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The Fibre Spectroscopy Cookbook

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1. 7 Instruments and Software Available The principal common user fibre fed spectrographs currently available to UK astronomers are e 2dF e WYFFOS AUTOFIB2 e FLAIR The characteristics of these instruments are summarised in Table Ijand they are described briefly below All three instruments have been described numerous times in the various conference proceedings listed in Section 2 In the following descriptions only the most recent of the references is given The three instruments each have their own data reduction software which is also described In the cases of WYFFOS AUTOFIB2 and FLAIR this software is based on the IRAF package dofibers Additional sections describe dofibers and the underlying IRAF environment gt There is always the chance of course that by inadvertence a random field object could be brought into the field of view of an individual fibre 19 SC 14 2 Instrument Telescope Field of view Maximum Multiplex minutes of arc resolving power advantage 2dF AAT 3 9m 120 4000 400 WYFFOS AUTOFIB2 WHT 4 2m 60 8000 150 FLAIR UKST 1 2m 390 2000 90 Table 1 Common user fibre fed spectrographs 71 2dF The 2dF Two degree Field instrument on the Anglo Australian 3 9m Telescope AAT has a two degree field of view as its name implies and 400 fibres The basic components of the system are the correction lens optics which give good images over a wide field a robot to position the fibres somewhat similar
2. An Introduction to IRAF 34 is a convenient starting point Reducing FLAIR observations with IRAF is similar to but more complicated than reducing Hydra observations which was described in the previous example Section 11 above Consequently it is sensible to work through the Hydra example before trying the present one The data used in this example are observations of some early type stars in the direction of the Galactic centre The stars are in the magnitude range 12 to 16 and the spectra cover the wavelength range 4000 4600A These data are unusual in that most FLAIR observations are of external galaxies Nonetheless they can be used to illustrate the reduction procedure which is as follows 1 Make your IRAF directory your current directory All the files used in the example are available in directory star examples sc14 flair Copy these files to your IRAF directory cp star examples sc14 flair The various files will be introduced as they are required However they are all listed in file OFLAIR LIS 2 Start IRAF See SG 12 for further details You should use the customisation file loginuser cl provided with SG 12 to ensure that IRAF is configured correctly to handle the large headers in FLAIR files if you do not use this customisation file you may or may not encounter problems depending on how IRAF is configured at your site 3 Load allthe various IRAF packages and sub packages which are required Type noao imred cc
3. a discussion of the IRAF data reduction environment These documents are mostly concerned with removing instrumental effects from direct images but are largely applicable to two dimensional spectra However the later stages of reducing direct images and spectra either fibre or slit differ In particular removing pixel sensitivity variations flat fielding is done differently Also there are some procedures such as identifying the spectra in the two dimensional image and extracting them which are peculiar to spectroscopy Some documents specifically about the reduction and calibration of spectroscopic data are e SC 7 Simple Spectroscopy Reductions 13 e A User s Guide to Reducing Slit Spectra with IRAFB3 e Guide to the Slit Spectra Reduction Task DOSLIT 45I These documents describe slit spectroscopy but are mostly also applicable to fibre spectroscopy Though they describe particular software packages they are still worth reading even if you do not intend to use the package described the techniques used are largely independent of the packages and thus the descriptions are still useful SC 7 is a particularly readable and informative document Note that it is usually not feasible to flux calibrate fibre spectra The features peculiar at least in part to fibre spectroscopy are Astronomers usually refer to spurious signals in CCD frames caused by ionising radiation as cosmic ray hits or cosmic ray events However these
4. a weaker signal than target object fibres 35 15 16 SC 14 2 e For the example data it so happens that dofibers makes several misidentifications in the first few fibres In this case it is less confusing to start with the highest numbered fibres and work down rather than vice versa You interact with the plot by positioning the cursor and issuing one or two character commands from the keyboard Help information about the commands available can be obtained by typing lt shift gt followed by hitting the space bar a few times to work through it and finally g to return to the interactive session However a few of the most useful commands are summarised below manipulating the plot w j resize the plot setting the left edge at the current cursor position w k resize the plot setting the right at the current cursor position t resize the plot setting the top at the current cursor position b resize the plot setting the bottom at the current cursor position a resize the plot auto scaling it to show all the data redraw the plot R3 3 amp renumbering spectra d delete the spectrum nearest to the cursor i renumber the spectrum nearest to the cursor you will be prompted to enter the new number q quit Once you have finally got the numbered spectra to agree with the entries in the aperture identifica tion file which will take some time type q to quit this stage and proceed to the next Next dofibers traces
5. along the entrance slit of a spectrograph The basics of fibre spectrographs are discussed further in Section Fibre spectroscopy is not the only technique for simultaneously observing the spectra of many objects Other techniques include multi slit spectroscopy and spectroscopy with objective prisms These techniques are beyond the scope of this cookbook However Section 9 gives a brief summary of their advantages and disadvantages relative to fibre spectroscopy in order to help you to judge whether fibre spectroscopy is appropriate for your purposes Conversely optical fibres have uses in astronomical spectroscopy other than allowing multiple targets to be observed simultaneously For example they can be used to bring the light from a single target to a large stable floor mounted spectrograph for high precision radial velocity determinations or interferometry Again these techniques are beyond the scope of this cookbook Fibre spectroscopy has been carried out at wavelengths ranging from the ultra violet 3500A to the infrared 2 3 micron The first fibre fed astronomical spectrograph was Medusa built by Hill et al 26 at the Steward obser vatory and first used in 1979 Since then many instruments have been built Parry 40 gives a list and the early development of the subject up to 1988 has been reviewed by Hill 25 Several fibre spectro graphs are available to the UK astronomical community as common user instruments The principal ones
6. and moves them to the reguired position The focal surface of a telescope is not necessarily a flat plane Fibre spectrographs of all types must accurately position the fibre heads to lie in the the focal surface This consideration is particularly important for systems such as FLAIR on the UKST because Schmidt telescopes have a spherical focal surface 6 Data Reduction Technigues Most of the principles of reducing data from fibre fed spectrographs are very similar to those for slit spectrographs though there are some procedures which are peculiar to fibre spectroscopy data The discussion here is a summary which emphasises the features peculiar to fibre spectroscopy If you are not familiar with slit spectroscopy then there are several good introductory documents which you can consult Some of these documents are listed below In modern slit and fibre spectrographs the detector will usually be a two dimensional CCD Various instrumental effects are present in the raw images read from the CCD and these must be removed or allowed for These effects include bad pixels bias in the electronics dark current and cosmic rayF and dust particles There are several introductory documents describing these effects and the technigues for handling them and the descriptions will not be repeated here For removing instrumental effects see e SC 5 The 2 D CCD Data Reduction Cookbook 18 e A User s Guide to CCD Reductions with IRAF 32 see Section below for
7. currently available are the Anglo Australian Telescope AAT 2dF WYFFOS AUTOFIB2 on the 5 SC 14 2 William Herschel Telescope WHT and FLAIR on the UK Schmidt Telescope UKST These instruments are briefly described in Section 7 Additional instruments are being built or are planned For example the 6dF 39 should replace FLAIR on the UKST around the year 2001 Numerous fibre spectrographs are also available or being developed at foreign observatories The most ambitious fibre spectroscopy instrument under development is the Chinese LAMOST project 12 which will have a dedicated 4m Schmidt telescope and be able to observe up to 4000 objects simultaneously A variation on the conventional fibre spectrograph is the Integral Field Unit IFU In a traditional fibre spectrograph the fibres are individually positioned so that they are illuminated by the objects being observed In an IFU the fibres are simply packed in a regular grid positioned in the focal surface of the telescope and thus produce a set of spectra at a grid of points on the sky Often the fibres will be arranged in a closely packed grid that is a hexagonal or honeycomb pattern rather than the more conventional rectangular grid IFUs are not yet in common use though they are likely to become important in the future For example the GMOS spectrographs 1 being built for the Gemini telescopes include an optional IFU as one of their modes of operation IFUs are not considered furthe
8. determine the spectrum of the target object it is necessary to estimate the contribution of the night sky and subtract it from the observed spectrum The accuracy with which the sky contribution can be estimated and the other calibrations made will largely determine the accuracy with which the spectrum of the target object can be determined The size of the sky correction varies with the angular size of the field of view of the fibre a fibre with a wide field of view will see more sky than one with a narrow field of view In principle the sky and scattered light contributions can vary in both space and time Indeed in principle the target object spectrum can also vary with time though in practice such variations can almost always be considered negligible on the time scale of a typical exposure and ignored The properties of the sky contribution is briefly discussed below and then the techniques for correcting for it considered 17 SC 14 2 6 7 1 Sky emission The main components of emission from the night sky are the aurora zodiacal light atmospheric emission and faint background astronomical sources The zodiacal light and faint astronomical sources have spectra similar to the Sun the zodiacal light is of course just sunlight reflected off interplanetary dust The aurora and atmospheric emission have primarily but not exclusively emission spectra Emission and absorption lines originating in the terrestrial atmosphere are often ca
9. fibre was pointing at sky then the object identification should be set to 999 If the fibre was broken blanked off or otherwise not in use it should be set to either 0 or 888 Summary of AutoFred fibre placement Date 06 29 98 Time 16 2 Field 454 For F 88 Smartt et al Fibred up by S Smartt 29 6 98 0 12 0 ouor 999 OANDOABAWN KY HHH HH HH RORRRR E q 10 4 18 Figure 6 Example FLAIR aperture identification file You should print out a copy of file apid txt to assist in identifying the spectra in the next step You might find it convenient to underline or otherwise highlight the fibres which are pointing at target objects or sky Wavelength calibrated sky subtracted one dimensional spectra can now be extracted from the combined image frame obj using dofibers This process is highly interactive Because there are multiple spectra in the frame some operations need to be done repeatedly once per spectrum Typically you will process the first one interactively to set the necessary parameters and then process the rest automatically IRAF has features to facilitate this sort of operation Some prompts can be answered with any of yes no YES or NO The lower case replies apply only to the current query The upper case replies apply to all similar queries To start dofibers type SC 14 2 34 dofibers apref flat dofibers throughput flat dofibers arcs1 arc dofibers obj Note that the master fla
