void QmitkQBallReconstructionView::NumericalQBallReconstruction (mitk::DataStorage::SetOfObjects::Pointer inImages, int normalization) { try { itk::TimeProbe clock; int nrFiles = inImages->size(); if (!nrFiles) return; QString status; mitk::ProgressBar::GetInstance()->AddStepsToDo(nrFiles); mitk::DataStorage::SetOfObjects::const_iterator itemiter( inImages->begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( inImages->end() ); std::vector<mitk::DataNode::Pointer> nodes; while ( itemiter != itemiterend ) // for all items { mitk::DiffusionImage<DiffusionPixelType>* vols = static_cast<mitk::DiffusionImage<DiffusionPixelType>*>( (*itemiter)->GetData()); std::string nodename; (*itemiter)->GetStringProperty("name", nodename); ++itemiter; // QBALL RECONSTRUCTION clock.Start(); MBI_INFO << "QBall reconstruction "; mitk::StatusBar::GetInstance()->DisplayText(status.sprintf( "QBall reconstruction for %s", nodename.c_str()).toAscii()); typedef itk::DiffusionQballReconstructionImageFilter <DiffusionPixelType, DiffusionPixelType, TTensorPixelType, QBALL_ODFSIZE> QballReconstructionImageFilterType; QballReconstructionImageFilterType::Pointer filter = QballReconstructionImageFilterType::New(); filter->SetGradientImage( vols->GetDirections(), vols->GetVectorImage() ); filter->SetNumberOfThreads( m_Controls->m_QBallReconstructionNumberThreadsSpinbox->value() ); filter->SetBValue(vols->GetB_Value()); filter->SetThreshold( m_Controls->m_QBallReconstructionThreasholdEdit->text().toFloat() ); switch(normalization) { case 0: { filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_STANDARD); break; } case 1: { filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_B_ZERO_B_VALUE); break; } case 2: { filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_B_ZERO); break; } case 3: { filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_NONE); break; } default: { filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_STANDARD); } } filter->Update(); clock.Stop(); MBI_DEBUG << "took " << clock.GetMeanTime() << "s." ; // ODFs TO DATATREE mitk::QBallImage::Pointer image = mitk::QBallImage::New(); image->InitializeByItk( filter->GetOutput() ); //image->SetImportVolume( filter->GetOutput()->GetBufferPointer(), 0, 0, mitk::Image::ImportMemoryManagementType::ManageMemory ); image->SetVolume( filter->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer node=mitk::DataNode::New(); node->SetData( image ); QString newname; newname = newname.append(nodename.c_str()); newname = newname.append("_QN%1").arg(normalization); SetDefaultNodeProperties(node, newname.toStdString()); nodes.push_back(node); // B-Zero TO DATATREE if(m_Controls->m_OutputB0Image->isChecked()) { mitk::Image::Pointer image4 = mitk::Image::New(); image4->InitializeByItk( filter->GetBZeroImage().GetPointer() ); image4->SetVolume( filter->GetBZeroImage()->GetBufferPointer() ); mitk::DataNode::Pointer node4=mitk::DataNode::New(); node4->SetData( image4 ); node4->SetProperty( "name", mitk::StringProperty::New( QString(nodename.c_str()).append("_b0").toStdString()) ); nodes.push_back(node4); } mitk::ProgressBar::GetInstance()->Progress(); } std::vector<mitk::DataNode::Pointer>::iterator nodeIt; for(nodeIt = nodes.begin(); nodeIt != nodes.end(); ++nodeIt) GetDefaultDataStorage()->Add(*nodeIt); mitk::StatusBar::GetInstance()->DisplayText(status.sprintf("Finished Processing %d Files", nrFiles).toAscii()); m_MultiWidget->RequestUpdate(); } catch (itk::ExceptionObject &ex) { MBI_INFO << ex ; return ; } }
