C++ Pointer::SetInput方法代码示例

void QmitkVirtualSurgery::MyCastPixelType(itk::Image<TPixel, VImageDimension> *itkImage, mitk::Image::Pointer *pointer)
{
	std::cout<< "Function MyCastPixelType :Begin."<<std::endl;

	/***************duplicate a image to clip 8 segment******************/
	typedef itk::Image<TPixel, VImageDimension> TImageType;
	typedef itk::ImageDuplicator< typename TImageType > DuplicatorType;
	DuplicatorType::Pointer duplicator = DuplicatorType::New();
	duplicator->SetInputImage( itkImage );
	duplicator->Update();
	typename TImageType::Pointer clonedImage = duplicator->GetOutput();
	mitk::Image::Pointer resultImage = mitk::ImportItkImage( clonedImage );
	mitk::DataTreeNode::Pointer newNode = mitk::DataTreeNode::New();
	newNode->SetData(resultImage);
	newNode->SetProperty("name", mitk::StringProperty::New("Liver Image"));
	newNode->SetProperty("opacity", mitk::FloatProperty::New(0.0));
	mitk::DataStorage::GetInstance()->Add( newNode );
	mitk::RenderingManager::GetInstance()->RequestUpdateAll();
	/*********************************************************************/

	//originalPixelType = (dynamic_cast<mitk::Image *>(selectedImage->Get()->GetData()))->GetPixelType();
	if (originalPixelType == typeid(float))
	{
		std::cout<< "Function MyCastPixelType : Origin image pixel type is float."<<std::endl;
		*pointer = mitk::ImportItkImage(itkImage);
	}
	else
	{
		typedef itk::Image<TPixel, VImageDimension> InputImageType;
		typedef float OutputImagePixelType;
		typedef itk::Image<OutputImagePixelType,  VImageDimension> OutputImageType;
		typedef itk::CastImageFilter<InputImageType, OutputImageType> CasterType;

		CasterType::Pointer caster = CasterType::New();
		caster->SetInput(itkImage);
		try
		{
			caster->Update();
		}
		catch( itk::ExceptionObject & excp )
		{
			std::cerr << "CastPixelType exception thrown." 
				<< std::endl;
			std::cerr << excp << std::endl;
			return ;
		}

		OutputImageType::Pointer output = caster->GetOutput();
		*pointer = mitk::ImportItkImage(output);
	}
	
	std::cout<< "Function MyCastPixelType End."<<std::endl;
	
}

typename itk::ShCoefficientImageImporter< float, shOrder >::QballImageType::Pointer TemplatedConvertShCoeffs(mitk::Image* mitkImg, int toolkit, bool noFlip = false)
{
    typedef itk::ShCoefficientImageImporter< float, shOrder > FilterType;
    typedef mitk::ImageToItk< itk::Image< float, 4 > > CasterType;
    CasterType::Pointer caster = CasterType::New();
    caster->SetInput(mitkImg);
    caster->Update();
    itk::Image< float, 4 >::Pointer itkImage = caster->GetOutput();
    typename FilterType::Pointer filter = FilterType::New();

    if (noFlip)
    {
        filter->SetInputImage(itkImage);
    }
    else
    {
        MITK_INFO << "Flipping image";
        itk::FixedArray<bool, 4> flipAxes;
        flipAxes[0] = true;
        flipAxes[1] = true;
        flipAxes[2] = false;
        flipAxes[3] = false;
        itk::FlipImageFilter< itk::Image< float, 4 > >::Pointer flipper = itk::FlipImageFilter< itk::Image< float, 4 > >::New();
        flipper->SetInput(itkImage);
        flipper->SetFlipAxes(flipAxes);
        flipper->Update();
        itk::Image< float, 4 >::Pointer flipped = flipper->GetOutput();
        itk::Matrix< double,4,4 > m = itkImage->GetDirection(); m[0][0] *= -1; m[1][1] *= -1;
        flipped->SetDirection(m);

        itk::Point< float, 4 > o = itkImage->GetOrigin();
        o[0] -= (flipped->GetLargestPossibleRegion().GetSize(0)-1);
        o[1] -= (flipped->GetLargestPossibleRegion().GetSize(1)-1);
        flipped->SetOrigin(o);
        filter->SetInputImage(flipped);
    }

