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 run_retry(macro, tries=5):
"""
The Fermi LAT sometimes fail with annoying Runtime errors,
try to catch them and re-run the macro that failed.
Do that up to 5 times with random waiting times.
"""
mes = Loggin.Message()
for retry in range(tries):
try:
macro.run()
except RuntimeError:
# Wait between 10 and 20 seconds to try again
mes.warning("An error ocurred, retrying ...")
sleep(10. * random() + 10.)
continue
else:
return (macro)
mes.error("An error ocurred and could not be recovered. Exiting!")
sys.exit(1)
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 GenAnalysisObjects(config, verbose=1, xmlfile=""):
mes = Loggin.Message()
#check is the summed likelihood method should be used and get the
#Analysis objects (observation and (Un)BinnedAnalysis objects)
folder = config['out']
# If there are no xml files, create it and print a warning
if len(glob.glob(config['file']['xml'].replace('.xml', '*.xml'))) == 0:
mes.warning("Xml not found, creating one for the given config %s" %
config['file']['xml'])
XmlMaker(config)
Fit = SummedLikelihood.SummedLikelihood()
if hasKey(config, 'ComponentAnalysis') == True:
# Create one obs instance for each component
configs = [None] * 4
Fits = [None] * 4
Analyses = [None] * 4
if isKey(config['ComponentAnalysis'], 'FrontBack') == 'yes':
from enrico.data import fermievtypes
mes.info("Breaking the analysis in Front/Back events")
# Set Summed Likelihood to True
oldxml = config['file']['xml']
for k, TYPE in enumerate(["FRONT", "BACK"]):
configs[k] = ConfigObj(config)
configs[k]['event']['evtype'] = fermievtypes[TYPE]
try:
Analyses[k] = Analysis(folder, configs[k], \
configgeneric=config,\
tag=TYPE, verbose = verbose)
if not (xmlfile == ""): Analyses[k].obs.xmlfile = xmlfile
Fits[k] = Analyses[k].CreateLikeObject()
Fit.addComponent(Fits[k])
except RuntimeError, e:
if 'RuntimeError: gtltcube execution failed' in str(e):
mes.warning("Event type %s is empty! Error is %s" %
(TYPE, str(e)))
FitRunner = Analyses[0]
def run(infile):
from enrico import utils
from enrico import energybin
from enrico.config import get_config
from enrico import Loggin
mes = Loggin.Message()
"""Run an entire Fermi analysis (spectrum) by reading a config file"""
config = get_config(infile)
folder = config['out']
utils.mkdir_p(folder)
FitRunner, Fit = GenAnalysisObjects(config)
# create all the fit files and run gtlike
FitRunner.PerformFit(Fit)
sedresult = None
#plot the SED and model map if possible and asked
if float(config['UpperLimit']['TSlimit']) < Fit.Ts(
config['target']['name']):
if config['Spectrum']['ResultPlots'] == 'yes':
from enrico.constants import SpectrumPath
utils.mkdir_p("%s/%s/" % (config['out'], SpectrumPath))
sedresult = FitRunner.ComputeSED(Fit, dump=True)
else:
sedresult = FitRunner.ComputeSED(Fit, dump=False)
if (config['energy']['decorrelation_energy'] == 'yes'):
#Update the energy scale to decorrelation energy
mes.info(
'Setting the decorrelation energy as new Scale for the spectral parameters'
)
spectrum = Fit[FitRunner.obs.srcname].funcs['Spectrum']
modeltype = spectrum.genericName()
genericName = Fit.model.srcs[
FitRunner.obs.srcname].spectrum().genericName()
varscale = None
if genericName == "PowerLaw2":
varscale = None
elif genericName in [
"PowerLaw", "PLSuperExpCutoff",
"EblAtten::PLSuperExpCutoff"
]:
varscale = "Scale"
elif genericName in ["LogParabola","EblAtten::LogParabola", \
"BrokenPowerLaw", "EblAtten::BrokenPowerLaw"]:
varscale = "Eb"
if varscale is not None:
spectrum.getParam(varscale).setValue(sedresult.decE)
FitRunner.PerformFit(Fit)
#Get and dump the target specific results
Result = FitRunner.GetAndPrintResults(Fit)
utils.DumpResult(Result, config)
# Make energy bins by running a *new* analysis
Nbin = config['Ebin']['NumEnergyBins']
FitRunner.config['file']['parent_config'] = infile
if config['Spectrum']['ResultParentPlots'] == "yes":
plot_sed_fromconfig(get_config(config['file']['parent_config']),
ignore_missing_bins=True)
if config['Spectrum']['ResultPlots'] == 'yes':
outXml = utils._dump_xml(config)
# the possibility of making the model map is checked inside the function
FitRunner.ModelMap(outXml)
if Nbin > 0:
FitRunner.config['Spectrum']['ResultParentPlots'] = "yes"
plot_sed_fromconfig(get_config(infile), ignore_missing_bins=True)
energybin.RunEbin(folder, Nbin, Fit, FitRunner, sedresult)
del (sedresult)
del (Result)
del (FitRunner)
plot_sed_fromconfig(get_config(config['file']['parent_config']),
ignore_missing_bins=True)
if config['Spectrum']['ResultPlots'] == 'yes':
outXml = utils._dump_xml(config)
# the possibility of making the model map is checked inside the function
FitRunner.ModelMap(outXml)
if Nbin > 0:
FitRunner.config['Spectrum']['ResultParentPlots'] = "yes"
plot_sed_fromconfig(get_config(infile), ignore_missing_bins=True)
energybin.RunEbin(folder, Nbin, Fit, FitRunner, sedresult)
del (sedresult)
del (Result)
del (FitRunner)
