# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
#
# Copyright 2021 The NiPreps Developers <nipreps@gmail.com>
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
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#
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# https://www.nipreps.org/community/licensing/
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"""Run the BOLD reference+mask workflow"""
import os
[docs]
def get_parser():
"""Build parser object."""
from argparse import ArgumentParser
from argparse import RawTextHelpFormatter, RawDescriptionHelpFormatter
parser = ArgumentParser(
description="""NiWorkflows Utilities""", formatter_class=RawTextHelpFormatter
)
subparsers = parser.add_subparsers(dest="command")
be_parser = subparsers.add_parser(
"brain-extract",
formatter_class=RawDescriptionHelpFormatter,
description="""Execute brain extraction and related operations (e.g., \
intensity nonuniformity correction, robust averaging, etc.)""",
)
be_parser.add_argument("input_file", action="store", help="the input file")
be_parser.add_argument("out_path", action="store", help="the output directory")
be_parser.add_argument(
"--modality",
"-m",
action="store",
choices=("bold", "t1w"),
default="bold",
help="the input file",
)
parser.add_argument(
"--omp-nthreads",
action="store",
type=int,
default=os.cpu_count(),
help="Number of CPUs available to individual processes",
)
parser.add_argument(
"--nprocs",
action="store",
type=int,
default=os.cpu_count(),
help="Number of processes that may run in parallel",
)
return parser
[docs]
def main(args=None):
"""Entry point."""
from nipype.utils.filemanip import hash_infile
from ..func.util import init_bold_reference_wf
opts = get_parser().parse_args(args=args)
wf = init_bold_reference_wf(
opts.omp_nthreads, gen_report=True, name=hash_infile(opts.input_file),
)
wf.inputs.inputnode.bold_file = opts.input_file
wf.base_dir = os.getcwd()
plugin = {
"plugin": "MultiProc",
"plugin_args": {"nprocs": opts.nprocs},
}
if opts.nprocs < 2:
plugin = {"plugin": "Linear"}
wf.run(**plugin)
if __name__ == "__main__":
from sys import argv
main(args=argv[1:])