diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt b/Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt index f81f7fd96f..a4a636d3c4 100644 --- a/Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt +++ b/Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt @@ -1,10 +1,9 @@ MITK_CREATE_MODULE_TESTS() mitkAddCustomModuleTest(mitkFiberBundleXReaderWriterTest mitkFiberBundleXReaderWriterTest ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX.fib) mitkAddCustomModuleTest(mitkGibbsTrackingTest mitkGibbsTrackingTest ${MITK_DATA_DIR}/DiffusionImaging/qBallImage.qbi ${MITK_DATA_DIR}/DiffusionImaging/diffusionImageMask.nrrd ${MITK_DATA_DIR}/DiffusionImaging/gibbsTrackingParameters.gtp ${MITK_DATA_DIR}/DiffusionImaging/gibbsTractogram.fib) mitkAddCustomModuleTest(mitkStreamlineTrackingTest mitkStreamlineTrackingTest ${MITK_DATA_DIR}/DiffusionImaging/tensorImage.dti ${MITK_DATA_DIR}/DiffusionImaging/diffusionImageMask.nrrd ${MITK_DATA_DIR}/DiffusionImaging/streamlineTractogram.fib) mitkAddCustomModuleTest(mitkPeakExtractionTest mitkPeakExtractionTest ${MITK_DATA_DIR}/DiffusionImaging/qBallImage_SHCoeffs.nrrd ${MITK_DATA_DIR}/DiffusionImaging/diffusionImageMask.nrrd ${MITK_DATA_DIR}/DiffusionImaging/qBallImage_VectorField.fib) -mitkAddCustomModuleTest(mitkPeakExtractionTest mitkPeakExtractionTest ${MITK_DATA_DIR}/DiffusionImaging/qBallImage_SHCoeffs.nrrd ${MITK_DATA_DIR}/DiffusionImaging/diffusionImageMask.nrrd ${MITK_DATA_DIR}/DiffusionImaging/qBallImage_VectorField.fib) -mitkAddCustomModuleTest(mitkLocalFiberPlausibilityTest mitkLocalFiberPlausibilityTest ${MITK_DATA_DIR}/DiffusionImaging/streamlineTractogram.fib ${MITK_DATA_DIR}/DiffusionImaging/LDFP_GT_DIRECTION_0.nrrd ${MITK_DATA_DIR}/DiffusionImaging/LDFP_GT_DIRECTION_1.nrrd ${MITK_DATA_DIR}/DiffusionImaging/LDFP_ERROR_IMAGE.nrrd ${MITK_DATA_DIR}/DiffusionImaging/LDFP_NUM_DIRECTIONS.nrrd ${MITK_DATA_DIR}/DiffusionImaging/LDFP_VECTOR_FIELD.fib) +mitkAddCustomModuleTest(mitkLocalFiberPlausibilityTest mitkLocalFiberPlausibilityTest ${MITK_DATA_DIR}/DiffusionImaging/streamlineTractogram.fib ${MITK_DATA_DIR}/DiffusionImaging/LDFP_GT_DIRECTION_0.nrrd ${MITK_DATA_DIR}/DiffusionImaging/LDFP_GT_DIRECTION_1.nrrd ${MITK_DATA_DIR}/DiffusionImaging/LDFP_ERROR_IMAGE.nrrd ${MITK_DATA_DIR}/DiffusionImaging/LDFP_NUM_DIRECTIONS.nrrd ${MITK_DATA_DIR}/DiffusionImaging/LDFP_VECTOR_FIELD.fib ${MITK_DATA_DIR}/DiffusionImaging/LDFP_OUT_DIRECTION_0.nrrd ${MITK_DATA_DIR}/DiffusionImaging/LDFP_OUT_DIRECTION_1.nrrd ${MITK_DATA_DIR}/DiffusionImaging/LDFP_OUT_DIRECTION_2.nrrd ${MITK_DATA_DIR}/DiffusionImaging/LDFP_ERROR_IMAGE_IGNORE.nrrd) mitkAddCustomModuleTest(mitkFiberTransformationTest mitkFiberTransformationTest ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_transformed.fib) mitkAddCustomModuleTest(mitkFiberExtractionTest mitkFiberExtractionTest ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_extracted.fib ${MITK_DATA_DIR}/DiffusionImaging/ROI1.pf ${MITK_DATA_DIR}/DiffusionImaging/ROI2.pf ${MITK_DATA_DIR}/DiffusionImaging/ROI3.pf ${MITK_DATA_DIR}/DiffusionImaging/ROIIMAGE.nrrd ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_inside.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_outside.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_passing-mask.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_ending-in-mask.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX-fiberBundleX_extracted.fib) diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkLocalFiberPlausibilityTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkLocalFiberPlausibilityTest.cpp index c052ba2009..223e67136a 100755 --- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkLocalFiberPlausibilityTest.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Testing/mitkLocalFiberPlausibilityTest.cpp @@ -1,149 +1,175 @@ /*=================================================================== 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 #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #define _USE_MATH_DEFINES #include using namespace std; int mitkLocalFiberPlausibilityTest(int argc, char* argv[]) { MITK_TEST_BEGIN("mitkLocalFiberPlausibilityTest"); - MITK_TEST_CONDITION_REQUIRED(argc==7,"check for input data") + MITK_TEST_CONDITION_REQUIRED(argc==11,"check for input data") string fibFile = argv[1]; vector< string > referenceImages; referenceImages.push_back(argv[2]); referenceImages.push_back(argv[3]); string LDFP_ERROR_IMAGE = argv[4]; string LDFP_NUM_DIRECTIONS = argv[5]; string LDFP_VECTOR_FIELD = argv[6]; float angularThreshold = 25; - bool ignore = false; try { RegisterDiffusionCoreObjectFactory(); RegisterFiberTrackingObjectFactory(); typedef itk::Image ItkUcharImgType; typedef itk::Image< itk::Vector< float, 3>, 3 > ItkDirectionImage3DType; typedef itk::VectorContainer< 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 (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(); // evaluate directions EvaluationFilterType::Pointer evaluationFilter = EvaluationFilterType::New(); evaluationFilter->SetImageSet(directionImageContainer); evaluationFilter->SetReferenceImageSet(referenceImageContainer); evaluationFilter->SetMaskImage(itkMaskImage); - evaluationFilter->SetIgnoreMissingDirections(ignore); + evaluationFilter->SetIgnoreMissingDirections(false); evaluationFilter->Update(); EvaluationFilterType::OutputImageType::Pointer angularErrorImage = evaluationFilter->GetOutput(0); ItkUcharImgType::Pointer numDirImage = fOdfFilter->GetNumDirectionsImage(); mitk::FiberBundleX::Pointer testDirections = fOdfFilter->GetOutputFiberBundle(); mitk::Image::Pointer mitkAngularErrorImage = mitk::Image::New(); mitkAngularErrorImage->InitializeByItk( angularErrorImage.GetPointer() ); mitkAngularErrorImage->SetVolume( angularErrorImage->GetBufferPointer() ); mitk::Image::Pointer mitkNumDirImage = mitk::Image::New(); mitkNumDirImage->InitializeByItk( numDirImage.GetPointer() ); mitkNumDirImage->SetVolume( numDirImage->GetBufferPointer() ); mitk::Image::Pointer gtAngularErrorImage = dynamic_cast(mitk::IOUtil::LoadDataNode(LDFP_ERROR_IMAGE)->GetData()); mitk::Image::Pointer gtNumTestDirImage = dynamic_cast(mitk::IOUtil::LoadDataNode(LDFP_NUM_DIRECTIONS)->GetData()); mitk::FiberBundleX::Pointer gtTestDirections = dynamic_cast(mitk::IOUtil::LoadDataNode(LDFP_VECTOR_FIELD)->GetData()); - MITK_TEST_CONDITION_REQUIRED(testDirections->Equals(gtTestDirections), "Check if vector fields are equal."); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(gtAngularErrorImage, mitkAngularErrorImage, 0.0001, true), "Check if error images are equal."); + MITK_TEST_CONDITION_REQUIRED(testDirections->Equals(gtTestDirections), "Check if vector fields are equal."); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(gtNumTestDirImage, mitkNumDirImage, 0.0001, true), "Check if num direction images are equal."); + + evaluationFilter = EvaluationFilterType::New(); + evaluationFilter->SetImageSet(directionImageContainer); + evaluationFilter->SetReferenceImageSet(referenceImageContainer); + //evaluationFilter->SetMaskImage(itkMaskImage); + evaluationFilter->SetIgnoreMissingDirections(true); + evaluationFilter->Update(); + angularErrorImage = evaluationFilter->GetOutput(0); + mitkAngularErrorImage = mitk::Image::New(); + mitkAngularErrorImage->InitializeByItk( angularErrorImage.GetPointer() ); + mitkAngularErrorImage->SetVolume( angularErrorImage->GetBufferPointer() ); + mitk::IOUtil::SaveImage(mitkAngularErrorImage, "test.nrrd"); + gtAngularErrorImage = dynamic_cast(mitk::IOUtil::LoadDataNode(argv[10])->GetData()); + MITK_TEST_CONDITION_REQUIRED(mitk::Equal(gtAngularErrorImage, mitkAngularErrorImage, 0.0001, true), "Check if error images with ignored missing directions are equal."); + + + for (int i=0; iSize(); i++) + { + MITK_INFO << "Checking direction image " << i; + itk::TractsToVectorImageFilter::ItkDirectionImageType::Pointer itkImg = directionImageContainer->GetElement(i); + mitk::Image::Pointer dirImage = mitk::Image::New(); + dirImage->InitializeByItk( itkImg.GetPointer() ); + dirImage->SetVolume( itkImg->GetBufferPointer() ); + + mitk::Image::Pointer refDirImage = dynamic_cast(mitk::IOUtil::LoadDataNode(argv[7+i])->GetData()); + MITK_TEST_CONDITION_REQUIRED(mitk::Equal(dirImage, refDirImage, 0.0001, true), "Check if direction images are equal."); + } } 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_TEST_END(); } diff --git a/Modules/DiffusionImaging/MiniApps/CMakeLists.txt b/Modules/DiffusionImaging/MiniApps/CMakeLists.txt index 0a4904d40c..98875684f4 100755 --- a/Modules/DiffusionImaging/MiniApps/CMakeLists.txt +++ b/Modules/DiffusionImaging/MiniApps/CMakeLists.txt @@ -1,61 +1,61 @@ OPTION(BUILD_DiffusionMiniApps "Build commandline tools for diffusion" OFF) IF(BUILD_DiffusionMiniApps) # include necessary modules here MitkExt QmitkExt MITK_CHECK_MODULE(_RESULT DiffusionCore FiberTracking ) IF(_RESULT) MESSAGE("Warning: DiffusionMiniApps is missing ${_RESULT}") ELSE(_RESULT) MITK_USE_MODULE( DiffusionCore FiberTracking ) # needed include directories INCLUDE_DIRECTORIES( ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR} ${ALL_INCLUDE_DIRECTORIES}) PROJECT( mitkDiffusionMiniApps ) # fill in the standalone executables here SET(DIFFUSIONMINIAPPS mitkDiffusionMiniApps ) # set additional files here SET(DIFFUSIONCORE_ADDITIONAL_FILES MiniAppManager.cpp FileFormatConverter.cpp TensorReconstruction.cpp QballReconstruction.cpp DiffusionIndices.cpp CopyGeometry.cpp GibbsTracking.cpp StreamlineTracking.cpp FiberProcessing.cpp - TractometerAngularErrorTool.cpp - TractogramAngularError.cpp + LocalDirectionalFiberPlausibility.cpp + #TractogramAngularError.cpp FiberDirectionExtraction.cpp PeakExtraction.cpp PeaksAngularError.cpp MultishellMethods.cpp FiberFoxProcessing.cpp ) # create an executable foreach tool (only one at the moment) FOREACH(tool ${DIFFUSIONMINIAPPS}) ADD_EXECUTABLE( ${tool} ${tool}.cpp ${DIFFUSIONCORE_ADDITIONAL_FILES} ) TARGET_LINK_LIBRARIES( ${tool} ${ALL_LIBRARIES} ) ENDFOREACH(tool) ENDIF() MITK_INSTALL_TARGETS(EXECUTABLES mitkDiffusionMiniApps ) ENDIF(BUILD_DiffusionMiniApps) diff --git a/Modules/DiffusionImaging/MiniApps/TractometerAngularErrorTool.cpp b/Modules/DiffusionImaging/MiniApps/LocalDirectionalFiberPlausibility.cpp similarity index 99% rename from Modules/DiffusionImaging/MiniApps/TractometerAngularErrorTool.cpp rename to Modules/DiffusionImaging/MiniApps/LocalDirectionalFiberPlausibility.cpp index a42916d2e4..e444ed3349 100755 --- a/Modules/DiffusionImaging/MiniApps/TractometerAngularErrorTool.cpp +++ b/Modules/DiffusionImaging/MiniApps/LocalDirectionalFiberPlausibility.cpp @@ -1,302 +1,302 @@ /*=================================================================== 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 #include #include #include #include #include #define _USE_MATH_DEFINES #include -int TractometerAngularErrorTool(int argc, char* argv[]) +int LocalDirectionalFiberPlausibility(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setArgumentPrefix("--", "-"); parser.addArgument("input", "i", ctkCommandLineParser::String, "input tractogram (.fib, vtk ascii file format)", us::Any(), false); parser.addArgument("reference", "r", ctkCommandLineParser::StringList, "reference direction images", us::Any(), false); parser.addArgument("out", "o", ctkCommandLineParser::String, "output root", us::Any(), false); parser.addArgument("mask", "m", ctkCommandLineParser::StringList, "mask images"); parser.addArgument("athresh", "a", ctkCommandLineParser::Float, "angular threshold in degrees. closer fiber directions are regarded as one direction and clustered together.", 25, true); parser.addArgument("verbose", "v", ctkCommandLineParser::Bool, "output optional and intermediate calculation results"); parser.addArgument("ignore", "n", ctkCommandLineParser::Bool, "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 { RegisterDiffusionCoreObjectFactory(); RegisterFiberTrackingObjectFactory(); typedef itk::Image ItkUcharImgType; typedef itk::Image< itk::Vector< float, 3>, 3 > ItkDirectionImage3DType; typedef itk::VectorContainer< 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 (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 (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 (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(TractometerAngularErrorTool); +RegisterDiffusionMiniApp(LocalDirectionalFiberPlausibility);