X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=vv%2FvvSlicerManager.cxx;h=fc6c6f2c3fc24df002b14852bdd5fedae4d19329;hb=488e466e7493439cb170bc263b4fb898f18183c1;hp=5afe71bd9a2df0ce2f5265916ba47f787a2ad78d;hpb=d3b2eb0b2a96f7925d95a195ba04a1ccf376c0b1;p=clitk.git

diff --git a/vv/vvSlicerManager.cxx b/vv/vvSlicerManager.cxx
index 5afe71b..fc6c6f2 100644
--- a/vv/vvSlicerManager.cxx
+++ b/vv/vvSlicerManager.cxx
@@ -25,6 +25,9 @@
 #include "vvMesh.h"
 #include "vvBlendImageActor.h"
 
+#include <vtkVersion.h>
+#include <vtkStreamingDemandDrivenPipeline.h>
+#include <vtkInformation.h>
 #include <vtkImageActor.h>
 #include <vtkImageData.h>
 #include <vtkRenderWindow.h>
@@ -43,7 +46,10 @@
 #include <QMessageBox>
 //----------------------------------------------------------------------------
 vvSlicerManager::vvSlicerManager(int numberOfSlicers)
-{
+{ 
+
+  connect(this, SIGNAL(callAddLandmark(float,float,float,float)), this, SLOT(AddLandmark(float,float,float,float)));
+
   mFileName = "";
   mId = "";
   mVFName = "";
@@ -73,8 +79,10 @@ vvSlicerManager::vvSlicerManager(int numberOfSlicers)
   mLandmarks = NULL;
   mLinkedId.resize(0);
 
-  for ( int i = 0; i < numberOfSlicers; i++)
+  for ( int i = 0; i < numberOfSlicers; i++) {
     mSlicers.push_back(vtkSmartPointer<vvSlicer>::New());
+    mSlicers[i]->SetSlicerNumber(i);
+  }
   mSelectedSlicer = -1;
   
   mPreviousSlice.resize(numberOfSlicers, 0);
@@ -88,7 +96,7 @@ vvSlicerManager::vvSlicerManager(int numberOfSlicers)
 
 //----------------------------------------------------------------------------
 vvSlicerManager::~vvSlicerManager()
-{
+{ 
   if (mLandmarks)
     delete mLandmarks;
 }
@@ -97,7 +105,7 @@ vvSlicerManager::~vvSlicerManager()
 
 //------------------------------------------------------------------------------
 void vvSlicerManager::SetFilename(std::string filename, int number)
-{
+{ 
   mFileName = filename;
   mFileName = vtksys::SystemTools::GetFilenameName(mFileName);
   mBaseFileName = vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(mFileName));
@@ -119,7 +127,7 @@ void vvSlicerManager::SetFilename(std::string filename, int number)
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::AddContour(vvMesh::Pointer contour,bool propagate)
-{
+{ 
   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
     mSlicers[i]->AddContour(contour,propagate);
   }
@@ -129,7 +137,7 @@ void vvSlicerManager::AddContour(vvMesh::Pointer contour,bool propagate)
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::ToggleContourSuperposition()
-{
+{ 
   for ( unsigned int i = 0; i < mSlicers.size(); i++)
     mSlicers[i]->ToggleContourSuperposition();
 }
@@ -137,7 +145,7 @@ void vvSlicerManager::ToggleContourSuperposition()
 
 //----------------------------------------------------------------------------
 std::string vvSlicerManager::GetListOfAbsoluteFilePathInOneString(const std::string &actorType)
-{
+{ 
   vvImageReader *reader = NULL;
 
   if(actorType=="image")
@@ -168,7 +176,7 @@ std::string vvSlicerManager::GetListOfAbsoluteFilePathInOneString(const std::str
 
 //----------------------------------------------------------------------------
 bool vvSlicerManager::SetImage(std::string filename, vvImageReader::LoadedImageType type, int n, unsigned int slice)
-{
+{ 
   mType = type;
   if (mReader.IsNull())
     mReader = vvImageReader::New();
@@ -203,7 +211,7 @@ bool vvSlicerManager::SetImage(std::string filename, vvImageReader::LoadedImageT
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::SetImage(vvImage::Pointer image)
-{
+{ 
   mImage=image;
   for (unsigned int i = 0; i < mSlicers.size(); i++) {
     mSlicers[i]->SetImage(image);
@@ -214,7 +222,7 @@ void vvSlicerManager::SetImage(vvImage::Pointer image)
 
 //----------------------------------------------------------------------------
 bool vvSlicerManager::SetImages(std::vector<std::string> filenames, vvImageReader::LoadedImageType type, int n)
-{
+{ 
   mType = type;
   std::string fileWithoutExtension = vtksys::SystemTools::GetFilenameWithoutExtension(filenames[0]);
   if (type == vvImageReader::DICOM)
@@ -254,7 +262,7 @@ bool vvSlicerManager::SetImages(std::vector<std::string> filenames, vvImageReade
 
