diff --git a/Modules/SurfaceInterpolation/mitkCreateDistanceImageFromSurfaceFilter.cpp b/Modules/SurfaceInterpolation/mitkCreateDistanceImageFromSurfaceFilter.cpp
index 5b3b8d8de1..efe5d9d340 100644
--- a/Modules/SurfaceInterpolation/mitkCreateDistanceImageFromSurfaceFilter.cpp
+++ b/Modules/SurfaceInterpolation/mitkCreateDistanceImageFromSurfaceFilter.cpp
@@ -1,622 +1,630 @@
 /*===================================================================
 
 The Medical Imaging Interaction Toolkit (MITK)
 
 Copyright (c) German Cancer Research Center,
 Division of Medical and Biological Informatics.
 All rights reserved.
 
 This software is distributed WITHOUT ANY WARRANTY; without
 even the implied warranty of MERCHANTABILITY or FITNESS FOR
 A PARTICULAR PURPOSE.
 
 See LICENSE.txt or http://www.mitk.org for details.
 
 ===================================================================*/
 
 #include "mitkCreateDistanceImageFromSurfaceFilter.h"
 
 mitk::CreateDistanceImageFromSurfaceFilter::CreateDistanceImageFromSurfaceFilter()
 {
   m_DistanceImageVolume = 50000;
   this->m_UseProgressBar = false;
   this->m_ProgressStepSize = 5;
 
   mitk::Image::Pointer output = mitk::Image::New();
   this->SetNthOutput(0, output.GetPointer());
 }
 
 
 mitk::CreateDistanceImageFromSurfaceFilter::~CreateDistanceImageFromSurfaceFilter()
 {
 }
 
 void mitk::CreateDistanceImageFromSurfaceFilter::GenerateData()
 {
   //First of all we have to build the equation-system from the existing contour-edge-points
   this->CreateSolutionMatrixAndFunctionValues();
+
+  if (this->m_UseProgressBar)
+    mitk::ProgressBar::GetInstance()->Progress(1);
+
   //Then we solve the equation-system via QR - decomposition. The interpolation weights are obtained in that way
   vnl_qr<double> solver (m_SolutionMatrix);
   m_Weights = solver.solve(m_FunctionValues);
 
   //Setting progressbar
   if (this->m_UseProgressBar)
     mitk::ProgressBar::GetInstance()->Progress(2);
 
   //The last step is to create the distance map with the interpolated distance function
   this->CreateDistanceImage();
+
+  if (this->m_UseProgressBar)
+    mitk::ProgressBar::GetInstance()->Progress(2);
+
   m_Centers.clear();
   m_FunctionValues.clear();
   m_Normals.clear();
   m_Weights.clear();
   m_SolutionMatrix.clear();
 
   //Setting progressbar
   if (this->m_UseProgressBar)
     mitk::ProgressBar::GetInstance()->Progress(3);
 }
 
 void mitk::CreateDistanceImageFromSurfaceFilter::CreateSolutionMatrixAndFunctionValues()
 {
   unsigned int numberOfInputs = this->GetNumberOfIndexedInputs();
 
   if (numberOfInputs == 0)
   {
     MITK_ERROR << "mitk::CreateDistanceImageFromSurfaceFilter: No input available. Please set an input!" << std::endl;
     itkExceptionMacro("mitk::CreateDistanceImageFromSurfaceFilter: No input available. Please set an input!");
     return;
   }
 
   //First of all we have to extract the nomals and the surface points.
   //Duplicated points can be eliminated
 
   Surface* currentSurface;
   vtkSmartPointer<vtkPolyData> polyData;
   vtkSmartPointer<vtkDoubleArray> currentCellNormals;
   vtkSmartPointer<vtkCellArray> existingPolys;
   vtkSmartPointer<vtkPoints> existingPoints;
 
   double p[3];
   PointType currentPoint;
   PointType normal;
 
   for (unsigned int i = 0; i < numberOfInputs; i++)
   {
     currentSurface = const_cast<Surface*>( this->GetInput(i) );
     polyData = currentSurface->GetVtkPolyData();
 
     if (polyData->GetNumberOfPolys() == 0)
     {
       MITK_INFO << "mitk::CreateDistanceImageFromSurfaceFilter: No input-polygons available. Please be sure the input surface consists of polygons!" << std::endl;
     }
 
     currentCellNormals = vtkDoubleArray::SafeDownCast(polyData->GetCellData()->GetNormals());
 
     existingPolys = polyData->GetPolys();
 
     existingPoints = polyData->GetPoints();
 
     existingPolys->InitTraversal();
 
     vtkIdType* cell (NULL);
     vtkIdType cellSize (0);
 
     for( existingPolys->InitTraversal(); existingPolys->GetNextCell(cellSize, cell);)
     {
       for ( vtkIdType j = 0; j < cellSize; j++ )
       {
         existingPoints->GetPoint(cell[j], p);
 
         currentPoint.copy_in(p);
 
         int count = std::count(m_Centers.begin() ,m_Centers.end(),currentPoint);
 
         if (count == 0)
         {
           double currentNormal[3];
           currentCellNormals->GetTuple(cell[j], currentNormal);
 
           normal.copy_in(currentNormal);
 
           m_Normals.push_back(normal);
 
           m_Centers.push_back(currentPoint);
         }
 
       }//end for all points
     }//end for all cells
   }//end for all outputs
 
   //For we can now calculate the exact size of the centers we initialize the data structures
   unsigned int numberOfCenters = m_Centers.size();
   m_Centers.reserve(numberOfCenters*3);
 
   m_FunctionValues.set_size(numberOfCenters*3);
   m_FunctionValues.fill(0);
 
