def Analysis(folder,
config,
configgeneric=None,
tag="",
convtyp='-1',
verbose=1):
import os
from enrico import utils
from enrico.gtfunction import Observation
from enrico.fitmaker import FitMaker
import Loggin
mes = Loggin.Message()
""" run an analysis"""
Obs = Observation(folder, config, tag=tag)
if verbose:
utils._log('SUMMARY: ' + tag)
Obs.printSum()
FitRunner = FitMaker(Obs, config) ##Class
if config['Spectrum']['FitsGeneration'] == 'yes':
FitRunner.FirstSelection(
configgeneric) #Generates fits files for the coarse selection
FitRunner.GenerateFits(
) #Generates fits files for the rest of the products
return FitRunner
def Analysis(folder, config, tag="", convtyp='-1', verbose = 1):
""" run an analysis"""
Obs = Observation(folder, config, convtyp, tag=tag)
if verbose:
utils._log('SUMMARY: ' + tag)
Obs.printSum()
FitRunner = FitMaker(Obs, config)##Class
if config['Spectrum']['FitsGeneration'] == 'yes':
FitRunner.GenerateFits() #Generates fits files
return FitRunner
def Analysis(folder, config, tag="", convtyp='-1', verbose=1):
""" run an analysis"""
Obs = Observation(folder, config, convtyp, tag=tag)
if verbose:
utils._log('SUMMARY: ' + tag)
Obs.printSum()
FitRunner = FitMaker(Obs, config) ##Class
if config['Spectrum']['FitsGeneration'] == 'yes':
FitRunner.GenerateFits() #Generates fits files
return FitRunner
def Runsrcprob(config):
config['space']['rad'] = config['srcprob']['rad']
Obs = Observation(config['out'], config, tag="srcprob")
_log("Summary")
Obs.printSum()
if config['srcprob']['FitsGeneration'] =='yes':
_log("Select data")
Obs.FirstCut()
if config['analysis']['ComputeDiffrsp'] == 'yes':
_log("Compute diffuse responses")
Obs.DiffResps()
_log("Run gtsrcprob")
Obs.SrcProb()
probfile=fits.open(Obs.Probfile)
srclist = open(config['srcprob']['srclist'],"r").readlines()
for src in srclist:
proba = probfile[1].data.field(string.split(src)[0])
energy = probfile[1].data.field("ENERGY")
ra = probfile[1].data.field("RA")
dec = probfile[1].data.field("DEC")
time = probfile[1].data.field("TIME")
indices = energy.argsort()
mes = Loggin.Message()
mes.info( "Results sorted by decreasing energy")
Print(indices,config,ra,dec,proba,energy,time)
print
mes.info( "Results sorted by decreasing probability")
indices = proba.argsort()
Print(indices,config,ra,dec,proba,energy,time)
def Analysis(folder, config, configgeneric=None, tag="", convtyp='-1', verbose = 1):
mes = Loggin.Message()
""" run an analysis"""
Obs = Observation(folder, config, tag=tag)
if verbose:
utils._log('SUMMARY: ' + tag)
Obs.printSum()
FitRunner = FitMaker(Obs, config)##Class
if config['Spectrum']['FitsGeneration'] == 'yes':
FitRunner.FirstSelection(configgeneric) #Generates fits files for the coarse selection
FitRunner.GenerateFits() #Generates fits files for the rest of the products
return FitRunner
def Analysis(folder, config, configgeneric=None, tag="", convtyp='-1', verbose = 1):
mes = Loggin.Message()
""" run an analysis"""
# If there are no xml files, create it and print a warning <--- This should be here?
#if len(glob.glob(config['file']['xml'].replace('.xml','*.xml')))==0:
if len(glob.glob(config['file']['xml']))==0: #.replace('.xml','*.xml')))==0:
mes.warning("Xml not found, creating one for the given config %s" %config['file']['xml'])
XmlMaker(config)
Obs = Observation(folder, config, tag=tag)
if verbose:
utils._log('SUMMARY: ' + tag)
Obs.printSum()
FitRunner = FitMaker(Obs, config)##Class
if config['Spectrum']['FitsGeneration'] == 'yes':
FitRunner.FirstSelection(configgeneric) #Generates fits files for the coarse selection
FitRunner.GenerateFits() #Generates fits files for the rest of the products
return FitRunner
def FindSrc(infile):
config = get_config(infile)
folder = config['out']
Obs = Observation(folder, config)
utils._log('SUMMARY: ')
Obs.printSum()
FitRunner = FitMaker(Obs, config)
if config["findsrc"]["FitsGeneration"]== "yes":
config['analysis']['likelihood'] = 'unbinned'
FitRunner.GenerateFits()
FitRunner._log('gtfindsrc', 'Optimize source position')
os.system("rm "+utils._dump_findsrcout(config))
Obs.FindSource()
try:
update_reg(config)
except:
pass
def PrepareEbin(Fit, FitRunner, sedresult=None):
""" Prepare the computation of spectral point in energy bins by
i) removing the weak sources (TS<1) # not true
ii) updating the config file (option and energy)
and save it in a new ascii file
iii) changing the spectral model and saving it in a new xml file.
A list of the ascii files is returned"""
mes = Loggin.Message()
NEbin = int(FitRunner.config['Ebin']['NumEnergyBins'])
config = FitRunner.config
config['verbose'] = 'no' #Be quiet
#Replace the evt file with the fits file produced before
#in order to speed up the production of the fits files
config['file']['event'] = FitRunner.obs.eventcoarse
#update the config to allow the fit in energy bins
config['UpperLimit']['envelope'] = 'no'
config['Ebin']['NumEnergyBins'] = '0' #no new bin in energy!
