Collaboration diagram for XML utilities:

Data Structures
struct	pni::io::nx::xml::attribute
	read and write attributes More...

class	pni::io::nx::xml::data_node
	node IO More...

struct	pni::io::nx::xml::write_no_data
	default data predicate More...

class	pni::io::nx::xml::dimensions
	reading and writing dimensions More...

struct	pni::io::nx::xml::field
	read and write field data More...

struct	pni::io::nx::xml::group
	read and write groups More...

struct	pni::io::nx::xml::io_node
	general IO objects More...

class	pni::io::nx::xml::link
	manages links in XML More...

Typedefs
typedef boost::mpl::map < boost::mpl::pair < pni::core::uint8, pni::core::uint64 > , boost::mpl::pair < pni::core::uint16, pni::core::uint64 > , boost::mpl::pair < pni::core::uint32, pni::core::uint64 > , boost::mpl::pair < pni::core::uint64, pni::core::uint64 > , boost::mpl::pair < pni::core::int8, pni::core::int64 > , boost::mpl::pair < pni::core::int16, pni::core::int64 > , boost::mpl::pair < pni::core::int32, pni::core::int64 > , boost::mpl::pair < pni::core::int64, pni::core::int64 > , boost::mpl::pair < pni::core::float32, pni::core::float128 > , boost::mpl::pair < pni::core::float64, pni::core::float128 > , boost::mpl::pair < pni::core::float128, pni::core::float128 > , boost::mpl::pair < pni::core::complex32, pni::core::complex128 > , boost::mpl::pair < pni::core::complex64, pni::core::complex128 > , boost::mpl::pair < pni::core::complex128, pni::core::complex128 > >	pni::io::nx::xml::max_type_map
	maximum type maps More...

typedef std::pair< size_t, size_t >	pni::io::nx::xml::index_value_type
	index-value type More...

using	pni::io::nx::xml::node = boost::property_tree::ptree
	alias for ptree More...

Functions
template<typename ATYPE >
ATYPE	pni::io::nx::xml::make_array (const node &data)
	generate an array More...

template<>
pni::core::array	pni::io::nx::xml::make_array (const node &data)
	generate an array type erasure More...

bool	pni::io::nx::xml::operator< (const index_value_type &lhs, const index_value_type &rhs)
	comparison operator for index_value_type More...

template<typename T , typename OTYPE >
void	pni::io::nx::xml::write_object_data (OTYPE &o, node &n)
	write data from Nexus to XML More...

template<typename OTYPE >
void	pni::io::nx::xml::write_object_data (OTYPE &p, node &n)
	write data from a Nexus object to XML More...

template<typename OTYPE , typename PTYPE >
void	pni::io::nx::xml::append_attributes (const OTYPE &parent, node &p, PTYPE &write_predicate)
	append attributes from a nexus type to XML More...

template<typename GTYPE , typename FTYPE , typename ATYPE , typename LTYPE , typename PTYPE >
void	pni::io::nx::xml::nexus_to_xml (nxobject< GTYPE, FTYPE, ATYPE, LTYPE > &p, node &n, PTYPE write_predicate)
	nexus to XML conversion More...

template<template< nximp_code > class OTYPE, nximp_code IMPID, typename PTYPE >
void	pni::io::nx::xml::nexus_to_xml (OTYPE< IMPID > &o, node &n, PTYPE write_predicate)
	nexus to XML conversion More...

template<typename GTYPE , typename FTYPE , typename ATYPE , typename LTYPE >
void	pni::io::nx::xml::nexus_to_xml (nxobject< GTYPE, FTYPE, ATYPE, LTYPE > &p, node &n)
	nexus to XML conversion More...

node	pni::io::nx::xml::create_from_string (const pni::core::string &s)
	create xml node from string More...

node	pni::io::nx::xml::create_from_file (const pni::core::string &s)
	create xml node from file More...

pni::core::string	pni::io::nx::xml::attribute_path (const pni::core::string &name)
	create an attribute path More...

