GIRAFFE data reduction cookbook
Contents
1. Log Messages Figure 10 Master BIAS reduction limari static 71 dfits fits fitsort pro catg FILE PRO CATG grating HR316 tfits GRATING DATA grating LR600 tfits GRATING DATA line catalog ThAr tfits LINE CATALOG slit geometry medusal tfits SLIT GEOMETRY MASTER Finally before we start keep in mind that ESO pipelines are in general QC oriented pipelines This means that the quality of your data reduction can be assessed by looking at the QC KW added to the image header by the pipeline 3 4 1 gimasterbias Select all BIAS FRAMES and pass them to the recipe gimasterbias as shown in the left panel of Fig 10 A new window appears right panel of Fig 10 where all parameters related to the recipe gimasterbias can be controlled For a full description of the parameters of each recipe please refer to the pipeline manual In this new window change the directory where the pipeline products are going to be placed and and add it to the gasgano list A similar window exist for all recipes There you have full control of the recipe parameters You can also change the input list and the output The log sub window at the bottom of the main window allows you to follow what is going on A copy of the log messages is dumped on the disk When you are happy with the parameters hit Execute The products master_bias_0000 fits and bad_pixel_map_000 fits now appear automatically in gasgago a2. GIRAFFE ESO calib giraf calib 1 0b cal slit geometry medusa1 H5 99 3 09 tfits group RAW level 2 INTERMEDIATE type 2 IMAGE tag ERROR 05 05 24 ERROR No dispersion solution present in frame set Aborting Completion status FAILURE Execution error Execution failed with code 1 Figure 8 In the log sub window of giscience we clearly see the reason for failure In the example shown here the file containing the dispersion solution is missing GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 17 home2 GIRAFFE ESO calib giraf calib 1 0b cal GI_PLOC_Medusa1_H599 3_09 fits group CALIB level INTERMEDIATE type IMAGE tag FF_LOCCENTROID home2 GIRAFFE ES0 calib giraf calib 1 0b cal GI_PLOW_Medusa1_H599 3_09 fits group CALIB level INTERMEDIATE type IMAGE tag FF_LOCWIDTH home2 GIRAFFE ESO calib giraf calib 1 0b cal grating_HR316 tfits group RAW level INTERMEDIATE type IMAGE tag GRATING_DATA home2 GIRAFFE ES0 calib giraf calib 1 0b cal slit_geometry_medusal_H599 3_09 tfits group RAW level INTERMEDIATE type IMAGE tag SLIT_GEOMETRY_SETUP 05 16 12 INFO No bad pixel map present in frame set 05 16 12 INFO No master bias present in frame set 05 16 12 INFO No scattered light model present in frame set ERROR 05 16 13 ERROR Missing master bias frame Selected bias removal method requires a master bias frame Completion status FAILURE Execution error Execution failed with code 1 Select the missing f
3. For this we use the command dtfits not dfits as above So the column INDEX corresponds to the aperture seen in the image Thus in the example above we were looking at the star ngc6253 mem4636 The column RP gives the GIRAFFE fibers allocated to the object Therefore ngc6253_mem4636 was allocated to fiber 18 20 VLT MAN ESO 13700 4034 GIRAFFE data reduction cookbook 699 847 978 LEG 9er 885 0 ST ST G i ER 9T 91 4899 cS8 S 4 pS 8T8IS ves cs 969 vac 9 0v3 81L vSC vVTTOTV 6 E9 ZS VEL vac T8929 8419 28 604 vS8C 18 94 cees cSa v4 vSC 3089 99 c8 10 ACNLINOVW 290 10 Kei 10 LNATYO S96TT 9 Z 9vtc9S 6vv pue eac9oSu SZPPOEO 9TVEOT OLEL 3nopueo esz923u 9 64400 T 6 Svc6 9g9pyueu ESZ9IBU G Z06Sv 0 T1T1480T G6EL 3nopue esz923U y 9924vC Ol ZvTYEST 4644 3nopueo esz9oSu e g01198 0 06Sv411 8044 3nopueo ESZ9IBU Z 10 10 WISTVO T VISHL U Lf 80 A TOW Td vT 2 IT 8 TON Td 9T 9 IT 6 TOW Td 8T S IT OT TOW Td OC IT TT TOW Td Z le IT GT TON Tdl vz Z IT luorqezqrTeO 1 T I dd xo35ez3eMu PI SUUnTo jo 1equny NOISNALX I n S311 0000 132edsuqi eoueros IZ 19 IS Ip le I IT D 19 IS lv IZ IT suorsu qax SE du NSSd NSS SdA X HUNT zou Sarj 0000 ei32edsuqi eoueros SITIIP 9e poonper ger doupyeT GIRAFFE
4. 2 RIA te e x vo o eo S gt gt E A 2 d DA Moin w 8 o Jo r A m a 55 lt x 9 A we m L Y Qv ey gt Ke e P ut e b P Ce Ae Met 3 E Ore O gt BI mS m d au di K 2 o gt e ks 079 550837 Sus Rip ansehen te SE G Marconi MP a gt oe x 2 ter She ge een gt Zaggy0_1 Zaggy0_2 Zaggy0_3 f Ag E pte sf e hand DB829 2 e 0 antc arn ES Figure 1 An example of the potentiality of multi fiber spectrographs In one shot up to 135 spectra are recorded by GIRAFFE and up 8 by UVES The figure a finding chart of a typical FLAMES observation Circles indicate science targets Sky positions are marked with crosses and the four FACBs used for centering the field are seen as squares GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 4 2 2 correcting frames for detector cosmetic effects determining the location of your data on the detector i e fiber tracing extraction of flat field spectrum and determination fiber transmission scattered light correction wavelength calibration extraction of science data sky subtraction Correcting detector cosmetic effects Data reduction of any nature starts by correcting the detector defects referred as cosmetics These effects and the way to correct them have largely described in different cookbooks Here we briefly described the main defects Subtracting the Bias level A bias voltage is routinely applied to CC
5. data reduction cookbook VLT MAN ESO 13700 4034 15 giscience v10000 AAA AS Noe E ae giraffe biasremoval fraction EE GI MBIA fits slit geometry medusa1 H599 3 _09 tfits emekmeo row Preis Figure 7 Pop up panel controlling the parameters and the arguments of girscience GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 16 k agiscience v10000 File Help iraffe biasremoval remove g Add to pool giraffe biasremoval method giraffe biasremoval areas JL giraffe biasremoval sigma giraffe biasremoval iterations giraffe biasremoval fraction Request Pool Filename Classification GIRAF 2005 07 01T00 28 08 811 fits play GI_MBIA fits Locate Display GI_PLOC_Medusal_H599 3_09 fits play GI_PLOW_Medusal_H599 3_09 fits Locate play grating HR3 16 tfits gt locate Display slit geometry medusa1 H5 99 3 oa us Execute Selected o Filename Classification home2 GIRAFFE ESO calib giraf calib 1 0b cal GI PLOC Medusal H5 99 3 09 fits group CALIB level INTERMEDIATE type IMAGE tag FF_U amp home2 GIRAFFE ESO calib giraf calib 1 0b cal Gl_PLOW_Medusal_H599 3_09 fits groups CALIB level 2 INTERMEDIATE type 2 IMAGE tag FF_ home2 GIRAFFE ESO calib giraf calib 1 0b cal grating HR3 16 tfits group RAW level 2 INTERMEDIATE type 2 IMAGE tag GRATING DATA jhome2
