def update(self,wsname,fname,storelist=[]):
"""Stores the current model (and observable) into a ROOT.Workspace,
persistified in a root file
Parameters
----------
wsname: str
Name to be given to the ROOT.Workspace
fname: str
Name to be given to the ROOT file
storelist: list(ROOT.RooDataSet,ROOT.RooRealVar,...), optional
List of RooFit objects to be stored in the same workspace
"""
import os
from ROOT import RooWorkspace, TFile
# Create the ws with the model and data available
w = RooWorkspace(wsname,'Workspace')
wsImport = getattr(w,'import')
# Put the models
for rawtuple in self.__models.values():
model = rawtuple[0]
anythingelse = rawtuple[1:]
wsImport(model)
# Put whatever the user want to store
for _item in storelist:
wsImport(_item)
# Check if the fname already exist
file_exist = os.path.isfile(fname)
if file_exist:
# Create a new auxiliar file, to provisionaly
# store the ws
auxfname = '_auxroot.root'
w.writeToFile(auxfname)
# Previously delete the old Workspace, if any
_rootfile = TFile(fname)
_rootfile.Delete(wsname+';*')
_rootfile.Delete("ProcessID*;*")
_rootfile.Close()
# Open the auxiliary file
_aux = TFile(auxfname)
# and copy the ws to the rootfile
w = _aux.Get(wsname)
# and copy the ws to the rootfile
w.writeToFile(fname,False)
if file_exist:
# And closing and removing auxfile
_aux.Close()
os.remove(auxfname)
def randomize_hists(filename, contains, seed=0):
print 'randomize hists in', filename,
work_file = TFile(filename, "UPDATE")
keys = work_file.GetListOfKeys()
hist_list = []
random.seed(seed)
for key in keys:
key = str(key.GetName())
#print key
if not contains in key: continue
hist = work_file.Get(key).Clone()
work_file.Delete(key + ';*')
for i in xrange(hist.GetNcells()):
error = hist.GetBinError(i)
#if error ==0 and hist.GetBinContent(i)==0: error =1
new = (random.random() * 2 - 1) * error + hist.GetBinContent(i)
m = 0
while (new < 0 and m < 1000):
m += 1
new = (random.random() * 2 - 1) * error + hist.GetBinContent(i)
if (new < 0): new = 0
print key, 'new content', new, 'old', hist.GetBinContent(
i), 'error', error
hist.SetBinContent(i, new)
hist_list.append(hist)
for item in hist_list:
item.Write()
def add_signal(fname, process, signal_file, signal, scale):
print 'adding signal', signal, ' with cross section', scale, 'to', process
print 'working file', fname, 'signal file', signal_file
signal_file = TFile(signal_file, 'READ')
work_file = TFile(fname, 'UPDATE')
keys = work_file.GetListOfKeys()
signal_keys = signal_file.GetListOfKeys()
original = []
for key in keys:
key = str(key.GetName())
if len(key.split('__')) > 3: continue
category = key.split("__")[0]
#print key, category
if '*' in process:
process_split = process.split('*')
if not all(part in key for part in process_split): continue
#print 'matched',process,'with',key
elif process not in key:
continue
for signal_key in signal_keys:
signal_key = str(signal_key.GetName())
#print 'comparing',key, signal_key
sig_cat = signal_key.split("__")[0]
#print signal, signal_key.split('__')[1]
if signal.replace('-',
'_') not in signal_key.split("__")[1].replace(
'-', '_'):
continue
#print category, sig_cat
if category == sig_cat:
print 'adding', signal_key, 'to', key
sig_hist = signal_file.Get(signal_key).Clone()
#original.append(work_file.Get(key).Clone(key))
#binning = get_binning(original[-1])
hist = work_file.Get(key).Clone(key)
work_file.Delete(key + ';*')
binning = get_binning(hist)
#print binning
if binning:
sig_hist = sig_hist.Rebin(
len(binning) - 1, key, array.array('d', binning))
