WSI reader

[bhashemian]

Fixes #1504

Description

Training models for pathology use cases requires loading patches from Whole Slide Imaging (WSI) scans. These images are enormous in size and usually much larger than user's available RAM (#1504). This PR provide a solution by implementing whole slide image readers for CuImage and OpenSlide.

Types of changes

• Non-breaking change (fix or new feature that would not break existing functionality).
• 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 --codeformat --coverage.
• Quick tests passed locally by running ./runtests.sh --quick.
• In-line docstrings updated.
• Documentation updated, tested make html command in the docs/ folder.

[bhashemian]

@wyli, @Nic-Ma
The mypy complains are for the existing code and I think they are due to the third-party libraries update. For instance, the first one is about np.eye, which I suspect it is because of the interface file ( __init__.pyi) that has been added after numpy==1.20 where the return type of np.eye is defined as Any. Have you encounter this in any other place in MONAI?

monai/data/image_reader.py:252:9: error: Returning Any from function declared to return "ndarray"  [no-any-return]
286
monai/data/image_reader.py:280:13: error: Returning Any from function declared to return "ndarray"  [no-any-return]
287
monai/data/image_reader.py:393:9: error: Returning Any from function declared to return "ndarray"  [no-any-return]

[bhashemian]

@wyli, @Nic-Ma
The mypy complains are for the existing code and I think they are due to the third-party libraries update. For instance, the first one is about np.eye, which I suspect it is because of the interface file ( __init__.pyi) that has been added after numpy==1.20 where the return type of np.eye is defined as Any. Have you encounter this in any other place in MONAI?

monai/data/image_reader.py:252:9: error: Returning Any from function declared to return "ndarray"  [no-any-return]
286
monai/data/image_reader.py:280:13: error: Returning Any from function declared to return "ndarray"  [no-any-return]
287
monai/data/image_reader.py:393:9: error: Returning Any from function declared to return "ndarray"  [no-any-return]

@wyli @Nic-Ma, what do you suggest here?

[wyli]

thanks, please see some initial comments inline, I'll try it out with an EA container soon...

[Nic-Ma]

Thanks for your quick update.
I put several minor comments inline, others look good to me.
And please add this new object to the "init.py" of mode/data/ and docs/sources/data.

Thanks.

[Nic-Ma]

Can it support images with channel = 1 or no channel?

[bhashemian]

It only supports RGB data as the output and it explicitly convert it to RGB, so the channels always should be 3.

[wyli]

thanks, the doc suggests RGBA (https://openslide.org/api/python/#openslide.OpenSlide.associated_images), I think we should make it clear in the docstring if we only support RGB

[Nic-Ma]

Suggest to use spatial_size, otherwise, it may be confusing whether it contains channel dim.

[bhashemian]

I kind of agree here but since both OpenSlide and cuClaraImage use size to define this input argument, I found using another name confusing for people who has ML in pathology background and has worked with WSI in the past.

[Nic-Ma]

Looks good to me.
Thanks for your quick update!