skeleton_utils

sleap.sleap_io_adaptors.skeleton_utils

Helper functions for sleap_io.Skeleton objects.

Functions:

Name	Description
cycles	Return a list of cycles in the skeleton.
delete_edge	Delete an edge between two nodes.
delete_symmetry	Delete symmetry for given node name.
edge_to_index	Return the index of edge from source to destination.
find_node	Find node in skeleton by name of node.
get_symmetry_node	Get symmetry node name for given node name.
in_degree_over_one	Return a list of nodes in the skeleton with in-degree over one.
is_arborescence	Return whether this skeleton graph forms an arborescence.
node_to_index	Return the index of the node, accepts either Node or name.
root_nodes	Return a list of root nodes in the skeleton.
to_graph	Return a graph representation of the skeleton.
to_subgraph_view	Return a view on the subgraph of body nodes and edges.

cycles(skeleton)

Return a list of cycles in the skeleton.

Source code in sleap/sleap_io_adaptors/skeleton_utils.py

def cycles(skeleton: Skeleton) -> List[List[Node]]:
    """Return a list of cycles in the skeleton."""
    graph = to_graph(skeleton)
    subgraph = to_subgraph_view(graph)
    return list(nx.algorithms.simple_cycles(subgraph))

delete_edge(skeleton, source, destination)

Delete an edge between two nodes. Args: skeleton: The skeleton to delete the edge from. source: The name of the source node. destination: The name of the destination node. Raises: ValueError: If skeleton does not have either source node, destination node, or edge between them. Returns: Skeleton: The skeleton with the edge deleted.

Source code in sleap/sleap_io_adaptors/skeleton_utils.py

def delete_edge(skeleton: Skeleton, source: str, destination: str):
    """Delete an edge between two nodes.
    Args:
        skeleton: The skeleton to delete the edge from.
        source: The name of the source node.
        destination: The name of the destination node.
    Raises:
        ValueError: If skeleton does not have either source node,
            destination node, or edge between them.
    Returns:
        Skeleton: The skeleton with the edge deleted.
    """
    if isinstance(source, Node):
        source = source.name

    if isinstance(destination, Node):
        destination = destination.name

    if source is None or source not in skeleton.node_names:
        raise ValueError("Skeleton does not have source node named ({})".format(source))

    if destination is None or destination not in skeleton.node_names:
        raise ValueError(
            "Skeleton does not have destination node named ({})".format(destination)
        )

    for edge_idx, edge in enumerate(skeleton.edges):
        if edge.source.name == source and edge.destination.name == destination:
            skeleton.edges.pop(edge_idx)
            return skeleton

    raise ValueError(
        "Skeleton has no edge between ({}) and ({}).".format(source, destination)
    )

delete_symmetry(skeleton, node1, node2)

Delete symmetry for given node name.

Source code in sleap/sleap_io_adaptors/skeleton_utils.py

def delete_symmetry(skeleton: Skeleton, node1: str, node2: str):
    """Delete symmetry for given node name."""
    for symmetry_idx, symmetry in enumerate(skeleton.symmetries):
        node_names = [n.name for n in symmetry.nodes]
        if node1 in node_names and node2 in node_names:
            skeleton.symmetries.pop(symmetry_idx)
    return skeleton

edge_to_index(skeleton, source, destination)

Return the index of edge from source to destination.

Source code in sleap/sleap_io_adaptors/skeleton_utils.py

def edge_to_index(
    skeleton: Skeleton, source: NodeOrIndex, destination: NodeOrIndex
) -> int:
    """Return the index of edge from source to destination."""
    source = source.name if isinstance(source, Node) else source
    destination = destination.name if isinstance(destination, Node) else destination
    for edge_idx, edge in enumerate(skeleton.edges):
        if edge.source.name == source and edge.destination.name == destination:
            return edge_idx
    return -1

find_node(skeleton, node_name)

Find node in skeleton by name of node.

