def anonymise_with_pseudo_cli(args):
if args.delete_unknown_tags:
handle_unknown_tags = True
elif args.ignore_unknown_tags:
handle_unknown_tags = False
else:
handle_unknown_tags = None
if not args.keywords_to_leave_unchanged:
keywords_to_leave_unchanged = ()
else:
keywords_to_leave_unchanged = args.keywords_to_leave_unchanged
replacement_strategy = None
if args.pseudo:
logging.info("Was run with pseudo!")
identifying_keywords_for_pseudo = get_default_pseudonymisation_keywords(
)
logging.info("Using pseudonymisation keywords")
replacement_strategy = strategy.pseudonymisation_dispatch
logging.info("Using pseudonymisation strategy")
if isfile(args.input_path):
anonymise_file(
dicom_filepath=args.input_path,
output_filepath=args.output_path,
delete_original_file=args.delete_original_files,
anonymise_filename=not args.preserve_filenames,
replace_values=not args.clear_values,
keywords_to_leave_unchanged=keywords_to_leave_unchanged,
delete_private_tags=not args.keep_private_tags,
delete_unknown_tags=handle_unknown_tags,
replacement_strategy=replacement_strategy,
identifying_keywords=identifying_keywords_for_pseudo,
)
elif isdir(args.input_path):
anonymise_directory(
dicom_dirpath=args.input_path,
output_dirpath=args.output_path,
delete_original_files=args.delete_original_files,
anonymise_filenames=not args.preserve_filenames,
replace_values=not args.clear_values,
keywords_to_leave_unchanged=keywords_to_leave_unchanged,
delete_private_tags=not args.keep_private_tags,
delete_unknown_tags=handle_unknown_tags,
replacement_strategy=replacement_strategy,
identifying_keywords=identifying_keywords_for_pseudo,
)
else:
raise FileNotFoundError(
"No file or directory was found at the supplied input path.")
def test_anonymise_file():
assert not is_anonymised_file(TEST_FILEPATH)
temp_basename = "{}_{}.dcm".format(".".join(TEST_FILEPATH.split(".")[:-1]),
uuid4())
temp_filepath = pjoin(dirname(TEST_FILEPATH), temp_basename)
anon_private_filepath = ""
anon_filepath_orig = ""
anon_filepath_pres = ""
try:
# Private tag handling
anon_private_filepath = anonymise_file(TEST_FILEPATH,
delete_private_tags=False)
assert not is_anonymised_file(anon_private_filepath,
ignore_private_tags=False)
assert is_anonymised_file(anon_private_filepath,
ignore_private_tags=True)
anon_private_filepath = anonymise_file(TEST_FILEPATH,
delete_private_tags=True)
assert is_anonymised_file(anon_private_filepath,
ignore_private_tags=False)
# Filename is anonymised?
assert basename(anon_private_filepath) == TEST_ANON_BASENAME
# Deletion of original file
copyfile(TEST_FILEPATH, temp_filepath)
anon_filepath_orig = anonymise_file(temp_filepath,
delete_original_file=True)
assert is_anonymised_file(anon_filepath_orig)
assert not exists(temp_filepath)
# Preservation of filename if desired
expected_filepath = "{}_Anonymised.dcm".format(".".join(
TEST_FILEPATH.split(".")[:-1]))
anon_filepath_pres = anonymise_file(TEST_FILEPATH,
anonymise_filename=False)
assert anon_filepath_pres == expected_filepath
finally:
remove_file(temp_filepath)
remove_file(anon_private_filepath)
remove_file(anon_filepath_orig)
remove_file(anon_filepath_pres)
def test_alternative_identifying_keywords():
alternative_keyword_list = copy.copy(get_default_identifying_keywords())
alternative_keyword_list.append("SOPInstanceUID")
test_file_path = get_treatment_record_test_file_path()
ds_test = pydicom.dcmread(test_file_path, force=True)
with tempfile.TemporaryDirectory() as output_directory:
anon_private_filepath = anonymise_file(
test_file_path,
output_filepath=output_directory,
delete_private_tags=True,
identifying_keywords=alternative_keyword_list,
)
ds_anon = pydicom.dcmread(anon_private_filepath, force=True)
assert is_anonymised_file(anon_private_filepath, ignore_private_tags=False)
assert ds_test["SOPInstanceUID"].value != ds_anon["SOPInstanceUID"].value
def _test_pseudonymise_file_at_path(
test_file_path, test_identifying_keywords=None, test_replacement_strategy=None
):
assert not is_anonymised_file(test_file_path)
if test_identifying_keywords is None:
identifying_keywords_for_pseudo = (
pseudonymisation_api.get_default_pseudonymisation_keywords()
)
logging.info("Using pseudonymisation keywords")
else:
identifying_keywords_for_pseudo = test_identifying_keywords
if test_replacement_strategy is None:
replacement_strategy = pseudonymisation_api.pseudonymisation_dispatch
logging.info("Using pseudonymisation strategy")
else:
replacement_strategy = test_replacement_strategy
with tempfile.TemporaryDirectory() as output_directory:
pseudonymised_file_path = anonymise_file(
dicom_filepath=test_file_path,
output_filepath=output_directory,
delete_original_file=False,
anonymise_filename=True,
replace_values=True,
# keywords_to_leave_unchanged=None,
delete_private_tags=True,
delete_unknown_tags=True,
replacement_strategy=replacement_strategy,
identifying_keywords=identifying_keywords_for_pseudo,
)
# debug print + Assert to force the print
# print("Pseudonymised file at: ", pseudonymised_file_path)
# assert False
assert exists(pseudonymised_file_path)
ds_input = pydicom.dcmread(test_file_path, force=True)
ds_pseudo = pydicom.dcmread(pseudonymised_file_path, force=True)
# simplistic stand-in to make sure *something* is happening
assert ds_input["PatientID"].value != ds_pseudo["PatientID"].value
# make sure that we are not accidentally using the hardcode replacement approach
assert ds_pseudo["PatientID"].value not in ["", "Anonymous"]
