void TestExtractChannels()
{
typedef itk::VectorImage<float, 2> VectorImageType;
VectorImageType::Pointer image = VectorImageType::New();
itk::Index<2> corner = {{0,0}};
itk::Size<2> size = {{100,100}};
itk::ImageRegion<2> region(corner, size);
image->SetRegions(region);
image->SetNumberOfComponentsPerPixel(3);
image->Allocate();
// Extract the first two channels
std::vector<unsigned int> channels;
channels.push_back(0);
channels.push_back(1);
typedef itk::VectorImage<float, 2> FloatScalarImageType;
FloatScalarImageType::Pointer floatScalarImage = FloatScalarImageType::New();
ITKHelpers::ExtractChannels(image.GetPointer(), channels, floatScalarImage.GetPointer());
typedef itk::VectorImage<unsigned char, 2> UnsignedCharScalarImageType;
UnsignedCharScalarImageType::Pointer unsignedCharScalarImage = UnsignedCharScalarImageType::New();
ITKHelpers::ExtractChannels(image.GetPointer(), channels, unsignedCharScalarImage.GetPointer());
}
void TestExtractChannel()
{
typedef itk::VectorImage<float, 2> VectorImageType;
VectorImageType::Pointer image = VectorImageType::New();
itk::Index<2> corner = {{0,0}};
itk::Size<2> size = {{100,100}};
itk::ImageRegion<2> region(corner, size);
image->SetRegions(region);
image->SetNumberOfComponentsPerPixel(2);
image->Allocate();
typedef itk::Image<float, 2> FloatScalarImageType;
FloatScalarImageType::Pointer floatScalarImage = FloatScalarImageType::New();
ITKHelpers::ExtractChannel(image.GetPointer(), 0, floatScalarImage.GetPointer());
typedef itk::Image<unsigned char, 2> UnsignedCharScalarImageType;
UnsignedCharScalarImageType::Pointer unsignedCharScalarImage = UnsignedCharScalarImageType::New();
ITKHelpers::ExtractChannel(image.GetPointer(), 0, unsignedCharScalarImage.GetPointer());
}
bool TestCreateLuminanceImage()
{
// From RGB image
{
itk::Index<2> imageCorner = {{0,0}};
itk::Size<2> imageSize = {{100,100}};
itk::ImageRegion<2> imageRegion(imageCorner, imageSize);
typedef itk::Image<itk::RGBPixel<unsigned char>, 2> RGBImageType;
RGBImageType::Pointer rgbImage = RGBImageType::New();
rgbImage->SetRegions(imageRegion);
rgbImage->Allocate();
typedef itk::Image<float, 2> LuminanceImageType;
LuminanceImageType::Pointer luminanceImage = LuminanceImageType::New();
ITKHelpers::CreateLuminanceImage(rgbImage.GetPointer(), luminanceImage.GetPointer());
}
// From Vector image
{
itk::Index<2> imageCorner = {{0,0}};
itk::Size<2> imageSize = {{100,100}};
itk::ImageRegion<2> imageRegion(imageCorner, imageSize);
typedef itk::Image<itk::CovariantVector<unsigned char, 3>, 2> VectorImageType;
VectorImageType::Pointer vectorImage = VectorImageType::New();
vectorImage->SetRegions(imageRegion);
vectorImage->Allocate();
typedef itk::Image<float, 2> LuminanceImageType;
LuminanceImageType::Pointer luminanceImage = LuminanceImageType::New();
ITKHelpers::CreateLuminanceImage(vectorImage.GetPointer(), luminanceImage.GetPointer());
}
return true;
}
bool TestExtractChannel()
{
// VectorImage
{
typedef itk::VectorImage<float, 2> VectorImageType;
VectorImageType::Pointer image = VectorImageType::New();
itk::Index<2> corner = {{0,0}};
itk::Size<2> size = {{100,100}};
itk::ImageRegion<2> region(corner, size);
image->SetRegions(region);
image->SetNumberOfComponentsPerPixel(2);
image->Allocate();
typedef itk::Image<float, 2> FloatScalarImageType;
FloatScalarImageType::Pointer floatScalarImage = FloatScalarImageType::New();
ITKHelpers::ExtractChannel(image.GetPointer(), 0, floatScalarImage.GetPointer());
typedef itk::Image<unsigned char, 2> UnsignedCharScalarImageType;
UnsignedCharScalarImageType::Pointer unsignedCharScalarImage = UnsignedCharScalarImageType::New();
