skeleton

`sleap_io.model.skeleton` ¶

Data model for skeletons.

Skeletons are collections of nodes and edges which describe the landmarks associated with a pose model. The edges represent the connections between them and may be used differently depending on the underlying pose model.

Classes:

Name	Description
`Edge`	A connection between two `Node` objects within a `Skeleton`.
`Node`	A landmark type within a `Skeleton`.
`Skeleton`	A description of a set of landmark types and connections between them.
`Symmetry`	A relationship between a pair of nodes denoting their left/right pairing.

Functions:

Name	Description
`is_node_or_index`	Check if an object is a `Node`, string name or integer index.

`Edge` ¶

A connection between two Node objects within a Skeleton.

This is a directed edge, representing the ordering of Nodes in the Skeleton tree.

Attributes:

Name	Type	Description
`source`	`Node`	The origin `Node`.
`destination`	`Node`	The destination `Node`.

Methods:

Name	Description
`__getitem__`	Return the source `Node` (`idx` is 0) or destination `Node` (`idx` is 1).

Source code in sleap_io/model/skeleton.py

@define(frozen=True)
class Edge:
    """A connection between two `Node` objects within a `Skeleton`.

    This is a directed edge, representing the ordering of `Node`s in the `Skeleton`
    tree.

    Attributes:
        source: The origin `Node`.
        destination: The destination `Node`.
    """

    source: Node
    destination: Node

    def __getitem__(self, idx) -> Node:
        """Return the source `Node` (`idx` is 0) or destination `Node` (`idx` is 1)."""
        if idx == 0:
            return self.source
        elif idx == 1:
            return self.destination
        else:
            raise IndexError("Edge only has 2 nodes (source and destination).")

`getitem(idx)` ¶

Return the source Node (idx is 0) or destination Node (idx is 1).

Source code in sleap_io/model/skeleton.py

def __getitem__(self, idx) -> Node:
    """Return the source `Node` (`idx` is 0) or destination `Node` (`idx` is 1)."""
    if idx == 0:
        return self.source
    elif idx == 1:
        return self.destination
    else:
        raise IndexError("Edge only has 2 nodes (source and destination).")

`Node` ¶

A landmark type within a Skeleton.

This typically corresponds to a unique landmark within a skeleton, such as the "left eye".

Attributes:

Name	Type	Description
`name`	`str`	Descriptive label for the landmark.

Source code in sleap_io/model/skeleton.py

@define(eq=False)
class Node:
    """A landmark type within a `Skeleton`.

    This typically corresponds to a unique landmark within a skeleton, such as the "left
    eye".

    Attributes:
        name: Descriptive label for the landmark.
    """

    name: str

`Skeleton` ¶

A description of a set of landmark types and connections between them.

Skeletons are represented by a directed graph composed of a set of Nodes (landmark types such as body parts) and Edges (connections between parts).

Attributes:

Name	Type	Description
`nodes`	`list[Node]`	A list of `Node`s. May be specified as a list of strings to create new nodes from their names.
`edges`	`list[Edge]`	A list of `Edge`s. May be specified as a list of 2-tuples of string names or integer indices of `nodes`. Each edge corresponds to a pair of source and destination nodes forming a directed edge.
`symmetries`	`list[Symmetry]`	A list of `Symmetry`s. Each symmetry corresponds to symmetric body parts, such as `"left eye", "right eye"`. This is used when applying flip (reflection) augmentation to images in order to appropriately swap the indices of symmetric landmarks.
`name`	`str \| None`	A descriptive name for the `Skeleton`.

Methods:

Name	Description
`__attrs_post_init__`	Ensure nodes are `Node`s, edges are `Edge`s, and `Node` map is updated.
`__contains__`	Check if a node is in the skeleton.
`__getitem__`	Return a `Node` when indexing by name or integer.
`__len__`	Return the number of nodes in the skeleton.
`__repr__`	Return a readable representation of the skeleton.
`add_edge`	Add an `Edge` to the skeleton.
`add_edges`	Add multiple `Edge`s to the skeleton.
`add_node`	Add a `Node` to the skeleton.
`add_nodes`	Add multiple `Node`s to the skeleton.
`add_symmetry`	Add a symmetry relationship to the skeleton.
`get_flipped_node_inds`	Returns node indices that should be switched when horizontally flipping.
`index`	Return the index of a node specified as a `Node` or string name.
`rebuild_cache`	Rebuild the node name/index to `Node` map caches.
`remove_node`	Remove a single node from the skeleton.
`remove_nodes`	Remove nodes from the skeleton.
`rename_node`	Rename a single node in the skeleton.
`rename_nodes`	Rename nodes in the skeleton.
`reorder_nodes`	Reorder nodes in the skeleton.
`require_node`	Return a `Node` object, handling indexing and adding missing nodes.

Attributes:

Name	Type	Description
`edge_inds`	`list[tuple[int, int]]`	Edges indices as a list of 2-tuples.
`edge_names`	`list[str, str]`	Edge names as a list of 2-tuples with string node names.
`node_names`	`list[str]`	Names of the nodes associated with this skeleton as a list of strings.
`symmetry_inds`	`list[tuple[int, int]]`	Symmetry indices as a list of 2-tuples.
`symmetry_names`	`list[str, str]`	Symmetry names as a list of 2-tuples with string node names.

Source code in sleap_io/model/skeleton.py

@define(eq=False)
class Skeleton:
    """A description of a set of landmark types and connections between them.

    Skeletons are represented by a directed graph composed of a set of `Node`s (landmark
    types such as body parts) and `Edge`s (connections between parts).

