diff --git a/Modules/DiffusionImaging/MiniApps/BatchedFolderRegistration.cpp b/Modules/DiffusionImaging/MiniApps/BatchedFolderRegistration.cpp index 5f6427c54b..20a4ec51ee 100644 --- a/Modules/DiffusionImaging/MiniApps/BatchedFolderRegistration.cpp +++ b/Modules/DiffusionImaging/MiniApps/BatchedFolderRegistration.cpp @@ -1,487 +1,487 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "MiniAppManager.h" // CTK #include "ctkCommandLineParser.h" #include #include #include #include #include #include #include "mitkNrrdDiffusionImageWriter.h" #include // ITK #include #include #include "itkLinearInterpolateImageFunction.h" #include "itkWindowedSincInterpolateImageFunction.h" #include "itkIdentityTransform.h" #include "itkResampleImageFilter.h" typedef std::vector FileListType; typedef itk::Image InputImageType; static mitk::Image::Pointer ExtractFirstTS(mitk::Image* image, std::string fileType) { if (fileType == ".dwi") return image; mitk::ImageTimeSelector::Pointer selector = mitk::ImageTimeSelector::New(); selector->SetInput(image); selector->SetTimeNr(0); selector->UpdateLargestPossibleRegion(); mitk::Image::Pointer img =selector->GetOutput()->Clone(); return img; } static std::vector &split(const std::string &s, char delim, std::vector &elems) { std::stringstream ss(s); std::string item; while (std::getline(ss, item, delim)) { elems.push_back(item); } return elems; } static std::vector split(const std::string &s, char delim) { std::vector < std::string > elems; return split(s, delim, elems); } /// Create list of all files in provided folder ending with same postfix static FileListType CreateFileList(std::string folder , std::string postfix) { itk::Directory::Pointer dir = itk::Directory::New(); FileListType fileList; if( dir->Load(folder.c_str() ) ) { int n = dir->GetNumberOfFiles(); for(int r=0;rGetFile( r ); if (filename == "." || filename == "..") continue; filename = folder + filename; if (!itksys::SystemTools::FileExists( filename.c_str())) continue; if (filename.substr(filename.length() -postfix.length() ) == postfix) fileList.push_back(filename); } } return fileList; } static std::string GetSavePath(std::string outputFolder, std::string fileName) { std::string fileType = itksys::SystemTools::GetFilenameExtension(fileName); std::string fileStem = itksys::SystemTools::GetFilenameWithoutExtension(fileName); std::string savePathAndFileName = outputFolder +fileStem + fileType; return savePathAndFileName; } static mitk::Image::Pointer ResampleBySpacing(mitk::Image *input, float *spacing, bool useLinInt = false) { InputImageType::Pointer itkImage = InputImageType::New(); CastToItkImage(input,itkImage); /** * 1) Resampling * */ // Identity transform. // We don't want any transform on our image except rescaling which is not // specified by a transform but by the input/output spacing as we will see // later. // So no transform will be specified. typedef itk::IdentityTransform T_Transform; // The resampler type itself. typedef itk::ResampleImageFilter T_ResampleFilter; // Prepare the resampler. // Instantiate the transform and specify it should be the id transform. T_Transform::Pointer _pTransform = T_Transform::New(); _pTransform->SetIdentity(); // Instantiate the resampler. Wire in the transform and the interpolator. T_ResampleFilter::Pointer _pResizeFilter = T_ResampleFilter::New(); _pResizeFilter->SetTransform(_pTransform); // Set the output origin. _pResizeFilter->SetOutputOrigin(itkImage->GetOrigin()); // Compute the size of the output. // The size (# of pixels) in the output is recomputed using // the ratio of the input and output sizes. InputImageType::SpacingType inputSpacing = itkImage->GetSpacing(); InputImageType::SpacingType outputSpacing; const InputImageType::RegionType& inputSize = itkImage->GetLargestPossibleRegion(); InputImageType::SizeType outputSize; typedef InputImageType::SizeType::SizeValueType SizeValueType; // Set the output spacing. outputSpacing[0] = spacing[0]; outputSpacing[1] = spacing[1]; outputSpacing[2] = spacing[2]; outputSize[0] = static_cast(inputSize.GetSize()[0] * inputSpacing[0] / outputSpacing[0] + .5); outputSize[1] = static_cast(inputSize.GetSize()[1] * inputSpacing[1] / outputSpacing[1] + .5); outputSize[2] = static_cast(inputSize.GetSize()[2] * inputSpacing[2] / outputSpacing[2] + .5); _pResizeFilter->SetOutputSpacing(outputSpacing); _pResizeFilter->SetSize(outputSize); typedef itk::LinearInterpolateImageFunction< InputImageType > LinearInterpolatorType; LinearInterpolatorType::Pointer lin_interpolator = LinearInterpolatorType::New(); typedef itk::Function::WelchWindowFunction<4> WelchWindowFunction; typedef itk::WindowedSincInterpolateImageFunction< InputImageType, 4,WelchWindowFunction> WindowedSincInterpolatorType; WindowedSincInterpolatorType::Pointer sinc_interpolator = WindowedSincInterpolatorType::New(); if (useLinInt) _pResizeFilter->SetInterpolator(lin_interpolator); else _pResizeFilter->SetInterpolator(sinc_interpolator); // Specify the input. _pResizeFilter->SetInput(itkImage); _pResizeFilter->Update(); mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk(_pResizeFilter->GetOutput()); mitk::GrabItkImageMemory( _pResizeFilter->GetOutput(), image); return image; } /// Build a derived file name from moving images e.g. xxx_T2.nrrd becomes xxx_GTV.nrrd static FileListType CreateDerivedFileList(std::string baseFN, std::string baseSuffix, std::vector derivedPatterns) { FileListType files; for (unsigned int i=0; i < derivedPatterns.size(); i++) { std::string derResourceSuffix = derivedPatterns.at(i); std::string derivedResourceFilename = baseFN.substr(0,baseFN.length() -baseSuffix.length()) + derResourceSuffix; MITK_INFO <<" Looking for file: " << derivedResourceFilename; if (!itksys::SystemTools::FileExists(derivedResourceFilename.c_str())) { MITK_INFO << "CreateDerivedFileList: File does not exit. Skipping entry."; continue; } files.push_back(derivedResourceFilename); } return files; } /// Save images according to file type static void SaveImage(std::string fileName, mitk::Image* image, std::string fileType ) { MITK_INFO << "----Save to " << fileName; if (fileType == "dwi") // IOUtil does not handle dwi files properly Bug 15772 { mitk::NrrdDiffusionImageWriter< short >::Pointer dwiwriter = mitk::NrrdDiffusionImageWriter< short >::New(); dwiwriter->SetInput( dynamic_cast* > (image)); dwiwriter->SetFileName( fileName ); try { dwiwriter->Update(); } catch( const itk::ExceptionObject& e) { MITK_ERROR << "Caught exception: " << e.what(); mitkThrow() << "Failed with exception from subprocess!"; } } else { mitk::IOUtil::SaveImage(image, fileName); } } /// Copy derived resources from first time step. Append _reg tag, but leave data untouched. static void CopyResources(FileListType fileList, std::string outputPath) { for (unsigned int j=0; j < fileList.size(); j++) { std::string derivedResourceFilename = fileList.at(j); std::string fileType = itksys::SystemTools::GetFilenameExtension(derivedResourceFilename); std::string fileStem = itksys::SystemTools::GetFilenameWithoutExtension(derivedResourceFilename); std::string savePathAndFileName = outputPath +fileStem + "." + fileType; MITK_INFO << "Copy resource " << savePathAndFileName; mitk::Image::Pointer resImage = ExtractFirstTS(mitk::IOUtil::LoadImage(derivedResourceFilename), fileType); mitk::IOUtil::SaveImage(resImage, savePathAndFileName); } } int BatchedFolderRegistration( int argc, char* argv[] ) { ctkCommandLineParser parser; parser.setArgumentPrefix("--","-"); parser.setTitle("Batched Folder Registraton"); parser.setCategory("Preprocessing Tools"); parser.setDescription(""); parser.setContributor("MBI"); // Add command line argument names parser.addArgument("help", "h",ctkCommandLineParser::Bool, "Help", "Show this help text"); //parser.addArgument("usemask", "u", QVariant::Bool, "Use segmentations (derived resources) to exclude areas from registration metrics"); - parser.addArgument("input", "i", ctkCommandLineParser::Directory, "Input:", "Input folder",us::Any(),false); - parser.addArgument("output", "o", ctkCommandLineParser::Directory, "Output:", "Output folder (ending with /)",us::Any(),false); + parser.addArgument("input", "i", ctkCommandLineParser::InputDirectory, "Input:", "Input folder",us::Any(),false); + parser.addArgument("output", "o", ctkCommandLineParser::OutputDirectory, "Output:", "Output folder (ending with /)",us::Any(),false); parser.addArgument("fixed", "f", ctkCommandLineParser::String, "Fixed images:", "Suffix for fixed image (if none is supplied first file matching moving pattern is chosen)",us::Any(),true); parser.addArgument("moving", "m", ctkCommandLineParser::String, "Moving images:", "Suffix for moving images",us::Any(),false); parser.addArgument("derived", "d", ctkCommandLineParser::String, "Derived resources:", "Derived resources suffixes (replaces suffix for moving images); comma separated",us::Any(),true); parser.addArgument("silent", "s", ctkCommandLineParser::Bool, "Silent:" "No xml progress output."); parser.addArgument("resample", "r", ctkCommandLineParser::String, "Resample (x,y,z)mm:", "Resample provide x,y,z spacing in mm (e.g. -r 1,1,3), is not applied to tensor data",us::Any()); parser.addArgument("binary", "b", ctkCommandLineParser::Bool, "Binary:", "Speficies that derived resource are binary (interpolation using nearest neighbor)",us::Any()); parser.addArgument("correct-origin", "c", ctkCommandLineParser::Bool, "Origin correction:", "Correct for large origin displacement. Switch when you reveive: Joint PDF summed to zero ",us::Any()); parser.addArgument("sinc-int", "s", ctkCommandLineParser::Bool, "Windowed-sinc interpolation:", "Use windowed-sinc interpolation (3) instead of linear interpolation ",us::Any()); map parsedArgs = parser.parseArguments(argc, argv); // Handle special arguments bool silent = false; bool isBinary = false; bool alignOrigin = false; bool useLinearInterpol = true; { if (parsedArgs.size() == 0) { MITK_ERROR << "Missig arguements" ; return EXIT_FAILURE; } if (parsedArgs.count("xml")) { MITK_ERROR << "This is to be handled by shell script"; return EXIT_SUCCESS; } if (parsedArgs.count("sinc-int")) useLinearInterpol = false; if (parsedArgs.count("silent")) silent = true; if (parsedArgs.count("binary")) isBinary = true; if (parsedArgs.count("correct-origin")) alignOrigin = true; // Show a help message if ( parsedArgs.count("help") || parsedArgs.count("h")) { std::cout << parser.helpText(); return EXIT_SUCCESS; } } std::string refPattern = ""; bool useFirstMoving = false; std::string movingImgPattern = us::any_cast(parsedArgs["moving"]); if (parsedArgs.count("fixed")) { refPattern = us::any_cast(parsedArgs["fixed"]); } else { useFirstMoving = true; refPattern = movingImgPattern; } std::string outputPath = us::any_cast(parsedArgs["output"]); std::string inputPath = us::any_cast(parsedArgs["input"]); //QString resampleReference = parsedArgs["resample"].toString(); //bool maskTumor = parsedArgs["usemask"].toBool(); // if derived sources pattern is provided, populate QStringList with possible filename postfixes std::vector derPatterns; if (parsedArgs.count("derived") || parsedArgs.count("d") ) { std::string arg = us::any_cast(parsedArgs["derived"]); derPatterns = split(arg ,','); } std::vector spacings; float spacing[3]; bool doResampling = false; if (parsedArgs.count("resample") || parsedArgs.count("d") ) { std::string arg = us::any_cast(parsedArgs["resample"]); spacings = split(arg ,','); spacing[0] = atoi(spacings.at(0).c_str()); spacing[1] = atoi(spacings.at(1).c_str()); spacing[2] = atoi(spacings.at(2).c_str()); doResampling = true; } MITK_INFO << "Input Folder : " << inputPath; MITK_INFO << "Looking for reference image ..."; FileListType referenceFileList = CreateFileList(inputPath,refPattern); if ((!useFirstMoving && referenceFileList.size() != 1) || (useFirstMoving && referenceFileList.size() == 0)) { MITK_ERROR << "None or more than one possible reference images (" << refPattern <<") found. Exiting." << referenceFileList.size(); MITK_INFO << "Choose a fixed arguement that is unique in the given folder!"; return EXIT_FAILURE; } std::string referenceFileName = referenceFileList.at(0); MITK_INFO << "Loading Reference (fixed) image: " << referenceFileName; std::string fileType = itksys::SystemTools::GetFilenameExtension(referenceFileName); mitk::Image::Pointer refImage = ExtractFirstTS(mitk::IOUtil::LoadImage(referenceFileName), fileType); mitk::Image::Pointer resampleReference = NULL; if (doResampling) { refImage = ResampleBySpacing(refImage,spacing); resampleReference = refImage; } if (refImage.IsNull()) MITK_ERROR << "Loaded fixed image is NULL"; // Copy reference image to destination std::string savePathAndFileName = GetSavePath(outputPath, referenceFileName); mitk::IOUtil::SaveImage(refImage, savePathAndFileName); // Copy all derived resources also to output folder, adding _reg suffix referenceFileList = CreateDerivedFileList(referenceFileName, movingImgPattern,derPatterns); CopyResources(referenceFileList, outputPath); std::string derivedResourceFilename; mitk::Image::Pointer referenceMask = NULL; // union of all segmentations if (!silent) { // XML Output to report progress std::cout << ""; std::cout << "Batched Registration"; std::cout << "Starting registration ... "; std::cout << ""; } // Now iterate over all files and register them to the reference image, // also register derived resources based on file patterns // ------------------------------------------------------------------------------ // Create File list FileListType movingImagesList = CreateFileList(inputPath, movingImgPattern); // TODO Reactivate Resampling Feature // mitk::Image::Pointer resampleImage = NULL; // if (QFileInfo(resampleReference).isFile()) // { // resampleImage = mitk::IOUtil::LoadImage(resampleReference.toStdString()); // } for (unsigned int i =0; i < movingImagesList.size(); i++) { std::string fileMorphName = movingImagesList.at(i); if (fileMorphName == referenceFileName) { // do not process reference image again continue; } MITK_INFO << "Processing image " << fileMorphName; // 1 Register morphological file to reference image if (!itksys::SystemTools::FileExists(fileMorphName.c_str())) { MITK_WARN << "File does not exit. Skipping entry."; continue; } // Origin of images is cancelled // TODO make this optional!! double transf[6]; double offset[3]; { std::string fileType = itksys::SystemTools::GetFilenameExtension(fileMorphName); mitk::Image::Pointer movingImage = ExtractFirstTS(mitk::IOUtil::LoadImage(fileMorphName), fileType); if (movingImage.IsNull()) MITK_ERROR << "Loaded moving image is NULL"; // Store transformation, apply it to morph file MITK_INFO << "----------Registering moving image to reference----------"; mitk::RegistrationWrapper::GetTransformation(refImage, movingImage, transf, offset, alignOrigin, referenceMask); mitk::RegistrationWrapper::ApplyTransformationToImage(movingImage, transf,offset, resampleReference); // , resampleImage savePathAndFileName = GetSavePath(outputPath, fileMorphName); if (fileType == ".dwi") fileType = "dwi"; SaveImage(savePathAndFileName,movingImage,fileType ); } if (!silent) { std::cout << "."; } // Now parse all derived resource and apply the above calculated transformation to them // ------------------------------------------------------------------------------------ FileListType fList = CreateDerivedFileList(fileMorphName, movingImgPattern,derPatterns); if (fList.size() > 0) MITK_INFO << "----------DERIVED RESOURCES ---------"; for (unsigned int j=0; j < fList.size(); j++) { derivedResourceFilename = fList.at(j); MITK_INFO << "----Processing derived resorce " << derivedResourceFilename << " ..."; std::string fileType = itksys::SystemTools::GetFilenameExtension(derivedResourceFilename); mitk::Image::Pointer derivedMovingResource = ExtractFirstTS(mitk::IOUtil::LoadImage(derivedResourceFilename), fileType); // Apply transformation to derived resource, treat derived resource as binary mitk::RegistrationWrapper::ApplyTransformationToImage(derivedMovingResource, transf,offset, resampleReference,isBinary); savePathAndFileName = GetSavePath(outputPath, derivedResourceFilename); SaveImage(savePathAndFileName,derivedMovingResource,fileType ); } } if (!silent) std::cout << ""; return EXIT_SUCCESS; } RegisterDiffusionMiniApp(BatchedFolderRegistration); diff --git a/Modules/DiffusionImaging/MiniApps/CopyGeometry.cpp b/Modules/DiffusionImaging/MiniApps/CopyGeometry.cpp index 2a1f009230..5f9c51eba6 100755 --- a/Modules/DiffusionImaging/MiniApps/CopyGeometry.cpp +++ b/Modules/DiffusionImaging/MiniApps/CopyGeometry.cpp @@ -1,97 +1,97 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "MiniAppManager.h" #include #include #include #include #include #include "ctkCommandLineParser.h" using namespace mitk; #include "ctkCommandLineParser.h" int CopyGeometry(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setTitle("Copy Geometry"); parser.setCategory("Preprocessing Tools"); parser.setDescription(""); parser.setContributor("MBI"); parser.setArgumentPrefix("--", "-"); - parser.addArgument("in", "i", ctkCommandLineParser::File, "Input:", "input image", us::Any(), false); - parser.addArgument("ref", "r", ctkCommandLineParser::File, "Reference:", "reference image", us::Any(), false); - parser.addArgument("out", "o", ctkCommandLineParser::File, "Output:", "output image", us::Any(), false); + parser.addArgument("in", "i", ctkCommandLineParser::InputFile, "Input:", "input image", us::Any(), false); + parser.addArgument("ref", "r", ctkCommandLineParser::InputFile, "Reference:", "reference image", us::Any(), false); + parser.addArgument("out", "o", ctkCommandLineParser::OutputFile, "Output:", "output image", us::Any(), false); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; // mandatory arguments string imageName = us::any_cast(parsedArgs["in"]); string refImage = us::any_cast(parsedArgs["ref"]); string outImage = us::any_cast(parsedArgs["out"]); try { MITK_INFO << "Loading image " << imageName; const std::string s1="", s2=""; std::vector infile = BaseDataIO::LoadBaseDataFromFile( refImage, s1, s2, false ); Image::Pointer source = dynamic_cast(infile.at(0).GetPointer()); infile = BaseDataIO::LoadBaseDataFromFile( imageName, s1, s2, false ); Image::Pointer target = dynamic_cast(infile.at(0).GetPointer()); mitk::BaseGeometry* s_geom = source->GetGeometry(); mitk::BaseGeometry* t_geom = target->GetGeometry(); t_geom->SetIndexToWorldTransform(s_geom->GetIndexToWorldTransform()); target->SetGeometry(t_geom); if ( dynamic_cast*>(target.GetPointer()) ) { MITK_INFO << "Writing " << outImage; DiffusionImage::Pointer dwi = dynamic_cast*>(target.GetPointer()); NrrdDiffusionImageWriter::Pointer writer = NrrdDiffusionImageWriter::New(); writer->SetFileName(outImage); writer->SetInput(dwi); writer->Update(); } else mitk::IOUtil::SaveImage(target, outImage); } 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; } RegisterDiffusionMiniApp(CopyGeometry); diff --git a/Modules/DiffusionImaging/MiniApps/DicomFolderDump.cpp b/Modules/DiffusionImaging/MiniApps/DicomFolderDump.cpp index 6779165e7a..e9500f7fcf 100644 --- a/Modules/DiffusionImaging/MiniApps/DicomFolderDump.cpp +++ b/Modules/DiffusionImaging/MiniApps/DicomFolderDump.cpp @@ -1,91 +1,91 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "MiniAppManager.h" #include "mitkDicomSeriesReader.h" #include "mitkProperties.h" // CTK #include "ctkCommandLineParser.h" #include "mitkIOUtil.h" int DicomFolderDump(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setTitle("Dicom Loader"); parser.setCategory("Preprocessing Tools"); parser.setDescription(""); parser.setContributor("MBI"); parser.setArgumentPrefix("--","-"); // Add command line argument names parser.addArgument("help", "h",ctkCommandLineParser::Bool, "Help:", "Show this help text"); // parser.addArgument("xml", "x",ctkCommandLineParser::Bool, "Print a XML description of this modules command line interface"); - parser.addArgument("input", "i", ctkCommandLineParser::Directory, "Input folder:", "Input folder",us::Any(),false); - parser.addArgument("output", "o", ctkCommandLineParser::Directory, "Output folder:", "Output folder (ending with /)",us::Any(),false); + parser.addArgument("input", "i", ctkCommandLineParser::InputDirectory, "Input folder:", "Input folder",us::Any(),false); + parser.addArgument("output", "o", ctkCommandLineParser::OutputDirectory, "Output folder:", "Output folder (ending with /)",us::Any(),false); parser.addArgument("filename", "f", ctkCommandLineParser::String, "Output name:", "Output filename (incl. .nrrd)",us::Any(),false); map parsedArgs = parser.parseArguments(argc, argv); // Show a help message if ( parsedArgs.count("help") || parsedArgs.count("h")) { std::cout << parser.helpText(); return EXIT_SUCCESS; } std::string inputFolder = us::any_cast(parsedArgs["input"]); std::string outputFolder = us::any_cast(parsedArgs["output"]); std::string outFileName = us::any_cast(parsedArgs["filename"]); //check if DICOMTags have been set as property for mitk::Image mitk::DicomSeriesReader::FileNamesGrouping seriesInFiles = mitk::DicomSeriesReader::GetSeries( inputFolder, true ); std::list images; std::map fileMap; // TODO sort series UIDs, implementation of map iterator might differ on different platforms (or verify this is a standard topic??) for (mitk::DicomSeriesReader::FileNamesGrouping::const_iterator seriesIter = seriesInFiles.begin(); seriesIter != seriesInFiles.end(); ++seriesIter) { mitk::DicomSeriesReader::StringContainer files = seriesIter->second.GetFilenames(); mitk::DataNode::Pointer node = mitk::DicomSeriesReader::LoadDicomSeries( files ); if (node.IsNotNull()) { mitk::Image::Pointer image = dynamic_cast( node->GetData() ); images.push_back( image ); fileMap.insert( std::pair(image,files)); } } // WARN: EXPECT ONLY ONE ITEM PER FOLDER for ( std::list::const_iterator imageIter = images.begin(); imageIter != images.end(); ++imageIter ) { const mitk::Image::Pointer image = *imageIter; mitk::IOUtil::SaveImage(image,outputFolder + outFileName); } return EXIT_SUCCESS; } RegisterDiffusionMiniApp(DicomFolderDump); diff --git a/Modules/DiffusionImaging/MiniApps/DiffusionIndices.cpp