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|
module mod_output
use mod_functions
use mod_globals
implicit none
contains
subroutine write_plaintext(realspec,fittedspectrum,continuum,skyspectrum,fittedlines,redshiftguess_overall,resolutionguess,normalisation,hbetaflux,outputbasename,totallines)
type(linelist), dimension(:), allocatable :: fittedlines
type(spectrum), dimension(:), allocatable :: realspec,fittedspectrum, skyspectrum, continuum
character(len=512) :: outputbasename
real :: redshiftguess_overall,resolutionguess
integer :: totallines
real :: normalisation, hbetaflux
integer :: omp_get_thread_num,threadnumber
threadnumber=omp_get_thread_num()
open(100+threadnumber,file=trim(outputdirectory)//trim(outputbasename)//"_fit")
write (100+threadnumber,*) "#alfa version ",VERSION
write (100+threadnumber,*) "#fit generated using: ",trim(commandline)
write (100+threadnumber,*) "#""wavelength"" ""input spectrum "" ""fitted spectrum"" ""cont-subbed orig"" ""continuum"" ""sky lines"" ""residuals"" ""uncertainty"""
do i=1,spectrumlength
write(100+threadnumber,"(F9.2, 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+threadnumber)
! now write out the line list.
if (maxval(fittedlines%peak) .lt. 0.1 .or. maxval(fittedlines%peak) .gt. 1.e7) then
fluxformat="ES12.3"
else
fluxformat="F12.3"
endif
if (messages) print *,gettime(),"writing output files ",trim(outputdirectory),trim(outputbasename),"_lines and ",trim(outputdirectory),trim(outputbasename),"_fit"
open(200+threadnumber,file=trim(outputdirectory)//trim(outputbasename)//"_lines")
write (200+threadnumber,*) "#wlen (obs) (rest) flux uncertainty peak FWHM"
!check whether to write out continuum fluxes
writeb1=0
writeb2=0
writep1=0
writep2=0
if (minval(continuum%wavelength)-3630.0 .lt.0..and. maxval(continuum%wavelength)-3630. .gt.0.) writeb1=minloc(abs(fittedlines%wavelength-3630.0),1)
if (minval(continuum%wavelength)-3700.0 .lt.0..and. maxval(continuum%wavelength)-3700. .gt.0.) writeb2=minloc(abs(fittedlines%wavelength-3700.0),1)
if (minval(continuum%wavelength)-8100.0 .lt.0..and. maxval(continuum%wavelength)-8100. .gt.0.) writep1=minloc(abs(fittedlines%wavelength-8100.0),1)
if (minval(continuum%wavelength)-8400.0 .lt.0..and. maxval(continuum%wavelength)-8400. .gt.0.) writep2=minloc(abs(fittedlines%wavelength-8400.0),1)
do i=1,totallines
if (i.eq.writeb1) then
write (200+threadnumber,"(2(F9.2),"//fluxformat//","//fluxformat//",' 0.0 0.0')") 3630.0, 3630.0, normalisation*continuum(minloc(abs(continuum%wavelength-3630.)))%flux, normalisation*realspec(minloc(abs(continuum%wavelength-3630.)))%uncertainty
endif
if (i.eq.writeb2) then
write (200+threadnumber,"(2(F9.2),"//fluxformat//","//fluxformat//",' 0.0 0.0')") 3700.0, 3700.0, normalisation*continuum(minloc(abs(continuum%wavelength-3700.)))%flux, normalisation*realspec(minloc(abs(continuum%wavelength-3700.)))%uncertainty
endif
if (i.eq.writep1) then
write (200+threadnumber,"(2(F9.2),"//fluxformat//","//fluxformat//",' 0.0 0.0')") 8100.0, 8100.0, normalisation*continuum(minloc(abs(continuum%wavelength-8100.)))%flux, normalisation*realspec(minloc(abs(continuum%wavelength-8100.)))%uncertainty
endif
if (i.eq.writep2) then
write (200+threadnumber,"(2(F9.2),"//fluxformat//","//fluxformat//",' 0.0 0.0')") 8400.0, 8400.0, normalisation*continuum(minloc(abs(continuum%wavelength-8400.)))%flux, normalisation*realspec(minloc(abs(continuum%wavelength-8400.)))%uncertainty
endif
if (fittedlines(i)%blended .eq. 0 .and. fittedlines(i)%uncertainty .gt. detectionlimit) then
write (200+threadnumber,"(2(F9.2),4("//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,fittedlines(i)%peak/normalisation, fittedlines(i)%wavelength/fittedlines(i)%resolution * 2.35482
elseif (fittedlines(i)%blended .ne. 0) then
if (fittedlines(fittedlines(i)%blended)%uncertainty .gt. detectionlimit) then
write (200+threadnumber,"(F9.2,F9.2,' * * * *')") 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. detectionlimit .and. upperlimits .eqv. .true.) then
write (200+threadnumber,"(2(F9.2),"//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 measured Hbeta flux if normalisation was applied, and resolution and velocity
if (hbetaflux .gt. 0.d0 .and. normalisation .ne. 1.d0) then
write (200+threadnumber,"(A,ES8.2)") "# measured flux of Hbeta: ",hbetaflux
endif
write (200+threadnumber,"(A,ES8.2)") "# spectral resolution: ",resolutionguess
write (200+threadnumber,"(A,ES8.2)") "# radial velocity: ",c*(redshiftguess_overall-1)
!done, close files
close(200+threadnumber)
end subroutine write_plaintext
subroutine write_latex(realspec,fittedspectrum,continuum,skyspectrum,fittedlines,redshiftguess_overall,resolutionguess,normalisation,hbetaflux,outputbasename,totallines)
type(linelist), dimension(:), allocatable :: fittedlines
type(spectrum), dimension(:), allocatable :: realspec,fittedspectrum, skyspectrum, continuum
character(len=512) :: outputbasename
real :: redshiftguess_overall,resolutionguess
integer :: totallines
real :: normalisation, hbetaflux
integer :: omp_get_thread_num,threadnumber
threadnumber=omp_get_thread_num()
open(100+threadnumber,file=trim(outputdirectory)//trim(outputbasename)//"_fit.tex")
write (100+threadnumber,*) "%alfa version ",VERSION
write (100+threadnumber,*) "%fit generated using: ",trim(commandline)
write (100+threadnumber,*) "#""wavelength"" ""input spectrum "" ""fitted spectrum"" ""cont-subbed orig"" ""continuum"" ""sky lines"" ""residuals"" ""uncertainty"""
do i=1,spectrumlength
write(100+threadnumber,"(F9.2, 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+threadnumber)
! now write out the line list.
