def cluster(model_tot,
file_map,
file_spec,
ClusterName='Cluster',
tscalc=True):
"""
Build a ctools model for the cluster.
Parameters
----------
- model_tot: a gammalib.GModels object
- file_map (str): the full name of the fits map
- file_spec (str): the full name of the text file spectrum
- ClusterName (str): the name of the source
- tscalc (bool): request TS computation or not
Outputs
--------
- the model is updated to include the cluster
"""
spatial = gammalib.GModelSpatialDiffuseMap(file_map)
spectral = gammalib.GModelSpectralFunc(file_spec, 1.0)
timing = gammalib.GModelTemporalConst(1)
model = gammalib.GModelSky(spatial, spectral, timing)
model.name(ClusterName)
model.tscalc(tscalc)
model_tot.append(model)
]
#masses = [0.300,0.400,0.600,0.700,0.800,0.900,2,3,4,5,6,7,8,9,10]
#jfactorname = "DM/jfactor/jfactorLMC.fits"
jfactorname = "DM/jfactor/annihil_LMC2D_FOVdiameter10.0deg_alphaint0.10deg_nside1024NFW-JFACTOR-Jsmooth-image.fits"
for mass in masses:
#Standarized name for the produced model so the other programs can use it easily:
#_______________________________________________________________________________
if mass < 1:
masstr = str(int(mass * 1000)) + 'GeV'
else:
masstr = str(mass) + 'TeV'
specname = 'flux' + particle + masstr + '.txt'
modelname = 'dm_LMC_' + particle + masstr
suf = '_jfactorNFW'
#_______________________________________________________________________________
for model in models:
modelcontainer = gammalib.GModels()
model.spectral().filename(
PATH_SPEC + specname
) #Put the spectrum for the specific mass in the model file
spectral = model.spectral()
spatial = gammalib.GModelSpatialDiffuseMap(DATA_PATH + jfactorname)
model = gammalib.GModelSky(spatial, spectral)
modelcontainer.append(model)
modelcontainer.save(PATH_MODELS + modelname + suf +
'.xml') #Save the model
beta = 0.1 # smoothness parameter
flux = 11.05e-12 # ph cm-2 s-1
flux_ethresh = gammalib.GEnergy(200., 'GeV')
# output files
out_fits = 'ic443_map.fits'
out_xml = 'ic443.xml'
###############################################################
# normalize template
normalize_template(in_fits, in_hdu, out_fits)
# create gammalib model
# spatial model
spatial = gammalib.GModelSpatialDiffuseMap(out_fits)
# spectral model
spectral = gammalib.GModelSpectralSmoothBrokenPlaw(1., index1, eref, index2,
ebreak, beta)
# change prefactor to get correct flux
norm = spectral.flux(flux_ethresh, gammalib.GEnergy(100, 'TeV'))
spectral['Prefactor'].value(flux / norm)
# create source model
source = gammalib.GModelSky(spatial, spectral)
# create model container and append source
models = gammalib.GModels()
models.append(source)
# write to disk
def set_source_model(srcmodel,
spec='plaw',
alpha=1.0,
mapname='../map_RXJ1713.fits'):
"""
Set source model
Parameters
----------
srcmodel : str
Source model name
spec : str, optional
Spectral model
alpha : float, optional
Map scaling factor
mapname : str, optional
Sky map name
Returns
-------
source : `~gammalib.GModelSky()`
Source model
"""
# Set spectral component
if spec == 'plaw':
spectral = gammalib.GModelSpectralPlaw(1.0e-17, -2.0,
gammalib.GEnergy(1.0, 'TeV'))
spectral['Prefactor'].min(1.0e-25)
elif spec == 'eplaw':
spectral = gammalib.GModelSpectralExpPlaw(
1.0e-17, -2.0, gammalib.GEnergy(1.0, 'TeV'),
gammalib.GEnergy(10.0, 'TeV'))
