Exemplo n.º 1
0
inline typename boost::enable_if<boost::mpl::and_<
    is_vector<T>, boost::is_fundamental<typename T::value_type>
>, T>::type
read_attribute(H5::H5Object const& object, std::string const& name)
{
    typedef typename T::value_type value_type;

    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();
    std::vector<value_type> value(size);
    attr.read(ctype<value_type>::hid(), &*value.begin());
    return value;
}
Exemplo n.º 2
0
inline typename boost::enable_if<is_multi_array<T>, T>::type
read_attribute(H5::H5Object const& object, std::string const& name)
{
    typedef typename T::element value_type;
    enum { rank = T::dimensionality };

    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 (!has_rank<rank>(attr)) {
        throw H5::AttributeIException("H5::attribute::as", "incompatible dataspace");
    }

    hsize_t dim[rank];
    ds.getSimpleExtentDims(dim);
    boost::array<size_t, rank> shape;
    std::copy(dim, dim + rank, shape.begin());
    boost::multi_array<value_type, rank> value(shape);
    attr.read(ctype<value_type>::hid(), value.origin());
    return value;
}
Exemplo n.º 3
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;
}
Exemplo n.º 4
0
 /// Return the attribute name of obj, and "" if the attribute does not exist.
 inline std::string read_string_attribute (H5::H5Object const * obj, std::string name ) { 
  std::string value ="";
  H5::Attribute attr;
  if (H5LTfind_attribute(obj -> getId(), name.c_str() )==0)  return value;// not present
  // can not find how to get the size with hl. Using full interface 
  //herr_t err2 =  H5LTget_attribute_string(gr.getId(), x.c_str(), name.c_str() , &(buf.front())  ) ;
  //value.append( &(buf.front()) );
  try { attr= obj->openAttribute(name.c_str());}
  catch (H5::AttributeIException) { return value;}
  try { 
   H5::DataSpace dataspace = attr.getSpace();
   int rank = dataspace.getSimpleExtentNdims();
   if (rank != 0) TRIQS_RUNTIME_ERROR << "Reading a string attribute and got rank !=0";
   size_t size = attr.getStorageSize();
   H5::StrType strdatatype(H5::PredType::C_S1, size+1);
   std::vector<char> buf(size+1, 0x00);
   attr.read(strdatatype, (void *)(&buf[0])); 
   value.append( &(buf.front()) );
  }
  TRIQS_ARRAYS_H5_CATCH_EXCEPTION;
  return value;
 } 
Exemplo n.º 5
0
void DataSet::readAttr(const H5::Attribute &attr, H5::DataType mem_type, const NDSize &size, std::string *data) {
    StringWriter writer(size, data);
    attr.read(mem_type, *writer);
    writer.finish();
    H5::DataSet::vlenReclaim(*writer, mem_type, attr.getSpace()); //recycle space?
}