    Attributes:
        nodes: A list of `Node`s. May be specified as a list of strings to create new
            nodes from their names.
        edges: A list of `Edge`s. May be specified as a list of 2-tuples of string names
            or integer indices of `nodes`. Each edge corresponds to a pair of source and
            destination nodes forming a directed edge.
        symmetries: A list of `Symmetry`s. Each symmetry corresponds to symmetric body
            parts, such as `"left eye", "right eye"`. This is used when applying flip
            (reflection) augmentation to images in order to appropriately swap the
            indices of symmetric landmarks.
        name: A descriptive name for the `Skeleton`.
    """

    def _nodes_on_setattr(self, attr, new_nodes):
        """Callback to update caches when nodes are set."""
        self.rebuild_cache(nodes=new_nodes)
        return new_nodes

    nodes: list[Node] = field(
        factory=list,
        on_setattr=_nodes_on_setattr,
    )
    edges: list[Edge] = field(factory=list)
    symmetries: list[Symmetry] = field(factory=list)
    name: str | None = None
    _name_to_node_cache: dict[str, Node] = field(init=False, repr=False, eq=False)
    _node_to_ind_cache: dict[Node, int] = field(init=False, repr=False, eq=False)

    def __attrs_post_init__(self):
        """Ensure nodes are `Node`s, edges are `Edge`s, and `Node` map is updated."""
        self._convert_nodes()
        self._convert_edges()
        self.rebuild_cache()

    def _convert_nodes(self):
        """Convert nodes to `Node` objects if needed."""
        if isinstance(self.nodes, np.ndarray):
            object.__setattr__(self, "nodes", self.nodes.tolist())
        for i, node in enumerate(self.nodes):
            if type(node) == str:
                self.nodes[i] = Node(node)

    def _convert_edges(self):
        """Convert list of edge names or integers to `Edge` objects if needed."""
        if isinstance(self.edges, np.ndarray):
            self.edges = self.edges.tolist()
        node_names = self.node_names
        for i, edge in enumerate(self.edges):
            if type(edge) == Edge:
                continue
            src, dst = edge
            if type(src) == str:
                try:
                    src = node_names.index(src)
                except ValueError:
                    raise ValueError(
                        f"Node '{src}' specified in the edge list is not in the nodes."
                    )
            if type(src) == int or (
                np.isscalar(src) and np.issubdtype(src.dtype, np.integer)
            ):
                src = self.nodes[src]

            if type(dst) == str:
                try:
                    dst = node_names.index(dst)
                except ValueError:
                    raise ValueError(
                        f"Node '{dst}' specified in the edge list is not in the nodes."
                    )
            if type(dst) == int or (
                np.isscalar(dst) and np.issubdtype(dst.dtype, np.integer)
            ):
                dst = self.nodes[dst]

            self.edges[i] = Edge(src, dst)

    def rebuild_cache(self, nodes: list[Node] | None = None):
        """Rebuild the node name/index to `Node` map caches.

        Args:
            nodes: A list of `Node` objects to update the cache with. If not provided,
                the cache will be updated with the current nodes in the skeleton. If
                nodes are provided, the cache will be updated with the provided nodes,
                but the current nodes in the skeleton will not be updated. Default is
                `None`.

        Notes:
            This function should be called when nodes or node list is mutated to update
            the lookup caches for indexing nodes by name or `Node` object.

            This is done automatically when nodes are added or removed from the skeleton
            using the convenience methods in this class.

            This method only needs to be used when manually mutating nodes or the node
            list directly.
        """
        if nodes is None:
            nodes = self.nodes
        self._name_to_node_cache = {node.name: node for node in nodes}
        self._node_to_ind_cache = {node: i for i, node in enumerate(nodes)}

    @property
    def node_names(self) -> list[str]:
        """Names of the nodes associated with this skeleton as a list of strings."""
        return [node.name for node in self.nodes]

    @property
    def edge_inds(self) -> list[tuple[int, int]]:
        """Edges indices as a list of 2-tuples."""
        return [
            (self.nodes.index(edge.source), self.nodes.index(edge.destination))
            for edge in self.edges
        ]

    @property
    def edge_names(self) -> list[str, str]:
        """Edge names as a list of 2-tuples with string node names."""
        return [(edge.source.name, edge.destination.name) for edge in self.edges]

    @property
    def symmetry_inds(self) -> list[tuple[int, int]]:
        """Symmetry indices as a list of 2-tuples."""
        return [
            tuple(sorted((self.index(symmetry[0]), self.index(symmetry[1]))))
            for symmetry in self.symmetries
        ]

    @property
    def symmetry_names(self) -> list[str, str]:
        """Symmetry names as a list of 2-tuples with string node names."""
        return [
            (self.nodes[i].name, self.nodes[j].name) for (i, j) in self.symmetry_inds
        ]

    def get_flipped_node_inds(self) -> list[int]:
        """Returns node indices that should be switched when horizontally flipping.

        This is useful as a lookup table for flipping the landmark coordinates when
        doing data augmentation.

        Example:
            >>> skel = Skeleton(["A", "B_left", "B_right", "C", "D_left", "D_right"])
            >>> skel.add_symmetry("B_left", "B_right")
            >>> skel.add_symmetry("D_left", "D_right")
            >>> skel.flipped_node_inds
            [0, 2, 1, 3, 5, 4]
            >>> pose = np.array([[0, 0], [1, 1], [2, 2], [3, 3], [4, 4], [5, 5]])
            >>> pose[skel.flipped_node_inds]
            array([[0, 0],
                   [2, 2],
                   [1, 1],
                   [3, 3],
                   [5, 5],
                   [4, 4]])
        """
        flip_idx = np.arange(len(self.nodes))
        if len(self.symmetries) > 0:
            symmetry_inds = np.array(
                [(self.index(a), self.index(b)) for a, b in self.symmetries]
            )
            flip_idx[symmetry_inds[:, 0]] = symmetry_inds[:, 1]
            flip_idx[symmetry_inds[:, 1]] = symmetry_inds[:, 0]

        flip_idx = flip_idx.tolist()
        return flip_idx

    def __len__(self) -> int:
        """Return the number of nodes in the skeleton."""
        return len(self.nodes)

    def __repr__(self) -> str:
        """Return a readable representation of the skeleton."""
        nodes = ", ".join([f'"{node}"' for node in self.node_names])
        return "Skeleton(" f"nodes=[{nodes}], " f"edges={self.edge_inds}" ")"

