void mitk::ProbeFilter::GenerateOutputInformation()
{
  mitk::Surface::ConstPointer input  = this->GetInput();
  mitk::Image::ConstPointer source = this->GetSource();
  mitk::Surface::Pointer output = this->GetOutput();

  if(input.IsNull()) return;
  if(source.IsNull()) return;

  if(input->GetGeometry()==NULL) return;
  if(source->GetGeometry()==NULL) return;

  if( (input->GetTimeGeometry()->CountTimeSteps()==1) && (source->GetTimeGeometry()->CountTimeSteps()>1) )
  {
    Geometry3D::Pointer geo3D = Geometry3D::New();
    BaseGeometry::Pointer geometry3D = dynamic_cast<BaseGeometry*>(geo3D.GetPointer());
    geometry3D->Initialize();
    geometry3D->SetBounds(source->GetTimeGeometry()->GetBoundsInWorld());

    ProportionalTimeGeometry::Pointer outputTimeGeometry = ProportionalTimeGeometry::New();
    outputTimeGeometry->Initialize(geometry3D, source->GetTimeGeometry()->CountTimeSteps());
    outputTimeGeometry->SetFirstTimePoint(source->GetTimeGeometry()->GetMinimumTimePoint());
    TimePointType stepDuration = source->GetTimeGeometry()->GetMaximumTimePoint(0) - source->GetTimeGeometry()->GetMinimumTimePoint(0);
    outputTimeGeometry->SetStepDuration(stepDuration);

    output->Expand(outputTimeGeometry->CountTimeSteps());
    output->SetTimeGeometry( outputTimeGeometry );
  }
  else
    output->SetGeometry( static_cast<BaseGeometry*>(input->GetGeometry()->Clone().GetPointer()) );

  itkDebugMacro(<<"GenerateOutputInformation()");
}

 //TODO_GOETZ
 // Remove old function, so only this one is working.
 bool
   RenderingManager
   ::InitializeViews(const BaseGeometry * dataGeometry, RequestType type, bool preserveRoughOrientationInWorldSpace)
 {
   ProportionalTimeGeometry::Pointer propTimeGeometry = ProportionalTimeGeometry::New();
   propTimeGeometry->Initialize(dynamic_cast<BaseGeometry *>(dataGeometry->Clone().GetPointer()), 1);
   return InitializeViews(propTimeGeometry, type, preserveRoughOrientationInWorldSpace);
 }

void mitk::PlanarFigure::InitializeTimeGeometry( unsigned int timeSteps )
{
  mitk::PlaneGeometry::Pointer geometry2D = mitk::PlaneGeometry::New();
  geometry2D->Initialize();

  // The geometry is propagated automatically to all time steps,
  // if EvenlyTimed is true...
  ProportionalTimeGeometry::Pointer timeGeometry = ProportionalTimeGeometry::New();
  timeGeometry->Initialize(geometry2D, timeSteps);
  SetTimeGeometry(timeGeometry);
}

void mitk::PlaneGeometryData::SetPlaneGeometry(mitk::PlaneGeometry *geometry2d)
{
  if(geometry2d != NULL)
  {
    ProportionalTimeGeometry::Pointer timeGeometry = ProportionalTimeGeometry::New();
    timeGeometry->Initialize(geometry2d, 1);
    SetTimeGeometry(timeGeometry);
    Modified();
  }
  else
    Superclass::SetGeometry(geometry2d);
}

itk::LightObject::Pointer mitk::ProportionalTimeGeometry::InternalClone() const
{
  itk::LightObject::Pointer parent = Superclass::InternalClone();
  ProportionalTimeGeometry::Pointer newTimeGeometry =
    dynamic_cast<ProportionalTimeGeometry * > (parent.GetPointer());
  newTimeGeometry->m_FirstTimePoint = this->m_FirstTimePoint;
  newTimeGeometry->m_StepDuration = this->m_StepDuration;
  newTimeGeometry->m_GeometryVector.clear();
  newTimeGeometry->Expand(this->CountTimeSteps());
  for (TimeStepType i =0; i < CountTimeSteps(); ++i)
  {
    BaseGeometry::Pointer tempGeometry = GetGeometryForTimeStep(i)->Clone();
    newTimeGeometry->SetTimeStepGeometry(tempGeometry, i);
  }
  return parent;
}

void mitk::PlanarFigure::InitializeTimeGeometry( unsigned int timeSteps )
{
  mitk::Geometry2D::Pointer geometry2D = mitk::Geometry2D::New();
  geometry2D->Initialize();

  if ( timeSteps > 1 )
  {
    mitk::ScalarType timeBounds[] = {0.0, 1.0};
    geometry2D->SetTimeBounds( timeBounds );
  }

