X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=itk%2FclitkSegmentationUtils.txx;h=2f0d935a7cbbc88d038000768d6bed04bfd2451f;hb=58b7f414d8d90e482b59075845e611ad54fa9810;hp=7f52aea61572e3591803aa805e7d408d7f37d4fb;hpb=c5fff0a0f4211d43cb7f9140883da46d84d05117;p=clitk.git

diff --git a/itk/clitkSegmentationUtils.txx b/itk/clitkSegmentationUtils.txx
index 7f52aea..2f0d935 100644
--- a/itk/clitkSegmentationUtils.txx
+++ b/itk/clitkSegmentationUtils.txx
@@ -3,7 +3,7 @@
 
   Authors belong to: 
   - University of LYON              http://www.universite-lyon.fr/
-  - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
+  - Léon Bérard cancer center       http://www.centreleonberard.fr
   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
 
   This software is distributed WITHOUT ANY WARRANTY; without even
@@ -18,248 +18,1441 @@
 
 // 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>
+#include <itkBinaryMorphologicalOpeningImageFilter.h>
+#include <itkImageDuplicator.h>
+#include <itkSignedMaurerDistanceMapImageFilter.h>
 
-//--------------------------------------------------------------------
-template<class ImageType>
-void clitk::ComputeBBFromImageRegion(typename ImageType::Pointer image, 
-                                     typename ImageType::RegionType region,
-                                     typename itk::BoundingBox<unsigned long, 
-                                     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];
-  }
-
-  typedef itk::BoundingBox<unsigned long, 
-    ImageType::ImageDimension> BBType;
-  typedef typename BBType::PointType PointType;
-  PointType lastPoint;
-  PointType firstPoint;
-  image->TransformIndexToPhysicalPoint(firstIndex, firstPoint);
-  image->TransformIndexToPhysicalPoint(lastIndex, lastPoint);
-
-  bb->SetMaximum(lastPoint);
-  bb->SetMinimum(firstPoint);
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<int Dimension>
-void clitk::ComputeBBIntersection(typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbo, 
-                                  typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi1, 
-                                  typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi2) {
-
-  typedef itk::BoundingBox<unsigned long, Dimension> BBType;
-  typedef typename BBType::PointType PointType;
-  PointType lastPoint;
-  PointType firstPoint;
-
-  for(unsigned int i=0; i<Dimension; i++) {
-    firstPoint[i] = std::max(bbi1->GetMinimum()[i], 
-                             bbi2->GetMinimum()[i]);
-    lastPoint[i] = std::min(bbi1->GetMaximum()[i], 
-                            bbi2->GetMaximum()[i]);
-  }
-
-  bbo->SetMaximum(lastPoint);
-  bbo->SetMinimum(firstPoint);
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class ImageType>
-void clitk::ComputeRegionFromBB(typename ImageType::Pointer image, 
-                                const typename itk::BoundingBox<unsigned long, 
-                                ImageType::ImageDimension>::Pointer bb, 
-                                typename ImageType::RegionType & region) {
-  // Types
-  typedef typename ImageType::IndexType  IndexType;
-  typedef typename ImageType::PointType  PointType;
-  typedef typename ImageType::RegionType RegionType;
-  typedef typename ImageType::SizeType   SizeType;
-
-  // Region starting point
-  IndexType regionStart;
-  PointType start = bb->GetMinimum();
-  image->TransformPhysicalPointToIndex(start, regionStart);
-    
-  // Region size
-  SizeType regionSize;
-  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]);
+namespace clitk {
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  void ComputeBBFromImageRegion(const ImageType * image, 
+                                typename ImageType::RegionType region,
+                                typename itk::BoundingBox<unsigned long, 
+                                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] = firstIndex[i]+region.GetSize()[i];
+    }
+
+    typedef itk::BoundingBox<unsigned long, 
+                             ImageType::ImageDimension> BBType;
+    typedef typename BBType::PointType PointType;
+    PointType lastPoint;
+    PointType firstPoint;
+    image->TransformIndexToPhysicalPoint(firstIndex, firstPoint);
+    image->TransformIndexToPhysicalPoint(lastIndex, lastPoint);
+
+    bb->SetMaximum(lastPoint);
+    bb->SetMinimum(firstPoint);
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<int Dimension>
+  void ComputeBBIntersection(typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbo, 
+                             typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi1, 
+                             typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi2) {
+
+    typedef itk::BoundingBox<unsigned long, Dimension> BBType;
+    typedef typename BBType::PointType PointType;
+    PointType lastPoint;
+    PointType firstPoint;
+
+    for(unsigned int i=0; i<Dimension; i++) {
+      firstPoint[i] = std::max(bbi1->GetMinimum()[i], 
+                               bbi2->GetMinimum()[i]);
+      lastPoint[i] = std::min(bbi1->GetMaximum()[i], 
+                              bbi2->GetMaximum()[i]);
+    }
+
+    bbo->SetMaximum(lastPoint);
+    bbo->SetMinimum(firstPoint);
   }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  void ComputeRegionFromBB(const ImageType * image, 
+                           const typename itk::BoundingBox<unsigned long, 
+                                                           ImageType::ImageDimension>::Pointer bb, 
+                           typename ImageType::RegionType & region) {
+    // Types
+    typedef typename ImageType::IndexType  IndexType;
+    typedef typename ImageType::PointType  PointType;
+    typedef typename ImageType::RegionType RegionType;
+    typedef typename ImageType::SizeType   SizeType;
+
+    // Region starting point
+    IndexType regionStart;
+    PointType start = bb->GetMinimum();
+    image->TransformPhysicalPointToIndex(start, regionStart);
+    
+    // Region size
+    SizeType regionSize;
+    PointType maxs = bb->GetMaximum();
