rename target_imaging_depth to average_container_depth

allensdk/brain_observatory/behavior/behavior_ophys_experiment.py

@@ -404,8 +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,
-            'target_imaging_depth':
-                self._metadata.ophys_metadata.target_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

@@ -145,7 +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,
-            target_imaging_depth=ophys_meta.target_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/target_imaging_depth.py → allensdk/brain_observatory/behavior/data_objects/metadata/ophys_experiment_metadata/average_container_depth.py

@@ -4,21 +4,21 @@
 from allensdk.internal.api import PostgresQueryMixin
 
 
-class TargetImagingDepth(
+class AverageContainerDepth(
     DataObject,
     LimsReadableInterface,
     NwbReadableInterface,
     JsonReadableInterface,
 ):
-    def __init__(self, target_imaging_depth: int):
+    def __init__(self, average_container_depth: int):
         super().__init__(
-            name="target_imaging_depth", value=target_imaging_depth
+            name="average_container_depth", value=average_container_depth
         )
 
     @classmethod
     def from_lims(
         cls, ophys_experiment_id: int, lims_db: PostgresQueryMixin
-    ) -> "TargetImagingDepth":
+    ) -> "AverageContainerDepth":
         query_container_id = """
             SELECT visual_behavior_experiment_container_id
             FROM ophys_experiments_visual_behavior_experiment_containers
@@ -41,14 +41,14 @@ def from_lims(
         )
 
         imaging_depths = lims_db.fetchall(query_depths)
-        target_imaging_depth = round(sum(imaging_depths) / len(imaging_depths))
-        return cls(target_imaging_depth=target_imaging_depth)
+        average_container_depth = round(sum(imaging_depths) / len(imaging_depths))
+        return cls(average_container_depth=average_container_depth)
 
     @classmethod
-    def from_json(cls, dict_repr: dict) -> "TargetImagingDepth":
-        return cls(target_imaging_depth=dict_repr["targeted_imaging_depth"])
+    def from_json(cls, dict_repr: dict) -> "AverageContainerDepth":
+        return cls(average_container_depth=dict_repr["targeted_imaging_depth"])
 
     @classmethod
-    def from_nwb(cls, nwbfile: NWBFile) -> "TargetImagingDepth":
+    def from_nwb(cls, nwbfile: NWBFile) -> "AverageContainerDepth":
         metadata = nwbfile.lab_meta_data["metadata"]
-        return cls(target_imaging_depth=metadata.target_imaging_depth)
+        return cls(average_container_depth=metadata.average_container_depth)

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

@@ -7,7 +7,7 @@
 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.target_imaging_depth import TargetImagingDepth  # NOQA
+from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.average_container_depth import AverageContainerDepth  # NOQA
 from allensdk.internal.api import PostgresQueryMixin
 
 
@@ -18,7 +18,7 @@ def __init__(self,
                  ophys_container_id: OphysContainerId,
                  field_of_view_shape: FieldOfViewShape,
                  imaging_depth: ImagingDepth,
-                 target_imaging_depth: TargetImagingDepth,
+                 average_container_depth: AverageContainerDepth,
                  imaging_plane_group: ImagingPlaneGroup,
                  project_code: ProjectCode):
         super().__init__(
@@ -27,7 +27,7 @@ def __init__(self,
             ophys_container_id=ophys_container_id,
             field_of_view_shape=field_of_view_shape,
             imaging_depth=imaging_depth,
-            target_imaging_depth=target_imaging_depth,
+            average_container_depth=average_container_depth,
             project_code=project_code
         )
         self._imaging_plane_group = imaging_plane_group
@@ -46,7 +46,7 @@ def from_lims(
             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,
-            target_imaging_depth=ophys_experiment_metadata._target_imaging_depth,  # noqa E501
+            average_container_depth=ophys_experiment_metadata._average_container_depth,  # noqa E501
             project_code=ophys_experiment_metadata._project_code,
             imaging_plane_group=imaging_plane_group
         )
@@ -61,7 +61,7 @@ def from_json(cls, dict_repr: dict) -> "MultiplaneMetadata":
             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,
-            target_imaging_depth=ophys_experiment_metadata._target_imaging_depth,  # noqa E501
+            average_container_depth=ophys_experiment_metadata._average_container_depth,  # noqa E501
             project_code=ophys_experiment_metadata._project_code,
             imaging_plane_group=imaging_plane_group
         )
@@ -76,7 +76,7 @@ def from_nwb(cls, nwbfile: NWBFile) -> "MultiplaneMetadata":
             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,
-            target_imaging_depth=ophys_experiment_metadata._target_imaging_depth,  # noqa E501
+            average_container_depth=ophys_experiment_metadata._average_container_depth,  # noqa E501
             project_code=ophys_experiment_metadata._project_code,
             imaging_plane_group=imaging_plane_group
         )

