ENH: better bundle endpoints maps #1047
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Hello @AntoineTheb, Thank you for updating ! There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻 Comment last updated at 2024-11-08 16:17:31 UTC |
AntoineTheb
commented
Nov 5, 2024
| point_to_select: int | ||
| Instead of computing the density based on the first and last points, | ||
| select more than one at each end. To support compressed streamlines, | ||
| a resampling to 0.5mm per segment is performed. |
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Narrator: this actually wasn't performed.
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #1047 +/- ##
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+ Coverage 68.79% 68.89% +0.10%
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Files 432 434 +2
Lines 22454 22646 +192
Branches 3041 3078 +37
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+ Hits 15448 15603 +155
- Misses 5706 5727 +21
- Partials 1300 1316 +16
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EmmaRenauld
approved these changes
Nov 7, 2024
| " of the streamlines. [%(default)s]") | ||
| p.add_argument('--mm', action='store_true', | ||
| help='Compute the endpoints in mm instead of nb. of ' | ||
| 'points. Useful for compressed streamlines.') |
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I think this could be a little clearer. Like, if user adds --mm, but not --nb_points, is it clear to them that it will take 1mm?
Maybe.... If set, the value --nb_points will instead be understood as the length, in mm. But I'm not sure that's perfect either.
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Quick description
This PR improves bundle endpoint maps computation. Before, the map was only computed on streamline points exactly, which may be problematic if the step size is too large (see fig. 1 for ref). Now, the map includes every voxel traversed by the endpoints (however many points are selected). Moreover, the user can now select
nmillimeters instead of points, which makes much more sense when dealing with compressed streamlines.Breaking change: the arguments of
scil_bundle_compute_endpoint_maps.pyare now slightly different.Type of change
Check the relevant options.
Provide data, screenshots, command line to test (if relevant)
Fig 1.: Before, 3 points
Fig. 2: After, 3 points
Fig. 3: After, 10mm.
Checklist