if (maxval(fittedlines%peak) .lt. 0.1 .or. maxval(fittedlines%peak) .gt. 1.e7) 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.tex"
open(200+threadnumber,file=trim(outputdirectory)//trim(outputbasename)//"_lines.tex")
write(200+threadnumber,*) "\\ \hline"
write(200+threadnumber,*) "Observed wavelength & Rest wavelength & Flux & Uncertainty & Peak & FWHM & Ion & Multiplet & Lower term & Upper term & g$_1$ & g$_2$ \\"
write(200+threadnumber,*) "\hline"
!check whether to write out continuum fluxes
writeb1=0
writeb2=0
writep1=0
writep2=0
if (minval(continuum%wavelength)-3630.0 .lt.0..and. maxval(continuum%wavelength)-3630. .gt.0.) writeb1=minloc(abs(fittedlines%wavelength-3630.0),1)
if (minval(continuum%wavelength)-3700.0 .lt.0..and. maxval(continuum%wavelength)-3700. .gt.0.) writeb2=minloc(abs(fittedlines%wavelength-3700.0),1)
if (minval(continuum%wavelength)-8100.0 .lt.0..and. maxval(continuum%wavelength)-8100. .gt.0.) writep1=minloc(abs(fittedlines%wavelength-8100.0),1)
if (minval(continuum%wavelength)-8400.0 .lt.0..and. maxval(continuum%wavelength)-8400. .gt.0.) writep2=minloc(abs(fittedlines%wavelength-8400.0),1)
do i=1,totallines
if (i.eq.writeb1) then
write (200+threadnumber,"(F9.2,' & & ',"//fluxformat//",' & ',"//fluxformat//",' & Balmer cont.\\')") 3630.0, normalisation*continuum(minloc(abs(continuum%wavelength-3630.)))%flux, normalisation*realspec(minloc(abs(continuum%wavelength-3630.)))%uncertainty
endif
if (i.eq.writeb2) then
write (200+threadnumber,"(F9.2,' & & ',"//fluxformat//",' & ',"//fluxformat//",' & Paschen cont.\\')") 3700.0, normalisation*continuum(minloc(abs(continuum%wavelength-3700.)))%flux, normalisation*realspec(minloc(abs(continuum%wavelength-3700.)))%uncertainty
endif
if (i.eq.writep1) then
write (200+threadnumber,"(F9.2,' & & ',"//fluxformat//",' & ',"//fluxformat//",' & Paschen cont.\\')") 8100.0, normalisation*continuum(minloc(abs(continuum%wavelength-8100.)))%flux, normalisation*realspec(minloc(abs(continuum%wavelength-8100.)))%uncertainty
endif
if (i.eq.writep2) then
write (200+threadnumber,"(F9.2,' & & ',"//fluxformat//",' & ',"//fluxformat//",' & Brackett cont.\\')") 8400.0, normalisation*continuum(minloc(abs(continuum%wavelength-8400.)))%flux, normalisation*realspec(minloc(abs(continuum%wavelength-8400.)))%uncertainty
endif
if (fittedlines(i)%blended .eq. 0 .and. fittedlines(i)%uncertainty .gt. detectionlimit) then
write (200+threadnumber,"(F9.2,' & ',F9.2,' & ',"//fluxformat//",' & ',"//fluxformat//",' & ',"//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)%peak/normalisation, fittedlines(i)%wavelength/fittedlines(i)%resolution * 2.35482, fittedlines(i)%ion
elseif (fittedlines(i)%blended .ne. 0) then
if (fittedlines(fittedlines(i)%blended)%uncertainty .gt. detectionlimit) then
write (200+threadnumber,"(F9.2,' & ',F9.2,' & * & * & * & *',A85)") fittedlines(i)%wavelength*fittedlines(i)%redshift,fittedlines(i)%wavelength,fittedlines(i)%ion
endif
! write out 3 sigma upper limit for non-detections if upperlimits flag is set
elseif (fittedlines(i)%uncertainty .le. detectionlimit .and. upperlimits .eqv. .true.) then
write (200+threadnumber,"(F9.2,' & ',F9.2,' & ',"//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)%ion
endif
enddo
!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) then
write (200+threadnumber,*) "\hline"
write (200+threadnumber,"(A,ES8.2,A)") "\multicolumn{10}{l}{Measured flux of H$\beta$: ",hbetaflux,"} \\"
endif
write (200+threadnumber,"(A,ES8.2,A)") "\multicolumn{10}{l}{Spectral resolution: ",resolutionguess,"} \\"
write (200+threadnumber,"(A,ES8.2,A)") "\multicolumn{10}{l}{Radial velocity: ",c*(redshiftguess_overall-1),"} \\"
write (200+threadnumber,*) "\hline"
!done, close files
close(200+threadnumber)
end subroutine write_latex
subroutine write_csv(realspec,fittedspectrum,continuum,skyspectrum,fittedlines,redshiftguess_overall,resolutionguess,normalisation,hbetaflux,outputbasename,totallines)
type(linelist), dimension(:), allocatable :: fittedlines
type(spectrum), dimension(:), allocatable :: realspec,fittedspectrum, skyspectrum, continuum
character(len=512) :: outputbasename
real :: redshiftguess_overall,resolutionguess
integer :: totallines
real :: normalisation, hbetaflux
integer :: omp_get_thread_num,threadnumber
threadnumber=omp_get_thread_num()
open(100+threadnumber,file=trim(outputdirectory)//trim(outputbasename)//"_fit.csv")
write (100+threadnumber,*) "#alfa version ",VERSION
write (100+threadnumber,*) "#fit generated using: ",trim(commandline)
write (100+threadnumber,*) "#wavelength,input spectrum,fitted spectrum,cont-subbed orig,continuum,sky lines,residuals,uncertainty"
do i=1,spectrumlength
write(100+threadnumber,"(F9.2, ',', 6(ES12.3,','), 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+threadnumber)
! now write out the line list.
