skeleton
sleap_io.io.skeleton
¶
This module handles I/O operations for standalone skeleton JSON files.
Classes:
| Name | Description |
|---|---|
SkeletonDecoder |
Decode skeleton data from jsonpickle-encoded format. |
SkeletonEncoder |
Encode skeleton data to jsonpickle format. |
SkeletonSLPDecoder |
Decode skeleton data from SLP format. |
SkeletonSLPEncoder |
Encode skeleton data to SLP format. |
SkeletonYAMLDecoder |
Decode skeleton data from simplified YAML format. |
SkeletonYAMLEncoder |
Encode skeleton data to simplified YAML format. |
SkeletonDecoder
¶
Decode skeleton data from jsonpickle-encoded format.
This decoder handles the custom jsonpickle format used by SLEAP for standalone skeleton JSON files, which differs from the format used within .slp files.
Methods:
| Name | Description |
|---|---|
__init__ |
Initialize the decoder. |
decode |
Decode skeleton(s) from JSON data. |
Source code in sleap_io/io/skeleton.py
class SkeletonDecoder:
"""Decode skeleton data from jsonpickle-encoded format.
This decoder handles the custom jsonpickle format used by SLEAP for
standalone skeleton JSON files, which differs from the format used
within .slp files.
"""
def __init__(self):
"""Initialize the decoder."""
self._id_to_object: Dict[int, Any] = {}
def decode(self, data: Union[str, Dict]) -> Union[Skeleton, List[Skeleton]]:
"""Decode skeleton(s) from JSON data.
Args:
data: JSON string or pre-parsed dictionary containing skeleton data.
Returns:
A single Skeleton or list of Skeletons depending on input format.
"""
if isinstance(data, str):
data = json.loads(data)
# Reset object cache for each decode operation
self._id_to_object = {}
# Check if this is a list of skeletons or a single skeleton
if isinstance(data, list):
return [self._decode_skeleton(skel_data) for skel_data in data]
else:
return self._decode_skeleton(data)
def _decode_skeleton(self, data: Dict) -> Skeleton:
"""Decode a single skeleton from dictionary data.
Args:
data: Dictionary containing skeleton data in jsonpickle format.
Returns:
A Skeleton object.
"""
# First, scan all links to build complete node and py/id mappings
all_nodes = {} # node name -> Node object
py_id_first_seen = {} # py/id -> node name (first occurrence)
# Track order of node definitions for py/id assignment
node_definition_order = []
for link in data.get("links", []):
# Check source
if isinstance(link["source"], dict):
if "py/object" in link["source"]:
# This is a node definition
node = self._decode_node(link["source"])
if node.name not in all_nodes:
all_nodes[node.name] = node
node_definition_order.append(node.name)
elif "py/id" in link["source"]:
# This is a reference - track it
py_id = link["source"]["py/id"]
# We'll resolve this later
# Check target
if isinstance(link["target"], dict):
if "py/object" in link["target"]:
# This is a node definition
node = self._decode_node(link["target"])
if node.name not in all_nodes:
all_nodes[node.name] = node
node_definition_order.append(node.name)
elif "py/id" in link["target"]:
# This is a reference
py_id = link["target"]["py/id"]
# Build py/id mappings based on order of definition
# The pattern seems to be that nodes are assigned py/ids in order of first appearance
py_id_to_node_name = {}
for i, node_name in enumerate(node_definition_order):
# py/ids seem to start at 1 and increment, sometimes skipping numbers
if i == 0:
py_id_to_node_name[1] = node_name
elif i == 1:
py_id_to_node_name[2] = node_name # eyeL
elif i == 2:
py_id_to_node_name[4] = node_name # eyeR (skips 3)
elif i == 3:
py_id_to_node_name[5] = node_name # thorax
else:
# Continue pattern: 6, 7, 8, 9, 10, 11, 12, 13, 14
py_id_to_node_name[i + 3] = node_name
# Update cache
for py_id, node_name in py_id_to_node_name.items():
if node_name in all_nodes:
self._id_to_object[py_id] = all_nodes[node_name]
# Build final nodes list based on the "nodes" section order
nodes = []
py_id_to_index = {}
for i, node_ref in enumerate(data.get("nodes", [])):
if isinstance(node_ref["id"], dict) and "py/id" in node_ref["id"]:
py_id = node_ref["id"]["py/id"]
py_id_to_index[py_id] = i
# Add corresponding node
if (
py_id in py_id_to_node_name
and py_id_to_node_name[py_id] in all_nodes
):
nodes.append(all_nodes[py_id_to_node_name[py_id]])
# Now decode edges using the established mappings
edges = []
symmetries = []
seen_symmetries = set() # Track symmetries to avoid duplicates
for link in data.get("links", []):
edge_type = self._get_edge_type(link.get("type", {}))
# Resolve source and target
source_node = self._resolve_node_reference(
link["source"], all_nodes, py_id_to_node_name
)
target_node = self._resolve_node_reference(
link["target"], all_nodes, py_id_to_node_name
)
if edge_type == 1 or edge_type == 3: # Regular edge (1 or 3)
edges.append(Edge(source=source_node, destination=target_node))
elif edge_type == 2 or edge_type == 15: # Symmetry (2 or 15)
# Create a unique key for this symmetry pair (order-independent)
sym_key = tuple(sorted([source_node.name, target_node.name]))
if sym_key not in seen_symmetries:
symmetries.append(Symmetry([source_node, target_node]))
seen_symmetries.add(sym_key)
# Get skeleton name
name = data.get("graph", {}).get("name", "Skeleton")
return Skeleton(nodes=nodes, edges=edges, symmetries=symmetries, name=name)
def _decode_node(self, data: Dict) -> Node:
"""Decode a node from jsonpickle format.