6. data reduction cookbook VLT MAN ESO 13700 4034 21 3 4 Case 2 Making your own calibration database If you are only interested in a quick look of your data you can probably use the database delivered with the GIRAFFE KIT However for any other scientific application you must use your most recent calibrations The position of the spectra on the CCD is a function of the ambient conditions temperature and pressure It also depends on the reproducibility of the grating which moves according to the set up chosen Thus the use of fresh calibrations ensures that the pipeline will extract your data on the right place In addition a better wavelength calibration is achieved since little shifts below 1 pixel level are expected to take place within the time gap between your science frame and your calibration probably a few hours and no more than 1 day Also your slit geometry determination is updated Even in the case we want to rebuild your calibration database a few static files are still needed Thus the best way to organize these static files is to create a directory called static to place these files In the example the data is organized as follow limari DATA 78 gt ls 1 raw reduced static e The raw data For each raw science frame a set of 5 biases 3 flat fields and 1 arc frame are produced as part of the FLAMES GIRAFFE calibration plan In the case of ARGUS and IFU a flux standard is also provided For ARGUS flat fields a nasm
7. fits MASTER BIAS FLAMES giraf cal bias 5 Users cmelo GIR COOKBOOK DATA raw CIRAF 2005 07 01T15 00 37 382 fits FLAMES GIRAF BIAS182 0001 fits UNCLASSIFIED Ee Extension HEADER ER Find in header Il C find Load Filter O Filter C Auto Display Output Frames Keyword Value SIMPLE I Filename BITPIX 16 0 master_bias_0000 fits MASTER yaxis 2 bad_pixel_map_0000 fits BAD PIXI NAXIS1 2148 NAXIS2 4096 EXTEND T PCOUNT 0 GCOUNT 1 Log Messages BZERO 32768 0 d bcs BSCALE 1 0 ORIGIN ESO DATE 2005 07 01T15 00 37 537 23 42 40 INFO Processing product frame master bias TELESCOP ESO VLT U2 Product frames INSTRUME GIRAFFE Users cmelo master_bias_0000 fits OBJECT BIAS Users cmelo bad_pixel_map_0000 fits EXPTIME 0 0605 Completion status SUCCESS MJD OBS 53552 62543266 C DATE OBS 2005 07 01T15 00 37 382 g gt E pa fS B x AT Figure 15 Apercu of the next release of the GIRAFFE pipeline running on a Mac OS machine A Preparing your sof file a first example Here a very basic example how you can automatize your data reduction using EsoRex We start with a generic sof The idea is to replace automatically the word _FILE_ by the real name of the raw science frame we want to reduce Let us call this generic sof file sample sof limari reduced 12 cat sample sof _FILE_ SCIENCE bad_pixel_map_0000 fits master_b
8. igesa dara adea piara cr anak 2 2 Correcting detector cosmetic effects w s s s s W a QW a e SU a 8 U Q S 220 Fiber localization and tracing ocre eae os XC ex c9 EN BS 2 4 Extraction flat field spectra and fiber transmission 2 0 Scattered light correction 5 2 44 44 ow Roo o ko HH ARA 2b Wavelength calibration lt c e s Lond o RR e nomm A 2 7 Extraction of the science 2242222299 a a S Q q W Q 2A OKY oco ono aa aaa A be ee e Ee p A 3 Pipeline in action Gasgano the friendly way al Belore VU ceca er a A A pee SIME PS o se sos saroia soe arar EESE BR 3 3 Case 1 your calibration data is up to date ccr 3 4 Case 2 Making your own calibration database 00 4 3 4 1 3 4 2 3 4 3 3 4 4 ma III IE a III MIWAVECQIIGTALION eec deco m de 9 eo eed AR AA a ck A Eee Oe ek k oe ee Mus 0 e Mus S Wa Wa 4 Pipeline in action scripting your data reduction with ESOrex A Preparing your sof file a first example B Note for Mac users k o cO na A NN 10 10 11 11 11 11 21 22 22 24 24 27 30 31 GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 1 Introduction 1 1 Purpose 1 2 Reference documents 1 3 Abbreviations and acronyms The following abbreviations and acronyms are used in this document SciOp Science Operations ESO European Southern Observatory Dec Declination eclipse ESO C Library Image Proces
9. monitoring Extension HEADER NAXIS2 4096 PCOUNT lo GCOUNT 1 EXTEND T BSCALE 1 BZERO o TELESCOP IESO VLT U2 INSTRUME GIRAFFE OBJECT BIAS MIN ABS 53552 A2542266 Figure 11 Gasgano automatically updates the list of files The reduced files created by gimasterbias are seen in the gasgano file list GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 24 GRATING_DATA here also you have to chose the right one in our example the data have been taken with the HR grating It s likely that you have to adjust the number of fibers to be found By default the recipe tries to find 136 but in practice we fit 135 on the chip and in addition there are always broken fibers In Fig 12 we see that the recipe failed because only 133 were found instead of 136 Fixing giraffe fibers nspectra in the Parameter sub window gimasterflat runs fine and pro duces a number of tables which are necessary to the extraction of the ThAr and the science spectra The FF spectra for each fiber is already extracted although still in the pixel space Fig 13 giraffe fibers nspectra should be used with care since it selects the nfibers from the left to right Consider the following example In the middle of the night a fiber just broken and had to be disabled In this case even though we can tell the pipeline to look for nfibers 1 accounting for the br
10. the quality of the scattered light correction and the final sky subtraction using the inter fiber regions and the broken fibers 3 Pipeline in action Gasgano the friendly way 3 1 Before you start In order to follow this cookbook you need e to have the GIRAF kit installed on your computer e to have downloaded the demo data from http www eso org instruments flames doc e to have the demo data organized in your disk under the following structure is it really important 3 2 Starting gasgano start gasgano by typing in command line shell 184dhcp125 GIR COOKBOOK 38 gt gasgano amp Add the directory containing your raw data the place where the reduced data will be placed and the giraffe calibration database delivered with the GIRAFFE kit to the list of gasgano directories by clicking on FILE and then ADD 3 3 Case 1 your calibration data is up to date In this case only the recipe called giscience is needed giscience does the final extraction of your science data using an existing calibration database As input for giscince you need your raw science along a number of calibration products page 49 Sec 9 4 1 of the GIRAFFE pipeline user manual These files are created at the moment you reduce your calibration from scratch see Sec 3 4 1 your science raw frame 2 MASTER_BIAS Two dimensional master bias frame produced by the recipe gibias it can be downloaded at http www eso org projects dfs dfs shared web vl
11. 12 1og Sun Apr 30 05 16 31 CLT 2006 GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 ba GASGANO Version 2 2 3 cmelo Linux File Selected files Tools Help amp ea CC Displaying 1023 files Unfiltered 9 Bd 075 C 0245 D GIRAFFE UNKNOWN 9 200150097 u2 9 INS SLIT NAME Medusal INS EXP MODE H599 fi GIRAF 2005 07 01T00 28 08 811 fits 9 id 60 4 9022 GIRAFFE FLAMES Operation Team 9 200117229 Calibration fi GIRAF 2005 07 01T15 00 37 382 fits fi GIRAF 2005 07 01T15 01 24 886 fits El cirar 2005 07 01T15 02 12 420 fits El cirar 2005 07 01T15 03 02 844 fits SCIEN El cirar 2005 07 01T15 03 50 308 fits B cl_BPix fits Gi ci MBlA fits e INS SLIT NAME Argus INS EXP MODE H412 4 GI INS SLIT NAME Argus INS EXP MODE H429 7 e INS SLIT NAME Argus INS EXP MODE H447 14 e zl INS SLIT NAME Arqus INS EXP MODE H447 1E Siess CLASSIFICATIO TPL ID ORIGFILE TPL EXPNO TPL NEXP 2 gimasterbias To Recipe Request Pool gimasterflat Report Move Copy Tar BAD PIXEL MAP FLAMES giraf MASTER_BIAS FLAMES giraf Figure 6 Passing a raw science frame to the recipe girscience using gasgano Files are first selected by holding CTRL key and clicking on the calibration and science files Then with the right button they are sent the a given recipe In the example below the input files are sent to the recipe giscience GIRAFFE
