:mod:`neuron_morphology.feature_extractor.run_feature_extraction`
=================================================================

.. py:module:: neuron_morphology.feature_extractor.run_feature_extraction


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


Functions
~~~~~~~~~

.. autoapisummary::

   neuron_morphology.feature_extractor.run_feature_extraction.resolve_reference_layer_depths
   neuron_morphology.feature_extractor.run_feature_extraction.hydrate_parameters
   neuron_morphology.feature_extractor.run_feature_extraction.setup_data
   neuron_morphology.feature_extractor.run_feature_extraction.run_feature_extraction


.. data:: well_known_marks
   :annotation: :Dict[str, Type[Mark]]

   

.. data:: item
   

   

.. data:: known_feature_sets
   

   

.. function:: resolve_reference_layer_depths(key=None, names=None, boundaries=None)

   Given either the name of a well known depths set or a set of names and 
   corresponding boundaries, produce a ReferenceLayerDepths


   :Parameters:

       **key** : of a well known reference layer
           ..

       **names** : the names of each layer in a custom sequence
           ..

       **boundaries** : the upper and lower depths of each layer in a custom sequence
           ..

   :Returns:

       the requested reference layer depths
           ..













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.. function:: hydrate_parameters(parameters: Dict[str, Any]) -> Dict[str, Any]

   Resolve argued feature parameters to a format comprehensible by 
   the features. e.g. loading data from a path.


   :Parameters:

       **parameters** : to be hydrated
           ..

   :Returns:

       The hydrated parameters
           ..













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.. function:: setup_data(reconstruction: Dict[str, Any], global_parameters: Dict[str, Any]) -> Tuple[str, Data]

   Construct a Data for extracting features from a single reconstruction.


   :Parameters:

       **reconstruction** : The reconstruction to be setup. Must specify an swc_path
           ..

       **global_parameters** : any cross-reconstruction feature parameters
           ..

   :Returns:

       **identifier** : a label for this reconstruction
           ..

       data suitable for feature extraction
           ..













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.. function:: run_feature_extraction(reconstruction_spec: Dict[str, Any], feature_set: str, only_marks: List[str], required_marks: List[str], global_parameter_spec: Dict[str, Any]) -> Tuple[str, Dict]

   Run feature extraction for a single reconstruction.


   :Parameters:

       **reconstruction_spec** : a dictionary specifying a reconstruction. Must
           have an swc_path.

       **feature_set** : names the set of features for which calculation will be
           attempted

       **only_marks** : names marks to which calculation will be restricted
           ..

       **required_marks** : raise an exception if these named marks fail validation
           ..

       **global_parameter_spec** : a dictionary specifying cross-reconstruction
           parameters

   :Returns:

       **identifier** : a label for this reconstruction
           ..

       A dict with keys:
           results - a dict, mapping features to calculated values
           selected_marks - the set of marks that passed validation
           selected features - the set of features for which calculation was 
               attempted













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