def main():
# Define basic vars
maps_dir = '/zfs/bsafdi/data/'
fermi_data_dir = '/zfs/tslatyer/fermimaps/allsky/'
work_dir = '/zfs/nrodd/NPTFWorking'
emin=0
emax=1
nside=256
eventclass=5
eventtype=3
newstyle=1
ps_file = '/zfs/nrodd/NPTFWorking/data/ps_data/ps_lists/3FGL_0to15_tiny.txt'
n_ps_run=10
indeg=True
loadforpsf = fp.fermi_plugin(maps_dir,fermi_data_dir=fermi_data_dir,work_dir=work_dir,CTB_en_min = emin,CTB_en_max=emax,nside=nside,eventclass=eventclass,eventtype=eventtype,newstyle=newstyle)
loadforpsf.load_psf(data_name='p8',fits_file_path = 'False',eventclass=eventclass,eventtype=eventtype)
sigma_PSF_deg = loadforpsf.sigma_PSF_deg[0:-1]
#print "exp map:",loadforpsf.CTB_exposure_maps
#print "len(loadforpsf.CTB_exposure_maps)",len(loadforpsf.CTB_exposure_maps)
#print "len(loadforpsf.CTB_exposure_maps[0])",len(loadforpsf.CTB_exposure_maps[0])
#print "mean(loadforpsf.CTB_exposure_maps[0])",np.mean(loadforpsf.CTB_exposure_maps[0])
#print "sum(loadforpsf.CTB_exposure_maps[0])",np.sum(loadforpsf.CTB_exposure_maps[0],axis=0)
#print "PSF_deg:",sigma_PSF_deg
larr,barr,n_ps,n_ps_border = trimorderpslist(ps_file,indeg,sigma_PSF_deg)
#print "n_ps:",n_ps
#print "n_ps_border:",n_ps_border
#print "l:",larr*180/np.pi
#print "b:",barr*180/np.pi
ps_norms=np.array([1,1,1,1])
loadforpsf.add_multiple_ps_king(larr,barr,rescale=ps_norms,comp='ps_comb')
print "MADE IT OUT"
n_groups = int(np.ceil(float(n_ps+n_ps_border)/float(n_ps_run)))
n_last_group = n_ps - (n_groups-1)*n_ps_run
def setup_fermi(self):
""" Setup the Fermi plugin """
eventclass=5 # 2 (Source) or 5 (UltracleanVeto)
eventtype=0 # 0 (all), 3 (bestpsf) or 5 (top3 quartiles)
mask_type='top300'
force_mask_at_bin_number=8
self.f1 = fp.fermi_plugin(maps_dir,fermi_data_dir=fermi_data_dir,work_dir=work_dir,CTB_en_min=0,CTB_en_max=40,nside=self.nside,eventclass=eventclass,eventtype=eventtype,newstyle=1,data_July16=True)
if mask_type != 'False':
self.f1.make_ps_mask(mask_type = mask_type,force_energy = True,energy_bin = force_mask_at_bin_number)
self.f1.add_diffuse_newstyle(comp = 'p7', eventclass = eventclass, eventtype = eventtype)
self.f1.add_bubbles(comp='bubs') #bubbles
self.f1.add_iso(comp='iso') #iso
self.f1.add_ps_model(comp='ps_model')
# Exposure correct J_map_arr
self.J_map_arr *= self.f1.CTB_exposure_maps
# Add J-factor map with mean 1 in each energy bin
self.f1.add_template_by_hand('J_map',np.array([self.J_map_arr[i]/np.mean(self.J_map_arr[i]) for i in range(40)]))
def setup_for_scan():
global f, b, new_template_dict, n_ps, newstyle
# Load Fermi Plugin and its basic functionality
f = fp.fermi_plugin(maps_dir,fermi_data_dir=fermi_data_dir,work_dir=work_dir,CTB_en_min = emin,CTB_en_max=emax,nside=nside,eventclass=eventclass,eventtype=eventtype,newstyle=newstyle)
if mask_type!='False':
f.make_ps_mask(mask_type=mask_type,force_energy=force_ps_mask,energy_bin=force_ps_mask_bin)
# Add appropriate templates
f.add_diffuse_newstyle(comp = diff, eventclass = eventclass, eventtype = eventtype)
if extraicstemp!='False':
f.add_diffuse_newstyle(comp = extraicstemp, eventclass = eventclass, eventtype = eventtype)
f.add_bubbles(comp = 'bubs')
f.add_iso(comp = 'iso')
if add_ps_model:
f.add_ps_model(comp = 'ps_model')
if nfw_dm:
f.add_nfw(comp = 'nfw')
f.add_template_from_file('disk',disk_file_name) # always add the disk here even if don't use as often needed for NPTF
if norm_file!='False':
if len(add_norm_file_for_comps) > 0 and add_norm_file != 'False':
print 'using first normalization file: ', norm_file
f.use_template_normalization_file(norm_file,key_suffix='-0',dont_use_keys=add_norm_file_for_comps)
print 'using second normalization file: ', add_norm_file
f.use_template_normalization_file(add_norm_file,key_suffix='-0',use_keys=add_norm_file_for_comps)
else:
f.use_template_normalization_file(norm_file,key_suffix='-0')
#### For now, combine diff, bubs, iso, ps_model, IC to reduce number of parameters
new_template_dict = {}
new_template_dict['back']=np.zeros(np.shape(f.template_dict['bubs']))
for key in f.template_dict.keys():
new_template_dict[key] = f.template_dict[key]
if key not in not_in_simplified_template_list: #key != 'nfw' and key != 'disk' and
print 'Including template', key, 'in background template'
new_template_dict['back']+=f.template_dict[key]
# else:
# new_template_dict[key] = f.template_dict[key]
# Load PSF - this is only required for NPTF scans
# This now uses a King function
if not poiss:
f.load_psf_kings()
f.make_f_ary_kings(psf_model,energy_averaged=True,psf_dir=psf_dir,psf_save_tag=run_tag_energy)
# Setup Bayesian scan for fermi
b = bsm.bayesian_scan_NPTF(tag=tag,work_dir = work_dir,psf_dir = psf_dir,nside=nside,nlive=nlive,k_max=k_max)
if fake_data:
data = np.loadtxt(fake_data_path)
else:
data = f.CTB_count_maps
b.load_external_data(f.CTB_en_bins,data,f.CTB_exposure_maps)
if use_simplified_templates:
b.add_new_template(new_template_dict)
if fixed_background:
b.add_fixed_templates({'back':new_template_dict['back']})
else:
b.add_new_template(f.template_dict)
if mask_type!='False':
b.make_mask_total(plane_mask=plane_mask, band_mask_range = [-pmval,pmval], lcut=lcut, lmin=lmin, lmax=lmax, bcut=bcut, bmin=bmin, bmax=bmax, mask_ring=mask_ring, inner=inner, outer=outer, ps_mask_array = f.ps_mask_array)
else:
b.make_mask_total(plane_mask=plane_mask, band_mask_range = [-pmval,pmval], lcut=lcut, lmin=lmin, lmax=lmax, bcut=bcut, bmin=bmin, bmax=bmax, mask_ring=mask_ring, inner=inner, outer=outer)
b.rebin_external_data(n_ebins)
b.compress_templates()
### Add in the Templates
if method != 'minuit':
if not min_prior_range:
b.add_poiss_model(diff,'$A_{diff}$',[-10,10],False)
if extraicstemp!='False':
b.add_poiss_model(extraicstemp,'$A_{ics}$',[-10,10],False)
b.add_poiss_model('iso','$A_{iso}$',[-10,10],False)
b.add_poiss_model('bubs','$A_{bubs}$',[-10,10],False)
else: # If already have priors, don't scan over such a large range
b.add_poiss_model(diff,'$A_{diff}$',[0.5,1.5],False)
if extraicstemp!='False':
b.add_poiss_model(extraicstemp,'$A_{ics}$',[0.5,1.5],False)
if high_lat:
b.add_poiss_model('iso','$A_{iso}$',[0.5,1.5],False)
else:
b.add_poiss_model('iso','$A_{iso}$',[0.8,1.2],False)
b.add_poiss_model('bubs','$A_{bubs}$',[0.5,1.5],False)
else:
b.add_poiss_model(diff,'$A_{diff}$',[0,2],False)
if extraicstemp!='False':
b.add_poiss_model(extraicstemp,'$A_{ics}$',[-2,2],False)
b.add_poiss_model('iso','$A_{iso}$',[0,2],False)
b.add_poiss_model('bubs','$A_{bubs}$',[0,4],False)
if add_ps_model:
if not min_prior_range:
b.add_poiss_model('ps_model','$A_{ps-model}$',[0,6],False)
else:
b.add_poiss_model('ps_model','$A_{ps-model}$',[0.5,1.5],False)
if nfw_dm: # leave this large as NFW struggles to converge at high E
b.add_poiss_model('nfw','$l10A_{nfw}$',[-6,6],True)
### Configure final details
def sb_string_mod(mod):
return ['${S_b^{' + mod + '}}^{'+str(i) + '}$' for i in range(n_ebins)]
if not poiss:
sb_string = ['$S_b^{'+str(i) + '}$' for i in range(n_ebins)]
sb_string_disk = ['${S_b^{disk}}^{'+str(i) + '}$' for i in range(n_ebins)]
sb_prior = [ [-3.,3.] for i in range(n_ebins)]
sb_prior_log = [True for i in range(n_ebins)]
if len(ps_fixed_filename_list) > 0:
for comp,filename in map(None,ps_fixed_list,ps_fixed_filename_list):
b.load_fixed_ps_model(filename,comp)
n_ps += len(ps_fixed_filename_list)
print 'n_ps changed to ', n_ps, ' because of fixed templates'
for mod in ps_list:
b.add_non_poiss_model(mod,['$A_{' +mod+'}$' ,'$n_1^{' +mod+'}$','$n_2^{' +mod+'}$']+sb_string_mod(mod),[[-6,6],[2.05,30],[-2,1.95]] + sb_prior, [True,False,False] + sb_prior_log)
if n_ps==1:
b.initiate_1_ps_edep_new_from_f_ary(f.f_ary_list,f.df_rho_div_f_ary_list)
elif n_ps==2:
b.initiate_2_ps_edep_new_from_f_ary(f.f_ary_list,f.df_rho_div_f_ary_list)
elif n_ps==3:
b.initiate_3_ps_edep_new_from_f_ary(f.f_ary_list,f.df_rho_div_f_ary_list)
print 'Performing an NPTF ...'
else:
b.initiate_poissonian_edep()
print 'Performing a standard template fit ...'
import argparse
nsim = 100
outstring = 'allhalos'
nside = 128
eventclass = 5 # 2 (Source) or 5 (UltracleanVeto)
eventtype = 0 # 0 (all), 3 (bestpsf) or 5 (top3 quartiles)
emin_bin = 0
emax_bin = 40 # Must match the norm file!
