; --- run .r prep_data if needed


;;IDL> tv, bytscl(scans[36,10,600:*,400:*],min=2000,max=3500)  
;;IDL> mycursor,/log,/rename,file='Rscan36',/cross, xstart=600,ystart=400


;;RESTORE,'/data3/2023sep07/aligned_results/vissr-aligned-xu.sav'
aprof=RF(averprof[0,*])

SET_PLOT,'X'
LOADCT, 0, /SILENT
CIRCLE, /FILL

pPos=[0.13,0.13,0.96,0.96]
xW=pPos[2]-pPos[0]
yW=pPos[3]-pPos[1]

figDir='~/article/2024/rbe_profiles/fig_profiles/1373-1069/'

padding=100

fname='/data3/2023sep07/aligned_results/1373-1069-scan38.log'
iWL=2 & wl='hab080' & tvSc=1.0
;---iWL=3 & wl='hab060' & tvSc=0.8
;---iWL=8 & wl='har040' & tvSc=0.6
;iWL=9 & wl='har060' & tvSc=0.9
iWL=10 & wl='har080' & tvSc=1.1
scStart=-2 & scStop=+1 & spPt=0 ; it will change to 2 further in the code

xy=READ_TABLE(fname)

; --- xy=REVERSE(xy,2)

pos1=STRPOS(fname,'scan',0)
pos2=STRPOS(fname,'.log',0)

scanC=STRMID(fname,pos1+4,pos2-pos1-4)
scanN=FIX(scanC)
;;print, scanN

fileTemp=FILE_BASENAME(fname,'.log')

dim=SIZE(xy,/DIM)
nPts=dim[1]
IF dim[0] EQ 3 THEN xy=xy[0:1,*]
dim=SIZE(xy,/DIM)
nPts=dim[1]

tmpImgb=REFORM(scans[scanN,2,MIN(xy[0,*])-padding:MAX(xy[0,*])+padding,MIN(xy[1,*])-padding:MAX(xy[1,*])+padding])
tmpImgr=REFORM(scans[scanN,10,MIN(xy[0,*])-padding:MAX(xy[0,*])+padding,MIN(xy[1,*])-padding:MAX(xy[1,*])+padding])

dimImgb=SIZE(tmpImgb,/DIM)
dx=dimImgb[0]
dy=dimImgb[1]

SET_PLOT,'X'
WINDOW, 0, XS=2*dx, YS=dy, /PIXMAP

TV, BYTSCL(tmpImgb,min=1700,max=3500),0,0
TV, BYTSCL(tmpImgr,min=1700,max=3500),dx,0

LOADCT, 3, /SILENT
PLOTS,xy[0,*]-min(xy[0,*])+padding,xy[1,*]-min(xy[1,*])+padding,/DEVICE, PSYM=8, SYMSIZE=0.3, COLOR=170
PLOTS,xy[0,0]-min(xy[0,*])+padding,xy[1,0]-min(xy[1,*])+padding,/DEVICE, PSYM=8, SYMSIZE=0.6, COLOR=170

PLOTS,xy[0,*]-min(xy[0,*])+padding+dx,xy[1,*]-min(xy[1,*])+padding,/DEVICE, PSYM=8, SYMSIZE=0.3, COLOR=170
PLOTS,xy[0,0]-min(xy[0,*])+padding+dx,xy[1,0]-min(xy[1,*])+padding,/DEVICE, PSYM=8, SYMSIZE=0.6, COLOR=170

;;;X2PNG, filename=figDir+fileTemp+'-image.png',/COLOR

LOADCT, 0

; --- makes a strip plot of all 13 Ha positions
WINDOW, 0, XS=13*dx, YS=dy, /PIXMAP

tvScale=[1.2,1.1,1.0,0.85,0.55,0.45,0.4,0.4,0.6,0.9,1.0,1.1,1.2]

for ii=0, 12 do begin
   tmpImg=REFORM(scans[scanN,ii,MIN(xy[0,*])-padding:MAX(xy[0,*])+padding,MIN(xy[1,*])-padding:MAX(xy[1,*])+padding])

   TV, BYTSCL(tmpImg,min=1700*tvSCale[ii],max=3500*tvScale[ii]),ii*dx,0

   LOADCT, 3, /SILENT
   PLOTS,xy[0,*]-min(xy[0,*])+padding+dx*ii,xy[1,*]-min(xy[1,*])+padding,/DEVICE, PSYM=8, SYMSIZE=0.2, COLOR=170
   ;;PLOTS,xy[0,0]-min(xy[0,*])+padding,xy[1,0]-min(xy[1,*])+padding,/DEVICE, PSYM=8, SYMSIZE=0.6, COLOR=170
   LOADCT, 0
   ;ENDIF
   ENDFOR

