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#!/usr/bin/env python
"""Apply MaxFilter.
Example usage:
$ mne maxfilter -i sample_audvis_raw.fif --st
This will apply MaxFilter with the MaxSt extension. The origin used
by MaxFilter is computed by mne-python by fitting a sphere to the
headshape points.
"""
# Authors : Martin Luessi <mluessi@nmr.mgh.harvard.edu>
import sys
import os
import mne
def run():
"""Run command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option("-i", "--in", dest="in_fname",
help="Input raw FIF file", metavar="FILE")
parser.add_option("-o", dest="out_fname",
help="Output FIF file (if not set, suffix '_sss' will "
"be used)", metavar="FILE", default=None)
parser.add_option("--origin", dest="origin",
help="Head origin in mm, or a filename to read the "
"origin from. If not set it will be estimated from "
"headshape points", default=None)
parser.add_option("--origin-out", dest="origin_out",
help="Filename to use for computed origin", default=None)
parser.add_option("--frame", dest="frame", type="string",
help="Coordinate frame for head center ('device' or "
"'head')", default="device")
parser.add_option("--bad", dest="bad", type="string",
help="List of static bad channels",
default=None)
parser.add_option("--autobad", dest="autobad", type="string",
help="Set automated bad channel detection ('on', 'off', "
"'n')", default="off")
parser.add_option("--skip", dest="skip",
help="Skips raw data sequences, time intervals pairs in "
"sec, e.g.: 0 30 120 150", default=None)
parser.add_option("--force", dest="force", action="store_true",
help="Ignore program warnings",
default=False)
parser.add_option("--st", dest="st", action="store_true",
help="Apply the time-domain MaxST extension",
default=False)
parser.add_option("--buflen", dest="st_buflen", type="float",
help="MaxSt buffer length in sec",
default=16.0)
parser.add_option("--corr", dest="st_corr", type="float",
help="MaxSt subspace correlation",
default=0.96)
parser.add_option("--trans", dest="mv_trans",
help="Transforms the data into the coil definitions of "
"in_fname, or into the default frame", default=None)
parser.add_option("--movecomp", dest="mv_comp", action="store_true",
help="Estimates and compensates head movements in "
"continuous raw data", default=False)
parser.add_option("--headpos", dest="mv_headpos", action="store_true",
help="Estimates and stores head position parameters, "
"but does not compensate movements", default=False)
parser.add_option("--hp", dest="mv_hp", type="string",
help="Stores head position data in an ascii file",
default=None)
parser.add_option("--hpistep", dest="mv_hpistep", type="float",
help="Sets head position update interval in ms",
default=None)
parser.add_option("--hpisubt", dest="mv_hpisubt", type="string",
help="Subtracts hpi signals: sine amplitudes, amp + "
"baseline, or switch off", default=None)
parser.add_option("--nohpicons", dest="mv_hpicons", action="store_false",
help="Do not check initial consistency isotrak vs "
"hpifit", default=True)
parser.add_option("--linefreq", dest="linefreq", type="float",
help="Sets the basic line interference frequency (50 or "
"60 Hz)", default=None)
parser.add_option("--nooverwrite", dest="overwrite", action="store_false",
help="Do not overwrite output file if it already exists",
default=True)
parser.add_option("--args", dest="mx_args", type="string",
help="Additional command line arguments to pass to "
"MaxFilter", default="")
options, args = parser.parse_args()
in_fname = options.in_fname
if in_fname is None:
parser.print_help()
sys.exit(1)
out_fname = options.out_fname
origin = options.origin
origin_out = options.origin_out
frame = options.frame
bad = options.bad
autobad = options.autobad
skip = options.skip
force = options.force
st = options.st
st_buflen = options.st_buflen
st_corr = options.st_corr
mv_trans = options.mv_trans
mv_comp = options.mv_comp
mv_headpos = options.mv_headpos
mv_hp = options.mv_hp
mv_hpistep = options.mv_hpistep
mv_hpisubt = options.mv_hpisubt
mv_hpicons = options.mv_hpicons
linefreq = options.linefreq
overwrite = options.overwrite
mx_args = options.mx_args
if in_fname.endswith('_raw.fif') or in_fname.endswith('-raw.fif'):
prefix = in_fname[:-8]
else:
prefix = in_fname[:-4]
if out_fname is None:
if st:
out_fname = prefix + '_tsss.fif'
else:
out_fname = prefix + '_sss.fif'
if origin is not None and os.path.exists(origin):
with open(origin, 'r') as fid:
origin = fid.readlines()[0].strip()
origin = mne.preprocessing.apply_maxfilter(
in_fname, out_fname, origin, frame,
bad, autobad, skip, force, st, st_buflen, st_corr, mv_trans,
mv_comp, mv_headpos, mv_hp, mv_hpistep, mv_hpisubt, mv_hpicons,
linefreq, mx_args, overwrite)
if origin_out is not None:
with open(origin_out, 'w') as fid:
fid.write(origin + '\n')
is_main = (__name__ == '__main__')
if is_main:
run()
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