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src/idl/dustem_check_data.pro 21.9 KB
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PRO dustem_check_data, data_sed, $
                       data_ext, $
                       sed=sed, $
                       ext=ext, $
                       polext=polext, $
                       polsed=polsed, $
                       polfrac=polfrac, $
                       psi_em=psi_em, $
                       qsed=qsed, $
                       used=used, $
                       qext=qext, $
                       uext=uext, $
                       psi_ext=psi_ext, $
                       fpolext=fpolext
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;+
; NAME:
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;    dustem_check_data
;
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; PURPOSE:
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;    Clean and modify the input DustEMWrap structure to meet the requirements of DustEMWrap. 
;    This is important for the subsequent internal handling/fitting of data. 
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;
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; CATEGORY:
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;    DustEMWrap, Mid-Level, Distributed, Initialization
;
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; CALLING SEQUENCE:
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;    dustem_check_data,data_sed,data_ext,sed=sed,ext=ext,polext=polext,polsed=polsed,polfrac=polfrac,psi_em=psi_em,qsed=qsed,used=used,qext=qext,uext=uext,psi_ext=psi_ext,fpolext=fpolext,[/help]
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;
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; INPUTS:
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;    data_sed : Emission DustEMWrap structure
;    data_ext : Extinction DustEMWrap structure
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;
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; OPTIONAL INPUT PARAMETERS:
;    None
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;
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; OUTPUTS: 
;    sed : modified emission structure 
;    ext : modified extinction structure
;    polext : modified polarized extinction structure
;    polsed : modified polarized emission structure 
;    polfrac : modified fractional polarized emission structure
;    psi_em  : modified emission polarization angle structure 
;    qsed : modified StokesQ emission structure
;    used : modified StokesU emission structure
;    qext : modified StokesQ extinction structure
;    uext : modified StokesU extinction structure
;    psi_ext : modified extinction polarization angle structure
;    fpolext : modified fractional extinction polarization structure
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;
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; OPTIONAL OUTPUT PARAMETERS:
;    None
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;
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; ACCEPTED KEY-WORDS:
;    help      = If set print this help
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;
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; COMMON BLOCKS:
;    None
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;
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; SIDE EFFECTS:
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;
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; RESTRICTIONS:
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;    The DustEMWrap IDL code must be installed
;
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; PROCEDURE:
;    None
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;
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; EXAMPLES
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;    dustem_check_data,data_sed,data_ext,sed=sed,ext=ext,polext=polext,polsed=polsed,polfrac=polfrac,psi_em=psi_em,qsed=qsed,used=used,qext=qext,uext=uext,psi_ext=psi_ext,fpolext=fpolext,[/help]
;    dustem_check_data,/help
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; MODIFICATION HISTORY:
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;    Written IC 2022
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;    Evolution details on the DustEMWrap gitlab.
;    See http://dustemwrap.irap.omp.eu/ for FAQ and help.   
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; COMMENTS:
;    Might still need a bit of cleaning. I am unsure of the availability of covariance data in polarized extinction.
;    Still regarding extinction, some of the error messages haven't been mirrored correctly with respect to the emission block.
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;-


IF keyword_set(help) THEN BEGIN
  doc_library,'dustem_check_data'
  goto,the_end
ENDIF

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;CHECKING THE FORMAT OF THE SED STRUCTURE
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IF KEYWORD_SET(data_sed) THEN BEGIN
            
