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   // Get the current support
  23   StartNewStep("[Station 3A] Get the current 3A suppport");
  24   m_Working_Support = m_ListOfSupports["S3A"];
  25   m_ListOfStations["3A"] = m_Working_Support;
  26   StopCurrentStep<MaskImageType>(m_Working_Support);
  27
  28   ExtractStation_3A_AntPost_S5();
  29   ExtractStation_3A_AntPost_S6();
  30   ExtractStation_3A_AntPost_Superiorly();
  31
  32   ExtractStation_3A_Remove_Structures();
  33
  34   Remove_Structures("3A", "Aorta");
  35   Remove_Structures("3A", "SubclavianArteryLeft");
  36   Remove_Structures("3A", "SubclavianArteryRight");
  37   Remove_Structures("3A", "Thyroid");
  38   Remove_Structures("3A", "CommonCarotidArteryLeft");
  39   Remove_Structures("3A", "CommonCarotidArteryRight");
  40   Remove_Structures("3A", "BrachioCephalicArtery");
  41   //  Remove_Structures("3A", "BrachioCephalicVein"); ?
  42
  43
  44   // ExtractStation_3A_Ant_Limits(); --> No, already in support; to remove
  45   // ExtractStation_3A_Post_Limits(); --> No, more complex, see Vessels etc
  46
  47   // Store image filenames into AFDB
  48   writeImage<MaskImageType>(m_ListOfStations["3A"], "seg/Station3A.mhd");
  49   GetAFDB()->SetImageFilename("Station3A", "seg/Station3A.mhd");
  50   WriteAFDB();
  51 }
  52 //--------------------------------------------------------------------
  53
  54
  55 //--------------------------------------------------------------------
  56 template <class ImageType>
  57 void
  58 clitk::ExtractLymphStationsFilter<ImageType>::
  59 ExtractStation_3A_Ant_Limits()
  60 {
  61   StartNewStep("[Station 3A] Ant limits with Sternum");
  62
  63   // Get Sternum, keep posterior part.
  64   MaskImagePointer Sternum = GetAFDB()->template GetImage<MaskImageType>("Sternum");
  65   m_Working_Support =
  66     clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support, Sternum, 2,
  67                                                        GetFuzzyThreshold("3A", "Sternum"), "PostTo",
  68                                                        false, 3, true, false);
  69   StopCurrentStep<MaskImageType>(m_Working_Support);
  70   m_ListOfStations["3A"] = m_Working_Support;
  71 }
  72 //--------------------------------------------------------------------
  73
  74
  75 //--------------------------------------------------------------------
  76 template <class ImageType>
  77 void
  78 clitk::ExtractLymphStationsFilter<ImageType>::
  79 ExtractStation_3A_Post_Limits()
  80 {
  81   StartNewStep("[Station 3A] Post limits with SubclavianArtery");
  82
  83   // Get Sternum, keep posterior part.
  84   MaskImagePointer SubclavianArteryLeft =
  85     GetAFDB()->template GetImage<MaskImageType>("SubclavianArteryLeft");
  86   MaskImagePointer SubclavianArteryRight =
  87     GetAFDB()->template GetImage<MaskImageType>("SubclavianArteryRight");
  88
  89   m_Working_Support =
  90     clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support, SubclavianArteryLeft, 2,
  91                                                        GetFuzzyThreshold("3A", "SubclavianArtery"), "AntTo",
  92                                                        false, 3, true, false);
  93   m_Working_Support =
  94     clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support, SubclavianArteryRight, 2,
  95                                                        GetFuzzyThreshold("3A", "SubclavianArtery"), "AntTo",
  96                                                        false, 3, true, false);
  97   StopCurrentStep<MaskImageType>(m_Working_Support);
  98   m_ListOfStations["3A"] = m_Working_Support;
  99 }
 100 //--------------------------------------------------------------------
 101
 102
 103 //--------------------------------------------------------------------
 104 template <class ImageType>
 105 void
 106 clitk::ExtractLymphStationsFilter<ImageType>::
 107 ExtractStation_3A_AntPost_S5()
 108 {
 109   StartNewStep("[Station 3A] Post limits around S5");
 110
 111   // First remove post to SVC
 112   MaskImagePointer SVC = GetAFDB()->template GetImage <MaskImageType>("SVC");
 113
 114   // Trial in 3D -> difficulties superiorly. Stay slice by slice.
 115   /*
 116   typedef clitk::AddRelativePositionConstraintToLabelImageFilter<MaskImageType> RelPosFilterType;
 117   typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New();
 118   relPosFilter->VerboseStepFlagOff();
 119   relPosFilter->WriteStepFlagOff();
 120   relPosFilter->SetBackgroundValue(GetBackgroundValue());
 121   relPosFilter->SetInput(m_Working_Support);
 122   relPosFilter->SetInputObject(SVC);
 123   relPosFilter->AddOrientationTypeString("PostTo");
 124   relPosFilter->SetInverseOrientationFlag(true);
 125   relPosFilter->SetIntermediateSpacing(4);
 126   relPosFilter->SetIntermediateSpacingFlag(false);
 127   relPosFilter->SetFuzzyThreshold(0.5);
 128   //  relPosFilter->AutoCropFlagOff(); // important ! because we join the slices after this loop
 129   relPosFilter->Update();
 130   m_Working_Support = relPosFilter->GetOutput();
 131   */
 132
 133   // Slice by slice not post to SVC. Use initial spacing
 134   m_Working_Support =
 135     clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support, SVC, 2,
 136                                                        GetFuzzyThreshold("3A", "SVC"),
 137                                                        "NotPostTo", true,
 138                                                        SVC->GetSpacing()[0], false, false);
 139
 140   // Consider Aorta, remove Left/Post part ; only around S5
 141   // Get S5 support and Aorta
 142   MaskImagePointer S5 = m_ListOfSupports["S5"];
 143   MaskImagePointer Aorta = GetAFDB()->template GetImage <MaskImageType>("Aorta");
 144   Aorta = clitk::ResizeImageLike<MaskImageType>(Aorta, S5, GetBackgroundValue());
 145
 146   // Inferiorly, Aorta has two CCL that merge into a single one when
 147   // S6 appears. Loop on Aorta slices, select the most ant one, detect
 148   // the most ant point.
 149   std::vector<MaskSlicePointer> slices;
 150   clitk::ExtractSlices<MaskImageType>(Aorta, 2, slices);
 151   std::vector<MaskImagePointType> points;
 152   for(uint i=0; i<slices.size(); i++) {
 153     // Select most ant CCL
 154     slices[i] = clitk::Labelize<MaskSliceType>(slices[i], GetBackgroundValue(), false, 1);
 155     std::vector<MaskSlicePointType> c;
 156     clitk::ComputeCentroids<MaskSliceType>(slices[i], GetBackgroundValue(), c);
 157     assert(c.size() == 3); // only 2 CCL
 158     typename MaskSliceType::PixelType l;
 159     if (c[1][1] > c[2][1]) { // We will remove the label=1
 160       l = 1;
 161     }
 162     else {
 163       l = 2;// We will remove the label=2
 164     }
 165     slices[i] = clitk::SetBackground<MaskSliceType, MaskSliceType>(slices[i], slices[i], l,
 166                                                                    GetBackgroundValue(), true);
 167
 168     // Detect the most ant point
 169     MaskSlicePointType p;
 170     MaskImagePointType pA;
 171     clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(slices[i], GetBackgroundValue(), 1, true, p);
 172     // Set the X coordinate to the X coordinate of the centroid
 173     if (l==1) p[0] = c[2][0];
 174     else p[0] = c[1][0];
 175
 176     // Convert in 3D and store
 177     clitk::PointsUtils<MaskImageType>::Convert2DTo3D(p, Aorta, i, pA);
 178     points.push_back(pA);
 179   }
 180
 181   // DEBUG
 182   // MaskImagePointer o = clitk::JoinSlices<MaskImageType>(slices, Aorta, 2);
 183   // writeImage<MaskImageType>(o, "o.mhd");
 184   // clitk::WriteListOfLandmarks<MaskImageType>(points, "Ant-Aorta.txt");
 185
 186   // Remove Post/Left to this point
 187   m_Working_Support =
 188     clitk::SliceBySliceSetBackgroundFromPoints<MaskImageType>(m_Working_Support,
 189                                                               GetBackgroundValue(), 2,
 190                                                               points,
