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1979 Enhance TTA to align with Invertd args and support no label#2654

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Nic-Ma merged 6 commits intoProject-MONAI:devfrom
Nic-Ma:1979-enhance-tta
Jul 26, 2021
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1979 Enhance TTA to align with Invertd args and support no label#2654
Nic-Ma merged 6 commits intoProject-MONAI:devfrom
Nic-Ma:1979-enhance-tta

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@Nic-Ma Nic-Ma commented Jul 23, 2021

Fixes #1979 .

Description

This PR enhanced the TTA module to align with Invertd transform args and support the inference case without label, just set orig_key to the same as image_key.

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.

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Nic-Ma commented Jul 23, 2021

I will also update the TTA tutorial when this PR merged.

Thanks.

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[DLMED] fix typo
be83558 
Signed-off-by: Nic Ma <[email protected]>
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Nic-Ma commented Jul 23, 2021

/black

@Nic-Ma Nic-Ma requested review from ericspod, rijobro and wyli July 23, 2021 15:49
wyli
wyli approved these changes Jul 24, 2021
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Thanks, perhaps @rijobro could confirm this change

@Nic-Ma Nic-Ma merged commit 325775b into Project-MONAI:dev Jul 26, 2021
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Nic-Ma commented Jul 26, 2021

The funtion in the tutorial is:

tt_aug = TestTimeAugmentation(
    val_transforms,
    batch_size=5,
    num_workers=0,
    inferrer_fn=partial(infer_seg, model=model),  # fn to infer segmentation
    device=device
)

Seems no need to update.

Thanks.

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@wyli wyli wyli approved these changes

@rijobro rijobro Awaiting requested review from rijobro

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

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TestTimeAugmentation assumes label is present

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