Add seedRadius option to clitkRegionGrowing

- Add seedRadius option to clitkRegionGrowing to allow ball of seeds
  instead of single pixel seed.

diff --git a/segmentation/clitkRegionGrowing.ggo b/segmentation/clitkRegionGrowing.ggo
index 59cb77c60a90a775aa080cca262b40d5574a4073..60bcae23c30e45150347d614630e6af94bf6f049 100644 (file)
--- a/segmentation/clitkRegionGrowing.ggo
+++ b/segmentation/clitkRegionGrowing.ggo
@@ -25,6 +25,7 @@ option "adaptLower"   -       "3,4: (locally) adapt lower thresholding"         flag          off
 option "adaptUpper"    -       "3,4: (locally) adapt upper thresholding"         flag          off
 option "multiplier"            m       "2-4: (2-3) accept if within mean+-mutiplier*SD, (4) explosion if size increases multiplier times"      double  no      default="2.0"
 option "seed"          s       "Seed index postion (in voxels)"                  int           multiple        no      default="0"     
+option "seedRadius"            -       "Radius used for seed dilatation(in voxel)"       int           multiple        no      default="0"     
 option "pad"           p       "The replace padding value"                       double        no              default="1.0"   
 option "radius"        r       "1-3: The radius of the neighborhood"             int           no              multiple        default="1"
 option "maxSD"         -       "3: Limit to SD"                                  double        no       

diff --git a/segmentation/clitkRegionGrowingGenericFilter.txx b/segmentation/clitkRegionGrowingGenericFilter.txx
index b92272788895fbd19e736e01b37a6ddbac1dedc2..43f5b08e167db7fdbda6d85029ca0b4b95175a23 100644 (file)
--- a/segmentation/clitkRegionGrowingGenericFilter.txx
+++ b/segmentation/clitkRegionGrowingGenericFilter.txx
@@ -17,6 +17,8 @@
 ===========================================================================**/
 #ifndef clitkRegionGrowingGenericFilter_txx
 #define clitkRegionGrowingGenericFilter_txx
+#include <itkBinaryBallStructuringElement.h>
+#include <itkConstShapedNeighborhoodIterator.h>
 
 namespace clitk
 {
@@ -75,17 +77,64 @@ namespace clitk
     typename InputImageType::Pointer input= reader->GetOutput();
 
     // Seed
-    typename  InputImageType::IndexType index;
+    typedef typename  std::vector<typename InputImageType::IndexType> SeedsType;
+    SeedsType seeds(1);
     if(m_ArgsInfo.seed_given==Dimension)
       for (unsigned int i=0; i<Dimension;i++)
-       index[i]=m_ArgsInfo.seed_arg[i];
+       seeds[0][i]=m_ArgsInfo.seed_arg[i];
     
     else if ( m_ArgsInfo.seed_given==1)
-      index.Fill(m_ArgsInfo.seed_arg[0]);
+      seeds[0].Fill(m_ArgsInfo.seed_arg[0]);
     
-    else index.Fill(m_ArgsInfo.seed_arg[0]);
-    if(m_Verbose)std::cout<<"Setting seed index to "<<index<<"..."<<std::endl;
+    else seeds[0].Fill(m_ArgsInfo.seed_arg[0]);
+    if(m_Verbose)std::cout<<"Setting seed seeds to "<<seeds[0]<<"..."<<std::endl;
 
+    if (m_ArgsInfo.seedRadius_given)
+    {
+      typedef itk::BinaryBallStructuringElement<PixelType, Dimension> BallType;
+      typename BallType::RadiusType r;
+
+      if (m_ArgsInfo.seedRadius_given == Dimension)
+        for (unsigned i = 0; i < Dimension; i++)
+          r[i] = m_ArgsInfo.seedRadius_arg[i];
+      else
+        r.Fill(m_ArgsInfo.seed_arg[0]);
+
+      BallType ball;
+      ball.SetRadius(r);
+      ball.CreateStructuringElement();
+
+      typedef itk::ConstShapedNeighborhoodIterator<InputImageType> IteratorType;
+      IteratorType it(ball.GetRadius(),
+          input,
+          input->GetLargestPossibleRegion());
+#if ITK_VERSION_MAJOR < 4
+      typename BallType::ConstIterator nit;
+      unsigned idx = 0;
+      for (nit = ball.Begin(); nit != ball.End(); ++nit, ++idx)
+      {
+        if (*nit)
+        {
+          it.ActivateOffset(it.GetOffset(idx));
+        }
+        else
+        {
+          it.DeactivateOffset(it.GetOffset(idx));
+        }
+      }
+#else
+      it.CreateActiveListFromNeighborhood(ball);
+      it.NeedToUseBoundaryConditionOff();
+#endif
+
+      it.SetLocation(seeds[0]);
+      for (typename IteratorType::ConstIterator i = it.Begin(); !i.IsAtEnd(); ++i)
+      {
+        typename InputImageType::IndexType id = seeds[0] + i.GetNeighborhoodOffset();
+        if (id != seeds[0] && input->GetLargestPossibleRegion().IsInside(id))
+          seeds.push_back(id);
+      }
+    }
 
     // Filter
     typedef itk::ImageToImageFilter<InputImageType, OutputImageType> ImageToImageFilterType;
@@ -101,7 +150,8 @@ namespace clitk
        f->SetLower(m_ArgsInfo.lower_arg);
        f->SetUpper(m_ArgsInfo.upper_arg);
        f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
-       f->SetSeed(index);
+        for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
+          f->AddSeed(*it);
        filter=f;
        if(m_Verbose)std::cout<<"Using the connected threshold image filter..."<<std::endl;
 
@@ -128,7 +178,8 @@ namespace clitk
        f->SetLower(m_ArgsInfo.lower_arg);
        f->SetUpper(m_ArgsInfo.upper_arg);
        f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
-       f->AddSeed(index);
+        for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
+          f->AddSeed(*it);
        f->SetRadius(size);
        filter=f;
        if(m_Verbose)std::cout<<"Using the neighborhood threshold connected image filter..."<<std::endl;
@@ -155,7 +206,8 @@ namespace clitk
 
        f->SetMultiplier( m_ArgsInfo.multiplier_arg );
        f->SetNumberOfIterations( m_ArgsInfo.multiplier_arg );
-       f->AddSeed( index );
+        for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
+          f->AddSeed(*it);
        f->SetNumberOfIterations( m_ArgsInfo.iter_arg);
        f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
        f->SetInitialNeighborhoodRadius(size[0]);
@@ -187,7 +239,8 @@ namespace clitk
        f->SetMultiplier(m_ArgsInfo.multiplier_arg);
        f->SetMaximumSDIsGiven(m_ArgsInfo.maxSD_given);
        if (m_ArgsInfo.maxSD_given) f->SetMaximumSD(m_ArgsInfo.maxSD_arg);
-       f->AddSeed(index);
+        for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
+          f->AddSeed(*it);
        f->SetRadius(size);
        filter=f;
        if(m_Verbose)std::cout<<"Using the locally adaptive threshold connected image filter..."<<std::endl;
@@ -221,7 +274,8 @@ namespace clitk
        f->SetThresholdStepSize(m_ArgsInfo.step_arg);
        f->SetMinimumThresholdStepSize(m_ArgsInfo.minStep_arg);
        f->SetFullyConnected(m_ArgsInfo.full_flag);
-       f->AddSeed(index);
+        for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
+          f->AddSeed(*it);
        filter=f;
        if(m_Verbose)std::cout<<"Using the explosion controlled threshold connected image filter..."<<std::endl;