def altdiff_followup(self, hypothesis, dist, halo, TS):
name = self.name
print dist, halo, TS
# Note, Gulli's alt diffuse models only go to 100GeV!
roi = self.reload_roi(hypothesis, fit_emax=1e5)
roi.print_summary()
print roi.get_source(name)
for source in get_background(roi):
roi.del_source(source)
print 'Loading alternate diffuse models'
diff = get_gulli_diffuse(dist=dist, halo=halo, TS=TS, version=2, event_class='source', verbosity=True)
print 'Adding alternate diffuse models to ROI'
for source in diff:
roi.add_source(source)
print 'Freezing insignificant diffuse models'
freeze_insignificant_diffuse(roi,allowed_fraction=0.03, verbosity=True)
print 'Printing ROI'
roi.print_summary()
print 'Doing gtlike analysis'
results=gtlike_analysis(roi, name=name,
max_free = self.max_free,
seddir=self.seddir, datadir=self.datadir, plotdir=self.plotdir,
hypothesis='%s_altdiff_dist_%s_halo_%s_TS_%s' % (hypothesis,dist,halo,TS),
upper_limit=False, do_bandfitter=False, do_sed=True,
)
savedict(results,'results_%s_altdiff_dist_%s_halo_%s_TS_%s_%s.yaml' % (name,dist,halo,TS,hypothesis))
def get_most_significant_diffuse(roi, allowed_fraction,max_n_models=1, verbosity=False):
from lande.fermi.likelihood.save import get_background
significant_list = []
for name in get_background(roi):
oc=observed_counts(roi)
mc=model_counts(roi,name)
fraction=float(mc)/oc
if verbosity:
print ' .. Source %s predicts %0.2f%% of total counts' % (name,fraction)
if fraction > allowed_fraction:
significant_list.append((name,)+(fraction,))
if verbosity: print 'keeping it.'
else:
if verbosity: print 'discarding it.'
sorted_list=sorted(significant_list, key=lambda frac: frac[1], reverse= True)
cut_list=[]
for i in sorted_list[:max_n_models]:
cut_list.append(i[0])
if verbosity:
print significant_list
print sorted_list
print cut_list
return cut_list
def get_most_significant_diffuse(roi, allowed_fraction,max_n_models=1, verbosity=False):
from lande.fermi.likelihood.save import get_background
significant_list = []
for name in get_background(roi):
oc=observed_counts(roi)
mc=model_counts(roi,name)
fraction=float(mc)/oc
if verbosity:
print ' .. Source %s predicts %0.2f%% of total counts' % (name,fraction)
if fraction > allowed_fraction:
significant_list.append((name,)+(fraction,))
if verbosity: print 'keeping it.'
else:
if verbosity: print 'discarding it.'
sorted_list=sorted(significant_list, key=lambda frac: frac[1], reverse= True)
cut_list=[]
for i in sorted_list[:max_n_models]:
cut_list.append(i[0])
if verbosity:
print significant_list
print sorted_list
print cut_list
return cut_list
def get_insignificant_diffuse(roi, allowed_fraction, verbosity=False):
insignificant_list = []
for source in get_background(roi):
if is_significant(roi, source, allowed_fraction, verbosity):
if verbosity: print '... keep source.'
else:
if verbosity: print "... Don't keep source."
insignificant_list.append(source)
return insignificant_list
def altdiff_followup(self, hypothesis, dist, halo, TS):
name = self.name
print dist, halo, TS
# Note, Gulli's alt diffuse models only go to 100GeV!
roi = self.reload_roi(hypothesis, fit_emax=1e5)
roi.print_summary()
print roi.get_source(name)
for source in get_background(roi):
roi.del_source(source)
print 'Loading alternate diffuse models'
diff = get_gulli_diffuse(dist=dist,
halo=halo,
TS=TS,
version=2,
event_class='source',
verbosity=True)
print 'Adding alternate diffuse models to ROI'
for source in diff:
roi.add_source(source)
print 'Freezing insignificant diffuse models'
freeze_insignificant_diffuse(roi,
allowed_fraction=0.03,
verbosity=True)
print 'Printing ROI'
roi.print_summary()
print 'Doing gtlike analysis'
results = gtlike_analysis(
roi,
name=name,
max_free=self.max_free,
seddir=self.seddir,
datadir=self.datadir,
plotdir=self.plotdir,
hypothesis='%s_altdiff_dist_%s_halo_%s_TS_%s' %
(hypothesis, dist, halo, TS),
upper_limit=False,
do_bandfitter=False,
do_sed=True,
)
savedict(
results, 'results_%s_altdiff_dist_%s_halo_%s_TS_%s_%s.yaml' %
(name, dist, halo, TS, hypothesis))
def _calculate(self,*args,**kwargs):
""" Convert all units into sympy arrays after the initial calculation. """
like = self.like
name = self.name
init_energes = like.energies[[0,-1]]
