Tractogram scripts part1

[EmmaRenauld]

Quick description

Verified the four first tractogram scripts.

1. scil_tractogram_apply_transform:
   • Fixed difference between the doc's explanation and the script's management of option --remove_invalid.
2. scil_tractogram_apply_transform_to_hdf5:
   • Made the same choices of management of invalid as in script 1.
   • ENCAPSULATED HDF5 MANAGEMENT IN SCILPY.IO.HDF5. (Many of these methods are not used here but will be in the next PR. I just wanted to make sure right now that everything fitted correctly).
3. scil_tractogram_assign_uniform_color:
   • Moved loading of the json file out of the loop.
   • Better explanation in parser
   • Better verifications in main
   • Encapsulated hexadecimal_to_RGB in viz.utils.
4. scil_tractogram_cut_streamlines:
   • Now the data_per_streamline is kept.

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

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 60.77586% with 91 lines in your changes are missing coverage. Please review.

Project coverage is 66.98%. Comparing base (7e80020) to head (560a89f). Report is 4 commits behind head on master.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #948 +/- ## ========================================== - Coverage 67.02% 66.98% -0.05% ========================================== Files 395 396 +1 Lines 21289 21393 +104 Branches 3225 3251 +26 ========================================== + Hits 14269 14330 +61 - Misses 5715 5749 +34 - Partials 1305 1314 +9 ``` | [Components](https://app.codecov.io/gh/scilus/scilpy/pull/948/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/948/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scilus) | `68.05% <75.00%> (+0.11%)` | :arrow_up: | | [Library](https://app.codecov.io/gh/scilus/scilpy/pull/948/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scilus) | `65.33% <51.42%> (-0.27%)` | :arrow_down: |

[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 15:56:06 UTC