Change mhd to mha

[clitk.git] / segmentation / clitkExtractLymphStation_Supports.txx

diff --git a/segmentation/clitkExtractLymphStation_Supports.txx b/segmentation/clitkExtractLymphStation_Supports.txx
index ad2e95792efec4095f1a999fbc86d9291c8aead2..2cde97dd98b7465ae1addea1e6bcfc11965a4281 100644 (file)
--- a/segmentation/clitkExtractLymphStation_Supports.txx
+++ b/segmentation/clitkExtractLymphStation_Supports.txx
@@ -8,8 +8,6 @@ void
 clitk::ExtractLymphStationsFilter<ImageType>::
 ExtractStationSupports()
 {
-  DD("ExtractStationSupports");
-
   // Get initial Mediastinum
   m_Working_Support = m_Mediastinum = this->GetAFDB()->template GetImage<MaskImageType>("Mediastinum", true);
 
@@ -23,10 +21,10 @@ ExtractStationSupports()
                                                      m_CarinaZ, true, GetBackgroundValue());
   m_ListOfSupports["Support_Superior_to_Carina"] = m_Support_Superior_to_Carina;
   m_ListOfSupports["Support_Inferior_to_Carina"] = m_Support_Inferior_to_Carina;
-  writeImage<MaskImageType>(m_Support_Inferior_to_Carina, "seg/Support_Inf_Carina.mhd");
-  this->GetAFDB()->SetImageFilename("Support_Inf_Carina", "seg/Support_Inf_Carina.mhd");
-  writeImage<MaskImageType>(m_Support_Superior_to_Carina, "seg/Support_Sup_Carina.mhd");
-  this->GetAFDB()->SetImageFilename("Support_Sup_Carina", "seg/Support_Sup_Carina.mhd");
+  writeImage<MaskImageType>(m_Support_Inferior_to_Carina, "seg/Support_Inf_Carina.mha");
+  this->GetAFDB()->SetImageFilename("Support_Inf_Carina", "seg/Support_Inf_Carina.mha");
+  writeImage<MaskImageType>(m_Support_Superior_to_Carina, "seg/Support_Sup_Carina.mha");
+  this->GetAFDB()->SetImageFilename("Support_Sup_Carina", "seg/Support_Sup_Carina.mha");
 
   // S1RL
   Support_SupInf_S1RL();
@@ -59,45 +57,45 @@ ExtractStationSupports()
   m_ListOfSupports["S11"] = clitk::Clone<MaskImageType>(m_Support_Inferior_to_Carina);
 
   // Store image filenames into AFDB 
-  writeImage<MaskImageType>(m_ListOfSupports["S1R"], "seg/Support_S1R.mhd");
-  this->GetAFDB()->SetImageFilename("Support_S1R", "seg/Support_S1R.mhd");
-  writeImage<MaskImageType>(m_ListOfSupports["S1L"], "seg/Support_S1L.mhd");
-  this->GetAFDB()->SetImageFilename("Support_S1L", "seg/Support_S1L.mhd");
+  writeImage<MaskImageType>(m_ListOfSupports["S1R"], "seg/Support_S1R.mha");
+  this->GetAFDB()->SetImageFilename("Support_S1R", "seg/Support_S1R.mha");
+  writeImage<MaskImageType>(m_ListOfSupports["S1L"], "seg/Support_S1L.mha");
+  this->GetAFDB()->SetImageFilename("Support_S1L", "seg/Support_S1L.mha");
 
-  writeImage<MaskImageType>(m_ListOfSupports["S2L"], "seg/Support_S2L.mhd");
-  this->GetAFDB()->SetImageFilename("Support_S2L", "seg/Support_S2L.mhd");
-  writeImage<MaskImageType>(m_ListOfSupports["S2R"], "seg/Support_S2R.mhd");
-  this->GetAFDB()->SetImageFilename("Support_S2R", "seg/Support_S2R.mhd");
+  writeImage<MaskImageType>(m_ListOfSupports["S2L"], "seg/Support_S2L.mha");
+  this->GetAFDB()->SetImageFilename("Support_S2L", "seg/Support_S2L.mha");
+  writeImage<MaskImageType>(m_ListOfSupports["S2R"], "seg/Support_S2R.mha");
+  this->GetAFDB()->SetImageFilename("Support_S2R", "seg/Support_S2R.mha");
 
