bug: Fix UID lookup and sequence field handling (#292)

* bug: Fix UID lookup and sequence field handling

Fix UID lookup for nested sequence fields in DICOM datasets

Previously, when processing DICOM sequence fields (VR=SQ), the UID lookup logic incorrectly handled nested items within sequences. This caused issues when trying to remove or manipulate specific nested fields using the field specification syntax like (0018,9346)__0__(0008,0104).

The fix ensures that:

Sequence fields with VR=SQ are properly identified and their items are correctly indexed
Each item within a sequence receives a proper UID that includes the parent sequence tag and item index
Nested fields can be targeted using the double-underscore notation with index (e.g., SequenceTag__ItemIndex__NestedTag)

* Update changelog and bump version

Author: Simlomb

CHANGELOG.md

@@ -14,6 +14,7 @@ and **Merged pull requests**. Critical items to know are:
 Referenced versions in headers are tagged on Github, in parentheses are for pypi.
 
 ## [vxx](https://github.com/pydicom/deid/tree/master) (master)
+- Fix UID lookup for nested sequence fields in DICOM datasets [#292](https://github.com/pydicom/deid/pull/292) (0.4.8)
 - Allow saving with a compressed transfer syntax [#290](https://github.com/pydicom/deid/pull/290) (0.4.7)
 - Improve performance of header deid with caching and lookup tables [#289](https://github.com/pydicom/deid/pull/289)
 - Fix REMOVE action to respect REPLACE or JITTER priority [#283](https://github.com/pydicom/deid/pull/283) (0.4.6)

deid/dicom/fields.py

@@ -329,6 +329,7 @@ def __init__(self, fields):
             "stripped_tag": defaultdict(list),
             "element_name": defaultdict(list),
             "element_keyword": defaultdict(list),
+            "uid": defaultdict(list),
         }
         for uid, field in fields.items():
             self._add_field_to_lookup(field)
@@ -347,6 +348,7 @@ def get_exact_matches(self, field):
             + self.lookup_tables["stripped_tag"][field]
             + self.lookup_tables["element_name"][field]
             + self.lookup_tables["element_keyword"][field]
+            + self.lookup_tables["uid"][field]
         )
         return exact_match_contenders
 
@@ -387,6 +389,8 @@ def _get_field_lookup_keys(self, field):
             lookup_keys["element_name"] = [field.element.name.lower()]
         if field.element.keyword:
             lookup_keys["element_keyword"] = [field.element.keyword.lower()]
+        if field.uid:
+            lookup_keys["uid"] = [field.uid.lower()]
         if field.element.is_private:
             lookup_keys["name"] = lookup_keys.get("name", []) + [
                 f'({field.element.tag.group:04X},"{field.element.private_creator}",{(field.element.tag.element & 0x00FF):02X})'.lower(),

deid/tests/test_remove_action.py

@@ -239,6 +239,38 @@ def test_remove_single_tag_private_creator_no_match(self):
         # Tag should still exist because private creator didn't match
         self.assertEqual(currentValue, outputfile[field_dicom].value)
 
+    def test_remove_specific_nested_sequence_tag(self):
+        """RECIPE RULE
+        REMOVE (0018,9346)__0__(0008,0104)
+        """
+        print("Test REMOVE specific nested sequence tag")
+        dicom_file = get_file(self.dataset)
+
+        Field = "(0018,9346)__0__(0008,0104)"  # Referenced SOP Instance UID inside Referenced Series Sequence
+        actions = [
+            {"action": "REMOVE", "field": Field},
+        ]
+        recipe = create_recipe(actions)
+
+        inputfile = utils.dcmread(dicom_file)
+        currentValue = inputfile["00189346"][0]["00080104"].value
+
+        self.assertNotEqual(None, currentValue)
+        self.assertNotEqual("", currentValue)
+
+        result = replace_identifiers(
+            dicom_files=dicom_file,
+            deid=recipe,
+            save=True,
+            remove_private=False,
+            strip_sequences=False,
+        )
+        outputfile = utils.dcmread(result[0])
+
+        self.assertEqual(1, len(result))
+        with self.assertRaises(KeyError):
+            _ = outputfile["00189346"][0]["00080104"].value
+
 
 if __name__ == "__main__":
     unittest.main()

deid/version.py

@@ -2,7 +2,7 @@
 __copyright__ = "Copyright 2016-2025, Vanessa Sochat"
 __license__ = "MIT"
 
-__version__ = "0.4.7"
+__version__ = "0.4.8"
 AUTHOR = "Vanessa Sochat"
 AUTHOR_EMAIL = "[email protected]"
 NAME = "deid"