+    PointType mins = bb->GetMinimum();
+    for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
+      regionSize[i] = lrint((maxs[i] - mins[i])/image->GetSpacing()[i]);
+    }
    
-  // Create region
-  region.SetIndex(regionStart);
-  region.SetSize(regionSize);
-}
-//--------------------------------------------------------------------
-
-//--------------------------------------------------------------------
-template<class ImageType, class TMaskImageType>
-typename ImageType::Pointer
-clitk::SetBackground(typename ImageType::ConstPointer input, 
-                     typename TMaskImageType::ConstPointer mask, 
-                     typename TMaskImageType::PixelType maskBG,
-                     typename ImageType::PixelType outValue) {
-  typedef clitk::SetBackgroundImageFilter<ImageType, TMaskImageType, ImageType> SetBackgroundImageFilterType;
-  typename SetBackgroundImageFilterType::Pointer setBackgroundFilter = SetBackgroundImageFilterType::New();
-  setBackgroundFilter->SetInput(input);
-  setBackgroundFilter->SetInput2(mask);
-  setBackgroundFilter->SetMaskValue(maskBG);
-  setBackgroundFilter->SetOutsideValue(outValue);
-  setBackgroundFilter->Update();
-  return setBackgroundFilter->GetOutput();
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class ImageType>
-typename ImageType::Pointer
-clitk::Labelize(typename ImageType::Pointer input, 
-                typename ImageType::PixelType BG, 
-                bool isFullyConnected, 
-                int minimalComponentSize) {
-
-  // Connected Component label 
-  typedef itk::ConnectedComponentImageFilter<ImageType, ImageType> ConnectFilterType;
-  typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
-  connectFilter->SetInput(input);
-  connectFilter->SetBackgroundValue(BG);
-  connectFilter->SetFullyConnected(isFullyConnected);
-  
-  // Sort by size and remove too small area.
-  typedef itk::RelabelComponentImageFilter<ImageType, ImageType> RelabelFilterType;
-  typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
-  relabelFilter->InPlaceOn();
-  relabelFilter->SetInput(connectFilter->GetOutput());
-  relabelFilter->SetMinimumObjectSize(minimalComponentSize);
-  relabelFilter->Update();
-
-  // Return result
-  return relabelFilter->GetOutput();
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class ImageType>
-typename ImageType::Pointer
-clitk::RemoveLabels(typename ImageType::Pointer input, 
-                    typename ImageType::PixelType BG,
-                    std::vector<typename ImageType::PixelType> & labelsToRemove) {
-  typename ImageType::Pointer working_image = input;
-  for (unsigned int i=0; i <labelsToRemove.size(); i++) {
-    typedef clitk::SetBackgroundImageFilter<ImageType, ImageType> SetBackgroundImageFilterType;
-    typename SetBackgroundImageFilterType::Pointer setBackgroundFilter = SetBackgroundImageFilterType::New();
+    // Create region
+    region.SetIndex(regionStart);
+    region.SetSize(regionSize);
+  }
+  //--------------------------------------------------------------------
+
+  //--------------------------------------------------------------------
+  template<class ImageType, class TMaskImageType>
+  typename ImageType::Pointer
+  SetBackground(const ImageType * input, 
+                const TMaskImageType * mask, 
+                typename TMaskImageType::PixelType maskBG,
+                typename ImageType::PixelType outValue, 
+                bool inPlace) {
+    typedef 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(input);
-    setBackgroundFilter->SetMaskValue(labelsToRemove[i]);
-    setBackgroundFilter->SetOutsideValue(BG);
+    setBackgroundFilter->SetInput2(mask);
+    setBackgroundFilter->SetMaskValue(maskBG);
+    setBackgroundFilter->SetOutsideValue(outValue);
     setBackgroundFilter->Update();
-    working_image = setBackgroundFilter->GetOutput();
+    return setBackgroundFilter->GetOutput();
   }
-  return working_image;
-}
-//--------------------------------------------------------------------
+  //--------------------------------------------------------------------
 
 
-//--------------------------------------------------------------------
-template<class ImageType>
-typename ImageType::Pointer
-clitk::KeepLabels(typename ImageType::Pointer input, 
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  int GetNumberOfConnectedComponentLabels(const ImageType * 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
+  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, 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<InternalImageType, ImageType> RelabelFilterType;
+    typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
+    //  relabelFilter->ReleaseDataFlagOn(); // if yes, fail when ExplosionControlledThresholdConnectedImageFilter ???
+    relabelFilter->SetInput(connectFilter->GetOutput());
+    relabelFilter->SetMinimumObjectSize(minimalComponentSize);
+    relabelFilter->Update();
+
+    // Return result
+    typename ImageType::Pointer output = relabelFilter->GetOutput();
+    return output;
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  /*
+    Warning : in this cas, we consider outputType like inputType, not
+    InternalImageType. Be sure it fits.
+  */
+  template<class ImageType>
+  typename ImageType::Pointer
+  LabelizeAndCountNumberOfObjects(const ImageType * input, 
+                                  typename ImageType::PixelType BG, 
+                                  bool isFullyConnected, 
+                                  int minimalComponentSize, 
+                                  int & nb) {
+    // InternalImageType for storing large number of component
+    typedef itk::Image<int, ImageType::ImageDimension> InternalImageType;
+  
+    // Connected Component label 
+    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<InternalImageType, ImageType> RelabelFilterType;
+    typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
+    //  relabelFilter->ReleaseDataFlagOn(); // if yes, fail when ExplosionControlledThresholdConnectedImageFilter ???
+    relabelFilter->SetInput(connectFilter->GetOutput());
+    relabelFilter->SetMinimumObjectSize(minimalComponentSize);
+    relabelFilter->Update();
+
+    nb = relabelFilter->GetNumberOfObjects();
+    // DD(relabelFilter->GetOriginalNumberOfObjects());
+    // DD(relabelFilter->GetSizeOfObjectsInPhysicalUnits()[0]);
+
+    // Return result
+    typename ImageType::Pointer output = relabelFilter->GetOutput();
+    return output;
+  }
+  //--------------------------------------------------------------------
+
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::Pointer
+  RemoveLabels(const ImageType * input, 
+               typename ImageType::PixelType BG,
+               std::vector<typename ImageType::PixelType> & labelsToRemove) {
+    assert(labelsToRemove.size() != 0);
+    typename ImageType::Pointer working_image;// = input;
+    for (unsigned int i=0; i <labelsToRemove.size(); i++) {
+      typedef SetBackgroundImageFilter<ImageType, ImageType> SetBackgroundImageFilterType;
+      typename SetBackgroundImageFilterType::Pointer setBackgroundFilter = SetBackgroundImageFilterType::New();
+      setBackgroundFilter->SetInput(input);
+      setBackgroundFilter->SetInput2(input);
+      setBackgroundFilter->SetMaskValue(labelsToRemove[i]);
+      setBackgroundFilter->SetOutsideValue(BG);
+      setBackgroundFilter->Update();
+      working_image = setBackgroundFilter->GetOutput();
+    }
+    return working_image;
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::Pointer
+  KeepLabels(const ImageType * input, 
+             typename ImageType::PixelType BG, 
+             typename ImageType::PixelType FG, 
+             typename ImageType::PixelType firstKeep, 
+             typename ImageType::PixelType lastKeep, 
+             bool useLastKeep) {
+    typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> BinarizeFilterType; 
+    typename BinarizeFilterType::Pointer binarizeFilter = BinarizeFilterType::New();
+    binarizeFilter->SetInput(input);
+    binarizeFilter->SetLowerThreshold(firstKeep);
+    if (useLastKeep) binarizeFilter->SetUpperThreshold(lastKeep);
+    binarizeFilter->SetInsideValue(FG);
+    binarizeFilter->SetOutsideValue(BG);
+    binarizeFilter->Update();
+    return binarizeFilter->GetOutput();
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::Pointer
+  LabelizeAndSelectLabels(const ImageType * input,
+                          typename ImageType::PixelType BG, 
+                          typename ImageType::PixelType FG, 
+                          bool isFullyConnected,
+                          int minimalComponentSize,
+                          LabelizeParameters<typename ImageType::PixelType> * param)
+  {
+    typename ImageType::Pointer working_image;
+    working_image = Labelize<ImageType>(input, BG, isFullyConnected, minimalComponentSize);
+    if (param->GetLabelsToRemove().size() != 0)
+      working_image = RemoveLabels<ImageType>(working_image, BG, param->GetLabelsToRemove());
+    working_image = KeepLabels<ImageType>(working_image, 
+                                          BG, FG, 
+                                          param->GetFirstKeep(), 
+                                          param->GetLastKeep(), 
+                                          param->GetUseLastKeep());
+    return working_image;
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::Pointer
+  ResizeImageLike(const ImageType * input,                       
+                  const itk::ImageBase<ImageType::ImageDimension> * like, 
+                  typename ImageType::PixelType backgroundValue) 
+  {
+    typedef CropLikeImageFilter<ImageType> CropFilterType;
+    typename CropFilterType::Pointer cropFilter = CropFilterType::New();
+    cropFilter->SetInput(input);
+    cropFilter->SetCropLikeImage(like);
+    cropFilter->SetBackgroundValue(backgroundValue);
+    cropFilter->Update();
+    return cropFilter->GetOutput();  
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class MaskImageType>
+  typename MaskImageType::Pointer
+  SliceBySliceRelativePosition(const MaskImageType * input,
+                               const MaskImageType * object,
+                               int direction, 
+                               double threshold, 
+                               std::string orientation, 
+                               bool uniqueConnectedComponent, 
+                               double spacing, 
+                               bool autocropFlag, 
+                               bool singleObjectCCL) 
+  {
+    typedef 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->SetIntermediateSpacingFlag((spacing != -1));
+    sliceRelPosFilter->SetIntermediateSpacing(spacing);
+    sliceRelPosFilter->SetUniqueConnectedComponentBySliceFlag(uniqueConnectedComponent);
+    sliceRelPosFilter->ObjectCCLSelectionFlagOff();
+    sliceRelPosFilter->SetUseTheLargestObjectCCLFlag(singleObjectCCL);
+    //    sliceRelPosFilter->SetInverseOrientationFlag(inverseflag); 
+    sliceRelPosFilter->SetAutoCropFlag(autocropFlag); 
+    sliceRelPosFilter->IgnoreEmptySliceObjectFlagOn();
+    sliceRelPosFilter->Update();
+    return sliceRelPosFilter->GetOutput();
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  bool
+  FindExtremaPointInAGivenDirection(const ImageType * input, 
+                                    typename ImageType::PixelType bg, 
+                                    int direction, bool opposite, 
+                                    typename ImageType::PointType & point)
+  {
+    typename ImageType::PointType dummy;
+    return FindExtremaPointInAGivenDirection(input, bg, direction, 
+                                             opposite, dummy, 0, point);
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  bool
+  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;
+    }
+    if (!found) return false;
+    input->TransformIndexToPhysicalPoint(max, point);
+    return true;
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::Pointer
+  CropImageRemoveGreaterThan(const ImageType * image, 
+                 int dim, double min, bool autoCrop,
+                 typename ImageType::PixelType BG) 
+  {
+    return CropImageAlongOneAxis<ImageType>(image, dim, 
+                                            image->GetOrigin()[dim], 
+                                            min,
+                                            autoCrop, BG);
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::Pointer
+  CropImageRemoveLowerThan(const ImageType * 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 CropImageAlongOneAxis<ImageType>(image, dim, max, p[dim], autoCrop, BG);
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::Pointer
+  CropImageAlongOneAxis(const ImageType * 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();
+    if (min > p[dim]) p[dim] = min; // Check if not outside the image
+    typename ImageType::IndexType start;
+    image->TransformPhysicalPointToIndex(p, start);
+    double m = image->GetOrigin()[dim] + size[dim]*image->GetSpacing()[dim];
+    if (max > m) p[dim] = m; // Check if not outside the image
+    else p[dim] = max;
+    typename ImageType::IndexType end;
+    image->TransformPhysicalPointToIndex(p, end);
+    size[dim] = abs(end[dim]-start[dim]);
+    region.SetIndex(start);
+    region.SetSize(size);
+  
+    // 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 = AutoCrop<ImageType>(result, BG);
+    }
+    return result;
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  void
+  ComputeCentroids(const ImageType * 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 BG 
+    //DS FIXME (not useful ! to change ..)
