#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"

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"

#### 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"

#### 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_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 [-5:5]
#set yrange [1e-7:]
set arrow 1 from graph 0.5,0 to graph 0.5,1 ls 0 lw 2 nohead


# plot exp_p_5ns_123_filename u (column(time)-exp_trigger_delay)/tau:bg_tran_prob:bg_tran_prob_err w yerrorl,\
#      exp_p_5ns_123_filename u (column(time)-exp_refl_delay)/tau:at_refl_prob:at_refl_prob_err w yerrorl,\
#      exp_p_5ns_5_filename u (column(time)-exp_trigger_delay)/tau:bg_tran_prob:bg_tran_prob_err w yerrorl,\
#      exp_p_5ns_5_filename u (column(time)-exp_refl_delay)/tau:at_refl_prob:at_refl_prob_err w yerrorl

#unset key
#set logscale y
set terminal postscript enhanced color eps
set output '../pulses/fluo_5ns_100.eps'
set title "t=5ns;n=123,117"
plot  exp_p_5ns_123_filename u (column(time)-exp_refl_delay)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'exp' ls 2,\
      sq_p_5ns_117_filename u (column(time)-sq_refl_delay)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'square' ls 1
#pause -1

set output '../pulses/fluo_5ns_500.eps'
set title "t=5ns;n=562,523"
plot  exp_p_5ns_562_filename u (column(time)-exp_refl_delay)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'exp' ls 2,\
      sq_p_5ns_523_filename u (column(time)-sq_refl_delay)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'square' ls 1
#pause -1

set output '../pulses/fluo_5ns_5.eps'
set title "t=5ns;n=5,6"
plot  exp_p_5ns_5_filename u (column(time)-exp_refl_delay)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'exp' ls 2,\
      sq_p_5ns_6_filename u (column(time)-sq_refl_delay)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'square' ls 1
#pause -1

set output '../pulses/fluo_5ns_1000.eps'
set title "t=5ns;n=1028,980"
plot  exp_p_5ns_1028_filename u (column(time)-exp_refl_delay)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'exp' ls 2,\
      sq_p_5ns_980_filename u (column(time)-sq_refl_delay)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'square' ls 1
#pause -1

set output '../pulses/fluo_15ns_6.eps'
set title "t=15ns;n=6.3,6.3"
plot  exp_p_15ns_6_filename u (column(time)-exp_refl_delay)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'exp' ls 2,\
      sq_p_15ns_6_filename u (column(time)-sq_refl_delay)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'square' ls 1
#pause -1

set output '../pulses/fluo_15ns_100.eps'
set title "t=15ns;n=104,110"
plot  exp_p_15ns_104_filename u (column(time)-exp_refl_delay)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'exp' ls 2,\
      sq_p_15ns_110_filename u (column(time)-sq_refl_delay)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'square' ls 1
#pause -1

set title "t=15ns;n=241,256"
plot  exp_p_15ns_241_filename u (column(time)-exp_refl_delay)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'exp' ls 2,\
      sq_p_15ns_256_filename u (column(time)-sq_refl_delay)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'square' ls 1
#pause -1

set output '../pulses/fluo_15ns_350.eps'
set title "t=15ns;n=342,374"
plot  exp_p_15ns_342_filename u (column(time)-exp_refl_delay)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'exp' ls 2,\
      sq_p_15ns_374_filename u (column(time)-sq_refl_delay)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'square' ls 1

set output '../pulses/fluo_15ns_600.eps'
set title "t=15ns;n=637,538"
plot  exp_p_15ns_637_filename u (column(time)-exp_refl_delay)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'exp' ls 2,\
      sq_p_15ns_538_filename u (column(time)-sq_refl_delay)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'square' ls 1
#pause -1

set output '../pulses/fluo_15ns_1300.eps'
set title "t=15ns;n=1229,1456"
plot  exp_p_15ns_1229_filename u (column(time)-exp_refl_delay)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'exp' ls 2,\
      sq_p_15ns_1456_filename u (column(time)-sq_refl_delay)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'square' ls 1
#pause -1


set xrange [-10:5]
unset arrow 1
set arrow 2 from graph 0.667,0 to graph 0.667,1 ls 0 lw 2 nohead
set output '../pulses/fluo_60ns_5.eps'
set title "t=60ns;n=4.5,4.5"
plot  exp_p_60ns_4_5_filename u (column(time)-exp_refl_delay2)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'exp' ls 2,\
      sq_p_60ns_4_5_filename u (column(time)-sq_refl_delay)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'square' ls 1
#pause -1

set output '../pulses/fluo_60ns_100.eps'
set title "t=60ns;n=90,80"
plot  exp_p_60ns_90_filename u (column(time)-exp_refl_delay)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'exp' ls 2,\
      sq_p_60ns_80_filename u (column(time)-sq_refl_delay)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'square' ls 1
#pause -1

set output '../pulses/fluo_60ns_1000.eps'
set title "t=60ns;n=913,1260"
plot  exp_p_60ns_913_filename u (column(time)-exp_refl_delay)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'exp' ls 2,\
      sq_p_60ns_1260_filename u (column(time)-sq_refl_delay)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'square' ls 1
#pause -1


set xrange [-15:5]
unset arrow 2
set arrow 3 from graph 0.75,0 to graph 0.75,1 ls 0 lw 2 nohead

set output '../pulses/fluo_250ns_3.eps'
set title "t=250ns;n=3.3,3.8"
plot  exp_p_250ns_3_3_filename u (column(time)-exp_refl_delay3)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'exp' ls 2,\
      sq_p_250ns_3_8_filename u (column(time)-sq_refl_delay)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'square' ls 1
#pause -1

set output '../pulses/fluo_250ns_150.eps'
set title "t=250ns;n=148,168"
plot  exp_p_250ns_148_filename u (column(time)-exp_refl_delay3)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'exp' ls 2,\
      sq_p_250ns_168_filename u (column(time)-sq_refl_delay)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'square' ls 1
#pause -1

set output '../pulses/fluo_250ns_400.eps'
set title "t=250ns;n=379,405"
plot  exp_p_250ns_379_filename u (column(time)-exp_refl_delay3)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'exp' ls 2,\
      sq_p_250ns_405_filename u (column(time)-sq_refl_delay)/tau:(rho(column(at_refl_prob))):(rho(column(at_refl_prob_err))) w yerrorl t 'square' ls 1
#pause -1