12. D detectors to ensure that as near as possible they are operating in a linear manner This current has the effect that a non zero count is recorded in all pixels Subtracting the dark current Dark current arises from thermal energy within the silicon lattice comprising the CCD Electrons are created over time that are independent of the light falling on the detector These electrons are captured by the CCD s potential wells and counted as signal Bad pixel correction Any detector has a certain number of pixels that are bad in the sense that these bad pixels record the information inaccurately This happens because either they are brighter than the others hot pixels or because they have low or no sensitivity at all dead pixels Bad pixels or bad columns are fixed by interpolating the signal in the neighbor pixels or columns Cosmic ray hits When a high energy particle hits the CCD it loses its energy by knocking the atoms constituting the chip itself That liberates many electrons that cause a bright spot on the image These high energy particle can either be genuine cosmic rays exotic particle produced by exploding supernovae black holes etc or just the product of the decay of some radioactive atoms present in the lenses just above the CCD Correction of pixel to pixel variations Pixels in a CCD have all different sensitiv ities This means that some of them will convert the light photons more efficiently into electrons than
13. EUROPEAN SOUTHERN OBSERVATORY ES Organisation Europ ene pour des Recherches Astronomiques dans l H misph re Austral O Europ ische Organisation f r astronomische Forschung in der s dlichen Hemisphare ESO European Southern Observatory Karl Schwarzschild Str 2 D 85748 Garching bei Miinchen Very Large Telescope Paranal Science Operations GIRAFFE data reduction cookbook Doc No VLT MAN ESO 13700 4034 Issue 79 0 Date 26 08 2006 C Melo Prepared EFT Date Signature G Marconi unns c Cs pa pes ee ea ee oe ee ees Date Signature 0 Hainaut Released 2 0 ok oe os sedo nde eS ER aa ne 54848 VERSE u Date Signature GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 This page was intentionally left blank GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 111 Change Record Issue Rev Date Section Parag affected Reason Initiation Documents Remarks 79 First version published GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 This page was intentionally left blank lv GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 Contents 1 Introduction LU TRIOS La ich Sos CR Oe A ERA OE WEE ee A 12 Reference documents 1 3 Abbreviations and acronyms o 9o REM EE EMG Eo la Stylistic OD VOD uou xd s w iaa e CER EE E Reo s 2 A brief overview of data reduction of multi fiber spectroscopy data 21 Mul BberspectroSCODY lt sc
14. Pixel R1 1 R212 Divide Std 2501 1000 3 500 3 03 O T T 645 650 655 660 665 670 675 680 1 Y 644 2 680 195 7200 x 184 functions re a 89 proce A 126 pgpl gistered DPUSER gt 8 256 256 DPUSER gt fits Users cmelo cookbook template science cube spectra 0000 fits O DPUSER gt r dfits Users cmelo cookbook template science cube spectra 0000 fits Y DPUSER gt Enter DPUSER commands a 000 amp QFitsView by Thomas Ott bufferl Users cmelo cookbook template science cube spectra 0000 fits e Son am ol o 9049 2716 Linemap x ae A 2200 A minmax linear jo I s x 42 966 872 i Minimum 0 Maximum 100 V Auto Scale Single Pixel 2 Divide Std 657 4 657 6 657 8 658 658 2 2609 657 242 658 392 2839 x 184 functions DPUSER gt fits 256 256 D DPUSER gt rl readfits Users cmelo cookbook_template science_cube_spectra_0000 fits DPUSER gt butter readfits Users cmelo cookbook template science cube spectra 0000 fits M DPUSER Enter DPUSER commands pm 89 procedures T 126 pgplot procedures registered rl Figure 14 Argus cube of an emission line object produced by the pipeline and visualized by QFitsView The upper panel show the flat image i e the whole wavelength range is considered Nothing is really seen with respect to the background In the lower panel one the c
15. RAFFE pipeline is given Like any other reduction package the GIRAFFE pipeline has many adjustable parameter allowing to fine tune the data reduction We refer to the user manual to a full description of these parameters 2 1 Multi fiber spectroscopy If you have already had a look at one of your raw science frames the advantage of using a multi fiber spectrograph is clear In one single shot hundreds of objects can be observed Fibers can be placed at almost any place within the telescope focal plane within 25arcmin in the case of FLAMES as shown in Fig 1 This multiplex capability has of course a cost Due to the limited size of the detectors only a small piece of the spectrum is recorded for each target Also the fibers most commonly used in astronomy have poor transmission in the blue region of spectrum There are number of multi fiber spectrographs around the world The main characteristics of some of them are given in Table 1 In the case of FLAMES the fibers are arranged in a circular pattern around a plate of the size of the telescope focal plane The fiber end looking into the sky has a magnetic button on it The magnetic side of this button sticks to the plate whereas the other side is open to leave the light of your target to get into the button All this is shown in Figure 1 In the case of FLAMES the light that enters into the button is deviated into the fibers by a tiny prism The other end of these fibers are arranged along
16. achieve an accurate sky subtraction 2 6 Wavelength calibration If you look at your spectrum after extraction you might already recognize a few features on it Hydrogen lines Li in the case of young stars etc But having that in pixel space is pretty much useless This is what the wavelength calibration lamp does Wavelength calibration is achieved using a Hallow Cathode Lamp An HCL usually consists of a glass tube containing a cathode made of the material of interest an anode and a buffer gas usually a noble gas A large voltage across the anode and cathode will cause the buffer gas to ionize creating a plasma These ions will then be accelerated into the cathode sputtering off atoms from the cathode These atoms will in turn be excited by collisions with other atoms particles in the plasma As these excited atoms decay to lower states they will emit photons which can then be detected and a spectrum can be determined The wavelengths of the emission line spectra of these lamps are known from laboratory tests From our ThAr frame we measure the x y position on the CCD for the emission lines From an atlas of emission lines we can associate a pixel to a wavelength By means of a polynomial fit we can compute the transformation function from pixel to wavelength space f x y 2 7 Extraction of the science The science data is extracted in the same fashion as described above for the flat field After extraction the scattere
