Ticket/2545/dev

allensdk/brain_observatory/behavior/behavior_ophys_experiment.py

@@ -2,44 +2,22 @@
 import pandas as pd
 from pynwb import NWBFile
 
-from allensdk.brain_observatory.behavior.behavior_session import (
-    BehaviorSession)
+from allensdk.brain_observatory.behavior.behavior_session import BehaviorSession  # NOQA
 from allensdk.brain_observatory.behavior.data_files import SyncFile
-from allensdk.brain_observatory.behavior.data_files\
-    .rigid_motion_transform_file import \
-    RigidMotionTransformFile
-from allensdk.brain_observatory.behavior.data_objects import \
-    BehaviorSessionId
-from allensdk.brain_observatory.behavior.data_objects.cell_specimens \
-    .cell_specimens import \
-    CellSpecimens, EventsParams
-from allensdk.brain_observatory.behavior.data_objects.metadata \
-    .behavior_metadata.date_of_acquisition import \
-    DateOfAcquisitionOphys, DateOfAcquisition
-from allensdk.brain_observatory.behavior.data_objects.metadata\
-    .behavior_ophys_metadata import \
-    BehaviorOphysMetadata
-from allensdk.brain_observatory.behavior.data_objects.metadata\
-    .ophys_experiment_metadata.multi_plane_metadata.imaging_plane_group \
-    import \
-    ImagingPlaneGroup
-from allensdk.brain_observatory.behavior.data_objects.metadata\
-    .ophys_experiment_metadata.multi_plane_metadata.multi_plane_metadata \
-    import \
-    MultiplaneMetadata
-from allensdk.brain_observatory.behavior.data_objects.motion_correction \
-    import \
-    MotionCorrection
-from allensdk.brain_observatory.behavior.data_objects.projections import \
-    Projections
-from allensdk.brain_observatory.behavior.data_objects.stimuli.util import \
-    calculate_monitor_delay
-from allensdk.brain_observatory.behavior.data_objects.timestamps \
-    .ophys_timestamps import \
-    OphysTimestamps, OphysTimestampsMultiplane
+from allensdk.brain_observatory.behavior.data_files.rigid_motion_transform_file import RigidMotionTransformFile  # NOQA
+from allensdk.brain_observatory.behavior.data_objects import BehaviorSessionId
+from allensdk.brain_observatory.behavior.data_objects.cell_specimens.cell_specimens import CellSpecimens, EventsParams  # NOQA
+from allensdk.brain_observatory.behavior.data_objects.metadata.behavior_metadata.date_of_acquisition import DateOfAcquisition, DateOfAcquisitionOphys  # NOQA
+from allensdk.brain_observatory.behavior.data_objects.metadata.behavior_ophys_metadata import BehaviorOphysMetadata  # NOQA
+from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.multi_plane_metadata.imaging_plane_group import ImagingPlaneGroup  # NOQA
+from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.multi_plane_metadata.multi_plane_metadata import MultiplaneMetadata  # NOQA
+from allensdk.brain_observatory.behavior.data_objects.motion_correction import MotionCorrection  # NOQA
+from allensdk.brain_observatory.behavior.data_objects.projections import Projections  # NOQA
+from allensdk.brain_observatory.behavior.data_objects.stimuli.util import calculate_monitor_delay  # NOQA
+from allensdk.brain_observatory.behavior.data_objects.timestamps.ophys_timestamps import OphysTimestamps, OphysTimestampsMultiplane  # NOQA
+from allensdk.brain_observatory.behavior.image_api import Image
 from allensdk.core.auth_config import LIMS_DB_CREDENTIAL_MAP
 from allensdk.deprecated import legacy
-from allensdk.brain_observatory.behavior.image_api import Image
 from allensdk.internal.api import db_connection_creator
 
 
@@ -426,6 +404,8 @@ def metadata(self):
             'field_of_view_width':
                 self._metadata.ophys_metadata.field_of_view_shape.width,
             'imaging_depth': self._metadata.ophys_metadata.imaging_depth,
+            'average_container_depth':
+                self._metadata.ophys_metadata.average_container_depth,
             'imaging_plane_group':
                 self._metadata.ophys_metadata.imaging_plane_group
                 if isinstance(self._metadata.ophys_metadata,

allensdk/brain_observatory/behavior/data_objects/metadata/behavior_ophys_metadata.py