f_global = fp.fermi_plugin(maps_dir,
fermi_data_dir=fermi_data_dir,
work_dir=work_dir,
CTB_en_min=emin_bin,
CTB_en_max=emax_bin,
nside=nside,
eventclass=eventclass,
eventtype=eventtype,
newstyle=1,
data_July16=True)
# Set up J_map
J_map = hp.ud_grade(np.load(
'/tigress/smsharma/public/GenMaps/GenMapsJumpAround/Jfactor_DS_true_map_100.0_100.0_100.0b2e+20_a3.16e+17.npy'
),
nside,
power=-2)
J_map /= GeV**2 * Centimeter**-5
# Exposure correct then smooth J_map latter must be done first
J_map_arr_ps = np.zeros(shape=(emax_bin - emin_bin, len(J_map)))
def scan(self):
################
# Fermi plugin #
################
# Load the Fermi plugin - always load all energy bins, extract what is needed
f_global = fp.fermi_plugin(maps_dir,
fermi_data_dir=fermi_data_dir,
work_dir=work_dir,
CTB_en_min=0,
CTB_en_max=40,
nside=self.nside,
eventclass=self.eventclass,
eventtype=self.eventtype,
newstyle=1,
data_July16=True)
# Load necessary templates
f_global.add_diffuse_newstyle(comp=self.diff,
eventclass=self.eventclass,
eventtype=self.eventtype)
f_global.add_iso()
ps_temp = np.load(work_dir + '/DataFiles/PS-Maps/ps_map.npy')
f_global.add_template_by_hand(comp='ps_model', template=ps_temp)
###################
# Get DM halo map #
###################
l = self.catalog.l.values[self.iobj]
b = self.catalog.b.values[self.iobj]
rs = self.catalog.rs.values[self.iobj] * 1e-3
if self.boost:
J0 = 10**self.catalog.mulog10J_inf.values[self.iobj]
else:
J0 = 10**self.catalog.mulog10Jnb_inf.values[self.iobj]
mk = mkDMMaps.mkDMMaps(z=self.catalog.z[self.iobj],
r_s=rs,
J_0=J0,
ell=l * np.pi / 180,
b=b * np.pi / 180,
nside=self.nside,
use_boost=self.use_boost,
Burkert=self.Burkert)
DM_template_base = mk.map
#########################################
# Loop over energy bins to get spectrum #
#########################################
# ROI where we will normalise our templates
ROI_mask = cm.make_mask_total(mask_ring=True,
inner=0,
outer=10,
ring_b=b,
ring_l=l)
ROI = np.where(ROI_mask == 0)[0]
# Setup output
output_cube = np.zeros((self.emax + 1 - self.emin, 5, len(ROI)))
for iebin, ebin in tqdm(enumerate(np.arange(self.emin, self.emax + 1)),
disable=1 - self.verbose):
######################
# Templates and maps #
######################
if self.verbose:
print "At bin", ebin
fermi_exposure = f_global.CTB_exposure_maps[ebin]
DM_template = DM_template_base * fermi_exposure / np.sum(
DM_template_base * fermi_exposure)
ksi = ks.king_smooth(maps_dir,
ebin,
self.eventclass,
self.eventtype,
threads=1)
DM_template_smoothed = ksi.smooth_the_map(DM_template)
DM_intensity_base = np.sum(DM_template_smoothed / fermi_exposure)
dif = f_global.template_dict[self.diff][ebin]
iso = f_global.template_dict['iso'][ebin]
psc = f_global.template_dict['ps_model'][ebin]
output_cube[iebin, 0] = ROI
output_cube[iebin, 1] = dif[ROI]
output_cube[iebin, 2] = iso[ROI]
output_cube[iebin, 3] = psc[ROI]
output_cube[iebin, 4] = DM_template_smoothed[ROI]
np.save(self.save_dir + 'cube_o' + str(self.iobj) + self.mc_tag,
output_cube)
def main():
keyfile = 'nptf/IG_NDI/FD_key_1.txt.gz'
jetbase = '/tigress/nrodd/FindPSOutput/psdata_2-12-15-m5-b1_roi/psdata_2-12-15-m5-b1_roi_ca_PT_R0p'
jetfiles = [jetbase+'15.txt.gz',jetbase+'2.txt.gz',jetbase+'25.txt.gz',jetbase+'3.txt.gz',jetbase+'4.txt.gz',jetbase+'5.txt.gz',jetbase+'6.txt.gz',jetbase+'7.txt.gz',jetbase+'8.txt.gz',jetbase+'9.txt.gz']
jetlabel = ['Jet R0p15','Jet R0p2','Jet R0p25','Jet R0p3','Jet R0p4','Jet R0p5','Jet R0p6','Jet R0p7','Jet R0p8','Jet R0p9']
jetrad = [0.15,0.2,0.25,0.3,0.4,0.5,0.6,0.7,0.8,0.9]
outname = '2-12-15-m5_b1'
fake_data_key_path = '/tigress/nrodd/NPTFWorking/FindPS/plots/' + keyfile
CTB_start_bin=8
CTB_end_bin=16
nside=512
data_type='p8'
npix = hp.nside2npix(nside)
theta, phi = hp.pix2ang(nside,range(npix))
larr_full = phi*180/np.pi
larr_full = ((larr_full + 180) % 360)-180
larr_full *= np.pi/180
barr_full = np.pi/2 - theta
band_mask_range_plot = [-1,1]
mask_ring_plot = True
outer_plot = 10
f = fp.fermi_plugin(maps_dir,CTB_en_min=CTB_start_bin,CTB_en_max=CTB_end_bin,nside=nside,data_name=data_type)
# Now calculate dndF from the sim key
fake_data_key_load = np.loadtxt(fake_data_key_path)
fake_data_key = np.zeros(shape=(len(fake_data_key_load),10))
fake_data_key[::,0:2] = fake_data_key_load[::,0:2]
fake_data_key[::,2:10] = fake_data_key_load[::,CTB_start_bin+2:CTB_end_bin+2]
# Now pick out point sources within the ROI we want to analyse
# NB: cuts in degrees, larr and barr in radians
pmfocus=3
ringfocus=10
barr = np.pi/2-fake_data_key[::,0]
larr = fake_data_key[::,1]*180/np.pi
larr = ((larr + 180) % 360)-180
larr *= np.pi/180
print np.min(larr)*180/np.pi
print np.max(larr)*180/np.pi
print np.min(barr)*180/np.pi
print np.max(barr)*180/np.pi
thetaarr = np.arccos(np.cos(larr)*np.cos(barr))
print np.min(thetaarr)*180/np.pi
print np.max(thetaarr)*180/np.pi
roi = np.where((np.abs(barr) > pmfocus*np.pi/180) & (thetaarr < ringfocus*np.pi/180))[0]
bigroi = np.where((np.abs(barr) > (pmfocus-0.9)*np.pi/180) & (thetaarr < (ringfocus+0.9)*np.pi/180))[0]
fake_data_keyroi = fake_data_key[roi,::]
key_bigroi = fake_data_key[bigroi,::]
larr_key = larr[bigroi]
barr_key = barr[bigroi]
print np.min(thetaarr[roi])*180/np.pi
print np.max(thetaarr[roi])*180/np.pi
print np.min(barr[roi])*180/np.pi
print np.min(thetaarr[bigroi])*180/np.pi
print np.max(thetaarr[bigroi])*180/np.pi
print np.min(barr[bigroi])*180/np.pi
#np.load('FAKE')
print "len(roi):",len(roi)
print "len(bigroi):",len(bigroi)
pfake3FGL = make_flux_histogram_local(fake_data_keyroi,f.CTB_exposure_maps,band_mask_range = band_mask_range_plot, mask_ring = mask_ring_plot, outer = outer_plot)
pfake3FGL.make_fake_data_flux_histogram(0.1,5000,10)
pfake3FGL.plot_fake_data_histogram(fmt = 'o', color='black',markersize=5,label='Sim PS')
# Now read in Jet data and create dndF plots from that
# First load the data and background model as we need these
jetcolors = ['red','orange','yellow','olive','green','blue','indigo','violet','deeppink','pink']
# Loop through the files
#for i in range(10):
for i in range(1):
print "At i =",i
jetload = np.loadtxt(jetfiles[i])
# extract (l,b) from array
larr = jetload[::,0]
phi = larr*180/np.pi
larr *= 180/np.pi
larr = ((larr + 180) % 360)-180
larr *= np.pi/180
barr = jetload[::,1]
theta = np.pi/2-barr
print np.min(larr)*180/np.pi
print np.max(larr)*180/np.pi
print np.min(larr_key)*180/np.pi
print np.max(larr_key)*180/np.pi
print np.min(barr)*180/np.pi
print np.max(barr)*180/np.pi
print np.min(barr_key)*180/np.pi
print np.max(barr_key)*180/np.pi
# Determine which are in the ROI
thetaarr = np.arccos(np.cos(larr)*np.cos(barr))
roi = np.where((np.abs(barr) > pmfocus*np.pi/180) & (thetaarr < ringfocus*np.pi/180))[0]
# Now build up the key for each ps in the ROI
jet_data_key = np.zeros(shape=(len(roi),10))
#print "len(larr):",len(larr)
#print "len(larr_key):",len(larr_key)
#print "len(roi):",len(roi)
count=0
for j in range(len(roi)):
print "j =",j
# First put theta and phi in
jet_data_key[j,0] = theta[roi[j]]
jet_data_key[j,1] = phi[roi[j]]
# Now input the counts - determine this by adding counts for sim PS within jetrad
thetaps = np.arccos(np.cos(larr[roi[j]]-larr_key)*np.cos(barr[roi[j]]-barr_key))
print np.min(thetaps)*180/np.pi
print np.max(thetaps)*180/np.pi
print len(thetaps)
if j==20:
np.load('Fake')
pstoadd = np.where(thetaps <= jetrad[i]*np.pi/180)[0]
#print "len(pstoadd)",len(pstoadd)
if len(pstoadd) > 0:
count += 1
print "count =",count
for k in range(8):
for m in range(len(pstoadd)):
print "key_bigroi[pstoadd[m],k+2]=",key_bigroi[pstoadd[m],k+2]
jet_data_key[j,k+2] += key_bigroi[pstoadd[m],k+2]
print "count:",count
# Now plot
pfake3FGL = make_flux_histogram_local(jet_data_key,f.CTB_exposure_maps,band_mask_range = band_mask_range_plot, mask_ring = mask_ring_plot, outer = outer_plot)
pfake3FGL.make_fake_data_flux_histogram(0.1,5000,10)
pfake3FGL.plot_fake_data_histogram(fmt = 'o', color=jetcolors[i],markersize=5,label=jetlabel[i])
plt.yscale('log')
plt.xscale('log')
plt.xlim([1e-12,1e-6])
plt.ylim([1e3,1e11])
plt.tick_params(axis='x', length=5,width=2,labelsize=18)
plt.tick_params(axis='y',length=5,width=2,labelsize=18)
plt.xlabel('$F$ [photons / cm$^2$ / s]', fontsize=18)
plt.ylabel('$dN/dF$ [photons$^{-1}$ cm$^2$ s deg$^{-2}$]', fontsize=18)
plt.legend(fontsize=16)
plt.savefig('./Plots/' + outname + '.pdf')
plt.close()
def scan(self):
################
# Fermi plugin #
################
# Load the Fermi plugin - always load all energy bins, extract what is needed
f_global = fp.fermi_plugin(maps_dir,
fermi_data_dir=fermi_data_dir,
work_dir=work_dir,
CTB_en_min=0,
CTB_en_max=40,
nside=self.nside,
eventclass=self.eventclass,
eventtype=self.eventtype,
newstyle=1,
data_July16=True)
# Load necessary templates
f_global.add_diffuse_newstyle(comp=self.diff,
eventclass=self.eventclass,
eventtype=self.eventtype)
f_global.add_iso()
ps_temp = np.load(work_dir + '/DataFiles/PS-Maps/ps_map.npy')
