Ejemplo n.º 1
0
inline typename boost::enable_if<boost::is_same<T, std::string>, T>::type
read_attribute(H5::H5Object const& object, std::string const& name)
{
    H5::Attribute attr;
    try {
        H5XX_NO_AUTO_PRINT(H5::AttributeIException);
        attr = object.openAttribute(name);
    }
    catch (H5::AttributeIException const&) {
        throw;
    }
    if (!has_scalar_space(attr)) {
        throw H5::AttributeIException("H5::attribute::as", "incompatible dataspace");
    }
    H5::DataType tid = attr.getDataType();
    std::string value;
    if (!tid.isVariableStr()) {
        // read fixed-size string, allocate space in advance and let the HDF5
        // library take care about NULLTERM and NULLPAD strings
        value.resize(tid.getSize(), std::string::value_type());
        attr.read(tid, &*value.begin());
    }
    else {
        // read variable-length string, memory will be allocated by HDF5 C
        // library and must be freed by us
        char *c_str;
        if (H5Aread(attr.getId(), tid.getId(), &c_str) < 0) {
            throw H5::AttributeIException("Attribute::read", "H5Aread failed");
        }
        value = c_str;  // copy '\0'-terminated string
        free(c_str);
    }
    return value;
}
Ejemplo n.º 2
0
DataSet DataSet::create(const H5::CommonFG &parent,
                        const std::string &name,
                        const H5::DataType &fileType,
                        const NDSize &size,
                        const NDSize &maxsize,
                        const NDSize &chunks,
                        bool max_size_unlimited,
                        bool guess_chunks)
{
    H5::DataSpace space;

    if (size) {
        if (maxsize) {
            space = DataSpace::create(size, maxsize);
        } else {
            space = DataSpace::create(size, max_size_unlimited);
        }
    }

    H5::DSetCreatPropList plcreate = H5::DSetCreatPropList::DEFAULT;

    if (chunks) {
        int rank = static_cast<int>(chunks.size());
        plcreate.setChunk(rank, chunks.data());
    } else if (guess_chunks) {
        NDSize guessedChunks = DataSet::guessChunking(size, fileType.getSize());
        plcreate.setChunk(static_cast<int>(guessedChunks.size()), guessedChunks.data());
    }

    H5::DataSet dset = parent.createDataSet(name, fileType, space);
    return DataSet(dset);
}
Ejemplo n.º 3
0
std::string hdfutil::ReadString (const H5::CommonFG& group, const std::string & dsname) {
    const H5::DataSet & dataset = group.openDataSet(dsname);
	try {
        H5::DataType type = dataset.getDataType();
        std::string retval;
        retval.resize(type.getSize());
		dataset.read(&retval[0], dataset.getStrType());
        return retval;
	} catch (H5::Exception e) {
        std::string error = "Unable to ReadString.";// + dsname;
        throw std::runtime_error(error.c_str());
	}
}
Ejemplo n.º 4
0
inline typename boost::enable_if<boost::mpl::and_<
    is_vector<T>
  , boost::is_same<typename T::value_type, std::string>
>, T>::type
read_attribute(H5::H5Object const& object, std::string const& name)
{
    H5::Attribute attr;
    try {
        H5XX_NO_AUTO_PRINT(H5::AttributeIException);
        attr = object.openAttribute(name);
    }
    catch (H5::AttributeIException const&) {
        throw;
    }

    H5::DataSpace ds(attr.getSpace());
    if (!ds.isSimple()) {
        throw H5::AttributeIException("H5::attribute::as", "incompatible dataspace");
    }
    size_t size = ds.getSimpleExtentNpoints();

    H5::DataType tid = attr.getDataType();
    if (tid.isVariableStr()) {
        throw error("reading non-scalar attribute of variable-length strings not supported");
    }
    size_t str_len = tid.getSize();

    // read to contiguous buffer and copy to std::vector
    std::vector<char> buffer(str_len * size);
    attr.read(tid, &*buffer.begin());

    T value;
    value.reserve(size);
    char const* s = buffer.data();
    for (size_t i = 0; i < size; ++i, s += str_len) {
        size_t len = strnlen(s, str_len);     // strings of str_len size are not '\0'-terminated
        value.push_back(std::string(s, len)); // copy len bytes from buffer
    }

    return value;
}
Ejemplo n.º 5
0
void ossim_hdf5::printAttribute( const H5::Attribute& attr,
                                 const std::string& prefix,
                                 std::ostream& out )
{
   std::string  name      = attr.getName();
   H5::DataType type      = attr.getDataType();
   H5T_class_t  typeClass = attr.getTypeClass();
   size_t       size      = type.getSize();
   
   std::string  value; // Initialized below.