node	pni::io::nx::xml::get_attribute (const node &parent, const pni::core::string &name)
	get attribute node More...

bool	pni::io::nx::xml::has_attribute (const node &parent, const pni::core::string &name)
	check for attribute existence More...

pni::core::string	pni::io::nx::xml::get_name (const node &n)
	get name of a node More...

std::ostream &	pni::io::nx::xml::operator<< (std::ostream &o, const node &n)
	XML stream output. More...

template<typename T , typename OTYPE >
void	pni::io::nx::xml::write_node_data (const OTYPE &object, const node &n)
	write data from buffer More...

template<typename OTYPE >
void	pni::io::nx::xml::write_node_data (const OTYPE &object, const node &n)
	write node data More...

template<typename GTYPE , typename FTYPE , typename ATYPE , typename LTYPE , typename PTYPE >
void	pni::io::nx::xml::xml_to_nexus (const node &t, const nxobject< GTYPE, FTYPE, ATYPE, LTYPE > &parent, PTYPE write_data)
	create objects from XML More...

template<typename GTYPE , typename FTYPE , typename ATYPE , typename LTYPE >
void	pni::io::nx::xml::xml_to_nexus (const node &t, const nxobject< GTYPE, FTYPE, ATYPE, LTYPE > &parent)
	create objects from XML More...

template<template< pni::io::nx::nximp_code > class OTYPE, pni::io::nx::nximp_code IMPID, typename PTYPE >
void	pni::io::nx::xml::xml_to_nexus (const node &t, const OTYPE< IMPID > &group, PTYPE write_data)
	create objects from XML More...

template<template< pni::io::nx::nximp_code > class OTYPE, pni::io::nx::nximp_code IMPID>
void	pni::io::nx::xml::xml_to_nexus (const node &t, const OTYPE< IMPID > &group)
	create objects from XML More...

Variables
static const std::map < pni::core::string, bool >	pni::io::nx::xml::bool_string_map {"1",true}
	bool representation map More...

Detailed Description

Creating the structure of a Nexus file can be rather tedious when coded statically. Additionally such an approach is usually rather inflexible and thus should be avoided at all. libpniio provides utility functions to create Nexus objects using XML templates. Fortunately, Nexus comes with its own XML dialect called NXDL which already defines the XML vocabulary necessary to describie Nexus files with XML.

Using NXDL makes programs much more flexible and gives users the possibility to customize the layout of a Nexus file without rewriting code.

Under the hood the XML/NXDL facility provided here is based on BOOST::property_tree providing a non-validating XML parser. However, for our purpose validation is not really required.

Typedef Documentation

typedef std::pair<size_t,size_t> pni::io::nx::xml::index_value_type

This type describes an index value pair used in NXDL to describe a single dimension. The first component is the index of the particular dimensions while the second one denotes the number of elements along this dimension.

typedef boost::mpl::map< boost::mpl::pair<pni::core::uint8,pni::core::uint64>, boost::mpl::pair<pni::core::uint16,pni::core::uint64>, boost::mpl::pair<pni::core::uint32,pni::core::uint64>, boost::mpl::pair<pni::core::uint64,pni::core::uint64>, boost::mpl::pair<pni::core::int8,pni::core::int64>, boost::mpl::pair<pni::core::int16,pni::core::int64>, boost::mpl::pair<pni::core::int32,pni::core::int64>, boost::mpl::pair<pni::core::int64,pni::core::int64>, boost::mpl::pair<pni::core::float32,pni::core::float128>, boost::mpl::pair<pni::core::float64,pni::core::float128>, boost::mpl::pair<pni::core::float128,pni::core::float128>, boost::mpl::pair<pni::core::complex32,pni::core::complex128>, boost::mpl::pair<pni::core::complex64,pni::core::complex128>, boost::mpl::pair<pni::core::complex128,pni::core::complex128> > pni::io::nx::xml::max_type_map

This map defines the maximum type for every numeric type provided by pnicore. It is used when reading data from an attribute or node.

