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); } }
void QmitkOdfMaximaExtractionView::GenerateDataFromDwi() { typedef itk::OdfMaximaExtractionFilter< float > MaximaExtractionFilterType; MaximaExtractionFilterType::Pointer filter = MaximaExtractionFilterType::New(); mitk::Geometry3D::Pointer geometry; if (!m_ImageNodes.empty()) { try{ Image::Pointer img = dynamic_cast<Image*>(m_ImageNodes.at(0)->GetData()); typedef ImageToItk< MaximaExtractionFilterType::CoefficientImageType > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(img); caster->Update(); filter->SetShCoeffImage(caster->GetOutput()); geometry = img->GetGeometry(); } catch(itk::ExceptionObject &e) { MITK_INFO << "wrong image type: " << e.what(); return; } } else return; filter->SetMaxNumPeaks(m_Controls->m_MaxNumPeaksBox->value()); filter->SetPeakThreshold(m_Controls->m_PeakThresholdBox->value()); if (!m_BinaryImageNodes.empty()) { ItkUcharImgType::Pointer itkMaskImage = ItkUcharImgType::New(); Image::Pointer mitkMaskImg = dynamic_cast<Image*>(m_BinaryImageNodes.at(0)->GetData()); CastToItkImage<ItkUcharImgType>(mitkMaskImg, itkMaskImage); filter->SetMaskImage(itkMaskImage); } switch (m_Controls->m_NormalizationBox->currentIndex()) { case 0: filter->SetNormalizationMethod(MaximaExtractionFilterType::NO_NORM); break; case 1: filter->SetNormalizationMethod(MaximaExtractionFilterType::MAX_VEC_NORM); break; case 2: filter->SetNormalizationMethod(MaximaExtractionFilterType::SINGLE_VEC_NORM); break; } filter->GenerateData(); ItkUcharImgType::Pointer numDirImage = filter->GetNumDirectionsImage(); if (m_Controls->m_OutputDirectionImagesBox->isChecked()) { typedef MaximaExtractionFilterType::ItkDirectionImageContainer ItkDirectionImageContainer; ItkDirectionImageContainer::Pointer container = filter->GetDirectionImageContainer(); for (int i=0; i<container->Size(); i++) { MaximaExtractionFilterType::ItkDirectionImage::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); } } if (m_Controls->m_OutputNumDirectionsBox->isChecked()) { mitk::Image::Pointer image2 = mitk::Image::New(); image2->InitializeByItk( numDirImage.GetPointer() ); image2->SetVolume( numDirImage->GetBufferPointer() ); DataNode::Pointer node = DataNode::New(); node->SetData(image2); QString name(m_ImageNodes.at(0)->GetName().c_str()); name += "_NumDirections"; node->SetName(name.toStdString().c_str()); GetDataStorage()->Add(node); } if (m_Controls->m_OutputVectorFieldBox->isChecked()) { 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); 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(minSpacing)); node->SetProperty("Fiber2DfadeEFX", mitk::BoolProperty::New(false)); GetDataStorage()->Add(node); } }