Dataspaces

An important concept in HDF5 are dataspaces. A dataspace describes the layout of dataelements (which are described by a datatype) on disk as well as in memory. In addition dataspaces are used to discribe selections in a dataset.

../_images/hdf5_dataspaces.svg

Currently two of the three dataspaces available in HDF5 are implemented in h5cpp

Dataspaces and related classes can be cound in namespace hdf5::dataspace. As shown above all dataspace classes derive from a common base class hdf5::dataspace::Dataspace which can be passed around whenever a dataspace is needed and the particular type is not relevant.

Dataspace inquery

The hdf5::dataspace::Dataspace class provides a couple of common inquery methods.

class Dataspace
size_t size()

returns the number of elements which can be stored in a dataspace independent of whether a selection has been applied or not.

Type type()

returns the type of the dataspace instance

The hdf5::dataspace::Type identifies the particular type of the dataspace there is currently

enum class Type
enumerator SIMPLE

for a simple datatype

enumerator SCALAR

for a scalar datatype

See Dataspace conversion for a good example of how to use the Dataspace::type() and the Type enumeration.

The scalar dataspace

A scalar dataspace can, as the name already suggests, store a single data element. Its construction is thus fairly easy

namespace hdf5;

dataspace::Scalar space;

A valid scalar dataspace can easily instantiated using the default constructor as there is nothing special to be set.

The simple dataspace

A simple dataspace can describe a multidimensional array of data elements. Such a dataspace has two basic properties

  • the rank of the dataspace which is the number of dimensions

  • and the dimensions which is the number of elements along each dimension.

In h5cpp a simple dataspace can be constructed using the hdf5::dataspace::Simple class. There are basically three configurations we could use

  • a dataspace of fixed size

  • an extensible dataspace with bounded maximum dimensions

  • an extensible dataspace with unbounded maximum dimensions

To create a simple dataspace with fixed dimensions use

using namespace hdf5;

dataspace::Simple space({2,3});

Dimensions current = space.current_dimensions(); // {2,3}
Dimensions maximum = space.maximum_dimensions(); // {2,3} too
../_images/static_dataspace.svg

which will result in a dataspace of rank 2 with 6 elements. To build an extensible dataspace with fixed bounds we could use

using namespace hdf5;

dataspace::Simple space({2,3},{10,10});

space.current_dimensions(); // {2,3}
space.maximum_dimensions(); // {10,10}
../_images/dynamic_dataspace_bounded.svg

Finally, for an extensible dataspace with an unlimited number of elements along a dimension we could use

using namespace hdf5;

dataspace::Simple space({1},{dataspace::Simple::UNLIMITED});
../_images/dynamic_dataspace_unbounded.svg

The initial size of the dataspace would be 1. However, we could extend it as much as we want (basically can). We will see later how to use this feature along with datasets.

A simple dataspace can be completely modified during the lifetime of an instance. For instance

using namespace hdf5;

dataspace::Simple space({3}); // rank=1,size=3
space.dimensions({2,3},{5,10}); // rank=2,size=6

Dataspace conversion

For all dataspace classes it is possible to construct a new instance from an instance of hdf5::dataspace::Dataspace as they provide a special conversion copy constructor

using namespace hdf5;

dataspace::Dataspace &general_dataspace = ...;
dataspace::Simple simple_dataspace(general_dataspace);

Using the inquery functions one could for instance use this along with an STL container to obtain all simple dataspaces in a collection sdfsdfsf

using namespace hdf5::dataspace;

std::vector<Dataspace> all_dataspaces = ...;
std::vector<Simple> simple_dataspaces;

std::copy_if(all_dataspaces.begin(),all_dataspaces.end(),
             std::back_inserter(simple_dataspaces),
             [](const Dataspace &space)
             {
                return space.type() == Type::SIMPLE;
             });