void Init()
  {

    im1 = mitk::ImageGenerator::GenerateRandomImage<double>(2,2,2,1,2,2,2,1,0);
    im2 = mitk::ImageGenerator::GenerateRandomImage<double>(3,3,3,1,3,3,3,3,2);
    im3 = mitk::ImageGenerator::GenerateRandomImage<double>(4,4,4,1,4,4,4,5,4);
    im4 = mitk::ImageGenerator::GenerateRandomImage<double>(5,5,5,1,5,5,5,7,6);

    dataCol1 = mitk::DataCollection::New();
    dataCol2 = mitk::DataCollection::New();

    dataCol1->AddData(im1.GetPointer(),"T1");

    dataCol1->AddData(im2.GetPointer(),"T2");

    dataCol2->AddData(im3.GetPointer(),"T1");
    dataCol2->AddData(im4.GetPointer(),"T2");

    col1 = mitk::DataCollection::New();

    col1->SetName("GnaBla");
    col1->AddData(dataCol1.GetPointer(), "0001");
    col1->AddData(dataCol2.GetPointer(), "0002");

    m_Collection = mitk::DataCollection::New();

    m_Collection->SetName("DummyCollection");
    m_Collection->AddData(col1.GetPointer(), "C1");


  }
void mitk::SurfaceInterpolationController::SetCurrentInterpolationSession(mitk::Image::Pointer currentSegmentationImage)
{
  if (currentSegmentationImage.GetPointer() == m_SelectedSegmentation)
    return;

  if (currentSegmentationImage.IsNull())
  {
    m_SelectedSegmentation = nullptr;
    return;
  }

  m_SelectedSegmentation = currentSegmentationImage.GetPointer();

  auto it = m_ListOfInterpolationSessions.find(currentSegmentationImage.GetPointer());
  // If the session does not exist yet create a new ContourPositionPairList otherwise reinitialize the interpolation pipeline
  if (it == m_ListOfInterpolationSessions.end())
  {
    ContourPositionInformationVec2D newList;
    m_ListOfInterpolationSessions.insert(std::pair<mitk::Image*, ContourPositionInformationVec2D>(m_SelectedSegmentation, newList));
    m_InterpolationResult = nullptr;
    m_CurrentNumberOfReducedContours = 0;

    itk::MemberCommand<SurfaceInterpolationController>::Pointer command = itk::MemberCommand<SurfaceInterpolationController>::New();
    command->SetCallbackFunction(this, &SurfaceInterpolationController::OnSegmentationDeleted);
    m_SegmentationObserverTags.insert( std::pair<mitk::Image*, unsigned long>( m_SelectedSegmentation, m_SelectedSegmentation->AddObserver( itk::DeleteEvent(), command ) ) );
  }

  this->ReinitializeInterpolation();
}
  void GetImageStatisticsWithImageAndMaskNotConnected()
  {
    //create rules connection + add statistics to dataStorage
    auto statisticsNode = mitk::CreateImageStatisticsNode(m_statisticsContainer, "testStatistics");
    CreateNodeRelationImage(m_statisticsContainer.GetPointer(), m_image.GetPointer());
    CreateNodeRelationMask(m_statisticsContainer.GetPointer(), m_mask.GetPointer());
    auto standaloneDataStorage = mitk::StandaloneDataStorage::New();
    standaloneDataStorage->Add(statisticsNode);

    //rule: (image-->statistics, mask-->statistics), 1 connected image --> test return nullptr
    mitk::ImageStatisticsContainer::ConstPointer statisticsWithImage;
    CPPUNIT_ASSERT_NO_THROW(statisticsWithImage = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image.GetPointer()));
    CPPUNIT_ASSERT_EQUAL(statisticsWithImage.IsNull(), true);

    //rule: (image-->statistics, mask-->statistics), 1 unconnected image, 1 unconnected mask --> test return nullptr
    mitk::ImageStatisticsContainer::ConstPointer statisticsWithImageNotConnectedAndMaskNotConnected;
    CPPUNIT_ASSERT_NO_THROW(statisticsWithImageNotConnectedAndMaskNotConnected = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image2.GetPointer(), m_mask2.GetPointer()));
    CPPUNIT_ASSERT_EQUAL(statisticsWithImageNotConnectedAndMaskNotConnected.IsNull(), true);

