[clitk-commits-list] Clitk branch master updated. v1.2.0-670-g5a7da4a

root root at tux.creatis.insa-lyon.fr
Thu Feb 2 17:07:14 CET 2012


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http://git.creatis.insa-lyon.fr/pubgit/?p=clitk.git;a=commitdiff;h=5a7da4aedae5c204bc55c187717193e5950f9a44

commit 5a7da4aedae5c204bc55c187717193e5950f9a44
Author: David Sarrut <david.sarrut at gmail.com>
Date:   Thu Feb 2 17:06:04 2012 +0100

    remove tools (now in tests_dav)

diff --git a/segmentation/CMakeLists.txt b/segmentation/CMakeLists.txt
index 353dcf3..f6c4096 100644
--- a/segmentation/CMakeLists.txt
+++ b/segmentation/CMakeLists.txt
@@ -26,53 +26,24 @@ IF(CLITK_BUILD_SEGMENTATION)
     TARGET_LINK_LIBRARIES(clitkExtractLung clitkSegmentationGgoLib clitkCommon ${ITK_LIBRARIES})
     SET(SEGMENTATION_INSTALL ${SEGMENTATION_INSTALL} clitkExtractLung)
 
-    # WRAP_GGO(clitkExtractAirwaysTreeInfo_GGO_C clitkExtractAirwaysTreeInfo.ggo)
-    # ADD_EXECUTABLE(clitkExtractAirwaysTreeInfo clitkExtractAirwaysTreeInfo.cxx ${clitkExtractAirwaysTreeInfo_GGO_C})
-    # TARGET_LINK_LIBRARIES(clitkExtractAirwaysTreeInfo clitkSegmentationGgoLib clitkCommon ${ITK_LIBRARIES})
-    # SET(SEGMENTATION_INSTALL ${SEGMENTATION_INSTALL} clitkExtractAirwaysTreeInfo)
-
     WRAP_GGO(clitkExtractBones_GGO_C clitkExtractBones.ggo)
     ADD_EXECUTABLE(clitkExtractBones clitkExtractBones.cxx ${clitkExtractBones_GGO_C})
     TARGET_LINK_LIBRARIES(clitkExtractBones clitkCommon ${ITK_LIBRARIES} clitkSegmentationGgoLib)
     SET(SEGMENTATION_INSTALL ${SEGMENTATION_INSTALL} clitkExtractBones)
 
-    WRAP_GGO(clitkBool_GGO_C clitkBool.ggo)
-    ADD_EXECUTABLE(clitkBool clitkBool.cxx ${clitkBool_GGO_C})
-    TARGET_LINK_LIBRARIES(clitkBool clitkCommon ${ITK_LIBRARIES} clitkSegmentationGgoLib)
-    SET(SEGMENTATION_INSTALL ${SEGMENTATION_INSTALL} clitkBool)
-
+ 
     WRAP_GGO(clitkRelativePosition_GGO_C ../tools/clitkRelativePosition.ggo)
 
-    WRAP_GGO(clitkExtractMediastinum_GGO_C clitkExtractMediastinum.ggo)
-    ADD_EXECUTABLE(clitkExtractMediastinum clitkExtractMediastinum.cxx ${clitkExtractMediastinum_GGO_C}  ${clitkRelativePosition_GGO_C})
-    TARGET_LINK_LIBRARIES(clitkExtractMediastinum clitkCommon clitkSegmentationGgoLib ${ITK_LIBRARIES})
-    SET(SEGMENTATION_INSTALL ${SEGMENTATION_INSTALL} clitkExtractMediastinum)
-
     WRAP_GGO(clitkExtractLymphStations_GGO_C clitkExtractLymphStations.ggo)
     ADD_EXECUTABLE(clitkExtractLymphStations clitkExtractLymphStations.cxx clitkFilterWithAnatomicalFeatureDatabaseManagement.cxx ${clitkExtractLymphStations_GGO_C} ${clitkRelativePosition_GGO_C})
     TARGET_LINK_LIBRARIES(clitkExtractLymphStations clitkSegmentationGgoLib clitkCommon vtkHybrid)
     SET(SEGMENTATION_INSTALL ${SEGMENTATION_INSTALL} clitkExtractLymphStations)
 
-    WRAP_GGO(clitkExtractMediastinalVessels_GGO_C clitkExtractMediastinalVessels.ggo)
-    ADD_EXECUTABLE(clitkExtractMediastinalVessels clitkExtractMediastinalVessels.cxx clitkFilterWithAnatomicalFeatureDatabaseManagement.cxx ${clitkExtractMediastinalVessels_GGO_C})
-    TARGET_LINK_LIBRARIES(clitkExtractMediastinalVessels clitkSegmentationGgoLib clitkCommon vtkHybrid)
-    SET(SEGMENTATION_INSTALL ${SEGMENTATION_INSTALL} clitkExtractMediastinalVessels)
-
-    WRAP_GGO(clitkMorphoMath_GGO_C clitkMorphoMath.ggo)
+     WRAP_GGO(clitkMorphoMath_GGO_C clitkMorphoMath.ggo)
     ADD_EXECUTABLE(clitkMorphoMath clitkMorphoMath.cxx ${clitkMorphoMath_GGO_C})
     TARGET_LINK_LIBRARIES(clitkMorphoMath clitkCommon ${ITK_LIBRARIES})
     SET(SEGMENTATION_INSTALL ${SEGMENTATION_INSTALL} clitkMorphoMath)
 
-    WRAP_GGO(clitkAnd_GGO_C clitkAnd.ggo)
-    ADD_EXECUTABLE(clitkAnd clitkAnd.cxx clitkAndGenericFilter.cxx ${clitkAnd_GGO_C})
-    TARGET_LINK_LIBRARIES(clitkAnd clitkCommon ${ITK_LIBRARIES} )
-    SET(SEGMENTATION_INSTALL ${SEGMENTATION_INSTALL} clitkAnd)
-
-    WRAP_GGO(clitkRegionGrowing_GGO_C clitkRegionGrowing.ggo)
-    ADD_EXECUTABLE(clitkRegionGrowing clitkRegionGrowing.cxx clitkRegionGrowingGenericFilter.cxx ${clitkRegionGrowing_GGO_C})
-    TARGET_LINK_LIBRARIES(clitkRegionGrowing clitkCommon ${ITK_LIBRARIES})
-    SET(SEGMENTATION_INSTALL ${SEGMENTATION_INSTALL} clitkRegionGrowing)
-
     WRAP_GGO(clitkDecomposeAndReconstruct_GGO_C clitkDecomposeAndReconstruct.ggo)
     ADD_EXECUTABLE(clitkDecomposeAndReconstruct clitkDecomposeAndReconstruct.cxx clitkDecomposeAndReconstructGenericFilter.cxx ${clitkDecomposeAndReconstruct_GGO_C})
     TARGET_LINK_LIBRARIES(clitkDecomposeAndReconstruct clitkCommon ${ITK_LIBRARIES})

http://git.creatis.insa-lyon.fr/pubgit/?p=clitk.git;a=commitdiff;h=2b4ec898fdd6dc8ea5780c0e30c7124272a4202e

commit 2b4ec898fdd6dc8ea5780c0e30c7124272a4202e
Author: David Sarrut <david.sarrut at gmail.com>
Date:   Thu Feb 2 17:03:43 2012 +0100

