X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=itk%2FclitkSegmentationUtils.txx;h=24ca5194853595a1ac2b815aeeee60533f5412e1;hb=1d3d35c2ac5c6b74d24d9f56d53de6aa990915d1;hp=afcefcf3077701a64abeb070374ece19c45ba044;hpb=6194949c0beb1589904e22381b9aba1bbface172;p=clitk.git

diff --git a/itk/clitkSegmentationUtils.txx b/itk/clitkSegmentationUtils.txx
index afcefcf..24ca519 100644
--- a/itk/clitkSegmentationUtils.txx
+++ b/itk/clitkSegmentationUtils.txx
@@ -34,92 +34,10 @@
 #include <itkImageSliceIteratorWithIndex.h>
 #include <itkBinaryMorphologicalOpeningImageFilter.h>
 #include <itkImageDuplicator.h>
+#include <itkSignedMaurerDistanceMapImageFilter.h>
 
 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
@@ -312,19 +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();
   }
   //--------------------------------------------------------------------
 
@@ -336,13 +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();
@@ -350,13 +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->SetUniqueConnectedComponentBySlice(uniqueConnectedComponent);
-    sliceRelPosFilter->CCLSelectionFlagOff();
-    sliceRelPosFilter->SetUseASingleObjectConnectedComponentBySliceFlag(singleObjectCCL);
-    //    sliceRelPosFilter->SetInverseOrientationFlag(inverseflag); 
+    sliceRelPosFilter->SetUniqueConnectedComponentBySliceFlag(uniqueConnectedComponent);
+    sliceRelPosFilter->ObjectCCLSelectionFlagOff();
+    sliceRelPosFilter->SetUseTheLargestObjectCCLFlag(singleObjectCCL);
+    sliceRelPosFilter->SetInverseOrientationFlag(inverseflag); 
     sliceRelPosFilter->SetAutoCropFlag(autocropFlag); 
     sliceRelPosFilter->IgnoreEmptySliceObjectFlagOn();
     sliceRelPosFilter->Update();
@@ -364,6 +302,7 @@ namespace clitk {
   }
   //--------------------------------------------------------------------
 
+
   //--------------------------------------------------------------------
   template<class ImageType>
   bool
@@ -378,6 +317,7 @@ namespace clitk {
   }
   //--------------------------------------------------------------------
 
+
   //--------------------------------------------------------------------
   template<class ImageType>
   bool
@@ -445,7 +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);
   }
   //--------------------------------------------------------------------
 
@@ -461,10 +405,12 @@ namespace clitk {
     typename ImageType::RegionType region;
     typename ImageType::SizeType size = image->GetLargestPossibleRegion().GetSize();
     typename ImageType::PointType p = image->GetOrigin();
-    p[dim] = min;
+    if (min > p[dim]) p[dim] = min; // Check if not outside the image
     typename ImageType::IndexType start;
     image->TransformPhysicalPointToIndex(p, start);
-    p[dim] = max;
+    double m = image->GetOrigin()[dim] + size[dim]*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]);
@@ -818,9 +764,9 @@ namespace clitk {
                                               int mainDirection, 
                                               double offsetToKeep)
   {
+    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();
@@ -839,7 +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]);
       
@@ -929,6 +874,34 @@ namespace clitk {
   //--------------------------------------------------------------------
 
 
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  void 
+  Or(ImageType * input, 
+     const ImageType * object, 
+     typename ImageType::PixelType BG)
+  {
+    typename ImageType::Pointer o;
+    bool resized=false;
+    if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input, object)) {
+      o = clitk::ResizeImageLike<ImageType>(object, input, BG);
+      resized = true;
+    }
+
+    typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
+    typename BoolFilterType::Pointer boolFilter = BoolFilterType::New(); 
+    boolFilter->InPlaceOn();
+    boolFilter->SetInput1(input);
+    if (resized) boolFilter->SetInput2(o);  
+    else boolFilter->SetInput2(object);
+    boolFilter->SetBackgroundValue1(BG);
+    boolFilter->SetBackgroundValue2(BG);
+    boolFilter->SetOperationType(BoolFilterType::Or);
+    boolFilter->Update();
+  }
+  //--------------------------------------------------------------------
+
+
   //--------------------------------------------------------------------
   template<class ImageType>
   typename ImageType::Pointer
@@ -1296,5 +1269,129 @@ namespace clitk {
   }
   //--------------------------------------------------------------------
 
