Redesign of WSIReader

[drbeh]

Right now WSIReader is based on ImageReader class with read and get_data methods. However, reading whole slide images regardless of the library to use have its own additional complexities that are not captured in the base class.
Also, currently, we have implemented different backends cuCIM, OpenSlide, and TiffFile` through if statements!

My suggestion would be to have a WSIReader base class that implements those additional functionalities such as evaluating the level based on ppm/resolution, validating the pyramidal levels, etc. along with abstract methods that each of the libraries has to implement. In this way, we can implement each backend in different classes like CuCIMReader (for cuCIM) inherited from WSIReader.

This not only makes the code cleaner and more readable but also decouples MONAI integration of third-party WSI reader libraries and makes the future contribution easier and safer.

The overall structure would look like this: (will update #4005)

[drbeh]

@wyli @Nic-Ma @ericspod @rijobro
Do you have any comment here? does it make sense to you?

[Nic-Ma]

Hi @drbeh ,

Thanks for the refactoring idea.
I think it overall looks good to me, maybe we can simplify it to a flattened file structure:
monai/data/wsireader.py and monai/data/wsidataset.py
What do you think?
CC @wyli @ericspod

Thanks.

[ericspod]

I think this is a good change though WSIReader should still inherit from ImageReader so that the API remains compatible. TiffFileReader isn't just reading TIFF images but specifically those storing slide data so this class should have a more specific name to not appear to be a general purpose TIFF image reader, PILReader is meant for that instead.

[drbeh]

Hi @drbeh ,

Thanks for the refactoring idea. I think it overall looks good to me, maybe we can simplify it to a flattened file structure: monai/data/wsireader.py and monai/data/wsidataset.py What do you think? CC @wyli @ericspod

Thanks.

Hi @Nic-Ma, thanks for your feedback. I agree with this naming too.
I just wanted to follow the previous suggestions with @wyli (#3868 (comment)) and @ericspod (#3868 (comment)).
Either way is fine with me, the benefit that I can see for having a wsi directory is to declutter data directory, and add all WSI related stuff, e.g. datasets.py, reader.py, writer.py (maybe in the future), under the same name space (monai.data.wsi).

What do you think? @wyli @ericspod @Nic-Ma

[drbeh]

I think this is a good change though WSIReader should still inherit from ImageReader so that the API remains compatible. TiffFileReader isn't just reading TIFF images but specifically those storing slide data so this class should have a more specific name to not appear to be a general purpose TIFF image reader, PILReader is meant for that instead.

You are right! Here we are implementing a specific use of tifffile library, so we should be more clear. I'll think of a better name for that.

[wyli]

It looks good, given that monai.data doesn't currently have subfolders, I suspect monai/data/wsireader.py and monai/data/wsidataset.py are more consistent with the rest of the module.

[drbeh]

Sure, that's fine with me. Follow the same format as image_*.py, I'll make wsi_*.py.