PRO dustem_stellarpopisrf_example,model=model $
                                 ,sed_file=sed_file $
                                 ,Nitermax=Nitermax $
                                 ,postscript=postscript $
                                 ,fits_save_and_restore=fits_save_and_restore $
                                 ,wait=wait $
                                 ,noobj=noobj $
                                 ,verbose=verbose $
                                 ,help=help

;+
; NAME:
;    dustem_fit_stellarpopisrf_example  
;
; PURPOSE:
; This routine is an example of how to fit an observational SED
; (StokesI only) with DustEM and DustEMWrap, and an ISRF that is due
; to a user-defined population of nearby main sequence stars.
;
; DustEMWrap reads information about the stellar spectral types (effective
; temperature, radius) from the EEM_dwarf_UBVIJHK_colors_Teff.txt file
; that is located in the Data/STELLARPOPS/ directory. This data file was
; authored by Prof. Erik Mamajek (see the file for more details).
;  
; For this example, we generate an SED using an input model and then
; launch the fit with a starting guess that has been shifted away from
; the true parameter values.
;
; CATEGORY:
;    DustEMWrap, Distributed, High-Level, User Example
;
; CALLING SEQUENCE:
;    dustem_fit_stellarpopisrf_example[,model=][sed_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
;    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.  
;    postscript = if set, final plot is saved as postscript in the
;                 current working directory
;    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
;    noobj     = if set, runs with no object graphics
;
; 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:
;    
;
; EXAMPLES
;    dustem_fit_stellarpopisrf_example
;    dustem_fit_stellarpopisrf_example,Nitermax=1,fits_save_and_restore='/tmp/mysavefile.fits'
;    dustem_fit_stellarpopisrf_example,model='DBP90'
;
; MODIFICATION HISTORY:
;    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_stellarpopisrf_example'
  goto,the_end
END

IF keyword_set(model) THEN BEGIN
  use_model=strupcase(model)
ENDIF ELSE BEGIN
  use_model='J13'    ;Default is last dustem model
ENDELSE

known_mdls=['MC10','DBP90','DL01','WD01_RV5P5B','DL07','J13','G17_MODELA','G17_MODELB','G17_MODELC','G17_MODELD'] 
test_model = where(known_mdls eq use_model,ct)
if ct eq 0 then begin
   message,'ISM dust model '+use_model+' unknown',/continue
   message,'Known models are MC10,DBP90,DL01,WD01_RV5P5B,DL07,J13,G17_MODELA,G17_MODELB,G17_MODELC,G17_MODELD',/continue
   stop
end


use_polarization=0   ; initialize Dustemwrap in no polarization mode 
use_verbose=0
if keyword_set(verbose) then use_verbose=1
use_Nitermax=5        ; maximum number of iterations for the fit
IF keyword_set(Nitermax) THEN use_Nitermax=Nitermax

dustem_define_la_common

;=== 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

;; ; example parameter initialisation for DBP90
;; pd = [ $
;;      '(*!dustem_params).grains(0).mdust_o_mh',$          ;PAH0 mass fraction
;;      '(*!dustem_params).grains(1).mdust_o_mh',$          ;VSG mass fraction
;;      '(*!dustem_params).grains(2).mdust_o_mh', $         ;amCBEx
;;      'dustem_plugin_stellar_population_O7V3',$           ;distance to O7V stars
;;      'dustem_plugin_stellar_population_O5V4']            ;number of O5V stars

;; rv =   [4.3e-4, 4.7e-4,6.4e-3,1.5,100.] ;rv because we're generating fake data and try to retrieve the original values
;; iv = rv+[5.00E-4,5.00E-4,5.00E-4,-1.,-30] ;###setting the initial parameter vector
        
;; Npar=n_elements(pd)
;; ulimed=replicate(0,Npar)
;; llimed=replicate(1,Npar)
;; llims=replicate(0.,Npar)         
              
;; ;fixed parameters
;; fpd=[ $
;;     'dustem_plugin_stellar_population_O7V4',$ ;number of O7V stars 
;;     'dustem_plugin_stellar_population_O5V3'$  ;  distance to O5V stars
;;     ]
;; ;initial parameter values for fixed parameters
;; fiv=[2., 45.]

