segmentation/clitkExtractLymphStation_7.txx

   1
   2 //--------------------------------------------------------------------
   3 template <class TImageType>
   4 void
   5 clitk::ExtractLymphStationsFilter<TImageType>::
   6 ExtractStation_7_SetDefaultValues()
   7 {
   8   SetFuzzyThreshold("7", "Bronchi", 0.1);
   9   SetFuzzyThreshold("7", "LeftSuperiorPulmonaryVein", 0.3);
  10   SetFuzzyThreshold("7", "RightSuperiorPulmonaryVein", 0.2);
  11   SetFuzzyThreshold("7", "RightPulmonaryArtery", 0.3);
  12   SetFuzzyThreshold("7", "LeftPulmonaryArtery", 0.5);
  13   SetFuzzyThreshold("7", "SVC", 0.2);
  14 }
  15 //--------------------------------------------------------------------
  16
  17
  18 //--------------------------------------------------------------------
  19 template <class TImageType>
  20 void
  21 clitk::ExtractLymphStationsFilter<TImageType>::
  22 ExtractStation_7_SI_Limits()
  23 {
  24   StartNewStep("[Station7] Inf/Sup mediastinum limits with carina/LLLBronchus");
  25   // Get Inputs
  26   MaskImagePointer Trachea = GetAFDB()->template GetImage <MaskImageType>("Trachea");
  27
  28   // We suppoe that CarinaZ was already computed (S8)
  29   double m_CarinaZ = GetAFDB()->GetDouble("CarinaZ");
  30
  31   //  double m_OriginOfRightMiddleLobeBronchusZ = GetAFDB()->GetPoint3D("OriginOfRightMiddleLobeBronchus", 2);
  32   // DD(m_OriginOfRightMiddleLobeBronchusZ);
  33   MaskImagePointer UpperBorderOfLLLBronchus = GetAFDB()->template GetImage<MaskImageType>("UpperBorderOfLLLBronchus");
  34
  35   // Search most inf point (WHY ? IS IT THE RIGHT STRUCTURE ??)
  36   MaskImagePointType ps = UpperBorderOfLLLBronchus->GetOrigin(); // initialise to avoid warning
  37   clitk::FindExtremaPointInAGivenDirection<MaskImageType>(UpperBorderOfLLLBronchus, GetBackgroundValue(), 2, true, ps);
  38   double m_UpperBorderOfLLLBronchusZ = ps[2];
  39
  40   /*
  41   std::vector<MaskImagePointType> centroids;
  42   clitk::ComputeCentroids<MaskImageType>(UpperBorderOfLLLBronchus, GetBackgroundValue(), centroids);
  43   double m_UpperBorderOfLLLBronchusZ = centroids[1][2];
  44   DD(m_UpperBorderOfLLLBronchusZ)
  45   */
  46
  47   /* Crop support */
  48   m_Working_Support =
  49     clitk::CropImageAlongOneAxis<MaskImageType>(m_Working_Support, 2,
  50                                                 m_UpperBorderOfLLLBronchusZ,
  51                                                 m_CarinaZ, true,
  52                                                 GetBackgroundValue());
  53   /* Crop trachea */
  54   m_Working_Trachea =
  55     clitk::CropImageAlongOneAxis<MaskImageType>(Trachea, 2,
  56                                                 m_UpperBorderOfLLLBronchusZ,
  57                                                 m_CarinaZ, true,
  58                                                 GetBackgroundValue());
  59
  60   StopCurrentStep<MaskImageType>(m_Working_Support);
  61   m_ListOfStations["7"] = m_Working_Support;
  62 }
  63 //--------------------------------------------------------------------
  64
  65
  66 //--------------------------------------------------------------------
  67 template <class TImageType>
  68 void
  69 clitk::ExtractLymphStationsFilter<TImageType>::
  70 ExtractStation_7_RL_Limits()
  71 {
  72   // ----------------------------------------------------------------
  73   StartNewStep("[Station7] Limits with bronchus : RightTo the left bronchus");
  74
  75   // First consider bronchus and keep the main CCL by slice
  76   m_RightBronchus = GetAFDB()->template GetImage <MaskImageType>("RightBronchus");
  77   m_LeftBronchus = GetAFDB()->template GetImage <MaskImageType>("LeftBronchus");
  78
  79   // Extract slices, Label, compute centroid, keep most central connected component
  80   std::vector<MaskSlicePointer> slices_leftbronchus;
  81   std::vector<MaskSlicePointer> slices_rightbronchus;
  82   clitk::ExtractSlices<MaskImageType>(m_LeftBronchus, 2, slices_leftbronchus);
  83   clitk::ExtractSlices<MaskImageType>(m_RightBronchus, 2, slices_rightbronchus);
  84
  85   // Loop on slices
  86   for(uint i=0; i<slices_leftbronchus.size(); i++) {
  87     slices_leftbronchus[i] = Labelize<MaskSliceType>(slices_leftbronchus[i], 0, false, 10);
  88     std::vector<typename MaskSliceType::PointType> c;
  89     clitk::ComputeCentroids<MaskSliceType>(slices_leftbronchus[i], GetBackgroundValue(), c);
  90     if (c.size() > 1) {
  91       double most_at_left = c[1][0];
  92       int most_at_left_index=1;
  93       for(uint j=1; j<c.size(); j++) {
  94         if (c[j][0] < most_at_left) {
  95           most_at_left = c[j][0];
  96           most_at_left_index = j;
  97         }
  98       }
  99       // Put all other CCL to Background
 100       slices_leftbronchus[i] =
 101         clitk::Binarize<MaskSliceType>(slices_leftbronchus[i], most_at_left_index,
 102                                        most_at_left_index, GetBackgroundValue(), GetForegroundValue());
 103     } // end c.size
 104   }
 105
 106   for(uint i=0; i<slices_rightbronchus.size(); i++) {
 107     slices_rightbronchus[i] = Labelize<MaskSliceType>(slices_rightbronchus[i], 0, false, 10);
 108     std::vector<typename MaskSliceType::PointType> c;
 109     clitk::ComputeCentroids<MaskSliceType>(slices_rightbronchus[i], GetBackgroundValue(), c);
 110     if (c.size() > 1) {
 111       double most_at_right = c[1][0];
 112       int most_at_right_index=1;
 113       for(uint j=1; j<c.size(); j++) {
 114         if (c[j][0] > most_at_right) {
 115           most_at_right = c[j][0];
 116           most_at_right_index = j;
 117         }
 118       }
 119       // Put all other CCL to Background
 120       slices_rightbronchus[i] =
 121         clitk::Binarize<MaskSliceType>(slices_rightbronchus[i], most_at_right_index,
 122                                        most_at_right_index, GetBackgroundValue(), GetForegroundValue());
 123     } // end c.size
 124   }
 125
 126   // Joint slices
 127   m_LeftBronchus = clitk::JoinSlices<MaskImageType>(slices_leftbronchus, m_LeftBronchus, 2);
 128   m_RightBronchus = clitk::JoinSlices<MaskImageType>(slices_rightbronchus, m_RightBronchus, 2);
 129
 130   writeImage<MaskImageType>(m_LeftBronchus, "step-left.mhd");
 131   writeImage<MaskImageType>(m_RightBronchus, "step-right.mhd");
 132
 133   m_Working_Support =
 134     clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support, m_LeftBronchus, 2,
 135                                                        GetFuzzyThreshold("7", "Bronchi"), "RightTo",
 136                                                        false, 3, false);
 137   StopCurrentStep<MaskImageType>(m_Working_Support);
 138
 139
 140   // ----------------------------------------------------------------
 141   StartNewStep("[Station7] Limits with bronchus : LeftTo the right bronchus");
 142   m_Working_Support =
 143     clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support, m_RightBronchus, 2,
 144                                                        GetFuzzyThreshold("7", "Bronchi"), "LeftTo",
 145                                                        false, 3, false);
 146   StopCurrentStep<MaskImageType>(m_Working_Support);
 147
 148
 149   // ----------------------------------------------------------------
 150   StartNewStep("[Station7] Limits with LeftSuperiorPulmonaryVein");
 151   try {
 152     MaskImagePointer LeftSuperiorPulmonaryVein = GetAFDB()->template GetImage<MaskImageType>("LeftSuperiorPulmonaryVein");
