tutorial.rst

Tutorial

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

In [0]: class Snek:

...: def __init__(self, length): ...: self.length = length ...: def __repr__(self): ...: return '≻:' + '=' * self.length + '>···' ...:

In [0]: Snek(10)

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 :pyh5py.File<File> or :pyh5py.Group<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.

Note

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 [0]: from fsc.hdf5_io import subscribe_hdf5, HDF5Enabled

In [0]: @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 [0]: HDF5Snek(12)

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 [0]: from fsc.hdf5_io import save, load

In [0]: from tempfile import NamedTemporaryFile

In [0]: mysnek = HDF5Snek(12)

In [0]: with NamedTemporaryFile() as f:

...: save(mysnek, f.name) ...: snek_clone = load(f.name)

In [0]: snek_clone

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

In [0]: with NamedTemporaryFile() as f:

...: save([HDF5Snek(2), HDF5Snek(4)], f.name) ...: snek_2, snek_4 = load(f.name)

In [0]: 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 [0]: from fsc.hdf5_io import SimpleHDF5Mapping

In [0]: @subscribe_hdf5('my_snek_module.simplified_snek')

...: class SimplifiedHDF5Snek(Snek, SimpleHDF5Mapping): ...: HDF5_ATTRIBUTES = ['length']

In [0]: new_snek = SimplifiedHDF5Snek(9)

In [0]: with NamedTemporaryFile() as f:

...: save(new_snek, f.name) ...: new_snek_clone = load(f.name)

In [0]: new_snek_clone

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

In [0]: @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 [0]: snek_with_friends = SnekWithFriends(3, friends=[mysnek, new_snek])

In [0]: snek_with_friends

In [0]: snek_with_friends.friends

In [0]: with NamedTemporaryFile() as f:

...: save(snek_with_friends, f.name) ...: snek_with_friends_clone = load(f.name)

In [0]: snek_with_friends_clone

In [0]: snek_with_friends_clone.friends