+    for(uint i=0; i<labelMap->GetNumberOfLabelObjects(); i++) {
+      int label = labelMap->GetLabels()[i];
+      centroids.push_back(labelMap->GetLabelObject(label)->GetCentroid());
+    } 
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType, class LabelType>
+  typename itk::LabelMap< itk::ShapeLabelObject<LabelType, ImageType::ImageDimension> >::Pointer
+  ComputeLabelMap(const ImageType * image, 
                   typename ImageType::PixelType BG, 
-                  typename ImageType::PixelType FG, 
-                  typename ImageType::PixelType firstKeep, 
-                  typename ImageType::PixelType lastKeep, 
-                  bool useLastKeep) {
-  typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> BinarizeFilterType; 
-  typename BinarizeFilterType::Pointer binarizeFilter = BinarizeFilterType::New();
-  binarizeFilter->SetInput(input);
-  binarizeFilter->SetLowerThreshold(firstKeep);
-  if (useLastKeep) binarizeFilter->SetUpperThreshold(lastKeep);
-  binarizeFilter->SetInsideValue(FG);
-  binarizeFilter->SetOutsideValue(BG);
-  binarizeFilter->Update();
-  return binarizeFilter->GetOutput();
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class ImageType>
-typename ImageType::Pointer
-clitk::LabelizeAndSelectLabels(typename ImageType::Pointer input,
+                  bool computePerimeterFlag) 
+  {
+    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->SetComputePerimeter(computePerimeterFlag);
+    statFilter->Update();
+    return statFilter->GetOutput();
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  void
+  ComputeCentroids2(const ImageType * 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());
+    } 
+    
+    for(uint i=1; i<labelMap->GetNumberOfLabelObjects()+1; i++) {
+      DD(labelMap->GetLabelObject(i)->GetBinaryPrincipalAxes());
+      DD(labelMap->GetLabelObject(i)->GetBinaryFlatness());
+      DD(labelMap->GetLabelObject(i)->GetRoundness ());      
+
+      // search for the point on the boundary alog PA
+
+    }
+
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  void
+  PointsUtils<ImageType>::Convert2DTo3D(const PointType2D & p2D, 
+                                        const ImageType * image, 
+                                        const int slice, 
+                                        PointType3D & p3D)  
+  {
+    IndexType3D index3D;
+    index3D[0] = index3D[1] = 0;
+    index3D[2] = image->GetLargestPossibleRegion().GetIndex()[2]+slice;
+    image->TransformIndexToPhysicalPoint(index3D, p3D);
+    p3D[0] = p2D[0]; 
+    p3D[1] = p2D[1];
+    //  p3D[2] = p[2];//(image->GetLargestPossibleRegion().GetIndex()[2]+slice)*image->GetSpacing()[2] 
+    //    + image->GetOrigin()[2];
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  void 
+  PointsUtils<ImageType>::Convert2DMapTo3DList(const MapPoint2DType & map, 
+                                            const ImageType * 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 
+  PointsUtils<ImageType>::Convert2DListTo3DList(const VectorPoint2DType & p2D, 
+                                                int slice,
+                                                const ImageType * image, 
+                                                VectorPoint3DType & list) 
+  {
+    for(uint i=0; i<p2D.size(); i++) {
+      PointType3D p;
+      Convert2DTo3D(p2D[i], image, slice, p);
+      list.push_back(p);
+    }
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  void 
+  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 
+  Dilate(const ImageType * 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 Dilate<ImageType>(image, r, BG, FG, extendSupport);
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::Pointer 
+  Dilate(const ImageType * 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 Dilate<ImageType>(image, r, BG, FG, extendSupport);
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::Pointer 
+  Dilate(const ImageType * 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();
+
+    typename ImageType::Pointer output;
+    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();
+      output = 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);
+    if (extendSupport) dilateFilter->SetInput(output);
+    else dilateFilter->SetInput(image);
+    dilateFilter->Update();
+    return dilateFilter->GetOutput();
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::Pointer 
+  Opening(const ImageType * image, typename ImageType::SizeType radius,
+         typename ImageType::PixelType BG,
+         typename ImageType::PixelType FG)
+  {
+    // Kernel 
+    typedef itk::BinaryBallStructuringElement<typename ImageType::PixelType, 
+                                              ImageType::ImageDimension> KernelType;    
+    KernelType structuringElement;
+    structuringElement.SetRadius(radius);
+    structuringElement.CreateStructuringElement();
+    
+    // Filter
+    typedef itk::BinaryMorphologicalOpeningImageFilter<ImageType, ImageType , KernelType> OpeningFilterType;
+    typename OpeningFilterType::Pointer open = OpeningFilterType::New();
+    open->SetInput(image);
+    open->SetBackgroundValue(BG);
+    open->SetForegroundValue(FG);
+    open->SetKernel(structuringElement);
+    open->Update();
+    return open->GetOutput();
+  }
+  //--------------------------------------------------------------------
+
+
+
+  //--------------------------------------------------------------------
+  template<class ValueType, class VectorType>
+  void 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
+
+    offsetToKeep = is used to determine which side of the line we
+    keep. The point along the mainDirection but 'offsetToKeep' mm away
+    is kept.