# @todo: Should this be a command line utility in bin?
if __name__ == '__main__':
import sys
from enrico import Loggin
mes = Loggin.Message()
try:
infile = sys.argv[1]
except:
print('Usage: ' + sys.argv[0] + ' <config file name>')
mes.error('Config file not found.')
run(infile)
def GenAnalysisObjects(config, verbose=1, xmlfile=""):
mes = Loggin.Message()
#check is the summed likelihood method should be used and get the
#Analysis objects (observation and (Un)BinnedAnalysis objects)
folder = config['out']
Fit = SummedLikelihood.SummedLikelihood()
EUnBinned = config['ComponentAnalysis']['EUnBinned']
emintotal = float(config['energy']['emin'])
emaxtotal = float(config['energy']['emax'])
evtnum = [config["event"]["evtype"]] #for std analysis
evtold = evtnum[0] #for std analysis
# Create one obs instance for each component
if isKey(config['ComponentAnalysis'], 'FrontBack') == 'yes':
evtnum = [1, 2]
if isKey(config['ComponentAnalysis'], 'PSF') == 'yes':
evtnum = [4, 8, 16, 32]
if isKey(config['ComponentAnalysis'], 'EDISP') == 'yes':
evtnum = [64, 128, 256, 521]
oldxml = config['file']['xml']
for k, evt in enumerate(evtnum):
config['event']['evtype'] = evt
config["file"]["xml"] = oldxml.replace(
".xml", "_" + typeirfs[evt] + ".xml").replace("_.xml", ".xml")
if EUnBinned > emintotal and EUnBinned < emaxtotal:
mes.info(
"Breaking the analysis in Binned (low energy) and Unbinned (high energies)"
)
analysestorun = ["lowE", "highE"]
for k, TYPE in enumerate(analysestorun):
tag = TYPE
if typeirfs[evt] != "":
tag += "_" + typeirfs[evt] # handle name of fits file
# Tune parameters
if TYPE is "lowE":
config['energy']['emin'] = emintotal
config['energy']['emax'] = min(config['energy']['emax'],
EUnBinned)
config['analysis']['likelihood'] = "binned"
config['analysis']['ComputeDiffrsp'] = "no"
elif TYPE is "highE":
config['energy']['emin'] = max(config['energy']['emin'],
EUnBinned)
config['energy']['emax'] = emaxtotal
config['analysis']['likelihood'] = "unbinned"
config['analysis']['ComputeDiffrsp'] = "yes"
Analyse = Analysis(folder, config, \
configgeneric=config,\
tag=TYPE,\
verbose=verbose)
Fit_component = Analyse.CreateLikeObject()
Fit.addComponent(Fit_component)
FitRunner = Analyse
FitRunner.obs.Emin = emintotal
FitRunner.obs.Emax = emaxtotal
else:
Analyse = Analysis(folder, config, \
configgeneric=config,\
tag=typeirfs[evt], verbose = verbose)
# if not(xmlfile ==""): Analyse.obs.xmlfile = xmlfile
Fit_component = Analyse.CreateLikeObject()
Fit.addComponent(Fit_component)
FitRunner = Analyse
config["event"]["evtype"] = evtold
FitRunner.config = config
return FitRunner, Fit
def GenAnalysisObjects(config, verbose=1, xmlfile=""):
import os
import os.path
import math
import SummedLikelihood
from enrico.xml_model import XmlMaker
from enrico.extern.configobj import ConfigObj
from utils import hasKey, isKey
import Loggin
mes = Loggin.Message()
#check is the summed likelihood method should be used and get the
#Analysis objects (observation and (Un)BinnedAnalysis objects)
SummedLike = config['Spectrum']['SummedLike']
folder = config['out']
# If there is no xml file, create it and print a warning
if (not os.path.isfile(config['file']['xml'])):
mes.warning("Xml not found, creating one for the given config %s" %
config['file']['xml'])
XmlMaker(config)
Fit = SummedLikelihood.SummedLikelihood()
if hasKey(config, 'ComponentAnalysis') == True:
# Create one obs instance for each component
configs = [None] * 4
Fits = [None] * 4
Analyses = [None] * 4
