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support for graph operations #334

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jnsbck opened this issue Apr 11, 2024 · 3 comments · May be fixed by #355
Open

support for graph operations #334

jnsbck opened this issue Apr 11, 2024 · 3 comments · May be fixed by #355
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@jnsbck
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enhancement New feature or request v1.0

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@jnsbck
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jnsbck commented Apr 11, 2024

Add .to_graph() and .from_graph() methods. See below. This is a long term thing though.

I agree, these things would be awesome to have, but I think we should add all of this functionality separately. Maybe in jaxley.graph_utils or something. Then the user could resample, clean, fix, edit, etc. however he wants directly on the graph. We could add a to_graph and from_graph method, that casts module.nodes to a networkx DiGraph object. Then graph_utils could operate on that.

Originally posted by @jnsbck in #238 (comment)
@jnsbck jnsbck added the enhancement New feature or request label Apr 11, 2024
@michaeldeistler
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Would be awesome if from_graph could be used to read swc...not sure if possible

@jnsbck
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jnsbck commented Apr 11, 2024

I.e. read swc into networkx DiGraph before running cell = Cell.from_graph(swc_graph) or something? Should work I think. MorphoPy does something like this.

https://github.com/berenslab/MorphoPy/blob/3ae9d1f51b6cac7d08a820cb1fcae931425bc797/morphopy/neurontree/utils.py#L356-L468

@michaeldeistler
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Yes it would be great if we could entirely remove my hand-written SWC reader. I would be open to use MorphoPy for this, or just networkx (not sure what is easier, I know neither of those two libraries well). The features we need are:

  • automatically reconstruct parents (i.e. the branch structure)
  • get length and radius of every reconstructed point in every branch
  • get the type of every branch

Anyways, let's maybe talk about this next week before starting to tackle it, but I think it could be worth it.

@jnsbck jnsbck self-assigned this Apr 25, 2024
@jnsbck jnsbck linked a pull request Apr 25, 2024 that will close this issue
Add support for graph operations #355
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Add support for graph operations jaxleyverse/jaxley
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