Converting from ASCII to hdf5, h5fromtxt?

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1

Hi everyone

I'm trying to convert an ASCII data file (/m rows x n columns/) to an hdf5
file. I've read about h5fromtxt but it only seems to get data from standard
input (console). Is it possible to pass an ASCII file as input to h5fromtxt?

Thanks in advance

···

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2

pacomet wrote:

Hi everyone

I'm trying to convert an ASCII data file (/m rows x n columns/) to an hdf5
file. I've read about h5fromtxt but it only seems to get data from standard
input (console). Is it possible to pass an ASCII file as input to h5fromtxt?

Greetings,

Try h5import.

If you need to do even moderate manipulation or parsing of the ASCII file you should consider using Python with h5py/numpy. This is what I use now instead of h5import.

--dan

···

Thanks in advance

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Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
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--
Daniel Kahn
Science Systems and Applications Inc.
301-867-2162

3

If this helps, here is a simple command line converter:
If it is made executable, it acts as expected. It requires NumPy and h5py.

Pierre

#!/usr/bin/env python
from sys import argv

if (__name__=="__main__"):
     if (len(argv)<3):
         print "Usage: ascii_data_to_h5.py 'file with ascii tabular data' outfile.h5"
         print "This program converts ascii data to a HDF5 file."
         exit()
     import numpy as np
     import h5py
     data = np.loadtxt(argv[1])
     h5file = h5py.File(argv[2],'w')
     h5file['data'] = data
     h5file.close()

···

Le 18 août 11 à 10:24, Daniel Kahn a écrit :

pacomet wrote:

Hi everyone

I'm trying to convert an ASCII data file (/m rows x n columns/) to an hdf5
file. I've read about h5fromtxt but it only seems to get data from standard
input (console). Is it possible to pass an ASCII file as input to h5fromtxt?

Greetings,

Try h5import.

If you need to do even moderate manipulation or parsing of the ASCII file you should consider using Python with h5py/numpy. This is what I use now instead of h5import.

--dan

Thanks in advance

--
View this message in context: http://hdf-forum.184993.n3.nabble.com/Converting-from-ASCII-to-hdf5-h5fromtxt-tp3264997p3264997.html
Sent from the hdf-forum mailing list archive at Nabble.com.

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

--
Daniel Kahn
Science Systems and Applications Inc.
301-867-2162

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org

-----------------------------------------------------------
Pierre de Buyl
Chemical Physics Theory Group - University of Toronto
Physique des Systèmes Complexes et Mécanique Statistique - Université Libre de Bruxelles
web: http://homepages.ulb.ac.be/~pdebuyl/
Tel: +1-416-946-0047
-----------------------------------------------------------

4

Thanks Pierre

Your script works fine and now I can convert any txt to h5.

Pacomet

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