Class for hdf5 attribute, which can be attached to groups and datasets. More...

#include <hdfattribute.hh>

Inheritance diagram for Utopia::DataIO::HDFAttribute:

Collaboration diagram for Utopia::DataIO::HDFAttribute:

[legend]

Public Types
using	Base = HDFObject< HDFCategory::attribute >
	alias base class More...

Public Member Functions
void	swap (HDFAttribute &other)
	Exchange states between caller and argument. More...

HDFDataspace	get_filespace ()
	Get the file-dataspace object. More...

auto	get_type ()
	Get the type object. More...

HDFIdentifier	get_parent_id ()
	Get the hdf5 identifier to which the attribute belongs. More...

void	close ()
	closes the attribute More...

auto	get_shape ()
	Get the shape object. More...

template<HDFCategory cat>
void	open (const HDFObject< cat > &parent, std::string name)
	Open a new attribute on HDFObject 'parent' with name 'name'. More...

void	open (const HDFIdentifier &parent, std::string name)
	Open a new attribute on HDFObject 'parent' with name 'name'. More...

template<typename Type >
auto	read ()
	Reads data from attribute, and returns the data and its shape in the form of a hsize_t vector. More...

template<typename Type >
void	read (Type &buffer)
	Reads data from attribute into a predefined buffer, and returns the data and its shape in the form of a hsize_t vector. User is responsible for providing a buffer which can hold the data and has the correct shape! More...

template<typename Type >
void	write (Type attribute_data, std::vector< hsize_t > shape={})
	Function for writing data to the attribute. More...

template<typename Iter , typename Adaptor >
void	write (Iter begin, Iter end, Adaptor adaptor=[](auto &value) { return value;}, [[maybe_unused]] std::vector< hsize_t > shape={})
	Function for writing data to the attribute. More...

	HDFAttribute ()=default
	Default constructor, deleted because of reference member. More...

	HDFAttribute (const HDFAttribute &other)=default
	Copy constructor. More...

	HDFAttribute (HDFAttribute &&other)=default
	Move constructor. More...

HDFAttribute &	operator= (const HDFAttribute &other)=default
	Copy assignment operator. More...

HDFAttribute &	operator= (HDFAttribute &&other)=default
	Attribute move assignment operator. More...

virtual	~HDFAttribute ()
	Destructor. More...

template<HDFCategory cat>
	HDFAttribute (const HDFObject< cat > &object, std::string name)
	Constructor for attribute. More...

Public Member Functions inherited from Utopia::DataIO::HDFObject< HDFCategory::attribute >
void	swap (HDFObject &other)
	swap the state of the caller with the state of the argument More...

std::string	get_path () const
	Get the name or path object. More...

auto	get_id_object () const
	Get the id object. More...

auto	get_logger () const
	Get the logger object. More...

hid_t	get_C_id () const
	Get the C id object. More...

auto	get_refcount ()
	Get the reference count of object. More...

virtual bool	is_valid () const
	Check if the object is still valid. More...

void	close ()
	Close function which takes care of correctly closing the object and managing the reference counter. More...

void	bind_to (hid_t id, std::function< herr_t(hid_t) > closing_func, std::string path={})
	Open the object and bind it to a HDF5 object identified by 'id' with name 'path'. Object should be created beforehand. More...

	HDFObject ()
	Construct HDFObject from the given arguments. More...

	HDFObject (HDFObject &&other)
	Construct HDFObject by moving. More...

	HDFObject (const HDFObject &other)=default
	Construct HDFObject by copying another object. More...

	HDFObject (hid_t id, std::function< herr_t(hid_t) > closing_func, std::string path={})
	Construct HDFObject from the given argument. More...

HDFObject &	operator= (const HDFObject &other)
	Copy assignment operator. More...

HDFObject &	operator= (HDFObject &&other)
	move assignment operator More...

virtual	~HDFObject ()
	Destroy the HDFObject object. Has to be implemented in subclass! More...

Private Member Functions
template<typename result_type >
void	__create_attribute__ (hsize_t typesize=0)
	private helper function for creation of attribute More...

template<typename Type >
herr_t	__write_container__ (Type attribute_data)
	Function for writing containers as attribute. More...

template<typename Type >
herr_t	__write_stringtype__ (Type attribute_data)

template<typename Type >
herr_t	__write_pointertype__ (Type attribute_data)

template<typename Type >
herr_t	__write_scalartype__ (Type attribute_data)

template<typename Type >
herr_t	__read_container__ (Type &buffer)

template<typename Type >
auto	__read_stringtype__ (Type &buffer)

template<typename Type >
auto	__read_pointertype__ (Type buffer)

template<typename Type >
auto	__read_scalartype__ (Type &buffer)

Private Attributes
std::vector< hsize_t >	_shape
	size of the attributes dataspace More...

HDFIdentifier	_parent_identifier
	Identifier of the parent object. More...

HDFDataspace	_dataspace
	Dataspace object that manages topology of data written and read. More...

HDFType	_type
	type done in the HDFAttribute More...