17. ch is the standard deviation of the resampled fluxes for each wavelength bin In the case of 3D spectroscopic observations with IFU or Argus a data cube containing the spatial information for each wavelength bin is generated An error cube is also generated as shown below rw r r 1 cmelo astro 6711 May 8 08 33 giscience 2007 05 05 17 09 52 Log IW r r 1 cmelo astro 5166720 May 8 08 34 science_exterrors_0000 fits IW r r 1 cmelo astro 5166720 May 8 08 34 science extpixels 0000 fits rw r r 1 cmelo astro 5166720 May 8 08 34 science exttraces 0000 fits rw r r 1 cmelo astro 9524160 May 8 08 34 science rbnspectra 0000 fits rw r r 1 cmelo astro 34560 May 8 08 34 science rcspectra 0000 fits rw r r 1 cmelo astro 34560 May 8 08 34 science rcerrors 0000 fits rw r r 1 cmelo astro 9524160 May 8 08 34 science rbnerrors 0000 fits rw r r 1 cmelo astro 33583680 May 8 08 34 science reduced 0000 fits rw r r 1 cmelo astro 5166720 May 8 08 34 science_extspectra_0000 fits rw r r 1 cmelo astro 8939520 May 8 08 34 science cube spectra 0000 fits rw r r 1 cmelo astro 8939520 May 8 08 34 science cube errors 0000 fits At the moment there is no dedicated tool for GIRAFFE data cubes A nice one which was developed for SINFONI is QfitsView written by Thomas Ott It is easy to install and has many nice functionalities to analyze your data There is a caveat though The world coordi nate system of the GIRAFFE cubes
18. d light is removed the science spectrum on each fiber is divided by its respective flat field spectrum correct for the fiber transmission variants and the keywords containing the information about the wavelength calibration are added to the fits header of the image Since the description of these keywords vary from package to package in most of the cases a process called rebin is carried out in which we resample our spectra in order to have a constant step in wavelength A cte The keywords used describing an evenly sampled spectrum obey the FITS standards and therefore is the same regardless the data reduction package you are using Also rebinned spectra can be easily read as a vector by your own programs written in FORTRAN C python etc Your spectra are ready to be analyzed 2 8 Sky subtraction In the case you are dealing with very faint source whose signal is close to the read out noise of the CCD you might want to carry out sky subtraction With some care sky subtraction as good as 1 can achieved This requires e proper bias and dark correction 3NOAO provides Spectral Atlases for different lamps at http www noao edu kpno specatlas index html GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 11 e scattered light correction e fiber to fiber transmission We refer to Wyse amp Gilmore 1992 MNRAS 257 1 for a very good discussion in the problem atic of achieving accurate sky subtraction and how to assess
19. direction The direction perpendicular to the dispersion is called cross dispersion direction or spatial direction in slit spectroscopy These directions are also indicate in Fig 2 Thus the first task in the data reduction process after cleaning the detector defects is to know where the spectra of each fiber actually are on your 2 dimensional CCD This processes is called fiber localization First a exposure with all fibers uniformly illuminated by a calibration lamp is taken This same exposure will be used to flat field the data latter Then a line is cut along the cross dispersion direction In the top panel of Fig 2 we see a series peaks more or less evenly spaced Each of these peaks corresponds to a fiber In many pipelines the fiber profiles is approximated by a gaussian function The pipeline fit each of those peaks with a guassian function and stores for each fiber its center and width In both panels of Fig 2 we can easily distinguish three packets of fibers with a larger gap GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 6 in between Each packet represents a GIRAFFE sub slit We might also find a gap within a given packet This happens when a fiber is broken In the bottom of Fig 2 we show an extract of a raw image of a flat fiel exposure Three packets of fibers are seen In the second one there is a missing broken fiber In order to deal with broken fibers the pipeline uses the fact that the size of the fiber
20. e image can vary according to the number of allocated fibers In the example pyraf Iraf module to python is used but any other data manipulation package can be used IRAF IDL Midas fitsio inside C or Fortran programs etc For those using pyraf iraf load onedspec and then change the dispersion axis PyRAF 1 1 20030ct17 Copyright c 2002 AURA Python 2 3 3 Copyright c 2001 2002 2003 Python Software Foundation Python CL command line wrapper help describes executive commands gt onedspec onedspec aidpars dopcor reidentify sensfunc specplot autoidentify fitprofs rspectext setairmass specshift bplot identify sapertures setjd splot calibrate lcalib sarith sfit standard continuum mkspec sbands sflip telluric deredden names scombine sinterp wspectext dispcor ndprep scoords skytweak disptrans refspectra scopy slist gt iraf onedspec dispaxis 2 then plot gt splot science_rbnspectra_0000 fits In the first fiber we see the ThAr spectra of the simultaneous calibration fiber of GIRAFFE Moving to the other apertures in the image we recognize a stellar spectrum in aperture 5 as GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 19 magraphicsl lt 2 gt 7777777777 Be Hle Edit Page Window Help per Figure 9 Stellar spectrum of a member of NGC6253 in aperture 5 shown in Figure 9 But to which target am I looking at The answer is found looking into the binary table
21. eady you simply call EsoRex as shown below limari reduced 63 esorex giscience giscience sof The log with the processing in flushed to the screen and also dumped into a log file 17 21 19 INFO giraffe rebin spectra Wavelength range Setup 17 21 35 INFO move products Created product home2 GIR COOKBOOK DATA reduced out 0000 fits 17 21 35 INFO move products Created product home2 GIR COOKBOOK DATA reduced out 0001 fits 17 21 35 INFO move products Created product home2 GIR COOKBOOK DATA reduced out 0002 fits 17 21 35 INFO move products Created product home2 GIR COOKBOOK DATA reduced out_0003 fits 17 21 35 INFO move_products Created product home2 GIR COOKBOOK DATA reduced out_0004 fits 17 21 35 INFO move products Created product home2 GIR COOKBOOK DATA reduced out_0005 fits 17 21 35 INFO move products Created product home2 GIR COOKBOOK DATA reduced out 0006 fits 17 21 35 INFO move products 7 products created Please consult the EsoRex manual GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 30 org eso gasgano Gasgano OE EJ Hom QD lt lt Charged EE Tuel0 22AM 3 d ooo gimasterbias v20202 y File Help Em es fanal Qui eoe GASGANO Version 2 2 7 cmelo Mac OS X File Selected files Tools Help Parameters Name va de Default grouping FS Cexpand Find entry DI 0 giraffe stacking method giraf
