From: tbaudier <thomas.baudier@creatis.insa-lyon.fr>
Date: Fri, 24 Nov 2017 15:27:25 +0000 (+0100)
Subject: Update README
X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=796954f9fff960cee1599e5a8960e0f424931900;p=clitk.git

Update README
---

diff --git a/README.md b/README.md
index 0e1ef10..a657222 100644
--- a/README.md
+++ b/README.md
@@ -10,56 +10,3 @@ You can download the binaries here:
  - [Linux 64bits](https://www.creatis.insa-lyon.fr/rio/vv?action=AttachFile&do=get&target=vv-1.4Qt4-linux64)
  - [Windows 32bits](https://www.creatis.insa-lyon.fr/rio/vv?action=AttachFile&do=get&target=vv-1.4Qt4-win32.zip)
  - [Windows 64bits](https://www.creatis.insa-lyon.fr/rio/vv?action=AttachFile&do=get&target=vv-1.4Qt4-win64.zip)
-
-### Installation
-To install vv with Linux (e.g.: OpenSuse 42.2), follow the instructions:
-
-#### Qt
-Install Qt5-devel and widget development library (Designer, Xml, Tools, Gui, Network, OpenGL, ...) with your package manager (e.g.: Yast)
-
-#### VTK
-mkdir vtk  
-cd vtk  
-mkdir src  
-git clone https://github.com/Kitware/VTK.git src  
-cd src  
-git checkout tags/v7.0.0  
-cd ..  
-mkdir bin  
-cd bin  
-ccmake ../src (use t to toggle, c to configure and g to generate)  
-Be sure to set (in toogle mode):
-  - Module_vtkGUISuppotQt to ON
-  - Module_vtkGUISuppotQtOpenGL to ON
-  - Module_vtkRenderingQt to ON
-  - Module_vtkViewQt to ON
-  - VTK_QT_VERSION to 5
-  - VTK_RENDERING_BACKEND to OpenGL
-  - All Qt5... DIR to /usr/local/Qt-5.../lib/cmake/QT5...  
-make  
-cd ../..  
-
-#### ITK
-mkdir itk  
-cd itk  
-mkdir src  
-git clone https://github.com/InsightSoftwareConsortium/ITK.git src  
-mkdir bin  
-ccmake ../src  
-Be sure to set (in toogle mode):
-  - Module_ITKReview to ON
-  - Module_ITKVtkGlue to ON
-  - BUILD_SHARED_LIBS to ON  
-make  
-cd ../..  
-
-#### vv
-mkdir vv  
-cd vv  
-mkdir src  
-git clone https://github.com/open-vv/vv.git src  
-mkdir bin  
-ccmake ../src  
-Be sure to set (the correct paths to Qt5 and ITK)  
-make  
-cd ../..  
diff --git a/common/clitkDicomRTStruct2ImageFilter.cxx b/common/clitkDicomRTStruct2ImageFilter.cxx
index bf515a4..bf4d4c4 100644
--- a/common/clitkDicomRTStruct2ImageFilter.cxx
+++ b/common/clitkDicomRTStruct2ImageFilter.cxx
@@ -103,6 +103,7 @@ void clitk::DicomRTStruct2ImageFilter::SetImage(vvImage::Pointer image)
   mOrigin.resize(3);
   mSize.resize(3);
   mDirection.resize(3);
+  mTransformMatrix = image->GetTransform()[0]->GetMatrix();
   for(unsigned int i=0; i<3; i++) {
     mSpacing[i] = image->GetSpacing()[i];
     mOrigin[i] = image->GetOrigin()[i];
@@ -179,7 +180,7 @@ void clitk::DicomRTStruct2ImageFilter::Update()
   }
 
   // Get Mesh
-  vtkPolyData * mesh = mROI->GetMesh();  
+  vtkPolyData * mesh = mROI->GetMesh();
 
   // Get bounds
   double *bounds=mesh->GetBounds();
@@ -229,7 +230,6 @@ void clitk::DicomRTStruct2ImageFilter::Update()
   extend[0] = ceil((bounds[1]-origin[0])/mSpacing[0]+4);
   extend[1] = ceil((bounds[3]-origin[1])/mSpacing[1]+4);
   extend[2] = ceil((bounds[5]-origin[2])/mSpacing[2]+4);
-
   // If no crop, set initial image size/origin
   if (!mCropMask) {
     for(int i=0; i<3; i++) {
@@ -238,6 +238,8 @@ void clitk::DicomRTStruct2ImageFilter::Update()
     }
   }
 
