principia_materia.io_interface.hdf5_wrapper module

class principia_materia.io_interface.hdf5_wrapper.HDF5Wrapper(title=None)

Bases: BaseDataWrapper

Save/load data in/from HDF5 file.

A object oriented wrapper to save and load data in and from HDF5 files. This allows us to easily save some custom defined data types into HDF5 supported types.

Parameters:

title (str, default to None) – A comment description for the file. The title is not used when saving/loading HDF5 files.

add_item(key, choices=None, dtype=None, load_dtype=None, save_dtype=None, optional=False)

Add an item of data to the container.

Parameters:

  • key (str) – The name of the item to be save in the data file.

  • dtype (str, default to None) – Data type of the item. The corresponding save/load functions will be used to save/load the item.

  • load_dtype (str or callable, default to None) – The function to load the item.

  • save_dtype (str or callable, default to None) – The function to save the item.

  • optional (bool, default to False) – Whether the item is optional.

  • help (str, default to None) – The description of the item.

  • alias (list of str, default to None) – A list aliases of the item keyword.

  • depends (list of str, default to None) – The keywords that are required when the item is present.

dump(data, filename, allow_missing=False, overwrite=False)

Save data into HDF5 file.

Parameters:

  • data (dict) – The dictionary containing data to be saved.

  • filename (str) – The name of the file to save the data into,

  • allow_missing (bool, optional, default to False) – Whether to allow a declared key not to exists in the data dictionary.

  • overwrite (bool, optional, default to False) – When the file exists, whether to replace the content of the file with the content to be saved.

dump_h5file(data, h5file, allow_missing=False)

Save data into HDF5 through a h5py.File/h5py.Group object.

This allows us to save data into a HDF5 group within a HDF5 file.

Parameters:

  • data (dict) – The dictionary containing data to be saved.

  • h5file (h5py.File/h5py.Group object) – The h5py.File/h5py.Group object to save the data into.

  • allow_missing (bool, optional, default to False) – Whether to allow a declared key not to exists in the data dictionary.

dumps(data, allow_missing=False)

Dump the data into string

Parameters:

  • data (dict) – The dictionary containing data to be saved.

  • allow_missing (bool, optional, default to False) – Whether to allow a declared key not to exists in the data dictionary.

load(filename, allow_missing=False)

Load data from HDF5 file

Parameters:

  • filename (str) – The name of the file to save the data into,

  • allow_missing (bool, optional, default to False) – Whether to allow a declared key not to exists in the data dictionary.

load_h5file(h5file, allow_missing=False)

Load data from HDF5 through a h5py.File/h5py.Group object.

This allows us to load data from a HDF5 group within a HDF5 file.

Parameters:

  • h5file (h5py.File/h5py.Group object) – The h5py.File/h5py.Group object to save the data into.

  • allow_missing (bool, optional, default to False) – Whether to allow a declared key not to exists in the data dictionary.

loads(text, allow_missing=False, allow_unknown=False, load_unknown=False)

Load the data from a string

Parameters:

  • text (str) – Data in text format,

  • allow_missing (bool, optional, default to False) – Whether to allow a declared key not to exists in the data dictionary.

  • allow_unknown (bool, optional, default to False) – Whether to allow keys not declared in the container. Though even if allowed, those keys will not be loaded if load_unknown == False.

  • load_unknown (bool, optional, default to False) – Whether to load keys not declared in the container to be loaded in raw.