def build_roi(name, snrdata, latdata):
snrdata=loaddict(snrdata)
latdata=loaddict(latdata)
roi_dir = SkyDir(*snrdata[name]['cel'])
snrsize = snrdata[name]['size']
if isinstance(snrsize,list) and len(snrsize) == 2:
snrradius = math.sqrt(snrsize[0]*snrsize[1])/2.0
else:
snrradius = snrsize/2.0
ds = DataSpecification(**latdata['data'])
sa = SpectralAnalysis(ds,
binsperdec = 4,
emin = 1e4,
emax = 10**5.5,
irf = "P7SOURCE_V6",
roi_dir = roi_dir,
maxROI = 10,
minROI = 10,
event_class= 0)
diffuse_sources = get_default_diffuse(**latdata['diffuse'])
catalog = Catalog2FGL(**latdata['catalog'])
roi=sa.roi(point_sources=[],
diffuse_sources=diffuse_sources,
catalogs=catalog)
print 'bins',roi.bin_edges
for source in roi.get_sources():
if np.degrees(source.skydir.difference(roi_dir)) < snrradius + 0.5:
roi.del_source(source)
snr = ExtendedSource(
name = name,
model = PowerLaw(),
spatial_model = Disk(sigma=snrradius, center=roi_dir)
)
roi.add_source(snr)
return roi
def setup_roi(name, snrdata, catalog_dict=dict(), roi_dict=dict()):
snr=yaml.load(open(snrdata))[name]
skydir=SkyDir(*snr['cel'])
size=snr['size']
ds=DataSpecification(
ft1files='$FERMILANDE/data/PWNCAT2/nov_30_2011/ft1_PWNCAT2_allsky.fits',
ft2files='$FERMILANDE/data/PWNCAT2/nov_30_2011/ft2_PWNCAT2_allsky.fits',
ltcube='$FERMILANDE/data/PWNCAT2/nov_30_2011/ltcube_PWNCAT2_allsky.fits',
binfile='$FERMILANDE/data/PWNCAT2/nov_30_2011/binned_%s.fits' % 4)
sa=SpectralAnalysis(ds,
binsperdec = 4,
roi_dir = skydir,
irf = 'P7SOURCE_V6',
maxROI = 10,
minROI = 10,
event_class = 0)
diffuse_sources = diffuse_sources = get_default_diffuse(
diffdir=e('$FERMILANDE/diffuse'),
gfile='ring_2year_P76_v0.fits',
ifile='isotrop_2year_P76_source_v0.txt')
catalogs = Catalog2FGL('$FERMILANDE/catalogs/gll_psc_v05.fit',
latextdir='$FERMILANDE/extended_archives/gll_psc_v05_templates/',
**catalog_dict)
roi = sa.roi(
catalogs = catalogs,
diffuse_sources = diffuse_sources,
**roi_dict)
return roi
def test_ps1(self):
if PointlikeTest.VERBOSE:
print '\nAnalyze a simulated point source against the galactic + isotropic diffuse\n'
center = SkyDir(0, 0)
diffuse_sources = get_default_diffuse(
diffdir='$GLAST_EXT/diffuseModels/v2r0p1/',
gfile='ring_2year_P76_v0.fits',
ifile='isotrop_2year_P76_source_v1.txt')
model = PowerLaw(index=2)
model.set_flux(1e-6)
ps_mc = PointSource(name='source', skydir=center, model=model)
ps_fit = ps_mc.copy()
point_sources = [ps_fit]
roi = PointlikeTest.get_roi('ps1', center, point_sources,
diffuse_sources)
global roi_pt
roi_pt = roi # helps with debugging
if PointlikeTest.VERBOSE:
print roi
roi.fit(use_gradient=PointlikeTest.USE_GRADIENT)
if PointlikeTest.VERBOSE: print roi
roi.localize(update=True)
roi.fit(use_gradient=PointlikeTest.USE_GRADIENT)
if PointlikeTest.VERBOSE:
roi.print_summary()
print roi
self.compare_model(ps_fit, ps_mc)
self.compare_spatial_model(ps_fit, ps_mc, roi.lsigma)
def setup_pwn(name,pwndata,phase, free_radius=5, tempdir=None, emin=1.0e2, emax=1.0e5,maxroi=10,model=None,**kwargs):
"""Name of the source
pwndata Yaml file
returns pointlike ROI.
