X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLymphStation_3P.txx;h=274fc867c740596227b8c2c92f84b31b4a5d5a02;hb=b2fd61648c05339dd302e102361c22c4b11d48ff;hp=effcd4fd6f51a88a6d407bd81faf0895c50b47c7;hpb=bf4928c59a1d39f53fe03deb4b73ecb7e1cf214b;p=clitk.git

diff --git a/segmentation/clitkExtractLymphStation_3P.txx b/segmentation/clitkExtractLymphStation_3P.txx
index effcd4f..274fc86 100644
--- a/segmentation/clitkExtractLymphStation_3P.txx
+++ b/segmentation/clitkExtractLymphStation_3P.txx
@@ -1,7 +1,4 @@
 
-#include <itkBinaryDilateImageFilter.h>
-#include <itkMirrorPadImageFilter.h>
-
 //--------------------------------------------------------------------
 template <class ImageType>
 void 
@@ -11,45 +8,275 @@ ExtractStation_3P_SetDefaultValues()
 }
 //--------------------------------------------------------------------
 
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void 
+clitk::ExtractLymphStationsFilter<TImageType>::
+ExtractStation_3P()
+{
+  if (!CheckForStation("3P")) return;
+
+  StartNewStep("Station 3P");
+  StartSubStep();  
+
+  // Get the current support 
+  StartNewStep("[Station 3P] Get the current 3P suppport");
+  m_Working_Support = m_ListOfSupports["S3P"];
+  m_ListOfStations["3P"] = m_Working_Support;
+  StopCurrentStep<MaskImageType>(m_Working_Support);
+
+  // Generic RelativePosition processes
+  m_ListOfStations["3P"] = this->ApplyRelativePositionList("Station_3P", m_ListOfStations["3P"]);
+  m_Working_Support = m_ListOfStations["3P"];
+  ExtractStation_8_Single_CCL_Limits(); // YES 8 !
+  ExtractStation_3P_Remove_Structures(); // after CCL
+  m_ListOfStations["3P"] = m_Working_Support;
+
+  // Old stuff
+  // LR limits superiorly => not here for the moment because not clear in the def
+  // ExtractStation_3P_LR_sup_Limits_2(); //TODO
+  // ExtractStation_3P_LR_sup_Limits();   // old version to change
+  // ExtractStation_3P_LR_inf_Limits();  // <-- done in RelPosList 
+
+  // Store image filenames into AFDB 
+  writeImage<MaskImageType>(m_ListOfStations["3P"], "seg/Station3P.mhd");
+  GetAFDB()->SetImageFilename("Station3P", "seg/Station3P.mhd"); 
+  WriteAFDB();   
+  StopSubStep();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void 
+clitk::ExtractLymphStationsFilter<ImageType>::
+ExtractStation_3P_Remove_Structures() 
+{
+  StartNewStep("[Station 3P] Remove some structures.");
+  Remove_Structures("3P", "Esophagus");
+  Remove_Structures("3P", "Thyroid");
+  Remove_Structures("3P", "VertebralArtery"); // (inside the station)
+  StopCurrentStep<MaskImageType>(m_Working_Support);
+  m_ListOfStations["3P"] = m_Working_Support;
+}
+//--------------------------------------------------------------------
+
+
 //--------------------------------------------------------------------
 template <class ImageType>
 void 
 clitk::ExtractLymphStationsFilter<ImageType>::
-ExtractStation_3P_SI_Limits() 
+ExtractStation_3P_LR_sup_Limits() 
 {
   /*
-    Apex of the chest & Carina.
-   */
-  StartNewStep("[Station 3P] Inf/Sup limits with apex of the chest and carina");
+    "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)."
 
-  writeImage<MaskImageType>(m_Working_Support, "support.mhd");
+    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) ");
 
-  // Get Carina position (has been determined in Station8)
-  m_CarinaZ = GetAFDB()->GetDouble("CarinaZ");
-  DD(m_CarinaZ);
+  // 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 Apex of the Chest
-  MaskImagePointer Lungs = GetAFDB()->template GetImage<MaskImageType>("Lungs");
-  DD("lung ok");
+  // 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;
-  bool found = clitk::FindExtremaPointInAGivenDirection<MaskImageType>(Lungs, 
-                                                                       GetBackgroundValue(), 
-                                                                       1, true, p);
-  DD(found);
-  DD(p);
-  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,
-                                                GetBackgroundValue());
+  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("RightTo");
+        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("AntTo");
+        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_sup_Limits_2() 
+{
+  /*
+    "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) ");
+  
+
+}
+//--------------------------------------------------------------------
+