segmentation/clitkExtractLymphStation_3A.txx

   1
   2 //--------------------------------------------------------------------
   3 template <class ImageType>
   4 void
   5 clitk::ExtractLymphStationsFilter<ImageType>::
   6 ExtractStation_3A_SetDefaultValues()
   7 {
   8   SetFuzzyThreshold("3A", "Sternum", 0.5);
   9   SetFuzzyThreshold("3A", "SubclavianArtery", 0.5);
  10 }
  11 //--------------------------------------------------------------------
  12
  13
  14 //--------------------------------------------------------------------
  15 template <class TImageType>
  16 void
  17 clitk::ExtractLymphStationsFilter<TImageType>::
  18 ExtractStation_3A()
  19 {
  20   if (!CheckForStation("3A")) return;
  21
  22   StartNewStep("Station 3A");
  23   StartSubStep();
  24
  25   // Get the current support
  26   StartNewStep("[Station 3A] Get the current 3A suppport");
  27   m_Working_Support = m_ListOfSupports["S3A"];
  28   m_ListOfStations["3A"] = m_Working_Support;
  29   StopCurrentStep<MaskImageType>(m_Working_Support);
  30
  31   ExtractStation_3A_AntPost_S5();
  32   ExtractStation_3A_AntPost_S6();
  33   ExtractStation_3A_AntPost_Superiorly();
  34   ExtractStation_3A_Remove_Structures();
  35
  36   Remove_Structures("3A", "Aorta");
  37   Remove_Structures("3A", "SubclavianArteryLeft");
  38   Remove_Structures("3A", "SubclavianArteryRight");
  39   Remove_Structures("3A", "Thyroid");
  40   Remove_Structures("3A", "CommonCarotidArteryLeft");
  41   Remove_Structures("3A", "CommonCarotidArteryRight");
  42   Remove_Structures("3A", "BrachioCephalicArtery");
  43
  44   ExtractStation_3A_PostToBones();
  45
  46   // Keep a single CCL
  47   m_ListOfStations["3A"] =
  48     clitk::SliceBySliceKeepMainCCL<MaskImageType>(m_ListOfStations["3A"],
  49                                                   GetBackgroundValue(),
  50                                                   GetForegroundValue());
  51
  52   // Store image filenames into AFDB
  53   writeImage<MaskImageType>(m_ListOfStations["3A"], "seg/Station3A.mhd");
  54   GetAFDB()->SetImageFilename("Station3A", "seg/Station3A.mhd");
  55   WriteAFDB();
  56   StopSubStep();
  57 }
  58 //--------------------------------------------------------------------
  59
  60
  61
  62 //--------------------------------------------------------------------
  63 template <class ImageType>
  64 void
  65 clitk::ExtractLymphStationsFilter<ImageType>::
  66 ExtractStation_3A_AntPost_S5()
  67 {
  68   StartNewStep("[Station 3A] Post limits around S5");
  69
  70   // First remove post to SVC
  71   MaskImagePointer SVC = GetAFDB()->template GetImage <MaskImageType>("SVC");
  72
  73   // Trial in 3D -> difficulties superiorly. Stay slice by slice.
  74   // Slice by slice not post to SVC. Use initial spacing
  75   m_Working_Support =
  76     clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support, SVC, 2,
  77                                                        GetFuzzyThreshold("3A", "SVC"),
  78                                                        "NotPostTo", true,
  79                                                        SVC->GetSpacing()[0], false, false);
  80
  81   // Consider Aorta, remove Left/Post part ; only around S5
  82   // Get S5 support and Aorta
  83   MaskImagePointer S5 = m_ListOfSupports["S5"];
  84   MaskImagePointer Aorta = GetAFDB()->template GetImage <MaskImageType>("Aorta");
  85   Aorta = clitk::ResizeImageLike<MaskImageType>(Aorta, S5, GetBackgroundValue());
  86
  87   // Inferiorly, Aorta has two CCL that merge into a single one when
  88   // S6 appears. Loop on Aorta slices, select the most ant one, detect
  89   // the most ant point.
