diff --git a/src/idl/dustem_brute_force_fit.pro b/src/idl/dustem_brute_force_fit.pro
index fc9c50c..0675d34 100644
--- a/src/idl/dustem_brute_force_fit.pro
+++ b/src/idl/dustem_brute_force_fit.pro
@@ -1,7 +1,7 @@
FUNCTION dustem_brute_force_fit,sed,table_name,filters,normalize=normalize,fact=fact,chi2=chi2,rchi2=rchi2,show_sed=show_sed
;stop
-;sed must be normalized to NH=1e21 H/cm2
+;sed must be normalized to NH=1e20 H/cm2
defsysv,'!dustem_grid',0,exist=exist
IF exist EQ 0 THEN BEGIN
diff --git a/src/idl/dustem_compute_sed.pro b/src/idl/dustem_compute_sed.pro
index e03d2dd..38a1de6 100755
--- a/src/idl/dustem_compute_sed.pro
+++ b/src/idl/dustem_compute_sed.pro
@@ -1,6 +1,7 @@
FUNCTION dustem_compute_sed,p_dim,$
st=st,$
sed_spec=sed_spec, $
+ use_previous_fortran=use_previous_fortran, $
help=help
;+
@@ -20,7 +21,7 @@ FUNCTION dustem_compute_sed,p_dim,$
; p_dim = parameter values
;
; OPTIONAL INPUT PARAMETERS:
-; st = Dustem output structure
+; st = Dustem Fortran output structure
;
; OUTPUTS:
; sed = computed SED for filters in !dustem_data
@@ -30,6 +31,7 @@ FUNCTION dustem_compute_sed,p_dim,$
; sed_spec = dustem emission spectrum
;
; ACCEPTED KEY-WORDS:
+; use_previous_fortran = if set, uses the output of the previous fortran run, and does not run the fortran.
; help = If set, print this help
;
; COMMON BLOCKS:
@@ -59,7 +61,7 @@ IF keyword_set(help) THEN BEGIN
ENDIF
IF not keyword_set(st) THEN BEGIN
- dustem_activate_plugins,p_dim/(*(*!dustem_fit).param_init_values),st=st
+ dustem_activate_plugins,p_dim/(*(*!dustem_fit).param_init_values),st=st,use_previous_fortran=use_previous_fortran
ENDIF
; Convert into MJy/sr/1d20
@@ -67,20 +69,22 @@ fact = 1.e4*(*!dustem_HCD)/(4.*!pi)/(3.e8/1.e-6/st.sed.wav)*1.e20/1.e7 ;this is
SED_spec = st.sed.em_tot * fact
;ADDING PLUGIN TO SPECTRUM----------------
-scopes=tag_names((*!dustem_plugin))
+Nplugins=n_elements(*!dustem_plugin)
+scopes=(*!dustem_plugin).scope
IF scopes[0] NE 'NONE' THEN BEGIN
-;IF ptr_valid(!dustem_plugin) THEN BEGIN
- for i=0L,n_tags(*!dustem_plugin)-1 do begin
- if total(strsplit((*(*!dustem_plugin).(i).scope),'+',/extract) eq 'ADD_SED') then SED_spec+=(*(*!dustem_plugin).(i).spec)[*,0]
- endfor
+ FOR i=0L,Nplugins-1 DO BEGIN
+ IF total(strsplit((*!dustem_plugin)[i].scope,'+',/extract) eq 'ADD_SED') THEN BEGIN
+ SED_spec+=(*(*!dustem_plugin)[i].spec)[*,0]
+ ENDIF
+ ENDFOR
ENDIF
;------------------------------------------
-if not isarray(SED_spec) THEN stop
+IF not isarray(SED_spec) THEN stop
;COMPUTE THE MODEL SED
-
+;JPB: problem there: we should be able to compute an SED even when there is no data in !dustem_data
dustem_sed = (*(*!dustem_data).sed).values * 0.
IF !dustem_do_cc NE 0 AND !dustem_never_do_cc EQ 0 THEN BEGIN
diff --git a/src/idl/dustem_fit_intensity_example.pro b/src/idl/dustem_fit_intensity_example.pro
index 1be4180..59ee653 100644
--- a/src/idl/dustem_fit_intensity_example.pro
+++ b/src/idl/dustem_fit_intensity_example.pro
@@ -257,7 +257,8 @@ if keyword_set(wait) then begin
end
;== INITIALISE DUSTEM
-dustem_init,model=use_model,polarization=use_polarization
+dustem_init,model=use_model,polarization=use_polarization,/show_plot
+;stop
!dustem_nocatch=1
!dustem_verbose=use_verbose
IF keyword_set(noobj) THEN !dustem_noobj=1
@@ -303,7 +304,7 @@ tit='FIT INTENSITY EXAMPLE' ; plot title
ytit=textoidl('I_\nu (MJy/sr) for N_H=10^{20} H/cm^2') ; y-axis title
xtit=textoidl('\lambda (\mum)') ; x-axis title
-
+;stop
;=== RUN THE FIT
t1=systime(0,/sec)
res=dustem_mpfit_data(tol=tol,Nitermax=use_Nitermax,gtol=gtol $
diff --git a/src/idl/dustem_fit_intensity_phangs_example.pro b/src/idl/dustem_fit_intensity_phangs_example.pro
index 90a5f22..8bc7d2d 100644
--- a/src/idl/dustem_fit_intensity_phangs_example.pro
+++ b/src/idl/dustem_fit_intensity_phangs_example.pro
@@ -10,7 +10,7 @@ PRO dustem_fit_intensity_phangs_example,model=model $
;+
; NAME:
-; dustem_fit_intensity_example
+; dustem_fit_intensity_phangs_example
;
; PURPOSE:
; This routine is an example of how to fit an observational SED
@@ -169,7 +169,9 @@ if keyword_set(wait) then begin
end
;== INITIALISE DUSTEM
-dustem_init,model=use_model,polarization=use_polarization
+;!dustem_show_plot=1
+dustem_init,model=use_model,polarization=use_polarization,/show_plot
+;stop
!dustem_nocatch=1
!dustem_verbose=use_verbose
IF keyword_set(noobj) THEN !dustem_noobj=1
diff --git a/src/idl/dustem_plugin_phangs_stellar_continuum.pro b/src/idl/dustem_plugin_phangs_stellar_continuum.pro
index d2c41c2..2d62321 100644
--- a/src/idl/dustem_plugin_phangs_stellar_continuum.pro
+++ b/src/idl/dustem_plugin_phangs_stellar_continuum.pro
@@ -31,6 +31,7 @@ FUNCTION dustem_plugin_phangs_stellar_continuum,key=key $
; paramtag = plugin parameter names as strings
; ACCEPTED KEY-WORDS:
; help = if set, print this help
+; method = SSP used. can be EMILES or CB19. default='EMILES'
; COMMON BLOCKS:
; None
; SIDE EFFECTS:
@@ -60,31 +61,25 @@ IF keyword_set(scope) THEN BEGIN
goto, the_scope
ENDIF
-;IF keyword_set(paramtag) THEN BEGIN
-; out=0
-; goto, the_paramtag
-;ENDIF
-
-;stop
-
-;default values of input parameters
+;use_method='EMILES'
+use_method='CB19'
age_values=[0.03, 0.05, 0.08, 0.15, 0.25, 0.40, 0.60, 1.0, 1.75, 3.0, 5.0, 8.5, 13.5]
metalicity_values=[-1.48630, -0.961400, -0.351200, +0.0600000, +0.255900, +0.397100]
;read template info
-info_st=dustem_read_emiles_stellar_templates(age_values,metalicity_values,/info_only)
-;stop
-age_values_emiles=info_st.age
-order=sort(age_values_emiles)
-age_values_emiles=age_values_emiles[order]
-un=uniq(age_values_emiles)
-age_values_emiles=age_values_emiles[un]
-met_values_emiles=info_st.z
-order=sort(met_values_emiles)
-met_values_emiles=met_values_emiles[order]
-un=uniq(met_values_emiles)
-met_values_emiles=met_values_emiles[un]
+;==== This is actually not used
+;info_st=dustem_read_emiles_stellar_templates(age_values,metalicity_values,/info_only)
+;age_values_emiles=info_st.age
+;order=sort(age_values_emiles)
+;age_values_emiles=age_values_emiles[order]
+;un=uniq(age_values_emiles)
+;age_values_emiles=age_values_emiles[un]
+;met_values_emiles=info_st.z
+;order=sort(met_values_emiles)
+;met_values_emiles=met_values_emiles[order]
+;un=uniq(met_values_emiles)
+;met_values_emiles=met_values_emiles[un]
;==== This does not work because the info files has many more entries than there are available ssps.