spectral['CutoffEnergy'].min(1.0e6)
spectral['CutoffEnergy'].max(1.0e8)
spectral['Prefactor'].min(1.0e-25)
elif spec == 'inveplaw':
spectral = gammalib.GModelSpectralExpInvPlaw(
1.0e-17, -2.0, gammalib.GEnergy(1.0, 'TeV'),
gammalib.GEnergy(10.0, 'TeV'))
spectral['Prefactor'].min(1.0e-25)
elif spec == 'logparabola':
spectral = gammalib.GModelSpectralLogParabola(
1.0e-17, -2.0, gammalib.GEnergy(1.0, 'TeV'), -0.3)
spectral['Prefactor'].min(1.0e-25)
elif spec == 'abdalla2018':
spectral = gammalib.GModelSpectralExpPlaw(
2.3e-17, -2.06, gammalib.GEnergy(1.0, 'TeV'),
gammalib.GEnergy(12.9, 'TeV'))
spectral['Prefactor'].fix()
spectral['Index'].fix()
spectral['CutoffEnergy'].fix()
elif spec == 'abdalla2018Ec':
spectral = gammalib.GModelSpectralExpPlaw(
2.3e-17, -2.06, gammalib.GEnergy(1.0, 'TeV'),
gammalib.GEnergy(12.9, 'TeV'))
spectral['CutoffEnergy'].fix()
spectral['Prefactor'].min(1.0e-25)
elif spec == 'aharonian2007':
spectral = gammalib.GModelSpectralLogParabola(
2.06e-17, -2.02, gammalib.GEnergy(1.0, 'TeV'), -0.29)
spectral['Prefactor'].fix()
spectral['Index'].fix()
spectral['Curvature'].fix()
# Set spatial component
if 'map' in srcmodel:
filename = '%s' % mapname
map = gammalib.GSkyMap(filename)
map = scale_map(map, alpha)
filename = 'map_RXJ1713_%.2f.fits' % alpha
map.save(filename, True)
spatial = gammalib.GModelSpatialDiffuseMap(filename)
elif 'disk' in srcmodel:
dir = gammalib.GSkyDir()
dir.radec_deg(258.3, -39.7)
spatial = gammalib.GModelSpatialRadialDisk(dir, 0.5)
spatial['RA'].free()
spatial['DEC'].free()
elif 'gauss' in srcmodel:
dir = gammalib.GSkyDir()
dir.radec_deg(258.3, -39.7)
spatial = gammalib.GModelSpatialRadialGauss(dir, 0.5)
spatial['RA'].free()
spatial['DEC'].free()
elif 'shell' in srcmodel:
dir = gammalib.GSkyDir()
dir.radec_deg(258.3, -39.7)
spatial = gammalib.GModelSpatialRadialShell(dir, 0.4, 0.2)
spatial['RA'].free()
spatial['DEC'].free()
# Set source model
source = gammalib.GModelSky(spatial, spectral)
source.name('RX J1713.7-3946')
source.tscalc(True)
# Return source model
return source
replaced += 1
else:
added += 1
# add templates
models_template = gammalib.GModels(
'../known-sources/templates/{}.xml'.format(name))
for model in models_template:
# if model contains spatial map take care of it
if model.spatial().type() == 'DiffuseMap':
# find model map name and path
filename = model.spatial().filename().file()
filepath = model.spatial().filename().path()
# copy file to output directory
shutil.copy(filepath + filename, './')
# replace file with the one in output directory
model.spatial(gammalib.GModelSpatialDiffuseMap(filename))
# if model contains spatial map take care of it
if model.spectral().type() == 'FileFunction':
# find spectrum file name and path
filename = model.spectral().filename().file()
filepath = model.spectral().filename().path()
# copy file to output directory
shutil.copy(filepath + filename, './')
# replace file with the one in output directory
model.spectral(
gammalib.GModelSpectralFunc(
gammalib.GFilename(filename),
model.spectral()['Normalization'].value()))
# append model to container
models.append(model)
def build_model_grid(cpipe,
subdir,
rad,
prof_ini,
spatial_value,
spatial_idx,
profile_reso,
includeIC=False,
rm_tmp=False):
"""
Build a grid of models for the cluster and background, using
as n_CRp(r) propto n_CRp_ref^scaling.