   //Create inner points
   for (unsigned int i = 0; i < numberOfCenters; i++)
   {
     currentPoint = m_Centers.at(i);
     normal = m_Normals.at(i);
 
     currentPoint[0] = currentPoint[0] - normal[0];
     currentPoint[1] = currentPoint[1] - normal[1];
     currentPoint[2] = currentPoint[2] - normal[2];
 
     m_Centers.push_back(currentPoint);
 
     m_FunctionValues.put(numberOfCenters+i, -1);
   }
 
   //Create outer points
   for (unsigned int i = 0; i < numberOfCenters; i++)
   {
     currentPoint = m_Centers.at(i);
     normal = m_Normals.at(i);
 
     currentPoint[0] = currentPoint[0] + normal[0];
     currentPoint[1] = currentPoint[1] + normal[1];
     currentPoint[2] = currentPoint[2] + normal[2];
 
     m_Centers.push_back(currentPoint);
 
     m_FunctionValues.put(numberOfCenters*2+i, 1);
   }
 
   //Now we have created all centers and all function values. Next step is to create the solution matrix
   numberOfCenters = m_Centers.size();
   m_SolutionMatrix.set_size(numberOfCenters, numberOfCenters);
 
   m_Weights.set_size(numberOfCenters);
 
   PointType p1;
   PointType p2;
   double norm;
 
   for (unsigned int i = 0; i < numberOfCenters; i++)
   {
     for (unsigned int j = 0; j < numberOfCenters; j++)
     {
       //Calculate the RBF value. Currently using Phi(r) = r with r is the euclidian distance between two points
       p1 = m_Centers.at(i);
       p2 = m_Centers.at(j);
       p1 = p1 - p2;
       norm = p1.two_norm();
       m_SolutionMatrix(i,j) = norm;
 
     }
   }
 
 }
 
 void mitk::CreateDistanceImageFromSurfaceFilter::CreateDistanceImage()
 {
   DistanceImageType::Pointer distanceImg = DistanceImageType::New();
 
   // Determine the bounds of the input points in index- and world-coordinates
   DistanceImageType::PointType minPointInWorldCoordinates, maxPointInWorldCoordinates;
   DistanceImageType::IndexType minPointInIndexCoordinates, maxPointInIndexCoordinates;
 
   DetermineBounds( minPointInWorldCoordinates, maxPointInWorldCoordinates,
                    minPointInIndexCoordinates, maxPointInIndexCoordinates );
 
 
   // Calculate the extent of the region that contains all given points in MM.
   // To do this, we take the difference between the maximal and minimal
   // index-coordinates (must not be less than 1) and multiply it with the
   // spacing of the reference-image.
   Vector3D extentMM;
   for (unsigned int dim = 0; dim < 3; ++dim)
   {
     extentMM[dim] = (int)
       (
                     (std::max( std::abs(maxPointInIndexCoordinates[dim] - minPointInIndexCoordinates[dim]),
                               (DistanceImageType::IndexType::IndexValueType) 1
                             ) + 1.0) // (max-index - min-index)+1 because the pixels between index 3 and 5 cover 2+1=3 pixels (pixel 3,4, and 5)
                     * m_ReferenceImage->GetSpacing()[dim]
       ) + 1; // (int) ((...) + 1) -> we round up to the next BIGGER int value
   }
 
   /*
   * Now create an empty distance image. The create image will always have the same sizeOfRegion, independent from
   * the original image (e.g. always consists of 500000 pixels) and will have an isotropic spacing.
   * The spacing is calculated like the following:
   * The image's volume = 500000 Pixels = extentX*spacing*extentY*spacing*extentZ*spacing
   * So the spacing is: spacing = ( 500000 / extentX*extentY*extentZ )^(1/3)
   */
   double basis = (extentMM[0]*extentMM[1]*extentMM[2]) / m_DistanceImageVolume;
   double exponent = 1.0/3.0;
   double distImgSpacing = pow(basis, exponent);
   int tempSpacing = (distImgSpacing+0.05)*10;
   m_DistanceImageSpacing = (double)tempSpacing/10.0;
 
   // calculate the number of pixels of the distance image for each direction
   unsigned int numberOfXPixel = extentMM[0] / m_DistanceImageSpacing;
   unsigned int numberOfYPixel = extentMM[1] / m_DistanceImageSpacing;
   unsigned int numberOfZPixel = extentMM[2] / m_DistanceImageSpacing;
 
   // We increase the sizeOfRegion by 4 as we decrease the origin by 2 later.
   // This expansion of the region is necessary to achieve a complete
   // interpolation.
   DistanceImageType::SizeType sizeOfRegion;
   sizeOfRegion[0] = numberOfXPixel + 4;
   sizeOfRegion[1] = numberOfYPixel + 4;
   sizeOfRegion[2] = numberOfZPixel + 4;
 
   // The region starts at index 0,0,0
   DistanceImageType::IndexType initialOriginAsIndex;
   initialOriginAsIndex.Fill(0);
 
   DistanceImageType::PointType originAsWorld = minPointInWorldCoordinates;
 
   DistanceImageType::RegionType lpRegion;
   lpRegion.SetSize(sizeOfRegion);
   lpRegion.SetIndex(initialOriginAsIndex);
 
   // We initialize the itk::Image with
   //  * origin and direction to have it correctly placed and rotated in the world
   //  * the largest possible region to set the extent to be calculated
   //  * the isotropic spacing that we have calculated above
   distanceImg->SetOrigin( originAsWorld );
   distanceImg->SetDirection( m_ReferenceImage->GetDirection() );
   distanceImg->SetRegions( lpRegion );
   distanceImg->SetSpacing( m_DistanceImageSpacing );
   distanceImg->Allocate();
 
   //First of all the image is initialized with the value 10 for each pixel
   distanceImg->FillBuffer(10);
 
   // Now we move the origin of the distanceImage 2 index-Coordinates
   // in all directions
   DistanceImageType::IndexType originAsIndex;
   distanceImg->TransformPhysicalPointToIndex( originAsWorld, originAsIndex );
   originAsIndex[0] -= 2;
   originAsIndex[1] -= 2;
   originAsIndex[2] -= 2;
   distanceImg->TransformIndexToPhysicalPoint( originAsIndex, originAsWorld );
   distanceImg->SetOrigin( originAsWorld );
 