    Moved from repository clitk to clitk.private/tests_dav

diff --git a/segmentation/clitkExtractMediastinum.cxx b/segmentation/clitkExtractMediastinum.cxx
deleted file mode 100644
index b79ae46..0000000
--- a/segmentation/clitkExtractMediastinum.cxx
+++ /dev/null
@@ -1,45 +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://www.centreleonberard.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 "clitkExtractMediastinum_ggo.h"
-#include "clitkExtractMediastinumGenericFilter.h"
-
-//--------------------------------------------------------------------
-int main(int argc, char * argv[])
-{
-
-  // Init command line
-  GGO(clitkExtractMediastinum, args_info);
-  CLITK_INIT;
-
-  // Filter
-  typedef clitk::ExtractMediastinumGenericFilter<args_info_clitkExtractMediastinum> FilterType;
-  FilterType::Pointer filter = FilterType::New();
-
-  filter->SetArgsInfo(args_info);
-
-  try {
-    filter->Update();
-  } catch(std::runtime_error e) {
-    std::cout << e.what() << std::endl;
-  }
-
-  return EXIT_SUCCESS;
-} // This is the end, my friend
-//--------------------------------------------------------------------
diff --git a/segmentation/clitkExtractMediastinum.ggo b/segmentation/clitkExtractMediastinum.ggo
deleted file mode 100644
index bd2bbe4..0000000
--- a/segmentation/clitkExtractMediastinum.ggo
+++ /dev/null
@@ -1,24 +0,0 @@
-#File clitkExtractMediastinum.ggo
-package "clitkExtractMediastinum"
-version "1.0"
-purpose "Extract mediastinum with help of patient/lungs/bones mask"
-
-option "config"	        -  "Config file"		  string  	no
-option "imagetypes"     -  "Display allowed image types"  flag          off
-option "verbose"        v  "Verbose"			  flag		off
-option "verboseStep"    -  "Verbose each step"		  flag		off
-option "writeStep"      w  "Write image at each step"	  flag		off
-option "verboseOption"  -  "Display options values"       flag          off
-option "verboseWarningOff" -  "Do not display warning"    flag          off
-option "verboseMemory"  -  "Display memory usage"         flag          off
-
-section "I/O"
-
-option "input"     i	"Input CT filename"               string  	yes
-option "output"    o 	"Output lungs mask filename"      string 	yes
-option "afdb"      a	"Input Anatomical Feature DB (needs Patient, Lungs, Trachea, VertebralBody)"     string  	no
-option "relpos" - "List of filenames for relativeposition operations" string no multiple
-
-option "useBones"  -    "If set : do use bones mask (when image is not injected)"  flag	off
-option "maxAntSpine"  - "Distance max to anterior part of the VertebralBody (spine) in mm"  double no default="10"
-
diff --git a/segmentation/clitkExtractMediastinumFilter.h b/segmentation/clitkExtractMediastinumFilter.h
deleted file mode 100644
index 3144c95..0000000
--- a/segmentation/clitkExtractMediastinumFilter.h
+++ /dev/null
@@ -1,173 +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://www.centreleonberard.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 CLITKEXTRACTMEDIASTINUMFILTER_H
-#define CLITKEXTRACTMEDIASTINUMFILTER_H
-
-#include "clitkStructuresExtractionFilter.h"
-
-namespace clitk {
-  
-  //--------------------------------------------------------------------
-  /*
-    Try to extract the mediastinum part of a thorax CT.
-    Input masks needed : 
-    - Patient
-    - Lungs 
-    - Bones [Optional]
-    - Trachea
-    - VertebralBody 
-  */
-  //--------------------------------------------------------------------
-  
-  template <class TImageType>
-  class ITK_EXPORT ExtractMediastinumFilter: 
-    public clitk::StructuresExtractionFilter<TImageType>
-  {
-
-  public:
-    /** Some convenient typedefs. */
-    typedef TImageType                       ImageType;
-    typedef typename ImageType::ConstPointer ImageConstPointer;
-    typedef typename ImageType::Pointer      ImagePointer;
-    typedef typename ImageType::RegionType   ImageRegionType; 
-    typedef typename ImageType::PixelType    ImagePixelType; 
-    typedef typename ImageType::SizeType     ImageSizeType; 
-    typedef typename ImageType::IndexType    ImageIndexType; 
-    typedef typename ImageType::PointType    ImagePointType; 
-        
-    /** Some convenient typedefs. */
-    typedef uchar MaskImagePixelType; 
-    typedef itk::Image<MaskImagePixelType, 3>    MaskImageType;
-    typedef typename MaskImageType::ConstPointer MaskImageConstPointer;
-    typedef typename MaskImageType::Pointer      MaskImagePointer;
-    typedef typename MaskImageType::RegionType   MaskImageRegionType; 
-    typedef typename MaskImageType::SizeType     MaskImageSizeType; 
-    typedef typename MaskImageType::IndexType    MaskImageIndexType; 
-    typedef typename MaskImageType::PointType    MaskImagePointType; 
-        
-    typedef itk::Image<MaskImagePixelType, 2>    MaskSliceType;
-    typedef typename MaskSliceType::Pointer      MaskSlicePointer;
-    typedef typename MaskSliceType::PointType    MaskSlicePointType;
-
-    /** Standard class typedefs. */
-    //    typedef itk::ImageToImageFilter<TImageType, MaskImageType> Superclass;
-    typedef clitk::StructuresExtractionFilter<TImageType> Superclass;
-    typedef ExtractMediastinumFilter            Self;
-    typedef itk::SmartPointer<Self>             Pointer;
-    typedef itk::SmartPointer<const Self>       ConstPointer;
-    
-    /** Method for creation through the object factory. */
-    itkNewMacro(Self);
-    
-    /** Run-time type information (and related methods). */
-    itkTypeMacro(ExtractMediastinumFilter, InPlaceImageFilter);
-    FILTERBASE_INIT;
-
-    /** Connect inputs */
-    void SetInput(const ImageType * image);
-    void SetInputPatientLabelImage(const MaskImageType * image, MaskImagePixelType bg=0);
-    void SetInputLungLabelImage(const MaskImageType * image, MaskImagePixelType bg=0, 
-                                MaskImagePixelType fgLeftLung=1, MaskImagePixelType fgRightLung=2);
-    void SetInputBonesLabelImage(const MaskImageType * image, MaskImagePixelType bg=0);
-    void SetInputTracheaLabelImage(const MaskImageType * image, MaskImagePixelType bg=0);
-
-    // Output filename  (for AFBD)
-    itkSetMacro(OutputMediastinumFilename, std::string);
-    itkGetConstMacro(OutputMediastinumFilename, std::string);
-
-    /** ImageDimension constants */
-    itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
-
-    // Background / Foreground
-    itkSetMacro(BackgroundValuePatient, MaskImagePixelType);
-    itkGetConstMacro(BackgroundValuePatient, MaskImagePixelType);
-    
-    itkSetMacro(BackgroundValueLung, MaskImagePixelType);
-    itkGetConstMacro(BackgroundValueLung, MaskImagePixelType);
-    
-    itkSetMacro(BackgroundValueBones, MaskImagePixelType);
-    itkGetConstMacro(BackgroundValueBones, MaskImagePixelType);
-    
-    itkSetMacro(ForegroundValueLeftLung, MaskImagePixelType);
-    itkGetConstMacro(ForegroundValueLeftLung, MaskImagePixelType);
-    
-    itkSetMacro(ForegroundValueRightLung, MaskImagePixelType);
-    itkGetConstMacro(ForegroundValueRightLung, MaskImagePixelType);
-    
-    itkSetMacro(BackgroundValueTrachea, MaskImagePixelType);
-    itkGetConstMacro(BackgroundValueTrachea, MaskImagePixelType);
-    
-    itkSetMacro(IntermediateSpacing, double);
-    itkGetConstMacro(IntermediateSpacing, double);
-
-    itkBooleanMacro(UseBones);
