#set multiplot layout 2,1

filename="processed_histogram_with_yerror_bars/results.sorted"
filename8="processed_histogram_with_yerror_bars_8ns_bin/results.sorted"
#rootdir="/mnt/buffalo/"
rootdir="./"
square="sq_pulse/"
exp="exp_pulse/vary_photon_number_perkin_elmer_"

#### Columns for square pulse ####
data_filename=1
p_tran=2
p_tran_err=3
od_used=4
photon_no=5
photon_err=6
p_refl_flou=7
p_refl_flou_err=8
p_refl_flou_bg=9
p_refl_flou_bg_err=10
p_refl_scat=11
p_refl_scat_err=12
flou_lifetime=13
flou_lifetime_err=14
max_p_refl=15
max_p_refl_err=16

#### "Columns for exponential pulse ####
exp_risetime=17
exp_risetime_err=18
fit_lambda=19
fit_lambda_err=20
fit_photon_no=21
fit_photon_err=22

#### End "Columns ####

currentdir="`pwd`"
cd rootdir

#### Styles ####

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

#### Normalising detection probablity to rho 22 ####
timebin=1.0
timebin8=8.0
lifetime=26.3
effiency=0.3
overlap=0.03
rho(x)=x/(overlap*effiency*(timebin/lifetime))
rho_d(x)=x/(overlap*effiency)
rho8(x)=x/(overlap*effiency*(timebin8/lifetime))
rho_d8(x)=x/(overlap*effiency)


#### Plotting maximum probability of detector click And Total probability of detector click for flourescence
####   	      	      		  vs average photon number for all square pulse times 

unset logscale xy
set logscale x
set key left
# plot square.'5ns/'.filename u photon_no:p_refl_flou:photon_err:p_refl_flou_err w xyerrorl,\
#      square.'5ns/'.filename u photon_no:max_p_refl:photon_err:max_p_refl_err w xyerror axes x1y2,\
#      square.'15ns/'.filename u photon_no:p_refl_flou:photon_err:p_refl_flou_err w xyerrorl,\
#      square.'15ns/'.filename u photon_no:max_p_refl:photon_err:max_p_refl_err w xyerror axes x1y2,\
#      square.'20ns/'.filename u photon_no:p_refl_flou:photon_err:p_refl_flou_err w xyerrorl,\
#      square.'20ns/'.filename u photon_no:max_p_refl:photon_err:max_p_refl_err w xyerror axes x1y2,\
#      square.'60ns/'.filename u photon_no:p_refl_flou:photon_err:p_refl_flou_err w xyerrorl,\
#      square.'60ns/'.filename u photon_no:max_p_refl:photon_err:max_p_refl_err w xyerror axes x1y2,\
#      square.'250ns/'.filename u photon_no:p_refl_flou:photon_err:p_refl_flou_err w xyerrorl,\
#      square.'250ns/'.filename u photon_no:max_p_refl:photon_err:max_p_refl_err w xyerror axes x1y2

#set xrange restore ; #[1:1000]

#### Plotting maximum probability of detector click And Total probability of detector click for flouroscence
####   	      	      		  vs average photon number for all exponential pulse times 

# plot exp.'5ns/'.filename u 7:9:8:10 w xyerrorl,\
#      exp.'5ns/'.filename u 7:17:8:18 axes x1y2 w xyerror,\
#      exp.'15ns/'.filename u 7:9:8:10 w xyerrorl,\
#      exp.'15ns/'.filename u 7:17:8:18 axes x1y2 w xyerror,\
#      exp.'25ns/'.filename u 7:9:8:10 w xyerrorl,\
#      exp.'25ns/'.filename u 7:17:8:18 axes x1y2 w xyerror,\
#      exp.'60ns/'.filename u 7:9:8:10 w xyerrorl,\
#      exp.'60ns/'.filename u 7:17:8:18 axes x1y2 w xyerror,\
#      exp.'250ns/'.filename u 7:9:8:10 w xyerrorl,\
#      exp.'250ns/'.filename u 7:17:8:18 axes x1y2 w xyerror