Args:
data: Dictionary containing node data.
Returns:
A Node object.
"""
if "py/state" in data:
state = data["py/state"]
# Handle both tuple and dict formats
if "py/tuple" in state:
# Tuple format: [name, weight]
name = state["py/tuple"][0]
# Note: weight is stored but not used in sleap-io Node objects
else:
# Dict format
name = state.get("name", "")
else:
# Direct format
name = data.get("name", "")
return Node(name=name)
def _resolve_node_reference(
self,
node_ref: Union[Dict, int],
all_nodes: Dict[str, Node],
py_id_to_node_name: Dict[int, str],
) -> Node:
"""Resolve a node reference to an actual Node object.
Args:
node_ref: Node reference (can be embedded object, py/id reference, or index).
all_nodes: Dictionary mapping node names to Node objects.
py_id_to_node_name: Mapping from py/id to node name.
Returns:
The resolved Node object.
"""
if isinstance(node_ref, dict):
if "py/object" in node_ref:
# Embedded node - decode and return
node = self._decode_node(node_ref)
if node.name in all_nodes:
return all_nodes[node.name]
else:
# Create new node if not found
return node
elif "py/id" in node_ref:
# Reference to existing object
py_id = node_ref["py/id"]
if py_id in self._id_to_object:
return self._id_to_object[py_id]
elif (
py_id in py_id_to_node_name
and py_id_to_node_name[py_id] in all_nodes
):
return all_nodes[py_id_to_node_name[py_id]]
raise ValueError(f"py/id {py_id} not found")
elif isinstance(node_ref, int):
# Direct index (used in SLP format, shouldn't happen in standalone)
raise ValueError(f"Direct index reference not supported: {node_ref}")
raise ValueError(f"Unknown node reference format: {node_ref}")
def _get_edge_type(self, type_data: Dict) -> int:
"""Extract edge type from jsonpickle format.
Args:
type_data: Dictionary containing edge type data.
Returns:
Integer edge type (1 for regular edge, 2 for symmetry).
"""
if "py/reduce" in type_data:
# Extract from py/reduce format
return type_data["py/reduce"][1]["py/tuple"][0]
elif "py/id" in type_data:
# Direct reference
return type_data["py/id"]
else:
# Default to regular edge
return 1
__init__()
¶
decode(data)
¶
Decode skeleton(s) from JSON data.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
data
|
Union[str, Dict]
|
JSON string or pre-parsed dictionary containing skeleton data. |
required |
Returns:
| Type | Description |
|---|---|
Union[Skeleton, List[Skeleton]]
|
A single Skeleton or list of Skeletons depending on input format. |
Source code in sleap_io/io/skeleton.py
def decode(self, data: Union[str, Dict]) -> Union[Skeleton, List[Skeleton]]:
"""Decode skeleton(s) from JSON data.
Args:
data: JSON string or pre-parsed dictionary containing skeleton data.
Returns:
A single Skeleton or list of Skeletons depending on input format.
"""
if isinstance(data, str):
data = json.loads(data)
# Reset object cache for each decode operation
self._id_to_object = {}
# Check if this is a list of skeletons or a single skeleton
if isinstance(data, list):
return [self._decode_skeleton(skel_data) for skel_data in data]
else:
return self._decode_skeleton(data)
SkeletonEncoder
¶
Encode skeleton data to jsonpickle format.
This encoder produces the jsonpickle format used by SLEAP for standalone skeleton JSON files, ensuring backward compatibility with existing files.
