Пример #1
0
mitk::DataNode::Pointer mitk::Tool::CreateEmptySegmentationNode( Image* original, const std::string& organName, const mitk::Color& color )
{
  // we NEED a reference image for size etc.
  if (!original) return NULL;

  // actually create a new empty segmentation
  PixelType pixelType(mitk::MakeScalarPixelType<DefaultSegmentationDataType>() );
  Image::Pointer segmentation = Image::New();

  if (original->GetDimension() == 2)
  {
    const unsigned int dimensions[] = { original->GetDimension(0), original->GetDimension(1), 1 };
    segmentation->Initialize(pixelType, 3, dimensions);
  }
  else
  {
    segmentation->Initialize(pixelType, original->GetDimension(), original->GetDimensions());
  }

  unsigned int byteSize = sizeof(DefaultSegmentationDataType);

  if(segmentation->GetDimension() < 4)
  {
    for (unsigned int dim = 0; dim < segmentation->GetDimension(); ++dim)
    {
      byteSize *= segmentation->GetDimension(dim);
    }

    mitk::ImageWriteAccessor writeAccess(segmentation, segmentation->GetVolumeData(0));

    memset( writeAccess.GetData(), 0, byteSize );
  }
  else
  {//if we have a time-resolved image we need to set memory to 0 for each time step
    for (unsigned int dim = 0; dim < 3; ++dim)
    {
      byteSize *= segmentation->GetDimension(dim);
    }

    for( unsigned int volumeNumber = 0; volumeNumber < segmentation->GetDimension(3); volumeNumber++)
    {
      mitk::ImageWriteAccessor writeAccess(segmentation, segmentation->GetVolumeData(volumeNumber));

      memset( writeAccess.GetData(), 0, byteSize );
    }
  }

  if (original->GetTimeGeometry() )
  {
    TimeGeometry::Pointer originalGeometry = original->GetTimeGeometry()->Clone();
    segmentation->SetTimeGeometry( originalGeometry );
  }
  else
  {
    Tool::ErrorMessage("Original image does not have a 'Time sliced geometry'! Cannot create a segmentation.");
    return NULL;
  }

  return CreateSegmentationNode( segmentation, organName, color );
}
void mitk::CorrectorAlgorithm::GenerateData()
{
  Image::Pointer inputImage = const_cast<Image*>(ImageToImageFilter::GetInput(0));

  if (inputImage.IsNull() || inputImage->GetDimension() != 2)
  {
    itkExceptionMacro("CorrectorAlgorithm needs a 2D image as input.");
  }

  if (m_Contour.IsNull())
  {
    itkExceptionMacro("CorrectorAlgorithm needs a Contour object as input.");
  }

  // copy the input (since m_WorkingImage will be changed later)
  m_WorkingImage = inputImage;

  TimeGeometry::Pointer originalGeometry = NULL;

  if (inputImage->GetTimeGeometry() )
  {
    originalGeometry = inputImage->GetTimeGeometry()->Clone();
    m_WorkingImage->SetTimeGeometry( originalGeometry );
  }
  else
  {
    itkExceptionMacro("Original image does not have a 'Time sliced geometry'! Cannot copy.");
  }

  Image::Pointer temporarySlice;
  // Convert to ipMITKSegmentationTYPE (because TobiasHeimannCorrectionAlgorithm relys on that data type)
  {
    itk::Image< ipMITKSegmentationTYPE, 2 >::Pointer correctPixelTypeImage;
    CastToItkImage( m_WorkingImage, correctPixelTypeImage );
    assert (correctPixelTypeImage.IsNotNull() );

