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mne/commands/mne_setup_source_space.py

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+# Authors: The MNE-Python contributors.
+# License: BSD-3-Clause
+# Copyright the MNE-Python contributors.
+
+"""Set up bilateral hemisphere surface-based source space with subsampling.
+
+Examples
+--------
+.. code-block:: console
+
+    $ mne setup_source_space --subject sample
+
+
+ .. note : Only one of --ico, --oct or --spacing options can be set at the same
+           time. Default to oct6.
+
+"""
+
+import sys
+
+import mne
+from mne.utils import _check_option
+
+
+def run():
+    """Run command."""
+    from mne.commands.utils import _add_verbose_flag, get_optparser
+
+    parser = get_optparser(__file__)
+
+    parser.add_option(
+        "-s", "--subject", dest="subject", help="Subject name (required)", default=None
+    )
+    parser.add_option(
+        "--src",
+        dest="fname",
+        help="Output file name. Use a name <dir>/<name>-src.fif",
+        metavar="FILE",
+        default=None,
+    )
+    parser.add_option(
+        "--morph",
+        dest="subject_to",
+        help="morph the source space to this subject",
+        default=None,
+    )
+    parser.add_option(
+        "--surf",
+        dest="surface",
+        help="The surface to use. (default to white)",
+        default="white",
+        type="string",
+    )
+    parser.add_option(
+        "--spacing",
+        dest="spacing",
+        help="Specifies the approximate grid spacing of the "
+        "source space in mm. (default to 7mm)",
+        default=None,
+        type="int",
+    )
+    parser.add_option(
+        "--ico",
+        dest="ico",
+        help="use the recursively subdivided icosahedron "
+        "to create the source space.",
+        default=None,
+        type="int",
+    )
+    parser.add_option(
+        "--oct",
+        dest="oct",
+        help="use the recursively subdivided octahedron to create the source space.",
+        default=None,
+        type="int",
+    )
+    parser.add_option(
+        "-d",
+        "--subjects-dir",
+        dest="subjects_dir",
+        help="Subjects directory",
+        default=None,
+    )
+    parser.add_option(
+        "-n",
+        "--n-jobs",
+        dest="n_jobs",
+        help="The number of jobs to run in parallel "
+        "(default 1). Requires the joblib package. "
+        "Will use at most 2 jobs"
+        " (one for each hemisphere).",
+        default=1,
+        type="int",
+    )
+    parser.add_option(
+        "--add-dist",
+        dest="add_dist",
+        help='Add distances. Can be "True", "False", or "patch" '
+        "to only compute cortical patch statistics (like the --cps option in MNE-C)",
+        default="True",
+    )
+    parser.add_option(
+        "-o",
+        "--overwrite",
+        dest="overwrite",
+        help="to write over existing files",
+        default=None,
+        action="store_true",
+    )
+    _add_verbose_flag(parser)
+
+    options, args = parser.parse_args()
+
+    if options.subject is None:
+        parser.print_help()
+        sys.exit(1)
+
+    subject = options.subject
+    subject_to = options.subject_to
+    fname = options.fname
+    subjects_dir = options.subjects_dir
+    spacing = options.spacing
+    ico = options.ico
+    oct_ = options.oct
+    surface = options.surface
+    n_jobs = options.n_jobs
+    add_dist = options.add_dist
+    _check_option("add_dist", add_dist, ("True", "False", "patch"))
+    add_dist = {"True": True, "False": False, "patch": "patch"}[add_dist]
+    verbose = True if options.verbose is not None else False
+    overwrite = True if options.overwrite is not None else False
+
+    # Parse source spacing option
+    spacing_options = [ico, oct_, spacing]
+    n_options = len([x for x in spacing_options if x is not None])
+    use_spacing = "oct6"
+    if n_options > 1:
+        raise ValueError("Only one spacing option can be set at the same time")
+    elif n_options == 0:
+        # Default to oct6
+        pass
+    elif n_options == 1:
+        if ico is not None:
+            use_spacing = "ico" + str(ico)
+        elif oct_ is not None:
+            use_spacing = "oct" + str(oct_)
+        elif spacing is not None:
+            use_spacing = spacing
+    del ico, oct_, spacing
+    # Generate filename
+    if fname is None:
+        if subject_to is None:
+            fname = subject + "-" + str(use_spacing) + "-src.fif"
+        else:
+            fname = subject_to + "-" + subject + "-" + str(use_spacing) + "-src.fif"
+    else:
+        if not (fname.endswith("_src.fif") or fname.endswith("-src.fif")):
+            fname = fname + "-src.fif"
+    # Create source space
+    src = mne.setup_source_space(
+        subject=subject,
+        spacing=use_spacing,
+        surface=surface,
+        subjects_dir=subjects_dir,
+        n_jobs=n_jobs,
+        add_dist=add_dist,
+        verbose=verbose,
+    )
+    # Morph source space if --morph is set
+    if subject_to is not None:
+        src = mne.morph_source_spaces(
+            src,
+            subject_to=subject_to,
+            subjects_dir=subjects_dir,
+            surf=surface,
+            verbose=verbose,
+        )
+
+    # Save source space to file
+    src.save(fname=fname, overwrite=overwrite)
+
+
+mne.utils.run_command_if_main()