Skip to content

correct_motion can't be set False in sorting = #3410

Open
@BEGINRX

Description

@BEGINRX

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.

Metadata

Metadata

Assignees

No one assigned

    Labels

    bugSomething isn't workingmotion correctionQuestions related to motion correction

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions