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SpikeInterface
SpikeInterface fails with spykingcircus2 spike sorting tetrode data
This is the full error output:
Exception has occurred: SpikeSortingError
Spike sorting error trace:
Traceback (most recent call last):
File "/home/m329786/anaconda3/envs/si_env/lib/python3.11/site-packages/spikeinterface/sorters/basesorter.py", line 270, in run_from_folder
SorterClass._run_from_folder(sorter_output_folder, sorter_params, verbose)
File "/home/m329786/anaconda3/envs/si_env/lib/python3.11/site-packages/spikeinterface/sorters/internal/spyking_circus2.py", line 199, in _run_from_folder
prototype, waveforms, _ = get_prototype_and_waveforms_from_recording(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/m329786/anaconda3/envs/si_env/lib/python3.11/site-packages/spikeinterface/sortingcomponents/tools.py", line 191, in get_prototype_and_waveforms_from_recording
prototype = np.nanmedian(waveforms[:, :, 0] / (np.abs(waveforms[:, nbefore, 0][:, np.newaxis])), axis=0)
~~~~~~~~~^^^^^^^^^^^^^^^
IndexError: index 0 is out of bounds for axis 1 with size 0
Spike sorting failed. You can inspect the runtime trace in /mnt/c/Users/m329786/Data/spikeinterface_output/spykingcircus2/sorter_output/sub-MSEL02698_ses-stim01_task-none_ieeg/spikeinterface_log.json.
File "/mnt/c/Users/m329786/code_repositories/nwb2spikesort/master_file.py", line 93, in <module>
folder=si_output_folder_specific, \
docker_image=docker_image, verbose=True, \
remove_existing_folder=True, **params)
print(sorting)
spikeinterface.sorters.utils.misc.SpikeSortingError: Spike sorting error trace:
Traceback (most recent call last):
File "/home/m329786/anaconda3/envs/si_env/lib/python3.11/site-packages/spikeinterface/sorters/basesorter.py", line 270, in run_from_folder
SorterClass._run_from_folder(sorter_output_folder, sorter_params, verbose)
File "/home/m329786/anaconda3/envs/si_env/lib/python3.11/site-packages/spikeinterface/sorters/internal/spyking_circus2.py", line 199, in _run_from_folder
prototype, waveforms, _ = get_prototype_and_waveforms_from_recording(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/m329786/anaconda3/envs/si_env/lib/python3.11/site-packages/spikeinterface/sortingcomponents/tools.py", line 191, in get_prototype_and_waveforms_from_recording
prototype = np.nanmedian(waveforms[:, :, 0] / (np.abs(waveforms[:, nbefore, 0][:, np.newaxis])), axis=0)
~~~~~~~~~^^^^^^^^^^^^^^^
IndexError: index 0 is out of bounds for axis 1 with size 0
Spike sorting failed. You can inspect the runtime trace in /mnt/c/Users/m329786/Data/spikeinterface_output/spykingcircus2/sorter_output/sub-MSEL02698_ses-stim01_task-none_ieeg/spikeinterface_log.json.
The parameters I am using are given below:
{'apply_motion_correction': (False,),
'apply_preprocessing': True,
'cache_preprocessing': {'delete_cache': True,
'memory_limit': 0.5,
'mode': 'memory'},
'clustering': {'legacy': True},
'debug': False,
'detection': {'detect_threshold': 5, 'peak_sign': 'neg'},
'filtering': {'filter_order': 2,
'freq_max': 7000,
'freq_min': 150,
'ftype': 'bessel',
'margin_ms': 10},
'general': {'ms_after': 0.001, 'ms_before': 0.001, 'radius_um': 70.0},
'job_kwargs': {'n_jobs': 0.5},
'matched_filtering': True,
'matching': {'method': 'circus-omp-svd'},
'merging': {'max_distance_um': 50},
'motion_correction': {'preset': 'dredge_fast'},
'multi_units_only': False,
'seed': 42,
'selection': {'method': 'uniform',
'min_n_peaks': 100000,
'n_peaks_per_channel': 5000,
'seed': 42,
'select_per_channel': False},
'sparsity': {'amplitude_mode': 'peak_to_peak',
'method': 'snr',
'threshold': 1},
'whitening': {'mode': 'local', 'regularize': False}}
I attach a probegroup to the recording based on the attached kilosort4 probe file.