  // The geometry is propagated automatically to all time steps,
  // if EvenlyTimed is true...
  ProportionalTimeGeometry::Pointer timeGeometry = ProportionalTimeGeometry::New();
  timeGeometry->Initialize(geometry2D, timeSteps);
  SetTimeGeometry(timeGeometry);
}

void mitk::PlaneFit::GenerateOutputInformation()
{
  mitk::PointSet::ConstPointer input  = this->GetInput();
  mitk::GeometryData::Pointer output  = this->GetOutput();

  itkDebugMacro(<<"GenerateOutputInformation()");

  if (input.IsNull()) return;

  if ( m_PointSet == NULL )
  {
    return;
  }

  bool update = false;
  if ( output->GetGeometry() == NULL || output->GetTimeGeometry() == NULL )
    update = true;
  if ( ( ! update ) && ( output->GetTimeGeometry()->CountTimeSteps() != input->GetTimeGeometry()->CountTimeSteps() ) )
    update = true;
  if ( update )
  {
    mitk::PlaneGeometry::Pointer planeGeometry = mitk::PlaneGeometry::New();

    ProportionalTimeGeometry::Pointer timeGeometry = dynamic_cast<ProportionalTimeGeometry *>(m_TimeGeometry.GetPointer());
    timeGeometry->Initialize(planeGeometry, m_PointSet->GetPointSetSeriesSize());
    //m_TimeGeometry->InitializeEvenlyTimed(
    //  planeGeometry, m_PointSet->GetPointSetSeriesSize() );

    TimeStepType timeStep;
    for ( timeStep = 0;
          (timeStep < m_PointSet->GetPointSetSeriesSize())
          && (timeStep < m_Planes.size());
          ++timeStep )
    {
      timeGeometry->SetTimeStepGeometry( m_Planes[timeStep], timeStep );
    }

    output->SetTimeGeometry( m_TimeGeometry );
  }
}

mitk::ExtrudedContour::ExtrudedContour()
  : m_Contour(NULL), m_ClippingGeometry(NULL), m_AutomaticVectorGeneration(false)
{
  ProportionalTimeGeometry::Pointer timeGeometry = ProportionalTimeGeometry::New();
  timeGeometry->Initialize(1);
  SetTimeGeometry(timeGeometry);

  FillVector3D(m_Vector, 0.0, 0.0, 1.0);
  m_RightVector.Fill(0.0);

  m_ExtrusionFilter = vtkLinearExtrusionFilter::New();

  m_ExtrusionFilter->CappingOff();
  m_ExtrusionFilter->SetExtrusionTypeToVectorExtrusion();

  double vtkvector[3]={0,0,1};

  // set extrusion vector
  m_ExtrusionFilter->SetVector(vtkvector);

  m_TriangleFilter = vtkTriangleFilter::New();
  m_TriangleFilter->SetInputConnection(m_ExtrusionFilter->GetOutputPort());

  m_SubdivisionFilter = vtkLinearSubdivisionFilter::New();
  m_SubdivisionFilter->SetInputConnection(m_TriangleFilter->GetOutputPort());
  m_SubdivisionFilter->SetNumberOfSubdivisions(4);

  m_ClippingBox = vtkPlanes::New();
  m_ClipPolyDataFilter = vtkClipPolyData::New();
  m_ClipPolyDataFilter->SetInputConnection(m_SubdivisionFilter->GetOutputPort());
  m_ClipPolyDataFilter->SetClipFunction(m_ClippingBox);
  m_ClipPolyDataFilter->InsideOutOn();

  m_Polygon = vtkPolygon::New();

