Do not write offset_to_uV and gain_to_uV in Electrodes (#803)

Co-authored-by: Cody Baker <[email protected]>

CHANGELOG.md

@@ -18,7 +18,7 @@
 * Keyword argument `field_name` of the `DatasetIOConfiguration.from_neurodata_object` method has been renamed to `dataset_name` to be more consistent with its usage. This only affects direct initialization of the model; usage via the `BackendConfiguration` constructor and its associated helper functions in `neuroconv.tools.nwb_helpers` is unaffected. [PR #767](https://github.com/catalystneuro/neuroconv/pull/767)
 * Manual construction of a `DatasetIOConfiguration` now requires the field `dataset_name`, and will be validated to match the final path of `location_in_file`. Usage via the automated constructors is unchanged. [PR #767](https://github.com/catalystneuro/neuroconv/pull/767)
 * Enhance `get_schema_from_method_signature` to extract descriptions from the method docval. [PR #771](https://github.com/catalystneuro/neuroconv/pull/771)
-
+* Avoid writing `channel_to_uV` and `offset_to_uV` in `add_electrodes`  [PR #803](https://github.com/catalystneuro/neuroconv/pull/803)
 
 
 # v0.4.7 (February 21, 2024)

src/neuroconv/tools/spikeinterface/spikeinterface.py

@@ -175,7 +175,12 @@ def add_electrode_groups(recording: BaseRecording, nwbfile: pynwb.NWBFile, metad
             nwbfile.create_electrode_group(**electrode_group_kwargs)
 
 
-def add_electrodes(recording: BaseRecording, nwbfile: pynwb.NWBFile, metadata: dict = None, exclude: tuple = ()):
+def add_electrodes(
+    recording: BaseRecording,
+    nwbfile: pynwb.NWBFile,
+    metadata: dict = None,
+    exclude: tuple = (),
+):
     """
     Add channels from recording object as electrodes to nwbfile object.
 
@@ -237,7 +242,7 @@ def add_electrodes(recording: BaseRecording, nwbfile: pynwb.NWBFile, metadata: d
     data_to_add = defaultdict(dict)
 
     recorder_properties = recording.get_property_keys()
-    excluded_properties = list(exclude) + ["contact_vector"]
+    excluded_properties = list(exclude) + ["offset_to_uV", "gain_to_uV", "contact_vector"]
     properties_to_extract = [property for property in recorder_properties if property not in excluded_properties]
 
     for property in properties_to_extract:

src/neuroconv/tools/testing/data_interface_mixins.py

@@ -290,7 +290,9 @@ def check_read_nwb(self, nwbfile_path: str):
 
             # Spikeinterface behavior is to load the electrode table channel_name property as a channel_id
             self.nwb_recording = NwbRecordingExtractor(
-                file_path=nwbfile_path, electrical_series_name=electrical_series_name
+                file_path=nwbfile_path,
+                electrical_series_name=electrical_series_name,
+                use_pynwb=True,
             )
 
             # Set channel_ids right for comparison

tests/test_on_data/test_gin_ecephys/test_raw_recordings.py

@@ -236,6 +236,17 @@ class TestConverter(NWBConverter):
         converter.run_conversion(nwbfile_path=nwbfile_path, overwrite=True, metadata=metadata)
         recording = converter.data_interface_objects["TestRecording"].recording_extractor
 
+        # Read NWB file
+        from pynwb import NWBHDF5IO
+
+        with NWBHDF5IO(path=nwbfile_path, mode="r") as io:
+            nwbfile = io.read()
+            electrodes = nwbfile.electrodes
+            electrodes_columns = electrodes.colnames
+
+            assert "offset_to_uV" not in electrodes_columns
+            assert "grain_to_uV" not in electrodes_columns
+
         es_key = converter.data_interface_objects["TestRecording"].es_key
         electrical_series_name = metadata["Ecephys"][es_key]["name"] if es_key else None
         if not isinstance(recording, BaseRecording):
@@ -244,7 +255,9 @@ class TestConverter(NWBConverter):
         # NWBRecordingExtractor on spikeinterface does not yet support loading data written from multiple segment.
         if recording.get_num_segments() == 1:
             # Spikeinterface behavior is to load the electrode table channel_name property as a channel_id
-            nwb_recording = NwbRecordingExtractor(file_path=nwbfile_path, electrical_series_name=electrical_series_name)
+            nwb_recording = NwbRecordingExtractor(
+                file_path=nwbfile_path, electrical_series_name=electrical_series_name, use_pynwb=True
+            )
             if "channel_name" in recording.get_property_keys():
                 renamed_channel_ids = recording.get_property("channel_name")
             else: