def get_config(infile, configspec=join(CONFIG_DIR, 'default.conf')):
"""Parse config file, and in addition:
- include default options
- exit with an error if a required option is missing"""
config = ConfigObj(infile, configspec=configspec, file_error=True)
validator = Validator()
# @todo: I'm not sure we always want to copy all default options here
results = config.validate(validator, copy=True)
mes = Loggin.Message()
utils.Checkevtclass(config['event']['evclass'])
if results != True:
for (section_list, key, _) in flatten_errors(config, results):
if key is not None:
mes.warning(
'The "%s" key in the section "%s" failed validation' %
(key, ', '.join(section_list)))
else:
mes.warning('The following section was missing:%s ' %
', '.join(section_list))
mes.warning(' Please check your config file for missing '
'and wrong options!')
mes.error('Config file is not valid.')
return config
def GetIRFS(evtclass, evttype):
from enrico import Loggin
mes = Loggin.Message()
classirfs = {
1: "P8R2_TRANSIENT100A",
2: "P8R2_TRANSIENT100E",
4: "P8R2_TRANSIENT100",
8: "P8R2_TRANSIENT020E",
16: "P8R2_TRANSIENT020",
32: "P8R2_TRANSIENT010E",
64: "P8R2_TRANSIENT010",
128: "P8R2_SOURCE",
256: "P8R2_CLEAN",
521: "P8R2_ULTRACLEAN",
1024: "P8R2_ULTRACLEANVETO",
32768: "P8R2_TRANSIENT100S",
65536: "P8R2_TRANSIENT015S",
16777216: "P8R2_LLE"
}
result = []
val = evttype
while val > 0:
deno = GetSDC(val)
result.append(2**deno)
val = val - result[-1]
typ = []
for t in result:
typ.append(typeirfs[t])
classirf = classirfs[evtclass] + "_V6"
#mes.info("Using IRFS for: class %s and type %s" %(str(classirf),str(typ)))
return classirf, typ
def Print(indices,config,ra,dec,proba,energy,time):
mes = Loggin.Message()
mes.info("Energy\tAngular Sep\tProba\tTime")
mes.info("[MeV] \t[Degrees]")
for i in xrange(min(config['srcprob']['numberPhoton'],indices.size)):
angSep = calcAngSepDeg(config['target']["ra"],config['target']["dec"],ra[indices[indices.size-1-i]],dec[indices[indices.size-1-i]])
print "%2.3e\t%2.3f\t\t%2.5f\t%2.1f"%(energy[indices[indices.size-1-i]],angSep,proba[indices[indices.size-1-i]],time[indices[indices.size-1-i]])
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 GetIRFS(evtclass, evttype, addversion=True):
from enrico import Loggin
mes = Loggin.Message()
classirfs = {
1: "P8R3_TRANSIENT100A",
2: "P8R3_TRANSIENT100E",
4: "P8R3_TRANSIENT100",
8: "P8R3_TRANSIENT020E",
16: "P8R3_TRANSIENT020",
32: "P8R3_TRANSIENT010E",
64: "P8R3_TRANSIENT010",
128: "P8R3_SOURCE",
256: "P8R3_CLEAN",
521: "P8R3_ULTRACLEAN",
1024: "P8R3_ULTRACLEANVETO",
32768: "P8R3_TRANSIENT100S",
65536: "P8R3_TRANSIENT015S",
16777216: "P8R3_LLE"
}
result = []
val = evttype
while val > 0:
deno = GetSDC(val)
result.append(2**deno)
val = val - result[-1]
typ = []
for t in result:
typ.append(typeirfs[t])
# P8R3_SOURCE_V2 is the irf, but iso_P8R3_SOURCE_V2_()_V2.txt does not exist,
# instead it is _V6_()_V2.txt. We need to get around this inconsistency.
if (addversion):
classirf = classirfs[evtclass] + "_V2"
else:
classirf = classirfs[evtclass]
#mes.info("Using IRFS for: class %s and type %s" %(str(classirf),str(typ)))
return classirf, typ
def Checkevtclass(evclass):
classirfs = {
1: "P8R2_TRANSIENT100A",
2: "P8R2_TRANSIENT100E",
4: "P8R2_TRANSIENT100",
8: "P8R2_TRANSIENT020E",
16: "P8R2_TRANSIENT020",
32: "P8R2_TRANSIENT010E",
64: "P8R2_TRANSIENT010",
128: "P8R2_SOURCE",
256: "P8R2_CLEAN",
521: "P8R2_ULTRACLEAN",
1024: "P8R2_ULTRACLEANVETO",
32768: "P8R2_TRANSIENT100S",
65536: "P8R2_TRANSIENT015S",
16777216: "P8R2_LLE"
}
try:
tmp = classirfs[evclass]
except:
from enrico import Loggin
mes = Loggin.Message()
mes.error("evclass value in config file not valid")
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
if __name__ == '__main__':
import sys
try:
infile = sys.argv[1]
except:
from enrico import Loggin
mes = Loggin.Message()
mes.error('Config file not found.')
FindSrc(infile)
def WriteXml(lib, doc, srclist, config):
from enrico import Loggin
mes = Loggin.Message()
"""Fill and write the library of sources into an XML file"""
emin = config['energy']['emin']
emax = config['energy']['emax']
Galname = "GalDiffModel"
Isoname = "IsoDiffModel"
#test if the user provides diffuse files. if not use the default one
if config['model']['diffuse_gal_dir'] == "":
Gal_dir = env.DIFFUSE_DIR
else:
Gal_dir = config['model']['diffuse_gal_dir']
if config['model']['diffuse_iso_dir'] == "":
Iso_dir = env.DIFFUSE_DIR
else:
Iso_dir = config['model']['diffuse_iso_dir']
if config['model']['diffuse_gal'] == "":
Gal = Gal_dir + "/" + env.DIFFUSE_GAL
else:
Gal = Gal_dir + "/" + config['model']['diffuse_gal']
if config['model']['diffuse_iso'] == "":
try:
Iso = utils.GetIso(config["event"]["evclass"],
config["event"]["evtype"])
if not (os.path.isfile(Iso)):
raise RuntimeError
except:
mes.warning("Cannot guess Iso file, please have a look")
Iso = Iso_dir + "/" + env.DIFFUSE_ISO_SOURCE
else:
Iso = Iso_dir + "/" + config['model']['diffuse_iso']
#add diffuse sources
addDiffusePL(lib, Iso, free=1, value=1.0, max=10.0, min=1.0, name=Isoname)
addGalprop(lib,
Gal,
free=1,
value=1.0,
scale=1.0,
max=10.0,
min=.010,
name=Galname)
print "Iso model file ", Iso
print "Galactic model file ", Gal
# loop over the list of sources and add it to the library
for i in xrange(len(srclist)):
name = srclist[i].get('name')
ra = srclist[i].get('ra')
dec = srclist[i].get('dec')
free = srclist[i].get('IsFree')
spectype = srclist[i].get('SpectrumType')
extendedName = srclist[i].get('ExtendedName')
# Check the spectrum model
if spectype == "PowerLaw":
addPSPowerLaw1(lib,
name,
ra,
dec,
eflux=srclist[i].get('scale'),
flux_free=free,
flux_value=srclist[i].get('flux'),
index_free=free,
index_value=srclist[i].get('index'),
extendedName=extendedName)
if spectype == "PowerLaw2":
addPSPowerLaw2(lib,
name,
ra,
dec,
emin=emin,
emax=emax,
flux_free=free,
flux_value=srclist[i].get('flux'),
index_free=free,
index_value=srclist[i].get('index'),
extendedName=extendedName)
if spectype == "LogParabola":
addPSLogparabola(lib,
name,
ra,
dec,
enorm=srclist[i].get('scale'),
norm_free=free,
norm_value=srclist[i].get('flux'),
alpha_free=free,
alpha_value=abs(srclist[i].get('index')),
beta_free=free,
beta_value=srclist[i].get('beta'),
extendedName=extendedName)
if spectype == "PLExpCutoff" or spectype == "PLSuperExpCutoff":
addPSPLSuperExpCutoff(lib,
name,
ra,
dec,
eflux=srclist[i].get('scale'),
flux_free=free,
flux_value=srclist[i].get('flux'),
index1_free=free,
index1_value=srclist[i].get('index'),
cutoff_free=free,
cutoff_value=srclist[i].get('cutoff'),
extendedName=extendedName)
folder = config['out']
os.system('mkdir -p ' + folder)
output = config['file']['xml']
mes.info("write the Xml file in " + output)
open(output, 'w').write(doc.toprettyxml(' ')) #save it
def GetlistFromFits(config, catalog):
from enrico import Loggin
mes = Loggin.Message()
"""Read the config and catalog file and generate the list of sources to include"""
#Get the informations for the config file
srcname = config['target']['name']
ra_src = config['target']['ra']
dec_src = config['target']['dec']
ra_space = config['space']['xref']
dec_space = config['space']['yref']
emin = config['energy']['emin']
roi = config['space']['rad'] + 2
max_radius = config['model']['max_radius']
min_significance = config['model']['min_significance']
model = config['target']['spectrum']
if model == "Generic":
mes.warning("Generic model found. Will turn it to PowerLaw")
model = "PowerLaw"
#read the catalog file
cfile = pyfits.open(catalog)
data = cfile[1].data
names = data.field('Source_Name')
ra = data.field('RAJ2000')
dec = data.field('DEJ2000')
flux = data.field('Flux_Density')
pivot = data.field('Pivot_Energy')
index = data.field('Spectral_Index')
try: # valid for the 2FGH, not for the 1FHL
cutoff = data.field('Cutoff')
beta = data.field('beta')
spectype = data.field('SpectrumType')
except:
cutoff = np.zeros(names.size)
beta = np.zeros(names.size)
spectype = np.array(names.size * ["PowerLaw"])
pivot *= 1e3 ## energy in the 1FHL are in GeV
flux *= 1e3
try:
extendedName = data.field('Extended_Source_Name')
extendedfits = cfile[5].data.field('Spatial_Filename')
extendedsrcname = cfile[5].data.field('Source_Name')
except:
mes.warning(
"Cannot find the extended source list: please check the xml")
extendedName = np.array(names.size * [""])
extendedsrcname = []
sigma = data.field('Signif_Avg')
sources = []
Nfree = 0
Nextended = 0
#loop over all the sources of the catalog
for i in xrange(len(names)):
#distance from the center of the maps
rspace = utils.calcAngSepDeg(float(ra[i]), float(dec[i]), ra_space,
dec_space)
#distance for the target
rsrc = utils.calcAngSepDeg(float(ra[i]), float(dec[i]), ra_src,
dec_src)
j = 0
extended_fitsfilename = ""
for extname in extendedsrcname:
if extname == extendedName[i]:
extended_fitsfilename = extendedfits[j]
j += 1
# if the source has a separation less than 0.1deg to the target and has
# the same model type as the one we want to use, insert as our target
# with our given coordinates
if rsrc < .1 and sigma[i] > min_significance and spectype[
i] == model and extended_fitsfilename == "":
Nfree += 1
sources.insert(
0, {
'name': srcname,
'ra': ra_src,
'dec': dec_src,
'flux': flux[i],
'index': -index[i],
'scale': pivot[i],
'cutoff': cutoff[i],
'beta': beta[i],
'IsFree': 1,
'SpectrumType': spectype[i],
'ExtendedName': extended_fitsfilename
})
elif rsrc < max_radius and rsrc > .1 and sigma[i] > min_significance:
# if the source is close to the target : add it as a free source
Nfree += 1
sources.append({
'name': names[i],
'ra': ra[i],
'dec': dec[i],
'flux': flux[i],
'index': -index[i],
'scale': pivot[i],
'cutoff': cutoff[i],
'beta': beta[i],
'IsFree': 1,
'SpectrumType': spectype[i],
'ExtendedName': extended_fitsfilename
})
if not (extended_fitsfilename == ""):
mes.info("Adding extended source " + extendedName[i] +
", Catalogue name is " + names[i])
Nextended += 1
else:
# if the source is inside the ROI: add it as a frozen source
if rspace < roi and rsrc > .1 and sigma[i] > min_significance:
sources.append({
'name': names[i],
'ra': ra[i],
'dec': dec[i],
'flux': flux[i],
'index': -index[i],
'scale': pivot[i],
'cutoff': cutoff[i],
'beta': beta[i],
'IsFree': 0,
'SpectrumType': spectype[i],
'ExtendedName': extended_fitsfilename
})
if not (extended_fitsfilename == ""):
mes.info("Adding extended source " + extendedName[i] +
", Catalogue name is " + names[i])
Nextended += 1
# if the target has not been added from catalog, add it now
if sources[0]['name'] != srcname:
Nfree += 1
#add the target to the list of sources in first position
sources.insert(
0, {
'name': srcname,
'ra': ra_src,
'dec': dec_src,
'flux': 1e-9,
'index': -2,
'scale': emin,
'cutoff': 1e4,
'beta': 0.1,
'IsFree': 1,
'SpectrumType': model,
'ExtendedName': ""
})
mes.info("Summary of the XML model generation")
print "Add ", len(sources), " sources in the ROI of ", roi, "(", config[
'space']['rad'], "+ 2 ) degrees"
print Nfree, " sources have free parameters inside ", max_radius, " degrees"
print Nextended, " source(s) is (are) extended"
#save log of the genration of the xml
save = "catalog: " + catalog + "\n"
save += "Add " + str(
len(sources)) + " sources in the ROI of " + str(roi) + "(" + str(
config['space']['rad']) + "+ 2 ) degrees\n"
save += " sources have free parameters inside " + str(
max_radius) + " degrees\n"
save += str(Nextended) + " source(s) is (are) extended\n"
savexml = open(
config['out'] + '/' + config['target']['name'] + "_" +
config['target']['spectrum'] + "_generation.log", "w")
savexml.write(save)
savexml.close()
return sources
def PlotDataPoints(config,pars):
"""Collect the data points/UL and generate a TGraph for the points
and a list of TArrow for the UL. All is SED format"""
#Preparation + declaration of arrays
arrows = []
NEbin = int(config['Ebin']['NumEnergyBins'])
lEmax = np.log10(float(config['energy']['emax']))
lEmin = np.log10(float(config['energy']['emin']))
Epoint = np.zeros(NEbin)
EpointErrp = np.zeros(NEbin)
EpointErrm = np.zeros(NEbin)
