minor fixes

src/cai_lab_to_nwb/zaki_2024/interfaces/miniscope_imaging_interface.py

@@ -248,16 +248,14 @@ def get_metadata(self) -> DeepDict:
 
         device_metadata = metadata["Ophys"]["Device"][0]
         miniscope_config = deepcopy(self._miniscope_config)
-        device_name = miniscope_config.pop("name")
+        miniscope_config.pop("name")
         description = (
             "The Miniscope is the head-mounted miniature microscope part of the UCLA Miniscope imaging platform."
         )
         device_metadata.update(description=description, **miniscope_config)
         # Add link to Device for ImagingPlane
         imaging_plane_metadata = metadata["Ophys"]["ImagingPlane"][0]
-        imaging_plane_metadata.update(
-            imaging_rate=self._metadata_frame_rate,
-        )
+        imaging_plane_metadata.update(imaging_rate=self._metadata_frame_rate)
         one_photon_series_metadata = metadata["Ophys"]["OnePhotonSeries"][0]
         one_photon_series_metadata.update(unit="px")
 

src/cai_lab_to_nwb/zaki_2024/zaki_2024_convert_conditioning_session.py

@@ -104,10 +104,7 @@ def session_to_nwb(
     else:
         print("No .edf file found at {}".format(edf_file_path))
 
-    ophys_metadata_path = Path(__file__).parent / "zaki_2024_ophys_metadata.yaml"
-    ophys_metadata = load_dict_from_file(ophys_metadata_path)
-
-    converter = Zaki2024NWBConverter(source_data=source_data, ophys_metadata=ophys_metadata)
+    converter = Zaki2024NWBConverter(source_data=source_data)
 
     # Add datetime to conversion
     metadata = converter.get_metadata()

src/cai_lab_to_nwb/zaki_2024/zaki_2024_metadata.yaml

@@ -39,3 +39,20 @@ Subject:
   species: Mus musculus
   age: P12W/P15W  # in ISO 8601, such as "P1W2D"
   sex: U  # One of M, F, U, or O
+Ophys:
+  OnePhotonSeries:
+    - name: OnePhotonSeries
+      description: Imaging data from Miniscope.
+      imaging_plane: ImagingPlane
+      unit: n.a.
+  ImagingPlane:
+    - name: ImagingPlane
+      description: Imaging plane for Miniscope imaging data.
+      excitation_lambda: 496.0
+      location: CA1
+      device: Microscope
+      optical_channel:
+        - name: OpticalChannel
+          description: Green channel of the microscope.
+          emission_lambda: 513.0
+      indicator: GCaMP6f

src/cai_lab_to_nwb/zaki_2024/zaki_2024_nwbconverter.py

@@ -30,27 +30,6 @@ class Zaki2024NWBConverter(NWBConverter):
         Video=VideoInterface,
     )
 
-    def __init__(
-        self,
-        source_data: Dict[str, dict],
-        verbose: bool = True,
-        ophys_metadata=Dict[str, dict],
-    ):
-        self.verbose = verbose
-        self._validate_source_data(source_data=source_data, verbose=self.verbose)
-        self.data_interface_objects = {
-            name: data_interface(**source_data[name])
-            for name, data_interface in self.data_interface_classes.items()
-            if name in source_data
-        }
-        self.ophys_metadata = ophys_metadata
-
-    def get_metadata(self) -> DeepDict:
-        metadata = super().get_metadata()
-        metadata["Ophys"]["OnePhotonSeries"] = self.ophys_metadata["Ophys"]["OnePhotonSeries"]
-        metadata["Ophys"]["ImagingPlane"] = self.ophys_metadata["Ophys"]["ImagingPlane"]
-        return metadata
-
 
 """
     # TODO decide which datastream set the session start time