    // possible bug in CastToItkImage ?
    // direction maxtrix is wrong/broken/not working after CastToItkImage, leading to a failed assertion in
    // mitk/Core/DataStructures/mitkSlicedGeometry3D.cpp, 479:
    // virtual void mitk::SlicedGeometry3D::SetSpacing(const mitk::Vector3D&): Assertion `aSpacing[0]>0 && aSpacing[1]>0 && aSpacing[2]>0' failed
    // solution here: we overwrite it with an unity matrix
    itk::Image< ipMITKSegmentationTYPE, 2 >::DirectionType imageDirection;
    imageDirection.SetIdentity();
    //correctPixelTypeImage->SetDirection(imageDirection);

    temporarySlice = this->GetOutput();
    //  temporarySlice = ImportItkImage( correctPixelTypeImage );
    m_FillColor = 1;
    m_EraseColor = 0;
    ImprovedHeimannCorrectionAlgorithm(correctPixelTypeImage);
    CastToMitkImage( correctPixelTypeImage, temporarySlice );
  }
  temporarySlice->SetTimeGeometry(originalGeometry);
}
Пример #3
0
  std::vector<BaseData::Pointer> ItkImageIO::Read()
  {
    std::vector<BaseData::Pointer> result;
    mitk::LocaleSwitch localeSwitch("C");

    Image::Pointer image = Image::New();

    const unsigned int MINDIM = 2;
    const unsigned int MAXDIM = 4;

    const std::string path = this->GetLocalFileName();

    MITK_INFO << "loading " << path << " via itk::ImageIOFactory... " << std::endl;

    // Check to see if we can read the file given the name or prefix
    if (path.empty())
    {
      mitkThrow() << "Empty filename in mitk::ItkImageIO ";
    }

    // Got to allocate space for the image. Determine the characteristics of
    // the image.
    m_ImageIO->SetFileName(path);
    m_ImageIO->ReadImageInformation();

    unsigned int ndim = m_ImageIO->GetNumberOfDimensions();
    if (ndim < MINDIM || ndim > MAXDIM)
    {
      MITK_WARN << "Sorry, only dimensions 2, 3 and 4 are supported. The given file has " << ndim
                << " dimensions! Reading as 4D.";
      ndim = MAXDIM;
    }

    itk::ImageIORegion ioRegion(ndim);
    itk::ImageIORegion::SizeType ioSize = ioRegion.GetSize();
    itk::ImageIORegion::IndexType ioStart = ioRegion.GetIndex();

    unsigned int dimensions[MAXDIM];
    dimensions[0] = 0;
    dimensions[1] = 0;
    dimensions[2] = 0;
    dimensions[3] = 0;

    ScalarType spacing[MAXDIM];
    spacing[0] = 1.0f;
    spacing[1] = 1.0f;
    spacing[2] = 1.0f;
    spacing[3] = 1.0f;

    Point3D origin;
    origin.Fill(0);

    unsigned int i;
    for (i = 0; i < ndim; ++i)
    {
      ioStart[i] = 0;
      ioSize[i] = m_ImageIO->GetDimensions(i);
      if (i < MAXDIM)
      {
        dimensions[i] = m_ImageIO->GetDimensions(i);
        spacing[i] = m_ImageIO->GetSpacing(i);
        if (spacing[i] <= 0)
          spacing[i] = 1.0f;
      }
      if (i < 3)
      {
        origin[i] = m_ImageIO->GetOrigin(i);
      }
    }

    ioRegion.SetSize(ioSize);
    ioRegion.SetIndex(ioStart);

    MITK_INFO << "ioRegion: " << ioRegion << std::endl;
    m_ImageIO->SetIORegion(ioRegion);
    void *buffer = new unsigned char[m_ImageIO->GetImageSizeInBytes()];
    m_ImageIO->Read(buffer);

    image->Initialize(MakePixelType(m_ImageIO), ndim, dimensions);
    image->SetImportChannel(buffer, 0, Image::ManageMemory);

    const itk::MetaDataDictionary &dictionary = m_ImageIO->GetMetaDataDictionary();

