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Add augmentation mri transforms #279

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@georgeyiasemis georgeyiasemis commented Jun 6, 2024

This PR:

  • Adds RescaleKspace, PadKspace trasnforms (these project the data to image domain, perform augmentation, and then transform back to k-space)
  • Adds CompressCoilModule transform which compresses the number of k-space coils using SVD
  • Adds tests for new transforms
  • Updates workflows for python v3.9 and v3.10

@github-actions github-actions bot added ci docker documentation Improvements or additions to documentation python labels Jun 6, 2024
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codecov bot commented Jun 6, 2024

Codecov Report

Attention: Patch coverage is 34.14634% with 108 lines in your changes missing coverage. Please review.

Project coverage is 83.94%. Comparing base (66dd5cd) to head (e824db2).
Report is 1 commits behind head on main.

Current head e824db2 differs from pull request most recent head f3aa68c

Please upload reports for the commit f3aa68c to get more accurate results.

Files Patch % Lines
direct/data/mri_transforms.py 24.77% 82 Missing ⚠️
direct/data/transforms.py 25.71% 26 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #279      +/-   ##
==========================================
- Coverage   85.03%   83.94%   -1.10%     
==========================================
  Files         100       98       -2     
  Lines        7531     7723     +192     
==========================================
+ Hits         6404     6483      +79     
- Misses       1127     1240     +113     

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@georgeyiasemis georgeyiasemis marked this pull request as ready for review June 6, 2024 13:53
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georgeyiasemis commented Jun 24, 2024

@jonasteuwen This is ready for merge.
Some updates:

  • I fixed pylint with py 3.10 (required a small import from skimage change)
  • For some reason it threw an issue for cnp.int_t in cython which I replaced witg cnp.int64_t
  • For docker, it needs more work and will do a seperate PR

@jonasteuwen jonasteuwen self-requested a review June 24, 2024 23:28
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LGTM. Nice work!

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