def run():
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
subjects_dir = mne.get_config('SUBJECTS_DIR')
parser.add_option('-s', '--subject', dest='subject',
help='Freesurfer subject id', type='str')
parser.add_option('-l', '--layers', dest='layers', default=1, type=int,
help='Number BEM layers.')
parser.add_option('-i', '--ico', dest='ico', default=4, type=int,
help='Triangle decimation number for single layer bem')
parser.add_option('-d', '--subjects-dir', dest='subjects_dir',
help='FS Subjects directory', default=subjects_dir)
parser.add_option('-o', '--overwrite', dest='overwrite', action='store_true',
help='Overwrite existing neuromag MRI and MNE BEM files.')
options, args = parser.parse_args()
subject = options.subject
subjects_dir = options.subjects_dir
if subject is None or subjects_dir is None:
parser.print_help()
sys.exit(1)
_run(subjects_dir, subject, options.layers, options.ico, options.overwrite)
def run():
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
subjects_dir = mne.get_config('SUBJECTS_DIR')
parser.add_option('-s', '--subject', dest='subject',
help='Freesurfer subject id', type='str')
parser.add_option('-r', '--raw-dir', dest='raw_dir',
help='Path to parent directory containing raw mri data', default='PARREC', metavar='FILE')
parser.add_option('-d', '--subjects-dir', dest='subjects_dir',
help='FS Subjects directory', default=subjects_dir)
parser.add_option('-f', '--force', dest='force', action='store_true',
help='Force FreeSurfer reconstruction.')
parser.add_option('-o', '--openmp', dest='openmp', default=2, type=str,
help='Number of CPUs to use for reconstruction routines.')
parser.add_option('-v', '--volume', dest='volume', default='MPRAGE', type=str,
help='Input raw volume file for nii conversion. Default is MPRAGE '
'it can also be MEMP_VBM.')
options, args = parser.parse_args()
subject = vars(options).get('subject', os.getenv('SUBJECT'))
subjects_dir = options.subjects_dir
raw_dir = options.raw_dir
if subject is None or subjects_dir is None:
parser.print_help()
sys.exit(1)
_run(subjects_dir, subject, raw_dir, options.force, options.openmp, options.volume)
def run():
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)
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=True,
help="Prevent the GUI from automatically guessing and "
"changing the MRI subject when a new head shape source "
"file is selected.")
options, args = parser.parse_args()
with ETSContext():
mne.gui.coregistration(options.tabbed, inst=options.inst,
subject=options.subject,
subjects_dir=options.subjects_dir,
guess_mri_subject=options.guess_mri_subject)
if is_main:
sys.exit(0)
def run():
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
subject = os.environ.get('SUBJECT')
subjects_dir = os.environ.get('SUBJECTS_DIR')
parser.add_option("-s", "--subject", dest="subject",
help="Subject name", default=subject)
parser.add_option("-d", "--subjects-dir", dest="subjects_dir",
help="Subjects directory", default=subjects_dir)
parser.add_option("-5", "--flash05", dest="flash05",
help=("Path to FLASH sequence with a spin angle of 5 "
"degrees in Nifti format"), metavar="FILE")
parser.add_option("-3", "--flash30", dest="flash30",
help=("Path to FLASH sequence with a spin angle of 30 "
"degrees in Nifti format"), metavar="FILE")
parser.add_option("-v", "--view", dest="show", action="store_true",
help="Show BEM model in 3D for visual inspection",
default=False)
options, args = parser.parse_args()
if options.flash05 is None or options.flash30 is None:
parser.print_help()
sys.exit(1)
subject = options.subject
subjects_dir = options.subjects_dir
flash05 = os.path.abspath(options.flash05)
flash30 = os.path.abspath(options.flash30)
show = options.show
make_flash_bem(subject, subjects_dir, flash05, flash30, show=show)
def run():
"""Run command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
subjects_dir = mne.get_config('SUBJECTS_DIR')
parser.add_option('-o', '--overwrite', dest='overwrite',
action='store_true',
help='Overwrite previously computed surface')
parser.add_option('-s', '--subject', dest='subject',
help='The name of the subject', type='str')
parser.add_option('-f', '--force', dest='force', action='store_true',
help='Force transformation of surface into bem.')
parser.add_option('-v', '--verbose', dest='verbose', action='store_true',
help='Print the debug messages.')
parser.add_option("-d", "--subjects-dir", dest="subjects_dir",
help="Subjects directory", default=subjects_dir)
parser.add_option("-n", "--no-decimate", dest="no_decimate",
help="Disable medium and sparse decimations "
"(dense only)", action='store_true')
options, args = parser.parse_args()
subject = vars(options).get('subject', os.getenv('SUBJECT'))
subjects_dir = options.subjects_dir
if subject is None or subjects_dir is None:
parser.print_help()
sys.exit(1)
_run(subjects_dir, subject, options.force, options.overwrite,
options.no_decimate, options.verbose)
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('--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
with ETSContext():
mne.gui.coregistration(options.tabbed, inst=options.inst,
subject=options.subject,
subjects_dir=options.subjects_dir,
guess_mri_subject=options.guess_mri_subject,
head_opacity=options.head_opacity,
head_high_res=head_high_res,
trans=options.trans,
verbose=options.verbose)
if is_main:
sys.exit(0)
def run():
"""Run command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option('--input', dest='input_fname',
help='Input data file name', metavar='filename')
parser.add_option('--mrk', dest='mrk_fname',
help='MEG Marker file name', metavar='filename')
parser.add_option('--elp', dest='elp_fname',
help='Headshape points file name', metavar='filename')
parser.add_option('--hsp', dest='hsp_fname',
help='Headshape file name', metavar='filename')
parser.add_option('--stim', dest='stim',
help='Colon Separated Stimulus Trigger Channels',
metavar='chs')
parser.add_option('--slope', dest='slope', help='Slope direction',
metavar='slope')
parser.add_option('--stimthresh', dest='stimthresh', default=1,
help='Threshold value for trigger channels',
metavar='value')
parser.add_option('--output', dest='out_fname',
help='Name of the resulting fiff file',
metavar='filename')
parser.add_option('--debug', dest='debug', action='store_true',
default=False,
help='Set logging level for terminal output to debug')
options, args = parser.parse_args()
if options.debug:
mne.set_log_level('debug')
input_fname = options.input_fname
if input_fname is None:
with ETSContext():
mne.gui.kit2fiff()
sys.exit(0)
hsp_fname = options.hsp_fname
elp_fname = options.elp_fname
mrk_fname = options.mrk_fname
stim = options.stim
slope = options.slope
stimthresh = options.stimthresh
out_fname = options.out_fname
if isinstance(stim, str):
stim = map(int, stim.split(':'))
raw = read_raw_kit(input_fname=input_fname, mrk=mrk_fname, elp=elp_fname,
hsp=hsp_fname, stim=stim, slope=slope,
stimthresh=stimthresh)
raw.save(out_fname)
raw.close()
sys.exit(0)
def run():
"""Run command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option("-s", "--subject", dest="subject",
help="Subject name", default=None)
parser.add_option("-d", "--subjects-dir", dest="subjects_dir",
help="Subjects directory", default=None)
parser.add_option("-3", "--noflash30", dest="noflash30",
action="store_true", default=False,
help=("Skip the 30-degree flip angle data"),)
parser.add_option("-n", "--noconvert", dest="noconvert",
action="store_true", default=False,
help=("Assume that the Flash MRI images have already "
"been converted to mgz files"))
parser.add_option("-u", "--unwarp", dest="unwarp",
action="store_true", default=False,
help=("Run grad_unwarp with -unwarp <type> option on "
"each of the converted data sets"))
parser.add_option("-o", "--overwrite", dest="overwrite",
action="store_true", default=False,
help="Write over existing .surf files in bem folder")
parser.add_option("-v", "--view", dest="show", action="store_true",
help="Show BEM model in 3D for visual inspection",
default=False)
parser.add_option("--copy", dest="copy",
help="Use copies instead of symlinks for surfaces",
action="store_true")
parser.add_option("-p", "--flash-path", dest="flash_path",
default=None,
help="The directory containing flash05.mgz and "
"flash30.mgz files (defaults to "
"$SUBJECTS_DIR/$SUBJECT/mri/flash/parameter_maps")
options, args = parser.parse_args()
subject = options.subject
subjects_dir = options.subjects_dir
flash30 = not options.noflash30
convert = not options.noconvert
unwarp = options.unwarp
overwrite = options.overwrite
show = options.show
flash_path = options.flash_path
copy = options.copy
if options.subject is None:
parser.print_help()
raise RuntimeError('The subject argument must be set')
convert_flash_mris(subject=subject, subjects_dir=subjects_dir,
flash30=flash30, convert=convert, unwarp=unwarp,
verbose=True)
make_flash_bem(subject=subject, subjects_dir=subjects_dir,
overwrite=overwrite, show=show, flash_path=flash_path,
copy=copy, verbose=True)
