Utopia
2
Framework for studying models of complex & adaptive systems.
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Namespaces | |
_chunk_helpers | |
_DMUtils | |
Default | |
Detail | |
GraphLoad | |
GraphUtilsHelper | |
Classes | |
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... | |
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... | |
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 | TaskFactory |
Functor for building a writetask from arguments. 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 | 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... | |
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 | MonitorTimer |
The MonitorTimer keeps track of the time when to emit monitor data. More... | |
class | MonitorManager |
The MonitorManager manages the monitor entries and MonitorTimer. More... | |
class | Monitor |
The Monitor monitors entries that are emitted if a given time has passed. More... | |
Typedefs | |
using | Config = YAML::Node |
Type of a variadic dictionary-like data structure used throughout Utopia. More... | |
Enumerations | |
enum class | TypeTag { plain , vertex_property , edge_property , vertex_descriptor , 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 class | HDFCategory { file = H5I_FILE , group = H5I_GROUP , datatype = H5I_DATATYPE , dataspace = H5I_DATASPACE , dataset = H5I_DATASET , 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. More... | |
std::string | to_string (const Config &node) |
Given a config node, returns a string representation of it. More... | |
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_. More... | |
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. More... | |
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. More... | |
std::string | get_abs_filepath (const Config &cfg) |
Extracts an absolute file path from a configuration. More... | |
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. More... | |
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. More... | |
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. More... | |
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. More... | |
void | swap (HDFDataset &lhs, HDFDataset &rhs) |
Exchange state between lhs and rhs. More... | |
void | swap (HDFDataspace &lhs, HDFDataspace &rhs) |
Swap states of lhs and rhs. More... | |
void | swap (HDFGroup &lhs, HDFGroup &rhs) |
Swap lhs and rhs. More... | |
bool | operator== (const HDFIdentifier &lhs, const HDFIdentifier &rhs) |
Comparsion operator for equality. More... | |
bool | operator!= (const HDFIdentifier &lhs, const HDFIdentifier &rhs) |
Comparsion operator for inequality. More... | |
void | swap (HDFIdentifier &lhs, HDFIdentifier &rhs) |
Exchange the states of lhs and rhs. More... | |
template<HDFCategory cat> | |
void | swap (HDFObject< cat > &lhs, HDFObject< cat > &rhs) |
Exchange state of lhs and rhs. More... | |
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. More... | |
bool | operator!= (const HDFType &lhs, const HDFType &rhs) |
TODO. More... | |
bool | check_validity (htri_t valid, const std::string_view object_name) |
Check for validity of a hdf5 htri_t type or similar. More... | |
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. More... | |
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. More... | |
template<HDFCategory category> | |
std::string | category_to_string () |
Turn category enum into a string that names it. More... | |
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. More... | |
template<typename Object > | |
hid_t | open_dataspace (Object &&object) |
Depending on object category, opens a dataset or attribute dataspace. More... | |
template<typename Object > | |
hid_t | open_type (Object &&object) |
Depending on object category, invokes H5Dget_type or H5Aget_type. More... | |