using pni::io::nx::xml::node = typedef boost::property_tree::ptree

This alias creates the new type name node which can be used within the xml namespace instead of boost::property_tree::ptree;

Function Documentation

template<typename OTYPE , typename PTYPE >

void pni::io::nx::xml::append_attributes	(	const OTYPE &	parent,
		node &	p,
		PTYPE &	write_predicate
	)

Reads all attribtues from a Nexus node and append them to an XML node. There are several attribute which are omitted as they are part of the XML tag

NX_class whose content is written in the type attribute
units which goes to the units attribute
long_name which goes to the long_name tag attribute

Whether or not data form the Nexus object is written to the XML output depends on the write_predicate. This is a callable which takes the Nexus object as its only argument and returns true if the data should be written or false otherwise.

Template Parameters

OTYPE	Nexus object type
PTYPE	write predicate type

Parameters

parent	the object with the attributes
p	XML node to which attribute tags should be appended
write_predicate	function object determinig when to write data to the XML output

pni::core::string pni::io::nx::xml::attribute_path ( const pni::core::string & name )

This function is intended for internal use only. It creates a valid attribute path from an attribute name.

Parameters

name	the name of the attribute

Returns: a valid property tree attribute path

node pni::io::nx::xml::create_from_file ( const pni::core::string & s )

Reads XML data from a file and returns an XML node refering to the root element of the XML tree.

Exceptions

pni::io::parser_error	in case of parsing issues
file_error	in case of problems opening the file

Parameters

s	name of the file

Returns: node instance

node pni::io::nx::xml::create_from_string ( const pni::core::string & s )

Parses a string provided by the user and returns an XML node from it.

Exceptions

parser_error in case of parsing problems

Parameters

s	string from which to read the data

Returns: node instance

node pni::io::nx::xml::get_attribute	(	const node &	parent,
		const pni::core::string &	name
	)

Returns an attribute node from its parent node.

Exceptions

key_error	if the attribute does not exist
parser_error	in case of any other error

Parameters

parent	the node from which to retrieve the attribute
name	the name of the attribute

Returns: node representing the attribute

string pni::io::nx::xml::get_name ( const node & n )

Return the name of a node as determined by the content of its name attribute. This is a convenience function. If the node does not have a name attribute an empty string is returned.

Parameters

n	node with name attribute

Returns: content of the name attribute of a tag

bool pni::io::nx::xml::has_attribute	(	const node &	parent,
		const pni::core::string &	name
	)

Returns true if the node parent has a an attribute name attached to it. Otherwise false is returned.

Parameters

parent	reference to the parent node
name	the attributes name

Returns: true if the attribute exists, false otherwise

template<typename ATYPE >

pni::core::array pni::io::nx::xml::make_array ( const node & data )

generate an array type erasure

This function template generates an instance of an mdarray from a data node and stores the data in this array. The data type is determined by the user and must match the data type stored in the array.

Parameters

data	the XML node holding the daata

Returns: instance of ATYPE with the data

template<>

pni::core::array pni::io::nx::xml::make_array ( const node & data )

This specialization of the make_array function template returns an array type erasure. This function is particularly useful in situations where we only need to transfer data and the data type is of no further important.

Parameters

data	the XML node with data

Returns: instance of array with the data

generate an array type erasure

This function template generates an instance of an mdarray from a data node and stores the data in this array. The data type is determined by the user and must match the data type stored in the array.

Parameters

data	the XML node holding the daata

Returns: instance of ATYPE with the data

template<typename GTYPE , typename FTYPE , typename ATYPE , typename LTYPE , typename PTYPE >

void pni::io::nx::xml::nexus_to_xml	(	nxobject< GTYPE, FTYPE, ATYPE, LTYPE > &	p,
		node &	n,
		PTYPE	write_predicate
	)

Converts the structure of a Nexus tree stored below p into an XML tree below n. The Nexus parent object p is provided as an instance of nxobject. Which data from the Nexus file goes to the XML output is determined by the write_predicate, a functor taking a single Nexus object as its argument and returns true if the data should be written and false otherwise.

