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.
id
property
id: int
Read-only property.
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
Adds a node to the tree. Apart from the mandatory position
parameter,
there are several optional parameters which can be used to encode
additional information. For example, the comment will be shown by the
WEBKNOSSOS UI.
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
Returns the highest node id.
get_node_by_id
get_node_by_id(node_id: int) -> Node
Returns the node in this tree with the requested id.
get_node_positions
get_node_positions() -> ndarray
Returns an numpy array with the positions of all nodes of this tree.
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. Despite the name, trees may contain cycles.
This class inherits from networkx.Graph
.
For further methods, please check the networkx documentation.
See Tree.init for more details.
A small usage example:
tree = skeleton.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)
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.
id
property
id: int
Read-only property.
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
Adds a node to the tree. Apart from the mandatory position
parameter,
there are several optional parameters which can be used to encode
additional information. For example, the comment will be shown by the
WEBKNOSSOS UI.
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
Returns the highest node id.
get_node_by_id
get_node_by_id(node_id: int) -> Node
Returns the node in this tree with the requested id.
get_node_positions
get_node_positions() -> ndarray
Returns an numpy array with the positions of all nodes of this tree.