  m_ProjectionPlane = mitk::PlaneGeometry::New();
}

void mitk::SlicedData::SetGeometry(BaseGeometry* aGeometry3D)
{
  if(aGeometry3D!=NULL)
  {
    ProportionalTimeGeometry::Pointer timeGeometry = ProportionalTimeGeometry::New();
    SlicedGeometry3D::Pointer slicedGeometry = dynamic_cast<SlicedGeometry3D*>(aGeometry3D);
    if(slicedGeometry.IsNull())
    {
      PlaneGeometry* geometry2d = dynamic_cast<PlaneGeometry*>(aGeometry3D);
      if(geometry2d!=NULL)
      {
        if((GetSlicedGeometry()->GetPlaneGeometry(0)==geometry2d) && (GetSlicedGeometry()->GetSlices()==1))
          return;
        slicedGeometry = SlicedGeometry3D::New();
        slicedGeometry->InitializeEvenlySpaced(geometry2d, 1);
      }
      else
      {
        slicedGeometry = SlicedGeometry3D::New();
        PlaneGeometry::Pointer planeGeometry = PlaneGeometry::New();
        planeGeometry->InitializeStandardPlane(aGeometry3D);
        slicedGeometry->InitializeEvenlySpaced(planeGeometry, (unsigned int)(aGeometry3D->GetExtent(2)));
      }
    }
    assert(slicedGeometry.IsNotNull());

    timeGeometry->Initialize(slicedGeometry, 1);
    Superclass::SetTimeGeometry(timeGeometry);
  }
  else
  {
    if(GetGeometry()==NULL)
      return;
    Superclass::SetGeometry(NULL);
  }
}

  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);
//.........这里部分代码省略.........

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)
//.........这里部分代码省略.........

void mitk::Image::Initialize(vtkImageData* vtkimagedata, int channels, int tDim, int sDim, int pDim)
{
  if(vtkimagedata==nullptr) return;

  m_Dimension=vtkimagedata->GetDataDimension();
  unsigned int i, *tmpDimensions=new unsigned int[m_Dimension>4?m_Dimension:4];
  for(i=0;i<m_Dimension;++i) tmpDimensions[i]=vtkimagedata->GetDimensions()[i];
  if(m_Dimension<4)
  {
    unsigned int *p;
    for(i=0,p=tmpDimensions+m_Dimension;i<4-m_Dimension;++i, ++p)
      *p=1;
  }

  if(pDim>=0)
  {
    tmpDimensions[1]=pDim;
    if(m_Dimension < 2)
      m_Dimension = 2;
  }
  if(sDim>=0)
  {
    tmpDimensions[2]=sDim;
    if(m_Dimension < 3)
      m_Dimension = 3;
  }
  if(tDim>=0)
  {
    tmpDimensions[3]=tDim;
    if(m_Dimension < 4)
      m_Dimension = 4;
  }

  mitk::PixelType pixelType(MakePixelType(vtkimagedata));
  Initialize(pixelType, m_Dimension, tmpDimensions, channels);

  const double *spacinglist = vtkimagedata->GetSpacing();
  Vector3D spacing;
  FillVector3D(spacing, spacinglist[0], 1.0, 1.0);
  if(m_Dimension>=2)
    spacing[1]=spacinglist[1];
  if(m_Dimension>=3)
    spacing[2]=spacinglist[2];

  // access origin of vtkImage
  Point3D origin;
  double vtkorigin[3];
  vtkimagedata->GetOrigin(vtkorigin);
  FillVector3D(origin, vtkorigin[0], 0.0, 0.0);
  if(m_Dimension>=2)
    origin[1]=vtkorigin[1];
  if(m_Dimension>=3)
    origin[2]=vtkorigin[2];

  SlicedGeometry3D* slicedGeometry = GetSlicedGeometry(0);

  // re-initialize PlaneGeometry with origin and direction
  PlaneGeometry* planeGeometry = static_cast<PlaneGeometry*>(slicedGeometry->GetPlaneGeometry(0));
  planeGeometry->SetOrigin(origin);

  // re-initialize SlicedGeometry3D
  slicedGeometry->SetOrigin(origin);
  slicedGeometry->SetSpacing(spacing);

