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CRIRES data reduction cookbook

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1. MarkAll UnMarkAll MarkAllPublic Instant download FTP or media Reset M HDR Release RA OB ID DPR DPR DPR TECH in s INS MODE Date Object DEC Progid pen CATG TYPE packs E Header 2011 01 15 HD 49331 06 47 36 94 08 59 52 5 MEER CRIRE 2011 01 15T04 46 56 780 500553 SCIENCE OBJECT SPECTRUM NODDING OTHER HD 49331 Spectroscopy EZ Header 2011 01 15 HD 49331 06 47 37 57 09 00 04 3 ao CRIRE 2011 01 15T04 47 50 972 500553 SCIENCE OBJECT SPECTRUM NODDING OTHER HD 49331 Spectroscopy E Header 2011 01 15 HD 49331 06 47 36 94 08 59 52 7 ma CRIRE 2011 01 15T04 49 29 646 500553 SCIENCE OBJECT SPECTRUM NODDING OTHER HD 49331 Spectroscopy E Header 2011 01 15 HD 49331 06 47 37 59 09 00 04 2 HET A CRIRE 2011 01 15T04 50 27 917 500553 SCIENCE OBJECT SPECTRUM NODDING OTHER HD 49331 Spectroscopy El Header 2011 01 15 HD 49331 06 47 36 93 08 59 52 8 EA CRIRE 2011 01 15T04 52 00 754 500553 SCIENCE OBJECT SEECTRUM NODDING OTHER HD 49331 Spectroscopy A L re I I T I lY T gt Figure 12 Result of ESO archive search shown in Fig 11 Two nodding spectra have been selected CRIRES data reduction cookbook VLT MAN ESO 14200 4032 23 LJ File Edit View History Bookmarks Tools Help v http dataportal eso
2. ADS MAPOD SNEWS GiAstroPH Goog SIM e Y MESO WFLA BiFLA INT WFLA QC MiJVS Sch MPSO EPSO Int Remedy MICRIRES SICRIRES Int ESO Science Arc X BiCRIRES SCIOPS 5 ESO Science Archive CRIRES Query Form Description This form provides access to observations performed with CRIRES that are stored on line in the Science Archive Facility in Garching Find more information about CRIRES data on the Paranal ambient conditions can be queried separately from here Search Reset query Help Status of Requests Target Name and Equatorial Coordinates Target HD 49331 SIMBAD name sl C Input Target List i Browse Search Box 00 10 00 If Simbad Ned name or coordinates given ee jg vec 32000 Format RA h DEC deg v Galactic Coordinates O Galactic Search Box OO 30 00 If galactic coord given D Galactic Longitude D Galactic Latitude degrees Observation and proposal parameters El MAME seen i DD MM YYYY of night begin 12 00 UT OR give a query range using the following two fields start end dates apio os 01012011 12hrs UT em 01062011 12 hrs UT M Progld PPP chui e g 073 C 0156 E Progrsistypa ass Any v U sv node All modes Hipnas i as Plonly O Proposal Title Generic File Information E h Garren ERE IE H archive file
3. Image X 7308 Image Y 2213 oF EL Equinox J Peak above bg 8185 7 Background level 6 9 FWHMX Y 23 21 Angle of X axis 141 6 Pixels in x y 20 0 r Figure 35 Top panel CRIRES ThAr wavelength calibration for detector 3 at 1087 3 nm The Y value for the ThAr lines on this detector ranges from 221 to 223 pixels Detector 1 has Y values some 15 pixels higher detector 2 values some 14 pixels higher and detector 4 values some 10 pixels lower Bottom panel determining the Y position of ThAr fibres for detector 3 From version 2 3 1 of the pipeline these are used to define the y pos cN values of the fibres in the crires spec wavecal recipe CRIRES data reduction cookbook VLT MAN ESO 14200 4032 67 23 13 20 INFO Refine the degree 2 polynomial 23 13 20 INFO Wl error 0 00244457 nm 0 48 pix 23 13 20 INFO Nb of samples 10 23 13 20 INFO Nb of candidates 1000 23 13 20 INFO Cross Correlation factor 0 147333 23 13 20 WARNING Cross correlation too low 0 147333 Use estimate What can we do to improve the correlation factor Well instead of performing the extraction over the whole detector we can perform the extraction of the ThAr lines in a window as shown in Fig 38 for v2 1 3 of the pipeline and 39 for versions v2 3 0 1 and upwards of the pipeline In particular for v2 3 0 and upwards of the pipeline if you measure the Y position of 6 ThAr fibres on each det
