allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.ophys_experiment_metadata module

class allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.ophys_experiment_metadata.OphysExperimentMetadata(ophys_experiment_id: int, ophys_session_id: ~allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.ophys_session_id.OphysSessionId, ophys_container_id: ~allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.ophys_container_id.OphysContainerId, field_of_view_shape: ~allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.field_of_view_shape.FieldOfViewShape, imaging_depth: ~allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.imaging_depth.ImagingDepth, targeted_imaging_depth: ~allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.targeted_imaging_depth.TargetedImagingDepth, project_code: ~allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.ophys_project_code.OphysProjectCode = <allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.ophys_project_code.OphysProjectCode object>)[source]

Bases: DataObject, LimsReadableInterface, JsonReadableInterface, NwbReadableInterface

Container class for ophys experiment metadata

property field_of_view_shape: FieldOfViewShape
classmethod from_json(dict_repr: dict) → OphysExperimentMetadata[source]

Populates a DataFile from a JSON compatible dict (likely parsed by argschema)

Returns:
DataObject:

An instantiated DataObject which has name and value properties

classmethod from_lims(ophys_experiment_id: int, lims_db: PostgresQueryMixin) → OphysExperimentMetadata[source]

Populate a DataObject from an internal database (likely LIMS)

Returns:
DataObject:

An instantiated DataObject which has name and value properties

classmethod from_nwb(nwbfile: NWBFile) → OphysExperimentMetadata[source]

Populate a DataObject from a pyNWB file object.

Parameters:
nwbfile:

The file object (NWBFile) of a pynwb dataset file.

Returns:
DataObject:

An instantiated DataObject which has name and value properties

property imaging_depth: int
property ophys_container_id: int
property ophys_experiment_id: int
property ophys_session_id: int
property project_code: str
property targeted_imaging_depth: int
update_targeted_imaging_depth(ophys_experiment_ids: List[int], lims_db: PostgresQueryMixin)[source]

Update the value for targeted imaging depth given a set of experiments to be published.

Compute the targeted_imaging_depth (average over experiments in a container) only for those experiments input.

Parameters:
ophys_experiment_idslist of ints

Set of experiments to calculate targeted_imaging_depth for. Needs to contain the experiment this metadata represents.

lims_dbPostgresQueryMixin

Connection to the LIMS2 database.