PRO dustem_fit_ext_pol_example,model=model $
                          ,sed=sed $
                          ,itermax=itermax $
                          ,postscript=postscript $
                          ,png=png $
                          ,save=save $
                          ,restore=restore $
                          ,help=help

IF keyword_set(help) THEN BEGIN
  doc_library,'dustem_fit_sed_readme'
  goto,the_end
END

IF keyword_set(model) THEN BEGIN
  use_model=strupcase(model)
ENDIF ELSE BEGIN
  use_model='G17_MODELA'    ;Default is last dustem model
ENDELSE

use_polarization=0.   ;default is no polarization in models
use_window=2       ; default graphics window number to use for plotting the results

;=== Set the (model-dependent) parameters that you want to fit
;=== Refer to the DustEM and DustEMWrap userguides for an explanation
;    of the different grain types

CASE use_model OF
      'DBP90':BEGIN
         pd = [ $
             '(*!dustem_params).G0', $      ;G0
             '(*!dustem_params).grains(0).mdust_o_mh',$  ;PAH0 mass fraction
             '(*!dustem_params).grains(1).mdust_o_mh',$     ;PAH1 mass fraction
             '(*!dustem_params).grains(2).mdust_o_mh', $    ;amCBEx
             'dustem_plugin_continuum_2']                ;Intensity of NIR continuum
        rv =   [1.0, 4.3e-4, 4.7e-4,6.4e-3,0.001]
        Npar=n_elements(pd)
        ulimed=replicate(0,Npar)
        llimed=replicate(1,Npar)
        llims=replicate(0.,Npar)
     END
      'DL01':BEGIN
         pd = [ $
             '(*!dustem_params).G0', $      ;G0
             '(*!dustem_params).grains(0).mdust_o_mh',$  ;PAH0 mass fraction
             '(*!dustem_params).grains(1).mdust_o_mh',$     ;PAH1 mass fraction
             '(*!dustem_params).grains(2).mdust_o_mh', $    ;Gra
             '(*!dustem_params).grains(3).mdust_o_mh', $    ;Gra
             '(*!dustem_params).grains(4).mdust_o_mh', $    ;aSil
             'dustem_plugin_continuum_2']                ;Intensity of NIR continuum
        rv =   [1.0,5.4e-4, 5.4e-4,1.8e-4,2.33e-3,8.27e-3,0.001]
        Npar=n_elements(pd)
        ulimed=replicate(0,Npar)
        llimed=replicate(1,Npar)
        llims=replicate(0.,Npar)
      END
      'WD01_RV5p5B':BEGIN
;;  ***COMMENT AH***
;; we need to implement this, or remove         
         message, 'WD01 model not yet implemented in DustEMWrap',/info
;;  ***END COMMENT AH***
       END
      'DL07':BEGIN
          pd = [ $
              '(*!dustem_params).G0', $      ;G0
              '(*!dustem_params).grains(0).mdust_o_mh',$  ;PAH0 mass fraction
              '(*!dustem_params).grains(1).mdust_o_mh',$     ;PAH1 mass fraction
              '(*!dustem_params).grains(2).mdust_o_mh', $    ;Gra
              '(*!dustem_params).grains(3).mdust_o_mh', $    ;Gra
              '(*!dustem_params).grains(4).mdust_o_mh', $    ;aSil
              'dustem_plugin_continuum_2']                ;Intensity of NIR continuum
                     
        rv =   [1.0,5.4e-4, 5.4e-4,1.8e-4,2.33e-3,8.27e-3,0.001];,10,1.,10.,1.]
        Npar=n_elements(pd)
        ulimed=replicate(0,Npar)
        llimed=replicate(1,Npar)
        llims=replicate(0.,Npar)
      END
      'MC10':BEGIN
        
