PRO dustem_write_fits_table,filename=filename,help=help

;+
; NAME:
;    dustem_write_fits_table
; PURPOSE:
;    Write a fits table with content of current Dustem system variables
; CATEGORY:
;    Dustem
; CALLING SEQUENCE:
;    dustem_write_fits_table,file[,/help]
; INPUTS:
;    file      = File name
; OPTIONAL INPUT PARAMETERS:
;    None
; OUTPUTS:
;    None
; OPTIONAL OUTPUT PARAMETERS:
;    None
; ACCEPTED KEY-WORDS:
;    help      = If set, print this help
; COMMON BLOCKS:
;    None
; SIDE EFFECTS:
;    File is stored.
; RESTRICTIONS:
;    The dustem idl wrapper must be installed
; PROCEDURE:
;    None
; EXAMPLES
;    
; MODIFICATION HISTORY:

;    Written by J.-Ph. Bernard July 2022
;    Evolution details on the DustEMWrap gitlab.
;    See http://dustemwrap.irap.omp.eu/ for FAQ and help.  

;-

; !DUSTEM_DAT = '/tmp/devteam1/scratch/'       
; !DUSTEM_DATA = -> <PtrHeapVar4>

; !DUSTEM_DO_CC =        1

; !DUSTEM_F90_EXEC = '/path_to_fortran_dustem/src/dustem'

; !DUSTEM_FILTERS = <PtrHeapVar570>
; !DUSTEM_FIT = <PtrHeapVar1>
; !DUSTEM_F_HI =       1.00000   
; !DUSTEM_IDL_CONTINUUM =       0.00000
; !DUSTEM_IDL_FREEFREE =       0.00000
; !DUSTEM_IDL_SYNCHROTRON =       0.00000
; !DUSTEM_INPUTS = <PtrHeapVar2>
; !DUSTEM_INSTRUMENT_DESCRIPTION = -> <Anonymous> Array[120]
; !DUSTEM_NEVER_DO_CC =        0 
; !DUSTEM_PARAMS = <PtrHeapVar15>
; !DUSTEM_PARINFO = <PtrHeapVar943>
; !DUSTEM_PREVIOUS_CC = <PtrHeapVar3346>

; !DUSTEM_RES = '/tmp/devteam1/scratch/'       

; !DUSTEM_SHOW_PLOT =        1 

; !DUSTEM_SOFT_DIR = '/path_to_fortran_dustem/'

; !DUSTEM_VERBOSE =        1

; !DUSTEM_WHICH = 'RELEASE'
; !DUSTEM_WRAP_SOFT_DIR = '/path_to_dustemwrap/'

; !FIT_RCHI2_WEIGHT = -> <Anonymous> Array[1]
; !RUN_ANIS =       0.00000
; !RUN_CIRC =       0.00000      
; !RUN_IONFRAC =       0.00000
; !RUN_LIN =       1.00000
; !RUN_POL =        1
; !RUN_RRF =       0.00000
; !RUN_TLS =       0.00000
; !RUN_UNIV =       0.00000

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

;===== run dustem to get predicted spectrum and sed
IF not keyword_set(function_name) THEN BEGIN 
  dustem_predicted_sed=dustem_compute_sed(*(*!dustem_fit).current_param_values,out_st=dustem_spectra_st)
ENDIF ELSE BEGIN
ENDELSE

Ngrains=n_tags(dustem_spectra_st.sed)-2

;===== define structures containing results
one_str_input_SED={FILTER:'',Wavelength:0.,I:0.,Q:0.,U:0.,varianceII:0.,varianceQQ:0.,varianceUU:0.}
one_str_predicted_SED={FILTER:'',Wavelength:0.,I:0.,Q:0.,U:0.}

;one_str_predicted_spectrum_tot={Wavelength:0.,I:0.,Q:0.,U:0.}
;one_str_predicted_spectrum_grain1={Wavelength:0.,I:0.,Q:0.,U:0.}

Nsed=n_elements((*(*!dustem_data).sed).filt_names)

str_input_SED=replicate(one_str_input_SED,Nsed)

str_input_SED.FILTER=(*(*!dustem_data).sed).filt_names
str_input_SED.Wavelength=(*(*!dustem_data).sed).wav
str_input_SED.I=(*(*!dustem_data).sed).values
str_input_SED.varianceII=(*(*!dustem_data).sed).sigma   ;should it be squared ??