-    itkSetMacro(UseBones, bool);
-    itkGetConstMacro(UseBones, bool);
-
-    itkSetMacro(DistanceMaxToAnteriorPartOfTheVertebralBody, double);
-    itkGetConstMacro(DistanceMaxToAnteriorPartOfTheVertebralBody, double);
-
-    void SetFuzzyThreshold(std::string tag, double value);
-    double GetFuzzyThreshold(std::string tag);
-
-  protected:
-    ExtractMediastinumFilter();
-    virtual ~ExtractMediastinumFilter() {}
-    
-    virtual void GenerateOutputInformation();
-    virtual void GenerateInputRequestedRegion();
-    virtual void GenerateData();
-         
-    MaskImagePixelType m_BackgroundValuePatient;
-    MaskImagePixelType m_BackgroundValueLung;
-    MaskImagePixelType m_BackgroundValueBones;
-    MaskImagePixelType m_BackgroundValueTrachea;
-    MaskImagePixelType m_ForegroundValueLeftLung;
-    MaskImagePixelType m_ForegroundValueRightLung;
-
-    MaskImagePointer output;
-    MaskImagePointer patient;
-    MaskImagePointer lung;
-    MaskImagePointer bones;
-    MaskImagePointer trachea;
-
-    std::map<std::string, double> m_FuzzyThreshold;
-    double m_IntermediateSpacing;
-    bool   m_UseBones;
-    double m_DistanceMaxToAnteriorPartOfTheVertebralBody;
-
-    void RemovePostPartOfVertebralBody();
-    
-    std::string m_OutputMediastinumFilename;
-    
-  private:
-    ExtractMediastinumFilter(const Self&); //purposely not implemented
-    void operator=(const Self&); //purposely not implemented
-    
-  }; // end class
-  //--------------------------------------------------------------------
-
-} // end namespace clitk
-//--------------------------------------------------------------------
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "clitkExtractMediastinumFilter.txx"
-#endif
-
-#endif
diff --git a/segmentation/clitkExtractMediastinumFilter.txx b/segmentation/clitkExtractMediastinumFilter.txx
deleted file mode 100644
index 6757180..0000000
--- a/segmentation/clitkExtractMediastinumFilter.txx
+++ /dev/null
@@ -1,533 +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://www.centreleonberard.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 CLITKEXTRACTMEDIASTINUMFILTER_TXX
-#define CLITKEXTRACTMEDIASTINUMFILTER_TXX
-
-// clitk
-#include "clitkCommon.h"
-#include "clitkExtractMediastinumFilter.h"
-#include "clitkAddRelativePositionConstraintToLabelImageFilter.h"
-#include "clitkSliceBySliceRelativePositionFilter.h"
-#include "clitkSegmentationUtils.h"
-#include "clitkExtractAirwaysTreeInfoFilter.h"
-#include "clitkCropLikeImageFilter.h"
-
-// std
-#include <deque>
-
-// itk
-#include "itkStatisticsLabelMapFilter.h"
-#include "itkLabelImageToStatisticsLabelMapFilter.h"
-#include "itkRegionOfInterestImageFilter.h"
-#include "itkBinaryThresholdImageFilter.h"
-#include "itkScalarImageKmeansImageFilter.h"
-
-// itk ENST
-#include "RelativePositionPropImageFilter.h"
-
-//--------------------------------------------------------------------
-template <class ImageType>
-clitk::ExtractMediastinumFilter<ImageType>::
-ExtractMediastinumFilter():
-  clitk::StructuresExtractionFilter<ImageType>()
-{
-  this->SetNumberOfRequiredInputs(1);
-  SetBackgroundValuePatient(0);
-  SetBackgroundValueLung(0);
-  SetBackgroundValueBones(0);
-  SetForegroundValueLeftLung(1);
-  SetForegroundValueRightLung(2);
-  SetDistanceMaxToAnteriorPartOfTheVertebralBody(10);  
-  SetOutputMediastinumFilename("mediastinum.mha");  
-  UseBonesOff();
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class ImageType>
-void 
-clitk::ExtractMediastinumFilter<ImageType>::
-SetInputPatientLabelImage(const MaskImageType * image, MaskImagePixelType bg) 
-{
-  this->SetNthInput(0, const_cast<MaskImageType *>(image));
-  m_BackgroundValuePatient = bg;
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class ImageType>
-void 
-clitk::ExtractMediastinumFilter<ImageType>::
-SetInputLungLabelImage(const MaskImageType * image, MaskImagePixelType bg, 
-                       MaskImagePixelType fgLeft, MaskImagePixelType fgRight) 
-{
-  this->SetNthInput(1, const_cast<MaskImageType *>(image));
-  m_BackgroundValueLung = bg;
-  m_ForegroundValueLeftLung = fgLeft;
-  m_ForegroundValueRightLung = fgRight;
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class ImageType>
-void 
-clitk::ExtractMediastinumFilter<ImageType>::
-SetInputBonesLabelImage(const MaskImageType * image, MaskImagePixelType bg) 
-{
-  this->SetNthInput(2, const_cast<MaskImageType *>(image));
-  m_BackgroundValueBones = bg;
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class ImageType>
-void 
-clitk::ExtractMediastinumFilter<ImageType>::
-SetInputTracheaLabelImage(const MaskImageType * image, MaskImagePixelType bg) 
-{
-  this->SetNthInput(3, const_cast<MaskImageType *>(image));
-  m_BackgroundValueTrachea = bg;
-}
-//--------------------------------------------------------------------
-
-//--------------------------------------------------------------------
-template <class ImageType>
-void 
-clitk::ExtractMediastinumFilter<ImageType>::
-SetFuzzyThreshold(std::string tag, double value)
-{
-  m_FuzzyThreshold[tag] = value;
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class ImageType>
-double 
-clitk::ExtractMediastinumFilter<ImageType>::
-GetFuzzyThreshold(std::string tag)
-{
-  if (m_FuzzyThreshold.find(tag) == m_FuzzyThreshold.end()) {
-    clitkExceptionMacro("Could not find options "+tag+" in the list of FuzzyThresholds.");
-    return 0.0;
-  }
-  
-  return m_FuzzyThreshold[tag]; 
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class ImageType>
-void 
-clitk::ExtractMediastinumFilter<ImageType>::
-GenerateInputRequestedRegion() 
-{
-  // DD("GenerateInputRequestedRegion");
-  // Do not call default
-  // Superclass::GenerateInputRequestedRegion();  
-  // DD("End GenerateInputRequestedRegion");
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class ImageType>
-void 
-clitk::ExtractMediastinumFilter<ImageType>::
-SetInput(const ImageType * image) 
-{
-  this->SetNthInput(0, const_cast<ImageType *>(image));
-}
-//--------------------------------------------------------------------
-
-
-
-//--------------------------------------------------------------------
-template <class ImageType>
-void 
-clitk::ExtractMediastinumFilter<ImageType>::
-GenerateOutputInformation() { 
-  // Do not call default
-  // Superclass::GenerateOutputInformation();
-
-  //--------------------------------------------------------------------
-  // Get input pointers
-  this->LoadAFDB();
-  ImageConstPointer input = dynamic_cast<const ImageType*>(itk::ProcessObject::GetInput(0));
-  MaskImagePointer patient, lung, bones, trachea;
-  patient = this->GetAFDB()->template GetImage <MaskImageType>("Patient");
-  lung = this->GetAFDB()->template GetImage <MaskImageType>("Lungs");
-  if (GetUseBones()) {
-    bones = this->GetAFDB()->template GetImage <MaskImageType>("Bones");  
-  }
-  trachea = this->GetAFDB()->template GetImage <MaskImageType>("Trachea");  
-
-  //this->VerboseImageSizeFlagOn();
-
-  //--------------------------------------------------------------------
-  // Step : Crop support (patient) to lung extend in RL
-  this->StartNewStep("[Mediastinum] Crop support like lungs along LR");
-  typedef clitk::CropLikeImageFilter<MaskImageType> CropFilterType;
-  typename CropFilterType::Pointer cropFilter = CropFilterType::New();
-  cropFilter->SetInput(patient);