        pd = [ $
              ;'(*!dustem_params).gas.G0', $      ;G0
             ; 'dustem_plugin_continuum_2', $      ;intensity of NIR continuum
             ; 'dustem_plugin_synchrotron_2',$
              '(*!dustem_params).grains(0).mdust_o_mh',$     ;PAH0 mass fraction
              '(*!dustem_params).grains(1).mdust_o_mh',$     ;PAH1 mass fraction
              '(*!dustem_params).grains(2).mdust_o_mh', $    ;amCBEx
              '(*!dustem_params).grains(3).mdust_o_mh', $    ;amCBEx
              '(*!dustem_params).grains(4).mdust_o_mh' $     ;aSilx
              ]
        ;initial parameter values for parameters to be fitted   
        rv =   [ $  
   ;       1.0, $
  ;       0.002,   $ ;intensity of NIR continuum
  ;        0.01,$    
          7.8e-4,  $ ;mass fraction of  PAH0  
          7.8e-4,  $ ;mass fraction of  PAH1  
          1.65e-4, $ ;mass fraction of  amCBEx
          1.45e-3, $ ;mass fraction of  amCBEx
          7.8e-3   $   ;mass fraction of aSilx
          ]
          
     
        Npar=n_elements(pd)
        
        ulimed=replicate(0,Npar)
        llimed=replicate(1,Npar)
        llims=replicate(0.,Npar)
        
        
        ;=== Fixed parameters
        ;parameter description of parameters to be set to a non-default value
;         fpd=[ $
;           '(*!dustem_params).gas.G0' ,  $     ;multiplicative factor to total ISRF
;           'dustem_plugin_continuum_2' $     ;intensity of NIR continuum
;             ]
;         ;initial parameter values for fixed parameters
;         fiv=[ $
;           1. , $        ;multiplicative factor to total ISRF
;           3.e-3$      ;intensity of NIR continuum
;             ]
;;  ***END COMMENT AH***
      END
     'J13':BEGIN
        pd = [ $
             '(*!dustem_params).G0', $      ;G0
             '(*!dustem_params).grains(1).mdust_o_mh',$     ;PAH1 mass fraction
             '(*!dustem_params).grains(0).mdust_o_mh',$  ;PAH0 mass fraction
             '(*!dustem_params).grains(2).mdust_o_mh', $    ;amCBEx
             '(*!dustem_params).grains(3).mdust_o_mh', $    ;amCBEx
             '(*!dustem_params).grains(4).mdust_o_mh', $      ;aSil
             'dustem_plugin_continuum_2']                ;Intensity of NIR continuum
        rv =   [1.0, 7.8e-4, 7.8e-4,1.65e-4,1.45e-3,7.8e-3,0.001]
        Npar=n_elements(pd)
        ulimed=replicate(0,Npar)
        llimed=replicate(1,Npar)
        llims=replicate(0.,Npar)
      END
      'G17_MODELA':BEGIN

         pd = [ $
             ;'(*!dustem_params).G0', $      ;G0
             '(*!dustem_params).grains(0).mdust_o_mh',$  ;PAH0 mass fraction
             '(*!dustem_params).grains(1).mdust_o_mh',$     ;PAH1 mass fraction
             '(*!dustem_params).grains(2).mdust_o_mh']    ;aSil
             ;'dustem_plugin_continuum_2']                ;Intensity of NIR continuum
        rv = [5.4e-4, 5.4e-4,1.8e-4]
        Npar=n_elements(pd)
        ulimed=replicate(0,Npar)
        llimed=replicate(1,Npar)
        llims=replicate(0.,Npar)
        use_polarization=0
        
        ;=== Fixed parameters
        ;parameter description of parameters to be set to a non-default value
        fpd=[ $
          '(*!dustem_params).gas.G0' ,  $     ;multiplicative factor to total ISRF
          'dustem_plugin_continuum_2' $     ;intensity of NIR continuum
            ]
        ;initial parameter values for fixed parameters
        fiv=[ $
          1. , $        ;multiplicative factor to total ISRF
          3.e-3$      ;intensity of NIR continuum
            ]
        