Template Parameters

GTYPE	Nexus group type
FTYPE	Nexus field type
ATYPE	Nexus attribute type
LTYPE	link type
PTYPE	write predicate type

Parameters

p	parent object
n	XML node
write_data	functor determining which data to write

template<template< nximp_code > class OTYPE, nximp_code IMPID, typename PTYPE >

void pni::io::nx::xml::nexus_to_xml	(	OTYPE< IMPID > &	o,
		node &	n,
		PTYPE	write_predicate
	)

Converts the content of Nexus object to XML. Here the Nexus object is is passed as an instance of nxattribute, nxgroup, or nxfield. The write_predicate functor determines which data is written to the XML output.

Template Parameters

OTYPE	Nexus object type
IMPID	implementation ID
PTYPE	predicate type

Parameters

o	parent object
n	XML node
write_predicate	the functor determining which data to write

template<typename GTYPE , typename FTYPE , typename ATYPE , typename LTYPE >

void pni::io::nx::xml::nexus_to_xml	(	nxobject< GTYPE, FTYPE, ATYPE, LTYPE > &	p,
		node &	n
	)

Converts the structure of a Nexus tree stored below p into an XML tree below n. The Nexus parent object p is provided as an instance of nxobject. This template function takes no write predicate and thus no data from the Nexus file is written to the XML output.

Template Parameters

GTYPE	Nexus group type
FTYPE	Nexus field type
ATYPE	Nexus attribute type
LTYPE	link type

Parameters

p	parent object
n	XML node

bool pni::io::nx::xml::operator<	(	const index_value_type &	lhs,
		const index_value_type &	rhs
	)

Operator required to sort containers using index_value_type as their element type. index-value pairs are ordered by their dimension index. This operator returns true if the index component of the LHS is smaller than the index component of the RHS.

Parameters

lhs	left handside of the operator
rhs	right handside of the operator

Returns: true if index of lhs is small than that of rhs, false otherwise

std::ostream & pni::io::nx::xml::operator<<	(	std::ostream &	o,
		const node &	n
	)

Write property tree structure as XML to an output stream.

Parameters

o	reference output stream
n	node to write to the output stream

Returns: modified output stream

template<typename T , typename OTYPE >

void pni::io::nx::xml::write_node_data	(	const OTYPE &	object,
		const node &	n
	)

Read data from the CDATA section of an XML tag and store it in an NeXus object. The data type used for reading the data is determined by the user supplied template parameter.

Exceptions

type_error	if the data type cannot be read or handled by the write function
parser_error	if the data could not be read from the CDATA section of the tag
invalid_object_error	if the target object is not valid
io_error	if writing the data fails
size_mismatch_error	if the amount of data read from CDATA does not match the size of the NeXus object
object_error	in case of any other error

Template Parameters

T	data type to use for writing
OTYPE	object type to which to write the data

Parameters

object	the object instance to which to write the data
n	the node holding the data

template<typename OTYPE >

void pni::io::nx::xml::write_node_data	(	const OTYPE &	object,
		const node &	n
	)

Write the data stored in an XML tag to a NeXus object. This is a utilty function which calles an appropriate instantiation of the write_node_data function template for every particular data type.

Exceptions

type_error	if the data type cannot be read or handled by the write function
parser_error	if the data could not be read from the CDATA section of the tag
invalid_object_error	if the target object is not valid
io_error	if writing the data fails
size_mismatch_error	if the amount of data read from CDATA does not match the size of the NeXus object
object_error	in case of any other error

Template Parameters

OTYPE object type to which to write the data

Parameters

object	the object instance to which to write the data
n	the node holding the data

template<typename T , typename OTYPE >

void pni::io::nx::xml::write_object_data	(	OTYPE &	o,
		node &	n
	)

This function template writes data from a Nexus object to the CDATA section of an XML tag.