    // access direction of itk::Image and include spacing
    mitk::Matrix3D matrix;
    matrix.SetIdentity();
    unsigned int j, itkDimMax3 = (ndim >= 3 ? 3 : ndim);
    for (i = 0; i < itkDimMax3; ++i)
      for (j = 0; j < itkDimMax3; ++j)
        matrix[i][j] = m_ImageIO->GetDirection(j)[i];

    // re-initialize PlaneGeometry with origin and direction
    PlaneGeometry *planeGeometry = image->GetSlicedGeometry(0)->GetPlaneGeometry(0);
    planeGeometry->SetOrigin(origin);
    planeGeometry->GetIndexToWorldTransform()->SetMatrix(matrix);

    // re-initialize SlicedGeometry3D
    SlicedGeometry3D *slicedGeometry = image->GetSlicedGeometry(0);
    slicedGeometry->InitializeEvenlySpaced(planeGeometry, image->GetDimension(2));
    slicedGeometry->SetSpacing(spacing);

    MITK_INFO << slicedGeometry->GetCornerPoint(false, false, false);
    MITK_INFO << slicedGeometry->GetCornerPoint(true, true, true);

    // re-initialize TimeGeometry
    TimeGeometry::Pointer timeGeometry;

    if (dictionary.HasKey(PROPERTY_NAME_TIMEGEOMETRY_TYPE) || dictionary.HasKey(PROPERTY_KEY_TIMEGEOMETRY_TYPE))
    { // also check for the name because of backwards compatibility. Past code version stored with the name and not with
      // the key
      itk::MetaDataObject<std::string>::ConstPointer timeGeometryTypeData = nullptr;
      if (dictionary.HasKey(PROPERTY_NAME_TIMEGEOMETRY_TYPE))
      {
        timeGeometryTypeData =
          dynamic_cast<const itk::MetaDataObject<std::string> *>(dictionary.Get(PROPERTY_NAME_TIMEGEOMETRY_TYPE));
      }
      else
      {
        timeGeometryTypeData =
          dynamic_cast<const itk::MetaDataObject<std::string> *>(dictionary.Get(PROPERTY_KEY_TIMEGEOMETRY_TYPE));
      }

      if (timeGeometryTypeData->GetMetaDataObjectValue() == ArbitraryTimeGeometry::GetStaticNameOfClass())
      {
        MITK_INFO << "used time geometry: " << ArbitraryTimeGeometry::GetStaticNameOfClass() << std::endl;
        typedef std::vector<TimePointType> TimePointVector;
        TimePointVector timePoints;

        if (dictionary.HasKey(PROPERTY_NAME_TIMEGEOMETRY_TIMEPOINTS))
        {
          timePoints = ConvertMetaDataObjectToTimePointList(dictionary.Get(PROPERTY_NAME_TIMEGEOMETRY_TIMEPOINTS));
        }
        else if (dictionary.HasKey(PROPERTY_KEY_TIMEGEOMETRY_TIMEPOINTS))
        {
          timePoints = ConvertMetaDataObjectToTimePointList(dictionary.Get(PROPERTY_KEY_TIMEGEOMETRY_TIMEPOINTS));
        }

        if (timePoints.size() - 1 != image->GetDimension(3))
        {
          MITK_ERROR << "Stored timepoints (" << timePoints.size() - 1 << ") and size of image time dimension ("
                     << image->GetDimension(3) << ") do not match. Switch to ProportionalTimeGeometry fallback"
                     << std::endl;
        }
        else
        {
          ArbitraryTimeGeometry::Pointer arbitraryTimeGeometry = ArbitraryTimeGeometry::New();
          TimePointVector::const_iterator pos = timePoints.begin();
          TimePointVector::const_iterator prePos = pos++;

          for (; pos != timePoints.end(); ++prePos, ++pos)
          {
            arbitraryTimeGeometry->AppendTimeStepClone(slicedGeometry, *pos, *prePos);
          }