    //rule: (image-->statistics, mask-->statistics), 1 unconnected image, 1 connected mask --> test return nullptr
    mitk::ImageStatisticsContainer::ConstPointer statisticsWithImageAndMaskNotConnected;
    CPPUNIT_ASSERT_NO_THROW(statisticsWithImageAndMaskNotConnected = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image2.GetPointer(), m_mask.GetPointer()));
    CPPUNIT_ASSERT_EQUAL(statisticsWithImageAndMaskNotConnected.IsNull(), true);

    //rule: (image-->statistics, mask-->statistics), 1 connected image, 1 unconnected planarFigure --> test return nullptr
    mitk::ImageStatisticsContainer::ConstPointer statisticsWithImageAndPlanarFigureNotConnected;
    CPPUNIT_ASSERT_NO_THROW(statisticsWithImageAndPlanarFigureNotConnected = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image.GetPointer(), m_planarFigure.GetPointer()));
    CPPUNIT_ASSERT_EQUAL(statisticsWithImageAndPlanarFigureNotConnected.IsNull(), true);

    //rule: (image-->statistics, mask-->statistics), 1 unconnected image, 1 unconnected planarFigure --> test return nullptr
    mitk::ImageStatisticsContainer::ConstPointer statisticsWithImageNotConnectedAndPlanarFigureNotConnected;
    CPPUNIT_ASSERT_NO_THROW(statisticsWithImageAndPlanarFigureNotConnected = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image2.GetPointer(), m_planarFigure.GetPointer()));
    CPPUNIT_ASSERT_EQUAL(statisticsWithImageAndPlanarFigureNotConnected.IsNull(), true);
  }
void mitk::SurfaceInterpolationController::SetCurrentInterpolationSession(mitk::Image::Pointer currentSegmentationImage)
{
  if (currentSegmentationImage.GetPointer() == m_SelectedSegmentation)
    return;

  m_ReduceFilter->Reset();
  m_NormalsFilter->Reset();
  m_InterpolateSurfaceFilter->Reset();

  if (currentSegmentationImage.IsNull())
  {
    m_SelectedSegmentation = 0;
    return;
  }
  ContourListMap::iterator it = m_ListOfInterpolationSessions.find(currentSegmentationImage.GetPointer());

  m_SelectedSegmentation = currentSegmentationImage.GetPointer();

  itk::ImageBase<3>::Pointer itkImage = itk::ImageBase<3>::New();
  AccessFixedDimensionByItk_1( m_SelectedSegmentation, GetImageBase, 3, itkImage );
  m_InterpolateSurfaceFilter->SetReferenceImage( itkImage.GetPointer() );

  if (it == m_ListOfInterpolationSessions.end())
  {
    ContourPositionPairList newList;
    m_ListOfInterpolationSessions.insert(std::pair<mitk::Image*, ContourPositionPairList>(m_SelectedSegmentation, newList));
    m_InterpolationResult = 0;
    m_CurrentNumberOfReducedContours = 0;

    itk::MemberCommand<SurfaceInterpolationController>::Pointer command = itk::MemberCommand<SurfaceInterpolationController>::New();
    command->SetCallbackFunction(this, &SurfaceInterpolationController::OnSegmentationDeleted);
    m_SegmentationObserverTags.insert( std::pair<mitk::Image*, unsigned long>( m_SelectedSegmentation, m_SelectedSegmentation->AddObserver( itk::DeleteEvent(), command ) ) );

