Moved from repository clitk to clitk.private/tests_dav

[clitk.git] / segmentation / clitkExtractLymphStation_1RL.txx

diff --git a/segmentation/clitkExtractLymphStation_1RL.txx b/segmentation/clitkExtractLymphStation_1RL.txx
deleted file mode 100644 (file)
index 6758ab8..0000000
--- a/segmentation/clitkExtractLymphStation_1RL.txx
+++ /dev/null
@@ -1,185 +0,0 @@
-
-
-// vtk
-#include <vtkAppendPolyData.h>
-#include <vtkPolyDataWriter.h>
-#include <vtkCellArray.h>
-
-// clitk
-#include "clitkMeshToBinaryImageFilter.h"
-
-// itk
-#include <itkImageDuplicator.h>
-
-//--------------------------------------------------------------------
-template <class ImageType>
-void 
-clitk::ExtractLymphStationsFilter<ImageType>::
-ExtractStation_1RL_SetDefaultValues()
-{
-  
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class TImageType>
-void 
-clitk::ExtractLymphStationsFilter<TImageType>::
-ExtractStation_1RL()
-{
-  if ((!CheckForStation("1R")) && (!CheckForStation("1L"))) return;
-
-  StartNewStep("Stations 1RL");
-  StartSubStep(); 
-
-  // Get the current support 
-  StartNewStep("[Station 1RL] Get the current 1RL suppport");
-  m_ListOfStations["1R"] = m_ListOfSupports["S1R"];
-  m_ListOfStations["1L"] = m_ListOfSupports["S1L"];
-  StopCurrentStep<MaskImageType>(m_ListOfStations["1R"]);
-    
-  // Specific processes
-  ExtractStation_1RL_Ant_Limits();
-  ExtractStation_1RL_Post_Limits();
-  m_Working_Support = m_ListOfStations["1R"];
-  Remove_Structures(" 1R", "ScaleneMuscleAnt");
-  Remove_Structures(" 1R", "RightCommonCarotidArtery");  
-  m_Working_Support = m_ListOfStations["1L"];
-  Remove_Structures(" 1L", "ScaleneMuscleAnt");
-  Remove_Structures(" 1L", "LeftCommonCarotidArtery");  
- 
-  // Generic RelativePosition processes
-  m_ListOfStations["1R"] = this->ApplyRelativePositionList("Station_1R", m_ListOfStations["1R"]);
-  m_ListOfStations["1L"] = this->ApplyRelativePositionList("Station_1L", m_ListOfStations["1L"]);
-
-  // Store image filenames into AFDB 
-  writeImage<MaskImageType>(m_ListOfStations["1R"], "seg/Station1R.mhd");
-  writeImage<MaskImageType>(m_ListOfStations["1L"], "seg/Station1L.mhd");
-  GetAFDB()->SetImageFilename("Station1R", "seg/Station1R.mhd"); 
-  GetAFDB()->SetImageFilename("Station1L", "seg/Station1L.mhd"); 
-  WriteAFDB(); 
-  StopSubStep();
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class ImageType>
-void 
-clitk::ExtractLymphStationsFilter<ImageType>::
-ExtractStation_1RL_Ant_Limits()
-{
-  // -----------------------------------------------------
-  StartNewStep("[Station 1RL] anterior limits with Trachea and Thyroid");
-  
-  /*
-    The idea here it to consider the most anterior points int the
-    Trachea or the Thyroid and cut all parts anterior to it. This is
-    an heuristic, not written explicitely in the articles.
