Convert HDF5 file to other formats

Question

I am having a few big files sets of HDF5 files and I am looking for an efficient way of converting the data in these files into XML, TXT or some other easily readable format. I tried working with the Python package (www.h5py.org), but I was not able to figure out any methods with which I can get this stuff done fast enough. I am not restricted to Python and can also code in Java, Scala or Matlab. Can someone give me some suggestions on how to proceed with this?

Thanks,

TM

Answer 1

You can use h5dump -o dset.asci -y -w 400 dset.h5

• -o dset.asci specifies the output file
• -y -w 400 specifies the dimension size multiplied by the number of positions and spaces needed to print each value. You should take a very large number here.
• dset.h5 is of course the hdf5 file you want to convert

I think this is the easiest way to convert it to an ascii file, which you can import to excel or whatever you want. I did it a couple of times, and it worked for me. I got his information from this website.

Answer 2

Mathias711's method is the best direct way. If you want to do it within python, then use pandas.HDFStore:

from pandas import HDFStore

store = HDFStore('inputFile.hd5')

store['table1Name'].to_csv('outputFileForTable1.csv')