bool CalculateSegmentationVolume::ThreadedUpdateFunction()
  {
    // get image
    Image::Pointer image;
    GetPointerParameter("Input", image);

    AccessFixedDimensionByItk(image.GetPointer(),
                              ItkImageProcessing,
                              3); // some magic to call the correctly templated function (we only do 3D images here!)

    // consider single voxel volume
    Vector3D spacing = image->GetSlicedGeometry()->GetSpacing();                           // spacing in mm
    float volumeML = (ScalarType)m_Volume * spacing[0] * spacing[1] * spacing[2] / 1000.0; // convert to ml

    DataNode *groupNode = GetGroupNode();
    if (groupNode)
    {
      groupNode->SetProperty("volume", FloatProperty::New(volumeML));
      groupNode->SetProperty("centerOfMass", Vector3DProperty::New(m_CenterOfMass));
      groupNode->SetProperty("boundingBoxMinimum", Vector3DProperty::New(m_MinIndexOfBoundingBox));
      groupNode->SetProperty("boundingBoxMaximum", Vector3DProperty::New(m_MaxIndexOfBoundingBox));
      groupNode->SetProperty("showVolume", BoolProperty::New(true));
    }

    return true;
  }
Example #2
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;
  }
Example #3
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;
}
Example #4
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;
}