def PlotUL(pars,config,ULFlux,Index):
#Compute the SED
E = np.logspace(np.log10(pars.Emin), np.log10(pars.Emax), pars.N)
SED = MEV_TO_ERG * E ** 2 * (-Index+1)*ULFlux* np.power(E,-Index)/(np.power(pars.Emax,-Index+1)-np.power(pars.Emin,-Index+1))
#Actually make the plot
plt.xlabel(r"E [MeV]")
plt.ylabel(r"$E^{2}dN/dE [ erg.cm^{-2}.s^{-1} ]$")
plt.loglog()
plt.plot(E,SED,"-",color='black')
# Plot the upper limits. For some reason, matplotlib draws the arrows inverted for uplim and lolim [?]
# This is a known issue fixed in matplotlib 1.4: https://github.com/matplotlib/matplotlib/pull/2452
if LooseVersion(matplotlib.__version__) < LooseVersion("1.4.0"):
plt.errorbar([E[0],E[-1]], [SED[0],SED[-1]], yerr=[SED[0]*0.8,SED[-1]*0.8],fmt='.',color='black',ls='None',lolims=[1,1])
else:
plt.errorbar([E[0],E[-1]], [SED[0],SED[-1]], yerr=[SED[0]*0.8,SED[-1]*0.8],fmt='.',color='black',ls='None',uplims=[1,1])
#save the plot
filebase = utils._SpecFileName(config)
plt.tight_layout()
plt.savefig(filebase + '.png', dpi=150, facecolor='w', edgecolor='w',
orientation='portrait', papertype=None, format=None,
transparent=False, bbox_inches=None, pad_inches=0.1,
frameon=None)
def plot_sed_fromconfig(config,ignore_missing_bins=False):
utils.mkdir_p(config["out"]+"/Spectrum")
srcname = config['target']['name']
Emin = config['energy']['emin']
Emax = config['energy']['emax']
filename = utils._SpecFileName(config)
Param = Params(srcname, Emin=Emin, Emax=Emax, PlotName=filename)
Result = utils.ReadResult(config)
# if the TS > ts limit plot the butterfly, if not draw UL
if Result["TS"]> config['UpperLimit']['TSlimit'] :
PlotSED(config,Param,ignore_missing_bins)
else :
try :
PlotUL(Param,config,Result['Ulvalue'],config['UpperLimit']['SpectralIndex'])
except :
print "Not able to plot an upper limit in a SED diagram. UL computed?"
def plot_sed_fromconfig(config, ignore_missing_bins=False):
utils.mkdir_p(config["out"] + "/Spectrum")
srcname = config['target']['name']
Emin = config['energy']['emin']
Emax = config['energy']['emax']
filename = utils._SpecFileName(config)
Param = Params(srcname, Emin=Emin, Emax=Emax, PlotName=filename)
Result = utils.ReadResult(config)
# if the TS > ts limit plot the butterfly, if not draw UL
if Result["TS"] > config['UpperLimit']['TSlimit']:
PlotSED(config, Param, ignore_missing_bins)
else:
try:
PlotUL(Param, config, Result['Ulvalue'],
config['UpperLimit']['SpectralIndex'])
except:
print "Not able to plot an upper limit in a SED diagram. UL computed?"
