Bases: Group
Representation of the skeleton of an Annotation.
It contains metadata to identify the related dataset and is the root-group of sub-groups and trees.
See the parent class Group for methods about group and tree handling.
To upload a skeleton to webknossos, please create an Annotation() with it.
A small usage example:
annotation = Annotation(
name="my_annotation", dataset_name="my_dataset", voxel_size=(11, 11, 24)
)
group = annotation.skeleton.add_group("a group")
tree = group.add_tree("a tree")
node_1 = tree.add_node(position=(0, 0, 0), comment="node 1")
node_2 = tree.add_node(position=(100, 100, 100), comment="node 2")
tree.add_edge(node_1, node_2)
Also see this example for a more complex interaction.
property
children: Iterator[GroupOrTree]
Returns all (immediate) children (groups and trees) as an iterator.
instance-attribute
dataset_name: str
class-attribute
instance-attribute
description: Optional[str] = None
property
groups: Iterator[Group]
Returns all (immediate) group children as an iterator. Use flattened_groups if you need also need groups within subgroups.
property
id: int
Read-only property.
class-attribute
instance-attribute
name: str = field(default='Root', init=False, eq=False, repr=False)
Should not be used with Skeleton, this attribute is only useful for sub-groups. Set to Root.
class-attribute
instance-attribute
organization_id: Optional[str] = None
property
writable
scale: Tuple[float, float, float]
Deprecated, please use voxel_size.
property
trees: Iterator[Tree]
Returns all (immediate) tree children as an iterator. Use flattened_trees if you need also need trees within subgroups.
instance-attribute
voxel_size: Vector3
add_graph(name: str, color: Optional[Union[Vector4, Vector3]] = None, _enforced_id: Optional[int] = None) -> Tree
Deprecated, please use add_tree.
add_group(name: str, _enforced_id: Optional[int] = None) -> Group
Adds a (sub) group to the current group with the provided name.
add_nx_graphs(tree_dict: Union[List[Graph], Dict[str, List[Graph]]]) -> None
A utility to add nx graphs NetworkX graph object to a wk skeleton object. Accepts both a simple list of multiple skeletons/trees or a dictionary grouping skeleton inputs.
Arguments: tree_dict (Union[List[nx.Graph], Dict[str, List[nx.Graph]]]): A list of wK tree-like structures as NetworkX graphs or a dictionary of group names and same lists of NetworkX tree objects.
add_tree(name_or_tree: Union[str, Tree], color: Optional[Union[Vector4, Vector3]] = None, _enforced_id: Optional[int] = None) -> Tree
Adds a tree to the current group. If the first parameter is a string, a new tree will be added with the provided name and color if specified. Otherwise, the first parameter is assumed to be a tree object (e.g., from another skeleton). A copy of that tree will then be added. If the id of the tree already exists, a new id will be generated.
as_nml_group() -> Group
Returns a named tuple representation of this group.
flattened_groups() -> Iterator[Group]
Returns an iterator of all groups within this group (and its subgroups).
flattened_trees() -> Iterator[Tree]
Returns an iterator of all trees within this group (and its subgroups).
staticmethod
from_path(file_path: Union[PathLike, str]) -> Skeleton
Deprecated. Use Skeleton.load instead.
get_group_by_id(group_id: int) -> Group
Returns the group which has the specified group id.
get_max_graph_id() -> int
Deprecated, please use get_max_tree_id.
get_max_node_id() -> int
Returns the highest node id of all nodes of all trees within this group (and its subgroups).
get_max_tree_id() -> int
Returns the highest tree id of all trees within this group (and its subgroups).
get_node_by_id(node_id: int) -> Node
Returns the node which has the specified node id.
get_total_node_count() -> int
Returns the total number of nodes of all trees within this group (and its subgroups).
get_tree_by_id(tree_id: int) -> Tree
Returns the tree which has the specified tree id.
has_tree_id(tree_id: int) -> bool
Returns true if this group (or a subgroup) contains a tree with the given id.
staticmethod
load(file_path: Union[PathLike, str]) -> Skeleton
Loads a .nml file or a .zip file containing an NML (and possibly also volume
layers). Returns the Skeleton object. Also see Annotation.load if you want to
have the annotation which wraps the skeleton.
remove_tree_by_id(tree_id: int) -> None
save(out_path: Union[str, PathLike]) -> None
Stores the skeleton as a zip or nml at the given path.
write(out_path: PathLike) -> None
Deprecated. Use Skeleton.save instead.