;age_values=age_values_emiles
@@ -132,8 +127,18 @@ IF exist EQ 0 THEN BEGIN
defsysv,'!dustem_plugin_phangs_stellar_continuum',st
ENDIF
IF not ptr_valid(!dustem_plugin_phangs_stellar_continuum.ssps) THEN BEGIN
- message,'Initializing SSP templates',/continue
- template_flux=dustem_read_emiles_stellar_templates(age_values,metalicity_values,template_wav=template_wav,Mstars=Mstars)
+ message,'Initializing SSP templates',/info
+ CASE use_method of
+ 'EMILES': BEGIN
+ template_flux=dustem_read_emiles_stellar_templates(age_values,metalicity_values,template_wav=template_wav,Mstars=Mstars)
+ END
+ 'CB19': BEGIN
+ ;== this is just to get the Mstars
+ bidon=dustem_read_emiles_stellar_templates(age_values,metalicity_values,template_wav=template_wav,Mstars=Mstars)
+ ;== This is to read in the CB19 templates
+ template_flux=dustem_read_cb19_stellar_templates(age_values=age_values,metalicity_values=metalicity_values,template_wav=template_wav,Mstars=Mstars)
+ END
+ ENDCASE
!dustem_plugin_phangs_stellar_continuum.ssps=ptr_new(template_flux)
!dustem_plugin_phangs_stellar_continuum.wavs=ptr_new(template_wav)
!dustem_plugin_phangs_stellar_continuum.mstars=ptr_new(Mstars)
@@ -157,7 +162,7 @@ FOR i=2L,Nparam-1 DO BEGIN
IF count NE 0 THEN BEGIN
ssp=*(*!dustem_plugin_phangs_stellar_continuum.ssps)[i-2]
output[ind,0]=output[ind,0]+paramvalues[i]*Mstar*interpol(ssp,wavs,lambir[ind])
- message,'Mstar='+strtrim(Mstar,2)+' paramvalue='+strtrim(paramvalues[i],2),/continue
+ message,'Mstar='+strtrim(Mstar,2)+' paramvalue='+strtrim(paramvalues[i],2),/info
ENDIF
ENDIF
ENDFOR
@@ -178,12 +183,12 @@ fact3=1./NHref ;[cm2/H] to go from ergs/s/cm2 to ergs/s/H
fact4=1.e4*(*!dustem_HCD)/(4.*!pi)/(3.e8/1.e-6/lambir)*1.e20/1.e7 ;This goes from ergs/s/H to MJy/sr (see dustem_plot_dataset)
fact=fact2*fact3*fact4
-print,'flux(1mic)=',interpol(flux,lambir,1.),' ergs/s/cm2/AA'
-print,'fact2=',interpol(fact2,lambir,1.)
-print,'fact3=',fact3
-print,'fact4=',interpol(fact4,lambir,1.)
-print,'fact=',interpol(fact,lambir,1.)
-print,'flux(1mic)=',interpol(flux,lambir,1.)*interpol(fact,lambir,1.),' MJy/sr'
+;print,'flux(1mic)=',interpol(flux,lambir,1.),' ergs/s/cm2/AA'
+;print,'fact2=',interpol(fact2,lambir,1.)
+;print,'fact3=',fact3
+;print,'fact4=',interpol(fact4,lambir,1.)
+;print,'fact=',interpol(fact,lambir,1.)
+;print,'flux(1mic)=',interpol(flux,lambir,1.)*interpol(fact,lambir,1.),' MJy/sr'
;goto,no_unred
@@ -213,7 +218,7 @@ output[*,0]=output[*,0]*fact
output[*,1]=output[*,1]*fact
output[*,2]=output[*,2]*fact
-print,'output=',interpol(output[*,0],lambir,1.),' MJy/sr'
+;print,'output=',interpol(output[*,0],lambir,1.),' MJy/sr'
;stop
the_scope:
diff --git a/src/idl/dustem_read_emiles_stellar_templates.pro b/src/idl/dustem_read_emiles_stellar_templates.pro
index c3f5fc5..af16ee5 100644
--- a/src/idl/dustem_read_emiles_stellar_templates.pro
+++ b/src/idl/dustem_read_emiles_stellar_templates.pro
@@ -39,7 +39,7 @@ FUNCTION dustem_read_emiles_stellar_templates,age_values, $
; PROCEDURES AND SUBROUTINES USED:
;
; EXAMPLES
-;
+; st=dustem_read_emiles_stellar_templates(age_values,Z_values)
; MODIFICATION HISTORY:
; Written by JPB June-2023
; Evolution details on the DustEMWrap gitlab.