4. 4 87 BERI Oly don do ee ee OHS Oe Roe AES X OOS EEE a 87 BEI IRAP dou rarene XR WA EG x PACK P dX S RE wR ES 87 8 10 Plotting reduced spectra 4 22 zelo oko x9 ee Sed ee oe EE 87 9 Utilities recipes 87 9 1 Examples of the use of the utilities 2 2 5 24 ee eee ee RR ww 89 Ola Cree ee aud eS E ee x8 ee A 89 DLT erres eee s pirea ona ee Ew Ree RE Bee Soe 90 OLS enesti wisshD 2 4 24 24 G26 4G bE PER REA EIER 6 EES Ee 90 DLA erbe util Wlassigh s nous uox Xe bee OSE de ROO A dede KER RS 90 915 ere cun genlines s so 49399 Reo Ew ee Row E 90 10 Limitations and problems 91 10 1 Wavelength calibration issues o 2229 9 9o Rc DR Rx Ux RR 91 10 1 1 Limited accuracy in the ThAr and OH linecatalogues 91 IDLS Too few TRAT ines dock ee ee X oder eK ee ROR KO RR OS 91 10 1 3 False identification of ThAr line features len 91 1012 Problems 19 acti ono nodos ed eee Ro e ew Rew AS OPE Se OSES 3 91 Wg IRAT Tee cog he we 4 GR SSR ESE EER ES ER 91 104 Correcting for non linearity ec o o ceuc hee dod tiesai teak 94 10 5 Problems in running gasgano saoao be ba o 95 100 Cannot ind recipe Deg ecr cce sre Goe greg Se eee ES eee oS ee k 96 10 7 Problems in running ebore s eae RES EASE E aE e eg oe 96 A Example IDL script to read in reduced data and produce ascii format output files 97 B Example IRAF script to read in reduced data and produce ascii format output files 100 CRIRES data reduction cookbook VLT MAN ESO
5. Product frames Completion status SUCCESS home jsmoker Instruments CRIRES Pipeline Data Raw crires_spec_dark_ Writing FITS propertyist product CALPRO DARK crires_spec_dark fits 0000 fits 4 Figure 27 Master dark creation within gasgano CAL_DARK CAL_DARK CAL_DARK CAL_WLLAMP CAL_WLLAMP CAL_WLLAMP CALPRO_DARK El CRIRE 2010 10 20713 56 57 981 fits El CRIRE 2010 10 20713 57 24 036 fits El CRIRE 2010 10 20713 57 52 040 fits CRIRE 2010 10 20T13 59 48 752 fits El CRIRE 2010 10 20T14 01 20 13 1 fits El CRIRE 2010 10 20714 02 47 227 fits U crires_spec_dark_OOOO fits gt 200165585 specphot Xi2Cet JHKLM CALPRO_DARK IMAGE IMAGE IMAGE SPECTRUM SPECTRUM SPECTRUM DARK DARK DARK WAVE LAMP WAVE LAMP WAVE LAMP 5219 100 5219 100 5219 100 1087 300 1087 300 1087 300 5050 4 E 5 000 5 000 5 000 52 3 000 52 52 11 3 000 3 000 FowlerNsamp FowlerNsamp FowlerNsamp FowlerNsamp FowlerNsamp 19 FowlerNsamp 3 FowlerNsamp wow w 19 zr 50 crires spec dark 0000 fits unknown orig name CALPRO DARK Extension IMAGE CHIP4 INT1 w Find in header QC A Filter Auto Display find Load Filter Ln Keyword Value DET CHIP GAIN 7 27 DET CHIP ID ESO Aladdin IDET CHIP LIVE IT DET CHIP NO 4 DET CHIP NX
6. e TPL ID contains an unique identifier describing the template which was used to produce the data e DPR CATG Data Product category SCIENCE CALIB Frame selection in the pipeline is mostly based on this keyword value e DPR TYPE Data Product type OBJECT SKY e DPR TECH Data Product acquisition technique e g IMAGE SPECTRUM NODDING SPECTRUM e TPL NEXP Number of scheduled exposures within the template e TPL EXPNO Exposure rank number within template A template may produce several different frame types Frames are discriminated by the value of the DPR keywords DPR CATG DPR TYPE and DPR TECH take different values depending on the observed frame type The offsets sent to the telescope for jitter observations only relevant if the Jitter width is greater than 0 are stored into 4 keywords This