+std::cout << "origin " << origin[0] << " " << origin[1] << " " << origin[2] << std::endl;
+std::cout << "extend " << extend[0] << " " << extend[1] << " " << extend[2] << std::endl;
   // Create new output image
   mBinaryImage = vtkSmartPointer<vtkImageData>::New();
 #if VTK_MAJOR_VERSION <= 5
diff --git a/common/clitkDicomRTStruct2ImageFilter.h b/common/clitkDicomRTStruct2ImageFilter.h
index 4943818..96de26d 100644
--- a/common/clitkDicomRTStruct2ImageFilter.h
+++ b/common/clitkDicomRTStruct2ImageFilter.h
@@ -23,6 +23,7 @@
 #include "clitkDicomRT_ROI.h"
 #include "clitkImageCommon.h"
 #include <vtkImageData.h>
+#include <vtkMatrix4x4.h>
 #include <itkImage.h>
 #include <itkVTKImageToImageFilter.h>
 
@@ -58,6 +59,7 @@ namespace clitk {
     std::vector<double> mOrigin;
     std::vector<unsigned long> mSize;
     std::vector< std::vector< double> > mDirection;
+    vtkSmartPointer<vtkMatrix4x4> mTransformMatrix;
     clitk::DicomRT_ROI * mROI;
     vtkSmartPointer<vtkImageData> mBinaryImage;
   };
diff --git a/common/clitkDicomRT_Contour.cxx b/common/clitkDicomRT_Contour.cxx
index 7fc7111..4bd4598 100644
--- a/common/clitkDicomRT_Contour.cxx
+++ b/common/clitkDicomRT_Contour.cxx
@@ -253,6 +253,14 @@ void clitk::DicomRT_Contour::SetMesh(vtkPolyData * mesh)
 //--------------------------------------------------------------------
 
 
+//--------------------------------------------------------------------
+void clitk::DicomRT_Contour::SetTransformMatrix(vtkMatrix4x4* matrix)
+{
+  mTransformMatrix = matrix;
+}
+//--------------------------------------------------------------------
+
+
 //--------------------------------------------------------------------
 void clitk::DicomRT_Contour::ComputeMeshFromDataPoints()
 {
@@ -263,13 +271,24 @@ void clitk::DicomRT_Contour::ComputeMeshFromDataPoints()
   mMesh->SetPoints(mPoints);
   vtkIdType ids[2];
   for (unsigned int idx=0 ; idx<mNbOfPoints ; idx++) {
+    double pointIn[4], pointOut[4];
+    for (unsigned int j=0 ; j<3; ++j)
+      pointIn[j] = mData->GetPoint(idx)[j];
+    pointIn[4] = 1.0;
+    /*mTransformMatrix->MultiplyPoint(pointIn, pointOut);
+    std::cout << pointOut[0] << " " << pointOut[1] << " " << pointOut[2] << " " << pointOut[3] << std::endl;
+    mMesh->GetPoints()->InsertNextPoint(pointOut[0],
+                                        pointOut[1],
+                                        pointOut[2]);*/
     mMesh->GetPoints()->InsertNextPoint(mData->GetPoint(idx)[0],
                                         mData->GetPoint(idx)[1],
                                         mData->GetPoint(idx)[2]);
+    //std::cout << mData->GetPoint(idx)[0] << " " << mData->GetPoint(idx)[1] << " " << mData->GetPoint(idx)[2] << std::endl;
     ids[0]=idx;
     ids[1]=(ids[0]+1) % mNbOfPoints; //0-1,1-2,...,n-1-0
     mMesh->GetLines()->InsertNextCell(2,ids);
   }
+  //std::cout << std::endl;
   mMeshIsUpToDate = true;
 }
 //--------------------------------------------------------------------
diff --git a/common/clitkDicomRT_Contour.h b/common/clitkDicomRT_Contour.h
index 78a5bfd..077599f 100644
--- a/common/clitkDicomRT_Contour.h
+++ b/common/clitkDicomRT_Contour.h
@@ -30,6 +30,7 @@
 #include <vtkPoints.h>
 #include <vtkPolyData.h>
 #include <vtkSmartPointer.h>
+#include <vtkMatrix4x4.h>
 
