diff --git a/Modules/DiffusionImaging/DiffusionCore/Algorithms/Registration/mitkRegistrationWrapper.cpp b/Modules/DiffusionImaging/DiffusionCore/Algorithms/Registration/mitkRegistrationWrapper.cpp index 96f2e44744..2819afa622 100644 --- a/Modules/DiffusionImaging/DiffusionCore/Algorithms/Registration/mitkRegistrationWrapper.cpp +++ b/Modules/DiffusionImaging/DiffusionCore/Algorithms/Registration/mitkRegistrationWrapper.cpp @@ -1,189 +1,183 @@ #include "mitkRegistrationWrapper.h" #include "mitkPyramidImageRegistrationMethod.h" #include "mitkDiffusionImage.h" #include #include "itkB0ImageExtractionImageFilter.h" #include #include #include #include void mitk::RegistrationWrapper::ApplyTransformationToImage(mitk::Image::Pointer img, const mitk::RegistrationWrapper::RidgidTransformType &transformation,double* offset, mitk::Image* resampleReference, bool binary) { typedef mitk::DiffusionImage DiffusionImageType; if (dynamic_cast (img.GetPointer()) == NULL) { ItkImageType::Pointer itkImage = ItkImageType::New(); - - MITK_ERROR << "imgCopy 0 " << "/" << img->GetReferenceCount(); - MITK_ERROR << "pixel type " << img->GetPixelType().GetComponentTypeAsString(); - CastToItkImage(img, itkImage); - - typedef itk::Euler3DTransform< double > RigidTransformType; RigidTransformType::Pointer rtransform = RigidTransformType::New(); RigidTransformType::ParametersType parameters(RigidTransformType::ParametersDimension); for (int i = 0; i<6;++i) parameters[i] = transformation[i]; rtransform->SetParameters( parameters ); mitk::Point3D origin = itkImage->GetOrigin(); origin[0]-=offset[0]; origin[1]-=offset[1]; origin[2]-=offset[2]; mitk::Point3D newOrigin = rtransform->GetInverseTransform()->TransformPoint(origin); itk::Matrix dir = itkImage->GetDirection(); itk::Matrix transM ( vnl_inverse(rtransform->GetMatrix().GetVnlMatrix())); itk::Matrix newDirection = transM * dir; itkImage->SetOrigin(newOrigin); itkImage->SetDirection(newDirection); // Perform Resampling if reference image is provided if (resampleReference != NULL) { typedef itk::ResampleImageFilter ResampleFilterType; ItkImageType::Pointer itkReference = ItkImageType::New(); CastToItkImage(resampleReference,itkReference); typedef itk::WindowedSincInterpolateImageFunction< ItkImageType, 3> WindowedSincInterpolatorType; WindowedSincInterpolatorType::Pointer sinc_interpolator = WindowedSincInterpolatorType::New(); typedef itk::NearestNeighborInterpolateImageFunction< ItkImageType, double > NearestNeighborInterpolatorType; NearestNeighborInterpolatorType::Pointer nn_interpolator = NearestNeighborInterpolatorType::New(); ResampleFilterType::Pointer resampler = ResampleFilterType::New(); resampler->SetInput(itkImage); resampler->SetReferenceImage( itkReference ); resampler->UseReferenceImageOn(); if (binary) resampler->SetInterpolator(nn_interpolator); else resampler->SetInterpolator(sinc_interpolator); resampler->Update(); GrabItkImageMemory(resampler->GetOutput(), img); } else { // !! CastToItk behaves very differently depending on the original data type // if the target type is the same as the original, only a pointer to the data is set // and an additional GrabItkImageMemory will cause a segfault when the image is destroyed // GrabItkImageMemory - is not necessary in this case since we worked on the original data // See Bug 17538. if (img->GetPixelType().GetComponentTypeAsString() != "double") img = GrabItkImageMemory(itkImage); } } else { DiffusionImageType::Pointer diffImages = dynamic_cast(img.GetPointer()); typedef itk::Euler3DTransform< double > RigidTransformType; RigidTransformType::Pointer rtransform = RigidTransformType::New(); RigidTransformType::ParametersType parameters(RigidTransformType::ParametersDimension); for (int i = 0; i<6;++i) { parameters[i] = transformation[i]; } rtransform->SetParameters( parameters ); mitk::Point3D b0origin = diffImages->GetVectorImage()->GetOrigin(); b0origin[0]-=offset[0]; b0origin[1]-=offset[1]; b0origin[2]-=offset[2]; mitk::Point3D