file hdf5printer/hdf5tools.hpp
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Namespaces
| Name |
|---|
| Gambit TODO: see if we can use this one: |
| Gambit::Printers Forward declaration. |
| Gambit::Printers::HDF5 |
Classes
Defines
| Name | |
|---|---|
| H5_OUTPUT_TYPES | |
| HDF5_STRING_MAX_LEN | |
| SPECIALISE_HDF5_DATA_TYPE_IF_NEEDED(TYPEDEFD_TYPE, RETURN_HDF5_TYPE) Provide template specialisation of get_hdf5_data_type only if the requested type hasn’t been used to define one already. |
Detailed Description
Author:
- Ben Farmer (benjamin.farmer@fysik.su.se)
- Pat Scott (p.scott@imperial.ac.uk)
- Tomas Gonzalo (tomas.gonzalo@monash.edu)
Date:
- 2015 May
- 2015 Jul
- 2020 June
A collection of tools for interacting with HDF5 databases.
Currently I am using the C++ bindings for HDF5, however they are a bit crap and it may be better to just write our own.
Authors (add name and date if you modify):
Macros Documentation
define H5_OUTPUT_TYPES
#define H5_OUTPUT_TYPES (char) \
(short) \
(int) \
(long) \
(long long) \
(unsigned char) \
(unsigned short) \
(unsigned int) \
(unsigned long) \
(unsigned long long) \
(float) \
(double) \
(long double) \
(bool) \
(std::string)
define HDF5_STRING_MAX_LEN
#define HDF5_STRING_MAX_LEN 100
define SPECIALISE_HDF5_DATA_TYPE_IF_NEEDED
#define SPECIALISE_HDF5_DATA_TYPE_IF_NEEDED(
TYPEDEFD_TYPE,
RETURN_HDF5_TYPE
)
template<typename T> \
struct get_hdf5_data_type<T, typename boost::enable_if_c< std::is_same<T, TYPEDEFD_TYPE>::value && \
!std::is_same<char, TYPEDEFD_TYPE>::value && \
!std::is_same<short, TYPEDEFD_TYPE>::value && \
!std::is_same<int, TYPEDEFD_TYPE>::value && \
!std::is_same<long, TYPEDEFD_TYPE>::value && \
!std::is_same<long long, TYPEDEFD_TYPE>::value && \
!std::is_same<unsigned char, TYPEDEFD_TYPE>::value && \
!std::is_same<unsigned short, TYPEDEFD_TYPE>::value && \
!std::is_same<unsigned int, TYPEDEFD_TYPE>::value && \
!std::is_same<unsigned long, TYPEDEFD_TYPE>::value && \
!std::is_same<unsigned long long, TYPEDEFD_TYPE>::value && \
!std::is_same<float, TYPEDEFD_TYPE>::value && \
!std::is_same<double, TYPEDEFD_TYPE>::value && \
!std::is_same<long double, TYPEDEFD_TYPE>::value && \
!std::is_same<bool, TYPEDEFD_TYPE>::value && \
!std::is_same<std::string, TYPEDEFD_TYPE>::value>::type > \
{ \
static hid_t type() { return RETURN_HDF5_TYPE; } \
}; \
Provide template specialisation of get_hdf5_data_type only if the requested type hasn’t been used to define one already.
Source code
// GAMBIT: Global and Modular BSM Inference Tool
// *********************************************
/// \file
///
/// A collection of tools for interacting with
/// HDF5 databases.
///
/// Currently I am using the C++ bindings for
/// HDF5, however they are a bit crap and it may
/// be better to just write our own.