  }
  else
  {
    for (unsigned int i = 0; i < m_ListOfInterpolationSessions[m_SelectedSegmentation].size(); i++)
    {
      m_ReduceFilter->SetInput(i, m_ListOfInterpolationSessions[m_SelectedSegmentation].at(i).contour);
    }

    m_ReduceFilter->Update();

    m_CurrentNumberOfReducedContours = m_ReduceFilter->GetNumberOfOutputs();

    for (unsigned int i = 0; i < m_CurrentNumberOfReducedContours; i++)
    {
      m_NormalsFilter->SetInput(i, m_ReduceFilter->GetOutput(i));
      m_InterpolateSurfaceFilter->SetInput(i, m_NormalsFilter->GetOutput(i));
    }
  }
  Modified();
}
Exemplo n.º 5
0
  /**
   * @brief AddColouredOverlay - Overlays the rgbImage with an coloured overlay
   *
   * For all positions in overlayImage not zero, its value is multiplied the the colour value and added
   * to the rgbImage.
   *
   * @param rgbImage - input rgbImage to which the coloured overlay is added
   * @param overlayImage
   * @param color
   */
  void AddColouredOverlay(mitk::Image::Pointer rgbImage, mitk::Image::Pointer overlayImage, mitk::Color color)
  {
    unsigned int *dim = rgbImage->GetDimensions();
    itk::Image<PixelType,3>::Pointer itkOverlayImage = itk::Image<PixelType,3>::New();
    mitk::CastToItkImage(overlayImage.GetPointer(), itkOverlayImage);
    mitk::ImagePixelWriteAccessor<RGBPixelType ,3> writeAcc(rgbImage);

    itk::Index<3> idx;
    itk::RGBPixel<PixelType> value;
    unsigned short overlayVal=0;
    // Fill rgb image with gray values
    for (idx[2] =0; (unsigned int)idx[2] < dim[2]; idx[2]++)
    {
      for (idx[1] =0; (unsigned int)idx[1] < dim[1]; idx[1]++)
      {
        for (idx[0] =0; (unsigned int)idx[0] < dim[0]; idx[0]++)
        {
          overlayVal = 255*itkOverlayImage->GetPixel(idx);
          value = writeAcc.GetPixelByIndex(idx);
          value[0] = std::min( (int)(value[0] + overlayVal * color[0]),254*255);
          value[1] =  std::min((int)(value[1] + overlayVal * color[1]),254*255) ;
          value[2] = std::min((int)(value[2] + overlayVal * color[2]),254*255);
          writeAcc.SetPixelByIndex(idx, value);
        }
      }
    }
  }
  void GetImageStatisticsWithImageConnected()
  {
    //create rules connection
    auto statisticsNode = mitk::CreateImageStatisticsNode(m_statisticsContainer, "testStatistics");
    CreateNodeRelationImage(m_statisticsContainer.GetPointer(), m_image.GetPointer());
    auto standaloneDataStorage = mitk::StandaloneDataStorage::New();
    standaloneDataStorage->Add(statisticsNode);

    //rule: (image-->statistics), 1 connected image --> test return image statistics
    mitk::ImageStatisticsContainer::ConstPointer statisticsWithImage;
    CPPUNIT_ASSERT_NO_THROW(statisticsWithImage = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image.GetPointer()));
    CPPUNIT_ASSERT_EQUAL(statisticsWithImage->GetUID(), m_statisticsContainer->GetUID());

    //new rule: (image2-->statistics2 AND mask --> statistics2)
    CreateNodeRelationImage(m_statisticsContainer2.GetPointer(), m_image2.GetPointer());
    CreateNodeRelationMask(m_statisticsContainer2.GetPointer(), m_mask.GetPointer());

    auto statisticsNode2 = mitk::CreateImageStatisticsNode(m_statisticsContainer2, "testStatistics2");
    standaloneDataStorage->Add(statisticsNode2);

    //--> test return (still) image statistics (!= statistics2)
    mitk::ImageStatisticsContainer::ConstPointer statisticsWithImageAgain;
    CPPUNIT_ASSERT_NO_THROW(statisticsWithImageAgain = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image.GetPointer()));
    CPPUNIT_ASSERT_EQUAL(statisticsWithImageAgain->GetUID(), m_statisticsContainer->GetUID());
    CPPUNIT_ASSERT_EQUAL(statisticsWithImageAgain->GetUID() != m_statisticsContainer2->GetUID(), true);