if (maxval(fittedlines%peak) .lt. 0.1 .or. maxval(fittedlines%peak) .gt. 1.e7) then
fluxformat="ES12.3"
else
fluxformat="F12.3"
endif
if (messages) print *,gettime(),"writing output files ",trim(outputdirectory),trim(outputbasename),"_lines.csv and ",trim(outputdirectory),trim(outputbasename),"_fit.csv"
open(200+threadnumber,file=trim(outputdirectory)//trim(outputbasename)//"_lines.csv")
write (200+threadnumber,*) "#wlen (obs),(rest),flux,uncertainty,peak,FWHM"
!check whether to write out continuum fluxes
writeb1=0
writeb2=0
writep1=0
writep2=0
if (minval(continuum%wavelength)-3630.0 .lt.0..and. maxval(continuum%wavelength)-3630. .gt.0.) writeb1=minloc(abs(fittedlines%wavelength-3630.0),1)
if (minval(continuum%wavelength)-3700.0 .lt.0..and. maxval(continuum%wavelength)-3700. .gt.0.) writeb2=minloc(abs(fittedlines%wavelength-3700.0),1)
if (minval(continuum%wavelength)-8100.0 .lt.0..and. maxval(continuum%wavelength)-8100. .gt.0.) writep1=minloc(abs(fittedlines%wavelength-8100.0),1)
if (minval(continuum%wavelength)-8400.0 .lt.0..and. maxval(continuum%wavelength)-8400. .gt.0.) writep2=minloc(abs(fittedlines%wavelength-8400.0),1)
do i=1,totallines
if (i.eq.writeb1) then
write (200+threadnumber,"(2(F9.2,','),"//fluxformat//",',',"//fluxformat//",', 0.0, 0.0')") 3630.0, 3630.0, normalisation*continuum(minloc(abs(continuum%wavelength-3630.)))%flux, normalisation*realspec(minloc(abs(continuum%wavelength-3630.)))%uncertainty
endif
if (i.eq.writeb2) then
write (200+threadnumber,"(2(F9.2,','),"//fluxformat//",',',"//fluxformat//",', 0.0, 0.0')") 3700.0, 3700.0, normalisation*continuum(minloc(abs(continuum%wavelength-3700.)))%flux, normalisation*realspec(minloc(abs(continuum%wavelength-3700.)))%uncertainty
endif
if (i.eq.writep1) then
write (200+threadnumber,"(2(F9.2,','),"//fluxformat//",',',"//fluxformat//",', 0.0, 0.0')") 8100.0, 8100.0, normalisation*continuum(minloc(abs(continuum%wavelength-8100.)))%flux, normalisation*realspec(minloc(abs(continuum%wavelength-8100.)))%uncertainty
endif
if (i.eq.writep2) then
write (200+threadnumber,"(2(F9.2,','),"//fluxformat//",',',"//fluxformat//",', 0.0, 0.0')") 8400.0, 8400.0, normalisation*continuum(minloc(abs(continuum%wavelength-8400.)))%flux, normalisation*realspec(minloc(abs(continuum%wavelength-8400.)))%uncertainty
endif
if (fittedlines(i)%blended .eq. 0 .and. fittedlines(i)%uncertainty .gt. detectionlimit) then
write (200+threadnumber,"(2(F9.2,','),3("//fluxformat//",','),"//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,fittedlines(i)%peak/normalisation, fittedlines(i)%wavelength/fittedlines(i)%resolution * 2.35482
elseif (fittedlines(i)%blended .ne. 0) then
if (fittedlines(fittedlines(i)%blended)%uncertainty .gt. detectionlimit) then
write (200+threadnumber,"(F9.2,','F9.2,',',3(A12,','),A12)") 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. detectionlimit .and. upperlimits .eqv. .true.) then
