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| # Authors: The MNE-Python contributors. | |
| # License: BSD-3-Clause | |
| # Copyright the MNE-Python contributors. | |
| """Import KIT / NYU data to fif file. | |
| Examples | |
| -------- | |
| .. code-block:: console | |
| $ mne kit2fiff --input input.sqd --output output.fif | |
| Use without arguments to invoke GUI: | |
| .. code-block:: console | |
| $ mne kt2fiff | |
| """ | |
| import sys | |
| import mne | |
| from mne.io import read_raw_kit | |
| 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: | |
| try: | |
| from mne_kit_gui import kit2fiff # noqa | |
| except ImportError: | |
| raise ImportError( | |
| "The mne-kit-gui package is required, install it using conda or pip" | |
| ) from None | |
| 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() | |
| mne.utils.run_command_if_main() | |