22. fe stacking ksigma low File CLASSIFICATION TPLID ORIGFILE TPL EXPNO TPL NEXP giraffe stacking ksigma high Y 98 200117229 Calibration giraffe stacking minmax minimum E GIRAF 2005 07 01T14 16 54 585 fits UNCLASSIFIED FLAMES_giraf_cal_flat FLAMES GIRA 1 3 giraffe stacking minmax maximum E GIRAF 2005 07 01T14 18 34 303 fits UNCLASSIFIED FLAMES_giraf_cal_flat FLAMES_GIRA 2 3 Input Frames 1 E GIRAF 2005 07 01T14 20 12 871 fits UNCLASSIFIED FLAMES giraf cal flat FLAMES GIRA 3 3 Include Filename Hi GiRAF 2005 07 01T14 22 34 861 fits UNCLASSIFIED FLAMES giraf_cal_wave FLAMES_GIRA 1 s GIAF 2005 07 01T15 00 37 382 fits E GIRAF 2005 07 01T15 00 37 382 fits UNCLASSIFIED FLAMES giraf cal_bias FLAMES GIRA 1 5 M GIRAF 2005 07 01T15 01 24 886 fits E GiRAF 2005 07 01T15 01 24 886 fits UNCLASSIFIED FLAMES giraf cal bias FLAMES GIRA 2 5 M GIRAF 2005 07 01T15 02 12 420 fits El GiRAF 2005 07 01T15 02 12 420 fits UNCLASSIFIED FLAMES giraf_cal_bias FLAMES GIRA 3 5 M GIRAF 2005 07 01T15 03 02 844 fits El GIRAF 2005 07 01T15 03 02 844 fits UNCLASSIFIED FLAMES giraf_cal_bias FLAMES GIRA 4 5 GIRAF 2005 07 01T15 03 50 308 fits E GIRAF 2005 07 01T15 03 50 308 fits UNCLASSIFIED FLAMES giraf cal bias FLAMES GIRA 5 5 i U bad pixel map fits BAD PIXEL MAP FLAMES giraf cal bias 5 Product Naming E bad pixel map 0000 fits BAD PIXEL MAP FLAMES grat cal bias 5 Product Root Directory Users cmelo B master bias
23. fication Log Messages 16 56 06 INFO Using raw spectra for localization 16 56 06 INFO Generating mask 136 spectra expected 16 56 13 WARNING Invalid number of spectra detected 133 136 ERROR 16 56 13 ERROR Spectrum localization computation failed ERROR 16 56 13 ERROR Spectrum localization failed Aborting Completion status FAILURE Execution error Execution failed with code 1 Figure 12 Recipe gimasterflat in action The recipe crashed due to the fact that the specified number of fibers was not found by the pipeline see Log Message window in the bottom of the panel GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 26 graphics File Edit Page Window Figure 13 Extract flat field spectrum for one the fibers Spectrum was produced by gimasterflat and will be wavelength calibrated by the next step carried out by giwavecalibration GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 27 giscience adds up the signal inside the PSF fitted by gimasterflat Optimum weighted extraction will be implemented in the next release giscience also flat field the data and corrects for the fiber to fiber transmission difference using the information produced by gimasterflat Flat field and transmission corrections can be controlled by the input parameters defined by the user Please refer to the user manual for more details giscience produces also an error spectrum whi
24. follow the Euro3D recommendations whereas QfitsView doesn t Therefore in order to make QfitsView to be able to read the wavelength calibration of the GIRAFFE pipeline you have to add a keyword called CDELT3 its value should be the same as the keyword CD3 3 already present in the fits header of the cube If you use IRAF or PyRAF you can do hedit science cube spectra 0000 fits CDELT3 CD3 3 add update add science cube spectra 0000 fits CDELT3 0 005 update science cube spectra 0000 fits yes Science cube spectra 0000 fits updated Now science cube spectra OO00fits can read by QFitsView as shown in Fig 14 4 Pipeline in action scripting your data reduction with ESOrex Using gasgano as pipeline GUI is a powerful way to get a feeling of how the GIRAFFE pipeline works It allows you to get quickly familiarized with the input files and tables optional and mandatory Most important it gives you the opportunity to play with the different parameters and check how they impact in your data product in real time GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 28 ane QFitsView by Thomas Ott buffer1 Users cmelo cookbook_template science_cube_spectra_0000 fits o ae S lole 1G 2 0 79 49 3525 Single x lt amp A 2200 YQ minmax linear k i x 7 439 1692 Eu Minimum 0 Maximum 100 Y Auto Scale Sinale
25. ias_0000 fits BAD_PIXEL_MAP MASTER_BIAS dispersion_solution_0000 tfits DISPERSION_SOLUTION ff_extspectra_0000 fits ff_loccentroid_0000 fits ff_locwidth_0000 fits static grating HR316 tfits FF EXTSPECTRA FF LOCCENTROID FF LOCWIDTH GRATING DATA static slit geometry medusai tfits SLIT GEOMETRY MASTER Now consider the within the same night you observed 3 different points with the same set up producing the raw frames f1 fits f2 fits f3 fits The script shown below uses the Unix command sed to replace the word FILE in the generic sof sample sof by the real GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 31 name of the file we want to reduce The result is put into a a sof file with the same name of the raw frame In the line below this newly created sof is passed to Esorex foreach f f1 fits f2 fits f3 fits cat sample sof sed s _FILE_ f gt f r sof esorex giscience f r sof end B Note for Mac users Although the new generation of ESO pipelines based on CPL Common Pipeline Libraries has no official Mac OS support some of the CPL pipelines were reported to compile without problems on Mac OS machines e g SINFONI and UVES The present version of the GIRAF pipeline does not work on Mac OS A new release will be available soon already running in Paranal This version compiles smoothly and can be used via esorex and or gasgano Figure 15 oho
26. ile contains two HDUs the first one with the image itself and a second one with a binary table with the information of the configuration file used for fiber allocation Any information in the image header can be easily retrieved with the dfits and fitsort commands for instance 184dhcp133 reduced 31 dfits science rbnspectra 0000 fits fitsort OBS TARG NAME EXPTIME FILE OBS TARG NAME EXPTIME Science rbnspectra 0000 fits NGC6253 center field 2699 9981 6dfits and fitsort are part of the ECLIPSE reduction routines and come with scisoft GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 18 also the header to fits table can be accessed with dfits 184dhcp133 reduced 32 gt dfits x 1 science_rbnspectra_0000 fits more gt file science_rbnspectra_0000 fits main lt gt xtension 1 XTENSION BINTABLE FITS Binary Table Extension BITPIX 8 8 bits character format NAXIS 2 Tables are 2 D char array NAXIS1 103 Bytes in row NAXIS2 84 No of rows in table PCOUNT O Parameter count always 0 GCOUNT 1 Group count always 1 TFIELDS 14 No of col in table TFORM1 1J gt Format of field TTYPE1 INDEX gt Field label TUNIT1 gt Physical unit of field TFORM2 1J gt Format of field TTYPE2 FPS Field label The image itself is a 2D frame with one of the axis being the dispersion direction and the other the object number Therefore the size of th