 153     typedef SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
 154     typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
 155     sliceRelPosFilter->SetInput(m_Working_Support);
 156     sliceRelPosFilter->SetInputObject(LeftSuperiorPulmonaryVein);
 157     sliceRelPosFilter->SetDirection(2);
 158     sliceRelPosFilter->SetFuzzyThreshold(GetFuzzyThreshold("7", "LeftSuperiorPulmonaryVein"));
 159     sliceRelPosFilter->AddOrientationTypeString("NotLeftTo");
 160     sliceRelPosFilter->AddOrientationTypeString("NotAntTo");
 161     sliceRelPosFilter->SetIntermediateSpacingFlag(true);
 162     sliceRelPosFilter->SetIntermediateSpacing(3);
 163     sliceRelPosFilter->SetUniqueConnectedComponentBySlice(false);
 164     sliceRelPosFilter->SetAutoCropFlag(false);
 165     sliceRelPosFilter->IgnoreEmptySliceObjectFlagOn();
 166     sliceRelPosFilter->Update();
 167     m_Working_Support = sliceRelPosFilter->GetOutput();
 168     StopCurrentStep<MaskImageType>(m_Working_Support);
 169   }
 170   catch (clitk::ExceptionObject e) {
 171     std::cout << "Not LeftSuperiorPulmonaryVein, skip" << std::endl;
 172   }
 173
 174   // ----------------------------------------------------------------
 175   StartNewStep("[Station7] Limits with RightSuperiorPulmonaryVein");
 176   try {
 177     MaskImagePointer RightSuperiorPulmonaryVein = GetAFDB()->template GetImage<MaskImageType>("RightSuperiorPulmonaryVein");
 178     typedef SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
 179     typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
 180     sliceRelPosFilter->SetInput(m_Working_Support);
 181     sliceRelPosFilter->SetInputObject(RightSuperiorPulmonaryVein);
 182     sliceRelPosFilter->SetDirection(2);
 183     sliceRelPosFilter->SetFuzzyThreshold(GetFuzzyThreshold("7", "RightSuperiorPulmonaryVein"));
 184     sliceRelPosFilter->AddOrientationTypeString("NotRightTo");
 185     sliceRelPosFilter->AddOrientationTypeString("NotAntTo");
 186     sliceRelPosFilter->AddOrientationTypeString("NotPostTo");
 187     sliceRelPosFilter->SetIntermediateSpacingFlag(true);
 188     sliceRelPosFilter->SetIntermediateSpacing(3);
 189     sliceRelPosFilter->SetUniqueConnectedComponentBySlice(false);
 190     sliceRelPosFilter->SetAutoCropFlag(false);
 191     sliceRelPosFilter->IgnoreEmptySliceObjectFlagOn();
 192     sliceRelPosFilter->Update();
 193     m_Working_Support = sliceRelPosFilter->GetOutput();
 194     StopCurrentStep<MaskImageType>(m_Working_Support);
 195   }
 196   catch (clitk::ExceptionObject e) {
 197     std::cout << "Not RightSuperiorPulmonaryVein, skip" << std::endl;
 198   }
 199
 200   // ----------------------------------------------------------------
 201   StartNewStep("[Station7] Limits with RightPulmonaryArtery");
 202   MaskImagePointer RightPulmonaryArtery = GetAFDB()->template GetImage<MaskImageType>("RightPulmonaryArtery");
 203   typedef SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
 204   typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
 205   sliceRelPosFilter->SetInput(m_Working_Support);
 206   sliceRelPosFilter->SetInputObject(RightPulmonaryArtery);
 207   sliceRelPosFilter->SetDirection(2);
 208   sliceRelPosFilter->SetFuzzyThreshold(GetFuzzyThreshold("7", "RightPulmonaryArtery"));
 209   sliceRelPosFilter->AddOrientationTypeString("NotAntTo");
 210   sliceRelPosFilter->SetIntermediateSpacingFlag(true);
 211   sliceRelPosFilter->SetIntermediateSpacing(3);
 212   sliceRelPosFilter->SetUniqueConnectedComponentBySlice(false);
 213   sliceRelPosFilter->SetAutoCropFlag(false);
 214   sliceRelPosFilter->IgnoreEmptySliceObjectFlagOn();
 215   sliceRelPosFilter->Update();
 216   m_Working_Support = sliceRelPosFilter->GetOutput();
 217   StopCurrentStep<MaskImageType>(m_Working_Support);
 218
 219   // ----------------------------------------------------------------
 220   StartNewStep("[Station7] Limits with LeftPulmonaryArtery");
 221   MaskImagePointer LeftPulmonaryArtery = GetAFDB()->template GetImage<MaskImageType>("LeftPulmonaryArtery");
 222   sliceRelPosFilter = SliceRelPosFilterType::New();
 223   sliceRelPosFilter->SetInput(m_Working_Support);
 224   sliceRelPosFilter->SetInputObject(LeftPulmonaryArtery);
 225   sliceRelPosFilter->SetDirection(2);
 226   sliceRelPosFilter->SetFuzzyThreshold(GetFuzzyThreshold("7", "LeftPulmonaryArtery"));
 227   sliceRelPosFilter->AddOrientationTypeString("NotAntTo");
 228   sliceRelPosFilter->SetIntermediateSpacingFlag(true);
 229   sliceRelPosFilter->SetIntermediateSpacing(3);
 230   sliceRelPosFilter->SetUniqueConnectedComponentBySlice(false);
 231   sliceRelPosFilter->SetAutoCropFlag(false);
 232   sliceRelPosFilter->IgnoreEmptySliceObjectFlagOn();
 233   sliceRelPosFilter->Update();
 234   m_Working_Support = sliceRelPosFilter->GetOutput();
 235   StopCurrentStep<MaskImageType>(m_Working_Support);
 236
 237   StartNewStep("[Station7] Limits with SVC");
 238   MaskImagePointer SVC = GetAFDB()->template GetImage<MaskImageType>("SVC");
 239   sliceRelPosFilter = SliceRelPosFilterType::New();
 240   sliceRelPosFilter->SetInput(m_Working_Support);
 241   sliceRelPosFilter->SetInputObject(SVC);
 242   sliceRelPosFilter->SetDirection(2);
 243   sliceRelPosFilter->SetFuzzyThreshold(GetFuzzyThreshold("7", "SVC"));
 244   sliceRelPosFilter->AddOrientationTypeString("NotRightTo");
 245   sliceRelPosFilter->AddOrientationTypeString("NotAntTo");
 246   sliceRelPosFilter->SetIntermediateSpacingFlag(true);
 247   sliceRelPosFilter->SetIntermediateSpacing(3);
 248   sliceRelPosFilter->SetUniqueConnectedComponentBySlice(false);
 249   sliceRelPosFilter->SetAutoCropFlag(true);
 250   sliceRelPosFilter->IgnoreEmptySliceObjectFlagOn();
 251   sliceRelPosFilter->Update();
 252   m_Working_Support = sliceRelPosFilter->GetOutput();
 253   StopCurrentStep<MaskImageType>(m_Working_Support);
 254
 255   // End
 256   m_ListOfStations["7"] = m_Working_Support;
 257 }
 258 //--------------------------------------------------------------------
 259
 260
 261 //--------------------------------------------------------------------
 262 template <class TImageType>
 263 void
 264 clitk::ExtractLymphStationsFilter<TImageType>::
 265 ExtractStation_7_Posterior_Limits()
 266 {
 267   StartNewStep("[Station7] Posterior limits -> must be AntTo post wall of the bronchi (OLD CLASSIF)");
 268
 269   // Search for points that are the most left/post/ant and most
 270   // right/post/ant of the left and right bronchus
 271
 272   // extract, loop slices, label/keep, find extrema x 3
 273   /*  FindExtremaPointsInBronchus(m_LeftBronchus, 0, 15, m_RightMostInLeftBronchus,
 274                               m_AntMostInLeftBronchus, m_PostMostInLeftBronchus);
 275   FindExtremaPointsInBronchus(m_RightBronchus, 1, 15, m_LeftMostInRightBronchus,
 276                               m_AntMostInRightBronchus, m_PostMostInRightBronchus);
 277   */
 278
 279   // First cut bronchus to the correct sup/inf support
 280   MaskImagePointer RightBronchus = clitk::ResizeImageLike<MaskImageType>(m_RightBronchus, m_Working_Support, GetBackgroundValue());
 281   MaskImagePointer LeftBronchus = clitk::ResizeImageLike<MaskImageType>(m_LeftBronchus, m_Working_Support, GetBackgroundValue());
 282
 283   // Find extrema points
 284   FindExtremaPointsInBronchus(RightBronchus, 0, 10, m_LeftMostInRightBronchus,
 285                               m_AntMostInRightBronchus, m_PostMostInRightBronchus);
 286
 287   FindExtremaPointsInBronchus(LeftBronchus, 1, 10, m_RightMostInLeftBronchus,