X2PNG, filename=figDir+fileTemp+'-all-scan.png',/COLOR






;------------------ -------------------- makes eps images of various wavelengths

IF STRMID(wl,2,1) EQ 'b' THEN wS='-' ELSE Ws='+' 

headLine=STRMID(list[scanN],48,8)+' '+STRMID(list[scanN],57,6)+'UT H!9a!X'+wS+'0.0'+STRMID(wl,4,1)+' nm'
tmpImg=REFORM(scans[scanN,iwl,MIN(xy[0,*])-padding:MAX(xy[0,*])+padding,MIN(xy[1,*])-padding:MAX(xy[1,*])+padding])


nx=(SIZE(tmpImg,/DIM))[0]
ny=(SIZE(tmpImg,/DIM))[1]

SET_PLOT,'X'
iScale=5
tmp=CONGRID(tmpImg,nx*iScale,ny*iScale,/INTER)

save,tmpImg, tmp, filename='ha-image-to-coalign.sav'

WINDOW, XS=nx*iScale, YS=ny*iScale, /PIXMAP
TV, BYTSCL(tmp,min=2000*tvSc,max=3700*tvSc)

LOADCT, 2, /SILENT
tmpPts=N_ELEMENTS(RF(xy[0,*]))
PLOTS,iScale*xy[0,1:tmpPts-2]-iScale*min(xy[0,*])+iScale*padding,iScale*xy[1,1:tmpPts-2]-iScale*min(xy[1,*])+iScale*padding,/DEVICE, PSYM=8, SYMSIZE=2., COLOR=30 ; 2/30 - green, 2/80 - red
PLOTS,iScale*xy[0,tmpPts-1]-iScale*min(xy[0,*])+iScale*padding,iScale*xy[1,tmpPts-1]-iScale*min(xy[1,*])+iScale*padding,/DEVICE, PSYM=8, SYMSIZE=2., COLOR=80 ; 2/30 - green, 2/80 - red
PLOTS,iScale*xy[0,0]-iScale*min(xy[0,*])+iScale*padding,iScale*xy[1,0]-iScale*min(xy[1,*])+iScale*padding,/DEVICE, PSYM=4, SYMSIZE=7.5, THICK=8, COLOR=0 ; 2/30 - green, 2/80 -

LOADCT, 0, /SILENT
tmp=TVRD(/TRUE)

SET_PLOT,'PS'
!P.CHARSIZE=0.5
DEVICE,XS=8, YS=8, filename=figDir+fileTemp+'-'+wl+'.eps',/COLOR, BITS_PER_PIXEL=8, /avantgarde,/book

TV, tmp, /TRUE, pPos[0], pPos[1], XS=xW, YS=yW, /NORM
PLOT, [0,0], [1,1], YR=[0, ny*0.029*0.725], XR=[0,nx*0.029*0.725], YTIT='Mm', XTIT='Mm', $
   POS=pPos,/NORM,/NODATA,/NOERASE,CHARSIZE=1

XYOUTS, 0.13, 4.5, headLine, CHARSIZE=0.9, COLOR=50
XYOUTS, 0.14, 4.51, headLine, CHARSIZE=0.9, COLOR=255
DEVICE, /CLOSE









; --- plots profile evolution at point spPt1
yspline=SPLINE(xscale, aprof, xspline)

pPos=[0.15,0.13,0.95,0.89]
xW=pPos[2]-pPos[0]
yW=pPos[3]-pPos[1]

SET_PLOT,'PS'
!P.CHARSIZE=0.5
DEVICE,XS=8.9, YS=8, filename=figDir+fileTemp+'-evolution-'+EXTENSION(spPt,LENGTH=2)+'.eps',/COLOR, /avantgarde,/book

spShift=0

PLOT, xspline/10., spShift+yspline, YR=[-20, 80], XR=[-0.15,0.15], XS=9, XTIT='nm', $
     LINESTYLE=1, YTIT='Relative Intensity',POS=pPos,CHARSIZE=0.9,THICK=4, /NORM
OPLOT, [-0.15,0.15],[0,0],LINESTYLE=1,THICK=2

AXIS, /XAXIS, XR=[-68.6,68.6],XS=1, CHARSIZE=0.9, xTITLE='km/s' ;this is km/s scale

XYOUTS,-0.01, 70, 'b)', CHARSIZE=0.9, /DATA

LOADCT, 13, /SILENT

contrastArr=FLTARR(scanN+scStart+1,N_ELEMENTS(yspline))

FOR i=scanN+scStart, scanN+scStop DO BEGIN
   nScans=ABS(scStart)+ABS(scStop)+1
   icnt=i-(scanN+scStart)
   color=0+125*(icnt)/FLOAT(nScans-1)
   sp=SPLINE(xscale, REFORM(scans[i,*,xy[0,spPt],xy[1,spPt]])/nKoef[spPt], xspline)