-  cropFilter->SetCropLikeImage(lung, 0);// Indicate that we only crop in X (Left-Right) axe
-  cropFilter->Update();
-  output = cropFilter->GetOutput();
-  this->template StopCurrentStep<MaskImageType>(output);
-
-  //--------------------------------------------------------------------
-  // Step : Crop support (previous) to bones extend in AP
-  if (GetUseBones()) {
-    this->StartNewStep("[Mediastinum] Crop support like bones along AP");
-    cropFilter = CropFilterType::New();
-    cropFilter->SetInput(output);
-    cropFilter->SetCropLikeImage(bones, 1);// Indicate that we only crop in Y (Ant-Post) axe
-    cropFilter->Update();
-    output = cropFilter->GetOutput();
-    this->template StopCurrentStep<MaskImageType>(output);
-  }
-
-  //--------------------------------------------------------------------
-  // Step : patient minus lungs, minus bones, minus trachea
-  this->StartNewStep("[Mediastinum] Patient contours minus lungs, trachea [and bones]");
-  typedef clitk::BooleanOperatorLabelImageFilter<MaskImageType> BoolFilterType;
-  typename BoolFilterType::Pointer boolFilter = BoolFilterType::New(); 
-  boolFilter->InPlaceOn();
-  boolFilter->SetInput1(output);
-  boolFilter->SetInput2(lung);    
-  boolFilter->SetOperationType(BoolFilterType::AndNot);
-  boolFilter->Update();    
-  if (GetUseBones()) {
-    boolFilter->SetInput1(boolFilter->GetOutput());
-    boolFilter->SetInput2(bones);
-    boolFilter->SetOperationType(BoolFilterType::AndNot);
-    boolFilter->Update(); 
-  }
-  boolFilter->SetInput1(boolFilter->GetOutput());
-  boolFilter->SetInput2(trachea);
-  boolFilter->SetOperationType(BoolFilterType::AndNot);
-  boolFilter->Update(); 
-  output = boolFilter->GetOutput();
-
-  // Auto crop to gain support area
-  output = clitk::AutoCrop<MaskImageType>(output, this->GetBackgroundValue()); 
-  this->template StopCurrentStep<MaskImageType>(output);
-
-  //--------------------------------------------------------------------
-  // Step : LR limits from lung (need separate lung ?)
-  // Get separate lung images to get only the right and left lung
-  // (because RelativePositionPropImageFilter only consider fg=1);
-  // (label must be '1' because right is greater than left).  (WE DO
-  // NOT NEED TO SEPARATE ? )
-  this->StartNewStep("[Mediastinum] Left/Right limits with lungs");
-  
-  // The following cannot be "inplace" because mask is the same than input ...
-  MaskImagePointer right_lung = 
-    clitk::SetBackground<MaskImageType, MaskImageType>(lung, lung, 2, 0, false);
-  MaskImagePointer left_lung = 
-    clitk::SetBackground<MaskImageType, MaskImageType>(lung, lung, 1, 0, false);
-  left_lung = clitk::SetBackground<MaskImageType, MaskImageType>(left_lung, left_lung, 2, 1, false);
-  right_lung = clitk::ResizeImageLike<MaskImageType>(right_lung, output, this->GetBackgroundValue());
-  left_lung = clitk::ResizeImageLike<MaskImageType>(left_lung, output, this->GetBackgroundValue());
-  this->GetAFDB()->template SetImage<MaskImageType>("RightLung", "seg/RightLung.mha", 
-                                                    right_lung, true);
-  this->GetAFDB()->template SetImage<MaskImageType>("LeftLung", "seg/LeftLung.mha", 
-                                                    left_lung, true);
-  this->GetAFDB()->Write();
-  this->template StopCurrentStep<MaskImageType>(output);
-
-  //--------------------------------------------------------------------
-  // Step : AP limits from bones
-  // Separate the bones in the ant-post middle
-  MaskImagePointer bones_ant;
-  MaskImagePointer bones_post;
-  MaskImagePointType middle_AntPost_position;
-  middle_AntPost_position.Fill(NumericTraits<MaskImagePointType::ValueType>::Zero);
-  if (GetUseBones()) { 
-    this->StartNewStep("[Mediastinum] Ant/Post limits with bones");
-
-    // To define ant and post part of the bones with a single horizontal line 
-    MaskImageIndexType index_bones_middle;
-
-    // Method1: cut in the middle (not optimal)
-    /*
-    middle_AntPost_position[0] = middle_AntPost_position[2] = 0;
-    middle_AntPost_position[1] = bones->GetOrigin()[1]+
-    (bones->GetLargestPossibleRegion().GetSize()[1]*bones->GetSpacing()[1])/2.0;
-    DD(middle_AntPost_position);
-    bones->TransformPhysicalPointToIndex(middle_AntPost_position, index_bones_middle);
-    */
-  
-    // Method2: Use VertebralBody, take most ant point
-    MaskImagePointer VertebralBody = this->GetAFDB()->template GetImage<MaskImageType>("VertebralBody");
-    FindExtremaPointInAGivenDirection<MaskImageType>(VertebralBody, this->GetBackgroundValue(), 
-                                                     1, true, middle_AntPost_position);
-    bones->TransformPhysicalPointToIndex(middle_AntPost_position, index_bones_middle);  
-
-    // Split bone image first into two parts (ant and post), and crop
-    // lateraly to get vertebral 
-    typedef itk::RegionOfInterestImageFilter<MaskImageType, MaskImageType> ROIFilterType;
-    //  typedef itk::ExtractImageFilter<MaskImageType, MaskImageType> ROIFilterType;
-    typename ROIFilterType::Pointer roiFilter = ROIFilterType::New();
-    MaskImageRegionType region = bones->GetLargestPossibleRegion();
-    MaskImageSizeType size = region.GetSize();
-    MaskImageIndexType index = region.GetIndex();
-    // ANT part
-    // crop LR to keep 1/4 center part
-    //    index[0] = size[0]/4+size[0]/8;
-    //size[0] = size[0]/4; 
-    // crop AP to keep first (ant) part
-    size[1] =  index_bones_middle[1]; //size[1]/2.0;
-    region.SetSize(size);
-    region.SetIndex(index);
-    roiFilter->SetInput(bones);
-    roiFilter->SetRegionOfInterest(region);
-    roiFilter->ReleaseDataFlagOff();
-    roiFilter->Update();
-    bones_ant = roiFilter->GetOutput();
-    //      writeImage<MaskImageType>(bones_ant, "b_ant.mhd");
-    // POST part
-    roiFilter = ROIFilterType::New();  
-    index[1] = bones->GetLargestPossibleRegion().GetIndex()[1] + size[1]-1;
-    size[1] =  bones->GetLargestPossibleRegion().GetSize()[1] - size[1];
-    region.SetIndex(index);
-    region.SetSize(size);
-    roiFilter->SetInput(bones);
-    roiFilter->SetRegionOfInterest(region);
-    roiFilter->ReleaseDataFlagOff();
-    roiFilter->Update();
-    bones_post = roiFilter->GetOutput();
-    // writeImage<MaskImageType>(bones_post, "b_post.mhd");
-
-    // Now, insert this image in the AFDB ==> (needed because used in the RelativePosition config file)
-    this->GetAFDB()->template SetImage<MaskImageType>("Bones_Post", "seg/Bones_Post.mha", 
-                                                 bones_post, true);
-    this->GetAFDB()->template SetImage<MaskImageType>("Bones_Ant", "seg/Bones_Ant.mha", 
-                                                 bones_ant, true);
-    this->GetAFDB()->Write();
-
-    this->template StopCurrentStep<MaskImageType>(output);
-  }
-
-  //--------------------------------------------------------------------
-  // Remove VertebralBody part
-  this->StartNewStep("[Mediastinum] Remove VertebralBody");  
-  MaskImagePointer VertebralBody = this->GetAFDB()->template GetImage<MaskImageType>("VertebralBody");
-  clitk::AndNot<MaskImageType>(output, VertebralBody, this->GetBackgroundValue());
-  this->template StopCurrentStep<MaskImageType>(output);
-
-  //--------------------------------------------------------------------
