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Add support for level in PatchWSIDataset#4036

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wyli merged 6 commits intoProject-MONAI:devfrom
bhashemian:fix_4034
Apr 2, 2022
Merged

Add support for level in PatchWSIDataset#4036
wyli merged 6 commits intoProject-MONAI:devfrom
bhashemian:fix_4034

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@bhashemian bhashemian commented Mar 31, 2022 •
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Fixes #4034

Description

Add supports in PatchWSIDataset to accept level as an argument and extract patches from the whole slide images at that level.

Status

Ready

Types of changes

  • Non-breaking change (fix or new feature that would not break existing functionality).
  • 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.

@bhashemian bhashemian requested review from Nic-Ma and wyli March 31, 2022 14:47
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Nic-Ma commented Apr 1, 2022 •
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Hi @drbeh ,

Thanks for your quick update according to user's feedback, I have 2 comments:

  1. Should we also add the level arg to other datasets in the file?
    Like SmartCachePatchWSIDataset, MaskedInferenceWSIDataset.
  2. As WSIReader also supports **kwargs, could you please help add it to the datasets?
    https://github.com/Project-MONAI/MONAI/blob/dev/monai/data/image_reader.py#L727
    Then I think it can help support more similar requirements in future.

What do you think?

Thanks.

@bhashemian
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bhashemian commented Apr 2, 2022 •
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Thank you @Nic-Ma, it was a very helpful comment.

Nic-Ma
Nic-Ma reviewed Apr 2, 2022
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@bhashemian
Update docstring
1d9b7b2 
Signed-off-by: Behrooz <[email protected]>
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Nic-Ma commented Apr 2, 2022

/black

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Nic-Ma commented Apr 2, 2022

/build

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wyli commented Apr 2, 2022

/build

@wyli wyli enabled auto-merge (squash) April 2, 2022 07:08
@wyli wyli merged commit de97391 into Project-MONAI:dev Apr 2, 2022
@bhashemian bhashemian deleted the fix_4034 branch April 4, 2022 13:17
@bhashemian bhashemian mentioned this pull request Apr 13, 2022
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@Nic-Ma Nic-Ma Nic-Ma approved these changes

@wyli wyli Awaiting requested review from wyli

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Support for chosen level in PatchWSIDataset

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@bhashemian @Nic-Ma @wyli