 //----------------------------------------------------------------------------
 bool vvSlicerManager::SetOverlay(std::vector<std::string> filenames,int dim, std::string component, vvImageReader::LoadedImageType type)
-{
+{ 
   mOverlayName = filenames[0];
   mOverlayComponent = component;
   if (dim > mImage->GetNumberOfDimensions()) {
@@ -279,20 +287,18 @@ bool vvSlicerManager::SetOverlay(std::vector<std::string> filenames,int dim, std
 
 
 //----------------------------------------------------------------------------
-bool vvSlicerManager::SetFusion(std::string filename,int dim, std::string component)
-{
-  mFusionName = filename;
+bool vvSlicerManager::SetFusion(std::vector<std::string> filenames,int dim, std::string component, vvImageReader::LoadedImageType type)
+{ 
+  mFusionName = filenames[0];
   mFusionComponent = component;
   if (dim > mImage->GetNumberOfDimensions()) {
-    mLastError = " Overlay dimension cannot be greater then reference image!";
+    mLastError = " Fusion dimension cannot be greater than reference image!";
     return false;
   }
   if (mFusionReader.IsNull())
     mFusionReader = vvImageReader::New();
-  std::vector<std::string> filenames;
-  filenames.push_back(filename);
   mFusionReader->SetInputFilenames(filenames);
-  mFusionReader->Update(mImage->GetNumberOfDimensions(),component.c_str(),mType);
+  mFusionReader->Update(type);
   if (mFusionReader->GetLastError().size() == 0) {
     for ( unsigned int i = 0; i < mSlicers.size(); i++) {
       mSlicers[i]->SetFusion(mFusionReader->GetOutput());
@@ -312,7 +318,7 @@ bool vvSlicerManager::SetFusion(std::string filename,int dim, std::string compon
 //----------------------------------------------------------------------------
 //this function is called by vvMainWindow::AddFusionSequence for the primary sequence (CT), while the given files constitute the secondary sequence.
 bool vvSlicerManager::SetFusionSequence(std::vector<std::string> filenames, int dim, std::string component, vvImageReader::LoadedImageType type)
-{
+{ 
 	mFusionSequenceInvolvementCode = 0;
 
 	mFusionName = filenames[0];
@@ -361,7 +367,7 @@ bool vvSlicerManager::SetFusionSequence(std::vector<std::string> filenames, int
 
 //----------------------------------------------------------------------------
 bool vvSlicerManager::SetVF(std::string filename)
-{
+{ 
   if (mVectorReader.IsNull())
     mVectorReader = vvImageReader::New();
   mVectorReader->SetInputFilename(filename);
@@ -381,7 +387,7 @@ bool vvSlicerManager::SetVF(std::string filename)
 
 //----------------------------------------------------------------------------
 bool vvSlicerManager::SetVF(vvImage::Pointer vf,std::string filename)
-{
+{ 
   if (vf->GetNumberOfDimensions() > mImage->GetNumberOfDimensions()) {
     mLastError = "Sorry, vector field dimension cannot be greater then reference image.";
     return false;
@@ -408,7 +414,7 @@ bool vvSlicerManager::SetVF(vvImage::Pointer vf,std::string filename)
 
 //----------------------------------------------------------------------------
 vvSlicer* vvSlicerManager::GetSlicer(int i)
-{
+{ 
   return mSlicers[i];
 }
 //----------------------------------------------------------------------------
@@ -416,7 +422,7 @@ vvSlicer* vvSlicerManager::GetSlicer(int i)
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::UpdateSlicer(int num, bool state)
-{
+{ 
   if (mSlicers[num]->GetImage()) {
     mSlicers[num]->SetDisplayMode(state);
   }
@@ -426,7 +432,7 @@ void vvSlicerManager::UpdateSlicer(int num, bool state)
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::SetSlicerWindow(int i, vtkRenderWindow* RW)
-{
+{ 
   mSlicers[i]->SetRenderWindow(i,RW);
 }
 //----------------------------------------------------------------------------
@@ -434,7 +440,7 @@ void vvSlicerManager::SetSlicerWindow(int i, vtkRenderWindow* RW)
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::SetInteractorStyleNavigator(int i, vtkInteractorStyle* style)
-{
+{ 
   vvSlicerManagerCommand *smc = vvSlicerManagerCommand::New();
   smc->SM = this;
   smc->SetSlicerNumber(i);
@@ -473,7 +479,7 @@ void vvSlicerManager::SetInteractorStyleNavigator(int i, vtkInteractorStyle* sty
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::LeftButtonReleaseEvent(int slicer)
-{
+{ 
   emit LeftButtonReleaseSignal(slicer);
 }
 //----------------------------------------------------------------------------
@@ -481,7 +487,7 @@ void vvSlicerManager::LeftButtonReleaseEvent(int slicer)
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::EmitMousePositionUpdated(int slicer)
-{
+{ 
   emit MousePositionUpdatedSignal(slicer);
 }
 //----------------------------------------------------------------------------
@@ -489,7 +495,7 @@ void vvSlicerManager::EmitMousePositionUpdated(int slicer)
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::EmitKeyPressed(std::string KeyPress)
-{
+{ 
   emit KeyPressedSignal(KeyPress);
 }
 //----------------------------------------------------------------------------
@@ -497,7 +503,7 @@ void vvSlicerManager::EmitKeyPressed(std::string KeyPress)
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::SetSliceOrientation(int slicer, int orientation)
-{
+{ 
   mSlicers[slicer]->SetSliceOrientation(orientation);
   emit UpdateOrientation(slicer, orientation);
 }
@@ -505,14 +511,14 @@ void vvSlicerManager::SetSliceOrientation(int slicer, int orientation)
 
