X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLymphStation_3P.txx;h=d1be71047093fb38dce38b1c25d571ff878a6230;hb=a339bdc482ea9752ec53195bc9a47e8b05dba582;hp=effcd4fd6f51a88a6d407bd81faf0895c50b47c7;hpb=9e5e119f00eb9051aa56e480aba3e86d053cdb80;p=clitk.git

diff --git a/segmentation/clitkExtractLymphStation_3P.txx b/segmentation/clitkExtractLymphStation_3P.txx
index effcd4f..d1be710 100644
--- a/segmentation/clitkExtractLymphStation_3P.txx
+++ b/segmentation/clitkExtractLymphStation_3P.txx
@@ -11,6 +11,7 @@ ExtractStation_3P_SetDefaultValues()
 }
 //--------------------------------------------------------------------
 
+
 //--------------------------------------------------------------------
 template <class ImageType>
 void 
@@ -19,37 +20,452 @@ ExtractStation_3P_SI_Limits()
 {
   /*
     Apex of the chest & Carina.
-   */
+  */
   StartNewStep("[Station 3P] Inf/Sup limits with apex of the chest and carina");
 
-  writeImage<MaskImageType>(m_Working_Support, "support.mhd");
-
   // Get Carina position (has been determined in Station8)
   m_CarinaZ = GetAFDB()->GetDouble("CarinaZ");
-  DD(m_CarinaZ);
   
-  // Get Apex of the Chest
+  // Get Apex of the Chest. The "lungs" structure is autocroped so we
+  // consider the most superior point.
   MaskImagePointer Lungs = GetAFDB()->template GetImage<MaskImageType>("Lungs");
-  DD("lung ok");
+  MaskImageIndexType index = Lungs->GetLargestPossibleRegion().GetIndex();
+  index += Lungs->GetLargestPossibleRegion().GetSize();
   MaskImagePointType p;
-  bool found = clitk::FindExtremaPointInAGivenDirection<MaskImageType>(Lungs, 
-                                                                       GetBackgroundValue(), 
-                                                                       1, true, p);
-  DD(found);
-  DD(p);
+  Lungs->TransformIndexToPhysicalPoint(index, p);
+  p[2] -= 5; // 5 mm below because the autocrop is slightly above the apex
   double m_ApexOfTheChest = p[2];
-  DD(m_ApexOfTheChest);
 
   /* Crop support :
      Superior limit = carina
      Inferior limit = Apex of the chest */
   m_Working_Support = 
     clitk::CropImageAlongOneAxis<MaskImageType>(m_Working_Support, 2, 
-                                                m_ApexOfTheChest,
-                                                m_CarinaZ, true,
+                                                m_CarinaZ,
+                                                m_ApexOfTheChest, true,
                                                 GetBackgroundValue());
 
   StopCurrentStep<MaskImageType>(m_Working_Support);
   m_ListOfStations["3P"] = m_Working_Support;
 }
 //--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void 
+clitk::ExtractLymphStationsFilter<ImageType>::
+ExtractStation_3P_Remove_Structures() 
+{
+  /*
+    3 - (sup) remove Aorta, VB, subcl
+    not LR subcl ! -> a séparer LR ?
+    (inf) remove Eso, Aorta, Azygousvein
+  */
+
+  StartNewStep("[Station 3P] Remove some structures.");
+
+  MaskImagePointer Aorta = GetAFDB()->template GetImage<MaskImageType>("Aorta");
+  clitk::AndNot<MaskImageType>(m_Working_Support, Aorta, GetBackgroundValue());
+
+  MaskImagePointer VertebralBody = GetAFDB()->template GetImage<MaskImageType>("VertebralBody");
+  clitk::AndNot<MaskImageType>(m_Working_Support, VertebralBody);
+
+  MaskImagePointer SubclavianArtery = GetAFDB()->template GetImage<MaskImageType>("SubclavianArtery");
+  clitk::AndNot<MaskImageType>(m_Working_Support, SubclavianArtery);
+
+  MaskImagePointer Esophagus = GetAFDB()->template GetImage<MaskImageType>("Esophagus");
+  clitk::AndNot<MaskImageType>(m_Working_Support, Esophagus);
+
+  MaskImagePointer AzygousVein = GetAFDB()->template GetImage<MaskImageType>("AzygousVein");
+  clitk::AndNot<MaskImageType>(m_Working_Support, AzygousVein);
+
+  MaskImagePointer Thyroid = GetAFDB()->template GetImage<MaskImageType>("Thyroid");
+  clitk::AndNot<MaskImageType>(m_Working_Support, Thyroid);
+
+  StopCurrentStep<MaskImageType>(m_Working_Support);
+  m_ListOfStations["3P"] = m_Working_Support;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void 
+clitk::ExtractLymphStationsFilter<ImageType>::
+ExtractStation_3P_Ant_Limits() 
+{
+  /*
+    Ant Post limit : 
+
+    Anteriorly, it is in contact with the posterior aspect of Stations
+    1–2 superiorly (Fig. 2A–C) and with Stations 4R and 4L inferiorly
+    (Fig. 2D–I and 3A–C). The anterior limit of Station 3P is kept
+    posterior to the trachea, which is defined by an imaginary
+    horizontal line running along the posterior wall of the trachea
+    (Fig. 2B,E, red line). Posteriorly, it is delineated along the
+    anterior and lateral borders of the vertebral body until an
+    imaginary horizontal line running 1 cm posteriorly to the
+    anterior border of the vertebral body (Fig. 2D).
+
+    1 - post to the trachea : define an imaginary line just post the
+    Trachea and remove what is anterior. 
+
+  */
+  StartNewStep("[Station 3P] Ant limits with Trachea ");
+
+  // Load Trachea
+  MaskImagePointer Trachea = GetAFDB()->template GetImage<MaskImageType>("Trachea");
+  
+  // Crop like current support (need by SliceBySliceSetBackgroundFromLineSeparation after)
+  Trachea = 
+    clitk::ResizeImageLike<MaskImageType>(Trachea, m_Working_Support, GetBackgroundValue());
+  
+  // Slice by slice, determine the most post point of the trachea (A)
+  // and consider a second point on the same horizontal line (B)
+  std::vector<MaskImagePointType> p_A;
+  std::vector<MaskImagePointType> p_B;
+  std::vector<typename MaskSliceType::Pointer> slices;
+  clitk::ExtractSlices<MaskImageType>(Trachea, 2, slices);
+  MaskImagePointType p;
+  typename MaskSliceType::PointType sp;
+  for(uint i=0; i<slices.size(); i++) {
+    // First only consider the main CCL (trachea, not bronchus)
+    slices[i] = Labelize<MaskSliceType>(slices[i], 0, true, 100);
+    slices[i] = KeepLabels<MaskSliceType>(slices[i], GetBackgroundValue(), 
+                                          GetForegroundValue(), 1, 1, true);
+    // Find most posterior point
+    clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(slices[i], GetBackgroundValue(), 
+                                                            1, false, sp);
+    clitk::PointsUtils<MaskImageType>::Convert2DTo3D(sp, Trachea, i, p);
+    p_A.push_back(p);
+    p[0] -= 20;
+    p_B.push_back(p);
+  }
+  clitk::WriteListOfLandmarks<MaskImageType>(p_A, "trachea-post.txt");
+
+  // Remove Ant part above those lines
+  clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(m_Working_Support, 
+                                                                    p_A, p_B,
+                                                                    GetBackgroundValue(), 
+                                                                    1, 10);
+  // End, release memory
+  GetAFDB()->template ReleaseImage<MaskImageType>("Trachea");
+  StopCurrentStep<MaskImageType>(m_Working_Support);
+  m_ListOfStations["3P"] = m_Working_Support;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void 
+clitk::ExtractLymphStationsFilter<ImageType>::
+ExtractStation_3P_Post_Limits() 
+{
+  /*
+    Ant Post limit : 
+
+    Anteriorly, it is in contact with the posterior aspect of Stations
+    1–2 superiorly (Fig. 2A–C) and with Stations 4R and 4L inferiorly
+    (Fig. 2D–I and 3A–C). The anterior limit of Station 3P is kept
+    posterior to the trachea, which is defined by an imaginary
+    horizontal line running along the posterior wall of the trachea
+    (Fig. 2B,E, red line). Posteriorly, it is delineated along the
+    anterior and lateral borders of the vertebral body until an
+    imaginary horizontal line running 1 cm posteriorly to the
+    anterior border of the vertebral body (Fig. 2D).
+
+    2 - post to the trachea : define an imaginary line just post the
+    Trachea and remove what is anterior. 
