NeXus HDF5 file reader with case-insensitive path lookup. More...

#include <PNeXus.h>

Public Member Functions
	PNeXus ()

	PNeXus (const std::string fln, const bool printDebug=false)

std::string	GetFileName () const
	Get the filename of the NeXus file.

std::string	GetHdf5LibVersion () const
	Get the HDF5 library version string.

std::string	GetHdf5Version () const
	Get the HDF5 version string from the file.

std::string	GetNeXusVersion () const
	Get the NeXus version of the file.

int	GetIdfVersion () const
	Get the Idf version of the file.

int	ReadNexusFile ()
	Read and parse the NeXus HDF5 file.

const std::map< std::string, std::any > &	GetDataMap () const
	Get the data map containing all datasets.

std::map< std::string, std::any > &	GetDataMap ()
	Get mutable reference to the data map.

bool	HasDataset (const std::string &path) const
	Check if a dataset path exists in the data map.

template<typename T>
void	SetDataset (const std::string &path, const PNXdata< T > &data)
	Add or update a dataset in the data map.

template<typename T>
PNXdata< T >	GetDataset (const std::string &path) const
	Get a dataset from the data map.

template<typename T>
PNXdata< T > &	GetDatasetRef (const std::string &path)
	Get a mutable reference to a dataset in the data map.

bool	RemoveDataset (const std::string &path)
	Remove a dataset from the data map.

void	ClearDataMap ()
	Clear all datasets from the data map.

size_t	GetNumDatasets () const
	Get the number of datasets in the data map.

template<typename T>
bool	UpdateDatasetData (const std::string &path, const std::vector< T > &newData)
	Update the data of an existing dataset.

template<typename T>
bool	UpdateDatasetDimensions (const std::string &path, const std::vector< hsize_t > &newDimensions)
	Update the dimensions of an existing dataset.

template<typename T>
bool	AddDatasetAttribute (const std::string &path, const std::string &attrName, const std::any &attrValue)
	Add or update an attribute for a dataset.

template<typename T>
bool	RemoveDatasetAttribute (const std::string &path, const std::string &attrName)
	Remove an attribute from a dataset.

template<typename T>
bool	AddDataset (const std::string &path, const std::vector< T > &data, const std::vector< hsize_t > &dimensions, const H5::DataType &dataType=H5::PredType::NATIVE_INT)
	Create and add a new dataset with data, dimensions, and optional attributes.

template<typename T>
bool	ModifyDataset (const std::string &path, const std::vector< T > &newData, const std::vector< hsize_t > &newDimensions)
	Modify an existing dataset's data and dimensions.

void	Dump ()

int	WriteNexusFile (const std::string &filename, int idfVersion=2)

bool	AddGroupAttribute (const std::string &groupPath, const std::string &attrName, const std::any &attrValue)

bool	RemoveGroupAttribute (const std::string &groupPath, const std::string &attrName)
	Remove an attribute from a group.

bool	HasGroupAttribute (const std::string &groupPath, const std::string &attrName) const
	Check if a group has a specific attribute.

std::any	GetGroupAttribute (const std::string &groupPath, const std::string &attrName) const
	Get an attribute value from a group.

const std::map< std::string, std::any > &	GetGroupAttributes (const std::string &groupPath) const
	Get all attributes for a group.

bool	ClearGroupAttributes (const std::string &groupPath)
	Clear all attributes from a group.

bool	AddRootAttribute (const std::string &attrName, const std::any &attrValue)

Private Member Functions
void	HandleIdfV1 (H5::H5File &file)
	Read datasets for IDF version 1 file structure.

void	HandleIdfV2 (H5::H5File &file)
	Read datasets for IDF version 2 file structure.

H5::Group	CreateGroupHierarchy (H5::H5File &file, const std::string &path)
	Create nested group hierarchy for a given path.

template<typename T>
void	WriteDatasetAttributes (H5::DataSet &dataset, const PNXdata< T > &data)
	Write dataset attributes from PNXdata object.

void	WriteGroupAttributes (H5::Group &group, const std::map< std::string, std::any > &attributes)
	Write attributes to a group.

void	WriteIntDataset (H5::H5File &file, const std::string &path, const PNXdata< int > &data)
	Write an integer dataset with attributes.

void	WriteFloatDataset (H5::H5File &file, const std::string &path, const PNXdata< float > &data)
	Write a float dataset with attributes.

void	WriteStringDataset (H5::H5File &file, const std::string &path, const PNXdata< std::string > &data)
	Write a string dataset with attributes.

void	WriteFileAttributes (H5::H5File &file)
	Write root-level file attributes.

std::string	FindAttributeName (H5::H5File &obj, const std::string &requestedName)

std::string	FindGroupPath (H5::H5File &parent, const std::string &requestedPath)

std::string	FindGroupPath (H5::Group &parent, const std::string &requestedPath)
	Find group path with case-insensitive matching (Group version)

std::string	FindDatasetPath (H5::H5File &parent, const std::string &requestedPath)

std::string	FindDatasetPath (H5::Group &parent, const std::string &requestedPath)
	Find dataset path with case-insensitive matching (Group version)

void	ReadIntDataset (H5::H5File &file, const std::string &path)
	Read an integer dataset and store in data map.

void	ReadFloatDataset (H5::H5File &file, const std::string &path)
	Read a float dataset and store in data map.

void	ReadStringDataset (H5::H5File &file, const std::string &path)
	Read a string dataset and store in data map.

template<typename T>
void	ReadDatasetAttributes (H5::DataSet &dataset, PNXdata< T > &data)
	Read dataset attributes and add to PNXdata object.