27. ile in the gasgano main window and try again If no problem occurs the Log Message indicates Completion status SUCCESS and the following files are placed in the reduced directory 184dhcp133 reduced 16 gt ls rtl total 42896 rw rw r 1 cmelo cmelo 2364 Apr 30 05 16 giscience_2006 04 30_05 16 12 log rw rw r 1 cmelo cmelo 33586560 Apr 30 05 18 science reduced 0000 fits rw rw r 1 cmelo cmelo 1425600 Apr 30 05 18 science extspectra 0000 fits rw rw r 1 cmelo cmelo 1425600 Apr 30 05 18 science extpixels 0000 fits rw rw r 1 cmelo cmelo 1425600 Apr 30 05 18 science exterrors 0000 fits rw rw r 1 cmelo cmelo 1425600 Apr 30 05 18 science exttraces 0000 fits rw rw r 1 cmelo cmelo 2269440 Apr 30 05 18 science rbnspectra 0000 fits rw rw r 1 cmelo cmelo 2269440 Apr 30 05 18 science rbnerrors 0000 fits rw rw r 1 cmelo cmelo 5204 Apr 30 05 18 giscience 2006 04 30 05 18 15 1og The name convention is the following The recipe name followed by the type of the product and a counter which increments automatically in order to avoid overwriting the products already present in the directory Let us have a look in the reduced spectra A description of the files produced by the girscience recipe is given at user manual of the GIRAFFE pipeline Sec 9 4 5 p 58 You most likely are interested in looking at the file containing your rebinned reduced spectra which according to the pipeline name scheme is science rbnspectra NNNN This f
28. ne while the coefficients of the polynomial are stored in the FITS table Another correction term is added during re binning by correcting for residual wavelength shifts computed from the simultaneous calibration fibers 3 4 4 giscience The recipegiscience can now be executed using the files produced by gimasterbias gimasterflat and giwavecalibration In the present version of the pipeline the extraction performed by For more details about the wavelength calibration process we refer to Royer et al 2002 which is available at http www eso org instruments flames doc spie_royer ps gz 8This is not yet implemented in the current version of the pipeline GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 25 gimasterflat v10000 Je fix File Help Current JANE E Parameters m giraffe fibers spectra Add to pool giraffe fibers nspectra giraffe biasremoval remove i Soo JL giraffe biasremoval method giraffe biasremoval areas giraffe biasremoval sigma Request Pool Filename bad pixel map 0000 fits master Dias 0000 fits GIRAF 2005 07 01T14 16 54 585 fits GIRAF 2005 07 01T14 18 34 303 fits GIRAF 2005 07 01T14 20 12 871 fits grating HR3 16 tfits Product Naming Product Root Directory home2 GIR COOKBOOK DATA reduced Browse Naming Scheme Numeric w JL Execute Selected Filename Classi
29. ns that after some manipulation your science frame can be divide by the flat field image In the case of fiber spectroscopy we have seen that the intensity of the pixels drops quickly on the edge of the fiber profile If the two frames are slightly miss aligned i e the two profiles don t match exactly each other the division will produce an sort of parabola instead of a GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 30 00 00 100 00 000 0 140 2120 WE o l l l 4 240 260 280 300 320 340 360 380 400 cross dispersion direction Figure 3 3D representation of the first packet seen in Fig 2 showing the gaussian tubes GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 8 Table 2 GIRAFFE fiber transmission The values given all losses focal ratio degradation op tics and coupling For wavelengths redder than 600nm the transmission is constant Variations of a few percent between different fibers are measured see Pasquini et al 2003 Fiber type 370nm 400nm 450 nm _ 600 nm MEDUSA _ 0 47 0 52 0 55 0 61 ARGUS 0 52 0 58 0 62 0 70 IFU 0 49 0 55 0 58 0 66 flat image Flat field are corrections are done in one dimension i e the extracted science data is divided by the flat field spectrum In this way we avoid introducing artifact due to the mismatch of the science and the flat field Fibers are not perfect devices A certain amount of photons that en
30. oken fiber the localization process will fail because it cannot find the flat field signal where it was supposed to be When this happens one has to explicitly tell the pipeline which fibers are enabled For this we use the parameters giraffe fibers spectra which gives the pipeline the list of enabled fibers For more details please refer to Sec 9 2 3 of the pipeline user manual 3 4 3 giwavecalibration The method used by the GIRAFFE pipeline is based on a simple optical model of the spec trograph Given the position of the fibers in the focal plane which is what is usually referred to as slit geometry and the wavelength of an arc lamp line the model predicts the position of this line on the CCD The line is searched around this initial position and a PSF profile not a Gaussian is fitted to the detected peak to get the centroid position Having determined the line positions for every line for every fiber the optical model is fitted to this data using the slit offset and slit rotation angle in the focal plane as free parameters The model is accurate to about one pixel and degrades towards the CCD edges To com pensate for that the residuals of the measured line positions with respect to the predicted positions is modeled by a 2D Chebyshev polynomial which is used as a corrective term when re binning the spectra The fitted optical model is described by FITS keywords in the header of the DISPER SION_SOLUTION product of the pipeli
31. omponents A smooth one covering the whole CCD which is proportional to the amount of light entering the spectrograph A second component is a local one and it is caused by the presence of bright objects or a simultaneous comparison lamp In this case it might happen that the charges of the CCD will jump to the neighbor pixels The smooth component is easy to be subtracted A two dimensional fit is carried out on the whole CCD using the points of the detector in the gap between two adjacent fibers The local component might require much detailed look in the light in the inter fiber regions to 2This paper is available at http www eso org instruments flames doc spie ps GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 9 800 600 Intensity ADU I I I I I I I 260 280 300 320 340 360 380 X pixels Figure 4 Cut across the fibers Solid and dashed lines show the minimum level before and after bias subtraction The remaning ADUs seen in the case of the bias subtracted frame are due to the dark current and scattered light GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 10 determine whether or not this is an issue The local component of the scattered light behaves like an extra continuum i e with no spectral features whose spectral energy distribution follows the one of the object causing the scattered light A good correction of the scattered light is essential to
32. ore of the emission is display The object pops up with respect to the background GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 29 However once you have found your ideal set of parameters for each recipe you might want to automatize your data reduction without have to highlight different files and tables At this point you need to use EsoRex EsoRex is a powerful parser which allows you to call a given recipe with a set of files as input parameters Moreover you can pass values to the different parameters of each recipe via command line options or via a configuration file Below we give a simple example of how to use EsoRex In order to use EsoRex you have to prepare your input sof files set of files which contains as expected a list of files to be used by a given recipe In the example below our raw science frame is raw GIRAF 2005 07 01T00 28 08 811 fits All other files or tables were produced by the reduction of the calibration frames or are static tables limari reduced 62 gt cat giscience sof raw GIRAF 2005 07 01T00 28 08 811 fits SCIENCE bad_pixel_map_0000 fits BAD_PIXEL_MAP master_bias_0000 fits MASTER_BIAS dispersion_solution_0000 tfits DISPERSION_SOLUTION ff_extspectra_0000 fits FF_EXTSPECTRA ff_loccentroid_0000 fits FF_LOCCENTROID ff_locwidth_0000 fits FF_LOCWIDTH static grating HR316 tfits GRATING DATA static slit geometry medusal tfits SLIT GEOMETRY MASTER Once you get your set of files r