#### Plotting maximum probability of detector click vs average photon number

set yrange [0:1]
y_stretch=1e0
set xrange [1:]
set xlabel 'N' font 'Helvetica, 20'
set ylabel 'P_{e,max}' font 'Helvetica, 20'
set xtics font 'Helvetica, 20'
set ytics font 'Helvetica, 20'
set terminal postscript enhanced color eps
set output '../rho22_max_p_vs_n.eps'
set key at 200,0.24 font 'Helvetica, 16' 
unset label
set multiplot layout 2,2
set label 1 '5 ns' font 'Helvetica, 18' at graph 0.05,0.90

plot square.'5ns/'.filename u (column(photon_no)):(rho(column(max_p_refl))*y_stretch):photon_err:(rho(column(max_p_refl_err))*y_stretch) w xyerror axes x1y1 t 'Square' ls 1,\
     exp.'5ns/'.filename u (column(photon_no)):(rho(column(max_p_refl))*y_stretch):photon_err:(rho(column(max_p_refl_err))*y_stretch) axes x1y1 w xyerror t 'Exp.' ls 2,\
     '../theory_plots/raw_data/evss_pmax_n/pmax_003_5.txt' u 1:2 w l lw 2 t '',\
     '../theory_plots/raw_data/evss_pmax_n/pmax_003_5.txt' u 1:3 w l lc 1 lw 2 t ''     

set label 1 '15 ns' font 'Helvetica, 18'

plot square.'15ns/'.filename u (column(photon_no)):(rho(column(max_p_refl))*y_stretch):photon_err:(rho(column(max_p_refl_err))*y_stretch) w xyerror axes x1y1 t 'Square' ls 1,\
     exp.'15ns/'.filename u (column(photon_no)):(rho(column(max_p_refl))*y_stretch):photon_err:(rho(column(max_p_refl_err))*y_stretch) axes x1y1 w xyerror t 'Exp.' ls 2,\
     '../theory_plots/raw_data/evss_pmax_n/pmax_003_15.txt' u 1:2 w l lw 2 t '',\
     '../theory_plots/raw_data/evss_pmax_n/pmax_003_15.txt' u 1:3 w l lc 1 lw 2 t '' 

set label 1 '60 ns' font 'Helvetica, 18'

plot square.'60ns/'.filename u (column(photon_no)):(rho(column(max_p_refl))*y_stretch):photon_err:(rho(column(max_p_refl_err))*y_stretch) w xyerror axes x1y1 t 'Square' ls 1,\
     exp.'60ns/'.filename u (column(photon_no)):(rho(column(max_p_refl))*y_stretch):photon_err:(rho(column(max_p_refl_err))*y_stretch) axes x1y1 w xyerror t 'Exp' ls 2,\
     '../theory_plots/raw_data/evss_pmax_n/pmax_003_60.txt' u 1:2 w l lw 2 t '' ,\
     '../theory_plots/raw_data/evss_pmax_n/pmax_003_60.txt' u 1:3 w l lc 1 lw 2 t ''

set label 1 '250 ns' font 'Helvetica, 18'

plot square.'250ns/'.filename8 u (column(photon_no)):(rho8(column(max_p_refl))*y_stretch):photon_err:(rho8(column(max_p_refl_err))*y_stretch) w xyerror axes x1y1 t 'Square' ls 1 ,\
     exp.'250ns/'.filename8 u (column(photon_no)):(rho8(column(max_p_refl))*y_stretch):photon_err:(rho8(column(max_p_refl_err))*y_stretch) axes x1y1 w xyerror t 'Exp' ls 2,\
     '../theory_plots/raw_data/EVSS/pmax_003_250.txt' u 1:2 w l lw 2 t '',\
     '../theory_plots/raw_data/EVSS/pmax_003_250.txt' u 1:3 w l lc 1 lw 2 t ''

