prepare.cube: Prepare a data cube for kinematic analysis
In oczoske/slacR: R-package to measure v and sigma from VIMOS IFU cubes

Description Usage Arguments Details Value Author(s) See Also

Read in an IFS data cube and prepare for kinematic analysis.

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prepare.cube(datacube, config = NULL, extension = 0, input.table = NULL,
             noisecube = NULL, mask = NULL, z = NULL, lambda.lim = NULL,
             verbose = FALSE, save.cube=FALSE, object = NULL, ...)

`datacube`	name of fits file containing the "data cube" in row-stacked form. Overrides name given in `config.file`.
`config`	name of list or file containing configuration data pertinent to the galaxy to be analysed
`extension`	name or number of the MEF extension of to be read from `datacube`. Defaults to 0 which is appropriate for the final reduced VIPGI cubes.
`input.table`	file or dataframe containing list of rows from "data cube" to be read in as well as translation to L/M coordinates
`noisecube`	name of fits file containing the "noise cube" in row-stacked form. Overrides name given in `config.file`.
`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.
`z`	redshift of the galaxy. Overrides keyword `z.lens` from `config`.
`lambda.lim`	Wavelength range to be cut from the data cube. Overrides keyword `lambda.spec.lim` from `config`.
`verbose`	be talkative
`save.cube`	logical or character string. Save the R representation of the data cube to a file using `save`. If `TRUE`, then the object and file names are generated automatically from the variable `object`, dropping the prefix "SDSS-". It is also possible to specify the file name as a character string. The file can later simply be `load`ed, which is significantly faster than using `prepare.cube` again.
`object`	optional name of the object. Overrides name given in `config.file`
`...`	Further parameters to be passed to `prepare.spectrum`, notably `normalize` and `order`.

Read in a subset of spectra from a "data cube" (actually a row-stacked representation of IFS data) as prepared by VIPGI. The list of rows to be read as well as the identification with two-dimensional position on the sky is given in an input table. A second data cube containing corresponding noise spectra can also be given.

a list of galaxy spectra. Each spectrum is in turn a list containing the following components:

`lambda`	wavelength grid
`value`	value of the spectrum
`noise`	value of the estimated noise
`contsub`	value of the spectrum after continuum subtraction
`name`	name of the fits file, including the filter to identify the row in the row-stacked representation
`object`	name of the object, including L and M
`L, M, F`	two-dimensional coordinates of the fibre in the data cube and the row-number in the row-stacked representation