def run():
"""Run command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option('-p', '--pdf', dest='pdf_fname',
help='Input data file name', metavar='FILE')
parser.add_option('-c', '--config', dest='config_fname',
help='Input config file name', metavar='FILE',
default='config')
parser.add_option('--head_shape', dest='head_shape_fname',
help='Headshape file name', metavar='FILE',
default='hs_file')
parser.add_option('-o', '--out_fname', dest='out_fname',
help='Name of the resulting fiff file',
default='as_data_fname')
parser.add_option('-r', '--rotation_x', dest='rotation_x', type='float',
help='Compensatory rotation about Neuromag x axis, deg',
default=2.0)
parser.add_option('-T', '--translation', dest='translation', type='str',
help='Default translation, meter',
default=(0.00, 0.02, 0.11))
parser.add_option('--ecg_ch', dest='ecg_ch', type='str',
help='4D ECG channel name',
default='E31')
parser.add_option('--eog_ch', dest='eog_ch', type='str',
help='4D EOG channel names',
default='E63,E64')
options, args = parser.parse_args()
pdf_fname = options.pdf_fname
if pdf_fname is None:
parser.print_help()
sys.exit(1)
config_fname = options.config_fname
head_shape_fname = options.head_shape_fname
out_fname = options.out_fname
rotation_x = options.rotation_x
translation = options.translation
ecg_ch = options.ecg_ch
eog_ch = options.ecg_ch.split(',')
if out_fname == 'as_data_fname':
out_fname = pdf_fname + '_raw.fif'
raw = read_raw_bti(pdf_fname=pdf_fname, config_fname=config_fname,
head_shape_fname=head_shape_fname,
rotation_x=rotation_x, translation=translation,
ecg_ch=ecg_ch, eog_ch=eog_ch)
raw.save(out_fname)
raw.close()
if is_main:
sys.exit(0)
def run():
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
options, args = parser.parse_args()
os.environ['ETS_TOOLKIT'] = 'qt4'
mne.gui.coregistration()
if is_main:
sys.exit(0)
def run():
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option('--input', dest='input_fname',
help='Input data file name', metavar='filename')
parser.add_option('--mrk', dest='mrk_fname',
help='MEG Marker file name', metavar='filename')
parser.add_option('--elp', dest='elp_fname',
help='Headshape points file name', metavar='filename')
parser.add_option('--hsp', dest='hsp_fname',
help='Headshape file name', metavar='filename')
parser.add_option('--stim', dest='stim',
help='Colon Separated Stimulus Trigger Channels',
metavar='chs')
parser.add_option('--slope', dest='slope', help='Slope direction',
metavar='slope')
parser.add_option('--stimthresh', dest='stimthresh', default=1,
help='Threshold value for trigger channels',
metavar='value')
parser.add_option('--output', dest='out_fname',
help='Name of the resulting fiff file',
metavar='filename')
options, args = parser.parse_args()
input_fname = options.input_fname
if input_fname is None:
os.environ['ETS_TOOLKIT'] = 'qt4'
mne.gui.kit2fiff()
sys.exit(0)
hsp_fname = options.hsp_fname
elp_fname = options.elp_fname
mrk_fname = options.mrk_fname
stim = options.stim
slope = options.slope
stimthresh = options.stimthresh
out_fname = options.out_fname
if isinstance(stim, str):
stim = stim.split(':')
raw = read_raw_kit(input_fname=input_fname, mrk=mrk_fname, elp=elp_fname,
hsp=hsp_fname, stim=stim, slope=slope,
stimthresh=stimthresh)
raw.save(out_fname)
raw.close()
sys.exit(0)
def run():
"""Run command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option("-s", "--subject", dest="subject",
help="Subject name (required)", default=None)
parser.add_option("-d", "--subjects-dir", dest="subjects_dir",
help="Subjects directory", default=None)
parser.add_option("-o", "--overwrite", dest="overwrite",
help="Write over existing files", action="store_true")
parser.add_option("-v", "--volume", dest="volume",
help="Defaults to T1", default='T1')
parser.add_option("-a", "--atlas", dest="atlas",
help="Specify the --atlas option for mri_watershed",
default=False, action="store_true")
parser.add_option("-g", "--gcaatlas", dest="gcaatlas",
help="Use the subcortical atlas", default=False,
action="store_true")
parser.add_option("-p", "--preflood", dest="preflood",
help="Change the preflood height", default=None)
parser.add_option("--copy", dest="copy",
help="Use copies instead of symlinks for surfaces",
action="store_true")
parser.add_option("--verbose", dest="verbose",
help="If not None, override default verbose level",
default=None)
options, args = parser.parse_args()
if options.subject is None:
parser.print_help()
sys.exit(1)
subject = options.subject
subjects_dir = options.subjects_dir
overwrite = options.overwrite
volume = options.volume
atlas = options.atlas
gcaatlas = options.gcaatlas
preflood = options.preflood
copy = options.copy
verbose = options.verbose
make_watershed_bem(subject=subject, subjects_dir=subjects_dir,
overwrite=overwrite, volume=volume, atlas=atlas,
gcaatlas=gcaatlas, preflood=preflood, copy=copy,
verbose=verbose)
def run():
"""Run command."""
from mne.commands.utils import get_optparser, _add_verbose_flag
parser = get_optparser(__file__)
subjects_dir = mne.get_config('SUBJECTS_DIR')
parser.add_option('-o',
'--overwrite',
dest='overwrite',
action='store_true',
help='Overwrite previously computed surface')
parser.add_option('-s',
'--subject',
dest='subject',
help='The name of the subject',
type='str')
parser.add_option('-f',
'--force',
dest='force',
action='store_true',
help='Force creation of the surface even if it has '
'some topological defects.')
parser.add_option("-d",
"--subjects-dir",
dest="subjects_dir",
help="Subjects directory",
default=subjects_dir)
parser.add_option("-n",
"--no-decimate",
dest="no_decimate",
help="Disable medium and sparse decimations "
"(dense only)",
action='store_true')
_add_verbose_flag(parser)
options, args = parser.parse_args()
subject = vars(options).get('subject', os.getenv('SUBJECT'))
subjects_dir = options.subjects_dir
if subject is None or subjects_dir is None:
parser.print_help()
sys.exit(1)
make_scalp_surfaces(subject=subject,
subjects_dir=subjects_dir,
force=options.force,
overwrite=options.overwrite,
no_decimate=options.no_decimate,
verbose=options.verbose)
def run():
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)
def run():
"""Run command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
subjects_dir = mne.get_config('SUBJECTS_DIR')
parser.add_option('-o',
'--overwrite',
dest='overwrite',
action='store_true',
help='Overwrite previously computed surface')
parser.add_option('-s',
'--subject',
dest='subject',
help='The name of the subject',
type='str')
parser.add_option('-f',
'--force',
dest='force',
action='store_true',
help='Force transformation of surface into bem.')
parser.add_option('-v',
'--verbose',
dest='verbose',
action='store_true',
help='Print the debug messages.')
parser.add_option("-d",
"--subjects-dir",
dest="subjects_dir",
help="Subjects directory",
default=subjects_dir)
parser.add_option("-n",
"--no-decimate",
dest="no_decimate",
help="Disable medium and sparse decimations "
"(dense only)",
action='store_true')
options, args = parser.parse_args()
subject = vars(options).get('subject', os.getenv('SUBJECT'))
subjects_dir = options.subjects_dir
if subject is None or subjects_dir is None:
parser.print_help()
sys.exit(1)
print(options.no_decimate)
_run(subjects_dir, subject, options.force, options.overwrite,
options.no_decimate, options.verbose)
def run():
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option("--input", dest="input_fname", help="Input data file name", metavar="filename")
parser.add_option("--mrk", dest="mrk_fname", help="MEG Marker file name", metavar="filename")
parser.add_option("--elp", dest="elp_fname", help="Headshape points file name", metavar="filename")
parser.add_option("--hsp", dest="hsp_fname", help="Headshape file name", metavar="filename")
parser.add_option("--stim", dest="stim", help="Colon Separated Stimulus Trigger Channels", metavar="chs")
parser.add_option("--slope", dest="slope", help="Slope direction", metavar="slope")
parser.add_option(
"--stimthresh", dest="stimthresh", default=1, help="Threshold value for trigger channels", metavar="value"
)
parser.add_option("--output", dest="out_fname", help="Name of the resulting fiff file", metavar="filename")
options, args = parser.parse_args()
input_fname = options.input_fname
if input_fname is None:
os.environ["ETS_TOOLKIT"] = "qt4"
mne.gui.kit2fiff()
sys.exit(0)
hsp_fname = options.hsp_fname
elp_fname = options.elp_fname
mrk_fname = options.mrk_fname
stim = options.stim
slope = options.slope
stimthresh = options.stimthresh
out_fname = options.out_fname
if isinstance(stim, str):
stim = map(int, stim.split(":"))
raw = read_raw_kit(
input_fname=input_fname,
mrk=mrk_fname,
elp=elp_fname,
hsp=hsp_fname,
stim=stim,
slope=slope,
stimthresh=stimthresh,
)
raw.save(out_fname)
raw.close()
sys.exit(0)
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=True,
help="Prevent the GUI from automatically guessing and "
"changing the MRI subject when a new head shape source "
"file is selected.")
options, args = parser.parse_args()
with ETSContext():
mne.gui.coregistration(options.tabbed,
inst=options.inst,
subject=options.subject,
subjects_dir=options.subjects_dir,
guess_mri_subject=options.guess_mri_subject)
if is_main:
sys.exit(0)
def run():
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option("-p", "--path", dest="path",
help="Path to folder who MNE-Report must be created")
parser.add_option("-i", "--info", dest="info_fname",
help="File from which info dictionary is to be read",
metavar="FILE")
parser.add_option("-d", "--subjects-dir", dest="subjects_dir",
help="The subjects directory")
parser.add_option("-s", "--subject", dest="subject",
help="The subject name")
parser.add_option("-v", "--verbose", dest="verbose",
action='store_true', help="run in verbose mode")
parser.add_option("--no-browser", dest="no_browser", action='store_false',
help="Do not open MNE-Report in browser")
parser.add_option("--overwrite", dest="overwrite", action='store_false',
help="Overwrite html report if it already exists")
parser.add_option("-j", "--jobs", dest="n_jobs", help="Number of jobs to"
" run in parallel")
parser.add_option("-m", "--mri-decim", type="int", dest="mri_decim",
default=2, help="Integer factor used to decimate "
"BEM plots")
options, args = parser.parse_args()
path = options.path
if path is None:
parser.print_help()
sys.exit(1)
info_fname = options.info_fname
subjects_dir = options.subjects_dir
subject = options.subject
mri_decim = int(options.mri_decim)
verbose = True if options.verbose is not None else False
open_browser = False if options.no_browser is not None else True
overwrite = True if options.overwrite is not None else False
n_jobs = int(options.n_jobs) if options.n_jobs is not None else 1
t0 = time.time()
report = Report(info_fname, subjects_dir=subjects_dir, subject=subject,
verbose=verbose)
report.parse_folder(path, verbose=verbose, n_jobs=n_jobs,
mri_decim=mri_decim)
log_elapsed(time.time() - t0, verbose=verbose)
report.save(open_browser=open_browser, overwrite=overwrite)
def run():
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option("-p", "--path", dest="path",
help="Path to folder who MNE-Report must be created")
parser.add_option("-i", "--info", dest="info_fname",
help="File from which info dictionary is to be read",
metavar="FILE")
parser.add_option("-d", "--subjects-dir", dest="subjects_dir",
help="The subjects directory")
parser.add_option("-s", "--subject", dest="subject",
help="The subject name")
parser.add_option("-v", "--verbose", dest="verbose",
action='store_true', help="run in verbose mode")
parser.add_option("--no-browser", dest="no_browser", action='store_false',
help="Do not open MNE-Report in browser")
parser.add_option("--overwrite", dest="overwrite", action='store_false',
help="Overwrite html report if it already exists")
parser.add_option("-j", "--jobs", dest="n_jobs", help="Number of jobs to"
" run in parallel")
parser.add_option("-m", "--mri-decim", type="int", dest="mri_decim",
default=2, help="Integer factor used to decimate "
"BEM plots")
options, args = parser.parse_args()
path = options.path
if path is None:
parser.print_help()
sys.exit(1)
info_fname = options.info_fname
subjects_dir = options.subjects_dir
subject = options.subject
mri_decim = int(options.mri_decim)
verbose = True if options.verbose is not None else False
open_browser = False if options.no_browser is not None else True
overwrite = True if options.overwrite is not None else False
n_jobs = int(options.n_jobs) if options.n_jobs is not None else 1
t0 = time.time()
report = Report(info_fname, subjects_dir=subjects_dir, subject=subject,
verbose=verbose)
report.parse_folder(path, verbose=verbose, n_jobs=n_jobs,
mri_decim=mri_decim)
log_elapsed(time.time() - t0, verbose=verbose)
report.save(open_browser=open_browser, overwrite=overwrite)
def run():
"""Run command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option("-s", "--subject", dest="subject",
help="Subject name", default=None)
parser.add_option("-d", "--subjects-dir", dest="subjects_dir",
help="Subjects directory", default=None)
parser.add_option("-3", "--noflash30", dest="noflash30",
action="store_true", default=False,
help=("Skip the 30-degree flip angle data"),)
parser.add_option("-n", "--noconvert", dest="noconvert",
action="store_true", default=False,
help=("Assume that the Flash MRI images have already "
"been converted to mgz files"))
parser.add_option("-u", "--unwarp", dest="unwarp",
action="store_true", default=False,
help=("Run grad_unwarp with -unwarp <type> option on "
"each of the converted data sets"))
parser.add_option("-o", "--overwrite", dest="overwrite",
action="store_true", default=False,
help="Write over existing .surf files in bem folder")
parser.add_option("-v", "--view", dest="show", action="store_true",
help="Show BEM model in 3D for visual inspection",
default=False)
options, args = parser.parse_args()
subject = options.subject
subjects_dir = options.subjects_dir
flash30 = not options.noflash30
convert = not options.noconvert
unwarp = options.unwarp
overwrite = options.overwrite
show = options.show
if options.subject is None:
parser.print_help()
raise RuntimeError('The subject argument must be set')
convert_flash_mris(subject=subject, subjects_dir=subjects_dir,
flash30=flash30, convert=convert, unwarp=unwarp)
make_flash_bem(subject=subject, subjects_dir=subjects_dir,
overwrite=overwrite, show=show, flash_path='.')
def run():
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option("-s", "--subject", dest="subject",
help="Subject name", default=None)
parser.add_option("-d", "--subjects-dir", dest="subjects_dir",
help="Subjects directory", default=None)
parser.add_option("-3", "--noflash30", dest="noflash30",
action="store_true", default=False,
help=("Skip the 30-degree flip angle data"),)
parser.add_option("-n", "--noconvert", dest="noconvert",
action="store_true", default=False,
help=("Assume that the Flash MRI images have already "
"been converted to mgz files"))
parser.add_option("-u", "--unwarp", dest="unwarp",
action="store_true", default=False,
help=("Run grad_unwarp with -unwarp <type> option on "
"each of the converted data sets"))
parser.add_option("-o", "--overwrite", dest="overwrite",
action="store_true", default=False,
help="Write over existing .surf files in bem folder")
parser.add_option("-v", "--view", dest="show", action="store_true",
help="Show BEM model in 3D for visual inspection",
default=False)
options, args = parser.parse_args()
subject = options.subject
subjects_dir = options.subjects_dir
flash30 = not options.noflash30
convert = not options.noconvert
unwarp = options.unwarp
overwrite = options.overwrite
show = options.show
if options.subject is None:
parser.print_help()
raise RuntimeError('The subject argument must be set')
convert_flash_mris(subject=subject, subjects_dir=subjects_dir,
flash30=flash30, convert=convert, unwarp=unwarp)
make_flash_bem(subject=subject, subjects_dir=subjects_dir,
overwrite=overwrite, show=show)
def run():
"""Run the calibration_to_bids command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__,
usage="usage: %prog options args",
prog_prefix='mne_bids',
version=mne_bids.__version__)
parser.add_option('--bids_root',
dest='bids_root',
help='The path of the folder containing the BIDS '
'dataset')
parser.add_option('--subject_id', dest='subject', help=('Subject name'))
parser.add_option('--session_id', dest='session', help='Session name')
parser.add_option('--file',
dest='fname',
help='The path of the crosstalk file')
parser.add_option('--verbose',
dest='verbose',
action='store_true',
help='Whether do generate additional diagnostic output')
opt, args = parser.parse_args()
if args:
parser.print_help()
parser.error(f'Please do not specify arguments without flags. '
f'Got: {args}.\n')
if opt.bids_root is None:
parser.print_help()
parser.error('You must specify bids_root')
if opt.subject is None:
parser.print_help()
parser.error('You must specify a subject')
bids_path = BIDSPath(subject=opt.subject,
session=opt.session,
root=opt.bids_root)
logger.info(f'Writing fine-calibration file {bids_path.basename} …')
write_meg_calibration(calibration=opt.fname,
bids_path=bids_path,
verbose=opt.verbose)
def run():
"""Run the raw_to_bids command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__,
usage="usage: %prog options args",
prog_prefix='mne_bids',
version=mne_bids.__version__)
parser.add_option('--bids_root',
dest='bids_root',
help='The path of the BIDS compatible folder.')
parser.add_option('--datatype',
dest='datatype',
default='auto',
help='The datatype to consider.')
parser.add_option('--describe',
dest='describe',
action="store_true",
help=('If set print the descriptive statistics '
'(min, max, etc.).'))
opt, args = parser.parse_args()
if len(args) > 0:
parser.print_help()
parser.error(
'Do not specify arguments without flags. Found: "{}".\n'.format(
args))
if not all([opt.bids_root]):
parser.print_help()
parser.error('Arguments missing. You need to specify the '
'--bids_root parameter.')
counts = count_events(opt.bids_root, datatype=opt.datatype)
if opt.describe:
counts = counts.describe()
print(counts)
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=True,
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=1.,
dest="head_opacity",
help="The opacity of the head surface, in the range "
"[0, 1].")
parser.add_option("--low-res-head",
action='store_true', default=False, dest="low_res_head",
help="Default to using a low-resolution head surface.")
parser.add_option('--verbose', action='store_true', dest='verbose',
help='Turn on verbose mode.')
options, args = parser.parse_args()
with ETSContext():
mne.gui.coregistration(options.tabbed, inst=options.inst,
subject=options.subject,
subjects_dir=options.subjects_dir,
guess_mri_subject=options.guess_mri_subject,
head_opacity=options.head_opacity,
head_high_res=not options.low_res_head,
verbose=options.verbose)
if is_main:
sys.exit(0)
def run():
"""Run command."""
from mne.commands.utils import get_optparser, _add_verbose_flag
parser = get_optparser(__file__)
parser.add_option('--bem',
dest='bem_fname',
help='The name of the file containing the '
'triangulations of the BEM surfaces and the '
'conductivities of the compartments. The standard '
'ending for this file is -bem.fif.',
metavar="FILE")
parser.add_option('--sol',
dest='bem_sol_fname',
help='The name of the resulting file containing BEM '
'solution (geometry matrix). It uses the linear '
'collocation approach. The file should end with '
'-bem-sof.fif.',
metavar='FILE',
default=None)
_add_verbose_flag(parser)
options, args = parser.parse_args()
bem_fname = options.bem_fname
bem_sol_fname = options.bem_sol_fname
verbose = True if options.verbose is not None else False
if bem_fname is None:
parser.print_help()
sys.exit(1)
if bem_sol_fname is None:
base, _ = os.path.splitext(bem_fname)
bem_sol_fname = base + '-sol.fif'
bem_model = mne.read_bem_surfaces(bem_fname,
patch_stats=False,
verbose=verbose)
bem_solution = mne.make_bem_solution(bem_model, verbose=verbose)
mne.write_bem_solution(bem_sol_fname, bem_solution)
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.")
options, args = parser.parse_args()
with ETSContext():
mne.gui.coregistration(options.tabbed,
inst=options.inst,
subject=options.subject,
subjects_dir=options.subjects_dir)
if is_main:
sys.exit(0)
def run():
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option("-s",
"--surf",
dest="surf",
help="Surface in Freesurfer format",
metavar="FILE")
parser.add_option("-f",
"--fif",
dest="fif",
help="FIF file produced",
metavar="FILE")
parser.add_option("-i",
"--id",
dest="id",
default=4,
help=("Surface Id (e.g. 4 sur head surface)"))
options, args = parser.parse_args()
if options.surf is None:
parser.print_help()
sys.exit(1)
print("Converting %s to BEM FIF file." % options.surf)
points, tris = mne.read_surface(options.surf)
points *= 1e-3
surf = dict(coord_frame=5,
id=int(options.id),
nn=None,
np=len(points),
ntri=len(tris),
rr=points,
sigma=1,
tris=tris)
mne.write_bem_surface(options.fif, surf)
def run():
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
subject = os.environ.get('SUBJECT')
subjects_dir = get_subjects_dir()
parser.add_option("-s", "--subject", dest="subject",
help="Subject name", default=subject)
parser.add_option("-d", "--subjects-dir", dest="subjects_dir",
help="Subjects directory", default=subjects_dir)
parser.add_option("-m", "--method", dest="method",
help=("Method used to generate the BEM model. "
"Can be flash or watershed."), metavar="FILE")
options, args = parser.parse_args()
subject = options.subject
subjects_dir = options.subjects_dir
method = options.method
freeview_bem_surfaces(subject, subjects_dir, method)
def run():
"""Run command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option("-s", "--surf", dest="surf",
help="Surface in Freesurfer format", metavar="FILE")
parser.add_option("-f", "--fif", dest="fif",
help="FIF file produced", metavar="FILE")
parser.add_option("-i", "--id", dest="id", default=4,
help=("Surface Id (e.g. 4 sur head surface)"))
options, args = parser.parse_args()
if options.surf is None:
parser.print_help()
sys.exit(1)
print("Converting %s to BEM FIF file." % options.surf)
surf = mne.bem._surfaces_to_bem([options.surf], [int(options.id)],
sigmas=[1])
mne.write_bem_surfaces(options.fif, surf)
def run():
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
subject = os.environ.get('SUBJECT')
subjects_dir = get_subjects_dir()
parser.add_option("-s", "--subject", dest="subject",
help="Subject name", default=subject)
parser.add_option("-d", "--subjects-dir", dest="subjects_dir",
help="Subjects directory", default=subjects_dir)
parser.add_option("-m", "--method", dest="method",
help=("Method used to generate the BEM model. "
"Can be flash or watershed."))
options, args = parser.parse_args()
subject = options.subject
subjects_dir = options.subjects_dir
method = options.method
freeview_bem_surfaces(subject, subjects_dir, method)
def run():
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.")
options, args = parser.parse_args()
with ETSContext():
mne.gui.coregistration(options.tabbed, inst=options.inst,
subject=options.subject,
subjects_dir=options.subjects_dir)
if is_main:
sys.exit(0)
def run():
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option("-s", "--surf", dest="surf",
help="Surface in Freesurfer format", metavar="FILE")
parser.add_option("-f", "--fif", dest="fif",
help="FIF file produced", metavar="FILE")
parser.add_option("-i", "--id", dest="id", default=4,
help=("Surface Id (e.g. 4 sur head surface)"))
options, args = parser.parse_args()
if options.surf is None:
parser.print_help()
sys.exit(1)
print("Converting %s to BEM FIF file." % options.surf)
points, tris = mne.read_surface(options.surf)
points *= 1e-3
surf = dict(coord_frame=5, id=int(options.id), nn=None, np=len(points),
ntri=len(tris), rr=points, sigma=1, tris=tris)
mne.write_bem_surface(options.fif, surf)
def run():
"""Run the raw_to_bids command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__,
usage="usage: %prog options args",
prog_prefix='mne_bids',
version=mne_bids.__version__)
parser.add_option('--subject_id',
dest='subject_id',
help=('subject name in BIDS compatible format '
'(01, 02, etc.)'))
parser.add_option('--task',
dest='task',
help='name of the task the data is based on')
parser.add_option('--raw',
dest='raw_fname',
help='path to the raw MEG file')
parser.add_option('--bids_root',
dest='bids_root',
help='The path of the BIDS compatible folder.')
parser.add_option('--session_id',
dest='session_id',
help='session name in BIDS compatible format')
parser.add_option('--run', dest='run', help='run number for this dataset')
parser.add_option('--acq',
dest='acq',
help='acquisition parameter for this dataset')
parser.add_option('--events_data',
dest='events_data',
help='events file (events.tsv)')
parser.add_option('--event_id',
dest='event_id',
help='event id dict',
metavar='eid')
parser.add_option('--hpi',
dest='hpi',
help='path to the MEG marker points')
parser.add_option('--electrode',
dest='electrode',
help='path to head-native digitizer points')
parser.add_option('--hsp', dest='hsp', help='path to headshape points')
parser.add_option('--config',
dest='config',
help='path to the configuration file')
parser.add_option('--overwrite',
dest='overwrite',
help="whether to overwrite existing data (BOOLEAN)")
parser.add_option('--line_freq',
dest='line_freq',
help="The frequency of the line noise in Hz "
"(e.g. 50 or 60). If unknown, pass None")
opt, args = parser.parse_args()
if len(args) > 0:
parser.print_help()
parser.error(
'Do not specify arguments without flags. Found: "{}".\n'.format(
args))
if not all([opt.subject_id, opt.task, opt.raw_fname, opt.bids_root]):
parser.print_help()
parser.error('Arguments missing. You need to specify at least the'
'following: --subject_id, --task, --raw, --bids_root.')
bids_path = BIDSPath(subject=opt.subject_id,
session=opt.session_id,
run=opt.run,
acquisition=opt.acq,
task=opt.task,
root=opt.bids_root)
allow_maxshield = False
if opt.raw_fname.endswith('.fif'):
allow_maxshield = True
raw = _read_raw(opt.raw_fname,
hpi=opt.hpi,
electrode=opt.electrode,
hsp=opt.hsp,
config=opt.config,
allow_maxshield=allow_maxshield)
if opt.line_freq is not None:
line_freq = None if opt.line_freq == "None" else opt.line_freq
raw.info['line_freq'] = line_freq
write_raw_bids(raw,
bids_path,
event_id=opt.event_id,
events_data=opt.events_data,
overwrite=opt.overwrite,
verbose=True)
def run():
import matplotlib.pyplot as plt
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option("--raw",
dest="raw_in",
help="Input raw FIF file",
metavar="FILE")
parser.add_option("--proj",
dest="proj_in",
help="Projector file",
metavar="FILE",
default='')
parser.add_option("--eve",
dest="eve_in",
help="Events file",
metavar="FILE",
default='')
parser.add_option("-d",
"--duration",
dest="duration",
type="float",
help="Time window for plotting (sec)",
default=10.0)
parser.add_option("-t",
"--start",
dest="start",
type="float",
help="Initial start time for plotting",
default=0.0)
parser.add_option("-n",
"--n_channels",
dest="n_channels",
type="int",
help="Number of channels to plot at a time",
default=20)
parser.add_option("-o",
"--order",
dest="order",
help="Order for plotting ('type' or 'original')",
default='type')
parser.add_option("-p",
"--preload",
dest="preload",
help="Preload raw data (for faster navigaton)",
default=False)
parser.add_option("-s",
"--show_options",
dest="show_options",
help="Show projection options dialog",
default=False)
parser.add_option("--allowmaxshield",
dest="maxshield",
help="Allow loading MaxShield processed data",
action="store_true")
parser.add_option("--highpass",
dest="highpass",
type="float",
help="Display high-pass filter corner frequency",
default=-1)
parser.add_option("--lowpass",
dest="lowpass",
type="float",
help="Display low-pass filter corner frequency",
default=-1)
parser.add_option("--filtorder",
dest="filtorder",
type="int",
help="Display filtering IIR order",
default=4)
parser.add_option("--clipping",
dest="clipping",
help="Enable trace clipping mode, either 'clip' or "
"'transparent'",
default=None)
options, args = parser.parse_args()
raw_in = options.raw_in
duration = options.duration
start = options.start
n_channels = options.n_channels
order = options.order
preload = options.preload
show_options = options.show_options
proj_in = options.proj_in
eve_in = options.eve_in
maxshield = options.maxshield
highpass = options.highpass
lowpass = options.lowpass
filtorder = options.filtorder
clipping = options.clipping
if raw_in is None:
parser.print_help()
sys.exit(1)
raw = mne.io.Raw(raw_in, preload=preload, allow_maxshield=maxshield)
if len(proj_in) > 0:
projs = mne.read_proj(proj_in)
raw.info['projs'] = projs
if len(eve_in) > 0:
events = mne.read_events(eve_in)
else:
events = None
highpass = None if highpass < 0 or filtorder <= 0 else highpass
lowpass = None if lowpass < 0 or filtorder <= 0 else lowpass
filtorder = 4 if filtorder <= 0 else filtorder
raw.plot(duration=duration,
start=start,
n_channels=n_channels,
order=order,
show_options=show_options,
events=events,
highpass=highpass,
lowpass=lowpass,
filtorder=filtorder,
clipping=clipping)
plt.show(block=True)
def run():
"""Run command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option('--input',
dest='input_fname',
help='Input data file name',
metavar='filename')
parser.add_option('--mrk',
dest='mrk_fname',
help='MEG Marker file name',
metavar='filename')
parser.add_option('--elp',
dest='elp_fname',
help='Headshape points file name',
metavar='filename')
parser.add_option('--hsp',
dest='hsp_fname',
help='Headshape file name',
metavar='filename')
parser.add_option('--stim',
dest='stim',
help='Colon Separated Stimulus Trigger Channels',
metavar='chs')
parser.add_option('--slope',
dest='slope',
help='Slope direction',
metavar='slope')
parser.add_option('--stimthresh',
dest='stimthresh',
default=1,
help='Threshold value for trigger channels',
metavar='value')
parser.add_option('--output',
dest='out_fname',
help='Name of the resulting fiff file',
metavar='filename')
options, args = parser.parse_args()
input_fname = options.input_fname
if input_fname is None:
with ETSContext():
mne.gui.kit2fiff()
sys.exit(0)
hsp_fname = options.hsp_fname
elp_fname = options.elp_fname
mrk_fname = options.mrk_fname
stim = options.stim
slope = options.slope
stimthresh = options.stimthresh
out_fname = options.out_fname
if isinstance(stim, str):
stim = map(int, stim.split(':'))
raw = read_raw_kit(input_fname=input_fname,
mrk=mrk_fname,
elp=elp_fname,
hsp=hsp_fname,
stim=stim,
slope=slope,
stimthresh=stimthresh)
raw.save(out_fname)
raw.close()
sys.exit(0)
def run():
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option("-p",
"--path",
dest="path",
help="Path to folder who MNE-Report must be created")
parser.add_option("-i",
"--info",
dest="info_fname",
help="File from which info dictionary is to be read",
metavar="FILE")
parser.add_option("-c",
"--cov",
dest="cov_fname",
help="File from which noise covariance is to be read",
metavar="FILE")
parser.add_option("--bmin",
dest="bmin",
help="Time at which baseline correction starts for "
"evokeds",
default=None)
parser.add_option("--bmax",
dest="bmax",
help="Time at which baseline correction stops for "
"evokeds",
default=None)
parser.add_option("-d",
"--subjects-dir",
dest="subjects_dir",
help="The subjects directory")
parser.add_option("-s",
"--subject",
dest="subject",
help="The subject name")
parser.add_option("-v",
"--verbose",
dest="verbose",
action='store_true',
help="run in verbose mode")
parser.add_option("--no-browser",
dest="no_browser",
action='store_false',
help="Do not open MNE-Report in browser")
parser.add_option("--overwrite",
dest="overwrite",
action='store_false',
help="Overwrite html report if it already exists")
parser.add_option("-j",
"--jobs",
dest="n_jobs",
help="Number of jobs to"
" run in parallel")
parser.add_option("-m",
"--mri-decim",
type="int",
dest="mri_decim",
default=2,
help="Integer factor used to decimate "
"BEM plots")
options, args = parser.parse_args()
path = options.path
if path is None:
parser.print_help()
sys.exit(1)
info_fname = options.info_fname
cov_fname = options.cov_fname
subjects_dir = options.subjects_dir
subject = options.subject
mri_decim = int(options.mri_decim)
verbose = True if options.verbose is not None else False
open_browser = False if options.no_browser is not None else True
overwrite = True if options.overwrite is not None else False
n_jobs = int(options.n_jobs) if options.n_jobs is not None else 1
bmin = float(options.bmin) if options.bmin is not None else None
bmax = float(options.bmax) if options.bmax is not None else None
# XXX: this means (None, None) cannot be specified through command line
if bmin is None and bmax is None:
baseline = None
else:
baseline = (bmin, bmax)
t0 = time.time()
report = Report(info_fname,
subjects_dir=subjects_dir,
subject=subject,
baseline=baseline,
cov_fname=cov_fname,
verbose=verbose)
report.parse_folder(path,
verbose=verbose,
n_jobs=n_jobs,
mri_decim=mri_decim)
log_elapsed(time.time() - t0, verbose=verbose)
report.save(open_browser=open_browser, overwrite=overwrite)
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)
def run():
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:
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]
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.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
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)
dspath = op.join(data_dir, dsname)
# install the dataset
print('datalad installing "{}"'.format(dsname))
dataset = dl.install(path=dspath, source=url)
# XXX: git-annex bug: https://github.com/datalad/datalad/issues/3583
# if datalad fails, use "get" twice, or set `n_jobs=1`
if dsname == 'ds003104':
n_jobs = 16
else:
n_jobs = 1
# get the first subject
for to_get in get_dict[dsname]:
print('datalad get data "{}" for "{}"'.format(to_get, dsname))
dataset.get(to_get, jobs=n_jobs)
if __name__ == '__main__':
parser = get_optparser(__file__, usage="usage: %prog -dataset DATASET")
parser.add_option('-d',
'--dataset',
dest='dataset',
help='Name of the dataset',
metavar='INPUT',
default=None)
opt, args = parser.parse_args()
dataset = opt.dataset if opt.dataset != '' else None
main(dataset)
def run():
"""Run command."""