  ProportionalTimeGeometry::Pointer timeGeometry = ProportionalTimeGeometry::New();
  timeGeometry->Initialize(slicedGeometry, m_Dimensions[3]);
  SetTimeGeometry(timeGeometry);

  delete [] tmpDimensions;
}

mitk::ProportionalTimeGeometry::Pointer mitk::ProportionalTimeGeometryToXML::FromXML(TiXmlElement *timeGeometryElement)
{
  if (!timeGeometryElement)
  {
    MITK_ERROR << "Cannot deserialize ProportionalTimeGeometry from nullptr.";
    return nullptr;
  }

  int numberOfTimeSteps = 0;

  if (TIXML_SUCCESS != timeGeometryElement->QueryIntAttribute("NumberOfTimeSteps", &numberOfTimeSteps))
  {
    MITK_WARN << "<ProportionalTimeGeometry> found without NumberOfTimeSteps attribute. Counting...";
  }

  // might be missing!
  TimePointType firstTimePoint;
  std::string firstTimePoint_s;
  TimePointType stepDuration;
  std::string stepDuration_s;
  try
  {
    if (TIXML_SUCCESS == timeGeometryElement->QueryStringAttribute("FirstTimePoint", &firstTimePoint_s))
    {
      firstTimePoint = boost::lexical_cast<double>(firstTimePoint_s);
    }
    else
    {
      firstTimePoint = -std::numeric_limits<TimePointType>::max();
    }

    if (TIXML_SUCCESS == timeGeometryElement->QueryStringAttribute("StepDuration", &stepDuration_s))
    {
      stepDuration = boost::lexical_cast<double>(stepDuration_s);
    }
    else
    {
      stepDuration = std::numeric_limits<TimePointType>::infinity();
    }
  }
  catch (boost::bad_lexical_cast &e)
  {
    MITK_ERROR << "Could not parse string as number: " << e.what();
    return nullptr;
  }

  // list of all geometries with their time steps
  std::multimap<TimeStepType, BaseGeometry::Pointer> allReadGeometries;

  int indexForUnlabeledTimeStep(-1);
  for (TiXmlElement *currentElement = timeGeometryElement->FirstChildElement(); currentElement != nullptr;
       currentElement = currentElement->NextSiblingElement())
  {
    // different geometries could have been inside a ProportionalTimeGeometry.
    // By now, we only support Geometry3D
    std::string tagName = currentElement->Value();
    if (tagName == "Geometry3D")
    {
      Geometry3D::Pointer restoredGeometry = Geometry3DToXML::FromXML(currentElement);
      if (restoredGeometry.IsNotNull())
      {
        int timeStep(-1);
        if (TIXML_SUCCESS != currentElement->QueryIntAttribute("TimeStep", &timeStep))
        {
          timeStep = indexForUnlabeledTimeStep--; // decrement index for next one
          MITK_WARN << "Found <Geometry3D> without 'TimeStep' attribute in <ProportionalTimeGeometry>. No guarantees "
                       "on order anymore.";
        }

        if (allReadGeometries.count(static_cast<TimeStepType>(timeStep)) > 0)
        {
          MITK_WARN << "Found <Geometry3D> tags with identical 'TimeStep' attribute in <ProportionalTimeGeometry>. No "
                       "guarantees on order anymore.";
        }

        allReadGeometries.insert(std::make_pair(static_cast<TimeStepType>(timeStep), restoredGeometry.GetPointer()));
      }
    }
    else
    {
      MITK_WARN << "Found unsupported tag <" << tagName << "> inside <ProportionalTimeGeometry>. Ignoring.";
    }
  }

  // now add all BaseGeometries that were read to a new instance
  // of ProportionalTimeGeometry
  ProportionalTimeGeometry::Pointer newTimeGeometry = ProportionalTimeGeometry::New();
  newTimeGeometry->SetFirstTimePoint(firstTimePoint);
  newTimeGeometry->SetStepDuration(stepDuration);
  newTimeGeometry->ReserveSpaceForGeometries(allReadGeometries.size());

  TimeStepType t(0);
  for (auto entry : allReadGeometries)
  {
    // We add items with newly assigned time steps.
    // This avoids great confusion when a file contains
    // bogus numbers.
    newTimeGeometry->SetTimeStepGeometry(entry.second, t++);
  }

//.........这里部分代码省略.........

std::vector<itk::SmartPointer<mitk::BaseData>> mitk::GeometryDataReaderService::Read()
{
  // Switch the current locale to "C"
  LocaleSwitch localeSwitch("C");

  std::vector<itk::SmartPointer<BaseData>> result;