33. others Thus an uniform light source like the bright sky or an illuminated screen will not appear uniform on the CCD This effect is corrected by taking uniformly illuminated images or flat fields Those images are used to construct a sensitivity map of the CCD In the case of spectroscopic data the first three steps are carried out in the same way as done in imaging data reduction whereas cosmic ray cleaning and flat field corrections are not The correction of these two effects will be discussed in the next sessions 1A good starting point is the cookbook A User s Guide to CCD Reductions with IRAF by Philip Massey which can be found in the IRAF website http iraf noao edu GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 5 dispersion direction X dispersion direction GIRAFFE sub slit Broken fiber Figure 2 An extract of a raw image of a flat filed frame is shown the bottom panel The sub slits packets of fibers defined in the previous figure a clear seen in the image As well as a broken fiber In the top panel a cross section of the frame is shown where the nearly gaussian profile of the fibers can be seen 2 3 Fiber localization and tracing As described above and in Fig 2 the fibers are arranged side by side along the spectrograph slit After being dispersed by the grating the spectrum of each is recorded on the CCD also side by side The direction along which the light is dispersed is called dispersion
34. quality information than others They all contribute with equal weight to the final spectrum Since the noise associated to each pixel is given by the squared root of the number of counts on this pixel Poisson noise we can easily see that give the same weight to pixel with lower counts means that we are adding noise to our final spectrum The shape of the fiber profile can be used as a weight function thus instead of a simple addition we weight its flux by its noise In this way better pixels will give a higher contribution to the final spectrum This is called optimum extraction e g Horne 1986 PASP 98 609 The optimum extraction has an additional advantage with respect to the standard extraction Since we know that the distribution of the intensity of the pixels should follow a smooth and continuous function any pixel deviating a few per cent of this profile is likely to be cosmic ray The pixel hit by a cosmic ray can be replaced by the interpolation of its neighbors cleaning the final spectrum Extraction of the spectrum of the flat lamp has two main functions The first is to correct the pixel to pixel variation in our science data Second the amount of light entering the fibers is supposed to be similar Thus any difference of the intensity of the extract flat field spectrum is due to differences in the fiber transmission In imaging or even in slit spectroscopy one can carry out a two dimensional flat field cor rection This mea
35. red with the giraffe kit home2 GIRAFFE ESO giraf calib 1 0 cal Since the actual filenames of item 2 7 are rather long in the table above we indicated the PRO CATG keyword FILE PRO CATG GI_PDIS_Medusal_H599 3_09 tfits DISPERSION SOLUTION GIPFEX Medusal H599 3 og nts FF EXTSPECTRA GIPLOC Medusal H599 3 09 ts FF LOCCENTROID GLPLOW_Medusa1_H599 3_09 fits FF LOCWIDTH GI MBIA fits MASTER BIAS Inside gasgano the keyword PRO CATG appears in the column CLASSFICATION Now we select in addition to the input science raw frame all corresponding calibrations In order to select multiple files in gasgano hold the CTRL key and click on the calibration and science files Once all files are selected click the right button to open a pull down menu from which you can choose to which recipe you want to send the input files you just selected Figure 6 As shown in Figure 7 a new window will open showing the input parameters for the recipe as well the input frames Choose the directory where the reduction product should go and the click on Execute In the Log Messages sub window you can follow what is going on If one of the mandatory input files is missing the recipe will stop and the cause of the crash is indicated in the Log window In the example above the input file DISPERSION SOLUTION is missing Figure 8 A log file is written in the directory chosen to have the reduced data 184dhcpi33 reduced 12 1s giscience 2006 04 30 05 16
36. s is known and the instrument is stable to a point that the center of the fibers don t move by more than 1 pixel So the pipeline knows where a given fiber should lie and if the localization algorithm cannot measure any signal there that fiber is declared as broken The second step once the initial position of the fibers is known is to determine the fiber profile along the dispersion direction Using the initial position for a given fiber the pipeline moves a couple of pixels along the dispersion direction and again it carries out a gaussian fit at this new position A new center and width are found This is repeated until the edge of the CCD is reached At the end the pipeline determine a sort of tube or tunnel where the science data will be recorded An example of these tubes are shown at Fig 3 2 4 Extraction flat field spectra and fiber transmission Once these tubes have been determined we can extract the signal on the CCD The first thing to be extracted using the same flat field frame is the flat field spectrum From Fig 2 we know already that the signal spreads over many pixels In the case of GI RAFFE the MEDUSA fiber profile is spread over 6 pixels There are two ways of summing the information spread over the fiber profile In the simplest case we add up all pixels inside the fiber profile This is what is called standard extraction The standard extraction ignores the fact that there pixels which contains more counts better
37. s shown in Fig 11 QC parameters returned by the recipes important 3 4 2 gimasterflat In order to reduce the FF we need two static tables In the case of the recipe gimasterflat the slit geometry CLASSIFICATION SLIT_GEOMETRY_MASTER make sure to chose the one corresponding to the plate used for the science data you want to reduce and the grating data GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 23 GASGANO Version 2 2 3 cmelo Linux File Selected files Tools Help D MEN esss z s File CLASSIFICATI ORIGFILE TPL EXPNO _TPL NEXP C Displaying 33 files Unfiltered pid 075 C 0245 D GIRAFFE UNKNOWN 9 pid 60 A 9022 GIRAFFE FLAMES Operation Team 9 200117229 Calibration 9 fi GIRAF 2005 07 01T15 00 37 382 fits BIAS FLAMES gir FLAMES_GIR H GIRAF 2005 07 01T15 01 24 886 fits BIAS FLAMES gir FLAMES_GIR DH GIRAF 2005 07 01T15 02 12 420 fits BIAS FLAMES gir FLAMES_GIR El CIRAF 2005 07 01T15 03 02 844 fits BIAS FLAMES gir FLAMES_GIR El cirar 2005 07 01T15 03 50 308 fits BIAS FLAMES gir FLAMES_GIR G bad pixel map 0000 fits BAD PIXEL FLAMES gir B master_bias_0000 fits MASTER BIAS FLAMES gir e INS SLIT NAME Medusal INS EXP MODE H572 8 e INS SLIT NAME Medusal INS EXP MODE H599 3 e INS SLIT NAME Medusal INS EXP MODE L543 1 e INS SLIT NAME Medusa2 INS EXP MODE H599 3 e INS SLIT NAME Medusa2 INS EXP MODE L543 1 e 200145733 FLAMES Daily