from mne.commands.utils import get_optparser, _add_verbose_flag
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('--simple-rendering', action='store_false',
dest='advanced_rendering',
help='Use simplified OpenGL rendering')
_add_verbose_flag(parser)
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)
import faulthandler
faulthandler.enable()
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,
advanced_rendering=options.advanced_rendering,
verbose=options.verbose)
def run():
"""Run command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option("-p", "--path", dest="path",
help="Path to folder who MNE-Report must be created")
parser.add_option("-i", "--info", dest="info_fname",
help="File from which info dictionary is to be read",
metavar="FILE")
parser.add_option("-c", "--cov", dest="cov_fname",
help="File from which noise covariance is to be read",
metavar="FILE")
parser.add_option("--bmin", dest="bmin",
help="Time at which baseline correction starts for "
"evokeds", default=None)
parser.add_option("--bmax", dest="bmax",
help="Time at which baseline correction stops for "
"evokeds", default=None)
parser.add_option("-d", "--subjects-dir", dest="subjects_dir",
help="The subjects directory")
parser.add_option("-s", "--subject", dest="subject",
help="The subject name")
parser.add_option("-v", "--verbose", dest="verbose",
action='store_true', help="run in verbose mode")
parser.add_option("--no-browser", dest="no_browser", action='store_false',
help="Do not open MNE-Report in browser")
parser.add_option("--overwrite", dest="overwrite", action='store_false',
help="Overwrite html report if it already exists")
parser.add_option("-j", "--jobs", dest="n_jobs", help="Number of jobs to"
" run in parallel")
parser.add_option("-m", "--mri-decim", type="int", dest="mri_decim",
default=2, help="Integer factor used to decimate "
"BEM plots")
options, args = parser.parse_args()
path = options.path
if path is None:
parser.print_help()
sys.exit(1)
info_fname = options.info_fname
cov_fname = options.cov_fname
subjects_dir = options.subjects_dir
subject = options.subject
mri_decim = int(options.mri_decim)
verbose = True if options.verbose is not None else False
open_browser = False if options.no_browser is not None else True
overwrite = True if options.overwrite is not None else False
n_jobs = int(options.n_jobs) if options.n_jobs is not None else 1
bmin = float(options.bmin) if options.bmin is not None else None
bmax = float(options.bmax) if options.bmax is not None else None
# XXX: this means (None, None) cannot be specified through command line
if bmin is None and bmax is None:
baseline = None
else:
baseline = (bmin, bmax)
t0 = time.time()
report = Report(info_fname, subjects_dir=subjects_dir,
subject=subject, baseline=baseline,
cov_fname=cov_fname, verbose=verbose)
report.parse_folder(path, verbose=verbose, n_jobs=n_jobs,
mri_decim=mri_decim)
log_elapsed(time.time() - t0, verbose=verbose)
report.save(open_browser=open_browser, overwrite=overwrite)
def run():
"""Run the raw_to_bids command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__,
usage="usage: %prog options args",
prog_prefix='mne_bids',
version=mne_bids.__version__)
parser.add_option('--subject_id',
dest='subject_id',
help=('The subject name in BIDS compatible format'
'(01,02, etc.)'))
parser.add_option('--task',
dest='task',
help='Name of the task the data is based on.')
parser.add_option('--raw',
dest='raw_fname',
help='The path to the raw MEG file.')
parser.add_option('--output_path',
dest='output_path',
help='The path of the BIDS compatible folder.')
parser.add_option('--session_id',
dest='session_id',
help='The session name in BIDS compatible format.')
parser.add_option('--run',
dest='run',
help='The run number for this dataset.')
parser.add_option('--acq', dest='acq', help='The acquisition parameter.')
parser.add_option('--events_data',
dest='events_data',
help='The events file.')
parser.add_option('--event_id',
dest='event_id',
help='The event id dict.',
metavar='eid')
parser.add_option('--hpi',
dest='hpi',
help='The path to the MEG Marker points')
parser.add_option('--electrode',
dest='electrode',
help='The path to head-native Digitizer points')
parser.add_option('--hsp',
dest='hsp',
help='The path to headshape points.')
parser.add_option('--config',
dest='config',
help='The path to the configuration file')
parser.add_option('--overwrite',
dest='overwrite',
help="Boolean. Whether to overwrite existing data")
parser.add_option('--allow_maxshield',
dest='allow_maxshield',
help="Boolean. Whether to allow non Maxfiltered data.",
action='store_true')
opt, args = parser.parse_args()
if len(args) > 0:
parser.print_help()
parser.error(
'Do not specify arguments without flags. Found: "{}".\n'.format(
args))
if not all([opt.subject_id, opt.task, opt.raw_fname, opt.output_path]):
parser.print_help()
parser.error('Arguments missing. You need to specify at least the'
'following: --subject_id, --task, --raw, --output_path.')
bids_basename = make_bids_basename(subject=opt.subject_id,
session=opt.session_id,
run=opt.run,
acquisition=opt.acq,
task=opt.task)
raw = _read_raw(opt.raw_fname,
hpi=opt.hpi,
electrode=opt.electrode,
hsp=opt.hsp,
config=opt.config,
allow_maxshield=opt.allow_maxshield)
write_raw_bids(raw,
bids_basename,
opt.output_path,
event_id=opt.event_id,
events_data=opt.events_data,
overwrite=opt.overwrite,
verbose=True)
def run():
t0 = time.time()
parser = get_optparser(__file__)
parser.add_option("--raw",
dest="raw_in",
help="Input raw FIF file",
metavar="FILE")
parser.add_option("--pos",
dest="pos",
default=None,
help="Position definition text file. Can be 'constant' "
"to hold the head position fixed",
metavar="FILE")
parser.add_option("--dipoles",
dest="dipoles",
default=None,
help="Dipole definition file",
metavar="FILE")
parser.add_option("--cov",
dest="cov",
help="Covariance to use for noise generation. Can be "
"'simple' to use a diagonal covariance, or 'off' to "
"omit noise",
metavar="FILE",
default='simple')
parser.add_option("--duration",
dest="duration",
default=None,
help="Duration of each epoch (sec). If omitted, the last"
" time point in the dipole definition file plus 200 ms "
"will be used",
type="float")
parser.add_option("-j",
"--jobs",
dest="n_jobs",
help="Number of jobs to"
" run in parallel",
type="int",
default=1)
parser.add_option("--out",
dest="raw_out",
help="Output raw filename",
metavar="FILE")
parser.add_option("--plot-dipoles",
dest="plot_dipoles",
help="Plot "
"input dipole positions",
action="store_true")
parser.add_option("--plot-raw",
dest="plot_raw",
help="Plot the resulting "
"raw traces",
action="store_true")
parser.add_option("--plot-evoked",
dest="plot_evoked",
help="Plot evoked "
"data",
action="store_true")
parser.add_option("-p",
"--plot",
dest="plot",
help="Plot dipoles, raw, "
"and evoked",
action="store_true")
parser.add_option("--overwrite",
dest="overwrite",
help="Overwrite the"
"output file if it exists",
action="store_true")
options, args = parser.parse_args()
raw_in = options.raw_in
pos = options.pos
raw_out = options.raw_out
dipoles = options.dipoles
n_jobs = options.n_jobs
plot = options.plot
plot_dipoles = options.plot_dipoles or plot
plot_raw = options.plot_raw or plot
plot_evoked = options.plot_evoked or plot
overwrite = options.overwrite
duration = options.duration
cov = options.cov
# check parameters
if not (raw_out or plot_raw or plot_evoked):
raise ValueError('data must either be saved (--out) or '
'plotted (--plot-raw or --plot_evoked)')
if raw_out and op.isfile(raw_out) and not overwrite:
raise ValueError('output file exists, use --overwrite (%s)' % raw_out)
if raw_in is None or pos is None or dipoles is None:
parser.print_help()
sys.exit(1)
s = 'Simulate raw data with head movements'