+  
+  */
+  template<class ImageType>
+  void 
+  SliceBySliceSetBackgroundFromLineSeparation(ImageType * input, 
+                                              std::vector<typename ImageType::PointType> & lA, 
+                                              std::vector<typename ImageType::PointType> & lB, 
+                                              typename ImageType::PixelType BG, 
+                                              int mainDirection, 
+                                              double offsetToKeep)
+  {
+    assert((mainDirection==0) || (mainDirection==1));
+    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() == lB.size());
+    while ((i<lA.size()) && (!siter.IsAtEnd())) {
+      // Check that the current slice correspond to the current point
+      input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
+      if ((fabs(C[2] - lA[i][2]))>0.01) { // is !equal with a tolerance of 0.01 mm
+      }
+      else {
+        // Define A,B,C points
+        A = lA[i];
+        B = lB[i];
+        C = A;
+      
+        // Check that the line is not a point (A=B)
+        bool p = (A[0] == B[0]) && (A[1] == B[1]);
+      
+        if (!p) {
+          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();
+          } // end loop slice
+        }      
+
+        ++i;
+      } // End of current slice
+      siter.NextSlice();
+    }
+  }                                                   
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  void 
+  AndNot(ImageType * input, 
+         const ImageType * object, 
+         typename ImageType::PixelType BG)
+  {
+    typename ImageType::Pointer o;
+    bool resized=false;
+    if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input, object)) {
+      o = clitk::ResizeImageLike<ImageType>(object, input, BG);
+      resized = true;
+    }
+
+    typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
+    typename BoolFilterType::Pointer boolFilter = BoolFilterType::New(); 
+    boolFilter->InPlaceOn();
+    boolFilter->SetInput1(input);
+    if (resized) boolFilter->SetInput2(o);  
+    else boolFilter->SetInput2(object);
+    boolFilter->SetBackgroundValue1(BG);
+    boolFilter->SetBackgroundValue2(BG);
+    boolFilter->SetOperationType(BoolFilterType::AndNot);
+    boolFilter->Update();
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  void 
+  And(ImageType * input, 
+      const ImageType * object, 
+      typename ImageType::PixelType BG)
+  {
+    typename ImageType::Pointer o;
+    bool resized=false;
+    if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input, object)) {
+      o = clitk::ResizeImageLike<ImageType>(object, input, BG);
+      resized = true;
+    }
+
+    typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
+    typename BoolFilterType::Pointer boolFilter = BoolFilterType::New(); 
+    boolFilter->InPlaceOn();
+    boolFilter->SetInput1(input);
+    if (resized) boolFilter->SetInput2(o);  
+    else boolFilter->SetInput2(object);
+    boolFilter->SetBackgroundValue1(BG);
+    boolFilter->SetBackgroundValue2(BG);
+    boolFilter->SetOperationType(BoolFilterType::And);
+    boolFilter->Update();
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  void 
+  Or(ImageType * input, 
+     const ImageType * object, 
+     typename ImageType::PixelType BG)
+  {
+    typename ImageType::Pointer o;
+    bool resized=false;
+    if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input, object)) {
+      o = clitk::ResizeImageLike<ImageType>(object, input, BG);
+      resized = true;
+    }
+
+    typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
+    typename BoolFilterType::Pointer boolFilter = BoolFilterType::New(); 
+    boolFilter->InPlaceOn();
+    boolFilter->SetInput1(input);
+    if (resized) boolFilter->SetInput2(o);  
+    else boolFilter->SetInput2(object);
+    boolFilter->SetBackgroundValue1(BG);
+    boolFilter->SetBackgroundValue2(BG);
+    boolFilter->SetOperationType(BoolFilterType::Or);
+    boolFilter->Update();
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::Pointer
+  Binarize(const ImageType * input, 
+           typename ImageType::PixelType lower, 
+           typename ImageType::PixelType upper, 
+           typename ImageType::PixelType BG,
+           typename ImageType::PixelType FG) 
+  {
+    typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> BinaryThresholdFilterType;
+    typename BinaryThresholdFilterType::Pointer binarizeFilter = BinaryThresholdFilterType::New();
+    binarizeFilter->SetInput(input);
+    binarizeFilter->InPlaceOff();
+    binarizeFilter->SetLowerThreshold(lower);
+    binarizeFilter->SetUpperThreshold(upper);
+    binarizeFilter->SetInsideValue(FG);
+    binarizeFilter->SetOutsideValue(BG);
+    binarizeFilter->Update();
+    return binarizeFilter->GetOutput();
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  void
+  GetMinMaxPointPosition(const ImageType * input, 
+                         typename ImageType::PointType & min,
+                         typename ImageType::PointType & max) 
+  {
+    typename ImageType::IndexType index = input->GetLargestPossibleRegion().GetIndex();
+    input->TransformIndexToPhysicalPoint(index, min);
+    index = index+input->GetLargestPossibleRegion().GetSize();
+    input->TransformIndexToPhysicalPoint(index, max);
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::PointType
+  FindExtremaPointInAGivenLine(const ImageType * input, 
+                               int dimension, 
+                               bool inverse, 
+                               typename ImageType::PointType p, 
                                typename ImageType::PixelType BG, 
-                               typename ImageType::PixelType FG, 
-                               bool isFullyConnected,
-                               int minimalComponentSize,
-                               LabelizeParameters<typename ImageType::PixelType> * param)
-{
-  typename ImageType::Pointer working_image;
-  working_image = Labelize<ImageType>(input, BG, isFullyConnected, minimalComponentSize);
-  working_image = RemoveLabels<ImageType>(working_image, BG, param->GetLabelsToRemove());
-  working_image = KeepLabels<ImageType>(working_image, 
-                                        BG, FG, 
-                                        param->GetFirstKeep(), 
-                                        param->GetLastKeep(), 
-                                        param->GetUseLastKeep());
-  return working_image;
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class ImageType>
-typename ImageType::Pointer
-clitk::EnlargeImageLike(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");
-  }
-
-  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]);
-  }
-  // DD(size);
-  typename ImageType::RegionType region;
-  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]);
-  }
-  // DD(index);
-  pasteFilter->SetSourceImage(input);
-  pasteFilter->SetDestinationImage(output);
-  pasteFilter->SetDestinationIndex(index);
-  pasteFilter->SetSourceRegion(input->GetLargestPossibleRegion());
-  pasteFilter->Update();
-  return pasteFilter->GetOutput();  
-}
-//--------------------------------------------------------------------
+                               double distanceMax) 
+  {
+    // Which direction ?  Increasing or decreasing.
