int StreamlineTracking(int argc, char* argv[])
{
ctkCommandLineParser parser;
parser.setArgumentPrefix("--", "-");
parser.addArgument("input", "i", ctkCommandLineParser::StringList, "input tensor image (.dti)", us::Any(), false);
parser.addArgument("seed", "si", ctkCommandLineParser::String, "binary seed image", us::Any(), true);
parser.addArgument("mask", "mi", ctkCommandLineParser::String, "binary mask image", us::Any(), true);
parser.addArgument("faImage", "fai", ctkCommandLineParser::String, "FA image", us::Any(), true);
parser.addArgument("minFA", "fa", ctkCommandLineParser::Float, "minimum fractional anisotropy threshold", 0.15, true);
parser.addArgument("minCurv", "c", ctkCommandLineParser::Float, "minimum curvature radius in mm (default = 0.5*minimum-spacing)");
parser.addArgument("stepSize", "s", ctkCommandLineParser::Float, "stepsize in mm (default = 0.1*minimum-spacing)");
parser.addArgument("tendf", "f", ctkCommandLineParser::Float, "Weighting factor between first eigenvector (f=1 equals FACT tracking) and input vector dependent direction (f=0).", 1.0, true);
parser.addArgument("tendg", "g", ctkCommandLineParser::Float, "Weighting factor between input vector (g=0) and tensor deflection (g=1 equals TEND tracking)", 0.0, true);
parser.addArgument("numSeeds", "n", ctkCommandLineParser::Int, "Number of seeds per voxel.", 1, true);
parser.addArgument("minLength", "l", ctkCommandLineParser::Float, "minimum fiber length in mm", 20, true);
parser.addArgument("interpolate", "ip", ctkCommandLineParser::Bool, "Use linear interpolation", false, true);
parser.addArgument("outFile", "o", ctkCommandLineParser::String, "output fiber bundle (.fib)", us::Any(), false);
map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
if (parsedArgs.size()==0)
return EXIT_FAILURE;
ctkCommandLineParser::StringContainerType inputImages = us::any_cast<ctkCommandLineParser::StringContainerType>(parsedArgs["input"]);
string dtiFileName;
string outFileName = us::any_cast<string>(parsedArgs["outFile"]);
float minFA = 0.15;
float minCurv = -1;
float stepSize = -1;
float tendf = 1;
float tendg = 0;
float minLength = 20;
int numSeeds = 1;
bool interpolate = false;
if (parsedArgs.count("minCurv"))
minCurv = us::any_cast<float>(parsedArgs["minCurv"]);
if (parsedArgs.count("minFA"))
minFA = us::any_cast<float>(parsedArgs["minFA"]);
if (parsedArgs.count("stepSize"))
stepSize = us::any_cast<float>(parsedArgs["stepSize"]);
if (parsedArgs.count("tendf"))
tendf = us::any_cast<float>(parsedArgs["tendf"]);
if (parsedArgs.count("tendg"))
tendg = us::any_cast<float>(parsedArgs["tendg"]);
if (parsedArgs.count("minLength"))
minLength = us::any_cast<float>(parsedArgs["minLength"]);
if (parsedArgs.count("numSeeds"))
numSeeds = us::any_cast<int>(parsedArgs["numSeeds"]);
if (parsedArgs.count("interpolate"))
interpolate = us::any_cast<bool>(parsedArgs["interpolate"]);
try
{
typedef itk::StreamlineTrackingFilter< float > FilterType;
FilterType::Pointer filter = FilterType::New();
MITK_INFO << "Loading tensor images ...";
typedef itk::Image< itk::DiffusionTensor3D<float>, 3 > ItkTensorImage;
dtiFileName = inputImages.at(0);
for (unsigned int i=0; i<inputImages.size(); i++)
{
try
{
mitk::TensorImage::Pointer img = dynamic_cast<mitk::TensorImage*>(mitk::IOUtil::LoadDataNode(inputImages.at(i))->GetData());
ItkTensorImage::Pointer itk_dti = ItkTensorImage::New();
mitk::CastToItkImage<ItkTensorImage>(img, itk_dti);
filter->SetInput(i, itk_dti);
}
catch(...){ MITK_INFO << "could not load: " << inputImages.at(i); }
}
MITK_INFO << "Loading seed image ...";
typedef itk::Image< unsigned char, 3 > ItkUCharImageType;
mitk::Image::Pointer mitkSeedImage = NULL;
if (parsedArgs.count("seed"))
mitkSeedImage = mitk::IOUtil::LoadImage(us::any_cast<string>(parsedArgs["seed"]));
MITK_INFO << "Loading mask image ...";
mitk::Image::Pointer mitkMaskImage = NULL;
if (parsedArgs.count("mask"))
mitkMaskImage = mitk::IOUtil::LoadImage(us::any_cast<string>(parsedArgs["mask"]));
// instantiate tracker
filter->SetSeedsPerVoxel(numSeeds);
filter->SetFaThreshold(minFA);
filter->SetMinCurvatureRadius(minCurv);