10. fits lis 1 rawflair IRAF version 2 11 rfits Ofits lis O rawflair Some twenty four files are included in the example comprising a mixture of bias flat field arc and object observations You need to know which file corresponds to which type of observation This information may be available from your observing log However if necessary it can be extracted from the data files themselves Type imhead rawflair imh gt heads txt Here task imhead extracts the header information and the IRAF cl Unix like output redirection mechanism is used to write it to file heads txt The contents of this file should be rawflair0001 imh rawflair0002 imh rawflair0003 imh rawflair0004 imh rawflair0005 imh rawflair0006 imh rawflair0007 imh rawflair0008 imh rawflair0009 imh rawflair0010 imh rawflair0011 imh rawflair0012 imh rawflair0013 imh rawflair0014 imh rawflair0015 imh rawflair0016 imh rawflair0017 imh rawflair0018 imh rawflair0019 imh rawflair0020 imh rawflair0021 imh rawflair0022 imh rawflair0023 imh rawflair0024 imh 420 578 short Bias 420 578 short Hg Cd 420 578 short F454 1 420 578 short F454 2 420 578 short F454 3 420 578 short F454 4 420 578 short F454 5 420 578 short Rb 420 578 short Rb 420 578 short Hg Cd 420 578 short Hg Cd 420 578 short Dome flat 420 578 short Dome flat 420 578 short Dome flat 420 578 short Bias 420 578 short Bias 420 578 short Bi
11. list of line identifications and residuals arcapid t ms Ap 28 4 4 4 4 1 08 1 45 3 5E 4 2 1E 11 arcapid t ms Ap 23 4 4 4 4 0 269 0 361 8 66E 5 8 0E 11 SC 14 2 38 arcapid t ms Ap 10 3 4 3 3 0 963 1 3 3 09E 4 3 9E 12 arcapid t ms Ap 8 4 4 4 4 0 904 1 22 2 91E 4 3 8E 11 arcapid t ms Ap 32 4 4 4 4 1 19 1 61 3 9E 4 1 2E 10 arcapid t ms Ap 83 4 4 4 4 0 285 0 383 9 3E 5 1 3E 10 arcapid t ms Ap 90 4 4 4 4 0 0497 0 0663 1 7E 5 4 0E 12 arcapid t ms Ap 91 4 4 4 4 0 789 1 06 2 6E 4 2 3E 12 arcapid t ms Ap 92 4 4 4 4 1 02 1 37 3 3E 4 6 7E 11 Dispersion correct arc arcapid t ms w1 3893 338768145233 w2 4729 910906658071 dw 1 323690092583605 nw 633 and prompt Change wavelength coordinate assignments yes no NO Again reply NO 17 A further series of messages will appear Extract object spectrum obj Assign arc spectra for obj Dispersion correct obj Sky subtract obj skybeams 0 Edit the sky spectra yes Reply yes and finally a plot of all the sky spectra will be drawn similar to Figure 10 Again you may need to adjust the axes to reproduce the plot shown You should delete any sky spectra which appear to deviate from the norm In the example data no sky spectra need to be deleted However the procedure to delete a spectrum is to position the cursor over it and type d Once you are happy with the remaining spectra type q to quit You will be prompted for the technique to be used to combine the
12. of the 2dFDR 2dF Data Reduction package for reducing 2dF observations 2dFDR was written at the AAO specifically for the reduction of 2dF data and it is the usual way to reduce these data The example works through a complete simple reduction but nonetheless only shows a few of the features of the 2dFDR package For a full description you should see the 2dF User Manual 3 You need a colour display to use 2dFDR A sample dataset is available from the AAO and it is used in the present example It is not included in the usual example directory for the present cookbook but rather you should download it from the AAO along with 2dFDR see below The data comprises observations of galaxies with Bj lt 19 7 and quasars with B i lt 21 They were acquired in January 1998 using 2dF plate 0 and spectrograph 1 and include arcs flat fields offset skys and target galaxy and quasar spectra Though the observations are genuine the celestial coordinates have been randomised to preserve the proprietary rights of the original observers The data are provided courtesy of the 2dF Bright Galaxy Survey and 2dF QSO Survey teams The procedure to use 2dFDR is as follows 1 Obtain copies of 2dFDR and the example data from the AAO See Section 7 1 for details 2dFDR is available for the Digital Alpha and Sun Solaris versions of Unix It reguires some 25Mb of disk space for the Digital Alpha version and the example data requires 40Mb Both the software and example
13. sky spectra Sky rejection option nonelminmaxlavsigclip none reply avsigclip dofibers then terminates 18 Sky subtracted wavelength calibrated spectra have now been computed and are stored in IRAF image obj ms ms for multiple spectra To plot them type splot obj ms You will be prompted Image line aperture to plot 0 1 A plot similar to Figure T1 should appear The axis ranges are adjusted in the usual way Use and to step through the spectra forwards and backwards respectively When you have finished inspecting the spectra type q to quit 12 1 Setup file customisation The FLAIR setup script flairsetup c1 is of course just a simple text file which can be listed or edited from the Unix shell In order to use the file with your own data there are a couple of items which may need to be changed You should set the items combine rdnoise and dofibers readnoise to the readout noise of the CCD chip The value can be obtained from the FLAIR Web pages You may also need to alter the extents of the bias and trim regions ccdproc biassec and ccdproc trimsec respectively If you are unsure about the appropriate values then the FLAIR support staff should be able to advise 39 SC 14 2 2500 1500 1000 500 4000 4200 4400 4600 Wavelength angstroms Figure 11 FLAIR sky subtracted wavelength calibrated object spectrum 13 Reducing 2dF Data Using 2dFDR This example demonstrates the use
14. 7 2 1 and 7 3 1 respectively which themselves use dofibers are optional IRAF packages The use of IRAF on Starlink systems is described in SG 12 An Introduction to IRAF 34 If you are not familiar with IRAF this document is a convenient introduction Another useful document is A Beginner s Guide to Using IRAF 8 SG 12 includes details of how to obtain copies of IRAF manuals IRAF is a complex and in some ways non intuitive system and it is well worth taking the time and trouble to learn the basics of its operation before attempting a complicated data reduction task The Beginner s Guide is an accessible and thorough document and is a good place to start Even if you are already familiar with IRAF it is still worthwhile having a look at the Beginner s Guide because it may well still contain useful information which is new to you IRAF is installed at most Starlink sites If it is not installed at your site and you wish to obtain a copy then SG 12 contains some useful notes However you will probably need to arrange for your site manager to carry out the actual installation 7 4 3 Using IRAF with fibre spectroscopy data FITS files containing observations made with fibre spectrographs usually have large headers because of all the bookkeeping associated with the individual fibres and this is the case with files generated by the 2dF WYFFOS AUTOFIB2 and FLAIR The headers generated by these instruments are larger SC 14 2 24 than IRAF acc
15. 88 Fiber Optics in Astronomy Astronomical Society of the Pacific Conference Series 3 5 S C Barden ed 1995 Fiber Optics in Astronomical Applications Proc SPIE 2476 6 S C Barden 1998 in Arribas et al op cit 2 pp14 19 7 S C Barden T Armandroff P Massey L Groves A C Rudeen D Vaughnn and G Muller 1993 in Gray op cit 21 pp185 202 8 J Barnes 1993 A Beginner s Guide to Using IRAF National Optical Astronomy Observatories Tucson See SG 12lop cit 34 for details of obtaining IRAF manuals 9 D V Bowen M Pettini and B J Boyle 1998 Mon Not R Astron Soc 297 pp239 250 10 R D Cannon 1997 in Kontizas et al op cit 28 pp33 40 11 J W Chamberlain 1961 Physics of the Aurora and Airflow International Geophysics Series 2 Aca demic Press New York 12 Y Chu 1997 in Kontizas et al op cit 28 pp67 72 13 MJ Clayton 1998 SC 7 2 Simple Spectroscopy Reductions Starlink 6 14 MJ Currie and D S Berry 1998 SUN 95 13 KAPPA Kernel Application Package Starlink 15 MJ Currie 1998 SC 4 2 C shell Cookbook Starlink 16 MJ Currie G J Privett AJ Chipperfield D S Berry and A C Davenhall 1998 SUN 55 10 CON VERT A Format conversion Package Starlink 17 er a 1998 SUN 190 6 CURSA Catalogue and Table Manipulation Applications Starlink 18 A C Davenhall G J Privett and M B Taylor 1999 SC 5 2 The 2 D
16. CCD Data Reduction Cookbook Starlink 6 19 P W Draper 1998 SUN 139 9 CCDPACK CCD Data Reduction Package Starlink 20 M Drinkwater and B Holman 1996 FLAIR Data Reduction with IRAF Anglo Australian Observa tory Sydney SC 14 2 Bibliography 46 21 P M Gray ed 1993 Fiber Optics in Astronomy II Astronomical Society of the Pacific Conference Series 37 22 W D Heacox and P Connes 1992 Astron Astrophys Rev 3 pp169 199 23 J Hecht 1998 Understanding Fiber Optics Prentice Hall Saddle River New Jersey 22 23 24 J Hecht 1999 City of Light Oxford University Press Oxford 25 J M Hill 1988 in Barden op cit 4 pp77 92 26 27 26 J M Hill J R P Angel J S Scott D Lindley and P Hintzen 1980 Astrophys J Lett 242 ppL69 L72 27 D C Kay and J R Levine 1995 Graphics File Formats second edition Windcrest McGraw Hill New York See in particular Chapter 18 pp235 244 6 28 E Kontizas M Kontizas D H Morgan and G P Vettolani eds 1997 Wide Field Spectroscopy Kluwer Academic Publishers Dordrecht 29 J R Lewis 1996 WYFFOS Data Reduction Manual Royal Greenwich Observatory Cambridge 30 C Lissandrini S Cristiani and F La Franca 1994 Publ Astron Soc Pacific 106 pp1157 1164 31 S J Maddox and A Arag n Salamanca eds 1995 Wide Field Spectroscopy and the Distant Universe the 35th Herstmonceux Conference World Scientif
17. IR support staff should be able to advise about where to find suitable wavelengths Proceed as follows SC 14 2 300 500 Line HOAGQ IRAF V2 i 0d roe ac uk Sun 16 54 53 20 Dec 9398 identify capid t ms Ap 46 24 4201 9281 4043 4586 4074 8583 A Figure 9 FLAIR line identification for wavelength calibration 37 SC 14 2 a Identify each line by placing the cursor Over it and typing m You will then be prompted to enter the appropriate wavelength in A b When you have identified all the lines type to perform a fit c By default a third order fit is used To change the order type order followed by the reguired order A second order fit is adeguate for the example data Type f again to re fit the points with the new order d Finally when you are happy with the fit type a dofibers makes a preliminary wavelength calibration using the lines you have given attempts to find further lines and displays all the additional lines it has found You are then invited to inspect and amend these additional identifications For the example data it is probably best to delete all the additional identifications The useful commands are z zoom on chosen line n plot the next line d delete line g quit 4000 4200 4400 4600 avelength angstroms Figure 10 FLAIR sky spectra You will then be prompted Fit dispersion function interactively nolyes NO YES NO Reply NO dofibers should display a
18. SC 14 2 Starlink Project Starlink Cookbook 14 2 A C Davenhall 11th June 1999 The Fibre Spectroscopy Cookbook SC 14 2 Abstract ii Abstract This cookbook is an introduction to fibre spectroscopy and in particular the technigues and software available for reducing fibre spectroscopy observations It covers the principal common user instruments available to UK astronomers the Anglo Australian Telescope 2dF WYFFOS AUTOFIB2 on the William Herschel Telescope and FLAIR on the UK Schmidt It is not a manual for any particular package though it does contain some worked examples Who Should Read this Cookbook This cookbook is aimed firmly at people who are new to fibre spectroscopy Typical readers might either be planning or considering their first programme of observations with a fibre fed spectrograph or have a set of fibre spectroscopy observations to reduce perhaps observed by a colleague No prior knowledge of fibre spectroscopy is assumed iii SC 14 2 Contents Contents I Introductory Material 3 es eee Gu tee hue eden Remi de Ee ee eee ek ho es 4 Further Redding dis sur tow ss Ga a GA san ee kena ee Bk An dee ee 5 fda tay ese a Can hy is es oe Ay oe a eae ee Se a e Ge ee 6 itp ape Boe GS GAAS E eh aud HE eee ee BE re ee 6 7 8 10 11 11 14 15 15 16 16 18 Z1 DEU ma obec cae ous tan en E eet Bae SO ea oa SB a Manga LAN te we Oh ee 19 7 2 WYFFOS AUTOFIB2 222 22 2 2 Como 21 7 3 ELA
19. Sub Plots Hard Setup Start Stop Information on Data DREXECI Free DREXEC2 Free Run 0 a File 3 A Class Abort Status Creating Group facdscratch fibres 2df sample data BIASGROUP Reduced File Creating Group facdscratch fibres 2df sample data DARKGROUP Creating Group facdscratch fibres 2df sample data TLMGROUP Creating Group facdscratch fibres 2df sample data MELATGROUP Show Plot Header Unreduce Creating Group facdscratch fibres 2df sample data LELATGROUP Raw Data Creating Group facdscratch fibres 2df sample data WAVEGROUP A Relea History Garen Creating Group facdscratch fibres 2df sample data THPUTGROUP 4 Hardcopy Fibres Messages Action INITIALISE Task DRCONTROL completed rl Figure 12 2dFDR main window 6 Click on the Commands menu the rightmost of the three items in the menu bar in the top left of the window and select the Find Fibres option A window similar to Figure 13 should appear You need to select a file to be used to locate the position of the fibres Click on file 29jan0033 sdf which is a flat field and consequently suitable Then click the OK button A stream of processing information should be displayed in the terminal window from which you are running drcontrol and the main window 41 Filter Selection ch fibres 2df sample data 29jan0033 sdf 3 Directories 3 acdscratch fibres 2df sample dat