 namespace clitk {
 
@@ -54,6 +55,7 @@ public:
   void SetMesh(vtkPolyData * mesh);
   vtkPoints * GetPoints() {return mData;}
   double GetZ() const {return mZ;}
+  void SetTransformMatrix(vtkMatrix4x4* matrix);
   
   
 protected:
@@ -64,6 +66,7 @@ protected:
   vtkSmartPointer<vtkPoints> mData;
   vtkSmartPointer<vtkPolyData> mMesh;
   vtkSmartPointer<vtkPoints> mPoints;
+  vtkSmartPointer<vtkMatrix4x4> mTransformMatrix;
   bool mMeshIsUpToDate;
   ///Z location of the contour
   double mZ;
diff --git a/common/clitkDicomRT_ROI.cxx b/common/clitkDicomRT_ROI.cxx
index b6af9c3..4135b31 100644
--- a/common/clitkDicomRT_ROI.cxx
+++ b/common/clitkDicomRT_ROI.cxx
@@ -211,6 +211,7 @@ bool clitk::DicomRT_ROI::Read(gdcm::Item * itemInfo, gdcm::Item * itemContour)
     {
       gdcm::Item & j = sqi2->GetItem(i+1); // Item start at #1
       DicomRT_Contour::Pointer c = DicomRT_Contour::New();
+      c->SetTransformMatrix(mTransformMatrix);
       bool b = c->Read(&j);
       if (b) {
         mListOfContours.push_back(c);
@@ -237,6 +238,7 @@ void clitk::DicomRT_ROI::Read(std::map<int, std::string> & rois, gdcm::SQItem *
     int i=0;
     for(gdcm::SQItem* j=contours->GetFirstSQItem(); j!=0; j=contours->GetNextSQItem()) {
       DicomRT_Contour::Pointer c = DicomRT_Contour::New();
+      c->SetTransformMatrix(mTransformMatrix);
       bool b = c->Read(j);
       if (b) {
         mListOfContours.push_back(c);
@@ -360,7 +362,6 @@ void clitk::DicomRT_ROI::SetFromBinaryImage(vvImage::Pointer image, int n,
                                             std::vector<double> color, 
                                             std::string filename)
 {
-
   // ROI number [Referenced ROI Number]
   mNumber = n;
 
@@ -388,6 +389,14 @@ vvImage * clitk::DicomRT_ROI::GetImage() const
 //--------------------------------------------------------------------
 
 
+//--------------------------------------------------------------------
+void clitk::DicomRT_ROI::SetTransformMatrix(vtkMatrix4x4* matrix)
+{
+  mTransformMatrix = matrix;
+}
+//--------------------------------------------------------------------
+
+
 //--------------------------------------------------------------------
 void clitk::DicomRT_ROI::ComputeContoursFromImage()
 {
@@ -519,6 +528,7 @@ void clitk::DicomRT_ROI::Read(vtkSmartPointer<vtkGDCMPolyDataReader> & reader, i
   // Get the contour
   mMesh =  reader->GetOutput(roiindex);  
   DicomRT_Contour::Pointer c = DicomRT_Contour::New();
+  c->SetTransformMatrix(mTransformMatrix);
   c->SetMesh(mMesh); // FIXME no GetZ, not GetPoints  
   mMeshIsUpToDate = true;
   mListOfContours.push_back(c);
diff --git a/common/clitkDicomRT_ROI.h b/common/clitkDicomRT_ROI.h
index 80cbacc..ec43538 100644
--- a/common/clitkDicomRT_ROI.h
+++ b/common/clitkDicomRT_ROI.h
@@ -23,6 +23,7 @@
 #include "clitkDicomRT_Contour.h"
 #include "vvImage.h"
 
+#include <vtkMatrix4x4.h>
 #include "clitkConfiguration.h"
 #if CLITK_USE_SYSTEM_GDCM == 1
 #include <vtkGDCMPolyDataReader.h>
@@ -66,6 +67,8 @@ public:
   void SetImage(vvImage::Pointer im);
   DicomRT_Contour* GetContour(int n);
 
+  void SetTransformMatrix(vtkMatrix4x4* matrix);
+
   // Compute a vtk mesh from the dicom contours
   void ComputeMeshFromContour();
   void ComputeContoursFromImage();
@@ -94,6 +97,7 @@ protected:
   std::vector<double> mColor;
   std::vector<DicomRT_Contour::Pointer> mListOfContours;
   vtkSmartPointer<vtkPolyData> mMesh;
+  vtkSmartPointer<vtkMatrix4x4> mTransformMatrix;
   bool mMeshIsUpToDate;
   vvImage::Pointer mImage;
   double mBackgroundValue;
diff --git a/common/clitkDicomRT_StructureSet.cxx b/common/clitkDicomRT_StructureSet.cxx
index 9fa96b3..49d90bd 100644
--- a/common/clitkDicomRT_StructureSet.cxx
+++ b/common/clitkDicomRT_StructureSet.cxx
@@ -91,6 +91,14 @@ const std::string & clitk::DicomRT_StructureSet::GetDate() const
 //--------------------------------------------------------------------
 
 
+//--------------------------------------------------------------------
+void clitk::DicomRT_StructureSet::SetTransformMatrix(vtkMatrix4x4* matrix)
+{
+  mTransformMatrix = matrix;
+}
+//--------------------------------------------------------------------
+
+
 //--------------------------------------------------------------------
 const std::string & clitk::DicomRT_StructureSet::GetTime() const
 {
@@ -439,6 +447,7 @@ void clitk::DicomRT_StructureSet::Read(const std::string & filename)
     int nb = i->first;//ReadROINumber(i);//mROIIndex[i];
     // Create the roi
     mROIs[nb] = DicomRT_ROI::New();
+    mROIs[nb]->SetTransformMatrix(mTransformMatrix);
     mROIs[nb]->Read(mMapOfROIInfo[nb], mMapOfROIContours[nb]);
   }
     
diff --git a/common/clitkDicomRT_StructureSet.h b/common/clitkDicomRT_StructureSet.h
index c26122e..7932051 100644
--- a/common/clitkDicomRT_StructureSet.h
+++ b/common/clitkDicomRT_StructureSet.h
@@ -24,6 +24,9 @@
 #include "clitkCommon.h" 
 #include "clitkDicomRT_ROI.h"
 
+//vtk
+#include "vtkMatrix4x4.h"
+
 // vv
 #include "vvImage.h"
 
@@ -58,6 +61,7 @@ public:
 
   void Print(std::ostream & os = std::cout) const;
   void Read(const std::string & filename);
+  void SetTransformMatrix(vtkMatrix4x4* matrix);
   bool IsDicomRTStruct(const std::string & filename);
   void Write(const std::string & filename);
 
@@ -90,6 +94,7 @@ protected:
   std::string mName;
   std::string mDate;
   std::string mTime;
+  vtkSmartPointer<vtkMatrix4x4> mTransformMatrix;
 