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    ans=''
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    wavs=data_sed.wave
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    ;=== Impose central wavelengths for photometric channels
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    ind=where(data_sed.filter NE 'SPECTRUM',count)
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    IF count NE 0 THEN BEGIN
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        wavs(ind)=dustem_filter2wav(data_sed(ind).filter)
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    ENDIF
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    ;=== Initializing observation structure
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    obs_EM={instru_names:data_sed.instru,filt_names:data_sed.filter,wav:wavs, values:data_sed.StokesI,sigma:sqrt(abs(data_sed.sigmaII))} 
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    ;INITIALIZING OUTPUT STRUCTURES
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    sed = obs_EM
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    qsed = sed
    used = sed
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    ;Test if there is StokesI data. If not move to polsed testing.
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    ind = where(data_sed.StokesI NE la_undef() and finite(data_sed.StokesI) EQ 1 and data_sed.sigmaII NE la_undef() and finite(data_sed.sigmaII) EQ 1,N_sed) ;Testing if the data and errors are set
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    IF N_sed EQ 0 THEN BEGIN
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        sed = ptr_new()
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        goto, qzone
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    ENDIF ELSE BEGIN 
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        ind = where(finite(data_sed.StokesI) EQ 0 or finite(data_sed.sigmaII) EQ 0, countnoki) ;Format is not okay if there are nan values but the wrapper recognizes the la_undef() value 
        IF countnoki NE 0 THEN BEGIN
            message, "SED format isn't met. NaN value(s) detected in StokesI data.",/continue
            message, 'Without automatic format fitering you cannot proceed.',/continue
            ;stop
            read, ans, prompt='Would you like automatic format filtering? (Y/N):'
            IF strupcase(ans) EQ 'N' THEN BEGIN
                message,'You have chosen not to use automatic filtering. Please adjust the SED format.',/continue
                message, 'Aborting ...'
            ENDIF
        ENDIF 
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        IF strupcase(ans) EQ 'Y' THEN message, 'You have chosen automatic format filtering. Removal of undefined data points...',/info $
        ELSE message, 'Data format is met. Removal of undefined data points...',/info
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        tdaerri=where((data_sed.sigmaII EQ la_undef() and data_sed.StokesI NE la_undef()) or (data_sed.sigmaII NE la_undef() and data_sed.StokesI EQ la_undef()),ctdaerri)
        IF ctdaerri NE 0 THEN BEGIN
            message, 'Data and errors do not match. Undefinded data detected. Aborting...',/continue
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        ENDIF
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        testi=where(data_sed.sigmaII NE 0. and finite(data_sed.sigmaII) EQ 1 and data_sed.sigmaII NE la_undef() and data_sed.StokesI NE la_undef() and finite(data_sed.StokesI) EQ 1,ctesti)                
        IF ctesti NE 0 THEN BEGIN 
            instru_names = sed.instru_names(testi)
            filt_names = sed.filt_names(testi)
            wav = sed.wav(testi)
            values = sed.values(testi)
            sigma = sed.sigma(testi)
            sed={instru_names:instru_names,filt_names:filt_names,wav:wav,values:values,sigma:sigma}
        ENDIF    
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    ENDELSE
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    qzone:
    ans=''
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    qsed.values=data_sed.StokesQ
    qsed.sigma=sqrt(abs(data_sed.sigmaQQ))
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    ;Testig if there is StokesQ data. If not move to used data
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    ind = where(data_sed.StokesQ NE la_undef() and finite(data_sed.StokesQ) EQ 1 and data_sed.sigmaQQ NE la_undef() and finite(data_sed.sigmaQQ) EQ 1,NQ)
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    IF NQ EQ 0 THEN BEGIN
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        qsed = ptr_new()
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        goto, uzone
    ENDIF ELSE BEGIN
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    ind = where(finite(data_sed.StokesQ) EQ 0 or finite(data_sed.sigmaQQ) EQ 0, countnokq) ;Format is not okay if there are nan values but the wrapper recognizes the la_undef() value 
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    IF countnokq NE 0 THEN BEGIN 
        message, "SED format isn't met. NaN value(s) detected in StokesQ data.",/continue
        message, 'Without automatic format fitering you cannot proceed.',/continue
        read, ans, prompt='Would you like automatic format filtering? (Y/N):' 
        IF strupcase(ans) EQ 'N' THEN BEGIN
            message,'You have chosen not to use automatic filtering. Please adjust the SED format.',/continue
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            message, 'Aborting ...'
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        ENDIF
    ENDIF
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    IF strupcase(ans) EQ 'Y' THEN message, 'You have chosen automatic format filtering. Removal of undefined data points...',/info $
    ELSE message, 'Data format is met. Removal of undefined data points...',/info
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    tdaerrq=where((data_sed.sigmaQQ EQ la_undef() and data_sed.StokesQ NE la_undef()) or (data_sed.sigmaQQ NE la_undef() and data_sed.StokesQ EQ la_undef()),ctdaerrq)
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    IF ctdaerrq NE 0 THEN BEGIN
        message, 'Data and errors in Stokes Q do not match. Undefinded data detected for these filters:',/continue
        print,data_sed[tdaerrq].filter
        ;message, 'Data and errors do not match. Undefinded data detected. Aborting...',/continue
        stop
    ENDIF
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    testq=where(data_sed.sigmaQQ NE 0. and finite(data_sed.sigmaQQ) EQ 1 and data_sed.sigmaQQ NE la_undef() and data_sed.StokesQ NE la_undef() and finite(data_sed.StokesQ) EQ 1,ctestq)                
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    IF ctestq NE 0 THEN BEGIN 
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        instru_names = qsed.instru_names(testq)
        filt_names = qsed.filt_names(testq)
        wav = qsed.wav(testq)
        values = qsed.values(testq)
        sigma = qsed.sigma(testq)
        qsed={instru_names:instru_names,filt_names:filt_names,wav:wav,values:values,sigma:sigma}
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    ENDIF
    ENDELSE
    uzone:
    ans=''
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    used.values=data_sed.StokesU
    used.sigma=sqrt(abs(data_sed.sigmaUU))
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    ;Testig if there is StokesU data. If not return empty value and end loop.
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    ind = where(data_sed.StokesU NE la_undef() and finite(data_sed.StokesU) EQ 1 and data_sed.sigmaUU NE la_undef() and finite(data_sed.sigmaUU) EQ 1,NU)
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    IF NU EQ 0 THEN BEGIN
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        used = ptr_new()
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        goto, psiemzone
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    ENDIF ELSE BEGIN
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    ind = where(finite(data_sed.StokesU) EQ 0 or finite(data_sed.sigmaUU) EQ 0, countnoku) ;Format is not okay if there are nan values but the wrapper recognizes the la_undef() value 
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    IF countnoku NE 0 THEN BEGIN 
        message, "SED format isn't met. NaN value(s) detected in StokesU data.",/continue
        message, 'Without automatic format fitering you cannot proceed.',/continue
        read, ans, prompt='Would you like automatic format filtering? (Y/N):' 
        IF strupcase(ans) EQ 'N' THEN BEGIN
            message,'You have chosen not to use automatic filtering. Please adjust the SED format.',/continue
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            message, 'Aborting ...'
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        ENDIF
    ENDIF  
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    IF strupcase(ans) EQ 'Y' THEN message, 'You have chosen automatic format filtering. Removal of undefined data points...',/info $
    ELSE message, 'Data format is met. Removal of undefined data points...',/info
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    tdaerru=where((data_sed.sigmaUU EQ la_undef() and data_sed.StokesU NE la_undef()) or (data_sed.sigmaUU NE la_undef() and data_sed.StokesU EQ la_undef()),ctdaerru)
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    IF ctdaerru NE 0 THEN BEGIN
        message, 'Data and errors in Stokes U do not match. Undefinded data detected for these filters:',/continue
        print,data_sed[tdaerru].filter
        stop
    ENDIF
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    testu=where(data_sed.sigmaUU NE 0. and finite(data_sed.sigmaUU) EQ 1 and data_sed.sigmaUU NE la_undef() and data_sed.StokesU NE la_undef() and finite(data_sed.StokesU) EQ 1,ctestu)                
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    IF ctestu NE 0 THEN BEGIN 
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        instru_names = used.instru_names(testu)
        filt_names = used.filt_names(testu)
        wav = used.wav(testu)
        values = used.values(testu)
        sigma = used.sigma(testu)
        used={instru_names:instru_names,filt_names:filt_names,wav:wav,values:values,sigma:sigma}
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    ENDIF
    ENDELSE
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    psiemzone:
    
