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#!/usr/bin/env python
r"""Compute SSP/PCA projections for EOG artifacts.
You can do for example:
$ mne compute_proj_eog -i sample_audvis_raw.fif \
--l-freq 1 --h-freq 35 \
--rej-grad 3000 --rej-mag 4000 --rej-eeg 100
or
$ mne compute_proj_eog -i sample_audvis_raw.fif \
--l-freq 1 --h-freq 35 \
--rej-grad 3000 --rej-mag 4000 --rej-eeg 100 \
--proj sample_audvis_ecg-proj.fif
to exclude ECG artifacts from projection computation.
"""
from __future__ import print_function
# Authors : Alexandre Gramfort, Ph.D.
# Martin Luessi, Ph.D.
from mne.externals.six import string_types
import os
import sys
import mne
def run():
"""Run command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option("-i", "--in", dest="raw_in",
help="Input raw FIF file", metavar="FILE")
parser.add_option("--tmin", dest="tmin", type="float",
help="Time before event in seconds", default=-0.2)
parser.add_option("--tmax", dest="tmax", type="float",
help="Time after event in seconds", default=0.2)
parser.add_option("-g", "--n-grad", dest="n_grad", type="int",
help="Number of SSP vectors for gradiometers",
default=2)
parser.add_option("-m", "--n-mag", dest="n_mag", type="int",
help="Number of SSP vectors for magnetometers",
default=2)
parser.add_option("-e", "--n-eeg", dest="n_eeg", type="int",
help="Number of SSP vectors for EEG", default=2)
parser.add_option("--l-freq", dest="l_freq", type="float",
help="Filter low cut-off frequency in Hz",
default=1)
parser.add_option("--h-freq", dest="h_freq", type="float",
help="Filter high cut-off frequency in Hz",
default=35)
parser.add_option("--eog-l-freq", dest="eog_l_freq", type="float",
help="Filter low cut-off frequency in Hz used for "
"EOG event detection", default=1)
parser.add_option("--eog-h-freq", dest="eog_h_freq", type="float",
help="Filter high cut-off frequency in Hz used for "
"EOG event detection", default=10)
parser.add_option("-p", "--preload", dest="preload",
help="Temporary file used during computation (to "
"save memory)", default=True)
parser.add_option("-a", "--average", dest="average", action="store_true",
help="Compute SSP after averaging",
default=False) # XXX: change to default=True in 0.17
parser.add_option("--proj", dest="proj",
help="Use SSP projections from a fif file.",
default=None)
parser.add_option("--filtersize", dest="filter_length", type="int",
help="Number of taps to use for filtering",
default=2048)
parser.add_option("-j", "--n-jobs", dest="n_jobs", type="int",
help="Number of jobs to run in parallel", default=1)
parser.add_option("--rej-grad", dest="rej_grad", type="float",
help="Gradiometers rejection parameter in fT/cm (peak "
"to peak amplitude)", default=2000)
parser.add_option("--rej-mag", dest="rej_mag", type="float",
help="Magnetometers rejection parameter in fT (peak to "
"peak amplitude)", default=3000)
parser.add_option("--rej-eeg", dest="rej_eeg", type="float",
help="EEG rejection parameter in uV (peak to peak "
"amplitude)", default=50)
parser.add_option("--rej-eog", dest="rej_eog", type="float",
help="EOG rejection parameter in uV (peak to peak "
"amplitude)", default=1e9)
parser.add_option("--avg-ref", dest="avg_ref", action="store_true",
help="Add EEG average reference proj",
default=False)
parser.add_option("--no-proj", dest="no_proj", action="store_true",
help="Exclude the SSP projectors currently in the "
"fiff file", default=False)
parser.add_option("--bad", dest="bad_fname",
help="Text file containing bad channels list "
"(one per line)", default=None)
parser.add_option("--event-id", dest="event_id", type="int",
help="ID to use for events", default=998)
parser.add_option("--event-raw", dest="raw_event_fname",
help="raw file to use for event detection", default=None)
parser.add_option("--tstart", dest="tstart", type="float",
help="Start artifact detection after tstart seconds",
default=0.)
parser.add_option("-c", "--channel", dest="ch_name", type="string",
help="Custom EOG channel(s), comma separated",
default=None)
options, args = parser.parse_args()
raw_in = options.raw_in
if raw_in is None:
parser.print_help()
sys.exit(1)
tmin = options.tmin
tmax = options.tmax
n_grad = options.n_grad
n_mag = options.n_mag
n_eeg = options.n_eeg
l_freq = options.l_freq
h_freq = options.h_freq
eog_l_freq = options.eog_l_freq
eog_h_freq = options.eog_h_freq
average = options.average
preload = options.preload
filter_length = options.filter_length
n_jobs = options.n_jobs
reject = dict(grad=1e-13 * float(options.rej_grad),
mag=1e-15 * float(options.rej_mag),
eeg=1e-6 * float(options.rej_eeg),
eog=1e-6 * float(options.rej_eog))
avg_ref = options.avg_ref
no_proj = options.no_proj
bad_fname = options.bad_fname
event_id = options.event_id
proj_fname = options.proj
raw_event_fname = options.raw_event_fname
tstart = options.tstart
ch_name = options.ch_name
if bad_fname is not None:
with open(bad_fname, 'r') as fid:
bads = [w.rstrip() for w in fid.readlines()]
print('Bad channels read : %s' % bads)
else:
bads = []
if raw_in.endswith('_raw.fif') or raw_in.endswith('-raw.fif'):
prefix = raw_in[:-8]
else:
prefix = raw_in[:-4]
eog_event_fname = prefix + '_eog-eve.fif'
if average:
eog_proj_fname = prefix + '_eog_avg-proj.fif'
else:
eog_proj_fname = prefix + '_eog-proj.fif'
raw = mne.io.read_raw_fif(raw_in, preload=preload)
if raw_event_fname is not None:
raw_event = mne.io.read_raw_fif(raw_event_fname)
else:
raw_event = raw
flat = None # XXX : not exposed to the user
projs, events = mne.preprocessing.compute_proj_eog(
raw=raw, raw_event=raw_event, tmin=tmin, tmax=tmax, n_grad=n_grad,
n_mag=n_mag, n_eeg=n_eeg, l_freq=l_freq, h_freq=h_freq,
average=average, filter_length=filter_length,
n_jobs=n_jobs, reject=reject, flat=flat, bads=bads,
avg_ref=avg_ref, no_proj=no_proj, event_id=event_id,
eog_l_freq=eog_l_freq, eog_h_freq=eog_h_freq,
tstart=tstart, ch_name=ch_name, copy=False)
raw.close()
if raw_event_fname is not None:
raw_event.close()
if proj_fname is not None:
print('Including SSP projections from : %s' % proj_fname)
# append the eog projs, so they are last in the list
projs = mne.read_proj(proj_fname) + projs
if isinstance(preload, string_types) and os.path.exists(preload):
os.remove(preload)
print("Writing EOG projections in %s" % eog_proj_fname)
mne.write_proj(eog_proj_fname, projs)
print("Writing EOG events in %s" % eog_event_fname)
mne.write_events(eog_event_fname, events)
is_main = (__name__ == '__main__')
if is_main:
run()
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