#include "MantidNexus/H5Util.h"
#include "MantidNexus/UniqueID.h"
#include <Poco/Logger.h>
#include <H5Cpp.h>
#include <algorithm>
#include <array>
#include <boost/numeric/conversion/cast.hpp>
#include <sstream>
#include <stdexcept>
#include <string>

Namespaces
namespace	Mantid
	Helper class which provides the Collimation Length for SANS instruments.

namespace	Mantid::Nexus
	Header for a base Nexus::Exception.

namespace	Mantid::Nexus::H5Util
	Operations for help with narrowing casts.

Macros
#define	RUN_H5UTIL_FUNCTION(dataType, func_name, ...)
	This macro matches the dataType in terms of PredType, with the actual primitive datatype.

Functions
MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::copyGroup (H5::H5Object &dest, const std::string &destGroupAddress, H5::H5Object &src, const std::string &srcGroupAddress)
	Copy a group and all of its contents, between the same or different HDF5 files or groups.

Group	Mantid::Nexus::H5Util::createGroupCanSAS (Group &group, const std::string &name, const std::string &nxtype, const std::string &cstype)

Group	Mantid::Nexus::H5Util::createGroupCanSAS (H5File &file, const std::string &name, const std::string &nxtype, const std::string &cstype)

Group	Mantid::Nexus::H5Util::createGroupNXS (Group &group, const std::string &name, const std::string &nxtype)

Group	Mantid::Nexus::H5Util::createGroupNXS (H5File &file, const std::string &name, const std::string &nxtype)

MANTID_NEXUS_DLL H5::FileAccPropList	Mantid::Nexus::H5Util::defaultFileAcc ()
	Default file access is H5F_CLOSE_STRONG.

MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::deleteObjectLink (H5::H5Object &h5, const std::string &target)
	Delete a target link for a group or dataset from a parent group.

MANTID_NEXUS_DLL H5::DataSpace	Mantid::Nexus::H5Util::getDataSpace (const size_t length)
	Create a 1D data-space to hold data of length.

template<typename NumT >
DataType	Mantid::Nexus::H5Util::getType ()
	Convert a primitive type to the appropriate H5::DataType.

template<>
MANTID_NEXUS_DLL DataType	Mantid::Nexus::H5Util::getType< bool > ()

template<>
MANTID_NEXUS_DLL DataType	Mantid::Nexus::H5Util::getType< char > ()

template<>
MANTID_NEXUS_DLL DataType	Mantid::Nexus::H5Util::getType< double > ()

template<>
MANTID_NEXUS_DLL DataType	Mantid::Nexus::H5Util::getType< float > ()

template<>
MANTID_NEXUS_DLL DataType	Mantid::Nexus::H5Util::getType< int16_t > ()

template<>
MANTID_NEXUS_DLL DataType	Mantid::Nexus::H5Util::getType< int32_t > ()

template<>
MANTID_NEXUS_DLL DataType	Mantid::Nexus::H5Util::getType< int64_t > ()

template<>
MANTID_NEXUS_DLL DataType	Mantid::Nexus::H5Util::getType< int8_t > ()

template<>
MANTID_NEXUS_DLL DataType	Mantid::Nexus::H5Util::getType< std::string > ()

template<>
MANTID_NEXUS_DLL DataType	Mantid::Nexus::H5Util::getType< uint16_t > ()

template<>
MANTID_NEXUS_DLL DataType	Mantid::Nexus::H5Util::getType< uint32_t > ()

template<>
MANTID_NEXUS_DLL DataType	Mantid::Nexus::H5Util::getType< uint64_t > ()

template<>
MANTID_NEXUS_DLL DataType	Mantid::Nexus::H5Util::getType< uint8_t > ()

MANTID_NEXUS_DLL bool	Mantid::Nexus::H5Util::groupExists (H5::H5Object const &h5, const std::string &groupAddress)
	Test if a group already exists within an HDF5 file or parent group.