   std::map<int, clitk::DicomRT_ROI::Pointer> mROIs;
   std::map<int, std::string> mMapOfROIName;
diff --git a/vv/vvBinaryImageOverlayActor.cxx b/vv/vvBinaryImageOverlayActor.cxx
index b5935c3..5068887 100644
--- a/vv/vvBinaryImageOverlayActor.cxx
+++ b/vv/vvBinaryImageOverlayActor.cxx
@@ -110,22 +110,45 @@ void vvBinaryImageOverlayActor::Initialize(bool IsVisible)
   // Create an actor for each time slice
   for (unsigned int numImage = 0; numImage < mSlicer->GetImage()->GetVTKImages().size(); numImage++) {
     // how many intensity ?
-    vtkSmartPointer<vtkImageMapToRGBA> mOverlayMapper = vtkSmartPointer<vtkImageMapToRGBA>::New();
-    if (mImage->IsTimeSequence())
-    {
- #if VTK_MAJOR_VERSION <= 5
-        mOverlayMapper->SetInput(mImage->GetVTKImages()[numImage]);
+    
+
+
+    if (!mFusionReslice) {
+      mFusionReslice = vtkSmartPointer<vtkImageReslice>::New();
+      mFusionReslice->SetInterpolationModeToLinear();
+      mFusionReslice->AutoCropOutputOn();
+      mFusionReslice->SetBackgroundColor(-1000,-1000,-1000,1);
+    }
+
+    mConcatenatedFusionTransform->Identity();
+    mConcatenatedFusionTransform->Concatenate(mImage->GetTransform()[0]);
+    mConcatenatedFusionTransform->Concatenate(mSlicer->GetSlicingTransform());
+    mFusionReslice->SetResliceAxes(mConcatenatedFusionTransform->GetMatrix());
+    if (mImage->IsTimeSequence()) {
+#if VTK_MAJOR_VERSION <= 5
+    mFusionReslice->SetInput(0, mImage->GetVTKImages()[numImage]);
+    mFusionReslice->UpdateInformation();
 #else
-        mOverlayMapper->SetInputData(mImage->GetVTKImages()[numImage]);
+    mFusionReslice->SetInputData(0, mImage->GetVTKImages()[numImage]);
 #endif
-    }
-    else {
+    } else {
 #if VTK_MAJOR_VERSION <= 5
-        mOverlayMapper->SetInput(mImage->GetVTKImages()[0]);
+    mFusionReslice->SetInput(0, mImage->GetVTKImages()[0]);
+    mFusionReslice->UpdateInformation();
 #else
-        mOverlayMapper->SetInputData(mImage->GetVTKImages()[0]);
+    mFusionReslice->SetInputData(0, mImage->GetVTKImages()[0]);
 #endif
     }
+    mFusionReslice->Update();
+
+
+    
+    vtkSmartPointer<vtkImageMapToRGBA> mOverlayMapper = vtkSmartPointer<vtkImageMapToRGBA>::New();
+#if VTK_MAJOR_VERSION <= 5
+    mOverlayMapper->SetInput(mFusionReslice->GetOutput());
+#else
+    mOverlayMapper->SetInputConnection(mFusionReslice->GetOutputPort(0));
+#endif
 
     double range[2];
     if (mImage->IsTimeSequence())
diff --git a/vv/vvBinaryImageOverlayActor.h b/vv/vvBinaryImageOverlayActor.h
index 9559bc7..2e575c3 100644
--- a/vv/vvBinaryImageOverlayActor.h
+++ b/vv/vvBinaryImageOverlayActor.h
@@ -27,6 +27,8 @@ class vtkActor;
 class vvImage;
 class vtkImageMapToRGBA;
 class vtkImageActor;
+class vtkImageReslice;
+class vtkTransform;
 
 //------------------------------------------------------------------------------
 class vvBinaryImageOverlayActor : public itk::LightObject
@@ -66,6 +68,8 @@ class vvBinaryImageOverlayActor : public itk::LightObject
 
   std::vector<vtkSmartPointer<vtkImageMapToRGBA> > mMapperList;
   std::vector<vtkSmartPointer<vtkImageActor> > mImageActorList;
+  vtkSmartPointer<vtkImageReslice> mFusionReslice;
+  vtkSmartPointer<vtkTransform> mConcatenatedFusionTransform;
 
   void ComputeExtent(int orientation, 
 		     int slice, 
diff --git a/vv/vvROIActor.cxx b/vv/vvROIActor.cxx
index 4e1a9dc..d6f5089 100644
--- a/vv/vvROIActor.cxx
+++ b/vv/vvROIActor.cxx
@@ -185,12 +185,11 @@ void vvROIActor::Initialize(double depth, bool IsVisible)
       mOverlayActors.push_back(vvBinaryImageOverlayActor::New());
 
       // BG or FG
-      if (m_modeBG) {
-	mOverlayActors[i]->SetImage(mROI->GetImage(), mROI->GetBackgroundValueLabelImage());
-      }
-      else {
-	mOverlayActors[i]->SetImage(mROI->GetImage(), mROI->GetForegroundValueLabelImage(), false);
-      }
+      if (m_modeBG)
+        mOverlayActors[i]->SetImage(mROI->GetImage(), mROI->GetBackgroundValueLabelImage());
+      else
+        mOverlayActors[i]->SetImage(mROI->GetImage(), mROI->GetForegroundValueLabelImage(), false);
+
 
 
       mOverlayActors[i]->SetColor(mROI->GetDisplayColor()[0],
@@ -236,7 +235,7 @@ void vvROIActor::Update(bool force)
 