# Freeze all sources except one to make sed of.
all_sources = like.sourceNames()
if name not in all_sources:
raise Exception("Cannot find source %s in list of sources" % name)
# make copy of parameter values + free parameters
saved_state = SuperState(like)
if self.verbosity: print 'Freezing background sources'
for other_name in get_background(like):
if self.freeze_bg_diffuse:
if self.verbosity: print ' * Freezing diffuse source %s' % other_name
modify(like, other_name, free=False)
else:
if self.verbosity: print ' * Freezing spectral shape for diffuse source %s' % other_name
modify(like, other_name, freeze_spectral_shape=True)
for other_name in get_sources(like):
if self.freeze_bg_sources:
if self.verbosity: print ' * Freezing bg source %s' % other_name
modify(like, other_name, free=False)
else:
if self.verbosity: print ' * Freezing spectral shape for bg source %s' % other_name
modify(like, other_name, freeze_spectral_shape=True)
self.raw_results = []
for i,(lower,upper) in enumerate(zip(self.lower,self.upper)):
like.setEnergyRange(float(lower)+1, float(upper)-1)
e = np.sqrt(lower*upper)
if self.verbosity: print 'Calculating SED from %.0dMeV to %.0dMeV' % (lower,upper)
""" Note, the most robust method I have found for computing SEDs in gtlike is:
(a) Create a generic spectral model with a fixed spectral index.
(b) Set the 'Scale' to sqrt(emin*emax) so the prefactor is dNdE in the middle
of the sed bin.
(b) Set the limits to go from norm/fit_range to norm*fit_range and set the scale to 'norm'
"""
old_flux = self.init_model.i_flux(emin=lower,emax=upper)
model = PowerLaw(index=self.powerlaw_index, e0=e)
model.set_flux(old_flux, emin=lower, emax=upper)
norm = model['norm']
model.set_limits('norm',norm/float(self.fit_range),norm*self.fit_range, scale=norm)
model.set_limits('index',-5,5)
model.freeze('index')
spectrum = build_gtlike_spectrum(model)
like.setSpectrum(name,spectrum)
like.syncSrcParams(name)
if self.verbosity:
print 'Before fitting SED from %.0dMeV to %.0dMeV' % (lower,upper)
print summary(like)
paranoid_gtlike_fit(like, verbosity=self.verbosity)
if self.verbosity:
print 'After fitting SED from %.0dMeV to %.0dMeV' % (lower,upper)
print summary(like)
d = dict()
self.raw_results.append(d)
d['energy'] = energy_dict(emin=lower, emax=upper, energy_units=self.energy_units)
d['flux'] = flux_dict(like, name, emin=lower,emax=upper, flux_units=self.flux_units,
errors=True, include_prefactor=True, prefactor_energy=e)
d['prefactor'] = powerlaw_prefactor_dict(like, name, errors=self.save_hesse_errors, minos_errors=True,
flux_units=self.flux_units)
d['TS'] = ts_dict(like, name, verbosity=self.verbosity)
if self.verbosity: print 'Calculating SED upper limit from %.0dMeV to %.0dMeV' % (lower,upper)
if self.always_upper_limit or d['TS']['reoptimize'] < self.min_ts:
ul = GtlikePowerLawUpperLimit(like, name,
cl=self.ul_confidence,
emin=lower,emax=upper,
flux_units=self.flux_units,
energy_units=self.energy_units,
upper_limit_kwargs=self.upper_limit_kwargs,
include_prefactor=True,
prefactor_energy=e,
verbosity=self.verbosity,
)
d['upper_limit'] = ul.todict()
# revert to old model
like.setEnergyRange(*init_energes)
saved_state.restore()
self._condense_results()
def update_roi(self):
roi = self.roi
if self.verbosity:
print "Replacing current diffuse file with Gulli's diffuse files"
if self.verbosity:
print 'Deleting previous background sources:'
for source in get_background(roi):
if self.verbosity:
print ' .. Deleting source %s' % source
roi.del_source(source)
if self.verbosity:
print 'Getting Gulli Diffuse:'
diffuse_sources = get_gulli_diffuse(verbosity=self.verbosity, **self.diffuse_kwargs)
if self.verbosity:
print 'Adding Gulli Diffuse files to ROI:'
for source in diffuse_sources:
if self.verbosity:
print ' .. adding file %s to the ROI' % source.name
roi.add_source(source)
galatic_sources = [i for i in diffuse_sources if isinstance(i.dmodel[0],DiffuseFunction)]
assert len(galatic_sources) == len(diffuse_sources) - 1, "Exactly one isotropic diffue source"
free_galatic_sources = [i for i in diffuse_sources if np.any(i.smodel.free)]
if self.verbosity:
print 'Testing significance of free Galactic sources (to see if they need to be merged):'
insignificant = [i for i in free_galatic_sources if not is_significant(roi, i.name, self.fraction, self.verbosity)]
if len(insignificant) == 0:
print 'No insignificant sources, returning!'
return
elif len(insignificant) == 0:
print 'Only one insignificant source (%s). Freezing it and returning' % insignificant[0].name
roi.modify(which=insignificant[0].name, free=False)
return
else:
if self.verbosity:
print 'Multiple insignificant sources in ROI. Merging them!'
