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 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.
- -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
- -o, --output-dir [DIRECTORY]
- The directory in which to put the output files. Default: current working
- -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
- -rtol1, --resolution-tolerance-1 [VALUE]
- Variation allowed in resolution in first pass. Default: equal to 0.9 x
- -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
- -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:
- -vtol2, --velocity-tolerance-2 [VALUE]
- Variation allowed in velocity in second pass of the fitting. Default: