Utopia::DataIO Namespace Reference

Namespaces
namespace	_chunk_helpers
namespace	_DMUtils
namespace	Default
namespace	Detail
namespace	GraphLoad
namespace	GraphUtilsHelper

Classes
class	DataManager
	Manage different tasks of writing out data from a source in a uniform yet flexible way. This is a class which, when being supplied with appropriate callables, manages their execution. More...
class	DataManagerFactory
	Factory function which produces a Datamanager of type Default::DefaultDataManager<Model> from a config and argumets from which to construct writetasks. More...
struct	DataManagerTraits
	Type traits for the DataManager This allows to specify custom types for the DataManager. Usually, you only need to touch this if you do not want to use the defaults or if you want to need to explicitly specify a common base class because it cannot be deduced automatically. More...
struct	DatasetDescriptor
	Descriptor for a dataset. Contains: path: string giving the path of the dataset in its group or file with_time_postfix: whether the current model time is appended to the dataset path dataset_capacity: vector giving capacity of the dataset per dimension dataset_chunksize: vector giving chunksize per dimension of the dataset dataset_compression: integer giving compression strength (0 to 10) More...
class	HDFAttribute
	Class for hdf5 attribute, which can be attached to groups and datasets. More...
class	HDFBufferFactory
	Class which turns non-vector or plain-array containers into vectors. If the value_types are containers themselves, these are turned into vectors as well, because HDF5 cannot write something else. More...
class	HDFDataset
	Class representing a HDFDataset, wich reads and writes data and attributes. More...
class	HDFDataspace
	Class that wraps an HDF5 dataspace and takes care of managing its resources. More...
class	HDFFile
	Class representing a HDF5 file. More...
class	HDFGroup
	Class represting a HDFGroup, an object analogous to a folder for HDFFiles. More...
class	HDFIdentifier
	Wrapper class around an hdf5 identifier, used to manage reference counts of the object this identifier refers to. More...
class	HDFObject
	Common base class for all HDF5 classes in the DATAIO Module i.e., for all classes that wrap HDF5-C-Library functionality like HDFDataset, HDFGroup, HDFFile. This class is not intendet as something to be used independently, but only as a base class to be inherited from. More...
class	HDFType
	Class which handles the conversion of C-types into hdf5types. More...
struct	is_callable
	Test whether an object is callable. More...
class	Monitor
	The Monitor monitors entries that are emitted if a given time has passed. More...
class	MonitorManager
	The MonitorManager manages the monitor entries and MonitorTimer. More...
class	MonitorTimer
	The MonitorTimer keeps track of the time when to emit monitor data. More...
class	TaskFactory
	Functor for building a writetask from arguments. More...
struct	WriteTask
	Encapsulate a task for writing data to a destination. Containes a callable 'writer' responisible for writing data to a held dataset. Contains a callabel 'build_dataset' which builds or opens a dataset for writing to in a held HDFGroup. A WriteTask is bound to a group for its entire lifetime. More...

Typedefs
using	Config = YAML::Node
	Type of a variadic dictionary-like data structure used throughout Utopia.

Enumerations
enum struct	TypeTag {   TypeTag::plain , TypeTag::vertex_property , TypeTag::edge_property , TypeTag::vertex_descriptor ,   TypeTag::edge_descriptor }
	TypeTag enumerates the kind of access which is used to write data. It became necessary after integrating graphs. Has 5 values: plain : use for everything that is not a graph vertex_property : for writing graphs using boost::vertex_property edge_property : for writing graphs using boost::edge_property vertex_descriptor : for writing graphs using boost::vertex_descriptor edge_descriptor : for writing graphs using boost::edge_descriptor. More...
enum struct	HDFCategory {   HDFCategory::file = H5I_FILE , HDFCategory::group = H5I_GROUP , HDFCategory::datatype = H5I_DATATYPE , HDFCategory::dataspace = H5I_DATASPACE ,   HDFCategory::dataset = H5I_DATASET , HDFCategory::attribute = H5I_ATTR }
	Enumerate the different HDF5 object types for use in HDFObject class. More...

