#!/usr/bin/gnuplot
f1 = 'combine_temp.dat'

#set terminal postscript eps color enhanced solid font "Helvetica,26" size 16cm,10cm
#set term pdf
#set output "temp_int.pdf"


attenuation = 0.0073 #0.012
fibercoupling = 0.65
apdeff = 0.52
opticalpath = 0.9
col_attn = 1.0 #0.726
bg_red = 180*20e-6 # bg per atom bin
bg_blue = 180*20e-6 # bg per atom bin

gamma = 1/26.24e-9
h = 6.626e-34
c = 3e8
lambda = 780.24e-9

eff_correction = 1/(fibercoupling*attenuation*opticalpath) 

#set title ", 11,12 July 2016 "
set xlabel "recapture probability after 30us"
set ylabel 'peak reflectivity (%)'
set ytics 0.05 nomirror
set y2tics 1
set y2label 'transmission extinction (%)'
#set key right bottom
set pointsize 0.5


plot f1 u 11:(($4-bg_blue*$6)/($5*eff_correction)*100):12:(sqrt ( (sqrt($4)/($5*eff_correction) )**2 + (sqrt($5)*$4/($5**2*eff_correction))**2 )*100) w xyerr pt 7 lw 2 t 'reflection', f1 u 11:((1-$8)*100):12:($9*100) w xye lt 9 lc 3 lw 2 axes x1y2 t 'extinction'
unset output

pause -1