dustem_fit_polarisation_example.pro
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PRO dustem_fit_polarisation_example,model=model $
,sed_file=sed_file $
,Nitermax=Nitermax $
,postscript=postscript $
,fits_save_and_restore=fits_save_and_restore $
,help=help $
,wait=wait $
,verbose=verbose
;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_polarisation_example
;
; PURPOSE:
; This is an example of how to fit observational SEDs (with
; measurements in Stokes IQU) using 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_polarisation_example[,model=][sed_file=][,postscript=][,Nitermax=][,fits_save_and_restore=][,/help,/wait,/verbose]
;
; INPUTS:
; None
;
; OPTIONAL INPUT PARAMETERS:
; None
;
; OUTPUTS:
; None
;
; OPTIONAL OUTPUT PARAMETERS:
; Plots, Results save 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). Default.
; 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_3.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
; 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
; 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_polarisation_example
; dustem_fit_polarisation_example,Nitermax=1,fits_save_and_restore='/tmp/mysavefile.fits'
; dustem_fit_polarisation_example,model='DBP90'
;
; MODIFICATION HISTORY:
; Written by JPB Apr-2022
; 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_polarisation_example'
goto,the_end
END
IF keyword_set(model) THEN BEGIN
use_model=strupcase(model)
ENDIF ELSE BEGIN
use_model='G17_MODELD' ;Default is one of the Guillet et al (2017) models since they treat dust polarisation properties
ENDELSE
known_mdls=['MC10','DBP90','DL01','WD01_RV5P5B','DL07','J13','G17_MODELA','G17_MODELB','G17_MODELC','G17_MODELD']
pol_mdls=['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
test_model = where(pol_mdls eq use_model,ct)
if ct eq 0 then begin
message,'The only models with polarisation are G17_MODELA,G17_MODELB,G17_MODELC,G17_MODELD',/continue
stop
end
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
;; ;=== AN EXAMPLE FOR G17_MODELA/B/C/D
;; ;=== Here we fit the dust abundances of the model, the dust
;; ;=== polarisation and a plug-in:
;; ;=== (i) synchrotron emission (also polarized)
;; ;=== The free parameters in the fit are all lower-bounded at zero. The
;; ;=== intensity of the dust-heating radiation field is fixed to 1.0*G0.
pd = [ $
'(*!dustem_params).grains(0).mdust_o_mh',$ ;PAH0 mass fraction
'(*!dustem_params).grains(1).mdust_o_mh',$ ;PAH0 mass fraction
'(*!dustem_params).grains(2).mdust_o_mh', $ ;PAH1 mass fraction
'dustem_plugin_modify_dust_pol_2', $ ;This will set the polarization angle
'dustem_plugin_synchrotron_2', $ ;Synchrotron amplitude at 10 mm
'dustem_plugin_synchrotron_3', $ ;Synchrotron polarization fraction
'dustem_plugin_synchrotron_4' $ ;Synchrotron polarization angle
]
p_truth=[7.8000E-04,7.8000E-04,7.8000E-04, 10. ,1.e-2, 0.3, 45.]
iv=p_truth+[1.e-4,-1.e-4,1.e-4,-5.,0.,0.1,10] ;initial values shifted from solution
Npar=n_elements(pd)
ulimed=replicate(0,Npar)
llimed=replicate(1,Npar)
llims=replicate(0.,Npar)
fpd=[ '(*!dustem_params).G0'] & fiv=[1.0]
Nfix=n_elements(fpd)
if n_elements(fiv) ne Nfix then begin
message,'Number of fixed parameters (fpd) does not equal number of initial values of fixed parameters (fiv)',/info
stop
end
;Final parameters : 1.0000000 0.00075715537 0.00075280676 0.00092480417 0.010006239 0.29981309 45.000163
;== INITIALISE DUSTEM
;dustem_init,mode=use_model,grain_keywords=['logn-chrg-spin','plaw-pol','plaw-pol'],polarization=1
dustem_init,mode=use_model,polarization=1
!dustem_verbose=1
!dustem_show_plot=1
!dustem_nocatch=1
;=== READ EXAMPLE SED DATA
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)
;== SET THE OBSERVATIONAL STRUCTURE
;== sed is passed twice -- the first occurrence is the SED that you
;== wish to fit, the second occurrence is the SED that you wish to visualise.
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;,tied=tied
;== INITIALIZE ANY PLUGINS
dustem_init_plugins,pd,fpd
;== INITIALIZE ANY FIXED PARAMETERS FOR PLUGINS
if Nfix gt 0 then dustem_init_fixed_params,fpd,fiv
;=== RUN fit
tol=1.e-16
xtol=1.e-16
Nitermax=30; just an initialization
xrange=[1.,2.e4]
yrange=[1e-4,1.e3]
loadct,13
t1=systime(0,/sec)
title='FIT POLARISATION EXAMPLE'
res=dustem_mpfit_data(tol=tol,xtol=xtol,Nitermax=Nitermax,xrange=xrange,/xstyle,yrange=yrange,/ysty,/ylog,/xlog,xtit='wavelength [mic]',ytit='Brightness []',title=title)
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
;=== MAKE THE 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,dummy,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(wait) then begin
message,'Made the plot of the final results',/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
;=== At this point, you could erase all dustem system variables, or exit idl... all the
;=== information needed to recover the results and remake the plots has been saved in the FITS table
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
dustemwrap_plot,res,dustem_spectra_st,xr=xr,/xstyle,yr=yr,/ysty,/ylog,/xlog,title=tit+' (From Saved FITS file)'
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
end
ENDIF
message,'Finished dustem_polarisation_example',/info
stop
the_end:
END