namespace for node like objects and related functions

Classes
class	ChunkedDataset
	dataset with chunked layout More...

class	Dataset

class	Group

class	GroupView
	base class for group views More...

class	LinkTarget
	link target descriptor More...

class	Link
	an HDF5 link More...

class	LinkIterator

class	LinkView

class	Node

class	NodeIterator
	bidirectional NodeIterator More...

class	NodeView

class	RecursiveLinkIterator
	recursive Link iterator More...

class	RecursiveNodeIterator
	recursive node iterator More...

class	VirtualDataset
	virtual dataset class More...

Typedefs
using	Type = NodeType
	alias type to ensure compatibility with existing code More...

Enumerations
enum class	NodeType : std::underlying_type< H5O_type_t >::type { Unknown = H5O_TYPE_UNKNOWN , Group = H5O_TYPE_GROUP , Dataset = H5O_TYPE_DATASET , Datatype = H5O_TYPE_NAMED_DATATYPE }
	enumeration for node type More...

enum class	LinkType : std::underlying_type< H5L_type_t >::type { Hard = H5L_TYPE_HARD , Soft = H5L_TYPE_SOFT , External = H5L_TYPE_EXTERNAL , Error = H5L_TYPE_ERROR }
	link type enumeration More...

Functions
void	resize_by (const Dataset &dataset, size_t dimension_index, ssize_t delta)
	resize a dataset by a particular offset More...

void	copy (const Node &source, const Group &base, const Path &relative_path, const property::ObjectCopyList &ocpl=property::ObjectCopyList(), const property::LinkCreationList &lcpl=property::LinkCreationList())
	copy node object More...

void	copy (const Node &source, const Group &destination, const property::ObjectCopyList &ocpl=property::ObjectCopyList(), const property::LinkCreationList &lcpl=property::LinkCreationList())
	copy node object More...

void	move (const Node &source, const Group &base, const Path &relative_path, const property::LinkCreationList &lcpl=property::LinkCreationList(), const property::LinkAccessList &lapl=property::LinkAccessList())
	move node object More...

void	move (const Node &source, const Group &destination, const property::LinkCreationList &lcpl=property::LinkCreationList(), const property::LinkAccessList &lapl=property::LinkAccessList())
	move node object More...

void	remove (const Group &base, const Path &object_path, const property::LinkAccessList &lapl=property::LinkAccessList())
	remove node from group More...

void	remove (const Node &object, const property::LinkAccessList &lapl=property::LinkAccessList())
	remove node from group More...

void	link (const Node &target, const Group &link_base, const Path &link_path, const property::LinkCreationList &lcpl=property::LinkCreationList(), const property::LinkAccessList &lapl=property::LinkAccessList())
	Create a soft or external link. More...

void	link (const Path &target_path, const Group &link_base, const Path &link_path, const property::LinkCreationList &lcpl=property::LinkCreationList(), const property::LinkAccessList &lapl=property::LinkAccessList())
	Create a soft link. More...

void	link (const fs::path &target_file, const Path &target_path, const Group &link_base, const Path &link_path, const property::LinkCreationList &lcpl=property::LinkCreationList(), const property::LinkAccessList &lapl=property::LinkAccessList())
	Create an external link. More...

Node	get_node (const Group &base, const Path &node_path, const property::LinkAccessList &lapl=property::LinkAccessList())
	get node More...

Group	get_real_base (const Group &base, const Path &path, const property::LinkAccessList &lapl=property::LinkAccessList())
	get real base of path More...

Group	get_group (const Group &base, const Path &path, const property::LinkAccessList &lapl=property::LinkAccessList())
	get group More...

Dataset	get_dataset (const Group &base, const Path &path, const property::LinkAccessList &lapl=property::LinkAccessList())
	get dataset More...

bool	is_group (const Node &node)
	predicate function returning true if node is a group More...

bool	is_dataset (const Node &node)
	predicate function returning true if a node is a dataset More...

bool	operator!= (const Link &lhs, const Link &rhs)

std::ostream &	operator<< (std::ostream &stream, const Link &link)

bool	operator== (const Node &lhs, const Node &rhs)

bool	operator!= (const Node &lhs, const Node &rhs)

std::ostream &	operator<< (std::ostream &stream, const NodeType &type)
	output stream operator for the NodeType enumeration More...

std::ostream &	operator<< (std::ostream &stream, const LinkType &type)
	output stream operator for the link type enumeration More...

