def plot_sec_spec():
particlePoints=1000
Eg=np.logspace(7.,13.,100)/1.e9
Ee=np.logspace(6.,15.,particlePoints)/1.e9
parameter=[1.,9.,-2.5,10.]
#Ne=spsh.bplcut(Ee,[49.4,-2.43,-2.7,1.69,5.])
Ne=spsh.sbplcuty(Ee,[49.4,1.,-1.5,1.176,-1.4,5.])
#Ne2=spsh.plcut()
ylist=[]
xlist=[]
taglist=[]
elist=[]
ppcrosspath='/Users/jogler/Physik/Fermi/scripts/pp_data/'
ppcross=crs.crossSection(ppcrosspath)
source=sed.source(6000,30.,3.e4)
source.set_radiation_densities(0.25,0.84,3.0e-3,0.9)#W51C densities Abdo et al 2009
source.set_radiation_photons(-8.,4.,0.1)
source.set_am_prop(10.,10.,1.)
fluxScale=Eg/(4.*np.pi*(source.dist*const.PARSEC*const.m2cm)**2.)/const.erg2GeV
print 'Scale: ',fluxScale
pp=mod.model(Ne,'pp',[],source,ppcross)
ppSpec=pp.nucFactor*pp.EdQdE_pp(Ne,Ee,Eg)
#secEPoints=np.logspace(np.log10(Eg[0]),np.log10(Eg[len(Eg)-1]),particlePoints)
eSecSpec=pp.nucFactor*(pp.EdQdE_pp(Ne,Ee,Ee,1)+pp.EdQdE_pp(Ne,Ee,Ee,2))*source.age*const.yr2s
print 'points in secondary spec: ',np.size(eSecSpec)
secBrems=pp.Brems_spec(eSecSpec,Ee,Eg)
secIC=pp.IC_spec_gamma(source.phTot,source.Eph,eSecSpec,Ee,Eg)
ylist.append(ppSpec*fluxScale)
ylist.append(secBrems*fluxScale)
ylist.append(secIC*fluxScale)
xlist.append(Eg)
xlist.append(Eg)
xlist.append(Eg)
elist.append(0)
elist.append(0)
elist.append(0)
taglist.append('pp')
taglist.append('brems sec')
taglist.append('IC sec')
fig=plot(xlist,ylist,[],elist,taglist,r'$\mathrm{E}_{\gamma}\, \mathrm{ [GeV]}$',r'$EF_{\gamma}\, [\mathrm{erg}\, \mathrm{ cm}^{-2} \mathrm{s}^{-1}]$')
plt.show(fig)
def run_sedfitter(inputfile,collumns,ispec,ipara,iprocess,erange,distance,size,shape,shellth,age,crosspath,testrun,testerror,config,confpath):
#print crosspath
print ipara,type(ipara)
if ipara!=[]:
ipara=ut.argparse_list_of_list_conv(ipara)
else:
fn=open(confpath)
confDict=eval(fn.read())
specname=[]
counter=0
for p in iprocess:
specname.append('%s_%s_%i'%(iprocess[counter],ispec[counter],counter))
counter+=1
print 'spectra: ',specname
ipara=ut.conv_dict2list(specname,['a','b','c','d','e','f','g','h'],confDict)
print 'parameters retrieved from config files:'
print ipara
print '\n'
if erange!=[]:
erange=ut.argparse_list_of_list_conv(erange)
else:
for p in iprocess:
erange.append([1e6,1e15])
#print erange,erange[0][0],erange[0][1]
if testrun:
'''generate test data only works with initial parameter
provided at the commandline
'''
print ispec[0]
test=testsed.testdata(15,ipara,erange[0][0],erange[0][1],ispec[0],testerror)
apara=ipara
print 'par' ,apara
data=test.make_data()
#print data
'''randomize the initial parameters'''
ipara=np.array(ipara)
ipara=np.random.normal(ipara,testerror*abs(ipara))
newerange=[[data[0][0],data[0][np.size(data[0])-1]]]
print "energyrange changed to data energy range: ",newerange
Fitroutine=sed.SEDfitter(data,ispec,ipara,newerange,iprocess,sed.source(),crosspath)
else:
metadata=[]
data=[[],[],[],[]]
''' read in the data files'''
if len(inputfile)==1:
datapart=ut.fill_array_from_txtfile(inputfile[0],collumns," ",8,4.,3,1)
print type(datapart)
metadata+=datapart