///
/// *********************************************
///
/// Authors (add name and date if you modify):
///
/// \author Ben Farmer
/// (benjamin.farmer@fysik.su.se)
/// \date 2015 May
///
/// \author Pat Scott
/// (p.scott@imperial.ac.uk)
/// \date 2015 Jul
///
/// \author Tomas Gonzalo
/// (tomas.gonzalo@monash.edu)
/// \date 2020 June
///
/// *********************************************
#ifndef __hdf5tools_hpp__
#define __hdf5tools_hpp__
// Standard library
#include <cstdint>
#include <memory>
#include <sstream>
#include <iostream>
#include <algorithm>
// GAMBIT
#include "gambit/Utils/standalone_error_handlers.hpp"
#include "gambit/Utils/mpiwrapper.hpp"
// HDF5
#include <hdf5.h>
// Boost
#include <boost/utility/enable_if.hpp>
// Maximum length of HDF5 strings
#define HDF5_STRING_MAX_LEN 100
/// Provide template specialisation of get_hdf5_data_type only if the requested type hasn't been used to define one already.
#define SPECIALISE_HDF5_DATA_TYPE_IF_NEEDED(TYPEDEFD_TYPE, RETURN_HDF5_TYPE) \
template<typename T> \
struct get_hdf5_data_type<T, typename boost::enable_if_c< std::is_same<T, TYPEDEFD_TYPE>::value && \
!std::is_same<char, TYPEDEFD_TYPE>::value && \
!std::is_same<short, TYPEDEFD_TYPE>::value && \
!std::is_same<int, TYPEDEFD_TYPE>::value && \
!std::is_same<long, TYPEDEFD_TYPE>::value && \
!std::is_same<long long, TYPEDEFD_TYPE>::value && \
!std::is_same<unsigned char, TYPEDEFD_TYPE>::value && \
!std::is_same<unsigned short, TYPEDEFD_TYPE>::value && \
!std::is_same<unsigned int, TYPEDEFD_TYPE>::value && \
!std::is_same<unsigned long, TYPEDEFD_TYPE>::value && \
!std::is_same<unsigned long long, TYPEDEFD_TYPE>::value && \
!std::is_same<float, TYPEDEFD_TYPE>::value && \
!std::is_same<double, TYPEDEFD_TYPE>::value && \
!std::is_same<long double, TYPEDEFD_TYPE>::value && \
!std::is_same<bool, TYPEDEFD_TYPE>::value && \
!std::is_same<std::string, TYPEDEFD_TYPE>::value>::type > \
{ \
static hid_t type() { return RETURN_HDF5_TYPE; } \
}; \
namespace Gambit
{
namespace Printers
{
/// Base template is left undefined in order to raise
/// a compile error if specialisation doesn't exist.
template<typename T, typename Enable=void>
struct get_hdf5_data_type;
namespace HDF5
{
/// @{ File and group manipulation
/// Create or open hdf5 file
// If overwrite=true then any existing file will be deleted and replaced. USE CAREFULLY!!!
// third argument "oldfile" is used to report whether an existing file was opened (true if yes)
hid_t openFile(const std::string& fname, bool overwrite, bool& oldfile, const char access_type='r');
hid_t openFile(const std::string& fname, bool overwrite=false, const char access_type='r');
/// Close hdf5 file
hid_t closeFile(hid_t file);
/// Check if hdf5 file exists and can be opened in read/write mode
bool checkFileReadable(const std::string& fname, std::string& msg);
/// Thin wrapper for the above to discard failure message
inline bool checkFileReadable(const std::string& fname)
{ std::string garbage; return checkFileReadable(fname, garbage); }
/// Check if a group exists and can be accessed
bool checkGroupReadable(hid_t location, const std::string& groupname, std::string& msg);
/// Thin wrapper for the above to discard failure message
inline bool checkGroupReadable(hid_t location, const std::string& groupname)
{ std::string garbage; return checkGroupReadable(location, groupname, garbage); }
/// Check if a dataset exists and can be read from fully
/// (Reads through entire dataset to make sure! May take some time)
std::pair<bool,std::size_t> checkDatasetReadable(hid_t location, const std::string& dsetname);
/// Create hdf5 file (always overwrite existing files)
hid_t createFile(const std::string& fname);
/// Create a group inside the specified location
// Argument "location" can be a pointer to either a file or another group
hid_t createGroup(hid_t location, const std::string& name);
/// Silence error report (e.g. while probing for file existence)
void errorsOff();
/// Restore error report
void errorsOn();
// Modified minimally from https://github.com/gregreen/h5utils/blob/master/src/h5utils.cpp#L92
// Credit: Gregory Green 2012
/*
* Opens a group, creating it if it does not exist. Nonexistent parent groups are also
* created. This works similarly to the Unix/Linux command
* mkdir -p /parent/subgroup/group
* in that if /parent and /parent/subgroup do not exist, they will be created.
