void QmitkPreprocessingView::DoAdcCalculation()
{
if (m_DiffusionImage.IsNull())
return;
typedef mitk::DiffusionImage< DiffusionPixelType > DiffusionImageType;
typedef itk::AdcImageFilter< DiffusionPixelType, double > FilterType;
for (unsigned int i=0; i<m_SelectedDiffusionNodes.size(); i++)
{
DiffusionImageType::Pointer inImage = dynamic_cast< DiffusionImageType* >(m_SelectedDiffusionNodes.at(i)->GetData());
FilterType::Pointer filter = FilterType::New();
filter->SetInput(inImage->GetVectorImage());
filter->SetGradientDirections(inImage->GetDirections());
filter->SetB_value(inImage->GetReferenceBValue());
filter->Update();
mitk::Image::Pointer image = mitk::Image::New();
image->InitializeByItk( filter->GetOutput() );
image->SetVolume( filter->GetOutput()->GetBufferPointer() );
mitk::DataNode::Pointer imageNode = mitk::DataNode::New();
imageNode->SetData( image );
QString name = m_SelectedDiffusionNodes.at(i)->GetName().c_str();
imageNode->SetName((name+"_ADC").toStdString().c_str());
GetDefaultDataStorage()->Add(imageNode);
}
}
/**
* Denoises DWI using the Nonlocal - Means algorithm
*/
int DwiDenoising(int argc, char* argv[])
{
ctkCommandLineParser parser;
parser.setArgumentPrefix("--", "-");
parser.addArgument("input", "i", ctkCommandLineParser::String, "input image (DWI)", us::Any(), false);
parser.addArgument("variance", "v", ctkCommandLineParser::Float, "noise variance", us::Any(), false);
parser.addArgument("mask", "m", ctkCommandLineParser::String, "brainmask for input image", us::Any(), true);
parser.addArgument("search", "s", ctkCommandLineParser::Int, "search radius", us::Any(), true);
parser.addArgument("compare", "c", ctkCommandLineParser::Int, "compare radius", us::Any(), true);
parser.addArgument("joint", "j", ctkCommandLineParser::Bool, "use joint information");
parser.addArgument("rician", "r", ctkCommandLineParser::Bool, "use rician adaption");
map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
if (parsedArgs.size()==0)
return EXIT_FAILURE;
string inFileName = us::any_cast<string>(parsedArgs["input"]);
double variance = static_cast<double>(us::any_cast<float>(parsedArgs["variance"]));
string maskName;
if (parsedArgs.count("mask"))
maskName = us::any_cast<string>(parsedArgs["mask"]);
string outFileName = inFileName;
boost::algorithm::erase_all(outFileName, ".dwi");
int search = 4;
if (parsedArgs.count("search"))
search = us::any_cast<int>(parsedArgs["search"]);
int compare = 1;
if (parsedArgs.count("compare"))
compare = us::any_cast<int>(parsedArgs["compare"]);
bool joint = false;
if (parsedArgs.count("joint"))
joint = true;
bool rician = false;
if (parsedArgs.count("rician"))
rician = true;
try
{
if( boost::algorithm::ends_with(inFileName, ".dwi"))
{
DiffusionImageType::Pointer dwi = dynamic_cast<DiffusionImageType*>(LoadFile(inFileName).GetPointer());
itk::NonLocalMeansDenoisingFilter<short>::Pointer filter = itk::NonLocalMeansDenoisingFilter<short>::New();
filter->SetNumberOfThreads(12);
filter->SetInputImage(dwi->GetVectorImage());
if (!maskName.empty())
{
mitk::Image::Pointer mask = dynamic_cast<mitk::Image*>(LoadFile(maskName).GetPointer());
ImageType::Pointer itkMask = ImageType::New();
mitk::CastToItkImage(mask, itkMask);
filter->SetInputMask(itkMask);
}
filter->SetUseJointInformation(joint);
filter->SetUseRicianAdaption(rician);
filter->SetSearchRadius(search);
filter->SetComparisonRadius(compare);
filter->SetVariance(variance);
filter->Update();
DiffusionImageType::Pointer output = DiffusionImageType::New();
output->SetVectorImage(filter->GetOutput());
output->SetReferenceBValue(dwi->GetReferenceBValue());
output->SetDirections(dwi->GetDirections());
output->InitializeFromVectorImage();
std::stringstream name;
name << outFileName << "_NLM_" << search << "-" << compare << "-" << variance << ".dwi";
MITK_INFO << "Writing: " << name.str();
mitk::NrrdDiffusionImageWriter<short>::Pointer writer = mitk::NrrdDiffusionImageWriter<short>::New();
writer->SetInput(output);
writer->SetFileName(name.str());
writer->Update();
MITK_INFO << "Finish!";
}
else
{
MITK_INFO << "Only supported for .dwi!";
}
}
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;
}
return EXIT_SUCCESS;
}