    def index(self, node: Node | str) -> int:
        """Return the index of a node specified as a `Node` or string name."""
        if type(node) == str:
            return self.index(self._name_to_node_cache[node])
        elif type(node) == Node:
            return self._node_to_ind_cache[node]
        else:
            raise IndexError(f"Invalid indexing argument for skeleton: {node}")

    def __getitem__(self, idx: NodeOrIndex) -> Node:
        """Return a `Node` when indexing by name or integer."""
        if type(idx) == int:
            return self.nodes[idx]
        elif type(idx) == str:
            return self._name_to_node_cache[idx]
        else:
            raise IndexError(f"Invalid indexing argument for skeleton: {idx}")

    def __contains__(self, node: NodeOrIndex) -> bool:
        """Check if a node is in the skeleton."""
        if type(node) == str:
            return node in self._name_to_node_cache
        elif type(node) == Node:
            return node in self.nodes
        elif type(node) == int:
            return 0 <= node < len(self.nodes)
        else:
            raise ValueError(f"Invalid node type for skeleton: {node}")

    def add_node(self, node: Node | str):
        """Add a `Node` to the skeleton.

        Args:
            node: A `Node` object or a string name to create a new node.

        Raises:
            ValueError: If the node already exists in the skeleton or if the node is
                not specified as a `Node` or string.
        """
        if node in self:
            raise ValueError(f"Node '{node}' already exists in the skeleton.")

        if type(node) == str:
            node = Node(node)

        if type(node) != Node:
            raise ValueError(f"Invalid node type: {node} ({type(node)})")

        self.nodes.append(node)

        # Atomic update of the cache.
        self._name_to_node_cache[node.name] = node
        self._node_to_ind_cache[node] = len(self.nodes) - 1

    def add_nodes(self, nodes: list[Node | str]):
        """Add multiple `Node`s to the skeleton.

        Args:
            nodes: A list of `Node` objects or string names to create new nodes.
        """
        for node in nodes:
            self.add_node(node)

    def require_node(self, node: NodeOrIndex, add_missing: bool = True) -> Node:
        """Return a `Node` object, handling indexing and adding missing nodes.

        Args:
            node: A `Node` object, name or index.
            add_missing: If `True`, missing nodes will be added to the skeleton. If
                `False`, an error will be raised if the node is not found. Default is
                `True`.

        Returns:
            The `Node` object.

        Raises:
            IndexError: If the node is not found in the skeleton and `add_missing` is
                `False`.
        """
        if node not in self:
            if add_missing:
                self.add_node(node)
            else:
                raise IndexError(f"Node '{node}' not found in the skeleton.")

        if type(node) == Node:
            return node

        return self[node]

    def add_edge(
        self,
        src: NodeOrIndex | Edge | tuple[NodeOrIndex, NodeOrIndex],
        dst: NodeOrIndex | None = None,
    ):
        """Add an `Edge` to the skeleton.

        Args:
            src: The source node specified as a `Node`, name or index.
            dst: The destination node specified as a `Node`, name or index.
        """
        edge = None
        if type(src) == tuple:
            src, dst = src

        if is_node_or_index(src):
            if not is_node_or_index(dst):
                raise ValueError("Destination node must be specified.")

            src = self.require_node(src)
            dst = self.require_node(dst)
            edge = Edge(src, dst)

        if type(src) == Edge:
            edge = src

        if edge not in self.edges:
            self.edges.append(edge)

    def add_edges(self, edges: list[Edge | tuple[NodeOrIndex, NodeOrIndex]]):
        """Add multiple `Edge`s to the skeleton.

        Args:
            edges: A list of `Edge` objects or 2-tuples of source and destination nodes.
        """
        for edge in edges:
            self.add_edge(edge)

    def add_symmetry(
        self, node1: Symmetry | NodeOrIndex = None, node2: NodeOrIndex | None = None
    ):
        """Add a symmetry relationship to the skeleton.

        Args:
            node1: The first node specified as a `Node`, name or index. If a `Symmetry`
                object is provided, it will be added directly to the skeleton.
            node2: The second node specified as a `Node`, name or index.
        """
        symmetry = None
        if type(node1) == Symmetry:
            symmetry = node1
            node1, node2 = symmetry

        node1 = self.require_node(node1)
        node2 = self.require_node(node2)

        if symmetry is None:
            symmetry = Symmetry({node1, node2})

        if symmetry not in self.symmetries:
            self.symmetries.append(symmetry)

    def rename_nodes(self, name_map: dict[NodeOrIndex, str] | list[str]):
        """Rename nodes in the skeleton.

        Args:
            name_map: A dictionary mapping old node names to new node names. Keys can be
                specified as `Node` objects, integer indices, or string names. Values
                must be specified as string names.

                If a list of strings is provided of the same length as the current
                nodes, the nodes will be renamed to the names in the list in order.

        Raises:
            ValueError: If the new node names exist in the skeleton or if the old node
                names are not found in the skeleton.

        Notes:
            This method should always be used when renaming nodes in the skeleton as it
            handles updating the lookup caches necessary for indexing nodes by name.

            After renaming, instances using this skeleton **do NOT need to be updated**
            as the nodes are stored by reference in the skeleton, so changes are
            reflected automatically.

        Example:
            >>> skel = Skeleton(["A", "B", "C"], edges=[("A", "B"), ("B", "C")])
            >>> skel.rename_nodes({"A": "X", "B": "Y", "C": "Z"})
            >>> skel.node_names
            ["X", "Y", "Z"]
            >>> skel.rename_nodes(["a", "b", "c"])
            >>> skel.node_names
            ["a", "b", "c"]
        """
        if type(name_map) == list:
            if len(name_map) != len(self.nodes):
                raise ValueError(
                    "List of new node names must be the same length as the current "
                    "nodes."
                )
            name_map = {node: name for node, name in zip(self.nodes, name_map)}

        for old_name, new_name in name_map.items():
            if type(old_name) == Node:
                old_name = old_name.name
            if type(old_name) == int:
                old_name = self.nodes[old_name].name

            if old_name not in self._name_to_node_cache:
                raise ValueError(f"Node '{old_name}' not found in the skeleton.")
            if new_name in self._name_to_node_cache:
                raise ValueError(f"Node '{new_name}' already exists in the skeleton.")

            node = self._name_to_node_cache[old_name]
            node.name = new_name
            self._name_to_node_cache[new_name] = node
            del self._name_to_node_cache[old_name]

    def rename_node(self, old_name: NodeOrIndex, new_name: str):
        """Rename a single node in the skeleton.

