changes in license header

[clitk.git] / common / clitkDicomRT_ROI.cxx

diff --git a/common/clitkDicomRT_ROI.cxx b/common/clitkDicomRT_ROI.cxx
index 119b63890323c4dc2fdf6f50c6eba546a2547d39..25a2f4322548a1de065c220654352490d7368219 100644 (file)
--- 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 +34,9 @@ clitk::DicomRT_ROI::DicomRT_ROI()
   mColor.resize(3);
   mColor[0] = mColor[1] = mColor[2] = 0;
   mMeshIsUpToDate = false;
+  mBackgroundValue = 0;
+  mForegroundValue = 1;
+  mZDelta = 0;
 }
 //--------------------------------------------------------------------
 
@@ -36,7 +44,6 @@ clitk::DicomRT_ROI::DicomRT_ROI()
 //--------------------------------------------------------------------
 clitk::DicomRT_ROI::~DicomRT_ROI()
 {
-
 }
 //--------------------------------------------------------------------
 
@@ -68,6 +75,14 @@ const std::string & clitk::DicomRT_ROI::GetName() const
 //--------------------------------------------------------------------
 
 
+//--------------------------------------------------------------------
+const std::string & clitk::DicomRT_ROI::GetFilename() const
+{
+  return mFilename;
+}
+//--------------------------------------------------------------------
+
+
 //--------------------------------------------------------------------
 const std::vector<double> & clitk::DicomRT_ROI::GetDisplayColor() const
 {
@@ -103,6 +118,83 @@ 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 ) )
+    {
+    }
+  const gdcm::DataElement& csq = nestedds.GetDataElement( tcsq );
+  gdcm::SmartPointer<gdcm::SequenceOfItems> sqi2 = csq.GetValueAsSQ();
+  if( !sqi2 || !sqi2->GetNumberOfItems() )
+    {
+    }
+  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();
+    }
+  }
+
+}
+#else
 void clitk::DicomRT_ROI::Read(std::map<int, std::string> & rois, gdcm::SQItem * item)
 {
 
@@ -121,12 +213,35 @@ 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 * c = new DicomRT_Contour;
+    DicomRT_Contour::Pointer c = DicomRT_Contour::New();
     bool b = c->Read(j);
-    if (b) mListOfContours.push_back(c);
+    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();
+    }
   }
 }
+#endif
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::DicomRT_ROI::SetImage(vvImage * image)
+{
+  mImage = image;
+}
 //--------------------------------------------------------------------
 
 
@@ -139,26 +254,32 @@ 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)
+void clitk::DicomRT_ROI::SetFromBinaryImage(vvImage * image, int n,
+                                           std::string name,
+                                           std::vector<double> color, 
+                                           std::string filename)
 {
 
   // ROI number [Referenced ROI Number]
@@ -166,6 +287,7 @@ void clitk::DicomRT_ROI::SetFromBinaryImage(vvImage::Pointer image, int n,
 
   // ROI Name
   mName = name;
+  mFilename = filename;
 
   // ROI Color [ROI Display Color]
   mColor = color;
@@ -180,7 +302,7 @@ 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;
 }