void
ResampleImage(itk::Image<TPixel, VImageDimension>* itkImage, float resolution, mitk::Image::Pointer& newImage)
{
typedef itk::Image<TPixel, VImageDimension> ImageType;
typedef itk::ResampleImageFilter<ImageType, ImageType> ResampleFilterType;
typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
auto spacing = itkImage->GetSpacing();
auto size = itkImage->GetLargestPossibleRegion().GetSize();
for (unsigned int i = 0; i < VImageDimension; ++i)
{
size[i] = size[i] / (1.0*resolution)*(1.0*spacing[i])+1.0;
}
spacing.Fill(resolution);
resampler->SetInput(itkImage);
resampler->SetSize(size);
resampler->SetOutputSpacing(spacing);
resampler->SetOutputOrigin(itkImage->GetOrigin());
resampler->SetOutputDirection(itkImage->GetDirection());
resampler->Update();
newImage->InitializeByItk(resampler->GetOutput());
mitk::GrabItkImageMemory(resampler->GetOutput(), newImage);
}
static void
ResampleMask(itk::Image<TPixel, VImageDimension>* itkMoving, mitk::Image::Pointer ref, mitk::Image::Pointer& newMask)
{
typedef itk::Image< TPixel, VImageDimension> LMaskImageType;
typedef itk::NearestNeighborInterpolateImageFunction< LMaskImageType> NearestNeighborInterpolateImageFunctionType;
typedef itk::ResampleImageFilter<LMaskImageType, LMaskImageType> ResampleFilterType;
typename NearestNeighborInterpolateImageFunctionType::Pointer nn_interpolator = NearestNeighborInterpolateImageFunctionType::New();
typename LMaskImageType::Pointer itkRef = LMaskImageType::New();
mitk::CastToItkImage(ref, itkRef);
typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
resampler->SetInput(itkMoving);
resampler->SetReferenceImage(itkRef);
resampler->UseReferenceImageOn();
resampler->SetInterpolator(nn_interpolator);
resampler->Update();
newMask->InitializeByItk(resampler->GetOutput());
mitk::GrabItkImageMemory(resampler->GetOutput(), newMask);
}
void WorkbenchUtils::resampleImageItk(itk::Image <PixelType, ImageDimension> *itkImage, Interpolator interpolType,
unsigned int *newDimensions, Image::Pointer outImage) {
typedef itk::Image <PixelType, ImageDimension> ImageType;
// get original image informations
const typename ImageType::RegionType &inputRegion = itkImage->GetLargestPossibleRegion();
const typename ImageType::SizeType &inputDimensions = inputRegion.GetSize();
const typename ImageType::SpacingType &inputSpacing = itkImage->GetSpacing();
// calculate spacing
double outputSpacing[ImageDimension];
itk::Size <ImageDimension> outputSize;
for (unsigned int i = 0; i < ImageDimension; ++i) {
outputSpacing[i] = inputSpacing[i] * (double) inputDimensions[i] / newDimensions[i];
outputSize[i] = newDimensions[i];
}
// transform
typedef itk::IdentityTransform<double, ImageDimension> TransformType;
typename TransformType::Pointer transform = TransformType::New();
transform->SetIdentity();
// interpolator typedefs
typedef double CoordinateType;
typedef itk::LinearInterpolateImageFunction <ImageType, CoordinateType> LinearInterpolatorType;
typedef itk::NearestNeighborInterpolateImageFunction <ImageType, CoordinateType> NearestNeighborInterpolatorType;
typedef itk::GaussianInterpolateImageFunction <ImageType, CoordinateType> GaussianInterpolatorType;
typedef itk::BSplineInterpolateImageFunction <ImageType, CoordinateType> BSplineInterpolatorType;
// set up the filter
typedef itk::ResampleImageFilter <ImageType, ImageType> ResampleFilterType;
typename ResampleFilterType::Pointer resampleFilter = ResampleFilterType::New();
resampleFilter->SetTransform(transform);
resampleFilter->SetOutputOrigin(itkImage->GetOrigin());
resampleFilter->SetOutputSpacing(outputSpacing);
resampleFilter->SetSize(outputSize);
switch (interpolType) {
case Interpolator::LINEAR: // the default;
resampleFilter->SetInterpolator(LinearInterpolatorType::New());
break;
case Interpolator::NEAREST_NEIGHBOR:
resampleFilter->SetInterpolator(NearestNeighborInterpolatorType::New());
break;
case Interpolator::GAUSSIAN:
resampleFilter->SetInterpolator(GaussianInterpolatorType::New());
break;
case Interpolator::BSPLINE:
resampleFilter->SetInterpolator(BSplineInterpolatorType::New());
break;
}
resampleFilter->SetInput(itkImage);
resampleFilter->UpdateLargestPossibleRegion();
// get the results and cast them back to mitk. return via out parameter.