@@ -91,8 +91,8 @@ metalicity_values_4str=string(metalicity_values_4str,format='(F5.2)')
FOR i=0L,n_elements(metalicity_values_4str)-1 DO metalicity_values_4str[i]=textoidl_str_replace(metalicity_values_4str[i],' ','p')
FOR i=0L,n_elements(metalicity_values_4str)-1 DO metalicity_values_4str[i]=textoidl_str_replace(metalicity_values_4str[i],'-','m')
-print,age_values
-print,metalicity_values
+;print,age_values
+;print,metalicity_values
;stop
;Ntemplates=n_elements(paramvalues)-1
@@ -119,11 +119,11 @@ FOR i=1L,Ntemplates DO BEGIN
met=metalicity_values[imet]
met_str=metalicity_values_4str[imet]
age_str=age_values_4str[iage]
- message,'reading template for Age '+age_str+' Met '+met_str,/continue
+ message,'reading template for Age '+age_str+' Met '+met_str,/info
file=dir_templates+file_start+'Z'+met_str+'T'+age_str+file_end
fi=file_info(file)
IF fi.exists THEN BEGIN
- message,'Reading SSP '+file,/continue
+ message,'Reading SSP '+file,/info
spec=readfits(file,h,2)
templates[ii]=ptr_new(spec)
make_axis,h,wavs
diff --git a/src/idl/dustem_sed_extractor.pro b/src/idl/dustem_sed_extractor.pro
index 568b63c..31e53ee 100644
--- a/src/idl/dustem_sed_extractor.pro
+++ b/src/idl/dustem_sed_extractor.pro
@@ -1,6 +1,6 @@
-FUNCTION dustem_sed_extractor,maps $
- ,index_roi $
- ,filters, $
+FUNCTION dustem_sed_extractor,maps, $
+ index_roi, $
+ filters, $
comments=comments, $
maps_order=maps_order, $
method=method, $
@@ -25,7 +25,7 @@ FUNCTION dustem_sed_extractor,maps $
; sed=sed_extractor(maps,index,filters[,comments=][,maps_order=][,method=][,mask_I_undef=][,/total_intensity_only])
;
; INPUTS:
-; maps : a set of Nmaps maps of same dimension [Nx,Ny,Nmaps,Ndata_sets]
+; maps : a set of Nmaps maps of same dimension [Nx,Ny,Nmaps,Ndata_sets]. Caution, maps are changed if set_undefined is set !
