Chapter 4
Applications Packages

When you run ICL and type:

you will be shown two lists of packages. The first contains Standard packages which are available at all Starlink sites. The other contains Options which are made available at a site only on request.

This Chapter gives a brief overview of each package, while Chapter 20 describes the specific commands available within each package. Further information can be obtained from their associated Starlink User Note (SUN) which is referenced at the top of each section. Starlink software as a whole is described in SUN/1.

An important part of the rationalization of Starlink software which the coming of ADAM made possible concerns data structures. The Hierarchical Data System (HDS) (see Chapter 10) is very flexible, and is capable of creating an infinite variety of data structures. Without recommending some standard structure there would be a danger of programmers writing applications which could not read each other’s data. If the standard is also implemented in a small number of routines, the restrictions imposed by the standard also make programming easier. The main unifying theme of Starlink applications is the standard data format defined by Starlink; this is the Extensible $N$-dimensional Data Format — NDF — described in Section 10.2. This is centred on an $n$-dimensional data array that can store most astronomical data such as spectra, images and spectral-line data cubes. The NDF may also contain such information as title, axis labels and units, and error and quality arrays. There is also a place to store ancillary data associated with the data array. These could be information about the original observing set-up, such as airmass during the observation or temperature of the detector; there may be calibration data or results produced during processing, for example spectral line fits. Groups of related parameters not defined by the NDF format itself are held in extensions.

A key component of Starlink software is KAPPA (Kernel Application Package). This does not process non-standard extensions, but neither does it lose them — it copies them to any NDFs which it creates. Other application packages may be able to process some, but not all, extensions. It is hoped that such packages will use KAPPA applications as templates, in procedures, or directly as appropriate.

Each section below contains a sketch of how to use the application being described. In these:

means “issue the command from DCL”, while:

means issue it from ICL. Remember that before using any of these packages, the commands:

should have been executed. Likewise, to run ICL you should type:

to get the ICL prompt.

The packages described in this chapter are listed below ordered by function. This should help you find a package which is appropriate for a particular purpose. The packages are then described in alphabetical order on separate pages.

4.1 ASTERIX — X-ray data analysis

[SUN/98]

This is a collection of programs to analyse astronomical data in the X-ray waveband. Many of the programs are general purpose and are capable of analysing any data in the correct format. It is instrument independent and currently has interfaces to the Exosat and Rosat instruments.

ASTERIX data are stored in HDS files and are therefore compatible with all ADAM packages. There are basically two different types: binned and event datasets. Binned data (e.g. time series, spectra, images) are stored in files whose structure is based on the Starlink standard NDF format (SGP/38). Data errors (stored in the form of variances) and quality are catered for. Event data sets store information about a set of photon ‘events’. Each event will have a set of properties, e.g. X position, Y position, time, raw pulse height.

The input data are first processed by an instrument interface. Event data are then processed and binned, and then the binned data are processed. Finally, graphical output is generated.

The commands may be classified as follows:

To run ASTERIX:

Demonstration:

4.2 CCDPACK — CCD data reduction

[SUN/139]

A package to perform the initial processing of CCD data. Its main advantage over previous methods is its enhanced functionality. It processes large amounts of data easily and efficiently, with a minimum of effort on the user’s part.

It includes routines for performing:

The following features are of particular note:

To run CCDPACK:

4.3 CONVERT — Data format conversion

[SUN/55]

This package converts data between the Starlink standard $n$-dimensional data format (NDF) and other formats. Currently, it can handle three data formats:

To run CONVERT:

Demonstration:

4.4 DAOPHOT — Stellar photometry

[SUN/42]

A stellar photometry package written by Peter Stetson at the Dominion Astrophysical Observatory, Victoria, B.C., Canada and adapted for use under ADAM. It performs the following tasks:

Profile fitting in crowded regions is performed iteratively, which improves the accuracy of the photometry. It does not directly use an image display (which aids portability), although three additional routines allow results to be displayed on an image device. It uses image data in NDF format.

To run DAOPHOT:

N.B. If you enter ‘DAOPHOT’ just to see what happens, you will be disappointed to receive the message ‘Value unacceptable –- please re-enter’. You will need to read the documentation and user manual before you can make any progress with this program.

