segmentation/clitkExtractLymphStation_3A.txx

   1
   2 //--------------------------------------------------------------------
   3 template <class ImageType>
   4 void
   5 clitk::ExtractLymphStationsFilter<ImageType>::
   6 ExtractStation_3A_SetDefaultValues()
   7 {
   8 }
   9 //--------------------------------------------------------------------
  10
  11
  12 //--------------------------------------------------------------------
  13 template <class TImageType>
  14 void
  15 clitk::ExtractLymphStationsFilter<TImageType>::
  16 ExtractStation_3A()
  17 {
  18   if (!CheckForStation("3A")) return;
  19
  20   StartNewStep("Station 3A");
  21   StartSubStep();
  22
  23   // Get the current support
  24   StartNewStep("[Station 3A] Get the current 3A suppport");
  25   m_Working_Support = m_ListOfSupports["S3A"];
  26   m_ListOfStations["3A"] = m_Working_Support;
  27   StopCurrentStep<MaskImageType>(m_Working_Support);
  28
  29   ExtractStation_3A_Post_Left_Limits_With_Aorta_S5_Support();
  30   ExtractStation_3A_Post_Limits_With_Dilated_Aorta_S6_Support();
  31   ExtractStation_3A_AntPost_Superiorly();
  32   ExtractStation_3A_Remove_Structures();
  33
  34   // Generic RelativePosition processes
  35   m_ListOfStations["3A"] = this->ApplyRelativePositionList("Station_3A", m_ListOfStations["3A"]);
  36
  37   // Keep a single CCL
  38   m_ListOfStations["3A"] =
  39     clitk::SliceBySliceKeepMainCCL<MaskImageType>(m_ListOfStations["3A"],
  40                                                   GetBackgroundValue(),
  41                                                   GetForegroundValue());
  42
  43   // Store image filenames into AFDB
  44   writeImage<MaskImageType>(m_ListOfStations["3A"], "seg/Station3A.mhd");
  45   GetAFDB()->SetImageFilename("Station3A", "seg/Station3A.mhd");
  46   WriteAFDB();
  47   StopSubStep();
  48 }
  49 //--------------------------------------------------------------------
  50
  51
  52
  53 //--------------------------------------------------------------------
  54 template <class ImageType>
  55 void
  56 clitk::ExtractLymphStationsFilter<ImageType>::
  57 ExtractStation_3A_Post_Left_Limits_With_Aorta_S5_Support()
  58 {
  59   StartNewStep("[Station 3A] Post limits in S5 support according to Aorta");
  60
  61    // Consider Aorta, remove Left/Post part ; only around S5
  62   // Get S5 support and Aorta
  63   MaskImagePointer S5 = m_ListOfSupports["S5"];
  64   MaskImagePointer Aorta = GetAFDB()->template GetImage <MaskImageType>("Aorta");
  65   Aorta = clitk::ResizeImageLike<MaskImageType>(Aorta, S5, GetBackgroundValue());
  66
  67   // Inferiorly, Aorta has two CCL that merge into a single one when
  68   // S6 appears. Loop on Aorta slices, select the most ant one, detect
  69   // the most ant point.