20. TRI ura o ne a TAN AT Opi de re he a ee K3 22 7 4 Additional software Cm on nr 23 EEE A es Foe Be A 24 fake mann Ca Buck Ma Eidos ee en ee ehe ge 25 9 1 Objective prism spectroscopy 2 ee 26 9 2 Multi slit spectroscopy ee 26 27 TO Introduction ssia cancer dm Re ew eA ERE ae ra EH 28 11 Reducing Hydra Data Using IRAFI 2 oa 29 12 Reducing FLAIR Data Using IRAF ee een 30 121 Setup file customisation ssh a soais es 38 AA ee wand eG ee ee bow er 39 Soa maan NG Ye ew o She Ge e at ae de ad o GD la TA an ar 44 Pee Rata Syn de oS a a Mieke ee ee Gee nk fo a ee te te tae in ees 45 SC 14 2 List of Figures List of Figures 1 Schematic of a traditional astronomical slit spectrograph 2 Fibre bundle for a fibre fed spectrograph o s s o in 3 CCD frame of target object spectra acquired with WYFFOS AUTOFIB2 5 Schematic diagram of the 2dF assembly o o ooo coco eee Bee Lane ee KERANA ME MD ci e SN E Ka A la E Ban Ka DAA ae A A ore Mo RAN Ta 11 FLAIR sky subtracted wavelength calibrated object spectrum 12 2dFDR main window An LN 17 2dFDR reduced galaxy spectrum aa 1 SC 14 2 List of Figures Revision history 1 21st December 1998 Version 1 Original version ACD 2 11th June 1999 Version 2 Removed the example of reducing FLAIR data with Figaro and also made various minor changes ACD SC 14 2 Li
21. User Manual The software is mostly written in Fortran and uses various Starlink subroutine libraries It is controlled from an easy to use graphical user interface GUI written in tcl tk 2d FDR is available for both the Digital Alpha and Sun Solaris versions of Unix A sample dataset is also available Both the software and sample data can be downloaded by anonymous ftp from the AAO If you are not familiar with the ftp utility then seek assistance from your site manager The details are as follows ftp site ftp aao gov au directory pub 2df files 2dfdr_alpha tar Z Digital Alpha version 2dfdr_solaris tar Z Sun Solaris version sample_data tar Z sample data SC 14 2 101 Figure 5 Schematic diagram of the 2dF assembly from Cannon 21 SC 14 2 The files are compressed tar archives Remember to set ftp to binary mode prior to retrieving copies Decompress the files using Unix command uncompress sic 2d FDR requires some 25Mb of disk space and sample data needs a further 40Mb Twice this amount is reguired if both the extracted files and the tar archives are to be resident on disk simultaneously See the README files included in the archives for further details Section 13 is an example of installing 2dFDR and using it to reduce sample data 2dF data files are stored using the standard Starlink NDF n dimensional Data Format see SUN 33 471 format They can be converted to the widely used s
22. a sdf 4 29jan0032 sdf 29jan0033 sdf 29jan0034 sdf 29jan0035 sdf 2 9jan0036 sdf 29jan0037 sdf OK Eiter Cancel Help Figure 13 2dFDR window to choose the file to locate the fibre positions SC 14 2 7 A plot similar to Figure 14 should appear in the window labelled DRPLOT1 Diagnostic Plots 2d FDR should find all 200 fibres and their positions should match the overlays down the middle of the plot ignore the edges at this point because the rotation is not yet fitted Click on the Quit button in the DRPLOT1 Diagnostic Plots window File fibposai dat should be created in the example data directory Eile Options Size Next Prev Colour Grey Counts Mag Min Max 95 Reset Guit Kak Axia 1 pixel Figure 14 2d FDR initial fibre positions SC 14 2 42 8 Move back to the main window Figure 12 Click on the Setup button in the Auto Reduction box towards the top right of the window The Setup Automatic Reduction window should appear as shown in Figure 15 Simply click on the OK button Further output should be displayed in the drcontrol terminal window Raw Data Directory acdscratch fibres 2df sample_data File Root Name 29jan File Extension sdf OK Cancel Figure 15 Window to setup 2dFDR for automatic reduction 9 Again move back to the main window Figure 12 Click on the Start button in the Auto Reduction box 2dFDR will process f
23. abases are sufficiently accurate for positioning 2dF fibres Currently the APM catalogue of the northern sky is available on line and a catalogue of the southern sky is being compiled Brief details of the catalogues are as follows The northern catalogue is based on O and E survey plates and covers most of the northern sky to within 20 of the Galactic plane The southern catalogue is based on the UKST J and SES R surveys Compilation 7see URL http www starlink ac uk archives 25 SC 14 2 of the catalogue is still in progress and data are added as they become available Further details of the catalogues and instructions on how to extract lists of target objects can be found on the Web pages of the Astronomy Survey Unitat the Institute of Astronomy Cambridge See URL http www ast cam ac uk mike casu apm apm html Currently SuperCOSMOS is scanning the J Rand I UKST surveys The South Galactic Cap and Magellanic Clouds have been scanned and will be available on line from Summer 1999 Additional fields are being added spiralling out from the South Galactic Cap If your target objects are in a region of sky which has not yet been scanned then it will usually be possible to locate and scan a suitable plate for you However you should consider this latter option as a method of last resort as the scanning schedule for the microdensitometer is planned well in advance An outline of the various procedures follows 1 Check the Sup
24. ank sky The sky spectrum is then determined from these fibres Usually 5 to 10 of the fibres are used in this wayf In Section 6 6 it was stated that the spectra should be wavelength calibrated prior to sky subtraction The reason for performing the operations in this order is that light from the sky and object falls on different parts of the detector and because of distortions in the spectrograph the shape of the spectra will not be identical If they are subtracted prior to wavelength calibration the pixels will not be properly aligned resulting in spurious artifacts such as residual P Cygni type profiled4 for the 3Typical numbers might be about twenty sky fibres for the 2dF between ten and twenty for WYFFOS AUTOFIB2 and three to ten for FLAIR 4A P Cygni line profile is one in which the line shows adjacent emission and absorption The name comes from the variable star P Cygni whose spectrum shows such features Of course in P Cygni and similar stars the effect is caused by physical processes in the stellar atmosphere not defective calibration SC 14 2 18 atmospheric lines The effect of poor wavelength calibration has been discussed comprehensively by Parry and Carrasco 42 As described in Section 6 7 1 if a rare relatively bright background galaxy happens to fall in the field of view of a fibre it will dominate the sky background in that fibre Consequently simply taking the mean of all the sky fibres is not usually t
25. are accurately positioned in the focal surface of the telescope so that each is illuminated by a target object in the field of view These fibres are then connected to a series of positions along a single entrance slit for a spectrograph see Figure A series of spectra one for each object are imaged on the CCD detector with say each spectrum dispersed along the rows and occupying a distinct separated range of columns In essence the operation of a fibre fed spectrograph is as simple as that There are of course a number of caveats and complications Firstly there is no simple correspondence between the position of any target object in the field of view and the position of its spectrum in the CCD image it is necessary to keep track of this information separately in order to reduce the observations Secondly the fibres have to be positioned so that they are illuminated by the target objects Thus they must be reconfigured in new positions for every field of target objects viewed Nonetheless with such an instrument spectra can be obtained simultaneously for large numbers of target objects with the possible number of targets corresponding roughly to the number of fibres though 9 SC 14 2 Figure 2 Fibre bundle for a fibre fed spectrograph from Parry 40 1 some fibres must be reserved for guiding and measuring the sky background Every technique has its own jargon and in fibre spectroscopy the number of spectra simultaneousl
26. as 420 578 short Bias 420 578 short Bias 420 578 short Bias 420 578 short Bias 420 578 short Bias 420 578 short Bias 420 578 short Bias A copy of the output is also provided in file flairheads txt for comparison It is obvious from this output which file contains which sort of observation The header information in the raw FLAIR data contain some oddities which must be fixed up before the data can be processed with IRAF The utility fixhead is provided as part of the FLAIR software for this purpose Type fixhead rawflair imh The corrected data are written to images called flair101 to flair124 and the original images are deleted SC 14 2 32 8 The next step is to combine the various bias frames into a single master bias frame In IRAF bias frames are usually called zeroes because they have zero exposure Rather than typing in the names of all the bias frames a list has been prepared in file zero 1is The master bias frame will simply be called zero Type zerocombine output zero zerocombine zero lis 9 The flat fields must be similarly combined using flatcombine Again there is a list of flat fields in file flat lis and the master flat field will be called flat Type flatcombine output flat flatcombine Oflat lis 10 The arc and object frames are now corrected using the bias frames Type ccdproc zero zero ccdproc ccdproc lis As usual the arc and object frames are liste
27. cing 2dF data using 2d FDR Section 13 The example of reducing Hydra data is available as part of the documentation for IRAF The procedure is similar to but simpler than the procedure for reducing FLAIR data Consequently it is sensible to work through the Hydra example before trying the FLAIR one All the examples assume that the requisite software is already installed at your site and ready for use If the software is not available at your site then Section 7 describes how to obtain it Note however that you will often reguire the assistance of your site manager to install the software Copies of the data files used in the examples are provided so that you can work through them yourself On Starlink systems they are kept in directory star examples sc14 Alternatively they can be retrieved by anonymous ftp from Edinburgh The details are as follows site ftp roe ac uk directory pub acd misc file sc14 tar Z Reply anonymous to the Name prompt and give your e mail address for the password Set ftp to binary mode before retrieving the file The file is a compressed tar archive and should be decompressed with the Unix command uncompress sic In order to work through the examples you should use a display capable of receiving X output typically an X terminal or a workstation console Strictly speaking the software will run on a black and white device but realistically you need a colour display Before starting you should ensur
28. d in file ccdproc lis The flat field frame flat should be similarly corrected Type ccdproc flat 11 In the example there are two arc frames containing a rubidium arc images flair108 and flair109 and two containing a mercury cadmium arc images flair110 and flair111 The spectra used in this example cover only a relatively narrow wavelength range and thus contain only a few lines Consequently the two types of arc must ultimately be added in order to provide enough lines for wavelength calibration However prior to this step the arcs of the same type are combined using combine which detects and rejects cosmic ray events in the images Type combine flair108 flair109 rb combine flairi10 flairiii hgcd imarith rb hgcd arc The final master arc frame is called arc 12 The five image frames must be similarly combined Incidentally the reasons for taking five separate image frames rather than one long exposure are twofold firstly to avoid possible saturation of the CCD by bright objects and secondly to allow cosmic ray events to be detected and removed each cosmic ray event will be present in only one image Again a list of object frames is included as file obj lis Type combine obj lis obj The master object frame is simply called obj 13 The next stage is to prepare an aperture identification file This file ties together the apertures in the image frame the fibres and the object or sky which each fibre was pointing at Fo