; index_roi : spatial index in Nx,Ny where the SED is to be extracted from (ROI=region of interest)
; filters : DustEMWrap filters corresponding to each dataset [Ndata_sets]
;
@@ -117,9 +117,10 @@ ENDIF ELSE BEGIN
ENDIF
ENDELSE
-used_maps=maps
+;used_maps=maps
IF keyword_set(set_undefined) THEN BEGIN
+ used_maps=maps
;===== do a map of saturated stokesI pixels
mask_I_undef=maps[*,*,0,0]
mask_I_undef[*]=0
@@ -132,8 +133,6 @@ IF keyword_set(set_undefined) THEN BEGIN
mask_I_undef[ind]=1
ENDIF
ENDFOR
-
- ;used_maps=maps
;set saturated stokesI pixels to la_undef in
indbad=where(mask_I_undef EQ 1,count)
IF count NE 0 THEN BEGIN
@@ -146,34 +145,36 @@ IF keyword_set(set_undefined) THEN BEGIN
ENDFOR
ENDFOR
ENDIF
+ maps=used_maps
+ used_maps=0
ENDIF
CASE use_method OF
'MEAN':BEGIN
- FOR j=0L,Nfilt-1 DO BEGIN
- this_map=used_maps[*,*,indI,j]
+ FOR j=0L,Nfilt-1 DO BEGIN
+ this_map=maps[*,*,indI,j]
sed[j].stokesI=la_mean(this_map[index_roi])
- this_map=used_maps[*,*,indII,j]
+ this_map=maps[*,*,indII,j]
sed[j].sigmaII=la_div(la_mean(this_map[index_roi]),count_roi)
IF not keyword_set(total_intensity_only) THEN BEGIN
- this_map=used_maps[*,*,indQ,j]
+ this_map=maps[*,*,indQ,j]
sed[j].stokesQ=la_mean(this_map[index_roi])
- this_map=used_maps[*,*,indU,j]
+ this_map=maps[*,*,indU,j]
sed[j].stokesU=la_mean(this_map[index_roi])
- this_map=used_maps[*,*,indQQ,j]
+ this_map=maps[*,*,indQQ,j]
sed[j].sigmaQQ=la_div(la_mean(this_map[index_roi]),count_roi)
- this_map=used_maps[*,*,indUU,j]
+ this_map=maps[*,*,indUU,j]
sed[j].sigmaUU=la_div(la_mean(this_map[index_roi]),count_roi)
- this_map=used_maps[*,*,indIQ,j]
+ this_map=maps[*,*,indIQ,j]
sed[j].sigmaIQ=la_div(la_mean(this_map[index_roi]),count_roi)
- this_map=used_maps[*,*,indIU,j]
+ this_map=maps[*,*,indIU,j]
sed[j].sigmaIU=la_div(la_mean(this_map[index_roi]),count_roi)
- this_map=used_maps[*,*,indQU,j]
+ this_map=maps[*,*,indQU,j]
sed[j].sigmaQU=la_div(la_mean(this_map[index_roi]),count_roi)
ENDIF
- ENDFOR
- END
+ ENDFOR
+ END
'MEAN_ONOFF': BEGIN ;This is mean ON - mean MEAN_ONOFF
IF not keyword_set(index_off) THEN BEGIN
message,'index_off keyword must be set with method '+use_method,/continue
@@ -182,36 +183,36 @@ CASE use_method OF
count_off=n_elements(index_off)
comments=[comments,'OFF has '+strtrim(count_off,2)+' map pixels']
FOR j=0L,Nfilt-1 DO BEGIN
- this_map=used_maps[*,*,indI,j]
+ this_map=maps[*,*,indI,j]
sed[j].stokesI=la_sub(la_mean(this_map[index_roi]),la_mean(this_map[index_off]))
- this_map=used_maps[*,*,indII,j]
+ this_map=maps[*,*,indII,j]
sig_on=la_div(la_mean(this_map[index_roi]),count_roi)
sig_off=la_div(la_mean(this_map[index_off]),count_off)
sed[j].sigmaII=la_add(sig_on,sig_off)
IF not keyword_set(total_intensity_only) THEN BEGIN
- this_map=used_maps[*,*,indQ,j]
+ this_map=maps[*,*,indQ,j]
sed[j].stokesQ=la_sub(la_mean(this_map[index_roi]),la_mean(this_map[index_off]))
- this_map=used_maps[*,*,indU,j]
+ this_map=maps[*,*,indU,j]
sed[j].stokesU=la_sub(la_mean(this_map[index_roi]),la_mean(this_map[index_off]))
;variances
- this_map=used_maps[*,*,indQQ,j]
+ this_map=maps[*,*,indQQ,j]
sig_on=la_div(la_mean(this_map[index_roi]),count_roi)
sig_off=la_div(la_mean(this_map[index_off]),count_off)
sed[j].sigmaQQ=la_add(sig_on,sig_off)