+    int d=1;
+    if (inverse) d=-1;
+  
+    // Transform to pixel index
+    typename ImageType::IndexType index;
+    input->TransformPhysicalPointToIndex(p, index);
+
+    // Loop while inside the mask;
+    while (input->GetPixel(index) != BG) {
+      index[dimension] += d;
+    }
+
+    // Transform back to Physical Units
+    typename ImageType::PointType result;
+    input->TransformIndexToPhysicalPoint(index, result);
+
+    // Check that is is not too far away
+    double distance = p.EuclideanDistanceTo(result);
+    if (distance > distanceMax) {
+      result = p; // Get back to initial value
+    }
+
+    return result;
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class PointType>
+  bool
+  IsOnTheSameLineSide(PointType C, PointType A, PointType B, PointType like) 
+  {
+    // Look at the position of point 'like' according to the AB line
+    double s = (B[0] - A[0]) * (like[1] - A[1]) - (B[1] - A[1]) * (like[0] - A[0]);
+    bool negative = s<0;
+  
+    // Look the C position
+    s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
+
+    if (negative && (s<=0)) return true;
+    if (!negative && (s>=0)) return true;
+    return false;
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  /* Consider an input object, for each slice, find the extrema
+     position according to a given direction and build a line segment
+     passing throught this point in a given direction.  Output is a
+     vector of line (from point A to B), for each slice;
+   */
+  template<class ImageType>
+  void 
+  SliceBySliceBuildLineSegmentAccordingToExtremaPosition(const ImageType * input, 
+                                                         typename ImageType::PixelType BG, 
+                                                         int sliceDimension, 
+                                                         int extremaDirection, 
+                                                         bool extremaOppositeFlag, 
+                                                         int lineDirection,
+                                                         double margin,
+                                                         std::vector<typename ImageType::PointType> & A, 
+                                                         std::vector<typename ImageType::PointType> & B)
+  {
+    // Type of a slice
+    typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
+    
+    // Build the list of slices
+    std::vector<typename SliceType::Pointer> slices;
+    clitk::ExtractSlices<ImageType>(input, sliceDimension, slices);
+
+    // Build the list of 2D points
+    std::map<int, typename SliceType::PointType> position2D;
+    for(uint i=0; i<slices.size(); i++) {
+      typename SliceType::PointType p;
+      bool found = 
+        clitk::FindExtremaPointInAGivenDirection<SliceType>(slices[i], BG, 
+                                                            extremaDirection, extremaOppositeFlag, p);
+      if (found) {
+        position2D[i] = p;
+      }
+    }
+    
+    // Convert 2D points in slice into 3D points
+    clitk::PointsUtils<ImageType>::Convert2DMapTo3DList(position2D, input, A);
+    
+    // Create additional point just right to the previous ones, on the
+    // given lineDirection, in order to create a horizontal/vertical line.
+    for(uint i=0; i<A.size(); i++) {
+      typename ImageType::PointType p = A[i];
+      p[lineDirection] += 10;
+      B.push_back(p);
+      // Margins ?
