X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;ds=sidebyside;f=itk%2FclitkSegmentationUtils.txx;h=de243adc2bc5394f0623ade2b1b490e976991ab6;hb=02f230e65dbfde06e84da374bb085643e29b5090;hp=adca988098ad8c78fee5cfb132b890fb0bef0c09;hpb=9ad931d0b92b6f5ae0f4eb4c2c90319eeb8316ef;p=clitk.git

diff --git a/itk/clitkSegmentationUtils.txx b/itk/clitkSegmentationUtils.txx
index adca988..de243ad 100644
--- a/itk/clitkSegmentationUtils.txx
+++ b/itk/clitkSegmentationUtils.txx
@@ -38,89 +38,6 @@
 
 namespace clitk {
 
-  //--------------------------------------------------------------------
-  template<class ImageType>
-  void ComputeBBFromImageRegion(const ImageType * image, 
-                                typename ImageType::RegionType region,
-                                typename itk::BoundingBox<unsigned long, 
-                                ImageType::ImageDimension>::Pointer bb) {
-    typedef typename ImageType::IndexType IndexType;
-    IndexType firstIndex;
-    IndexType lastIndex;
-    for(unsigned int i=0; i<image->GetImageDimension(); i++) {
-      firstIndex[i] = region.GetIndex()[i];
-      lastIndex[i] = firstIndex[i]+region.GetSize()[i];
-    }
-
-    typedef itk::BoundingBox<unsigned long, 
-                             ImageType::ImageDimension> BBType;
-    typedef typename BBType::PointType PointType;
-    PointType lastPoint;
-    PointType firstPoint;
-    image->TransformIndexToPhysicalPoint(firstIndex, firstPoint);
-    image->TransformIndexToPhysicalPoint(lastIndex, lastPoint);
-
-    bb->SetMaximum(lastPoint);
-    bb->SetMinimum(firstPoint);
-  }
-  //--------------------------------------------------------------------
-
-
-  //--------------------------------------------------------------------
-  template<int Dimension>
-  void ComputeBBIntersection(typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbo, 
-                             typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi1, 
-                             typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi2) {
-
-    typedef itk::BoundingBox<unsigned long, Dimension> BBType;
-    typedef typename BBType::PointType PointType;
-    PointType lastPoint;
-    PointType firstPoint;
-
-    for(unsigned int i=0; i<Dimension; i++) {
-      firstPoint[i] = std::max(bbi1->GetMinimum()[i], 
-                               bbi2->GetMinimum()[i]);
-      lastPoint[i] = std::min(bbi1->GetMaximum()[i], 
-                              bbi2->GetMaximum()[i]);
-    }
-
-    bbo->SetMaximum(lastPoint);
-    bbo->SetMinimum(firstPoint);
-  }
-  //--------------------------------------------------------------------
-
-
-  //--------------------------------------------------------------------
-  template<class ImageType>
-  void ComputeRegionFromBB(const ImageType * image, 
-                           const typename itk::BoundingBox<unsigned long, 
-                                                           ImageType::ImageDimension>::Pointer bb, 
-                           typename ImageType::RegionType & region) {
-    // Types
-    typedef typename ImageType::IndexType  IndexType;
-    typedef typename ImageType::PointType  PointType;
-    typedef typename ImageType::RegionType RegionType;
-    typedef typename ImageType::SizeType   SizeType;
-
-    // Region starting point
-    IndexType regionStart;
-    PointType start = bb->GetMinimum();
-    image->TransformPhysicalPointToIndex(start, regionStart);
-    
-    // Region size
-    SizeType regionSize;
-    PointType maxs = bb->GetMaximum();
-    PointType mins = bb->GetMinimum();
-    for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
-      regionSize[i] = lrint((maxs[i] - mins[i])/image->GetSpacing()[i]);
-    }
-   
-    // Create region
-    region.SetIndex(regionStart);
-    region.SetSize(regionSize);
-  }
-  //--------------------------------------------------------------------
-
   //--------------------------------------------------------------------
   template<class ImageType, class TMaskImageType>
   typename ImageType::Pointer
@@ -313,19 +230,37 @@ namespace clitk {
 
