Moved from repository clitk to clitk.private/tests_dav

diff --git a/segmentation/CMakeLists.txt b/segmentation/CMakeLists.txt
index 7e40973435bea5558edc713df650cd16adea14a5..f26ec74c203d0ee38e5df3dba5192b250d459a44 100644 (file)
--- a/segmentation/CMakeLists.txt
+++ b/segmentation/CMakeLists.txt
@@ -1,7 +1,7 @@
 #=========================================================
 
 # Add Libraries used in vv and clitk to avoid recompilation
 #=========================================================
 
 # Add Libraries used in vv and clitk to avoid recompilation

-FOREACH(clitkTool clitkExtractLung clitkExtractPatient clitkConnectedComponentLabeling)
+FOREACH(clitkTool clitkExtractLung clitkExtractPatient clitkConnectedComponentLabeling clitkRegionGrowing)

     WRAP_GGO(${clitkTool}_GGO_C ${clitkTool}.ggo)
     SET(GGO_C_FILES ${GGO_C_FILES} ${${clitkTool}_GGO_C})
 ENDFOREACH(clitkTool)
     WRAP_GGO(${clitkTool}_GGO_C ${clitkTool}.ggo)
     SET(GGO_C_FILES ${GGO_C_FILES} ${${clitkTool}_GGO_C})
 ENDFOREACH(clitkTool)


@@ -46,6 +46,10 @@ IF(CLITK_BUILD_SEGMENTATION)
     TARGET_LINK_LIBRARIES(clitkMotionMask clitkCommon ${ITK_LIBRARIES})
     SET(SEGMENTATION_INSTALL ${SEGMENTATION_INSTALL} clitkMotionMask)
     
     TARGET_LINK_LIBRARIES(clitkMotionMask clitkCommon ${ITK_LIBRARIES})
     SET(SEGMENTATION_INSTALL ${SEGMENTATION_INSTALL} clitkMotionMask)
     

+    WRAP_GGO(clitkRegionGrowing_GGO_C clitkRegionGrowing.ggo)
+    ADD_EXECUTABLE(clitkRegionGrowing clitkRegionGrowing.cxx ${clitkRegionGrowing_GGO_C} ${clitkRelativePosition_GGO_C})
+    TARGET_LINK_LIBRARIES(clitkRegionGrowing clitkCommon ${ITK_LIBRARIES})
+

     SET_TARGET_PROPERTIES(${SEGMENTATION_INSTALL} PROPERTIES INSTALL_RPATH "${VTK_DIR}:${ITK_DIR}" )  
     INSTALL (TARGETS ${SEGMENTATION_INSTALL} DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_EXECUTE WORLD_EXECUTE)
 
     SET_TARGET_PROPERTIES(${SEGMENTATION_INSTALL} PROPERTIES INSTALL_RPATH "${VTK_DIR}:${ITK_DIR}" )  
     INSTALL (TARGETS ${SEGMENTATION_INSTALL} DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_EXECUTE WORLD_EXECUTE)
 

diff --git a/segmentation/clitkRegionGrowing.cxx b/segmentation/clitkRegionGrowing.cxx
index 83aa816c403cff88c84f89744f6890e696798c2b..d24d2f72d9f3ec21ec4eb6708a0f4c297eac8519 100644 (file)
--- a/segmentation/clitkRegionGrowing.cxx
+++ b/segmentation/clitkRegionGrowing.cxx
@@ -16,22 +16,11 @@
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
 ===========================================================================**/
 
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
 ===========================================================================**/
 

-/* =================================================
- * @file   clitkRegionGrowing.cxx
- * @author 
- * @date   
- * 
- * @brief 
- * 
- ===================================================*/
-
-

 // clitk
 #include "clitkRegionGrowing_ggo.h"
 #include "clitkIO.h"
 #include "clitkRegionGrowingGenericFilter.h"
 
 // clitk
 #include "clitkRegionGrowing_ggo.h"
 #include "clitkIO.h"
 #include "clitkRegionGrowingGenericFilter.h"
 

-

 //--------------------------------------------------------------------
 int main(int argc, char * argv[]) {
 
 //--------------------------------------------------------------------
 int main(int argc, char * argv[]) {
 


