Question

How to (1) batch select all arrays under a hdf5 file, then (2) apply calculations on those arrays and finally (3) batch create new arrays in another hdf5 file?

for example:

import numpy
import tables

file = openFile('file1',"r")

array1 = file.root.array1
array1_cal = (array1 <= 1)
newfile.createArray('/','array1_cal',array1_cal)

array2 = file.root.array2
array2_cal = (array2 <= 1)
newfile.createArray('/','array2_cal',array2_cal)

I have 100+ arrays under a single hdf5 file and several hdf5 files, how can I batch process them? Thanks a lot.

Answer 1

With PyTables you can use the walkNodes function to recursively iterate through nodes. Here is an example:

# Recursively print all the nodes hanging from '/detector'.
print "Nodes hanging from group '/detector':"
for node in h5file.walkNodes('/detector', classname='EArray'):
    data = node[:]
    // do some calculation 
    // store new array in second file