allensdk.brain_observatory.behavior.schemas module

class allensdk.brain_observatory.behavior.schemas.BehaviorMetadataSchema(only=None, exclude=(), many=False, context=None, load_only=(), dump_only=(), partial=False, unknown=None)

Bases: allensdk.brain_observatory.behavior.schemas.RaisingSchema

This schema contains metadata pertaining to behavior.

neurodata_doc = 'Metadata for behavior and behavior + ophys experiments'

neurodata_skip = {'experiment_datetime'}

neurodata_type = 'BehaviorMetadata'

neurodata_type_inc = 'LabMetaData'

opts = <marshmallow.schema.SchemaOpts object>

class allensdk.brain_observatory.behavior.schemas.BehaviorTaskParametersSchema(only=None, exclude=(), many=False, context=None, load_only=(), dump_only=(), partial=False, unknown=None)

Bases: allensdk.brain_observatory.behavior.schemas.RaisingSchema

This schema encompasses task parameters used for behavior or ophys + behavior.

neurodata_doc = 'Metadata for behavior or behavior + ophys task parameters'

neurodata_type = 'BehaviorTaskParameters'

neurodata_type_inc = 'LabMetaData'

opts = <marshmallow.schema.SchemaOpts object>

class allensdk.brain_observatory.behavior.schemas.CompleteOphysBehaviorMetadataSchema(only=None, exclude=(), many=False, context=None, load_only=(), dump_only=(), partial=False, unknown=None)

Bases: allensdk.brain_observatory.behavior.schemas.OphysBehaviorMetadataSchema, allensdk.brain_observatory.behavior.schemas.SubjectMetadataSchema

This schema combines fields from behavior, ophys, and subject schemas. Metadata info is passed by the behavior+ophys session in a combined lump containing all the field types.

opts = <marshmallow.schema.SchemaOpts object>

class allensdk.brain_observatory.behavior.schemas.EyeTrackingRigGeometry(only=None, exclude=(), many=False, context=None, load_only=(), dump_only=(), partial=False, unknown=None)

Bases: allensdk.brain_observatory.behavior.schemas.RaisingSchema

Eye tracking rig geometry

opts = <marshmallow.schema.SchemaOpts object>

class allensdk.brain_observatory.behavior.schemas.NwbOphysMetadataSchema(only=None, exclude=(), many=False, context=None, load_only=(), dump_only=(), partial=False, unknown=None)

Bases: allensdk.brain_observatory.behavior.schemas.RaisingSchema

This schema contains fields that will be stored in pyNWB base classes pertaining to optical physiology.

opts = <marshmallow.schema.SchemaOpts object>

class allensdk.brain_observatory.behavior.schemas.OphysBehaviorMetadataSchema(only=None, exclude=(), many=False, context=None, load_only=(), dump_only=(), partial=False, unknown=None)

Bases: allensdk.brain_observatory.behavior.schemas.BehaviorMetadataSchema, allensdk.brain_observatory.behavior.schemas.OphysMetadataSchema

This schema contains fields pertaining to ophys+behavior. It is used as a template for generating our custom NWB behavior + ophys extension.

neurodata_doc = 'Metadata for behavior + ophys experiments'

neurodata_skip = {'emission_lambda', 'excitation_lambda', 'experiment_datetime', 'indicator', 'ophys_frame_rate', 'targeted_structure'}

neurodata_type = 'OphysBehaviorMetadata'

neurodata_type_inc = 'BehaviorMetadata'

opts = <marshmallow.schema.SchemaOpts object>

class allensdk.brain_observatory.behavior.schemas.OphysEyeTrackingRigMetadataSchema(only=None, exclude=(), many=False, context=None, load_only=(), dump_only=(), partial=False, unknown=None)

Bases: allensdk.brain_observatory.behavior.schemas.RaisingSchema

This schema encompasses metadata for ophys experiment rig

neurodata_doc = 'Metadata for ophys experiment rig'

neurodata_type = 'OphysEyeTrackingRigMetadata'

neurodata_type_inc = 'NWBDataInterface'

opts = <marshmallow.schema.SchemaOpts object>

class allensdk.brain_observatory.behavior.schemas.OphysMetadataSchema(only=None, exclude=(), many=False, context=None, load_only=(), dump_only=(), partial=False, unknown=None)

Bases: allensdk.brain_observatory.behavior.schemas.NwbOphysMetadataSchema

This schema contains metadata pertaining to optical physiology (ophys).

opts = <marshmallow.schema.SchemaOpts object>

class allensdk.brain_observatory.behavior.schemas.RaisingSchema(only=None, exclude=(), many=False, context=None, load_only=(), dump_only=(), partial=False, unknown=None)

Bases: marshmallow.schema.Schema

class Meta

Bases: object

unknown = 'raise'

opts = <marshmallow.schema.SchemaOpts object>

class allensdk.brain_observatory.behavior.schemas.SubjectMetadataSchema(only=None, exclude=(), many=False, context=None, load_only=(), dump_only=(), partial=False, unknown=None)

Bases: allensdk.brain_observatory.behavior.schemas.RaisingSchema

This schema contains metadata pertaining to a subject in either a behavior or behavior + ophys experiment.

neurodata_doc = 'Metadata for an AIBS behavior or behavior + ophys subject'

neurodata_skip = {'age', 'genotype', 'sex', 'subject_id'}

neurodata_type = 'BehaviorSubject'

neurodata_type_inc = 'Subject'

opts = <marshmallow.schema.SchemaOpts object>