@@ -40,7 +29,8 @@ int main(int argc, char * argv[]) {
   CLITK_INIT;
 
   // Filter
   CLITK_INIT;
 
   // Filter

-  clitk::RegionGrowingGenericFilter::Pointer genericFilter=clitk::RegionGrowingGenericFilter::New();
+  typedef clitk::RegionGrowingGenericFilter<args_info_clitkRegionGrowing> FilterType;
+  FilterType::Pointer genericFilter = FilterType::New();

   
   genericFilter->SetArgsInfo(args_info);
   genericFilter->Update();
   
   genericFilter->SetArgsInfo(args_info);
   genericFilter->Update();

diff --git a/segmentation/clitkRegionGrowing.ggo b/segmentation/clitkRegionGrowing.ggo
index 60bcae23c30e45150347d614630e6af94bf6f049..cd2d03e22c6cc4be5cd5a8bc3b2e08ab4837fffd 100644 (file)
--- a/segmentation/clitkRegionGrowing.ggo
+++ b/segmentation/clitkRegionGrowing.ggo
@@ -15,8 +15,8 @@ option "output"       o       "Output image filename"           string        yes
 section "Parameters"
 
 option "type"          t       "Region growing filter type: 0=threshold , 1=neighborhood-threshold , 2=confidence , 3= locally-adaptive-threshold, 4= explosion-controlled-threshold" int      no      default="0"
 section "Parameters"
 
 option "type"          t       "Region growing filter type: 0=threshold , 1=neighborhood-threshold , 2=confidence , 3= locally-adaptive-threshold, 4= explosion-controlled-threshold" int      no      default="0"

-option "lower"         l       "1,2,3,4: Lower threshold value"                  double        no      default="0"
-option "upper"         u       "1,2,3,4: Upper threshold value"                  double        no      default="1"
+option "lower"         l       "1,2,3,4: Lower threshold value"                  double        no      default="310"
+option "upper"         u       "1,2,3,4: Upper threshold value"                  double        no      default="4000"

 option "maxUpper"      -       "4: Maximum upper threshold value"                double        no      default="2000"
 option "minLower"      -       "4: Minimum lower threshold value"                double        no      default="-1000"
 option "step"          -       "4: Threshold step size"                          double        no      default="64.0"
 option "maxUpper"      -       "4: Maximum upper threshold value"                double        no      default="2000"
 option "minLower"      -       "4: Minimum lower threshold value"                double        no      default="-1000"
 option "step"          -       "4: Threshold step size"                          double        no      default="64.0"

diff --git a/segmentation/clitkRegionGrowingGenericFilter.h b/segmentation/clitkRegionGrowingGenericFilter.h
index 6f7872a24a6b991c94af8fbdac3fd97d300f12e2..225619d716a4d3b64aa3a948ea139336cd0c24d9 100644 (file)
--- a/segmentation/clitkRegionGrowingGenericFilter.h
+++ b/segmentation/clitkRegionGrowingGenericFilter.h
@@ -15,24 +15,13 @@
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
 ===========================================================================**/
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
 ===========================================================================**/

-#ifndef clitkRegionGrowingGenericFilter_h
-#define clitkRegionGrowingGenericFilter_h
-
-/* =================================================
- * @file   clitkRegionGrowingGenericFilter.h
- * @author 
- * @date   
- * 
- * @brief 
- * 
- ===================================================*/

 
 

+#ifndef CLITKREGIONGROWINGGENERICFILTER_H
+#define CLITKREGIONGROWINGGENERICFILTER_H

 
 // clitk include
 #include "clitkIO.h"
 
 // clitk include
 #include "clitkIO.h"

-#include "clitkCommon.h"
-#include "clitkImageCommon.h"
-#include "clitkRegionGrowing_ggo.h"
+#include "clitkImageToImageGenericFilter.h"

 #include "clitkLocallyAdaptiveThresholdConnectedImageFilter.h"
 #include "clitkExplosionControlledThresholdConnectedImageFilter.h"
 
 #include "clitkLocallyAdaptiveThresholdConnectedImageFilter.h"
 #include "clitkExplosionControlledThresholdConnectedImageFilter.h"
 


@@ -43,79 +32,45 @@
 #include "itkConfidenceConnectedImageFilter.h"
 #include "itkConfidenceConnectedImageFilter.h"
 
 #include "itkConfidenceConnectedImageFilter.h"
 #include "itkConfidenceConnectedImageFilter.h"
 

+//--------------------------------------------------------------------

 namespace clitk 
 {
 namespace clitk 
 {

-
-
-  class ITK_EXPORT RegionGrowingGenericFilter : public itk::LightObject
+  template<class ArgsInfoType>
+  class ITK_EXPORT RegionGrowingGenericFilter: 
+    public ImageToImageGenericFilter<RegionGrowingGenericFilter<ArgsInfoType> >

   {
   {

+

   public:
     //----------------------------------------
   public:
     //----------------------------------------

-    // ITK
+    RegionGrowingGenericFilter();
+

     //----------------------------------------
     //----------------------------------------

-    typedef RegionGrowingGenericFilter                   Self;
-    typedef itk::LightObject                   Superclass;
+    typedef RegionGrowingGenericFilter         Self;

     typedef itk::SmartPointer<Self>            Pointer;
     typedef itk::SmartPointer<const Self>      ConstPointer;
    
     typedef itk::SmartPointer<Self>            Pointer;
     typedef itk::SmartPointer<const Self>      ConstPointer;
    

-    // Method for creation through the object factory
+    //----------------------------------------

     itkNewMacro(Self);  
     itkNewMacro(Self);  

-
-    // Run-time type information (and related methods)

     itkTypeMacro( RegionGrowingGenericFilter, LightObject );
 
     itkTypeMacro( RegionGrowingGenericFilter, LightObject );
 

+    //--------------------------------------------------------------------
+    void SetArgsInfo(const ArgsInfoType & a);

 
 

-    //----------------------------------------
-    // Typedefs
-    //----------------------------------------
-
-
-    //----------------------------------------
-    // Set & Get
-    //----------------------------------------    
-    void SetArgsInfo(const args_info_clitkRegionGrowing & a)
-    {
-      m_ArgsInfo=a;
-      m_Verbose=m_ArgsInfo.verbose_flag;
-      m_InputFileName=m_ArgsInfo.input_arg;
-    }
-    
-    
-    //----------------------------------------  
-    // Update
-    //----------------------------------------  
-    void Update();
+    //--------------------------------------------------------------------
+    // Main function called each time the filter is updated
+    template<class ImageType>  
+    void UpdateWithInputImageType();

 
   protected:
 
   protected:

+    void Modified() {} // Need for using itkMacros
+    template<unsigned int Dim> void InitializeImageType();
+    ArgsInfoType mArgsInfo;

 
 

-    //----------------------------------------  
-    // Constructor & Destructor
-    //----------------------------------------  
-    RegionGrowingGenericFilter();
-    ~RegionGrowingGenericFilter() {};
-
-    
-    //----------------------------------------  
-    // Templated members
-    //----------------------------------------  
-    template <unsigned int Dimension>  void UpdateWithDim(std::string PixelType);
-    template <unsigned int Dimension, class PixelType>  void UpdateWithDimAndPixelType();
-
-
-    //----------------------------------------  
-    // Data members
-    //----------------------------------------
-    args_info_clitkRegionGrowing m_ArgsInfo;
-    bool m_Verbose;
-    std::string m_InputFileName;
-
-  };
-
-
+  }; // end class

 } // end namespace clitk
 
 #ifndef ITK_MANUAL_INSTANTIATION
 #include "clitkRegionGrowingGenericFilter.txx"
 #endif
 
 } // end namespace clitk
 
 #ifndef ITK_MANUAL_INSTANTIATION
 #include "clitkRegionGrowingGenericFilter.txx"
 #endif
 

-#endif // #define clitkRegionGrowingGenericFilter_h
+#endif // #define CLITKREGIONGROWINGGENERICFILTER_H

diff --git a/segmentation/clitkRegionGrowingGenericFilter.txx b/segmentation/clitkRegionGrowingGenericFilter.txx
index eead0d5174341a4acf08a3a05a93cff55b6ae387..e8f365317661d7a7e5d83ab28d98440561607ca9 100644 (file)
--- a/segmentation/clitkRegionGrowingGenericFilter.txx
+++ b/segmentation/clitkRegionGrowingGenericFilter.txx
@@ -14,91 +14,93 @@
 
