sleap.skeleton

Implementation of skeleton data structure and API.

This module implements and API for creating animal skeletons. The goal is to provide a common interface for defining the parts of the animal, their connection to each other, and needed meta-data.

class sleap.skeleton.EdgeType(value)[source]

The skeleton graph can store different types of edges to represent different things. All edges must specify one or more of the following types:

  • BODY - these edges represent connections between parts or landmarks.

  • SYMMETRY - these edges represent symmetrical relationships between parts (e.g. left and right arms)

class sleap.skeleton.Node(name: str, weight: float = 1.0)[source]

The class Node represents a potential skeleton node. (But note that nodes can exist without being part of a skeleton.)

classmethod as_node(node: Union[str, Node])sleap.skeleton.Node[source]

Convert given node to Node object (if not already).

static from_names(name_list: str) → List[sleap.skeleton.Node][source]

Convert list of node names to list of nodes objects.

matches(other: sleap.skeleton.Node) → bool[source]

Check whether all attributes match between two nodes.

Parameters

other – The Node to compare to this one.

Returns

True if all attributes match, False otherwise.

class sleap.skeleton.Skeleton(name: str = None)[source]

The main object for representing animal skeletons.

The skeleton represents the constituent parts of the animal whose pose is being estimated.

An index variable used to give skeletons a default name that should be unique across all skeletons.

add_edge(source: str, destination: str)[source]

Add an edge between two nodes.

Parameters
  • source – The name of the source node.

  • destination – The name of the destination node.

Raises

ValueError – If source or destination nodes cannot be found, or if edge already exists between those nodes.

Returns

None.

add_node(name: str)[source]

Add a node representing an animal part to the skeleton.

Parameters

name – The name of the node to add to the skeleton. This name must be unique within the skeleton.

Raises

ValueError – If name is not unique.

Returns

None

add_nodes(name_list: List[str])[source]

Add a list of nodes representing animal parts to the skeleton.

Parameters

name_list – List of strings representing the nodes.

Returns

None

add_symmetry(node1: str, node2: str)[source]

Specify that two parts (nodes) in skeleton are symmetrical.

Certain parts of an animal body can be related as symmetrical parts in a pair. For example, left and right hands of a person.

Parameters
  • node1 – The name of the first part in the symmetric pair

  • node2 – The name of the second part in the symmetric pair

Raises

ValueError – If node1 and node2 match, or if there is already a symmetry between them.

Returns

None

clear_edges()[source]

Deletes all edges in skeleton.

delete_edge(source: str, destination: str)[source]

Delete an edge between two nodes.

Parameters
  • 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

None

delete_node(name: str)[source]

Remove a node from the skeleton.

The method removes a node from the skeleton and any edge that is connected to it.

Parameters

name – The name of the node to remove

Raises

ValueError – If node cannot be found.

Returns

None

delete_symmetry(node1: Union[str, Node], node2: Union[str, Node])[source]

Deletes a previously established symmetry between two nodes.

Parameters
  • node1 – One node (by Node object or name) in symmetric pair.

  • node2 – Other node in symmetric pair.

Raises

ValueError – If there’s no symmetry between node1 and node2.

Returns

None

property edge_inds

Get a list of edges as node indices.

Returns

A list of (src_node_ind, dst_node_ind), where indices are subscripts into the Skeleton.nodes list.

property edge_names

Get a list of edge name tuples.

Returns

list of (src_node.name, dst_node.name)

edge_to_index(source: Union[str, Node], destination: Union[str, Node])[source]

Returns the index of edge from source to destination.

property edges

Get a list of edge tuples.

Returns

list of (src_node, dst_node)

property edges_full

Get a list of edge tuples with keys and attributes.

Returns

list of (src_node, dst_node, key, attributes)

find_node(name: Union[str, Node])sleap.skeleton.Node[source]

Find node in skeleton by name of node.

Parameters

name – The name of the Node (or a Node)

Returns

Node, or None if no match found

static find_unique_nodes(skeletons: List[Skeleton]) → List[sleap.skeleton.Node][source]

Find all unique nodes from a list of skeletons.

Parameters

skeletons – The list of skeletons.

Returns

A list of unique Node objects.

classmethod from_dict(d: Dict, node_to_idx: Dict[sleap.skeleton.Node, int] = None)sleap.skeleton.Skeleton[source]

Create skeleton from dict; used for loading from JSON.

