kilosort3 run time 353.29s
Traceback (most recent call last):
File "/home/software/python3/lib/python3.9/site-packages/IPython/core/interactiveshell.py", line 3361, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "", line 5, in <cell line: 5>
sortingk = ss.run_sorter('kilosort3', rec_cmr, output_folder=foldername,
File "/home/software/python3/lib/python3.9/site-packages/spikeinterface/sorters/runsorter.py", line 67, in run_sorter
return run_sorter_local(sorter_name, recording, output_folder=output_folder,
File "/home/software/python3/lib/python3.9/site-packages/spikeinterface/sorters/runsorter.py", line 91, in run_sorter_local
sorting = SorterClass.get_result_from_folder(output_folder)
File "/home/software/python3/lib/python3.9/site-packages/spikeinterface/sorters/basesorter.py", line 258, in get_result_from_folder
recording = load_extractor(output_folder / 'spikeinterface_recording.json')
File "/home/software/python3/lib/python3.9/site-packages/spikeinterface/core/base.py", line 821, in load_extractor
def _load_extractor_from_dict(dic):
File "/home/software/python3/lib/python3.9/site-packages/spikeinterface/core/base.py", line 513, in load
return extractor
File "/home/software/python3/lib/python3.9/site-packages/spikeinterface/core/base.py", line 340, in from_dict
folder_metadata = d.get('folder_metadata', None)
File "/home/software/python3/lib/python3.9/site-packages/spikeinterface/core/base.py", line 767, in _load_extractor_from_dict
for path in d[k]:
File "/home/software/python3/lib/python3.9/site-packages/spikeinterface/toolkit/preprocessing/common_reference.py", line 87, in init
groups = [self.ids_to_indices(g) for g in groups]
File "/home/software/python3/lib/python3.9/site-packages/spikeinterface/toolkit/preprocessing/common_reference.py", line 87, in
groups = [self.ids_to_indices(g) for g in groups]
File "/home/software/python3/lib/python3.9/site-packages/spikeinterface/core/base.py", line 89, in ids_to_indices
indices = np.array([_main_ids.index(id) for id in ids])
ValueError: 0 is not in list
Hi @jkb521
sorry for our very late reply. Could you provide some more info? What is the code you are running? How are you preprocessing the data?
SpikeInterface