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
 
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html

-===========================================================================**/
-#ifndef clitkRegionGrowingGenericFilter_txx
-#define clitkRegionGrowingGenericFilter_txx
-#include <itkBinaryBallStructuringElement.h>
-#include <itkConstShapedNeighborhoodIterator.h>
+  ===========================================================================**/

 
 

-namespace clitk
-{
+#ifndef CLITKREGIONGROWINGGENERICFILTER_TXX
+#define CLITKREGIONGROWINGGENERICFILTER_TXX

 
 

-  //-------------------------------------------------------------------
-  // Update with the number of dimensions
-  //-------------------------------------------------------------------
-  template<unsigned int Dimension>
-  void 
-  RegionGrowingGenericFilter::UpdateWithDim(std::string PixelType)
-  {
-    if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<"..."<<std::endl;
-
-    if(PixelType == "short"){  
-      if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
-      UpdateWithDimAndPixelType<Dimension, signed short>(); 
-    }
-    //    else if(PixelType == "unsigned_short"){  
-    //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
-    //       UpdateWithDimAndPixelType<Dimension, unsigned short>(); 
-    //     }
-    
-    else if (PixelType == "unsigned_char"){ 
-      if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
-      UpdateWithDimAndPixelType<Dimension, unsigned char>();
-    }
-    
-    //     else if (PixelType == "char"){ 
-    //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
-    //       UpdateWithDimAndPixelType<Dimension, signed char>();
-    //     }
-    else {
-      if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
-      UpdateWithDimAndPixelType<Dimension, float>();
-    }
-  }
+#include <itkBinaryBallStructuringElement.h>
+#include <itkConstShapedNeighborhoodIterator.h>

 
 
 
 

-  //-------------------------------------------------------------------
-  // Update with the number of dimensions and the pixeltype
-  //-------------------------------------------------------------------
-  template <unsigned int Dimension, class  PixelType> 
-  void 
-  RegionGrowingGenericFilter::UpdateWithDimAndPixelType()
-  {
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+clitk::RegionGrowingGenericFilter<ArgsInfoType>::RegionGrowingGenericFilter():
+  ImageToImageGenericFilter<Self>("RegionGrowing") 
+{
+  InitializeImageType<2>();
+  InitializeImageType<3>();
+  //InitializeImageType<4>();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<unsigned int Dim>
+void clitk::RegionGrowingGenericFilter<ArgsInfoType>::InitializeImageType() 
+{  
+  ADD_IMAGE_TYPE(Dim, uchar);
+  ADD_IMAGE_TYPE(Dim, short);
+  // ADD_IMAGE_TYPE(Dim, int);
+  ADD_IMAGE_TYPE(Dim, float);
+}
+//--------------------------------------------------------------------
+  

 
 

-    // ImageTypes
-    typedef itk::Image<PixelType, Dimension> InputImageType;
-    typedef itk::Image<PixelType, Dimension> OutputImageType;
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+void clitk::RegionGrowingGenericFilter<ArgsInfoType>::SetArgsInfo(const ArgsInfoType & a) 
+{
+  mArgsInfo=a;
+  this->SetIOVerbose(mArgsInfo.verbose_flag);
+  if (mArgsInfo.input_given)   this->AddInputFilename(mArgsInfo.input_arg);
+  if (mArgsInfo.output_given)  this->SetOutputFilename(mArgsInfo.output_arg);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<class ImageType>
+void clitk::RegionGrowingGenericFilter<ArgsInfoType>::UpdateWithInputImageType() 
+{ 
+  DD("UpdateWithInputImageType");
+  const int Dimension = ImageType::ImageDimension;
+
+  // ImageTypes
+  typedef ImageType InputImageType;
+  typedef ImageType OutputImageType;
+  typedef typename ImageType::PixelType PixelType;

     
     

