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[WIP] Fibertube Tracking #971
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Hello @VincentBeaud, Thank you for updating ! There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻 Comment last updated at 2024-10-25 21:03:20 UTC |
@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 ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #971 +/- ##
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- Coverage 68.78% 68.50% -0.28%
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Files 429 439 +10
Lines 22265 23388 +1123
Branches 3324 3174 -150
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+ Hits 15314 16022 +708
- Misses 5665 6040 +375
- Partials 1286 1326 +40
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First 2 files of the PR tested and commented. Great job! Great start.
Major comments to discussion with @CHrlS98 and maybe @arnaudbore
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Should we rename all files that contain ft or fibertube. If not, how do we make sure our users know what ft means?
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@VincentBeaud I think you should create a small documentation in docs/source/documentation/ to show the typical order of execution of your scripts.
- scil_tractogram_filter_collisions.py GT_tracks.trk diameter.txt GT_tracks_wo_collisions.trk --single_diameter --save_colliders --save_collided
- scil_ft_visualize_collisions.py GT_tracks_wo_collisions_colliders.trk
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And maybe ask @arnaudbore where you could put a small toy exemple of trk and diameters.
Yes I think we should replace |
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Reviewed everything but did not test anything. This is a big PR. Ask me if you have any questions. My comments are mostly about scilpy coding standards and some renaming suggestions. Good work!
Co-authored-by: Charles Poirier <[email protected]>
New script names: |
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Good job @VincentBeaud . Massive PR and lots of nice work.
- Good news. Everything runs well.
- My comments are mostly regarding clarity of the docstring and --help messages. I'm picky on terminology and coherence across scripts. Addressing my comments will help your paper and demo
docs/fibertube/DEMO.md
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Should you and could you propose a figure to illustrate these? A bit like you did above?
…r fibertube. Not just END.
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