add final opening

[clitk.git] / itk / clitkSegmentationUtils.txx

diff --git a/itk/clitkSegmentationUtils.txx b/itk/clitkSegmentationUtils.txx
index 16c184c0d1e36ff0e3ace5cec61df5c94de295a4..b432188aec93aa8e34a21f1047ea3d22991a2c25 100644 (file)
--- a/itk/clitkSegmentationUtils.txx
+++ b/itk/clitkSegmentationUtils.txx
@@ -32,6 +32,8 @@
 #include <itkBinaryDilateImageFilter.h>
 #include <itkConstantPadImageFilter.h>
 #include <itkImageSliceIteratorWithIndex.h>
+#include <itkBinaryMorphologicalOpeningImageFilter.h>
+#include <itkImageDuplicator.h>
 
 namespace clitk {
 
@@ -464,7 +466,7 @@ namespace clitk {
     p[dim] = max;
     typename ImageType::IndexType end;
     image->TransformPhysicalPointToIndex(p, end);
-    size[dim] = fabs(end[dim]-start[dim]);
+    size[dim] = abs(end[dim]-start[dim]);
     region.SetIndex(start);
     region.SetSize(size);
   
@@ -510,7 +512,6 @@ namespace clitk {
     typename ImageType::PointType dummy;
     centroids.push_back(dummy); // label 0 -> no centroid, use dummy point for BG 
     //DS FIXME (not useful ! to change ..)
-    DD(labelMap->GetNumberOfLabelObjects());
     for(uint i=0; i<labelMap->GetNumberOfLabelObjects(); i++) {
       int label = labelMap->GetLabels()[i];
       centroids.push_back(labelMap->GetLabelObject(label)->GetCentroid());
@@ -519,6 +520,30 @@ namespace clitk {
   //--------------------------------------------------------------------
 
 
+  //--------------------------------------------------------------------
+  template<class ImageType, class LabelType>
+  typename itk::LabelMap< itk::ShapeLabelObject<LabelType, ImageType::ImageDimension> >::Pointer
+  ComputeLabelMap(const ImageType * image, 
+                  typename ImageType::PixelType BG, 
+                  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
@@ -560,25 +585,6 @@ namespace clitk {
   //--------------------------------------------------------------------
 
 
-  //--------------------------------------------------------------------
-  template<class ImageType>
-  void
-  ExtractSlices(const ImageType * image, int direction, 
-                std::vector<typename itk::Image<typename ImageType::PixelType, 
-                                                ImageType::ImageDimension-1>::Pointer > & slices) 
-  {
-    typedef ExtractSliceFilter<ImageType> ExtractSliceFilterType;
-    typedef typename ExtractSliceFilterType::SliceType SliceType;
-    typename ExtractSliceFilterType::Pointer 
-      extractSliceFilter = ExtractSliceFilterType::New();
-    extractSliceFilter->SetInput(image);
-    extractSliceFilter->SetDirection(direction);
-    extractSliceFilter->Update();
-    extractSliceFilter->GetOutputSlices(slices);
-  }
-  //--------------------------------------------------------------------
-
-
   //--------------------------------------------------------------------
   template<class ImageType>
   void
@@ -730,6 +736,34 @@ namespace clitk {
   //--------------------------------------------------------------------
 
 
+  //--------------------------------------------------------------------
+  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, 
@@ -1020,5 +1054,46 @@ namespace clitk {
   //--------------------------------------------------------------------
 
 
+  //--------------------------------------------------------------------
+  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();
+  }
+  //--------------------------------------------------------------------
+
+
 } // end of namespace