    switch (toolkit)
    {
    case 0:
        filter->SetToolkit(FilterType::FSL);
        break;
    case 1:
        filter->SetToolkit(FilterType::MRTRIX);
        break;
    default:
        filter->SetToolkit(FilterType::FSL);
    }
    filter->GenerateData();
    return filter->GetQballImage();
}

  void CompareImages(mitk::PeakImage::ItkPeakImageType::Pointer testImage, std::string name)
  {
    typedef mitk::ImageToItk< mitk::PeakImage::ItkPeakImageType > CasterType;
    CasterType::Pointer caster = CasterType::New();
    caster->SetInput(mitk::IOUtil::Load<mitk::Image>(GetTestDataFilePath("DiffusionImaging/FiberFit/out/" + name)));
    caster->Update();
    mitk::PeakImage::ItkPeakImageType::Pointer refImage = caster->GetOutput();


    itk::ImageRegionConstIterator< mitk::PeakImage::ItkPeakImageType > it1(testImage, testImage->GetLargestPossibleRegion());
    itk::ImageRegionConstIterator< mitk::PeakImage::ItkPeakImageType > it2(refImage, refImage->GetLargestPossibleRegion());

    while(!it1.IsAtEnd())
    {
      if (it2.Get()>0.0001)
      {
        if (fabs( it1.Get()/it2.Get()-1 )>0.01)
        {
          itk::ImageFileWriter< mitk::PeakImage::ItkPeakImageType >::Pointer writer = itk::ImageFileWriter< mitk::PeakImage::ItkPeakImageType >::New();
          writer->SetInput(testImage);
          writer->SetFileName(mitk::IOUtil::GetTempPath()+name);
          writer->Update();

          MITK_INFO << it1.Get() << " - " << it2.Get();

          CPPUNIT_ASSERT_MESSAGE("Peak images should be equal 1", false);
        }
      }
      else if (it1.Get()>0.0001)
      {
        itk::ImageFileWriter< mitk::PeakImage::ItkPeakImageType >::Pointer writer = itk::ImageFileWriter< mitk::PeakImage::ItkPeakImageType >::New();
        writer->SetInput(testImage);
        writer->SetFileName(mitk::IOUtil::GetTempPath()+name);
        writer->Update();

        CPPUNIT_ASSERT_MESSAGE("Peak images should be equal 2", false);
      }

      ++it1;
      ++it2;
    }
  }

// ------------------------------------------------------------------------
void OpenCVValve::ConvertImage(const ImageType::Pointer &input, MatPtr &mat)
{
	// cast the image to uchar 
	typedef itk::Image<unsigned char, 2> OutputImageType;
	typedef itk::RescaleIntensityImageFilter<ImageType, OutputImageType> CasterType;
	CasterType::Pointer caster = CasterType::New();
	caster->SetOutputMaximum(255);
	caster->SetOutputMinimum(0);
	caster->SetInput(input);
	caster->Update();


	OutputImageType::Pointer output = caster->GetOutput();


	typedef itk::ImageFileWriter<OutputImageType> WriterType;
	WriterType::Pointer writer = WriterType::New();
	writer->SetImageIO(itk::PNGImageIO::New());
	writer->SetInput(output);
	writer->SetFileName("test.png");
	writer->Update();



	ImageType::SizeType size = input->GetLargestPossibleRegion().GetSize();
	unsigned int rows = size[1];
	unsigned int cols = size[0];

	mat = new MatType(rows,cols, CV_8UC1);


	itk::ImageRegionConstIterator<OutputImageType> it(output, output->GetLargestPossibleRegion());
	it.GoToBegin();
	while(!it.IsAtEnd())
	{
		OutputImageType::IndexType index = it.GetIndex();
		unsigned char val = it.Get();
		mat->at<unsigned char>(cv::Point(index[0], index[1])) = val;
		++it;
	}
}

  void setUp() override
  {
    std::vector<mitk::FiberBundle::Pointer> tracts;
    tracts.push_back(LoadFib("Cluster_0.fib"));
    tracts.push_back(LoadFib("Cluster_1.fib"));
    tracts.push_back(LoadFib("Cluster_2.fib"));
    tracts.push_back(LoadFib("Cluster_3.fib"));
    tracts.push_back(LoadFib("Cluster_4.fib"));

    mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Peak Image"}, {});
    mitk::PeakImage::Pointer peaks = mitk::IOUtil::Load<mitk::PeakImage>(GetTestDataFilePath("DiffusionImaging/FiberFit/csd_peak_image.nii.gz"), &functor);


    typedef mitk::ImageToItk< mitk::PeakImage::ItkPeakImageType > CasterType;
    CasterType::Pointer caster = CasterType::New();
    caster->SetInput(peaks);
    caster->Update();
    mitk::PeakImage::ItkPeakImageType::Pointer peak_image = caster->GetOutput();

    fitter = FitterType::New();
    fitter->SetPeakImage(peak_image);
    fitter->SetTractograms(tracts);
  }

typename itk::ShCoefficientImageImporter< float, shOrder >::QballImageType::Pointer TemplatedConvertShCoeffs(mitk::Image* mitkImg, int toolkit)
{
    typedef itk::ShCoefficientImageImporter< float, shOrder > FilterType;
    typedef mitk::ImageToItk< itk::Image< float, 4 > > CasterType;
    CasterType::Pointer caster = CasterType::New();
    caster->SetInput(mitkImg);
    caster->Update();

    typename FilterType::Pointer filter = FilterType::New();
    switch (toolkit)
    {
    case 0:
        filter->SetToolkit(FilterType::FSL);
        break;
    case 1:
        filter->SetToolkit(FilterType::MRTRIX);
        break;
    default:
        filter->SetToolkit(FilterType::FSL);
    }
    filter->SetInputImage(caster->GetOutput());
    filter->GenerateData();
    return filter->GetQballImage();
}

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
    {
        typedef itk::Image<unsigned char, 3>                                    ItkUcharImgType;
        typedef itk::Image< itk::Vector< float, 3>, 3 >                         ItkDirectionImage3DType;
        typedef itk::VectorContainer< unsigned int, ItkDirectionImage3DType::Pointer >   ItkDirectionImageContainerType;
        typedef itk::EvaluateDirectionImagesFilter< float >                     EvaluationFilterType;

        // load fiber bundle
        mitk::FiberBundleX::Pointer inputTractogram = dynamic_cast<mitk::FiberBundleX*>(mitk::IOUtil::LoadDataNode(fibFile)->GetData());

        // load reference directions
        ItkDirectionImageContainerType::Pointer referenceImageContainer = ItkDirectionImageContainerType::New();
        for (unsigned int i=0; i<referenceImages.size(); i++)
        {
            try
            {
                mitk::Image::Pointer img = dynamic_cast<mitk::Image*>(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<float>::Pointer fOdfFilter = itk::TractsToVectorImageFilter<float>::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::Image*>(mitk::IOUtil::LoadDataNode(LDFP_ERROR_IMAGE_IGNORE)->GetData());
        mitk::Image::Pointer gtAngularErrorImage = dynamic_cast<mitk::Image*>(mitk::IOUtil::LoadDataNode(LDFP_ERROR_IMAGE)->GetData());
        mitk::Image::Pointer gtNumTestDirImage = dynamic_cast<mitk::Image*>(mitk::IOUtil::LoadDataNode(LDFP_NUM_DIRECTIONS)->GetData());
        mitk::FiberBundleX::Pointer gtTestDirections = dynamic_cast<mitk::FiberBundleX*>(mitk::IOUtil::LoadDataNode(LDFP_VECTOR_FIELD)->GetData());
//.........这里部分代码省略.........

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<string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
    if (parsedArgs.size()==0)
        return EXIT_FAILURE;

    ctkCommandLineParser::StringContainerType referenceImages = us::any_cast<ctkCommandLineParser::StringContainerType>(parsedArgs["reference"]);
    ctkCommandLineParser::StringContainerType maskImages;
    if (parsedArgs.count("mask"))
        maskImages = us::any_cast<ctkCommandLineParser::StringContainerType>(parsedArgs["mask"]);

    string fibFile = us::any_cast<string>(parsedArgs["input"]);

    float angularThreshold = 25;
    if (parsedArgs.count("athresh"))
        angularThreshold = us::any_cast<float>(parsedArgs["athresh"]);

    string outRoot = us::any_cast<string>(parsedArgs["out"]);

    bool verbose = false;
    if (parsedArgs.count("verbose"))
        verbose = us::any_cast<bool>(parsedArgs["verbose"]);

    bool ignore = false;
    if (parsedArgs.count("ignore"))
        ignore = us::any_cast<bool>(parsedArgs["ignore"]);

    try
    {
        RegisterDiffusionCoreObjectFactory();
        RegisterFiberTrackingObjectFactory();

        typedef itk::Image<unsigned char, 3>                                    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::FiberBundleX*>(mitk::IOUtil::LoadDataNode(fibFile)->GetData());

