neuron_morphology.features.path

Module Contents

Functions

_calculate_max_path_distance(morphology, root, node_types)
calculate_max_path_distance(morphology, root, node_types=None) Helper for max_path_distance. See below for more information.
max_path_distance(data: MorphologyLike, node_types: Optional[List[int]] = None) → float Calculate the distance, following the path of adjacent neurites, from
early_branch_path(data: MorphologyLike, node_types: Optional[List[int]] = None, soma: Optional[Dict] = None) → float Returns the ratio of the longest ‘short’ branch from a bifurcation to
_calculate_mean_contraction(morphology, reference, root, node_types) Calculate the average contraction of all sections. In other words,
calculate_mean_contraction(morphology, root=None, node_types=None) See mean_contraction
mean_contraction(data: MorphologyLike, node_types: Optional[List[int]] = None) → float Calculate the average contraction of all sections. In other words,
neuron_morphology.features.path._calculate_max_path_distance(morphology, root, node_types)
neuron_morphology.features.path.calculate_max_path_distance(morphology, root, node_types=None)

Helper for max_path_distance. See below for more information.

neuron_morphology.features.path.max_path_distance(data: MorphologyLike, node_types: Optional[List[int]] = None) → float

Calculate the distance, following the path of adjacent neurites, from the soma to the furthest compartment. This is equivalent to the distance to the furthest SWC node.

Parameters:
data : the input reconstruction
node_types : if provided, restrict the calculation to nodes of these

types

Returns:
The along-path distance from the soma to the farthest (in the along-path
sense) node.
neuron_morphology.features.path.early_branch_path(data: MorphologyLike, node_types: Optional[List[int]] = None, soma: Optional[Dict] = None) → float

Returns the ratio of the longest ‘short’ branch from a bifurcation to the maximum path length of the tree. In other words, for each bifurcation, the maximum path length below that branch is calculated, and the shorter of these values is used. The maximum of these short values is divided by the maximum path length.

Parameters:
data : the input reconstruction
node_types : if provided, restrict the calculation to nodes of these

types

soma : if provided, use this node as the root, otherwise infer the root

from the argued morphology

Returns:
ratio of max short branch to max path length
neuron_morphology.features.path._calculate_mean_contraction(morphology, reference, root, node_types)

Calculate the average contraction of all sections. In other words, calculate the average ratio of euclidean distance to path distance between all bifurcations in the morphology. Trifurcations are treated as bifurcations.

Parameters:
morphology: Morphology object
reference: dict
This is the node of the previous bifurcation
root: dict
This is the node from which to measure branch contraction under
node_types: list (AXON, BASAL_DENDRITE, APICAL_DENDRITE)
Type to restrict search to
Returns:
Two scalars: euclidean distance, path distance
These are the total bif-bif and bif-tip distances under this root
neuron_morphology.features.path.calculate_mean_contraction(morphology, root=None, node_types=None)

See mean_contraction

neuron_morphology.features.path.mean_contraction(data: MorphologyLike, node_types: Optional[List[int]] = None) → float

Calculate the average contraction of all sections. In other words, calculate the average ratio of euclidean distance to path distance between all bifurcations in the morphology. Trifurcations are treated as bifurcations.

Parameters:
data : the input reconstruction
node_types : if provided, restrict the calculation to nodes of these

types

Returns:
The average contraction across all sections in this reconstruction