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plot_fig5.py
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plot_fig5.py
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##To plot polarization position angle profile comparisons between our Obl+Schw and arcmancer
#import:
import matplotlib
matplotlib.use('Agg')
from numpy import linspace, logspace, empty, zeros, ones, array, fromfile
from numpy import pi, exp, log, sqrt, sin, cos, arccos, arctan2
from numpy import absolute, sign, floor, ceil
from numpy.polynomial.laguerre import laggauss
from numpy.polynomial.legendre import leggauss
from scipy.interpolate import interp1d
from scipy.special import kn
from matplotlib.pyplot import *
from bisect import bisect
import find_best_phshift
def shift_phase(phi,shift):
return (phi + shift) % 1
#physical constants:
evere=.5109989e6 # electron volts in elecron rest energy
G=13275412528e1 # G*M_sol in km^3/s^2
c=299792458e-3 # speed of light in km/s
NPhase = 150#500#150#128*2#120#128#120 # Number of equidistant phase points
NBend= 20 # Number of knots in light bending integrations
NBendPhase= 1000 # Number of psi/aplha grid points
IntBend = leggauss(NBend)
NEnergy = 281 # 50# 101 # number of energy points (x)
phi,phi_weight=linspace(0,2*pi,num=NPhase,endpoint=False,retstep=True) #Size of spacing between samples = phi_weight
nu=600#1#100#600#700#600 # star rotation frequency in Hz
M=1.4#1.6#1.4 # star mass in solar masses
R_g=M*2.95 # gravitational Schwarzschild radius
R_e=12.0 # equatorial radius of the star in kilometers
incl=pi*4/18#50.0*pi/180.0#pi*4/18#1.5 # line of sight colatitude #in radians
#i=pi/180.0*80.0
theta = [pi/3,pi-pi/3]#[50.0*pi/180.0]#[pi/3,pi-pi/3] # spot colatitude
#theta = [pi/180.0*15.0,pi-pi/180.0*15.0] # spot colatitude
rho = 10#1#10
#Try switching:
#theta_new = [i,pi-i] # spot colatitude
#i = theta[0] # spot colatitude
#theta = theta_new
tau_T= .6 # Thomson optical depth of thermalization
x_l, x_u = -3.7 , .3 # lower and upper bounds of the log_10 energy span
Theta = 0.1 # dimensionless electron gas temperature (Theta = k T_e / m_e c^2) # it's about 0.1
T = 0.002 # 10/evere # dimensionless photon black body temperature T = k T_bb / m_e c^2
IntEnergy = logspace(x_l,x_u,NEnergy), log(1e1)*(x_u-x_l)/(NEnergy-1.) # sample points and weights for integrations over the spectrum computing sorce function
x_ene,x_weight=IntEnergy
#figA=figure(2,figsize=(14,18))
#figA.clear()
#rc("text", usetex=True)
#figA = figure(figsize=(14,18), dpi=300) #8,6
figA = figure(figsize=(14,30), dpi=300)
#figA = figure(figsize=(14,16), dpi=300) #8,6
#rc("font", family="serif")
#rc("font",serif="Times")
matplotlib.pyplot.figure(1)
lbfontsz = 25#35#30#25
lwidth= 2.5#3.5#3.0#2.5#2.0#1.5
wpad = 10
rc("xtick", labelsize=lbfontsz)
rc("ytick", labelsize=lbfontsz)
rc("axes", linewidth=lwidth)
#figA.clear()
matplotlib.pyplot.rcParams.update({'axes.titlesize': lbfontsz})
matplotlib.pyplot.rcParams.update({'font.size': lbfontsz})
matplotlib.pyplot.rcParams.update({'lines.linewidth': lwidth})
matplotlib.pyplot.rcParams.update({'ytick.major.width': lwidth})
matplotlib.pyplot.rcParams.update({'xtick.major.width': lwidth})
matplotlib.pyplot.rcParams.update({'ytick.major.size': 10.0})
matplotlib.pyplot.rcParams.update({'xtick.major.size': 10.0})
matplotlib.pyplot.rcParams.update({'font.family': 'serif'})
#matplotlib.pyplot.rcParams.update({'font.serif': 'Times'})
plot_only_I = False
plot_all = True
plot_QU = False#True
two_spots = False#True
plot5 = True