Fluxpoint = np.zeros(NEbin)
FluxpointErrp = np.zeros(NEbin)
FluxpointErrm = np.zeros(NEbin)
ener = np.logspace(lEmin, lEmax, NEbin + 1)
mes = Loggin.Message()
mes.info("Save Ebin results in ",pars.PlotName+".Ebin.dat")
dumpfile = open(pars.PlotName+".Ebin.dat",'w')
dumpfile.write("# Energy (MeV)\tEmin (MeV)\tEmax (MeV)\tE**2. dN/dE (erg.cm-2s-1)\tGaussianError\tMinosNegativeError\tMinosPositiveError\n")
from enrico.constants import EbinPath
for i in xrange(NEbin):#Loop over the energy bins
E = int(pow(10, (np.log10(ener[i + 1]) + np.log10(ener[i])) / 2))
filename = (config['out'] + '/'+EbinPath+str(NEbin)+'/' + config['target']['name'] +
"_" + str(i) + ".conf")
try:#read the config file of each data points
CurConf = get_config(filename)
mes.info("Reading "+filename)
results = utils.ReadResult(CurConf)
except:
mes.warning("cannot read the Results of energy "+ str(E))
continue
#fill the energy arrays
Epoint[i] = E
EpointErrm[i] = E - results.get("Emin")
EpointErrp[i] = results.get("Emax") - E
dprefactor = 0
#Compute the flux or the UL (in SED format)
if results.has_key('Ulvalue'):
PrefUl = utils.Prefactor(results.get("Ulvalue"),results.get("Index"),
results.get("Emin"),results.get("Emax"),E)
Fluxpoint[i] = MEV_TO_ERG * PrefUl * Epoint[i] ** 2
arrows.append(ROOT.TArrow(Epoint[i], Fluxpoint[i], Epoint[i],
Fluxpoint[i] * 0.5, 0.02, "|>"))
else : #Not an UL : compute points + errors
Fluxpoint[i] = MEV_TO_ERG * results.get("Prefactor") * Epoint[i] ** 2
dprefactor = results.get("dPrefactor")
try:
down = abs(results.get("dPrefactor-"))
up = results.get("dPrefactor+")
if down==0 or up ==0 :
mes.error("cannot get Error value")
FluxpointErrp[i] = MEV_TO_ERG * up * Epoint[i] ** 2
FluxpointErrm[i] = MEV_TO_ERG * down * Epoint[i] ** 2
except:
try:
err = MEV_TO_ERG * dprefactor * Epoint[i] ** 2
FluxpointErrp[i] = err
FluxpointErrm[i] = err
except:
pass
mes.info("Energy bins results")
print "Energy = ",Epoint[i]
print "E**2. dN/dE = ",Fluxpoint[i]," + ",FluxpointErrp[i]," - ",FluxpointErrm[i]
#Save the data point in a ascii file
dumpfile.write(str(Epoint[i])+"\t"+str(results.get("Emin"))+"\t"+str( results.get("Emax"))+"\t"+str(Fluxpoint[i])+"\t"+str( MEV_TO_ERG * dprefactor * Epoint[i] ** 2)+"\t"+str(FluxpointErrm[i])+"\t"+str(FluxpointErrp[i])+"\n")
#create a TGraph for the points
tgpoint = ROOT.TGraphAsymmErrors(NEbin, Epoint, Fluxpoint, EpointErrm,
EpointErrp, FluxpointErrm, FluxpointErrp)
tgpoint.SetMarkerStyle(20)
dumpfile.close()
return tgpoint, arrows
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 GetlistFromFits(config, catalog):
from enrico import Loggin
mes = Loggin.Message()
"""Read the config and catalog file and generate the list of sources to include"""
#Get the informations for the config file
srcname = config['target']['name']
ra_src = config['target']['ra']
dec_src = config['target']['dec']
redshift = config['target']['redshift']
ebl_model = config['target']['ebl_model']
ra_space = config['space']['xref']
dec_space = config['space']['yref']
emin = config['energy']['emin']
roi = config['space']['rad']+2
max_radius = config['model']['max_radius']
min_significance = config['model']['min_significance']
model = config['target']['spectrum']
if model == "Generic":
mes.warning("Generic model found. Will turn it to PowerLaw")
model = "PowerLaw"
#read the catalog file
cfile = fits.open(catalog)
data = cfile[1].data
names = data.field('Source_Name')
ra = data.field('RAJ2000')
dec = data.field('DEJ2000')
flux = data.field('Flux_Density')
pivot = data.field('Pivot_Energy')
spectype = data.field('SpectrumType')
is8yr = 'FL8Y' in cfile[1].header['CDS-NAME']
try : # valid for the 2FGH, not for the 1FHL
if is8yr:
spectype = data.field('SpectrumType')
index = np.zeros(names.size)
cutoff = np.zeros(names.size)
expfac = np.zeros(names.size)
beta = np.zeros(names.size)
for k,spec in enumerate(spectype):
if spec == 'PowerLaw':
index[k] = data.field('PL_Index')[k]
if spec == 'LogParabola':
index[k] = data.field('LP_Index')[k]
beta[k] = data.field('LP_beta')[k]
if spec == 'PLSuperExpCutoff2':