Static Private Member Functions
static bool	CaseInsensitiveEquals (const std::string &a, const std::string &b)
	Compare two strings case-insensitively.

static std::vector< std::string >	SplitPath (const std::string &path)

Private Attributes
bool	fPrintDebug {false}
	if true print additional debug information

std::string	fFileName {""}
	NeXus HDF5 filename.

int	fIdfVersion {-1}
	IDF version of the NeXus file.

std::string	fHdf5LibVersion {"n/a"}
	HDF5 library version used when calling PNeXus.

std::string	fHdf5Version {""}
	HDF5 version of the file.

std::string	fNeXusVersion {""}
	NeXus version of the file.

std::string	fFileNameNxs {""}

std::string	fFileTimeNxs {""}

std::string	fCreatorNxs {""}

std::string	fUserV1 {""}

std::map< std::string, std::any >	fDataMap
	Map of HDF5 paths to PNXdata objects.

std::map< std::string, std::map< std::string, std::any > >	fGroupAttributes
	Map of group paths to their attributes.

Detailed Description

NeXus HDF5 file reader with case-insensitive path lookup.

The PNeXus class provides functionality for reading ISIS muon NeXus HDF5 files using the HDF5 C++ API. It implements case-insensitive path lookup for datasets, groups, and attributes to handle files with varying path casings.

Key features:

Automatic file reading upon construction
Case-insensitive path resolution for datasets and groups
Case-insensitive attribute name matching
Comprehensive exception handling with HDF5 C++ exceptions

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 1463 of file PNeXus.h.

Constructor & Destructor Documentation

◆ PNeXus() [1/2]

nxH5::PNeXus::PNeXus ( )

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp, and /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 3451 of file PNeXus.cpp.

References fHdf5LibVersion, and status.

◆ PNeXus() [2/2]

nxH5::PNeXus::PNeXus	(	const std::string	fln,
		const bool	printDebug = false )

Definition at line 3490 of file PNeXus.cpp.

References fFileName, fHdf5LibVersion, fPrintDebug, ReadNexusFile(), and status.

Member Function Documentation

◆ AddDataset()

template<typename T>

bool nxH5::PNeXus::AddDataset	(	const std::string &	path,
		const std::vector< T > &	data,
		const std::vector< hsize_t > &	dimensions,
		const H5::DataType &	dataType = H5::PredType::NATIVE_INT )

inline

Create and add a new dataset with data, dimensions, and optional attributes.

Template Parameters

T	Data type of the PNXdata object

Parameters

path	HDF5 path for the new dataset
data	Data vector
dimensions	Dimensions vector
dataType	HDF5 DataType (optional, uses default if not provided)

Returns: true if dataset was created, false if path already exists

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 1723 of file PNeXus.h.

References fDataMap, HasDataset(), nxH5::PNXdata< T >::SetData(), and nxH5::PNXdata< T >::SetDimensions().

◆ AddDatasetAttribute()

template<typename T>

bool nxH5::PNeXus::AddDatasetAttribute	(	const std::string &	path,
		const std::string &	attrName,
		const std::any &	attrValue )

inline

Add or update an attribute for a dataset.

Template Parameters

T	Data type of the PNXdata object

Parameters

path	HDF5 path of the dataset
attrName	Attribute name
attrValue	Attribute value (stored as std::any)

Returns: true if attribute was added, false if dataset doesn't exist

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 1677 of file PNeXus.h.

References fDataMap, and HasDataset().

◆ AddGroupAttribute()

bool nxH5::PNeXus::AddGroupAttribute	(	const std::string &	groupPath,
		const std::string &	attrName,
		const std::any &	attrValue )

Add or update an attribute for a group.

Parameters

groupPath	HDF5 path of the group (e.g., "/raw_data_1")
attrName	Attribute name
attrValue	Attribute value (stored as std::any)

Returns: true if attribute was added successfully

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp, and /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 5605 of file PNeXus.cpp.

References fGroupAttributes.

Referenced by AddRootAttribute().

◆ AddRootAttribute()

bool nxH5::PNeXus::AddRootAttribute	(	const std::string &	attrName,
		const std::any &	attrValue )

Add or update an attribute at the root level "/". This is a convenience method that calls AddGroupAttribute("/", attrName, attrValue).

Parameters

attrName	Attribute name
attrValue	Attribute value (stored as std::any)

Returns: true if attribute was added successfully

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp, and /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 5712 of file PNeXus.cpp.

References AddGroupAttribute().

◆ CaseInsensitiveEquals()

bool nxH5::PNeXus::CaseInsensitiveEquals	(	const std::string &	a,
		const std::string &	b )

staticprivate

Compare two strings case-insensitively.

Parameters

a	First string to compare
b	Second string to compare

Returns: true if strings are equal (ignoring case), false otherwise

Note: Uses std::tolower for character-by-character comparison

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp, and /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 3015 of file PNeXus.cpp.

Referenced by FindAttributeName(), FindDatasetPath(), FindDatasetPath(), FindGroupPath(), and FindGroupPath().