 //----------------------------------------------------------------------------
 int vvSlicerManager::GetTSlice()
-{
+{ 
   return mSlicers[0]->GetTSlice();
 }
 //----------------------------------------------------------------------------
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::SetTSlice(int slice, bool updateLinkedImages)
-{
+{ 
 	if (!updateLinkedImages) { //for fusionSequence, TMax / MaxCurrentTSlice are irrelevant.
 		for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 			mSlicers[i]->SetTSlice(slice, updateLinkedImages);
@@ -539,7 +545,7 @@ void vvSlicerManager::SetTSlice(int slice, bool updateLinkedImages)
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::SetFusionSequenceTSlice(int slice)
-{
+{ 
 	for ( unsigned int i = 0; i < mSlicers.size(); i++) {
 		mSlicers[i]->SetFusionSequenceTSlice(slice);
 		UpdateTSlice(i);
@@ -550,12 +556,11 @@ void vvSlicerManager::SetFusionSequenceTSlice(int slice)
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::SetNextTSlice(int originating_slicer)
-{
+{ 
   int t = mSlicers[0]->GetMaxCurrentTSlice();
   t++;
   if (t > mSlicers[0]->GetTMax())
     t = 0;
-  //std::cout << "vvSlicerManager::SetNextTSlice" << std::endl;
   emit UpdateTSlice(originating_slicer,t, mFusionSequenceInvolvementCode);
 }
 //----------------------------------------------------------------------------
@@ -563,12 +568,11 @@ void vvSlicerManager::SetNextTSlice(int originating_slicer)
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::SetPreviousTSlice(int originating_slicer)
-{
+{ 
   int t = mSlicers[0]->GetMaxCurrentTSlice();
   t--;
   if (t < 0)
     t = mSlicers[0]->GetTMax();
-  //std::cout << "vvSlicerManager::SetPreviousTSlice" << std::endl;
   emit UpdateTSlice(originating_slicer,t, mFusionSequenceInvolvementCode);
 }
 //----------------------------------------------------------------------------
@@ -576,7 +580,7 @@ void vvSlicerManager::SetPreviousTSlice(int originating_slicer)
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::ToggleInterpolation()
-{
+{ 
   bool interpolate=!(mSlicers[0]->GetImageActor()->GetInterpolate());
   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
     mSlicers[i]->GetImageActor()->SetInterpolate(interpolate);
@@ -591,7 +595,7 @@ void vvSlicerManager::ToggleInterpolation()
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::SetTSliceInSlicer(int tslice, int slicer)
-{
+{ 
   if (tslice < 0)
     tslice = 0;
   else if (tslice > mSlicers[slicer]->GetTMax())
@@ -617,7 +621,7 @@ void vvSlicerManager::SetTSliceInSlicer(int tslice, int slicer)
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::SetColorWindow(double s)
-{
+{ 
   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
     mSlicers[i]->SetColorWindow(s);
   }
@@ -626,7 +630,7 @@ void vvSlicerManager::SetColorWindow(double s)
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::SetColorLevel(double s)
-{
+{ 
   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
     mSlicers[i]->SetColorLevel(s);
   }
@@ -635,7 +639,7 @@ void vvSlicerManager::SetColorLevel(double s)
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::SetOverlayColorWindow(double s)
-{
+{ 
   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
     mSlicers[i]->SetOverlayColorWindow(s);
   }
@@ -644,7 +648,7 @@ void vvSlicerManager::SetOverlayColorWindow(double s)
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::SetOverlayColorLevel(double s)
-{
+{ 
   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
     mSlicers[i]->SetOverlayColorLevel(s);
   }
@@ -653,7 +657,7 @@ void vvSlicerManager::SetOverlayColorLevel(double s)
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::SetLinkOverlayWindowLevel(bool b)
-{
+{ 
   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
     mSlicers[i]->SetLinkOverlayWindowLevel(b);
   }
@@ -662,7 +666,7 @@ void vvSlicerManager::SetLinkOverlayWindowLevel(bool b)
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::SetCursorAndCornerAnnotationVisibility(int s)
-{
+{ 