-  writeImage<MaskImageType>(m_ListOfSupports["S3P"], "seg/Support_S3P.mhd");
-  this->GetAFDB()->SetImageFilename("Support_S3P", "seg/Support_S3P.mhd");
-  writeImage<MaskImageType>(m_ListOfSupports["S3A"], "seg/Support_S3A.mhd");
-  this->GetAFDB()->SetImageFilename("Support_S3A", "seg/Support_S3A.mhd");
+  writeImage<MaskImageType>(m_ListOfSupports["S3P"], "seg/Support_S3P.mha");
+  this->GetAFDB()->SetImageFilename("Support_S3P", "seg/Support_S3P.mha");
+  writeImage<MaskImageType>(m_ListOfSupports["S3A"], "seg/Support_S3A.mha");
+  this->GetAFDB()->SetImageFilename("Support_S3A", "seg/Support_S3A.mha");
 
-  writeImage<MaskImageType>(m_ListOfSupports["S4L"], "seg/Support_S4L.mhd");
-  this->GetAFDB()->SetImageFilename("Support_S4L", "seg/Support_S4L.mhd");
-  writeImage<MaskImageType>(m_ListOfSupports["S4R"], "seg/Support_S4R.mhd");
-  this->GetAFDB()->SetImageFilename("Support_S4R", "seg/Support_S4R.mhd");
+  writeImage<MaskImageType>(m_ListOfSupports["S4L"], "seg/Support_S4L.mha");
+  this->GetAFDB()->SetImageFilename("Support_S4L", "seg/Support_S4L.mha");
+  writeImage<MaskImageType>(m_ListOfSupports["S4R"], "seg/Support_S4R.mha");
+  this->GetAFDB()->SetImageFilename("Support_S4R", "seg/Support_S4R.mha");
 
-  writeImage<MaskImageType>(m_ListOfSupports["S5"], "seg/Support_S5.mhd");
-  this->GetAFDB()->SetImageFilename("Support_S5", "seg/Support_S5.mhd");
-  writeImage<MaskImageType>(m_ListOfSupports["S6"], "seg/Support_S6.mhd");
-  this->GetAFDB()->SetImageFilename("Support_S6", "seg/Support_S6.mhd");
+  writeImage<MaskImageType>(m_ListOfSupports["S5"], "seg/Support_S5.mha");
+  this->GetAFDB()->SetImageFilename("Support_S5", "seg/Support_S5.mha");
+  writeImage<MaskImageType>(m_ListOfSupports["S6"], "seg/Support_S6.mha");
+  this->GetAFDB()->SetImageFilename("Support_S6", "seg/Support_S6.mha");
 
-  writeImage<MaskImageType>(m_ListOfSupports["S7"], "seg/Support_S7.mhd");
-  this->GetAFDB()->SetImageFilename("Support_S7", "seg/Support_S7.mhd");
+  writeImage<MaskImageType>(m_ListOfSupports["S7"], "seg/Support_S7.mha");
+  this->GetAFDB()->SetImageFilename("Support_S7", "seg/Support_S7.mha");
 
-  writeImage<MaskImageType>(m_ListOfSupports["S8"], "seg/Support_S8.mhd");
-  this->GetAFDB()->SetImageFilename("Support_S8", "seg/Support_S8.mhd");
+  writeImage<MaskImageType>(m_ListOfSupports["S8"], "seg/Support_S8.mha");
+  this->GetAFDB()->SetImageFilename("Support_S8", "seg/Support_S8.mha");
 
-  writeImage<MaskImageType>(m_ListOfSupports["S9"], "seg/Support_S9.mhd");
-  this->GetAFDB()->SetImageFilename("Support_S9", "seg/Support_S9.mhd");
+  writeImage<MaskImageType>(m_ListOfSupports["S9"], "seg/Support_S9.mha");
+  this->GetAFDB()->SetImageFilename("Support_S9", "seg/Support_S9.mha");
 
-  writeImage<MaskImageType>(m_ListOfSupports["S10"], "seg/Support_S10.mhd");
-  this->GetAFDB()->SetImageFilename("Support_S10", "seg/Support_S10.mhd");  
+  writeImage<MaskImageType>(m_ListOfSupports["S10"], "seg/Support_S10.mha");
+  this->GetAFDB()->SetImageFilename("Support_S10", "seg/Support_S10.mha");  
 
