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monofonIC/include/HDF_IO.hh

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#pragma once
#if defined(USE_HDF5)
#define H5_USE_16_API
/*
HDF_IO.hh -- templated C++ HDF5 front-end functions, v1.2b
Copyright (C) 2006-7 Oliver Hahn -- ojha@gmx.de
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#include <fstream>
#include <iostream>
#include <string>
#include <sstream>
#include <typeinfo>
#include <vector>
#include <cstdlib>
#include "hdf5.h"
template<typename T>
hid_t GetDataType( void )
{
if( typeid(T) == typeid(int) )
return H5T_NATIVE_INT;
if( typeid(T) == typeid(unsigned) )
return H5T_NATIVE_UINT;
if( typeid(T) == typeid(float) )
return H5T_NATIVE_FLOAT;
if( typeid(T) == typeid(double) )
return H5T_NATIVE_DOUBLE;
if( typeid(T) == typeid(long long) )
return H5T_NATIVE_LLONG;
if( typeid(T) == typeid(unsigned long long) )
return H5T_NATIVE_ULLONG;
if( typeid(T) == typeid(size_t) )
return H5T_NATIVE_ULLONG;
std::cerr << " - Error: [HDF_IO] trying to evaluate unsupported type in GetDataType\n\n";
return -1;
}
#include <stdexcept>
class HDFException : public std::runtime_error {
public:
HDFException( const std::string &errtxt ) : std::runtime_error(errtxt) { }
};
inline bool DoesFileExist( std::string Filename ){
bool flag = false;
std::fstream fin(Filename.c_str(),std::ios::in|std::ios::binary);
if( fin.is_open() )
flag=true;
fin.close();
return flag;
}
inline void AssertFileOpen( std::string Filename )
{
if( !DoesFileExist( Filename ) ){
std::fstream fout( Filename.c_str(), std::ios::out|std::ios::binary);
fout.close();
}
}
inline void HDFCreateFile( std::string Filename )
{
hid_t HDF_FileID;
HDF_FileID = H5Fcreate( Filename.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT );
H5Fclose( HDF_FileID );
}
template< typename T>
inline void HDFReadVector( const std::string Filename, const std::string ObjName, std::vector<T> &Data )
{
HDFReadDataset( Filename, ObjName, Data );
}
inline void HDFGetDatasetExtent( const std::string Filename, const std::string ObjName, std::vector<int> &Extent )
{
hid_t HDF_FileID, HDF_DatasetID, HDF_DataspaceID;
HDF_FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT );
//... save old error handler
herr_t (*old_func)(void*);
void *old_client_data;
H5Eget_auto(&old_func, &old_client_data);
//... turn off error handling by hdf5 library
H5Eset_auto(NULL, NULL);
//... probe dataset opening
HDF_DatasetID = H5Dopen( HDF_FileID, ObjName.c_str() );
//... restore previous error handler
H5Eset_auto(old_func, old_client_data);
//... dataset did not exist or was empty
if( HDF_DatasetID < 0 ){
std::stringstream ss;
ss << " - Warning: dataset \'" << ObjName.c_str() << "\' does not exist or is empty.\n";
H5Fclose( HDF_FileID );
throw HDFException(ss.str());
return;
}
//... get space associated with dataset and its extensions
HDF_DataspaceID = H5Dget_space( HDF_DatasetID );
int ndims = H5Sget_simple_extent_ndims( HDF_DataspaceID );
hsize_t *dimsize = new hsize_t[ndims];
H5Sget_simple_extent_dims( HDF_DataspaceID, dimsize, NULL );
Extent.clear();
for(int i=0; i<ndims; ++i )
Extent.push_back( dimsize[i] );
delete[] dimsize;
H5Sclose( HDF_DataspaceID );
H5Dclose( HDF_DatasetID );
H5Fclose( HDF_FileID );
}
template< typename T >
inline void HDFReadDataset( const std::string Filename, const std::string ObjName, std::vector<T> &Data )