  70
  71
  72
  73   // ====> TO BE CHANGED USING AscendingAorta and DescendingAorta
  74
  75
  76
  77   std::vector<MaskSlicePointer> slices;
  78   clitk::ExtractSlices<MaskImageType>(Aorta, 2, slices);
  79   std::vector<MaskImagePointType> points;
  80   for(uint i=0; i<slices.size(); i++) {
  81     // Select most ant CCL
  82     slices[i] = clitk::Labelize<MaskSliceType>(slices[i], GetBackgroundValue(), false, 1);
  83     std::vector<MaskSlicePointType> c;
  84     clitk::ComputeCentroids<MaskSliceType>(slices[i], GetBackgroundValue(), c);
  85     assert(c.size() == 3); // only 2 CCL
  86     typename MaskSliceType::PixelType l;
  87     if (c[1][1] > c[2][1]) { // We will remove the label=1
  88       l = 1;
  89     }
  90     else {
  91       l = 2;// We will remove the label=2
  92     }
  93     slices[i] = clitk::SetBackground<MaskSliceType, MaskSliceType>(slices[i], slices[i], l,
  94                                                                    GetBackgroundValue(), true);
  95
  96     // Detect the most ant point
  97     MaskSlicePointType p;
  98     MaskImagePointType pA;
  99     clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(slices[i], GetBackgroundValue(), 1, true, p);
 100     // Set the X coordinate to the X coordinate of the centroid
 101     if (l==1) p[0] = c[2][0];
 102     else p[0] = c[1][0];
 103
 104     // Convert in 3D and store
 105     clitk::PointsUtils<MaskImageType>::Convert2DTo3D(p, Aorta, i, pA);
 106     points.push_back(pA);
 107   }
 108
 109   // DEBUG
 110   // MaskImagePointer o = clitk::JoinSlices<MaskImageType>(slices, Aorta, 2);
 111   // writeImage<MaskImageType>(o, "o.mhd");
 112   // clitk::WriteListOfLandmarks<MaskImageType>(points, "Ant-Aorta.txt");
 113
 114   // Remove Post/Left to this point
 115   m_Working_Support =
 116     clitk::SliceBySliceSetBackgroundFromPoints<MaskImageType>(m_Working_Support,
 117                                                               GetBackgroundValue(), 2,
 118                                                               points,
 119                                                               true, // Set BG if X greater than point[x], and
 120                                                               true); // if Y greater than point[y]
 121
 122   StopCurrentStep<MaskImageType>(m_Working_Support);
 123   m_ListOfStations["3A"] = m_Working_Support;
 124 }
 125 //--------------------------------------------------------------------
 126
 127
 128 //--------------------------------------------------------------------
 129 template <class ImageType>
 130 void
 131 clitk::ExtractLymphStationsFilter<ImageType>::
 132 ExtractStation_3A_Post_Limits_With_Dilated_Aorta_S6_Support()
 133 {
 134   StartNewStep("[Station 3A] Post limits with dilated Aorta");
 135
 136   // Consider Aorta
 137   MaskImagePointer Aorta = GetAFDB()->template GetImage <MaskImageType>("Aorta");
 138
 139   // Limits the support to S6
 140   MaskImagePointer S6 = m_ListOfSupports["S6"];
 141   Aorta = clitk::ResizeImageLike<MaskImageType>(Aorta, S6, GetBackgroundValue());
 142
 143   // Extend 1cm anteriorly
 144   MaskImagePointType radius; // in mm
 145   radius[0] = 10;
 146   radius[1] = 10;
 147   radius[2] = 0; // required
 148   Aorta = clitk::Dilate<MaskImageType>(Aorta, radius, GetBackgroundValue(), GetForegroundValue(), false);
 149
 150   // Now, insert this image in the AFDB (but do not store on disk)
 151   GetAFDB()->template SetImage<MaskImageType>("Aorta_Dilated_Anteriorly", "bidon",
 152                                               Aorta, false);
 153   /*
 154   // Not Post to
 155   m_Working_Support =
 156     clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support, Aorta, 2,
 157                                                        GetFuzzyThreshold("3A", "Aorta"),
 158                                                        "NotPostTo", true,
 159                                                        Aorta->GetSpacing()[0], false, false);
 160
 161   */
 162
 163
 164   StopCurrentStep<MaskImageType>(m_Working_Support);
 165   m_ListOfStations["3A"] = m_Working_Support;
 166 }
 167 //--------------------------------------------------------------------
 168
 169
 170 //--------------------------------------------------------------------
 171 template <class ImageType>
 172 void
 173 clitk::ExtractLymphStationsFilter<ImageType>::
 174 ExtractStation_3A_AntPost_Superiorly()
 175 {