matplotlib.pyplot.subplots_adjust(wspace=0, hspace=0)
if(plot_all):
if not(plot5):
plotAF=figA.add_subplot(4,1,1,yscale='linear')
plotAp=figA.add_subplot(4,1,2) #
plotAc=figA.add_subplot(4,1,3) #
plotAd=figA.add_subplot(4,1,4) #
if(plot5):
plotAFF=figA.add_subplot(5,1,1,yscale='linear')
plotAF=figA.add_subplot(5,1,2)
plotAp=figA.add_subplot(5,1,3)
plotAc=figA.add_subplot(5,1,4)
plotAd=figA.add_subplot(5,1,5)
else:
plotAc=figA.add_subplot(2,1,1) #
plotAd=figA.add_subplot(2,1,2) #
#shapes = ["Sphere","AlGendy"]
#colors = ["yellow","black","red"]
colors = ["yellow","blue","green"]
#colors = ["blue"]
shapes = np.copy(colors)
for ish in range(1,2):#len(shapes)):
#oblateness='AlGendy'#'Sphere'#'AlGendy'
oblateness=shapes[ish]
print(ish)
#AtmName='res/B/C1obl' # the prefix for all result files related to the set of parameters
#AtmName='res/B/B0P2' # the prefix for all result files related to the set of parameters
if(ish == 0):
PulsName='res/B/lbb_rhoinf_chi-1'
if(ish == 1):
#PulsName='res/B/lbb_rhoinf_sp1_f001_p100_ires'#THIS one was the first shown to work with arcmancer
#PulsName='res/B/lbb_rho10_sp1_f600_obl'
#PulsName='res/B/lbb_rho10_sp1_f600_obl_eqnew'
#PulsName='res/B/lbb_rho10_sp1_f600_obl_accspot'#test'#accspot' #this was used in the first results
PulsName='pOS_pulses/lbb_rho10_sp1_f600_obl_burst2_dt'
#PulsName='res/B/lbb_rho10_sp1_f001_obl_accspot'
#PulsName='res/B/B0Ptest'
#PulsName='res/B/lbb_rhoinf_chi0'
if(ish == 2):
#PulsName='res/B/B0Ptest'
#PulsName='res/B/lbb_rhoinf_sp1_f001_p100_ires_swit'
PulsName='res/B/lbb_rho10_sp1_f600_sph'#_accspot'
#PulsName='res/B/B0Ptest'
#PulsName=AtmName+'P1'
computePulse= True
plotAtm=not True
plotPulse=True
mod=True
#outF = open(PulsName + 'F.bin','w')
#outf = open(PulsName + 'f.bin','w')
#Flux.tofile(outF,format="%e")
#phi.tofile(outf,format="%e")
print(PulsName)
inFlux = open(PulsName+'FF.bin')
inphi = open(PulsName+'ff.bin')
Flux1 = fromfile(inFlux)
phi = fromfile(inphi)
#print(phi, Flux1)
fluxlcurve0 = Flux1[0:len(Flux1):3*NEnergy] #light curve with lowest E
fluxspec0 = Flux1[0:3*NEnergy:3] #spectrum at phase=0
#print(fluxlcurve0)
#print(" ")
#print(fluxspec0)
ene = 118#166#140#166#140 #The chosen energy index
print("The chosen energy (keV): ", x_ene[ene]*evere/1e3)
fluxlcurve_Iene = Flux1[0+ene*3:len(Flux1):3*NEnergy]
fluxlcurve_Qene = Flux1[1+ene*3:len(Flux1):3*NEnergy]
fluxlcurve_Uene = Flux1[2+ene*3:len(Flux1):3*NEnergy]
#Flux=zeros((NPhase,NEnergy,3))
#print(fluxlcurve_Iene)
#print(fluxlcurve_Qene)
#print(fluxlcurve_Uene)
labelsize=40#30#20
fontsize=35#50#35#25
ticksize=25
#phase=list(phi/2/pi)+[1.]
phase=list(phi)+[1.]
I=zeros(NPhase+1)
Q=zeros(NPhase+1)
U=zeros(NPhase+1)
for t in range(NPhase+1):
#I[t],Q[t],U[t]=Flux[t-1,e]*x[e]
I[t],Q[t],U[t]=fluxlcurve_Iene[t-1]*x_ene[ene] ,fluxlcurve_Qene[t-1]*x_ene[ene] ,fluxlcurve_Uene[t-1]*x_ene[ene]
p=sqrt(Q**2+U**2)/I*100
#PA=arctan2(-U,-Q)*90/pi+90
PA=arctan2(U,Q)*90/pi+90
#figA.suptitle(r'$\nu={:5.0f}Hz$'.format(nu)+
# r'$,\,R_e={:5.1f}km$'.format(R_e)+
# #r'$,\,R_e=11,12,14km$'.format(R_e)+
# #r'$,\,M=1.0, 1.5, 2.0$'+r'$M_{\odot}$'+',\n'+
# r'$,\,M=$'+str(M)+r'$M_{\odot}$'+',\n'+
# r'$\,\theta={:5.1f}\degree$'.format(theta[0]*180/pi)+#r'$,{:5.1f}\degree$'.format(40.0)+
# r'$,\,i={:5.1f}\degree$'.format(incl*180/pi)+',\n'#r'$,{:5.1f}\degree$'.format(60.0)+',\n'
# r'$\rho={:5.1f}\degree$'.format(rho)+', '+
# r'$\,E={:6.2f}keV$'.format(x[ene]*evere/1e3),fontsize=fontsize)
if not(plot_only_I):
if(plot_QU):
print("plot_QU option not valid in this version!")
