2525 Add decollate logic to DeepGrow module (8/July)

[Nic-Ma]

Fixes #2525 .

Description

This PR updated the DeepGrow module based on the latest decollate logic.

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.
• In-line docstrings updated.
• Documentation updated, tested make html command in the docs/ folder.

[Nic-Ma]

Hi @wyli @SachidanandAlle ,

There is a potential issue in this PR that I am not very sure how to fix and want to discuss with you guys here:
As DeepGrow is slightly different from regular training, it needs to run several iterations inference / interactions, so we need to inference -> decollate -> click transforms -> collate -> inference as what I changed in this PR.
But some random click transforms may output data with different size, so we can't collate them into a batch for next inference, like the "guidance" generated by AddRandomGuidanced here: https://github.com/Project-MONAI/tutorials/blob/master/deepgrow/ignite/train.py#L98

Can we pad the data and collate? Or any other idea to avoid collate?

Thanks in advance.

[Nic-Ma]

/black

[SachidanandAlle]

This fix looks ok to me.. we can Vish to verify sample 2D deepgrow training.. for accuracy

[Nic-Ma]

This fix looks ok to me.. we can Vish to verify sample 2D deepgrow training.. for accuracy

Hi @SachidanandAlle ,

Thanks for your review, do you mean to use pad_collate to solve the size issue when collating again?
@wyli @rijobro what do you guys think?

Thanks in advance.

[Nic-Ma]

/black

[Nic-Ma]

Hi @wyli ,

Thanks for @SachidanandAlle 's analysis and help, this PR is ready for review now.
Could you please help also review it?

Thanks in advance.

[wyli]

looks good according to @SachidanandAlle