{
hid_t HDF_Type, HDF_FileID, HDF_DatasetID, HDF_DataspaceID;
hsize_t HDF_StorageSize;
HDF_Type = GetDataType<T>();
HDF_FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT );
//... save old error handler
herr_t (*old_func)(void*);
void *old_client_data;
H5Eget_auto(&old_func, &old_client_data);
//... turn off error handling by hdf5 library
H5Eset_auto(NULL, NULL);
//... probe dataset opening
HDF_DatasetID = H5Dopen( HDF_FileID, ObjName.c_str() );
//... restore previous error handler
H5Eset_auto(old_func, old_client_data);
//... dataset did not exist or was empty
if( HDF_DatasetID < 0 ){
std::stringstream ss;
ss << " - Warning: dataset \'" << ObjName.c_str() << "\' does not exist or is empty.\n";
Data.clear();
H5Fclose( HDF_FileID );
throw HDFException(ss.str());
return;
}
//... get space associated with dataset and its extensions
HDF_DataspaceID = H5Dget_space( HDF_DatasetID );
int ndims = H5Sget_simple_extent_ndims( HDF_DataspaceID );
hsize_t dimsize[ndims];
H5Sget_simple_extent_dims( HDF_DataspaceID, dimsize, NULL );
HDF_StorageSize = 1;
for(int i=0; i<ndims; ++i )
HDF_StorageSize *= dimsize[i];
//... adjust the array size to hold the data
Data.clear();
Data.reserve( HDF_StorageSize );
Data.assign( HDF_StorageSize, (T)1 );
if( Data.capacity() < HDF_StorageSize ){
std::cerr << " - Error: not enough memory to store all data in HDFReadDataset!\n\n";
abort();
}
//... read the dataset
H5Dread( HDF_DatasetID, HDF_Type, H5S_ALL, H5S_ALL, H5P_DEFAULT, &Data[0] );
if( Data.size() != HDF_StorageSize ){
std::cerr << " - Error: something went wrong while reading!\n\n";
abort();
}
H5Sclose( HDF_DataspaceID );
H5Dclose( HDF_DatasetID );
H5Fclose( HDF_FileID );
}
template<typename T >
inline void HDFReadSelect( const std::string Filename, const std::string ObjName, const std::vector<unsigned>& ii, std::vector<T> &Data ){
hid_t HDF_Type, HDF_FileID, HDF_DatasetID, HDF_DataspaceID, HDF_MemspaceID;
hsize_t HDF_StorageSize;
HDF_Type = GetDataType<T>();
HDF_FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT );
//... save old error handler
herr_t (*old_func)(void*);
void *old_client_data;
H5Eget_auto(&old_func, &old_client_data);
//... turn off error handling by hdf5 library
H5Eset_auto(NULL, NULL);
//... probe dataset opening
HDF_DatasetID = H5Dopen( HDF_FileID, ObjName.c_str() );
//... restore previous error handler
H5Eset_auto(old_func, old_client_data);
//... dataset did not exist or was empty
if( HDF_DatasetID < 0 ){
std::stringstream ss;
ss << " - Warning: dataset \'" << ObjName.c_str() << "\' does not exist or is empty.\n";
Data.clear();
H5Fclose( HDF_FileID );
throw HDFException(ss.str());
}
//... get space associated with dataset and its extensions
HDF_DataspaceID = H5Dget_space( HDF_DatasetID );
hsize_t block[2];
block[0] = ii.size();
block[1] = 1;
Data.clear();
Data.reserve( block[0]*block[1] );
Data.assign( block[0]*block[1], (T)1 );
HDF_MemspaceID = H5Screate_simple( 2, block, NULL );
// H5Sselect_hyperslab( FilespaceID, H5S_SELECT_SET, offset, stride, count, block );
H5Sselect_elements( HDF_DataspaceID, H5S_SELECT_SET, ii.size(), (const hsize_t *)&ii[0] );
H5Dread( HDF_DatasetID, HDF_Type, HDF_MemspaceID, HDF_DataspaceID, H5P_DEFAULT, &Data[0] );
H5Sclose( HDF_DataspaceID );
H5Sclose( HDF_MemspaceID );