if isKey(config['ComponentAnalysis'], 'FrontBack') == 'yes':
from enrico.data import fermievtypes
mes.info("Breaking the analysis in Front/Back events")
# Set Summed Likelihood to True
config['Spectrum']['SummedLike'] = 'yes'
oldxml = config['file']['xml']
for k, TYPE in enumerate(["FRONT", "BACK"]):
configs[k] = ConfigObj(config)
configs[k]['event']['evtype'] = fermievtypes[TYPE]
try:
Analyses[k] = Analysis(folder, configs[k], \
configgeneric=config,\
tag=TYPE, verbose = verbose)
if not (xmlfile == ""): Analyses[k].obs.xmlfile = xmlfile
Fits[k] = Analyses[k].CreateLikeObject()
Fit.addComponent(Fits[k])
except RuntimeError, e:
if 'RuntimeError: gtltcube execution failed' in str(e):
mes.warning("Event type %s is empty! Error is %s" %
(TYPE, str(e)))
FitRunner = Analyses[0]
elif isKey(config['ComponentAnalysis'], 'PSF') == 'yes':
from enrico.data import fermievtypes
mes.info("Breaking the analysis in PSF 0,1,2,3.")
# Clone the configs
# Set Summed Likelihood to True
config['Spectrum']['SummedLike'] = 'yes'
for k, TYPE in enumerate(["PSF0", "PSF1", "PSF2", "PSF3"]):
configs[k] = ConfigObj(config)
configs[k]['event']['evtype'] = fermievtypes[TYPE]
try:
Analyses[k] = Analysis(folder, configs[k], \
configgeneric=config,\
tag=TYPE, verbose = verbose)
if not (xmlfile == ""): Analyses[k].obs.xmlfile = xmlfile
Fits[k] = Analyses[k].CreateLikeObject()
Fit.addComponent(Fits[k])
except RuntimeError, e:
if 'RuntimeError: gtltcube execution failed' in str(e):
mes.warning("Event type %s is empty! Error is %s" %
(TYPE, str(e)))
FitRunner = Analyses[0]
def GenAnalysisObjects(config, verbose = 1, xmlfile =""):
# Array containing the list of analysis objects (needed to produce the individual residual maps)
ListOfAnalysisObjects = []
mes = Loggin.Message()
#check is the summed likelihood method should be used and get the
#Analysis objects (observation and (Un)BinnedAnalysis objects)
folder = config['out']
# If there are no xml files, create it and print a warning <--- Not sure if this is needed here.
Fit = SummedLikelihood.SummedLikelihood()
EUnBinned = config['ComponentAnalysis']['EUnBinned']
emintotal = float(config['energy']['emin'])
emaxtotal = float(config['energy']['emax'])
evtnum = [config["event"]["evtype"]] #for std analysis
evtold = evtnum[0] #for std analysis
# Create one obs instance for each component.
# The first 3 can be combined with splitting in energy. The 4th tries to mimick 4FGL.
if isKey(config['ComponentAnalysis'],'FrontBack') == 'yes':
evtnum = [1, 2]
config['analysis']['likelihood'] = "binned"
elif isKey(config['ComponentAnalysis'],'PSF') == 'yes':
evtnum = [4,8,16,32]
config['analysis']['likelihood'] = "binned"
elif isKey(config['ComponentAnalysis'],'EDISP') == 'yes':
evtnum = [64,128,256,521]
config['analysis']['likelihood'] = "binned"
elif isKey(config['ComponentAnalysis'],'FGL4') == 'yes':
# Special case of the PSF component analysis,
# where up to 15 components (energy+PSF) are created following
# 4FGL prescription.
from catalogComponents import evtnum, energybins, nbinsbins, zmaxbins, ringwidths, pixelsizes
config['analysis']['likelihood'] = "binned"
oldxml = config['file']['xml']
bin_i = 0
roi = 0
# energybins is a dictionary containing an index and a pair of energies
for ebin_i in energybins:
# Restrict the analysis to the specified energy range in all cases.
if emintotal>=energybins[ebin_i][1]:
continue
if emaxtotal<=energybins[ebin_i][0]:
continue
if (roi==0): roi = 2.*ringwidths[ebin_i]+4.