-  writeImage<MaskImageType>(m_ListOfSupports["S11"], "seg/Support_S11.mhd");
-  this->GetAFDB()->SetImageFilename("Support_S11", "seg/Support_S11.mhd");  
+  writeImage<MaskImageType>(m_ListOfSupports["S11"], "seg/Support_S11.mha");
+  this->GetAFDB()->SetImageFilename("Support_S11", "seg/Support_S11.mha");  
   WriteAFDB();
 }
 //--------------------------------------------------------------------
@@ -204,8 +202,10 @@ Support_SupInf_S2R_S2L()
   MaskImagePointer BrachioCephalicVein = this->GetAFDB()->template GetImage<MaskImageType>("BrachioCephalicVein");
   MaskImagePointType p;
   clitk::FindExtremaPointInAGivenDirection<MaskImageType>(BrachioCephalicVein, GetBackgroundValue(), 2, true, p);
-  // I add slightly more than a slice
-  double CaudalMarginOfLeftBrachiocephalicVeinZ=p[2]+ 1.1*m_Working_Support->GetSpacing()[2];
+
+  // I add slightly more than a slice --> NO !!
+  double CaudalMarginOfLeftBrachiocephalicVeinZ=p[2];//+ 1.1*m_Working_Support->GetSpacing()[2];
+
   this->GetAFDB()->SetDouble("CaudalMarginOfLeftBrachiocephalicVeinZ", CaudalMarginOfLeftBrachiocephalicVeinZ);
   MaskImagePointer S2R = 
     clitk::CropImageRemoveLowerThan<MaskImageType>(m_Working_Support, 2, 
@@ -266,7 +266,6 @@ Support_SupInf_S2R_S2L()
 
 
 
-
 //--------------------------------------------------------------------
 template <class ImageType>
 void 
@@ -313,24 +312,32 @@ Support_SupInf_S4R_S4L()
   */
   StartNewStep("[Support] Sup-Inf limits of 4R/4L");
 
-  // Start from the support, remove 2R and 2L
+  // Start from the support
   MaskImagePointer S4RL = clitk::Clone<MaskImageType>(m_Working_Support);
+  MaskImagePointer S4R = clitk::Clone<MaskImageType>(S4RL);
+  MaskImagePointer S4L = clitk::Clone<MaskImageType>(S4RL);
+
+  // Keep only what is lower than S2
   MaskImagePointer S2R = m_ListOfSupports["S2R"];
   MaskImagePointer S2L = m_ListOfSupports["S2L"];
-  clitk::AndNot<MaskImageType>(S4RL, S2R, GetBackgroundValue());
-  clitk::AndNot<MaskImageType>(S4RL, S2L, GetBackgroundValue());
-  S4RL = clitk::AutoCrop<MaskImageType>(S4RL, GetBackgroundValue());
+  MaskImagePointType p;
+  // Right part
+  clitk::FindExtremaPointInAGivenDirection<MaskImageType>(S2R, GetBackgroundValue(), 
+                                                          2, true, p);
+  S4R = clitk::CropImageRemoveGreaterThan<MaskImageType>(S4R, 2, 
+                                                       p[2], true, GetBackgroundValue());
+  // Left part
+  clitk::FindExtremaPointInAGivenDirection<MaskImageType>(S2L, GetBackgroundValue(), 
+                                                          2, true, p);
+  S4L = clitk::CropImageRemoveGreaterThan<MaskImageType>(S4L, 2, 
+                                                         p[2], true, GetBackgroundValue());
 
