PRO dustem_fit_sed_ext_pol_example,model=model $
                                  ,sed_file=sed_file $
                                  ,ext_file=ext_file $
                                  ,Nitermax=Nitermax $
                                  ,fits_save_and_restore=fits_save_and_restore $
                                  ,wait=wait $
                                  ,help=help

;+
; NAME:
;    dustem_fit_sed_ext_pol_example  
;
; PURPOSE:
; This routine is an example of how to fit an observational emission + extinction SED
; (StokesI,Q,U) with DustEM and DustEMWrap. The objective is to
; illustrate how to use DustEMWrap and not to do science -- the fit
; obtained by running this example is likely to be poor.
;  
; See the DustEMWrap User Guide for more information.
;
; CATEGORY:
;    DustEMWrap, Distributed, High-Level, User Example
;
; CALLING SEQUENCE:
;    dustem_fit_ext_pol_example[,model=][sed_file=][ext_file=][,postscript=][,Nitermax=][,fits_save_and_restore=][,/help,/wait,/verbose]
;
; INPUTS:
;    None
;
; OPTIONAL INPUT PARAMETERS:
;    None
;
; OUTPUTS:
;    None
;
; OPTIONAL OUTPUT PARAMETERS:
;    Plots, results structure in binary FITS table format
;
; ACCEPTED KEY-WORDS:
;    model = specifies the interstellar dust mixture used by DustEM
;           'MC10' model from Compiegne et al 2010 
;           'DBP90' model from Desert et al 1990
;           'DL01' model from Draine & Li 2001
;           'WD01_RV5p5B' model from Weingartner & Draine 2002 with Rv=5.5
;           'DL07' model from Draine & Li 2007
;           'J13' model from Jones et al 2013, as updated in
;                 Koehler et al 2014
;           'G17_ModelA' model A from Guillet et al (2018). Includes
;                 polarisation. See Tables 2 and 3 of that paper for details.
;           'G17_ModelB' model B from Guillet et al (2018)
;           'G17_ModelC' model C from Guillet et al (2018)
;           'G17_ModelD' model A from Guillet et al (2018)
;    sed_file = string naming the path to text file in .xcat format that
;          describes the observational SED. If not set, the file
;          'Data/EXAMPLE_OBSDATA/example_SED_2.xcat' is used.  
;    ext_file = string naming the path to text file in .xcat format that
;          describes the observational extinction SED. If not set, the file
;          'Data/EXAMPLE_OBSDATA/Mathis1990_DISM.xcat' is used.  
;    Nitermax = maximum number of fit iterations. Default is 5.
;    fits_save_and_restore = if set, save the fit results in a binary
;               FITS file. The code then restore this file and plots
;               the results using the saved results information.
;    help      = if set, print this help
;    wait      = if set, wait this many seconds between each step of
;                the code (for illustration purposes)
;    verbose      = if set, subroutines will run in verbose mode
;
; COMMON BLOCKS:
;    None
;
; SIDE EFFECTS:
;    None
;
; RESTRICTIONS:
;    The DustEM fortran code must be installed
;    The DustEMWrap IDL code must be installed
;
; PROCEDURES AND SUBROUTINES USED:
;    *** COMMENT AH --> is this really NONE? ****
;
; EXAMPLES
;    dustem_fit_sed_ext_pol_example
;    dustem_fit_sed_ext_pol_example,Nitermax=1,fits_save_and_restore='/tmp/mysavefile.fits'
;    dustem_fit_sed_ext_pol_example,model='DBP90'
;
; MODIFICATION HISTORY:
;    Written by JPB Apr-2011
;    Evolution details on the DustEMWrap gitlab.
;    See http://dustemwrap.irap.omp.eu/ for FAQ and help.  
;-

IF keyword_set(help) THEN BEGIN
  doc_library,'dustem_fit_sed_ext_pol_example'
  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

;IC: NOT NEEDED SINCE PLOTTING HAPPENS INTERNALLY
;Leaving as is because maybe it's used for something else?
 
use_window=2       ; default graphics window number to use for plotting the results
use_verbose=0
if keyword_set(verbose) then use_verbose=1

;=== 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_modify_dust_polx_2' ]
             ;'dustem_plugin_continuum_2']                ;Intensity of NIR continuum
        rv = [5.4e-4, 5.4e-4,1.8e-4,50]
        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=use_verbose
;!dustem_show_plot=1
!EXCEPT=2 ;so I can locate the plotting error...


