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Fix SpikeInterface API compatibility in neuropixels_pipeline.py

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- Change stream_name to stream_id in read_spikeglx() call
- Change output_folder to folder in run_sorter() call

These parameters were renamed in SpikeInterface ≥0.100.

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
This commit is contained in:
Robert
2025-12-17 11:13:09 -05:00
parent 312f18ae60
commit 1e00b1536e
1 changed files with 3 additions and 3 deletions
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6
scientific-skills/neuropixels-analysis/scripts/neuropixels_pipeline.py
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@@ -19,7 +19,7 @@ import spikeinterface.full as si
import numpy as np import numpy as np
def load_recording(data_path: str, stream_name: str = 'imec0.ap') -> si.BaseRecording: def load_recording(data_path: str, stream_id: str = 'imec0.ap') -> si.BaseRecording:
"""Load a SpikeGLX or Open Ephys recording.""" """Load a SpikeGLX or Open Ephys recording."""
data_path = Path(data_path) data_path = Path(data_path)
@@ -29,7 +29,7 @@ def load_recording(data_path: str, stream_name: str = 'imec0.ap') -> si.BaseReco
# SpikeGLX format # SpikeGLX format
streams, _ = si.get_neo_streams('spikeglx', data_path) streams, _ = si.get_neo_streams('spikeglx', data_path)
print(f"Available streams: {streams}") print(f"Available streams: {streams}")
recording = si.read_spikeglx(data_path, stream_name=stream_name) recording = si.read_spikeglx(data_path, stream_id=stream_id)
elif any(data_path.rglob('*.oebin')): elif any(data_path.rglob('*.oebin')):
# Open Ephys format # Open Ephys format
recording = si.read_openephys(data_path) recording = si.read_openephys(data_path)
@@ -184,7 +184,7 @@ def run_spike_sorting(
sorting = si.run_sorter( sorting = si.run_sorter(
sorter, sorter,
recording, recording,
output_folder=sorter_folder, folder=sorter_folder,
verbose=True verbose=True
) )