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!Copyright (C) 2013- Roger Wesson
!Free under the terms of the GNU General Public License v3
! this is the general fitting routine, which first subtracts a continuum, then fits sky lines if requested, then fits the emission lines
! it is called from within parallelised wrappers for 2D and 3D data, and simply called for 1D data.
! subtract the continuum
if (messages) print *,gettime(),"fitting continuum"
call fit_continuum(realspec,spectrumlength, continuum)
! now do the fitting
! first get guesses for the redshift and resolution
if (.not. resolution_estimated) then
! estimate resolution assuming nyquist sampling
resolutionguess=2*realspec(2)%wavelength/(realspec(3)%wavelength-realspec(1)%wavelength)
if (messages) print *,gettime(),"estimated spectrograph resolution assuming Nyquist sampling: ",resolutionguess
else
if (messages) print *,gettime(),"estimated spectrograph resolution from user input: ",resolutionguess
endif
if (rtol1 .eq. 0.d0) then
rtol1=0.9*resolutionguess ! user didn't specify a value, default behaviour is to allow resolution to vary between 0.1 and 1.9x the initial guess on the first pass
endif
if (messages) print "(X,A,A,F8.1,A,F7.1)",gettime(),"initial guesses for velocity and resolution: ",c*(redshiftguess-1),"km/s, R=",resolutionguess
! first, subtract sky spectrum if requested. do in chunks of 400 units. no overlap necessary because velocity is zero
allocate(skyspectrum(spectrumlength))
skyspectrum%wavelength=realspec%wavelength
skyspectrum%flux=0.d0
if (subtractsky) then
if (messages) print *,gettime(),"fitting sky emission"
!get an array for all the sky lines in the range
call selectlines(skylines_catalogue,realspec(1)%wavelength, realspec(size(realspec))%wavelength, skylines, nlines)
linearraypos=1
!if there are any sky lines to fit, then go though in chunks of 400 units
if (nlines .gt. 0) then
do i=1,spectrumlength,400
if (i+400 .gt. spectrumlength) then
endpos=spectrumlength
else
endpos=i+400
endif
allocate(spectrumchunk(endpos-i+1))
spectrumchunk = realspec(i:endpos)
!read in sky lines in chunk
call selectlines(skylines_catalogue, realspec(i)%wavelength, realspec(endpos)%wavelength, skylines_section, nlines)
if (nlines .gt. 0) then
call fit(spectrumchunk, 1., resolutionguess, skylines_section, 0., rtol2, generations, popsize, pressure)
skylines(linearraypos:linearraypos+nlines-1)=skylines_section!(1:nlines)
linearraypos=linearraypos+nlines
endif
deallocate(spectrumchunk)
enddo
! make full sky spectrum and subtract at end
call makespectrum(skylines,skyspectrum)
realspec%flux = realspec%flux - skyspectrum%flux
else
print *,gettime(),"no sky lines in wavelength range covered by spectrum"
endif ! nlines .gt. 0
endif ! subtractsky
! select the lines from the catalogue
call selectlines(stronglines_catalogue, minval(realspec%wavelength), maxval(realspec%wavelength), fittedlines, nlines)
if (nlines .eq. 0) then
if (messages) print *,gettime(),"Warning: no reference lines detected, using default guesses for velocity and resolution"
redshiftguess_overall=1.d0
else
if (messages) print *,gettime(),"estimating resolution and velocity using ",nlines," lines"
!create an array containing just the regions around lines of interest
!otherwise far more data is being processed than necessary
!for each line, take 50 data points nearest to wavelength
!should be way more than enough and still far more efficient than fitting the whole spectrum
!todo: calculate the number of points from vtol1
allocate(stronglines(50*nlines))
do i=1,nlines
linelocation=minloc(abs(stronglines_catalogue(i)%wavelength*redshiftguess-realspec%wavelength),1)
stronglines(50*(i-1)+1:50*i) = realspec(linelocation-24:linelocation+25)
enddo
!now fit the strong lines
call fit(stronglines, redshiftguess, resolutionguess, fittedlines, vtol1, rtol1, generations, popsize, pressure)
if (messages) print *,gettime(),"estimated velocity and resolution: ",c*(fittedlines(1)%redshift-1),fittedlines(1)%resolution
redshiftguess_overall = fittedlines(1)%redshift ! when fitting chunks, use this redshift to get lines in the right range from the catalogue. if velocity from each chunk is used, then there's a chance that a line could be missed or double counted due to variations in the calculated velocity between chunks.