 191                                                               true, // Set BG if X greater than point[x], and
 192                                                               true); // if Y greater than point[y]
 193
 194   StopCurrentStep<MaskImageType>(m_Working_Support);
 195   m_ListOfStations["3A"] = m_Working_Support;
 196 }
 197 //--------------------------------------------------------------------
 198
 199
 200 //--------------------------------------------------------------------
 201 template <class ImageType>
 202 void
 203 clitk::ExtractLymphStationsFilter<ImageType>::
 204 ExtractStation_3A_AntPost_S6()
 205 {
 206   StartNewStep("[Station 3A] Post limits around S6");
 207
 208   // Consider Aorta
 209   MaskImagePointer Aorta = GetAFDB()->template GetImage <MaskImageType>("Aorta");
 210
 211   // Limits the support to S6
 212   MaskImagePointer S6 = m_ListOfSupports["S6"];
 213   Aorta = clitk::ResizeImageLike<MaskImageType>(Aorta, S6, GetBackgroundValue());
 214
 215   // Extend 1cm anteriorly
 216   MaskImagePointType radius; // in mm
 217   radius[0] = 10;
 218   radius[1] = 10;
 219   radius[2] = 0; // required
 220   Aorta = clitk::Dilate<MaskImageType>(Aorta, radius, GetBackgroundValue(), GetForegroundValue(), false);
 221
 222   // Not Post to
 223   m_Working_Support =
 224     clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support, Aorta, 2,
 225                                                        GetFuzzyThreshold("3A", "Aorta"),
 226                                                        "NotPostTo", true,
 227                                                        Aorta->GetSpacing()[0], false, false);
 228
 229   StopCurrentStep<MaskImageType>(m_Working_Support);
 230   m_ListOfStations["3A"] = m_Working_Support;
 231 }
 232 //--------------------------------------------------------------------
 233
 234
 235 //--------------------------------------------------------------------
 236 template <class ImageType>
 237 void
 238 clitk::ExtractLymphStationsFilter<ImageType>::
 239 ExtractStation_3A_AntPost_Superiorly()
 240 {
 241   StartNewStep("[Station 3A] Post limits superiorly");
 242
 243   /*
 244  MaskImagePointer BrachioCephalicVein = GetAFDB()->template GetImage <MaskImageType>("BrachioCephalicVein");
 245  MaskImagePointer BrachioCephalicArtery = GetAFDB()->template GetImage <MaskImageType>("BrachioCephalicArtery");
 246  MaskImagePointer CommonCarotidArteryLeft = GetAFDB()->template GetImage <MaskImageType>("CommonCarotidArteryLeft");
 247  MaskImagePointer CommonCarotidArteryRight = GetAFDB()->template GetImage <MaskImageType>("CommonCarotidArteryRight");
 248  MaskImagePointer SubclavianArteryLeft = GetAFDB()->template GetImage <MaskImageType>("SubclavianArteryLeft");
 249  MaskImagePointer SubclavianArteryRight = GetAFDB()->template GetImage <MaskImageType>("SubclavianArteryRight");
 250
 251   // Not Post to
 252 #define RP(STRUCTURE)                                                   \
 253  m_Working_Support =                                                    \
 254    clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support, STRUCTURE, 2, \
 255                                                       0.5,              \
 256                                                       "NotPostTo", true, \
 257                                                       STRUCTURE->GetSpacing()[0], false, false);
 258
 259  // RP(BrachioCephalicVein);
 260  RP(BrachioCephalicArtery);
 261  RP(CommonCarotidArteryRight);
 262  RP(CommonCarotidArteryLeft);
 263  RP(SubclavianArteryRight);
 264  RP(SubclavianArteryLeft);
 265   */
 266
 267   // Get or compute the binary mask that separate Ant/Post part
 268   // according to vessels
