This is obvious, but it is important to remember.
import pandas as pd, pylab, cProfile def create_file(): r = pylab.randn(10000,1000) p = pd.DataFrame(r) with pd.get_store('test.h5','w') as store: store['data'] = p def analyze(p): return [(p[c] > 0).size for c in [0,1,2,3,4,5,6,7,8,9]] def copy1(): print 'Working on copy of data' with pd.get_store('test.h5','r') as store: p = store['data'] idx = analyze(p) print idx def copy2(): print 'Working on copy of data' with pd.get_store('test.h5','r') as store: idx = analyze(store['data']) print idx def ref(): print 'Working on hdf5 store reference' with pd.get_store('test.h5','r') as store: idx = [(store['data'][c] > 0).size for c in [0,1,2,3,4,5,6,7,8,9]] print idx #create_file() cProfile.run('copy1()') cProfile.run('copy1()') cProfile.run('copy2()') cProfile.run('ref()')When run with
python test.py | grep "function calls"
gives us
5340 function calls (5256 primitive calls) in 0.094 seconds 2080 function calls (2040 primitive calls) in 0.048 seconds 2080 function calls (2040 primitive calls) in 0.050 seconds 5661 function calls (5621 primitive calls) in 0.402 secondsSo, if you are going to do multiple operations on the data in a node it is better to copy it over once (if you have the memory).
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