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