applies to AutoNodOnSlit GenericOffset and SpectroAstrometry templates e SEQ CUMOFFSETX and SEQ CUMOFFSETY for cumulative offsets in pixels e SEQ CUMOFFSETA and SEQ CUMOFFSETD for cumulative offsets in arcseconds alpha delta Cumulative offsets are always relative to the first frame in the batch TPL EXPNO 1 If the same guide star is used before and after an offset the offsetting accuracy is about 0 1 arc seconds All recipes looking for offset information take this into account and will use the header offset information as a first guess and will refine the offset through cross correlation techniques The j
7. 1024 DET CHIP NY 1024 IDET CHIP PXSPACE 2 7E 05 IDET CHIP RON 10 DET CHIP X DET CHIP XGAP DET CHIP Y DET CHIP YGAP IDET WIN NX IDET WIN NY IDET WIN STARTX IDET WIN STARTY 6 8746721627819 QC RON2 6 77970798213789 QC DARKMED 2 94444449742635 Lehi Figure 28 Master dark result within gasgano showing quality control parameters for derived readout noise CRIRES data reduction cookbook VLT MAN ESO 14200 4032 51 8 2 2 Reduction of darks within esorex for flats and science frames To obtain the same result within esorex one has to have an input file containing the names of the darks like this cat Darks sof CRIRE 2010 10 19T15 16 07 776 fits CAL DARK CRIRE 2010 10 19T15 16 35 681 fits CAL DARK CRIRE 2010 10 19T15 17 03 820 fits CAL DARK And then run esorex using the following command esorex output dir home2 jsmoker Instruments CRIRES Pipeline Data Reduced Xxx ESO Recipe Execution Tool version 3 9 0 crires spec dark Darks sof 28K KKK INFO crires spec dark pbob ooo oook kkk INFO crires spec dark Detector 1 Y 1 gt Y 512 pixels INFO crires spec dark Detector 2 Y 1 gt Y 512 pixels INFO crires spec dark Detector 3 Y 1 gt Y 512 pixels INFO crires spec dark Detector 4 Y 1 gt Y 512 pixels INFO crires spec dark pbob ooo oook kkk INFO crires spec dark DIT valu
8. HIERARCH ESO TPL ID is short ened to TPL ID A classification example could be both commands are equivalent since fitsort is case insensitive CRIRES data reduction cookbook VLT MAN ESO 14200 4032 4 dfits CR fits fitsort TPL ID DPR TYPE INS WLEN REF INS SLIT1 WID AOS RTC LOOP STATE DET DIT DET NDIT dfits CR fits fitsort tpl id dpr type ins wlen ref ins sliti wid aos rtc loop state det dit det ndit The output from this combination is something like CRIRES SPEC DARK108 0013 fits CRIRES spec cal Darks DARK 4092 900 0 200 2 0000000 3 all on one CRIRES SPEC FLAT108 0001 fits CRIRES spec cal LampFlats FLAT 4092 900 0 200 10 0000000 6 all on one CRIRES_SPEC_STDO76_0011 fits CRIRES spec cal AutoNodOnSlit STD 2287 000 0 400 20 0000000 4 all on one CRIRES SPEC STDO76 0012 fits CRIRES spec cal AutoNodOnSlit STD 2287 000 0 400 20 0000000 4 all on one Which shows the filename name of template used to produce the file data product type reference wavelength slit width loop status i e if the adaptive optics was deployed or not DIT and NDIT This kind of table is useful in getting an idea of what is present in a directory or list of direc tories Loading such a summary table into a spreadsheet program also makes it conveniently readable Another easy way to visualise the content of a FITS file is using the graphical Gasgano tool which is the data management tool currently used at VLT Gasgano off
