X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=common%2FclitkDicomRT_ROI.cxx;h=88bab72d80ad025c8e2dba52fe2a97d8cad0bb3f;hb=d91a03193e84e5a74aeeb8bda9686c48108890c6;hp=fb7b0ca21dec0739d6d1b90be03d041ccdbf2dfd;hpb=0f41173383ece2736e285fb44e8b06569bd8d201;p=clitk.git

diff --git a/common/clitkDicomRT_ROI.cxx b/common/clitkDicomRT_ROI.cxx
index fb7b0ca..88bab72 100644
--- a/common/clitkDicomRT_ROI.cxx
+++ b/common/clitkDicomRT_ROI.cxx
@@ -4,7 +4,7 @@
 
   Authors belongs to:
   - University of LYON           http://www.universite-lyon.fr/
-  - Léon Bérard cancer center    http://oncora1.lyon.fnclcc.fr
+  - Léon Bérard cancer center    http://www.centreleonberard.fr
   - CREATIS CNRS laboratory      http://www.creatis.insa-lyon.fr
 
   This software is distributed WITHOUT ANY WARRANTY; without even
@@ -21,6 +21,11 @@
 #include <vtkSmartPointer.h>
 #include <vtkAppendPolyData.h>
 
+#if GDCM_MAJOR_VERSION == 2
+#include "gdcmAttribute.h"
+#include "gdcmItem.h"
+#endif
+
 //--------------------------------------------------------------------
 clitk::DicomRT_ROI::DicomRT_ROI()
 {
@@ -29,6 +34,8 @@ clitk::DicomRT_ROI::DicomRT_ROI()
   mColor.resize(3);
   mColor[0] = mColor[1] = mColor[2] = 0;
   mMeshIsUpToDate = false;
+  mBackgroundValue = 0;
+  mForegroundValue = 1;
 }
 //--------------------------------------------------------------------
 
@@ -36,7 +43,6 @@ clitk::DicomRT_ROI::DicomRT_ROI()
 //--------------------------------------------------------------------
 clitk::DicomRT_ROI::~DicomRT_ROI()
 {
-
 }
 //--------------------------------------------------------------------
 
@@ -111,6 +117,72 @@ double clitk::DicomRT_ROI::GetBackgroundValueLabelImage() const
 
 
 //--------------------------------------------------------------------
+void clitk::DicomRT_ROI::SetForegroundValueLabelImage(double bg)
+{
+  mForegroundValue = bg;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+double clitk::DicomRT_ROI::GetForegroundValueLabelImage() const
+{
+  return mForegroundValue;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+#if GDCM_MAJOR_VERSION == 2
+void clitk::DicomRT_ROI::Read(std::map<int, std::string> & rois, gdcm::Item const & item)
+{
+  const gdcm::DataSet& nestedds = item.GetNestedDataSet();
+
+  gdcm::Attribute<0x3006,0x0084> referencedroinumber;
+  referencedroinumber.SetFromDataSet( nestedds );
+  // Change number if needed
+
+  // TODO
+
+  // ROI number [Referenced ROI Number]
+  mNumber = referencedroinumber.GetValue();
+
+  // Retrieve ROI Name
+  mName = rois[mNumber];
+
+  // ROI Color [ROI Display Color]
+  gdcm::Attribute<0x3006,0x002a> color = {};
+  color.SetFromDataSet( nestedds );
+  assert( color.GetNumberOfValues() == 3 );
+  mColor[0] = color.GetValue(0);
+  mColor[1] = color.GetValue(1);
+  mColor[2] = color.GetValue(2);
+
+  // Read contours [Contour Sequence]
+  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;
+      return;
+    }
+  const gdcm::DataElement& csq = nestedds.GetDataElement( tcsq );
+  gdcm::SmartPointer<gdcm::SequenceOfItems> sqi2 = csq.GetValueAsSQ();
+  if( !sqi2 || !sqi2->GetNumberOfItems() )
+    {
+    }
+  unsigned int nitems = sqi2->GetNumberOfItems();
+
+  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);
+      }
+    }
+}
+#else
 void clitk::DicomRT_ROI::Read(std::map<int, std::string> & rois, gdcm::SQItem * item)
 {
 
@@ -129,12 +201,22 @@ void clitk::DicomRT_ROI::Read(std::map<int, std::string> & rois, gdcm::SQItem *
 
   // Read contours [Contour Sequence]
   gdcm::SeqEntry * contours=item->GetSeqEntry(0x3006,0x0040);
-  for(gdcm::SQItem* j=contours->GetFirstSQItem(); j!=0; j=contours->GetNextSQItem()) {
-    DicomRT_Contour * c = new DicomRT_Contour;
-    bool b = c->Read(j);
-    if (b) mListOfContours.push_back(c);
+  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;
   }
 }
+#endif
 //--------------------------------------------------------------------
 
 
@@ -155,27 +237,32 @@ vtkPolyData * clitk::DicomRT_ROI::GetMesh()
   return mMesh;
 }
 //--------------------------------------------------------------------
-
+clitk::DicomRT_Contour * clitk::DicomRT_ROI::GetContour(int n)
+{
+  return mListOfContours[n];
+}
 
 //--------------------------------------------------------------------
 void clitk::DicomRT_ROI::ComputeMesh()
 {
-  vtkAppendPolyData * append = vtkAppendPolyData::New();
+  vtkSmartPointer<vtkAppendPolyData> append = vtkSmartPointer<vtkAppendPolyData>::New();
   for(unsigned int i=0; i<mListOfContours.size(); i++) {
     append->AddInput(mListOfContours[i]->GetMesh());
   }
   append->Update();
-  mMesh = append->GetOutput();
+ 
+  mMesh = vtkSmartPointer<vtkPolyData>::New();
+  mMesh->DeepCopy(append->GetOutput());
   mMeshIsUpToDate = true;
 }
 //--------------------------------------------------------------------
 
 
 //--------------------------------------------------------------------
-void clitk::DicomRT_ROI::SetFromBinaryImage(vvImage::Pointer image, int n,
-					    std::string name,
-					    std::vector<double> color, 
-					    std::string filename)
+void clitk::DicomRT_ROI::SetFromBinaryImage(vvImage * image, int n,
+                                            std::string name,
+                                            std::vector<double> color, 
+                                            std::string filename)
 {
 
   // ROI number [Referenced ROI Number]
@@ -198,7 +285,7 @@ void clitk::DicomRT_ROI::SetFromBinaryImage(vvImage::Pointer image, int n,
 
 
 //--------------------------------------------------------------------
-const vvImage::Pointer clitk::DicomRT_ROI::GetImage() const
+vvImage * clitk::DicomRT_ROI::GetImage() const
 {
   return mImage;
 }