X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=itk%2FclitkSegmentationUtils.txx;h=dccfc35df72daee8087047b54757168e1909ed46;hb=c0274b5a8535f5ed75fe9939f3a12f86e8e1ef3c;hp=0f5ebfbd58b9f7a9888e906091129b48909737e2;hpb=48f513811d9b13e6c7df67d8dc16fa073aa0751a;p=clitk.git

diff --git a/itk/clitkSegmentationUtils.txx b/itk/clitkSegmentationUtils.txx
index 0f5ebfb..dccfc35 100644
--- a/itk/clitkSegmentationUtils.txx
+++ b/itk/clitkSegmentationUtils.txx
@@ -18,29 +18,37 @@
 
 // clitk
 #include "clitkSetBackgroundImageFilter.h"
+#include "clitkSliceBySliceRelativePositionFilter.h"
+#include "clitkCropLikeImageFilter.h"
+#include "clitkMemoryUsage.h"
 
 // itk
 #include <itkConnectedComponentImageFilter.h>
 #include <itkRelabelComponentImageFilter.h>
 #include <itkBinaryThresholdImageFilter.h>
 #include <itkPasteImageFilter.h>
+#include <itkStatisticsLabelMapFilter.h>
+#include <itkBinaryBallStructuringElement.h>
+#include <itkBinaryDilateImageFilter.h>
+#include <itkConstantPadImageFilter.h>
+#include <itkImageSliceIteratorWithIndex.h>
 
 //--------------------------------------------------------------------
 template<class ImageType>
 void clitk::ComputeBBFromImageRegion(typename ImageType::Pointer image, 
                                      typename ImageType::RegionType region,
                                      typename itk::BoundingBox<unsigned long, 
-                                     ImageType::ImageDimension>::Pointer bb) {
+                                                               ImageType::ImageDimension>::Pointer bb) {
   typedef typename ImageType::IndexType IndexType;
   IndexType firstIndex;
   IndexType lastIndex;
   for(unsigned int i=0; i<image->GetImageDimension(); i++) {
     firstIndex[i] = region.GetIndex()[i];
-    lastIndex[i] = region.GetSize()[i];
+    lastIndex[i] = firstIndex[i]+region.GetSize()[i];
   }
 
   typedef itk::BoundingBox<unsigned long, 
-    ImageType::ImageDimension> BBType;
+                           ImageType::ImageDimension> BBType;
   typedef typename BBType::PointType PointType;
   PointType lastPoint;
   PointType firstPoint;
@@ -99,7 +107,11 @@ void clitk::ComputeRegionFromBB(typename ImageType::Pointer image,
   PointType maxs = bb->GetMaximum();
   PointType mins = bb->GetMinimum();
   for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
-    regionSize[i] = floor((maxs[i] - mins[i])/image->GetSpacing()[i]);
+    // DD(maxs[i]);
+    // DD(mins[i]);
+    // DD((maxs[i] - mins[i])/image->GetSpacing()[i]);
+    regionSize[i] = lrint((maxs[i] - mins[i])/image->GetSpacing()[i]);
+    // DD(regionSize[i]);
   }
    
   // Create region
@@ -111,12 +123,17 @@ void clitk::ComputeRegionFromBB(typename ImageType::Pointer image,
 //--------------------------------------------------------------------
 template<class ImageType, class TMaskImageType>
 typename ImageType::Pointer
-clitk::SetBackground(typename ImageType::ConstPointer input, 
-                     typename TMaskImageType::ConstPointer mask, 
+clitk::SetBackground(const ImageType * input, 
+                     const TMaskImageType * mask, 
                      typename TMaskImageType::PixelType maskBG,
-                     typename ImageType::PixelType outValue) {
-  typedef clitk::SetBackgroundImageFilter<ImageType, TMaskImageType, ImageType> SetBackgroundImageFilterType;
-  typename SetBackgroundImageFilterType::Pointer setBackgroundFilter = SetBackgroundImageFilterType::New();
+                     typename ImageType::PixelType outValue, 
+                     bool inPlace) {
+  typedef clitk::SetBackgroundImageFilter<ImageType, TMaskImageType, ImageType> 
+    SetBackgroundImageFilterType;
+  typename SetBackgroundImageFilterType::Pointer setBackgroundFilter 
+    = SetBackgroundImageFilterType::New();
+  //  if (inPlace) setBackgroundFilter->ReleaseDataFlagOn(); // No seg fault
+  setBackgroundFilter->SetInPlace(inPlace); // This is important to keep memory low
   setBackgroundFilter->SetInput(input);
   setBackgroundFilter->SetInput2(mask);
   setBackgroundFilter->SetMaskValue(maskBG);
@@ -129,28 +146,55 @@ clitk::SetBackground(typename ImageType::ConstPointer input,
 
