neuron_morphology.features.path
¶
Module Contents¶
Functions¶
_calculate_max_path_distance (morphology, root, node_types) |
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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, |
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neuron_morphology.features.path.
_calculate_max_path_distance
(morphology, root, node_types)¶
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neuron_morphology.features.path.
calculate_max_path_distance
(morphology, root, node_types=None)¶ Helper for max_path_distance. See below for more information.
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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.
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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
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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
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neuron_morphology.features.path.
calculate_mean_contraction
(morphology, root=None, node_types=None)¶ See mean_contraction
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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