        Args:
            old_name: The name of the node to rename. Can also be specified as an
                integer index or `Node` object.
            new_name: The new name for the node.
        """
        self.rename_nodes({old_name: new_name})

    def remove_nodes(self, nodes: list[NodeOrIndex]):
        """Remove nodes from the skeleton.

        Args:
            nodes: A list of node names, indices, or `Node` objects to remove.

        Notes:
            This method handles updating the lookup caches necessary for indexing nodes
            by name.

            Any edges and symmetries that are connected to the removed nodes will also
            be removed.

        Warning:
            **This method does NOT update instances** that use this skeleton to reflect
            changes.

            It is recommended to use the `Labels.remove_nodes()` method which will
            update all contained to reflect the changes made to the skeleton.

            To manually update instances after this method is called, call
            `instance.update_nodes()` on each instance that uses this skeleton.
        """
        # Standardize input and make a pre-mutation copy before keys are changed.
        rm_node_objs = [self.require_node(node, add_missing=False) for node in nodes]

        # Remove nodes from the skeleton.
        for node in rm_node_objs:
            self.nodes.remove(node)
            del self._name_to_node_cache[node.name]

        # Remove edges connected to the removed nodes.
        self.edges = [
            edge
            for edge in self.edges
            if edge.source not in rm_node_objs and edge.destination not in rm_node_objs
        ]

        # Remove symmetries connected to the removed nodes.
        self.symmetries = [
            symmetry
            for symmetry in self.symmetries
            if symmetry.nodes.isdisjoint(rm_node_objs)
        ]

        # Update node index map.
        self.rebuild_cache()

    def remove_node(self, node: NodeOrIndex):
        """Remove a single node from the skeleton.

        Args:
            node: The node to remove. Can be specified as a string name, integer index,
                or `Node` object.

        Notes:
            This method handles updating the lookup caches necessary for indexing nodes
            by name.

            Any edges and symmetries that are connected to the removed node will also be
            removed.

        Warning:
            **This method does NOT update instances** that use this skeleton to reflect
            changes.

            It is recommended to use the `Labels.remove_nodes()` method which will
            update all contained instances to reflect the changes made to the skeleton.

            To manually update instances after this method is called, call
            `Instance.update_skeleton()` on each instance that uses this skeleton.
        """
        self.remove_nodes([node])

    def reorder_nodes(self, new_order: list[NodeOrIndex]):
        """Reorder nodes in the skeleton.

        Args:
            new_order: A list of node names, indices, or `Node` objects specifying the
                new order of the nodes.

        Raises:
            ValueError: If the new order of nodes is not the same length as the current
                nodes.

        Notes:
            This method handles updating the lookup caches necessary for indexing nodes
            by name.

        Warning:
            After reordering, instances using this skeleton do not need to be updated as
            the nodes are stored by reference in the skeleton.

            However, the order that points are stored in the instances will not be
            updated to match the new order of the nodes in the skeleton. This should not
            matter unless the ordering of the keys in the `Instance.points` dictionary
            is used instead of relying on the skeleton node order.

            To make sure these are aligned, it is recommended to use the
            `Labels.reorder_nodes()` method which will update all contained instances to
            reflect the changes made to the skeleton.

            To manually update instances after this method is called, call
            `Instance.update_skeleton()` on each instance that uses this skeleton.
        """
        if len(new_order) != len(self.nodes):
            raise ValueError(
                "New order of nodes must be the same length as the current nodes."
            )

        new_nodes = [self.require_node(node, add_missing=False) for node in new_order]
        self.nodes = new_nodes

`edge_inds: list[tuple[int, int]]` `property` ¶

Edges indices as a list of 2-tuples.

`edge_names: list[str, str]` `property` ¶

Edge names as a list of 2-tuples with string node names.

`node_names: list[str]` `property` ¶

Names of the nodes associated with this skeleton as a list of strings.

`symmetry_inds: list[tuple[int, int]]` `property` ¶

Symmetry indices as a list of 2-tuples.

`symmetry_names: list[str, str]` `property` ¶

Symmetry names as a list of 2-tuples with string node names.

`__attrs_post_init__()` ¶

Ensure nodes are Nodes, edges are Edges, and Node map is updated.

Source code in sleap_io/model/skeleton.py

def __attrs_post_init__(self):
    """Ensure nodes are `Node`s, edges are `Edge`s, and `Node` map is updated."""
    self._convert_nodes()
    self._convert_edges()
    self.rebuild_cache()

`contains(node)` ¶

Check if a node is in the skeleton.

Source code in sleap_io/model/skeleton.py

def __contains__(self, node: NodeOrIndex) -> bool:
    """Check if a node is in the skeleton."""
    if type(node) == str:
        return node in self._name_to_node_cache
    elif type(node) == Node:
        return node in self.nodes
    elif type(node) == int:
        return 0 <= node < len(self.nodes)
    else:
        raise ValueError(f"Invalid node type for skeleton: {node}")

`getitem(idx)` ¶

Return a Node when indexing by name or integer.

Source code in sleap_io/model/skeleton.py

def __getitem__(self, idx: NodeOrIndex) -> Node:
    """Return a `Node` when indexing by name or integer."""
    if type(idx) == int:
        return self.nodes[idx]
    elif type(idx) == str:
        return self._name_to_node_cache[idx]
    else:
        raise IndexError(f"Invalid indexing argument for skeleton: {idx}")

`len()` ¶

Return the number of nodes in the skeleton.

Source code in sleap_io/model/skeleton.py

def __len__(self) -> int:
    """Return the number of nodes in the skeleton."""
    return len(self.nodes)

`repr()` ¶

Return a readable representation of the skeleton.

