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();
}