Parameters
----------
Outputs files
-------------
-
"""
# Save the cluster model before modification
cluster_tmp = copy.deepcopy(cpipe.cluster)
#----- Loop changing profile
spatial_npt = len(spatial_value)
for imod in range(spatial_npt):
print('--- Building model template ' + str(1 + imod) + '/' +
str(spatial_npt))
#---------- Indexing
spatial_i = spatial_value[imod]
exti = 'TMP_' + str(imod)
print(' spatial = ', str(spatial_i), ', ext = ', exti)
#---------- Compute the model spectrum, map, and xml model file
# Re-scaling
cluster_tmp.density_crp_model = {
'name': 'User',
'radius': rad,
'profile': prof_ini.value**spatial_i
}
# Cluster model
make_cluster_template.make_map(cluster_tmp,
subdir + '/Model_Map_' + exti + '.fits',
Egmin=cpipe.obs_setup.get_emin(),
Egmax=cpipe.obs_setup.get_emax(),
includeIC=includeIC)
make_cluster_template.make_spectrum(
cluster_tmp,
subdir + '/Model_Spectrum_' + exti + '.txt',
energy=np.logspace(-1, 5, 1000) * u.GeV,
includeIC=includeIC)
# xml model
model_tot = gammalib.GModels(cpipe.output_dir +
'/Ana_Model_Input_Stack.xml')
clencounter = 0
for i in range(len(model_tot)):
if model_tot[i].name() == cluster_tmp.name:
spefn = subdir + '/Model_Spectrum_' + exti + '.txt'
model_tot[i].spectral().filename(spefn)
spafn = subdir + '/Model_Map_' + exti + '.fits'
model_tot[i].spatial(gammalib.GModelSpatialDiffuseMap(spafn))
clencounter += 1
if clencounter != 1:
raise ValueError('No cluster encountered in the input stack model')
model_tot.save(subdir + '/Model_Input_' + exti + '.xml')
#---------- Likelihood fit
like = ctools.ctlike()
like['inobs'] = cpipe.output_dir + '/Ana_Countscube.fits'
like['inmodel'] = subdir + '/Model_Input_' + exti + '.xml'
like['expcube'] = cpipe.output_dir + '/Ana_Expcube.fits'
like['psfcube'] = cpipe.output_dir + '/Ana_Psfcube.fits'
like['bkgcube'] = cpipe.output_dir + '/Ana_Bkgcube.fits'
like['edispcube'] = cpipe.output_dir + '/Ana_Edispcube.fits'
like['edisp'] = cpipe.spec_edisp
like['outmodel'] = subdir + '/Model_Output_' + exti + '.xml'
like['outcovmat'] = 'NONE'
like['statistic'] = cpipe.method_stat
like['refit'] = False
like['like_accuracy'] = 0.005
like['max_iter'] = 50
like['fix_spat_for_ts'] = False
like['logfile'] = subdir + '/Model_Output_log_' + exti + '.txt'
like.logFileOpen()
like.execute()
like.logFileClose()
#---------- Compute the 3D residual cube
cpipe._rm_source_xml(subdir + '/Model_Output_' + exti + '.xml',
subdir + '/Model_Output_Cluster_' + exti + '.xml',
cluster_tmp.name)
modcube = cubemaking.model_cube(
cpipe.output_dir,
cpipe.map_reso,
cpipe.map_coord,
cpipe.map_fov,
cpipe.spec_emin,
cpipe.spec_emax,
cpipe.spec_enumbins,
cpipe.spec_ebinalg,
edisp=cpipe.spec_edisp,
stack=cpipe.method_stack,
silent=True,
logfile=subdir + '/Model_Cube_log_' + exti + '.txt',
inmodel_usr=subdir + '/Model_Output_' + exti + '.xml',
outmap_usr=subdir + '/Model_Cube_' + exti + '.fits')
modcube_Cl = cubemaking.model_cube(
cpipe.output_dir,
cpipe.map_reso,
cpipe.map_coord,
cpipe.map_fov,
cpipe.spec_emin,