sig_hist.Scale(scale)
#print 'adding',sig_hist.GetIntegral(), 'to', original[-1].GetIntegral()
#original[-1].Add(sig_hist)
hist.Add(sig_hist)
original.append(hist) #.Write('',TObject.kOverwrite)
break
signal_file.Close()
work_file.cd()
for item in original:
item.Write('') #,TObject.kOverwrite);
work_file.Close()
def rename_hists(filename, from_s, to_s):
print 'rename hists in', filename, 'from', from_s, 'to', to_s
work_file = TFile(filename, "UPDATE")
keys = work_file.GetListOfKeys()
hist_list = []
for key in keys:
key = str(key.GetName())
if from_s in key:
hist = work_file.Get(key).Clone(key.replace(from_s, to_s))
hist_list.append(hist)
work_file.Delete(key + ';*')
for item in hist_list:
item.Write()
def hist_title(filename, histtitel):
print 'rename hist titel in', filename, 'to', histtitel
work_file = TFile(filename, "UPDATE")
keys = work_file.GetListOfKeys()
hist_list = []
for key in keys:
key = str(key.GetName())
hist = work_file.Get(key).Clone()
work_file.Delete(key + ';*')
hist.SetTitle(histtitel)
hist_list.append(hist)
for item in hist_list:
item.Write()
work_file.Close()
def set_sqrt_errors(filename):
print 'sqrt error hists in', filename,
work_file = TFile(filename, "UPDATE")
keys = work_file.GetListOfKeys()
hist_list = []
for key in keys:
key = str(key.GetName())
#print key
hist = work_file.Get(key).Clone()
work_file.Delete(key + ';*')
for i in xrange(hist.GetNcells()):
hist.SetBinError(i, math.sqrt(hist.GetBinContent(i)))
hist_list.append(hist)
for item in hist_list:
item.Write()
def fixed_rebin(filename, rebin_values, hist_contains=''):
work_file = TFile(filename, "UPDATE")
keys = work_file.GetListOfKeys()
hists = []
for key in keys:
key = str(key.GetName())
if not hist_contains in key: continue
hists.append(work_file.Get(key).Clone())
if isinstance(rebin_values, (int, long)):
hists[-1] = hists[-1].Rebin(rebin_values)
else:
print rebin_values
hists[-1] = hists[-1].Rebin(len(rebin_values), hists[-1].GetName(),
array.array('d', rebin_values))
work_file.Delete(key + ';*')
for item in hists:
item.Write('', TObject.kOverwrite)
work_file.Close()
def blind_final(filename, obs, exp):
print 'starting to calculate chi2 for file', filename
work_file = TFile(filename, 'UPDATE')
keys = work_file.GetListOfKeys()
categories_done = []
hist_list = []
for key in keys:
key = str(key.GetName())
category = key.split("__")[0]
if category in categories_done: continue
exp_hist = work_file.Get(category + '__' + exp).Clone(category + '__' +
obs)
hist_list.append(exp_hist)
work_file.Delete(key + ';*')
categories_done.append(category)
for item in hist_list:
item.Write('', TObject.kOverwrite)
work_file.Close()
def copyOneFile(dataset):
# If the input and output files are defined outside the loop, histograms after the first instance are not found.
# I did not track down what the cause of this behavior was. --Wells
fin = TFile(condor_dir + "/pu.root", "READ")
fout = TFile(
os.environ['CMSSW_BASE'] +
"/src/OSUT3Analysis/Configuration/data/pu.root", "UPDATE")
print "Copying histogram " + dataset + " from " + fin.GetName(
) + " to " + fout.GetName()
fin.cd()
h = fin.Get(dataset)
if not h:
print " Could not find hist named " + dataset + " in " + fin.GetName()
return
fout.cd()
if dataset != h.GetName():
# print " Resetting name from " + h.GetName() + " to " + dataset
h.SetName(dataset)
# Check if the histogram already exists in the destination file
h2 = fout.Get(dataset)
if h2:
print " The histogram " + h2.GetName(
) + " already exists in the destination file."
