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#!/usr/bin/env python
"""Clean a raw file from EOG and ECG artifacts with PCA (ie SSP).
You can do for example:
$ mne clean_eog_ecg -i in_raw.fif -o clean_raw.fif -e -c
"""
from __future__ import print_function
# Authors : Dr Engr. Sheraz Khan, P.Eng, Ph.D.
# Engr. Nandita Shetty, MS.
# Alexandre Gramfort, Ph.D.
import sys
import mne
def clean_ecg_eog(in_fif_fname, out_fif_fname=None, eog=True, ecg=True,
ecg_proj_fname=None, eog_proj_fname=None,
ecg_event_fname=None, eog_event_fname=None, in_path='.',
quiet=False):
"""Clean ECG from raw fif file.
Parameters
----------
in_fif_fname : str
Raw fif File
eog_event_fname : str
name of EOG event file required.
eog : bool
Reject or not EOG artifacts.
ecg : bool
Reject or not ECG artifacts.
ecg_event_fname : str
name of ECG event file required.
in_path : str
Path where all the files are.
"""
if not eog and not ecg:
raise Exception("EOG and ECG cannot be both disabled")
# Reading fif File
raw_in = mne.io.read_raw_fif(in_fif_fname)
if in_fif_fname.endswith('_raw.fif') or in_fif_fname.endswith('-raw.fif'):
prefix = in_fif_fname[:-8]
else:
prefix = in_fif_fname[:-4]
if out_fif_fname is None:
out_fif_fname = prefix + '_clean_ecg_eog_raw.fif'
if ecg_proj_fname is None:
ecg_proj_fname = prefix + '_ecg-proj.fif'
if eog_proj_fname is None:
eog_proj_fname = prefix + '_eog-proj.fif'
if ecg_event_fname is None:
ecg_event_fname = prefix + '_ecg-eve.fif'
if eog_event_fname is None:
eog_event_fname = prefix + '_eog-eve.fif'
print('Implementing ECG and EOG artifact rejection on data')
kwargs = dict() if quiet else dict(stdout=None, stderr=None)
if ecg:
ecg_events, _, _ = mne.preprocessing.find_ecg_events(raw_in)
print("Writing ECG events in %s" % ecg_event_fname)
mne.write_events(ecg_event_fname, ecg_events)
print('Computing ECG projector')
command = ('mne_process_raw', '--cd', in_path, '--raw', in_fif_fname,
'--events', ecg_event_fname, '--makeproj',
'--projtmin', '-0.08', '--projtmax', '0.08',
'--saveprojtag', '_ecg-proj', '--projnmag', '2',
'--projngrad', '1', '--projevent', '999', '--highpass', '5',
'--lowpass', '35', '--projmagrej', '4000',
'--projgradrej', '3000')
mne.utils.run_subprocess(command, **kwargs)
if eog:
eog_events = mne.preprocessing.find_eog_events(raw_in)
print("Writing EOG events in %s" % eog_event_fname)
mne.write_events(eog_event_fname, eog_events)
print('Computing EOG projector')
command = ('mne_process_raw', '--cd', in_path, '--raw', in_fif_fname,
'--events', eog_event_fname, '--makeproj',
'--projtmin', '-0.15', '--projtmax', '0.15',
'--saveprojtag', '_eog-proj', '--projnmag', '2',
'--projngrad', '2', '--projevent', '998', '--lowpass', '35',
'--projmagrej', '4000', '--projgradrej', '3000')
mne.utils.run_subprocess(command, **kwargs)
if out_fif_fname is not None:
# Applying the ECG EOG projector
print('Applying ECG EOG projector')
command = ('mne_process_raw', '--cd', in_path, '--raw', in_fif_fname,
'--proj', in_fif_fname, '--projoff', '--save',
out_fif_fname, '--filteroff',
'--proj', ecg_proj_fname, '--proj', eog_proj_fname)
mne.utils.run_subprocess(command, **kwargs)
print('Done removing artifacts.')
print("Cleaned raw data saved in: %s" % out_fif_fname)
print('IMPORTANT : Please eye-ball the data !!')
else:
print('Projection not applied to raw data.')
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("-o", "--out", dest="raw_out",
help="Output raw FIF file", metavar="FILE",
default=None)
parser.add_option("-e", "--no-eog", dest="eog", action="store_false",
help="Remove EOG", default=True)
parser.add_option("-c", "--no-ecg", dest="ecg", action="store_false",
help="Remove ECG", default=True)
parser.add_option("-q", "--quiet", dest="quiet", action="store_true",
help="Suppress mne_process_raw output", default=False)
options, args = parser.parse_args()
if options.raw_in is None:
parser.print_help()
sys.exit(1)
raw_in = options.raw_in
raw_out = options.raw_out
eog = options.eog
ecg = options.ecg
quiet = options.quiet
clean_ecg_eog(raw_in, raw_out, eog=eog, ecg=ecg, quiet=quiet)
is_main = (__name__ == '__main__')
if is_main:
run()
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