PRO dustem_fit_sed_polsed_readme,postcript=postcript,mode=mode,help=help

;This Readme describes how to fit total intensity and polarization SEDs jointly
;Obviously, the dustem package must have been installed succesfully
;see DustemWrap documentation for install instructions.

;+
; NAME:
;    dustem_fit_sed_polsed_readme
; PURPOSE:
;    This is an example of how to fit total intensity and polarization SEDs jointly
;    It is meant to be an example to follow when writing your own
;    programs using the dustem IDL wrapper.
; CATEGORY:
;    Dustem
; CALLING SEQUENCE:
;    dustem_fit_sed_polsed_readme,postcript=postcript,mode=mode,help=help
; INPUTS:
;    None
; OPTIONAL INPUT PARAMETERS:
;    None
; OUTPUTS:
;    None
; OPTIONAL OUTPUT PARAMETERS:
;    None
; ACCEPTED KEY-WORDS:
;    postcript = if set plot is done in DUSTEM/Docs/Figures/Last_dustem_fit.ps
;    help      = If set print this help
; COMMON BLOCKS:
;    None
; SIDE EFFECTS:
;    None
; RESTRICTIONS:
;    The dustem idl wrapper must be installed
; PROCEDURE:
;    None
; EXAMPLES
;    dustem_fit_sed_polsed_readme
; MODIFICATION HISTORY:
;    Written by J.P. Bernard June 29th 2011
;    see evolution details on the dustem cvs maintained at CESR
;    Contact J.-Ph. Bernard (Jean-Philippe.Bernard@cesr.fr) in case of problems.
;-

IF keyword_set(help) THEN BEGIN
  doc_library,'dustem_fit_sed_polsed_readme'
  goto,the_end
ENDIF

dustem_define_la_common

;=== initialise dustem
;dustem_init,mode='COMPIEGNE_ETAL2010',/pol

;use_mode='G17_MODELA'

use_mode='G17_MODELC';'DBP90';'G17_MODELA';'THEMIS';;'USER_MODEL';'THEMIS';;'THEMIS';'G17_MODELA';'THEMIS';'NY_MODELA';'G17_MODELA';'DBP90';'USER_MODEL';'THEMIS';'NY_MODELA';'G17_MODELA';'DBP90';'COMPIEGNE_ETAL2010'
;,/pol
dustem_init,mode=use_mode,kwords=['logn-chrg-spin','plaw-pol','plaw-pol'],/pol;,kwords=['plaw-ed','logn','logn'];,/pol;kwords=['plaw-ed-chrg-spin'],/pol;,kwords=['plaw-ed'];kwords=['plaw-ed-chrg-spin'];,/pol;

!dustem_verbose=1
!dustem_show_plot=1
!dustem_nocatch=1
;help,!run_pol

;stop


;filters=['DIRBE1','DIRBE2','DIRBE3','DIRBE4','IRAS1','IRAS2','IRAS3','IRAS4','PACS3','SPIRE1','SPIRE2','SPIRE3','HFI2','HFI3','HFI4','HFI5','HFI6','LFI1','LFI2','LFI3']
filters=['IRAS1','IRAS2','IRAS3','IRAS4','PACS3','SPIRE1','SPIRE2','SPIRE3','HFI2','HFI3','HFI4','HFI5','HFI6','LFI1','LFI2','LFI3']
Nfilt=n_elements(filters)
sed=dustem_initialize_sed(Nfilt)
sed.filter=filters
sed.wave=dustem_filter2wav(filters)
sed.instru=dustem_filter2instru(filters)

;INITIALIZING IQU and associated errors to avoid problems when checking SED in dustem_set_data.pro
sed[*].StokesI=1.
sed.StokesQ=sed.StokesI/100.
sed.StokesU=sed.StokesI/100.
sed.SigmaII=sed.StokesI/100.
sed.SigmaQQ=sed.StokesI/100.
sed.SigmaUU=sed.StokesI/100.
sed.SigmaIQ=sed.StokesI/100.
sed.SigmaIU=sed.StokesI/100.
sed.SigmaQU=sed.StokesI/100.

;st=dustem_set_data(ext=ext,polsed=polsed,polext=polext,sed=sed,polfrac=polfrac,rchi2_weight=rchi2_weight,f_HI=f_HI,qsed=qsed,used=used,qext=qext,uext=uext)

;INITIALIZING THE !dustem_data tags that will be internally used 
;st=dustem_set_data(sed=sed,rchi2_weight=rchi2_weight,f_HI=f_HI)
st=dustem_set_data(m_fit=sed)

;st=dustem_set_data() ;this should be one of the tests


;=== Set which parameters you want to fit
pd = [ $
             '(*!dustem_params).G0', $      ;G0
             '(*!dustem_params).grains(0).mdust_o_mh',$  ;PAH0 mass fraction
             '(*!dustem_params).grains(1).mdust_o_mh',$  ;PAH0 mass fraction   
             '(*!dustem_params).grains(2).mdust_o_mh' $    ;PAH1 mass fraction
             ;'(*!dustem_params).grains(3).mdust_o_mh',$    ;amCBEx
             ;'dustem_plugin_synchrotron_2', $               ;Synchrotron amplitude
             ;'dustem_plugin_synchrotron_4', $               ;Synchrotron polarization angle
             ;'dustem_plugin_modify_dust_polarization_2', $ ;Polarization angle applied to the Fortran dust model via a core plugin
             ;'dustem_plugin_modify_spinning_polarization_1', $
             ;'dustem_plugin_modify_spinning_polarization_2' $
              ]                   

