Method DoRead

Modules/Multilabel/autoload/IO/mitkMultiLabelSegmentationStackReader.cpp:194–327

  }

  std::vector<mitk::BaseData::Pointer> mitk::MultiLabelSegmentationStackReader::DoRead()
  {
    std::vector<BaseData::Pointer> result;

    std::ifstream input(this->GetLocalFileName());
    if (!input.is_open())
    {
      return result;
    }

    auto filePathBase = itksys::SystemTools::GetFilenamePath(this->GetLocalFileName());

    nlohmann::json fileContent;
    try
    {
      input >> fileContent;
    }
    catch (const nlohmann::json::parse_error& e)
    {
      MITK_ERROR << "Cannot reader data due to parsing error. Parse error: " << e.what() << '\n';
      throw;
    }

    //check version
    int version = 0;

    if (!MultiLabelIOHelper::GetValueFromJson<int>(fileContent, "version", version))
    {
      MITK_INFO << "Data has unknown version. Assuming that it can be read. Result might be invalid.";
    }

    if (version > MULTILABEL_SEGMENTATION_VERSION_VALUE)
    {
      mitkThrow() << "Data to read has unsupported version. Software is to old to ensure correct reading. Please use a compatible version of MITK or store data in another format. Version of data: " << version << "; Supported versions up to: "<<MULTILABEL_SEGMENTATION_VERSION_VALUE;
    }

    auto segmentation = MultiLabelSegmentation::New();
    bool segInitialized = false;

    //get pixel content
    auto groupInfos = MultiLabelIOHelper::DeserializeMultiLabelGroupsFromJSON(fileContent["groups"]);

    for (const auto& groupInfo : groupInfos)
    {
      auto groupImage = LoadImageBasedOnFileProperty(groupInfo.properties, filePathBase);
      auto cleanedLabels = MultiLabelSegmentation::ConvertLabelVectorConst(MultiLabelIOHelper::CloneLabelsWithoutMetaProperties(groupInfo.labels));

      if (!segInitialized)
      {
        //this is the first group, we need to initialize the segmentation first to ensure the
        //correct geometry.
        mitk::Image::Pointer initImage = groupImage;
        if (initImage.IsNull())
        {
          //seems to be a stack only defined with label images
          //search for the first defined file and use it for initialization.
          //not the most efficient way, but it is robust.
          auto firstFileName = FindFirstFileInJson(fileContent["groups"]);