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extractor.read_spikeglx results in ValueError

See original GitHub issue

I’m attempting to read a raw ephys data file acquired using neuropixels 1.0 probes and spikeGLX to export it as a NWB file and I’m running into the following ValueError when using the extractors.read_spikeglx() function:

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In [42], line 1
----> 1 extractor = extractors.read_spikeglx(npx_dir)

File c:\Users\kusha\miniconda3\envs\mapEphysNWB\lib\site-packages\spikeinterface\core\core_tools.py:27, in define_function_from_class.<locals>.reader_func(*args, **kwargs)
     25 @copy_signature(source_class)
     26 def reader_func(*args, **kwargs):
---> 27     return source_class(*args, **kwargs)

File c:\Users\kusha\miniconda3\envs\mapEphysNWB\lib\site-packages\spikeinterface\extractors\neoextractors\spikeglx.py:70, in SpikeGLXRecordingExtractor.__init__(self, folder_path, load_sync_channel, stream_id, stream_name, all_annotations)
     67 probe = pi.read_spikeglx(meta_filename)
     69 if probe.shank_ids is not None:
---> 70     self.set_probe(probe, in_place=True, group_mode="by_shank")
     71 else:
     72     self.set_probe(probe, in_place=True)

File c:\Users\kusha\miniconda3\envs\mapEphysNWB\lib\site-packages\spikeinterface\core\baserecordingsnippets.py:74, in BaseRecordingSnippets.set_probe(self, probe, group_mode, in_place)
     72 probegroup = ProbeGroup()
     73 probegroup.add_probe(probe)
---> 74 return self.set_probes(probegroup, group_mode=group_mode, in_place=in_place)

File c:\Users\kusha\miniconda3\envs\mapEphysNWB\lib\site-packages\spikeinterface\core\baserecordingsnippets.py:141, in BaseRecordingSnippets.set_probes(self, probe_or_probegroup, group_mode, in_place)
    139 # check
    140 if np.max(list(inds) + [0]) >= self.get_num_channels():
...
    142         'The given Probe have "device_channel_indices" that do not match channel count')
    143 new_channel_ids = self.get_channel_ids()[inds]
    144 arr = arr[order]

ValueError: The given Probe have "device_channel_indices" that do not match channel count

The export was working without this error for the same files ~ Sept. 15, 2022. Please let me know if you have any suggestions to solve this or further questions about my code and set up.

Issue Analytics

State:
Created a year ago
Comments:6 (4 by maintainers)

Top GitHub Comments

1reaction

alejoe91commented, Nov 21, 2022

you can use @samuelgarcia and my email as they appear on our github page 😉

0reactions

alejoe91commented, Nov 23, 2022

Great! Closing then 😃

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