          timeGeometry = arbitraryTimeGeometry;
        }
      }
    }

    if (timeGeometry.IsNull())
    { // Fallback. If no other valid time geometry has been created, create a ProportionalTimeGeometry
      MITK_INFO << "used time geometry: " << ProportionalTimeGeometry::GetStaticNameOfClass() << std::endl;
      ProportionalTimeGeometry::Pointer propTimeGeometry = ProportionalTimeGeometry::New();
      propTimeGeometry->Initialize(slicedGeometry, image->GetDimension(3));
      timeGeometry = propTimeGeometry;
    }

    image->SetTimeGeometry(timeGeometry);

    buffer = NULL;
    MITK_INFO << "number of image components: " << image->GetPixelType().GetNumberOfComponents() << std::endl;

    for (itk::MetaDataDictionary::ConstIterator iter = dictionary.Begin(), iterEnd = dictionary.End(); iter != iterEnd;
         ++iter)
    {
      if (iter->second->GetMetaDataObjectTypeInfo() == typeid(std::string))
      {
        const std::string &key = iter->first;
        std::string assumedPropertyName = key;
        std::replace(assumedPropertyName.begin(), assumedPropertyName.end(), '_', '.');

        std::string mimeTypeName = GetMimeType()->GetName();

        // Check if there is already a info for the key and our mime type.
        IPropertyPersistence::InfoResultType infoList = mitk::CoreServices::GetPropertyPersistence()->GetInfoByKey(key);

        auto predicate = [mimeTypeName](const PropertyPersistenceInfo::ConstPointer &x) {
          return x.IsNotNull() && x->GetMimeTypeName() == mimeTypeName;
        };
        auto finding = std::find_if(infoList.begin(), infoList.end(), predicate);

        if (finding == infoList.end())
        {
          auto predicateWild = [](const PropertyPersistenceInfo::ConstPointer &x) {
            return x.IsNotNull() && x->GetMimeTypeName() == PropertyPersistenceInfo::ANY_MIMETYPE_NAME();
          };
          finding = std::find_if(infoList.begin(), infoList.end(), predicateWild);
        }

        PropertyPersistenceInfo::ConstPointer info;

        if (finding != infoList.end())
        {
          assumedPropertyName = (*finding)->GetName();
          info = *finding;
        }
        else
        { // we have not found anything suitable so we generate our own info
          PropertyPersistenceInfo::Pointer newInfo = PropertyPersistenceInfo::New();
          newInfo->SetNameAndKey(assumedPropertyName, key);
          newInfo->SetMimeTypeName(PropertyPersistenceInfo::ANY_MIMETYPE_NAME());
          info = newInfo;
        }

        std::string value =
          dynamic_cast<itk::MetaDataObject<std::string> *>(iter->second.GetPointer())->GetMetaDataObjectValue();

        mitk::BaseProperty::Pointer loadedProp = info->GetDeserializationFunction()(value);

        image->SetProperty(assumedPropertyName.c_str(), loadedProp);

        // Read properties should be persisted unless they are default properties
        // which are written anyway
        bool isDefaultKey(false);

        for (const auto &defaultKey : m_DefaultMetaDataKeys)
        {
          if (defaultKey.length() <= assumedPropertyName.length())
          {
            // does the start match the default key
            if (assumedPropertyName.substr(0, defaultKey.length()).find(defaultKey) != std::string::npos)
            {
              isDefaultKey = true;
              break;
            }
          }
        }

        if (!isDefaultKey)
        {
          mitk::CoreServices::GetPropertyPersistence()->AddInfo(info);
        }
      }
    }

    MITK_INFO << "...finished!" << std::endl;

    result.push_back(image.GetPointer());
    return result;
  }
Пример #4
0
std::vector<BaseData::Pointer> LabelSetImageIO::Read()
{
  const std::string& locale = "C";
  const std::string& currLocale = setlocale( LC_ALL, NULL );

  if ( locale.compare(currLocale)!=0 )
  {
    try
    {
      setlocale(LC_ALL, locale.c_str());
    }
    catch(...)
    {
      mitkThrow() << "Could not set locale.";
    }
  }