;p_truth=[1.,7.8000E-04,7.8000E-04,7.8000E-04,1.6500E-04,68.,4e-3,20]
;iv=p_truth+[0.,8.e-4,8.e-4,8.e-4,8.e-4,-10.,2e-4,10]      ;shifted from solution

;p_truth=[1.,7.8000E-04,7.8000E-04,7.8000E-04,1.6500E-04,5e-3,20.,68.,1.2,20]    
p_truth=[1.,7.8000E-04,7.8000E-04,7.8000E-04]
iv=p_truth+[0.,8.e-4,8.e-4,8.e-4]      ;shifted from solution

Npar=n_elements(pd)  
ulimed=replicate(0,Npar)
llimed=replicate(1,Npar)
llims=replicate(0,Npar)

;stop

dustem_init_parinfo,pd,iv,up_limited=ulimed,lo_limited=llimed,up_limits=ulims,lo_limits=llims;,tied=tied
;stop
dustem_init_plugins,pd

;Here fortran fails when pluggins are activated and/or type-keywods exist
sed.StokesI=dustem_compute_sed(p_truth,ssti)   ;sst is not set on purpose, for dustem_compute_sed to compute the sed using fortran code
sed.sigmaII=abs(sed.StokesI*0.000001)

;sed.largeP=dustem_compute_polsed(p_truth,sstp)
;sed.sigma_largep=abs(sed.largeP*0.000001)

toto=dustem_compute_stokes(p_truth,sstqu,dustem_qsed,dustem_used) ;this procedure also allows for the extraction of the spectra

sed.StokesQ=dustem_qsed
sed.sigmaQQ=abs(sed.StokesQ*0.000001)

sed.StokesU=dustem_used
sed.sigmaUU=abs(sed.StokesU*0.000001)

message,'Fake polarization SED has been set',/continue
stop


;=== SET THE OBSERVATION STRUCTURE

ind=where(sed.wave GE 0.1)

st_bidon=dustem_set_data(m_fit=sed[ind],rchi2_weight=rchi2_weight,f_HI=f_HI) ; comment if second line is to be used

;=== RUN fit
tol=1.e-16
xtol=1.e-16
Nitermax=30; just an initialization
;for i=0L,n_tags(!dustem_data)-1 do begin
;if ptr_valid(!dustem_data.(i)) then Nitermax+=1
;endfor
;Nitermax=4           ;maximum number of iteration. This is the criterion which will stop the fit procedure

xrange=[1.,2.e4]
yrange=[1e-4,1.e3]

loadct,13
;!y.range=[1e-8,100]              ;This is to ajust plot range from outside the routine
t1=systime(0,/sec)
title='CACA'    ;does not work if title is undefined ....
res=dustem_mpfit_data(tol=tol,xtol=xtol,Nitermax=Nitermax,xrange=xrange,/xstyle,yrange=yrange,/ysty,/ylog,/xlog,xtit='wavelength [mic]',ytit='Brightness []',title=title)
t2=systime(0,/sec)

stop

print,(res-p_truth)/p_truth*100.

;help,(*!dustem_fit),/STRUCTURE

;=== SAVE FIT RESULTS
file_out='/tmp/DUSTEM_polsed_fit_example.sav'
dustem_save_system_variables,file_out
message,'Saved '+file_out,/continue

;stop

;======================================
;====You can exit IDL here and re-enter   -   THIS PART APPEARS TO BE FAULTY. NEEDS INVESTIGATION 
;======================================
file='/tmp/DUSTEM_polsed_fit_example.sav'
dustem_restore_system_variables,file

;=== Plot best fit
win=1
window,win & win=win+1
xrange=[1.,2.e4]
yrange=[1e-4,1.e3]

;=== recover best fit values
res=*(*!dustem_fit).current_param_values
chi2=(*!dustem_fit).chi2
rchi2=(*!dustem_fit).rchi2
;errors=*(*!dustem_fit).current_param_errors
errors=(*(*!dustem_fit).current_param_errors)*(*(*!dustem_fit).param_init_values)

;=== Plot best fit
tit='DUSTEM polarization dust Example (Saved)'
ytit=textoidl('I_\nu (MJy/sr) for N_H=10^{20} H/cm^2')
xtit=textoidl('\lambda (\mum)')

loadct,13
IF keyword_set(postcript) THEN BEGIN
  set_plot,'PS'
  ps_file=!dustem_wrap_soft_dir+'/Docs/'+'Last_dustem_spinning_fit.ps';'/Docs/Figures/'+'Last_dustem_spinning_fit.ps'
  device,filename=ps_file,/color
ENDIF

dustem_sed_plot,*(*!dustem_fit).current_param_values,ytit=ytit,xtit=xtit,title=tit,yr=yrange,xr=xrange,/ysty,/xsty,res=res,errors=errors,chi2=chi2,rchi2=rchi2,/xlog,/ylog,/pol

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

print,'dustem_mpfit_sed executed in ',t2-t1,' sec'

the_end:

END