+      A[i][extremaDirection] += margin;
+      B[i][extremaDirection] += margin;
+    }
+
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::Pointer
+  SliceBySliceKeepMainCCL(const ImageType * input, 
+                          typename ImageType::PixelType BG,
+                          typename ImageType::PixelType FG)  {
+    
+    // Extract slices
+    const int d = ImageType::ImageDimension-1;
+    typedef typename itk::Image<typename ImageType::PixelType, d> SliceType;
+    std::vector<typename SliceType::Pointer> slices;
+    clitk::ExtractSlices<ImageType>(input, d, slices);
+    
+    // Labelize and keep the main one
+    std::vector<typename SliceType::Pointer> o;
+    for(uint i=0; i<slices.size(); i++) {
+      o.push_back(clitk::Labelize<SliceType>(slices[i], BG, false, 1));
+      o[i] = clitk::KeepLabels<SliceType>(o[i], BG, FG, 1, 1, true);
+    }
+    
+    // Join slices
+    typename ImageType::Pointer output;
+    output = clitk::JoinSlices<ImageType>(o, input, d);
+    return output;
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::Pointer
+  Clone(const ImageType * input) {
+    typedef itk::ImageDuplicator<ImageType> DuplicatorType;
+    typename DuplicatorType::Pointer duplicator = DuplicatorType::New();
+    duplicator->SetInputImage(input);
+    duplicator->Update();
+    return duplicator->GetOutput();
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  /* Consider an input object, start at A, for each slice (dim1): 
+     - compute the intersection between the AB line and the current slice
+     - remove what is at lower or greater according to dim2 of this point
+     - stop at B
+  */
+  template<class ImageType>
+  typename ImageType::Pointer
+  SliceBySliceSetBackgroundFromSingleLine(const ImageType * input, 
+                                          typename ImageType::PixelType BG, 
+                                          typename ImageType::PointType & A, 
+                                          typename ImageType::PointType & B, 
+                                          int dim1, int dim2, bool removeLowerPartFlag)
+    
+  {
+    // Extract slices
+    typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
+    typedef typename SliceType::Pointer SlicePointer;
+    std::vector<SlicePointer> slices;
+    clitk::ExtractSlices<ImageType>(input, dim1, slices);
+
+    // Start at slice that contains A, and stop at B
+    typename ImageType::IndexType Ap;
+    typename ImageType::IndexType Bp;
+    input->TransformPhysicalPointToIndex(A, Ap);
+    input->TransformPhysicalPointToIndex(B, Bp);
+    
+    // Determine slice largest region
+    typename SliceType::RegionType region = slices[0]->GetLargestPossibleRegion();
+    typename SliceType::SizeType size = region.GetSize();
+    typename SliceType::IndexType index = region.GetIndex();
+
+    // Line slope
+    double a = (Bp[dim2]-Ap[dim2])/(Bp[dim1]-Ap[dim1]);
+    double b = Ap[dim2];
+
+    // Loop from slice A to slice B
+    for(uint i=0; i<(Bp[dim1]-Ap[dim1]); i++) {
+      // Compute intersection between line AB and current slice for the dim2
+      double p = a*i+b;
+      // Change region (lower than dim2)
+      if (removeLowerPartFlag) {
+        size[dim2] = p-Ap[dim2];
+      }
+      else {
+        size[dim2] = slices[0]->GetLargestPossibleRegion().GetSize()[dim2]-p;
+        index[dim2] = p;
+      }
+      region.SetSize(size);
+      region.SetIndex(index);
+      // Fill region with BG (simple region iterator)
+      FillRegionWithValue<SliceType>(slices[i+Ap[dim1]], BG, region);
+      /*
+      typedef itk::ImageRegionIterator<SliceType> IteratorType;
+      IteratorType iter(slices[i+Ap[dim1]], region);
+      iter.GoToBegin();
+      while (!iter.IsAtEnd()) {
+        iter.Set(BG);
+        ++iter;
+      }
+      */
+      // Loop
+    }
+    
+    // Merge slices
+    typename ImageType::Pointer output;
+    output = clitk::JoinSlices<ImageType>(slices, input, dim1);
+    return output;
+  }
+  //--------------------------------------------------------------------
+
+  //--------------------------------------------------------------------
+  /* Consider an input object, slice by slice, use the point A and set
+     pixel to BG according to their position relatively to A
+  */
+  template<class ImageType>
+  typename ImageType::Pointer
+  SliceBySliceSetBackgroundFromPoints(const ImageType * input, 
+                                      typename ImageType::PixelType BG, 
+                                      int sliceDim,
+                                      std::vector<typename ImageType::PointType> & A, 
+                                      bool removeGreaterThanXFlag,
+                                      bool removeGreaterThanYFlag)
+    
+  {
+    // Extract slices
+    typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
+    typedef typename SliceType::Pointer SlicePointer;
+    std::vector<SlicePointer> slices;
+    clitk::ExtractSlices<ImageType>(input, sliceDim, slices);
+
+    // Start at slice that contains A
+    typename ImageType::IndexType Ap;
+    
+    // Determine slice largest region
+    typename SliceType::RegionType region = slices[0]->GetLargestPossibleRegion();
+    typename SliceType::SizeType size = region.GetSize();
+    typename SliceType::IndexType index = region.GetIndex();
+
+    // Loop from slice A to slice B
+    for(uint i=0; i<A.size(); i++) {
+      input->TransformPhysicalPointToIndex(A[i], Ap);
+      uint sliceIndex = Ap[2] - input->GetLargestPossibleRegion().GetIndex()[2];
+      if ((sliceIndex < 0) || (sliceIndex >= slices.size())) {
+        continue; // do not consider this slice
+      }
+      
+      // Compute region for BG
+      if (removeGreaterThanXFlag) {
+        index[0] = Ap[0];
+        size[0] = region.GetSize()[0]-(index[0]-region.GetIndex()[0]);
+      }
+      else {
+        index[0] = region.GetIndex()[0];
+        size[0] = Ap[0] - index[0];
+      }
+
+      if (removeGreaterThanYFlag) {
+        index[1] = Ap[1];
+        size[1] = region.GetSize()[1]-(index[1]-region.GetIndex()[1]);
+      }
+      else {
+        index[1] = region.GetIndex()[1];
+        size[1] = Ap[1] - index[1];
+      }
+
