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mne/commands/mne_kit2fiff.py

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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()