Template Parameters

T	data type to use
OTYPE	Nexus object type

Parameters

o	Nexus object from which to read the data
n	XML tag where to store the data

template<typename OTYPE >

void pni::io::nx::xml::write_object_data	(	OTYPE &	p,
		node &	n
	)

Read data from a Nexus object and store it to the CDATA section of an XML tag. This function template only does type dispatching.

Template Parameters

OTYPE Nexus object type

Parameters

p	the Nexus object from which to read the data
n	the XML node where to store the data

template<typename GTYPE , typename FTYPE , typename ATYPE , typename LTYPE , typename PTYPE >

void pni::io::nx::xml::xml_to_nexus	(	const node &	t,
		const nxobject< GTYPE, FTYPE, ATYPE, LTYPE > &	parent,
		PTYPE	write_data
	)

Recursively creates the objects as described in the XML file below parent. The parent is passed as a reference to an instance of nxobject.

Exceptions

parser_error	in case of XML parsing problems
invalid_object_error	if the parent object is not valid
io_error	if data or metadata write failed
type_error	if a data type is involved that cannot be handled
object_error	in case of any other error

Template Parameters

GTYPE	group type
FTYPE	field type
ATYPE	attribute type
LTYPE	link type

Parameters

t	ptree instance with the XML data
parent	instance of nxobject
write_data	predicate function determining when data should be written

template<typename GTYPE , typename FTYPE , typename ATYPE , typename LTYPE >

void pni::io::nx::xml::xml_to_nexus	(	const node &	t,
		const nxobject< GTYPE, FTYPE, ATYPE, LTYPE > &	parent
	)

A version of xml_to_nexus where no data is written to the file at all. The parent is passed as a reference to nxobject.

Exceptions

parser_error	in case of XML parsing problems
invalid_object_error	if the parent object is not valid
io_error	if data or metadata write failed
type_error	if a data type is involved that cannot be handled
object_error	in case of any other error

Template Parameters

GTYPE	group type
FTYPE	field type
ATYPE	attribute type
LTYPE	link type

Parameters

t	ptree instance with the XML data
parent	instance of nxobject

template<template< pni::io::nx::nximp_code > class OTYPE, pni::io::nx::nximp_code IMPID, typename PTYPE >

void pni::io::nx::xml::xml_to_nexus	(	const node &	t,
		const OTYPE< IMPID > &	group,
		PTYPE	write_data
	)

An overload of the xml_to_nexus function template where the parent is passed as an instance of nxgroup.

Exceptions

parser_error	in case of XML parsing problems
invalid_object_error	if the parent object is not valid
io_error	if data or metadata write failed
type_error	if a data type is involved that cannot be handled
object_error	in case of any other error

Template Parameters

OTYPE	parent template
IMPID	implementation ID
PTYPE	data writer predicate

Parameters

t	XML node from which to construct the Nexus structure
group	the parent group below which the structure should be generated
write_data	predicate to determine whether or tag data should be written to the file

template<template< pni::io::nx::nximp_code > class OTYPE, pni::io::nx::nximp_code IMPID>

void pni::io::nx::xml::xml_to_nexus	(	const node &	t,
		const OTYPE< IMPID > &	group
	)

An overload of the xml_to_nexus function template where the parent is passed as an instance of nxgroup.

Exceptions

parser_error	in case of XML parsing problems
invalid_object_error	if the parent object is not valid
io_error	if data or metadata write failed
type_error	if a data type is involved that cannot be handled
object_error	in case of any other error

Template Parameters

OTYPE	parent template
IMPID	implementation ID
PTYPE	data writer predicate

Parameters

t	XML node from which to construct the Nexus structure
group	the parent group below which the structure should be generated
write_data	predicate to determine whether or tag data should be written to the file

Variable Documentation

const std::map<pni::core::string,bool> pni::io::nx::xml::bool_string_map {"1",true}

static

A static map with all valid representations of boolean values.

Data Structures

Typedefs

Functions

Variables

Detailed Description

Typedef Documentation

Function Documentation

Variable Documentation