b/Modules/DiffusionImaging/MiniApps/DiffusionIndices.cpp index 4eaf1233e1..e4b634d5a5 100644 --- a/Modules/DiffusionImaging/MiniApps/DiffusionIndices.cpp +++ b/Modules/DiffusionImaging/MiniApps/DiffusionIndices.cpp @@ -1,152 +1,152 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "MiniAppManager.h" #include #include #include #include #include #include #include #include #include "ctkCommandLineParser.h" #include #include #include /** * Calculate indices derived from Qball or tensor images */ int DiffusionIndices(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setTitle("Diffusion Indices"); parser.setCategory("Diffusion Related Measures"); parser.setDescription(""); parser.setContributor("MBI"); parser.setArgumentPrefix("--", "-"); - parser.addArgument("input", "i", ctkCommandLineParser::File, "Input:", "input image (tensor, Q-ball or FSL/MRTrix SH-coefficient image)", us::Any(), false); + parser.addArgument("input", "i", ctkCommandLineParser::InputFile, "Input:", "input image (tensor, Q-ball or FSL/MRTrix SH-coefficient image)", us::Any(), false); parser.addArgument("index", "idx", ctkCommandLineParser::String, "Index:", "index (fa, gfa, ra, ad, rd, ca, l2, l3, md)", us::Any(), false); - parser.addArgument("outFile", "o", ctkCommandLineParser::File, "Output:", "output file", us::Any(), false); + parser.addArgument("outFile", "o", ctkCommandLineParser::OutputFile, "Output:", "output file", us::Any(), false); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; string inFileName = us::any_cast(parsedArgs["input"]); string index = us::any_cast(parsedArgs["index"]); string outFileName = us::any_cast(parsedArgs["outFile"]); string ext = itksys::SystemTools::GetFilenameLastExtension(outFileName); if (ext.empty()) outFileName += ".nrrd"; try { // load input image const std::string s1="", s2=""; std::vector infile = mitk::BaseDataIO::LoadBaseDataFromFile( inFileName, s1, s2, false ); if( boost::algorithm::ends_with(inFileName, ".qbi") && index=="gfa" ) { typedef itk::Vector OdfVectorType; typedef itk::Image ItkQballImageType; mitk::QBallImage::Pointer mitkQballImage = dynamic_cast(infile.at(0).GetPointer()); ItkQballImageType::Pointer itk_qbi = ItkQballImageType::New(); mitk::CastToItkImage(mitkQballImage, itk_qbi); typedef itk::DiffusionQballGeneralizedFaImageFilter GfaFilterType; GfaFilterType::Pointer gfaFilter = GfaFilterType::New(); gfaFilter->SetInput(itk_qbi); gfaFilter->SetComputationMethod(GfaFilterType::GFA_STANDARD); gfaFilter->Update(); MITK_INFO << "Writing " << outFileName; itk::ImageFileWriter< itk::Image >::Pointer fileWriter = itk::ImageFileWriter< itk::Image >::New(); fileWriter->SetInput(gfaFilter->GetOutput()); fileWriter->SetFileName(outFileName); fileWriter->Update(); } else if( boost::algorithm::ends_with(inFileName, ".dti") ) { typedef itk::Image< itk::DiffusionTensor3D, 3 > ItkTensorImage; mitk::TensorImage::Pointer mitkTensorImage = dynamic_cast(infile.at(0).GetPointer()); ItkTensorImage::Pointer itk_dti = ItkTensorImage::New(); mitk::CastToItkImage(mitkTensorImage, itk_dti); typedef itk::TensorDerivedMeasurementsFilter MeasurementsType; MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New(); measurementsCalculator->SetInput(itk_dti.GetPointer() ); if(index=="fa") measurementsCalculator->SetMeasure(MeasurementsType::FA); else if(index=="ra") measurementsCalculator->SetMeasure(MeasurementsType::RA); else if(index=="ad") measurementsCalculator->SetMeasure(MeasurementsType::AD); else if(index=="rd") measurementsCalculator->SetMeasure(MeasurementsType::RD); else if(index=="ca") measurementsCalculator->SetMeasure(MeasurementsType::CA); else if(index=="l2") measurementsCalculator->SetMeasure(MeasurementsType::L2); else if(index=="l3") measurementsCalculator->SetMeasure(MeasurementsType::L3); else if(index=="md") measurementsCalculator->SetMeasure(MeasurementsType::MD); else { MITK_WARN << "No valid diffusion index for input image (tensor image) defined"; return EXIT_FAILURE; } measurementsCalculator->Update(); MITK_INFO << "Writing " << outFileName; itk::ImageFileWriter< itk::Image >::Pointer fileWriter = itk::ImageFileWriter< itk::Image >::New(); fileWriter->SetInput(measurementsCalculator->GetOutput()); fileWriter->SetFileName(outFileName); fileWriter->Update(); } else MITK_INFO << "Diffusion index " << index << " not supported for supplied file type."; } 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; } RegisterDiffusionMiniApp(DiffusionIndices); diff --git a/Modules/DiffusionImaging/MiniApps/DwiDenoising.cpp b/Modules/DiffusionImaging/MiniApps/DwiDenoising.cpp index 76dfc7c19a..5574d3ef2a 100644 --- a/Modules/DiffusionImaging/MiniApps/DwiDenoising.cpp +++ b/Modules/DiffusionImaging/MiniApps/DwiDenoising.cpp @@ -1,169 +1,168 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "MiniAppManager.h" #include #include #include "ctkCommandLineParser.h" #include #include #include #include #include typedef mitk::DiffusionImage DiffusionImageType; typedef itk::Image ImageType; mitk::BaseData::Pointer LoadFile(std::string filename) { if( filename.empty() ) return NULL; const std::string s1="", s2=""; std::vector infile = mitk::BaseDataIO::LoadBaseDataFromFile( filename, s1, s2, false ); if( infile.empty() ) { MITK_INFO << "File " << filename << " could not be read!"; return NULL; } mitk::BaseData::Pointer baseData = infile.at(0); return baseData; } /** * Denoises DWI using the Nonlocal - Means algorithm */ int DwiDenoising(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setTitle("DWI Denoising"); parser.setCategory("Preprocessing Tools"); parser.setContributor("MBI"); parser.setDescription("Denoising for diffusion weighted images using a non-local means algorithm."); parser.setArgumentPrefix("--", "-"); - parser.addArgument("input", "i", ctkCommandLineParser::File, "Input:", "input image (DWI)", us::Any(), false); + parser.addArgument("input", "i", ctkCommandLineParser::InputFile, "Input:", "input image (DWI)", us::Any(), false); parser.addArgument("variance", "v", ctkCommandLineParser::Float, "Variance:", "noise variance", us::Any(), false); - parser.addArgument("mask", "m", ctkCommandLineParser::File, "Mask:", "brainmask for input image", us::Any(), true); + + parser.addArgument("mask", "m", ctkCommandLineParser::InputFile, "Mask:", "brainmask for input image", us::Any(), true); parser.addArgument("search", "s", ctkCommandLineParser::Int, "Search radius:", "search radius", us::Any(), true); parser.addArgument("compare", "c", ctkCommandLineParser::Int, "Comparison radius:", "comparison radius", us::Any(), true); parser.addArgument("joint", "j", ctkCommandLineParser::Bool, "Joint information:", "use joint information"); parser.addArgument("rician", "r", ctkCommandLineParser::Bool, "Rician adaption:", "use rician adaption"); + parser.changeParameterGroup("Output", "Output of this miniapp"); + parser.addArgument("output", "o", ctkCommandLineParser::OutputFile, "Output:", "output image (DWI)", us::Any(), false); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; string inFileName = us::any_cast(parsedArgs["input"]); double variance = static_cast(us::any_cast(parsedArgs["variance"])); string maskName; if (parsedArgs.count("mask")) maskName = us::any_cast(parsedArgs["mask"]); - string outFileName = inFileName; - boost::algorithm::erase_all(outFileName, ".dwi"); + string outFileName = us::any_cast(parsedArgs["output"]); +// boost::algorithm::erase_all(outFileName, ".dwi"); int search = 4; if (parsedArgs.count("search")) search = us::any_cast(parsedArgs["search"]); int compare = 1; if (parsedArgs.count("compare")) compare = us::any_cast(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(LoadFile(inFileName).GetPointer()); itk::NonLocalMeansDenoisingFilter::Pointer filter = itk::NonLocalMeansDenoisingFilter::New(); filter->SetNumberOfThreads(12); filter->SetInputImage(dwi->GetVectorImage()); if (!maskName.empty()) { mitk::Image::Pointer mask = dynamic_cast(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"; +// std::stringstream name; +// name << outFileName << "_NLM_" << search << "-" << compare << "-" << variance << ".dwi"; - MITK_INFO << "Writing: " << name.str(); + MITK_INFO << "Writing: " << outFileName; mitk::NrrdDiffusionImageWriter::Pointer writer = mitk::NrrdDiffusionImageWriter::New(); writer->SetInput(output); - writer->SetFileName(name.str()); + writer->SetFileName(outFileName/*.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; } RegisterDiffusionMiniApp(DwiDenoising); diff --git a/Modules/DiffusionImaging/MiniApps/ExportShImage.cpp b/Modules/DiffusionImaging/MiniApps/ExportShImage.cpp index 0f1faa94aa..e81690ffb5 100755 --- a/Modules/DiffusionImaging/MiniApps/ExportShImage.cpp +++ b/Modules/DiffusionImaging/MiniApps/ExportShImage.cpp @@ -1,140 +1,140 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "MiniAppManager.h" #include #include #include #include #include #include "ctkCommandLineParser.h" #include #include #include #include #include #include #include #define _USE_MATH_DEFINES #include template int StartShConversion(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setTitle("Export SH Image"); parser.setCategory("Preprocessing Tools"); parser.setDescription(""); parser.setContributor("MBI"); parser.setArgumentPrefix("--", "-"); - parser.addArgument("input", "i", ctkCommandLineParser::File, "Input:", "MITK SH image", us::Any(), false); - parser.addArgument("output", "o", ctkCommandLineParser::File, "Output", "MRtrix SH image", us::Any(), false); + parser.addArgument("input", "i", ctkCommandLineParser::InputFile, "Input:", "MITK SH image", us::Any(), false); + parser.addArgument("output", "o", ctkCommandLineParser::InputFile, "Output", "MRtrix SH image", us::Any(), false); parser.addArgument("shOrder", "sh", ctkCommandLineParser::Int, "SH order:", "spherical harmonics order"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; string inFile = us::any_cast(parsedArgs["input"]); string outFile = us::any_cast(parsedArgs["output"]); try { typedef itk::Image< float, 4 > OutImageType; typedef itk::Image< itk::Vector< float, (shOrder*shOrder + shOrder + 2)/2 + shOrder >, 3 > InputImageType; typename InputImageType::Pointer itkInImage = InputImageType::New(); typedef itk::ImageFileReader< InputImageType > ReaderType; typename ReaderType::Pointer reader = ReaderType::New(); MITK_INFO << "reading " << inFile; reader->SetFileName(inFile.c_str()); reader->Update(); itkInImage = reader->GetOutput(); // extract directions from fiber bundle typename itk::ShCoefficientImageExporter::Pointer filter = itk::ShCoefficientImageExporter::New(); filter->SetInputImage(itkInImage); filter->GenerateData(); OutImageType::Pointer outImage = filter->GetOutputImage(); typedef itk::ImageFileWriter< OutImageType > WriterType; WriterType::Pointer writer = WriterType::New(); MITK_INFO << "writing " << outFile; writer->SetFileName(outFile.c_str()); writer->SetInput(outImage); writer->Update(); MITK_INFO << "DONE"; } 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; } int ExportShImage(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setArgumentPrefix("--", "-"); - parser.addArgument("input", "i", ctkCommandLineParser::File, "Input image", "MITK SH image", us::Any(), false); - parser.addArgument("output", "o", ctkCommandLineParser::File, "Output image", "MRtrix SH image", us::Any(), false); + parser.addArgument("input", "i", ctkCommandLineParser::InputFile, "Input image", "MITK SH image", us::Any(), false); + parser.addArgument("output", "o", ctkCommandLineParser::OutputFile, "Output image", "MRtrix SH image", us::Any(), false); parser.addArgument("shOrder", "sh", ctkCommandLineParser::Int, "Spherical harmonics order", "spherical harmonics order"); parser.setCategory("Preprocessing Tools"); parser.setTitle("Export SH Image"); parser.setDescription(""); parser.setContributor("MBI"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; int shOrder = -1; if (parsedArgs.count("shOrder")) shOrder = us::any_cast(parsedArgs["shOrder"]); switch (shOrder) { case 4: return StartShConversion<4>(argc, argv); case 6: return StartShConversion<6>(argc, argv); case 8: return StartShConversion<8>(argc, argv); case 10: return StartShConversion<10>(argc, argv); case 12: return StartShConversion<12>(argc, argv); } return EXIT_FAILURE; } RegisterDiffusionMiniApp(ExportShImage); diff --git a/Modules/DiffusionImaging/MiniApps/ExtractImageStatistics.cpp b/Modules/DiffusionImaging/MiniApps/ExtractImageStatistics.cpp index 24015cb965..62ba8be51a 100644 --- a/Modules/DiffusionImaging/MiniApps/ExtractImageStatistics.cpp +++ b/Modules/DiffusionImaging/MiniApps/ExtractImageStatistics.cpp @@ -1,127 +1,127 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "MiniAppManager.h" #include "ctkCommandLineParser.h" #include "mitkImage.h" #include "mitkImageStatisticsCalculator.h" #include "mitkIOUtil.h" #include #include #include int ExtractImageStatistics(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setTitle("Extract Image Statistics"); parser.setCategory("Preprocessing Tools"); parser.setDescription(""); parser.setContributor("MBI"); parser.setArgumentPrefix("--", "-"); parser.addArgument("help", "h", ctkCommandLineParser::String, "Help:", "Show this help text"); - parser.addArgument("input", "i", ctkCommandLineParser::File, "Input:", "input image", us::Any(),false); - parser.addArgument("mask", "m", ctkCommandLineParser::File, "Mask:", "mask image / roi image denotin area on which statistics are calculated", us::Any(),false); - parser.addArgument("out", "o", ctkCommandLineParser::File, "Output", "output file (default: filenameOfRoi.nrrd_statistics.txt)", us::Any()); + parser.addArgument("input", "i", ctkCommandLineParser::InputFile, "Input:", "input image", us::Any(),false); + parser.addArgument("mask", "m", ctkCommandLineParser::InputFile, "Mask:", "mask image / roi image denotin area on which statistics are calculated", us::Any(),false); + parser.addArgument("out", "o", ctkCommandLineParser::OutputFile, "Output", "output file (default: filenameOfRoi.nrrd_statistics.txt)", us::Any()); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0 || parsedArgs.count("help") || parsedArgs.count("h")) { std::cout << "\n\n MiniApp Description: \nCalculates statistics on the supplied image using given mask." << endl; std::cout << "Output is written to the designated output file in this order:" << endl; std::cout << "Mean, Standard Deviation, RMS, Max, Min, Number of Voxels, Volume [mm3]" << endl; std::cout << "\n\n Parameters:"<< endl; std::cout << parser.helpText(); return EXIT_SUCCESS; } // Parameters: bool ignoreZeroValues = false; unsigned int timeStep = 0; std::string inputImageFile = us::any_cast(parsedArgs["input"]); std::string maskImageFile = us::any_cast(parsedArgs["mask"]); std::string outFile; if (parsedArgs.count("out") || parsedArgs.count("o") ) outFile = us::any_cast(parsedArgs["out"]); else outFile = inputImageFile + "_statistics.txt"; // Load image and mask mitk::Image::Pointer maskImage = mitk::IOUtil::LoadImage(maskImageFile); mitk::Image::Pointer inputImage = mitk::IOUtil::LoadImage(inputImageFile); // Calculate statistics mitk::ImageStatisticsCalculator::Statistics statisticsStruct; mitk::ImageStatisticsCalculator::Pointer calculator = mitk::ImageStatisticsCalculator::New(); try { calculator->SetImage(inputImage); calculator->SetImageMask(maskImage); calculator->SetMaskingModeToImage(); } catch( const itk::ExceptionObject& e) { MITK_ERROR << "Statistic Calculation Failed - ITK Exception:" << e.what(); return -1; } calculator->SetDoIgnorePixelValue(ignoreZeroValues); calculator->SetIgnorePixelValue(0); try { calculator->ComputeStatistics(timeStep); } catch ( mitk::Exception& e) { MITK_ERROR<< "MITK Exception: " << e.what(); return -1; } statisticsStruct = calculator->GetStatistics(timeStep); // Calculate Volume double volume = 0; const mitk::BaseGeometry *geometry = inputImage->GetGeometry(); if ( geometry != NULL ) { const mitk::Vector3D &spacing = inputImage->GetGeometry()->GetSpacing(); volume = spacing[0] * spacing[1] * spacing[2] * (double) statisticsStruct.N; } // Write Results to file std::ofstream output; output.open(outFile.c_str()); output << statisticsStruct.Mean << " , "; output << statisticsStruct.Sigma << " , "; output << statisticsStruct.RMS << " , "; output << statisticsStruct.Max << " , "; output << statisticsStruct.Min << " , "; output << statisticsStruct.N << " , "; output << volume << "\n"; output.flush(); output.close(); return 0; } RegisterDiffusionMiniApp(ExtractImageStatistics); diff --git a/Modules/DiffusionImaging/MiniApps/FiberDirectionExtraction.cpp b/Modules/DiffusionImaging/MiniApps/FiberDirectionExtraction.cpp index 0b868f4a8b..29a4cc8444 100755 --- a/Modules/DiffusionImaging/MiniApps/FiberDirectionExtraction.cpp +++ b/Modules/DiffusionImaging/MiniApps/FiberDirectionExtraction.cpp @@ -1,169 +1,169 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "MiniAppManager.h" #include #include #include #include #include #include "ctkCommandLineParser.h" #include #include #include #include #include #include #include #define _USE_MATH_DEFINES #include int FiberDirectionExtraction(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setTitle("Fiber Direction Extraction"); parser.setCategory("Fiber Tracking and Processing Methods"); parser.setDescription(""); parser.setContributor("MBI"); parser.setArgumentPrefix("--", "-"); - parser.addArgument("input", "i", ctkCommandLineParser::File, "Input:", "input tractogram (.fib, vtk ascii file format)", us::Any(), false); - parser.addArgument("out", "o", ctkCommandLineParser::Directory, "Output:", "output root", us::Any(), false); - parser.addArgument("mask", "m", ctkCommandLineParser::File, "Mask:", "mask image"); + parser.addArgument("input", "i", ctkCommandLineParser::InputFile, "Input:", "input tractogram (.fib, vtk ascii file format)", us::Any(), false); + parser.addArgument("out", "o", ctkCommandLineParser::OutputDirectory, "Output:", "output root", us::Any(), false); + parser.addArgument("mask", "m", ctkCommandLineParser::InputFile, "Mask:", "mask image"); parser.addArgument("athresh", "a", ctkCommandLineParser::Float, "Angular threshold:", "angular threshold in degrees. closer fiber directions are regarded as one direction and clustered together.", 25, true); parser.addArgument("verbose", "v", ctkCommandLineParser::Bool, "Verbose:", "output optional and intermediate calculation results"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; string fibFile = us::any_cast(parsedArgs["input"]); string maskImage(""); if (parsedArgs.count("mask")) maskImage = us::any_cast(parsedArgs["mask"]); float angularThreshold = 25; if (parsedArgs.count("athresh")) angularThreshold = us::any_cast(parsedArgs["athresh"]); string outRoot = us::any_cast(parsedArgs["out"]); bool verbose = false; if (parsedArgs.count("verbose")) verbose = us::any_cast(parsedArgs["verbose"]); try { typedef itk::Image ItkUcharImgType; typedef itk::Image< itk::Vector< float, 3>, 3 > ItkDirectionImage3DType; typedef itk::VectorContainer< unsigned int, ItkDirectionImage3DType::Pointer > ItkDirectionImageContainerType; // load fiber bundle mitk::FiberBundleX::Pointer inputTractogram = dynamic_cast(mitk::IOUtil::LoadDataNode(fibFile)->GetData()); // load/create mask image ItkUcharImgType::Pointer itkMaskImage = NULL; if (maskImage.compare("")!