diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkLocalFiberPlausibilityTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkLocalFiberPlausibilityTest.cpp index cf54859c1b..357eed14ca 100755 --- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkLocalFiberPlausibilityTest.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Testing/mitkLocalFiberPlausibilityTest.cpp @@ -1,162 +1,163 @@ /*=================================================================== 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==8,"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]; 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->SetNumberOfThreads(1); fOdfFilter->Update(); ItkDirectionImageContainerType::Pointer directionImageContainer = fOdfFilter->GetDirectionImageContainer(); // 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); mitk::Image::Pointer mitkAngularErrorImage = mitk::Image::New(); mitkAngularErrorImage->InitializeByItk( angularErrorImage.GetPointer() ); mitkAngularErrorImage->SetVolume( angularErrorImage->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."); } 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/FiberTracking/Testing/mitkPeakExtractionTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkPeakExtractionTest.cpp index bd3bd7bfa8..90309912c6 100755 --- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkPeakExtractionTest.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Testing/mitkPeakExtractionTest.cpp @@ -1,115 +1,116 @@ /*=================================================================== 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 #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(); RegisterDiffusionCoreObjectFactory(); RegisterFiberTrackingObjectFactory(); mitk::Image::Pointer image = mitk::IOUtil::LoadImage(shCoeffFileName); mitk::Image::Pointer mitkMaskImage = mitk::IOUtil::LoadImage(maskFileName); 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::FiberBundleX::Pointer fib1 = filter->GetOutputFiberBundle(); MITK_INFO << "Loading reference ..."; const std::string s1="", s2=""; std::vector infile = mitk::BaseDataIO::LoadBaseDataFromFile( referenceFileName, s1, s2, false ); mitk::FiberBundleX::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(); } diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkStreamlineTrackingTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkStreamlineTrackingTest.cpp index 14c6008ed0..ade4aa983d 100755 --- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkStreamlineTrackingTest.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Testing/mitkStreamlineTrackingTest.cpp @@ -1,129 +1,130 @@ /*=================================================================== 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 using namespace std; int mitkStreamlineTrackingTest(int argc, char* argv[]) { MITK_TEST_BEGIN("mitkStreamlineTrackingTest"); MITK_TEST_CONDITION_REQUIRED(argc>3,"check for input data") string dtiFileName = argv[1]; string maskFileName = argv[2]; string referenceFileName = argv[3]; MITK_INFO << "DTI file: " << dtiFileName; MITK_INFO << "Mask file: " << maskFileName; MITK_INFO << "Reference fiber file: " << referenceFileName; float minFA = 0.05; float minCurv = -1; float stepSize = -1; float tendf = 1; float tendg = 0; float minLength = 20; int numSeeds = 1; bool interpolate = false; try { RegisterDiffusionCoreObjectFactory(); RegisterFiberTrackingObjectFactory(); // load input image const std::string s1="", s2=""; std::vector infile = mitk::BaseDataIO::LoadBaseDataFromFile( dtiFileName, s1, s2, false ); 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); MITK_INFO << "Loading seed image ..."; typedef itk::Image< unsigned char, 3 > ItkUCharImageType; mitk::Image::Pointer mitkSeedImage = mitk::IOUtil::LoadImage(maskFileName); MITK_INFO << "Loading mask image ..."; mitk::Image::Pointer mitkMaskImage = mitk::IOUtil::LoadImage(maskFileName); // instantiate tracker typedef itk::StreamlineTrackingFilter< float > FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetInput(itk_dti); filter->SetSeedsPerVoxel(numSeeds); filter->SetFaThreshold(minFA); filter->SetMinCurvatureRadius(minCurv); filter->SetStepSize(stepSize); filter->SetF(tendf); filter->SetG(tendg); filter->SetInterpolate(interpolate); filter->SetMinTractLength(minLength); + filter->SetNumberOfThreads(1); 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(); mitk::FiberBundleX::Pointer fib1 = mitk::FiberBundleX::New(fiberBundle); infile = mitk::BaseDataIO::LoadBaseDataFromFile( referenceFileName, s1, s2, false ); mitk::FiberBundleX::Pointer fib2 = dynamic_cast(infile.at(0).GetPointer()); MITK_TEST_CONDITION_REQUIRED(fib2.IsNotNull(), "Check if reference tractogram is not null."); 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(); }