cpipe.spec_emax,
cpipe.spec_enumbins,
cpipe.spec_ebinalg,
edisp=cpipe.spec_edisp,
stack=cpipe.method_stack,
silent=True,
logfile=subdir + '/Model_Cube_Cluster_log_' + exti + '.txt',
inmodel_usr=subdir + '/Model_Output_Cluster_' + exti + '.xml',
outmap_usr=subdir + '/Model_Cube_Cluster_' + exti + '.fits')
#----- Build the data
hdul = fits.open(cpipe.output_dir + '/Ana_Countscube.fits')
header = hdul[0].header
header.remove('NAXIS3')
header['NAXIS'] = 2
cntmap = np.sum(hdul[0].data, axis=0)
hdul.close()
r_dat, p_dat, err_dat = radial_profile_cts(
cntmap, [
cpipe.cluster.coord.icrs.ra.to_value('deg'),
cpipe.cluster.coord.icrs.dec.to_value('deg')
],
stddev=np.sqrt(cntmap),
header=header,
binsize=profile_reso.to_value('deg'),
stat='POISSON',
counts2brightness=True)
tabdat = Table()
tabdat['radius'] = r_dat
tabdat['radius_min'] = r_dat - profile_reso.to_value('deg') / 2.0
tabdat['radius_max'] = r_dat + profile_reso.to_value('deg') / 2.0
tabdat['profile'] = p_dat
dat_hdu = fits.BinTableHDU(tabdat)
#----- Build the grid
modgrid_bk = np.zeros((spatial_npt, len(p_dat)))
modgrid_cl = np.zeros((spatial_npt, len(p_dat)))
for imod in range(spatial_npt):
exti = 'TMP_' + str(imod)
# Extract the profile
hdul = fits.open(subdir + '/Model_Cube_' + exti + '.fits')
cntmap = np.sum(hdul[0].data, axis=0)
hdul.close()
hdul_cl = fits.open(subdir + '/Model_Cube_Cluster_' + exti + '.fits')
cntmap_cl = np.sum(hdul_cl[0].data, axis=0)
hdul_cl.close()
map_cl = cntmap - cntmap_cl
map_bk = cntmap_cl
r_cl, p_cl, err_cl = radial_profile_cts(
map_cl, [
cpipe.cluster.coord.icrs.ra.to_value('deg'),
cpipe.cluster.coord.icrs.dec.to_value('deg')
],
stddev=np.sqrt(map_cl),
header=header,
binsize=profile_reso.to_value('deg'),
stat='POISSON',
counts2brightness=True)
r_bk, p_bk, err_bk = radial_profile_cts(
map_bk, [
cpipe.cluster.coord.icrs.ra.to_value('deg'),
cpipe.cluster.coord.icrs.dec.to_value('deg')
],
stddev=np.sqrt(map_bk),
header=header,
binsize=profile_reso.to_value('deg'),
stat='POISSON',
counts2brightness=True)
modgrid_bk[imod, :] = p_bk
modgrid_cl[imod, :] = p_cl
grid_cl_hdu = fits.ImageHDU(modgrid_cl)
grid_bk_hdu = fits.ImageHDU(modgrid_bk)
#----- Make the index table
scal = Table()
scal['index'] = spatial_idx
scal['value'] = spatial_value
scal_hdu = fits.BinTableHDU(scal)
#----- Make and save HDUlist
hdul = fits.HDUList()
hdul.append(scal_hdu)
hdul.append(dat_hdu)
hdul.append(grid_cl_hdu)
hdul.append(grid_bk_hdu)
hdul.writeto(subdir + '/Grid_Sampling.fits', overwrite=True)
#----- Save the properties of the last computation run
np.save(subdir + '/Grid_Parameters.npy', [cpipe.cluster, spatial_value],
allow_pickle=True)
#----- remove TMP files
if rm_tmp:
for imod in range(spatial_npt):
exti = 'TMP_' + str(imod)
os.remove(subdir + '/Model_Map_' + exti + '.fits')
os.remove(subdir + '/Model_Spectrum_' + exti + '.txt')
os.remove(subdir + '/Model_Cube_' + exti + '.fits')
os.remove(subdir + '/Model_Cube_log_' + exti + '.txt')
os.remove(subdir + '/Model_Cube_Cluster_' + exti + '.fits')