 //------------------------------------------------------------------------------
 void vvROIActor::UpdateSlice(int slicer, int slices, int force)
-{ 
+{
   if (!mROI->GetImage())  return;
   if ((!mIsVisible) && (!mIsContourVisible)) return; 
   if (!mSlicerManager) {
diff --git a/vv/vvROIActor.h b/vv/vvROIActor.h
index 04c9029..799d339 100644
--- a/vv/vvROIActor.h
+++ b/vv/vvROIActor.h
@@ -70,7 +70,7 @@ public slots:
   vvSlicerManager * mSlicerManager;
   std::vector<vvImageContour::Pointer> mImageContour;
   std::vector< vvBinaryImageOverlayActor::Pointer > mOverlayActors;
-  
+
   bool mIsVisible;
   bool mIsContourVisible;
   double mOpacity;
diff --git a/vv/vvToolROIManager.cxx b/vv/vvToolROIManager.cxx
index 4c2832e..00eff1d 100644
--- a/vv/vvToolROIManager.cxx
+++ b/vv/vvToolROIManager.cxx
@@ -55,7 +55,7 @@ vvToolROIManager::vvToolROIManager(vvMainWindowBase * parent, Qt::WindowFlags f)
   QWidget(parent->GetTab()),
   vvToolBase<vvToolROIManager>(parent),
   Ui::vvToolROIManager()
-{ 
+{
   // Store parent
   mMainWindow = parent;
 
@@ -95,7 +95,7 @@ vvToolROIManager::vvToolROIManager(vvMainWindowBase * parent, Qt::WindowFlags f)
 
 //------------------------------------------------------------------------------
 vvToolROIManager::~vvToolROIManager()
-{ 
+{
   mROIActorsList.clear();
 }
 //------------------------------------------------------------------------------
@@ -104,7 +104,7 @@ vvToolROIManager::~vvToolROIManager()
 //------------------------------------------------------------------------------
 // STATIC
 void vvToolROIManager::Initialize()
-{ 
+{
   SetToolName("ROIManager");
   SetToolMenuName("Open ROI (binary image or RT-STRUCT)");
   SetToolIconFilename(":/common/icons/tool-roi.png");
@@ -117,7 +117,7 @@ void vvToolROIManager::Initialize()
 
 //------------------------------------------------------------------------------
 void  vvToolROIManager::InitializeNewTool(bool ReadStateFlag)
-{ 
+{
   // Check if we need to start a new tool or read in the state file to load
   if (ReadStateFlag == false) {
     // Select the current image as the target
@@ -224,7 +224,7 @@ void  vvToolROIManager::InitializeNewTool(bool ReadStateFlag)
 
 //------------------------------------------------------------------------------
 void vvToolROIManager::InputIsSelected(vvSlicerManager *m)
-{ 
+{
   // Initialization
   mCurrentSlicerManager = m;
   mCurrentImage = mCurrentSlicerManager->GetImage();
@@ -240,7 +240,7 @@ void vvToolROIManager::InputIsSelected(vvSlicerManager *m)
 
 //------------------------------------------------------------------------------
 void vvToolROIManager::AnImageIsBeingClosed(vvSlicerManager * m)
-{ 
+{
   if (m == mCurrentSlicerManager) {
     close();
     return;
@@ -249,7 +249,7 @@ void vvToolROIManager::AnImageIsBeingClosed(vvSlicerManager * m)
 //------------------------------------------------------------------------------
 
 void vvToolROIManager::RemoveROI()
-{ 
+{
 
   // Search the indice of the selected ROI
   QList<QTreeWidgetItem *> l = mTree->selectedItems();
@@ -288,7 +288,7 @@ void vvToolROIManager::RemoveROI()
 
 //------------------------------------------------------------------------------
 void vvToolROIManager::close()
-{ 
+{
   disconnect(mTree, SIGNAL(itemSelectionChanged()), this, SLOT(SelectedItemChangedInTree()));
   disconnect(mCheckBoxShow, SIGNAL(toggled(bool)), this, SLOT(VisibleROIToggled(bool)));
   disconnect(mOpacitySlider, SIGNAL(valueChanged(int)), this, SLOT(OpacityChanged(int)));
@@ -315,7 +315,7 @@ void vvToolROIManager::close()
 
