[VV] New feature to jump on image origin

[clitk.git] / segmentation / clitkExtractLymphStation_8.txx

diff --git a/segmentation/clitkExtractLymphStation_8.txx b/segmentation/clitkExtractLymphStation_8.txx
index 545780e7e1c151d4a29c333d709ea78883e2816b..fc39203ebf7ee646fbc2b169adfad864d9aabd92 100644 (file)
--- a/segmentation/clitkExtractLymphStation_8.txx
+++ b/segmentation/clitkExtractLymphStation_8.txx
@@ -14,7 +14,7 @@ ExtractStation_8_SetDefaultValues()
   SetEsophagusDiltationForAnt(p);
   p[0] = 5; p[1] = 10; p[2] = 1;
   SetEsophagusDiltationForRight(p);
-  SetFuzzyThresholdForS8(0.5);
+  SetFuzzyThreshold("8", "Esophagus", 0.5);
   SetInjectedThresholdForS8(150);
 }
 //--------------------------------------------------------------------
@@ -163,9 +163,9 @@ ExtractStation_8_Post_Limits()
 
   // Convert 2D points in slice into 3D points
   std::vector<MaskImagePointType> vertebralAntPositions;
-  clitk::PointsUtils<MaskImageType>::Convert2DTo3DList(vertebralAntPositionBySlice, 
-                                                       VertebralBody, 
-                                                       vertebralAntPositions);
+  clitk::PointsUtils<MaskImageType>::Convert2DMapTo3DList(vertebralAntPositionBySlice, 
+                                                          VertebralBody, 
+                                                          vertebralAntPositions);
 
   // DEBUG : write list of points
   clitk::WriteListOfLandmarks<MaskImageType>(vertebralAntPositions, 
@@ -241,7 +241,7 @@ ExtractStation_8_Ant_Sup_Limits()
   MaskImagePointer Trachea = GetAFDB()->template GetImage<MaskImageType>("Trachea");
  
   MaskImagePointer m_Working_Trachea = 
-    clitk::CropImageAbove<MaskImageType>(Trachea, 2, m_CarinaZ, true, // AutoCrop
+    clitk::CropImageRemoveGreaterThan<MaskImageType>(Trachea, 2, m_CarinaZ, true, // AutoCrop
                                          GetBackgroundValue());
 
   // Seprate into two main bronchi
@@ -322,12 +322,12 @@ ExtractStation_8_Ant_Sup_Limits()
   OriginOfRightMiddleLobeBronchus->Delete();
 
   RightBronchus = 
-    clitk::CropImageBelow<MaskImageType>(RightBronchus, 2, 
+    clitk::CropImageRemoveLowerThan<MaskImageType>(RightBronchus, 2, 
                                          m_OriginOfRightMiddleLobeBronchusZ, 
                                          true, // AutoCrop
                                          GetBackgroundValue());
   LeftBronchus = 
-    clitk::CropImageBelow<MaskImageType>(LeftBronchus, 2, 
+    clitk::CropImageRemoveLowerThan<MaskImageType>(LeftBronchus, 2, 
                                          m_OriginOfRightMiddleLobeBronchusZ, 
                                          true, // AutoCrop
                                          GetBackgroundValue());
@@ -431,7 +431,7 @@ ExtractStation_8_Ant_Inf_Limits()
 
   // Crop Esophagus : keep only below the OriginOfRightMiddleLobeBronchusZ
   m_Esophagus = 
-    clitk::CropImageAbove<MaskImageType>(m_Esophagus, 2, 
+    clitk::CropImageRemoveGreaterThan<MaskImageType>(m_Esophagus, 2, 
                                          m_OriginOfRightMiddleLobeBronchusZ, 
                                          true, // AutoCrop
                                          GetBackgroundValue());
@@ -468,7 +468,7 @@ ExtractStation_8_Ant_Inf_Limits()
   relPosFilter->UniqueConnectedComponentBySliceOff();
   relPosFilter->SetIntermediateSpacing(3);
   relPosFilter->IntermediateSpacingFlagOn();
-  relPosFilter->SetFuzzyThreshold(GetFuzzyThresholdForS8());
+  relPosFilter->SetFuzzyThreshold(GetFuzzyThreshold("8", "Esophagus"));
   relPosFilter->RemoveObjectFlagOff(); // Do not exclude here because it is dilated
   relPosFilter->CombineWithOrFlagOff(); // NO !
   relPosFilter->IgnoreEmptySliceObjectFlagOn();
@@ -849,7 +849,7 @@ ExtractStation_8_LR_Limits_old2()
     clitk::ComputeCentroids<MaskSliceType>(eso_slices[i], GetBackgroundValue(), c);
     if (c.size() >1) {
       eso_slices[i] = 
-        clitk::CropImageAbove<MaskSliceType>(eso_slices[i], 1, c[1][1], false, GetBackgroundValue());
+        clitk::CropImageRemoveGreaterThan<MaskSliceType>(eso_slices[i], 1, c[1][1], false, GetBackgroundValue());
       eso_slices[i] = 
         clitk::ResizeImageLike<MaskSliceType>(eso_slices[i], aorta_slices[i], GetBackgroundValue());
       // writeImage<MaskSliceType>(eso_slices[i], "eso-slice-"+toString(i)+".mhd");
@@ -1040,7 +1040,7 @@ ExtractStation_8_LR_Limits()
 
     // Crop the vertebralbody below this most post line
     vert_slices[j] = 
-      clitk::CropImageAbove<MaskSliceType>(vert_slices[j], 1, sp_MostAntVertebralBody[1], false, GetBackgroundValue());
+      clitk::CropImageRemoveGreaterThan<MaskSliceType>(vert_slices[j], 1, sp_MostAntVertebralBody[1], false, GetBackgroundValue());
     vert_slices[j] = 
       clitk::ResizeImageLike<MaskSliceType>(vert_slices[j], aorta_slices[i], GetBackgroundValue());
     //    writeImage<MaskSliceType>(vert_slices[i], "vert-slice-"+toString(i)+".mhd");
@@ -1131,8 +1131,8 @@ ExtractStation_8_Remove_Structures()
   //--------------------------------------------------------------------
   StartNewStep("[Station8] remove some structures");
 
-  Remove_Structures("Aorta");
-  Remove_Structures("Esophagus");
+  Remove_Structures("8", "Aorta");
+  Remove_Structures("8", "Esophagus");
 
   // END
   StopCurrentStep<MaskImageType>(m_Working_Support);
@@ -1161,7 +1161,7 @@ EnlargeEsophagusDilatationRadiusInferiorly(MaskImagePointer & Esophagus)
     clitk::FindExtremaPointInAGivenDirection<MaskImageType>(Esophagus, GetBackgroundValue(), 2, true, pt);
     DD(pt);
     Esophagus = 
-      clitk::CropImageBelow<MaskImageType>(Esophagus, 2, 
+      clitk::CropImageRemoveLowerThan<MaskImageType>(Esophagus, 2, 
                                            pt[2], 
                                            false, // AutoCrop
                                            GetBackgroundValue());