quit()
else:
plotAc.set_xlim(0,1)
plotAc.set_ylim(0,180)
#plotAc.set_ylim(40,140)
#plotAc.set_yticks([0,30,60,90,120,150,180])
#plotAc.set_ylim(-180,180)
#plotAc.set_yticks([0,30,60,90,120,150,180])
plotAc.tick_params(axis='both', which='major', labelsize=ticksize,direction='in',top=True,right = True)
plotAc.set_ylabel(r'$\chi\,[\mathrm{deg}]$',fontsize=fontsize)
#plotAc.set_xlabel(r'$\varphi\,[360\degree]$',fontsize=fontsize)
if(plot_all):
plotAp.set_xlim(0,1)
plotAp.tick_params(axis='both', which='major', labelsize=ticksize,direction='in',top=True,right = True)
plotAp.set_ylabel(r'$p\,[ \% ]$',fontsize=fontsize)
##plotAp.set_ylabel(r'$|\frac{F_{\mathrm{vp}}-F_{\mathrm{acm}}}{F_{\mathrm{vp}}}|$',fontsize=fontsize)
plotAp.set_ylabel(r'$\delta F_{\mathrm{Q,U}} / F_{\mathrm{Q,U}}$',fontsize=fontsize)
##plotAp.set_ylabel(r'$F_{\mathrm{Q}}(\varphi)/F_{\mathrm{Q}}^{\mathrm{max}}$',fontsize=fontsize)
plotAF.set_xlim(0,1)
## plotAF.locator_params(axis='y', nbins=10)
#plotAF.set_ylabel(r"$F_{\mathrm{x}}(\varphi)/F_{\mathrm{x}}^{\mathrm{max}}$",fontsize=fontsize)
if(plot5):
plotAFF.set_xlim(0,1)
plotAFF.tick_params(axis='both', which='major', labelsize=ticksize,direction='in',top=True,right = True)
plotAF.set_ylabel(r"$F_{\mathrm{Q,U}}/F_{\mathrm{I}}$",fontsize=fontsize)
plotAFF.set_ylabel(r"$F_{\mathrm{I}}/F_{\mathrm{I}}^{\mathrm{max}}$",fontsize=fontsize)
else:
plotAF.set_ylabel(r"$F_{\mathrm{x}}$",fontsize=fontsize)
##plotAF.set_ylabel(r'$F_{\mathrm{I}}(\varphi)/F_{\mathrm{I}}^{\mathrm{max}}$',fontsize=fontsize)
##plotAd.set_ylabel(r'$F_{\mathrm{U}}(\varphi)/F_{\mathrm{U}}^{\mathrm{max}}$',fontsize=fontsize)
plotAd.tick_params(axis='both', which='major', labelsize=ticksize,direction='in',top=True,right = True)
plotAd.set_xlim(0,1)
plotAF.tick_params(axis='both', which='major', labelsize=ticksize,direction='in',top=True,right = True)
#col=colors[(e*NColors)//NEnergy]
col = colors[ish]
PA_VP04 = PA
phase_VP04 = phase
if(ish == 1):
#find best-phasehift: #This would work now only if running arcmancer part fist...
#phshift1, gf1 = find_best_phshift.find_best_phshift(np.array(phase),PA,phase_acm0,PA_acm0)
#phshift1 = phshift1 -1.0
#print(phshift1)
#quit()
#in the end, setting the shift by hand seems still to produce better results
phshift1 = -0.047590550687164 #0.0#-0.048315#-0.2517#0.019#0.0#0.019#0.195#-0.07#-0.2517#0.0#0.001#0.008#0.2421#0.2517#0.2535#0.069#0.0#-0.195#-0.18#-0.172#0.0
phase_new = shift_phase(np.array(phase),phshift1)
for ipha in range(0,len(phase_new)-1):
if(phase_new[ipha+1] > phase_new[ipha]):
#print(PA[ipha],PA[ipha+1])
if(PA[ipha] > 100.0*PA[ipha+1]):
plotAc.plot(phase_new[ipha:ipha+2],[PA[ipha],180.0],"-",color="blue")
#print("pass!")
