# this is an adapted file for plotting the sample pulses for 15 nsec
#  characteristic time. Original file: plot_pulses.gnu
# This is cleaned up to only contain two traces, and for generating the 
# publication figure



#set terminal postscript eps color enhanced size 8.6cm,6cm font "Helvetica,16pt"
set terminal postscript eps color enhanced size 8.6cm,4.5cm font "Helvetica,16pt"
# set output "pulseshapes_lin.eps"
set output "pulseshapes_log.eps"

set multiplot


rootdir="./"
square="sq_pulse/"
dir1="/processed_histogram_with_yerror_bars/"
exp="exp_pulse/vary_photon_number_perkin_elmer_"


#### 15 ns pulses ####
exp_p_15ns_6_filename=exp."15ns".dir1."OD_in_1.8_0.51_OD_out_2.9_after_histo"
exp_p_15ns_104_filename=exp."15ns".dir1."OD_in_1.1_OD_out_1.4_2.9_after_histo"
exp_p_15ns_241_filename=exp."15ns".dir1."OD_in_0.76_OD_out_1.4_2.9_after_histo"
exp_p_15ns_637_filename=exp."15ns".dir1."OD_in_0.16_OD_out_1.8_2.9_after_histo"
exp_p_15ns_342_filename=exp."15ns".dir1."OD_in_0.32_OD_out_1.8_2.9_after_histo"
exp_p_15ns_1229_filename=exp."15ns".dir1."OD_in_0.00_OD_out_1.8_2.9_after_histo"

sq_p_15ns_6_filename=square."15ns".dir1."OD_in_0.76_2.3_OD_out_2.9_after_histo"
sq_p_15ns_110_filename=square."15ns".dir1."OD_in_1.8_OD_out_1.1_2.9_after_histo"
sq_p_15ns_256_filename=square."15ns".dir1."OD_in_1.4_OD_out_1.1_2.9_after_histo"
sq_p_15ns_538_filename=square."15ns".dir1."OD_in_0.98_OD_out_2.2_2.9_after_histo"
sq_p_15ns_374_filename=square."15ns".dir1."OD_in_1.1_OD_out_2.2_2.9_after_histo"
sq_p_15ns_1456_filename=square."15ns".dir1."OD_in_0.51_OD_out_2.2_2.9_after_histo"

#### Columns for pulse data file ####
bin=1
time=2
at_tran_count=3
at_refl_count=4
at_tran_prob=5
at_refl_prob=6
at_tran_prob_err=7
at_refl_prob_err=8
bg_tran_count=9
bg_refl_count=10
bg_tran_prob=11
bg_refl_prob=12
bg_tran_prob_err=13
bg_refl_prob_err=14

#### Styles ####

set style line 1 lc 1 lw 1 ps 1.5
set style line 2 lc 3 lw 1 ps 1.5
set style line 3 lc 4 lw 2 ps 1.5
set style line 4 lc 2 lw 3 ps 1.5

#### Some experimental parameters ####

exp_trigger_delay=555
exp_refl_delay=295+exp_trigger_delay
exp_refl_delay2=480+exp_refl_delay
sq_trigger_delay=324
sq_refl_delay=302+sq_trigger_delay
tau=26.24

#### Fit results?
f(x)= eta*lambda*exp((x-x0)/tau0)*(exp(time_width/tau0)-1)
x0=exp_trigger_delay; time_width=1
tau0=15.3907
eta=0.3
lambda=0.00381085*14750000


# set title "t=15ns;n=104,110"
# plot  exp_p_15ns_104_filename u (column(time)-exp_refl_delay)/tau:at_refl_prob:at_refl_prob_err w yerrorl t 'exp' ls 2,\
#       sq_p_15ns_110_filename u (column(time)-sq_refl_delay)/tau:at_refl_prob:at_refl_prob_err w yerrorl t 'square' ls 1


# Here starts plot formatting
set xrange [-80:30]

set ylabel "Events" offset 1,0

set xtics 
# set ytics 500
set logscale y

# square pulse plot

set origin 0,0
# set size 1,0.58
set size 1,0.60

set xlabel 't (ns)' offset 0,0.3

# set output '../pulses/excitation_sq_pulse_15ns_n100.eps'

# set yrange [0:2950]
set yrange [1:5000] ; # for log scale
set label 1 'ND2: 40 dB' at -70,500; # for log scale
# set label 1 'ND2: 40 dB' at -70,2000  ; # for lin scale
plot  sq_p_15ns_110_filename u  \
      (column(time)-sq_trigger_delay):bg_tran_count \
      w p pt 7 ps 0.7 lc rgbcolor "blue"  notitle


# Exponential pulse plot

set origin 0,0.5
set size 1,0.5

set format x "" ; # no labels and ticks on top plot
set xlabel ""

# set terminal postscript enhanced color eps
# set yrange [1:1600]
lambda=0.00381085*14750000

# set label 1 'ND2: 43 dB' at -70,1200 ; # for lin scale
set label 1 'ND2: 43 dB' at -70,500 ; # for log scale

plot  exp_p_15ns_104_filename u \
      (column(time)-exp_trigger_delay):bg_tran_count \
      w p pt 7 ps 0.7 lc rgbcolor "red"  notitle,\
      f((x+x0)) lt 3 lw 2 lc rgbcolor "black" notitle