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GIRAFFE data reduction cookbook

1. 20 522 4 Wavelength 522 8 523 2 523 6 524 0 Flux 1 Iz 205 00 EFIT 90 r 85 L 80 F e Z r 70 65 F 60 L SSON 50 522 4 BH144 2004 07 03 amp 2005 01 06 E 522 8 523 2 523 6 524 0 Wavelength 50 Figure 28 Reduced spectra of a single star in the cluster BH144 taken on 2004 07 03 compared with three other dates Black line 2004 07 03 Red lines D 2004 12 24 E 2005 01 06 and F 2005 02 18 Green lines show the ratio of the normalised spectra compared with 2004 07 03 GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 51 BH144 2004 07 03 A BH144 2004 07 03 B 1 05 14 05 rz T T T T T 1 00 1 00 pe AE Pn ieee a 95 Fr 295 F 90 Fr 90 r s je 85 L x BD L x 80 r 3 5 cl H B 75 H 25 L 70 F 70 F 65 Fr 65 L 60 F 60 L 55 F xB 50 L L L L L L L L L 50 L L L L L L L L L 522 4 522 8 523 2 523 6 524 0 522 4 522 8 523 2 523 6 524 0 Wavelength Wavelength BH144 2004 07 03 C 1 05 T T 1 T T 1 1 00 495 F 90 4 05 F x 80 L 5 Ge RB 28 xd e 4865 F 60 F YS FF 250 L L L L L 1 1 L 1 522 4 522 8 523 2 523 6 524 0 Wavelength Figure 29 Reduced spectra of a single star in the cluster BH144 taken on 2004 07 03 and reduced using calibrations taken on different dates A Data calibrated using 2004 07 03 and 2004
2. The standard extraction ignores the fact that there pixels which contains more counts better 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 Note that at present optimal extraction is only present for Medusa and not for Argus or IFU 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
3. suorsu qax SE du NSSd NSS 944 1 XSQNI zou Sarj 0000 ei32edsuqi eoueros SFJP 9e poonper Cc Td PYST GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 23 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 fram
4. true wcal lfoffset 20 wcal lswidth 20 20 20 20 20 000 WAVE Medusa2 OPT 2003 04 14 s0f all on one line jsmoker ESO mv esorex log 000 WAVE Medusai SUM NewSG 2004 06 14 Log jsmoker ESO mv slit geometry setup fits slit geometry setup SUM NewSG fits Now the second pass to determine an improved wavelength solution using the created slit geomtry table jsmoker ESO esorex recipe dir path giwavecalibration wcal slit true wcal lfoffset 10 wcal lswidth 10 10 10 10 10 000 WAVE Medusa2 SUM NewSG 2003 04 14 sof all on one line jsmoker ESO mv esorex log 000 WAVE Medusai SUM NewSG 2004 06 14 10g Now do the science reduction jsmoker eso esorex recipe dir path giscience extr method OPTIMAL flat apply true transmission apply false remove bias true bsremove method PROFILE 000 SCIENCE Medusa2 Flat OPT 2003 04 14 s0f all on one line jsmoker eso mv esorex log 000 SCIENCE Medusa2 Flat OPT 2003 04 14 1og Which will produced the final fits files of the rebinned spectra ready for further analysis GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 48 6 Automating data reduction using EsOrEx 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 cmelo
5. ERROR Spectrum localization computation failed ERROR 21 11 48 ERROR Spectrum localization failed Aborting Completion status FAILURE Execution error Execution failed with code 1 Figure 14 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 28 the Parameter sub window gimasterflat to 1 26 28 135 ignores fibre 27 therefore runs fine see Fig 16 and produces 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 17 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 broken 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 as described above which gives the pipeline the list of enabled fibers For more details please refer also to Sec 9 2 3 of the pipeline u
6. iraffe sgcalibration iterations iraffe sgcalibration zmax 10000 0 iraffe sgcalibration cc domain 0 0 iraffe sgcalibration rv limits iraffe sgcalibration rv iterations 3 iraffe sgcalibration rv wfactor iraffe sgcalibration peak iterations iraffe sgcalibration peak tests iraffe sgcalibration peak dchisquare 4 Filename GIRAF 2003 04 15T00 36 45 624 fits F e ff loccentroid 0000 fits grating HR3 16 fits MR line catalog THAP fits INE CAT line mask ThAr H395 8 014 fits slit geometry medusa2 fits Product Naming Product Root Directory Ihome2 Jjsmoker Instruments FLAMES Pipelines Comparison Srmartt Gasgano Browse Naming Scheme 1 PGT TR ET UI Filename Classification arc extspectra 0001 fits ARC EXTSPECTRA arc exterrors 0001 fits ARC EXTERRORS arc extpixels 0001 fits A arc_exttraces_0001 fits dispersion_solution_0001 fits line_data_0001 fits Jhome2 jsmoker Instruments FLAMES Pipelines Comparison Smartt Gasgano line data 0001 fits Tome jsmoker Instruments FLAMES Pipelines Comparison Smartt Gasgano slit geometry setup 0000 fits Jhome 2 jsmoker Instruments FLAMES Pipelines Comparison Smartt Gasgano arc rbnspectra 0001 fits home jsmoker Instruments FLAMES Pipelines Comparison
7. Any information in the image header can be easily retrieved with the dfits and fitsort commands for instance 6dfits and fitsort are part of the ECLIPSE reduction routines and come with scisoft GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 19 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_Medusa1_H599 3_09 fits play j GI_PLOW_Medusal_H599 3_09 fits Locate play grating HR3 16 tfits locate Display slit geometry medusa1 H5 99 3 oa us Execute Selected v Filename Classification fhome2 GIRAFFE ESO calib giraf calipb 1 0b cal GI_PLOC_Medusal_H599 3_09 fits group CALIB level INTERMEDIATE type IMAGE tag FF_U amp fhome2 GIRAFFE ESO calib giraf calipb 1 0b cal GI_PLOW_Medusal_H599 3_09 fits group 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 GIRAFFE ESO calib giraf calib 1 0b cal slit geometry medusa1 H5 99 3 09 tfits group RAW level 2 INTERMEDIATE type 2 IMAGE
8. last 90 days close up QC data range 2008 12 15 2009 03 14 20 LR DX 6 5 4 3 2 1 0 1 AX px fo Figure 30 Shift of GIRAFFE X axis with temperature in late 2008 early 2009 Calibrations are taken the day after the science and the temperatures are inspected so that they are within 1 5 C GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 55 8 4 Cannot create local file error The following error sometimes occurs in within giscience when one of the input files ff extspectra fits contains zeros ERROR 11 03 13 ERROR Cannot create local file Aborting Completion status FAILURE Execution error Execution failed with code 1 This error is related to the new GIRAFFE CCD sensitivity to cosmic rays It was normally not a problem with the old CCD so there was no check necessary but with the new CCD you can be unfortunate that all pixels belonging to a wavelength bin of a fiber are considered as bad pixels i e the pixel value in the extracted flat field is set to 0 A workaround for old versions of the pipeline is to add a small constant 0 000001 to ff extspectra fits and now giscience should successfully complete the reduction Newer versions of the pipelines do not produce this error 8 5 Spectrum localization computation failed within gimaster flat This error can be caused by a number of reasons One common one is that the number of fibres traced is not correct In the following case t