-  // Generic RelativePosition processes
-  output = this->ApplyRelativePositionList("Mediastinum", output);
-
-
-  //--------------------------------------------------------------------
-  // FIXME --> do not put this limits here !
-  /*
-  // Step : SI limits It is better to do this limit *AFTER* the
-  // RelativePosition to avoid some issue due to superior boundaries.
-  this->StartNewStep("[Mediastinum] Keep inferior to CricoidCartilag");
-  // load Cricoid, get centroid, cut above (or below), lower bound
-  MaskImagePointType p;
-  try {
-    MaskImagePointer CricoidCartilag = this->GetAFDB()->template GetImage <MaskImageType>("CricoidCartilag");
-    p[0] = p[1] = p[2] =  0.0; // to avoid warning
-    clitk::FindExtremaPointInAGivenDirection<MaskImageType>(CricoidCartilag, 
-                                                            this->GetBackgroundValue(), 2, true, p);
-  } catch (clitk::ExceptionObject e) {
-    //DD("CricoidCartilag image not found, try CricoidCartilagZ");
-    this->GetAFDB()->GetPoint3D("CricoidCartilagPoint", p);
-  }
-  output = clitk::CropImageRemoveGreaterThan<MaskImageType>(output, 2, p[2], true, this->GetBackgroundValue());
-  this->template StopCurrentStep<MaskImageType>(output);
-  */
-
-  //--------------------------------------------------------------------
-  // Step: Get CCL
-  this->StartNewStep("[Mediastinum] Keep main connected component");
-  output = clitk::Labelize<MaskImageType>(output, this->GetBackgroundValue(), false, 500);
-  // output = RemoveLabels<MaskImageType>(output, BG, param->GetLabelsToRemove());
-  output = clitk::KeepLabels<MaskImageType>(output, this->GetBackgroundValue(), 
-                                            this->GetForegroundValue(), 1, 1, 0);
-  this->template StopCurrentStep<MaskImageType>(output);
-
-  //--------------------------------------------------------------------
-  // Step: Remove post part from VertebralBody
-  this->StartNewStep("[Mediastinum] Remove post part according to VertebralBody");
-  RemovePostPartOfVertebralBody();
-  this->template StopCurrentStep<MaskImageType>(output);
-
-  //--------------------------------------------------------------------
-  // Step: Slice by Slice CCL
-  this->StartNewStep("[Mediastinum] Slice by Slice keep only one component");
-  typedef clitk::ExtractSliceFilter<MaskImageType> ExtractSliceFilterType;
-  //  typename ExtractSliceFilterType::Pointer 
-  ExtractSliceFilterType::Pointer extractSliceFilter = ExtractSliceFilterType::New();
-  extractSliceFilter->SetInput(output);
-  extractSliceFilter->SetDirection(2);
-  extractSliceFilter->Update();
-  typedef typename ExtractSliceFilterType::SliceType SliceType;
-  std::vector<typename SliceType::Pointer> mSlices;
-  extractSliceFilter->GetOutputSlices(mSlices);
-  for(unsigned int i=0; i<mSlices.size(); i++) {
-    mSlices[i] = Labelize<SliceType>(mSlices[i], 0, true, 100);
-    mSlices[i] = KeepLabels<SliceType>(mSlices[i], 0, 1, 1, 1, true);
-  }
-  typedef itk::JoinSeriesImageFilter<SliceType, MaskImageType> JoinSeriesFilterType;
-  typename JoinSeriesFilterType::Pointer joinFilter = JoinSeriesFilterType::New();
-  joinFilter->SetOrigin(output->GetOrigin()[2]);
-  joinFilter->SetSpacing(output->GetSpacing()[2]);
-  for(unsigned int i=0; i<mSlices.size(); i++) {
-    joinFilter->PushBackInput(mSlices[i]);
-  }
-  joinFilter->Update();
-  output = joinFilter->GetOutput();
-  this->template StopCurrentStep<MaskImageType>(output);
-
-  //--------------------------------------------------------------------
-  // Step 10 : AutoCrop
-  this->StartNewStep("[Mediastinum] AutoCrop");
-  output = clitk::AutoCrop<MaskImageType>(output, this->GetBackgroundValue()); 
-  this->template StopCurrentStep<MaskImageType>(output);
-
-  // End, set the real size
-  this->GetOutput(0)->SetRegions(output->GetLargestPossibleRegion());
-  this->GetOutput(0)->SetLargestPossibleRegion(output->GetLargestPossibleRegion());
-  this->GetOutput(0)->SetRequestedRegion(output->GetLargestPossibleRegion());
-  this->GetOutput(0)->SetBufferedRegion(output->GetLargestPossibleRegion());
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class ImageType>
-void 
-clitk::ExtractMediastinumFilter<ImageType>::
-GenerateData() 
-{
-  this->GraftOutput(output);
-  // Store image filenames into AFDB 
-  this->GetAFDB()->SetImageFilename("Mediastinum", this->GetOutputMediastinumFilename());  
-  this->WriteAFDB();
-}
-//--------------------------------------------------------------------
-
-  
-//--------------------------------------------------------------------
-template <class ImageType>
-void 
-clitk::ExtractMediastinumFilter<ImageType>::
-RemovePostPartOfVertebralBody()
-{
-  
-  /*
-    Posteriorly, Station 8 abuts the descending aorta and the anterior
-    aspect of the vertebral body until an imaginary horizontal line
-    running 1 cm posterior to the anterior border of the vertebral
-    body (Fig. 3C).
-    
-    => We use this definition for all the mediastinum
-
-   Find most Ant point in VertebralBody. Consider the horizontal line
-   which is 'DistanceMaxToAnteriorPartOfTheVertebralBody' away from
-   the most ant point.
-  */
-
-  // Get VertebralBody mask image
-  MaskImagePointer VertebralBody = 
-    this->GetAFDB()->template GetImage <MaskImageType>("VertebralBody");  
-
-  // Consider vertebral body slice by slice
-  std::vector<MaskSlicePointer> vertebralSlices;
-  clitk::ExtractSlices<MaskImageType>(VertebralBody, 2, vertebralSlices);
-
-  // For each slice, compute the most anterior point
-  std::map<int, MaskSlicePointType> vertebralAntPositionBySlice;
-  for(uint i=0; i<vertebralSlices.size(); i++) {
-    MaskSlicePointType p;
-    bool found = clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(vertebralSlices[i], 
-                                                                     this->GetBackgroundValue(), 
-                                                                     1, true, p);
-    if (found) {
-      vertebralAntPositionBySlice[i] = p;
-    }
-    else { 
-      // It should not happen ! But sometimes, a contour is missing or
-      // the VertebralBody is not delineated enough inferiorly ... in
-      // those cases, we consider the first found slice.
-      //        std::cerr << "No foreground pixels in this VertebralBody slices !?? I try with the previous/next slice" << std::endl;
-      // [ Possible alternative -> consider previous limit ]
-    }
-  }
-
-  // Convert 2D points in slice into 3D points
-  std::vector<MaskImagePointType> vertebralAntPositions;
-  clitk::PointsUtils<MaskImageType>::Convert2DMapTo3DList(vertebralAntPositionBySlice, 
-                                                          VertebralBody, 
-                                                          vertebralAntPositions);
-
-  // DEBUG : write list of points
-  clitk::WriteListOfLandmarks<MaskImageType>(vertebralAntPositions, 
-                                             "VertebralBodyMostAnteriorPoints.txt");
-
-  // Cut support posteriorly 1cm the most anterior point of the
-  // VertebralBody. Do nothing below and above the VertebralBody. To
-  // do that compute several region, slice by slice and fill. 
-  MaskImageRegionType region;
-  MaskImageSizeType size;
-  MaskImageIndexType start;
-  size[2] = 1; // a single slice