H5Dclose( HDF_DatasetID );
H5Fclose( HDF_FileID );
}
template<typename T >
inline void HDFReadVectorSelect( const std::string Filename, const std::string ObjName, const std::vector<unsigned>& ii, std::vector<T> &Data ){
hid_t HDF_Type, HDF_FileID, HDF_DatasetID, HDF_DataspaceID, HDF_MemspaceID;
// hsize_t HDF_StorageSize;
HDF_Type = GetDataType<T>();
HDF_FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT );
//... save old error handler
herr_t (*old_func)(void*);
void *old_client_data;
H5Eget_auto(&old_func, &old_client_data);
//... turn off error handling by hdf5 library
H5Eset_auto(NULL, NULL);
//... probe dataset opening
HDF_DatasetID = H5Dopen( HDF_FileID, ObjName.c_str() );
//... restore previous error handler
H5Eset_auto(old_func, old_client_data);
//... dataset did not exist or was empty
if( HDF_DatasetID < 0 ){
std::stringstream ss;
ss << " - Warning: dataset \'" << ObjName.c_str() << "\' does not exist or is empty.\n";
Data.clear();
H5Fclose( HDF_FileID );
throw HDFException(ss.str());
return;
}
//... get space associated with dataset and its extensions
HDF_DataspaceID = H5Dget_space( HDF_DatasetID );
int ndims = H5Sget_simple_extent_ndims( HDF_DataspaceID );
hsize_t dimsize[ndims];
H5Sget_simple_extent_dims( HDF_DataspaceID, dimsize, NULL );
hsize_t block[2];
block[0] = ii.size();
block[1] = 3;
std::vector<hsize_t> coord;
for( unsigned i=0; i<ii.size(); ++i )
for( unsigned k=0; k<3; ++k ){
coord.push_back(ii[i]);
coord.push_back(k);
}
//std::vector<unsigned>().swap(ii);
if( ii.size() == 0 ){
std::cerr << "attempted to read empty block. skipping....\n";
return;
}
//std::cerr << "starting 2 read...\n";
H5Sselect_none( HDF_DataspaceID );
if( H5Sselect_elements( HDF_DataspaceID, H5S_SELECT_SET, coord.size()/2, (const hsize_t *)&coord[0] ) < 0 )//(const hsize_t**)&coord[0] ) < 0 )
std::cerr << " - could not select elements properly\n";
if(H5Sselect_valid( HDF_DataspaceID )<=0 ){
std::cerr << "\n - sorry, invalid element selection in file \'"<< Filename.c_str() << "\'. \n - dumping 10 first indices...\n";
/*for( unsigned i=0; i<10; ++i ){
for( unsigned k=0; k<3; ++k ){
std::cerr << coord[3*i+k] << " ";
}
std::cerr << "\n";
}*/
return;
}
std::vector<hsize_t>().swap(coord);
Data.assign( block[0]*block[1], (T)0 );
HDF_MemspaceID = H5Screate_simple( 2, &block[0], NULL );
H5Dread( HDF_DatasetID, HDF_Type, HDF_MemspaceID, HDF_DataspaceID, H5P_DEFAULT, &Data[0] );
H5Sclose( HDF_DataspaceID );
H5Sclose( HDF_MemspaceID );
H5Dclose( HDF_DatasetID );
H5Fclose( HDF_FileID );
}
template< typename T >
inline void HDFReadVectorSlab( const std::string Filename, const std::string ObjName, unsigned nStart, unsigned nCount, std::vector<T> &Data )
{
hsize_t
offset[2],
stride[2],
count[2],
block[2];
hid_t MemspaceID, FilespaceID, DatasetID, FileID;
hid_t Type = GetDataType<T>();
FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT );
//... save old error handler
herr_t (*old_func)(void*);
void *old_client_data;
H5Eget_auto(&old_func, &old_client_data);
//... turn off error handling by hdf5 library
H5Eset_auto(NULL, NULL);
//... probe dataset opening
DatasetID = H5Dopen( FileID, ObjName.c_str() );
//... restore previous error handler
H5Eset_auto(old_func, old_client_data);
//... dataset did not exist or was empty
if( DatasetID < 0 ){
std::stringstream ss;
