Method decodeBase64Arrays

src/openms/source/FORMAT/HANDLERS/MzMLHandlerHelper.cpp:138–266

  }

  void MzMLHandlerHelper::decodeBase64Arrays(std::vector<BinaryData>& data, const bool skipXMLCheck)
  {
    // decode all base64 arrays
    for (auto& bindata : data)
    {
      // remove whitespaces from binary data
      // this should not be necessary, but line breaks inside the base64 data are unfortunately no exception
      if (!skipXMLCheck)
      {
        bindata.base64.removeWhitespaces();
      }

      // Catch proteowizard invalid conversion where 
      // (i) no data type is set 
      // (ii) data type is set to integer for pic compression
      //
      // Since numpress arrays are always 64 bit and decode to double arrays,
      // this should be safe. However, we cannot generally assume that DT_NONE
      // means that we are dealing with a 64 bit float type. 
      if (bindata.np_compression != MSNumpressCoder::NONE && 
          bindata.data_type == BinaryData::DT_NONE)
      {
        MzMLHandlerHelper::warning(0, String("Invalid mzML format: Numpress-compressed binary data array '") + 
            bindata.meta.getName() + "' has no child term of MS:1000518 (binary data type) set. Assuming 64 bit float data type.");
        bindata.data_type = BinaryData::DT_FLOAT;
        bindata.precision = BinaryData::PRE_64;
      }
      if (bindata.np_compression == MSNumpressCoder::PIC && 
          bindata.data_type == BinaryData::DT_INT)
      {
        bindata.data_type = BinaryData::DT_FLOAT;
        bindata.precision = BinaryData::PRE_64;
      }

      // decode data and check if the length of the decoded data matches the expected length
      if (bindata.data_type == BinaryData::DT_FLOAT)
      {
        if (bindata.np_compression != MSNumpressCoder::NONE)
        {
          // If its numpress, we don't distinguish 32 / 64 bit as the numpress
          // decoder always works with 64 bit (takes std::vector<double>)
          MSNumpressCoder::NumpressConfig config;
          config.np_compression = bindata.np_compression;
          MSNumpressCoder().decodeNP(bindata.base64, bindata.floats_64,  bindata.compression, config);

          // Next, ensure that we only look at the float array even if the
          // mzML tags say 32 bit data (I am looking at you, proteowizard)
          bindata.precision = BinaryData::PRE_64;
        }
        else if (bindata.precision == BinaryData::PRE_64)
        {
          Base64::decode(bindata.base64, Base64::BYTEORDER_LITTLEENDIAN, bindata.floats_64, bindata.compression);
          if (bindata.size != bindata.floats_64.size())
          {
            MzMLHandlerHelper::warning(0, String("Float binary data array '") + bindata.meta.getName() + 
                "' has length " + bindata.floats_64.size() + ", but should have length " + bindata.size + ".");
            bindata.size = bindata.floats_64.size();
          }