f_global.add_template_by_hand(comp='ps_model', template=ps_temp)
###################
# Get DM halo map #
###################
l = self.catalog.l.values[self.iobj]
b = self.catalog.b.values[self.iobj]
rs = self.catalog.rs.values[self.iobj] * 1e-3
if self.boost:
J0 = 10**self.catalog.mulog10J_inf.values[self.iobj]
else:
J0 = 10**self.catalog.mulog10Jnb_inf.values[self.iobj]
mk = mkDMMaps.mkDMMaps(z=self.catalog.z[self.iobj],
r_s=rs,
J_0=J0,
ell=l * np.pi / 180,
b=b * np.pi / 180,
nside=self.nside,
use_boost=self.use_boost,
Burkert=self.Burkert)
DM_template_base = mk.map
#########################################
# Loop over energy bins to get spectrum #
#########################################
# 10 deg mask for the analysis
analysis_mask_base = cm.make_mask_total(mask_ring=True,
inner=0,
outer=10,
ring_b=b,
ring_l=l)
# ROI where we will normalise our templates
ROI_mask = cm.make_mask_total(mask_ring=True,
inner=0,
outer=2,
ring_b=b,
ring_l=l)
ROI = np.where(ROI_mask == 0)[0]
# Setup output
output_norms = np.zeros((self.emax + 1 - self.emin, 4, 2))
for iebin, ebin in tqdm(enumerate(np.arange(self.emin, self.emax + 1)),
disable=1 - self.verbose):
######################
# Templates and maps #
######################
if self.verbose:
print "At bin", ebin
data = f_global.CTB_count_maps[ebin].astype(np.float64)
# Add large scale mask to analysis mask
els_str = [
'0.20000000', '0.25178508', '0.31697864', '0.39905246',
'0.50237729', '0.63245553', '0.79621434', '1.0023745',
'1.2619147', '1.5886565', '2.0000000', '2.5178508',
'3.1697864', '3.9905246', '5.0237729', '6.3245553',
'7.9621434', '10.023745', '12.619147', '15.886565',
'20.000000', '25.178508', '31.697864', '39.905246',
'50.237729', '63.245553', '79.621434', '100.23745',
'126.19147', '158.86565', '200.00000', '251.78508',
'316.97864', '399.05246', '502.37729', '632.45553',
'796.21434', '1002.3745', '1261.9147', '1588.6565'
]
ls_mask_load = fits.open(
'/tigress/nrodd/LargeObjMask/Allpscmask_3FGL-energy' +
els_str[ebin] + 'large-obj.fits')
ls_mask = np.array([
np.round(val) for val in hp.ud_grade(
ls_mask_load[0].data, self.nside, power=0)
])
analysis_mask = np.vectorize(bool)(analysis_mask_base + ls_mask)
fermi_exposure = f_global.CTB_exposure_maps[ebin]
DM_template = DM_template_base * fermi_exposure / np.sum(
DM_template_base * fermi_exposure)
ksi = ks.king_smooth(maps_dir,
ebin,
self.eventclass,
self.eventtype,
threads=1)
DM_template_smoothed = ksi.smooth_the_map(DM_template)
DM_intensity_base = np.sum(DM_template_smoothed / fermi_exposure)
dif = f_global.template_dict[self.diff][ebin]
iso = f_global.template_dict['iso'][ebin]
psc = f_global.template_dict['ps_model'][ebin]
# Get mean values in ROI
dif_mu = np.mean(dif[ROI])
iso_mu = np.mean(iso[ROI])
psc_mu = np.mean(psc[ROI])
DM_mu = np.mean(DM_template_smoothed[ROI])
exp_mu = np.mean(fermi_exposure[ROI])
####################
# NPTFit norm scan #
####################
n = nptfit.NPTF(tag='norm_o' + str(self.iobj) + '_E' + str(ebin) +
self.mc_tag)
n.load_data(data, fermi_exposure)
n.load_mask(analysis_mask)
n.add_template(dif, self.diff)
n.add_template(iso, 'iso')
n.add_template(psc, 'psc')
n.add_template(DM_template_smoothed, 'DM')
n.add_poiss_model(self.diff, '$A_\mathrm{dif}$', [0, 10], False)
n.add_poiss_model('iso', '$A_\mathrm{iso}$', [0, 20], False)
n.add_poiss_model('psc', '$A_\mathrm{psc}$', [0, 10], False)
n.add_poiss_model('DM', '$A_\mathrm{DM}$', [0, 1000], False)
n.configure_for_scan()
##########
# Minuit #
##########
keys = n.poiss_model_keys
limit_dict = {}
init_val_dict = {}
step_size_dict = {}
for key in keys:
if key == 'DM':
limit_dict['limit_' + key] = (0, 1000)
else:
limit_dict['limit_' + key] = (0, 50)
init_val_dict[key] = 0.0
step_size_dict['error_' + key] = 1.0
other_kwargs = {'print_level': self.verbose, 'errordef': 1}
z = limit_dict.copy()
z.update(other_kwargs)
z.update(limit_dict)
z.update(init_val_dict)
z.update(step_size_dict)
f = call_ll(len(keys), n.ll, keys)
m = Minuit(f, **z)
m.migrad(ncall=30000, precision=1e-14)
# Output spectra in E^2 dN/dE, in units [GeV/cm^2/s/sr] as mean in 2 degrees
output_norms[iebin, 0, 0] = m.values[
'p8'] * dif_mu / exp_mu * self.emid[iebin]**2 / self.de[iebin]
output_norms[iebin, 0, 1] = m.errors[
'p8'] * dif_mu / exp_mu * self.emid[iebin]**2 / self.de[iebin]
output_norms[iebin, 1, 0] = m.values[
'iso'] * iso_mu / exp_mu * self.emid[iebin]**2 / self.de[iebin]
output_norms[iebin, 1, 1] = m.errors[
'iso'] * iso_mu / exp_mu * self.emid[iebin]**2 / self.de[iebin]
output_norms[iebin, 2, 0] = m.values[
'psc'] * psc_mu / exp_mu * self.emid[iebin]**2 / self.de[iebin]
output_norms[iebin, 2, 1] = m.errors[
'psc'] * psc_mu / exp_mu * self.emid[iebin]**2 / self.de[iebin]
output_norms[iebin, 3, 0] = m.values[
'DM'] * DM_mu / exp_mu * self.emid[iebin]**2 / self.de[iebin]
output_norms[iebin, 3, 1] = m.errors[
'DM'] * DM_mu / exp_mu * self.emid[iebin]**2 / self.de[iebin]
###################################
# NPTFit fixed DM and bkg profile #
###################################
# Make background sum and initiate second scan
# If was no data leave bkg_sum as 0
bkg_sum = np.zeros(len(data))
if np.sum(data * np.logical_not(analysis_mask)) != 0:
for key in keys:
if key != 'DM': # Don't add DM in here
if m.values[key] != 0:
bkg_sum += n.templates_dict[key] * m.values[key]
else: # If zero, use ~parabolic error
bkg_sum += n.templates_dict[key] * m.errors[
key] / 2.
nDM = nptfit.NPTF(tag='dm_o' + str(self.iobj) + '_E' + str(ebin) +
self.mc_tag)
nDM.load_data(data, fermi_exposure)
nDM.add_template(bkg_sum, 'bkg_sum')
# If there is no data, only go over pixels where DM is non-zero
if np.sum(data * np.logical_not(analysis_mask)) != 0:
nDM.load_mask(analysis_mask)
else:
nodata_mask = DM_template_smoothed == 0
nDM.load_mask(nodata_mask)
nDM.add_poiss_model('bkg_sum',
'$A_\mathrm{bkg}$',
fixed=True,
fixed_norm=1.0)
np.save(self.save_dir + 'spec_o' + str(self.iobj) + self.mc_tag,
output_norms)
n_flux_bins=15
error_range=0.68 #for plotting uncertanties
######disk filename
disk_file_name= 'thindiskmodel_ec.fits' #'simplediskmodel_ec.fits'
####################
##########Internal code
###################
##Fermi plugin instance
f = fp.fermi_plugin(maps_dir,fermi_data_dir=fermi_data_dir,work_dir=work_dir,CTB_en_min=CTB_start_bin,CTB_en_max=CTB_end_bin+1,nside=nside,eventclass=eventclass,eventtype=eventtype,newstyle=newstyle)
#f.make_ps_mask(mask_type = mask_type,energy_bin = energy_bin_mask,force_energy=force_energy)
f.add_diffuse_newstyle(comp = 'p6', eventclass = eventclass, eventtype = eventtype)
f.add_bubbles() #bubbles
f.add_iso() #iso
f.add_nfw() #NFW-DM
f.add_template_from_file('disk',disk_file_name) #we will call template 'disk'
if mask_type != 'False':
f.make_ps_mask(mask_type = mask_type,energy_bin = energy_bin_mask,force_energy=force_energy)
f.use_template_normalization_file(norm_file_path,key_suffix='-0')
def main():
global plot_ll_profile, eachps_dict, eachts_dict, eachps_En_center, TSbkg, TS, ps_norms_loop1, ps_norms
# Determine PSF using fermi plugin, for use in the ps ordering
loadforpsf = fp.fermi_plugin(maps_dir,fermi_data_dir=fermi_data_dir,work_dir=work_dir,CTB_en_min = emin,CTB_en_max=emax,nside=nside,eventclass=eventclass,eventtype=eventtype,newstyle=newstyle)
loadforpsf.load_psf(data_name='p8',fits_file_path = 'False')
sigma_PSF_deg = loadforpsf.sigma_PSF_deg[0:-1]
# Get an ordered list of the l and b values by ranking - cutting those outside of region
# End of list contains those sources outside region but within 1 PSF of the border
larr,barr,n_ps,n_ps_border = trimorderpslist(ps_file,indeg,sigma_PSF_deg)
n_groups = int(np.ceil(float(n_ps+n_ps_border)/float(n_ps_run)))
n_last_group = n_ps+n_ps_border - (n_groups-1)*n_ps_run
# Establish array of norms for the point sources - starting at 1 and adjusted throughout the run
ps_norms_loop1 = np.ones(n_ps+n_ps_border)
ps_norms = np.ones(n_ps)
# The strategy from here is as follows:
# Break the point source lists up into groups of n_ps_run, in order of ranking
# For each group we float each point source individually and extract its normalisation
# Next we create a template combining each of the point sources just fitted
# This is done at the analysis step
# Then we repeat this for the next group, but add in a template of all the point sources
# already run, and repeat this process till all point sources have been run
# After this we perform a run with the full ps map to get its spectrum
# Then we rerun each ps one by one to get its TS while fixing the rest
print 'Determining initial value for each point source...'
for i in range(n_groups):
if i+1 == n_groups:
n_ps_groupi = n_last_group
else:
n_ps_groupi = n_ps_run
# Setup for scan
if method=='minuit' and run==False:
pass
else:
print 'setting up the scan. the method is', method
setup_for_scan(i=i,n_ps_groupi=n_ps_groupi,larr=larr,barr=barr,
psloop1=True)
print 'finished setting up the scan.'
