segmentation/clitkExtractLymphStation_7.txx

   1
   2 //--------------------------------------------------------------------
   3 template <class TImageType>
   4 void
   5 clitk::ExtractLymphStationsFilter<TImageType>::
   6 ExtractStation_7_SetDefaultValues()
   7 {
   8   SetFuzzyThresholdForS7("Bronchi", 0.1);
   9   SetFuzzyThresholdForS7("LeftSuperiorPulmonaryVein", 0.3);
  10   SetFuzzyThresholdForS7("RightSuperiorPulmonaryVein", 0.2);
  11   SetFuzzyThresholdForS7("RightPulmonaryArtery", 0.3);
  12   SetFuzzyThresholdForS7("LeftPulmonaryArtery", 0.5);
  13   SetFuzzyThresholdForS7("SVC", 0.2);
  14 }
  15 //--------------------------------------------------------------------
  16
  17 //--------------------------------------------------------------------
  18 template <class TImageType>
  19 void
  20 clitk::ExtractLymphStationsFilter<TImageType>::
  21 SetFuzzyThresholdForS7(std::string tag, double value)
  22 {
  23   m_FuzzyThresholdForS7[tag] = value;
  24 }
  25 //--------------------------------------------------------------------
  26
  27
  28 //--------------------------------------------------------------------
  29 template <class TImageType>
  30 double
  31 clitk::ExtractLymphStationsFilter<TImageType>::
  32 GetFuzzyThresholdForS7(std::string tag)
  33 {
  34   if (m_FuzzyThresholdForS7.find(tag) != m_FuzzyThresholdForS7.end()) {
  35     return m_FuzzyThresholdForS7[tag];
  36   }
  37   else {
  38     clitkExceptionMacro("Could not find options "+tag+" in the m_FuzzyThresholdForS7 list");
  39   }
  40 }
  41 //--------------------------------------------------------------------
  42
  43
  44 //--------------------------------------------------------------------
  45 template <class TImageType>
  46 void
  47 clitk::ExtractLymphStationsFilter<TImageType>::
  48 ExtractStation_7_SI_Limits()
  49 {
  50   StartNewStep("[Station7] Inf/Sup mediastinum limits with carina/LLLBronchus");
  51   // Get Inputs
  52   MaskImagePointer Trachea = GetAFDB()->template GetImage <MaskImageType>("Trachea");
  53
  54   // We suppoe that CarinaZ was already computed (S8)
  55   double m_CarinaZ = GetAFDB()->GetDouble("CarinaZ");
  56
  57   //  double m_OriginOfRightMiddleLobeBronchusZ = GetAFDB()->GetPoint3D("OriginOfRightMiddleLobeBronchus", 2);
  58   // DD(m_OriginOfRightMiddleLobeBronchusZ);
  59   MaskImagePointer UpperBorderOfLLLBronchus = GetAFDB()->template GetImage<MaskImageType>("UpperBorderOfLLLBronchus");
  60
  61   // Search most inf point (WHY ? IS IT THE RIGHT STRUCTURE ??)
  62   MaskImagePointType ps = UpperBorderOfLLLBronchus->GetOrigin(); // initialise to avoid warning
  63   clitk::FindExtremaPointInAGivenDirection<MaskImageType>(UpperBorderOfLLLBronchus, GetBackgroundValue(), 2, true, ps);
  64   double m_UpperBorderOfLLLBronchusZ = ps[2];
  65
  66   /*
  67   std::vector<MaskImagePointType> centroids;
  68   clitk::ComputeCentroids<MaskImageType>(UpperBorderOfLLLBronchus, GetBackgroundValue(), centroids);
  69   double m_UpperBorderOfLLLBronchusZ = centroids[1][2];
  70   DD(m_UpperBorderOfLLLBronchusZ)
  71   */
  72
  73   /* Crop support */
  74   m_Working_Support =
  75     clitk::CropImageAlongOneAxis<MaskImageType>(m_Working_Support, 2,
  76                                                 m_UpperBorderOfLLLBronchusZ,
  77                                                 m_CarinaZ, true,
  78                                                 GetBackgroundValue());
  79   /* Crop trachea */
  80   m_Working_Trachea =
  81     clitk::CropImageAlongOneAxis<MaskImageType>(Trachea, 2,
  82                                                 m_UpperBorderOfLLLBronchusZ,
  83                                                 m_CarinaZ, true,
  84                                                 GetBackgroundValue());
  85
  86   StopCurrentStep<MaskImageType>(m_Working_Support);
  87   m_ListOfStations["7"] = m_Working_Support;
  88 }
  89 //--------------------------------------------------------------------
  90
  91
  92 //--------------------------------------------------------------------
  93 template <class TImageType>
  94 void
  95 clitk::ExtractLymphStationsFilter<TImageType>::
  96 ExtractStation_7_RL_Limits()
  97 {
  98   // ----------------------------------------------------------------
  99   StartNewStep("[Station7] Limits with bronchus : RightTo the left bronchus");
 100
 101   // First consider bronchus and keep the main CCL by slice
 102   m_RightBronchus = GetAFDB()->template GetImage <MaskImageType>("RightBronchus");
 103   m_LeftBronchus = GetAFDB()->template GetImage <MaskImageType>("LeftBronchus");
 104
 105   // Extract slices, Label, compute centroid, keep most central connected component
 106   std::vector<MaskSlicePointer> slices_leftbronchus;
 107   std::vector<MaskSlicePointer> slices_rightbronchus;
 108   clitk::ExtractSlices<MaskImageType>(m_LeftBronchus, 2, slices_leftbronchus);
 109   clitk::ExtractSlices<MaskImageType>(m_RightBronchus, 2, slices_rightbronchus);
 110
 111   // Loop on slices
 112   for(uint i=0; i<slices_leftbronchus.size(); i++) {
 113     slices_leftbronchus[i] = Labelize<MaskSliceType>(slices_leftbronchus[i], 0, false, 10);
 114     std::vector<typename MaskSliceType::PointType> c;
 115     clitk::ComputeCentroids<MaskSliceType>(slices_leftbronchus[i], GetBackgroundValue(), c);
 116     if (c.size() > 1) {
 117       double most_at_left = c[1][0];
 118       int most_at_left_index=1;
 119       for(uint j=1; j<c.size(); j++) {
 120         if (c[j][0] < most_at_left) {
 121           most_at_left = c[j][0];
 122           most_at_left_index = j;
 123         }
 124       }
 125       // Put all other CCL to Background
 126       slices_leftbronchus[i] =
 127         clitk::Binarize<MaskSliceType>(slices_leftbronchus[i], most_at_left_index,
 128                                        most_at_left_index, GetBackgroundValue(), GetForegroundValue());
 129     } // end c.size
 130   }
 131
 132   for(uint i=0; i<slices_rightbronchus.size(); i++) {
 133     slices_rightbronchus[i] = Labelize<MaskSliceType>(slices_rightbronchus[i], 0, false, 10);
 134     std::vector<typename MaskSliceType::PointType> c;
 135     clitk::ComputeCentroids<MaskSliceType>(slices_rightbronchus[i], GetBackgroundValue(), c);
 136     if (c.size() > 1) {
 137       double most_at_right = c[1][0];
 138       int most_at_right_index=1;
 139       for(uint j=1; j<c.size(); j++) {
 140         if (c[j][0] > most_at_right) {
 141           most_at_right = c[j][0];
 142           most_at_right_index = j;
 143         }
 144       }
 145       // Put all other CCL to Background
 146       slices_rightbronchus[i] =
 147         clitk::Binarize<MaskSliceType>(slices_rightbronchus[i], most_at_right_index,
 148                                        most_at_right_index, GetBackgroundValue(), GetForegroundValue());
 149     } // end c.size
 150   }
 151
 152   // Joint slices
 153   m_LeftBronchus = clitk::JoinSlices<MaskImageType>(slices_leftbronchus, m_LeftBronchus, 2);
 154   m_RightBronchus = clitk::JoinSlices<MaskImageType>(slices_rightbronchus, m_RightBronchus, 2);
 155
 156   writeImage<MaskImageType>(m_LeftBronchus, "step-left.mhd");
 157   writeImage<MaskImageType>(m_RightBronchus, "step-right.mhd");
 158
 159   m_Working_Support =
 160     clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support, m_LeftBronchus, 2,
 161                                                        GetFuzzyThresholdForS7("Bronchi"), "RightTo",
 162                                                        false, 3, false);
 163   StopCurrentStep<MaskImageType>(m_Working_Support);
 164
 165
 166   // ----------------------------------------------------------------
 167   StartNewStep("[Station7] Limits with bronchus : LeftTo the right bronchus");
 168   m_Working_Support =
 169     clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support, m_RightBronchus, 2,
 170                                                        GetFuzzyThresholdForS7("Bronchi"), "LeftTo",
 171                                                        false, 3, false);
 172   StopCurrentStep<MaskImageType>(m_Working_Support);
 173
 174
 175   // ----------------------------------------------------------------
 176   StartNewStep("[Station7] Limits with LeftSuperiorPulmonaryVein");
 177   try {
 178     MaskImagePointer LeftSuperiorPulmonaryVein = GetAFDB()->template GetImage<MaskImageType>("LeftSuperiorPulmonaryVein");
 179     typedef SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
 180     typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
 181     sliceRelPosFilter->SetInput(m_Working_Support);
 182     sliceRelPosFilter->SetInputObject(LeftSuperiorPulmonaryVein);
 183     sliceRelPosFilter->SetDirection(2);
 184     sliceRelPosFilter->SetFuzzyThreshold(GetFuzzyThresholdForS7("LeftSuperiorPulmonaryVein"));
 185     sliceRelPosFilter->AddOrientationTypeString("NotLeftTo");
 186     sliceRelPosFilter->AddOrientationTypeString("NotAntTo");
 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 LeftSuperiorPulmonaryVein, skip" << std::endl;
 198   }
 199
 200   // ----------------------------------------------------------------
 201   StartNewStep("[Station7] Limits with RightSuperiorPulmonaryVein");
 202   try {
 203     MaskImagePointer RightSuperiorPulmonaryVein = GetAFDB()->template GetImage<MaskImageType>("RightSuperiorPulmonaryVein");
 204     typedef SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
 205     typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
 206     sliceRelPosFilter->SetInput(m_Working_Support);
 207     sliceRelPosFilter->SetInputObject(RightSuperiorPulmonaryVein);
 208     sliceRelPosFilter->SetDirection(2);
 209     sliceRelPosFilter->SetFuzzyThreshold(GetFuzzyThresholdForS7("RightSuperiorPulmonaryVein"));
 210     sliceRelPosFilter->AddOrientationTypeString("NotRightTo");
 211     sliceRelPosFilter->AddOrientationTypeString("NotAntTo");
 212     sliceRelPosFilter->AddOrientationTypeString("NotPostTo");
 213     sliceRelPosFilter->SetIntermediateSpacingFlag(true);
 214     sliceRelPosFilter->SetIntermediateSpacing(3);
 215     sliceRelPosFilter->SetUniqueConnectedComponentBySlice(false);
 216     sliceRelPosFilter->SetAutoCropFlag(false);
 217     sliceRelPosFilter->IgnoreEmptySliceObjectFlagOn();
 218     sliceRelPosFilter->Update();
 219     m_Working_Support = sliceRelPosFilter->GetOutput();
 220     StopCurrentStep<MaskImageType>(m_Working_Support);
 221   }
 222   catch (clitk::ExceptionObject e) {
 223     std::cout << "Not RightSuperiorPulmonaryVein, skip" << std::endl;
 224   }
 225
 226   // ----------------------------------------------------------------
 227   StartNewStep("[Station7] Limits with RightPulmonaryArtery");
 228   MaskImagePointer RightPulmonaryArtery = GetAFDB()->template GetImage<MaskImageType>("RightPulmonaryArtery");
 229   typedef SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
 230   typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
 231   sliceRelPosFilter->SetInput(m_Working_Support);
 232   sliceRelPosFilter->SetInputObject(RightPulmonaryArtery);
 233   sliceRelPosFilter->SetDirection(2);
 234   sliceRelPosFilter->SetFuzzyThreshold(GetFuzzyThresholdForS7("RightPulmonaryArtery"));
 235   sliceRelPosFilter->AddOrientationTypeString("NotAntTo");
 236   sliceRelPosFilter->SetIntermediateSpacingFlag(true);
 237   sliceRelPosFilter->SetIntermediateSpacing(3);
 238   sliceRelPosFilter->SetUniqueConnectedComponentBySlice(false);
 239   sliceRelPosFilter->SetAutoCropFlag(false);
 240   sliceRelPosFilter->IgnoreEmptySliceObjectFlagOn();
 241   sliceRelPosFilter->Update();
 242   m_Working_Support = sliceRelPosFilter->GetOutput();
 243   StopCurrentStep<MaskImageType>(m_Working_Support);
 244
 245   // ----------------------------------------------------------------
 246   StartNewStep("[Station7] Limits with LeftPulmonaryArtery");
 247   MaskImagePointer LeftPulmonaryArtery = GetAFDB()->template GetImage<MaskImageType>("LeftPulmonaryArtery");
 248   sliceRelPosFilter = SliceRelPosFilterType::New();
 249   sliceRelPosFilter->SetInput(m_Working_Support);
 250   sliceRelPosFilter->SetInputObject(LeftPulmonaryArtery);
 251   sliceRelPosFilter->SetDirection(2);
 252   sliceRelPosFilter->SetFuzzyThreshold(GetFuzzyThresholdForS7("LeftPulmonaryArtery"));
 253   sliceRelPosFilter->AddOrientationTypeString("NotAntTo");
 254   sliceRelPosFilter->SetIntermediateSpacingFlag(true);
 255   sliceRelPosFilter->SetIntermediateSpacing(3);
 256   sliceRelPosFilter->SetUniqueConnectedComponentBySlice(false);
 257   sliceRelPosFilter->SetAutoCropFlag(false);
 258   sliceRelPosFilter->IgnoreEmptySliceObjectFlagOn();
 259   sliceRelPosFilter->Update();
 260   m_Working_Support = sliceRelPosFilter->GetOutput();
 261   StopCurrentStep<MaskImageType>(m_Working_Support);
 262
 263   StartNewStep("[Station7] Limits with SVC");
 264   MaskImagePointer SVC = GetAFDB()->template GetImage<MaskImageType>("SVC");
 265   sliceRelPosFilter = SliceRelPosFilterType::New();
 266   sliceRelPosFilter->SetInput(m_Working_Support);
 267   sliceRelPosFilter->SetInputObject(SVC);
 268   sliceRelPosFilter->SetDirection(2);
 269   sliceRelPosFilter->SetFuzzyThreshold(GetFuzzyThresholdForS7("SVC"));
 270   sliceRelPosFilter->AddOrientationTypeString("NotRightTo");
 271   sliceRelPosFilter->AddOrientationTypeString("NotAntTo");
 272   sliceRelPosFilter->SetIntermediateSpacingFlag(true);
 273   sliceRelPosFilter->SetIntermediateSpacing(3);
 274   sliceRelPosFilter->SetUniqueConnectedComponentBySlice(false);
 275   sliceRelPosFilter->SetAutoCropFlag(true);
 276   sliceRelPosFilter->IgnoreEmptySliceObjectFlagOn();
 277   sliceRelPosFilter->Update();
 278   m_Working_Support = sliceRelPosFilter->GetOutput();
 279   StopCurrentStep<MaskImageType>(m_Working_Support);
 280
 281   // End
 282   m_ListOfStations["7"] = m_Working_Support;
 283 }
 284 //--------------------------------------------------------------------
 285
 286
 287 //--------------------------------------------------------------------
 288 template <class TImageType>
 289 void
 290 clitk::ExtractLymphStationsFilter<TImageType>::
 291 ExtractStation_7_Posterior_Limits()
 292 {
 293   StartNewStep("[Station7] Posterior limits -> must be AntTo post wall of the bronchi (OLD CLASSIF)");
 294
 295   // Search for points that are the most left/post/ant and most
 296   // right/post/ant of the left and right bronchus
 297
 298   // extract, loop slices, label/keep, find extrema x 3
 299   /*  FindExtremaPointsInBronchus(m_LeftBronchus, 0, 15, m_RightMostInLeftBronchus,
 300                               m_AntMostInLeftBronchus, m_PostMostInLeftBronchus);
 301   FindExtremaPointsInBronchus(m_RightBronchus, 1, 15, m_LeftMostInRightBronchus,
 302                               m_AntMostInRightBronchus, m_PostMostInRightBronchus);
 303   */
 304
 305   // First cut bronchus to the correct sup/inf support
 306   MaskImagePointer RightBronchus = clitk::ResizeImageLike<MaskImageType>(m_RightBronchus, m_Working_Support, GetBackgroundValue());
 307   MaskImagePointer LeftBronchus = clitk::ResizeImageLike<MaskImageType>(m_LeftBronchus, m_Working_Support, GetBackgroundValue());
 308
 309   // Find extrema points
 310   FindExtremaPointsInBronchus(RightBronchus, 0, 10, m_LeftMostInRightBronchus,
