Merge pull request #85 from howardpchen/fix/jitter_timestamp

jitter_timestamp with variable name change

deid/dicom/actions.py

@@ -41,6 +41,7 @@
 import os
 import re
 import sys
+import datetime
 
 
 # Actions
@@ -118,7 +119,7 @@ def _perform_action(dicom, field, action, value=None, item=None):
             if value is not None:
 
                 # Jitter the field by the supplied value
-                dicom = jitter_timestamp(item=dicom,
+                dicom = jitter_timestamp(dicom=dicom,
                                          field=field,
                                          value=value)
             else:
@@ -156,6 +157,35 @@ def jitter_timestamp(dicom, field, value):
         value = int(value)
 
     original = dicom.get(field,None)
+
     if original is not None:
-        dicom[field] = original + value
+        dcmvr = dicom.data_element(field).VR
+        '''
+        DICOM Value Representation can be either DA (Date) DT (Timestamp),
+        or something else, which is not supported.
+        '''
+        if (dcmvr == 'DA'):
+            '''
+            NEMA-compliant format for DICOM date is YYYYMMDD
+            '''
+            new_value = get_timestamp(original, jitter_days=value, 
+                                      format='%Y%m%d')
+
+        elif (dcmvr == 'DT'):
+            '''
+            NEMA-compliant format for DICOM timestamp is
+            YYYYMMDDHHMMSS.FFFFFF&ZZXX
+            '''
+            new_value = get_timestamp(original, jitter_days=value,
+                                      format='%Y%m%d%H%M%S.%f%z')
+        else:
+            # Do nothing and issue a warning.
+            new_value = None
+            bot.warning("JITTER not supported for %s with VR=%s" % (field, 
+                                                                    dcmvr))
+        if (new_value is not None and new_value != original):
+            # Only update if there's something to update AND there's been change
+            dicom = update_tag(dicom,
+                               field=field,
+                               value=new_value)
     return dicom

deid/tests/test_dicom_utils.py

@@ -160,6 +160,61 @@ def generate_uid(item, value, field):
         updated = perform_action(dicom=dicom, action=ACTION, item=item)
         self.assertEqual(updated.PatientID, "pancakes")
 
+    def test_jitter_timestamp(self):
+
+        from deid.dicom.actions import jitter_timestamp
+        dicom = get_dicom(self.dataset)
+
+        print("Testing test_jitter_timestamp")
+
+        print("Case 1: Testing jitter_timestamp with DICOM Date (DA)")
+        dicom.StudyDate = '20131210'
+        dicom.data_element("StudyDate").VR = 'DA'
+        jitter_timestamp(dicom, "StudyDate", 10) 
+        expected = '20131220'
+        self.assertEqual(dicom.StudyDate, expected)
+
+        print("Case 2: Testing with DICOM timestamp (DT)")
+        dicom.AcquisitionDateTime = '20131210081530'
+        dicom.data_element("AcquisitionDateTime").VR = 'DT'
+        jitter_timestamp(dicom, "AcquisitionDateTime", 10) 
+        expected = '20131220081530.000000' 
+        self.assertEqual(dicom.AcquisitionDateTime, expected)
+
+        print("Case 3: Testing with non-standard DICOM date (DA)")
+        dicom.StudyDate = '2013/12/10'
+        dicom.data_element("StudyDate").VR = 'DA'
+        jitter_timestamp(dicom, "StudyDate", 10) 
+        expected = '20131220'
+        self.assertEqual(dicom.StudyDate, expected)
+
+        print("Case 4: Testing negative jitter value")
+        dicom.StudyDate = '20131210'
+        jitter_timestamp(dicom, "StudyDate", -5) 
+        expected = '20131205'
+        self.assertEqual(dicom.StudyDate, expected)
+
+        print("Case 5: Testing with empty field")
+        dicom.StudyDate = expected = ''
+        jitter_timestamp(dicom, "StudyDate", 10) 
+        self.assertEqual(dicom.StudyDate, expected)
+
+        print('Case 6: Testing with nonexistent field')
+        del dicom.StudyDate
+        jitter_timestamp(dicom, "StudyDate", 10) 
+        self.assertTrue("StudyDate" not in dicom)  
+
+        print("Case 7: Testing JITTER recipe action")
+        from deid.dicom.actions import perform_action
+        dicom.StudyDate = '20131210'
+        dicom.data_element("StudyDate").VR = 'DA'
+        JITTER = { "action":"JITTER",
+                   "field":"StudyDate",
+                   "value":"-5" } 
+        expected = '20131205'
+        dicom = perform_action(dicom=dicom,action=JITTER)
+        self.assertTrue(dicom.StudyDate, expected)  
+
 
 def get_dicom(dataset):
     '''helper function to load a dicom