neuron.py 文件源码

def calc_arc_choord(anno, nxg=None):
    """
    Calculates the arc choord length of an annotation object as a measure of
    the tortuosity of an annotation. The return value is 1 for a completely
    straight skeleton. It uses the two most distant end nodes in an
    annotation and divides it by the graph path length between them.
    :param anno:
    :param nxg:
    :return: float
    """

    if not nxg:
        nxg = su.annoToNXGraph(anno)

    # find end nodes
    e_nodes = list({k for k, v in nxg.degree().iteritems() if v == 1})
    # get euclidian distance between end nodes max away
    # this can be done more efficiently by computing a convex hull first,
    # but the naive implementation should be fast enough for now
    dists = []
    for pair in itertools.permutations(e_nodes, 2):
        dists.append((pair, pair[0].distance_scaled(pair[1])))
    dists = sorted(dists, key=lambda x: x[1])
    try:
        path_len = nx.shortest_path_length(nxg, source=dists[-1][0][0],
                                           target=dists[-1][0][1],
                                           weight='weight')
    except:
        # print('No path between nodes for tortuosity calculation for neuron %s' %
        #       anno.filename)
        return 0
    return dists[-1][1] / path_len