webknossos.skeleton.skeleton ¶

Classes:

Skeleton –

Representation of the skeleton of an Annotation.

Skeleton ¶

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.

Methods:

add_graph –

Deprecated, please use add_tree.
add_group –

Adds a (sub) group to the current group with the provided name.
add_nx_graphs –

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.
add_tree –

Adds a tree to the current group. If the first parameter is a string,
as_nml_group –

Returns a named tuple representation of this group.
flattened_graphs –

Deprecated, please use flattened_trees.
flattened_groups –

Returns an iterator of all groups within this group (and its subgroups).
flattened_trees –

Returns an iterator of all trees within this group (and its subgroups).
from_path –

Deprecated. Use Skeleton.load instead.
get_graph_by_id –

Deprecated, please use get_tree_by_id.
get_group_by_id –

Returns the group which has the specified group id.
get_max_graph_id –

Deprecated, please use get_max_tree_id.
get_max_node_id –

Returns the highest node id of all nodes of all trees within this group (and its subgroups).
get_max_tree_id –

Returns the highest tree id of all trees within this group (and its subgroups).
get_node_by_id –

Returns the node which has the specified node id.
get_total_node_count –

Returns the total number of nodes of all trees within this group (and its subgroups).
get_tree_by_id –

Returns the tree which has the specified tree id.
has_tree_id –

Returns true if this group (or a subgroup) contains a tree with the given id.
load –

Loads a .nml file or a .zip file containing an NML (and possibly also volume
remove_tree_by_id –
save –

Stores the skeleton as a zip or nml at the given path.
write –

Deprecated. Use Skeleton.save instead.

Attributes:

children (Iterator[GroupOrTree]) –

Returns all (immediate) children (groups and trees) as an iterator.
dataset_name (str) –
description (Optional[str]) –
graphs (Iterator[Tree]) –

Deprecated, please use trees.
groups (Iterator[Group]) –

Returns all (immediate) group children as an iterator.
id (int) –

Read-only property.
name (str) –

Should not be used with Skeleton, this attribute is only useful for sub-groups. Set to Root.
organization_id (Optional[str]) –
scale (Tuple[float, float, float]) –

Deprecated, please use voxel_size.
trees (Iterator[Tree]) –

Returns all (immediate) tree children as an iterator.
voxel_size (Vector3) –

children `property` ¶

children: Iterator[GroupOrTree]

Returns all (immediate) children (groups and trees) as an iterator.

dataset_name `instance-attribute` ¶

dataset_name: str

description `class-attribute` `instance-attribute` ¶

description: Optional[str] = None

graphs `property` ¶

graphs: Iterator[Tree]

Deprecated, please use trees.

groups `property` ¶

groups: Iterator[Group]

Returns all (immediate) group children as an iterator. Use flattened_groups if you need also need groups within subgroups.

id `property` ¶

id: int

Read-only property.

name `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.

organization_id `class-attribute` `instance-attribute` ¶

organization_id: Optional[str] = None

scale `property` `writable` ¶

scale: Tuple[float, float, float]

Deprecated, please use voxel_size.

trees `property` ¶

trees: Iterator[Tree]

Returns all (immediate) tree children as an iterator. Use flattened_trees if you need also need trees within subgroups.

voxel_size `instance-attribute` ¶

voxel_size: Vector3

add_graph ¶

add_graph(name: str, color: Optional[Union[Vector4, Vector3]] = None, _enforced_id: Optional[int] = None) -> Tree

Deprecated, please use add_tree.

add_group ¶

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 ¶

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 ¶

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 ¶

as_nml_group() -> Group

Returns a named tuple representation of this group.

flattened_graphs ¶

flattened_graphs() -> Iterator[Tree]

Deprecated, please use flattened_trees.

flattened_groups ¶

flattened_groups() -> Iterator[Group]

Returns an iterator of all groups within this group (and its subgroups).

flattened_trees ¶

flattened_trees() -> Iterator[Tree]

Returns an iterator of all trees within this group (and its subgroups).

from_path `staticmethod` ¶

from_path(file_path: Union[PathLike, str]) -> Skeleton

Deprecated. Use Skeleton.load instead.

get_graph_by_id ¶

get_graph_by_id(graph_id: int) -> Tree

Deprecated, please use get_tree_by_id.

get_group_by_id ¶

get_group_by_id(group_id: int) -> Group

Returns the group which has the specified group id.

get_max_graph_id ¶

get_max_graph_id() -> int

Deprecated, please use get_max_tree_id.

get_max_node_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 ¶

get_max_tree_id() -> int

Returns the highest tree id of all trees within this group (and its subgroups).

get_node_by_id ¶

get_node_by_id(node_id: int) -> Node

Returns the node which has the specified node id.

get_total_node_count ¶

get_total_node_count() -> int

Returns the total number of nodes of all trees within this group (and its subgroups).

get_tree_by_id ¶

get_tree_by_id(tree_id: int) -> Tree

Returns the tree which has the specified tree id.

has_tree_id ¶

has_tree_id(tree_id: int) -> bool

Returns true if this group (or a subgroup) contains a tree with the given id.

load `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 ¶

remove_tree_by_id(tree_id: int) -> None

save ¶

save(out_path: Union[str, PathLike]) -> None

Stores the skeleton as a zip or nml at the given path.

write ¶

write(out_path: PathLike) -> None

Deprecated. Use Skeleton.save instead.