print('\n%s\n%s\n%s\n' % ('-' * len(s), s, '-' * len(s)))
# setup the simulation
with printer('Reading dipole definitions'):
if not op.isfile(dipoles):
raise IOError('dipole file not found:\n%s' % dipoles)
dipoles = np.loadtxt(dipoles, skiprows=1, dtype=float)
n_dipoles = dipoles.shape[0]
if dipoles.shape[1] != 8:
raise ValueError('dipoles must have 8 columns')
rr = dipoles[:, :3] * 1e-3
nn = dipoles[:, 3:6]
t = dipoles[:, 6:8]
duration = t.max() + 0.2 if duration is None else duration
if (t[:, 0] > t[:, 1]).any():
raise ValueError('found tmin > tmax in dipole file')
if (t < 0).any():
raise ValueError('found t < 0 in dipole file')
if (t > duration).any():
raise ValueError('found t > duration in dipole file')
amp = np.sqrt(np.sum(nn * nn, axis=1)) * 1e-9
mne.surface._normalize_vectors(nn)
nn[(nn == 0).all(axis=1)] = (1, 0, 0)
src = mne.SourceSpaces([
dict(rr=rr,
nn=nn,
inuse=np.ones(n_dipoles, int),
coord_frame=FIFF.FIFFV_COORD_HEAD)
])
for key in ['pinfo', 'nuse_tri', 'use_tris', 'patch_inds']:
src[0][key] = None
trans = {
'from': FIFF.FIFFV_COORD_HEAD,
'to': FIFF.FIFFV_COORD_MRI,
'trans': np.eye(4)
}
if (amp > 100e-9).any():
print('')
warnings.warn('Largest dipole amplitude %0.1f > 100 nA' %
(amp.max() * 1e9))
if pos == 'constant':
print('Holding head position constant')
pos = None
else:
with printer('Loading head positions'):
pos = mne.get_chpi_positions(pos)
with printer('Loading raw data file'):
with warnings.catch_warnings(record=True):
raw = mne.io.Raw(raw_in,
preload=False,
allow_maxshield=True,
verbose=False)
if cov == 'simple':
print('Using diagonal covariance for brain noise')
elif cov == 'off':
print('Omitting brain noise in the simulation')
cov = None
else:
with printer('Loading covariance file for brain noise'):
cov = mne.read_cov(cov)
with printer('Setting up spherical model'):
bem = mne.bem.make_sphere_model('auto',
'auto',
raw.info,
verbose=False)
# check that our sources are reasonable
rad = bem['layers'][0]['rad']
r0 = bem['r0']
outside = np.sqrt(np.sum((rr - r0)**2, axis=1)) >= rad
n_outside = outside.sum()
if n_outside > 0:
print('')
raise ValueError(
'%s dipole%s outside the spherical model, are your positions '
'in mm?' % (n_outside, 's were' if n_outside != 1 else ' was'))
with printer('Constructing source estimate'):
tmids = t.mean(axis=1)
t = np.round(t * raw.info['sfreq']).astype(int)
t[:, 1] += 1 # make it inclusive
n_samp = int(np.ceil(duration * raw.info['sfreq']))
data = np.zeros((n_dipoles, n_samp))
for di, (t_, amp_) in enumerate(zip(t, amp)):
data[di, t_[0]:t_[1]] = amp_ * np.hanning(t_[1] - t_[0])
stc = mne.VolSourceEstimate(data, np.arange(n_dipoles), 0,
1. / raw.info['sfreq'])
# do the simulation
print('')
raw_mv = simulate_raw(raw,
stc,
trans,
src,
bem,
cov=cov,
head_pos=pos,
chpi=True,
n_jobs=n_jobs,
verbose=True)
print('')
if raw_out:
with printer('Saving data'):
raw_mv.save(raw_out, overwrite=overwrite)
# plot results -- must be *after* save because we low-pass filter
if plot_dipoles:
with printer('Plotting dipoles'):
fig, axs = plt.subplots(1, 3, figsize=(10, 3), facecolor='w')
fig.canvas.set_window_title('Dipoles')
meg_info = mne.pick_info(
raw.info, mne.pick_types(raw.info, meg=True, eeg=False))
helmet_rr = [
ch['coil_trans'][:3, 3].copy() for ch in meg_info['chs']
]
helmet_nn = np.zeros_like(helmet_rr)
helmet_nn[:, 2] = 1.
surf = dict(rr=helmet_rr,
nn=helmet_nn,
coord_frame=FIFF.FIFFV_COORD_DEVICE)
helmet_rr = mne.surface.transform_surface_to(
surf, 'head', meg_info['dev_head_t'])['rr']
p = np.linspace(0, 2 * np.pi, 40)
x_sphere, y_sphere = rad * np.sin(p), rad * np.cos(p)
for ai, ax in enumerate(axs):
others = np.setdiff1d(np.arange(3), [ai])
ax.plot(helmet_rr[:, others[0]],
helmet_rr[:, others[1]],
marker='o',
linestyle='none',
alpha=0.1,
markeredgecolor='none',
markerfacecolor='b',
zorder=-2)
ax.plot(x_sphere + r0[others[0]],
y_sphere + r0[others[1]],
color='y',
alpha=0.25,
zorder=-1)
ax.quiver(rr[:, others[0]],
rr[:, others[1]],
amp * nn[:, others[0]],
amp * nn[:, others[1]],
angles='xy',
units='x',
color='k',
alpha=0.5)
ax.set_aspect('equal')
ax.set_xlabel(' - ' + 'xyz'[others[0]] + ' + ')
ax.set_ylabel(' - ' + 'xyz'[others[1]] + ' + ')
ax.set_xticks([])
ax.set_yticks([])
plt.setp(list(ax.spines.values()), color='none')
plt.tight_layout()
if plot_raw or plot_evoked:
with printer('Low-pass filtering simulated data'):
events = mne.find_events(raw_mv, 'STI101', verbose=False)
b, a = signal.butter(4,
40. / (raw.info['sfreq'] / 2.),
'low',
analog=False)
raw_mv.filter(None,
40.,
method='iir',
iir_params=dict(b=b, a=a),
verbose=False,
n_jobs=n_jobs)
if plot_raw:
with printer('Plotting raw data'):
raw_mv.plot(clipping='transparent', events=events, show=False)
if plot_evoked:
with printer('Plotting evoked data'):
picks = mne.pick_types(raw_mv.info, meg=True, eeg=True)
events[:, 2] = 1
evoked = mne.Epochs(raw_mv, events, {
'Simulated': 1
}, 0, duration, None, picks).average()
evoked.plot_topomap(np.unique(tmids), show=False)
print('\nTotal time: %0.1f sec' % (time.time() - t0))
sys.stdout.flush()
if any([plot_dipoles, plot_raw, plot_evoked]):
plt.show(block=True)
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=0.4)
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) # 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("-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:
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]
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.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_ecg(
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, str) 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)
def run():
"""Run command."""
from mne.commands.utils import get_optparser, _add_verbose_flag
parser = get_optparser(__file__)
parser.add_option("-s",
"--subject",
dest="subject",
help="Subject name (required)",
default=None)
parser.add_option("-d",
"--subjects-dir",
dest="subjects_dir",
help="Subjects directory",
default=None)
parser.add_option("-o",
"--overwrite",
dest="overwrite",
help="Write over existing files",
action="store_true")
parser.add_option("-v",
"--volume",
dest="volume",
help="Defaults to T1",
default='T1')
parser.add_option("-a",
"--atlas",
dest="atlas",
help="Specify the --atlas option for mri_watershed",
default=False,
action="store_true")
parser.add_option("-g",
"--gcaatlas",
dest="gcaatlas",
help="Specify the --brain_atlas option for "
"mri_watershed",
default=False,
action="store_true")
parser.add_option("-p",
"--preflood",
dest="preflood",
help="Change the preflood height",
default=None)
parser.add_option("--copy",
dest="copy",
help="Use copies instead of symlinks for surfaces",
action="store_true")
parser.add_option("-t",
"--T1",
dest="T1",
help="Whether or not to pass the -T1 flag "
"(can be true, false, 0, or 1). "
"By default it takes the same value as gcaatlas.",
default=None)
parser.add_option("-b",
"--brainmask",
dest="brainmask",
help="The filename for the brainmask output file "
"relative to the "
"$SUBJECTS_DIR/$SUBJECT/bem/watershed/ directory.",
default="ws")
_add_verbose_flag(parser)
options, args = parser.parse_args()
if options.subject is None:
parser.print_help()
sys.exit(1)
subject = options.subject
subjects_dir = options.subjects_dir
overwrite = options.overwrite
volume = options.volume
atlas = options.atlas
gcaatlas = options.gcaatlas
preflood = options.preflood
copy = options.copy
brainmask = options.brainmask
T1 = options.T1
if T1 is not None:
T1 = T1.lower()
_check_option("--T1", T1, ('true', 'false', '0', '1'))
T1 = T1 in ('true', '1')
verbose = options.verbose
make_watershed_bem(subject=subject,
subjects_dir=subjects_dir,
overwrite=overwrite,
volume=volume,
atlas=atlas,
gcaatlas=gcaatlas,
preflood=preflood,
copy=copy,
T1=T1,
brainmask=brainmask,
verbose=verbose)
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.')
