Merge pull request #94 from catalystneuro/adjust_processing_submodules

Adjust behavior modules

src/ibl_to_nwb/_scripts/convert_brainwide_map_processed_only.py

@@ -51,8 +51,6 @@
             one=ibl_client,
             session=session_id,
             camera_name=camera_name,
-            include_video=False,
-            include_pose=True,
             revision=revision,
         )
     )

src/ibl_to_nwb/datainterfaces/_lick_times.py

@@ -29,5 +29,5 @@ def add_to_nwbfile(self, nwbfile: NWBFile, metadata: dict):
             ],
         )
 
-        behavior_module = get_module(nwbfile=nwbfile, name="behavior", description="Processed behavioral data.")
-        behavior_module.add(lick_events_table)
+        camera_module = get_module(nwbfile=nwbfile, name="camera", description="Processed camera data.")
+        camera_module.add(lick_events_table)

src/ibl_to_nwb/datainterfaces/_pose_estimation.py

@@ -90,5 +90,6 @@ def add_to_nwbfile(self, nwbfile: NWBFile, metadata: dict) -> None:
             nodes=body_parts,
         )
         pose_estimation_container = PoseEstimation(**pose_estimation_kwargs)
-        behavior_module = get_module(nwbfile=nwbfile, name="behavior", description="Processed behavioral data.")
-        behavior_module.add(pose_estimation_container)
+
+        camera_module = get_module(nwbfile=nwbfile, name="camera", description="Processed camera data.")
+        camera_module.add(pose_estimation_container)

src/ibl_to_nwb/datainterfaces/_pupil_tracking.py

@@ -45,5 +45,5 @@ def add_to_nwbfile(self, nwbfile, metadata: dict):
         # in this case I'd say LeftPupilTracking and RightPupilTracking reads better
         pupil_tracking = PupilTracking(name=f"{left_or_right.capitalize()}PupilTracking", time_series=pupil_time_series)
 
-        behavior_module = get_module(nwbfile=nwbfile, name="behavior", description="Processed behavioral data.")
-        behavior_module.add(pupil_tracking)
+        camera_module = get_module(nwbfile=nwbfile, name="camera", description="Processed camera data.")
+        camera_module.add(pupil_tracking)

src/ibl_to_nwb/datainterfaces/_roi_motion_energy.py

@@ -38,5 +38,5 @@ def add_to_nwbfile(self, nwbfile, metadata: dict):
             unit="a.u.",
         )
 
-        behavior_module = get_module(nwbfile=nwbfile, name="behavior", description="Processed behavioral data.")
-        behavior_module.add(motion_energy_series)
+        camera_module = get_module(nwbfile=nwbfile, name="camera", description="Processed camera data.")
+        camera_module.add(motion_energy_series)

src/ibl_to_nwb/datainterfaces/_wheel_movement.py

@@ -78,7 +78,7 @@ def add_to_nwbfile(self, nwbfile, metadata: dict):
             unit="rad/s^2",
         )
 
-        behavior_module = get_module(nwbfile=nwbfile, name="behavior", description="Processed behavioral data.")
+        behavior_module = get_module(nwbfile=nwbfile, name="wheel", description="Processed wheel data.")
         behavior_module.add(wheel_movement_intervals)
         behavior_module.add(compass_direction)
         behavior_module.add(velocity_series)

src/ibl_to_nwb/testing/_consistency_checks.py

@@ -27,9 +27,9 @@ def check_written_nwbfile_for_consistency(*, one: ONE, nwbfile_path: Path):
 
 
 def _check_wheel_data(*, eid: str, one: ONE, nwbfile: NWBFile, revision: str = None):
-    processing_module = nwbfile.processing["behavior"]
+    processing_module = nwbfile.processing["wheel"]
     wheel_position_series = processing_module.data_interfaces["CompassDirection"].spatial_series["WheelPositionSeries"]
-    wheel_movement_table = nwbfile.processing["behavior"].data_interfaces["WheelMovementIntervals"][:]
+    wheel_movement_table = processing_module.data_interfaces["WheelMovementIntervals"][:]
 
     # wheel position
     data_from_ONE = one.load_dataset(id=eid, dataset="_ibl_wheel.position", collection="alf")
@@ -44,7 +44,7 @@ def _check_wheel_data(*, eid: str, one: ONE, nwbfile: NWBFile, revision: str = N
     # wheel movement intervals
     data_from_ONE = one.load_dataset(id=eid, dataset="_ibl_wheelMoves.intervals", collection="alf")
     data_from_NWB = wheel_movement_table[["start_time", "stop_time"]].values
-    assert_frame_equal(left=data_from_ONE, right=data_from_NWB)
+    assert_array_equal(x=data_from_ONE, y=data_from_NWB)
 
     # peak amplitude of wheel movement
     data_from_ONE = one.load_dataset(id=eid, dataset="_ibl_wheelMoves.peakAmplitude", collection="alf")
@@ -53,7 +53,7 @@ def _check_wheel_data(*, eid: str, one: ONE, nwbfile: NWBFile, revision: str = N
 
 
 def _check_lick_data(*, eid: str, one: ONE, nwbfile: NWBFile):
-    processing_module = nwbfile.processing["behavior"]
+    processing_module = nwbfile.processing["camera"]
     lick_times_table = processing_module.data_interfaces["LickTimes"][:]
 
     data_from_NWB = lick_times_table["lick_time"].values
@@ -62,7 +62,7 @@ def _check_lick_data(*, eid: str, one: ONE, nwbfile: NWBFile):
 
 
 def _check_roi_motion_energy_data(*, eid: str, one: ONE, nwbfile: NWBFile):
-    processing_module = nwbfile.processing["behavior"]
+    processing_module = nwbfile.processing["camera"]
 
     camera_views = ["body", "left", "right"]
     for view in camera_views:
@@ -80,7 +80,7 @@ def _check_roi_motion_energy_data(*, eid: str, one: ONE, nwbfile: NWBFile):
 
 
 def _check_pose_estimation_data(*, eid: str, one: ONE, nwbfile: NWBFile, revision: str = None):
-    processing_module = nwbfile.processing["behavior"]
+    processing_module = nwbfile.processing["camera"]
 
     camera_views = ["body", "left", "right"]
     for view in camera_views:
@@ -142,7 +142,7 @@ def _check_trials_data(*, eid: str, one: ONE, nwbfile: NWBFile):
 
 
 def _check_pupil_tracking_data(*, eid: str, one: ONE, nwbfile: NWBFile):
-    processing_module = nwbfile.processing["behavior"]
+    processing_module = nwbfile.processing["camera"]
 
     camera_views = ["left", "right"]
     for view in camera_views:
@@ -165,7 +165,6 @@ def _check_pupil_tracking_data(*, eid: str, one: ONE, nwbfile: NWBFile):
 
 
 def _check_spike_sorting_data(*, eid: str, one: ONE, nwbfile: NWBFile, revision: str = None):
-
     units_table = nwbfile.units[:]
     probe_names = units_table["probe_name"].unique()