zmax = zmaxbins[ebin_i]
nbinsE = nbinsbins[ebin_i]
energybin = energybins[ebin_i]
for k,evt in enumerate(evtnum):
pixel_size = pixelsizes[ebin_i][k]
if pixel_size<0: continue
tag = "{0}_En{1}".format(typeirfs[evt],ebin_i)
# Approximation, in the 4FGL the core radius changes from src to src!
mes.info("Breaking the analysis in bins ~ 4FGL")
config['event']['evtype'] = evt
config["file"]["xml"] = oldxml.replace(".xml","_")+typeirfs[evt]+"_"+\
"En{0}.xml".format(ebin_i)
config["energy"]["emin"] = max(emintotal,energybin[0])
config["energy"]["emax"] = min(emaxtotal,energybin[1])
config["analysis"]["likelihood"] = "binned"
config["analysis"]["ComputeDiffrsp"] = "no"
config["analysis"]["enumbins_per_decade"] = \
int(1.*nbinsE/math.log10(energybin[1]/energybin[0])+0.5)
config["space"]["rad"] = roi
config["analysis"]["zmax"] = zmax
Analyse = Analysis(folder, config, \
configgeneric=config,\
tag=tag, verbose=verbose)
ListOfAnalysisObjects.append(Analyse)
if not(xmlfile ==""): Analyse.obs.xmlfile = xmlfile
mes.info('Creating Likelihood object for component.')
Fit_component = Analyse.CreateLikeObject()
mes.info('Adding component to the summed likelihood.')
Fit.addComponent(Fit_component)
FitRunner = Analyse
FitRunner.obs.Emin = emintotal
FitRunner.obs.Emax = emaxtotal
config["energy"]["emin"] = emintotal
config["energy"]["emax"] = emaxtotal
config["event"]["evtype"] = evtold
FitRunner.config = config
return FitRunner,Fit,ListOfAnalysisObjects
# Standard (non-4FGL) analysis components
oldxml = config['file']['xml']
for k,evt in enumerate(evtnum):
config['event']['evtype'] = evt
if typeirfs[evt] != "":
config["file"]["xml"] = oldxml.replace(".xml","_"+typeirfs[evt]+".xml")
if EUnBinned>emintotal and EUnBinned<emaxtotal:
mes.info("Breaking the analysis in Binned (low energy) and Unbinned (high energies)")
analysestorun = ["lowE","highE"]
for j,TYPE in enumerate(analysestorun):
tag = TYPE
if typeirfs[evt] != "" : tag += "_"+typeirfs[evt]# handle name of fits file
config["file"]["xml"] = oldxml.replace(".xml","_"+tag+".xml")
# Tune parameters
if TYPE is "lowE":
config['energy']['emin'] = emintotal
config['energy']['emax'] = min(config['energy']['emax'],EUnBinned)
config['analysis']['likelihood'] = "binned"
config['analysis']['ComputeDiffrsp'] = "no"
elif TYPE is "highE":
config['energy']['emin'] = max(config['energy']['emin'],EUnBinned)
config['energy']['emax'] = emaxtotal
config['analysis']['likelihood'] = "unbinned"
config['analysis']['ComputeDiffrsp'] = "yes"
Analyse = Analysis(folder, config, \
configgeneric=config,\
tag=tag,\
verbose=verbose)
ListOfAnalysisObjects.append(Analyse)
mes.info('Creating Likelihood object for component.')
Fit_component = Analyse.CreateLikeObject()
mes.info('Adding component to the summed likelihood.')
Fit.addComponent(Fit_component)
FitRunner = Analyse
FitRunner.obs.Emin = emintotal
FitRunner.obs.Emax = emaxtotal
config["energy"]["emin"] = emintotal
config["energy"]["emax"] = emaxtotal
else:
Analyse = Analysis(folder, config, \
configgeneric=config,\
tag=typeirfs[evt], verbose = verbose)
ListOfAnalysisObjects.append(Analyse)
if not(xmlfile ==""): Analyse.obs.xmlfile = xmlfile
mes.info('Creating Likelihood object for component.')
Fit_component = Analyse.CreateLikeObject()
mes.info('Adding component to the summed likelihood.')
Fit.addComponent(Fit_component)
FitRunner = Analyse
config["event"]["evtype"] = evtold
FitRunner.config = config
return FitRunner,Fit,ListOfAnalysisObjects