   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
     mSlicers[i]->SetCursorVisibility(s);
     mSlicers[i]->SetCornerAnnotationVisibility(s);
@@ -672,7 +676,7 @@ void vvSlicerManager::SetCursorAndCornerAnnotationVisibility(int s)
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::SetOpacity(int i, double factor)
-{
+{ 
   mSlicers[i]->SetOpacity(1/factor);
 }
 //----------------------------------------------------------------------------
@@ -680,7 +684,7 @@ void vvSlicerManager::SetOpacity(int i, double factor)
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::UpdateViews(int current,int slicer)
-{
+{ 
   double p[3], pt[3];
   p[0] = mSlicers[slicer]->GetCurrentPosition()[0];
   p[1] = mSlicers[slicer]->GetCurrentPosition()[1];
@@ -693,13 +697,24 @@ void vvSlicerManager::UpdateViews(int current,int slicer)
     /mSlicers[slicer]->GetInput()->GetSpacing()[1];
   double z = (pt[2] - mSlicers[slicer]->GetInput()->GetOrigin()[2])
     /mSlicers[slicer]->GetInput()->GetSpacing()[2];
-
+#if VTK_MAJOR_VERSION <= 5
   if (x >= mSlicers[slicer]->GetInput()->GetWholeExtent()[0]-0.5 &&
       x <= mSlicers[slicer]->GetInput()->GetWholeExtent()[1]+0.5 &&
       y >= mSlicers[slicer]->GetInput()->GetWholeExtent()[2]-0.5 &&
       y <= mSlicers[slicer]->GetInput()->GetWholeExtent()[3]+0.5 &&
       z >= mSlicers[slicer]->GetInput()->GetWholeExtent()[4]-0.5 &&
-      z <= mSlicers[slicer]->GetInput()->GetWholeExtent()[5]+0.5) {
+      z <= mSlicers[slicer]->GetInput()->GetWholeExtent()[5]+0.5)
+#else
+int extentImageReslice[6];
+mSlicers[slicer]->GetRegisterExtent(extentImageReslice);
+  if (x >= extentImageReslice[0]-0.5 &&
+      x <= extentImageReslice[1]+0.5 &&
+      y >= extentImageReslice[2]-0.5 &&
+      y <= extentImageReslice[3]+0.5 &&
+      z >= extentImageReslice[4]-0.5 &&
+      z <= extentImageReslice[5]+0.5)
+#endif
+  {
     mSlicers[slicer]->UpdateCursorPosition();
     mSlicers[slicer]->SetCursorColor(10,212,255);
     mSelectedSlicer = slicer;
@@ -766,7 +781,7 @@ void vvSlicerManager::UpdateViews(int current,int slicer)
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::UpdateLinked(int slicer)
-{
+{ 
   double p[3], pt[3];
   p[0] = mSlicers[slicer]->GetCurrentPosition()[0];
   p[1] = mSlicers[slicer]->GetCurrentPosition()[1];
@@ -775,13 +790,24 @@ void vvSlicerManager::UpdateLinked(int slicer)
   double x = (pt[0] - mSlicers[slicer]->GetInput()->GetOrigin()[0]) / mSlicers[slicer]->GetInput()->GetSpacing()[0];
   double y = (pt[1] - mSlicers[slicer]->GetInput()->GetOrigin()[1]) / mSlicers[slicer]->GetInput()->GetSpacing()[1];
   double z = (pt[2] - mSlicers[slicer]->GetInput()->GetOrigin()[2]) / mSlicers[slicer]->GetInput()->GetSpacing()[2];
-
+#if VTK_MAJOR_VERSION <= 5
   if (x >= mSlicers[slicer]->GetInput()->GetWholeExtent()[0]-0.5 &&
       x <= mSlicers[slicer]->GetInput()->GetWholeExtent()[1]+0.5 &&
       y >= mSlicers[slicer]->GetInput()->GetWholeExtent()[2]-0.5 &&
       y <= mSlicers[slicer]->GetInput()->GetWholeExtent()[3]+0.5 &&
       z >= mSlicers[slicer]->GetInput()->GetWholeExtent()[4]-0.5 &&
-      z <= mSlicers[slicer]->GetInput()->GetWholeExtent()[5]+0.5) {
+      z <= mSlicers[slicer]->GetInput()->GetWholeExtent()[5]+0.5)
+#else
+int extentImageReslice[6];
+mSlicers[slicer]->GetRegisterExtent(extentImageReslice);
+  if (x >= extentImageReslice[0]-0.5 &&
+      x <= extentImageReslice[1]+0.5 &&
+      y >= extentImageReslice[2]-0.5 &&
+      y <= extentImageReslice[3]+0.5 &&
+      z >= extentImageReslice[4]-0.5 &&
+      z <= extentImageReslice[5]+0.5)
+#endif
+  {
     for (std::list<std::string>::const_iterator i = mLinkedId.begin(); i != mLinkedId.end(); i++) {
 		if (this->IsInvolvedInFusionSequence()) {
 			//this SlicerManager is involved in fusionSequence => do not synchronize the times
@@ -797,7 +823,7 @@ void vvSlicerManager::UpdateLinked(int slicer)
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::UpdateLinkedNavigation(vvSlicer *refSlicer, bool bPropagate)
-{
+{ 
   vtkCamera *refCam = refSlicer->GetRenderer()->GetActiveCamera();
 
