Meta tensor load image #4130

rijobro · 2022-04-13T16:35:42Z

This shows how I would propose to modify LoadImage to deal with MetaTensor.

This caused a lot of errors throughout our codebase, which I solved with FromMetaTensord wherever necessary.

This is a temporary fix and the usages of FromMetaTensord will be deleted as other parts of the codebase are updated to be compatible with MetaTensor.

This is a breaking change, so the PR is to MONAI/MetaTensor instead of dev.

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.
In-line docstrings updated.

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

…llate

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

rijobro · 2022-04-22T15:21:56Z

@Nic-Ma @ericspod @wyli
This branch seems to be working. Also all of the monai tutorials correctly run on this modified branch: https://github.com/Project-MONAI/tutorials/tree/MetaTensor. Could you please review this PR when you have the chance?

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

ericspod

Looks good, I have a few optional suggestions.

monai/transforms/io/array.py

monai/transforms/utility/dictionary.py

monai/transforms/io/array.py

wyli · 2022-04-27T12:38:25Z

Hi @rijobro, branches with the name pattern 'feature/*' will trigger more integration tests

MONAI/.github/workflows/setupapp.yml

Line 9 in 641a079

- feature/*

after this PR, I'll rename this MetaTensor branch to feature/MetaTensor to benefit from this...

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

rijobro · 2022-04-29T10:30:13Z

@ericspod thanks for the code review. I've incorporated all suggestions in 9e7b3d6.

rijobro · 2022-04-29T10:31:24Z

@wyli Any idea what's going wrong with the checks? Some jobs are failing before starting with:

Reading package lists...
W: GPG error: https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64  InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY A4B469963BF863CC
E: The repository 'https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64  InRelease' is not signed.
Error: Process completed with exit code 100.

wyli · 2022-04-29T10:45:11Z

@wyli Any idea what's going wrong with the checks? Some jobs are failing before starting with:

Reading package lists...
W: GPG error: https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64  InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY A4B469963BF863CC
E: The repository 'https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64  InRelease' is not signed.
Error: Process completed with exit code 100.

it's a known NGC issue and the team is working on it, (https://forums.developer.nvidia.com/t/invalid-public-key-for-cuda-apt-repository/212901)

wyli · 2022-05-02T09:02:45Z

for the record for more tests, after this PR I'll

rename MetaTensor branch to feature/MetaTensor
update the cron task to fetch the tutorial branch https://github.com/Project-MONAI/tutorials/tree/MetaTensor

(we also need a torch_function benchmark such as: https://github.com/pytorch/pytorch/tree/c371542efc31b1abfe6f388042aa3ab0cef935f2/benchmarks/overrides_benchmark

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

wyli · 2022-05-03T15:24:38Z

/build

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

rijobro · 2022-05-04T08:12:26Z

monai/data/meta_obj.py


    def __repr__(self) -> str:
        """String representation of class."""
-        out: str = super().__repr__()


I think this line should be reverted, I think the output should be the same as torch.Tensor, but with the extra metadata (now we have metadata instead of voxel data). @wyli what do you think?

sure, please feel free to change, the corresponding test case is this line:

MONAI/tests/test_meta_tensor.py

Line 201 in 18fca88

self.assertTrue(str(out).startswith("\nMetaData"))

* collate , decollate, dataset, dataloader, out= Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * mypy Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * skip decollation for pytorch 1.7 Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * add batch index testing Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fixes Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * load image meta tensor Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * splitdims fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * flake8 Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix test_nifti_rw Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * test_smartcachedataset Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * test fixes Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * test fixes Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fixes Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fixes Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * fix wsi test Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> * changes after code review Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com> Signed-off-by: Wenqi Li <wenqil@nvidia.com>

rijobro requested review from Nic-Ma and wyli April 13, 2022 16:35

Nic-Ma requested a review from ericspod April 14, 2022 04:17

rijobro added 13 commits April 14, 2022 15:36

collate , decollate, dataset, dataloader, out=

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Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

mypy

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Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

skip decollation for pytorch 1.7

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Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

fix

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Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

fix

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Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

Merge branch 'dev' into MetaTensor_collate_decollate

c6ae90d

add batch index testing

12afd4a

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

Merge remote-tracking branch 'MONAI/dev' into MetaTensor_collate_deco…

f7a583e

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fixes

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Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

fix

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fix

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Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

fix

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Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

fix

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Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

rijobro force-pushed the MetaTensorLoadImage branch 4 times, most recently from 1d57add to 6c4c3d0 Compare April 20, 2022 14:20

load image meta tensor

f9fd14a

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

rijobro force-pushed the MetaTensorLoadImage branch from 6c4c3d0 to f9fd14a Compare April 20, 2022 14:24

rijobro added 2 commits April 20, 2022 15:24

Merge branch 'MetaTensor_collate_decollate' into MetaTensorLoadImage

9a4bbb4

splitdims fix

b227fdd

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

rijobro force-pushed the MetaTensorLoadImage branch from 78728d2 to b227fdd Compare April 20, 2022 15:17

rijobro added 5 commits April 20, 2022 16:52

flake8

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Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

Merge branch 'MetaTensor' into MetaTensorLoadImage

226b104

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

fix test_nifti_rw

91eff3a

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

test_smartcachedataset

0f548c6

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

test fixes

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Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

rijobro added 6 commits April 21, 2022 15:13

test fixes

549c2ee

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

Merge remote-tracking branch 'MONAI/dev' into MetaTensorLoadImage

3563bc3

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

fix

55f483a

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

fixes

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Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

fix

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Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

fixes

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Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

Merge remote-tracking branch 'MONAI/dev' into MetaTensorLoadImage

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Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

ericspod approved these changes Apr 26, 2022

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wyli and others added 3 commits April 27, 2022 22:43

Merge branch 'MetaTensor' into MetaTensorLoadImage

b1e19eb

fix wsi test

ad1d780

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

changes after code review

9e7b3d6

Signed-off-by: Richard Brown <33289025+rijobro@users.noreply.github.com>

wyli and others added 3 commits May 2, 2022 13:24

Merge branch 'MetaTensor' into MetaTensorLoadImage

8cb4634

fixes unit tests

ad58d79

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

fixes: TypeError: __str__ returned non-string (type list)

2fb16f9

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

wyli force-pushed the MetaTensorLoadImage branch from be69305 to 56cb925 Compare May 3, 2022 16:52

fixes unit test tests.test_lr_finder

c74f0b3

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

wyli force-pushed the MetaTensorLoadImage branch from 56cb925 to c74f0b3 Compare May 3, 2022 16:59

wyli merged commit 18fca88 into Project-MONAI:MetaTensor May 3, 2022

rijobro commented May 4, 2022

View reviewed changes

rijobro deleted the MetaTensorLoadImage branch May 19, 2022 11:07

Meta tensor load image #4130

Meta tensor load image #4130

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