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AAOmega Software

News

Configure7.9 "import allocations" option re-enabled - 25 October 2007
2dfdr version 3.76 now available - 6 July 2007
Configure7.4 fixes a minor bug in the "Generate Sky Grid" routine - 24 August 2006
Configure7.3 introduces the Simulated Annealing configure algoritham - 8 August 2006

Fibre-to-slit mapping fix for early AAOmega data  - 7 July 2006
Pre August 2006 AAOmega data has errors in the fibre-to-slit mapping.  Find out more on the "Whats new" page, or below.

See the 2dfdr CookBook for the latest 2dfdr News.

AAOmega Software

This page lists the dedicated software the AAO has written for astronomers to facilitate preparation for observations and data reduction with the 2dF/AAOmega system.

The items are:

  1. Field configuration - configure
    - Version 7 required for AAOmega operations.
    - Latest AAOmega astrometric and fibre files.
  2. Data Reduction - 2dfdr - upgraded version for use with AAOmega data   
  3. FITS conversion - ndf2fits/fits2ndf
  4. Fixing 2dF Fibre Headers - tdffix
  5. Editing individual fibre details - edit_headers
  6. Fixing fibre-to-slit position mapping errors in AAOmega - fdtswap

Manuals can be found on the documentation page.

1) Field configuration - Configure

The configure software allows astronomers to prepare input files for the fibre positioner. It reads an ASCII formatted catalog and allows astronomers to automatically or manually allocate fibres to targets using a graphical user interface. Binary files can be saved which can then be directly loaded into the 2dF system.

The current version of configure is 7.9 (released October 25, 2007); it is a version for AAOmega, 2dF, 6dF, and Ozpoz, and may be downloaded from the ftp site.  Configure 7.3 was a major new release for the AAOmega system, subsequent upgrades improve utility. It includes the resent upgrade of the Configure code to implement Simulated Annealing. See ReleaseNote_configure7.#.txt on the ftp site.  For most users, even those familiar with Configure, it will also be ESSENTIAL to read the Guide to using SAconfigure.  There are currently versions available for Linux (RH3E) and Mac-OS.  Note, the Mac version is code named Darwin by the Operating system.  This should run on most modern flavors of the hardware.  The older Configure7, is still available for Solaris, Linux and Darwin.

For users who do not wish to use Simulated Annealing, the a version of configure which uses the original "Oxford" algorithm is also package with Configure7.3 and later packages.

Installing Configure7.#

All you have to do is unzip the appropriate gzipped (.gz) file, and then untar the .tar file. e.g. for the Linux version:

tar -zxvf configure-7.#.Linux.tar.gz

Then you just have to run the Configure executable.

Running Configure 

To run Configure, First set the environment variable:

tcsh
setenv CONFIG_FILES /path/configure-7.#.Linux/data_files/

Download the relevant astrometry files (see below) to this CONFIG_FILES directory.  Then

configure-7.#/Linux/configure          --- For the (default) Simulated Annealing code
Or
configure-7.#/Linux/configureTrad   --- For the original "Oxford" algorithm

Please read the "How to prepare for an AAOmega observing run" guide.  For the new SAconfigure routine, please also review the Guide to using SAconfigure.

To run configure, you will also need files giving the 2dF astrometry model: tdFlinear0.sds, tdFlinear1.sds are the linear astrometric coefficients for plate 0 and plate 1, respectively; tdFdistortion0.sds, tdFdistortion1.sds are the distortion maps for plate 0 and plate 1, respectively. Plus you will need the file giving the current fibre information (availability and park positions for all fibres [1-400]): tdFconstants400.sds. In addition, the fibre information file (tdFconstants400.sds) may change throughout the run, as fibres become broken (and sometimes fixed!). Thus, before configuring, you should get the most recent version of these files: they can be fetched from anonymous ftp at the AAO. In that directory, you will see the tdFconstants400.sds file, which is updated daily at 7:30am local time. Please configure your fields with the latest astrometric and fibre information.

NOTE: Even if you do use the most current fibre and astrometric information, you (or your 2dF support astronomer) will still have to tweak your fields at the telescope, since things can and do change on very short notice. This is especially true if you are not able to use the astrometric information for the 2dF run when your observations are being done (i.e. in the normal case when you are configuring your fields before your 2dF run has started).

There is now a Configure manual available from the documentation page.  The operation of configure is also documented in Chapter 6 of the 2dF manual. Additionally see Chapters 4 and 5 for instructions on 2dF astrometry and how to choose fiducial stars.

Bug reports about configure should be addressed to Chris Ramage and Rob Sharp. Older versions of configure can be found here.

2) Data Reduction-2dfdr

2dfdr is an automatic data reduction pipeline dedicated to reducing multi-fibre spectroscopy data (with current implementations for AAOmega with either the 2dF or IFU top ends, 2dF, 6dF, FMOS and the older Spiral).  A graphical user interface is provided to control data reduction and allow inspection of the reduced spectra. It is being continually developed at the AAO in response to user feedback and the changing face of AAOmega projects. You can reduce most of your data by simply pressing SETUP+START in the Graphical User Interface.

The software can be downloaded from the ftp site ftp://ftp.aao.gov.au/pub/2df/.  The software is distributed as an executable binary and is currently only supported for Redhat Linux, although it has been found to run correctly under many other flavours of PC Linux.

