X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=itk%2FclitkSegmentationUtils.txx;h=aef202f00ec849a3cb6e3428b59680c339864135;hb=97e94d6d86e558d1d377486bf2db1549c06f4fd1;hp=716e2872a2f402cb2f8fd4ce89a609581e39ef81;hpb=825277ddef9bbde1f378fec8d140c1ee335dab1b;p=clitk.git

diff --git a/itk/clitkSegmentationUtils.txx b/itk/clitkSegmentationUtils.txx
index 716e287..aef202f 100644
--- a/itk/clitkSegmentationUtils.txx
+++ b/itk/clitkSegmentationUtils.txx
@@ -14,20 +14,29 @@
 
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-======================================================================-====*/
+  ======================================================================-====*/
+
+// clitk
+#include "clitkSetBackgroundImageFilter.h"
+
+// itk
+#include <itkConnectedComponentImageFilter.h>
+#include <itkRelabelComponentImageFilter.h>
+#include <itkBinaryThresholdImageFilter.h>
+#include <itkPasteImageFilter.h>
 
 //--------------------------------------------------------------------
 template<class ImageType>
 void clitk::ComputeBBFromImageRegion(typename ImageType::Pointer image, 
-                              typename ImageType::RegionType region,
-                              typename itk::BoundingBox<unsigned long, 
+                                     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];
+    lastIndex[i] = firstIndex[i]+region.GetSize()[i];
   }
 
   typedef itk::BoundingBox<unsigned long, 
@@ -47,8 +56,8 @@ void clitk::ComputeBBFromImageRegion(typename ImageType::Pointer image,
 //--------------------------------------------------------------------
 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) {
+                                  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;
@@ -70,31 +79,212 @@ void clitk::ComputeBBIntersection(typename itk::BoundingBox<unsigned long, Dimen
 
 //--------------------------------------------------------------------
 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);
+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]);
-    }
+  // Region size
+  SizeType regionSize;
+  PointType maxs = bb->GetMaximum();
+  PointType mins = bb->GetMinimum();
+  for(unsigned int i=0; i<ImageType::ImageDimension; 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
-    region.SetIndex(regionStart);
-    region.SetSize(regionSize);
+  // Create region
+  region.SetIndex(regionStart);
+  region.SetSize(regionSize);
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template<class ImageType, class TMaskImageType>
+typename ImageType::Pointer
+clitk::SetBackground(//typename ImageType::ConstPointer input, 
+                     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();
+  setBackgroundFilter->SetInput(input);
+  setBackgroundFilter->SetInput2(mask);
+  setBackgroundFilter->SetMaskValue(maskBG);
+  setBackgroundFilter->SetOutsideValue(outValue);
+  setBackgroundFilter->Update();
+  return setBackgroundFilter->GetOutput();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+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();
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template<class ImageType>
+typename ImageType::Pointer
+clitk::Labelize(typename ImageType::Pointer 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->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->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();
+    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
+clitk::KeepLabels(typename ImageType::Pointer 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
+clitk::LabelizeAndSelectLabels(typename ImageType::Pointer 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);
+  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();  
+}
+//--------------------------------------------------------------------