emodelrunner.factsheets.morphology_features

Computation of morphology features.

Classes

AverageDiameter(morphology, neurite_name, ...)

Average diameter (weighted by section length) feature for a neurite type.

AverageSectionLength(morphology, ...)

Average section length feature.

AverageSegmentLength(morphology, ...)

Average segment length feature.

HippocampusMorphologyFactsheetBuilder(morph_path)

Morphology factsheet builder for Hippocampus packages.

MaxBranchOrder(morphology, neurite_name, ...)

Maximum branch order feature.

MaxSectionLength(morphology, neurite_name, ...)

Maximum section length feature.

MeanNeuriteVolumes(morphology, neurite_name, ...)

Mean neurite volume feature.

MorphologyFactsheetBuilder(morph_path)

Computes the factsheet values for a morphology.

MorphologyFeature()

Morphology feature representation.

NumberOfSections(morphology, neurite_name, ...)

Number of sections feature.

NumberOfSegments(morphology, neurite_name, ...)

Number of segments feature.

SSCXMorphologyFactsheetBuilder(morph_path)

Morphology factsheet builder for SSCX packages.

SomaDiamater(morphology)

Soma diameter feature.

SomaSurfaceArea(morphology)

Soma surface area feature.

SomaVolume(morphology)

Soma volume feature.

ThalamusMorphologyFactsheetBuilder(morph_path)

Morphology factsheet builder for Thalamus packages.

TotalArea(morphology, neurite_name, neurite_type)

Total area feature.

TotalDepth(morphology, neurite_name, ...)

Total depth feature.

TotalHeight(morphology, neurite_name, ...)

Total height feature.

TotalLength(morphology, neurite_name, ...)

Total length feature.

TotalVolume(morphology, neurite_name, ...)

Total volume feature.

TotalWidth(morphology, neurite_name, ...)

Total width feature.

class emodelrunner.factsheets.morphology_features.AverageDiameter(morphology, neurite_name, neurite_type)[source]

Bases: MorphologyFeature

Average diameter (weighted by section length) feature for a neurite type.

class emodelrunner.factsheets.morphology_features.AverageSectionLength(morphology, neurite_name, neurite_type)[source]

Bases: MorphologyFeature

Average section length feature.

name

name of the feature

Type

str

value

value of the feature

Type

float

unit

unit of the feature

Type

str

class emodelrunner.factsheets.morphology_features.AverageSegmentLength(morphology, neurite_name, neurite_type)[source]

Bases: MorphologyFeature

Average segment length feature.

name

name of the feature

Type

str

value

value of the feature

Type

float

unit

unit of the feature

Type

str

class emodelrunner.factsheets.morphology_features.HippocampusMorphologyFactsheetBuilder(morph_path)[source]

Bases: MorphologyFactsheetBuilder

Morphology factsheet builder for Hippocampus packages.

class emodelrunner.factsheets.morphology_features.MaxBranchOrder(morphology, neurite_name, neurite_type)[source]

Bases: MorphologyFeature

Maximum branch order feature.

name

name of the feature

Type

str

value

value of the feature

Type

int

unit

unit of the feature

Type

str

class emodelrunner.factsheets.morphology_features.MaxSectionLength(morphology, neurite_name, neurite_type)[source]

Bases: MorphologyFeature

Maximum section length feature.

name

name of the feature

Type

str

value

value of the feature

Type

float

unit

unit of the feature

Type

str

class emodelrunner.factsheets.morphology_features.MeanNeuriteVolumes(morphology, neurite_name, neurite_type)[source]

Bases: MorphologyFeature

Mean neurite volume feature.

name

name of the feature

Type

str

value

value of the feature

Type

float

unit

unit of the feature

Type

str

class emodelrunner.factsheets.morphology_features.MorphologyFactsheetBuilder(morph_path)[source]

Bases: object

Computes the factsheet values for a morphology.

morphology

morphology of the neuron

Type

neurom.core.morphology.Morphology

neurites

list of neurites to be considered

Type

list

neurite_features

list of neurite feature to be used

Type

list

soma_features

list of soma features to be used

Type

list

factsheet_dict()[source]

Returns the factsheet as a dict.

get_feature_values()[source]

Returns the values of all features in a list.

get_neurites()[source]

Return neurite names (str) and types (neurom type).