9. of the GIRAFFE or UVES pipelines If so make sure that you are using the correct one GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 53 For example jsmoker 184dhcp22 ESO which esorex home jsmoker UVES DRS CPL bin esorex an old version fails as the EsOrEx version was out of date However when we use the correct version the spectra are reduced without problems jsmoker 184dhcp22 ESO which esorex home jsmoker GIRAFFE DRS giraf kit 2 6 0 bin esorex 8 3 Mis allignment between calibration data and science frames Because GIRAFFE is not a thermally controlled instrument there can be shifts in the cross dispersion position of the fibres when comparing science and calibration frames ESO tries to minimise these shifts by taking calibrations as close as possible in time to the science frames and by re scheduling observations if the shift is so big that data cannot be reduced by the nearest calibrations The shift as a function in temperature for both gratings can be found on the following webpage www eso org observing dfo quality GIRAFFE reports HEALTH trend report STABILITY HC html Examples of the shifts in the HR and LR gratings in the x axis with temperature are shown in Fig 30 If your reduction is not working it may be a good idea to look at the temperature at which the science and calibrations were taken by looking at the keyword INS TEMP53 viz jsmoker 184dhcp22 ES0 dfits GIR fits grep
10. 12 24 calibrations B Data calibrated using 2004 07 03 and 2005 01 06 calibrations C Data calibrated using 2004 07 03 and 2005 02 18 calibrations Green lines show the ratio of the reduced spectra calibrated using the different dates GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 52 8 Common problems during data reduction 8 1 Incorrect input files Many times problems with the GIRAFFE pipeline are caused by incorrect input files Unfor tunately the error reporting is not always intuitive and will be improved in future versions Hence you should take a lot of care in ensuring that the input files are correct An example is given below of an esorex command to create a fibre flatfield jsmoker 184dhcp22 ESO cat Fibre Flat Medusa1 Bad Sof sof GIRAF 2008 01 05T14 02 23 360 fits FIBER FLAT GIRAF 2008 01 05T14 04 18 900 fits FIBER FLAT GIRAF 2008 01 05T14 06 13 719 fits FIBER_FLAT path giraf 2 6 0 cal grating_HR316 fits GRATING_DATA path giraf 2 6 0 cal line_mask_ThAr_L682 2_03 fits LINE_MASK path giraf 2 6 0 cal slit_geometry_medusal fits SLIT_GEOMETRY_MASTER gimasterbias_2008 01 05 fits MASTER_BIAS gibadpixelmap_2008 01 05 fits BAD_PIXEL_MAP Let s try and run it where path is where your recipe directory lies jsmoker 184dhcp22 ESO esorex recipe dir path gimasterflat fiber splist 1 26 28 135 extr method SUM Fibre Flat Medusai Bad Sof sof all on one line ERROR gimasterflat Rel
11. 2 6 0 cal grating_HR316 fits ARC_SPECTRUM MASTER_BIAS BAD_PIXEL_MAP FF_LOCCENTROID FF_PSFCENTROID FF_LOCWIDTH PSF_WIDTH FIBER_PROFILE GRATING_DATA path giraf 2 6 0 cal line_mask_ThAr_H395 8_014 fits path giraf 2 6 0 cal slit_geometry_medusa2 fits path giraf 2 6 0 cal line_catalog ThAr fits LINE_MASK SLIT_GEOMETRY_MASTER LINE_CATALOG here although we have specified FF_LOCCENTROID LOCWIDTH and FF_PSFCENTROID PSF_WIDTH by default the FF_PSF is preferred For the input file to create the dispersion solution and a new slit geometry file second pass of recipe giwavecalibration within esorex smoker ESO cat OO0O0_WAVE_Medusa2_OPT_NewSG_2003 04 14 sof GIRAF 2003 04 15T00 36 45 624 fits gimasterbias_2003 04 15 fits gibadpixelmap_2003 04 15 fits ff loccentroid OPT fits ff psfcentroid OPT fits ff_locwidth_OPT fits ff_psfwidth_OPT fits fiber_profile_OPT fits slit_geometry_setup_OPT_NewSG fits path giraf 2 6 0 cal grating_HR316 fits ARC_SPECTRUM MASTER_BIAS BAD_PIXEL_MAP FF_LOCCENTROID FF_PSFCENTROID FF_LOCWIDTH PSF_WIDTH FIBER_PROFILE SLIT_GEOMETRY_MASTER GRATING_DATA path giraf 2 6 0 cal line_mask_ThAr_H395 8_014 fits path giraf 2 6 0 cal line_catalog_ThAr fits and finally the sof file for the science reduction LINE MASK LINE CATALOG smoker ESO cat 000 SCIENCE Medusa2 Flat GIRAF 2003 04 14T05 49 22 7740 fits gimasterbias_2003 04 15 fits MASTER_B gibadpixelmap_2003 04 15 fits BAD
12. 37 High 20600 _Auto Set Cut Levels LUTTE LZ g Figure 15 A Medusal flatfield image in which fibre 27 about a quarter from the left is missing Note that for ARGUS the counting is done from right to left and not from left to right as in Medusa or IFU GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 30 File Help Current Queued Executing Parameters Name Default Range giraffe fibers spectra giraffe fibers nspectra 0 2147483646 giraffe biasremoval remove giraffe biasremoval method giraffe biasremoval areas giraffe biasremoval sigma giraffe biasremoval iterations giraffe biasremoval fraction giraffe biasremoval xorder giraffe biasremoval yorder Request Pool Include Filename Classification vi GIRAF 2008 01 05T14 02 23 360 fits GIRAF 2008 01 05T14 04 18 900 fits GIRAF 2008 01 05T14 06 13 719 fits gibadpixelmap 2008 01 05 fits grating LR600 fits line mask ThAr L682 2 03 fits slit geometry medusa1 fits Product Naming Product Root Directory home2 jsmoker Instruments FLAMES Pipelines Comparison Barrado Naming Scheme JL Execute Selected Filename Classification master fiber flat 0000 fits MASTER FIBER FLAT Iff loccentroid 0000 fits FF LOCCENTROID Iff Iocwidth 0000 fits FF LOCWIDTH If
13. 9 200150097 u2 9 INS SLIT NAME Medusal INS EXP MODE H599 D GIRAF 2005 07 01T00 28 08 811 fits 9 EZ 60 4 9022 GIRAFFE FLAMES Operation Team 9 200117229 Calibration D GIRAF 2005 07 01T15 00 37 382 fits D GIRAF 2005 07 01T15 01 24 886 fits El CIRAF 2005 07 01T15 02 12 420 fits Ei CIRAF 2005 07 01715 03 02 84 4 fits El cIRAF 2005 07 01T15 03 50 308 fits B cl_Bpix fits B ci_MBIA fits GI INS SLIT NAME Argus INS EXP MODE H412 4 GI INS SLIT NAME Argus INS EXP MODE H429 7 GI INS SLIT NAME Argus INS EXP MODE H447 14 GI INS SLIT NAME Arqus INS EXP MODE H447 1B TPL NEXP SCIEN Display BOUT asa S gimasterbias To Recipe Request Pool gt gimasterflat Report Move Copy Tar Run BAD PIXEL MAP FLAMES giraf MASTER_BIAS FLAMES giraf giwavecalibration home2 GIR COOKBOOK DATA raw GIRAF 2005 07 01T00 28 08 811 fits FLAMES GIRAF OBS182 0001 fits SCIENCE Extension HEADER gt Find in header find Load Fitter Fitter Auto Displa M Figure 8 Passing a raw science frame to the recipe giscience 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 FILE PRO CATG GI_PDIS_Medusa1_H599 3_09 tf
14. PIXE ff loccentroid OPT fits FF_LOCCENTROID ff psfcentroid OPT fits ER PSFCENTROID ff_locwidth_OPT fits FF_LOCWIDTH ff_psfwidth_OPT fits PSF_WIDTH fiber_profile_OPT fits FIBER_PROFILE ff_extspectra_OPT fits FF_EXTSPECTRA ff_exterrors_OPT fits FF EXTERRORS master_fiber_flat_OPT fits MASTER_F dispersion_solution_OPT fits DISPERSI slit_geometry_setup_OPT fits SLIT GEO path giraf 2 6 0 cal grating HR316 fits path giraf 2 6 0 cal line mask ThAr H39 _OPT_2003 04 14 sof SCIENCE TAS L_MAP IBER_FLAT ON_SOLUTION METRY MASTER GRATING_DATA 5 8_014 fits LINE MASK GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 47 Once you get your set of files ready you simply call EsoRex as shown below where in this case path is equivalent to home jsmoker GIRAFFE DRS giraf 2 6 recipes libs First make the master bias and bad pixel map jsmoker ESO esorex recipe dir path gimasterbias 000 BIAS 2003 04 15 txt jsmoker ESO mv esorex log 000 BIAS 2003 04 15 esorex log Now the master flat and the fibre localisation jsmoker ESO esorex recipe dir path gimasterflat fiber splist 1 26 28 136 extr method O PTIMAL 000 FIBRE FLAT Medusa2 2003 04 15 sof all on one line jsmoker ESO mv esorex log 000 FIBRE PLAT Medusa2 OPT 2003 04 15 1og Now the first pass to determine the wavelength solution and to make a new slit ge ometry table jsmoker ESO esorex recipe dir path giwavecalibration wcal slit
15. cmelo 33586560 Apr 30 05 18 science reduced 0000 fits cmelo cmelo 1425600 Apr 30 05 18 science extspectra 0000 fits cmelo cmelo 1425600 Apr 30 05 18 science extpixels 0000 fits 1 rw rw r 1 1 1 rw rw r 1 cmelo cmelo 1425600 Apr 30 05 18 science exterrors 0000 fits 1 1 1 1 rw rw r rw rw r rw rw r cmelo cmelo 1425600 Apr 30 05 18 science exttraces 0000 fits cmelo cmelo 2269440 Apr 30 05 18 science rbnspectra 0000 fits cmelo cmelo 2269440 Apr 30 05 18 science rbnerrors 0000 fits cmelo cmelo 5204 Apr 30 05 18 giscience 2006 04 30 05 18 15 1og rw rw r rw rw r rw rw r 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 Note that the incrment only will work if you have Naming Scheme Numeric as opposed to Naming Scheme Overwrite 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 file 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
