FUNCTION dustem_compute_stokes,p_dim,$
                               st=st,$
                               Q_spec=Q_spec,$
                               U_spec=U_spec,$
                               PSI_spec=PSI_spec,$
                               dustem_psi_em=dustem_psi_em,$
                               help=help

;+
; NAME:
;    dustem_compute_stokes
;
; PURPOSE:
;    Computes Stokes Parmeters SEDs for a given Dustem spectrum
;
; CATEGORY:
;    Dustem
;
; CALLING SEQUENCE:
;    out=dustem_compute_stokes(p_dim[,st=][,Q_spec=][,U_spec=][,PSI_spec=][,dustem_psi_em=][,/help])
;
; INPUTS:
;    p_dim      = parameter values
;
; OPTIONAL INPUT PARAMETERS:
;    st        = Dustem structure
;
; OUTPUTS:
;    out        = List Containing the Stokes parameters emission for spectrum points in !dustem_data 
;    out[0]     = Computed Stokes Q emission for spectrum points in !dustem_data
;    out[1]     = Computed Stokes U emission for spectrum points in !dustem_data 
;
; OPTIONAL OUTPUT PARAMETERS:
;    st          = Dustem output structure
;    Q_spec        = Dustem Stokes Q emission 
;    U_spec        = Dustem Stokes U emission
;    PSI_spec      = Dustem Polarization angle output in emission
;    dustem_psi_em = Computed Polarization angle ouput for spectrum points in !dustem_data
;
; ACCEPTED KEY-WORDS:
;    help      = If set, print this help
;
; COMMON BLOCKS:
;    None
;
; SIDE EFFECTS:
;    None
;
; RESTRICTIONS:
;    The DustEMWrap IDL code must be installed
;
; PROCEDURES:
;    None
;
; EXAMPLES
;    
; MODIFICATION HISTORY:
;    Written by J.-Ph. Bernard 2021
;    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_compute_stokes'
    out=0.
    goto,the_end
ENDIF

IF not keyword_set(st) THEN $
    dustem_activate_plugins,p_dim/(*(*!dustem_fit).param_init_values),st=st

fact = 1.e4*(*!dustem_HCD)/(4.*!pi)/(3.e8/1.e-6/(st.polsed).wav)*1.e20/1.e7
stI = st.sed.em_tot * fact    ;This is Total intensity I
P = st.polsed.em_tot * fact   ;This is Polarized intensity P

Nwaves=(size(stI))[1]

frac=P/stI
tes=where(finite(frac) eq 0)
frac(tes)=0.

scopes=tag_names((*!dustem_plugin))
IF scopes[0] NE 'NONE' THEN BEGIN
  FOR i=0L,n_tags(*!dustem_plugin)-1 DO BEGIN   
      
      IF total(strsplit((*(*!dustem_plugin).(i).scope),'+',/extract) EQ 'REPLACE_POLSED') THEN BEGIN
          
          Q_spec = (*(*!dustem_plugin).(i).spec)[*,1]
          U_spec = (*(*!dustem_plugin).(i).spec)[*,2]
          
      ENDIF 

  ENDFOR    
  
ENDIF

  IF ~isa(Q_spec) && ~isa(U_spec) THEN BEGIN
      polar_ippsi2iqu,stI,Q_spec,U_spec,frac,replicate(!dustem_psi,Nwaves);     
  ENDIF    

IF scopes[0] NE 'NONE' THEN BEGIN          
  FOR i=0L,n_tags(*!dustem_plugin)-1 DO BEGIN
      
      IF total(strsplit((*(*!dustem_plugin).(i).scope),'+',/extract) EQ 'ADD_POLSED') THEN BEGIN
          
          Q_spec+=(*(*!dustem_plugin).(i).spec)[*,1]
          U_spec+=(*(*!dustem_plugin).(i).spec)[*,2]
          
      
      ENDIF

  ENDFOR

ENDIF
;-----------------------------------------
ind=where(finite(U_spec) NE 1 OR finite(Q_spec) NE 1,count)
IF count NE 0 THEN BEGIN
  message,'Q or U is NaN',/continue
  stop
ENDIF

;Hard-coded block so that atan(U,Q) does not return wrong values when Q eq -0
testnzero = where(Q_spec EQ -0., ct_nzero)
if ct_nzero ne 0 then Q_spec[testnzero] = 0
testnzero = where(U_spec EQ -0., ct_nzero)
if ct_nzero ne 0 then U_spec[testnzero] = 0


PSI_spec = 0.5*atan(U_spec,Q_spec)/!dtor
;polar_iqu2ippsi,stI,Q_spec,U_spec,p_bidon,PSI_spec ;same but this line runs several commands for each iteration of this current procedure

;INITIALIZING THE STOKES SEDS
dustem_qsed = (*(*!dustem_data).qsed).values * 0.
dustem_used = (*(*!dustem_data).used).values * 0.
;using a list because the arrays can have different dimensions
;this doesn't change anything ...
out=list(fltarr(n_elements(dustem_qsed)),fltarr(n_elements(dustem_used)))
if not isarray(stI) THEN stop ; I don't get this test. It is unnecessary.

;Performing color corrections on the dustem spectra and generating the SEDs at the given filters 

IF !dustem_do_cc NE 0 AND !dustem_never_do_cc EQ 0 THEN BEGIN
    message,'DOING color correction calculations',/info
ENDIF ELSE BEGIN
    message,'SKIPPING color correction calculations',/info
ENDELSE

ind_qsed=where((*(*!dustem_data).qsed).filt_names NE 'SPECTRUM',count_qsed)
ind_used=where((*(*!dustem_data).used).filt_names NE 'SPECTRUM',count_used)
  
  
IF count_qsed NE 0 THEN BEGIN 
  filter_names=((*(*!dustem_data).qsed).filt_names)[ind_qsed]
  if isa(dustem_qsed) then begin 
    sqsed=dustem_cc(st.polsed.wav,Q_spec,filter_names,cc=cc)
    dustem_qsed[ind_qsed]=sqsed
  endif
ENDIF

IF count_used NE 0 THEN BEGIN
  filter_names=((*(*!dustem_data).used).filt_names)[ind_used]
  if isa(dustem_used) then begin
    sused=dustem_cc(st.polsed.wav,U_spec,filter_names,cc=cc)
    dustem_used[ind_used]=sused
  endif
ENDIF


;For spectrum data points, interpolate in log-logdustem_compute_stokes.pro
;Linear interpolation leads to wrong values, in particular where few
;wavelengths points exist in the model (long wavelengths).

ind_qspec=where((*(*!dustem_data).qsed).filt_names EQ 'SPECTRUM',count_qspec)
ind_uspec=where((*(*!dustem_data).used).filt_names EQ 'SPECTRUM',count_uspec)

IF count_qspec NE 0 THEN BEGIN
  if isa(dustem_qsed) then dustem_qsed[ind_qspec]=interpol(Q_spec,st.polsed.wav,(((*(*!dustem_data).qsed).wav)[ind_qspec]))  
ENDIF

IF count_uspec NE 0 THEN BEGIN
  if isa(dustem_used) then dustem_used[ind_uspec]=interpol(U_spec,st.polsed.wav,(((*(*!dustem_data).used).wav)[ind_uspec]))
ENDIF

;generating interpolates for Psi_em
dustem_psi_em = 0.5*atan(dustem_used,dustem_qsed)/!dtor

out[0]=dustem_qsed
out[1]=dustem_used

;clean pointers
heap_gc

the_end:

RETURN,out

END