alfa(1)                          alfa man page                         alfa(1)

       alfa - automated line fitting algorithm

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

       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

       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.

       -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.

              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

       -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


       No known bugs.

       Roger Wesson

1.0                               26 Aug 2016                          alfa(1)