config['target']['redshift'] = '0' #Disable EBL correction
config['out'] = FitRunner.config['out'] + '/' + EbinPath + str(NEbin)
config['Spectrum']['ResultPlots'] = 'no' #no SED plot/modelmap
#copy the chose of the user for the enery bin computing
config['Spectrum']['FitsGeneration'] = config['Ebin']['FitsGeneration']
config['UpperLimit']['TSlimit'] = config['Ebin']['TSEnergyBins']
tag = FitRunner.config['file']['tag']
lEmax = np.log10(float(FitRunner.config['energy']['emax']))
lEmin = np.log10(float(FitRunner.config['energy']['emin']))
utils._log("Preparing submission of fit into energy bins")
print(" Emin = ", float(FitRunner.config['energy']['emin']), " Emax = ",
float(FitRunner.config['energy']['emax']), " Nbins = ", NEbin)
if config['Ebin']['DistEbins'] in ['TS', 'mix'] and sedresult != None:
# Make the bins equispaced in sum(SED/SEDerr) - using the butterfly
ipo = 0
iTS = sedresult.SED / sedresult.Err
TScumula = 0
TSperbin = 1. * sum(iTS) / NEbin
ener = [10**lEmin]
while ipo < len(sedresult.E) - 1:
TScumula += iTS[ipo]
if TScumula / TSperbin > 1:
ener.append(sedresult.E[ipo])
TScumula -= TSperbin
ipo += 1
ener.append(10**lEmax)
ener = np.array(ener)
# intermediate approach (between both TS-spaced and logE spaced)
if config['Ebin']['DistEbins'] == 'mix':
ener = 0.5 * (ener + np.logspace(lEmin, lEmax, NEbin + 1))
else:
# Make the bins equispaced in logE (standard)
ener = np.logspace(lEmin, lEmax, NEbin + 1)
os.system("mkdir -p " + config['out'])
paramsfile = []
srcname = FitRunner.config['target']['name']
if config['UpperLimit']['TSlimit'] > Fit.Ts(srcname):
utils._log('Re-optimize', False)
print "An upper limit has been computed. The fit need to be re-optmized"
Fit.optimize(0)
Pref = utils.ApproxPref(Fit, ener, srcname)
Gamma = utils.ApproxGamma(Fit, ener, srcname)
Model_type = Fit.model.srcs[srcname].spectrum().genericName()
# if the model is not PowerLaw : change the model
if not (Model_type == 'PowerLaw'):
for comp in Fit.components:
comp.logLike.getSource(srcname).setSpectrum(
"PowerLaw") #Change model
config['target']['spectrum'] = "PowerLaw"
xmltag_list = [""] #handle summed like analysis
if config['ComponentAnalysis']['FrontBack'] == "yes":
xmltag_list = ["_FRONT", "_BACK"]
mes.info("Splitting Front/Back events")
elif config['ComponentAnalysis']['PSF'] == "yes":
xmltag_list = ["_PSF0", "_PSF1", "_PSF2"]
mes.info("Splitting PSF events")
elif config['ComponentAnalysis']['EDISP'] == "yes":
xmltag_list = ["_EDISP0", "_EDISP1", "_EDISP2", "_EDISP3"]
mes.info("Splitting EDISP events")
for ibin in xrange(NEbin): #Loop over the energy bins
E = utils.GetE0(ener[ibin + 1], ener[ibin])
mes.info("Submitting # " + str(ibin) + " at energy " + str(E))
#Update the model for the bin
for comp, xmltag in zip(Fit.components, xmltag_list):
NewFitObject = ChangeModel(comp, ener[ibin], ener[ibin + 1],
srcname, Pref[ibin], Gamma[ibin])
Xmlname = (config['out'] + "/" + srcname + "_" + str(ibin) +
xmltag + ".xml")
NewFitObject.writeXml(Xmlname) # dump the corresponding xml file
config['file']['xml'] = Xmlname.replace(xmltag, "")
#update the energy bounds
config['energy']['emin'] = str(ener[ibin])
config['energy']['emax'] = str(ener[ibin + 1])
config['energy']['decorrelation_energy'] = "no"
# Change the spectral index to follow the Estimated Gamma
# if approximated Gamma is outside of bounds set it to limit
Gamma_min = -5
Gamma_max = 0.5
config['UpperLimit']['SpectralIndex'] = -min(
max(Gamma_min, Gamma[ibin]), Gamma_max)
config['file']['tag'] = tag + '_Ebin' + str(NEbin) + '_' + str(ibin)
filename = config['target']['name'] + "_" + str(ibin) + ".conf"
paramsfile.append(filename)
config.write(open(config['out'] + '/' + paramsfile[ibin],
'w')) #save the config file in a ascii file
return paramsfile
def VariabilityIndex(self):
"""Compute the variability index as in the 2FLG catalogue. (see Nolan et al, 2012)"""
LcOutPath = self.LCfolder + self.config['target']['name']
utils._log('Computing Variability index ')
self.config['Spectrum']['FitsGeneration'] = 'no'
# ValueDC = self.GetDCValue()
ResultDicDC = utils.ReadResult(self.config)
LogL1 = []
LogL0 = []
Time = []
for i in xrange(self.Nbin):
CurConfig = get_config(self.configfile[i])
#Read the result. If it fails, it means that the bins has not bin computed. A warning message is printed
try :
ResultDic = utils.ReadResult(CurConfig)
except :
print "WARNING : fail reading the config file : ",CurConfig
print "Job Number : ",i
print "Please have a look at this job log file"
continue
# LogL1.append(ResultDic.get("log_like"))
#Update the time and time error array
Time.append((ResultDic.get("tmax")+ResultDic.get("tmin"))/2.)
##############################################################
# Compute the loglike value using the DC flux or prefactor
##############################################################
# Create one obs instance
CurConfig['Spectrum']['FitsGeneration'] = 'no'
_,Fit = GenAnalysisObjects(CurConfig,verbose=0)#be quiet
Fit.ftol = float(self.config['fitting']['ftol'])
#Spectral index management!
utils.FreezeParams(Fit, self.srcname, 'Index', -2)
LogL1.append(-Fit.fit(0,optimizer=CurConfig['fitting']['optimizer']))
Model_type = Fit.model.srcs[self.srcname].spectrum().genericName()
if (Model_type == 'PowerLaw') :
utils.FreezeParams(Fit, self.srcname, 'Prefactor', utils.fluxNorm(ResultDicDC['Prefactor']))
if (Model_type == 'PowerLaw2') :
utils.FreezeParams(Fit, self.srcname, 'Integral', utils.fluxNorm(ResultDicDC['Integral']))
LogL0.append(-Fit.fit(0,optimizer=CurConfig['fitting']['optimizer']))
del Fit #Clean memory
Can = _GetCanvas()
TgrDC = ROOT.TGraph(len(Time),np.array(Time),np.array(LogL0))
TgrDC.Draw("ALP*")
TgrDC = ROOT.TGraph(len(Time),np.array(Time),np.array(LogL0))
TgrDC.SetMarkerColor(2)
TgrDC.Draw("PL*")
#Save the canvas in the LightCurve subfolder
Can.Print(LcOutPath+'_VarIndex.eps')
Can.Print(LcOutPath+'_VarIndex.C')
print
print "\t TSvar = ",2*(sum(LogL1)-sum(LogL0))
print "\t NDF = ",len(LogL0)-1
print "\t Chi2 prob = ",ROOT.TMath.Prob(2*(sum(LogL1)-sum(LogL0)),len(LogL0)-1)
print
def PrepareEbin(Fit, FitRunner):
""" Prepare the computation of spectral point in energy bins by
i) removing the weak sources (TS<1) # not true
ii) updating the config file (option and energy)
and save it in a new ascii file
iii) changing the spectral model and saving it in a new xml file.