print 'Insignificant free Galactic diffuse sources are:'
for i in insignificant:
print ' .. %s' % i.name
if self.verbosity:
print 'Deleting (and the merging) the insignificant free Galactic sources'
for source in insignificant:
if self.verbosity:
print ' .. Deleting (and then merging) %s' % source.name
roi.del_source(source.name)
merged = merge_diffuse(insignificant, mergefile=self.mergefile, verbosity=self.verbosity, short_name=self.short_name , compress=self.compress)
if self.verbosity:
print 'Adding merged Galactic diffuse source %s to ROI:' % (merged.name)
roi.add_source(merged)
if self.verbosity:
print 'Testing if the merged Galactic diffuse source is significant'
if is_significant(roi, merged.name, self.fraction, self.verbosity):
if self.verbosity:
print 'Keeping free the merged Galactic diffuse sources!'
else:
if self.verbosity:
print 'Freezing the insignificant merged Galactic diffuse sources!'
roi.modify(which=merged.name, free=False)
def _calculate(self, *args, **kwargs):
""" Convert all units into sympy arrays after the initial calculation. """
like = self.like
name = self.name
init_energes = like.energies[[0, -1]]
# Freeze all sources except one to make sed of.
all_sources = like.sourceNames()
if name not in all_sources:
raise Exception("Cannot find source %s in list of sources" % name)
# make copy of parameter values + free parameters
saved_state = SuperState(like)
if self.verbosity: print 'Freezing background sources'
for other_name in get_background(like):
if self.freeze_bg_diffuse:
if self.verbosity:
print ' * Freezing diffuse source %s' % other_name
modify(like, other_name, free=False)
else:
if self.verbosity:
print ' * Freezing spectral shape for diffuse source %s' % other_name
modify(like, other_name, freeze_spectral_shape=True)
for other_name in get_sources(like):
if self.freeze_bg_sources:
if self.verbosity:
print ' * Freezing bg source %s' % other_name
modify(like, other_name, free=False)
else:
if self.verbosity:
print ' * Freezing spectral shape for bg source %s' % other_name
modify(like, other_name, freeze_spectral_shape=True)
self.raw_results = []
for i, (lower, upper) in enumerate(zip(self.lower, self.upper)):
like.setEnergyRange(float(lower) + 1, float(upper) - 1)
e = np.sqrt(lower * upper)
if self.verbosity:
print 'Calculating SED from %.0dMeV to %.0dMeV' % (lower,
upper)
""" Note, the most robust method I have found for computing SEDs in gtlike is:
(a) Create a generic spectral model with a fixed spectral index.
(b) Set the 'Scale' to sqrt(emin*emax) so the prefactor is dNdE in the middle
of the sed bin.
(b) Set the limits to go from norm/fit_range to norm*fit_range and set the scale to 'norm'
"""
old_flux = self.init_model.i_flux(emin=lower, emax=upper)
model = PowerLaw(index=self.powerlaw_index, e0=e)
model.set_flux(old_flux, emin=lower, emax=upper)
norm = model['norm']
model.set_limits('norm',
norm / float(self.fit_range),
norm * self.fit_range,
scale=norm)
model.set_limits('index', -5, 5)
model.freeze('index')
spectrum = build_gtlike_spectrum(model)
like.setSpectrum(name, spectrum)
like.syncSrcParams(name)
if self.verbosity:
print 'Before fitting SED from %.0dMeV to %.0dMeV' % (lower,
upper)
print summary(like)
paranoid_gtlike_fit(like, verbosity=self.verbosity)
if self.verbosity:
print 'After fitting SED from %.0dMeV to %.0dMeV' % (lower,
upper)
print summary(like)
d = dict()
self.raw_results.append(d)
d['energy'] = energy_dict(emin=lower,
emax=upper,
energy_units=self.energy_units)
d['flux'] = flux_dict(like,
name,
emin=lower,
emax=upper,
flux_units=self.flux_units,
errors=True,
include_prefactor=True,
prefactor_energy=e)
d['prefactor'] = powerlaw_prefactor_dict(
like,
name,
errors=self.save_hesse_errors,
minos_errors=True,
flux_units=self.flux_units)
d['TS'] = ts_dict(like, name, verbosity=self.verbosity)
if self.verbosity:
print 'Calculating SED upper limit from %.0dMeV to %.0dMeV' % (
lower, upper)
if self.always_upper_limit or d['TS']['reoptimize'] < self.min_ts:
ul = GtlikePowerLawUpperLimit(
like,
name,
cl=self.ul_confidence,
emin=lower,
emax=upper,
flux_units=self.flux_units,
energy_units=self.energy_units,
upper_limit_kwargs=self.upper_limit_kwargs,
include_prefactor=True,
prefactor_energy=e,
verbosity=self.verbosity,
)
d['upper_limit'] = ul.todict()
# revert to old model
like.setEnergyRange(*init_energes)
saved_state.restore()
self._condense_results()