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 );
}