ss << " - Warning: dataset \'" << ObjName.c_str() << "\' does not exist or is empty.\n";
Data.clear();
H5Fclose( FileID );
throw HDFException(ss.str());
return;
}
FilespaceID = H5Dget_space( DatasetID );
offset[0] = nStart;
offset[1] = 0;
count[0] = 1;
count[1] = 1;
stride[0] = 1;
stride[1] = 1;
block[0] = nCount;
block[1] = 3;
Data.clear();
Data.reserve( block[0]*block[1] );
Data.assign( block[0]*block[1], (T)1 );
MemspaceID = H5Screate_simple( 2, block, NULL );
H5Sselect_hyperslab( FilespaceID, H5S_SELECT_SET, offset, stride, count, block );
H5Dread( DatasetID, Type, MemspaceID, FilespaceID, H5P_DEFAULT, &Data[0] );
H5Sclose( FilespaceID );
H5Sclose( MemspaceID );
H5Dclose( DatasetID );
H5Fclose( FileID );
}
template< typename T >
inline void HDFReadDatasetSlab( const std::string Filename, const std::string ObjName, unsigned nStart, unsigned nCount, std::vector<T> &Data )
{
hsize_t
offset[2],
stride[2],
count[2],
block[2];
hid_t MemspaceID, FilespaceID, DatasetID, FileID;
hid_t Type = GetDataType<T>();
FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT );
//... save old error handler
herr_t (*old_func)(void*);
void *old_client_data;
H5Eget_auto(&old_func, &old_client_data);
//... turn off error handling by hdf5 library
H5Eset_auto(NULL, NULL);
//... probe dataset opening
DatasetID = H5Dopen( FileID, ObjName.c_str() );
//... restore previous error handler
H5Eset_auto(old_func, old_client_data);
//... dataset did not exist or was empty
if( DatasetID < 0 ){
std::stringstream ss;
ss << " - Warning: dataset \'" << ObjName.c_str() << "\' does not exist or is empty.\n";
Data.clear();
H5Fclose( FileID );
throw HDFException(ss.str());
return;
}
FilespaceID = H5Dget_space( DatasetID );
offset[0] = nStart;
offset[1] = 0;
count[0] = 1;
count[1] = 1;
stride[0] = 1;
stride[1] = 1;
block[0] = nCount;
block[1] = 1;
Data.clear();
Data.reserve( block[0]*block[1] );
Data.assign( block[0]*block[1], (T)1 );
MemspaceID = H5Screate_simple( 2, block, NULL );
H5Sselect_hyperslab( FilespaceID, H5S_SELECT_SET, offset, stride, count, block );
H5Dread( DatasetID, Type, MemspaceID, FilespaceID, H5P_DEFAULT, &Data[0] );
H5Sclose( FilespaceID );
H5Sclose( MemspaceID );
H5Dclose( DatasetID );
H5Fclose( FileID );
}
template< typename T>
inline void HDFReadGroupAttribute( const std::string Filename, const std::string GroupName, const std::string ObjName, T &Data )
{
hid_t HDF_Type, HDF_FileID, HDF_GroupID, HDF_AttributeID;
// hsize_t HDF_StorageSize;
HDF_Type = GetDataType<T>();
//... save old error handler
herr_t (*old_func)(void*);
void *old_client_data;
H5Eget_auto(&old_func, &old_client_data);
//... turn off error handling by hdf5 library
H5Eset_auto(NULL, NULL);
//... attempt to open attribute
HDF_FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT );
HDF_GroupID = H5Gopen( HDF_FileID, GroupName.c_str() );
HDF_AttributeID = H5Aopen_name( HDF_GroupID, ObjName.c_str() );
if( HDF_FileID < 0 || HDF_GroupID < 0 || HDF_AttributeID < 0 ){
std::stringstream ss;
ss << " - Warning: attribute \'" << GroupName.c_str() << "/" << ObjName.c_str() << "\' does not exist or is empty.\n";
H5Fclose( HDF_FileID );
throw HDFException(ss.str());
return;
}
H5Aread( HDF_AttributeID, HDF_Type, &Data );
//... restore previous error handler
H5Eset_auto(old_func, old_client_data);
H5Aclose( HDF_AttributeID );
H5Gclose( HDF_GroupID );
