BundleSeg exploration viewer for filtering

[frheault]

Quick description

Implemented a new BundleSeg slider feature for filtering
Improved code to limit RAM usage by processing FreeSurfer surfaces (FSS) in chunks, making it easier to handle larger datasets.

New Features:

• Exploration Mode (--exploration_mode):
  This mode searches all bundles at a higher pruning threshold (12mm).
  A second script then visualizes the results and can save outputs in the specified folder.
• Distance Threshold Modification (--modify_distance_thr):
  Allows customization of the pruning distance threshold for all bundles.
  Default value is 0.0, but this parameter can be adjusted based on the user's requirements.

Performance Improvements:
Slight speed optimization, especially for large datasets. For example, processing a 2GB tractogram with 6M streamlines and 51 atlas bundles takes approximately 5 minutes on 4 processes.
RAM usage is now optimized, allowing for smoother handling of large subjects on machines with limited resources (e.g., 5 large subjects processed on 4 CPUs with 32GB RAM).

Note: Using more than 4 processes (e.g., 8 or 16) doesn't significantly improve speed in this scenario.

Title:
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Type of change

Check the relevant options.

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• This change requires a documentation update

Provide data, screenshots, command line to test (if relevant)

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Checklist

• My code follows the style guidelines of this project (run autopep8)
• I added relevant citations to scripts, modules and functions docstrings and descriptions
• I have performed a self-review of my code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I moved all functions from the script file (except the argparser and main) to scilpy modules
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes

[pep8speaks]

Hello @frheault, Thank you for updating !

• In the file scilpy/segment/bundleseg.py:

Line 152:80: E501 line too long (81 > 79 characters)
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• In the file scilpy/segment/voting_scheme.py:

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• In the file scripts/scil_bundle_explore_bundleseg.py:

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• In the file scripts/scil_tractogram_segment_with_bundleseg.py:

Line 25:80: E501 line too long (80 > 79 characters)

Comment last updated at 2024-11-19 14:02:24 UTC

[codecov]

Codecov Report

Attention: Patch coverage is 18.96956% with 346 lines in your changes missing coverage. Please review.

Project coverage is 68.08%. Comparing base (e7337af) to head (6ec2906).

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1035      +/-   ##
==========================================
- Coverage   68.93%   68.08%   -0.86%     
==========================================
  Files         438      439       +1     
  Lines       22889    23219     +330     
  Branches     3106     3135      +29     
==========================================
+ Hits        15779    15809      +30     
- Misses       5793     6088     +295     
- Partials     1317     1322       +5     

Components	Coverage Δ
Scripts	68.47% <3.90%> (-1.37%)	⬇️
Library	67.52% <48.27%> (-0.14%)	⬇️

---- 🚨 Try these New Features:

• Flaky Tests Detection - Detect and resolve failed and flaky tests

[frheault]

@GuillaumeTh Testing BundleSeg on a random big tractogram with the new --exploration_mode option and then using the viewer would be great for a tumor case showcase.