      END
      'G17_MODELB':BEGIN
         pd = [ $
             '(*!dustem_params).G0', $      ;G0
             '(*!dustem_params).grains(0).mdust_o_mh',$  ;PAH0 mass fraction
             '(*!dustem_params).grains(1).mdust_o_mh',$     ;PAH1 mass fraction
             '(*!dustem_params).grains(2).mdust_o_mh', $    ;Gra
             '(*!dustem_params).grains(3).mdust_o_mh', $    ;Gra
             '(*!dustem_params).grains(4).mdust_o_mh', $    ;aSil
             'dustem_plugin_continuum_2']                ;Intensity of NIR continuum
        rv = [1.0,5.4e-4, 5.4e-4,1.8e-4,2.33e-3,8.27e-3,0.001]
        Npar=n_elements(pd)
        ulimed=replicate(0,Npar)
        llimed=replicate(1,Npar)
        llims=replicate(0.,Npar)
        use_polarization=1
     END
      'G17_MODELC':BEGIN

         pd = [ $
             '(*!dustem_params).G0', $      ;G0
             '(*!dustem_params).grains(0).mdust_o_mh',$  ;PAH0 mass fraction
             '(*!dustem_params).grains(1).mdust_o_mh',$     ;PAH1 mass fraction
             '(*!dustem_params).grains(2).mdust_o_mh', $    ;Gra
             '(*!dustem_params).grains(3).mdust_o_mh', $    ;Gra
             '(*!dustem_params).grains(4).mdust_o_mh', $    ;aSil
             'dustem_plugin_continuum_2']                ;Intensity of NIR continuum
        rv =   [1.0,5.4e-4, 5.4e-4,1.8e-4,2.33e-3,8.27e-3,0.001]
        Npar=n_elements(pd)
        ulimed=replicate(0,Npar)
        llimed=replicate(1,Npar)
        llims=replicate(0.,Npar)
        use_polarization=1
      END
      'G17_MODELD':BEGIN
         pd = [ $
             '(*!dustem_params).G0', $      ;G0
             '(*!dustem_params).grains(0).mdust_o_mh',$  ;PAH0 mass fraction
             '(*!dustem_params).grains(1).mdust_o_mh',$     ;PAH1 mass fraction
             '(*!dustem_params).grains(2).mdust_o_mh', $    ;Gra
             '(*!dustem_params).grains(3).mdust_o_mh', $    ;Gra
             '(*!dustem_params).grains(4).mdust_o_mh', $    ;aSil
             'dustem_plugin_continuum_2']                ;Intensity of NIR continuum
        rv =   [1.0,5.4e-4, 5.4e-4,1.8e-4,2.33e-3,8.27e-3,0.001]
        Npar=n_elements(pd)
        ulimed=replicate(0,Npar)
        llimed=replicate(1,Npar)
        llims=replicate(0.,Npar)
        use_polarization=1
     END
      'ELSE':BEGIN
         message,'model '+model+' unknown',/continue
         message,'Known models are MC10,DBP90,DL01,DL07,J13,G17_MODELA,G17_MODELB,G17_MODELC,G17_MODELD',/continue
         stop
      END
ENDCASE



;== INITIALISE DUSTEM
;;  ***COMMENT AH***
;; do we need the use_polarization key word activated here? -->
;; len(kwords) must match Npar_dust (i.e. without plugins), otherwise
;; fails in dustem_read_grain -- should set this within the above case statement?
;; IC: yes good idea. Maybe by default set 'kwords' to the original dust keywords and let the user modify kwords(i) where i is the index of the dust species.
dustem_init,model=use_model,/pol;,kwords=['logn','plaw','plaw'];,polarization=use_polarization
;;  ***END COMMENT AH***
!dustem_nocatch=1
!dustem_verbose=1
!dustem_show_plot=1
!EXCEPT=2 ;so I can locate the plotting error...


