dustem_fit_sed_ext_pol_example.pro
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PRO dustem_fit_sed_ext_pol_example,model=model $
,sed_file=sed_file $
,ext_file=ext_file $
,Nitermax=Nitermax $
,fits_save_and_restore=fits_save_and_restore $
,wait=wait $
,noobj=noobj $
,help=help $
,verbose=verbose
;+
; NAME:
; dustem_fit_sed_ext_pol_example
;
; PURPOSE: This routine is an example of how to fit an observational
; data in emission + extinction SED (StokesI,Q,U) with DustEM and
; DustEMWrap.
;
; See the DustEMWrap User Guide for more information.
;
; CATEGORY:
; DustEMWrap, Distributed, High-Level, User Example
;
; CALLING SEQUENCE:
; dustem_fit_sed_ext_pol_example[,model=][sed_file=][ext_file=][,Nitermax=][,fits_save_and_restore=][,/help,/wait,/verbose,/noobj]
;
; INPUTS:
; None
;
; OPTIONAL INPUT PARAMETERS:
; None
;
; OUTPUTS:
; None
;
; OPTIONAL OUTPUT PARAMETERS:
; Plots, results structure in binary FITS table format
;
; ACCEPTED KEY-WORDS:
; model = specifies the interstellar dust mixture used by DustEM
; 'MC10' model from Compiegne et al 2010
; 'DBP90' model from Desert et al 1990
; 'DL01' model from Draine & Li 2001
; 'WD01_RV5P5B' model from Weingartner & Draine 2002 with Rv=5.5
; 'DL07' model from Draine & Li 2007
; 'J13' model from Jones et al 2013, as updated in
; Koehler et al 2014
; 'G17_ModelA' model A from Guillet et al (2018). Includes
; polarisation. See Tables 2 and 3 of that paper for details.
; 'G17_ModelB' model B from Guillet et al (2018)
; 'G17_ModelC' model C from Guillet et al (2018)
; 'G17_ModelD' model A from Guillet et al (2018)
; sed_file = string naming the path to text file in .xcat format that
; describes the observational SED. If not set, the file
; 'Data/EXAMPLE_OBSDATA/example_SED_2.xcat' is used.
; ext_file = string naming the path to text file in .xcat format that
; describes the observational extinction SED. If not set, the file
; 'Data/EXAMPLE_OBSDATA/Mathis90Fitz99_DISM_NH20.xcat' is used.
; Nitermax = maximum number of fit iterations. Default is 5.
; fits_save_and_restore = if set, save the fit results in a binary
; FITS file. The code then restore this file and plots
; the results using the saved results information.
; help = if set, print this help
; wait = if set, wait this many seconds between each step of
; the code (for illustration purposes)
; verbose = if set, subroutines will run in verbose mode
; noobj = if set, runs with no object graphics
;
; COMMON BLOCKS:
; None
;
; SIDE EFFECTS:
; None
;
; RESTRICTIONS:
; The DustEM fortran code must be installed
; The DustEMWrap IDL code must be installed
;
; PROCEDURES AND SUBROUTINES USED:
;
; EXAMPLES
; dustem_fit_sed_ext_pol_example
; dustem_fit_sed_ext_pol_example,Nitermax=1,fits_save_and_restore='/tmp/mysavefile.fits'
; dustem_fit_sed_ext_pol_example,model='DBP90'
;
; MODIFICATION HISTORY:
; Written by JPB Apr-2011
; 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_fit_sed_ext_pol_example'
goto,the_end
END
IF keyword_set(model) THEN BEGIN
use_model=strupcase(model)
ENDIF ELSE BEGIN
use_model='G17_MODELD'
ENDELSE
known_mdls=['MC10','DBP90','DL01','WD01_RV5P5B','DL07','J13','G17_MODELA','G17_MODELB','G17_MODELC','G17_MODELD']
test_model = where(known_mdls eq use_model,ct)
if ct eq 0 then begin
message,'ISM dust model '+use_model+' unknown',/continue
message,'Known models are MC10,DBP90,DL01,WD01_RV5P5B,DL07,J13,G17_MODELA,G17_MODELB,G17_MODELC,G17_MODELD',/continue
stop
end
use_polarization=0. ;default is no polarization in models
use_window=2 ; default graphics window number to use for plotting the results
use_verbose=0
if keyword_set(verbose) then use_verbose=1
use_Nitermax=5 ; maximum number of iterations for the fit
IF keyword_set(Nitermax) THEN use_Nitermax=Nitermax
dustem_define_la_common
;=== Set the (model-dependent) parameters that you want to fit
;=== Refer to the DustEM and DustEMWrap userguides for an explanation
; of the different grain types
;=== Set the (model-dependent) parameters that you want to fit (pd),
;=== their initial values (iv)
;=== and whether they are bounded (ulimed,llimed,llims,ulims).