◆ ClearDataMap()

void nxH5::PNeXus::ClearDataMap ( )

inline

Clear all datasets from the data map.

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 1622 of file PNeXus.h.

References fDataMap.

◆ ClearGroupAttributes()

bool nxH5::PNeXus::ClearGroupAttributes ( const std::string & groupPath )

Clear all attributes from a group.

Parameters

groupPath HDF5 path of the group

Returns: true if group was found and attributes cleared, false otherwise

Clear all attributes from a group.

Parameters

groupPath HDF5 path of the group

Returns: true if group was found and attributes cleared, false otherwise

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp, and /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 5693 of file PNeXus.cpp.

References fGroupAttributes.

◆ CreateGroupHierarchy()

H5::Group nxH5::PNeXus::CreateGroupHierarchy	(	H5::H5File &	file,
		const std::string &	path )

private

Create nested group hierarchy for a given path.

Parameters

file	HDF5 file object
path	Full path (e.g., "/raw_data_1/detector_1")

Returns: H5::Group handle to the deepest created/opened group

Exceptions

H5::GroupIException if group creation fails

Create nested group hierarchy for a given path. Groups are created recursively if they don't exist. If a group already exists, it is opened and returned.

Parameters

file	HDF5 file object
path	Full path (e.g., "/raw_data_1/detector_1")

Returns: H5::Group handle to the deepest created/opened group

Exceptions

H5::GroupIException if group creation fails

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp, and /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 5027 of file PNeXus.cpp.

References fGroupAttributes, fPrintDebug, SplitPath(), and WriteGroupAttributes().

Referenced by WriteFloatDataset(), WriteIntDataset(), and WriteStringDataset().

◆ Dump()

void nxH5::PNeXus::Dump ( )

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp, and /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 3761 of file PNeXus.cpp.

References fDataMap, fFileName, fFileNameNxs, fFileTimeNxs, fHdf5Version, fIdfVersion, fNeXusVersion, and fUserV1.

◆ FindAttributeName()

std::string nxH5::PNeXus::FindAttributeName	(	H5::H5File &	obj,
		const std::string &	requestedName )

private

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp, and /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 3090 of file PNeXus.cpp.

References CaseInsensitiveEquals().

Referenced by HandleIdfV1(), HandleIdfV2(), and ReadNexusFile().

◆ FindDatasetPath() [1/2]

std::string nxH5::PNeXus::FindDatasetPath	(	H5::Group &	parent,
		const std::string &	requestedPath )

private

Find dataset path with case-insensitive matching (Group version)

Parameters

parent	HDF5 Group object to start search from
requestedPath	Requested dataset path (any case)

Returns: Correctly-cased dataset path as it exists in the file

Exceptions

H5::DataSetIException if dataset not found or path invalid

Note: Validates that final path component is actually a dataset

Definition at line 3372 of file PNeXus.cpp.

References CaseInsensitiveEquals(), and SplitPath().

◆ FindDatasetPath() [2/2]

std::string nxH5::PNeXus::FindDatasetPath	(	H5::H5File &	parent,
		const std::string &	requestedPath )

private

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp, and /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 3292 of file PNeXus.cpp.

References CaseInsensitiveEquals(), and SplitPath().

Referenced by ReadFloatDataset(), ReadIntDataset(), ReadNexusFile(), and ReadStringDataset().

◆ FindGroupPath() [1/2]

std::string nxH5::PNeXus::FindGroupPath	(	H5::Group &	parent,
		const std::string &	requestedPath )

private

Find group path with case-insensitive matching (Group version)

Parameters

parent	HDF5 Group object to start search from
requestedPath	Requested group path (any case)

Returns: Correctly-cased group path as it exists in the file

Exceptions

H5::GroupIException if group not found or path invalid

Definition at line 3200 of file PNeXus.cpp.

References CaseInsensitiveEquals(), and SplitPath().

◆ FindGroupPath() [2/2]

std::string nxH5::PNeXus::FindGroupPath	(	H5::H5File &	parent,
		const std::string &	requestedPath )

private

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp, and /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 3131 of file PNeXus.cpp.

References CaseInsensitiveEquals(), and SplitPath().

◆ GetDataMap() [1/2]

std::map< std::string, std::any > & nxH5::PNeXus::GetDataMap ( )

inline

Get mutable reference to the data map.

Returns: Reference to the data map

Definition at line 1559 of file PNeXus.h.

References fDataMap.

◆ GetDataMap() [2/2]

const std::map< std::string, std::any > & nxH5::PNeXus::GetDataMap ( ) const

inline

Get the data map containing all datasets.

Returns: Reference to the data map (path -> PNXdata stored in std::any)

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 1553 of file PNeXus.h.

References fDataMap.

◆ GetDataset()

template<typename T>

PNXdata< T > nxH5::PNeXus::GetDataset ( const std::string & path ) const

inline

Get a dataset from the data map.

Template Parameters

T	Data type of the PNXdata object

Parameters

path	HDF5 path of the dataset

Returns: PNXdata object

Exceptions

std::out_of_range	if path doesn't exist
std::bad_any_cast	if type T doesn't match stored type

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 1588 of file PNeXus.h.

References fDataMap.

