Ejemplo n.º 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 nullptr;

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

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

  mitk::Label::Pointer label = mitk::Label::New();
  label->SetName(organName);
  label->SetColor(color);
  label->SetValue(1);
  segmentation->GetActiveLabelSet()->AddLabel(label);
  segmentation->GetActiveLabelSet()->SetActiveLabel(1);

  unsigned int byteSize = sizeof(mitk::Label::PixelType);

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

    mitk::ImageWriteAccessor writeAccess(segmentation.GetPointer(), 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.GetPointer(), 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 nullptr;
  }

  // Add some DICOM Tags as properties to segmentation image
  PropertyList::Pointer dicomSegPropertyList = mitk::DICOMSegmentationPropertyHandler::GetDICOMSegmentationProperties(original->GetPropertyList());
  segmentation->GetPropertyList()->ConcatenatePropertyList(dicomSegPropertyList);
  mitk::DICOMSegmentationPropertyHandler::GetDICOMSegmentProperties(segmentation->GetActiveLabel(segmentation->GetActiveLayer()));

  return CreateSegmentationNode(segmentation, organName, color);
}
  std::vector<BaseData::Pointer> DICOMSegmentationIO::Read()
  {
    mitk::LocaleSwitch localeSwitch("C");

    LabelSetImage::Pointer labelSetImage;
    std::vector<BaseData::Pointer> result;

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

    MITK_INFO << "loading " << path << std::endl;

    if (path.empty())
      mitkThrow() << "Empty filename in mitk::ItkImageIO ";

    try
    {
      // Get the dcm data set from file path
      DcmFileFormat dcmFileFormat;
      OFCondition status = dcmFileFormat.loadFile(path.c_str());
      if (status.bad())
        mitkThrow() << "Can't read the input file!";

      DcmDataset *dataSet = dcmFileFormat.getDataset();
      if (dataSet == nullptr)
        mitkThrow() << "Can't read data from input file!";

      // Read the DICOM SEG images (segItkImages) and DICOM tags (metaInfo)
      dcmqi::ImageSEGConverter *converter = new dcmqi::ImageSEGConverter();
      pair<map<unsigned, ImageType::Pointer>, string> dcmqiOutput = converter->dcmSegmentation2itkimage(dataSet);

      map<unsigned, ImageType::Pointer> segItkImages = dcmqiOutput.first;

      // For each itk image add a layer to the LabelSetImage output
      for (auto &element : segItkImages)
      {
        // Get the labeled image and cast it to mitkImage
        typedef itk::CastImageFilter<itkInternalImageType, itkInputImageType> castItkImageFilterType;
        castItkImageFilterType::Pointer castFilter = castItkImageFilterType::New();
        castFilter->SetInput(element.second);
        castFilter->Update();

        Image::Pointer layerImage;
        CastToMitkImage(castFilter->GetOutput(), layerImage);

        // Get pixel value of the label
        itkInternalImageType::ValueType segValue = 1;
        typedef itk::ImageRegionIterator<const itkInternalImageType> IteratorType;
        // Iterate over the image to find the pixel value of the label
        IteratorType iter(element.second, element.second->GetLargestPossibleRegion());
        iter.GoToBegin();
        while (!iter.IsAtEnd())
        {
          itkInputImageType::PixelType value = iter.Get();
          if (value != 0)
          {
            segValue = value;
            break;
          }
          ++iter;
        }

        dcmqi::JSONSegmentationMetaInformationHandler metaInfo(dcmqiOutput.second.c_str());
        metaInfo.read();
        MITK_INFO << "Input " << metaInfo.getJSONOutputAsString();
        // TODO: Read all DICOM Tags

        // Get the label information from segment attributes
        vector<map<unsigned, dcmqi::SegmentAttributes *>>::const_iterator segmentIter =
          metaInfo.segmentsAttributesMappingList.begin();
        map<unsigned, dcmqi::SegmentAttributes *> segmentMap = (*segmentIter);
        map<unsigned, dcmqi::SegmentAttributes *>::const_iterator segmentMapIter = (*segmentIter).begin();
        dcmqi::SegmentAttributes *segmentAttr = (*segmentMapIter).second;

        OFString labelName;

        if (segmentAttr->getSegmentedPropertyTypeCodeSequence() != nullptr)
          segmentAttr->getSegmentedPropertyTypeCodeSequence()->getCodeMeaning(labelName);
        else
        {
          labelName = std::to_string(segmentAttr->getLabelID()).c_str();
          if (labelName.empty())
            labelName = "Unnamed";
        }

        float tmp[3] = {0.0, 0.0, 0.0};
        if (segmentAttr->getRecommendedDisplayRGBValue() != nullptr)
        {
          tmp[0] = segmentAttr->getRecommendedDisplayRGBValue()[0] / 255.0;
          tmp[1] = segmentAttr->getRecommendedDisplayRGBValue()[1] / 255.0;
          tmp[2] = segmentAttr->getRecommendedDisplayRGBValue()[2] / 255.0;
        }

        // If labelSetImage do not exists (first image)
        if (labelSetImage.IsNull())
        {
          // Initialize the labelSetImage with the read image
          labelSetImage = LabelSetImage::New();
          labelSetImage->InitializeByLabeledImage(layerImage);
          // Already a label was generated, so set the information to this
          Label *activeLabel = labelSetImage->GetActiveLabel(labelSetImage->GetActiveLayer());
          activeLabel->SetName(labelName.c_str());
          activeLabel->SetColor(Color(tmp));
          activeLabel->SetValue(segValue);
        }
        else
        {
          // Add a new layer to the labelSetImage. Background label is set automatically
          labelSetImage->AddLayer(layerImage);

          // Add new label
          Label *newLabel = new Label;
          newLabel->SetName(labelName.c_str());
          newLabel->SetColor(Color(tmp));
          newLabel->SetValue(segValue);

          labelSetImage->GetLabelSet(labelSetImage->GetActiveLayer())->AddLabel(newLabel);
        }

        ++segmentIter;
      }
      // Clean up
      if (converter != nullptr)
        delete converter;
    }
    catch (const std::exception &e)
    {
      MITK_ERROR << "An error occurred while reading the DICOM Seg file: " << e.what();
      return result;
    }

    // Set active layer to th first layer of the labelset image
    if (labelSetImage->GetNumberOfLayers() > 1 && labelSetImage->GetActiveLayer() != 0)
      labelSetImage->SetActiveLayer(0);

    result.push_back(labelSetImage.GetPointer());

    return result;
  }