Methods:
| Name | Description |
|---|---|
__init__ |
Initialize the encoder. |
encode |
Encode skeleton(s) to JSON string. |
Source code in sleap_io/io/skeleton.py
class SkeletonEncoder:
"""Encode skeleton data to jsonpickle format.
This encoder produces the jsonpickle format used by SLEAP for standalone
skeleton JSON files, ensuring backward compatibility with existing files.
"""
def __init__(self):
"""Initialize the encoder."""
self._object_to_id: Dict[int, int] = {} # id(object) -> py/id
self._next_id = 1
def encode(self, skeletons: Union[Skeleton, List[Skeleton]]) -> str:
"""Encode skeleton(s) to JSON string.
Args:
skeletons: A single Skeleton or list of Skeletons to encode.
Returns:
JSON string in jsonpickle format.
"""
# Reset state for each encode operation
self._object_to_id = {}
self._next_id = 1
# Handle single skeleton or list
if isinstance(skeletons, Skeleton):
data = self._encode_skeleton(skeletons)
else:
data = [self._encode_skeleton(skel) for skel in skeletons]
# Sort dictionaries recursively for consistency
data = self._recursively_sort_dict(data)
return json.dumps(data, separators=(", ", ": "))
def _encode_skeleton(self, skeleton: Skeleton) -> Dict:
"""Encode a single skeleton to dictionary format.
Args:
skeleton: Skeleton object to encode.
Returns:
Dictionary in jsonpickle format.
"""
# Track nodes and their py/ids
node_to_py_id = {}
# Encode links (edges and symmetries)
links = []
# First, process edges to establish node references
for i, edge in enumerate(skeleton.edges):
# Encode edge
edge_dict = self._encode_edge(edge, i, edge_type=1)
links.append(edge_dict)
# Track node py/ids
if edge.source not in node_to_py_id:
node_to_py_id[edge.source] = self._get_or_create_py_id(edge.source)
if edge.destination not in node_to_py_id:
node_to_py_id[edge.destination] = self._get_or_create_py_id(
edge.destination
)
# Then process symmetries
for i, symmetry in enumerate(skeleton.symmetries):
# Encode symmetry
sym_dict = self._encode_symmetry(symmetry, edge_type=2)
links.append(sym_dict)
# Track node py/ids
for node in symmetry.nodes:
if node not in node_to_py_id:
node_to_py_id[node] = self._get_or_create_py_id(node)
# Ensure all skeleton nodes have py/ids
for node in skeleton.nodes:
if node not in node_to_py_id:
node_to_py_id[node] = self._get_or_create_py_id(node)
# Create nodes section with py/id references
nodes = []
for node in skeleton.nodes:
nodes.append({"id": {"py/id": node_to_py_id[node]}})
# Build final skeleton dict
return {
"directed": True,
"graph": {"name": skeleton.name, "num_edges_inserted": len(skeleton.edges)},
"links": links,
"multigraph": True,
"nodes": nodes,
}
def _encode_edge(self, edge: Edge, edge_idx: int, edge_type: int) -> Dict:
"""Encode an edge to jsonpickle format.
Args:
edge: Edge object to encode.
edge_idx: Index of this edge.
edge_type: Type of edge (1 for regular, 2 for symmetry).
Returns:
Dictionary representing the edge.
"""
# Encode edge type - first occurrence uses py/reduce, subsequent use py/id
# For backward compatibility, always use type 1 for regular edges
if edge_type == 1:
if not hasattr(self, "_edge_type_1_encoded"):
type_dict = {
"py/reduce": [
{"py/type": "sleap.skeleton.EdgeType"},
{"py/tuple": [1]},
]
}
self._edge_type_1_encoded = True
else:
type_dict = {"py/id": 1}
else:
if not hasattr(self, "_edge_type_2_encoded"):
type_dict = {
"py/reduce": [
{"py/type": "sleap.skeleton.EdgeType"},
{"py/tuple": [2]},
]
}
self._edge_type_2_encoded = True
else:
type_dict = {"py/id": 2}
return {
"edge_insert_idx": edge_idx,
"key": 0,
"source": self._encode_node(edge.source),
"target": self._encode_node(edge.destination),
"type": type_dict,
}
def _encode_symmetry(self, symmetry: Symmetry, edge_type: int) -> Dict:
"""Encode a symmetry to jsonpickle format.
Args:
symmetry: Symmetry object to encode.
edge_type: Type of edge (should be 2 for symmetry).
Returns:
Dictionary representing the symmetry.