A list of the ascii files is returned"""
NEbin = int(FitRunner.config['Ebin']['NumEnergyBins'])
config = FitRunner.config
config['verbose'] ='no' #Be quiet
#Replace the evt file with the fits file produced before
#in order to speed up the production of the fits files
config['file']['event'] = FitRunner.obs.eventfile
#update the config to allow the fit in energy bins
config['UpperLimit']['envelope'] = 'no'
config['Ebin']['NumEnergyBins'] = '0'#no new bin in energy!
config['out'] = FitRunner.config['out'] + '/'+EbinPath + str(NEbin)
config['Spectrum']['ResultPlots'] = 'no' #no SED plot/modelmap
#copy the chose of the user for the enery bin computing
config['Spectrum']['FitsGeneration'] = config['Ebin']['FitsGeneration']
config['UpperLimit']['TSlimit'] = config['Ebin']['TSEnergyBins']
tag = FitRunner.config['file']['tag']
lEmax = np.log10(float(FitRunner.config['energy']['emax']))
lEmin = np.log10(float(FitRunner.config['energy']['emin']))
utils._log("Preparing submission of fit into energy bins")
print("Emin = ", float(FitRunner.config['energy']['emin']),
" Emax = ", float(FitRunner.config['energy']['emax']),
" Nbins = ", NEbin)
ener = np.logspace(lEmin, lEmax, NEbin + 1)
os.system("mkdir -p " + config['out'])
paramsfile = []
srcname = FitRunner.config['target']['name']
if config['UpperLimit']['TSlimit']>Fit.Ts(srcname) :
utils._log('Re-optimize', False)
print "An upper limit has been computed. The fit need to be re-optmized"
Fit.optimize(0)
# utils.RemoveWeakSources(Fit,srcname)#remove source with TS<1 to be sure that MINUIT will converge
Pref = utils.ApproxPref(Fit, ener, srcname)
Gamma = utils.ApproxGamma(Fit, ener, srcname)
Model_type = Fit.model.srcs[srcname].spectrum().genericName()
# if the model is not PowerLaw : change the model
if not(Model_type == 'PowerLaw') :
Fit.logLike.getSource(srcname).setSpectrum("PowerLaw") #Change model
for ibin in xrange(NEbin):#Loop over the energy bins
E = utils.GetE0(ener[ibin + 1],ener[ibin])
print "Submition # ", ibin, " at energy ", E
#Update the model for the bin
NewFitObject = ChangeModel(Fit, ener[ibin], ener[ibin + 1], srcname, Pref[ibin] ,Gamma[ibin])
Xmlname = (config['out'] + "/" + srcname +
"_" + str(ibin) + ".xml")
NewFitObject.writeXml(Xmlname)# dump the corresponding xml file
config['file']['xml'] = Xmlname
#update the energy bounds
config['energy']['emin'] = str(ener[ibin])
config['energy']['emax'] = str(ener[ibin + 1])
config['file']['tag'] = tag + '_Ebin' + str(NEbin) + '_' + str(ibin)
filename = config['target']['name'] + "_" + str(ibin) + ".conf"
paramsfile.append(filename)
config.write(open(config['out'] + '/' +paramsfile[ibin], 'w')) #save the config file in a ascii file
return paramsfile
def PrepareEbin(Fit, FitRunner):
""" Prepare the computation of spectral point in energy bins by
i) removing the weak sources (TS<1) # not true
ii) updating the config file (option and energy)
and save it in a new ascii file
iii) changing the spectral model and saving it in a new xml file.
A list of the ascii files is returned"""
NEbin = int(FitRunner.config['Ebin']['NumEnergyBins'])
config = FitRunner.config
config['verbose'] = 'no' #Be quiet
#Replace the evt file with the fits file produced before
#in order to speed up the production of the fits files
config['file']['event'] = FitRunner.obs.eventcoarse
#update the config to allow the fit in energy bins
config['UpperLimit']['envelope'] = 'no'
config['Ebin']['NumEnergyBins'] = '0' #no new bin in energy!
config['target']['redshift'] = '0' #Disable EBL correction
config['out'] = FitRunner.config['out'] + '/' + EbinPath + str(NEbin)
config['Spectrum']['ResultPlots'] = 'no' #no SED plot/modelmap
#copy the chose of the user for the enery bin computing
config['Spectrum']['FitsGeneration'] = config['Ebin']['FitsGeneration']
config['UpperLimit']['TSlimit'] = config['Ebin']['TSEnergyBins']
tag = FitRunner.config['file']['tag']
lEmax = np.log10(float(FitRunner.config['energy']['emax']))
lEmin = np.log10(float(FitRunner.config['energy']['emin']))
utils._log("Preparing submission of fit into energy bins")
print(" Emin = ", float(FitRunner.config['energy']['emin']), " Emax = ",
float(FitRunner.config['energy']['emax']), " Nbins = ", NEbin)
ener = np.logspace(lEmin, lEmax, NEbin + 1)
os.system("mkdir -p " + config['out'])
paramsfile = []
srcname = FitRunner.config['target']['name']
if config['UpperLimit']['TSlimit'] > Fit.Ts(srcname):
utils._log('Re-optimize', False)
print "An upper limit has been computed. The fit need to be re-optmized"
Fit.optimize(0)
Pref = utils.ApproxPref(Fit, ener, srcname)
Gamma = utils.ApproxGamma(Fit, ener, srcname)
Model_type = Fit.model.srcs[srcname].spectrum().genericName()
# if the model is not PowerLaw : change the model
if not (Model_type == 'PowerLaw'):
for comp in Fit.components:
comp.logLike.getSource(srcname).setSpectrum(
"PowerLaw") #Change model
config['target']['spectrum'] = "PowerLaw"
for ibin in xrange(NEbin): #Loop over the energy bins
E = utils.GetE0(ener[ibin + 1], ener[ibin])
from enrico import Loggin
mes = Loggin.Message()
mes.info("Submition # " + str(ibin) + " at energy " + str(E))
#Update the model for the bin
NewFitObject = ChangeModel(Fit, ener[ibin], ener[ibin + 1], srcname,
Pref[ibin], Gamma[ibin])
Xmlname = (config['out'] + "/" + srcname + "_" + str(ibin) + ".xml")
NewFitObject.writeXml(Xmlname) # dump the corresponding xml file
config['file']['xml'] = Xmlname
#update the energy bounds
config['energy']['emin'] = str(ener[ibin])
config['energy']['emax'] = str(ener[ibin + 1])
config['energy']['decorrelation_energy'] = "no"
# Change the spectral index to follow the Estimated Gamma
# if approximated Gamma is outside of bounds set it to limit
Gamma_min = -5
Gamma_max = 0.5
config['UpperLimit']['SpectralIndex'] = -min(
max(Gamma_min, Gamma[ibin]), Gamma_max)
config['file']['tag'] = tag + '_Ebin' + str(NEbin) + '_' + str(ibin)
filename = config['target']['name'] + "_" + str(ibin) + ".conf"
paramsfile.append(filename)
config.write(open(config['out'] + '/' + paramsfile[ibin],
'w')) #save the config file in a ascii file
return paramsfile
def VariabilityIndex(self):
"""Compute the variability index as in the 2FGL catalogue. (see Nolan et al, 2012)"""
LcOutPath = self.LCfolder + self.config['target']['name']
utils._log('Computing Variability index ')
self.config['Spectrum']['FitsGeneration'] = 'no'
try :
ResultDicDC = utils.ReadResult(self.generalconfig)
except :
self.warning("No results file found; please run enrico_sed first.")