16. d ad ig e NE e v E 74 DA LS 1 lt x e m D d D vi ES Ke SEL P t Wa e ut e b P Ce A ab Y Be Q LE o ST d X Z AY K A sa 4 Gt e PASS 079 550837 Sus de ansehen T SE Guerebht tick EE Sege 1 Zaggy0 2 Seege 3 4 KL X LN x a band DB829 amp 7 D BONNET CUPIT et xt 4 e v Z e a Figure 1 An example of the potential of multi fiber spectrographs In one shot up to 135 spectra are recorded by GIRAFFE and up 8 by UVES The figure is 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 The basic steps of the reduction of multi fiber spectroscopy data are the following 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 standard star calibration in the case of IFU or ARGUS 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 defec
17. 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 15 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 giscience 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 gimasterbias but see section 3 4 1 about the bias history effect 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 FF_PSFCENTROID 6 FF_PSFWDITH You can use either the FF LOCCENTROID WIDTH or the FF PSFCENTROID WIDTH files as i
18. 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 components A smooth one covering the whole CCD which is proportional to the amount of light entering the spectrograph This 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 U 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 remaining 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 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 subtract 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 determine whether or not this is an issue The local component of the scattered light behaves like an extra conti
19. 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 10 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 20 184dhcp133 reduced 31 gt dfits science_rbnspectra_0000 fits fitsort OBS TARG NAME EXPTIME FILE science_rbnspectra_0000 fits OBS TARG NAME NGC6253_center_field EXPTIME 2699 9981 also the header to fits table can be accessed with dfits 184dhcp133 reduced 32 dfits x 1 science rbnspectra 0000 fits more file science rbnspectra 0000 fits main 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 Format of field TTYPE1 INDEX Field label TUNIT1 gt 77 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 the image can vary according to
20. 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 aidparsQ 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 iraf onedspec dispaxis 2 GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 21 7777777775 a ALA DR EAP ALLP REBRE LRRD EEEAPEREA A eis Page Window Help File Edit yn Figure 11 Stellar spectrum of a member of NGC6253 in aperture 5 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 shown in Figure 11 But to which target am I looking at The answer is found looking into the binary table For th
21. the relevant calibrations and science frames the first thing you should do is to check the INS TEMP53 value in the headers and make sure that they are within 1 5 C see Sect 8 3 In any case the cross dispersion value of your calibration data and science targets should match to within less than 0 8 of a pixel or else there may be problems with the data reduction Fig 28 shows GIRAFFE observations of a part of an order for a single star in BH 144 taken at different dates Fig 29 shows a single dates observations 2004 07 03 but reduced using calibrations taken on 2004 07 03 2004 12 24 2005 01 06 and 2005 02 18 The region of interest was normalised by fitting a Oth order polynomial and the wavelengths forced to match The conclusion for these Medusa observations is that the flatfielding at least worked well with data taken far away with time but with similar values of cross dispersion Whether this generally holds true is not clear and we again remind the reader that the wavelength calibration would be very inaccurate GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 Flux Flux Li Ls 95 F 90 r 285 r 80 F XS 430 F 65 F 460 7 55r 4S0 lt 05 80 F ELEAF 70 F 465 F BLU F 495 F 05 00 BH144 2004 07 03 amp 2004 1 H 2 24 D 522 4 BH144 Wavelength 522 8 523 2 523 6 524 0 2004 07 03 amp 2005 02 18 F
22. 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 scattered 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 AA 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 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 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 3 can achieved This requires e proper bias and dark correction e scattered light corre
23. 034 This page was intentionally left blank iv GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 v Contents 1 Introduction 1 RE TRIOS La ich Ce E Oe WEE A RECEN AO OE WEE EE A 1 1 2 Reference documents 4 26 be kee EEN EE NR eR ee we Ee 1 1 3 Abbreviations and acronyms NEE ook REX EE EMG Eo 1 1 4 Stylistic OD VOD uou so s w adn s w X he Re E pee E Reo s 1 2 A brief overview of data reduction of multi fiber spectroscopy data 2 21 Mul BberspectroSCODY lt sc igesa a ena ERA REEL cr anak 2 2 2 Correcting detector cosmetic effects coe soep s s s p a QW a e SU a 8 U Q S 4 220 Fiber localization and tracing es keas ed kuka escasas HERE EO EEE BO 5 2 4 Extraction flat field spectra and fiber transmission 6 2 0 Scattered light correction 5 2 45 44 e e He Eo oos 8 2b Wavelength calibration lt c lt s oed ss aca bee S E RO ESO 2 10 of Wetraction of thescienc 222252393 xo EES ee EX GU Eo 10 2A OKY OUTRO A ocak s a S wq Ke ee be OR Ew RR eee A Q 11 3 Pipeline in action Gasgano the friendly way 14 al Belore H e A sed ede er Se Y sus eos h ROEUER OE X XU EUR RO s s kos 14 pee GE Phe uox odo saroia soe kue w ox cR E QU K Qua E EL Y Q e s 14 3 3 Case 1 your calibration data is up to date 4 o Ron 15 3 4 Case 2 Making your own calibration database ss 23 Baal pHDASSUSPDIQS wt Q s A AIR EE EE a Ae QUQ e SU e e 24 e c lt e a s a sss ua w Q y S QU S w W Qh W Qum OSO W Qum Q
24. 2 8 1 at the time of writing For the input file to create the master bias and bad pixel map smoker ESO cat 000 BIAS 2003 04 15 txt GIRAF 2003 04 15T00 47 11 122 fits BIAS GIRAF 2003 04 15T00 47 58 821 fits BIAS GIRAF 2003 04 15T00 48 46 582 fits BIAS GIRAF 2003 04 15T00 49 37 202 fits BIAS GIRAF 2003 04 15T00 50 24 933 fits BIAS For the input file to create the master flatfield and localisation centroids smoker ESO cat 000 FIBRE FLAT Medusa2 2003 04 15 s0of GIRAF 2003 04 15T00 11 23 320 fits FIBER FLAT GIRAF 2003 04 15T00 17 29 884 fits FIBER FLAT GIRAF 2003 04 15T00 23 36 497 fits FIBER FLAT path giraf 2 6 0 cal grating HR316 fits GRATING DATA path giraf 2 6 0 cal line mask ThAr H395 8 oi4 fits LINE MASK path giraf 2 6 0 cal slit geometry medusa2 fits SLIT GEOMETRY MASTER gimasterbias 2003 04 15 fits MASTER BIAS gibadpixelmap 2003 04 15 fits BAD PIXEL MAP 8Please consult the EsoRex manual GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 46 For the input file to create the dispersion solution and new slit geometry table using the default slit geometry file first pass of recipe giwavecalibration within esorex smoker ESO cat 000 WAVE Medusa2 OPT 2002 04 14 sof GIRAF 2003 04 15T00 36 45 624 fits gimasterbias_2003 04 15 fits gibadpixelmap_2003 04 15 fits ff loccentroid OPT fits ff psfcentroid OPT fits ff_locwidth_OPT fits ff_psfwidth_OPT fits fiber_profile_OPT fits path giraf
