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mhhennig / HS2

Software for high density electrophysiology
GNU General Public License v3.0
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Cant run herdingspikes #64

Closed franciscomiqueles closed 4 months ago

franciscomiqueles commented 2 years ago

Hello,

I have been testing Spikeinterface using the tutorials in the github. I tried to sort through herdingspikes using the database provided in the tutorial but i have the following error in the code

sorting_HS = ss.run_herdingspikes(recording_loaded, output_folder='results_HS', filter=False, verbose=True) print('Found', len(sorting_HS.get_unit_ids()), 'units')

Generating new position and neighbor files from data file Not Masking any Channels Sampling rate: 20000 Localization On Number of recorded channels: 16 Few recording channels: not subtracing mean from activity Analysing frames: 6000000; Seconds: 300.0 Frames before spike in cutout: 6 Frames after spike in cutout: 36 tcuts: 26 56 tInc: 100000 Detection completed, time taken: 0:00:00.854102 Time per frame: 0:00:00.000142 Time per sample: 0:00:00.000009 Loaded 0 spikes. Error running herdingspikes Traceback (most recent call last): File "/home/brontodegus/anaconda3/envs/si090/lib/python3.8/site-packages/spikeinterface/sorters/basesorter.py", line 200, in run_from_folder SorterClass._run_from_folder(output_folder, sorter_params, verbose) File "/home/brontodegus/anaconda3/envs/si090/lib/python3.8/site-packages/spikeinterface/sorters/herdingspikes/herdingspikes.py", line 226, in _run_from_folder uids = C.spikes.cl.unique() File "/home/brontodegus/anaconda3/envs/si090/lib/python3.8/site-packages/pandas/core/generic.py", line 5575, in getattr return object.getattribute(self, name) AttributeError: 'DataFrame' object has no attribute 'cl'

Also, i tried changing "filter=True" but i still having the same error .

Thanks for your help.

nasnass commented 2 years ago

Hi! Were you able to find a solution - I am currently also struggling running herdingspikes on SI

b-grimaud commented 2 years ago

As you can see here : Loaded 0 spikes., it seems HS2 found zero spikes. Since the C.spikes DataFrame is most likely empty, HS2 failed. Either there is something with your raw or processed data, or the detection threshold is too high.

mhhennig commented 1 year ago

Correct, this means no spikes were detected (falsely leads to an error, this is internal to HS as it then tries to extract features). Is this still an issue?