return
LogL1 = []
LogL0 = []
Time = []
for i in xrange(self.Nbin):
CurConfig = get_config(self.configfile[i])
#Read the result. If it fails, it means that the bins has not bin computed. A warning message is printed
try :
ResultDic = utils.ReadResult(CurConfig)
except :
self._errorReading("Fail reading the config file ",i)
continue
# LogL1.append(ResultDic.get("log_like"))
#Update the time and time error array
Time.append((ResultDic.get("tmax")+ResultDic.get("tmin"))/2.)
##############################################################
# Compute the loglike value using the DC flux or prefactor
##############################################################
# Create one obs instance
CurConfig['Spectrum']['FitsGeneration'] = 'no'
_,Fit = GenAnalysisObjects(CurConfig,verbose=0)#be quiet
Fit.ftol = float(self.config['fitting']['ftol'])
#Spectral index management!
parameters = dict()
parameters['Index'] = -2.
parameters['alpha'] = +2.
parameters['Index1'] = -2.
parameters['beta'] = 0
parameters['Index2'] = 2.
parameters['Cutoff'] = 100000. # set the cutoff to be high
for key in parameters.keys():
try:
utils.FreezeParams(Fit, self.srcname, key, parameters[key])
except:
continue
LogL1.append(-Fit.fit(0,optimizer=CurConfig['fitting']['optimizer']))
for key in ["norm","Prefactor","Integral"]:
try:
utils.FreezeParams(Fit,self.srcname,key, utils.fluxNorm(ResultsDicDC[key]))
except:
continue
LogL0.append(-Fit.fit(0,optimizer=CurConfig['fitting']['optimizer']))
del Fit #Clean memory
plt.figure()
plt.xlabel("Time")
plt.ylabel("Log(Like) Variability")
plt.errorbar(Time,LogL0,fmt='o',color='black',ls='None')
plt.xlim(xmin=max(plt.xlim()[0],1.02*min(Time)-0.02*max(Time)),
xmax=min(plt.xlim()[1],1.02*max(Time)-0.02*min(Time)))
# Move the offset to the axis label
ax = plt.gca()
ax.get_yaxis().get_major_formatter().set_useOffset(False)
offset_factor = int(np.mean(np.log10(np.abs(ax.get_ylim()))))
if (offset_factor != 0):
ax.set_yticklabels([float(round(k,5)) \
for k in ax.get_yticks()*10**(-offset_factor)])
ax.yaxis.set_label_text(ax.yaxis.get_label_text() +\
r" [${\times 10^{%d}}$]" %offset_factor)
# Secondary axis with MJD
mjdaxis = ax.twiny()
mjdaxis.set_xlim([utils.met_to_MJD(k) for k in ax.get_xlim()])
mjdaxis.set_xlabel(r"Time (MJD)")
mjdaxis.xaxis.set_major_formatter(matplotlib.ticker.ScalarFormatter(useOffset=False))
plt.setp( mjdaxis.xaxis.get_majorticklabels(), rotation=15 )
plt.tight_layout()
plt.savefig(LcOutPath+"_VarIndex.png", dpi=150, facecolor='w', edgecolor='w',
orientation='portrait', papertype=None, format=None,
transparent=False, bbox_inches=None, pad_inches=0.1,
frameon=None)
self.info("Variability index calculation")
print "\t TSvar = ",2*(sum(LogL1)-sum(LogL0))
print "\t NDF = ",len(LogL0)-1
print "\t Chi2 prob = ",1 - chi2.cdf(2*(sum(LogL1)-sum(LogL0)),len(LogL0)-1)
print
def VariabilityIndex(self):
"""Compute the variability index as in the 2FLG catalogue. (see Nolan et al, 2012)"""
LcOutPath = self.LCfolder + self.config['target']['name']
utils._log('Computing Variability index ')
self.config['Spectrum']['FitsGeneration'] = 'no'
# ValueDC = self.GetDCValue()
ResultDicDC = utils.ReadResult(self.config)
LogL1 = []
LogL0 = []
Time = []
for i in xrange(self.Nbin):
CurConfig = get_config(self.configfile[i])
#Read the result. If it fails, it means that the bins has not bin computed. A warning message is printed
try:
ResultDic = utils.ReadResult(CurConfig)
except:
self._errorReading("fail reading the config file ", i)
# print "WARNING : fail reading the config file : ",CurConfig
# print "Job Number : ",i
# print "Please have a look at this job log file"
continue
# LogL1.append(ResultDic.get("log_like"))
#Update the time and time error array
Time.append((ResultDic.get("tmax") + ResultDic.get("tmin")) / 2.)
##############################################################
# Compute the loglike value using the DC flux or prefactor
##############################################################
# Create one obs instance
CurConfig['Spectrum']['FitsGeneration'] = 'no'
_, Fit = GenAnalysisObjects(CurConfig, verbose=0) #be quiet
Fit.ftol = float(self.config['fitting']['ftol'])
#Spectral index management!
self.info("Spectral index frozen to a value of 2")
utils.FreezeParams(Fit, self.srcname, 'Index', -2)
LogL1.append(
-Fit.fit(0, optimizer=CurConfig['fitting']['optimizer']))
Model_type = Fit.model.srcs[self.srcname].spectrum().genericName()
if (Model_type == 'PowerLaw'):
utils.FreezeParams(Fit, self.srcname, 'Prefactor',
utils.fluxNorm(ResultDicDC['Prefactor']))
if (Model_type == 'PowerLaw2'):
utils.FreezeParams(Fit, self.srcname, 'Integral',
utils.fluxNorm(ResultDicDC['Integral']))
LogL0.append(
-Fit.fit(0, optimizer=CurConfig['fitting']['optimizer']))
del Fit #Clean memory
Can = _GetCanvas()
TgrDC = ROOT.TGraph(len(Time), np.array(Time), np.array(LogL0))
TgrDC.Draw("ALP*")
TgrDC = ROOT.TGraph(len(Time), np.array(Time), np.array(LogL0))
TgrDC.SetMarkerColor(2)
TgrDC.Draw("PL*")
#Save the canvas in the LightCurve subfolder
Can.Print(LcOutPath + '_VarIndex.eps')
Can.Print(LcOutPath + '_VarIndex.C')
self.info("Variability index calculation")
print "\t TSvar = ", 2 * (sum(LogL1) - sum(LogL0))
print "\t NDF = ", len(LogL0) - 1
print "\t Chi2 prob = ", ROOT.TMath.Prob(2 * (sum(LogL1) - sum(LogL0)),
len(LogL0) - 1)
print
def PrepareEbin(Fit, FitRunner, sedresult=None):
""" Prepare the computation of spectral point in energy bins by
i) removing the weak sources (TS<1) # not true
ii) updating the config file (option and energy)
and save it in a new ascii file
iii) changing the spectral model and saving it in a new xml file.
