X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLymphStationsFilter.txx;h=aab78d85c01730c9778c4be1cf81d99c28726728;hb=5cc64cb817d78d671eb20d219cc19f9ad5b1e5c1;hp=0bcb447d2a90804f1643dd28a17e7b418760e698;hpb=e008d74b0ecdc4ca2eaae8c429901a78f9ef5c31;p=clitk.git

diff --git a/segmentation/clitkExtractLymphStationsFilter.txx b/segmentation/clitkExtractLymphStationsFilter.txx
index 0bcb447..aab78d8 100644
--- a/segmentation/clitkExtractLymphStationsFilter.txx
+++ b/segmentation/clitkExtractLymphStationsFilter.txx
@@ -23,17 +23,18 @@
 #include "clitkCommon.h"
 #include "clitkExtractLymphStationsFilter.h"
 #include "clitkAddRelativePositionConstraintToLabelImageFilter.h"
-#include "clitkSegmentationFunctions.h"
+#include "clitkSegmentationUtils.h"
 #include "clitkAutoCropFilter.h"
-#include "clitkSegmentationFunctions.h"
+#include "clitkSegmentationUtils.h"
+#include "clitkSliceBySliceRelativePositionFilter.h"
 
 // itk
-#include <deque>
 #include <itkStatisticsLabelMapFilter.h>
 #include <itkLabelImageToStatisticsLabelMapFilter.h>
 #include <itkRegionOfInterestImageFilter.h>
 #include <itkBinaryThresholdImageFilter.h>
 #include <itkImageSliceConstIteratorWithIndex.h>
+#include <itkBinaryThinningImageFilter.h>
 
 // itk ENST
 #include "RelativePositionPropImageFilter.h"
@@ -118,7 +119,7 @@ GenerateOutputInformation() {
   // ----------------------------------------------------------------
   // Superior limit = carena
   // Inferior limit = origine middle lobe bronchus
-  StartNewStep("Inf/Sup limits with carena/bronchus");
+  StartNewStep("Inf/Sup mediastinum limits with carena/bronchus");
   ImageRegionType region = m_mediastinum->GetLargestPossibleRegion(); DD(region);
   ImageSizeType size = region.GetSize();
   ImageIndexType index = region.GetIndex();
@@ -143,7 +144,7 @@ GenerateOutputInformation() {
   // ----------------------------------------------------------------
   // ----------------------------------------------------------------
   // Separate trachea in two CCL
-  StartNewStep("Separate trachea");
+  StartNewStep("Separate trachea under carena");
   // DD(region);
   ImageRegionType trachea_region = m_trachea->GetLargestPossibleRegion();
   for(int i=0; i<3; i++) {
@@ -175,8 +176,7 @@ GenerateOutputInformation() {
 
   // Labelize and consider two main labels
   m_working_trachea = Labelize<ImageType>(m_working_trachea, 0, true, 1);
-  StopCurrentStep<ImageType>(m_working_trachea);
-  
+
   // Detect wich label is at Left
   typedef itk::ImageSliceConstIteratorWithIndex<ImageType> SliceIteratorType;
   SliceIteratorType iter(m_working_trachea, m_working_trachea->GetLargestPossibleRegion());
@@ -185,6 +185,7 @@ GenerateOutputInformation() {
   iter.GoToBegin();
   bool stop = false;
   ImagePixelType leftLabel;
+  ImagePixelType rightLabel;
   while (!stop) {
     if (iter.Get() != m_BackgroundValueTrachea) {
       //     DD(iter.GetIndex());
@@ -194,52 +195,65 @@ GenerateOutputInformation() {
     }
     ++iter;
   }
+  if (leftLabel == 1) rightLabel = 2;
+  else rightLabel = 1;
   DD((int)leftLabel);
+  DD((int)rightLabel);  
+
+  // End step
+  StopCurrentStep<ImageType>(m_working_trachea);
   
-  // Relative position 
-  StartNewStep("Left/Right limits with trachea");
+  //-----------------------------------------------------
+  /*  DD("TEST Skeleton");
+  typedef itk::BinaryThinningImageFilter<ImageType, ImageType> SkeletonFilterType;
+  typename SkeletonFilterType::Pointer skeletonFilter = SkeletonFilterType::New();
+  skeletonFilter->SetInput(m_working_trachea);
+  skeletonFilter->Update();
+  writeImage<ImageType>(skeletonFilter->GetOutput(), "skel.mhd");
+  writeImage<ImageType>(skeletonFilter->GetThinning(), "skel2.mhd");  
+  */
 