        // load reference directions
        ItkDirectionImageContainerType::Pointer referenceImageContainer = ItkDirectionImageContainerType::New();
        for (int i=0; i<referenceImages.size(); i++)
        {
            try
            {
                mitk::Image::Pointer img = dynamic_cast<mitk::Image*>(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<float>::Pointer fOdfFilter = itk::TractsToVectorImageFilter<float>::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() );
//.........这里部分代码省略.........

//.........这里部分代码省略.........
                std::cout << "Using FSL SH-basis";
            }
            else if ( boost::algorithm::equals(convention, "MRtrix") )
            {
                toolkitConvention = 2;
                std::cout << "Using MRtrix SH-basis";
            }
            else
                std::cout << "Using MITK SH-basis";
        }
        else
            std::cout << "Using MITK SH-basis";

        ItkUcharImgType::Pointer itkMaskImage = nullptr;
        if (mask.IsNotNull())
        {
            try{
                itkMaskImage = ItkUcharImgType::New();
                mitk::CastToItkImage(mask, itkMaskImage);
                filter->SetMaskImage(itkMaskImage);
            }
            catch(...)
            {

            }
        }

        if (toolkitConvention>0)
        {
            std::cout << "Converting coefficient image to MITK format";
            typedef itk::ShCoefficientImageImporter< float, shOrder > ConverterType;
            typedef mitk::ImageToItk< itk::Image< float, 4 > > CasterType;
            CasterType::Pointer caster = CasterType::New();
            caster->SetInput(image);
            caster->Update();
            itk::Image< float, 4 >::Pointer itkImage = caster->GetOutput();

            typename ConverterType::Pointer converter = ConverterType::New();

            if (noFlip)
            {
                converter->SetInputImage(itkImage);
            }
            else
            {
                std::cout << "Flipping image";
                itk::FixedArray<bool, 4> flipAxes;
                flipAxes[0] = true;
                flipAxes[1] = true;
                flipAxes[2] = false;
                flipAxes[3] = false;
                itk::FlipImageFilter< itk::Image< float, 4 > >::Pointer flipper = itk::FlipImageFilter< itk::Image< float, 4 > >::New();
                flipper->SetInput(itkImage);
                flipper->SetFlipAxes(flipAxes);
                flipper->Update();
                itk::Image< float, 4 >::Pointer flipped = flipper->GetOutput();
                itk::Matrix< double,4,4 > m = itkImage->GetDirection(); m[0][0] *= -1; m[1][1] *= -1;
                flipped->SetDirection(m);

                itk::Point< float, 4 > o = itkImage->GetOrigin();
                o[0] -= (flipped->GetLargestPossibleRegion().GetSize(0)-1);
                o[1] -= (flipped->GetLargestPossibleRegion().GetSize(1)-1);
                flipped->SetOrigin(o);
                converter->SetInputImage(flipped);
            }

/*!
\brief Copies transformation matrix of one image to another
*/
int main(int argc, char* argv[])
{
  mitkCommandLineParser parser;

  parser.setTitle("Flip Peaks");
  parser.setCategory("Preprocessing Tools");
  parser.setDescription("Flips the peaks of the input peak image along the given dimensions.");
  parser.setContributor("MIC");

  parser.setArgumentPrefix("--", "-");
  parser.addArgument("", "i", mitkCommandLineParser::String, "Input", "input image", us::Any(), false, false, false, mitkCommandLineParser::Input);
  parser.addArgument("", "o", mitkCommandLineParser::String, "Output", "output image", us::Any(), false, false, false, mitkCommandLineParser::Output);
  parser.addArgument("", "x", mitkCommandLineParser::Bool, "Flip x", "flip along x-axis");
  parser.addArgument("", "y", mitkCommandLineParser::Bool, "Flip y", "flip along y-axis");
  parser.addArgument("", "z", mitkCommandLineParser::Bool, "Flip z", "flip along z-axis");

