Merge remote-tracking branch 'upstream/master' into other-vr-jitter

CHANGELOG.md

@@ -17,6 +17,7 @@ Referenced versions in headers are tagged on Github, in parentheses are for pypi
  - updated pydicom dependency from 1.3.0 to 2.1.1 [#171] (https://github.com/pydicom/deid/issues/171) (0.2.25)
  - bug fix for multivalued fields in %values lists [#174](https://github.com/pydicom/deid/issues/174)
  - allowing other VR types for jitter [#175](https://github.com/pydicom/deid/issues/175)
+ - ensuring that an add/replace of an existing value is also updated in fields [#173](https://github.com/pydicom/deid/issues/173)
  - change to correct issue with deidentifying RGB images [#165](https://github.com/pydicom/deid/issues/165) (0.2.24)
  - removing verbosity of debug logger (0.2.23)
  - changing iteration technique through fields to properly add nested uids [#153](https://github.com/pydicom/deid/issues/153) (0.2.22)

deid/dicom/header.py

@@ -127,7 +127,6 @@ def replace_identifiers(
     and saving new files. If you want to replace sequences, they need
     to be extracted with get_identifiers and expand_sequences to True.
     """
-
     if not isinstance(dicom_files, list):
         dicom_files = [dicom_files]
 

deid/dicom/parser.py

@@ -393,6 +393,7 @@ def add_field(self, field, value):
                     while not hasattr(element, "value"):
                         element = element.element
                     element.value = value
+                    self.dicom.add(element)
 
                 else:
                     element = DataElement(tag["tag"], tag["VR"], value)
@@ -426,6 +427,13 @@ def _run_action(self, field, action, value=None):
             )
             if value is not None:
 
+                # Cut out early if the field isn't in the dicom
+                if field.name not in self.dicom:
+                    return
+
+                # Preserve the old value in case we need to update
+                old_value = self.dicom[field.name].value
+
                 # Jitter the field by the supplied value
                 new_val = jitter_timestamp(field=field, value=value)
                 self.replace_field(field, new_val)

deid/tests/test_replace_identifiers.py

@@ -164,6 +164,41 @@ def test_replace_with_constant(self):
         self.assertEqual(newvalue1, result[0][newfield1].value)
         self.assertEqual(newvalue2, result[0][newfield2].value)
 
+    def test_jitter_replace_compounding(self):
+        """RECIPE RULE
+        JITTER AcquisitonDate 1
+        REPLACE AcquisitionDate 20210330
+        """
+
+        print("Test replace tags with constant values")
+        dicom_file = get_file(self.dataset)
+
+        newfield1 = "AcquisitionDate"
+        newvalue1 = "20210330"
+
+        actions = [
+            {"action": "JITTER", "field": newfield1, "value": "1"},
+            {"action": "REPLACE", "field": newfield1, "value": newvalue1},
+        ]
+        recipe = create_recipe(actions)
+
+        inputfile = read_file(dicom_file)
+        currentValue = inputfile[newfield1].value
+
+        self.assertNotEqual(newvalue1, currentValue)
+
+        result = replace_identifiers(
+            dicom_files=dicom_file,
+            deid=recipe,
+            save=True,
+            remove_private=False,
+            strip_sequences=False,
+        )
+
+        outputfile = read_file(result[0])
+        self.assertEqual(1, len(result))
+        self.assertEqual(newvalue1, outputfile[newfield1].value)
+
     def test_remove(self):
         """RECIPE RULE
         REMOVE InstitutionName