def test_load_deid(self):
print("Case 1: Test loading deid directly")
from deid.config import load_deid
config = load_deid(self.deid)
self.assertTrue('format' in config)
print("Case 2: Loading from folder")
config = load_deid(os.path.dirname(self.deid))
self.assertTrue('format' in config)
print("Case 3: Testing error on non-existing load")
with self.assertRaises(SystemExit) as cm:
config = load_deid(self.tmpdir)
self.assertEqual(cm.exception.code, 1)
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
if args.action == "all":
bot.info("GET and PUT identifiers from %s" % (basename))
do_get = True
do_put = True
elif args.action == "get":
do_get = True
bot.info("GET and PUT identifiers from %s" % (basename))
elif args.action == "put":
bot.info("PUT identifiers from %s" % (basename))
do_put = True
if args.ids is None:
bot.exit(
"To PUT without GET you must provide a json file with ids.")
ids = args.ids
# GET identifiers
if do_get is True:
ids = get_identifiers(dicom_files)
if do_put is True:
cleaned_files = replace_identifiers(
dicom_files=dicom_files,
ids=ids,
deid=args.deid,
overwrite=args.overwrite,
output_folder=output_folder,
)
bot.info("%s %s files at %s" %
(len(cleaned_files), args.format, output_folder))
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)
print("\nSUMMARY ================================\n")
if result["clean"]:
bot.custom(
prefix="CLEAN", message="%s files" % len(result["clean"]), color="CYAN"
)
if result["flagged"]:
for group, files in result["flagged"].items():
bot.flag("%s %s files" % (group, len(files)))
if args.save:
folders = "-".join([os.path.basename(folder) for folder in base])
outfile = "pixel-flag-results-%s-%s.tsv" % (
folders,
datetime.datetime.now().strftime("%y-%m-%d"),
)
with open(outfile, "w") as filey:
filey.writelines("dicom_file\tpixels_flagged\tflag_list\treason\n")
for clean in result["clean"]:
filey.writelines("%s\tCLEAN\t\t\n" % clean)
for flagged, details in result["flagged"].items():
if details["flagged"] is True:
for result in details["results"]:
group = result["group"]
reason = result["reason"]
filey.writelines(
"%s\tFLAGGED\t%s\t%s\n" % (flagged, group, reason)
)
print("Result written to %s" % outfile)
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
'''
# Global output folder
#output_folder = args.outfolder
#if output_folder is None:
# output_folder = tempfile.mkdtemp()
# 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)
print('\nSUMMARY ================================\n')
if len(result['clean']) > 0:
bot.custom(prefix='CLEAN',
message="%s files" % len(result['clean']),
color="CYAN")
if len(result['flagged']) > 0:
for group, files in result['flagged'].items():
bot.flag("%s %s files" % (group, len(files)))
if args.save is True:
folders = '-'.join([os.path.basename(folder) for folder in base])
outfile = "pixel-flag-results-%s-%s.tsv" % (
folders, datetime.datetime.now().strftime('%y-%m-%d'))
with open(outfile, 'w') as filey:
filey.writelines('dicom_file\tpixels_flagged\tflag_list\treason\n')
for clean in result['clean']:
filey.writelines('%s\tCLEAN\t\t\n' % clean)
for flagged, details in result['flagged'].items():
if details['flagged'] is True:
for result in details['results']:
group = result['group']
reason = result['reason']
filey.writelines('%s\tFLAGGED\t%s\t%s\n' %
(flagged, group, reason))
print('Result written to %s' % outfile)
def test_load_deid(self):
print("Case 1: Test loading deid directly")
from deid.config import load_deid
config = load_deid(self.deid)
self.assertTrue("format" in config)
print("Case 2: Loading from folder")
config = load_deid(os.path.dirname(self.deid))
self.assertTrue("format" in config)
print("Case 3: Testing error on non-existing load of file")
with self.assertRaises(SystemExit) as cm:
config = load_deid(os.path.join(self.tmpdir, "deid.doesnt-exist"))
self.assertEqual(cm.exception.code, 1)
print("Case 4: Testing load of default deid.")
config = load_deid(self.tmpdir)
#**
# Here you might save them in your special (IRB approvied) places
# And then provide replacement anonymous ids to put back in the data
# A cookie tumor example is below
#**
# Load your custom deid parameters (see deid folder under examples)
from deid.utils import get_installdir
from deid.config import load_deid
import os
path = os.path.abspath("%s/../examples/deid/" % get_installdir())
# If you are intereseted to see it, but you don't have to do this,
# this happens internally
deid = load_deid(path)
# Let's add the fields that we specify to add in our deid, a source_id for SOPInstanceUID,
# and an id for PatientID
count = 0
updated_ids = dict()
for image, fields in ids.items():
fields['id'] = 'cookiemonster'
fields['source_id'] = "cookiemonster-image-%s" % (count)
updated_ids[image] = fields
count += 1
# Run again, provided the path to deid, and the updated ids
cleaned_files = replace_identifiers(dicom_files=dicom_files,
deid=path,
ids=updated_ids)