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Description
I have a problem. The error information is following:
Traceback (most recent call last):
File "/home/NITD/lxr/code/spike_sorting/run_sorter0913.py", line 628, in <module>
start_sorting(manual,
File "/home/NITD/lxr/code/spike_sorting/run_sorter0913.py", line 530, in start_sorting
sorting = run_sorter_sc2(rec_w_sub, detection, general, selection, matching, apply_preprocessing, output_folder=sorter_path)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/NITD/lxr/code/spike_sorting/run_sorter0913.py", line 347, in run_sorter_sc2
sort_res = si.run_sorter('spykingcircus2', recording,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/NITD/anaconda3/envs/si_env_rolling/lib/python3.11/site-packages/spikeinterface/sorters/runsorter.py", line 216, in run_sorter
return run_sorter_local(**common_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/NITD/anaconda3/envs/si_env_rolling/lib/python3.11/site-packages/spikeinterface/sorters/runsorter.py", line 276, in run_sorter_local
SorterClass.run_from_folder(folder, raise_error, verbose)
File "/home/NITD/anaconda3/envs/si_env_rolling/lib/python3.11/site-packages/spikeinterface/sorters/basesorter.py", line 301, in run_from_folder
raise SpikeSortingError(
spikeinterface.sorters.utils.misc.SpikeSortingError: Spike sorting error trace:
Traceback (most recent call last):
File "/home/NITD/anaconda3/envs/si_env_rolling/lib/python3.11/site-packages/spikeinterface/sorters/basesorter.py", line 261, in run_from_folder
SorterClass._run_from_folder(sorter_output_folder, sorter_params, verbose)
File "/home/NITD/anaconda3/envs/si_env_rolling/lib/python3.11/site-packages/spikeinterface/sorters/internal/spyking_circus2.py", line 116, in _run_from_folder
recording = cls.load_recording_from_folder(sorter_output_folder.parent, with_warnings=False)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/NITD/anaconda3/envs/si_env_rolling/lib/python3.11/site-packages/spikeinterface/sorters/basesorter.py", line 212, in load_recording_from_folder
recording = load_extractor(json_file, base_folder=output_folder)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/NITD/anaconda3/envs/si_env_rolling/lib/python3.11/site-packages/spikeinterface/core/base.py", line 1185, in load_extractor
return BaseExtractor.load(file_or_folder_or_dict, base_folder=base_folder)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/NITD/anaconda3/envs/si_env_rolling/lib/python3.11/site-packages/spikeinterface/core/base.py", line 769, in load
extractor = BaseExtractor.from_dict(d, base_folder=base_folder)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/NITD/anaconda3/envs/si_env_rolling/lib/python3.11/site-packages/spikeinterface/core/base.py", line 515, in from_dict
extractor = _load_extractor_from_dict(dictionary)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/NITD/anaconda3/envs/si_env_rolling/lib/python3.11/site-packages/spikeinterface/core/base.py", line 1109, in _load_extractor_from_dict
new_kwargs[name] = [transform_dict_to_extractor(e) for e in value]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/NITD/anaconda3/envs/si_env_rolling/lib/python3.11/site-packages/spikeinterface/core/base.py", line 1109, in <listcomp>
new_kwargs[name] = [transform_dict_to_extractor(e) for e in value]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/NITD/anaconda3/envs/si_env_rolling/lib/python3.11/site-packages/spikeinterface/core/base.py", line 1101, in <lambda>
transform_dict_to_extractor = lambda x: _load_extractor_from_dict(x) if is_dict_extractor(x) else x
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/NITD/anaconda3/envs/si_env_rolling/lib/python3.11/site-packages/spikeinterface/core/base.py", line 1105, in _load_extractor_from_dict
new_kwargs[name] = _load_extractor_from_dict(value)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/NITD/anaconda3/envs/si_env_rolling/lib/python3.11/site-packages/spikeinterface/core/base.py", line 1124, in _load_extractor_from_dict
extractor = extractor_class(**new_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/NITD/anaconda3/envs/si_env_rolling/lib/python3.11/site-packages/spikeinterface/sortingcomponents/motion/motion_interpolation.py", line 302, in __init__
assert channel_locations.ndim >= motion.dim, (
^^^^^^^^^^
AttributeError: 'dict' object has no attribute 'dim'
Then I set apply_motion_correction=False
, like
sort_res = si.run_sorter('spykingcircus2', recording,
detection=detection,
general=general,
selection=selection,
matching=matching,
apply_preprocessing=apply_preprocessing,
apply_motion_correction=False,
remove_existing_folder=True,
verbose=False,
output_folder=output_folder)
But it doesn't seem to work.