Additional Inherited Members
Static Public Attributes inherited from Utopia::DataIO::HDFObject< HDFCategory::attribute >
static constexpr HDFCategory	category
	Named variable for template arg. More...

Protected Attributes inherited from Utopia::DataIO::HDFObject< HDFCategory::attribute >
HDFIdentifier	_id
	Identifier object that binds an instance of this class to an HDF5 object. More...

std::string	_path
	Name of the object. More...

std::shared_ptr< spdlog::logger >	_log
	pointer to the logger for dataio More...

Detailed Description

Class for hdf5 attribute, which can be attached to groups and datasets.

Template Parameters

HDFObject the object class

Member Typedef Documentation

◆ Base

using Utopia::DataIO::HDFAttribute::Base = HDFObject< HDFCategory::attribute >

alias base class

Constructor & Destructor Documentation

◆ HDFAttribute() [1/4]

Utopia::DataIO::HDFAttribute::HDFAttribute ( )

default

Default constructor, deleted because of reference member.

◆ HDFAttribute() [2/4]

Utopia::DataIO::HDFAttribute::HDFAttribute ( const HDFAttribute & other )

default

Copy constructor.

Parameters

other The other

◆ HDFAttribute() [3/4]

Utopia::DataIO::HDFAttribute::HDFAttribute ( HDFAttribute && other )

default

Move constructor.

Parameters

other The other

◆ ~HDFAttribute()

virtual Utopia::DataIO::HDFAttribute::~HDFAttribute ( )

inlinevirtual

Destructor.

◆ HDFAttribute() [4/4]

template<HDFCategory cat>

Utopia::DataIO::HDFAttribute::HDFAttribute	(	const HDFObject< cat > &	object,
		std::string	name
	)

inline

Constructor for attribute.

Parameters

object	the object to create the attribute at
name	the name of the attribute
size	the size of the attribute if known, else 1

Member Function Documentation

◆ __create_attribute__()

template<typename result_type >

void Utopia::DataIO::HDFAttribute::__create_attribute__ ( hsize_t typesize = 0 )

inlineprivate

private helper function for creation of attribute

Parameters

[in] typesize The typesize

Template Parameters

result_type Type of the resulting attribute

Returns: hid_t

◆ __read_container__()

template<typename Type >

herr_t Utopia::DataIO::HDFAttribute::__read_container__ ( Type & buffer )

inlineprivate

◆ __read_pointertype__()

template<typename Type >

auto Utopia::DataIO::HDFAttribute::__read_pointertype__ ( Type buffer )

inlineprivate

◆ __read_scalartype__()

template<typename Type >

auto Utopia::DataIO::HDFAttribute::__read_scalartype__ ( Type & buffer )

inlineprivate

◆ __read_stringtype__()

template<typename Type >

auto Utopia::DataIO::HDFAttribute::__read_stringtype__ ( Type & buffer )

inlineprivate

◆ __write_container__()

template<typename Type >

herr_t Utopia::DataIO::HDFAttribute::__write_container__ ( Type attribute_data )

inlineprivate

Function for writing containers as attribute.

Only buffers if necessary, i.e. if non-vector containers or nested containers or containers of strings have to be written.

◆ __write_pointertype__()

template<typename Type >

herr_t Utopia::DataIO::HDFAttribute::__write_pointertype__ ( Type attribute_data )

inlineprivate

◆ __write_scalartype__()

template<typename Type >

herr_t Utopia::DataIO::HDFAttribute::__write_scalartype__ ( Type attribute_data )

inlineprivate

◆ __write_stringtype__()

template<typename Type >

herr_t Utopia::DataIO::HDFAttribute::__write_stringtype__ ( Type attribute_data )

inlineprivate

◆ close()

void Utopia::DataIO::HDFAttribute::close ( )

inline

closes the attribute

◆ get_filespace()

HDFDataspace Utopia::DataIO::HDFAttribute::get_filespace ( )

inline

Get the file-dataspace object.

Returns: HDFDataspace

◆ get_parent_id()

HDFIdentifier Utopia::DataIO::HDFAttribute::get_parent_id ( )

inline

Get the hdf5 identifier to which the attribute belongs.

Returns: weak pointer to HDFObject

◆ get_shape()

auto Utopia::DataIO::HDFAttribute::get_shape ( )

inline

Get the shape object.

Returns: std::vector<hsize_t>

◆ get_type()

auto Utopia::DataIO::HDFAttribute::get_type ( )

inline

Get the type object.

Returns: hid_t

◆ open() [1/2]

void Utopia::DataIO::HDFAttribute::open	(	const HDFIdentifier &	parent,
		std::string	name
	)

inline

Open a new attribute on HDFObject 'parent' with name 'name'.

Parameters

parent	HDFIdentifier to open the attribute on
name	The attribute's name

◆ open() [2/2]

template<HDFCategory cat>

void Utopia::DataIO::HDFAttribute::open	(	const HDFObject< cat > &	parent,
		std::string	name
	)

inline

Open a new attribute on HDFObject 'parent' with name 'name'.