    //--> test return image statistics 2
    CPPUNIT_ASSERT_NO_THROW(statisticsWithImageAgain = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image2.GetPointer(), m_mask.GetPointer()));
    CPPUNIT_ASSERT_EQUAL(statisticsWithImageAgain->GetUID(), m_statisticsContainer2->GetUID());
    CPPUNIT_ASSERT_EQUAL(statisticsWithImageAgain->GetUID() != m_statisticsContainer->GetUID(), true);

    //add another newer statistic: should return this newer one
    auto statisticsContainerNew = mitk::ImageStatisticsContainer::New();
    CreateNodeRelationImage(statisticsContainerNew.GetPointer(), m_image.GetPointer());

    auto statisticsNodeNew = mitk::CreateImageStatisticsNode(statisticsContainerNew, "testStatisticsNew");
    standaloneDataStorage->Add(statisticsNodeNew);
    statisticsContainerNew->Modified();

    mitk::ImageStatisticsContainer::ConstPointer statisticsWithImageNew;
    CPPUNIT_ASSERT_NO_THROW(statisticsWithImageNew = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image.GetPointer()));
    CPPUNIT_ASSERT_EQUAL(statisticsWithImageNew->GetUID(), statisticsContainerNew->GetUID());
    CPPUNIT_ASSERT_EQUAL(statisticsWithImageNew->GetUID() != m_statisticsContainer->GetUID(), true);
  }
  void GetImageStatisticsWithImageAndMaskConnected()
  {
    //create rules connection + add statistics to dataStorage
    auto statisticsNode = mitk::CreateImageStatisticsNode(m_statisticsContainer, "testStatistics");

    CreateNodeRelationImage(m_statisticsContainer.GetPointer(), m_image.GetPointer());
    CreateNodeRelationMask(m_statisticsContainer.GetPointer(), m_mask.GetPointer());
    auto standaloneDataStorage = mitk::StandaloneDataStorage::New();
    standaloneDataStorage->Add(statisticsNode);

    //rule: (image-->statistics, mask-->statistics), 1 connected image, 1 connected mask --> test return statistics
    mitk::ImageStatisticsContainer::ConstPointer statisticsWithImageAndMask;
    CPPUNIT_ASSERT_NO_THROW(statisticsWithImageAndMask = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image.GetPointer(), m_mask.GetPointer()));
    CPPUNIT_ASSERT_EQUAL(statisticsWithImageAndMask.IsNull(), false);
    CPPUNIT_ASSERT_EQUAL(statisticsWithImageAndMask->GetUID(), m_statisticsContainer->GetUID());

    //new rule: (image-->statistics2) --> returns statistic because statistic2 has no mask connection
    CreateNodeRelationImage(m_statisticsContainer2.GetPointer(), m_image.GetPointer());
    
    auto statisticsNode2 = mitk::CreateImageStatisticsNode(m_statisticsContainer2, "testStatistics2");
    standaloneDataStorage->Add(statisticsNode2);

    mitk::ImageStatisticsContainer::ConstPointer statisticsWithImageAndMaskAgain;
    CPPUNIT_ASSERT_NO_THROW(statisticsWithImageAndMaskAgain = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image.GetPointer(), m_mask.GetPointer()));
    CPPUNIT_ASSERT_EQUAL(statisticsWithImageAndMaskAgain->GetUID(), m_statisticsContainer->GetUID());
    CPPUNIT_ASSERT_EQUAL(statisticsWithImageAndMaskAgain->GetUID() != m_statisticsContainer2->GetUID(), true);

    //add another newer statistic: should return this newer one
    auto statisticsContainerNew = mitk::ImageStatisticsContainer::New();

    mitk::PropertyRelations::RuleResultVectorType rules4;
    CreateNodeRelationImage(statisticsContainerNew.GetPointer(), m_image.GetPointer());
    CreateNodeRelationMask(statisticsContainerNew.GetPointer(), m_mask.GetPointer());
    auto statisticsNodeNew = mitk::CreateImageStatisticsNode(statisticsContainerNew, "testStatisticsNew");
    standaloneDataStorage->Add(statisticsNodeNew);