;=== READ EXAMPLE DATA: EXTINCTION

;NB:HERE WE ARE NOT FITTING THE DATA. WE'RE JUST USING THE EXISTING FILTERS.

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_file) then file=ext_file ; not really needed for the tests
ext=read_xcat(file,/silent)

dir=!dustem_wrap_soft_dir+'/Data/EXAMPLE_OBSDATA/'
file=dir+'example_SED_2.xcat'
if keyword_set(sed_file) then file=sed_file ; not really needed for the tests
sed=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

;=== initializing IQU and associated errors to avoid problems when checking SED in dustem_set_data.pro
sed.StokesI=1.
for i=4l,n_tags(sed)-1 do begin
    sed.(i) = sed.StokesI/1E10
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 
dustem_set_data,sed,sed,ext,ext 

iv = rv+[10.00E-4,10.00E-4,10.00E-4,-30] ;###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=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 ;using the plugin instead

;stop
ext.EXT_I = dustem_compute_ext(rv,st=st)
toto = dustem_compute_stokext(rv,st=st,Qext_spec=dustem_qext,Uext_spec=dustem_uext)
ext.EXT_Q = toto[0]
ext.EXT_U = toto[1]

sed.StokesI = dustem_compute_sed(rv,st=st)
toto = dustem_compute_stokes(rv,st=st,Q_spec=dustem_qsed,U_spec=dustem_used)
sed.StokesQ = toto[0]
sed.StokesU = toto[1]


;;  ***END COMMENT AH***

;== SET THE OBSERVATIONAL STRUCTURE
dustem_set_data, sed,sed,ext,ext

; dustem_init_fixed_params,fpd,fiv

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

xr_x = [0.01,30]
yr_x = [5.00E-8,10]

xr_m = [1.,5e5]
yr_m = [5e-8,1.00e6]


tit='Spectral Energy Distribution'
ytit=textoidl('I_\nu (MJy/sr) for N_H=10^{20} H/cm^2')
xtit=textoidl('\lambda (\mum)')
;Set show_plot to 0 to hide plot
;Commented or set to 1 is the same since !dustem_show_plot (existing sysvar) is initialized to 1 in dustem_init
;show_plot = 0 
t1=systime(0,/sec)
res=dustem_mpfit_data(tol=tol,Nitermax=use_Nitermax,gtol=gtol $
                      ,/xlog,/ylog,xr=xr,yr=yr,xr_m=xr_m,yr_m=yr_m,xr_x=xr_x,yr_x=yr_x,xtit=xtit,ytit=ytit,title=tit $
                      ,legend_xpos=legend_xpos,legend_ypos=legend_ypos $
                      ,errors=errors,chi2=chi2,rchi2=rchi2,show_plot=show_plot)
t2=systime(0,/sec)

IF keyword_set(fits_save_and_restore) THEN BEGIN
   message,'Writing out results structure: '+fits_save_and_restore,/info
   dustem_write_fits_table,filename=fits_save_and_restore,help=help
;=== At this point, you could erase all dustem system variables, or exit idl... all the
;=== information needed to recover the results and remake the plots has been saved in the FITS table
  ;stop
  dustem_read_fits_table,filename=fits_save_and_restore,dustem_spectra_st=dustem_spectra_st
  ;==== plot result taken from the saved fits table
  res=*(*!dustem_fit).CURRENT_PARAM_VALUES
  IF !dustem_noobj THEN BEGIN
     dustemwrap_plot_noobj,res,dustem_spectra_st,xr=xr,/xstyle,yr=yr,/ysty,/ylog,/xlog,title=tit+' (From Saved FITS file)'
  ENDIF ELSE BEGIN
    dustemwrap_plot,res,dustem_spectra_st,xr=xr,/xstyle,yr=yr,/ysty,/ylog,/xlog,title=tit+' (From Saved FITS file)'
  ENDELSE
  IF keyword_set(wait) THEN BEGIN
     message,'Saved the results as FITS in the file: '+fits_save_and_restore+', and made a plot using the data in this file',/info
     wait,wait
  ENDIF
ENDIF

message,'Finished dustem_fit_sed_ext_pol_example',/info

the_end:

END