Source code for allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.imaging_depth

from pynwb import NWBFile

from allensdk.core import DataObject
from allensdk.core import \
    JsonReadableInterface, LimsReadableInterface, NwbReadableInterface
from allensdk.internal.api import PostgresQueryMixin


class ImagingDepth(DataObject, LimsReadableInterface, NwbReadableInterface,
                   JsonReadableInterface):
    """Data object loads and stores the imaging_depth (microns) for an
    experiments. This is the calculated difference between measured
    z-depths of the surface and imaging_depth.
    """
    def __init__(self, imaging_depth: int):
        super().__init__(name='imaging_depth', value=imaging_depth)

    @classmethod
    def from_lims(cls, ophys_experiment_id: int,
                  lims_db: PostgresQueryMixin) -> "ImagingDepth":
        query = """
                SELECT imd.depth
                FROM ophys_experiments oe
                JOIN ophys_sessions os ON oe.ophys_session_id = os.id
                LEFT JOIN imaging_depths imd ON imd.id = oe.imaging_depth_id
                WHERE oe.id = {};
                """.format(ophys_experiment_id)
        imaging_depth = lims_db.fetchone(query, strict=True)
        return cls(imaging_depth=imaging_depth)

    @classmethod
    def from_json(cls, dict_repr: dict) -> "ImagingDepth":
        # TODO remove all of the from_json loading and validation step
        # ticket 2607
        return cls(imaging_depth=dict_repr['targeted_depth'])

    @classmethod
    def from_nwb(cls, nwbfile: NWBFile) -> "ImagingDepth":
        metadata = nwbfile.lab_meta_data['metadata']
        return cls(imaging_depth=metadata.imaging_depth)