allensdk.brain_observatory.behavior.schemas module¶
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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.
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neurodata_doc
= 'Metadata for behavior and behavior + ophys experiments'¶
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neurodata_skip
= {'date_of_acquisition'}¶
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neurodata_type
= 'BehaviorMetadata'¶
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neurodata_type_inc
= 'LabMetaData'¶
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opts
= <marshmallow.schema.SchemaOpts object>¶
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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.
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neurodata_doc
= 'Metadata for behavior or behavior + ophys task parameters'¶
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neurodata_type
= 'BehaviorTaskParameters'¶
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neurodata_type_inc
= 'LabMetaData'¶
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opts
= <marshmallow.schema.SchemaOpts object>¶
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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.
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opts
= <marshmallow.schema.SchemaOpts object>¶
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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
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opts
= <marshmallow.schema.SchemaOpts object>¶
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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.
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opts
= <marshmallow.schema.SchemaOpts object>¶
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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.
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neurodata_doc
= 'Metadata for behavior + ophys experiments'¶
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neurodata_skip
= {'date_of_acquisition', 'emission_lambda', 'excitation_lambda', 'indicator', 'ophys_frame_rate', 'targeted_structure'}¶
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neurodata_type
= 'OphysBehaviorMetadata'¶
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neurodata_type_inc
= 'BehaviorMetadata'¶
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opts
= <marshmallow.schema.SchemaOpts object>¶
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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
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neurodata_doc
= 'Metadata for ophys experiment rig'¶
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neurodata_type
= 'OphysEyeTrackingRigMetadata'¶
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neurodata_type_inc
= 'NWBDataInterface'¶
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opts
= <marshmallow.schema.SchemaOpts object>¶
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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).
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opts
= <marshmallow.schema.SchemaOpts object>¶
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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
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opts
= <marshmallow.schema.SchemaOpts object>¶
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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.
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neurodata_doc
= 'Metadata for an AIBS behavior or behavior + ophys subject'¶
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neurodata_skip
= {'age_in_days', 'genotype', 'sex', 'subject_id'}¶
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neurodata_type
= 'BehaviorSubject'¶
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neurodata_type_inc
= 'Subject'¶
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opts
= <marshmallow.schema.SchemaOpts object>¶
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