Pydcmio Dicomreader

Example automatically generated from package script.

# System import
from __future__ import print_function
import argparse
import os

# Bredala import
try:
    import bredala
    bredala.USE_PROFILER = False
    bredala.register("pydcmio.dcmreader.reader",
                     names=["get_values"])
except:
    pass

# Dcmio import
from pydcmio import __version__ as version
from pydcmio.dcmreader.reader import walk
from pydcmio.dcmreader.reader import get_values
from pydcmio.dcmreader.reader import STANDARD_EXTRACTOR

# Parameters to keep trace
__hopla__ = ["tool", "version"]


# Script documentation
doc = """
Dicom reader and value extractor
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This code enables us to extract any kind of information from a Dicom file.

Dicom field sequences are parsed recursively (deep search) to handle
enhanced storage parsing.

Steps:

Chose which mode you want to use:

* free (you provide the dicom tags)
* guided (tags are automatically provided)

Command:

python $HOME/git/pydcmio/pydcmio/scripts/pydcmio_dicomreader \
    -t 0x0018 0x1312 \
    -f /volatile/nsap/dcm2nii/dicom/dcm.dcm \
    -s

or

python $HOME/git/pydcmio/pydcmio/scripts/pydcmio_dicomreader \
    -a get_sequence_name \
    -f /volatile/nsap/dcm2nii/dicom/dcm.dcm
"""


def is_file(filearg):
    """ Type for argparse - checks that output file exists.
    """
    if not os.path.isfile(filearg):
        raise argparse.ArgumentError(
            "The file '{0}' does not exist!".format(filearg))
    return filearg


parser = argparse.ArgumentParser(description=doc)
parser.add_argument(
    "-v", "--verbose", dest="verbose", type=int, choices=[0, 1, 2], default=0,
    help="increase the verbosity level: 0 silent, [1, 2] verbose.")
group = parser.add_mutually_exclusive_group()
group.add_argument(
    "-t", "--tag", dest="dcmtag",
    help=("the tags you wich to extract from the dicom file, string such as "
          "type(repr(<tag>)) == tuple."),
    type=str, nargs=2)
group.add_argument(
    "-a", "--extractor", dest="extractor", choices=STANDARD_EXTRACTOR.keys(),
    help="use an already provided extractor: {}".format(
        STANDARD_EXTRACTOR.keys()))
parser.add_argument(
    "-f", "--dcmfile", dest="dcmfile", required=True, metavar="PATH",
    help="the dicom file to parse",
    type=is_file)
parser.add_argument(
    "-s", "--stack", dest="stack", action="store_true",
    help=("if specified, the output file will contain all values that "
          "correspond to a given tag, not only the first one."))
args = parser.parse_args()

Welcome message

if args.verbose > 0:
    print("[info] Start dicom tag extraction...")
    print("[info] Dicom file: {0}.".format(args.dcmfile))

Get tag

if args.dcmtag:
    print(args.dcmtag, ": ",
          walk(args.dcmfile, args.dcmtag, stack_values=args.stack))

Get extractor

if args.extractor:
    print(args.extractor, STANDARD_EXTRACTOR[args.extractor], ": ",
          get_values(args.dcmfile, args.extractor))

Total running time of the script: ( 0 minutes 0.000 seconds)