update Flip/Rotate/Resize spatial transforms support MetaTensor #4429

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Merged

wyli merged 63 commits into Project-MONAI:feature/MetaTensor from wyli:some-spatial

Jun 14, 2022

Contributor

wyli commented Jun 1, 2022 •

edited

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trasforms in monai.transforms.spatial to support metatensor

Name	Array impl.	Dict impl.	Array test	Dict test
Flip	done	done	done	done
RandFlip	done	done	done	done
Rotate	done	done	done	done
RandRotate	done	done	done	done
RandAxisFlip	done	done	done	done
Resize	done	done	done	done
Zoom	done	done	done	done
RandZoom	done	done	done	done
Affine	done	done	done	done
RandAffine	done	done	done	done
Rotate90	done	done	done	done
RandRotate90	done	done	done	done

Status

Ready/Work in progress/Hold

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

wyli and others added 8 commits

May 31, 2022 04:09


          fixes integration tests

53f7385

Signed-off-by: Wenqi Li <wenqil@nvidia.com>


          [MONAI] code formatting

a62d029

Signed-off-by: monai-bot <monai.miccai2019@gmail.com>


          original spatial shape

98c0df0

Signed-off-by: Wenqi Li <wenqil@nvidia.com>


          fixes tests

8de2fd5

Signed-off-by: Wenqi Li <wenqil@nvidia.com>


          flip/flipd

40a0226

Signed-off-by: Wenqi Li <wenqil@nvidia.com>


          rand flip/flipd

7be5fd7

Signed-off-by: Wenqi Li <wenqil@nvidia.com>


          rotate/rotated

9cbf068

Signed-off-by: Wenqi Li <wenqil@nvidia.com>


          rand rotate/rotated

1e9e033

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

wyli requested a review from rijobro

June 1, 2022 12:53

wyli and others added 3 commits

June 1, 2022 13:59


          Merge branch 'feature/MetaTensor' into some-spatial

a09e657


          RandAxisFlip/RandAxisFlipd

e4a4643

Signed-off-by: Wenqi Li <wenqil@nvidia.com>


          fixes local var

0ac653a

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

wyli force-pushed the some-spatial branch from 9f86777 to 0ac653a Compare

June 1, 2022 14:16

wyli and others added 11 commits

June 1, 2022 15:42


          Merge branch 'feature/MetaTensor' into some-spatial

c0de4d6


          consistency tests

2b3c96c

Signed-off-by: Wenqi Li <wenqil@nvidia.com>


          Merge branch 'feature/MetaTensor' into some-spatial

c655b4d


          test tests.test_rand_axis_flip

b5f8433

Signed-off-by: Wenqi Li <wenqil@nvidia.com>


          fixes tests

7e01968

Signed-off-by: Wenqi Li <wenqil@nvidia.com>


          error -> warnings

8af8014

Signed-off-by: Wenqi Li <wenqil@nvidia.com>


          fixes tests

31ae028

Signed-off-by: Wenqi Li <wenqil@nvidia.com>


          update tests

46de0be

Signed-off-by: Wenqi Li <wenqil@nvidia.com>


          adds resize/resized

254f347

Signed-off-by: Wenqi Li <wenqil@nvidia.com>


          adds zoom/zoomd/randzoom/randzoomd

a1ca082

Signed-off-by: Wenqi Li <wenqil@nvidia.com>


          fixes test inverse

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

wyli changed the title ~~update Flip/Rotate spatial transforms support MetaTensor~~ update Flip/Rotate/Resize spatial transforms support MetaTensor

wyli added 5 commits

June 7, 2022 21:14


          fixes inverse

201a415

Signed-off-by: Wenqi Li <wenqil@nvidia.com>


          fixes typing

1fdbb32

Signed-off-by: Wenqi Li <wenqil@nvidia.com>


          resume collate

5bbf995

Signed-off-by: Wenqi Li <wenqil@nvidia.com>


          fixes unit tests

0f4a46c

Signed-off-by: Wenqi Li <wenqil@nvidia.com>


          affine/affined

6bad2ac

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

wyli added 4 commits

June 9, 2022 23:01


          fixes cpp ext metatensor

0cb78bf

Signed-off-by: Wenqi Li <wenqil@nvidia.com>


          Merge branch 'feature/MetaTensor' into some-spatial

5da66fe

Signed-off-by: Wenqi Li <wenqil@nvidia.com>


          autofix

8b3e52d

Signed-off-by: Wenqi Li <wenqil@nvidia.com>


          fixes type convertion

4152b95

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

wyli force-pushed the some-spatial branch from b89f5ad to 4152b95 Compare

June 10, 2022 08:00

wyli added 2 commits

June 12, 2022 11:46


          update randrotate90d tests

549e491

Signed-off-by: Wenqi Li <wenqil@nvidia.com>


          revert unecessary changes

83c58d1

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

wyli marked this pull request as ready for review

June 12, 2022 18:26


          sliding window inferer to preserve type

f607055

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

wyli force-pushed the some-spatial branch from 75a4590 to f607055 Compare

June 12, 2022 21:27


          tests sliding window

b7f6511

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

wyli force-pushed the some-spatial branch from 4da8e2a to b7f6511 Compare

June 13, 2022 09:54


          update integration tests

9c04da4

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Contributor Author

wyli commented Jun 13, 2022 •

edited

Loading

/black


          fixes torch.mode

4df1563

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

wyli force-pushed the some-spatial branch from a408fe4 to 4df1563 Compare

June 13, 2022 10:59


          [MONAI] code formatting

39c79af

Signed-off-by: monai-bot <monai.miccai2019@gmail.com>

wyli force-pushed the some-spatial branch from 010f529 to 39c79af Compare

June 13, 2022 11:06

Contributor Author

wyli commented Jun 13, 2022 •

edited

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/integration-test
/build

wyli added 2 commits

June 13, 2022 12:37


          fixes tests

af2ae1d

Signed-off-by: Wenqi Li <wenqil@nvidia.com>


          fixes return types

2dff3f1

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

wyli force-pushed the some-spatial branch from 4c96ff8 to 2dff3f1 Compare

June 13, 2022 13:34


          fixes unit tests

bc52321

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

rijobro reviewed

View reviewed changes

monai/data/image_writer.py Show resolved Hide resolved

wyli added 2 commits

June 13, 2022 22:39


          Merge branch 'feature/MetaTensor' into some-spatial

325a9b4

Signed-off-by: Wenqi Li <wenqil@nvidia.com>


          fixes integration tests

9d6fdfe

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

Contributor Author

wyli commented Jun 14, 2022

Most of the unit/integration tests are working fine now (apart from these documented #4462), I plan to merge this PR to the metatensor branch today.

Then the feature branch will cover two major areas of supporting metatensor, padcrop and spatial transforms. We should review the diff and have a plan for merging metatensor into dev dev...feature/MetaTensor mainly to polish the API and ensure backward compatibility cc @rijobro @Nic-Ma @ericspod

Contributor Author

wyli commented Jun 14, 2022

/build

wyli merged commit 3583ea0 into Project-MONAI:feature/MetaTensor

wyli deleted the some-spatial branch

June 14, 2022 12:30

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