overwrite = raw_input(" Do you want to overwrite it? (y/n): ")
if not (overwrite is "y"):
print " Will not overwrite existing histogram."
return # Only overwrite if the user enters "y"
# delete all previously existing instances of the histogram
print " Will overwrite existing histogram."
fout.Delete(dataset + ";*")
h.Write()
fin.Close()
fout.Close()
def scale_hists(fname, process, factors):
print 'scaling', fname, process
work_file = TFile(fname, 'UPDATE')
keys = work_file.GetListOfKeys()
hist_list = []
for key in keys:
key = str(key.GetName())
#if len(key.split('__'))>2: continue
category = key.split("__")[0]
if process not in key.split("__")[1]: continue
#print key, category
if (isinstance(factors, list)):
for factor in factors:
catname = factor[0]
catname = catname.replace('Anti-b-tag_rate', 'AntiBTag')
catname = catname.replace('1-b-tag_rate', '1_BTag')
catname = catname.replace('2-b-tag_rate', '2_BTag')
catname = catname.replace('W-tag_rate', 'WTag')
catname = catname.replace('top-tag_rate', 'TopTag')
#print category, catname
if catname in category:
print 'scaling', key, 'by', factor[1]
hist = work_file.Get(key)
hist.Scale(factor[1])
hist_list.append(hist)
work_file.Delete(key + ';*')
#hist.Write('',TObject.kOverwrite);
else:
print 'scaling', key, 'by', factors
hist = work_file.Get(key)
hist.Scale(factors)
hist_list.append(hist)
for item in hist_list:
item.Write('', TObject.kOverwrite)
item.SetDirectory(0)
work_file.Close()
del hist_list
# print h_Info[0],h_Info[1],h_Info[2]
# tree.Draw("%s>>%s_%s"%(h_Info[0],h_Info[1],sample),evtWeight)
tree.Draw("%s:%s>>%s_%s"%(h_Info[0],h_Info[1],h_Info[2],sample),evtWeight,"colz")
#outputFile = TFile(outputhistName,"update")
# if not onlyAddPlots:
# outputFile.rmdir(sample)
# outputFile.mkdir(sample)
# outputFile.cd(sample)
# for h in histograms:
# if onlyAddPlots:
# gDirectory.Delete("%s;*"%(h.GetName()))
# h.Write()
# outputFile.Close()
if not os.path.exists(outputhistName):
os.makedirs(outputhistName)
outputFile = TFile("%s/%s.root"%(outputhistName,sample),"update")
for h in histograms:
outputFile.Delete("%s;*"%h.GetName())
if onlyAddPlots:
gDirectory.Delete("%s;*"%(h.GetName()))
h.Write()
outputFile.Close()
r_values = []
output = output.splitlines()
output.sort()
for line in output:
for i in range(nBin):
if line.find('r_' + str(i) + ' ') != -1:
r_values.append(getValues(line.split()))
## Diff plots
h_diff_name = 'diff_' + observable
if asimov != '':
h_diff_name += '_' + asimov
h_uncor = TH1F(h_diff_name + '_uncorrelated', h_diff_name + '_uncorrelated',
nBin, 0, nBin)
for i in range(nBin):
h_uncor.SetBinContent(i + 1, r_values[i][1])
h_uncor.SetBinError(i + 1, r_values[i][3])
## Save plots
output_file = TFile('./results/histograms_24bins_time_' + year + '.root',
'UPDATE')
for l in output_file.GetListOfKeys():
if l.GetName() == h_diff_name + '_uncorrelated':
output_file.Delete(h_diff_name + '_uncorrelated' + ';1')
h_uncor.Write()
output_file.Close()
def AnalyseWaveforms(topology, PATH, PMT_data_filenames, root_filename,
pre_PULSE_region, waveform_length):
try: # Will not create a new file if one exists already
waveformfile = open(root_filename, "r")
print(">>> File exists")