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    if nu eq 0 and nq eq 0 then goto, end_sed
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    degtorad = !pi/180
    
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    ;Generation of POLFRAC,POLSED and PSI data by default   
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    ;Testing on the presence of covariances otherwise an error is returned
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    ;The testing happens here because covariances are needed for the error estimation of P,p and PSI. (Also cannot test before because we're not in !run_pol mode) 
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    tstcovu = where((data_sed(testu).sigmaIU) EQ la_undef() or (data_sed(testu).sigmaQU) EQ la_undef(), ctcovu)
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    if ctcovu NE 0  then BEGIN
        ;message, 'Covariance data is missing in StokesU data. Data, errors and covariances do not match. Aborting...',/continue
        message, 'IU or QU Covariance data is missing in StokesU data. Data, errors and covariances do not match for the following filters.',/continue
        print,data_sed[testu[tstcovu]].filter
        stop
    ENDIF
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    tstcovq = where((data_sed(testq).sigmaIQ) EQ la_undef() or (data_sed(testq).sigmaQU) EQ la_undef(), ctcovq)
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    if ctcovq NE 0  then BEGIN
        message, 'IQ or QU Covariance data is missing in StokesQ data. Data, errors and covariances do not match for the following filters.',/continue
        print,data_sed[testq[tstcovq]].filter
        stop
    ENDIF
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    ;Matching both filter and spectrum points 
    
