diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt b/Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt index c9c558e4f2..b4aa62b258 100644 --- a/Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt +++ b/Modules/DiffusionImaging/FiberTracking/Testing/CMakeLists.txt @@ -1,21 +1,18 @@ MITK_CREATE_MODULE_TESTS() if("${CMAKE_SIZEOF_VOID_P}" EQUAL "8") mitkAddCustomModuleTest(mitkFiberBundleReaderWriterTest mitkFiberBundleReaderWriterTest) # Temporarily disabled. Since method relies on random numbers, the behaviour is not consistent across different systems. Solution? #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) - -# mitkLocalFiberPlausibilityTest needs to use new direction image -# 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_subtracted.fib ${MITK_DATA_DIR}/DiffusionImaging/fiberBundleX_added.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) mitkAddCustomModuleTest(mitkFiberfoxSignalGenerationTest mitkFiberfoxSignalGenerationTest) mitkAddCustomModuleTest(mitkMachineLearningTrackingTest mitkMachineLearningTrackingTest) mitkAddCustomModuleTest(mitkStreamlineTractographyTest mitkStreamlineTractographyTest) mitkAddCustomModuleTest(mitkFiberProcessingTest mitkFiberProcessingTest) ENDIF() diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/files.cmake b/Modules/DiffusionImaging/FiberTracking/Testing/files.cmake index f760eddcd6..7190a886e0 100644 --- a/Modules/DiffusionImaging/FiberTracking/Testing/files.cmake +++ b/Modules/DiffusionImaging/FiberTracking/Testing/files.cmake @@ -1,15 +1,14 @@ SET(MODULE_CUSTOM_TESTS mitkFiberBundleReaderWriterTest.cpp mitkGibbsTrackingTest.cpp mitkStreamlineTractographyTest.cpp - mitkPeakExtractionTest.cpp mitkLocalFiberPlausibilityTest.cpp mitkFiberTransformationTest.cpp mitkFiberExtractionTest.cpp mitkFiberGenerationTest.cpp mitkFiberfoxSignalGenerationTest.cpp mitkMachineLearningTrackingTest.cpp mitkFiberProcessingTest.cpp ) diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkPeakExtractionTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkPeakExtractionTest.cpp deleted file mode 100755 index 43f0fa8af6..0000000000 --- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkPeakExtractionTest.cpp +++ /dev/null @@ -1,106 +0,0 @@ -/*=================================================================== - -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 - -using namespace std; - -int mitkPeakExtractionTest(int argc, char* argv[]) -{ - MITK_TEST_BEGIN("mitkStreamlineTrackingTest"); - - MITK_TEST_CONDITION_REQUIRED(argc>3,"check for input data") - - string shCoeffFileName = argv[1]; - string maskFileName = argv[2]; - string referenceFileName = argv[3]; - - MITK_INFO << "SH-coefficient file: " << shCoeffFileName; - MITK_INFO << "Mask file: " << maskFileName; - MITK_INFO << "Reference fiber file: " << referenceFileName; - - try - { - mitk::CoreObjectFactory::GetInstance(); - - mitk::Image::Pointer image = dynamic_cast(mitk::IOUtil::Load(shCoeffFileName)[0].GetPointer()); - mitk::Image::Pointer mitkMaskImage = dynamic_cast(mitk::IOUtil::Load(maskFileName)[0].GetPointer()); - - typedef itk::Image ItkUcharImgType; - typedef itk::FiniteDiffOdfMaximaExtractionFilter< float, 4, 20242 > MaximaExtractionFilterType; - MaximaExtractionFilterType::Pointer filter = MaximaExtractionFilterType::New(); - - MITK_INFO << "Casting mask image ..."; - ItkUcharImgType::Pointer itkMask = ItkUcharImgType::New(); - mitk::CastToItkImage(mitkMaskImage, itkMask); - filter->SetMaskImage(itkMask); - - MITK_INFO << "Casting SH image ..."; - typedef mitk::ImageToItk< MaximaExtractionFilterType::CoefficientImageType > CasterType; - CasterType::Pointer caster = CasterType::New(); - caster->SetInput(image); - caster->Update(); - filter->SetInput(caster->GetOutput()); - filter->SetMaxNumPeaks(2); - filter->SetPeakThreshold(0.4); - filter->SetAbsolutePeakThreshold(0.01); - filter->SetAngularThreshold(25); - filter->SetNormalizationMethod(MaximaExtractionFilterType::MAX_VEC_NORM); - filter->SetNumberOfThreads(1); - MITK_INFO << "Starting extraction ..."; - filter->Update(); -// mitk::FiberBundle::Pointer fib1 = filter->GetOutputFiberBundle(); - -// MITK_INFO << "Loading reference ..."; -// std::vector infile = mitk::IOUtil::Load( referenceFileName ); -// mitk::FiberBundle::Pointer fib2 = dynamic_cast(infile.at(0).GetPointer()); - -// // TODO: reduce epsilon. strange issues with differing values between windows and linux. -// MITK_TEST_CONDITION_REQUIRED(fib1->Equals(fib2), "Check if tractograms 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(); -}