◆ GetDatasetRef()

template<typename T>

PNXdata< T > & nxH5::PNeXus::GetDatasetRef ( const std::string & path )

inline

Get a mutable reference to a dataset in the data map.

Template Parameters

T	Data type of the PNXdata object

Parameters

path	HDF5 path of the dataset

Returns: Reference to PNXdata object

Exceptions

std::out_of_range	if path doesn't exist
std::bad_any_cast	if type T doesn't match stored type

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 1601 of file PNeXus.h.

References fDataMap.

◆ GetFileName()

std::string nxH5::PNeXus::GetFileName ( ) const

inline

Get the filename of the NeXus file.

Returns: The filename as a string

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 1514 of file PNeXus.h.

References fFileName.

◆ GetGroupAttribute()

std::any nxH5::PNeXus::GetGroupAttribute	(	const std::string &	groupPath,
		const std::string &	attrName ) const

Get an attribute value from a group.

Parameters

groupPath	HDF5 path of the group
attrName	Attribute name

Returns: The attribute value as std::any

Exceptions

std::out_of_range if group or attribute doesn't exist

Get an attribute value from a group.

Parameters

groupPath	HDF5 path of the group
attrName	Attribute name

Returns: The attribute value as std::any

Exceptions

std::out_of_range if group or attribute doesn't exist

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp, and /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 5666 of file PNeXus.cpp.

References fGroupAttributes.

◆ GetGroupAttributes()

const std::map< std::string, std::any > & nxH5::PNeXus::GetGroupAttributes ( const std::string & groupPath ) const

Get all attributes for a group.

Parameters

groupPath HDF5 path of the group

Returns: Map of attribute names to values

Get all attributes for a group.

Parameters

groupPath HDF5 path of the group

Returns: Map of attribute names to values

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp, and /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 5677 of file PNeXus.cpp.

References fGroupAttributes.

◆ GetHdf5LibVersion()

std::string nxH5::PNeXus::GetHdf5LibVersion ( ) const

inline

Get the HDF5 library version string.

Returns: The HDF5 version as a string (e.g., "1.10.4")

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 1520 of file PNeXus.h.

References fHdf5LibVersion.

◆ GetHdf5Version()

std::string nxH5::PNeXus::GetHdf5Version ( ) const

inline

Get the HDF5 version string from the file.

Returns: The HDF5 version as a string (e.g., "1.10.4")

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 1526 of file PNeXus.h.

References fHdf5Version.

◆ GetIdfVersion()

int nxH5::PNeXus::GetIdfVersion ( ) const

inline

Get the Idf version of the file.

Returns: The Idf version tag

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 1538 of file PNeXus.h.

References fIdfVersion.

◆ GetNeXusVersion()

std::string nxH5::PNeXus::GetNeXusVersion ( ) const

inline

Get the NeXus version of the file.

Returns: The NeXus version as a string

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 1532 of file PNeXus.h.

References fNeXusVersion.

◆ GetNumDatasets()

size_t nxH5::PNeXus::GetNumDatasets ( ) const

inline

Get the number of datasets in the data map.

Returns: Number of datasets stored

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 1628 of file PNeXus.h.

References fDataMap.

◆ HandleIdfV1()

void nxH5::PNeXus::HandleIdfV1 ( H5::H5File & file )

private

Read datasets for IDF version 1 file structure.

Reads datasets specific to the IDF version 1 NeXus format, which uses a "/run/" group hierarchy. Datasets are organized under paths like:

/run/IDF_version, /run/number, /run/title
/run/sample/temperature, /run/sample/magnetic_field
/run/histogram_data_1/counts, /run/histogram_data_1/raw_time

Parameters

file	HDF5 file object to read from

Note: IDF v1 is an older format primarily used by ISIS facilities

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp, and /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 3631 of file PNeXus.cpp.

References FindAttributeName(), fPrintDebug, fUserV1, ReadFloatDataset(), ReadIntDataset(), and ReadStringDataset().

Referenced by ReadNexusFile().

◆ HandleIdfV2()

void nxH5::PNeXus::HandleIdfV2 ( H5::H5File & file )

private

Read datasets for IDF version 2 file structure.

Reads datasets specific to the IDF version 2 NeXus format, which uses a "/raw_data_1/" group hierarchy. Datasets are organized under paths like:

/raw_data_1/IDF_version, /raw_data_1/run_number, /raw_data_1/title
/raw_data_1/instrument/detector_1/counts
/raw_data_1/instrument/detector_1/resolution

Parameters

file	HDF5 file object to read from

Note: IDF v2 is the current standard format for ISIS muon NeXus files

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp, and /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 3693 of file PNeXus.cpp.

References fFileNameNxs, fFileTimeNxs, FindAttributeName(), fPrintDebug, ReadFloatDataset(), ReadIntDataset(), and ReadStringDataset().

Referenced by ReadNexusFile().

◆ HasDataset()

bool nxH5::PNeXus::HasDataset ( const std::string & path ) const

inline

Check if a dataset path exists in the data map.

Parameters

path	HDF5 path to check

Returns: true if path exists, false otherwise

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 1566 of file PNeXus.h.

References fDataMap.

Referenced by AddDataset(), AddDatasetAttribute(), ModifyDataset(), RemoveDatasetAttribute(), UpdateDatasetData(), and UpdateDatasetDimensions().

