jaxley.morphology.distance_direct

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jaxley.morphology.distance_direct#

distance_direct(startpoint, endpoints)[source]#

Returns the direct distance between a root and other compartments.

This function uses cell.nodes[['x', 'y', 'z']] and computes the euclidean distance (i.e., the line of sight distance).

Parameters:

  • startpoint (View) – A single compartment from which to compute the distance.

  • endpoints (Branch | Cell | View) – One or multiple compartments to which to compute the distance to.

Returns:

A list of distances.

Return type:

List[float]

Example usage#

The following computes the direct (line of sight) distance between the zero-eth soma compartment and all other compartments. It then saves this distance in cell.nodes[“direct_dist_from_soma”].

from jaxley.morphology import distance_pathwise

cell.compute_compartment_centers()  # necessary if you modified branch length.
direct_dists = distance_direct(cell.soma.branch(0).comp(0), cell)
cell.nodes["direct_dist_from_soma"] = direct_dists
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