Parameters

parent	HDFObject to open the attribute on
name	The attribute's name

◆ operator=() [1/2]

HDFAttribute& Utopia::DataIO::HDFAttribute::operator= ( const HDFAttribute & other )

default

Copy assignment operator.

Parameters

other Object to copy assign from

Returns: HDFAttribute&

◆ operator=() [2/2]

HDFAttribute& Utopia::DataIO::HDFAttribute::operator= ( HDFAttribute && other )

default

Attribute move assignment operator.

Parameters

other Object to move assing from

Returns: HDFAttribute&

◆ read() [1/2]

template<typename Type >

auto Utopia::DataIO::HDFAttribute::read ( )

inline

Reads data from attribute, and returns the data and its shape in the form of a hsize_t vector.

This function has a quirk:

N-dimensional data are read into 1d arrays, and the shape has to be used to regain the original layout via index arithmetic.

Depending on the type 'Type', the data will be returned as:

if Type is a container other than vector: Will throw runtime_error
if Type is a vector or vector of vectors: Will return this, filled with data
if Type is a stringtype, i.e. char*, const char*, std::string: Will return std::string
if Type is a plain type, will return plain type
if Type as a pointer type, it will return a shared_ptr, i.e. Type = double*, return will be std::shared_ptr<double>;

Template Parameters

Type	which can hold elements in the attribute and which will be returned

Returns: tuple containing (shape, data)

◆ read() [2/2]

template<typename Type >

void Utopia::DataIO::HDFAttribute::read ( Type & buffer )

inline

Reads data from attribute into a predefined buffer, and returns the data and its shape in the form of a hsize_t vector. User is responsible for providing a buffer which can hold the data and has the correct shape!

Template Parameters

Type	which can hold elements in the attribute and which will be returned

◆ swap()

void Utopia::DataIO::HDFAttribute::swap ( HDFAttribute & other )

inline

Exchange states between caller and argument.

Parameters

other

◆ write() [1/2]

template<typename Iter , typename Adaptor >

void Utopia::DataIO::HDFAttribute::write	(	Iter	begin,
		Iter	end,
		Adaptor	adaptor = `[](auto& value) { return value; }`,
		[[maybe_unused] ] std::vector< hsize_t >	shape = `{}`
	)

inline

Function for writing data to the attribute.

Template Parameters

Iter	Iterator type
Adaptor	Adaptor which allows for extraction of a value from compound types, i.e. classes or structs

Parameters

begin	Start of iterator range
end	End of iterator range
adaptor	Function which turns the elements of the iterator into the objects to be written. Should (auto&) argument (simplest), but else must have (typename Iter::value_type&) argument

◆ write() [2/2]

template<typename Type >

void Utopia::DataIO::HDFAttribute::write	(	Type	attribute_data,
		std::vector< hsize_t >	shape = `{}`
	)

inline

Function for writing data to the attribute.

Template Parameters

Type	Automatically determined type of the data to write

Parameters

attribute_data	Data to write
shape	Layout of the data, i.e. {20, 50} would indicate a 2d array like int a[20][50]; The parameter has only to be given if the data to be written is given as plain pointers, because the shape cannot be determined automatically then.
typelen	If the elements of the data to be written are arrays of equal length, and the data should be written as 1d attribute, then we can give the length of the arrays in order to speed up the memory allocation and avoid unecessary buffering. This can be useful for grids for instance.

Member Data Documentation

◆ _dataspace

HDFDataspace Utopia::DataIO::HDFAttribute::_dataspace

private

Dataspace object that manages topology of data written and read.

◆ _parent_identifier

HDFIdentifier Utopia::DataIO::HDFAttribute::_parent_identifier

private

Identifier of the parent object.

◆ _shape

std::vector< hsize_t > Utopia::DataIO::HDFAttribute::_shape

private

size of the attributes dataspace

◆ _type

HDFType Utopia::DataIO::HDFAttribute::_type

private

type done in the HDFAttribute

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

include/utopia/data_io/hdfattribute.hh

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ Base

Constructor & Destructor Documentation

◆ HDFAttribute() [1/4]

◆ HDFAttribute() [2/4]

◆ HDFAttribute() [3/4]

◆ ~HDFAttribute()

◆ HDFAttribute() [4/4]

Member Function Documentation

◆ __create_attribute__()

◆ __read_container__()

◆ __read_pointertype__()

◆ __read_scalartype__()

◆ __read_stringtype__()

◆ __write_container__()

◆ __write_pointertype__()

◆ __write_scalartype__()

◆ __write_stringtype__()

◆ close()

◆ get_filespace()

◆ get_parent_id()

◆ get_shape()

◆ get_type()

◆ open() [1/2]

◆ open() [2/2]

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ read() [1/2]

◆ read() [2/2]

◆ swap()

◆ write() [1/2]

◆ write() [2/2]

Member Data Documentation

◆ _dataspace

◆ _parent_identifier

◆ _shape

◆ _type