dustem_fit_intensity_example.pro
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PRO dustem_fit_intensity_example,model=model $
,sed_file=sed_file $
,Nitermax=Nitermax $
,postscript=postscript $
,fits_save_and_restore=fits_save_and_restore $
,help=help
;This routine is an example of how to fit observational SEDs with
;DustEM and DustEMWrap. The objective is to illustrate how to use DustEMWrap
; (and not to do science -- the fit obtained by running this example is
; likely to be poor!)
;
;For this example, the code uses the SED in the file example_SED_1.xcat,
;which is distributed in the Data/EXAMPLE_OBSDATA/ directory
;
;The example SED has Stokes I photometric data points from SPITZER
;IRAC and MIPS and IRAS. Examples illustrating running DustEMWrap to
;fit data with spectral data, polarisation data and extinction data
;are provided in other _readme routines in the src/idl/ directory.
;; ***COMMENT AH***
;; Remove or update the next few lines -->>
;; No spectrum data points.
;;SPECTRUM data points can be included and the corresponding filter
;;filed must read SPECTRUM. Note that its is note necessary
;;to use the .xcat file format, and data SED can be provided
;;manually, but the observation structure must have the structure shown below.
;;For the example to work, the DustEM and DustEMWrap packages must have
;;been configured and installed succesfully.
;;See dustem_cvs_readme.txt for install instructions).
;; *** END COMMENT AH***
;+
; NAME:
; dustem_fit_intensity_example
; PURPOSE:
; This is an example of how to fit SEDs with DustEMWrap.
; It is intended as an example to follow when writing your own
; programs to analyse data with DustEMWrap.
; CATEGORY:
; DustEMWrap, Distributed, High-Level, User Example
; CALLING SEQUENCE:
; dustem_fit_intensity_example[,model=][sed_file=][,postscript=][,Nitermax=][,fits_save_and_restore=][,/help]
; INPUTS:
; None
; OPTIONAL INPUT PARAMETERS:
; None
; OUTPUTS:
; None
; OPTIONAL OUTPUT PARAMETERS:
; Plots, Results save structure
; ACCEPTED KEY-WORDS:
; model = specifies the interstellar dust mixture used by DustEM
; 'MC10' model from Compiegne et al 2010 (default)
; '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/SEDs/sample_SED.xcat' is used.
; postscript = if set, final plot is saved as postscript in the
; current working directory
; Nitermax = maximum number of fit iterations. Default is 5.
; fits_save_and_restore = if set, saves results in a fits file, restore the file and plot restored results
; help = if set, print this help
; 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:
; *** COMMENT AH --> is this really NONE? ****
; EXAMPLES
; dustem_fit_intensity_example
; dustem_fit_intensity_example,Nitermax=1,fits_save_and_restore='/tmp/mysavefile.fits'
; dustem_fit_intensity_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_intensity_example'
goto,the_end
END
IF keyword_set(model) THEN BEGIN
use_model=strupcase(model)
ENDIF ELSE BEGIN
use_model='MC10' ;Default is last dustem model
ENDELSE
use_polarization=0. ;default is no polarization in models
use_window=2 ; default graphics window number to use for plotting the results
;=== 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
CASE use_model OF
'DBP90':BEGIN
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_plugin_continuum_2'] ;Intensity of NIR continuum
iv = [1.0, 4.3e-4, 4.7e-4,6.4e-3,0.001]
Npar=n_elements(pd)
ulimed=replicate(0,Npar)
llimed=replicate(1,Npar)
llims=replicate(0.,Npar)
END
'DL01':BEGIN
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', $ ;Gra
'(*!dustem_params).grains(3).mdust_o_mh', $ ;Gra
'(*!dustem_params).grains(4).mdust_o_mh', $ ;aSil
'dustem_plugin_continuum_2'] ;Intensity of NIR continuum
iv = [1.0,5.4e-4, 5.4e-4,1.8e-4,2.33e-3,8.27e-3,0.001]
Npar=n_elements(pd)
ulimed=replicate(0,Npar)
llimed=replicate(1,Npar)
llims=replicate(0.,Npar)
END
'WD01_RV5p5B':BEGIN
;; ***COMMENT AH***
;; we need to implement this, or remove
message, 'WD01 model not yet implemented in DustEMWrap',/info
;; ***END COMMENT AH***
END
'DL07':BEGIN
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', $ ;Gra
'(*!dustem_params).grains(3).mdust_o_mh', $ ;Gra
'(*!dustem_params).grains(4).mdust_o_mh', $ ;aSil
'dustem_plugin_continuum_2'] ;Intensity of NIR continuum
iv = [1.0,5.4e-4, 5.4e-4,1.8e-4,2.33e-3,8.27e-3,0.001];,10,1.,10.,1.]
