/**
* Denoises DWI using the Nonlocal - Means algorithm
*/
int main(int argc, char* argv[])
{
mitkCommandLineParser parser;
parser.setTitle("DWI Denoising");
parser.setCategory("Preprocessing Tools");
parser.setContributor("MIC");
parser.setDescription("Denoising for diffusion weighted images using a non-local means algorithm.");
parser.setArgumentPrefix("--", "-");
parser.addArgument("input", "i", mitkCommandLineParser::InputFile, "Input:", "input image (DWI)", us::Any(), false);
parser.addArgument("variance", "v", mitkCommandLineParser::Float, "Variance:", "noise variance", us::Any(), false);
parser.addArgument("mask", "m", mitkCommandLineParser::InputFile, "Mask:", "brainmask for input image", us::Any(), true);
parser.addArgument("search", "s", mitkCommandLineParser::Int, "Search radius:", "search radius", us::Any(), true);
parser.addArgument("compare", "c", mitkCommandLineParser::Int, "Comparison radius:", "comparison radius", us::Any(), true);
parser.addArgument("joint", "j", mitkCommandLineParser::Bool, "Joint information:", "use joint information");
parser.addArgument("rician", "r", mitkCommandLineParser::Bool, "Rician adaption:", "use rician adaption");
parser.changeParameterGroup("Output", "Output of this miniapp");
parser.addArgument("output", "o", mitkCommandLineParser::OutputFile, "Output:", "output image (DWI)", us::Any(), false);
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 = us::any_cast<string>(parsedArgs["output"]);
// 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
{
mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Diffusion Weighted Images"}, {});
DiffusionImageType::Pointer dwi = dynamic_cast<mitk::Image*>(mitk::IOUtil::LoadImage(inFileName, &functor).GetPointer());
mitk::DiffusionPropertyHelper::ImageType::Pointer itkVectorImagePointer = mitk::DiffusionPropertyHelper::ImageType::New();
mitk::CastToItkImage(dwi, itkVectorImagePointer);
itk::NonLocalMeansDenoisingFilter<short>::Pointer filter = itk::NonLocalMeansDenoisingFilter<short>::New();
filter->SetNumberOfThreads(12);
filter->SetInputImage( itkVectorImagePointer );
if (!maskName.empty())
{
mitk::Image::Pointer mask = dynamic_cast<mitk::Image*>(mitk::IOUtil::Load(maskName)[0].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 = mitk::GrabItkImageMemory( filter->GetOutput() );
output->GetPropertyList()->ReplaceProperty( mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str(), mitk::FloatProperty::New( mitk::DiffusionPropertyHelper::GetReferenceBValue(dwi) ) );
output->GetPropertyList()->ReplaceProperty( mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str(), mitk::GradientDirectionsProperty::New( mitk::DiffusionPropertyHelper::GetGradientContainer(dwi) ) );
mitk::DiffusionPropertyHelper propertyHelper( output );
propertyHelper.InitializeImage();
// std::stringstream name;
// name << outFileName << "_NLM_" << search << "-" << compare << "-" << variance << ".dwi";
mitk::IOUtil::Save(output, outFileName.c_str());
}
catch (itk::ExceptionObject e)
{
std::cout << e;
return EXIT_FAILURE;
}
catch (std::exception e)
{
std::cout << e.what();
return EXIT_FAILURE;
}
catch (...)
{
std::cout << "ERROR!?!";
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
