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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()
|
