diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxSignalGenerationTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxSignalGenerationTest.cpp index a6628b1bf8..3af9506e81 100644 --- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxSignalGenerationTest.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxSignalGenerationTest.cpp @@ -1,325 +1,337 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include /**Documentation * Test the Fiberfox simulation functions (fiberBundle -> diffusion weighted image) */ bool CompareDwi(itk::VectorImage< short, 3 >* dwi1, itk::VectorImage< short, 3 >* dwi2) { typedef itk::VectorImage< short, 3 > DwiImageType; try{ itk::ImageRegionIterator< DwiImageType > it1(dwi1, dwi1->GetLargestPossibleRegion()); itk::ImageRegionIterator< DwiImageType > it2(dwi2, dwi2->GetLargestPossibleRegion()); while(!it1.IsAtEnd()) { if (it1.Get()!=it2.Get()) return false; ++it1; ++it2; } } catch(...) { return false; } return true; } void StartSimulation(FiberfoxParameters parameters, FiberBundleX::Pointer fiberBundle, mitk::DiffusionImage::Pointer refImage, string message) { itk::TractsToDWIImageFilter< short >::Pointer tractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New(); tractsToDwiFilter->SetUseConstantRandSeed(true); tractsToDwiFilter->SetSimulateEddyCurrents(parameters.m_DoSimulateEddyCurrents); tractsToDwiFilter->SetEddyGradientStrength(parameters.m_EddyStrength); tractsToDwiFilter->SetAddGibbsRinging(parameters.m_AddGibbsRinging); tractsToDwiFilter->SetSimulateRelaxation(parameters.m_DoSimulateRelaxation); tractsToDwiFilter->SetImageRegion(parameters.m_ImageRegion); tractsToDwiFilter->SetSpacing(parameters.m_ImageSpacing); tractsToDwiFilter->SetOrigin(parameters.m_ImageOrigin); tractsToDwiFilter->SetDirectionMatrix(parameters.m_ImageDirection); tractsToDwiFilter->SetFiberBundle(fiberBundle); tractsToDwiFilter->SetFiberModels(parameters.m_FiberModelList); tractsToDwiFilter->SetNonFiberModels(parameters.m_NonFiberModelList); tractsToDwiFilter->SetNoiseModel(parameters.m_NoiseModel); tractsToDwiFilter->SetkOffset(parameters.m_KspaceLineOffset); tractsToDwiFilter->SettLine(parameters.m_tLine); tractsToDwiFilter->SettInhom(parameters.m_tInhom); tractsToDwiFilter->SetTE(parameters.m_tEcho); tractsToDwiFilter->SetNumberOfRepetitions(parameters.m_Repetitions); tractsToDwiFilter->SetEnforcePureFiberVoxels(parameters.m_DoDisablePartialVolume); tractsToDwiFilter->SetInterpolationShrink(parameters.m_InterpolationShrink); tractsToDwiFilter->SetFiberRadius(parameters.m_AxonRadius); tractsToDwiFilter->SetSignalScale(parameters.m_SignalScale); if (parameters.m_InterpolationShrink>0) tractsToDwiFilter->SetUseInterpolation(true); tractsToDwiFilter->SetTissueMask(parameters.m_MaskImage); tractsToDwiFilter->SetFrequencyMap(parameters.m_FrequencyMap); tractsToDwiFilter->SetSpikeAmplitude(parameters.m_SpikeAmplitude); tractsToDwiFilter->SetSpikes(parameters.m_Spikes); tractsToDwiFilter->SetWrap(parameters.m_Wrap); tractsToDwiFilter->SetAddMotionArtifact(parameters.m_DoAddMotion); tractsToDwiFilter->SetMaxTranslation(parameters.m_Translation); tractsToDwiFilter->SetMaxRotation(parameters.m_Rotation); tractsToDwiFilter->SetRandomMotion(parameters.m_RandomMotion); tractsToDwiFilter->Update(); mitk::DiffusionImage::Pointer testImage = mitk::DiffusionImage::New(); testImage->SetVectorImage( tractsToDwiFilter->GetOutput() ); testImage->SetB_Value(parameters.m_Bvalue); testImage->SetDirections(parameters.m_GradientDirections); testImage->InitializeFromVectorImage(); if (refImage.IsNotNull()) { - MITK_TEST_CONDITION_REQUIRED(CompareDwi(testImage->GetVectorImage(), refImage->GetVectorImage()), message); + bool cond = CompareDwi(testImage->GetVectorImage(), refImage->GetVectorImage()); + if (!cond) + { + NrrdDiffusionImageWriter::Pointer writer = NrrdDiffusionImageWriter::New(); + writer->SetFileName("/tmp/testImage.dwi"); + writer->SetInput(testImage); + writer->Update(); + + writer->SetFileName("/tmp/refImage.dwi"); + writer->SetInput(refImage); + writer->Update(); + } + MITK_TEST_CONDITION_REQUIRED(cond, message); } else { MITK_INFO << "Saving test image to " << message; NrrdDiffusionImageWriter::Pointer writer = NrrdDiffusionImageWriter::New(); writer->SetFileName(message); writer->SetInput(testImage); writer->Update(); } } int mitkFiberfoxSignalGenerationTest(int argc, char* argv[]) { RegisterDiffusionCoreObjectFactory(); 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(fibReader->GetOutput()); // reference diffusion weighted images mitk::DiffusionImage::Pointer stickBall = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[2])->GetData()); mitk::DiffusionImage::Pointer stickAstrosticks = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[3])->GetData()); mitk::DiffusionImage::Pointer