;xy_offsets
;
;PURPOSE:
;	This script will return the difference in coordinates between a 
;	ShackHartman image centroid and the corresponding point on the 
;	reference grid
;
;	Since the center of the grid seems to be drifting 

pro cn_ind_log_depth_variance_avg_sub,Date=Date,stats_directory=stats_directory,$
	x_center_file=x_center_file,y_center_file=y_center_file,$
	depth=depth,x_off=x_off,y_off=y_off


If (not keyword_set(Date)) then Date='10'
If (not keyword_set(stats_directory)) then stats_directory='stats'
If (not keyword_set(x_center_file)) then x_center_file='x_centers.txt'
If (not keyword_set(y_center_file)) then y_center_file='y_centers.txt'
If (not keyword_set(depth)) then depth=1
If (not keyword_set(postscript_dir)) then postscript_dir='postscripts'
If (not keyword_set(x_off)) then x_off=0
If (not keyword_set(y_off)) then y_off=0

if Date eq '10' then begin
  letter=['hr5132a','hr5132b','hr5132c','hr5132d','hr5132e','hr5132f',$
          'hr5132g','hr5132h','hr5132i']
endif else if Date eq '11' then begin
  letter=['h5132g','h5132h','h5132i','hr5132a','hr5132b','hr5132c','hr5132d',$
          'hr5132e','hr5132f','hr5132g','hr5132h']
endif else if Date eq '12' then begin
  letter=['hr5132a','hr5132b','hr5132c','hr5132d','hr5132e','hr5132f',$
           'hr5132g','hr5132h','hr5132i']
endif

stats_directory='/a/pippin01/Volumes/u08/lsst/CPanalysis/2005-05-'+Date+$
	  '/ShackHartman/'+stats_directory+'/'
postscript_dir='/a/pippin01/Volumes/u08/lsst/CPanalysis/2005-05-'+Date+$
          '/ShackHartman/'+postscript_dir+'/'
Cor_directory='/a/pippin01/Volumes/u08/lsst/CPanalysis/2005-05-'+Date+$
          '/ShackHartman/correlations/'

;ARRAYS OF FILES
average_offset_file=stats_directory+'average_offsets.txt'
readcol,average_offset_file,x_off_avg,y_off_avg,format='x,f,f,'

;CONSTANTS
num=25
grid_spots=625
index=findgen(625)

set_plot,'ps'
device,filename=Postscript_dir+'Log_depth_individual'+string(strtrim(depth,2))+'_cn_5_'+Date+'_05.ps'
                                                                                    
loadct,39                       ;load color table 39
device,/color                   ;allow color on the postscript
device,ysize=8.5,/inches        ;Height of plot in y
device,xsize=10.0,/inches        ;Width of plot in x
device,yoffset=1.0,/inches      ;Y position of lower left corner
                                                                                    
white='FFFFFF'x
black='000000'x
!P.CHARSIZE=.7
!P.THICK=4.
                                                                                    
items_time=['t=0']
sym_time=[1]
items_k_tran=['Data Points','n!e-7/32!n','n!e-13/64!n','n!e-27/128!n']
sym_k_tran=[1,0,0,0]
line_k_tran=[0,1,2,3]
items_k_lon=['Data Points','n!e-1/3!n']
sym_k_long=[0,1]
colors_time=[0]


for j=0, N_elements(letter)-1 do begin
                                                                                
                                                                                
offset_files=file_search(stats_directory+letter(j)+'*offsets.txt',count=num_stats_files)

;HUGE DATA CUBE
x_offset_hor=fltarr(num_stats_files,grid_spots)
y_offset_hor=fltarr(num_stats_files,grid_spots)
x_offset_ver=fltarr(num_stats_files,grid_spots)
y_offset_ver=fltarr(num_stats_files,grid_spots)

;Correlations
Cxt_full=fltarr(num_stats_files,num,depth)
Cxl_full=fltarr(num_stats_files,num,depth)
Cyt_full=fltarr(num_stats_files,num,depth)
Cyl_full=fltarr(num_stats_files,num,depth)


;FILL THE DATA CUBES
for file_number=0,num_stats_files-1 do begin

	;Take the results from the offset.txt files and fill the cube
	readcol,offset_files(file_number),x_offset,y_offset,format='X,X,f,X,f'
	not_fitted=where(x_offset eq -10,complement=fitted)
	
	;Obtain the difference ordered in COLUMN, ROW between centroid and grid 	point
	x_offset_hor(file_number,*)=x_offset
	y_offset_hor(file_number,*)=y_offset