25. 3 6 93 1984 32 1402 0 7579 0 112 0 143417 0 00348608 15964 5 93 1965 31 6202 0 7643 0 1392 0 159096 0 00355957 16134 7 93 2076 31 1002 0 7707 0 166 0 0835813 0 00356177 16183 5 93 3142 30 2499 0 475 0 0971 0 254631 0 00339826 16405 8 93 3028 29 7299 0 4803 0 0723 0 25714 0 0034156 16460 93 2904 29 2099 0 4855 0 0479 0 194354 0 0035145 16221 2 93 2805 28 69 0 4908 0 0238 0 158393 0 00347458 16283 6 93 2729 28 17 0 4961 0 0 14358 0 00347986 16352 7 93 2623 21 65 0 5014 0 0234 0 0466289 0 00338651 16075 93 254 27 1301 0 5067 0 0465 0 0954385 0 00346265 16109 5 93 2455 26 6101 0 512 0 0693 0 016709 0 00342234 16061 93 2309 26 0901 0 5173 0 0917 0 037551 0 00357151 16040 4 93 2135 25 2399 0 3179 0 0803 0 0624736 0 00347723 16380 9 93 2039 24 7199 0 3223 0 0597 0 153443 0 00352105 16818 6 93 2041 24 2 0 3266 0 0395 0 107512 0 00348652 16381 4 93 1995 23 68 0 331 0 0196 0 163205 0 00342611 16267 4 93 1971 23 16 0 3353 0 0 138406 0 00347739 15987 93 1884 22 64 0 3397 0 0192 0 185514 0 00351302 16054 6 93 1862 22 12 0 344 0 0381 0 195105 0 00347557 16198 4 93 1859 21 6001 0 3484 0 0567 0 186927 0 00346506 16050 1 93 1743 21 0801 0 3527 0 0749 0 223937 0 00346037 16116 3 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 3 3 3 7 7 3 3 3 3 Figure 22 New slit geometry table created by giwavecalibration The errors in Radial Velocity are in kms 1 Note that errors in the wavelength calibration for the sc
26. 4 34 E zoom Object gt 1 3 5 v 2170 0 Value cc 8 Equinox 4 Min 46 1745 Max 134729 Bitpix 32 Low 5000 High 20000 Auto Set Cut Levels DOO i G image WB select object W scroll image RH measure WCS Contr Figure 19 Original rebinned arc line spectrum arc rbnspectra fits created by giwavecalibra tion Jumps in the y position signify that this is not a good wavelength solution and should be improved by creating a new slit geometry table GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 35 3 4 4 giwavecalibration remaking the slit geometry table If you see jumps in your arc_rbnspectra fits file it is probably wise to remake the slit geometry table by re running giwavecalibration To do this you have to enable the giraffe wcal slitgeometry flag within giwavecalibration and re run it Typical inputs using gasgano are shown in Fig 20 On the first pass of giwavecalibration you may choose to run 8 iterations with a box of 20 pixels 20 20 20 20 20 20 20 20 and in the 2nd go you use 10 10 10 10 10 5 times After giwavecalibration has been run again you should look anew at the arc rbnspectra fits file to see if there has been any improvement An example is shown in Fig 21 The jumps in vi have now disappeared so the wavelength solution appears to be good This can be checked by looking at the radial velocity error RV
27. ERR in the slit geometry table as shown in Fig 22 In the example shown the errors are typically 0 003 kms 1 or 3 ms We note that the radial velocity accuracy of your science targets will be much worse than this the best achieved velocity accuracy to date being around 30 m s over a period of 5 days Loeillet et al A amp A 479 865 2008 3 4 5 giscience The recipe giscience can now be executed using the files produced by gimasterbias gimasterflat and giwavecalibration In the present version of the pipeline the extraction performed by giscience adds up the signal inside the PSF fitted by gimasterflat Optimum weighted extraction is now available that also does the background not sky subtraction too 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 which is the standard deviation of the re sampled fluxes for each wavelength bin GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 36 File Help Current Executing Parameters Name E Default y iraffe rebinning Istep 050 0 0050 A00 to pool raffe rebinning scalemethod iraffe rebinning size 0 1 iraffe rebinning range i Request Pool raffe wcal slitgeometry Ll FAR SSS Espia
28. ESO gt cat sample sof _FILE_ 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 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 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 fi fits f2 fits f3 fits cat sample sof sed s FILE f gt f r sof esorex giscience f r sof end GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 49 7 Reducing data using calibrations taken far away in time Note that it is not recommended to reduce data taken using calibrations taken a long time away from the science data In particular wavelength calibration accuracy should not be trusted due to shifts in the instrument That said if there are no nearby calibrations taken then you may consider it worthwhile to search the archive for matching calibrations taken further away in time After downloading
29. EUROPEAN SOUTHERN OBSERVATORY ES Organisation Europ ene pour des Recherches Astronomiques dans l H misph re Austral Q Europ ische Organisation f r astronomische Forschung in der s dlichen Hemisph re ESO European Southern Observatory Karl Schwarzschild Str 2 D 85748 Garching bei M nchen Very Large Telescope Paranal Science Operations GIRAFFE data reduction cookbook Doc No VLT MAN ESO 13700 4034 Issue 85 0 Date 29 08 2009 C Melo J Smoker luci nuc pes soras bie gt raaa w han k pau aiid E E ERS Date Signature G Marconi Approved desc Ete ten aimo ea ea a Nas deg dE ca dies Date Signature C Dumas Released 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 ili Change Record Issue Rev Date Section Parag affected Reason Initiation Documents Remarks 79 26 08 2006 First version 85 29 08 2009 All Update Bias history effect How to make slit geometry table ESOrex section expanded Sects on common problems in reducing data and on reducing data with old calibrations added Example of sky lines added IFU and Argus section improved Issues to be covered in a future version Different extraction methods Sky subtraction example Argus data reduction GIRAFFE data reduction cookbook VLT MAN ESO 13700 4
30. Smartt Gasgano arc rbnerrors 0001 fits Completion status SUCCESS Figure 20 Inputs to giwavecalibration using gasgano in order to create a new slit geometry table GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 37 Ir Zoom Object arc rbnspe ctr Value 263 193 Equinox Min 46 252 Max 143514 Bitpix 32 Low 5000 High 20000 Auto Set Cut Levels Scale H Z zi S Site E i image WB select object W scroll image RH measure WCS Contr Figure 21 Rebinned arc line spectrum arc rbnspectra fits created by giwavecalibration after making a new slit geometry table The jumps in y are much less pronounced than in Fig 19 GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 38 Hle Edit Options Data Servers Search Results 136 ZF ZDEFOCUS RV RVERR RESOLUTION 93 1782 37 3398 0 6937 0 1782 0 231945 0 00323477 14984 8 93 184 36 8198 0 7001 0 1477 0 171355 0 00342404 16472 6 93 1825 36 2998 0 7065 0 1174 0 182567 0 00340234 16274 1 93 1839 35 7799 0 7129 0 0876 0 147593 0 00358495 16634 6 93 1835 35 2599 0 7194 0 058 0 176119 0 00354971 16500 9 93 1902 34 74 0 7258 0 0289 0 16136 0 00347851 16357 1 93 1962 34 22 0 7322 0 0 154024 0 00335576 16882 93 1976 33 7 0 7386 0 0285 0 159423 0 00347449 16200 7 93 1985 33 1801 0 7451 0 0567 0 137595 0 00343178 16138 3 93 1995 32 6601 0 7515 0 0845 0 128764 0 00343981 1605
31. T15 00 37 867 H cipor 2005 07 01115 01 24 81 product Root Diesen rere ES T s Brest mej l E gun Frames Log Messages Figure 12 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 A list of these is available in the GIRAFFE pipeline manual 3 4 1 gimasterbias Until July 7th 2008 there was a history effect for biases that meant that the first bias in the sequence of 5 had lower flux than the remaining four The effect was upto 2 ADU for the new CCD Carreras and perhaps 0 3 ADU for the old CCD Bruce See www eso org sci facilities paranal instruments flames inst features FLAMES GIRAFFE Bias History Effect html This history effect when present can cause the master bias to be too high compared with the science data and hence cause over subtraction of the bias level To avoid this one can use the PROFILE option of bias removal in the s