int mitkImageReconstructionTest(int argc, char* argv[]) { MITK_TEST_BEGIN("mitkImageReconstructionTest"); MITK_TEST_CONDITION_REQUIRED(argc>1,"check for input data") try { mitk::DiffusionImage<short>::Pointer dwi = dynamic_cast<mitk::DiffusionImage<short>*>(mitk::IOUtil::LoadDataNode(argv[1])->GetData()); { MITK_INFO << "Tensor reconstruction " << argv[2]; mitk::TensorImage::Pointer tensorImage = dynamic_cast<mitk::TensorImage*>(mitk::IOUtil::LoadDataNode(argv[2])->GetData()); typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, float > TensorReconstructionImageFilterType; TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New(); filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() ); filter->SetBValue(dwi->GetB_Value()); filter->Update(); mitk::TensorImage::Pointer testImage = mitk::TensorImage::New(); testImage->InitializeByItk( filter->GetOutput() ); testImage->SetVolume( filter->GetOutput()->GetBufferPointer() ); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(testImage, tensorImage, 0.0001, true), "tensor reconstruction test."); } { MITK_INFO << "Numerical Q-ball reconstruction " << argv[3]; mitk::QBallImage::Pointer qballImage = dynamic_cast<mitk::QBallImage*>(mitk::IOUtil::LoadDataNode(argv[3])->GetData()); typedef itk::DiffusionQballReconstructionImageFilter<short, short, float, QBALL_ODFSIZE> QballReconstructionImageFilterType; QballReconstructionImageFilterType::Pointer filter = QballReconstructionImageFilterType::New(); filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() ); filter->SetBValue(dwi->GetB_Value()); filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_STANDARD); filter->Update(); mitk::QBallImage::Pointer testImage = mitk::QBallImage::New(); testImage->InitializeByItk( filter->GetOutput() ); testImage->SetVolume( filter->GetOutput()->GetBufferPointer() ); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(testImage, qballImage, 0.0001, true), "Numerical Q-ball reconstruction test."); } { MITK_INFO << "Standard Q-ball reconstruction " << argv[4]; mitk::QBallImage::Pointer qballImage = dynamic_cast<mitk::QBallImage*>(mitk::IOUtil::LoadDataNode(argv[4])->GetData()); typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,4,QBALL_ODFSIZE> FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() ); filter->SetBValue(dwi->GetB_Value()); filter->SetLambda(0.006); filter->SetNormalizationMethod(FilterType::QBAR_STANDARD); filter->Update(); mitk::QBallImage::Pointer testImage = mitk::QBallImage::New(); testImage->InitializeByItk( filter->GetOutput() ); testImage->SetVolume( filter->GetOutput()->GetBufferPointer() ); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(testImage, qballImage, 0.0001, true), "Standard Q-ball reconstruction test."); } { MITK_INFO << "CSA Q-ball reconstruction " << argv[5]; mitk::QBallImage::Pointer qballImage = dynamic_cast<mitk::QBallImage*>(mitk::IOUtil::LoadDataNode(argv[5])->GetData()); typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,4,QBALL_ODFSIZE> FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() ); filter->SetBValue(dwi->GetB_Value()); filter->SetLambda(0.006); filter->SetNormalizationMethod(FilterType::QBAR_SOLID_ANGLE); filter->Update(); mitk::QBallImage::Pointer testImage = mitk::QBallImage::New(); testImage->InitializeByItk( filter->GetOutput() ); testImage->SetVolume( filter->GetOutput()->GetBufferPointer() ); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(testImage, qballImage, 0.0001, true), "CSA Q-ball reconstruction test."); } { MITK_INFO << "ADC profile reconstruction " << argv[6]; mitk::QBallImage::Pointer qballImage = dynamic_cast<mitk::QBallImage*>(mitk::IOUtil::LoadDataNode(argv[6])->GetData()); typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,4,QBALL_ODFSIZE> FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() ); filter->SetBValue(dwi->GetB_Value()); filter->SetLambda(0.006); filter->SetNormalizationMethod(FilterType::QBAR_ADC_ONLY); filter->Update(); mitk::QBallImage::Pointer testImage = mitk::QBallImage::New(); testImage->InitializeByItk( filter->GetOutput() ); testImage->SetVolume( filter->GetOutput()->GetBufferPointer() ); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(testImage, qballImage, 0.0001, true), "ADC profile reconstruction test."); } { MITK_INFO << "Raw signal modeling " << argv[7]; mitk::QBallImage::Pointer qballImage = dynamic_cast<mitk::QBallImage*>(mitk::IOUtil::LoadDataNode(argv[7])->GetData()); typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,4,QBALL_ODFSIZE> FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() ); filter->SetBValue(dwi->GetB_Value()); filter->SetLambda(0.006); filter->SetNormalizationMethod(FilterType::QBAR_RAW_SIGNAL); filter->Update(); mitk::QBallImage::Pointer testImage = mitk::QBallImage::New(); testImage->InitializeByItk( filter->GetOutput() ); testImage->SetVolume( filter->GetOutput()->GetBufferPointer() ); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(testImage, qballImage, 0.0001, true), "Raw signal modeling test."); } } catch (itk::ExceptionObject e) { MITK_INFO << e; return EXIT_FAILURE; } catch (std::exception e) { MITK_INFO << e.what(); return EXIT_FAILURE; } catch (...) { MITK_INFO << "ERROR!?!"; return EXIT_FAILURE; } MITK_TEST_END(); }
int mitkImageReconstructionTest(int argc, char* argv[]) { MITK_TEST_BEGIN("mitkImageReconstructionTest"); MITK_TEST_CONDITION_REQUIRED(argc>1,"check for input data") try { mitk::Image::Pointer dwi = dynamic_cast<mitk::Image*>(mitk::IOUtil::Load(argv[1])[0].GetPointer()); itk::VectorImage<short,3>::Pointer itkVectorImagePointer = itk::VectorImage<short,3>::New(); mitk::CastToItkImage(dwi, itkVectorImagePointer); float b_value = mitk::DiffusionPropertyHelper::GetReferenceBValue( dwi ); mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer gradients = mitk::DiffusionPropertyHelper::GetGradientContainer(dwi); { MITK_INFO << "Tensor reconstruction " << argv[2]; mitk::TensorImage::Pointer tensorImage = dynamic_cast<mitk::TensorImage*>(mitk::IOUtil::Load(argv[2])[0].GetPointer()); typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, float > TensorReconstructionImageFilterType; TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New(); filter->SetBValue( b_value ); filter->SetGradientImage( gradients, itkVectorImagePointer ); filter->Update(); mitk::TensorImage::Pointer testImage = mitk::TensorImage::New(); testImage->InitializeByItk( filter->GetOutput() ); testImage->SetVolume( filter->GetOutput()->GetBufferPointer() ); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(*testImage, *tensorImage, 0.0001, true), "tensor reconstruction test."); } { MITK_INFO << "Numerical Q-ball reconstruction " << argv[3]; mitk::OdfImage::Pointer odfImage = dynamic_cast<mitk::OdfImage*>(mitk::IOUtil::Load(argv[3])[0].GetPointer()); typedef itk::DiffusionQballReconstructionImageFilter<short, short, float, ODF_SAMPLING_SIZE> QballReconstructionImageFilterType; QballReconstructionImageFilterType::Pointer filter = QballReconstructionImageFilterType::New(); filter->SetBValue( b_value ); filter->SetGradientImage( gradients, itkVectorImagePointer ); filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_STANDARD); filter->Update(); mitk::OdfImage::Pointer testImage = mitk::OdfImage::New(); testImage->InitializeByItk( filter->GetOutput() ); testImage->SetVolume( filter->GetOutput()->GetBufferPointer() ); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(*testImage, *odfImage, 0.0001, true), "Numerical Q-ball reconstruction test."); } { MITK_INFO << "Standard Q-ball reconstruction " << argv[4]; mitk::OdfImage::Pointer odfImage = dynamic_cast<mitk::OdfImage*>(mitk::IOUtil::Load(argv[4])[0].GetPointer()); typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,4,ODF_SAMPLING_SIZE> FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetBValue( b_value ); filter->SetGradientImage( gradients, itkVectorImagePointer ); filter->SetLambda(0.006); filter->SetNormalizationMethod(FilterType::QBAR_STANDARD); filter->Update(); mitk::OdfImage::Pointer testImage = mitk::OdfImage::New(); testImage->InitializeByItk( filter->GetOutput() ); testImage->SetVolume( filter->GetOutput()->GetBufferPointer() ); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(*testImage, *odfImage, 0.0001, true), "Standard Q-ball reconstruction test."); } { MITK_INFO << "CSA Q-ball reconstruction " << argv[5]; mitk::OdfImage::Pointer odfImage = dynamic_cast<mitk::OdfImage*>(mitk::IOUtil::Load(argv[5])[0].GetPointer()); typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,4,ODF_SAMPLING_SIZE> FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetBValue( b_value ); filter->SetGradientImage( gradients, itkVectorImagePointer ); filter->SetLambda(0.006); filter->SetNormalizationMethod(FilterType::QBAR_SOLID_ANGLE); filter->Update(); mitk::OdfImage::Pointer testImage = mitk::OdfImage::New(); testImage->InitializeByItk( filter->GetOutput() ); testImage->SetVolume( filter->GetOutput()->GetBufferPointer() ); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(*testImage, *odfImage, 0.0001, true), "CSA Q-ball reconstruction test."); } { MITK_INFO << "ADC profile reconstruction " << argv[6]; mitk::OdfImage::Pointer odfImage = dynamic_cast<mitk::OdfImage*>(mitk::IOUtil::Load(argv[6])[0].GetPointer()); typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,4,ODF_SAMPLING_SIZE> FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetBValue( b_value ); filter->SetGradientImage( gradients, itkVectorImagePointer ); filter->SetLambda(0.006); filter->SetNormalizationMethod(FilterType::QBAR_ADC_ONLY); filter->Update(); mitk::OdfImage::Pointer testImage = mitk::OdfImage::New(); testImage->InitializeByItk( filter->GetOutput() ); testImage->SetVolume( filter->GetOutput()->GetBufferPointer() ); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(*testImage, *odfImage, 0.0001, true), "ADC profile reconstruction test."); } { MITK_INFO << "Raw signal modeling " << argv[7]; mitk::OdfImage::Pointer odfImage = dynamic_cast<mitk::OdfImage*>(mitk::IOUtil::Load(argv[7])[0].GetPointer()); typedef itk::AnalyticalDiffusionQballReconstructionImageFilter<short,short,float,4,ODF_SAMPLING_SIZE> FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetBValue( b_value ); filter->SetGradientImage( gradients, itkVectorImagePointer ); filter->SetLambda(0.006); filter->SetNormalizationMethod(FilterType::QBAR_RAW_SIGNAL); filter->Update(); mitk::OdfImage::Pointer testImage = mitk::OdfImage::New(); testImage->InitializeByItk( filter->GetOutput() ); testImage->SetVolume( filter->GetOutput()->GetBufferPointer() ); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(*testImage, *odfImage, 0.0001, true), "Raw signal modeling test."); } } catch (itk::ExceptionObject e) { MITK_INFO << e; return EXIT_FAILURE; } catch (std::exception e) { MITK_INFO << e.what(); return EXIT_FAILURE; } catch (...) { MITK_INFO << "ERROR!?!"; return EXIT_FAILURE; } MITK_TEST_END(); }