Merge branch 'master' of /home/dsarrut/clitk3.server

[clitk.git] / common / clitkDicomRT_ROI.cxx

diff --git a/common/clitkDicomRT_ROI.cxx b/common/clitkDicomRT_ROI.cxx
index 25a2f4322548a1de065c220654352490d7368219..73d25b99cf038934b5479b61edca6237e74e9075 100644 (file)
--- a/common/clitkDicomRT_ROI.cxx
+++ b/common/clitkDicomRT_ROI.cxx
@@ -36,7 +36,7 @@ clitk::DicomRT_ROI::DicomRT_ROI()
   mMeshIsUpToDate = false;
   mBackgroundValue = 0;
   mForegroundValue = 1;
-  mZDelta = 0;
+  SetDicomUptodateFlag(false);
 }
 //--------------------------------------------------------------------
 
@@ -135,21 +135,38 @@ double clitk::DicomRT_ROI::GetForegroundValueLabelImage() const
 
 //--------------------------------------------------------------------
 #if GDCM_MAJOR_VERSION == 2
-void clitk::DicomRT_ROI::Read(std::map<int, std::string> & rois, gdcm::Item const & item)
+bool clitk::DicomRT_ROI::Read(gdcm::Item * itemInfo, gdcm::Item * itemContour)
 {
-  const gdcm::DataSet& nestedds = item.GetNestedDataSet();
-
+  // Keep dicom item
+  mItemInfo = itemInfo;
+  mItemContour = itemContour;
+  // DD(mItemInfo);
+  
+  // ROI number [Referenced ROI Number]
+  const gdcm::DataSet & nesteddsInfo = mItemInfo->GetNestedDataSet();
+  gdcm::Attribute<0x3006,0x0022> roinumber;
+  roinumber.SetFromDataSet( nesteddsInfo );
+  int nb1 = roinumber.GetValue();
+  
+  // Check this is the same with the other item
+  const gdcm::DataSet & nestedds = mItemContour->GetNestedDataSet();
   gdcm::Attribute<0x3006,0x0084> referencedroinumber;
   referencedroinumber.SetFromDataSet( nestedds );
-  // Change number if needed
-
-  // TODO
-
-  // ROI number [Referenced ROI Number]
-  mNumber = referencedroinumber.GetValue();
+  int nb2 = referencedroinumber.GetValue();
+  
+  // Must never be different
+  if (nb1 != nb2) {
+    DD(nb2);
+    DD(nb1);
+    FATAL("nb1 must equal nb2" << std::endl);
+  }
+  mNumber = nb1;
 
-  // Retrieve ROI Name
-  mName = rois[mNumber];
+  // Retrieve ROI Name (in the info item)
+  gdcm::Attribute<0x3006,0x26> roiname;
+  roiname.SetFromDataSet( nesteddsInfo );
+  mName = roiname.GetValue();
+  // DD(mName);
 
   // ROI Color [ROI Display Color]
   gdcm::Attribute<0x3006,0x002a> color = {};
@@ -163,6 +180,9 @@ void clitk::DicomRT_ROI::Read(std::map<int, std::string> & rois, gdcm::Item cons
   gdcm::Tag tcsq(0x3006,0x0040);
   if( !nestedds.FindDataElement( tcsq ) )
     {
+      std::cerr << "Warning. Could not read contour for structure <" << mName << ">, number" << mNumber << " ? I ignore it" << std::endl;
+      SetDicomUptodateFlag(true);
+      return false;
     }
   const gdcm::DataElement& csq = nestedds.GetDataElement( tcsq );
   gdcm::SmartPointer<gdcm::SequenceOfItems> sqi2 = csq.GetValueAsSQ();
@@ -171,37 +191,21 @@ void clitk::DicomRT_ROI::Read(std::map<int, std::string> & rois, gdcm::Item cons
     }
   unsigned int nitems = sqi2->GetNumberOfItems();
 