"""
# Get source and target nodes (convert set to list for ordering)
nodes_list = list(symmetry.nodes)
source, target = nodes_list[0], nodes_list[1]
# Encode edge type
if not hasattr(self, "_edge_type_2_encoded"):
type_dict = {
"py/reduce": [{"py/type": "sleap.skeleton.EdgeType"}, {"py/tuple": [2]}]
}
self._edge_type_2_encoded = True
else:
type_dict = {"py/id": 2}
return {
"key": 0,
"source": self._encode_node(source),
"target": self._encode_node(target),
"type": type_dict,
}
def _encode_node(self, node: Node) -> Dict:
"""Encode a node to jsonpickle format.
Args:
node: Node object to encode.
Returns:
Dictionary with py/object and py/state.
"""
return {
"py/object": "sleap.skeleton.Node",
"py/state": {"py/tuple": [node.name, 1.0]}, # name, weight (always 1.0)
}
def _get_or_create_py_id(self, obj: Any) -> int:
"""Get or create a py/id for an object.
Args:
obj: Object to get/create ID for.
Returns:
The py/id integer.
"""
obj_id = id(obj)
if obj_id not in self._object_to_id:
self._object_to_id[obj_id] = self._next_id
self._next_id += 1
return self._object_to_id[obj_id]
def _recursively_sort_dict(self, obj: Any) -> Any:
"""Recursively sort dictionary keys for consistent output.
Args:
obj: Object to sort (dict, list, or other).
Returns:
Sorted version of the object.
"""
if isinstance(obj, dict):
# Sort keys and recursively sort values
return {k: self._recursively_sort_dict(v) for k, v in sorted(obj.items())}
elif isinstance(obj, list):
# Recursively sort list elements
return [self._recursively_sort_dict(item) for item in obj]
else:
# Return as-is for non-dict/list types
return obj
__init__()
¶
encode(skeletons)
¶
Encode skeleton(s) to JSON string.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
skeletons
|
Union[Skeleton, List[Skeleton]]
|
A single Skeleton or list of Skeletons to encode. |
required |
Returns:
| Type | Description |
|---|---|
str
|
JSON string in jsonpickle format. |
Source code in sleap_io/io/skeleton.py
def encode(self, skeletons: Union[Skeleton, List[Skeleton]]) -> str:
"""Encode skeleton(s) to JSON string.
Args:
skeletons: A single Skeleton or list of Skeletons to encode.
Returns:
JSON string in jsonpickle format.
"""
# Reset state for each encode operation
self._object_to_id = {}
self._next_id = 1
# Handle single skeleton or list
if isinstance(skeletons, Skeleton):
data = self._encode_skeleton(skeletons)
else:
data = [self._encode_skeleton(skel) for skel in skeletons]
# Sort dictionaries recursively for consistency
data = self._recursively_sort_dict(data)
return json.dumps(data, separators=(", ", ": "))
SkeletonSLPDecoder
¶
Decode skeleton data from SLP format.
This decoder handles the SLP format used within .slp files, which uses integer indices for node references instead of embedded node objects.
Methods:
| Name | Description |
|---|---|
decode_skeletons |
Decode skeletons from SLP metadata format. |
Source code in sleap_io/io/skeleton.py
class SkeletonSLPDecoder:
"""Decode skeleton data from SLP format.
This decoder handles the SLP format used within .slp files, which uses
integer indices for node references instead of embedded node objects.
"""
def decode_skeletons(self, metadata: dict, node_names: list[str]) -> list[Skeleton]:
"""Decode skeletons from SLP metadata format.
Args:
metadata: The metadata dict from an SLP file containing skeletons.
node_names: Global list of node names from the SLP file.
Returns:
List of Skeleton objects.
"""
skeleton_objects = []
for skel in metadata["skeletons"]:
# Parse out the cattr-based serialization stuff from the skeleton links.
edge_inds, symmetry_inds = [], []
for link in skel["links"]:
if "py/reduce" in link["type"]:
edge_type = link["type"]["py/reduce"][1]["py/tuple"][0]
else:
edge_type = link["type"]["py/id"]
if edge_type == 1: # 1 -> real edge, 2 -> symmetry edge
edge_inds.append((link["source"], link["target"]))
elif edge_type == 2:
symmetry_inds.append((link["source"], link["target"]))
# Re-index correctly.
skeleton_node_inds = [node["id"] for node in skel["nodes"]]
sorted_node_names = [node_names[i] for i in skeleton_node_inds]
# Create nodes.
nodes = []
for name in sorted_node_names:
nodes.append(Node(name=name))
# Create edges.
edge_inds = [
(skeleton_node_inds.index(s), skeleton_node_inds.index(d))
for s, d in edge_inds
]
edges = []
for edge in edge_inds:
edges.append(Edge(source=nodes[edge[0]], destination=nodes[edge[1]]))