Do you have any suggestions on how to address this issue? I can provide the binary or NWB file that I use to produce the error.
Just so we have all the info. What version of spikeinterface were you using? @yger works on SC2 so he can comment on that.
If I can have the data (rec+probes+anything related that might be necessary) to reproduce the error, I'll fix it. This is strange because this implies that no waveforms are found..
This is the ks4_probe file probe_ks4.json
And this is the link to download the recording https://drive.google.com/file/d/1KQV-RKrONYZJ0WHUaSGJCotSRG7ZhAi4/view?usp=sharing
Let me know if you need anything else. Thanks
Can I get a probe in the probeinterface file format ? Or alternatively give the script you are using to process the raw recording with spikeinterface
I have also tried using a different file and loading from a binary file instead of NWB and I get a very similar output:
Error running spykingcircus2
Traceback (most recent call last):
File "/mnt/c/Users/m329786/code_repositories/nwb2spikesort/run_spykingcircus2.py", line 115, in <module>
sorting = ss.run_sorter(sorter_name=sorter, recording=recording, # type: ignore \
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/m329786/anaconda3/envs/si_env/lib/python3.11/site-packages/spikeinterface/sorters/runsorter.py", line 198, in run_sorter
return run_sorter_local(**common_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/m329786/anaconda3/envs/si_env/lib/python3.11/site-packages/spikeinterface/sorters/runsorter.py", line 260, in run_sorter_local
SorterClass.run_from_folder(folder, raise_error, verbose)
File "/home/m329786/anaconda3/envs/si_env/lib/python3.11/site-packages/spikeinterface/sorters/basesorter.py", line 310, in run_from_folder
raise SpikeSortingError(
spikeinterface.sorters.utils.misc.SpikeSortingError: Spike sorting error trace:
Traceback (most recent call last):
File "/home/m329786/anaconda3/envs/si_env/lib/python3.11/site-packages/spikeinterface/sorters/basesorter.py", line 270, in run_from_folder
SorterClass._run_from_folder(sorter_output_folder, sorter_params, verbose)
File "/home/m329786/anaconda3/envs/si_env/lib/python3.11/site-packages/spikeinterface/sorters/internal/spyking_circus2.py", line 193, in _run_from_folder
prototype, waveforms, _ = get_prototype_and_waveforms_from_recording(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/m329786/anaconda3/envs/si_env/lib/python3.11/site-packages/spikeinterface/sortingcomponents/tools.py", line 191, in get_prototype_and_waveforms_from_recording
prototype = np.nanmedian(waveforms[:, :, 0] / (np.abs(waveforms[:, nbefore, 0][:, np.newaxis])), axis=0)
~~~~~~~~~^^^^^^^^^^^^^^^
IndexError: index 0 is out of bounds for axis 1 with size 0
Spike sorting failed. You can inspect the runtime trace in /mnt/c/Users/m329786/Data/spikeinterface_output/spykingcircus2/sorter_output/msel_02750_ICU02a_micro_data/dump/spikeinterface_log.json.
The link to the binary file is below: https://drive.google.com/file/d/17tyA0VQNA1gdLC88uNia0PC5wvVNx-9k/view?usp=sharing
Also, can you try to view the data with sw.plot_traces? You can also use the backend="ipywidgets" for an interactive plot in Jupyter. Since many sorters fail, I suspect something is wrong in the data loading/parsing
SOrry, I was away last week for conferences. I have your data and the probe, but you just sent me a raw binary. So what are the metadata info (dtype, nchannels I can guess, but also sampling rate) ? Or at least a script to show me how do you load the data to reproduce the bug
@yger you can find the probe here: https://github.com/SpikeInterface/spikeinterface/issues/3909#issuecomment-2898649051
It's KS4 json, but easy to convert. I was able to run SC2 and it found some units, but mainly noisy. @dervinism here's my script:
import spikeinterface.full as si
import json
import numpy as np
rec = si.read_nwb_recording("/home/alessio/Downloads/msel_02698_ICU03.nwb",
electrical_series_path="acquisition/TimeSeries_32000_Hz")
rec.reset_times()
# load probe and groups
with open("/home/alessio/Downloads/probe_ks4.json") as f:
probe_info = json.load(f)
groups = probe_info["kcoords"]
locations = np.zeros((rec.get_num_channels(), 2))
locations[:, 0] = probe_info["xc"]
locations[:, 1] = probe_info["yc"]
rec.set_channel_locations(locations)
rec.set_channel_groups(groups)
# preprocess
rec_pre = si.bandpass_filter(rec)
rec_cmr = si.common_reference(rec_pre)
# run MS5
sort_ms5 = si.run_sorter_by_property("mountainsort5", rec_cmr, grouping_property="group", folder="by_prop_ms5")
print(sort_ms5)
sort_sc2 = si.run_sorter_by_property("spykingcircus2", rec_cmr, grouping_property="group", folder="by_prop_sc2")
print(sort_sc2)
So both sorters run, but they find bad units, probably due to the high contamination of the recording. Did KS4 find any good unit?