def PlotUL(pars, config, ULFlux, Index):
ROOT.gROOT.SetBatch(ROOT.kTRUE)
root_style.RootStyle()
# Compute the SED
E = np.logspace(np.log10(pars.Emin), np.log10(pars.Emax), pars.N)
SED = (
MEV_TO_ERG
* E ** 2
* (-Index + 1)
* ULFlux
* np.power(E, -Index)
/ (np.power(pars.Emax, -Index + 1) - np.power(pars.Emin, -Index + 1))
)
# Actually make the plot
c_plot = ROOT.TCanvas(pars.PlotName)
c_plot.SetLogx()
c_plot.SetLogy()
xmin, xmax = E[0] * 0.7, E[-1] * 1.6
ymin = min(SED[0], SED[-1]) * 0.15
ymax = max(SED[0], SED[-1]) * 3
ghSED = ROOT.TH2F("ghSED", "", 10000, xmin, xmax, 100, ymin, ymax)
ghSED.SetStats(000)
ghSED.SetTitle(pars.PlotName)
ghSED.SetXTitle("E [MeV]")
ghSED.SetYTitle("E^{2}dN/dE [ erg cm^{-2} s^{-1} ] ")
ghSED.Draw()
tgr = ROOT.TGraph(pars.N, np.array(E), np.array(SED))
tgr.Draw("L")
Ar_1 = ROOT.TArrow(E[0], SED[0] * 0.2, E[0], SED[0], 0.02)
Ar_2 = ROOT.TArrow(E[-1], SED[-1] * 0.2, E[-1], SED[-1], 0.02)
Ar_2.Draw("<|")
Ar_1.Draw("<|")
# save the canvas
filebase = utils._SpecFileName(config)
c_plot.Print(filebase + ".C")
c_plot.Print(filebase + ".eps")
c_plot.Print(filebase + ".png")
def PlotUL(pars, config, ULFlux, Index):
#Compute the SED
E = np.logspace(np.log10(pars.Emin), np.log10(pars.Emax), pars.N)
SED = MEV_TO_ERG * E**2 * (-Index + 1) * ULFlux * np.power(E, -Index) / (
np.power(pars.Emax, -Index + 1) - np.power(pars.Emin, -Index + 1))
#Actually make the plot
plt.xlabel(r"E [MeV]")
plt.ylabel(r"$E^{2}dN/dE [ erg.cm^{-2}.s^{-1} ]$")
plt.loglog()
plt.plot(E, SED, "-", color='black')
# Plot the upper limits. For some reason, matplotlib draws the arrows inverted for uplim and lolim [?]
# This is a known issue fixed in matplotlib 1.4: https://github.com/matplotlib/matplotlib/pull/2452
if LooseVersion(matplotlib.__version__) < LooseVersion("1.4.0"):
plt.errorbar([E[0], E[-1]], [SED[0], SED[-1]],
yerr=[SED[0] * 0.8, SED[-1] * 0.8],
fmt='.',
color='black',
ls='None',
lolims=[1, 1])
else:
plt.errorbar([E[0], E[-1]], [SED[0], SED[-1]],
yerr=[SED[0] * 0.8, SED[-1] * 0.8],
fmt='.',
color='black',
ls='None',
uplims=[1, 1])
#save the plot
filebase = utils._SpecFileName(config)
plt.tight_layout()
plt.savefig(filebase + '.png',
dpi=150,
facecolor='w',
edgecolor='w',
orientation='portrait',
papertype=None,
format=None,
transparent=False,
bbox_inches=None,
pad_inches=0.1,
frameon=None)
def PlotUL(pars, config, ULFlux, Index):
ROOT.gROOT.SetBatch(ROOT.kTRUE)
root_style.RootStyle()
#Compute the SED
E = np.logspace(np.log10(pars.Emin), np.log10(pars.Emax), pars.N)
SED = MEV_TO_ERG * E**2 * (-Index + 1) * ULFlux * np.power(E, -Index) / (
np.power(pars.Emax, -Index + 1) - np.power(pars.Emin, -Index + 1))
#Actually make the plot