write (200+threadnumber,"(2(F9.2,','),"//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 measured Hbeta flux if normalisation was applied
if (hbetaflux .gt. 0.d0 .and. normalisation .ne. 1.d0) then
write (200+threadnumber,"(A,ES8.2)") "# measured flux of Hbeta: ",hbetaflux
endif
write (200+threadnumber,"(A,ES8.2)") "# spectral resolution: ",resolutionguess
write (200+threadnumber,"(A,ES8.2)") "# radial velocity: ",c*(redshiftguess_overall-1)
!done, close files
close(200+threadnumber)
end subroutine write_csv
subroutine write_fits(realspec,fittedspectrum,continuum,skyspectrum,fittedlines,redshiftguess_overall,resolutionguess,normalisation,hbetaflux,outputbasename,totallines)
!create a single fits file with two extensions, one with the fit and one with the linelist
implicit none
integer :: status,unit,readwrite,blocksize,tfields,varidat
character(len=16) :: extname
character(len=16),dimension(8) :: ttype_fit,tform_fit,tunit_fit
character(len=16),dimension(12) :: ttype_lines,tform_lines,tunit_lines
character(len=16),dimension(4) :: ttype_qc,tform_qc,tunit_qc
real,dimension(:),allocatable :: linefluxes,linesigmas,linelambdas
type(linelist), dimension(:), allocatable :: fittedlines
type(spectrum), dimension(:), allocatable :: realspec,fittedspectrum, skyspectrum, continuum
character(len=512) :: outputbasename
real :: redshiftguess_overall,resolutionguess
integer :: totallines,detectedlines,i,rownumber
real :: normalisation, hbetaflux
character(len=8) :: writevalue
character(len=30) :: cfitsioerror
integer :: omp_get_thread_num,threadnumber
threadnumber=omp_get_thread_num()
status=0
readwrite=1
! initialise
! call ftgiou(unit,status)
unit=51+threadnumber
call ftinit(unit,"!"//trim(outputdirectory)//trim(outputbasename)//"_fit.fits",blocksize,status)
call ftphps(unit,16,0,0,status)
! add history keyword to primary HDU
call ftpdat(unit,status)
call ftphis(unit,trim(commandline),status)
! first extension for the fit
ttype_fit=(/"Wavelength ","InputSpec ","FittedSpec ","ContSubbedInput ","Continuum ","SkyLines ","Residuals ","Uncertainty "/)
tform_fit=(/"1E","1E","1E","1E","1E","1E","1E","1E"/)
tunit_fit=(/"Angstrom ","Flux ","Flux ","Flux ","Flux ","Flux ","Flux ","Flux "/)
extname='FIT'
varidat=0
tfields=8
call ftibin(unit,spectrumlength,tfields,ttype_fit,tform_fit,tunit_fit,extname,varidat,status)
! record version, date and setting used in comments
call ftpcom(unit,"Produced by alfa version "//VERSION,status)
call ftpcom(unit,"Command line: '"//trim(commandline)//"'",status)
call ftpcom(unit,"input file: "//trim(spectrumfile),status)
! if (len(trim(imagesection)).gt.0) print *," fitting section: ",imagesection
if (.not.normalise) then
call ftpcom(unit,"normalisation: using measured value of Hb",status)
else
if (normalisation.eq.0.d0) then
call ftpcom(unit,"normalisation: no normalisation",status)
else
write(writevalue,"(F8.3)") normalisation
call ftpcom(unit,"normalisation: to Hb="//writevalue,status)
endif
endif
if (subtractcontinuum) then
call ftpcom(unit,"continuum fitting: enabled",status)
