Merge branch 'master' of git.creatis.insa-lyon.fr:clitk

[clitk.git] / itk / clitkSegmentationUtils.txx

diff --git a/itk/clitkSegmentationUtils.txx b/itk/clitkSegmentationUtils.txx
index 8fe69a0b13cdfaad0a98819090d35d0ba765a731..b7a5de50693c5f078b19ea2245076f3c384c4657 100644 (file)
--- a/itk/clitkSegmentationUtils.txx
+++ b/itk/clitkSegmentationUtils.txx
@@ -288,7 +288,7 @@ namespace clitk {
     sliceRelPosFilter->SetDirection(direction);
     sliceRelPosFilter->SetFuzzyThreshold(threshold);
     //    sliceRelPosFilter->AddOrientationTypeString(orientation);
-    sliceRelPosFilter->AddAngles(angle, 0.0);
+    sliceRelPosFilter->AddAnglesInRad(angle, 0.0);
     sliceRelPosFilter->SetIntermediateSpacingFlag((spacing != -1));
     sliceRelPosFilter->SetIntermediateSpacing(spacing);
     sliceRelPosFilter->SetUniqueConnectedComponentBySliceFlag(uniqueConnectedComponent);
@@ -385,7 +385,11 @@ namespace clitk {
     typename ImageType::PointType p;
     image->TransformIndexToPhysicalPoint(image->GetLargestPossibleRegion().GetIndex()+
                                          image->GetLargestPossibleRegion().GetSize(), p);
-    return CropImageAlongOneAxis<ImageType>(image, dim, max, p[dim], autoCrop, BG);
+    // 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);
   }
   //--------------------------------------------------------------------
 
@@ -762,8 +766,7 @@ namespace clitk {
   {
     assert((mainDirection==0) || (mainDirection==1));
     typedef itk::ImageSliceIteratorWithIndex<ImageType> SliceIteratorType;
-    SliceIteratorType siter = SliceIteratorType(input, 
-                                                input->GetLargestPossibleRegion());
+    SliceIteratorType siter = SliceIteratorType(input, input->GetLargestPossibleRegion());
     siter.SetFirstDirection(0);
     siter.SetSecondDirection(1);
     siter.GoToBegin();
@@ -782,7 +785,6 @@ namespace clitk {
         A = lA[i];
         B = lB[i];
         C = A;
-      
         // Check that the line is not a point (A=B)
         bool p = (A[0] == B[0]) && (A[1] == B[1]);
       
@@ -1369,6 +1371,7 @@ namespace clitk {
     iter2.GoToBegin();
     double dmin = 100000.0;
     typename ImageType::IndexType indexmin;
+    indexmin.Fill(0);
     while (!iter1.IsAtEnd()) {
       if (iter1.Get() != BG) {
         double d = iter2.Get();
@@ -1389,6 +1392,30 @@ namespace clitk {
   //--------------------------------------------------------------------
      
 
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::Pointer
+  RemoveNegativeIndexFromRegion(ImageType * input) {
+    typedef itk::ChangeInformationImageFilter< ImageType > InfoFilterType; 
+    typename InfoFilterType::Pointer indexChangeFilter = InfoFilterType::New(); 
+    indexChangeFilter->ChangeRegionOn(); 
+    // The next line is commented because not exist in itk 3
+    // typename InfoFilterType::OutputImageOffsetValueType indexShift[3];
+    long indexShift[3];
+    typename ImageType::IndexType index = input->GetLargestPossibleRegion().GetIndex();
+    for(uint i=0;i<ImageType::ImageDimension; i++)
+      indexShift[i] = (index[i]<0 ? -index[i]:0);
+    typename ImageType::PointType origin;
+    for(uint i=0;i<ImageType::ImageDimension; i++)
+    origin[i] = input->GetOrigin()[i] - indexShift[i]*input->GetSpacing()[i];
+    indexChangeFilter->SetOutputOffset( indexShift ); 
+    indexChangeFilter->SetInput(input); 
+    indexChangeFilter->SetOutputOrigin(origin);
+    indexChangeFilter->ChangeOriginOn();
+    indexChangeFilter->Update();
+    return indexChangeFilter->GetOutput();
+  }
+  //--------------------------------------------------------------------
 
 
 } // end of namespace