   /*
   * Now we must calculate the distance for each pixel. But instead of calculating the distance value
   * for all of the image's pixels we proceed similar to the region growing algorithm:
   *
   * 1. Take the first pixel from the narrowband_point_list and calculate the distance for each neighbor (6er)
   * 2. If the current index's distance value is below a certain threshold push it into the list
   * 3. Next iteration take the next index from the list and originAsIndex with 1. again
   *
   * This is done until the narrowband_point_list is empty.
   */
   std::queue<DistanceImageType::IndexType> narrowbandPoints;
   PointType currentPoint = m_Centers.at(0);
   double distance = this->CalculateDistanceValue(currentPoint);
 
   // create itk::Point from vnl_vector
   DistanceImageType::PointType currentPointAsPoint;
   currentPointAsPoint[0] = currentPoint[0];
   currentPointAsPoint[1] = currentPoint[1];
   currentPointAsPoint[2] = currentPoint[2];
 
   // Transform the input point in world-coordinates to index-coordinates
   DistanceImageType::IndexType currentIndex;
   distanceImg->TransformPhysicalPointToIndex( currentPointAsPoint, currentIndex );
 
   assert( lpRegion.IsInside(currentIndex) ); // we are quite certain this should hold
 
   narrowbandPoints.push(currentIndex);
   distanceImg->SetPixel(currentIndex, distance);
 
   NeighborhoodImageIterator::RadiusType radius;
   radius.Fill(1);
   NeighborhoodImageIterator nIt(radius, distanceImg, distanceImg->GetLargestPossibleRegion());
   unsigned int relativeNbIdx[] = {4, 10, 12, 14, 16, 22};
 
   bool isInBounds = false;
   while ( !narrowbandPoints.empty() )
   {
 
     nIt.SetLocation(narrowbandPoints.front());
     narrowbandPoints.pop();
 
     unsigned int* relativeNb = &relativeNbIdx[0];
     for (int i = 0; i < 6; i++)
     {
       nIt.GetPixel(*relativeNb, isInBounds);
       if( isInBounds && nIt.GetPixel(*relativeNb) == 10)
       {
         currentIndex = nIt.GetIndex(*relativeNb);
 
         // Transform the currently checked point from index-coordinates to
         // world-coordinates
         distanceImg->TransformIndexToPhysicalPoint( currentIndex, currentPointAsPoint );
 
         // create a vnl_vector
         currentPoint[0] = currentPointAsPoint[0];
         currentPoint[1] = currentPointAsPoint[1];
         currentPoint[2] = currentPointAsPoint[2];
 
         // and check the distance
         distance = this->CalculateDistanceValue(currentPoint);
         if ( abs(distance) <= m_DistanceImageSpacing )
         {
           nIt.SetPixel(*relativeNb, distance);
           narrowbandPoints.push(currentIndex);
         }
       }
       relativeNb++;
     }
   }
 
 
   ImageIterator imgRegionIterator (distanceImg, distanceImg->GetLargestPossibleRegion());
   imgRegionIterator.GoToBegin();
 
   double prevPixelVal = 1;
 
   DistanceImageType::IndexType _size;
   _size.Fill(-1);
   _size += sizeOfRegion;
 
   //Set every pixel inside the surface to -10 except the edge point (so that the received surface is closed)
   while (!imgRegionIterator.IsAtEnd()) {
 
     if ( imgRegionIterator.Get() == 10 && prevPixelVal < 0 )
     {
 
       while (imgRegionIterator.Get() == 10)
       {
         if (imgRegionIterator.GetIndex()[0] == _size[0] || imgRegionIterator.GetIndex()[1] == _size[1] || imgRegionIterator.GetIndex()[2] == _size[2]
             || imgRegionIterator.GetIndex()[0] == 0U || imgRegionIterator.GetIndex()[1] == 0U || imgRegionIterator.GetIndex()[2] == 0U )
         {
           imgRegionIterator.Set(10);
           prevPixelVal = 10;
           ++imgRegionIterator;
           break;
         }
         else
         {
           imgRegionIterator.Set(-10);
           ++imgRegionIterator;
           prevPixelVal = -10;
         }
 
       }
 
     }
     else if (imgRegionIterator.GetIndex()[0] == _size[0] || imgRegionIterator.GetIndex()[1] == _size[1] || imgRegionIterator.GetIndex()[2] == _size[2]
              || imgRegionIterator.GetIndex()[0] == 0U || imgRegionIterator.GetIndex()[1] == 0U || imgRegionIterator.GetIndex()[2] == 0U)
 
     {
       imgRegionIterator.Set(10);
       prevPixelVal = 10;
       ++imgRegionIterator;
     }
     else
     {
       prevPixelVal = imgRegionIterator.Get();
       ++imgRegionIterator;
     }
   }
 
   Image::Pointer resultImage = this->GetOutput();
 
   // Cast the created distance-Image from itk::Image to the mitk::Image
   // that is our output.
   CastToMitkImage(distanceImg, resultImage);
 }
 
 void mitk::CreateDistanceImageFromSurfaceFilter::FillImageRegion(DistanceImageType::RegionType reqRegion,
                                                                  DistanceImageType::PixelType pixelValue, DistanceImageType::Pointer image)
 {
   image->SetRequestedRegion(reqRegion);
   ImageIterator it (image, image->GetRequestedRegion());
   while (!it.IsAtEnd())
   {
     it.Set(pixelValue);
     ++it;
   }
 
 }
 
 
 double mitk::CreateDistanceImageFromSurfaceFilter::CalculateDistanceValue(PointType p)
 {
   double distanceValue (0);
   PointType p1;
   PointType p2;
   double norm;
 
   CenterList::iterator centerIter;
   InterpolationWeights::iterator weightsIter;
 
   for ( centerIter=m_Centers.begin(), weightsIter=m_Weights.begin();
     centerIter!=m_Centers.end() && weightsIter!=m_Weights.end();
     centerIter++, weightsIter++ )
   {
     p1 = *centerIter;
     p2 = p-p1;
     norm = p2.two_norm();
     distanceValue = distanceValue + norm* (*weightsIter);
   }
   return distanceValue;
 }
 
 void mitk::CreateDistanceImageFromSurfaceFilter::GenerateOutputInformation()
 {
 }
 
 void mitk::CreateDistanceImageFromSurfaceFilter::PrintEquationSystem()
 {
   std::stringstream out;
   out<<"Nummber of rows: "<<m_SolutionMatrix.rows()<<" ****** Number of columns: "<<m_SolutionMatrix.columns()<<endl;
   out<<"[ ";
   for (unsigned int i = 0; i < m_SolutionMatrix.rows(); i++)
   {
     for (unsigned int j = 0; j < m_SolutionMatrix.columns(); j++)
     {
       out<<m_SolutionMatrix(i,j)<<"   ";
     }
     out<<";"<<endl;
   }
   out<<" ]\n\n\n";
 
   for (unsigned int i = 0; i < m_Centers.size(); i++)
   {
     out<<m_Centers.at(i)<<";"<<endl;
   }
   std::cout<<"Equation system: \n\n\n"<<out.str();
 }
 
 
 
 void mitk::CreateDistanceImageFromSurfaceFilter::SetInput( const mitk::Surface* surface )
 {
     this->SetInput( 0, const_cast<mitk::Surface*>( surface ) );
 }
 
 
 void mitk::CreateDistanceImageFromSurfaceFilter::SetInput( unsigned int idx, const mitk::Surface* surface )
 {
     if ( this->GetInput(idx) != surface )
     {
         this->SetNthInput( idx, const_cast<mitk::Surface*>( surface ) );
         this->Modified();
     }
 }
 
 
 const mitk::Surface* mitk::CreateDistanceImageFromSurfaceFilter::GetInput()
 {
     if (this->GetNumberOfIndexedInputs() < 1)
         return NULL;
 
     return static_cast<const mitk::Surface*>(this->ProcessObject::GetInput(0));
 }
 
 
 const mitk::Surface* mitk::CreateDistanceImageFromSurfaceFilter::GetInput( unsigned int idx)
 {
     if (this->GetNumberOfIndexedInputs() < 1)
         return NULL;
 
     return static_cast<const mitk::Surface*>(this->ProcessObject::GetInput(idx));
 }
 
 void mitk::CreateDistanceImageFromSurfaceFilter::RemoveInputs(mitk::Surface* input)
 {
   DataObjectPointerArraySizeType nb = this->GetNumberOfIndexedInputs();
 
   for(DataObjectPointerArraySizeType i = 0; i < nb; i++)
   {
     if( this->GetInput(i) == input )
     {
       this->RemoveInput(i);
       return;
     }
   }
 }
 
 void mitk::CreateDistanceImageFromSurfaceFilter::Reset()
 {
   for (unsigned int i = 0; i < this->GetNumberOfIndexedInputs(); i++)
   {
     this->PopBackInput();
   }
   this->SetNumberOfIndexedInputs(0);
   this->SetNumberOfIndexedOutputs(1);
 
   mitk::Image::Pointer output = mitk::Image::New();
   this->SetNthOutput(0, output.GetPointer());
 }
 
 void mitk::CreateDistanceImageFromSurfaceFilter::SetUseProgressBar(bool status)
 {
   this->m_UseProgressBar = status;
 }
 
 void mitk::CreateDistanceImageFromSurfaceFilter::SetProgressStepSize(unsigned int stepSize)
 {
   this->m_ProgressStepSize = stepSize;
 }
 
 void mitk::CreateDistanceImageFromSurfaceFilter::SetReferenceImage( itk::ImageBase<3>::Pointer referenceImage )
 {
  m_ReferenceImage = referenceImage;
 }
 
 void mitk::CreateDistanceImageFromSurfaceFilter::DetermineBounds( DistanceImageType::PointType &minPointInWorldCoordinates,
                                                                   DistanceImageType::PointType &maxPointInWorldCoordinates,
                                                                   DistanceImageType::IndexType &minPointInIndexCoordinates,
                                                                   DistanceImageType::IndexType &maxPointInIndexCoordinates )
 {
   PointType firstCenter = m_Centers.at(0);
   DistanceImageType::PointType tmpPoint;
   tmpPoint[0] = firstCenter[0];
   tmpPoint[1] = firstCenter[1];
   tmpPoint[2] = firstCenter[2];
 
   // transform the first point from world-coordinates to index-coordinates
   DistanceImageType::IndexType tmpIndex;
   m_ReferenceImage->TransformPhysicalPointToIndex( tmpPoint, tmpIndex );
 
   // initialize the variables with this first point
   int xmin = tmpIndex[0];
   int ymin = tmpIndex[1];
   int zmin = tmpIndex[2];
   int xmax = tmpIndex[0];
   int ymax = tmpIndex[1];
   int zmax = tmpIndex[2];
 
   // iterate over the rest of the points
   CenterList::iterator centerIter = m_Centers.begin();
   for ( ++centerIter; centerIter!=m_Centers.end(); centerIter++)
   {
     tmpPoint[0] = (*centerIter)[0];
     tmpPoint[1] = (*centerIter)[1];
     tmpPoint[2] = (*centerIter)[2];
 
     // transform each point from world-coordinates to index-coordinates
     m_ReferenceImage->TransformPhysicalPointToIndex( tmpPoint, tmpIndex );
 
     // and set the variables accordingly to find the minimum
     // and maximum in all directions in index-coordinates
     if (xmin > tmpIndex[0])
     {
       xmin = tmpIndex[0];
     }
     if (ymin > tmpIndex[1])
     {
       ymin = tmpIndex[1];
     }
     if (zmin > tmpIndex[2])
     {
       zmin = tmpIndex[2];
     }
     if (xmax < tmpIndex[0])
     {
       xmax = tmpIndex[0];
     }
     if (ymax < tmpIndex[1])
     {
       ymax = tmpIndex[1];
     }
     if (zmax < tmpIndex[2])
     {
       zmax = tmpIndex[2];
     }
   }
 
