AAOmega File Format (or, which spectrum is which object?)

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When analysing data from an AAOmega run, one needs to be able to map the combined spectra returned from the reduction task back to individual objects from the input catalogue. All the relevant information is contained within the combined output file(s). The page that follows attempts to describe how to recover this information. The process is simple, once one follows the logic. However, it can seem rather convoluted at first sight. Please send any questions, comments and suggestion you may have on how to make this information more digestible, to Rob Sharp (rgs@aao.gov.au).

The table below gives a summary of the 2dfdr output file content, for either the individual frame ....red.fits files or a combined_frames.fits file. The file is a standard Multi-Extension FITS file (FITS MEF).

>IRAF format

>Contents

>WxN image containing the spectrum  (W pixels long) for each fibre of the N spectra

>First Extension

>.fits[1]

>WxN image containing the Variance array for the data

>Second Extension

=.fits[2]

>binary table, with N rows, one for each fibre

Each Row contains information for each object such as RA, Dec, 2dF Pivot number and more

Details to be added

Seventh Extension

.fits[7]

Sky spectrum

Stored as a FITS binary table, with W rows.

Each row contains the one element of the 'typical' sky spectrum used in the data reduction ('typical' because for a combined frame it is not obvious how the final sky spectrum for each fibre should be represented here).

Note: The variance information is correctly propagated, the sky spectrum is not presented here for this purpose.

These extension can be accessed in a number of ways. A number of example are provided below, if you have an alternate suggestion or an example that should be added to this list (or if something does not seem to work), please contact Rob Sharp (rgs@aao.gov.au).

The primary image in the MEF fits file is a WxN image where N is the number of spectra which are represented.  This is  400 for AAOmega data, 392 science fibres and 8 guide fibres.  Unused science fibres and Sky spectra, are included in the output file along with the guide fibres spectra, even though the spectra contain no information, as this is seen to simplify book keeping, and is a small disc space overhead.  In the case where multiple sets of AAOmega datasets, which contained a subset of common objects,  have been combined, the format is a little more complex, and is explained separately below.

An important note on 2dF Fibre-Pivot number and 2dfdr Fibre number

There are two very important, and very different, number which one must understand in order to recover the information on which object each fibres was allocated to.  Fibre slit position AND 2dF Fibre-Pivot position.  For the most part there is a one-to-one correspondence between these number.  Usually the fibre at AAOmega slit position 1 (bottom of the CCD image) will map directly to 2dF Pivot position 1,  and 400 will map to 400 (note, 400 is a guide fibre and so maps to a blank space at the top of the CCD image).  However, during manufacture or repair of each of the AAOmega slit units, it is some times possible for the order of fibres in each of the AAOmega slits to fall out of synchronization with the 2dF Pivot numbering (2 slit block on each plate currently (April 2007) are like this).  It is not practical to mechanically alter either position so each of the two fibre numbers (slit position and Pivot position) are propagated in the binary table extension.

In the primary image (and also the variance array, stored in the first extension) the fibre at the bottom of the image, which is the fibre at slit position 1, corresponds to the first row in the binary table extension (the second fits extension).  The table contains a column entry, PIVOT, which gives the 2dF pivot position for this fibre.  This is the fibre number seen be the Configure software.  The very top fibre in a CCD image corresponds to the very last entry in the binary table (which will be an AAOmega guide fibre in the case of a single AAOmega data set).  There is ALWAYS a one-to-one correspondence between each spectrum position in the image and the binary table.  There is typically a one-to-one correspondence between slit position and 2dF pivot position but with a number of known mismatches and discontinuities which are tracked via the PIVOT column of the binary table.

Combining multiple AAOmega data sets which contain a common subset of targets

To be added

Binary Table columns

Column	Column name	Description
1	Name	Object name, as given in the .fld file
2	RA	Right Ascension from the .fld file
3	Dec	Declination from the .fld file
4	X	2dF field plate X co-ordinate (in microns)
5	y	2dF field plate Y co-ordinate (in microns)
6	Xerr	Reported error in X in final fibre placement
7	Yerr	Reported error in Y in final fibre placement
8	Theta	Angle of fibre on field plate
9	Type	Fibre type (P-program, S - Sky, U-unused etc...)
10	Pivot	2dF fibre pivot number
11	Magnitude	Object magnitude, as given in the .fld file
12	PID
13	Comment	Comment from the .fld file
14	Retractor	2dF retractor number
15	Switch Field
16	Switch Partner	For cross beam switched data, the paired fibre is indicated (fibre slit position number)
17	Wlen

 

Example for accessing the fits Binary table information

This list is not exhaustive, if your favorite option is missing, send an e-mail to Rob Sharp (rgs@aao.gov.au) and we'll add it to the list.

With Configure

One can save a list file (file menu -> ..list) which contains the allocated 2dF Fibre-Pivot number for each allocated fibre.  Note, this is the Pivot number for 2dF NOT the fibre number in the reduced 2D spectra file.

Within 2dfdr

To be added

2dfinfo

The 2dfinfo procedure comes packaged with 2dfdr.  It can be used to recover information on the fibre from either a .fits or .sdf file.  The syntax for the command is :

2dfinfo file.fits <option>

If the <option> is omitted then the list of options is given.  To recover the fibre table information one would use:

2dfinfo file.fits fibres

IRAF

The IRAF/STSDAS package TABLES has a number of routines designed, unsurprisingly, for manipulating tables.  A simple example might be:

IRAF> tdump combined_frame.fits[2] > output.txt

This would create a complete, if rather inelegant, listing of the fibre info binary table and pipe it to a ascii text file.   Formating the output can be achieved with:

IRAF> tprint combined_frame.fits[2] columns="NAME,RA,DEC" > output.txt

IDL

For users of IDL, the NASA IDL astronomy library has some excellent fits data access routines

Starting from a combined fits frame, combined_frame.fits, one might use the following code extracts to manipulate AAOmega data.

 Notes, there are much cleverer (and quicker) ways to perform the operations below with the NASA astrolib tasks, the code here is given as a set of simple examples.

file='combined_frame.fits'

;; Read in the spectral image, store the header information

spec=mrdfits(dir+file_comb,0,header0)

;; And the variance array

spec_var=mrdfits(dir+file_comb,1)

;; Make a wavelength vector, note the use of CRPIX1, which is often not expected by many users.

;; If missed, the wavelength solution will tend to be wrong by half a CCD width

crpix=fxpar(header0,'crpix1')

crval=fxpar(header0,'crval1')

cdelt=fxpar(header0,'cdelt1')

wave=((findgen(n_elements(spec[*,0]))-crpix)*cdelt)+crval

;; Read in the object identification information

fxbopen,unit,file,2

fxbreadm,unit $

  ,['name','ra','dec','x','y','xerr','yerr','theta','type','pivot','magnitude'] $

  ,id,ra,dec,x,y,xerr,yerr,theta,type,pivot,mag

fxbclose,unit

;; And read a copy of the sky spectrum subtracted from the data.

;; Note, for a combined frame, this is the sky spectrum from the first file in the list of combined frames.

;; It is a good representative sky spectrum, but should be used with caution for the combined spectral data.

fxbopen,unit,file,7

fxbreadm,unit,['SKY'],sky

fxbclose,unit

Rob Sharp (rgs@aao.gov.au)