error running `wave_clus`

[marcoistasy]

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]

Hi, It looks like your matlab have issues with the command 'quit', could it be ?? can you try running quit(0) in Matlab and check if that works?

The other error looks like an issue between h5py and the matfile, which matlab version are you using?

[marcoistasy]

@ferchaure hello! yes, that's what I thought -- so I ran both quit and quit(0)in Matlab and they both worked fine (i.e ask me if i want to save changes and then quit Matlab). I am runningh5py=3.2.1andmatlab=R2021Bwithsave -v7.3enabled by default to ensure that the.mat` files can be larger than 2gb. Any ideas what might be causing this?

[ferchaure]

I will take a look at the matlabhelpers function, @samuelgarcia do you remember if h5py has some issue loading structs from matlab?

@marcoistasy, can you try disabling the -v7.3 by default? The sorting results should be smaller than 2gb and wave_clus will use the old format.

[marcoistasy]

@ferchaure thank you! unfortunately, I had to enable -v7.3 as I ran into an issue saying that spikes could not be saved as it was larger than 2gb. For reference, I am sorting 48 channels sampled at 32KHz for 1 hour. Would you like me to disable it and copy the exact error?

[ferchaure]

That's odd, wave_clus has a few try-catch to save automatically with -v7.3 in files larger than 2gb. If you can disable it and run it again, it will be nice, but put the error as an in issue on https://github.com/csn-le/wave_clus because that is not spikeinterface related.

Notice that waveclus is developed to handle single-channel and low density probes like tetrodes. It won't escalate well with that amount of channels. I would recommend sort channel by channel (like combinato) or by sectors of less than 10 channels.

[ferchaure]

I found the bug in how the wave_clus sorter called the MatlabHelper.

[marcoistasy]

@ferchaure oh that's great!!! so should the problem be fixed now? I also am waiting for my code to run so that i can get the exact output to report to the wave_clus repo about files saving with -v7.3.

[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).

[marcoistasy]

hi @ferchaure! i'm just commenting again as I ran into this error message that I believe directly related to the Matlab Helper:

waveclus run time 10986.35s
Exception ignored in: <function MatlabHelper.__del__ at 0x7fa3a245ff80>
Traceback (most recent call last):
  File "/home/marco/anaconda/envs/visification/lib/python3.7/site-packages/spikeinterface-0.91.1.dev0-py3.7.egg/spikeinterface/extractors/matlabhelpers.py", line 64, in __del__
  File "/home/marco/anaconda/envs/visification/lib/python3.7/site-packages/h5py/_hl/files.py", line 464, in close
  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 "h5py/h5f.pyx", line 275, in h5py.h5f.get_obj_ids
  File "h5py/h5i.pyx", line 40, in h5py.h5i.wrap_identifier
ImportError: sys.meta_path is None, Python is likely shutting down

Do you know why this exceptional would occur?

[ferchaure]

I don't know, looks like something related to how multiprocessing is closed, any ideas @samuelgarcia ?

[ferchaure]

I'm trying to reproduce the error, @marcoistasy could you tell me more details of how are you running the sorter?

[marcoistasy]

hey @ferchaure! it was definitelysomething to do with the multi processer -- I ran the same code but did not specify the backend_engine and did not run into this issue.