   double refPosition[3];
@@ -840,7 +866,7 @@ void vvSlicerManager::UpdateLinkedNavigation(vvSlicer *refSlicer, bool bPropagat
 
 //----------------------------------------------------------------------------
 double vvSlicerManager::GetColorWindow() const
-{
+{ 
   if (mSlicers.size())
     return mSlicers[0]->GetColorWindow();
   return -1;
@@ -850,7 +876,7 @@ double vvSlicerManager::GetColorWindow() const
 
 //----------------------------------------------------------------------------
 double vvSlicerManager::GetColorLevel() const
-{
+{ 
   if (mSlicers.size())
     return mSlicers[0]->GetColorLevel();
   return -1;
@@ -859,7 +885,7 @@ double vvSlicerManager::GetColorLevel() const
 
 //----------------------------------------------------------------------------
 double vvSlicerManager::GetOverlayColorWindow() const
-{
+{ 
   if (mSlicers.size())
     return mSlicers[0]->GetOverlayColorWindow();
   return -1;
@@ -868,7 +894,7 @@ double vvSlicerManager::GetOverlayColorWindow() const
 
 //----------------------------------------------------------------------------
 double vvSlicerManager::GetOverlayColorLevel() const
-{
+{ 
   if (mSlicers.size())
     return mSlicers[0]->GetOverlayColorLevel();
   return -1;
@@ -877,7 +903,7 @@ double vvSlicerManager::GetOverlayColorLevel() const
 
 //----------------------------------------------------------------------------
 bool vvSlicerManager::GetLinkOverlayWindowLevel() const
-{
+{ 
   if (mSlicers.size())
     return mSlicers[0]->GetLinkOverlayWindowLevel();
   return -1;
@@ -886,7 +912,7 @@ bool vvSlicerManager::GetLinkOverlayWindowLevel() const
 
 //------------------------------------------------------------------------------
 void vvSlicerManager::ResetTransformationToIdentity(const std::string actorType)
-{
+{ 
   if(actorType == "image")
     for(unsigned int i=0; i<this->GetImage()->GetTransform().size(); i++)
       this->GetImage()->GetTransform()[i]->Identity();
@@ -915,7 +941,7 @@ void vvSlicerManager::ResetTransformationToIdentity(const std::string actorType)
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::Render()
-{
+{ 
   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
     mSlicers[i]->Render();
   }
@@ -925,7 +951,7 @@ void vvSlicerManager::Render()
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::GenerateDefaultLookupTable()
-{
+{ 
   SetPreset(mPreset);
   SetColorMap(mColorMap);
 }
@@ -934,7 +960,7 @@ void vvSlicerManager::GenerateDefaultLookupTable()
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::Reload()
-{
+{ 
   mReader->Update(mType);
   mImage=mReader->GetOutput();
   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
@@ -951,7 +977,7 @@ void vvSlicerManager::Reload()
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::ReloadFusion()
-{
+{ 
   mFusionReader->Update(mImage->GetNumberOfDimensions(),mFusionComponent.c_str(),mType);
 
   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
@@ -964,7 +990,7 @@ void vvSlicerManager::ReloadFusion()
 //----------------------------------------------------------------------------
 //the secondary sequence is being reloaded.
 void vvSlicerManager::ReloadFusionSequence()
-{
+{ 
   //  this is to keep the slice thickness, which needs to be artificially increased for visualization
   double sp_x, sp_y, sp_z;
   this->GetImage()->GetVTKImages()[0]->GetSpacing(sp_x, sp_y, sp_z);
@@ -1001,7 +1027,7 @@ void vvSlicerManager::ReloadFusionSequence()
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::ReloadOverlay()
-{
+{ 
   mOverlayReader->Update(mImage->GetNumberOfDimensions(),mOverlayComponent.c_str(),mType);
   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
     mSlicers[i]->SetOverlay(mOverlayReader->GetOutput());
@@ -1013,7 +1039,7 @@ void vvSlicerManager::ReloadOverlay()
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::ReloadVF()
-{
+{ 
   mVectorReader->Update(vvImageReader::VECTORFIELD); //deletes the old images through the VF::Init() function
   mVF=mVectorReader->GetOutput();
   for ( unsigned int i = 0; i < mSlicers.size(); i++) {
@@ -1026,7 +1052,7 @@ void vvSlicerManager::ReloadVF()
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::RemoveActor(const std::string& actor_type, int overlay_index)
-{
+{ 
   if (actor_type =="overlay")
     mOverlayReader = NULL;
 
