Artefacts are provided but label 0 has no value!

[EstherXSD]

Hi,

I'm doing preprocessing. I removed the artifacts and wanted to use kilosort4 to do spikesorting.

rec_removed = spre.remove_artifacts(recording=recording_cmr, list_triggers=laser_on_times, mode='median') sorting_KS4 = ss.run_sorter('kilosort4', recording=rec_removed) sorting_analyzer = si.create_sorting_analyzer(sorting_KS4, recording=rec_removed) sorting_analyzer.compute(['random+_spikes','templates','quality_metrics']) sexp.export_to_phy(sorting_analyzer, output_folder=f"{npx_path}/phy")

However, after the cell ran for an hour, an error occurred. I don't know how to fix it.

Thank you!

---

SpikeSortingError                         Traceback (most recent call last)
Cell In[7], line 1
----> 1 sorting_KS4 = ss.run_sorter('kilosort4', recording=rec_removed)
      2 sorting_analyzer = si.create_sorting_analyzer(sorting_KS4, recording=rec_removed)
      3 sorting_analyzer.compute(['random+_spikes','templates','quality_metrics'])

File c:\Users\username\anaconda3\envs\si_env\Lib\site-packages\spikeinterface\sorters\runsorter.py:198, in run_sorter(sorter_name, recording, folder, remove_existing_folder, delete_output_folder, verbose, raise_error, docker_image, singularity_image, delete_container_files, with_output, output_folder, **sorter_params)
    187             raise RuntimeError(
    188                 "The python `spython` package must be installed to "
    189                 "run singularity. Install with `pip install spython`"
    190             )
    192     return run_sorter_container(
    193         container_image=container_image,
    194         mode=mode,
    195         **common_kwargs,
    196     )
--> 198 return run_sorter_local(**common_kwargs)

File c:\Users\username\anaconda3\envs\si_env\Lib\site-packages\spikeinterface\sorters\runsorter.py:260, in run_sorter_local(sorter_name, recording, folder, remove_existing_folder, delete_output_folder, verbose, raise_error, with_output, output_folder, **sorter_params)
    258 SorterClass.setup_recording(recording, folder, verbose=verbose)
    259 # This NEEDS to happen in the docker because of dependencies
--> 260 SorterClass.run_from_folder(folder, raise_error, verbose)
    261 if with_output:
    262     sorting = SorterClass.get_result_from_folder(folder, register_recording=True, sorting_info=True)

File c:\Users\username\anaconda3\envs\si_env\Lib\site-packages\spikeinterface\sorters\basesorter.py:310, in BaseSorter.run_from_folder(cls, output_folder, raise_error, verbose)
    307         print(f"{sorter_name} run time {run_time:0.2f}s")
    309 if has_error and raise_error:
--> 310     raise SpikeSortingError(
    311         f"Spike sorting error trace:\n{error_log_to_display}\n"
    312         f"Spike sorting failed. You can inspect the runtime trace in {output_folder}/spikeinterface_log.json."
    313     )
    315 return run_time

SpikeSortingError: Spike sorting error trace:
Traceback (most recent call last):
  File "c:\Users\username\anaconda3\envs\si_env\Lib\site-packages\spikeinterface\sorters\basesorter.py", line 270, in run_from_folder
    SorterClass._run_from_folder(sorter_output_folder, sorter_params, verbose)
  File "c:\Users\username\anaconda3\envs\si_env\Lib\site-packages\spikeinterface\sorters\external\kilosort4.py", line 224, in _run_from_folder
    recording = cls.load_recording_from_folder(sorter_output_folder.parent, with_warnings=False)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "c:\Users\username\anaconda3\envs\si_env\Lib\site-packages\spikeinterface\sorters\basesorter.py", line 221, in load_recording_from_folder
    recording = load(json_file, base_folder=output_folder)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "c:\Users\username\anaconda3\envs\si_env\Lib\site-packages\spikeinterface\core\loading.py", line 100, in load
    return _load_object_from_dict(d, object_type, base_folder=base_folder)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "c:\Users\username\anaconda3\envs\si_env\Lib\site-packages\spikeinterface\core\loading.py", line 175, in _load_object_from_dict
    return BaseExtractor.from_dict(d, base_folder=base_folder)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "c:\Users\username\anaconda3\envs\si_env\Lib\site-packages\spikeinterface\core\base.py", line 567, in from_dict
    extractor = _load_extractor_from_dict(dictionary)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "c:\Users\username\anaconda3\envs\si_env\Lib\site-packages\spikeinterface\core\base.py", line 1123, in _load_extractor_from_dict
    extractor = extractor_class(**new_kwargs)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "c:\Users\username\anaconda3\envs\si_env\Lib\site-packages\spikeinterface\preprocessing\remove_artifacts.py", line 166, in __init__
    assert l in artifacts.keys(), f"Artefacts are provided but label {l} has no value!"
           ^^^^^^^^^^^^^^^^^^^^^
AssertionError: Artefacts are provided but label 0 has no value!

Spike sorting failed. You can inspect the runtime trace in c:\Users\username\Desktop\Code\Functions\kilosort4_output/spikeinterface_log.json.

spikeinterface_log.json