;=== READ EXAMPLE DATA: EXTINCTION

dir=!dustem_wrap_soft_dir+'/Data/EXAMPLE_OBSDATA/'
file=dir+'Mathis1990_DISM.xcat' ;We should add the serkowski xcat's content into the MATHIS one right?
;if keyword_set(ext) then file=ext ; not really needed for the tests
ext=read_xcat(file,/silent)


;=== GENERATE EXAMPLE DATA: EXTINCTION

;filters=['IRAS1','IRAS2','IRAS3','IRAS4','PACS3','SPIRE1','SPIRE2','SPIRE3','HFI2','HFI3','HFI4','HFI5','HFI6','LFI1','LFI2','LFI3']
;Nfilt=n_elements(filters)

;ext=dustem_initialize_ext(Nfilt)
;ext.filter=replicate('SPECTRUM',Nfilt)
;Using these filters to set the wavelengths
;ext.wave=dustem_filter2wav(filters)
;ext.instru=replicate('EXTINCTION', Nfilt);don't really know what to put here ;dustem_filter2instru(filters)


;=== initializing IQU and associated errors to avoid problems when checking SED in dustem_set_data.pro
ext.EXT_I=1.
for i=4l,n_tags(ext)-1 do begin
    ext.(i) = ext.EXT_I/1E13
endfor

; ind=where(spec.sigextII EQ 0.,count)
; IF count NE 0 THEN spec[ind].sigextII=(0.2*spec(ind).EXT_I)^2
; ind=where(spec.instru EQ 'FIRAS',count) ; I do  not know what this is for (WHY FIRAS)... maybe an old remnant of the older procedures 
; IF count NE 0 THEN spec[ind].sigextII=(0.2*spec(ind).EXT_I)^2


;###Before merging any xcat files we'll just displace the initial parameter array.

;###Creating fake extinction data: (already replaced iv by rv)

;###Creating observational strcture using xcat file (for simplicity)

;###Initializing the structure tags so that dustem_set_data sets said tags in !dustem_data

; for i=4l,n_tags(spec) -1 do begin
; 
;     ;initial loop
;     ;actually only data pertaining to Q and U need to be set. 
;     ;but dustem_set_data will take care of the tags of the !dustem_data structure pertaining to other polarization quantities
;     ;The content of the xcat file shouldn't not/isn't used after this in the main procedure 
;     if (tag_names(spec))[i] ne 'SIGEXTII' then begin
;         spec.(i) = spec.(3)/1E12 ;just to fill the tags...
;         ;This gives really high sigma values       
;     endif
;     
; endfor

;###first call to dustem_set_data so that the !dustem_data tags that are used in the 'compute_' procedures are set
dustem_set_data,m_fit,m_show,ext,ext 


iv = rv+[10.00E-4,10.00E-4,10.00E-4] ;###setting the initial parameter vector

;== SET INITIAL VALUES AND LIMITS OF THE PARAMETERS THAT WILL BE
;== ADJUSTED DURING THE FIT
dustem_init_parinfo,pd,iv,up_limited=ulimed,lo_limited=llimed,up_limits=ulims,lo_limits=llims

;== INITIALIZE ANY PLUGINS
dustem_init_plugins, pd,fpd 

dustem_init_fixed_params,fpd,fiv


;generation of the fake data (since dustem_set_data takes ONE structure containing all the info)
!dustem_psi_ext=25

ext.EXT_I = dustem_compute_ext(rv,st)
toto = dustem_compute_stokext(rv,st,dustem_qext,dustem_uext)
ext.EXT_Q = dustem_qext
ext.EXT_U = dustem_uext
stop




;;  ***END COMMENT AH***

;== SET THE OBSERVATIONAL STRUCTURE
dustem_set_data, m_fit,m_show,ext,ext;sed=spec)

