#include <itkImageSliceIteratorWithIndex.h>
#include <itkBinaryMorphologicalOpeningImageFilter.h>
#include <itkImageDuplicator.h>
+#include <itkSignedMaurerDistanceMapImageFilter.h>
namespace clitk {
sliceRelPosFilter->AddOrientationTypeString(orientation);
sliceRelPosFilter->SetIntermediateSpacingFlag((spacing != -1));
sliceRelPosFilter->SetIntermediateSpacing(spacing);
- sliceRelPosFilter->SetUniqueConnectedComponentBySlice(uniqueConnectedComponent);
- sliceRelPosFilter->CCLSelectionFlagOff();
- sliceRelPosFilter->SetUseASingleObjectConnectedComponentBySliceFlag(singleObjectCCL);
+ sliceRelPosFilter->SetUniqueConnectedComponentBySliceFlag(uniqueConnectedComponent);
+ sliceRelPosFilter->ObjectCCLSelectionFlagOff();
+ sliceRelPosFilter->SetUseTheLargestObjectCCLFlag(singleObjectCCL);
// sliceRelPosFilter->SetInverseOrientationFlag(inverseflag);
sliceRelPosFilter->SetAutoCropFlag(autocropFlag);
sliceRelPosFilter->IgnoreEmptySliceObjectFlagOn();
}
//--------------------------------------------------------------------
+
//--------------------------------------------------------------------
template<class ImageType>
bool
}
//--------------------------------------------------------------------
+
//--------------------------------------------------------------------
template<class ImageType>
bool
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]);
int mainDirection,
double offsetToKeep)
{
+ assert((mainDirection==0) || (mainDirection==1));
typedef itk::ImageSliceIteratorWithIndex<ImageType> SliceIteratorType;
SliceIteratorType siter = SliceIteratorType(input,
input->GetLargestPossibleRegion());
//--------------------------------------------------------------------
+ //--------------------------------------------------------------------
+ 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
}
//--------------------------------------------------------------------
+
+ //--------------------------------------------------------------------
+ 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
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff