void StartSimulation(FiberfoxParameters<double> parameters, FiberBundleX::Pointer fiberBundle, mitk::DiffusionImage<short>::Pointer refImage, string message) { itk::TractsToDWIImageFilter< short >::Pointer tractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New(); tractsToDwiFilter->SetUseConstantRandSeed(true); tractsToDwiFilter->SetParameters(parameters); tractsToDwiFilter->SetFiberBundle(fiberBundle); tractsToDwiFilter->Update(); mitk::DiffusionImage<short>::Pointer testImage = mitk::DiffusionImage<short>::New(); testImage->SetVectorImage( tractsToDwiFilter->GetOutput() ); testImage->SetB_Value(parameters.m_Bvalue); testImage->SetDirections(parameters.GetGradientDirections()); testImage->InitializeFromVectorImage(); if (refImage.IsNotNull()) { bool cond = CompareDwi(testImage->GetVectorImage(), refImage->GetVectorImage()); if (!cond) { mitk::IOUtil::SaveBaseData(testImage, "/tmp/testImage.dwi"); mitk::IOUtil::SaveBaseData(refImage, "/tmp/refImage.dwi"); } MITK_TEST_CONDITION_REQUIRED(cond, message); } else { MITK_INFO << "Saving test image to " << message; mitk::IOUtil::SaveBaseData(testImage, message); } }
void StartSimulation(string testFileName) { mitk::DiffusionImage<short>::Pointer refImage = NULL; if (!testFileName.empty()) CPPUNIT_ASSERT(refImage = dynamic_cast<mitk::DiffusionImage<short>*>(mitk::IOUtil::LoadDataNode(testFileName)->GetData())); itk::AddArtifactsToDwiImageFilter< short >::Pointer artifactsToDwiFilter = itk::AddArtifactsToDwiImageFilter< short >::New(); artifactsToDwiFilter->SetUseConstantRandSeed(true); artifactsToDwiFilter->SetInput(m_InputDwi->GetVectorImage()); artifactsToDwiFilter->SetParameters(m_Parameters); CPPUNIT_ASSERT_NO_THROW(artifactsToDwiFilter->Update()); mitk::DiffusionImage<short>::Pointer testImage = mitk::DiffusionImage<short>::New(); testImage->SetVectorImage( artifactsToDwiFilter->GetOutput() ); testImage->SetB_Value(m_Parameters.m_Bvalue); testImage->SetDirections(m_Parameters.GetGradientDirections()); testImage->InitializeFromVectorImage(); if (refImage.IsNotNull()) { bool ok = CompareDwi(testImage->GetVectorImage(), refImage->GetVectorImage()); if (!ok) { mitk::IOUtil::SaveBaseData(testImage, "/tmp/test2.dwi"); mitk::IOUtil::SaveBaseData(refImage, "/tmp/ref2.dwi"); } CPPUNIT_ASSERT_MESSAGE(testFileName, ok); } else { mitk::IOUtil::SaveBaseData(testImage, "/local/distortions2.dwi"); } }
int mitkFiberfoxSignalGenerationTest(int argc, char* argv[]) { MITK_TEST_BEGIN("mitkFiberfoxSignalGenerationTest"); MITK_TEST_CONDITION_REQUIRED(argc>=19,"check for input data"); // input fiber bundle FiberBundleXReader::Pointer fibReader = FiberBundleXReader::New(); fibReader->SetFileName(argv[1]); fibReader->Update(); FiberBundleX::Pointer fiberBundle = dynamic_cast<FiberBundleX*>(fibReader->GetOutput()); // reference diffusion weighted images mitk::DiffusionImage<short>::Pointer stickBall = dynamic_cast<mitk::DiffusionImage<short>*>(mitk::IOUtil::LoadDataNode(argv[2])->GetData()); mitk::DiffusionImage<short>::Pointer stickAstrosticks = dynamic_cast<mitk::DiffusionImage<short>*>(mitk::IOUtil::LoadDataNode(argv[3])->GetData()); mitk::DiffusionImage<short>::Pointer stickDot = dynamic_cast<mitk::DiffusionImage<short>*>(mitk::IOUtil::LoadDataNode(argv[4])->GetData()); mitk::DiffusionImage<short>::Pointer tensorBall = dynamic_cast<mitk::DiffusionImage<short>*>(mitk::IOUtil::LoadDataNode(argv[5])->GetData()); mitk::DiffusionImage<short>::Pointer stickTensorBall = dynamic_cast<mitk::DiffusionImage<short>*>(mitk::IOUtil::LoadDataNode(argv[6])->GetData()); mitk::DiffusionImage<short>::Pointer stickTensorBallAstrosticks = dynamic_cast<mitk::DiffusionImage<short>*>(mitk::IOUtil::LoadDataNode(argv[7])->GetData()); mitk::DiffusionImage<short>::Pointer gibbsringing = dynamic_cast<mitk::DiffusionImage<short>*>(mitk::IOUtil::LoadDataNode(argv[8])->GetData()); mitk::DiffusionImage<short>::Pointer ghost = dynamic_cast<mitk::DiffusionImage<short>*>(mitk::IOUtil::LoadDataNode(argv[9])->GetData()); mitk::DiffusionImage<short>::Pointer aliasing = dynamic_cast<mitk::DiffusionImage<short>*>(mitk::IOUtil::LoadDataNode(argv[10])->GetData()); mitk::DiffusionImage<short>::Pointer eddy = dynamic_cast<mitk::DiffusionImage<short>*>(mitk::IOUtil::LoadDataNode(argv[11])->GetData()); mitk::DiffusionImage<short>::Pointer linearmotion = dynamic_cast<mitk::DiffusionImage<short>*>(mitk::IOUtil::LoadDataNode(argv[12])->GetData()); mitk::DiffusionImage<short>::Pointer randommotion = dynamic_cast<mitk::DiffusionImage<short>*>(mitk::IOUtil::LoadDataNode(argv[13])->GetData()); mitk::DiffusionImage<short>::Pointer spikes = dynamic_cast<mitk::DiffusionImage<short>*>(mitk::IOUtil::LoadDataNode(argv[14])->GetData()); mitk::DiffusionImage<short>::Pointer riciannoise = dynamic_cast<mitk::DiffusionImage<short>*>(mitk::IOUtil::LoadDataNode(argv[15])->GetData()); mitk::DiffusionImage<short>::Pointer chisquarenoise = dynamic_cast<mitk::DiffusionImage<short>*>(mitk::IOUtil::LoadDataNode(argv[16])->GetData()); mitk::DiffusionImage<short>::Pointer distortions = dynamic_cast<mitk::DiffusionImage<short>*>(mitk::IOUtil::LoadDataNode(argv[17])->GetData()); mitk::Image::Pointer mitkFMap = dynamic_cast<mitk::Image*>(mitk::IOUtil::LoadDataNode(argv[18])->GetData()); typedef itk::Image<double, 3> ItkDoubleImgType; ItkDoubleImgType::Pointer fMap = ItkDoubleImgType::New(); mitk::CastToItkImage<ItkDoubleImgType>(mitkFMap, fMap); FiberfoxParameters<double> parameters; parameters.m_DoSimulateRelaxation = true; parameters.m_SignalScale = 10000; parameters.m_ImageRegion = stickBall->GetVectorImage()->GetLargestPossibleRegion(); parameters.m_ImageSpacing = stickBall->GetVectorImage()->GetSpacing(); parameters.m_ImageOrigin = stickBall->GetVectorImage()->GetOrigin(); parameters.m_ImageDirection = stickBall->GetVectorImage()->GetDirection(); parameters.m_Bvalue = stickBall->GetB_Value(); parameters.SetGradienDirections(stickBall->GetDirections()); // intra and inter axonal compartments mitk::StickModel<double> stickModel; stickModel.SetBvalue(parameters.m_Bvalue); stickModel.SetT2(110); stickModel.SetDiffusivity(0.001); stickModel.SetGradientList(parameters.GetGradientDirections()); mitk::TensorModel<double> tensorModel; tensorModel.SetT2(110); stickModel.SetBvalue(parameters.m_Bvalue); tensorModel.SetDiffusivity1(0.001); tensorModel.SetDiffusivity2(0.00025); tensorModel.SetDiffusivity3(0.00025); tensorModel.SetGradientList(parameters.GetGradientDirections()); // extra axonal compartment models mitk::BallModel<double> ballModel; ballModel.SetT2(80); ballModel.SetBvalue(parameters.m_Bvalue); ballModel.SetDiffusivity(0.001); ballModel.SetGradientList(parameters.GetGradientDirections()); mitk::AstroStickModel<double> astrosticksModel; astrosticksModel.SetT2(80); astrosticksModel.SetBvalue(parameters.m_Bvalue); astrosticksModel.SetDiffusivity(0.001); astrosticksModel.SetRandomizeSticks(true); astrosticksModel.SetSeed(0); astrosticksModel.SetGradientList(parameters.GetGradientDirections()); mitk::DotModel<double> dotModel; dotModel.SetT2(80); dotModel.SetGradientList(parameters.GetGradientDirections()); // noise models mitk::RicianNoiseModel<double>* ricianNoiseModel = new mitk::RicianNoiseModel<double>(); ricianNoiseModel->SetNoiseVariance(1000000); ricianNoiseModel->SetSeed(0); // Rician noise mitk::ChiSquareNoiseModel<double>* chiSquareNoiseModel = new mitk::ChiSquareNoiseModel<double>(); chiSquareNoiseModel->SetNoiseVariance(1000000); chiSquareNoiseModel->SetSeed(0); try { // Stick-Ball parameters.m_FiberModelList.push_back(&stickModel); parameters.m_NonFiberModelList.push_back(&ballModel); StartSimulation(parameters, fiberBundle, stickBall, argv[2]); // Srick-Astrosticks parameters.m_NonFiberModelList.clear(); parameters.m_NonFiberModelList.push_back(&astrosticksModel); StartSimulation(parameters, fiberBundle, stickAstrosticks, argv[3]); // Stick-Dot parameters.m_NonFiberModelList.clear(); parameters.m_NonFiberModelList.push_back(&dotModel); StartSimulation(parameters, fiberBundle, stickDot, argv[4]); // Tensor-Ball parameters.m_FiberModelList.clear(); parameters.m_FiberModelList.push_back(&tensorModel); parameters.m_NonFiberModelList.clear(); parameters.m_NonFiberModelList.push_back(&ballModel); StartSimulation(parameters, fiberBundle, tensorBall, argv[5]); // Stick-Tensor-Ball parameters.m_FiberModelList.clear(); parameters.m_FiberModelList.push_back(&stickModel); parameters.m_FiberModelList.push_back(&tensorModel); parameters.m_NonFiberModelList.clear(); parameters.m_NonFiberModelList.push_back(&ballModel); StartSimulation(parameters, fiberBundle, stickTensorBall, argv[6]); // Stick-Tensor-Ball-Astrosticks parameters.m_NonFiberModelList.push_back(&astrosticksModel); StartSimulation(parameters, fiberBundle, stickTensorBallAstrosticks, argv[7]); // Gibbs ringing parameters.m_FiberModelList.clear(); parameters.m_FiberModelList.push_back(&stickModel); parameters.m_NonFiberModelList.clear(); parameters.m_NonFiberModelList.push_back(&ballModel); parameters.m_DoAddGibbsRinging = true; StartSimulation(parameters, fiberBundle, gibbsringing, argv[8]); // Ghost parameters.m_DoAddGibbsRinging = false; parameters.m_KspaceLineOffset = 0.25; StartSimulation(parameters, fiberBundle, ghost, argv[9]); // Aliasing parameters.m_KspaceLineOffset = 0; parameters.m_CroppingFactor = 0.4; parameters.m_SignalScale = 1000; StartSimulation(parameters, fiberBundle, aliasing, argv[10]); // Eddy currents parameters.m_CroppingFactor = 1; parameters.m_SignalScale = 10000; parameters.m_EddyStrength = 0.05; StartSimulation(parameters, fiberBundle, eddy, argv[11]); // Motion (linear) parameters.m_EddyStrength = 0.0; parameters.m_DoAddMotion = true; parameters.m_DoRandomizeMotion = false; parameters.m_Translation[1] = 10; parameters.m_Rotation[2] = 90; StartSimulation(parameters, fiberBundle, linearmotion, argv[12]); // Motion (random) parameters.m_DoRandomizeMotion = true; parameters.m_Translation[1] = 5; parameters.m_Rotation[2] = 45; StartSimulation(parameters, fiberBundle, randommotion, argv[13]); // Spikes parameters.m_DoAddMotion = false; parameters.m_Spikes = 5; parameters.m_SpikeAmplitude = 1; StartSimulation(parameters, fiberBundle, spikes, argv[14]); // Rician noise parameters.m_Spikes = 0; parameters.m_NoiseModel = ricianNoiseModel; StartSimulation(parameters, fiberBundle, riciannoise, argv[15]); delete parameters.m_NoiseModel; // Chi-square noise parameters.m_NoiseModel = chiSquareNoiseModel; StartSimulation(parameters, fiberBundle, chisquarenoise, argv[16]); delete parameters.m_NoiseModel; // Distortions parameters.m_NoiseModel = NULL; parameters.m_FrequencyMap = fMap; StartSimulation(parameters, fiberBundle, distortions, argv[17]); } catch (std::exception &e) { MITK_TEST_CONDITION_REQUIRED(false, e.what()); } // always end with this! MITK_TEST_END(); }