A list of the ascii files is returned"""
mes = Loggin.Message()
NEbin = int(FitRunner.config['Ebin']['NumEnergyBins'])
config = FitRunner.config
config['verbose'] = 'no' #Be quiet
#Replace the evt file with the fits file produced before
#in order to speed up the production of the fits files
config['file']['event'] = FitRunner.obs.eventcoarse
#update the config to allow the fit in energy bins
config['UpperLimit']['envelope'] = 'no'
config['Ebin']['NumEnergyBins'] = '0' #no new bin in energy!
config['target']['redshift'] = '0' #Disable EBL correction
config['out'] = FitRunner.config['out'] + '/' + EbinPath + str(NEbin)
config['Spectrum']['ResultPlots'] = 'no' #no SED plot/modelmap
#copy the chose of the user for the enery bin computing
config['Spectrum']['FitsGeneration'] = config['Ebin']['FitsGeneration']
config['UpperLimit']['TSlimit'] = config['Ebin']['TSEnergyBins']
tag = FitRunner.config['file']['tag']
Emax = float(FitRunner.config['energy']['emax'])
Emin = float(FitRunner.config['energy']['emin'])
lEmax = np.log10(Emax)
lEmin = np.log10(Emin)
utils._log("Preparing submission of fit into energy bins")
print("Emin = {0} MeV".format(Emin), "Emax = {0} MeV".format(Emax),
"Nbins = {0}".format(NEbin))
ener = utils.string_to_list(config['Ebin']['DistEbins'])
if ener is None:
if (config['ComponentAnalysis']['FGL4'] == 'yes'
or config['Ebin']['DistEbins'] == 'FGL4'):
ener = np.asarray([50, 1e2, 3e2, 1e3, 3e3, 1e4, 3e4, 3e5])
NEbin = len(ener) - 1
elif config['Ebin']['DistEbins'] in ['TS', 'mix'
] and sedresult != None:
# Make the bins equispaced in sum(SED/SEDerr) - using the butterfly
ipo = 0
iTS = sedresult.SED / sedresult.Err
TScumula = 0
TSperbin = 1. * sum(iTS) / NEbin
ener = [10**lEmin]
while ipo < len(sedresult.E) - 1:
TScumula += iTS[ipo]
if TScumula / TSperbin > 1:
ener.append(sedresult.E[ipo])
TScumula -= TSperbin
ipo += 1
ener.append(10**lEmax)
ener = np.array(ener)
# intermediate approach (between both TS-spaced and logE spaced)
if config['Ebin']['DistEbins'] == 'mix':
ener = 0.5 * (ener + np.logspace(lEmin, lEmax, NEbin + 1))
else:
# Make the bins equispaced in logE (standard)
ener = np.logspace(lEmin, lEmax, NEbin + 1)
# 1. Remove bins that are out of the range covered by the data
# 2. Limit the bin extend to the range covered by the data.
# Get elements strictly above threshold +1 element to the left for the left side
# Get elements strictly below limit +1 element to the right side.
# example. [1,2,3,4,5] -> if Emin=3.4, Emax=3.9 we want to keep [3.4,3.9].
ener = np.asarray(ener)
print("Energy bins (before energy cuts): {0}".format(str(ener)))
if len(ener) == 0:
print("** Warning: energy bin array is empty")
return (None)
available_left = ener > Emin # In the example FFFTT -> [4,5]
for k, use in enumerate(available_left[:-1]):
if not use and available_left[k + 1]:
available_left[k] = True # In the example FFTTT -> [3,5]
available_right = ener < Emax # In the example TTTFF -> [1,3]
for k, use in enumerate(available_right[1:]):
if not use and available_right[k]:
available_right[k + 1] = True # In the example TTTTF -> [1,4]
available = available_left * available_right
ener = ener[available] # In the example FFTTF -> [3,4]