os.remove(subdir + '/Model_Cube_Cluster_log_' + exti + '.txt')
os.remove(subdir + '/Model_Input_' + exti + '.xml')
os.remove(subdir + '/Model_Output_' + exti + '.xml')
os.remove(subdir + '/Model_Output_log_' + exti + '.txt')
os.remove(subdir + '/Model_Output_Cluster_' + exti + '.xml')
# divide pixel value by distance (1/r profile as in Aharonian+ 2019)
hdu.data /= r
# clip tempate
# calculate median flux at max rad
low_flux = np.median(
hdu.data[np.abs(r * out_res - rad_max[s]) < 4 * out_res])
# clip at this flux level
hdu.data[hdu.data < low_flux] = 0.
# normalize map
hdu.data /= np.sum(hdu.data)
# create fits map file
hdu.verify('fix')
mapname = name + '_map.fits'
hdu.writeto(mapname, overwrite=True)
# create gammalib spatial model component based on map
spatial = gammalib.GModelSpatialDiffuseMap(mapname)
# create model and save as xml
model = gammalib.GModelSky(spatial, spectral_models[s])
model.name(name)
models = gammalib.GModels()
models.append(model)
models.save(name + '.xml')
# move output files to template directory
os.system('mv {}* {}'.format(name, outdir))
def _gen_model_anna(self, i) :
"""
in-fly Creation of GModel
Return
------
GModel for a dark matter annihilation
"""
# Create xml element for the spectral type
# These are the min and max values that can take
# the prefactor parameter
# Note: I am not sure why I need to rise so much
# the maxval to specify the valid range od the
# parameter
# I hope this issue change when implementing the
# GModelSpectralDMMmodel class
minval = 1.0e-20
maxval = 1.0e+20
# Model type
modtype = self['modtype'].string()
# recover filename created with _gen_dmfile_anna
srcname = self['srcname'].string()
# Create spectral container using GModelSpectralTable
# and setup the mass, channel and normalization of the model
ch_number = self._get_channel_key()
dmmass = self._masses[i]
jfactor = math.pow(10., self['logastfactor'].real())
sigmav = math.pow(10., self['logsigmav'].real())
fluxnorm = sigmav * jfactor / 8. / gammalib.pi / dmmass / dmmass
fluxnorm *= 1.e-3
ffile = self['dmspecfits'].filename()
dmspec = gammalib.GModelSpectralTable()
dmspec.load(ffile)
dmspec['Mass'].value(dmmass)
dmspec['Channel'].value(ch_number)
dmspec['Channel'].scale(1)
dmspec['Normalization'].value(fluxnorm)
dmspec['Normalization'].range(minval, maxval)
# Mass and Channel parameters should be fixed
# But, just to be sure
dmspec['Mass'].fix()
dmspec['Channel'].fix()
dmspec['Normalization'].free()
# Creating Spatial container
if self[ 'modtype' ].string() == 'PointSource' :
ra = self['ra'].real()
dec = self['dec'].real()
dmspat = gammalib.GModelSpatialPointSource(ra, dec)
elif self[ 'modtype' ].string() == 'DiffuseSource' :
mfile = self['map_fits'].filename()
dmspat = gammalib.GModelSpatialDiffuseMap(mfile)
# Then generate GModel from spatial and spectral part
# This must avoid to create a lot of XML Templates
# to specify DM models :P
dmmodel = gammalib.GModelSky(dmspat, dmspec)
dmmodel.name(srcname)
dmmodel.tscalc(True)
# Return
return dmmodel