 311                               m_AntMostInRightBronchus, m_PostMostInRightBronchus);
 312
 313   FindExtremaPointsInBronchus(LeftBronchus, 1, 10, m_RightMostInLeftBronchus,
 314                               m_AntMostInLeftBronchus, m_PostMostInLeftBronchus);
 315
 316
 317
 318   // DEBUG
 319   std::ofstream osrl; openFileForWriting(osrl, "osrl.txt"); osrl << "LANDMARKS1" << std::endl;
 320   std::ofstream osal; openFileForWriting(osal, "osal.txt"); osal << "LANDMARKS1" << std::endl;
 321   std::ofstream ospl; openFileForWriting(ospl, "ospl.txt"); ospl << "LANDMARKS1" << std::endl;
 322   std::ofstream osrr; openFileForWriting(osrr, "osrr.txt"); osrr << "LANDMARKS1" << std::endl;
 323   std::ofstream osar; openFileForWriting(osar, "osar.txt"); osar << "LANDMARKS1" << std::endl;
 324   std::ofstream ospr; openFileForWriting(ospr, "ospr.txt"); ospr << "LANDMARKS1" << std::endl;
 325
 326   for(uint i=0; i<m_RightMostInLeftBronchus.size(); i++) {
 327     osrl << i << " " << m_RightMostInLeftBronchus[i][0] << " " << m_RightMostInLeftBronchus[i][1]
 328          << " " << m_RightMostInLeftBronchus[i][2] << " 0 0 " << std::endl;
 329     osal << i << " " << m_AntMostInLeftBronchus[i][0] << " " << m_AntMostInLeftBronchus[i][1]
 330          << " " << m_AntMostInLeftBronchus[i][2] << " 0 0 " << std::endl;
 331     ospl << i << " " << m_PostMostInLeftBronchus[i][0] << " " << m_PostMostInLeftBronchus[i][1]
 332          << " " << m_PostMostInLeftBronchus[i][2] << " 0 0 " << std::endl;
 333   }
 334
 335   for(uint i=0; i<m_LeftMostInRightBronchus.size(); i++) {
 336     osrr << i << " " << m_LeftMostInRightBronchus[i][0] << " " << m_LeftMostInRightBronchus[i][1]
 337          << " " << m_LeftMostInRightBronchus[i][2] << " 0 0 " << std::endl;
 338     osar << i << " " << m_AntMostInRightBronchus[i][0] << " " << m_AntMostInRightBronchus[i][1]
 339          << " " << m_AntMostInRightBronchus[i][2] << " 0 0 " << std::endl;
 340     ospr << i << " " << m_PostMostInRightBronchus[i][0] << " " << m_PostMostInRightBronchus[i][1]
 341          << " " << m_PostMostInRightBronchus[i][2] << " 0 0 " << std::endl;
 342   }
 343   osrl.close();
 344   osal.close();
 345   ospl.close();
 346   osrr.close();
 347   osar.close();
 348   ospr.close();
 349
 350   clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(m_Working_Support,
 351                                                                     m_PostMostInRightBronchus,
 352                                                                     m_PostMostInLeftBronchus,
 353                                                                     GetBackgroundValue(), 1, -10);
 354   // If needed -> can do the same with AntMost.
 355
 356   // End
 357   StopCurrentStep<MaskImageType>(m_Working_Support);
 358   m_ListOfStations["7"] = m_Working_Support;
 359 }
 360 //--------------------------------------------------------------------
 361
 362 //--------------------------------------------------------------------
 363 template <class ImageType>
 364 void
 365 clitk::ExtractLymphStationsFilter<ImageType>::
 366 ExtractStation_7_Remove_Structures()
 367 {
 368
 369   //--------------------------------------------------------------------
 370   StartNewStep("[Station7] remove some structures");
 371
 372   Remove_Structures("AzygousVein");
 373   Remove_Structures("Aorta");
 374   Remove_Structures("Esophagus");
 375   Remove_Structures("RightPulmonaryArtery");
 376   Remove_Structures("LeftPulmonaryArtery");
 377   Remove_Structures("LeftSuperiorPulmonaryVein");
 378   Remove_Structures("PulmonaryTrunk");
 379   Remove_Structures("VertebralBody");
 380
 381   // END
 382   StopCurrentStep<MaskImageType>(m_Working_Support);
 383   m_ListOfStations["7"] = m_Working_Support;
 384   return;
 385 }
 386 //--------------------------------------------------------------------
 387
 388
 389