 
   //--------------------------------------------------------------------
-  template<class ImageType>
-  typename ImageType::Pointer
-  ResizeImageLike(const ImageType * input,                       
-                  const itk::ImageBase<ImageType::ImageDimension> * like, 
-                  typename ImageType::PixelType backgroundValue) 
+  template<class MaskImageType>
+  typename MaskImageType::Pointer
+  SliceBySliceRelativePosition(const MaskImageType * input,
+                               const MaskImageType * object,
+                               int direction, 
+                               double threshold, 
+                               std::string orientation, 
+                               bool uniqueConnectedComponent, 
+                               double spacing, 
+                               bool autocropFlag, 
+                               bool singleObjectCCL) 
   {
-    typedef CropLikeImageFilter<ImageType> CropFilterType;
-    typename CropFilterType::Pointer cropFilter = CropFilterType::New();
-    cropFilter->SetInput(input);
-    cropFilter->SetCropLikeImage(like);
-    cropFilter->SetBackgroundValue(backgroundValue);
-    cropFilter->Update();
-    return cropFilter->GetOutput();  
+    typedef clitk::SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
+    typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
+    sliceRelPosFilter->VerboseStepFlagOff();
+    sliceRelPosFilter->WriteStepFlagOff();
+    sliceRelPosFilter->SetInput(input);
+    sliceRelPosFilter->SetInputObject(object);
+    sliceRelPosFilter->SetDirection(direction);
+    sliceRelPosFilter->SetFuzzyThreshold(threshold);
+    sliceRelPosFilter->AddOrientationTypeString(orientation);
+    sliceRelPosFilter->SetIntermediateSpacingFlag((spacing != -1));
+    sliceRelPosFilter->SetIntermediateSpacing(spacing);
+    sliceRelPosFilter->SetUniqueConnectedComponentBySliceFlag(uniqueConnectedComponent);
+    sliceRelPosFilter->ObjectCCLSelectionFlagOff();
+    sliceRelPosFilter->SetUseTheLargestObjectCCLFlag(singleObjectCCL);
+    //    sliceRelPosFilter->SetInverseOrientationFlag(inverseflag); 
+    sliceRelPosFilter->SetAutoCropFlag(autocropFlag); 
+    sliceRelPosFilter->IgnoreEmptySliceObjectFlagOn();
+    sliceRelPosFilter->Update();
+    return sliceRelPosFilter->GetOutput();
   }
   //--------------------------------------------------------------------
 
@@ -337,13 +272,14 @@ namespace clitk {
                                const MaskImageType * object,
                                int direction, 
                                double threshold, 
-                               std::string orientation, 
+                               double angle,
+                               bool inverseflag,
                                bool uniqueConnectedComponent, 
                                double spacing, 
                                bool autocropFlag, 
                                bool singleObjectCCL) 
   {
-    typedef SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
+    typedef clitk::SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
     typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
     sliceRelPosFilter->VerboseStepFlagOff();
     sliceRelPosFilter->WriteStepFlagOff();
@@ -351,13 +287,14 @@ namespace clitk {
     sliceRelPosFilter->SetInputObject(object);
     sliceRelPosFilter->SetDirection(direction);
     sliceRelPosFilter->SetFuzzyThreshold(threshold);
-    sliceRelPosFilter->AddOrientationTypeString(orientation);
+    //    sliceRelPosFilter->AddOrientationTypeString(orientation);
+    sliceRelPosFilter->AddAnglesInRad(angle, 0.0);
     sliceRelPosFilter->SetIntermediateSpacingFlag((spacing != -1));
     sliceRelPosFilter->SetIntermediateSpacing(spacing);
     sliceRelPosFilter->SetUniqueConnectedComponentBySliceFlag(uniqueConnectedComponent);
     sliceRelPosFilter->ObjectCCLSelectionFlagOff();
     sliceRelPosFilter->SetUseTheLargestObjectCCLFlag(singleObjectCCL);
-    //    sliceRelPosFilter->SetInverseOrientationFlag(inverseflag); 
+    sliceRelPosFilter->SetInverseOrientationFlag(inverseflag); 
     sliceRelPosFilter->SetAutoCropFlag(autocropFlag); 
     sliceRelPosFilter->IgnoreEmptySliceObjectFlagOn();
     sliceRelPosFilter->Update();
@@ -417,7 +354,7 @@ namespace clitk {
       ++iter;
     }
     if (!found) return false;
-    input->TransformIndexToPhysicalPoint(max, point);
+    input->TransformIndexToPhysicalPoint(max, point); // half of the pixel
     return true;
   }
   //--------------------------------------------------------------------
@@ -445,9 +382,11 @@ 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);
+
     return CropImageAlongOneAxis<ImageType>(image, dim, max, p[dim], autoCrop, BG);
   }
   //--------------------------------------------------------------------
@@ -463,14 +402,24 @@ namespace clitk {
     // Compute region size
     typename ImageType::RegionType region;
     typename ImageType::SizeType size = image->GetLargestPossibleRegion().GetSize();
-    typename ImageType::PointType p = image->GetOrigin();
-    p[dim] = min;
+    
+    // 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);
-    p[dim] = max;
+
+    // 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);
   
@@ -823,8 +772,7 @@ 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();
@@ -843,7 +791,6 @@ 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]);
       
@@ -1380,11 +1327,11 @@ 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);
@@ -1430,6 +1377,7 @@ 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();
@@ -1450,6 +1398,30 @@ 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