unset multiplot
set term wxt
#!gv 'max_p_vs_n.eps' &

#### Plotting total probability of detector click for flourescence vs average photon number

y_stretch=1e0
set xlabel 'N' font 'Helvetica, 20'
set ylabel 'P_{e,tot}' font 'Helvetica, 20'
set xtics font 'Helvetica, 20'
set ytics font 'Helvetica, 20'
#set ylabel '{/Symbol=20 \362@_{/=9 0}^{/=12 \245}}{/Symbol r}_{22}(t){/Symbol t}'
set xrange [1:]
set yrange [0:]
unset key
set terminal postscript enhanced color eps
set output '../rho22_flou_vs_n.eps'
set multiplot layout 2,2
set label 1 '5 ns' at graph 0.05, 0.90

plot square.'5ns/'.filename u (column(photon_no)):(rho_d(column(p_refl_flou))*y_stretch):photon_err:(rho_d(column(p_refl_flou_err))*y_stretch) w xyerror t 'Square pulse 5ns' ls 1,\
     exp.'5ns/'.filename u photon_no:(rho_d(column(p_refl_flou))*y_stretch):photon_err:(rho_d(column(p_refl_flou_err))*y_stretch) w xyerror t 'Exponential pulse 5ns' ls 2,\
     '../theory_plots/raw_data/evss_pt0_n/pt0_003_5.txt' u 1:2 w l lw 2 t '',\
     '../theory_plots/raw_data/evss_pt0_n/pt0_003_5.txt' u 1:3 w l lc 1 lw 2 t ''

#exp.'5ns/'.filename u fit_photon_no:(rho_d(column(p_refl_flou))*y_stretch):fit_photon_err:(rho_d(column(p_refl_flou_err))*y_stretch) w xyerror t 'Exponential pulse 5ns' ls 3
set label 1 '15 ns'
plot square.'15ns/'.filename u (column(photon_no)):(rho_d(column(p_refl_flou))*y_stretch):photon_err:(rho_d(column(p_refl_flou_err))*y_stretch) w xyerror t 'Square pulse 5ns' ls 1,\
     exp.'15ns/'.filename u photon_no:(rho_d(column(p_refl_flou))*y_stretch):photon_err:(rho_d(column(p_refl_flou_err))*y_stretch) w xyerror t 'Exponential pulse 5ns' ls 2,\
     '../theory_plots/raw_data/evss_pt0_n/pt0_003_15.txt' u 1:2 w l lw 2 t '',\
     '../theory_plots/raw_data/evss_pt0_n/pt0_003_15.txt' u 1:3 w l lc 1 lw 2 t ''

#exp.'15ns/'.filename u fit_photon_no:(rho_d(column(p_refl_flou))*y_stretch):fit_photon_err:(rho_d(column(p_refl_flou_err))*y_stretch) w xyerror t 'Exponential pulse 5ns' ls 3
set label 1 '60 ns'
plot square.'60ns/'.filename u (column(photon_no)):(rho_d(column(p_refl_flou))*y_stretch):photon_err:(rho_d(column(p_refl_flou_err))*y_stretch) w xyerror t 'Square pulse 5ns' ls 1,\
     exp.'60ns/'.filename u photon_no:(rho_d(column(p_refl_flou))*y_stretch):photon_err:(rho_d(column(p_refl_flou_err))*y_stretch) w xyerror t 'Exponential pulse 5ns' ls 2,\
     '../theory_plots/raw_data/evss_pt0_n/pt0_003_60.txt' u 1:2 w l lw 2 t '',\
     '../theory_plots/raw_data/evss_pt0_n/pt0_003_60.txt' u 1:3 w l lc 1 lw 2 t ''

