Extraction of S1RL

diff --git a/segmentation/clitkExtractLymphStation_1RL.txx b/segmentation/clitkExtractLymphStation_1RL.txx
new file mode 100644 (file)
index 0000000..608fdc9
--- /dev/null
+++ b/segmentation/clitkExtractLymphStation_1RL.txx
@@ -0,0 +1,185 @@
+
+
+// vtk
+#include <vtkAppendPolyData.h>
+#include <vtkPolyDataWriter.h>
+#include <vtkCellArray.h>
+
+// clitk
+#include "clitkMeshToBinaryImageFilter.h"
+
+// itk
+#include <itkImageDuplicator.h>
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void 
+clitk::ExtractLymphStationsFilter<ImageType>::
+ExtractStation_1RL_SetDefaultValues()
+{
+  
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void 
+clitk::ExtractLymphStationsFilter<TImageType>::
+ExtractStation_1RL()
+{
+  if ((!CheckForStation("1R")) && (!CheckForStation("1L"))) return;
+
+  StartNewStep("Stations 1RL");
+  StartSubStep(); 
+
+  // Get the current support 
+  StartNewStep("[Station 1RL] Get the current 1RL suppport");
+  m_ListOfStations["1R"] = m_ListOfSupports["S1R"];
+  m_ListOfStations["1L"] = m_ListOfSupports["S1L"];
+  StopCurrentStep<MaskImageType>(m_ListOfStations["1R"]);
+    
+  // Specific processes
+  ExtractStation_1RL_Ant_Limits();
+  ExtractStation_1RL_Post_Limits();
+  m_Working_Support = m_ListOfStations["1R"];
+  Remove_Structures(" 1R", "ScaleneMuscleAnt");
+  Remove_Structures(" 1R", "CommonCarotidArteryRight");  
+  m_Working_Support = m_ListOfStations["1L"];
+  Remove_Structures(" 1L", "ScaleneMuscleAnt");
+  Remove_Structures(" 1L", "CommonCarotidArteryLeft");  
+ 
+  // Generic RelativePosition processes
+  m_ListOfStations["1R"] = this->ApplyRelativePositionList("Station_1R", m_ListOfStations["1R"]);
+  m_ListOfStations["1L"] = this->ApplyRelativePositionList("Station_1L", m_ListOfStations["1L"]);
+
+  // Store image filenames into AFDB 
+  writeImage<MaskImageType>(m_ListOfStations["1R"], "seg/Station1R.mhd");
+  writeImage<MaskImageType>(m_ListOfStations["1L"], "seg/Station1L.mhd");
+  GetAFDB()->SetImageFilename("Station1R", "seg/Station1R.mhd"); 
+  GetAFDB()->SetImageFilename("Station1L", "seg/Station1L.mhd"); 
+  WriteAFDB(); 
+  StopSubStep();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void 
+clitk::ExtractLymphStationsFilter<ImageType>::
+ExtractStation_1RL_Ant_Limits()
+{
+  // -----------------------------------------------------
+  StartNewStep("[Station 1RL] anterior limits with Trachea and Thyroid");
+  
+  /*
+    The idea here it to consider the most anterior points int the
+    Trachea or the Thyroid and cut all parts anterior to it. This is
+    an heuristic, not written explicitely in the articles.
+  */
+
+  MaskImagePointer Trachea = GetAFDB()->template GetImage<MaskImageType>("Trachea");
+  MaskImagePointer Thyroid = GetAFDB()->template GetImage<MaskImageType>("Thyroid");
+  MaskImagePointer S1R = m_ListOfStations["1R"];
+  MaskImagePointer S1L = m_ListOfStations["1L"];
+  MaskImagePointer support = m_ListOfSupports["S1RL"];
+ 
+  // Resize like S1R. Warning: for Thyroid, only Right part is thus
+  // taken into account
+  Trachea = clitk::ResizeImageLike<MaskImageType>(Trachea, S1R, GetBackgroundValue());
+  Thyroid = clitk::ResizeImageLike<MaskImageType>(Thyroid, S1R, GetBackgroundValue());
+
+  // Search for most Ant point, slice by slice, between Trachea and Thyroid
+  std::vector<MaskSlicePointer> Trachea_slices;
+  clitk::ExtractSlices<MaskImageType>(Trachea, 2, Trachea_slices);
+  std::vector<MaskSlicePointer> Thyroid_slices;
+  clitk::ExtractSlices<MaskImageType>(Thyroid, 2, Thyroid_slices);
+  std::vector<typename ImageType::PointType> A;
+  std::vector<typename ImageType::PointType> B;
+  for(uint i=0; i<Trachea_slices.size(); i++) {
+    MaskSlicePointType p;
+    MaskSlicePointType q;
+    FindExtremaPointInAGivenDirection<MaskSliceType>(Trachea_slices[i], 
+                                                     GetBackgroundValue(), 
+                                                     1, true, p);
+    FindExtremaPointInAGivenDirection<MaskSliceType>(Thyroid_slices[i], 
+                                                     GetBackgroundValue(), 
+                                                     1, true, q);
+    if (q[1] < p[1]) p = q; // Now p is the most ant.