Source code in sleap/sleap_io_adaptors/skeleton_utils.py

def find_node(skeleton: Skeleton, node_name: str) -> Node:
    """Find node in skeleton by name of node."""
    for node in skeleton.nodes:
        if node.name == node_name:
            return node
    return None

get_symmetry_node(skeleton, node_name)

Get symmetry node name for given node name.

Source code in sleap/sleap_io_adaptors/skeleton_utils.py

def get_symmetry_node(skeleton: Skeleton, node_name: str) -> str:
    """Get symmetry node name for given node name."""
    for symmetry in skeleton.symmetries:
        if node_name in [n.name for n in symmetry.nodes]:
            # Return the other node in the symmetry pair
            return next((n.name for n in symmetry.nodes if n.name != node_name), None)
    return None

in_degree_over_one(skeleton)

Return a list of nodes in the skeleton with in-degree over one.

Source code in sleap/sleap_io_adaptors/skeleton_utils.py

def in_degree_over_one(skeleton: Skeleton) -> List[Node]:
    """Return a list of nodes in the skeleton with in-degree over one."""
    graph = to_graph(skeleton)
    subgroup = to_subgraph_view(graph)
    return [node for node, in_degree in subgroup.in_degree if in_degree > 1]

is_arborescence(skeleton)

Return whether this skeleton graph forms an arborescence.

Source code in sleap/sleap_io_adaptors/skeleton_utils.py

def is_arborescence(skeleton: Skeleton) -> bool:
    """Return whether this skeleton graph forms an arborescence."""
    graph = to_graph(skeleton)
    subgroup = to_subgraph_view(graph)
    return nx.algorithms.tree.recognition.is_arborescence(subgroup)

node_to_index(skeleton, node)

Return the index of the node, accepts either Node or name. Args: node: The name of the node or the Node object. Raises: ValueError if node cannot be found in skeleton. Returns: The index of the node in the graph.

Source code in sleap/sleap_io_adaptors/skeleton_utils.py

def node_to_index(skeleton: Skeleton, node: NodeOrIndex) -> int:
    """Return the index of the node, accepts either `Node` or name.
    Args:
        node: The name of the node or the Node object.
    Raises:
        ValueError if node cannot be found in skeleton.
    Returns:
        The index of the node in the graph.
    """
    node_list = skeleton.node_names
    if isinstance(node, Node):
        node = node.name
    if node in node_list:
        return node_list.index(node)
    else:
        raise ValueError(f"Node {node} not found in skeleton.")

root_nodes(skeleton)

Return a list of root nodes in the skeleton.

Source code in sleap/sleap_io_adaptors/skeleton_utils.py

def root_nodes(skeleton: Skeleton) -> List[Node]:
    """Return a list of root nodes in the skeleton."""
    graph = to_graph(skeleton)
    return [node for node, in_degree in graph.in_degree if in_degree == 0]

to_graph(skeleton)

Return a graph representation of the skeleton.

Source code in sleap/sleap_io_adaptors/skeleton_utils.py

def to_graph(skeleton: Skeleton):
    """Return a graph representation of the skeleton."""
    graph = nx.MultiDiGraph(name=skeleton.name, num_edges_inserted=0)

    # Add nodes
    for node in skeleton.nodes:
        graph.add_node(node.name)

    # Add edges
    for edge in skeleton.edges:
        graph.add_edge(
            edge.source.name,
            edge.destination.name,
            type=1,  # BODY
            edge_insert_idx=graph.graph["num_edges_inserted"],
        )
        graph.graph["num_edges_inserted"] += 1

    return graph

to_subgraph_view(graph)

Return a view on the subgraph of body nodes and edges.

Source code in sleap/sleap_io_adaptors/skeleton_utils.py

def to_subgraph_view(graph: nx.MultiDiGraph):
    """Return a view on the subgraph of body nodes and edges."""

    def edge_filter_fn(src, dst, edge_key):
        edge_data = graph.get_edge_data(src, dst, edge_key)
        return edge_data["type"] == 1  # BODY

    return nx.subgraph_view(graph, filter_edge=edge_filter_fn)