#exp.'60ns/'.filename u fit_photon_no:(rho_d(column(p_refl_flou))*y_stretch):fit_photon_err:(rho_d(column(p_refl_flou_err))*y_stretch) w xyerror t 'Exponential pulse 5ns' ls 3
set label 1 '250 ns'
plot square.'250ns/'.filename8 u (column(photon_no)):(rho_d8(column(p_refl_flou))*y_stretch):photon_err:(rho_d8(column(p_refl_flou_err))*y_stretch) w xyerror t 'Square pulse 5ns' ls 1,\
     exp.'250ns/'.filename8 u photon_no:(rho_d8(column(p_refl_flou))*y_stretch):photon_err:(rho_d8(column(p_refl_flou_err))*y_stretch) w xyerror t 'Exponential pulse 5ns' ls 2,\
     '../theory_plots/raw_data/evss_pt0_n/pt0_003_250.txt' u 1:2 w l lw 2 t '',\
     '../theory_plots/raw_data/evss_pt0_n/pt0_003_250.txt' u 1:3 w l lc 1 lw 2 t ''

#exp.'250ns/'.filename u fit_photon_no:(rho_d(column(p_refl_flou))*y_stretch):fit_photon_err:(rho_d(column(p_refl_flou_err))*y_stretch) w xyerror t 'Exponential pulse 5ns' ls 3

unset multiplot
set term wxt
#!gv '../rho22_flou_vs_n.eps' &


# #### Plotting stuff vs average photon number, for optimal bandwidths

y_stretch=1e0
unset label 1
set yrange [0:]
set xlabel 'N' font 'Helvetica, 20'
set ylabel 'P_{e,max}' font 'Helvetica, 20'
set xtics font 'Helvetica, 20'
set ytics font 'Helvetica, 20'
unset key
set key at 200,0.24 font 'Helvetica, 16'
set terminal postscript enhanced color eps
set output '../rho22_max_optimal_bandwidth.eps'
#set multiplot layout 2,2

#set label 1 'a) Max {/Symbol r}_{22}' at graph 0.05,0.90
plot square.'20ns/'.filename u (column(photon_no)):(rho(column(max_p_refl))*y_stretch):photon_err:(rho(column(max_p_refl_err))*y_stretch) w xyerror axes x1y1 t 'Square pulse 20 ns' ls 1,\
      exp.'15ns/'.filename u (column(photon_no)):(rho(column(max_p_refl))*y_stretch):photon_err:(rho(column(max_p_refl_err))*y_stretch) axes x1y1 w xyerror t 'Exponential pulse 15 ns' ls 2 

set output '../rho22_flou_optimal_bandwidth.eps'
set ylabel '{/Symbol=20 \362@_{/=9 0}^{/=12 \245}}{/Symbol r}_{22}(t){/Symbol t}'
# set label 1 'b) {/Symbol r}_{22}P flourescence'
 plot square.'20ns/'.filename u (column(photon_no)):(rho_d(column(p_refl_flou))*y_stretch):photon_err:(rho_d(column(p_refl_flou_err))*y_stretch) w xyerror t 'Square pulse 5ns' ls 1,\
      exp.'15ns/'.filename u photon_no:(rho_d(column(p_refl_flou))*y_stretch):photon_err:(rho_d(column(p_refl_flou_err))*y_stretch) w xyerror t 'Exponential pulse 5ns' ls 2


# set label 1 'c) P scattering'
# plot square.'20ns/'.filename u (column(photon_no)):(column(p_refl_scat)*y_stretch):photon_err:(column(p_refl_scat_err)*y_stretch) w xyerror t 'Square pulse 5ns' ls 1,\
#      exp.'15ns/'.filename u photon_no:(column(p_refl_scat)*y_stretch):photon_err:(column(p_refl_scat_err)*y_stretch) w xyerror t 'Exponential pulse 5ns' ls 2


# set label 1 'd) P combined'
# plot square.'20ns/'.filename u photon_no:((column(p_refl_scat)+column(p_refl_flou))*y_stretch):photon_err:((column(p_refl_scat_err)+column(p_refl_flou_err))*y_stretch) w  xyerror ls 1,\
#      exp.'15ns/'.filename u photon_no:((column(p_refl_scat)+column(p_refl_flou))*y_stretch):photon_err:((column(p_refl_scat_err)+column(p_refl_flou_err))*y_stretch) w  xyerror ls 2


#unset multiplot
unset output

set term wxt

cd currentdir