hdfdict helps h5py to dump and load python dictionaries

If you have a hierarchical data structure of e.g. numpy arrays in a dictionary for example, you can use this tool to save this dictionary into a h5py File() or Group() and load it again. This tool just maps the hdf Groups to dict keys and the Datset to dict values. Only types supported by h5py can be used. The dictionary-keys need to be strings.

A lazy loading option is activated per default. So big h5 files are not loaded at once. Instead, a dataset gets only loaded if it is accessed from the LazyHdfDict instance.

Datetimes are serialized as isoformat from version 0.5.0 on. You won't notice that directly on the python side but e.g. timezone aware datetimes would be also loaded as timezone aware again.

You should be aware of the fact, that load will not return exactly the same types as you put them into the dump function. Many types are loaded by h5py as numpy types and will not be changed by hdfdict to the original type.

Example

import hdfdict
import numpy as np


d = {
    'a': np.random.randn(10),
    'b': [1, 2, 3],
    'c': 'Hallo',
    'd': np.array(['a', 'b']).astype('S'),
    'e': True,
    'f': (True, False),
}
fname = 'test_hdfdict.h5'
hdfdict.dump(d, fname)
res = hdfdict.load(fname)

print(res)

Output: {'a': <HDF5 dataset "a": shape (10,), type "<f8">, 'b': <HDF5 dataset "b": shape (3,), type "<i8">, 'c': <HDF5 dataset "c": shape (), type "|O">, 'd': <HDF5 dataset "d": shape (2,), type "|S1">, 'e': <HDF5 dataset "e": shape (), type "|b1">, 'f': <HDF5 dataset "f": shape (2,), type "|b1">}

This are all lazy loding fields in the result res. Just call res.unlazy() or dict(res) to get all fields loaded. If you only want to load specific fields, just use item access e.g. res['a'] so only field 'a' will be loaded from the file.

print(dict(res))

Output: {'a': array([ 1.20991242, 0.74938763, -0.02199212, -0.08664085, -0.11950787, -0.12527781, -1.26821192, -1.20105904, -0.37933725, -0.16289392]), 'b': [1, 2, 3], 'c': 'Hallo', 'd': array([b'a', b'b'], dtype='|S1'), 'e': True, 'f': (True, False)}

Installation

• pip install git+https://github.com/SiggiGue/hdfdict.git