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   std::vector<MaskSlicePointer> slices;
  71   clitk::ExtractSlices<MaskImageType>(Aorta, 2, slices);
  72   std::vector<MaskImagePointType> points;
  73   for(uint i=0; i<slices.size(); i++) {
  74     // Select most ant CCL
  75     slices[i] = clitk::Labelize<MaskSliceType>(slices[i], GetBackgroundValue(), false, 1);
  76     std::vector<MaskSlicePointType> c;
  77     clitk::ComputeCentroids<MaskSliceType>(slices[i], GetBackgroundValue(), c);
  78     assert(c.size() == 3); // only 2 CCL
  79     typename MaskSliceType::PixelType l;
  80     if (c[1][1] > c[2][1]) { // We will remove the label=1
  81       l = 1;
  82     }
  83     else {
  84       l = 2;// We will remove the label=2
  85     }
  86     slices[i] = clitk::SetBackground<MaskSliceType, MaskSliceType>(slices[i], slices[i], l,
  87                                                                    GetBackgroundValue(), true);
  88
  89     // Detect the most ant point
  90     MaskSlicePointType p;
  91     MaskImagePointType pA;
  92     clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(slices[i], GetBackgroundValue(), 1, true, p);
  93     // Set the X coordinate to the X coordinate of the centroid
  94     if (l==1) p[0] = c[2][0];
  95     else p[0] = c[1][0];
  96
  97     // Convert in 3D and store
  98     clitk::PointsUtils<MaskImageType>::Convert2DTo3D(p, Aorta, i, pA);
  99     points.push_back(pA);
 100   }
 101
 102   // DEBUG
 103   // MaskImagePointer o = clitk::JoinSlices<MaskImageType>(slices, Aorta, 2);
 104   // writeImage<MaskImageType>(o, "o.mhd");
 105   // clitk::WriteListOfLandmarks<MaskImageType>(points, "Ant-Aorta.txt");
 106
 107   // Remove Post/Left to this point
 108   m_Working_Support =
 109     clitk::SliceBySliceSetBackgroundFromPoints<MaskImageType>(m_Working_Support,
 110                                                               GetBackgroundValue(), 2,
 111                                                               points,
 112                                                               true, // Set BG if X greater than point[x], and
 113                                                               true); // if Y greater than point[y]
 114
 115   StopCurrentStep<MaskImageType>(m_Working_Support);
 116   m_ListOfStations["3A"] = m_Working_Support;
 117 }
 118 //--------------------------------------------------------------------
 119
 120
 121 //--------------------------------------------------------------------
 122 template <class ImageType>
 123 void
 124 clitk::ExtractLymphStationsFilter<ImageType>::
 125 ExtractStation_3A_Post_Limits_With_Dilated_Aorta_S6_Support()
 126 {
 127   StartNewStep("[Station 3A] Post limits with dilated Aorta");
 128
 129   // Consider Aorta
 130   MaskImagePointer Aorta = GetAFDB()->template GetImage <MaskImageType>("Aorta");
 131
 132   // Limits the support to S6
 133   MaskImagePointer S6 = m_ListOfSupports["S6"];
 134   Aorta = clitk::ResizeImageLike<MaskImageType>(Aorta, S6, GetBackgroundValue());
 135
 136   // Extend 1cm anteriorly
 137   MaskImagePointType radius; // in mm
 138   radius[0] = 10;
 139   radius[1] = 10;
 140   radius[2] = 0; // required
 141   Aorta = clitk::Dilate<MaskImageType>(Aorta, radius, GetBackgroundValue(), GetForegroundValue(), false);
 142
 143   // Now, insert this image in the AFDB (but do not store on disk)
 144   GetAFDB()->template SetImage<MaskImageType>("Aorta_Dilated_Anteriorly", "bidon",
 145                                               Aorta, false);
 146   /*
 147   // Not Post to
 148   m_Working_Support =
 149     clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support, Aorta, 2,
 150                                                        GetFuzzyThreshold("3A", "Aorta"),
 151                                                        "NotPostTo", true,
 152                                                        Aorta->GetSpacing()[0], false, false);
 153
 154   */
 155
 156
 157   StopCurrentStep<MaskImageType>(m_Working_Support);
 158   m_ListOfStations["3A"] = m_Working_Support;
 159 }
 160 //--------------------------------------------------------------------
 161
 162
 163 //--------------------------------------------------------------------
 164 template <class ImageType>
 165 void
 166 clitk::ExtractLymphStationsFilter<ImageType>::
 167 ExtractStation_3A_AntPost_Superiorly()
 168 {
 169   StartNewStep("[Station 3A] Post limits superiorly");