# From the makeFL8Yxml.py script
index[k] = data.field('PLEC_Index')[k]
expfac = data.field('PLEC_Expfactor')[k]
expind = data.field('PLEC_Exp_Index')[k]
cutoff[k] =(1./expfac)**(1./expind)
#cutoff = data.field('Cutoff')
#beta = data.field('LP_beta')
else:
index = data.field('Spectral_Index')
cutoff = data.field('Cutoff')
beta = data.field('beta')
except :
raise
index = data.field('Spectral_Index')
cutoff = np.zeros(names.size)
beta = np.zeros(names.size)
spectype = np.array(names.size*["PowerLaw"])
pivot *= 1e3 ## energy in the 1FHL are in GeV
flux *= 1e3
try :
extendedName = data.field('Extended_Source_Name')
if is8yr:
extendedfits = cfile[2].data.field('Spatial_Filename')
extendedsrcname = cfile[2].data.field('Source_Name')
else:
extendedfits = cfile[5].data.field('Spatial_Filename')
extendedsrcname = cfile[5].data.field('Source_Name')
except:
raise
mes.warning("Cannot find the extended source list: please check the xml")
extendedName = np.array(names.size*[""])
extendedsrcname = []
sigma = data.field('Signif_Avg')
sources = []
Nfree = 0
Nextended = 0
#loop over all the sources of the catalog
for i in xrange(len(names)):
#distance from the center of the maps
rspace = utils.calcAngSepDeg(float(ra[i]), float(dec[i]), ra_space, dec_space)
#distance for the target
rsrc = utils.calcAngSepDeg(float(ra[i]), float(dec[i]), ra_src, dec_src)
j=0
extended_fitsfilename = ""
for extname in extendedsrcname:
if extname == extendedName[i]:
extended_fitsfilename = extendedfits[j]
j+=1
# if the source has a separation less than 0.1deg to the target and has
# the same model type as the one we want to use, insert as our target
# with our given coordinates
if rsrc < .1 and sigma[i] > min_significance and spectype[i] == model and extended_fitsfilename=="":
Nfree += 1
mes.info("Adding [free] target source, Catalog name is %s, dist is %.2f and TS is %.2f" %(names[i],rsrc,sigma[i]) )
sources.insert(0,{'name': srcname, 'ra': ra_src, 'dec': dec_src,
'flux': flux[i], 'index': -index[i], 'scale': pivot[i],
'cutoff': cutoff[i], 'beta': beta[i], 'IsFree': 1,
'SpectrumType': spectype[i], 'ExtendedName': extended_fitsfilename})
elif rsrc < max_radius and rsrc > .1 and sigma[i] > min_significance:
# if the source is close to the target : add it as a free source
Nfree += 1
mes.info("Adding [free] source, Catalog name is %s, dist is %.2f and TS is %.2f" %(names[i],rsrc,sigma[i]) )
if not(extended_fitsfilename==""):
if not os.path.isfile(extended_fitsfilename):
mes.warning("Filename %s for extended source %s does not exist. Skipping." %(extended_fitsfilename,extendedName[i]))
continue
mes.info("Adding extended source "+extendedName[i]+", Catalogue name is "+names[i])
Nextended+=1
sources.append({'name': names[i], 'ra': ra[i], 'dec': dec[i],
'flux': flux[i], 'index': -index[i], 'scale': pivot[i],
'cutoff': cutoff[i], 'beta': beta[i], 'IsFree': 1,
'SpectrumType': spectype[i], 'ExtendedName': extended_fitsfilename})
# srcs that were kept fixed in the 3FGL: add them as fixed srcs
elif rspace < roi and sigma[i] == -np.inf:
mes.info("Adding [fixed in 3FGL] source, Catalog name is %s, dist is %.2f and TS is %.2f" %(names[i],rspace,sigma[i]) )
if not(extended_fitsfilename==""):
if not os.path.isfile(extended_fitsfilename):
mes.warning("Filename %s for extended source %s does not exist. Skipping." %(extended_fitsfilename,extendedName[i]))
continue
mes.info("Adding extended source "+extendedName[i]+", Catalogue name is "+names[i])
Nextended+=1
sources.append({'name': names[i], 'ra': ra[i], 'dec': dec[i],
'flux': flux[i], 'index': -index[i], 'scale': pivot[i],
'cutoff': cutoff[i], 'beta': beta[i], 'IsFree': 0,
'SpectrumType': spectype[i],'ExtendedName': extended_fitsfilename})
else:
# if the source is inside the ROI: add it as a frozen source
if rspace < roi and rsrc > .1 and sigma[i] > min_significance:
mes.info("Adding [fixed] source, Catalog name is %s, dist is %.2f and TS is %.2f" %(names[i],rsrc,sigma[i]) )
if not(extended_fitsfilename==""):
if not os.path.isfile(extended_fitsfilename):