Npar=n_elements(pd)
ulimed=replicate(0,Npar)
llimed=replicate(1,Npar)
llims=replicate(0.,Npar)
END
'MC10':BEGIN
pd = [ $
;'(*!dustem_params).gas.G0', $ ;G0
; 'dustem_plugin_continuum_2', $ ;intensity of NIR continuum
; 'dustem_plugin_synchrotron_2',$
'(*!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_params).grains(3).mdust_o_mh', $ ;amCBEx
'(*!dustem_params).grains(4).mdust_o_mh' $ ;aSilx
]
;initial parameter values for parameters to be fitted
iv = [ $
; 1.0, $
; 0.002, $ ;intensity of NIR continuum
; 0.01,$
7.8e-4, $ ;mass fraction of PAH0
7.8e-4, $ ;mass fraction of PAH1
1.65e-4, $ ;mass fraction of amCBEx
1.45e-3, $ ;mass fraction of amCBEx
7.8e-3 $ ;mass fraction of aSilx
]
Npar=n_elements(pd)
ulimed=replicate(0,Npar)
llimed=replicate(1,Npar)
llims=replicate(0.,Npar)
;=== Fixed parameters
;parameter description of parameters to be set to a non-default value
fpd=[ $
'(*!dustem_params).gas.G0' , $ ;multiplicative factor to total ISRF
'dustem_plugin_continuum_2' $ ;intensity of NIR continuum
]
;initial parameter values for fixed parameters
fiv=[ $
1. , $ ;multiplicative factor to total ISRF
3.e-3$ ;intensity of NIR continuum
]
;; ***END COMMENT AH***
END
'J13':BEGIN
pd = [ $
'(*!dustem_params).G0', $ ;G0
'(*!dustem_params).grains(1).mdust_o_mh',$ ;PAH1 mass fraction
'(*!dustem_params).grains(0).mdust_o_mh',$ ;PAH0 mass fraction
'(*!dustem_params).grains(2).mdust_o_mh', $ ;amCBEx
'(*!dustem_params).grains(3).mdust_o_mh', $ ;amCBEx
'(*!dustem_params).grains(4).mdust_o_mh', $ ;aSil
'dustem_plugin_continuum_2'] ;Intensity of NIR continuum
iv = [1.0, 7.8e-4, 7.8e-4,1.65e-4,1.45e-3,7.8e-3,0.001]
Npar=n_elements(pd)
ulimed=replicate(0,Npar)
llimed=replicate(1,Npar)
llims=replicate(0.,Npar)
END
'G17_MODELA':BEGIN
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', $ ;Gra
'(*!dustem_params).grains(3).mdust_o_mh', $ ;Gra
'(*!dustem_params).grains(4).mdust_o_mh', $ ;aSil
'dustem_plugin_continuum_2'] ;Intensity of NIR continuum
iv = [1.0,5.4e-4, 5.4e-4,1.8e-4,2.33e-3,8.27e-3,0.001]
Npar=n_elements(pd)
ulimed=replicate(0,Npar)
llimed=replicate(1,Npar)
llims=replicate(0.,Npar)
use_polarization=0
END
'G17_MODELB':BEGIN
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', $ ;Gra
'(*!dustem_params).grains(3).mdust_o_mh', $ ;Gra
'(*!dustem_params).grains(4).mdust_o_mh', $ ;aSil
'dustem_plugin_continuum_2'] ;Intensity of NIR continuum
iv = [1.0,5.4e-4, 5.4e-4,1.8e-4,2.33e-3,8.27e-3,0.001]
Npar=n_elements(pd)
ulimed=replicate(0,Npar)
llimed=replicate(1,Npar)
llims=replicate(0.,Npar)
use_polarization=1
END
'G17_MODELC':BEGIN
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', $ ;Gra
'(*!dustem_params).grains(3).mdust_o_mh', $ ;Gra
'(*!dustem_params).grains(4).mdust_o_mh', $ ;aSil
'dustem_plugin_continuum_2'] ;Intensity of NIR continuum
iv = [1.0,5.4e-4, 5.4e-4,1.8e-4,2.33e-3,8.27e-3,0.001]
Npar=n_elements(pd)
ulimed=replicate(0,Npar)
llimed=replicate(1,Npar)
llims=replicate(0.,Npar)
use_polarization=1
END
'G17_MODELD':BEGIN
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', $ ;Gra
'(*!dustem_params).grains(3).mdust_o_mh', $ ;Gra
'(*!dustem_params).grains(4).mdust_o_mh', $ ;aSil
'dustem_plugin_continuum_2'] ;Intensity of NIR continuum
iv = [1.0,5.4e-4, 5.4e-4,1.8e-4,2.33e-3,8.27e-3,0.001]
Npar=n_elements(pd)
ulimed=replicate(0,Npar)
llimed=replicate(1,Npar)
llims=replicate(0.,Npar)
use_polarization=1
END
'ELSE':BEGIN
message,'model '+model+' unknown',/continue
message,'Known models are MC10,DBP90,DL01,DL07,J13,G17_MODELA,G17_MODELB,G17_MODELC,G17_MODELD',/continue
stop
END
ENDCASE
;== INITIALISE DUSTEM
;; ***COMMENT AH***
;; do we need the use_polarization key word activated here? -->
;; len(kwords) must match Npar_dust (i.e. without plugins), otherwise
;; fails in dustem_read_grain -- should set this within the above case statement?
