neuron_morphology.feature_extractor.mark

Module Contents

Classes

Mark	A tag, intended for use in feature selection.
RequiresLayerAnnotations	A tag, intended for use in feature selection.
Intrinsic	Indicates intrinsic features that don’t rely on a ccf or scale.
Geometric	Indicates features that change depending on coordinate frame.
AllNeuriteTypes	Indicates features that are calculated for all neurite types.
RequiresDendrite	This feature can only be calculated for neurons with at least one
RequiresRelativeSomaDepth	This feature can only be calculated for relative soma depth
RequiresSoma	Indicates that these features require a soma.
RequiresApical	Indicates that these features require an apical dendrite.
RequiresBasal	Indicates that these features require a basal dendrite.
RequiresAxon	Indicates that these features require an axon.
RequiresRoot	Indicates that this features require a root. Warns if the root
BifurcationFeatures	Indicates a feature calculated on bifurcations.
CompartmentFeatures	Indicates a feature calculated on compartments.
TipFeatures	Indicates a feature calculated on tips (leaf nodes).
NeuriteTypeComparison	Indicates a feature that is a comparison between neurite types.
RequiresRadii	This feature can only be calculated if the radii of nodes are annotated.
RequiresReferenceLayerDepths	This feature can only be calculated if a referenceset of average depths
RequiresLayeredPointDepths	This feature can only be calculated if (cortical) points are annotated
RequiresRegularPointSpacing	This features can only be (meaningfully) calculated if the points (e.g.

Functions

check_nodes_have_key(data: Data, key: str) → bool

Checks whether each node in a morphology is annotated with some key.

neuron_morphology.feature_extractor.mark.Mr

class neuron_morphology.feature_extractor.mark.Mark

A tag, intended for use in feature selection.

classmethod validate(cls, data: Data)

Determine if this feature is calculable from the provided data.

Parameters:

data : Data from a single morphological reconstruction

Returns:

whether marked features can be calculated from these data

classmethod factory(cls: Type[Mr], name: str)

class neuron_morphology.feature_extractor.mark.RequiresLayerAnnotations

Bases: neuron_morphology.feature_extractor.mark.Mark

A tag, intended for use in feature selection.

classmethod validate(cls, data: Data)

Checks whether each node in the data’s morphology is annotated with a cortical layer. Returns False if any are missing.

class neuron_morphology.feature_extractor.mark.Intrinsic

Bases: neuron_morphology.feature_extractor.mark.Mark

Indicates intrinsic features that don’t rely on a ccf or scale.

class neuron_morphology.feature_extractor.mark.Geometric

Bases: neuron_morphology.feature_extractor.mark.Mark

Indicates features that change depending on coordinate frame.

class neuron_morphology.feature_extractor.mark.AllNeuriteTypes

Bases: neuron_morphology.feature_extractor.mark.Mark

Indicates features that are calculated for all neurite types.

class neuron_morphology.feature_extractor.mark.RequiresDendrite

Bases: neuron_morphology.feature_extractor.mark.Mark

This feature can only be calculated for neurons with at least one dendrite node

classmethod validate(cls, data: Data)

Determine if this feature is calculable from the provided data.

Parameters:

data : Data from a single morphological reconstruction

Returns:

whether marked features can be calculated from these data

class neuron_morphology.feature_extractor.mark.RequiresRelativeSomaDepth

Bases: neuron_morphology.feature_extractor.mark.Mark

This feature can only be calculated for relative soma depth

classmethod validate(cls, data: Data)

Determine if this feature is calculable from the provided data.

Parameters:

data : Data from a single morphological reconstruction

Returns:

whether marked features can be calculated from these data

class neuron_morphology.feature_extractor.mark.RequiresSoma

Bases: neuron_morphology.feature_extractor.mark.Mark

Indicates that these features require a soma.

classmethod validate(cls, data: Data)

Determine if this feature is calculable from the provided data.