    match2,used.wav,qsed.wav,qpts,upts
    
    ;removing -1 values from the indices (qpts & upts)
    indnotq = where(qpts eq -1, cnotq)
    if cnotq ne 0 then remove, indnotq, qpts
    indnotu = where(upts eq -1, cnotu)
    if cnotu ne 0 then remove, indnotu, upts
    
    match2, sed.wav, qsed.wav(qpts), qtmp, sedpts
    indnoti = where(sedpts eq -1, cnoti)
    if cnoti ne 0 then remove, indnoti, sedpts
    
    instru_names = used.instru_names(upts)
    filt_names = used.filt_names(upts)
    wav = used.wav(upts)
    values = 0.5*atan(used.values(upts),qsed.values(qpts))/degtorad
    polar_variance_iqu2ippsi,sed.values(sedpts),qsed.values(qpts),used.values(upts),(data_sed(testi).sigmaII)(sedpts),(data_sed(testq).sigmaQQ)(qpts),(data_sed(testu).sigmaUU)(upts),(data_sed(testi).sigmaIQ)(sedpts),(data_sed(testi).sigmaIU)(sedpts),(data_sed(testi).sigmaQU)(sedpts),variance_smallp,variance_psi,variance_largep
    sigma = sqrt(variance_psi)
    psi_em={instru_names:instru_names,filt_names:filt_names,wav:wav,values:values,sigma:sigma}
    
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    polsed = psi_em
    polsed.values = sqrt(used.values(upts)^2+qsed.values(qpts)^2) 
    polsed.sigma = sqrt(variance_largep)
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    polfrac = psi_em
    polfrac.values = polsed.values/sed.values(sedpts) 
    polfrac.sigma = sqrt(variance_smallp)
    
    goto, end_sed
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    end_sed:
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ENDIF


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;EXTINCTION
;
;Covariances?... 
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IF KEYWORD_SET(data_ext) THEN begin
    
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    ans=''
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    wavs=data_ext.wave
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    ;=== Impose central wavelengths for photometric channels
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    ind=where(data_ext.filter NE 'SPECTRUM',count)
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    IF count NE 0 THEN BEGIN
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        wavs(ind)=dustem_filter2wav(data_ext(ind).filter)
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    ENDIF
    ;=== define observations structure 
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    obs_EXT={instru_names:data_ext.instru,filt_names:data_ext.filter,wav:wavs, values:data_ext.EXT_I,sigma:sqrt(abs(data_ext.sigextII))} 
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    ;INITIALIZING OUTPUT STRUCTURES
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    ext = obs_EXT
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    qext = ext
    uext = ext
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    ind = where(data_ext.EXT_I NE la_undef() and finite(data_ext.EXT_I) EQ 1 and data_ext.sigextII NE la_undef() and finite(data_ext.sigextII) EQ 1,N_ext) ;Testing if the data and errors are set
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    IF N_ext EQ 0 THEN BEGIN
3ff9cac3   Ilyes Choubani   general update
292
        ext = ptr_new()
303de20d   Ilyes Choubani   updating check_data
293
        goto, qexzone
09e61d64   Ilyes Choubani   cleaned set_data ...
294
    ENDIF ELSE BEGIN
3ff9cac3   Ilyes Choubani   general update
295
    ind = where(finite(data_ext.EXT_I) EQ 0 or finite(data_ext.sigextII) EQ 0, countnokex) ;Format is not okay if there are nan values but the wrapper recognizes the la_undef() value 
09e61d64   Ilyes Choubani   cleaned set_data ...
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    IF countnokex NE 0 THEN BEGIN 
        message, "SED format isn't met. NaN value(s) detected in EXT_I data.",/continue
        message, 'Without automatic format fitering you cannot proceed.',/continue
        ans=''
        read, ans, prompt='Would you like automatic format filtering? (Y/N):' 
        IF strupcase(ans) EQ 'N' THEN BEGIN
            message,'You have chosen not to use automatic filtering. Please adjust the SED format.',/continue
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303
            message, 'Aborting ...'
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        ENDIF
    ENDIF      
5eebdedb   Jean-Philippe Bernard   changed plugin st...
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    IF strupcase(ans) EQ 'Y' THEN message, 'You have chosen automatic format filtering. Removal of undefined data points...',/info $ 
    ELSE message, 'Data format is met. Removal of undefined data points...',/info
3ff9cac3   Ilyes Choubani   general update
308
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    tdaerrex=where((data_ext.sigextII EQ la_undef() and data_ext.EXT_I NE la_undef()) or (data_ext.sigextII NE la_undef() and data_ext.EXT_I EQ la_undef()),ctdaerrex)
    IF ctdaerrex NE 0 THEN message, 'Data and errors do not match. Undefinded data detected. Aborting...'
    testex=where(data_ext.sigextII NE 0. and finite(data_ext.sigextII) EQ 1 and data_ext.sigextII NE la_undef() and data_ext.EXT_I NE la_undef() and finite(data_ext.EXT_I) EQ 1,ctestex)                
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311
    IF ctestex NE 0 THEN BEGIN 
3ff9cac3   Ilyes Choubani   general update
312
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        instru_names = ext.instru_names(testex)
        filt_names = ext.filt_names(testex)
        wav = ext.wav(testex)
        values = ext.values(testex)
        sigma = ext.sigma(testex)
        ext={instru_names:instru_names,filt_names:filt_names,wav:wav,values:values,sigma:sigma}
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    ENDIF 
    ENDELSE
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320
    