N_predicted_sed=n_elements(dustem_predicted_sed)
str_predicted_SED=replicate(one_str_predicted_SED,N_predicted_sed)

str_predicted_SED.FILTER=(*(*!dustem_data).sed).filt_names    ;taken from input SED
str_predicted_SED.Wavelength=(*(*!dustem_data).sed).wav       ;taken from input SED

str_predicted_SED.I=dustem_predicted_sed    ;but where is Q,U ??
;str_predicted_SED.Q=
;str_predicted_SED.U=

;str_predicted_spectrum_grains=ptrarr(Ngrains)
;FOR i=0L,Ngrains-1 DO BEGIN
;	str_predicted_spectrum_grains[i]=ptr_new(dustem_spectra_st.sed)
;ENDFOR

N_predicted_spectra=n_elements(dustem_spectra_st.sed)

;str_predicted_spectrum_tot=replicate(one_str_predicted_spectrum_tot,N_predicted_spectra)
;str_predicted_spectrum_tot.Wavelength=dustem_spectra_st.SED.wav
;str_predicted_spectrum_tot.I=dustem_spectra_st.SED.em_tot

;str_predicted_spectrum_tot.Q=dustem_spectra_st.polsed         ;not exactly, should have Q,U
;str_predicted_spectrum_tot.U=dustem_spectra_st.polsed         ;not exactly, should have Q,U

;===== Fill in header with parameter values
parameters_desc=*(*!dustem_fit).PARAM_DESCS
parameters_init_values=*(*!dustem_fit).PARAM_INIT_VALUES
best_parameters=*(*!dustem_fit).CURRENT_PARAM_VALUES
best_parameters_uncertainties=*(*!dustem_fit).CURRENT_PARAM_ERRORS
best_fit_chi2=(*!dustem_fit).CHI2
best_fit_rchi2=(*!dustem_fit).RCHI2

Nparams=n_elements(parameters_desc)

;unit_input_sed=1
;unit_predicted_sed=2
;unit_predicted_spectra=3
;unit_predicted_extinctions=4

;stop

file='./dustem_wrap_output.fits'

;==== Write the observed SED in extension 1

unit=1L

mwrfits,str_input_SED,file,/create

unit_input_sed=unit
unit=unit+1

;==== add the predicted SED in extension 2
mwrfits,str_predicted_SED,file

unit_predicted_sed=unit
unit=unit+1

;==== add the predicted total spectrum in extension 3

;mwrfits,str_predicted_spectrum_tot,file
;==== add the predicted per-grain spectrum in extension 4
;stop
mwrfits,dustem_spectra_st.sed,file
unit_predicted_spectra=unit
unit=unit+1
;==== add the predicted per-grain extinction in extension 5
mwrfits,dustem_spectra_st.ext,file
unit_predicted_extinctions=unit
;FOR i=0L,Ngrains-1 DO BEGIN
;	mwrfits,*str_predicted_spectrum_grains[i],file
;ENDFOR

;print,unit_input_sed,unit_predicted_sed,unit_predicted_spectra,unit_predicted_extinctions
;stop

;===== read back extensions to get proper extension headers

file='./dustem_wrap_output.fits'

sst_input_sed=mrdfits(file,unit_input_sed,header_input_sed)
sst_predicted_SED=mrdfits(file,unit_predicted_sed,header_predicted_SED)
;sst_predicted_spectrum_tot=mrdfits(file,3,header_predicted_spectrum_tot)
dustem_spectra_st.sed=mrdfits(file,unit_predicted_spectra,header_predicted_spectra)
dustem_spectra_st.ext=mrdfits(file,unit_predicted_extinctions,header_predicted_extinctions)
;FOR i=0L,Ngrains-1 DO BEGIN
;	str_predicted_spectrum_grains[i]=ptr_new(dustem_spectra_st.sed.(i+1))
;ENDFOR
;headers_predicted_spectrum_grain=ptrarr(Ngrains)
;FOR i=0L,Ngrains-1 DO BEGIN
;	*str_predicted_spectrum_grains[i]=mrdfits(file,3+i+1,hh)
;	headers_predicted_spectrum_grain[i]=ptr_new(hh)
;ENDFOR

;===== complement extension header for input SED
sxaddpar,header_input_sed,'TITLE','OBSERVED INPUT SED TO DUSTEMWRAP',before='COMMENT'
sxaddpar,header_input_sed,'TTYPE1','FILTER','Dustemwrap Filter name'
sxaddpar,header_input_sed,'TTYPE2','WAVELENGTH','Dustemwrap Filter reference wavelength [microns]'
sxaddpar,header_input_sed,'TTYPE3','I','Observed Total Stokes I Intensity [??]'
sxaddpar,header_input_sed,'TTYPE4','Q','Observed Stokes Q Intensity [??]'
sxaddpar,header_input_sed,'TTYPE5','U','Observed Stokes U Intensity [??]'
sxaddpar,header_input_sed,'TTYPE6','VARIANCEII','Observed Total Stokes I Variance [??]'
sxaddpar,header_input_sed,'TTYPE7','VARIANCEQQ','Observed Stokes Q Variance [??]'
sxaddpar,header_input_sed,'TTYPE8','VARIANCEUU','Observed Stokes U Variance [??]'

