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

;=== initialise dustem
;dustem_init,mode='COMPIEGNE_ETAL2010',/pol
use_mode='G17_MODELA'
dustem_init,mode=use_mode,/pol

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

;stop

;=== make a fake one out for given filters
;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)
polsed=sed
;polext=sed 

;stokes fake parameters
qsed=sed
used=sed

; ;stokes extinction fake parameters
; qext=sed
; uext=sed

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)

;=== 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',$     ;PAH1 mass fraction
             '(*!dustem_params).grains(2).mdust_o_mh',$    ;amCBEx
             'dustem_create_synchrotron_2',$ 
             'dustem_create_stokes_1',$ ;Polarization angle psi_ref_dust
             'dustem_create_stokes_2',$;Polarization angle psi_ref_synch
             'dustem_create_stokes_3'$;Polarization fraction of synchrotron spectrum
             ;'dustem_create_stext_1'$;Polarization angle in extinction PSI_ext
              ]                   

p_truth=[1.,7.8000E-04,7.8000E-04,1.6500E-04,5e-3,70,20,0.2]    
;p_truth=[1.,7.8000E-04,7.8000E-04,1.6500E-04,25]    





dustem_init_plugins, pd

;=== set initial value of parameters you want to fit
;iv=p_truth   ;exact solution
iv=p_truth+[0.,3.e-5,1.e-5,-2.e-5,5e-2,5,5,0.2];shifted from solution

;iv=p_truth+[0.,3.e-5,1.e-5,-2.e-5,5];shifted from solution


ulimed=[0   ,0   ,0   ,0   ,0   ,0   , 0   ,0] ;Polarization angles exist in the range [0-180] degress

;ulimed=[0   ,0   ,0   ,0   ,0] ;Polarization angles exist in the range [0-180] degress


llimed=[1   , 1   ,1   ,1   ,1   ,1   ,1   ,1]
;llimed=[1   , 1   ,1   ,1   ,1]

llims =[0.  ,0.   ,0.  ,0.   , 0.   ,0.   ,0.   ,0.]
;llims =[0.  ,0.   ,0.  ,0.   ,0.]

;== SET THE FITTED PARAMETERS (now done in dustem_init_parinfo)
dustem_init_parinfo,pd,iv,up_limited=ulimed,lo_limited=llimed,up_limits=ulims,lo_limits=llims

;dustem_init_fixed_params,fpd,fiv
    
;(*!dustem_params).grains[0].TYPE_KEYWORDS='logn-chrg-spin'
;(*!dustem_params).grains[1].TYPE_KEYWORDS='logn-chrg-spin'
;(*!dustem_params).grains[4].TYPE_KEYWORDS='pol-plaw-ed'

help,*!dustem_fit

help,!run_pol

sed.spec=dustem_compute_sed(p_truth,sst,_extra=extra)   ;sst is not set on purpose, for dustem_compute_sed to compute the sed using fortran code
sed.error=(sed.spec*0.1);>0.1

polsed.spec=dustem_compute_polsed(p_truth,sstp,_extra=extra,dustem_qsed,dustem_used)   ;sst is not set on purpose, for dustem_compute_sed to compute the sed using fortran code
polsed.error=(polsed.spec*0.1)


;creating fake polext
  
;polext.spec=dustem_compute_polext(p_truth,ssttp,dustem_qext,dustem_uext)
;polext.error=(polext.spec*0.1)
;  


;SET qsed and used data
qsed.spec=dustem_qsed
qsed.error=qsed.spec*0.1


used.spec=dustem_used
used.error=used.spec*0.1


; ;SET qext and uext data
; qext.spec=dustem_qext
; qext.error=qext.spec*0.1
; 
; 
; uext.spec=dustem_uext
; uext.error=uext.spec*0.1
; 

;=== SET THE OBSERVATION STRUCTURE

ind=where(sed.wave GE 0.1)

st=dustem_set_data(polsed=polsed[ind],sed=sed[ind],qsed=qsed[ind],used=used[ind])
;st=dustem_set_data(sed=sed[ind],polext=polext[ind],qext=qext[ind],uext=uext[ind])

;=== RUN fit
tol=1.e-12
xtol=1.e-12
Nitermax=0 ; 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)
res=dustem_mpfit_data(tol=tol,xtol=xtol,Nitermax=Nitermax,xrange=xrange,/xstyle,yrange=yrange,/ysty,/ylog,/xlog,xtit='wavelength [mic]',ytit='Brightness []')
t2=systime(0,/sec)

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
;======================================
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/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