redshiftguess=fittedlines(1)%redshift
resolutionguess=fittedlines(1)%resolution
deallocate(stronglines)
endif
! then again in chunks with tighter tolerance
linearraypos=1
!get total number of lines and an array to put them all in
call selectlines(deeplines_catalogue, realspec(1)%wavelength/redshiftguess_overall, realspec(size(realspec))%wavelength/redshiftguess_overall, fittedlines, totallines)
if (messages) print *, gettime(),"fitting full spectrum with ",totallines," lines"
!now go through spectrum in chunks of 440 units. Each one overlaps by 20 units with the previous and succeeding chunk, to avoid the code attempting to fit part of a line profile
!at beginning and end, padding is only to the right and left respectively
do i=1,spectrumlength,400
overlap=nint(2*vtol2/(1-realspec(i)%wavelength/realspec(i+1)%wavelength))
if (i .eq. 1) then
startpos=1
startwlen=realspec(1)%wavelength/redshiftguess_overall
else
startpos=i-overlap
startwlen=realspec(i)%wavelength/redshiftguess_overall
endif
if (i+400+overlap-1 .gt. spectrumlength) then
endpos=spectrumlength
endwlen=realspec(spectrumlength)%wavelength/redshiftguess_overall
else
endpos=i+400+overlap-1
endwlen=realspec(i+400)%wavelength/redshiftguess_overall
endif
allocate(spectrumchunk(endpos-startpos+1))
spectrumchunk = realspec(startpos:endpos)
call selectlines(deeplines_catalogue, startwlen, endwlen, fittedlines_section, nlines)
if (nlines .gt. 0) then
if (messages) print "(' ',A,A,F7.1,A,F7.1,A,I3,A)",gettime(),"fitting from ",spectrumchunk(1)%wavelength," to ",spectrumchunk(size(spectrumchunk))%wavelength," with ",nlines," lines"
call fit(spectrumchunk, redshiftguess, resolutionguess, fittedlines_section, vtol2, rtol2, generations, popsize, pressure)
!use redshift and resolution from this chunk as initial values for next chunk
redshiftguess=fittedlines_section(1)%redshift
resolutionguess=fittedlines_section(1)%resolution
!copy results back
fittedlines(linearraypos:linearraypos+nlines-1)=fittedlines_section
linearraypos=linearraypos+nlines
!report any errors
if (maxval(fittedlines_section%wavelength*fittedlines_section%redshift) .gt. maxval(spectrumchunk%wavelength) .or. minval(fittedlines_section%wavelength*fittedlines_section%redshift) .lt. minval(spectrumchunk%wavelength)) then
if (messages) print *," Warning: some lines ended up outside the fitting region."
if (messages) print *," Try reducing the value of vtol2, which is currently set to ",c*vtol2
endif
endif
deallocate(spectrumchunk)
enddo
!make the fitted spectrum
call makespectrum(fittedlines, fittedspectrum)
!account for blends - for each line, determine if the subsequent line is separated by less than the resolution
!if it is, then flag that line with the lineid of the first member of the blend
if (messages) print *
if (messages) print *,gettime(),"flagging blends"
fittedlines%blended = 0
do i=1,totallines-1
if (abs(fittedlines(i)%wavelength-fittedlines(i+1)%wavelength) .lt. 0.75*fittedlines(i)%wavelength/fittedlines(i)%resolution) then
if (fittedlines(i)%blended .gt. 0) then
fittedlines(i+1)%blended = fittedlines(i)%blended
else
fittedlines(i+1)%blended = i
endif
endif
enddo
! now, go through the list and add all blended line fluxes to the first line in the blend
! uncertainty at a given wavelength is independent of the line flux, so the uncertainty calculated
! at the position of the blend will apply to the total flux.