 //------------------------------------------------------------------------------
 void vvToolROIManager::SelectedImageHasChanged(vvSlicerManager * m)
-{ 
+{
   if (mCurrentSlicerManager == NULL) return;
   if (m == NULL) return;
   if (m != mCurrentSlicerManager) hide();
@@ -328,7 +328,7 @@ void vvToolROIManager::SelectedImageHasChanged(vvSlicerManager * m)
 
 //------------------------------------------------------------------------------
 void vvToolROIManager::Open()
-{ 
+{
   // Open images
   QString Extensions = "Images or Dicom-Struct files ( *.mha *.mhd *.hdr *.his *.dcm RS*)";
   Extensions += ";;All Files (*)";
@@ -349,7 +349,7 @@ void vvToolROIManager::Open()
 
 //------------------------------------------------------------------------------
 void vvToolROIManager::OpenBinaryImage(QStringList & filename)
-{ 
+{
   if (filename.size() == 0) return;
 
   vvProgressDialog p("Reading ROI ...", true);
@@ -393,7 +393,7 @@ void vvToolROIManager::OpenBinaryImage(QStringList & filename)
 
 //------------------------------------------------------------------------------
 void vvToolROIManager::OpenDicomImage(std::string filename)
-{ 
+{
   // GUI selector of roi
   vvMeshReader reader;
   reader.SetFilename(filename);
@@ -409,6 +409,9 @@ void vvToolROIManager::OpenDicomImage(std::string filename)
 
     // Read information
     clitk::DicomRT_StructureSet::Pointer s = clitk::DicomRT_StructureSet::New();
+    vtkSmartPointer<vtkMatrix4x4> transformMatrix = vtkSmartPointer<vtkMatrix4x4>::New();
+    transformMatrix = mCurrentImage->GetTransform()[0]->GetMatrix();
+    s->SetTransformMatrix(transformMatrix);
     s->Read(filename);
 
     // Loop on selected struct
@@ -445,7 +448,7 @@ void vvToolROIManager::AddImage(vvImage * binaryImage,
                                 std::string name,
                                 std::string filename,
                                 double BG, bool modeBG)
-{ 
+{
   // Check Dimension
   int dim = mCurrentImage->GetNumberOfDimensions();
   int bin_dim = binaryImage->GetNumberOfDimensions();
@@ -547,7 +550,7 @@ void vvToolROIManager::AddImage(vvImage * binaryImage,
 
 //------------------------------------------------------------------------------
 void vvToolROIManager::UpdateAllContours()
-{ 
+{
   if (mCurrentSlicerManager == NULL) return;
   // Render loaded ROIs (the first is sufficient)
   for(unsigned int i=0; i<mROIList.size(); i++) {
@@ -560,7 +563,7 @@ void vvToolROIManager::UpdateAllContours()
 
 //------------------------------------------------------------------------------
 void vvToolROIManager::UpdateAllROIStatus()
-{ 
+{
   int nbVisible = 0;
   int nbContourVisible = 0;
   int nb = mROIList.size();
@@ -594,7 +597,7 @@ void vvToolROIManager::UpdateAllROIStatus()
 
 //------------------------------------------------------------------------------
 void vvToolROIManager::SelectedItemChangedInTree()
-{ 
+{
   // Search which roi is selected
   QList<QTreeWidgetItem *> l = mTree->selectedItems();
   if (l.size() == 0) {
@@ -679,7 +682,7 @@ void vvToolROIManager::SelectedItemChangedInTree()
 
 //------------------------------------------------------------------------------
 void vvToolROIManager::VisibleROIToggled(bool b)
-{ 
+{
   if (mCurrentROIActor == NULL) return;
   if (b == mCurrentROIActor->IsVisible()) return; // nothing to do
   mCurrentROIActor->SetVisible(b);
@@ -691,7 +694,7 @@ void vvToolROIManager::VisibleROIToggled(bool b)
 
 //------------------------------------------------------------------------------
 void vvToolROIManager::VisibleContourROIToggled(bool b)
-{ 
+{
   if (mCurrentROIActor == NULL) return;
   if (mCurrentROIActor->IsContourVisible() == b) return; // nothing to do
   mCurrentROIActor->SetContourVisible(b);
@@ -704,7 +707,7 @@ void vvToolROIManager::VisibleContourROIToggled(bool b)
 