parser.add_option('--simple-rendering', action='store_false',
dest='advanced_rendering',
help='Use simplified OpenGL rendering')
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,
advanced_rendering=options.advanced_rendering,
verbose=options.verbose)
if is_main:
sys.exit(0)
def run():
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')
def run():
t0 = time.time()
parser = get_optparser(__file__)
parser.add_option("--raw", dest="raw_in",
help="Input raw FIF file", metavar="FILE")
parser.add_option("--pos", dest="pos", default=None,
help="Position definition text file. Can be 'constant' "
"to hold the head position fixed", metavar="FILE")
parser.add_option("--dipoles", dest="dipoles", default=None,
help="Dipole definition file", metavar="FILE")
parser.add_option("--cov", dest="cov",
help="Covariance to use for noise generation. Can be "
"'simple' to use a diagonal covariance, or 'off' to "
"omit noise",
metavar="FILE", default='simple')
parser.add_option("--duration", dest="duration", default=None,
help="Duration of each epoch (sec). If omitted, the last"
" time point in the dipole definition file plus 200 ms "
"will be used", type="float")
parser.add_option("-j", "--jobs", dest="n_jobs", help="Number of jobs to"
" run in parallel", type="int", default=1)
parser.add_option("--out", dest="raw_out",
help="Output raw filename", metavar="FILE")
parser.add_option("--plot-dipoles", dest="plot_dipoles", help="Plot "
"input dipole positions", action="store_true")
parser.add_option("--plot-raw", dest="plot_raw", help="Plot the resulting "
"raw traces", action="store_true")
parser.add_option("--plot-evoked", dest="plot_evoked", help="Plot evoked "
"data", action="store_true")
parser.add_option("-p", "--plot", dest="plot", help="Plot dipoles, raw, "
"and evoked", action="store_true")
parser.add_option("--overwrite", dest="overwrite", help="Overwrite the"
"output file if it exists", action="store_true")
options, args = parser.parse_args()
raw_in = options.raw_in
pos = options.pos
raw_out = options.raw_out
dipoles = options.dipoles
n_jobs = options.n_jobs
plot = options.plot
plot_dipoles = options.plot_dipoles or plot
plot_raw = options.plot_raw or plot
plot_evoked = options.plot_evoked or plot
overwrite = options.overwrite
duration = options.duration
cov = options.cov
# check parameters
if not (raw_out or plot_raw or plot_evoked):
raise ValueError('data must either be saved (--out) or '
'plotted (--plot-raw or --plot_evoked)')
if raw_out and op.isfile(raw_out) and not overwrite:
raise ValueError('output file exists, use --overwrite (%s)' % raw_out)
if raw_in is None or pos is None or dipoles is None:
parser.print_help()
sys.exit(1)
s = 'Simulate raw data with head movements'
print('\n%s\n%s\n%s\n' % ('-' * len(s), s, '-' * len(s)))
# setup the simulation
with printer('Reading dipole definitions'):
if not op.isfile(dipoles):
raise IOError('dipole file not found:\n%s' % dipoles)
dipoles = np.loadtxt(dipoles, skiprows=1, dtype=float)
n_dipoles = dipoles.shape[0]
if dipoles.shape[1] != 8:
raise ValueError('dipoles must have 8 columns')
rr = dipoles[:, :3] * 1e-3
nn = dipoles[:, 3:6]
t = dipoles[:, 6:8]
duration = t.max() + 0.2 if duration is None else duration
if (t[:, 0] > t[:, 1]).any():
raise ValueError('found tmin > tmax in dipole file')
if (t < 0).any():
raise ValueError('found t < 0 in dipole file')
if (t > duration).any():
raise ValueError('found t > duration in dipole file')
amp = np.sqrt(np.sum(nn * nn, axis=1)) * 1e-9
mne.surface._normalize_vectors(nn)
nn[(nn == 0).all(axis=1)] = (1, 0, 0)
src = mne.SourceSpaces([
dict(rr=rr, nn=nn, inuse=np.ones(n_dipoles, int),
coord_frame=FIFF.FIFFV_COORD_HEAD)])
for key in ['pinfo', 'nuse_tri', 'use_tris', 'patch_inds']:
src[0][key] = None
trans = {'from': FIFF.FIFFV_COORD_HEAD, 'to': FIFF.FIFFV_COORD_MRI,
'trans': np.eye(4)}
if (amp > 100e-9).any():
print('')
warnings.warn('Largest dipole amplitude %0.1f > 100 nA'
% (amp.max() * 1e9))
if pos == 'constant':
print('Holding head position constant')
pos = None
else:
with printer('Loading head positions'):
pos = mne.get_chpi_positions(pos)
with printer('Loading raw data file'):
with warnings.catch_warnings(record=True):
raw = mne.io.Raw(raw_in, preload=False, allow_maxshield=True,
verbose=False)
if cov == 'simple':
print('Using diagonal covariance for brain noise')
elif cov == 'off':
print('Omitting brain noise in the simulation')
cov = None
else:
with printer('Loading covariance file for brain noise'):
cov = mne.read_cov(cov)
with printer('Setting up spherical model'):
bem = mne.bem.make_sphere_model('auto', 'auto', raw.info,
verbose=False)
# check that our sources are reasonable
rad = bem['layers'][0]['rad']
r0 = bem['r0']
outside = np.sqrt(np.sum((rr - r0) ** 2, axis=1)) >= rad
n_outside = outside.sum()
if n_outside > 0:
print('')
raise ValueError(
'%s dipole%s outside the spherical model, are your positions '
'in mm?' % (n_outside, 's were' if n_outside != 1 else ' was'))
with printer('Constructing source estimate'):
tmids = t.mean(axis=1)
t = np.round(t * raw.info['sfreq']).astype(int)
t[:, 1] += 1 # make it inclusive
n_samp = int(np.ceil(duration * raw.info['sfreq']))
data = np.zeros((n_dipoles, n_samp))
for di, (t_, amp_) in enumerate(zip(t, amp)):
data[di, t_[0]:t_[1]] = amp_ * np.hanning(t_[1] - t_[0])
stc = mne.VolSourceEstimate(data, np.arange(n_dipoles),
0, 1. / raw.info['sfreq'])
# do the simulation
print('')
raw_mv = simulate_raw(raw, stc, trans, src, bem, cov=cov, head_pos=pos,
chpi=True, n_jobs=n_jobs, verbose=True)
print('')
if raw_out:
with printer('Saving data'):
raw_mv.save(raw_out, overwrite=overwrite)
# plot results -- must be *after* save because we low-pass filter
if plot_dipoles:
with printer('Plotting dipoles'):
fig, axs = plt.subplots(1, 3, figsize=(10, 3), facecolor='w')
fig.canvas.set_window_title('Dipoles')
meg_info = mne.pick_info(raw.info,
mne.pick_types(raw.info,
meg=True, eeg=False))
helmet_rr = [ch['coil_trans'][:3, 3].copy()
for ch in meg_info['chs']]
helmet_nn = np.zeros_like(helmet_rr)
helmet_nn[:, 2] = 1.
surf = dict(rr=helmet_rr, nn=helmet_nn,
coord_frame=FIFF.FIFFV_COORD_DEVICE)
helmet_rr = mne.surface.transform_surface_to(
surf, 'head', meg_info['dev_head_t'])['rr']
p = np.linspace(0, 2 * np.pi, 40)
x_sphere, y_sphere = rad * np.sin(p), rad * np.cos(p)
for ai, ax in enumerate(axs):
others = np.setdiff1d(np.arange(3), [ai])
ax.plot(helmet_rr[:, others[0]], helmet_rr[:, others[1]],
marker='o', linestyle='none', alpha=0.1,
markeredgecolor='none', markerfacecolor='b', zorder=-2)
ax.plot(x_sphere + r0[others[0]], y_sphere + r0[others[1]],
color='y', alpha=0.25, zorder=-1)
ax.quiver(rr[:, others[0]], rr[:, others[1]],
amp * nn[:, others[0]], amp * nn[:, others[1]],
angles='xy', units='x', color='k', alpha=0.5)
ax.set_aspect('equal')
ax.set_xlabel(' - ' + 'xyz'[others[0]] + ' + ')
ax.set_ylabel(' - ' + 'xyz'[others[1]] + ' + ')
ax.set_xticks([])
ax.set_yticks([])
plt.setp(list(ax.spines.values()), color='none')
plt.tight_layout()
if plot_raw or plot_evoked:
with printer('Low-pass filtering simulated data'):
events = mne.find_events(raw_mv, 'STI101', verbose=False)
b, a = signal.butter(4, 40. / (raw.info['sfreq'] / 2.), 'low',
analog=False)
raw_mv.filter(None, 40., method='iir', iir_params=dict(b=b, a=a),
verbose=False, n_jobs=n_jobs)
if plot_raw:
with printer('Plotting raw data'):
raw_mv.plot(clipping='transparent', events=events,
show=False)
if plot_evoked:
with printer('Plotting evoked data'):
picks = mne.pick_types(raw_mv.info, meg=True, eeg=True)
events[:, 2] = 1
evoked = mne.Epochs(raw_mv, events, {'Simulated': 1},
0, duration, None, picks).average()
evoked.plot_topomap(np.unique(tmids), show=False)
print('\nTotal time: %0.1f sec' % (time.time() - t0))
sys.stdout.flush()
if any([plot_dipoles, plot_raw, plot_evoked]):
plt.show(block=True)
def run():
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)
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.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
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)
def run():
"""Run command."""
