def run_spike_sorting_ibl(bin_file):
_logger = logging.getLogger("pykilosort")
START_TIME = datetime.datetime.now()
out_dir = Path("/datadisk/Data/spike_sorting/datasets").joinpath(
'_'.join(list(bin_file.parts[-6:-3]) + [bin_file.parts[-2]]))
out_dir.mkdir(exist_ok=True, parents=True)
add_default_handler(level='DEBUG')
add_default_handler(
level='DEBUG',
filename=out_dir.joinpath(f"{START_TIME.isoformat()}_kilosort.log"))
files_chmap = Path(
"/home/olivier/Documents/MATLAB/Kilosort2/configFiles/neuropixPhase3A_kilosortChanMap.mat"
)
matdata = Bunch(scipy.io.loadmat(files_chmap))
probe = Bunch()
probe.NchanTOT = 385
# WARNING: indexing mismatch with MATLAB hence the -1
probe.chanMap = (matdata.chanMap - 1).squeeze()
probe.xc = matdata.xcoords.squeeze()
probe.yc = matdata.ycoords.squeeze()
probe.kcoords = probe.yc * 0 + 1
try:
_logger.info(f"Starting KS, output in {out_dir}")
run(bin_file,
probe=probe,
dir_path=out_dir,
n_channels=385,
dtype=np.int16,
sample_rate=3e4)
except Exception as e:
_logger.exception("Error in the main loop")
[_logger.removeHandler(h) for h in _logger.handlers]
dat_path = Path("test/test.bin").absolute()
dir_path = dat_path.parent
ka.set_config(fr="default_readonly")
recording_path = "sha1dir://c0879a26f92e4c876cd608ca79192a84d4382868.manual_franklab/tetrode_600s/sorter1_1"
recording = AutoRecordingExtractor(recording_path, download=True)
recording.write_to_binary_dat_format(str(dat_path))
n_channels = len(recording.get_channel_ids())
probe = Bunch()
probe.NchanTOT = n_channels
probe.chanMap = np.array(range(0, n_channels))
probe.kcoords = np.ones(n_channels)
probe.xc = recording.get_channel_locations()[:, 0]
probe.yc = recording.get_channel_locations()[:, 1]
add_default_handler(level="DEBUG")
params = {"nfilt_factor": 8, "AUCsplit": 0.85, "nskip": 5}
run(
dat_path,
params=params,
probe=probe,
dir_path=dir_path,
n_channels=probe.NchanTOT,
dtype=np.int16,
sample_rate=recording.get_sampling_frequency(),
)
eng.workspace['rootZ'] = rootZ
rez = eng.function_kilosort(rootZ, ops)
os.listdir(MATLAB_SORTING_RESULTS_DIR)
# ## Sort simulated data using pykilosort
# In[40]:
import pykilosort
from pathlib import Path
from importlib import reload
from pykilosort import main
reload(main)
pykilosort.add_default_handler()
# In[35]:
np.load(PYKILOSORT_SORTING_RESULTS_DIR +
'/.kilosort/sim_binary.imec.ap/igood.npy')
# In[43]:
probe = pykilosort.Bunch()
probe.NchanTOT = int(opts['NchanTOT'])
probe.chanMap = np.load(BASE_PATH + '/chanMap.npy').flatten().astype(int)
probe.kcoords = np.ones(int(opts['NchanTOT']))
probe.xc = np.load(BASE_PATH + '/xc.npy').flatten()
probe.yc = np.load(BASE_PATH + '/yc.npy').flatten()
from math import ceil
from pathlib import Path
from pytest import fixture
import numpy as np
from pykilosort.utils import Bunch, read_data
from pykilosort import add_default_handler
add_default_handler(level='DEBUG')
from math import ceil
from pathlib import Path
from pytest import fixture
import numpy as np
@fixture
def data_path():
path = (Path(__file__).parent / '../../data/').resolve()
assert path.exists()
return path
@fixture
def dat_path(data_path):
return data_path / 'imec_385_100s.bin'
@fixture