[ENH] Add an option to cut streamlines

[arnaudbore]

Quick description

When you want to cut streamlines between two regions from a label file, you now have the possibility to either:

• Keep all points inside the two ROIS. (default)
• Keep one point inside each ROI (--one_point_in_roi)
• No point in ROI ( use --no_point_in_roi)

I checked with MI-Brain and I'm not sure it works, I can filter the no_point_in_roi.trk with the mask :|

Here are some data.tar.gz with the command line:

scil_tractogram_cut_streamlines.py tractogram.trk --labels labels.nii.gz one_point_in_roi.trk -f --one_point_in_roi
scil_tractogram_cut_streamlines.py tractogram.trk --labels labels.nii.gz no_point_in_roi.trk -f --no_point_in_roi
scil_tractogram_cut_streamlines.py tractogram.trk --labels labels.nii.gz points_in_roi.trk -f

...

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)

...

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 @arnaudbore, Thank you for updating !

• In the file scilpy/tractograms/streamline_and_mask_operations.py:

Line 460:80: E501 line too long (87 > 79 characters)
Line 461:80: E501 line too long (85 > 79 characters)
Line 541:80: E501 line too long (105 > 79 characters)

Comment last updated at 2025-01-17 12:18:59 UTC

[codecov]

Codecov Report

Attention: Patch coverage is 55.88235% with 15 lines in your changes missing coverage. Please review.

Project coverage is 69.53%. Comparing base (0ac4461) to head (0b63c48).
Report is 7 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1119      +/-   ##
==========================================
- Coverage   69.56%   69.53%   -0.04%     
==========================================
  Files         448      448              
  Lines       24078    24103      +25     
  Branches     3290     3298       +8     
==========================================
+ Hits        16751    16761      +10     
- Misses       5934     5946      +12     
- Partials     1393     1396       +3     

Components	Coverage Δ
Scripts	70.27% <66.66%> (+0.01%)	⬆️
Library	68.56% <53.57%> (-0.10%)	⬇️

[frheault]

I see a potential error in all three I think. If you look at all streamlines going through the no_point you will see some are going in and out and in again. And these few streamlines are present in a three.

This could be acceptable for the default (longest segment could be longest final segment)

[AntoineTheb]

LGTM, however I think some unit tests would be nice to ensure no regression happens when we inevitably revisit this script later on.

[frheault]

Would it be possible to make a unit with synthetic data A 3x3x3 grid with a single central voxel as mask.

And try a straight line going through, a straight going in and out and in again, starting in going out, fully in, fully out.

We change/broke/fix this like 3 times and 2 years.

Juste the easiest case