/** * 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; }