webknossos.skeleton.tree ¶

Graph ¶

Graph(name: str, group: Group, skeleton: Skeleton, color: Optional[Vector4] = None, enforced_id: Optional[int] = None)

Bases: Tree

Deprecated, please use Tree instead.

color `instance-attribute` ¶

color = color

group `instance-attribute` ¶

group = group

id `property` ¶

id: int

The unique identifier of the tree.

Returns:

int ( int ) –

A unique identifier for this tree instance.

Note

This is a read-only property that is set during tree creation.

name `instance-attribute` ¶

name = name

node_dict_factory `class-attribute` `instance-attribute` ¶

node_dict_factory = _NodeDict

add_node ¶

add_node(position: Vec3IntLike, comment: Optional[str] = None, radius: Optional[float] = None, rotation: Optional[Vector3] = None, inVp: Optional[int] = None, inMag: Optional[int] = None, bitDepth: Optional[int] = None, interpolation: Optional[bool] = None, time: Optional[int] = None, is_branchpoint: bool = False, branchpoint_time: Optional[int] = None, _enforced_id: Optional[int] = None) -> Node

Add a new node to the tree.

Creates a new node at the specified position and adds it to the tree.

Parameters:

position (Vec3IntLike) –

The 3D coordinates (x, y, z) of the node.
comment (Optional[str], default: None ) –

A text comment associated with the node. Visible in the WEBKNOSSOS UI. Defaults to None.
radius (Optional[float], default: None ) –

Node radius for visualization. Defaults to None.
rotation (Optional[Vector3], default: None ) –

3D rotation vector for the node. Defaults to None.
inVp (Optional[int], default: None ) –

Viewport information. Defaults to None.
inMag (Optional[int], default: None ) –

Magnification level. Defaults to None.
bitDepth (Optional[int], default: None ) –

Bit depth for node data. Defaults to None.
interpolation (Optional[bool], default: None ) –

Whether to use interpolation. Defaults to None.
time (Optional[int], default: None ) –

Timestamp for the node. Defaults to None.
is_branchpoint (bool, default: False ) –

Whether this node is a branch point. Defaults to False.
branchpoint_time (Optional[int], default: None ) –

Timestamp for branch point creation. Defaults to None.
_enforced_id (Optional[int], default: None ) –

Internal use only. Forces a specific node ID. Defaults to None.

Returns:

Node ( Node ) –

The newly created and added node.

Examples:

# Add a simple node with just position
node1 = tree.add_node(position=(100, 200, 300))

# Add a node with additional properties
node2 = tree.add_node(
    position=(150, 250, 350),
    comment="Dendrite branch point",
    radius=2.5,
    is_branchpoint=True
)

adjlist_inner_dict_factory ¶

adjlist_inner_dict_factory() -> _AdjDict

adjlist_outer_dict_factory ¶

adjlist_outer_dict_factory() -> _AdjDict

get_max_node_id ¶

get_max_node_id() -> int

Get the highest node ID in the tree.

Returns:

int ( int ) –

The maximum node ID present in the tree. Returns 0 if the tree has no nodes.

get_node_by_id ¶

get_node_by_id(node_id: int) -> Node

Retrieve a node using its unique identifier.

Parameters:

node_id (int) –

The unique identifier of the node to retrieve.

Returns:

Node ( Node ) –

The node with the specified ID.

Raises:

KeyError –

If no node exists with the given ID in this tree.

get_node_positions ¶

get_node_positions() -> ndarray

Get positions of all nodes in the tree.

Returns:

ndarray –

np.ndarray: A numpy array of shape (N, 3) containing the 3D positions of all N nodes in the tree. Each row represents a node's (x, y, z) coordinates.

Tree ¶

Tree(name: str, group: Group, skeleton: Skeleton, color: Optional[Vector4] = None, enforced_id: Optional[int] = None)

Bases: Graph

Contains a collection of nodes and edges in a graph structure.

Despite the name, trees may contain cycles. This class inherits from networkx.Graph and provides additional functionality specific to neural annotation tasks.

Parameters:

name (str) –

The name of the tree.
group (Group) –

The group this tree belongs to.
skeleton (Skeleton) –

The skeleton this tree is part of.
color (Optional[Vector4], default: None ) –

RGBA color values for the tree. Defaults to None.
enforced_id (Optional[int], default: None ) –

Specific ID to use for the tree. Defaults to None.

Returns:

Tree –

A new Tree instance that represents a collection of nodes and edges.

Raises:

ValueError –

If the tree name is empty or if the group or skeleton is None.
TypeError –

If the color value is not a valid Vector4 type when provided.

Note

It is recommended to create trees using Skeleton.add_tree or Group.add_tree instead of instantiating this class directly. This ensures proper parent-child relationships are maintained.

