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_4R() {
  18   if (!CheckForStation("4R")) return;
  19   StartNewStep("Stations 4R");
  20   StartSubStep();
  21
  22   // Get the current support
  23   StartNewStep("[Station 4R] Get the current 4RL suppport");
  24   m_ListOfStations["4R"] = m_ListOfSupports["S4R"];
  25   StopCurrentStep<MaskImageType>(m_ListOfStations["4R"]);
  26
  27   // Generic RelativePosition processes
  28   m_ListOfStations["4R"] = this->ApplyRelativePositionList("Station_4R", m_ListOfStations["4R"]);
  29
  30   // Store image filenames into AFDB
  31   WriteImageStation("4R");
  32   StopSubStep();
  33   ComputeOverlapWithRef("4R");
  34 }
  35 //--------------------------------------------------------------------
  36
  37
  38 //--------------------------------------------------------------------
  39 template <class TImageType>
  40 void
  41 clitk::ExtractLymphStationsFilter<TImageType>::
  42 ExtractStation_4L() {
  43   if (!CheckForStation("4L")) return;
  44   StartNewStep("Stations 4L");
  45   StartSubStep();
  46
  47   // Get the current support
  48   StartNewStep("[Station 4L] Get the current 4RL suppport");
  49   m_ListOfStations["4L"] = m_ListOfSupports["S4L"];
  50   StopCurrentStep<MaskImageType>(m_ListOfStations["4L"]);
  51
  52   // Generic RelativePosition processes
  53   m_ListOfStations["4L"] = this->ApplyRelativePositionList("Station_4L", m_ListOfStations["4L"]);
  54
  55   // Separation Ant/Post
  56   m_Working_Support = m_ListOfStations["4L"];
  57   ExtractStation_S4L_S5_Limits_Aorta_LeftPulmonaryArtery(10);
  58   m_ListOfStations["4L"] = m_Working_Support;
  59
  60   // Keep only one single CCL by slice
  61   StartNewStep("[Station 4L] Keep only one CCL by slice");
  62   m_ListOfStations["4L"] = SliceBySliceKeepMainCCL<MaskImageType>(m_ListOfStations["4L"],
  63                                                                   GetBackgroundValue(),
  64                                                                   GetForegroundValue());
  65   StopCurrentStep<MaskImageType>(m_ListOfStations["4L"]);
  66
  67   // Store image filenames into AFDB
  68   WriteImageStation("4L");
  69   StopSubStep();
  70   ComputeOverlapWithRef("4L");
  71 }
  72 //--------------------------------------------------------------------
  73
  74
  75 //--------------------------------------------------------------------
  76 template <class TImageType>
  77 void
  78 clitk::ExtractLymphStationsFilter<TImageType>::
  79 ExtractStation_S4L_S5_Limits_Aorta_LeftPulmonaryArtery(int KeepPoint)
  80 {
  81   // ----------------------------------------------------------
  82   StartNewStep("[Station 4L] Limits between Asc and Desc Aorta, and with LeftPulmonaryArtery ");
  83
  84   // Separate Aorta into DescendingAorta AscendingAorta
  85   MaskImagePointer AscendingAorta = GetAFDB()->template GetImage<MaskImageType>("AscendingAorta");
  86   MaskImagePointer DescendingAorta = GetAFDB()->template GetImage<MaskImageType>("DescendingAorta");
  87
  88   // Crop like support (inferiorly)
  89   m_Working_Support = clitk::AutoCrop<MaskImageType>(m_Working_Support, GetBackgroundValue());
  90   AscendingAorta =
  91     clitk::ResizeImageLike<MaskImageType>(AscendingAorta, m_Working_Support, GetBackgroundValue());
  92   DescendingAorta =
  93     clitk::ResizeImageLike<MaskImageType>(DescendingAorta, m_Working_Support, GetBackgroundValue());
  94
  95   // Crop superior part (when AscendingAorta and DescendingAorta join)
  96   MaskImagePointType p;
  97   clitk::FindExtremaPointInAGivenDirection<MaskImageType>(AscendingAorta,
  98                                                           GetBackgroundValue(), 2, false, p);
  99   double max = p[2]+AscendingAorta->GetSpacing()[2];
 100   AscendingAorta =