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename itk::Image<float, ImageType::ImageDimension>::Pointer
+  DistanceMap(const ImageType * input, typename ImageType::PixelType BG)//, 
+  //              typename itk::Image<float, ImageType::ImageDimension>::Pointer dmap) 
+  {
+    typedef itk::Image<float,ImageType::ImageDimension> FloatImageType;
+    typedef itk::SignedMaurerDistanceMapImageFilter<ImageType, FloatImageType> DistanceMapFilterType;
+    typename DistanceMapFilterType::Pointer filter = DistanceMapFilterType::New();
+    filter->SetInput(input);
+    filter->SetUseImageSpacing(true);
+    filter->SquaredDistanceOff();
+    filter->SetBackgroundValue(BG);
+    filter->Update();
+    return filter->GetOutput();
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  void 
+  SliceBySliceBuildLineSegmentAccordingToMinimalDistanceBetweenStructures(const ImageType * S1, 
+                                                                          const ImageType * S2, 
+                                                                          typename ImageType::PixelType BG, 
+                                                                          int sliceDimension, 
+                                                                          std::vector<typename ImageType::PointType> & A, 
+                                                                          std::vector<typename ImageType::PointType> & B)
+  {
+    // Extract slices
+    typedef typename itk::Image<typename ImageType::PixelType, 2> SliceType;
+    typedef typename SliceType::Pointer SlicePointer;
+    std::vector<SlicePointer> slices_s1;
+    std::vector<SlicePointer> slices_s2;
+    clitk::ExtractSlices<ImageType>(S1, sliceDimension, slices_s1);
+    clitk::ExtractSlices<ImageType>(S2, sliceDimension, slices_s2);
+
+    assert(slices_s1.size() == slices_s2.size());
+
+    // Prepare dmap
+    typedef itk::Image<float,2> FloatImageType;
+    typedef itk::SignedMaurerDistanceMapImageFilter<SliceType, FloatImageType> DistanceMapFilterType;
+    std::vector<typename FloatImageType::Pointer> dmaps1;
+    std::vector<typename FloatImageType::Pointer> dmaps2;
+    typename FloatImageType::Pointer dmap;
+
+    // loop on slices
+    for(uint i=0; i<slices_s1.size(); i++) {
+      // 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");
+      // Compute dmap for S2
+      dmap = clitk::DistanceMap<SliceType>(slices_s2[i], BG);
+      dmaps2.push_back(dmap);
+      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);
+      typename ImageType::PointType p3D;
+      clitk::PointsUtils<ImageType>::Convert2DTo3D(p, S1, i, p3D);
+      A.push_back(p3D);
+
+      // Look in S2 for the point the closest to S1
+      p = ComputeClosestPoint<SliceType>(slices_s2[i], dmaps1[i], BG);
+      clitk::PointsUtils<ImageType>::Convert2DTo3D(p, S2, i, p3D);
+      B.push_back(p3D);
+
+    }
+
+    // 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");
+    */
+  }
+  //--------------------------------------------------------------------
+
+
+  //--------------------------------------------------------------------
+  template<class ImageType>
+  typename ImageType::PointType
+  ComputeClosestPoint(const ImageType * input, 
+                      const itk::Image<float, ImageType::ImageDimension> * dmap, 
+                      typename ImageType::PixelType & BG) 
+  {
+    // Loop dmap + S2, if FG, get min
+    typedef itk::Image<float,ImageType::ImageDimension> FloatImageType;
+    typedef itk::ImageRegionConstIteratorWithIndex<ImageType> ImageIteratorType;
+    typedef itk::ImageRegionConstIterator<FloatImageType> DMapIteratorType;
+    ImageIteratorType iter1(input, input->GetLargestPossibleRegion());
+    DMapIteratorType iter2(dmap, dmap->GetLargestPossibleRegion());
+    
+    iter1.GoToBegin();
+    iter2.GoToBegin();
+    double dmin = 100000.0;
+    typename ImageType::IndexType indexmin;
+    while (!iter1.IsAtEnd()) {
+      if (iter1.Get() != BG) {
+        double d = iter2.Get();
+        if (d<dmin) {
+          indexmin = iter1.GetIndex();
+          dmin = d;
+        }
+      }
+      ++iter1;
+      ++iter2;
+    }
+    
+    // Convert in Point
+    typename ImageType::PointType p;
+    input->TransformIndexToPhysicalPoint(indexmin, p);
+    return p;
+  }
+  //--------------------------------------------------------------------
+     
+
+
+
 } // end of namespace