ITKHelpers::ExtractChannel(image.GetPointer(), 0, unsignedCharScalarImage.GetPointer());
}
// VectorImage different output type
{
typedef itk::VectorImage<float, 2> VectorImageType;
VectorImageType::Pointer image = VectorImageType::New();
itk::Index<2> corner = {{0,0}};
itk::Size<2> size = {{100,100}};
itk::ImageRegion<2> region(corner, size);
image->SetRegions(region);
image->SetNumberOfComponentsPerPixel(2);
image->Allocate();
typedef itk::Image<unsigned char, 2> UnsignedCharScalarImageType;
UnsignedCharScalarImageType::Pointer unsignedCharScalarImage = UnsignedCharScalarImageType::New();
ITKHelpers::ExtractChannel(image.GetPointer(), 0, unsignedCharScalarImage.GetPointer());
}
// Scalar Image
{
typedef itk::Image<float, 2> VectorImageType;
VectorImageType::Pointer image = VectorImageType::New();
itk::Index<2> corner = {{0,0}};
itk::Size<2> size = {{100,100}};
itk::ImageRegion<2> region(corner, size);
image->SetRegions(region);
image->Allocate();
typedef itk::Image<float, 2> FloatScalarImageType;
FloatScalarImageType::Pointer floatScalarImage = FloatScalarImageType::New();
ITKHelpers::ExtractChannel(image.GetPointer(), 0, floatScalarImage.GetPointer());
typedef itk::Image<unsigned char, 2> UnsignedCharScalarImageType;
UnsignedCharScalarImageType::Pointer unsignedCharScalarImage = UnsignedCharScalarImageType::New();
ITKHelpers::ExtractChannel(image.GetPointer(), 0, unsignedCharScalarImage.GetPointer());
}
// Image<CovariantVector>
{
typedef itk::Image<itk::CovariantVector<float, 3>, 2> VectorImageType;
VectorImageType::Pointer image = VectorImageType::New();
itk::Index<2> corner = {{0,0}};
itk::Size<2> size = {{100,100}};
itk::ImageRegion<2> region(corner, size);
image->SetRegions(region);
image->Allocate();
typedef itk::Image<float, 2> FloatScalarImageType;
FloatScalarImageType::Pointer floatScalarImage = FloatScalarImageType::New();
ITKHelpers::ExtractChannel(image.GetPointer(), 0, floatScalarImage.GetPointer());
}
// Image<Vector>
{
typedef itk::Image<itk::Vector<float, 3>, 2> VectorImageType;
VectorImageType::Pointer image = VectorImageType::New();
itk::Index<2> corner = {{0,0}};
itk::Size<2> size = {{100,100}};
itk::ImageRegion<2> region(corner, size);
image->SetRegions(region);
image->Allocate();
typedef itk::Image<float, 2> FloatScalarImageType;
FloatScalarImageType::Pointer floatScalarImage = FloatScalarImageType::New();
ITKHelpers::ExtractChannel(image.GetPointer(), 0, floatScalarImage.GetPointer());
}
return true;
}
QVector<double> PerfusionMapCalculatorThread::deconvolve(QVector<double> tissue)
{
QVector<double> residuefunc(tissue.size());
int i;
//std::cout<<"?"<<std::endl;
/*for(i=0;i<tissue.size();i++)
{
std::cout<<tissue[i]<<" "<<std::flush;
}*/
//std::cout<<"?"<<std::endl;
typedef std::complex<double> complexd;
complexd num1, num2, num3;
// //Usant fftw
// fftw_complex* in;
// fftw_complex* out;
//
// in = new fftw_complex[tissue.size()];
// out = new fftw_complex[tissue.size()];
//
// fftw_plan pf, pb;
//
// pf = fftw_plan_dft_1d(tissue.size(), in, out, FFTW_FORWARD, FFTW_ESTIMATE);
// pb = fftw_plan_dft_1d(tissue.size(), in, out, FFTW_BACKWARD, FFTW_ESTIMATE);
//
// int i;
// for(i=0;i<tissue.size();i++)
// {
// in[i][0]=tissue[i];
// in[i][1]=0.0;
// }
//
// fftw_execute(pf);
//
// for(i=0;i<tissue.size();i++)
// {
// num1=complexd(fftaifreal[i],fftaifimag[i]);
// num2=complexd(out[i][0],out[i][1]);
//
// if((reg_fact > 1e-6) || ((fabs(num1.real()) + fabs(num1.imag()))> 1e-6))
// {
// num3 = num2* (conj(num1) / (num1*conj(num1) + reg_fact*pow(-1,reg_exp)*pow(omega[i],2*reg_exp)));
// in[i][0] = num3.real();
// in[i][1] = num3.imag();
// }
// else
// {