H5Fclose( HDF_FileID );
}
template< typename T>
inline void HDFReadGroupAttribute( const std::string Filename, const std::string GroupName, const std::string ObjName, std::vector<T> &Data )
{
hid_t HDF_Type, HDF_FileID, HDF_GroupID, HDF_AttributeID, HDF_DataspaceID;
hsize_t HDF_StorageSize;
HDF_Type = GetDataType<T>();
//... save old error handler
herr_t (*old_func)(void*);
void *old_client_data;
H5Eget_auto(&old_func, &old_client_data);
//... turn off error handling by hdf5 library
H5Eset_auto(NULL, NULL);
//... attempt to open attribute
HDF_FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT );
HDF_GroupID = H5Gopen( HDF_FileID, GroupName.c_str() );
HDF_AttributeID = H5Aopen_name( HDF_GroupID, ObjName.c_str() );
if( HDF_FileID < 0 || HDF_GroupID < 0 || HDF_AttributeID < 0 ){
std::stringstream ss;
ss << " - Warning: attribute \'" << GroupName.c_str() << "/" << ObjName.c_str() << "\' does not exist or is empty.\n";
H5Fclose( HDF_FileID );
throw HDFException(ss.str());
return;
}
//... get space associated with dataset and its extensions
HDF_DataspaceID = H5Aget_space( HDF_AttributeID );
int ndims = H5Sget_simple_extent_ndims( HDF_DataspaceID );
hsize_t dimsize[ndims];
H5Sget_simple_extent_dims( HDF_DataspaceID, dimsize, NULL );
HDF_StorageSize = 1;
for(int i=0; i<ndims; ++i )
HDF_StorageSize *= dimsize[i];
//... adjust the array size to hold the data
Data.clear();
Data.reserve( HDF_StorageSize );
Data.assign( HDF_StorageSize, (T)1 );
H5Aread( HDF_AttributeID, HDF_Type, &Data[0] );
//... restore previous error handler
H5Eset_auto(old_func, old_client_data);
H5Aclose( HDF_AttributeID );
H5Sclose( HDF_DataspaceID );
H5Gclose( HDF_GroupID );
H5Fclose( HDF_FileID );
}
template< typename T >
inline void HDFWriteDataset( const std::string Filename, const std::string ObjName, const std::vector<T> &Data )
{
hid_t
HDF_FileID,
HDF_DatasetID,
HDF_DataspaceID,
HDF_Type;
hsize_t HDF_Dims;
HDF_FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT );
HDF_Type = GetDataType<T>();
HDF_Dims = Data.size();
HDF_DataspaceID = H5Screate_simple(1, &HDF_Dims, NULL);
HDF_DatasetID = H5Dcreate( HDF_FileID, ObjName.c_str(), HDF_Type,
HDF_DataspaceID, H5P_DEFAULT );
H5Dwrite( HDF_DatasetID, HDF_Type, H5S_ALL, H5S_ALL,
H5P_DEFAULT, &Data[0] );
H5Dclose( HDF_DatasetID );
H5Sclose( HDF_DataspaceID );
H5Fclose( HDF_FileID );
}
template< typename T >
inline void HDFWriteGroupDataset( const std::string Filename, const std::string GrpName, const std::string ObjName, const std::vector<T> &Data )
{
hid_t
HDF_FileID,
HDF_GroupID,
HDF_DatasetID,
HDF_DataspaceID,
HDF_Type;
hsize_t HDF_Dims;
HDF_FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT );
HDF_GroupID = H5Gopen( HDF_FileID, GrpName.c_str() );
HDF_Type = GetDataType<T>();
HDF_Dims = Data.size();
HDF_DataspaceID = H5Screate_simple(1, &HDF_Dims, NULL);
HDF_DatasetID = H5Dcreate( HDF_GroupID, ObjName.c_str(), HDF_Type,
HDF_DataspaceID, H5P_DEFAULT );
H5Dwrite( HDF_DatasetID, HDF_Type, H5S_ALL, H5S_ALL,
H5P_DEFAULT, &Data[0] );
H5Dclose( HDF_DatasetID );
H5Sclose( HDF_DataspaceID );
H5Gclose( HDF_GroupID );
H5Fclose( HDF_FileID );
}
template< typename T >
inline void HDFWriteDataset2D( const std::string Filename, const std::string ObjName, const std::vector< std::vector<T> > &Data )
{
hid_t
HDF_FileID,
HDF_DatasetID,
HDF_DataspaceID,
