Move utils.streamlines methods

[EmmaRenauld]

Quick description

• All methods in utils.streamlines moved elsewhere.
  - Changed: get_color_streamlines_from_angle is now only get_angle. The color is managed separately.
  - Changed: get_color_streamlines_along_length is now only get_values_along_length. The color is managed separately.

• tractanalysis.feature is renamed tractanalysis.bundle_operation (it could also go in tractograms if you prefer). Some of its methods have been moved to tractogram.tractogram_operations or tractogram.streamline_operations if they didn't really concern bundles.

• Script scil_tractogram_assign_custom_color strongly modified:
  - LUT was loaded but not used, and re-loaded later in sub-function.
  - Sometimes, data was loaded as data = ..., sometimes as values, lbound, ubound = ..., but actually, the same call to clip_and_normalize_data_for_cmap was always done, just very unclear. That's why they are removed from the two methods described above.
  - Tried to remove access to hidden ._data when possible.
  - Encapsulated main script to new dps_and_dpp_management method.

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

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 @EmmaRenauld, Thank you for updating !

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2024-03-27 12:42:11 UTC

[codecov]

Codecov Report

Attention: Patch coverage is 64.50512% with 104 lines in your changes are missing coverage. Please review.

Project coverage is 67.02%. Comparing base (234b88c) to head (7e80020).

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #950      +/-   ##
==========================================
+ Coverage   66.86%   67.02%   +0.16%     
==========================================
  Files         396      395       -1     
  Lines       21290    21289       -1     
  Branches     3225     3225              
==========================================
+ Hits        14235    14269      +34     
+ Misses       5756     5715      -41     
- Partials     1299     1305       +6     

Components	Coverage Δ
Scripts	67.93% <60.71%> (+0.18%)	⬆️
Library	65.59% <65.40%> (+0.12%)	⬆️

[CHrlS98]

I read the code. Some minor comments. Good to go once they are addressed.

[arnaudbore]

GTG