MANTID_NEXUS_DLL bool	Mantid::Nexus::H5Util::hasAttribute (const H5::H5Object &object, const char *attributeName)

MANTID_NEXUS_DLL bool	Mantid::Nexus::H5Util::isHdf5 (std::string const &filename)
	Determine if a given file can be opened with HDF5 using the CORRECT file access level (H5F_CLOSE_STRONG)

MANTID_NEXUS_DLL bool	Mantid::Nexus::H5Util::keyHasValue (H5::H5Object const &h5, const std::string &key, const std::string &value)
	Test if an attribute is present and has a specific string value for an HDF5 group or dataset.

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::readArray1DCoerce (const DataSet &dataset, std::vector< char > &output, const size_t length, const size_t offset)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::readArray1DCoerce (const DataSet &dataset, std::vector< double > &output, const size_t length, const size_t offset)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::readArray1DCoerce (const DataSet &dataset, std::vector< float > &output, const size_t length, const size_t offset)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::readArray1DCoerce (const DataSet &dataset, std::vector< int16_t > &output, const size_t length, const size_t offset)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::readArray1DCoerce (const DataSet &dataset, std::vector< int32_t > &output, const size_t length, const size_t offset)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::readArray1DCoerce (const DataSet &dataset, std::vector< int64_t > &output, const size_t length, const size_t offset)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::readArray1DCoerce (const DataSet &dataset, std::vector< int8_t > &output, const size_t length, const size_t offset)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::readArray1DCoerce (const DataSet &dataset, std::vector< uint16_t > &output, const size_t length, const size_t offset)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::readArray1DCoerce (const DataSet &dataset, std::vector< uint32_t > &output, const size_t length, const size_t offset)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::readArray1DCoerce (const DataSet &dataset, std::vector< uint64_t > &output, const size_t length, const size_t offset)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::readArray1DCoerce (const DataSet &dataset, std::vector< uint8_t > &output, const size_t length, const size_t offset)

template<typename OutT , Narrowing narrow>
void	Mantid::Nexus::H5Util::readArray1DCoerce (const H5::DataSet &dataset, std::vector< OutT > &output, const size_t length, const size_t offset)
	Read a standard vector from a dataset, coerced to type of OutT.

template<typename OutT , Narrowing narrow>
std::vector< OutT >	Mantid::Nexus::H5Util::readArray1DCoerce (const H5::Group &group, const std::string &name)

template MANTID_NEXUS_DLL std::vector< float >	Mantid::Nexus::H5Util::readArray1DCoerce (const H5::Group &group, const std::string &name)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::readArray1DCoerce (const H5::Group &group, const std::string &name, std::vector< double > &output)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::readArray1DCoerce (const H5::Group &group, const std::string &name, std::vector< float > &output)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::readArray1DCoerce (const H5::Group &group, const std::string &name, std::vector< int32_t > &output)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::readArray1DCoerce (const H5::Group &group, const std::string &name, std::vector< int64_t > &output)

template<typename OutT , Narrowing narrow>
void	Mantid::Nexus::H5Util::readArray1DCoerce (const H5::Group &group, const std::string &name, std::vector< OutT > &output)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::readArray1DCoerce (const H5::Group &group, const std::string &name, std::vector< uint32_t > &output)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::readArray1DCoerce (const H5::Group &group, const std::string &name, std::vector< uint64_t > &output)

template<typename OutT , Narrowing narrow>
std::vector< OutT >	Mantid::Nexus::H5Util::readNumArrayAttributeCoerce (const H5::H5Object &object, const std::string &attributeName)
	Read a numerical array from an attribute, coerced to type of OutT.

template MANTID_NEXUS_DLL std::vector< float >	Mantid::Nexus::H5Util::readNumArrayAttributeCoerce (const H5::H5Object &object, const std::string &attributeName)

template<typename OutT , Narrowing narrow>
OutT	Mantid::Nexus::H5Util::readNumAttributeCoerce (const H5::H5Object &object, const std::string &attributeName)
	Read a single quantity from an attribute, coerced to type of OutT.

template MANTID_NEXUS_DLL float	Mantid::Nexus::H5Util::readNumAttributeCoerce (const H5::H5Object &object, const std::string &attributeName)

MANTID_NEXUS_DLL std::string	Mantid::Nexus::H5Util::readString (const H5::DataSet &dataset)