  90   std::vector<MaskSlicePointer> slices;
  91   clitk::ExtractSlices<MaskImageType>(Aorta, 2, slices);
  92   std::vector<MaskImagePointType> points;
  93   for(uint i=0; i<slices.size(); i++) {
  94     // Select most ant CCL
  95     slices[i] = clitk::Labelize<MaskSliceType>(slices[i], GetBackgroundValue(), false, 1);
  96     std::vector<MaskSlicePointType> c;
  97     clitk::ComputeCentroids<MaskSliceType>(slices[i], GetBackgroundValue(), c);
  98     assert(c.size() == 3); // only 2 CCL
  99     typename MaskSliceType::PixelType l;
 100     if (c[1][1] > c[2][1]) { // We will remove the label=1
 101       l = 1;
 102     }
 103     else {
 104       l = 2;// We will remove the label=2
 105     }
 106     slices[i] = clitk::SetBackground<MaskSliceType, MaskSliceType>(slices[i], slices[i], l,
 107                                                                    GetBackgroundValue(), true);
 108
 109     // Detect the most ant point
 110     MaskSlicePointType p;
 111     MaskImagePointType pA;
 112     clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(slices[i], GetBackgroundValue(), 1, true, p);
 113     // Set the X coordinate to the X coordinate of the centroid
 114     if (l==1) p[0] = c[2][0];
 115     else p[0] = c[1][0];
 116
 117     // Convert in 3D and store
 118     clitk::PointsUtils<MaskImageType>::Convert2DTo3D(p, Aorta, i, pA);
 119     points.push_back(pA);
 120   }
 121
 122   // DEBUG
 123   // MaskImagePointer o = clitk::JoinSlices<MaskImageType>(slices, Aorta, 2);
 124   // writeImage<MaskImageType>(o, "o.mhd");
 125   // clitk::WriteListOfLandmarks<MaskImageType>(points, "Ant-Aorta.txt");
 126
 127   // Remove Post/Left to this point
 128   m_Working_Support =
 129     clitk::SliceBySliceSetBackgroundFromPoints<MaskImageType>(m_Working_Support,
 130                                                               GetBackgroundValue(), 2,
 131                                                               points,
 132                                                               true, // Set BG if X greater than point[x], and
 133                                                               true); // if Y greater than point[y]
 134
 135   StopCurrentStep<MaskImageType>(m_Working_Support);
 136   m_ListOfStations["3A"] = m_Working_Support;
 137 }
 138 //--------------------------------------------------------------------
 139
 140
 141 //--------------------------------------------------------------------
 142 template <class ImageType>
 143 void
 144 clitk::ExtractLymphStationsFilter<ImageType>::
 145 ExtractStation_3A_AntPost_S6()
 146 {
 147   StartNewStep("[Station 3A] Post limits around S6");
 148
 149   // Consider Aorta
 150   MaskImagePointer Aorta = GetAFDB()->template GetImage <MaskImageType>("Aorta");
 151
 152   // Limits the support to S6
 153   MaskImagePointer S6 = m_ListOfSupports["S6"];
 154   Aorta = clitk::ResizeImageLike<MaskImageType>(Aorta, S6, GetBackgroundValue());
 155
 156   // Extend 1cm anteriorly
 157   MaskImagePointType radius; // in mm
 158   radius[0] = 10;
 159   radius[1] = 10;
 160   radius[2] = 0; // required
 161   Aorta = clitk::Dilate<MaskImageType>(Aorta, radius, GetBackgroundValue(), GetForegroundValue(), false);
 162
 163   // Not Post to
 164   m_Working_Support =
 165     clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support, Aorta, 2,
 166                                                        GetFuzzyThreshold("3A", "Aorta"),
 167                                                        "NotPostTo", true,
 168                                                        Aorta->GetSpacing()[0], false, false);
 169
 170   StopCurrentStep<MaskImageType>(m_Working_Support);
 171   m_ListOfStations["3A"] = m_Working_Support;
 172 }
 173 //--------------------------------------------------------------------
 174
 175
 176 //--------------------------------------------------------------------
 177 template <class ImageType>
 178 void
 179 clitk::ExtractLymphStationsFilter<ImageType>::
 180 ExtractStation_3A_AntPost_Superiorly()
 181 {
 182   StartNewStep("[Station 3A] Post limits superiorly");
 183
 184   /*
 185  MaskImagePointer BrachioCephalicVein = GetAFDB()->template GetImage <MaskImageType>("BrachioCephalicVein");
 186  MaskImagePointer BrachioCephalicArtery = GetAFDB()->template GetImage <MaskImageType>("BrachioCephalicArtery");
 187  MaskImagePointer CommonCarotidArteryLeft = GetAFDB()->template GetImage <MaskImageType>("CommonCarotidArteryLeft");
 188  MaskImagePointer CommonCarotidArteryRight = GetAFDB()->template GetImage <MaskImageType>("CommonCarotidArteryRight");
 189  MaskImagePointer SubclavianArteryLeft = GetAFDB()->template GetImage <MaskImageType>("SubclavianArteryLeft");
 190  MaskImagePointer SubclavianArteryRight = GetAFDB()->template GetImage <MaskImageType>("SubclavianArteryRight");
 191
 192   // Not Post to
 193 #define RP(STRUCTURE)                                                   \
 194  m_Working_Support =                                                    \
 195    clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support, STRUCTURE, 2, \
 196                                                       0.5,              \
 197                                                       "NotPostTo", true, \
 198                                                       STRUCTURE->GetSpacing()[0], false, false);
 199
 200  // RP(BrachioCephalicVein);