-    // Read the input
-    typedef itk::ImageFileReader<InputImageType> InputReaderType;
-    typename InputReaderType::Pointer reader = InputReaderType::New();
-    reader->SetFileName( m_InputFileName);
-    reader->Update();
-    typename InputImageType::Pointer input= reader->GetOutput();
-
-    // Seed
-    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++)
-       seeds[0][i]=m_ArgsInfo.seed_arg[i];
+  // Reading input
+  typename ImageType::Pointer input = this->template GetInput<ImageType>(0);
+
+  // Seed
+  typedef typename  std::vector<typename InputImageType::IndexType> SeedsType;
+  SeedsType seeds(1);
+  if (mArgsInfo.seed_given==Dimension)
+    for (unsigned int i=0; i<Dimension;i++)
+      seeds[0][i]=mArgsInfo.seed_arg[i];

     
     

-    else if ( m_ArgsInfo.seed_given==1)
-      seeds[0].Fill(m_ArgsInfo.seed_arg[0]);
+  else if ( mArgsInfo.seed_given==1)
+    seeds[0].Fill(mArgsInfo.seed_arg[0]);

     
     

-    else seeds[0].Fill(m_ArgsInfo.seed_arg[0]);
-    if(m_Verbose)std::cout<<"Setting seed seeds to "<<seeds[0]<<"..."<<std::endl;
+  else seeds[0].Fill(mArgsInfo.seed_arg[0]);
+  if (mArgsInfo.verbose_flag) std::cout<<"Setting seed seeds to "<<seeds[0]<<"..."<<std::endl;

 
 

-    if (m_ArgsInfo.seedRadius_given)
+  if (mArgsInfo.seedRadius_given)

     {
       typedef itk::BinaryBallStructuringElement<PixelType, Dimension> BallType;
       typename BallType::RadiusType r;
 
     {
       typedef itk::BinaryBallStructuringElement<PixelType, Dimension> BallType;
       typename BallType::RadiusType r;
 

-      if (m_ArgsInfo.seedRadius_given == Dimension)
+      if (mArgsInfo.seedRadius_given == Dimension)

         for (unsigned i = 0; i < Dimension; i++)
         for (unsigned i = 0; i < Dimension; i++)

-          r[i] = m_ArgsInfo.seedRadius_arg[i];
+          r[i] = mArgsInfo.seedRadius_arg[i];

       else
       else

-        r.Fill(m_ArgsInfo.seedRadius_arg[0]);
+        r.Fill(mArgsInfo.seedRadius_arg[0]);

 
       BallType ball;
       ball.SetRadius(r);
 
       BallType ball;
       ball.SetRadius(r);


@@ -106,22 +108,22 @@ namespace clitk
 
       typedef itk::ConstShapedNeighborhoodIterator<InputImageType> IteratorType;
       IteratorType it(ball.GetRadius(),
 
       typedef itk::ConstShapedNeighborhoodIterator<InputImageType> IteratorType;
       IteratorType it(ball.GetRadius(),

-          input,
-          input->GetLargestPossibleRegion());
+                      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 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));
+          if (*nit)
+            {
+              it.ActivateOffset(it.GetOffset(idx));
+            }
+          else
+            {
+              it.DeactivateOffset(it.GetOffset(idx));
+            }

         }
         }

-        else
-        {
-          it.DeactivateOffset(it.GetOffset(idx));
-        }
-      }

 #else
       it.CreateActiveListFromNeighborhood(ball);
       it.NeedToUseBoundaryConditionOff();
 #else
       it.CreateActiveListFromNeighborhood(ball);
       it.NeedToUseBoundaryConditionOff();


@@ -129,174 +131,170 @@ namespace clitk
 
       it.SetLocation(seeds[0]);
       for (typename IteratorType::ConstIterator i = it.Begin(); !i.IsAtEnd(); ++i)
 
       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);
-      }
+        {
+          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;
-    typename ImageToImageFilterType::Pointer filter;
+  // Filter
+  typedef itk::ImageToImageFilter<InputImageType, OutputImageType> ImageToImageFilterType;
+  typename ImageToImageFilterType::Pointer filter;

 
 

-    switch (m_ArgsInfo.type_arg)
-      {
-      case 0: {
+  switch (mArgsInfo.type_arg)
+    {
+    case 0: {

                
                