	;Obtain the difference ordered in ROW, COLUMN
	x_offset_ver(file_number,*)=x_offset((index mod 25)*25+index/25)
	y_offset_ver(file_number,*)=y_offset((index mod 25)*25+index/25)
	
endfor
	
;DATA CUBEs are now in place. Begin the covariance

;Loop through all of the files in the 
for file_number=0,num_stats_files-depth do begin

  ;CORRELATIONS
  Cxl=fltarr(num,depth)
  Cxt=fltarr(num,depth)
  Cyl=fltarr(num,depth)
  Cyt=fltarr(num,depth)

     for time=0, depth-1 do begin

	for spacing=0, num-1 do begin
	
	  Cxl_arr=fltarr(num*num)
       	  Cxt_arr=fltarr(num*num)
	  Cyl_arr=fltarr(num*num)
	  Cyt_arr=fltarr(num*num)

	  ;SCAN FIRST ALONG THE ROWS
	
	  for column_index=0, num-1 do begin
	     for row_index=0, num -1 do begin
		 spot_index=column_index*num+row_index
			
		 ;If we have reached the edge, start on the next row
		 If (row_index+spacing) ge num then break
		 ;Check to see if both have valid values
		 If (x_offset_hor(file_number,spot_index) ne -10) and $
		    (x_offset_hor(file_number+time,spot_index+spacing) ne -10) $
		    then begin
		    ;add offset in to tweek the plots
		    Cxl_arr(spot_index)=(x_offset_hor(file_number,spot_index)+x_off)*$
		    (x_offset_hor(file_number+time,spot_index+spacing)+x_off)
		    Cxt_arr(spot_index)=(y_offset_hor(file_number,spot_index)+y_off)*$
                    (y_offset_hor(file_number+time,spot_index+spacing)+y_off)
		    ;print,FORMAT='(%"%i\t%i\t")',spot_index,spot_index+spacing
	
		 endif

	      endfor
	   endfor
		
	   correlated=where(Cxl_arr ne 0)
	   If correlated(0) ne -1 then begin
		Cxl(spacing,time)=mean(Cxl_arr(correlated))
		Cxt(spacing,time)=mean(Cxt_arr(correlated))
	   endif else begin
		Cxl(spacing,time)=-10
		Cxt(spacing,time)=-10
	   endelse
		
	   ;printf,xcor,FORMAT='(%"%f\t%f\t%i")',Cxl(spacing-1),Cxt(spacing-1),N_elements(correlated)
		
	
           ;SCAN SECOND ALONG Y

           for column_index=0, num-1 do begin
               for row_index=0, num -1 do begin
                   spot_index=column_index*num+row_index
	
        	   ;If we have reached the edge, start on the next row
                   If (row_index+spacing) ge num then break
                   ;Check to see if both have valid values
                   If (y_offset_ver(file_number,spot_index) ne -10) and $
                   (y_offset_ver(file_number+time,spot_index+spacing) ne -10) $
		   then begin

                   Cyl_arr(spot_index)=(y_offset_ver(file_number,spot_index)+y_off)*$
                   (y_offset_ver(file_number+time,spot_index+spacing)+y_off)
                   Cyt_arr(spot_index)=(x_offset_ver(file_number,spot_index)+x_off)*$
                   (x_offset_ver(file_number+time,spot_index+spacing)+x_off)
                   ;print,FORMAT='(%"%i\t%i\t")',spot_index,spot_index+spacing

          	   endif

                   endfor
            endfor

            correlated=where(Cyl_arr ne 0)
            If correlated(0) ne -1 then begin
                 Cyl(spacing,time)=mean(Cyl_arr(correlated))
                 Cyt(spacing,time)=mean(Cyt_arr(correlated))
            endif else begin
                 Cyl(spacing,time)=-10
                 Cyt(spacing,time)=-10
            endelse

            ;printf,ycor,FORMAT='(%"%f\t%f\t%i")',Cyl(spacing-1),Cyt(spacing-1),N_elements(correlated)

     	  endfor
	
	endfor	
	;partvelvec,x_offset(fitted),y_offset(fitted),gridx(fitted),$
	;	gridy(fitted),yrange=[150,800],xrange=[200,850]

