Spike sorting error

[AbhiSwamiUConn]

When I try running a sorter with either openephys or plexon files, I get an error stating that I need at least one array to concatenate. Previously, this error did not show up and the files I tried ran without issue. Is this something on my end?

SpikeSortingError                         Traceback (most recent call last)
Cell In[3], line 28
     26 print(filtered_recording.is_filtered())
     27 #sort and analyze
---> 28 sorting = ss.run_sorter(sorter_name=sorter_name, recording=recording, output_folder=output_folder1, remove_existing_folder=True)
     29 Sanalyzer = si.waveform_extractor.extract_waveforms(recording=recording, sorting=sorting, folder = output_folder2, overwrite= True)
     30 recording.analyze_extractor(Sanalyzer)

File ~\anaconda3\Lib\site-packages\spikeinterface\sorters\runsorter.py:175, in run_sorter(sorter_name, recording, output_folder, remove_existing_folder, delete_output_folder, verbose, raise_error, docker_image, singularity_image, delete_container_files, with_output, **sorter_params)
    168             container_image = singularity_image
    169     return run_sorter_container(
    170         container_image=container_image,
    171         mode=mode,
    172         **common_kwargs,
    173     )
--> 175 return run_sorter_local(**common_kwargs)

File ~\anaconda3\Lib\site-packages\spikeinterface\sorters\runsorter.py:225, in run_sorter_local(sorter_name, recording, output_folder, remove_existing_folder, delete_output_folder, verbose, raise_error, with_output, **sorter_params)
    223 SorterClass.set_params_to_folder(recording, output_folder, sorter_params, verbose)
    224 SorterClass.setup_recording(recording, output_folder, verbose=verbose)
--> 225 SorterClass.run_from_folder(output_folder, raise_error, verbose)
    226 if with_output:
    227     sorting = SorterClass.get_result_from_folder(output_folder, register_recording=True, sorting_info=True)

File ~\anaconda3\Lib\site-packages\spikeinterface\sorters\basesorter.py:293, in BaseSorter.run_from_folder(cls, output_folder, raise_error, verbose)
    290         print(f"{sorter_name} run time {run_time:0.2f}s")
    292 if has_error and raise_error:
--> 293     raise SpikeSortingError(
    294         f"Spike sorting error trace:\n{log['error_trace']}\n"
    295         f"Spike sorting failed. You can inspect the runtime trace in {output_folder}/spikeinterface_log.json."
    296     )
    298 return run_time

SpikeSortingError: Spike sorting error trace:
Traceback (most recent call last):
  File "C:\Users\User\anaconda3\Lib\site-packages\spikeinterface\sorters\basesorter.py", line 258, in run_from_folder
    SorterClass._run_from_folder(sorter_output_folder, sorter_params, verbose)
  File "C:\Users\User\anaconda3\Lib\site-packages\spikeinterface\sorters\internal\spyking_circus2.py", line 118, in _run_from_folder
    recording_f = zscore(recording_f, dtype="float32")
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\User\anaconda3\Lib\site-packages\spikeinterface\preprocessing\normalize_scale.py", line 296, in __init__
    random_data = get_random_data_chunks(recording, return_scaled=False, **random_chunk_kwargs)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\User\anaconda3\Lib\site-packages\spikeinterface\core\recording_tools.py", line 569, in get_random_data_chunks
    return np.concatenate(chunk_list, axis=0)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: need at least one array to concatenate

Spike sorting failed. You can inspect the runtime trace in C:\Users\User\Desktop\Abhinav\files1/spikeinterface_log.json.

[alejoe91]

Can you print(recording)?

[h-mayorquin]

Maybe another check to add in general is that the memmaps have data (with shape I guess). From here we don't know if some preprocessing step fail or if the data just failed to reload.

[AbhiSwamiUConn]

I get this when I try to print the recording: BandpassFilterRecording: 16 channels - 30.0kHz - 0 segments - 0 samples - 0.00s (0.00 ms) int16 dtype - 0.00 B. My filter was set between 250 and 2500 hertz.

[alejoe91]

That's the problem! You have no samples in your recording! Can you print the recording before the bandpass filter? You did you load it?

[AbhiSwamiUConn]

I definitely loaded the recording. When loading before the filter, I get: SelectSegmentRecording: 16 channels - 30.0kHz - 0 segments - 0 samples - 0.00s (0.00 ms) int16 dtype - 0.00 B. Is the issue that I am trying to access segments in a recording that does not have multiple segments?

[AbhiSwamiUConn]

I was utilizing user input and I had an statement set up where if there are no recording segments, the step of selecting specific segments would be skipped. This statement was getting skipped and an empty list was being passed. When I try running my script with the change I made, it now works. Sorry for taking your time.

[h-mayorquin]

You don't even have data in that recording, check the number of samples.

[AbhiSwamiUConn]

I do have data. I unknowingly passed an empty list to the segment recording extractor. Here is the recording with all data: OpenEphysBinaryRecordingExtractor: 16 channels - 30.0kHz - 1 segments - 18,272,400 samples 609.08s (10.15 minutes) - int16 dtype - 557.63 MiB

[h-mayorquin]

I meant at the point of the print above. It says you have zero samples.

[AbhiSwamiUConn]

Yes, and I have stated it is now fixed. Here is the recording after the check for multiple segements and after it has been filtered: BandpassFilterRecording: 16 channels - 30.0kHz - 1 segments - 18,272,400 samples 609.08s (10.15 minutes) - int16 dtype - 557.63 MiB

[h-mayorquin]

Glad it worked for you : )