Python 3 library to extract skeletons from 3D meshes
Unlike its namesake, this Python 3 library does not (yet) seek to conquer Eternia but to turn meshes into skeletons.
1.0.0 introduced some breaking changes and major reorganizations.
Please see the changelog
pip3 install skeletor
For the dev version:
pip3 install git+https://github.com/navis-org/skeletor@master
Automatically installed with
Optional because not strictly required for the core functions but highly recommended:
- pyglet is required by trimesh to preview meshes/skeletons in 3D:
pip3 install pyglet
- fastremap for sizeable speed-ups with some methods:
pip3 install fastremap
Please see the documentation for details.
The changelog can be found here.
For the impatient a quick example:
>>> import skeletor as sk >>> mesh = sk.example_mesh() >>> fixed = sk.pre.fix_mesh(mesh, remove_disconnected=5, inplace=False) >>> skel = sk.skeletonize.by_wavefront(fixed, waves=1, step_size=1) >>> skel <Skeleton(vertices=(1258, 3), edges=(1194, 2), method=wavefront)>
All skeletonization methods return a
Skeleton object. These are just
convenient objects to represent and inspect the results.
>>> # location of vertices (nodes) >>> skel.vertices array([[16744, 36720, 26407], ..., [22076, 23217, 24472]]) >>> # child -> parent edges >>> skel.edges array([[ 64, 31], ..., [1257, 1252]]) >>> # Mapping for mesh to skeleton vertex indices >>> skel.mesh_map array([ 157, 158, 1062, ..., 525, 474, 547]) >>> # SWC table >>> skel.swc.head() node_id parent_id x y z radius 0 0 -1 16744.005859 36720.058594 26407.902344 0.000000 1 1 -1 5602.751953 22266.756510 15799.991211 7.542587 2 2 -1 16442.666667 14999.978516 10887.916016 5.333333 >>> # Save SWC file >>> skel.save_swc('skeleton.swc')
If you installed
pyglet (see above) you can also use
capabilities to inspect the results:
were run on a 2018 MacBook Pro (2.2 GHz Core i7, 32Gb memory) with optional
fastremap dependency installed. Note some of these functions (e.g.
contraction and TEASAR/vertex cluster skeletonization) can vary a lot in
speed based on parameterization.
Pull requests are always welcome!
References & Acknowledgments
Mesh contraction and the edge collapse approach are based on this paper:
 Au OK, Tai CL, Chu HK, Cohen-Or D, Lee TY. Skeleton extraction by mesh contraction. ACM Transactions on Graphics (TOG). 2008 Aug 1;27(3):44.
The abstract and the paper can be found here.
Also see this YouTube video.
Some of the code in skeletor was modified from the Py_BL_MeshSkeletonization addon for Blender 3D created by #0K Srinivasan Ramachandran and published under GPL3.
The mesh TEASAR approach was adapted from the implementation in meshparty by Sven Dorkenwald, Casey Schneider-Mizell and Forrest Collman.
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