segmentation/clitkExtractLymphStation_5.txx

   1
   2
   3 //--------------------------------------------------------------------
   4 template <class ImageType>
   5 void
   6 clitk::ExtractLymphStationsFilter<ImageType>::
   7 ExtractStation_5_SetDefaultValues()
   8 {
   9 }
  10 //--------------------------------------------------------------------
  11
  12
  13 //--------------------------------------------------------------------
  14 template <class TImageType>
  15 void
  16 clitk::ExtractLymphStationsFilter<TImageType>::
  17 ExtractStation_5() {
  18   if ((!CheckForStation("5")) && (!CheckForStation("5"))) return;
  19
  20   StartNewStep("Stations 5");
  21   StartSubStep();
  22
  23   // Get the current support
  24   StartNewStep("[Station 5] Get the current 5 suppport");
  25   m_ListOfStations["5"] = m_ListOfSupports["S5"];
  26   StopCurrentStep<MaskImageType>(m_ListOfStations["5"]);
  27
  28   // Generic RelativePosition processes
  29   m_ListOfStations["5"] = this->ApplyRelativePositionList("Station_5", m_ListOfStations["5"]);
  30
  31   // Separation Ant/Post -> Like 4SL !
  32   m_Working_Support = m_ListOfStations["5"];
  33   ExtractStation_S4L_S5_Limits_Aorta_LeftPulmonaryArtery(-10);
  34   m_ListOfStations["5"] = m_Working_Support;
  35
  36   // Ant limit
  37   m_Working_Support = m_ListOfStations["5"];
  38   ExtractStation_5_Limits_AscendingAorta_Ant();
  39   m_ListOfStations["5"] = m_Working_Support;
  40
  41   // Keep only one single CCL by slice
  42   StartNewStep("[Station 5] Keep only one CCL by slice");
  43   m_ListOfStations["5"] = SliceBySliceKeepMainCCL<MaskImageType>(m_ListOfStations["5"],
  44                                                                   GetBackgroundValue(),
  45                                                                   GetForegroundValue());
  46
  47   // AutoCrop
  48   m_ListOfStations["5"] = clitk::AutoCrop<MaskImageType>(m_ListOfStations["5"], GetBackgroundValue());
  49   StopCurrentStep<MaskImageType>(m_ListOfStations["5"]);
  50
  51   // Store image filenames into AFDB
  52   writeImage<MaskImageType>(m_ListOfStations["5"], "seg/Station5.mhd");
  53   GetAFDB()->SetImageFilename("Station5", "seg/Station5.mhd");
  54   WriteAFDB();
  55   StopSubStep();
  56
  57 }
  58 //--------------------------------------------------------------------
  59
  60
  61 //--------------------------------------------------------------------
  62 template <class TImageType>
  63 void
  64 clitk::ExtractLymphStationsFilter<TImageType>::
  65 ExtractStation_5_Limits_AscendingAorta_Ant()
  66 {
  67   // ----------------------------------------------------------
  68   StartNewStep("[Station 5] Limits with Ant part of AscendingAorta");
  69
  70   // Get AscendingAorta
  71   MaskImagePointer AscendingAorta = GetAFDB()->template GetImage<MaskImageType>("AscendingAorta");
  72
  73   // Crop and select most Ant points
  74   AscendingAorta =
  75     clitk::ResizeImageLike<MaskImageType>(AscendingAorta, m_Working_Support, GetBackgroundValue());
  76   std::vector<MaskImagePointType> A;
  77   std::vector<MaskImagePointType> B;
  78   clitk::SliceBySliceBuildLineSegmentAccordingToExtremaPosition<MaskImageType>(AscendingAorta,
  79                                                                                GetBackgroundValue(),
  80                                                                                2, 1, true, 0, -1, A, B);
  81   //1 mm margin
  82
  83   // Separate according to AB lines
  84   // clitk::WriteListOfLandmarks<MaskImageType>(A, "A.txt");
  85   // clitk::WriteListOfLandmarks<MaskImageType>(B, "B.txt");
  86   clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(m_Working_Support, A, B,
  87                                                                     GetBackgroundValue(),
  88                                                                     1, 10); // Keep point along axis 1
  89   // End
  90   StopCurrentStep<MaskImageType>(m_Working_Support);
  91 }
  92 //--------------------------------------------------------------------
  93
  94