segmentation/clitkExtractLymphStation_4RL.txx

   1
   2
   3 //--------------------------------------------------------------------
   4 template <class ImageType>
   5 void
   6 clitk::ExtractLymphStationsFilter<ImageType>::
   7 ExtractStation_4RL_SetDefaultValues()
   8 {
   9 }
  10 //--------------------------------------------------------------------
  11
  12
  13 //--------------------------------------------------------------------
  14 template <class TImageType>
  15 void
  16 clitk::ExtractLymphStationsFilter<TImageType>::
  17 ExtractStation_4RL() {
  18   if ((!CheckForStation("4R")) && (!CheckForStation("4L"))) return;
  19
  20   StartNewStep("Stations 4RL");
  21   StartSubStep();
  22
  23   // Get the current support
  24   StartNewStep("[Station 4RL] Get the current 4RL suppport");
  25   m_ListOfStations["4R"] = m_ListOfSupports["S4R"];
  26   m_ListOfStations["4L"] = m_ListOfSupports["S4L"];
  27   StopCurrentStep<MaskImageType>(m_ListOfStations["4R"]);
  28
  29   // Generic RelativePosition processes
  30   m_ListOfStations["4R"] = this->ApplyRelativePositionList("Station_4R", m_ListOfStations["4R"]);
  31   m_ListOfStations["4L"] = this->ApplyRelativePositionList("Station_4L", m_ListOfStations["4L"]);
  32
  33   // Separation Ant/Post
  34   m_Working_Support = m_ListOfStations["4L"];
  35   ExtractStation_S4L_S5_Limits_Aorta_LeftPulmonaryArtery(10);
  36   m_ListOfStations["4L"] = m_Working_Support;
  37
  38   // Keep only one single CCL by slice
  39   StartNewStep("[Station 4L] Keep only one CCL by slice");
  40   m_ListOfStations["4L"] = SliceBySliceKeepMainCCL<MaskImageType>(m_ListOfStations["4L"],
  41                                                                   GetBackgroundValue(),
  42                                                                   GetForegroundValue());
  43   StopCurrentStep<MaskImageType>(m_ListOfStations["4L"]);
  44
  45   // Store image filenames into AFDB
  46   writeImage<MaskImageType>(m_ListOfStations["4R"], "seg/Station4R.mhd");
  47   writeImage<MaskImageType>(m_ListOfStations["4L"], "seg/Station4L.mhd");
  48   GetAFDB()->SetImageFilename("Station4R", "seg/Station4R.mhd");
  49   GetAFDB()->SetImageFilename("Station4L", "seg/Station4L.mhd");
  50   WriteAFDB();
  51   StopSubStep();
  52
  53 }
  54 //--------------------------------------------------------------------
  55
  56
  57 //--------------------------------------------------------------------
  58 template <class TImageType>
  59 void
  60 clitk::ExtractLymphStationsFilter<TImageType>::
  61 ExtractStation_S4L_S5_Limits_Aorta_LeftPulmonaryArtery(int KeepPoint)
  62 {
  63   // ----------------------------------------------------------
  64   StartNewStep("[Station 4L] Limits between Asc and Desc Aorta, and with LeftPulmonaryArtery ");
  65
  66   // Separate Aorta into DescendingAorta AscendingAorta
  67   MaskImagePointer AscendingAorta = GetAFDB()->template GetImage<MaskImageType>("AscendingAorta");
  68   MaskImagePointer DescendingAorta = GetAFDB()->template GetImage<MaskImageType>("DescendingAorta");
  69
  70   // Crop like support (inferiorly)
  71   m_Working_Support = clitk::AutoCrop<MaskImageType>(m_Working_Support, GetBackgroundValue());
  72   AscendingAorta =
  73     clitk::ResizeImageLike<MaskImageType>(AscendingAorta, m_Working_Support, GetBackgroundValue());
  74   DescendingAorta =
  75     clitk::ResizeImageLike<MaskImageType>(DescendingAorta, m_Working_Support, GetBackgroundValue());
  76
  77   // Crop superior part (when AscendingAorta and DescendingAorta join)
  78   MaskImagePointType p;
  79   clitk::FindExtremaPointInAGivenDirection<MaskImageType>(AscendingAorta,
  80                                                           GetBackgroundValue(), 2, false, p);
  81   double max = p[2]+AscendingAorta->GetSpacing()[2];
  82   AscendingAorta =