 //------------------------------------------------------------------------------
 void vvToolROIManager::OpacityChanged(int v)
-{ 
+{
   if (mCurrentROIActor == NULL) return;
   mCurrentROIActor->SetOpacity((double)v/100.0);
   mCurrentROIActor->UpdateColor();
@@ -715,7 +718,7 @@ void vvToolROIManager::OpacityChanged(int v)
 
 //------------------------------------------------------------------------------
 void vvToolROIManager::AllVisibleROIToggled(int b)
-{ 
+{
   disconnect(mCheckBoxShowAll, SIGNAL(stateChanged(int)), this, SLOT(AllVisibleROIToggled(int)));
   bool status = false;
   if ((mCheckBoxShowAll->checkState() == Qt::Checked) ||
@@ -735,7 +738,7 @@ void vvToolROIManager::AllVisibleROIToggled(int b)
 
 //------------------------------------------------------------------------------
 void vvToolROIManager::AllVisibleContourROIToggled(int b)
-{ 
+{
   disconnect(mContourCheckBoxShowAll, SIGNAL(stateChanged(int)), this, SLOT(AllVisibleContourROIToggled(int)));
   bool status = false;
   if ((mContourCheckBoxShowAll->checkState() == Qt::Checked) ||
@@ -756,7 +759,7 @@ void vvToolROIManager::AllVisibleContourROIToggled(int b)
 
 //------------------------------------------------------------------------------
 void vvToolROIManager::ChangeColor()
-{ 
+{
   if (mCurrentROIActor == NULL) return;
   QColor color;
   color.setRgbF(mCurrentROIActor->GetROI()->GetDisplayColor()[0],
@@ -782,7 +785,7 @@ void vvToolROIManager::ChangeColor()
 
 //------------------------------------------------------------------------------
 void vvToolROIManager::ChangeContourColor()
-{ 
+{
   if (mCurrentROIActor == NULL) return;
   QColor color;
   color.setRgbF(mCurrentROIActor->GetContourColor()[0],
@@ -800,7 +803,7 @@ void vvToolROIManager::ChangeContourColor()
 
 //------------------------------------------------------------------------------
 void vvToolROIManager::ChangeContourWidth(int n)
-{ 
+{
   if (mCurrentROIActor == NULL) return;
   mCurrentROIActor->SetContourWidth(n);
   mCurrentROIActor->UpdateColor();
@@ -811,7 +814,7 @@ void vvToolROIManager::ChangeContourWidth(int n)
 
 //------------------------------------------------------------------------------
 void vvToolROIManager::ChangeDepth(int n)
-{ 
+{
   if (mCurrentROIActor == NULL) return;
   mCurrentROIActor->SetDepth(n);
   // mCurrentROIActor->UpdateImage(); // FIXME
@@ -825,7 +828,7 @@ void vvToolROIManager::ChangeDepth(int n)
 
 //------------------------------------------------------------------------------
 void vvToolROIManager::ReloadCurrentROI()
-{ 
+{
   if (mCurrentROI->GetFilename() == "") {
     return; // do nothing (contour from rt struct do not reload)
   }
@@ -870,7 +873,7 @@ void  vvToolROIManager::SaveState(std::shared_ptr<QXmlStreamWriter> & m_XmlWrite
 #else
 void  vvToolROIManager::SaveState(std::auto_ptr<QXmlStreamWriter> & m_XmlWriter)
 #endif
-{ 
+{
   // Get index of the image
   int n = mMainWindow->GetSlicerManagers().size();
   int index=-1;
@@ -916,7 +919,7 @@ void  vvToolROIManager::SaveState(std::auto_ptr<QXmlStreamWriter> & m_XmlWriter)
 
 //------------------------------------------------------------------------------
 void vvToolROIManager::ReadXMLInformation()
-{ 
+{
   std::string value="";
   mInitialImageIndex = -1;
   while (!(m_XmlReader->isEndElement() && value == GetToolName().toStdString())) {
@@ -938,7 +941,7 @@ void vvToolROIManager::ReadXMLInformation()
 
 //------------------------------------------------------------------------------
 void vvToolROIManager::ReadXMLInformation_ROI()
-{ 
+{
   QString s;
   std::string value="";
   QSharedPointer<vvROIActor> param = QSharedPointer<vvROIActor>(new vvROIActor);