[WIP] Fibertube Tracking

[VincentBeaud]

Quick description

Please include a summary of the changes and the related issue(s) or improvement(s). Please also include relevant motivation and context. List any dependencies that are required for this change if needed.

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Type of change

Check the relevant options.

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

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

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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
• [ ] 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
• [ ] New and existing unit tests pass locally with my changes

[pep8speaks]

Hello @VincentBeaud, Thank you for updating !

• In the file scripts/scil_fibertube_tracking.py:

Line 183:80: E501 line too long (85 > 79 characters)

• In the file scripts/scil_tractogram_filter_collisions.py:

Line 44:80: E501 line too long (81 > 79 characters)

• In the file scripts/tests/test_fibertube_tracking.py:

Line 80:80: E501 line too long (84 > 79 characters)

Comment last updated at 2024-10-02 18:55:46 UTC

[VincentBeaud]

@mdesco et @CHrlS98 Voici la grosse PR! Il me reste un peu de job à faire alors elle est en draft. Aussi, je viens de faire plusieurs petits changements et je n'ai pas retesté chaque script. Je vais donc le faire maintenant en créant un fichier de test pour chaque.

Je vais aussi rajouter une description détaillée dès que j'aurai terminé ça.

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 59.80498% with 371 lines in your changes missing coverage. Please review.

Project coverage is 68.51%. Comparing base (1d6f848) to head (4adc5eb).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #971 +/- ## ========================================== - Coverage 68.78% 68.51% -0.27% ========================================== Files 429 436 +7 Lines 22265 23186 +921 Branches 3324 3464 +140 ========================================== + Hits 15314 15886 +572 - Misses 5665 5987 +322 - Partials 1286 1313 +27 ``` | [Components](https://app.codecov.io/gh/scilus/scilpy/pull/971/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/971/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scilus) | `69.85% <77.67%> (+0.19%)` | :arrow_up: | | [Library](https://app.codecov.io/gh/scilus/scilpy/pull/971/components?src=pr&el=component&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scilus) | `66.69% <50.41%> (-0.85%)` | :arrow_down: |

[CHrlS98]

@mdesco

1. Should we rename all files that contain ft or fibertube. If not, how do we make sure our users know what ft means?

Yes I think we should replace ft by fibertube. We will want our example in the documentation to clearly explain what fibertubes are too.

[VincentBeaud]

New script names: scil_tractogram_filter_collisions.py -> unchanged scil_ft_visualize_collisions.py -> scil_viz_tractogram_collisions.py scil_ft_fibers_metrics.py -> deleted. Code is in "scil_tractogram_filter_collisions.py" scil_ft_tracking.py -> scil_fibertube_tracking.py scil_ft_reconstruction_metrics.py -> scil_fibertube_score_tractogram.py