   if ( ( typeClass == H5T_INTEGER ) || ( typeClass == H5T_FLOAT ) )
   {
      H5::IntType intType = attr.getIntType();

      ossimScalarType scalar = ossim_hdf5::getScalarType( intType.getId() );
      
      ossimByteOrder order = ossim_hdf5::getByteOrder( &attr );
      ossimEndian* endian = 0;
      if ( ( size > 1 ) && ( order != ossim::byteOrder() ) )
      {
         endian = new ossimEndian(); // If set used as flag to byte swap.
      }
      
      if ( typeClass == H5T_INTEGER )
      {
         switch ( scalar )
         {
            case OSSIM_UINT8:
            {
               if ( size == 1 )
               {
                  ossim_uint8 i;
                  attr.read( type, (void*)&i );
                  value = ossimString::toString( ossim_int32(i) ).string();
               }
               break;
            }
            case OSSIM_SINT8:
            {
               if ( size == 1 )
               {
                  ossim_sint8 i;
                  attr.read( type, (void*)&i );
                  value = ossimString::toString( ossim_int32(i) ).string();
               }
               break;
            }
            case OSSIM_UINT16:            
            {
               if ( size == 2 )
               {
                  ossim_uint16 i;
                  attr.read( type, (void*)&i );
                  if ( endian )
                  {
                     endian->swap( i );
                  }  
                  value = ossimString::toString( i ).string();
               }
               break;
            }
            case OSSIM_SINT16:
            {
               if ( size == 2 )
               {
                  ossim_sint16 i;
                  attr.read( type, (void*)&i );
                  if ( endian )
                  {
                     endian->swap( i );
                  }
                  value = ossimString::toString( i ).string();
               }
               break;
            }
            case OSSIM_UINT32:        
            {
               if ( size == 4 )
               {
                  ossim_uint32 i;
                  attr.read( type, (void*)&i );
                  if ( endian )
                  {
                     endian->swap( i );
                  }  
                  value = ossimString::toString( i ).string();
               }
               break;
            }
            case OSSIM_SINT32:
            {
               if ( size == 4 )
               {
                  ossim_sint32 i;
                  attr.read( type, (void*)&i );
                  if ( endian )
                  {
                     endian->swap( i );
                  }
                  value = ossimString::toString( i ).string();
               }
               break;
            }
            case OSSIM_UINT64:        
            {
               if ( size == 8 )
               {
                  ossim_uint64 i;
                  attr.read( type, (void*)&i );
                  if ( endian )
                  {
                     endian->swap( i );
                  }  
                  value = ossimString::toString( i ).string();
               }
               break;
            }
            case OSSIM_SINT64:
            {
               if ( size == 8 )
               {
                  ossim_sint32 i;
                  attr.read( type, (void*)&i );
                  if ( endian )
                  {
                     endian->swap( i );
                  }
                  value = ossimString::toString( i ).string();
               }
               break;
            }
            default:
               break;
         }
      }
      else if ( typeClass == H5T_FLOAT )
      {
         if ( scalar == OSSIM_FLOAT32 )
         {
            if ( size == 4 )
            {
               ossim_float32 f;
               attr.read( type, (void*)&f );
               if ( endian )
               {
                  endian->swap( f );
               }
               value = ossimString::toString( f ).string();
            }
         }
         if ( scalar == OSSIM_FLOAT64 )
         {
            if ( size == 8 )
            {
               ossim_float64 f;
               attr.read( type, (void*)&f );
               if ( endian )
               {
                  endian->swap( f );
               }
               value = ossimString::toString( f ).string();
            }
         }
      }

      if ( endian )
      {
         delete endian;
         endian = 0;
      }
   }
   else if ( typeClass == H5T_STRING )
   {
      attr.read( type, value );
   }
   else
   {
      ossimNotify(ossimNotifyLevel_DEBUG)
         << "ossimH5Util::printAttribute WARN: Unhandled type class: " << typeClass
         << std::endl;
   }

   out << prefix << "." << name << ": " << value << std::endl;
   
} // End: ossim_hdf5::printAttribute