Pandas can't read hdf5 file created with h5py
I've worked a little on the pytables module in pandas.io and from what I know pandas interaction with HDF files is limited to specific structures that pandas understands. To see what these look like, you can try
import pandas as pdimport numpy as nppd.Series(np.zeros((3,5),dtype=np.float32).to_hdf('test.h5','test')If you open 'test.h5' in HDFView, you will see a path /test with 4 items that are needed to recreate the DataFrame.
So I think your only option for reading in NumPy arrays is to read them in directly and then convert these to Pandas objects.