# Perform scan / load scan
if run:
print 'The nside for this scan is ', b.nside
if method=='multinest':
b.perform_scan(run_tag = run_tag_energy)
do_analysis(i=i,n_ps_groupi=n_ps_groupi,minuit_new=False,psloop1=True)
elif method=='minuit':
b.perform_scan_minuit(run_tag = run_tag_energy)
b.save_minuit()
do_analysis(i=i,n_ps_groupi=n_ps_groupi,minuit_new=True,psloop1=True)
# Now perform run to extract to spectrum of all point sources combined
print 'Determining spectrum of combined point source template...'
# Setup for scan
if method=='minuit' and run==False:
pass
else:
print 'setting up the scan. the method is', method
setup_for_scan(larr=larr,barr=barr,pscomball=True)
print 'finished setting up the scan.'
# Perform scan / load scan
if run:
print 'The nside for this scan is ', b.nside
if method=='multinest':
b.perform_scan(run_tag = run_tag_energy)
do_analysis(pscomball=True,minuit_new=False)
elif method=='minuit':
b.perform_scan_minuit(run_tag = run_tag_energy)
b.save_minuit()
do_analysis(pscomball=True,minuit_new=True)
# Now loop over all point sources, floating one at a time with the others fixed
print 'Calculating spectrum and significance of each point source in ROI...'
# From this we want to extract their TS and spectrum
# Initialise empty dictionary to put the spectra in
eachps_dict = {}
eachts_dict = {}
# Now run through loop - need to do this twice for each, once with and once without the point source, in order to determine the TS
for i in range(n_ps):
TSbkg=0.
TS=0.
# Setup for scan
if method=='minuit' and run==False:
pass
else:
print 'setting up the scan. the method is', method
setup_for_scan(i=i,larr=larr,barr=barr,psloop2bkg=True)
print 'finished setting up the scan.'
# Perform scan / load scan
if run:
print 'The nside for this scan is ', b.nside
if method=='multinest':
b.perform_scan(run_tag = run_tag_energy)
do_analysis(i=i,minuit_new=False,psloop2bkg=True)
elif method=='minuit':
b.perform_scan_minuit(run_tag = run_tag_energy)
b.save_minuit()
print "MINUIT doesn't currently save TS - need to add this in if want minuit"
do_analysis(i=i,minuit_new=True,psloop2bkg=True)
# Setup for scan
if method=='minuit' and run==False:
pass
else:
print 'setting up the scan. the method is', method
setup_for_scan(i=i,larr=larr,barr=barr,psloop2=True)
print 'finished setting up the scan.'
# Perform scan / load scan
if run:
print 'The nside for this scan is ', b.nside
if method=='multinest':
b.perform_scan(run_tag = run_tag_energy)
do_analysis(i=i,minuit_new=False,psloop2=True)
elif method=='minuit':
b.perform_scan_minuit(run_tag = run_tag_energy)
b.save_minuit()
print "MINUIT doesn't currently save TS - need to add this in if want minuit"
do_analysis(i=i,minuit_new=True,psloop2=True)
# Finally save the spectra, norm and ts details
# Create norm dictionary and a dictionary where we convert this to a spectrum
eachnormloop1_dict={}
eachnorm_dict={}
for i in range(n_ps+n_ps_border):
eachnormloop1_dict['ps_' + str(i+1)] = ps_norms_loop1[i]
for i in range(n_ps):
eachnorm_dict['ps_' + str(i+1)] = ps_norms[i]*ps_norms_loop1[i]
# NB: norm is from the initial scan, spectra and ts from the final scan
eachps_savefile = ps_spec_dir + save_spect_label_ps
eachnormloop1_savefile = ps_spec_dir + save_norm_loop1_label_ps
eachnorm_savefile = ps_spec_dir + save_norm_label_ps
eachts_savefile = ps_spec_dir + save_ts_label
print 'saving spectra, norm and ts spectra'
spect = [[ eachps_En_center, eachps_dict]]
np.save(eachps_savefile,np.array(spect))
normloop1 = [[ eachps_En_center, eachnormloop1_dict]]
np.save(eachnormloop1_savefile,np.array(normloop1))
norm = [[ eachps_En_center, eachnorm_dict]]
np.save(eachnorm_savefile,np.array(norm))
outts = [[ eachps_En_center, eachts_dict]]
np.save(eachts_savefile,np.array(outts))
band_mask_range = [-band_mask, band_mask] #measured from the Galactic plane
mask_ring = False
mask_type = 'top300' #can also be '0.99', 'top300', or 'False'
force_energy = True #we will force the PS mask from a specific energy bin
energy_bin_mask = 10
norm_file_path = '/tigress/nrodd/2mass2furious/MakeMC/P8UCVA_norm'
spect_file_path = '/tigress/nrodd/2mass2furious/MakeMC/P8UCVA_spec'
f_total = fp.fermi_plugin(maps_dir,
fermi_data_dir=fermi_data_dir,
CTB_en_min=CTB_start_bin,
CTB_en_max=CTB_end_bin + 1,
nside=nside,
eventclass=eventclass,
eventtype=eventtype,
newstyle=newstyle,
data_July16=data_July16)
#f_total.make_ps_mask(mask_type = mask_type,energy_bin = energy_bin_mask,force_energy=force_energy)
f_total.make_ps_mask(mask_type=mask_type,
energy_bin=energy_bin_mask,
force_energy=force_energy)
f_total.add_diffuse_newstyle(comp='p7',
eventclass=eventclass,
eventtype=eventtype) #diffuse
f_total.add_bubbles() #bubbles
f_total.add_iso() #iso
f_total.add_ps_model()
parser.add_argument('-d', action='store', dest='tag',type=str)
parser.add_argument('-t', action='store', dest='run_tag',type=str)
parser.add_argument('-m', action='store', dest='maps_dir',type=str)
results = parser.parse_args()
run=results.run
analysis=results.analysis
tag = results.tag
run_tag = results.run_tag
maps_dir = results.maps_dir
print 'maps_dir is ', maps_dir
#########################
#configure for fermi
f = fp.fermi_plugin(maps_dir)
f.make_ps_mask()
f.add_diffuse(comp = 'p6')
f.add_bubbles()
f.add_iso()
f.add_nfw()
f.add_ps(0,0)
#########################
#setup bayesian scan for fermi
b = bsm.bayesian_scan_NPTF(tag=tag)
b.load_external_data(f.CTB_en_bins,f.CTB_count_maps,f.CTB_exposure_maps)
b.add_new_template(f.template_dict)
b.make_mask_total(ps_mask_array = f.ps_mask_array)
def main():
keyfile = 'nptf/IG_NDI/FD_key_1.txt.gz'
datafile = 'nptf/IG_NDI/FD_1.txt.gz'
jetbase = '/tigress/nrodd/FindPSOutput/psdata_29-11-15-m4-b2_roi/psdata_29-11-15-m4-b2_roi_ca_PT_R0p'
jetfiles = [jetbase+'2.txt.gz',jetbase+'3.txt.gz',jetbase+'4.txt.gz',jetbase+'5.txt.gz',jetbase+'6.txt.gz',jetbase+'7.txt.gz',jetbase+'8.txt.gz',jetbase+'9.txt.gz']
outname = '29-11-15-m4_b2'
fake_data_key_path = '/tigress/nrodd/NPTFWorking/FindPS/plots/' + keyfile
CTB_start_bin=8
CTB_end_bin=16
nside=512
data_type='p8'
npix = hp.nside2npix(nside)
theta, phi = hp.pix2ang(nside,range(npix))
larr_full = phi*180/np.pi
larr_full = ((larr_full + 180) % 360)-180
larr_full *= np.pi/180
barr_full = np.pi/2 - theta
band_mask_range_plot = [-1,1]
mask_ring_plot = True
outer_plot = 10
f = fp.fermi_plugin(maps_dir,CTB_en_min=CTB_start_bin,CTB_en_max=CTB_end_bin,nside=nside,data_name=data_type)
f.add_diffuse(comp = 'p6') #diffuse
f.add_bubbles() #bubbles
f.add_iso() #iso
f.add_nfw()
f.load_psf()
sigma_PSF_deg = f.sigma_PSF_deg[0:-1]
# Create background model in each energy bin
norm_file='/tigress/nrodd/NPTFWorking/FindPS/data/spect/findps_norm.npy'
loadnorm = np.load(norm_file)
bkg = np.zeros(shape=(CTB_end_bin-CTB_start_bin,npix))
for i in range(CTB_start_bin,CTB_end_bin):
comb = f.template_dict['p6'][i-CTB_start_bin]*loadnorm[i][1]['p6-0']
comb += f.template_dict['iso'][i-CTB_start_bin]*loadnorm[i][1]['iso-0']
comb += f.template_dict['bubs'][i-CTB_start_bin]*loadnorm[i][1]['bubs-0']
comb += f.template_dict['nfw'][i-CTB_start_bin]*(10**(loadnorm[i][1]['nfw-0']))
bkg[i-CTB_start_bin,::] = comb
# Load the fake data map
load = np.loadtxt('/tigress/nrodd/NPTFWorking/FindPS/plots/' + datafile)
fakemap = load[CTB_start_bin:CTB_end_bin,::]
# Now calculate dndF from the sim key
fake_data_key_load = np.loadtxt(fake_data_key_path)
fake_data_key = np.zeros(shape=(len(fake_data_key_load),10))
fake_data_key[::,0:2] = fake_data_key_load[::,0:2]
fake_data_key[::,2:10] = fake_data_key_load[::,CTB_start_bin+2:CTB_end_bin+2]
# Now pick out point sources within the ROI we want to analyse
# NB: cuts in degrees, larr and barr in radians
pmfocus=3
ringfocus=10
barr = np.pi/2-fake_data_key[::,0]
larr = fake_data_key[::,1]*180/np.pi
larr = ((larr + 180) % 360)-180
larr *= np.pi/180
thetaarr = np.arccos(np.cos(larr)*np.cos(barr))
roi = np.where((np.abs(barr) > pmfocus*np.pi/180) & (thetaarr < ringfocus*np.pi/180))[0]
fake_data_keyroi = fake_data_key[roi,::]