29. d spectrum Clearly a slice across an absorption line would show a smaller peak and a slice across the centre of a dark absorption line might hardly deviate from the background In general the spectrum will be spread across a range of pixels as in Figure 4 The actual number depends on the telescope and spectrograph optics and the physical size of the CCD pixels but it is SC 14 2 12 Figure 3 CCD frame containing spectra of target objects observed with the WYFFOS AUTOFIB2 fibre spectrograph on the WHT Each horizontal line is an individual spectrum obtained through a single fibre The prominent dark features seen in all the spectra mostly in the left half of the frame are night sky emission lines In most fibre spectrographs the corresponding night sky lines in the various spectra more or less line up in a row perpendicular to the dispersion direction However in order to try to save space on the WYFFOS AUTOFIB2 detector the fibre ends were positioned in three parallel rows in the spectrograph entrance slit rather than the conventional single row This arrangement causes the distinctive and unusual staggered pattern of the night sky lines seen in the figure The blemishes scattered throughout the frame are not associated with the spectra but are spurious signals caused by cosmic ray events The objects observed here are low redshift galaxies z lt 0 2 of the sort which are thought to be responsible for the Lya absorption lines obser
30. data are retrieved as compressed tar files If you wish to have both the extracted files and the decompressed tar files resident on disk simultaneously then double the amount of disk space required All that is required to install 2dFDR is to simply extract the files from the tar archive Similarly the SC 14 2 40 example data are just extracted from the archive For further details see file README included with each tar archive 2 Prior to using 2dFDR you should set the environment variable DRCONTROL_DIR to the name of the directory where you have copied the files For example if I had put the files in directory home acd 2dfdr I would type setenv DRCONTROL_DIR home acd 2dfdr To set up for running 2dFDR type source DRCONTROL_DIR 2dfdr_setup 3 2dFDR requires a large number of the colours on your display Before starting it you should shut down any other applications which use many colours Likely candidates are Netscape SAOIMAGE or GAIA If 2dFDR cannot obtain sufficient colours it will not start correctly 4 Make the directory where you have copied the example data your current directory Then type drcontrol amp The amp is of course simply to run drcontrol as a detached process A series of windows should appear 5 Find the main window which is called 2dF Data Reduction It is shown in Figure 12 Eile Options Commands Auto Reduction Files nj Reduced Ei Data General Combine Extract Sky
31. dred specred astutil flair If any of the packages are not found then the most likely explanation is that they are not installed at your site ask your site manager to install them See Section 7 3 for details of how to obtain the FLAIR software and SG 12 for the standard IRAF packages 4 Several IRAF tasks have to be run in order to reduce FLAIR data and for most of them hidden parameters have to be set The FLAIR manual 20 gives the necessary details However for convenience the script flairsetup cl is provided with the example It simply sets all the required values It is correct for the example data and can simply be used unaltered However if you wish to use it with your own data there are couple of items which may need to be changed Section 12 1 gives the details To define and run the script simply type task flairsetup home flairsetup cl flairsetup For information the script echoes the values that it sets to the IRAF command line 31 5 6 7 SC 14 2 FLAIR data are provided as FITS files of file type fts They must be converted to the IRAF OIF format Rather than specifying all the file names individually they have previously been listed in file fits lis provided with the example you might like to examine this file and check that it is just a list of file names The procedure for making the conversion differs slightly depending on which version of IRAF you are using IRAF version 2 10 rfits
32. e aspects to defining the footprint of each spectrum locating its position defining the shape parallel to the dispersion direction and defining the shape perpendicular to the dispersion direction The need to locate the position is obvious The remaining two aspects are described below Shape parallel to the dispersion direction Ideally each spectrum is a straight line perfectly aligned along either the rows or columns of the CCD In practice the spectra are usually slightly curved rather than perfectly straight This curvature can be caused by distortions introduced by the spectrograph optics and refraction in the terrestrial atmosphere Spectra imaged on different parts of the CCD frame will not necessarily have precisely the same shape Even if the spectra are perfectly straight they will not usually be perfectly aligned with the CCD grid In order to define the shape along the dispersion direction a locus of points along the middle of the spectrum is defined over its whole length This process is called tracing the spectrum and the locus is called the trace of the spectrum Shape perpendicular to the dispersion direction Figure 4 shows a row of pixels or slice extracted from the CCD frame The slice is centred on a spectrum and aligned perpendicular to the dispersion direction The peak in the plot is the spectrum and the flat outer regions the ambient background signal in the CCD frame Here the slice is crossing the continuum in a well expose
33. e that your display is configured to receive X output Finally the examples show only some of the features of the various packages used In all cases they have additional features which are not described here You should see the appropriate user manuals for full details 29 SC 14 2 11 Reducing Hydra Data Using IRAF Hydra is a fibre spectrograph available at the Kitt Peak National Observatory KPNO Tucson see for example Barden et al 7 Observations acquired with it are usually reduced using the IRAF task dohydra dohydra is very similar to the IRAF task dofibers which is used to reduce FLAIR and WYF FOS AUTOFIB2 data A worked example of using dohydra is available as part of the IRAF documenta tion This example is similar to though simpler and easier than the example of reducing FLAIR data given in Section 12 below Thus it is sensible to work through the Hydra example before trying the FLAIR one even though you are unlikely to observe with Hydra Before trying the Hydra or FLAIR example you should already be familiar with the rudiments of IRAF and have an IRAF directory prepared which you will use for running IRAF If you are not au fait with IRAF then you must familiarise yourself with it before proceeding SG 12 An Introduction to IRAF 34 is a convenient starting point The dohydra tutorial is available at URL http www starlink ac uk iraf web tutorials dohydra dohydra html You can simply follow the i
34. erCOSMOS on line databases to see whether the region of sky containing your objects is available The databases can be accessed from the SuperCOSMOS Web pages at URL http www roe ac uk cosmos scosmos html You should retrieve the catalogue of objects found in your region of sky formatted as a FITS table 2 If your region of sky is not yet available then you will need to identify a suitable plate of the region You can search the UKST plate catalogue from URL http www roe ac uk ukstu ukst html Once you have identified a plate you can arrange for it to be measured by SuperCOSMOS Details are available at URL http www roe ac uk cosmos applic html For further information send an e mail message to username hmg roe ac uk You should specify that the list of objects detected the TAM data file in SuperCOSMOS jargon is to be returned to you formatted as a FITS table Usually there will be a delay of a couple of weeks before your plate is scanned 3 Typically SuperCOSMOS finds upwards of some hundreds of thousands of objects on a Schmidt plate You need to identify the few hundred corresponding to your target objects from amongst all the objects that SuperCOSMOS has detected in the selected region You can identify your objects using the catalogue manipulation package CURSA see SUN 190 171 First prepare a table contain ing the known approximate coordinates of your objects formatted as a CURSA STL list which is
35. for unusual objects such as quasars blue stars and emission line objects Considerable archives of prism plates have been accumulated at various observatories around the world and various programmes are still in progress for example with the UKST For recent reviews of objective prism work see Parker and Hartley 38 and references therein There is a brief introduction to objective prism techniques in Walker 46 pp164 165 9 2 Multi slit spectroscopy Multi slit spectroscopy is a realistic alternative to fibre spectroscopy Multi slit spectroscopy is identical to traditional spectroscopy of one object using a single slit except that as its name implies there are several slits in the field of view each allowing light from a different object to pass into the spectrograph and form spectra on the detector The engineering problem of configuring the slits to be in the correct positions to pass light from the target objects is usually solved by preparing a separate plate or mask for each field observed The required slits are simply drilled in the appropriate positions This approach is analogous to preparing a plug plate in fibre spectroscopy The advantages of multi slit spectroscopy are that it has all the accuracy and capabilities of single slit spectroscopy It is feasible to carry out flux calibration Accurate sky subtraction is certainly easier and perhaps more accurate though the arguments are not simple see Section 6 7labove and Wyse a
36. he best way to estimate the most likely sky spectrum Rather it is better to find the total counts for each spectrum and exclude the extreme spectra in the resulting distribution thus avoiding contamination by rare relatively bright background galaxies Clearly the simultaneous sky exposure technique does not work well if the sky background is not flat Separate sky frames Here before or after acquiring spectra of the target objects or both the pointing of the telescope is offset slightly so that all the fibres point at the night skyPland a frame of spectra of the sky background acquired The genuine target spectra can then be sky subtracted using the sky spectrum from the corresponding fibre in the sky frame Here there is less need for fibre throughput and vignetting corrections as both the object and the sky used to correct it are measured through the same fibre The technique is viable only if the sky background is constant on time scales longer than the exposure time It also makes less effective use of the telescope than the simultaneous sky exposure technique because approximately half the observing time is spent observing sky However a few separate sky frames can provide a useful check that the simultaneous sky exposure technique is working correctly 6 7 3 Other techniques Various more complicated techniques have been proposed for example by Lissandrini et al 30 or Watson et al 49 though these are not usually in routine use
37. ic Singapore 32 P Massey 1997 A User s Guide to CCD Reductions with IRAF National Optical Astronomy Observa tories Tucson See SG 12 op cit 34 for details of obtaining IRAF manuals g 33 P Massey F Valdes and J Barnes 1992 A User s Guide to Reducing Slit Spectra with IRAF National Optical Astronomy Observatories Tucson See SG 12 op cit 34 for details of obtaining IRAF manuals 6 34 R Morris G J Privett and A C Davenhall 1998 SG 12 1 IRAF Image Reduction Analysis Facility Starlink 35 R Morris and G J Privett 1966 SUN 166 4 SAOIMAGE Astronomical Image Display Starlink 36 G W Nelson 1988 in Barden op cit 4 pp2 22 37 Q A Parker 1997 in Kontizas et al op cit 28 pp25 31 38 Q A Parker and M Hartley 1997 in Kontizas et al op cit BEN pp17 23 39 Q A Parker F G Watson and S Miziarski 1998 in Arribas et al op cit 2 pp80 91 40 LR Parry 1997 in Kontizas et al op cit 28 pp3 16 41 LR Parry 1998 in Arribas et al op cit PI pp3 13 42 42 LR Parry and E Carrasco 1990 in Instrumentation in Astronomy VII Proc SPIE 1235 pp702 708 6 7 2 43 K T Shortridge H Meyerdierks M J Currie MJ Clayton J Lockley A C Charles A C Davenhall and M B Taylor 1998 SUN 86 16 FIGARO A General Data Reduction System Starlink 44 F Valdes 1992 Guide to the Multifiber Reduction Task DOFIBERS National Op
