Hello Klustakwik2 contributors,
I am currently using spike interface and I am stuck in the section that involves using Klusta. I am running these lines
The code runs but halfway through I then encounter the following errors
14:52:29 [I] launch:218 Spike detection done! 53594 spikes found in shank 0
C:\Users\HiveTeam6\Anaconda\envs\spiketutorial\lib\site-packages\klusta\kwik\h5.py:55: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details.
with h5py.File(path, driver='sec2') as f:
14:52:29 [I] launch:249 Starting clustering on shank 0/1.
14:52:29 [I] launch:252 Clustering group 0 (53594 spikes).
14:52:29 [I] launch:123 Starting KK...
INFO klustakwik: KlustaKwik2 version 0.2.0
ValueError: There is no parameter num_starting_clusters
---------------------------------------------------------------------------
Exception Traceback (most recent call last)
C:\Users\HiveTeam6\Anaconda\envs\spiketutorial\lib\site-packages\spikesorters\basesorter.py in run(self, raise_error, parallel, n_jobs, joblib_backend)
157 for i, recording in enumerate(self.recording_list):
--> 158 self._run(recording, self.output_folders[i])
159 else:
C:\Users\HiveTeam6\Anaconda\envs\spiketutorial\lib\site-packages\spikesorters\klusta\klusta.py in _run(self, recording, output_folder)
151 if retcode != 0:
--> 152 raise Exception('klusta returned a non-zero exit code')
153
Exception: klusta returned a non-zero exit code
During handling of the above exception, another exception occurred:
SpikeSortingError Traceback (most recent call last)
<ipython-input-43-bb497d375e72> in <module>
1 # run spike sorting on entire recording
----> 2 sorting_KL_all = ss.run_klusta(recording_cache, output_folder='results_all_klusta', adjacency_radius=50, verbose=True)
3 print('Found', len(sorting_KL_all.get_unit_ids()), 'units')
C:\Users\HiveTeam6\Anaconda\envs\spiketutorial\lib\site-packages\spikesorters\sorterlist.py in run_klusta(*args, **kwargs)
267 The spike sorted data
268 """
--> 269 return run_sorter('klusta', *args, **kwargs)
270
271
C:\Users\HiveTeam6\Anaconda\envs\spiketutorial\lib\site-packages\spikesorters\sorterlist.py in run_sorter(sorter_name_or_class, recording, output_folder, delete_output_folder, grouping_property, parallel, verbose, raise_error, n_jobs, joblib_backend, **params)
91 verbose=verbose, delete_output_folder=delete_output_folder)
92 sorter.set_params(**params)
---> 93 sorter.run(raise_error=raise_error, parallel=parallel, n_jobs=n_jobs, joblib_backend=joblib_backend)
94 sortingextractor = sorter.get_result(raise_error=raise_error)
95
C:\Users\HiveTeam6\Anaconda\envs\spiketutorial\lib\site-packages\spikesorters\basesorter.py in run(self, raise_error, parallel, n_jobs, joblib_backend)
167 except Exception as err:
168 if raise_error:
--> 169 raise SpikeSortingError(f"Spike sorting failed: {err}. You can inspect the runtime trace in "
170 f"the {self.sorter_name}.log of the output folder.'")
171 else:
SpikeSortingError: Spike sorting failed: klusta returned a non-zero exit code. You can inspect the runtime trace in the klusta.log of the output folder.'
I am working on window 10 pro. Anything helps, thank you.
alejoe91
commented
2 years ago
Hello Klustakwik2 contributors, I am currently using spike interface and I am stuck in the section that involves using Klusta. I am running these lines
The code runs but halfway through I then encounter the following errors
I am working on window 10 pro. Anything helps, thank you.