#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>'
set ylabel 'Max {/Symbol r}_{22}'
set terminal postscript enhanced color eps
set output '../rho22_max_p_vs_n.eps'
unset key
unset label
set multiplot layout 2,2
set label 1 'a)' 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 pulse 5ns' 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 'Exponential pulse 5ns' ls 2 
set label 1 'b)'

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 pulse 15ns' 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 15ns' ls 2
set label 1 'c)'

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 pulse 60ns' 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 'Exponential pulse 60ns' ls 2
set label 1 'd)'

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 pulse 250ns' 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 'Exponential pulse 250ns' ls 2

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 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 'a)' 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
#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 'b)'
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
#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 'c)'
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
#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 'd)'
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
#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:]
unset key
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
set ylabel 'Max {/Symbol r}_{22} '
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 5ns' 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 5ns' 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