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    qexzone:
    ans=''
3ff9cac3   Ilyes Choubani   general update
323
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    qext.values=data_ext.EXT_Q
    qext.sigma=sqrt(abs(data_ext.sigextQQ))
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325
    ;Testig if there is EXT_P data. If not move to EXT_U testing
3ff9cac3   Ilyes Choubani   general update
326
    ind = where(data_ext.EXT_Q NE la_undef() and finite(data_ext.EXT_Q) EQ 1 and data_ext.sigextQQ NE la_undef() and finite(data_ext.sigextQQ) EQ 1,NQ_ext) ;Testing if the data and errors are set
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327
    ;dustem_set_data.prostop   
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328
    IF NQ_ext EQ 0 THEN BEGIN
3ff9cac3   Ilyes Choubani   general update
329
        qext = ptr_new()
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        goto, uexzone
    ENDIF ELSE BEGIN
3ff9cac3   Ilyes Choubani   general update
332
    ind = where(finite(data_ext.EXT_Q) EQ 0 or finite(data_ext.sigextQQ) EQ 0, countnokqex) ;Format is not okay if there are nan values but the wrapper recognizes the la_undef() value 
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333
    IF countnokqex NE 0 THEN BEGIN 
3ff9cac3   Ilyes Choubani   general update
334
        message, "SED format isn't met. NaN value(s) detected in EXT_Q data.",/continue
09e61d64   Ilyes Choubani   cleaned set_data ...
335
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        message, 'Without automatic format fitering you cannot proceed.',/continue
        ans=''
        read, ans, prompt='Would you like automatic format filtering? (Y/N):' 
        IF strupcase(ans) EQ 'N' THEN BEGIN
            message,'You have chosen not to use automatic filtering. Please adjust the SED format.',/continue
266ae799   Ilyes Choubani   General update
340
            message, 'Aborting ...'
09e61d64   Ilyes Choubani   cleaned set_data ...
341
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        ENDIF
    ENDIF
5eebdedb   Jean-Philippe Bernard   changed plugin st...
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    IF strupcase(ans) EQ 'Y' THEN message, 'You have chosen automatic format filtering. Removal of undefined data points...',/info $
    ELSE message, 'Data format is met. Removal of undefined data points...',/info
3ff9cac3   Ilyes Choubani   general update
345
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    tdaerrqex=where((data_ext.sigextQQ EQ la_undef() and data_ext.EXT_Q NE la_undef()) or (data_ext.sigextQQ NE la_undef() and data_ext.EXT_Q EQ la_undef()),ctdaerrqex)
    IF ctdaerrqex NE 0 THEN message, 'Data and errors do not match. Undefinded data detected. Aborting...'
    testqex=where(data_ext.sigextQQ NE 0. and finite(data_ext.sigextQQ) EQ 1 and data_ext.sigextQQ NE la_undef() and data_ext.EXT_Q NE la_undef() and finite(data_ext.EXT_Q) EQ 1,ctestqex)                
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348
    IF ctestqex NE 0 THEN BEGIN 
3ff9cac3   Ilyes Choubani   general update
349
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        instru_names = qext.instru_names(testqex)
        filt_names = qext.filt_names(testqex)
        wav = qext.wav(testqex)
        values = qext.values(testqex)
        sigma = qext.sigma(testqex)
        qext={instru_names:instru_names,filt_names:filt_names,wav:wav,values:values,sigma:sigma}
09e61d64   Ilyes Choubani   cleaned set_data ...
355
356
    ENDIF 
    ENDELSE
303de20d   Ilyes Choubani   updating check_data
357
    
