Well, it's a bit tricky to reproduce, because it is a conversion script from
the ROOT file format to pytables.
I'll try to reproduce it without the ROOT dependency.
For now, maybe the script itself can be of help.
convertChain.py reads a ROOT file and attempts to map the pytables structure
in CommonBaryonTuple.py
Cheers,
Jan
PS: The problem could also be related to my installation of pytables-1.4, so
I'll try that one again, too...
#!/usr/bin/env python2.4
from RootPython.Samples import RooTuple
from ROOT import SigmaPbarGammaEvent, CommonBaryonEvent
from ROOT import TVector3, TLorentzVector
from optparse import OptionParser
from tables import *
from numpy import array
import psyco
psyco.full()
def vector3_to_array(vector):
return array([vector.x(), vector.y(), vector.z()])
def vector4_to_array(vector):
return array([vector.T(), vector.X(), vector.Y(), vector.Z()])
def convertEventHeader(table, chain, event):
row = table.row
nEntries = chain.GetEntries()
print 'starting to convert file (%d Events)' % nEntries,
header = event.eventHeader
for iEv in xrange(nEntries):
if iEv % 500 == 0:
print '.',
chain.GetEntry(iEv)
row['eventCMS'] = vector4_to_array(header.eventCMS)
row['r2'] = header.r2
row['event_id'] = iEv
row['upperID'] = header.upperID
row['lowerID'] = header.lowerID
row.append()
table.attrs.nevents = chain.GetEntries()
table.flush()
def fillProperty(row, columnName, itemName, candidate):
if isinstance(itemName, tuple):
columnName += itemName[0] + '/'
daughter = candidate.__getattribute__(itemName[0])
for name in itemName[1]:
fillProperty(row, columnName, name, daughter)
elif isinstance(itemName, str):
columnName += itemName
if itemName in ('event_id', 'upperID', 'lowerID'):
return
data = candidate.__getattribute__(itemName)
if isinstance(data, TVector3):
row[columnName] = vector3_to_array(data)
elif isinstance(data, TLorentzVector):
row[columnName] = vector4_to_array(data)
else:
row[columnName] = data
else:
print "Unknown column type %s. This is bad !" % itemName
def convertB_Candidates(table, chain, event):
row = table.row
nEntries = chain.GetEntries()
print 'starting to convert file (%d Events)' % nEntries,
for iEv in xrange(nEntries):
if iEv % 500 == 0:
print '.',
chain.GetEntry(iEv)
bList = event.bList
upperID = event.eventHeader.upperID
lowerID = event.eventHeader.lowerID
for B in bList:
# just fill the Tuple with everything
# hopefully the attribute names are the same.
for item in table.colnames:
fillProperty(row, '', item, B)
row['event_id'] = iEv
row['upperID'] = upperID
row['lowerID'] = lowerID
row.append()
# this isn't really the correct number
table.attrs.nevents = chain.GetEntries()
table.flush()
print 'done'
def processSigmaSample(sample, candidate_class, event_class, baseDir='/data1/BaryonicPenguins/Analysis-32/RooTuples/SigmaTuples'):
s = RooTuple(sample, baseDir, SigmaPbarGammaEvent, 'SigmaPbarGammaAnalysis')
f = openFile('/u/br/jstrube/work/Tuples/%s_SigmaTuples.h5' % sample, 'w')
group = f.createGroup(f.root, 'events')
# be careful with the expected events. The number of B is not the number of events
# trick ROOT into telling us -- it's a hack but the best we can do here
s.chain.Draw('bList.mES >> dummy')
number_of_B = s.chain.GetSelectedRows()
print 'number of B:', number_of_B, 'total events:', s.chain.GetEntries()
candidates = f.createTable(group, 'B_candidates', candidate_class, 'reconstructed B candidates', filters=Filters(complevel=9, complib='lzo'), expectedrows=number_of_B)
events = f.createTable(group, 'eventHeader', event_class, 'event information', filters=Filters(complevel=9, complib='lzo'), expectedrows=s.chain.GetEntries())
candidates.attrs.reconstruction = '%s_Sigma' % sample
convertB_Candidates(candidates, s.chain, s.event)
convertEventHeader(events, s.chain, s.event)
f.close()
def processLambdaSample(sample, candidate_class, event_class, baseDir='/data1/BaryonicPenguins/Analysis-32/RooTuples/LambdaTuples'):