Parameters:

data : Data from a single morphological reconstruction

Returns:

whether marked features can be calculated from these data

class neuron_morphology.feature_extractor.mark.RequiresApical

Bases: neuron_morphology.feature_extractor.mark.Mark

Indicates that these features require an apical dendrite.

classmethod validate(cls, data: Data)

Determine if this feature is calculable from the provided data.

Parameters:

data : Data from a single morphological reconstruction

Returns:

whether marked features can be calculated from these data

class neuron_morphology.feature_extractor.mark.RequiresBasal

Bases: neuron_morphology.feature_extractor.mark.Mark

Indicates that these features require a basal dendrite.

classmethod validate(cls, data: Data)

Determine if this feature is calculable from the provided data.

Parameters:

data : Data from a single morphological reconstruction

Returns:

whether marked features can be calculated from these data

class neuron_morphology.feature_extractor.mark.RequiresAxon

Bases: neuron_morphology.feature_extractor.mark.Mark

Indicates that these features require an axon.

classmethod validate(cls, data: Data)

Determine if this feature is calculable from the provided data.

Parameters:

data : Data from a single morphological reconstruction

Returns:

whether marked features can be calculated from these data

class neuron_morphology.feature_extractor.mark.RequiresRoot

Bases: neuron_morphology.feature_extractor.mark.Mark

Indicates that this features require a root. Warns if the root is not unique

classmethod validate(cls, data: Data)

Determine if this feature is calculable from the provided data.

Parameters:

data : Data from a single morphological reconstruction

Returns:

whether marked features can be calculated from these data

class neuron_morphology.feature_extractor.mark.BifurcationFeatures

Bases: neuron_morphology.feature_extractor.mark.Mark

Indicates a feature calculated on bifurcations.

class neuron_morphology.feature_extractor.mark.CompartmentFeatures

Bases: neuron_morphology.feature_extractor.mark.Mark

Indicates a feature calculated on compartments.

class neuron_morphology.feature_extractor.mark.TipFeatures

Bases: neuron_morphology.feature_extractor.mark.Mark

Indicates a feature calculated on tips (leaf nodes).

class neuron_morphology.feature_extractor.mark.NeuriteTypeComparison

Bases: neuron_morphology.feature_extractor.mark.Mark

Indicates a feature that is a comparison between neurite types.

Function should be decorated with the appropriate RequiresType marks

class neuron_morphology.feature_extractor.mark.RequiresRadii

Bases: neuron_morphology.feature_extractor.mark.Mark

This feature can only be calculated if the radii of nodes are annotated.

classmethod validate(cls, data: Data)

Determine if this feature is calculable from the provided data.

Parameters:

data : Data from a single morphological reconstruction

Returns:

whether marked features can be calculated from these data

class neuron_morphology.feature_extractor.mark.RequiresReferenceLayerDepths

Bases: neuron_morphology.feature_extractor.mark.Mark

This feature can only be calculated if a referenceset of average depths for cortical layers is provided. See features.layer.reference_layer_depths for more information.

classmethod validate(cls, data: Data)

Determine if this feature is calculable from the provided data.

Parameters:

data : Data from a single morphological reconstruction

Returns:

whether marked features can be calculated from these data

class neuron_morphology.feature_extractor.mark.RequiresLayeredPointDepths

Bases: neuron_morphology.feature_extractor.mark.Mark

This feature can only be calculated if (cortical) points are annotated with a collection of within-layer depths. See features.layer.layered_point_depths for more information.

classmethod validate(cls, data: Data)

Determine if this feature is calculable from the provided data.

Parameters:

data : Data from a single morphological reconstruction

Returns:

whether marked features can be calculated from these data

class neuron_morphology.feature_extractor.mark.RequiresRegularPointSpacing

Bases: neuron_morphology.feature_extractor.mark.Mark

This features can only be (meaningfully) calculated if the points (e.g. node positions) on which it is based are resampled to have regular spacing.

neuron_morphology.feature_extractor.mark.check_nodes_have_key(data: Data, key: str) → bool

Checks whether each node in a morphology is annotated with some key.