FileNotFoundError: cuda/mexThSpkPC.cu

[DradeAW]

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:

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.

Hope this helps!