parseargs.py

#! /usr/bin/env python

import argparse


class disableFilter(argparse.Action):
    def __call__(self, parser, args, values, option_string=None):
        # print("action, baby!", self.dest, values)
        # print(args, type(args))
        noval = 'no'+values
        if isinstance(args.filters, type(None)):
            args.filters = [noval]
        else:
            args.filters.append(noval)


class enableAnisotropic(argparse.Action):
    def __init__(self, nargs=0, **kw):
        super().__init__(nargs=nargs, **kw)

    def __call__(self, parser, args, values, option_string=None):
        # x = getattr(args, 'filters')
        if isinstance(args.filters, type(None)):
            args.filters = ['anisotropic']
        # args.filters.append('anisotropic')


class enableLargest(argparse.Action):
    def __init__(self, nargs=0, **kw):
        super().__init__(nargs=nargs, **kw)

    def __call__(self, parser, args, values, option_string=None):
        x = getattr(args, 'filters')
        x.append('largest')


def parseargs():
    parser = argparse.ArgumentParser()

    parser.add_argument('filenames', nargs='*')

    parser.add_argument('--verbose', '-v', action='store_true', default=False,
                        dest='verbose', help='Enable verbose messages')

    parser.add_argument('--debug', '-D', action='store_true', default=False,
                        dest='debug',
                        help="""Enable debugging messages
                        """)

    parser.add_argument('--output', '-o', action='store', dest='output',
                        default='result.stl',
                        help='Output file name (default=result.stl)')

    parser.add_argument('--meta', '-m', action='store', dest='meta',
                        help='Output metadata file')

    parser.add_argument('--ct', action='store_true', default=False,
                        dest='ctonly', help='Only allow CT Dicom as input')

    parser.add_argument('--clean', '-c', action='store_true', default=False,
                        dest='clean', help='Clean up temp files')

    parser.add_argument('--temp', '-T', action='store', dest='temp',
                        help='Temporary directory')

    parser.add_argument('--search', '-s', action='store', dest='search',
                        help='Dicom series search string')

    # Options that apply to the volumetric portion of the pipeline
    vol_group = parser.add_argument_group('Volume options')

    vol_group.add_argument('--type', '-t', action='store', dest='tissue',
                           choices=['skin', 'bone', 'soft_tissue', 'fat'],
                           help='CT tissue type')

    vol_group.add_argument('--anisotropic', '-a', action=enableAnisotropic,
                           help='Apply anisotropic smoothing to the volume')

    vol_group.add_argument('--isovalue', '-i', action='store', dest='isovalue',
                           type=float, default=0.0, help='Iso-surface value')

    vol_group.add_argument('--double', '-d', action='store',
                           dest='double_threshold',
                           help="""Double threshold with 4 semicolon separated floats
                                """)

    # Options that apply to the mesh processing portion of the pipeline
    mesh_group = parser.add_argument_group('Mesh options')
    mesh_group.add_argument('--largest', '-l', action=enableLargest,
                            help='Only keep the largest connected sub-mesh')

    mesh_group.add_argument('--rotaxis', action='store', dest='rotaxis',
                            default='Y', choices=['X', 'Y', 'Z'],
                            help='Rotation axis (default=Y)')

    mesh_group.add_argument('--rotangle', action='store', dest='rotangle',
                            type=float, default=0.0,
                            help='Rotation angle in degrees (default=180)')

    mesh_group.add_argument('--smooth', action='store', dest='smooth',
                            type=int, default=25,
                            help='Mesh smoothing iterations (default=25)')

    mesh_group.add_argument('--reduce', action='store', dest='reduce',
                            type=float, default=.9,
                            help='Mesh reduction factor (default=.9)')

    # Filtering options
    filter_group = parser.add_argument_group('Filtering options')
    filter_group.add_argument('--enable', action='append', dest='filters',
                              choices=['anisotropic', 'shrink',
                                       'median', 'largest', 'rotation'],
                              help='Enable filtering options')
    filter_group.add_argument('--disable', action=disableFilter,
                              dest='filters',
                              choices=['anisotropic', 'shrink', 'median',
                                       'largest', 'rotation'],
                              help='Disable filtering options')
    args = parser.parse_args()
    return args