s = RooTuple(sample, baseDir, CommonBaryonEvent, 'CommonBaryonAnalysis')
f = openFile('/u/br/jstrube/work/Tuples/%s_LambdaTuples.h5' % sample, 'w')
group = f.createGroup(f.root, 'events')
# be careful with the expected events. The number of B is not the number of events
# trick ROOT into telling us -- it's a hack but the best we can do here
s.chain.Draw('bList.mES >> dummy')
number_of_B = s.chain.GetSelectedRows()
print 'number of B:', number_of_B, 'total events:', s.chain.GetEntries()
candidates = f.createTable(group, 'B_candidates', candidate_class, 'reconstructed B candidates', filters=Filters(complevel=9, complib='lzo'), expectedrows=number_of_B)
candidates.attrs.reconstruction = '%s_Lambda' % sample
events = f.createTable(group, 'eventHeader', event_class, 'event information', filters=Filters(complevel=9, complib='lzo'), expectedrows=s.chain.GetEntries())
convertB_Candidates(candidates, s.chain, s.event)
convertEventHeader(events, s.chain, s.event)
f.close()
if __name__ == '__main__':
parser = OptionParser()
parser.add_option('-b', action='store_true', help='batch mode, passed on to ROOT')
parser.add_option('--sample', help='Select the id for the input sample')
parser.add_option('--mode', help='Select Lambda or Sigma0 reconstruction. Allowed values are "Lambda" and "Sigma0"')
parser.add_option('--directory', help='Base Directory for the files in the chain')
options, args = parser.parse_args()
if options.mode == 'Lambda':
modulename = 'TablePython.CommonBaryonTuple'
processor = processLambdaSample
elif options.mode == 'Sigma0':
modulename = 'TablePython.SigmaPbarGammaTuple'
processor = processSigmaSample
else:
parser.print_help()
parser.error('This is not a valid reconstruction mode. Aborting.')
tupleModule = __import__(modulename, globals(), locals(), ['B_Candidate'])
B_Candidate = vars(tupleModule)['B_Candidate']
Event = vars(tupleModule)['Event']
processor(options.sample, B_Candidate, Event, options.directory)
from tables import *
# note: inheritance from IsDescription does not copy columns
# this is a bug in pytables
class Event(IsDescription):
_v_flavor = "numpy"
event_id = UInt32Col(pos=0, indexed=True)
upperID = UInt32Col(pos=1, indexed=True)
lowerID = UInt32Col(pos=2, indexed=True)
# decayString = StringCol(500)
r2 = Float32Col(pos=3)
eventCMS = Float32Col(shape=4, pos=4)
class Baryon1(IsDescription):
_v_flavor = "numpy"
isTruthMatched = UInt8Col()
uid = UInt32Col()
mass = Float32Col()
chi2 = Float32Col()
nDOF = Int32Col()
decayLength = Float32Col()
decayLengthError = Float32Col()
decayVector = Float32Col(shape=3)
class Baryon2(IsDescription):
_v_flavor = "numpy"
isTruthMatched = UInt8Col()
uid = UInt32Col()
pidMask = Int32Col()
pidStatus = Int32Col()
pidWeight = Float32Col()
pidError = Float32Col()
class Gamma(IsDescription):
_v_flavor = "numpy"
isTruthMatched = UInt8Col()
uid = UInt32Col()
momentum = Float32Col(shape=3)
minNeutralDistance = Float32Col()
minTrackDistance = Float32Col()
minTrackDTheta = Float32Col()
bestEtaMass = Float32Col()
bestPi0Mass = Float32Col()
cmsEnergy = Float32Col()
labEnergy = Float32Col()
# Particle description
class B_Candidate(IsDescription):
_v_flavor = "numpy"
event_id = UInt32Col(indexed=True) # event id (indexed)
upperID = UInt32Col(indexed=True)
lowerID = UInt32Col(indexed=True)
isTruthMatched = UInt8Col()
momentum = Float32Col(shape=3) # momentum of the particle
mass = Float32Col() # mass of the particle
uid = UInt32Col()
charge = Int8Col()
chi2 = Float32Col()
nDOF = Int32Col()
legendreRatio = Float32Col()
decayLength = Float32Col()
decayLengthError = Float32Col()
decayVector = Float32Col(shape=3)
btaB_Status = Int32Col()
mES = Float32Col()
mMiss = Float32Col()
deltaE = Float32Col()
Gamma = Gamma()
Baryon1 = Baryon1()
Baryon2 = Baryon2()
-------------------------------------------------------------------------
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