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

@@ -7,7 +7,7 @@
 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_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.target_imaging_depth import TargetImagingDepth  # NOQA
+from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.average_container_depth import AverageContainerDepth  # NOQA
 from allensdk.core import DataObject, JsonReadableInterface, LimsReadableInterface, NwbReadableInterface  # NOQA
 from allensdk.internal.api import PostgresQueryMixin
 
@@ -21,7 +21,7 @@ def __init__(self,
                  ophys_container_id: OphysContainerId,
                  field_of_view_shape: FieldOfViewShape,
                  imaging_depth: ImagingDepth,
-                 target_imaging_depth: TargetImagingDepth,
+                 average_container_depth: AverageContainerDepth,
                  project_code: Optional[ProjectCode] = None):
         super().__init__(name='ophys_experiment_metadata', value=None,
                          is_value_self=True)
@@ -30,7 +30,7 @@ def __init__(self,
         self._ophys_container_id = ophys_container_id
         self._field_of_view_shape = field_of_view_shape
         self._imaging_depth = imaging_depth
-        self._target_imaging_depth = target_imaging_depth
+        self._average_container_depth = average_container_depth
         self._project_code = project_code
 
         # project_code needs to be excluded from comparison
@@ -49,7 +49,7 @@ def from_lims(
             ophys_experiment_id=ophys_experiment_id, lims_db=lims_db)
         imaging_depth = ImagingDepth.from_lims(
             ophys_experiment_id=ophys_experiment_id, lims_db=lims_db)
-        target_imaging_depth = TargetImagingDepth.from_lims(
+        average_container_depth = AverageContainerDepth.from_lims(
             ophys_experiment_id=ophys_experiment_id, lims_db=lims_db)
         project_code = ProjectCode.from_lims(
             ophys_experiment_id=ophys_experiment_id, lims_db=lims_db)
@@ -60,7 +60,7 @@ def from_lims(
             ophys_container_id=ophys_container_id,
             field_of_view_shape=field_of_view_shape,
             imaging_depth=imaging_depth,
-            target_imaging_depth=target_imaging_depth,
+            average_container_depth=average_container_depth,
             project_code=project_code
         )
 
@@ -72,7 +72,7 @@ def from_json(cls, dict_repr: dict) -> "OphysExperimentMetadata":
         ophys_experiment_id = dict_repr['ophys_experiment_id']
         field_of_view_shape = FieldOfViewShape.from_json(dict_repr=dict_repr)
         imaging_depth = ImagingDepth.from_json(dict_repr=dict_repr)
-        target_imaging_depth = TargetImagingDepth.from_json(
+        average_container_depth = AverageContainerDepth.from_json(
             dict_repr=dict_repr
         )
 
@@ -82,7 +82,7 @@ def from_json(cls, dict_repr: dict) -> "OphysExperimentMetadata":
             ophys_container_id=ophys_container_id,
             field_of_view_shape=field_of_view_shape,
             imaging_depth=imaging_depth,
-            target_imaging_depth=target_imaging_depth
+            average_container_depth=average_container_depth
         )
 
     @classmethod
@@ -93,15 +93,15 @@ def from_nwb(cls, nwbfile: NWBFile) -> "OphysExperimentMetadata":
             nwbfile=nwbfile)
         field_of_view_shape = FieldOfViewShape.from_nwb(nwbfile=nwbfile)
         imaging_depth = ImagingDepth.from_nwb(nwbfile=nwbfile)
-        target_imaging_depth = TargetImagingDepth.from_nwb(nwbfile=nwbfile)
+        average_container_depth = AverageContainerDepth.from_nwb(nwbfile=nwbfile)
 
         return OphysExperimentMetadata(
             ophys_experiment_id=ophys_experiment_id,
             ophys_session_id=ophys_session_id,
             ophys_container_id=ophys_container_id,
             field_of_view_shape=field_of_view_shape,
             imaging_depth=imaging_depth,
-            target_imaging_depth=target_imaging_depth
+            average_container_depth=average_container_depth
         )
 