# Limit the range to the real energies that are covered by our data
# If the energy bins are well placed this should not do anything.
ener[0] = np.max([Emin, ener[0]])
ener[-1] = np.min([Emax, ener[-1]])
NEbin = len(ener) - 1
print("Energy bins (after energy cuts): {0}".format(str(ener)))
if len(ener) == 0:
print("** Warning: energy bin array is empty")
return (None)
utils.mkdir_p(config['out'])
paramsfile = []
srcname = FitRunner.config['target']['name']
try:
TSsrc = Fit.Ts(srcname)
except RuntimeError:
TSsrc = 0
if config['UpperLimit']['TSlimit'] > TSsrc:
utils._log('Re-optimize', False)
print "An upper limit has been computed. The fit need to be re-optimized"
Fit.optimize(0)
Pref = utils.ApproxPref(Fit, ener, srcname)
Gamma = utils.ApproxGamma(Fit, ener, srcname)
Model_type = Fit.model.srcs[srcname].spectrum().genericName()
# if the model is not PowerLaw : change the model
if not (Model_type == 'PowerLaw'):
for comp in Fit.components:
comp.logLike.getSource(srcname).setSpectrum(
"PowerLaw") #Change model
config['target']['spectrum'] = "PowerLaw"
xmltag_list = [""] #handle summed like analysis
if config['ComponentAnalysis']['FrontBack'] == "yes":
xmltag_list = ["_FRONT", "_BACK"]
mes.info("Splitting Front/Back events")
elif config['ComponentAnalysis']['PSF'] == "yes":
xmltag_list = ["_PSF0", "_PSF1", "_PSF2", "_PSF3"]
mes.info("Splitting PSF events")
elif config['ComponentAnalysis']['EDISP'] == "yes":
xmltag_list = ["_EDISP0", "_EDISP1", "_EDISP2", "_EDISP3"]
mes.info("Splitting EDISP events")
elif config['ComponentAnalysis']['FGL4'] == "yes":
from catalogComponents import evtnum, energybins, pixelsizes
xmltag_list = []
for ebin_i in energybins:
for k, evt in enumerate(evtnum):
#if pixelsizes[ebin_i][k] > 0:
try:
xmltag_list.append("_{0}_En{1}".format(
utils.typeirfs[k], ebin_i))
except KeyError:
continue
for ibin in xrange(NEbin): #Loop over the energy bins
E = utils.GetE0(ener[ibin + 1], ener[ibin])
mes.info("Submitting # " + str(ibin) + " at energy " + str(E))
#Update the model for the bin
for comp, xmltag in zip(Fit.components, xmltag_list):
NewFitObject = ChangeModel(comp, ener[ibin], ener[ibin + 1],
srcname, Pref[ibin], Gamma[ibin])
Xmlname = (config['out'] + "/" + srcname + "_" + str(ibin) +
xmltag + ".xml")
NewFitObject.writeXml(Xmlname) # dump the corresponding xml file
config['file']['xml'] = Xmlname.replace(xmltag, "")
#update the energy bounds
config['energy']['emin'] = str(ener[ibin])
config['energy']['emax'] = str(ener[ibin + 1])
config['energy']['decorrelation_energy'] = "no"
# Change the spectral index to follow the Estimated Gamma
# if approximated Gamma is outside of bounds set it to limit
Gamma_min = -5
Gamma_max = -0.501
Gamma_bin = -max(min(Gamma_max, Gamma[ibin]), Gamma_min)
config['Spectrum']['FrozenSpectralIndex'] = Gamma_bin
config['UpperLimit']['SpectralIndex'] = Gamma_bin
config['file']['tag'] = tag + '_Ebin' + str(NEbin) + '_' + str(ibin)
filename = config['target']['name'] + "_" + str(ibin) + ".conf"
paramsfile.append(filename)
config.write(open(config['out'] + '/' + filename,
'w')) #save the config file in a ascii file
return paramsfile
def VariabilityIndex(self):
"""Compute the variability index as in the 2FGL catalogue. (see Nolan et al, 2012)"""
LcOutPath = self.LCfolder + self.config['target']['name']
utils._log('Computing Variability index ')
self.config['Spectrum']['FitsGeneration'] = 'no'
try :
ResultDicDC = utils.ReadResult(self.generalconfig)
except :
self.warning("No results file found; please run enrico_sed first.")
return
LogL1 = []
LogL0 = []
Time = []
for i in xrange(self.Nbin):
CurConfig = get_config(self.configfile[i])
#Read the result. If it fails, it means that the bins has not bin computed. A warning message is printed
try :
ResultDic = utils.ReadResult(CurConfig)
except :
self._errorReading("Fail reading the config file ",i)
continue
# LogL1.append(ResultDic.get("log_like"))
#Update the time and time error array
Time.append((ResultDic.get("tmax")+ResultDic.get("tmin"))/2.)
##############################################################
# Compute the loglike value using the DC flux or prefactor
##############################################################
# Create one obs instance
CurConfig['Spectrum']['FitsGeneration'] = 'no'
_,Fit = GenAnalysisObjects(CurConfig,verbose=0)#be quiet
Fit.ftol = float(self.config['fitting']['ftol'])
#Spectral index management!
parameters = dict()
parameters['Index'] = -2.
parameters['alpha'] = +2.
parameters['Index1'] = -2.
parameters['beta'] = 0
parameters['Index2'] = 2.
parameters['Cutoff'] = 30000. # set the cutoff to be high
for key in parameters.keys():
try:
utils.FreezeParams(Fit, self.srcname, key, parameters[key])
except:
continue
LogL1.append(-Fit.fit(0,optimizer=CurConfig['fitting']['optimizer']))
for key in ["norm","Prefactor","Integral"]:
try:
utils.FreezeParams(Fit,self.srcname,key, utils.fluxNorm(ResultsDicDC[key]))
except:
continue
LogL0.append(-Fit.fit(0,optimizer=CurConfig['fitting']['optimizer']))
del Fit #Clean memory
plt.figure()
plt.xlabel("Time")
plt.ylabel("Log(Like) Variability")
plt.errorbar(Time,LogL0,fmt='o',color='black',ls='None')
plt.xlim(xmin=max(plt.xlim()[0],1.02*min(Time)-0.02*max(Time)),
xmax=min(plt.xlim()[1],1.02*max(Time)-0.02*min(Time)))
# Move the offset to the axis label
ax = plt.gca()
ax.get_yaxis().get_major_formatter().set_useOffset(False)
offset_factor = int(np.mean(np.log10(np.abs(ax.get_ylim()))))
if (offset_factor != 0):
ax.set_yticklabels([float(round(k,5)) \
for k in ax.get_yticks()*10**(-offset_factor)])
ax.yaxis.set_label_text(ax.yaxis.get_label_text() +\
r" [${\times 10^{%d}}$]" %offset_factor)
# Secondary axis with MJD
mjdaxis = ax.twiny()
mjdaxis.set_xlim([utils.met_to_MJD(k) for k in ax.get_xlim()])
mjdaxis.set_xlabel(r"Time (MJD)")
mjdaxis.xaxis.set_major_formatter(matplotlib.ticker.ScalarFormatter(useOffset=False))
plt.setp( mjdaxis.xaxis.get_majorticklabels(), rotation=15 )
plt.tight_layout()
plt.savefig(LcOutPath+"_VarIndex.png", dpi=150, facecolor='w', edgecolor='w',
orientation='portrait', papertype=None, format=None,
transparent=False, bbox_inches=None, pad_inches=0.1,
frameon=None)
self.info("Variability index calculation")
print "\t TSvar = ",2*(sum(LogL1)-sum(LogL0))
print "\t NDF = ",len(LogL0)-1
print "\t Chi2 prob = ",1 - chi2.cdf(2*(sum(LogL1)-sum(LogL0)),len(LogL0)-1)
print
def VariabilityIndex(self):
"""Compute the variability index as in the 2FLG catalogue. (see Nolan et al, 2012)"""
LcOutPath = self.LCfolder + self.config["target"]["name"]
utils._log("Computing Variability index ")
self.config["Spectrum"]["FitsGeneration"] = "no"
# ValueDC = self.GetDCValue()
ResultDicDC = utils.ReadResult(self.config)
LogL1 = []
LogL0 = []
Time = []
for i in xrange(self.Nbin):
CurConfig = get_config(self.configfile[i])
# Read the result. If it fails, it means that the bins has not bin computed. A warning message is printed
try:
ResultDic = utils.ReadResult(CurConfig)
except:
self._errorReading("fail reading the config file ", i)
# print "WARNING : fail reading the config file : ",CurConfig
# print "Job Number : ",i
# print "Please have a look at this job log file"
continue
# LogL1.append(ResultDic.get("log_like"))
# Update the time and time error array
Time.append((ResultDic.get("tmax") + ResultDic.get("tmin")) / 2.0)
##############################################################
# Compute the loglike value using the DC flux or prefactor
##############################################################
# Create one obs instance
CurConfig["Spectrum"]["FitsGeneration"] = "no"
_, Fit = GenAnalysisObjects(CurConfig, verbose=0) # be quiet
Fit.ftol = float(self.config["fitting"]["ftol"])