// in[i][0] = 0.0;
// in[i][1] = 0.0;
// }
// }
// fftw_execute(pb);
// for(i=0;i<tissue.size();i++)
// {
// residuefunc[i]=out[i][0]/tissue.size();
// }
// fftw_destroy_plan(pf);
// fftw_destroy_plan(pb);
// free(in);
// free(out);
//Usant itk's
//std::cout<<"Usant itk's"<<std::endl;
typedef itk::Image< double, 1 > VectorImageType;
VectorImageType::RegionType region;
VectorImageType::IndexType start;
start[0]=0;
VectorImageType::SizeType size;
size[0] = m_sizet; //les mostres temporals
region.SetSize(size);
region.SetIndex(start);
//std::cout<<"&"<<std::endl;
VectorImageType::Pointer tissueImage = VectorImageType::New();
tissueImage->SetRegions(region);
try
{
tissueImage->Allocate();
}
catch(itk::ExceptionObject & excp)
{
std::cerr << "Error: " << std::endl;
std::cerr << excp << std::endl;
return residuefunc;
}
//std::cout<<"$"<<std::endl;
typedef itk::ImageRegionIterator<VectorImageType> VectorIteratorType;
VectorIteratorType tissueIter(tissueImage, tissueImage->GetLargestPossibleRegion());
//std::cout<<"@"<<tissueImage->GetLargestPossibleRegion().GetSize()[0]<<std::endl;
typedef itk::VnlFFTRealToComplexConjugateImageFilter< double, 1 > FFTFilterType;
FFTFilterType::Pointer fftFilter = FFTFilterType::New();
//std::cout<<"#"<<std::endl;
tissueIter.GoToBegin();
//std::cout<<"%"<<std::endl;
for(i=0;i<tissue.size();i++)
{
tissueIter.Set(tissue[i]);
++tissueIter;
}
fftFilter->SetInput(tissueImage);
try
{
fftFilter->Update();
}
catch(itk::ExceptionObject & excp)
{
std::cerr << "Error: " << std::endl;
std::cerr << excp << std::endl;
return residuefunc;
}
typedef FFTFilterType::OutputImageType ComplexImageType;
ComplexImageType::Pointer residualFFTImage = ComplexImageType::New();
residualFFTImage->SetRegions(region);
residualFFTImage->Allocate();
typedef itk::ImageRegionIterator<ComplexImageType> ComplexIteratorType;
ComplexIteratorType fftTissueIter(fftFilter->GetOutput(), fftFilter->GetOutput()->GetLargestPossibleRegion());
fftTissueIter.GoToBegin();
ComplexIteratorType fftResidualIter(residualFFTImage, residualFFTImage->GetLargestPossibleRegion());
fftResidualIter.GoToBegin();
//std::cout<<"!"<<fftFilter->GetOutput()->GetLargestPossibleRegion().GetSize()[0]<<std::endl;
for(i=0;i<tissue.size();i++)
{
num1=complexd(fftaifreal[i],fftaifimag[i]);
num2=complexd(fftTissueIter.Get().real(),fftTissueIter.Get().imag());
if((reg_fact > 1e-6) || ((fabs(num1.real()) + fabs(num1.imag()))> 1e-6))
{
num3 = num2* (conj(num1) / (num1*conj(num1) + reg_fact*pow(-1,reg_exp)*pow(omega[i],2*reg_exp)));
fftResidualIter.Set(num3);
}
else
{
num3 = complexd(0.0, 0.0);
fftResidualIter.Set(num3);
}
++fftTissueIter;
++fftResidualIter;
}
typedef itk::VnlFFTComplexConjugateToRealImageFilter< double, 1 > IFFTFilterType;
IFFTFilterType::Pointer fftInverseFilter = IFFTFilterType::New();
fftInverseFilter->SetInput(residualFFTImage);
try
{
fftInverseFilter->Update();
}
catch(itk::ExceptionObject & excp)
{
std::cerr << "Error: " << std::endl;
std::cerr << excp << std::endl;
return residuefunc;
}
//std::cout<<"*"<<fftInverseFilter->GetOutput()->GetLargestPossibleRegion().GetSize()[0]<<std::endl;
VectorIteratorType residualIter(fftInverseFilter->GetOutput(), fftInverseFilter->GetOutput()->GetLargestPossibleRegion());
residualIter.GoToBegin();
for(i=0;i<residuefunc.size();i++)
{
//if(residuefunc[i]!=residualIter.Get()) std::cout<<"Resultat residuefunc diferent: "<<residuefunc[i]<<" ," <<residualIter.Get()/tissue.size()<<std::endl;
residuefunc[i]=residualIter.Get();
++residualIter;
}
for(i=0;i<residuefunc.size();i++)
{
//std::cout<<residuefunc[i]<<" "<<std::flush;
}
//std::cout<<"?"<<std::endl;
return residuefunc;
}