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Hi,
I tried pykilosort for the first time today, and I encountered an error that I was able to solve, so I'm sharing it here.
pykilosort
My code is the following:
import numpy as np import pathlib import pykilosort as kilosort kilosort.add_default_handler(level="DEBUG") dat_path = pathlib.Path("amplifier.dat") dir_path = dat_path.parent probe = kilosort.Bunch() probe.NchanTOT = 64 probe.chanMap = np.arange(64) probe.kcoords = np.ones(64) coords = np.zeros([64, 2], dtype=np.float64) for i in range(64): coords[i] = (250*(i//16) + 12.5*(i%2), 12.5*(i%16)) probe.xc = coords[:, 0] probe.yc = coords[:, 1] kilosort.run(dat_path, probe=probe, dir_path=dir_path, n_channels=64, dtype=np.int16, sample_rate=30000)
The error was the following:
$ python test.py 16:17:18.254 [I] main:56 Loaded raw data with 64 channels, 48825600 samples. 16:17:18.254 [D] utils:273 Loading Wrot.npy 16:17:18.258 [I] utils:334 Starting step reorder. Clustering spikes: 0%| | 0/746 [00:00<?, ?it/s] Traceback (most recent call last): File "test.py", line 22, in <module> kilosort.run(dat_path, probe=probe, dir_path=dir_path, n_channels=64, dtype=np.int16, sample_rate=30000) File "/users/nsr/wyngaard/.conda/envs/kilosort/lib/python3.7/site-packages/pykilosort-2.0.0a0-py3.7.egg/pykilosort/main.py", line 164, in run out = clusterSingleBatches(ctx) File "/users/nsr/wyngaard/.conda/envs/kilosort/lib/python3.7/site-packages/pykilosort-2.0.0a0-py3.7.egg/pykilosort/cluster.py", line 481, in clusterSingleBatches proc, params, probe, wPCA, min(nBatches - 2, ibatch), iC, Nbatch) File "/users/nsr/wyngaard/.conda/envs/kilosort/lib/python3.7/site-packages/pykilosort-2.0.0a0-py3.7.egg/pykilosort/cluster.py", line 339, in extractPCbatch2 uS, idchan = mexThSpkPC(Params, dataRAW, wPCA, iC) File "/users/nsr/wyngaard/.conda/envs/kilosort/lib/python3.7/site-packages/pykilosort-2.0.0a0-py3.7.egg/pykilosort/cluster.py", line 249, in mexThSpkPC code, constants = get_cuda('mexThSpkPC') File "/users/nsr/wyngaard/.conda/envs/kilosort/lib/python3.7/site-packages/pykilosort-2.0.0a0-py3.7.egg/pykilosort/utils.py", line 115, in get_cuda code = path.read_text() File "/users/nsr/wyngaard/.conda/envs/kilosort/lib/python3.7/pathlib.py", line 1221, in read_text with self.open(mode='r', encoding=encoding, errors=errors) as f: File "/users/nsr/wyngaard/.conda/envs/kilosort/lib/python3.7/pathlib.py", line 1208, in open opener=self._opener) File "/users/nsr/wyngaard/.conda/envs/kilosort/lib/python3.7/pathlib.py", line 1063, in _opener return self._accessor.open(self, flags, mode) FileNotFoundError: [Errno 2] No such file or directory: '/users/nsr/wyngaard/.conda/envs/kilosort/lib/python3.7/site-packages/pykilosort-2.0.0a0-py3.7.egg/pykilosort/cuda/mexThSpkPC.cu' (kilosort) wyngaard@nspc05:~/Documents/bug/kilosort$ locate mexThSpkPC.cu /export/home1/users/nsr/wyngaard/dev/kilosort/pykilosort/pykilosort/cuda/mexThSpkPC.cu
I was able to solve the issue my modifying line 115 of the file pykilosort/utils.py to match where my mexThSpkPC.cu was.
pykilosort/utils.py
mexThSpkPC.cu
Hope this helps!
The text was updated successfully, but these errors were encountered:
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Hi,
I tried
pykilosort
for the first time today, and I encountered an error that I was able to solve, so I'm sharing it here.My code is the following:
The error was the following:
I was able to solve the issue my modifying line 115 of the file
pykilosort/utils.py
to match where mymexThSpkPC.cu
was.Hope this helps!
The text was updated successfully, but these errors were encountered: