Add S3A, correct minors for S7

[clitk.git] / segmentation / clitkExtractLymphStation_3A.txx

diff --git a/segmentation/clitkExtractLymphStation_3A.txx b/segmentation/clitkExtractLymphStation_3A.txx
new file mode 100644 (file)
index 0000000..3e70059
--- /dev/null
+++ b/segmentation/clitkExtractLymphStation_3A.txx
@@ -0,0 +1,66 @@
+
+#include <itkBinaryDilateImageFilter.h>
+#include <itkMirrorPadImageFilter.h>
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void 
+clitk::ExtractLymphStationsFilter<ImageType>::
+ExtractStation_3A_SetDefaultValues()
+{
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void 
+clitk::ExtractLymphStationsFilter<ImageType>::
+ExtractStation_3A_SI_Limits() 
+{
+  // Apex of the chest or Sternum & Carina.
+  StartNewStep("[Station 3A] Inf/Sup limits with Sternum and Carina");
+
+  // Get Carina position (has been determined in Station8)
+  m_CarinaZ = GetAFDB()->GetDouble("CarinaZ");
+  
+  // Get Sternum and search for the upper position
+  MaskImagePointer Sternum = GetAFDB()->template GetImage<MaskImageType>("Sternum");
+
+  // Search most sup point
+  MaskImagePointType ps = Sternum->GetOrigin(); // initialise to avoid warning 
+  clitk::FindExtremaPointInAGivenDirection<MaskImageType>(Sternum, GetBackgroundValue(), 2, false, ps);
+  double m_SternumZ = ps[2]+Sternum->GetSpacing()[2]; // One more slice, because it is below this point
+
+  //* Crop support :
+  m_Working_Support = 
+    clitk::CropImageAlongOneAxis<MaskImageType>(m_Working_Support, 2, 
+                                                m_CarinaZ, m_SternumZ, true,
+                                                GetBackgroundValue());
+
+  StopCurrentStep<MaskImageType>(m_Working_Support);
+  m_ListOfStations["3A"] = m_Working_Support;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void 
+clitk::ExtractLymphStationsFilter<ImageType>::
+ExtractStation_3A_Ant_Limits() 
+{
+  StartNewStep("[Station 3A] Ant limits with Sternum");
+
+  // Get Sternum, keep posterior part.
+  MaskImagePointer Sternum = GetAFDB()->template GetImage<MaskImageType>("Sternum");
+  m_Working_Support = 
+    clitk::SliceBySliceRelativePosition<MaskImageType>(m_Working_Support, Sternum, 2, 
+                                                       0.5, "PostTo", 
+                                                       false, 3, true, false);
+  StopCurrentStep<MaskImageType>(m_Working_Support);
+  m_ListOfStations["3A"] = m_Working_Support;
+}
+//--------------------------------------------------------------------
+
+