newOrigin = rtransform->GetInverseTransform()->TransformPoint(b0origin); itk::Matrix dir = diffImages->GetVectorImage()->GetDirection(); itk::Matrix transM ( vnl_inverse(rtransform->GetMatrix().GetVnlMatrix())); itk::Matrix newDirection = transM * dir; diffImages->GetVectorImage()->SetOrigin(newOrigin); diffImages->GetVectorImage()->SetDirection(newDirection); diffImages->Modified(); mitk::DiffusionImageCorrectionFilter::Pointer correctionFilter = mitk::DiffusionImageCorrectionFilter::New(); // For Diff. Images: Need to rotate the gradients (works in-place) correctionFilter->SetImage(diffImages); correctionFilter->CorrectDirections(transM.GetVnlMatrix()); img = diffImages; } } void mitk::RegistrationWrapper::GetTransformation(mitk::Image* fixedImage, mitk::Image* movingImage, RidgidTransformType transformation,double* offset, mitk::Image* mask) { // Handle the case that fixed/moving image is a DWI image mitk::DiffusionImage* fixedDwi = dynamic_cast*> (fixedImage); mitk::DiffusionImage* movingDwi = dynamic_cast*> (movingImage); itk::B0ImageExtractionImageFilter::Pointer b0Extraction = itk::B0ImageExtractionImageFilter::New(); offset[0]=offset[1]=offset[2]=0; if (fixedDwi != NULL) { // Set b0 extraction as fixed image b0Extraction->SetInput(fixedDwi->GetVectorImage()); b0Extraction->SetDirections(fixedDwi->GetDirections()); b0Extraction->Update(); mitk::Image::Pointer tmp = mitk::Image::New(); tmp->InitializeByItk(b0Extraction->GetOutput()); tmp->SetVolume(b0Extraction->GetOutput()->GetBufferPointer()); fixedImage = tmp; } if (movingDwi != NULL) { // Set b0 extraction as moving image b0Extraction->SetInput(movingDwi->GetVectorImage()); b0Extraction->SetDirections(movingDwi->GetDirections()); b0Extraction->Update(); mitk::Image::Pointer tmp = mitk::Image::New(); tmp->InitializeByItk(b0Extraction->GetOutput()); tmp->SetVolume(b0Extraction->GetOutput()->GetBufferPointer()); movingImage = tmp; } // align the offsets of the two images. this is done to avoid non-overlapping initialization Point3D origin = fixedImage->GetGeometry()->GetOrigin(); Point3D originMoving = movingImage->GetGeometry()->GetOrigin(); offset[0] = originMoving[0]-origin[0]; offset[1] = originMoving[1]-origin[1]; offset[2] = originMoving[2]-origin[2]; mitk::Image::Pointer tmpImage = movingImage->Clone(); tmpImage->GetGeometry()->SetOrigin(origin); // Start registration mitk::PyramidImageRegistrationMethod::Pointer registrationMethod = mitk::PyramidImageRegistrationMethod::New(); registrationMethod->SetFixedImage( fixedImage ); if (mask != NULL) { registrationMethod->SetFixedImageMask(mask); registrationMethod->SetUseFixedImageMask(true); } else { registrationMethod->SetUseFixedImageMask(false); } registrationMethod->SetTransformToRigid(); registrationMethod->SetCrossModalityOn(); registrationMethod->SetMovingImage(tmpImage); registrationMethod->Update(); registrationMethod->GetParameters(transformation); // first three: euler angles, last three translation } diff --git a/Modules/DiffusionImaging/MiniApps/BatchedFolderRegistration.cpp b/Modules/DiffusionImaging/MiniApps/BatchedFolderRegistration.cpp index 3625bc16ee..665b7a0f01 100644 --- a/Modules/DiffusionImaging/MiniApps/BatchedFolderRegistration.cpp +++ b/Modules/DiffusionImaging/MiniApps/BatchedFolderRegistration.cpp @@ -1,341 +1,338 @@ /*=================================================================== 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" // ITK #include #include typedef std::vector FileListType; 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; } /// Add '_reg' tag to file name 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 + "_reg" + fileType; return savePathAndFileName; } /// 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 + "_reg." + fileType; MITK_INFO << "Copy resource " << savePathAndFileName; mitk::Image::Pointer resImage = mitk::IOUtil::LoadImage(derivedResourceFilename); mitk::IOUtil::SaveImage(resImage, savePathAndFileName); } } int