Functions
template<class Exc >
YAML::Exception	improve_yaml_exception (const Exc &e, const Config &node, std::string prefix={})
	Improves yaml-cpp exceptions occurring for a given node.
std::string	to_string (const Config &node)
	Given a config node, returns a string representation of it.
template<typename CVecT , DimType dim = 0>
CVecT	get_as_arma_vec (const std::string &key, const DataIO::Config &node)
	Retrieve a config entry as Armadillo column vector using get_.
template<class BGB , class DW , class DB , class AWG , class AWD >
void	swap (WriteTask< BGB, DW, DB, AWG, AWD > &lhs, WriteTask< BGB, DW, DB, AWG, AWD > &rhs)
	Swaps the state of lhs and rhs.
template<typename Basegroupbuilder , typename Writertype , typename Buildertype , typename AWritertypeG , typename AWritertypeD >
	WriteTask (Basegroupbuilder &&bgb, Writertype &&w, Buildertype &&b, AWritertypeG &&ad, AWritertypeD &&ag) -> WriteTask< std::decay_t< Basegroupbuilder >, std::decay_t< Writertype >, std::decay_t< Buildertype >, std::decay_t< AWritertypeG >, std::decay_t< AWritertypeD > >
std::string	expanduser (const std::string &path)
	Expands a path with a leading ~ character into an absolute path.
std::string	get_abs_filepath (const Config &cfg)
	Extracts an absolute file path from a configuration.
template<typename Graph >
std::shared_ptr< HDFGroup >	create_graph_group (const Graph &g, const std::shared_ptr< HDFGroup > &parent_grp, const std::string &name)
template<typename Graph >
void	save_graph (const Graph &g, const std::shared_ptr< HDFGroup > &grp)
	Write function for a boost::Graph.
template<typename Graph , typename PropertyMap >
void	save_graph (const Graph &g, const std::shared_ptr< HDFGroup > &grp, const PropertyMap vertex_ids)
	Write function for a boost::Graph.
template<IterateOver iterate_over, typename Graph , typename... Adaptors>
void	save_graph_entity_properties (const Graph &g, const std::shared_ptr< HDFGroup > &nw_grp, const std::string &label, const std::tuple< Adaptors... > &adaptor_tuple)
template<typename Graph , typename... Adaptors>
void	save_vertex_properties (Graph &&g, const std::shared_ptr< HDFGroup > &nw_grp, const std::string &label, const std::tuple< Adaptors... > &adaptor_tuple)
template<typename Graph , typename... Adaptors>
void	save_edge_properties (Graph &&g, const std::shared_ptr< HDFGroup > &nw_grp, const std::string &label, const std::tuple< Adaptors... > &adaptor_tuple)
void	swap (HDFAttribute &lhs, HDFAttribute &rhs)
	Swaps the states of Attributes rhs and lhs.
template<typename Cont = std::vector< hsize_t >>
const Cont	calc_chunksize (const hsize_t typesize, const Cont io_extend, Cont max_extend={}, const bool opt_inf_dims=true, const bool larger_high_dims=true, const unsigned int CHUNKSIZE_MAX=1048576, const unsigned int CHUNKSIZE_MIN=8192, const unsigned int CHUNKSIZE_BASE=262144)
	Try to guess a good chunksize for a dataset.
void	swap (HDFDataset &lhs, HDFDataset &rhs)
	Exchange state between lhs and rhs.
void	swap (HDFDataspace &lhs, HDFDataspace &rhs)
	Swap states of lhs and rhs.
void	swap (HDFGroup &lhs, HDFGroup &rhs)
	Swap lhs and rhs.
bool	operator== (const HDFIdentifier &lhs, const HDFIdentifier &rhs)
	Comparsion operator for equality.
bool	operator!= (const HDFIdentifier &lhs, const HDFIdentifier &rhs)
	Comparsion operator for inequality.
void	swap (HDFIdentifier &lhs, HDFIdentifier &rhs)
	Exchange the states of lhs and rhs.
template<HDFCategory cat>
void	swap (HDFObject< cat > &lhs, HDFObject< cat > &rhs)
	Exchange state of lhs and rhs.
bool	operator== (const HDFType &lhs, const HDFType &rhs)
	Check equality of argument typefactories. Two typefactories are considered equal when they refer to the same HDF5 type, e.g., H5T_INTEGER, or H5T_VLEN.
bool	operator!= (const HDFType &lhs, const HDFType &rhs)
	TODO.
bool	check_validity (htri_t valid, const std::string_view object_name)
	Check for validity of a hdf5 htri_t type or similar.
htri_t	path_exists (hid_t loc_id, std::string path, hid_t link_property_list=H5P_DEFAULT)
	Checks iteratively if each segment of a path exists.
auto	path_is_valid (hid_t id, std::string path)
	Check if the path given relative to the object identified by 'id' exists and points to a valid hdf5 object.
template<HDFCategory category>
std::string	category_to_string ()
	Turn category enum into a string that names it.
template<class Object >
std::string	generate_object_name (const Object &object)
	Use category and path variable of object to make a string that identifies the object it is applied to.
template<typename Object >
hid_t	open_dataspace (Object &&object)
	Depending on object category, opens a dataset or attribute dataspace.
template<typename Object >
hid_t	open_type (Object &&object)
	Depending on object category, invokes H5Dget_type or H5Aget_type.