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#!/usr/bin/env python
# Authors: Christian Brodbeck <christianbrodbeck@nyu.edu>
"""Open the coregistration GUI.
example usage: $ mne coreg
"""
import os.path as op
import sys
import mne
from mne.utils import ETSContext
def run():
"""Run command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option("-d", "--subjects-dir", dest="subjects_dir",
default=None, help="Subjects directory")
parser.add_option("-s", "--subject", dest="subject", default=None,
help="Subject name")
parser.add_option("-f", "--fiff", dest="inst", default=None,
help="FIFF file with digitizer data for coregistration")
parser.add_option("-t", "--tabbed", dest="tabbed", action="store_true",
default=False, help="Option for small screens: Combine "
"the data source panel and the coregistration panel "
"into a single panel with tabs.")
parser.add_option("--no-guess-mri", dest="guess_mri_subject",
action='store_false', default=None,
help="Prevent the GUI from automatically guessing and "
"changing the MRI subject when a new head shape source "
"file is selected.")
parser.add_option("--head-opacity", type=float, default=None,
dest="head_opacity",
help="The opacity of the head surface, in the range "
"[0, 1].")
parser.add_option("--high-res-head",
action='store_true', default=False, dest="high_res_head",
help="Use a high-resolution head surface.")
parser.add_option("--low-res-head",
action='store_true', default=False, dest="low_res_head",
help="Use a low-resolution head surface.")
parser.add_option('--trans', dest='trans', default=None,
help='Head<->MRI transform FIF file ("-trans.fif")')
parser.add_option('--project-eeg', dest='project_eeg',
action='store_true', default=None,
help="Project EEG electrodes to the head surface ("
"for visualization purposes only)")
parser.add_option('--orient-to-surface',
action='store_true', default=None,
dest='orient_to_surface',
help='Orient points to the surface.')
parser.add_option('--scale-by-distance',
action='store_true', default=None,
dest='scale_by_distance',
help='Scale points by distance from the surface.')
parser.add_option('--mark-inside',
action='store_true', default=None,
dest='mark_inside',
help='Mark points inside the head using a different '
'color.')
parser.add_option('--interaction',
type=str, default=None, dest='interaction',
help='Interaction style to use, can be "trackball" or '
'"terrain".')
parser.add_option('--scale',
type=float, default=None, dest='scale',
help='Scale factor for the scene.')
parser.add_option('--verbose', action='store_true', dest='verbose',
help='Turn on verbose mode.')
options, args = parser.parse_args()
if options.low_res_head:
if options.high_res_head:
raise ValueError("Can't specify --high-res-head and "
"--low-res-head at the same time.")
head_high_res = False
elif options.high_res_head:
head_high_res = True
else:
head_high_res = None
# expanduser allows ~ for --subjects-dir
subjects_dir = options.subjects_dir
if subjects_dir is not None:
subjects_dir = op.expanduser(subjects_dir)
trans = options.trans
if trans is not None:
trans = op.expanduser(trans)
try:
import faulthandler
faulthandler.enable()
except ImportError:
pass # old Python2
with ETSContext():
mne.gui.coregistration(
options.tabbed, inst=options.inst, subject=options.subject,
subjects_dir=subjects_dir,
guess_mri_subject=options.guess_mri_subject,
head_opacity=options.head_opacity, head_high_res=head_high_res,
trans=trans, scrollable=True, project_eeg=options.project_eeg,
orient_to_surface=options.orient_to_surface,
scale_by_distance=options.scale_by_distance,
mark_inside=options.mark_inside, interaction=options.interaction,
scale=options.scale, verbose=options.verbose)
if is_main:
sys.exit(0)
is_main = (__name__ == '__main__')
if is_main:
run()
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