diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt b/Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt index 9a6eac7ed7..d46f8c63b2 100644 --- a/Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt +++ b/Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt @@ -1,11 +1,11 @@ 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(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(mitkLocalFiberPlausibilityTest mitkLocalFiberPlausibilityTest ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX.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_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_subtracted.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_subtracted.fib) mitkAddCustomModuleTest(mitkFiberGenerationTest mitkFiberGenerationTest ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/Fiducial_0.pf ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/Fiducial_1.pf ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/Fiducial_2.pf ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/uniform.fib ${MITK_DATA_DIR}/DiffusionImaging/Fiberfox/gaussian.fib) # TODO: fiberfox signalgen diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkLocalFiberPlausibilityTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkLocalFiberPlausibilityTest.cpp index 223e67136a..cf54859c1b 100755 --- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkLocalFiberPlausibilityTest.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Testing/mitkLocalFiberPlausibilityTest.cpp @@ -1,175 +1,162 @@ /*=================================================================== 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==11,"check for input data") + MITK_TEST_CONDITION_REQUIRED(argc==8,"check for input data") string fibFile = argv[1]; - vector< string > referenceImages; referenceImages.push_back(argv[2]); referenceImages.push_back(argv[3]); + 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]; + string LDFP_ERROR_IMAGE_IGNORE = argv[7]; float angularThreshold = 25; 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 + // Get directions and num directions image + ItkUcharImgType::Pointer numDirImage = fOdfFilter->GetNumDirectionsImage(); + mitk::Image::Pointer mitkNumDirImage = mitk::Image::New(); + mitkNumDirImage->InitializeByItk( numDirImage.GetPointer() ); + mitkNumDirImage->SetVolume( numDirImage->GetBufferPointer() ); + mitk::FiberBundleX::Pointer testDirections = fOdfFilter->GetOutputFiberBundle(); + + // evaluate directions with missing directions EvaluationFilterType::Pointer evaluationFilter = EvaluationFilterType::New(); evaluationFilter->SetImageSet(directionImageContainer); evaluationFilter->SetReferenceImageSet(referenceImageContainer); evaluationFilter->SetMaskImage(itkMaskImage); 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() ); + // evaluate directions without missing directions + evaluationFilter->SetIgnoreMissingDirections(true); + evaluationFilter->Update(); + + EvaluationFilterType::OutputImageType::Pointer angularErrorImageIgnore = evaluationFilter->GetOutput(0); + mitk::Image::Pointer mitkAngularErrorImageIgnore = mitk::Image::New(); + mitkAngularErrorImageIgnore->InitializeByItk( angularErrorImageIgnore.GetPointer() ); + mitkAngularErrorImageIgnore->SetVolume( angularErrorImageIgnore->GetBufferPointer() ); + mitk::Image::Pointer gtAngularErrorImageIgnore = dynamic_cast(mitk::IOUtil::LoadDataNode(LDFP_ERROR_IMAGE_IGNORE)->GetData()); 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(mitk::Equal(gtAngularErrorImageIgnore, mitkAngularErrorImageIgnore, 0.0001, true), "Check if error images are equal (ignored missing directions)."); 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(); }