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:

Line 176:1: W293 blank line contains whitespace
Line 214:80: E501 line too long (81 > 79 characters)
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Line 391:80: E501 line too long (81 > 79 characters)

• In the file scripts/scil_bundle_explore_bundleseg.py:

Line 192:80: E501 line too long (80 > 79 characters)
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Line 458:80: E501 line too long (81 > 79 characters)
Line 465:80: E501 line too long (80 > 79 characters)

• In the file scripts/scil_tractogram_segment_with_bundleseg.py:

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

Comment last updated at 2024-12-12 18:58:07 UTC

[codecov]

Codecov Report

Attention: Patch coverage is 19.65443% with 372 lines in your changes missing coverage. Please review.

Project coverage is 72.02%. Comparing base (3ddae5d) to head (5492585).
Report is 37 commits behind head on master.

❌ Your patch status has failed because the patch coverage (19.65%) is below the target coverage (90.00%). You can increase the patch coverage or adjust the target coverage.
❌ Your project status has failed because the head coverage (72.02%) is below the target coverage (75.00%). You can increase the head coverage or adjust the target coverage.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1035      +/-   ##
==========================================
- Coverage   73.18%   72.02%   -1.16%     
==========================================
  Files         451      452       +1     
  Lines       24872    25232     +360     
  Branches     3424     3452      +28     
==========================================
- Hits        18202    18174      -28     
- Misses       5207     5597     +390     
+ Partials     1463     1461       -2     

Components	Coverage Δ
Scripts	74.02% <3.93%> (-1.54%)	⬇️
Library	69.39% <50.00%> (-0.71%)	⬇️

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[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.

[arnaudbore]

Some comments, works as expected. Can you move the viewer from scil_bundle_explore_bundleseg.py somewhere else ?