Source code in sleap_io/model/skeleton.py

def __repr__(self) -> str:
    """Return a readable representation of the skeleton."""
    nodes = ", ".join([f'"{node}"' for node in self.node_names])
    return "Skeleton(" f"nodes=[{nodes}], " f"edges={self.edge_inds}" ")"

`add_edge(src, dst=None)` ¶

Add an Edge to the skeleton.

Parameters:

Name	Type	Description	Default
`src`	`NodeOrIndex \| Edge \| tuple[NodeOrIndex, NodeOrIndex]`	The source node specified as a `Node`, name or index.	required
`dst`	`NodeOrIndex \| None`	The destination node specified as a `Node`, name or index.	`None`

Source code in sleap_io/model/skeleton.py

def add_edge(
    self,
    src: NodeOrIndex | Edge | tuple[NodeOrIndex, NodeOrIndex],
    dst: NodeOrIndex | None = None,
):
    """Add an `Edge` to the skeleton.

    Args:
        src: The source node specified as a `Node`, name or index.
        dst: The destination node specified as a `Node`, name or index.
    """
    edge = None
    if type(src) == tuple:
        src, dst = src

    if is_node_or_index(src):
        if not is_node_or_index(dst):
            raise ValueError("Destination node must be specified.")

        src = self.require_node(src)
        dst = self.require_node(dst)
        edge = Edge(src, dst)

    if type(src) == Edge:
        edge = src

    if edge not in self.edges:
        self.edges.append(edge)

`add_edges(edges)` ¶

Add multiple Edges to the skeleton.

Parameters:

Name	Type	Description	Default
`edges`	`list[Edge \| tuple[NodeOrIndex, NodeOrIndex]]`	A list of `Edge` objects or 2-tuples of source and destination nodes.	required

Source code in sleap_io/model/skeleton.py

def add_edges(self, edges: list[Edge | tuple[NodeOrIndex, NodeOrIndex]]):
    """Add multiple `Edge`s to the skeleton.

    Args:
        edges: A list of `Edge` objects or 2-tuples of source and destination nodes.
    """
    for edge in edges:
        self.add_edge(edge)

`add_node(node)` ¶

Add a Node to the skeleton.

Parameters:

Name	Type	Description	Default
`node`	`Node \| str`	A `Node` object or a string name to create a new node.	required

Raises:

Type	Description
`ValueError`	If the node already exists in the skeleton or if the node is not specified as a `Node` or string.

Source code in sleap_io/model/skeleton.py

def add_node(self, node: Node | str):
    """Add a `Node` to the skeleton.

    Args:
        node: A `Node` object or a string name to create a new node.

    Raises:
        ValueError: If the node already exists in the skeleton or if the node is
            not specified as a `Node` or string.
    """
    if node in self:
        raise ValueError(f"Node '{node}' already exists in the skeleton.")

    if type(node) == str:
        node = Node(node)

    if type(node) != Node:
        raise ValueError(f"Invalid node type: {node} ({type(node)})")

    self.nodes.append(node)

    # Atomic update of the cache.
    self._name_to_node_cache[node.name] = node
    self._node_to_ind_cache[node] = len(self.nodes) - 1

`add_nodes(nodes)` ¶

Add multiple Nodes to the skeleton.

Parameters:

Name	Type	Description	Default
`nodes`	`list[Node \| str]`	A list of `Node` objects or string names to create new nodes.	required

Source code in sleap_io/model/skeleton.py

def add_nodes(self, nodes: list[Node | str]):
    """Add multiple `Node`s to the skeleton.

    Args:
        nodes: A list of `Node` objects or string names to create new nodes.
    """
    for node in nodes:
        self.add_node(node)

`add_symmetry(node1=None, node2=None)` ¶

Add a symmetry relationship to the skeleton.

Parameters:

Name	Type	Description	Default
`node1`	`Symmetry \| NodeOrIndex`	The first node specified as a `Node`, name or index. If a `Symmetry` object is provided, it will be added directly to the skeleton.	`None`
`node2`	`NodeOrIndex \| None`	The second node specified as a `Node`, name or index.	`None`

Source code in sleap_io/model/skeleton.py

def add_symmetry(
    self, node1: Symmetry | NodeOrIndex = None, node2: NodeOrIndex | None = None
):
    """Add a symmetry relationship to the skeleton.

    Args:
        node1: The first node specified as a `Node`, name or index. If a `Symmetry`
            object is provided, it will be added directly to the skeleton.
        node2: The second node specified as a `Node`, name or index.
    """
    symmetry = None
    if type(node1) == Symmetry:
        symmetry = node1
        node1, node2 = symmetry

    node1 = self.require_node(node1)
    node2 = self.require_node(node2)

    if symmetry is None:
        symmetry = Symmetry({node1, node2})

    if symmetry not in self.symmetries:
        self.symmetries.append(symmetry)

`get_flipped_node_inds()` ¶

Returns node indices that should be switched when horizontally flipping.

This is useful as a lookup table for flipping the landmark coordinates when doing data augmentation.

Example

skel = Skeleton(["A", "B_left", "B_right", "C", "D_left", "D_right"]) skel.add_symmetry("B_left", "B_right") skel.add_symmetry("D_left", "D_right") skel.flipped_node_inds [0, 2, 1, 3, 5, 4] pose = np.array([[0, 0], [1, 1], [2, 2], [3, 3], [4, 4], [5, 5]]) pose[skel.flipped_node_inds] array([[0, 0], [2, 2], [1, 1], [3, 3], [5, 5], [4, 4]])

Source code in sleap_io/model/skeleton.py

def get_flipped_node_inds(self) -> list[int]:
    """Returns node indices that should be switched when horizontally flipping.

    This is useful as a lookup table for flipping the landmark coordinates when
    doing data augmentation.