import matplotlib.pyplot as plt
from mne.commands.utils import get_optparser, _add_verbose_flag
parser = get_optparser(__file__, usage='usage: %prog raw [options]')
parser.add_option("--raw", dest="raw_in",
help="Input raw FIF file (can also be specified "
"directly as an argument without the --raw prefix)",
metavar="FILE")
parser.add_option("--proj", dest="proj_in",
help="Projector file", metavar="FILE",
default='')
parser.add_option("--eve", dest="eve_in",
help="Events file", metavar="FILE",
default='')
parser.add_option("-d", "--duration", dest="duration", type="float",
help="Time window for plotting (sec)",
default=10.0)
parser.add_option("-t", "--start", dest="start", type="float",
help="Initial start time for plotting",
default=0.0)
parser.add_option("-n", "--n_channels", dest="n_channels", type="int",
help="Number of channels to plot at a time",
default=20)
parser.add_option("-o", "--order", dest="group_by",
help="Order to use for grouping during plotting "
"('type' or 'original')", default='type')
parser.add_option("-p", "--preload", dest="preload",
help="Preload raw data (for faster navigaton)",
default=False, action="store_true")
parser.add_option("-s", "--show_options", dest="show_options",
help="Show projection options dialog",
default=False)
parser.add_option("--allowmaxshield", dest="maxshield",
help="Allow loading MaxShield processed data",
action="store_true")
parser.add_option("--highpass", dest="highpass", type="float",
help="Display high-pass filter corner frequency",
default=-1)
parser.add_option("--lowpass", dest="lowpass", type="float",
help="Display low-pass filter corner frequency",
default=-1)
parser.add_option("--filtorder", dest="filtorder", type="int",
help="Display filtering IIR order (or 0 to use FIR)",
default=4)
parser.add_option("--clipping", dest="clipping",
help="Enable trace clipping mode, either 'clamp' or "
"'transparent'", default=None)
parser.add_option("--filterchpi", dest="filterchpi",
help="Enable filtering cHPI signals.", default=None,
action="store_true")
_add_verbose_flag(parser)
options, args = parser.parse_args()
if len(args):
raw_in = args[0]
else:
raw_in = options.raw_in
duration = options.duration
start = options.start
n_channels = options.n_channels
group_by = options.group_by
preload = options.preload
show_options = options.show_options
proj_in = options.proj_in
eve_in = options.eve_in
maxshield = options.maxshield
highpass = options.highpass
lowpass = options.lowpass
filtorder = options.filtorder
clipping = options.clipping
filterchpi = options.filterchpi
verbose = options.verbose
if raw_in is None:
parser.print_help()
sys.exit(1)
raw = mne.io.read_raw_fif(raw_in, preload=preload,
allow_maxshield=maxshield)
if len(proj_in) > 0:
projs = mne.read_proj(proj_in)
raw.info['projs'] = projs
if len(eve_in) > 0:
events = mne.read_events(eve_in)
else:
events = None
if filterchpi:
if not preload:
raise RuntimeError(
'Raw data must be preloaded for chpi, use --preload')
raw = mne.chpi.filter_chpi(raw)
highpass = None if highpass < 0 or filtorder < 0 else highpass
lowpass = None if lowpass < 0 or filtorder < 0 else lowpass
raw.plot(duration=duration, start=start, n_channels=n_channels,
group_by=group_by, show_options=show_options, events=events,
highpass=highpass, lowpass=lowpass, filtorder=filtorder,
clipping=clipping, verbose=verbose)
plt.show(block=True)
# Martin Luessi <*****@*****.**>
# Alexandre Gramfort <*****@*****.**>
# Matti Hamalainen <*****@*****.**>
# Yuval Harpaz <*****@*****.**>
#
# simplified bsd-3 license
import sys
from mne.fiff.bti import read_raw_bti
if __name__ == '__main__':
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option('-p',
'--pdf',
dest='pdf_fname',
help='Input data file name',
metavar='FILE')
parser.add_option('-c',
'--config',
dest='config_fname',
help='Input config file name',
metavar='FILE',
default='config')
parser.add_option('--head_shape',
dest='head_shape_fname',
help='Headshape file name',
def run():
"""Run command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option('-p',
'--pdf',
dest='pdf_fname',
help='Input data file name',
metavar='FILE')
parser.add_option('-c',
'--config',
dest='config_fname',
help='Input config file name',
metavar='FILE',
default='config')
parser.add_option('--head_shape',
dest='head_shape_fname',
help='Headshape file name',
metavar='FILE',
default='hs_file')
parser.add_option('-o',
'--out_fname',
dest='out_fname',
help='Name of the resulting fiff file',
default='as_data_fname')
parser.add_option('-r',
'--rotation_x',
dest='rotation_x',
type='float',
help='Compensatory rotation about Neuromag x axis, deg',
default=2.0)
parser.add_option('-T',
'--translation',
dest='translation',
type='str',
help='Default translation, meter',
default=(0.00, 0.02, 0.11))
parser.add_option('--ecg_ch',
dest='ecg_ch',
type='str',
help='4D ECG channel name',
default='E31')
parser.add_option('--eog_ch',
dest='eog_ch',
type='str',
help='4D EOG channel names',
default='E63,E64')
options, args = parser.parse_args()
pdf_fname = options.pdf_fname
if pdf_fname is None:
parser.print_help()
sys.exit(1)
config_fname = options.config_fname
head_shape_fname = options.head_shape_fname
out_fname = options.out_fname
rotation_x = options.rotation_x
translation = options.translation
ecg_ch = options.ecg_ch
eog_ch = options.ecg_ch.split(',')
if out_fname == 'as_data_fname':
out_fname = pdf_fname + '_raw.fif'
raw = read_raw_bti(pdf_fname=pdf_fname,
config_fname=config_fname,
head_shape_fname=head_shape_fname,
rotation_x=rotation_x,
translation=translation,
ecg_ch=ecg_ch,
eog_ch=eog_ch)
raw.save(out_fname)
raw.close()
if is_main:
sys.exit(0)
def run():
import matplotlib.pyplot as plt
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option("--raw", dest="raw_in",
help="Input raw FIF file", metavar="FILE")
parser.add_option("--proj", dest="proj_in",
help="Projector file", metavar="FILE",
default='')
parser.add_option("--eve", dest="eve_in",
help="Events file", metavar="FILE",
default='')
parser.add_option("-d", "--duration", dest="duration", type="float",
help="Time window for plotting (sec)",
default=10.0)
parser.add_option("-t", "--start", dest="start", type="float",
help="Initial start time for plotting",
default=0.0)
parser.add_option("-n", "--n_channels", dest="n_channels", type="int",
help="Number of channels to plot at a time",
default=20)
parser.add_option("-o", "--order", dest="order",
help="Order for plotting ('type' or 'original')",
default='type')
parser.add_option("-p", "--preload", dest="preload",
help="Preload raw data (for faster navigaton)",
default=False)
parser.add_option("-s", "--show_options", dest="show_options",
help="Show projection options dialog",
default=False)
options, args = parser.parse_args()
raw_in = options.raw_in
duration = options.duration
start = options.start
n_channels = options.n_channels
order = options.order
preload = options.preload
show_options = options.show_options
proj_in = options.proj_in
eve_in = options.eve_in
if raw_in is None:
parser.print_help()
sys.exit(1)
raw = mne.io.Raw(raw_in, preload=preload)
if len(proj_in) > 0:
projs = mne.read_proj(proj_in)
raw.info['projs'] = projs
if len(eve_in) > 0:
events = mne.read_events(eve_in)
else:
events = None
raw.plot(duration=duration, start=start, n_channels=n_channels,
order=order, show_options=show_options, events=events)
plt.show(block=True)
def run():
import matplotlib.pyplot as plt
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option("--raw",
dest="raw_in",
help="Input raw FIF file",
metavar="FILE")
parser.add_option("--proj",
dest="proj_in",
help="Projector file",
metavar="FILE",
default='')
parser.add_option("--eve",
dest="eve_in",
help="Events file",
metavar="FILE",
default='')
parser.add_option("-d",
"--duration",
dest="duration",
type="float",
help="Time window for plotting (sec)",
default=10.0)
parser.add_option("-t",
"--start",
dest="start",
type="float",
help="Initial start time for plotting",
default=0.0)
parser.add_option("-n",
"--n_channels",
dest="n_channels",
type="int",
help="Number of channels to plot at a time",
default=20)
parser.add_option("-o",
"--order",
dest="order",
help="Order for plotting ('type' or 'original')",
default='type')
parser.add_option("-p",
"--preload",
dest="preload",
help="Preload raw data (for faster navigaton)",
default=False)
parser.add_option("-s",
"--show_options",
dest="show_options",
help="Show projection options dialog",
default=False)
options, args = parser.parse_args()
raw_in = options.raw_in
duration = options.duration
start = options.start
n_channels = options.n_channels
order = options.order
preload = options.preload
show_options = options.show_options
proj_in = options.proj_in
eve_in = options.eve_in
if raw_in is None:
parser.print_help()
sys.exit(1)
raw = mne.io.Raw(raw_in, preload=preload)
if len(proj_in) > 0:
projs = mne.read_proj(proj_in)
raw.info['projs'] = projs
if len(eve_in) > 0:
events = mne.read_events(eve_in)
else:
events = None
raw.plot(duration=duration,
start=start,
n_channels=n_channels,
order=order,
show_options=show_options,
events=events)
plt.show(block=True)
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
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=0.2)
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)
def run():
"""Run command."""
import matplotlib.pyplot as plt
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option("--raw", dest="raw_in", help="Input raw FIF file", metavar="FILE")
parser.add_option("--proj", dest="proj_in", help="Projector file", metavar="FILE", default="")
parser.add_option("--eve", dest="eve_in", help="Events file", metavar="FILE", default="")
parser.add_option(
"-d", "--duration", dest="duration", type="float", help="Time window for plotting (sec)", default=10.0
)
parser.add_option("-t", "--start", dest="start", type="float", help="Initial start time for plotting", default=0.0)
parser.add_option(
"-n", "--n_channels", dest="n_channels", type="int", help="Number of channels to plot at a time", default=20
)
parser.add_option("-o", "--order", dest="order", help="Order for plotting ('type' or 'original')", default="type")
parser.add_option("-p", "--preload", dest="preload", help="Preload raw data (for faster navigaton)", default=False)
parser.add_option("-s", "--show_options", dest="show_options", help="Show projection options dialog", default=False)
parser.add_option(
"--allowmaxshield", dest="maxshield", help="Allow loading MaxShield processed data", action="store_true"
)
parser.add_option(
"--highpass", dest="highpass", type="float", help="Display high-pass filter corner frequency", default=-1
)
parser.add_option(
"--lowpass", dest="lowpass", type="float", help="Display low-pass filter corner frequency", default=-1
)
parser.add_option("--filtorder", dest="filtorder", type="int", help="Display filtering IIR order", default=4)
parser.add_option(
"--clipping",
dest="clipping",
help="Enable trace clipping mode, either 'clip' or " "'transparent'",
default=None,
)
parser.add_option("--filterchpi", dest="filterchpi", help="Enable filtering cHPI signals.", default=None)
options, args = parser.parse_args()
raw_in = options.raw_in
duration = options.duration
start = options.start
n_channels = options.n_channels
order = options.order
preload = options.preload
show_options = options.show_options
proj_in = options.proj_in
eve_in = options.eve_in
maxshield = options.maxshield
highpass = options.highpass
lowpass = options.lowpass
filtorder = options.filtorder
clipping = options.clipping
filterchpi = options.filterchpi
if raw_in is None:
parser.print_help()
sys.exit(1)
raw = mne.io.read_raw_fif(raw_in, preload=preload, allow_maxshield=maxshield)
if len(proj_in) > 0:
projs = mne.read_proj(proj_in)
raw.info["projs"] = projs
if len(eve_in) > 0:
events = mne.read_events(eve_in)
else:
events = None
if filterchpi:
if not preload:
raise RuntimeError("Raw data must be preloaded for chpi, use --preload")
raw = mne.chpi.filter_chpi(raw)
highpass = None if highpass < 0 or filtorder <= 0 else highpass
lowpass = None if lowpass < 0 or filtorder <= 0 else lowpass
filtorder = 4 if filtorder <= 0 else filtorder
raw.plot(
duration=duration,
start=start,
n_channels=n_channels,
order=order,
show_options=show_options,
events=events,
highpass=highpass,
lowpass=lowpass,
filtorder=filtorder,
clipping=clipping,
)
plt.show(block=True)
