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.

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

Checklist

• [X] My code follows the style guidelines of this project (run autopep8)
• [] I added relevant citations to scripts, modules and functions docstrings and descriptions
• [X] 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
• [x] 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
• [x] 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! :beers:

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

[codecov[bot]]

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

```diff @@ 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](https://app.codecov.io/gh/scilus/scilpy/pull/950/components?src=pr&el=components&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scilus) | Coverage Δ | | |---|---|---| | [Scripts](https://app.codecov.io/gh/scilus/scilpy/pull/950/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scilus) | `67.93% <60.71%> (+0.18%)` | :arrow_up: | | [Library](https://app.codecov.io/gh/scilus/scilpy/pull/950/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scilus) | `65.59% <65.40%> (+0.12%)` | :arrow_up: |