FUNCTION dustem_check_data,data_sed=data_sed,data_ext=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


;NOTA BENE: No testing is done on the covariances. These will be used when debiasing the large P.       


;CHECKING THE FORMAT OF THE SED STRUCTURE
IF KEYWORD_SET(data_sed) THEN BEGIN
            
    ans=''
    wavs=data_sed.wave
    ;=== Impose central wavelengths for photometric channels
    ind=where(data_sed.filter NE 'SPECTRUM',count)
    IF count NE 0 THEN BEGIN
        wavs(ind)=dustem_filter2wav(data_sed(ind).filter)
    ENDIF
    ;=== Initializing observation structure
    ;it doesn't matter that data.StokesI is used, further test will take care of what is necessary. 
    obs_EM={instru_names:data_sed.instru,filt_names:data_sed.filter,wav:wavs, values:data_sed.StokesI,sigma:sqrt(abs(data_sed.sigmaII))} 
    ;INITIALIZING OUTPUT STRUCTURES
    sed = obs_EM
    qsed = sed
    used = sed
    
    ;Test if there is StokesI data. If not move to polsed testing.
    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
    IF N_sed EQ 0 THEN BEGIN
        sed = ptr_new()
        goto, qzone
    ENDIF ELSE BEGIN 
    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
        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 
    IF strupcase(ans) EQ 'Y' THEN message, 'You have chosen automatic format filtering. Removal of undefined data points...',/continue $
    ELSE message, 'Data format is met. Removal of undefined data points...',/continue
    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 message, 'Data and errors do not match. Undefinded data detected. Aborting...'
    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    
    ENDELSE
    qzone:
    ans=''
    qsed.values=data_sed.StokesQ
    qsed.sigma=sqrt(abs(data_sed.sigmaQQ))
    ;Testig if there is StokesQ data. If not move to used data
    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)
    IF NQ EQ 0 THEN BEGIN
        qsed = ptr_new()
        goto, uzone
    ENDIF ELSE BEGIN
    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 
    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
            message, 'Aborting ...'
        ENDIF
    ENDIF
    IF strupcase(ans) EQ 'Y' THEN message, 'You have chosen automatic format filtering. Removal of undefined data points...',/continue $
    ELSE message, 'Data format is met. Removal of undefined data points...',/continue
    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)
    IF ctdaerrq NE 0 THEN message, 'Data and errors do not match. Undefinded data detected. Aborting...'
    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)                
    IF ctestq NE 0 THEN BEGIN 
        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}
    ENDIF
    ENDELSE
    uzone:
    ans=''
    used.values=data_sed.StokesU
    used.sigma=sqrt(abs(data_sed.sigmaUU))
    ;Testig if there is StokesU data. If not return empty value and end loop.
    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)
    IF NU EQ 0 THEN BEGIN
        used = ptr_new()
        goto, psiemzone
    ENDIF ELSE BEGIN
    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 
    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
            message, 'Aborting ...'
        ENDIF
    ENDIF  
    IF strupcase(ans) EQ 'Y' THEN message, 'You have chosen automatic format filtering. Removal of undefined data points...',/continue $
    ELSE message, 'Data format is met. Removal of undefined data points...',/continue
    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)
    IF ctdaerru NE 0 THEN message, 'Data and errors do not match. Undefinded data detected. Aborting...'
    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)                
    IF ctestu NE 0 THEN BEGIN 
        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}
    ENDIF
    ENDELSE
    psiemzone:
    
    degtorad = !pi/180
    
    ;INSTEAD OF USING THE DATA THAT IS IN THE XCAT FILE WE WILL CODE IT ANEW.  
    
    ;Testing on the presence of covariances otherwise an error is returned
    ;The testing happens here because covariances are needed for P,p and PSI.   
     
    tstcovu = where((data_sed(testu).sigmaIU) EQ la_undef() or (data_sed(testu).sigmaQU) EQ la_undef(), ctcovu)
    if ctcovu NE 0 and ctestu EQ 0 then message, 'Covariance data is missing in StokesU data. Data, errors and covariances do not match. Aborting...'
    tstcovq = where((data_sed(testq).sigmaIQ) EQ la_undef() or (data_sed(testq).sigmaQU) EQ la_undef(), ctcovq)
    if ctcovq NE 0 and ctestq EQ 0 then message, 'Covariance data is missing in StokesQ data. Data, errors and covariances do not match. Aborting...'
    
