bulky.py

#!/usr/bin/env python

from pathlib import Path
from argparse import ArgumentParser, Namespace, ArgumentDefaultsHelpFormatter

from chris_plugin import chris_plugin, PathMapper
import shutil

__version__ = "1.0.0"

DISPLAY_TITLE = r"""
 _           _ _                                      
| |         | | |                                     
| |__  _   _| | | ___ __  _ __ ___   ___ ___  ___ ___ 
| '_ \| | | | | |/ / '_ \| '__/ _ \ / __/ _ \/ __/ __|
| |_) | |_| | |   <| |_) | | | (_) | (_|  __/\__ \__ \
|_.__/ \__,_|_|_|\_\ .__/|_|  \___/ \___\___||___/___/
                   | |                                
                   |_|                                
"""


parser = ArgumentParser(
    description="""
    A dummy bulk processor. Move along. Not much to see here.
                        """,
    formatter_class=ArgumentDefaultsHelpFormatter,
)
parser.add_argument(
    "--pattern", default="**/*.dcm", type=str, help="input file filter glob"
)
parser.add_argument("--version", action="version", version=f"%(prog)s {__version__}")


# The main function of this *ChRIS* plugin is denoted by this ``@chris_plugin`` "decorator."
# Some metadata about the plugin is specified here. There is more metadata specified in setup.py.
#
# documentation: https://fnndsc.github.io/chris_plugin/chris_plugin.html#chris_plugin
@chris_plugin(
    parser=parser,
    title="A bulk processor",
    category="",  # ref. https://chrisstore.co/plugins
    min_memory_limit="100Mi",  # supported units: Mi, Gi
    min_cpu_limit="1000m",  # millicores, e.g. "1000m" = 1 CPU core
    min_gpu_limit=0,  # set min_gpu_limit=1 to enable GPU
)
def main(options: Namespace, inputdir: Path, outputdir: Path):
    """
    *ChRIS* plugins usually have two positional arguments: an **input directory** containing
    input files and an **output directory** where to write output files. Command-line arguments
    are passed to this main method implicitly when ``main()`` is called below without parameters.

    :param options: non-positional arguments parsed by the parser given to @chris_plugin
    :param inputdir: directory containing (read-only) input files
    :param outputdir: directory where to write output files
    """
    print(DISPLAY_TITLE)

    # Typically it's easier to think of programs as operating on individual files
    # rather than directories. The helper functions provided by a ``PathMapper``
    # object make it easy to discover input files and write to output files inside
    # the given paths.
    #
    # Refer to the documentation for more options, examples, and advanced uses e.g.
    # adding a progress bar and parallelism.
    mapper = PathMapper.file_mapper(
        inputdir, outputdir, glob=options.pattern, suffix=".bak.dcm"
    )
    for input_file, output_file in mapper:
        # The code block below is a small and easy example of how to use a ``PathMapper``.
        # It is recommended that you put your functionality in a helper function, so that
        # it is more legible and can be unit tested.
        print(f"copying {input_file} to {output_file}")
        shutil.copy(input_file, output_file)


if __name__ == "__main__":
    main()