-       typedef itk::ConnectedThresholdImageFilter<InputImageType, OutputImageType> ImageFilterType;
-       typename ImageFilterType::Pointer f= ImageFilterType::New();
+      typedef itk::ConnectedThresholdImageFilter<InputImageType, OutputImageType> ImageFilterType;
+      typename ImageFilterType::Pointer f= ImageFilterType::New();

        
        

-       f->SetLower(m_ArgsInfo.lower_arg);
-       f->SetUpper(m_ArgsInfo.upper_arg);
-       f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
-        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;
-
-       break;
-      }
-
-      case 1: {
+      f->SetLower(mArgsInfo.lower_arg);
+      f->SetUpper(mArgsInfo.upper_arg);
+      f->SetReplaceValue(static_cast<PixelType>(mArgsInfo.pad_arg));
+      for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
+        f->AddSeed(*it);
+      filter=f;
+      if (mArgsInfo.verbose_flag) std::cout<<"Using the connected threshold image filter..."<<std::endl;
+
+      break;
+    }
+
+    case 1: {

                
                

-       typedef itk::NeighborhoodConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
-       typename ImageFilterType::Pointer f= ImageFilterType::New();
+      typedef itk::NeighborhoodConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
+      typename ImageFilterType::Pointer f= ImageFilterType::New();

        
        

-       // Radius
-       typename  InputImageType::SizeType size;
-       if(m_ArgsInfo.radius_given==Dimension)
-         for (unsigned int i=0; i<Dimension;i++)
-           size[i]=m_ArgsInfo.radius_arg[i];
+      // Radius
+      typename  InputImageType::SizeType size;
+      if (mArgsInfo.radius_given==Dimension)
+        for (unsigned int i=0; i<Dimension;i++)
+          size[i]=mArgsInfo.radius_arg[i];

        
        

-       else if ( m_ArgsInfo.radius_given==1)
-         size.Fill(m_ArgsInfo.radius_arg[0]);
+      else if ( mArgsInfo.radius_given==1)
+        size.Fill(mArgsInfo.radius_arg[0]);

        
        

-       else size.Fill(m_ArgsInfo.radius_arg[0]);
-       if(m_Verbose)std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
-
-       f->SetLower(m_ArgsInfo.lower_arg);
-       f->SetUpper(m_ArgsInfo.upper_arg);
-       f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
-        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;
-
-       break;
-      }
-
-      case 2: {
+      else size.Fill(mArgsInfo.radius_arg[0]);
+      if (mArgsInfo.verbose_flag) std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
+
+      f->SetLower(mArgsInfo.lower_arg);
+      f->SetUpper(mArgsInfo.upper_arg);
+      f->SetReplaceValue(static_cast<PixelType>(mArgsInfo.pad_arg));
+      for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
+        f->AddSeed(*it);
+      f->SetRadius(size);
+      filter=f;
+      if (mArgsInfo.verbose_flag) std::cout<<"Using the neighborhood threshold connected image filter..."<<std::endl;
+
+      break;
+    }
+
+    case 2: {

        
        

-       typedef itk::ConfidenceConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
-       typename ImageFilterType::Pointer f= ImageFilterType::New();
+      typedef itk::ConfidenceConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
+      typename ImageFilterType::Pointer f= ImageFilterType::New();

        
        

-       // Radius
-       typename  InputImageType::SizeType size;
-       if(m_ArgsInfo.radius_given==Dimension)
-         for (unsigned int i=0; i<Dimension;i++)
-           size[i]=m_ArgsInfo.radius_arg[i];
+      // Radius
+      typename  InputImageType::SizeType size;
+      if (mArgsInfo.radius_given==Dimension)
+        for (unsigned int i=0; i<Dimension;i++)
+          size[i]=mArgsInfo.radius_arg[i];

        
        

-       else if ( m_ArgsInfo.radius_given==1)
-         size.Fill(m_ArgsInfo.radius_arg[0]);
+      else if ( mArgsInfo.radius_given==1)
+        size.Fill(mArgsInfo.radius_arg[0]);

        
        

