#set multiplot layout 2,1

filename="processed_histogram_with_yerror_bars/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

#### 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:*]
y_stretch=1e4
set xrange [1:1e4]
set xlabel '<n>'
set ylabel 'Max P_{detector click} (10^{-4})'
set terminal postscript enhanced color eps
set output '../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)):(column(max_p_refl)*y_stretch):photon_err:(column(max_p_refl_err)*y_stretch) w xyerror axes x1y1 t 'Square pulse 5ns' ls 1,\
     exp.'5ns/'.filename u (column(photon_no)):(column(max_p_refl)*y_stretch):photon_err:(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)):(column(max_p_refl)*y_stretch):photon_err:(column(max_p_refl_err)*y_stretch) w xyerror axes x1y1 t 'Square pulse 15ns' ls 1,\
     exp.'15ns/'.filename u (column(photon_no)):(column(max_p_refl)*y_stretch):photon_err:(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)):(column(max_p_refl)*y_stretch):photon_err:(column(max_p_refl_err)*y_stretch) w xyerror axes x1y1 t 'Square pulse 60ns' ls 1,\
     exp.'60ns/'.filename u (column(photon_no)):(column(max_p_refl)*y_stretch):photon_err:(column(max_p_refl_err)*y_stretch) axes x1y1 w xyerror t 'Exponential pulse 60ns' ls 2
set label 1 'd)'

plot square.'250ns/'.filename u (column(photon_no)):(column(max_p_refl)*y_stretch):photon_err:(column(max_p_refl_err)*y_stretch) w xyerror axes x1y1 t 'Square pulse 250ns' ls 1 ,\
     exp.'250ns/'.filename u (column(photon_no)):(column(max_p_refl)*y_stretch):photon_err:(column(max_p_refl_err)*y_stretch) axes x1y1 w xyerror t 'Exponential pulse 250ns' ls 2

unset multiplot
#!gv 'max_p_vs_n.eps' &

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

y_stretch=1e3
set ylabel 'P_{detector click} (10^{-3})'
set xrange [1:]
set yrange [0:*]
unset key
set terminal postscript enhanced color eps
set output '../p_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)):(column(p_refl_flou)*y_stretch):photon_err:(column(p_refl_flou_err)*y_stretch) w xyerror t 'Square pulse 5ns' ls 1,\
     exp.'5ns/'.filename u photon_no:(column(p_refl_flou)*y_stretch):photon_err:(column(p_refl_flou_err)*y_stretch) w xyerror t 'Exponential pulse 5ns' ls 2
#exp.'5ns/'.filename u fit_photon_no:(column(p_refl_flou)*y_stretch):fit_photon_err:(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)):(column(p_refl_flou)*y_stretch):photon_err:(column(p_refl_flou_err)*y_stretch) w xyerror t 'Square pulse 5ns' ls 1,\
     exp.'15ns/'.filename u photon_no:(column(p_refl_flou)*y_stretch):photon_err:(column(p_refl_flou_err)*y_stretch) w xyerror t 'Exponential pulse 5ns' ls 2
#exp.'15ns/'.filename u fit_photon_no:(column(p_refl_flou)*y_stretch):fit_photon_err:(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)):(column(p_refl_flou)*y_stretch):photon_err:(column(p_refl_flou_err)*y_stretch) w xyerror t 'Square pulse 5ns' ls 1,\
     exp.'60ns/'.filename u photon_no:(column(p_refl_flou)*y_stretch):photon_err:(column(p_refl_flou_err)*y_stretch) w xyerror t 'Exponential pulse 5ns' ls 2
#exp.'60ns/'.filename u fit_photon_no:(column(p_refl_flou)*y_stretch):fit_photon_err:(column(p_refl_flou_err)*y_stretch) w xyerror t 'Exponential pulse 5ns' ls 3
set label 1 'd)'
plot square.'250ns/'.filename u (column(photon_no)):(column(p_refl_flou)*y_stretch):photon_err:(column(p_refl_flou_err)*y_stretch) w xyerror t 'Square pulse 5ns' ls 1,\
     exp.'250ns/'.filename u photon_no:(column(p_refl_flou)*y_stretch):photon_err:(column(p_refl_flou_err)*y_stretch) w xyerror t 'Exponential pulse 5ns' ls 2
#exp.'250ns/'.filename u fit_photon_no:(column(p_refl_flou)*y_stretch):fit_photon_err:(column(p_refl_flou_err)*y_stretch) w xyerror t 'Exponential pulse 5ns' ls 3

