blech_hdf5_repack.py

import os
import tables
import easygui

# Get directory where the hdf5 file sits, and change to that directory
dir_name = easygui.diropenbox()
os.chdir(dir_name)

# Look for the hdf5 file in the directory
file_list = os.listdir('./')
hdf5_name = ''
for files in file_list:
	if files[-2:] == 'h5':
		hdf5_name = files

# Use ptrepack to save a clean and fresh copy of the hdf5 file as tmp.hf5
os.system("ptrepack --chunkshape=auto --propindexes --complevel=9 --complib=blosc " + hdf5_name + " " +  "tmp.h5")

# Delete the old hdf5 file
os.remove(hdf5_name)

# And rename the new file with the same old name
os.rename("tmp.h5", hdf5_name)