##pass
else:
plotAc.plot(phase_new[ipha:ipha+2],PA[ipha:ipha+2],"-",color="blue")#,markersize="1.0")
if(plot_all):
if plot5:
plotAFF.plot(phase_new[ipha:ipha+2],I[ipha:ipha+2]/I.max(),color=col)
plotAF.plot(phase_new[ipha:ipha+2],Q[ipha:ipha+2]/I[ipha:ipha+2],color="red")
plotAF.plot(phase_new[ipha:ipha+2],U[ipha:ipha+2]/I[ipha:ipha+2],color="darkorange")
else:
plotAF.plot(phase_new[ipha:ipha+2],I[ipha:ipha+2]/I.max(),color=col)
plotAF.plot(phase_new[ipha:ipha+2],Q[ipha:ipha+2]/I[ipha:ipha+2],color="red")
plotAF.plot(phase_new[ipha:ipha+2],U[ipha:ipha+2]/I[ipha:ipha+2],color="darkorange")
#plotAp.plot(phase_new[ipha:ipha+2],Q[ipha:ipha+2]/Q.max(),color=col)
#plotAd.plot(phase_new[ipha:ipha+2],U[ipha:ipha+2]/U.max(),color=col)
PA0_VP04 = PA
F0_VP04 = I/I.max()
Q0_VP04 = Q/I
U0_VP04 = U/I
phase0_VP04 = phase
if(ish == 2):
phshift2 = 0.0
phase_new = shift_phase(np.array(phase),phshift)
#find best-phasehift:#not working now
phshift2, gf2 = find_best_phshift.find_best_phshift(np.array(phase),PA,phase_acm0,PA_acm0)
phshift2 = phshift2 -1.0
print(phshift2)
#phshift2 = -0.2517#0.0#0.001#0.008#0.2421#0.2517#0.2535#0.069#0.0#-0.195#-0.18#-0.172#0.0
phase_new = shift_phase(np.array(phase),phshift2)
print(len(phase_new))
for ipha in range(0,len(phase_new)-1):
if(phase_new[ipha+1] > phase_new[ipha]):
plotAc.plot(phase_new[ipha:ipha+2],PA[ipha:ipha+2],"-",color=col,markersize="1.0")
if(plot_all):
plotAF.plot(phase_new[ipha:ipha+2],I[ipha:ipha+2]/I.max(),color=col)
#plotAF.plot(phase_new[ipha:ipha+2],Q[ipha:ipha+2]/Q.max(),color="darkgreen")
#plotAF.plot(phase_new[ipha:ipha+2],U[ipha:ipha+2]/U.max(),color="lightgreen")
plotAp.plot(phase_new[ipha:ipha+2],Q[ipha:ipha+2]/Q.max(),color=col)
plotAd.plot(phase_new[ipha:ipha+2],U[ipha:ipha+2]/U.max(),color=col)
PA0_VP04_2 = PA
F0_VP04_2 = I/I.max()
Q0_VP04_2 = Q/Q.max()
U0_VP04_2 = U/U.max()
phase0_VP04_2 = phase
#else:
# #plotAc.plot(phase,PA,color=col,marker="o",markersize=1.0)
# print("...")
compare_to_arcmancer = True
if(compare_to_arcmancer):
#colors = ["green","blue","black"]
colors = ["black","black","black"]
for ic in range(0,1):
if(ic == 0):
#datafile = "../arcmancer/out3/polar_f001_bb_r12_m1.4_d60_i40_x10_agm.csv"# (copy).csv"
#datafile = "../arcmancer/out3/polar_f001_bb_r12_m1.4_d60_i40_x10_obl_img1000.csv"# (copy).csv"
#datafile = "../arcmancer/out3/polar_f600_bb_r12_m1.4_d60_i40_x10_obl.csv"# this was used in old results
datafile = "arcman_res/polar_acc_f600_burst_r12_m1.4_d60_i40_x10_obl.csv"# (copy).csv"
if(ic == 1):
datafile = "../arcmancer/out3/polar_f001_bb_r12_m1.4_d40_i60_x01_sph.csv"
#datafile = "../arcmancer/out3/polar_f700_bb_r12_m1.6_d50_i50_x05.csv"
#datafile = "../arcmancer/out3/polar_f001_bb_r12_m1.4_d60_i40_x01.csv"# (copy).csv"
#input = file(datafile, 'r')
input = open(datafile, 'r')
lines = input.readlines()
input.close()
Nchain_size = sum(1 for line in open(datafile))
#c_lines = 21#28
c_lines = 1
#egrid = 3
egrid = 6#5#3
#full_chain= [[] for x in xrange(egrid+1)]
full_chain= [[] for x in range(egrid+1)]
#input = file(datafile, 'r')
input = open(datafile, 'r')
lines = input.readlines()
input.close()
for j in range(0,len(full_chain)):
for i in range(c_lines,Nchain_size): #not reading comment lines
parts = lines[i].split(",")
#print parts
full_chain[j].append(float(parts[j]))
parts = lines[c_lines].split(",")
full_chain = np.array(full_chain)
#print full_chain[0,:]
#print full_chain[30,:]
#energy_keV = [2.0,6.0,12.0]
energy_keV = [4.94]
phase = full_chain[0,:]
norm_obsF = np.zeros((len(phase), egrid))
obsF = np.zeros((len(phase),egrid))
for i in range(1,egrid+1):
#norm_obsF[:,i-1] = full_chain[i,:]*energy_keV[i-1]/np.max(full_chain[i,:]*energy_keV[i-1])
#norm_obsF[:,i-1] = full_chain[i,:]/np.max(full_chain[i,:])
if(i==1):
norm_obsF[:,i-1] = full_chain[i,:]/np.max(full_chain[1,:])
else:
norm_obsF[:,i-1] = full_chain[i,:]/full_chain[1,:]
obsF[:,i-1] = full_chain[i,:]
#for i in range(0,egrid):
#print energy_keV
ene = 0
print("energy_keV = ", energy_keV[ene])
phshift = 0.0#0.2517#0.25#0.2421#0.2517#0.2535#0.069#0.0#-0.195#-0.18#-0.172#0.0
phase_new = shift_phase(phase,phshift)
fluxsp1 = full_chain[1,:]
#phase_new = shift_phase(phase,-phshift)
col = colors[ic]
if not(plot_only_I):
if(plot_QU):
print("plot_QU option not valid in this version!")