     @property
@@ -117,8 +117,8 @@ def imaging_depth(self) -> int:
         return self._imaging_depth.value
 
     @property
-    def target_imaging_depth(self) -> int:
-        return self._target_imaging_depth.value
+    def average_container_depth(self) -> int:
+        return self._average_container_depth.value
 
     @property
     def ophys_experiment_id(self) -> int:

allensdk/brain_observatory/behavior/schemas.py

@@ -148,7 +148,7 @@ class OphysMetadataSchema(NwbOphysMetadataSchema):
              'targeted for two-photon acquisition'),
         required=True,
     )
-    target_imaging_depth = fields.Int(
+    average_container_depth = fields.Int(
         doc=(
             "Average Depth (microns) below the cortical surface "
             "across experiments of a container."

allensdk/brain_observatory/nwb/ndx-aibs-behavior-ophys.extension.yaml

@@ -119,7 +119,7 @@ groups:
   - name: imaging_depth
     dtype: int
     doc: Depth (microns) below the cortical surface targeted for two-photon acquisition
-  - name: target_imaging_depth
+  - name: average_container_depth
     dtype: int
     doc: Average imaging_depth (microns) across experiments in a container
 - neurodata_type_def: OphysEyeTrackingRigMetadata

allensdk/test/brain_observatory/behavior/data_objects/metadata/test_behavior_ophys_metadata.py

@@ -15,7 +15,7 @@
 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.target_imaging_depth import TargetImagingDepth  # NOQA
+from allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.average_container_depth import AverageContainerDepth  # NOQA
 from allensdk.core.auth_config import LIMS_DB_CREDENTIAL_MAP
 from allensdk.internal.api import db_connection_creator
 from allensdk.test.brain_observatory.behavior.data_objects.metadata.behavior_metadata.test_behavior_metadata import TestBehaviorMetadata  # NOQA
@@ -38,7 +38,7 @@ def _get_meta():
                 ophys_container_id=5678),
             field_of_view_shape=FieldOfViewShape(width=4, height=4),
             imaging_depth=ImagingDepth(imaging_depth=375),
-            target_imaging_depth=TargetImagingDepth(target_imaging_depth=375)
+            average_container_depth=AverageContainerDepth(average_container_depth=375)
         )
 
         behavior_metadata = TestBehaviorMetadata()
@@ -62,7 +62,7 @@ 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,
-            target_imaging_depth=ophys_experiment_metadata._target_imaging_depth,  # noqa E501
+            average_container_depth=ophys_experiment_metadata._average_container_depth,  # noqa E501
             project_code=ophys_experiment_metadata._project_code,
             imaging_plane_group=imaging_plane_group
         )
@@ -99,7 +99,7 @@ def test_from_lims(self, meso):
             assert isinstance(bom.ophys_metadata,
                               MultiplaneMetadata)
             assert bom.ophys_metadata.imaging_depth == 150
-            assert bom.ophys_metadata.target_imaging_depth == 150
+            assert bom.ophys_metadata.average_container_depth == 150
             assert bom.behavior_metadata.session_type == 'OPHYS_1_images_A'
             assert bom.behavior_metadata.subject_metadata.reporter_line == \
                    'Ai148(TIT2L-GC6f-ICL-tTA2)'
@@ -113,7 +113,7 @@ def test_from_lims(self, meso):
         else:
             assert isinstance(bom.ophys_metadata, OphysExperimentMetadata)
             assert bom.ophys_metadata.imaging_depth == 175
-            assert bom.ophys_metadata.target_imaging_depth == 175
+            assert bom.ophys_metadata.average_container_depth == 175
             assert bom.behavior_metadata.session_type == 'OPHYS_4_images_A'
             assert bom.behavior_metadata.subject_metadata.reporter_line == \
                    'Ai93(TITL-GCaMP6f)'

allensdk/test/brain_observatory/behavior/test_behavior_ophys_experiment.py

@@ -103,7 +103,7 @@ def test_visbeh_ophys_data_set():
             datetime.datetime(2018, 11, 30, 23, 28, 37)),
         'ophys_frame_rate': 31.0,
         'imaging_depth': 375,
-        'target_imaging_depth': 375,
+        'average_container_depth': 375,
         'mouse_id': 416369,
         'ophys_container_id': 814796558,
         'targeted_structure': 'VISp',