09e61d64   Ilyes Choubani   cleaned set_data ...
358
359
    uexzone:
    ans=''
3ff9cac3   Ilyes Choubani   general update
360
361
    uext.values=data_ext.EXT_U
    uext.sigma=sqrt(abs(data_ext.sigextUU))
09e61d64   Ilyes Choubani   cleaned set_data ...
362
    ;Testig if there is EXT_P data. If not return empty value and end loop.
3ff9cac3   Ilyes Choubani   general update
363
    ind = where(data_ext.EXT_U NE la_undef() and finite(data_ext.EXT_U) EQ 1 and data_ext.sigextUU NE la_undef() and finite(data_ext.sigextUU) EQ 1,NU_ext) ;Testing if the data and errors are set
09e61d64   Ilyes Choubani   cleaned set_data ...
364
    IF NU_ext EQ 0 THEN BEGIN
3ff9cac3   Ilyes Choubani   general update
365
        uext = ptr_new()
303de20d   Ilyes Choubani   updating check_data
366
        goto, psiexzone
09e61d64   Ilyes Choubani   cleaned set_data ...
367
    ENDIF ELSE BEGIN
3ff9cac3   Ilyes Choubani   general update
368
    ind = where(finite(data_ext.EXT_U) EQ 0 or finite(data_ext.sigextUU) EQ 0, countnokuex) ;Format is not okay if there are nan values but the wrapper recognizes the la_undef() value 
09e61d64   Ilyes Choubani   cleaned set_data ...
369
    IF countnokuex NE 0 THEN BEGIN 
3ff9cac3   Ilyes Choubani   general update
370
        message, "SED format isn't met. NaN value(s) detected in EXT_U data.",/continue
09e61d64   Ilyes Choubani   cleaned set_data ...
371
372
373
374
375
        message, 'Without automatic format fitering you cannot proceed.',/continue
        ans=''
        read, ans, prompt='Would you like automatic format filtering? (Y/N):' 
        IF strupcase(ans) EQ 'N' THEN BEGIN
            message,'You have chosen not to use automatic filtering. Please adjust the SED format.',/continue
266ae799   Ilyes Choubani   General update
376
            message, 'Aborting ...'
09e61d64   Ilyes Choubani   cleaned set_data ...
377
378
        ENDIF
    ENDIF
5eebdedb   Jean-Philippe Bernard   changed plugin st...
379
380
    IF strupcase(ans) EQ 'Y' THEN message, 'You have chosen automatic format filtering. Removal of undefined data points...',/info $
    ELSE message, 'Data format is met. Removal of undefined data points...',/info
3ff9cac3   Ilyes Choubani   general update
381
382
383
    tdaerruex=where((data_ext.sigextUU EQ la_undef() and data_ext.EXT_U NE la_undef()) or (data_ext.sigextUU NE la_undef() and data_ext.EXT_U EQ la_undef()),ctdaerruex)
    IF ctdaerruex NE 0 THEN message, 'Data and errors do not match. Undefinded data detected. Aborting...'
    testuex=where(data_ext.sigextUU NE 0. and finite(data_ext.sigextUU) EQ 1 and data_ext.sigextUU NE la_undef() and data_ext.EXT_U NE la_undef() and finite(data_ext.EXT_U) EQ 1,ctestuex)                
09e61d64   Ilyes Choubani   cleaned set_data ...
384
    IF ctestuex NE 0 THEN BEGIN 
3ff9cac3   Ilyes Choubani   general update
385
386
387
388
389
390
        instru_names = uext.instru_names(testuex)
        filt_names = uext.filt_names(testuex)
        wav = uext.wav(testuex)
        values = uext.values(testuex)
        sigma = uext.sigma(testuex)
        uext={instru_names:instru_names,filt_names:filt_names,wav:wav,values:values,sigma:sigma}
09e61d64   Ilyes Choubani   cleaned set_data ...
391
392
    ENDIF 
    ENDELSE
303de20d   Ilyes Choubani   updating check_data
393
394
395
    
    psiexzone: ;Starting the analogy here. 
    
