def test_anonymise_directory():
temp_anon_filepath = label_dicom_filepath_as_anonymised(temp_filepath)
try:
makedirs(temp_dirpath, exist_ok=True)
copyfile(test_filepath, temp_filepath)
assert not is_anonymised_directory(temp_dirpath)
# Test file deletion
anonymise_directory(temp_dirpath,
delete_original_files=False,
anonymise_filenames=False)
# # File should be anonymised but not dir, since original file
# # is still present.
assert is_anonymised_file(temp_anon_filepath)
assert exists(temp_filepath)
assert not is_anonymised_directory(temp_dirpath)
remove_file(temp_anon_filepath)
anonymise_directory(temp_dirpath,
delete_original_files=True,
anonymise_filenames=False)
# # File and dir should be anonymised since original file should
# # have been deleted.
assert is_anonymised_file(temp_anon_filepath)
assert not exists(temp_filepath)
assert is_anonymised_directory(temp_dirpath)
finally:
remove_file(temp_anon_filepath)
remove_dir(temp_dirpath)
def compare_dicom_cli(command, original, expected):
# TODO: Extract CLI definition from subpackages and test separately
if "SUBPACKAGE" not in os.environ:
pydicom.write_file(ORIGINAL_DICOM_FILENAME, original)
try:
subprocess.check_call(command)
cli_adjusted_ds = pydicom.read_file(ADJUSTED_DICOM_FILENAME,
force=True)
assert str(cli_adjusted_ds) == str(expected)
finally:
remove_file(ORIGINAL_DICOM_FILENAME)
remove_file(ADJUSTED_DICOM_FILENAME)
def _check_is_anonymised_dataset_file_and_dir(
ds, tmp_path, anon_is_expected=True, ignore_private_tags=False
):
temp_filepath = str(tmp_path / "test.dcm")
try:
ds.is_little_endian = True
ds.is_implicit_VR = True
ds.file_meta = TEST_FILE_META
ds.save_as(temp_filepath, write_like_original=False)
if anon_is_expected:
assert is_anonymised_dataset(ds, ignore_private_tags)
assert is_anonymised_file(temp_filepath, ignore_private_tags)
assert is_anonymised_directory(tmp_path, ignore_private_tags)
else:
assert not is_anonymised_dataset(ds, ignore_private_tags)
assert not is_anonymised_file(temp_filepath, ignore_private_tags)
assert not is_anonymised_directory(tmp_path, ignore_private_tags)
finally:
remove_file(temp_filepath)
def _check_is_anonymised_dataset_file_and_dir(ds,
anon_is_expected=True,
ignore_private_tags=False):
try:
makedirs(temp_dirpath, exist_ok=True)
ds.is_little_endian = True
ds.is_implicit_VR = True
ds.file_meta = file_meta
ds.save_as(temp_filepath, write_like_original=False)
if anon_is_expected:
assert is_anonymised_dataset(ds, ignore_private_tags)
assert is_anonymised_file(temp_filepath, ignore_private_tags)
assert is_anonymised_directory(temp_dirpath, ignore_private_tags)
else:
assert not is_anonymised_dataset(ds, ignore_private_tags)
assert not is_anonymised_file(temp_filepath, ignore_private_tags)
assert not is_anonymised_directory(temp_dirpath,
ignore_private_tags)
finally:
remove_file(temp_filepath)
remove_dir(temp_dirpath)
def test_anonymise_file():
assert not is_anonymised_file(test_filepath)
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
temp_basename = "{}_{}.dcm".format(
'.'.join(test_filepath.split('.')[:-1]), uuid4())
temp_filepath = pjoin(dirname(test_filepath), temp_basename)
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_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_anonymise_cli():
try:
makedirs(temp_dirpath, exist_ok=True)
copyfile(test_filepath, temp_filepath)
temp_anon_filepath = pjoin(temp_dirpath, test_anon_basename)
# Basic file anonymisation
assert not is_anonymised_file(temp_filepath)
assert not exists(temp_anon_filepath)
anon_file_command = ('pymedphys dicom anonymise'.split() +
[temp_filepath])
try:
subprocess.check_call(anon_file_command)
assert is_anonymised_file(temp_anon_filepath)
assert exists(temp_filepath)
finally:
remove_file(temp_anon_filepath)
# File anonymisation - preserve filenames
assert not is_anonymised_file(temp_filepath)
expected_anon_filepath = label_dicom_filepath_as_anonymised(
temp_filepath)
assert not exists(expected_anon_filepath)
anon_file_pres_command = ('pymedphys dicom anonymise -f'.split() +
[temp_filepath])
try:
subprocess.check_call(anon_file_pres_command)
assert is_anonymised_file(expected_anon_filepath)
assert exists(temp_filepath)
finally:
remove_file(expected_anon_filepath)
# File anonymisation - clear values
assert not is_anonymised_file(temp_filepath)
assert not exists(temp_anon_filepath)
anon_file_clear_command = ('pymedphys dicom anonymise -c'.split() +
[temp_filepath])
try:
subprocess.check_call(anon_file_clear_command)
assert is_anonymised_file(temp_anon_filepath)
assert pydicom.dcmread(temp_anon_filepath).PatientName == ''
assert exists(temp_filepath)
finally:
remove_file(temp_anon_filepath)
# File anonymisation - leave keywords unchanged
assert not is_anonymised_file(temp_filepath)
assert not exists(temp_anon_filepath)
anon_file_keep_command = ('pymedphys dicom anonymise'.split() +
[temp_filepath] + '-k PatientName'.split())
try:
subprocess.check_call(anon_file_keep_command)
assert not is_anonymised_file(temp_anon_filepath)
ds = pydicom.dcmread(temp_anon_filepath)
ds.PatientName = "Anonymous"
assert is_anonymised_dataset(ds)
assert exists(temp_filepath)
finally:
remove_file(temp_anon_filepath)
# File anonymisation - private tag handling
assert not is_anonymised_file(temp_filepath)
assert not exists(temp_anon_filepath)
anon_file_private_command = ('pymedphys dicom anonymise -p'.split() +
[temp_filepath])
try:
subprocess.check_call(anon_file_private_command)
assert not is_anonymised_file(temp_anon_filepath)
assert is_anonymised_file(temp_anon_filepath,
ignore_private_tags=True)
assert exists(temp_filepath)
finally:
remove_file(temp_anon_filepath)