  83     clitk::CropImageRemoveGreaterThan<MaskImageType>(AscendingAorta, 2, max, false, GetBackgroundValue());
  84   DescendingAorta =
  85     clitk::CropImageRemoveGreaterThan<MaskImageType>(DescendingAorta, 2, max, false, GetBackgroundValue());
  86
  87   // Crop inferior part, where LeftPulmonaryArtery start
  88   MaskImagePointer AscendingAortaCopy = clitk::Clone<MaskImageType>(AscendingAorta);
  89   MaskImagePointer LeftPulmonaryArtery = GetAFDB()->template GetImage<MaskImageType>("LeftPulmonaryArtery");
  90   clitk::FindExtremaPointInAGivenDirection<MaskImageType>(LeftPulmonaryArtery,
  91                                                           GetBackgroundValue(), 2, false, p);
  92   max = p[2]+LeftPulmonaryArtery->GetSpacing()[2];
  93   AscendingAorta =
  94     clitk::CropImageRemoveLowerThan<MaskImageType>(AscendingAorta, 2, max, false, GetBackgroundValue());
  95   DescendingAorta =
  96     clitk::CropImageRemoveLowerThan<MaskImageType>(DescendingAorta, 2, max, false, GetBackgroundValue());
  97
  98   // Find closest points
  99   std::vector<MaskImagePointType> A;
 100   std::vector<MaskImagePointType> B;
 101   clitk::SliceBySliceBuildLineSegmentAccordingToMinimalDistanceBetweenStructures<MaskImageType>(AscendingAorta,
 102                                                                                                 DescendingAorta,
 103                                                                                                 GetBackgroundValue(),
 104                                                                                                 2, A, B);
 105   // Separate according to AB lines
 106   // clitk::WriteListOfLandmarks<MaskImageType>(A, "A.txt");
 107   // clitk::WriteListOfLandmarks<MaskImageType>(B, "B.txt");
 108   clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(m_Working_Support, A, B,
 109                                                                     GetBackgroundValue(),
 110                                                                     1, KeepPoint); // Keep point along axis 1
 111
 112   // Now, same principle between AscendingAorta and LeftPulmonaryArtery
 113   AscendingAorta =
 114     clitk::ResizeImageLike<MaskImageType>(AscendingAortaCopy, m_Working_Support, GetBackgroundValue());
 115   LeftPulmonaryArtery =
 116     clitk::ResizeImageLike<MaskImageType>(LeftPulmonaryArtery, m_Working_Support, GetBackgroundValue());
 117   AscendingAorta =
 118     clitk::CropImageRemoveGreaterThan<MaskImageType>(AscendingAorta, 2, max, false, GetBackgroundValue());
 119   LeftPulmonaryArtery =
 120     clitk::CropImageRemoveGreaterThan<MaskImageType>(LeftPulmonaryArtery, 2, max, false, GetBackgroundValue());
 121   A.clear();
 122   B.clear();
 123   clitk::SliceBySliceBuildLineSegmentAccordingToMinimalDistanceBetweenStructures<MaskImageType>(AscendingAorta,
 124                                                                                                 LeftPulmonaryArtery,
 125                                                                                                 GetBackgroundValue(),
 126                                                                                                 2, A, B);
 127   clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(m_Working_Support, A, B,
 128                                                                     GetBackgroundValue(),
 129                                                                     1, KeepPoint); // Keep point along axis 1
 130
 131   // AutoCrop
 132   m_Working_Support = clitk::AutoCrop<MaskImageType>(m_Working_Support, GetBackgroundValue());
 133
 134   // End
 135   StopCurrentStep<MaskImageType>(m_Working_Support);
 136 }
 137 //--------------------------------------------------------------------
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