If basal or apical are not present, name them ‘dendrite’.

Returns

(neurite_names, neurite_types)

Return type

list of tuple

class emodelrunner.factsheets.morphology_features.MorphologyFeature[source]

Bases: object

Morphology feature representation.

name

name of the feature

Type

str

value

value of the feature

Type

float or list

unit

unit of the feature

Type

str

static replace_empty_value(value)[source]

Replaces the empty value with 0 or [0].

Attrs:

value (float or list): the value to be replaced if empty

Returns

float/int or non-empty list

to_dict()[source]

Returns a dictionary from the fields.

class emodelrunner.factsheets.morphology_features.NumberOfSections(morphology, neurite_name, neurite_type)[source]

Bases: MorphologyFeature

Number of sections feature.

name

name of the feature

Type

str

value

value of the feature

Type

float

unit

unit of the feature

Type

str

class emodelrunner.factsheets.morphology_features.NumberOfSegments(morphology, neurite_name, neurite_type)[source]

Bases: MorphologyFeature

Number of segments feature.

name

name of the feature

Type

str

value

value of the feature

Type

float

unit

unit of the feature

Type

str

class emodelrunner.factsheets.morphology_features.SSCXMorphologyFactsheetBuilder(morph_path)[source]

Bases: MorphologyFactsheetBuilder

Morphology factsheet builder for SSCX packages.

class emodelrunner.factsheets.morphology_features.SomaDiamater(morphology)[source]

Bases: MorphologyFeature

Soma diameter feature.

name

name of the feature

Type

str

value

value of the feature

Type

float

unit

unit of the feature

Type

str

class emodelrunner.factsheets.morphology_features.SomaSurfaceArea(morphology)[source]

Bases: MorphologyFeature

Soma surface area feature.

name

name of the feature

Type

str

value

value of the feature

Type

float

unit

unit of the feature

Type

str

class emodelrunner.factsheets.morphology_features.SomaVolume(morphology)[source]

Bases: MorphologyFeature

Soma volume feature.

name

name of the feature

Type

str

value

value of the feature

Type

float

unit

unit of the feature

Type

str

class emodelrunner.factsheets.morphology_features.ThalamusMorphologyFactsheetBuilder(morph_path)[source]

Bases: MorphologyFactsheetBuilder

Morphology factsheet builder for Thalamus packages.

class emodelrunner.factsheets.morphology_features.TotalArea(morphology, neurite_name, neurite_type)[source]

Bases: MorphologyFeature

Total area feature.

name

name of the feature

Type

str

value

value of the feature

Type

float

unit

unit of the feature

Type

str

class emodelrunner.factsheets.morphology_features.TotalDepth(morphology, neurite_name, neurite_type)[source]

Bases: MorphologyFeature

Total depth feature.

name

name of the feature

Type

str

value

value of the feature

Type

float

unit

unit of the feature

Type

str

class emodelrunner.factsheets.morphology_features.TotalHeight(morphology, neurite_name, neurite_type)[source]

Bases: MorphologyFeature

Total height feature.

name

name of the feature

Type

str

value

value of the feature

Type

float

unit

unit of the feature

Type

str

class emodelrunner.factsheets.morphology_features.TotalLength(morphology, neurite_name, neurite_type)[source]

Bases: MorphologyFeature

Total length feature.

name

name of the feature

Type

str

value

value of the feature

Type

float

unit

unit of the feature

Type

str

class emodelrunner.factsheets.morphology_features.TotalVolume(morphology, neurite_name, neurite_type)[source]

Bases: MorphologyFeature

Total volume feature.

name

name of the feature

Type

str

value

value of the feature

Type

float

unit

unit of the feature

Type

str

class emodelrunner.factsheets.morphology_features.TotalWidth(morphology, neurite_name, neurite_type)[source]

Bases: MorphologyFeature

Total width feature.

name

name of the feature

Type

str

value

value of the feature

Type

float

unit

unit of the feature

Type

str