=0) { MITK_INFO << "Using mask image"; itkMaskImage = ItkUcharImgType::New(); mitk::Image::Pointer mitkMaskImage = dynamic_cast(mitk::IOUtil::LoadDataNode(maskImage)->GetData()); mitk::CastToItkImage(mitkMaskImage, itkMaskImage); } // extract directions from fiber bundle itk::TractsToVectorImageFilter::Pointer fOdfFilter = itk::TractsToVectorImageFilter::New(); fOdfFilter->SetFiberBundle(inputTractogram); fOdfFilter->SetMaskImage(itkMaskImage); fOdfFilter->SetAngularThreshold(cos(angularThreshold*M_PI/180)); fOdfFilter->SetNormalizeVectors(false); fOdfFilter->SetUseWorkingCopy(false); fOdfFilter->Update(); ItkDirectionImageContainerType::Pointer directionImageContainer = fOdfFilter->GetDirectionImageContainer(); // write direction images for (unsigned int i=0; iSize(); i++) { itk::TractsToVectorImageFilter::ItkDirectionImageType::Pointer itkImg = directionImageContainer->GetElement(i); typedef itk::ImageFileWriter< itk::TractsToVectorImageFilter::ItkDirectionImageType > WriterType; WriterType::Pointer writer = WriterType::New(); string outfilename = outRoot; outfilename.append("_DIRECTION_"); outfilename.append(boost::lexical_cast(i)); outfilename.append(".nrrd"); MITK_INFO << "writing " << outfilename; writer->SetFileName(outfilename.c_str()); writer->SetInput(itkImg); writer->Update(); } if (verbose) { // write vector field mitk::FiberBundleX::Pointer directions = fOdfFilter->GetOutputFiberBundle(); mitk::CoreObjectFactory::FileWriterList fileWriters = mitk::CoreObjectFactory::GetInstance()->GetFileWriters(); for (mitk::CoreObjectFactory::FileWriterList::iterator it = fileWriters.begin() ; it != fileWriters.end() ; ++it) { if ( (*it)->CanWriteBaseDataType(directions.GetPointer()) ) { string outfilename = outRoot; outfilename.append("_VECTOR_FIELD.fib"); (*it)->SetFileName( outfilename.c_str() ); (*it)->DoWrite( directions.GetPointer() ); } } // write num direction image { ItkUcharImgType::Pointer numDirImage = fOdfFilter->GetNumDirectionsImage(); typedef itk::ImageFileWriter< ItkUcharImgType > WriterType; WriterType::Pointer writer = WriterType::New(); string outfilename = outRoot; outfilename.append("_NUM_DIRECTIONS.nrrd"); MITK_INFO << "writing " << outfilename; writer->SetFileName(outfilename.c_str()); writer->SetInput(numDirImage); writer->Update(); } } MITK_INFO << "DONE"; } 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; } RegisterDiffusionMiniApp(FiberDirectionExtraction); diff --git a/Modules/DiffusionImaging/MiniApps/FiberProcessing.cpp b/Modules/DiffusionImaging/MiniApps/FiberProcessing.cpp index 987bdbd2b6..9b6a7db5e7 100644 --- a/Modules/DiffusionImaging/MiniApps/FiberProcessing.cpp +++ b/Modules/DiffusionImaging/MiniApps/FiberProcessing.cpp @@ -1,240 +1,240 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "MiniAppManager.h" #include #include #include #include #include #include #include #include #include #include #include #include "ctkCommandLineParser.h" #include #include mitk::FiberBundleX::Pointer LoadFib(std::string filename) { const std::string s1="", s2=""; std::vector fibInfile = mitk::BaseDataIO::LoadBaseDataFromFile( filename, s1, s2, false ); if( fibInfile.empty() ) MITK_INFO << "File " << filename << " could not be read!"; mitk::BaseData::Pointer baseData = fibInfile.at(0); return dynamic_cast(baseData.GetPointer()); } int FiberProcessing(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setTitle("Fiber Processing"); parser.setCategory("Fiber Tracking and Processing Methods"); parser.setDescription(""); parser.setContributor("MBI"); parser.setArgumentPrefix("--", "-"); - parser.addArgument("input", "i", ctkCommandLineParser::File, "Input:", "input fiber bundle (.fib)", us::Any(), false); - parser.addArgument("outFile", "o", ctkCommandLineParser::File, "Output:", "output fiber bundle (.fib)", us::Any(), false); + parser.addArgument("input", "i", ctkCommandLineParser::InputFile, "Input:", "input fiber bundle (.fib)", us::Any(), false); + parser.addArgument("outFile", "o", ctkCommandLineParser::OutputFile, "Output:", "output fiber bundle (.fib)", us::Any(), false); parser.addArgument("resample", "r", ctkCommandLineParser::Float, "Resample:", "Resample fiber with the given point distance (in mm)"); parser.addArgument("smooth", "s", ctkCommandLineParser::Float, "Smooth:", "Smooth fiber with the given point distance (in mm)"); parser.addArgument("minLength", "l", ctkCommandLineParser::Float, "Minimum length:", "Minimum fiber length (in mm)"); parser.addArgument("maxLength", "m", ctkCommandLineParser::Float, "Maximum length:", "Maximum fiber length (in mm)"); parser.addArgument("minCurv", "a", ctkCommandLineParser::Float, "Minimum curvature radius:", "Minimum curvature radius (in mm)"); parser.addArgument("mirror", "p", ctkCommandLineParser::Int, "Invert coordinates:", "Invert fiber coordinates XYZ (e.g. 010 to invert y-coordinate of each fiber point)"); parser.addArgument("copyAndJoin", "c", ctkCommandLineParser::Bool, "Copy & Join:", "Create a copy of the input fiber bundle (applied after resample/smooth/minLength/maxLength/minCurv/mirror) and join copy with original (applied after rotate/scale/translate)"); //parser.addArgument("join", "j", ctkCommandLineParser::Bool, "Join the original and copied fiber bundle (applied after rotate/scale/translate)"); parser.addArgument("rotate-x", "rx", ctkCommandLineParser::Float, "Rotate x-axis:", "Rotate around x-axis (if copy is given the copy is rotated, in deg)"); parser.addArgument("rotate-y", "ry", ctkCommandLineParser::Float, "Rotate y-axis:", "Rotate around y-axis (if copy is given the copy is rotated, in deg)"); parser.addArgument("rotate-z", "rz", ctkCommandLineParser::Float, "Rotate z-axis:", "Rotate around z-axis (if copy is given the copy is rotated, in deg)"); parser.addArgument("scale-x", "sx", ctkCommandLineParser::Float, "Scale x-axis:", "Scale in direction of x-axis (if copy is given the copy is scaled)"); parser.addArgument("scale-y", "sy", ctkCommandLineParser::Float, "Scale y-axis:", "Scale in direction of y-axis (if copy is given the copy is scaled)"); parser.addArgument("scale-z", "sz", ctkCommandLineParser::Float, "Scale z-axis", "Scale in direction of z-axis (if copy is given the copy is scaled)"); parser.addArgument("translate-x", "tx", ctkCommandLineParser::Float, "Translate x-axis:", "Translate in direction of x-axis (if copy is given the copy is translated, in mm)"); parser.addArgument("translate-y", "ty", ctkCommandLineParser::Float, "Translate y-axis:", "Translate in direction of y-axis (if copy is given the copy is translated, in mm)"); parser.addArgument("translate-z", "tz", ctkCommandLineParser::Float, "Translate z-axis:", "Translate in direction of z-axis (if copy is given the copy is translated, in mm)"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; float pointDist = -1; if (parsedArgs.count("resample")) pointDist = us::any_cast(parsedArgs["resample"]); float smoothDist = -1; if (parsedArgs.count("smooth")) smoothDist = us::any_cast(parsedArgs["smooth"]); float minFiberLength = -1; if (parsedArgs.count("minLength")) minFiberLength = us::any_cast(parsedArgs["minLength"]); float maxFiberLength = -1; if (parsedArgs.count("maxLength")) maxFiberLength = us::any_cast(parsedArgs["maxLength"]); float curvThres = -1; if (parsedArgs.count("minCurv")) curvThres = us::any_cast(parsedArgs["minCurv"]); int axis = 0; if (parsedArgs.count("mirror")) axis = us::any_cast(parsedArgs["mirror"]); bool copyAndJoin = false; if(parsedArgs.count("copyAndJoin")) copyAndJoin = us::any_cast(parsedArgs["copyAndJoin"]); float rotateX = 0; if (parsedArgs.count("rotate-x")) rotateX = us::any_cast(parsedArgs["rotate-x"]); float rotateY = 0; if (parsedArgs.count("rotate-y")) rotateY = us::any_cast(parsedArgs["rotate-y"]); float rotateZ = 0; if (parsedArgs.count("rotate-z")) rotateZ = us::any_cast(parsedArgs["rotate-z"]); float scaleX = 0; if (parsedArgs.count("scale-x")) scaleX = us::any_cast(parsedArgs["scale-x"]); float scaleY = 0; if (parsedArgs.count("scale-y")) scaleY = us::any_cast(parsedArgs["scale-y"]); float scaleZ = 0; if (parsedArgs.count("scale-z")) scaleZ = us::any_cast(parsedArgs["scale-z"]); float translateX = 0; if (parsedArgs.count("translate-x")) translateX = us::any_cast(parsedArgs["translate-x"]); float translateY = 0; if (parsedArgs.count("translate-y")) translateY = us::any_cast(parsedArgs["translate-y"]); float translateZ = 0; if (parsedArgs.count("translate-z")) translateZ = us::any_cast(parsedArgs["translate-z"]); string inFileName = us::any_cast(parsedArgs["input"]); string outFileName = us::any_cast(parsedArgs["outFile"]); try { mitk::FiberBundleX::Pointer fib = LoadFib(inFileName); if (minFiberLength>0) fib->RemoveShortFibers(minFiberLength); if (maxFiberLength>0) fib->RemoveLongFibers(maxFiberLength); if (curvThres>0) fib->ApplyCurvatureThreshold(curvThres, false); if (pointDist>0) fib->ResampleFibers(pointDist); if (smoothDist>0) fib->DoFiberSmoothing(smoothDist); if (axis/100==1) fib->MirrorFibers(0); if ((axis%100)/10==1) fib->MirrorFibers(1); if (axis%10==1) fib->MirrorFibers(2); if (copyAndJoin == true) { MITK_INFO << "Create copy"; mitk::FiberBundleX::Pointer fibCopy = fib->GetDeepCopy(); if (rotateX > 0 || rotateY > 0 || rotateZ > 0){ MITK_INFO << "Rotate " << rotateX << " " << rotateY << " " << rotateZ; fibCopy->RotateAroundAxis(rotateX, rotateY, rotateZ); } if (translateX > 0 || translateY > 0 || translateZ > 0) fibCopy->TranslateFibers(translateX, translateY, translateZ); if (scaleX > 0 || scaleY > 0 || scaleZ > 0) fibCopy->ScaleFibers(scaleX, scaleY, scaleZ); MITK_INFO << "Join copy with original"; fib = fib->AddBundle(fibCopy.GetPointer()); } else { if (rotateX > 0 || rotateY > 0 || rotateZ > 0){ MITK_INFO << "Rotate " << rotateX << " " << rotateY << " " << rotateZ; fib->RotateAroundAxis(rotateX, rotateY, rotateZ); } if (translateX > 0 || translateY > 0 || translateZ > 0){ fib->TranslateFibers(translateX, translateY, translateZ); } if (scaleX > 0 || scaleY > 0 || scaleZ > 0) fib->ScaleFibers(scaleX, scaleY, scaleZ); } 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()) ) { MITK_INFO << "writing " << outFileName; (*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; } return EXIT_SUCCESS; } RegisterDiffusionMiniApp(FiberProcessing); diff --git a/Modules/DiffusionImaging/MiniApps/FileFormatConverter.cpp b/Modules/DiffusionImaging/MiniApps/FileFormatConverter.cpp index 381b160e8c..675b71e0f2 100755 --- a/Modules/DiffusionImaging/MiniApps/FileFormatConverter.cpp +++ b/Modules/DiffusionImaging/MiniApps/FileFormatConverter.cpp @@ -1,100 +1,100 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "MiniAppManager.h" #include #include #include #include #include #include #include #include "ctkCommandLineParser.h" #include "ctkCommandLineParser.cpp" using namespace mitk; int FileFormatConverter(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setTitle("Format Converter"); parser.setCategory("Fiber Tracking and Processing Methods"); parser.setDescription(""); parser.setContributor("MBI"); parser.setArgumentPrefix("--", "-"); - parser.addArgument("in", "i", ctkCommandLineParser::File, "Input:", "input file", us::Any(), false); - parser.addArgument("out", "o", ctkCommandLineParser::File, "Output:", "output file", us::Any(), false); + parser.addArgument("in", "i", ctkCommandLineParser::InputFile, "Input:", "input file", us::Any(), false); + parser.addArgument("out", "o", ctkCommandLineParser::OutputFile, "Output:", "output file", us::Any(), false); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; // mandatory arguments string inName = us::any_cast(parsedArgs["in"]); string outName = us::any_cast(parsedArgs["out"]); try { MITK_INFO << "Loading " << inName; const std::string s1="", s2=""; std::vector infile = BaseDataIO::LoadBaseDataFromFile( inName, s1, s2, false ); mitk::BaseData::Pointer baseData = infile.at(0); if ( dynamic_cast*>(baseData.GetPointer()) ) { MITK_INFO << "Writing " << outName; DiffusionImage::Pointer dwi = dynamic_cast*>(baseData.GetPointer()); NrrdDiffusionImageWriter::Pointer writer = NrrdDiffusionImageWriter::New(); writer->SetFileName(outName); writer->SetInput(dwi); writer->Update(); } else if ( dynamic_cast(baseData.GetPointer()) ) { Image::Pointer image = dynamic_cast(baseData.GetPointer()); mitk::IOUtil::SaveImage(image, outName); } else if ( dynamic_cast(baseData.GetPointer()) ) { MITK_INFO << "Writing " << outName; FiberBundleXWriter::Pointer fibWriter = FiberBundleXWriter::New(); fibWriter->SetFileName(outName.c_str()); fibWriter->DoWrite( dynamic_cast(baseData.GetPointer()) ); } else MITK_INFO << "File type currently not supported!"; } 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; } RegisterDiffusionMiniApp(FileFormatConverter); diff --git a/Modules/DiffusionImaging/MiniApps/GibbsTracking.cpp b/Modules/DiffusionImaging/MiniApps/GibbsTracking.cpp index ff95feaba6..507c64a57b 100755 --- a/Modules/DiffusionImaging/MiniApps/GibbsTracking.cpp +++ b/Modules/DiffusionImaging/MiniApps/GibbsTracking.cpp @@ -1,251 +1,251 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "MiniAppManager.h" #include #include #include #include #include #include #include #include #include #include #include "ctkCommandLineParser.h" #include #include #include template typename itk::ShCoefficientImageImporter< float, shOrder >::QballImageType::Pointer TemplatedConvertShCoeffs(mitk::Image* mitkImg, int toolkit, bool noFlip = false) { typedef itk::ShCoefficientImageImporter< float, shOrder > FilterType; typedef mitk::ImageToItk< itk::Image< float, 4 > > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(mitkImg); caster->Update(); itk::Image< float, 4 >::Pointer itkImage = caster->GetOutput(); typename FilterType::Pointer filter = FilterType::New(); if (noFlip) { filter->SetInputImage(itkImage); } else { MITK_INFO << "Flipping image"; itk::FixedArray flipAxes; flipAxes[0] = true; flipAxes[1] = true; flipAxes[2] = false; flipAxes[3] = false; itk::FlipImageFilter< itk::Image< float, 4 > >::Pointer flipper = itk::FlipImageFilter< itk::Image< float, 4 > >::New(); flipper->SetInput(itkImage); flipper->SetFlipAxes(flipAxes); flipper->Update(); itk::Image< float, 4 >::Pointer flipped = flipper->GetOutput(); itk::Matrix< double,4,4 > m = itkImage->GetDirection(); m[0][0] *= -1; m[1][1] *= -1; flipped->SetDirection(m); itk::Point< float, 4 > o = itkImage->GetOrigin(); o[0] -= (flipped->GetLargestPossibleRegion().GetSize(0)-1); o[1] -= (flipped->GetLargestPossibleRegion().GetSize(1)-1); flipped->SetOrigin(o); filter->SetInputImage(flipped); } switch (toolkit) { case 0: filter->SetToolkit(FilterType::FSL); break; case 1: filter->SetToolkit(FilterType::MRTRIX); break; default: filter->SetToolkit(FilterType::FSL); } filter->GenerateData(); return filter->GetQballImage(); } int GibbsTracking(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setTitle("Gibbs Tracking"); parser.setCategory("Fiber Tracking and Processing Methods"); parser.setDescription(""); parser.setContributor("MBI"); parser.setArgumentPrefix("--", "-"); - parser.addArgument("input", "i", ctkCommandLineParser::File, "Input:", "input image (tensor, Q-ball or FSL/MRTrix SH-coefficient image)", us::Any(), false); - parser.addArgument("parameters", "p", ctkCommandLineParser::File, "Parameters:", "parameter file (.gtp)", us::Any(), false); - parser.addArgument("mask", "m", ctkCommandLineParser::File, "Mask:", "binary mask image"); + parser.addArgument("input", "i", ctkCommandLineParser::InputFile, "Input:", "input image (tensor, Q-ball or FSL/MRTrix SH-coefficient image)", us::Any(), false); + parser.addArgument("parameters", "p", ctkCommandLineParser::InputFile, "Parameters:", "parameter file (.gtp)", us::Any(), false); + parser.addArgument("mask", "m", ctkCommandLineParser::InputFile, "Mask:", "binary mask image"); parser.addArgument("shConvention", "s", ctkCommandLineParser::String, "SH coefficient:", "sh coefficient convention (FSL, MRtrix)", string("FSL"), true); - parser.addArgument("outFile", "o", ctkCommandLineParser::File, "Output:", "output fiber bundle (.fib)", us::Any(), false); + parser.addArgument("outFile", "o", ctkCommandLineParser::OutputFile, "Output:", "output fiber bundle (.fib)", us::Any(), false); parser.addArgument("noFlip", "f", ctkCommandLineParser::Bool, "No flip:", "do not flip input image to match MITK coordinate convention"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; string inFileName = us::any_cast(parsedArgs["input"]); string paramFileName = us::any_cast(parsedArgs["parameters"]); string outFileName = us::any_cast(parsedArgs["outFile"]); bool noFlip = false; if (parsedArgs.count("noFlip")) noFlip = us::any_cast(parsedArgs["noFlip"]); try { // instantiate gibbs tracker typedef itk::Vector OdfVectorType; typedef itk::Image ItkQballImageType; typedef itk::GibbsTrackingFilter GibbsTrackingFilterType; GibbsTrackingFilterType::Pointer gibbsTracker = GibbsTrackingFilterType::New(); // load input image const std::string s1="", s2=""; std::vector infile = mitk::BaseDataIO::LoadBaseDataFromFile( inFileName, s1, s2, false ); mitk::Image::Pointer mitkImage = dynamic_cast(infile.at(0).GetPointer()); // try to cast to qball image if( boost::algorithm::ends_with(inFileName, ".qbi") ) { MITK_INFO << "Loading qball image ..."; mitk::QBallImage::Pointer mitkQballImage = dynamic_cast(infile.at(0).GetPointer()); ItkQballImageType::Pointer itk_qbi = ItkQballImageType::New(); mitk::CastToItkImage(mitkQballImage, itk_qbi); gibbsTracker->SetQBallImage(itk_qbi.GetPointer()); } else if( boost::algorithm::ends_with(inFileName, ".dti") ) { MITK_INFO << "Loading tensor image ..."; typedef itk::Image< itk::DiffusionTensor3D, 3 > ItkTensorImage; mitk::TensorImage::Pointer mitkTensorImage = dynamic_cast(infile.at(0).GetPointer()); ItkTensorImage::Pointer itk_dti = ItkTensorImage::New(); mitk::CastToItkImage(mitkTensorImage, itk_dti); gibbsTracker->SetTensorImage(itk_dti); } else if ( boost::algorithm::ends_with(inFileName, ".nii") ) { MITK_INFO << "Loading sh-coefficient image ..."; int nrCoeffs = mitkImage->GetLargestPossibleRegion().GetSize()[3]; int c=3, d=2-2*nrCoeffs; double D = c*c-4*d; int shOrder; if (D>0) { shOrder = (-c+sqrt(D))/2.0; if (shOrder<0) shOrder = (-c-sqrt(D))/2.0; } else if (D==0) shOrder = -c/2.0; MITK_INFO << "using SH-order " << shOrder; int toolkitConvention = 0; if (parsedArgs.count("shConvention")) { string convention = us::any_cast(parsedArgs["shConvention"]).c_str(); if ( boost::algorithm::equals(convention, "MRtrix") ) { toolkitConvention = 1; MITK_INFO << "Using MRtrix style sh-coefficient convention"; } else MITK_INFO << "Using FSL style sh-coefficient convention"; } else MITK_INFO << "Using FSL style sh-coefficient convention"; switch (shOrder) { case 4: gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<4>(mitkImage, toolkitConvention, noFlip)); break; case 6: gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<6>(mitkImage, toolkitConvention, noFlip)); break; case 8: gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<8>(mitkImage, toolkitConvention, noFlip)); break; case 10: gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<10>(mitkImage, toolkitConvention, noFlip)); break; case 12: gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<12>(mitkImage, toolkitConvention, noFlip)); break; default: MITK_INFO << "SH-order " << shOrder << " not supported"; } } else return EXIT_FAILURE; // global tracking if (parsedArgs.count("mask")) { typedef itk::Image MaskImgType; mitk::Image::Pointer mitkMaskImage = mitk::IOUtil::LoadImage(us::any_cast(parsedArgs["mask"])); MaskImgType::Pointer itk_mask = MaskImgType::New(); mitk::CastToItkImage(mitkMaskImage, itk_mask); gibbsTracker->SetMaskImage(itk_mask); } gibbsTracker->SetDuplicateImage(false); gibbsTracker->SetLoadParameterFile( paramFileName ); // gibbsTracker->SetLutPath( "" ); gibbsTracker->Update(); mitk::FiberBundleX::Pointer mitkFiberBundle = mitk::FiberBundleX::New(gibbsTracker->GetFiberBundle()); mitkFiberBundle->SetReferenceImage(mitkImage); mitk::CoreObjectFactory::FileWriterList fileWriters = mitk::CoreObjectFactory::GetInstance()->GetFileWriters(); for (mitk::CoreObjectFactory::FileWriterList::iterator it = fileWriters.begin() ; it != fileWriters.end() ; ++it) { if ( (*it)->CanWriteBaseDataType(mitkFiberBundle.GetPointer()) ) { (*it)->SetFileName( outFileName.c_str() ); (*it)->DoWrite( mitkFiberBundle.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; } return EXIT_SUCCESS; } RegisterDiffusionMiniApp(GibbsTracking); diff --git a/Modules/DiffusionImaging/MiniApps/LocalDirectionalFiberPlausibility.cpp b/Modules/DiffusionImaging/MiniApps/LocalDirectionalFiberPlausibility.cpp index 6f3bfd4bc4..559e154593 100755 --- a/Modules/DiffusionImaging/MiniApps/LocalDirectionalFiberPlausibility.cpp +++ b/Modules/DiffusionImaging/MiniApps/LocalDirectionalFiberPlausibility.cpp @@ -1,304 +1,304 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "MiniAppManager.h" #include #include #include #include #include #include #include "ctkCommandLineParser.h" #include #include #include #include #include #include #include #include #include #define _USE_MATH_DEFINES #include int LocalDirectionalFiberPlausibility(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setTitle("Local Directional Fiber Plausibility"); parser.setCategory("Fiber Tracking and Processing Methods"); parser.setDescription(""); parser.setContributor("MBI"); parser.setArgumentPrefix("--", "-"); - parser.addArgument("input", "i", ctkCommandLineParser::File, "Input:", "input tractogram (.fib, vtk ascii file format)", us::Any(), false); + parser.addArgument("input", "i", ctkCommandLineParser::InputFile, "Input:", "input tractogram (.fib, vtk ascii file format)", us::Any(), false); parser.addArgument("reference", "r", ctkCommandLineParser::StringList, "Reference images:", "reference direction images", us::Any(), false); - parser.addArgument("out", "o", ctkCommandLineParser::Directory, "Output:", "output root", us::Any(), false); + parser.addArgument("out", "o", ctkCommandLineParser::OutputDirectory, "Output:", "output root", us::Any(), false); parser.addArgument("mask", "m", ctkCommandLineParser::StringList, "Masks:", "mask images"); parser.addArgument("athresh", "a", ctkCommandLineParser::Float, "Angular threshold:", "angular threshold in degrees. closer fiber directions are regarded as one direction and clustered together.", 25, true); parser.addArgument("verbose", "v", ctkCommandLineParser::Bool, "Verbose:", "output optional and intermediate calculation results"); parser.addArgument("ignore", "n", ctkCommandLineParser::Bool, "Ignore:", "don't increase error for missing or too many directions"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; ctkCommandLineParser::StringContainerType referenceImages = us::any_cast(parsedArgs["reference"]); ctkCommandLineParser::StringContainerType maskImages; if (parsedArgs.count("mask")) maskImages = us::any_cast(parsedArgs["mask"]); string fibFile = us::any_cast(parsedArgs["input"]); float angularThreshold = 25; if (parsedArgs.count("athresh")) angularThreshold = us::any_cast(parsedArgs["athresh"]); string outRoot = us::any_cast(parsedArgs["out"]); bool verbose = false; if (parsedArgs.count("verbose")) verbose = us::any_cast(parsedArgs["verbose"]); bool ignore = false; if (parsedArgs.count("ignore")) ignore = us::any_cast(parsedArgs["ignore"]); try { typedef itk::Image ItkUcharImgType; typedef itk::Image< itk::Vector< float, 3>, 3 > ItkDirectionImage3DType; typedef itk::VectorContainer< unsigned int, ItkDirectionImage3DType::Pointer > ItkDirectionImageContainerType; typedef itk::EvaluateDirectionImagesFilter< float > EvaluationFilterType; // load fiber bundle mitk::FiberBundleX::Pointer inputTractogram = dynamic_cast(mitk::IOUtil::LoadDataNode(fibFile)->GetData()); // load reference directions ItkDirectionImageContainerType::Pointer referenceImageContainer = ItkDirectionImageContainerType::New(); for (unsigned int i=0; i(mitk::IOUtil::LoadDataNode(referenceImages.at(i))->GetData()); typedef mitk::ImageToItk< ItkDirectionImage3DType > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(img); caster->Update(); ItkDirectionImage3DType::Pointer itkImg = caster->GetOutput(); referenceImageContainer->InsertElement(referenceImageContainer->Size(),itkImg); } catch(...){ MITK_INFO << "could not load: " << referenceImages.at(i); } } ItkUcharImgType::Pointer itkMaskImage = ItkUcharImgType::New(); ItkDirectionImage3DType::Pointer dirImg = referenceImageContainer->GetElement(0); itkMaskImage->SetSpacing( dirImg->GetSpacing() ); itkMaskImage->SetOrigin( dirImg->GetOrigin() ); itkMaskImage->SetDirection( dirImg->GetDirection() ); itkMaskImage->SetLargestPossibleRegion( dirImg->GetLargestPossibleRegion() ); itkMaskImage->SetBufferedRegion( dirImg->GetLargestPossibleRegion() ); itkMaskImage->SetRequestedRegion( dirImg->GetLargestPossibleRegion() ); itkMaskImage->Allocate(); itkMaskImage->FillBuffer(1); // extract directions from