◆ HasGroupAttribute()

bool nxH5::PNeXus::HasGroupAttribute	(	const std::string &	groupPath,
		const std::string &	attrName ) const

Check if a group has a specific attribute.

Parameters

groupPath	HDF5 path of the group
attrName	Attribute name to check

Returns: true if attribute exists, false otherwise

Check if a group has a specific attribute.

Parameters

groupPath	HDF5 path of the group
attrName	Attribute name to check

Returns: true if attribute exists, false otherwise

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp, and /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 5648 of file PNeXus.cpp.

References fGroupAttributes.

◆ ModifyDataset()

template<typename T>

bool nxH5::PNeXus::ModifyDataset	(	const std::string &	path,
		const std::vector< T > &	newData,
		const std::vector< hsize_t > &	newDimensions )

inline

Modify an existing dataset's data and dimensions.

Template Parameters

T	Data type of the PNXdata object

Parameters

path	HDF5 path of the dataset
newData	New data vector
newDimensions	New dimensions vector

Returns: true if modification succeeded, false if path doesn't exist

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 1743 of file PNeXus.h.

References fDataMap, and HasDataset().

◆ ReadDatasetAttributes()

template<typename T>

void nxH5::PNeXus::ReadDatasetAttributes	(	H5::DataSet &	dataset,
		PNXdata< T > &	data )

private

Read dataset attributes and add to PNXdata object.

Template Parameters

T	The data type of the PNXdata object

Parameters

dataset	HDF5 dataset object
data	PNXdata object to add attributes to

Reads all attributes from an HDF5 dataset and adds them to a PNXdata object. Attributes can be integers, floats, or strings.

Template Parameters

T	The data type of the PNXdata object

Parameters

dataset	HDF5 dataset object
data	PNXdata object to add attributes to

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp, and /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 4971 of file PNeXus.cpp.

References nxH5::PNXdata< T >::AddAttribute(), and fPrintDebug.

Referenced by ReadFloatDataset(), ReadIntDataset(), and ReadStringDataset().

◆ ReadFloatDataset()

void nxH5::PNeXus::ReadFloatDataset	(	H5::H5File &	file,
		const std::string &	path )

private

Read a float dataset and store in data map.

Parameters

file	HDF5 file object
path	Path to the dataset

Exceptions

H5::Exception if reading fails

Reads a float dataset from the HDF5 file and stores it in the data map. Handles multi-dimensional datasets by flattening them into a vector.

Parameters

file	HDF5 file object
path	Path to the dataset

Exceptions

H5::Exception if reading fails

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp, and /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 4835 of file PNeXus.cpp.

References fDataMap, FindDatasetPath(), fPrintDebug, ReadDatasetAttributes(), nxH5::PNXdata< T >::SetData(), and nxH5::PNXdata< T >::SetDimensions().

Referenced by HandleIdfV1(), and HandleIdfV2().

◆ ReadIntDataset()

void nxH5::PNeXus::ReadIntDataset	(	H5::H5File &	file,
		const std::string &	path )

private

Read an integer dataset and store in data map.

Parameters

file	HDF5 file object
path	Path to the dataset

Exceptions

H5::Exception if reading fails

Reads an integer dataset from the HDF5 file and stores it in the data map. Handles multi-dimensional datasets by flattening them into a vector.

Parameters

file	HDF5 file object
path	Path to the dataset

Exceptions

H5::Exception if reading fails

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp, and /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 4769 of file PNeXus.cpp.

References fDataMap, FindDatasetPath(), fPrintDebug, ReadDatasetAttributes(), nxH5::PNXdata< T >::SetData(), and nxH5::PNXdata< T >::SetDimensions().

Referenced by HandleIdfV1(), and HandleIdfV2().

◆ ReadNexusFile()

int nxH5::PNeXus::ReadNexusFile ( )

Read and parse the NeXus HDF5 file.

Returns: 0 on success, 1 on error

Exceptions

H5::FileIException	if file cannot be opened
H5::AttributeIException	if required attributes are missing
H5::DataSetIException	if required datasets are missing

Reads and parses the NeXus HDF5 file. Opens the file in read-only mode, loads the NeXus version attribute, and reads the IDF version dataset. Uses case-insensitive path lookup to handle varying path casings.

Returns: 0 on success, 1 on error

Exceptions

H5::FileIException	if file cannot be opened
H5::AttributeIException	if NeXus_version attribute is missing
H5::DataSetIException	if IDF_version dataset is missing

Note: This method is called automatically by the constructor. It performs case-insensitive lookups for both attributes and datasets to handle NeXus files with varying naming conventions.

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp, and /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 3531 of file PNeXus.cpp.

References fFileName, fHdf5Version, fIdfVersion, FindAttributeName(), FindDatasetPath(), fNeXusVersion, fPrintDebug, HandleIdfV1(), and HandleIdfV2().

Referenced by PNeXus().

◆ ReadStringDataset()

void nxH5::PNeXus::ReadStringDataset	(	H5::H5File &	file,
		const std::string &	path )

private

Read a string dataset and store in data map.

Parameters

file	HDF5 file object
path	Path to the dataset

Exceptions

H5::Exception if reading fails

Reads a string dataset from the HDF5 file and stores it in the data map.

Parameters

file	HDF5 file object
path	Path to the dataset

Exceptions

H5::Exception if reading fails

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp, and /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 4900 of file PNeXus.cpp.

