✨ Add PatchPredictor Engine

[shaneahmed]

• 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

All modified and coverable lines are covered by tests ✅

Project coverage is 91.47%. Comparing base (dba269c) to head (156179d).
Report is 1 commits behind head on dev-define-engines-abc.

Additional details and impacted files

@@                    Coverage Diff                     @@
##           dev-define-engines-abc     #865      +/-   ##
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+ Coverage                   91.34%   91.47%   +0.13%     
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  Files                          71       71              
  Lines                        8892     8920      +28     
  Branches                     1180     1185       +5     
==========================================================
+ Hits                         8122     8160      +38     
+ Misses                        751      744       -7     
+ Partials                       19       16       -3     

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[shaneahmed]

I left a couple of specific comments, but also a general comment - there seems to be a lot of duplication of code/docstrings/text in general, with PatchPredictor mostly just calling the superclass with all of its methods apart from 1. It is a ~500 line file which is almost functionally equivalent to the EngineABC class apart from infer_wsi() method. The proliferation of the amount of text you need to go through in various files to get down to where the actual things are being done/identify what is the key difference a specific subclass introduces, is something we should try to avoid, in my opinion.

Thanks @measty. I have removed duplicated code as well.

[mostafajahanifar]

Thanks Shan for doing this PR. All looks good to me. I only made a couple of minor comments.

However, I also have a question: I don't understand the reason for needing "PatchPredictor" class to serve "PatchClassifer" as a parent class. Would be great if you can let me know why you have decided to do it like this (you most probably have discussed it before, but I'm very forgetful, I'm sorry :-s).

[shaneahmed]

Thanks Shan for doing this PR. All looks good to me. I only made a couple of minor comments.

However, I also have a question: I don't understand the reason for needing "PatchPredictor" class to serve "PatchClassifer" as a parent class. Would be great if you can let me know why you have decided to do it like this (you most probably have discussed it before, but I'm very forgetful, I'm sorry :-s).

Thanks @mostafajahanifar. This was a suggestion by Fayyaz to separate the two. In some cases, we do not need classification. For example, in semantic segmentor we need the raw predictions which are then converted to segmentation. In other cases, where we are building a pipeline where we need raw predictions instead of classification, this can simplify the pipeline by using just the predictor.