Kilosort
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Initial Usage Error(s): NumPy array is not writable, 0 spikes extracted
Describe the issue:
upon"LOAD"-ing the data: C:\ProgramData\anaconda3\envs\KS4\lib\site-packages\kilosort\io.py:498: UserWarning: The given NumPy array is not writable, and PyTorch does not support non-writable tensors. This means writing to this tensor will result in undefined behavior. You may want to copy the array to protect its data or make it writable before converting it to a tensor. This type of warning will be suppressed for the rest of this program. (Triggered internally at C:\cb\pytorch_1000000000000\work\torch\csrc\utils\tensor_numpy.cpp:212.) X[:, self.nt : self.nt+nsamp] = torch.from_numpy(data).to(self.device).float()
If I proceed anyways, and "RUN", I get:
Preprocessing filters computed in 0.20s; total 0.20s computing drift Re-computing universal templates from data.
C:\ProgramData\anaconda3\envs\KS4\lib\site-packages\threadpoolctl.py:1223: RuntimeWarning: Found Intel OpenMP ('libiomp') and LLVM OpenMP ('libomp') loaded at the same time. Both libraries are known to be incompatible and this can cause random crashes or deadlocks on Linux when loaded in the same Python program. Using threadpoolctl may cause crashes or deadlocks. For more information and possible workarounds, please see https://github.com/joblib/threadpoolctl/blob/master/multiple_openmp.md
warnings.warn(msg, RuntimeWarning)
0%| | 0/155 [00:00<?, ?it/s] 0%| | 0/155 [00:10<?, ?it/s] 100%|################################################################################| 155/155 [00:19<00:00, 7.81it/s] drift computed in 20.98s; total 21.18s
Extracting spikes using templates Re-computing universal templates from data. 0%| | 0/155 [00:00<?, ?it/s] 100%|################################################################################| 155/155 [00:17<00:00, 8.66it/s]
0 spikes extracted in 18.44s; total 39.61s
Traceback (most recent call last):
File "C:\ProgramData\anaconda3\envs\KS4\lib\site-packages\kilosort\gui\sorter.py", line 82, in run
st, tF, Wall0, clu0 = detect_spikes(ops, self.device, bfile, tic0=tic0,
File "C:\ProgramData\anaconda3\envs\KS4\lib\site-packages\kilosort\run_kilosort.py", line 397, in detect_spikes
raise ValueError('No spikes detected, cannot continue sorting.')
ValueError : No spikes detected, cannot continue sorting.
******* DUMP SETTINGS:
{'data_file_path': WindowsPath('C:/DATA/Spikes/tempData.dat'), 'results_dir': WindowsPath('C:/DATA/Spikes/kilosort4'), 'probe': {'xc': array([ 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 0., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500., 500.], dtype=float32), 'yc': array([ 0., 20., 40., 60., 80., 100., 120., 140., 160., 180., 200., 220., 240., 260., 280., 300., 320., 340., 360., 380., 400., 420., 440., 460., 480., 500., 520., 540., 560., 580., 600., 620., 640., 660., 680., 700., 720., 740., 760., 780., 800., 820., 840., 860., 880., 900., 920., 940., 960., 980., 1000., 1020., 1040., 1060., 1080., 1100., 1120., 1140., 1160., 1180., 1200., 1220., 1240., 1260., 0., 20., 40., 60., 80., 100., 120., 140., 160., 180., 200., 220., 240., 260., 280., 300., 320., 340., 360., 380., 400., 420., 440., 460., 480., 500., 520., 540., 560., 580., 600., 620., 640., 660., 680., 700., 720., 740., 760., 780., 800., 820., 840., 860., 880., 900., 920., 940., 960., 980., 1000., 1020., 1040., 1060., 1080., 1100., 1120., 1140., 1160., 1180., 1200., 1220., 1240., 1260.], dtype=float32), 'kcoords': array([1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2.], dtype=float32), 'chanMap': array([ 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79]), 'n_chan': 128}, 'probe_name': 'chanMap128.mat', 'data_dtype': 'int16', 'n_chan_bin': 128, 'fs': 30000.0, 'batch_size': 60000, 'nblocks': 1, 'Th_universal': 9.0, 'Th_learned': 8.0, 'tmin': 0.0, 'tmax': inf, 'nt': 61, 'artifact_threshold': inf, 'nskip': 25, 'whitening_range': 32, 'binning_depth': 5.0, 'sig_interp': 20.0, 'nt0min': None, 'dmin': None, 'dminx': None, 'min_template_size': 10.0, 'template_sizes': 5, 'nearest_chans': 10, 'nearest_templates': 100, 'templates_from_data': True, 'n_templates': 6, 'n_pcs': 6, 'Th_single_ch': 6.0, 'acg_threshold': 0.2, 'ccg_threshold': 0.25, 'cluster_downsampling': 20, 'cluster_pcs': 64, 'duplicate_spike_bins': 15}