@@ -2,26 +2,13 @@
 
 from pynwb import NWBFile
 
-from allensdk.core import DataObject
 from allensdk.brain_observatory.behavior.data_objects import BehaviorSessionId
-from allensdk.core import \
-    JsonReadableInterface, NwbReadableInterface, \
-    LimsReadableInterface
-from allensdk.core import \
-    NwbWritableInterface
-from allensdk.brain_observatory.behavior.data_objects.metadata\
-    .behavior_metadata.behavior_metadata import \
-    BehaviorMetadata
-from allensdk.brain_observatory.behavior.data_objects.metadata\
-    .ophys_experiment_metadata.multi_plane_metadata\
-    .multi_plane_metadata import \
-    MultiplaneMetadata
-from allensdk.brain_observatory.behavior.data_objects.metadata\
-    .ophys_experiment_metadata.ophys_experiment_metadata import \
-    OphysExperimentMetadata
-from allensdk.brain_observatory.behavior.schemas import \
-    OphysBehaviorMetadataSchema
+from allensdk.brain_observatory.behavior.data_objects.metadata.behavior_metadata.behavior_metadata import BehaviorMetadata  # NOQA
+from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.multi_plane_metadata.multi_plane_metadata import MultiplaneMetadata  # NOQA
+from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.ophys_experiment_metadata import OphysExperimentMetadata  # NOQA
+from allensdk.brain_observatory.behavior.schemas import OphysBehaviorMetadataSchema  # NOQA
 from allensdk.brain_observatory.nwb import load_pynwb_extension
+from allensdk.core import DataObject, JsonReadableInterface, LimsReadableInterface, NwbReadableInterface, NwbWritableInterface  # NOQA
 from allensdk.internal.api import PostgresQueryMixin
 
 
@@ -158,6 +145,7 @@ def to_nwb(self, nwbfile: NWBFile) -> NWBFile:
             session_type=behavior_meta.session_type,
             equipment_name=behavior_meta.equipment.value,
             imaging_depth=ophys_meta.imaging_depth,
+            average_container_depth=ophys_meta.average_container_depth,
             behavior_session_uuid=str(behavior_meta.behavior_session_uuid),
             behavior_session_id=behavior_meta.behavior_session_id
         )

allensdk/brain_observatory/behavior/data_objects/metadata/ophys_experiment_metadata/average_container_depth.py

@@ -0,0 +1,58 @@
+from pynwb import NWBFile
+
+from allensdk.core import DataObject, JsonReadableInterface, LimsReadableInterface, NwbReadableInterface  # NOQA
+from allensdk.internal.api import PostgresQueryMixin
+
+
+class AverageContainerDepth(
+    DataObject,
+    LimsReadableInterface,
+    NwbReadableInterface,
+    JsonReadableInterface,
+):
+    """Data object loads and stores the average `imaging_depth`s
+    (microns) across experiments in the container that an experiment is
+    associated with.
+    """
+    def __init__(self, average_container_depth: int):
+        super().__init__(
+            name="average_container_depth", value=average_container_depth
+        )
+
+    @classmethod
+    def from_lims(
+        cls, ophys_experiment_id: int, lims_db: PostgresQueryMixin
+    ) -> "AverageContainerDepth":
+        query_container_id = """
+            SELECT visual_behavior_experiment_container_id
+            FROM ophys_experiments_visual_behavior_experiment_containers
+            WHERE ophys_experiment_id = {}
+        """.format(
+            ophys_experiment_id
+        )
+
+        container_id = lims_db.fetchone(query_container_id, strict=True)
+
+        query_depths = """
+            SELECT AVG(imd.depth)
+            FROM ophys_experiments_visual_behavior_experiment_containers ec
+            JOIN ophys_experiments oe ON oe.id = ec.ophys_experiment_id
+            LEFT JOIN imaging_depths imd ON imd.id = oe.imaging_depth_id
+            WHERE ec.visual_behavior_experiment_container_id = {};
+        """.format(
+            container_id
+        )
+
+        average_container_depth = int(lims_db.fetchone(query_depths))
+        return cls(average_container_depth=average_container_depth)
+
+    @classmethod
+    def from_json(cls, dict_repr: dict) -> "AverageContainerDepth":
+        # TODO remove all of the from_json loading and validation step
+        # ticket 2607
+        return cls(average_container_depth=dict_repr["targeted_depth"])
+
+    @classmethod
+    def from_nwb(cls, nwbfile: NWBFile) -> "AverageContainerDepth":
+        metadata = nwbfile.lab_meta_data["metadata"]
+        return cls(average_container_depth=metadata.average_container_depth)

allensdk/brain_observatory/behavior/data_objects/metadata/ophys_experiment_metadata/imaging_depth.py

@@ -8,24 +8,30 @@
 
 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 id.depth
+                SELECT imd.depth
                 FROM ophys_experiments oe
                 JOIN ophys_sessions os ON oe.ophys_session_id = os.id
-                LEFT JOIN imaging_depths id ON id.id = oe.imaging_depth_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

allensdk/brain_observatory/behavior/data_objects/metadata/ophys_experiment_metadata/multi_plane_metadata/multi_plane_metadata.py

