jaxley.io.graph.from_graph

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jaxley.io.graph.from_graph#

from_graph(comp_graph, assign_groups=True, solve_root=None, traverse_for_solve_order=True)[source]#

Return a Jaxley module from a compartmentalized networkX graph.

This method is currently limited to graphs that have the same number of compartments in each branch. If this is not the case then the method will raise an AssertionError.

Parameters:

  • comp_graph (DiGraph) – The compartment graph built with build_compartment_graph() or with to_graph().

  • assign_groups (bool) – Whether to assign groups to the nodes.

  • solve_root (int | None) – The root node to traverse the graph for identifying the solve order.

  • traverse_for_solve_order (bool) – Whether to traverse the graph for identifying the solve order. Should only be set to False if you are confident that the comp_graph is in a form in which it can be solved (i.e. its branch indices, compartment indices, and node names are correct). Typically, this is the case only if you exported a module to a comp_graph via to_graph, did not modify the graph, and now re-import it as a module with from_graph.

Returns:

A jx.Module representing the graph.

Example usage#

from jaxley.io.graph import to_swc_graph, build_compartment_graph, from_graph
swc_graph = to_swc_graph("path_to_swc.swc")
comp_graph = build_compartment_graph(swc_graph, ncomp=1)
cell = from_graph(comp_graph)
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