 101     clitk::CropImageRemoveGreaterThan<MaskImageType>(AscendingAorta, 2, max, false, GetBackgroundValue());
 102   DescendingAorta =
 103     clitk::CropImageRemoveGreaterThan<MaskImageType>(DescendingAorta, 2, max, false, GetBackgroundValue());
 104
 105   // Crop inferior part, where LeftPulmonaryArtery start
 106   MaskImagePointer AscendingAortaCopy = clitk::Clone<MaskImageType>(AscendingAorta);
 107   MaskImagePointer LeftPulmonaryArtery = GetAFDB()->template GetImage<MaskImageType>("LeftPulmonaryArtery");
 108   clitk::FindExtremaPointInAGivenDirection<MaskImageType>(LeftPulmonaryArtery,
 109                                                           GetBackgroundValue(), 2, false, p);
 110   max = p[2]+LeftPulmonaryArtery->GetSpacing()[2];
 111   AscendingAorta =
 112     clitk::CropImageRemoveLowerThan<MaskImageType>(AscendingAorta, 2, max, false, GetBackgroundValue());
 113   DescendingAorta =
 114     clitk::CropImageRemoveLowerThan<MaskImageType>(DescendingAorta, 2, max, false, GetBackgroundValue());
 115
 116   // Find closest points
 117   std::vector<MaskImagePointType> A;
 118   std::vector<MaskImagePointType> B;
 119   clitk::SliceBySliceBuildLineSegmentAccordingToMinimalDistanceBetweenStructures<MaskImageType>(AscendingAorta,
 120                                                                                                 DescendingAorta,
 121                                                                                                 GetBackgroundValue(),
 122                                                                                                 2, A, B);
 123   // Separate according to AB lines
 124   // clitk::WriteListOfLandmarks<MaskImageType>(A, "A.txt");
 125   // clitk::WriteListOfLandmarks<MaskImageType>(B, "B.txt");
 126   clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(m_Working_Support, A, B,
 127                                                                     GetBackgroundValue(),
 128                                                                     1, KeepPoint); // Keep point along axis 1
 129
 130   // Now, same principle between AscendingAorta and LeftPulmonaryArtery
 131   AscendingAorta =
 132     clitk::ResizeImageLike<MaskImageType>(AscendingAortaCopy, m_Working_Support, GetBackgroundValue());
 133   LeftPulmonaryArtery =
 134     clitk::ResizeImageLike<MaskImageType>(LeftPulmonaryArtery, m_Working_Support, GetBackgroundValue());
 135   AscendingAorta =
 136     clitk::CropImageRemoveGreaterThan<MaskImageType>(AscendingAorta, 2, max, false, GetBackgroundValue());
 137   LeftPulmonaryArtery =
 138     clitk::CropImageRemoveGreaterThan<MaskImageType>(LeftPulmonaryArtery, 2, max, false, GetBackgroundValue());
 139   A.clear();
 140   B.clear();
 141   clitk::SliceBySliceBuildLineSegmentAccordingToMinimalDistanceBetweenStructures<MaskImageType>(AscendingAorta,
 142                                                                                                 LeftPulmonaryArtery,
 143                                                                                                 GetBackgroundValue(),
 144                                                                                                 2, A, B);
 145   clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(m_Working_Support, A, B,
 146                                                                     GetBackgroundValue(),
 147                                                                     1, KeepPoint); // Keep point along axis 1
 148
 149   // AutoCrop
 150   m_Working_Support = clitk::AutoCrop<MaskImageType>(m_Working_Support, GetBackgroundValue());
 151
 152   // End
 153   StopCurrentStep<MaskImageType>(m_Working_Support);
 154 }
 155 //--------------------------------------------------------------------
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