pfake3FGL = make_flux_histogram_local(fake_data_keyroi,f.CTB_exposure_maps,band_mask_range = band_mask_range_plot, mask_ring = mask_ring_plot, outer = outer_plot)
pfake3FGL.make_fake_data_flux_histogram(0.1,5000,50)
pfake3FGL.plot_fake_data_histogram(fmt = 'o', color='black',markersize=5,label='Sim PS')
# Now read in Jet data and create dndF plots from that
# First load the data and background model as we need these
jetcolors = ['red','orange','yellow','green','blue','indigo','violet','pink']
# Loop through the files
for i in range(8):
print "At i =",i
jetload = np.loadtxt(jetfiles[i])
# extract (l,b) from array
larr = jetload[::,0]
phi = larr*180/np.pi
larr = ((larr + 180) % 360)-180
larr *= np.pi/180
barr = jetload[::,1]
theta = np.pi/2-barr
# Determine which are in the ROI
thetaarr = np.arccos(np.cos(larr)*np.cos(barr))
roi = np.where((np.abs(barr) > pmfocus*np.pi/180) & (thetaarr < ringfocus*np.pi/180))[0]
# Now build up the key for each ps in the ROI
jet_data_key = np.zeros(shape=(len(roi),10))
for j in range(len(roi)):
# First put theta and phi in
jet_data_key[j,0] = theta[roi[j]]
jet_data_key[j,1] = phi[roi[j]]
# Now input the counts - determine this from data-bkg in within 1 PSF of the source
# Then rescale up as this is just the 68% containment radius
thetaps = np.arccos(np.cos(larr[roi[j]]-larr_full)*np.cos(barr[roi[j]]-barr_full))
for k in range(8):
PSF = sigma_PSF_deg[k]
psroi = np.where(thetaps < PSF*np.pi/180)[0]
jet_data_key[j,k+2] = np.sum(bkg[k,psroi]-fakemap[k,psroi])/0.68
# Now plot
pfake3FGL = make_flux_histogram_local(jet_data_key,f.CTB_exposure_maps,band_mask_range = band_mask_range_plot, mask_ring = mask_ring_plot, outer = outer_plot)
pfake3FGL.make_fake_data_flux_histogram(0.1,5000,50)
pfake3FGL.plot_fake_data_histogram(fmt = 'o', color=jetcolors[i],markersize=5,label='Jet R0p'+str(i+2))
plt.yscale('log')
plt.xscale('log')
plt.xlim([1e-12,1e-6])
plt.ylim([1e3,1e11])
plt.tick_params(axis='x', length=5,width=2,labelsize=18)
plt.tick_params(axis='y',length=5,width=2,labelsize=18)
plt.xlabel('$F$ [photons / cm$^2$ / s]', fontsize=18)
plt.ylabel('$dN/dF$ [photons$^{-1}$ cm$^2$ s deg$^{-2}$]', fontsize=18)
plt.legend(fontsize=16)
plt.savefig('./Plots/' + outname + '.pdf')
plt.close()
def setup_for_scan(larr=[0],barr=[0],add_group_ps=False,ps_number=0,fdn=True,fdrun=False):
global f, b, new_template_dict, sigma_PSF_deg, sigma_PSF_deg_red, n_ps, newstyle, ps_norms, diffnormfix
# Load Fermi Plugin and its basic functionality
f = fp.fermi_plugin(maps_dir,fermi_data_dir=fermi_data_dir,work_dir=work_dir,CTB_en_min = emin,CTB_en_max=emax,nside=nside,eventclass=eventclass,eventtype=eventtype,newstyle=newstyle)
if mask_type!='False':
f.make_ps_mask(mask_type=mask_type,force_energy=force_ps_mask,energy_bin=force_ps_mask_bin)
# Add appropriate templates
f.add_diffuse_newstyle(comp = diff, eventclass = eventclass, eventtype = eventtype)
if extraicstemp!='False':
f.add_diffuse_newstyle(comp = extraicstemp, eventclass = eventclass, eventtype = eventtype)
f.add_bubbles(comp = 'bubs')
f.add_iso(comp = 'iso')
if add_ps_model:
f.add_ps_model(comp = 'ps_model')
if fdn:
f.add_nfw(comp = 'nfw')
# Throughout we use a king function or Gaussian for the point sources
if add_group_ps:
if use_king:
f.add_multiple_ps_king_fast(larr[0:ps_number],barr[0:ps_number],rescale=ps_norms[0:ps_number],comp='ps_comb')
else:
# Add in Gaussian point source - need the PSF for this
f.load_psf(data_name='p8',fits_file_path = 'False')
sigma_PSF_deg = f.sigma_PSF_deg[0:-1]
f.add_multiple_ps(larr[0:ps_number],barr[0:ps_number],sigma_PSF_deg[0],rescale=ps_norms[0:ps_number],comp='ps_comb')
if norm_file!='False':
if len(add_norm_file_for_comps) > 0 and add_norm_file != 'False':
print 'using first normalization file: ', norm_file
f.use_template_normalization_file(norm_file,key_suffix='-0',dont_use_keys=add_norm_file_for_comps)
print 'using second normalization file: ', add_norm_file
f.use_template_normalization_file(add_norm_file,key_suffix='-0',use_keys=add_norm_file_for_comps)
else:
f.use_template_normalization_file(norm_file,key_suffix='-0')
# Setup Bayesian scan for fermi
b = bsm.bayesian_scan_NPTF(tag=tag,work_dir = work_dir,psf_dir = psf_dir,nside=nside,nlive=nlive,k_max=k_max)
if fake_data_file=='False':
print 'Using real data'
count_maps=f.CTB_count_maps
new_count_maps = f.CTB_count_maps
else:
print 'Using fake data from the file', fake_data_file
count_maps=np.loadtxt(fake_data_file)[fake_data_emin:fake_data_emax]
new_count_maps = np.zeros( (len(count_maps),hp.nside2npix(nside) ) )
for i in range(len(count_maps)):
new_count_maps[i] = hp.ud_grade(count_maps[i],nside,power=-2)
b.load_external_data(f.CTB_en_bins,new_count_maps,f.CTB_exposure_maps)
if use_simplified_templates:
b.add_new_template(new_template_dict)
if fixed_background:
b.add_fixed_templates({'back':new_template_dict['back']})
else:
b.add_new_template(f.template_dict)
if mask_type!='False':
b.make_mask_total(plane_mask=plane_mask, band_mask_range = [-pmval,pmval], lcut=lcut, lmin=lmin, lmax=lmax, bcut=bcut, bmin=bmin, bmax=bmax, mask_ring=mask_ring, inner=inner, outer=outer, ps_mask_array = f.ps_mask_array)
else:
b.make_mask_total(plane_mask=plane_mask, band_mask_range = [-pmval,pmval], lcut=lcut, lmin=lmin, lmax=lmax, bcut=bcut, bmin=bmin, bmax=bmax, mask_ring=mask_ring, inner=inner, outer=outer)
b.rebin_external_data(1)
b.compress_templates()
### Add in the Templates
if method != 'minuit':
if not min_prior_range:
if not fdrun:
b.add_fixed_templates({diff:[f.template_dict[diff][0]*diffnormfix]})
else:
b.add_poiss_model(diff,'$A_{diff}$',[-5,5],False)
if extraicstemp!='False':
b.add_poiss_model(extraicstemp,'$A_{ics}$',[-5,5],False)
b.add_poiss_model('iso','$A_{iso}$',[-3,3],False)
b.add_poiss_model('bubs','$A_{bubs}$',[-3,3],False)
else: # If already have priors, don't scan over such a large range
if not fdrun:
b.add_fixed_templates({diff:f.template_dict[diff]*diffnormfix})
else:
b.add_poiss_model(diff,'$A_{diff}$',[0.5,1.5],False)
if extraicstemp!='False':
b.add_poiss_model(extraicstemp,'$A_{ics}$',[0.5,1.5],False)
if high_lat:
b.add_poiss_model('iso','$A_{iso}$',[0.5,1.5],False)
else:
b.add_poiss_model('iso','$A_{iso}$',[0.8,1.2],False)
b.add_poiss_model('bubs','$A_{bubs}$',[0.5,1.5],False)
else:
if not fdrun:
b.add_fixed_templates({diff:f.template_dict[diff]*diffnormfix})
else:
b.add_poiss_model(diff,'$A_{diff}$',[0,2],False)
if extraicstemp!='False':
b.add_poiss_model(extraicstemp,'$A_{ics}$',[-2,2],False)
b.add_poiss_model('iso','$A_{iso}$',[0,2],False)
b.add_poiss_model('bubs','$A_{bubs}$',[0,4],False)
if add_ps_model:
if not min_prior_range:
b.add_poiss_model('ps_model','$A_{ps-model}$',[0,6],False)
else:
b.add_poiss_model('ps_model','$A_{ps-model}$',[0.5,1.5],False)
if fdn:
b.add_poiss_model('nfw','$l10A_{nfw}$',[-6,6],True)
if add_group_ps:
b.add_poiss_model('ps_comb','$A_{ps-comb}$',[-5,5],False)
### Configure final details
def sb_string_mod(mod):
return ['${S_b^{' + mod + '}}^{'+str(i) + '}$' for i in range(1)]
b.initiate_poissonian_edep()
print 'Performing a standard template fit ...'
def main():
global plot_ll_profile, full_dict, eachps_En_center, n_ps, ps_norms, diffnormfix
diffnormfix=1.
# Determine PSF using fermi plugin, for use in the ps ordering
loadforpsf = fp.fermi_plugin(maps_dir,fermi_data_dir=fermi_data_dir,work_dir=work_dir,CTB_en_min = emin,CTB_en_max=emax,nside=nside,eventclass=eventclass,eventtype=eventtype,newstyle=newstyle)
loadforpsf.load_psf(data_name='p8',fits_file_path = 'False')
sigma_PSF_deg = loadforpsf.sigma_PSF_deg[0:-1]
# Get an ordered list of the l and b values by ranking - cutting those outside of region
# End of list contains those sources outside region but within 1 PSF of the border
larr,barr,n_ps,n_ps_border = trimorderpslist(ps_file,indeg,sigma_PSF_deg)
# Define empty dictionary
full_dict={}
# First run to get diff norm
# Setup for scan
if method=='minuit' and run==False:
pass
else:
print 'setting up the scan. the method is', method
setup_for_scan(larr=larr,barr=barr,add_group_ps=True,ps_number=n_ps,fdn=fixdiffnfw,fdrun=True)
print 'finished setting up the scan.'