*
* If no accessmode has H5Utils::DONOTCREATE flag set, then returns NULL if group
* does not yet exist.
*
*/
hid_t openGroup(hid_t file_id, const std::string& name, bool nocreate=false, bool fatal=true);
/// Close group
hid_t closeGroup(hid_t group);
/// List object names in a group
std::vector<std::string> lsGroup(hid_t group_id);
/// Get type of an object in a group
hid_t getH5DatasetType(hid_t group_id, const std::string& dset_name);
/// Release datatype identifier
hid_t closeType(hid_t type_id);
/// @}
/// @{ Dataset and dataspace manipulation
/// Open dataset
hid_t openDataset(hid_t dset_id, const std::string& name, bool error_off=false);
/// Close dataset
hid_t closeDataset(hid_t dset_id);
/// Get dataspace
hid_t getSpace(hid_t dset_id);
/// Close dataspace
hid_t closeSpace(hid_t space_id);
/// Get simple dataspace extent
hssize_t getSimpleExtentNpoints(hid_t dset_id);
/// Get name of dataset
std::string getName(hid_t dset_id);
/// Select a simple hyperslab in a 1D dataset
std::pair<hid_t,hid_t> selectChunk(const hid_t dset_id, std::size_t offset, std::size_t length);
/// Check if an object in a group is a dataset
bool isDataSet(hid_t group_id, const std::string& name);
/// Retrieve a chunk of data from a simple dataset
/// NOTE! Doesn't work for T=bool! Have a custom specialisation in the source file for that.
template<class T>
std::vector<T> getChunk(const hid_t dset_id, std::size_t offset, std::size_t length)
{
// Buffer to receive data (and return from function)
std::vector<T> chunkdata(length);
// Select hyperslab
std::pair<hid_t,hid_t> selection_ids = selectChunk(dset_id,offset,length);
hid_t memspace_id = selection_ids.first;
hid_t dspace_id = selection_ids.second;
// Buffer to receive data
void* buffer = chunkdata.data(); // pointer to contiguous memory within the buffer vector
// Get the data from the hyperslab.
hid_t hdftype_id = get_hdf5_data_type<T>::type(); // It is assumed that you already know this is the right type for the dataset!
herr_t err_read = H5Dread(dset_id, hdftype_id, memspace_id, dspace_id, H5P_DEFAULT, buffer);
if(err_read<0)
{
std::ostringstream errmsg;
errmsg << "Error retrieving chunk (offset="<<offset<<", length="<<length<<") from dataset in HDF5 file. H5Dread failed." << std::endl;
errmsg << " offset+length = "<< offset+length << std::endl;
printer_error().raise(LOCAL_INFO, errmsg.str());
}
H5Sclose(dspace_id);
H5Sclose(memspace_id);
return chunkdata;
}
// Bool version to deal with bool weirdness
template<>
std::vector<bool> getChunk(const hid_t dset_id, std::size_t offset, std::size_t length);
// Match fixed integers to HDF5 types
int inttype_from_h5type(hid_t h5type);
// Query whether type integer indicates general 'float' or 'int'
bool is_float_type(int inttype);
/// @}
}
/// True types
/// @{
template<> struct get_hdf5_data_type<char> { static hid_t type() { return H5T_NATIVE_CHAR ; } };
template<> struct get_hdf5_data_type<short> { static hid_t type() { return H5T_NATIVE_SHORT ; } };
template<> struct get_hdf5_data_type<int> { static hid_t type() { return H5T_NATIVE_INT ; } };
template<> struct get_hdf5_data_type<long> { static hid_t type() { return H5T_NATIVE_LONG ; } };
template<> struct get_hdf5_data_type<long long> { static hid_t type() { return H5T_NATIVE_LLONG ; } };
