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fix: recording_extractor_full_dict is deprecated (SpikeInterface/spikeinterface#3153)
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-11
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element_array_ephys/spike_sorting/si_spike_sorting.py

Lines changed: 16 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -111,25 +111,30 @@ def make(self, key):
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)
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spikeglx_recording.validate_file("ap")
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data_dir = spikeglx_meta_filepath.parent
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si_extractor = si.extractors.neoextractors.spikeglx.SpikeGLXRecordingExtractor
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stream_names, stream_ids = si.extractors.get_neo_streams(
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acq_software, folder_path=data_dir
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)
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si_recording: si.BaseRecording = si_extractor(
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folder_path=data_dir, stream_name=stream_names[0]
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)
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elif acq_software == "Open Ephys":
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oe_probe = ephys.get_openephys_probe_data(key)
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assert len(oe_probe.recording_info["recording_files"]) == 1
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data_dir = oe_probe.recording_info["recording_files"][0]
126+
si_extractor = si.extractors.neoextractors.openephys.OpenEphysBinaryRecordingExtractor
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128+
stream_names, stream_ids = si.extractors.get_neo_streams(
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acq_software, folder_path=data_dir
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)
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si_recording: si.BaseRecording = si_extractor(
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folder_path=data_dir, stream_name=stream_names[0]
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)
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else:
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raise NotImplementedError(
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f"SpikeInterface processing for {acq_software} not yet implemented."
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)
122-
acq_software = acq_software.replace(" ", "").lower()
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si_extractor: si.extractors.neoextractors = (
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si.extractors.extractorlist.recording_extractor_full_dict[acq_software]
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) # data extractor object
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stream_names, stream_ids = si.extractors.get_neo_streams(
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acq_software, folder_path=data_dir
129-
)
130-
si_recording: si.BaseRecording = si_extractor(
131-
folder_path=data_dir, stream_name=stream_names[0]
132-
)
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# Add probe information to recording object
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electrodes_df = (

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