# TODO: File anonymisation - unknown tag handling
# # Calling a subprocess reloads BaselineDicomDictionary...
# Basic dir anonymisation
assert not is_anonymised_directory(DATA_DIR)
assert not exists(temp_anon_filepath)
anon_dir_command = ('pymedphys dicom anonymise'.split() +
[temp_dirpath])
try:
subprocess.check_call(anon_dir_command)
assert is_anonymised_file(temp_anon_filepath)
assert exists(temp_filepath)
finally:
remove_file(temp_anon_filepath)
finally:
remove_file(temp_filepath)
remove_dir(temp_dirpath)
def test_anonymise_cli(tmp_path):
temp_filepath = str(tmp_path / "test.dcm")
try:
copyfile(TEST_FILEPATH, temp_filepath)
temp_anon_filepath = str(tmp_path / TEST_ANON_BASENAME)
# Basic file anonymisation
assert not is_anonymised_file(temp_filepath)
assert not exists(temp_anon_filepath)
anon_file_command = "pymedphys dicom anonymise".split() + [temp_filepath]
try:
subprocess.check_call(anon_file_command)
assert is_anonymised_file(temp_anon_filepath)
assert exists(temp_filepath)
finally:
remove_file(temp_anon_filepath)
# File anonymisation - preserve filenames
assert not is_anonymised_file(temp_filepath)
expected_anon_filepath = label_dicom_filepath_as_anonymised(temp_filepath)
assert not exists(expected_anon_filepath)
anon_file_pres_command = "pymedphys dicom anonymise -f".split() + [
temp_filepath
]
try:
subprocess.check_call(anon_file_pres_command)
assert is_anonymised_file(expected_anon_filepath)
assert exists(temp_filepath)
finally:
remove_file(expected_anon_filepath)
# File anonymisation - clear values
assert not is_anonymised_file(temp_filepath)
assert not exists(temp_anon_filepath)
temp_cleared_anon_filepath = str(tmp_path / TEST_ANON_BASENAME)
anon_file_clear_command = "pymedphys dicom anonymise -c".split() + [
temp_filepath
]
try:
subprocess.check_call(anon_file_clear_command)
assert is_anonymised_file(temp_cleared_anon_filepath)
assert pydicom.dcmread(temp_cleared_anon_filepath).PatientName == ""
assert exists(temp_filepath)
finally:
remove_file(temp_cleared_anon_filepath)
# File anonymisation - leave keywords unchanged
assert not is_anonymised_file(temp_filepath)
assert not exists(temp_anon_filepath)
anon_file_keep_command = (
"pymedphys dicom anonymise".split()
+ [temp_filepath]
+ "-k PatientName".split()
)
try:
subprocess.check_call(anon_file_keep_command)
assert not is_anonymised_file(temp_anon_filepath)
ds = pydicom.dcmread(temp_anon_filepath)
ds.PatientName = "Anonymous"
assert is_anonymised_dataset(ds)
assert exists(temp_filepath)
finally:
remove_file(temp_anon_filepath)
# File anonymisation - private tag handling
assert not is_anonymised_file(temp_filepath)
assert not exists(temp_anon_filepath)
anon_file_private_command = "pymedphys dicom anonymise -p".split() + [
temp_filepath
]
try:
subprocess.check_call(anon_file_private_command)
assert not is_anonymised_file(temp_anon_filepath)
assert is_anonymised_file(temp_anon_filepath, ignore_private_tags=True)
assert exists(temp_filepath)
finally:
remove_file(temp_anon_filepath)
# TODO: File anonymisation - unknown tag handling
# # Calling a subprocess reloads BASELINE_DICOM_DICT...
# Basic dir anonymisation
assert not is_anonymised_directory(tmp_path)
assert not exists(temp_anon_filepath)
anon_dir_command = "pymedphys dicom anonymise".split() + [str(tmp_path)]
try:
subprocess.check_call(anon_dir_command)
assert is_anonymised_file(temp_anon_filepath)
assert exists(temp_filepath)
finally:
remove_file(temp_anon_filepath)
finally:
remove_file(temp_filepath)