# Perform scan / load scan
if run:
print 'The nside for this scan is ', b.nside
if method=='multinest':
b.perform_scan(run_tag = run_tag_energy)
do_analysis(minuit_new=False,add_group_ps=False,ps_number=0,fdn=fixdiffnfw,fdrun=True)
elif method=='minuit':
b.perform_scan_minuit(run_tag = run_tag_energy)
b.save_minuit()
do_analysis(minuit_new=True,add_group_ps=False,ps_number=0,fdn=fixdiffnfw,fdrun=True)
# Setup for scan
if method=='minuit' and run==False:
pass
else:
print 'setting up the scan. the method is', method
setup_for_scan(larr=larr,barr=barr,add_group_ps=False,ps_number=0)
print 'finished setting up the scan.'
# Perform scan / load scan
if run:
print 'The nside for this scan is ', b.nside
if method=='multinest':
b.perform_scan(run_tag = run_tag_energy)
do_analysis(minuit_new=False,add_group_ps=False,ps_number=0)
elif method=='minuit':
b.perform_scan_minuit(run_tag = run_tag_energy)
b.save_minuit()
do_analysis(minuit_new=True,add_group_ps=False,ps_number=0)
# Setup for scan
if method=='minuit' and run==False:
pass
else:
print 'setting up the scan. the method is', method
setup_for_scan(larr=larr,barr=barr,add_group_ps=True,ps_number=10)
print 'finished setting up the scan.'
#hp.mollview(np.sum(f.template_dict['ps_comb'],axis=0),max=1)
#plt.show()
# Perform scan / load scan
if run:
print 'The nside for this scan is ', b.nside
if method=='multinest':
b.perform_scan(run_tag = run_tag_energy)
do_analysis(minuit_new=False,add_group_ps=True,ps_number=10)
elif method=='minuit':
b.perform_scan_minuit(run_tag = run_tag_energy)
b.save_minuit()
do_analysis(minuit_new=True,add_group_ps=True,ps_number=10)
# Setup for scan
if method=='minuit' and run==False:
pass
else:
print 'setting up the scan. the method is', method
setup_for_scan(larr=larr,barr=barr,add_group_ps=True,ps_number=100)
print 'finished setting up the scan.'
# Perform scan / load scan
if run:
print 'The nside for this scan is ', b.nside
if method=='multinest':
b.perform_scan(run_tag = run_tag_energy)
do_analysis(minuit_new=False,add_group_ps=True,ps_number=100)
elif method=='minuit':
b.perform_scan_minuit(run_tag = run_tag_energy)
b.save_minuit()
do_analysis(minuit_new=True,add_group_ps=True,ps_number=100)
# Setup for scan
if method=='minuit' and run==False:
pass
else:
print 'setting up the scan. the method is', method
setup_for_scan(larr=larr,barr=barr,add_group_ps=True,ps_number=n_ps)
print 'finished setting up the scan.'
# Perform scan / load scan
if run:
print 'The nside for this scan is ', b.nside
if method=='multinest':
b.perform_scan(run_tag = run_tag_energy)
do_analysis(minuit_new=False,add_group_ps=True,ps_number=n_ps)
elif method=='minuit':
b.perform_scan_minuit(run_tag = run_tag_energy)
b.save_minuit()
do_analysis(minuit_new=True,add_group_ps=True,ps_number=n_ps)
# Finally save the spectra, norm and ts details
# Create norm dictionary and a dictionary where we convert this to a spectrum
nfwps_savefile = psnfw_spec_dir + save_nfwps_label
spect = [[ eachps_En_center, full_dict]]
np.save(nfwps_savefile,np.array(spect))
band_mask_range=[-1.,1.]
mask_ring=True
outer=30
mask_type='top300' # If don't want to include this, make it 'False'
force_energy=True
energy_bin_mask=8
# Setup npix, l and b
npix = hp.nside2npix(nside)
theta, phi = hp.pix2ang(nside,range(npix))
larr = phi
barr = np.pi/2 - theta
# Setup Fermi module which we need to extract data and determine the background model
f = fp.fermi_plugin('/tigress/smsharma/public/CTBCORE/',CTB_en_min=CTB_start_bin,CTB_en_max=CTB_end_bin,nside=nside,data_name='p8')
f.add_diffuse(comp = 'p6') #diffuse
f.add_bubbles() #bubbles
f.add_iso() #iso
f.add_nfw()
# Load the real data map
realdata = np.sum(f.CTB_count_maps,axis=0)
# Create the masks
if mask_type != 'False':
f.make_ps_mask(mask_type = mask_type,energy_bin = energy_bin_mask,force_energy=force_energy)
b = bsm.bayesian_scan_NPTF(nside=nside)
b.load_external_data(f.CTB_en_bins,f.CTB_count_maps,f.CTB_exposure_maps)
b2 = copy.deepcopy(b)
b.make_mask_total(band_mask_range=band_mask_range,mask_ring=mask_ring,outer=outer)
def setup_for_scan(i=0,n_ps_groupi=0,larr=[0],barr=[0],psloop1=False,pscomball=False,psloop2bkg=False,psloop2=False):
global f, b, new_template_dict, sigma_PSF_deg, sigma_PSF_deg_red, n_ps, newstyle, ps_norms_loop1, ps_norms
# Load Fermi Plugin and its basic functionality
f = fp.fermi_plugin(maps_dir,fermi_data_dir=fermi_data_dir,work_dir=work_dir,CTB_en_min = emin,CTB_en_max=emax,nside=nside,eventclass=eventclass,eventtype=eventtype,newstyle=newstyle)
if mask_type!='False':
f.make_ps_mask(mask_type=mask_type,force_energy=force_ps_mask,energy_bin=force_ps_mask_bin)
# Add appropriate templates
f.add_diffuse_newstyle(comp = diff, eventclass = eventclass, eventtype = eventtype)
if extraicstemp!='False':
f.add_diffuse_newstyle(comp = extraicstemp, eventclass = eventclass, eventtype = eventtype)
f.add_bubbles(comp = 'bubs')
f.add_iso(comp = 'iso')
if add_ps_model:
f.add_ps_model(comp = 'ps_model')
if nfw_dm:
f.add_nfw(comp = 'nfw')
if psloop1:
# Throughout we use a king function or Gaussian for the point sources
if use_king:
for j in range(n_ps_groupi):
f.add_ps_king_fast(larr[i*n_ps_run+j],barr[i*n_ps_run+j],comp ='ps_' + str(i*n_ps_run+j+1))
if i != 0:
f.add_multiple_ps_king_fast(larr[0:i*n_ps_run],barr[0:i*n_ps_run],rescale=ps_norms_loop1[0:i*n_ps_run],comp='ps_comb')
else:
# Add in Gaussian point source - need the PSF for this
f.load_psf(data_name='p8',fits_file_path = 'False')
sigma_PSF_deg = f.sigma_PSF_deg[0:-1]
for j in range(n_ps_groupi):
f.add_ps(larr[i*n_ps_run+j],barr[i*n_ps_run+j],sigma_PSF_deg[0],comp ='ps_' + str(i*n_ps_run+j+1))
if i != 0:
f.add_multiple_ps(larr[0:i*n_ps_run],barr[0:i*n_ps_run],sigma_PSF_deg[0],rescale=ps_norms_loop1[0:i*n_ps_run],comp='ps_comb')
if pscomball:
if use_king:
f.add_multiple_ps_king_fast(larr,barr,rescale=ps_norms_loop1,comp='ps_comb')
else:
f.load_psf(data_name='p8',fits_file_path = 'False')
sigma_PSF_deg = f.sigma_PSF_deg[0:-1]
f.add_multiple_ps(larr,barr,sigma_PSF_deg[0],rescale=ps_norms_loop1,comp='ps_comb')
if psloop2bkg:
if use_king:
f.add_multiple_ps_king_fast(larr,barr,rescale=ps_norms_loop1,comp='ps_comb',excluded=i)
else:
f.load_psf(data_name='p8',fits_file_path = 'False')
sigma_PSF_deg = f.sigma_PSF_deg[0:-1]
f.add_multiple_ps(larr,barr,sigma_PSF_deg[0],rescale=ps_norms_loop1,comp='ps_comb',excluded=i)
if psloop2:
if use_king:
f.add_ps_king_fast(larr[i],barr[i],rescale=ps_norms_loop1[i],comp ='ps_' + str(i+1))
f.add_multiple_ps_king_fast(larr,barr,rescale=ps_norms_loop1,comp='ps_comb',excluded=i)
else:
f.load_psf(data_name='p8',fits_file_path = 'False')
sigma_PSF_deg = f.sigma_PSF_deg[0:-1]
f.add_ps(larr[i],barr[i],sigma_PSF_deg[0],rescale=ps_norms_loop1[i],comp ='ps_' + str(i+1))
f.add_multiple_ps(larr,barr,sigma_PSF_deg[0],rescale=ps_norms_loop1,comp='ps_comb',excluded=i)
if norm_file!='False':
if len(add_norm_file_for_comps) > 0 and add_norm_file != 'False':
print 'using first normalization file: ', norm_file
f.use_template_normalization_file(norm_file,key_suffix='-0',dont_use_keys=add_norm_file_for_comps)
print 'using second normalization file: ', add_norm_file
f.use_template_normalization_file(add_norm_file,key_suffix='-0',use_keys=add_norm_file_for_comps)
else:
f.use_template_normalization_file(norm_file,key_suffix='-0')
# Setup Bayesian scan for fermi
b = bsm.bayesian_scan_NPTF(tag=tag,work_dir = work_dir,psf_dir = psf_dir,nside=nside,nlive=nlive,k_max=k_max)
if fake_data:
data = np.loadtxt(fake_data_path)
else:
data = f.CTB_count_maps
b.load_external_data(f.CTB_en_bins,data,f.CTB_exposure_maps)
if use_simplified_templates:
b.add_new_template(new_template_dict)
if fixed_background:
b.add_fixed_templates({'back':new_template_dict['back']})
else:
b.add_new_template(f.template_dict)
if mask_type!='False':
b.make_mask_total(plane_mask=plane_mask, band_mask_range = [-pmval,pmval], lcut=lcut, lmin=lmin, lmax=lmax, bcut=bcut, bmin=bmin, bmax=bmax, mask_ring=mask_ring, inner=inner, outer=outer, ps_mask_array = f.ps_mask_array)
else:
b.make_mask_total(plane_mask=plane_mask, band_mask_range = [-pmval,pmval], lcut=lcut, lmin=lmin, lmax=lmax, bcut=bcut, bmin=bmin, bmax=bmax, mask_ring=mask_ring, inner=inner, outer=outer)
b.rebin_external_data(1)
b.compress_templates()
### Add in the Templates
if method != 'minuit':
if not min_prior_range:
b.add_poiss_model(diff,'$A_{diff}$',[-5,5],False)
if extraicstemp!='False':
b.add_poiss_model(extraicstemp,'$A_{ics}$',[-5,5],False)
b.add_poiss_model('iso','$A_{iso}$',[-3,3],False)
b.add_poiss_model('bubs','$A_{bubs}$',[-3,3],False)
else: # If already have priors, don't scan over such a large range
b.add_poiss_model(diff,'$A_{diff}$',[0.5,1.5],False)
if extraicstemp!='False':
b.add_poiss_model(extraicstemp,'$A_{ics}$',[0.5,1.5],False)
if high_lat:
b.add_poiss_model('iso','$A_{iso}$',[0.5,1.5],False)
else:
b.add_poiss_model('iso','$A_{iso}$',[0.8,1.2],False)
b.add_poiss_model('bubs','$A_{bubs}$',[0.5,1.5],False)
else:
b.add_poiss_model(diff,'$A_{diff}$',[0,2],False)
if extraicstemp!='False':
b.add_poiss_model(extraicstemp,'$A_{ics}$',[-2,2],False)
b.add_poiss_model('iso','$A_{iso}$',[0,2],False)
b.add_poiss_model('bubs','$A_{bubs}$',[0,4],False)
if add_ps_model:
if not min_prior_range:
b.add_poiss_model('ps_model','$A_{ps-model}$',[0,6],False)
else:
b.add_poiss_model('ps_model','$A_{ps-model}$',[0.5,1.5],False)
if nfw_dm: # leave this large as NFW struggles to converge at high E
b.add_poiss_model('nfw','$l10A_{nfw}$',[-6,6],True)
if psloop1:
for j in range(n_ps_groupi):
b.add_poiss_model('ps_' + str(i*n_ps_run+j+1),'$l10A_{ps' + str(i*n_ps_run+j+1) + '}$',[-10,10],True)
if i != 0:
b.add_poiss_model('ps_comb','$A_{ps-comb}$',[0.5,1.5],False)
if pscomball:
b.add_poiss_model('ps_comb','$A_{ps-comb}$',[0.5,1.5],False)
if psloop2bkg:
b.add_poiss_model('ps_comb','$A_{ps-comb}$',[0.5,1.5],False)
if psloop2:
b.add_poiss_model('ps_' + str(i+1),'$A_{ps' + str(i+1) + '}$',[0.5,1.5],False)
b.add_poiss_model('ps_comb','$A_{ps-comb}$',[0,3],False)
# Ideally want to basically fix this component, but if make too small minuit crashes
### Configure final details
def sb_string_mod(mod):
return ['${S_b^{' + mod + '}}^{'+str(i) + '}$' for i in range(1)]
b.initiate_poissonian_edep()
print 'Performing a standard template fit ...'
