graph_extraction.py

# Copyright CNRS/Inria/UNS
# Contributor(s): Eric Debreuve (since 2019), Morgane Nadal (2020)
#
# eric.debreuve@cnrs.fr
#
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import re as re_
import numpy as np_

from brick.component.soma import soma_t
from brick.general.type import array_t
from typing import Tuple, Dict, Union, Any


def FindGraphsRootWithEdges(soma: soma_t, ext_nfo: Dict[str, Union[array_t, Any]]) -> dict:
    """
    Finds the soma roots of the graph extension.
    """
    # For a given soma, find the roots of the graphs
    root_nodes = {}

    # Finds the primary extensions
    primary_extension_uids = tuple(extension.uid for extension in soma.extensions)
    print(primary_extension_uids, '\nn = ', len(primary_extension_uids))

    # List of the degree 1 nodes of the graph
    for node1_id, node2_id, edge_nfo in soma.skl_graph.edges.data('as_edge_t'):
        if (soma.skl_graph.degree[node1_id] == 1) or (soma.skl_graph.degree[node2_id] == 1):

            # Find the pixels of the terminal extension
            sites = ext_nfo['lmp'][edge_nfo.sites]
            ext_uid = np_.unique(sites)[-1]
            # sites > 0 because ext_nfo['lmp'] do not contain the connexions

            # Save the root node candidates (one-degree nodes)
            if ext_uid in primary_extension_uids:
                if soma.skl_graph.degree[node1_id] == 1:
                    root_node = node1_id
                else:
                    root_node = node2_id

                # Get the node coordinates and extend them to the 26 neighboring voxels
                root_node_coor = GetNodesCoordinates((root_node,))[0]  # tuple('x-y-z') -> list[(x,y,z)]

                root_sites = set(
                    (root_node_coor[0] + i, root_node_coor[1] + j, root_node_coor[2] + k)
                    for i in (-1, 0, 1)
                    for j in (-1, 0, 1)
                    for k in (-1, 0, 1)
                    if i != 0 or j != 0 or k != 0)

                # Find the intersection between the extended root node candidate and the soma contour points
                intersections = set(soma.contour_points).intersection(root_sites)

                # if the graph root sites are included in the soma extensions sites (non-nul intersection):
                if len(intersections) > 0:
                    # Keep the info of the root node. Key = ext uid, Value = root node
                    root_nodes[ext_uid] = root_node
                        ## By construction, only one root node possible for an ext

    return root_nodes  # TODO: find out why there are less root points than extensions !!


def FindGraphsRootWithNodes(soma: soma_t) -> dict:
    """
    Find the roots of the {extension+connexion} graphs to be lined to the soma.
    Add a key "root" (bool) in the dict of nodes attributes.
    """

    node_degree_bool = tuple(degree == 1 for _, degree in soma.skl_graph.degree)
    node_coord = tuple(xyz for xyz, _ in soma.skl_graph.degree)

    root_nodes = {}

    # get the coordinates of the nodes (x,y,z)
    coordinates = GetNodesCoordinates(node_coord)

    # get a list with elements = (soma_uid, extension_uid, root coordinates)
    roots = GetListRoots(soma)

    # for each node in the graph, search among the degree 1 nodes the nodes that are roots (linked to soma)
    for node in range(len(coordinates)):
        if node_degree_bool[node]:
            # compare the coor with end points
            for ext_root in roots:
                if ext_root[1] == coordinates[node]:
                    root_nodes[ext_root[0]] = node_coord[node]

    return root_nodes


def GetListRoots(soma: soma_t) -> list:
    """
    Gives a list containing the following information for all somas: [soma id: int, extension id: int, root = (x,y,z): tuple]
    """
    roots = []
    for ext_id, ext_root in enumerate(soma.ext_roots):
        roots.append((soma.extensions[ext_id].uid, ext_root))
    return roots


def GetNodesCoordinates(node_coord: Tuple[str, ...]) -> list:
    """
    Input: nodes attributes -> Tuple('x1-y1-z1', 'x2-y2-z2', ...) .
    Output: coordinates -> List[Tuple(x1,y1,z1), Tuple(x2,y2,z2), ...]
    """
    coord = []
    for c in node_coord:
        coord.append(c)

    for node in range(len(node_coord)):
        coord_node = coord[node]
        pattern = '\d+'
        coord_node = re_.findall(pattern, coord_node)
        coor = []
        for i in range(3):
            coor.append(int(coord_node[i]))
        coor = tuple(coor)
        coord[node] = coor

    return coord