Move metatensor support into dev branch (crop/pad) #4548

Nic-Ma · 2022-06-21T04:50:22Z

Description

This PR added MetaTensor support for all the crop & pad transforms.

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

merge master

Signed-off-by: Nic Ma <nma@nvidia.com>

Nic-Ma · 2022-06-21T05:01:01Z

Hi @wyli , @rijobro ,

Thanks for sharing the implementation in the metatensor branch, I refer to the PR #4536 and made the change for Pad transform in this PR, could you please help take a look first then I will dive into more transforms?
The main differences between this PR and the implementation in #4536:

The transform can accept tensor, metatensor or numpy, but the computation backend is always tensor.
The output of the transform is always tensor or metatensor, I see the typehints in metatensor branch are torch.Tensor for transforms input/output now.
The value modification are in-place for the image and metadata, same as our current existing transforms.

Thanks.

Signed-off-by: Nic Ma <nma@nvidia.com>

Nic-Ma · 2022-06-28T07:30:16Z

Hi @wyli @rijobro ,

I have integrated all the crop and pad transforms and migrated all the crop & pad unit tests from #4536.
Could you please help review it?
Please note that:

Some CI tests can't pass so far because having some other dependencies need to update.
I dropped the inverse operation of "crop samples" transforms.

Thanks.

wyli

thanks, I put some initial comments inline, please help fix the docs error: https://github.com/Project-MONAI/MONAI/runs/7087792214?check_suite_focus=true

monai/transforms/croppad/array.py

monai/transforms/croppad/dictionary.py

Signed-off-by: Nic Ma <nma@nvidia.com>

wyli

looks good to me

* [DLMED] adapt Pad transform for MetaTensor Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] format code Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update inverse and spatial_pad Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update border pad Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update divisible pad Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update spatial crop Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] make thread safe Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update CenterSpatialCrop Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update scale crop Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix flake8 Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update random spatial crop Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update random scale crop Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update random spatial crop samples Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] adjust Pad design Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update CropForeground Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update random weighted crop Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update RandCropPosNeg Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update rand crop by label classes Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update ResizeCropOrPad Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] restore numpy pad Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update dict spatial pad Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update border pad and divisible pad Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update spatial crop dict Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update center spatial crop Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update rand scale crop dict Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update rand spatial crop samples dict Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update crop foreground dict Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update rand weighted crop dict Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update pos neg crop dict Signed-off-by: Nic Ma <nma@nvidia.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [DLMED] update crop by labels dict Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update resize with pad or crop dict Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update format Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix all the mypy errors Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add crop / pad base tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update border pad test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update spatial crop Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update pad transforms Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update samples crop Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update crop tests Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add test for deepcopy Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update docs Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Nic-Ma and others added 8 commits February 1, 2021 19:15

Merge pull request #19 from Project-MONAI/master

42a45e0

merge master

Merge pull request #32 from Project-MONAI/master

cd16a13

merge master

Merge pull request #180 from Project-MONAI/dev

6f87afd

merge master

Merge pull request #214 from Project-MONAI/dev

f398298

merge master

Merge pull request #397 from Project-MONAI/dev

ec463d6

merge master

Merge pull request #424 from Project-MONAI/dev

9c13c88

merge master

[DLMED] adapt Pad transform for MetaTensor

577bb65

Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] format code

0c0c32d

Signed-off-by: Nic Ma <nma@nvidia.com>

Nic-Ma changed the title ~~[WIP] Add MetaTensor support for all the crop & pad transforms~~ [WIP] Move metatensor support into dev branch (crop/pad) Jun 21, 2022

Nic-Ma added 20 commits June 22, 2022 10:22

Merge branch 'dev' into metatensor-croppad

000f035

[DLMED] update inverse and spatial_pad

63e36b6

Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] update border pad

8f9814b

Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] update divisible pad

549fe2a

Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] update spatial crop

382b3e2

Signed-off-by: Nic Ma <nma@nvidia.com>

Merge branch 'dev' into metatensor-croppad

55b9101

Merge branch 'dev' into metatensor-croppad

6fe4132

[DLMED] make thread safe

d3962e4

Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] update CenterSpatialCrop

57f635a

Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] update scale crop

41c38b0

Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] fix flake8

ad85387

Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] update random spatial crop

647b239

Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] update random scale crop

3c84236

Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] update random spatial crop samples

0e1a322

Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] adjust Pad design

b6c4811

Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] update CropForeground

e432e03

Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] update random weighted crop

0807a10

Signed-off-by: Nic Ma <nma@nvidia.com>

Merge branch 'dev' into metatensor-croppad

2ca683a

[DLMED] update RandCropPosNeg

6706d07

Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] update rand crop by label classes

d7fa644

Signed-off-by: Nic Ma <nma@nvidia.com>

Nic-Ma added 8 commits June 27, 2022 18:59

[DLMED] fix all the mypy errors

52d1818

Signed-off-by: Nic Ma <nma@nvidia.com>

Merge branch 'integration-metatensor' into metatensor-croppad

e3a718d

[DLMED] add crop / pad base tests

da5195b

Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] update border pad test

7a573fa

Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] update spatial crop

e8de8e3

Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] update pad transforms

a91cfa3

Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] update samples crop

bf10855

Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] update crop tests

c43a87d

Signed-off-by: Nic Ma <nma@nvidia.com>

Nic-Ma marked this pull request as ready for review June 28, 2022 07:30

Nic-Ma changed the title ~~[WIP] Move metatensor support into dev branch (crop/pad)~~ Move metatensor support into dev branch (crop/pad) Jun 28, 2022

Nic-Ma requested review from wyli, rijobro and ericspod June 28, 2022 07:31

wyli reviewed Jun 28, 2022

View reviewed changes

wyli mentioned this pull request Jun 28, 2022

MetaTensor: re-enable full tests #4462

Closed

12 tasks

Nic-Ma added 5 commits June 28, 2022 22:33

[DLMED] update according to comments

e65c609

Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] update according to comments

65bda07

Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] update according to comments

5514c69

Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] update according to comments

f8e2379

Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] add test for deepcopy

ca7e11d

Signed-off-by: Nic Ma <nma@nvidia.com>

Nic-Ma requested a review from wyli June 29, 2022 06:12

Nic-Ma added 2 commits June 29, 2022 14:35

[DLMED] fix typo

b0ff943

Signed-off-by: Nic Ma <nma@nvidia.com>

[DLMED] update docs

bb37a2b

Signed-off-by: Nic Ma <nma@nvidia.com>

wyli approved these changes Jun 29, 2022

View reviewed changes

Nic-Ma merged commit 06c9eb7 into Project-MONAI:integration-metatensor Jun 29, 2022

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Move metatensor support into dev branch (crop/pad) #4548

Move metatensor support into dev branch (crop/pad) #4548

Nic-Ma commented Jun 21, 2022 •

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Move metatensor support into dev branch (crop/pad) #4548

Move metatensor support into dev branch (crop/pad) #4548

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Nic-Ma commented Jun 21, 2022 • edited Loading

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Nic-Ma commented Jun 21, 2022 •

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