quit()
else:
#p = full_chain[3,:]*100.0
#PA = full_chain[2,:]*180.0/pi+90.0
p = full_chain[5,:]*100.0
PA = full_chain[4,:]*180.0/pi+90.0
if(two_spots):
U1 = full_chain[3,:]
Q1 = full_chain[2,:]
datafile = "../arcmancer/out3/polar_f600_bb_r12_m1.4_d120_i40_x10_obl2.csv"# (copy).csv"
input = open(datafile, 'r')
lines = input.readlines()
input.close()
Nchain_size = sum(1 for line in open(datafile))
print(Nchain_size)
egrid = 6#5#3
full_chain= [[] for x in range(egrid+1)]
for j in range(0,len(full_chain)):
for i in range(c_lines,Nchain_size): #not reading comment lines
parts = lines[i].split(",")
#print parts
full_chain[j].append(float(parts[j]))
parts = lines[c_lines].split(",")
full_chain = np.array(full_chain)
U2 = full_chain[3,:]
Q2 = full_chain[2,:]
#make 0.5 phase shift
U2_1 = U2[0:int(len(U2)/2)]
U2_2 = U2[int(len(U2)/2):len(U2)]
Q2_1 = Q2[0:int(len(Q2)/2)]
Q2_2 = Q2[int(len(Q2)/2):len(Q2)]
U2_new = np.append(U2_2,U2_1)
Q2_new = np.append(Q2_2,Q2_1)
Utot = U1+U2_new
Qtot = Q1+Q2_new
PA=arctan2(Utot,Qtot)*90/pi+90
use_PA_avg = False#True
if use_PA_avg:
PA = full_chain[6,:]*180/pi+90.0#full_chain[4,:]*180.0/pi+90.0
#PA = np.array(list(reversed(full_chain[6,:])))*180/pi+90.0#full_chain[4,:]*180.0/pi+90.0
for qwe in range(0,len(PA)):
if(PA[qwe] < 0.0):
PA[qwe] = PA[qwe]+180.0
if(PA[qwe] > 180.0):
PA[qwe] = PA[qwe]-180.0
for ipha in range(0,len(phase_new)-1):
if(phase_new[ipha+1] > phase_new[ipha]):
if(PA[ipha] > 100.0*PA[ipha+1]):
plotAc.plot(phase_new[ipha:ipha+2],[PA[ipha],180.0],"--",color=col,dashes=[2,2])
else:
plotAc.plot(phase_new[ipha:ipha+2],PA[ipha:ipha+2],"--",color=col,dashes=[2,2])
if(ic == 0):
PA_acm0 = PA#norm_obsF[:,ene]#PA
F_acm0 = norm_obsF[:,ene]#obsF[:,ene]
Q_acm0 = norm_obsF[:,ene+1]#norm_obsF[:,ene+1]
U_acm0 = norm_obsF[:,ene+2]#norm_obsF[:,ene+2]
phase_acm0 = phase_new
phase_acm0[len(phase_acm0)-1]=1.0
if(ic == 1):
PA_acm = PA#norm_obsF[:,ene]#PA
phase_acm = phase_new
phase_acm[len(phase_acm)-1]=1.0
if(plot_all):
if(two_spots):
datafile = "../arcmancer/out3/polar_f600_bb_r12_m1.4_d120_i40_x10_obl2.csv"# (copy).csv"
input = open(datafile, 'r')
lines = input.readlines()
input.close()
Nchain_size = sum(1 for line in open(datafile))
print(Nchain_size)
egrid = 6#5#3
full_chain= [[] for x in range(egrid+1)]
for j in range(0,len(full_chain)):
for i in range(c_lines,Nchain_size): #not reading comment lines
parts = lines[i].split(",")
#print parts
full_chain[j].append(float(parts[j]))
parts = lines[c_lines].split(",")
full_chain = np.array(full_chain)
fluxsp2 = full_chain[1,:]
fluxsp2_1 = fluxsp2[0:int(len(fluxsp2)/2)]
fluxsp2_2 = fluxsp2[int(len(fluxsp2)/2):len(fluxsp2)]
fluxsp2_new = np.append(fluxsp2_2,fluxsp2_1)
print(fluxsp2_new)
norm_obsF[:,ene] = (fluxsp1 + fluxsp2_new)/(np.max(fluxsp1 + fluxsp2_new))
#for i in range(ene,ene+1):
sind=0
if(plot5):
sind=1
for ipha in range(0,len(phase_new)-1):
if(phase_new[ipha+1] > phase_new[ipha]):
plotAFF.plot(phase_new[ipha:ipha+2],norm_obsF[ipha:ipha+2,0],"--",color=colors[0],dashes=[2,2])
for i in range(sind,ene+3): #sind=0 if plotting all stokes fluxes to same plot
for ipha in range(0,len(phase_new)-1):
if(phase_new[ipha+1] > phase_new[ipha]):
plotAF.plot(phase_new[ipha:ipha+2],norm_obsF[ipha:ipha+2,i],"--",color=colors[i],dashes=[2,2])#,marker="o",markersize="1.0")
#if(i == 0):
# plotAF.plot(phase_new[ipha:ipha+2],norm_obsF[ipha:ipha+2,i],color=colors[i],markersize="1.0")
#if(i == 1):
# plotAp.plot(phase_new[ipha:ipha+2],norm_obsF[ipha:ipha+2,i],color=colors[i],markersize="1.0")
#if(i == 2):
# plotAd.plot(phase_new[ipha:ipha+2],norm_obsF[ipha:ipha+2,i],color=colors[i],markersize="1.0")
#This is not updated for long time:...
