Test speed of data retrieval from HDF5 file. UPDATED with absolute/relative path comparison.

PyTables_speed_test.py

# It seems slightly faster to skip getting the groups/tables

import timeit

r = timeit.Timer(stmt="read = tables.openFile('Angle_120301_120314.h5', 'r');"
                      "group = read.root.s503;"
                      "blobs = group.blobs;"
                      "events = group.events;"
                      "event = events[-1];"
                      "trace_id = event['traces'];"
                      "trace = [zlib.decompress(blobs[trace_id[0]]).split(','),"
                               "zlib.decompress(blobs[trace_id[1]]).split(','),"
                               "zlib.decompress(blobs[trace_id[2]]).split(','),"
                               "zlib.decompress(blobs[trace_id[3]]).split(',')];"
                      "read.close()",
                 setup='import tables; import zlib')
min(r.repeat(2000, 1))
# 0.000643014907836914 (absolute path)
# 0.004560947418212891 (relative path)


r_direct = timeit.Timer(stmt="read = tables.openFile('Angle_120301_120314.h5', 'r');"
                             "event = read.root.s503.events[-1];"
                             "trace_id = event['traces'];"
                             "trace = [read.root.s503.blobs[trace_id[0]],"
                                      "read.root.s503.blobs[trace_id[1]],"
                                      "read.root.s503.blobs[trace_id[2]],"
                                      "read.root.s503.blobs[trace_id[3]]];"
                             "read.close()",
                        setup='import tables')
min(r_direct.repeat(2000, 1))
# 0.0005998611450195312 (absolute path)
# 0.0045261383056640625 (relative path)

setup = """
import tables
def get_trace():
    read = tables.openFile('Angle_120301_120314.h5', 'r')
    event = read.root.s503.events[-1]
    trace_id = event['traces']
    trace = [read.root.s503.blobs[trace_id[0]],
            read.root.s503.blobs[trace_id[1]],
            read.root.s503.blobs[trace_id[2]],
            read.root.s503.blobs[trace_id[3]]]
    read.close()"""

r_function = timeit.Timer(stmt="get_trace()", setup=setup)
min(r_function.repeat(2000, 1))
# 0.000604152679443359 (absolute path)
# 0.004538059234619141 (relative path)