fiber bundle itk::TractsToVectorImageFilter::Pointer fOdfFilter = itk::TractsToVectorImageFilter::New(); fOdfFilter->SetFiberBundle(inputTractogram); fOdfFilter->SetMaskImage(itkMaskImage); fOdfFilter->SetAngularThreshold(cos(angularThreshold*M_PI/180)); fOdfFilter->SetNormalizeVectors(true); fOdfFilter->SetUseWorkingCopy(false); fOdfFilter->Update(); ItkDirectionImageContainerType::Pointer directionImageContainer = fOdfFilter->GetDirectionImageContainer(); if (verbose) { // write vector field mitk::FiberBundleX::Pointer directions = fOdfFilter->GetOutputFiberBundle(); mitk::CoreObjectFactory::FileWriterList fileWriters = mitk::CoreObjectFactory::GetInstance()->GetFileWriters(); for (mitk::CoreObjectFactory::FileWriterList::iterator it = fileWriters.begin() ; it != fileWriters.end() ; ++it) { if ( (*it)->CanWriteBaseDataType(directions.GetPointer()) ) { string outfilename = outRoot; outfilename.append("_VECTOR_FIELD.fib"); (*it)->SetFileName( outfilename.c_str() ); (*it)->DoWrite( directions.GetPointer() ); } } // write direction images for (unsigned int i=0; iSize(); i++) { itk::TractsToVectorImageFilter::ItkDirectionImageType::Pointer itkImg = directionImageContainer->GetElement(i); typedef itk::ImageFileWriter< itk::TractsToVectorImageFilter::ItkDirectionImageType > WriterType; WriterType::Pointer writer = WriterType::New(); string outfilename = outRoot; outfilename.append("_DIRECTION_"); outfilename.append(boost::lexical_cast(i)); outfilename.append(".nrrd"); MITK_INFO << "writing " << outfilename; writer->SetFileName(outfilename.c_str()); writer->SetInput(itkImg); writer->Update(); } // write num direction image { ItkUcharImgType::Pointer numDirImage = fOdfFilter->GetNumDirectionsImage(); typedef itk::ImageFileWriter< ItkUcharImgType > WriterType; WriterType::Pointer writer = WriterType::New(); string outfilename = outRoot; outfilename.append("_NUM_DIRECTIONS.nrrd"); MITK_INFO << "writing " << outfilename; writer->SetFileName(outfilename.c_str()); writer->SetInput(numDirImage); writer->Update(); } } string logFile = outRoot; logFile.append("_ANGULAR_ERROR.csv"); ofstream file; file.open (logFile.c_str()); if (maskImages.size()>0) { for (unsigned int i=0; i(mitk::IOUtil::LoadDataNode(maskImages.at(i))->GetData()); mitk::CastToItkImage(mitkMaskImage, itkMaskImage); // evaluate directions EvaluationFilterType::Pointer evaluationFilter = EvaluationFilterType::New(); evaluationFilter->SetImageSet(directionImageContainer); evaluationFilter->SetReferenceImageSet(referenceImageContainer); evaluationFilter->SetMaskImage(itkMaskImage); evaluationFilter->SetIgnoreMissingDirections(ignore); evaluationFilter->Update(); if (verbose) { EvaluationFilterType::OutputImageType::Pointer angularErrorImage = evaluationFilter->GetOutput(0); typedef itk::ImageFileWriter< EvaluationFilterType::OutputImageType > WriterType; WriterType::Pointer writer = WriterType::New(); string outfilename = outRoot; outfilename.append("_ERROR_IMAGE.nrrd"); MITK_INFO << "writing " << outfilename; writer->SetFileName(outfilename.c_str()); writer->SetInput(angularErrorImage); writer->Update(); } string sens = itksys::SystemTools::GetFilenameWithoutExtension(itksys::SystemTools::GetFilenameName(fibFile)); sens.append(","); sens.append(itksys::SystemTools::GetFilenameWithoutExtension(itksys::SystemTools::GetFilenameName(maskImages.at(i)))); sens.append(","); sens.append(boost::lexical_cast(evaluationFilter->GetMeanAngularError())); sens.append(","); sens.append(boost::lexical_cast(evaluationFilter->GetMedianAngularError())); sens.append(","); sens.append(boost::lexical_cast(evaluationFilter->GetMaxAngularError())); sens.append(","); sens.append(boost::lexical_cast(evaluationFilter->GetMinAngularError())); sens.append(","); sens.append(boost::lexical_cast(std::sqrt(evaluationFilter->GetVarAngularError()))); sens.append(";\n"); file << sens; } } else { // evaluate directions EvaluationFilterType::Pointer evaluationFilter = EvaluationFilterType::New(); evaluationFilter->SetImageSet(directionImageContainer); evaluationFilter->SetReferenceImageSet(referenceImageContainer); evaluationFilter->SetMaskImage(itkMaskImage); evaluationFilter->SetIgnoreMissingDirections(ignore); evaluationFilter->Update(); if (verbose) { EvaluationFilterType::OutputImageType::Pointer angularErrorImage = evaluationFilter->GetOutput(0); typedef itk::ImageFileWriter< EvaluationFilterType::OutputImageType > WriterType; WriterType::Pointer writer = WriterType::New(); string outfilename = outRoot; outfilename.append("_ERROR_IMAGE.nrrd"); MITK_INFO << "writing " << outfilename; writer->SetFileName(outfilename.c_str()); writer->SetInput(angularErrorImage); writer->Update(); } string sens = itksys::SystemTools::GetFilenameWithoutExtension(itksys::SystemTools::GetFilenameName(fibFile)); sens.append(","); sens.append("FULL"); sens.append(","); sens.append(boost::lexical_cast(evaluationFilter->GetMeanAngularError())); sens.append(","); sens.append(boost::lexical_cast(evaluationFilter->GetMedianAngularError())); sens.append(","); sens.append(boost::lexical_cast(evaluationFilter->GetMaxAngularError())); sens.append(","); sens.append(boost::lexical_cast(evaluationFilter->GetMinAngularError())); sens.append(","); sens.append(boost::lexical_cast(std::sqrt(evaluationFilter->GetVarAngularError()))); sens.append(";\n"); file << sens; } file.close(); MITK_INFO << "DONE"; } 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; } RegisterDiffusionMiniApp(LocalDirectionalFiberPlausibility); diff --git a/Modules/DiffusionImaging/MiniApps/MultishellMethods.cpp b/Modules/DiffusionImaging/MiniApps/MultishellMethods.cpp index d1a52851d9..0368b6b6a0 100644 --- a/Modules/DiffusionImaging/MiniApps/MultishellMethods.cpp +++ b/Modules/DiffusionImaging/MiniApps/MultishellMethods.cpp @@ -1,230 +1,230 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "MiniAppManager.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "ctkCommandLineParser.h" #include #include #include #include #include #include #include int MultishellMethods(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setTitle("Multishell Methods"); parser.setCategory("Fiber Tracking and Processing Methods"); parser.setDescription(""); parser.setContributor("MBI"); parser.setArgumentPrefix("--", "-"); - parser.addArgument("in", "i", ctkCommandLineParser::File, "Input:", "input file", us::Any(), false); - parser.addArgument("out", "o", ctkCommandLineParser::File, "Output:", "output file", us::Any(), false); + parser.addArgument("in", "i", ctkCommandLineParser::InputFile, "Input:", "input file", us::Any(), false); + parser.addArgument("out", "o", ctkCommandLineParser::OutputFile, "Output:", "output file", us::Any(), false); parser.addArgument("adc", "D", ctkCommandLineParser::Bool, "ADC:", "ADC Average", us::Any(), false); parser.addArgument("akc", "K", ctkCommandLineParser::Bool, "Kurtosis fit:", "Kurtosis Fit", us::Any(), false); parser.addArgument("biexp", "B", ctkCommandLineParser::Bool, "BiExp fit:", "BiExp fit", us::Any(), false); parser.addArgument("targetbvalue", "b", ctkCommandLineParser::String, "b Value:", "target bValue (mean, min, max)", us::Any(), false); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; // mandatory arguments string inName = us::any_cast(parsedArgs["in"]); string outName = us::any_cast(parsedArgs["out"]); bool applyADC = us::any_cast(parsedArgs["adc"]); bool applyAKC = us::any_cast(parsedArgs["akc"]); bool applyBiExp = us::any_cast(parsedArgs["biexp"]); string targetType = us::any_cast(parsedArgs["targetbvalue"]); try { MITK_INFO << "Loading " << inName; const std::string s1="", s2=""; std::vector infile = mitk::BaseDataIO::LoadBaseDataFromFile( inName, s1, s2, false ); mitk::BaseData::Pointer baseData = infile.at(0); if ( dynamic_cast*>(baseData.GetPointer()) ) { MITK_INFO << "Writing " << outName; mitk::DiffusionImage::Pointer dwi = dynamic_cast*>(baseData.GetPointer()); typedef itk::RadialMultishellToSingleshellImageFilter FilterType; typedef itk::DwiGradientLengthCorrectionFilter CorrectionFilterType; CorrectionFilterType::Pointer roundfilter = CorrectionFilterType::New(); roundfilter->SetRoundingValue( 1000 ); roundfilter->SetReferenceBValue(dwi->GetReferenceBValue()); roundfilter->SetReferenceGradientDirectionContainer(dwi->GetDirections()); roundfilter->Update(); dwi->SetReferenceBValue( roundfilter->GetNewBValue() ); dwi->SetDirections( roundfilter->GetOutputGradientDirectionContainer()); // filter input parameter const mitk::DiffusionImage::BValueMap &originalShellMap = dwi->GetBValueMap(); const mitk::DiffusionImage::ImageType *vectorImage = dwi->GetVectorImage(); const mitk::DiffusionImage::GradientDirectionContainerType::Pointer gradientContainer = dwi->GetDirections(); const unsigned int &bValue = dwi->GetReferenceBValue(); // filter call vnl_vector bValueList(originalShellMap.size()-1); double targetBValue = bValueList.mean(); mitk::DiffusionImage::BValueMap::const_iterator it = originalShellMap.begin(); ++it; int i = 0 ; for(; it != originalShellMap.end(); ++it) bValueList.put(i++,it->first); if( targetType == "mean" ) targetBValue = bValueList.mean(); else if( targetType == "min" ) targetBValue = bValueList.min_value(); else if( targetType == "max" ) targetBValue = bValueList.max_value(); if(applyADC) { FilterType::Pointer filter = FilterType::New(); filter->SetInput(vectorImage); filter->SetOriginalGradientDirections(gradientContainer); filter->SetOriginalBValueMap(originalShellMap); filter->SetOriginalBValue(bValue); itk::ADCAverageFunctor::Pointer functor = itk::ADCAverageFunctor::New(); functor->setListOfBValues(bValueList); functor->setTargetBValue(targetBValue); filter->SetFunctor(functor); filter->Update(); // create new DWI image mitk::DiffusionImage::Pointer outImage = mitk::DiffusionImage::New(); outImage->SetVectorImage( filter->GetOutput() ); outImage->SetReferenceBValue( targetBValue ); outImage->SetDirections( filter->GetTargetGradientDirections() ); outImage->InitializeFromVectorImage(); mitk::NrrdDiffusionImageWriter::Pointer writer = mitk::NrrdDiffusionImageWriter::New(); writer->SetFileName((string(outName) + "_ADC.dwi")); writer->SetInput(outImage); writer->Update(); } if(applyAKC) { FilterType::Pointer filter = FilterType::New(); filter->SetInput(vectorImage); filter->SetOriginalGradientDirections(gradientContainer); filter->SetOriginalBValueMap(originalShellMap); filter->SetOriginalBValue(bValue); itk::KurtosisFitFunctor::Pointer functor = itk::KurtosisFitFunctor::New(); functor->setListOfBValues(bValueList); functor->setTargetBValue(targetBValue); filter->SetFunctor(functor); filter->Update(); // create new DWI image mitk::DiffusionImage::Pointer outImage = mitk::DiffusionImage::New(); outImage->SetVectorImage( filter->GetOutput() ); outImage->SetReferenceBValue( targetBValue ); outImage->SetDirections( filter->GetTargetGradientDirections() ); outImage->InitializeFromVectorImage(); mitk::NrrdDiffusionImageWriter::Pointer writer = mitk::NrrdDiffusionImageWriter::New(); writer->SetFileName((string(outName) + "_AKC.dwi")); writer->SetInput(outImage); writer->Update(); } if(applyBiExp) { FilterType::Pointer filter = FilterType::New(); filter->SetInput(vectorImage); filter->SetOriginalGradientDirections(gradientContainer); filter->SetOriginalBValueMap(originalShellMap); filter->SetOriginalBValue(bValue); itk::BiExpFitFunctor::Pointer functor = itk::BiExpFitFunctor::New(); functor->setListOfBValues(bValueList); functor->setTargetBValue(targetBValue); filter->SetFunctor(functor); filter->Update(); // create new DWI image mitk::DiffusionImage::Pointer outImage = mitk::DiffusionImage::New(); outImage->SetVectorImage( filter->GetOutput() ); outImage->SetReferenceBValue( targetBValue ); outImage->SetDirections( filter->GetTargetGradientDirections() ); outImage->InitializeFromVectorImage(); mitk::NrrdDiffusionImageWriter::Pointer writer = mitk::NrrdDiffusionImageWriter::New(); writer->SetFileName((string(outName) + "_BiExp.dwi")); writer->SetInput(outImage); writer->Update(); } } } 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; } RegisterDiffusionMiniApp(MultishellMethods); diff --git a/Modules/DiffusionImaging/MiniApps/NetworkCreation.cpp b/Modules/DiffusionImaging/MiniApps/NetworkCreation.cpp index 394cb74058..45eda8cf9f 100644 --- a/Modules/DiffusionImaging/MiniApps/NetworkCreation.cpp +++ b/Modules/DiffusionImaging/MiniApps/NetworkCreation.cpp @@ -1,143 +1,143 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "MiniAppManager.h" // std includes #include // CTK includes #include "ctkCommandLineParser.h" // MITK includes #include #include "mitkConnectomicsNetworkCreator.h" #include int NetworkCreation(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setArgumentPrefix("--", "-"); - parser.addArgument("fiberImage", "f", ctkCommandLineParser::File, "Input image", "input fiber image (.fib)", us::Any(), false); - parser.addArgument("parcellation", "p", ctkCommandLineParser::File, "Parcellation image", "parcellation image", us::Any(), false); + parser.addArgument("fiberImage", "f", ctkCommandLineParser::InputFile, "Input image", "input fiber image (.fib)", us::Any(), false); + parser.addArgument("parcellation", "p", ctkCommandLineParser::InputFile, "Parcellation image", "parcellation image", us::Any(), false); parser.addArgument("outputNetwork", "o", ctkCommandLineParser::String, "Output network", "where to save the output (.cnf)", us::Any(), false); parser.addArgument("radius", "r", ctkCommandLineParser::Int, "Radius", "Search radius in mm", 15, true); parser.addArgument("noCenterOfMass", "com", ctkCommandLineParser::Bool, "No center of mass", "Do not use center of mass for node positions"); parser.setCategory("Connectomics"); parser.setTitle("Network Creation"); parser.setDescription(""); parser.setContributor("MBI"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; //default values int searchRadius( 15 ); bool noCenterOfMass( false ); // parse command line arguments std::string fiberFilename = us::any_cast(parsedArgs["fiberImage"]); std::string parcellationFilename = us::any_cast(parsedArgs["parcellation"]); std::string outputFilename = us::any_cast(parsedArgs["outputNetwork"]); if (parsedArgs.count("radius")) searchRadius = us::any_cast(parsedArgs["radius"]); if (parsedArgs.count("noCenterOfMass")) noCenterOfMass = us::any_cast(parsedArgs["noCenterOfMass"]); try { const std::string s1="", s2=""; // load fiber image std::vector fiberInfile = mitk::BaseDataIO::LoadBaseDataFromFile( fiberFilename, s1, s2, false ); if( fiberInfile.empty() ) { std::string errorMessage = "Fiber Image at " + fiberFilename + " could not be read. Aborting."; MITK_ERROR << errorMessage; return EXIT_FAILURE; } mitk::BaseData* fiberBaseData = fiberInfile.at(0); mitk::FiberBundleX* fiberBundle = dynamic_cast( fiberBaseData ); // load parcellation std::vector parcellationInFile = mitk::BaseDataIO::LoadBaseDataFromFile( parcellationFilename, s1, s2, false ); if( parcellationInFile.empty() ) { std::string errorMessage = "Parcellation at " + parcellationFilename + " could not be read. Aborting."; MITK_ERROR << errorMessage; return EXIT_FAILURE; } mitk::BaseData* parcellationBaseData = parcellationInFile.at(0); mitk::Image* parcellationImage = dynamic_cast( parcellationBaseData ); // do creation mitk::ConnectomicsNetworkCreator::Pointer connectomicsNetworkCreator = mitk::ConnectomicsNetworkCreator::New(); connectomicsNetworkCreator->SetSegmentation( parcellationImage ); connectomicsNetworkCreator->SetFiberBundle( fiberBundle ); if( !noCenterOfMass ) { connectomicsNetworkCreator->CalculateCenterOfMass(); } connectomicsNetworkCreator->SetEndPointSearchRadius( searchRadius ); connectomicsNetworkCreator->CreateNetworkFromFibersAndSegmentation(); mitk::ConnectomicsNetwork::Pointer network = connectomicsNetworkCreator->GetNetwork(); MITK_INFO << "searching writer"; mitk::CoreObjectFactory::FileWriterList fileWriters = mitk::CoreObjectFactory::GetInstance()->GetFileWriters(); for (mitk::CoreObjectFactory::FileWriterList::iterator it = fileWriters.begin() ; it != fileWriters.end() ; ++it) { if ( (*it)->CanWriteBaseDataType(network.GetPointer()) ) { MITK_INFO << "writing"; (*it)->SetFileName( outputFilename.c_str() ); (*it)->DoWrite( network.GetPointer() ); } } return EXIT_SUCCESS; } 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; } RegisterDiffusionMiniApp(NetworkCreation); diff --git a/Modules/DiffusionImaging/MiniApps/NetworkStatistics.cpp b/Modules/DiffusionImaging/MiniApps/NetworkStatistics.cpp index e395e6e6ec..2c961df8e8 100644 --- a/Modules/DiffusionImaging/MiniApps/NetworkStatistics.cpp +++ b/Modules/DiffusionImaging/MiniApps/NetworkStatistics.cpp @@ -1,518 +1,518 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include // std includes #include #include #include #include #include #include // boost includes #include // ITK includes #include // CTK includes #include "ctkCommandLineParser.h" // MITK includes #include #include #include #include int NetworkStatistics(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setArgumentPrefix("--", "-"); - parser.addArgument("inputNetwork", "i", ctkCommandLineParser::File, "Input network", "input connectomics network (.cnf)", us::Any(), false); - parser.addArgument("outputFile", "o", ctkCommandLineParser::File, "Output file", "name of output file", us::Any(), false); + parser.addArgument("inputNetwork", "i", ctkCommandLineParser::InputFile, "Input network", "input connectomics network (.cnf)", us::Any(), false); + parser.addArgument("outputFile", "o", ctkCommandLineParser::OutputFile, "Output file", "name of output file", us::Any(), false); parser.addArgument("noGlobalStatistics", "g", ctkCommandLineParser::Bool, "No global statistics", "Do not calculate global statistics"); parser.addArgument("createConnectivityMatriximage", "I", ctkCommandLineParser::Bool, "Write connectivity matrix image", "Write connectivity matrix image"); parser.addArgument("binaryConnectivity", "b", ctkCommandLineParser::Bool, "Binary connectivity", "Whether to create a binary connectivity matrix"); parser.addArgument("rescaleConnectivity", "r", ctkCommandLineParser::Bool, "Rescale connectivity", "Whether to rescale the connectivity matrix"); parser.addArgument("localStatistics", "L", ctkCommandLineParser::StringList, "Local statistics", "Provide a list of node labels for local statistics", us::Any()); parser.addArgument("regionList", "R", ctkCommandLineParser::StringList, "Region list", "A space separated list of regions. Each region has the format\n regionname;label1;label2;...;labelN", us::Any()); parser.addArgument("granularity", "gr", ctkCommandLineParser::Int, "Granularity", "How finely to test the density range and how many thresholds to consider"); parser.addArgument("startDensity", "d", ctkCommandLineParser::Bool, "Start Density", "Largest density for the range"); parser.addArgument("thresholdStepSize", "t", ctkCommandLineParser::Int, "Step size threshold", "Distance of two adjacent thresholds"); parser.setCategory("Connectomics"); parser.setTitle("Network Statistics"); parser.setDescription(""); parser.setContributor("MBI"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; //default values bool noGlobalStatistics( false ); bool binaryConnectivity( false ); bool rescaleConnectivity( false ); bool createConnectivityMatriximage( false ); unsigned int granularity( 1 ); double startDensity( 1.0 ); unsigned int thresholdStepSize( 3 ); // parse command line arguments std::string networkName = us::any_cast(parsedArgs["inputNetwork"]); std::string outName = us::any_cast(parsedArgs["outputFile"]); ctkCommandLineParser::StringContainerType localLabels; if(parsedArgs.count("localStatistics")) { localLabels = us::any_cast(parsedArgs["localStatistics"]); } ctkCommandLineParser::StringContainerType unparsedRegions; std::map< std::string, std::vector > parsedRegions; std::map< std::string, std::vector >::iterator parsedRegionsIterator; if(parsedArgs.count("regionList")) { unparsedRegions = us::any_cast(parsedArgs["regionList"]); for(unsigned int index(0); index < unparsedRegions.size(); index++ ) { std::vector< std::string > tempRegionVector; boost::split(tempRegionVector, unparsedRegions.at(index), boost::is_any_of(";")); std::vector< std::string >::const_iterator begin = tempRegionVector.begin(); std::vector< std::string >::const_iterator last = tempRegionVector.begin() + tempRegionVector.size(); std::vector< std::string > insertRegionVector(begin + 1, last); if( parsedRegions.count( tempRegionVector.at(0) ) == 0 ) { parsedRegions.insert( std::pair< std::string, std::vector >( tempRegionVector.at(0), insertRegionVector) ); } else { MITK_ERROR << "Region already exists. Skipping second occurrence."; } } } if (parsedArgs.count("noGlobalStatistics")) noGlobalStatistics = us::any_cast(parsedArgs["noGlobalStatistics"]); if (parsedArgs.count("binaryConnectivity")) binaryConnectivity = us::any_cast(parsedArgs["binaryConnectivity"]); if (parsedArgs.count("rescaleConnectivity")) rescaleConnectivity = us::any_cast(parsedArgs["rescaleConnectivity"]); if (parsedArgs.count("createConnectivityMatriximage")) createConnectivityMatriximage = us::any_cast(parsedArgs["createConnectivityMatriximage"]); if (parsedArgs.count("granularity")) granularity = us::any_cast(parsedArgs["granularity"]); if (parsedArgs.count("startDensity")) startDensity = us::any_cast(parsedArgs["startDensity"]); if (parsedArgs.count("thresholdStepSize")) thresholdStepSize = us::any_cast(parsedArgs["thresholdStepSize"]); try { const std::string s1="", s2=""; // load network std::vector networkFile = mitk::BaseDataIO::LoadBaseDataFromFile( networkName, s1, s2, false ); if( networkFile.empty() ) { std::string errorMessage = "File at " + networkName + " could not be read. Aborting."; MITK_ERROR << errorMessage; return EXIT_FAILURE; } mitk::BaseData* networkBaseData = networkFile.at(0); mitk::ConnectomicsNetwork* network = dynamic_cast( networkBaseData ); if( !network ) { std::string errorMessage = "Read file at " + networkName + " could not be recognized as network. Aborting."; MITK_ERROR << errorMessage; return EXIT_FAILURE; } // streams std::stringstream globalHeaderStream; globalHeaderStream << "NumberOfVertices " << "NumberOfEdges " << "AverageDegree " << "ConnectionDensity " << "NumberOfConnectedComponents " << "AverageComponentSize " << "LargestComponentSize " << "RatioOfNodesInLargestComponent " << "HopPlotExponent " << "EffectiveHopDiameter " << "AverageClusteringCoefficientsC " << "AverageClusteringCoefficientsD " << "AverageClusteringCoefficientsE " << "AverageVertexBetweennessCentrality " << "AverageEdgeBetweennessCentrality " << "NumberOfIsolatedPoints " << "RatioOfIsolatedPoints " << "NumberOfEndPoints " << "RatioOfEndPoints " << "Diameter " << "Diameter90 " << "Radius " << "Radius90 " << "AverageEccentricity " << "AverageEccentricity90 " << "AveragePathLength " << "NumberOfCentralPoints " << "RatioOfCentralPoints " << "SpectralRadius " << "SecondLargestEigenValue " << "AdjacencyTrace " << "AdjacencyEnergy " << "LaplacianTrace " << "LaplacianEnergy " << "LaplacianSpectralGap " << "NormalizedLaplacianTrace " << "NormalizedLaplacianEnergy " << "NormalizedLaplacianNumberOf2s " << "NormalizedLaplacianNumberOf1s " << "NormalizedLaplacianNumberOf0s " << "NormalizedLaplacianLowerSlope " << "NormalizedLaplacianUpperSlope " << "SmallWorldness" << std::endl; std::stringstream localHeaderStream; std::stringstream regionalHeaderStream; std::stringstream globalDataStream; std::stringstream localDataStream; std::stringstream regionalDataStream; std::string globalOutName = outName + "_global.txt"; std::string localOutName = outName + "_local.txt"; std::string regionalOutName = outName + "_regional.txt"; bool firstRun( true ); // iterate over all three possible methods for(unsigned int method( 0 ); method < 3; method++) { // 0 - Random removal threshold // 1 - Largest density below threshold // 2 - Threshold based // iterate over possible targets for( unsigned int step( 0 ); step < granularity; step++ ) { double targetValue( 0.0 ); bool newStep( true ); switch ( method ) { case mitk::ConnectomicsNetworkThresholder::RandomRemovalOfWeakest : case mitk::ConnectomicsNetworkThresholder::LargestLowerThanDensity : targetValue = startDensity * (1 - static_cast( step ) / ( granularity + 0.5 ) ); break; case mitk::ConnectomicsNetworkThresholder::ThresholdBased : targetValue = static_cast( thresholdStepSize * step ); break; default: MITK_ERROR << "Invalid thresholding method called, aborting."; return EXIT_FAILURE; break; } mitk::ConnectomicsNetworkThresholder::Pointer thresholder = mitk::ConnectomicsNetworkThresholder::New(); thresholder->SetNetwork( network ); thresholder->SetTargetThreshold( targetValue ); thresholder->SetTargetDensity( targetValue ); thresholder->SetThresholdingScheme( static_cast(method) ); mitk::ConnectomicsNetwork::Pointer thresholdedNetwork = thresholder->GetThresholdedNetwork(); mitk::ConnectomicsStatisticsCalculator::Pointer statisticsCalculator = mitk::ConnectomicsStatisticsCalculator::New(); statisticsCalculator->SetNetwork( thresholdedNetwork ); statisticsCalculator->Update(); // global statistics if( !noGlobalStatistics ) { globalDataStream << statisticsCalculator->GetNumberOfVertices() << " " << statisticsCalculator->GetNumberOfEdges() << " " << statisticsCalculator->GetAverageDegree() << " " << statisticsCalculator->GetConnectionDensity() << " " << statisticsCalculator->GetNumberOfConnectedComponents() << " " << statisticsCalculator->GetAverageComponentSize() << " " << statisticsCalculator->GetLargestComponentSize() << " " << statisticsCalculator->GetRatioOfNodesInLargestComponent() << " " << statisticsCalculator->GetHopPlotExponent() << " " << statisticsCalculator->GetEffectiveHopDiameter() << " " << statisticsCalculator->GetAverageClusteringCoefficientsC() << " " << statisticsCalculator->GetAverageClusteringCoefficientsD() << " " << statisticsCalculator->GetAverageClusteringCoefficientsE() << " " << statisticsCalculator->GetAverageVertexBetweennessCentrality() << " " << statisticsCalculator->GetAverageEdgeBetweennessCentrality() << " " << statisticsCalculator->GetNumberOfIsolatedPoints() << " " << statisticsCalculator->GetRatioOfIsolatedPoints() << " " << statisticsCalculator->GetNumberOfEndPoints() << " " << statisticsCalculator->GetRatioOfEndPoints() << " " << statisticsCalculator->GetDiameter() << " " << statisticsCalculator->GetDiameter90() << " " << statisticsCalculator->GetRadius() << " " << statisticsCalculator->GetRadius90() << " " << statisticsCalculator->GetAverageEccentricity() << " " << statisticsCalculator->GetAverageEccentricity90() << " " << statisticsCalculator->GetAveragePathLength() << " " << statisticsCalculator->GetNumberOfCentralPoints() << " " << statisticsCalculator->GetRatioOfCentralPoints() << " " << statisticsCalculator->GetSpectralRadius() << " " << statisticsCalculator->GetSecondLargestEigenValue() << " " << statisticsCalculator->GetAdjacencyTrace() << " " << statisticsCalculator->GetAdjacencyEnergy() << " " << statisticsCalculator->GetLaplacianTrace() << " " << statisticsCalculator->GetLaplacianEnergy() << " " << statisticsCalculator->GetLaplacianSpectralGap() << " " << statisticsCalculator->GetNormalizedLaplacianTrace() << " " << statisticsCalculator->GetNormalizedLaplacianEnergy() << " " << statisticsCalculator->GetNormalizedLaplacianNumberOf2s() << " " << statisticsCalculator->GetNormalizedLaplacianNumberOf1s() << " " << statisticsCalculator->GetNormalizedLaplacianNumberOf0s() << " " << statisticsCalculator->GetNormalizedLaplacianLowerSlope() << " " << statisticsCalculator->GetNormalizedLaplacianUpperSlope() << " " << statisticsCalculator->GetSmallWorldness() << std::endl; } // end global statistics //create connectivity matrix png if( createConnectivityMatriximage ) { std::string connectivity_png_postfix = "_connectivity"; if( binaryConnectivity ) { connectivity_png_postfix += "_binary"; } else if( rescaleConnectivity ) { connectivity_png_postfix += "_rescaled"; } connectivity_png_postfix += ".png"; /* File format * A png file depicting the binary connectivity matrix */ itk::ConnectomicsNetworkToConnectivityMatrixImageFilter::Pointer filter = itk::ConnectomicsNetworkToConnectivityMatrixImageFilter::New(); filter->SetInputNetwork( network ); filter->SetBinaryConnectivity( binaryConnectivity ); filter->SetRescaleConnectivity( rescaleConnectivity ); filter->Update(); typedef itk::ConnectomicsNetworkToConnectivityMatrixImageFilter::OutputImageType connectivityMatrixImageType; itk::ImageFileWriter< connectivityMatrixImageType >::Pointer connectivityWriter = itk::ImageFileWriter< connectivityMatrixImageType >::New(); connectivityWriter->SetInput( filter->GetOutput() ); connectivityWriter->SetFileName( outName + connectivity_png_postfix); connectivityWriter->Update(); MITK_INFO << "Connectivity matrix image written."; } // end create connectivity matrix png /* * We can either calculate local indices for specific nodes, or specific regions */ // Create LabelToIndex translation std::map< std::string, int > labelToIdMap; std::vector< mitk::ConnectomicsNetwork::NetworkNode > nodeVector = thresholdedNetwork->GetVectorOfAllNodes(); for(int loop(0); loop < nodeVector.size(); loop++) { labelToIdMap.insert( std::pair< std::string, int>(nodeVector.at(loop).label, nodeVector.at(loop).id) ); } std::vector< int > degreeVector = thresholdedNetwork->GetDegreeOfNodes(); std::vector< double > ccVector = thresholdedNetwork->GetLocalClusteringCoefficients( ); std::vector< double > bcVector = thresholdedNetwork->GetNodeBetweennessVector( ); // calculate local indices { // only add to header for the first step of the first method if( firstRun ) { localHeaderStream << "Th_method " << "Th_target " << "density"; } double density = statisticsCalculator->GetConnectionDensity(); localDataStream << "\n" << method << " " << targetValue << " " << density; for(unsigned int loop(0); loop < localLabels.size(); loop++ ) { if( network->CheckForLabel(localLabels.at( loop )) ) { if( firstRun ) { localHeaderStream << " " << localLabels.at( loop ) << "_Degree " << localLabels.at( loop ) << "_CC " << localLabels.at( loop ) << "_BC"; } localDataStream << " " << degreeVector.at( labelToIdMap.find( localLabels.at( loop ) )->second ) << " " << ccVector.at( labelToIdMap.find( localLabels.at( loop ) )->second ) << " " << bcVector.at( labelToIdMap.find( localLabels.at( loop ) )->second ); } else { MITK_ERROR << "Illegal label. Label: \"" << localLabels.at( loop ) << "\" not found."; } } } // calculate regional indices { // only add to header for the first step of the first method if( firstRun ) { regionalHeaderStream << "Th_method " << "Th_target " << "density"; } double density = statisticsCalculator->GetConnectionDensity(); regionalDataStream << "\n" << method << " " << targetValue << " " << density; for( parsedRegionsIterator = parsedRegions.begin(); parsedRegionsIterator != parsedRegions.end(); parsedRegionsIterator++ ) { std::vector regionLabelsVector = parsedRegionsIterator->second; std::string regionName = parsedRegionsIterator->first; double sumDegree( 0 ); double sumCC( 0 ); double sumBC( 0 ); double count( 0 ); for( int loop(0); loop < regionLabelsVector.size(); loop++ ) { if( thresholdedNetwork->CheckForLabel(regionLabelsVector.at( loop )) ) { sumDegree = sumDegree + degreeVector.at( labelToIdMap.find( regionLabelsVector.at( loop ) )->second ); sumCC = sumCC + ccVector.at( labelToIdMap.find( regionLabelsVector.at( loop ) )->second ); sumBC = sumBC + bcVector.at( labelToIdMap.find( regionLabelsVector.at( loop ) )->second ); count = count + 1; } else { MITK_ERROR << "Illegal label. Label: \"" << regionLabelsVector.at( loop ) << "\" not found."; } } // only add to header for the first step of the first method if( firstRun ) { regionalHeaderStream << " " << regionName << "_LocalAverageDegree " << regionName << "_LocalAverageCC " << regionName << "_LocalAverageBC " << regionName << "_NumberOfNodes"; } regionalDataStream << " " << sumDegree / count << " " << sumCC / count << " " << sumBC / count << " " << count; } } firstRun = false; } }// end calculate local averages if( !noGlobalStatistics ) { MITK_INFO << "Writing to " << globalOutName; std::ofstream glocalOutFile( globalOutName.c_str(), ios::out ); if( ! glocalOutFile.is_open() ) { std::string errorMessage = "Could not open " + globalOutName + " for writing."; MITK_ERROR << errorMessage; return EXIT_FAILURE; } glocalOutFile << globalHeaderStream.str() << globalDataStream.str(); glocalOutFile.close(); } if( localLabels.size() > 0 ) { MITK_INFO << "Writing to " << localOutName; std::ofstream localOutFile( localOutName.c_str(), ios::out ); if( ! localOutFile.is_open() ) { std::string errorMessage = "Could not open " + localOutName + " for writing."; MITK_ERROR << errorMessage; return EXIT_FAILURE; } localOutFile << localHeaderStream.str() << localDataStream.str(); localOutFile.close(); } if( parsedRegions.size() > 0 ) { MITK_INFO << "Writing to " << regionalOutName; std::ofstream regionalOutFile( regionalOutName.c_str(), ios::out ); if( ! regionalOutFile.is_open() ) { std::string errorMessage = "Could not open " + regionalOutName + " for writing."; MITK_ERROR << errorMessage; return EXIT_FAILURE; } regionalOutFile << regionalHeaderStream.str() << regionalDataStream.str(); regionalOutFile.close(); } return EXIT_SUCCESS; } 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; } RegisterDiffusionMiniApp(NetworkStatistics); diff --git a/Modules/DiffusionImaging/MiniApps/PeakExtraction.cpp b/Modules/DiffusionImaging/MiniApps/PeakExtraction.cpp index d6821d3ffd..8bf7146349 100755 --- a/Modules/DiffusionImaging/MiniApps/PeakExtraction.cpp +++ b/Modules/DiffusionImaging/MiniApps/PeakExtraction.cpp @@ -1,382 +1,382 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "MiniAppManager.h" #include #include #include #include #include #include #include #include #include #include #include "ctkCommandLineParser.h" #include #include #include #include #include mitk::Image::Pointer LoadData(std::string filename) { if( filename.empty() ) return NULL; const std::string s1="", s2=""; std::vector infile = mitk::BaseDataIO::LoadBaseDataFromFile( filename, s1, s2, false ); if( infile.empty() ) { MITK_INFO << "File " << filename << " could not be read!"; return NULL; } mitk::BaseData::Pointer baseData = infile.at(0); return dynamic_cast(baseData.GetPointer()); } template int StartPeakExtraction(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setArgumentPrefix("--", "-"); - parser.addArgument("image", "i", ctkCommandLineParser::File, "Input image", "sh coefficient image", us::Any(), false); - parser.addArgument("outroot", "o", ctkCommandLineParser::Directory, "Output directory", "output root", us::Any(), false); - parser.addArgument("mask", "m", ctkCommandLineParser::File, "Mask", "mask image"); + parser.addArgument("image", "i", ctkCommandLineParser::InputFile, "Input image", "sh coefficient image", us::Any(), false); + parser.addArgument("outroot", "o", ctkCommandLineParser::OutputDirectory, "Output directory", "output root", us::Any(), false); + parser.addArgument("mask", "m", ctkCommandLineParser::InputFile, "Mask", "mask image"); parser.addArgument("normalization", "n", ctkCommandLineParser::Int, "Normalization", "0=no norm, 1=max norm, 2=single vec norm", 1, true); parser.addArgument("numpeaks", "p", ctkCommandLineParser::Int, "Max. number of peaks", "maximum number of extracted peaks", 2, true); parser.addArgument("peakthres", "r", ctkCommandLineParser::Float, "Peak threshold", "peak threshold relative to largest peak", 0.4, true); parser.addArgument("abspeakthres", "a", ctkCommandLineParser::Float, "Absolute peak threshold", "absolute peak threshold weighted with local GFA value", 0.06, true); parser.addArgument("shConvention", "s", ctkCommandLineParser::String, "Use specified SH-basis", "use specified SH-basis (MITK, FSL, MRtrix)", string("MITK"), true); parser.addArgument("noFlip", "f", ctkCommandLineParser::Bool, "No flip", "do not flip input image to match MITK coordinate convention"); parser.setCategory("Preprocessing Tools"); parser.setTitle("Peak Extraction"); parser.setDescription(""); parser.setContributor("MBI"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; // mandatory arguments string imageName = us::any_cast(parsedArgs["image"]); string outRoot = us::any_cast(parsedArgs["outroot"]); // optional arguments string maskImageName(""); if (parsedArgs.count("mask")) maskImageName = us::any_cast(parsedArgs["mask"]); int normalization = 1; if (parsedArgs.count("normalization")) normalization = us::any_cast(parsedArgs["normalization"]); int numPeaks = 2; if (parsedArgs.count("numpeaks")) numPeaks = us::any_cast(parsedArgs["numpeaks"]); float peakThres = 0.4; if (parsedArgs.count("peakthres")) peakThres = us::any_cast(parsedArgs["peakthres"]); float absPeakThres = 0.06; if (parsedArgs.count("abspeakthres")) absPeakThres = us::any_cast(parsedArgs["abspeakthres"]); bool noFlip = false; if (parsedArgs.count("noFlip")) noFlip = us::any_cast(parsedArgs["noFlip"]); MITK_INFO << "image: " << imageName; MITK_INFO << "outroot: " << outRoot; if (!maskImageName.empty()) MITK_INFO << "mask: " << maskImageName; else MITK_INFO << "no mask image selected"; MITK_INFO << "numpeaks: " << numPeaks; MITK_INFO << "peakthres: " << peakThres; MITK_INFO << "abspeakthres: " << absPeakThres; MITK_INFO << "shOrder: " << shOrder; try { mitk::Image::Pointer image = LoadData(imageName); mitk::Image::Pointer mask = LoadData(maskImageName); typedef itk::Image ItkUcharImgType; typedef itk::FiniteDiffOdfMaximaExtractionFilter< float, shOrder, 20242 > MaximaExtractionFilterType; typename MaximaExtractionFilterType::Pointer filter = MaximaExtractionFilterType::New(); int toolkitConvention = 0; if (parsedArgs.count("shConvention")) { string convention = us::any_cast(parsedArgs["shConvention"]).c_str(); if ( boost::algorithm::equals(convention, "FSL") ) { toolkitConvention = 1; MITK_INFO << "Using FSL SH-basis"; } else if ( boost::algorithm::equals(convention, "MRtrix") ) { toolkitConvention = 2; MITK_INFO << "Using MRtrix SH-basis"; } else MITK_INFO << "Using MITK SH-basis"; } else MITK_INFO << "Using MITK SH-basis"; ItkUcharImgType::Pointer itkMaskImage = NULL; if (mask.IsNotNull()) { try{ itkMaskImage = ItkUcharImgType::New(); mitk::CastToItkImage(mask, itkMaskImage); filter->SetMaskImage(itkMaskImage); } catch(...) { } } if (toolkitConvention>0) { MITK_INFO << "Converting coefficient image to MITK format"; typedef itk::ShCoefficientImageImporter< float, shOrder > ConverterType; typedef mitk::ImageToItk< itk::Image< float, 4 > > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(image); caster->Update(); itk::Image< float, 4 >::Pointer itkImage = caster->GetOutput(); typename ConverterType::Pointer converter = ConverterType::New(); if (noFlip) { converter->SetInputImage(itkImage); } else { MITK_INFO << "Flipping image"; itk::FixedArray flipAxes; flipAxes[0] = true; flipAxes[1] = true; flipAxes[2] = false; flipAxes[3] = false; itk::FlipImageFilter< itk::Image< float, 4 > >::Pointer flipper = itk::FlipImageFilter< itk::Image< float, 4 > >::New(); flipper->SetInput(itkImage); flipper->SetFlipAxes(flipAxes); flipper->Update(); itk::Image< float, 4 >::Pointer flipped = flipper->GetOutput(); itk::Matrix< double,4,4 > m = itkImage->GetDirection(); m[0][0] *= -1; m[1][1] *= -1; flipped->SetDirection(m); itk::Point< float, 4 > o = itkImage->GetOrigin(); o[0] -= (flipped->GetLargestPossibleRegion().GetSize(0)-1); o[1] -= (flipped->GetLargestPossibleRegion().GetSize(1)-1); flipped->SetOrigin(o); converter->SetInputImage(flipped); } MITK_INFO << "Starting conversion"; switch (toolkitConvention) { case 1: converter->SetToolkit(ConverterType::FSL); filter->SetToolkit(MaximaExtractionFilterType::FSL); break; case 2: converter->SetToolkit(ConverterType::MRTRIX); filter->SetToolkit(MaximaExtractionFilterType::MRTRIX); break; default: converter->SetToolkit(ConverterType::FSL); filter->SetToolkit(MaximaExtractionFilterType::FSL); break; } converter->GenerateData(); filter->SetInput(converter->GetCoefficientImage()); } else { try{ typedef mitk::ImageToItk< typename MaximaExtractionFilterType::CoefficientImageType > CasterType; typename CasterType::Pointer caster = CasterType::New(); caster->SetInput(image); caster->Update(); filter->SetInput(caster->GetOutput()); } catch(...) { MITK_INFO << "wrong image type"; return EXIT_FAILURE; } } filter->SetMaxNumPeaks(numPeaks); filter->SetPeakThreshold(peakThres); filter->SetAbsolutePeakThreshold(absPeakThres); filter->SetAngularThreshold(1); switch (normalization) { case 0: filter->SetNormalizationMethod(MaximaExtractionFilterType::NO_NORM); break; case 1: filter->SetNormalizationMethod(MaximaExtractionFilterType::MAX_VEC_NORM); break; case 2: filter->SetNormalizationMethod(MaximaExtractionFilterType::SINGLE_VEC_NORM); break; } MITK_INFO << "Starting extraction"; filter->Update(); // write direction images { typedef typename MaximaExtractionFilterType::ItkDirectionImageContainer ItkDirectionImageContainer; typename ItkDirectionImageContainer::Pointer container = filter->GetDirectionImageContainer(); for (unsigned int i=0; iSize(); i++) { typename MaximaExtractionFilterType::ItkDirectionImage::Pointer itkImg = container->GetElement(i); if (itkMaskImage.IsNotNull()) { itkImg->SetDirection(itkMaskImage->GetDirection()); itkImg->SetOrigin(itkMaskImage->GetOrigin()); } string outfilename = outRoot; outfilename.append("_DIRECTION_"); outfilename.append(boost::lexical_cast(i)); outfilename.append(".nrrd"); MITK_INFO << "writing " << outfilename; typedef itk::ImageFileWriter< typename MaximaExtractionFilterType::ItkDirectionImage > WriterType; typename WriterType::Pointer writer = WriterType::New(); writer->SetFileName(outfilename); writer->SetInput(itkImg); writer->Update(); } } // write num directions image { ItkUcharImgType::Pointer numDirImage = filter->GetNumDirectionsImage(); if (itkMaskImage.IsNotNull()) { numDirImage->SetDirection(itkMaskImage->GetDirection()); numDirImage->SetOrigin(itkMaskImage->GetOrigin()); } string outfilename = outRoot.c_str(); outfilename.append("_NUM_DIRECTIONS.nrrd"); MITK_INFO << "writing " << outfilename; typedef itk::ImageFileWriter< ItkUcharImgType > WriterType; WriterType::Pointer writer = WriterType::New(); writer->SetFileName(outfilename); writer->SetInput(numDirImage); writer->Update(); } // write vector field { mitk::FiberBundleX::Pointer directions = filter->GetOutputFiberBundle(); string outfilename = outRoot.c_str(); outfilename.append("_VECTOR_FIELD.fib"); mitk::FiberBundleXWriter::Pointer fibWriter = mitk::FiberBundleXWriter::New(); fibWriter->SetFileName(outfilename.c_str()); fibWriter->DoWrite(directions.