schlegelp
commented
3 years ago Hi. It looks to me like your mesh is not fully connected - i.e. it consists of multiple disconnected shapes that only appear to be a closed surface. sk.pre.fix_mesh then removes some of these disconnected pieces because of the remove_disconnected parameter.
You can check this like so:
>>> import networkx as nx
>>> cc = nx.connected_components(mesh.vertex_adjacency_graph)
>>> print(f'Mesh consists of {len(list(cc))} connected components')
Mesh consists of 70 connected componentsWithout having seen what your Matrixvertices and triangle look like, I can't tell whether it's the input data that's wrong or whether trimesh does something funny. Normally, trimesh will merge vertices that occupy the same position in space but your process=False deactivates that behaviour.
Also another heads-up: I know it's somewhat counterintuitive but skeletonization of small primitives such as your cylinder often produce suboptimal results. You might be able to get better results by increasing the number of vertices (e.g. by subdividing).
bsaunois
Hi, I have a set of vertices and faces that I have given to Trimesh (my mesh is a perfect cylinder (all surface are closed)) . But when I compute the skeletonization, it seems that something wrong has happened. The mesh isn't complete and so the skeletonization didn't work... What did I do wrong ?
Here is my code for that part :
mesh = trimesh.Trimesh(vertices=Matrixvertices,faces=triangle,process=False)trimesh.Scene(mesh).show()fixed = sk.pre.fix_mesh(mesh, remove_disconnected=5, inplace=False)skel = sk.skeletonize.by_wavefront(fixed, waves=1, step_size=1)skel.mesh_mapskel.swc.head()skel.show(mesh=True)