prepare.spectrum: Read and prepare a one-dimensional spectrum
In oczoske/slacR: R-package to measure v and sigma from VIMOS IFU cubes

Description Usage Arguments Details Value Author(s) See Also

Read a one-dimensional spectrum from a fits file or ASCII data table and prepare for the kinematic analysis

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prepare.spectrum(file, config = NULL, noise = NULL, mask = NULL,
  order = 16,z = NULL, lambda.lim = NULL, normalize = FALSE,
  contsub = FALSE, contdiv = FALSE, verbose = TRUE, object = "")

`file`	name of the fits file containing the spectrum. Filters are allowed, as understood by cfitsio.
`config`	name of a configuration file. Specifying this is enough to read in a spectrum. Parameters than can be overridden explicitely are `file` (`configuration$spectrum`), `noise` (`configuration$noise.1d`), `z` (`configuration$z.lens`), `lambda.lim` (`configuration$lambda.spec.lim`), `object` (`configuration$object`).
`noise`	name of a fits file containing the noise spectrum, or a noise `spectrum`, or a numeric vector containing the noise spectrum or a number giving the noise level
`mask`	a mask in any format that can be read and converted by `convert.mask`. Most of the time, this will be a file or data.frame with components `x1` and `x2` giving the left and right limits of the wavelength regions to be masked.
`order`	order of a polynomial fit to the continuum
`z`	redshift of the galaxy. Defaults to 0.
`lambda.lim`	wavelength range to be cut from the data cube. If `NULL`, use the entire range.
`normalize`	logical. If TRUE, the spectrum is normalized to mean of unity over the range defined by `lambda.lim`
`contsub`	logical. if TRUE a polynomial fit to the continuum will be subtracted from the spectrum
`contdiv`	logical. If TRUE, the spectrum will be divided by a polynomial fit to the continuum
`verbose`	logical. If TRUE, give some progress report.
`object`	an optional name of the object

A one-dimensional spectrum is read from a file and returned in the form of a list. Optionally, a noise vector is added. The spectrum is deredshifted and optionally a polynomial fit to the continuum is subtracted from the spectrum. The input file can be either a fits file or an ASCII file in the format of a data table with at least columns lambda and value.

a list containing the following elements:

`lambda`	the wavelength values of the deredshifted spectrum
`value`	the original values of the spectrum
`noise`	the estimated noise for each wavelength pixel
`mask`	a logical vector with `TRUE` for good and `FALSE` for bad pixels
`contsub`	(optional) the values of the spectrum after subtraction of a continuum fit
`contdiv`	(optional) the values of the spectrum after division by a continuum fit
`name`	the name of the input fits file
`object`	the name of the object