    mitk::ImageStatisticsContainer::ConstPointer statisticsWithImageAndMaskNew;
    CPPUNIT_ASSERT_NO_THROW(statisticsWithImageAndMaskNew = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image.GetPointer(), m_mask.GetPointer()));
    CPPUNIT_ASSERT_EQUAL(statisticsContainerNew->GetUID(), statisticsWithImageAndMaskNew->GetUID());
    CPPUNIT_ASSERT_EQUAL(statisticsWithImageAndMaskNew->GetUID() != m_statisticsContainer->GetUID(), true);
  }
  void GetImageStatisticsInvalid()
  {
    CreateNodeRelationImage(m_statisticsContainer.GetPointer(), m_image.GetPointer());

    CPPUNIT_ASSERT_THROW(mitk::ImageStatisticsContainerManager::GetImageStatistics(nullptr, m_image.GetPointer()), mitk::Exception);

    auto standaloneDataStorage = mitk::StandaloneDataStorage::New();

    CPPUNIT_ASSERT_THROW(mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), nullptr), mitk::Exception);
    CPPUNIT_ASSERT_THROW(mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), nullptr, m_mask.GetPointer()), mitk::Exception);
    CPPUNIT_ASSERT_THROW(mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), nullptr, m_planarFigure.GetPointer()), mitk::Exception);
  }
bool mitk::SurfaceInterpolationController::ReplaceInterpolationSession(mitk::Image::Pointer oldSession, mitk::Image::Pointer newSession)
{
  if (oldSession.IsNull() || newSession.IsNull())
    return false;

  if (oldSession.GetPointer() == newSession.GetPointer())
    return false;

  if (!mitk::Equal(*(oldSession->GetGeometry()), *(newSession->GetGeometry()), mitk::eps, false))
    return false;

  auto it = m_ListOfInterpolationSessions.find(oldSession.GetPointer());

  if (it == m_ListOfInterpolationSessions.end())
    return false;

  ContourPositionInformationVec2D oldList = (*it).second;
  m_ListOfInterpolationSessions.insert(std::pair<mitk::Image*, ContourPositionInformationVec2D>(newSession.GetPointer(), oldList));
  itk::MemberCommand<SurfaceInterpolationController>::Pointer command = itk::MemberCommand<SurfaceInterpolationController>::New();
  command->SetCallbackFunction(this, &SurfaceInterpolationController::OnSegmentationDeleted);
  m_SegmentationObserverTags.insert( std::pair<mitk::Image*, unsigned long>( newSession, newSession->AddObserver( itk::DeleteEvent(), command ) ) );

  if (m_SelectedSegmentation == oldSession)
    m_SelectedSegmentation = newSession;

  mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New();
  timeSelector->SetInput( m_SelectedSegmentation );
  timeSelector->SetTimeNr( m_CurrentTimeStep );
  timeSelector->SetChannelNr( 0 );
  timeSelector->Update();
  mitk::Image::Pointer refSegImage = timeSelector->GetOutput();
  m_NormalsFilter->SetSegmentationBinaryImage(refSegImage);

  this->RemoveInterpolationSession(oldSession);
  return true;
}
Exemplo n.º 10
0
void mitk::RegistrationWrapper::ApplyTransformationToImage(mitk::Image::Pointer img, const mitk::RegistrationWrapper::RidgidTransformType &transformation,double* offset, mitk::Image* resampleReference,  bool binary)
{
  typedef mitk::DiffusionImage<short> DiffusionImageType;

  if (dynamic_cast<DiffusionImageType*> (img.GetPointer()) == NULL)
  {

    ItkImageType::Pointer itkImage = ItkImageType::New();


    MITK_ERROR << "imgCopy  0 " <<  "/" << img->GetReferenceCount();
    MITK_ERROR << "pixel type  " << img->GetPixelType().GetComponentTypeAsString();