References fDataMap, FindDatasetPath(), fPrintDebug, ReadDatasetAttributes(), nxH5::PNXdata< T >::SetData(), and nxH5::PNXdata< T >::SetDimensions().

Referenced by HandleIdfV1(), and HandleIdfV2().

◆ RemoveDataset()

bool nxH5::PNeXus::RemoveDataset ( const std::string & path )

inline

Remove a dataset from the data map.

Parameters

path	HDF5 path of the dataset to remove

Returns: true if dataset was removed, false if path didn't exist

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 1610 of file PNeXus.h.

References fDataMap.

◆ RemoveDatasetAttribute()

template<typename T>

bool nxH5::PNeXus::RemoveDatasetAttribute	(	const std::string &	path,
		const std::string &	attrName )

inline

Remove an attribute from a dataset.

Template Parameters

T	Data type of the PNXdata object

Parameters

path	HDF5 path of the dataset
attrName	Attribute name to remove

Returns: true if attribute was removed, false if dataset doesn't exist or attribute not found

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 1697 of file PNeXus.h.

References fDataMap, and HasDataset().

◆ RemoveGroupAttribute()

bool nxH5::PNeXus::RemoveGroupAttribute	(	const std::string &	groupPath,
		const std::string &	attrName )

Remove an attribute from a group.

Parameters

groupPath	HDF5 path of the group
attrName	Attribute name to remove

Returns: true if attribute was removed, false if group or attribute not found

Remove an attribute from a group.

Parameters

groupPath	HDF5 path of the group
attrName	Attribute name to remove

Returns: true if attribute was removed, false if group or attribute not found

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp, and /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 5619 of file PNeXus.cpp.

References fGroupAttributes.

◆ SetDataset()

template<typename T>

void nxH5::PNeXus::SetDataset	(	const std::string &	path,
		const PNXdata< T > &	data )

inline

Add or update a dataset in the data map.

Template Parameters

T	Data type of the PNXdata object

Parameters

path	HDF5 path for the dataset
data	PNXdata object to store

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 1575 of file PNeXus.h.

References fDataMap.

◆ SplitPath()

std::vector< std::string > nxH5::PNeXus::SplitPath ( const std::string & path )

staticprivate

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp, and /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 3052 of file PNeXus.cpp.

Referenced by CreateGroupHierarchy(), FindDatasetPath(), FindDatasetPath(), FindGroupPath(), and FindGroupPath().

◆ UpdateDatasetData()

template<typename T>

bool nxH5::PNeXus::UpdateDatasetData	(	const std::string &	path,
		const std::vector< T > &	newData )

inline

Update the data of an existing dataset.

Template Parameters

T	Data type of the PNXdata object

Parameters

path	HDF5 path of the dataset
newData	New data vector to set

Returns: true if update succeeded, false if path doesn't exist

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 1638 of file PNeXus.h.

References fDataMap, and HasDataset().

◆ UpdateDatasetDimensions()

template<typename T>

bool nxH5::PNeXus::UpdateDatasetDimensions	(	const std::string &	path,
		const std::vector< hsize_t > &	newDimensions )

inline

Update the dimensions of an existing dataset.

Template Parameters

T	Data type of the PNXdata object

Parameters

path	HDF5 path of the dataset
newDimensions	New dimensions vector to set

Returns: true if update succeeded, false if path doesn't exist

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 1657 of file PNeXus.h.

References fDataMap, and HasDataset().

◆ WriteDatasetAttributes()

template<typename T>

void nxH5::PNeXus::WriteDatasetAttributes	(	H5::DataSet &	dataset,
		const PNXdata< T > &	data )

private

Write dataset attributes from PNXdata object.

Template Parameters

T	The data type of the PNXdata object

Parameters

dataset	HDF5 dataset object to write attributes to
data	PNXdata object containing attributes

Writes all attributes from a PNXdata object to an HDF5 dataset. Supports int, float, and string attribute types.

Template Parameters

T	The data type of the PNXdata object

Parameters

dataset	HDF5 dataset object to write attributes to
data	PNXdata object containing attributes

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp, and /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 5089 of file PNeXus.cpp.

References fPrintDebug, and nxH5::PNXdata< T >::GetAttributes().

Referenced by WriteFloatDataset(), WriteIntDataset(), and WriteStringDataset().

◆ WriteFileAttributes()

void nxH5::PNeXus::WriteFileAttributes ( H5::H5File & file )

private

Write root-level file attributes.

Parameters

file	HDF5 file object

Exceptions

H5::Exception if writing fails

Writes root-level file attributes such as NeXus_version, HDF5_version, file_name, and file_time to the HDF5 file.

Parameters

file	HDF5 file object

Exceptions

H5::Exception if writing fails

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp, and /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 5479 of file PNeXus.cpp.

References fFileNameNxs, fFileTimeNxs, fGroupAttributes, fHdf5Version, fNeXusVersion, and fPrintDebug.

Referenced by WriteNexusFile().

◆ WriteFloatDataset()

void nxH5::PNeXus::WriteFloatDataset	(	H5::H5File &	file,
		const std::string &	path,
		const PNXdata< float > &	data )

private

Write a float dataset with attributes.

