dicom_validate.py

#!/usr/bin/env python

import pydicom
from pathlib import Path
from argparse import ArgumentParser, Namespace, ArgumentDefaultsHelpFormatter
from loguru import logger
import pydicom
from chris_plugin import chris_plugin, PathMapper
import sys

LOG = logger.debug

logger_format = (
    "<green>{time:YYYY-MM-DD HH:mm:ss}</green> │ "
    "<level>{level: <5}</level> │ "
    "<yellow>{name: >28}</yellow>::"
    "<cyan>{function: <30}</cyan> @"
    "<cyan>{line: <4}</cyan> ║ "
    "<level>{message}</level>"
)
logger.remove()
logger.add(sys.stderr, format=logger_format)

__version__ = '1.0.0'

DISPLAY_TITLE = r"""
       _           _ _                                _ _     _       _       
      | |         | (_)                              | (_)   | |     | |      
 _ __ | |______ __| |_  ___ ___  _ __ ___ __   ____ _| |_  __| | __ _| |_ ___ 
| '_ \| |______/ _` | |/ __/ _ \| '_ ` _ \\ \ / / _` | | |/ _` |/ _` | __/ _ \
| |_) | |     | (_| | | (_| (_) | | | | | |\ V / (_| | | | (_| | (_| | ||  __/
| .__/|_|      \__,_|_|\___\___/|_| |_| |_| \_/ \__,_|_|_|\__,_|\__,_|\__\___|
| |                                     ______                                
|_|                                    |______|                               
"""


parser = ArgumentParser(description='A ChRIS plugin to validate DICOMs.'
                                    'The plugin offers automated structural validation of DICOM files ',
                        formatter_class=ArgumentDefaultsHelpFormatter)
parser.add_argument('-p', '--pattern', default='**/*.dcm', type=str,
                    help='input file filter glob')
parser.add_argument('-V', '--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 ChRIS plugin to validate DICOMs',
    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
    """

    LOG(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)
    for input_file, output_file in mapper:
        try:
            logger.debug(f"Validating input file: ----> {input_file} <----")
            ds = pydicom.dcmread(input_file)
            logger.debug(f"DICOM is readable. Saving output file: ----> {output_file} <----")
            ds.save_as(output_file)
        except Exception as ex:
            logger.error(f"DICOM is unreadable: {ex}")


if __name__ == '__main__':
    main()