X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractMediastinumFilter.txx;h=d3ba557b97d863cb7a486aab5c59c742a4f371b0;hb=765020625fbc092d283e221e36c83e60a1844cb7;hp=fde335c28ada90f738bc5051673d7554027e2546;hpb=6e16222234a90c6079a8f4696c92de7349a496bb;p=clitk.git

diff --git a/segmentation/clitkExtractMediastinumFilter.txx b/segmentation/clitkExtractMediastinumFilter.txx
index fde335c..d3ba557 100644
--- a/segmentation/clitkExtractMediastinumFilter.txx
+++ b/segmentation/clitkExtractMediastinumFilter.txx
@@ -3,7 +3,7 @@
 
   Authors belong to: 
   - University of LYON              http://www.universite-lyon.fr/
-  - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.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
@@ -14,7 +14,7 @@
 
   - 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
@@ -23,15 +23,20 @@
 #include "clitkCommon.h"
 #include "clitkExtractMediastinumFilter.h"
 #include "clitkAddRelativePositionConstraintToLabelImageFilter.h"
+#include "clitkSliceBySliceRelativePositionFilter.h"
 #include "clitkSegmentationUtils.h"
-#include "clitkExtractAirwayTreeInfoFilter.h"
+#include "clitkExtractAirwaysTreeInfoFilter.h"
+#include "clitkCropLikeImageFilter.h"
 
-// itk
+// std
 #include <deque>
+
+// itk
 #include "itkStatisticsLabelMapFilter.h"
 #include "itkLabelImageToStatisticsLabelMapFilter.h"
 #include "itkRegionOfInterestImageFilter.h"
 #include "itkBinaryThresholdImageFilter.h"
+#include "itkScalarImageKmeansImageFilter.h"
 
 // itk ENST
 #include "RelativePositionPropImageFilter.h"
@@ -41,9 +46,10 @@ template <class ImageType>
 clitk::ExtractMediastinumFilter<ImageType>::
 ExtractMediastinumFilter():
   clitk::FilterBase(),
-  itk::ImageToImageFilter<ImageType, ImageType>()
+  clitk::FilterWithAnatomicalFeatureDatabaseManagement(),
+  itk::ImageToImageFilter<ImageType, MaskImageType>()
 {
-  this->SetNumberOfRequiredInputs(4);
+  this->SetNumberOfRequiredInputs(1);
 
   SetBackgroundValuePatient(0);
   SetBackgroundValueLung(0);
@@ -54,8 +60,13 @@ ExtractMediastinumFilter():
   SetForegroundValue(1);
 
   SetIntermediateSpacing(6);
-  SetFuzzyThreshold1(0.6);
-  SetFuzzyThreshold2(0.7);
+  SetFuzzyThreshold1(0.5);
+  SetFuzzyThreshold2(0.6);
+  SetFuzzyThreshold3(0.05);
+  
+  SetOutputMediastinumFilename("mediastinum.mhd");
+  
+  UseBonesOff();
 }
 //--------------------------------------------------------------------
 
@@ -64,9 +75,9 @@ ExtractMediastinumFilter():
 template <class ImageType>
 void 
 clitk::ExtractMediastinumFilter<ImageType>::
-SetInputPatientLabelImage(const ImageType * image, ImagePixelType bg) 
+SetInputPatientLabelImage(const MaskImageType * image, MaskImagePixelType bg) 
 {
-  this->SetNthInput(0, const_cast<ImageType *>(image));
+  this->SetNthInput(0, const_cast<MaskImageType *>(image));
   m_BackgroundValuePatient = bg;
 }
 //--------------------------------------------------------------------
@@ -76,10 +87,10 @@ SetInputPatientLabelImage(const ImageType * image, ImagePixelType bg)
 template <class ImageType>
 void 
 clitk::ExtractMediastinumFilter<ImageType>::
-SetInputLungLabelImage(const ImageType * image, ImagePixelType bg, 
-                       ImagePixelType fgLeft, ImagePixelType fgRight) 
+SetInputLungLabelImage(const MaskImageType * image, MaskImagePixelType bg, 
+                       MaskImagePixelType fgLeft, MaskImagePixelType fgRight) 
 {
-  this->SetNthInput(1, const_cast<ImageType *>(image));
+  this->SetNthInput(1, const_cast<MaskImageType *>(image));
   m_BackgroundValueLung = bg;
   m_ForegroundValueLeftLung = fgLeft;
   m_ForegroundValueRightLung = fgRight;
@@ -91,9 +102,9 @@ SetInputLungLabelImage(const ImageType * image, ImagePixelType bg,
 template <class ImageType>
 void 
 clitk::ExtractMediastinumFilter<ImageType>::
-SetInputBonesLabelImage(const ImageType * image, ImagePixelType bg) 
+SetInputBonesLabelImage(const MaskImageType * image, MaskImagePixelType bg) 
 {
-  this->SetNthInput(2, const_cast<ImageType *>(image));
+  this->SetNthInput(2, const_cast<MaskImageType *>(image));
   m_BackgroundValueBones = bg;
 }
 //--------------------------------------------------------------------
@@ -103,9 +114,9 @@ SetInputBonesLabelImage(const ImageType * image, ImagePixelType bg)
 template <class ImageType>
 void 
 clitk::ExtractMediastinumFilter<ImageType>::
-SetInputTracheaLabelImage(const ImageType * image, ImagePixelType bg) 
+SetInputTracheaLabelImage(const MaskImageType * image, MaskImagePixelType bg) 
 {
-  this->SetNthInput(3, const_cast<ImageType *>(image));
+  this->SetNthInput(3, const_cast<MaskImageType *>(image));
   m_BackgroundValueTrachea = bg;
 }
 //--------------------------------------------------------------------
@@ -113,39 +124,16 @@ SetInputTracheaLabelImage(const ImageType * image, ImagePixelType bg)
 
 //--------------------------------------------------------------------
 template <class ImageType>
-template<class ArgsInfoType>
 void 
 clitk::ExtractMediastinumFilter<ImageType>::
-SetArgsInfo(ArgsInfoType mArgsInfo)
+GenerateInputRequestedRegion() 
 {
-  SetVerboseOption_GGO(mArgsInfo);
-  SetVerboseStep_GGO(mArgsInfo);
-  SetWriteStep_GGO(mArgsInfo);
-  SetVerboseWarningOff_GGO(mArgsInfo);
-
-  SetBackgroundValuePatient_GGO(mArgsInfo);
-  SetBackgroundValueLung_GGO(mArgsInfo);
-  SetBackgroundValueTrachea_GGO(mArgsInfo);
-
-  SetForegroundValueLeftLung_GGO(mArgsInfo);
-  SetForegroundValueRightLung_GGO(mArgsInfo);
-
-  SetIntermediateSpacing_GGO(mArgsInfo);
-  SetFuzzyThreshold1_GGO(mArgsInfo);
-  SetFuzzyThreshold2_GGO(mArgsInfo);
+  // DD("GenerateInputRequestedRegion");
+  // Do not call default
+  // Superclass::GenerateInputRequestedRegion();  
+  // DD("End GenerateInputRequestedRegion");
 }
-//--------------------------------------------------------------------
-
 
-//--------------------------------------------------------------------
-template <class ImageType>
-void 
-clitk::ExtractMediastinumFilter<ImageType>::
-GenerateOutputInformation() { 
-  ImagePointer input = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
-  ImagePointer outputImage = this->GetOutput(0);
-  outputImage->SetRegions(outputImage->GetLargestPossibleRegion());
-}
 //--------------------------------------------------------------------
 
 
@@ -153,20 +141,9 @@ GenerateOutputInformation() {
 template <class ImageType>
 void 
 clitk::ExtractMediastinumFilter<ImageType>::
-GenerateInputRequestedRegion() 
+SetInput(const ImageType * image) 
 {
-  // Call default
-  Superclass::GenerateInputRequestedRegion();  
-  // Get input pointers
-  ImagePointer patient = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
-  ImagePointer lung    = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(1));
-  ImagePointer bones   = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(2));
-  ImagePointer trachea = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(3));
-    
-  patient->SetRequestedRegion(patient->GetLargestPossibleRegion());
-  lung->SetRequestedRegion(lung->GetLargestPossibleRegion());
-  bones->SetRequestedRegion(bones->GetLargestPossibleRegion());
-  trachea->SetRequestedRegion(trachea->GetLargestPossibleRegion());
+  this->SetNthInput(0, const_cast<ImageType *>(image));
 }
 //--------------------------------------------------------------------
 
@@ -175,170 +152,412 @@ GenerateInputRequestedRegion()
 template <class ImageType>
 void 
 clitk::ExtractMediastinumFilter<ImageType>::
-GenerateData() 
-{
+GenerateOutputInformation() { 
+  // Do not call default
+  // Superclass::GenerateOutputInformation();
+
+  //--------------------------------------------------------------------
   // Get input pointers
-  ImageConstPointer patient = dynamic_cast<const ImageType*>(itk::ProcessObject::GetInput(0));
-  ImageConstPointer lung    = dynamic_cast<const ImageType*>(itk::ProcessObject::GetInput(1));
-  ImageConstPointer bones   = dynamic_cast<const ImageType*>(itk::ProcessObject::GetInput(2));
-  ImageConstPointer trachea = dynamic_cast<const ImageType*>(itk::ProcessObject::GetInput(3));
+  clitk::PrintMemory(GetVerboseMemoryFlag(), "Initial memory"); // OK
+  LoadAFDB();
+  ImageConstPointer input = dynamic_cast<const ImageType*>(itk::ProcessObject::GetInput(0));
+  MaskImagePointer patient = GetAFDB()->template GetImage <MaskImageType>("Patient");  
+  MaskImagePointer lung = GetAFDB()->template GetImage <MaskImageType>("Lungs");
+  MaskImagePointer bones;
+  if (GetUseBones()) {
+    bones = GetAFDB()->template GetImage <MaskImageType>("Bones");  
+  }
+  MaskImagePointer trachea = GetAFDB()->template GetImage <MaskImageType>("Trachea");  
     
-  // Get output pointer
-  ImagePointer output;
-
-  // Step 1: patient minus lungs, minus bones
-  StartNewStep("Patient contours minus lungs and minus bones");
-  typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
+  clitk::PrintMemory(GetVerboseMemoryFlag(), "After read patient, lung"); 
+  
+  //--------------------------------------------------------------------
+  // Step 1: Crop support (patient) to lung extend in RL
+  StartNewStep("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 2: Crop support (previous) to bones extend in AP
+  if (GetUseBones()) {
+    StartNewStep("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 3: patient minus lungs, minus bones, minus trachea
+  StartNewStep("Patient contours minus lungs, trachea [and bones]");
+  typedef clitk::BooleanOperatorLabelImageFilter<MaskImageType> BoolFilterType;
   typename BoolFilterType::Pointer boolFilter = BoolFilterType::New(); 
   boolFilter->InPlaceOn();
-  boolFilter->SetInput1(patient);
+  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(bones);
+  boolFilter->SetInput2(trachea);
   boolFilter->SetOperationType(BoolFilterType::AndNot);
   boolFilter->Update(); 
   output = boolFilter->GetOutput();
 
   // Auto crop to gain support area
-  output = clitk::AutoCrop<ImageType>(output, GetBackgroundValue()); 
-  this->template StopCurrentStep<ImageType>(output);
-
-  // Step 2: LR limits from lung (need separate lung ?)
+  output = clitk::AutoCrop<MaskImageType>(output, GetBackgroundValue()); 
+  this->template StopCurrentStep<MaskImageType>(output);
+
+  //--------------------------------------------------------------------
+  // Step 4: 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 ? )
   StartNewStep("Left/Right limits with lungs");
-
-  /* // WE DO NOT NEED THE FOLLOWING
-     // Get separate lung images to get only the right and left lung
-     // (label must be '1' because right is greater than left).
-     ImagePointer right_lung = clitk::SetBackground<ImageType, ImageType>(lung, lung, 2, 0);
-     ImagePointer left_lung = clitk::SetBackground<ImageType, ImageType>(lung, lung, 1, 0);
-     writeImage<ImageType>(right_lung, "right.mhd");
-     writeImage<ImageType>(left_lung, "left.mhd");
-  */
-
-  typedef clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType> RelPosFilterType;
+  
+  // 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);
+  right_lung = clitk::ResizeImageLike<MaskImageType>(right_lung, output, GetBackgroundValue());
+  left_lung = clitk::ResizeImageLike<MaskImageType>(left_lung, output, GetBackgroundValue());
+  // writeImage<MaskImageType>(right_lung, "right.mhd");
+  // writeImage<MaskImageType>(left_lung, "left.mhd");
+
+  typedef clitk::AddRelativePositionConstraintToLabelImageFilter<MaskImageType> RelPosFilterType;
   typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New();
   relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
-  relPosFilter->VerboseStepOff();
-  relPosFilter->WriteStepOff();
+  relPosFilter->VerboseStepFlagOff();
+  relPosFilter->WriteStepFlagOff();
   relPosFilter->SetInput(output); 
-  DD(output->GetLargestPossibleRegion().GetIndex());
-  //  relPosFilter->SetInputObject(left_lung); 
-  relPosFilter->SetInputObject(lung); 
-  relPosFilter->SetOrientationType(RelPosFilterType::LeftTo); // warning left lung is at right ;)
+  relPosFilter->SetInputObject(left_lung); 
+  //  relPosFilter->SetInputObject(lung); 
+  relPosFilter->AddOrientationType(RelPosFilterType::AtRightTo); // warning left lung is at right ;)
   relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
   relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold1());
   relPosFilter->Update();
   output = relPosFilter->GetOutput();
-  DD(output->GetLargestPossibleRegion());
+  //writeImage<MaskImageType>(right_lung, "step4-left.mhd");
 