Parameters

file	HDF5 file object
path	Dataset path (groups created automatically)
data	PNXdata object containing data, dimensions, and attributes

Exceptions

H5::Exception if writing fails

Writes a float dataset to the HDF5 file with all its attributes. The parent group hierarchy is created automatically if it doesn't exist.

Parameters

file	HDF5 file object
path	Dataset path (groups created automatically)
data	PNXdata object containing data, dimensions, and attributes

Exceptions

H5::Exception if writing fails

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp, and /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 5248 of file PNeXus.cpp.

References CreateGroupHierarchy(), fPrintDebug, nxH5::PNXdata< T >::GetData(), nxH5::PNXdata< T >::GetDimensions(), nxH5::PNXdata< T >::GetNumElements(), and WriteDatasetAttributes().

Referenced by WriteNexusFile().

◆ WriteGroupAttributes()

void nxH5::PNeXus::WriteGroupAttributes	(	H5::Group &	group,
		const std::map< std::string, std::any > &	attributes )

private

Write attributes to a group.

Parameters

group	HDF5 group object to write attributes to
attributes	Map of attribute names to values

Writes attributes to an HDF5 group object. Supports int, float, and string attribute types.

Parameters

group	HDF5 group object to write attributes to
attributes	Map of attribute names to values (stored as std::any)

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp, and /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 5396 of file PNeXus.cpp.

References fPrintDebug.

Referenced by CreateGroupHierarchy().

◆ WriteIntDataset()

void nxH5::PNeXus::WriteIntDataset	(	H5::H5File &	file,
		const std::string &	path,
		const PNXdata< int > &	data )

private

Write an integer dataset with attributes.

Parameters

file	HDF5 file object
path	Dataset path (groups created automatically)
data	PNXdata object containing data, dimensions, and attributes

Exceptions

H5::Exception if writing fails

Writes an integer dataset to the HDF5 file with all its attributes. The parent group hierarchy is created automatically if it doesn't exist.

Parameters

file	HDF5 file object
path	Dataset path (groups created automatically)
data	PNXdata object containing data, dimensions, and attributes

Exceptions

H5::Exception if writing fails

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp, and /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 5176 of file PNeXus.cpp.

References CreateGroupHierarchy(), fPrintDebug, nxH5::PNXdata< T >::GetData(), nxH5::PNXdata< T >::GetDimensions(), nxH5::PNXdata< T >::GetNumElements(), and WriteDatasetAttributes().

Referenced by WriteNexusFile().

◆ WriteNexusFile()

int nxH5::PNeXus::WriteNexusFile	(	const std::string &	filename,
		int	idfVersion = 2 )

Writes the data map contents to a new NeXus HDF5 file. This is the main public API for writing NeXus files.

Parameters

filename	Path to the output NeXus HDF5 file
idfVersion	IDF version to write (default: 2)

Returns: 0 on success, 1 on error

Exceptions

H5::FileIException	if file cannot be created
H5::GroupIException	if group creation fails
H5::DataSetIException	if dataset writing fails

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp, and /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 5731 of file PNeXus.cpp.

References fDataMap, fPrintDebug, WriteFileAttributes(), WriteFloatDataset(), WriteIntDataset(), and WriteStringDataset().

◆ WriteStringDataset()

void nxH5::PNeXus::WriteStringDataset	(	H5::H5File &	file,
		const std::string &	path,
		const PNXdata< std::string > &	data )

private

Write a string dataset with attributes.

Parameters

file	HDF5 file object
path	Dataset path (groups created automatically)
data	PNXdata object containing data, dimensions, and attributes

Exceptions

H5::Exception if writing fails

Writes a string dataset to the HDF5 file with all its attributes. The parent group hierarchy is created automatically if it doesn't exist. Handles both scalar strings and arrays of strings.

Parameters

file	HDF5 file object
path	Dataset path (groups created automatically)
data	PNXdata object containing data, dimensions, and attributes

Exceptions

H5::Exception if writing fails

Examples: /workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp, and /workspace/LMU/musrfit/src/external/nexus/PNeXus.h.

Definition at line 5321 of file PNeXus.cpp.

References CreateGroupHierarchy(), fPrintDebug, nxH5::PNXdata< T >::GetData(), nxH5::PNXdata< T >::GetDimensions(), and WriteDatasetAttributes().

Referenced by WriteNexusFile().

Member Data Documentation

◆ fCreatorNxs

std::string nxH5::PNeXus::fCreatorNxs {""}

private

Definition at line 1882 of file PNeXus.h.

◆ fDataMap

std::map<std::string, std::any> nxH5::PNeXus::fDataMap

private

Map of HDF5 paths to PNXdata objects.

Definition at line 1884 of file PNeXus.h.

Referenced by AddDataset(), AddDatasetAttribute(), ClearDataMap(), Dump(), GetDataMap(), GetDataMap(), GetDataset(), GetDatasetRef(), GetNumDatasets(), HasDataset(), ModifyDataset(), ReadFloatDataset(), ReadIntDataset(), ReadStringDataset(), RemoveDataset(), RemoveDatasetAttribute(), SetDataset(), UpdateDatasetData(), UpdateDatasetDimensions(), and WriteNexusFile().

◆ fFileName

std::string nxH5::PNeXus::fFileName {""}

private

NeXus HDF5 filename.

Definition at line 1875 of file PNeXus.h.

