dustem_fit_ext_pol_example.pro
17.6 KB
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PRO dustem_fit_ext_pol_example,model=model $
,ext_file=ext_file $
,Nitermax=Nitermax $
,fits_save_and_restore=fits_save_and_restore $
,wait=wait $
,help=help
;+
; NAME:
; dustem_fit_ext_pol_example
;
; PURPOSE:
; This routine is an example of how to fit an observational extinction SED
; (StokesI,Q,U) 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.
;
; See the DustEMWrap User Guide for more information.
;
; CATEGORY:
; DustEMWrap, Distributed, High-Level, User Example
;
; CALLING SEQUENCE:
; dustem_fit_ext_pol_example[,model=][ext_file=][,postscript=][,Nitermax=][,fits_save_and_restore=][,/help,/wait,/verbose]
;
; 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)
; 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/Mathis1990_DISM.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
;
; 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_ext_pol_example
; dustem_fit_ext_pol_example,Nitermax=1,fits_save_and_restore='/tmp/mysavefile.fits'
; dustem_fit_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_ext_pol_example'
goto,the_end
END
IF keyword_set(model) THEN BEGIN
use_model=strupcase(model)
ENDIF ELSE BEGIN
use_model='G17_MODELA' ;Default is last dustem model
ENDELSE
use_polarization=0. ;default is no polarization in models
;IC: NOT NEEDED SINCE THE PLOTTING IS INTERNAL
use_window=2 ; default graphics window number to use for plotting the results
use_verbose=0
if keyword_set(verbose) then use_verbose=1
;=== 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
rv = [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
rv = [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
rv = [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
rv = [ $
; 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
rv = [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'] ;aSil
;'dustem_plugin_continuum_2'] ;Intensity of NIR continuum
rv = [5.4e-4, 5.4e-4,1.8e-4]
Npar=n_elements(pd)
ulimed=replicate(0,Npar)
llimed=replicate(1,Npar)
llims=replicate(0.,Npar)
use_polarization=0
;=== 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
'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
rv = [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
rv = [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
rv = [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,/pol;,kwords=['logn','plaw','plaw'];,polarization=use_polarization
;; ***END COMMENT AH***
!dustem_nocatch=1
!dustem_verbose=use_verbose
;!dustem_show_plot=1
!EXCEPT=2
;=== READ EXAMPLE DATA: EXTINCTION
dir=!dustem_wrap_soft_dir+'/Data/EXAMPLE_OBSDATA/'
file=dir+'Mathis1990_DISM.xcat' ;We should add the serkowski xcat's content into the MATHIS one right?
;if keyword_set(ext) then file=ext ; not really needed for the tests
IF keyword_set(ext_file) THEN file=ext_file
ext=read_xcat(file,/silent)
;=== GENERATE EXAMPLE DATA: EXTINCTION
;filters=['IRAS1','IRAS2','IRAS3','IRAS4','PACS3','SPIRE1','SPIRE2','SPIRE3','HFI2','HFI3','HFI4','HFI5','HFI6','LFI1','LFI2','LFI3']
;Nfilt=n_elements(filters)
;ext=dustem_initialize_ext(Nfilt)
;ext.filter=replicate('SPECTRUM',Nfilt)
;Using these filters to set the wavelengths
;ext.wave=dustem_filter2wav(filters)
;ext.instru=replicate('EXTINCTION', Nfilt);don't really know what to put here ;dustem_filter2instru(filters)
;=== initializing IQU and associated errors to avoid problems when checking SED in dustem_set_data.pro
ext.EXT_I=1.
for i=4l,n_tags(ext)-1 do begin
ext.(i) = ext.EXT_I/1E13
endfor
; ind=where(spec.sigextII EQ 0.,count)
; IF count NE 0 THEN spec[ind].sigextII=(0.2*spec(ind).EXT_I)^2
; ind=where(spec.instru EQ 'FIRAS',count) ; I do not know what this is for (WHY FIRAS)... maybe an old remnant of the older procedures
; IF count NE 0 THEN spec[ind].sigextII=(0.2*spec(ind).EXT_I)^2
;###Before merging any xcat files we'll just displace the initial parameter array.
;###Creating fake extinction data: (already replaced iv by rv)
;###Creating observational strcture using xcat file (for simplicity)
;###Initializing the structure tags so that dustem_set_data sets said tags in !dustem_data
; for i=4l,n_tags(spec) -1 do begin
;
; ;initial loop
; ;actually only data pertaining to Q and U need to be set.
; ;but dustem_set_data will take care of the tags of the !dustem_data structure pertaining to other polarization quantities
; ;The content of the xcat file shouldn't not/isn't used after this in the main procedure
; if (tag_names(spec))[i] ne 'SIGEXTII' then begin
; spec.(i) = spec.(3)/1E12 ;just to fill the tags...
; ;This gives really high sigma values
; endif
;
; endfor
;###first call to dustem_set_data so that the !dustem_data tags that are used in the 'compute_' procedures are set
dustem_set_data,m_fit,m_show,ext,ext
;stop
iv = rv+[10.00E-4,10.00E-4,10.00E-4] ;###setting the initial parameter vector
;== 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=fpd
dustem_init_fixed_params,fpd,fiv
;generation of the fake data (since dustem_set_data takes ONE structure containing all the info)
!dustem_psi_ext=25
ext.EXT_I = dustem_compute_ext(rv,st=st)
toto = dustem_compute_stokext(rv,st=st,qext_spec=dustem_qext,uext_spec=dustem_uext)
ext.EXT_Q = toto[0]
ext.EXT_U = toto[1]
;stop
;==== JPB
;below m_fit does not exist, so there is no emission data to plot, and therefore, no emission data to plot.
;; ***END COMMENT AH***
;== SET THE OBSERVATIONAL STRUCTURE
dustem_set_data, m_fit,m_show,ext,ext;sed=spec)
; dustem_init_fixed_params,fpd,fiv
;== RUN THE FIT
tol=1.e-10
use_Nitermax=30 ;maximum number of iterations.
IF keyword_set(Nitermax) THEN use_Nitermax=Nitermax
xr_x=[0.01,30]
yr_x=[1.00E-10,10]
tit='Spectral Energy Distribution'
ytit=textoidl('I_\nu (MJy/sr) for N_H=10^{20} H/cm^2')
xtit=textoidl('\lambda (\mum)')
;Set show_plot to 0 to hide plot
;Commented or set to 1 is the same since !dustem_show_plot (existing sysvar) is initialized to 1 in dustem_init
;show_plot = 0
t1=systime(0,/sec)
res=dustem_mpfit_data(tol=tol,Nitermax=use_Nitermax,gtol=gtol $
,/xlog,/ylog,xr_x=xr_x,yr_x=yr_x,xtit=xtit,ytit=ytit,title=tit $
,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(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
;stop
dustem_read_fits_table,filename=fits_save_and_restore,dustem_st=dustem_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_st,xr=xr,/xstyle,yr=yr,/ysty,/ylog,/xlog,title=tit+' (From Saved FITS file)'
ENDIF ELSE BEGIN
dustemwrap_plot,res,dustem_st,xr=xr,/xstyle,yr=yr,/ysty,/ylog,/xlog,title=tit+' (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_ext_pol_example',/info
the_end:
END