mes.warning("Filename %s for extended source %s does not exist. Skipping." %(extended_fitsfilename,extendedName[i]))
continue
mes.info("Adding extended source "+extendedName[i]+", Catalogue name is "+names[i])
Nextended+=1
sources.append({'name': names[i], 'ra': ra[i], 'dec': dec[i],
'flux': flux[i], 'index': -index[i], 'scale': pivot[i],
'cutoff': cutoff[i], 'beta': beta[i], 'IsFree': 0,
'SpectrumType': spectype[i],'ExtendedName': extended_fitsfilename})
# if the target has not been added from catalog, add it now
if sources[0]['name']!=srcname:
Nfree += 1
#add the target to the list of sources in first position
sources.insert(0,{'name':srcname, 'ra': ra_src, 'dec': dec_src,
'flux': 1e-9, 'index':-2, 'scale': emin,
'cutoff': 1e4, 'beta': 0.1, 'IsFree': 1,
'SpectrumType': model,'ExtendedName': ""})
mes.info("Summary of the XML model generation")
print "Add ", len(sources), " sources in the ROI of ", roi, "(",config['space']['rad'],"+ 2 ) degrees"
print Nfree, " sources have free parameters inside ", max_radius, " degrees"
print Nextended, " source(s) is (are) extended"
#save log of the generation of the xml
save = "catalog: "+catalog+"\n"
save += "Add "+str(len(sources))+" sources in the ROI of "+str(roi)+ "("+str(config['space']['rad'])+"+ 2 ) degrees\n"
save += " sources have free parameters inside "+str(max_radius)+" degrees\n"
save += str(Nextended)+" source(s) is (are) extended\n"
savexml = open(config['out']+'/'+ config['target']['name']+"_"+config['target']['spectrum']+"_generation.log","w")
savexml.write(save)
savexml.close()
return sources
def query_config():
import os
"""Make a new config object, asking the user for required options"""
config = ConfigObj(indent_type='\t')
mes = Loggin.Message()
mes.info('Please provide the following required options [default] :')
config['out'] = os.getcwd()
out = raw_input('Output directory [' + config['out'] + '] : ')
if not (out == ''):
config['out'] = out
# Informations about the source
config['target'] = {}
config['target']['name'] = raw_input('Target Name : ')
config['target']['ra'] = raw_input('Right Ascension: ')
config['target']['dec'] = raw_input('Declination: ')
config['target']['redshift'] = '0'
redshift = raw_input('redshift, no effect if null [0] : ')
if not (redshift == ''):
config['target']['redshift'] = redshift
config['target']['ebl_model'] = raw_input(
'ebl model to used\n'
'0=Kneiske, 1=Primack05, 2=Kneiske_HighUV, 3=Stecker05, '
'4=Franceschini, 5=Finke, 6=Gilmore : ')
message = (
'Options are : PowerLaw, PowerLaw2, LogParabola, '
'PLExpCutoff, Generic\nGeneric is design to allow the user to fit with non-supported models\n'
'EBL absorption can be added for PowerLaw2, LogParabola, PLExpCutoff\n'
'Spectral Model [PowerLaw] : ')
config['target']['spectrum'] = 'PowerLaw'
model = raw_input(message)
if not (model == ''):
config['target']['spectrum'] = model
# informations about the ROI
config['space'] = {}
config['space']['xref'] = config['target']['ra']
config['space']['yref'] = config['target']['dec']
config['space']['rad'] = '15'
roi = raw_input('ROI Size [15] : ')
if not (roi == ''):
config['space']['rad'] = roi
# informations about the input files
config['file'] = {}
if USE_FULLMISSION_SPACECRAFT:
config['file'][
'spacecraft'] = DOWNLOAD_DIR + '/lat_spacecraft_merged.fits'
else:
config['file']['spacecraft'] = '@' + DOWNLOAD_DIR + '/spacecraft.lis'
ft2 = raw_input('FT2 file [' + config['file']['spacecraft'] + '] : ')
if not (ft2 == ''):
config['file']['spacecraft'] = ft2
config['file']['event'] = DOWNLOAD_DIR + '/events.lis'
ft1list = raw_input('FT1 list of files [' + config['file']['event'] +
'] : ')
if not (ft1list == ''):
config['file']['event'] = ft1list
config['file']['xml'] = config['out'] + '/' + config['target'][
'name'] + '_' + config['target']['spectrum'] + '_model.xml'
tag = raw_input('tag [LAT_Analysis] : ')
if not (tag == ''):
config['file']['tag'] = tag
else:
config['file']['tag'] = 'LAT_Analysis'
# informations about the time
config['time'] = {}
tmin = raw_input('Start time [-1=START] : ')
ft2 = config['file']['spacecraft']
if not (tmin == '') and float(tmin) >= 0:
