"""Add standard command line options."""
# Copyright (c) 2013-2022 Erling Andersen, Haukeland University Hospital, Bergen, Norway
import sys
import argparse
import copy
import logging
from . import __version__
from .formats import str_to_sort_on, str_to_input_order, str_to_dtype
from .formats import SORT_ON_SLICE
from .formats import INPUT_ORDER_AUTO
[docs]
class DictAction(argparse.Action):
def __init__(self, option_strings, dest, nargs=None, **kwargs):
if nargs is not None:
raise ValueError("nargs not allowed")
super(DictAction, self).__init__(option_strings, dest, **kwargs)
def __call__(self, _parser, namespace, values, option_string=None):
try:
k, v = values.split("=", 1)
except ValueError:
raise argparse.ArgumentError(self, "Format must be key=value")
# noinspection PyProtectedMember
items = copy.copy(getattr(namespace, self.dest, {})) # Default mutables, use copy!
items[k] = v
setattr(namespace, self.dest, items)
[docs]
class CommaSepAction(argparse.Action):
def __init__(self, option_strings, dest, nargs=None, **kwargs):
if nargs is not None:
raise ValueError("nargs not allowed")
super(CommaSepAction, self).__init__(option_strings, dest, **kwargs)
def __call__(self, _parser, namespace, values, option_string=None):
# print('%r %r %r' % (namespace, values, option_string))
commasep = values.split(',')
setattr(namespace, self.dest, commasep)
[docs]
class SortOnAction(argparse.Action):
def __init__(self, option_strings, dest, nargs=None, **kwargs):
if nargs is not None:
raise ValueError("nargs not allowed")
super(SortOnAction, self).__init__(option_strings, dest, **kwargs)
def __call__(self, _parser, namespace, values, option_string=None):
# print('%r %r %r' % (namespace, values, option_string))
sort = str_to_sort_on(values)
setattr(namespace, self.dest, sort)
[docs]
class DtypeAction(argparse.Action):
def __init__(self, option_strings, dest, nargs=None, **kwargs):
if nargs is not None:
raise ValueError("nargs not allowed")
super(DtypeAction, self).__init__(option_strings, dest, **kwargs)
def __call__(self, _parser, namespace, values, option_string=None):
# print('%r %r %r' % (namespace, values, option_string))
output_dtype = str_to_dtype(values)
setattr(namespace, self.dest, output_dtype)
def add_argparse_options(parser):
parser.add_argument('--of', dest="output_format", action=OutputFormatAction,
help="Output format [dicom|itk|nifti|biff|mat|ps] (default: dicom). "
"Replaces %%p in output path.",
choices=['dicom', 'itk', 'nifti', 'biff', 'mat', 'ps'],
default=[])
parser.add_argument('--sort', dest="output_sort", action=SortOnAction,
help="Sort output file on slice or input order 'tag' (default: slice)",
choices=['slice', 'tag'], default=SORT_ON_SLICE)
parser.add_argument('--order', dest="input_order",
action=InputOrderAction,
help="How to sort input file (time, b-value, fa, te) (default: none)",
choices=['auto', 'none', 'time', 'b', 'fa', 'te', 'faulty'],
default=INPUT_ORDER_AUTO)
# readdata.str_to_dtype() will convert choice to numpy dtype
parser.add_argument('--dtype', action=DtypeAction,
help="Specify output datatype. Otherwise keep input datatype",
choices=['uint8', 'uint16', 'int16', 'int', 'float', 'float32',
'float64', 'double'],
default=None)
parser.add_argument('--psopt',
help="Postscript options (opt=value,opt=value) where opt can be: " +
"dpi= (Resolution in pixels/inch of image, default=150); " +
"driver=png16m/pnggray (default=png16m); "
"rotate=90 (default=0)",
default=None)
parser.add_argument('--odir', dest="output_dir",
help="Store all images in a single or multiple directories "
"(default: single)",
choices=['single', 'multi'], default='single')
parser.add_argument('--template', default=None,
help="Source to get DICOM template from")
parser.add_argument('--geometry', default=None,
help="Second DICOM template for geometry attributes")
parser.add_argument('--frame',
help="Set DICOM frame of reference uid")
parser.add_argument('--SOPClassUID', help="Set DICOM SOP Class UID", default=None)
parser.add_argument('--sernum', type=int,
help="Set DICOM series number")
parser.add_argument('--serdes',
help="Set DICOM series description")
parser.add_argument('--input_serinsuid',
help="Only read images with specified Series Instance UID",
default=None)
parser.add_argument('--input_acquisition',
help="Only read images with specified Acquisition Number",
default=None)
parser.add_argument('--input_echo',
help="Only read images with specified Echo Number",
default=None)
parser.add_argument('--imagetype', action=CommaSepAction,
help="Set DICOM image type, comma-separated list")
parser.add_argument('--input_options', action=DictAction,
help="Set input options (e.g. time=TriggerTime)",
default={
'time': 'AcquisitionTime',
'fa': 'FlipAngle',
'te': 'EchoTime'
})
parser.add_argument('--calling_aet',
help='Calling AEtitle',
default=None)
parser.add_argument('--correct_acq', action='store_true',
help="Correct acquisition time on dynamic series (DICOM only) "
"(implies --order time)")
parser.add_argument('--headers_only', action='store_true',
help="Read headers only")
parser.add_argument('--input_shape',
help="How to shape input data (t)x(z), e.g. 10x30 for 10 tags, 30 slices",
default=None)
parser.add_argument('--input_sort', action=SortOnAction,
help="Sort input file on slice or input order 'tag' (default: slice)",
choices=['slice', 'tag'], default=SORT_ON_SLICE)
parser.add_argument('-d', '--debug',
help="Print lots of debugging statements",
action="store_const", dest="loglevel",
const=logging.DEBUG,
default=logging.WARNING)
parser.add_argument('-v', '--verbose',
help="Be verbose",
action="store_const", dest="loglevel",
const=logging.INFO)
parser.add_argument('-V', '--version',
help='Show program version',
action='version',
version='{} {}'.format(sys.argv[0], __version__))