neuron_morphology.feature_extractor.mark module

class neuron_morphology.feature_extractor.mark.AllNeuriteTypes[source]

Bases: neuron_morphology.feature_extractor.mark.Mark

Indicates features that are calculated for all neurite types.

Methods

validate(data) Determine if this feature is calculable from the provided data.
factory  
class neuron_morphology.feature_extractor.mark.BifurcationFeatures[source]

Bases: neuron_morphology.feature_extractor.mark.Mark

Indicates a feature calculated on bifurcations.

Methods

validate(data) Determine if this feature is calculable from the provided data.
factory  
class neuron_morphology.feature_extractor.mark.CompartmentFeatures[source]

Bases: neuron_morphology.feature_extractor.mark.Mark

Indicates a feature calculated on compartments.

Methods

validate(data) Determine if this feature is calculable from the provided data.
factory  
class neuron_morphology.feature_extractor.mark.Geometric[source]

Bases: neuron_morphology.feature_extractor.mark.Mark

Indicates features that change depending on coordinate frame.

Methods

validate(data) Determine if this feature is calculable from the provided data.
factory  
class neuron_morphology.feature_extractor.mark.Intrinsic[source]

Bases: neuron_morphology.feature_extractor.mark.Mark

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

Methods

validate(data) Determine if this feature is calculable from the provided data.
factory  
class neuron_morphology.feature_extractor.mark.Mark[source]

Bases: object

A tag, intended for use in feature selection.

Methods

validate(data) Determine if this feature is calculable from the provided data.
factory  
classmethod factory(name: str) → Type[~Mr][source]
classmethod validate(data: neuron_morphology.feature_extractor.data.Data) → bool[source]

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.NeuriteTypeComparison[source]

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

Methods

validate(data) Determine if this feature is calculable from the provided data.
factory  
class neuron_morphology.feature_extractor.mark.RequiresApical[source]

Bases: neuron_morphology.feature_extractor.mark.Mark

Indicates that these features require an apical dendrite.

Methods

validate(data) Determine if this feature is calculable from the provided data.
factory  
classmethod validate(data: neuron_morphology.feature_extractor.data.Data) → bool[source]

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[source]

Bases: neuron_morphology.feature_extractor.mark.Mark

Indicates that these features require an axon.

Methods

validate(data) Determine if this feature is calculable from the provided data.
factory  
classmethod validate(data: neuron_morphology.feature_extractor.data.Data) → bool[source]

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[source]

Bases: neuron_morphology.feature_extractor.mark.Mark

Indicates that these features require a basal dendrite.

Methods

validate(data) Determine if this feature is calculable from the provided data.
factory  
classmethod validate(data: neuron_morphology.feature_extractor.data.Data) → bool[source]

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.RequiresDendrite[source]

Bases: neuron_morphology.feature_extractor.mark.Mark

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

Methods

validate(data) Determine if this feature is calculable from the provided data.
factory  
classmethod validate(data: neuron_morphology.feature_extractor.data.Data) → bool[source]

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.RequiresLayerAnnotations[source]

Bases: neuron_morphology.feature_extractor.mark.Mark

Methods

validate(data) Checks whether each node in the data’s morphology is annotated with a cortical layer.
factory  
classmethod validate(data: neuron_morphology.feature_extractor.data.Data) → bool[source]

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.RequiresLayeredPointDepths[source]

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.

Methods

validate(data) Determine if this feature is calculable from the provided data.
factory  
classmethod validate(data: neuron_morphology.feature_extractor.data.Data) → bool[source]

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.RequiresRadii[source]

Bases: neuron_morphology.feature_extractor.mark.Mark

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

Methods

validate(data) Determine if this feature is calculable from the provided data.
factory  
classmethod validate(data: neuron_morphology.feature_extractor.data.Data) → bool[source]

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[source]

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.

Methods

validate(data) Determine if this feature is calculable from the provided data.
factory  
classmethod validate(data: neuron_morphology.feature_extractor.data.Data) → bool[source]

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[source]

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.

Methods

validate(data) Determine if this feature is calculable from the provided data.
factory  
class neuron_morphology.feature_extractor.mark.RequiresRelativeSomaDepth[source]

Bases: neuron_morphology.feature_extractor.mark.Mark

This feature can only be calculated for relative soma depth

Methods

validate(data) Determine if this feature is calculable from the provided data.
factory  
classmethod validate(data: neuron_morphology.feature_extractor.data.Data) → bool[source]

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[source]

Bases: neuron_morphology.feature_extractor.mark.Mark

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

Methods

validate(data) Determine if this feature is calculable from the provided data.
factory  
classmethod validate(data: neuron_morphology.feature_extractor.data.Data) → bool[source]

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[source]

Bases: neuron_morphology.feature_extractor.mark.Mark

Indicates that these features require a soma.

Methods

validate(data) Determine if this feature is calculable from the provided data.
factory  
classmethod validate(data: neuron_morphology.feature_extractor.data.Data) → bool[source]

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.TipFeatures[source]

Bases: neuron_morphology.feature_extractor.mark.Mark

Indicates a feature calculated on tips (leaf nodes).

Methods

validate(data) Determine if this feature is calculable from the provided data.
factory  
neuron_morphology.feature_extractor.mark.check_nodes_have_key(data: neuron_morphology.feature_extractor.data.Data, key: str) → bool[source]

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