update conversion script

src/dombeck_lab_to_nwb/he_embargo_2024/he_embargo_2024_convert_session.py

@@ -11,6 +11,7 @@
 def session_to_nwb(
     abf_file_path: Union[str, Path],
     optogenetic_stimulation_file_path: Union[str, Path],
+    fiber_photometry_file_path: Union[str, Path],
     nwbfile_path: Union[str, Path],
     stub_test: bool = False,
 ):
@@ -52,6 +53,13 @@ def session_to_nwb(
         )
     )
 
+    # Add fiber photometry data
+    source_data.update(
+        dict(
+            FiberPhotometry=dict(file_path=str(fiber_photometry_file_path), session_id=session_id),
+        )
+    )
+
     converter = HeEmbargo2024NWBConverter(source_data=source_data)
 
     # Add datetime to conversion
@@ -72,6 +80,13 @@ def session_to_nwb(
     ophys_metadata = load_dict_from_file(ophys_metadata_path)
     metadata = dict_deep_update(metadata, ophys_metadata)
 
+    # Update fiber photometry metadata
+    fiber_photometry_metadata_path = (
+        Path(__file__).parent / "metadata" / "he_embargo_2024_fiber_photometry_metadata.yaml"
+    )
+    fiber_photometry_metadata = load_dict_from_file(fiber_photometry_metadata_path)
+    metadata = dict_deep_update(metadata, fiber_photometry_metadata)
+
     # Update conversion options
     # Retrieve the sampling frequency from the abf file
     sampling_frequency = converter.data_interface_objects["AxonBinaryTimeSeries"]._sampling_frequency
@@ -87,6 +102,10 @@ def session_to_nwb(
                 stub_test=stub_test,
             ),
             TTL=dict(stub_test=stub_test),
+            FiberPhotometry=dict(
+                sampling_frequency=100.0,
+                stub_test=stub_test,
+            ),
         )
     )
 
@@ -107,6 +126,10 @@ def session_to_nwb(
     # The path to the opto file
     opto_file_path = "/Volumes/LaCie/CN_GCP/Dombeck/sample_data/AnT60/stimulation/processed/AnT60-new.mat"
 
+    fiber_photometry_file_path = (
+        "/Volumes/LaCie/CN_GCP/Dombeck/sample_data/AnT60/stimulation/processed/AnT60_data4-new.mat"
+    )
+
     # The path to the NWB file to be created.
     nwbfile_path = Path("/Volumes/LaCie/CN_GCP/Dombeck/nwbfiles/AnT60-2024-01-09-0003.nwb")
 
@@ -115,6 +138,7 @@ def session_to_nwb(
     session_to_nwb(
         abf_file_path=abf_file_path,
         optogenetic_stimulation_file_path=opto_file_path,
+        fiber_photometry_file_path=fiber_photometry_file_path,
         nwbfile_path=nwbfile_path,
         stub_test=stub_test,
     )