+  relPosFilter = RelPosFilterType::New();
   relPosFilter->SetInput(output); 
   relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
-  relPosFilter->VerboseStepOff();
-  relPosFilter->WriteStepOff();
-  //  relPosFilter->SetInputObject(right_lung);
-  relPosFilter->SetInputObject(lung); 
-  relPosFilter->SetOrientationType(RelPosFilterType::RightTo);
+  relPosFilter->VerboseStepFlagOff();
+  relPosFilter->WriteStepFlagOff();
+  relPosFilter->SetInput(output); 
+  relPosFilter->SetInputObject(right_lung);
+  //relPosFilter->SetInputObject(lung); 
+  relPosFilter->AddOrientationType(RelPosFilterType::AtLeftTo);
   relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
   relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold1());
   relPosFilter->Update();   
   output = relPosFilter->GetOutput();
-  DD(output->GetLargestPossibleRegion());
-  this->template StopCurrentStep<ImageType>(output);
-
-  // Step 3: AP limits from bones
-  StartNewStep("Ant/Post limits with bones");
-  ImageConstPointer bones_ant;
-  ImageConstPointer bones_post;
-
-  // Find ant-post coordinate of trachea (assume the first point is a
-  // good estimation of the ant-post position of the trachea)
-  typedef clitk::ExtractAirwayTreeInfoFilter<ImageType> AirwayFilter;
-  typename AirwayFilter::Pointer airwayfilter = AirwayFilter::New();
-  airwayfilter->SetInput(trachea);
-  airwayfilter->Update();
-  DD(airwayfilter->GetFirstTracheaPoint());
-  ImagePointType point_trachea = airwayfilter->GetFirstTracheaPoint();
-  ImageIndexType index_trachea;
-  bones->TransformPhysicalPointToIndex(point_trachea, index_trachea);
-  DD(index_trachea);
+  this->template StopCurrentStep<MaskImageType>(output);
+
+  //--------------------------------------------------------------------
+  // Step 5: AP limits from bones
+  // Separate the bones in the ant-post middle
+  MaskImageConstPointer bones_ant;
+  MaskImageConstPointer bones_post;
+  MaskImagePointType middle_AntPost__position;
+  if (GetUseBones()) { 
+    StartNewStep("Ant/Post limits with bones");
+    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;
+    MaskImageIndexType index_bones_middle;
+    bones->TransformPhysicalPointToIndex(middle_AntPost__position, index_bones_middle);
   