compare_to_fortran_vlad = False#True
if(compare_to_fortran_vlad):
#colors = ["green","blue","black"]
colors = ["green"]
for ic in range(0,1):
#datafile = "../../MCMC/results_obl_vlad_rhotest.txt"
#datafile = "../../MCMC/results_obl_vlad_rho10f600_sp2.txt"
datafile = "../../MCMC/results_sph_vlad_rho10f001.txt"
input = open(datafile, 'r')
lines = input.readlines()
input.close()
Nchain_size = sum(1 for line in open(datafile))
c_lines = 29
egrid = 5#3
full_chain= [[] for x in range(egrid+1)]
for j in range(0,len(full_chain)):
for i in range(c_lines,Nchain_size): #not reading comment lines
parts = lines[i].split()
full_chain[j].append(float(parts[j]))
parts = lines[c_lines].split()
full_chain = np.array(full_chain)
energy_keV = [4.94]
phase = full_chain[0,:]
phase = np.append(phase,1.0)
norm_obsF = np.zeros((len(phase), egrid))
for i in range(1,egrid+1):
#norm_obsF[:,i-1] = full_chain[i,:]*energy_keV[i-1]/np.max(full_chain[i,:]*energy_keV[i-1])
norm_obsF[0:len(phase)-1,i-1] = full_chain[i,:]/np.max(full_chain[i,:])
norm_obsF[len(phase)-1,i-1] = full_chain[i,0]/np.max(full_chain[i,:])
ene = 0
print("energy_keV = ", energy_keV[ene])
#phshift = -0.07#-0.24486510062979483#-0.2519665385268506#-0.01#-0.02#0.0#-0.195#-0.18#-0.172#0.0
phshift = 0.0#0.195#-0.6184895833333334
phase_new = shift_phase(np.array(phase),phshift)
#print phase_new
if(plot_all):
for i in range(ene,ene+1):
#for i in range(0,egrid):
for ipha in range(0,len(phase_new)-1):
if(phase_new[ipha+1] > phase_new[ipha]):
plotAF.plot(phase_new[ipha:ipha+2],norm_obsF[ipha:ipha+2,i],"-",markersize=1.0,color=colors[i])
#testing these:
plotAp.plot(phase_new[ipha:ipha+2],norm_obsF[ipha:ipha+2,i+1],"-",markersize=1.0,color=colors[i])
plotAd.plot(phase_new[ipha:ipha+2],norm_obsF[ipha:ipha+2,i+2],"-",markersize=1.0,color=colors[i])
#phase_new = shift_phase(phase,-phshift)
col = colors[ic]
if not(plot_only_I):
#p = full_chain[3,:]*100.0
#PA = full_chain[2,:]*180.0/pi+90.0
p = full_chain[5,:]
PA = arctan2(full_chain[3,:],full_chain[2,:])*90/pi+90#full_chain[4,:]*180.0/pi+90.0#arctan2(full_chain[3,:],full_chain[2,:])*90/pi+90#full_chain[4,:]*180.0/pi+90.0
PA = np.append(PA,PA[0])
for ipha in range(0,len(phase_new)-1):
if(phase_new[ipha+1] > phase_new[ipha]):
plotAc.plot(phase_new[ipha:ipha+2],"--",PA[ipha:ipha+2],color=col,dashes=[2,2])
plot_PA_residuals = True
if(plot_QU):
plot_PA_residuals = False
if(plot_PA_residuals):
col = "black"
plotAd.set_xlim(0,1)
#plotAd.set_ylim(0.97,1.06)
#plotAd.set_ylim(0.0,0.11)
#plotAd.set_ylim(-4.0,3.0)
#plotAd.set_ylim(-0.02,0.02)
#plotAd.set_ylim(-0.005,0.005)
#plotAd.set_ylim(-1.0,1.0)
plotAd.set_ylim(-0.3,0.3)
#plotAd.set_ylim(-10.0,10.0)
#plotAF.set_ylim(-1.2,1.2)
#plotAd.set_yticks([0,30,60,90,120,150,180])
plotAd.tick_params(axis='both', which='major', labelsize=ticksize,direction='in')
#plotAd.tick_params(axis='y', which='major', labelsize=8)
plotAd.tick_params(axis='x', which='major', labelsize=labelsize)
#plotAd.set_ylabel(r'$\chi_{\mathrm{acm}}/\chi_{\mathrm{vp}}$',fontsize=fontsize)