32. TER BIAS FLAMES gir 5 B INS SLIT NAME Medusal INS EXP MODE H572 8 Ke INS SLIT NAME Medusal INS EXP MODE H599 3 S INS SLIT NAME Medusal INS EXP MODE L543 1 Ke INS SLIT NAME Medusa2 INS EXP MODE H599 3 e INS SLIT NAME Medusa2 INS EXP MODE L543 1 5 200145733 FLAMES Daily monitoring bad pixel map 0000 fits unknown orig name gt BAD PIXEL MAP Find in header find Load Finer Filter Figure 13 Gasgano automatically updates the list of files The reduced files created by gimasterbias are seen in the gasgano file list 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 gasgano as shown in Fig 13 Note that the default stacking method is average which generally gives a lower noise on the combined master bias than median
33. Y 0 517048258124353 Median master bias level ADU Mean master bias level ADU RMS of master bias level ADU Readout noise raw Readout noise master Structure along the x axis Structure along the y axis Gb OF 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 GRATING DATA here also you have to chose the right one in our example the data have been taken with the LR 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 Note that it is best to do this by explicitly defining the fibres using giraffe fibers spectra see below As a first pass we run the recipe with the default number of fibres and by removing the bias using the overscan region giraffe biasremoval method PROFILE In Fig 14 we see that the recipe failed because only 134 were found instead of 136 fibres The best way to get things working is to display the flatfield and see what fibre or fibres are missing Fig 15 shows an example in which Fibre 27 counting left to right for Medusa about a quarter of the way from the left has no flux Fixing giraffe fibers
34. allowing to fine tune the data reduction We refer to the pipeline 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 the spectrum An advantage in fibres over Multi Object Spectroscopy MOS is that there are no issues with slit centering which can impact on radial velocities with slits 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 at 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 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
35. aphics Real time Help Object ff loccentroid SUM fits x 34 5 Y 2129 2 Value 537 066 K B Equinox Min 23 0648 Max 2044 3 Bitpix 32 Low 19 High 2046 Auto Set Cut Levels Scale 3x Zl z SI Si ty Figure 18 Localisation centroid frame ff loccentroid fits produced by gimasterflat The x coordinate is fibre number the vi coordinate the y position on the CCD and the value at each point the x coordinate of the localisation centroid For a perfect fit there is an offset of 1 pixel between the value in ff loccentroid fits and the x centre within each fi bre in master_fiber_flat fits i e value for ff loccentroid fits for fibre x N is x value for master fiber Hat hrs 1 GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 33 the simultaneous calibration fibre is used The amount corrected is given in the table and the user can undo the correction After you have run giwavecalibration you should check the products to see that they look sensible In particular the file arc_rbnspectra fits file should be displayed The results of our first run are shown in Fig 19 Note that in this figure there are big jumps in the y direction between the fibres If you see shifts like these in your data then a good idea would be to remake the slit geometry table GIRAFFE data reduction cookbook VLT MAN ESO 13700 403
36. are arranged along 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 fiber instruments differ from each other in technical details the basic idea is the same for all of them GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 ae H CN 6 5 D ar e A f e e d oo Py e A z d F t D D e Ser EE E T Ee A DIESE P e e e 7 s CH a k m H e lt x a e Set j 3 A T s gq 72 8 28 en ZER e 2 e 2 we e er e D s D CH ge Ka v s f gt E A 4 L b s e Rp 4 Wi e e we n 200 s e RK s KS Ge i F 99 ar a Ee Des pe GES E e Ta C s D e D E p 1 v t S w LI K 4 o 4 O we 3 Je e X e X s D aga e ag N Ae M w e ed d TX 1 Le SORGE EE ie iu tae Os Z eu ur te E eg s xs 9 ei di e d e Ta AA Pg S Wh e lt t L L i t s ap T e A Y C W wei 3 M H d e ag D et E IS 2 3 a e ss r wir 3 K e 2 lt SO SA d en 2 P ST BO e LC RT x te e o Se Qs eo o X S S D c A e A 2
37. at the expense of possible problems with bad pixels or cosmic rays QC parameters produced by gimasterbias are logged in qc 000N paf an example is shown below jsmoker 184dhcp22 Smartt Gasgano more qc0000 paf GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 26 PAF HDR START PAF TYPE QC1 parameters Type of parameter file PAF ID PAF NAME qc0000 paf Name of PAF PAF DESC Short description of PAF PAF CRTE NAME jsmoker Name of creator PAF CRTE DAYTIM 2009 03 14T20 38 11 000 Civil time for creation PAF LCHG NAME Author of par file PAF LCHG DAYTIM Timestamp for last change PAF CHCK NAME Name of appl checking PAF CHCK DAYTIM Time for checking PAF CHCK CHECKSUM Checksum for the PAF PAF HDR END e ee e EE ee ee QC DID ESO0 VLT DIC GIRAFFE QC 0 2 QC1 dictionary ARCFILE GIRAF 2003 04 15T00 47 11 122 fits Archive File Name TPL ID FLAMES giraf cal bias Template signature ID PRO CATG MASTER BIAS Pipeline product category PRO DATAAVG 158 56187685038 Mean of pixel values PRO DATARMS 29 4017477751589 Standard deviation of pixel values PRO DATAMED 158 2 Median of pixel values PRO DATANCOM 5 QC BIAS MASTER MEDIAN 158 199996948242 QC BIAS MASTER MEAN 158 26553557018 QC BIAS MASTER RMS 2 06290380948411 QC OUT1 RON RAW 1 84526219570382 QC OUT1 RON MASTER 0 834264929284362 QC O0UT1 STRUCT X 0 0620529817523003 QC O0UT1 STRUCT
38. ative transmission computation failed Aborting ERROR esorex Execution of recipe gimasterflat failed status 1 lt snip gt INFO gimasterflat Average of in borders pixels per spectra 3 447e 04 INFO gimasterflat Average lost pixels per spectra 0 09938 INFO gimasterflat Average lost pixels at upper border 1 039 INFO gimasterflat Average lost pixels at lower border 0 9396 INFO gimasterflat Average spectrum width 10 3 2 286 min max 0 10 91 INFO gimasterflat Writing fiber localization WARNING gimasterflat Missing dark value property ESO PRO DARK VALUE will be set to 0 00 INFO gimasterflat Fitting fiber profiles INFO gimasterflat Fitting PSF profile parameters INFO gimasterflat Writing fiber traces INFO gimasterflat Extracting spectra INFO gimasterflat Computing relative fiber transmission L L What is the problem Well in this case it was the fact that we used grating HR3106 fits for the GRATING DATA and not grating LR600 fits If we run with grating LR600 fits then the reduction runs fine Similar problems would be encountered if you use an incorrect LINE MASK Often such errors are caused by editing old versions of sof files used for other setups and forgetting to change all the input files 8 2 Old versions of EsoReX Sometimes you may have different versions of EsOrEx on your system from previous version
39. by side The direction along which the light is dispersed is called the dispersion direction The direction perpendicular to the dispersion is called the cross dispersion direction or spatial direction in slit spectroscopy These directions are also indicated in Fig 2 Thus the first task in the data reduction process after cleaning the detector defects is to know where the spectrum of each fiber actually is 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 later Then a line is cut along the cross GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 6 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 Gaussian 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 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 field exposure Three packets of fibers are seen In the second one there is a missing broken fiber I
