConfig` to `ModelIOConfigABC` - Use `ModelIOConfigABC` for `PatchPredictor` instead of `IOSegmentorConfig` --------- Signed-off-by: Shan E Ahmed Raza <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: John Pocock <[email protected]> Co-authored-by: Mark Eastwood <[email protected]> Co-authored-by: Mostafa Jahanifar <[email protected]> Co-authored-by: Adam Shephard <[email protected]>
6 people authoredJul 31, 2023 -
♻️ Move Dataset Classes to
dataset_abc.py(#637)- Move `WSIStreamDataset`, `PatchDatasetABC` and `WSIPatchDataset` to `dataset_abc.py` --------- Signed-off-by: Shan E Ahmed Raza <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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🎨 New
EngineABCDesign forPatches(#635)- New `EngineABC` design - Update `PatchPredictor` based on the new design - Move `model_to` from `utils.misc` to `model_abc` - Define `load_torch_model` in `model_abc` --------- Signed-off-by: Shan E Ahmed Raza <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: measty <[email protected]> Co-authored-by: abishekrajvg <[email protected]>
4 people authoredOct 31, 2023 -
Commits on Nov 15, 2023
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🔀 Merge develop into dev-define-engines-abc
Signed-off-by: Shan E Ahmed Raza <[email protected]>
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🥅 Fix merge errors in classification.py
Signed-off-by: Shan E Ahmed Raza <[email protected]>
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✨ Add WSI processing to
EngineABC(#737)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]>
3 people authoredApr 26, 2024
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🧑💻 Define
PatchPredictor(#783)- 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>
3 people authoredSep 20, 2024 -
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🐛 Fix
mypyType Checks forcli/common.py(#864)- Fix `mypy` Type Checks for `cli/common.py`
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✨ Add
PatchPredictorEngine (#865)- 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]>
5 people authoredNov 20, 2024
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