;===== complement extension header for predicted SED
sxaddpar,header_predicted_SED,'TITLE','OUTPUT BEST FIT SED BY DUSTEMWRAP'
sxaddpar,header_predicted_SED,'TTYPE1','FILTER','Dustemwrap Filter name'
sxaddpar,header_predicted_SED,'TTYPE2','WAVELENGTH','Dustemwrap Filter reference wavelength [microns]'
sxaddpar,header_predicted_SED,'TTYPE3','I','Observed Total Stokes I Intensity [??]'
sxaddpar,header_predicted_SED,'TTYPE4','Q','Observed Stokes Q Intensity [??]'
sxaddpar,header_predicted_SED,'TTYPE5','U','Observed Stokes U Intensity [??]'
sxaddpar,header_predicted_SED,'CHI2',best_fit_chi2,'Dustemwrap best fit chi2 [-]'
sxaddpar,header_predicted_SED,'RCHI2',best_fit_rchi2,'Dustemwrap best fit reduced chi2 [-]'

sxaddpar,header_predicted_SED,'NGRAINS',Ngrains,'Number of grain species'

;====== write dustem wrap parameter names
sxaddpar,header_predicted_SED,'COMMENT','======= Dustemwrap parameter names ======',after='RCHI2'

sxaddpar,header_predicted_SED,'NPARAMS',Nparams,' Number of DustemWrap free parameters'

FOR i=0L,Nparams-1 DO BEGIN
	sxaddpar,header_predicted_SED,'PARN'+strtrim(i+1,2),parameters_desc[i],' DustemWrap parameter name'
ENDFOR
sxaddpar,header_predicted_SED,'COMMENT','===================================================',after='PARN'+strtrim(i,2)

;====== write dustem wrap parameter best fit values

sxaddpar,header_predicted_SED,'COMMENT','======= Dustemwrap parameter best fit values ======',after='COMMENT'
FOR i=0L,Nparams-1 DO BEGIN
	sxaddpar,header_predicted_SED,'PARV'+strtrim(i+1,2),best_parameters[i],'Param. '+parameters_desc[i]
ENDFOR
sxaddpar,header_predicted_SED,'COMMENT','===================================================',after='PARV'+strtrim(i,2)

;====== write dustem wrap parameter best fit values uncertainties
sxaddpar,header_predicted_SED,'COMMENT','======= Dustemwrap best fit parameter uncertainties ======',after='COMMENT'
FOR i=0L,Nparams-1 DO BEGIN
	sxaddpar,header_predicted_SED,'PARU'+strtrim(i+1,2),best_parameters_uncertainties[i],'Param. '+parameters_desc[i]
ENDFOR
sxaddpar,header_predicted_SED,'COMMENT','===================================================',after='PARIU'+strtrim(i,2)

;====== write dustem wrap parameter initial fit values
sxaddpar,header_predicted_SED,'COMMENT','======= Dustemwrap parameter initial fit values ======',after='COMMENT'
FOR i=0L,Nparams-1 DO BEGIN
	sxaddpar,header_predicted_SED,'PARI'+strtrim(i+1,2),parameters_init_values[i],'Param. '+parameters_desc[i]
ENDFOR
sxaddpar,header_predicted_SED,'COMMENT','===================================================',after='PARIV'+strtrim(i,2)

;===== complement extension header for predicted spectrum total
sxaddpar,header_predicted_spectrum_tot,'TITLE','OUTPUT BEST FIT TOTAL SPECTRUM BY DUSTEMWRAP'

sxaddpar,header_predicted_spectra,'TITLE','OUTPUT BEST FIT PER-GRAIN AND TOTAL EMISSION SPECTRA BY DUSTEMWRAP'
sxaddpar,header_predicted_extinctions,'TITLE','OUTPUT BEST FIT PER-GRAIN AND TOTAL EXTINCTION BY DUSTEMWRAP'

;FOR i=0L,Ngrains-1 DO BEGIN
;	hh=*headers_predicted_spectrum_grain[i]
;	sxaddpar,hh,'TITLE','OUTPUT BEST FIT SPECTRUM BY DUSTEMWRAP FOR GRAIN '+strtrim(i+1,2)
;	*headers_predicted_spectrum_grain[i]=hh
;ENDFOR

;write final file
IF keyword_set(filename) THEN BEGIN
	file=filename
ENDIF ELSE BEGIN
	file='/tmp/dustem_wrap_ouput_final.fits'
ENDELSE

;==== Write the observed SED in extension 1
mwrfits,str_input_SED,file,header_input_sed,/create

unit=unit+1

;==== add the predicted SED in extension 2
mwrfits,str_predicted_SED,file,header_predicted_SED
;==== add the predicted total spectrum in extension 3

;mwrfits,str_predicted_spectrum_tot,file,header_predicted_spectrum_tot
;==== add the predicted spectrum for each grain type in extension 4 - 4+Ngrains
;FOR i=0L,Ngrains-1 DO BEGIN
;	mwrfits,*str_predicted_spectrum_grains[i],file,*headers_predicted_spectrum_grain[i]
;ENDFOR
;==== add the predicted per-grain spectrum in extension 3
;stop
mwrfits,dustem_spectra_st.sed,file,header_predicted_spectra
;==== add the predicted per-grain extinction in extension 4
mwrfits,dustem_spectra_st.ext,file,header_predicted_extinctions

message,'Wrote '+file,/info

;stop
;hprint,header_input_sed
;hprint,header_predicted_SED

the_end:

END