-  // Split bone image first into two parts (ant and post)
-  typedef itk::RegionOfInterestImageFilter<ImageType, ImageType> CropFilterType;
-  //  typedef itk::ExtractImageFilter<ImageType, ImageType> CropFilterType;
-  typename CropFilterType::Pointer cropFilter = CropFilterType::New();
-  ImageRegionType region = bones->GetLargestPossibleRegion();
-  ImageSizeType size = region.GetSize();
-  DD(size);
-  size[1] =  index_trachea[1]; //size[1]/2.0;
-  DD(size);
-  region.SetSize(size);
-  cropFilter->SetInput(bones);
-  //  cropFilter->SetExtractionRegion(region);
-  cropFilter->SetRegionOfInterest(region);
-  cropFilter->ReleaseDataFlagOff();
-  cropFilter->Update();
-  bones_ant = cropFilter->GetOutput();
-  writeImage<ImageType>(bones_ant, "b_ant.mhd");
-  
-  //  cropFilter->ResetPipeline();// = CropFilterType::New();  
-  cropFilter = CropFilterType::New();  
-  ImageIndexType index = region.GetIndex();
-  size[1] =  bones->GetLargestPossibleRegion().GetSize()[1] - size[1];
-  index[1] = bones->GetLargestPossibleRegion().GetIndex()[1] + size[1]-1;
-  DD(size);
-  region.SetIndex(index);
-  region.SetSize(size);
-  cropFilter->SetInput(bones);
-  //  cropFilter->SetExtractionRegion(region);
-  cropFilter->SetRegionOfInterest(region);
-  cropFilter->ReleaseDataFlagOff();
-  cropFilter->Update();
-  bones_post = cropFilter->GetOutput();
-  writeImage<ImageType>(bones_post, "b_post.mhd");
+    // 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");
+
+    // Go ! 
+    relPosFilter->SetCurrentStepNumber(0);
+    relPosFilter->ResetPipeline();// = RelPosFilterType::New();
+    relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
+    relPosFilter->VerboseStepFlagOff();
+    relPosFilter->WriteStepFlagOff();
+    relPosFilter->SetInput(output); 
+    relPosFilter->SetInputObject(bones_post); 
+    relPosFilter->AddOrientationType(RelPosFilterType::AntTo);
+    relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
+    relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold2());
+    relPosFilter->Update();
+    output = relPosFilter->GetOutput();
+    //    writeImage<MaskImageType>(output, "post.mhd");
+
+    relPosFilter->SetInput(relPosFilter->GetOutput()); 
+    relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
+    relPosFilter->VerboseStepFlagOff();
+    relPosFilter->WriteStepFlagOff();
+    relPosFilter->SetInput(output); 
+    relPosFilter->SetInputObject(bones_ant); 
+    relPosFilter->AddOrientationType(RelPosFilterType::PostTo);
+    relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
+    relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold2());
+    relPosFilter->Update();   
+    output = relPosFilter->GetOutput();
+    this->template StopCurrentStep<MaskImageType>(output);
+  }
+
+  //--------------------------------------------------------------------
+  // Step 6: Get CCL
+  StartNewStep("Keep main connected component");
+  output = clitk::Labelize<MaskImageType>(output, GetBackgroundValue(), false, 500);
+  // output = RemoveLabels<MaskImageType>(output, BG, param->GetLabelsToRemove());
+  output = clitk::KeepLabels<MaskImageType>(output, GetBackgroundValue(), 
+                                            GetForegroundValue(), 1, 1, 0);
+  this->template StopCurrentStep<MaskImageType>(output);
+
+
+  //--------------------------------------------------------------------
+  // Step 8: Trial segmentation KMeans
+  if (0) {
+    StartNewStep("K means");
+    // Take input, crop like current mask
+    typedef CropLikeImageFilter<ImageType> CropLikeFilterType;
+    typename CropLikeFilterType::Pointer cropLikeFilter = CropLikeFilterType::New();
+    cropLikeFilter->SetInput(input);
+    cropLikeFilter->SetCropLikeImage(output);
+    cropLikeFilter->Update();
+    ImagePointer working_input = cropLikeFilter->GetOutput();
+    writeImage<ImageType>(working_input, "crop-input.mhd");
+    // Set bG at -1000
+    working_input = clitk::SetBackground<ImageType, MaskImageType>(working_input, output, GetBackgroundValue(), -1000, true);
+    writeImage<ImageType>(working_input, "crop-input2.mhd");
+    // Kmeans
+    typedef itk::ScalarImageKmeansImageFilter<ImageType> KMeansFilterType;
+    typename KMeansFilterType::Pointer kmeansFilter = KMeansFilterType::New();
+    kmeansFilter->SetInput(working_input);
+    //  const unsigned int numberOfInitialClasses = 3;
+    // const unsigned int useNonContiguousLabels = 0;
+    kmeansFilter->AddClassWithInitialMean(-1000);
+    kmeansFilter->AddClassWithInitialMean(30);
+    kmeansFilter->AddClassWithInitialMean(-40);  // ==> I want this one
+    DD("Go!");
+    kmeansFilter->Update();
+    DD("End");
+    typename KMeansFilterType::ParametersType estimatedMeans = kmeansFilter->GetFinalMeans();
+    const unsigned int numberOfClasses = estimatedMeans.Size();
+    for ( unsigned int i = 0 ; i < numberOfClasses ; ++i ) {
+      std::cout << "cluster[" << i << "] ";
+      std::cout << "    estimated mean : " << estimatedMeans[i] << std::endl;
+    }
+    MaskImageType::Pointer kmeans = kmeansFilter->GetOutput();
+    kmeans = clitk::SetBackground<MaskImageType, MaskImageType>(kmeans, kmeans, 
+                                                                1, GetBackgroundValue(), true);
+    writeImage<MaskImageType>(kmeans, "kmeans.mhd");
