Closed ceesem closed 3 years ago
Merging #64 into master will decrease coverage by
14.67%
. The diff coverage is54.12%
.
@@ Coverage Diff @@
## master #64 +/- ##
===========================================
- Coverage 76.25% 61.58% -14.68%
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Files 12 18 +6
Lines 1946 3512 +1566
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+ Hits 1484 2163 +679
- Misses 462 1349 +887
Impacted Files | Coverage Δ | |
---|---|---|
meshparty/skeleton_io.py | 89.02% <ø> (ø) |
|
meshparty/meshwork/algorithms.py | 7.31% <7.31%> (ø) |
|
meshparty/skeletonize.py | 52.74% <21.34%> (-34.48%) |
:arrow_down: |
meshparty/ray_tracing.py | 35.39% <35.39%> (ø) |
|
meshparty/utils.py | 64.84% <48.48%> (+8.55%) |
:arrow_up: |
meshparty/trimesh_io.py | 68.84% <50.90%> (-3.04%) |
:arrow_down: |
meshparty/meshwork/meshwork_io.py | 52.03% <52.03%> (ø) |
|
meshparty/meshwork/meshwork.py | 57.62% <57.62%> (ø) |
|
meshparty/meshwork/utils.py | 59.74% <59.74%> (ø) |
|
meshparty/mesh_filters.py | 82.27% <84.78%> (-0.18%) |
:arrow_down: |
... and 12 more |
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This PR adds a new object that integrates meshes, skeletons, and point annotations into a so-called "meshwork" object. This required a significant rewrite of the Skeleton class so that it handles masking while maintaining its original topology.
This also adds a few algorithms that have come in handy: 1) Adds optional support for a branch-level soma/neurite split. The default is the current system. 2) Axon/dendrite split via point of maximal input-to-output paths. 3) Cone-based SDF measurement. Again, the default is the current
I tried to make everything fully compatible with previous code, but it's possible one or two things have changed. Tests pass, but I might have neglected some combination of arguments.
The obvious to-do before merging is updating the docs, but I wanted to start this processes.