    Example:
        >>> skel = Skeleton(["A", "B_left", "B_right", "C", "D_left", "D_right"])
        >>> skel.add_symmetry("B_left", "B_right")
        >>> skel.add_symmetry("D_left", "D_right")
        >>> skel.flipped_node_inds
        [0, 2, 1, 3, 5, 4]
        >>> pose = np.array([[0, 0], [1, 1], [2, 2], [3, 3], [4, 4], [5, 5]])
        >>> pose[skel.flipped_node_inds]
        array([[0, 0],
               [2, 2],
               [1, 1],
               [3, 3],
               [5, 5],
               [4, 4]])
    """
    flip_idx = np.arange(len(self.nodes))
    if len(self.symmetries) > 0:
        symmetry_inds = np.array(
            [(self.index(a), self.index(b)) for a, b in self.symmetries]
        )
        flip_idx[symmetry_inds[:, 0]] = symmetry_inds[:, 1]
        flip_idx[symmetry_inds[:, 1]] = symmetry_inds[:, 0]

    flip_idx = flip_idx.tolist()
    return flip_idx

`index(node)` ¶

Return the index of a node specified as a Node or string name.

Source code in sleap_io/model/skeleton.py

def index(self, node: Node | str) -> int:
    """Return the index of a node specified as a `Node` or string name."""
    if type(node) == str:
        return self.index(self._name_to_node_cache[node])
    elif type(node) == Node:
        return self._node_to_ind_cache[node]
    else:
        raise IndexError(f"Invalid indexing argument for skeleton: {node}")

`rebuild_cache(nodes=None)` ¶

Rebuild the node name/index to Node map caches.

Parameters:

Name	Type	Description	Default
`nodes`	`list[Node] \| None`	A list of `Node` objects to update the cache with. If not provided, the cache will be updated with the current nodes in the skeleton. If nodes are provided, the cache will be updated with the provided nodes, but the current nodes in the skeleton will not be updated. Default is `None`.	`None`

Notes

This function should be called when nodes or node list is mutated to update the lookup caches for indexing nodes by name or Node object.

This is done automatically when nodes are added or removed from the skeleton using the convenience methods in this class.

This method only needs to be used when manually mutating nodes or the node list directly.

Source code in sleap_io/model/skeleton.py

def rebuild_cache(self, nodes: list[Node] | None = None):
    """Rebuild the node name/index to `Node` map caches.

    Args:
        nodes: A list of `Node` objects to update the cache with. If not provided,
            the cache will be updated with the current nodes in the skeleton. If
            nodes are provided, the cache will be updated with the provided nodes,
            but the current nodes in the skeleton will not be updated. Default is
            `None`.

    Notes:
        This function should be called when nodes or node list is mutated to update
        the lookup caches for indexing nodes by name or `Node` object.

        This is done automatically when nodes are added or removed from the skeleton
        using the convenience methods in this class.

        This method only needs to be used when manually mutating nodes or the node
        list directly.
    """
    if nodes is None:
        nodes = self.nodes
    self._name_to_node_cache = {node.name: node for node in nodes}
    self._node_to_ind_cache = {node: i for i, node in enumerate(nodes)}

`remove_node(node)` ¶

Remove a single node from the skeleton.

Parameters:

Name	Type	Description	Default
`node`	`NodeOrIndex`	The node to remove. Can be specified as a string name, integer index, or `Node` object.	required

Notes

This method handles updating the lookup caches necessary for indexing nodes by name.

Any edges and symmetries that are connected to the removed node will also be removed.

Warning

This method does NOT update instances that use this skeleton to reflect changes.

It is recommended to use the Labels.remove_nodes() method which will update all contained instances to reflect the changes made to the skeleton.

To manually update instances after this method is called, call Instance.update_skeleton() on each instance that uses this skeleton.

Source code in sleap_io/model/skeleton.py

def remove_node(self, node: NodeOrIndex):
    """Remove a single node from the skeleton.

    Args:
        node: The node to remove. Can be specified as a string name, integer index,
            or `Node` object.

    Notes:
        This method handles updating the lookup caches necessary for indexing nodes
        by name.

        Any edges and symmetries that are connected to the removed node will also be
        removed.

    Warning:
        **This method does NOT update instances** that use this skeleton to reflect
        changes.

        It is recommended to use the `Labels.remove_nodes()` method which will
        update all contained instances to reflect the changes made to the skeleton.

        To manually update instances after this method is called, call
        `Instance.update_skeleton()` on each instance that uses this skeleton.
    """
    self.remove_nodes([node])

`remove_nodes(nodes)` ¶

Remove nodes from the skeleton.

Parameters:

Name	Type	Description	Default
`nodes`	`list[NodeOrIndex]`	A list of node names, indices, or `Node` objects to remove.	required

Notes

This method handles updating the lookup caches necessary for indexing nodes by name.

Any edges and symmetries that are connected to the removed nodes will also be removed.

Warning

This method does NOT update instances that use this skeleton to reflect changes.

It is recommended to use the Labels.remove_nodes() method which will update all contained to reflect the changes made to the skeleton.

To manually update instances after this method is called, call instance.update_nodes() on each instance that uses this skeleton.

Source code in sleap_io/model/skeleton.py

def remove_nodes(self, nodes: list[NodeOrIndex]):
    """Remove nodes from the skeleton.

    Args:
        nodes: A list of node names, indices, or `Node` objects to remove.

    Notes:
        This method handles updating the lookup caches necessary for indexing nodes
        by name.

        Any edges and symmetries that are connected to the removed nodes will also
        be removed.

    Warning:
        **This method does NOT update instances** that use this skeleton to reflect
        changes.

        It is recommended to use the `Labels.remove_nodes()` method which will
        update all contained to reflect the changes made to the skeleton.

        To manually update instances after this method is called, call
        `instance.update_nodes()` on each instance that uses this skeleton.
    """
    # Standardize input and make a pre-mutation copy before keys are changed.
    rm_node_objs = [self.require_node(node, add_missing=False) for node in nodes]

    # Remove nodes from the skeleton.
    for node in rm_node_objs:
        self.nodes.remove(node)
        del self._name_to_node_cache[node.name]

    # Remove edges connected to the removed nodes.
    self.edges = [
        edge
        for edge in self.edges
        if edge.source not in rm_node_objs and edge.destination not in rm_node_objs
    ]

    # Remove symmetries connected to the removed nodes.
    self.symmetries = [
        symmetry
        for symmetry in self.symmetries
        if symmetry.nodes.isdisjoint(rm_node_objs)
    ]

    # Update node index map.
    self.rebuild_cache()

`rename_node(old_name, new_name)` ¶

Rename a single node in the skeleton.