4.5 FIGARO — General spectral reduction

[SUN/86]

This is a general data reduction system written by Keith Shortridge at Caltech and the AAO. Most people find it of greatest use in the reduction of spectroscopic data, though it also has powerful image and data cube manipulation facilities. Starlink recommends FIGARO as the most complete spectroscopic data reduction system in the Collection. Examples of its facilities are:

At present, a number of related packages are bundled with FIGARO. In future, these may be released as separate items. They include:

TWODSPEC

[SUN/16]

This reduces and analyses long-slit and optical-fibre array spectra. A number of its functions are useful outside the area of spectroscopy. The main application areas are:

• Line profile analysis; LONGSLIT analyses calibrated long-slit spectra. For example, it can fit Gaussians, either manually or automatically, in batch. It can handle data with two spatial dimensions, such as TAURUS data. FIBDISP provides further options useful for such data, although it is primarily designed for fibre array data. An extensive range of options is available, especially for output.
• Two-dimensional arc calibration.
• Geometrical distortion correction; S-distortion and Line curvature.
• Conversion between FIGARO and IRAF data formats.
• Display programs.
• Removing continua.

To run FIGARO:

4.6 IRCAM — Infrared camera data reduction

[SUN/41]

This package reduces, displays, and analyses 2-dimensional images from the UKIRT infrared camera (IRCAM). The image data reduction facilities available are:

The graphics and image display facilities available are:

To run IRCAM:

4.7 KAPPA — Kernel applications

[SUN/95]

The Kernel Application Package runs under ADAM, using the NDF data format, and provides general-purpose applications. It is the backbone of the software reorganization around the ADAM environment, and its applications integrate with other packages such as PHOTOM, PISA, and FIGARO. It is usable as a single large program from the ADAM command language ICL, or as individual applications from DCL.

It handles bad pixels, and processes quality and variance information within NDF data files. Although oriented towards image processing, many applications will work on NDFs of arbitrary dimension. Its graphics are device independent. Currently, KAPPA has about 140 commands and provides the following facilities for data processing:

There are also many applications for data visualization:

To run KAPPA:

4.8 PHOTOM — Aperture photometry

[SUN/45]

This performs aperture photometry. It has two basic modes of operation:

The aperture is circular or elliptical, and the size and shape can be varied interactively on the display, or by entering values from the keyboard or parameter system. The background sky level can be sampled interactively by manually positioning the aperture, or automatically from an annulus surrounding the object.

To run PHOTOM:

4.9 PISA — Object finding and analysis

[SUN/109]

The Position, Intensity and Shape Analysis package, PISA, locates and parameterizes objects in an image frame. The core of the package is a routine which performs image analysis on a 2-dimensional data frame. It searches for objects having a minimum number of connected pixels above a given threshold, and extracts the image parameters (position, intensity, shape) for each object. The parameters can be determined using thresholding techniques, or an analytical stellar profile can be used to fit the objects. In crowded regions, deblending of overlapping sources can be performed.

The package derives from the APM IMAGES routine originally written by Mike Irwin at the University of Cambridge to analyse output from the Automatic Photographic Measuring system.

To run PISA:

Demonstration:

4.10 SCAR — Star catalogue database system

[SUN/70, 106]

The Starlink Catalogue Access and Reporting system is a relational database management system. It was designed principally for extracting information from astronomical catalogues, but it can be used to process any data stored in relational form. A large number of catalogues are available, including the IRAS catalogues. For general database requirements, REXEC may be preferable. SCAR can perform the following functions:

A distinctive feature of SCAR is the use of index files which you can create and which contain pointers to rows in one or more catalogues. This is a compact and flexible method of accessing catalogues; for example, a very large catalogue may be physically ordered by declination, but you can create an index giving access to it ordered by flux.

To run SCAR:

Demonstration:

4.11 SPECDRE — Spectroscopy data reduction

[SUN/140]

A package for spectroscopy data reduction and analysis. It fills the gap between FIGARO and KAPPA — on the one hand, all its routines conform with Starlink’s concept of bad values and variances, on the other hand, they offer spectroscopy applications hitherto available only in FIGARO. In general, it can work on data sets with seven or less axes. Often an application will take just a one-dimensional subset as a spectrum. In most cases the spectroscopy axis can be any axis, but for some applications must be the first axis.

To run SPECDRE:

4.12 SST — Simple software tools

[SUN/110]

The Simple Software Tools package helps produce software and documentation, with particular emphasis on ADAM programming using Fortran 77. It performs fairly simple manipulations of software, and also tackles some of the commonly encountered problems which are not catered for in the more sophisticated commercial software tools (such as FORCHECK and VAXset) available on Starlink.

The main purpose of the first version is to extract information from subroutine ‘prologues’, and to format it to produce various forms of user documentation. A simple source-code and comment statistics tool is also included.

There are five applications:

To run SST:

Demonstration:

4.13 TSP — Time-series and polarimetry analysis

[SUN/66]

This is a data reduction package for time-series and polarimetric data. These facilities are missing from most existing data reduction packages which are usually oriented towards either spectroscopy or image processing or both. Currently TSP can process the following data:

To run TSP:

Demonstration: