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SPTABLE Package for Tabular Spectra Now Available
- Wednesday, September 24 2014 @ 04:35 PM GMT
- Contributed by: fitz
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The SPTABLE external package is the first release of the IRAF spectral tasks intended to support data in various tabular formats. These formats currently include text files and FITS tables (direct support for the VOTable format is still pending) that are increasingly being used to store spectra as multi-column tables of wavelength/frequency and flux in a variety of formats.
The new package may be installed on a V2.16 system using the commands:
% cd $iraf/extern
% make self_update
% ./configure # even if done earlier
% make sptable
This release of the SPTABLE package should be considered an Alpha release as many possible table formats or use-cases have not yet thoroughly been tested. The detailed guide to the package below provides additional information on using the package and adding your data files to the list of recognized formats. Please report any problems or questions to the forums.
Guide to Spectral Tables
Spectral tables are file formats for one dimensional spectra represented as multi-column tables. These formats include text files and FITS binary tables. In the future this could also include XML tables such as VOTABLES. Typically such tables include a column for the dispersion coordinates such as wavelength or frequency. This guide describes how spectral tables may be used with the IRAF spectral packages ONEDSPEC and RV.
Spectral tables provide a very wide range of possible formats, particularly since there are minimal standards.
The Spectrum Table Database and Package Parameters
It would be highly inconvenient to require specifying all the details of a spectral table in each IRAF task. Instead these details are specified through package parameters; i.e. onedspec and rv. The principle is that one normally will work with one type of format with, possibly, many spectra and many tasks. Setting information for the package allows this to be done once in this case.
While there can be a wide variety of formats it is common that data providers will use one format for spectral data from an observatory, instrument, or pipeline. So a way to simplify describing spectral tables is with a database of formats. This is called a spectrum table database. Users can use the database provided with the IRAF package as well as easily customizing thier own version and make additions. Because there is no standard for identifying a particular format the spectrum table database applies a heuristic that generally works well. This heuristic consist of identifying a format by the set of column names, including their order, in the file. This set of column names act like a fingerprint that the database translates into the detailed description of the table.
Spectrum Table Package Parameters
The fundamental requirement for defining a spectrum table is the column identifications. Columns are defined by range lists of column numbers. A range list is one or more comma separated ranges. A range may be a single number, a pair of hypen separated numbers, and some less common variations as described in the help page "ranges". Column numbers are used instead of column names in order to allow for more complex situations as well as for simple text tables without column names.
The simplest spectrum table consists of the most basic type of column, the flux values, which might be instrumental numbers or some calibrated photon unit. There can be multiple flux columns, each of which is considered a different spectrum. In these cases the dispersion values are just the row numbers which are akin to pixels in an image. The flux columns are specified by the package parameter "tbspec".
The second basic column type is the dispersion coordinate. There can only be one dispersion column, though one could use the same file with different dispersion columns specified as separate spectrum table descriptions. The dispersion column is specified by the package parameter "tbdisp".
There may also be two types of optional associated quantities; an error spectrum and an associated spectrum. These are defined by the parameters "tberr" and "tbassoc". An associated spectrum might be an uncalibrated version of the spectrum, a different type of extraction, or even more creative types.
There are also two parameters specifying the flux units, "tbfunits", and dispersion units, "tbdunits". Ideally these should be specified by the units attribute of named columns. These parameters are mostly intended for the case of simple text tables that don't have named columns. The units understood are found in the help for "onedspec.package", "disptrans", or "splot". For instance, common dispersion units are "angstroms" and "nm".
A final convenience package parameter, "tbextn", specifies a default extension. Note the period is not included in this parameter. This allows using tasks with names that don't include the extension. For example, if all the spectra are ".fits" or ".txt" you can refer to spec.fits or spec.txt as just spec.
Spectrum Table Database Format
The spectrum table database is a text file with lines consisting of 1) a list of column names, 2) an identifier, 3) the dispersion column, 4) the flux columns, 5) any flux error columns, and 6) and associated data columns. The column fields are range lists and a value of NULL may be used if there are no columns of a particular type (though a minimum of a single flux column is required). Each field may not contain blanks. Additionally there may be blank and comment lines with '#' as the comment character. The identifier is not currently used by the tasks.
The column names are those understood by the "nttools" package. In particular, simple text tables without column definitions have column names "C1", "C2", etc. Note that the matching is case insensitive.
Below are some examples:
# A simple ASCII file with a single column. C1 SIMPLE_ASCII NULL 1 NULL NULL
# A simple ASCII file with a two columns: dispersion, spectrum. C1,C2 SIMPLE_ASCII 1 2 NULL NULL
# Some simple common defaults. WAVE,FLUX SIMPLE_TABLE 1 2 NULL NULL FLUX,WAVE1 SIMPLE_TABLE 2 1 NULL NULL FLUX,WAVE1,WAVE2 SIMPLE_TABLE 2 1 NULL NULL
# A STIS format. WAVE,FLUX,DATA_QUALITY,SIGMA STIS 1 2 NULL NULL
# An IUE format. WAVE,FLUX,SIGMA,QUALITY IUE 1 2 NULL NULL
# An STECF format. SPORDER,NELEM,WAVELENGTH,GROSS,BACKGROUND,NET,FLUX,ERROR, NET_ERROR,DQ,A2CENTER,EXTRSIZE,MAXSRCH,BK1SIZE,BK2SIZE, BK1OFFST,BK2OFFST,EXTRLOCY,OFFSET STECF 3 7 8 6
Note the last example is shown wrapped to illustrate the complexity of the columns but in the database file this would be a single line.
As mentioned previously, the association between a particular table file and its description is through the comma separated list of all the column names in order. So, for instance, all files having just the two columns WAVE and FLUX would match the SIMPLE_TABLE entry but would not match either WAVELENGTH/FLUX, WAVE/SPECTRUM, or WAVE/FLUX/ERR.
The spectrum table database is specified by the "sptabledb" package parameter. A default is supplied but the user may copy the file to the working or home directory and modify it, or simply create their own as described above.
IRAF Spectral Tasks
Spectrum tables are understood by the onedspec and rv package tasks. These tasks have a spectrum data model which includes the concepts of multiple spectra, called apertures, and associated elements, called bands. These may be thought of in the same way as the spectrum image formats of onedspec, equispec or multispec, and echelle. A description of these may be found under the topic "specwcs". In these formats multiple spectra are stored as rows in a 2D or 3D image and as bands in a 3D image. Note there can be a 3D image with a single row. The main effect of understanding this is that when a table has multiple flux, error, and associated columns defined by range lists they manifest in the task parameters as apertures and bands.
Physical File Formats
Tables are accessed using the IRAF tables library, which is inherited from the STSDAS tables system. This means that any format understood by the nttools package may a spectrum table. The formats currently supported by this library are text tables with and without column descriptors, FITS binary tables, and STSDAS tables. For FITS binary tables the FITS extension syntax also applies if there are multiple extensions. Also the row and column selector syntax may be used (see below).
The most important thing to note, as mentioned earlier, is that simple ASCII text tables consisting only of lines with the same number of whitespace separated columns may be used and, when necessary, the implied column names are C1, C2, etc, which are case insensitive. ASCII tables may have headers and column descriptors as supported by the tables library and which have lines beginning with "#k" for keywords and "#c" for columns definitions. If you want to add column names and units see the help for "tcreate".
Another special case is FITS binary tables with array cells. In this case each column would have a one-dimensional array and only one row may be present.
It should be obvious, but all the vectors must have the same length. In other words, for column tables there must be the same number of rows while for array cells each array must be the same length.
Table Selector Syntax
The table selector syntax, see the help topic "selectors", allows on-the-fly selection of rows and columns. For simply cutting out a dispersion region this could be done with a selector but some of the common spectral tasks have this facility; e.g. SPLOT.
However, one interesting case is for multi-order (e.g. echelle) spectra in a format where there is a just one dispersion, flux, and order column. So different orders have to be separated based on the order column. For instance, if the order column is called "order" then
ondspec> splot myechelle.fits[r:order=5]
plots order 5.
The ONEDSPEC tasks applicable to an echelle do not directly deal with this concatenated order format. Rather, an echelle format requires each order to be a separate column. The table selector syntax and SCOPY could be used to convert to the echelle format. The NTTOOLS package, described next, may provide an easier method to convert.
Any spectral table format may be manipulated with the NTTOOLS package, which is essentially a version of the STSDAS TABLES package added to the IRAF core system. There are a wide variety of spectral format manipulations that can be performed with these tools. These can include changing formats, expressions, and joining, projecting, and merging. In effect, these supplement the more spectroscopy oriented tasks in the ONEDSPEC and RV package in a nice symbiosis.
See Also specwcs, onedspec, rv, ranges, nttools, selectors