    CastToItkImage(img, itkImage);



    typedef itk::Euler3DTransform< double > RigidTransformType;
    RigidTransformType::Pointer rtransform = RigidTransformType::New();
    RigidTransformType::ParametersType parameters(RigidTransformType::ParametersDimension);

    for (int i = 0; i<6;++i)
      parameters[i] = transformation[i];

    rtransform->SetParameters( parameters );

    mitk::Point3D origin = itkImage->GetOrigin();
    origin[0]-=offset[0];
    origin[1]-=offset[1];
    origin[2]-=offset[2];

    mitk::Point3D newOrigin = rtransform->GetInverseTransform()->TransformPoint(origin);

    itk::Matrix<double,3,3> dir = itkImage->GetDirection();
    itk::Matrix<double,3,3> transM  ( vnl_inverse(rtransform->GetMatrix().GetVnlMatrix()));
    itk::Matrix<double,3,3> newDirection = transM * dir;

    itkImage->SetOrigin(newOrigin);
    itkImage->SetDirection(newDirection);

    // Perform Resampling if reference image is provided
    if (resampleReference != NULL)
    {
      typedef itk::ResampleImageFilter<ItkImageType, ItkImageType>  ResampleFilterType;

      ItkImageType::Pointer itkReference = ItkImageType::New();
      CastToItkImage(resampleReference,itkReference);

      typedef itk::WindowedSincInterpolateImageFunction< ItkImageType, 3> WindowedSincInterpolatorType;
      WindowedSincInterpolatorType::Pointer sinc_interpolator = WindowedSincInterpolatorType::New();

      typedef itk::NearestNeighborInterpolateImageFunction< ItkImageType, double > NearestNeighborInterpolatorType;
      NearestNeighborInterpolatorType::Pointer nn_interpolator = NearestNeighborInterpolatorType::New();


      ResampleFilterType::Pointer resampler = ResampleFilterType::New();
      resampler->SetInput(itkImage);
      resampler->SetReferenceImage( itkReference );
      resampler->UseReferenceImageOn();
      if (binary)
        resampler->SetInterpolator(nn_interpolator);
      else
        resampler->SetInterpolator(sinc_interpolator);

      resampler->Update();

      GrabItkImageMemory(resampler->GetOutput(), img);
    }
    else
    {
      // !! CastToItk behaves very differently depending on the original data type
      // if the target type is the same as the original, only a pointer to the data is set
      // and an additional GrabItkImageMemory will cause a segfault when the image is destroyed
      // GrabItkImageMemory - is not necessary in this case since we worked on the original data
      // See Bug 17538.
      if (img->GetPixelType().GetComponentTypeAsString() != "double")
        img = GrabItkImageMemory(itkImage);
    }
  }
  else
  {
    DiffusionImageType::Pointer diffImages = dynamic_cast<DiffusionImageType*>(img.GetPointer());

    typedef itk::Euler3DTransform< double > RigidTransformType;
    RigidTransformType::Pointer rtransform = RigidTransformType::New();
    RigidTransformType::ParametersType parameters(RigidTransformType::ParametersDimension);

    for (int i = 0; i<6;++i)
    {
      parameters[i] = transformation[i];
    }

    rtransform->SetParameters( parameters );

    mitk::Point3D b0origin = diffImages->GetVectorImage()->GetOrigin();
    b0origin[0]-=offset[0];
    b0origin[1]-=offset[1];
    b0origin[2]-=offset[2];

    mitk::Point3D newOrigin = rtransform->GetInverseTransform()->TransformPoint(b0origin);

    itk::Matrix<double,3,3> dir = diffImages->GetVectorImage()->GetDirection();
    itk::Matrix<double,3,3> transM  ( vnl_inverse(rtransform->GetMatrix().GetVnlMatrix()));
    itk::Matrix<double,3,3> newDirection = transM * dir;

    diffImages->GetVectorImage()->SetOrigin(newOrigin);
    diffImages->GetVectorImage()->SetDirection(newDirection);
    diffImages->Modified();

    mitk::DiffusionImageCorrectionFilter<short>::Pointer correctionFilter = mitk::DiffusionImageCorrectionFilter<short>::New();