-  // Select LeftLabel (set label 1 to 0)
-  ImagePointer temp = SetBackground<ImageType, ImageType>(m_working_trachea, m_working_trachea, 1, 0);
+  //-----------------------------------------------------
+  StartNewStep("Left limits with bronchus (slice by slice)");  
+  // Select LeftLabel (set right label to 0)
+  ImagePointer temp = SetBackground<ImageType, ImageType>(m_working_trachea, m_working_trachea, rightLabel, 0);
   writeImage<ImageType>(temp, "temp1.mhd");
 
-  // Left relative position
-  typedef clitk::AddRelativePositionConstraintToLabelImageFilter<TImageType> RelPosFilterType;
-  typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New();
-  relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
-  relPosFilter->VerboseStepOff();
-  relPosFilter->WriteStepOff();
-  relPosFilter->SetInput(m_working_image); 
-  relPosFilter->SetInputObject(temp); 
-  relPosFilter->SetOrientationType(RelPosFilterType::RightTo);
-  relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
-  relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold1());
-  relPosFilter->Update();
-  m_working_image = relPosFilter->GetOutput();
-
-  // Select RightLabel (set label 2 to 0)
-  temp = SetBackground<ImageType, ImageType>(m_working_trachea, m_working_trachea, 2, 0);
-  writeImage<ImageType>(temp, "temp2.mhd");
-
-  // Left relative position
-  relPosFilter = RelPosFilterType::New();
-  relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
-  relPosFilter->VerboseStepOn();
-  relPosFilter->WriteStepOn();
-  relPosFilter->SetInput(m_working_image); 
-  relPosFilter->SetInputObject(temp); 
-  relPosFilter->SetOrientationType(RelPosFilterType::LeftTo);
-  relPosFilter->SetIntermediateSpacing(GetIntermediateSpacing());
-  relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold1());
-  relPosFilter->Update();
-  m_working_image = relPosFilter->GetOutput();
+  typedef clitk::SliceBySliceRelativePositionFilter<ImageType> SliceRelPosFilterType;
+  typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
+  sliceRelPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
+  sliceRelPosFilter->VerboseStepOn();
+  sliceRelPosFilter->WriteStepOn();
+  sliceRelPosFilter->SetInput(m_working_image);
+  sliceRelPosFilter->SetInputObject(temp);
+  sliceRelPosFilter->SetDirection(2);
+  sliceRelPosFilter->SetFuzzyThreshold(0.5);
+  sliceRelPosFilter->SetOrientationType(SliceRelPosFilterType::RelPosFilterType::RightTo);
+  sliceRelPosFilter->Update();
+  m_working_image = sliceRelPosFilter->GetOutput();
+  writeImage<ImageType>(m_working_image, "afterslicebyslice.mhd");
 
 
   //-----------------------------------------------------
-  //  StartNewStep("Left/Right limits with trachea (slice by slice");
-  //  typedef SliceBySliceImageFilter<ImageType, ImageType, 
+  StartNewStep("Right limits with bronchus (slice by slice)");
+  // Select LeftLabel (set right label to 0)
+  temp = SetBackground<ImageType, ImageType>(m_working_trachea, m_working_trachea, leftLabel, 0);
+  writeImage<ImageType>(temp, "temp2.mhd");
+
+  sliceRelPosFilter = SliceRelPosFilterType::New();
+  sliceRelPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
+  sliceRelPosFilter->VerboseStepOn();
+  sliceRelPosFilter->WriteStepOn();
+  sliceRelPosFilter->SetInput(m_working_image);
+  sliceRelPosFilter->SetInputObject(temp);
+  sliceRelPosFilter->SetDirection(2);
+  sliceRelPosFilter->SetFuzzyThreshold(0.5);
+  sliceRelPosFilter->SetOrientationType(SliceRelPosFilterType::RelPosFilterType::LeftTo);
+  sliceRelPosFilter->Update();
+  m_working_image = sliceRelPosFilter->GetOutput();
+  writeImage<ImageType>(m_working_image, "afterslicebyslice.mhd");
+
 
-  
   DD("end");
   m_output = m_working_image;
   StopCurrentStep<ImageType>(m_output);