Provide environment info:
active environment : KS4
active env location : C:\ProgramData\anaconda3\envs\KS4
shell level : 2
user config file : C:\Users\wehr\.condarc
populated config files : conda version : 24.1.0 conda-build version : 3.27.0 python version : 3.11.5.final.0 solver : libmamba (default) virtual packages : __archspec=1=x86_64 __conda=24.1.0=0 __cuda=12.2=0 __win=0=0 base environment : C:\ProgramData\anaconda3 (writable) conda av data dir : C:\ProgramData\anaconda3\etc\conda conda av metadata url : None channel URLs : https://repo.anaconda.com/pkgs/main/win-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/win-64 https://repo.anaconda.com/pkgs/r/noarch https://repo.anaconda.com/pkgs/msys2/win-64 https://repo.anaconda.com/pkgs/msys2/noarch package cache : C:\ProgramData\anaconda3\pkgs C:\Users\wehr.conda\pkgs C:\Users\wehr\AppData\Local\conda\conda\pkgs envs directories : C:\ProgramData\anaconda3\envs C:\Users\wehr.conda\envs C:\Users\wehr\AppData\Local\conda\conda\envs platform : win-64 user-agent : conda/24.1.0 requests/2.31.0 CPython/3.11.5 Windows/10 Windows/10.0.19045 solver/libmamba conda-libmamba-solver/24.1.0 libmambapy/1.5.6 aau/0.4.3 c/jUGHLyl0bHLouE7eQQlcaQ s/WWJUok-a5hEuXJiceMfI9A e/UhGP7xmY_2PAV0B0v2HiFA administrator : True netrc file : None offline mode : False
Operating system information:
OS Name Microsoft Windows 10 Pro Version 10.0.19045 Build 19045
@kipkeller Can you please confirm if you're using the latest version of Kilosort4 (v4.0.5), and reinstall if not (pip install --upgrade kilosort). This looks like it's coming from an older release.
OK - did this:
Installing collected packages: tbb, intel-openmp, mkl, kilosort
Attempting uninstall: kilosort
Found existing installation: kilosort 4.0.2
Uninstalling kilosort-4.0.2:
Successfully uninstalled kilosort-4.0.2
Successfully installed intel-openmp-2021.4.0 kilosort-4.0.5 mkl-2021.4.0 tbb-2021.12.0
****** , now have this:
(KS4) C:\Windows\system32>python -m kilosort
Traceback (most recent call last):
File "C:\ProgramData\anaconda3\envs\KS4\lib\runpy.py", line 197, in _run_module_as_main
return run_code(code, main_globals, None,
File "C:\ProgramData\anaconda3\envs\KS4\lib\runpy.py", line 87, in run_code
exec(code, run_globals)
File "C:\ProgramData\anaconda3\envs\KS4\lib\site-packages\kilosort_main.py", line 2, in
You might need to do pip install kilosort again without the --upgrade part then, that should have installed qtpy as well.
did: pip install kilosort everything was listed as 'satisfied' and did not list qtpy running: python -m kilosort gives the same error
can I just pip install qtpy ? should I specify a version or source?
Yeah, try that, just qtpy with no version. It's just odd that it didn't do that automatically.
OK - now running, with a few glitches to attend to tomorrow:
None not allowed for parameter probe. - maybe this solved when I loaded the probe>?
then:
INFO: The correct number of channels has been estimated to be 128.
None not allowed for parameter dminx.
I could set this to some value, but what? Is there info somewhere on what all these settings mean and suggested values? thnx !!!
Yes, parameters are documented in kilosort.parameters.py. You can also see the same information by mousing over the parameter name in the GUI for about half a second. The default value for dminx was changed to 32, and corresponds to horizontal spacing between contacts on the probe, in microns. I'm not sure what's going on with the probe error, it's probably because of the version change. I would recommend clicking the "reset gui" and "clear cache" buttons at the top right to make sure everything is set correctly for the updated version.