40. cience reduction and not the master bias After July 7th 2008 the levels in all biases should be the same The above noted one should still run the gimasterbias command to produce the bad pixel map If you decide to use the master bias for the science reduction then be sure to compare the bias subtracted science frame To produce the master bias and bad pixel map select all BIAS FRAMES and pass them to the recipe gimasterbias as shown in the left panel of Fig 12 A new window appears right panel of Fig 12 where all parameters related to the recipe gimasterbias can be controlled GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 25 GASGANO Version 2 2 3 cmelo Linux Bam Default grouping expand File J CLASSIFICATI TPL ID ORIGFILE TPL EXPNO TPL NEXP C Displaying 33 files Unfiltered pid 075 C 0245 D GIRAFFE UNKNOWN pid 60 4 9022 GIRAFFE FLAMES Operation Team 9 5 200117229 Calibration File Selected files Tools Help 9 Wl CIRAF 2005 07 01T15 00 37 382 fits BIAS FLAMES gir FLAMES_GIR 1 5 Ei CIRAF 2005 07 01T15 01 24 886 fits BIAS FLAMES gir FLAMES_CIR 2 5 El CIRAF 2005 07 01T15 02 12 420 fits BIAS FLAMES gir FLAMES_GIR 3 5 Wl CIRAF 2005 07 01T15 03 02 84 4 fits BIAS FLAMES gir FLAMES_GIR 4 5 GIRAF 2005 07 01T15 03 50 308 fits BIAS FLAMES gir FLAMES_GIR 5 5 B bad_pixel_map_0000 fits BAD PIXEL FLAMES gir 5 B master bias 0000 fits MAS
41. ction e fiber to fiber transmission Before submitting a proposal PIs should consider downloading previous GIRAFFE spectra from the ESO archive to see how badly their spectra will be contaminated by sky lines Figures 5 and 6 show how strong sky lines can be in the red We note that the current version of the GIRAFFE pipeline does not perform sky subtraction PIs should consider referring to the following articles amongst others on how to remove sky features in FLAMES data e Battaglia et al 2008 MNRAS 383 183 Contains a detailed description of how sky lines can removed from FLAMES GIRAFFE spectra e Koch et al 2007 AJ 134 566 An estimate in the final accuracy of sky subtraction of 3 per cent is given for Leo spectra e Koch et al 2006 AJ 131 895 An estimate in the final accuracy of sky subtraction of 2 per cent is given for Carina spectra Finally we refer to Wyse amp Gilmore 1992 MNRAS 257 1 for a very good discussion in the problematic of achieving accurate sky subtraction and how to assess the quality of the scattered light correction and the final sky subtraction using the inter fiber regions and the broken fibers GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 12 Ka serr Hier ISSF 1 SIT Figure 5 This image shows how especially in the red that there are many sky lines Re moving them can be critical to obtaining good science output The exposure was taken using GIRAFFE at L881 7 n
42. e 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 nasmyth 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 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 Looking at the rebinned arc spectrum produced by the wavelength calibration recipe will give you an idea if you have to remake it Sections 3 4 4 and 8 describe how to make this slit geometry table in gasgano and ESOrex GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 24 H cigar 2005 07 01
43. extract flat field spectrum is due to differences in the fiber transmission GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 70 00 00 100 100 000 0 140 2120 WE 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 In imaging or even in slit spectroscopy one can carry out a two dimensional flat field correc tion This means that after some manipulation your science frame can be divided by the flat field image In the case of fiber spectroscopy we have seen that the intensity of the pixels drops quickly at 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 flat image Flat field are corrections are done in one dimension i e the extracted science data is divided by t
44. f locfit 0000 fits FF_LOCFIT Iff psfcentroid 0000 fits FF PSFCENTROID Iff psfwidth 0000 fits FF PSFWIDTH Iff psffit 0000 fits FF PSFFIT fiber profile 0000 fits FIBER PROFILE ff extsnertra NANNA fits EF EXTSPECTRA home jsmoker Instruments FLAMES Pipelines Comparison Barrado ff psfwidth 0000 fits fhome2 jsmoker Instruments FLAMES Pipelines Comparison Barrado ff psffit 0000 fits home2 jsmoker Instruments FLAMES Pipelines Comparison Barrado fiber profile 0000 fits fhome2 jsmoker Instruments FLAMES Pipelines Comparison Barrado ff extspectra 0000 fits Jhome2 jsmoker Instruments FLAMES Pipelines Comparison Barrado ff exterrors 0000 fits Jhome2 jsmoker Instruments FLAMES Pipelines Comparison Barrado ff extpixels 0000 fits home2 jsmoker Instruments FLAMES Pipelines Comparison Barrado ff exttraces 0000 fits Completion status SUCCESS Figure 16 Recipe gimasterflat in action The recipe runs fine as we have told it which fibres in the flat have signal by changing the parameter giraffe fibers spectra to 1 26 28 135 GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 31 graphics File Edit Page Window Figure 17 Extracted flat field spectrum for one the fibers The spectrum was pro duced by gimasterflat and will be wavelength calibrated by the next step carried out by giwavecalibration GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 32 File View Gr
45. f them will convert the light photons more efficiently into electrons than 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 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 are clearly 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 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 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
46. h respect to the background In the lower panel one the core of the emission is display The object pops up with respect to the background GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 A W Cuts 1 Pixel Values v curs T Pixel Values Value 17405 0 Figure 24 Raw GIRAFFE IFU images of the solar spectrum on plate 1 top and plate 2 bottom Variations in the IFU responses are clear 42 VLT MAN ESO 13700 4034 GIRAFFE data reduction cookbook nmi 165 183 203 219 237 253 007 K Kol ME ul H ol eo o o Los B m B if Rea Figure 25 Raw GIRAFFE image of a field in which 15 IFU units were deployed The recon structed image is shown in Fig GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 43 219 237 253 183 203 113 131 059 077 095 025 043 Figure 26 Reconstructed image of 15 IFU units produced by the pipeline The raw image is shown in Fig 25 GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 44 ARGUS PA 45 degrees original position E E Reconstructed image ARGUS PA 45 degrees Tel moved 1 N and 1 E E Reconstructed image Figure 27 Argus reconstructed image with Position angle in the acquisition set to 45 degrees Top panel Original pointing Bottom panel Telescope moved by 1 0 arcseconds North and 1 0 a
47. he default of 137 fibres was used for a H395 8 setting cat gimasterflat 2009 04 15 14 36 37 1og Snip 14 36 44 INFO Generating mask 137 spectra expected 14 36 50 INFO 137 spectra detected in 1 wavelength bins 14 36 50 INFO Computing spectrum positions and widths in pixel range 2053 2053 14 36 50 INFO Not enough data points 1 for 4 order fit ERROR 14 36 50 ERROR Spectrum localization computation failed ERROR 14 36 50 ERROR Spectrum localization failed Aborting Completion status FAILURE Execution error Execution failed with code 1 However if giraffe fibers spectra was set within gimasterflat in gasgano the recipe works fine cat gimasterflat 2009 04 15 14 41 06 1og Snip 14 41 12 INFO Fiber setup taken from flat field frame home2 jsmoker Instruments FLAMES Pipelines Comparison Smartt Gasgano GIRAF 2003 04 15T00 11 23 320 fits 14 41 12 INFO Setting number of fibers ESO PRO SLIT NFIBRES to 136 14 41 12 INFO Bias sigma value 2 39 e Snip home2 jsmoker Instruments FLAMES Pipelines Comparison Smartt Gasgano GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 56 ff exterrors fits home2 jsmoker Instruments FLAMES Pipelines Comparison Smartt_Gasgano ff_extpixels fits home2 jsmoker Instruments FLAMES Pipelines Comparison Smartt_Gasgano ff_exttraces fits Completion status SUCCESS and the spectra are reduced GIRAFFE data reduction cookboo