# Spectral index management!
self.info("Spectral index frozen to a value of 2")
utils.FreezeParams(Fit, self.srcname, "Index", -2)
LogL1.append(-Fit.fit(0, optimizer=CurConfig["fitting"]["optimizer"]))
Model_type = Fit.model.srcs[self.srcname].spectrum().genericName()
if Model_type == "PowerLaw":
utils.FreezeParams(Fit, self.srcname, "Prefactor", utils.fluxNorm(ResultDicDC["Prefactor"]))
if Model_type == "PowerLaw2":
utils.FreezeParams(Fit, self.srcname, "Integral", utils.fluxNorm(ResultDicDC["Integral"]))
LogL0.append(-Fit.fit(0, optimizer=CurConfig["fitting"]["optimizer"]))
del Fit # Clean memory
Can = _GetCanvas()
TgrDC = ROOT.TGraph(len(Time), np.array(Time), np.array(LogL0))
TgrDC.Draw("ALP*")
TgrDC = ROOT.TGraph(len(Time), np.array(Time), np.array(LogL0))
TgrDC.SetMarkerColor(2)
TgrDC.Draw("PL*")
# Save the canvas in the LightCurve subfolder
Can.Print(LcOutPath + "_VarIndex.eps")
Can.Print(LcOutPath + "_VarIndex.C")
self.info("Variability index calculation")
print "\t TSvar = ", 2 * (sum(LogL1) - sum(LogL0))
print "\t NDF = ", len(LogL0) - 1
print "\t Chi2 prob = ", ROOT.TMath.Prob(2 * (sum(LogL1) - sum(LogL0)), len(LogL0) - 1)
print
def PrepareEbin(Fit, FitRunner,sedresult=None):
""" Prepare the computation of spectral point in energy bins by
i) removing the weak sources (TS<1) # not true
ii) updating the config file (option and energy)
and save it in a new ascii file
iii) changing the spectral model and saving it in a new xml file.
A list of the ascii files is returned"""
mes = Loggin.Message()
NEbin = int(FitRunner.config['Ebin']['NumEnergyBins'])
config = FitRunner.config
config['verbose'] ='no' #Be quiet
#Replace the evt file with the fits file produced before
#in order to speed up the production of the fits files
config['file']['event'] = FitRunner.obs.eventcoarse
#update the config to allow the fit in energy bins
config['UpperLimit']['envelope'] = 'no'
config['Ebin']['NumEnergyBins'] = '0'#no new bin in energy!
config['target']['redshift'] = '0'#Disable EBL correction
config['out'] = FitRunner.config['out'] + '/'+EbinPath + str(NEbin)
config['Spectrum']['ResultPlots'] = 'no' #no SED plot/modelmap
#copy the chose of the user for the enery bin computing
config['Spectrum']['FitsGeneration'] = config['Ebin']['FitsGeneration']
config['UpperLimit']['TSlimit'] = config['Ebin']['TSEnergyBins']
tag = FitRunner.config['file']['tag']
lEmax = np.log10(float(FitRunner.config['energy']['emax']))
lEmin = np.log10(float(FitRunner.config['energy']['emin']))
utils._log("Preparing submission of fit into energy bins")
print(" Emin = ", float(FitRunner.config['energy']['emin']),
" Emax = ", float(FitRunner.config['energy']['emax']),
" Nbins = ", NEbin)
if config['Ebin']['DistEbins'] in ['TS','mix'] and sedresult!=None:
# Make the bins equispaced in sum(SED/SEDerr) - using the butterfly
ipo = 0
iTS = sedresult.SED/sedresult.Err
TScumula = 0
TSperbin = 1.*sum(iTS)/NEbin
ener = [10**lEmin]
while ipo<len(sedresult.E)-1:
TScumula += iTS[ipo]
if TScumula/TSperbin > 1:
ener.append(sedresult.E[ipo])
TScumula -= TSperbin
ipo += 1
ener.append(10**lEmax)
ener = np.array(ener)
# intermediate approach (between both TS-spaced and logE spaced)
if config['Ebin']['DistEbins'] == 'mix':
ener = 0.5*(ener + np.logspace(lEmin, lEmax, NEbin + 1))
else:
# Make the bins equispaced in logE (standard)
ener = np.logspace(lEmin, lEmax, NEbin + 1)
utils.mkdir_p(config['out'])
paramsfile = []
srcname = FitRunner.config['target']['name']
if config['UpperLimit']['TSlimit']>Fit.Ts(srcname) :
utils._log('Re-optimize', False)
print "An upper limit has been computed. The fit need to be re-optmized"
Fit.optimize(0)
Pref = utils.ApproxPref(Fit, ener, srcname)
Gamma = utils.ApproxGamma(Fit, ener, srcname)
Model_type = Fit.model.srcs[srcname].spectrum().genericName()
# if the model is not PowerLaw : change the model
if not(Model_type == 'PowerLaw'):
for comp in Fit.components:
comp.logLike.getSource(srcname).setSpectrum("PowerLaw") #Change model
config['target']['spectrum'] = "PowerLaw"
xmltag_list = [""]#handle summed like analysis
if config['ComponentAnalysis']['FrontBack'] == "yes":
xmltag_list = ["_FRONT","_BACK"]
mes.info("Splitting Front/Back events")
elif config['ComponentAnalysis']['PSF'] == "yes":
xmltag_list = ["_PSF0","_PSF1","_PSF2","_PSF3"]
mes.info("Splitting PSF events")
elif config['ComponentAnalysis']['EDISP'] == "yes":
xmltag_list = ["_EDISP0","_EDISP1","_EDISP2","_EDISP3"]
mes.info("Splitting EDISP events")
for ibin in xrange(NEbin):#Loop over the energy bins
E = utils.GetE0(ener[ibin + 1],ener[ibin])
mes.info("Submitting # "+str(ibin)+" at energy "+str(E))
#Update the model for the bin
for comp,xmltag in zip(Fit.components, xmltag_list):
NewFitObject = ChangeModel(comp, ener[ibin], ener[ibin + 1], srcname, Pref[ibin] ,Gamma[ibin])
Xmlname = (config['out'] + "/" + srcname + "_" + str(ibin) +xmltag+ ".xml")
NewFitObject.writeXml(Xmlname)# dump the corresponding xml file
config['file']['xml'] = Xmlname.replace(xmltag,"")
#update the energy bounds
config['energy']['emin'] = str(ener[ibin])
config['energy']['emax'] = str(ener[ibin + 1])
config['energy']['decorrelation_energy'] = "no"
# Change the spectral index to follow the Estimated Gamma
# if approximated Gamma is outside of bounds set it to limit
Gamma_min=-5
Gamma_max=0.5
config['UpperLimit']['SpectralIndex'] = -min(max(Gamma_min,Gamma[ibin]),Gamma_max)
config['file']['tag'] = tag + '_Ebin' + str(NEbin) + '_' + str(ibin)
filename = config['target']['name'] + "_" + str(ibin) + ".conf"
paramsfile.append(filename)
config.write(open(config['out'] + '/' +paramsfile[ibin], 'w')) #save the config file in a ascii file
return paramsfile
def VariabilityIndex(self):
"""Compute the variability index as in the 2FLG catalogue. (see Nolan et al, 2012)"""
LcOutPath = self.LCfolder + self.config['target']['name']
utils._log('Computing Variability index ')
self.config['Spectrum']['FitsGeneration'] = 'no'
try :
ResultDicDC = utils.ReadResult(self.generalconfig)
except :
self.warning("No results file found; please run enrico_sed first.")
