h5_read (h5::group_or_file f, std::string const & name, S & A) {
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 << "triqs::array::h5::read. Rank mismatch : expecting a scalar (rank =0)"
<<" while the array stored in the hdf5 file has rank = "<<rank;
ds.read( (void *)(&A), data_type_mem_scalar(A), DataSpace() , DataSpace() );
}
TRIQS_ARRAYS_H5_CATCH_EXCEPTION;
}
/**
* \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;
}
inline DataSpace DataSpace::From(const boost::multi_array<Value, Dims> & container){
std::vector<size_t> dims(Dims);
for(std::size_t i = 0; i < Dims; ++i){
dims[i] = container.shape()[i];
}
return DataSpace(dims);
}
/**
* \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 DataSpace DataSpace::From(const std::vector<Value> & container){
return DataSpace(details::get_dim_vector<Value>(container));
}
DataSpace DataSet::getSpace () const {
return DataSpace (Exception::check ("H5Dget_space", H5Dget_space (handle ())));
}
int WriteHDF5DoubleAttribute(string filename , string datasetname, string attr_name, int attr_dims, double* attr_data)
{
hsize_t dims[1] = { attr_dims };
// Try block to detect exceptions raised by any of the calls inside it
try
{
// Turn off the auto-printing when failure occurs so that we can
// handle the errors appropriately
Exception::dontPrint();
// Open an existing file and dataset.
H5File file(filename, H5F_ACC_RDWR );
DataSet dataset = file.openDataSet(datasetname);
// Create the data space for the attribute.
DataSpace attr_dataspace = DataSpace (1, dims );
// Create a dataset attribute.
Attribute attribute = dataset.createAttribute(attr_name, PredType::NATIVE_DOUBLE,
attr_dataspace, PropList::DEFAULT);
// Write the attribute data.
attribute.write( PredType::NATIVE_DOUBLE, attr_data);
} // end of try block
// catch failure caused by the H5File operations
catch( DataSpaceIException error )
{
error.printError();
return -1;
}
// catch failure caused by the H5File operations
catch( AttributeIException error )
{
error.printError();
return -1;
}
// catch failure caused by the H5File operations
catch( FileIException error )
{
error.printError();
return -1;
}
// catch failure caused by the DataSet operations
catch( DataSetIException error )
{
error.printError();
return -1;
}
return 0; // successfully terminated
}