hdfwriter

A tableio plugin for writing HDF5 files.

Usage

I3HDFTableService provides output to HDF5 tables. Use it like any other writer service:

from icecube import icetray
from I3Tray import I3Tray
from icecube.tableio import I3TableWriter
from icecube.hdfwriter import I3HDFTableService

tray = I3Tray()
tray.AddModule('I3Reader','reader',filename = 'foo.i3.gz')

hdf = I3HDFTableService('foo.hd5')

tray.AddModule(I3TableWriter,'writer',
               tableservice = hdf,
               keys         = ['LineFit','InIceRawData']
              )

tray.AddModule('TrashCan','yeswecan')
tray.Execute()
tray.Finish()

Reading with pytables

I3HDFTableService creates a flat structure of tables under the file root. Since the HDF5 high-level Table API does not explicitly support units and docstrings, these are stored in the attributes FIELD_N_UNIT and FIELD_N_DOC for each field N. Support for reading these attributes is provided by the hdfwriter.pytables_ext module:

In [1]: from icecube.hdfwriter import pytables_ext
In [2]: import tables
In [3]: f=tables.openFile('foo.hdf5')
In [4]: f.root.LineFit.coldoc
Out[4]:
['run number',
 'event number',
 'object was found in the frame',
 'x-position of particle',
 'y-position of particle',
 'z-position of particle',
 'origin time of particle',
 'zenith angle of particle origin',
 'azimuthal angle of particle origin',
 'energy of particle',
 'particle speed',
 'length of track',
 '',
 '',
 '',
 '']
In [5]: f.root.LineFit.colunits
Out[5]:
['',
 '',
 'bool',
 'm',
 'm',
 'm',
 'ns',
 'radian',
 'radian',
 'GeV',
 'Gm/s',
 'm',
 '',
 '',
 '',
 '']

Using the built-in HDF5 libraries on your system

If your system comes with HDF5 libraries, it is better to use the system-provided ones rather than those in I3_PORTS, particularly if you’re using a system-provided build of pytables. You can tell cmake to use the system libraries using the SYSTEM_PACKAGES option.