;'J13':BEGIN
pd = [ $
     '(*!dustem_params).grains(1).mdust_o_mh',$          ;CM20 mass fraction
     '(*!dustem_params).grains(0).mdust_o_mh',$          ;CM20 mass fraction
     '(*!dustem_params).grains(2).mdust_o_mh', $         ;aPyM5
     '(*!dustem_params).grains(3).mdust_o_mh', $         ;aPyM5
     'dustem_plugin_stellar_population_O5V4']            ; number of pop O5V stars

rv =   [7.8e-4, 7.8e-4,1.65e-4,1.45e-3,35] ; real values
iv = rv + [2.e-4,-1.e-4,3.e-5,5.e-4,-5] ; starting guess values
        
Npar=n_elements(pd)
ulimed=replicate(0,Npar)
llimed=replicate(1,Npar)
llims=replicate(0.,Npar)

;fixed parameters and their values
fpd = ['dustem_plugin_stellar_population_O5V3' $ ;distance to stellar population O5V
       ,'(*!dustem_params).G0'] ; Mathis field
fiv  = [5.,1.e-12]
      
dustem_init,model=use_model,polarization=use_polarization

!dustem_nocatch=1
!dustem_verbose=1
;!dustem_show_plot=1
;; !EXCEPT=2 ;so I can locate the plotting error...
;; ;!dustem_dim=1 ; this option is to dim the stellar population ISRF with the current Dustem extinction
;; ;We're fitting total optical depths so the dimmed-ISRF scenario is a reasonable assumption.
;; ;Because of this the final parameter values are slightly lower than the initial (real) values.
;; ;But this is because the first run was not extinct with the current dustem extinction 
;; ;since it comes prior to the dustem run. Meaning the first ISRF has to be extinct to see if the paramters are retrieved.
IF keyword_set(noobj) THEN !dustem_noobj=1

!dustem_isrf_file=ptr_new(!dustem_soft_dir+'data/ISRF_MATHIS.DAT')

;=== READ EXAMPLE DATA:

;NB: HERE WE ARE READING AN SED FILE JUST TO SET-UP THE SED STRUCTURE
;AND FILTERS. WE REPLACE THE STOKES I and STOKES I UNCERTAINTIES LATER
dir=!dustem_wrap_soft_dir+'/Data/EXAMPLE_OBSDATA/'
file=dir+'example_SED_1.xcat'
IF keyword_set(sed_file) THEN file=sed_file
sed=read_xcat(file,/silent)

if keyword_set(wait) then begin
   message,'Finished reading SED data: '+file,/info
   wait,wait
end


;=== GENERATE EXAMPLE DATA:

;=== initializing IQU and associated errors to avoid problems when checking SED in dustem_set_data.pro
;sed.StokesI=1.
;setting the errors (well equating all the tags to the sigmaii array but this is an initialization)
for i=4l,n_tags(sed)-1 do begin
    sed.(i) = sed.sigmaii
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,sed,sed

; ;== 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

dustem_init_params,use_model,pd,iv,fpd=fpd,fiv=fiv,ulimed=ulimed,llimed=llimed,ulims=ulims,llims=llims

;Generating the fake emission data
sed.StokesI = dustem_compute_sed(rv,st=st)

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


if keyword_set(wait) then begin
   message,'Finished initializing DustEMWrap, including plugins and fixed parameters',/info
   wait,wait
end

;== RUN THE FIT
tol=1.e-18

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_m=xr_m,yr_m=yr_m,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(wait) then begin
   message,'Finished running DustEMWrap, using Niters: '+strtrim(string(use_Nitermax),2),/info
   message,'Time taken [sec]: '+sigfig(t2-t1,2,/sci),/info
   wait,wait
end


;=== MAKE THE FINAL PLOT
IF keyword_set(postscript) THEN BEGIN
    dir_ps='./'
    set_plot,'PS'
    ps_file=dir_ps+postscript
    device,filename=ps_file,/color
ENDIF

IF !dustem_noobj THEN BEGIN
  dustemwrap_plot_noobj,*(*!dustem_fit).CURRENT_PARAM_VALUES,dummy,xr=xr,/xstyle,yr=yr,/ysty,/ylog,/xlog,title=tit+' (Final fit)'
 ENDIF ELSE BEGIN
  dustemwrap_plot,*(*!dustem_fit).CURRENT_PARAM_VALUES,dummy,xr=xr,/xstyle,yr=yr,/ysty,/ylog,/xlog,title=tit+' (Final fit)'
ENDELSE

IF keyword_set(postscript) THEN BEGIN
  set_plot,'X'
  device,/close
  message,'Wrote '+ps_file,/info
ENDIF

if keyword_set(wait) then begin
   message,'Made the plot of the final results',/info
   wait,wait
end

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_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_stellarpopisrf_example',/info


the_end:

END