Allow swc files without a soma to be loaded

[IgorTatarnikov]

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Description

What is this PR

• [x] Bug fix
• [ ] Addition of a new feature
• [ ] Other

Why is this PR needed? See https://forum.image.sc/t/brainrender-error-when-rendering-my-own-neuron-morphology/95389/5

What does this PR do? Allows the load_from_swc and create_mesh functions to run when the provided swc file/Neuron object has no soma.

References

Please reference any existing issues/PRs that relate to this PR.

How has this PR been tested?

Tested using the user provided swc file, along with the standard brainrender swc test file. Both are able to be rendered without errors now.

Is this a breaking change?

No.

Does this PR require an update to the documentation?

No.

Checklist:

• [x] The code has been tested locally
• [x] The code has been formatted with pre-commit

[adamltyson]

@IgorTatarnikov when I run it on the data without a soma, I get:

morphio._morphio.MissingParentError: Sample id: 1 refers to non-existant parent ID: 0

Am I missing something?

[IgorTatarnikov]

Hmm, that's odd. Which swc file are you using?

[adamltyson]

wl3_local_registered.swc from the image.sc issue. Running it with the latest brainrender & this branch of morphapi:

from brainrender import Scene
from brainrender.actors import Neuron

scene = Scene()
scene.add(Neuron('wl3_local_registered.swc'))
scene.render()

[IgorTatarnikov]

I'm able to run it with the same file. I'll try downloading the file again and running it in a fresh environment.

[IgorTatarnikov]

I can't seem to replicate it, everything runs smoothly in a fresh environment.

[adamltyson]

Ok finally after starting from scratch with everything, it works fine. No idea what's going on with my system.

[adamltyson]

Will release and report back on image.sc.