inline typename boost::enable_if<boost::mpl::and_<
is_vector<T>
, boost::is_same<typename T::value_type, std::string>
>, void>::type
write_attribute(H5::H5Object const& object, std::string const& name, T const& value)
{
size_t size = value.size();
// size of longest string
size_t str_len = 0;
for (size_t i = 0; i < size; ++i) {
str_len = std::max(str_len, value[i].size());
}
// remove attribute if it exists and re-create with proper String datatype
// and simple dataspace
if (exists_attribute(object, name)) {
object.removeAttr(name);
}
hsize_t dim[1] = { size };
H5::DataSpace ds(1, dim);
H5::StrType tid(H5::PredType::C_S1, str_len);
H5::Attribute attr = object.createAttribute(name, tid, ds);
// copy strings to contiguous buffer
std::vector<char> buffer(size * str_len);
for (size_t i = 0; i < size; ++i) {
value[i].copy(buffer.data() + i * str_len, str_len);
}
attr.write(tid, &*buffer.begin());
}
inline typename boost::enable_if<boost::mpl::and_<is_array<T>, boost::is_same<typename T::value_type, char const*> >, void>::type
write_attribute(H5::H5Object const& object, std::string const& name, T const& value)
{
enum { size = T::static_size };
hsize_t dim[1] = { size };
H5::DataSpace ds(1, dim);
size_t max_len = 0;
for (size_t i = 0; i < size; ++i) {
max_len = std::max(max_len, strlen(value[i]));
}
H5::StrType tid(H5::PredType::C_S1, max_len);
// remove attribute if it exists
try {
H5XX_NO_AUTO_PRINT(H5::AttributeIException);
object.removeAttr(name);
}
catch (H5::AttributeIException const&) {}
H5::Attribute attr = object.createAttribute(name, tid, ds);
std::vector<char> data(max_len * size);
for (size_t i = 0; i < size; ++i) {
strncpy(&*data.begin() + i * max_len, value[i], max_len);
}
attr.write(tid, &*data.begin());
}
inline typename boost::enable_if<boost::is_same<T, char const*>, void>::type
write_attribute(H5::H5Object const& object, std::string const& name, T value)
{
H5::StrType tid(H5::PredType::C_S1, strlen(value));
// remove attribute if it exists
try {
H5XX_NO_AUTO_PRINT(H5::AttributeIException);
object.removeAttr(name);
}
catch (H5::AttributeIException const&) {}
H5::Attribute attr = object.createAttribute(name, tid, H5S_SCALAR);
attr.write(tid, value);
}
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;
}
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;
}
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;
}
/**
* determine whether attribute exists in file/group/dataset
*/
inline bool exists_attribute(H5::H5Object const& object, std::string const& name)
{
htri_t tri = H5Aexists(object.getId(), name.c_str());
if (tri < 0) {
throw error("failed to determine whether attribute \"" + name + "\" exists");
}
return (tri > 0);
}
inline typename boost::enable_if<boost::is_fundamental<T>, void>::type
write_attribute(H5::H5Object const& object, std::string const& name, T const& value)
{
H5::Attribute attr;
try {
H5XX_NO_AUTO_PRINT(H5::AttributeIException);
attr = object.openAttribute(name);
if (!has_type<T>(attr) || !has_scalar_space(attr)) {
// recreate attribute with proper type
object.removeAttr(name);
throw H5::AttributeIException();
}
}
catch (H5::AttributeIException const&) {
attr = object.createAttribute(name, ctype<T>::hid(), H5S_SCALAR);
}
attr.write(ctype<T>::hid(), &value);
}
inline typename boost::enable_if<boost::mpl::and_<is_array<T>, boost::is_fundamental<typename T::value_type> >, void>::type
write_attribute(H5::H5Object const& object, std::string const& name, T const& value)
{
typedef typename T::value_type value_type;
enum { size = T::static_size };
H5::Attribute attr;
try {
H5XX_NO_AUTO_PRINT(H5::AttributeIException);
attr = object.openAttribute(name);
if (!has_type<T>(attr) || !has_extent<T>(attr)) {
// recreate attribute with proper type and size
object.removeAttr(name);
throw H5::AttributeIException();
}
}
catch (H5::AttributeIException const&) {
hsize_t dim[1] = { size };
H5::DataSpace ds(1, dim);
attr = object.createAttribute(name, ctype<value_type>::hid(), ds);
}
attr.write(ctype<value_type>::hid(), &*value.begin());
}
inline typename boost::enable_if<is_multi_array<T>, void>::type
write_attribute(H5::H5Object const& object, std::string const& name, T const& value)
{
typedef typename T::element value_type;
enum { rank = T::dimensionality };
H5::Attribute attr;
try {
H5XX_NO_AUTO_PRINT(H5::AttributeIException);
attr = object.openAttribute(name);
if (!has_type<T>(attr) || !has_extent<T>(attr, value.shape())) {
// recreate attribute with proper type and size
object.removeAttr(name);
throw H5::AttributeIException();
}
}
catch (H5::AttributeIException const&) {
hsize_t dim[rank];
std::copy(value.shape(), value.shape() + rank, dim);
H5::DataSpace ds(rank, dim);
attr = object.createAttribute(name, ctype<value_type>::hid(), ds);
}
attr.write(ctype<value_type>::hid(), value.origin());
}
void File::doAddAttribute(H5::H5Object&loc, std::string name, void*data) {
double v;
//hsize_t size;
H5::Group *d = (H5::Group *)data;
H5::Attribute a(loc.openAttribute(name));
//size = loc.getStorageSize();
//FIXME: double
a.read( H5::PredType::NATIVE_DOUBLE, &v );
hsize_t dataSize = 1;
H5::DataSpace spaceParameters(1,&dataSize,&dataSize);
H5::Attribute b(d->createAttribute(name,H5::PredType::NATIVE_DOUBLE,
spaceParameters));
b.write( H5::PredType::NATIVE_DOUBLE, &v );
}
inline typename boost::enable_if<boost::is_fundamental<T>, 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");
}
T value;
attr.read(ctype<T>::hid(), &value);
return value;
}
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;
}
inline typename boost::enable_if<boost::mpl::and_<is_array<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;
enum { size = T::static_size };
H5::Attribute attr;
try {
H5XX_NO_AUTO_PRINT(H5::AttributeIException);
attr = object.openAttribute(name);
}
catch (H5::AttributeIException const&) {
throw;
}
if (!has_extent<T>(attr)) {
throw H5::AttributeIException("H5::attribute::as", "incompatible dataspace");
}
T value;
attr.read(ctype<value_type>::hid(), &*value.begin());
return value;
}
