115 lines
2.7 KiB
Python
115 lines
2.7 KiB
Python
# Authors: The MNE-Python contributors.
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# License: BSD-3-Clause
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# Copyright the MNE-Python contributors.
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"""Import KIT / NYU data to fif file.
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Examples
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--------
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.. code-block:: console
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$ mne kit2fiff --input input.sqd --output output.fif
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Use without arguments to invoke GUI:
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.. code-block:: console
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$ mne kt2fiff
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"""
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import sys
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import mne
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from mne.io import read_raw_kit
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def run():
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"""Run command."""
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from mne.commands.utils import get_optparser
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parser = get_optparser(__file__)
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parser.add_option(
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"--input", dest="input_fname", help="Input data file name", metavar="filename"
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)
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parser.add_option(
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"--mrk", dest="mrk_fname", help="MEG Marker file name", metavar="filename"
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)
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parser.add_option(
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"--elp", dest="elp_fname", help="Headshape points file name", metavar="filename"
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)
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parser.add_option(
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"--hsp", dest="hsp_fname", help="Headshape file name", metavar="filename"
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)
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parser.add_option(
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"--stim",
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dest="stim",
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help="Colon Separated Stimulus Trigger Channels",
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metavar="chs",
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)
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parser.add_option("--slope", dest="slope", help="Slope direction", metavar="slope")
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parser.add_option(
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"--stimthresh",
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dest="stimthresh",
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default=1,
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help="Threshold value for trigger channels",
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metavar="value",
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)
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parser.add_option(
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"--output",
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dest="out_fname",
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help="Name of the resulting fiff file",
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metavar="filename",
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)
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parser.add_option(
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"--debug",
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dest="debug",
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action="store_true",
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default=False,
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help="Set logging level for terminal output to debug",
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)
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options, args = parser.parse_args()
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if options.debug:
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mne.set_log_level("debug")
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input_fname = options.input_fname
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if input_fname is None:
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try:
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from mne_kit_gui import kit2fiff # noqa
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except ImportError:
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raise ImportError(
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"The mne-kit-gui package is required, install it using conda or pip"
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) from None
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kit2fiff()
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sys.exit(0)
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hsp_fname = options.hsp_fname
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elp_fname = options.elp_fname
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mrk_fname = options.mrk_fname
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stim = options.stim
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slope = options.slope
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stimthresh = options.stimthresh
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out_fname = options.out_fname
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if isinstance(stim, str):
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stim = map(int, stim.split(":"))
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raw = read_raw_kit(
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input_fname=input_fname,
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mrk=mrk_fname,
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elp=elp_fname,
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hsp=hsp_fname,
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stim=stim,
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slope=slope,
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stimthresh=stimthresh,
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)
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raw.save(out_fname)
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raw.close()
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mne.utils.run_command_if_main()
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