#set multiplot layout 2,1

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

#### 5 ns pulses ####
exp_p_5ns_123_filename=exp."5ns".dir1."OD_in_0.32_OD_out_2.2_2.9_after_4_histo"
exp_p_5ns_5_filename=exp."5ns".dir1."OD_in_2.3_OD_out_1.4_1.1_after_histo"
exp_p_5ns_562_filename=exp."5ns".dir1."OD_in_0.16_OD_out_2.2_2.9_after_histo"
exp_p_5ns_1028_filename=exp."5ns".dir1."OD_in_0.16_OD_out_2.3_2.9_after_4_histo"
exp_p_5ns_260_filename=exp."5ns".dir1."OD_in_0.16_OD_out_2.2_2.9_after_5_histo"

sq_p_5ns_117_filename=square."5ns".dir1."OD_in_0.98_OD_out_1.1_2.9_after_histo"
sq_p_5ns_6_filename=square."5ns".dir1."OD_in_2.3_OD_out_2.9_after_histo"
sq_p_5ns_43_filename=square."5ns".dir1."OD_in_1.4_OD_out_1.1_2.9_after_histo"
sq_p_5ns_523_filename=square."5ns".dir1."OD_in_0.32_OD_out_2.2_2.9_after_2_histo"
sq_p_5ns_980_filename=square."5ns".dir1."OD_in_0.00_OD_out_2.2_2.9_after_histo"
sq_p_5ns_246_filename=square."5ns".dir1."OD_in_0.32_OD_out_2.2_2.9_after_histo"

#### 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"

#### 25ns pulses ####

exp_p_25ns_2_7_filename=exp."25ns".dir1."OD_in_2.0_OD_out_1.8_after_histo"
exp_p_25ns_5_7_filename=exp."25ns".dir1."OD_in_1.5_OD_out_2.9_after_histo"

#### 60ns pulses ####
exp_p_60ns_4_5_filename=exp."60ns".dir1."OD_in_1.1_1.5_OD_out_2.9_after_histo"
exp_p_60ns_90_filename=exp."60ns".dir1."OD_in_1.4_OD_out_0.51_2.9_after_histo"
exp_p_60ns_913_filename=exp."60ns".dir1."OD_in_0.51_OD_out_1.5_2.9_after_histo"

sq_p_60ns_2_1_filename=square."60ns".dir1."OD_in_2.0_2.0_OD_out_2.9_after_1_histo"
sq_p_60ns_4_5_filename=square."60ns".dir1."OD_in_1.1_2.0_OD_out_2.9_after_3_histo"
sq_p_60ns_80_filename=square."60ns".dir1."OD_in_0.32_2.0_OD_out_2.2_2.9_after_histo"
sq_p_60ns_1260_filename=square."60ns".dir1."OD_in_0.32_1.0_OD_out_2.2_2.9_after_histo"

#### 250ns pulses ####

exp_p_250ns_3_3_filename=exp."250ns".dir1."OD_in_0.51_2.2_OD_out_2.9_after_histo"
exp_p_250ns_148_filename=exp."250ns".dir1."OD_in_0.16_1.1_OD_out_2.9_after_histo"
exp_p_250ns_379_filename=exp."250ns".dir1."OD_in_0.16_1.1_OD_out_2.9_after_2_histo"

sq_p_250ns_3_8_filename=square."250ns".dir1."OD_in_1.0_1.1_2.2_OD_out_2.9_after_1_histo"
sq_p_250ns_168_filename=square."250ns".dir1."OD_in_2.0_OD_out_2.2_2.9_after_1_histo"
sq_p_250ns_405_filename=square."250ns".dir1."OD_in_2.0_OD_out_2.2_2.9_after_2_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 2 ps 1.5

#### Normalising detection probablity to rho 22 ####
timebin=1.0
lifetime=26.3
effiency=0.3
overlap=0.03
rho(x)=x/(overlap*effiency*(timebin/lifetime))
rho_d(x)=x/(overlap*effiency*(timebin))

#### Some experimental parameters ####

exp_trigger_delay=555
exp_refl_delay=295+exp_trigger_delay
exp_refl_delay2=480+exp_refl_delay
exp_refl_delay3=700+480+130+exp_refl_delay
sq_trigger_delay=324
sq_refl_delay=302+sq_trigger_delay
tau=26.24

#set xrange [-100:100]
set xlabel 't {/Symbol G}'
set ylabel 'P_{e}(t)'

set arrow 1 from graph 0.5,0 to graph 0.5,1 lt 0 lw 2 nohead

set terminal postscript enhanced color eps size 8.6cm,5cm font "Helvetica,16pt"

set xlabel 't (ns)' offset 0,0.3
set ylabel 'P_{e}(t)' offset 1,0

unset output
set xrange [-100:100]
#set yrange [0:1]
set output '../pulses/figure6_corr_5_photons.eps'
#set format y "%4.0f"
set key off
set label 1 at -70,0.12 "exponential\npulse" tc lt 3
set label 2 at 40,0.12 "square\npulse" tc lt 1

plot  exp_p_25ns_5_7_filename every 3 u (column(time)-exp_refl_delay):(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorbar pt 6 ps 1 lt 1 lc 3 lw 1,\
sq_p_60ns_4_5_filename every 3 u (column(time)-sq_refl_delay):(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorbar pt 7 ps 1 lt 1 lc 1 lw 1,\
"../theory_plots/raw_data/pt_003/pt_003_exp_5_25.txt" every 20 u ($1*1000000000):2 w l lc 3 lw 2 lt 1,\
"../theory_plots/raw_data/pt_003/pt_003_square_5_60.txt" every 20 u ($1*1000000000):2 w l lc 1 lw 2 lt 1