Follow up #9

src/howe_lab_to_nwb/vu2024/interfaces/vu2024_behaviorinterface.py

@@ -211,6 +211,8 @@ def add_binary_signals(self, nwbfile: NWBFile, metadata: dict):
 
         event_dfs = []
         for event_name in ["lick", "reward", "stimulus_led", "stimulus_sound"]:
+            if event_name not in behavior_data:
+                continue
             start_times, end_times = self._get_start_end_times(binary_event_data=behavior_data[event_name])
             if not len(start_times):
                 continue

src/howe_lab_to_nwb/vu2024/vu2024_convert_dual_wavelength_session.py

@@ -76,6 +76,7 @@ def dual_wavelength_session_to_nwb(
         ttl_file_path=ttl_file_path,
         ttl_stream_name=ttl_stream_names[0],
         motion_corrected_imaging_file_path=motion_corrected_imaging_file_paths[0],
+        behavior_file_path=behavior_file_paths[0],
         stub_test=stub_test,
     )
 
@@ -111,6 +112,11 @@ def dual_wavelength_session_to_nwb(
         session_folder_path / "R600_AP9_117_crop_MC_ROIs_new.mat",
     ]
 
+    behavior_file_paths = [
+        session_folder_path / "chatdat600_AP9_470_570_2021.08.21_10.48.07_aligned_ttlIn1_movie1.mat",
+        session_folder_path / "chatdat600_AP9_470_570_2021.08.21_10.48.07_aligned_ttlIn2_movie1.mat",
+    ]
+
     ttl_file_path = session_folder_path / "chatdat600_AP9_470_570_2021.08.21_10.48.07.mat"
     ttl_stream_names = ["ttlIn1", "ttlIn2"]
 
@@ -130,6 +136,7 @@ def dual_wavelength_session_to_nwb(
         fiber_locations_file_path=fiber_locations_file_path,
         excitation_wavelengths_in_nm=excitation_wavelengths_in_nm,
         indicators=indicators,
+        behavior_file_paths=behavior_file_paths,
         nwbfile_path=nwbfile_path,
         stub_test=stub_test,
     )

src/howe_lab_to_nwb/vu2024/vu2024_convert_single_wavelength_session.py

@@ -20,12 +20,11 @@ def single_wavelength_session_to_nwb(
     indicator: str,
     ttl_file_path: Union[str, Path],
     ttl_stream_name: str,
-    behavior_file_path: Union[str, Path],
+    behavior_file_path: Optional[Union[str, Path]] = None,
     motion_corrected_imaging_file_path: Optional[Union[str, Path]] = None,
     frame_indices: Optional[List[int]] = None,
     nwbfile_path: Optional[Union[str, Path]] = None,
     nwbfile: Optional[NWBFile] = None,
-    behavior_avi_file_path: Union[str, Path] = None,
     sampling_frequency: float = None,
     stub_test: bool = False,
 ) -> NWBFile:
@@ -58,7 +57,7 @@ def single_wavelength_session_to_nwb(
         An in-memory NWBFile object to add the data to. If None, a new NWBFile object will be created.
     motion_corrected_imaging_file_path : Union[str, Path]
         The path to the .tif file containing the motion corrected imaging data.
-    behavior_file_path : Union[str, Path]
+    behavior_file_path : Union[str, Path], optional
         The path to the .mat file containing the processed behavior data.
     nwbfile_path : Union[str, Path]
         The path to the NWB file to be created.
@@ -92,12 +91,12 @@ def single_wavelength_session_to_nwb(
     conversion_options.update(dict(FiberPhotometry=dict(stub_test=stub_test)))
 
     # Add motion corrected imaging data
+    if sampling_frequency is None:
+        ome_metadata = extract_ome_metadata(file_path=raw_imaging_file_path)
+        parsed_metadata = parse_ome_metadata(metadata=ome_metadata)
+        sampling_frequency = parsed_metadata["sampling_frequency"]
     if motion_corrected_imaging_file_path is not None:
         # We need the sampling frequency from the raw imaging data
-        if sampling_frequency is None:
-            ome_metadata = extract_ome_metadata(file_path=raw_imaging_file_path)
-            parsed_metadata = parse_ome_metadata(metadata=ome_metadata)
-            sampling_frequency = parsed_metadata["sampling_frequency"]
         source_data.update(
             dict(
                 ProcessedImaging=dict(
@@ -126,8 +125,9 @@ def single_wavelength_session_to_nwb(
     conversion_options.update(dict(Segmentation=dict(stub_test=stub_test)))
 
     # Add behavior
-    source_data.update(dict(Behavior=dict(file_path=str(behavior_file_path))))
-    conversion_options.update(dict(Behavior=dict(stub_test=stub_test)))
+    if behavior_file_path is not None:
+        source_data.update(dict(Behavior=dict(file_path=str(behavior_file_path))))
+        conversion_options.update(dict(Behavior=dict(stub_test=stub_test)))
 
     # Add behavior camera recording (optional)
     subject_id = raw_fiber_photometry_file_path.parent.parent.name