    // For Diff. Images: Need to rotate the gradients (works in-place)
    correctionFilter->SetImage(diffImages);
    correctionFilter->CorrectDirections(transM.GetVnlMatrix());
    img = diffImages;
  }
}
Exemplo n.º 11
0
void KurtosisMapComputation( mitk::Image::Pointer input,
                             std::string output_prefix ,
                             std::string output_type,
                             std::string maskPath,
                             bool omitBZero,
                             double lower,
                             double upper )
{
  DPH::ImageType::Pointer vectorImage = DPH::ImageType::New();
  mitk::CastToItkImage( input, vectorImage );

  typedef itk::DiffusionKurtosisReconstructionImageFilter< short, double > KurtosisFilterType;
  KurtosisFilterType::Pointer kurtosis_filter = KurtosisFilterType::New();
  kurtosis_filter->SetInput( GetBlurredVectorImage( vectorImage, 1.5 ) );
  kurtosis_filter->SetReferenceBValue( DPH::GetReferenceBValue( input.GetPointer() ) );
  kurtosis_filter->SetGradientDirections( DPH::GetGradientContainer( input.GetPointer() ) );
//  kurtosis_filter->SetNumberOfThreads(1);
  kurtosis_filter->SetOmitUnweightedValue(omitBZero);
  kurtosis_filter->SetBoundariesForKurtosis(-lower,upper);
//  kurtosis_filter->SetInitialSolution(const vnl_vector<double>& x0 );


  if(maskPath != "")
  {
    mitk::Image::Pointer segmentation;
    segmentation = dynamic_cast<mitk::Image*>(mitk::IOUtil::Load(maskPath)[0].GetPointer());
    typedef itk::Image< short , 3>            MaskImageType;
    MaskImageType::Pointer vectorSeg = MaskImageType::New() ;
    mitk::CastToItkImage( segmentation, vectorSeg );
    kurtosis_filter->SetImageMask(vectorSeg) ;
  }

  try
  {
    kurtosis_filter->Update();
  }
  catch( const itk::ExceptionObject& e)
  {
    mitkThrow() << "Kurtosis fit failed with an ITK Exception: " << e.what();
  }

  mitk::Image::Pointer d_image = mitk::Image::New();
  d_image->InitializeByItk( kurtosis_filter->GetOutput(0) );
  d_image->SetVolume( kurtosis_filter->GetOutput(0)->GetBufferPointer() );

  mitk::Image::Pointer k_image = mitk::Image::New();
  k_image->InitializeByItk( kurtosis_filter->GetOutput(1) );
  k_image->SetVolume( kurtosis_filter->GetOutput(1)->GetBufferPointer() );

  std::string outputD_FileName = output_prefix + "_ADC_map." + output_type;
  std::string outputK_FileName = output_prefix + "_AKC_map." + output_type;

  try
  {
    mitk::IOUtil::Save(  d_image,  outputD_FileName );
    mitk::IOUtil::Save(  k_image,  outputK_FileName );
  }
  catch( const itk::ExceptionObject& e)
  {
    mitkThrow() << "Failed to save the KurtosisFit Results due to exception: " << e.what();
  }

}
  void GetImageStatisticsNoRules() {
    auto statisticsNode = mitk::CreateImageStatisticsNode(m_statisticsContainer, "testStatistics");
    auto standaloneDataStorage = mitk::StandaloneDataStorage::New();
    standaloneDataStorage->Add(statisticsNode);

    //no rules + 1 image --> test return nullptr
    mitk::ImageStatisticsContainer::ConstPointer emptyStatistic;
    CPPUNIT_ASSERT_NO_THROW(emptyStatistic = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image.GetPointer()));
    CPPUNIT_ASSERT_EQUAL(emptyStatistic.IsNull(), true);

    //no rules + 1 image + 1 mask --> test return nullptr
    CPPUNIT_ASSERT_NO_THROW(emptyStatistic = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image.GetPointer(), m_mask.GetPointer()));
    CPPUNIT_ASSERT_EQUAL(emptyStatistic.IsNull(), true);

    //no rules + 1 image + 1 planarFigure --> test return nullptr
    CPPUNIT_ASSERT_NO_THROW(emptyStatistic = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image.GetPointer(), m_planarFigure.GetPointer()));
    CPPUNIT_ASSERT_EQUAL(emptyStatistic.IsNull(), true);
  }