;;;;;;;;;;;;   OPLOT, xspline/10., spShift+yspline-3*i, pSYM=-3, SYMSIZE=0.15, LINESTYLE=1, THICK=1, COLOR=0
   OPLOT, xspline/10., spShift+sp-3*icnt, pSYM=-3, SYMSIZE=0.15, LINESTYLE=0, THICK=4, COLOR=color

   contrastProf=sp-yspline
   contrastArr[icnt,*]=contrastProf
   OPLOT, xspline/10., contrastProf, PSYM=-3, SYMSIZE=2, THICK=4, COLOR=color

   ENDFOR
   DEVICE, /CLOSE

LOADCT, 0, /SILENT


; --- plots profile evolution at point spPt2
SpPt=2
yspline=SPLINE(xscale, aprof, xspline)

pPos=[0.15,0.13,0.95,0.89]
xW=pPos[2]-pPos[0]
yW=pPos[3]-pPos[1]

SET_PLOT,'PS'
!P.CHARSIZE=0.5
DEVICE,XS=8.9, YS=8, filename=figDir+fileTemp+'-evolution-'+EXTENSION(spPt,LENGTH=2)+'.eps',/COLOR, /avantgarde,/book

spShift=0

PLOT, xspline/10., spShift+yspline, YR=[-20, 80], XR=[-0.15,0.15], XS=9, XTIT='nm', $
     LINESTYLE=1, YTIT='Relative Intensity',POS=pPos,CHARSIZE=0.9,THICK=4, /NORM
OPLOT, [-0.15,0.15],[0,0],LINESTYLE=1,THICK=2

AXIS, /XAXIS, XR=[-68.6,68.6],XS=1, CHARSIZE=0.9, xTITLE='km/s' ;this is km/s scale

XYOUTS,-0.01, 70, 'c)', CHARSIZE=0.9, /DATA

LOADCT, 13, /SILENT

contrastArr=FLTARR(scanN+scStart+1,N_ELEMENTS(yspline))

FOR i=scanN+scStart, scanN+scStop DO BEGIN
   nScans=ABS(scStart)+ABS(scStop)+1
   icnt=i-(scanN+scStart)
   color=0+125*(icnt)/FLOAT(nScans-1)
   sp=SPLINE(xscale, REFORM(scans[i,*,xy[0,spPt],xy[1,spPt]])/nKoef[spPt], xspline)

;;;;;;;;;;;;   OPLOT, xspline/10., spShift+yspline-3*i, pSYM=-3, SYMSIZE=0.15, LINESTYLE=1, THICK=1, COLOR=0
   OPLOT, xspline/10., spShift+sp-3*icnt, pSYM=-3, SYMSIZE=0.15, LINESTYLE=0, THICK=4, COLOR=color

   contrastProf=sp-yspline
   contrastArr[icnt,*]=contrastProf
   OPLOT, xspline/10., contrastProf, PSYM=-3, SYMSIZE=2, THICK=4, COLOR=color

   ENDFOR
   DEVICE, /CLOSE

LOADCT, 0, /SILENT






; --- plots profiles along the spine

yspline=SPLINE(xscale, aprof, xspline)
pPos=[0.15,0.13,0.95,0.89]

SET_PLOT,'PS'
!P.CHARSIZE=0.5
DEVICE,XS=8.9, YS=8, filename=figDir+fileTemp+'-profiles.eps',/COLOR, /avantgarde,/book

spShift=0

PLOT, xspline/10., spShift+yspline, YR=[-20, 80], XR=[-0.15,0.15], XS=9, XTIT='nm', $
     LINESTYLE=1, YTIT='Relative Intensity',POS=pPos,CHARSIZE=0.9,THICK=4,/NORM
OPLOT, [-0.15,0.15],[0,0],LINESTYLE=1,THICK=2

AXIS, /XAXIS, XR=[-68.6,68.6],XS=1, CHARSIZE=0.9, xTITLE='km/s' ;this is km/s scale

XYOUTS,-0.01, 70, 'a)', CHARSIZE=0.9, /DATA

LOADCT, 13, /SILENT

contrastArr=FLTARR(nPts,N_ELEMENTS(yspline))

FOR i=0, nPts-1 DO BEGIN
   color=255*i/FLOAT(nPts-1)
   sp=SPLINE(xscale, REFORM(scans[scanN,*,xy[0,i],xy[1,i]])/nKoef[i], xspline)

