GLSbin

defaultopt=""    # place here your personal default options
                 # e.g. "-k", (leading minus required)

set -- $defaultopt $@  # concatenates default options and command line

kep="#"; Kep=""; igls="#"; chi=""; calmass="#"
while getopts ':cfhHikKmMrsvx-?' opt; do
   case $opt in
      i)  igls="";;
      r)  replot="yes";;
      s)  silent="yes";;
      m)  calmass="";;
      M)  calmass=""; silent="yes";;
      k)  kep="";;
      v)  chi="#";;
      K)  kep="";Kep="#";;
      -|c|v|f|m) ;;      # do nothing; options processed by GLS.f
      x)  rm -f {,i}RV{Sin,Kep}Res.plt iGLS{fit,Kep,Sin}.log {GLS,fit}.log GLS{,Kep,Fit,}.plt GLS{,RV}.{ps,pdf}; exit;;
      H)  less $GLSDir/ReadMe.txt; exit;;
      h|?) help="yes";;
   esac;
done;

### output of help
if [ "$help" ]; then
	cat <<-EOF
	
		##################################################
		### GLS - Generalised Lomb-Scargle Periodogram ###
		##################################################
		
		syntax:  GLS [OPTIONS] FILE fbeg fend mass
		input file format: JD RV [RV_err]
		
		available options for the GLS program:
		  -c       chi2 (weight errors, default)
		  -f       fast computation of the Keplerian periodogram
		  -h -?    help
		  -H       view the ReadMe.txt
		  -i       improve (refines the best GLS solution)
		  -k       compute Keplerian periodogram
		  -K       plot only Keplerian periodogram and orbit (no GLS)
		  -m       companion mass calculation
		  -M       only companion mass calculation (no periodogram)
		           syntax: GLS -M mass[Msun] semi-amplitude[m/s] period[d] eccentricity
		  -r       only replot
		  -s       silent, no graphical output
		  -v       variance (unweighted mode)
		  -x       delete GLS product files
		
		you can set default options in the ~/bin/GLS script
		see also ReadMe.txt for more information
		         by Mathias Zechmeister 2012-08-03 (v2.3.02)
	EOF
   exit
fi


#### execute the GLS ####
[ $replot ] || $GLSDir/GLS.e $@ || exit

#### refine the GLS solution ####
           refinefile="$GLSDir/fitsin.gnu"
eval $kep  refinefile="$GLSDir/fitkep.gnu"
eval $igls gnuplot - <<<"chi='$chi'; calmass='$calmass'"  $refinefile 2>/dev/null

#### graphical output ####
if [ ! "$silent" ]; then
   kep="kep='$kep'; Kep='$Kep'; igls='$igls'; chi='$chi'"

   ### output periodogram ###
   [ ! "$igls" ] && [ "$replot" ] || (echo $kep; cat $GLSDir/GLSplot.gnu $GLSDir/zoom.gnu; echo pause mouse key) | gnuplot &

   ### output RV curves ###
#   echo -e "$kep; load '$GLSDir/GLSRVandPhased.gnu'\n pause mouse key" | gnuplot &
   (echo $kep; cat $GLSDir/GLSRVandPhased.gnu $GLSDir/zoom.gnu; echo pause mouse key) | gnuplot &
   sed '/term post/s/^#//' - <<<"$kep" $GLSDir/GLSRVandPhased.gnu    | gnuplot  # ps and pdf plots
   epstopdf GLSRV.ps
   #   echo -e "$kep ; load '$GLSDir/GLSRV.gnu';\n  pause mouse key" | gnuplot &
fi

# END

# Changes in version v2.3.01 (2011-09-13):
# new: output of refine mode more similar to standard mode
# new: output of mass function
# new: option -M (only companion mass calculation)
# new: option -H (view the ReadMe)
# new: option -x (clear the directory from GLS products)
# fix: pseudo error bars are not shown in unweighted mode
# fix: refine option in unweighted mode
# change: physical constants updated
# improved: interactive x11 (gnuplot >v4.2; for gnuplot v4.2 there is now at least a unzoom key 'u')
# NOTE: this version does not work with the old GLS.log file!

# Changes in version v2.3.02 (2012-08-03):
# fix: exit immediately when file does not exits
# fix: no gnuplot zombies even when exit with 'q' (v4.2)
# new: zoom and pan with arrow keys
# fix: precision of pi