"""
sources=yaml.load(open(pwndata))
catalog_name=sources[name]['catalog']
ltcube=sources[name]['ltcube']
pulsar_position=SkyDir(*sources[name]['dir'])
ft2=sources[name]['ft2']
ft1=sources[name]['ft1']
# in case no list was passed
if len(phase)==2 and isinstance(phase[0],numbers.Real) and \
isinstance(phase[1],numbers.Real):
# write in case phase wraps around.
if phase[0]>phase[1]:
phase=[[phase[0],1.0],[0.0,phase[1]]]
else:
phase = [phase]
phase_factor=get_phase_factor(phase)
print "phase"
print phase
print "phase_factor=%.2f"%phase_factor
catalog=FermiCatalog(e("$FERMI/catalogs/gll_psc_v02.fit"),free_radius=free_radius)
catalog_source=[i for i in catalog.get_sources(SkyDir(),180) if i.name==catalog_name][0]
center=catalog_source.skydir
if tempdir is None: tempdir=mkdtemp(prefix='/scratch/')
binfile=j(tempdir,'binned_phased.fits')
# apply phase cut to ft1 file
phased_ft1 = j(tempdir,'ft1_phased.fits')
phasetools.phase_cut(ft1,phased_ft1,phaseranges=phase)
# create a temporary ltcube scaled by the phase factor
# phased_ltcube=j(tempdir,'phased_ltcube.fits')
# phase_ltcube(ltcube,phased_ltcube, phase=phase)
phased_ltcube=ltcube
from uw.like.pointspec import DataSpecification
data_specification = DataSpecification(
ft1files = phased_ft1,
ft2files = ft2,
ltcube = phased_ltcube,
binfile = binfile)
spectral_analysis = SpectralAnalysis(data_specification,
binsperdec = 4,
emin = 100,
emax = 100000,
irf = "P6_V3_DIFFUSE",
roi_dir = center,
maxROI = maxroi,
minROI = maxroi)
if model == None :
roi=spectral_analysis.roi(
roi_dir=center,
diffuse_sources=get_default_diffuse(diffdir=e("$FERMI/diffuse"),
gfile="gll_iem_v02.fit",
ifile="isotropic_iem_v02.txt"),
catalogs = catalog,
phase_factor = 1.0,
fit_emin = [emin,emin],
fit_emax = [emax,emax],
**kwargs)
else :
roi=spectral_analysis.roi(
roi_dir=center,
xmlfile = model,
phase_factor =1.0,
fit_emin = [emin,emin],
fit_emax = [emax,emax],
**kwargs)
print "---------------------Energy range--------------------"
print "emin="+str(roi.bands[0].emin)+"\n"
print "emax="+str(roi.bands[len(roi.bands)-1].emax)+"\n"
# keep overall flux of catalog source,
# but change the starting index to 2.
roi.modify(which=catalog_name, name=name, index=2,
keep_old_flux=True)
return roi
from lande.utilities.random import random_on_sphere
from lande.utilities.tools import savedict
for roi_dir in [SkyDir(0,0, SkyDir.GALACTIC), SkyDir(70,85, SkyDir.GALACTIC)]:
savedir='/nfs/slac/g/ki/ki03/lande/fermi/data/monte_carlo/test_mapcube_cutting/plot_example/datadir_l_%d_b_%d' % (roi_dir.l(), roi_dir.b())
emin=1e3
emax=1e5
diffdir='/afs/slac/g/glast/groups/diffuse/rings/2year/'
diffuse_sources = get_default_diffuse(diffdir=diffdir,
gfile='ring_2year_P76_v0.fits',
ifile='isotrop_2year_P76_source_v0.txt')
ft2 = dict2fgl['ft2']
ltcube = dict2fgl['ltcube']
ft1 = join(savedir,'ft1.fits')
m=MonteCarlo(
sources=diffuse_sources,
emin = emin,
emax = emax,
irf='P7SOURCE_V6',
roi_dir=roi_dir,
maxROI=10,
def setup_pointlike(name,pwnlist,phasing=True):
"""Name of the source
pwnlist Yaml file