 176   StartNewStep("[Station 3A] Post limits superiorly");
 177
 178   // Get or compute the binary mask that separate Ant/Post part
 179   // according to vessels
 180   MaskImagePointer binarizedContour = FindAntPostVessels2();
 181   binarizedContour = clitk::ResizeImageLike<MaskImageType>(binarizedContour,
 182                                                            m_Working_Support,
 183                                                            GetBackgroundValue());
 184
 185   // remove from support
 186   typedef clitk::BooleanOperatorLabelImageFilter<MaskImageType> BoolFilterType;
 187   typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
 188   boolFilter->InPlaceOn();
 189   boolFilter->SetInput1(m_Working_Support);
 190   boolFilter->SetInput2(binarizedContour);
 191   boolFilter->SetBackgroundValue1(GetBackgroundValue());
 192   boolFilter->SetBackgroundValue2(GetBackgroundValue());
 193   boolFilter->SetOperationType(BoolFilterType::AndNot);
 194   boolFilter->Update();
 195   m_Working_Support = boolFilter->GetOutput();
 196
 197   StopCurrentStep<MaskImageType>(m_Working_Support);
 198   m_ListOfStations["3A"] = m_Working_Support;
 199 }
 200 //--------------------------------------------------------------------
 201
 202
 203 //--------------------------------------------------------------------
 204 template <class ImageType>
 205 void
 206 clitk::ExtractLymphStationsFilter<ImageType>::
 207 ExtractStation_3A_Remove_Structures()
 208 {
 209   Remove_Structures(" 3A", "Aorta");
 210   Remove_Structures(" 3A", "SubclavianArteryLeft");
 211   Remove_Structures(" 3A", "SubclavianArteryRight");
 212   Remove_Structures(" 3A", "Thyroid");
 213   Remove_Structures(" 3A", "CommonCarotidArteryLeft");
 214   Remove_Structures(" 3A", "CommonCarotidArteryRight");
 215   Remove_Structures(" 3A", "BrachioCephalicArtery");
 216   //  Remove_Structures("3A", "Bones"); --> should be in extractmediastinum
 217   //  Remove_Structures("3A", "BrachioCephalicVein"); ?
 218
 219   StartNewStep("[Station 3A] Remove part of BrachioCephalicVein");
 220   // resize like support, extract slices
 221   // while single CCL -> remove
 222   // when two remove only the most post
 223   MaskImagePointer BrachioCephalicVein =
 224     GetAFDB()->template GetImage <MaskImageType>("BrachioCephalicVein");
 225   BrachioCephalicVein = clitk::ResizeImageLike<MaskImageType>(BrachioCephalicVein,
 226                                                               m_Working_Support,
 227                                                               GetBackgroundValue());
 228   std::vector<MaskSlicePointer> slices;
 229   std::vector<MaskSlicePointer> slices_BCV;
 230   clitk::ExtractSlices<MaskImageType>(m_Working_Support, 2, slices);
 231   clitk::ExtractSlices<MaskImageType>(BrachioCephalicVein, 2, slices_BCV);
 232   for(uint i=0; i<slices.size(); i++) {
 233     // Labelize slices_BCV
 234     slices_BCV[i] = Labelize<MaskSliceType>(slices_BCV[i], 0, true, 1);
 235
 236     // Compute centroids
 237     std::vector<typename MaskSliceType::PointType> centroids;
 238     ComputeCentroids<MaskSliceType>(slices_BCV[i], GetBackgroundValue(), centroids);
 239
 240     // If several centroid, select the one most anterior
 241     if (centroids.size() > 2) {
 242       // Only keep the one most post
 243       typename MaskSliceType::PixelType label;
 244       if (centroids[1][1] > centroids[2][1]) {
 245         label = 2;
 246       }
 247       else {
 248         label = 1;
 249       }
 250       // "remove" the CCL
 251       slices_BCV[i] = clitk::SetBackground<MaskSliceType, MaskSliceType>(slices_BCV[i],
 252                                                                          slices_BCV[i],
 253                                                                          label,
 254                                                                          GetBackgroundValue(),
 255                                                                          true);
 256     }
 257
 258     // Remove from the support
 259     clitk::AndNot<MaskSliceType>(slices[i], slices_BCV[i], GetBackgroundValue());
 260   }
 261
 262   // Joint
 263   m_Working_Support = clitk::JoinSlices<MaskImageType>(slices, m_Working_Support, 2);
 264
 265   StopCurrentStep<MaskImageType>(m_Working_Support);
 266   m_ListOfStations["3A"] = m_Working_Support;
 267 }
 268 //--------------------------------------------------------------------
 269
 270