From: David Sarrut <david.sarrut@creatis.insa-lyon.fr>
Date: Mon, 25 Jul 2011 07:17:54 +0000 (+0200)
Subject: Merge branch 'master' of /home/dsarrut/clitk3.server
X-Git-Tag: v1.3.0~274
X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=9a80ea6d6a4cb304435b2bbdc4dda677036b0e2b;hp=cbd1fd38ff1782f4a06dc4d8133abfbaf17c929d;p=clitk.git

Merge branch 'master' of /home/dsarrut/clitk3.server
---

diff --git a/itk/clitkForwardWarpImageFilter.txx b/itk/clitkForwardWarpImageFilter.txx
index 5e1bb13..e99ef0f 100644
--- a/itk/clitkForwardWarpImageFilter.txx
+++ b/itk/clitkForwardWarpImageFilter.txx
@@ -154,6 +154,7 @@ void HelperClass1<InputImageType, OutputImageType, DeformationFieldType>::Thread
   //define some temp variables
   signed long baseIndex[ImageDimension];
   double distance[ImageDimension];
+  for(uint i=0; i<ImageDimension; i++) distance[i] = 0.0; // to avoid warning
   unsigned int dim, counter, upper;
   double overlap, totalOverlap;
   typename OutputImageType::IndexType neighIndex;
@@ -195,7 +196,7 @@ void HelperClass1<InputImageType, OutputImageType, DeformationFieldType>::Thread
         upper = counter;  // each bit indicates upper/lower neighbour
 
         // get neighbor index and overlap fraction
-        for( dim = 0; dim < 3; dim++ ) {
+        for( dim = 0; dim < ImageDimension; dim++ ) {
           if ( upper & 1 ) {
             neighIndex[dim] = baseIndex[dim] + 1;
             overlap *= distance[dim];
diff --git a/itk/clitkSegmentationUtils.h b/itk/clitkSegmentationUtils.h
index 85f2591..6204c9c 100644
--- a/itk/clitkSegmentationUtils.h
+++ b/itk/clitkSegmentationUtils.h
@@ -444,11 +444,32 @@ namespace clitk {
                                           int dim1, int dim2, bool removeLowerPartFlag);
   //--------------------------------------------------------------------
   
-  
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::Pointer
+  SliceBySliceSetBackgroundFromPoints(const ImageType * input, 
+                                      typename ImageType::PixelType BG, 
+                                      int sliceDim,
+                                      std::vector<typename ImageType::PointType> & A, 
+                                      bool removeGreaterThanXFlag,
+                                      bool removeGreaterThanYFlag);
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  void
+  FillRegionWithValue(ImageType * input, typename ImageType::PixelType value, 
+                      typename ImageType::RegionType & region);
+  //--------------------------------------------------------------------
+
+
   //--------------------------------------------------------------------
   template<class ImageType>
   void
-  FillRegionWithValue(ImageType * input, typename ImageType::PixelType value, typename ImageType::RegionType & region);
+  GetMinMaxBoundary(ImageType * input, typename ImageType::PointType & min, 
+                    typename ImageType::PointType & max);
   //--------------------------------------------------------------------
 
 }
diff --git a/itk/clitkSegmentationUtils.txx b/itk/clitkSegmentationUtils.txx
index b328315..afcefcf 100644
--- a/itk/clitkSegmentationUtils.txx
+++ b/itk/clitkSegmentationUtils.txx
@@ -730,7 +730,8 @@ namespace clitk {
     dilateFilter->SetForegroundValue(FG);
     dilateFilter->SetBoundaryToForeground(false);
     dilateFilter->SetKernel(structuringElement);
-    dilateFilter->SetInput(output);
+    if (extendSupport) dilateFilter->SetInput(output);
+    else dilateFilter->SetInput(image);
     dilateFilter->Update();
     return dilateFilter->GetOutput();
   }
@@ -831,9 +832,6 @@ namespace clitk {
     while ((i<lA.size()) && (!siter.IsAtEnd())) {
       // Check that the current slice correspond to the current point
       input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
-      // DD(C);
-      // DD(i);
-      // DD(lA[i]);
       if ((fabs(C[2] - lA[i][2]))>0.01) { // is !equal with a tolerance of 0.01 mm
       }
       else {
@@ -841,9 +839,6 @@ namespace clitk {
         A = lA[i];
         B = lB[i];
         C = A;
-        // DD(A);
-        // DD(B);
-        // DD(C);
       