-  start[0] = output->GetLargestPossibleRegion().GetIndex()[0];
-  size[0] = output->GetLargestPossibleRegion().GetSize()[0];
-  for(uint i=0; i<vertebralAntPositions.size(); i++) {
-    typedef typename itk::ImageRegionIterator<MaskImageType> IteratorType;
-    IteratorType iter = 
-      IteratorType(output, output->GetLargestPossibleRegion());
-    MaskImageIndexType index;
-    // Consider some cm posterior to most anterior positions (usually
-    // 1 cm).
-    vertebralAntPositions[i][1] += GetDistanceMaxToAnteriorPartOfTheVertebralBody();
-    // Get index of this point
-    output->TransformPhysicalPointToIndex(vertebralAntPositions[i], index);
-    // Compute region (a single slice)
-    start[2] = index[2];
-    start[1] = output->GetLargestPossibleRegion().GetIndex()[1]+index[1];
-    size[1] = output->GetLargestPossibleRegion().GetSize()[1]-start[1];
-    region.SetSize(size);
-    region.SetIndex(start);
-    // Fill region
-    if (output->GetLargestPossibleRegion().IsInside(start))  {
-      itk::ImageRegionIterator<MaskImageType> it(output, region);
-      it.GoToBegin();
-      while (!it.IsAtEnd()) {
-        it.Set(this->GetBackgroundValue());
-        ++it;
-      }
-    }
-  }  
-}
-//--------------------------------------------------------------------
-
-
-#endif //#define CLITKBOOLEANOPERATORLABELIMAGEFILTER_TXX
diff --git a/segmentation/clitkExtractMediastinumGenericFilter.h b/segmentation/clitkExtractMediastinumGenericFilter.h
deleted file mode 100644
index 22339e4..0000000
--- a/segmentation/clitkExtractMediastinumGenericFilter.h
+++ /dev/null
@@ -1,76 +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://www.centreleonberard.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 CLITKEXTRACTMEDIASTINUMSGENERICFILTER_H
-#define CLITKEXTRACTMEDIASTINUMSGENERICFILTER_H
-
-#include "clitkIO.h"
-#include "clitkImageToImageGenericFilter.h"
-#include "clitkExtractMediastinumFilter.h"
-
-//--------------------------------------------------------------------
-namespace clitk 
-{
-  
-  template<class ArgsInfoType>
-  class ITK_EXPORT ExtractMediastinumGenericFilter: 
-    public ImageToImageGenericFilter<ExtractMediastinumGenericFilter<ArgsInfoType> >
-  {
-    
-  public:
-    //--------------------------------------------------------------------
-    ExtractMediastinumGenericFilter();
-
-    //--------------------------------------------------------------------
-    typedef ExtractMediastinumGenericFilter      Self;
-    typedef ImageToImageGenericFilter<ExtractMediastinumGenericFilter<ArgsInfoType> > Superclass;
-    typedef itk::SmartPointer<Self>       Pointer;
-    typedef itk::SmartPointer<const Self> ConstPointer;
-
-    //--------------------------------------------------------------------
-    itkNewMacro(Self);  
-    itkTypeMacro(ExtractMediastinumGenericFilter, LightObject);
-
-    //--------------------------------------------------------------------
-    // Options for the GenericFilter
-    void SetArgsInfo(const ArgsInfoType & a);
-    
-    //--------------------------------------------------------------------
-    // Options for the Filter
-    template<class FilterType> 
-    void SetOptionsFromArgsInfoToFilter(FilterType * f) ;
-
-    //--------------------------------------------------------------------
-    // Main function called each time the filter is updated
-    template<class ImageType>  
-    void UpdateWithInputImageType();
-
-  protected:
-    template<unsigned int Dim> void InitializeImageType();
-    ArgsInfoType mArgsInfo;
-    
-  }; // end class
-  //--------------------------------------------------------------------
-    
-} // end namespace clitk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "clitkExtractMediastinumGenericFilter.txx"
-#endif
-
-#endif // #define CLITKEXTRACTMEDIASTINUMSGENERICFILTER_H
diff --git a/segmentation/clitkExtractMediastinumGenericFilter.txx b/segmentation/clitkExtractMediastinumGenericFilter.txx
deleted file mode 100644
index 679fb36..0000000
--- a/segmentation/clitkExtractMediastinumGenericFilter.txx
+++ /dev/null
@@ -1,116 +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://www.centreleonberard.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 CLITKEXTRACTMEDIASTINUMSGENERICFILTER_TXX
-#define CLITKEXTRACTMEDIASTINUMSGENERICFILTER_TXX
-
-#include "clitkImageCommon.h"
-  
-//--------------------------------------------------------------------
-template<class ArgsInfoType>
-clitk::ExtractMediastinumGenericFilter<ArgsInfoType>::
-ExtractMediastinumGenericFilter():
-  ImageToImageGenericFilter<Self>("ExtractMediastinum") 
-{
-  // Default values
-  cmdline_parser_clitkExtractMediastinum_init(&mArgsInfo);
-  InitializeImageType<3>();
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class ArgsInfoType>
-template<unsigned int Dim>
-void 
-clitk::ExtractMediastinumGenericFilter<ArgsInfoType>::
-InitializeImageType() 
-{  
-  ADD_IMAGE_TYPE(Dim, short);
-}
-//--------------------------------------------------------------------
-  
-
-//--------------------------------------------------------------------
-template<class ArgsInfoType>
-void 
-clitk::ExtractMediastinumGenericFilter<ArgsInfoType>::
-SetArgsInfo(const ArgsInfoType & a) 
-{
-  mArgsInfo=a;
-  SetIOVerbose(mArgsInfo.verbose_flag);
-  if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
-  if (mArgsInfo.input_given) AddInputFilename(mArgsInfo.input_arg);
-  if (mArgsInfo.output_given)  AddOutputFilename(mArgsInfo.output_arg);
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template<class ArgsInfoType>
-template<class FilterType>
-void 
-clitk::ExtractMediastinumGenericFilter<ArgsInfoType>::
-SetOptionsFromArgsInfoToFilter(FilterType * f)
-{
-  f->SetVerboseOptionFlag(mArgsInfo.verbose_flag);
-  f->SetVerboseStepFlag(mArgsInfo.verboseStep_flag);
-  f->SetWriteStepFlag(mArgsInfo.writeStep_flag);
-  f->SetAFDBFilename(mArgsInfo.afdb_arg);  
-  f->SetOutputMediastinumFilename(mArgsInfo.output_arg);
-  f->SetVerboseMemoryFlag(mArgsInfo.verboseMemory_flag);
-
-  f->SetDistanceMaxToAnteriorPartOfTheVertebralBody(mArgsInfo.maxAntSpine_arg);
-  f->SetUseBones(mArgsInfo.useBones_flag);
-
-  // Set RelativePositionList filenames
-  for(uint i=0; i<mArgsInfo.relpos_given; i++) {
-    f->AddRelativePositionListFilename(mArgsInfo.relpos_arg[i]);
-  }
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-// Update with the number of dimensions and the pixeltype
-//--------------------------------------------------------------------
-template<class ArgsInfoType>
-template<class ImageType>
-void clitk::ExtractMediastinumGenericFilter<ArgsInfoType>::UpdateWithInputImageType() 
-{ 
-  // Reading input
-  typename ImageType::Pointer input = this->template GetInput<ImageType>(0);
-
-  // Create filter
-  typedef clitk::ExtractMediastinumFilter<ImageType> FilterType;
-  typename FilterType::Pointer filter = FilterType::New();
-    
-  // Set global Options 
-  filter->SetInput(input);
-  SetOptionsFromArgsInfoToFilter<FilterType>(filter);
-
-  // Go !
-  filter->Update();
-
-  // Write/Save results
-  typename FilterType::MaskImageType::Pointer output = filter->GetOutput();
-  this->template SetNextOutput<typename FilterType::MaskImageType>(output); 
-}
-//--------------------------------------------------------------------
-
-#endif //#define CLITKEXTRACTMEDIASTINUMSGENERICFILTER_TXX