-       else size.Fill(m_ArgsInfo.radius_arg[0]);
-       if(m_Verbose)std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
-
-       f->SetMultiplier( m_ArgsInfo.multiplier_arg );
-       f->SetNumberOfIterations( m_ArgsInfo.multiplier_arg );
-        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]);
-       filter=f;
-       if(m_Verbose)std::cout<<"Using the confidence threshold connected image filter..."<<std::endl;
+      else size.Fill(mArgsInfo.radius_arg[0]);
+      if (mArgsInfo.verbose_flag) std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
+
+      f->SetMultiplier( mArgsInfo.multiplier_arg );
+      f->SetNumberOfIterations( mArgsInfo.multiplier_arg );
+      for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
+        f->AddSeed(*it);
+      f->SetNumberOfIterations( mArgsInfo.iter_arg);
+      f->SetReplaceValue(static_cast<PixelType>(mArgsInfo.pad_arg));
+      f->SetInitialNeighborhoodRadius(size[0]);
+      filter=f;
+      if (mArgsInfo.verbose_flag) std::cout<<"Using the confidence threshold connected image filter..."<<std::endl;

        
        

-       break;
-      }
+      break;
+    }

 
 

-      case 3: {
+    case 3: {

                
                

-       typedef clitk::LocallyAdaptiveThresholdConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
-       typename ImageFilterType::Pointer f= ImageFilterType::New();
+      typedef clitk::LocallyAdaptiveThresholdConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
+      typename ImageFilterType::Pointer f= ImageFilterType::New();

        
        

-       // Radius
-       typename  InputImageType::SizeType size;
-       if(m_ArgsInfo.radius_given==Dimension)
-         for (unsigned int i=0; i<Dimension;i++)
-           size[i]=m_ArgsInfo.radius_arg[i];
-       else size.Fill(m_ArgsInfo.radius_arg[0]);
-       if(m_Verbose)std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
-
-       // params
-       f->SetLower(m_ArgsInfo.lower_arg);
-       f->SetUpper(m_ArgsInfo.upper_arg);
-       f->SetLowerBorderIsGiven(m_ArgsInfo.adaptLower_flag);
-       f->SetLowerBorderIsGiven(m_ArgsInfo.adaptUpper_flag);
-       f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
-       f->SetMultiplier(m_ArgsInfo.multiplier_arg);
-       f->SetMaximumSDIsGiven(m_ArgsInfo.maxSD_given);
-       if (m_ArgsInfo.maxSD_given) f->SetMaximumSD(m_ArgsInfo.maxSD_arg);
-        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;
-
-       break;
-      }
+      // Radius
+      typename  InputImageType::SizeType size;
+      if (mArgsInfo.radius_given==Dimension)
+        for (unsigned int i=0; i<Dimension;i++)
+          size[i]=mArgsInfo.radius_arg[i];
+      else size.Fill(mArgsInfo.radius_arg[0]);
+      if (mArgsInfo.verbose_flag) std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
+
+      // params
+      f->SetLower(mArgsInfo.lower_arg);
+      f->SetUpper(mArgsInfo.upper_arg);
+      f->SetLowerBorderIsGiven(mArgsInfo.adaptLower_flag);
+      f->SetLowerBorderIsGiven(mArgsInfo.adaptUpper_flag);
+      f->SetReplaceValue(static_cast<PixelType>(mArgsInfo.pad_arg));
+      f->SetMultiplier(mArgsInfo.multiplier_arg);
+      f->SetMaximumSDIsGiven(mArgsInfo.maxSD_given);
+      if (mArgsInfo.maxSD_given) f->SetMaximumSD(mArgsInfo.maxSD_arg);
+      for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
+        f->AddSeed(*it);
+      f->SetRadius(size);
+      filter=f;
+      if (mArgsInfo.verbose_flag) std::cout<<"Using the locally adaptive threshold connected image filter..."<<std::endl;
+
+      break;
+    }

   
   

-      case 4: {
+    case 4: {

                
                

-       typedef clitk::ExplosionControlledThresholdConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
-       typename ImageFilterType::Pointer f= ImageFilterType::New();
+      typedef clitk::ExplosionControlledThresholdConnectedImageFilter<InputImageType, OutputImageType> ImageFilterType;
+      typename ImageFilterType::Pointer f= ImageFilterType::New();