# Create symmetries.
symmetry_inds = [
(skeleton_node_inds.index(s), skeleton_node_inds.index(d))
for s, d in symmetry_inds
]
symmetries = []
for symmetry in symmetry_inds:
symmetries.append(Symmetry([nodes[symmetry[0]], nodes[symmetry[1]]]))
# Create the full skeleton.
skel = Skeleton(
nodes=nodes,
edges=edges,
symmetries=symmetries,
name=skel["graph"]["name"],
)
skeleton_objects.append(skel)
return skeleton_objects
decode_skeletons(metadata, node_names)
¶
Decode skeletons from SLP metadata format.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
metadata
|
dict
|
The metadata dict from an SLP file containing skeletons. |
required |
node_names
|
list[str]
|
Global list of node names from the SLP file. |
required |
Returns:
| Type | Description |
|---|---|
list[Skeleton]
|
List of Skeleton objects. |
Source code in sleap_io/io/skeleton.py
def decode_skeletons(self, metadata: dict, node_names: list[str]) -> list[Skeleton]:
"""Decode skeletons from SLP metadata format.
Args:
metadata: The metadata dict from an SLP file containing skeletons.
node_names: Global list of node names from the SLP file.
Returns:
List of Skeleton objects.
"""
skeleton_objects = []
for skel in metadata["skeletons"]:
# Parse out the cattr-based serialization stuff from the skeleton links.
edge_inds, symmetry_inds = [], []
for link in skel["links"]:
if "py/reduce" in link["type"]:
edge_type = link["type"]["py/reduce"][1]["py/tuple"][0]
else:
edge_type = link["type"]["py/id"]
if edge_type == 1: # 1 -> real edge, 2 -> symmetry edge
edge_inds.append((link["source"], link["target"]))
elif edge_type == 2:
symmetry_inds.append((link["source"], link["target"]))
# Re-index correctly.
skeleton_node_inds = [node["id"] for node in skel["nodes"]]
sorted_node_names = [node_names[i] for i in skeleton_node_inds]
# Create nodes.
nodes = []
for name in sorted_node_names:
nodes.append(Node(name=name))
# Create edges.
edge_inds = [
(skeleton_node_inds.index(s), skeleton_node_inds.index(d))
for s, d in edge_inds
]
edges = []
for edge in edge_inds:
edges.append(Edge(source=nodes[edge[0]], destination=nodes[edge[1]]))
# Create symmetries.
symmetry_inds = [
(skeleton_node_inds.index(s), skeleton_node_inds.index(d))
for s, d in symmetry_inds
]
symmetries = []
for symmetry in symmetry_inds:
symmetries.append(Symmetry([nodes[symmetry[0]], nodes[symmetry[1]]]))
# Create the full skeleton.
skel = Skeleton(
nodes=nodes,
edges=edges,
symmetries=symmetries,
name=skel["graph"]["name"],
)
skeleton_objects.append(skel)
return skeleton_objects
SkeletonSLPEncoder
¶
Encode skeleton data to SLP format.
This encoder produces the SLP format used within .slp files, which uses integer indices for node references instead of embedded node objects.
Methods:
| Name | Description |
|---|---|
encode_skeletons |
Serialize a list of Skeleton objects to SLP format. |
Source code in sleap_io/io/skeleton.py
class SkeletonSLPEncoder:
"""Encode skeleton data to SLP format.
This encoder produces the SLP format used within .slp files, which uses
integer indices for node references instead of embedded node objects.
"""
def encode_skeletons(
self, skeletons: list[Skeleton]
) -> tuple[list[dict], list[dict]]:
"""Serialize a list of Skeleton objects to SLP format.
Args:
skeletons: A list of Skeleton objects.
Returns:
A tuple of (skeletons_dicts, nodes_dicts).
nodes_dicts is a list of dicts containing the nodes in all the skeletons.
skeletons_dicts is a list of dicts containing the skeletons.
"""
# Create global list of nodes with all nodes from all skeletons.
nodes_dicts = []
node_to_id = {}
for skeleton in skeletons:
for node in skeleton.nodes:
if node not in node_to_id:
node_to_id[node] = len(node_to_id)
nodes_dicts.append({"name": node.name, "weight": 1.0})
skeletons_dicts = []
for skeleton in skeletons:
# Build links dicts for normal edges.
edges_dicts = []
for edge_ind, edge in enumerate(skeleton.edges):
if edge_ind == 0:
edge_type = {
"py/reduce": [
{"py/type": "sleap.skeleton.EdgeType"},
{"py/tuple": [1]}, # 1 = real edge, 2 = symmetry edge
]
}
else:
edge_type = {"py/id": 1}
edges_dicts.append(
{
"edge_insert_idx": edge_ind,
"key": 0, # Always 0.
