Tractogram scripts part7: segmentation scripts

[EmmaRenauld]

Quick description

The four segmentation scripts. (Renaming = made changes in many files). Improved doc everywhere to reference each other.

1) scil_tractogram_segment_bundles_with_bundleseg.py:

• Was ok! Clarified verifications.

2) scil_tractogram_segment_connections_from_labels.py:

• A lot of the lines have changed because I moved most of the processing to scilpy.tractanalysis.connectivity_segmentation! Will be difficult to review, sorry.
• Added an option to save the final streamlines in out_dir. Previously, they were saved as soon as you added option --out_dir.
• Added a lot of prints at debug level.
• Only saving intermediate files if that step was processed.
• Reusing the same variable (current_sft) rather than a separate sft name at each step to avoid multiplying data in memory. Using current_sft.streamlines rather than a separate streamlines = current_sft.streamlines, for the same reason.
• Separating the method remove_loops_and_sharp_turns into two: remove_loops, remove_sharp turns for more clarification; the "remove_loops" part was used twice (option args.loop_max_angle), once at the remove loops step, once at the remove_sharp_turn steps. Unnecessary processing removed.
• Encapsulating the "remove overlapping points" section in scilpy.tractograms.streamline_operations
• Using the existing function "filter_streamlines_by_length" rather than the local _prune_length method.

3) scil_tractogram_tractogram_segment_with_recobundles.py:

• Fixed the verbose. Still had a if args.verbose.
• Explained more the space and origin management. Added a to_rasmm, to_center to clarify, but it's the default when loading.
• Used new scilpy's save_tractogram, that checks if empty first.

4) scil_tractogram_tractogram_segment_with_ROI_and_score.py:

• Considering that I already have a 30-script PR, let's do it in another PR!!

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)
• [x] I added relevant citations to scripts, modules and functions docstrings and descriptions
• [x] I have performed a self-review of my code
• [x] I have commented my code, particularly in hard-to-understand areas
• [x] I have made corresponding changes to the documentation
• [x] My changes generate no new warnings
• [x] I moved all functions from the script file (except the argparser and main) to scilpy modules
• [x] 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 2024-05-31 00:18:40 UTC

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 79.34509% with 82 lines in your changes are missing coverage. Please review.

Project coverage is 68.23%. Comparing base (17b9a4a) to head (dd02451).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #993 +/- ## ========================================== + Coverage 68.14% 68.23% +0.09% ========================================== Files 419 419 Lines 21369 21388 +19 Branches 3216 3206 -10 ========================================== + Hits 14561 14594 +33 + Misses 5533 5527 -6 + Partials 1275 1267 -8 ``` | [Components](https://app.codecov.io/gh/scilus/scilpy/pull/993/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/993/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scilus) | `69.19% <78.24%> (+0.05%)` | :arrow_up: | | [Library](https://app.codecov.io/gh/scilus/scilpy/pull/993/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scilus) | `66.85% <80.66%> (+0.18%)` | :arrow_up: |