n_flux_bins=15
error_range=0.68 #for plotting uncertanties
######disk filename
disk_file_name= 'thindiskmodel_ec.fits' #'simplediskmodel_ec.fits'
####################
##########Internal code
###################
##Fermi plugin instance
f = fp.fermi_plugin(maps_dir,CTB_en_min=CTB_start_bin,CTB_en_max=CTB_end_bin,nside=nside,data_name=data_type)
#f.make_ps_mask(mask_type = mask_type,energy_bin = energy_bin_mask,force_energy=force_energy)
f.add_diffuse(comp = 'p6') #diffuse
f.add_bubbles() #bubbles
f.add_iso() #iso
f.add_nfw() #NFW-DM
f.add_template_from_file('disk',disk_file_name) #we will call template 'disk'
if mask_type != 'False':
f.make_ps_mask(mask_type = mask_type,energy_bin = energy_bin_mask,force_energy=force_energy)
f.use_template_normalization_file(norm_file_path,key_suffix='-0')
def __init__(self,Emin,eventclass=5,eventtype=3,fermi_data_dir = '/mnt/hepheno/FermiData/', maps_dir = '/mnt/hepheno/CTBCORE/',nside=128,mask_type='top300',force_energy=False,newstyle=1,diff='p8',data_July16=True):
self.f = fp.fermi_plugin(maps_dir,fermi_data_dir=fermi_data_dir,CTB_en_min=Emin,CTB_en_max=Emin+1,nside=nside,eventclass=eventclass,eventtype=eventtype,newstyle=newstyle,data_July16=data_July16)
self._setup_f(mask_type,Emin,force_energy,eventclass,eventtype,diff)
self.extract()
ps_string = ['ps-l-'+str(round(ell_i,3)) + '-b-'+str(round(b_i,3)) for ell_i, b_i in map(None,ell_0,b_0)]
inner=0
##################
#################
####figure out the mask
if mask_string!='False':
mask = hp.ud_grade( np.array(np.loadtxt(mask_string)), nside)
#########################
#configure for fermi
f = fp.fermi_plugin(maps_dir,work_dir=work_dir,CTB_en_min = emin,CTB_en_max=emax,nside=nside)
if mask_type!='False':
f.make_ps_mask(mask_type = mask_type,force_energy = False) #
f.add_diffuse(comp = diff)
f.add_bubbles(comp='bubs')
f.add_iso(comp='iso')
######Need to figure out the PSF
f.load_psf(data_name='p8',fits_file_path = 'False')
sigma_PSF_deg = f.sigma_PSF_deg[0]
print 'The psf is', sigma_PSF_deg
######
for ell_i, b_i,ps_string_i in map(None,ell_0,b_0,ps_string):
f.add_ps(ell_i,b_i,f.sigma_PSF_deg[0],comp = ps_string_i)
############
def scan(self):
print("Getting into scan")
################
# Fermi plugin #
################
print("Loading Fermi plugin...")
# Load the Fermi plugin - always load all energy bins, extract what is needed
f_global = fp.fermi_plugin(maps_dir,fermi_data_dir=fermi_data_dir,work_dir=work_dir,CTB_en_min=0,CTB_en_max=40,nside=self.nside,eventclass=self.eventclass,eventtype=self.eventtype,newstyle=1,data_July16=True)
print("... done")
# Load necessary templates
f_global.add_diffuse_newstyle(comp = self.diff,eventclass = self.eventclass, eventtype = self.eventtype)
f_global.add_iso()
ps_temp = np.load(work_dir + '/DataFiles/PS-Maps/ps_map.npy')
f_global.add_template_by_hand(comp='ps_model',template=ps_temp)
f_global.add_bubbles()
# If Asimov normalize the templates and create a summed map
if self.Asimov:
norm_file = work_dir + '/DataFiles/Misc/P8UCVA_norm.npy'
f_global.use_template_normalization_file(norm_file,key_suffix='-0')
Asimov_data = np.zeros((40,hp.nside2npix(self.nside)))
for key in f_global.template_dict.keys():
Asimov_data += np.array(f_global.template_dict[key])
###################
# Get DM halo map #
###################
print("Getting halo map...")
if not self.randlocs: # If doing random locations
l = self.catalog.l.values[self.iobj]
b = self.catalog.b.values[self.iobj]
else:
badval = True
while (badval):
test_ell = np.random.uniform(0.,2*np.pi)
test_b = np.arccos(np.random.uniform(-1.,1.))-np.pi/2.
test_pixval = hp.ang2pix(self.nside, test_b+np.pi/2, test_ell)
ps0p5_mask = np.load(work_dir + '/DataFiles/Misc/mask0p5_3FGL.npy') > 0
# Check if not masked with plan or PS mask
if ( (np.abs(test_b)*180./np.pi > 20. ) & (ps0p5_mask[test_pixval] == 0)):
badval = False
l = test_ell*180./np.pi
b = test_b*180./np.pi
np.savetxt(self.save_dir + "/lb_obj"+str(self.iobj) + ".dat", np.array([l, b]))
rs = self.catalog.rs.values[self.iobj]*1e-3
if self.boost:
J0 = 10**self.catalog.mulog10J_inf.values[self.iobj]
else:
J0 = 10**self.catalog.mulog10Jnb_inf.values[self.iobj]
mk = mkDMMaps.mkDMMaps(z = self.catalog.z[self.iobj], r_s = rs , J_0 = J0, ell = l*np.pi/180, b = b*np.pi/180, nside=self.nside, use_boost=self.use_boost, Burkert=self.Burkert)
DM_template_base = mk.map
print("...done")
#########################################
# Loop over energy bins to get xsec LLs #
#########################################
A_ary = 10**np.linspace(-6,6,200)
LL_inten_ary = np.zeros((len(self.ebins)-1,len(A_ary)))
inten_ary = np.zeros((len(self.ebins)-1,len(A_ary)))
# 10 deg mask for the analysis
analysis_mask = cm.make_mask_total(mask_ring = True, inner = 0, outer = 10, ring_b = b, ring_l = l)
for iebin, ebin in tqdm(enumerate(np.arange(self.emin,self.emax+1)), disable = 1 - self.verbose):
######################
# Templates and maps #
######################
if self.verbose:
print "At bin", ebin
if self.imc != -1:
data = np.load(mc_dir + 'MC_allhalos_p7_' + self.dm_string + '_v' + str(self.imc)+'.npy')[ebin].astype(np.float64)
else:
data = f_global.CTB_count_maps[ebin].astype(np.float64)
fermi_exposure = f_global.CTB_exposure_maps[ebin]
DM_template = DM_template_base*fermi_exposure/np.sum(DM_template_base*fermi_exposure)
print("Loading smoothing class...")
ksi = ks.king_smooth(maps_dir, ebin, self.eventclass, self.eventtype, threads=1)
print("...done!")
print("Beginning to smooth...")
DM_template_smoothed = ksi.smooth_the_map(DM_template)
print("...done!")