stickDot = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[4])->GetData()); mitk::DiffusionImage::Pointer tensorBall = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[5])->GetData()); mitk::DiffusionImage::Pointer stickTensorBall = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[6])->GetData()); mitk::DiffusionImage::Pointer stickTensorBallAstrosticks = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[7])->GetData()); mitk::DiffusionImage::Pointer gibbsringing = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[8])->GetData()); mitk::DiffusionImage::Pointer ghost = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[9])->GetData()); mitk::DiffusionImage::Pointer aliasing = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[10])->GetData()); mitk::DiffusionImage::Pointer eddy = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[11])->GetData()); mitk::DiffusionImage::Pointer linearmotion = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[12])->GetData()); mitk::DiffusionImage::Pointer randommotion = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[13])->GetData()); mitk::DiffusionImage::Pointer spikes = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[14])->GetData()); mitk::DiffusionImage::Pointer riciannoise = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[15])->GetData()); mitk::DiffusionImage::Pointer chisquarenoise = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[16])->GetData()); mitk::DiffusionImage::Pointer distortions = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[17])->GetData()); mitk::Image::Pointer mitkFMap = dynamic_cast(mitk::IOUtil::LoadDataNode(argv[18])->GetData()); typedef itk::Image ItkDoubleImgType; ItkDoubleImgType::Pointer fMap = ItkDoubleImgType::New(); mitk::CastToItkImage(mitkFMap, fMap); FiberfoxParameters 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(); mitk::DiffusionImage::GradientDirectionContainerType::Pointer dirs = stickBall->GetDirections(); parameters.m_NumGradients = 0; for (unsigned int i=0; iSize(); i++) { DiffusionSignalModel::GradientType g; g[0] = dirs->at(i)[0]; g[1] = dirs->at(i)[1]; g[2] = dirs->at(i)[2]; parameters.m_GradientDirections.push_back(g); if (dirs->at(i).magnitude()>0.0001) parameters.m_NumGradients++; } // intra and inter axonal compartments mitk::StickModel stickModel; stickModel.SetBvalue(parameters.m_Bvalue); stickModel.SetT2(110); stickModel.SetDiffusivity(0.001); stickModel.SetGradientList(parameters.m_GradientDirections); mitk::TensorModel tensorModel; tensorModel.SetT2(110); stickModel.SetBvalue(parameters.m_Bvalue); tensorModel.SetDiffusivity1(0.001); tensorModel.SetDiffusivity2(0.00025); tensorModel.SetDiffusivity3(0.00025); tensorModel.SetGradientList(parameters.m_GradientDirections); // extra axonal compartment models mitk::BallModel ballModel; ballModel.SetT2(80); ballModel.SetBvalue(parameters.m_Bvalue); ballModel.SetDiffusivity(0.001); ballModel.SetGradientList(parameters.m_GradientDirections); mitk::AstroStickModel astrosticksModel; astrosticksModel.SetT2(80); astrosticksModel.SetBvalue(parameters.m_Bvalue); astrosticksModel.SetDiffusivity(0.001); astrosticksModel.SetRandomizeSticks(true); astrosticksModel.SetSeed(0); astrosticksModel.SetGradientList(parameters.m_GradientDirections); mitk::DotModel dotModel; dotModel.SetT2(80); dotModel.SetGradientList(parameters.m_GradientDirections); // noise models mitk::RicianNoiseModel* ricianNoiseModel = new mitk::RicianNoiseModel(); ricianNoiseModel->SetNoiseVariance(1000000); ricianNoiseModel->SetSeed(0); // Rician noise mitk::ChiSquareNoiseModel* chiSquareNoiseModel = new mitk::ChiSquareNoiseModel(); chiSquareNoiseModel->SetDOF(500000); 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_AddGibbsRinging = true; StartSimulation(parameters, fiberBundle, gibbsringing, argv[8]); // Ghost parameters.m_AddGibbsRinging = false; parameters.m_KspaceLineOffset = 0.25; StartSimulation(parameters, fiberBundle, ghost, argv[9]); // Aliasing parameters.m_KspaceLineOffset = 0; parameters.m_Wrap = 0.4; parameters.m_SignalScale = 1000; StartSimulation(parameters, fiberBundle, aliasing, argv[10]); // Eddy currents parameters.m_Wrap = 1; parameters.m_SignalScale = 10000; parameters.m_DoSimulateEddyCurrents = true; parameters.m_EddyStrength = 0.05; StartSimulation(parameters, fiberBundle, eddy, argv[11]); // Motion (linear) parameters.m_DoSimulateEddyCurrents = false; parameters.m_EddyStrength = 0.0; parameters.m_DoAddMotion = true; parameters.m_RandomMotion = false; parameters.m_Translation[1] = 10; parameters.m_Rotation[2] = 90; StartSimulation(parameters, fiberBundle, linearmotion, argv[12]); // Motion (random) parameters.m_RandomMotion = 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(); }