write(writevalue,"(I8)") continuumwindow
call ftpcom(unit,"continuum window: "//writevalue,status)
else
call ftpcom(unit,"continuum fitting: disabled",status)
endif
write(writevalue,"(F8.2)") baddata
call ftpcom(unit,"spectrum fitted if max value > "//writevalue,status)
write(writevalue,"(F8.2)") wavelengthscaling
call ftpcom(unit,"Angstroms per wavelength unit: "//writevalue,status)
if (tablewavelengthcolumn.ne.1) then
write(writevalue,"(I2)") tablewavelengthcolumn
call ftpcom(unit,"table wavelength column: "//writevalue,status)
endif
if (tablefluxcolumn.ne.2) then
write(writevalue,"(I2)") tablefluxcolumn
call ftpcom(unit,"table flux column: "//writevalue,status)
endif
if (collapse) then
call ftpcom(unit,"multiple spectra: collapsed to 1D",status)
else
call ftpcom(unit,"multiple spectra: fitted individually",status)
endif
! call ftpcom(unit,"velocity guess: ",status)
! call ftpcom(unit,redshiftguess_initial,status)
! call ftpcom(unit,"resolution guess: ",status)
! call ftpcom(unit,resolutionguess_initial,status)
write(writevalue,"(F8.2)") vtol1*c
call ftpcom(unit,"first pass velocity tolerance: "//writevalue,status)
write(writevalue,"(F8.2)") vtol2*c
call ftpcom(unit,"second pass velocity tolerance: "//writevalue,status)
write(writevalue,"(F8.2)") rtol1
call ftpcom(unit,"first pass resolution tolerance: "//writevalue,status)
write(writevalue,"(F8.2)") rtol2
call ftpcom(unit,"second pass resolution tolerance: "//writevalue,status)
if (subtractsky) then
call ftpcom(unit,"sky line fitting: enabled",status)
call ftpcom(unit,"sky line catalogue: "//trim(skylinelistfile),status)
else
call ftpcom(unit,"sky line fitting: disabled",status)
endif
call ftpcom(unit,"strong line catalogue: "//trim(stronglinelistfile),status)
call ftpcom(unit,"deep line catalogue: "//trim(deeplinelistfile),status)
! if (exclusioncount .gt. 0) then
! call ftpcom(unit,"lines excluded from fitting: "//exclusions,status)
! endif
if (rebinfactor .gt. 1) then
write(writevalue,"(I8)") rebinfactor
call ftpcom(unit,"spectra rebinned by factor of: "//writevalue,status)
endif
write(writevalue,"(I8)") generations
call ftpcom(unit,"number of generations: "//writevalue,status)
write(writevalue,"(I8)") popsize
call ftpcom(unit,"population size: "//writevalue,status)
write(writevalue,"(F8.2)") pressure
call ftpcom(unit,"pressure factor: "//writevalue,status)
call ftpcom(unit,"output directory: "//trim(outputdirectory),status)
call ftpcom(unit,"output format: "//outputformat,status)
call ftpcle(unit,1,1,1,spectrumlength,fittedspectrum%wavelength,status)
call ftpcle(unit,2,1,1,spectrumlength,realspec%flux + continuum%flux,status)
call ftpcle(unit,3,1,1,spectrumlength,fittedspectrum%flux + continuum%flux + skyspectrum%flux,status)
call ftpcle(unit,4,1,1,spectrumlength,realspec%flux,status)
call ftpcle(unit,5,1,1,spectrumlength,continuum%flux,status)
call ftpcle(unit,6,1,1,spectrumlength,skyspectrum%flux,status)