  std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
  if (parsedArgs.size()==0)
    return EXIT_FAILURE;

  std::string imageName = us::any_cast<std::string>(parsedArgs["i"]);
  std::string outImage = us::any_cast<std::string>(parsedArgs["o"]);

  bool x = false;
  if (parsedArgs.count("x"))
    x = us::any_cast<bool>(parsedArgs["x"]);

  bool y = false;
  if (parsedArgs.count("y"))
    y = us::any_cast<bool>(parsedArgs["y"]);

  bool z = false;
  if (parsedArgs.count("z"))
    z = us::any_cast<bool>(parsedArgs["z"]);

  try
  {
    mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Peak Image"}, {});
    mitk::PeakImage::Pointer image = mitk::IOUtil::Load<mitk::PeakImage>(imageName, &functor);

    typedef mitk::ImageToItk< mitk::PeakImage::ItkPeakImageType > CasterType;
    CasterType::Pointer caster = CasterType::New();
    caster->SetInput(image);
    caster->Update();
    mitk::PeakImage::ItkPeakImageType::Pointer itkImg = caster->GetOutput();

    itk::FlipPeaksFilter< float >::Pointer flipper = itk::FlipPeaksFilter< float >::New();
    flipper->SetInput(itkImg);
    flipper->SetFlipX(x);
    flipper->SetFlipY(y);
    flipper->SetFlipZ(z);
    flipper->Update();

    mitk::Image::Pointer resultImage = dynamic_cast<mitk::Image*>(mitk::PeakImage::New().GetPointer());
    mitk::CastToMitkImage(flipper->GetOutput(), resultImage);
    resultImage->SetVolume(flipper->GetOutput()->GetBufferPointer());

    mitk::IOUtil::Save(resultImage, outImage);
  }
  catch (itk::ExceptionObject e)
  {
    std::cout << e;
    return EXIT_FAILURE;
  }
  catch (std::exception e)
  {
    std::cout << e.what();
    return EXIT_FAILURE;
  }
  catch (...)
  {
    std::cout << "ERROR!?!";
    return EXIT_FAILURE;
  }
  return EXIT_SUCCESS;
}

int TractogramAngularError(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::String, "mask image");
    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");
    parser.addArgument("trilinear", "t", ctkCommandLineParser::Bool, "use trilinear instead of nearest neighbor interpolation");

    map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
    if (parsedArgs.size()==0)
        return EXIT_FAILURE;

    ctkCommandLineParser::StringContainerType referenceImages = us::any_cast<ctkCommandLineParser::StringContainerType>(parsedArgs["reference"]);

    string fibFile = us::any_cast<string>(parsedArgs["input"]);

    string maskImage("");
    if (parsedArgs.count("mask"))
        maskImage = us::any_cast<string>(parsedArgs["mask"]);

    string outRoot = us::any_cast<string>(parsedArgs["out"]);

    bool verbose = false;
    if (parsedArgs.count("verbose"))
        verbose = us::any_cast<bool>(parsedArgs["verbose"]);

    bool ignore = false;
    if (parsedArgs.count("ignore"))
        ignore = us::any_cast<bool>(parsedArgs["ignore"]);

    bool interpolate = false;
    if (parsedArgs.count("interpolate"))
        interpolate = us::any_cast<bool>(parsedArgs["interpolate"]);

    try
    {
        RegisterDiffusionCoreObjectFactory();
        RegisterFiberTrackingObjectFactory();

        typedef itk::Image<unsigned char, 3>                                    ItkUcharImgType;
        typedef itk::Image< itk::Vector< float, 3>, 3 >                         ItkDirectionImage3DType;
        typedef itk::VectorContainer< int, ItkDirectionImage3DType::Pointer >   ItkDirectionImageContainerType;
        typedef itk::EvaluateTractogramDirectionsFilter< float >                EvaluationFilterType;

        // load fiber bundle
        mitk::FiberBundleX::Pointer inputTractogram = dynamic_cast<mitk::FiberBundleX*>(mitk::IOUtil::LoadDataNode(fibFile)->GetData());
        if (!inputTractogram)
            return EXIT_FAILURE;