+    // Add a little margin, 3mm
+    p[1] -= 3;
+    // Convert in 3D
+    ImagePointType x; //dummy
+    A.push_back(x);
+    B.push_back(x);
+    clitk::PointsUtils<MaskImageType>::Convert2DTo3D(p, Trachea, i, A[i]);
+    p[0] += 10;    
+    clitk::PointsUtils<MaskImageType>::Convert2DTo3D(p, Trachea, i, B[i]);
+  }  
+
+  // Remove anterior to this line (keep +10 offset)
+  clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(S1R, A, B, 
+                                                                    GetBackgroundValue(), 1, +10);
+  m_ListOfStations["1R"] = S1R;
+
+  clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(S1L, A, B, 
+                                                                    GetBackgroundValue(), 1, +10);
+  StopCurrentStep<MaskImageType>(S1L);
+  m_ListOfStations["1L"] = S1L;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void 
+clitk::ExtractLymphStationsFilter<ImageType>::
+ExtractStation_1RL_Post_Limits()
+{
+  // -----------------------------------------------------
+  StartNewStep("[Station 1RL] Posterior limits with VertebralArtery");
+  
+  MaskImagePointer VertebralArtery = GetAFDB()->template GetImage<MaskImageType>("VertebralArtery");
+  MaskImagePointer S1R = m_ListOfStations["1R"];
+  MaskImagePointer S1L = m_ListOfStations["1L"];
+
+  // Resize like S1R.
+  VertebralArtery = clitk::ResizeImageLike<MaskImageType>(VertebralArtery, S1R, GetBackgroundValue());
+
+  // Search for most Ant point, slice by slice, between Trachea and Thyroid
+  std::vector<MaskSlicePointer> VertebralArtery_slices;
+  clitk::ExtractSlices<MaskImageType>(VertebralArtery, 2, VertebralArtery_slices);
+  std::vector<typename ImageType::PointType> A;
+  std::vector<typename ImageType::PointType> B;
+  for(uint i=0; i<VertebralArtery_slices.size(); i++) {
+    MaskSlicePointType p;
+    FindExtremaPointInAGivenDirection<MaskSliceType>(VertebralArtery_slices[i], 
+                                                     GetBackgroundValue(), 
+                                                     1, false, p);
+    // Add a little margin ? No.
+    //p[1] += 0;
+    //DD(p);
+    // Convert in 3D
+    ImagePointType x; //dummy
+    A.push_back(x);
+    B.push_back(x);
+    clitk::PointsUtils<MaskImageType>::Convert2DTo3D(p, VertebralArtery, i, A[i]);
+    p[0] += 10;    
+    clitk::PointsUtils<MaskImageType>::Convert2DTo3D(p, VertebralArtery, i, B[i]);
+  }  
+
+  // Remove anterior to this line (keep -10 offset)
+  clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(S1R, A, B, 
+                                                                    GetBackgroundValue(), 1, -10);
+  m_ListOfStations["1R"] = S1R;
+
+  // Remove anterior to this line (keep -10 offset)
+  clitk::SliceBySliceSetBackgroundFromLineSeparation<MaskImageType>(S1L, A, B, 
+                                                                    GetBackgroundValue(), 1, -10);
+  StopCurrentStep<MaskImageType>(S1L);
+  m_ListOfStations["1L"] = S1L;
+}
+//--------------------------------------------------------------------
+
+