data=ut.build_fitdata(data,datapart)
else:
for infile in inputfile:
if inputfile.index(infile)==len(inputfile)-1:
datapart=ut.fill_array_from_txtfile(infile,[1,2,3,-1,4,-1]," ")
#print 'type: ',type(datapart)
#print datapart
datapart=ut.conv_magic_sed(datapart)
#print len(datapart)
#print 'type: ',type(datapart),datapart
else:
datapart=ut.fill_array_from_txtfile(infile,collumns," ",8,2.,3,1)
print type(datapart)
metadata+=datapart
data=ut.build_fitdata(data,datapart)
#print metadata
#testspec=sed.spectrum(spsh.test,ipara,data[0][0],data[0][np.size(data[0])-1],np.size(data[0]))
Fitroutine=sed.SEDfitter(data,ispec,ipara,erange,iprocess,sed.source(),crosspath)
'''SNR specific setting of source parameters'''
'''W51C'''
Fitroutine.set_source(distance,size,age,shape,shellth)
Fitroutine.source.set_radiation_photons(-7.,2.,0.05)
Fitroutine.set_im(10,0,150)
Fitroutine.source.set_radiation_densities(0.25,0.84,3.0e-3,0.9)
if config:
Fitroutine.set_config_dict(confpath)
modelSpec=Fitroutine.get_model_func()[0]
modelval=modelSpec(ipara[0])
def pp2T_func(ppFunc,MParticle):
# newfunc=np.sqrt((ppFunc*const.C)**2+MParticle**2*const.C**4)-MParticle*const.C**2
newfunc=np.sqrt(ppFunc**2+MParticle**2)#-MParticle
return newfunc
def dp2dT_func(ppFunc,MParticle,p):
newfunc=ppFunc/((np.sqrt(p**2+MParticle**2)*p-MParticle**2))
return newfunc
protonPVal=Fitroutine.parentspec[0].get_xvals()
protonEnergy=Fitroutine.parentspec[0].get_xvals()
protonSpecVal=dp2dT_func(Fitroutine.parentspec[0].value(),const.ME_GeV*1.e3,protonPVal)
finalPar,finalParError,finalChi2,finalVal,func,fineGamma,xFineGamma=Fitroutine.fit(config)
#print 'type func: ',type(func),func
if testrun:
print 'simulation parameter: ',apara
'''
Prepare the plotting of the data and the fit functions
in a pretty way
'''
xvals=[]
yvals=[]
yerrors=[]
yerrflaq=[]
tags=['Fermi/LAT','MAGIC']
counter=0
Fscale=const.MeV2erg
for p in iprocess:
''' if p =="pp_wos":
tags.append('pp $\chi^2:$ %.1f'%(finalChi2[counter]))
else: '''
tags.append('%s $\chi^2:$ %.1f'%(p,finalChi2[counter]))
counter+=1
#tags=['Fermi/LAT','MAGIC','%s $\chi^2:$ %.1f'%(finalChi2[0]),'Brems $\chi^2:$ %.1f'%(finalChi2[1]),'IC $\chi^2:$ %.1f'%(finalChi2[2])]
counter=0
for i in range(len(metadata)/4):
xvals.append(metadata[counter])
yvals.append(metadata[counter+1]*Fscale)
yerrors.append(metadata[counter+3]*Fscale)
yerrflaq.append(1)
counter+=4
for f in fineGamma:
if type(f)==list:# required for secondaries in pp process
for ff in f:
yvals.append(ff*Fscale)
tags.append('sub')
yerrflaq.append(0)
else:
yvals.append(f*Fscale)
yerrflaq.append(0)
for xf in xFineGamma:
if type(xf)==list:# required for secondaries in pp process
for xxf in xf:
tags.append('sub')
xvals.append(xxf)
else:
xvals.append(xf)
if len(xvals)!= len(yvals):
print 'ERROR: number of x arrays not equal to y arrays'
exit()
tags.append('pp only')
tags.append('sec brems')
tags.append('sec IC')
#print xvals,yvals
#print len(xvals),len(yvals),len(yerrflaq),len(tags)
fig=ut.plot(xvals,yvals,yerrors,yerrflaq,tags,res=False,onlybands=False,forceLog=True,ytitle=r'E$^{2}$ dN/dE [erg $\mathrm{cm}^{-2} \mathrm{ s}^{-1}$]')
fig.show()
'''
xvals=[data[0]]
finalVal.insert(0,data[1])
for f in fineGamma:
finalVal.append(f)
xvals.append(data[0]) # adds the xvals for the rough model fucntions
for xf in xFineGamma:
xvals.append(xf)# adds the xvals for the fine model fucntions
if len(finalVal)!=len(xvals):
print 'ERROR: number of plotted x and y lists is not equal'
exit()
plot(xvals,finalVal,data[3])
'''
#plot([data[0],data[0],func.get_xvals()/1.e6],[data[1],finalVal,func.value()],data[4])
#plot([data[0],10**np.arange(-2.+3.,4.+3.,0.1),protonEnergy],[data[1],modelval,protonSpecVal],data[4])
#plot([data[0],data[0],protonEnergy],[data[1],modelval,protonSpecVal],data[4])
plt.figure()
#print 'protonPVal: ',protonPVal
#print 'Ep: ',protonEnergy
#print 'Fp: ',protonSpecVal
'''
print 'test: ',Fitroutine.parentspec[0].get_parameters()
Fitroutine.parentspec[0].set_precision(np.size(protonEnergy))
plt.loglog(protonEnergy,Fitroutine.parentspec[0].value())
plt.loglog(protonEnergy,protonSpecVal)
plt.show()
plt.figure()
plt.loglog(protonEnergy,protonPVal)
plt.show()
'''
var=raw_input("Press enter to exit")
def plot_spectrum(typ=['ic','brems','pp']):
'''plots spectra'''
Eg=np.logspace(6.,12.,100)
Ee=np.logspace(6.,15.,1000)
parameter=[1.,9.,-2.5,10.]
#Ne2=spsh.bplcut(Ee,[49.4,-1.5,-2.9,10.176,13.])
Ne2=spsh.sbplcut(Ee,[49.4,9.,-1.5,10.301,2.3,13.])
#print Ne
Ne=spsh.sbplcuty(Ee,[49.4,9.,-1.5,10.301,2.3,13.])#W51C values abdo et al 2009
ENe=Ee*Ne2
spec=sed.spectrum(spsh.sbplcut,[49.4,9.,-1.5,10.301,2.3,13.],1.e6,1.e15,1000.)
#Ne2=spsh.plcut()
ylist=[]
xlist=[]
taglist=[]
elist=[]
source=sed.source()
source.set_radiation_densities(0.25,0.84,3.0e-3,0.9)#W51C densities Abdo et al 2009
source.set_radiation_photons(-8.,4.,0.1)
source.set_am_prop(10.,10.,1.)
ppcrosspath='/Users/jogler/Physik/Fermi/scripts/pp_data/'
ppcross=crs.crossSection(ppcrosspath)
if 'brems' in typ:
brems=mod.model(spec,'brems',[],source,ppcross)
En=brems.spec.get_xvals()*brems.spec.value()
print En-ENe
ylist.append((Eg/1.e9)*brems.Brems_spec(ENe,Ee/1.e9,Eg/1.e9))
#ylist.append(brems.Brems_spec(ENe,Ee/10**9,Eg/10**9))
# ylist.append(brems.Brems_spec_ee(Ne,Ee,Eg))
xlist.append(Eg)
#xlist.append(Eg)
taglist.append('Brems N')
#taglist.append('Brems ee')
elist.append(0)
#elist.append(0)
if 'ic' in typ:
for ph in [source.phTot,source.phCMB,source.phDust,source.phStar]:
ic=mod.model(Ne,'ic',[],source,ppcrosspath)
ylist.append(Eg/1.e9*ic.IC_spec_gamma(ph/source.Eph,source.Eph,ENe,Ee/10**9,Eg/10**9))
xlist.append(Eg)
elist.append(0)
for t in['IC total','IC CMB','IC Dust','IC Star']:
taglist.append(t)
if 'pp' in typ:
pp=mod.model(Ne,'pp',[],source,ppcross)
ylist.append(pp.EdQdE_pp(Ne,Ee/10**9,Eg/10**9))
xlist.append(Eg)
elist.append(0)
taglist.append(r'$\mathrm{pp}_{\gamma} $')
''' plot e+ e- sec spec'''
ylist.append(pp.EdQdE_pp(Ne,Ee/10**9,Eg/10**9,1))
xlist.append(Eg)
elist.append(0)
taglist.append('pp_e-')
ylist.append(pp.EdQdE_pp(Ne,Ee/10**9,Eg/10**9,2))