        // load reference directions
        ItkDirectionImageContainerType::Pointer referenceImageContainer = ItkDirectionImageContainerType::New();
        for (int i=0; i<referenceImages.size(); i++)
        {
            try
            {
                mitk::Image::Pointer img = dynamic_cast<mitk::Image*>(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);
            }
        }

        // load/create mask image
        ItkUcharImgType::Pointer itkMaskImage = ItkUcharImgType::New();
        if (maskImage.compare("")==0)
        {
            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);
        }
        else
        {
            mitk::Image::Pointer mitkMaskImage = dynamic_cast<mitk::Image*>(mitk::IOUtil::LoadDataNode(maskImage)->GetData());
            mitk::CastToItkImage<ItkUcharImgType>(mitkMaskImage, itkMaskImage);
        }

        // evaluate directions
        EvaluationFilterType::Pointer evaluationFilter = EvaluationFilterType::New();
        evaluationFilter->SetTractogram(inputTractogram);
        evaluationFilter->SetReferenceImageSet(referenceImageContainer);
        evaluationFilter->SetMaskImage(itkMaskImage);
        evaluationFilter->SetIgnoreMissingDirections(ignore);
        evaluationFilter->SetUseInterpolation(interpolate);
        evaluationFilter->Update();
//.........这里部分代码省略.........

//.........这里部分代码省略.........
    for (auto item : fib_files)
    {
      if ( ist::FileIsDirectory(item) )
      {
        for ( auto fibFile : get_file_list(item) )
        {
          mitk::FiberBundle::Pointer inputTractogram = mitk::IOUtil::Load<mitk::FiberBundle>(fibFile);
          if (inputTractogram.IsNull())
            continue;
          input_tracts.push_back(inputTractogram);
          fib_names.push_back(fibFile);
        }
      }
      else
      {
        mitk::FiberBundle::Pointer inputTractogram = mitk::IOUtil::Load<mitk::FiberBundle>(item);
        if (inputTractogram.IsNull())
          continue;
        input_tracts.push_back(inputTractogram);
        fib_names.push_back(item);
      }
    }
    std::cout.rdbuf (old);              // <-- restore

    itk::FitFibersToImageFilter::Pointer fitter = itk::FitFibersToImageFilter::New();

    mitk::BaseData::Pointer inputData = mitk::IOUtil::Load(input_image_name, &functor)[0].GetPointer();
    mitk::Image::Pointer mitk_image = dynamic_cast<mitk::Image*>(inputData.GetPointer());
    mitk::PeakImage::Pointer mitk_peak_image = dynamic_cast<mitk::PeakImage*>(inputData.GetPointer());
    if (mitk_peak_image.IsNotNull())
    {
      typedef mitk::ImageToItk< mitk::PeakImage::ItkPeakImageType > CasterType;
      CasterType::Pointer caster = CasterType::New();
      caster->SetInput(mitk_peak_image);
      caster->Update();
      mitk::PeakImage::ItkPeakImageType::Pointer peak_image = caster->GetOutput();
      fitter->SetPeakImage(peak_image);
    }
    else if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(mitk_image))
    {
      fitter->SetDiffImage(mitk::DiffusionPropertyHelper::GetItkVectorImage(mitk_image));
      mitk::TensorModel<>* model = new mitk::TensorModel<>();
      model->SetBvalue(1000);
      model->SetDiffusivity1(0.0010);
      model->SetDiffusivity2(0.00015);
      model->SetDiffusivity3(0.00015);
      model->SetGradientList(mitk::DiffusionPropertyHelper::GetGradientContainer(mitk_image));
      fitter->SetSignalModel(model);
    }
    else if (mitk_image->GetDimension()==3)
    {
      itk::FitFibersToImageFilter::DoubleImgType::Pointer scalar_image = itk::FitFibersToImageFilter::DoubleImgType::New();
      mitk::CastToItkImage(mitk_image, scalar_image);
      fitter->SetScalarImage(scalar_image);
    }
    else
    {
      MITK_INFO << "Input image invalid. Valid options are peak image, 3D scalar image or raw diffusion-weighted image.";
      return EXIT_FAILURE;
    }

    fitter->SetTractograms(input_tracts);
    fitter->SetFitIndividualFibers(single_fib);
    fitter->SetMaxIterations(max_iter);
    fitter->SetGradientTolerance(g_tol);
    fitter->SetLambda(lambda);