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 PeakExtraction(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setArgumentPrefix("--", "-"); - parser.addArgument("image", "i", ctkCommandLineParser::File, "Input image", "sh coefficient image", us::Any(), false); + parser.addArgument("image", "i", ctkCommandLineParser::InputFile, "Input image", "sh coefficient image", us::Any(), false); parser.addArgument("shOrder", "sh", ctkCommandLineParser::Int, "Spherical harmonics order", "spherical harmonics order"); - parser.addArgument("outroot", "o", ctkCommandLineParser::Directory, "Output directory", "output root", us::Any(), false); - parser.addArgument("mask", "m", ctkCommandLineParser::File, "Mask", "mask image"); + parser.addArgument("outroot", "o", ctkCommandLineParser::OutputDirectory, "Output directory", "output root", us::Any(), false); + parser.addArgument("mask", "m", ctkCommandLineParser::InputFile, "Mask", "mask image"); parser.addArgument("normalization", "n", ctkCommandLineParser::Int, "Normalization", "0=no norm, 1=max norm, 2=single vec norm", 1, true); parser.addArgument("numpeaks", "p", ctkCommandLineParser::Int, "Max. number of peaks", "maximum number of extracted peaks", 2, true); parser.addArgument("peakthres", "r", ctkCommandLineParser::Float, "Peak threshold", "peak threshold relative to largest peak", 0.4, true); parser.addArgument("abspeakthres", "a", ctkCommandLineParser::Float, "Absolute peak threshold", "absolute peak threshold weighted with local GFA value", 0.06, true); parser.addArgument("shConvention", "s", ctkCommandLineParser::String, "Use specified SH-basis", "use specified SH-basis (MITK, FSL, MRtrix)", string("MITK"), true); parser.addArgument("noFlip", "f", ctkCommandLineParser::Bool, "No flip", "do not flip input image to match MITK coordinate convention"); parser.setCategory("Preprocessing Tools"); parser.setTitle("Peak Extraction"); parser.setDescription(""); parser.setContributor("MBI"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; int shOrder = -1; if (parsedArgs.count("shOrder")) shOrder = us::any_cast(parsedArgs["shOrder"]); switch (shOrder) { case 4: return StartPeakExtraction<4>(argc, argv); case 6: return StartPeakExtraction<6>(argc, argv); case 8: return StartPeakExtraction<8>(argc, argv); case 10: return StartPeakExtraction<10>(argc, argv); case 12: return StartPeakExtraction<12>(argc, argv); } return EXIT_FAILURE; } RegisterDiffusionMiniApp(PeakExtraction); diff --git a/Modules/DiffusionImaging/MiniApps/PeaksAngularError.cpp b/Modules/DiffusionImaging/MiniApps/PeaksAngularError.cpp index ef4f84b569..07ac417141 100755 --- a/Modules/DiffusionImaging/MiniApps/PeaksAngularError.cpp +++ b/Modules/DiffusionImaging/MiniApps/PeaksAngularError.cpp @@ -1,210 +1,210 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "MiniAppManager.h" #include #include #include #include #include #include #include "ctkCommandLineParser.h" #include #include #include #include #include #include #include #define _USE_MATH_DEFINES #include int PeaksAngularError(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setArgumentPrefix("--", "-"); parser.addArgument("test", "t", ctkCommandLineParser::StringList, "Test images", "test direction images", us::Any(), false); parser.addArgument("reference", "r", ctkCommandLineParser::StringList, "Reference images", "reference direction images", us::Any(), false); - parser.addArgument("out", "o", ctkCommandLineParser::Directory, "Output directory", "output root", us::Any(), false); - parser.addArgument("mask", "m", ctkCommandLineParser::File, "Mask", "mask image"); + parser.addArgument("out", "o", ctkCommandLineParser::OutputDirectory, "Output directory", "output root", us::Any(), false); + parser.addArgument("mask", "m", ctkCommandLineParser::InputFile, "Mask", "mask image"); parser.addArgument("verbose", "v", ctkCommandLineParser::Bool, "Verbose", "output optional and intermediate calculation results"); parser.addArgument("ignore", "i", ctkCommandLineParser::Bool, "Ignore", "don't increase error for missing or too many directions"); parser.setCategory("Preprocessing Tools"); parser.setTitle("Peaks Angular Error"); parser.setDescription(""); parser.setContributor("MBI"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; ctkCommandLineParser::StringContainerType testImages = us::any_cast(parsedArgs["test"]); ctkCommandLineParser::StringContainerType referenceImages = us::any_cast(parsedArgs["reference"]); string maskImage(""); if (parsedArgs.count("mask")) maskImage = us::any_cast(parsedArgs["mask"]); string outRoot = us::any_cast(parsedArgs["out"]); bool verbose = false; if (parsedArgs.count("verbose")) verbose = us::any_cast(parsedArgs["verbose"]); bool ignore = false; if (parsedArgs.count("ignore")) ignore = us::any_cast(parsedArgs["ignore"]); try { typedef itk::Image ItkUcharImgType; typedef itk::Image< itk::Vector< float, 3>, 3 > ItkDirectionImage3DType; typedef itk::VectorContainer< unsigned int, ItkDirectionImage3DType::Pointer > ItkDirectionImageContainerType; typedef itk::EvaluateDirectionImagesFilter< float > EvaluationFilterType; ItkDirectionImageContainerType::Pointer directionImageContainer = ItkDirectionImageContainerType::New(); for (unsigned int i=0; i(mitk::IOUtil::LoadDataNode(testImages.at(i))->GetData()); typedef mitk::ImageToItk< ItkDirectionImage3DType > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(img); caster->Update(); ItkDirectionImage3DType::Pointer itkImg = caster->GetOutput(); directionImageContainer->InsertElement(directionImageContainer->Size(),itkImg); } catch(...){ MITK_INFO << "could not load: " << referenceImages.at(i); } } // load reference directions ItkDirectionImageContainerType::Pointer referenceImageContainer = ItkDirectionImageContainerType::New(); for (unsigned int i=0; i(mitk::IOUtil::LoadDataNode(referenceImages.at(i))->GetData()); typedef mitk::ImageToItk< ItkDirectionImage3DType > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(img); caster->Update(); ItkDirectionImage3DType::Pointer itkImg = caster->GetOutput(); referenceImageContainer->InsertElement(referenceImageContainer->Size(),itkImg); } catch(...){ MITK_INFO << "could not load: " << referenceImages.at(i); } } // load/create mask image ItkUcharImgType::Pointer itkMaskImage = ItkUcharImgType::New(); if (maskImage.compare("")==0) { ItkDirectionImage3DType::Pointer dirImg = referenceImageContainer->GetElement(0); itkMaskImage->SetSpacing( dirImg->GetSpacing() ); itkMaskImage->SetOrigin( dirImg->GetOrigin() ); itkMaskImage->SetDirection( dirImg->GetDirection() ); itkMaskImage->SetLargestPossibleRegion( dirImg->GetLargestPossibleRegion() ); itkMaskImage->SetBufferedRegion( dirImg->GetLargestPossibleRegion() ); itkMaskImage->SetRequestedRegion( dirImg->GetLargestPossibleRegion() ); itkMaskImage->Allocate(); itkMaskImage->FillBuffer(1); } else { mitk::Image::Pointer mitkMaskImage = dynamic_cast(mitk::IOUtil::LoadDataNode(maskImage)->GetData()); mitk::CastToItkImage(mitkMaskImage, itkMaskImage); } // evaluate directions EvaluationFilterType::Pointer evaluationFilter = EvaluationFilterType::New(); evaluationFilter->SetImageSet(directionImageContainer); evaluationFilter->SetReferenceImageSet(referenceImageContainer); evaluationFilter->SetMaskImage(itkMaskImage); evaluationFilter->SetIgnoreMissingDirections(ignore); evaluationFilter->Update(); if (verbose) { EvaluationFilterType::OutputImageType::Pointer angularErrorImage = evaluationFilter->GetOutput(0); typedef itk::ImageFileWriter< EvaluationFilterType::OutputImageType > WriterType; WriterType::Pointer writer = WriterType::New(); string outfilename = outRoot; outfilename.append("_ERROR_IMAGE.nrrd"); MITK_INFO << "writing " << outfilename; writer->SetFileName(outfilename.c_str()); writer->SetInput(angularErrorImage); writer->Update(); } string logFile = outRoot; logFile.append("_ANGULAR_ERROR.csv"); ofstream file; file.open (logFile.c_str()); string sens = "Mean:"; sens.append(","); sens.append(boost::lexical_cast(evaluationFilter->GetMeanAngularError())); sens.append(";\n"); sens.append("Median:"); sens.append(","); sens.append(boost::lexical_cast(evaluationFilter->GetMedianAngularError())); sens.append(";\n"); sens.append("Maximum:"); sens.append(","); sens.append(boost::lexical_cast(evaluationFilter->GetMaxAngularError())); sens.append(";\n"); sens.append("Minimum:"); sens.append(","); sens.append(boost::lexical_cast(evaluationFilter->GetMinAngularError())); sens.append(";\n"); sens.append("STDEV:"); sens.append(","); sens.append(boost::lexical_cast(std::sqrt(evaluationFilter->GetVarAngularError()))); sens.append(";\n"); file << sens; file.close(); MITK_INFO << "DONE"; } 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; } RegisterDiffusionMiniApp(PeaksAngularError); diff --git a/Modules/DiffusionImaging/MiniApps/QballReconstruction.cpp b/Modules/DiffusionImaging/MiniApps/QballReconstruction.cpp index b1994e085c..d0531a20ba 100644 --- a/Modules/DiffusionImaging/MiniApps/QballReconstruction.cpp +++ b/Modules/DiffusionImaging/MiniApps/QballReconstruction.cpp @@ -1,244 +1,244 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "MiniAppManager.h" #include "mitkBaseDataIOFactory.h" #include #include "mitkDiffusionImage.h" #include "itkAnalyticalDiffusionQballReconstructionImageFilter.h" #include #include "ctkCommandLineParser.h" #include #include using namespace mitk; /** * Perform Q-ball reconstruction using a spherical harmonics basis */ int QballReconstruction(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setArgumentPrefix("--", "-"); - parser.addArgument("input", "i", ctkCommandLineParser::File, "Input file", "input raw dwi (.dwi or .fsl/.fslgz)", us::Any(), false); - parser.addArgument("outFile", "o", ctkCommandLineParser::File, "Output file", "output file", us::Any(), false); + parser.addArgument("input", "i", ctkCommandLineParser::InputFile, "Input file", "input raw dwi (.dwi or .fsl/.fslgz)", us::Any(), false); + parser.addArgument("outFile", "o", ctkCommandLineParser::OutputFile, "Output file", "output file", us::Any(), false); parser.addArgument("shOrder", "sh", ctkCommandLineParser::Int, "Spherical harmonics order", "spherical harmonics order", 4, true); parser.addArgument("b0Threshold", "t", ctkCommandLineParser::Int, "b0 threshold", "baseline image intensity threshold", 0, true); parser.addArgument("lambda", "r", ctkCommandLineParser::Float, "Lambda", "ragularization factor lambda", 0.006, true); parser.addArgument("csa", "csa", ctkCommandLineParser::Bool, "Constant solid angle consideration", "use constant solid angle consideration"); parser.addArgument("outputCoeffs", "shc", ctkCommandLineParser::Bool, "Output coefficients", "output file containing the SH coefficients"); parser.addArgument("mrtrix", "mb", ctkCommandLineParser::Bool, "MRtrix", "use MRtrix compatible spherical harmonics definition"); parser.setCategory("Preprocessing Tools"); parser.setTitle("Qball Reconstruction"); parser.setDescription(""); parser.setContributor("MBI"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; std::string inFileName = us::any_cast(parsedArgs["input"]); std::string outfilename = us::any_cast(parsedArgs["outFile"]); outfilename = itksys::SystemTools::GetFilenamePath(outfilename)+"/"+itksys::SystemTools::GetFilenameWithoutExtension(outfilename); int threshold = 0; if (parsedArgs.count("b0Threshold")) threshold = us::any_cast(parsedArgs["b0Threshold"]); int shOrder = 4; if (parsedArgs.count("shOrder")) shOrder = us::any_cast(parsedArgs["shOrder"]); float lambda = 0.006; if (parsedArgs.count("lambda")) lambda = us::any_cast(parsedArgs["lambda"]); int normalization = 0; if (parsedArgs.count("csa") && us::any_cast(parsedArgs["csa"])) normalization = 6; bool outCoeffs = false; if (parsedArgs.count("outputCoeffs")) outCoeffs = us::any_cast(parsedArgs["outputCoeffs"]); bool mrTrix = false; if (parsedArgs.count("mrtrix")) mrTrix = us::any_cast(parsedArgs["mrtrix"]); try { MITK_INFO << "Loading image ..."; const std::string s1="", s2=""; std::vector infile = BaseDataIO::LoadBaseDataFromFile( inFileName, s1, s2, false ); DiffusionImage::Pointer dwi = dynamic_cast*>(infile.at(0).GetPointer()); dwi->AverageRedundantGradients(0.001); mitk::QBallImage::Pointer image = mitk::QBallImage::New(); mitk::Image::Pointer coeffsImage = mitk::Image::New(); MITK_INFO << "SH order: " << shOrder; MITK_INFO << "lambda: " << lambda; MITK_INFO << "B0 threshold: " << threshold; switch ( shOrder ) { case 4: { typedef itk::AnalyticalDiffusionQballReconstructionImageFilter FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() ); filter->SetBValue(dwi->GetReferenceBValue()); filter->SetThreshold( threshold ); filter->SetLambda(lambda); filter->SetUseMrtrixBasis(mrTrix); if (normalization==0) filter->SetNormalizationMethod(FilterType::QBAR_STANDARD); else filter->SetNormalizationMethod(FilterType::QBAR_SOLID_ANGLE); filter->Update(); image->InitializeByItk( filter->GetOutput() ); image->SetVolume( filter->GetOutput()->GetBufferPointer() ); coeffsImage->InitializeByItk( filter->GetCoefficientImage().GetPointer() ); coeffsImage->SetVolume( filter->GetCoefficientImage()->GetBufferPointer() ); break; } case 6: { typedef itk::AnalyticalDiffusionQballReconstructionImageFilter FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() ); filter->SetBValue(dwi->GetReferenceBValue()); filter->SetThreshold( threshold ); filter->SetLambda(lambda); filter->SetUseMrtrixBasis(mrTrix); if (normalization==0) filter->SetNormalizationMethod(FilterType::QBAR_STANDARD); else filter->SetNormalizationMethod(FilterType::QBAR_SOLID_ANGLE); filter->Update(); image->InitializeByItk( filter->GetOutput() ); image->SetVolume( filter->GetOutput()->GetBufferPointer() ); coeffsImage->InitializeByItk( filter->GetCoefficientImage().GetPointer() ); coeffsImage->SetVolume( filter->GetCoefficientImage()->GetBufferPointer() ); break; } case 8: { typedef itk::AnalyticalDiffusionQballReconstructionImageFilter FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() ); filter->SetBValue(dwi->GetReferenceBValue()); filter->SetThreshold( threshold ); filter->SetLambda(lambda); filter->SetUseMrtrixBasis(mrTrix); if (normalization==0) filter->SetNormalizationMethod(FilterType::QBAR_STANDARD); else filter->SetNormalizationMethod(FilterType::QBAR_SOLID_ANGLE); filter->Update(); image->InitializeByItk( filter->GetOutput() ); image->SetVolume( filter->GetOutput()->GetBufferPointer() ); coeffsImage->InitializeByItk( filter->GetCoefficientImage().GetPointer() ); coeffsImage->SetVolume( filter->GetCoefficientImage()->GetBufferPointer() ); break; } case 10: { typedef itk::AnalyticalDiffusionQballReconstructionImageFilter FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() ); filter->SetBValue(dwi->GetReferenceBValue()); filter->SetThreshold( threshold ); filter->SetLambda(lambda); filter->SetUseMrtrixBasis(mrTrix); if (normalization==0) filter->SetNormalizationMethod(FilterType::QBAR_STANDARD); else filter->SetNormalizationMethod(FilterType::QBAR_SOLID_ANGLE); filter->Update(); image->InitializeByItk( filter->GetOutput() ); image->SetVolume( filter->GetOutput()->GetBufferPointer() ); coeffsImage->InitializeByItk( filter->GetCoefficientImage().GetPointer() ); coeffsImage->SetVolume( filter->GetCoefficientImage()->GetBufferPointer() ); break; } case 12: { typedef itk::AnalyticalDiffusionQballReconstructionImageFilter FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() ); filter->SetBValue(dwi->GetReferenceBValue()); filter->SetThreshold( threshold ); filter->SetLambda(lambda); if (normalization==0) filter->SetNormalizationMethod(FilterType::QBAR_STANDARD); else filter->SetNormalizationMethod(FilterType::QBAR_SOLID_ANGLE); filter->Update(); image->InitializeByItk( filter->GetOutput() ); image->SetVolume( filter->GetOutput()->GetBufferPointer() ); coeffsImage->InitializeByItk( filter->GetCoefficientImage().GetPointer() ); coeffsImage->SetVolume( filter->GetCoefficientImage()->GetBufferPointer() ); break; } default: { MITK_INFO << "Supplied SH order not supported. Using default order of 4."; typedef itk::AnalyticalDiffusionQballReconstructionImageFilter FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() ); filter->SetBValue(dwi->GetReferenceBValue()); filter->SetThreshold( threshold ); filter->SetLambda(lambda); filter->SetUseMrtrixBasis(mrTrix); if (normalization==0) filter->SetNormalizationMethod(FilterType::QBAR_STANDARD); else filter->SetNormalizationMethod(FilterType::QBAR_SOLID_ANGLE); filter->Update(); image->InitializeByItk( filter->GetOutput() ); image->SetVolume( filter->GetOutput()->GetBufferPointer() ); coeffsImage->InitializeByItk( filter->GetCoefficientImage().GetPointer() ); coeffsImage->SetVolume( filter->GetCoefficientImage()->GetBufferPointer() ); } } std::string coeffout = outfilename; coeffout += "_shcoeffs.nrrd"; outfilename += ".qbi"; MITK_INFO << "writing image " << outfilename; mitk::IOUtil::SaveBaseData(image, outfilename); if (outCoeffs) mitk::IOUtil::SaveImage(coeffsImage, coeffout); } catch ( itk::ExceptionObject &err) { MITK_INFO << "Exception: " << err; } catch ( std::exception err) { MITK_INFO << "Exception: " << err.what(); } catch ( ... ) { MITK_INFO << "Exception!"; } return EXIT_SUCCESS; } RegisterDiffusionMiniApp(QballReconstruction); diff --git a/Modules/DiffusionImaging/MiniApps/StreamlineTracking.cpp b/Modules/DiffusionImaging/MiniApps/StreamlineTracking.cpp index 2605d62b90..61d3f78b2f 100755 --- a/Modules/DiffusionImaging/MiniApps/StreamlineTracking.cpp +++ b/Modules/DiffusionImaging/MiniApps/StreamlineTracking.cpp @@ -1,187 +1,187 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "MiniAppManager.h" #include #include #include #include #include #include #include #include "ctkCommandLineParser.h" #include #include int StreamlineTracking(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setArgumentPrefix("--", "-"); parser.addArgument("input", "i", ctkCommandLineParser::StringList, "Input image", "input tensor image (.dti)", us::Any(), false); - parser.addArgument("seed", "si", ctkCommandLineParser::File, "Seed image", "binary seed image", us::Any(), true); - parser.addArgument("mask", "mi", ctkCommandLineParser::File, "Mask", "binary mask image", us::Any(), true); - parser.addArgument("faImage", "fai", ctkCommandLineParser::File, "FA image", "FA image", us::Any(), true); + parser.addArgument("seed", "si", ctkCommandLineParser::InputFile, "Seed image", "binary seed image", us::Any(), true); + parser.addArgument("mask", "mi", ctkCommandLineParser::InputFile, "Mask", "binary mask image", us::Any(), true); + parser.addArgument("faImage", "fai", ctkCommandLineParser::InputFile, "FA image", "FA image", us::Any(), true); parser.addArgument("minFA", "fa", ctkCommandLineParser::Float, "Min. FA threshold", "minimum fractional anisotropy threshold", 0.15, true); parser.addArgument("minCurv", "c", ctkCommandLineParser::Float, "Min. curvature radius", "minimum curvature radius in mm (default = 0.5*minimum-spacing)"); parser.addArgument("stepSize", "s", ctkCommandLineParser::Float, "Step size", "step size in mm (default = 0.1*minimum-spacing)"); parser.addArgument("tendf", "f", ctkCommandLineParser::Float, "Weight f", "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, "Weight g", "Weighting factor between input vector (g=0) and tensor deflection (g=1 equals TEND tracking)", 0.0, true); parser.addArgument("numSeeds", "n", ctkCommandLineParser::Int, "Seeds per voxel", "Number of seeds per voxel.", 1, true); parser.addArgument("minLength", "l", ctkCommandLineParser::Float, "Min. fiber length", "minimum fiber length in mm", 20, true); parser.addArgument("interpolate", "ip", ctkCommandLineParser::Bool, "Interpolate", "Use linear interpolation", false, true); parser.addArgument("outFile", "o", ctkCommandLineParser::String, "Output file", "output fiber bundle (.fib)", us::Any(), false); parser.setCategory("Fiber Tracking and Processing Methods"); parser.setTitle("Streamline Tracking"); parser.setDescription(""); parser.setContributor("MBI"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; ctkCommandLineParser::StringContainerType inputImages = us::any_cast(parsedArgs["input"]); string dtiFileName; string outFileName = us::any_cast(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(parsedArgs["minCurv"]); if (parsedArgs.count("minFA")) minFA = us::any_cast(parsedArgs["minFA"]); if (parsedArgs.count("stepSize")) stepSize = us::any_cast(parsedArgs["stepSize"]); if (parsedArgs.count("tendf")) tendf = us::any_cast(parsedArgs["tendf"]); if (parsedArgs.count("tendg")) tendg = us::any_cast(parsedArgs["tendg"]); if (parsedArgs.count("minLength")) minLength = us::any_cast(parsedArgs["minLength"]); if (parsedArgs.count("numSeeds")) numSeeds = us::any_cast(parsedArgs["numSeeds"]); if (parsedArgs.count("interpolate")) interpolate = us::any_cast(parsedArgs["interpolate"]); try { typedef itk::StreamlineTrackingFilter< float > FilterType; FilterType::Pointer filter = FilterType::New(); mitk::Image::Pointer mitkImage = NULL; MITK_INFO << "Loading tensor images ..."; typedef itk::Image< itk::DiffusionTensor3D, 3 > ItkTensorImage; dtiFileName = inputImages.at(0); for (unsigned int i=0; i(mitk::IOUtil::LoadDataNode(inputImages.at(i))->GetData()); mitk::TensorImage::Pointer img = dynamic_cast(mitk::IOUtil::LoadDataNode(inputImages.at(i))->GetData()); ItkTensorImage::Pointer itk_dti = ItkTensorImage::New(); mitk::CastToItkImage(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(parsedArgs["seed"])); MITK_INFO << "Loading mask image ..."; mitk::Image::Pointer mitkMaskImage = NULL; if (parsedArgs.count("mask")) mitkMaskImage = mitk::IOUtil::LoadImage(us::any_cast(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(mitkSeedImage, mask); filter->SetSeedImage(mask); } if (mitkMaskImage.IsNotNull()) { ItkUCharImageType::Pointer mask = ItkUCharImageType::New(); mitk::CastToItkImage(mitkMaskImage, mask); filter->SetMaskImage(mask); } filter->Update(); vtkSmartPointer 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); fib->SetReferenceImage(mitkImage); 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; } RegisterDiffusionMiniApp(StreamlineTracking); diff --git a/Modules/DiffusionImaging/MiniApps/TensorDerivedMapsExtraction.cpp b/Modules/DiffusionImaging/MiniApps/TensorDerivedMapsExtraction.cpp index 77aec36383..ba06963c47 100644 --- a/Modules/DiffusionImaging/MiniApps/TensorDerivedMapsExtraction.cpp +++ b/Modules/DiffusionImaging/MiniApps/TensorDerivedMapsExtraction.cpp @@ -1,195 +1,195 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "MiniAppManager.h" #include #include "mitkImage.h" #include #include "mitkITKImageImport.h" #include #include #include #include #include "itkTensorDerivedMeasurementsFilter.h" #include "itkDiffusionTensor3DReconstructionImageFilter.h" #include "ctkCommandLineParser.h" #include #include #include typedef short DiffusionPixelType; typedef double TTensorPixelType; static void ExtractMapsAndSave(mitk::TensorImage::Pointer tensorImage, std::string filename, std::string postfix = "") { mitk::Image* image = dynamic_cast (tensorImage.GetPointer()); typedef itk::DiffusionTensor3D< TTensorPixelType > TensorPixelType; typedef itk::Image< TensorPixelType, 3 > TensorImageType; TensorImageType::Pointer itkvol = TensorImageType::New(); mitk::CastToItkImage(image, itkvol); typedef itk::TensorDerivedMeasurementsFilter MeasurementsType; MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New(); measurementsCalculator->SetInput(itkvol.GetPointer() ); mitk::Image::Pointer map = mitk::Image::New(); // FA measurementsCalculator->SetMeasure(MeasurementsType::FA); measurementsCalculator->Update(); map->InitializeByItk( measurementsCalculator->GetOutput() ); map->SetVolume( measurementsCalculator->GetOutput()->GetBufferPointer() ); mitk::IOUtil::SaveImage(map, filename + "_dti_FA" + postfix + ".nrrd"); // MD measurementsCalculator->SetMeasure(MeasurementsType::MD); measurementsCalculator->Update(); map->InitializeByItk( measurementsCalculator->GetOutput() ); map->SetVolume( measurementsCalculator->GetOutput()->GetBufferPointer() ); mitk::IOUtil::SaveImage(map, filename + "_dti_MD" + postfix + ".nrrd"); // AD measurementsCalculator->SetMeasure(MeasurementsType::AD); measurementsCalculator->Update(); map->InitializeByItk( measurementsCalculator->GetOutput() ); map->SetVolume( measurementsCalculator->GetOutput()->GetBufferPointer() ); mitk::IOUtil::SaveImage(map, filename + "_dti_AD" + postfix + ".nrrd"); // CA measurementsCalculator->SetMeasure(MeasurementsType::CA); measurementsCalculator->Update(); map->InitializeByItk( measurementsCalculator->GetOutput() ); map->SetVolume( measurementsCalculator->GetOutput()->GetBufferPointer() ); mitk::IOUtil::SaveImage(map, filename + "_dti_CA" + postfix + ".nrrd"); // RA measurementsCalculator->SetMeasure(MeasurementsType::RA); measurementsCalculator->Update(); map->InitializeByItk( measurementsCalculator->GetOutput() ); map->SetVolume( measurementsCalculator->GetOutput()->GetBufferPointer() ); mitk::IOUtil::SaveImage(map, filename + "_dti_RA" + postfix + ".nrrd"); // RD measurementsCalculator->SetMeasure(MeasurementsType::RD); measurementsCalculator->Update(); map->InitializeByItk( measurementsCalculator->GetOutput() ); map->SetVolume( measurementsCalculator->GetOutput()->GetBufferPointer() ); mitk::IOUtil::SaveImage(map, filename + "_dti_RD" + postfix + ".nrrd"); } int TensorDerivedMapsExtraction(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setArgumentPrefix("--", "-"); parser.addArgument("help", "h", ctkCommandLineParser::String, "Help", "Show this help text"); - parser.addArgument("input", "i", ctkCommandLineParser::File, "Input file", "input dwi file", us::Any(),false); + parser.addArgument("input", "i", ctkCommandLineParser::InputFile, "Input file", "input dwi file", us::Any(),false); parser.addArgument("out", "o", ctkCommandLineParser::String, "Output folder", "output folder and base name, e.g. /tmp/outPatient1 ", us::Any(),false); parser.setCategory("Diffusion Related Measures"); parser.setTitle("Tensor Derived Maps Extraction"); parser.setDescription(""); parser.setContributor("MBI"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0 || parsedArgs.count("help") || parsedArgs.count("h")) { std::cout << "\n\nMiniApp Description: \nPerforms tensor reconstruction on DWI file," << endl; std::cout << "and computes tensor derived measures." << endl; std::cout << "\n\n For out parameter /tmp/outPatient1 it will produce :"<< endl; std::cout << " /tmp/outPatient1_dti.dti , /tmp/outPatient1_dti_FA.nrrd, ..."