Tree graph

class dendrotweaks.morphology.trees.Node(idx: int | str, parent_idx: int | str)

Bases: object

Represents a node in a tree.

A node can be a 3D point in a neuron morphology, a segment, a section, or even a tree.

Parameters:

• idx (Union[int, str]) – The index of the node.

• parent_idx (Union[int, str]) – The index of the parent node.

property parent

property is_root: bool

Check if the node is the root of the tree.

Returns:

True if the node is the root, False otherwise.

Return type:

bool

property topological_type: str

The topological type of the node based on the number of children.

Returns:

The topological type of the node: ‘continuation’, ‘bifurcation’, or ‘termination’.

Return type:

str

property subtree: list

Gets the subtree of the node (including the node itself) using an iterative depth-first traversal.

Returns:

A list of nodes in the subtree.

Return type:

list

property subtree_size

Gets the size of the subtree of the node.

Returns:

The size of the subtree of the node.

Return type:

int

property depth

Computes the depth of the node in the tree iteratively.

property siblings

Gets the siblings of the node.

Returns:

A list of nodes that share the same parent as the node.

Return type:

list

property nearest_neighbours

Gets the nearest neighbours of the node.

Returns:

A list of nodes that share the same parent or children as the node.

Return type:

list

property ancestors

Get all ancestors of this node up to the root.

path_to_ancestor(ancestor=None, include_self=True, include_ancestor=True)

Get the path from this node to a given ancestor node.

Parameters:

• ancestor (Node, optional) – The ancestor node to get the path to. If None, the path to the root is returned.

• include_self (bool, optional) – Whether to include this node in the path. Defaults to True.

• include_ancestor (bool, optional) – Whether to include the ancestor node in the path. Defaults to True.

Returns:

A list of nodes representing the path from this node to the ancestor node.

Return type:

list

find_common_ancestor(other)

Find the common ancestor between this node and another node.

path(other, include_self=True, include_other=True, include_ancestor=True)

Get the path between this node and another node.

Parameters:

• other (Node) – The other node to get the path to.

• include_self (bool) – Whether to include this node in the path.

• include_other (bool) – Whether to include the other node in the path.

• include_ancestor (bool) – Whether to include the lowest common ancestor (LCA) in the path. Only relevant when self and other are in parallel subtrees, ignored otherwise.

Returns:

A list of nodes representing the path from this node to the other node.

Return type:

list

connect_to_parent(parent)

Attach the node to a parent node.

Warning

This method should not be used directly when working with trees as it doesn’t add the node to the tree’s list of nodes. Use the Tree class to insert nodes into the tree.

Args:

parent (Node): The parent node to attach the node to.

disconnect_from_parent()

Detach the node from its parent.

Examples

for child in node.children: child.disconnect_from_parent()

class dendrotweaks.morphology.trees.Tree(nodes: list)

Bases: object

A class to represent a tree data structure.

A tree graph is a hierarchical data structure that consists of nodes connected by edges.

Parameters:

nodes (list) – A list of nodes in the tree.

root

The root node of the tree.

Type:

Node

property is_connected

Whether the tree is connected i.e. each node can be reached from the root.

Returns:

• bool – True if the root node’s subtree contains exactly the same nodes

• as the entire tree. False otherwise.

property is_sorted

Whether the nodes in the tree are sorted by index.

Returns:

True if the nodes are sorted by index. False otherwise.

Return type:

bool

property bifurcations

The bifurcation nodes in the tree.

Returns:

A list of bifurcation nodes in the tree.

Return type:

list

property terminations

property edges: list

Returns a list of edges in the tree.

Returns:

A list of edges in the tree.

Return type:

list[tuple[Node, Node]]

traverse(root=None)

Iterate over the nodes in the tree using a stack-based depth-first traversal.

Parameters:

root (Node, optional) – The root node to start the traversal from. Defaults to None.

sort(sort_children=True, force=False)

Sort the nodes in the tree using a stack-based depth-first traversal.

Parameters:

• sort_children (bool, optional) – Whether to sort the children of each node based on the number of bifurcations in their subtrees. Defaults to True.

• force (bool, optional) – Whether to force the sorting of the tree even if it is already sorted. Defaults to False.

remove_node(node)

Remove a node from the tree.

Parameters:

node (Node) – The node to remove.

Raises:

ValueError – If the tree is not sorted.

remove_subtree(node)

Remove a subtree from the tree.

Parameters:

node (Node) – The root node of the subtree to remove.

add_subtree(node, parent)

Add a subtree to the tree.

Parameters:

• node (Node) – The root node of the subtree to add.

• parent (Node) – The parent node to attach the subtree to.

insert_node_after(new_node, existing_node)

Insert a node after a given node in the tree.

Parameters:

• new_node (Node) – The new node to insert.

• existing_node (Node) – The existing node after which to insert the new node.

insert_node_before(new_node, existing_node)

Insert a node before a given node in the tree.

Parameters:

• new_node (Node) – The new node to insert.

• existing_node (Node) – The existing node before which to insert the new node.

reposition_subtree(node, new_parent_node, origin=None)

Reposition a subtree in the tree.

Parameters:

• node (Node) – The root node of the subtree to reposition.

• new_parent_node (Node) – The new parent node of the subtree.

• origin (Node, optional) – The origin node to use as the reference point for the repositioning. Defaults to None.

Note

Treats differently the children of the root node.

topology()

Print the topology of the tree with a visual tree structure.