allensdk.brain_observatory.behavior.schemas module

class allensdk.brain_observatory.behavior.schemas.BehaviorMetadataSchema(*, only: types.StrSequenceOrSet | None = None, exclude: types.StrSequenceOrSet = (), many: bool = False, context: dict | None = None, load_only: types.StrSequenceOrSet = (), dump_only: types.StrSequenceOrSet = (), partial: bool | types.StrSequenceOrSet | None = None, unknown: str | None = None)

Bases: RaisingSchema

This schema contains metadata pertaining to behavior.

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

neurodata_skip = {'date_of_acquisition'}

neurodata_type = 'BehaviorMetadata'

neurodata_type_inc = 'LabMetaData'

opts: SchemaOpts = <marshmallow.schema.SchemaOpts object>

class allensdk.brain_observatory.behavior.schemas.BehaviorTaskParametersSchema(*, only: types.StrSequenceOrSet | None = None, exclude: types.StrSequenceOrSet = (), many: bool = False, context: dict | None = None, load_only: types.StrSequenceOrSet = (), dump_only: types.StrSequenceOrSet = (), partial: bool | types.StrSequenceOrSet | None = None, unknown: str | None = None)

Bases: 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: SchemaOpts = <marshmallow.schema.SchemaOpts object>

class allensdk.brain_observatory.behavior.schemas.CompleteOphysBehaviorMetadataSchema(*, only: types.StrSequenceOrSet | None = None, exclude: types.StrSequenceOrSet = (), many: bool = False, context: dict | None = None, load_only: types.StrSequenceOrSet = (), dump_only: types.StrSequenceOrSet = (), partial: bool | types.StrSequenceOrSet | None = None, unknown: str | None = None)

Bases: OphysBehaviorMetadataSchema, 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.

dump_fields: Dict[str, ma_fields.Field]

exclude: set[Any] | MutableSet[Any]

fields: Dict[str, ma_fields.Field]

Dictionary mapping field_names -> Field objects

load_fields: Dict[str, ma_fields.Field]

opts: SchemaOpts = <marshmallow.schema.SchemaOpts object>

class allensdk.brain_observatory.behavior.schemas.EyeTrackingRigGeometry(*, only: types.StrSequenceOrSet | None = None, exclude: types.StrSequenceOrSet = (), many: bool = False, context: dict | None = None, load_only: types.StrSequenceOrSet = (), dump_only: types.StrSequenceOrSet = (), partial: bool | types.StrSequenceOrSet | None = None, unknown: str | None = None)

Bases: RaisingSchema

Eye tracking rig geometry

opts: SchemaOpts = <marshmallow.schema.SchemaOpts object>

class allensdk.brain_observatory.behavior.schemas.NwbOphysMetadataSchema(*, only: types.StrSequenceOrSet | None = None, exclude: types.StrSequenceOrSet = (), many: bool = False, context: dict | None = None, load_only: types.StrSequenceOrSet = (), dump_only: types.StrSequenceOrSet = (), partial: bool | types.StrSequenceOrSet | None = None, unknown: str | None = None)

Bases: RaisingSchema

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

opts: SchemaOpts = <marshmallow.schema.SchemaOpts object>

class allensdk.brain_observatory.behavior.schemas.OphysBehaviorMetadataSchema(*, only: types.StrSequenceOrSet | None = None, exclude: types.StrSequenceOrSet = (), many: bool = False, context: dict | None = None, load_only: types.StrSequenceOrSet = (), dump_only: types.StrSequenceOrSet = (), partial: bool | types.StrSequenceOrSet | None = None, unknown: str | None = None)

Bases: BehaviorMetadataSchema, OphysMetadataSchema

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

dump_fields: Dict[str, ma_fields.Field]

exclude: set[Any] | MutableSet[Any]

fields: Dict[str, ma_fields.Field]

Dictionary mapping field_names -> Field objects

load_fields: Dict[str, ma_fields.Field]

neurodata_doc = 'Metadata for behavior + ophys experiments'

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

neurodata_type = 'OphysBehaviorMetadata'

neurodata_type_inc = 'BehaviorMetadata'

opts: SchemaOpts = <marshmallow.schema.SchemaOpts object>

class allensdk.brain_observatory.behavior.schemas.OphysEyeTrackingRigMetadataSchema(*, only: types.StrSequenceOrSet | None = None, exclude: types.StrSequenceOrSet = (), many: bool = False, context: dict | None = None, load_only: types.StrSequenceOrSet = (), dump_only: types.StrSequenceOrSet = (), partial: bool | types.StrSequenceOrSet | None = None, unknown: str | None = None)

Bases: RaisingSchema

This schema encompasses metadata for ophys experiment rig

neurodata_doc = 'Metadata for ophys experiment rig'

neurodata_type = 'OphysEyeTrackingRigMetadata'

neurodata_type_inc = 'NWBDataInterface'

opts: SchemaOpts = <marshmallow.schema.SchemaOpts object>

class allensdk.brain_observatory.behavior.schemas.OphysMetadataSchema(*, only: types.StrSequenceOrSet | None = None, exclude: types.StrSequenceOrSet = (), many: bool = False, context: dict | None = None, load_only: types.StrSequenceOrSet = (), dump_only: types.StrSequenceOrSet = (), partial: bool | types.StrSequenceOrSet | None = None, unknown: str | None = None)

Bases: NwbOphysMetadataSchema

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

dump_fields: Dict[str, ma_fields.Field]

exclude: set[Any] | MutableSet[Any]

fields: Dict[str, ma_fields.Field]

Dictionary mapping field_names -> Field objects

load_fields: Dict[str, ma_fields.Field]

opts: SchemaOpts = <marshmallow.schema.SchemaOpts object>

class allensdk.brain_observatory.behavior.schemas.RaisingSchema(*, only: types.StrSequenceOrSet | None = None, exclude: types.StrSequenceOrSet = (), many: bool = False, context: dict | None = None, load_only: types.StrSequenceOrSet = (), dump_only: types.StrSequenceOrSet = (), partial: bool | types.StrSequenceOrSet | None = None, unknown: str | None = None)

Bases: Schema

class Meta

Bases: object

unknown = 'raise'

opts: SchemaOpts = <marshmallow.schema.SchemaOpts object>

class allensdk.brain_observatory.behavior.schemas.SubjectMetadataSchema(*, only: types.StrSequenceOrSet | None = None, exclude: types.StrSequenceOrSet = (), many: bool = False, context: dict | None = None, load_only: types.StrSequenceOrSet = (), dump_only: types.StrSequenceOrSet = (), partial: bool | types.StrSequenceOrSet | None = None, unknown: str | None = None)

Bases: RaisingSchema

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

dump_fields: Dict[str, ma_fields.Field]

exclude: set[Any] | MutableSet[Any]

fields: Dict[str, ma_fields.Field]

Dictionary mapping field_names -> Field objects

load_fields: Dict[str, ma_fields.Field]

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

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

neurodata_type = 'BehaviorSubject'

neurodata_type_inc = 'Subject'

opts: SchemaOpts = <marshmallow.schema.SchemaOpts object>