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sys.exit(0)
# Initialize the message bot, with level above
from deid.logger import bot
from deid.dicom import get_files
from deid.data import get_dataset
output_folder = args.outfolder
if output_folder is None:
if args.do_print is False:
output_folder = tempfile.mkdtemp()
# If a deid is given, check against format
if args.deid is not None:
from deid.config import load_deid
params = load_deid(args.deid)
if params['format'] != args.format:
bot.error("Format in deid (%s) doesn't match choice here (%s) exiting." %(params['format'],
args.format))
# Get list of dicom files
base = args.folder
if base is None:
bot.info("No input folder specified, will use demo dicom-cookies.")
base = get_dataset('dicom-cookies')
basename = os.path.basename(base)
dicom_files = get_files(base)
# Does the user want to inspect files?
if args.action == "inspect":
from deid.dicom import has_burned_pixels
has_burned_pixels(dicom_files)
def main(args, parser):
# Global output folder
output_folder = args.outfolder
if output_folder is None:
output_folder = tempfile.mkdtemp()
# If a deid is given, check against format
if args.deid is not None:
params = load_deid(args.deid)
if params["format"] != args.format:
bot.error(
"Format in deid (%s) doesn't match choice here (%s) exiting."
% (params["format"], args.format)
)
# Get list of dicom files
base = args.input
if base is None:
bot.info("No input folder specified, will use demo dicom-cookies.")
base = get_dataset("dicom-cookies")
basename = os.path.basename(base)
dicom_files = list(get_files(base)) # todo : consider using generator functionality
do_get = False
do_put = False
ids = None
def main(args, parser):
"""inspect currently serves to inspect the header fields of a set
of dicom files against a standard, and flag images that don't
pass the different levels of criteria
"""
# If a deid is given, check against format
deid = args.deid
if deid is not None:
params = load_deid(deid)
if params["format"] != args.format:
bot.error(
"Format in deid (%s) doesn't match choice here (%s) exiting."
% (params["format"], args.format)
)
# Get list of dicom files
base = args.folder
if base is None:
bot.info("No input folder specified, will use demo dicom-cookies.")
base = get_dataset("dicom-cookies")
dicom_files = list(
get_files(base, pattern=args.pattern)
) # todo : consider using generator functionality
result = has_burned_pixels(dicom_files, deid=deid)