  InputStream stream(this);

  TiXmlDocument doc;
  stream >> doc;
  if (!doc.Error())
  {
    TiXmlHandle docHandle(&doc);

    for (TiXmlElement *geomDataElement = docHandle.FirstChildElement("GeometryData").ToElement();
         geomDataElement != nullptr;
         geomDataElement = geomDataElement->NextSiblingElement())
    {
      for (TiXmlElement *currentElement = geomDataElement->FirstChildElement(); currentElement != nullptr;
           currentElement = currentElement->NextSiblingElement())
      {
        // different geometries could have been serialized from a GeometryData
        // object:
        std::string tagName = currentElement->Value();
        if (tagName == "Geometry3D")
        {
          Geometry3D::Pointer restoredGeometry = Geometry3DToXML::FromXML(currentElement);
          if (restoredGeometry.IsNotNull())
          {
            GeometryData::Pointer newGeometryData = GeometryData::New();
            newGeometryData->SetGeometry(restoredGeometry);
            result.push_back(newGeometryData.GetPointer());
          }
          else
          {
            MITK_ERROR << "Invalid <Geometry3D> tag encountered. Skipping.";
          }
        }
        else if (tagName == "ProportionalTimeGeometry")
        {
          ProportionalTimeGeometry::Pointer restoredTimeGeometry =
            ProportionalTimeGeometryToXML::FromXML(currentElement);
          if (restoredTimeGeometry.IsNotNull())
          {
            GeometryData::Pointer newGeometryData = GeometryData::New();
            newGeometryData->SetTimeGeometry(restoredTimeGeometry);
            result.push_back(newGeometryData.GetPointer());
          }
          else
          {
            MITK_ERROR << "Invalid <ProportionalTimeGeometry> tag encountered. Skipping.";
          }
        }
      } // for child of <GeometryData>
    }   // for <GeometryData>
  }
  else
  {
    mitkThrow() << "Parsing error at line " << doc.ErrorRow() << ", col " << doc.ErrorCol() << ": " << doc.ErrorDesc();
  }

  if (result.empty())
  {
    mitkThrow() << "Did not read a single GeometryData object from input.";
  }

  return result;
}

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 )
//.........这里部分代码省略.........

void mitk::Image::Initialize(const mitk::PixelType& type, unsigned int dimension, const unsigned int *dimensions, unsigned int channels)
{
  Clear();

  m_Dimension=dimension;

  if(!dimensions)
    itkExceptionMacro(<< "invalid zero dimension image");

  unsigned int i;
  for(i=0;i<dimension;++i)
  {
    if(dimensions[i]<1)
      itkExceptionMacro(<< "invalid dimension[" << i << "]: " << dimensions[i]);
  }

  // create new array since the old was deleted
  m_Dimensions = new unsigned int[MAX_IMAGE_DIMENSIONS];

  // initialize the first four dimensions to 1, the remaining 4 to 0
  FILL_C_ARRAY(m_Dimensions, 4, 1u);
  FILL_C_ARRAY((m_Dimensions+4), 4, 0u);

  // copy in the passed dimension information
  std::memcpy(m_Dimensions, dimensions, sizeof(unsigned int)*m_Dimension);

  this->m_ImageDescriptor = mitk::ImageDescriptor::New();
  this->m_ImageDescriptor->Initialize( this->m_Dimensions, this->m_Dimension );

  for(i=0;i<4;++i)
  {
    m_LargestPossibleRegion.SetIndex(i, 0);
    m_LargestPossibleRegion.SetSize (i, m_Dimensions[i]);
  }
  m_LargestPossibleRegion.SetIndex(i, 0);
  m_LargestPossibleRegion.SetSize(i, channels);

  if(m_LargestPossibleRegion.GetNumberOfPixels()==0)
  {
    delete [] m_Dimensions;
    m_Dimensions = NULL;
    return;
  }

  for( unsigned int i=0u; i<channels; i++)
  {
    this->m_ImageDescriptor->AddNewChannel( type );
  }

  PlaneGeometry::Pointer planegeometry = PlaneGeometry::New();
  planegeometry->InitializeStandardPlane(m_Dimensions[0], m_Dimensions[1]);