   // put the found coordinates into Index-Points
   minPointInIndexCoordinates[0] = xmin;
   minPointInIndexCoordinates[1] = ymin;
   minPointInIndexCoordinates[2] = zmin;
 
   maxPointInIndexCoordinates[0] = xmax;
   maxPointInIndexCoordinates[1] = ymax;
   maxPointInIndexCoordinates[2] = zmax;
 
   // and transform them into world-coordinates
   m_ReferenceImage->TransformIndexToPhysicalPoint( minPointInIndexCoordinates, minPointInWorldCoordinates );
   m_ReferenceImage->TransformIndexToPhysicalPoint( maxPointInIndexCoordinates, maxPointInWorldCoordinates );
 }
 
diff --git a/Modules/SurfaceInterpolation/mitkSurfaceInterpolationController.cpp b/Modules/SurfaceInterpolation/mitkSurfaceInterpolationController.cpp
index a676ff4c0c..7fbaf75c57 100644
--- a/Modules/SurfaceInterpolation/mitkSurfaceInterpolationController.cpp
+++ b/Modules/SurfaceInterpolation/mitkSurfaceInterpolationController.cpp
@@ -1,541 +1,538 @@
 /*===================================================================
 
 The Medical Imaging Interaction Toolkit (MITK)
 
 Copyright (c) German Cancer Research Center,
 Division of Medical and Biological Informatics.
 All rights reserved.
 
 This software is distributed WITHOUT ANY WARRANTY; without
 even the implied warranty of MERCHANTABILITY or FITNESS FOR
 A PARTICULAR PURPOSE.
 
 See LICENSE.txt or http://www.mitk.org for details.
 
 ===================================================================*/
 
 #include "mitkSurfaceInterpolationController.h"
 #include "mitkMemoryUtilities.h"
 #include "mitkImageAccessByItk.h"
 #include "mitkImageCast.h"
 
 #include "mitkImageToSurfaceFilter.h"
 
 // Check whether the given contours are coplanar
 bool ContoursCoplanar(mitk::SurfaceInterpolationController::ContourPositionInformation leftHandSide, mitk::SurfaceInterpolationController::ContourPositionInformation rightHandSide)
 {
   // Here we check two things:
   // 1. Whether the normals of both contours are at least parallel
   // 2. Whether both contours lie in the same plane
 
   // Check for coplanarity:
   // a. Span a vector between two points one from each contour
   // b. Calculate dot product for the vector and one of the normals
   // c. If the dot is zero the two vectors are orthogonal and the contours are coplanar
 
   double vec[3];
   vec[0] = leftHandSide.contourPoint[0] - rightHandSide.contourPoint[0];
   vec[1] = leftHandSide.contourPoint[1] - rightHandSide.contourPoint[1];
   vec[2] = leftHandSide.contourPoint[2] - rightHandSide.contourPoint[2];
   double n[3];
   n[0] = rightHandSide.contourNormal[0];
   n[1] = rightHandSide.contourNormal[1];
   n[2] = rightHandSide.contourNormal[2];
   double dot = vtkMath::Dot(n, vec);
 
   double n2[3];
   n2[0] = leftHandSide.contourNormal[0];
   n2[1] = leftHandSide.contourNormal[1];
   n2[2] = leftHandSide.contourNormal[2];
 
   // The normals of both contours have to be parallel but not of the same orientation
   double lengthLHS = leftHandSide.contourNormal.GetNorm();
   double lengthRHS = rightHandSide.contourNormal.GetNorm();
   double dot2 = vtkMath::Dot(n, n2);
   bool contoursParallel = mitk::Equal(fabs(lengthLHS*lengthRHS), fabs(dot2), 0.001);
 
   if (mitk::Equal(dot, 0.0, 0.001) && contoursParallel)
     return true;
   else
     return false;
 }
 
 mitk::SurfaceInterpolationController::ContourPositionInformation CreateContourPositionInformation(mitk::Surface::Pointer contour)
 {
   mitk::SurfaceInterpolationController::ContourPositionInformation contourInfo;
   contourInfo.contour = contour;
   double n[3];
   double p[3];
   contour->GetVtkPolyData()->GetPoints()->GetPoint(0, p);
   vtkPolygon::ComputeNormal(contour->GetVtkPolyData()->GetPoints(), n);
   contourInfo.contourNormal = n;
   contourInfo.contourPoint = p;
   return contourInfo;
 }
 
 mitk::SurfaceInterpolationController::SurfaceInterpolationController()
   :m_SelectedSegmentation(0)
 {
   m_ReduceFilter = ReduceContourSetFilter::New();
   m_NormalsFilter = ComputeContourSetNormalsFilter::New();
   m_InterpolateSurfaceFilter = CreateDistanceImageFromSurfaceFilter::New();
 
   m_ReduceFilter->SetUseProgressBar(false);
-  m_NormalsFilter->SetUseProgressBar(false);
-  m_InterpolateSurfaceFilter->SetUseProgressBar(false);
+//  m_ReduceFilter->SetProgressStepSize(1);
+  m_NormalsFilter->SetUseProgressBar(true);
+  m_NormalsFilter->SetProgressStepSize(1);
+  m_InterpolateSurfaceFilter->SetUseProgressBar(true);
+  m_InterpolateSurfaceFilter->SetProgressStepSize(7);
 
   m_Contours = Surface::New();
 
   m_PolyData = vtkSmartPointer<vtkPolyData>::New();
   m_PolyData->SetPoints(vtkPoints::New());
 
   m_InterpolationResult = 0;
   m_CurrentNumberOfReducedContours = 0;
 }
 
 mitk::SurfaceInterpolationController::~SurfaceInterpolationController()
 {
   //Removing all observers
   std::map<mitk::Image*, unsigned long>::iterator dataIter = m_SegmentationObserverTags.begin();
   for (; dataIter != m_SegmentationObserverTags.end(); ++dataIter )
   {
     (*dataIter).first->RemoveObserver( (*dataIter).second );
   }
   m_SegmentationObserverTags.clear();
 }
 
 mitk::SurfaceInterpolationController* mitk::SurfaceInterpolationController::GetInstance()
 {
   static mitk::SurfaceInterpolationController* m_Instance;
 
