Storing Pandas objects along with regular Python objects in HDF5

hdf5, pandas, python

Solution

Here's the example from the cookbook: http://pandas.pydata.org/pandas-docs/stable/cookbook.html#hdfstore

You can store arbitrary objects as the attributes of a node. I belive there is a 64kb limit (I think its total attribute data for that node). The objects are pickled

In [1]: df = DataFrame(np.random.randn(8,3))

In [2]: store = HDFStore('test.h5')

In [3]: store['df'] = df

# you can store an arbitrary python object via pickle
In [4]: store.get_storer('df').attrs.my_attribute = dict(A = 10)

In [5]: store.get_storer('df').attrs.my_attribute
{'A': 10}

Problem

Pandas has a nice interface that facilitates storing things like Dataframes and Series in an HDF5: ``` random_matrix = np.random.random_integers(0,10, m_size) my_dataframe = pd.DataFrame(random_matrix) store = pd.HDFStore('some_file.h5',complevel=9, complib='bzip2') store['my_dataframe'] = my_dataframe store.close() ``` But if I try to save some other regular Python objects in the same file, it complains: ``` my_dictionary = dict() my_dictionary['a'] = 2 # <--- ERROR my_dictionary['b'] = [2,3,4] store['my_dictionary'] = my_dictionary store.close() ``` with ``` TypeError: cannot properly create the storer for: [_TYPE_MAP] [group->/par ameters (Group) u'',value-><type 'dict'>,table->None,append->False,kwargs- >{}] ``` How can I store regular Python data structures in the same HDF5 where I store other Pandas objects ?

Original source