except IOError:
print(">>> File not found")
print(">>> Creating .root file with the Average Waveforms")
root_file = TFile(root_filename, 'RECREATE')
# First create all the conatiners for the histograms
map_HT = TH2I("Mapping_HT", "Mapping_HT", topology[0], 0, topology[0],
topology[1], 0, topology[1])
map_LTO = TH2I("Mapping_LTO", "Mapping_LTO", topology[0], 0,
topology[0], topology[1], 0, topology[1])
map = TH2I("Mapping", "Mapping", topology[0], 0, topology[0],
topology[1], 0, topology[1])
Spectra_hist_vector = []
Spectra_cal_hist_vector = []
Peak_Cell_hist_vector = []
Rise_Time_hist_vector = []
Amplitude_hist_vector = []
Ratio_hist_vector = []
amp_shape_vector = []
Average_Waveform_hist_vector = []
# Create a blank waveform for each OM
average_pulse_trace_vector = []
average_pulse_counter_vector = []
event_num_HT_vector = []
event_num_LTO_vector = []
blank_num_vector = []
# Fill the containers with the objects for each OM in this Loop
for slot_num in range(topology[0]):
Spectra_hist_vector.append([])
Spectra_cal_hist_vector.append([])
Peak_Cell_hist_vector.append([])
Rise_Time_hist_vector.append([])
Amplitude_hist_vector.append([])
Ratio_hist_vector.append([])
Average_Waveform_hist_vector.append([])
average_pulse_trace_vector.append([])
average_pulse_counter_vector.append([])
event_num_HT_vector.append([])
event_num_LTO_vector.append([])
amp_shape_vector.append([])
blank_num_vector.append([])
for channel_num in range(topology[1]):
Spectra_hist = TH1F(
"Spectra_" + str(slot_num) + "_" + str(channel_num),
"Spectra_" + str(slot_num) + "_" + str(channel_num), 200,
0, 200000)
Spectra_hist.GetXaxis().SetTitle("Raw Charge")
Spectra_hist_vector[slot_num].append(Spectra_hist)
Spectra_cal_hist = TH1F(
"Spectra_cal_" + str(slot_num) + "_" + str(channel_num),
"Spectra_cal_" + str(slot_num) + "_" + str(channel_num),
200, 0, 200000)
Spectra_cal_hist.GetXaxis().SetTitle("Raw Charge")
Spectra_cal_hist_vector[slot_num].append(Spectra_cal_hist)
Peak_Cell_hist = TH1F(
"Peak_Cell_" + str(slot_num) + "_" + str(channel_num),
"Peak_Cell_" + str(slot_num) + "_" + str(channel_num),
waveform_length, 0, waveform_length)
Peak_Cell_hist.GetXaxis().SetTitle(
"Peak Cell Position /Sample Number")
Peak_Cell_hist_vector[slot_num].append(Peak_Cell_hist)
Rise_Time_hist = TH1F(
"Rise_Time_" + str(slot_num) + "_" + str(channel_num),
"Rise_Time_" + str(slot_num) + "_" + str(channel_num), 200,
50, 200)
Rise_Time_hist.GetXaxis().SetTitle("Rise Time")
Rise_Time_hist_vector[slot_num].append(Rise_Time_hist)
Amplitude_hist = TH1F(
"Amplitudes_" + str(slot_num) + "_" + str(channel_num),
"Amplitudes_" + str(slot_num) + "_" + str(channel_num),
200, 0, 2100)
Amplitude_hist.GetXaxis().SetTitle("Amplitude /ADC Counts")
Amplitude_hist_vector[slot_num].append(Amplitude_hist)
Ratio_hist = TH1F(
"Ratio_" + str(slot_num) + "_" + str(channel_num),
"Ratio_" + str(slot_num) + "_" + str(channel_num), 200, 0,
0.05)
Ratio_hist.GetXaxis().SetTitle("Amplitude/Raw Charge")
Ratio_hist_vector[slot_num].append(Ratio_hist)
amp_shape_hist = TH2F(
"amp_shape" + str(slot_num) + "_" + str(channel_num),
"amp_shape" + str(slot_num) + "_" + str(channel_num), 100,
