Source code for niworkflows.cli.boldref

# 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>
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# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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#
#     http://www.apache.org/licenses/LICENSE-2.0
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# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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"""Run the BOLD reference+mask workflow"""

import os




def get_parser():
    """Build parser object."""
    from argparse import ArgumentParser, RawDescriptionHelpFormatter, RawTextHelpFormatter

    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





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:])