@@ -1,27 +1,13 @@
 from pynwb import NWBFile
 
-from allensdk.brain_observatory.behavior.data_objects.metadata \
-    .ophys_experiment_metadata.ophys_container_id import \
-    OphysContainerId
-from allensdk.brain_observatory.behavior.data_objects.metadata \
-    .ophys_experiment_metadata.field_of_view_shape import \
-    FieldOfViewShape
-from allensdk.brain_observatory.behavior.data_objects.metadata \
-    .ophys_experiment_metadata.imaging_depth import \
-    ImagingDepth
-from allensdk.brain_observatory.behavior.data_objects.metadata \
-    .ophys_experiment_metadata.multi_plane_metadata \
-    .imaging_plane_group import \
-    ImagingPlaneGroup
-from allensdk.brain_observatory.behavior.data_objects.metadata \
-    .ophys_experiment_metadata.ophys_experiment_metadata import \
-    OphysExperimentMetadata
-from allensdk.brain_observatory.behavior.data_objects.metadata \
-    .ophys_experiment_metadata.ophys_session_id import \
-    OphysSessionId
-from allensdk.brain_observatory.behavior.data_objects.metadata \
-    .ophys_experiment_metadata.project_code import \
-    ProjectCode
+from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.field_of_view_shape import FieldOfViewShape  # NOQA
+from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.imaging_depth import ImagingDepth  # NOQA
+from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.multi_plane_metadata.imaging_plane_group import ImagingPlaneGroup  # NOQA
+from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.ophys_container_id import OphysContainerId  # NOQA
+from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.ophys_experiment_metadata import OphysExperimentMetadata  # NOQA
+from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.ophys_session_id import OphysSessionId  # NOQA
+from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.project_code import ProjectCode  # NOQA
+from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.average_container_depth import AverageContainerDepth  # NOQA
 from allensdk.internal.api import PostgresQueryMixin
 
 
@@ -32,6 +18,7 @@ def __init__(self,
                  ophys_container_id: OphysContainerId,
                  field_of_view_shape: FieldOfViewShape,
                  imaging_depth: ImagingDepth,
+                 average_container_depth: AverageContainerDepth,
                  imaging_plane_group: ImagingPlaneGroup,
                  project_code: ProjectCode):
         super().__init__(
@@ -40,6 +27,7 @@ def __init__(self,
             ophys_container_id=ophys_container_id,
             field_of_view_shape=field_of_view_shape,
             imaging_depth=imaging_depth,
+            average_container_depth=average_container_depth,
             project_code=project_code
         )
         self._imaging_plane_group = imaging_plane_group
@@ -55,9 +43,10 @@ def from_lims(
         return cls(
             ophys_experiment_id=ophys_experiment_metadata.ophys_experiment_id,
             ophys_session_id=ophys_experiment_metadata._ophys_session_id,
-            ophys_container_id=ophys_experiment_metadata._ophys_container_id,     # noqa E501
+            ophys_container_id=ophys_experiment_metadata._ophys_container_id,
             field_of_view_shape=ophys_experiment_metadata._field_of_view_shape,
             imaging_depth=ophys_experiment_metadata._imaging_depth,
+            average_container_depth=ophys_experiment_metadata._average_container_depth,  # noqa E501
             project_code=ophys_experiment_metadata._project_code,
             imaging_plane_group=imaging_plane_group
         )
@@ -69,9 +58,10 @@ def from_json(cls, dict_repr: dict) -> "MultiplaneMetadata":
         return cls(
             ophys_experiment_id=ophys_experiment_metadata.ophys_experiment_id,
             ophys_session_id=ophys_experiment_metadata._ophys_session_id,
-            ophys_container_id=ophys_experiment_metadata._ophys_container_id, # noqa E501
+            ophys_container_id=ophys_experiment_metadata._ophys_container_id,
             field_of_view_shape=ophys_experiment_metadata._field_of_view_shape,
             imaging_depth=ophys_experiment_metadata._imaging_depth,
+            average_container_depth=ophys_experiment_metadata._average_container_depth,  # noqa E501
             project_code=ophys_experiment_metadata._project_code,
             imaging_plane_group=imaging_plane_group
         )
@@ -83,9 +73,10 @@ def from_nwb(cls, nwbfile: NWBFile) -> "MultiplaneMetadata":
         return cls(
             ophys_experiment_id=ophys_experiment_metadata.ophys_experiment_id,
             ophys_session_id=ophys_experiment_metadata._ophys_session_id,
-            ophys_container_id=ophys_experiment_metadata._ophys_container_id, # noqa E501
+            ophys_container_id=ophys_experiment_metadata._ophys_container_id,
             field_of_view_shape=ophys_experiment_metadata._field_of_view_shape,
             imaging_depth=ophys_experiment_metadata._imaging_depth,
+            average_container_depth=ophys_experiment_metadata._average_container_depth,  # noqa E501
             project_code=ophys_experiment_metadata._project_code,
             imaging_plane_group=imaging_plane_group
         )