 288                               m_AntMostInLeftBronchus, m_PostMostInLeftBronchus);
 289
 290
 291
 292   // DEBUG
 293   std::ofstream osrl; openFileForWriting(osrl, "osrl.txt"); osrl << "LANDMARKS1" << std::endl;
 294   std::ofstream osal; openFileForWriting(osal, "osal.txt"); osal << "LANDMARKS1" << std::endl;
 295   std::ofstream ospl; openFileForWriting(ospl, "ospl.txt"); ospl << "LANDMARKS1" << std::endl;
 296   std::ofstream osrr; openFileForWriting(osrr, "osrr.txt"); osrr << "LANDMARKS1" << std::endl;
 297   std::ofstream osar; openFileForWriting(osar, "osar.txt"); osar << "LANDMARKS1" << std::endl;
 298   std::ofstream ospr; openFileForWriting(ospr, "ospr.txt"); ospr << "LANDMARKS1" << std::endl;
 299
 300   for(uint i=0; i<m_RightMostInLeftBronchus.size(); i++) {
 301     osrl << i << " " << m_RightMostInLeftBronchus[i][0] << " " << m_RightMostInLeftBronchus[i][1]
 302          << " " << m_RightMostInLeftBronchus[i][2] << " 0 0 " << std::endl;
 303     osal << i << " " << m_AntMostInLeftBronchus[i][0] << " " << m_AntMostInLeftBronchus[i][1]
 304          << " " << m_AntMostInLeftBronchus[i][2] << " 0 0 " << std::endl;
 305     ospl << i << " " << m_PostMostInLeftBronchus[i][0] << " " << m_PostMostInLeftBronchus[i][1]
 306          << " " << m_PostMostInLeftBronchus[i][2] << " 0 0 " << std::endl;
 307   }
 308
 309   for(uint i=0; i<m_LeftMostInRightBronchus.size(); i++) {
 310     osrr << i << " " << m_LeftMostInRightBronchus[i][0] << " " << m_LeftMostInRightBronchus[i][1]
 311          << " " << m_LeftMostInRightBronchus[i][2] << " 0 0 " << std::endl;
 312     osar << i << " " << m_AntMostInRightBronchus[i][0] << " " << m_AntMostInRightBronchus[i][1]
 313          << " " << m_AntMostInRightBronchus[i][2] << " 0 0 " << std::endl;
 314     ospr << i << " " << m_PostMostInRightBronchus[i][0] << " " << m_PostMostInRightBronchus[i][1]
 315          << " " << m_PostMostInRightBronchus[i][2] << " 0 0 " << std::endl;
 316   }
 317   osrl.close();
 318   osal.close();
 319   ospl.close();
 320   osrr.close();
 321   osar.close();
 322   ospr.close();
 323
 324   clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(m_Working_Support,
 325                                                                     m_PostMostInRightBronchus,
 326                                                                     m_PostMostInLeftBronchus,
 327                                                                     GetBackgroundValue(), 1, -10);
 328   // If needed -> can do the same with AntMost.
 329
 330   // End
 331   StopCurrentStep<MaskImageType>(m_Working_Support);
 332   m_ListOfStations["7"] = m_Working_Support;
 333 }
 334 //--------------------------------------------------------------------
 335
 336 //--------------------------------------------------------------------
 337 template <class ImageType>
 338 void
 339 clitk::ExtractLymphStationsFilter<ImageType>::
 340 ExtractStation_7_Remove_Structures()
 341 {
 342
 343   //--------------------------------------------------------------------
 344   StartNewStep("[Station7] remove some structures");
 345
 346   Remove_Structures("7", "AzygousVein");
 347   Remove_Structures("7", "Aorta");
 348   Remove_Structures("7", "Esophagus");
 349   Remove_Structures("7", "RightPulmonaryArtery");
 350   Remove_Structures("7", "LeftPulmonaryArtery");
 351   Remove_Structures("7", "LeftSuperiorPulmonaryVein");
 352   Remove_Structures("7", "PulmonaryTrunk");
 353   Remove_Structures("7", "VertebralBody");
 354
 355   // END
 356   StopCurrentStep<MaskImageType>(m_Working_Support);
 357   m_ListOfStations["7"] = m_Working_Support;
 358   return;
 359 }
 360 //--------------------------------------------------------------------
 361
 362
 363