Python utils.get_optparser函数代码示例

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=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__)
    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():
    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():
    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():
    """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("-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('--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('-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():
    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():
    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)