def get_sessionmaker(dbpath, echo=True, autocommit=True, **kw):
from sqlalchemy import create_engine
from sqlalchemy.orm import sessionmaker
path = Path(dbpath)
engine = create_engine('sqlite:///{}'.format(dbpath),
echo=echo, **kw) if path.is_file() else recreate('', echo=echo)
return sessionmaker(engine, autocommit=autocommit)
def import_ephys(filepath):
"""
filepath = '/Volumes/Users/ht/dev/current/pacu/tmp/Jack/jzg1/day1/day1_000_007.txt'
risings = import_ephys(filepath)
"""
path = Path(filepath)
if not path.is_file():
raise NoRawDataError('Can not find raw data {!r}'.format(path.name))
try:
raw = np.genfromtxt(path.str,
delimiter=' ',
names=['TTL', 'ON'],
dtype='b')
first_frame = find_nth_rising(raw['TTL'])
data = raw[first_frame:]
data['ON'][data['ON'] == 60] = 1
edges = np.diff(data['TTL']) > 0
ed_indices = np.where(edges)[0] + 1
on_chunks = np.split(data['ON'], ed_indices)
return np.array([chunk.any() for chunk in on_chunks])
except Exception as e:
raise RawDataParseError(e)
def from_metadata_filename(cls, filename, meta):
sbxpath = Path(filename).with_suffix('.sbx')
if sbxpath.is_file():
return cls(sbxpath.str, meta)