:mod:`neuron_morphology.features.path`
======================================

.. py:module:: neuron_morphology.features.path


Module Contents
---------------


Functions
~~~~~~~~~

.. autoapisummary::

   neuron_morphology.features.path._calculate_max_path_distance
   neuron_morphology.features.path.calculate_max_path_distance
   neuron_morphology.features.path.max_path_distance
   neuron_morphology.features.path.early_branch_path
   neuron_morphology.features.path._calculate_mean_contraction
   neuron_morphology.features.path.calculate_mean_contraction
   neuron_morphology.features.path.mean_contraction


.. function:: _calculate_max_path_distance(morphology, root, node_types)


.. function:: calculate_max_path_distance(morphology, root, node_types=None)

   Helper for max_path_distance. See below for more information.
















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.. function:: 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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.. function:: 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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.. function:: _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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.. function:: calculate_mean_contraction(morphology, root=None, node_types=None)

   See mean_contraction
















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.. function:: 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
           ..













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