HDF_Type;
hsize_t HDF_Dims[2];
HDF_FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT );
HDF_Type = GetDataType<T>();
HDF_Dims[0] = Data.size();
HDF_Dims[1] = Data[0].size();
HDF_DataspaceID = H5Screate_simple(2, HDF_Dims, NULL);
HDF_DatasetID = H5Dcreate( HDF_FileID, ObjName.c_str(), HDF_Type,
HDF_DataspaceID, H5P_DEFAULT );
T *tmp = new T[HDF_Dims[0]*HDF_Dims[1]];
unsigned k=0;
for(unsigned i=0; i<HDF_Dims[0]; ++i )
for(unsigned j=0; j<HDF_Dims[1]; ++j ){
tmp[k++] = (Data[i])[j];
}
H5Dwrite( HDF_DatasetID, HDF_Type, H5S_ALL, H5S_ALL,
H5P_DEFAULT, tmp );
delete[] tmp;
H5Dclose( HDF_DatasetID );
H5Sclose( HDF_DataspaceID );
H5Fclose( HDF_FileID );
}
template< typename T >
inline void HDFWriteDataset3D( const std::string Filename, const std::string ObjName, unsigned nd[3], const std::vector< T > &Data )
{
hid_t
HDF_FileID,
HDF_DatasetID,
HDF_DataspaceID,
HDF_Type;
hsize_t HDF_Dims[3];
HDF_FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT );
HDF_Type = GetDataType<T>();
HDF_Dims[0] = nd[0];
HDF_Dims[1] = nd[1];
HDF_Dims[2] = nd[2];
//std::cerr << nd[0]<<nd[1]<<nd[2]<<"\n";
HDF_DataspaceID = H5Screate_simple(3, HDF_Dims, NULL);
HDF_DatasetID = H5Dcreate( HDF_FileID, ObjName.c_str(), HDF_Type,
HDF_DataspaceID, H5P_DEFAULT );
H5Dwrite( HDF_DatasetID, HDF_Type, H5S_ALL, H5S_ALL,
H5P_DEFAULT, &Data[0] );
H5Dclose( HDF_DatasetID );
H5Sclose( HDF_DataspaceID );
H5Fclose( HDF_FileID );
}
template< typename T >
struct HDFHyperslabWriter3Ds
{
hid_t dset_id_, type_id_, file_id_;
HDFHyperslabWriter3Ds( const std::string Filename, const std::string ObjName, size_t nd[3] )
{
hid_t filespace;
hsize_t sizes[4] = { 1, nd[0], nd[1], nd[2] };
type_id_ = GetDataType<T>();
file_id_ = H5Fopen( Filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT );
//std::cerr << "creating filespace : 1 x " << nd[0] << " x " << nd[1] << " x " << nd[2] << std::endl;
filespace = H5Screate_simple( 4, sizes, NULL );
dset_id_ = H5Dcreate( file_id_, ObjName.c_str(), type_id_, filespace, H5P_DEFAULT );
H5Sclose(filespace);
}
~HDFHyperslabWriter3Ds()
{
H5Dclose( dset_id_ );
H5Fclose( file_id_ );
}
void write_slab( T* data, size_t* count, size_t* offset )
{
hsize_t counts[4] = { 1, count[0], count[1], count[2] };
hsize_t offsets[4] = { 0, offset[0], offset[1], offset[2] };
hid_t filespace = H5Dget_space(dset_id_);
//std::cerr << "creating memspace : 1 x " << count[0] << " x " << count[1] << " x " << count[2] << std::endl;
hid_t memspace = H5Screate_simple(4, counts, NULL);
H5Sselect_hyperslab( filespace, H5S_SELECT_SET, offsets, NULL, counts, NULL );
//herr_t status;
//status =
H5Dwrite(dset_id_, type_id_, memspace, filespace, H5P_DEFAULT, reinterpret_cast<void*>(data));
H5Sclose(filespace);
H5Sclose(memspace);
}
};
template< typename T >
inline void HDFWriteDataset3Ds( const std::string Filename, const std::string ObjName, unsigned nd[3], const std::vector< T > &Data )
{
hid_t
HDF_FileID,
HDF_DatasetID,
HDF_DataspaceID,
HDF_Type;
hsize_t HDF_Dims[4];
HDF_FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT );
HDF_Type = GetDataType<T>();
HDF_Dims[0] = 1;
HDF_Dims[1] = nd[0];
HDF_Dims[2] = nd[1];
HDF_Dims[3] = nd[2];
//std::cerr << nd[0]<<nd[1]<<nd[2]<<"\n";
HDF_DataspaceID = H5Screate_simple(4, HDF_Dims, NULL);
HDF_DatasetID = H5Dcreate( HDF_FileID, ObjName.c_str(), HDF_Type,
HDF_DataspaceID, H5P_DEFAULT );
H5Dwrite( HDF_DatasetID, HDF_Type, H5S_ALL, H5S_ALL,
H5P_DEFAULT, &Data[0] );
H5Dclose( HDF_DatasetID );
H5Sclose( HDF_DataspaceID );
H5Fclose( HDF_FileID );
}
template< typename T >
inline void HDFWriteDatasetVector( const std::string Filename, const std::string ObjName, const std::vector<T> &Data )
{
hid_t
HDF_FileID,
HDF_DatasetID,
HDF_DataspaceID,
HDF_Type;
hsize_t HDF_Dims[2];
// hsize_t HDF_Dims;
HDF_FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT );
HDF_Type = GetDataType<T>();
HDF_Dims[0] = (hsize_t)(Data.size()/3);
HDF_Dims[1] = 3;
if( Data.size() % 3 != 0 ){
std::cerr << " - Warning: Trying to write vector data in HDFWriteDatasetVector\n"
<< " but array length not divisible by 3!\n\n";
}
HDF_DataspaceID = H5Screate_simple(2, HDF_Dims, NULL);
HDF_DatasetID = H5Dcreate( HDF_FileID, ObjName.c_str(), H5T_NATIVE_FLOAT,
HDF_DataspaceID, H5P_DEFAULT );
H5Dwrite( HDF_DatasetID, HDF_Type, H5S_ALL, H5S_ALL,
H5P_DEFAULT, &Data[0] );
H5Dclose( HDF_DatasetID );
H5Sclose( HDF_DataspaceID );
H5Fclose( HDF_FileID );
}
inline void HDFCreateGroup( const std::string Filename, const std::string GroupName )
{
hid_t HDF_FileID, HDF_GroupID;
HDF_FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT );
HDF_GroupID = H5Gcreate( HDF_FileID, GroupName.c_str(), 0 );
H5Gclose( HDF_GroupID );
H5Fclose( HDF_FileID );
}
inline void HDFCreateSubGroup( const std::string Filename, const std::string SuperGroupName, const std::string GroupName )
{
hid_t HDF_FileID, HDF_GroupID, HDF_SuperGroupID;
HDF_FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT );
HDF_SuperGroupID = H5Gopen( HDF_FileID, SuperGroupName.c_str() );
HDF_GroupID = H5Gcreate( HDF_SuperGroupID, GroupName.c_str(), 0 );
H5Gclose( HDF_GroupID );
H5Gclose( HDF_SuperGroupID );
H5Fclose( HDF_FileID );
}
template< typename T >
inline void HDFWriteGroupAttribute( const std::string Filename, const std::string GroupName, const std::string ObjName, const std::vector< T > &Data )
{
hid_t HDF_FileID,
HDF_GroupID,
HDF_AttributeID,
HDF_DataspaceID,
HDF_DatatypeID;
hsize_t HDF_Dims;
HDF_DatatypeID = GetDataType<T>();
HDF_Dims = (hsize_t)(Data.size());
HDF_FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT );
HDF_GroupID = H5Gopen( HDF_FileID, GroupName.c_str() );
HDF_DataspaceID = H5Screate_simple(1, &HDF_Dims, NULL);
HDF_AttributeID = H5Acreate(HDF_GroupID, ObjName.c_str(), HDF_DatatypeID, HDF_DataspaceID, H5P_DEFAULT);
H5Awrite( HDF_AttributeID, HDF_DatatypeID, &Data[0] );
H5Aclose( HDF_AttributeID );
H5Sclose( HDF_DataspaceID );
H5Gclose( HDF_GroupID );
H5Fclose( HDF_FileID );
}
template< typename T >
inline void HDFWriteDatasetAttribute( const std::string Filename, const std::string DatasetName, const std::string ObjName, const std::vector< T > &Data )
{
hid_t HDF_FileID,
HDF_DatasetID,
HDF_AttributeID,
HDF_DataspaceID,
HDF_DatatypeID;
hsize_t HDF_Dims;
HDF_DatatypeID = GetDataType<T>();
HDF_Dims = (hsize_t)(Data.size());
HDF_FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT );
HDF_DatasetID = H5Dopen( HDF_FileID, DatasetName.c_str() );
HDF_DataspaceID = H5Screate_simple(1, &HDF_Dims, NULL);
HDF_AttributeID = H5Acreate(HDF_DatasetID, ObjName.c_str(), HDF_DatatypeID, HDF_DataspaceID, H5P_DEFAULT);
H5Awrite( HDF_AttributeID, HDF_DatatypeID, &Data[0] );
H5Aclose( HDF_AttributeID );
H5Sclose( HDF_DataspaceID );