BatchedFolderRegistration( int argc, char* argv[] ) { ctkCommandLineParser parser; parser.setArgumentPrefix("--","-"); // Add command line argument names parser.addArgument("help", "h",ctkCommandLineParser::Bool, "Show this help text"); parser.addArgument("xml", "x",ctkCommandLineParser::Bool, "Print a XML description of this modules command line interface"); //parser.addArgument("usemask", "u", QVariant::Bool, "Use segmentations (derived resources) to exclude areas from registration metrics"); parser.addArgument("input", "i", ctkCommandLineParser::String, "Input folder",us::Any(),false); parser.addArgument("output", "o", ctkCommandLineParser::String, "Output folder (ending with /)",us::Any(),false); parser.addArgument("fixed", "f", ctkCommandLineParser::String, "Suffix for fixed image",us::Any(),false); parser.addArgument("moving", "m", ctkCommandLineParser::String, "Suffix for moving images",us::Any(),false); parser.addArgument("derived", "d", ctkCommandLineParser::String, "Derived resources suffixes (replaces suffix for moving images); comma separated",us::Any(),true); parser.addArgument("silent", "s", ctkCommandLineParser::Bool, "No xml progress output."); // Feature currently disabled //parser.addArgument("resample", "r", QVariant::String, "Reference Image for resampling (optional), is not applied to tensor data"); map parsedArgs = parser.parseArguments(argc, argv); // Handle special arguments bool silent = false; { 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("silent")) silent = true; // Show a help message if ( parsedArgs.count("help") || parsedArgs.count("h")) { std::cout << parser.helpText(); return EXIT_SUCCESS; } } std::string outputPath = us::any_cast(parsedArgs["output"]); std::string refPattern = us::any_cast(parsedArgs["fixed"]); std::string inputPath = us::any_cast(parsedArgs["input"]); std::string movingImgPattern = us::any_cast(parsedArgs["moving"]); //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 ,','); } MITK_INFO << "Input Folder : " << inputPath; MITK_INFO << "Looking for reference image ..."; FileListType referenceFileList = CreateFileList(inputPath,refPattern); if (referenceFileList.size() != 1) { 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; mitk::Image::Pointer refImage = mitk::IOUtil::LoadImage(referenceFileName); 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]; { mitk::Image::Pointer movingImage = mitk::IOUtil::LoadImage(fileMorphName); - MITK_ERROR << "REF COUNT MOVING 0 " << movingImage->GetReferenceCount(); 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_ERROR << "REF COUNT MOVING 1 " << movingImage->GetReferenceCount(); - //mitk::RegistrationWrapper::GetTransformation(refImage, movingImage, transf, offset, referenceMask); - MITK_ERROR << "REF COUNT MOVING 2 " << movingImage->GetReferenceCount(); - + mitk::RegistrationWrapper::GetTransformation(refImage, movingImage, transf, offset, referenceMask); mitk::RegistrationWrapper::ApplyTransformationToImage(movingImage, transf,offset, NULL); // , resampleImage - MITK_ERROR << "REF COUNT MOVING 3 " << movingImage->GetReferenceCount(); + savePathAndFileName = GetSavePath(outputPath, fileMorphName); std::string fileType = itksys::SystemTools::GetFilenameExtension(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 resource " << derivedResourceFilename << " ..."; mitk::Image::Pointer derivedMovingResource = mitk::IOUtil::LoadImage(derivedResourceFilename); // Apply transformation to derived resource, treat derived resource as binary mitk::RegistrationWrapper::ApplyTransformationToImage(derivedMovingResource, transf,offset, NULL, true); savePathAndFileName = GetSavePath(outputPath, derivedResourceFilename); std::string fileType = itksys::SystemTools::GetFilenameExtension(derivedResourceFilename); SaveImage(savePathAndFileName,derivedMovingResource,fileType ); } } if (!silent) std::cout << ""; return EXIT_SUCCESS; } RegisterDiffusionMiniApp(BatchedFolderRegistration);