Parameters
  • d – the dict from which to deserialize

  • node_to_idx – optional dict which maps Node`sto index in some list. This is used when saving :class:`Labels`where we want to serialize the :class:`Nodes outside the Skeleton object. If given, then we replace each Node with specified index before converting Skeleton. Otherwise, we convert Node objects with the rest of the Skeleton.

Returns

Skeleton.

classmethod from_json(json_str: str, idx_to_node: Dict[int, sleap.skeleton.Node] = None)sleap.skeleton.Skeleton[source]

Instantiate Skeleton from JSON string.

Parameters
  • json_str – The JSON encoded Skeleton.

  • idx_to_node – optional dict which maps an int (indexing a list of Node objects) to the already deserialized Node. This should invert node_to_idx we used when saving. If not given, then we’ll assume each Node was left in the Skeleton when it was saved.

Returns

An instance of the Skeleton object decoded from the JSON.

classmethod from_names_and_edge_inds(node_names: List[str], edge_inds: List[Tuple[int, int]] = None)sleap.skeleton.Skeleton[source]

Create skeleton from a list of node names and edge indices.

Parameters
  • node_names – List of strings defining the nodes.

  • edge_inds – List of tuples in the form (src_node_ind, dst_node_ind). If not specified, the resulting skeleton will have no edges.

Returns

The instantiated skeleton.

get_symmetry(node: Union[str, Node]) → Optional[sleap.skeleton.Node][source]

Returns the node symmetric with the specified node.

Parameters

node – Node (by Node object or name) to query.

Raises

ValueError – If node has more than one symmetry.

Returns

The symmetric Node, None if no symmetry.

get_symmetry_name(node: Union[str, Node]) → Optional[str][source]

Returns the name of the node symmetric with the specified node.

Parameters

node – Node (by Node object or name) to query.

Returns

Name of symmetric node, None if no symmetry.

property graph

Returns subgraph of BODY edges for skeleton.

property graph_symmetry

Returns subgraph of symmetric edges for skeleton.

has_edge(source_name: str, dest_name: str) → bool[source]

Check whether the skeleton has an edge.

Parameters
  • source_name – The name of the source node for the edge.

  • dest_name – The name of the destination node for the edge.

Returns

True is yes, False if no.

has_node(name: str) → bool[source]

Check whether the skeleton has a node.

Parameters

name – The name of the node to check for.

Returns

True for yes, False for no.

has_nodes(names: Iterable[str]) → bool[source]

Check whether the skeleton has a list of nodes.

Parameters

names – The list names of the nodes to check for.

Returns

True for yes, False for no.

classmethod load_all_hdf5(file: Union[str, h5py._hl.files.File], return_dict: bool = False) → Union[List[sleap.skeleton.Skeleton], Dict[str, sleap.skeleton.Skeleton]][source]

Load all skeletons found in the HDF5 file.

Parameters
  • file – The file name or open h5.File

  • return_dict – Whether the the return value should be a dict where the keys are skeleton names and values the corresponding skeleton. If False, then method will return just a list of the skeletons.

Returns

The skeleton instances stored in the HDF5 file. Either in List or Dict form.

classmethod load_hdf5(file: Union[str, h5py._hl.files.File], name: str) → List[sleap.skeleton.Skeleton][source]

Load a specific skeleton (by name) from the HDF5 file.

Parameters
  • file – The file name or open h5.File

  • name – The name of the skeleton.

Returns

The specified Skeleton instance stored in the HDF5 file.

classmethod load_json(filename: str, idx_to_node: Dict[int, sleap.skeleton.Node] = None)sleap.skeleton.Skeleton[source]

Load a skeleton from a JSON file.

This method will load the Skeleton from JSON file saved with; save_json()

Parameters
  • filename – The file that contains the JSON.

  • idx_to_node – optional dict which maps an int (indexing a list of Node objects) to the already deserialized Node. This should invert node_to_idx we used when saving. If not given, then we’ll assume each Node was left in the Skeleton when it was saved.

Returns

The Skeleton object stored in the JSON filename.

classmethod load_mat(filename: str)sleap.skeleton.Skeleton[source]

Load the skeleton from a Matlab MAT file.

This is to support backwards compatibility with old LEAP MATLAB code and datasets.

Parameters

filename – The name of the skeleton file

Returns

An instance of the skeleton.

static make_cattr(idx_to_node: Dict[int, sleap.skeleton.Node] = None) → cattr.converters.Converter[source]

Make cattr.Convert() for Skeleton.