phasing=true : apply phase cut
phasing=false : don't do it"""
sources=yaml.load(open(pwnlist))
catalog_name=sources[name]['catalog']
phase=sources[name]['phase']
ltcube=sources[name]['ltcube']
pulsar_position=SkyDir(*sources[name]['dir'])
if phasing==True:
phase_factor=phase[1]-phase[0] if phase[1]>phase[0] else (1-phase[0]) + (phase[1]-0)
ft1=sources[name]['ft1']
else :
phase_factor=1.0
raise Exception("Unable to phase data")
catalog=FermiCatalog(e("$FERMI/catalogs/gll_psc_v02.fit"),free_radius=5)
catalog_source=[i for i in catalog.get_sources(SkyDir(),180) if i.name==catalog_name][0]
center=catalog_source.skydir
from uw.like.pointspec import DataSpecification
data_specification = DataSpecification(
ft1files = ft1,
ltcube = ltcube,
binfile = "binned_%s.fits" % name)
spectral_analysis = SpectralAnalysis(data_specification,
binsperdec = 8,
emin = 100,
emax = 100000,
irf = "P6_V3_DIFFUSE",
roi_dir = center,
maxROI = 10,
minROI = 10)
roi=LandeROI(spectral_analysis.roi(
roi_dir=center,
diffuse_sources=get_default_diffuse(diffdir=e("$FERMI/diffuse"),
gfile="gll_iem_v02.fit",
ifile="isotropic_iem_v02.txt"),
catalogs = catalog,
fit_emin = 100,
fit_emax = 100000,
catalog_include_radius = 20,
phase_factor = phase_factor)
)
roi.del_source(catalog_name)
# make residual TS map
# add in PWN Candidate
source=PointSource(
name=name,
model=PowerLaw(p=[1,2]),
skydir=pulsar_position
)
source.model.set_flux(1e-7,emin=100,emax=100000)
roi.add_source(source)
return roi
def build_roi(self, name, fast):
if fast:
roi_size=5
binsperdec = 2
max_free=2
free_radius=2
else:
roi_size = 10
binsperdec = 4
max_free=5
free_radius=5
catalog = Catalog2FGL('$FERMI/catalogs/gll_psc_v05.fit',
latextdir='$FERMI/extended_archives/gll_psc_v05_templates',
prune_radius=0,
max_free=max_free,
free_radius=free_radius,
limit_parameters=True)
ft1 = self.radiopsr_loader.get_ft1(name)
ft2 = self.radiopsr_loader.get_ft2(name)
ltcube = self.radiopsr_loader.get_ltcube(name)
binfile = self.radiopsr_loader.get_binfile(name, binsperdec)
roi_dir = self.radiopsr_loader.get_skydir(name)
ds = DataSpecification(
ft1files = ft1,
ft2files = ft2,
ltcube = ltcube,
binfile = binfile)
sa = SpectralAnalysis(ds,
binsperdec = binsperdec,
emin = 100,
emax = 1000000,
irf = "P7SOURCE_V6",
roi_dir = roi_dir,
maxROI = roi_size,
minROI = roi_size,
event_class= 0)
fit_emin = 1e2
fit_emax = 10**5.5
model=PowerLaw(index=2, e0=np.sqrt(fit_emin*fit_emax))
model.set_limits('index',-5,5)
ps = PointSource(name=name, model=model, skydir=roi_dir)
point_sources = [ps]
diffuse_sources = get_default_diffuse(diffdir="/afs/slac/g/glast/groups/diffuse/rings/2year",
gfile="ring_2year_P76_v0.fits",
ifile="isotrop_2year_P76_source_v0.txt",
limit_parameters=True)
roi=sa.roi(point_sources=point_sources,
diffuse_sources=diffuse_sources,
catalogs=catalog,
fit_emin=fit_emin, fit_emax=fit_emax)
return roi
def setup_region(name,pwndata,phase, free_radius=5, tempdir=None, maxroi=10,
xml=None, **kwargs):
"""Name of the source
pwndata Yaml file
returns pointlike ROI.
