NAME

       alfa - automated line fitting algorithm

SYNOPSIS

       alfa [OPTION] [VALUE]... [FILE]

DESCRIPTION

       alfa rapidly fits emission line spectra, using a genetic algorithm to optimise fitting parameters.  It is
       intended  to  be  entirely automated, but while the default values should work well in many situations, a
       good fit to your observed spectrum may require some adjustments to the input parameters.  It is optimised
       for optical spectra, but can be applied to any wavelength range if a suitable line catalogue is provided.

       alfa reads one dimensional spectra in either plain text or FITS format.  Plain text input should  consist
       of  two columns, giving wavelength and flux.  It can also read data cubes and row-stacked spectra in FITS
       format.  Results are written out in plain text, to  files  containing  the  fit  (total  fit,  continuum-
       subtracted original, continuum, sky lines and residuals), and the line flux measurements.

OPTIONS

       -b, --bad-data [REAL]
              If  all values in a spectrum are below the value specified, alfa will not fit it.  Most useful for
              avoiding wasting time on low signal regions of data cubes.

       --citation
              Prints out the bibliographic details of the paper to cite if you use alfa in your research.

       -g, --generations [INTEGER]
              The number of generations used in the genetic algorithm. Default: 500

       -n, --normalise [VALUE]
              Normalise to Hb=100 assuming that F(Hb)=VALUE.  If VALUE is zero, no normalisation is applied.  If
              this option is not specified, fluxes are normalised using the  measured  value  of  Hb  if  it  is
              detected, and not normalised otherwise.

       -o, --output-dir [DIRECTORY]
              The directory in which to put the output files. Default: current working directory.

       -pr, --pressure [REAL]
              The  fraction of the population retained from each generation. The product of the pressure and the
              population size should be an integer.  Default: 0.3

       -ps, --populationsize [INTEGER]
              The size of the population used in the genetic algorithm. Default: 30

       -rg, --resolution-guess [VALUE]
              Initial guess for the resolution [lambda/delta lambda]. Default: estimated using the  sampling  of
              the input spectrum, assuming that it is Nyquist sampled.

       -rtol1, --resolution-tolerance-1 [VALUE]
              Variation allowed in resolution in first pass. Default: equal to 0.9 x resolution guess.

       -rtol2, --resolution-tolerance-2 [VALUE]
              Variation allowed in resolution in second pass. Default: 500.

       -skycat, -strongcat, -deepcat [FILENAME]
              The  files  containing the line catalogues to be used for the removal of sky lines, the estimation
              of velocity and resolution, and the full line fitting.   The  default  catalogues  are  stored  in
              /usr/share/alfa .  If you wish to create your own catalogue, the required format is that each line
              should  be  85  characters  wide,  with  a  wavelength  in  the  first column, and the rest of the
              characters are not used by the code but are transferred to the output files.   They  can  thus  be
              used, as in the supplied catalogues, for line transition data.

       -ss, --subtract-sky
              Fit and subtract night sky emission lines before fitting nebular emission lines.

       -ul, --upper-limits
              Write out upper limits for all lines searched for and not detected.

       -vg, --velocity-guess [VALUE]
              Initial guess for the velocity of the object [km/s]. Default: 0.

       -vtol1, --velocity-tolerance-1 [VALUE]
              Variation allowed in velocity in first pass of the fitting. Default: 900km/s

       -vtol2, --velocity-tolerance-2 [VALUE]
              Variation allowed in velocity in second pass of the fitting. Default: 60km/s

SEE ALSO

       neat

BUGS

       No known bugs.

AUTHOR

       Roger Wesson

1.0                                                26 Aug 2016                                           alfa(1)