  // begin regular image loading, adapted from mitkItkImageIO
  itk::NrrdImageIO::Pointer nrrdImageIO = itk::NrrdImageIO::New();
  Image::Pointer image = Image::New();

  const unsigned int MINDIM = 2;
  const unsigned int MAXDIM = 4;

  const std::string path = this->GetLocalFileName();

  MITK_INFO << "loading " << path << " via itk::ImageIOFactory... " << std::endl;

  // Check to see if we can read the file given the name or prefix
  if (path.empty())
  {
    mitkThrow() << "Empty filename in mitk::ItkImageIO ";
  }

  // Got to allocate space for the image. Determine the characteristics of
  // the image.
  nrrdImageIO->SetFileName(path);
  nrrdImageIO->ReadImageInformation();

  unsigned int ndim = nrrdImageIO->GetNumberOfDimensions();
  if (ndim < MINDIM || ndim > MAXDIM)
  {
    MITK_WARN << "Sorry, only dimensions 2, 3 and 4 are supported. The given file has " << ndim << " dimensions! Reading as 4D.";
    ndim = MAXDIM;
  }

  itk::ImageIORegion ioRegion(ndim);
  itk::ImageIORegion::SizeType ioSize = ioRegion.GetSize();
  itk::ImageIORegion::IndexType ioStart = ioRegion.GetIndex();

  unsigned int dimensions[MAXDIM];
  dimensions[0] = 0;
  dimensions[1] = 0;
  dimensions[2] = 0;
  dimensions[3] = 0;

  ScalarType spacing[MAXDIM];
  spacing[0] = 1.0f;
  spacing[1] = 1.0f;
  spacing[2] = 1.0f;
  spacing[3] = 1.0f;

  Point3D origin;
  origin.Fill(0);

  unsigned int i;
  for (i = 0; i < ndim; ++i)
  {
    ioStart[i] = 0;
    ioSize[i] = nrrdImageIO->GetDimensions(i);
    if (i<MAXDIM)
    {
      dimensions[i] = nrrdImageIO->GetDimensions(i);
      spacing[i] = nrrdImageIO->GetSpacing(i);
      if (spacing[i] <= 0)
        spacing[i] = 1.0f;
    }
    if (i<3)
    {
      origin[i] = nrrdImageIO->GetOrigin(i);
    }
  }

  ioRegion.SetSize(ioSize);
  ioRegion.SetIndex(ioStart);

  MITK_INFO << "ioRegion: " << ioRegion << std::endl;
  nrrdImageIO->SetIORegion(ioRegion);
  void* buffer = new unsigned char[nrrdImageIO->GetImageSizeInBytes()];
  nrrdImageIO->Read(buffer);

  image->Initialize(MakePixelType(nrrdImageIO), ndim, dimensions);
  image->SetImportChannel(buffer, 0, Image::ManageMemory);

  // access direction of itk::Image and include spacing
  mitk::Matrix3D matrix;
  matrix.SetIdentity();
  unsigned int j, itkDimMax3 = (ndim >= 3 ? 3 : ndim);
  for (i = 0; i < itkDimMax3; ++i)
    for (j = 0; j < itkDimMax3; ++j)
      matrix[i][j] = nrrdImageIO->GetDirection(j)[i];

  // re-initialize PlaneGeometry with origin and direction
  PlaneGeometry* planeGeometry = image->GetSlicedGeometry(0)->GetPlaneGeometry(0);
  planeGeometry->SetOrigin(origin);
  planeGeometry->GetIndexToWorldTransform()->SetMatrix(matrix);