+    // Get final results, and remove from current mask
+    boolFilter = BoolFilterType::New(); 
+    boolFilter->InPlaceOn();
+    boolFilter->SetInput1(output);
+    boolFilter->SetInput2(kmeans);    
+    boolFilter->SetOperationType(BoolFilterType::And);
+    boolFilter->Update();    
+    output = boolFilter->GetOutput();
+    writeImage<MaskImageType>(output, "out-kmean.mhd");
+    this->template StopCurrentStep<MaskImageType>(output);
+
+    // TODO -> FillMASK ?
+    // comment speed ? mask ? 2 class ?
+
+
+    //TODO 
+    // Confidence connected ?
+
+  }
+
+  //--------------------------------------------------------------------
+  // Step 8: Lower limits from lung (need separate lung ?)
+  if (0) {
+    // StartNewStep("Trial : minus segmented struct");
+    // MaskImagePointer heart = GetAFDB()->template GetImage <MaskImageType>("heart");  
+    // boolFilter = BoolFilterType::New(); 
+    // boolFilter->InPlaceOn();
+    // boolFilter->SetInput1(output);
+    // boolFilter->SetInput2(heart);
+    // boolFilter->SetOperationType(BoolFilterType::AndNot);
+    // boolFilter->Update();  
+    //  output = boolFilter->GetOutput(); // not needed because InPlace
+    
+    // Not below the heart
+    // relPosFilter = RelPosFilterType::New();
+    // relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
+    // relPosFilter->VerboseStepFlagOff();
+    // relPosFilter->WriteStepFlagOff();
+    // relPosFilter->SetInput(output); 
+    // relPosFilter->SetInputObject(heart);
+    // relPosFilter->SetOrientationType(RelPosFilterType::SupTo);
+    // relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
+    // relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold3());
+    // relPosFilter->Update();
+    // output = relPosFilter->GetOutput();
+  }
+
+  //--------------------------------------------------------------------
+  // Step 8: Lower limits from lung (need separate lung ?)
+  if (0) {
+    StartNewStep("Lower limits with lungs");
+    // TODO BOFFF ????
+    relPosFilter = RelPosFilterType::New();
+    relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
+    relPosFilter->VerboseStepFlagOff();
+    relPosFilter->WriteStepFlagOff();
+    relPosFilter->SetInput(output); 
+    //  relPosFilter->SetInputObject(left_lung); 
+    relPosFilter->SetInputObject(lung); 
+    relPosFilter->AddOrientationType(RelPosFilterType::SupTo);
+    relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
+    relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold3());
+    relPosFilter->Update();
+    output = relPosFilter->GetOutput();
+    this->template StopCurrentStep<MaskImageType>(output);
+  }
+
+  //--------------------------------------------------------------------
+  // Step 10: Slice by Slice CCL
+  StartNewStep("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 9: Binarize to remove too high HU
+  // --> warning CCL slice by slice must be done before
+  if (0) {
+    StartNewStep("Remove hypersignal (bones and injected part");
+    // Crop initial ct like current support
+    typedef CropLikeImageFilter<ImageType> CropLikeFilterType;
+    typename CropLikeFilterType::Pointer cropLikeFilter = CropLikeFilterType::New();
+    cropLikeFilter->SetInput(input);
+    cropLikeFilter->SetCropLikeImage(output);
+    cropLikeFilter->Update();
+    ImagePointer working_input = cropLikeFilter->GetOutput();
+    //  writeImage<ImageType>(working_input, "crop-ct.mhd");
+    // Binarize
+    typedef itk::BinaryThresholdImageFilter<ImageType, MaskImageType> InputBinarizeFilterType; 
+    typename InputBinarizeFilterType::Pointer binarizeFilter=InputBinarizeFilterType::New();
+    binarizeFilter->SetInput(working_input);
+    binarizeFilter->SetLowerThreshold(GetLowerThreshold());
+    binarizeFilter->SetUpperThreshold(GetUpperThreshold());
+    binarizeFilter->SetInsideValue(this->GetBackgroundValue());  // opposite
+    binarizeFilter->SetOutsideValue(this->GetForegroundValue()); // opposite
+    binarizeFilter->Update();
+    MaskImagePointer working_bin = binarizeFilter->GetOutput();
+    // writeImage<MaskImageType>(working_bin, "bin.mhd");
+    // Remove from support
+    boolFilter = BoolFilterType::New(); 
+    boolFilter->InPlaceOn();
+    boolFilter->SetInput1(output);
+    boolFilter->SetInput2(working_bin);    
+    boolFilter->SetOperationType(BoolFilterType::AndNot);
+    boolFilter->Update();
+    output = boolFilter->GetOutput();
+    StopCurrentStep<MaskImageType>(output);
+  }
+
+  //--------------------------------------------------------------------
+  // Step 10 : AutoCrop
+  StartNewStep("AutoCrop");
+  output = clitk::AutoCrop<MaskImageType>(output, GetBackgroundValue()); 
+  this->template StopCurrentStep<MaskImageType>(output);
+
+  // Bones ? pb with RAM ? FillHoles ?
+
+  // how to do with post part ? spine /lung ?
+  // POST the spine (should be separated from the rest) 
+  /// DO THAT ---->>
+  // histo Y on the whole bones_post (3D) -> result is the Y center on the spine (?)
+  // by slice on bones_post
+  //       find the most ant point in the center
+  //       from this point go to post until out of bones.
+  //       
+
+
+  // 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());
+}
+//--------------------------------------------------------------------
 
