Working with files

Todo

For the time being, h5cpp provides no interface to the metadata cache. This feature might be added in future.

The first things you have to do when using HDF5 is to create a new file or open an already existing one. This chapter deals with this very basic topic. Unlike in the C-API filenames are not represented by mere strings but by instances of boost::filesystem::path. This avoids problems when using different seperator characters in a path on different platforms. Additionally a file system path has a particular semantic which is not reflecetd by a simple string.

Identifying an HDF5 file

Before opening an HDF5 file we should check whether or not the filesystem object referenced by boost::filesystem::path is indeed an HDF5 file. The simpliest way to achieve this goal is to use the hdf5::file::is_hdf5_file() utiltiy function function.

boost::filesystem::path file_path = ...;

if(!hdf5::file::is_hdf5_file(file_path))
{
   //deal with the error situation
}

//continue with opening the file

Creating files

The first thing one may wants to do is to create a new file. Use the hdf5::file::create() function

#include <h5cpp/hdf5.hpp>
#include <boost/filesystem.hpp>

using namespace hdf5;
using namespace fs = boost::filesystem;

int main()
{
  //creating a new file
  fs::path file_path("data.h5");
  file::File f1 = file::create(file_path);

  //do something with the file
}

By default, the hdf5::file::create() function will throw an exception if the file already exists. To overwrite an already existing file use

file::File f1 = file::create(file_path,file::AccessFlags::Truncate);

HDF5 uses property lists to pass additional information to API functions. The hdf5::file::create() function accepts two additional arguments

• a reference to a file creation property list (hdf5::property::FileCreateList)

• and a reference to a file access property list (hdf5::property::FileAccessList)

There are several situations when you have to use these property lists to create a file. The most common might be

• you want better control over object and link iteration

• you want to use the SWMR feature introduced with HDF5 1.10.

We will deal with the iterator problem a bit later. For now we have a look on the SWMR feature. Provided you link h5cpp against HDF5 1.10.0 or higher you have to provide a custom file access property list

property::FileCreationList fcpl; //can use the default here
property::FileAccessList fapl;

//we need to set the appropriate version flags
fapl.library_version_bounds(property::LibVersion::Latest,
                            property::LibVersion::Latest);

file::File f = file::create("swmr_file.h5",
                            file::AccessFlags::Truncate,
                            fcpl,fapl);

Opening an existing file

To open a file use the hdf5::file::open() function

#include <h5cpp/hdf5.hpp>
#include <boost/filesystem.hpp>

using namespace hdf5;
using namespace fs = boost::filesystem;

int main()
{
  //creating a new file
  fs::path file_path("data.h5");
  file::File f1 = file::open(file_path);

  //do something with the file
}

By default, files are opened in read only mode to avoid accidental modification of the file. To write to an existing file use

file::File f1 = file::open(file_path,file::AccessFlags::ReadWrite);

The only additional argument hdf5::file::open() takes is a reference to file access property list. We have to use this to open a file for SWMR access. However, in addition we need some custom flags to use SWMR. To open a file for writing in SWMR mode use

property::FileAccessList fapl;
//we need to set the appropriate version flags
fapl.library_version_bounds(property::LibVersion::Latest,
                            property::LibVersion::Latest);

file::File write_fiel = file::open(file_path,
                                   file::AccessFlags::ReadWrite |
                                   file::AccessFlags::SWMRWrite,
                                   fapl);

and to open a file for reading in SWMR mode use

property::FileAccessList fapl;
//we need to set the appropriate version flags
fapl.library_version_bounds(property::LibVersion::Latest,
                            property::LibVersion::Latest);

file::File write_fiel = file::open(file_path,
                                   file::AccessFlags::ReadOnly |
                                   file::AccessFlags::SWMRRead,
                                   fapl);

Getting access to the object tree

Unlike in the C-API an instance of hdf5::File is not a valid parent object. For this purpose the root group of the file must be obtained using the File::root() method of a file instance

hdf5::file::File f = ....;
hdf5::node::Group root_group = f.root();

Rational

Though in the C-API the ID of a group and a file can both act as valid parent object, this approach does not run well with an object oriented appraoch. It would mean that hdf5::file::File and hdf5::node::Gruop would have to provide a common, group-like interface.

In order to avoid code duplications we hdf5::file::File would have to derive from hdf5::node::Group making it also a valid group object. From the point of semantics this is simply wrong. A file is not a group.

Though the approach choosen here requires a single line of code more to obtain the root group of a file before doing any useful work on the file, however, I think a clean difference between hdf5::file::File and hdf5::node::Group is worth the additional effort.