void udgPerfusionEstimator<TPerfuImage,TMaskImage, TTransform>::ComputeEstimation()
{
if(m_perfuImage.IsNull()){
std::cout<<"Not Perfusion Image defined"<<std::endl;
return;
}
if(m_ventricleMask.IsNull()){
std::cout<<"Not Ventricle Mask Image defined"<<std::endl;
return;
}
if(m_strokeMask.IsNull()){
std::cout<<"Not Stroke Mask Image defined"<<std::endl;
return;
}
if(m_Transform.IsNull()){
std::cout<<"Not Transform defined"<<std::endl;
return;
}
m_estimatedImage = PerfuImageType::New();
m_estimatedImage->SetRegions( m_perfuImage->GetLargestPossibleRegion() );
m_estimatedImage->SetSpacing( m_perfuImage->GetSpacing() );
m_estimatedImage->SetOrigin( m_perfuImage->GetOrigin() );
m_estimatedImage->Allocate();
//Definim la regi�molt probablement infartada
typename MaskImageType::Pointer m_strokeInfluence = MaskImageType::New();
m_strokeInfluence->SetRegions( m_strokeMask->GetLargestPossibleRegion() );
m_strokeInfluence->SetSpacing( m_strokeMask->GetSpacing() );
m_strokeInfluence->SetOrigin( m_strokeMask->GetOrigin() );
m_strokeInfluence->Allocate();
typename DilateFilterType::Pointer binaryDilate = DilateFilterType::New();
binaryDilate->SetDilateValue( 255 ); //suposem que el valor alt ser�255
StructuringElementType structuringElementDilate;
structuringElementDilate.SetRadius( 2 ); // 3x3 structuring element
structuringElementDilate.CreateStructuringElement();
binaryDilate->SetKernel( structuringElementDilate );
binaryDilate->SetInput( m_strokeMask );
binaryDilate->Update();
m_strokeInfluence = binaryDilate->GetOutput();
//Fi regi�molt probablement infartada
typename ResampleFilterType::Pointer resample = ResampleFilterType::New();
typename TransformType::Pointer inverse = TransformType::New();
if (!m_Transform->GetInverse( inverse ))
{
std::cout<<"ERROR! udgPerfusionEstimator<TPerfuImage,TMaskImage, TTransform>::ComputeEstimation() No hi ha inversa!"<<std::endl;
}
resample->SetTransform( inverse );
resample->SetInput( m_ventricleMask);
resample->SetSize( m_perfuImage->GetLargestPossibleRegion().GetSize() );
resample->SetOutputOrigin( m_perfuImage->GetOrigin() );
resample->SetOutputSpacing( m_perfuImage->GetSpacing() );
resample->SetDefaultPixelValue( 0 );
resample->SetInterpolator( m_InterpolatorVentricle );
resample->Update();
Ventricles = resample->GetOutput();
typename ResampleFilterType::Pointer resample2 = ResampleFilterType::New();
resample2->SetTransform( inverse );
resample2->SetInput( m_strokeInfluence);
resample2->SetSize( m_perfuImage->GetLargestPossibleRegion().GetSize() );
resample2->SetOutputOrigin( m_perfuImage->GetOrigin() );
resample2->SetOutputSpacing( m_perfuImage->GetSpacing() );
resample2->SetDefaultPixelValue( 0 );
resample2->SetInterpolator( m_InterpolatorStroke );
resample2->Update();
//Creem les finestres mostrant les imatges registrades
Stroke = resample2->GetOutput();
PerfuIteratorType estimatedIt(m_estimatedImage, m_estimatedImage->GetBufferedRegion());
PerfuIteratorType perfuIt(m_perfuImage, m_perfuImage->GetBufferedRegion());
PerfuIteratorType VentIt(Ventricles, Ventricles->GetBufferedRegion());
PerfuIteratorType StkIt(Stroke, Stroke->GetBufferedRegion());
RadiusNeighborType radius;
radius.Fill(2);
m_InterpolatorVentricle->SetInputImage( m_ventricleMask );