@@ -1050,7 +1076,7 @@ void vvSlicerManager::RemoveActor(const std::string& actor_type, int overlay_ind
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::RemoveActors()
-{
+{ 
   ///This method leaks a few objects. See RemoveActor for what a
   ///correct implementation would look like
   //DS -> probably due to the reader (now released in the
@@ -1065,7 +1091,7 @@ void vvSlicerManager::RemoveActors()
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::UpdateInfoOnCursorPosition(int slicer)
-{
+{ 
   //  int view = mSlicers[slicer]->GetSliceOrientation();
   //  int slice = mSlicers[slicer]->GetSlice();
   double x = mSlicers[slicer]->GetCursorPosition()[0];
@@ -1077,19 +1103,41 @@ void vvSlicerManager::UpdateInfoOnCursorPosition(int slicer)
     mSlicers[slicer]->GetInput()->GetSpacing()[1];
   double Z = (z - mSlicers[slicer]->GetInput()->GetOrigin()[2])/
     mSlicers[slicer]->GetInput()->GetSpacing()[2];
+  double xyz[3], xyzTransform[3];
+  xyz[0] = x;
+  xyz[1] = y;
+  xyz[2] = z;
+  mSlicers[slicer]->GetConcatenatedTransform()->TransformPoint(xyz, xyzTransform);
+  double XTransform = (xyzTransform[0] - mSlicers[slicer]->GetImage()->GetVTKImages()[GetTSlice()]->GetOrigin()[0])/
+    mSlicers[slicer]->GetImage()->GetVTKImages()[GetTSlice()]->GetSpacing()[0];
+  double YTransform = (xyzTransform[1] - mSlicers[slicer]->GetImage()->GetVTKImages()[GetTSlice()]->GetOrigin()[1])/
+    mSlicers[slicer]->GetImage()->GetVTKImages()[GetTSlice()]->GetSpacing()[1];
+  double ZTransform = (xyzTransform[2] - mSlicers[slicer]->GetImage()->GetVTKImages()[GetTSlice()]->GetOrigin()[2])/
+    mSlicers[slicer]->GetImage()->GetVTKImages()[GetTSlice()]->GetSpacing()[2];
   double value = -VTK_DOUBLE_MAX;
   int displayVec = 0;
   double xVec=0, yVec=0, zVec=0, valueVec=0;
   int displayOver = 0;
   int displayFus = 0;
   double valueOver=0, valueFus=0;
-  if (X >= mSlicers[slicer]->GetInput()->GetWholeExtent()[0] &&
-      X <= mSlicers[slicer]->GetInput()->GetWholeExtent()[1] &&
-      Y >= mSlicers[slicer]->GetInput()->GetWholeExtent()[2] &&
-      Y <= mSlicers[slicer]->GetInput()->GetWholeExtent()[3] &&
-      Z >= mSlicers[slicer]->GetInput()->GetWholeExtent()[4] &&
-      Z <= mSlicers[slicer]->GetInput()->GetWholeExtent()[5]) {
-
+#if VTK_MAJOR_VERSION <= 5
+    if (XTransform >= mSlicers[slicer]->GetInput()->GetWholeExtent()[0] -0.5 &&
+      XTransform <= mSlicers[slicer]->GetInput()->GetWholeExtent()[1] +0.5 &&
+      YTransform >= mSlicers[slicer]->GetInput()->GetWholeExtent()[2] -0.5 &&
+      YTransform <= mSlicers[slicer]->GetInput()->GetWholeExtent()[3] +0.5 &&
+      ZTransform >= mSlicers[slicer]->GetInput()->GetWholeExtent()[4] -0.5 &&
+      ZTransform <= mSlicers[slicer]->GetInput()->GetWholeExtent()[5] +0.5)
+#else
+int extentImageReslice[6];
+mSlicers[slicer]->GetRegisterExtent(extentImageReslice);
+    if (XTransform >= extentImageReslice[0] -0.5 &&
+      XTransform <= extentImageReslice[1] +0.5 &&
+      YTransform >= extentImageReslice[2] -0.5 &&
+      YTransform <= extentImageReslice[3] +0.5 &&
+      ZTransform >= extentImageReslice[4] -0.5 &&
+      ZTransform <= extentImageReslice[5] +0.5)
+#endif
+    {
     value = this->GetScalarComponentAsDouble(mSlicers[slicer]->GetInput(), X, Y, Z);
 
     if (mSlicers[slicer]->GetVFActor() ) {
@@ -1137,7 +1185,7 @@ void vvSlicerManager::UpdateInfoOnCursorPosition(int slicer)
 	}
 
     emit UpdatePosition(mSlicers[slicer]->GetCursorVisibility(),
-                        x,y,z,X,Y,Z,value);
+                        x,y,z,XTransform,YTransform,ZTransform,value);
     emit UpdateVector(displayVec,xVec, yVec, zVec, valueVec);
     emit UpdateOverlay(displayOver,valueOver,value);
     emit UpdateFusion(displayFus,valueFus);
@@ -1148,7 +1196,7 @@ void vvSlicerManager::UpdateInfoOnCursorPosition(int slicer)
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::Activated()
-{
+{ 
   emit currentImageChanged(mId);
 }
 //----------------------------------------------------------------------------
@@ -1156,7 +1204,7 @@ void vvSlicerManager::Activated()
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::Picked()
-{
+{ 
   emit currentPickedImageChanged(mId);
 }
 //----------------------------------------------------------------------------
@@ -1164,7 +1212,7 @@ void vvSlicerManager::Picked()
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::UpdateWindowLevel()
-{
+{ 
   emit WindowLevelChanged();
 }
 //----------------------------------------------------------------------------
@@ -1172,12 +1220,11 @@ void vvSlicerManager::UpdateWindowLevel()
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::UpdateSlice(int slicer)
-{
+{ 
   if (mPreviousSlice[slicer] == mSlicers[slicer]->GetSlice()) {
     //DD("============= NOTHING");
     return;
   }
-  //std::cout << "vvSlicerManager::UpdateSlice " << slicer << " " << mSlicers[slicer]->GetSlice() << std::endl;
   emit UpdateSlice(slicer, mSlicers[slicer]->GetSlice());
   mSlicers[slicer]->Render(); // DS <-- I add this, this could/must be the only Render ...
   mPreviousSlice[slicer] = mSlicers[slicer]->GetSlice();
@@ -1187,7 +1234,7 @@ void vvSlicerManager::UpdateSlice(int slicer)
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::UpdateTSlice(int slicer)
-{
+{ 
   int slice = mSlicers[slicer]->GetSlice();
 
