Foreground Tissue Mask

[bhashemian]

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.

[Nic-Ma]

Thanks for the new feature, it overall looks good to me, put some minor comments inline.

[Nic-Ma]

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.

[bhashemian]

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

[Nic-Ma]

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.

[Nic-Ma]

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]

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

[bhashemian]

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

[Nic-Ma]

Thanks for the quick update!
Looks good to me.

Thanks.

[Nic-Ma]

/black

[Nic-Ma]

/build