	;close,xcor
	;free_lun,xcor		
	;close,ycor
	;free_lun,ycor
	
	Cxt_full(file_number,*,*)=Cxt
	Cxl_full(file_number,*,*)=Cxl
	Cyt_full(file_number,*,*)=Cyt
	Cyl_full(file_number,*,*)=Cyl


endfor	
		

Cxt_means=fltarr(num,depth)
Cxl_means=fltarr(num,depth)
Cyt_means=fltarr(num,depth)
Cyl_means=fltarr(num,depth)

for m=0, depth-1 do begin
	
   get_lun,correlations
   openw,correlations,stats_directory+'Depth_ind_hr5132'+letter(j)+string(strtrim(m,2))+'Correlations.ps'
   printf,correlations,$
   FORMAT='(%"%s\t%s\t%s\t%s")','Long. X Cor.','Trans. X Cor.','Long. Y Cor.','Trans. Y Cor'

   for n=0, num-1 do begin
	
	not_inc_cxt=where(Cxt_full(*,n,m) eq -10,complement=inc_cxt)
        Cxt_means(n,m)=mean(Cxt_full(inc_cxt,n,m))
        not_inc_cxl=where(cxl_full(*,n,m) eq -10,complement=inc_cxl)
        Cxl_means(n,m)=mean(Cxl_full(inc_cxl,n,m))
        not_inc_cyl=where(Cyl_full(*,n,m) eq -10,complement=inc_cyl)
        Cyl_means(n,m)=mean(Cyl_full(inc_cyl,n,m))
        not_inc_cyt=where(Cyt_full(*,n,m) eq -10,complement=inc_cyt)
        Cyt_means(n,m)=mean(Cyt_full(inc_cyt,n,m))
	printf,correlations,FORMAT='(%"%f\t%f\t%f\t%f")',$
	                    Cxl_means(n,m),Cxt_means(n,m),Cyl_means(n,m),Cyt_means(n,m)
	
   endfor
   close,correlations
   free_lun,correlations

endfor


;*************FIRST PLOT
!P.multi=[0,1,1]

plot,Cxt_means(*,0),psym=1,title="Transverse correlation along X direction"+$
	       letter(j),$
               xtitle="n",ytitle="Covariance",$
               background=white,color=black,$
               yrange=[1e-3,1e1],$
               POSITION=[0.10,0.10,0.9,0.9],/ylog

;Over Plot the various separations in time and also generate legends

for i=1,depth-1 do begin

        oplot,Cxt_means(*,i),psym=1,color=20*i
        sym_time=[sym_time,1]
        items_time=[items_time,string(strtrim(i*7,2))+' seconds']
        colors_time=[colors_time,20*i]

endfor

legend,items_time,psym=sym_time,position=[.7,.8],colors=colors_time,/normal


!p.multi=[0,1,1]
;***************FIFTH PLOT
plot,Cxl_means(*,0),psym=1,title="Longitudinal correlation along X direction"+$
               letter(j),$
	       xtitle="n",ytitle="Covariance (Pixels Squared)",$
               background=white,color=black,$
               yrange=[1e-3,1e1],$
               POSITION=[0.10,0.10,0.9,0.9],/ylog

for i=1,depth-1 do begin

        oplot,Cxl_means(*,i),psym=1,color=20*i

endfor

legend,items_time,psym=sym_time,position=[.2,.4],/normal,colors=colors_time

!P.multi=[0,1,1]

;**************NINTH PLOT
plot,Cyt_means(*,0),psym=1,title="Transverse correlation along Y direction"+$
               letter(j),$
	       xtitle="n",ytitle="Covariance (Pixels Squared)",$
               background=white,color=black,$
               yrange=[1e-3,1e1],$
               POSITION=[0.10,0.10,0.9,0.9],/ylog

for i=1,depth-1 do begin

        oplot,Cyt_means(*,i),psym=1,color=20*i

endfor

legend,items_time,psym=sym_time,position=[.6,.8],/normal,colors=colors_time

;***************THIRTEENTH PLOT
!p.multi=[0,1,1]

plot,Cyl_means(*,0),psym=1,title="Longitudinal correlation along Y direction"+$
	       letter(j),$
               xtitle="n",ytitle="Covariance (Pixels Squared)",$
               background=white,color=black,$
               yrange=[1e-3,1e1],$
               POSITION=[0.10,0.10,0.9,0.9],/ylog

for i=1,depth-1 do begin

        oplot,Cyl_means(*,i),psym=1,color=20*i

endfor

legend,items_time,psym=sym_time,position=[.6,.8],/normal,colors=colors_time

endfor

device,/close
set_plot,'X'

end