def test_tags_to_anonymise_in_dicom_dict_baseline( save_new_identifying_keywords=False, save_new_baselines=False): baseline_keywords = [val[4] for val in get_baseline_dicom_dict().values()] assert set(IDENTIFYING_KEYWORDS).issubset(baseline_keywords) if save_new_identifying_keywords: with open(IDENTIFYING_KEYWORDS_FILEPATH, "w") as outfile: json.dump(IDENTIFYING_KEYWORDS, outfile, indent=2, sort_keys=True) # TODO: Keywords to add if/when anonymisation of UIDs is implemented: # "AffectedSOPInstanceUID", # "ConcatenationUID", # "ContextGroupExtensionCreatorUID", # "CreatorVersionUID", # "DeviceUID", # "DigitalSignatureUID", # "DimensionOrganizationUID", # "DoseReferenceUID", # "FailedSOPInstanceUIDList", # "FiducialUID", # "FrameOfReferenceUID", # "InstanceCreatorUID", # "IrradiationEventUID", # "LargePaletteColorLookupTableUID", # "MediaStorageSOPInstanceUID", # "PaletteColorLookupTableUID", # "ReferencedFrameOfReferenceUID", # "ReferencedGeneralPurposeScheduledProcedureStepTransactionUID", # "ReferencedSOPInstanceUID", # "ReferencedSOPInstanceUIDInFile", # "RelatedFrameOfReferenceUID", # "RequestedSOPInstanceUID", # "SeriesInstanceUID", # "SOPInstanceUID", # "StorageMediaFileSetUID", # "StudyInstanceUID", # "SynchronizationFrameOfReferenceUID", # "TemplateExtensionCreatorUID", # "TemplateExtensionOrganizationUID", # "TransactionUID", # "UID", if save_new_baselines: with open(BASELINE_DICOM_DICT_FILEPATH, "w") as outfile: json.dump(get_baseline_dicom_dict(), outfile, indent=2, sort_keys=True) with open(BASELINE_DICOM_REPEATERS_DICT_FILEPATH, "w") as outfile: json.dump(get_baseline_dicom_repeaters_dict(), outfile, indent=2, sort_keys=True)
def test_tags_to_anonymise_in_dicom_dict_baseline(save_new_identifying_keywords=False): baseline_keywords = [val[4] for val in get_baseline_dicom_dict().values()] assert set(IDENTIFYING_KEYWORDS).issubset(baseline_keywords) if save_new_identifying_keywords: with open(IDENTIFYING_KEYWORDS_FILEPATH, "w") as outfile: json.dump(IDENTIFYING_KEYWORDS, outfile, indent=2, sort_keys=True)
def test_anonymise_dataset_and_all_is_anonymised_functions(tmp_path): # Create dataset with one instance of every identifying keyword and # run basic anonymisation tests ds = pydicom.dataset.Dataset() for keyword in IDENTIFYING_KEYWORDS: # Ignore file meta elements for now tag = hex(pydicom.datadict.tag_for_keyword(keyword)) if pydicom.tag.Tag(tag).group == 0x0002: continue value = _get_non_anonymous_replacement_value(keyword) setattr(ds, keyword, value) _check_is_anonymised_dataset_file_and_dir(ds, tmp_path, anon_is_expected=False) ds_anon = anonymise_dataset(ds) _check_is_anonymised_dataset_file_and_dir(ds_anon, tmp_path, anon_is_expected=True) # Test the anonymisation and check functions for each identifying # element individually. for elem in ds_anon.iterall(): # TODO: AffectedSOPInstanceUID and RequestedSOPInstanceUID # are not writing to file. Investigate when UID anonymisation is # implemented. if elem.keyword in ("AffectedSOPInstanceUID", "RequestedSOPInstanceUID"): continue ds_single_non_anon_value = deepcopy(ds_anon) setattr( ds_single_non_anon_value, elem.keyword, _get_non_anonymous_replacement_value(elem.keyword), ) _check_is_anonymised_dataset_file_and_dir( ds_single_non_anon_value, tmp_path, anon_is_expected=False ) ds_single_anon = anonymise_dataset(ds_single_non_anon_value) _check_is_anonymised_dataset_file_and_dir( ds_single_anon, tmp_path, anon_is_expected=True ) # Test correct handling of private tags ds_anon.add(pydicom.dataset.DataElement(0x0043102B, "SS", [4, 4, 0, 0])) _check_is_anonymised_dataset_file_and_dir( ds_anon, tmp_path, anon_is_expected=False, ignore_private_tags=False ) _check_is_anonymised_dataset_file_and_dir( ds_anon, tmp_path, anon_is_expected=True, ignore_private_tags=True ) ds_anon.remove_private_tags() _check_is_anonymised_dataset_file_and_dir( ds_anon, tmp_path, anon_is_expected=True, ignore_private_tags=False ) # Test blank anonymisation # # Sanity check _check_is_anonymised_dataset_file_and_dir(ds, tmp_path, anon_is_expected=False) ds_anon_blank = anonymise_dataset(ds, replace_values=False) _check_is_anonymised_dataset_file_and_dir( ds_anon_blank, tmp_path, anon_is_expected=True ) # Test handling of unknown tags by removing PatientName from # baseline dict patient_name_tag = pydicom.datadict.tag_for_keyword("PatientName") try: patient_name = get_baseline_dicom_dict().pop(patient_name_tag) with pytest.raises(ValueError) as e_info: anonymise_dataset(ds) assert str(e_info.value).count( "At least one of the non-private tags " "within your DICOM file is not within " "PyMedPhys's copy of the DICOM dictionary." ) ds_anon_delete_unknown = anonymise_dataset(ds, delete_unknown_tags=True) _check_is_anonymised_dataset_file_and_dir( ds_anon_delete_unknown, tmp_path, anon_is_expected=True ) with pytest.raises(AttributeError) as e_info: ds_anon_delete_unknown.PatientName # pylint: disable = pointless-statement assert str(e_info.value).count( "'Dataset' object has no attribute " "'PatientName'" ) ds_anon_ignore_unknown = anonymise_dataset(ds, delete_unknown_tags=False) _check_is_anonymised_dataset_file_and_dir( ds_anon_ignore_unknown, tmp_path, anon_is_expected=True ) assert patient_name_tag in ds_anon_ignore_unknown finally: get_baseline_dicom_dict().setdefault(patient_name_tag, patient_name) # Test copy_dataset=False: anonymise_dataset(ds, copy_dataset=False) assert is_anonymised_dataset(ds)