void QmitkOdfMaximaExtractionView::ConvertPeaksFromMrtrix()
{
if (m_ImageNodes.empty())
return;
typedef itk::Image< float, 4 > ItkImageType;
typedef itk::MrtrixPeakImageConverter< float > FilterType;
FilterType::Pointer filter = FilterType::New();
// cast to itk
mitk::Image::Pointer mitkImg = dynamic_cast<mitk::Image*>(m_ImageNodes.at(0)->GetData());
mitk::Geometry3D::Pointer geom = mitkImg->GetGeometry();
typedef mitk::ImageToItk< FilterType::InputImageType > CasterType;
CasterType::Pointer caster = CasterType::New();
caster->SetInput(mitkImg);
caster->Update();
FilterType::InputImageType::Pointer itkImg = caster->GetOutput();
filter->SetInputImage(itkImg);
filter->GenerateData();
mitk::Vector3D outImageSpacing = geom->GetSpacing();
float maxSpacing = 1;
if(outImageSpacing[0]>outImageSpacing[1] && outImageSpacing[0]>outImageSpacing[2])
maxSpacing = outImageSpacing[0];
else if (outImageSpacing[1] > outImageSpacing[2])
maxSpacing = outImageSpacing[1];
else
maxSpacing = outImageSpacing[2];
mitk::FiberBundleX::Pointer directions = filter->GetOutputFiberBundle();
directions->SetGeometry(geom);
DataNode::Pointer node = DataNode::New();
node->SetData(directions);
QString name(m_ImageNodes.at(0)->GetName().c_str());
name += "_VectorField";
node->SetName(name.toStdString().c_str());
node->SetProperty("Fiber2DSliceThickness", mitk::FloatProperty::New(maxSpacing));
node->SetProperty("Fiber2DfadeEFX", mitk::BoolProperty::New(false));
GetDataStorage()->Add(node);
typedef FilterType::DirectionImageContainerType DirectionImageContainerType;
DirectionImageContainerType::Pointer container = filter->GetDirectionImageContainer();
for (int i=0; i<container->Size(); i++)
{
ItkDirectionImage3DType::Pointer itkImg = container->GetElement(i);
mitk::Image::Pointer img = mitk::Image::New();
img->InitializeByItk( itkImg.GetPointer() );
img->SetVolume( itkImg->GetBufferPointer() );
DataNode::Pointer node = DataNode::New();
node->SetData(img);
QString name(m_ImageNodes.at(0)->GetName().c_str());
name += "_Direction";
name += QString::number(i+1);
node->SetName(name.toStdString().c_str());
GetDataStorage()->Add(node);
}
}
void QmitkDwiSoftwarePhantomView::GeneratePhantom()
{
typedef itk::DwiPhantomGenerationFilter< short > FilterType;
FilterType::GradientListType gradientList;
m_SignalRegions.clear();
for (int i=0; i<m_SignalRegionNodes.size(); i++)
{
mitk::Image::Pointer mitkBinaryImg = dynamic_cast<mitk::Image*>(m_SignalRegionNodes.at(i)->GetData());
ItkUcharImgType::Pointer signalRegion = ItkUcharImgType::New();
mitk::CastToItkImage<ItkUcharImgType>(mitkBinaryImg, signalRegion);
m_SignalRegions.push_back(signalRegion);
}
switch(m_Controls->m_TensorsToDWINumDirsSelect->currentIndex())
{
case 0:
gradientList = MakeGradientList<12>();
break;
case 1:
gradientList = MakeGradientList<42>();
break;
case 2:
gradientList = MakeGradientList<92>();
break;
case 3:
gradientList = MakeGradientList<162>();
break;
case 4:
gradientList = MakeGradientList<252>();
break;
case 5:
gradientList = MakeGradientList<362>();
break;
case 6:
gradientList = MakeGradientList<492>();
break;
case 7:
gradientList = MakeGradientList<642>();
break;
case 8:
gradientList = MakeGradientList<812>();
break;
case 9:
gradientList = MakeGradientList<1002>();
break;
default:
gradientList = MakeGradientList<92>();
}
double bVal = m_Controls->m_TensorsToDWIBValueEdit->value();
itk::ImageRegion<3> imageRegion;
imageRegion.SetSize(0, m_Controls->m_SizeX->value());
imageRegion.SetSize(1, m_Controls->m_SizeY->value());
imageRegion.SetSize(2, m_Controls->m_SizeZ->value());
mitk::Vector3D spacing;
spacing[0] = m_Controls->m_SpacingX->value();
spacing[1] = m_Controls->m_SpacingY->value();
