PRO dustem_set_data,m_fit=m_fit $
                    ,m_show=m_show $
                    ,x_fit=x_fit $
                    ,x_show=x_show $
                    ,rchi2_weight=rchi2_weight $
                    ,f_HI=f_HI $
                    ,help=help

;+
; NAME:
;    dustem_set_data

;

; PURPOSE:

;    Set the *!dustem data (and *!dustem_show) datasets in emission and/or extinction from input data structures
;    *!dustem_data is important for the fitting of data and its general handling by DustEMWrap.

; CATEGORY:

;    DustEMWrap, Mid-Level, Distributed, Initialization

;

; CALLING SEQUENCE:

;    dustem_set_data,[,m_fit=,x_fit=][,m_show=,x_show=],[,rchi2_weight=][,f_HI=][,/help]

;

; INPUTS:

;    None

;

; OPTIONAL INPUT PARAMETERS:

;    m_fit : DustEMWrap structure contaning emission data to be fitted 
;    m_show : DustEMWrap structure containing emission data to be displayed
;    x_fit : DusteEMWrap structure containing extinction data to be fitted
;    x_show : DustEMWrap structure containing extinctiond data to be displayed
;    rchi2_weight : DustEMWrap structure containing the wieghts for chi2 calculation

;    f_HI : multiplicative factor for the SED values (extinction and emission)

;

; OUTPUTS:

;    None/ALL OF THE ABOVE? 

;

; OPTIONAL OUTPUT PARAMETERS:
;    None

;

; ACCEPTED KEY-WORDS:
;    help      = If set print this help

;

; COMMON BLOCKS:
;    None

;

; SIDE EFFECTS:

;    initializes !dustem_data and !dustem_show
;    wavelengths are forced to be the central filter wavelength for photometric data

;

; RESTRICTIONS:

;    The DustEMWrap IDL code must be installed
; 

; PROCEDURE:
;    None

;

; EXAMPLES
;    dustem_init

;    dir=!dustem_wrap_soft_dir+'/Data/EXAMPLE_OBSDATA/'
;    file=dir+'example_SED_1.xcat'

;    spec=read_xcat(file,/silent)

;    dustem_set_data,m_fit=spec,m_show=spec
;    nb: in this example *!dustem_data and *!dustem_show end up identical

;

; MODIFICATION HISTORY:

;    Written by J.-Ph. Bernard 2007

;    V. Guillet (2012) : dustem_set_data is turned into a function which can be used 
;                        indifferently for sed, ext, polext

;    I. Choubani (2022): dustem_set_data is turned into a procedure for emission/extinction with/without polarization.

;    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_set_data'
  goto,the_end
ENDIF

;Cleaninig fitting/showing structure(s) 

for i=0L,n_tags(*!dustem_data)-1 do begin
    (*!dustem_data).(i) = ptr_new()
    (*!dustem_show).(i) = ptr_new()

endfor

;Outputs have the format required by !dustem_data and the subsequent fitting process.
dustem_check_data, m_fit,x_fit,sed=sed,ext=ext,polext=polext, $
                   polsed=polsed,polfrac=polfrac,psi_em=psi_em, $
                   qsed=qsed,used=used,qext=qext,uext=uext, $
                   psi_ext=psi_ext,fpolext=fpolext

;FITTING STRUCTURE INITIALIZATION

IF isa(sed) THEN (*!dustem_data).sed = ptr_new(sed)
IF isa(ext) THEN (*!dustem_data).ext = ptr_new(ext)

;####################

;RELIC. For Annie to judge if this is necessary

; If f_HI is specified, multiply the data by f_HI

If keyword_set(f_HI) and ptr_valid((*!dustem_data).sed) then begin
    if f_HI gt 0 then (*(*!dustem_data).sed).values *= f_HI else f_HI = 1.

endif else f_HI = 1.

if keyword_set(f_HI) and ptr_valid((*!dustem_data).ext) then begin
    if f_HI gt 0 then (*(*!dustem_data).ext).values *= f_HI else f_HI = 1.

endif else f_HI = 1.
defsysv,'!dustem_f_HI',f_HI
;####################

;Problem here is that the user can activate !run_pol without wanting to be in polarization mode. 

;reinitialze !run_pol here? IC - January 2023
; March 2023 -- Annie commented following lines since they prevent using a model to
; generate SEDs.
;; If !run_pol THEN BEGIN
;;    If tag_exist(*!dustem_show,'QSED') THEN BEGIN
;;         IF ~isa((*!dustem_data).qsed) THEN !run_pol=0 
;;     ENDIF ELSE !run_pol=0
;; ENDIF

if !run_pol then begin

    if keyword_set(m_fit) then begin

        teststks = isa(qsed) and isa(used)

        IF ~teststks  then message, 'Stokes parameters are not set correctly. Please check the input structure. Aborting...'

        message, 'Polarization component(s) to fit: QSED and USED' ,/continue

        IF isa(qsed) THEN BEGIN        

            (*!dustem_data).qsed = ptr_new(qsed)

            ;RELIC

            if keyword_set(f_HI) then if f_HI gt 0 then $

          	(*(*!dustem_data).qsed).values *= f_HI

        ENDIF    

        if isa(used) then BEGIN

            (*!dustem_data).used = ptr_new(used)

            ;RELIC

            if keyword_set(f_HI) then if f_HI gt 0 then $

          	(*(*!dustem_data).used).values *= f_HI

        ENDIF

        
        if isa(polsed) then BEGIN
            

            (*!dustem_data).polsed = ptr_new(polsed)

            ;RELIC

            if keyword_set(f_HI) then if f_HI gt 0 then $

          	(*(*!dustem_data).polsed).values *= f_HI

            
        ENDIF 
        
        if isa(polfrac) then BEGIN
            

            (*!dustem_data).polfrac = ptr_new(polfrac)

            ;RELIC

            if keyword_set(f_HI) then if f_HI gt 0 then $

          	(*(*!dustem_data).polfrac).values *= f_HI

        ENDIF

        
        if isa(psi_em) then BEGIN
            

            (*!dustem_data).psi_em = ptr_new(psi_em)

            ;RELIC

            if keyword_set(f_HI) then if f_HI gt 0 then $

          	(*(*!dustem_data).psi_em).values *= f_HI

        
        ENDIF 
        

    endif

    if keyword_set(x_fit) then begin

        testexstks = isa(qext) and isa(uext)

        IF ~testexstks then message, 'Extinction stokes parameters/Polarization data is not set correctly. Please check the input structure. Aborting...'
         

        ;EXTINCTION - 
        

        message, 'Extinction polarization component(s) to fit: QEXT and UEXT',/continue
       

        if isa(polext) then BEGIN        

            (*!dustem_data).polext = ptr_new(polext)

            if keyword_set(f_HI) then if f_HI gt 0 then $

           	(*(*!dustem_data).polext).values *= f_HI

        ENDIF

        IF isa(qext) THEN BEGIN        

            (*!dustem_data).qext = ptr_new(qext)

            if keyword_set(f_HI) then if f_HI gt 0 then $

           	(*(*!dustem_data).qext).values *= f_HI

        ENDIF

        if isa(uext) then BEGIN 

            (*!dustem_data).uext = ptr_new(uext)

            if keyword_set(f_HI) then if f_HI gt 0 then $

           	(*(*!dustem_data).uext).values *= f_HI

        ENDIF

        if isa(psi_ext) then BEGIN 

            (*!dustem_data).psi_ext = ptr_new(psi_ext)

            if keyword_set(f_HI) then if f_HI gt 0 then $

           	(*(*!dustem_data).psi_ext).values *= f_HI

        ENDIF
        

        ;added for completeness 
        if isa(fpolext) then BEGIN        

            (*!dustem_data).fpolext = ptr_new(fpolext)

            if keyword_set(f_HI) then if f_HI gt 0 then $

           	(*(*!dustem_data).fpolext).values *= f_HI

        ENDIF
        

    endif

endif

;SHOWING STRUCTURE / IT IS NEEDED TO BE ABLE TO LOCATE THE HIDDEN DATA POINTS WHEN COMPARING WITH !dustem_data.
;when creating the HUGE system variable JP wants to create. We'll be able to omit it from DusteEMWrap for good.

if keyword_set(m_fit) and not keyword_set(m_show) then m_show=m_fit
if keyword_set(x_fit) and not keyword_set(x_show) then x_show = x_fit

dustem_check_data, m_show,x_show,sed=sed,ext=ext,polext=polext, $
                   polsed=polsed,polfrac=polfrac,psi_em=psi_em, $
                   qsed=qsed,used=used,qext=qext,uext=uext, $
                   psi_ext=psi_ext,fpolext=fpolext

IF isa(sed) THEN (*!dustem_show).sed = ptr_new(sed)
IF isa(ext) THEN (*!dustem_show).ext = ptr_new(ext)

  
;####################

;RELIC

; If f_HI is specified, multiply the data by f_HI

If keyword_set(f_HI) and ptr_valid((*!dustem_show).sed) then begin
    if f_HI gt 0 then (*(*!dustem_show).sed).values *= f_HI else f_HI = 1.

endif else f_HI = 1.

if keyword_set(f_HI) and ptr_valid((*!dustem_show).ext) then begin
    if f_HI gt 0 then (*(*!dustem_show).ext).values *= f_HI else f_HI = 1.

endif else f_HI = 1.
defsysv,'!dustem_f_HI',f_HI
;####################

if !run_pol then begin

    if isa(m_show) then begin ; because sometimes this keyword isn't set.

        
        teststks = isa(qsed) and isa(used)
        

        IF (~teststks and ~isa(polsed)) or (~teststks and ~isa(polfrac)) then message, 'Stokes parameters/Polarization showing data is not set correctly. Please check the input structure. Aborting...'

