In this tutorial we’ll see how to add HDF5 serialization to classes. Let’s start with defining a simple class:

In [1]: class Snek:
   ...:     def __init__(self, length):
   ...:         self.length = length
   ...:     def __repr__(self):
   ...:         return '≻:' + '=' * self.length + '>···'

In [2]: Snek(10)
Out[2]: ≻:==========>···

To make this Snek HDF5 serializable, we need to answer these questions three:

  1. How is the Snek serialized to HDF5?
  2. How is the HDF5 converted back into a Snek?
  3. What is your favourite colour the unique tag identifying the Snek class?

To define how the Snek is serialized to HDF5, we add a to_hdf5 method. This method is passed a hdf5_handle, which is a h5py.File or h5py.Group defining the (current) root of the HDF5 file where the object should be added.

For de-serialization, the from_hdf5 classmethod should be implemented. Again, this method is passed a hdf5_handle. It should return the deserialized object.

Finally, the subscribe_hdf5() class decorator is used to define a unique type_tag which identifies this class.


The type_tag needs to be unique across all projects using fsc.hdf5_io. For this reason, you should always prepend it with the name of your module.

In [3]: from fsc.hdf5_io import subscribe_hdf5, HDF5Enabled

In [4]: @subscribe_hdf5('my_snek_module.snek')
   ...: class HDF5Snek(Snek, HDF5Enabled):
   ...:     def to_hdf5(self, hdf5_handle):
   ...:         hdf5_handle['length'] = self.length
   ...:     @classmethod
   ...:     def from_hdf5(cls, hdf5_handle):
   ...:         return cls(hdf5_handle['length'][()])

In [5]: HDF5Snek(12)
Out[5]: ≻:============>···

Notice also that we inherit from HDF5Enabled. This abstract base class checks for the existence of the HDF5 (de-)serialization functions, and adds methods to_hdf5_file and from_hdf5_file to save and load directly to a file.

Now we can use the save() and load() methods to save and load Sneks in HDF5 format:

In [6]: from fsc.hdf5_io import save, load

In [7]: from tempfile import NamedTemporaryFile

In [8]: mysnek = HDF5Snek(12)

In [9]: with NamedTemporaryFile() as f:
   ...:     save(mysnek, f.name)
   ...:     snek_clone = load(f.name)

In [10]: snek_clone
Out[10]: ≻:============>···

You can also save and load lists or dictionaries containing Sneks:

In [11]: with NamedTemporaryFile() as f:
   ....:     save([HDF5Snek(2), HDF5Snek(4)], f.name)
   ....:     snek_2, snek_4 = load(f.name)

In [12]: print(snek_2, snek_4)
≻:==>··· ≻:====>···

A common use case is to serialize all the attributes of an object, a base class SimpleHDF5Mapping exists for this case. A subclass needs to define a lists HDF5_ATTRIBUTES of attributes that should be serialized. The attribute names must be the same as the arguments accepted by the constructor.

We can re-write the Snek as

In [13]: from fsc.hdf5_io import SimpleHDF5Mapping

In [14]: @subscribe_hdf5('my_snek_module.simplified_snek')
   ....: class SimplifiedHDF5Snek(Snek, SimpleHDF5Mapping):
   ....:     HDF5_ATTRIBUTES = ['length']

In [15]: new_snek = SimplifiedHDF5Snek(9)

In [16]: with NamedTemporaryFile() as f:
   ....:     save(new_snek, f.name)
   ....:     new_snek_clone = load(f.name)

In [17]: new_snek_clone
Out[17]: ≻:=========>···

We can extend the Snek functionality by adding a list of friends:

In [18]: @subscribe_hdf5('my_snek_module.snek_with_friends')
   ....: class SnekWithFriends(SimplifiedHDF5Snek):
   ....:     HDF5_ATTRIBUTES = SimplifiedHDF5Snek.HDF5_ATTRIBUTES + ['friends']
   ....:     def __init__(self, length, friends):
   ....:         super().__init__(length)
   ....:         self.friends = friends

In [19]: snek_with_friends = SnekWithFriends(3, friends=[mysnek, new_snek])

In [20]: snek_with_friends
Out[20]: ≻:===>···

In [21]: snek_with_friends.friends
Out[21]: [≻:============>···, ≻:=========>···]

In [22]: with NamedTemporaryFile() as f:
   ....:     save(snek_with_friends, f.name)
   ....:     snek_with_friends_clone = load(f.name)

In [23]: snek_with_friends_clone
Out[23]: ≻:===>···

In [24]: snek_with_friends_clone.friends
Out[24]: [≻:============>···, ≻:=========>···]