Trouble running Herdingspikes on Spikeinterface

[nasnass]

Hi! I am having a bit of difficulties getting Herdingspikes to run using Spike interface. This is the error I am getting:

The extractor was not dumpable Error running herdingspikes Traceback (most recent call last): File "C:\Users\nasya\anaconda3\envs\herdingspikes\lib\site-packages\spikeinterface\sorters\basesorter.py", line 200, in run_from_folder SorterClass._run_from_folder(output_folder, sorter_params, verbose) File "C:\Users\nasya\anaconda3\envs\herdingspikes\lib\site-packages\spikeinterface\sorters\herdingspikes\herdingspikes.py", line 170, in _run_from_folder recording = st.normalize_by_quantile( File "C:\Users\nasya\anaconda3\envs\herdingspikes\lib\site-packages\spikeinterface\toolkit\preprocessing\normalize_scale.py", line 196, in normalize_by_quantile return NormalizeByQuantileRecording(*args, **kwargs) File "C:\Users\nasya\anaconda3\envs\herdingspikes\lib\site-packages\spikeinterface\toolkit\preprocessing\normalize_scale.py", line 60, in init random_data = get_random_data_chunks(recording, **random_chunk_kwargs) File "C:\Users\nasya\anaconda3\envs\herdingspikes\lib\site-packages\spikeinterface\toolkit\utils.py", line 36, in get_random_data_chunks for segment_index in range(recording.get_num_segments()): AttributeError: 'NoneType' object has no attribute 'get_num_segments'

Here is how I am running it:

sorting_HS = ss.run_herdingspikes(recording, output_folder='results_HS', filter=False, verbose=True)

Whenever I try to pre-process it, and then run the sorter, the Kernel dies.

recording_f = st.bandpass_filter(recording, freq_min=100, freq_max=3000) recording = recording_f.save(format='binary')

I have only take a small chunk of my data (not even 1GB) just to try and get it to work. Would be very thankful for any hints! I have already talked to the team at Herdingspikes and they are saying it might have something to do with the pre-processing of SI.

[samuelgarcia]

Hi thanks for report.

@mhhennig : could you help on this ?

@nasnass : you should update your spikeinterface isntallation with the source installation from github.

[nasnass]

@samuelgarcia I have updated it, still same issue.

[alejoe91]

@nasnass how are you running HerdingSpikes? I think there might be an error in how you pass the arguments, because the recording seems to be None...

[alejoe91]

Closing for inactivity, feel free to reopen