38. ield of view of FLAIR see Section 7 3 means that spatial variations on scales of degrees are more important for it than for other instruments with smaller fields of view 6 7 2 Correction procedure This section considers the procedures for correcting for sky emission Two techniques are in common use simultaneous sky exposure and separate sky frames In both cases the target object spectra should previously have been corrected for instrumental scattered light and flat fielded Recall that for isolated objects far from the Galactic plane and bright galaxies there is usually no structure in the sky background on spatial scales ranging from seconds of arc to degrees but there are temporal variations on the time scale of a typical exposure Consequently there is no advantage in measuring the sky background very close to the target object measurements within a degree or so are just as good Conversely because the background varies with time there is an advantage in measuring it simultaneously with measuring the target objects As its name implies the simultaneous sky exposure technique measures the sky and target objects simultaneously whereas in the separate sky frames technique they are measured sequentially Thus the simultaneous sky exposure technique is usually preferable Simultaneous sky exposure When the target objects are being observed a few fibres are not allocated to targets but rather are positioned so that they point at patches of bl
39. ing FLAIR observations and has been used successfully to reduce 2dF data The reduction procedures for WYFFOS AUTOFIB2 are based on dofibers but it cannot be used directly in this case because in WYFFOS AUTOFIB2 the fibre ends are positioned in three parallel rows in the spectrograph slit rather than the single row expected by dofibers dof ibers is documented in the Guide to the Multifiber Reduction Task DOFIBERS 44 Both the software and manual are available as part of IRAF see the following section 7 4 2 IRAF IRAF Image Reduction and Analysis Facility is a powerful and comprehensive environment for reducing and analysing astronomical data It was developed at the National Optical Astronomy Observatories NOAO Tucson and is in widespread use around the world IRAF has its own data file format command language on line help system and programming language It is a modular system The basic core which is always present provides general facilities for image processing and data reduction For more specialised tasks such as reducing spectroscopic data additional packages are loaded to augment the core system Software for processing most sorts of astronomical data is available for the IRAF environment For example dofibers the general purpose package for processing fibre spectroscopy data discussed in Sec tion 7 4 1 runs as part of IRAF Similarly the special purpose packages for reducing WYEFOS AUTOFIB2 and FLAIR data see Section
40. lair iraf ps Z are compressed Remember to set ftp binary mode prior to retrieving them Decompress the files using Unix command uncompress sic See file README for details of installing the IRAF scripts FLAIR data are usually exported as FITS files and then converted to the IRAF format using the IRAF command rfits Note however that as for WYFFOS AUTOFIB2 the IRAF parameter min_lenuserarea must be increased before importing the data in order to accommodate the FLAIR headers See Section 7 4 3 below and the Setup section of the FLAIR II data reduction manual for details 23 SC 14 2 Section 12 is an example of reducing FLAIR observations with dofibers FLAIR data can also be reduced using the Starlink packages Figaro see SUN 86 43 CCDPACK see SUN 139 19 and KAPPA see SUN 95 14 though this is unusual 7 4 Additional software The WYFFOS AUTOFIB2 and FLAIR software is based on the package dofibers which itself runs under the IRAF environment These items are briefly described below 7 41 dofibers dofibers is a general purpose IRAF application written by Francisco Valdes for reducing fibre spec troscopy observations and is not tied to any particular instrument It provides facilities for the extraction flat fielding fibre throughput correction wavelength calibration and sky subtraction of fibre spectra It is an IRAF command language script which invokes other IRAF applications dofibers is the usual method of reduc
41. lled telluric lines Wyse and Gilmore 51 give summary details of the atmospheric emission and Chamberlain 11 gives a thorough description However the upshot is that atmospheric emission is more important in the red than the blue with the OH Meinel bands often being particularly prominent at wavelengths longer than about 6500A The atmospheric components variously show spatial changes on scales of a degree or more and of less than a second of arc but not on intermediate scales They can however show temporal changes on time scales which are short compared to a typical astronomical exposure Of the astronomical sources complex resolved backgrounds such as diffuse Galactic light or a resolved galaxy can show spatial variations on all scales up to degrees However away from the Galactic plane and large nearby galaxies such complex backgrounds are rare and the astronomical background is usually dominated by light from faint unresolved galaxies This distribution is variable on scales of less than a second of arc but not on larger scales unless the region observed is in a galaxy cluster Furthermore the galaxy luminosity function is such that usually the field of view probably will not contain a rare relatively bright background galaxy but if by chance it does then this galaxy will dominate the observed background This property of the luminosity function has consequences for determining the background level see below The uniquely wide f
42. merous people who contributed their time expertise and data during the preparation of this cookbook Nigel Hambly provided the data used in Section12Jand demonstrated the reduction of FLAIR data with IRAF Dave Bowen provided the data used in Figures Band land demonstrated the reduction of WYFFOS AUTOFIB2 data with IRAF Martin Clayton did much of the preliminary work on which the document is based Ihad extremely useful discussions with Malcolm Currie and Ouentin Parker All the above and also Karl Glazebrook Fred Watson Don Pollacco Jim Lewis Harvey MacGillivray Martin Bly and Rodney Warren Smith either answered gueries and or provided useful comments on the draft version of the cookbook Any mistakes of course are my own 45 SC 14 2 Bibliography Bibliography 1 J Allington Smith P Bettess E Chadwick R Content R Davies G Dodsworth R Haynes D Lee I Lewis J Webster E Atad S Beard R Bennett M Ellis P Hastings P Williams T Bond D Crampton T Davidge M Fletcher B Leckie C Morbey R Murowinski S Roberts L Saddle myer J Sebesta J Stilburn and K Szeto 1997 in Kontizas et al op cit 28 pp73 79 2 S Arribas E Mediavilla and F G Watson eds 1998 Fiber Optics in Astronomy III Astronomical Society of the Pacific Conference Series 152 2 6 89 41 49 3 J A Bailey and K Glazebrook 1997 2dF User Manual Anglo Australian Observatory Sydney 4 S C Barden ed 19
43. n grating and thence it is re imaged on a two dimensional panoramic detector Historically this detector would have been a photographic plate or even a human eye observing through a travelling eyepiece though now it is usually a CCD Charge Coupled Device The slit spectrograph and detector are so aligned that the dispersion direction corresponds to one axis of the two dimensional CCD array say the rows for example The other axis say the columns corresponds to positions along the slit Thus the central columns of the CCD see dispersed light from the target object and neighbouring columns see dispersed light from the night sky adjacent to the object Slit Disperser OCD Figure 1 Schematic of a traditional astronomical slit spectrograph Such an instrument is not making full use of the imaging capabilities of the telescope several objects are simultaneously imaged in the field of view but only one is detected One way of addressing this deficiency is to place several slits in the field of view positioned so that light from a separate object passes through each Many such multi slit spectrographs have been built A full discussion is beyond the scope of this cookbook However multi slit spectroscopy has different advantages than fibre spectroscopy and the technigues are briefly compared in Section Fibre fed spectrographs are another attempt to address the problem and the basics of their operation are simple A set of optical fibres
44. nd Gilmore BTJ Also there are no throughput losses associated with passing light through the fibres The disadvantages are that both the field of view and the multiplex advantage are usually smaller than for fibre spectroscopy A modern multi slit spectrograph might typically have a field of view of 10 minutes of arc in diameter compared with for example the 2 diameter field of the 2dF Also in order to avoid overlapping spectra the number of spectra which can be simultaneously recorded is usually limited to tens rather than hundreds although Allington Smith et al T quote the theoretical maximum multiplex advantage of the GMOS multi slit spectrographs being built for the Gemini telescopes as 600 Of course this maximum value will not be attainable in most fields The necessity of avoiding overlapping spectra can also limit the positioning of the slits to locations that are not optimal for the scientific investigation being conducted A final consideration is that a multi slit spectrograph attached directly to the telescope may be less stable than a fibre spectrograph mounted on the dome floor or a Nasmyth platform Part III Worked Examples SC 14 2 SC 14 2 28 10 Introduction This part of the cookbook provides a set of worked examples of reducing fibre spectroscopy observations from various instruments The examples are e reducing Hydra data using IRAF Section 11 e reducing FLAIR data using IRAF Section 12 e redu
45. nstructions given and there is no need to repeat them here There are however a couple of caveats which you should be aware of 1 The sequence of IRAF packages to load given in the tutorial is slightly incorrect The correct sequence is noao imred hydra 2 An IRAF script is provided with the present cookbook to automatically set all the dohydra parame ters recommended in the tutorial It is available as file star examples sc14 hydra hydrasetup cl You should make a copy of this file in your IRAF home directory Then from the IRAF command line type task hydrasetup home hydrasetup cl hydrasetup For information the script echoes the values that it sets to the IRAF command line SC 14 2 30 12 Reducing FLAIR Data Using IRAF FLAIR observations are usually reduced using IRAF see Section 7 3 1 and this example is a simple demonstration of the procedure The reduction of FLAIR data is documented in the manual FLAIR Data Reduction with IRAF 20 The present example gives all the steps involved in a simple reduction but nonetheless you will find it useful to have a copy of the manual to hand as you work through it for further explanation of each step and future reference The example assumes that you are familiar with the rudiments of IRAF and already have an IRAF directory prepared which you will use for running IRAF If you are not au fait with IRAF then you must familiarise yourself with it before proceeding SG 12
46. nstrumental signature fibre throughput losses and vignetting superimposed Note that the individual pixel sensitivity variations will have been averaged perpendicular to the dispersion direction when the one dimensional spectrum was constructed The flat field spectrum is normalised and depending on the characteristics of the data either smoothed or fit by a low order polynomial It is then simply divided into the target object spectrum to remove the various multiplicative effects Remember however that the spectrum of the continuum calibration lamp is not flat so the target object spectra will still show sensitivity variations with wavelength The flat field correction is unique to each fibre in each configuration and must be redefined when the fibres are repositioned for example because the fibre will be in a different position in the focal surface SC 14 2 16 and hence the vignetting will be different Flat field frames should have a high signal to noise ratio that is contain well exposed images of the lamp in order to reduce noise in the calibration lamp spectra Conseguently flat field frames are also usually suitable for tramlining see above 6 6 Wavelength calibration Each extracted spectrum consists of a list of the intensity at a series of positions along the central locus of spectrum Because the spectra are usually both bent and misaligned with the CCD grid these positions will not generally correspond precisely to the p