38. sing Software Environment ESO MIDAS ESO s Munich Image Data Analysis System FITS Flexible Image Transport System IRAF Image Reduction and Analysis Facility PAF PArameter File RA Right Ascension UT Unit Telecope VLT Very Large Telescope 1 4 Stylistic conventions The following styles are used bold in the text for commands etc as they have to be typed italic for parts that have to be substituted with real content box for buttons to click on teletype for examples and filenames with path in the text Bold and italic are also used to highlight words GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 2 Table 1 A few multifiber spectrographs around the world Instrument Telescope Observatory Number of objects Hectospec 6 7 m MMT MMT 300 6dF 1 2 m UK Schmidt AAO 150 2dF 3 9 m AAT AAO 400 Hydra 3 5 m WYIN KPNO 90 FLAMES 8 2 UT2 VLT 135 8 2 A brief overview of data reduction of multi fiber spec troscopy data This section aims at making a brief description of the reduction of multi fiber spectroscopic data If you are a beginner who just got your first data set this section is probably worth reading Although the data collected with FLAMES GIRAFFE is used as an example the steps outlined here are the typical ones for data reduction of any multi fiber spectrograph The experienced user might want to jump this section going directly to Sec 3 where an example of the use of the ESO GI
39. t vlt instrument pipelines html It contains the GIRAFFE pipeline and its manual the calibration database gasgano and esorex 5 Gasgano is a powerful file organizer with many different functionalities For a detailed description please refer to the GASGANO user manual GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 12 4 GASGANO Version 2 2 3 cmelo Linux BSA Berane rowing smi enano TH Ema mM Displaying 0 files Unfiltered l Figure 5 Entry screen of gasgano GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 13 3 FF_LOCCENTROID Table created by giflatfield containing the center of the PSF pro files fitted for each wavelength bin along the dispersion direction Gaussian fit is not the default but rather a particular case of the function PSF x A x e eenter W 4 background The GIRAFFE pipeline allows for different fitting functions and methods to derive the centroid 4 FF_LOCWIDTH Also created by giflatfield to store the FWHM the fitted PSF function fit as above along the dispersion direction 5 DISPERSION SOLUTION Wavelength calibration solution found with giwavecal 6 SLIT_GEOMETRY_SETUP Table containing the off set table to be applied to each fiber in order to correct for the curvature along of the GIRAFFE slit 7 GRATING_DATA Static table containing information about the physical model of GI RAFFE Files 2 7 are located in the calibration database delive
40. ter in one end don t make it to the other end of the fibers The amount of lost photons depends of their energy or wavelength Typical transmissions as a function of wavelength for the different fiber systems of FLAMES GIRAFFE are given in Table 2 Values are taken form Pasquini et al 2003 SPIE 4841 1682 Now if you consider a set of fibers sharing the same characteristics like the MEDUSA fibers in FLAMES for instance although they have a similar behavior they are not exactly similar to each other Some of them carry light better than others In a flat field frame the amount of light entering the fibers is assumed to be the same for all fibers Thus comparing the intensity of the extracted flat field spectra we can derive what is called the fiber relative transmission This is important when one wants to do additive operations with the fibers and critical in operations like sky subtraction as described in Sec 2 8 and in Wyse amp Gilmore 1992 MNRAS 257 1 2 5 Scattered light correction A better idea of what scattered light is given in Fig 4 In this figure we show a zoom in of the base of a packet of fibers The solid line and dashed lines represent the fiber profiles before and after the bias subtraction We see that even after the bias removal the signal doesn t go to zero This remaining signal is the scattered light This is because part of the light is scattered inside the spectrograph This scattered light has two c
41. the long slit of the spectrograph Once the light of the fibers get inside the spectrograph the desired spectral order is selected by order sorting filters It is then reflected into a double pass collimator and goes to the grating After an intermediate spectrum is formed the light is finally re imaged on the CCD Although all multi fibers differ from each other in technical details the basic idea is the same for all of them The basic steps of the reduction of multi fiber spectroscopy data are the following GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 3 gt e z e D 28 H e e elit a gt ie avn AS D e r D e ere S 374 T nte e MN DD SO E ACT e A H F e P D 22 it y AM 5 Q SH D G I e dos z Ka X QUE e 3 E E M e ab 66 det 2 D A V ka ge x s de x a As ks e D 5 ye Ld e we e O a 200 s e RK s A e UE E Of ar Ha Ee Des pe GES E 34 q n d e t S LI e K 4 o 4 O D Ds A een X gt e DU ne a 28 x S w e e d lt 3 e 1 Leo Es w bk e WW 6 M POF vi X Os Y m e e e o DM ER ES AA k ap 4 Fa GAL a lt e e I H F t s AL Mg e A Ly RUE AR P e QA S da s oz ddr y 3 Ke e er PS amp e e OF PO wf KA D e d en 00 P ST BO e y
42. yth screen is used instead the robot flat These screen flats provide by far a more uniform illumination and a better correction of the fiber to fiber variations limari raw 67 gt dfits fits fitsort dpr type FILE DPR TYPE GIRAF 2005 07 01T00 28 08 811 fits OBJECT SimCal GIRAF 2005 07 01T14 16 54 585 fits LAMP FLAT GIRAF 2005 07 01T14 18 34 303 fits LAMP FLAT GIRAF 2005 07 01T14 20 12 871 fits LAMP FLAT GIRAF 2005 07 01T14 22 34 861 fits LAMP WAVE GIRAF 2005 07 01T15 00 37 382 fits BIAS GIRAF 2005 07 01T15 01 24 886 fits BIAS GIRAF 2005 07 01T15 02 12 420 fits BIAS GIRAF 2005 07 01T15 03 02 844 fits BIAS GIRAF 2005 07 01T15 03 50 308 fits BIAS e The static data The static data are fits table containing information about the physical model of GIRAFFE gratings a catalogue of ThAr lines and the slit geometry table Whereas the two first tables are really static the slit geometry does change although in a very long time scale months It is not clear when we should determine a new slit geometry For the moment we recommend to redo it for observations separated by more than a 2 weeks GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 22 Bi airar 2005 07 01715 00 37 38 E cipor 2005 07 01115 01 24 81 Produc Root Diesen rere EES Browse mej l E gun Frames
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