return
LogL1 = []
LogL0 = []
Time = []
for i in xrange(self.Nbin):
CurConfig = get_config(self.configfile[i])
#Read the result. If it fails, it means that the bins has not bin computed. A warning message is printed
try :
ResultDic = utils.ReadResult(CurConfig)
except :
self._errorReading("Fail reading the config file ",i)
continue
# LogL1.append(ResultDic.get("log_like"))
#Update the time and time error array
Time.append((ResultDic.get("tmax")+ResultDic.get("tmin"))/2.)
##############################################################
# Compute the loglike value using the DC flux or prefactor
##############################################################
# Create one obs instance
CurConfig['Spectrum']['FitsGeneration'] = 'no'
_,Fit = GenAnalysisObjects(CurConfig,verbose=0)#be quiet
Fit.ftol = float(self.config['fitting']['ftol'])
#Spectral index management!
parameters = dict()
parameters['Index'] = -2.
parameters['alpha'] = +2.
parameters['Index1'] = -2.
parameters['beta'] = 0
parameters['Index2'] = 2.
parameters['Cutoff'] = 30000. # set the cutoff to be high
for key in parameters.keys():
try:
utils.FreezeParams(Fit, self.srcname, key, parameters[key])
except:
continue
LogL1.append(-Fit.fit(0,optimizer=CurConfig['fitting']['optimizer']))
for key in ["norm","Prefactor","Integral"]:
try:
utils.FreezeParams(Fit,self.srcname,key, utils.fluxNorm(ResultsDicDC[key]))
except:
continue
LogL0.append(-Fit.fit(0,optimizer=CurConfig['fitting']['optimizer']))
del Fit #Clean memory
plt.figure()
plt.xlabel("Time")
plt.ylabel("Log(Like) Variability")
plt.errorbar(Time,LogL0,fmt='o',color='black',ls='None')
plt.savefig(LcOutPath+"_VarIndex.png", dpi=150, facecolor='w', edgecolor='w',
orientation='portrait', papertype=None, format=None,
transparent=False, bbox_inches=None, pad_inches=0.1,
frameon=None)
self.info("Variability index calculation")
print "\t TSvar = ",2*(sum(LogL1)-sum(LogL0))
print "\t NDF = ",len(LogL0)-1
print "\t Chi2 prob = ",1 - chi2.cdf(2*(sum(LogL1)-sum(LogL0)),len(LogL0)-1)
print
def VariabilityIndex(self):
"""Compute the variability index as in the 2FLG catalogue. (see Nolan et al, 2012)"""
LcOutPath = self.LCfolder + self.config['target']['name']
utils._log('Computing Variability index ')
self.config['Spectrum']['FitsGeneration'] = 'no'
try:
ResultDicDC = utils.ReadResult(self.generalconfig)
except:
self.warning("No results file found; please run enrico_sed first.")
return
LogL1 = []
LogL0 = []
Time = []
for i in xrange(self.Nbin):
CurConfig = get_config(self.configfile[i])
#Read the result. If it fails, it means that the bins has not bin computed. A warning message is printed
try:
ResultDic = utils.ReadResult(CurConfig)
except:
self._errorReading("fail reading the config file ", i)
# print "WARNING : fail reading the config file : ",CurConfig
# print "Job Number : ",i
# print "Please have a look at this job log file"
continue
# LogL1.append(ResultDic.get("log_like"))
#Update the time and time error array
Time.append((ResultDic.get("tmax") + ResultDic.get("tmin")) / 2.)
##############################################################
# Compute the loglike value using the DC flux or prefactor
##############################################################
# Create one obs instance
CurConfig['Spectrum']['FitsGeneration'] = 'no'
_, Fit = GenAnalysisObjects(CurConfig, verbose=0) #be quiet
Fit.ftol = float(self.config['fitting']['ftol'])
#Spectral index management!
parameters = dict()
parameters['Index'] = -2.
parameters['alpha'] = +2.
parameters['Index1'] = -2.
parameters['beta'] = 0
parameters['Index2'] = 2.
parameters['Cutoff'] = 30000. # set the cutoff to be high
for key in parameters.keys():
try:
utils.FreezeParams(Fit, self.srcname, key, parameters[key])
except:
continue
LogL1.append(
-Fit.fit(0, optimizer=CurConfig['fitting']['optimizer']))
for key in ["norm", "Prefactor", "Integral"]:
try:
utils.FreezeParams(Fit, self.srcname, key,
utils.fluxNorm(ResultsDicDC[key]))
except:
continue
LogL0.append(
-Fit.fit(0, optimizer=CurConfig['fitting']['optimizer']))
del Fit #Clean memory
Can = _GetCanvas()
TgrDC = ROOT.TGraph(len(Time), np.array(Time), np.array(LogL0))
TgrDC.Draw("ALP*")
TgrDC = ROOT.TGraph(len(Time), np.array(Time), np.array(LogL0))
TgrDC.SetMarkerColor(2)
TgrDC.Draw("PL*")
#Save the canvas in the LightCurve subfolder
Can.Print(LcOutPath + '_VarIndex.eps')
Can.Print(LcOutPath + '_VarIndex.C')
self.info("Variability index calculation")
print "\t TSvar = ", 2 * (sum(LogL1) - sum(LogL0))
print "\t NDF = ", len(LogL0) - 1
print "\t Chi2 prob = ", ROOT.TMath.Prob(2 * (sum(LogL1) - sum(LogL0)),
len(LogL0) - 1)
print