Parameters:

Name	Type	Description	Default
`old_name`	`NodeOrIndex`	The name of the node to rename. Can also be specified as an integer index or `Node` object.	required
`new_name`	`str`	The new name for the node.	required

Source code in sleap_io/model/skeleton.py

def rename_node(self, old_name: NodeOrIndex, new_name: str):
    """Rename a single node in the skeleton.

    Args:
        old_name: The name of the node to rename. Can also be specified as an
            integer index or `Node` object.
        new_name: The new name for the node.
    """
    self.rename_nodes({old_name: new_name})

`rename_nodes(name_map)` ¶

Rename nodes in the skeleton.

Parameters:

Name	Type	Description	Default
`name_map`	`dict[NodeOrIndex, str] \| list[str]`	A dictionary mapping old node names to new node names. Keys can be specified as `Node` objects, integer indices, or string names. Values must be specified as string names. If a list of strings is provided of the same length as the current nodes, the nodes will be renamed to the names in the list in order.	required

Raises:

Type	Description
`ValueError`	If the new node names exist in the skeleton or if the old node names are not found in the skeleton.

Notes

This method should always be used when renaming nodes in the skeleton as it handles updating the lookup caches necessary for indexing nodes by name.

After renaming, instances using this skeleton do NOT need to be updated as the nodes are stored by reference in the skeleton, so changes are reflected automatically.

Example

skel = Skeleton(["A", "B", "C"], edges=[("A", "B"), ("B", "C")]) skel.rename_nodes({"A": "X", "B": "Y", "C": "Z"}) skel.node_names ["X", "Y", "Z"] skel.rename_nodes(["a", "b", "c"]) skel.node_names ["a", "b", "c"]

Source code in sleap_io/model/skeleton.py

def rename_nodes(self, name_map: dict[NodeOrIndex, str] | list[str]):
    """Rename nodes in the skeleton.

    Args:
        name_map: A dictionary mapping old node names to new node names. Keys can be
            specified as `Node` objects, integer indices, or string names. Values
            must be specified as string names.

            If a list of strings is provided of the same length as the current
            nodes, the nodes will be renamed to the names in the list in order.

    Raises:
        ValueError: If the new node names exist in the skeleton or if the old node
            names are not found in the skeleton.

    Notes:
        This method should always be used when renaming nodes in the skeleton as it
        handles updating the lookup caches necessary for indexing nodes by name.

        After renaming, instances using this skeleton **do NOT need to be updated**
        as the nodes are stored by reference in the skeleton, so changes are
        reflected automatically.

    Example:
        >>> skel = Skeleton(["A", "B", "C"], edges=[("A", "B"), ("B", "C")])
        >>> skel.rename_nodes({"A": "X", "B": "Y", "C": "Z"})
        >>> skel.node_names
        ["X", "Y", "Z"]
        >>> skel.rename_nodes(["a", "b", "c"])
        >>> skel.node_names
        ["a", "b", "c"]
    """
    if type(name_map) == list:
        if len(name_map) != len(self.nodes):
            raise ValueError(
                "List of new node names must be the same length as the current "
                "nodes."
            )
        name_map = {node: name for node, name in zip(self.nodes, name_map)}

    for old_name, new_name in name_map.items():
        if type(old_name) == Node:
            old_name = old_name.name
        if type(old_name) == int:
            old_name = self.nodes[old_name].name

        if old_name not in self._name_to_node_cache:
            raise ValueError(f"Node '{old_name}' not found in the skeleton.")
        if new_name in self._name_to_node_cache:
            raise ValueError(f"Node '{new_name}' already exists in the skeleton.")

        node = self._name_to_node_cache[old_name]
        node.name = new_name
        self._name_to_node_cache[new_name] = node
        del self._name_to_node_cache[old_name]

`reorder_nodes(new_order)` ¶

Reorder nodes in the skeleton.

Parameters:

Name	Type	Description	Default
`new_order`	`list[NodeOrIndex]`	A list of node names, indices, or `Node` objects specifying the new order of the nodes.	required

Raises:

Type	Description
`ValueError`	If the new order of nodes is not the same length as the current nodes.

Notes

This method handles updating the lookup caches necessary for indexing nodes by name.

Warning

After reordering, instances using this skeleton do not need to be updated as the nodes are stored by reference in the skeleton.

However, the order that points are stored in the instances will not be updated to match the new order of the nodes in the skeleton. This should not matter unless the ordering of the keys in the Instance.points dictionary is used instead of relying on the skeleton node order.

To make sure these are aligned, it is recommended to use the Labels.reorder_nodes() method which will update all contained instances to reflect the changes made to the skeleton.

To manually update instances after this method is called, call Instance.update_skeleton() on each instance that uses this skeleton.

Source code in sleap_io/model/skeleton.py

def reorder_nodes(self, new_order: list[NodeOrIndex]):
    """Reorder nodes in the skeleton.

    Args:
        new_order: A list of node names, indices, or `Node` objects specifying the
            new order of the nodes.

    Raises:
        ValueError: If the new order of nodes is not the same length as the current
            nodes.

    Notes:
        This method handles updating the lookup caches necessary for indexing nodes
        by name.

    Warning:
        After reordering, instances using this skeleton do not need to be updated as
        the nodes are stored by reference in the skeleton.

        However, the order that points are stored in the instances will not be
        updated to match the new order of the nodes in the skeleton. This should not
        matter unless the ordering of the keys in the `Instance.points` dictionary
        is used instead of relying on the skeleton node order.

        To make sure these are aligned, it is recommended to use the
        `Labels.reorder_nodes()` method which will update all contained instances to
        reflect the changes made to the skeleton.

