add AutoCrop function

diff --git a/itk/clitkSegmentationUtils.h b/itk/clitkSegmentationUtils.h
index 3b7a1e5525a2ae2d04603aafd7dda3031dda8c42..277dfc791401b3a475c389821ae1eecb50b6e8e7 100644 (file)
--- a/itk/clitkSegmentationUtils.h
+++ b/itk/clitkSegmentationUtils.h
@@ -20,6 +20,8 @@
 #define CLITKSEGMENTATIONUTILS_H
 
 #include "clitkCommon.h"
+#include "clitkAutoCropFilter.h"
+#include "clitkLabelizeParameters.h"
 #include <itkBoundingBox.h>
 
 namespace clitk {
@@ -43,7 +45,94 @@ namespace clitk {
                            const typename itk::BoundingBox<unsigned long, 
                            ImageType::ImageDimension>::Pointer bb, 
                            typename ImageType::RegionType & region);
+  //--------------------------------------------------------------------
+  template<class TInternalImageType, class TMaskInternalImageType>
+  typename TInternalImageType::Pointer
+  SetBackground(typename TInternalImageType::ConstPointer input,
+                typename TMaskInternalImageType::ConstPointer mask, 
+                typename TMaskInternalImageType::PixelType maskBG, 
+                typename TInternalImageType::PixelType outValue);
+  //--------------------------------------------------------------------
+
+    
+  //--------------------------------------------------------------------
+  template<class TInternalImageType, class TMaskInternalImageType>
+  typename TInternalImageType::Pointer
+  SetBackground(typename TInternalImageType::Pointer input, 
+                typename TMaskInternalImageType::Pointer mask, 
+                typename TMaskInternalImageType::PixelType maskBG, 
+                typename TInternalImageType::PixelType outValue) {
+    return SetBackground<TInternalImageType, TMaskInternalImageType>
+      (static_cast<typename TInternalImageType::ConstPointer>(input),  
+       static_cast<typename TMaskInternalImageType::ConstPointer>(mask), 
+       maskBG, outValue);
+  }
+  //--------------------------------------------------------------------
+
+
+  //-------------------------------------------------------------------- 
+  template<class TImageType>
+  typename TImageType::Pointer
+  Labelize(typename TImageType::Pointer input, 
+           typename TImageType::PixelType BG, 
+           bool isFullyConnected, 
+           int minimalComponentSize);
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class TImageType>
+  typename TImageType::Pointer
+  RemoveLabels(typename TImageType::Pointer input, 
+               typename TImageType::PixelType BG, 
+               std::vector<typename TImageType::PixelType> & labelsToRemove);
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+    typename ImageType::Pointer
+    AutoCrop(typename ImageType::Pointer input, 
+            typename ImageType::PixelType BG) {
+      typedef clitk::AutoCropFilter<ImageType> AutoCropFilterType;
+      typename AutoCropFilterType::Pointer autoCropFilter = AutoCropFilterType::New();
+      autoCropFilter->SetInput(input);
+      autoCropFilter->Update();   
+      return autoCropFilter->GetOutput();
+  }
+
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class TImageType>
+  typename TImageType::Pointer
+  KeepLabels(typename TImageType::Pointer input,
+             typename TImageType::PixelType BG, 
+             typename TImageType::PixelType FG,  
+             typename TImageType::PixelType firstKeep, 
+             typename TImageType::PixelType lastKeep, 
+             bool useLastKeep);
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class TImageType>
+  typename TImageType::Pointer
+  LabelizeAndSelectLabels(typename TImageType::Pointer input,
+                          typename TImageType::PixelType BG, 
+                          typename TImageType::PixelType FG, 
+                          bool isFullyConnected,
+                          int minimalComponentSize,
+                          LabelizeParameters<typename TImageType::PixelType> * param);
 
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::Pointer
+  EnlargeImageLike(typename ImageType::Pointer input,
+                   typename ImageType::Pointer like, 
+                   typename ImageType::PixelType BG);
+  
 }
 
 #include "clitkSegmentationUtils.txx"

diff --git a/itk/clitkSegmentationUtils.txx b/itk/clitkSegmentationUtils.txx
index 716e2872a2f402cb2f8fd4ce89a609581e39ef81..7f52aea61572e3591803aa805e7d408d7f37d4fb 100644 (file)
--- a/itk/clitkSegmentationUtils.txx
+++ b/itk/clitkSegmentationUtils.txx
@@ -14,13 +14,22 @@
 
   - 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;
@@ -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 +79,187 @@ 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++) {
+    regionSize[i] = floor((maxs[i] - mins[i])/image->GetSpacing()[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, 
+                     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();
+    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();  
+}
+//--------------------------------------------------------------------