Collaboration diagram for HDF5 implementation classes:

Modules
	HDF5 implementation error classes

Data Structures
class	pni::io::nx::h5::attribute_imp
	attribute implementation More...

class	pni::io::nx::h5::field_factory
	factory for field construction More...

class	pni::io::nx::h5::field_imp
	dataset object More...

class	pni::io::nx::h5::file_imp
	HDF5 file implementation. More...

class	pni::io::nx::h5::group_imp
	HDF5 group object. More...

class	pni::io::nx::h5::h5dataspace
	dataspace object More...

class	pni::io::nx::h5::h5datatype
	HDF5 type wrapper. More...

class	pni::io::nx::h5::h5deflate_filter
	HDF5 deflate filter. More...

class	pni::io::nx::h5::h5filter
	base class for filter implementations More...

class	pni::io::nx::h5::h5link

class	pni::io::nx::h5::object_imp
	basic HDF5 ID wrapper More...

class	pni::io::nx::h5::selection
	describe a selection in an HDF5 file More...

class	pni::io::nx::h5::selection_guard< STYPE >
	selection guard More...

struct	pni::io::nx::h5::type_imp
	provide implementation specific types More...

Typedefs
typedef std::vector< char * >	pni::io::nx::h5::char_ptr_vector_type
	vector tyep for char pointers More...

typedef std::vector< const char * >	pni::io::nx::h5::char_const_ptr_vector_type
	vector type for const char pointers More...

Enumerations
enum	pni::io::nx::h5::h5object_type { pni::io::nx::h5::h5object_type::FILE, pni::io::nx::h5::h5object_type::GROUP, pni::io::nx::h5::h5object_type::DATATYPE, pni::io::nx::h5::h5object_type::DATASPACE, pni::io::nx::h5::h5object_type::DATASET, pni::io::nx::h5::h5object_type::ATTRIBUTE, pni::io::nx::h5::h5object_type::PLIST, pni::io::nx::h5::h5object_type::BADID }
	HDF5 object type enumerations. More...

Functions
bool	pni::io::nx::h5::has_attribute (const object_imp &parent, const pni::core::string &name)
	checks for an attributes existence More...

void	pni::io::nx::h5::delete_attribute (const object_imp &parent, const pni::core::string &name)
	Deletes an attribute. More...

object_imp	pni::io::nx::h5::create_attribute (const object_imp &parent, const pni::core::string &name, const h5datatype &type, const h5dataspace &space, bool overwrite)
	create a new attribute at parent More...

object_imp	pni::io::nx::h5::get_attribute_by_name (const object_imp &parent, const pni::core::string &n)
	open attribute by name More...

size_t	pni::io::nx::h5::get_number_of_attributes (const object_imp &parent)
	get number of attributes More...

object_imp	pni::io::nx::h5::get_attribute_by_index (const object_imp &parent, size_t i)
	open attribute by index More...

std::ostream &	pni::io::nx::h5::operator<< (std::ostream &o, const h5dataspace &s)
	output operator More...

bool	pni::io::nx::h5::operator== (const h5datatype &a, const h5datatype &b)
	equality comparison More...

bool	pni::io::nx::h5::operator!= (const h5datatype &a, const h5datatype &b)
	inequality More...

pni::core::type_id_t	pni::io::nx::h5::type_id (const h5datatype &o)
	get type code More...

const h5datatype &	pni::io::nx::h5::get_type (pni::core::type_id_t id)
	get reference to type More...

h5datatype	pni::io::nx::h5::make_type (pni::core::type_id_t id)
	create new type More...

h5object_type	pni::io::nx::h5::get_hdf5_type (const object_imp &o)
	return HDF5 type More...

pni::io::nx::nxobject_type	pni::io::nx::h5::get_nexus_type (const object_imp &o)
	return Nexus type More...

pni::core::string	pni::io::nx::h5::get_filename (const object_imp &object)
	get object filename More...

pni::core::string	pni::io::nx::h5::get_path (const object_imp &object)
	get object path More...

pni::core::string	pni::io::nx::h5::get_name (const object_imp &obj)
	return object name More...

pni::core::string	pni::io::nx::h5::get_parent_path (const object_imp &object)
	get parent path More...

object_imp	pni::io::nx::h5::get_parent (const object_imp &obj)
	return the parent object More...

bool	pni::io::nx::h5::operator== (const object_imp &a, const object_imp &b)
	equality operator More...

