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Twixtools and orientation matrix extraction #157

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merged 9 commits into from
Jul 12, 2024
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mbertrait
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This PR solves #153 by moving from mapVBVD to twixtools to read Siemens Twix scan files and storing the orientation matrix in the hdr dict.

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@paquiteau paquiteau left a comment

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Nice ! I have made a suggestion for more pythonic code. Also you need to run black/ ruff on your code

src/mrinufft/io/siemens.py Outdated Show resolved Hide resolved
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@chaithyagr chaithyagr left a comment

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LGTM, I think Only Pierre's comments makes sense and some code linting. Ideally we need a test, but thats hard as we need to create dummy data. Lets skip testing this module but maybe @mbertrait can you open an issue if its not already present to track the need for a test?

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A minor comment, if you can it could help to just tell here is twixtools is faster or pymapvbvd. It doesnt have to be an extensive test. Careful though, we dont want bad numbers just because data was in cache.

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Please also change pymapvbvd to twixtools with the right github link in pyproject.toml
@paquiteau to comment how to specify gitghub link, as twixtools is not released by authors.

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LGTM, I think Only Pierre's comments makes sense and some code linting. Ideally we need a test, but thats hard as we need to create dummy data. Lets skip testing this module but maybe @mbertrait can you open an issue if its not already present to track the need for a test?

I thought about tests but then as you mentioned we need dummy data so I set them aside for the moment.

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mbertrait commented Jul 11, 2024

Please also change pymapvbvd to twixtools with the right github link in pyproject.toml @paquiteau to comment how to specify gitghub link, as twixtools is not released by authors.

@paquiteau I found a syntax you can find in 612cfd9. Need your expertise on this

@paquiteau paquiteau merged commit 20a77aa into master Jul 12, 2024
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@chaithyagr chaithyagr deleted the siemens_twix_quat branch July 25, 2024 06:58
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3 participants