"source": node_to_id[edge.source],
"target": node_to_id[edge.destination],
"type": edge_type,
}
)
# Build links dicts for symmetry edges.
for symmetry_ind, symmetry in enumerate(skeleton.symmetries):
if symmetry_ind == 0:
edge_type = {
"py/reduce": [
{"py/type": "sleap.skeleton.EdgeType"},
{"py/tuple": [2]}, # 1 = real edge, 2 = symmetry edge
]
}
else:
edge_type = {"py/id": 2}
src, dst = tuple(symmetry.nodes)
edges_dicts.append(
{
"key": 0,
"source": node_to_id[src],
"target": node_to_id[dst],
"type": edge_type,
}
)
# Create skeleton dict.
skeletons_dicts.append(
{
"directed": True,
"graph": {
"name": skeleton.name,
"num_edges_inserted": len(skeleton.edges),
},
"links": edges_dicts,
"multigraph": True,
"nodes": [{"id": node_to_id[node]} for node in skeleton.nodes],
}
)
return skeletons_dicts, nodes_dicts
encode_skeletons(skeletons)
¶
Serialize a list of Skeleton objects to SLP format.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
skeletons
|
list[Skeleton]
|
A list of Skeleton objects. |
required |
Returns:
| Type | Description |
|---|---|
tuple[list[dict], list[dict]]
|
A tuple of (skeletons_dicts, nodes_dicts). nodes_dicts is a list of dicts containing the nodes in all the skeletons. skeletons_dicts is a list of dicts containing the skeletons. |
Source code in sleap_io/io/skeleton.py
def encode_skeletons(
self, skeletons: list[Skeleton]
) -> tuple[list[dict], list[dict]]:
"""Serialize a list of Skeleton objects to SLP format.
Args:
skeletons: A list of Skeleton objects.
Returns:
A tuple of (skeletons_dicts, nodes_dicts).
nodes_dicts is a list of dicts containing the nodes in all the skeletons.
skeletons_dicts is a list of dicts containing the skeletons.
"""
# Create global list of nodes with all nodes from all skeletons.
nodes_dicts = []
node_to_id = {}
for skeleton in skeletons:
for node in skeleton.nodes:
if node not in node_to_id:
node_to_id[node] = len(node_to_id)
nodes_dicts.append({"name": node.name, "weight": 1.0})
skeletons_dicts = []
for skeleton in skeletons:
# Build links dicts for normal edges.
edges_dicts = []
for edge_ind, edge in enumerate(skeleton.edges):
if edge_ind == 0:
edge_type = {
"py/reduce": [
{"py/type": "sleap.skeleton.EdgeType"},
{"py/tuple": [1]}, # 1 = real edge, 2 = symmetry edge
]
}
else:
edge_type = {"py/id": 1}
edges_dicts.append(
{
"edge_insert_idx": edge_ind,
"key": 0, # Always 0.
"source": node_to_id[edge.source],
"target": node_to_id[edge.destination],
"type": edge_type,
}
)
# Build links dicts for symmetry edges.
for symmetry_ind, symmetry in enumerate(skeleton.symmetries):
if symmetry_ind == 0:
edge_type = {
"py/reduce": [
{"py/type": "sleap.skeleton.EdgeType"},
{"py/tuple": [2]}, # 1 = real edge, 2 = symmetry edge
]
}
else:
edge_type = {"py/id": 2}
src, dst = tuple(symmetry.nodes)
edges_dicts.append(
{
"key": 0,
"source": node_to_id[src],
"target": node_to_id[dst],
"type": edge_type,
}
)
# Create skeleton dict.
skeletons_dicts.append(
{
"directed": True,
"graph": {
"name": skeleton.name,
"num_edges_inserted": len(skeleton.edges),
},
"links": edges_dicts,
"multigraph": True,
"nodes": [{"id": node_to_id[node]} for node in skeleton.nodes],
}
)
return skeletons_dicts, nodes_dicts
SkeletonYAMLDecoder
¶
Decode skeleton data from simplified YAML format.
This decoder handles a simplified YAML format that is more human-readable than the jsonpickle format.
Methods:
| Name | Description |
|---|---|
decode |
Decode skeleton(s) from YAML data. |
decode_dict |
Decode a single skeleton from a dictionary. |
Source code in sleap_io/io/skeleton.py
class SkeletonYAMLDecoder:
"""Decode skeleton data from simplified YAML format.
This decoder handles a simplified YAML format that is more human-readable
than the jsonpickle format.