  SlicedGeometry3D::Pointer slicedGeometry = SlicedGeometry3D::New();
  slicedGeometry->InitializeEvenlySpaced(planegeometry, m_Dimensions[2]);

  if(dimension>=4)
  {
    TimeBounds timebounds;
    timebounds[0] = 0.0;
    timebounds[1] = 1.0;
    slicedGeometry->SetTimeBounds(timebounds);
  }

  ProportionalTimeGeometry::Pointer timeGeometry = ProportionalTimeGeometry::New();
  timeGeometry->Initialize(slicedGeometry, m_Dimensions[3]);
  for (TimeStepType step = 0; step < timeGeometry->CountTimeSteps(); ++step)
  {
    timeGeometry->GetGeometryForTimeStep(step)->ImageGeometryOn();
  }
  SetTimeGeometry(timeGeometry);

  ImageDataItemPointer dnull=NULL;

  m_Channels.assign(GetNumberOfChannels(), dnull);

  m_Volumes.assign(GetNumberOfChannels()*m_Dimensions[3], dnull);

  m_Slices.assign(GetNumberOfChannels()*m_Dimensions[3]*m_Dimensions[2], dnull);

  ComputeOffsetTable();

  Initialize();

  m_Initialized = true;
}

 bool RenderingManager::InitializeView(vtkRenderWindow * renderWindow, const BaseGeometry * geometry, bool initializeGlobalTimeSNC)
 {
   ProportionalTimeGeometry::Pointer propTimeGeometry = ProportionalTimeGeometry::New();
   propTimeGeometry->Initialize(dynamic_cast<BaseGeometry *>(geometry->Clone().GetPointer()), 1);
   return InitializeView(renderWindow, propTimeGeometry, initializeGlobalTimeSNC);
 }

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;
}

//.........这里部分代码省略.........
  {
    tmpDimensions[2]=sDim;
    if(m_Dimension < 3)
      m_Dimension = 3;
  }
  if(tDim>=0)
  {
    tmpDimensions[3]=tDim;
    if(m_Dimension < 4)
      m_Dimension = 4;
  }


  switch ( vtkimagedata->GetScalarType() )
  {
  case VTK_BIT:
  case VTK_CHAR:
    //pixelType.Initialize(typeid(char), vtkimagedata->GetNumberOfScalarComponents());
    Initialize(mitk::MakeScalarPixelType<char>(), m_Dimension, tmpDimensions, channels);
    break;
  case VTK_UNSIGNED_CHAR:
    //pixelType.Initialize(typeid(unsigned char), vtkimagedata->GetNumberOfScalarComponents());
    Initialize(mitk::MakeScalarPixelType<unsigned char>(), m_Dimension, tmpDimensions, channels);
    break;
  case VTK_SHORT:
    //pixelType.Initialize(typeid(short), vtkimagedata->GetNumberOfScalarComponents());
    Initialize(mitk::MakeScalarPixelType<short>(), m_Dimension, tmpDimensions, channels);
    break;
  case VTK_UNSIGNED_SHORT:
    //pixelType.Initialize(typeid(unsigned short), vtkimagedata->GetNumberOfScalarComponents());
    Initialize(mitk::MakeScalarPixelType<unsigned short>(), m_Dimension, tmpDimensions, channels);
    break;
  case VTK_INT:
    //pixelType.Initialize(typeid(int), vtkimagedata->GetNumberOfScalarComponents());
    Initialize(mitk::MakeScalarPixelType<int>(), m_Dimension, tmpDimensions, channels);
    break;
  case VTK_UNSIGNED_INT:
    //pixelType.Initialize(typeid(unsigned int), vtkimagedata->GetNumberOfScalarComponents());
    Initialize(mitk::MakeScalarPixelType<unsigned int>(), m_Dimension, tmpDimensions, channels);
    break;
  case VTK_LONG:
    //pixelType.Initialize(typeid(long), vtkimagedata->GetNumberOfScalarComponents());
    Initialize(mitk::MakeScalarPixelType<long>(), m_Dimension, tmpDimensions, channels);
    break;
  case VTK_UNSIGNED_LONG:
    //pixelType.Initialize(typeid(unsigned long), vtkimagedata->GetNumberOfScalarComponents());
    Initialize(mitk::MakeScalarPixelType<unsigned long>(), m_Dimension, tmpDimensions, channels);
    break;
  case VTK_FLOAT:
    //pixelType.Initialize(typeid(float), vtkimagedata->GetNumberOfScalarComponents());
    Initialize(mitk::MakeScalarPixelType<float>(), m_Dimension, tmpDimensions, channels);
    break;
  case VTK_DOUBLE:
    //pixelType.Initialize(typeid(double), vtkimagedata->GetNumberOfScalarComponents());
    Initialize(mitk::MakeScalarPixelType<double>(), m_Dimension, tmpDimensions, channels);
    break;
  default:
    break;
  }
  /*
  Initialize(pixelType,
    m_Dimension,
    tmpDimensions,
    channels);
*/

