Meta tensor load image

[rijobro]

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.

[rijobro]

@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?

[ericspod]

Looks good, I have a few optional suggestions.

[wyli]

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...

[rijobro]

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

[rijobro]

@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]

@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]

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

[wyli]

/build

[rijobro]

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?

[wyli]

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"))