Make a cattr.Converter() that registers structure/unstructure hooks for Skeleton objects to handle serialization of skeletons.

Parameters

idx_to_node – A dict that maps node index to Node objects.

Returns

A cattr.Converter() instance for skeleton serialization and deserialization.

matches(other: sleap.skeleton.Skeleton) → bool[source]

Compare this Skeleton to another, ignoring skeleton name and the identities of the Node objects in each graph.

Parameters

other – The other skeleton.

Returns

True if match, False otherwise.

property name

Get the name of the skeleton.

Returns

A string representing the name of the skeleton.

property node_names

Get a list of node names.

Returns

A list of node names.

node_to_index(node: Union[str, Node]) → int[source]

Return the index of the node, accepts either Node or name.

Parameters

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.

property nodes

Get a list of :class:`Node`s.

Returns

A list of :class:`Node`s

relabel_node(old_name: str, new_name: str)[source]

Relabel a single node to a new name.

Parameters
  • old_name – The old name of the node.

  • new_name – The new name of the node.

Returns

None

relabel_nodes(mapping: Dict[str, str])[source]

Relabel the nodes of the skeleton.

Parameters

mapping – A dictionary with the old labels as keys and new labels as values. A partial mapping is allowed.

Raises

ValueError – If node already present with one of the new names.

Returns

None

classmethod rename_skeleton(skeleton: sleap.skeleton.Skeleton, name: str)sleap.skeleton.Skeleton[source]

Make copy of skeleton with new name.

This property is immutable because it is used to hash skeletons. If you want to rename a Skeleton you must use this class method.

>>> new_skeleton = Skeleton.rename_skeleton(
>>>     skeleton=old_skeleton, name="New Name")
Parameters
  • skeleton – The skeleton to copy.

  • name – The name of the new skeleton.

Returns

A new deep copied skeleton with the changed name.

classmethod save_all_hdf5(file: Union[str, h5py._hl.files.File], skeletons: List[Skeleton])[source]

Convenience method to save a list of skeletons to HDF5 file.

Skeletons are saved as attributes of a /skeleton group in the file.

Parameters
  • file – The filename or the open h5.File object.

  • skeletons – The list of skeletons to save.

Raises

ValueError – If multiple skeletons have the same name.

Returns

None

save_hdf5(file: Union[str, h5py._hl.files.File])[source]

Wrapper for HDF5 saving which takes either filename or h5.File.

Parameters

file – can be filename (string) or h5.File object

Returns

None

save_json(filename: str, node_to_idx: Optional[Dict[sleap.skeleton.Node, int]] = None)[source]

Save the Skeleton as JSON file.

Output the complete skeleton to a file in JSON format.

Parameters
  • filename – The filename to save the JSON to.

  • node_to_idx – optional dict which maps Node`sto index in some list. This is used when saving :class:`Labels`where we want to serialize the :class:`Nodes outside the Skeleton object. If given, then we replace each Node with specified index before converting Skeleton. Otherwise, we convert Node objects with the rest of the Skeleton.

Returns

None

property symmetries

Get a list of all symmetries without duplicates.

Returns

list of (node1, node2)

property symmetries_full

Get a list of all symmetries with keys and attributes.

Note: The returned list will contain duplicates (node1, node2) and (node2, node1).

Returns

list of (node1, node2, key, attr)

static to_dict(obj: sleap.skeleton.Skeleton, node_to_idx: Optional[Dict[sleap.skeleton.Node, int]] = None) → Dict[source]

Convert skeleton to dict; used for saving as JSON.

Parameters
  • obj – the :object:`Skeleton` to convert

  • node_to_idx – optional dict which maps Node`sto index in some list. This is used when saving :class:`Labels`where we want to serialize the :class:`Nodes outside the Skeleton object. If given, then we replace each Node with specified index before converting Skeleton. Otherwise, we convert Node objects with the rest of the Skeleton.

Returns

dict with data from skeleton

to_json(node_to_idx: Optional[Dict[sleap.skeleton.Node, int]] = None) → str[source]

Convert the Skeleton to a JSON representation.

Parameters

node_to_idx – optional dict which maps Node`sto index in some list. This is used when saving :class:`Labels`where we want to serialize the :class:`Nodes outside the Skeleton object. If given, then we replace each Node with specified index before converting Skeleton. Otherwise, we convert Node objects with the rest of the Skeleton.

Returns

A string containing the JSON representation of the skeleton.