unset multiplot
#!gv 'p_flou_vs_n.eps' &

# #### Plotting total probability of detector click from scattering vs average photon number

y_stretch=1e3
set ylabel 'P_{detector click} (10^{-3})'
set yrange [0:*]
unset key
set terminal postscript enhanced color eps
set output '../p_scat_vs_n.eps'
set multiplot layout 2,2
set label 1 'a)'
plot square.'5ns/'.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.'5ns/'.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
#exp.'5ns/'.filename u fit_photon_no:(column(p_refl_scat)*y_stretch):fit_photon_err:(column(p_refl_scat_err)*y_stretch) w xyerror t 'Exponential pulse 5ns' ls 3
set label 1 'b)'
plot square.'15ns/'.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
#exp.'15ns/'.filename u fit_photon_no:(column(p_refl_scat)*y_stretch):fit_photon_err:(column(p_refl_scat_err)*y_stretch) w xyerror t 'Exponential pulse 5ns' ls 3
set label 1 'c)'
plot square.'60ns/'.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.'60ns/'.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
#exp.'60ns/'.filename u fit_photon_no:(column(p_refl_scat)*y_stretch):fit_photon_err:(column(p_refl_scat_err)*y_stretch) w xyerror t 'Exponential pulse 5ns' ls 3
set label 1 'd)'
plot square.'250ns/'.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.'250ns/'.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
#exp.'250ns/'.filename u fit_photon_no:(column(p_refl_scat)*y_stretch):fit_photon_err:(column(p_refl_scat_err)*y_stretch) w xyerror t 'Exponential pulse 5ns' ls 3

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

# #### Plotting total probability of detector click (scattering and flourescence) vs average photon number

y_stretch=1e3
set ylabel 'P_{detector click} (10^{-3})'
#set yrange [0:]
unset key
set terminal postscript enhanced color eps
set output '../p_total_vs_n.eps'
set multiplot layout 2,2
set label 1 'a)'
plot square.'5ns/'.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.'5ns/'.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

set label 1 'b)'
plot square.'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 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

set label 1 'c)'
plot square.'60ns/'.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.'60ns/'.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

set label 1 'd)'
plot square.'250ns/'.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.'250ns/'.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
#!gv 'p_total_vs_n.eps' &

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

y_stretch=1e3
set ylabel 'P_{detector click} (10^{-3})'
#set yrange [0:]
unset key
set terminal postscript enhanced color eps
set output '../optimal_bandwidths.eps'
set multiplot layout 2,2

set label 1 'a) Max P' at graph 0.05,0.90
plot square.'20ns/'.filename u (column(photon_no)):(column(max_p_refl)*y_stretch):photon_err:(column(max_p_refl_err)*y_stretch) w xyerror axes x1y1 t 'Square pulse 5ns' ls 1,\
     exp.'15ns/'.filename u (column(photon_no)):(column(max_p_refl)*y_stretch):photon_err:(column(max_p_refl_err)*y_stretch) axes x1y1 w xyerror t 'Exponential pulse 5ns' ls 2 


 set label 1 'b) P flourescence'
 plot square.'20ns/'.filename u (column(photon_no)):(column(p_refl_flou)*y_stretch):photon_err:(column(p_refl_flou_err)*y_stretch) w xyerror t 'Square pulse 5ns' ls 1,\
      exp.'15ns/'.filename u photon_no:(column(p_refl_flou)*y_stretch):photon_err:(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