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mri utils added#4552

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wyli merged 26 commits intoProject-MONAI:devfrom
mersad95zd:00-mri-utils
Jun 29, 2022
Merged

mri utils added#4552
wyli merged 26 commits intoProject-MONAI:devfrom
mersad95zd:00-mri-utils

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@mersad95zd
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@mersad95zd mersad95zd commented Jun 21, 2022

Signed-off-by: mersad95zd [email protected]

Fixes #4566.

(Fixes #4606 to unblock the merging)

Description

The file contains a few required transforms for MRI reconstruction.

Status

Work in progress

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.

Signed-off-by: mersad95zd <[email protected]>
@Can-Zhao
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Can-Zhao commented Jun 21, 2022

Thank you for submitting your first PR!

Would you mind taking a look at the code format check flake8?
You could run runtests.sh --autofix
or run isort, black, flake8 one by one
Then run mypy ${your_added_script}

@Can-Zhao Can-Zhao added this to the MRI Reconstruction Module milestone Jun 23, 2022
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After you finalize the code, please add docstring reference in docs/source/apps.rst and make sure the document looks correct.
Please refer to https://github.com/Project-MONAI/MONAI/blob/dev/CONTRIBUTING.md#building-the-documentation
Thanks!

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Please move the unit test to tests folder, not monai.apps

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Looks good to me

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Have you added rst for the script in monai.networks.blocks?

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Please solve this error:
AttributeError: module 'torch.fft' has no attribute 'ifftshift'

@mersad95zd
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Sorry I somehow missed this comment yesterday.
Could you provide more details? Is your pytorch up-to-date?

torch.fft.ifftshift is supported in the latest pytorch release: https://pytorch.org/docs/stable/generated/torch.fft.ifftshift.html

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Can-Zhao commented Jun 27, 2022

Sorry I somehow missed this comment yesterday. Could you provide more details? Is your pytorch up-to-date?

torch.fft.ifftshift is supported in the latest pytorch release: https://pytorch.org/docs/stable/generated/torch.fft.ifftshift.html

Please see https://github.com/Project-MONAI/MONAI/runs/7056882942?check_suite_focus=true
The PR could not be merged if it does not pass this test. Actually all the tests labeled as "Required" need to be passed. Please click "Details" to find the issues.
Thanks!

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wyli commented Jun 29, 2022

/black

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wyli commented Jun 29, 2022

/build

@wyli wyli enabled auto-merge (squash) June 29, 2022 07:54
@wyli wyli merged commit 25d6208 into Project-MONAI:dev Jun 29, 2022
@mersad95zd mersad95zd deleted the 00-mri-utils branch June 29, 2022 15:52
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typing error with torch 1.12 N-D FFT is missing

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