fix_mesh does not support MeshNeuron

[dokato]

Is there a reason why:

> mesh = navis.MeshNeuron("meshes/720575940577508022.ply")
> type(mesh1)
Out[5]: navis.core.neurons.MeshNeuron

> fixed = sk.pre.fix_mesh(mesh, remove_disconnected=5, inplace=False)

throws silent assertion error?

---> 68     assert isinstance(mesh, tm.Trimesh)
     69 
     70     if not inplace:

AssertionError: 

For convenience of using preprocessing functions it would be nice to support MeshNeuron objects.

[schlegelp]

The reason in this case is the inplace parameter that allows you to have the fixes applied to the original mesh instead of making a copy and fixing + returning that:

The whole point of this setting is to save some memory and overhead by not making a copy. But editing inplace=True would be a bit pointless if we had to first generate a trimesh (e.g. from a MeshNeuron) anyway.

There were already a few ways to work around this:

Use skeletor.utilities.make_trimesh - this function is very flexibly and will take pretty much anything with vertices and faces. Setting validate=True will also automatically run fix_mesh.

>>> fixed = sk.utilities.make_trimesh(mesh, validate=True)

Explicitly use the trimesh representation of your neuron: MeshNeuron.trimesh

>>> fixed = sk.pre.fix_mesh(mesh.trimesh, remove_disconnected=5, inplace=False)

On the code side, I just pushed a small update with aeb9112 that makes fix_mesh more flexible: it now accepts any mesh-like object (including MeshNeuron) but will ignore inplace=True if the input is not already a trimesh. So your original code approach will now also work.

[schlegelp]

I'm closing this as the issue has been fixed with the release of skeletor 1.0.0