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plot_fig6.py
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plot_fig6.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,x_weight=IntEnergy
##figA=figure(2,figsize=(10,14))
#figA=figure(2,figsize=(14,18))
#figA.clear()
#rc("text", usetex=True)
figA = figure(figsize=(14,30), dpi=300)
#figA = figure(figsize=(14,18), dpi=300) #8,6
#rc("font", family="serif")
#rc("font",serif="Times")
matplotlib.pyplot.figure(1)
lbfontsz = 35 #25 #35 #25 #30#25
lwidth= 3.0 #2.5 #3.5 #3.0 #2.5 #3.0#2.5#2.0#1.5
lpad = 10 #12
labelsize=lbfontsz#40#30#20
fontsize=lbfontsz#35#25
ticksize=lbfontsz#25
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'})
#matplotlib.pyplot.tight_layout()
plot_only_I = False
plot_all = True
plot_QU = False#True
two_spots = False#True
plot_resid = True
matplotlib.pyplot.subplots_adjust(wspace=0, hspace=0)
if(plot_all):
if not (plot_resid):
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) #
plotAd=figA.add_subplot(4,1,3) #
plotAc=figA.add_subplot(4,1,4) #
else:
plotAF=figA.add_subplot(5,1,1,yscale='linear')
plotAp=figA.add_subplot(5,1,2)
plotAd=figA.add_subplot(5,1,3)
plotAc=figA.add_subplot(5,1,4)
plotAr=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(1,3):#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_f001_obl_accspot'
#PulsName='res/B/lbb_rho10_sp1_f600_obl'#obl_accspot used in old results
PulsName='pOS_pulses/lbb_rho10_sp1_f600_obl_burst2_dt'#test'
#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_dmr2'#_accspot' #used in the previous results
PulsName='pOS_pulses/lbb_rho10_sp1_f600_sph_burst2_dt'#_dmr2_test'
#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(x)
#print(evere)
print("The chosen energy (keV): ", x[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)
#phase=list(phi/2/pi)+[1.]
#phase=list(phi)#+[1.]
phil = list(phi)
phase=zeros(NPhase)
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] ,fluxlcurve_Qene[t-1]*x[ene] ,fluxlcurve_Uene[t-1]*x[ene]
phase[t] = phil[t]
#I[t],Q[t],U[t]=fluxlcurve_Iene[t]*x[ene] ,fluxlcurve_Qene[t]*x[ene] ,fluxlcurve_Uene[t]*x[ene]
p=sqrt(Q**2+U**2)/I*100
#PA=arctan2(-U,-Q)*90/pi+90
PA=arctan2(U,Q)*90/pi+90
#print("ish=",ish)
#for t in range(NPhase):
# print(phase[t], I[t])
#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=fontsize,direction='in',pad=lpad,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=fontsize,direction='in',pad=lpad,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'$F_{\mathrm{Q}}(\varphi)/F_{\mathrm{Q}}^{\mathrm{max}}$',fontsize=fontsize)
plotAF.set_xlim(0,1)
# plotAF.locator_params(axis='y', nbins=10)
#plotAF.set_ylabel(r"$F_{x}(\varphi)/F_{x}^{\mathrm{max}}$",fontsize=fontsize)
plotAF.set_ylabel(r'$F_{\mathrm{I}}/F_{\mathrm{I}}^{\mathrm{max}}$',fontsize=fontsize)
#plotAd.set_ylabel(r'$F_{\mathrm{U}}(\varphi)/F_{\mathrm{U}}^{\mathrm{max}}$',fontsize=fontsize)
plotAp.set_ylabel(r'$F_{\mathrm{Q}}/F_{\mathrm{I}}$',fontsize=fontsize)
plotAd.set_ylabel(r'$F_{\mathrm{U}}/F_{\mathrm{I}}$',fontsize=fontsize)
plotAd.tick_params(axis='both', which='major', labelsize=fontsize,direction='in',pad=lpad,top=True,right = True)
plotAd.set_xlim(0,1)
plotAF.tick_params(axis='both', which='major', labelsize=fontsize,direction='in',pad=lpad,top=True,right = True)
#plotAp.yaxis.set_major_formatter(matplotlib.pyplot.NullFormatter())
#plotAp.set_yticks([-0.9,0.0,0.9])
#plotAp.set_yticklabels(["-0.9","0.0","0.9"],fontstyle="normal")
plotAF.set_ylim(0.0,1.1)#(0.1,1.1)
plotAF.yaxis.set_major_formatter(matplotlib.pyplot.NullFormatter())
#plotAF.set_yticks([0.25,0.5,0.75,1.0])
#plotAF.set_yticklabels(["0.25","0.50","0.75","1.00"],fontstyle="normal")
plotAF.set_yticks([0.0,0.2,0.4,0.6,0.8,1.0])
plotAF.set_yticklabels(["0","0.2","0.4","0.6","0.8","1.0"],fontstyle="normal")
#col=colors[(e*NColors)//NEnergy]
col = colors[ish]
PA_VP04 = PA
phase_VP04 = phase
if(ish == 1):
#find best-phasehift:
#phshift1, gf1 = find_best_phshift.find_best_phshift(np.array(phase),PA,phase_acm0,PA_acm0)
#phshift1 = phshift1 -1.0
#print("Phaseshift for oblate star: ",phshift1)
#quit()
#in the end, setting the shift by hand seems still to produce better results
#phshift1 = 0.0 #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
phshift1 = -0.018#695# -0.016830883531243623#-0.025#-0.048315
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]):
if(PA[ipha] > 50.0*PA[ipha+1]):
plotAc.plot(phase_new[ipha:ipha+2],[PA[ipha],180.0],"-",color="blue",linewidth=lwidth)
else:
plotAc.plot(phase_new[ipha:ipha+2],PA[ipha:ipha+2],"-",color="blue",linewidth=lwidth)
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="darkblue")
##plotAF.plot(phase_new[ipha:ipha+2],U[ipha:ipha+2]/U.max(),color="lightblue")
#plotAp.plot(phase_new[ipha:ipha+2],Q[ipha:ipha+2]/Q.max(),color=col,linewidth=lwidth)
#plotAd.plot(phase_new[ipha:ipha+2],U[ipha:ipha+2]/U.max(),color=col,linewidth=lwidth)
plotAp.plot(phase_new[ipha:ipha+2],Q[ipha:ipha+2]/I[ipha:ipha+2],color=col,linewidth=lwidth)
plotAd.plot(phase_new[ipha:ipha+2],U[ipha:ipha+2]/I[ipha:ipha+2],color=col,linewidth=lwidth)
PA0_VP04 = PA
F0_VP04 = I/I.max()
Q0_VP04 = Q/Q.max()
U0_VP04 = U/U.max()
phase0_VP04 = phase
if(ish == 2):
#phshift2 = 0.0
#phase_new = shift_phase(np.array(phase),phshift)
##find best-phasehift:
#phshift2, gf2 = find_best_phshift.find_best_phshift(np.array(phase),PA,phase_acm0,PA_acm0)
phshift2 = -0.022371326512027778 #phshift2 -1.0
print("phaseshift for spherical star: ",phshift2)
#phshift2 = 0.0 #0.1 #-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]):
if(PA[ipha] > 30.0*PA[ipha+1]):
plotAc.plot(phase_new[ipha:ipha+2],[PA[ipha],180.0],"-",color="blue",linewidth=lwidth)
else:
plotAc.plot(phase_new[ipha:ipha+2],PA[ipha:ipha+2],"-",color=col,linewidth=lwidth)
if(plot_all):
plotAF.plot(phase_new[ipha:ipha+2],I[ipha:ipha+2]/I.max(),"--",color=col,linewidth=lwidth)
###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,linewidth=lwidth)
##plotAd.plot(phase_new[ipha:ipha+2],U[ipha:ipha+2]/U.max(),color=col,linewidth=lwidth)#,linestyle="dashed")
plotAp.plot(phase_new[ipha:ipha+2],Q[ipha:ipha+2]/I[ipha:ipha+2],"-",color=col,linewidth=lwidth)
plotAd.plot(phase_new[ipha:ipha+2],U[ipha:ipha+2]/I[ipha:ipha+2],"-",color=col,linewidth=lwidth)
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 = "arcman_res/polar_f600_bb_r12_m1.4_d60_i40_x10_agm.csv"# used in old results
datafile = "../arcmancer/out3/polar_acc_f600_burst_r12_m1.4_d60_i40_x10_agm.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"# (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 ix 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))
for i in range(2,egrid+1): #(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,:])
norm_obsF[:,i-1] = full_chain[i,:]/full_chain[1,:]
norm_obsF[:,0] = full_chain[1,:]/np.max(full_chain[1,:])
#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 ix 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]):