blendpeak = 0.d0
do i=1,totallines-1
if (fittedlines(i+1)%blended .gt. 0 .and. blendpeak .eq. 0.d0) then
!line is first in blend. add line flux to temporary variable, store line number
blendpeak = blendpeak + fittedlines(i)%peak
elseif (fittedlines(i+1)%blended .gt. 0 .and. blendpeak .gt. 0) then
!line is part of multiple blend. add line flux to temporary variable, leave line number alone
blendpeak = blendpeak + fittedlines(i)%peak
fittedlines(i)%peak = 0.d0
! elseif (fittedlines(i)%blended .eq. 0 .and. blendpeak .eq. 0.d0)
!line is isolated, nothing to be done
elseif (fittedlines(i+1)%blended .eq. 0 .and. blendpeak .gt. 0) then
!line was last component of blend. total flux needs to be attributed to first line in blend
blendpeak = blendpeak + fittedlines(i)%peak
fittedlines(i)%peak = 0.d0
fittedlines(fittedlines(i)%blended)%peak = blendpeak
blendpeak = 0.d0
endif
enddo
! calculate the uncertainties
if (messages) print *,gettime(),"estimating uncertainties"
call get_uncertainties(fittedspectrum, realspec, fittedlines)
! write out the fitted spectrum
open(100+tid,file=trim(outputdirectory)//trim(outputbasename)//"_fit")
write (100+tid,*) """wavelength"" ""input spectrum "" ""fitted spectrum"" ""cont-subbed orig"" ""continuum"" ""sky lines"" ""residuals"""
do i=1,spectrumlength
write(100+tid,"(F8.2, 7(ES12.3))") fittedspectrum(i)%wavelength,realspec(i)%flux + continuum(i)%flux, fittedspectrum(i)%flux + continuum(i)%flux + skyspectrum(i)%flux, realspec(i)%flux, continuum(i)%flux, skyspectrum(i)%flux, realspec(i)%flux - fittedspectrum(i)%flux, realspec(i)%uncertainty
enddo
close(100+tid)
! normalise if H beta is present and user did not specify a normalisation
hbetaflux=0.d0
do i=1,totallines
if (abs(fittedlines(i)%wavelength - 4861.33) .lt. 0.005) then
hbetaflux = gaussianflux(fittedlines(i)%peak,(fittedlines(i)%wavelength/fittedlines(i)%resolution))
endif
enddo
if (.not. normalise) then
normalisation = 0.d0
if (hbetaflux .gt. 0.d0) then
normalisation = 100./hbetaflux
if (messages) print "(' ',A,A,ES9.3,A)",gettime(),"H beta detected with flux ",hbetaflux," - normalising to 100.0"
endif
if (normalisation .eq. 0.d0) then
if (messages) print *,gettime(),"no H beta detected, no normalisation applied"
normalisation = 1.d0
endif
else
if (normalisation .eq. 0.0) then
if (messages) print *,gettime(),"no normalisation applied, measured fluxes will be reported"
normalisation = 1.d0
else
if (messages) print *,gettime(),"normalising to H beta = 100.0 assuming flux of ",normalisation
normalisation = 100./normalisation
endif
endif
fittedlines%peak = fittedlines%peak * normalisation
continuum%flux = continuum%flux * normalisation !for continuum jumps to be scaled
realspec%uncertainty = realspec%uncertainty * normalisation !for continuum jumps to be scaled
! now write out the line list.
if (maxval(fittedlines%peak) .lt. 0.1) then
fluxformat="ES12.3"
else
fluxformat="F12.3"
endif
if (messages) print *,gettime(),"writing output files ",trim(outputdirectory),trim(outputbasename),"_lines.tex and ",trim(outputdirectory),trim(outputbasename),"_fit"
if (messages) open(100+tid,file=trim(outputdirectory)//trim(outputbasename)//"_lines.tex")
open(200+tid,file=trim(outputdirectory)//trim(outputbasename)//"_lines")
if (messages) write(100+tid,*) "Observed wavelength & Rest wavelength & Flux & Uncertainty & Ion & Multiplet & Lower term & Upper term & g$_1$ & g$_2$ \\"
do i=1,totallines
if (fittedlines(i)%blended .eq. 0 .and. fittedlines(i)%uncertainty .gt. 3.0) then
if (messages) write (100+tid,"(F8.2,' & ',F8.2,' & ',"//fluxformat//",' & ',"//fluxformat//",A85)") fittedlines(i)%wavelength*fittedlines(i)%redshift,fittedlines(i)%wavelength,gaussianflux(fittedlines(i)%peak,(fittedlines(i)%wavelength/fittedlines(i)%resolution)), gaussianflux(fittedlines(i)%peak,(fittedlines(i)%wavelength/fittedlines(i)%resolution))/fittedlines(i)%uncertainty, fittedlines(i)%linedata