  const double *spacinglist = vtkimagedata->GetSpacing();
  Vector3D spacing;
  FillVector3D(spacing, spacinglist[0], 1.0, 1.0);
  if(m_Dimension>=2)
    spacing[1]=spacinglist[1];
  if(m_Dimension>=3)
    spacing[2]=spacinglist[2];

  // access origin of vtkImage
  Point3D origin;
  double vtkorigin[3];
  vtkimagedata->GetOrigin(vtkorigin);
  FillVector3D(origin, vtkorigin[0], 0.0, 0.0);
  if(m_Dimension>=2)
    origin[1]=vtkorigin[1];
  if(m_Dimension>=3)
    origin[2]=vtkorigin[2];

  SlicedGeometry3D* slicedGeometry = GetSlicedGeometry(0);

  // re-initialize PlaneGeometry with origin and direction
  PlaneGeometry* planeGeometry = static_cast<PlaneGeometry*>(slicedGeometry->GetGeometry2D(0));
  planeGeometry->SetOrigin(origin);

  // re-initialize SlicedGeometry3D
  slicedGeometry->SetOrigin(origin);
  slicedGeometry->SetSpacing(spacing);

  ProportionalTimeGeometry::Pointer timeGeometry = ProportionalTimeGeometry::New();
  timeGeometry->Initialize(slicedGeometry, m_Dimensions[3]);
  SetTimeGeometry(timeGeometry);

  delete [] tmpDimensions;
}

void mitk::ExtrudedContour::BuildGeometry()
{
  if(m_Contour.IsNull())
    return;

//  Initialize(1);

  Vector3D nullvector; nullvector.Fill(0.0);
  float xProj[3];
  unsigned int i;
  unsigned int numPts = 20; //m_Contour->GetNumberOfPoints();
  mitk::Contour::PathPointer path = m_Contour->GetContourPath();
  mitk::Contour::PathType::InputType cstart = path->StartOfInput();
  mitk::Contour::PathType::InputType cend   = path->EndOfInput();
  mitk::Contour::PathType::InputType cstep  = (cend-cstart)/numPts;
  mitk::Contour::PathType::InputType ccur;

  // Part I: guarantee/calculate legal vectors

  m_Vector.Normalize();
  itk2vtk(m_Vector, m_Normal);
  // check m_Vector
  if(mitk::Equal(m_Vector, nullvector) || m_AutomaticVectorGeneration)
  {
    if ( m_AutomaticVectorGeneration == false)
      itkWarningMacro("Extrusion vector is 0 ("<< m_Vector << "); trying to use normal of polygon");

    vtkPoints *loopPoints = vtkPoints::New();
    //mitk::Contour::PointsContainerIterator pointsIt = m_Contour->GetPoints()->Begin();
    double vtkpoint[3];

    unsigned int i=0;
    for(i=0, ccur=cstart; i<numPts; ++i, ccur+=cstep)
    {
      itk2vtk(path->Evaluate(ccur), vtkpoint);
      loopPoints->InsertNextPoint(vtkpoint);
    }

    // Make sure points define a loop with a m_Normal
    vtkPolygon::ComputeNormal(loopPoints, m_Normal);
    loopPoints->Delete();

    vtk2itk(m_Normal, m_Vector);
    if(mitk::Equal(m_Vector, nullvector))
    {
      itkExceptionMacro("Cannot calculate normal of polygon");
    }
  }
  // check m_RightVector
  if((mitk::Equal(m_RightVector, nullvector)) || (mitk::Equal(m_RightVector*m_Vector, 0.0)==false))
  {
    if(mitk::Equal(m_RightVector, nullvector))
    {
      itkDebugMacro("