        If isa(polsed) then BEGIN    ;Apply changes to !dustem_data here.      

            (*!dustem_show).polsed = ptr_new(polsed)

            if keyword_set(f_HI) then if f_HI gt 0 then $

           	(*(*!dustem_show).polsed).values *= f_HI

        ENDIF
        If isa(polfrac) then BEGIN        

            (*!dustem_show).polfrac = ptr_new(polfrac)

            if keyword_set(f_HI) then if f_HI gt 0 then $

           	(*(*!dustem_show).polfrac).values *= f_HI

        ENDIF
        IF isa(qsed) THEN BEGIN        

            (*!dustem_show).qsed = ptr_new(qsed)

            if keyword_set(f_HI) then if f_HI gt 0 then $

           	(*(*!dustem_show).qsed).values *= f_HI

        ENDIF    
        if isa(used) then BEGIN

            (*!dustem_show).used = ptr_new(used)

            if keyword_set(f_HI) then if f_HI gt 0 then $

           	(*(*!dustem_show).used).values *= f_HI

        ENDIF
        if isa(psi_em) then BEGIN

            (*!dustem_show).psi_em = ptr_new(psi_em)

            if keyword_set(f_HI) then if f_HI gt 0 then $

            (*(*!dustem_show).psi_em).values *= f_HI

        ENDIF        
    endif

    if isa(x_show) then begin

        teststks = isa(qext) and isa(uext)
        

        IF (~teststks) then message, 'Extinction stokes parameters/Polarization data is not set correctly. Please check the input structure. Aborting...'

        ;EXTINCTION
        if isa(polext) then BEGIN        

            (*!dustem_show).polext = ptr_new(polext)

            if keyword_set(f_HI) then if f_HI gt 0 then $

           	(*(*!dustem_show).polext).values *= f_HI

        ENDIF
        IF isa(qext) THEN BEGIN        

            (*!dustem_show).qext = ptr_new(qext)

            if keyword_set(f_HI) then if f_HI gt 0 then $

           	(*(*!dustem_show).qext).values *= f_HI

        ENDIF
        if isa(uext) then BEGIN 

            (*!dustem_show).uext = ptr_new(uext)

            if keyword_set(f_HI) then if f_HI gt 0 then $

           	(*(*!dustem_show).uext).values *= f_HI

        ENDIF
        if isa(psi_ext) then BEGIN 

            (*!dustem_show).psi_ext = ptr_new(psi_ext)

            if keyword_set(f_HI) then if f_HI gt 0 then $

           	(*(*!dustem_show).psi_ext).values *= f_HI

        ENDIF

        
        ;Added for completeness
        
        if isa(fpolext) then BEGIN        

            (*!dustem_show).fpolext = ptr_new(fpolext)

            if keyword_set(f_HI) then if f_HI gt 0 then $

           	(*(*!dustem_show).fpolext).values *= f_HI

        ENDIF
        

    endif
endif

IF keyword_set(rchi2_weight) THEN BEGIN

	(*!fit_rchi2_weight).sed     = rchi2_weight.sed
	(*!fit_rchi2_weight).ext     = rchi2_weight.ext

	IF !run_pol THEN BEGIN

    	IF isa(qsed) THEN (*!fit_rchi2_weight).qsed  = rchi2_weight.qsed
    	IF isa(used) THEN (*!fit_rchi2_weight).used  = rchi2_weight.used

    	IF isa(qext) THEN (*!fit_rchi2_weight).qext  = rchi2_weight.qext
    	IF isa(uext) THEN (*!fit_rchi2_weight).uext  = rchi2_weight.uext

    ENDIF
    

ENDIF ELSE BEGIN

    (*!fit_rchi2_weight).sed=1.
    (*!fit_rchi2_weight).ext=1.

    
    If !run_pol THEN BEGIN

        IF isa(qsed) THEN (*!fit_rchi2_weight).qsed=1.
        IF isa(used) THEN (*!fit_rchi2_weight).used=1.

        IF isa(qext) THEN (*!fit_rchi2_weight).qext=1.
        IF isa(uext) THEN (*!fit_rchi2_weight).uext=1.

    ENDIF

ENDELSE

; ;Setting the data and wavelength tags in '!dustem_fit'
; ;ask about it because !dustem_fit's tag was initially empty...s
; ((*!dustem_fit).data)=ptr_new(!dustem_data)

IF not ptr_valid((*!dustem_data).sed) AND not ptr_valid((*!dustem_data).ext) THEN BEGIN
  message,'dustemwrap system variable was not set properly.',/continue
  message,'Check the existence of at least some non undefined values in StokesI and sigmaII.',/continue
  stop
ENDIF

the_end:

END