moved $CLITK3/vv/scripts to $CLITK3/scripts

[clitk.git] / segmentation / clitkExtractLymphStation_8.txx

diff --git a/segmentation/clitkExtractLymphStation_8.txx b/segmentation/clitkExtractLymphStation_8.txx
index dd3fdca3cafcf96622b035e4a42f9999c693cb6f..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());
@@ -462,13 +462,13 @@ ExtractStation_8_Ant_Inf_Limits()
   relPosFilter->WriteStepFlagOff();
   relPosFilter->SetInput(m_Working_Support);
   relPosFilter->SetInputObject(m_Esophagus);
-  relPosFilter->AddOrientationTypeString("P");
-  relPosFilter->InverseOrientationFlagOff();
+  relPosFilter->AddOrientationTypeString("PostTo");
+  //  relPosFilter->InverseOrientationFlagOff();
   relPosFilter->SetDirection(2); // Z axis
   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();
@@ -635,7 +635,7 @@ clitk::ExtractLymphStationsFilter<ImageType>::
 ExtractStation_8_Single_CCL_Limits() 
 {
   //--------------------------------------------------------------------
-  StartNewStep("[Station8] Single CCL");
+  StartNewStep("[Station8 or 3P] Slice by slice, keep a single CCL (the closest to VertebralBody)");
 
   // Consider slices
   std::vector<typename MaskSliceType::Pointer> slices;
@@ -654,15 +654,11 @@ ExtractStation_8_Single_CCL_Limits()
     std::vector<typename MaskSliceType::PointType> c;
     clitk::ComputeCentroids<MaskSliceType>(slices[i], GetBackgroundValue(), centroids);
     clitk::ComputeCentroids<MaskSliceType>(slices_vb[i], GetBackgroundValue(), c);
-    // DD(c.size());
-    // DD(centroids.size());
     if ((c.size() > 1) && (centroids.size() > 1)) {
       // keep the one which is the closer to vertebralbody centroid
       double distance=1000000;
       int index=0;
-      //      DD(c[1]);
       for(uint j=1; j<centroids.size(); j++) {
-        // DD(centroids[j]);
         double d = centroids[j].EuclideanDistanceTo(c[1]);
         if (d<distance) {
           distance = d;
@@ -852,9 +848,8 @@ ExtractStation_8_LR_Limits_old2()
     std::vector<typename MaskSliceType::PointType> c;
     clitk::ComputeCentroids<MaskSliceType>(eso_slices[i], GetBackgroundValue(), c);
     if (c.size() >1) {
-      // DD(c[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");
@@ -1041,12 +1036,11 @@ ExtractStation_8_LR_Limits()
         j++;
       }
     }
-    // DD(j);
     sp_MostAntVertebralBody[1] += GetDistanceMaxToAnteriorPartOfTheSpine(); // Consider offset
 
     // 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");
@@ -1065,8 +1059,6 @@ ExtractStation_8_LR_Limits()
     clitk::PointsUtils<MaskImageType>::Convert2DTo3D(sp_MostLeftVertebralBody, VertebralBody, i, p);
     p_MostLeftVertebralBody.push_back(p);
 
-    // DD(p_MostLeftVertebralBody.back());
-
     /* -------------------------------------------------------------------------------------
        Find most Left point in Esophagus
      */
@@ -1082,14 +1074,12 @@ ExtractStation_8_LR_Limits()
       //   p_MostLeftEsophagus.push_back(p);
       //   sp_MostLeftEsophagus = sp_temp; // Retrieve previous 2D position
       //   found = true;
-      //   DD(p);
       // }
     }
     else {
       clitk::PointsUtils<MaskImageType>::Convert2DTo3D(sp_MostLeftEsophagus, EsophagusForSlice, i, p);
       p_MostLeftEsophagus.push_back(p);
       // sp_temp = sp_MostLeftEsophagus; // Store previous 2D position
-      // // DD(p_MostLeftEsophagus.back());
     }
       
     /* -------------------------------------------------------------------------------------
@@ -1141,11 +1131,8 @@ ExtractStation_8_Remove_Structures()
   //--------------------------------------------------------------------
   StartNewStep("[Station8] remove some structures");
 
-  MaskImagePointer Aorta = GetAFDB()->template GetImage<MaskImageType>("Aorta");
-  clitk::AndNot<MaskImageType>(m_Working_Support, Aorta, GetBackgroundValue());
-
-  MaskImagePointer Esophagus = GetAFDB()->template GetImage<MaskImageType>("Esophagus");
-  clitk::AndNot<MaskImageType>(m_Working_Support, Esophagus, GetBackgroundValue());
+  Remove_Structures("8", "Aorta");
+  Remove_Structures("8", "Esophagus");
 
   // END
   StopCurrentStep<MaskImageType>(m_Working_Support);
@@ -1174,7 +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());
@@ -1243,8 +1230,8 @@ ExtractStation_8_LR_Limits_old()
   relPosFilter->WriteStepFlagOff();
   relPosFilter->SetInput(m_Working_Support);
   relPosFilter->SetInputObject(Esophagus);
-  relPosFilter->AddOrientationTypeString("L");
-  relPosFilter->InverseOrientationFlagOn(); // Not Left to
+  relPosFilter->AddOrientationTypeString("NotLeftTo");
+  //  relPosFilter->InverseOrientationFlagOn(); // Not Left to
   relPosFilter->SetDirection(2); // Z axis
   relPosFilter->UniqueConnectedComponentBySliceOff(); // important
   relPosFilter->SetIntermediateSpacing(4);