segmentation/clitkExtractLymphStation_2RL.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_2RL_SetDefaultValues()
  19 {
  20 }
  21 //--------------------------------------------------------------------
  22
  23
  24 //--------------------------------------------------------------------
  25 template <class TImageType>
  26 void
  27 clitk::ExtractLymphStationsFilter<TImageType>::
  28 ExtractStation_2RL()
  29 {
  30   if ((!CheckForStation("2R")) && (!CheckForStation("2L"))) return;
  31
  32   StartNewStep("Stations 2RL");
  33   StartSubStep();
  34
  35   // Get the current support
  36   StartNewStep("[Station 2RL] Get the current 2RL suppport");
  37   m_ListOfStations["2R"] = m_ListOfSupports["S2R"];
  38   m_ListOfStations["2L"] = m_ListOfSupports["S2L"];
  39   StopCurrentStep<MaskImageType>(m_ListOfStations["2R"]);
  40
  41   // Do the same limits for R & L
  42   m_Working_Support = m_ListOfStations["2R"];
  43   ExtractStation_2RL_Ant_Limits("2R");
  44   ExtractStation_2RL_Remove_Structures(" 2R");
  45   m_ListOfStations["2R"] = m_Working_Support;
  46
  47   m_Working_Support = m_ListOfStations["2L"];
  48   ExtractStation_2RL_Ant_Limits("2L");
  49   ExtractStation_2RL_Remove_Structures(" 2L");
  50   m_ListOfStations["2L"] = m_Working_Support;
  51
  52   // Remove superior part to BrachioCephalicVein (used then by RelPos)
  53   ExtractStation_2RL_Cut_BrachioCephalicVein_superiorly_when_it_split();
  54
  55   // Generic RelativePosition processes
  56   m_ListOfStations["2R"] = this->ApplyRelativePositionList("Station_2R", m_ListOfStations["2R"]);
  57   m_ListOfStations["2L"] = this->ApplyRelativePositionList("Station_2L", m_ListOfStations["2L"]);
  58
  59   // Store image filenames into AFDB
  60   writeImage<MaskImageType>(m_ListOfStations["2R"], "seg/Station2R.mhd");
  61   writeImage<MaskImageType>(m_ListOfStations["2L"], "seg/Station2L.mhd");
  62   GetAFDB()->SetImageFilename("Station2R", "seg/Station2R.mhd");
  63   GetAFDB()->SetImageFilename("Station2L", "seg/Station2L.mhd");
  64   WriteAFDB();
  65   StopSubStep();
  66 }
  67 //--------------------------------------------------------------------
  68
  69
  70 //--------------------------------------------------------------------
  71 template <class ImageType>
  72 void
  73 clitk::ExtractLymphStationsFilter<ImageType>::
  74 ExtractStation_2RL_Ant_Limits(std::string s)
  75 {
  76   // -----------------------------------------------------
  77   StartNewStep("[Station "+s+"] Ant limits with vessels centroids");
  78
  79   // WARNING, as I used "And" after, empty slice in binarizedContour
  80   // lead to remove part of the support, although we want to keep
  81   // unchanged. So we decide to ResizeImageLike but pad with
  82   // ForegroundValue instead of BG
  83
  84   // Get or compute the binary mask that separate Ant/Post part
  85   // according to vessels
  86   MaskImagePointer binarizedContour = FindAntPostVessels2();
  87   binarizedContour = clitk::ResizeImageLike<MaskImageType>(binarizedContour,
  88                                                            m_Working_Support,
  89                                                            GetForegroundValue());
  90   // remove from support
  91   typedef clitk::BooleanOperatorLabelImageFilter<MaskImageType> BoolFilterType;
  92   typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
  93   boolFilter->InPlaceOn();
  94   boolFilter->SetInput1(m_Working_Support);
  95   boolFilter->SetInput2(binarizedContour);
  96   boolFilter->SetBackgroundValue1(GetBackgroundValue());
  97   boolFilter->SetBackgroundValue2(GetBackgroundValue());
  98   boolFilter->SetOperationType(BoolFilterType::And);
  99   boolFilter->Update();
 100   m_Working_Support = boolFilter->GetOutput();
 101
 102   // End
 103   StopCurrentStep<MaskImageType>(m_Working_Support);