filter->SetStepSize(stepSize);
filter->SetF(tendf);
filter->SetG(tendg);
filter->SetInterpolate(interpolate);
filter->SetMinTractLength(minLength);
if (mitkSeedImage.IsNotNull())
{
ItkUCharImageType::Pointer mask = ItkUCharImageType::New();
mitk::CastToItkImage<ItkUCharImageType>(mitkSeedImage, mask);
filter->SetSeedImage(mask);
}
if (mitkMaskImage.IsNotNull())
{
ItkUCharImageType::Pointer mask = ItkUCharImageType::New();
mitk::CastToItkImage<ItkUCharImageType>(mitkMaskImage, mask);
filter->SetMaskImage(mask);
}
filter->Update();
vtkSmartPointer<vtkPolyData> fiberBundle = filter->GetFiberPolyData();
if ( fiberBundle->GetNumberOfLines()==0 )
{
MITK_INFO << "No fibers reconstructed. Check parametrization.";
return EXIT_FAILURE;
}
mitk::FiberBundleX::Pointer fib = mitk::FiberBundleX::New(fiberBundle);
mitk::CoreObjectFactory::FileWriterList fileWriters = mitk::CoreObjectFactory::GetInstance()->GetFileWriters();
for (mitk::CoreObjectFactory::FileWriterList::iterator it = fileWriters.begin() ; it != fileWriters.end() ; ++it)
{
if ( (*it)->CanWriteBaseDataType(fib.GetPointer()) ) {
(*it)->SetFileName( outFileName.c_str() );
(*it)->DoWrite( fib.GetPointer() );
}
}
}
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_INFO << "DONE";
return EXIT_SUCCESS;
}
int mitkStreamlineTrackingTest(int argc, char* argv[])
{
MITK_TEST_BEGIN("mitkStreamlineTrackingTest");
MITK_TEST_CONDITION_REQUIRED(argc>3,"check for input data")
string dtiFileName = argv[1];
string maskFileName = argv[2];
string referenceFileName = argv[3];
MITK_INFO << "DTI file: " << dtiFileName;
MITK_INFO << "Mask file: " << maskFileName;
MITK_INFO << "Reference fiber file: " << referenceFileName;
float minFA = 0.05;
float minCurv = -1;
float stepSize = -1;
float tendf = 1;
float tendg = 0;
float minLength = 20;
int numSeeds = 1;
bool interpolate = true;
try
{
MITK_INFO << "Loading tensor image ...";
typedef itk::Image< itk::DiffusionTensor3D<float>, 3 > ItkTensorImage;
mitk::TensorImage::Pointer mitkTensorImage = dynamic_cast<mitk::TensorImage*>(mitk::IOUtil::LoadDataNode(dtiFileName)->GetData());
ItkTensorImage::Pointer itk_dti = ItkTensorImage::New();
mitk::CastToItkImage(mitkTensorImage, itk_dti);
MITK_INFO << "Loading seed image ...";
typedef itk::Image< unsigned char, 3 > ItkUCharImageType;
mitk::Image::Pointer mitkSeedImage = mitk::IOUtil::LoadImage(maskFileName);
MITK_INFO << "Loading mask image ...";
mitk::Image::Pointer mitkMaskImage = mitk::IOUtil::LoadImage(maskFileName);
// instantiate tracker
typedef itk::StreamlineTrackingFilter< float > FilterType;
FilterType::Pointer filter = FilterType::New();
filter->SetInput(itk_dti);
filter->SetSeedsPerVoxel(numSeeds);
filter->SetFaThreshold(minFA);
filter->SetMinCurvatureRadius(minCurv);
filter->SetStepSize(stepSize);
filter->SetF(tendf);
filter->SetG(tendg);
filter->SetInterpolate(interpolate);
filter->SetMinTractLength(minLength);
filter->SetNumberOfThreads(1);
if (mitkSeedImage.IsNotNull())
{
ItkUCharImageType::Pointer mask = ItkUCharImageType::New();
mitk::CastToItkImage(mitkSeedImage, mask);
filter->SetSeedImage(mask);
}
if (mitkMaskImage.IsNotNull())
{
ItkUCharImageType::Pointer mask = ItkUCharImageType::New();
mitk::CastToItkImage(mitkMaskImage, mask);
filter->SetMaskImage(mask);
}
filter->Update();
vtkSmartPointer<vtkPolyData> fiberBundle = filter->GetFiberPolyData();
mitk::FiberBundleX::Pointer fib1 = mitk::FiberBundleX::New(fiberBundle);
mitk::FiberBundleX::Pointer fib2 = dynamic_cast<mitk::FiberBundleX*>(mitk::IOUtil::LoadDataNode(referenceFileName)->GetData());
MITK_TEST_CONDITION_REQUIRED(fib2.IsNotNull(), "Check if reference tractogram is not null.");
bool ok = fib1->Equals(fib2);
if (!ok)
{
MITK_WARN << "TEST FAILED. TRACTOGRAMS ARE NOT EQUAL!";
mitk::IOUtil::SaveBaseData(fib1, mitk::IOUtil::GetTempPath()+"testBundle.fib");
mitk::IOUtil::SaveBaseData(fib2, mitk::IOUtil::GetTempPath()+"refBundle.fib");
MITK_INFO << "OUTPUT: " << mitk::IOUtil::GetTempPath();
}
MITK_TEST_CONDITION_REQUIRED(ok, "Check if tractograms are equal.");
}
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();
}
