files merged in SegmentationUtils

diff --git a/itk/clitkSegmentationFunctions.h b/itk/clitkSegmentationFunctions.h
deleted file mode 100644 (file)
index e39c3e5..0000000
--- a/itk/clitkSegmentationFunctions.h
+++ /dev/null
@@ -1,111 +0,0 @@
-/*=========================================================================
-  Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
-
-  Authors belong to: 
-  - University of LYON              http://www.universite-lyon.fr/
-  - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
-  - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
-
-  This software is distributed WITHOUT ANY WARRANTY; without even
-  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-  PURPOSE.  See the copyright notices for more information.
-
-  It is distributed under dual licence
-
-  - BSD        See included LICENSE.txt file
-  - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-  ======================================================================-====*/
-
-#ifndef CLITKSEGMENTATIONFUNCTIONS_H
-#define CLITKSEGMENTATIONFUNCTIONS_H
-
-#include "clitkAutoCropFilter.h"
-
-//--------------------------------------------------------------------
-namespace clitk {
-
-  //--------------------------------------------------------------------
-  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);
-}
-//--------------------------------------------------------------------
-
-#include "clitkSegmentationFunctions.txx"
-//--------------------------------------------------------------------
-                      
-#endif

diff --git a/itk/clitkSegmentationFunctions.txx b/itk/clitkSegmentationFunctions.txx
deleted file mode 100644 (file)
index 6da6b7b..0000000
--- a/itk/clitkSegmentationFunctions.txx
+++ /dev/null
@@ -1,139 +0,0 @@
-/*=========================================================================
-  Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
-
-  Authors belong to: 
-  - University of LYON              http://www.universite-lyon.fr/
-  - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
-  - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
-
-  This software is distributed WITHOUT ANY WARRANTY; without even
-  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-  PURPOSE.  See the copyright notices for more information.
-
-  It is distributed under dual licence
-
-  - 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>
-
-//--------------------------------------------------------------------
-template<class TImageType, class TMaskImageType>
-typename TImageType::Pointer
-clitk::SetBackground(typename TImageType::ConstPointer input, 
-                     typename TMaskImageType::ConstPointer mask, 
-                     typename TMaskImageType::PixelType maskBG,
-                     typename TImageType::PixelType outValue) {
-  typedef clitk::SetBackgroundImageFilter<TImageType, TMaskImageType, TImageType> 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 TImageType>
-typename TImageType::Pointer
-clitk::Labelize(typename TImageType::Pointer input, 
-                typename TImageType::PixelType BG, 
-                bool isFullyConnected, 
-                int minimalComponentSize) {
-
-  // Connected Component label 
-  typedef itk::ConnectedComponentImageFilter<TImageType, TImageType> 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<TImageType, TImageType> 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 TImageType>
-typename TImageType::Pointer
-clitk::RemoveLabels(typename TImageType::Pointer input, 
-                    typename TImageType::PixelType BG,
-                    std::vector<typename TImageType::PixelType> & labelsToRemove) {
-  typename TImageType::Pointer working_image = input;
-  for (unsigned int i=0; i <labelsToRemove.size(); i++) {
-    typedef clitk::SetBackgroundImageFilter<TImageType, TImageType> 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 TImageType>
-typename TImageType::Pointer
-clitk::KeepLabels(typename TImageType::Pointer input, 
-                  typename TImageType::PixelType BG, 
-                  typename TImageType::PixelType FG, 
-                  typename TImageType::PixelType firstKeep, 
-                  typename TImageType::PixelType lastKeep, 
-                  bool useLastKeep) {
-  typedef itk::BinaryThresholdImageFilter<TImageType, TImageType> 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 TImageType>
-typename TImageType::Pointer
-clitk::LabelizeAndSelectLabels(typename TImageType::Pointer input,
-                               typename TImageType::PixelType BG, 
-                               typename TImageType::PixelType FG, 
-                               bool isFullyConnected,
-                               int minimalComponentSize,
-                               LabelizeParameters<typename TImageType::PixelType> * param)
-{
-  typename TImageType::Pointer working_image;
-  working_image = Labelize<TImageType>(input, BG, isFullyConnected, minimalComponentSize);
-  working_image = RemoveLabels<TImageType>(working_image, BG, param->GetLabelsToRemove());
-  working_image = KeepLabels<TImageType>(working_image, 
-                                         BG, FG, 
-                                         param->GetFirstKeep(), 
-                                         param->GetLastKeep(), 
-                                         param->GetUseLastKeep());
-  return working_image;
-}
-//--------------------------------------------------------------------