   if ( m_Instance == 0)
   {
     m_Instance = new SurfaceInterpolationController();
   }
   return m_Instance;
 }
 
 void mitk::SurfaceInterpolationController::AddNewContour (mitk::Surface::Pointer newContour)
 {
   ContourPositionInformation contourInfo = CreateContourPositionInformation(newContour);
   this->AddToInterpolationPipeline(contourInfo);
 
   this->Modified();
 }
 
 void mitk::SurfaceInterpolationController::AddNewContours(std::vector<mitk::Surface::Pointer> newContours)
 {
   for (unsigned int i = 0; i < newContours.size(); ++i)
   {
     ContourPositionInformation contourInfo = CreateContourPositionInformation(newContours.at(i));
     this->AddToInterpolationPipeline(contourInfo);
   }
   this->Modified();
 }
 
 void mitk::SurfaceInterpolationController::AddToInterpolationPipeline(ContourPositionInformation contourInfo)
 {
   int pos (-1);
   ContourPositionInformationList currentContourList = m_ListOfInterpolationSessions[m_SelectedSegmentation];
   mitk::Surface* newContour = contourInfo.contour;
   for (unsigned int i = 0; i < currentContourList.size(); i++)
   {
     ContourPositionInformation contourFromList = currentContourList.at(i);
     if (ContoursCoplanar(contourInfo, contourFromList))
     {
       pos = i;
       break;
     }
   }
 
   //Don't save a new empty contour
   if (pos == -1 && newContour->GetVtkPolyData()->GetNumberOfPoints() > 0)
   {
     m_ReduceFilter->SetInput(m_ListOfInterpolationSessions[m_SelectedSegmentation].size(), newContour);
     m_ListOfInterpolationSessions[m_SelectedSegmentation].push_back(contourInfo);
   }
   else if (pos != -1 && newContour->GetVtkPolyData()->GetNumberOfPoints() > 0)
   {
     m_ListOfInterpolationSessions[m_SelectedSegmentation].at(pos) = contourInfo;
     m_ReduceFilter->SetInput(pos, newContour);
   }
   else if (newContour->GetVtkPolyData()->GetNumberOfPoints() == 0)
   {
     this->RemoveContour(contourInfo);
   }
 
   m_ReduceFilter->Update();
   m_CurrentNumberOfReducedContours = m_ReduceFilter->GetNumberOfOutputs();
 
   for (unsigned int i = 0; i < m_CurrentNumberOfReducedContours; i++)
   {
     m_NormalsFilter->SetInput(i, m_ReduceFilter->GetOutput(i));
     m_InterpolateSurfaceFilter->SetInput(i, m_NormalsFilter->GetOutput(i));
   }
 }
 
 bool mitk::SurfaceInterpolationController::RemoveContour(ContourPositionInformation contourInfo)
 {
   ContourPositionInformationList::iterator it = m_ListOfInterpolationSessions[m_SelectedSegmentation].begin();
   while (it !=  m_ListOfInterpolationSessions[m_SelectedSegmentation].end())
   {
     ContourPositionInformation currentContour = (*it);
     if (ContoursCoplanar(currentContour, contourInfo))
     {
       m_ListOfInterpolationSessions[m_SelectedSegmentation].erase(it);
       this->ReinitializeInterpolation();
       return true;
     }
     ++it;
   }
   return false;
 }
 
 const mitk::Surface* mitk::SurfaceInterpolationController::GetContour(ContourPositionInformation contourInfo)
 {
   ContourPositionInformationList contourList = m_ListOfInterpolationSessions[m_SelectedSegmentation];
   for (unsigned int i = 0; i < contourList.size(); ++i)
   {
     ContourPositionInformation currentContour = contourList.at(i);
     if (ContoursCoplanar(contourInfo, currentContour))
       return currentContour.contour;
   }
   return 0;
 }
 
 unsigned int mitk::SurfaceInterpolationController::GetNumberOfContours()
 {
   return m_ListOfInterpolationSessions[m_SelectedSegmentation].size();
 }
 
 void mitk::SurfaceInterpolationController::Interpolate()
 {
   if (m_CurrentNumberOfReducedContours< 2)
   {
     //If no interpolation is possible reset the interpolation result
     m_InterpolationResult = 0;
     return;
   }
 
   //Setting up progress bar
-   /*
-    * Removed due to bug 12441. ProgressBar messes around with Qt event queue which is fatal for segmentation
-    */
-  //mitk::ProgressBar::GetInstance()->AddStepsToDo(8);
+  mitk::ProgressBar::GetInstance()->AddStepsToDo(10);
 
   // create a surface from the distance-image
   mitk::ImageToSurfaceFilter::Pointer imageToSurfaceFilter = mitk::ImageToSurfaceFilter::New();
   imageToSurfaceFilter->SetInput( m_InterpolateSurfaceFilter->GetOutput() );
   imageToSurfaceFilter->SetThreshold( 0 );
   imageToSurfaceFilter->SetSmooth(true);
   imageToSurfaceFilter->SetSmoothIteration(20);
   imageToSurfaceFilter->Update();
   m_InterpolationResult = imageToSurfaceFilter->GetOutput();
 
   vtkSmartPointer<vtkAppendPolyData> polyDataAppender = vtkSmartPointer<vtkAppendPolyData>::New();
   for (unsigned int i = 0; i < m_ListOfInterpolationSessions[m_SelectedSegmentation].size(); i++)
   {
     polyDataAppender->AddInputData(m_ListOfInterpolationSessions[m_SelectedSegmentation].at(i).contour->GetVtkPolyData());
   }
   polyDataAppender->Update();
   m_Contours->SetVtkPolyData(polyDataAppender->GetOutput());
 
