X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=itk%2FclitkSegmentationUtils.txx;h=0d758e447caa88e0a33745a00d6b2faffc772ea2;hb=3b072585d9fc4e6b21940531196cec798ee74796;hp=b7a5de50693c5f078b19ea2245076f3c384c4657;hpb=fb01ed73088a1440263acba4cad589b15e180eef;p=clitk.git

diff --git a/itk/clitkSegmentationUtils.txx b/itk/clitkSegmentationUtils.txx
index b7a5de5..0d758e4 100644
--- a/itk/clitkSegmentationUtils.txx
+++ b/itk/clitkSegmentationUtils.txx
@@ -354,7 +354,7 @@ namespace clitk {
       ++iter;
     }
     if (!found) return false;
-    input->TransformIndexToPhysicalPoint(max, point);
+    input->TransformIndexToPhysicalPoint(max, point); // half of the pixel
     return true;
   }
   //--------------------------------------------------------------------
@@ -382,14 +382,12 @@ namespace clitk {
                  int dim, double max, bool autoCrop,
                  typename ImageType::PixelType BG) 
   {
-    typename ImageType::PointType p;
+    typename ImageType::PointType p; 
+    
     image->TransformIndexToPhysicalPoint(image->GetLargestPossibleRegion().GetIndex()+
                                          image->GetLargestPossibleRegion().GetSize(), p);
-    // Add GetSpacing because remove Lower or equal than
-    // DD(max);
-    // DD(p);
-    // DD(max+image->GetSpacing()[dim]);
-    return CropImageAlongOneAxis<ImageType>(image, dim, max+image->GetSpacing()[dim], p[dim], autoCrop, BG);
+
+    return CropImageAlongOneAxis<ImageType>(image, dim, max, p[dim], autoCrop, BG);
   }
   //--------------------------------------------------------------------
 
@@ -404,16 +402,24 @@ namespace clitk {
     // Compute region size
     typename ImageType::RegionType region;
     typename ImageType::SizeType size = image->GetLargestPossibleRegion().GetSize();
-    typename ImageType::PointType p = image->GetOrigin();
+    
+    // Starting index
+    typename ImageType::PointType p = image->GetOrigin(); // not at pixel center !
     if (min > p[dim]) p[dim] = min; // Check if not outside the image
     typename ImageType::IndexType start;
     image->TransformPhysicalPointToIndex(p, start);
-    double m = image->GetOrigin()[dim] + size[dim]*image->GetSpacing()[dim];
+
+    // Size of the region
+    // -1 because last point is size -1
+    double m = image->GetOrigin()[dim] + (size[dim]-1)*image->GetSpacing()[dim];
     if (max > m) p[dim] = m; // Check if not outside the image
     else p[dim] = max;
+
     typename ImageType::IndexType end;
     image->TransformPhysicalPointToIndex(p, end);
-    size[dim] = abs(end[dim]-start[dim]);
+    size[dim] = abs(end[dim]-start[dim])+1;// +1 because we want to include the point. 
+    
+    // Set region
     region.SetIndex(start);
     region.SetSize(size);
   
@@ -762,9 +768,24 @@ namespace clitk {
                                               std::vector<typename ImageType::PointType> & lB, 
                                               typename ImageType::PixelType BG, 
                                               int mainDirection, 
-                                              double offsetToKeep)
+                                              double offsetToKeep,
+                                              bool keepIfEqual)
   {
     assert((mainDirection==0) || (mainDirection==1));
+    typename ImageType::PointType offset;
+    offset[0] = offset[1] = offset[2] = 0.0;
+    offset[mainDirection] = offsetToKeep;
+    SliceBySliceSetBackgroundFromLineSeparation<ImageType>(input, lA, lB, BG, offset, keepIfEqual);
+  }
+  template<class ImageType>
+  void 
+  SliceBySliceSetBackgroundFromLineSeparation(ImageType * input, 
+                                              std::vector<typename ImageType::PointType> & lA, 
+                                              std::vector<typename ImageType::PointType> & lB, 
+                                              typename ImageType::PixelType BG, 
+                                              typename ImageType::PointType offsetToKeep,
+                                              bool keepIfEqual)
+  {
     typedef itk::ImageSliceIteratorWithIndex<ImageType> SliceIteratorType;
     SliceIteratorType siter = SliceIteratorType(input, input->GetLargestPossibleRegion());
     siter.SetFirstDirection(0);
@@ -789,7 +810,10 @@ namespace clitk {
         bool p = (A[0] == B[0]) && (A[1] == B[1]);
       
         if (!p) {
-          C[mainDirection] += offsetToKeep; // I know I must keep this point
+          //C[mainDirection] += offsetToKeep; // I know I must keep this point
+          C[0] += offsetToKeep[0];
+          C[1] += offsetToKeep[1];
+          //C[2] += offsetToKeep[2]; 
           double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
           bool isPositive = s<0;
           while (!siter.IsAtEndOfSlice()) {
@@ -797,7 +821,9 @@ namespace clitk {
               // Very slow, I know ... but image should be very small
               input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
               double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
-              if (s == 0) siter.Set(BG); // on the line, we decide to remove
+              if (s == 0) {
+                if (!keepIfEqual) siter.Set(BG); // on the line, we decide to remove
+              }
               if (isPositive) {
                 if (s > 0) siter.Set(BG);
               }
@@ -1321,11 +1347,11 @@ namespace clitk {
       // Compute dmap for S1 *TO PUT IN FONCTION*
       dmap = clitk::DistanceMap<SliceType>(slices_s1[i], BG);
       dmaps1.push_back(dmap);
-      writeImage<FloatImageType>(dmap, "dmap1.mha");
+      //writeImage<FloatImageType>(dmap, "dmap1.mha");
       // Compute dmap for S2
       dmap = clitk::DistanceMap<SliceType>(slices_s2[i], BG);
       dmaps2.push_back(dmap);
-      writeImage<FloatImageType>(dmap, "dmap2.mha");
+      //writeImage<FloatImageType>(dmap, "dmap2.mha");
       
       // Look in S2 for the point the closest to S1
       typename SliceType::PointType p = ComputeClosestPoint<SliceType>(slices_s1[i], dmaps2[i], BG);
@@ -1340,14 +1366,14 @@ namespace clitk {
 
     }
 
-    // Debug dmap
     /*
-      typedef itk::Image<float,3> FT;
-      FT::Pointer f = FT::New();
-      typename FT::Pointer d1 = clitk::JoinSlices<FT>(dmaps1, S1, 2);
-      typename FT::Pointer d2 = clitk::JoinSlices<FT>(dmaps2, S2, 2);
-      writeImage<FT>(d1, "d1.mha");
-      writeImage<FT>(d2, "d2.mha");
+    // Debug dmap
+    typedef itk::Image<float,3> FT;
+    FT::Pointer f = FT::New();
+    typename FT::Pointer d1 = clitk::JoinSlices<FT>(dmaps1, S1, 2);
+    typename FT::Pointer d2 = clitk::JoinSlices<FT>(dmaps2, S2, 2);
+    writeImage<FT>(d1, "d1.mha");
+    writeImage<FT>(d2, "d2.mha");
     */
   }
   //--------------------------------------------------------------------