Tractogram scripts parts3

[EmmaRenauld]

Quick description

Next step of scripts verification.

• scil_tractogram_detect_loops:
  • Clarified the argparser: arguments --qb and --threshold were either both required or both not used, so they were basically the same argument. Merged.
  • Added a --no_empty option.
• scil_tractogram_dpp_math:
  • argument --out_name was not really the output tractogram name, but the output dpp/dps name. Confusing. Changed to --out_key_name.
  • Moved some checks higher to do them before loading stuff.
  • Added more tests for better code coverage.
• scil_tractogram_extract_ushape:
  • Using ranged_type; verifications not needed anymore.
  • Moving stuff a bit.
  • There was a return (old line 88) that could potentially prevent the rest of happening (print counts, save remaining_tractogram). Fixed.
• scil_tractogram_smooth: Just improving doc!

Other changes:

• New compression_arg in all script using compression.
• New method that saves an emtpy tractogram only if not --no_empty.
• Deleted the filter_tractogram_data method. Confirmed with François: All this is just the equivalent of sft[idx].

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

Provide data, screenshots, command line to test (if relevant)

...

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 2024-04-12 14:18:48 UTC

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 70.52632% with 28 lines in your changes are missing coverage. Please review.

Project coverage is 68.17%. Comparing base (48911be) to head (4a86479).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #958 +/- ## ========================================== + Coverage 67.99% 68.17% +0.17% ========================================== Files 397 397 Lines 21396 21357 -39 Branches 3239 3229 -10 ========================================== + Hits 14549 14560 +11 + Misses 5532 5493 -39 + Partials 1315 1304 -11 ``` | [Components](https://app.codecov.io/gh/scilus/scilpy/pull/958/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/958/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scilus) | `69.24% <76.92%> (+0.25%)` | :arrow_up: | | [Library](https://app.codecov.io/gh/scilus/scilpy/pull/958/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scilus) | `66.55% <56.66%> (+0.06%)` | :arrow_up: |