+      // Set region
+      region.SetSize(size);
+      region.SetIndex(index);
+
+      // Fill region with BG (simple region iterator)
+      FillRegionWithValue<SliceType>(slices[sliceIndex], BG, region);
+      // Loop
+    }
+    
+    // Merge slices
+    typename ImageType::Pointer output;
+    output = clitk::JoinSlices<ImageType>(slices, input, sliceDim);
+    return output;
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  void
+  FillRegionWithValue(ImageType * input, typename ImageType::PixelType value, typename ImageType::RegionType & region)
+  {
+    typedef itk::ImageRegionIterator<ImageType> IteratorType;
+    IteratorType iter(input, region);
+    iter.GoToBegin();
+    while (!iter.IsAtEnd()) {
+      iter.Set(value);
+      ++iter;
+    }    
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  void
+  GetMinMaxBoundary(ImageType * input, typename ImageType::PointType & min, 
+                    typename ImageType::PointType & max)
+  {
+    typedef typename ImageType::PointType PointType;
+    typedef typename ImageType::IndexType IndexType;
+    IndexType min_i, max_i;
+    min_i = input->GetLargestPossibleRegion().GetIndex();
+    for(uint i=0; i<ImageType::ImageDimension; i++)
+      max_i[i] = input->GetLargestPossibleRegion().GetSize()[i] + min_i[i];
+    input->TransformIndexToPhysicalPoint(min_i, min);
+    input->TransformIndexToPhysicalPoint(max_i, max);  
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename itk::Image<float, ImageType::ImageDimension>::Pointer
+  DistanceMap(const ImageType * input, typename ImageType::PixelType BG)//, 
+  //              typename itk::Image<float, ImageType::ImageDimension>::Pointer dmap) 
+  {
+    typedef itk::Image<float,ImageType::ImageDimension> FloatImageType;
+    typedef itk::SignedMaurerDistanceMapImageFilter<ImageType, FloatImageType> DistanceMapFilterType;
+    typename DistanceMapFilterType::Pointer filter = DistanceMapFilterType::New();
+    filter->SetInput(input);
+    filter->SetUseImageSpacing(true);
+    filter->SquaredDistanceOff();
+    filter->SetBackgroundValue(BG);
+    filter->Update();
+    return filter->GetOutput();
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  void 
+  SliceBySliceBuildLineSegmentAccordingToMinimalDistanceBetweenStructures(const ImageType * S1, 
+                                                                          const ImageType * S2, 
+                                                                          typename ImageType::PixelType BG, 
+                                                                          int sliceDimension, 
+                                                                          std::vector<typename ImageType::PointType> & A, 
+                                                                          std::vector<typename ImageType::PointType> & B)
+  {
+    // Extract slices
+    typedef typename itk::Image<typename ImageType::PixelType, 2> SliceType;
+    typedef typename SliceType::Pointer SlicePointer;
+    std::vector<SlicePointer> slices_s1;
+    std::vector<SlicePointer> slices_s2;
+    clitk::ExtractSlices<ImageType>(S1, sliceDimension, slices_s1);
+    clitk::ExtractSlices<ImageType>(S2, sliceDimension, slices_s2);
+
+    assert(slices_s1.size() == slices_s2.size());
+
+    // Prepare dmap
+    typedef itk::Image<float,2> FloatImageType;
+    typedef itk::SignedMaurerDistanceMapImageFilter<SliceType, FloatImageType> DistanceMapFilterType;
+    std::vector<typename FloatImageType::Pointer> dmaps1;
+    std::vector<typename FloatImageType::Pointer> dmaps2;
+    typename FloatImageType::Pointer dmap;
+
+    // loop on slices
+    for(uint i=0; i<slices_s1.size(); i++) {
+      // Compute dmap for S1 *TO PUT IN FONCTION*
+      dmap = clitk::DistanceMap<SliceType>(slices_s1[i], BG);
+      dmaps1.push_back(dmap);
+      writeImage<FloatImageType>(dmap, "dmap1.mha");
+      // Compute dmap for S2
+      dmap = clitk::DistanceMap<SliceType>(slices_s2[i], BG);
+      dmaps2.push_back(dmap);
+      writeImage<FloatImageType>(dmap, "dmap2.mha");
+      
+      // Look in S2 for the point the closest to S1
+      typename SliceType::PointType p = ComputeClosestPoint<SliceType>(slices_s1[i], dmaps2[i], BG);
+      typename ImageType::PointType p3D;
+      clitk::PointsUtils<ImageType>::Convert2DTo3D(p, S1, i, p3D);
+      A.push_back(p3D);
+
+      // Look in S2 for the point the closest to S1
+      p = ComputeClosestPoint<SliceType>(slices_s2[i], dmaps1[i], BG);
+      clitk::PointsUtils<ImageType>::Convert2DTo3D(p, S2, i, p3D);
+      B.push_back(p3D);
+
+    }
+
+    // Debug dmap
+    /*
+      typedef itk::Image<float,3> FT;
+      FT::Pointer f = FT::New();
+      typename FT::Pointer d1 = clitk::JoinSlices<FT>(dmaps1, S1, 2);
+      typename FT::Pointer d2 = clitk::JoinSlices<FT>(dmaps2, S2, 2);
+      writeImage<FT>(d1, "d1.mha");
+      writeImage<FT>(d2, "d2.mha");
+    */
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::PointType
+  ComputeClosestPoint(const ImageType * input, 
+                      const itk::Image<float, ImageType::ImageDimension> * dmap, 
+                      typename ImageType::PixelType & BG) 
+  {
+    // Loop dmap + S2, if FG, get min
+    typedef itk::Image<float,ImageType::ImageDimension> FloatImageType;
+    typedef itk::ImageRegionConstIteratorWithIndex<ImageType> ImageIteratorType;
+    typedef itk::ImageRegionConstIterator<FloatImageType> DMapIteratorType;
+    ImageIteratorType iter1(input, input->GetLargestPossibleRegion());
+    DMapIteratorType iter2(dmap, dmap->GetLargestPossibleRegion());
+    
+    iter1.GoToBegin();
+    iter2.GoToBegin();
+    double dmin = 100000.0;
+    typename ImageType::IndexType indexmin;
+    while (!iter1.IsAtEnd()) {
+      if (iter1.Get() != BG) {
+        double d = iter2.Get();
+        if (d<dmin) {
+          indexmin = iter1.GetIndex();
+          dmin = d;
+        }
+      }
+      ++iter1;
+      ++iter2;
+    }
+    
+    // Convert in Point
+    typename ImageType::PointType p;
+    input->TransformIndexToPhysicalPoint(indexmin, p);
+    return p;
+  }
+  //--------------------------------------------------------------------
+     
+
+
+
+} // end of namespace
+