- this_map=used_maps[*,*,indUU,j]
+ this_map=maps[*,*,indUU,j]
sig_on=la_div(la_mean(this_map[index_roi]),count_roi)
sig_off=la_div(la_mean(this_map[index_off]),count_off)
sed[j].sigmaUU=la_add(sig_on,sig_off)
;co-variances
- this_map=used_maps[*,*,indIQ,j]
+ this_map=maps[*,*,indIQ,j]
sig_on=la_div(la_mean(this_map[index_roi]),count_roi)
sig_off=la_div(la_mean(this_map[index_off]),count_off)
sed[j].sigmaIQ=la_add(sig_on,sig_off)
- this_map=used_maps[*,*,indIU,j]
+ this_map=maps[*,*,indIU,j]
sig_on=la_div(la_mean(this_map[index_roi]),count_roi)
sig_off=la_div(la_mean(this_map[index_off]),count_off)
sed[j].sigmaIU=la_add(sig_on,sig_off)
- this_map=used_maps[*,*,indQU,j]
+ this_map=maps[*,*,indQU,j]
sig_on=la_div(la_mean(this_map[index_roi]),count_roi)
sig_off=la_div(la_mean(this_map[index_off]),count_off)
sed[j].sigmaQU=la_add(sig_on,sig_off)
@@ -232,21 +233,21 @@ CASE use_method OF
message,'reference filter '+reference_filter+' not found in provided filter list',/continue
stop
ENDIF
- mapI_ref=used_maps[*,*,indI,indf]
- mapQ_ref=used_maps[*,*,indQ,indf]
- mapU_ref=used_maps[*,*,indU,indf]
- mapII_ref=used_maps[*,*,indII,indf]
- mapQQ_ref=used_maps[*,*,indQQ,indf]
- mapUU_ref=used_maps[*,*,indUU,indf]
+ mapI_ref=maps[*,*,indI,indf]
+ mapQ_ref=maps[*,*,indQ,indf]
+ mapU_ref=maps[*,*,indU,indf]
+ mapII_ref=maps[*,*,indII,indf]
+ mapQQ_ref=maps[*,*,indQQ,indf]
+ mapUU_ref=maps[*,*,indUU,indf]
Iref=la_mean(mapI_ref[index_roi])
Qref=la_mean(mapQ_ref[index_roi])
Uref=la_mean(mapU_ref[index_roi])
FOR j=0L,Nfilt-1 DO BEGIN
;==== do the correlation in Stokes I
x=mapI_ref[index_roi]
- y=(used_maps[*,*,indI,j])[index_roi]
+ y=(maps[*,*,indI,j])[index_roi]
sx=la_power(mapII_ref[index_roi],0.5)
- sy=la_power((used_maps[*,*,indI,j])[index_roi],0.5)
+ sy=la_power((maps[*,*,indI,j])[index_roi],0.5)
ind_good=where(x NE la_undef() AND y NE la_undef() AND sx NE la_undef() and sy NE la_undef(),count_good)
comments=[comments,'I corelation has '+strtrim(count_good,2)+' map pixels']
IF count_good NE 0 THEN BEGIN
@@ -268,9 +269,9 @@ CASE use_method OF
ENDIF
;Do the correlation between Q maps
x=[mapQ_ref[index_roi],mapU_ref[index_roi]]
- y=[(used_maps[*,*,indQ,j])[index_roi],(used_maps[*,*,indU,j])[index_roi]]
+ y=[(maps[*,*,indQ,j])[index_roi],(maps[*,*,indU,j])[index_roi]]
sx=la_power([mapQQ_ref[index_roi],mapUU_ref[index_roi]],0.5)
- sy=la_power([(used_maps[*,*,indQ,j])[index_roi],(used_maps[*,*,indU,j])[index_roi]],0.5)
+ sy=la_power([(maps[*,*,indQ,j])[index_roi],(maps[*,*,indU,j])[index_roi]],0.5)
ind_good=where(x NE la_undef() AND y NE la_undef() AND sx NE la_undef() and sy NE la_undef(),count_good)
comments=[comments,'QU corelation has '+strtrim(count_good,2)+' map pixels']
IF count_good NE 0 THEN BEGIN
diff --git a/src/idl/dustem_write_chrg.pro b/src/idl/dustem_write_chrg.pro
index 8ccf24a..be14472 100755
--- a/src/idl/dustem_write_chrg.pro
+++ b/src/idl/dustem_write_chrg.pro
@@ -94,7 +94,7 @@ FOR i=0L,Nst-1 DO BEGIN
fv=str_sep(ffile,'/')
file=dir+fv(n_elements(fv)-1)
;Open file
- message,'Will write CHRG file '+file,/continue
+ message,'Will write CHRG file '+file,/info
openw,unit,file,/get_lun
;Print comments
IF Ncomments NE 0 THEN BEGIN
--
libgit2 0.21.2