"""
phase = PhaseRange(phase)
sources=yaml.load(open(pwndata))
catalog_name=sources[name]['catalog']['2fgl']
ltcube=sources[name]['ltcube']
pulsar_position=SkyDir(*sources[name]['dir'])
ft2=sources[name]['ft2']
ft1=sources[name]['ft1']
catalog=FermiCatalog(e("$FERMI/catalogs/gll_psc_v02.fit"))
catalog=Catalog2FGL('$FERMI/catalogs/gll_psc_v05.fit',
latextdir='$FERMI/extended_archives/gll_psc_v05_templates',
free_radius=free_radius)
catalog_source=catalog.get_source(catalog_name)
center=catalog_source.skydir
if tempdir is None: tempdir=mkdtemp(prefix='/scratch/')
binfile=j(tempdir,'binned_phased.fits')
if np.allclose(phase.phase_fraction,1):
phased_ltcube = ltcube
phased_ft1 = ft1
else:
# create a temporary ltcube scaled by the phase factor
phased_ltcube=j(tempdir,'phased_ltcube.fits')
phase_ltcube(ltcube,phased_ltcube, phase=phase)
# apply phase cut to ft1 file
phased_ft1 = j(tempdir,'ft1_phased.fits')
phasetools.phase_cut(ft1,phased_ft1,phaseranges=phase.tolist(dense=False))
from uw.like.pointspec import DataSpecification
ds = DataSpecification(
ft1files = phased_ft1,
ft2files = ft2,
ltcube = phased_ltcube,
binfile = binfile)
sa = SpectralAnalysis(ds,
binsperdec = 8,
emin = 100,
emax = 100000,
irf = "P6_V11_DIFFUSE",
roi_dir = center,
maxROI = maxroi,
minROI = maxroi)
if xml is None:
roi=sa.roi(
diffuse_sources=get_default_diffuse(diffdir="/afs/slac/g/glast/groups/diffuse/mapcubes",
gfile="gll_iem_v02.fit",
ifile="isotropic_iem_v02.txt"),
catalogs = catalog,
phase_factor =1,
**kwargs)
else:
roi=sa.roi_from_xml(
roi_dir=center,
xmlfile = xml,
phase_factor =1,
**kwargs)
print 'bins ',roi.bin_edges
roi.del_source(catalog_name)
return roi
#indices_and_galcenter_fluxes = [[1.5, 2.2e-8], [2.0, 1.2e-7], [2.5, 5.7e-7], [3.0, 2.7e-6]]
# v11
#indices_and_galcenter_fluxes = [[1.5, 2.3e-8], [2.0, 1.3e-7], [2.5, 4.5e-7], [3.0, 1.2e-6]]
# v12
indices_and_galcenter_fluxes = [[1.5, 2.3e-8], [2.0, 1.2e-7], [2.5, 4.5e-7], [3.0, 2e-6]]
np.random.shuffle(indices_and_galcenter_fluxes)
for index,galcenter_flux in indices_and_galcenter_fluxes:
diffuse=gal,iso=get_default_diffuse(diffdir='/afs/slac/g/glast/groups/diffuse/rings/2year',
gfile='ring_2year_P76_v0.fits',
ifile='isotrop_2year_P76_source_v0.txt')
def integral(skydir):
i = lambda m: m.integral(skydir, emin, emax)
return i(gal.dmodel[0]) + i(iso.dmodel[0])
bg_ratio = integral(SkyDir(0,0,SkyDir.GALACTIC))/integral(roi_dir)
flux = galcenter_flux*bg_ratio**-0.5
print 'index=%.1f, galcenter_flux=%.1e, bg_ratio=%.2f, l,b=%.2f,%.2f, flux=%.1e' % \
(index,galcenter_flux,bg_ratio,roi_dir.l(),roi_dir.b(),flux)
name = 'source_index_%g' % index
tempdir = mkdtemp(prefix='/scratch/')
roi_dir=SkyDir(94.30999756,22.57999992)
elif name == 'W51C':
ft1='/u/gl/funk/data3/ExtendedSources/NewAnalysis/gtlike/W51C/SmoothBrokenPowerlaw/W51C-ft1.fits'
ltcube='/u/gl/funk/data3/ExtendedSources/NewAnalysis/gtlike/W51C/ltcube_239557414_334152002.fits'
roi_dir=SkyDir(290.81799316,14.14500046)
else:
raise Exception("...")
ds = DataSpecification(
ft1files=ft1,
ft2files=ft2,
ltcube=ltcube,
binfile='binned_ct=%s.fits' % conv_type)
diffuse_sources = get_default_diffuse(
diffdir=expandvars('$diffuse'),
gfile="gal_2yearp7v6_v0.fits",
ifile="iso_p7v6source_extrapolated.txt")
catalog = Catalog2FGL(expandvars('$catalogs/gll_psc_v07.fit'),
latextdir=expandvars('$extended_archives/gll_psc_v07_templates'),
free_radius=5,
)
if args.test:
roi_size=5
else:
roi_size=10*np.sqrt(2)
print 'conv',conv_type
sa = SpectralAnalysis(ds,
def setup_pwn(name,pwndata,phase, free_radius=5, tempdir=None, **kwargs):
"""Name of the source
pwndata Yaml file
returns pointlike ROI.