Referenced by Dump(), GetFileName(), PNeXus(), and ReadNexusFile().

◆ fFileNameNxs

std::string nxH5::PNeXus::fFileNameNxs {""}

private

Definition at line 1880 of file PNeXus.h.

Referenced by Dump(), HandleIdfV2(), and WriteFileAttributes().

◆ fFileTimeNxs

std::string nxH5::PNeXus::fFileTimeNxs {""}

private

Definition at line 1881 of file PNeXus.h.

Referenced by Dump(), HandleIdfV2(), and WriteFileAttributes().

◆ fGroupAttributes

std::map<std::string, std::map<std::string, std::any> > nxH5::PNeXus::fGroupAttributes

private

Map of group paths to their attributes.

Definition at line 1885 of file PNeXus.h.

Referenced by AddGroupAttribute(), ClearGroupAttributes(), CreateGroupHierarchy(), GetGroupAttribute(), GetGroupAttributes(), HasGroupAttribute(), RemoveGroupAttribute(), and WriteFileAttributes().

◆ fHdf5LibVersion

std::string nxH5::PNeXus::fHdf5LibVersion {"n/a"}

private

HDF5 library version used when calling PNeXus.

Definition at line 1877 of file PNeXus.h.

Referenced by GetHdf5LibVersion(), PNeXus(), and PNeXus().

◆ fHdf5Version

std::string nxH5::PNeXus::fHdf5Version {""}

private

HDF5 version of the file.

Definition at line 1878 of file PNeXus.h.

Referenced by Dump(), GetHdf5Version(), ReadNexusFile(), and WriteFileAttributes().

◆ fIdfVersion

int nxH5::PNeXus::fIdfVersion {-1}

private

IDF version of the NeXus file.

Definition at line 1876 of file PNeXus.h.

Referenced by Dump(), GetIdfVersion(), and ReadNexusFile().

◆ fNeXusVersion

std::string nxH5::PNeXus::fNeXusVersion {""}

private

NeXus version of the file.

Definition at line 1879 of file PNeXus.h.

Referenced by Dump(), GetNeXusVersion(), ReadNexusFile(), and WriteFileAttributes().

◆ fPrintDebug

bool nxH5::PNeXus::fPrintDebug {false}

private

if true print additional debug information

Definition at line 1874 of file PNeXus.h.

Referenced by CreateGroupHierarchy(), HandleIdfV1(), HandleIdfV2(), PNeXus(), ReadDatasetAttributes(), ReadFloatDataset(), ReadIntDataset(), ReadNexusFile(), ReadStringDataset(), WriteDatasetAttributes(), WriteFileAttributes(), WriteFloatDataset(), WriteGroupAttributes(), WriteIntDataset(), WriteNexusFile(), and WriteStringDataset().

◆ fUserV1

std::string nxH5::PNeXus::fUserV1 {""}

private

Definition at line 1883 of file PNeXus.h.

Referenced by Dump(), and HandleIdfV1().

The documentation for this class was generated from the following files:

/workspace/LMU/musrfit/src/external/nexus/PNeXus.h
/workspace/LMU/musrfit/src/external/nexus/PNeXus.cpp

Public Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PNeXus() [1/2]

◆ PNeXus() [2/2]

Member Function Documentation

◆ AddDataset()

◆ AddDatasetAttribute()

◆ AddGroupAttribute()

◆ AddRootAttribute()

◆ CaseInsensitiveEquals()

◆ ClearDataMap()

◆ ClearGroupAttributes()

◆ CreateGroupHierarchy()

◆ Dump()

◆ FindAttributeName()

◆ FindDatasetPath() [1/2]

◆ FindDatasetPath() [2/2]

◆ FindGroupPath() [1/2]

◆ FindGroupPath() [2/2]

◆ GetDataMap() [1/2]

◆ GetDataMap() [2/2]

◆ GetDataset()

◆ GetDatasetRef()

◆ GetFileName()

◆ GetGroupAttribute()

◆ GetGroupAttributes()

◆ GetHdf5LibVersion()

◆ GetHdf5Version()

◆ GetIdfVersion()

◆ GetNeXusVersion()

◆ GetNumDatasets()

◆ HandleIdfV1()

◆ HandleIdfV2()

◆ HasDataset()

◆ HasGroupAttribute()

◆ ModifyDataset()

◆ ReadDatasetAttributes()

◆ ReadFloatDataset()

◆ ReadIntDataset()

◆ ReadNexusFile()

◆ ReadStringDataset()

◆ RemoveDataset()

◆ RemoveDatasetAttribute()

◆ RemoveGroupAttribute()

◆ SetDataset()

◆ SplitPath()

◆ UpdateDatasetData()

◆ UpdateDatasetDimensions()

◆ WriteDatasetAttributes()

◆ WriteFileAttributes()

◆ WriteFloatDataset()

◆ WriteGroupAttributes()

◆ WriteIntDataset()

◆ WriteNexusFile()

◆ WriteStringDataset()

Member Data Documentation

◆ fCreatorNxs

◆ fDataMap

◆ fFileName

◆ fFileNameNxs

◆ fFileTimeNxs

◆ fGroupAttributes

◆ fHdf5LibVersion

◆ fHdf5Version

◆ fIdfVersion

◆ fNeXusVersion

◆ fPrintDebug

◆ fUserV1