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mne_compute_proj_ecg.py
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#!/usr/bin/env python
"""Compute SSP/PCA projections for ECG artifacts
You can do for example:
$ mne compute_proj_ecg -i sample_audvis_raw.fif -c "MEG 1531" --l-freq 1 --h-freq 100 --rej-grad 3000 --rej-mag 4000 --rej-eeg 100
"""
from __future__ import print_function
# Authors : Alexandre Gramfort, Ph.D.
# Martin Luessi, Ph.D.
from ..externals.six import string_types
import os
import sys
import mne
if __name__ == '__main__':
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=0.4)
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=100)
parser.add_option("--ecg-l-freq", dest="ecg_l_freq", type="float",
help="Filter low cut-off frequency in Hz used "
"for ECG event detection",
default=5)
parser.add_option("--ecg-h-freq", dest="ecg_h_freq", type="float",
help="Filter high cut-off frequency in Hz used "
"for ECG event detection",
default=35)
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)
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("-c", "--channel", dest="ch_name",
help="Channel to use for ECG detection "
"(Required if no ECG found)",
default=None)
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=250)
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=999)
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("--qrsthr", dest="qrs_threshold", type="string",
help="QRS detection threshold. Between 0 and 1. Can "
"also be 'auto' for automatic selection",
default='auto')
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
ecg_l_freq = options.ecg_l_freq
ecg_h_freq = options.ecg_h_freq
average = options.average
preload = options.preload
filter_length = options.filter_length
n_jobs = options.n_jobs
ch_name = options.ch_name
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
qrs_threshold = options.qrs_threshold
if qrs_threshold != 'auto':
try:
qrs_threshold = float(qrs_threshold)
except ValueError:
raise ValueError('qrsthr must be "auto" or a float')
if bad_fname is not None:
bads = [w.rstrip().split()[0] for w in open(bad_fname).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]
ecg_event_fname = prefix + '_ecg-eve.fif'
if average:
ecg_proj_fname = prefix + '_ecg_avg_proj.fif'
else:
ecg_proj_fname = prefix + '_ecg_proj.fif'
raw = mne.io.Raw(raw_in, preload=preload)
if raw_event_fname is not None:
raw_event = mne.io.Raw(raw_event_fname)
else:
raw_event = raw
flat = None # XXX : not exposed to the user
cpe = mne.preprocessing.compute_proj_ecg
projs, events = cpe(raw, raw_event, tmin, tmax, n_grad, n_mag, n_eeg,
l_freq, h_freq, average, filter_length, n_jobs,
ch_name, reject, flat, bads, avg_ref, no_proj,
event_id, ecg_l_freq, ecg_h_freq, tstart,
qrs_threshold, 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 ecg 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 ECG projections in %s" % ecg_proj_fname)
mne.write_proj(ecg_proj_fname, projs)
print("Writing ECG events in %s" % ecg_event_fname)
mne.write_events(ecg_event_fname, events)