Tree graph¶

class dendrotweaks.morphology.trees.Node(idx: int | str, parent_idx: int | str)[source]¶

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.
Examples –
```
>>> node = Node(0, -1)
>>> node
•0
```

property parent¶

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

connect_to_parent(parent)[source]¶

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()[source]¶

Detach the node from its parent.

Examples

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

class dendrotweaks.morphology.trees.Tree(nodes: list)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

Remove a node from the tree.

Parameters:: node (Node) – The node to remove.
Raises:: ValueError – If the tree is not sorted.

remove_subtree(node)[source]¶

Remove a subtree from the tree.

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

add_subtree(node, parent)[source]¶

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)[source]¶

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)[source]¶

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)[source]¶

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()[source]¶: Print the topology of the tree with a visual tree structure.