Typedef Documentation

◆ Type

using hdf5::node::Type = typedef NodeType

This alias ensures, that existing code still using the old Type enumeration type is still working. Since NodeType and Type are equivalent from a structural point of view this should be no issue.

Enumeration Type Documentation

◆ LinkType

enum hdf5::node::LinkType : std::underlying_type< H5L_type_t >::type

strong

Enumeration type to distinguish the various link types in HDF5.

Enumerator
Hard
Soft
External
Error

◆ NodeType

enum hdf5::node::NodeType : std::underlying_type< H5O_type_t >::type

strong

Enumerator
Unknown
Group
Dataset
Datatype

Function Documentation

◆ copy() [1/2]

void hdf5::node::copy	(	const Node &	source,
		const Group &	base,
		const Path &	relative_path,
		const property::ObjectCopyList &	ocpl = `property::ObjectCopyList()`,
		const property::LinkCreationList &	lcpl = `property::LinkCreationList()`
	)

Copy source object to a new relative_path under base Group. If an object of same name already exists an exception will be thrown.

The copy operation should also work across file boundaries. In all cases the source object as well as the destination group must exist.

Parameters

source	object to be copied
base	the destination base group where the new copy will be stored
relative_path	the destination relative path under the base group
ocpl	optional object copy property list
lcpl	optional link creation property list

Exceptions

std::runtime_error in case of a failure

◆ copy() [2/2]

void hdf5::node::copy	(	const Node &	source,
		const Group &	destination,
		const property::ObjectCopyList &	ocpl = `property::ObjectCopyList()`,
		const property::LinkCreationList &	lcpl = `property::LinkCreationList()`
	)

Copy source object to a new location under destination Group using the original object's name. For instance, if we have

source path /detector/data
destination path /recorded/detectors

then the copy will appear as /recorded/detectors/data. If an object of same name already exists an exception will be thrown.

The copy operation should also work across file boundaries. In all cases the source object as well as the destination group must exist.

Parameters

source	object to be copied
destination	the destination group where the new copy will be stored
ocpl	optional object copy property list
lcpl	optional link creation property list

Exceptions

std::runtime_error in case of a failure

◆ get_dataset()

Dataset hdf5::node::get_dataset	(	const Group &	base,
		const Path &	path,
		const property::LinkAccessList &	lapl = `property::LinkAccessList()`
	)

A convenience function for get_node. Returns a Dataset instance if the node referenced by path is a dataset, otherwise throws an exception. Use this function whenever you want to work with a Dataset temporarily.

For instance

Group root = file.root();

Dataspace space = get_dataset(root,"run_01/sensors/temperature").dataspace();

hdf5::node::Dataset::dataspace

dataspace::Dataspace dataspace() const

get dataspace of dataset

hdf5::file::SearchFlags::Group

@ Group

hdf5::node::get_dataset

Dataset get_dataset(const Group &base, const Path &path, const property::LinkAccessList &lapl=property::LinkAccessList())

get dataset

Exceptions

std::runtime_error in case of a failure

Parameters

base	base group
path	path to dataset
lapl	optional link access property list

Returns: new Group instance

See also: get_node; get_dataset

◆ get_group()

Group hdf5::node::get_group	(	const Group &	base,
		const Path &	path,
		const property::LinkAccessList &	lapl = `property::LinkAccessList()`
	)

A convenience function for get_node. Returns a Group instance if the node referenced by path is a group, otherwise throws an exception. Use this function whenever you want to work with a Group temporarily.

For instance

Group root = file.root();
if(get_group(root,"run_01/sensors").nodes.size()!=0)
{
 
}

Exceptions

std::runtime_error in case of a failure

Parameters

base	base group
path	path to group
lapl	optional link access property list

Returns: new Group instance

See also: get_node; get_dataset

◆ get_node()

Node hdf5::node::get_node	(	const Group &	base,
		const Path &	node_path,
		const property::LinkAccessList &	lapl = `property::LinkAccessList()`
	)

Get a node from a base group.

Exceptions

std::runtime_error in case of a failure

Parameters

base	reference to the base group
node_path	reference to the path of the node
lapl	optional link access property list

Returns: new node instance

◆ get_real_base()

Group hdf5::node::get_real_base	(	const Group &	base,
		const Path &	path,
		const property::LinkAccessList &	lapl = `property::LinkAccessList()`
	)

Helper function to facilitate a number of convenience functions in the wrapper. Gets the most proximate parent Group of path. If path is absolute, base will only be used to obtain the root node of the file. If the parent node does not exist or is not a Group, an exception will be thrown.

Exceptions

std::runtime_error in case of a failure

Parameters

base	base group for link
path	path of desired node
lapl	optional link access property list

Returns: most recent parent Group of path

◆ is_dataset()

bool hdf5::node::is_dataset ( const Node & node )

This predicate function is used to filter dataset nodes. A typical application would be for instance

std::vector<Dataset> datasets;

std::copy_if(root.nodes.begin(),root.nodes.end(),std::back_inserter(datasets),is_dataset);

hdf5::node::is_dataset

bool is_dataset(const Node &node)

predicate function returning true if a node is a dataset

or whenever you want to partition a vector

std::vector<Nodes> nodes;
std::copy(root.nodes.begin(),root.nodes.end(),std::back_inserter(nodes));
auto first_group = std::partition_by(nodes.begin(),nodes.end(),is_dataset);

Exceptions

std::runtime_error in case of a failure

Parameters

node	reference to the node

Returns: true if the node is a dataset, false otherwise

◆ is_group()

bool hdf5::node::is_group ( const Node & node )

This predicate function is used to filter group nodes. A typical application would be for instance

std::vector<Group> groups;

std::copy_if(root.nodes.begin(),root.nodes.end(),std::back_inserter(groups),is_group);

hdf5::node::is_group

bool is_group(const Node &node)

predicate function returning true if node is a group

or whenever you want to partition a vector

std::vector<Node> nodes;
std::copy(root.nodes.begin(),root.nodes.end(),std::back_inserter(nodes));
auto first_dset = std::partition_by(nodes.begin(),nodes.end(),is_group);

Exceptions

std::runtime_error in case of a failure

Parameters

node	reference to the node

Returns: true if the node is a group, false otherwise

◆ link() [1/3]

void hdf5::node::link	(	const fs::path &	target_file,
		const Path &	target_path,
		const Group &	link_base,
		const Path &	link_path,
		const property::LinkCreationList &	lcpl = `property::LinkCreationList()`,
		const property::LinkAccessList &	lapl = `property::LinkAccessList()`
	)

Create an external link to an object stored in a different file. The target object is determined by the target file and an absolute path within this file. The location of the link is given by a base group and a relative or absolute path. If link_path is a relative path the new link will be relative to link_base. Otherwise link_base is only used to determine the root group (and thus the file within which the link is placed).

Exceptions

std::runtime_error in case of a failure

Parameters

target_file	the file where the link target is stored
target_path	absolute path to the object which we want to reference in the target file
link_base	base group for the link
link_path	absolute or relative path to the new link
lcpl	optional link creation property list
lapl	optional link access property list

Precondition: target_path must be an absolute path; link_base must be a valid HDF5 object

◆ link() [2/3]

void hdf5::node::link	(	const Node &	target,
		const Group &	link_base,
		const Path &	link_path,
		const property::LinkCreationList &	lcpl = `property::LinkCreationList()`,
		const property::LinkAccessList &	lapl = `property::LinkAccessList()`
	)

Create a link from link_path under link_base to object at target_path under target_base. A soft link will be created if link_base and target_base reside in the same file. Otherwise an external link is created.

The target for the link is determined by target_base and target_path. If the latter one is a relative path the target location is assumed relative to target_base. If it is an absolute path, target_base is used to retrieve the root group of the specific file.

Parameters

target	the target node (could also be path here?)
link_base	the base group for the link location
link_path	path to the new link (either relative or absolute)
lcpl	optional link creation property list
lapl	optional link access property list

◆ link() [3/3]

void hdf5::node::link	(	const Path &	target_path,
		const Group &	link_base,
		const Path &	link_path,
		const property::LinkCreationList &	lcpl = `property::LinkCreationList()`,
		const property::LinkAccessList &	lapl = `property::LinkAccessList()`
	)

Create a link from link_path under link_base to object at target_path. The object at target_path need not already exist at this time.

If the target_path is a relative path the target location is assumed relative to link_base. If absolute, the path is assumed to be on the same file as link_base.

Parameters

target_path	the target node (could also be path here?)
link_base	the base group for the link location
link_path	path to the new link (either relative or absolute)
lcpl	optional link creation property list
lapl	optional link access property list

◆ move() [1/2]

void hdf5::node::move	(	const Node &	source,
		const Group &	base,
		const Path &	relative_path,
		const property::LinkCreationList &	lcpl = `property::LinkCreationList()`,
		const property::LinkAccessList &	lapl = `property::LinkAccessList()`
	)

Move source object to a new relative_path under base Group. If an object of same name already exists an exception will be thrown. In all cases the source object as well as the destination group must exist.