-  // Go ! 
-  relPosFilter->SetCurrentStepNumber(0);
-  relPosFilter->ResetPipeline();// = RelPosFilterType::New();
-  relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
-  relPosFilter->VerboseStepOff();
-  relPosFilter->WriteStepOff();
-  relPosFilter->SetInput(output); 
-  relPosFilter->SetInputObject(bones_post); 
-  relPosFilter->SetOrientationType(RelPosFilterType::AntTo);
-  relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
-  relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold2());
-  relPosFilter->Update();
-  output = relPosFilter->GetOutput();
-  writeImage<ImageType>(output, "post.mhd");
 
-  relPosFilter->SetInput(relPosFilter->GetOutput()); 
-  relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
-  relPosFilter->VerboseStepOff();
-  relPosFilter->WriteStepOff();
-  relPosFilter->SetInput(output); 
-  relPosFilter->SetInputObject(bones_ant); 
-  relPosFilter->SetOrientationType(RelPosFilterType::PostTo);
-  relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
-  relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold2());
-  relPosFilter->Update();   
-  output = relPosFilter->GetOutput();
-  this->template StopCurrentStep<ImageType>(output);
-  // Get CCL
-  output = clitk::Labelize<ImageType>(output, GetBackgroundValue(), true, 100);
-  // output = RemoveLabels<ImageType>(output, BG, param->GetLabelsToRemove());
-  output = clitk::KeepLabels<ImageType>(output, GetBackgroundValue(), 
-                                        GetForegroundValue(), 1, 1, 0);
-
-  output = clitk::AutoCrop<ImageType>(output, GetBackgroundValue()); 
-  //  cropFilter = CropFilterType::New();
-  //cropFilter->SetInput(output);
-  //cropFilter->Update();   
-  //output = cropFilter->GetOutput();
-
-  // Final Step -> set output
-  this->SetNthOutput(0, output);
+//--------------------------------------------------------------------
+template <class ImageType>
+void 
+clitk::ExtractMediastinumFilter<ImageType>::
+GenerateData() 
+{
+  this->GraftOutput(output);
+  // Store image filenames into AFDB 
+  GetAFDB()->SetImageFilename("Mediastinum", this->GetOutputMediastinumFilename());  
+  WriteAFDB();
 }
 //--------------------------------------------------------------------