+
+  */
+  StartNewStep("[Station 3P] Post limits with VertebralBody ");
+
+  // Load VertebralBody
+  MaskImagePointer VertebralBody = GetAFDB()->template GetImage<MaskImageType>("VertebralBody");
+  
+  // Crop like current support (need by SliceBySliceSetBackgroundFromLineSeparation after)
+  VertebralBody = clitk::ResizeImageLike<MaskImageType>(VertebralBody, m_Working_Support, GetBackgroundValue());
+  
+  writeImage<MaskImageType>(VertebralBody, "vb.mhd");
+  
+  // Compute VertebralBody most Ant position (again because slices
+  // changes). Slice by slice, determine the most post point of the
+  // trachea (A) and consider a second point on the same horizontal
+  // line (B)
+  std::vector<MaskImagePointType> p_A;
+  std::vector<MaskImagePointType> p_B;
+  std::vector<typename MaskSliceType::Pointer> slices;
+  clitk::ExtractSlices<MaskImageType>(VertebralBody, 2, slices);
+  MaskImagePointType p;
+  typename MaskSliceType::PointType sp;
+  for(uint i=0; i<slices.size(); i++) {
+    // Find most anterior point
+    bool found = clitk::FindExtremaPointInAGivenDirection<MaskSliceType>(slices[i], GetBackgroundValue(), 
+                                                                         1, true, sp);
+    
+    // If the VertebralBody stop superiorly before the end of
+    // m_Working_Support, we consider the same previous point.
+    if (!found) {
+      p = p_A.back();
+      p[2] += VertebralBody->GetSpacing()[2];
+      p_A.push_back(p);
+      p = p_B.back();
+      p[2] += VertebralBody->GetSpacing()[2];
+      p_B.push_back(p);
+    }
+    else {
+      clitk::PointsUtils<MaskImageType>::Convert2DTo3D(sp, VertebralBody, i, p);
+      p[1] += 10; // Consider 10 mm more post
+      p_A.push_back(p);
+      p[0] -= 20;
+      p_B.push_back(p);
+    }
+  }
+  clitk::WriteListOfLandmarks<MaskImageType>(p_A, "vb-ant.txt");
+  
+
+  // Remove Ant part above those lines
+  clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(m_Working_Support, 
+                                                                    p_A, p_B,
+                                                                    GetBackgroundValue(), 
+                                                                    1, -10);
+  writeImage<MaskImageType>(m_Working_Support, "a.mhd");
+
+  StopCurrentStep<MaskImageType>(m_Working_Support);
+  m_ListOfStations["3P"] = m_Working_Support;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void 
+clitk::ExtractLymphStationsFilter<ImageType>::
+ExtractStation_3P_LR_sup_Limits() 
+{
+  /*
+    "On the right side, the limit is defined by the air–soft-tissue
+    interface. On the left side, it is defined by the air–tissue
+    interface superiorly (Fig. 2A–C) and the aorta inferiorly
+    (Figs. 2D–I and 3A–C)."
+
+    sup : 
+    Resizelike support : Trachea, SubclavianArtery
+    Trachea, slice by slice, get centroid trachea
+    SubclavianArtery, slice by slice, CCL
+    prendre la 1ère à L et R, not at Left
+    
+  */
+  StartNewStep("[Station 3P] Left/Right limits (superior part) ");
+
+  // Load structures
+  MaskImagePointer Trachea = GetAFDB()->template GetImage<MaskImageType>("Trachea");
+  MaskImagePointer SubclavianArtery = GetAFDB()->template GetImage<MaskImageType>("SubclavianArtery");
+  
+  // Crop like current support
+  Trachea = clitk::ResizeImageLike<MaskImageType>(Trachea, m_Working_Support, GetBackgroundValue());
+  SubclavianArtery = clitk::ResizeImageLike<MaskImageType>(SubclavianArtery, m_Working_Support, GetBackgroundValue());
+  
+  writeImage<MaskImageType>(Trachea, "tr.mhd");
+  writeImage<MaskImageType>(SubclavianArtery, "sca.mhd");
+  
+  // Get list of slices
+  std::vector<MaskSlicePointer> slices_support;
+  std::vector<MaskSlicePointer> slices_trachea;
+  std::vector<MaskSlicePointer> slices_subclavianartery;
+  clitk::ExtractSlices<MaskImageType>(m_Working_Support, 2, slices_support);
+  clitk::ExtractSlices<MaskImageType>(Trachea, 2, slices_trachea);
+  clitk::ExtractSlices<MaskImageType>(SubclavianArtery, 2, slices_subclavianartery);
+
+  // Loop on slices
+  std::vector<MaskImagePointType> points;
+  MaskImagePointType p;
+  for(uint i=0; i<slices_support.size(); i++) {
+    // Get Trachea centroid
+    std::vector<typename MaskSliceType::PointType> centroids;
+    typename MaskSliceType::PointType c;
+    ComputeCentroids<MaskSliceType>(slices_trachea[i], GetBackgroundValue(), centroids);
+    c = centroids[1];
+
+    // [debug] Store point
+    clitk::PointsUtils<MaskImageType>::Convert2DTo3D(centroids[1], Trachea, i, p);
+    points.push_back(p);
+    
+    // Get Right and Left CCL in SubclavianArtery
+    slices_subclavianartery[i] = Labelize<MaskSliceType>(slices_subclavianartery[i], 0, true, 10);
+    ComputeCentroids<MaskSliceType>(slices_subclavianartery[i], GetBackgroundValue(), centroids);
+
+    if (centroids.size() > 1) {
+      // Determine the one at Right/Left -> first after Trachea
+      // centroid 
+      typename MaskSliceType::PointType right;
+      typename MaskSliceType::PointType left;
+      int label_right=-1;
+      int label_left=-1;
+      right[0] = c[0]-100;
+      left[0] = c[0]+100;
+      for(uint j=1; j<centroids.size(); j++) {
+        if (centroids[j][0] < c[0]) { // At Right of Trachea centroid
+          if (centroids[j][0] >= right[0]) {
+            right = centroids[j];
+            label_right = j;
+          }
+        }
+        if (centroids[j][0] > c[0]) { // At Left of Trachea centroid
+          if (centroids[j][0] <= left[0]) {
+            left = centroids[j];
+            label_left = j;
+          }
+        }
+      }
+
+      if (label_right != -1) {
+    
+        // Debug points
+        clitk::PointsUtils<MaskImageType>::Convert2DTo3D(centroids[label_right], SubclavianArtery, i, p);
+        points.push_back(p);
+
+        // Set Background and ForegroundValue according to label_right
+        MaskSlicePointer object = 
+          clitk::Binarize<MaskSliceType>(slices_subclavianartery[i], label_right, label_right, 
+                                         GetBackgroundValue(), GetForegroundValue());
+      
+        // Relative Position : not at Right
+        typedef clitk::AddRelativePositionConstraintToLabelImageFilter<MaskSliceType> RelPosFilterType;
+        typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New();
+        relPosFilter->VerboseStepFlagOff();
+        relPosFilter->WriteStepFlagOff();
+        relPosFilter->SetBackgroundValue(GetBackgroundValue());
+        relPosFilter->SetInput(slices_support[i]); 
+        relPosFilter->SetInputObject(object); 
+        relPosFilter->AddOrientationTypeString("R");
+        relPosFilter->SetInverseOrientationFlag(true);
+        //      relPosFilter->SetIntermediateSpacing(3);
+        relPosFilter->SetIntermediateSpacingFlag(false);
+        relPosFilter->SetFuzzyThreshold(0.7);
+        relPosFilter->AutoCropFlagOff(); // important ! because we join the slices after this loop
+        relPosFilter->Update();
+        slices_support[i] = relPosFilter->GetOutput();
+
+        // Relative Position : not Anterior
+        relPosFilter = RelPosFilterType::New();
+        relPosFilter->VerboseStepFlagOff();
+        relPosFilter->WriteStepFlagOff();
+        relPosFilter->SetBackgroundValue(GetBackgroundValue());
+        relPosFilter->SetInput(slices_support[i]); 
+        relPosFilter->SetInputObject(object); 
+        relPosFilter->AddOrientationTypeString("A");
+        relPosFilter->SetInverseOrientationFlag(true);
+        //      relPosFilter->SetIntermediateSpacing(3);
+        relPosFilter->SetIntermediateSpacingFlag(false);
+        relPosFilter->SetFuzzyThreshold(0.7);
+        relPosFilter->AutoCropFlagOff(); // important ! because we join the slices after this loop
+        relPosFilter->Update();
+        slices_support[i] = relPosFilter->GetOutput();
+
+      } // End RelativePosition for Right
+
+
+      if (label_left != -1) {
+    
+        // Debug points
+        clitk::PointsUtils<MaskImageType>::Convert2DTo3D(centroids[label_left], SubclavianArtery, i, p);
