Ticket #2 (new defect)

Opened 2 years ago

Converting ASCII column separated values to hdf5

Reported by: emuller Assigned to: somebody
Priority: major Milestone:
Component: component1 Version:
Keywords: Cc:

Description

How to convert a table of values with columns separated by commas/tabs to hdf5?

Given the following example text file: 

v ge gi
0.1 0.2 0.3
0.11 0.22 0.33
0.111 0.222 0.333

Assume it is stored locally as "data.txt" 

import tables
import pylab

# load the text file, skipping the "labels" row
d = pylab.load('data.txt',skiprows=1)

# get column names from first line
column_names = [x.strip() for x in file('data.txt').readline().split(' ')]

# open new file in write mode
h5 = tables.openFile('data.h5','w')

# write columns

for i,name in enumerate(column_names):
    h5.createArray('/',name,d[:,i])

h5.close()

# read it back

h5 = tables.openFile('data.h5')

ge = h5.root.ge.read()
gi = h5.root.gi.read()
v = h5.root.v.read()

h5.close()