-  bool contour_processed=false;
-  bool delta_computed=false;
-  double last_z=0;
   for(unsigned int i = 0; i < nitems; ++i)
     {
-    const gdcm::Item & j = sqi2->GetItem(i+1); // Item start at #1
-    DicomRT_Contour::Pointer c = DicomRT_Contour::New();
-    bool b = c->Read(j);
-    if (b) {
-      mListOfContours.push_back(c);
-      if (contour_processed) {
-        double delta=c->GetZ() - last_z;
-        if (delta_computed)
-          assert(mZDelta == delta);
-        else
-          mZDelta = delta;
-      } else
-        contour_processed=true;
-      last_z=c->GetZ();
+      const gdcm::Item & j = sqi2->GetItem(i+1); // Item start at #1
+      DicomRT_Contour::Pointer c = DicomRT_Contour::New();
+      bool b = c->Read(j);
+      if (b) {
+        mListOfContours.push_back(c);
+      }
     }
-  }
-
+  SetDicomUptodateFlag(true);
+  return true;
 }
 #else
 void clitk::DicomRT_ROI::Read(std::map<int, std::string> & rois, gdcm::SQItem * item)
 {
-
-  // Change number if needed
-
-  // TODO
-
   // ROI number [Referenced ROI Number]
   mNumber = atoi(item->GetEntryValue(0x3006,0x0084).c_str());
 
@@ -213,25 +217,21 @@ void clitk::DicomRT_ROI::Read(std::map<int, std::string> & rois, gdcm::SQItem *
 
   // Read contours [Contour Sequence]
   gdcm::SeqEntry * contours=item->GetSeqEntry(0x3006,0x0040);
-  bool contour_processed=false;
-  bool delta_computed=false;
-  double last_z=0;
-  for(gdcm::SQItem* j=contours->GetFirstSQItem(); j!=0; j=contours->GetNextSQItem()) {
-    DicomRT_Contour::Pointer c = DicomRT_Contour::New();
-    bool b = c->Read(j);
-    if (b) {
-      mListOfContours.push_back(c);
-      if (contour_processed) {
-        double delta=c->GetZ() - last_z;
-        if (delta_computed)
-          assert(mZDelta == delta);
-        else
-          mZDelta = delta;
-      } else
-        contour_processed=true;
-      last_z=c->GetZ();
+  if (contours) {
+    int i=0;
+    for(gdcm::SQItem* j=contours->GetFirstSQItem(); j!=0; j=contours->GetNextSQItem()) {
+      DicomRT_Contour::Pointer c = DicomRT_Contour::New();
+      bool b = c->Read(j);
+      if (b) {
+        mListOfContours.push_back(c);
+      }
+      ++i;
     }
   }
+  else {
+    std::cerr << "Warning. Could not read contour for structure <" << mName << ">, number" << mNumber << " ? I ignore it" << std::endl;
+  }
+  SetDicomUptodateFlag(true);
 }
 #endif
 //--------------------------------------------------------------------
@@ -253,11 +253,16 @@ vtkPolyData * clitk::DicomRT_ROI::GetMesh()
   }
   return mMesh;
 }
+//--------------------------------------------------------------------
+
+
 //--------------------------------------------------------------------
 clitk::DicomRT_Contour * clitk::DicomRT_ROI::GetContour(int n)
 {
   return mListOfContours[n];
 }
+//--------------------------------------------------------------------
+
 
 //--------------------------------------------------------------------
 void clitk::DicomRT_ROI::ComputeMesh()
@@ -275,11 +280,39 @@ void clitk::DicomRT_ROI::ComputeMesh()
 //--------------------------------------------------------------------
 
 
+#if GDCM_MAJOR_VERSION == 2
+
+//--------------------------------------------------------------------
+void clitk::DicomRT_ROI::UpdateDicomItem()
+{
+  if (GetDicomUptoDateFlag()) return;
+  DD("ROI::UpdateDicomItem");
+  DD(GetName());  
+
+  // From now, only some item can be modified
+
+  // Set ROI Name 0x3006,0x26> 
+  gdcm::Attribute<0x3006,0x26> roiname;
+  roiname.SetValue(GetName());
+  gdcm::DataElement de = roiname.GetAsDataElement();
+  gdcm::DataSet & ds = mItemInfo->GetNestedDataSet();  
+  ds.Replace(de);
+
+  // Update contours
+  for(uint i=0; i<mListOfContours.size(); i++) {
+    DD(i);
+    DicomRT_Contour::Pointer roi = mListOfContours[i];
+    roi->UpdateDicomItem(mItemContour);
+  }
+}
+//--------------------------------------------------------------------
+#endif
+
 //--------------------------------------------------------------------
 void clitk::DicomRT_ROI::SetFromBinaryImage(vvImage * image, int n,
-                                           std::string name,
-                                           std::vector<double> color, 
-                                           std::string filename)
+                                            std::string name,
+                                            std::vector<double> color, 
+                                            std::string filename)
 {
 
   // ROI number [Referenced ROI Number]