call ftpcle(unit,7,1,1,spectrumlength,realspec%flux - fittedspectrum%flux,status)
call ftpcle(unit,8,1,1,spectrumlength,realspec%uncertainty,status)
if (status .gt. 0) then
call ftgerr(status,cfitsioerror)
print *,gettime(),"[107] CFITSIO error: ",status,cfitsioerror
print *,gettime(),"thread ",threadnumber,", unit ",unit
call exit(107)
else
print *,gettime(),"Wrote fit to extension FIT of output file ",trim(outputdirectory)//trim(outputbasename)//"_fit.fits"
endif
! second extension for the lines
status=0
extname="LINES"
tfields=12
ttype_lines=(/"WlenObserved ","WlenRest ","Flux ","Uncertainty ","Peak ","FWHM ","Ion ","Multiplet ","LowerTerm ","Upperterm ","g1 ","g2 "/)
tform_lines=(/"1E ","1E ","1E ","1E ","1E ","1E ","12A","12A","12A","12A","1I ","1I "/)
tunit_lines=(/"Angstrom ","Angstrom ","Flux ","Flux ","Flux ","Angstrom "," "," "," "," "," "," "/)
call ftibin(unit,totallines,tfields,ttype_lines,tform_lines,tunit_lines,extname,varidat,status)
allocate(linefluxes(totallines))
allocate(linesigmas(totallines))
allocate(linelambdas(totallines))
! replicates gaussianflux function. why can't that be vectorised?
! should replace this with calculation at time of fitting?
linefluxes=fittedlines%peak*(fittedlines%wavelength/fittedlines%resolution)*(2*3.14159265359)**0.5
linesigmas=linefluxes/fittedlines%uncertainty
linelambdas=fittedlines%wavelength*fittedlines%redshift
! deal with blends and upper limits
detectedlines=totallines
do i=1,totallines
if (fittedlines(i)%blended .ne. 0) then
linelambdas(i)=0
if (fittedlines(fittedlines(i)%blended)%uncertainty .gt. detectionlimit) then
linefluxes(i)=0
linesigmas(i)=0
else ! blends of non-detections. todo: save with null value
linelambdas(i)=0
linefluxes(i)=-999.
linesigmas(i)=-999.
detectedlines=detectedlines-1
endif
! write out 3 sigma upper limit as a negative flux for non-detections
elseif (fittedlines(i)%uncertainty .le. detectionlimit) then
linefluxes(i)=-detectionlimit*linesigmas(i)
linesigmas(i)=-linesigmas(i)
detectedlines=detectedlines-1
endif
enddo
call ftpcle(unit,1,1,1,totallines,linelambdas,status)
call ftpcle(unit,2,1,1,totallines,fittedlines%wavelength,status)
call ftpcle(unit,3,1,1,totallines,linefluxes,status)
call ftpcle(unit,4,1,1,totallines,linesigmas,status)
call ftpcle(unit,5,1,1,totallines,fittedlines%peak/normalisation,status)
call ftpcle(unit,6,1,1,totallines,fittedlines%wavelength/fittedlines%resolution * 2.35482,status)
call ftpcls(unit,7,1,1,totallines,fittedlines%ion,status)
call ftpcls(unit,8,1,1,totallines,fittedlines%multiplet,status)
call ftpcls(unit,9,1,1,totallines,fittedlines%lowerterm,status)
call ftpcls(unit,10,1,1,totallines,fittedlines%upperterm,status)
call ftpclj(unit,11,1,1,totallines,fittedlines%g1,status)
call ftpclj(unit,12,1,1,totallines,fittedlines%g2,status)
!write out continuum fluxes if measured
rownumber=totallines
if (minval(continuum%wavelength)-3630.0 .lt.0..and. maxval(continuum%wavelength)-3630. .gt.0.) then
call ftirow(unit,rownumber,1,status)
