error running `wave_clus`

Hello,

I run into the following error when running wave_clus

1 of 1 'spikes' files done.
1 of 1 'spikes' files done.
1 of 1 'times' files finished.
1 of 1 'times' files finished.
Computations Done (1364.28s).
Computations Done (1364.28s).
Elapsed time is 1364.309871 seconds.
Elapsed time is 1364.309871 seconds.
Error using quit
Unrecognized function or variable 'Settings'.
Error in run_waveclus (line 35)
quit(0);
 
Error using quit
Unrecognized function or variable 'Settings'.
Error in run_waveclus (line 35)
quit(0);
 
Error using quit
Unrecognized function or variable 'Settings'.
Error in run_waveclus (line 35)
quit(0);
 
Error using quit
Unrecognized function or variable 'Settings'.
Error in run_waveclus (line 35)
quit(0);
 
/home/marco/anaconda/envs/visification/lib/python3.7/site-packages/spikeinterface/sorters/basesorter.py:198: ResourceWarning: unclosed file <_io.TextIOWrapper name=10 encoding='UTF-8'>
  SorterClass._run_from_folder(output_folder, sorter_params, verbose)
ResourceWarning: Enable tracemalloc to get the object allocation traceback
waveclus run time 8126.42s
Traceback (most recent call last):
  File "/home/marco/anaconda/envs/visification/lib/python3.7/site-packages/IPython/core/interactiveshell.py", line 3441, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "<ipython-input-3-e89336859e78>", line 11, in <module>
    verbose=True)
  File "/home/marco/anaconda/envs/visification/lib/python3.7/site-packages/spikeinterface/sorters/launcher.py", line 291, in run_sorters
    _run_one(task_args)
  File "/home/marco/anaconda/envs/visification/lib/python3.7/site-packages/spikeinterface/sorters/launcher.py", line 35, in _run_one
    delete_output_folder, verbose, raise_error, with_output)
  File "/home/marco/anaconda/envs/visification/lib/python3.7/site-packages/spikeinterface/sorters/runsorter.py", line 85, in run_sorter_local
    sorting = SorterClass.get_result_from_folder(output_folder)
  File "/home/marco/anaconda/envs/visification/lib/python3.7/site-packages/spikeinterface/sorters/basesorter.py", line 254, in get_result_from_folder
    sorting = cls._get_result_from_folder(output_folder)
  File "/home/marco/anaconda/envs/visification/lib/python3.7/site-packages/spikeinterface/sorters/waveclus/waveclus.py", line 255, in _get_result_from_folder
    file_path=result_fname, keep_good_only=keep_good_only)
  File "/home/marco/anaconda/envs/visification/lib/python3.7/site-packages/spikeinterface/extractors/waveclustextractors.py", line 19, in __init__
    par = self._getfield("par")
  File "/home/marco/anaconda/envs/visification/lib/python3.7/site-packages/spikeinterface/extractors/matlabhelpers.py", line 76, in _getfield
    return self._data[fieldname][()]
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "/home/marco/anaconda/envs/visification/lib/python3.7/site-packages/h5py/_hl/group.py", line 288, in __getitem__
    oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
  File "/home/marco/anaconda/envs/visification/lib/python3.7/site-packages/h5py/_hl/base.py", line 200, in _e
    name = name.encode('ascii')
AttributeError: 'tuple' object has no attribute 'encode'

I am not sure if the error messages output by Matlab are what is causing AttributeError.

[ferchaure]

They have to accept the change, etc. But maybe you could do the change yourself in your local pc (check the commit, it’s a quite small change).

[samuelgarcia]

Hi here. Honestly I don’t known what is going here abotu this matlab helper. I think Alessio did it. I see here a __del__ method that force the file to be closed. Honestly normaly I would remove to test if it works. Normaly this close should also append in the del of h5py itself.