Source code for pymialsrtk.parser

# Copyright © 2016-2023 Medical Image Analysis Laboratory, University Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland
#
#  This software is distributed under the open-source license Modified BSD.

"""MIALSRTK BIDS App Commandline Parser."""

import argparse

from pymialsrtk.info import __version__
from pymialsrtk.info import __release_date__


def get_parser():
    """Create and return the parser object of the BIDS App."""
    p = argparse.ArgumentParser(description="Argument parser of the MIALSRTK BIDS App")

    p.add_argument("bids_dir",
                   help="The directory with the input dataset "
                        "formatted according to the BIDS standard.")

    p.add_argument(
        "output_dir",
        help="The directory where the output files "
             "should be stored. If you are running group level analysis "
             "this folder should be prepopulated with the results of the "
             "participant level analysis.",
    )

    p.add_argument(
        "analysis_level",
        help="Level of the analysis that will be performed. " "Only participant is available",
        choices=["participant"],
    )

    p.add_argument(
        "--run_type",
        help="Type of pipeline that is run. Can choose between "
             "running the super-resolution pipeline (`sr`) "
             "or only preprocessing (`preprocessing`).",
        choices=["sr", "preprocessing"],
        default="sr"
    )

    p.add_argument(
        "--participant_label",
        help="The label(s) of the participant(s) that should be analyzed. "
             "The label corresponds to sub-<participant_label> from the BIDS spec "
             '(so it does not include "sub-"). If this parameter is not '
             "provided all subjects should be analyzed. Multiple "
             "participants can be specified with a space separated list.",
        nargs="+",
    )

    p.add_argument(
        "--param_file",
        help="Path to a JSON file containing subjects' exams "
             "information and super-resolution total variation parameters.",
        default="/bids_dir/code/participants_params.json",
        type=str,
    )

    p.add_argument(
        "--openmp_nb_of_cores",
        help="Specify number of cores used by OpenMP threads "
             "Especially useful for NLM denoising and slice-to-volume registration. "
             "(Default: 0, meaning it will be determined automatically)",
        default=0,
        type=int,
    )

    p.add_argument(
        "--nipype_nb_of_cores",
        help="Specify number of cores used by the Niype workflow library to distribute "
             "the execution of independent processing workflow nodes (i.e. interfaces) "
             "(Especially useful in the case of slice-by-slice bias field correction and "
             "intensity standardization steps for example). "
             "(Default: 0, meaning it will be determined automatically)",
        default=0,
        type=int,
    )

    p.add_argument(
        "--memory",
        help="Limit the workflow to using the amount of specified memory [in gb] "
             "(Default: 0, the workflow memory consumption is not limited)",
        default=0,
        type=int,
    )

    p.add_argument(
        "--masks_derivatives_dir",
        help="Use manual brain masks found in "
             "``<output_dir>/<masks_derivatives_dir>/`` directory",
    )

    p.add_argument(
        "--labels_derivatives_dir",
        help="Use low-resolution labelmaps found in "
             "``<output_dir>/<labels_derivatives_dir>/`` directory.",
    )

    p.add_argument(
        '--all_outputs',
        action='store_true',
        default=False,
        help="Whether or not all outputs should be kept"
             "(e.g. preprocessed LR images)",
    )

    p.add_argument(
        "-v",
        "--version",
        action="version",
        version=f"BIDS-App MIALSRTK version {__version__} (Released: {__release_date__})",
    )

    p.add_argument(
        '--verbose',
        action='store_true',
        default=False,
        help="Verbose mode",
    )
    return p


def get_wrapper_parser(container_type):
    """Create and return the parser object of the python wrappers of the BIDS App."""
    p = get_parser()
    p.description = f"Argument parser of the python wrapper of MIALSRTK BIDS App ({container_type})"
    p.add_argument(
        '--track_carbon_footprint',
        dest='track_carbon_footprint',
        action='store_true',
        help="Track carbon footprint with `codecarbon <https://codecarbon.io/>`_ and save results in "
             "a CSV file called ``emissions.csv`` in the ``<bids_dir>/code`` directory.",
    )
    return p


def get_singularity_wrapper_parser():
    """Create and return the parser object of the python wrappers of the BIDS App."""
    p = get_wrapper_parser('Singularity')
    p.description = f"Argument parser of the python wrapper of MIALSRTK BIDS App via Singularity"
    p.add_argument(
        '--singularity_image',
        dest='singularity_image',
        default=f'library://tourbier/mialsuperresolutiontoolkit-bidsapp:v{__version__}',
        type=str,
        help="Specify the path to the singularity image. "
             f"If not specified, library://tourbier/mialsuperresolutiontoolkit-bidsapp:v{__version__} is used.",
    )
    return p