m_InterpolatorStroke->SetInputImage( m_strokeInfluence );
PerfuPointType inputPoint;
PerfuPixelType perfuValue;
PerfuPixelType VentValue;
PerfuPixelType StkValue;
typename PerfuImageType::IndexType index;
MaskPointType transformedPoint;
perfuIt.GoToBegin();
VentIt.GoToBegin();
StkIt.GoToBegin();
estimatedIt.GoToBegin();
++perfuIt;
++VentIt;
++StkIt;
++estimatedIt;
while (!perfuIt.IsAtEnd())
{
perfuValue = perfuIt.Value();
// if(perfuValue == 0) // ((maskValue == m_insideValue)&&(perfuValue == 0))
if ( perfuValue < 32 ) // ((maskValue == m_insideValue)&&(perfuValue == 0))
{ //és a dir, és un punt negre
index = perfuIt.GetIndex();
m_perfuImage->TransformIndexToPhysicalPoint(index, inputPoint);
transformedPoint = m_Transform->TransformPoint(inputPoint); //transformed point és el punt corresponent en difusió
if (m_InterpolatorVentricle->IsInsideBuffer(transformedPoint))
{
// m_Interpolator->SetInputImage( m_ventricleMask );
//const RealType VentriclemaskValue = m_InterpolatorVentricle->Evaluate(transformedPoint);
VentValue = VentIt.Value();
// if(VentriclemaskValue!=0)
if(VentValue!=0)
{
estimatedIt.Set(0);//estimatedIt.Set(1);
}
else
{
/*
const RealType strokemaskValue = m_InterpolatorStroke->Evaluate(transformedPoint);
if(strokemaskValue!=0){
estimatedIt.Set(1);//estimatedIt.Set(255);
}
*/
StkValue = StkIt.Value();
if(StkValue != 0)
{
estimatedIt.Set(255);
}
else
{
estimatedIt.Set(0);
}
}
}
}
else
{
estimatedIt.Set( perfuValue ); //estimatedIt.Set( perfuValue );
}
++perfuIt;
++VentIt;
++StkIt;
++estimatedIt;
}
//Aqu�determinem els punts que no s� ni infart ni ventricle, fent una mitjana dels valors veins
//La imatge s'actualitza sobre ella mateixa, per�no sembla que aix�hagi de portar problemes
/*
double med, cont;
PerfuNeighborIteratorType perfuNeighborIt(radius, m_estimatedImage, m_estimatedImage->GetBufferedRegion());
perfuNeighborIt.GoToBegin();
perfuIt.GoToBegin();
estimatedIt.GoToBegin();
++perfuNeighborIt;
++estimatedIt;
while (!estimatedIt.IsAtEnd())
{
perfuValue = estimatedIt.Get();
if (perfuValue == 0) //� a dir, � un punt negre
{
med=0;
cont=0;
for (unsigned int i = 0; i < perfuNeighborIt.Size(); i++)
{
if ( perfuNeighborIt.GetPixel(i) != 0 && perfuNeighborIt.GetPixel(i)<1000 )
{
med += perfuNeighborIt.GetPixel(i);
cont ++;
}
}
estimatedIt.Set(static_cast<PerfuPixelType> (med/cont));
}
++perfuNeighborIt;
++estimatedIt;
}
*/
//Suavitzem la sortida --> S'hauria de fer per�d�a errors
/*
typename SmoothingFilterType::Pointer smoothFilter = SmoothingFilterType::New();
// smoothFilter->SetInput(m_estimatedImage);
smoothFilter->SetInput(m_perfuImage);
// smoothFilter->SetNumberOfIterations(5);
// smoothFilter->SetTimeStep(0.0625);
// smoothFilter->SetConductanceParameter(1);
//std::cout<<"hola 1"<<std::endl;
smoothFilter->SetVariance(1);
smoothFilter->SetMaximumKernelWidth(6);
//smoothFilter->Update();
RescaleFilterType::Pointer rescaler = RescaleFilterType::New();
rescaler->SetOutputMinimum( 0 );
rescaler->SetOutputMaximum( 255 );
//std::cout<<"hola 2"<<std::endl;
rescaler->SetInput(smoothFilter->GetOutput());
rescaler->Update();
//std::cout<<"hola 3"<<std::endl;
m_estimatedImage = rescaler->GetOutput();
*/
}
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 );
}