Redesign PatchWSIDataset

[bhashemian]

Fixes #3930

Description

This PR refactor PatchWSIDataset and uses new WSIReader as the backend.

Status

Ready

Types of changes

• Breaking change (fix or new feature that would cause existing functionality to change).
• New tests added to cover the changes.
• Integration tests passed locally by running ./runtests.sh -f -u --net --coverage.
• Quick tests passed locally by running ./runtests.sh --quick --unittests --disttests.
• In-line docstrings updated.
• Documentation updated, tested make html command in the docs/ folder.

[Nic-Ma]

Hi @drbeh ,

BTW, about the SmartCachePatchWSIDataset, I think your previous suggestion was correct, we can slightly optimize the CacheDataset and SmartCacheDataset, etc. Then we can use them as decorators on another dataset object in future.

For now, you can use PatchWSIDataset as the data arg of SmartCacheDataset in your program to replace:
https://github.com/Project-MONAI/MONAI/blob/dev/monai/apps/pathology/data/datasets.py#L166

We must implement SmartCachePatchWSIDataset before because Clara 4.0 only supports 1 dataset in the config, now it's not necessary anymore.

Thanks.

[bhashemian]

Hi @drbeh ,

BTW, about the SmartCachePatchWSIDataset, I think your previous suggestion was correct, we can slightly optimize the CacheDataset and SmartCacheDataset, etc. Then we can use them as decorators on another dataset object in future.

For now, you can use PatchWSIDataset as the data arg of SmartCacheDataset in your program to replace: https://github.com/Project-MONAI/MONAI/blob/dev/monai/apps/pathology/data/datasets.py#L166

We must implement SmartCachePatchWSIDataset before because Clara 4.0 only supports 1 dataset in the config.

Thanks.

Sure, will add SmartCache in a seperate PR as the test cases need some attention.

[bhashemian]

Hi @Nic-Ma, any other comment here? thanks :)

[Nic-Ma]

Thanks for the quick update.
Looks good to me.

[Nic-Ma]

/black

[Nic-Ma]

/build