        
        

-       //      // Radius
-       //      typename  InputImageType::SizeType size;
-       //      if(m_ArgsInfo.radius_given==Dimension)
-       //        for (unsigned int i=0; i<Dimension;i++)
-       //          size[i]=m_ArgsInfo.radius_arg[i];
-       //      else size.Fill(m_ArgsInfo.radius_arg[0]);
-       //      if(m_Verbose)std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;
+      //       // Radius
+      //       typename  InputImageType::SizeType size;
+      //       if (mArgsInfo.radius_given==Dimension)
+      //         for (unsigned int i=0; i<Dimension;i++)
+      //           size[i]=mArgsInfo.radius_arg[i];
+      //       else size.Fill(mArgsInfo.radius_arg[0]);
+      //       if (mArgsInfo.verbose_flag) std::cout<<"Setting neighborhood radius to "<<size<<"..."<<std::endl;

        
        

-       // params
-       f->SetVerbose(m_ArgsInfo.verbose_flag);
-       f->SetLower(m_ArgsInfo.lower_arg);
-       f->SetUpper(m_ArgsInfo.upper_arg);
-       f->SetMinimumLowerThreshold(m_ArgsInfo.minLower_arg);
-       f->SetMaximumUpperThreshold(m_ArgsInfo.maxUpper_arg);
-       f->SetAdaptLowerBorder(m_ArgsInfo.adaptLower_flag);
-       f->SetAdaptUpperBorder(m_ArgsInfo.adaptUpper_flag);
-       f->SetReplaceValue(static_cast<PixelType>(m_ArgsInfo.pad_arg));
-       f->SetMultiplier(m_ArgsInfo.multiplier_arg);
-       f->SetThresholdStepSize(m_ArgsInfo.step_arg);
-       f->SetMinimumThresholdStepSize(m_ArgsInfo.minStep_arg);
-       f->SetFullyConnected(m_ArgsInfo.full_flag);
-        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;
-
-       break;
-      }
+      // params
+      f->SetVerbose(mArgsInfo.verbose_flag);
+      f->SetLower(mArgsInfo.lower_arg);
+      f->SetUpper(mArgsInfo.upper_arg);
+      f->SetMinimumLowerThreshold(mArgsInfo.minLower_arg);
+      f->SetMaximumUpperThreshold(mArgsInfo.maxUpper_arg);
+      f->SetAdaptLowerBorder(mArgsInfo.adaptLower_flag);
+      f->SetAdaptUpperBorder(mArgsInfo.adaptUpper_flag);
+      f->SetReplaceValue(static_cast<PixelType>(mArgsInfo.pad_arg));
+      f->SetMultiplier(mArgsInfo.multiplier_arg);
+      f->SetThresholdStepSize(mArgsInfo.step_arg);
+      f->SetMinimumThresholdStepSize(mArgsInfo.minStep_arg);
+      f->SetFullyConnected(mArgsInfo.full_flag);
+      for (typename SeedsType::const_iterator it = seeds.begin(); it != seeds.end(); ++it)
+        f->AddSeed(*it);
+      filter=f;
+      if (mArgsInfo.verbose_flag) std::cout<<"Using the explosion controlled threshold connected image filter..."<<std::endl;
+
+      break;
+    }

   
     }
 
 
   
     }
 
 

-    filter->SetInput(input);
-    filter->Update();
-    typename OutputImageType::Pointer output=filter->GetOutput();
+  filter->SetInput(input);
+  filter->Update();
+  typename OutputImageType::Pointer output=filter->GetOutput();

 
 

-    // Output
-    typedef itk::ImageFileWriter<OutputImageType> WriterType;
-    typename WriterType::Pointer writer = WriterType::New();
-    writer->SetFileName(m_ArgsInfo.output_arg);
-    writer->SetInput(output);
-    writer->Update();
-  }
+  // Write/Save results
+  this->template SetNextOutput<OutputImageType>(output); 
+}
+//--------------------------------------------------------------------

 
 

-}//end clitk

  
  

-#endif //#define clitkRegionGrowingGenericFilter_txx
+#endif //#define CLITKREGIONGROWINGGENERICFILTER_TXX