allensdk.brain_observatory.behavior.schemas module

class allensdk.brain_observatory.behavior.schemas.BehaviorMetadataSchema(*, only: Union[Sequence[str], Set[str], None] = None, exclude: Union[Sequence[str], Set[str]] = (), many: bool = False, context: Optional[Dict[KT, VT]] = None, load_only: Union[Sequence[str], Set[str]] = (), dump_only: Union[Sequence[str], Set[str]] = (), partial: Union[bool, Sequence[str], Set[str]] = False, unknown: Optional[str] = None)[source]

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 = {'date_of_acquisition'}
neurodata_type = 'BehaviorMetadata'
neurodata_type_inc = 'LabMetaData'
opts = <marshmallow.schema.SchemaOpts object>
class allensdk.brain_observatory.behavior.schemas.BehaviorTaskParametersSchema(*, only: Union[Sequence[str], Set[str], None] = None, exclude: Union[Sequence[str], Set[str]] = (), many: bool = False, context: Optional[Dict[KT, VT]] = None, load_only: Union[Sequence[str], Set[str]] = (), dump_only: Union[Sequence[str], Set[str]] = (), partial: Union[bool, Sequence[str], Set[str]] = False, unknown: Optional[str] = None)[source]

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: Union[Sequence[str], Set[str], None] = None, exclude: Union[Sequence[str], Set[str]] = (), many: bool = False, context: Optional[Dict[KT, VT]] = None, load_only: Union[Sequence[str], Set[str]] = (), dump_only: Union[Sequence[str], Set[str]] = (), partial: Union[bool, Sequence[str], Set[str]] = False, unknown: Optional[str] = None)[source]

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: Union[Sequence[str], Set[str], None] = None, exclude: Union[Sequence[str], Set[str]] = (), many: bool = False, context: Optional[Dict[KT, VT]] = None, load_only: Union[Sequence[str], Set[str]] = (), dump_only: Union[Sequence[str], Set[str]] = (), partial: Union[bool, Sequence[str], Set[str]] = False, unknown: Optional[str] = None)[source]

Bases: allensdk.brain_observatory.behavior.schemas.RaisingSchema

Eye tracking rig geometry

opts = <marshmallow.schema.SchemaOpts object>
class allensdk.brain_observatory.behavior.schemas.NwbOphysMetadataSchema(*, only: Union[Sequence[str], Set[str], None] = None, exclude: Union[Sequence[str], Set[str]] = (), many: bool = False, context: Optional[Dict[KT, VT]] = None, load_only: Union[Sequence[str], Set[str]] = (), dump_only: Union[Sequence[str], Set[str]] = (), partial: Union[bool, Sequence[str], Set[str]] = False, unknown: Optional[str] = None)[source]

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: Union[Sequence[str], Set[str], None] = None, exclude: Union[Sequence[str], Set[str]] = (), many: bool = False, context: Optional[Dict[KT, VT]] = None, load_only: Union[Sequence[str], Set[str]] = (), dump_only: Union[Sequence[str], Set[str]] = (), partial: Union[bool, Sequence[str], Set[str]] = False, unknown: Optional[str] = None)[source]

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 = {'date_of_acquisition', 'emission_lambda', 'excitation_lambda', '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: Union[Sequence[str], Set[str], None] = None, exclude: Union[Sequence[str], Set[str]] = (), many: bool = False, context: Optional[Dict[KT, VT]] = None, load_only: Union[Sequence[str], Set[str]] = (), dump_only: Union[Sequence[str], Set[str]] = (), partial: Union[bool, Sequence[str], Set[str]] = False, unknown: Optional[str] = None)[source]

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: Union[Sequence[str], Set[str], None] = None, exclude: Union[Sequence[str], Set[str]] = (), many: bool = False, context: Optional[Dict[KT, VT]] = None, load_only: Union[Sequence[str], Set[str]] = (), dump_only: Union[Sequence[str], Set[str]] = (), partial: Union[bool, Sequence[str], Set[str]] = False, unknown: Optional[str] = None)[source]

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: Union[Sequence[str], Set[str], None] = None, exclude: Union[Sequence[str], Set[str]] = (), many: bool = False, context: Optional[Dict[KT, VT]] = None, load_only: Union[Sequence[str], Set[str]] = (), dump_only: Union[Sequence[str], Set[str]] = (), partial: Union[bool, Sequence[str], Set[str]] = False, unknown: Optional[str] = None)[source]

Bases: marshmallow.schema.Schema

class Meta[source]

Bases: object

unknown = 'raise'
opts = <marshmallow.schema.SchemaOpts object>
class allensdk.brain_observatory.behavior.schemas.SubjectMetadataSchema(*, only: Union[Sequence[str], Set[str], None] = None, exclude: Union[Sequence[str], Set[str]] = (), many: bool = False, context: Optional[Dict[KT, VT]] = None, load_only: Union[Sequence[str], Set[str]] = (), dump_only: Union[Sequence[str], Set[str]] = (), partial: Union[bool, Sequence[str], Set[str]] = False, unknown: Optional[str] = None)[source]

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_in_days', 'genotype', 'sex', 'subject_id'}
neurodata_type = 'BehaviorSubject'
neurodata_type_inc = 'Subject'
opts = <marshmallow.schema.SchemaOpts object>