0, 2000, 100, 0, 1)
amp_shape_hist.GetXaxis().SetTitle("Amplitude /mV")
amp_shape_hist.GetYaxis().SetTitle("Shape")
amp_shape_vector[slot_num].append(amp_shape_hist)
average_pulse_trace_vector[slot_num].append([0] *
waveform_length)
average_pulse_counter_vector[slot_num].append(0)
event_num_HT_vector[slot_num].append(0)
event_num_LTO_vector[slot_num].append(0)
blank_num_vector[slot_num].append(0)
average_pulse_trace_hist = TH1F(
"Waveform_" + str(slot_num) + "_" + str(channel_num) +
"_average", "Waveform_" + str(slot_num) + "_" +
str(channel_num) + "_average", waveform_length, 0,
waveform_length)
average_pulse_trace_hist.GetXaxis().SetTitle("Sample Number")
average_pulse_trace_hist.GetYaxis().SetTitle(
"Averaged ADC Counts /AU")
Average_Waveform_hist_vector[slot_num].append(
average_pulse_trace_hist)
del Spectra_hist
del Spectra_cal_hist
del Peak_Cell_hist
del Rise_Time_hist
del Amplitude_hist
del Ratio_hist
del average_pulse_trace_hist
print(">>> Create Templates... ")
template = createTemplate(PATH + PMT_data_filenames[0].rstrip(),
topology, waveform_length, pre_PULSE_region)
# Now run ove the files
print(">>> Reading Data Files... ")
processing_start = time.time()
temp_start = processing_start
for file_num in range(len(PMT_data_filenames)):
print(">>> File: ", PATH + PMT_data_filenames[file_num].rstrip())
Read_Data(PATH + PMT_data_filenames[file_num].rstrip(),
pre_PULSE_region, average_pulse_counter_vector,
event_num_HT_vector, event_num_LTO_vector,
average_pulse_trace_vector, Spectra_hist_vector,
Spectra_cal_hist_vector, Rise_Time_hist_vector,
Peak_Cell_hist_vector, Amplitude_hist_vector,
Ratio_hist_vector, amp_shape_vector, blank_num_vector,
waveform_length, template)
intermidiate = time.time()
time_length = intermidiate - processing_start
print(">>>\n>>> %.3f seconds.\n" % (intermidiate - temp_start))
temp_start = intermidiate
print("Processed %.2f of data..." %
(float(file_num + 1) / float(len(PMT_data_filenames)) * 100))
Estimate = (time_length / float(file_num + 1)) * (
len(PMT_data_filenames) - file_num - 1)
print(">>> Estimated time till termination %.3f seconds\n\n" %
Estimate)
for slot_num in range(topology[0]):
root_file.mkdir("Slot" + str(slot_num))
root_file.GetDirectory("Slot" + str(slot_num)).cd()
Channel_Check = topology[1]
for channel_num in range(topology[1]):
root_file.GetDirectory("Slot" +
str(slot_num)).mkdir("Channel" +
str(channel_num))
root_file.GetDirectory("Slot" + str(slot_num)).GetDirectory(
"Channel" + str(channel_num)).cd()
Spectra_hist_vector[slot_num][channel_num].Write(
"", TFile.kOverwrite)
Spectra_cal_hist_vector[slot_num][channel_num].Write(
"", TFile.kOverwrite)
Rise_Time_hist_vector[slot_num][channel_num].Write(
"", TFile.kOverwrite)
Amplitude_hist_vector[slot_num][channel_num].Write(
"", TFile.kOverwrite)
Peak_Cell_hist_vector[slot_num][channel_num].Write(
"", TFile.kOverwrite)
Ratio_hist_vector[slot_num][channel_num].Write(
"", TFile.kOverwrite)
amp_shape_vector[slot_num][channel_num].Write(
"", TFile.kOverwrite)
for bin in range(
len(average_pulse_trace_vector[slot_num]
[channel_num])):
# Avoid dividing by zero
if average_pulse_counter_vector[slot_num][
channel_num] == 0:
