Merge pull request #62 from dj-sciops/update-lfp

fix: `_build_si_recording_object` for new version of SI

Author: MilagrosMarin

element_array_ephys/spike_sorting/si_spike_sorting.py

@@ -143,65 +143,75 @@ def make(self, key):
         )  # get the row indices of the port
 
         # Create SI recording extractor object
-        si_extractor: si.extractors.neoextractors = (
-            si.extractors.extractorlist.recording_extractor_full_dict[
-                acq_software.replace(" ", "").lower()
-            ]
-        )  # data extractor object
+        from spikeinterface.extractors.extractor_classes import (
+            recording_extractor_full_dict,
+        )
+
+        acq_key = acq_software.replace(" ", "").lower()
+        try:
+            si_extractor = recording_extractor_full_dict[acq_key]
+        except KeyError:
+            raise ValueError(f"Unsupported acquisition software: {acq_software}")
 
         files, file_times = (
             ephys.EphysRawFile
             & key
             & f"file_time BETWEEN '{key['start_time']}' AND '{key['end_time']}'"
         ).fetch("file_path", "file_time", order_by="file_time")
 
-        si_recording = None
+        # Detect stream name from the first file
+        first_file_path = find_full_path(ephys.get_ephys_root_data_dir(), files[0])
+        available_streams = si_extractor.get_streams(first_file_path)[0]
+        amplifier_streams = [s for s in available_streams if "amplifier" in s.lower()]
+
+        if not amplifier_streams:
+            raise ValueError(
+                f"No amplifier stream found in {first_file_path}. "
+                f"Available streams: {available_streams}"
+            )
+
+        stream_name = amplifier_streams[0]
+
         # Read data. Concatenate if multiple files are found.
+        si_recording = None
         for file_path in (
             find_full_path(ephys.get_ephys_root_data_dir(), f) for f in files
         ):
             if not si_recording:
-                stream_name = [
-                    s
-                    for s in si_extractor.get_streams(file_path)[0]
-                    if "amplifier" in s
-                ][0]
-                si_recording: si.BaseRecording = si_extractor(
-                    file_path, stream_name=stream_name
-                )
+                si_recording = si_extractor(file_path, stream_name=stream_name)
             else:
-                si_recording: si.BaseRecording = si.concatenate_recordings(
+                si_recording = si.concatenate_recordings(
                     [
                         si_recording,
                         si_extractor(file_path, stream_name=stream_name),
                     ]
                 )
 
+        # Restrict to channels from the target port
         si_recording = si_recording.channel_slice(
             si_recording.channel_ids[port_indices]
-        )  # select only the port data
+        )
 
-        # Create SI probe object
+        # Apply probe geometry
         si_probe = readers.probe_geometry.to_probeinterface(electrodes_df)
         si_probe.set_device_channel_indices(electrodes_df["channel_idx"].values)
         si_recording.set_probe(probe=si_probe, in_place=True)
 
-        # Account for additional electrodes being removed
+        # Remove unused electrodes
         if unused_electrodes:
             chn_ids_to_remove = [
                 f"{probe_info['port_id']}-{electrodes_df.channel_idx.iloc[elec]:03d}"
                 for elec in unused_electrodes
             ]
-        else:
-            chn_ids_to_remove = []
-
-        si_recording = si_recording.remove_channels(
-            remove_channel_ids=chn_ids_to_remove
-        )
+            si_recording = si_recording.remove_channels(
+                remove_channel_ids=chn_ids_to_remove
+            )
 
-        # Run preprocessing and save results to output folder
+        # Preprocess
         si_preproc_func = getattr(si_preprocessing, params["SI_PREPROCESSING_METHOD"])
         si_recording = si_preproc_func(si_recording)
+
+        # Save to pickle
         si_recording.dump_to_pickle(file_path=recording_file, relative_to=output_dir)
 
         self.insert1(