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Masked Patch WSI Dataset#4410

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bhashemian merged 73 commits intoProject-MONAI:devfrom
bhashemian:masked_wsi_dataset
Jun 3, 2022
Merged

Masked Patch WSI Dataset#4410
bhashemian merged 73 commits intoProject-MONAI:devfrom
bhashemian:masked_wsi_dataset

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@bhashemian bhashemian commented May 31, 2022 •
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Fixes #4014
Fixes #4398

Description

This PR implements MaskedPatchWSIDataset, which uses a whole slide image at a lower resolution to create a mask and extract patches based on that.
It also updates WSIReader to be able to set channel_last, and some other updates to make sure all components are properly working together.

Status

Ready

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 -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.

bhashemian added 30 commits May 26, 2022 01:34
@bhashemian
Implement foreground mask
2b2a31e 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Add unittests for foreground mask
381ac73 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Add several test cases
ba45b62 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Merge branch 'dev' of github.com:Project-MONAI/MONAI into tissue-mask
582caf7
@bhashemian
Add ForegroundMaskd
7294c87 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Add unittests for ForegroundMaskd
cb86da5 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Update init
a2feb79 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Update docstring
d271d98 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Merge branch 'dev' of github.com:Project-MONAI/MONAI into tissue-mask
aff1005
@bhashemian
Merge branch 'dev' of github.com:Project-MONAI/MONAI into tissue-mask
be4a7d5
@bhashemian
Update to less or equal for RGB threshold
32313ec 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Update RGB and HSV mask combination
4771712 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Add support for torch.Tensor
7a72eb9 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Update docsting and dict tests
d393e35 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Add docs
8902a8a 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Merge branch 'dev' into tissue-mask
5209c52
@bhashemian
Add skipunless for skimage
4a8aa14 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Exclude form min tests
33fc743 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
fix a typo
aa11706 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Merge branch 'dev' into tissue-mask
558314a
@bhashemian
Merge branch 'dev' into tissue-mask
48aece9
@bhashemian
Update no or wrong threshold cases
de94b00 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Merge branch 'dev' of github.com:Project-MONAI/MONAI into tissue-mask
2849958
@bhashemian
Update docstring
ebde248 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Merge branch 'dev' of github.com:Project-MONAI/MONAI into tissue-mask
b84b63b
@bhashemian
Implement MaskedPatchWSIDataset
0bfb77b 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Add unittests
1c8a106 
Signed-off-by: Behrooz <[email protected]>
@bhashemian
Merge branch 'dev' into tissue-mask
6e860a3
@bhashemian
pMerge branch 'tissue-mask' of github.com:behxyz/MONAI into tissue-mask
deaab9e
@bhashemian
Update the min verison for skimage to 0.19.0
6411373 
Signed-off-by: Behrooz <[email protected]>
@bhashemian bhashemian marked this pull request as ready for review June 1, 2022 16:16
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bhashemian commented Jun 1, 2022

/black

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bhashemian commented Jun 1, 2022 •
edited
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@Nic-Ma it is ready for review. Do you have any idea what's the issue with flake8 tests? It seems that they are failing for an unrelated issue to this PR, doesn't it?

Hopefully, this is the last PR for MONAI code and then I will finish up the pathology bundle and pipelines.

Thanks

@bhashemian bhashemian enabled auto-merge (squash) June 1, 2022 19:50
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bhashemian commented Jun 1, 2022

Since this PR had pulls from other branches, the commit list was a bit messy, so I cleaned it up for autho-merge.

@bhashemian bhashemian disabled auto-merge June 2, 2022 00:29
@bhashemian bhashemian enabled auto-merge (squash) June 2, 2022 00:31
Nic-Ma
Nic-Ma reviewed Jun 2, 2022
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Nic-Ma approved these changes Jun 2, 2022
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Thanks for the quick update.
Looks good to me now.

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Nic-Ma commented Jun 2, 2022

/black

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Nic-Ma commented Jun 2, 2022

/build

@bhashemian bhashemian merged commit 07306c0 into Project-MONAI:dev Jun 3, 2022
@bhashemian bhashemian deleted the masked_wsi_dataset branch June 3, 2022 03:43
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WSIReader get_patch => ChannelFirst behvaiour should be controlled through argument Refactor MaskedInferenceWSIDataset

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