average_pulse_counter_vector[slot_num][channel_num] = 1
Average_Waveform_hist_vector[
slot_num][channel_num].SetBinContent(
bin,
(average_pulse_trace_vector[slot_num][channel_num]
[bin] / average_pulse_counter_vector[slot_num]
[channel_num]) * 1000.0)
Average_Waveform_hist_vector[slot_num][
channel_num].SetBinError(bin, 1.0)
Average_Waveform_hist_vector[slot_num][channel_num].Write(
"", TFile.kOverwrite)
map.Fill(
slot_num, channel_num,
event_num_HT_vector[slot_num][channel_num] +
event_num_LTO_vector[slot_num][channel_num])
map_HT.Fill(slot_num, channel_num,
event_num_HT_vector[slot_num][channel_num])
map_LTO.Fill(slot_num, channel_num,
event_num_LTO_vector[slot_num][channel_num])
if event_num_HT_vector[slot_num][
channel_num] + event_num_LTO_vector[slot_num][
channel_num] + blank_num_vector[slot_num][
channel_num] == 0:
root_file.GetDirectory("Slot" + str(slot_num)).Delete(
"Channel" + str(channel_num) + ";1")
#print("\n>>> Deleted Slot: ",slot_num, " Channel: ", channel_num, " as there were no events\n")
Channel_Check = Channel_Check - 1
if Channel_Check == 0:
root_file.Delete("Slot" + str(slot_num) + ";1")
print('\n>>> Deleted Slot: ', slot_num,
' as there were no events\n')
root_file.cd()
map.Write("", TFile.kOverwrite)
map_HT.Write("", TFile.kOverwrite)
map_LTO.Write("", TFile.kOverwrite)
root_file.Close()
print(">>>")
def Modify_AlignmentDBFile(dbfilename=None, planenumber=None, mode=None, value=None):
"""
Change single position or angle in alignment DB file
:@dbfilename Name of the output root file
:@planenumber Planenumber to be modified (starting with 0)
:@mode Mode to be modified ['x','y','z','alpha','beta','gamma']
:@value New value in mm or rad
:author: [email protected]
"""
if dbfilename == None:
return None
if planenumber == None:
return None
if mode == None:
return None
if value == None:
return None
if os.path.isfile(dbfilename):
dbfile = TFile( dbfilename, 'UPDATE' )
else:
raise ValueError('alignment DB ('+dbfilename+') file not found')
# Get access to histogram
if mode=='x':
histo = dbfile.Get("hPositionX")
dbfile.Delete("hPositionX;1")
elif mode=='y':
histo = dbfile.Get("hPositionY")
dbfile.Delete("hPositionY;1")
elif mode=='z':
histo = dbfile.Get("hPositionZ")
dbfile.Delete("hPositionZ;1")
elif mode=='alpha':
histo = dbfile.Get("hRotationAlpha")
dbfile.Delete("hRotationAlpha:1")
elif mode=='beta':
histo = dbfile.Get("hRotationBeta")
dbfile.Delete("hRotationBeta;1")
elif mode=='gamma':
histo = dbfile.Get("hRotationGamma")
dbfile.Delete("hRotationGamma;1")
else:
return None
histo.SetBinContent(planenumber+1,value)
dbfile.Write()
dbfile.Close()
# all_integrals_gamma=np.append(all_integrals_gamma,inte)
# elif("PhS1" in sims):
# all_integrals_elecphs1=np.append(all_integrals_elecphs1,inte)
# else:
# all_integrals_elec=np.append(all_integrals_elec,inte)
# print("exists")
except:
print("file is",filename)
print("!!!corrupt!!!")
if (fi.IsZombie()):
print("zombie")
fi.Close()
fi.Delete()
plt.plot(all_integrals)
plt.pause(0.01)
input("")
# plt.plot(all_integrals_gamma)
# plt.pause(0.01)
# input("")
# plt.clf()
# plt.cla()
# plt.plot(all_integrals_gamma)
# plt.pause(0.01)
# input("")
# plt.clf()
