void HDF5IO::saveMatrix(const std::string& GroupName, const std::string& Name,
const ComplexMatrixType& M)
{
try{
H5::CompType ComplexDataType = this->openCompType("complex");
hsize_t Dims[2] = {hsize_t(M.rows()),hsize_t(M.cols())};
H5::DataSpace dataspace(2,Dims);
H5::Group FG = getGroup( GroupName );
try{
H5::Exception::dontPrint();
H5::DataSet dset = FG.openDataSet(Name.c_str());
// dset.extend( Dims );not working
dset.write(M.data(), ComplexDataType);
} catch ( const H5::GroupIException not_found_error ){
H5::DataSet dset = FG.createDataSet(Name.c_str(), ComplexDataType, dataspace);
dset.write(M.data(), ComplexDataType);
} catch ( const H5::DataSetIException error ){
error.printError();
RUNTIME_ERROR("HDF5IO::saveComplexMatrix at ");
}
FG.close();
} catch( const H5::Exception error ){
error.printError();
RUNTIME_ERROR("HDF5IO::saveComplexMatrix at ");
}
}
void HDF5IO::saveStdVector(const std::string& GroupName, const std::string& Name,
const std::vector<std::complex<double> >& V)
{
try{
H5::CompType ComplexDataType = openCompType("complex");
hsize_t Dim[1] = {hsize_t(V.size())};
H5::DataSpace dataspace(1,Dim);
H5::Group FG = getGroup( GroupName.c_str() );
try{
H5::Exception::dontPrint();
H5::DataSet dataset = FG.openDataSet(Name.c_str());
dataset.write(V.data(), ComplexDataType, dataspace);
} catch( const H5::GroupIException not_found_error ){
H5::DataSet dataset = FG.createDataSet(Name.c_str(), ComplexDataType,
dataspace);
dataset.write(V.data(), ComplexDataType);
} catch( const H5::FileIException error){
error.printError();
} catch( const H5::DataSetIException error){
error.printError();
}
FG.close();
} catch( const H5::Exception err ){
err.printError();
RUNTIME_ERROR("HDF5IO::saveComplexStdVector. ");
}
}
void BufferedHDF2DArray<T>::Create(H5::CommonFG *_container, string _datasetName, unsigned int _rowLength) {
container = _container;
datasetName = _datasetName;
rowLength = (unsigned int)_rowLength;
//
// Make life easy if the buffer is too small to fit a row --
// resize it so that rows may be copied and written out in an
// atomic unit.
//
if (this->bufferSize < rowLength) {
// When the buffer size is greater than 0, the write buffer
// should exist.
if (this->bufferSize > 0) {
assert(this->writeBuffer != NULL);
delete[] this->writeBuffer;
}
this->writeBuffer = new T[rowLength];
this->bufferSize = rowLength;
}
hsize_t dataSize[2] = {0, hsize_t(rowLength)};
hsize_t maxDataSize[2] = {H5S_UNLIMITED, hsize_t(rowLength)};
H5::DataSpace fileSpace(2, dataSize, maxDataSize);
H5::DSetCreatPropList cparms;
/*
* For some reason, chunking must be enabled when creating a dataset
* that has an unlimited dimension. Of course, this is not
* mentioned in the hdf5 c++ documentation, because that
* docuemntation was written for people who enjoy learning how to
* use an API by reading comments in source code.
*/
hsize_t chunkDims[2] = {16384, hsize_t(rowLength)};
cparms.setChunk( 2, chunkDims );
TypedCreate(fileSpace, cparms);
fileSpace.close();
//
// Set some flags that indicate this dataset is ready for writing.
//
fileDataSpaceInitialized = true;
isInitialized = true;
}
void HDF5IO::saveMatrix(const std::string& GroupName, const std::string& Name,
const RealMatrixType& M)
{
try{
hsize_t Dims[2] = {hsize_t(M.rows()),hsize_t(M.cols())};
H5::DataSpace dataspace(2,Dims);
H5::Group FG = getGroup( GroupName );
try{
H5::Exception::dontPrint();
H5::DataSet DataSet = FG.openDataSet(Name.c_str());
DataSet.write(M.data(),H5::PredType::NATIVE_DOUBLE,dataspace);
} catch ( const H5::GroupIException not_found_error ){
H5::DataSet DataSet = FG.createDataSet(Name.c_str(),H5::PredType::NATIVE_DOUBLE,dataspace);
DataSet.write(M.data(),H5::PredType::NATIVE_DOUBLE);
}
FG.close();
} catch( const H5::Exception err ){
RUNTIME_ERROR("HDF5IO::saveRealMatrix");
}
}
/* only for Eigen3 matrix/vector */
void HDF5IO::saveVector(const std::string& GroupName,
const std::string& Name, const RealVectorType& V)
{
hsize_t Dim[1] = {hsize_t(V.size())};
H5::DataSpace dspace(1,Dim);
H5::Group FG = getGroup( GroupName );
try{
H5::Exception::dontPrint();
H5::DataSet DataSet = FG.openDataSet(Name.c_str());
DataSet.write(V.data(),H5::PredType::NATIVE_DOUBLE, dspace);
} catch ( const H5::GroupIException not_found_error ){
H5::DataSet DataSet = FG.createDataSet(Name.c_str(),
H5::PredType::NATIVE_DOUBLE,dspace);
DataSet.write(V.data(),H5::PredType::NATIVE_DOUBLE);
}
FG.close();
}
void HDF5IO::saveStdVector(const std::string& GroupName, const std::string& Name,
const std::vector<double>& V)
{
try{
hsize_t Dim[1] = {hsize_t(V.size())};
H5::DataSpace dataspace(1,Dim);
H5::Group FG = getGroup( GroupName );
try{
H5::Exception::dontPrint();
H5::DataSet dataset = FG.openDataSet(Name.c_str());
dataset.write(V.data(),H5::PredType::NATIVE_DOUBLE, dataspace);
} catch ( const H5::GroupIException not_found_error ){
H5::DataSet dataset = FG.createDataSet(Name.c_str(),
H5::PredType::NATIVE_DOUBLE,dataspace);
dataset.write(V.data(),H5::PredType::NATIVE_DOUBLE);
}
FG.close();
} catch( const H5::Exception err ){
RUNTIME_ERROR("HDF5IO::saveRealStdVector");
}
}
void HDF5IO::saveVector(const std::string& GroupName,
const std::string& Name, const ComplexVectorType& V)
{
try{
H5::CompType ComplexDataType = this->openCompType("complex");
hsize_t Dim[1] = {hsize_t(V.size())};
H5::DataSpace dspace(1,Dim);
H5::Group FG = getGroup( GroupName );
try{
H5::Exception::dontPrint();
H5::DataSet DataSet = FG.openDataSet(Name.c_str());
DataSet.write(V.data(), ComplexDataType, dspace);
} catch ( const H5::GroupIException not_found_error ){
H5::DataSet DataSet = FG.createDataSet(Name.c_str(), ComplexDataType,
dspace);
DataSet.write(V.data(), ComplexDataType);
}
FG.close();
} catch ( const H5::DataSetIException error ){
error.printError();
RUNTIME_ERROR("HDF5IO::saveComplexVector at ");
}
}
inline DataSpace::DataSpace(const size_t dim1){
const hsize_t dims = hsize_t(dim1);
if( (_hid = H5Screate_simple(1, &dims, NULL) ) < 0){
throw DataSpaceException("Unable to create dataspace");
}
}