plotAd.set_ylabel(r'$\chi_{\mathrm{arc}}-\chi_{\mathrm{obl}} \ [\mathrm{deg}]$',fontsize=fontsize)
#plotAd.set_ylabel(r'$\frac{\chi_{\mathrm{acm}}-\chi_{\mathrm{vp}}}{\chi_{\mathrm{max}}-\chi_{\mathrm{min}}}$',fontsize=fontsize)
#plotAd.set_xlabel(r'$\varphi\,[360\degree]$',fontsize=fontsize)
#print(len(phase_VP04),len(phase_acm))
PA_VP04_interp = interp1d(phase_VP04,PA_VP04)#,"cubic")
#PA0_VP04_interp = interp1d(phase0_VP04,PA0_VP04)#,"cubic")
#print(shift_phase(np.array(phase0_VP04),phshift1),PA0_VP04)
#quit()
#PA0_VP04_interp = interp1d(shift_phase(np.array(phase0_VP04),phshift0),PA0_VP04)#,"cubic")
PA0_VP04_interp = interp1d(shift_phase(np.array(phase0_VP04),phshift1),PA0_VP04,fill_value='extrapolate')# workd with newer scipy
#PA0_VP04_2_interp = interp1d(shift_phase(np.array(phase0_VP04_2),phshift2),PA0_VP04_2,fill_value='extrapolate')# workd with newer scipy
norm = 1.0#abs(np.max(PA_acm0)-np.min(PA_acm0))
#print(phase_acm0)
res_PA = (PA_acm0-PA0_VP04_interp(phase_acm0))/norm
plotAd.plot(phase_acm0[abs(res_PA) < 5.0],res_PA[abs(res_PA) < 5.0],"-",markersize=5,color="black")#"red")
#res_PA_2 = (PA_acm0-PA0_VP04_2_interp(phase_acm0))/norm
#plotAd.plot(phase_acm0[abs(res_PA_2) < 20.0],res_PA_2[abs(res_PA_2) < 20.0],color="green")
#for ipha in range(0,len(phase_acm0)-1):
# #if(phase_new[ipha+1] > phase_new[ipha]):
# if(phase_acm0[ipha+1] > phase_acm0[ipha]):
# plotAd.plot(phase_acm0[ipha:ipha+2],(PA_acm0[ipha:ipha+2]-PA0_VP04_interp(phase_acm0[ipha:ipha+2]))/norm,color="blue")
# #plotAd.plot(phase_acm0[ipha:ipha+2],(PA_acm0[ipha:ipha+2]-PA_VP04_interp(phase_acm0[ipha:ipha+2]))/norm,color="green")
print("sum_PA_err=",sum(res_PA[abs(res_PA)<5.0]))
plotAp.set_ylim(-0.03,0.03)
#plotAp.set_ylim(0.0,0.5)
F0_VP04_interp = interp1d(shift_phase(np.array(phase0_VP04),phshift1),F0_VP04,fill_value='extrapolate')# workd with newer scipy
Q0_VP04_interp = interp1d(shift_phase(np.array(phase0_VP04),phshift1),Q0_VP04,fill_value='extrapolate')# workd with newer scipy
U0_VP04_interp = interp1d(shift_phase(np.array(phase0_VP04),phshift1),U0_VP04,fill_value='extrapolate')# workd with newer scipy
res_F = (F_acm0-F0_VP04_interp(phase_acm0))/F_acm0#abs((F_acm0-F0_VP04_interp(phase_acm0))/F_acm0)
res_Q = (Q_acm0-Q0_VP04_interp(phase_acm0))/Q_acm0
res_U = (U_acm0-U0_VP04_interp(phase_acm0))/U_acm0
#print(res_F)
#print(res_Q)
#print(res_U)
plotAp.plot(phase_acm0,res_F,"-",markersize=5,color="blue")
plotAp.plot(phase_acm0[abs(res_Q) < 0.02],res_Q[abs(res_Q) < 0.02],"-",markersize=5,color="red")#"darkblue")
plotAp.plot(phase_acm0[abs(res_U) < 0.02],res_U[abs(res_U) < 0.02],"-",markersize=5,color="darkorange")#"lightblue")
#F0_VP04_2_interp = interp1d(shift_phase(np.array(phase0_VP04),phshift2),F0_VP04_2,fill_value='extrapolate')# workd with newer scipy
#Q0_VP04_2_interp = interp1d(shift_phase(np.array(phase0_VP04),phshift2),Q0_VP04_2,fill_value='extrapolate')# workd with newer scipy