bool	pni::io::nx::h5::operator!= (const object_imp &a, const object_imp &b)
	inequality operator More...

size_t	pni::io::nx::h5::effective_rank (const selection &s) noexcept
	get effective rank More...

type_imp::index_vector_type	pni::io::nx::h5::effective_shape (const selection &s)
	get effective shape More...

size_t	pni::io::nx::h5::size (const selection &s) noexcept
	get selection size More...

selection	pni::io::nx::h5::create_selection (const type_imp::selection_vector_type &s)

type_imp::selection_vector_type	pni::io::nx::h5::create_slice_vector (const selection &s)

bool	pni::io::nx::h5::is_vl_string (const h5datatype &type)
	check variable length string More...

bool	pni::io::nx::h5::is_static_string (const h5datatype &type)
	check if static length string More...

size_t	pni::io::nx::h5::static_string_size (const h5datatype &type)
	get static string size More...

void	pni::io::nx::h5::copy_from_vector (const char_vector_type &vector, size_t nstrs, size_t strsize, pni::core::string *strings, const formatter_ptr &formatter)
	copy char vector to strings More...

void	pni::io::nx::h5::copy_from_vector (const char_ptr_vector_type &vector, size_t nstrs, pni::core::string *strings, const formatter_ptr &formatter)
	copy strings from vector to a pointer of strings More...

Detailed Description

HDF5 implementation of the Nexus file format. This module describes the implementation classes which are used to instantiate the low level class templates.

Typedef Documentation

typedef std::vector<const char*> pni::io::nx::h5::char_const_ptr_vector_type

This type is mainly used for writing strings of variable length to a field or attribute

typedef std::vector<char*> pni::io::nx::h5::char_ptr_vector_type

Mainly used for reading strings of variable length from a field or attribute.

Enumeration Type Documentation

enum pni::io::nx::h5::h5object_type

strong

This enumeration class defines type-codes for different kinds of HDF5 objects. As all HDF5 objects are derived from H5Object an thus can be convereted into such an object we need this codes to identify the particular object type of an instance of H5Object.

Enumerator
FILE	HDF5 file code.
GROUP	HDF5 group code.
DATATYPE	HDF5 datatype code.
DATASPACE	HDF5 dataspace code.
DATASET	HDF5 dataset code.
ATTRIBUTE	HDF5 attribute.
PLIST	HDF5 property list.
BADID	unknown object

Function Documentation

void pni::io::nx::h5::copy_from_vector	(	const char_vector_type &	vector,
		size_t	nstrs,
		size_t	strsize,
		pni::core::string *	strings,
		const formatter_ptr &	formatter
	)

Copies the content of char vector to a set of strings. An exception is throws if the total number of required characters does not match the size of the vector.

Exceptions

size_mismatch_error if nstrs*strsize!=vector.size()

Parameters

vector	the vector with characters
nstrs	number of strings
strsize	size of the strings
strings	pointer to the first string instance

void pni::io::nx::h5::copy_from_vector	(	const char_ptr_vector_type &	vector,
		size_t	nstrs,
		pni::core::string *	strings,
		const formatter_ptr &	formatter
	)

Copies the content of a pointer of stringsa

Exceptions

size_mismatch_error if number of strings and vector size do not match

Parameters

vector	the vector with char poitners
nstrs	number of strings
strings	pointer to the first string

object_imp pni::io::nx::h5::create_attribute	(	const object_imp &	parent,
		const pni::core::string &	name,
		const h5datatype &	type,
		const h5dataspace &	space,
		bool	overwrite
	)

Create a new attribute attached to a parent.

Exceptions

invalid_objet_error	if the parent object is not valid
object_error	in case of any errors

Parameters

parent	the parent object for the attribute
name	the name for the attribute
type	an HDF5 data type
space	the dataspace for the attribute
overwrite	if true overwrite an existing attribute

Returns: the attribute as h5object

selection pni::io::nx::h5::create_selection ( const type_imp::selection_vector_type & s )

Create a selection from a slice vector.

Parameters

s	reference to the slice vector

Returns: selection instance

type_imp::selection_vector_type pni::io::nx::h5::create_slice_vector ( const selection & s )

Create a slice vector from a selection. Such a slice vector might be used to create an array selection from an mdarray instance.

Parameters

s	reference to the selection object

Returns: slice vector

void pni::io::nx::h5::delete_attribute	(	const object_imp &	parent,
		const pni::core::string &	name
	)

Deletes an attribute from the object.