DM_intensity_base = np.sum(DM_template_smoothed/fermi_exposure)
dif = f_global.template_dict[self.diff][ebin]
iso = f_global.template_dict['iso'][ebin]
psc = f_global.template_dict['ps_model'][ebin]
bub = f_global.template_dict['bubs'][ebin]
# If doing Asimov this first scan is irrelevant, but takes no time so run
####################
# NPTFit norm scan #
####################
n = nptfit.NPTF(tag='norm_o'+str(self.iobj)+'_E'+str(ebin)+self.mc_tag)
n.load_data(data, fermi_exposure)
n.load_mask(analysis_mask)
n.add_template(dif, self.diff)
n.add_template(iso, 'iso')
n.add_template(psc, 'psc')
n.add_template(bub, 'bub')
n.add_poiss_model(self.diff, '$A_\mathrm{dif}$', [0,10], False)
n.add_poiss_model('iso', '$A_\mathrm{iso}$', [0,20], False)
if (np.sum(bub*np.logical_not(analysis_mask)) != 0):
n.add_poiss_model('bub', '$A_\mathrm{bub}$', [0,10], False)
# # Add PS at halo location
# ps_halo_map = np.zeros(hp.nside2npix(self.nside))
# ps_halo_idx = hp.ang2pix(self.nside, np.pi/2. - b*np.pi/180., l*np.pi/180.) # ell and b are in rad
# ps_halo_map[ps_halo_idx] = 1.
# ps_halo_map_smoothed = ksi.smooth_the_map(ps_halo_map) # smooth it
# n.add_template(ps_halo_map_smoothed,'ps_halo')
# n.add_poiss_model('ps_halo', 'ps_halo', [0,100], False)
if self.floatDM:
if ebin >= 7:
# Don't float DM in initial scan for < 1 GeV. Below here
# Fermi PSF is so large that we find the DM often picks up
# spurious excesses in MC.
n.add_template(DM_template_smoothed, 'DM')
n.add_poiss_model('DM', '$A_\mathrm{DM}$', [0,1000], False)
if self.float_ps_together:
n.add_poiss_model('psc', '$A_\mathrm{psc}$', [0,10], False)
else:
# Astropy-formatted coordinates of cluster
c2 = SkyCoord("galactic", l=[l]*u.deg, b=[b]*u.deg)
idx3fgl_10, _, _, _ = c2.search_around_sky(self.c3, 10*u.deg)
idx3fgl_18, _, _, _ = c2.search_around_sky(self.c3, 18*u.deg)
ps_map_outer = np.zeros(hp.nside2npix(self.nside))
for i3fgl in idx3fgl_18:
ps_file = np.load(ps_indiv_dir + '/ps_temp_128_5_'+str(self.eventtype)+'_'+str(i3fgl)+'.npy')
ps_map = np.zeros(hp.nside2npix(self.nside))
ps_map[np.vectorize(int)(ps_file[::,ebin,0])] = ps_file[::,ebin,1]
if i3fgl in idx3fgl_10: # If within 10 degrees, float individually
n.add_template(ps_map, 'ps_'+str(i3fgl))
n.add_poiss_model('ps_'+str(i3fgl), '$A_\mathrm{ps'+str(i3fgl)+'}$', [0,10], False)
else: # Otherwise, add to be floated together
ps_map_outer += ps_map
if np.sum(ps_map_outer) != 0:
n.add_template(ps_map_outer, 'ps_outer')
n.add_poiss_model('ps_outer', '$A_\mathrm{ps_outer}$', [0,10], False)
n.configure_for_scan()
##########
# Minuit #
##########
# Skip this step if there is 0 data (higher energy bins)
if np.sum(data*np.logical_not(analysis_mask)) != 0:
keys = n.poiss_model_keys
limit_dict = {}
init_val_dict = {}
step_size_dict = {}
for key in keys:
if key == 'DM':
limit_dict['limit_'+key] = (0,1000)
else:
limit_dict['limit_'+key] = (0,50)
init_val_dict[key] = 0.0
step_size_dict['error_'+key] = 1.0
other_kwargs = {'print_level': self.verbose, 'errordef': 1}
z = limit_dict.copy()
z.update(other_kwargs)
z.update(limit_dict)
z.update(init_val_dict)
z.update(step_size_dict)
f = call_ll(len(keys),n.ll,keys)
m = Minuit(f,**z)
m.migrad(ncall=30000, precision=1e-14)
###################################
# NPTFit fixed DM and bkg profile #
###################################
# Make background sum and initiate second scan
# If was no data leave bkg_sum as 0
bkg_sum = np.zeros(len(data))
if np.sum(data*np.logical_not(analysis_mask)) != 0:
for key in keys:
if key != 'DM': # Don't add DM in here
if m.values[key] != 0:
bkg_sum += n.templates_dict[key]*m.values[key]
else: # If zero, use ~parabolic error
bkg_sum += n.templates_dict[key]*m.errors[key]/2.
nDM = nptfit.NPTF(tag='dm_o'+str(self.iobj)+'_E'+str(ebin)+self.mc_tag)
if self.Asimov: # Use background expectation for the data
nDM.load_data(Asimov_data[ebin], fermi_exposure)
nDM.add_template(Asimov_data[ebin], 'bkg_sum')
else:
nDM.load_data(data, fermi_exposure)
nDM.add_template(bkg_sum, 'bkg_sum')
# If there is no data, only go over pixels where DM is non-zero
if np.sum(data*np.logical_not(analysis_mask)) != 0:
nDM.load_mask(analysis_mask)
else:
nodata_mask = DM_template_smoothed == 0
nDM.load_mask(nodata_mask)
nDM.add_poiss_model('bkg_sum', '$A_\mathrm{bkg}$', fixed=True, fixed_norm=1.0)
#####################
# Get intensity LLs #
#####################
for iA, A in enumerate(A_ary):
new_n2 = copy.deepcopy(nDM)
new_n2.add_template(A*DM_template_smoothed,'DM')
new_n2.add_poiss_model('DM','DM',False,fixed=True,fixed_norm=1.0)
new_n2.configure_for_scan()
max_LL = new_n2.ll([])
LL_inten_ary[iebin, iA] = max_LL
inten_ary[iebin, iA] = DM_intensity_base*A
np.savez(self.save_dir + 'LL_inten_o'+str(self.iobj)+self.mc_tag, LL=LL_inten_ary, intens=inten_ary)
xsec=results.xsec
#IC file name
force_mask_at_bin_number = emin #hard-coded for now
#for the scan
run_tag_energy = run_tag #+ '-' +str(emin) + '-' + str(emax)
print 'maps_dir is ', maps_dir
newstyle=1 # This is a keyword to activate some of my newstyle codes whilst we keep the old around for legacy reasons
#########################
#configure for fermi
f = fp.fermi_plugin(maps_dir,fermi_data_dir=fermi_data_dir,work_dir=work_dir,CTB_en_min = emin,CTB_en_max=emax,nside=nside,eventclass=eventclass,eventtype=eventtype,newstyle=newstyle)
if mask_type!='False':
f.make_ps_mask(mask_type = mask_type,force_energy = True,energy_bin = force_mask_at_bin_number) #
f.add_diffuse_newstyle(comp = diff, eventclass = eventclass, eventtype = eventtype)
f.add_bubbles(comp='bubs')
f.add_iso(comp='iso')
if ps_model:
f.add_ps_model(comp = 'ps_model')
# f.add_ps(0,0,0.15)
if norm_file!='False':
f.use_template_normalization_file(norm_file)
#######################################
###PSF
f.load_psf(data_name='p8',fits_file_path = 'False',eventclass=eventclass,eventtype=eventtype)
def main():
global plot_ll_profile, eachps_dict, eachps_En_center
# Need the PSF a number of times in this calculation. Rather than continually calculating it, do it once and for all here using the fermi plugin
# NB: will later want to compute the King function parameters here too
# Determine PSF using fermi plugin
loadforpsf = fp.fermi_plugin(maps_dir,fermi_data_dir=fermi_data_dir,work_dir=work_dir,CTB_en_min = emin,CTB_en_max=emax,nside=nside,eventclass=eventclass,eventtype=eventtype,newstyle=newstyle)
loadforpsf.load_psf(data_name='p8',fits_file_path = 'False',eventclass=eventclass,eventtype=eventtype)
sigma_PSF_deg = loadforpsf.sigma_PSF_deg[0:-1]
# The strategy from here is as follows:
# Break the point source lists up into groups of n_ps_run, in order of ranking
# For each group we float each point source individually and extract its normalisation
# Next we create a template combining each of the point sources just fitted
# This is done at the analysis step
# Then we repeat this for the next group, but add in a template of all the point sources
# already run, and repeat this process till all point sources have been run
# After this we perform a run with the full ps map to get its spectrum
# Then we rerun each ps one by one to get its TS while fixing the rest
for i in range(n_groups):
if i+1 == n_groups:
n_ps_groupi = n_last_group
else:
n_ps_groupi = n_ps_run
# Setup for scan
if method=='minuit' and run==False:
pass
else:
print 'setting up the scan. the method is', method
setup_for_scan(i=i,n_ps_groupi=n_ps_groupi,larr=larr,barr=barr,
psloop1=True)
print 'finished setting up the scan.'
# Perform scan / load scan
if run:
print 'The nside for this scan is ', b.nside
if method=='multinest':
b.perform_scan(run_tag = run_tag_energy)
do_analysis(i=i,n_ps_groupi=n_ps_groupi,minuit_new=False,psloop1=True)
elif method=='minuit':
b.perform_scan_minuit(run_tag = run_tag_energy)
b.save_minuit()
do_analysis(i=i,n_ps_groupi=n_ps_groupi,minuit_new=True,psloop1=True)
# Now perform run to extract to spectrum of all point sources combined
# Setup for scan
if method=='minuit' and run==False:
pass
else:
print 'setting up the scan. the method is', method
setup_for_scan(pscomball=True)
print 'finished setting up the scan.'
# Perform scan / load scan
if run:
print 'The nside for this scan is ', b.nside
if method=='multinest':
b.perform_scan(run_tag = run_tag_energy)
do_analysis(pscomball=True,minuit_new=False)
elif method=='minuit':
b.perform_scan_minuit(run_tag = run_tag_energy)
b.save_minuit()
do_analysis(pscomball=True,minuit_new=True)
# Now loop over all point sources, floating one at a time with the others fixed
# From this we want to extract their TS and spectrum
# Initialise empty dictionary to put the spectra in
eachps_dict = {}
# Now run through loop
for i in range(n_ps):
# Setup for scan
if method=='minuit' and run==False:
pass
else:
print 'setting up the scan. the method is', method
setup_for_scan(i=i,larr=larr,barr=barr,psloop2=True)
print 'finished setting up the scan.'
# Perform scan / load scan
if run:
print 'The nside for this scan is ', b.nside
if method=='multinest':
b.perform_scan(run_tag = run_tag_energy)
do_analysis(i=i,minuit_new=False,psloop2=True)
elif method=='minuit':
b.perform_scan_minuit(run_tag = run_tag_energy)
b.save_minuit()
do_analysis(i=i,minuit_new=True,psloop2=True)
# Finally save the spectra dictionary
eachps_savefile = ps_spec_dir + save_spect_label_ps
if os.path.isfile(eachps_savefile + '.npy'):
print 'appending to eachps spectrum ...'
spect = list(np.load(eachps_savefile + '.npy'))
spect += [[ eachps_En_center, eachps_dict]]
np.save(eachps_savefile,np.array(spect))
else:
print 'saving eachps spectra for first time'
spect = [[ eachps_En_center, eachps_dict]]
np.save(eachps_savefile,np.array(spect))
