Merge pull request #4 from catalystneuro/video

Video

src/schneider_lab_to_nwb/schneider_2024/schneider_2024_behaviorinterface.py

@@ -8,7 +8,7 @@
 from ndx_events import EventTypesTable, EventsTable, Task, TimestampVectorData
 
 from neuroconv.basedatainterface import BaseDataInterface
-from neuroconv.utils import DeepDict
+from neuroconv.utils import DeepDict, get_base_schema
 from neuroconv.tools import nwb_helpers
 
 
@@ -26,6 +26,41 @@ def get_metadata(self) -> DeepDict:
 
         return metadata
 
+    def get_metadata_schema(self) -> dict:
+        metadata_schema = super().get_metadata_schema()
+        metadata_schema["properties"]["Behavior"] = get_base_schema(tag="Behavior")
+        metadata_schema["properties"]["Behavior"]["properties"]["TimeSeries"] = {
+            "type": "array",
+            "items": {
+                "type": "object",
+                "properties": {
+                    "name": {"type": "string"},
+                    "description": {"type": "string"},
+                },
+            },
+        }
+        metadata_schema["properties"]["Behavior"]["properties"]["Events"] = {
+            "type": "array",
+            "items": {
+                "type": "object",
+                "properties": {
+                    "name": {"type": "string"},
+                    "description": {"type": "string"},
+                },
+            },
+        }
+        metadata_schema["properties"]["Behavior"]["properties"]["ValuedEvents"] = {
+            "type": "array",
+            "items": {
+                "type": "object",
+                "properties": {
+                    "name": {"type": "string"},
+                    "description": {"type": "string"},
+                },
+            },
+        }
+        return metadata_schema
+
     def add_to_nwbfile(self, nwbfile: NWBFile, metadata: dict):
         # Read Data
         file_path = self.source_data["file_path"]

src/schneider_lab_to_nwb/schneider_2024/schneider_2024_convert_session.py

@@ -19,6 +19,11 @@ def session_to_nwb(data_dir_path: Union[str, Path], output_dir_path: Union[str,
     recording_folder_path = data_dir_path / "Raw Ephys" / "m69_2023-10-31_17-24-15_Day1_A1"
     sorting_folder_path = data_dir_path / "Processed Ephys" / "m69_2023-10-31_17-24-15_Day1_A1"
     behavior_file_path = data_dir_path / "Behavior" / "m69_231031" / "raw_m69_231031_001.mat"
+    video_folder_path = data_dir_path / "Video" / "m69_231031"
+    video_file_paths = [
+        file_path for file_path in video_folder_path.glob("*.mp4") if not file_path.name.startswith("._")
+    ]
+    video_file_paths = sorted(video_file_paths)
     if stub_test:
         output_dir_path = output_dir_path / "nwb_stub"
         recording_folder_path = recording_folder_path.with_name(recording_folder_path.name + "_stubbed")
@@ -43,6 +48,12 @@ def session_to_nwb(data_dir_path: Union[str, Path], output_dir_path: Union[str,
     source_data.update(dict(Behavior=dict(file_path=behavior_file_path)))
     conversion_options.update(dict(Behavior=dict()))
 
+    # Add Video(s)
+    for i, video_file_path in enumerate(video_file_paths):
+        metadata_key_name = f"VideoCamera{i+1}"
+        source_data.update({metadata_key_name: dict(file_paths=[video_file_path], metadata_key_name=metadata_key_name)})
+        conversion_options.update({metadata_key_name: dict()})
+
     converter = Schneider2024NWBConverter(source_data=source_data)
 
     # Add datetime to conversion
@@ -74,6 +85,11 @@ def session_to_nwb(data_dir_path: Union[str, Path], output_dir_path: Union[str,
     )
     metadata["Ecephys"]["Device"] = editable_metadata["Ecephys"]["Device"]
 
+    # Overwrite video metadata
+    for i, video_file_path in enumerate(video_file_paths):
+        metadata_key_name = f"VideoCamera{i+1}"
+        metadata["Behavior"][metadata_key_name] = editable_metadata["Behavior"][metadata_key_name]
+
     # Run conversion
     converter.run_conversion(metadata=metadata, nwbfile_path=nwbfile_path, conversion_options=conversion_options)
 

src/schneider_lab_to_nwb/schneider_2024/schneider_2024_metadata.yaml

@@ -51,6 +51,15 @@ Behavior:
   ValuedEvents:
     - name: tuningTones
       description: Times at which tuning tones are played to an animal after a behavioral experiment during ephys recording sessions.
+  VideoCamera1:
+    - name: video_camera_1
+      description: Three IR video cameras (AAK CA20 600TVL 2.8MM) are used to monitor the experiments from different angles of interest, allowing for offline analysis of body movements, pupillometry, and other behavioral data if necessary.
+      unit: Frames
+  VideoCamera2:
+    - name: video_camera_2
+      description: Three IR video cameras (AAK CA20 600TVL 2.8MM) are used to monitor the experiments from different angles of interest, allowing for offline analysis of body movements, pupillometry, and other behavioral data if necessary.
+      unit: Frames
 
 Sorting:
   units_description: Neural spikes will be sorted offline using Kilosort 2.5 and Phy2 software and manually curated to ensure precise spike time acquisition.
+

src/schneider_lab_to_nwb/schneider_2024/schneider_2024_notes.md

@@ -5,6 +5,9 @@
 - TuningTones has a values field with integers, what does this correspond to?
 - 'push' is basically some kind of trials table, but need descriptions for variables ex. ITI_respect?
 
+## Video
+- In research overview, 3 cameras are mentioned, but only 2 appear in example data. Missing camera? Or incorrect description?
+
 ## Data Requests
 - Mice sexes
 - Remaining data for Grant's project
@@ -13,3 +16,4 @@
     - stereotactic coordinates of the whole probe
 - Detailed description of the behavioral paradigm
 - Description of lickometer and lever/treadmill quadrature encoder.
+- Detailed description of temporal alignment procedure.

src/schneider_lab_to_nwb/schneider_2024/schneider_2024_nwbconverter.py

@@ -3,7 +3,9 @@
 from neuroconv.datainterfaces import (
     OpenEphysRecordingInterface,
     PhySortingInterface,
+    VideoInterface,
 )
+from neuroconv.basedatainterface import BaseDataInterface
 
 from schneider_lab_to_nwb.schneider_2024 import Schneider2024BehaviorInterface
 
@@ -15,4 +17,7 @@ class Schneider2024NWBConverter(NWBConverter):
         Recording=OpenEphysRecordingInterface,
         Sorting=PhySortingInterface,
         Behavior=Schneider2024BehaviorInterface,
+        VideoCamera1=VideoInterface,
+        VideoCamera2=VideoInterface,
+        VideoCamera3=VideoInterface,
     )