         // Check that the line is not a point (A=B)
         bool p = (A[0] == B[0]) && (A[1] == B[1]);
@@ -1063,7 +1058,7 @@ namespace clitk {
                                                             extremaDirection, extremaOppositeFlag, p);
       if (found) {
         position2D[i] = p;
-      }    
+      }
     }
     
     // Convert 2D points in slice into 3D points
@@ -1076,8 +1071,8 @@ namespace clitk {
       p[lineDirection] += 10;
       B.push_back(p);
       // Margins ?
-      A[i][1] += margin;
-      B[i][1] += margin;
+      A[i][extremaDirection] += margin;
+      B[i][extremaDirection] += margin;
     }
 
   }
@@ -1196,6 +1191,78 @@ namespace clitk {
   }
   //--------------------------------------------------------------------
 
+  //--------------------------------------------------------------------
+  /* Consider an input object, slice by slice, use the point A and set
+     pixel to BG according to their position relatively to A
+  */
+  template<class ImageType>
+  typename ImageType::Pointer
+  SliceBySliceSetBackgroundFromPoints(const ImageType * input, 
+                                      typename ImageType::PixelType BG, 
+                                      int sliceDim,
+                                      std::vector<typename ImageType::PointType> & A, 
+                                      bool removeGreaterThanXFlag,
+                                      bool removeGreaterThanYFlag)
+    
+  {
+    // Extract slices
+    typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
+    typedef typename SliceType::Pointer SlicePointer;
+    std::vector<SlicePointer> slices;
+    clitk::ExtractSlices<ImageType>(input, sliceDim, slices);
+
+    // Start at slice that contains A
+    typename ImageType::IndexType Ap;
+    
+    // Determine slice largest region
+    typename SliceType::RegionType region = slices[0]->GetLargestPossibleRegion();
+    typename SliceType::SizeType size = region.GetSize();
+    typename SliceType::IndexType index = region.GetIndex();
+
+    // Loop from slice A to slice B
+    for(uint i=0; i<A.size(); i++) {
+      input->TransformPhysicalPointToIndex(A[i], Ap);
+      uint sliceIndex = Ap[2] - input->GetLargestPossibleRegion().GetIndex()[2];
+      if ((sliceIndex < 0) || (sliceIndex >= slices.size())) {
+        continue; // do not consider this slice
+      }
+      
+      // Compute region for BG
+      if (removeGreaterThanXFlag) {
+        index[0] = Ap[0];
+        size[0] = region.GetSize()[0]-(index[0]-region.GetIndex()[0]);
+      }
+      else {
+        index[0] = region.GetIndex()[0];
+        size[0] = Ap[0] - index[0];
+      }
+
+      if (removeGreaterThanYFlag) {
+        index[1] = Ap[1];
+        size[1] = region.GetSize()[1]-(index[1]-region.GetIndex()[1]);
+      }
+      else {
+        index[1] = region.GetIndex()[1];
+        size[1] = Ap[1] - index[1];
+      }
+
+      // Set region
+      region.SetSize(size);
+      region.SetIndex(index);
+
+      // Fill region with BG (simple region iterator)
+      FillRegionWithValue<SliceType>(slices[sliceIndex], BG, region);
+      // Loop
+    }
+    
+    // Merge slices
+    typename ImageType::Pointer output;
+    output = clitk::JoinSlices<ImageType>(slices, input, sliceDim);
+    return output;
+  }
+  //--------------------------------------------------------------------
+
+
   //--------------------------------------------------------------------
   template<class ImageType>
   void
@@ -1211,5 +1278,23 @@ namespace clitk {
   }
   //--------------------------------------------------------------------
 
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  void
+  GetMinMaxBoundary(ImageType * input, typename ImageType::PointType & min, 
+                    typename ImageType::PointType & max)
+  {
+    typedef typename ImageType::PointType PointType;
+    typedef typename ImageType::IndexType IndexType;
+    IndexType min_i, max_i;
+    min_i = input->GetLargestPossibleRegion().GetIndex();
+    for(uint i=0; i<ImageType::ImageDimension; i++)
+      max_i[i] = input->GetLargestPossibleRegion().GetSize()[i] + min_i[i];
+    input->TransformIndexToPhysicalPoint(min_i, min);
+    input->TransformIndexToPhysicalPoint(max_i, max);  
+  }
+  //--------------------------------------------------------------------
+
 } // end of namespace