47. ommodates by default when it reads FITS files Thus it is necessary to reset the parameter min lenuserarea which specifies the maximum header size prior to importing the FITS files Table 2 gives the minimum required value for each instrument larger values may of course be used The sim plest way to reset min_lenuserarea is to use the IRAF customisation login file supplied with SG 12 34 In this case the parameter is set to an appropriate value when IRAF starts Alternatively you can reset the value manually from the IRAF command line For example for WYFFOS AUTOFIB2 you would type reset min lenuserarea 300000 Instrument min lenuserarea 2dF 128 000 WYFFOS AUTOFIB2 300 000 FLAIR 40 000 Table 2 Minimum permitted values of IRAF parameter min_lenuserarea for use with fibre spectrographs 8 Generating Target Positions Positioning the fibres correctly in the focal surface so that light from the target objects falls on them is perhaps the greatest technical challenge of fibre spectroscopy However most of the difficulties and complexities of mechanically positioning the fibres will not concern you as a user Nonetheless you will need to compile a list of accurate celestial coordinates for all your target objects Typically some time before the observations are made you will supply this list to the support staff of the telescope where you are planing to observe Usually each fibre has a limited field of view and hence accurate coordina
48. opy photographic plate of the field to be observed The plate was placed in a modified plate holder with the fibres on the illuminated side of the plate Small prisms on the head of the fibres directed the incident light along the fibres Currently the fibres are mounted on top of a film copy of the target field using magnetic buttons FLAIR should be replaced by the 6dF 39 around the year 2001 FLAIR has been described by Parker 37 and further information is available on the AAO s Web pages at URL http www aao gov au astro flair html including a hypertext user manual 7 3 1 Software FLAIR data are reduced using a set of IRAF scripts based around the IRAF application dofibers see Section 741 Before running the FLAIR scripts the CCD frames must be corrected for instrumental effects allowing for bad pixels flat fielding debiasing etc These operations are also most conveniently done with IRAF A manual for reducing FLAIR observations is available FLAIR Data Reduction with IRAF 20 Another useful document is A User s Guide to CCD Reductions with IRAF 33 Copies of the FLAIR software and the manual can be downloaded from the FLAIR section on the AAO Web pages see Section 7 3 Alternatively they be retrieved by anonymous ftp The details are as follows ftp site ftp aao gov au directory pub flair files README instructions flair tar Z FLAIR IRAF scripts flair iraf ps Z user manual postscript Files flair tar Z and f
49. or a few minutes and a whole stream of output will be displayed in the drcontrol terminal window and the main window 10 Still in the main window Figure 12 click on the Commands menu again and this time choose the Combine Reduced Runs option A window similar to Figure 16 should appear For the purposes of the example you should combine files 29jan0034 sdf 29jan0035 sdf and 29jan0036 sdf These files contain object frames and by combining them cosmic ray events can be removed First click on file 29jan0034 sdf in the Files box and then click on the gt ADD gt button The file name with a complete directory specification should appear in the Files to be Combined box on the right hand side of the window Repeat the procedure for files 29jan0035 sdf and 29jan0036 sdf When you are finished the appearance of the window should be similar to Figure 16 If you add the wrong file by mistake then simply click on the REMOVE button When you have assembled the correct list of files click on the OK button Further output will be displayed in the drcontrol terminal window 11 When the processing finishes the reduction is complete Move to the main window Figure 12 and close 2dFDR by clicking on the File menu the leftmost item in the menu bar at the top of the screen and choosing the Exit option 12 The reduced spectra are stored in file combined frames sdf This file is a two dimensional array with one axis corresponding to the fibre number
50. ositions of pixels in the CCD However they are in units of pixel positions The next step is to convert the positions into genuine wavelengths typically in ngstr m This calibration is achieved using calibration frames Arc calibration frames are produced by illuminating the fibres with an arc calibration lamp The spectrum of such a lamp is primarily a set of emission lines Briefly the emission lines have a known wavelength and their positions in the calibration spectra can be measured It is then possible to fit the relation between position and wavelength using a low order polynomial This relation is applied to the spectra of the target objects to calibrate them into wavelength The details of the way in which the calibration lines are identified and the fit made vary You may be required to identify some or all of the emission lines from a spectral atlas or the identification may be completely automatic If you have to identify the lines manually you should try to ensure that you find lines spread along the entire range of the spectrum to minimise errors of interpolation and extrapolation You will probably also have to choose the order of the polynomial fit between wavelength and position too low an order will leave systematic residuals and too high an order will introduce spurious effects The traditional wisdom is that arc frames should be exposed both before and after target object frames and the results averaged in order to reduce sys
51. pectrograph on the 3 9m Anglo Australian Telescope can observe 400 spectra simultaneously In a single observation it can acquire spectra which would require 400 consecutive observations using a traditional single object spectrograph Of course there are limitations on using fibre spectrographs to observe multiple objects In particular multiple objects can only be observed if they are simultaneously in the field of view of the telescope Also in order to obtain the maximum advantage from the instrument the various objects being observed should be of similar brightness otherwise the duration of the observation must be set by the faintest object and some of the advantage of simultaneous observation is lost These constraints favour telescope designs with wide fields of view Nonetheless the increase by one or two orders of magnitude in the number of spectra which can be acquired in a given amount of observing time has lead to a veritable revolution in astronomical spectroscopy Numerous large scale surveys and smaller individual projects which would hitherto have been infeasible are now regularly carried out Multiple object spectroscopy is now common and indeed on some telescopes the norm rather than the exception The basic principle of fibre spectroscopy is simple A set of optical fibres are positioned in the focal surface of the telescope so that each is illuminated by one of the objects being observed The other ends of the fibres are positioned
52. r see URL Though FITS is basically an astronomical format it is sometimes mentioned in books about standard image formats See for example Graphics File Formats by Kay and Levine 27 SC 14 2 22 There is no example of reducing WYFFOS AUTOFIB2 data in the present cookbook However the examples of reducing Hydra Section IT and FLAIR Section 12 data with IRAF are sufficiently similar because they also use dofibers or the closely related dohydra that it is worthwhile trying them before attempting to reduce WYFFOS AUTOFIB2 data 73 FLAIR FLAIR Fibre Linked Array Image Reformatter is a fibre fed spectrograph for the 1 2m UK Schmidt Telescope UKST Strictly speaking the current version of the instrument is FLAIR II a development of the original FLAIR However for simplicity it will simply be referred to as FLAIR in the present cookbook FLAIR is able to exploit the 40 sguare degree wide field of view of the UK Schmidt Telescope giving it a uniguely wide field of view for a fibre fed spectroscopic system Typical dwell times on single fields are one to two hours though long dwell times of up to seven hours are possible FLAIR is suitable for observing moderately faint objects B lt 18 with number densities in the range 1 10 per square degree The spectrograph is mounted on the dome floor and consequently is extremely stable Originally the fibres were positioned using a technique unique to FLAIR They were cemented onto a c
53. r FLAIR data an aperture identification file can be created automatically from the log file produced when the fibres were positioned This log file is usually called af log Simply type reformat af log apid txt 33 14 SC 14 2 where apid txt is the new aperture identification file Alternatively the file can be created from scratch using a text editor and your notes on positioning the fibres However you create the file you need to be familiar with its format and contents for subseguent operations Figure elshows the first few lines of a typical file The lines beginning with a hash character are comments and can be ignored Each remaining line corresponds to one fibre and there is one line for every fibre in the instrument The three items on each line are from left to right fibre number a sequential running count identifying each fibre fibre type a code indicating what the fibre is pointing at The options are target astronomical object 1 sky 0 broken or blanked off fibre 1or1 A broken or blanked off fibre is one which is not in use If a code of 1 is used for such a fibre then it is distinguished from target objects by the object identification below object identification if the fibre is pointing at a target object then the target identification should be a unique number identifying the object in your records of the observation It allows you to determine which object the fibre was pointing at If the
54. r done using an image frame where the fibres were illuminated using a bright continuous source in order that all the spectra are well defined along their entire length Sometimes special frames are acquired for this purpose Alternatively flat field frames see below are usually suitable It is usually acceptable to apply the footprints defined from one frame say a flat field to another frame say a target object or arc frame as long as the instrumental configuration remains unchanged 6 3 Extraction Extraction as its name implies is the process of extracting a series of one dimensional spectra one per fibre from the two dimensional CCD frame It consists of determining the intensity of each spectrum at a series of equally spaced points along the locus of the spectrum using its trace defined during the tramlining The simplest way to determine the intensity at each point along the spectrum is simply to average all the points across the width of the spectrum that is perpendicular to the dispersion direction again using the the width determined during the tramlining A more sophisticated technique is optimal extraction which gives high weight to high signal to noise pixels close to the centre of the spectrum and lower 15 SC 14 2 weight to lower signal to noise pixels close to the edge see Figurel4 Optimal extraction offers significant advantages for faint noisy spectra and does no harm for less noisy well exposed spectra Extrac
55. r here though many of their features are similar to traditional fibre spectrographs This cookbook is an overview and is not specific to any particular instrument However it does contain both numerous references for further information and some worked examples The structure of the cookbook is Part I background material Part II worked examples If you are familiar with the principles of fibre spectroscopy then you can omit Part I and proceed straight to the worked examples On Starlink systems example datasets are distributed with the cookbook so that you can try the examples for yourself 2 Further Reading Fibre fed spectrographs are a relatively recent innovation and are rarely described in textbooks on astronomical instrumentation However they are mentioned briefly in Astronomical Observations by Walker 46 pp167 169 and pp115 116 There have been a number of conferences in whole or part about fibre spectroscopy and proceedings are usually available These conferences include the following e Fiber Optics in Astronomy 1 4 1988 e Fiber Optics in Astronomy II 21 1993 e Wide Field Spectroscopy and the Distant Universe 31 1995 e Fiber Optics in Astronomical Applications 5 1995 e Wide Field Spectroscopy 28 1997 e Fiber Optics in Astronomy III 2 1998 1The principal advantage of a hexagonal grid over a rectangular one is that for a given size of fibre it achieves a denser sampling of the region of
