neuron_morphology.feature_extractor.run_feature_extraction

Module Contents

Functions

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
hydrate_parameters(parameters: Dict[str, Any]) → Dict[str, Any]	Resolve argued feature parameters to a format comprehensible by
setup_data(reconstruction: Dict[str, Any], global_parameters: Dict[str, Any]) → Tuple[str, Data]	Construct a Data for extracting features from a single reconstruction.
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.

neuron_morphology.feature_extractor.run_feature_extraction.well_known_marks :Dict[str, Type[Mark]]

neuron_morphology.feature_extractor.run_feature_extraction.item

neuron_morphology.feature_extractor.run_feature_extraction.known_feature_sets

neuron_morphology.feature_extractor.run_feature_extraction.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

neuron_morphology.feature_extractor.run_feature_extraction.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

neuron_morphology.feature_extractor.run_feature_extraction.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

neuron_morphology.feature_extractor.run_feature_extraction.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