;; IC: yes good idea. Maybe by default set 'kwords' to the original dust keywords and let the user modify kwords(i) where i is the index of the dust species.
dustem_init,model=use_model;,kwords=['plaw-ed','logn','plaw-ed','plaw-ed','plaw-ed'];,polarization=use_polarization
;; ***END COMMENT AH***
!dustem_nocatch=1
!dustem_verbose=1
!dustem_show_plot=1
;=== READ EXAMPLE Intensity SED DATA
dir=!dustem_wrap_soft_dir+'/Data/EXAMPLE_OBSDATA/'
file=dir+'example_SED_1.xcat'
IF keyword_set(sed_file) THEN file=sed_file
sed=read_xcat(file,/silent)
;; ***COMMENT AH***
;; explain what we are doing here -->
ind=where(sed.sigmaII EQ 0.,count)
IF count NE 0 THEN sed[ind].sigmaII=(0.2*sed[ind].StokesI)^2
ind=where(sed.instru EQ 'FIRAS',count)
IF count NE 0 THEN sed[ind].sigmaII=(0.2*sed[ind].StokesI)^2
;; ***END COMMENT AH***
;== SET THE OBSERVATIONAL STRUCTURE
;st=dustem_set_data(m_fit=sed,m_show=sed)
dustem_set_data,sed,sed
;== SET INITIAL VALUES AND LIMITS OF THE PARAMETERS THAT WILL BE
;== ADJUSTED DURING THE FIT
dustem_init_parinfo,pd,iv,up_limited=ulimed,lo_limited=llimed,up_limits=ulims,lo_limits=llims
;== INITIALIZE ANY PLUGINS
dustem_init_plugins,pd,fpd
;== INITIALIZE ANY FIXED PARAMETERS FOR PLUGINS
dustem_init_fixed_params,fpd,fiv
;== RUN THE FIT
tol=1.e-16 ;fit tolerence
use_Nitermax=5 ;maximum number of iterations.
IF keyword_set(Nitermax) THEN use_Nitermax=Nitermax
yr=[1.00e-4,1.00E2]
xr=[1.00E0,6.00e4]
tit='Spectral Energy Distribution'
ytit=textoidl('I_\nu (MJy/sr) for N_H=10^{20} H/cm^2')
xtit=textoidl('\lambda (\mum)')
t1=systime(0,/sec)
res=dustem_mpfit_data(tol=tol,Nitermax=use_Nitermax,gtol=gtol $
,/xlog,/ylog,xr=xr,yr=yr,xtit=xtit,ytit=ytit,title=tit $
,legend_xpos=legend_xpos,legend_ypos=legend_ypos $
,errors=errors,chi2=chi2,rchi2=rchi2)
t2=systime(0,/sec)
;=== Do final plot
IF keyword_set(postscript) THEN BEGIN
dir_ps='./'
set_plot,'PS'
ps_file=dir_ps+postscript
device,filename=ps_file,/color
ENDIF
dustemwrap_plot,*(*!dustem_fit).CURRENT_PARAM_VALUES,bidon,xr=xr,/xstyle,yr=yr,/ysty,/ylog,/xlog,title=tit+' (Final fit)'
IF keyword_set(postscript) THEN BEGIN
set_plot,'X'
device,/close
message,'Wrote '+ps_file,/info
ENDIF
IF keyword_set(fits_save_and_restore) THEN BEGIN
dustem_write_fits_table,filename=fits_save_and_restore,help=help
;could erase all dustem system variables here
dustem_read_fits_table,filename=fits_save_and_restore,dustem_spectra_st=dustem_spectra_st
;==== plot result taken from the saved fits table
res=*(*!dustem_fit).CURRENT_PARAM_VALUES
; try=dustem_run(*(*!dustem_fit).CURRENT_PARAM_VALUES)
stop
dustemwrap_plot,res,dustem_spectra_st,xr=xr,/xstyle,yr=yr,/ysty,/ylog,/xlog,title=tit+' (From Saved Fits)'
ENDIF
message,'Finished dustem_fit_sed_readme',/info
the_end:
END