added docstring and reformatted average_container_depth query

AllenInstitute · Nov 14, 2022 · f2b35fe · f2b35fe
1 parent b6d9d21
commit f2b35fe
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Showing 3 changed files with 14 additions and 8 deletions.
diff --git a/...atory/behavior/data_objects/metadata/ophys_experiment_metadata/average_container_depth.py b/...atory/behavior/data_objects/metadata/ophys_experiment_metadata/average_container_depth.py
@@ -10,6 +10,10 @@ class AverageContainerDepth(
     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
@@ -30,19 +34,16 @@ def from_lims(
         container_id = lims_db.fetchone(query_container_id, strict=True)
 
         query_depths = """
-            SELECT id.depth
+            SELECT AVG(id.depth)
             FROM ophys_experiments_visual_behavior_experiment_containers ec
             JOIN ophys_experiments oe ON oe.id = ec.ophys_experiment_id
-            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 ec.visual_behavior_experiment_container_id = {};
         """.format(
             container_id
         )
 
-        imaging_depths = lims_db.fetchall(query_depths)
-        average_container_depth = round(sum(imaging_depths) /
-                                        len(imaging_depths))
+        average_container_depth = lims_db.fetchone(query_depths)
         return cls(average_container_depth=average_container_depth)
 
     @classmethod

diff --git a/...ain_observatory/behavior/data_objects/metadata/ophys_experiment_metadata/imaging_depth.py b/...ain_observatory/behavior/data_objects/metadata/ophys_experiment_metadata/imaging_depth.py
@@ -8,6 +8,10 @@
 
 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)
 
@@ -18,7 +22,7 @@ def from_lims(cls, ophys_experiment_id: int,
                 SELECT id.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)

diff --git a/...sdk/test/brain_observatory/behavior/data_objects/metadata/test_behavior_ophys_metadata.py b/...sdk/test/brain_observatory/behavior/data_objects/metadata/test_behavior_ophys_metadata.py
@@ -63,7 +63,8 @@ def _get_multiplane_meta(self):
             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
+            average_container_depth=ophys_experiment_metadata.
+            _average_container_depth,
             project_code=ophys_experiment_metadata._project_code,
             imaging_plane_group=imaging_plane_group
         )