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Foreground Tissue Mask#4379

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bhashemian merged 36 commits intoProject-MONAI:devfrom
bhashemian:tissue-mask
May 31, 2022
Merged

Foreground Tissue Mask#4379
bhashemian merged 36 commits intoProject-MONAI:devfrom
bhashemian:tissue-mask

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@bhashemian bhashemian commented May 28, 2022 •
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Fixes #4380
Prerequisite for #4014

Description

This PR implements ForegroundMask transform that creates a foreground mask with various thresholding. For digital pathology use cases, this transform is helpful to create sliding-window patches that covers only the tissue.

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.
  • Documentation updated, tested make html command in the docs/ folder.

bhashemian added 16 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 bhashemian linked an issue May 28, 2022 that may be closed by this pull request
iter_patch_slices Patch Order #4287
Closed
@bhashemian bhashemian removed a link to an issue May 28, 2022
iter_patch_slices Patch Order #4287
Closed
@bhashemian bhashemian marked this pull request as ready for review May 28, 2022 21:06
Nic-Ma
Nic-Ma reviewed May 30, 2022
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Thanks for the new feature, it overall looks good to me, put some minor comments inline.

@bhashemian bhashemian enabled auto-merge (squash) May 30, 2022 19:23
Nic-Ma
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Thanks for the quick update, it overall looks good to me.
Put some minor comments inline.
As it's a typical use case for images and in the core transforms, could you please help add the sample image in the doc? Following: https://github.com/Project-MONAI/MONAI/blob/dev/monai/transforms/utils_create_transform_ims.py

Thanks.

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bhashemian commented May 31, 2022

Thanks for the quick update, it overall looks good to me. Put some minor comments inline. As it's a typical use case for 2D image and in the core transforms, could you please help add the sample image in the doc? Following: https://github.com/Project-MONAI/MONAI/blob/dev/monai/transforms/utils_create_transform_ims.py

Thanks.

@Nic-Ma, I think it has the same blocker that has not been resolved: #4161

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Nic-Ma commented May 31, 2022

Thanks for the quick update.
Looks good to me except for the missing sample image in doc.
@rijobro Could you please help guide @drbeh the basic steps to add a sample transform image?

Thanks in advance.

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Nic-Ma commented May 31, 2022

Hi @drbeh ,

I feel this transform is different from #4161 as this transform seems like a general-purpose intensity transform for 2D/3D images?
@ericspod @rijobro Please feel free to correct me if I misunderstood it.

Thanks.

@bhashemian
Add enums
2c1b868 
Signed-off-by: Behrooz <[email protected]>
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bhashemian commented May 31, 2022

HI @Nic-Ma, alright, let me see if I can create an image with the existing data for this transform.

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bhashemian commented May 31, 2022

@Nic-Ma, I've added the images for this transform: Project-MONAI/DocImages#12, and updated this PR. Can you check they are fine?

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Thanks for the quick update!
Looks good to me.

Thanks.

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Nic-Ma commented May 31, 2022

/black

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Nic-Ma commented May 31, 2022

/build

@bhashemian bhashemian merged commit 27c37f2 into Project-MONAI:dev May 31, 2022
@bhashemian bhashemian deleted the tissue-mask branch February 22, 2023 15:31
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@Nic-Ma Nic-Ma Nic-Ma approved these changes

@wyli wyli Awaiting requested review from wyli

@ericspod ericspod Awaiting requested review from ericspod ericspod is a code owner

@rijobro rijobro Awaiting requested review from rijobro

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Tissue Foreground Mask

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