9. Science User Information gt ESO User Portal gt ESO Archive Requests Jonathan Smoker Logout ESO User Portal EX Request 427 577 by Jonathan Smoker ata Access Control ESO Query SAF HD 49331 two wavelength download for cookbook example Science Archive Download Selected ive Requests reams Requested Datasets UNIX Linux Shell script if you prefer command line download of complete requesffiownloadRequest27577 script sh Select Dataset File Category Access PI Pack Requests n Y SAF CRIRE 2011 01 15T04 46 56 780 FAQ H V SAF CRIRE 2011 01 18705 05 20 631 Files 1 94 of 94 333 5MB NGRH 1 4 10 ESO Data Flow Infrastructure Send us your comments Subscribe to Newsletter Privacy Statement Figure 14 Query result hitting will show the associated calibrations that were associated with the science spectra queried in Fig 13 A shell script can be saved to download the data and calibrations red ellipse or a java applet run Fig 16 CRIRES data reduction cookbook VLT MAN ESO 14200 4032 24 9 File Edit View History Bookmarks Tools Help 8 http dataportal eso org rh requests JSMOKER 27577 2 iv a d HADS KIAPOD SNEWS GAstroPH 4SGoog SIM e Y ESO WFLA EFLA INT WFLA QC INJVS Sch IPSO BiPSO Int is Remedy MICRIRES BiCRIRES Int gt ESO PSO home 6 Eso Request Han BECRIRES SCIOPS ESO Archive Requests Reaching New Heights in Astronomy e Jonathan
10. by fitting them or alternatively use a second telluric standard that does not have helium or hydrogen lines so that these lines can be removed from the hot star If required users should provide their own telluric standard s In the case where there is a problem with the provided telluric typically an observatory standard will be taken In these cases the CRIRES FITS header does not contain the full target name of the telluric standard and sometimes operators forget to include it in the night report To find out which telluric standard was used look at the RA and DEC of the target and consult the following link CRIRES data reduction cookbook VLT MAN ESO 14200 4032 29 http www eso org sci facilities paranal sciops catsearch html 5 7 Flux calibration The first step is to obtain a relative flux calibration The second step is to do absolute flux calibration If the telluric standard was a hot star then a blackbody curve can be used to model the continuum of the standard The spectral type of the star can be used to give an idea of what temperature to use The blackbody curve is then multiplied into the object spectrum For solar type stars a blackbody curve is a good enough description of the spectral energy dis tribution above 1 6 microns Below 1 6 microns a more accurate description of the continuum is required The second step is absolute flux calibration If the magnitude of the target is known one can determine the appr
11. crire crires spec jitter wl err crire crires spec jitter wl xclimit crire crires spec jitter waves crire crires spec jitter rej crire crires spec jitter spec zone crire crires spec jitter comb used crire crires spec jitter refine crire crires spec jitter onlyA crire crires spec jitter onlyB crire crires spec jitter blind crire crires spec jitter wl log crire crires spec jitter wl nolimit crire crires spec jitter wl clean HOO Input Frames Include Filename Classification CRIRE 2010 10 20T03 21 52 798 fits LS SS T DOT Locate Display master dark 5pOs fits l j Locate CD isplay master flat 1087p3 fits Locate Display crires spec wavecal tab 0022 fits RO Locate Display M CRIRES 2010 09 21T17 04 57 320 fits DE Locate Display M CRIRES 2010 09 21T17 05 07 420 fits DE Locate Dispay M CRIRES 2010 09 21T17 05 13 214 fits Locate X Display Product Naming T Root Directory home ismoker CRIRES Reduced Browse Naming Scheme Figure 44 Dark subtraction flatfielding wavelength calibration non linearity correction extraction and combination of simple nodding observations using gasgano CRIRES data reducti