xlist.append(Eg)
elist.append(0)
taglist.append('pp_e+')
if 'comp' in typ:
if 'brems' in typ:
print 'nH: %.2f nHeff: %.2f Zeff: %.2f'%(source.nH,source.nHeff,source.Zeff)
bremsSp=gs.brems_spectrum(ENe,Ee/10**9,source.nHeff)
ylist.append(Eg/10**9*bremsSp(Eg/10**9))
xlist.append(Eg)
elist.append(0)
taglist.append('brems dima')
if 'ic' in typ:
icSp=gs.IC_spectrum(source.phTot/source.Eph,source.Eph,ENe,Ee/10**9)
ylist.append(Eg/10**9*icSp(Eg/10**9))
xlist.append(Eg)
elist.append(0)
taglist.append('ic dima')
if 'pp' in typ:
ppSp=gs.EdQdE_pp(Ne,Ee/10**9,source.nH,0)
ylist.append(ppSp(Eg/10**9))
xlist.append(Eg)
elist.append(0)
taglist.append('pp dima')
fig0=plot(xlist,ylist,[],elist,taglist,r'$\mathrm{E}_{\gamma}\, \mathrm{ [eV]}$',r'$E^2F_{\gamma}\, [\mathrm{erg}\,\mathrm{ cm}^{-3} \mathrm{s}^{-1}]$')
#plt.show(fig0)
xlist=[]
ylist=[]
elist=[]
taglist=[]
xlist.append(Ee)
xlist.append(Ee)
ylist.append(Ne)
ylist.append(Ne2)
elist.append(0)
elist.append(0)
taglist.append('Ne')
taglist.append('Ne2')
fig1=plot(xlist,ylist,[],elist,taglist,r'$\mathrm{E}_{\gamma}\, \mathrm{ [eV]}$',r'$N_e\, [\mathrm{N}_{e}\mathrm{ cm}^{-3} \mathrm{s}^{-1}]$')
plt.show()
def plot_cross(typ=['ic','brems','pp']):
Eg=np.logspace(6.,12.,300)
Ee=np.logspace(7.,15.,100)
Ne=spsh.plcut(Ee,[1.,9.,-3.,14.])
Ne2=spsh.plcut(Ee,[1.,9.,-2.0,11.])
ylist=[]
xlist=[]
taglist=[]
elist=[]
if 'brems' in typ:
Ee/=10**9
Eg/=10**9
ylist.append(const.C*const.m2cm*crs.sigma_brems(Eg,Ee,Ne))
print const.C*const.m2cm*crs.sigma_brems(Eg,Ee,Ne)
#ylist.append(crs.sigma_brems(Eg,Ee,Ne2))
ylist.append(const.C*const.m2cm*crs.sigma_brems_ee(Eg,Ee,Ne))
#ylist.append(crs.sigma_brems_ee(Eg,Ee,Ne2))
ylist.append(const.C*const.m2cm*gs.sigmaB_test(Ne,Eg,Ee))
xlist.append(Eg)
xlist.append(Eg)
xlist.append(Eg)
#xlist.append(Eg)
#xlist.append(Eg)
for t in['brems_N -1.5','brems_ee -1.5','brems dima']:
taglist.append(t)
elist.append(0)
if 'ic' in typ:
Ee/=10**9
Eg/=10**9
#print Ee,Eg
source=sed.source()
source.set_radiation_densities(0.25,0.84,3.0e-3,0.9)#W51C densities Abdo et al 2009
source.set_radiation_photons(-8.,4.,0.1)
'''
print 'CMB: ',source.phCMB
print 'Dust : ',source.phDust
print 'Star: ',source.phStar
print 'tot: ',source.phTot
'''
for ph in [source.phTot,source.phCMB,source.phDust,source.phStar]:
def sigma_fcn(x):
sigma=crs.sigma_ic(x,source.Eph,Ee)
#print 'sigma: ',np.size(sigma)
return const.C*const.m2cm*np.dot(ph,np.dot(sigma,np.ones_like(Ee)))
sigma=np.frompyfunc(sigma_fcn,1,1)
ylist.append(sigma(Eg))
xlist.append(Eg)
elist.append(0)
for t in['IC total','IC CMB','IC Dust','IC Star']:
taglist.append(t)
plot([source.Eph,source.Eph,source.Eph,source.Eph],[source.phTot,source.phCMB,source.phDust,source.phStar],[],elist,['Tot','CMB','Dust','Star'],r'E [eV]',r'$N_{ph}$')
#print ylist
plot(xlist,ylist,[],elist,taglist,r'E [eV]',r'$N_{e}\times \sigma_{\mathrm{brems}}$')
#plot([source.Eph,source.Eph,source.Eph,source.Eph],[source.phTot,source.phCMB,source.phDust,source.phStar],[],elist,['Tot','CMB','Dust','Star'],r'E [eV]',r'$N_{ph}$')
plt.show()