-  // Copy, stop 4R at AzygousVein and 4L at LeftPulmonaryArtery
-  MaskImagePointer S4R = clitk::Clone<MaskImageType>(S4RL);
-  MaskImagePointer S4L = clitk::Clone<MaskImageType>(S4RL);
-  
   // Get AzygousVein and limit according to LowerBorderAzygousVein
   MaskImagePointer LowerBorderAzygousVein 
     = this->GetAFDB()->template GetImage<MaskImageType>("LowerBorderAzygousVein");
   std::vector<MaskImagePointType> c;
   clitk::ComputeCentroids<MaskImageType>(LowerBorderAzygousVein, GetBackgroundValue(), c);
-  S4R = clitk::CropImageRemoveLowerThan<MaskImageType>(S4RL, 2, 
+  S4R = clitk::CropImageRemoveLowerThan<MaskImageType>(S4R, 2, 
                                                        c[1][2], true, GetBackgroundValue());
   S4R = clitk::AutoCrop<MaskImageType>(S4R, GetBackgroundValue());
   m_ListOfSupports["S4R"] = S4R;
@@ -339,10 +346,9 @@ Support_SupInf_S4R_S4L()
   // Limit according to LeftPulmonaryArtery
   MaskImagePointer LeftPulmonaryArtery 
     = this->GetAFDB()->template GetImage<MaskImageType>("LeftPulmonaryArtery");
-  MaskImagePointType p;
   clitk::FindExtremaPointInAGivenDirection<MaskImageType>(LeftPulmonaryArtery, GetBackgroundValue(), 
                                                           2, false, p);
-  S4L = clitk::CropImageRemoveLowerThan<MaskImageType>(S4RL, 2, 
+  S4L = clitk::CropImageRemoveLowerThan<MaskImageType>(S4L, 2, 
                                                        p[2], true, GetBackgroundValue());
   S4L = clitk::AutoCrop<MaskImageType>(S4L, GetBackgroundValue());
   m_ListOfSupports["S4L"] = S4L;
@@ -423,7 +429,7 @@ LimitsWithTrachea(MaskImageType * input, int extremaDirection, int lineDirection
                                                                                GetBackgroundValue(), 2, 
                                                                                extremaDirection, false, // Left
                                                                                lineDirection, // Vertical line 
-                                                                               1, // margins 
+                                                                               -1, // margins 
                                                                                tracheaLeftPositionsA, 
                                                                                tracheaLeftPositionsB);
   // Do not consider trachea above the limit
@@ -519,7 +525,7 @@ Support_S3A()
   MaskImagePointType p;
   p[0] = p[1] = p[2] =  0.0; // to avoid warning
   clitk::FindExtremaPointInAGivenDirection<MaskImageType>(Sternum, GetBackgroundValue(), 2, false, p);
-
+  p[2] += Sternum->GetSpacing()[2]; // we add one slice to stop 3A at the same slice than Sternum stop
   S3A = 
     clitk::CropImageRemoveGreaterThan<MaskImageType>(S3A, 2, 
                                                      //m_ApexOfTheChest
@@ -538,20 +544,22 @@ void
 clitk::ExtractLymphStationsFilter<ImageType>::
 Support_S5()
 {
-  StartNewStep("[Support] Sup-Inf limits S5 with aorta");
+  StartNewStep("[Support] Sup-Inf limits S5 with Aorta and MainPulmonaryArtery");
 
   // Initial S5 support
-  MaskImagePointer S5 = clitk::Clone<MaskImageType>(this->GetAFDB()->template GetImage<MaskImageType>("Mediastinum", true));
+  MaskImagePointer S5 = 
+    clitk::Clone<MaskImageType>(this->GetAFDB()->template GetImage<MaskImageType>("Mediastinum", true));
 
   // Sup limits with Aorta
   double sup = FindInferiorBorderOfAorticArch();
   
   // Inf limits with "upper rim of the left main pulmonary artery"
   // For the moment only, it will change.
-  MaskImagePointer PulmonaryTrunk = this->GetAFDB()->template GetImage<MaskImageType>("PulmonaryTrunk");
+  MaskImagePointer MainPulmonaryArtery = this->GetAFDB()->template GetImage<MaskImageType>("MainPulmonaryArtery");
   MaskImagePointType p;
   p[0] = p[1] = p[2] =  0.0; // to avoid warning
-  clitk::FindExtremaPointInAGivenDirection<MaskImageType>(PulmonaryTrunk, GetBackgroundValue(), 2, false, p);
+  clitk::FindExtremaPointInAGivenDirection<MaskImageType>(MainPulmonaryArtery, GetBackgroundValue(), 2, false, p);
+  p[2] += MainPulmonaryArtery->GetSpacing()[2];
   
   // Cut Sup/Inf
   S5 = clitk::CropImageAlongOneAxis<MaskImageType>(S5, 2, p[2], sup, true, GetBackgroundValue());