write (200+tid,"(2(F8.2),2("//fluxformat//"))") fittedlines(i)%wavelength*fittedlines(i)%redshift, fittedlines(i)%wavelength, gaussianflux(fittedlines(i)%peak,(fittedlines(i)%wavelength/fittedlines(i)%resolution)), gaussianflux(fittedlines(i)%peak,(fittedlines(i)%wavelength/fittedlines(i)%resolution))/fittedlines(i)%uncertainty
elseif (fittedlines(i)%blended .ne. 0) then
if (fittedlines(fittedlines(i)%blended)%uncertainty .gt. 3.0) then
if (messages) write (100+tid,"(F8.2,' & ',F8.2,' & * & *',A85)") fittedlines(i)%wavelength*fittedlines(i)%redshift,fittedlines(i)%wavelength,fittedlines(i)%linedata
write (200+tid,"(F8.2,F8.2,' * *')") fittedlines(i)%wavelength*fittedlines(i)%redshift,fittedlines(i)%wavelength
endif
! write out 3 sigma upper limit for non-detections if upperlimits flag is set
elseif (fittedlines(i)%uncertainty .le. 3.0 .and. upperlimits .eqv. .true.) then
if (messages) write (100+tid,"(F8.2,' & ',F8.2,' & ',"//fluxformat//",' & upper limit ',A85)") fittedlines(i)%wavelength*fittedlines(i)%redshift,fittedlines(i)%wavelength, 3.*gaussianflux(fittedlines(i)%peak,(fittedlines(i)%wavelength/fittedlines(i)%resolution))/fittedlines(i)%uncertainty, fittedlines(i)%linedata
write (200+tid,"(2(F8.2),"//fluxformat//",' upper limit')") fittedlines(i)%wavelength*fittedlines(i)%redshift, fittedlines(i)%wavelength, 3.*gaussianflux(fittedlines(i)%peak,(fittedlines(i)%wavelength/fittedlines(i)%resolution))/fittedlines(i)%uncertainty
endif
enddo
!write out continuum jump fluxes. Take continuum at 3630 and 3700A as representative, but write them out as 3645.5 and 3646.5 for input into NEAT
!Balmer
if (minval(abs(continuum%wavelength-3630.)) .lt. 3630./fittedlines(1)%resolution) then
if (messages) write (100+tid,"(F8.2,' & & ',"//fluxformat//",' & ',"//fluxformat//",' & Balmer jump-\\')") 3645.5, continuum(minloc(abs(continuum%wavelength-3630.)))%flux, realspec(minloc(abs(continuum%wavelength-3630.)))%uncertainty
write (200+tid,"(2(F8.2),"//fluxformat//","//fluxformat//")"), 3645.5, 3645.5, continuum(minloc(abs(continuum%wavelength-3630.)))%flux, realspec(minloc(abs(continuum%wavelength-3630.)))%uncertainty
endif
if (minval(abs(continuum%wavelength-3700.)) .lt. 3700./fittedlines(1)%resolution) then
if (messages) write (100+tid,"(F8.2,' & & ',"//fluxformat//",' & ',"//fluxformat//",' & Balmer jump+\\')") 3646.5, continuum(minloc(abs(continuum%wavelength-3700.)))%flux, realspec(minloc(abs(continuum%wavelength-3700. )))%uncertainty
write (200+tid,"(2(F8.2),"//fluxformat//","//fluxformat//")"), 3646.5, 3646.5, continuum(minloc(abs(continuum%wavelength-3700.)))%flux, realspec(minloc(abs(continuum%wavelength-3700.)))%uncertainty
endif
!paschen
if (minval(abs(continuum%wavelength-8100.)) .lt. 8100./fittedlines(1)%resolution) then
if (messages) write (100+tid,"(F8.2,' & & ',"//fluxformat//",' & ',"//fluxformat//",' & Paschen jump-\\')") 8100.0, continuum(minloc(abs(continuum%wavelength-8100.)))%flux, realspec(minloc(abs(continuum%wavelength-8100. )))%uncertainty
write (200+tid,"(2(F8.2),"//fluxformat//","//fluxformat//")"), 8100.0, 8100.0, continuum(minloc(abs(continuum%wavelength-8100.)))%flux, realspec(minloc(abs(continuum%wavelength-8100.)))%uncertainty
endif
if (minval(abs(continuum%wavelength-8400.)) .lt. 8400./fittedlines(1)%resolution) then
if (messages) write (100+tid,"(F8.2,' & & ',"//fluxformat//",' & ',"//fluxformat//",' & Paschen jump+\\')") 8400.0, continuum(minloc(abs(continuum%wavelength-8400.)))%flux, realspec(minloc(abs(continuum%wavelength-8400. )))%uncertainty
write (200+tid,"(2(F8.2),"//fluxformat//","//fluxformat//")"), 8400.0, 8400.0, continuum(minloc(abs(continuum%wavelength-8400.)))%flux, realspec(minloc(abs(continuum%wavelength-8400.)))%uncertainty
endif
!write out measured Hbeta flux to latex table, if normalisation was applied and if output is required
if (hbetaflux .gt. 0.d0 .and. normalisation .ne. 1.d0 .and. messages) then
write (100+tid,*) "\hline"
write (100+tid,"(A,ES8.2)") "Measured flux of H$\beta$: ",hbetaflux
write (100+tid,*) "\hline"
endif
!done, close files
close(200+tid)
if (messages) close(100+tid)
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