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read_spikegadgets broken for neuropixel recordings

Open RobertoDF opened this issue 6 months ago • 15 comments

Hi, The read_spikegadgets from spikeinterface was working with neuropixel probes with this committ 83a84b2 but now it is broken.

 File "C:\Users\SciencePerson\miniforge3\envs\spikesorting\lib\site-packages\IPython\core\interactiveshell.py", line 3550, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-6-3052bc77e239>", line 1, in <module>
    raw_rec = read_spikegadgets(r"X:\13\ephys\20231213_155419.rec\20231213_155419.rec" )
  File "C:\Users\SciencePerson\miniforge3\envs\spikesorting\lib\site-packages\spikeinterface\extractors\neoextractors\spikegadgets.py", line 45, in __init__
    NeoBaseRecordingExtractor.__init__(
  File "C:\Users\SciencePerson\miniforge3\envs\spikesorting\lib\site-packages\spikeinterface\extractors\neoextractors\neobaseextractor.py", line 188, in __init__
    _NeoBaseExtractor.__init__(self, block_index, **neo_kwargs)
  File "C:\Users\SciencePerson\miniforge3\envs\spikesorting\lib\site-packages\spikeinterface\extractors\neoextractors\neobaseextractor.py", line 27, in __init__
    self.neo_reader = self.get_neo_io_reader(self.NeoRawIOClass, **neo_kwargs)
  File "C:\Users\SciencePerson\miniforge3\envs\spikesorting\lib\site-packages\spikeinterface\extractors\neoextractors\neobaseextractor.py", line 66, in get_neo_io_reader
    neo_reader.parse_header()
  File "C:\Users\SciencePerson\miniforge3\envs\spikesorting\lib\site-packages\neo\rawio\baserawio.py", line 189, in parse_header
    self._parse_header()
  File "C:\Users\SciencePerson\miniforge3\envs\spikesorting\lib\site-packages\neo\rawio\spikegadgetsrawio.py", line 227, in _parse_header
    signal_channels = signal_channels[keep]
IndexError: list index out of range

Environment:

  • OS: Windows
  • Python 3.9
  • Neo 0.13.1dev1
  • NumPy 1.26.4

RobertoDF avatar Jul 30 '24 19:07 RobertoDF