MANTID_NEXUS_DLL std::string	Mantid::Nexus::H5Util::readString (const H5::Group &group, const std::string &name)

MANTID_NEXUS_DLL std::string	Mantid::Nexus::H5Util::readString (H5::H5File &file, const std::string &address)

MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::readStringAttribute (const H5::H5Object &object, const std::string &attributeName, std::string &output)

std::vector< std::string >	Mantid::Nexus::H5Util::readStringVector (DataSet &dataset)

std::vector< std::string >	Mantid::Nexus::H5Util::readStringVector (Group &group, const std::string &name)
	Returns 1D vector of variable length strings.

MANTID_NEXUS_DLL H5::DSetCreatPropList	Mantid::Nexus::H5Util::setCompressionAttributes (const std::size_t length, const int deflateLevel=6)
	Sets up the chunking and compression rate.

void	Mantid::Nexus::H5Util::write (Group &group, const std::string &name, const std::string &value)

template<typename NumT >
void	Mantid::Nexus::H5Util::writeArray1D (Group &group, const std::string &name, const std::vector< NumT > &values)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeArray1D (H5::Group &group, const std::string &name, const std::vector< double > &values)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeArray1D (H5::Group &group, const std::string &name, const std::vector< float > &values)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeArray1D (H5::Group &group, const std::string &name, const std::vector< int32_t > &values)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeArray1D (H5::Group &group, const std::string &name, const std::vector< int64_t > &values)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeArray1D (H5::Group &group, const std::string &name, const std::vector< uint32_t > &values)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeArray1D (H5::Group &group, const std::string &name, const std::vector< uint64_t > &values)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeNumAttribute (const H5::H5Object &object, const std::string &name, const char &value)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeNumAttribute (const H5::H5Object &object, const std::string &name, const double &value)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeNumAttribute (const H5::H5Object &object, const std::string &name, const float &value)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeNumAttribute (const H5::H5Object &object, const std::string &name, const int16_t &value)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeNumAttribute (const H5::H5Object &object, const std::string &name, const int32_t &value)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeNumAttribute (const H5::H5Object &object, const std::string &name, const int64_t &value)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeNumAttribute (const H5::H5Object &object, const std::string &name, const int8_t &value)

template<typename NumT >
void	Mantid::Nexus::H5Util::writeNumAttribute (const H5::H5Object &object, const std::string &name, const NumT &value)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeNumAttribute (const H5::H5Object &object, const std::string &name, const std::vector< char > &value)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeNumAttribute (const H5::H5Object &object, const std::string &name, const std::vector< double > &value)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeNumAttribute (const H5::H5Object &object, const std::string &name, const std::vector< float > &value)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeNumAttribute (const H5::H5Object &object, const std::string &name, const std::vector< int16_t > &value)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeNumAttribute (const H5::H5Object &object, const std::string &name, const std::vector< int32_t > &value)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeNumAttribute (const H5::H5Object &object, const std::string &name, const std::vector< int64_t > &value)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeNumAttribute (const H5::H5Object &object, const std::string &name, const std::vector< int8_t > &value)

template<typename NumT >
void	Mantid::Nexus::H5Util::writeNumAttribute (const H5::H5Object &object, const std::string &name, const std::vector< NumT > &value)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeNumAttribute (const H5::H5Object &object, const std::string &name, const std::vector< uint16_t > &value)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeNumAttribute (const H5::H5Object &object, const std::string &name, const std::vector< uint32_t > &value)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeNumAttribute (const H5::H5Object &object, const std::string &name, const std::vector< uint64_t > &value)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeNumAttribute (const H5::H5Object &object, const std::string &name, const std::vector< uint8_t > &value)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeNumAttribute (const H5::H5Object &object, const std::string &name, const uint16_t &value)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeNumAttribute (const H5::H5Object &object, const std::string &name, const uint32_t &value)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeNumAttribute (const H5::H5Object &object, const std::string &name, const uint64_t &value)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeNumAttribute (const H5::H5Object &object, const std::string &name, const uint8_t &value)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeScalarDataSetWithStrAttributes (H5::Group &group, const std::string &name, const double &value, const std::map< std::string, std::string > &attributes)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeScalarDataSetWithStrAttributes (H5::Group &group, const std::string &name, const float &value, const std::map< std::string, std::string > &attributes)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeScalarDataSetWithStrAttributes (H5::Group &group, const std::string &name, const int32_t &value, const std::map< std::string, std::string > &attributes)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeScalarDataSetWithStrAttributes (H5::Group &group, const std::string &name, const int64_t &value, const std::map< std::string, std::string > &attributes)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeScalarDataSetWithStrAttributes (H5::Group &group, const std::string &name, const std::string &value, const std::map< std::string, std::string > &attributes)

template<typename T >
void	Mantid::Nexus::H5Util::writeScalarDataSetWithStrAttributes (H5::Group &group, const std::string &name, const T &value, const std::map< std::string, std::string > &attributes)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeScalarDataSetWithStrAttributes (H5::Group &group, const std::string &name, const uint32_t &value, const std::map< std::string, std::string > &attributes)

template MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeScalarDataSetWithStrAttributes (H5::Group &group, const std::string &name, const uint64_t &value, const std::map< std::string, std::string > &attributes)

MANTID_NEXUS_DLL void	Mantid::Nexus::H5Util::writeStrAttribute (const H5::H5Object &object, const std::string &name, const std::string &value)

Macro Definition Documentation

◆ RUN_H5UTIL_FUNCTION

#define RUN_H5UTIL_FUNCTION	(	dataType,
		func_name,
		...
	)

Value:

  if (dataType == PredType::NATIVE_FLOAT) {                                                                            \
    func_name<float, OutT, narrow>(__VA_ARGS__);                                                                       \
  } else if (dataType == PredType::NATIVE_DOUBLE) {                                                                    \
    func_name<double, OutT, narrow>(__VA_ARGS__);                                                                      \
  } else if (dataType == PredType::NATIVE_INT8) {                                                                      \
    func_name<int8_t, OutT, narrow>(__VA_ARGS__);                                                                      \
  } else if (dataType == PredType::NATIVE_UINT8) {                                                                     \
    func_name<uint8_t, OutT, narrow>(__VA_ARGS__);                                                                     \
  } else if (dataType == PredType::NATIVE_INT16) {                                                                     \
    func_name<int16_t, OutT, narrow>(__VA_ARGS__);                                                                     \
  } else if (dataType == PredType::NATIVE_UINT16) {                                                                    \
    func_name<uint16_t, OutT, narrow>(__VA_ARGS__);                                                                    \
  } else if (dataType == PredType::NATIVE_INT32) {                                                                     \
    func_name<int32_t, OutT, narrow>(__VA_ARGS__);                                                                     \
  } else if (dataType == PredType::NATIVE_UINT32) {                                                                    \
    func_name<uint32_t, OutT, narrow>(__VA_ARGS__);                                                                    \
  } else if (dataType == PredType::NATIVE_INT64) {                                                                     \
    func_name<int64_t, OutT, narrow>(__VA_ARGS__);                                                                     \
  } else if (dataType == PredType::NATIVE_UINT64) {                                                                    \
    func_name<uint64_t, OutT, narrow>(__VA_ARGS__);                                                                    \
  } else if (dataType == PredType::C_S1) {                                                                             \
    func_name<char, OutT, narrow>(__VA_ARGS__);                                                                        \
  } else {                                                                                                             \
    std::string msg = "H5Util: error in narrowing, unknown H5Cpp PredType ";                                           \
    msg += dataType.fromClass() + ".";                                                                                 \
    throw DataTypeIException(msg);                                                                                     \
  }

This macro matches the dataType in terms of PredType, with the actual primitive datatype.

The macro assumes it is called from inside a function where OutT, narrow are defined. It assumes that func_name is a template function with parameters <InT, OutT, narrow> It will set InT to the proper value, based on dataType.

Definition at line 90 of file H5Util.cpp.

Namespaces

Macros

Functions

Macro Definition Documentation

◆ RUN_H5UTIL_FUNCTION