c_plot = ROOT.TCanvas(pars.PlotName)
c_plot.SetLogx()
c_plot.SetLogy()
xmin, xmax = E[0] * 0.7, E[-1] * 1.6
ymin = min(SED[0], SED[-1]) * 0.15
ymax = max(SED[0], SED[-1]) * 3
ghSED = ROOT.TH2F("ghSED", "", 10000, xmin, xmax, 100, ymin, ymax)
ghSED.SetStats(000)
ghSED.SetTitle(pars.PlotName)
ghSED.SetXTitle("E [MeV]")
ghSED.SetYTitle("E^{2}dN/dE [ erg cm^{-2} s^{-1} ] ")
ghSED.Draw()
tgr = ROOT.TGraph(pars.N, np.array(E), np.array(SED))
tgr.Draw("L")
Ar_1 = ROOT.TArrow(E[0], SED[0] * 0.2, E[0], SED[0], 0.02)
Ar_2 = ROOT.TArrow(E[-1], SED[-1] * 0.2, E[-1], SED[-1], 0.02)
Ar_2.Draw("<|")
Ar_1.Draw("<|")
#save the canvas
filebase = utils._SpecFileName(config)
c_plot.Print(filebase + '.C')
c_plot.Print(filebase + '.eps')
c_plot.Print(filebase + '.png')
def PlotSED(config,pars):
"""plot a nice SED with a butterfly and points"""
ROOT.gROOT.SetBatch(ROOT.kTRUE)
root_style.RootStyle()
# Read the ascii file where the butterfly is stored
filebase = utils._SpecFileName(config)
lines = open(filebase + '.dat', 'r').readlines()
SED = []
E = []
Err = []
for i in xrange(len(lines) - 1):
words = lines[i + 1].split()
if float(words[0])<pars.Emax :
E.append(float(words[0]))
SED.append(float(words[1]))
Err.append(float(words[2]))
ilen = len(SED)
#From dN/dE to SED
Fluxp = np.array(SED)*np.exp(np.array(Err)/np.array(SED))
Fluxm = np.array(SED)*np.exp(-np.array(Err)/np.array(SED))
ErrorFlux = np.zeros(2 * ilen + 1)
ErrorE = np.zeros(2 * ilen + 1)
#Compute the butterfly and close it
for i in xrange(ilen):
ErrorFlux[i] = Fluxp[i]
ErrorE[i] = E[i]
for i in xrange(ilen):
ErrorFlux[ilen + i] = Fluxm[ilen - i - 1]
ErrorE[ilen + i] = E[ilen - i - 1]
ErrorFlux[-1] = Fluxp[0]
ErrorE[-1] = E[0]
#Actually make the plot
c_plot = ROOT.TCanvas(pars.PlotName)
c_plot.SetLogx()
c_plot.SetLogy()
xmin, xmax = E[0] * 0.8, E[-1] * 1.5
ymin = min(np.array(SED) - np.array(Err)) * 0.2
ymax = max(np.array(SED) + np.array(Err)) * 3
ghSED = ROOT.TH2F("ghSED", "", 10000, xmin, xmax, 100, ymin, ymax)
ghSED.SetStats(000)
ghSED.SetTitle(pars.PlotName)
ghSED.SetXTitle("E [MeV]")
ghSED.SetYTitle("E^{2}dN/dE [ erg cm^{-2} s^{-1} ] ")
ghSED.Draw()
tgr = ROOT.TGraph(ilen, np.array(E), np.array(SED))
tgr.SetLineWidth(2)
tgr.SetLineColor(pars.LineColor)
tgr.Draw("L")
tgerr = ROOT.TGraph(2 * ilen + 1, ErrorE, ErrorFlux)
tgerr.SetLineColor(pars.LineColor)
tgerr.Draw("L")
#Plot points
NEbin = int(config['Ebin']['NumEnergyBins'])
if NEbin > 0:
tgpoint, Arrow = PlotDataPoints(config,pars) #collect data points
tgpoint.SetLineColor(pars.PointColor)
tgpoint.SetMarkerColor(pars.PointColor)
tgpoint.Draw("pz")
for i in xrange(len(Arrow)):
Arrow[i].SetLineColor(pars.PointColor)