12. x v x 2 x L4 L4 x CRIRE 2011 01 15704 46 56 780 xml ASSOCIATION TREE 89KB M SAFSCRIRE 2011 01 18T05 05 20 631 333 5MB NGRHAL 4 16 ESO Data Flow Infrastructure Send us your comments Subscribe to Newsletter Privacy Statement Figure 15 Results of query of the raw data and associated calibrations that can either be downloaded using the java applet or the shell script highlighted by the red ellipse shown in Fig 14 CRIRES data reduction cookbook VLT MAN ESO 14200 4032 25 CRIRE 2011 01 15T04 47 50 972 fits Z CRIRE 2011 01 15T04 45 54 946 fits Z mr CRIRE 2011 01 15T10 03 52 997 fits Z Queued CRIRE 2011 01 15T12 33 25 959 fits Z Queued CRIRE 2011 01 15T12 34 45 559 fits Z Queued CRIRE 2011 01 15T12 36 09 493 fits Z Queued CRIRE 2011 01 15T13 48 41 291 fits Z Queued CRIRE 2011 01 15T14 05 22 521 fits Z Queued P CRIRE 2011 01 15T14 22 03 756 fits Z Queued M CRIRE 2011 01 15T16 03 26 476 fits Z Queued CRIRE 2011 01 15T16 03 48 841 fits Z ETTUTTES 7 0 0 0 0 5 CRIRE 2011 01 15T16 04 06 893 fits Z Queued Mr CRIRE 2011 01 15T16 04 48 613 fits Z mr CRIRE 2011 01 15T16 05 34 183 fits Z Queued 777 0 0 03 CRIRE 2011 01 15T16 06 17 779 fits Z Queued CRIRE 2011 01 15T16 07 23 407 fits Z Queued MO CRIRE 2011 01 15T16 07 51 257 fits Z rm 22 44 32 CRIRE 2011 01 15104 46 56 780 fits Z Queued lt gt 22 44 32 Downloading 22 44 32 CRIRE 2011 01 15T04 47 50 972 fit
13. 1087 1088 1083 1080 0 1084 1085 1086 1087 1088 1089 1090 Wavelength nm llavelenath nm Figure 46 Dark subtraction flatfielding wavelength calibration non linearity correction extraction and combination of simple nodding observations In this case optimal extraction gives an improved S N ratio CRIRES data reduction cookbook VLT MAN ESO 14200 4032 86 1150 Extracted Spectrum 1100 1050 H ud e o py e ceo o row e e o Intensity OPT ADU sec Intensity OPT ADU sec 5 s Mofes 36 1085 38 1086 1086 02 1086 04 1086 06 1086 08 1086 1 1085 1 986221086 241086 261086 28 1086 3 1085 321086 541085 351086 38 1086 E 1120 1150 1100 1100 as eo o uw c o pes e E o wo a o Intensity OPT RDU sec 5 8 res oS n2 o Intensity OPT ADU sec E o wo c o 1005 5 5 1085 98 1008 1006 02 1008 0 1000 08 1000 08 1086 1 1088 1 aoe A ZETORE E KE zu CHILE De nri Wavelength nm Wavelength i 1089 99 y 1085 45 xz 1090 16 y 802 787 1140 1120 3 3 1100 3 S 1050 E 1080 Es amp 1000 51060 2 4 z 9 1040 o i n 300 1020 Combined j P B8 3 10g tae 36 1085 98 1085 TX 02 TX 04 TX 06 TX 08 TE 1 1086 1 sibs 221085 241085 XU 28 1086 3 TX TUE THO TI 38 1086 Rae pay Wavelength nm a Wavelength nm Figure 47 Extraction of NodA alone NodB alone and the combined spectra Slight shifts between NodA and NodB are app
14. 632 fits CRIRE 2011 04 10T03 10 13 780 fits 607 0 Y 408 0 Value 300 0 Y 3840 14025 3 s at a ae Equinox 407 625 6384 88 Bitpix e Min 320 193 Max 151441 E 32 200 375 High 334 375 Auto Set Cut Levels Low 9535 38 High 148261 J e zz m zl nl Auto Set Cut Levels Zz a Zin 3 i Graph plot image pixel values along line 2 zoom restore Figure 8 Detector linearity frames taken at 4007 0 nm Left panel DIT 2 0 s Right panel DIT 100 0 s Figure 9 Example of ghost observed with a reference wavelength of 1153 8 nm The ghost is visible in a staring frame top left on detector 2 Also a diagonal scratch right edge of detector 2 and a vertical scratch middle of detector 4 are visible CRIRES data reduction cookbook VLT MAN ESO 14200 4032 20 E Pick Object 1 Peak count in remnant ADU 100 3200 300 400 0 0 50 100 Minutes since saturation Figure 10 Left plot Example of remanence on a 600 s dark image on Detector 1 taken after the detector was saturated with a ThAr arc exposure Right plot Decay of remanence with time for the four detectors CRIRES data reduction cookbook VLT MAN ESO 14200 4032 21 File Edit View History Bookmarks Tools Help http archive eso org wdb wdb eso crires form Lm Q Sv Google UK ala