48. he 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 enter 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
49. i temp grep 53 HIERARCH ESO INS TEMP53 NAME Surface table temperature top Temperature sen HIERARCH ESO INS TEMP53 VAL 13 500000 Temperature Sensor numeric value HIERARCH ESO INS TEMP53 NAME Surface table temperature top Temperature sen HIERARCH ESO INS TEMP53 VAL 13 830000 Temperature Sensor numeric value HIERARCH ESO INS TEMP53 NAME Surface table temperature top Temperature sen HIERARCH ESO INS TEMP53 VAL 13 830000 Temperature Sensor numeric value HIERARCH ESO INS TEMP53 NAME Surface table temperature top Temperature sen HIERARCH ESO INS TEMP53 VAL 13 840000 Temperature Sensor numeric value HIERARCH ESO INS TEMP53 NAME Surface table temperature top Temperature sen HIERARCH ESO INS TEMP53 VAL 13 840000 Temperature Sensor numeric value In the case above all data were taken within a temperature of 0 34 Celcius so shifts between science and calibrations should be small You can double check this by displaying an image and measuring the x y position of the centre of a science fibre and flatfield If the x position is shifted by more than 0 8 pixels then it is possible that the pipeline will not be able to flatfield the data GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 54 GIRAFFE grating stability last 90 days close up QC data range 2008 12 15 2009 03 14 20 HR DX 15 10 T oC 6 5 4 3 2 ss 0 1 2 GIRAFFE grating stability
50. ience will be larger than this due to S N constraints or because of instrumental shifts between science and calibration images GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 39 4 IFU and Argus image reconstruction 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 1og rw r r 1 cmelo astro 5166720 May 8 08 34 science exterrors 0000 fits rw r r 1 cmelo astro 5166720 May 8 08 34 science extpixels 0000 fits PLw r r 1 cmelo astro 5166720 May 8 08 34 science exttraces 0000 fits fw 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 and
51. ight 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 FOV Resolution Hectospec 6 7 m MMT MMT 300 1 deg 1000 2500 6dF 1 2 m UK Schmidt AAO 150 5 7 deg 2dF 3 9 m AAT AAO 400 2 deg Hydra 3 5 m WYIN KPNO 90 1 deg FLAMES 8 2 UT2 VLT 135 8 25 arcmin 5600 46000 48000 2 A brief overview of data reduction of multi fiber spec troscopy data This section presents 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 Al though 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 Sect 3 where an exam ple of the use of the ESO GIRAFFE pipeline is given Like any other reduction package the GIRAFFE pipeline has many adjustable parameters
52. inimum 0 Maximum 100 WV Auto Scale Sinale Pixel R1 1 R212 gt 0 Divide Std 2501 1000 3 500 3 93 e LL q T T 645 650 655 660 665 670 675 680 1 644 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 D DPUSER gt r dfits Users cmelo cookbook template science cube spectra 0000 fits Y DPUSER gt Enter DPUSER commands a OOO amp QFitsView by Thomas Ott bufferl Users cmelo cookbook template science cube spectra 0000 fits uokl oov STT 9049 2716 Summe x ae J2 2200 A minmax Z linear jo I s x 42966872 S ln Minimum 0 Maximum 100 V Auto Scale Single Pixel 7 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 0 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 23 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 wit
53. is 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 22 VLT MAN ESO 13700 4034 GIRAFFE data reduction cookbook 699 847 9v8 LEG SCT 88C 0 ST ST TL ER 9T 91 4899 cS8 S 4 vSC T TS 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 o Vu 10 LNATYO Seqrj Surssriu o4 anp zequnu 944 eua se owes eu4 eq shemTe JOU TTT STUL Agut ur unij2eds eut yoTds nok gen umous sr et zequnu edqn4iedy eua sr XHCNI eua I4 SON S9611 9 Z 9vtc9S 6vv pue cac9oSu SZPPOEO 9TPEOST OLEL 3nopueo esz923u 9 64400 T 6 Svc6 9g9pyueu egzgosu g Z06Sv 0 T1T1480T G6EL 3nopue esz923U y 9924vC Ol ZvTYEST 4644 3nopueo esz9oSu e g01198 0 06Sv411 8044 3nopueo egg29 3u z 10 Io WISTVO T VISHL U Lf 80 A TOW Td vT L IT 8 TON Td 9T 9 IT 6 TOW Td 8T S IT OT TOW Td OC IT TI TOW Td ec IT CI TOWN Td vo Z IT luorqezqrTeO 1 T I 0941101961160 PI suunjoo jo zequnw NOISNALX I n S311 0000 132edsuqi eoueros 2 19 IS Ip lE IZ IT D 19 E lv IZ IT
54. its GI_PFEX_Medusal_H599 3_09 fits GI_PLOC_Medusal1_H599 3_09 fits GI PLOW Medusa1 H599 3 09 fits GI MBIA fits DISPERSION SOLUTION FF EXTSPECTRA FF LOCCENTROID FF LOCWIDTH MASTER BIAS Inside gasgano the keyword PRO CATG appears in the column CLASSIFICATION 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 8 As shown in Figure 9 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 then 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 10 A GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 17 giscience v10000 SSeS nS E TEE None aaa ae giraffe biasremoval fraction EE GI MBIA fits slit geometry medusa1 H599 3 _09 tfits assi T r Figure 9 Pop up panel controlling the parameters and the arguments of girscience GIRAFFE data reducti
55. k VLT MAN ESO 13700 4034 57 A 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 have been reported to compile without problems on Mac OS machines e g SINFONI and UVES Care must be taken however because even if the pipeline appears to work there may be subtle effects that cause incorrect results 000
56. m for 2750 s GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 13 L MIN del 8 AN J ne 850 855 860 Wavelength angstroms T 113 ny l Lise N 850 875 300 Wavelength angstroms Figure 6 Extracted spectra of the image in Fig 5 showing a number of bright sky emission lines GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 14 w GASGANO Version 2 2 3 cmelo Linux x File Selected files Tools Help Ea L Default grouping expand mmm lE ml u File CLASSIFICATION TPL ID ORIGFILE T TPL EXPNO C Displaying 0 files Unfiltered Figure 7 Entry screen of gasgano 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 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 it can be downloaded at http www eso org sci data processing software pipelines It contains the GIRAFFE pipeline and its manual the calibration database gasgano and
57. n order to deal with broken fibers the pipeline uses the fact that the size of the fibers 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 or summed extraction
58. n 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 pipeline 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 This is done in the science frame when For more details about the wavelength calibration process we refer to Royer et al 2002 which is available at http d www eso org instruments flames doc spie royer ps gz GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 29 File View Graphics Real time Help Object LAMP FLAT x 440 v 22750 Value GC ST 8 F g Equinox E j Min 371 Max 20000 Bitpx 16 Low