 201  RP(BrachioCephalicArtery);
 202  RP(CommonCarotidArteryRight);
 203  RP(CommonCarotidArteryLeft);
 204  RP(SubclavianArteryRight);
 205  RP(SubclavianArteryLeft);
 206   */
 207
 208   // Get or compute the binary mask that separate Ant/Post part
 209   // according to vessels
 210   MaskImagePointer binarizedContour = FindAntPostVessels2();
 211   binarizedContour = clitk::ResizeImageLike<MaskImageType>(binarizedContour,
 212                                                            m_Working_Support,
 213                                                            GetBackgroundValue());
 214
 215   // remove from support
 216   typedef clitk::BooleanOperatorLabelImageFilter<MaskImageType> BoolFilterType;
 217   typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
 218   boolFilter->InPlaceOn();
 219   boolFilter->SetInput1(m_Working_Support);
 220   boolFilter->SetInput2(binarizedContour);
 221   boolFilter->SetBackgroundValue1(GetBackgroundValue());
 222   boolFilter->SetBackgroundValue2(GetBackgroundValue());
 223   boolFilter->SetOperationType(BoolFilterType::AndNot);
 224   boolFilter->Update();
 225   m_Working_Support = boolFilter->GetOutput();
 226
 227   StopCurrentStep<MaskImageType>(m_Working_Support);
 228   m_ListOfStations["3A"] = m_Working_Support;
 229 }
 230 //--------------------------------------------------------------------
 231
 232
 233 //--------------------------------------------------------------------
 234 template <class ImageType>
 235 void
 236 clitk::ExtractLymphStationsFilter<ImageType>::
 237 ExtractStation_3A_Remove_Structures()
 238 {
 239   Remove_Structures("3A", "Aorta");
 240   Remove_Structures("3A", "SubclavianArteryLeft");
 241   Remove_Structures("3A", "SubclavianArteryRight");
 242   Remove_Structures("3A", "Thyroid");
 243   Remove_Structures("3A", "CommonCarotidArteryLeft");
 244   Remove_Structures("3A", "CommonCarotidArteryRight");
 245   Remove_Structures("3A", "BrachioCephalicArtery");
 246   //  Remove_Structures("3A", "BrachioCephalicVein"); ?
 247
 248   StartNewStep("[Station 3A] Remove part of BrachioCephalicVein");
 249   // resize like support, extract slices
 250   // while single CCL -> remove
 251   // when two remove only the most post
 252   MaskImagePointer BrachioCephalicVein =
 253     GetAFDB()->template GetImage <MaskImageType>("BrachioCephalicVein");
 254   BrachioCephalicVein = clitk::ResizeImageLike<MaskImageType>(BrachioCephalicVein,
 255                                                               m_Working_Support,
 256                                                               GetBackgroundValue());
 257   std::vector<MaskSlicePointer> slices;
 258   std::vector<MaskSlicePointer> slices_BCV;
 259   clitk::ExtractSlices<MaskImageType>(m_Working_Support, 2, slices);
 260   clitk::ExtractSlices<MaskImageType>(BrachioCephalicVein, 2, slices_BCV);
 261   for(uint i=0; i<slices.size(); i++) {
 262     // Labelize slices_BCV
 263     slices_BCV[i] = Labelize<MaskSliceType>(slices_BCV[i], 0, true, 1);
 264
 265     // Compute centroids
 266     std::vector<typename MaskSliceType::PointType> centroids;
 267     ComputeCentroids<MaskSliceType>(slices_BCV[i], GetBackgroundValue(), centroids);
 268
 269     // If several centroid, select the one most anterior
 270     if (centroids.size() > 2) {
 271       // Only keep the one most post
 272       typename MaskSliceType::PixelType label;
 273       if (centroids[1][1] > centroids[2][1]) {
 274         label = 2;
 275       }
 276       else {
 277         label = 1;
 278       }
 279       // "remove" the CCL
 280       slices_BCV[i] = clitk::SetBackground<MaskSliceType, MaskSliceType>(slices_BCV[i],
 281                                                                          slices_BCV[i],
 282                                                                          label,
 283                                                                          GetBackgroundValue(),
 284                                                                          true);
 285     }
 286
 287     // Remove from the support
 288     clitk::AndNot<MaskSliceType>(slices[i], slices_BCV[i], GetBackgroundValue());
 289   }
 290
 291   // Joint
 292   m_Working_Support = clitk::JoinSlices<MaskImageType>(slices, m_Working_Support, 2);
 293
 294   StopCurrentStep<MaskImageType>(m_Working_Support);
 295   m_ListOfStations["3A"] = m_Working_Support;
 296 }
 297 //--------------------------------------------------------------------
 298
 299
 300 //--------------------------------------------------------------------
 301 template <class ImageType>
 302 void
 303 clitk::ExtractLymphStationsFilter<ImageType>::
 304 ExtractStation_3A_PostToBones()
 305 {
 306   StartNewStep("[Station 3A] Post limits with bones");
 307
 308   // limits with bones
 309   MaskImagePointer Bones = GetAFDB()->template GetImage<MaskImageType>("Bones");
 310   m_Working_Support =
 311     clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support, Bones, 2,
 312                                                        GetFuzzyThreshold("3A", "Bones"), "NotAntTo",
 313                                                        false, 3, true, false);
 314
 315   StopCurrentStep<MaskImageType>(m_Working_Support);
 316   m_ListOfStations["3A"] = m_Working_Support;
 317 }
 318 //--------------------------------------------------------------------
 319