From 5e1d163792db82f6cf17e41bece4a6fb4f0f56fc Mon Sep 17 00:00:00 2001
From: Andrey Fedorov <andrey.fedorov@gmail.com>
Date: Wed, 26 Jun 2024 10:59:21 -0400
Subject: [PATCH] initialize references

---
 libsrc/Itk2DicomConverter.cpp | 47 +++++++++++++++++++++++------------
 1 file changed, 31 insertions(+), 16 deletions(-)

diff --git a/libsrc/Itk2DicomConverter.cpp b/libsrc/Itk2DicomConverter.cpp
index 098d6c08..694cc9e4 100644
--- a/libsrc/Itk2DicomConverter.cpp
+++ b/libsrc/Itk2DicomConverter.cpp
@@ -109,6 +109,22 @@ namespace dcmqi {
       delete pixmsr;
     }
 
+    // Iterate over the files and labels available in each file, create a segment for each label,
+    // initialize segment frames and add to the document
+
+    OFString seriesInstanceUID, classUID;
+    set<OFString> instanceUIDs;
+
+    IODCommonInstanceReferenceModule &commref = segdoc->getCommonInstanceReference();
+    OFVector<IODSeriesAndInstanceReferenceMacro::ReferencedSeriesItem*> &refseries = commref.getReferencedSeriesItems();
+
+    IODSeriesAndInstanceReferenceMacro::ReferencedSeriesItem* refseriesItem = new IODSeriesAndInstanceReferenceMacro::ReferencedSeriesItem;
+
+    OFVector<SOPInstanceReferenceMacro*> &refinstances = refseriesItem->getReferencedInstanceItems();
+
+    CHECK_COND(dcmDatasets[0]->findAndGetOFString(DCM_SeriesInstanceUID, seriesInstanceUID));
+    CHECK_COND(refseriesItem->setSeriesInstanceUID(seriesInstanceUID));
+
     // Shared FGs: DerivationImageSequence
     if(!referencesGeometryCheck && dcmDatasets.size() > 1){
       FGDerivationImage *fgder = new FGDerivationImage();
@@ -122,26 +138,25 @@ namespace dcmqi {
       derimgItem->addSourceImageItems(dcmDatasets, 
         CodeSequenceMacro(code_seg.CodeValue,code_seg.CodingSchemeDesignator, code_seg.CodeMeaning), srcimgItems, OFTrue /*skip file errors */);
 
+      for(size_t src_image_cnt=0;src_image_cnt<srcimgItems.size();src_image_cnt++){
+        // initialize class UID and series instance UID
+        ImageSOPInstanceReferenceMacro &instRef = srcimgItems[src_image_cnt]->getImageSOPInstanceReference();
+        OFString instanceUID;
+        CHECK_COND(instRef.getReferencedSOPClassUID(classUID));
+        CHECK_COND(instRef.getReferencedSOPInstanceUID(instanceUID));
+
+        if(instanceUIDs.find(instanceUID) == instanceUIDs.end()){
+          SOPInstanceReferenceMacro *refinstancesItem = new SOPInstanceReferenceMacro();
+          CHECK_COND(refinstancesItem->setReferencedSOPClassUID(classUID));
+          CHECK_COND(refinstancesItem->setReferencedSOPInstanceUID(instanceUID));
+          refinstances.push_back(refinstancesItem);
+          instanceUIDs.insert(instanceUID);
+        }
+      }
       CHECK_COND(segdoc->addForAllFrames(*fgder));
       delete fgder;
     }
 
-    // Iterate over the files and labels available in each file, create a segment for each label,
-    // initialize segment frames and add to the document
-
-    OFString seriesInstanceUID, classUID;
-    set<OFString> instanceUIDs;
-
-    IODCommonInstanceReferenceModule &commref = segdoc->getCommonInstanceReference();
-    OFVector<IODSeriesAndInstanceReferenceMacro::ReferencedSeriesItem*> &refseries = commref.getReferencedSeriesItems();
-
-    IODSeriesAndInstanceReferenceMacro::ReferencedSeriesItem* refseriesItem = new IODSeriesAndInstanceReferenceMacro::ReferencedSeriesItem;
-
-    OFVector<SOPInstanceReferenceMacro*> &refinstances = refseriesItem->getReferencedInstanceItems();
-
-    CHECK_COND(dcmDatasets[0]->findAndGetOFString(DCM_SeriesInstanceUID, seriesInstanceUID));
-    CHECK_COND(refseriesItem->setSeriesInstanceUID(seriesInstanceUID));
-
     int uidfound = 0, uidnotfound = 0;
     Uint8 *frameData = new Uint8[frameSize];