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. |
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neuron_morphology.feature_extractor.mark.
Mr
¶
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class
neuron_morphology.feature_extractor.mark.
Mark
¶ A tag, intended for use in feature selection.
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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
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classmethod
factory
(cls: Type[Mr], name: str)¶
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classmethod
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class
neuron_morphology.feature_extractor.mark.
RequiresLayerAnnotations
¶ Bases:
neuron_morphology.feature_extractor.mark.Mark
A tag, intended for use in feature selection.
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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.
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classmethod
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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.
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class
neuron_morphology.feature_extractor.mark.
Geometric
¶ Bases:
neuron_morphology.feature_extractor.mark.Mark
Indicates features that change depending on coordinate frame.
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class
neuron_morphology.feature_extractor.mark.
AllNeuriteTypes
¶ Bases:
neuron_morphology.feature_extractor.mark.Mark
Indicates features that are calculated for all neurite types.
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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
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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
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classmethod
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class
neuron_morphology.feature_extractor.mark.
RequiresRelativeSomaDepth
¶ Bases:
neuron_morphology.feature_extractor.mark.Mark
This feature can only be calculated for relative soma depth
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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
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classmethod
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class
neuron_morphology.feature_extractor.mark.
RequiresSoma
¶ Bases:
neuron_morphology.feature_extractor.mark.Mark
Indicates that these features require a soma.
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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
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classmethod
-
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
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classmethod
-
class
neuron_morphology.feature_extractor.mark.
RequiresBasal
¶ Bases:
neuron_morphology.feature_extractor.mark.Mark
Indicates that these features require a basal dendrite.
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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
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classmethod
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class
neuron_morphology.feature_extractor.mark.
RequiresAxon
¶ Bases:
neuron_morphology.feature_extractor.mark.Mark
Indicates that these features require an axon.
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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
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classmethod
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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
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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
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classmethod
-
class
neuron_morphology.feature_extractor.mark.
BifurcationFeatures
¶ Bases:
neuron_morphology.feature_extractor.mark.Mark
Indicates a feature calculated on bifurcations.
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class
neuron_morphology.feature_extractor.mark.
CompartmentFeatures
¶ Bases:
neuron_morphology.feature_extractor.mark.Mark
Indicates a feature calculated on compartments.
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class
neuron_morphology.feature_extractor.mark.
TipFeatures
¶ Bases:
neuron_morphology.feature_extractor.mark.Mark
Indicates a feature calculated on tips (leaf nodes).
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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
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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.
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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
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classmethod
-
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.
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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
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classmethod
-
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.
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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
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classmethod
-
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.
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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.