def test_reject_kogsps_fail(dataset):
"""Datasets that should be rejected"""
with pytest.raises(DeidentificationException):
Core(profile=Profile(rule_sets=[]), bouncers=[RejectKOGSPS()]).deidentify(
dataset
)
def create_core(profile: Profile, location_list: PIILocationList = None,) -> Core:
"""A deidentification core with defaults
Which rejects non-standard dicom and encapsulated pdfs
and inserts some tags that indicate deidentification has been performed
Parameters
----------
profile: Profile,
The deidentification profile to use
location_list: PIILocationList, optional
Definition of where to remove burnt in information from images.
Defaults to simply rejecting all datasets that might have burnt in
information
"""
# insert some info on what type of deidentification was performed
insertions = [
get_idis_code_sequence([x.name for x in profile.rule_sets]),
PATIENT_IDENTITY_REMOVED,
get_deidentification_method(),
]
bouncers = [RejectEncapsulatedImageStorage(), RejectNonStandardDicom()]
core = Core(
profile=profile,
insertions=insertions,
bouncers=bouncers,
pixel_processor=PixelProcessor(PIILocationList(location_list)),
)
return core
def test_core_description():
"""Human readable answer to the question 'what does this deidentifier do?'"""
sets = DICOMRuleSets()
profile = Profile(rule_sets=[
sets.basic_profile,
sets.clean_descriptors,
sets.clean_graphics,
sets.retain_modified_dates,
sets.retain_safe_private,
])
final_set = profile.flatten()
assert len(final_set.rules) == 442
core = Core(profile=profile, bouncers=[RejectKOGSPS])
test = core.description()
print(test)
def test_realistic_profile():
"""Run a file through a profile that has several options"""
sets = DICOMRuleSets()
profile = Profile(rule_sets=[
sets.basic_profile,
sets.clean_descriptors,
sets.clean_graphics,
sets.retain_modified_dates,
sets.retain_safe_private,
])
final_set = profile.flatten()
assert len(final_set.rules) == 442
core = Core(profile=profile)
dataset = CTDatasetFactory()
original = deepcopy(dataset)
deidentified = core.deidentify(dataset)
assert original.PatientID != deidentified.PatientID
def test_reject_non_standard():
a_core = Core(profile=Profile(rule_sets=[]), bouncers=[RejectNonStandardDicom()])
# this should not raise anything
a_core.deidentify(quick_dataset(SOPClassUID="1.2.840.10008"))
with pytest.raises(DeidentificationException):
a_core.deidentify(quick_dataset(SOPClassUID="123"))
def test_core_deidentify_safe_private(a_dataset, a_safe_private_definition):
"""Private elements marked as safe should not be removed by Clean()"""
assert Tag("00b10010") in a_dataset # a private creator tag
assert Tag("00b11001") in a_dataset # and a private tag
# A core instance that should clean() private tags, but one tag is deemed safe
ruleset = RuleSet(
[Rule(PrivateTags(), Clean(safe_private=a_safe_private_definition))])
core = Core(profile=Profile([ruleset]))
# One tag should be kept
deltas = extract_signature(deidentifier=core, dataset=a_dataset)
assert {x.tag: x for x in deltas}[Tag("00b10010")].status == "REMOVED"
assert {x.tag: x for x in deltas}[Tag("00b11001")].status == "UNCHANGED"
# but only so long as dataset has modality = CT
a_dataset.Modality = "US"
deltas = extract_signature(deidentifier=core, dataset=a_dataset)
assert {x.tag: x for x in deltas}[Tag("00b10010")].status == "REMOVED"
assert {x.tag: x for x in deltas}[Tag("00b11001")].status == "REMOVED"
"""You can set your own rules for specific DICOM tags. Be aware that this might
mean the deidentification is no longer DICOM-complient
"""
import pydicom
from idiscore.core import Core, Profile
from idiscore.defaults import get_dicom_rule_sets
from idiscore.identifiers import RepeatingGroup, SingleTag
from idiscore.operators import Hash, Remove
from idiscore.rules import Rule, RuleSet
# Custom rules that will hash the patient name and remove all curve data
my_ruleset = RuleSet(
rules=[
Rule(SingleTag("PatientName"), Hash()),
Rule(RepeatingGroup("50xx,xxxx"), Remove()),
],
name="My Custom RuleSet",
)
sets = get_dicom_rule_sets() # Contains official DICOM deidentification rules
profile = Profile( # add custom rules to basic profile
rule_sets=[sets.basic_profile, my_ruleset])
core = Core(profile) # Create an deidentification core
# read a DICOM dataset from file and write to another
core.deidentify(pydicom.read("my_file.dcm")).save_as("deidentified.dcm")
def test_reject_kogsps_pass(dataset):
"""Datasets that should be passed"""
# should not raise exceptions
assert Core(profile=Profile(rule_sets=[]), bouncers=[RejectKOGSPS()]).deidentify(
dataset
)
def a_core_with_some_rules(some_rules) -> Core:
"""Core instance with a three-rule profile"""
return Core(profile=Profile([RuleSet(some_rules)]))