graph_utils

navis.graph.graph_utils.match_mesh_skeleton

Match vertices of MeshNeuron to nodes of TreeNeuron.

PARAMETER	DESCRIPTION
mesh	MeshNeuron to match. TYPE: MeshNeuron
skeleton	Skeleton to match. TYPE: TreeNeuron

RETURNS	DESCRIPTION
np.ndarray	Array of skeleton node IDs for each vertex in the mesh.

Source code in navis/graph/graph_utils.py

def match_mesh_skeleton(mesh, skeleton):
    """Match vertices of MeshNeuron to nodes of TreeNeuron.

    Parameters
    ----------
    mesh :      MeshNeuron
                MeshNeuron to match.
    skeleton :  TreeNeuron
                Skeleton to match.

    Returns
    -------
    np.ndarray
                Array of skeleton node IDs for each vertex in the mesh.

    """
    if not isinstance(mesh, core.MeshNeuron):
        raise TypeError(f"Expected MeshNeuron, got {type(mesh)}")

    if not isinstance(skeleton, core.TreeNeuron):
        raise TypeError(f"Expected TreeNeuron, got {type(skeleton)}")

    # Generate a KDTree for the skeleton
    tree = graph.neuron2KDTree(skeleton)

    # Find closest node for each vertex
    dist, ix = tree.query(mesh.vertices, k=1)

    return skeleton.nodes.node_id.values[ix]