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CMRxRecon challenge 2023 participation scripts #274

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merged 17 commits into from
Apr 9, 2024
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@georgeyiasemis georgeyiasemis commented Apr 4, 2024

This PR incrorporates code used for DIRECT team participation at the CMRxRecon challenge 2023:

  • CMRxReconDataset which allows for 2D or 3D data loading.
  • Cartesian subsampling functions (similar to :class:FastMRI, but instead of center_fractions representing the fraction of center lines to the original size, here, it represents the actual number of center lines).
  • Training and inference scripts (yaml, lst files) for reproducing our experiments.

Also it introduces improvements to documentation and typing for edited files.

@github-actions github-actions bot added documentation Improvements or additions to documentation python labels Apr 4, 2024
@georgeyiasemis georgeyiasemis self-assigned this Apr 4, 2024
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codecov bot commented Apr 4, 2024

Codecov Report

Attention: Patch coverage is 88.01498% with 32 lines in your changes are missing coverage. Please review.

Project coverage is 84.80%. Comparing base (79543f0) to head (99d4b7a).

❗ Current head 99d4b7a differs from pull request most recent head 4caa1fb. Consider uploading reports for the commit 4caa1fb to get more accurate results

Files Patch % Lines
direct/data/datasets.py 82.66% 26 Missing ⚠️
direct/common/subsample.py 94.17% 6 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #274      +/-   ##
==========================================
+ Coverage   84.76%   84.80%   +0.03%     
==========================================
  Files          96       96              
  Lines        6963     7185     +222     
==========================================
+ Hits         5902     6093     +191     
- Misses       1061     1092      +31     

☔ View full report in Codecov by Sentry.
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@jonasteuwen jonasteuwen left a comment

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Some comments, in general:

  • Might it be possible to deduplicate or define more abstract base classes?
  • Use pathlib
  • Avoid randomness in the dataset classes

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Looks good to me

@jonasteuwen jonasteuwen merged commit df99d4e into main Apr 9, 2024
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@jonasteuwen jonasteuwen deleted the feature/cmrxrecon branch April 9, 2024 18:38
@georgeyiasemis georgeyiasemis mentioned this pull request Jun 27, 2024
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