#U0_VP04_2_interp = interp1d(shift_phase(np.array(phase0_VP04),phshift2),U0_VP04_2,fill_value='extrapolate')# workd with newer scipy
#res_F = abs((F_acm0-F0_VP04_2_interp(phase_acm0))/F_acm0)
#res_Q = abs((Q_acm0-Q0_VP04_2_interp(phase_acm0))/Q_acm0)
#res_U = abs((U_acm0-U0_VP04_2_interp(phase_acm0))/U_acm0)
#plotAp.plot(phase_acm0,res_F,"-",markersize=5,color="green")
#plotAp.plot(phase_acm0[res_Q < 0.5],res_Q[res_Q < 0.5],"-",markersize=5,color="darkgreen")
#plotAp.plot(phase_acm0[res_U < 0.5],res_U[res_U < 0.5],"-",markersize=5,color="lightgreen")
#figA.savefig('res/C2/obl_sph_comp.pdf')#.format(e))
#Fine tuning:
#plotAF.axes.get_xaxis().set_ticks([])
#plotAp.axes.get_xaxis().set_ticks([])
#plotAc.axes.get_xaxis().set_ticks([])
plotAFF.margins(x=0,y=0)
plotAF.margins(x=0,y=0)
plotAp.margins(x=0,y=0)
plotAc.margins(x=0,y=0)
plotAd.margins(x=0)
plotAF.xaxis.set_major_formatter(matplotlib.pyplot.NullFormatter())
plotAp.xaxis.set_major_formatter(matplotlib.pyplot.NullFormatter())
plotAc.xaxis.set_major_formatter(matplotlib.pyplot.NullFormatter())
#plotAd.xaxis.set_major_formatter(matplotlib.pyplot.NullFormatter())
#plotAc.set_xlabel(r'$\varphi\,[360\degree]$',fontsize=fontsize)
plotAd.set_xlabel(r'$\varphi / (2\pi)$',fontsize=fontsize)
#These are already defined elsewhere and top=True,right = True used there (this is used just to adjust labelsizes and pads):
plotAF.tick_params(axis='both', which='major', labelsize=fontsize,pad=wpad)
plotAp.tick_params(axis='both', which='major', labelsize=fontsize,pad=wpad)
plotAc.tick_params(axis='both', which='major', labelsize=fontsize,pad=wpad)
plotAd.tick_params(axis='both', which='major', labelsize=fontsize,pad=wpad)
#figA.tight_layout()
figA.subplots_adjust(wspace=0, hspace=0)
figA.subplots_adjust(left=0.15)
#figA.align_ylabels(plotAF)
#figA.align_ylabels(plotAp)
#align manually instead:
labelx = -0.14#-0.16
plotAFF.yaxis.set_label_coords(labelx, 0.5)
plotAF.yaxis.set_label_coords(labelx, 0.5)
plotAp.yaxis.set_label_coords(labelx, 0.5)
plotAc.yaxis.set_label_coords(labelx, 0.5)
plotAd.yaxis.set_label_coords(labelx, 0.5)
plotAF.set_yticks([-0.04,-0.02,0.0,0.02])
plotAF.set_yticklabels(["-0.04","-0.02","0","0.02"],fontstyle="normal")
plotAF.set_ylim(-0.05,0.03)
plotAp.set_yticks([-0.02,0.0,0.02])
plotAp.set_yticklabels(["-0.02","0","0.02"],fontstyle="normal")
plotAd.set_yticks([-0.2,0.0,0.2])
plotAd.set_yticklabels(["-0.2","0","0.2"],fontstyle="normal")
if(plot5):
plotAFF.xaxis.set_major_formatter(matplotlib.pyplot.NullFormatter())
plotAFF.tick_params(axis='both', which='major', labelsize=fontsize, pad=wpad)
plotAFF.set_ylim(0.0,1.1)
plotAFF.set_yticks([0.0,0.2,0.4,0.6,0.8,1.0])
plotAFF.set_yticklabels(["0","0.2","0.4","0.6","0.8","1.0"],fontstyle="normal")
plotAc.set_yticks([0,50,100,150])
plotAc.set_yticklabels(["0","50","100","150"],fontstyle="normal")
figA.subplots_adjust(0.15)#(left=0.175)
else:
figA.subplots_adjust(left=0.15)
#figA.savefig('res/C2/obl_sph_comp.pdf')#.format(e))
figA.savefig('res/B/plot.pdf',bbox_inches='tight')#.format(e))
figA.clf()