04efbaa5   Ilyes Choubani   Correcting set_da...
396
    if NU_EXT eq 0 and NQ_EXT eq 0 then goto, end_ext
303de20d   Ilyes Choubani   updating check_data
397
398
399
400
401
402
    degtorad = !pi/180
    
    ;Generation of POLEXT and PSI_EXT data by default   
    ;Testing on the presence of covariances otherwise an error is returned
    ;The testing happens here because covariances are needed for the error estimation of EXT_P,PSI_EXT.   
    
0e955322   Ilyes Choubani   fixing small typo...
403
    tstcovuex = where((data_ext(testuex).sigextIU) EQ la_undef() or (data_ext(testuex).sigextQU) EQ la_undef(), ctcovuex)
303de20d   Ilyes Choubani   updating check_data
404
405
406
407
408
409
410
411
412
413
414
415
416
    if ctcovuex NE 0  then message, 'Covariance data is missing in the extinction data pertaining to the StokesU parameter. Data, errors and covariances do not match. Aborting...'
    tstcovqex = where((data_ext(testqex).sigextIQ) EQ la_undef() or (data_ext(testqex).sigextQU) EQ la_undef(), ctcovqex)
    if ctcovqex NE 0  then message, 'Covariance data is missing in the extinction pertaining to the StokesQ parameter. Data, errors and covariances do not match. Aborting...'
    
    ;Matching both filter and spectrum points 
    match2,uext.wav,qext.wav,qexpts,uexpts
    
    ;removing -1 values from the indices (qpts & upts)
    indnotqex = where(qexpts eq -1, cnotqex)
    if cnotqex ne 0 then remove, indnotqex, qexpts
    indnotuex = where(uexpts eq -1, cnotuex)
    if cnotuex ne 0 then remove, indnotuex, uexpts
    
0e955322   Ilyes Choubani   fixing small typo...
417
    match2, ext.wav, qext.wav(qexpts), qextmp, extpts
303de20d   Ilyes Choubani   updating check_data
418
419
420
421
422
423
424
    indnotx = where(extpts eq -1, cnotx)
    if cnotx ne 0 then remove, indnotx, extpts
    
    instru_names = uext.instru_names(uexpts)
    filt_names = uext.filt_names(uexpts)
    wav = uext.wav(uexpts)
    values = 0.5*atan(uext.values(uexpts),qext.values(qexpts))/degtorad
0e955322   Ilyes Choubani   fixing small typo...
425
    polar_variance_iqu2ippsi,ext.values(extpts),qext.values(qexpts),uext.values(uexpts),(data_ext(testex).sigextII)(extpts),(data_ext(testqex).sigextQQ)(qexpts),(data_ext(testuex).sigextUU)(uexpts),(data_ext(testex).sigextIQ)(extpts),(data_ext(testex).sigextIU)(extpts),(data_ext(testex).sigextQU)(extpts),variance_smallp,variance_psi,variance_largep
303de20d   Ilyes Choubani   updating check_data
426
    sigma = sqrt(variance_psi)
5a2643a4   Ilyes Choubani   cleaning/improvin...
427
    psi_ext={instru_names:instru_names,filt_names:filt_names,wav:wav,values:values,sigma:sigma}
07372e26   Ilyes Choubani   Corrected huge pl...
428
429


303de20d   Ilyes Choubani   updating check_data
430
    polext = psi_ext
0e955322   Ilyes Choubani   fixing small typo...
431
    polext.values = sqrt(uext.values(uexpts)^2+qext.values(qexpts)^2) 
303de20d   Ilyes Choubani   updating check_data
432
    polext.sigma = sqrt(variance_largep)
67bd858a   Ilyes Choubani   Replication of th...
433
434
435
436
437
    
    fpolext = psi_ext
    fpolext.values = polext.values/ext.values(extpts) 
    fpolext.sigma = sqrt(variance_smallp)
    
303de20d   Ilyes Choubani   updating check_data
438
439
    goto, end_ext
    
67bd858a   Ilyes Choubani   Replication of th...
440
    
09e61d64   Ilyes Choubani   cleaned set_data ...
441
442
    end_ext:
ENDIF
04efbaa5   Ilyes Choubani   Correcting set_da...
443
444
445

the_end:

09e61d64   Ilyes Choubani   cleaned set_data ...
446
447

END