template<> struct get_hdf5_data_type<unsigned char> { static hid_t type() { return H5T_NATIVE_UCHAR ; } };
template<> struct get_hdf5_data_type<unsigned short> { static hid_t type() { return H5T_NATIVE_USHORT ; } };
template<> struct get_hdf5_data_type<unsigned int> { static hid_t type() { return H5T_NATIVE_UINT ; } };
template<> struct get_hdf5_data_type<unsigned long> { static hid_t type() { return H5T_NATIVE_ULONG ; } };
template<> struct get_hdf5_data_type<unsigned long long>{ static hid_t type() { return H5T_NATIVE_ULLONG ; } };
template<> struct get_hdf5_data_type<float> { static hid_t type() { return H5T_NATIVE_FLOAT ; } };
template<> struct get_hdf5_data_type<double> { static hid_t type() { return H5T_NATIVE_DOUBLE ; } };
template<> struct get_hdf5_data_type<long double> { static hid_t type() { return H5T_NATIVE_LDOUBLE; } };
// Bools are a bit trickier because C has no built-in boolean type (until recently; anyway
// the HDF5 libraries were written in C before this existed). We also want something that
// will be recognised as a bool by h5py. For now we just use an unsigned int.
template<> struct get_hdf5_data_type<bool> { static hid_t type() { return H5T_NATIVE_UINT8 ; } };
// The hdf5 native type H5T_C_S1 is a string of a single character.
// To use longer strings we copy the type and extend it.
template<> struct get_hdf5_data_type<std::string> { static hid_t type() { hid_t strtype = H5Tcopy(H5T_C_S1); H5Tset_size (strtype, H5T_VARIABLE); return strtype; } };
// Macro sequence for iterating over all allowed output types
#define H5_OUTPUT_TYPES \
(char) \
(short) \
(int) \
(long) \
(long long) \
(unsigned char) \
(unsigned short) \
(unsigned int) \
(unsigned long) \
(unsigned long long) \
(float) \
(double) \
(long double) \
(bool) \
(std::string)
/// DEBUG: print to stdout all HDF5 type IDs
void printAllH5Types(void);
/// @}
/// Typedef'd types; enabled only where they differ from the true types.
/// @{
SPECIALISE_HDF5_DATA_TYPE_IF_NEEDED(int8_t, H5T_NATIVE_INT8)
SPECIALISE_HDF5_DATA_TYPE_IF_NEEDED(uint8_t, H5T_NATIVE_UINT8)
SPECIALISE_HDF5_DATA_TYPE_IF_NEEDED(int16_t, H5T_NATIVE_INT16)
SPECIALISE_HDF5_DATA_TYPE_IF_NEEDED(uint16_t, H5T_NATIVE_UINT16)
SPECIALISE_HDF5_DATA_TYPE_IF_NEEDED(int32_t, H5T_NATIVE_INT32)
SPECIALISE_HDF5_DATA_TYPE_IF_NEEDED(uint32_t, H5T_NATIVE_UINT32)
SPECIALISE_HDF5_DATA_TYPE_IF_NEEDED(int64_t, H5T_NATIVE_INT64)
SPECIALISE_HDF5_DATA_TYPE_IF_NEEDED(uint64_t, H5T_NATIVE_UINT64)
/// @}
// Template function to match datatypes to fixed integers
template<class T> constexpr int h5v2_type() {return -1;}
template<> constexpr int h5v2_type<int >() {return 0;}
template<> constexpr int h5v2_type<unsigned int >() {return 1;}
template<> constexpr int h5v2_type<long >() {return 2;}
template<> constexpr int h5v2_type<unsigned long >() {return 3;}
template<> constexpr int h5v2_type<long long >() {return 4;}
template<> constexpr int h5v2_type<unsigned long long>() {return 5;}
template<> constexpr int h5v2_type<float >() {return 6;}
template<> constexpr int h5v2_type<double >() {return 7;}
//!_______________________________________________________________________________________
}
}
#endif
Updated on 2024-07-18 at 13:53:33 +0000