Module xelo2.io.events
Expand source code
from numpy import empty
from wonambi.dataset import UnrecognizedFormat
from sys import maxsize
from logging import getLogger
from .utils import localize_blackrock
from ..api.utils import get_dtypes
lg = getLogger(__name__)
def read_events_from_ephys(file, run=None, rec=None, db=None):
"""Read events from ephys file. If you specify both run and rec, then it only
read the events in the period inside the run period
Parameters
----------
file : File
instance of File
run : Run
instance of Run
rec : Recording
instance of Recording
db : database
only necessary if you don't specify run
Notes
-----
Make sure that rec.onset is in the good direction
"""
try:
d = localize_blackrock(file.path)
except UnrecognizedFormat:
lg.warning(f'cannot parse poorly edited BCI2000 file ({file.path})')
return None
except FileNotFoundError:
lg.warning(f'{file.path} does not exist')
return None
markers = d.read_markers()
if run is None:
start_t = 0
else:
start_t = (run.start_time - d.header['start_time']).total_seconds() + rec.offset
if run.duration is not None:
end_t = start_t + run.duration
else:
end_t = maxsize
markers = [m for m in markers if start_t <= m['start'] <= end_t]
if run is not None:
DTYPES = run.events.dtype
else:
DTYPES = get_dtypes(db['tables']['events'])
events = empty(len(markers), dtype=DTYPES)
events['value'] = [m['name'] for m in markers]
events['onset'] = [m['start'] - start_t for m in markers]
events['duration'] = 0
return events
def find_eegfile_in_run(run):
for rec in run.list_recordings():
for file in rec.list_files():
if file.format in ('micromed', 'bci2000', 'blackrock'):
return rec, file
return None, NoneFunctions
def find_eegfile_in_run(run)-
Expand source code
def find_eegfile_in_run(run): for rec in run.list_recordings(): for file in rec.list_files(): if file.format in ('micromed', 'bci2000', 'blackrock'): return rec, file return None, None def read_events_from_ephys(file, run=None, rec=None, db=None)-
Read events from ephys file. If you specify both run and rec, then it only read the events in the period inside the run period
Parameters
file:File- instance of File
run:Run- instance of Run
rec:Recording- instance of Recording
db:database- only necessary if you don't specify run
Notes
Make sure that rec.onset is in the good direction
Expand source code
def read_events_from_ephys(file, run=None, rec=None, db=None): """Read events from ephys file. If you specify both run and rec, then it only read the events in the period inside the run period Parameters ---------- file : File instance of File run : Run instance of Run rec : Recording instance of Recording db : database only necessary if you don't specify run Notes ----- Make sure that rec.onset is in the good direction """ try: d = localize_blackrock(file.path) except UnrecognizedFormat: lg.warning(f'cannot parse poorly edited BCI2000 file ({file.path})') return None except FileNotFoundError: lg.warning(f'{file.path} does not exist') return None markers = d.read_markers() if run is None: start_t = 0 else: start_t = (run.start_time - d.header['start_time']).total_seconds() + rec.offset if run.duration is not None: end_t = start_t + run.duration else: end_t = maxsize markers = [m for m in markers if start_t <= m['start'] <= end_t] if run is not None: DTYPES = run.events.dtype else: DTYPES = get_dtypes(db['tables']['events']) events = empty(len(markers), dtype=DTYPES) events['value'] = [m['name'] for m in markers] events['onset'] = [m['start'] - start_t for m in markers] events['duration'] = 0 return events