PRO dustem_fit_sed_ext_stokesi_example,model=model $ ,sed_file=sed_file $ ,ext_file=ext_file $ ,Nitermax=Nitermax $ ,postscript=postscript $ ,fits_save=fits_save $ ,wait=wait $ ,noobj=noobj $ ,help=help $ ,verbose=verbose ;+ ; NAME: ; dustem_fit_sed_ext_stokesi_example ; ; PURPOSE: This routine is an example of how to fit an observational ; data in emission + extinction SED (StokesI only) 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_stokesi_example[,model=][sed_file=][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_test_model_exists.pro ; for more details about available models in current ; release. Default for this example is J13. ; 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 to ; identify the filters, and the model is used to generate a ; predicted SED. ; 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 identify the wavelength range, and the dust model ; is used to generate the corresponding extinction. ; 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. ; 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_stokesi_example ; dustem_fit_sed_ext_stokesi_example,Nitermax=1,fits_save='/tmp/mysavefile.fits' ; dustem_fit_sed_ext_stokesi_example,model='MC10' ; ; 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_stokesi_example' goto,the_end END IF keyword_set(model) THEN BEGIN use_model=strupcase(model) ENDIF ELSE BEGIN use_model='J13' ENDELSE exists=dustem_test_model_exists(use_model) if exists ne 1 then $ message,'Unknown 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=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. ;; ;=== AN EXAMPLE FOR J13 ;; ;=== Here we fit the dust abundances of the J13 model, the ;; ;=== intensity of the dust-heating radiation field as well as two plug-ins: ;; ;=== (i) free-free emission ;; ;=== (ii)continuum due to a blackbody ;; ;=== The temperature of the blackbody is fixed to 1000K ;; ;=== The free parameters in the fit are all lower-bounded at zero. ;=== If you choose a different dust model, you will need to adjust the ;=== parameter information accordingly. pd = [ $ '(*!dustem_params).G0' $ ;G0 ,'(*!dustem_params).grains(0).mdust_o_mh'$ ;CM20 -- power law size distribution ,'(*!dustem_params).grains(1).mdust_o_mh'$ ;CM20 -- logN size distribution ,'(*!dustem_params).grains(2).mdust_o_mh' $ ;aPyM5 ,'(*!dustem_params).grains(3).mdust_o_mh' $ ;aOlM5 ,'dustem_plugin_continuum_2'] ;Intensity at peak of the BB continuum true_vals = [1.5,1.8e-3, 6.e-4, 3.5e-3, 3.55e-3, 0.003] iv = [1.2,1.7e-3, 6.3e-4, 2.55e-3, 2.55e-3, 0.001] Npar=n_elements(pd) ulimed=replicate(0,Npar) llimed=replicate(1,Npar) llims=replicate(1.e-15,Npar) fpd=[ 'dustem_plugin_continuum_1'] ; Temperature of the BB fiv=[1000.] 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 TEMPLATE 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+' dust model',/info ext.EXT_I=1. ENDIF ;=== READ TEMPLATE 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_2.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+' dust model',/info sed.StokesI=1. 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 ;== GENERATE THE EXTINCTION DATA USING THE MODEL AND TRUE VALUES if not keyword_set(ext_file) then $ ext.EXT_I = dustem_compute_ext(true_vals,st=st) ;== GENERATE THE EMISSION DATA USING THE MODEL AND TRUE VALUES IF not keyword_set(sed_file) THEN $ sed.StokesI = dustem_compute_sed(true_vals,st=st) ;=== 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, m_fit=sed,m_show=sed,x_fit=ext,x_show=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 ;=== MAKE THE FINAL PLOT IF keyword_set(postscript) THEN BEGIN ; dir_ps='./' mydevice=!d.name set_plot,'PS' ps_file=postscript device,filename=ps_file,/color ENDIF IF !dustem_noobj THEN BEGIN dustemwrap_plot_noobj,(*(*!dustem_fit).CURRENT_PARAM_VALUES),st=dummy,xr=xr,/xstyle,yr=yr,/ysty,/ylog,/xlog,tit_m=tit_m+' (Final fit)',tit_x=tit_x+' (Final fit)' ENDIF ELSE BEGIN dustemwrap_plot,(*(*!dustem_fit).CURRENT_PARAM_VALUES),st=dummy,xr=xr,/xstyle,yr=yr,/ysty,/ylog,/xlog,tit_m=tit_m+' (Final fit)',tit_x=tit_x+' (Final fit)' ENDELSE IF keyword_set(postscript) THEN BEGIN device,/close set_plot,mydevice 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) 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 ;; dustem_read_fits_table,filename=fits_save,dustem_st=dustem_spectra_st ;; ;==== plot result taken from the saved fits table ;; res=*(*!dustem_fit).CURRENT_PARAM_VALUES ;; ;If the user prefers non-OOP plotting then reset !dustem_noobj=1 here since dustem_init is called in reads_fits_table. ;; IF !dustem_noobj THEN BEGIN ;; dustemwrap_plot_noobj,res,st=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,st=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,/info wait,wait ENDIF ENDIF the_end: message,'Finished dustem_fit_sed_ext_stokesi_example',/info END