;=== Fixed parameters (fpd) and their values (fiv) are also set here.
;=== Refer to the DustEM and DustEMWrap User guides for an explanation
;=== of the physical meaning of dust model and plug-in parameters, and
;=== how to specify them.
;=== Example is provided for G17_MODELD
;=== If you choose a different dust model, you will need to adjust the
;=== parameter information accordingly.
pd = [ $
'(*!dustem_params).grains(0).mdust_o_mh',$ ;PAH0 mass fraction
'(*!dustem_params).grains(1).mdust_o_mh',$ ;amCBE mass fraction
'(*!dustem_params).grains(2).mdust_o_mh',$ ;aSil
'dustem_plugin_modify_dust_pol_2', $
'dustem_plugin_modify_dust_polx_2' ]
true_vals = [5.4e-4, 6.4e-4,4.8e-4, 48., 52] ; these are the true values that will be used to generate the data
iv = true_vals+[2.00E-4,-2.00E-4,2.00E-4,10, -10] ; this is the vector of starting guesses for the fit
Npar=n_elements(pd)
ulimed=replicate(0,Npar)
llimed=replicate(1,Npar) & llimed[3]=0 & llimed[4]=0
llims=replicate(1.e-15,Npar)
use_polarization=1
;=== Fixed parameters
fpd=[ $
'(*!dustem_params).G0' , $ ;multiplicative factor to total ISRF
'dustem_plugin_continuum_2' $ ;intensity of a BB continuum
]
;=== Initial parameter values for fixed parameters
fiv=[ $
1. , $ ;multiplicative factor to total ISRF
3.e-3$ ;intensity of BB continuum
]
if keyword_set(wait) then begin
message,'Finished setting dust model and plug-in parameters: '+use_model,/info
wait,wait
end
;== INITIALISE DUSTEM
dustem_init,model=use_model,polarization=use_polarization
!dustem_nocatch=1
!dustem_verbose=use_verbose
IF keyword_set(noobj) THEN !dustem_noobj=1
!EXCEPT=2 ; for debugging
;=== READ OBSERVATIONAL EXTINCTION DATA
;=== IF THE USER DOES NOT PROVIDE AN EXTINCTION CURVE FILE , WE READ MATHIS TO INITIALISE THE OBSERVATIONAL STRUCTURE.
dir=!dustem_wrap_soft_dir+'/Data/EXAMPLE_OBSDATA/'
use_ext_file=dir+'Mathis90Fitz99_DISM_NH20.xcat'
IF keyword_set(ext_file) THEN use_ext_file=ext_file
ext=read_xcat(use_ext_file,/silent)
IF not keyword_set(ext_file) THEN BEGIN
message, 'You have not provided an extinction curve. I will generate one from the '+use_model+' model',/info
;;=== CREATE ENTRIES FOR ALL STOKES (OTHERWISE NEXT CALL TO
;;=== DUSTEM_SET_DATA WILL COMPLAIN SINCE WE HAVE INITIALISED
;;=== DUSTEM IN POLARIZATION MODE
;;=== WE ASSUME THAT A USER-PROVIDED EXT CURVE WILL SATISFY ALL REQUIREMENTS
ext.EXT_I=1.
for i=4l,n_tags(ext)-1 do begin
ext.(i) = 1.E-15
endfor
ENDIF
;=== READ OBSERVATIONAL EMISSION DATA
;=== IF THE USER DOES NOT PROVIDE A SED FILE , WE READ AN EXAMPLE_SED FILE TO INITIALISE THE OBSERVATIONAL STRUCTURE.
dir=!dustem_wrap_soft_dir+'/Data/EXAMPLE_OBSDATA/'
file=dir+'example_SED_3.xcat'
if keyword_set(sed_file) then file=sed_file
sed=read_xcat(file,/silent)
IF not keyword_set(sed_file) THEN BEGIN
message, 'You have not provided an SED. I will generate one from the '+use_model+' model',/info
;;=== CREATE ENTRIES FOR ALL STOKES (OTHERWISE NEXT CALL TO
;;=== DUSTEM_SET_DATA WILL COMPLAIN SINCE WE HAVE INITIALISED
;;=== DUSTEM IN POLARIZATION MODE
;;=== WE ASSUME THAT A USER-PROVIDED SED CURVE WILL SATISFY ALL REQUIREMENTS
sed.StokesI=1.