;;;;;;;;;;;;   OPLOT, xspline/10., spShift+yspline-3*i, pSYM=-3, SYMSIZE=0.15, LINESTYLE=1, THICK=1, COLOR=0
   OPLOT, xspline/10., spShift+sp-3*i, pSYM=-3, SYMSIZE=0.15, LINESTYLE=0, THICK=4, COLOR=color

   contrastProf=sp-yspline
   contrastArr[i,*]=contrastProf
   OPLOT, xspline/10., contrastProf, PSYM=-3, SYMSIZE=2, THICK=4, COLOR=color

   ENDFOR
   DEVICE, /CLOSE

LOADCT, 0, /SILENT


; --- plots doppler and deapth of contrast profiles
pPos=[0.15,0.13,0.95,0.89]

DEVICE,XS=8.9, YS=8, filename=figDir+fileTemp+'-contrast.eps',/COLOR, /avantgarde,/book

cogBlue=FLTARR(nPts)
cogRed=FLTARR(nPts)
maxBlue=FLTARR(nPts)
maxRed=FLTARR(nPts)
areaBlue=FLTARR(nPts)
areaRed=FLTARR(nPts)

FOR i=0, nPts-1 DO BEGIN
 
      tmp1=xspline[0:12] & tmp2=REFORM(contrastArr[i,0:12])
      ind=WHERE(tmp2 LT 0)
      IF TOTAL(ind) GT 0 THEN BEGIN
      areaBlue[i]=TOTAL(tmp2[ind])
      cogBlue[i]=TOTAL(tmp2[ind]*tmp1[ind])/areaBlue[i]
         ENDIF ELSE BEGIN
                  areaBlue[i]=0
                  cogBlue[i]=0
                  ENDELSE      
      tmp1=xspline[12:24] & tmp2=REFORM(contrastArr[i,12:24])
      ind=WHERE(tmp2 LT 0)

      IF TOTAL(ind) GT 0 THEN BEGIN
         areaRed[i]=TOTAL(tmp2[ind])
         cogRed[i]=TOTAL(tmp2[ind]*tmp1[ind])/areaRed[i]
         ENDIF ELSE BEGIN
                  areaRed[i]=0
                  cogRed[i]=0
                  ENDELSE

   ENDFOR

CIRCLE, /FILL

imgNum=FINDGEN(nPts)+1

PLOT, cogBlue/10, imgNum, XTIT='!9l!X!Dcog!N, nm', LINESTYLE=0, PSYM=-5, YTIT='Data Point Number along the Spine', $
      POS=pPos,/NORM, YR=[0.9,MAX(imgNum)+0.1],YS=1,XR=[-0.2,0.2],XS=9,CHARSIZE=0.9,/NODATA

AXIS, /XAXIS, XR=[-91.5,91.5],XS=1,XMINOR=5, CHARSIZE=0.9, xTITLE='km/s' ;this is km/s scale68

tmp=areaBlue/1000
tmpbx=[0,tmp,0]
tmpby=[1,imgNum,MAX(imgNum)]
LOADCT, 1, /SILENT
;OPLOT, tmpbx, tmpby, PSYM=-3, SYMSIZE=0.15, COLOR=230
polyfill, tmpbx,tmpby,color=230

; sign change for AreaRed and areaBlue for plotting purposed only
tmp=-areaRed/1000
tmprx=[0,tmp,0]
tmpry=[1,imgNum,MAX(imgNum)]

LOADCT, 3, /SILENT
OPLOT, tmprx, tmpry, PSYM=-3, SYMSIZE=0.15, COLOR=200
polyfill, tmprx,tmpry,color=160

;OPLOT, tmprx, tmpry, PSYM=-3, SYMSIZE=0.15, COLOR=140
;OPLOT, cogRed/10,  imgNUm, PSYM=-3, SYMSIZE=0.3, THICK=4, COLOR=100
;OPLOT, cogRed/10,  imgNUm, PSYM=8, SYMSIZE=0.2, THICK=0, COLOR=255
;OPLOT, cogRed/10,  imgNUm, PSYM=8, SYMSIZE=0.15, THICK=0, COLOR=180

LOADCT,1 , /SILENT
OPLOT, tmpbx, tmpby, PSYM=-3, SYMSIZE=0.15, COLOR=180
OPLOT, cogBlue/10, imgNUm, PSYM=-3, SYMSIZE=0.2, THICK=4, COLOR=100
OPLOT, cogBlue/10, imgNUm, PSYM=8, SYMSIZE=0.2, COLOR=255
OPLOT, cogBlue/10, imgNUm, PSYM=8, SYMSIZE=0.15, COLOR=180

LOADCT, 0, /SILENT
OPLOT, [0,0],[0,nPts], LINESTYLE=1

XYOUTS,-0.01, 3.75, 'd)', CHARSIZE=0.9, /DATA

DEVICE, /CLOSE

LOADCT, 0, /SILENT

SET_PLOT,'X'
END