;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 new_xy_offsets_cn_depth,Date=Date,stats_directory=stats_directory,$
	x_center_file=x_center_file,y_center_file=y_center_file,$
	depth=depth


If (not keyword_set(Date)) then Date='10'
If (not keyword_set(stats_directory)) then stats_directory='stats_temp'
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=2
If (not keyword_set(postscript_dir)) then postscript_dir='postscripts'

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+'/'

;ARRAYS OF FILES
offset_files=file_search(stats_directory+'*5132*offsets.txt',count=num_stats_files)

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

;ARRAY REFERENCE 25x25=625 FOR GRID
subx=2*indgen(num)-25           ;The x-reference numbers
suby=indgen(num)-12             ;The y-reference numbers

;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 -1,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 -1) and $
		    (x_offset_hor(file_number+time,spot_index+spacing) ne -1) $
		    then begin

		    Cxl_arr(spot_index)=x_offset_hor(file_number,spot_index)*$
		    x_offset_hor(file_number+time,spot_index+spacing)
		    Cxt_arr(spot_index)=y_offset_hor(file_number,spot_index)*$
                    y_offset_hor(file_number+time,spot_index+spacing)
		    ;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)=0
		Cxt(spacing,time)=0
	   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 -1) and $
                   (y_offset_ver(file_number+time,spot_index+spacing) ne -1) $
		   then begin

                   Cyl_arr(spot_index)=y_offset_ver(file_number,spot_index)*$
                   y_offset_ver(file_number+time,spot_index+spacing)
                   Cyt_arr(spot_index)=x_offset_ver(file_number,spot_index)*$
                   x_offset_ver(file_number+time,spot_index+spacing)
                   ;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)=0
                 Cyt(spacing,time)=0
            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 n=0, num-1 do begin
	for m=0, depth-1 do begin

	Cxt_means(n,m)=mean(Cxt_full(*,n,m))
	Cxl_means(n,m)=mean(Cxl_full(*,n,m))
	Cyl_means(n,m)=mean(Cyl_full(*,n,m))
	Cyt_means(n,m)=mean(Cyt_full(*,n,m))

	endfor
endfor

set_plot,'ps'
device,filename=Postscript_dir+'new_cn_time'+string(strtrim(depth,2))+'.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=1.2
!P.THICK=4.

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

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]

;*************FIRST PLOT
plot,Cxt_means(*,0),psym=1,title="Transverse correlation along X direction",$
               xtitle="n",ytitle="Covariance",$
               background=white,color=black,$
               yrange=[min(Cxt_means(*,0))-.5,max(Cxt_means(*,0))+.5],$
               POSITION=[0.10,0.10,0.9,0.9]

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

for i=1,depth-1 do begin

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

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

;*************SECOND PLOT
plot,(Cxt_means(*,0)-Cxt_means(*,depth-1)),psym=1,$
	       title="Transverse correlation along X direction for t=0-t="+$
	       strtrim(string(depth*7),2)+' seconds',$
               xtitle="n",ytitle="Covariance",$
               background=white,color=black,$
               yrange=[0,2],$
               POSITION=[0.10,0.10,0.9,0.9]

oplot,findgen(num-1)+1,(findgen(num-1)+1)^(-7./32.),psym=0,color=black,$
        linestyle=1
oplot,findgen(num-1)+1,(findgen(num-1)+1)^(-13./64.),psym=0,color=black,$
        linestyle=2
oplot,findgen(num-1)+1,(findgen(num-1)+1)^(-27./128.),psym=0,color=black,$
	linestyle=3

legend,items_k_tran,linestyle=line_k_tran,position=[.6,.8],/normal

;***************THIRD PLOT
plot,Cxl_means(*,0),psym=1,title="Longitudinal correlation along X direction",$
               xtitle="n",ytitle="Covariance (Pixels Squared)",$
               background=white,color=black,$
               yrange=[min(Cxl_means(*,0))-.5,max(Cxl_means(*,0))+.5],$
               POSITION=[0.10,0.10,0.9,0.9]

for i=1,depth-1 do begin
	
        oplot,Cxl_means(*,i),psym=i+1
	
endfor

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

;**************FOURTH PLOT
plot,(Cxl_means(*,0)-Cxl_means(*,depth-1)),psym=1,$
               title="Longitudinal correlation along X direction for t=0-t="+$
               strtrim(string(depth*7),2)+' seconds',$
               xtitle="n",ytitle="Covariance",$
               background=white,color=black,$
               yrange=[0,max(Cxl_means(*,0)-Cxl_means(*,depth-1))+.5],$
               POSITION=[0.10,0.10,0.9,0.9]

oplot,findgen(num-1)+1,(findgen(num-1)+1)^(-1./3.),psym=0,color=black

legend,items_k_lon,linestyle=line_k_lon,position=[.6,.8],/normal


;**************FIFTH PLOT
plot,Cyt_means(*,0),psym=1,title="Transverse correlation along Y direction",$
               xtitle="n",ytitle="Covariance (Pixels Squared)",$
               background=white,color=black,$
               yrange=[min(Cyt_means(*,0))-.5,max(Cyt_means(*,0))+.5],$
               POSITION=[0.10,0.10,0.9,0.9]

for i=1,depth-1 do begin

        oplot,Cyt_means(*,i),psym=i+1

endfor

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

;***************SIXTH PLOT
plot,(Cyt_means(*,0)-Cyt_means(*,depth-1)),psym=1,$
               title="Transverse correlation along Y direction for t=0-t="+$
               strtrim(string(depth*7),2)+' seconds',$
               xtitle="n",ytitle="Covariance",$
               background=white,color=black,$
               yrange=[min(Cyt_means(*,0)-Cyt_means(*,depth-1))-.5,$
                       max(Cyt_means(*,0)-Cyt_means(*,depth-1))+.5],$
               POSITION=[0.10,0.10,0.9,0.9]

oplot,findgen(num-1)+1,(findgen(num-1)+1)^(-7./32.),psym=0,color=black,$
        linestyle=1
oplot,findgen(num-1)+1,(findgen(num-1)+1)^(-13./64.),psym=0,color=black,$
        linestyle=2
oplot,findgen(num-1)+1,(findgen(num-1)+1)^(-27./128.),psym=0,color=black,$
        linestyle=3                                                                        
legend,items_k_tran,linestyle=line_k_tran,position=[.6,.8],/normal

;***************SEVENTH PLOT
plot,Cyl_means(*,0),psym=1,title="Longitudinal correlation along Y direction",$
               xtitle="n",ytitle="Covariance (Pixels Squared)",$
               background=white,color=black,$
               yrange=[min(Cyl_means(*,0))-.5,max(Cyl_means(*,0))+.5],$
               POSITION=[0.10,0.10,0.9,0.9]

for i=1,depth-1 do begin

        oplot,Cyl_means(*,i),psym=i+1

endfor

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

;***************EIGTH PLOT
plot,(Cyl_means(*,0)-Cyl_means(*,depth-1)),psym=1,$
               title="Longitudinal correlation along Y direction for t=0-t="+$
               strtrim(string(depth*7),2)+' seconds',$
               xtitle="n",ytitle="Covariance",$
               background=white,color=black,$
               yrange=[0,max(Cyl_means(*,0)-Cyl_means(*,depth-1))+.5],$
               POSITION=[0.10,0.10,0.9,0.9]

oplot,findgen(num-1)+1,(findgen(num-1)+1)^(-1./3.),psym=0,color=black

legend,items_k_lon,linestyle=line_k_lon,position=[.6,.8],/normal


device,/close
set_plot,'X'



end