#plotAc.plot(phase_new[ipha:ipha+2],PA[ipha:ipha+2],"-o",color=col,markersize="1.0")
#plotAc.plot(phase_new[ipha:ipha+2],PA[ipha:ipha+2],"-",color=col,markersize="1.0")
if(PA[ipha] > 50.0*PA[ipha+1]):
plotAc.plot(phase_new[ipha:ipha+2],[PA[ipha],180.0],"--",color=col,linewidth=lwidth,dashes=[2,2])
else:
plotAc.plot(phase_new[ipha:ipha+2],PA[ipha:ipha+2],"--",color=col,linewidth=lwidth,dashes=[2,2])
#linePA.set_dashes([2, 2, 2, 2])
if(ic == 0):
PA_acm0 = PA#norm_obsF[:,ene]#PA
F_acm0 = norm_obsF[:,ene]
Q_acm0 = norm_obsF[:,ene+1]
U_acm0 = 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 ix 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):
for i in range(0,ene+3): #this 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],marker="o",markersize="1.0")
if(i == 0):
plotAF.plot(phase_new[ipha:ipha+2],norm_obsF[ipha:ipha+2,i],"--",color=colors[i],linewidth=lwidth,dashes=[2,2])
if(i == 1):
plotAp.plot(phase_new[ipha:ipha+2],norm_obsF[ipha:ipha+2,i],"--",color=colors[i],linewidth=lwidth,dashes=[2,2])
if(i == 2):
plotAd.plot(phase_new[ipha:ipha+2],norm_obsF[ipha:ipha+2,i],"--",color=colors[i],linewidth=lwidth,dashes=[2,2])
#plot_PA_residuals = True
#if(plot_QU):
# plot_PA_residuals = False
#if(plot_PA_residuals):
if(plot_resid):
col = "black"
plotAr.set_xlim(0,1)
plotAr.set_ylim(-10.0,10.0)
plotAr.tick_params(axis='both', which='major', labelsize=fontsize,direction='in',pad=lpad,top=True,right = True)
#plotAd.set_yticks([0,30,60,90,120,150,180])
#plotAr.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)
plotAr.set_ylabel(r'$\Delta \chi \ [\mathrm{deg}]$',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)
plotAr.yaxis.set_major_formatter(matplotlib.pyplot.NullFormatter())
plotAr.set_yticks([-5.0,0.0,5.0])
plotAr.set_yticklabels(["-5","0","5"],fontstyle="normal")
#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
plotAr.plot(phase_acm0[abs(res_PA) < 10.0],res_PA[abs(res_PA) < 10.0],"-",markersize=5,color="red")
res_PA_2 = (PA_acm0-PA0_VP04_2_interp(phase_acm0))/norm
plotAr.plot(phase_acm0[abs(res_PA_2) < 10.0],res_PA_2[abs(res_PA_2) < 10.0],color="darkorange")
#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")
#plotAp.set_ylim(0.0,0.02)
#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([])
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)
if not (plot_resid):
plotAc.set_xlabel(r'$\varphi / (2\pi)$',fontsize=fontsize)
else:
plotAc.xaxis.set_major_formatter(matplotlib.pyplot.NullFormatter())
plotAr.set_xlabel(r'$\varphi / (2\pi)$',fontsize=fontsize)
plotAc.set_yticks([0,50,100,150])
plotAc.set_yticklabels(["0","50","100","150"],fontstyle="normal")
#align manuallyl ylabels:
labelx = -0.16
plotAF.yaxis.set_label_coords(labelx, 0.5)
plotAd.yaxis.set_label_coords(labelx, 0.5)
plotAp.yaxis.set_label_coords(labelx, 0.5)
plotAc.yaxis.set_label_coords(labelx, 0.5)
plotAF.margins(x =0, y=0)
plotAd.margins(x =0, y=0)
plotAp.margins(x =0, y=0)
plotAc.margins(x =0, y=0)
#Adjusting the ticks and their labels ....
plotAp.set_ylim(-0.05,0.03)
plotAp.set_yticks([-0.04,-0.02,0.0,0.02])
plotAp.set_yticklabels(["-0.04","-0.02","0","0.02"],fontstyle="normal")
plotAd.set_ylim(-0.04,0.04)
plotAd.set_yticks([-0.02,0.0,0.02])
plotAd.set_yticklabels(["-0.02","0","0.02"],fontstyle="normal")
if(plot_resid):
plotAr.margins(x =0)
plotAr.yaxis.set_label_coords(labelx, 0.5)
#figA.tight_layout()
figA.subplots_adjust(wspace=0, hspace=0)
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()