15. CRIRES Pipeline Data Rawj crires spec jitter contrib fits home jsmoker Instruments CRIRES Pipeline Data Rawj crires spec jitter prof fits home jsmoker Instruments CRIRES Pipeline Data Raw crires spec jitter bgmap fits home jsmoker Instruments CRIRES Pipeline Data Rawj crires spec jitter wlmap fits home jsmoker Instruments CRIRES Pipeline Data Rawj crires spec jitter extracted fits Completion status SUCCESS Figure 21 Successful reduction using the crires spec jitter recipe Note that this is the simplest reduction possible for example there is NO correction for the odd even effect flatfielding or good wavelength calibration CRIRES data reduction cookbook VLT MAN ESO 14200 4032 41 GASGANO Version 2 4 0 jsmoker Linux File Selected files Tools Help n a a Default grouping x expand Find entry find 1 File CLASSIFICATION PRO CATG DPR TECH DPR TYPE JINS GRAT O INS WLEN DET DIT DET NDIT DET NCORRS NA Displaying 55 files Unfiltered a pid 60 A 9051 4 CRIRES UNKNOWN e 200163466 Calibration 200165585 specphot Xi2Cet JHKLM i CRIRE 2010 10 20T03 21 52 798 fits CAL NOD SPECTRUM NODDI STD 52 1087 300 5 00 2 FowlerNsamp i CRIRE 2010 10 20T03 22 23 810 fits CAL NOD SPECTRUM NODDI STD 52 1087 300 5 00 2 FowlerNsamp i CRIRE 2010 10 20
16. DIT of both science and flat field larger than 2 sec then you can still get a good correction with residuals smaller than 1 of the non linearity of the detectors in cluding the odd even effect by downloading non linearity corrections appropriate to the data of observation from the following webpage http www eso org observing dfo quality CRIRES pipeline pipe calib html Data taken with DITs shorter than 2 sec are affected by the finite reset time of the detector arrays Sections 8 3 and 10 4 describe how to obtain the non linearity coefficients and their limitations at low and high light levels 3 4 4 Remnants from bright sources If the array is exposed to a bright source and is saturated a remnant becomes visible The amplitude of the remnant and the time it lasts depend on the brightness of the source see Fig 10 for an example They are a nuisance and by Murphy s law are bound to land on your spectrum Hence in Service Mode no saturation of the detectors is permitted 3 4 5 Fringing No extreme detector fringes are detected in the wavelength range useful for science observa tions Strong fringes are only visible beyond 5 um outside the atmospheric window 4 Downloading CRIRES raw data and calibrations Users must have an ESO user portal ID that is also used to submit proposals It is easily obtained by registering at http www eso org UserPortal Once registered raw CRIRES spectra and calibrations should be downlo
17. Figure 18 Adding files in gasgano CRIRES data reduction cookbook VLT MAN ESO 14200 4032 36 7 The ESO CRIRES pipeline Quick look data reduc tion of CRIRES nodding and stare images using the recipe crires_spec_jitter We will describe the data reduction of a standard star at two wavelengths 1087 3 nm and 3611 0 nm using both gasgano and esorex The first example will be of spectra taken by nodding along the slit finally an example of a quick look reduction of a stare image will be presented Your first quick reduction will use just two scientific spectra one in each nodding position and the recipe crires_spec_jitter 7 1 Data reduction of nodding spectra using gasgano Within gasgano we click on the file or files that we wish to reduce in this case CRIRES 2010 10 20T03 28 13 918 which is a spectrum of wavelength 3611 