Exceptions

invalid_object_error	if the object is not a valid HDF5 object
object_error	in case of all other errors
key_error	if attribute does not exist

Parameters

parent	reference to the parent object
name	the name of the attribute to delete

size_t pni::io::nx::h5::effective_rank ( const selection & s )

noexcept

The effective rank for a selection is the number of dimension for whome the count value is >1.

Parameters

s	selection instance

Returns: effective rank

type_imp::index_vector_type pni::io::nx::h5::effective_shape ( const selection & s )

The effective shape of a selection is basically the count buffer with those entries removed where its value is 1.

Parameters

s	selection instance

Returns: vector with effective shape

object_imp pni::io::nx::h5::get_attribute_by_index	(	const object_imp &	parent,
		size_t	i
	)

Opens an attribute reference by index i. If i exceeds the number of attributes attached to this object an exception will be thrown.

Exceptions

invalid_object_error	if parent object is not valid
index_error	if i exceeds the total number of attributes attached to the parent object
object_error	in case of any other error

Parameters

parent	the parent object from which to retrieve the attribute
i	index of the attribute

Returns: instance of H5Attribute

object_imp pni::io::nx::h5::get_attribute_by_name	(	const object_imp &	parent,
		const pni::core::string &	n
	)

Open an existing attribute and returns it to the callee. If the object does not exist key_error is thrown. In case of any other error oject_error;

Exceptions

invalid_object_error	if the parent object is not valid
key_error	if attribute does not exist
object_error	in case of other errors

Parameters

parent	reference to the parent object of the attribute
n	name of the attribute

Returns: attribute object

string pni::io::nx::h5::get_filename ( const object_imp & object )

Returns the name of the file an HDF5 object belongs too. This function works with the following objects

an HDF5 dataset
an HDF5 group
or an HDF5 attribute

Exceptions

invalid_object_error	if the object is not valid
io_error	if object data cannot be retrieveda
object_error	if validity check fails for some other reason
type_error	if the passed object is of inappropriate type

Parameters

object HDF5 object

Returns: string with the file name

h5object_type pni::io::nx::h5::get_hdf5_type ( const object_imp & o )

Returns the HDF5 type of an instance of h5object. Currently this can be

an HDF5 file
an HDF5 group
an HDF5 dataspace
an HDF5 dataset
an HDF5 attribute
an HDF5 property list

An exception is thrown in case of an unknown type.

Exceptions

type_error	in case of an unkown object type
invalid_object_error	if the object is not valid
object_error	in case of any other error

Parameters

o	reference to h5object

Returns: HDF5 object type

string pni::io::nx::h5::get_name ( const object_imp & obj )

Returns the name of an object. This function works for the following HDF5 types

groups
datasets
attributes

Exceptions

object_error	if validity check fails
invalid_object_error	if obj is not valid
io_error	in case of data retrieval issues
type_error	if object type cannot be determined

Parameters

obj	reference to the object from which to retrieve the name

Returns: name of the object

pni::nx::nexus_type pni::io::nx::h5::get_nexus_type ( const object_imp & o )

Return the Nexus type of an instance of h5object. This can be either a

Nexus group
Nexus field
Nexus attribute
Nexus file

An exception is thrown if the type is unkown.

Exceptions

type_error	in the case of an unkown object type
invalid_object_error	if the object is not valid
object_error	in case of any other error

Parameters

o	reference to h5object instance

Returns: Nexus type

size_t pni::io::nx::h5::get_number_of_attributes ( const object_imp & parent )

Method returns the number of attributes attached to this object.

Exceptions

invalid_object_error	if the parent is not valid
object_error	in case of any other error

Parameters

parent the parent object with attributes

Returns: number of attributes

object_imp pni::io::nx::h5::get_parent ( const object_imp & obj )

Returns the parent object. If the current object is group or a field the returned object is always a group. In the case of an attribute the parent can be either a group or a field.

