PRO lambdacal
;NAME:lambdacal
;
;PURPOSE:calibrate the wavelength for the SED mode 
;
;CALLING SEQUENCE:
;
;INPUTS:name of fits image (one telescope position) this will have 12
;on/off pairs
;
;OPTIONAL KEYWORD:
;
;OUTPUTS:LambdaCal.txt - list of wavelength, row number for a col number
;
;SIDE EFFECTS:chages the color
;
;RESTRICTIONS:??
;
;EXAMPLES:
;
;MODIFICATION HISTORY:started on 2/26/03
;
;------------------------------------
PRINT,'On a separate IDL prompt,run lambdalook.pro with the same file.'
;set the color right
loadct,39
pcolor=[20,40,70,100,150,190,20,40,70,100,150,190,25 ]

;name='ffene3.fits'
;name='ffene2.fits'
;name='fhear2.fits'
;name='fobject2.fits'
Print, 'Some test files are ffene3.fits, ffene2.fits, fhear2.fits,'
print, 'and fobject2.fits'
name=''
READ, name, PROMPT='Enter file name:'

;cube=RDFITSCUBE(name)
;ffile=cube(0)
ffile=READFITS(name)


CLOSE, 10
OPENW,10,'LambdaCal.txt',/APPEND
PRINTF,10, '#For file',name
PRINTF,10,'# Wavelength       Row #        StartCol     EndCol'

top=max(ffile, MIN=bottom)

PLOT,ffile(0,*),background=255, color=0,xtit='row # (wavelength)',$
  ytit='Flux (mJans/ster)',yrange=[0,top]
for i=1,23 do begin
OPLOT, ffile(i,*), color=i*10
endfor

;PRINT, 'Type .c to continue'
;stop
;slaffi,ffile
READ,num,PROMPT='How many wavelengths will be fit in this file?'

;PRINT, 'Which cols would you like to use? Max range = 0 to 23'
;READ,startcol,PROMPT='Which col to start on?'
;READ,endcol,PROMPT='Which col to end on?'
;PRINT, 'Number of cols per bin can be: 1,2,3,4,6,8,12 or 24'
;READ, nbin2, PROMPT='How many cols in each bin?'
;nbin=24/nbin2

;lambda=fltarr(nbin,num)
;maxcol=fltarr(nbin,num)
;xs=fltarr(nbin*num)
;xys=fltarr(nbin*num)
;xsquare=fltarr(nbin*num)
;k=0
again=''
ll=''
flip=''
;iter=24/nbin

PRINT, 'You can combine columns (spacial direction) for a better flux.'
PRINT, 'If you do not want to do this, choose 24 bins.'
READ, nbin, PROMPT='How many bins would you like?'


IF (nbin eq 24) then begin
bin=ffile
startbin=dindgen(24)
endbin=dindgen(24)
GOTO, maxbins
Endif


;bin the columns
startbin=fltarr(nbin)
endbin=fltarr(nbin)
bin=fltarr(nbin,32)
for i=0,nbin-1 do BEGIN 
PRINT, 'For bin #',i
PRINT, 'Bin counting starts at 0'
READ, sb,PROMPT= 'What col to start the bin?'
startbin(i)=sb
READ, eb,PROMPT= 'What col to end the bin?'
endbin(i)=eb
;   bin(i,*)=TOTAL(ffile((i*iter):(i+1)*iter-1,*),1)
   bin(i,*)=TOTAL(ffile(startbin(i):endbin(i),*),1)
endfor


maxbins:
FOr ii=0,num-1 DO Begin  ;for each wavelength
;PLOT,TOTAL(ffile(0:23,*),1),background=255, color=0
;PLOT,TOTAL(ffile(startcol:endcol+1,*),1),background=255, color=0
;start with fitting all rows
fit1=0
fit2=31

READ,lam, PROMPT='What wavelength (in microns) is this fitting?'
READ, flip,PROMPT='Is this an emission or absorbtion line? (em/ab):'
;PRINT, flip
;IF (flip eq 'ab') then  bin=MAX(bin)-bin


;lambda(k,ii)=lam
;fit the bined rows
for i=0,nbin-1 DO Begin
;for i=startcol, endcol Do Begin
fitloop:
;Plot, bin(*,i), Title='Bin '+STRING(i),ytit='fluxes in DN/sec',$
;  xtit='col #',background=255, color=0, xticklen=1,xgridstyle=1,$
;   xticks=7

y=dindgen(fit2-fit1+1)
for j=0,(fit2-fit1) do y(j)=fit1+j

;fit with mpfitpeak
A=fltarr(4)
yfit=MPFITPEAK(y,bin(i,fit1:fit2) , A)
PRINT, 'Coeff: ', A
Mcol=A(1)
;maxcol(k)=mcol
PRINT, 'Max Row: ',MCOl


;get finer grid for gaussian check
y2=fltarr(n_elements(y)*4)
y2(0)=y(0)
y2(n_elements(y2)-1)=y(n_elements(y)-1)
yrange=y(n_elements(y)-1)-y(0)
for j=1,n_elements(y2)-2 do y2(j)=y2(0)+j*(yrange/n_elements(y2))
z=(y2-A(1))/A(2)
check=A(0)*EXP(-0.5*z^2)+A(3)
checkbig=MAX(check)

PLOT, y,bin(i,fit1:fit2),title='Fits to Col/Bin'+STRING(i), ytit='Flux',$
   xtit='Row #', background=255, color=0,yrange=[0,checkbig]
OPLOT,y2, check, linestyle=3,color=40

If (flip eq 'ab') then begin
Minrow=MIN(bin(i,fit1:fit2),mr)
PRINT, 'Do you want to use the min row? (r) It is row',mr+fit1
endif 
If (flip eq 'em') then begin
Maxrow=MAX(bin(i,fit1:fit2),mr)
PRINT,'Do you want to use the max row? (r) It is row',mr+fit1 
endif

READ, again, PROMPT='Is this fit ok?(y/n) Or should it be skipped (s): '
If (again eq 's') Then Goto, skipped
If (again eq 'r') THen Mcol=mr+fit1
IF (again eq 'n') Then begin
;get which cols to fit:
READ, fit1,Prompt='Where should the fit start?'
READ, fit2,PROMPT='Where should the fit end?'
for j=0,fit1-1 do bin(i,j)=ffile(i, fit1)
for j=fit2+1,31 do bin(i,j)=ffile(i,fit2)
goto, fitloop
endif


PRINTF,10, lam, FLOAT(Mcol), startbin(i),endbin(i)

;k=k+1
skipped:
endfor;fitting cols

endfor ;wavelength

PRINT, 'Info written to LambdaCal.txt'
CLOSE,10
END