"""
sources=yaml.load(open(pwndata))
catalog_name=sources[name]['catalog']
ltcube=sources[name]['ltcube']
pulsar_position=SkyDir(*sources[name]['dir'])
ft2=sources[name]['ft2']
ft1=sources[name]['ft1']
# in case no list was passed
if len(phase)==2 and isinstance(phase[0],numbers.Real) and \
isinstance(phase[1],numbers.Real):
# write in case phase wraps around.
if phase[0]>phase[1]:
phase=[[phase[0],1.0],[0.0,phase[1]]]
else:
phase = [phase]
phase_factor=get_phase_factor(phase)
catalog=FermiCatalog(e("$FERMI/catalogs/gll_psc_v02.fit"),free_radius=free_radius)
catalog_source=[i for i in catalog.get_sources(SkyDir(),180) if i.name==catalog_name][0]
center=catalog_source.skydir
if tempdir is None: tempdir=mkdtemp(prefix='/scratch/')
binfile=j(tempdir,'binned_phased.fits')
# apply phase cut to ft1 file
phased_ft1 = j(tempdir,'ft1_phased.fits')
phasetools.phase_cut(ft1,phased_ft1,phaseranges=phase)
# create a temporary ltcube scaled by the phase factor
# phased_ltcube=j(tempdir,'phased_ltcube.fits')
# phase_ltcube(ltcube,phased_ltcube, phase=[0.0,1.0])
phased_ltcube=ltcube
from uw.like.pointspec import DataSpecification
data_specification = DataSpecification(
ft1files = phased_ft1,
ft2files = ft2,
ltcube = phased_ltcube,
binfile = binfile)
spectral_analysis = SpectralAnalysis(data_specification,
binsperdec = 4,
emin = 100,
emax = 100000,
irf = "P6_V3_DIFFUSE",
roi_dir = center,
maxROI = 10,
minROI = 10)
roi=spectral_analysis.roi(
roi_dir=center,
diffuse_sources=get_default_diffuse(diffdir=e("$FERMI/diffuse"),
gfile="gll_iem_v02.fit",
ifile="isotropic_iem_v02.txt"),
catalogs = catalog,
phase_factor = phase_factor,
**kwargs) # phaseing already done to the ltcube
print "phase_factor=%.2f"%phase_factor
# keep overall flux of catalog source,
# but change the starting index to 2.
roi.modify(which=catalog_name, name=name, index=2,
keep_old_flux=True)
roi.toXML(filename="essai")
print roi
roi.print_summary()
for names in roi.get_names():
try :
roi.modify(names,Norm=roi.get_model(names)[0]*roi.phase_factor)
except :
try :
roi.modify(names,Int_flux=roi.get_model(names)[0]*roi.phase_factor)
except :
print names
table=roi.get_names()
print roi.modify(which=table[len(table)-2],model=PowerLaw(p=[1.0*phase_factor,0.1]),free=[True,False])
print roi.modify(which=table[len(table)-1],model=PowerLaw(p=[1.0*phase_factor,0.1]),free=[True,False])
# print roi.modify(which='eg_v02',free=[False])
print roi
return roi
def get_background():
return get_default_diffuse(diffdir="/afs/slac/g/glast/groups/diffuse/rings/2year",
gfile="ring_2year_P76_v0.fits",
ifile="isotrop_2year_P76_source_v0.txt",
limit_parameters=True)
ft1 = 'simulated_ft1.fits'
catalog = Catalog2FGL('/afs/slac/g/glast/groups/catalog/2FGL/gll_psc_v05.fit',
latextdir='/afs/slac/g/glast/groups/catalog/2FGL/gll_psc_v05_templates')
if source == 'W44':
skydir = SkyDir(284.005,1.345)
gtifile = '/u/gl/funk/data/GLAST/ExtendedSources/NewAnalysis/gtlike/W44/sel_W44_60_100000.fits'
elif source == 'IC443':
skydir = SkyDir(94.310,22.580)
gtifile = '/u/gl/funk/data/GLAST/ExtendedSources/NewAnalysis/gtlike/IC443/sel_IC443_60_100000.fits'
if args.diffuse == 'galactic':
ds = get_default_diffuse(
diffdir="/nfs/slac/g/ki/ki03/lande/fermi/diffuse/",
gfile="gal_2yearp7v6_v0.fits",
ifile="iso_p7v6source.txt")
elif args.diffuse == 'sreekumar':
ds = [ get_sreekumar() ]
elif args.diffuse == 'nobackground':
ds = []
elif args.diffuse == 'extrapolated':
ds = get_background(
"/afs/slac/g/glast/groups/scienceTools/bugs/Likelihood/energy_dispersion/Simulations/galdif_extended.fits",
'/nfs/slac/g/ki/ki03/lande/fermi/diffuse/iso_p7v6source_extrapolated.txt')
else:
raise Exception("...")
ps,ds = catalog.merge_lists(skydir, radius=15, user_diffuse_list=ds)
def get_background():
return get_default_diffuse(
diffdir="/afs/slac/g/glast/groups/diffuse/rings/2year",
gfile="ring_2year_P76_v0.fits",
ifile="isotrop_2year_P76_source_v0.txt",
limit_parameters=True)