   //Last progress step
-  /*
-   * Removed due to bug 12441. ProgressBar messes around with Qt event queue which is fatal for segmentation
-   */
-  //mitk::ProgressBar::GetInstance()->Progress(8);
+  mitk::ProgressBar::GetInstance()->Progress(2);
 
   m_InterpolationResult->DisconnectPipeline();
 }
 
 mitk::Surface::Pointer mitk::SurfaceInterpolationController::GetInterpolationResult()
 {
     return m_InterpolationResult;
 }
 
 mitk::Surface* mitk::SurfaceInterpolationController::GetContoursAsSurface()
 {
   return m_Contours;
 }
 
 void mitk::SurfaceInterpolationController::SetDataStorage(DataStorage::Pointer ds)
 {
   m_DataStorage = ds;
 }
 
 void mitk::SurfaceInterpolationController::SetMinSpacing(double minSpacing)
 {
   m_ReduceFilter->SetMinSpacing(minSpacing);
 }
 
 void mitk::SurfaceInterpolationController::SetMaxSpacing(double maxSpacing)
 {
   m_ReduceFilter->SetMaxSpacing(maxSpacing);
   m_NormalsFilter->SetMaxSpacing(maxSpacing);
 }
 
 void mitk::SurfaceInterpolationController::SetDistanceImageVolume(unsigned int distImgVolume)
 {
   m_InterpolateSurfaceFilter->SetDistanceImageVolume(distImgVolume);
 }
 
 mitk::Image::Pointer mitk::SurfaceInterpolationController::GetCurrentSegmentation()
 {
   return m_SelectedSegmentation;
 }
 
 mitk::Image* mitk::SurfaceInterpolationController::GetImage()
 {
   return m_InterpolateSurfaceFilter->GetOutput();
 }
 
 double mitk::SurfaceInterpolationController::EstimatePortionOfNeededMemory()
 {
   double numberOfPointsAfterReduction = m_ReduceFilter->GetNumberOfPointsAfterReduction()*3;
   double sizeOfPoints = pow(numberOfPointsAfterReduction,2)*sizeof(double);
   double totalMem = mitk::MemoryUtilities::GetTotalSizeOfPhysicalRam();
   double percentage = sizeOfPoints/totalMem;
   return percentage;
 }
 
 unsigned int mitk::SurfaceInterpolationController::GetNumberOfInterpolationSessions()
 {
   return m_ListOfInterpolationSessions.size();
 }
 
 template<typename TPixel, unsigned int VImageDimension>
 void mitk::SurfaceInterpolationController::GetImageBase(itk::Image<TPixel, VImageDimension>* input, itk::ImageBase<3>::Pointer& result)
 {
   result->Graft(input);
 }
 
 void mitk::SurfaceInterpolationController::SetCurrentSegmentationInterpolationList(mitk::Image::Pointer segmentation)
 {
   this->SetCurrentInterpolationSession(segmentation);
 }
 
 void mitk::SurfaceInterpolationController::SetCurrentInterpolationSession(mitk::Image::Pointer currentSegmentationImage)
 {
   if (currentSegmentationImage.GetPointer() == m_SelectedSegmentation)
     return;
 
   if (currentSegmentationImage.IsNull())
   {
     m_SelectedSegmentation = 0;
     return;
   }
 
   m_SelectedSegmentation = currentSegmentationImage.GetPointer();
 
   ContourListMap::iterator it = m_ListOfInterpolationSessions.find(currentSegmentationImage.GetPointer());
   // If the session does not exist yet create a new ContourPositionPairList otherwise reinitialize the interpolation pipeline
   if (it == m_ListOfInterpolationSessions.end())
   {
     ContourPositionInformationList newList;
     m_ListOfInterpolationSessions.insert(std::pair<mitk::Image*, ContourPositionInformationList>(m_SelectedSegmentation, newList));
     m_InterpolationResult = 0;
     m_CurrentNumberOfReducedContours = 0;
 
     itk::MemberCommand<SurfaceInterpolationController>::Pointer command = itk::MemberCommand<SurfaceInterpolationController>::New();
     command->SetCallbackFunction(this, &SurfaceInterpolationController::OnSegmentationDeleted);
     m_SegmentationObserverTags.insert( std::pair<mitk::Image*, unsigned long>( m_SelectedSegmentation, m_SelectedSegmentation->AddObserver( itk::DeleteEvent(), command ) ) );
   }
 
   this->ReinitializeInterpolation();
 }
 
 void mitk::SurfaceInterpolationController::RemoveSegmentationFromContourList(mitk::Image *segmentation)
 {
   this->RemoveInterpolationSession(segmentation);
 }
 
 void mitk::SurfaceInterpolationController::RemoveInterpolationSession(mitk::Image::Pointer segmentationImage)
 {
   if (segmentationImage)
   {
     if (m_SelectedSegmentation == segmentationImage)
     {
       m_NormalsFilter->SetSegmentationBinaryImage(NULL);
       m_SelectedSegmentation = 0;
     }
     m_ListOfInterpolationSessions.erase(segmentationImage);
     // Remove observer
     std::map<mitk::Image*, unsigned long>::iterator pos = m_SegmentationObserverTags.find(segmentationImage);
     if (pos != m_SegmentationObserverTags.end())
     {
       segmentationImage->RemoveObserver((*pos).second);
       m_SegmentationObserverTags.erase(pos);
     }
   }
 }
 
 void mitk::SurfaceInterpolationController::RemoveAllInterpolationSessions()
 {
   //Removing all observers
   std::map<mitk::Image*, unsigned long>::iterator dataIter = m_SegmentationObserverTags.begin();
   while (dataIter != m_SegmentationObserverTags.end())
   {
     mitk::Image* image = (*dataIter).first;
     image->RemoveObserver((*dataIter).second);
     ++dataIter;
   }
 
   m_SegmentationObserverTags.clear();
   m_SelectedSegmentation = 0;
   m_ListOfInterpolationSessions.clear();
 }
 
 void mitk::SurfaceInterpolationController::ReinitializeInterpolation(mitk::Surface::Pointer contours)
 {
   // 1. detect coplanar contours
   // 2. merge coplanar contours into a single surface
   // 4. add contour to pipeline
 