H5Dclose( HDF_DatasetID );
H5Fclose( HDF_FileID );
}
template< typename T >
inline void HDFWriteGroupAttribute( const std::string Filename, const std::string GroupName, const std::string ObjName, T
Data )
{
hid_t
HDF_FileID,
HDF_GroupID,
HDF_AttributeID,
HDF_DataspaceID,
HDF_DatatypeID;
HDF_DatatypeID = GetDataType<T>();
HDF_FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT );
HDF_GroupID = H5Gopen( HDF_FileID, GroupName.c_str() );
HDF_DataspaceID = H5Screate(H5S_SCALAR);
HDF_AttributeID = H5Acreate(HDF_GroupID, ObjName.c_str(), HDF_DatatypeID,
HDF_DataspaceID, H5P_DEFAULT);
H5Awrite( HDF_AttributeID, HDF_DatatypeID, &Data );
H5Aclose( HDF_AttributeID );
H5Sclose( HDF_DataspaceID );
H5Gclose( HDF_GroupID );
H5Fclose( HDF_FileID );
}
template< typename T >
inline void HDFWriteDatasetAttribute( const std::string Filename, const std::string DatasetName, const std::string ObjName, T Data )
{
hid_t
HDF_FileID,
HDF_DatasetID,
HDF_AttributeID,
HDF_DataspaceID,
HDF_DatatypeID;
HDF_DatatypeID = GetDataType<T>();
HDF_FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT );
HDF_DatasetID = H5Dopen( HDF_FileID, DatasetName.c_str() );
HDF_DataspaceID = H5Screate(H5S_SCALAR);
HDF_AttributeID = H5Acreate(HDF_DatasetID, ObjName.c_str(), HDF_DatatypeID,
HDF_DataspaceID, H5P_DEFAULT);
H5Awrite( HDF_AttributeID, HDF_DatatypeID, &Data );
H5Aclose( HDF_AttributeID );
H5Sclose( HDF_DataspaceID );
H5Dclose( HDF_DatasetID );
H5Fclose( HDF_FileID );
}
template< typename T >
inline void HDFWriteSubGroupAttribute( const std::string Filename, const std::string GroupName, const std::string SubGroupName, const std::string ObjName, T
Data )
{
hid_t
HDF_FileID,
HDF_GroupID,
HDF_SubGroupID,
HDF_AttributeID,
HDF_DataspaceID,
HDF_DatatypeID;
HDF_DatatypeID = GetDataType<T>();
HDF_FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT );
std::cerr << "opening " << GroupName.c_str() << std::endl;
HDF_GroupID = H5Gopen( HDF_FileID, GroupName.c_str() );
std::cerr << "opening " << SubGroupName.c_str() << std::endl;
HDF_SubGroupID = H5Gopen( HDF_GroupID, SubGroupName.c_str() );
HDF_DataspaceID = H5Screate(H5S_SCALAR);
HDF_AttributeID = H5Acreate(HDF_SubGroupID, ObjName.c_str(), HDF_DatatypeID,
HDF_DataspaceID, H5P_DEFAULT);
H5Awrite( HDF_AttributeID, HDF_DatatypeID, &Data );
H5Aclose( HDF_AttributeID );
H5Sclose( HDF_DataspaceID );
H5Gclose( HDF_SubGroupID );
H5Gclose( HDF_GroupID );
H5Fclose( HDF_FileID );
}
template<>
inline void HDFWriteGroupAttribute<std::string>( const std::string Filename, const std::string GroupName, const std::string ObjName, std::string Data )
{
hid_t
HDF_FileID,
HDF_GroupID,
HDF_AttributeID,
HDF_DataspaceID,
HDF_DatatypeID;
HDF_DatatypeID = H5Tcopy( H5T_C_S1 );
H5Tset_size( HDF_DatatypeID, Data.size() );
H5Tset_strpad(HDF_DatatypeID, H5T_STR_NULLPAD);
HDF_FileID = H5Fopen( Filename.c_str(), H5F_ACC_RDWR, H5P_DEFAULT );
HDF_GroupID = H5Gopen( HDF_FileID, GroupName.c_str() );
HDF_DataspaceID = H5Screate(H5S_SCALAR);
HDF_AttributeID = H5Acreate(HDF_GroupID, ObjName.c_str(), HDF_DatatypeID,
HDF_DataspaceID, H5P_DEFAULT);
H5Awrite( HDF_AttributeID, HDF_DatatypeID, Data.c_str() );
H5Aclose( HDF_AttributeID );
H5Sclose( HDF_DataspaceID );
H5Gclose( HDF_GroupID );
H5Fclose( HDF_FileID );
}
#endif // USE_HDF5
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