You are running it differently though. What is the difference between run_sorter and run_sorter_by_property?
You are running it differently though. What is the difference between
run_sorterandrun_sorter_by_property?
It also completed with run_sorter. run_sorter_by_property will run spike sorting separately for each tetrode and aggregate the results
Ok, so the key appears to be this line:
recording.set_channel_groups(groups)
Also a question. You filter and whiten the data prior to passing it to the spike sorter but you can also instruct the sorter to do the same via parameters. Do I understand it correctly? Does the spike sorter also perform CAR or does it have to be done as a separate step prior to spike sorting?
It wouldn't run with run_sorter. I'm guessing that recordings have to be split beforehand in this case, like:
recording.split_by(property="group")
*Edit: Apparently that doesn't help
Or that's just unique to SpykingCircus which wouldn't run:
Traceback (most recent call last):
File "/mnt/c/Users/m329786/code_repositories/nwb2spikesort/master_file.py", line 176, in <module>
sorting = ss.run_sorter_by_property(sorter_name=sorter, recording=recording, # type: ignore \
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/m329786/anaconda3/envs/si_env/lib/python3.11/site-packages/spikeinterface/sorters/launcher.py", line 308, in run_sorter_by_property
sorting_list = run_sorter_jobs(job_list, engine=engine, engine_kwargs=engine_kwargs, return_output=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/m329786/anaconda3/envs/si_env/lib/python3.11/site-packages/spikeinterface/sorters/launcher.py", line 106, in run_sorter_jobs
sorting = run_sorter(**kwargs)
^^^^^^^^^^^^^^^^^^^^
File "/home/m329786/anaconda3/envs/si_env/lib/python3.11/site-packages/spikeinterface/sorters/runsorter.py", line 198, in run_sorter
return run_sorter_local(**common_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/m329786/anaconda3/envs/si_env/lib/python3.11/site-packages/spikeinterface/sorters/runsorter.py", line 260, in run_sorter_local
SorterClass.run_from_folder(folder, raise_error, verbose)
File "/home/m329786/anaconda3/envs/si_env/lib/python3.11/site-packages/spikeinterface/sorters/basesorter.py", line 310, in run_from_folder
raise SpikeSortingError(
spikeinterface.sorters.utils.misc.SpikeSortingError: Spike sorting error trace:
Traceback (most recent call last):
File "/home/m329786/anaconda3/envs/si_env/lib/python3.11/site-packages/spikeinterface/sorters/basesorter.py", line 270, in run_from_folder
SorterClass._run_from_folder(sorter_output_folder, sorter_params, verbose)
File "/home/m329786/anaconda3/envs/si_env/lib/python3.11/site-packages/spikeinterface/sorters/internal/spyking_circus2.py", line 193, in _run_from_folder
prototype, waveforms, _ = get_prototype_and_waveforms_from_recording(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/m329786/anaconda3/envs/si_env/lib/python3.11/site-packages/spikeinterface/sortingcomponents/tools.py", line 191, in get_prototype_and_waveforms_from_recording
prototype = np.nanmedian(waveforms[:, :, 0] / (np.abs(waveforms[:, nbefore, 0][:, np.newaxis])), axis=0)
~~~~~~~~~^^^^^^^^^^^^^^^
IndexError: index 0 is out of bounds for axis 1 with size 0
Spike sorting failed. You can inspect the runtime trace in /mnt/c/Users/m329786/Data/spikeinterface_output/spykingcircus2/sorter_output/msel_02750_ICU02a_micro_data/0.0/spikeinterface_log.json.
Sorting fails when peak_sign = 'both'. So this is the reason why spykingcircus is not failing.
Why do you want peak_sign set to both? I suggest keeping the default (neg)