spacing[2] = m_Controls->m_SpacingZ->value();
FilterType::Pointer filter = FilterType::New();
filter->SetGradientList(gradientList);
filter->SetBValue(bVal);
filter->SetSNR(m_Controls->m_NoiseLevel->value());
filter->SetSignalScale(m_Controls->m_SignalScale->value());
filter->SetImageRegion(imageRegion);
filter->SetSpacing(spacing);
filter->SetSignalRegions(m_SignalRegions);
filter->SetGreyMatterAdc(m_Controls->m_GmAdc->value());
std::vector< float > tensorFA;
std::vector< float > tensorADC;
std::vector< float > tensorWeight;
std::vector< vnl_vector_fixed<double, 3> > tensorDirection;
for (int i=0; i<m_SpinFa.size(); i++)
{
tensorFA.push_back(m_SpinFa.at(i)->value());
tensorADC.push_back(m_SpinAdc.at(i)->value());
vnl_vector_fixed<double, 3> dir;
dir[0] = m_SpinX.at(i)->value();
dir[1] = m_SpinY.at(i)->value();
dir[2] = m_SpinZ.at(i)->value();
dir.normalize();
tensorDirection.push_back(dir);
tensorWeight.push_back(m_SpinWeight.at(i)->value());
}
filter->SetTensorFA(tensorFA);
filter->SetTensorADC(tensorADC);
filter->SetTensorWeight(tensorWeight);
filter->SetTensorDirection(tensorDirection);
filter->Update();
mitk::DiffusionImage<short>::Pointer image = mitk::DiffusionImage<short>::New();
image->SetVectorImage( filter->GetOutput() );
image->SetB_Value(bVal);
image->SetDirections(gradientList);
image->InitializeFromVectorImage();
mitk::DataNode::Pointer node = mitk::DataNode::New();
node->SetData( image );
node->SetName(m_Controls->m_ImageName->text().toStdString());
GetDataStorage()->Add(node);
if (m_Controls->m_OutputNumDirectionsBox->isChecked())
{
ItkUcharImgType::Pointer numDirImage = filter->GetNumDirectionsImage();
mitk::Image::Pointer image2 = mitk::Image::New();
image2->InitializeByItk( numDirImage.GetPointer() );
image2->SetVolume( numDirImage->GetBufferPointer() );
mitk::DataNode::Pointer node2 = mitk::DataNode::New();
node2->SetData(image2);
QString name(m_Controls->m_ImageName->text());
name += "_NumDirections";
node2->SetName(name.toStdString().c_str());
GetDataStorage()->Add(node2);
}
if (m_SignalRegionNodes.size()==0)
return;
if (m_Controls->m_OutputDirectionImagesBox->isChecked())
{
typedef FilterType::ItkDirectionImageContainer ItkDirectionImageContainer;
ItkDirectionImageContainer::Pointer container = filter->GetDirectionImageContainer();
for (int i=0; i<container->Size(); i++)
{
FilterType::ItkDirectionImage::Pointer itkImg = container->GetElement(i);
mitk::Image::Pointer img = mitk::Image::New();
img->InitializeByItk( itkImg.GetPointer() );
img->SetVolume( itkImg->GetBufferPointer() );
mitk::DataNode::Pointer node = mitk::DataNode::New();
node->SetData(img);
QString name(m_Controls->m_ImageName->text());
name += "_Direction";
name += QString::number(i+1);
node->SetName(name.toStdString().c_str());
GetDataStorage()->Add(node);
}
}
if (m_Controls->m_OutputVectorFieldBox->isChecked())
{
mitk::Geometry3D::Pointer geometry = image->GetGeometry();
mitk::Vector3D outImageSpacing = geometry->GetSpacing();
float minSpacing = 1;
if(outImageSpacing[0]<outImageSpacing[1] && outImageSpacing[0]<outImageSpacing[2])
minSpacing = outImageSpacing[0];
else if (outImageSpacing[1] < outImageSpacing[2])
minSpacing = outImageSpacing[1];
else
minSpacing = outImageSpacing[2];
mitk::FiberBundleX::Pointer directions = filter->GetOutputFiberBundle();
directions->SetGeometry(geometry);
mitk::DataNode::Pointer node = mitk::DataNode::New();
node->SetData(directions);
QString name(m_Controls->m_ImageName->text());
name += "_VectorField";
node->SetName(name.toStdString().c_str());
node->SetProperty("Fiber2DSliceThickness", mitk::FloatProperty::New(minSpacing));
node->SetProperty("Fiber2DfadeEFX", mitk::BoolProperty::New(false));
GetDataStorage()->Add(node);
}
}