-  */
-
-  MaskImagePointer Trachea = GetAFDB()->template GetImage<MaskImageType>("Trachea");
-  MaskImagePointer Thyroid = GetAFDB()->template GetImage<MaskImageType>("Thyroid");
-  MaskImagePointer S1R = m_ListOfStations["1R"];
-  MaskImagePointer S1L = m_ListOfStations["1L"];
-  MaskImagePointer support = m_ListOfSupports["S1RL"];
- 
-  // Resize like S1R. Warning: for Thyroid, only Right part is thus
-  // taken into account
-  Trachea = clitk::ResizeImageLike<MaskImageType>(Trachea, S1R, GetBackgroundValue());
-  Thyroid = clitk::ResizeImageLike<MaskImageType>(Thyroid, S1R, GetBackgroundValue());
-
-  // Search for most Ant point, slice by slice, between Trachea and Thyroid
-  std::vector<MaskSlicePointer> Trachea_slices;
-  clitk::ExtractSlices<MaskImageType>(Trachea, 2, Trachea_slices);
-  std::vector<MaskSlicePointer> Thyroid_slices;
-  clitk::ExtractSlices<MaskImageType>(Thyroid, 2, Thyroid_slices);
-  std::vector<typename ImageType::PointType> A;
-  std::vector<typename ImageType::PointType> B;
-  for(uint i=0; i<Trachea_slices.size(); i++) {
-    MaskSlicePointType p;
-    MaskSlicePointType q;
-    FindExtremaPointInAGivenDirection<MaskSliceType>(Trachea_slices[i], 
-                                                     GetBackgroundValue(), 
-                                                     1, true, p);
-    FindExtremaPointInAGivenDirection<MaskSliceType>(Thyroid_slices[i], 
-                                                     GetBackgroundValue(), 
-                                                     1, true, q);
-    if (q[1] < p[1]) p = q; // Now p is the most ant.
-    // Add a little margin, 3mm
-    p[1] -= 3;
-    // Convert in 3D
-    ImagePointType x; //dummy
-    A.push_back(x);
-    B.push_back(x);
-    clitk::PointsUtils<MaskImageType>::Convert2DTo3D(p, Trachea, i, A[i]);
-    p[0] += 10;    
-    clitk::PointsUtils<MaskImageType>::Convert2DTo3D(p, Trachea, i, B[i]);
-  }  
-
-  // Remove anterior to this line (keep +10 offset)
-  clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(S1R, A, B, 
-                                                                    GetBackgroundValue(), 1, +10);
-  m_ListOfStations["1R"] = S1R;
-
-  clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(S1L, A, B, 
-                                                                    GetBackgroundValue(), 1, +10);
-  StopCurrentStep<MaskImageType>(S1L);
-  m_ListOfStations["1L"] = S1L;
-}
-//--------------------------------------------------------------------
-
-
-//--------------------------------------------------------------------
-template <class ImageType>
-void 
-clitk::ExtractLymphStationsFilter<ImageType>::
-ExtractStation_1RL_Post_Limits()
-{
-  // -----------------------------------------------------
-  StartNewStep("[Station 1RL] Posterior limits with VertebralArtery");
-  
-  MaskImagePointer VertebralArtery = GetAFDB()->template GetImage<MaskImageType>("VertebralArtery");
-  MaskImagePointer S1R = m_ListOfStations["1R"];
-  MaskImagePointer S1L = m_ListOfStations["1L"];
-
-  // Resize like S1R.
-  VertebralArtery = clitk::ResizeImageLike<MaskImageType>(VertebralArtery, S1R, GetBackgroundValue());
-
-  // Search for most Ant point
-  std::vector<MaskSlicePointer> VertebralArtery_slices;
-  clitk::ExtractSlices<MaskImageType>(VertebralArtery, 2, VertebralArtery_slices);
-  std::vector<typename ImageType::PointType> A;
-  std::vector<typename ImageType::PointType> B;
-  for(uint i=0; i<VertebralArtery_slices.size(); i++) {
-    MaskSlicePointType p;
-    FindExtremaPointInAGivenDirection<MaskSliceType>(VertebralArtery_slices[i], 
-                                                     GetBackgroundValue(), 
-                                                     1, false, p);
-    // Add a little margin ? No.
-    //p[1] += 0;
-    //DD(p);
-    // Convert in 3D
-    ImagePointType x; //dummy
-    A.push_back(x);
-    B.push_back(x);
-    clitk::PointsUtils<MaskImageType>::Convert2DTo3D(p, VertebralArtery, i, A[i]);
-    p[0] += 10;    
-    clitk::PointsUtils<MaskImageType>::Convert2DTo3D(p, VertebralArtery, i, B[i]);
-  }  
-
-  // Remove anterior to this line (keep -10 offset)
-  clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(S1R, A, B, 
-                                                                    GetBackgroundValue(), 1, -10);
-  m_ListOfStations["1R"] = S1R;
-
-  // Remove anterior to this line (keep -10 offset)
-  clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(S1L, A, B, 
-                                                                    GetBackgroundValue(), 1, -10);
-  StopCurrentStep<MaskImageType>(S1L);
-  m_ListOfStations["1L"] = S1L;
-}
-//--------------------------------------------------------------------
-
-