for i=4l,n_tags(sed)-1 do begin
sed.(i) = 1.E-15
endfor
ENDIF
;=== HERE WE SET THE DATA SO THAT THE COMPUTE_ FUNCTIONS BELOW HAVE
;=== THE NECESSARY FIELDS AND INFORMATION
dustem_set_data,m_fit=sed,m_show=sed,x_fit=ext,x_show=ext
;== SET INITIAL VALUES AND LIMITS OF THE PARAMETERS FOR THE FIT
;== AND ACTIVATE ANY PLUGINS (HENCE WE NEED TO DO THIS BEFORE THE COMPUTE_ CALLS)
dustem_init_params,use_model,pd,iv,fpd=fpd,fiv=fiv,ulimed=ulimed,llimed=llimed,ulims=ulims,llims=llims,polarization=use_polarization
if keyword_set(wait) then begin
message,'Finished initializing DustEMWrap, including plugins and fixed parameters',/info
wait,wait
end
if not keyword_set(ext_file) then begin
;== GENERATE THE EXTINCTION DATA USING THE MODEL AND TRUE VALUES
ext.EXT_I = dustem_compute_ext(true_vals,st=st)
toto = dustem_compute_stokext(true_vals,st=st,Qext_spec=dustem_qext,Uext_spec=dustem_uext)
ext.EXT_Q = toto[0]
ext.EXT_U = toto[1]
end
IF not keyword_set(sed_file) THEN BEGIN
;== GENERATE THE EMISSION DATA USING THE MODEL AND TRUE VALUES
sed.StokesI = dustem_compute_sed(true_vals,st=st)
toto = dustem_compute_stokes(true_vals,st=st,Q_spec=dustem_qsed,U_spec=dustem_used)
sed.StokesQ = toto[0]
sed.StokesU = toto[1]
end
;=== RESET THE OBSERVATIONAL STRUCTURE IF WE HAVE GENERATED DATA USING
;=== A MODEL
if not keyword_set(ext_file) or not keyword_set(sed_file) THEN BEGIN
dustem_set_data, sed,sed,ext,ext
if keyword_set(wait) then begin
message,'Finished generating data from the model '+use_model,/info
wait,wait
end
end
;== INFORMATION TO RUN THE FIT
tol=1.e-10 ;fit tolerence
;=== INFORMATION TO MAKE THE PLOT
;=== _x/_extinction means extinction plots, _m/_emissions means emission plots
xr_x = [0.01,30]
yr_x = [5.00E-8,10]
xr_m = [1.,5e5]
yr_m = [5e-8,1.00e6]
tit_m='Spectral Energy Distribution'
tit_x='Dust Optical Depth'
;=== RUN THE FIT
t1=systime(0,/sec)
res=dustem_mpfit_data(tol=tol,Nitermax=use_Nitermax,gtol=gtol $
,/xlog,/ylog,xr_m=xr_m,yr_m=yr_m,xr_x=xr_x,yr_x=yr_x,xtit=xtit,ytit=ytit,tit_m=tit_m,tit_x=tit_x $
,legend_xpos=legend_xpos,legend_ypos=legend_ypos $
,errors=errors,chi2=chi2,rchi2=rchi2,show_plot=show_plot)
t2=systime(0,/sec)
if keyword_set(wait) then begin
message,'Finished running DustEMWrap, using Niters: '+strtrim(string(use_Nitermax),2),/info
message,'Time taken [sec]: '+sigfig(t2-t1,2,/sci),/info
wait,wait
end
IF keyword_set(fits_save_and_restore) THEN BEGIN
message,'Writing out results structure: '+fits_save_and_restore,/info
dustem_write_fits_table,filename=fits_save_and_restore,help=help
dustem_read_fits_table,filename=fits_save_and_restore,dustem_st=dustem_spectra_st
;==== plot result taken from the saved fits table
res=*(*!dustem_fit).CURRENT_PARAM_VALUES
IF !dustem_noobj THEN BEGIN
dustemwrap_plot_noobj,res,dustem_spectra_st,xr=xr,/xstyle,yr=yr,/ysty,/ylog,/xlog,tit_m=tit_m+' (From Saved FITS file)',tit_x=tit_x+' (From Saved FITS file)'
ENDIF ELSE BEGIN
dustemwrap_plot,res,dustem_spectra_st,xr=xr,/xstyle,yr=yr,/ysty,/ylog,/xlog,tit_m=tit_m+' (From Saved FITS file)',tit_x=tit_x+' (From Saved FITS file)'
ENDELSE
IF keyword_set(wait) THEN BEGIN
message,'Saved the results as FITS in the file: '+fits_save_and_restore+', and made a plot using the data in this file',/info
wait,wait
ENDIF
ENDIF
message,'Finished dustem_fit_sed_ext_pol_example',/info
the_end:
END