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#!/usr/bin/env python
r"""Create mne report for a folder.
Example usage
mne report -p MNE-sample-data/ -i \
MNE-sample-data/MEG/sample/sample_audvis-ave.fif -d MNE-sample-data/subjects/ \
-s sample
"""
import sys
import time
from mne.report import Report
from mne.utils import verbose, logger
@verbose
def log_elapsed(t, verbose=None):
"""Log elapsed time."""
logger.info('Report complete in %s seconds' % round(t, 1))
def run():
"""Run command."""
from mne.commands.utils import get_optparser
parser = get_optparser(__file__)
parser.add_option("-p", "--path", dest="path",
help="Path to folder who MNE-Report must be created")
parser.add_option("-i", "--info", dest="info_fname",
help="File from which info dictionary is to be read",
metavar="FILE")
parser.add_option("-c", "--cov", dest="cov_fname",
help="File from which noise covariance is to be read",
metavar="FILE")
parser.add_option("--bmin", dest="bmin",
help="Time at which baseline correction starts for "
"evokeds", default=None)
parser.add_option("--bmax", dest="bmax",
help="Time at which baseline correction stops for "
"evokeds", default=None)
parser.add_option("-d", "--subjects-dir", dest="subjects_dir",
help="The subjects directory")
parser.add_option("-s", "--subject", dest="subject",
help="The subject name")
parser.add_option("-v", "--verbose", dest="verbose",
action='store_true', help="run in verbose mode")
parser.add_option("--no-browser", dest="no_browser", action='store_false',
help="Do not open MNE-Report in browser")
parser.add_option("--overwrite", dest="overwrite", action='store_false',
help="Overwrite html report if it already exists")
parser.add_option("-j", "--jobs", dest="n_jobs", help="Number of jobs to"
" run in parallel")
parser.add_option("-m", "--mri-decim", type="int", dest="mri_decim",
default=2, help="Integer factor used to decimate "
"BEM plots")
parser.add_option("--image-format", type="str", dest="image_format",
default='png', help="Image format to use "
"(can be 'png' or 'svg')")
options, args = parser.parse_args()
path = options.path
if path is None:
parser.print_help()
sys.exit(1)
info_fname = options.info_fname
cov_fname = options.cov_fname
subjects_dir = options.subjects_dir
subject = options.subject
image_format = options.image_format
mri_decim = int(options.mri_decim)
verbose = True if options.verbose is not None else False
open_browser = False if options.no_browser is not None else True
overwrite = True if options.overwrite is not None else False
n_jobs = int(options.n_jobs) if options.n_jobs is not None else 1
bmin = float(options.bmin) if options.bmin is not None else None
bmax = float(options.bmax) if options.bmax is not None else None
# XXX: this means (None, None) cannot be specified through command line
if bmin is None and bmax is None:
baseline = None
else:
baseline = (bmin, bmax)
t0 = time.time()
report = Report(info_fname, subjects_dir=subjects_dir,
subject=subject, baseline=baseline,
cov_fname=cov_fname, verbose=verbose,
image_format=image_format)
report.parse_folder(path, verbose=verbose, n_jobs=n_jobs,
mri_decim=mri_decim)
log_elapsed(time.time() - t0, verbose=verbose)
report.save(open_browser=open_browser, overwrite=overwrite)
is_main = (__name__ == '__main__')
if is_main:
run()
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