59. nput The information they contain is the same but they are determined by different methods The FF LOCCENTROID is computed as the location of the barycen ter of the flux distribution within the extraction region and the corresponding width is the half width of the extraction region The FF PSFCENTROID is computed from the fit of the fiber profile and the half width from the FWHM You can even mix the 2 kind of frames i e use for instance the FF LOCCENTROID together with the FF PSFWIDTH If you provide both kinds for the centroid or the width the FF PSF variant is preferred 7 DISPERSION SOLUTION Wavelength calibration solution found with giwavecal 8 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 9 GRATING DATA Static table containing information about the physical model of GI RAFFE Files 2 7 are located in the calibration database delivered 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 GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 16 ba GASGANO Version 2 2 3 cmelo Linux File Selected files Tools Help amp Default grouping sl expand Find entry D find File CLASSIFICATION TPL ID ORIGFILE TPL EXPNO C Displaying 1023 files Unfiltered 9 pid 075 C 0245 D GIRAFFE UNKNOWN
60. nuum 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 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
61. on cookbook VLT MAN ESO 13700 4034 18 log file is written in the directory chosen to have the reduced data 184dhcp133 reduced 12 gt 1s giscience_2006 04 30_05 16 12 log Sun Apr 30 05 16 31 CLT 2006 home2 GIRAFFE ESO calib giraf calib 1 0b cal GI_PLOC_Medusai_H599 3_09 fits group CALIB level INTERMEDIATE type IMAGE tag FF_LOCCENTROID home2 GIRAFFE ESO calib giraf calib 1 0b cal GI_PLOW_Medusa1_H599 3_09 fits group CALIB level INTERMEDIATE type IMAGE tag FF_LOCWIDTH hnome2 GIRAFFE ESO calib giraf calib 1 0b cal grating_HR316 tfits group RAW level INTERMEDIATE type IMAGE tag GRATING_DATA home2 GIRAFFE ESO calib giraf calib 1 0b cal slit geometry medusai H599 3 o9 tfits group RAW level INTERMEDIATE type IMAGE tag SLIT GEOMETRY SETUP 05 16 12 L INFO No bad pixel map present in frame set 05 16 12 L INFO No master bias present in frame set 05 16 12 L 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 file 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 184dhcpi33 reduced 16 gt ls rtl total 42896 rw rw r cmelo cmelo 2364 Apr 30 05 16 giscience 2006 04 30 05 16 12 1og cmelo
62. rcseconds East i e the object moves 1 0 arcseconds South and 1 0 arcseconds West on ARGUS GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 45 5 Pipeline in action scripting your data reduction with ESOrex and sof files 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 importantly it gives you the opportunity to play with the different parameters and check how they impact in your data product in real time 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 con tains as expected a list of files to be used by a given recipe In the example below our raw science frame is GIRAF 2003 04 14T05 49 22 740 fits and path is equivalent to home jsmoker GIRAFFE DRS giraf kit 2 6 0 calib note that you should use a more up to date version of the pipline like
63. s 26 S43 rwaveealbsablOH e e secr eer s wee ed wok w 39 RETE da QUY n 28 3 44 giwavecalibration remaking the slit geometry table 35 201 T T TC uc AE xo Ek EC QUE EROR X De os RR BEE OLE EES 35 4 IFU and Argus image reconstruction 39 5 Pipeline in action scripting your data reduction with ESOrex and sof files 45 6 Automating data reduction using EsOrEx 48 7 Reducing data using calibrations taken far away in time 49 8 Common problems during data reduction 52 8 1 Incorrect input files i s sac seoa o s ER NI m sa s EROR RO lt w SQ 52 82 Old versions of BSORG ou 44 64 w ac RO e REM ERR EE ec 52 8 3 Mis allignment between calibration data and science frames 53 8 4 Cannot create local file error do da eed wo ER RR S 55 8 5 Spectrum localization computation failed within gimasterflat 55 GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 A Note for Mac users vi 57 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 Processing 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 R
64. ser manual After creating your master flat you may want to make sure that the fibre localisation has worked In order to do this it is necessary to look at the product ff_loccentroid fits as shown in Fig 18 and compare with the master flatfield In the product ff loccentroid fits the x coordinate responds to the fibre number the y coordinate to the y coordinate on the detector and the value to the x coordinate of the fitted localisation of the fibre If we move the mouse to position 10 2000 in ff loccentroid fits say we see the value of 160 62 Now if we display master fiber flat fits and move the mouse to the position of fibre 10 counting left to right for Medusa then we see that the centre of this fibre is x 161 67 an offset of about 1 pixel Note that this is just due to the difference in counting convention in the two products which always show this offset In this case this means that the localisation centroid ff loccentroid for the master fiber flat are identical to within 0 05 pixels Shifts of more than a pixel should be investigated as they may indicate problems with the data reduction 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 o
65. spectra in GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 File Help Current Queued Executing Parameters Name value Default Range giraffe fibers spectra giraffe fibers nspectra giraffe biasremoval remove giraffe biasremoval method giraffe biasremoval areas giraffe biasremoval sigma giraffe biasremoval iterations giraffe biasremoval fraction giraffe biasremoval xorder giraffe biasremoval yorder giraffe biasremoval xstep Cx 0 2147483646 N La lra lra lra lm Filename Classification GIRAF 2008 01 05T14 02 23 360 fits GIRAF 2008 01 05T14 04 18 900 fits GIRAF 2008 01 05T14 06 13 719 fits gibadpixelmap 2008 01 05 fits grating LR6O0 fits line mask ThAr L682 2 03 fits slit geometry medusal fits Product Naming Product Root Directory home jsmoker Instruments FLAMES Pipelines Comparison Barrado Browse Naming Scheme gt Beane y A Request Pool Execute Selected Ka Filename Classification 21 11 40 INFO Setting equilizing filter to 16 pxl for slit configuration Medusal 21 11 40 INFO Using raw spectra for localization 21 11 41 INFO Generating mask 136 spectra expected 21 11 48 WARNING Invalid number of spectra detected 134 136 ERROR 21 11 48
66. ts Subtracting the Bias level A bias voltage is routinely applied to CCD 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 o
67. which comes with scisoft released by ESO You can also install it yourself by downloading it from http www mpe mpg de ott QFitsView It has many nice functionalities to analyze and visualise your data The new version of QFitsView will read Argus cubes straight out of the box without any need for changes to the GIRAFFE headers You need to look for a HIERARCH ESO PRO CATG of SCI ENCE CUBE SPECTRA which will be something like r GIRAF 2009 02 14T02 39 37 821 0009 fits Note that at present that cubes are only produced for ARGUS but a future version will also make them for the IFU fibres An alternative is gaia which is available at http star www dur ac uk pdraper gaia gaia html Now science cube spectra 0000fits can be read by QFitsView as shown in Fig 23 The IFUs on the two plates have somewhat different responses Fig 24 shows a sky spectrum taken on plate 1 and and on plate 2 Fig 25 shows an example of a raw GIRAFFE image in which 15 stars were observed using IFU mode with Fig 26 displaying the reconstructed image of the same field that is produced by the pipeline GIRAFFE data reduction cookbook VLT MAN ESO 13700 4034 40 ane QFitsView by Thomas Ott buffer1 Users cmelo cookbook_template science_cube_spectra_0000 fits co mio lole Ta 79 49 3s25 sme i x lt amp A 2200 YQ minmax linear k i x 7 439 1692 M

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