   int tslice = mSlicers[slicer]->GetMaxCurrentTSlice();
@@ -1209,7 +1256,7 @@ void vvSlicerManager::UpdateTSlice(int slicer)
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::UpdateSliceRange(int slicer)
-{
+{ 
   emit UpdateSliceRange(slicer,
                         mSlicers[slicer]->GetSliceRange()[0], mSlicers[slicer]->GetSliceRange()[1],
                         0,mSlicers[slicer]->GetTMax());
@@ -1218,7 +1265,7 @@ void vvSlicerManager::UpdateSliceRange(int slicer)
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::SetSlicingPreset(SlicingPresetType preset)
-{
+{ 
   if(mSlicingPreset==preset)
     return;
 
@@ -1240,8 +1287,15 @@ void vvSlicerManager::SetSlicingPreset(SlicingPresetType preset)
       return;
     }
     s->ForceUpdateDisplayExtent();
+#if VTK_MAJOR_VERSION <= 5
     s->SetSlice((s->GetInput()->GetWholeExtent()[s->GetSliceOrientation()*2+1]
                 +s->GetInput()->GetWholeExtent()[s->GetSliceOrientation()*2])/2.0);
+#else
+    int extentImageReslice[6];
+    s->GetRegisterExtent(extentImageReslice);
+    s->SetSlice((extentImageReslice[s->GetSliceOrientation()*2+1]
+                +extentImageReslice[s->GetSliceOrientation()*2])/2.0);
+#endif
     s->ResetCamera();
     s->Render();
   }
@@ -1254,7 +1308,7 @@ void vvSlicerManager::SetSlicingPreset(SlicingPresetType preset)
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::SetPreset(int preset)
-{
+{ 
 
   //vtkLookupTable* LUT = static_cast<vtkLookupTable*>(mSlicers[0]->GetWindowLevel()->GetLookupTable());
   double window = mSlicers[0]->GetColorWindow();
@@ -1313,7 +1367,7 @@ void vvSlicerManager::SetPreset(int preset)
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::SetLocalColorWindowing(const int slicer, const bool bCtrlKey)
-{
+{ 
   double min, max;
   if(bCtrlKey && this->mSlicers[slicer]->GetFusion()) {
     int t = mSlicers[slicer]->GetFusionTSlice();
@@ -1354,7 +1408,7 @@ void vvSlicerManager::SetLocalColorWindowing(const int slicer, const bool bCtrlK
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::SetColorMap(int colormap)
-{
+{ 
   double range[2];
 
   range[0] = mSlicers[0]->GetInput()->GetScalarRange()[0];
@@ -1453,7 +1507,6 @@ void vvSlicerManager::SetColorMap(int colormap)
 
     fusLUT->ForceBuild();
     double v[4];
-
     // set color table transparency
     //double alpha_range=(double)mFusionThresOpacity/10;
     double range_end = fusRange[0] + (double)mFusionThresOpacity*(fusRange[1] - fusRange[0])/100;
@@ -1509,7 +1562,7 @@ void vvSlicerManager::SetColorMap(int colormap)
 
 //----------------------------------------------------------------------------
 vvLandmarks* vvSlicerManager::GetLandmarks()
-{
+{ 
   if (mLandmarks == NULL) {
     mLandmarks = new vvLandmarks(mSlicers[0]->GetTMax()+1);
     for (unsigned int i = 0; i < mSlicers.size(); i++)
@@ -1518,44 +1571,89 @@ vvLandmarks* vvSlicerManager::GetLandmarks()
   return mLandmarks;
 }
 //----------------------------------------------------------------------------
-
+void vvSlicerManager::AddNewLandmark(float x,float y,float z,float t)
+{ 
+    emit callAddLandmark(x,y,z,t);
+}
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::AddLandmark(float x,float y,float z,float t)
-{
+{ 
   double x_index = (x - mSlicers[0]->GetInput()->GetOrigin()[0])/mSlicers[0]->GetInput()->GetSpacing()[0];
   double y_index = (y - mSlicers[0]->GetInput()->GetOrigin()[1])/mSlicers[0]->GetInput()->GetSpacing()[1];
   double z_index = (z - mSlicers[0]->GetInput()->GetOrigin()[2])/mSlicers[0]->GetInput()->GetSpacing()[2];
+#if VTK_MAJOR_VERSION <= 5
   if (x_index >= mSlicers[0]->GetInput()->GetWholeExtent()[0]-0.5 &&
       x_index <= mSlicers[0]->GetInput()->GetWholeExtent()[1]+0.5 &&
       y_index >= mSlicers[0]->GetInput()->GetWholeExtent()[2]-0.5 &&
       y_index <= mSlicers[0]->GetInput()->GetWholeExtent()[3]+0.5 &&
       z_index >= mSlicers[0]->GetInput()->GetWholeExtent()[4]-0.5 &&
-      z_index <= mSlicers[0]->GetInput()->GetWholeExtent()[5]+0.5) {
-    double value = this->GetScalarComponentAsDouble(mSlicers[0]->GetInput(), x_index, y_index, z_index);
+      z_index <= mSlicers[0]->GetInput()->GetWholeExtent()[5]+0.5)
+#else
+  int extentImageReslice[6];
+  mSlicers[0]->GetRegisterExtent(extentImageReslice);
+  if (x_index >= extentImageReslice[0]-0.5 &&
+      x_index <= extentImageReslice[1]+0.5 &&
+      y_index >= extentImageReslice[2]-0.5 &&
+      y_index <= extentImageReslice[3]+0.5 &&
+      z_index >= extentImageReslice[4]-0.5 &&
+      z_index <= extentImageReslice[5]+0.5)
+#endif
+  {
+    double value = this->GetScalarComponentAsDouble(mSlicers[mSelectedSlicer]->GetInput(), x_index, y_index, z_index); //Value in selected Slicer (not 0): bug #2848
     this->GetLandmarks()->AddLandmark(x,y,z,t,value);
     emit LandmarkAdded();
   }
 }
 //----------------------------------------------------------------------------
 
+//----------------------------------------------------------------------------
+void vvSlicerManager::AddLandmarkProfile(float x,float y,float z,float t)
+{ 
+  double x_index = (x - mSlicers[0]->GetInput()->GetOrigin()[0])/mSlicers[0]->GetInput()->GetSpacing()[0];
+  double y_index = (y - mSlicers[0]->GetInput()->GetOrigin()[1])/mSlicers[0]->GetInput()->GetSpacing()[1];
+  double z_index = (z - mSlicers[0]->GetInput()->GetOrigin()[2])/mSlicers[0]->GetInput()->GetSpacing()[2];
+#if VTK_MAJOR_VERSION <= 5
+  if (x_index >= mSlicers[0]->GetInput()->GetWholeExtent()[0]-0.5 &&
+      x_index <= mSlicers[0]->GetInput()->GetWholeExtent()[1]+0.5 &&
+      y_index >= mSlicers[0]->GetInput()->GetWholeExtent()[2]-0.5 &&
+      y_index <= mSlicers[0]->GetInput()->GetWholeExtent()[3]+0.5 &&
+      z_index >= mSlicers[0]->GetInput()->GetWholeExtent()[4]-0.5 &&
+      z_index <= mSlicers[0]->GetInput()->GetWholeExtent()[5]+0.5)
+#else
+  int extentImageReslice[6];
+  mSlicers[0]->GetRegisterExtent(extentImageReslice);
+  if (x_index >= extentImageReslice[0]-0.5 &&
+      x_index <= extentImageReslice[1]+0.5 &&
+      y_index >= extentImageReslice[2]-0.5 &&
+      y_index <= extentImageReslice[3]+0.5 &&
+      z_index >= extentImageReslice[4]-0.5 &&
+      z_index <= extentImageReslice[5]+0.5)
+#endif
+  {
+    double value = this->GetScalarComponentAsDouble(mSlicers[mSelectedSlicer]->GetInput(), x_index, y_index, z_index); //Value in selected Slicer (not 0): bug #2848
+    this->GetLandmarks()->AddLandmark(x,y,z,t,value);
+  }
+}
+//----------------------------------------------------------------------------
+
 //----------------------------------------------------------------------------
 void vvSlicerManager::PrevImage(int slicer)
-{
+{ 
   emit ChangeImageWithIndexOffset(this, slicer, -1);
 }
 //----------------------------------------------------------------------------
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::NextImage(int slicer)
-{
+{ 
   emit ChangeImageWithIndexOffset(this, slicer,  1);
 }
 //----------------------------------------------------------------------------
 
 //----------------------------------------------------------------------------
 void vvSlicerManager::VerticalSliderHasChanged(int slicer, int slice)
-{
+{ 
   emit AVerticalSliderHasChanged(slicer, slice);
 }
 
@@ -1563,7 +1661,7 @@ void vvSlicerManager::VerticalSliderHasChanged(int slicer, int slice)
 
 //----------------------------------------------------------------------------
 double vvSlicerManager::GetScalarComponentAsDouble(vtkImageData *image, double X, double Y, double Z, int component)
-{
+{ 
   int ix, iy, iz;
   return mSlicers[0]->GetScalarComponentAsDouble(image, X, Y, Z, ix, iy, iz, component);
 }