static int CalculateGlSZMatrix(itk::Image<TPixel, VImageDimension>* itkImage, itk::Image<unsigned short, VImageDimension>* mask, std::vector<itk::Offset<VImageDimension> > offsets, bool estimateLargestRegion, mitk::GreyLevelSizeZoneMatrixHolder &holder) { typedef itk::Image<TPixel, VImageDimension> ImageType; typedef itk::Image<unsigned short, VImageDimension> MaskImageType; typedef typename ImageType::IndexType IndexType; typedef itk::ImageRegionIteratorWithIndex<ImageType> ConstIterType; typedef itk::ImageRegionIteratorWithIndex<MaskImageType> ConstMaskIterType; auto region = mask->GetLargestPossibleRegion(); typename MaskImageType::RegionType newRegion; newRegion.SetSize(region.GetSize()); newRegion.SetIndex(region.GetIndex()); ConstIterType imageIter(itkImage, itkImage->GetLargestPossibleRegion()); ConstMaskIterType maskIter(mask, mask->GetLargestPossibleRegion()); typename MaskImageType::Pointer visitedImage = MaskImageType::New(); visitedImage->SetRegions(newRegion); visitedImage->Allocate(); visitedImage->FillBuffer(0); int largestRegion = 0; while (!maskIter.IsAtEnd()) { if (maskIter.Value() > 0 ) { auto startIntensityIndex = holder.IntensityToIndex(imageIter.Value()); std::vector<IndexType> indices; indices.push_back(maskIter.GetIndex()); unsigned int steps = 0; while (indices.size() > 0) { auto currentIndex = indices.back(); indices.pop_back(); if (!region.IsInside(currentIndex)) { continue; } auto wasVisited = visitedImage->GetPixel(currentIndex); auto newIntensityIndex = holder.IntensityToIndex(itkImage->GetPixel(currentIndex)); auto isInMask = mask->GetPixel(currentIndex); if ((isInMask > 0) && (newIntensityIndex == startIntensityIndex) && (wasVisited < 1)) { ++steps; visitedImage->SetPixel(currentIndex, 1); for (auto offset : offsets) { auto newIndex = currentIndex + offset; indices.push_back(newIndex); newIndex = currentIndex - offset; indices.push_back(newIndex); } } } if (steps > 0) { largestRegion = std::max<int>(steps, largestRegion); steps = std::min<unsigned int>(steps, holder.m_MaximumSize); if (!estimateLargestRegion) { holder.m_Matrix(startIntensityIndex, steps - 1) += 1; } } } ++imageIter; ++maskIter; } return largestRegion; }
void PartialVolumeAnalysisClusteringCalculator::InternalQuantify( const itk::Image< TPixel, VImageDimension > *image, mitk::Image::Pointer clusteredImage, double* retval, mitk::Image::Pointer mask ) const { typedef itk::Image< TPixel, VImageDimension > ImageType; typedef itk::Image< float, VImageDimension > ProbImageType; typedef itk::Image< unsigned char, VImageDimension > MaskImageType; typedef mitk::ImageToItk<ProbImageType> CastFilterType; typename CastFilterType::Pointer castFilter = CastFilterType::New(); castFilter->SetInput( clusteredImage ); castFilter->Update(); typename ProbImageType::Pointer clusterImage = castFilter->GetOutput(); typename MaskImageType::Pointer itkmask = 0; if(mask.IsNotNull()) { typedef mitk::ImageToItk<MaskImageType> CastFilterType2; typename CastFilterType2::Pointer castFilter2 = CastFilterType2::New(); castFilter2->SetInput( mask ); castFilter2->Update(); itkmask = castFilter2->GetOutput(); } else { itkmask = MaskImageType::New(); itkmask->SetSpacing( clusterImage->GetSpacing() ); // Set the image spacing itkmask->SetOrigin( clusterImage->GetOrigin() ); // Set the image origin itkmask->SetDirection( clusterImage->GetDirection() ); // Set the image direction itkmask->SetRegions( clusterImage->GetLargestPossibleRegion() ); itkmask->Allocate(); itkmask->FillBuffer(1); } itk::ImageRegionConstIterator<ImageType> itimage(image, image->GetLargestPossibleRegion()); itk::ImageRegionConstIterator<ProbImageType> itprob(clusterImage, clusterImage->GetLargestPossibleRegion()); itk::ImageRegionConstIterator<MaskImageType> itmask(itkmask, itkmask->GetLargestPossibleRegion()); itimage.GoToBegin(); itprob.GoToBegin(); itmask.GoToBegin(); double totalProb = 0; double measurement = 0; double error = 0; while( !itimage.IsAtEnd() && !itprob.IsAtEnd() && !itmask.IsAtEnd() ) { double valImag = itimage.Get(); double valProb = itprob.Get(); double valMask = itmask.Get(); typename ProbImageType::PixelType prop = valProb * valMask; totalProb += prop; measurement += valImag * prop; error += valImag * valImag * prop; ++itimage; ++itprob; ++itmask; } measurement = measurement / totalProb; error = error / totalProb; retval[0] = measurement; retval[1] = sqrt( error - measurement*measurement ); }