Arrow[i].SetFillColor(pars.PointColor)
Arrow[i].Draw()
#save the canvas
c_plot.Print(filebase + '.C')
c_plot.Print(filebase + '.eps')
c_plot.Print(filebase + '.png')
def PlotSED(config, pars, ignore_missing_bins=False):
"""plot a nice SED with a butterfly and points"""
# Read the ascii file where the butterfly is stored
filebase = utils._SpecFileName(config)
lines = open(filebase + '.dat', 'r').readlines()
SED = []
E = []
Err = []
for i in xrange(len(lines) - 1):
words = lines[i + 1].split()
if float(words[0]) < pars.Emax:
E.append(float(words[0]))
SED.append(float(words[1]))
Err.append(float(words[2]))
ilen = len(SED)
#From dN/dE to SED
Fluxp = np.array(SED) * np.exp(np.array(Err) / np.array(SED))
Fluxm = np.array(SED) * np.exp(-np.array(Err) / np.array(SED))
ErrorFlux = np.zeros(2 * ilen + 1)
ErrorE = np.zeros(2 * ilen + 1)
#Compute the butterfly and close it
for i in xrange(ilen):
ErrorFlux[i] = Fluxp[i]
ErrorE[i] = E[i]
for i in xrange(ilen):
ErrorFlux[ilen + i] = Fluxm[ilen - i - 1]
ErrorE[ilen + i] = E[ilen - i - 1]
ErrorFlux[-1] = Fluxp[0]
ErrorE[-1] = E[0]
#Actually make the plot
plt.figure()
plt.title(pars.PlotName.split("/")[-1].replace('_', '\_'))
name = pars.PlotName.split("/")[-1]
plt.loglog()
plt.xlabel(r"Energy (MeV)")
plt.ylabel(r"$\mathrm{E^2\ dN/dE}\ \mathrm{(erg\ cm^{-2} s^{-1})}$")
plt.plot(E, SED, "-r", label='LAT model')
plt.plot(ErrorE, ErrorFlux, "-r")
#Plot points
NEbin = int(config['Ebin']['NumEnergyBins'])
if NEbin > 0:
Epoint, Fluxpoint, EpointErrm, EpointErrp, FluxpointErrm, FluxpointErrp, uplim = GetDataPoints(
config, pars, ignore_missing_bins) #collect data points
plot_errorbar_withuls(Epoint, EpointErrm, EpointErrp, Fluxpoint,
FluxpointErrm, FluxpointErrp, uplim)
#print uplim
#print FluxpointErrm
#print FluxpointErrp
#Set meaningful axes limits
xlim = plt.xlim()
ylim = plt.ylim()
xlim = (max([20, xlim[0]]), min([2e6, xlim[1]]))
ylim = (max([1e-13, ylim[0]]), min([1e-8, ylim[1]]))
plt.xlim(xlim)
plt.ylim(ylim)
# turn them into log10 scale
#xticks = plt.xticks()[0]
#xticklabels = np.array(np.log10(xticks),dtype=int)
#plt.xticks(xticks,xticklabels)
#plt.xlabel('$\mathrm{\log_{10}\mathbf{(Energy)} \\ \\ [MeV]}$')
plt.legend(fontsize='small',ncol=1,\
loc=3,numpoints=1)#,framealpha=0.75)
#Upper horizontal secondary axis with frequency
#Plt2 = plt.twiny()
#Plt2.set_xscale('log')
#Plt2.set_xlim(2.417990504024163e+20 *np.array(xlim))
#Plt2.set_xticklabels(np.array(np.log10(Plt2.get_xticks()),dtype=int))
#Plt2.set_xlabel('$\mathrm{\log_{10}\mathbf{(Frequency)} \\ \\ [Hz]}$')
#save the canvas
#plt.grid()
plt.tight_layout()
plt.savefig("%s.png" % filebase,
dpi=150,
facecolor='w',
edgecolor='w',
orientation='portrait',