http://git.creatis.insa-lyon.fr/pubgit/?p=clitk.git;a=commitdiff;h=595624eb4297e747630105d45017de69733caef2

commit 595624eb4297e747630105d45017de69733caef2
Author: David Sarrut <david.sarrut at gmail.com>
Date:   Thu Feb 2 17:01:20 2012 +0100

    Moved from repository clitk to clitk.private/tests_dav

diff --git a/segmentation/clitkAnd.cxx b/segmentation/clitkAnd.cxx
deleted file mode 100644
index e8be880..0000000
--- a/segmentation/clitkAnd.cxx
+++ /dev/null
@@ -1,51 +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://www.centreleonberard.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
-===========================================================================**/
-
-/* =================================================
- * @file   clitkAnd.cxx
- * @author 
- * @date   
- * 
- * @brief 
- * 
- ===================================================*/
-
-
-// clitk
-#include "clitkAnd_ggo.h"
-#include "clitkIO.h"
-#include "clitkAndGenericFilter.h"
-
-
-//--------------------------------------------------------------------
-int main(int argc, char * argv[]) {
-
-  // Init command line
-  GGO(clitkAnd, args_info);
-  CLITK_INIT;
-
-  // Filter
-  clitk::AndGenericFilter::Pointer genericFilter=clitk::AndGenericFilter::New();
-  
-  genericFilter->SetArgsInfo(args_info);
-  genericFilter->Update();
-
-  return EXIT_SUCCESS;
-}// end main
-
-//--------------------------------------------------------------------
diff --git a/segmentation/clitkAnd.ggo b/segmentation/clitkAnd.ggo
deleted file mode 100644
index 8455845..0000000
--- a/segmentation/clitkAnd.ggo
+++ /dev/null
@@ -1,13 +0,0 @@
-#File clitkAnd.ggo
-package "clitkAnd"
-version "1.0"
-purpose "Perform a pixel-wise logical AND between to images"
-
-option "config"	  	-	"Config file"			  string  	no
-option "verbose"   	v   	"Verbose"			  flag		off
-
-option "input"		i	"Input image filename"		  string  	yes
-option "input2"		j	"Input image filename"		  string  	yes
-option "output"    	o   	"Output image filename"		  string 	yes
-
-
diff --git a/segmentation/clitkAndGenericFilter.cxx b/segmentation/clitkAndGenericFilter.cxx
deleted file mode 100644
index e81757b..0000000
--- a/segmentation/clitkAndGenericFilter.cxx
+++ /dev/null
@@ -1,72 +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://www.centreleonberard.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 clitkAndGenericFilter_cxx
-#define clitkAndGenericFilter_cxx
-
-/* =================================================
- * @file   clitkAndGenericFilter.cxx
- * @author 
- * @date   
- * 
- * @brief 
- * 
- ===================================================*/
-
-#include "clitkAndGenericFilter.h"
-
-
-namespace clitk
-{
-
-
-  //-----------------------------------------------------------
-  // Constructor
-  //-----------------------------------------------------------
-  AndGenericFilter::AndGenericFilter()
-  {
-    m_Verbose=false;
-    m_InputFileName="";
-  }
-
-
-  //-----------------------------------------------------------
-  // Update
-  //-----------------------------------------------------------
-  void AndGenericFilter::Update()
-  {
-    // Read the Dimension and PixelType
-    int Dimension;
-    std::string PixelType;
-    ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType);
-
-    
-    // Call UpdateWithDim
-    if(Dimension==2) UpdateWithDim<2>(PixelType);
-    else if(Dimension==3) UpdateWithDim<3>(PixelType);
-    // else if (Dimension==4)UpdateWithDim<4>(PixelType); 
-    else 
-      {
-	std::cout<<"Error, Only for 2 or 3  Dimensions!!!"<<std::endl ;
-	return;
-      }
-  }
-
-
-} //end clitk
-
-#endif  //#define clitkAndGenericFilter_cxx
diff --git a/segmentation/clitkAndGenericFilter.h b/segmentation/clitkAndGenericFilter.h
deleted file mode 100644
index d67f4da..0000000
--- a/segmentation/clitkAndGenericFilter.h
+++ /dev/null
@@ -1,117 +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://www.centreleonberard.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 clitkAndGenericFilter_h
-#define clitkAndGenericFilter_h
-
-/* =================================================
- * @file   clitkAndGenericFilter.h
- * @author 
- * @date   
- * 
- * @brief 
- * 
- ===================================================*/
-
-
-// clitk include
-#include "clitkIO.h"
-#include "clitkCommon.h"
-#include "clitkImageCommon.h"
-#include "clitkAnd_ggo.h"
-
-//itk include
-#include "itkLightObject.h"
-#include "itkAndImageFilter.h"
-#include "itkCastImageFilter.h"
-
-namespace clitk 
-{
-
-
-  class ITK_EXPORT AndGenericFilter : public itk::LightObject
-  {
-  public:
-    //----------------------------------------
-    // ITK
-    //----------------------------------------
-    typedef AndGenericFilter                   Self;
-    typedef itk::LightObject                   Superclass;
-    typedef itk::SmartPointer<Self>            Pointer;
-    typedef itk::SmartPointer<const Self>      ConstPointer;
-   
-    // Method for creation through the object factory
-    itkNewMacro(Self);  
-
-    // Run-time type information (and related methods)
-    itkTypeMacro( AndGenericFilter, LightObject );
-
-
-    //----------------------------------------
-    // Typedefs
-    //----------------------------------------
-
-
-    //----------------------------------------
-    // Set & Get
-    //----------------------------------------    
-    void SetArgsInfo(const args_info_clitkAnd & a)
-    {
-      m_ArgsInfo=a;
-      m_Verbose=m_ArgsInfo.verbose_flag;
-      m_InputFileName=m_ArgsInfo.input_arg;
-    }
-    
-    
-    //----------------------------------------  
-    // Update
-    //----------------------------------------  
-    void Update();
-
-  protected:
