def test_remove_all_func(self):
"""
%header
REMOVE ALL func:contains_hibbard
"""
print("Test tag removal by")
dicom_file = get_file(self.dataset)
def contains_hibbard(dicom, value, field, item):
from pydicom.tag import Tag
tag = Tag(field.element.tag)
if tag in dicom:
currentvalue = str(dicom.get(tag).value).lower()
if "hibbard" in currentvalue:
return True
return False
actions = [{
"action": "REMOVE",
"field": "ALL",
"value": "func:contains_hibbard"
}]
recipe = create_recipe(actions)
# Create a parser, define function for it
parser = DicomParser(dicom_file, recipe=recipe)
parser.define("contains_hibbard", contains_hibbard)
parser.parse()
self.assertEqual(156, len(parser.dicom))
with self.assertRaises(KeyError):
check1 = parser.dicom["ReferringPhysicianName"].value
with self.assertRaises(KeyError):
check2 = parser.dicom["PhysiciansOfRecord"].value
with self.assertRaises(KeyError):
check3 = parser.dicom["RequestingPhysician"].value
with self.assertRaises(KeyError):
check4 = parser.dicom["00331019"].value
def test_extract_groups(self):
print("Test deid.dicom.groups extract_values_list")
from deid.dicom.groups import extract_values_list, extract_fields_list
dicom = get_dicom(self.dataset)
fields = get_fields(dicom)
# Test split action
actions = [{
"action": "SPLIT",
"field": "PatientID",
"value": 'by="^";minlength=4'
}]
expected_names = dicom.get("PatientID").split("^")
actual = extract_values_list(dicom, actions)
self.assertEqual(actual, expected_names)
# Test field action
actions = [{"action": "FIELD", "field": "startswith:Operator"}]
expected_operator = [
x.element.value for uid, x in fields.items()
if x.element.keyword.startswith("Operator")
]
actual = extract_values_list(dicom, actions)
self.assertEqual(actual, expected_operator)
print("Test deid.dicom.groups extract_fields_list")
actions = [{"action": "FIELD", "field": "contains:Instance"}]
expected = {
uid: x
for uid, x in fields.items() if "Instance" in x.element.keyword
}
actual = extract_fields_list(dicom, actions)
for uid in expected:
assert uid in actual
# Get identifiers for file
ids = get_identifiers(dicom)
self.assertTrue(isinstance(ids, dict))
# Add keys to be used for replace to ids - these first are for values
parser = DicomParser(dicom, recipe=self.deid)
parser.define("cookie_names", expected_names)
parser.define("operator_names", expected_operator)
# This is for fields
parser.define("instance_fields", expected)
parser.define("id", "new-cookie-id")
parser.define("source_id", "new-operator-id")
parser.parse()
# Were the changes made?
assert parser.dicom.get("PatientID") == "new-cookie-id"
assert parser.dicom.get("OperatorsName") == "new-operator-id"
# Instance fields should be removed based on recipe
for uid, field in parser.lookup["instance_fields"].items():
self.assertTrue(field.element.keyword not in parser.dicom)
# Start over
dicom = get_dicom(self.dataset)
# We need to provide ids with variables "id" and "source_id"
ids = {
dicom.filename: {
"id": "new-cookie-id",
"source_id": "new-operator-id"
}
}
# Returns list of updated dicom, since save is False
replaced = replace_identifiers(dicom,
save=False,
deid=self.deid,
ids=ids)
cleaned = replaced.pop()
self.assertEqual(cleaned.get("PatientID"), "new-cookie-id")
self.assertEqual(cleaned.get("OperatorsName"), "new-operator-id")