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import os
import odil
def add_subparser(subparsers):
parser = subparsers.add_parser(
"dicomdir",
help="Create a DICOMDIR")
parser.add_argument(
"names", nargs="+", metavar="name", help="DICOM files or directories")
parser.add_argument(
"directory", help="Output directory for the DICOMDIR file")
parser.add_argument(
"--patient-key", "-p", default=[], action="append",
help="User-defined keys for PATIENT-level records, "
"expressed as KEYWORD[:TYPE]. TYPE defaults to 3.")
parser.add_argument(
"--study-key", "-S", default=[], action="append",
help="User-defined keys for STUDY-level records")
parser.add_argument(
"--series-key", "-s", default=[], action="append",
help="User-defined keys for SERIES-level records")
parser.add_argument(
"--image-key", "-i", default=[], action="append",
help="User-defined keys for IMAGE-level records")
parser.set_defaults(function=create_dicomdir)
return parser
def create_dicomdir(
names, directory, patient_key, study_key, series_key, image_key):
files = []
for name in names:
if os.path.isfile(name):
files.append(os.path.abspath(name))
elif os.path.isdir(name):
for dirpath, _, filenames in os.walk(name):
dirpath = os.path.abspath(dirpath)
filenames = [os.path.join(dirpath, x) for x in filenames]
dicom_files = []
for filename in filenames:
try:
odil.Reader.read_file(
filename, halt_condition=lambda x: True)
except Exception:
# Not a DICOM file
pass
else:
dicom_files.append(filename)
files.extend(dicom_files)
directory = os.path.abspath(directory)
if not all(x.startswith(directory) for x in files):
raise Exception("All files must be under {}".format(directory))
files = [x[len(directory)+1:] for x in files]
keys = {}
for level in ["patient", "study", "series", "image"]:
for entry in locals()["{}_key".format(level)]:
if ":" in entry:
tag, type_ = entry.split(":")
else:
tag, type_ = entry, "3"
tag = getattr(odil.registry, tag)
type_ = int(type_)
keys.setdefault(level.upper(), []).append((tag, type_))
creator = odil.BasicDirectoryCreator(directory, files, keys)
creator()
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