PRO normalise_msst, scope

;; normalise_msst
;;
;; Purpose:
;;
;;  Normalise MSST 4m time-series spectroscopy 
;;
;; Use:
;;
;;  normalise_msst, <scope>
;;
;; Example:
;;
;;  normalise_msst, 'apo_red'
;;  normalise_msst, 'twin_blue'
;;  normalise_msst, 'twin_red'
;;
;;


;; Standard FAST common blocks
COMMON fileblock, nfiles, folder, flabel, nruns, nbomit, nwomit
COMMON fitsblock,  time, wave, spec, nwave, nspec
COMMON procblock,  specf, specr, specm
COMMON pspecblock, freq, twod_dft
COMMON xcorblock,  ccfx, ccfy, ccf2y, ccf2n, nccf, afits, template


;; identify the dataset with an index
IF scope EQ 'apo_red'   THEN isc = 0
IF scope EQ 'twin_blue' THEN isc = 1
IF scope EQ 'twin_red'  THEN isc = 2


;; define continum regions for normalising the data
creg = fltarr(3,12)
  creg(0,0:3) = [3.806,3.810, 3.820,3.825 ]
  creg(1,*)   = [3.587,3.588, 3.593,3.596, 3.603,3.608, 3.615,3.630, 3.637,3.682, 3.688, 3.695]
  creg(2,0:3) = [3.806,3.810, 3.820,3.826 ]



;; read in a previous dataset stored using "save_msst"

  restore, filename=scope

  wave = w
  time = t
  spec = s

IF ( isc EQ 2 OR isc EQ 0 ) THEN BEGIN
mask = WHERE ( w GE alog10(6400) AND w LE alog10 (6700) ) 
  wave = w(mask)
  spec = s(mask,*)
ENDIF


  nwave=n_elements(wave)
  nspec=n_elements(time)
  nwomit = 0

;; display raw data

  IF (strupcase(!d.name) EQ 'X') THEN BEGIN
    window,1
    shade_surf,spec,wave,time
  ENDIF


;; compute and analyse the light variations

  lightcurve, wave, time, spec, lc, dm
   
  IF (strupcase(!d.name) EQ 'X') THEN BEGIN
    window,0
    plot,time,dm,xtitle='day',ytitle='dmag'
  ENDIF

;; normalise the data

  normalise, creg(isc,*)

  IF (strupcase(!d.name) EQ 'X') THEN BEGIN
    window,0
    plot,wave,specm
    window,1
    shade_surf,spec,wave,time
  ENDIF


  save, filename=scope+'_norm', /All
  RETURN

;; clean the data

  cleandata
  specf = spec

  IF (strupcase(!d.name) EQ 'X') THEN BEGIN
    window,0
    plot,wave,specm,xtitle='Angstrom',ytitle='F/Fc'
    window,1
    shade_surf,specr,wave,time
  ENDIF

END