1866 Add TransformInverter handler

[Nic-Ma]

Fixes #1866 .

Description

This PR added the ignite handler to invert transforms for model output data.

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.

[rijobro]

Thanks for looking into this @Nic-Ma. I notice an issue here that I hadn't thought about previously.

During training/validation/testing, there will typically be a ground truth label attached, and we'll want to use those transforms for the inverse.

At deployment, we'll probably only be using images (no labels). And typically for labels, we'll use nearest-neighbour interpolation, whereas for images we'll use something else (e.g., linear). So if we do the inverse as you've suggested in this PR, we'll probably be using non-nearest neighbour interpolation on our labels.

I wonder if this would be solved by simply doing AsDiscrete at the end. A little messy. cc @wyli @ericspod.

[Nic-Ma]

/black

[Nic-Ma]

Hi @rijobro ,

Thanks for your review, there are another 2 minor issues about inverse logic:

1. You didn't implement the inverse for ToTensorD transform, so it will run with Tensor data, fixed in this PR.
2. The BatchInverseTransform requires the transform must be InvertibleTransform while the allow_missing_keys_mode requires Compose or MapTransform, it will cause some typehints issue, I ignored in the PR.

About the sampling question you proposed, it's a good point, let me add another arg as_discrete.

Thanks.

[Nic-Ma]

/black

[rijobro]

test is basic, but I suppose testing shape is sufficient here, as voxel values are tested in test_inverse.py. Thanks!

Have you tested this personally to check it works as you expect?

[Nic-Ma]

Hi @rijobro ,

Thanks for your review, I already tested it with the workflow example:
https://github.com/Project-MONAI/tutorials/blob/master/modules/engines/unet_evaluation_dict.py

And I will write another PR to solve the interpolation mode issue soon.

Thanks.

[wyli]

thanks @rijobro chat with Nic offline that we plan to update to store/use the inverse parameters such as mode and align_corners in EXTRA_INFO