Starlink Project
STARLINK Cookbook 16.2

A. Allan & Malcolm J. Currie

2008 July 4

The IFU Data-Product Cookbook

Version 1.3



This cookbook is a collection of material covering IFU data reduction and analysis. Along with this material are pointers to more advanced documents dealing with the various packages, and hints and tips about how to deal with commonly occurring problems.


1 Introduction
2 The Datacube Package
3 Data reduction
 3.1 Reduction paradigms
 3.2 INTEGRAL data
 3.3 OASIS data
 3.4 SAURON data
 3.5 GMOS data
 3.6 CIRPASS data
 3.7 SMIRFS data
 3.8 TEIFU data
 3.9 UIST data
 3.10 VIMOS data
 3.11 Other IFU instruments
4 File formats
 4.1 The GMOS working format
 4.2 The new IRAF spectral format
 4.3 The UK data-cube format
 4.4 MEF to data-cube format
 4.5 Format conversion
  4.5.1 GMOS MEF to NDF
  4.5.2 TEIFU FITS to NDF
 4.6 GMOS vs. TEIFU format
 4.7 FITS header manipulation
  4.7.1 Native FITS files
  4.7.2 The NDF FITS extension
 4.8 FITS I/O with IDL
 4.9 NDF I/O with IDL
5 Data-cube manipulation
 5.1 Existing software
  5.1.1 Arithmetic Operations
  5.1.2 Cube manipulation
  5.1.3 Two-dimensional manipulation
  5.1.4 Pixel Operations
  5.1.5 Other tools and file manipulation
  5.1.6 Visualisation
  5.1.7 Mosaics
  5.1.8 Spectral fitting
 5.2 Locating Features
 5.3 Dealing with Graphical Devices
  5.3.1 Devices and Globals
  5.3.2 The Graphics Database
  5.3.3 Pseudo Colour and LUTs
 5.4 Dealing with WCS Information
 5.5 GAIA data visualisation
  5.5.1 Cube toolbox
  5.5.2 Spectral plot
  5.5.3 Volume Visualisation
 5.6 IDL and data visualisation
  5.6.1 Display problems
  5.6.2 Slicer3
  5.6.3 The IDL Astronomy Library
  5.6.4 ATV Image Viewer
 5.7 IRAF and the Starlink software
 5.8 Visualisation using the DATACUBE scripts
  5.8.1 How do I create a white-light image?
  5.8.2 How do I create a passband image?
  5.8.3 How do I step through passband images?
  5.8.4 How do I extract individual spectra?
  5.8.5 How do I compare spectra?
  5.8.6 How do I plot stacked spectra?
  5.8.7 How do I create a grid of spectra?
  5.8.8 How do I create a velocity map?
  5.8.9 How do I create line-strength map?
  5.8.10 But they don’t handle blended lines!
  5.8.11 How do I create line-ratio map?
 5.9 Mosaicking
6 Writing csh scripts
 6.1 How do I get pixel positions using the cursor?
 6.2 How do I get real world co-ordinate positions using the cursor?
 6.3 How do I overplot contours from one image on to another?
 6.4 How do I use scientific notation in bc?
 6.5 My file has been converted to NDF. How do I access FITS header keywords?
 6.6 How do I create an NDF file from an ASCII file?
 6.7 How to make a simple GUI
7 Instrument information sources
8 Other information sources

Revision history

1st September 2000; Version 0.1 Original version (AA)
24th November 2000; Version 0.2 Added VIMOS information (AA)
12th December 2000; Version 0.3 Added IDL procedures (AA)
30th December 2000; Version 0.4 Cleanup for release (AA)
2nd January 2001; Version 1.0 Release version (AA)
30th September 2002; Version 1.0-1 Minor changes (AA)
2005 October; Version 1.1 Updated for DATACUBE version 1.1 and major tidy. (MJC)
2006 March 17; Version 1.1-1 Add illustrated velmoment and gridspec sections; mention CLINPLOT. (MJC)
2006 June 16; Version 1.1.-2 Introduce GAIA ‘3D’ in a new illustrated subsection. List CHANMAP, and smoothing of planes by BLOCK and GAUSMOOTH. (MJC)
2008 July 4; Version 1.2 Add section on locating features with CUPID and STILTS. Update GAIA section and graphics; add new illustrated subsection on three-dimensional rendering. Mention PLUCK and PERMAXES. (MJC)


Economou F., Bridger A., Wright G.S., Jenness T., Currie M.J., Adamson A., Astronomical Data Analysis Software and Systems VIII, Mehringer D.M., Plante R.L., Roberts D.A. (eds.), 1999, p.p. 11, ASP Conf. Ser., Vol. 172


In compiling this document I (AA) have again leant heavily on already available material, and the help of many people in the IFS community. However, special thanks should go to Rachel Johnston, Jeremy Allington-Smith, James Turner and Frank Valdes for their co-operation and contributions.

Up-to-date information about UIST data reduction was provided by Stephen Todd who wrote the original ORAC-DR IFU recipes for the instrument.