Segment tree

class dendrotweaks.morphology.seg_trees.Segment(idx, parent_idx, sim_seg, section)[source]

Bases: Node

A class representing a segment.

A segment is a part of a section used to discretize the section in space for the purpose of numerical simulations.

Parameters:

  • idx (int) – The index of the segment.

  • parent_idx (int) – The index of the parent segment.

  • sim_seg (h.Segment) – The segment object from a simulator (e.g. NEURON).

  • section (Section) – The section to which the segment belongs.

_section

The section to which the segment belongs.

Type:

Section

_ref

The segment object from a simulator (e.g. NEURON).

Type:

h.Segment

property domain

The morphological or functional domain of the segment.

property subtree_size

The number of sections in the subtree rooted at the segment.

property Ra

The axial resistance of the segment (from NEURON).

path_distance(within_domain=False)[source]
property distance
property domain_distance
set_param_value(param_name, value)[source]

Set the value of a parameter of the segment.

Parameters:

  • param_name (str) – The name of the parameter to set.

  • value (float) – The value to set the parameter to.

get_param_value(param_name)[source]

Get the value of a parameter of the segment.

Parameters:

param_name (str) – The name of the parameter to get.

Returns:

The value of the parameter.

Return type:

float

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.

property depth

Computes the depth of the node in the tree iteratively.

disconnect_from_parent()

Detach the node from its parent.

Examples

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

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 parent
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 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 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

class dendrotweaks.morphology.seg_trees.SegmentTree(segments: list[Segment])[source]

Bases: Tree

A class representing a tree graph of segments.

property segments

The segments in the segment tree. Alias for self._nodes

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.

property bifurcations

The bifurcation nodes in the tree.

Returns:

A list of bifurcation nodes in the tree.

Return type:

list

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]]

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.

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

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.

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.

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.

property terminations
topology()

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

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.