 170
 171   // Get or compute the binary mask that separate Ant/Post part
 172   // according to vessels
 173   MaskImagePointer binarizedContour = FindAntPostVessels2();
 174   binarizedContour = clitk::ResizeImageLike<MaskImageType>(binarizedContour,
 175                                                            m_Working_Support,
 176                                                            GetBackgroundValue());
 177
 178   // remove from support
 179   typedef clitk::BooleanOperatorLabelImageFilter<MaskImageType> BoolFilterType;
 180   typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
 181   boolFilter->InPlaceOn();
 182   boolFilter->SetInput1(m_Working_Support);
 183   boolFilter->SetInput2(binarizedContour);
 184   boolFilter->SetBackgroundValue1(GetBackgroundValue());
 185   boolFilter->SetBackgroundValue2(GetBackgroundValue());
 186   boolFilter->SetOperationType(BoolFilterType::AndNot);
 187   boolFilter->Update();
 188   m_Working_Support = boolFilter->GetOutput();
 189
 190   StopCurrentStep<MaskImageType>(m_Working_Support);
 191   m_ListOfStations["3A"] = m_Working_Support;
 192 }
 193 //--------------------------------------------------------------------
 194
 195
 196 //--------------------------------------------------------------------
 197 template <class ImageType>
 198 void
 199 clitk::ExtractLymphStationsFilter<ImageType>::
 200 ExtractStation_3A_Remove_Structures()
 201 {
 202   Remove_Structures(" 3A", "Aorta");
 203   Remove_Structures(" 3A", "SubclavianArteryLeft");
 204   Remove_Structures(" 3A", "SubclavianArteryRight");
 205   Remove_Structures(" 3A", "Thyroid");
 206   Remove_Structures(" 3A", "CommonCarotidArteryLeft");
 207   Remove_Structures(" 3A", "CommonCarotidArteryRight");
 208   Remove_Structures(" 3A", "BrachioCephalicArtery");
 209   //  Remove_Structures("3A", "Bones"); --> should be in extractmediastinum
 210   //  Remove_Structures("3A", "BrachioCephalicVein"); ?
 211
 212   StartNewStep("[Station 3A] Remove part of BrachioCephalicVein");
 213   // resize like support, extract slices
 214   // while single CCL -> remove
 215   // when two remove only the most post
 216   MaskImagePointer BrachioCephalicVein =
 217     GetAFDB()->template GetImage <MaskImageType>("BrachioCephalicVein");
 218   BrachioCephalicVein = clitk::ResizeImageLike<MaskImageType>(BrachioCephalicVein,
 219                                                               m_Working_Support,
 220                                                               GetBackgroundValue());
 221   std::vector<MaskSlicePointer> slices;
 222   std::vector<MaskSlicePointer> slices_BCV;
 223   clitk::ExtractSlices<MaskImageType>(m_Working_Support, 2, slices);
 224   clitk::ExtractSlices<MaskImageType>(BrachioCephalicVein, 2, slices_BCV);
 225   for(uint i=0; i<slices.size(); i++) {
 226     // Labelize slices_BCV
 227     slices_BCV[i] = Labelize<MaskSliceType>(slices_BCV[i], 0, true, 1);
 228
 229     // Compute centroids
 230     std::vector<typename MaskSliceType::PointType> centroids;
 231     ComputeCentroids<MaskSliceType>(slices_BCV[i], GetBackgroundValue(), centroids);
 232
 233     // If several centroid, select the one most anterior
 234     if (centroids.size() > 2) {
 235       // Only keep the one most post
 236       typename MaskSliceType::PixelType label;
 237       if (centroids[1][1] > centroids[2][1]) {
 238         label = 2;
 239       }
 240       else {
 241         label = 1;
 242       }
 243       // "remove" the CCL
 244       slices_BCV[i] = clitk::SetBackground<MaskSliceType, MaskSliceType>(slices_BCV[i],
 245                                                                          slices_BCV[i],
 246                                                                          label,
 247                                                                          GetBackgroundValue(),
 248                                                                          true);
 249     }
 250
 251     // Remove from the support
 252     clitk::AndNot<MaskSliceType>(slices[i], slices_BCV[i], GetBackgroundValue());
 253   }
 254
 255   // Joint
 256   m_Working_Support = clitk::JoinSlices<MaskImageType>(slices, m_Working_Support, 2);
 257
 258   StopCurrentStep<MaskImageType>(m_Working_Support);
 259   m_ListOfStations["3A"] = m_Working_Support;
 260 }
 261 //--------------------------------------------------------------------
 262
 263