        To manually update instances after this method is called, call
        `Instance.update_skeleton()` on each instance that uses this skeleton.
    """
    if len(new_order) != len(self.nodes):
        raise ValueError(
            "New order of nodes must be the same length as the current nodes."
        )

    new_nodes = [self.require_node(node, add_missing=False) for node in new_order]
    self.nodes = new_nodes

`require_node(node, add_missing=True)` ¶

Return a Node object, handling indexing and adding missing nodes.

Parameters:

Name	Type	Description	Default
`node`	`NodeOrIndex`	A `Node` object, name or index.	required
`add_missing`	`bool`	If `True`, missing nodes will be added to the skeleton. If `False`, an error will be raised if the node is not found. Default is `True`.	`True`

Returns:

Type	Description
`Node`	The `Node` object.

Raises:

Type	Description
`IndexError`	If the node is not found in the skeleton and `add_missing` is `False`.

Source code in sleap_io/model/skeleton.py

def require_node(self, node: NodeOrIndex, add_missing: bool = True) -> Node:
    """Return a `Node` object, handling indexing and adding missing nodes.

    Args:
        node: A `Node` object, name or index.
        add_missing: If `True`, missing nodes will be added to the skeleton. If
            `False`, an error will be raised if the node is not found. Default is
            `True`.

    Returns:
        The `Node` object.

    Raises:
        IndexError: If the node is not found in the skeleton and `add_missing` is
            `False`.
    """
    if node not in self:
        if add_missing:
            self.add_node(node)
        else:
            raise IndexError(f"Node '{node}' not found in the skeleton.")

    if type(node) == Node:
        return node

    return self[node]

`Symmetry` ¶

A relationship between a pair of nodes denoting their left/right pairing.

Attributes:

Name	Type	Description
`nodes`	`set[Node]`	A set of two `Node`s.

Methods:

Name	Description
`__getitem__`	Return the first node.
`__iter__`	Iterate over the symmetric nodes.

Source code in sleap_io/model/skeleton.py

@define
class Symmetry:
    """A relationship between a pair of nodes denoting their left/right pairing.

    Attributes:
        nodes: A set of two `Node`s.
    """

    nodes: set[Node] = field(converter=set, validator=lambda _, __, val: len(val) == 2)

    def __iter__(self):
        """Iterate over the symmetric nodes."""
        return iter(self.nodes)

    def __getitem__(self, idx) -> Node:
        """Return the first node."""
        for i, node in enumerate(self.nodes):
            if i == idx:
                return node

`getitem(idx)` ¶

Return the first node.

Source code in sleap_io/model/skeleton.py

def __getitem__(self, idx) -> Node:
    """Return the first node."""
    for i, node in enumerate(self.nodes):
        if i == idx:
            return node

`iter()` ¶

Iterate over the symmetric nodes.

Source code in sleap_io/model/skeleton.py

def __iter__(self):
    """Iterate over the symmetric nodes."""
    return iter(self.nodes)

`is_node_or_index(obj)` ¶

Check if an object is a Node, string name or integer index.

Parameters:

Name	Type	Description	Default
`obj`	`Any`	The object to check.	required

Notes

This is mainly for backwards compatibility with Python versions < 3.10 where generics can't be used with isinstance. In newer Python, this is equivalent to isinstance(obj, NodeOrIndex).

Source code in sleap_io/model/skeleton.py

def is_node_or_index(obj: typing.Any) -> bool:
    """Check if an object is a `Node`, string name or integer index.

    Args:
        obj: The object to check.

    Notes:
        This is mainly for backwards compatibility with Python versions < 3.10 where
        generics can't be used with `isinstance`. In newer Python, this is equivalent
        to `isinstance(obj, NodeOrIndex)`.
    """
    return isinstance(obj, (Node, str, int))

skeleton

sleap_io.model.skeleton ¶

Edge ¶

__getitem__(idx) ¶

Node ¶

Skeleton ¶

edge_inds: list[tuple[int, int]] property ¶

edge_names: list[str, str] property ¶

node_names: list[str] property ¶

symmetry_inds: list[tuple[int, int]] property ¶

symmetry_names: list[str, str] property ¶

__attrs_post_init__() ¶

__contains__(node) ¶

__getitem__(idx) ¶

__len__() ¶

__repr__() ¶

add_edge(src, dst=None) ¶

add_edges(edges) ¶

add_node(node) ¶

add_nodes(nodes) ¶

add_symmetry(node1=None, node2=None) ¶

get_flipped_node_inds() ¶

index(node) ¶

rebuild_cache(nodes=None) ¶

remove_node(node) ¶

remove_nodes(nodes) ¶

rename_node(old_name, new_name) ¶

rename_nodes(name_map) ¶

reorder_nodes(new_order) ¶

require_node(node, add_missing=True) ¶

Symmetry ¶

__getitem__(idx) ¶

__iter__() ¶

is_node_or_index(obj) ¶

`sleap_io.model.skeleton` ¶

`Edge` ¶

`getitem(idx)` ¶

`Node` ¶

`Skeleton` ¶

`edge_inds: list[tuple[int, int]]` `property` ¶

`edge_names: list[str, str]` `property` ¶

`node_names: list[str]` `property` ¶

`symmetry_inds: list[tuple[int, int]]` `property` ¶

`symmetry_names: list[str, str]` `property` ¶

`__attrs_post_init__()` ¶

`contains(node)` ¶

`getitem(idx)` ¶

`len()` ¶

`repr()` ¶

`add_edge(src, dst=None)` ¶

`add_edges(edges)` ¶

`add_node(node)` ¶

`add_nodes(nodes)` ¶

`add_symmetry(node1=None, node2=None)` ¶

`get_flipped_node_inds()` ¶

`index(node)` ¶

`rebuild_cache(nodes=None)` ¶

`remove_node(node)` ¶

`remove_nodes(nodes)` ¶

`rename_node(old_name, new_name)` ¶

`rename_nodes(name_map)` ¶

`reorder_nodes(new_order)` ¶

`require_node(node, add_missing=True)` ¶

`Symmetry` ¶

`getitem(idx)` ¶

`iter()` ¶

`is_node_or_index(obj)` ¶