 104 }
 105 //--------------------------------------------------------------------
 106
 107
 108 //--------------------------------------------------------------------
 109 template <class ImageType>
 110 void
 111 clitk::ExtractLymphStationsFilter<ImageType>::
 112 ExtractStation_2RL_Cut_BrachioCephalicVein_superiorly_when_it_split()
 113 {
 114   // -----------------------------------------------------
 115   StartNewStep("[Station 2RL] Cut BrachioCephalicVein superiorly (when it split)");
 116
 117   // Get BrachioCephalicVein
 118   MaskImagePointer BrachioCephalicVein = GetAFDB()->template GetImage<MaskImageType>("BrachioCephalicVein");
 119
 120   // Remove the part superior to the slice where BrachioCephalicVein
 121   // divide in two CCL
 122   std::vector<MaskSlicePointer> BCV_slices;
 123   clitk::ExtractSlices<MaskImageType>(BrachioCephalicVein, 2, BCV_slices);
 124   bool stop = false;
 125   uint i=0;
 126   while (!stop) {
 127     // Count the number of CCL
 128     int nb;
 129     clitk::LabelizeAndCountNumberOfObjects<MaskSliceType>(BCV_slices[i], GetBackgroundValue(), true, 1, nb);
 130     if (nb>1) stop = true;
 131     i++;
 132   }
 133   // Convert slice into coordinate
 134   MaskImagePointType p;
 135   MaskImageIndexType index;
 136   index[0] = index[1] = 0;
 137   index[2] = i;
 138   BrachioCephalicVein->TransformIndexToPhysicalPoint(index, p);
 139   BrachioCephalicVein =
 140     clitk::CropImageRemoveGreaterThan<MaskImageType>(BrachioCephalicVein, 2,
 141                                                      p[2], true,
 142                                                      GetBackgroundValue());
 143
 144   // Now, insert this image in the AFDB (but do not store on disk)
 145   GetAFDB()->template SetImage<MaskImageType>("BrachioCephalicVein_ForS2RL", "bidon",
 146                                               BrachioCephalicVein, false);
 147   // End
 148   StopCurrentStep<MaskImageType>(BrachioCephalicVein);
 149 }
 150 //--------------------------------------------------------------------
 151
 152
 153 //--------------------------------------------------------------------
 154 // Build a vtk mesh from a list of slice number/closed-contours
 155 template <class ImageType>
 156 vtkSmartPointer<vtkPolyData>
 157 clitk::ExtractLymphStationsFilter<ImageType>::
 158 Build3DMeshFrom2DContour(const std::vector<ImagePointType> & points)
 159 {
 160   // create a contour, polydata.
 161   vtkSmartPointer<vtkPolyData> mesh = vtkSmartPointer<vtkPolyData>::New();
 162   mesh->Allocate(); //for cell structures
 163   mesh->SetPoints(vtkPoints::New());
 164   vtkIdType ids[2];
 165   int point_number = points.size();
 166   for (unsigned int i=0; i<points.size(); i++) {
 167     mesh->GetPoints()->InsertNextPoint(points[i][0],points[i][1],points[i][2]);
 168     ids[0]=i;
 169     ids[1]=(ids[0]+1)%point_number; //0-1,1-2,...,n-1-0
 170     mesh->GetLines()->InsertNextCell(2,ids);
 171   }
 172   // Return
 173   return mesh;
 174 }
 175 //--------------------------------------------------------------------
 176
 177
 178 //--------------------------------------------------------------------
 179 template <class ImageType>
 180 void
 181 clitk::ExtractLymphStationsFilter<ImageType>::
 182 ExtractStation_2RL_Remove_Structures(std::string s)
 183 {
 184   // m_Working_Support must be set
 185   Remove_Structures(s, "BrachioCephalicVein");
 186   Remove_Structures(s, "BrachioCephalicArtery");
 187   Remove_Structures(s, "LeftCommonCarotidArtery");
 188   Remove_Structures(s, "RightCommonCarotidArtery");
 189   Remove_Structures(s, "LeftSubclavianArtery");
 190   Remove_Structures(s, "RightSubclavianArtery");
 191   Remove_Structures(s, "Thyroid");
 192   Remove_Structures(s, "Aorta");
 193 }
 194 //--------------------------------------------------------------------
 195
 196