⚡ Improve Engine Performance and Implementation

[shaneahmed]

• Improve Engines performance and implementation
• 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.
• Fix mypy Type Checks for cli/common.py
• 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.
• 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

[codecov]

Codecov Report

Attention: Patch coverage is 83.48348% with 110 lines in your changes missing coverage. Please review.

Project coverage is 91.53%. Comparing base (4a1940d) to head (f6ba41f).

Files with missing lines	Patch %	Lines
tiatoolbox/models/dataset/dataset_abc.py	70.99%	38 Missing ⚠️
tiatoolbox/models/engine/io_config.py	56.16%	32 Missing ⚠️
tiatoolbox/utils/misc.py	57.81%	26 Missing and 1 partial ⚠️
tiatoolbox/models/engine/semantic_segmentor.py	29.41%	12 Missing ⚠️
tiatoolbox/cli/nucleus_instance_segment.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #578      +/-   ##
===========================================
- Coverage    99.90%   91.53%   -8.38%     
===========================================
  Files           69       71       +2     
  Lines         8715     8930     +215     
  Branches      1149     1184      +35     
===========================================
- Hits          8707     8174     -533     
- Misses           3      742     +739     
- Partials         5       14       +9     

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