papertype=None,
format=None,
transparent=False,
bbox_inch=None,
pad_inches=0.1,
frameon=None)
def PlotSED(config,pars,ignore_missing_bins=False):
"""plot a nice SED with a butterfly and points"""
# Read the ascii file where the butterfly is stored
filebase = utils._SpecFileName(config)
lines = open(filebase + '.dat', 'r').readlines()
SED = []
E = []
Err = []
for i in xrange(len(lines) - 1):
words = lines[i + 1].split()
if float(words[0])<pars.Emax :
E.append(float(words[0]))
SED.append(float(words[1]))
Err.append(float(words[2]))
ilen = len(SED)
#From dN/dE to SED
Fluxp = np.array(SED)*np.exp(np.array(Err)/np.array(SED))
Fluxm = np.array(SED)*np.exp(-np.array(Err)/np.array(SED))
ErrorFlux = np.zeros(2 * ilen + 1)
ErrorE = np.zeros(2 * ilen + 1)
#Compute the butterfly and close it
for i in xrange(ilen):
ErrorFlux[i] = Fluxp[i]
ErrorE[i] = E[i]
for i in xrange(ilen):
ErrorFlux[ilen + i] = Fluxm[ilen - i - 1]
ErrorE[ilen + i] = E[ilen - i - 1]
ErrorFlux[-1] = Fluxp[0]
ErrorE[-1] = E[0]
#Actually make the plot
plt.figure()
plt.title(pars.PlotName.split("/")[-1].replace('_','\_'))
name = pars.PlotName.split("/")[-1]
plt.loglog()
plt.xlabel(r"Energy (MeV)")
plt.ylabel(r"$\mathrm{E^2\ dN/dE}\ \mathrm{(erg\ cm^{-2} s^{-1})}$")
plt.plot(E,SED,"-r",label='LAT model')
plt.plot(ErrorE,ErrorFlux,"-r")
#Plot points
NEbin = int(config['Ebin']['NumEnergyBins'])
if NEbin > 0:
Epoint, Fluxpoint, EpointErrm, EpointErrp, FluxpointErrm, FluxpointErrp, uplim = GetDataPoints(config,pars,ignore_missing_bins) #collect data points
plot_errorbar_withuls(Epoint,EpointErrm,EpointErrp,Fluxpoint,FluxpointErrm,FluxpointErrp,uplim)
#print uplim
#print FluxpointErrm
#print FluxpointErrp
#Set meaningful axes limits
xlim = plt.xlim()
ylim = plt.ylim()
xlim = (max([20,xlim[0]]),min([2e6,xlim[1]]))
ylim = (max([1e-13,ylim[0]]),min([1e-8,ylim[1]]))
plt.xlim(xlim)
plt.ylim(ylim)
# turn them into log10 scale
#xticks = plt.xticks()[0]
#xticklabels = np.array(np.log10(xticks),dtype=int)
#plt.xticks(xticks,xticklabels)
#plt.xlabel('$\mathrm{\log_{10}\mathbf{(Energy)} \\ \\ [MeV]}$')
plt.legend(fontsize='small',ncol=1,\
loc=3,numpoints=1)#,framealpha=0.75)
#Upper horizontal secondary axis with frequency
#Plt2 = plt.twiny()
#Plt2.set_xscale('log')
#Plt2.set_xlim(2.417990504024163e+20 *np.array(xlim))
#Plt2.set_xticklabels(np.array(np.log10(Plt2.get_xticks()),dtype=int))
#Plt2.set_xlabel('$\mathrm{\log_{10}\mathbf{(Frequency)} \\ \\ [Hz]}$')
#save the canvas
#plt.grid()
plt.tight_layout()
plt.savefig("%s.png" %filebase, dpi=150, facecolor='w', edgecolor='w',
orientation='portrait', papertype=None, format=None,
transparent=False, bbox_inch=None, pad_inches=0.1,
frameon=None)