outImage->InitializeByItk(resampleFilter->GetOutput());
CastToMitkImage(resampleFilter->GetOutput(), outImage);
}
/**
* @brief 3D resample data to new grid size
*
* @param M Incoming data
* @param f Resampling factor in all 3 dimensions
* @param im Interpolation method (LINEAR|BSPLINE)
*
* @return Resampled data
*/
template<class T> static Matrix<T>
resample (const Matrix<T>& M, const Matrix<double>& f, const InterpMethod& im) {
Matrix <T> res = M;
#ifdef HAVE_INSIGHT
typedef typename itk::OrientedImage< T, 3 > InputImageType;
typedef typename itk::OrientedImage< T, 3 > OutputImageType;
typedef typename itk::IdentityTransform< double, 3 > TransformType;
typedef typename itk::LinearInterpolateImageFunction< InputImageType, double > InterpolatorType;
typedef typename itk::ResampleImageFilter< InputImageType, InputImageType > ResampleFilterType;
typename InterpolatorType::Pointer linterp = InterpolatorType::New();
TransformType::Pointer trafo = TransformType::New();
trafo->SetIdentity();
typename InputImageType::SpacingType space;
space[0] = 1.0/f[0];
space[1] = 1.0/f[1];
space[2] = 1.0/f[2];
typedef typename InputImageType::SizeType::SizeValueType SizeValueType;
typename InputImageType::SizeType size;
size[0] = static_cast<SizeValueType>(res.Dim(0));
size[1] = static_cast<SizeValueType>(res.Dim(1));
size[2] = static_cast<SizeValueType>(res.Dim(2));
typename itk::OrientedImage< T, 3 >::Pointer input = itk::OrientedImage< T, 3 >::New();
typename itk::OrientedImage< T, 3 >::Pointer output = itk::OrientedImage< T, 3 >::New();
typename itk::Image< T, 3 >::IndexType ipos;
ipos[0] = 0; ipos[1] = 0; ipos[2] = 0;
typename itk::Image< T, 3 >::IndexType opos;
opos[0] = 0; opos[1] = 0; opos[2] = 0;
typename itk::Image< T, 3 >::RegionType ireg;
ireg.SetSize(size);
ireg.SetIndex(ipos);
input->SetRegions(ireg);
input->Allocate();
typename itk::Image< T, 3 >::RegionType oreg;
oreg.SetSize(size);
ireg.SetIndex(opos);
output->SetRegions(oreg);
output->Allocate();
for (size_t z = 0; z < res.Dim(2); z++)
for (size_t y = 0; y < res.Dim(1); y++)
for (size_t x = 0; x < res.Dim(0); x++) {
ipos[0] = x; ipos[1] = y; ipos[2] = z;
input->SetPixel (ipos, res.At(x,y,z));
}
typename ResampleFilterType::Pointer rs = ResampleFilterType::New();
rs->SetInput( input );
rs->SetTransform( trafo );
rs->SetInterpolator( linterp );
rs->SetOutputOrigin ( input->GetOrigin());
rs->SetOutputSpacing ( space );
rs->SetOutputDirection ( input->GetDirection());
rs->SetSize ( size );
rs->Update ();
output = rs->GetOutput();
res = Matrix<T> (res.Dim(0)*f[0], res.Dim(1)*f[1], res.Dim(2)*f[2]);
res.Res(0) = res.Res(0)/f[0];
res.Res(1) = res.Dim(1)/f[1];
res.Res(2) = res.Dim(2)/f[2];
for (size_t z = 0; z < res.Dim(2); z++)
for (size_t y = 0; y < res.Dim(1); y++)
for (size_t x = 0; x < res.Dim(0); x++) {
opos[0] = x; opos[1] = y; opos[2] = z;
res.At(x,y,z) = output->GetPixel (opos);
}
#else
printf ("ITK ERROR - Resampling not performed without ITK!\n");
#endif
return res;
}
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();
*/
}