   // Split the surface into separate polygons
   vtkSmartPointer<vtkCellArray> existingPolys;
   vtkSmartPointer<vtkPoints> existingPoints;
   existingPolys = contours->GetVtkPolyData()->GetPolys();
   existingPoints = contours->GetVtkPolyData()->GetPoints();
   existingPolys->InitTraversal();
 
   vtkSmartPointer<vtkIdList> ids = vtkSmartPointer<vtkIdList>::New();
 
   typedef std::pair<mitk::Vector3D, mitk::Point3D> PointNormalPair;
   std::vector<ContourPositionInformation> list;
   std::vector<vtkSmartPointer<vtkPoints> > pointsList;
   int count (0);
   for( existingPolys->InitTraversal(); existingPolys->GetNextCell(ids);)
   {
     // Get the points
     vtkSmartPointer<vtkPoints> points = vtkSmartPointer<vtkPoints>::New();
     existingPoints->GetPoints(ids, points);
     ++count;
     pointsList.push_back(points);
 
 
     PointNormalPair p_n;
     double n[3];
     vtkPolygon::ComputeNormal(points, n);
     p_n.first = n;
     double p[3];
 
     existingPoints->GetPoint(ids->GetId(0), p);
     p_n.second = p;
 
     ContourPositionInformation p_info;
     p_info.contourNormal = n;
     p_info.contourPoint = p;
     list.push_back(p_info);
     continue;
   }
 
   // Detect and sort coplanar polygons
   std::vector<ContourPositionInformation>::iterator outer = list.begin();
   std::vector< std::vector< vtkSmartPointer<vtkPoints> > > relatedPoints;
   while (outer != list.end())
   {
     std::vector<ContourPositionInformation>::iterator inner = outer;
     ++inner;
     std::vector< vtkSmartPointer<vtkPoints> > rel;
     std::vector< vtkSmartPointer<vtkPoints> >::iterator pointsIter = pointsList.begin();
     rel.push_back((*pointsIter));
     pointsIter = pointsList.erase(pointsIter);
 
     while (inner != list.end())
     {
       if(ContoursCoplanar((*outer),(*inner)))
       {
         inner = list.erase(inner);
         rel.push_back((*pointsIter));
         pointsIter = pointsList.erase(pointsIter);
       }
       else
       {
         ++inner;
         ++pointsIter;
       }
     }
     relatedPoints.push_back(rel);
     ++outer;
   }
 
   // Build the separate surfaces again
   std::vector<mitk::Surface::Pointer> finalSurfaces;
   for (unsigned int i = 0; i < relatedPoints.size(); ++i)
   {
     vtkSmartPointer<vtkPolyData> contourSurface = vtkSmartPointer<vtkPolyData>::New();
     vtkSmartPointer<vtkPoints> points = vtkSmartPointer<vtkPoints>::New();
     vtkSmartPointer<vtkCellArray> polygons = vtkSmartPointer<vtkCellArray>::New();
     unsigned int pointId (0);
     for (unsigned int j = 0; j < relatedPoints.at(i).size(); ++j)
     {
       unsigned int numPoints = relatedPoints.at(i).at(j)->GetNumberOfPoints();
       vtkSmartPointer<vtkPolygon> polygon = vtkSmartPointer<vtkPolygon>::New();
       polygon->GetPointIds()->SetNumberOfIds(numPoints);
       polygon->GetPoints()->SetNumberOfPoints(numPoints);
       vtkSmartPointer<vtkPoints> currentPoints = relatedPoints.at(i).at(j);
       for (unsigned k = 0; k < numPoints; ++k)
       {
         points->InsertPoint(pointId, currentPoints->GetPoint(k));
         polygon->GetPointIds()->SetId(k, pointId);
         ++pointId;
       }
       polygons->InsertNextCell(polygon);
     }
     contourSurface->SetPoints(points);
     contourSurface->SetPolys(polygons);
     contourSurface->BuildLinks();
     mitk::Surface::Pointer surface = mitk::Surface::New();
     surface->SetVtkPolyData(contourSurface);
     finalSurfaces.push_back(surface);
   }
 
   // Add detected contours to interpolation pipeline
   this->AddNewContours(finalSurfaces);
 }
 
 void mitk::SurfaceInterpolationController::OnSegmentationDeleted(const itk::Object *caller, const itk::EventObject &/*event*/)
 {
   mitk::Image* tempImage = dynamic_cast<mitk::Image*>(const_cast<itk::Object*>(caller));
   if (tempImage)
   {
     if (m_SelectedSegmentation == tempImage)
     {
       m_NormalsFilter->SetSegmentationBinaryImage(NULL);
       m_SelectedSegmentation = 0;
     }
     m_SegmentationObserverTags.erase(tempImage);
     m_ListOfInterpolationSessions.erase(tempImage);
   }
 }
 
 void mitk::SurfaceInterpolationController::ReinitializeInterpolation()
 {
   m_NormalsFilter->SetSegmentationBinaryImage(m_SelectedSegmentation);
 
   // If session has changed reset the pipeline
   m_ReduceFilter->Reset();
   m_NormalsFilter->Reset();
   m_InterpolateSurfaceFilter->Reset();
 
   itk::ImageBase<3>::Pointer itkImage = itk::ImageBase<3>::New();
   AccessFixedDimensionByItk_1( m_SelectedSegmentation, GetImageBase, 3, itkImage );
   m_InterpolateSurfaceFilter->SetReferenceImage(itkImage.GetPointer());
 
   for (unsigned int i = 0; i < m_ListOfInterpolationSessions[m_SelectedSegmentation].size(); i++)
   {
     m_ReduceFilter->SetInput(i, m_ListOfInterpolationSessions[m_SelectedSegmentation].at(i).contour);
   }
 
   m_ReduceFilter->Update();
 
   m_CurrentNumberOfReducedContours = m_ReduceFilter->GetNumberOfOutputs();
 
   for (unsigned int i = 0; i < m_CurrentNumberOfReducedContours; i++)
   {
     m_NormalsFilter->SetInput(i, m_ReduceFilter->GetOutput(i));
     m_InterpolateSurfaceFilter->SetInput(i, m_NormalsFilter->GetOutput(i));
   }
   Modified();
 }