config['time']['tmin'] = tmin
else:
config['time']['tmin'] = get_times_from_spacecraft(ft2,
target=['tmin'])[0]
tmax = raw_input('End time [-1=END] : ')
if not (tmax == '') and float(tmax) >= 0:
config['time']['tmax'] = tmax
else:
config['time']['tmax'] = get_times_from_spacecraft(ft2,
target=['tmax'])[1]
# informations about the energy
config['energy'] = {}
emin = raw_input('Emin [100] : ')
if not (emin == ''):
config['energy']['emin'] = emin
else:
config['energy']['emin'] = '100'
emax = raw_input('Emax [300000] : ')
if not (emax == ''):
config['energy']['emax'] = emax
else:
config['energy']['emax'] = '300000'
# informations about the event class
config['event'] = {}
irfs = raw_input('IRFs [CALDB] : ')
if not (irfs == ''):
config['event']['irfs'] = irfs
else:
config['event']['irfs'] = 'CALDB'
if irfs == '':
ok = False
while not (ok):
evclass = raw_input('evclass [128] : ')
if not (evclass == ''):
config['event']['evclass'] = evclass
else:
config['event']['evclass'] = '128'
evtype = raw_input('evtype [3] : ')
if not (evtype == ''):
config['event']['evtype'] = evtype
else:
config['event']['evtype'] = '3'
print "Corresponding IRFs\t=\t", utils.GetIRFS(
float(config['event']['evclass']),
float(config['event']['evtype']))
ans = raw_input('Is this ok? [y] : ')
if ans == "y" or ans == '':
ok = True
config['analysis'] = {}
zmax = utils.GetZenithCut(float(config['event']['evclass']),
float(config['event']['evtype']),
float(config['energy']['emin']))
print "Corresponding zmax = ", zmax
config["analysis"]["zmax"] = zmax
return get_config(config)
def Contour(config):
# ROOT.gROOT.SetBatch(ROOT.kTRUE)
# cres = ROOT.TCanvas("Contour")
config["Spectrum"]["FitsGeneration"] = "no"
parname1 = config["Contours"]["parname1"]
parname2 = config["Contours"]["parname2"]
FitRunner,Fit = RunGTlike.GenAnalysisObjects(config)
spectrum = Fit[FitRunner.obs.srcname].funcs['Spectrum']
ParName = spectrum.paramNames
mes = Loggin.Message()
mes.info("Computing Contours for "+parname1+" and "+parname2)
### Check part !!!!
findpar2 = findpar1 = False
for par in ParName : #Loop over the parameters to check
if par == parname1:
findpar1 = True
if not(spectrum.getParam(par).isFree()):
mes.error(parname1+" is not a free parameter")
if par == parname2:
findpar2 = True
if not(spectrum.getParam(par).isFree()):
mes.error(parname2+" is not a free parameter")
if not(findpar1):
mes.error(parname1+" is not a valid parameter")
if not(findpar2):
mes.error(parname2+" is not a valid parameter")
bestloglike = Fit.fit(0,covar=False,optimizer=config['fitting']['optimizer'])
print spectrum
print "Min LogLikelihood =",bestloglike
## get values
ParValue1 = spectrum.getParam(parname1).value()
ParError1 = spectrum.getParam(parname1).error()
bmin1,bmax1 = spectrum.getParam(parname1).getBounds()
bmin1 = max(bmin1,ParValue1-20*ParError1)
bmax1 = min(bmax1,ParValue1+20*ParError1)
ParValue2 = spectrum.getParam(parname2).value()
ParError2 = spectrum.getParam(parname2).error()
bmin2,bmax2 = spectrum.getParam(parname2).getBounds()
bmin2 = max(bmin2,ParValue2-20*ParError2)
bmax2 = min(bmax2,ParValue2+20*ParError2)
N = 100
param2 = numpy.zeros(N)
loglike = ROOT.TH2F("loglike","Contours (68%, 95%, 99%)",N,bmin1,bmax1,N,bmin2,bmax2)
spectrum.getParam(parname2).setFree(0)
mes.info("Boundaries for "+parname1+" ["+str(bmin1)+","+str(bmax1)+"]")
mes.info("Boundaries for "+parname2+" ["+str(bmin2)+","+str(bmax2)+"]")
for i in xrange(N):
param2[i] = bmin2 + (bmax2-bmin2)*i/(N-1.)
spectrum.getParam(parname2).setValue(param2[i])
param1,ll = MakeScan(Fit,spectrum,parname1,bmin1,bmax1,config['fitting']['optimizer'],N)
for j in xrange(N):
loglike.Fill(param1[j],param2[i],ll[j])
os.system("mkdir -p "+config["out"]+"/"+cst.ScanPath)
cres = ROOT.TCanvas("Contours")
loglike.SetMinimum(bestloglike);
loglike.SetMaximum(bestloglike+3);
loglike.SetXTitle(parname1);
loglike.SetYTitle(parname2);
loglike.SetStats(000)
loglike.SetContour(3)
loglike.SetContourLevel(0,bestloglike+0.5)
loglike.SetContourLevel(1,bestloglike+4./2.)
loglike.SetContourLevel(2,bestloglike+6.63/2.)