 //--------------------------------------------------------------------
 template<class ImageType>
+int clitk::GetNumberOfConnectedComponentLabels(typename ImageType::Pointer input, 
+                                               typename ImageType::PixelType BG, 
+                                               bool isFullyConnected) {
+  // Connected Component label 
+  typedef itk::ConnectedComponentImageFilter<ImageType, ImageType> ConnectFilterType;
+  typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
+  connectFilter->SetInput(input);
+  connectFilter->SetBackgroundValue(BG);
+  connectFilter->SetFullyConnected(isFullyConnected);
+  connectFilter->Update();
+  
+  // Return result
+  return connectFilter->GetObjectCount();
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+/*
+  Warning : in this cas, we consider outputType like inputType, not
+  InternalImageType. Be sure it fits.
+ */
+template<class ImageType>
 typename ImageType::Pointer
-clitk::Labelize(typename ImageType::Pointer input, 
+clitk::Labelize(const ImageType * input, 
                 typename ImageType::PixelType BG, 
                 bool isFullyConnected, 
                 int minimalComponentSize) {
+  // InternalImageType for storing large number of component
+  typedef itk::Image<int, ImageType::ImageDimension> InternalImageType;
+  
   // Connected Component label 
-  typedef itk::ConnectedComponentImageFilter<ImageType, ImageType> ConnectFilterType;
+  typedef itk::ConnectedComponentImageFilter<ImageType, InternalImageType> ConnectFilterType;
   typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
+  //  connectFilter->ReleaseDataFlagOn(); 
   connectFilter->SetInput(input);
   connectFilter->SetBackgroundValue(BG);
   connectFilter->SetFullyConnected(isFullyConnected);
   
   // Sort by size and remove too small area.
-  typedef itk::RelabelComponentImageFilter<ImageType, ImageType> RelabelFilterType;
+  typedef itk::RelabelComponentImageFilter<InternalImageType, ImageType> RelabelFilterType;
   typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
-  relabelFilter->InPlaceOn();
+  //  relabelFilter->ReleaseDataFlagOn(); // if yes, fail when ExplosionControlledThresholdConnectedImageFilter ???
   relabelFilter->SetInput(connectFilter->GetOutput());
   relabelFilter->SetMinimumObjectSize(minimalComponentSize);
   relabelFilter->Update();
 
   // Return result
-  return relabelFilter->GetOutput();
+  typename ImageType::Pointer output = relabelFilter->GetOutput();
+  return output;
 }
 //--------------------------------------------------------------------
 
@@ -180,7 +224,7 @@ clitk::RemoveLabels(typename ImageType::Pointer input,
 //--------------------------------------------------------------------
 template<class ImageType>
 typename ImageType::Pointer
-clitk::KeepLabels(typename ImageType::Pointer input, 
+clitk::KeepLabels(const ImageType * input, 
                   typename ImageType::PixelType BG, 
                   typename ImageType::PixelType FG, 
                   typename ImageType::PixelType firstKeep, 
@@ -225,40 +269,477 @@ clitk::LabelizeAndSelectLabels(typename ImageType::Pointer input,
 //--------------------------------------------------------------------
 template<class ImageType>
 typename ImageType::Pointer
-clitk::EnlargeImageLike(typename ImageType::Pointer input,
-                        typename ImageType::Pointer like, 
-                        typename ImageType::PixelType backgroundValue) 
+clitk::ResizeImageLike(typename ImageType::Pointer input,
+                       typename ImageType::Pointer like, 
+                       typename ImageType::PixelType backgroundValue) 
 {
-  if (!HaveSameSpacing<ImageType, ImageType>(input, like)) {
-    FATAL("Images must have the same spacing");
-  }
+  typedef clitk::CropLikeImageFilter<ImageType> CropFilterType;
+  typename CropFilterType::Pointer cropFilter = CropFilterType::New();
+  cropFilter->SetInput(input);
+  cropFilter->SetCropLikeImage(like);
+  cropFilter->SetBackgroundValue(backgroundValue);
+  cropFilter->Update();
+  return cropFilter->GetOutput();  
+}
+//--------------------------------------------------------------------
 