rownumber=rownumber+1
call ftpcle(unit,1,rownumber,1,1,(/3630.0/),status)
call ftpcle(unit,2,rownumber,1,1,(/3630.0/),status)
call ftpcle(unit,3,rownumber,1,1,normalisation*continuum(minloc(abs(continuum%wavelength-3630.)))%flux,status)
call ftpcle(unit,4,rownumber,1,1,normalisation*realspec(minloc(abs(continuum%wavelength-3630.)))%uncertainty,status)
endif
if (minval(continuum%wavelength)-3700.0 .lt.0..and. maxval(continuum%wavelength)-3700. .gt.0.) then
call ftirow(unit,rownumber,1,status)
rownumber=rownumber+1
call ftpcle(unit,1,rownumber,1,1,(/3700.0/),status)
call ftpcle(unit,2,rownumber,1,1,(/3700.0/),status)
call ftpcle(unit,3,rownumber,1,1,normalisation*continuum(minloc(abs(continuum%wavelength-3700.)))%flux,status)
call ftpcle(unit,4,rownumber,1,1,normalisation*realspec(minloc(abs(continuum%wavelength-3700.)))%uncertainty,status)
endif
if (minval(continuum%wavelength)-8100.0 .lt.0..and. maxval(continuum%wavelength)-8100. .gt.0.) then
call ftirow(unit,rownumber,1,status)
rownumber=rownumber+1
call ftpcle(unit,1,rownumber,1,1,(/8100.0/),status)
call ftpcle(unit,2,rownumber,1,1,(/8100.0/),status)
call ftpcle(unit,3,rownumber,1,1,normalisation*continuum(minloc(abs(continuum%wavelength-8100.)))%flux,status)
call ftpcle(unit,4,rownumber,1,1,normalisation*realspec(minloc(abs(continuum%wavelength-8100.)))%uncertainty,status)
endif
if (minval(continuum%wavelength)-8400.0 .lt.0..and. maxval(continuum%wavelength)-8400. .gt.0.) then
call ftirow(unit,rownumber,1,status)
rownumber=rownumber+1
call ftpcle(unit,1,rownumber,1,1,(/8400.0/),status)
call ftpcle(unit,2,rownumber,1,1,(/8400.0/),status)
call ftpcle(unit,3,rownumber,1,1,normalisation*continuum(minloc(abs(continuum%wavelength-8400.)))%flux,status)
call ftpcle(unit,4,rownumber,1,1,normalisation*realspec(minloc(abs(continuum%wavelength-8400.)))%uncertainty,status)
endif
if (status .gt. 0) then
call ftgerr(status,cfitsioerror)
print *,gettime(),"[107] CFITSIO error: ",status,cfitsioerror
call exit(107)
else
print *,gettime(),"Wrote line list to extension LINES"
endif
! third extension for nlines, f(hb), rv, resolution
status=0
extname="QC"
tfields=4
ttype_qc=(/"NumberOfLines ","HbetaFlux ","RadialVelocity ","Resolution "/)
tform_qc=(/"1J","1E","1E","1E"/)
tunit_qc=(/" ","SameAsInputFlux ","kms-1 "," "/)
call ftibin(unit,1,tfields,ttype_qc,tform_qc,tunit_qc,extname,varidat,status)
call ftpclj(unit,1,1,1,1,(/detectedlines/),status)
call ftpcle(unit,2,1,1,1,(/hbetaflux/),status)
call ftpcle(unit,3,1,1,1,(/c*(redshiftguess_overall-1)/),status)
call ftpcle(unit,4,1,1,1,(/resolutionguess/),status)
if (status .gt. 0) then
call ftgerr(status,cfitsioerror)
print *,gettime(),"[107] CFITSIO error: ",status,cfitsioerror
call exit(107)
else
print *,gettime(),"Wrote QC info to extension QC"
endif
! close
call ftclos(unit, status)
call ftfiou(unit, status)
end subroutine write_fits
end module mod_output
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