+        points.push_back(p);
+
+        // Set Background and ForegroundValue according to label_right
+        MaskSlicePointer object = 
+          clitk::Binarize<MaskSliceType>(slices_subclavianartery[i], label_left, label_left, 
+                                         GetBackgroundValue(), GetForegroundValue());
+      
+        // Relative Position : not at Right
+        typedef clitk::AddRelativePositionConstraintToLabelImageFilter<MaskSliceType> RelPosFilterType;
+        typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New();
+        relPosFilter->VerboseStepFlagOff();
+        relPosFilter->WriteStepFlagOff();
+        relPosFilter->SetBackgroundValue(GetBackgroundValue());
+        relPosFilter->SetInput(slices_support[i]); 
+        relPosFilter->SetInputObject(object); 
+        relPosFilter->AddOrientationTypeString("L");
+        relPosFilter->SetInverseOrientationFlag(true);
+        //      relPosFilter->SetIntermediateSpacing(3);
+        relPosFilter->SetIntermediateSpacingFlag(false);
+        relPosFilter->SetFuzzyThreshold(0.7);
+        relPosFilter->AutoCropFlagOff(); // important ! because we join the slices after this loop
+        relPosFilter->Update();
+        slices_support[i] = relPosFilter->GetOutput();
+
+        // Relative Position : not Anterior
+        relPosFilter = RelPosFilterType::New();
+        relPosFilter->VerboseStepFlagOff();
+        relPosFilter->WriteStepFlagOff();
+        relPosFilter->SetBackgroundValue(GetBackgroundValue());
+        relPosFilter->SetInput(slices_support[i]); 
+        relPosFilter->SetInputObject(object); 
+        relPosFilter->AddOrientationTypeString("A");
+        relPosFilter->SetInverseOrientationFlag(true);
+        //      relPosFilter->SetIntermediateSpacing(3);
+        relPosFilter->SetIntermediateSpacingFlag(false);
+        relPosFilter->SetFuzzyThreshold(0.7);
+        relPosFilter->AutoCropFlagOff(); // important ! because we join the slices after this loop
+        relPosFilter->Update();
+        slices_support[i] = relPosFilter->GetOutput();
+
+      }
+
+    
+    } // if centroids.size > 1
+  } // End loop slices
+
+  // Joint slices
+  m_Working_Support = clitk::JoinSlices<MaskImageType>(slices_support, m_Working_Support, 2);
+
+  // Save list points
+  clitk::WriteListOfLandmarks<MaskImageType>(points, "subcl-lr.txt");
+
+
+  StopCurrentStep<MaskImageType>(m_Working_Support);
+  m_ListOfStations["3P"] = m_Working_Support;
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void 
+clitk::ExtractLymphStationsFilter<ImageType>::
+ExtractStation_3P_LR_inf_Limits() 
+{
+  /*
+    "On the right side, the limit is defined by the air–soft-tissue
+    interface. On the left side, it is defined by the air–tissue
+    interface superiorly (Fig. 2A–C) and the aorta inferiorly
+    (Figs. 2D–I and 3A–C)."
+
+    inf : not Right to Azygousvein    
+  */
+  StartNewStep("[Station 3P] Left/Right limits (inferior part) ");
+
+  // Load structures
+  MaskImagePointer AzygousVein = GetAFDB()->template GetImage<MaskImageType>("AzygousVein");
+
+  typedef clitk::AddRelativePositionConstraintToLabelImageFilter<MaskImageType> RelPosFilterType;
+  typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New();
+  relPosFilter->VerboseStepFlagOff();
+  relPosFilter->WriteStepFlagOff();
+  relPosFilter->SetBackgroundValue(GetBackgroundValue());
+  relPosFilter->SetInput(m_Working_Support); 
+  relPosFilter->SetInputObject(AzygousVein); 
+  relPosFilter->AddOrientationTypeString("R");
+  relPosFilter->SetInverseOrientationFlag(true);
+  //      relPosFilter->SetIntermediateSpacing(3);
+  relPosFilter->SetIntermediateSpacingFlag(false);
+  relPosFilter->SetFuzzyThreshold(0.7);
+  relPosFilter->AutoCropFlagOn();
+  relPosFilter->Update();
+  m_Working_Support = relPosFilter->GetOutput();
+
+  StopCurrentStep<MaskImageType>(m_Working_Support);
+  m_ListOfStations["3P"] = m_Working_Support;
+}
+//--------------------------------------------------------------------