Parameters

source	object to be moved
base	the destination base group where the object will be moved
relative_path	the destination relative path under the base group
lcpl	optional link creation property list
lapl	optional link access property list

Exceptions

std::runtime_error in case of a failure

◆ move() [2/2]

void hdf5::node::move	(	const Node &	source,
		const Group &	destination,
		const property::LinkCreationList &	lcpl = `property::LinkCreationList()`,
		const property::LinkAccessList &	lapl = `property::LinkAccessList()`
	)

Move source object to a new location under destination Group using the original object's name. For instance, if we have

source path /detector/data
destination path /recorded/detectors

then the moved object will appear as /recorded/detectors/data. If an object of same name already exists an exception will be thrown. In all cases the source object as well as the destination group must exist.

Parameters

source	object to be moved
destination	the new group where the object should be located
lcpl	optional link creation property list
lapl	optional link access property list

Exceptions

std::runtime_error in case of a failure

◆ operator!=() [1/2]

bool hdf5::node::operator!=	(	const Link &	lhs,
		const Link &	rhs
	)

◆ operator!=() [2/2]

bool hdf5::node::operator!=	(	const Node &	lhs,
		const Node &	rhs
	)

◆ operator<<() [1/3]

std::ostream& hdf5::node::operator<<	(	std::ostream &	stream,
		const Link &	link
	)

◆ operator<<() [2/3]

std::ostream& hdf5::node::operator<<	(	std::ostream &	stream,
		const LinkType &	type
	)

This operator writes a textual representation of the link type to the output stream.

Parameters

stream	refernce to the output stream
type	reference to the link type

Returns: modified output stream

◆ operator<<() [3/3]

std::ostream& hdf5::node::operator<<	(	std::ostream &	stream,
		const NodeType &	type
	)

This operator writes a text representation of the node type to the output stream.

Parameters

stream	reference to the output stream
type	the actual type to write to the stream

Returns: modified output stream

◆ operator==()

bool hdf5::node::operator==	(	const Node &	lhs,
		const Node &	rhs
	)

◆ remove() [1/2]

void hdf5::node::remove	(	const Group &	base,
		const Path &	object_path,
		const property::LinkAccessList &	lapl = `property::LinkAccessList()`
	)

Removes link at object_path within the base Group. If there are more references (links) to this particular object, they remain active. Additionally: removing an object entirely from an HDF5 file means removing all links to this object and thus rendering it inaccessible. No storage space in the file will be cleared. In order to reduce the size of the file h5repack must be used which will simply not copy objects which cannot be referenced.

Exceptions

std::runtime_error in case of a failure

Parameters

base	group relative to which the link or object resides
object_path	path relative to base determining the link or object to remove
lapl	optional link access property list

◆ remove() [2/2]

void hdf5::node::remove	(	const Node &	object,
		const property::LinkAccessList &	lapl = `property::LinkAccessList()`
	)

Removes link to object from parent Group via which it was accessed.

Exceptions

std::runtime_error in case of a failure

Parameters

object the object which to remove

Precondition: object must be a valid HDF5 object instance

Parameters

lapl	optional link access property list

See also: remove(const Node &base, const Path &object_path)

◆ resize_by()

void hdf5::node::resize_by	(	const Dataset &	dataset,
		size_t	dimension_index,
		ssize_t	delta
	)

Resizes a dataset along the dimension determined by dimension_index by delta elements. As delta is a signed integer one can either enlarge or shrink the dataset.

Parameters

dataset	reference to the dataset to resize
dimension_index	the index of the dimension to resize
delta	the number of elements about which the dataset should be resized

Exceptions

std::runtime_error in case of any failure

Classes

Typedefs

Enumerations

Functions

Typedef Documentation

◆ Type

Enumeration Type Documentation

◆ LinkType

◆ NodeType

Function Documentation

◆ copy() [1/2]

◆ copy() [2/2]

◆ get_dataset()

◆ get_group()

◆ get_node()

◆ get_real_base()

◆ is_dataset()

◆ is_group()

◆ link() [1/3]

◆ link() [2/3]

◆ link() [3/3]

◆ move() [1/2]

◆ move() [2/2]

◆ operator!=() [1/2]

◆ operator!=() [2/2]

◆ operator<<() [1/3]

◆ operator<<() [2/3]

◆ operator<<() [3/3]

◆ operator==()

◆ remove() [1/2]

◆ remove() [2/2]

◆ resize_by()