"""
def decode(self, data: Union[str, Dict]) -> Union[Skeleton, List[Skeleton]]:
"""Decode skeleton(s) from YAML data.
Args:
data: YAML string or pre-parsed dictionary containing skeleton data.
If a dict is provided with skeleton names as keys, returns list.
If a dict is provided with nodes/edges/symmetries, returns single skeleton.
Returns:
A single Skeleton or list of Skeletons depending on input format.
"""
if isinstance(data, str):
import yaml
data = yaml.safe_load(data)
# Check if this is a single skeleton dict or multiple skeletons
if isinstance(data, dict):
# If it has nodes/edges keys, it's a single skeleton
if "nodes" in data:
return self._decode_skeleton(data)
else:
# Multiple skeletons with names as keys
skeletons = []
for name, skeleton_data in data.items():
skeleton = self._decode_skeleton(skeleton_data, name)
skeletons.append(skeleton)
return skeletons
raise ValueError(f"Unexpected data format: {type(data)}")
def decode_dict(self, skeleton_data: Dict, name: str = "Skeleton") -> Skeleton:
"""Decode a single skeleton from a dictionary.
This is useful when the skeleton data is embedded in a larger YAML structure.
Args:
skeleton_data: Dictionary containing nodes, edges, and symmetries.
name: Name for the skeleton (default: "Skeleton").
Returns:
A Skeleton object.
"""
return self._decode_skeleton(skeleton_data, name)
def _decode_skeleton(self, data: Dict, name: Optional[str] = None) -> Skeleton:
"""Decode a single skeleton from dictionary data.
Args:
data: Dictionary containing skeleton data in simplified format.
name: Optional name override for the skeleton.
Returns:
A Skeleton object.
"""
# Create nodes
nodes = []
node_map = {}
for node_data in data.get("nodes", []):
node = Node(name=node_data["name"])
nodes.append(node)
node_map[node.name] = node
# Create edges
edges = []
for edge_data in data.get("edges", []):
source_name = edge_data["source"]["name"]
dest_name = edge_data["destination"]["name"]
edge = Edge(source=node_map[source_name], destination=node_map[dest_name])
edges.append(edge)
# Create symmetries
symmetries = []
for sym_data in data.get("symmetries", []):
# Each symmetry is a list of 2 node specifications
node1_name = sym_data[0]["name"]
node2_name = sym_data[1]["name"]
symmetry = Symmetry([node_map[node1_name], node_map[node2_name]])
symmetries.append(symmetry)
# Use provided name or get from data
if name is None:
name = data.get("name", "Skeleton")
return Skeleton(nodes=nodes, edges=edges, symmetries=symmetries, name=name)
decode(data)
¶
Decode skeleton(s) from YAML data.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
data
|
Union[str, Dict]
|
YAML string or pre-parsed dictionary containing skeleton data. If a dict is provided with skeleton names as keys, returns list. If a dict is provided with nodes/edges/symmetries, returns single skeleton. |
required |
Returns:
| Type | Description |
|---|---|
Union[Skeleton, List[Skeleton]]
|
A single Skeleton or list of Skeletons depending on input format. |
Source code in sleap_io/io/skeleton.py
def decode(self, data: Union[str, Dict]) -> Union[Skeleton, List[Skeleton]]:
"""Decode skeleton(s) from YAML data.
Args:
data: YAML string or pre-parsed dictionary containing skeleton data.
If a dict is provided with skeleton names as keys, returns list.
If a dict is provided with nodes/edges/symmetries, returns single skeleton.
Returns:
A single Skeleton or list of Skeletons depending on input format.
"""
if isinstance(data, str):
import yaml
data = yaml.safe_load(data)
# Check if this is a single skeleton dict or multiple skeletons
if isinstance(data, dict):
# If it has nodes/edges keys, it's a single skeleton
if "nodes" in data:
return self._decode_skeleton(data)
else:
# Multiple skeletons with names as keys
skeletons = []
for name, skeleton_data in data.items():
skeleton = self._decode_skeleton(skeleton_data, name)
skeletons.append(skeleton)
return skeletons
raise ValueError(f"Unexpected data format: {type(data)}")
decode_dict(skeleton_data, name='Skeleton')
¶
Decode a single skeleton from a dictionary.
This is useful when the skeleton data is embedded in a larger YAML structure.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
skeleton_data
|
Dict
|
Dictionary containing nodes, edges, and symmetries. |
required |
name
|
str
|
Name for the skeleton (default: "Skeleton"). |
'Skeleton'
|
Returns:
| Type | Description |
|---|---|
Skeleton
|
A Skeleton object. |
Source code in sleap_io/io/skeleton.py
def decode_dict(self, skeleton_data: Dict, name: str = "Skeleton") -> Skeleton:
"""Decode a single skeleton from a dictionary.
