PRO dustem_fit_ext_pol_example,model=model $ ,ext_file=ext_file $ ,Nitermax=Nitermax $ ,postscript=postscript $ ,fits_save=fits_save $ ,wait=wait $ ,noobj=noobj $ ,help=help $ ,verbose=verbose ;+ ; 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. ; ; 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=][,/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. See userguide or dustem_init.pro for more details about ; available models. ; 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 to define the observational structure, and a synthetic ; observation is generated using the dust model. ; Nitermax = maximum number of fit iterations. Default is 5. ; postscript = if set, final plot is saved as postscript file ; fits_save = if set, save the fit results in a binary ; FITS file. ; 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_ext_pol_example ; dustem_fit_ext_pol_example,Nitermax=1,fits_save='/tmp/mysavefile.fits' ; dustem_fit_ext_pol_example,model='G17_MODELD' ; ; MODIFICATION HISTORY: ; Written by JPB Apr-2021 ; 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_MODELD' ENDELSE exists=dustem_test_model_exists(use_model,/pol) if exists ne 1 then $ message,'Unknown/unpolarised dust model: '+use_model 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=1 ; 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_polx_2' ] true_vals = [7.1e-4, 1.3e-3,5.6e-3,35.] ; these are the true values that will be used to generate the data if no ext_file is specified iv = true_vals+[5.00E-4,-7.00E-4,8.00E-4,5] ; 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 llims=replicate(1.e-15,Npar) use_polarization=1 ;=== Fixed parameters fpd=[] ;==initial parameter values for fixed parameters fiv=[] 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) ;;=== 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) = ext.EXT_I/1.E10 endfor ENDIF ;=== HERE WE SET THE DATA SO THAT THE COMPUTE_ FUNCTIONS BELOW HAVE ;=== THE NECESSARY FIELDS AND INFORMATION ;== note that m_fit and m_show do not exist -- this is deliberate ;== since we are not treating emission data dustem_set_data, m_fit=m_fit,m_show=m_show,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 with parameters and plugins',/info wait,wait ENDIF ;stop if not keyword_set(ext_file) then begin ;== GENERATE THE 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) ext.EXT_Q = toto[0] ext.EXT_U = toto[1] ;stop ;== RESET THE OBSERVATIONAL STRUCTURE ;== note that m_fit and m_show do not exist -- this is deliberate ;== since we are not treating emission data dustem_set_data, m_fit=m_fit,m_show=m_show,x_fit=ext,x_show=ext IF keyword_set(wait) THEN BEGIN message,'Finished generating a synthetic EXT from the model '+use_model,/info wait,wait ENDIF end ;stop ;== INFORMATION TO RUN THE FIT tol=1.e-10 ;=== INFORMATION TO MAKE THE PLOTS ;=== _x/_extinction means extinction plots, _m/_emissions means emission plots xr_x=[0.01,30] yr_fpolext=[1.00E-10,50] ;yr_fpolext=[1e-4,30] tit='Dust Optical Depth' ;=== RUN THE FIT ;stop t1=systime(0,/sec) res=dustem_mpfit_data(tol=tol,Nitermax=use_Nitermax,gtol=gtol $ ,/xlog,/ylog,xr_x=xr_x,yr_fpolext=yr_fpolext,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(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='./' mydevice=!d.name set_plot,'PS' ; ps_file=dir_ps+postscript ps_file=postscript device,filename=ps_file,/color ENDIF ;stop IF !dustem_noobj THEN BEGIN dustemwrap_plot_noobj,*(*!dustem_fit).CURRENT_PARAM_VALUES,st=dummy,xr=xr,/xstyle,yr=yr,/ysty,/ylog,/xlog,title=tit+' (Final fit)' ENDIF ELSE BEGIN dustemwrap_plot,*(*!dustem_fit).CURRENT_PARAM_VALUES,st=dummy,xr=xr,/xstyle,yr=yr,/ysty,/ylog,/xlog,title=tit+' (Final fit)' ENDELSE IF keyword_set(postscript) THEN BEGIN device,/close set_plot,mydevice message,'Wrote '+ps_file,/info ENDIF IF keyword_set(fits_save) THEN BEGIN message,'Writing out results structure: '+fits_save,/info dustem_write_fits_table,filename=fits_save,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 ;; Moved the following to dustem_fitsio_example.pro ;; dustem_read_fits_table,filename=fits_save,dustem_st=dustem_st ;; ;==== plot result taken from the saved fits table ;; res=*(*!dustem_fit).CURRENT_PARAM_VALUES ;; !dustem_end=-1; subsequent calls to the fit. 0 is intialization an 1 is for the last iteration. It's initialized to 0 after the creation of the fits file. ;; IF !dustem_noobj THEN BEGIN ;; dustemwrap_plot_noobj,res,st=dustem_st,xr=xr,/xstyle,yr=yr,/ysty,/ylog,/xlog,title=tit+' (From Saved FITS file)' ;; ENDIF ELSE BEGIN ;; dustemwrap_plot,res,st=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 made a plot using the data in this file',/info wait,wait ENDIF ENDIF the_end: message,'Finished dustem_fit_ext_pol_example',/info END