 269   MaskImagePointer binarizedContour = FindAntPostVessels2();
 270   binarizedContour = clitk::ResizeImageLike<MaskImageType>(binarizedContour,
 271                                                            m_Working_Support,
 272                                                            GetBackgroundValue());
 273
 274   // remove from support
 275   typedef clitk::BooleanOperatorLabelImageFilter<MaskImageType> BoolFilterType;
 276   typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
 277   boolFilter->InPlaceOn();
 278   boolFilter->SetInput1(m_Working_Support);
 279   boolFilter->SetInput2(binarizedContour);
 280   boolFilter->SetBackgroundValue1(GetBackgroundValue());
 281   boolFilter->SetBackgroundValue2(GetBackgroundValue());
 282   boolFilter->SetOperationType(BoolFilterType::AndNot);
 283   boolFilter->Update();
 284   m_Working_Support = boolFilter->GetOutput();
 285
 286   StopCurrentStep<MaskImageType>(m_Working_Support);
 287   m_ListOfStations["3A"] = m_Working_Support;
 288 }
 289 //--------------------------------------------------------------------
 290
 291
 292 //--------------------------------------------------------------------
 293 template <class ImageType>
 294 void
 295 clitk::ExtractLymphStationsFilter<ImageType>::
 296 ExtractStation_3A_Remove_Structures()
 297 {
 298   Remove_Structures("3A", "Aorta");
 299   Remove_Structures("3A", "SubclavianArteryLeft");
 300   Remove_Structures("3A", "SubclavianArteryRight");
 301   Remove_Structures("3A", "Thyroid");
 302   Remove_Structures("3A", "CommonCarotidArteryLeft");
 303   Remove_Structures("3A", "CommonCarotidArteryRight");
 304   Remove_Structures("3A", "BrachioCephalicArtery");
 305   //  Remove_Structures("3A", "BrachioCephalicVein"); ?
 306
 307   StartNewStep("[Station 3A] Remove part of BrachioCephalicVein");
 308   // resize like support, extract slices
 309   // while single CCL -> remove
 310   // when two remove only the most post
 311   BrachioCephalicVein = clitk::ResizeImageLike<MaskImageType>(BrachioCephalicVein,
 312                                                               m_Working_Support,
 313                                                               GetBackgroundValue());
 314   std::vector<MaskSlicePointer> slices;
 315   std::vector<MaskSlicePointer> slices_BCV;
 316   clitk::ExtractSlices<MaskImageType>(m_Working_Support, 2, slices);
 317   clitk::ExtractSlices<MaskImageType>(BrachioCephalicVein, 2, slices_BCV);
 318   for(uint i=0; i<slices.size(); i++) {
 319     // Labelize slices_BCV
 320     slices_BCV[i] = Labelize<MaskSliceType>(slices_BCV[i], 0, true, 1);
 321     // Compute centroids
 322     std::vector<typename MaskSliceType::PointType> centroids;
 323     ComputeCentroids<MaskSliceType>(slices_BCV[i], GetBackgroundValue(), centroids);
 324     if (centroids.size() > 1) {
 325       // Only keep the one most post
 326       typename MaskSliceType::PixelType label;
 327       if (centroids[1][1] > centroids[2][1]) {
 328         label = 1;
 329       }
 330       else {
 331         label = 2;
 332       }
 333
 334       HERE
 335
 336       slices_BCV[i] = clitk::SetBackground<MaskSliceType>(slices_BCV[i], slices_BCV[i],
 337                                                           label,
 338                                                           GetBackgroundValue(), true);
 339     }
 340     // Remove from the support
 341     slices[i] = clitk::AndNot(slices[i], slices_BCV[i], GetBackgroundValue());
 342   }
 343
 344   // Joint
 345   m_Working_Support = clitk::JoinSlices<MaskImageType>(slices, m_Working_Support, 2);
 346
 347   StopCurrentStep<MaskImageType>(m_Working_Support);
 348   m_ListOfStations["3A"] = m_Working_Support;
 349 }
 350 //--------------------------------------------------------------------