    ;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}
    
    goto, pzone ; Not forgetting that the variances for polfrac and polsed were already computed. 
        
    pzone:
    
    polsed = psi_em
    polsed.values = sqrt(used.values(upts)^2+qsed.values(qpts)^2) 
    polsed.sigma = sqrt(variance_largep)
    goto, fpzone
    
    fpzone:
    
    polfrac = psi_em
    polfrac.values = polsed.values/sed.values(sedpts) 
    polfrac.sigma = sqrt(variance_smallp)
    
    goto, end_sed
    end_sed:
ENDIF



;EXTINCTION HASN'T BEEN TREATED YET 


IF KEYWORD_SET(data_ext) THEN begin
    
    ans=''
    wavs=data_ext.wave
    ;=== Impose central wavelengths for photometric channels
    ind=where(data_ext.filter NE 'SPECTRUM',count)
    IF count NE 0 THEN BEGIN
        wavs(ind)=dustem_filter2wav(data_ext(ind).filter)
    ENDIF
    ;=== define observations structure 
    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))} 
    ;INITIALIZING OUTPUT STRUCTURES
    ext = obs_EXT
    polext = ext
    qext = ext
    uext = ext
    psi_ext = ext
    
    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
    IF N_ext EQ 0 THEN BEGIN
        ext = ptr_new()
        goto, pexzone
    ENDIF ELSE BEGIN
    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 
    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
            message, 'Aborting ...'
        ENDIF
    ENDIF      
    IF strupcase(ans) EQ 'Y' THEN message, 'You have chosen automatic format filtering. Removal of undefined data points...',/continue $ 
    ELSE message, 'Data format is met. Removal of undefined data points...',/continue
    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)                
    IF ctestex NE 0 THEN BEGIN 
        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}
    ENDIF 
    ENDELSE
    pexzone:
    ans=''
    polext.values=data_ext.EXT_P
    polext.sigma=sqrt(abs(data_ext.sigextP))
    ;Testig if there is EXT_P data. If not move to EXT_Q testing
    ind = where(data_ext.EXT_P NE la_undef() and finite(data_ext.EXT_P) EQ 1 and data_ext.sigextP NE la_undef() and finite(data_ext.sigextP) EQ 1,NP_ext) ;Testing if the data and errors are set
    IF NP_ext EQ 0 THEN BEGIN
        polext = ptr_new()
        goto, qexzone
    ENDIF ELSE BEGIN
    ind = where(finite(data_ext.EXT_P) EQ 0 or finite(data_ext.sigextP) EQ 0, countnokpex) ;Format is not okay if there are nan values but the wrapper recognizes the la_undef() value 
    IF countnokpex NE 0 THEN BEGIN 
        message, "SED format isn't met. NaN value(s) detected in EXT_P 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
            message, 'Aborting ...'
        ENDIF
    ENDIF
    IF strupcase(ans) EQ 'Y' THEN message, 'You have chosen automatic format filtering. Removal of undefined data points...',/continue $ 
    ELSE message, 'Data format is met. Removal of undefined data points...',/continue
    tdaerrpex=where((data_ext.sigextP EQ la_undef() and data_ext.EXT_P NE la_undef()) or (data_ext.sigextP NE la_undef() and data_ext.EXT_P EQ la_undef()),ctdaerrpex)
    IF ctdaerrpex NE 0 THEN message, 'Data and errors do not match. Undefinded data detected. Aborting...'
    testpex=where(data_ext.sigextP NE 0. and finite(data_ext.sigextP) EQ 1 and data_ext.sigextP NE la_undef() and data_ext.EXT_P NE la_undef() and finite(data_ext.EXT_P) EQ 1,ctestpex)                
    IF ctestpex NE 0 THEN BEGIN 
        instru_names = polext.instru_names(testpex)
        filt_names = polext.filt_names(testpex)
        wav = polext.wav(testpex)
        values = polext.values(testpex)
        sigma = polext.sigma(testpex)
        polext={instru_names:instru_names,filt_names:filt_names,wav:wav,values:values,sigma:sigma}
    ENDIF 
    ENDELSE
    psiexzone:
    ans=''
    psi_ext.values=data_ext.psi
    psi_ext.sigma=sqrt(abs(data_ext.sigextpsi))
    ;Testig if there is EXT_P data. If not move to EXT_Q testing