  // re-initialize SlicedGeometry3D
  SlicedGeometry3D* slicedGeometry = image->GetSlicedGeometry(0);
  slicedGeometry->InitializeEvenlySpaced(planeGeometry, image->GetDimension(2));
  slicedGeometry->SetSpacing(spacing);

  MITK_INFO << slicedGeometry->GetCornerPoint(false, false, false);
  MITK_INFO << slicedGeometry->GetCornerPoint(true, true, true);

  // re-initialize TimeGeometry
  ProportionalTimeGeometry::Pointer timeGeometry = ProportionalTimeGeometry::New();
  timeGeometry->Initialize(slicedGeometry, image->GetDimension(3));
  image->SetTimeGeometry(timeGeometry);

  buffer = NULL;
  MITK_INFO << "number of image components: " << image->GetPixelType().GetNumberOfComponents() << std::endl;

  const itk::MetaDataDictionary& dictionary = nrrdImageIO->GetMetaDataDictionary();
  for (itk::MetaDataDictionary::ConstIterator iter = dictionary.Begin(), iterEnd = dictionary.End();
    iter != iterEnd; ++iter)
  {
    std::string key = std::string("meta.") + iter->first;
    if (iter->second->GetMetaDataObjectTypeInfo() == typeid(std::string))
    {
      std::string value = dynamic_cast<itk::MetaDataObject<std::string>*>(iter->second.GetPointer())->GetMetaDataObjectValue();
      image->SetProperty(key.c_str(), mitk::StringProperty::New(value));
    }
  }

  // end regular image loading

  LabelSetImage::Pointer output = LabelSetImageConverter::ConvertImageToLabelSetImage(image);

  // get labels and add them as properties to the image
  char keybuffer[256];

  unsigned int numberOfLayers = GetIntByKey(dictionary, "layers");
  std::string _xmlStr;
  mitk::Label::Pointer label;

  for (unsigned int layerIdx = 0; layerIdx < numberOfLayers; layerIdx++)
  {
    sprintf(keybuffer, "layer_%03d", layerIdx);
    int numberOfLabels = GetIntByKey(dictionary, keybuffer);

    mitk::LabelSet::Pointer labelSet = mitk::LabelSet::New();

    for (int labelIdx = 0; labelIdx < numberOfLabels; labelIdx++)
    {
      TiXmlDocument doc;
      sprintf(keybuffer, "label_%03d_%05d", layerIdx, labelIdx);
      _xmlStr = GetStringByKey(dictionary, keybuffer);
      doc.Parse(_xmlStr.c_str());

      TiXmlElement * labelElem = doc.FirstChildElement("Label");
      if (labelElem == 0)
        mitkThrow() << "Error parsing NRRD header for mitk::LabelSetImage IO";

      label = LoadLabelFromTiXmlDocument(labelElem);

      if (label->GetValue() == 0) // set exterior label is needed to hold exterior information
        output->SetExteriorLabel(label);
      labelSet->AddLabel(label);
      labelSet->SetLayer(layerIdx);
    }
    output->AddLabelSetToLayer(layerIdx, labelSet);
  }

  MITK_INFO << "...finished!" << std::endl;

  try
  {
    setlocale(LC_ALL, currLocale.c_str());
  }
  catch(...)
  {
    mitkThrow() << "Could not reset locale!";
  }

  std::vector<BaseData::Pointer> result;
  result.push_back(output.GetPointer());
  return result;
}
Пример #5
0
mitk::Image::Pointer mitk::PicFileReader::CreateImage()
{
  Image::Pointer output = Image::New();

  std::string fileName = this->GetLocalFileName();

  mitkIpPicDescriptor *header = mitkIpPicGetHeader(const_cast<char *>(fileName.c_str()), NULL);

  if (!header)
  {
    mitkThrow() << "File could not be read.";
  }

  header = mitkIpPicGetTags(const_cast<char *>(fileName.c_str()), header);

  int channels = 1;

