+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ SliceBySliceKeepMainCCL(const ImageType * input,
+ typename ImageType::PixelType BG,
+ typename ImageType::PixelType FG) {
+
+ // Extract slices
+ const int d = ImageType::ImageDimension-1;
+ typedef typename itk::Image<typename ImageType::PixelType, d> SliceType;
+ std::vector<typename SliceType::Pointer> slices;
+ clitk::ExtractSlices<ImageType>(input, d, slices);
+
+ // Labelize and keep the main one
+ std::vector<typename SliceType::Pointer> o;
+ for(uint i=0; i<slices.size(); i++) {
+ o.push_back(clitk::Labelize<SliceType>(slices[i], BG, false, 1));
+ o[i] = clitk::KeepLabels<SliceType>(o[i], BG, FG, 1, 1, true);
+ }
+
+ // Join slices
+ typename ImageType::Pointer output;
+ output = clitk::JoinSlices<ImageType>(o, input, d);
+ return output;
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ template<class ImageType>
+ typename ImageType::Pointer
+ Clone(const ImageType * input) {
+ typedef itk::ImageDuplicator<ImageType> DuplicatorType;
+ typename DuplicatorType::Pointer duplicator = DuplicatorType::New();
+ duplicator->SetInputImage(input);
+ duplicator->Update();
+ return duplicator->GetOutput();
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ /* Consider an input object, start at A, for each slice (dim1):
+ - compute the intersection between the AB line and the current slice
+ - remove what is at lower or greater according to dim2 of this point
+ - stop at B
+ */
+ template<class ImageType>
+ typename ImageType::Pointer
+ SliceBySliceSetBackgroundFromSingleLine(const ImageType * input,
+ typename ImageType::PixelType BG,
+ typename ImageType::PointType & A,
+ typename ImageType::PointType & B,
+ int dim1, int dim2, bool removeLowerPartFlag)
+
+ {
+ // 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, dim1, slices);
+
+ // Start at slice that contains A, and stop at B
+ typename ImageType::IndexType Ap;
+ typename ImageType::IndexType Bp;
+ input->TransformPhysicalPointToIndex(A, Ap);
+ input->TransformPhysicalPointToIndex(B, Bp);
+
+ // Determine slice largest region
+ typename SliceType::RegionType region = slices[0]->GetLargestPossibleRegion();
+ typename SliceType::SizeType size = region.GetSize();
+ typename SliceType::IndexType index = region.GetIndex();
+
+ // Line slope
+ double a = (Bp[dim2]-Ap[dim2])/(Bp[dim1]-Ap[dim1]);
+ double b = Ap[dim2];
+
+ // Loop from slice A to slice B
+ for(uint i=0; i<(Bp[dim1]-Ap[dim1]); i++) {
+ // Compute intersection between line AB and current slice for the dim2
+ double p = a*i+b;
+ // Change region (lower than dim2)
+ if (removeLowerPartFlag) {
+ size[dim2] = p-Ap[dim2];
+ }
+ else {
+ size[dim2] = slices[0]->GetLargestPossibleRegion().GetSize()[dim2]-p;
+ index[dim2] = p;
+ }
+ region.SetSize(size);
+ region.SetIndex(index);
+ // Fill region with BG (simple region iterator)
+ FillRegionWithValue<SliceType>(slices[i+Ap[dim1]], BG, region);
+ /*
+ typedef itk::ImageRegionIterator<SliceType> IteratorType;
+ IteratorType iter(slices[i+Ap[dim1]], region);
+ iter.GoToBegin();
+ while (!iter.IsAtEnd()) {
+ iter.Set(BG);
+ ++iter;
+ }
+ */
+ // Loop
+ }
+
+ // Merge slices
+ typename ImageType::Pointer output;
+ output = clitk::JoinSlices<ImageType>(slices, input, dim1);
+ return output;
+ }
+ //--------------------------------------------------------------------
+
+ //--------------------------------------------------------------------
+ /* 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
+ FillRegionWithValue(ImageType * input, typename ImageType::PixelType value, typename ImageType::RegionType & region)
+ {
+ typedef itk::ImageRegionIterator<ImageType> IteratorType;
+ IteratorType iter(input, region);
+ iter.GoToBegin();
+ while (!iter.IsAtEnd()) {
+ iter.Set(value);
+ ++iter;
+ }
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ 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);
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ 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;
+ indexmin.Fill(0);
+ 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;
+ }
+ //--------------------------------------------------------------------
+
+
+ //--------------------------------------------------------------------
+ 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();
+ }
+ //--------------------------------------------------------------------
+
+