segmentation/clitkExtractLymphStation_1RL.txx

   1
   2
   3 // vtk
   4 #include <vtkAppendPolyData.h>
   5 #include <vtkPolyDataWriter.h>
   6 #include <vtkCellArray.h>
   7
   8 // clitk
   9 #include "clitkMeshToBinaryImageFilter.h"
  10
  11 // itk
  12 #include <itkImageDuplicator.h>
  13
  14 //--------------------------------------------------------------------
  15 template <class ImageType>
  16 void
  17 clitk::ExtractLymphStationsFilter<ImageType>::
  18 ExtractStation_1RL_SetDefaultValues()
  19 {
  20
  21 }
  22 //--------------------------------------------------------------------
  23
  24
  25 //--------------------------------------------------------------------
  26 template <class TImageType>
  27 void
  28 clitk::ExtractLymphStationsFilter<TImageType>::
  29 ExtractStation_1RL()
  30 {
  31   if ((!CheckForStation("1R")) && (!CheckForStation("1L"))) return;
  32
  33   StartNewStep("Stations 1RL");
  34   StartSubStep();
  35
  36   // Get the current support
  37   StartNewStep("[Station 1RL] Get the current 1RL suppport");
  38   m_ListOfStations["1R"] = m_ListOfSupports["S1R"];
  39   m_ListOfStations["1L"] = m_ListOfSupports["S1L"];
  40   StopCurrentStep<MaskImageType>(m_ListOfStations["1R"]);
  41
  42   // Specific processes
  43   ExtractStation_1RL_Ant_Limits();
  44   ExtractStation_1RL_Post_Limits();
  45   m_Working_Support = m_ListOfStations["1R"];
  46   Remove_Structures(" 1R", "ScaleneMuscleAnt");
  47   Remove_Structures(" 1R", "RightCommonCarotidArtery");
  48   m_Working_Support = m_ListOfStations["1L"];
  49   Remove_Structures(" 1L", "ScaleneMuscleAnt");
  50   Remove_Structures(" 1L", "LeftCommonCarotidArtery");
  51
  52   // Generic RelativePosition processes
  53   m_ListOfStations["1R"] = this->ApplyRelativePositionList("Station_1R", m_ListOfStations["1R"]);
  54   m_ListOfStations["1L"] = this->ApplyRelativePositionList("Station_1L", m_ListOfStations["1L"]);
  55
  56   // Store image filenames into AFDB
  57   writeImage<MaskImageType>(m_ListOfStations["1R"], "seg/Station1R.mhd");
  58   writeImage<MaskImageType>(m_ListOfStations["1L"], "seg/Station1L.mhd");
  59   GetAFDB()->SetImageFilename("Station1R", "seg/Station1R.mhd");
  60   GetAFDB()->SetImageFilename("Station1L", "seg/Station1L.mhd");
  61   WriteAFDB();
  62   StopSubStep();
  63 }
  64 //--------------------------------------------------------------------
  65
  66
  67 //--------------------------------------------------------------------
  68 template <class ImageType>
  69 void
  70 clitk::ExtractLymphStationsFilter<ImageType>::
  71 ExtractStation_1RL_Ant_Limits()
  72 {
  73   // -----------------------------------------------------
  74   StartNewStep("[Station 1RL] anterior limits with Trachea and Thyroid");
  75
  76   /*
  77     The idea here it to consider the most anterior points int the
  78     Trachea or the Thyroid and cut all parts anterior to it. This is
  79     an heuristic, not written explicitely in the articles.
  80   */
  81
  82   MaskImagePointer Trachea = GetAFDB()->template GetImage<MaskImageType>("Trachea");
  83   MaskImagePointer Thyroid = GetAFDB()->template GetImage<MaskImageType>("Thyroid");
  84   MaskImagePointer S1R = m_ListOfStations["1R"];
  85   MaskImagePointer S1L = m_ListOfStations["1L"];
  86   MaskImagePointer support = m_ListOfSupports["S1RL"];
  87
  88   // Resize like S1R. Warning: for Thyroid, only Right part is thus
  89   // taken into account
  90   Trachea = clitk::ResizeImageLike<MaskImageType>(Trachea, S1R, GetBackgroundValue());
  91   Thyroid = clitk::ResizeImageLike<MaskImageType>(Thyroid, S1R, GetBackgroundValue());
  92
  93   // Search for most Ant point, slice by slice, between Trachea and Thyroid
  94   std::vector<MaskSlicePointer> Trachea_slices;
  95   clitk::ExtractSlices<MaskImageType>(Trachea, 2, Trachea_slices);
  96   std::vector<MaskSlicePointer> Thyroid_slices;
  97   clitk::ExtractSlices<MaskImageType>(Thyroid, 2, Thyroid_slices);
  98   std::vector<typename ImageType::PointType> A;
  99   std::vector<typename ImageType::PointType> B;
 100   for(uint i=0; i<Trachea_slices.size(); i++) {
 101     MaskSlicePointType p;
 102     MaskSlicePointType q;
 103     FindExtremaPointInAGivenDirection<MaskSliceType>(Trachea_slices[i],
 104                                                      GetBackgroundValue(),
 105                                                      1, true, p);
 106     FindExtremaPointInAGivenDirection<MaskSliceType>(Thyroid_slices[i],
 107                                                      GetBackgroundValue(),
 108                                                      1, true, q);
 109     if (q[1] < p[1]) p = q; // Now p is the most ant.