  mitkIpPicTSV_t *tsv;
  if ((tsv = mitkIpPicQueryTag(header, "SOURCE HEADER")) != NULL)
  {
    if (tsv->n[0] > 1e+06)
    {
      mitkIpPicTSV_t *tsvSH;
      tsvSH = mitkIpPicDelTag(header, "SOURCE HEADER");
      mitkIpPicFreeTag(tsvSH);
    }
  }
  if ((tsv = mitkIpPicQueryTag(header, "ICON80x80")) != NULL)
  {
    mitkIpPicTSV_t *tsvSH;
    tsvSH = mitkIpPicDelTag(header, "ICON80x80");
    mitkIpPicFreeTag(tsvSH);
  }
  if ((tsv = mitkIpPicQueryTag(header, "VELOCITY")) != NULL)
  {
    ++channels;
    mitkIpPicDelTag(header, "VELOCITY");
  }

  if (header == NULL || header->bpe == 0)
  {
    mitkThrow() << " Could not read file " << fileName;
  }

  // if pic image only 2D, the n[2] value is not initialized
  unsigned int slices = 1;
  if (header->dim == 2)
  {
    header->n[2] = slices;
  }

  // First initialize the geometry of the output image by the pic-header
  SlicedGeometry3D::Pointer slicedGeometry = mitk::SlicedGeometry3D::New();
  PicHelper::InitializeEvenlySpaced(header, header->n[2], slicedGeometry);

  // if pic image only 3D, the n[3] value is not initialized
  unsigned int timesteps = 1;
  if (header->dim > 3)
  {
    timesteps = header->n[3];
  }

  slicedGeometry->ImageGeometryOn();
  ProportionalTimeGeometry::Pointer timeGeometry = ProportionalTimeGeometry::New();
  timeGeometry->Initialize(slicedGeometry, timesteps);

  // Cast the pic descriptor to ImageDescriptor and initialize the output

  output->Initialize(CastToImageDescriptor(header));
  output->SetTimeGeometry(timeGeometry);
  mitkIpPicFree(header);

  return output;
}
Пример #6
0
std::vector<BaseData::Pointer> ItkImageIO::Read()
{
  std::vector<BaseData::Pointer> result;

  const std::string& locale = "C";
  const std::string& currLocale = setlocale( LC_ALL, NULL );

  if ( locale.compare(currLocale)!=0 )
  {
    try
    {
      setlocale(LC_ALL, locale.c_str());
    }
    catch(...)
    {
      MITK_INFO << "Could not set locale " << locale;
    }
  }

  Image::Pointer image = Image::New();

  const unsigned int MINDIM = 2;
  const unsigned int MAXDIM = 4;

  const std::string path = this->GetLocalFileName();

  MITK_INFO << "loading " << path << " via itk::ImageIOFactory... " << std::endl;

  // Check to see if we can read the file given the name or prefix
  if (path.empty())
  {
    mitkThrow() << "Empty filename in mitk::ItkImageIO ";
  }

  // Got to allocate space for the image. Determine the characteristics of
  // the image.
  m_ImageIO->SetFileName( path );
  m_ImageIO->ReadImageInformation();

  unsigned int ndim = m_ImageIO->GetNumberOfDimensions();
  if ( ndim < MINDIM || ndim > MAXDIM )
  {
    MITK_WARN << "Sorry, only dimensions 2, 3 and 4 are supported. The given file has " << ndim << " dimensions! Reading as 4D.";
    ndim = MAXDIM;
  }

  itk::ImageIORegion ioRegion( ndim );
  itk::ImageIORegion::SizeType ioSize = ioRegion.GetSize();
  itk::ImageIORegion::IndexType ioStart = ioRegion.GetIndex();

  unsigned int dimensions[ MAXDIM ];
  dimensions[ 0 ] = 0;
  dimensions[ 1 ] = 0;
  dimensions[ 2 ] = 0;
  dimensions[ 3 ] = 0;

