void read_1darray_vector_of_string_impl (group_or_file f, std::string const & name, ArrayVectorOfStringType & V) {
if (!h5::exists(f, name)) TRIQS_RUNTIME_ERROR << "no such dataset : "<<name <<" in file ";
try {
DataSet ds = f->openDataSet( name.c_str() );
DataSpace dataspace = ds.getSpace();
mini_vector<hsize_t,1> dims_out;
int ndims = dataspace.getSimpleExtentDims( &dims_out[0], NULL);
if (ndims !=1) TRIQS_RUNTIME_ERROR << "triqs::h5 : Trying to read 1d array/vector . Rank mismatch : the array stored in the hdf5 file has rank = "<<ndims;
size_t Len = dims_out[0];
V.resize(Len);
size_t size = ds.getStorageSize();
StrType strdatatype(PredType::C_S1, size);
std::vector<char> buf(Len*(size+1), 0x00);
mini_vector<hsize_t,1> L; L[0]=V.size();
mini_vector<hsize_t,1> S; S[0]=1;
auto d_space = dataspace_from_LS<1,false > (L,L,S);
ds.read( (void *)(&buf[0]),strdatatype, d_space );
size_t i=0; for (auto & x : V) { x = ""; x.append(&buf[i*(size)]); ++i;}
}
TRIQS_ARRAYS_H5_CATCH_EXCEPTION;
}
/**
* \brief Write a string into an hdf5 file
* \param f The h5 file or group of type H5::H5File or H5::Group
* \param name The name of the hdf5 array in the file/group where the stack will be stored
* \param value The string
* \exception The HDF5 exceptions will be caught and rethrown as TRIQS_RUNTIME_ERROR (with a full stackstrace, cf triqs doc).
*/
inline void h5_write (h5::group_or_file f, std::string const & name, std::string const & value) {
try {
DataSet ds;
StrType strdatatype(PredType::C_S1, value.size());
ds = f->createDataSet( name.c_str(), strdatatype, DataSpace() );
ds.write((void*)(value.c_str()), strdatatype );
}
TRIQS_ARRAYS_H5_CATCH_EXCEPTION;
}
inline void write_attribute ( DataSet & dataset, std::string name, std::string value ) {
DataSpace attr_dataspace = DataSpace(H5S_SCALAR);
// Create new string datatype for attribute
StrType strdatatype(PredType::C_S1, value.size());
// Set up write buffer for attribute
const H5std_string strwritebuf (value);
// Create attribute and write to it
Attribute myatt_in = dataset.createAttribute(name, strdatatype, attr_dataspace);
myatt_in.write(strdatatype, strwritebuf);
}
inline void write_string_attribute ( H5::H5Object const * obj, std::string name, std::string value ) {
H5::DataSpace attr_dataspace = H5::DataSpace(H5S_SCALAR);
// Create new string datatype for attribute
H5::StrType strdatatype(H5::PredType::C_S1, value.size());
// Set up write buffer for attribute
//const H5std_string strwritebuf (value);
// Create attribute and write to it
H5::Attribute myatt_in = obj->createAttribute(name.c_str(), strdatatype, attr_dataspace);
//myatt_in.write(strdatatype, strwritebuf);
myatt_in.write(strdatatype, (void *)(value.c_str()));
}
/**
* \brief Read a string from an hdf5 file
* \param f The h5 file or group of type H5::H5File or H5::Group
* \param name The name of the hdf5 array in the file/group where the stack will be stored
* \param value The string to fill
* \exception The HDF5 exceptions will be caught and rethrown as TRIQS_RUNTIME_ERROR (with a full stackstrace, cf triqs doc).
*/
inline void h5_read (h5::group_or_file f, std::string const & name, std::string & value) {
if (!f.exists(name)) TRIQS_RUNTIME_ERROR << "no such dataset : "<<name <<" in file ";
try {
DataSet ds = f->openDataSet( name.c_str() );
DataSpace dataspace = ds.getSpace();
int rank = dataspace.getSimpleExtentNdims();
if (rank != 0) TRIQS_RUNTIME_ERROR << "Reading a string and got rank !=0";
size_t size = ds.getStorageSize();
StrType strdatatype(PredType::C_S1, size);
std::vector<char> buf(size+1, 0x00);
ds.read( (void *)(&buf[0]), strdatatype, DataSpace(), DataSpace() );
value = ""; value.append( &(buf.front()) );
}
TRIQS_ARRAYS_H5_CATCH_EXCEPTION;
}
void write_1darray_vector_of_string_impl (group_or_file f, std::string const & name, ArrayVectorOfStringType const & V) {
size_t s=0; for (auto & x : V) s = std::max(s,x.size());
try {
if (h5::exists(f, name)) f->unlink( name.c_str()); // put some option here ?
DataSet ds;
StrType strdatatype(PredType::C_S1, s);
const size_t n = V.size();
std::vector<char> buf(n*s, 0x00);
size_t i=0; for (auto & x : V) {strcpy( &buf[i*s], x.c_str()); ++i;}
mini_vector<hsize_t,1> L; L[0]=V.size();
mini_vector<hsize_t,1> S; S[0]=1;
auto d_space = dataspace_from_LS<1,false > (L,L,S);
ds = f->createDataSet( name.c_str(), strdatatype, d_space );
ds.write( (void *)(&buf[0]),strdatatype, d_space );
}
TRIQS_ARRAYS_H5_CATCH_EXCEPTION;
}
/// 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;
}
