initial commit

mne/commands/mne_coreg.py

@@ -0,0 +1,116 @@
+# Authors: The MNE-Python contributors.
+# License: BSD-3-Clause
+# Copyright the MNE-Python contributors.
+
+"""Open the coregistration GUI.
+
+Examples
+--------
+.. code-block:: console
+
+    $ mne coreg
+
+"""
+
+import os.path as op
+
+import mne
+
+
+def run():
+    """Run command."""
+    from mne.commands.utils import _add_verbose_flag, 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(
+        "--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(
+        "--interaction",
+        type=str,
+        default=None,
+        dest="interaction",
+        help='Interaction style to use, can be "trackball" or "terrain".',
+    )
+    _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(
+        inst=options.inst,
+        subject=options.subject,
+        subjects_dir=subjects_dir,
+        head_opacity=options.head_opacity,
+        head_high_res=head_high_res,
+        trans=trans,
+        interaction=options.interaction,
+        show=True,
+        block=True,
+        verbose=options.verbose,
+    )
+
+
+mne.utils.run_command_if_main()