  ScalarType spacing[ MAXDIM ];
  spacing[ 0 ] = 1.0f;
  spacing[ 1 ] = 1.0f;
  spacing[ 2 ] = 1.0f;
  spacing[ 3 ] = 1.0f;

  Point3D origin;
  origin.Fill(0);

  unsigned int i;
  for ( i = 0; i < ndim ; ++i )
  {
    ioStart[ i ] = 0;
    ioSize[ i ] = m_ImageIO->GetDimensions( i );
    if(i<MAXDIM)
    {
      dimensions[ i ] = m_ImageIO->GetDimensions( i );
      spacing[ i ] = m_ImageIO->GetSpacing( i );
      if(spacing[ i ] <= 0)
        spacing[ i ] = 1.0f;
    }
    if(i<3)
    {
      origin[ i ] = m_ImageIO->GetOrigin( i );
    }
  }

  ioRegion.SetSize( ioSize );
  ioRegion.SetIndex( ioStart );

  MITK_INFO << "ioRegion: " << ioRegion << std::endl;
  m_ImageIO->SetIORegion( ioRegion );
  void* buffer = new unsigned char[m_ImageIO->GetImageSizeInBytes()];
  m_ImageIO->Read( buffer );

  image->Initialize( MakePixelType(m_ImageIO), ndim, dimensions );
  image->SetImportChannel( buffer, 0, Image::ManageMemory );

  // access direction of itk::Image and include spacing
  mitk::Matrix3D matrix;
  matrix.SetIdentity();
  unsigned int j, itkDimMax3 = (ndim >= 3? 3 : ndim);
  for ( i=0; i < itkDimMax3; ++i)
    for( j=0; j < itkDimMax3; ++j )
      matrix[i][j] = m_ImageIO->GetDirection(j)[i];

  // re-initialize PlaneGeometry with origin and direction
  PlaneGeometry* planeGeometry = image->GetSlicedGeometry(0)->GetPlaneGeometry(0);
  planeGeometry->SetOrigin(origin);
  planeGeometry->GetIndexToWorldTransform()->SetMatrix(matrix);

  // re-initialize SlicedGeometry3D
  SlicedGeometry3D* slicedGeometry = image->GetSlicedGeometry(0);
  slicedGeometry->InitializeEvenlySpaced(planeGeometry, image->GetDimension(2));
  slicedGeometry->SetSpacing(spacing);

  MITK_INFO << slicedGeometry->GetCornerPoint(false,false,false);
  MITK_INFO << slicedGeometry->GetCornerPoint(true,true,true);

  // re-initialize TimeGeometry
  ProportionalTimeGeometry::Pointer timeGeometry = ProportionalTimeGeometry::New();
  timeGeometry->Initialize(slicedGeometry, image->GetDimension(3));
  image->SetTimeGeometry(timeGeometry);

  buffer = NULL;
  MITK_INFO << "number of image components: "<< image->GetPixelType().GetNumberOfComponents() << std::endl;

  const itk::MetaDataDictionary& dictionary = m_ImageIO->GetMetaDataDictionary();
  for (itk::MetaDataDictionary::ConstIterator iter = dictionary.Begin(), iterEnd = dictionary.End();
       iter != iterEnd; ++iter)
  {
    std::string key = std::string("meta.") + iter->first;
    if (iter->second->GetMetaDataObjectTypeInfo() == typeid(std::string))
    {
      std::string value = dynamic_cast<itk::MetaDataObject<std::string>*>(iter->second.GetPointer())->GetMetaDataObjectValue();
      image->SetProperty(key.c_str(), mitk::StringProperty::New(value));
    }
  }

  MITK_INFO << "...finished!" << std::endl;

  try
  {
    setlocale(LC_ALL, currLocale.c_str());
  }
  catch(...)
  {
    MITK_INFO << "Could not reset locale " << currLocale;
  }

  result.push_back(image.GetPointer());
  return result;
}