 110     // Add a little margin, 3mm
 111     p[1] -= 3;
 112     // Convert in 3D
 113     ImagePointType x; //dummy
 114     A.push_back(x);
 115     B.push_back(x);
 116     clitk::PointsUtils<MaskImageType>::Convert2DTo3D(p, Trachea, i, A[i]);
 117     p[0] += 10;
 118     clitk::PointsUtils<MaskImageType>::Convert2DTo3D(p, Trachea, i, B[i]);
 119   }
 120
 121   // Remove anterior to this line (keep +10 offset)
 122   clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(S1R, A, B,
 123                                                                     GetBackgroundValue(), 1, +10);
 124   m_ListOfStations["1R"] = S1R;
 125
 126   clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(S1L, A, B,
 127                                                                     GetBackgroundValue(), 1, +10);
 128   StopCurrentStep<MaskImageType>(S1L);
 129   m_ListOfStations["1L"] = S1L;
 130 }
 131 //--------------------------------------------------------------------
 132
 133
 134 //--------------------------------------------------------------------
 135 template <class ImageType>
 136 void
 137 clitk::ExtractLymphStationsFilter<ImageType>::
 138 ExtractStation_1RL_Post_Limits()
 139 {
 140   // -----------------------------------------------------
 141   StartNewStep("[Station 1RL] Posterior limits with VertebralArtery");
 142
 143   MaskImagePointer VertebralArtery = GetAFDB()->template GetImage<MaskImageType>("VertebralArtery");
 144   MaskImagePointer S1R = m_ListOfStations["1R"];
 145   MaskImagePointer S1L = m_ListOfStations["1L"];
 146
 147   // Resize like S1R.
 148   VertebralArtery = clitk::ResizeImageLike<MaskImageType>(VertebralArtery, S1R, GetBackgroundValue());
 149
 150   // Search for most Ant point
 151   std::vector<MaskSlicePointer> VertebralArtery_slices;
 152   clitk::ExtractSlices<MaskImageType>(VertebralArtery, 2, VertebralArtery_slices);
 153   std::vector<typename ImageType::PointType> A;
 154   std::vector<typename ImageType::PointType> B;
 155   for(uint i=0; i<VertebralArtery_slices.size(); i++) {
 156     MaskSlicePointType p;
 157     FindExtremaPointInAGivenDirection<MaskSliceType>(VertebralArtery_slices[i],
 158                                                      GetBackgroundValue(),
 159                                                      1, false, p);
 160     // Add a little margin ? No.
 161     //p[1] += 0;
 162     //DD(p);
 163     // Convert in 3D
 164     ImagePointType x; //dummy
 165     A.push_back(x);
 166     B.push_back(x);
 167     clitk::PointsUtils<MaskImageType>::Convert2DTo3D(p, VertebralArtery, i, A[i]);
 168     p[0] += 10;
 169     clitk::PointsUtils<MaskImageType>::Convert2DTo3D(p, VertebralArtery, i, B[i]);
 170   }
 171
 172   // Remove anterior to this line (keep -10 offset)
 173   clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(S1R, A, B,
 174                                                                     GetBackgroundValue(), 1, -10);
 175   m_ListOfStations["1R"] = S1R;
 176
 177   // Remove anterior to this line (keep -10 offset)
 178   clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(S1L, A, B,
 179                                                                     GetBackgroundValue(), 1, -10);
 180   StopCurrentStep<MaskImageType>(S1L);
 181   m_ListOfStations["1L"] = S1L;
 182 }
 183 //--------------------------------------------------------------------
 184
 185