Run `ss.sorter` without `set_probe()`

Hello,

I am trying to sort data from Behnke Fried contacts. However, the exact or even approximate geometry of the contacts is unable to be determined and so I left the probe property empty.

However, when running any of the sorters, I get the following error asking me to set the probe:

ValueError                                Traceback (most recent call last)
~/d/n2b/n2b-visification/n2b-visification/scripts/test_sort.py in <module>
----> 16 sorting = ss.run_spykingcircus(recording=recording, output_folder='tmp_TDC_5' )

~/anaconda/envs/visification/lib/python3.7/site-packages/spikeinterface/sorters/runsorter.py in run_spykingcircus(*args, **kwargs)
    367 
    368 def run_spykingcircus(*args, **kwargs):
--> 369     return run_sorter('spykingcircus', *args, **kwargs)
    370 
    371 

~/anaconda/envs/visification/lib/python3.7/site-packages/spikeinterface/sorters/runsorter.py in run_sorter(sorter_name, recording, output_folder, remove_existing_folder, delete_output_folder, verbose, raise_error, docker_image, with_output, **sorter_params)
     59                                    remove_existing_folder=remove_existing_folder,
     60                                    delete_output_folder=delete_output_folder,
---> 61                                    verbose=verbose, raise_error=raise_error, with_output=with_output, **sorter_params)
     62     else:
     63         sorting = run_sorter_docker(sorter_name, recording, docker_image, output_folder=output_folder,

~/anaconda/envs/visification/lib/python3.7/site-packages/spikeinterface/sorters/runsorter.py in run_sorter_local(sorter_name, recording, output_folder, remove_existing_folder, delete_output_folder, verbose, raise_error, with_output, **sorter_params)
     80     output_folder = SorterClass.initialize_folder(recording, output_folder, verbose, remove_existing_folder)
     81     SorterClass.set_params_to_folder(recording, output_folder, sorter_params, verbose)
---> 82     SorterClass.setup_recording(recording, output_folder, verbose=verbose)
     83     SorterClass.run_from_folder(output_folder, raise_error, verbose)
     84     if with_output:

~/anaconda/envs/visification/lib/python3.7/site-packages/spikeinterface/sorters/basesorter.py in setup_recording(cls, recording, output_folder, verbose)
    167             all_params = json.load(f)
    168             sorter_params = all_params['sorter_params']
--> 169         cls._setup_recording(recording, output_folder, sorter_params, verbose)
    170 
    171     @classmethod

~/anaconda/envs/visification/lib/python3.7/site-packages/spikeinterface/sorters/spyking_circus/spyking_circus.py in _setup_recording(cls, recording, output_folder, params, verbose)
    108         # note: only one group here, the split is done in basesorter
    109         prb_file = output_folder / 'probe.prb'
--> 110         probegroup = recording.get_probegroup()
    111         write_prb(prb_file, probegroup,
    112                   total_nb_channels=recording.get_num_channels(),

~/anaconda/envs/visification/lib/python3.7/site-packages/spikeinterface/core/baserecording.py in get_probegroup(self)
    326             positions = self.get_property('location')
    327             if positions is None:
--> 328                 raise ValueError('There is not Probe attached to recording. use set_probe(...)')
    329             else:
    330                 warn('There is no Probe attached to this recording. Creating a dummy one with contact positions')

ValueError: There is not Probe attached to recording. use set_probe(...)

Is there anyway to run the sorters without setting the probe?

[samuelgarcia]

I was not mentioning the shape of the probe but the configuration (location) of the contacts. The probe shape is not taken in account by sorters but only contact location.

Have a look to this. https://probeinterface.readthedocs.io/en/main/examples/ex_01_generate_probe_from_sratch.html https://probeinterface.readthedocs.io/en/main/examples/ex_09_more_complicated_probe.html

When you don’t have contact geometry you have 2 solutions:

1. all contacts are in the same neighborhood and you want to tell the sorter they are close to each other. So locating contact as a circle will minimize the distance between contact.
2. all contacts are far away from each other (e.g. utah array) in that case you should split your recording into groups one one electrode see https://github.com/SpikeInterface/spikeinterface/issues/317#issuecomment-946750275

[samuelgarcia]

If you don’t have location and wants to make dummmy ones maybe the best are to make a fake geometry with contact with a circle map.