loglike.Draw("CONT1");
tgrres = ROOT.TGraphErrors(2,array.array('f',[ParValue1,ParValue1]),array.array('f',[ParValue2,ParValue2]),array.array('f',[ParError1,ParError1]),array.array('f',[ParError2,ParError2]))
tgrres.Draw(".pz")
cres.Print(config["out"]+"/"+cst.ScanPath+ "/Contours_"+parname1+"_"+parname2+".eps")
cres.Print(config["out"]+"/"+cst.ScanPath+ "/Contours_"+parname1+"_"+parname2+".C")
cres.Print(config["out"]+"/"+cst.ScanPath+ "/Contours_"+parname1+"_"+parname2+".png")
mes.success("Scan Performed")
def WriteXml(lib, doc, srclist, config):
from enrico import Loggin
mes = Loggin.Message()
"""Fill and write the library of sources into an XML file"""
emin = config['energy']['emin']
emax = config['energy']['emax']
Galname = "GalDiffModel"
Isoname = "IsoDiffModel"
#test if the user provides diffuse files. if not use the default one
if config['model']['diffuse_gal_dir'] == "":
Gal_dir = env.DIFFUSE_DIR
else:
Gal_dir = config['model']['diffuse_gal_dir']
if config['model']['diffuse_iso_dir'] == "":
Iso_dir = env.DIFFUSE_DIR
else:
Iso_dir = config['model']['diffuse_iso_dir']
if config['model']['diffuse_gal'] == "":
Gal = Gal_dir + "/" + env.DIFFUSE_GAL
else:
Gal = Gal_dir + "/" + config['model']['diffuse_gal']
if config['model']['diffuse_iso'] == "":
try :
Iso = utils.GetIso(config["event"]["evclass"],config["event"]["evtype"])
if not(os.path.isfile(Iso)):
raise RuntimeError
except:
mes.warning("Cannot find Iso file %s, please have a look. Switching to default one" %Iso)
Iso = Iso_dir + "/" + env.DIFFUSE_ISO_SOURCE
else:
Iso = Iso_dir + "/" + config['model']['diffuse_iso']
#add diffuse sources
addDiffusePL(lib, Iso, free=1, value=1.0,
max=10.0, min=1.0, name=Isoname)
addGalprop(lib, Gal, free=1, value=1.0, scale=1.0,
max=10.0, min=.010, name=Galname)
print "Iso model file ",Iso
print "Galactic model file ",Gal
yesnodict = {}
for y in ['yes',True,'true',1,1.0,'1','1.0']:
yesnodict[y] = 1
for n in ['no',False,'false',0,0.0,'0','0.0']:
yesnodict[n] = 0
try:
ebldict = {}
ebldict['tau_norm'] = 1.0
ebldict['free_redshift'] = 0 # NOTE:ToDo
ebldict['free_tau_norm'] = yesnodict[config['target']['fit_tau']]
ebldict['redshift'] = float(config['target']['redshift'])
ebldict['model'] = int(config['target']['ebl_model'])
if ebldict['redshift'] < 1.e-3:
ebldict = None
except NameError:
ebldict = None
# loop over the list of sources and add it to the library
for i in xrange(len(srclist)):
name = srclist[i].get('name')
if (name == config['target']['name']):
ebl = ebldict
else:
ebl = None
ra = srclist[i].get('ra')
dec = srclist[i].get('dec')
free = srclist[i].get('IsFree')
spectype = srclist[i].get('SpectrumType')
extendedName = srclist[i].get('ExtendedName')
# Check the spectrum model
if spectype.strip() == "PowerLaw":
if (ebl==None):
addPSPowerLaw1(lib, name, ra, dec, "None",
eflux=srclist[i].get('scale'),
flux_free=free, flux_value=srclist[i].get('flux'),
index_free=free, index_value=srclist[i].get('index'),extendedName=extendedName)
if (ebl!=None):
addPSLogparabola(lib, name, ra, dec, ebl,
norm_free=free, norm_value=srclist[i].get('flux'),
alpha_free=free, alpha_value=abs(srclist[i].get('index')),
beta_free=0, beta_min=0, beta_max=0,
beta_value=0,extendedName=extendedName)
elif spectype.strip() == "PowerLaw2":
addPSPowerLaw2(lib, name, ra, dec, ebl,
emin=emin, emax=emax,
flux_free=free, flux_value=srclist[i].get('flux'),
index_free=free, index_value=srclist[i].get('index'),extendedName=extendedName)
elif spectype.strip() == "LogParabola":
addPSLogparabola(lib, name, ra, dec, ebl, enorm=srclist[i].get('scale'),
norm_free=free, norm_value=srclist[i].get('flux'),
alpha_free=free, alpha_value=abs(srclist[i].get('index')),
beta_free=free, beta_value=srclist[i].get('beta'),extendedName=extendedName)
elif spectype.strip() == "PLExpCutoff" or spectype == "PLSuperExpCutoff" or spectype == "PLSuperExpCutoff2":
addPSPLSuperExpCutoff(lib, name, ra, dec, ebl,
eflux=srclist[i].get('scale'),
flux_free=free, flux_value=srclist[i].get('flux'),
index1_free=free, index1_value=srclist[i].get('index'),
cutoff_free=free, cutoff_value=srclist[i].get('cutoff'),extendedName=extendedName)
else:
print('Warning!!!, unknown model %s' %spectype.strip())
folder = config['out']
utils.mkdir_p(folder)
output = config['file']['xml']
mes.info("write the Xml file in "+output)
open(output, 'w').write(doc.toprettyxml(' '))#save it
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 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