56. ranging from 1 to 200 and the other to wavelength The individual spectra can be plotted for example with Figaro see SUN 86 43 Type figaro To start Figaro Then type soft xw splot combined_frames 90 autoscale yes soft xw As is usual for Starlink software the file name is specified without the sdf file type Also note how the backslash is used to prevent the brackets being interpreted by the Unix shell the use of Starlink applications from the Unix shell is discussed further in SC 4 C shell Cookbook 15 Simply hit return in response to the additional prompts from splot Here spectrum number 90 is being displayed A plot similar to Figure 17 should appear 43 2000 3000 4000 1000 Combined File combined_frames sdf Filter tchifibres 2df sample_data red sdf 3 Directories Selection 5 Files 29jand032red sdf 29jan0033red sdf 2 9jan0034red sdf 2 9jan0035red sdf 29jan0036red sdf 29jan0037red sdf 29jan0038red sdf 2 9jan0039red sdf 29jan0041red sdf Zdf sample_data 2ajan0035red sdf 3 Files to be Combined SC 14 2 net reaxp04 acdscratch fibres 2c net reaxpO4 acdscratchifibres 2c net reaxpO4 acdscratch fibres 2c REMOVE 4000 Figure 16 2dFDR window to combine reduced runs 4500 5000 5500 5009 6500 7000 7500 Wavelength Angstroms Figure 17 2dFDR reduced galaxy spectrum 8000 SC 14 2 44 Acknowledgements Iam grateful to nu
57. rder The word fibre or fiber is spelt differently on opposite sides of the Atlantic Both spellings are common in the literature In this cookbook I have used the British spelling throughout except that I have tried to follow the preferences of authors and editors for the titles of manuals conference proceedings etc 4 Typographic Conventions Technical terms are shown in a bold font like this the first time that they are used Also Anything that is to be typed into a computer program via the keyboard or output from one via the screen is indicated by a typewriter or courier font like this However items appearing in graphical windows such as those used by 2dFDR are shown in a sans serif font like this SC 14 2 Part II Background Material SC 14 2 8 5 Fibre fed Spectrographs Figure shows a very schematic diagram of a traditional astronomical single slit spectrograph Such an instrument is capable of observing only one object at a time Typically a flat opaque plate is placed in the field of view of the telescope perpendicular to the optical axis The star field being observed is imaged on this plate The plate contains a long thin slit and the telescope pointing is adjusted until the object being observed the target object is imaged on the centre of this slit Light from the target object passes through the slit into the spectrograph where it is dispersed almost invariably by a diffractio
58. roscopy such effects include e the instrumental signature small scale variations in the throughput of the instrument optics e throughput losses in the fibres which usually vary between different fibres in the instrument e vignetting the dimming of objects observed towards the edge of the telescope field of view e pixel to pixel sensitivity variations in the CCD detector In fibre spectroscopy it is usually not possible to correct for the sensitivity variations of individual pixels in the detector and the effects of these variations remain as noise in the data Flat field corrections in fibre spectroscopy differ from the corresponding operations in direct imaging or single object spectroscopy In direct imaging with CCDs the flat field correction is made in order to correct for the individual pixel sensitivity variations in the detector Image frames are obtained in which the detector is uniformly illuminated see SC 5 The object frame is then simply divided by the flat field frame Flat field corrections for single object spectroscopy are described in SC 7 Section 4 5 To flat field fibre spectroscopy data the fibres are illuminated with a continuum calibration lamp The flat field spectra are extracted from the two dimensional image and converted to one dimensional spectra in a similar fashion to the target objects The observed spectrum consists of the intrinsic spectrum of the lamp which will be more or less a black body with the i
59. simply an easy to prepare text file see SUN 190 for details Then find the objects in the SuperCOS MOS data file with similar coordinates using CURSA application catpair The output catalogue generated by catpair will include the accurate coordinates determined by SuperCOSMOS 9 Comparison With Other Techniques In addition to fibre spectroscopy there are two other major techniques for obtaining multiple spectra simultaneously objective prism spectroscopy and multi slit spectroscopy This final section briefly compares fibre spectroscopy with these techniques They are discussed separately below SC 14 2 26 91 Objective prism spectroscopy Objective prism spectroscopy is rather different to fibre spectroscopy and is not really a direct alternative A low dispersion prism or a grating is placed in front of the telescope objective and produces low resolution spectra in the focal surface of all the objects in the field of view The technigue has been used for many years mostly in conjunction with Schmidt telescopes Because spectra are produced throughout the field of view which is typically large for Schmidt telescopes the images are usually recorded on photographic plates A good guality low dispersion prism plate obtained with the UKST might typically contain some 60 000 images However it is only possible to produce spectra with relatively low dispersion Objective prism spectra are typically used for classification surveys and searches
60. sky observed Also each fibre is equidistant from all its nearest neighbours which is a desideratum of some aspects of information theory However the representation and analysis of data sampled on a hexagonal grid is more complicated than the rectangular case SC 14 2 6 Note that as mentioned above wide field spectroscopy includes a number of technigues of which fibre spectroscopy is but one although perhaps currently the most important Most of the proceedings carry progress and status reports for the major instruments as they are built and subseguently operated it is possible to see them developing over a number of years In general the more recent proceedings are the most useful In particular Wide Field Spectroscopy and Fiber Optics in Astronomy III include excellent reviews by Parry 40 41 which are strongly recommended The construction and properties of optical fibres are beyond the scope of this cookbook for details see the reviews by Bardenf6 Heacox and Connes 22 and Nelson 36 Of course the major uses of optical fibres are outside astronomy For an accessible introduction to these wider uses see and for the history of the subject see his City of Light 24 If you do read any non astronomical literature about optical fibres you should be aware that various different types are available only some of which are usually used in astronomical instrumentation 3 Lexicography A brief note about lexicography is probably in o
61. st of Figures SC 14 2 Part I Introductory Material SC 14 2 4 1 Introduction Now Argus had a hundred eyes in his head and never went to sleep with more than two at a time so that he kept watch of Io constantly The Age of Fable Thomas Bulfinch 1855 This cookbook is an introduction to and overview of fibre spectroscopy and in particular the techniques and software available for reducing observations made with fibre fed spectrographs It is intended as a starting point for astronomers with such observations to reduce No prior knowledge of fibre spectroscopy is assumed Fibre fed spectrographs or fibre spectrographs for short have become common in recent years and several are available as common user instruments for the UK astronomical community A traditional astronomical spectrograph can observe only a single astronomical object at a given time The essential feature of fibre spectrographs is that they can observe many objects simultaneously typically over a hundred objects for a modern instrument Furthermore the spectra obtained with fibre spectrographs are similar in terms of wavelength range resolution sensitivity and accuracy to those obtained with traditional single object spectrographs Thus fibre spectrographs act as a telescope multiplier a given set of objects can be observed with a fibre spectrograph in much less time than with the equivalent single object spectrograph For example the 2dF fibre s
62. t field frame flat is being used to define the apertures and for the throughput corrections The following messages and prompts appear Set reference apertures for flat Resize apertures for flat yes Edit apertures for flat yes NOADZIRAF F 10 14 Figure 7 Slice through FLAIR tramlines perpendicular to the dispersion direction Reply yes to the prompts or just hit return A plot similar to Figure 7 should appear It shows a slice through the tramlines frame perpendicular to the dispersion direction dofibers has attempted to identify the spectra but it will undoubtedly have made some mistakes which you will need to correct You need to ensure that each genuine spectrum object or sky is correctly identified and no blanked off spectra are identified by mistake You do this by comparing the identifications shown in the plot with the entries in the aperture identification file apid txt and changing the identifications in the plot until they agree with the file The following points might be useful e A plot through the entire set of tramlines will probably be too crowded to read and you will need to expand it into segments and work through them sequentially Figure 7 shows such a segment e The number shown above each spectrum is the fibre number that is the first column in the aperture identification file e Remember that a flat field frame not a target object frame is plotted here Hence do not expect sky fibres to show
63. tandard FIT Flexible Image Transport System format using the Starlink CONVERT package see SUN 55 16 Use application ndf2fits with the proexts propagate extensions option The auxiliary information in the NDF giving details of the individual fibres is appended to the FITS files as a binary table extension This binary table can be accessed using the catalogue and table manipulation package CURSA see SUN 190 17 2dF FITS files can be converted back to the original NDF format using the CONVERT application fits2ndf 2dF data can also be successfully reduced using the IRAF package dofibers see Section 7 4 1 The AAO Web pages include some tips on using dofibers with 2dF data You are likely to need to increase parameter min lenuserarea before using IRAF with 2dF data see Section for details 7 2 WYFFOS AUTOFIB2 The 4 2m William Herschel Telescope WHT has a prime focus corrector and associated atmospheric dispersion compensator with a one degree field of view The WYFFOS AUTOFIB2 system exploits this field of view with up to about 150 fibres WYFFOS and AUTOFIB2 are separate components AUTOFIB2 is an auto fib type robot fibre positioner indeed it is a descendent of the original auto fib mounted at the WHT prime focus WYFFOS WYde Field Fibre Optics Spectrograph is a fibre fed spectrograph It is permanently mounted on one of the Nasmyth platforms and consequently is very stable WYFFOS AUTOFIB2 has been described by Watson 48 and f
64. tematic effects However spectrographs mounted on a Nasmyth platform or the dome floor are usually extremely stable and in these cases fewer arc frames may be adequate Applying the wavelength calibration to the target spectra is often called making the dispersion correction Wavelength calibration is discussed further in SC 7 Section 4 7 In fibre spectroscopy it is usually necessary to perform wavelength calibration prior to sky subtraction 6 7 Sky subtraction Sky subtraction is one of the most critical areas of fibre spectroscopy It is closely related to the correction for scattered light see Section 6 4 and the flat field correction see Section 6 5 for throughput losses in the fibres and vignetting The corrections are more difficult to estimate than in the case of slit spectroscopy However if the appropriate procedures are applied carefully then it is possible to obtain accurate results In a seminal paper Wyse and Gilmore 51 give a detailed and thorough description of the sources of error and discuss how to correct for them The following discussion is largely based on this paper though it is still well worth reading the original Another useful and detailed description is given by Watson et al 49 Consider a spectrum corrected for scattered light flat fielded and wavelength calibrated as described above The resulting spectrum is the sum of the spectra of the astronomical target object and emission from the night sky In order to
65. terms are slightly misleading as the ionising events are as likely to be due to background terrestrial radiation as cosmic rays 11 SC 14 2 bookkeeping aperture definition tramlining extraction scattered light correction flat fielding wavelength calibration e sky subtraction These points are discussed individually below 6 1 Bookkeeping The most obvious addition to traditional spectroscopic techniques required for fibre spectroscopy is the additional bookkeeping needed to keep track of which fibre was targeted on which object and consequently which object each spectrum was obtained from It is important that this information is kept track of carefully otherwise you will become hopelessly confused A collection of spectra of unknown objects however well reduced and calibrated is more or less useless Usually the data reduction software will keep track of the bookkeeping automatically If it does not then you must do it manually yourself 6 2 Aperture definition or tramlining Figure 8 shows a CCD frame obtained with the WYFFOS AUTOFIB2 fibre spectrograph Most fibre spectrographs produce frames of broadly similar appearance The series of horizontal lines are the individual spectra obtained through the various fibres In order to extract each spectrum from the image it is necessary to define its spatial extent or aperture software aperture or in this cookbook footprint on the CCD frame There are really thre
66. tes are required For example for the 2dF they should be accurate to within 0 25 seconds of arc The manual for the instrument that you are using should give the required tolerance You will necessarily know some details about your target objects otherwise you would not be intending to observe them and these details will almost certainly include their celestial coordinates expressed to some level of accuracy If you know the coordinates to the accuracy required by the instrument then you can simply compile a list without further ado This section gives a couple of hints about how you might proceed if you know only approximate coordinates which are insufficiently accurate to position the fibres If your objects are included in one of the general purpose on line object databases such as for Galactic objects or NED for external galaxied then you can use the coordinates that they give for your objects You should be aware however that these databases contain heterogeneous information obtained from a variety of sources and you should ensure that the coordinates given are of sufficient accuracy If you cannot obtain sufficiently accurate coordinates from published sources or general purpose on line databases then it may be possible to use the catalogues and databases compiled by scanning Schmidt survey plates with either the APM or SuperCOSMOS fast microdensitometers in Cambridge and Edinburgh respectively The coordinates in these catalogues and dat
67. the positions along the dispersion axis Fit traced positions for flat interactively yes Fit curve to aperture 2 of flat interactively yes A plot similar to Figure 8 appears For the example data you can simply accept the fit and type q and proceed to the next step However for other data you might want to edit the fit dof ibers then prompts Fit curve to aperture 3 of flat interactively yes Reply NO in upper case so that the trace is applied to all subsequent spectra The next step is to wavelength calibrate the spectra The following messages appear Create response function flatflatapid t ms Extract flat field flat Extract throughput image flat Correct flat field to throughput image Create the normalized response flatflatapid t ms Extract arc reference image arc Determine dispersion solution for arc A plot similar to Figure Plis drawn You may need to adjust the plot limits to make your plot appear similar to Figure 9 use the plot manipulation commands given above You need to identify the lines and enter their wavelengths For the example data the wavelengths are marked on the plot The example data contain unusually few lines of which four are suitable for wavelength calibration Using this small number of lines is conveniently simple for the example However the FLAIR arc lamps usually produce spectra with more lines and it is often desirable to have as many lines as practical in order to improve the calibration FLA
68. tical Astronomy Observatories Tucson See SG 12lop cit 34 for details of obtaining IRAF manuals 45 F Valdes 1992 Guide to the Slit Spectra Reduction Task DOSLIT National Optical Astronomy Obser vatories Tucson See SG 12 op cit 34 for details of obtaining IRAF manuals El 46 G Walker 1987 Astronomical Observations An Optical Perspective Cambridge University Press Cambridge 47 SC 14 2 Bibliography 47 R F Warren Smith 1998 SUN 33 6 NDF Routines for Accessing the Extensible N Dimensional Data Format Starlink 48 F G Watson 1995 in Maddox and Arag n Salamanca op cit BI pp25 32 49 F G Watson A R Offer I J Lewis J A Bailey and K Glazebrook 1998 in Arribas et al op cit PI pp50 59 50 D C Wells E W Greisen and R H Harten 1981 Astron Astrophys Suppl 44 pp363 370 6 51 EG Wyse and G Gilmore 1992 Mon Not R Astron Soc 257 pp1 10
69. tion is discussed further in SC 7 Section 4 6 6 4 Scattered light correction The signal recorded on the CCD detector for each spectrum includes a contribution from light scattered inside the spectrograph Typically this scattered light will comprise a uniform component and a local component The uniform component is as its name implies uniform across the detector and is simply proportional to the total light input into the spectrograph The local component is caused by light scattered from the spectra of bright objects illuminating regions of the detector in the footprints of adjacent spectra For emission from a source external to the instrument either a genuine target object or a sky source such as emission from the terrestrial atmosphere the strength of the recorded signal is simply proportional to the fraction of the light lost in the optical system Important sources of losses are typically the throughput of the fibres and vignetting in the telescope and they are removed by flat fielding see Section 6 5 below However the intensity of the scattered light does not scale in this fashion and therefore it must be identified and treated separately For example in dofibers see Section 7 4 1 it is estimated from the signal recorded in parts of the detector which are outside the footprints of the spectra 6 5 Flat fielding Flat field corrections are made in order to allow for simple multiplicative effects in the data In fibre spect
70. to auto fib and two identical spectrographs each accommodating 200 fibres The whole assembly is mounted on a self contained top end ring which can be removed from the telescope see Figure B The typical time for the robot to position the fibres is about an hour approximately eight seconds per fibre similar to typical exposure times In order to avoid wasting observing time two complete sets of fibres are provided attached to a rotating tumbler mechanism One set is configured whilst the other is being used to observe When the observation finishes the tumbler rotates to bring the newly configured set of fibres into the optical path ready for the next observation The 2dF has been described by Cannon 1O and a user guide is available 3 Further information can be found on the Anglo Australian Observatory AAO s Web pages at URL http www aao gov au 2df including a hypertext version of the manual and a postscript version which can be downloaded and printed 7 1 1 Software A comprehensive suite of software 2dFDR has been developed specifically for reducing 2dF data It was mostly written by Jeremy Bailey of the AAO It includes the following facilities bias and dark subtraction tram line mapping of the spectra from individual fibres on the CCD and their extraction arc identification wavelength calibration fibre throughput calibration and sky subtraction The 2dF data reduction software is comprehensively documented in the 2dF
71. urther information is available on the Instituto de Astrofisica de Canarias Web pages at URL http www ing iac es including a hypertext user manual 7 21 Software WYFFOS AUTOFIB2 data are reduced using wyf_red a special purpose IRAF script written by Jim Lewis This script uses the IRAF application dof ibers see Section 7 4 1 below and other IRAF applications Unlike the basic dofibers it will automatically perform the routine CCD processing bad pixel removal flat fielding debaising etc wyf_red will also handle wavelength calibration and sky subtraction A comprehensive manual for wyf_red the WYFFOS Data Reduction Manual 29 is available Copies of the software and manual can be downloaded from the WYFFOS AUTOFIB2 section of the IAC Web pages WYFFOS AUTOFIB2 data are exported as FITS files Prior to using wyf_red they must be converted to the IRAF format using the IRAF command rfits Note however that the IRAF parameter min_lenuserarea must be increased in order to accommodate WYFFOS headers This change must be made before running rfits to import the files See Section 7 4 3 below and the Getting Started section of the wyf_red manual for details The original FITS format was proposed by Wells et al 50 in 1981 However it has been developed and enhanced over the years The FITS standard is now maintained and documented by the FITS Support Office of the Astrophysics Data Facility at the NASA Goddard Space Flight Cente
72. ve been given by Barden 6 Heacox and Connes 22 and Nelson 36 Clearly the positions of the fibres which must be such that light from the target objects falls on them are unique to each field and the fibres must be moved to different positions when the telescope views a new field Indeed positioning the fibres with sufficient accuracy is the greatest technical problem of fibre spectroscopy Broadly three different types of system have been used to position fibres plug plate systems auto fib type systems and MX type systems Auto fib and MX were early fibre spectrographs In a plug plate system an opaque plate is placed in the focal surface of the telescope with holes drilled in the plate at the positions of the target objects and fibres attached to the holes Clearly a separate plug plate must SC 14 2 10 be prepared in advance for each field viewed In an MX type system each fibre is held at the tip of an arm and positioned independently each arm being controlled by a two axis actuator The arms are arranged around the circumference of the field of view in a fishermen round the pond arrangement In autofib type systems an opague plate usually steel lies in the focal surface of the telescope The fibres lie flat along the illuminated side of the plate with a small prism at their head to direct light incident on the fibre head along the fibre A magnetic button holds the fibre head in place A single robot picks up the fibre heads
73. ved in QSO spectra see Bowen et al 9 13 SC 14 2 typically a dozen or so the spectrum in the figure is actually rather narrower being about half a dozen pixels wide The main information which must be determined is the width of the spectrum in pixels However for more sophisticated methods of extracting the spectrum from the frame the shape or profile of the spectrum across the slice may also be important SC 14 2 14 2500 a 9 pow on X a 9 9 a Q oO 760 765 779 775 780 785 PIXEL Figure 4 A slice across a spectrum The plot shows a row of about twenty eight pixels centred on the spectrum and aligned perpendicular to the dispersion direction The description up to this point is egually applicable to extracting either multiple spectra from fibre spectrograph data or an individual spectrum from single slit spectrograph data Indeed there is a good description of the latter in SC 7 Sections 4 3land 4 4 which is mostly applicable to the fibre spectroscopy case However the essential difference for fibre spectroscopy data is that instead of a single spectrum to be extracted there is a whole set of more or less parallel spectra to be extracted recall Figure Defining the footprints of the set of spectra on the CCD frame is called tramlining because of the resemblance of the spectra to a set of tramlines In principle the tramlining could be carried out on the object frame However it is bette
74. y observable is known as the multiplex advantage or multiplex gain though it is simply the approximate number of fibres The multiplex advantage or number of fibres is not the sole criterion for assessing the usefulness of a fibre spectrograph Clearly a fibre fed system can only be used to its full advantage if there are sufficient objects of interest in a single field of view to occupy all the available fibres This requirement in turn leads to telescope designs with wide fields of view Another consideration is the proximity with which fibres can be positioned in the focal plane In addition there are the usual criteria for a spectrograph wavelength range resolution stability sensitivity etc The optical fibres are acting as light pipes they simply conduct light emitted by the target objects from the focal plane to the spectrograph entrance slit and emit it effectively unchanged However inevitably there is some loss and degradation of the signal In particular fibres output a beam with a smaller focal ratio than the input beam that is one which is faster This phenomenon is known as focal ratio degradation FRD The effects of FRD can be minimised by careful design of the optical system Similarly various types of fibres are available which operate over a range of wavelengths from the near ultraviolet to the near infra red The construction and properties of fibres are beyond the scope of this cookbook but useful reviews ha

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