-  typename ImageType::Pointer output = ImageType::New();
-  typename ImageType::SizeType size;
-  for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
-    size[i] = lrint((like->GetLargestPossibleRegion().GetSize()[i]*like->GetSpacing()[i])/
-                    (double)like->GetSpacing()[i]);
+
+//--------------------------------------------------------------------
+template<class MaskImageType>
+typename MaskImageType::Pointer
+clitk::SliceBySliceRelativePosition(const MaskImageType * input,
+				    const MaskImageType * object,
+				    int direction, 
+				    double threshold, 
+				    std::string orientation, 
+                                    bool uniqueConnectedComponent, 
+                                    double spacing, 
+				    bool inverseflag) 
+{
+  typedef clitk::SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
+  typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
+  sliceRelPosFilter->VerboseStepFlagOff();
+  sliceRelPosFilter->WriteStepFlagOff();
+  sliceRelPosFilter->SetInput(input);
+  sliceRelPosFilter->SetInputObject(object);
+  sliceRelPosFilter->SetDirection(direction);
+  sliceRelPosFilter->SetFuzzyThreshold(threshold);
+  sliceRelPosFilter->AddOrientationTypeString(orientation);
+  sliceRelPosFilter->SetResampleBeforeRelativePositionFilter((spacing != -1));
+  sliceRelPosFilter->SetIntermediateSpacing(spacing);
+  sliceRelPosFilter->SetUniqueConnectedComponentBySlice(uniqueConnectedComponent);
+  sliceRelPosFilter->SetInverseOrientationFlag(inverseflag);
+  //  sliceRelPosFilter->SetAutoCropFlag(true); ??
+  sliceRelPosFilter->Update();
+  return sliceRelPosFilter->GetOutput();
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template<class ImageType>
+bool
+clitk::FindExtremaPointInAGivenDirection(const ImageType * input, 
+                                         typename ImageType::PixelType bg, 
+                                         int direction, bool opposite, 
+                                         typename ImageType::PointType & point)
+{
+  typename ImageType::PointType dummy;
+  return clitk::FindExtremaPointInAGivenDirection(input, bg, direction, 
+                                                  opposite, dummy, 0, point);
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template<class ImageType>
+bool
+clitk::FindExtremaPointInAGivenDirection(const ImageType * input, 
+                                         typename ImageType::PixelType bg, 
+                                         int direction, bool opposite, 
+                                         typename ImageType::PointType refpoint,
+                                         double distanceMax, 
+                                         typename ImageType::PointType & point)
+{
+  /*
+    loop over input pixels, store the index in the fg that is max
+    according to the given direction. 
+  */
+  typedef itk::ImageRegionConstIteratorWithIndex<ImageType> IteratorType;
+  IteratorType iter(input, input->GetLargestPossibleRegion());
+  iter.GoToBegin();
+  typename ImageType::IndexType max = input->GetLargestPossibleRegion().GetIndex();
+  if (opposite) max = max+input->GetLargestPossibleRegion().GetSize();
+  bool found=false;
+  while (!iter.IsAtEnd()) {
+    if (iter.Get() != bg) {
+      bool test = iter.GetIndex()[direction] >  max[direction];
+      if (opposite) test = !test;
+      if (test) {
+        typename ImageType::PointType p;
+        input->TransformIndexToPhysicalPoint(iter.GetIndex(), p);
+        if ((distanceMax==0) || (p.EuclideanDistanceTo(refpoint) < distanceMax)) {
+          max = iter.GetIndex();
+          found = true;
+        }
+      }
+    }
+    ++iter;
   }
-  // DD(size);
+  if (!found) return false;
+  input->TransformIndexToPhysicalPoint(max, point);
+  return true;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ImageType>
+typename ImageType::Pointer
+clitk::CropImageAbove(typename ImageType::Pointer image, 
+                      int dim, double min, 
+                      bool autoCrop,
+                      typename ImageType::PixelType BG) 
+{
+  return clitk::CropImageAlongOneAxis<ImageType>(image, dim, 
+                                                 image->GetOrigin()[dim], 
+                                                 min,
+                                                 autoCrop, BG);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ImageType>
+typename ImageType::Pointer
+clitk::CropImageBelow(typename ImageType::Pointer image, 
+                      int dim, double max, 
+                      bool autoCrop,
+                      typename ImageType::PixelType BG) 
+{
+  typename ImageType::PointType p;
+  image->TransformIndexToPhysicalPoint(image->GetLargestPossibleRegion().GetIndex()+
+                                       image->GetLargestPossibleRegion().GetSize(), p);
+  return clitk::CropImageAlongOneAxis<ImageType>(image, dim, max, p[dim], autoCrop, BG);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ImageType>
+typename ImageType::Pointer
+clitk::CropImageAlongOneAxis(typename ImageType::Pointer image, 
+                             int dim, double min, double max, 
+                             bool autoCrop,
+                             typename ImageType::PixelType BG) 
+{
+  // Compute region size
   typename ImageType::RegionType region;
+  typename ImageType::SizeType size = image->GetLargestPossibleRegion().GetSize();
+  typename ImageType::PointType p = image->GetOrigin();
+  p[dim] = min;
+  typename ImageType::IndexType start;
+  image->TransformPhysicalPointToIndex(p, start);
+  p[dim] = max;
+  typename ImageType::IndexType end;
+  image->TransformPhysicalPointToIndex(p, end);
+  size[dim] = fabs(end[dim]-start[dim]);
+  region.SetIndex(start);
   region.SetSize(size);
-  output->SetRegions(region);
-  output->SetSpacing(like->GetSpacing());
-  output->SetOrigin(like->GetOrigin());
-  output->Allocate();
-  output->FillBuffer(backgroundValue);
-  typedef itk::PasteImageFilter<ImageType,ImageType> PasteFilterType;
-  typename PasteFilterType::Pointer pasteFilter = PasteFilterType::New();
-  typename PasteFilterType::InputImageIndexType index;
-  for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
-    index[i] = lrint((input->GetOrigin()[i] - like->GetOrigin()[i])/(double)input->GetSpacing()[i]);
+  
+  // Perform Crop
+  typedef itk::RegionOfInterestImageFilter<ImageType, ImageType> CropFilterType;
+  typename CropFilterType::Pointer cropFilter = CropFilterType::New();
+  cropFilter->SetInput(image);
+  cropFilter->SetRegionOfInterest(region);
+  cropFilter->Update();
+  typename ImageType::Pointer result = cropFilter->GetOutput();
+  
+  // Auto Crop
+  if (autoCrop) {
+    result = clitk::AutoCrop<ImageType>(result, BG);
   }
-  // DD(index);
-  pasteFilter->SetSourceImage(input);
-  pasteFilter->SetDestinationImage(output);
-  pasteFilter->SetDestinationIndex(index);
-  pasteFilter->SetSourceRegion(input->GetLargestPossibleRegion());
-  pasteFilter->Update();
-  return pasteFilter->GetOutput();  
+  return result;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ImageType>
+void
+clitk::ComputeCentroids(typename ImageType::Pointer image, 
+                        typename ImageType::PixelType BG, 
+                        std::vector<typename ImageType::PointType> & centroids) 
+{
+  typedef long LabelType;
+  static const unsigned int Dim = ImageType::ImageDimension;
+  typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
+  typedef itk::LabelMap< LabelObjectType > LabelMapType;
+  typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
+  typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New(); 
+  typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType; 
+  typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
+  imageToLabelFilter->SetBackgroundValue(BG);
+  imageToLabelFilter->SetInput(image);
+  statFilter->SetInput(imageToLabelFilter->GetOutput());
+  statFilter->Update();
+  typename LabelMapType::Pointer labelMap = statFilter->GetOutput();
+
+  centroids.clear();
+  typename ImageType::PointType dummy;
+  centroids.push_back(dummy); // label 0 -> no centroid, use dummy point
+  for(uint i=1; i<labelMap->GetNumberOfLabelObjects()+1; i++) {
+    centroids.push_back(labelMap->GetLabelObject(i)->GetCentroid());
+  } 
 }
 //--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ImageType>
+void
+clitk::ExtractSlices(typename ImageType::Pointer image, 
+		     int direction, 
+		     std::vector<typename itk::Image<typename ImageType::PixelType, 
+		     ImageType::ImageDimension-1>::Pointer > & slices) 
+{
+  typedef clitk::ExtractSliceFilter<ImageType> ExtractSliceFilterType;
+  typedef typename ExtractSliceFilterType::SliceType SliceType;
+  typename ExtractSliceFilterType::Pointer 
+    extractSliceFilter = ExtractSliceFilterType::New();
+  extractSliceFilter->SetInput(image);
+  extractSliceFilter->SetDirection(direction);
+  extractSliceFilter->Update();
+  extractSliceFilter->GetOutputSlices(slices);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ImageType>
+typename ImageType::Pointer
+clitk::JoinSlices(std::vector<typename itk::Image<typename ImageType::PixelType, 
+		  ImageType::ImageDimension-1>::Pointer > & slices, 
+		  typename ImageType::Pointer input, 
+		  int direction) {
+  typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
+  typedef itk::JoinSeriesImageFilter<SliceType, ImageType> JoinSeriesFilterType;
+  typename JoinSeriesFilterType::Pointer joinFilter = JoinSeriesFilterType::New();
+  joinFilter->SetOrigin(input->GetOrigin()[direction]);
+  joinFilter->SetSpacing(input->GetSpacing()[direction]);
+  for(unsigned int i=0; i<slices.size(); i++) {
+    joinFilter->PushBackInput(slices[i]);
+  }
+  joinFilter->Update();
+  return joinFilter->GetOutput();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ImageType>
+void
+clitk::PointsUtils<ImageType>::Convert2DTo3D(const PointType2D & p, 
+                                             ImagePointer image, 
+                                             const int slice, 
+                                             PointType3D & p3D)  
+{
+  p3D[0] = p[0]; 
+  p3D[1] = p[1];
+  p3D[2] = (image->GetLargestPossibleRegion().GetIndex()[2]+slice)*image->GetSpacing()[2] 
+    + image->GetOrigin()[2];
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ImageType>
+void 
+clitk::PointsUtils<ImageType>::Convert2DTo3DList(const MapPoint2DType & map, 
+                                                 ImagePointer image, 
+                                                 VectorPoint3DType & list)
+{
+  typename MapPoint2DType::const_iterator iter = map.begin();
+  while (iter != map.end()) {
+    PointType3D p;
+    Convert2DTo3D(iter->second, image, iter->first, p);
+    list.push_back(p);
+    ++iter;
+  }
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template<class ImageType>
+void 
+clitk::WriteListOfLandmarks(std::vector<typename ImageType::PointType> points, 
+                            std::string filename)
+{
+  std::ofstream os; 
+  openFileForWriting(os, filename); 
+  os << "LANDMARKS1" << std::endl;  
+  for(uint i=0; i<points.size(); i++) {
+    const typename ImageType::PointType & p = points[i];
+    // Write it in the file
+    os << i << " " << p[0] << " " << p[1] << " " << p[2] << " 0 0 " << std::endl;
+  }
+  os.close();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ImageType>
+typename ImageType::Pointer 
+clitk::Dilate(typename ImageType::Pointer image, 
+              double radiusInMM,               
+              typename ImageType::PixelType BG,
+              typename ImageType::PixelType FG,  
+              bool extendSupport)
+{
+  typename ImageType::SizeType r;
+  for(uint i=0; i<ImageType::ImageDimension; i++) 
+    r[i] = (uint)lrint(radiusInMM/image->GetSpacing()[i]);
+  return clitk::Dilate<ImageType>(image, r, BG, FG, extendSupport);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ImageType>
+typename ImageType::Pointer 
+clitk::Dilate(typename ImageType::Pointer image, 
+              typename ImageType::PointType radiusInMM, 
+              typename ImageType::PixelType BG, 
+              typename ImageType::PixelType FG, 
+              bool extendSupport)
+{
+  typename ImageType::SizeType r;
+  for(uint i=0; i<ImageType::ImageDimension; i++) 
+    r[i] = (uint)lrint(radiusInMM[i]/image->GetSpacing()[i]);
+  return clitk::Dilate<ImageType>(image, r, BG, FG, extendSupport);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ImageType>
+typename ImageType::Pointer 
+clitk::Dilate(typename ImageType::Pointer image, 
+              typename ImageType::SizeType radius, 
+              typename ImageType::PixelType BG, 
+              typename ImageType::PixelType FG, 
+              bool extendSupport)
+{
+  // Create kernel for dilatation
+  typedef itk::BinaryBallStructuringElement<typename ImageType::PixelType, 
+                                            ImageType::ImageDimension> KernelType;
+  KernelType structuringElement;
+  structuringElement.SetRadius(radius);
+  structuringElement.CreateStructuringElement();
+
+  if (extendSupport) {
+    typedef itk::ConstantPadImageFilter<ImageType, ImageType> PadFilterType;
+    typename PadFilterType::Pointer padFilter = PadFilterType::New();
+    padFilter->SetInput(image);
+    typename ImageType::SizeType lower;
+    typename ImageType::SizeType upper;
+    for(uint i=0; i<3; i++) {
+      lower[i] = upper[i] = 2*(radius[i]+1);
+    }
+    padFilter->SetPadLowerBound(lower);
+    padFilter->SetPadUpperBound(upper);
+    padFilter->Update();
+    image = padFilter->GetOutput();
+  }
+
+  // Dilate  filter
+  typedef itk::BinaryDilateImageFilter<ImageType, ImageType , KernelType> DilateFilterType;
+  typename DilateFilterType::Pointer dilateFilter = DilateFilterType::New();
+  dilateFilter->SetBackgroundValue(BG);
+  dilateFilter->SetForegroundValue(FG);
+  dilateFilter->SetBoundaryToForeground(false);
+  dilateFilter->SetKernel(structuringElement);
+  dilateFilter->SetInput(image);
+  dilateFilter->Update();
+  return image = dilateFilter->GetOutput();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ValueType, class VectorType>
+void clitk::ConvertOption(std::string optionName, uint given, 
+                          ValueType * values, VectorType & p, 
+                          uint dim, bool required) 
+{
+  if (required && (given == 0)) {
+    clitkExceptionMacro("The option --" << optionName << " must be set and have 1 or " 
+                        << dim << " values.");
+  }
+  if (given == 1) {
+    for(uint i=0; i<dim; i++) p[i] = values[0];
+    return;
+  }
+  if (given == dim) {
+    for(uint i=0; i<dim; i++) p[i] = values[i];
+    return;
+  }
+  if (given == 0) return;
+  clitkExceptionMacro("The option --" << optionName << " must have 1 or " 
+                      << dim << " values.");
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+/*
+  http://www.gamedev.net/community/forums/topic.asp?topic_id=542870
+  Assuming the points are (Ax,Ay) (Bx,By) and (Cx,Cy), you need to compute:
+  (Bx - Ax) * (Cy - Ay) - (By - Ay) * (Cx - Ax)
+  This will equal zero if the point C is on the line formed by
+  points A and B, and will have a different sign depending on the
+  side. Which side this is depends on the orientation of your (x,y)
+  coordinates, but you can plug test values for A,B and C into this
+  formula to determine whether negative values are to the left or to
+  the right.
+  => to accelerate, start with formula, when change sign -> stop and fill
+*/
+template<class ImageType>
+void 
+clitk::SliceBySliceSetBackgroundFromLineSeparation(typename ImageType::Pointer input, 
+                                                   std::vector<typename ImageType::PointType> & lA, 
+                                                   std::vector<typename ImageType::PointType> & lB, 
+                                                   typename ImageType::PixelType BG, 
+                                                   int mainDirection, 
+                                                   double offsetToKeep)
+{
+  
+  typedef itk::ImageSliceIteratorWithIndex<ImageType> SliceIteratorType;
+  SliceIteratorType siter = SliceIteratorType(input, 
+                                              input->GetLargestPossibleRegion());
+  siter.SetFirstDirection(0);
+  siter.SetSecondDirection(1);
+  siter.GoToBegin();
+  uint i=0;
+  typename ImageType::PointType A;
+  typename ImageType::PointType B;
+  typename ImageType::PointType C;
+  assert(lA.size() == B.size());
+  //  DD(lA.size());
+  //DD(input->GetLargestPossibleRegion().GetSize());
+  while ((i<lA.size()) && (!siter.IsAtEnd())) {
+    // Check that the current slice correspond to the current point
+    input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
+    if (C[2] != lA[i][2]) {
+      // DD(C);
+      // DD(lA[i]);
+    }
+    else {
+      // Define A,B,C points
+      A = lA[i];
+      B = lB[i];
+      C = A;
+      C[mainDirection] += offsetToKeep; // I know I must keep this point
+      double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
+      bool isPositive = s<0;
+      while (!siter.IsAtEndOfSlice()) {
+        while (!siter.IsAtEndOfLine()) {
+          // Very slow, I know ... but image should be very small
+          input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
+          double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
+          if (s == 0) siter.Set(BG); // on the line, we decide to remove
+          if (isPositive) {
+            if (s > 0) siter.Set(BG);
+          }
+          else {
+            if (s < 0) siter.Set(BG); 
+          }
+          ++siter;
+        }
+        siter.NextLine();
+      }
+      ++i;
+    }
+    siter.NextSlice();
+  }
+}                                                   
+//--------------------------------------------------------------------