-
-    //----------------------------------------  
-    // Constructor & Destructor
-    //----------------------------------------  
-    AndGenericFilter();
-    ~AndGenericFilter() {};
-
-    
-    //----------------------------------------  
-    // Templated members
-    //----------------------------------------  
-    template <unsigned int Dimension>  void UpdateWithDim(std::string PixelType);
-    template <unsigned int Dimension, class PixelType>  void UpdateWithDimAndPixelType();
-
-
-    //----------------------------------------  
-    // Data members
-    //----------------------------------------
-    args_info_clitkAnd m_ArgsInfo;
-    bool m_Verbose;
-    std::string m_InputFileName;
-
-  };
-
-
-} // end namespace clitk
-
-#ifndef ITK_MANUAL_INSTANTIATION
-#include "clitkAndGenericFilter.txx"
-#endif
-
-#endif // #define clitkAndGenericFilter_h
diff --git a/segmentation/clitkAndGenericFilter.txx b/segmentation/clitkAndGenericFilter.txx
deleted file mode 100644
index 6bf0ccc..0000000
--- a/segmentation/clitkAndGenericFilter.txx
+++ /dev/null
@@ -1,127 +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://www.centreleonberard.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 clitkAndGenericFilter_txx
-#define clitkAndGenericFilter_txx
-
-/* =================================================
- * @file   clitkAndGenericFilter.txx
- * @author 
- * @date   
- * 
- * @brief 
- * 
- ===================================================*/
-
-
-namespace clitk
-{
-
-  //-------------------------------------------------------------------
-  // Update with the number of dimensions
-  //-------------------------------------------------------------------
-  template<unsigned int Dimension>
-  void 
-  AndGenericFilter::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>();
-    }
-  }
-
-
-  //-------------------------------------------------------------------
-  // Update with the number of dimensions and the pixeltype
-  //-------------------------------------------------------------------
-  template <unsigned int Dimension, class  PixelType> 
-  void 
-  AndGenericFilter::UpdateWithDimAndPixelType()
-  {
-
-    // ImageTypes
-    typedef itk::Image<PixelType, Dimension> InputImageType;
-    typedef itk::Image<int, Dimension> InternalImageType;
-    typedef itk::Image<PixelType, Dimension> OutputImageType;
-    
-    // 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();
-
-    // Read the second input
-    typename InputReaderType::Pointer reader2 = InputReaderType::New();
-    reader2->SetFileName( m_ArgsInfo.input2_arg);
-    reader2->Update();
-    typename InputImageType::Pointer input2= reader2->GetOutput();
-
-
-    // Cast
-    typedef itk::CastImageFilter<InputImageType, InternalImageType> InputCastImageFilterType;
-    typename InputCastImageFilterType::Pointer caster= InputCastImageFilterType::New();
-    caster->SetInput(input);
-    typename InputCastImageFilterType::Pointer caster2= InputCastImageFilterType::New();
-    caster->SetInput(input2);
-    
-    // Filter
-    typedef    itk::AndImageFilter< InternalImageType , InternalImageType , InternalImageType> AndFilterType;
-    typename   AndFilterType::Pointer andFilter = AndFilterType::New();
-    andFilter->SetInput1(caster->GetOutput());
-    andFilter->SetInput2(caster2->GetOutput());
-    if (m_Verbose) std::cout<<"Performing a logical AND..."<<std::endl;
-
-    // Cast
-    typedef itk::CastImageFilter<InternalImageType, OutputImageType> OutputCastImageFilterType;
-    typename OutputCastImageFilterType::Pointer caster3= OutputCastImageFilterType::New();
-    caster3->SetInput(andFilter->GetOutput());
-    typename OutputImageType::Pointer output =caster3->GetOutput();
-    
-    // Output
-    typedef itk::ImageFileWriter<OutputImageType> WriterType;
-    typename WriterType::Pointer writer = WriterType::New();
-    writer->SetFileName(m_ArgsInfo.output_arg);
-    writer->SetInput(output);
-    writer->Update();
-
-  }
-
-
-}//end clitk
- 
-#endif //#define clitkAndGenericFilter_txx

-----------------------------------------------------------------------

Summary of changes:
 segmentation/CMakeLists.txt                        |   33 +--
 segmentation/clitkAnd.cxx                          |   51 --
 segmentation/clitkAnd.ggo                          |   13 -
 segmentation/clitkAndGenericFilter.cxx             |   72 ---
 segmentation/clitkAndGenericFilter.h               |  117 -----
 segmentation/clitkAndGenericFilter.txx             |  127 -----
 segmentation/clitkExtractMediastinum.cxx           |   45 --
 segmentation/clitkExtractMediastinum.ggo           |   24 -
 segmentation/clitkExtractMediastinumFilter.h       |  173 -------
 segmentation/clitkExtractMediastinumFilter.txx     |  533 --------------------
 .../clitkExtractMediastinumGenericFilter.h         |   76 ---
 .../clitkExtractMediastinumGenericFilter.txx       |  116 -----
 12 files changed, 2 insertions(+), 1378 deletions(-)
 delete mode 100644 segmentation/clitkAnd.cxx
 delete mode 100644 segmentation/clitkAnd.ggo
 delete mode 100644 segmentation/clitkAndGenericFilter.cxx
 delete mode 100644 segmentation/clitkAndGenericFilter.h
 delete mode 100644 segmentation/clitkAndGenericFilter.txx
 delete mode 100644 segmentation/clitkExtractMediastinum.cxx
 delete mode 100644 segmentation/clitkExtractMediastinum.ggo
 delete mode 100644 segmentation/clitkExtractMediastinumFilter.h
 delete mode 100644 segmentation/clitkExtractMediastinumFilter.txx
 delete mode 100644 segmentation/clitkExtractMediastinumGenericFilter.h
 delete mode 100644 segmentation/clitkExtractMediastinumGenericFilter.txx


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