<< endl; std::cout << "\n\n Parameters:"<< endl; std::cout << parser.helpText(); return EXIT_SUCCESS; } std::string inputFile = us::any_cast(parsedArgs["input"]); std::string baseFileName = us::any_cast(parsedArgs["out"]); std::string dtiFileName = "_dti.dti"; MITK_INFO << "BaseFileName: " << baseFileName; mitk::Image::Pointer inputImage = mitk::IOUtil::LoadImage(inputFile); mitk::DiffusionImage* diffusionImage = static_cast*>(inputImage.GetPointer()); if (diffusionImage == NULL) // does NULL pointer check make sense after static cast ? { MITK_ERROR << "Invalid Input Image. Must be DWI. Aborting."; return -1; } mitk::DiffusionImage* vols = dynamic_cast *> (inputImage.GetPointer()); typedef itk::DiffusionTensor3DReconstructionImageFilter< DiffusionPixelType, DiffusionPixelType, TTensorPixelType > TensorReconstructionImageFilterType; TensorReconstructionImageFilterType::Pointer tensorReconstructionFilter = TensorReconstructionImageFilterType::New(); typedef mitk::DiffusionImage DiffusionImageType; typedef DiffusionImageType::GradientDirectionContainerType GradientDirectionContainerType; GradientDirectionContainerType::Pointer gradientContainerCopy = GradientDirectionContainerType::New(); for(GradientDirectionContainerType::ConstIterator it = vols->GetDirections()->Begin(); it != vols->GetDirections()->End(); it++) { gradientContainerCopy->push_back(it.Value()); } tensorReconstructionFilter->SetGradientImage( gradientContainerCopy, vols->GetVectorImage() ); tensorReconstructionFilter->SetBValue(vols->GetReferenceBValue()); tensorReconstructionFilter->SetThreshold(50); tensorReconstructionFilter->Update(); typedef itk::Image, 3> TensorImageType; TensorImageType::Pointer tensorImage = tensorReconstructionFilter->GetOutput(); tensorImage->SetDirection( vols->GetVectorImage()->GetDirection() ); mitk::TensorImage::Pointer tensorImageMitk = mitk::TensorImage::New(); tensorImageMitk->InitializeByItk(tensorImage.GetPointer()); tensorImageMitk->SetVolume( tensorImage->GetBufferPointer() ); itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New(); io->SetFileType( itk::ImageIOBase::Binary ); io->UseCompressionOn(); itk::ImageFileWriter< itk::Image< itk::DiffusionTensor3D< double >, 3 > >::Pointer writer = itk::ImageFileWriter< itk::Image< itk::DiffusionTensor3D< double >, 3 > >::New(); writer->SetInput(tensorReconstructionFilter->GetOutput()); writer->SetFileName(baseFileName + dtiFileName); writer->SetImageIO(io); writer->UseCompressionOn(); writer->Update(); ExtractMapsAndSave(tensorImageMitk,baseFileName); return EXIT_SUCCESS; } RegisterDiffusionMiniApp(TensorDerivedMapsExtraction); diff --git a/Modules/DiffusionImaging/MiniApps/TensorReconstruction.cpp b/Modules/DiffusionImaging/MiniApps/TensorReconstruction.cpp index a9111bc8d5..446bcb6dfa 100644 --- a/Modules/DiffusionImaging/MiniApps/TensorReconstruction.cpp +++ b/Modules/DiffusionImaging/MiniApps/TensorReconstruction.cpp @@ -1,102 +1,102 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "MiniAppManager.h" #include "mitkBaseDataIOFactory.h" #include "mitkDiffusionImage.h" #include "mitkBaseData.h" #include #include #include #include #include "ctkCommandLineParser.h" #include using namespace mitk; /** * Convert files from one ending to the other */ int TensorReconstruction(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setArgumentPrefix("--", "-"); - parser.addArgument("input", "i", ctkCommandLineParser::File, "Input file", "input raw dwi (.dwi or .fsl/.fslgz)", us::Any(), false); - parser.addArgument("outFile", "o", ctkCommandLineParser::File, "Output file", "output file", us::Any(), false); + parser.addArgument("input", "i", ctkCommandLineParser::InputFile, "Input file", "input raw dwi (.dwi or .fsl/.fslgz)", us::Any(), false); + parser.addArgument("outFile", "o", ctkCommandLineParser::OutputFile, "Output file", "output file", us::Any(), false); parser.addArgument("b0Threshold", "t", ctkCommandLineParser::Int, "b0 threshold", "baseline image intensity threshold", 0, true); parser.setCategory("Preprocessing Tools"); parser.setTitle("Tensor Reconstruction"); parser.setDescription(""); parser.setContributor("MBI"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; std::string inFileName = us::any_cast(parsedArgs["input"]); std::string outfilename = us::any_cast(parsedArgs["outFile"]); outfilename = itksys::SystemTools::GetFilenamePath(outfilename)+"/"+itksys::SystemTools::GetFilenameWithoutExtension(outfilename); outfilename += ".dti"; int threshold = 0; if (parsedArgs.count("b0Threshold")) threshold = us::any_cast(parsedArgs["b0Threshold"]); try { MITK_INFO << "Loading image ..."; const std::string s1="", s2=""; std::vector infile = BaseDataIO::LoadBaseDataFromFile( inFileName, s1, s2, false ); DiffusionImage::Pointer dwi = dynamic_cast*>(infile.at(0).GetPointer()); MITK_INFO << "B0 threshold: " << threshold; typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, float > TensorReconstructionImageFilterType; TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New(); filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() ); filter->SetBValue(dwi->GetReferenceBValue()); filter->SetThreshold(threshold); filter->Update(); // Save tensor image MITK_INFO << "writing image " << outfilename; itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New(); io->SetFileType( itk::ImageIOBase::Binary ); io->UseCompressionOn(); itk::ImageFileWriter< itk::Image< itk::DiffusionTensor3D< float >, 3 > >::Pointer writer = itk::ImageFileWriter< itk::Image< itk::DiffusionTensor3D< float >, 3 > >::New(); writer->SetInput(filter->GetOutput()); writer->SetFileName(outfilename); writer->SetImageIO(io); writer->UseCompressionOn(); writer->Update(); } catch ( itk::ExceptionObject &err) { MITK_INFO << "Exception: " << err; } catch ( std::exception err) { MITK_INFO << "Exception: " << err.what(); } catch ( ... ) { MITK_INFO << "Exception!"; } return EXIT_SUCCESS; } RegisterDiffusionMiniApp(TensorReconstruction); diff --git a/Modules/DiffusionImaging/MiniApps/ctkCommandLineParser.cpp b/Modules/DiffusionImaging/MiniApps/ctkCommandLineParser.cpp index 721e07c08e..dc3637c135 100755 --- a/Modules/DiffusionImaging/MiniApps/ctkCommandLineParser.cpp +++ b/Modules/DiffusionImaging/MiniApps/ctkCommandLineParser.cpp @@ -1,845 +1,881 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ /*========================================================================= Library: CTK Copyright (c) Kitware Inc. Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0.txt Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. =========================================================================*/ // STL includes #include // CTK includes #include "ctkCommandLineParser.h" using namespace std; namespace { // -------------------------------------------------------------------------- class CommandLineParserArgumentDescription { public: CommandLineParserArgumentDescription( const string& longArg, const string& longArgPrefix, const string& shortArg, const string& shortArgPrefix, ctkCommandLineParser::Type type, const string& argHelp, const string& argLabel, const us::Any& defaultValue, bool ignoreRest, - bool deprecated, bool optional) + bool deprecated, bool optional, string& argGroup, string& groupDescription) : LongArg(longArg), LongArgPrefix(longArgPrefix), ShortArg(shortArg), ShortArgPrefix(shortArgPrefix), ArgHelp(argHelp), ArgLabel(argLabel), IgnoreRest(ignoreRest), NumberOfParametersToProcess(0), - Deprecated(deprecated), DefaultValue(defaultValue), Value(type), ValueType(type), Optional(optional) + Deprecated(deprecated), DefaultValue(defaultValue), Value(type), ValueType(type), Optional(optional), ArgGroup(argGroup), ArgGroupDescription(groupDescription) { Value = defaultValue; switch (type) { case ctkCommandLineParser::String: { NumberOfParametersToProcess = 1; } break; case ctkCommandLineParser::Bool: { NumberOfParametersToProcess = 0; } break; case ctkCommandLineParser::StringList: { NumberOfParametersToProcess = -1; } break; case ctkCommandLineParser::Int: { NumberOfParametersToProcess = 1; } break; case ctkCommandLineParser::Float: { NumberOfParametersToProcess = 1; } break; - case ctkCommandLineParser::Directory: + case ctkCommandLineParser::OutputDirectory: + case ctkCommandLineParser::InputDirectory: { NumberOfParametersToProcess = 1; } break; - case ctkCommandLineParser::File: + + case ctkCommandLineParser::OutputFile: + case ctkCommandLineParser::InputFile: { NumberOfParametersToProcess = 1; } break; default: MITK_INFO << "Type not supported: " << static_cast(type); } } ~CommandLineParserArgumentDescription(){} bool addParameter(const string& value); string helpText(); string LongArg; string LongArgPrefix; string ShortArg; string ShortArgPrefix; string ArgHelp; string ArgLabel; + string ArgGroup; + string ArgGroupDescription; bool IgnoreRest; int NumberOfParametersToProcess; bool Deprecated; bool Optional; us::Any DefaultValue; us::Any Value; ctkCommandLineParser::Type ValueType; }; // -------------------------------------------------------------------------- bool CommandLineParserArgumentDescription::addParameter(const string &value) { switch (ValueType) { case ctkCommandLineParser::String: { Value = value; } break; case ctkCommandLineParser::Bool: { if (value.compare("true")==0) Value = true; else Value = false; } break; case ctkCommandLineParser::StringList: { try { ctkCommandLineParser::StringContainerType list = us::any_cast(Value); list.push_back(value); Value = list; } catch(...) { ctkCommandLineParser::StringContainerType list; list.push_back(value); Value = list; } } break; case ctkCommandLineParser::Int: { stringstream ss(value); int i; ss >> i; Value = i; } break; case ctkCommandLineParser::Float: { stringstream ss(value); float f; ss >> f; Value = f; } break; - case ctkCommandLineParser::Directory: + case ctkCommandLineParser::InputDirectory: + case ctkCommandLineParser::OutputDirectory: { Value = value; } break; - case ctkCommandLineParser::File: + case ctkCommandLineParser::InputFile: + case ctkCommandLineParser::OutputFile: { Value = value; } break; default: return false; } return true; } // -------------------------------------------------------------------------- string CommandLineParserArgumentDescription::helpText() { string text; string shortAndLongArg; if (!this->ShortArg.empty()) { shortAndLongArg = " "; shortAndLongArg += this->ShortArgPrefix; shortAndLongArg += this->ShortArg; } if (!this->LongArg.empty()) { if (this->ShortArg.empty()) shortAndLongArg.append(" "); else shortAndLongArg.append(", "); shortAndLongArg += this->LongArgPrefix; shortAndLongArg += this->LongArg; } text = text + shortAndLongArg + ", " + this->ArgHelp; if (this->Optional) text += " (optional)"; if (!this->DefaultValue.Empty()) { text = text + ", (default: " + this->DefaultValue.ToString() + ")"; } text += "\n"; return text; } } // -------------------------------------------------------------------------- // ctkCommandLineParser::ctkInternal class // -------------------------------------------------------------------------- class ctkCommandLineParser::ctkInternal { public: ctkInternal() : Debug(false), FieldWidth(0), StrictMode(false) {} ~ctkInternal() { } CommandLineParserArgumentDescription* argumentDescription(const string& argument); vector ArgumentDescriptionList; map ArgNameToArgumentDescriptionMap; map > GroupToArgumentDescriptionListMap; StringContainerType UnparsedArguments; StringContainerType ProcessedArguments; string ErrorString; bool Debug; int FieldWidth; string LongPrefix; string ShortPrefix; string CurrentGroup; string DisableQSettingsLongArg; string DisableQSettingsShortArg; bool StrictMode; }; // -------------------------------------------------------------------------- // ctkCommandLineParser::ctkInternal methods // -------------------------------------------------------------------------- CommandLineParserArgumentDescription* ctkCommandLineParser::ctkInternal::argumentDescription(const string& argument) { string unprefixedArg = argument; if (!LongPrefix.empty() && argument.compare(0, LongPrefix.size(), LongPrefix)==0) { // Case when (ShortPrefix + UnPrefixedArgument) matches LongPrefix if (argument == LongPrefix && !ShortPrefix.empty() && argument.compare(0, ShortPrefix.size(), ShortPrefix)==0) { unprefixedArg = argument.substr(ShortPrefix.size(),argument.size()); } else { unprefixedArg = argument.substr(LongPrefix.size(),argument.size()); } } else if (!ShortPrefix.empty() && argument.compare(0, ShortPrefix.size(), ShortPrefix)==0) { unprefixedArg = argument.substr(ShortPrefix.size(),argument.size()); } else if (!LongPrefix.empty() && !ShortPrefix.empty()) { return 0; } if (ArgNameToArgumentDescriptionMap.count(unprefixedArg)) { return this->ArgNameToArgumentDescriptionMap[unprefixedArg]; } return 0; } // -------------------------------------------------------------------------- // ctkCommandLineParser methods // -------------------------------------------------------------------------- ctkCommandLineParser::ctkCommandLineParser() { this->Internal = new ctkInternal(); this->Category = string(); this->Title = string(); this->Contributor = string(); this->Description = string(); + this->ParameterGroupName = "Parameters"; + this->ParameterGroupDescription = "Groupbox containing parameters."; } // -------------------------------------------------------------------------- ctkCommandLineParser::~ctkCommandLineParser() { delete this->Internal; } // -------------------------------------------------------------------------- map ctkCommandLineParser::parseArguments(const StringContainerType& arguments, bool* ok) { // Reset this->Internal->UnparsedArguments.clear(); this->Internal->ProcessedArguments.clear(); this->Internal->ErrorString.clear(); // foreach (CommandLineParserArgumentDescription* desc, this->Internal->ArgumentDescriptionList) for (unsigned int i=0; iArgumentDescriptionList.size(); i++) { CommandLineParserArgumentDescription* desc = Internal->ArgumentDescriptionList.at(i); desc->Value = us::Any(desc->ValueType); if (!desc->DefaultValue.Empty()) { desc->Value = desc->DefaultValue; } } bool error = false; bool ignoreRest = false; CommandLineParserArgumentDescription * currentArgDesc = 0; vector parsedArgDescriptions; for(unsigned int i = 1; i < arguments.size(); ++i) { string argument = arguments.at(i); if (this->Internal->Debug) { MITK_DEBUG << "Processing" << argument; } if (!argument.compare("--xml") || !argument.compare("-xml") || !argument.compare("--XML") || !argument.compare("-XML")) { - this->GetXML("lala", "lalalalalalalalalalalalalalalla"); + this->GetXML(); return map(); } // should argument be ignored ? if (ignoreRest) { if (this->Internal->Debug) { MITK_DEBUG << " Skipping: IgnoreRest flag was been set"; } this->Internal->UnparsedArguments.push_back(argument); continue; } // Skip if the argument does not start with the defined prefix if (!(argument.compare(0, Internal->LongPrefix.size(), Internal->LongPrefix)==0 || argument.compare(0, Internal->ShortPrefix.size(), Internal->ShortPrefix)==0)) { if (this->Internal->StrictMode) { this->Internal->ErrorString = "Unknown argument "; this->Internal->ErrorString += argument; error = true; break; } if (this->Internal->Debug) { MITK_DEBUG << " Skipping: It does not start with the defined prefix"; } this->Internal->UnparsedArguments.push_back(argument); continue; } // Skip if argument has already been parsed ... bool alreadyProcessed = false; for (unsigned int i=0; iProcessedArguments.size(); i++) if (argument.compare(Internal->ProcessedArguments.at(i))==0) { alreadyProcessed = true; break; } if (alreadyProcessed) { if (this->Internal->StrictMode) { this->Internal->ErrorString = "Argument "; this->Internal->ErrorString += argument; this->Internal->ErrorString += " already processed !"; error = true; break; } if (this->Internal->Debug) { MITK_DEBUG << " Skipping: Already processed !"; } continue; } // Retrieve corresponding argument description currentArgDesc = this->Internal->argumentDescription(argument); // Is there a corresponding argument description ? if (currentArgDesc) { // If the argument is deprecated, print the help text but continue processing if (currentArgDesc->Deprecated) { MITK_WARN << "Deprecated argument " << argument << ": " << currentArgDesc->ArgHelp; } else { parsedArgDescriptions.push_back(currentArgDesc); } this->Internal->ProcessedArguments.push_back(currentArgDesc->ShortArg); this->Internal->ProcessedArguments.push_back(currentArgDesc->LongArg); int numberOfParametersToProcess = currentArgDesc->NumberOfParametersToProcess; ignoreRest = currentArgDesc->IgnoreRest; if (this->Internal->Debug && ignoreRest) { MITK_DEBUG << " IgnoreRest flag is True"; } // Is the number of parameters associated with the argument being processed known ? if (numberOfParametersToProcess == 0) { currentArgDesc->addParameter("true"); } else if (numberOfParametersToProcess > 0) { string missingParameterError = "Argument %1 has %2 value(s) associated whereas exacly %3 are expected."; for(int j=1; j <= numberOfParametersToProcess; ++j) { if (i + j >= arguments.size()) { // this->Internal->ErrorString = // missingParameterError.arg(argument).arg(j-1).arg(numberOfParametersToProcess); // if (this->Internal->Debug) { MITK_DEBUG << this->Internal->ErrorString; } if (ok) { *ok = false; } return map(); } string parameter = arguments.at(i + j); if (this->Internal->Debug) { MITK_DEBUG << " Processing parameter" << j << ", value:" << parameter; } if (this->argumentAdded(parameter)) { // this->Internal->ErrorString = // missingParameterError.arg(argument).arg(j-1).arg(numberOfParametersToProcess); // if (this->Internal->Debug) { MITK_DEBUG << this->Internal->ErrorString; } if (ok) { *ok = false; } return map(); } if (!currentArgDesc->addParameter(parameter)) { // this->Internal->ErrorString = string( // "Value(s) associated with argument %1 are incorrect. %2"). // arg(argument).arg(currentArgDesc->ExactMatchFailedMessage); // if (this->Internal->Debug) { MITK_DEBUG << this->Internal->ErrorString; } if (ok) { *ok = false; } return map(); } } // Update main loop increment i = i + numberOfParametersToProcess; } else if (numberOfParametersToProcess == -1) { if (this->Internal->Debug) { MITK_DEBUG << " Proccessing StringList ..."; } int j = 1; while(j + i < arguments.size()) { if (this->argumentAdded(arguments.at(j + i))) { if (this->Internal->Debug) { MITK_DEBUG << " No more parameter for" << argument; } break; } string parameter = arguments.at(j + i); if (parameter.compare(0, Internal->LongPrefix.size(), Internal->LongPrefix)==0 || parameter.compare(0, Internal->ShortPrefix.size(), Internal->ShortPrefix)==0) { j--; break; } if (this->Internal->Debug) { MITK_DEBUG << " Processing parameter" << j << ", value:" << parameter; } if (!currentArgDesc->addParameter(parameter)) { // this->Internal->ErrorString = string( // "Value(s) associated with argument %1 are incorrect. %2"). // arg(argument).arg(currentArgDesc->ExactMatchFailedMessage); // if (this->Internal->Debug) { MITK_DEBUG << this->Internal->ErrorString; } if (ok) { *ok = false; } return map(); } j++; } // Update main loop increment i = i + j; } } else { if (this->Internal->StrictMode) { this->Internal->ErrorString = "Unknown argument "; this->Internal->ErrorString += argument; error = true; break; } if (this->Internal->Debug) { MITK_DEBUG << " Skipping: Unknown argument"; } this->Internal->UnparsedArguments.push_back(argument); } } if (ok) { *ok = !error; } map parsedArguments; int obligatoryArgs = 0; vector::iterator it; for(it = Internal->ArgumentDescriptionList.begin(); it != Internal->ArgumentDescriptionList.end();++it) { CommandLineParserArgumentDescription* desc = *it; if(!desc->Optional) obligatoryArgs++; } int parsedObligatoryArgs = 0; for(it = parsedArgDescriptions.begin(); it != parsedArgDescriptions.end();++it) { CommandLineParserArgumentDescription* desc = *it; string key; if (!desc->LongArg.empty()) { key = desc->LongArg; } else { key = desc->ShortArg; } if(!desc->Optional) parsedObligatoryArgs++; std::pair elem; elem.first = key; elem.second = desc->Value; parsedArguments.insert(elem); } if (obligatoryArgs>parsedObligatoryArgs) { parsedArguments.clear(); cout << helpText(); } return parsedArguments; } // ------------------------------------------------------------------------- map ctkCommandLineParser::parseArguments(int argc, char** argv, bool* ok) { StringContainerType arguments; // Create a StringContainerType of arguments for(int i = 0; i < argc; ++i) arguments.push_back(argv[i]); return this->parseArguments(arguments, ok); } // ------------------------------------------------------------------------- string ctkCommandLineParser::errorString() const { return this->Internal->ErrorString; } // ------------------------------------------------------------------------- const ctkCommandLineParser::StringContainerType& ctkCommandLineParser::unparsedArguments() const { return this->Internal->UnparsedArguments; } // -------------------------------------------------------------------------- void ctkCommandLineParser::addArgument(const string& longarg, const string& shortarg, Type type, const string& argLabel, const string& argHelp, const us::Any& defaultValue, bool optional, bool ignoreRest, bool deprecated) { if (longarg.empty() && shortarg.empty()) { return; } /* Make sure it's not already added */ bool added = this->Internal->ArgNameToArgumentDescriptionMap.count(longarg); if (added) { return; } added = this->Internal->ArgNameToArgumentDescriptionMap.count(shortarg); if (added) { return; } CommandLineParserArgumentDescription* argDesc = new CommandLineParserArgumentDescription(longarg, this->Internal->LongPrefix, shortarg, this->Internal->ShortPrefix, type, - argHelp, argLabel, defaultValue, ignoreRest, deprecated, optional); + argHelp, argLabel, defaultValue, ignoreRest, deprecated, optional, ParameterGroupName, ParameterGroupDescription); int argWidth = 0; if (!longarg.empty()) { this->Internal->ArgNameToArgumentDescriptionMap[longarg] = argDesc; argWidth += longarg.size() + this->Internal->LongPrefix.size(); } if (!shortarg.empty()) { this->Internal->ArgNameToArgumentDescriptionMap[shortarg] = argDesc; argWidth += shortarg.size() + this->Internal->ShortPrefix.size() + 2; } argWidth += 5; // Set the field width for the arguments if (argWidth > this->Internal->FieldWidth) { this->Internal->FieldWidth = argWidth; } this->Internal->ArgumentDescriptionList.push_back(argDesc); this->Internal->GroupToArgumentDescriptionListMap[this->Internal->CurrentGroup].push_back(argDesc); } // -------------------------------------------------------------------------- void ctkCommandLineParser::addDeprecatedArgument( const string& longarg, const string& shortarg, const string& argLabel, const string& argHelp) { addArgument(longarg, shortarg, StringList, argLabel, argHelp, us::Any(), false, true, false); } // -------------------------------------------------------------------------- int ctkCommandLineParser::fieldWidth() const { return this->Internal->FieldWidth; } // -------------------------------------------------------------------------- void ctkCommandLineParser::beginGroup(const string& description) { this->Internal->CurrentGroup = description; } // -------------------------------------------------------------------------- void ctkCommandLineParser::endGroup() { this->Internal->CurrentGroup.clear(); } // -------------------------------------------------------------------------- string ctkCommandLineParser::helpText() const { string text; vector deprecatedArgs; // Loop over grouped argument descriptions map >::iterator it; for(it = Internal->GroupToArgumentDescriptionListMap.begin(); it != Internal->GroupToArgumentDescriptionListMap.end();++it) { if (!(*it).first.empty()) { text = text + "\n" + (*it).first + "\n"; } vector::iterator it2; for(it2 = (*it).second.begin(); it2 != (*it).second.end(); ++it2) { CommandLineParserArgumentDescription* argDesc = *it2; if (argDesc->Deprecated) { deprecatedArgs.push_back(argDesc); } else { text += argDesc->helpText(); } } } if (!deprecatedArgs.empty()) { text += "\nDeprecated arguments:\n"; vector::iterator it2; for(it2 = deprecatedArgs.begin(); it2 != deprecatedArgs.end(); ++it2) { CommandLineParserArgumentDescription* argDesc = *it2; text += argDesc->helpText(); } } return text; } // -------------------------------------------------------------------------- bool ctkCommandLineParser::argumentAdded(const string& argument) const { return this->Internal->ArgNameToArgumentDescriptionMap.count(argument); } // -------------------------------------------------------------------------- bool ctkCommandLineParser::argumentParsed(const string& argument) const { for (unsigned int i=0; iProcessedArguments.size(); i++) if (argument.compare(Internal->ProcessedArguments.at(i))==0) return true; return false; } // -------------------------------------------------------------------------- void ctkCommandLineParser::setArgumentPrefix(const string& longPrefix, const string& shortPrefix) { this->Internal->LongPrefix = longPrefix; this->Internal->ShortPrefix = shortPrefix; } // -------------------------------------------------------------------------- void ctkCommandLineParser::setStrictModeEnabled(bool strictMode) { this->Internal->StrictMode = strictMode; } -void ctkCommandLineParser::GetXML(std::string title, std::string description) +void ctkCommandLineParser::GetXML() { std::stringstream xml; xml << "" << endl; xml << "" << Category << "" << endl; xml << "" << Title <<"" << endl; xml << "" << Description << "" << endl; xml << "" << Contributor << "" << endl; xml << "" << endl; - //TODO: nicht hard coded!! - xml << "" << endl; - xml << "TestTest" << endl; - - std::vector::iterator it; + + std::string lastParameterGroup = ""; for (it = this->Internal->ArgumentDescriptionList.begin(); it != this->Internal->ArgumentDescriptionList.end(); it++) { std::string type; switch ((*it)->ValueType) { case ctkCommandLineParser::String: type = "string"; break; case ctkCommandLineParser::Bool: type = "boolean"; break; case ctkCommandLineParser::StringList: type = "string-vector"; break; case ctkCommandLineParser::Int: type = "integer"; break; case ctkCommandLineParser::Float: type = "float"; break; - case ctkCommandLineParser::Directory: + case ctkCommandLineParser::OutputDirectory: + case ctkCommandLineParser::InputDirectory: type = "directory"; break; - case ctkCommandLineParser::File: + case ctkCommandLineParser::OutputFile: + case ctkCommandLineParser::InputFile: type = "file"; break; } + if (lastParameterGroup.compare((*it)->ArgGroup)) + { + if (it != this->Internal->ArgumentDescriptionList.begin()) + { + xml << "" << endl; + xml << "" << endl; + } + xml << "" << endl; + xml << "" << (*it)->ArgGroupDescription << "" << endl; + lastParameterGroup = (*it)->ArgGroup; + } + xml << "<" << type << ">" << endl; + xml << "" << (*it)->LongArg << "" << endl; xml << "" << endl; xml << "" << (*it)->ArgHelp << "" << endl; xml << "" << (*it)->LongArg << "" << endl; xml << "" << (*it)->ShortArg << "" << endl; + + if ((*it)->ValueType == ctkCommandLineParser::InputDirectory || (*it)->ValueType == ctkCommandLineParser::InputFile) + { + xml << "input" << endl; + } + else if ((*it)->ValueType == ctkCommandLineParser::OutputDirectory || (*it)->ValueType == ctkCommandLineParser::OutputFile) + { + xml << "output" << endl; + } xml << "" << endl; } xml << "" << endl; xml << "" << endl; cout << xml.str(); } void ctkCommandLineParser::setTitle(string title) { Title = title; } void ctkCommandLineParser::setContributor(string contributor) { Contributor = contributor; } void ctkCommandLineParser::setCategory(string category) { Category = category; } void ctkCommandLineParser::setDescription(string description) { Description = description; } + +void ctkCommandLineParser::changeParameterGroup(string name, string description) +{ + ParameterGroupName = name; + ParameterGroupDescription = description; +} diff --git a/Modules/DiffusionImaging/MiniApps/ctkCommandLineParser.h b/Modules/DiffusionImaging/MiniApps/ctkCommandLineParser.h index 44370c7272..202fef074d 100755 --- a/Modules/DiffusionImaging/MiniApps/ctkCommandLineParser.h +++ b/Modules/DiffusionImaging/MiniApps/ctkCommandLineParser.h @@ -1,436 +1,441 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ /*========================================================================= Library: CTK Copyright (c) Kitware Inc. Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0.txt Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. =========================================================================*/ #ifndef __ctkCommandLineParser_h #define __ctkCommandLineParser_h #include #include /** * \ingroup Core * * The CTK command line parser. * * Use this class to add information about the command line arguments * your program understands and to easily parse them from a given list * of strings. * * This parser provides the following features: * *
    *
  • Add arguments by supplying a long name and/or a short name. * Arguments are validated using a regular expression. They can have * a default value and a help string.
    • *
  • Deprecated arguments.
    • *
  • Custom regular expressions for argument validation.
    • *
  • Set different argument name prefixes for native platform look and feel.
    • *
  • QSettings support. Default values for arguments can be read from * a QSettings object.
    • *
  • Create a help text for the command line arguments with support for * grouping arguments.
    • *
* * Here is an example how to use this class inside a main function: * * \code * #include * #include * #include * * int main(int argc, char** argv) * { * QCoreApplication app(argc, argv); * // This is used by QSettings * QCoreApplication::setOrganizationName("MyOrg"); * QCoreApplication::setApplicationName("MyApp"); * * ctkCommandLineParser parser; * // Use Unix-style argument names * parser.setArgumentPrefix("--", "-"); * // Enable QSettings support * parser.enableSettings("disable-settings"); * * // Add command line argument names * parser.addArgument("disable-settings", "", us::Any::Bool, "Do not use QSettings"); * parser.addArgument("help", "h", us::Any::Bool, "Show this help text"); * parser.addArgument("search-paths", "s", us::Any::StringList, "A list of paths to search"); * * // Parse the command line arguments * bool ok = false; * map parsedArgs = parser.parseArguments(QCoreApplication::arguments(), &ok); * if (!ok) * { * QTextStream(stderr, QIODevice::WriteOnly) << "Error parsing arguments: " * << parser.errorString() << "\n"; * return EXIT_FAILURE; * } * * // Show a help message * if (parsedArgs.contains("help") || parsedArgs.contains("h")) * { * QTextStream(stdout, QIODevice::WriteOnly) << parser.helpText(); * return EXIT_SUCCESS; * } * * // Do something * * return EXIT_SUCCESS; * } * \endcode */ using namespace std; class ctkCommandLineParser { public: enum Type { String = 0, Bool = 1, StringList = 2, Int = 3, Float = 4, - Directory = 5, - File = 6 + InputDirectory = 5, + InputFile = 6, + OutputDirectory = 7, + OutputFile = 8 }; typedef std::vector< std::string > StringContainerType; /** * Constructs a parser instance. * * If QSettings support is enabled by a call to enableSettings() * a default constructed QSettings instance will be used when parsing * the command line arguments. Make sure to call QCoreApplication::setOrganizationName() * and QCoreApplication::setApplicationName() before using default * constructed QSettings objects. * * @param newParent The QObject parent. */ ctkCommandLineParser(); ~ctkCommandLineParser(); /** * Parse a given list of command line arguments. * * This method parses a list of string elements considering the known arguments * added by calls to addArgument(). If any one of the argument * values does not match the corresponding regular expression, * ok is set to false and an empty map object is returned. * * The keys in the returned map object correspond to the long argument string, * if it is not empty. Otherwise, the short argument string is used as key. The * us::Any values can safely be converted to the type specified in the * addArgument() method call. * * @param arguments A StringContainerType containing command line arguments. Usually * given by QCoreApplication::arguments(). * @param ok A pointer to a boolean variable. Will be set to true * if all regular expressions matched, false otherwise. * @return A map object mapping the long argument (if empty, the short one) * to a us::Any containing the value. */ map parseArguments(const StringContainerType &arguments, bool* ok = 0); /** * Convenient method allowing to parse a given list of command line arguments. * @see parseArguments(const StringContainerType &, bool*) */ map parseArguments(int argc, char** argv, bool* ok = 0); /** * Returns a detailed error description if a call to parseArguments() * failed. * * @return The error description, empty if no error occured. * @see parseArguments(const StringContainerType&, bool*) */ string errorString() const; /** * This method returns all unparsed arguments, i.e. all arguments * for which no long or short name has been registered via a call * to addArgument(). * * @see addArgument() * * @return A list containing unparsed arguments. */ const StringContainerType& unparsedArguments() const; /** * Checks if the given argument has been added via a call * to addArgument(). * * @see addArgument() * * @param argument The argument to be checked. * @return true if the argument was added, false * otherwise. */ bool argumentAdded(const string& argument) const; /** * Checks if the given argument has been parsed successfully by a previous * call to parseArguments(). * * @param argument The argument to be checked. * @return true if the argument was parsed, false * otherwise. */ bool argumentParsed(const string& argument) const; /** * Adds a command line argument. An argument can have a long name * (like --long-argument-name), a short name (like -l), or both. The type * of the argument can be specified by using the type parameter. * The following types are supported: * * * * * * * * *
Type# of parametersDefault regular exprExample
us::Any::String1.*--test-string StringParameter
us::Any::Bool0does not apply--enable-something
us::Any::StringList-1.*--test-list string1 string2
us::Any::Int1-?[0-9]+--test-int -5
* * The regular expressions are used to validate the parameters of command line * arguments. You can restrict the valid set of parameters by calling * setExactMatchRegularExpression() for your argument. * * Optionally, a help string and a default value can be provided for the argument. If * the us::Any type of the default value does not match type, an * exception is thrown. Arguments with default values are always returned by * parseArguments(). * * You can also declare an argument deprecated, by setting deprecated * to true. Alternatively you can add a deprecated argument by calling * addDeprecatedArgument(). * * If the long or short argument has already been added, or if both are empty strings, * the method call has no effect. * * @param longarg The long argument name. * @param shortarg The short argument name. * @param type The argument type (see the list above for supported types). * @param argHelp A help string describing the argument. * @param defaultValue A default value for the argument. * @param ignoreRest All arguments after the current one will be ignored. * @param deprecated Declares the argument deprecated. * * @see setExactMatchRegularExpression() * @see addDeprecatedArgument() * @throws std::logic_error If the us::Any type of defaultValue * does not match type, a std::logic_error is thrown. */ void addArgument(const string& longarg, const string& shortarg, Type type, const string& argLabel, const string& argHelp = string(), const us::Any& defaultValue = us::Any(), bool optional=true, bool ignoreRest = false, bool deprecated = false); /** * Adds a deprecated command line argument. If a deprecated argument is provided * on the command line, argHelp is displayed in the console and * processing continues with the next argument. * * Deprecated arguments are grouped separately at the end of the help text * returned by helpText(). * * @param longarg The long argument name. * @param shortarg The short argument name. * @param argHelp A help string describing alternatives to the deprecated argument. */ void addDeprecatedArgument(const string& longarg, const string& shortarg, const string& argLabel, const string& argHelp); /** * Sets a custom regular expression for validating argument parameters. The method * errorString() can be used the get the last error description. * * @param argument The previously added long or short argument name. * @param expression A regular expression which the arugment parameters must match. * @param exactMatchFailedMessage An error message explaining why the parameter did * not match. * * @return true if the argument was found and the regular expression was set, * false otherwise. * * @see errorString() */ bool setExactMatchRegularExpression(const string& argument, const string& expression, const string& exactMatchFailedMessage); /** * The field width for the argument names without the help text. * * @return The argument names field width in the help text. */ int fieldWidth() const; /** * Creates a help text containing properly formatted argument names and help strings * provided by calls to addArgument(). The arguments can be grouped by * using beginGroup() and endGroup(). * * @param charPad The padding character. * @return The formatted help text. */ string helpText() const; /** * Sets the argument prefix for long and short argument names. This can be used * to create native command line arguments without changing the calls to * addArgument(). For example on Unix-based systems, long argument * names start with "--" and short names with "-", while on Windows argument names * always start with "/". * * Note that all methods in ctkCommandLineParser which take an argument name * expect the name as it was supplied to addArgument. * * Example usage: * * \code * ctkCommandLineParser parser; * parser.setArgumentPrefix("--", "-"); * parser.addArgument("long-argument", "l", us::Any::String); * StringContainerType args; * args << "program name" << "--long-argument Hi"; * parser.parseArguments(args); * \endcode * * @param longPrefix The prefix for long argument names. * @param shortPrefix The prefix for short argument names. */ void setArgumentPrefix(const string& longPrefix, const string& shortPrefix); /** * Begins a new group for documenting arguments. All newly added arguments via * addArgument() will be put in the new group. You can close the * current group by calling endGroup() or be opening a new group. * * Note that groups cannot be nested and all arguments which do not belong to * a group will be listed at the top of the text created by helpText(). * * @param description The description of the group */ void beginGroup(const string& description); /** * Ends the current group. * * @see beginGroup(const string&) */ void endGroup(); /** * Enables QSettings support in ctkCommandLineParser. If an argument name is found * in the QSettings instance with a valid us::Any, the value is considered as * a default value and overwrites default values registered with * addArgument(). User supplied values on the command line overwrite * values in the QSettings instance, except for arguments with multiple parameters * which are merged with QSettings values. Call mergeSettings(false) * to disable merging. * * See ctkCommandLineParser(QSettings*) for information about how to * supply a QSettings instance. * * Additionally, a long and short argument name can be specified which will disable * QSettings support if supplied on the command line. The argument name must be * registered as a regular argument via addArgument(). * * @param disableLongArg Long argument name. * @param disableShortArg Short argument name. * * @see ctkCommandLineParser(QSettings*) */ void enableSettings(const string& disableLongArg = "", const string& disableShortArg = ""); /** * Controlls the merging behavior of user values and QSettings values. * * If merging is on (the default), user supplied values for an argument * which can take more than one parameter are merged with values stored * in the QSettings instance. If merging is off, the user values overwrite * the QSettings values. * * @param merge true enables QSettings merging, false * disables it. */ void mergeSettings(bool merge); /** * Can be used to check if QSettings support has been enabled by a call to * enableSettings(). * * @return true if QSettings support is enabled, false * otherwise. */ bool settingsEnabled() const; /** * Can be used to teach the parser to stop parsing the arguments and return False when * an unknown argument is encountered. By default StrictMode is disabled. * * @see parseArguments(const StringContainerType &, bool*) */ void setStrictModeEnabled(bool strictMode); - void GetXML(std::string title, std::string description); + void GetXML(); void setTitle(std::string title); void setContributor(std::string contributor); void setCategory(std::string category); void setDescription(std::string description); + void changeParameterGroup(std::string name, std::string description); private: class ctkInternal; ctkInternal * Internal; string Title; string Contributor; string Category; string Description; + string ParameterGroupName; + string ParameterGroupDescription; }; #endif