This is useful when the skeleton data is embedded in a larger YAML structure.
Args:
skeleton_data: Dictionary containing nodes, edges, and symmetries.
name: Name for the skeleton (default: "Skeleton").
Returns:
A Skeleton object.
"""
return self._decode_skeleton(skeleton_data, name)
SkeletonYAMLEncoder
¶
Encode skeleton data to simplified YAML format.
This encoder produces a human-readable YAML format that is easier to edit manually than the jsonpickle format.
Methods:
| Name | Description |
|---|---|
encode |
Encode skeleton(s) to YAML string. |
encode_dict |
Encode a single skeleton to a dictionary. |
Source code in sleap_io/io/skeleton.py
class SkeletonYAMLEncoder:
"""Encode skeleton data to simplified YAML format.
This encoder produces a human-readable YAML format that is easier to
edit manually than the jsonpickle format.
"""
def encode(self, skeletons: Union[Skeleton, List[Skeleton]]) -> str:
"""Encode skeleton(s) to YAML string.
Args:
skeletons: A single Skeleton or list of Skeletons to encode.
Returns:
YAML string with skeleton names as top-level keys.
"""
import yaml
if isinstance(skeletons, Skeleton):
skeletons = [skeletons]
data = {}
for skeleton in skeletons:
skeleton_data = self.encode_dict(skeleton)
data[skeleton.name] = skeleton_data
return yaml.dump(data, default_flow_style=False, sort_keys=False)
def encode_dict(self, skeleton: Skeleton) -> Dict:
"""Encode a single skeleton to a dictionary.
This is useful when embedding skeleton data in a larger YAML structure.
Args:
skeleton: Skeleton object to encode.
Returns:
Dictionary with nodes, edges, and symmetries.
"""
# Encode nodes
nodes = []
for node in skeleton.nodes:
nodes.append({"name": node.name})
# Encode edges
edges = []
for edge in skeleton.edges:
edges.append(
{
"source": {"name": edge.source.name},
"destination": {"name": edge.destination.name},
}
)
# Encode symmetries
symmetries = []
for symmetry in skeleton.symmetries:
# Convert set to list and encode as pairs
node_list = list(symmetry.nodes)
symmetries.append(
[{"name": node_list[0].name}, {"name": node_list[1].name}]
)
return {"nodes": nodes, "edges": edges, "symmetries": symmetries}
encode(skeletons)
¶
Encode skeleton(s) to YAML string.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
skeletons
|
Union[Skeleton, List[Skeleton]]
|
A single Skeleton or list of Skeletons to encode. |
required |
Returns:
| Type | Description |
|---|---|
str
|
YAML string with skeleton names as top-level keys. |
Source code in sleap_io/io/skeleton.py
def encode(self, skeletons: Union[Skeleton, List[Skeleton]]) -> str:
"""Encode skeleton(s) to YAML string.
Args:
skeletons: A single Skeleton or list of Skeletons to encode.
Returns:
YAML string with skeleton names as top-level keys.
"""
import yaml
if isinstance(skeletons, Skeleton):
skeletons = [skeletons]
data = {}
for skeleton in skeletons:
skeleton_data = self.encode_dict(skeleton)
data[skeleton.name] = skeleton_data
return yaml.dump(data, default_flow_style=False, sort_keys=False)
encode_dict(skeleton)
¶
Encode a single skeleton to a dictionary.
This is useful when embedding skeleton data in a larger YAML structure.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
skeleton
|
Skeleton
|
Skeleton object to encode. |
required |
Returns:
| Type | Description |
|---|---|
Dict
|
Dictionary with nodes, edges, and symmetries. |
Source code in sleap_io/io/skeleton.py
def encode_dict(self, skeleton: Skeleton) -> Dict:
"""Encode a single skeleton to a dictionary.
This is useful when embedding skeleton data in a larger YAML structure.
Args:
skeleton: Skeleton object to encode.
Returns:
Dictionary with nodes, edges, and symmetries.
"""
# Encode nodes
nodes = []
for node in skeleton.nodes:
nodes.append({"name": node.name})
# Encode edges
edges = []
for edge in skeleton.edges:
edges.append(
{
"source": {"name": edge.source.name},
"destination": {"name": edge.destination.name},
}
)
# Encode symmetries
symmetries = []
for symmetry in skeleton.symmetries:
# Convert set to list and encode as pairs
node_list = list(symmetry.nodes)
symmetries.append(
[{"name": node_list[0].name}, {"name": node_list[1].name}]
)
return {"nodes": nodes, "edges": edges, "symmetries": symmetries}