Examples:

Create a new tree with nodes and edges:

# First create a skeleton (parent object)
skeleton = Skeleton("example_skeleton")

# Add a new tree to the skeleton
tree = skeleton.add_tree("dendrite_1")

# Add nodes with 3D positions
soma = tree.add_node(position=(0, 0, 0), comment="soma")
branch1 = tree.add_node(position=(100, 0, 0), comment="branch1")
branch2 = tree.add_node(position=(0, 100, 0), comment="branch2")

# Connect nodes with edges
tree.add_edge(soma, branch1)
tree.add_edge(soma, branch2)

# Access node positions
positions = tree.get_node_positions()  # Returns numpy array of all positions

For additional graph operations, see the networkx documentation.

To create a tree, it is recommended to use Skeleton.add_tree or Group.add_tree. That way, the newly created tree is automatically attached as a child to the object the method was called on.

color `instance-attribute` ¶

color = color

group `instance-attribute` ¶

group = group

id `property` ¶

id: int

The unique identifier of the tree.

Returns:

int ( int ) –

A unique identifier for this tree instance.

Note

This is a read-only property that is set during tree creation.

name `instance-attribute` ¶

name = name

node_dict_factory `class-attribute` `instance-attribute` ¶

node_dict_factory = _NodeDict

add_node ¶

add_node(position: Vec3IntLike, comment: Optional[str] = None, radius: Optional[float] = None, rotation: Optional[Vector3] = None, inVp: Optional[int] = None, inMag: Optional[int] = None, bitDepth: Optional[int] = None, interpolation: Optional[bool] = None, time: Optional[int] = None, is_branchpoint: bool = False, branchpoint_time: Optional[int] = None, _enforced_id: Optional[int] = None) -> Node

Add a new node to the tree.

Creates a new node at the specified position and adds it to the tree.

Parameters:

position (Vec3IntLike) –

The 3D coordinates (x, y, z) of the node.
comment (Optional[str], default: None ) –

A text comment associated with the node. Visible in the WEBKNOSSOS UI. Defaults to None.
radius (Optional[float], default: None ) –

Node radius for visualization. Defaults to None.
rotation (Optional[Vector3], default: None ) –

3D rotation vector for the node. Defaults to None.
inVp (Optional[int], default: None ) –

Viewport information. Defaults to None.
inMag (Optional[int], default: None ) –

Magnification level. Defaults to None.
bitDepth (Optional[int], default: None ) –

Bit depth for node data. Defaults to None.
interpolation (Optional[bool], default: None ) –

Whether to use interpolation. Defaults to None.
time (Optional[int], default: None ) –

Timestamp for the node. Defaults to None.
is_branchpoint (bool, default: False ) –

Whether this node is a branch point. Defaults to False.
branchpoint_time (Optional[int], default: None ) –

Timestamp for branch point creation. Defaults to None.
_enforced_id (Optional[int], default: None ) –

Internal use only. Forces a specific node ID. Defaults to None.

Returns:

Node ( Node ) –

The newly created and added node.

Examples:

# Add a simple node with just position
node1 = tree.add_node(position=(100, 200, 300))

# Add a node with additional properties
node2 = tree.add_node(
    position=(150, 250, 350),
    comment="Dendrite branch point",
    radius=2.5,
    is_branchpoint=True
)

adjlist_inner_dict_factory ¶

adjlist_inner_dict_factory() -> _AdjDict

adjlist_outer_dict_factory ¶

adjlist_outer_dict_factory() -> _AdjDict

get_max_node_id ¶

get_max_node_id() -> int

Get the highest node ID in the tree.

Returns:

int ( int ) –

The maximum node ID present in the tree. Returns 0 if the tree has no nodes.

get_node_by_id ¶

get_node_by_id(node_id: int) -> Node

Retrieve a node using its unique identifier.

Parameters:

node_id (int) –

The unique identifier of the node to retrieve.

Returns:

Node ( Node ) –

The node with the specified ID.

Raises:

KeyError –

If no node exists with the given ID in this tree.

get_node_positions ¶

get_node_positions() -> ndarray

Get positions of all nodes in the tree.

Returns:

ndarray –

np.ndarray: A numpy array of shape (N, 3) containing the 3D positions of all N nodes in the tree. Each row represents a node's (x, y, z) coordinates.

webknossos.skeleton.tree ¶

Graph ¶

color instance-attribute ¶

group instance-attribute ¶

id property ¶

name instance-attribute ¶

node_dict_factory class-attribute instance-attribute ¶

add_node ¶

adjlist_inner_dict_factory ¶

adjlist_outer_dict_factory ¶

get_max_node_id ¶

get_node_by_id ¶

get_node_positions ¶

Tree ¶

color instance-attribute ¶

group instance-attribute ¶

id property ¶

name instance-attribute ¶

node_dict_factory class-attribute instance-attribute ¶

add_node ¶

adjlist_inner_dict_factory ¶

adjlist_outer_dict_factory ¶

get_max_node_id ¶

get_node_by_id ¶

get_node_positions ¶

color `instance-attribute` ¶

group `instance-attribute` ¶

id `property` ¶

name `instance-attribute` ¶

node_dict_factory `class-attribute` `instance-attribute` ¶

color `instance-attribute` ¶

group `instance-attribute` ¶

id `property` ¶

name `instance-attribute` ¶

node_dict_factory `class-attribute` `instance-attribute` ¶