    ind = where(data_ext.psi NE la_undef() and finite(data_ext.psi) EQ 1 and data_ext.sigextpsi NE la_undef() and finite(data_ext.sigextpsi) EQ 1,NPSIEXT) ;Testing if the data and errors are set
    IF NPSIEXT EQ 0 THEN BEGIN
        psi_ext = ptr_new()
        goto, qexzone
    ENDIF ELSE BEGIN
    ind = where(finite(data_ext.psi) EQ 0 or finite(data_ext.sigextpsi) EQ 0, countnokpsiex) ;Format is not okay if there are nan values but the wrapper recognizes the la_undef() value 
    IF countnokpsiex NE 0 THEN BEGIN 
        message, "SED format isn't met. NaN value(s) detected in PSI_EXT 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
            message, 'Aborting ...'
        ENDIF
    ENDIF
    IF strupcase(ans) EQ 'Y' THEN message, 'You have chosen automatic format filtering. Removal of undefined data points...',/continue $ 
    ELSE message, 'Data format is met. Removal of undefined data points...',/continue
    tdaerrpsiex=where((data_ext.sigextpsi EQ la_undef() and data_ext.psi NE la_undef()) or (data_ext.sigextpsi NE la_undef() and data_ext.psi EQ la_undef()),ctdaerrpsiex)
    IF ctdaerrpsiex NE 0 THEN message, 'Data and errors do not match. Undefinded data detected. Aborting...'
    testpsiex=where(data_ext.sigextpsi NE 0. and finite(data_ext.sigextpsi) EQ 1 and data_ext.sigextpsi NE la_undef() and data_ext.psi NE la_undef() and finite(data_ext.psi) EQ 1,ctestpsiex)                
    IF ctestpsiex NE 0 THEN BEGIN 
        instru_names = psi_ext.instru_names(testpsiex)
        filt_names = psi_ext.filt_names(testpsiex)
        wav = psi_ext.wav(testpsiex)
        values = psi_ext.values(testpsiex)
        sigma = psi_ext.sigma(testpsiex)
        psi_ext={instru_names:instru_names,filt_names:filt_names,wav:wav,values:values,sigma:sigma}
    ENDIF 
    ENDELSE
    qexzone:
    ans=''
    qext.values=data_ext.EXT_Q
    qext.sigma=sqrt(abs(data_ext.sigextQQ))
    ;Testig if there is EXT_P data. If not move to EXT_U testing
    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
    ;dustem_set_data.prostop   
    IF NQ_ext EQ 0 THEN BEGIN
        qext = ptr_new()
        goto, uexzone
    ENDIF ELSE BEGIN
    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 
    IF countnokqex NE 0 THEN BEGIN 
        message, "SED format isn't met. NaN value(s) detected in EXT_Q 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
            message, 'Aborting ...'
        ENDIF
    ENDIF
    IF strupcase(ans) EQ 'Y' THEN message, 'You have chosen automatic format filtering. Removal of undefined data points...',/continue $
    ELSE message, 'Data format is met. Removal of undefined data points...',/continue
    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)                
    IF ctestqex NE 0 THEN BEGIN 
        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}
    ENDIF 
    ENDELSE
    uexzone:
    ans=''
    uext.values=data_ext.EXT_U
    uext.sigma=sqrt(abs(data_ext.sigextUU))
    ;Testig if there is EXT_P data. If not return empty value and end loop.
    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
    IF NU_ext EQ 0 THEN BEGIN
        uext = ptr_new()
        goto, end_ext
    ENDIF ELSE BEGIN
    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 
    IF countnokuex NE 0 THEN BEGIN 
        message, "SED format isn't met. NaN value(s) detected in EXT_U 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
            message, 'Aborting ...'
        ENDIF
    ENDIF
    IF strupcase(ans) EQ 'Y' THEN message, 'You have chosen automatic format filtering. Removal of undefined data points...',/continue $
    ELSE message, 'Data format is met. Removal of undefined data points...',/continue
    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)                
    IF ctestuex NE 0 THEN BEGIN 
        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}
    ENDIF 
    ENDELSE
    end_ext:
ENDIF
;stop
RETURN, 0.


END