; dustem_init_fixed_params,fpd,fiv

;== RUN THE FIT
tol=1.e-10
use_Nitermax=30 ;maximum number of iterations. 
IF keyword_set(itermax) THEN use_Nitermax=itermax

xr=[0.01,30]
yr=[1.00E-10,10]

tit='Spectral Energy Distribution'
ytit=textoidl('I_\nu (MJy/sr) for N_H=10^{20} H/cm^2')
xtit=textoidl('\lambda (\mum)')

t1=systime(0,/sec)
res=dustem_mpfit_data(tol=tol,Nitermax=use_Nitermax,gtol=gtol $
                      ,/xlog,/ylog,xr=xr,yr=yr,xtit=xtit,ytit=ytit,title=tit $
                      ,legend_xpos=legend_xpos,legend_ypos=legend_ypos $
                      ,errors=errors,chi2=chi2,rchi2=rchi2)
t2=systime(0,/sec)

;=== SAVE FIT RESULTS
;file_out='/tmp/DUSTEM_fit_example.sav'
if keyword_set(save) then begin
   dir_sav='./'
   dustem_save_system_variables,dir_sav+save
   message,'Saved fit results in '+dir_sav+save,/continue
   if not keyword_set(restore) then $
      restore=dir_sav+save
end
message,'The fit executed in '+strtrim(t2-t1,2)+' sec',/info

;======================================
;====You could exit IDL here. The remaining lines of code (essentially
;====plotting the results) would work by returning to this point
;====restoring the IDL output file that was created above.
;======================================

;file='/tmp/DUSTEM_fit_example.sav'
if keyword_set(restore) then begin
   file=restore
   dustem_restore_system_variables,file
end
 
;== PLOT THE FIT RESULTS RESTORED FROM .SAV FILE
; tit='Spectral Energy Distribution (Saved)'
; ytit=textoidl('I_\nu (MJy/sr) for N_H=10^{20} H/cm^2')
; xtit=textoidl('\lambda (\mum)')
; errors=(*(*!dustem_fit).current_param_errors)*(*(*!dustem_fit).param_init_values)
; chi2=(*!dustem_fit).chi2
; rchi2=(*!dustem_fit).rchi2
; 
; res=*(*!dustem_fit).current_param_values
; chi2=(*!dustem_fit).chi2
; rchi2=(*!dustem_fit).rchi2
; errors=(*(*!dustem_fit).current_param_errors)*(*(*!dustem_fit).param_init_values)

;=== PLOT FIT RESULTS AND SAVE TO GRAPHICS FILE IF REQUESTED
; window,use_window
; loadct,13
IF keyword_set(postscript) THEN BEGIN
;  dir_ps=!dustem_dat+'/Figures/'
  dir_ps='./'
;  force_mkdir,dir_ps
  set_plot,'PS'
  ps_file=dir_ps+postscript
  device,filename=ps_file,/color
ENDIF

;dustemwrap_plot,res,stp,xr=xr,/xstyle,yr=yr,/ysty,/ylog,/xlog,title=tit

; dustem_sed_plot,*(*!dustem_fit).current_param_values $
;                 ,ytit=ytit,xtit=xtit,title=tit $
;                 ,yr=yr,xr=xr,/ysty,/xsty $
;                 ,res=res,errors=errors,chi2=chi2,rchi2=rchi2 $
;                 ,/xlog,/ylog,legend_xpos=legend_xpos,legend_ypos=legend_ypos


IF keyword_set(postscript) THEN BEGIN
  device,/close
  set_plot,'X'
  message,'Wrote '+ps_file,/info
  stop
ENDIF
IF keyword_set(png) THEN BEGIN
;  dir_png=!dustem_dat+'/Figures/'
  dir_png='./'
;  force_mkdir,dir_png
  file_png=dir_png+png
  write_png,file_png,tvrd(/true)
  message,'Wrote '+file_png,/info
ENDIF

message,'Finished dustem_fit_sed_readme',/info

the_end:

END