Exceptions

invalid_object_error	if object not valid
object_error	in case of any other error
type_error	if the type of the object is unkown or could not be determined
io_error	in case of any IO related errors

Parameters

obj	reference to the object from which to retrieve the parent

Returns: object instance of the parent

string pni::io::nx::h5::get_parent_path ( const object_imp & object )

Return the path to the parent of a particular object. Supported HDf5 types are

groups
datasets

Exceptions

invalid_object_error	if object is not valid
io_error	in case of errors
object_error	if validity check fails
type_error	if the object is of an inappropriate type

Parameters

object the HDF5 object from which to retrieve the parent path

Returns: path to the parent

string pni::io::nx::h5::get_path ( const object_imp & object )

Return the path of an HDF5 object as a string. This function works for the following HDF5 object types

group
dataset

Exceptions

object_error	if object validity cannot be verified
invalid_object_error	if the object is not valid
io_error	in case of any IO related error.
type_error	object is not a group or dataset

Parameters

object reference to the object from which to retrieve the path

Returns: path as string

const h5datatype& pni::io::nx::h5::get_type ( pni::core::type_id_t id )

Exceptions

type_error if id has no corresponding HDF5 data type

Parameters

id	type id for which to requeste an HDF5 datatype

Returns: reference to a predefined data type

bool pni::io::nx::h5::has_attribute	(	const object_imp &	parent,
		const pni::core::string &	name
	)

Checks if an attribute exists and returns true if it does. Otherwise false will be returned.

Exceptions

invalid_object_error	if parent object not valid
object_error	in case of any other errors

Parameters

parent	the parent object where we look for the attribute
name	the name of the attribute to look for

Returns: true if exists, false otherwise

bool pni::io::nx::h5::is_static_string ( const h5datatype & type )

Returns true if the data type represents a static length string. If type is not a string type at all false will be returned.

Exceptions

object_error	if information retrieval fails
invalid_object_error	if object not valid
type_error	if data type is not supported

Parameters

type	instance of h5datatype

Returns: true if static string type, false otherwise

bool pni::io::nx::h5::is_vl_string ( const h5datatype & type )

Returns true if the data type represents a variable length string type.

Exceptions

object_error	if type inquery fails
invalid_object_error	if type is not valid
type_error	if the datatype is not supported

Parameters

type	a type instance

Returns: true if VL string type, false otherwise

h5datatype pni::io::nx::h5::make_type ( pni::core::type_id_t id )

Exceptions

type_error if the ID has no HDF5 counterpart

Parameters

id type id

Returns: h5datatype instance

bool pni::io::nx::h5::operator!=	(	const h5datatype &	a,
		const h5datatype &	b
	)

Exceptions

object_error if comparison fails

Parameters

a	lhs value of the operator
b	rhs value of the operator

Returns: true if not equal

bool pni::io::nx::h5::operator!=	(	const object_imp &	a,
		const object_imp &	b
	)

Simply the inverse of the equality operator.

Exceptions

object_error	in case of errors
type_error	if object type cannot be determined

Parameters

a	lhs value of the operator
b	rhs value of the operator

Returns: true if not equal, false otherwise

std::ostream & pni::io::nx::h5::operator<<	(	std::ostream &	o,
		const h5dataspace &	s
	)

Exceptions

invalid_object_error if dataspace is not valid

Parameters

o	output stream
s	HDF5 dataspace

Returns: modified output stream

bool pni::io::nx::h5::operator==	(	const h5datatype &	a,
		const h5datatype &	b
	)

Exceptions

object_error if comparison fails

Parameters

a	lhs value of the operator
b	rhs value of the operator

Returns: true if types are equal

bool pni::io::nx::h5::operator==	(	const object_imp &	a,
		const object_imp &	b
	)

Operator checks if two HDF5 object are equal. This check is done by comparing the address of the objects in the file. If they share the same address the objects should be equal. Invalid objects are considered as not equal.

Exceptions

object_error	in case of errors
type_error	if object type cannot be determined

Parameters

a	lhs value of the operator
b	rhs value of the operator

Returns: true if equal, false otherwise

size_t pni::io::nx::h5::size ( const selection & s )

noexcept

Get the number of elements referenced by the selection.

Parameters

s	selection instance

Returns: number of selected elements

size_t pni::io::nx::h5::static_string_size ( const h5datatype & type )

Return the size of the strings for a static string size type.

Exceptions

type_error	if type is not a static string type
invalid_type_error	if the type is not valid
object_error	in any other case

Parameters

type	the datatype from which to retrieve the string size

Returns: number of characters in each string

type_id_t pni::io::nx::h5::type_id ( const h5datatype & o )

Obtain the type code of a datatype object

Exceptions

type_error	if the passed datatype is not known
invalid_object_error	if the data type instance is not valid
object_error	in case of any other error

Parameters

o	instance of an HDF5 datat type

Returns: type_id_t value for the data type

Modules

Data Structures

Typedefs

Enumerations

Functions

Detailed Description

Typedef Documentation

Enumeration Type Documentation

Function Documentation