def phycli(ctx):
"""Interactive visualization and manual spike sorting of large-scale ephys data."""
add_default_handler(level='DEBUG' if DEBUG else 'INFO',
logger=logging.getLogger('phy'))
add_default_handler(level='DEBUG' if DEBUG else 'INFO',
logger=logging.getLogger('phylib'))
add_default_handler(level='DEBUG' if DEBUG else 'INFO',
logger=logging.getLogger('mtscomp'))
import warnings
import matplotlib
import numpy as np
from pytest import fixture
from phylib import add_default_handler
#------------------------------------------------------------------------------
# Common fixtures
#------------------------------------------------------------------------------
logger = logging.getLogger('phylib')
logger.setLevel(10)
add_default_handler(5, logger=logger)
# Fix the random seed in the tests.
np.random.seed(2015)
warnings.filterwarnings('ignore', category=matplotlib.cbook.mplDeprecation)
warnings.filterwarnings("ignore", message="numpy.dtype size changed")
warnings.filterwarnings("ignore", message="numpy.ufunc size changed")
@fixture
def tempdir():
curdir = os.getcwd()
tempdir = tempfile.mkdtemp()
os.chdir(tempdir)
yield Path(tempdir)
def launch_phy(probe_name,
eid=None,
subj=None,
date=None,
sess_no=None,
one=None):
"""
Launch phy given an eid and probe name.
TODO calculate metrics and save as .tsvs to include in GUI when launching?
"""
# This is a first draft, no error handling and a draft dataset list.
# Load data from probe #
# -------------------- #
if one is None:
one = ONE()
dtypes = [
'spikes.times',
'spikes.clusters',
'spikes.amps',
'spikes.templates',
'spikes.samples',
'spikes.depths',
'templates.waveforms',
'templates.waveformsChannels',
'clusters.uuids',
'clusters.metrics',
'clusters.waveforms',
'clusters.waveformsChannels',
'clusters.depths',
'clusters.amps',
'clusters.channels',
'channels.probes',
'channels.rawInd',
'channels.localCoordinates',
# 'ephysData.raw.ap'
'_phy_spikes_subset.waveforms',
'_phy_spikes_subset.spikes',
'_phy_spikes_subset.channels'
]
if eid is None:
eid = one.search(subject=subj, date=date, number=sess_no)[0]
_ = one.load(eid, dataset_types=dtypes, download_only=True)
ses_path = one.path_from_eid(eid)
alf_probe_dir = os.path.join(ses_path, 'alf', probe_name)
ephys_file_dir = os.path.join(ses_path, 'raw_ephys_data', probe_name)
raw_files = glob.glob(os.path.join(ephys_file_dir, '*ap.*bin'))
raw_file = [raw_files[0]] if raw_files else None
# TODO download ephys meta-data, and extract TemplateController input arg params
# Launch phy #
# -------------------- #
add_default_handler('DEBUG', logging.getLogger("phy"))
add_default_handler('DEBUG', logging.getLogger("phylib"))
create_app()
controller = TemplateController(
dat_path=raw_file,
dir_path=alf_probe_dir,
dtype=np.int16,
n_channels_dat=384,
sample_rate=3e4,
plugins=['IBLMetricsPlugin'],
plugin_dirs=[Path(__file__).resolve().parent / 'plugins'])
gui = controller.create_gui()
gui.show()
run_app()
gui.close()
controller.model.close()