See the 2dfdr CookBook to get started. Users familiar with 2dF data reduction many still benefit from a quick look at this, which highlights many operational changes.

The complete 2dfdr Users Manual is available in [Word] or [pdf] format. THE MANUAL IS LARGELY OUT OF DATE due to ongoing development work since the upgrade from 2dF to AAOmega. It is probably best to see the above CookBook first as it is the first place to be updated when changes are made.

The operation of 2dfdr is also documented in Chapter 8 of the 2dF manual.

2dfdr also comes with utility programs to convert NDF format to and from FITS files preserving fibre information (ndf2fits/fits2ndf) and to list fibre information to an ASCII file (2dfinfo).

Please send bug reports, problems or suggestions to Rob Sharp.

3) FITS conversion - ndf2fits/fits2ndf

AAOmega data files come embedded with a complete description of the configuration and all the objects observed as well as the raw CCD data.  The fibres info is just too big to go in to a standard FITS header - and is therefore written into a FITS binary table extension.

To this end we have worked  with Malcolm Currie at  STARLINK  to enhance the FITS converters in the CONVERT package to support the 2dF FIBRES extension.  These are included with the 2dfdr package. and their use is described in the AAOmega manual.  They also handle correctly other AAOmega extensions, for example the VARIANCE array (giving the errors as computed from Poission statistics + readout noise) which is present in the reduced data files from 2dfdr.

A recent release of the STARLINK software appears to have introduced a bug which prevents the correct operation of the ndf2fits/fits2ndf programs. With the demise of the STARLINK project, the AAO is investigating alternatives for these and other software issues. Recent releases of the 2dfdr package have include these unfortunate versions of ndf2fits and fits2ndf. Correctly operating version can be found at the ftp site (ftp://ftp.aao.gov.au/pub/2df/ndf2fits/). Please read the README file and download convert_mon_ix86 and the two .ifc files.

As an example, the command structure below will convert a STARLINK .sdf file to a Multi-extension FITS .fits file, propagating the variance and sky extensions. Note the missing .sdf extension and the presence of the .fits extension.

     ./ndf2fits proexts input_file output_file.fits

Note, the input should not have the .sdf extension, the output should have the .fits extension.

4) 2dfinfo

The FITS header information in 2dfdr files can be accessed using the 2dfinfo command. It can be used in a number of ways as follows:

    2dfinfo run0001.sdf fits

lists the FITS header of run0001.sdf.

    2dfinfo run0001 fibres

lists the fibre configuration information for the same file (note that the .sdf extension is optional).

    2dfinfo run0001red history

lists the reduction history of the reduced file run0001red.sdf.

It is also possible to request information for an individual fibre or an individual FITS keyword as follows:

    2dfinfo run0001 fibre 37

lists the information on fibre number 37.

    2dfinfo run0001 fits—item GRATID

lists the value of the fits header item GRATID (grating ID).

5) Fixing 2dF Fibre Headers - tdffix

A utility called `tdffix' has been developed at AAO to add or correct headers in data with an error (potentially a problem after major system work). It takes as input the .sds file produced by the configure software and a text file listing the ordering of fibres along the slit on both plates (normally called `aspect_fibres.txt') and writes the information into a data structure in the SDF data file. This can then be used in 2dfdr for fully automatic reduction and is preserved in the FITS archive. Additionally tdffix can be used to fix other header details such as the plate and spectrograph ID.  This is documented in a UNIX man page included with the software.

A Solaris binary of tdffix is available by anonymous ftp from ftp://ftp.aao.gov.au/pub/2df/tdffix-1.4.tar.Z.  Unfortunately the source code links against elements of the AAO drama software environment and so source code cannot usefully be distributed at this time.

6) Editing individual fibre details - edit_headers

From time to time it may be necessary to alter the object details within 2dF frames. For example if a missing fibre has not been correctly flagged in the 2dF setup file the extraction and sky subtractions routines may fall over when no object flux is identified. The fibre should then be set to N or U to prevent the software trying to use it.

Scott Croom has written a simple FORTRAN routine to allow editing of objects information in .sdf files.

The FORTRAN code edit_headers.f requires starlink libraries. A Solaris binary, edit_headers, is also available.

Running the code provides usage information.

NOTE : the procedure runs on .sdf files not .fits files.

> edit_fibres
edit_fibres version 1.1

usage:
edit_fibres NDF_name
or
edit_fibres NDF_name fibre_number new_name new_type

7)Fixing fibre-to-slit position mapping errors in AAOmega

A number of errors where found in the slit position-to-fibre mapping during the early stages of AAOmega commissioning.  All data taken with AAOmega before August 2006 are affected.  In total 4 banks of fibres (2 retractors, of 10 fibres each, and on each field plate) where out of sequence.   A Tcl script has been written to alter the fibre table in raw and/or reduced AAOmega data to correct the problem.

The script (fdtswap.tcl) and the new fibre files (spec_fibres.txt, spec_fibres.txt_old060630) can be downloaded from the ftp site:

ftp://ftp.aao.gov.au/pub/2df/fdtswap/

Download the tar.gz archive (which contains the fitsTcl library), and the two spec_fibres files and follow the instructions in the README file.

Rob Sharp (rgs@aao.gov.au)