Merge branch 'nwatters' into main

catalystneuro · Dec 20, 2023 · 54b431b · 54b431b
2 parents 101a2da + 7eb0f4f
commit 54b431b
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Showing 3 changed files with 23 additions and 26 deletions.
diff --git a/src/jazayeri_lab_to_nwb/watters/main_convert_session.py b/src/jazayeri_lab_to_nwb/watters/main_convert_session.py
@@ -291,12 +291,10 @@ def session_to_nwb(
 
     # Check if session_start_time was found/set
     if "session_start_time" not in metadata["NWBFile"]:
-        try:
-            date = datetime.datetime.strptime(session, "%Y-%m-%d")
-            date = date.replace(tzinfo=ZoneInfo("US/Eastern"))
-        except:
-            raise ValueError("Session start time was not auto-detected. Please provide it " "in `metadata.yaml`")
-        metadata["NWBFile"]["session_start_time"] = date
+        raise ValueError("Session start time was not auto-detected. Please provide it " "in `metadata.yaml`")
+    session_start_time = metadata["NWBFile"]["session_start_time"]
+    metadata["NWBFile"]["session_start_time"] = session_start_time.replace(
+        tzinfo=ZoneInfo("US/Eastern"))
 
     # Run conversion
     logging.info("Running processed conversion")

diff --git a/src/jazayeri_lab_to_nwb/watters/recording_interface.py b/src/jazayeri_lab_to_nwb/watters/recording_interface.py
@@ -46,23 +46,14 @@ def __init__(
         self.probe_name = probe_name
 
         # add probe information
-        probe_metadata = None
-        if probe_metadata_file is not None and probe_key is not None:
-            with open(probe_metadata_file, "r") as f:
-                all_probe_metadata = json.load(f)
-            for entry in all_probe_metadata:
-                if entry["label"] == probe_key:
-                    probe_metadata = entry
+        with open(probe_metadata_file, "r") as f:
+            all_probe_metadata = json.load(f)
+        for entry in all_probe_metadata:
+            if entry["label"] == probe_key:
+                probe_metadata = entry
 
-        if probe_metadata is not None and "electrodes_locations" in probe_metadata:
-            # Grab electrode position from metadata
-            locations_array = np.array(probe_metadata["electrodes_locations"])
-            ndim = locations_array.shape[1]
-            probe = probeinterface.Probe(ndim=ndim)
-            probeinterface.set_contacts(locations_array)
-        else:
-            # Generate V-probe geometry: 64 channels arranged vertically with 50 um spacing
-            probe = probeinterface.generate_linear_probe(num_elec=channel_count, ypitch=50)
+        # Generate V-probe geometry: 64 channels arranged vertically with 50 um spacing
+        probe = probeinterface.generate_linear_probe(num_elec=channel_count, ypitch=50)
         probe.set_device_channel_indices(np.arange(channel_count))
         probe.name = probe_name
 

diff --git a/src/jazayeri_lab_to_nwb/watters/timeseries_interface.py b/src/jazayeri_lab_to_nwb/watters/timeseries_interface.py
@@ -71,6 +71,8 @@ def __init__(self, folder_path: FolderPathType):
         self._eye_pos = np.stack([eye_h_values, eye_v_values], axis=1)
 
     def add_to_nwbfile(self, nwbfile: NWBFile, metadata: dict):
+        del metadata
+
         # Make SpatialSeries
         eye_position = SpatialSeries(
             name="eye_position",
@@ -83,7 +85,7 @@ def add_to_nwbfile(self, nwbfile: NWBFile, metadata: dict):
         )
 
         # Get processing module
-        module_description = "Contains behavioral data from experiment."
+        module_description = "Contains behavior, audio, and reward data from experiment."
         processing_module = get_module(nwbfile=nwbfile, name="behavior", description=module_description)
 
         # Add data to module
@@ -107,6 +109,8 @@ def __init__(self, folder_path: FolderPathType):
         self._pupil_size = np.array(pupil_size_data["values"])
 
     def add_to_nwbfile(self, nwbfile: NWBFile, metadata: dict):
+        del metadata
+
         # Make TimeSeries
         pupil_size = TimeSeries(
             name="pupil_size",
@@ -118,7 +122,7 @@ def add_to_nwbfile(self, nwbfile: NWBFile, metadata: dict):
         )
 
         # Get processing module
-        module_description = "Contains behavioral data from experiment."
+        module_description = "Contains behavior, audio, and reward data from experiment."
         processing_module = get_module(nwbfile=nwbfile, name="behavior", description=module_description)
 
         # Add data to module
@@ -142,6 +146,8 @@ def __init__(self, folder_path: FolderPathType):
         self._reward_line = reward_line_data["values"]
 
     def add_to_nwbfile(self, nwbfile: NWBFile, metadata: dict):
+        del metadata
+
         # Make LabeledEvents
         reward_line = LabeledEvents(
             name="reward_line",
@@ -152,7 +158,7 @@ def add_to_nwbfile(self, nwbfile: NWBFile, metadata: dict):
         )
 
         # Get processing module
-        module_description = "Contains audio and reward data from experiment."
+        module_description = "Contains behavior, audio, and reward data from experiment."
         processing_module = get_module(nwbfile=nwbfile, name="behavior", description=module_description)
 
         # Add data to module
@@ -181,6 +187,8 @@ def __init__(self, folder_path: FolderPathType):
         self._sound_codes = [sound_to_code[x] for x in audio]
 
     def add_to_nwbfile(self, nwbfile: NWBFile, metadata: dict):
+        del metadata
+
         # Make LabeledEvents
         audio = LabeledEvents(
             name="audio",
@@ -191,7 +199,7 @@ def add_to_nwbfile(self, nwbfile: NWBFile, metadata: dict):
         )
 
         # Get processing module
-        module_description = "Contains audio and reward data from experiment."
+        module_description = "Contains behavior, audio, and reward data from experiment."
         processing_module = get_module(nwbfile=nwbfile, name="behavior", description=module_description)
 
         # Add data to module