00 nm Then go to Selected Files To Recipe Load Recipe and crires spec jitter Fig 19 At this point a further window will appear crires spec jitter v20103 Going from top to bottom there are several sub windows which are explained as follows e Parameters For the crires spec jitter recipe there are 23 parameters that you can alter as you please in order to tune the data reduction top panel of Fig 20 e Input frames In this case we have only incorrectly added one input frame You will notice that gasgano has classified this frame as CAL NOD using the classification rules Note tha
18. GuideMocle Rst crires spec jitter extracted fits unknown orig name gt STD_EXTRACT_WL_TAB Extension Find in header v find Load Filter Filter Ke ord Value gt a IL 2011 09 29T 16 20 34 ESO Paranal ESO VLT U1 k CRIRES STD 02 28 09 5 08 27 39 82 2000 FS 55489 14460553 2010 10 20T03 28 13 9182 Figure 22 Gasgano raw and reduced data obtained with crires spec jitter CRIRES data reduction cookbook VLT MAN ESO 14200 4032 42 7 2 Quick data reduction of nodding spectra using esorex For the simplest data reduction of nod jitter observations using ESOREX one needs only the following sof file cat Science_Frames_1087p3 sof CRIRE 2010 10 20T03 21 52 798 fits CAL NOD CRIRE 2010 10 20T03 22 23 810 fits CAL NOD And then run the following command esorex output dir home2 jsmoker Instruments CRIRES Pipeline Data Reduced crires spec jitter Science Frames 1087p3 sof mv out 0000 fits std combined ima 1087p3 fits mv out O001 fits std contribution ima 1087p3 fits mv out 0002 fits std profile ima 1087p3 fits mv out O003 fits std bgd map ima 1087p3 fits mv out O004 fits std wl map ima 1087p3 fits mv out O005 fits std extract wl tab 1087p3 fits and run something similar for the other wavelength setting with a different sof file Note that these dat
19. INFO crires_spec_wavecal Calibrate chip number 1 INFO crires_spec_wavecal Wavelength range 1070 57 1076 24 INFO crires_spec_wavecal Correct the bad pixels INFO crires spec wavecal Correct for the dark INFO crires spec wavecal Correct for the flat field lt snip gt WARNING crires_spec_wavecal Cross correlation too low 0 0640687 Use estimate lt snip gt INFO crires_spec_wavecal Calibrate chip number 3 INFO crires_spec_wavecal Wavelength range 1084 7 1089 91 INFO crires_spec_wavecal Correct the bad pixels INFO crires_spec_wavecal Correct for the dark INFO crires_spec_wavecal Correct for the flat field lt snip gt WARNING crires_spec_wavecal Cannot fit a gaussian at 918 928 INFO crires_spec_wavecal Save the product INFO crires_spec_wavecal Writing FITS propertylist product WL_MAP_IMA crires_spec_wavecal_ima fits INFO crires_spec_wavecal Writing FITS table product CALPRO_WAVE crires_spec_wavecal_tab fits INFO esorex Created product home2 jsmoker Instruments CRIRES Pipeline Data Reduced out_0000 fits INFO esorex Created product home2 jsmoker Instruments CRIRES Pipeline Data Reduced out_0001 fits CRIRES data reduction cookbook VLT MAN ESO 14200 4032 72 INFO esorex 2 products created mv home2 jsmoker Instruments CRIRES Pipeline Data Reduced out_0000 fits home2 jsmoker Instruments CRIRES Pipeline Data Reduced ThAr
20. IWVSTD START Standard deviation of the Integrated Water Vapor measure ments towards zenith over the previous 2 min at start of exposure Implemented soon Instrument Keywords Here is a non exhaustive list of instrument keywords INS SLIT1 WID Entrance slit width since Oct 2011 set to 0 2 or 0 4 arcseconds INS WLEN REF Reference wavelength microns INS WLEN CWLEN Central wavelength microns INS WLEN END1 Wavelength at the end of detector 1 microns INS WLEN END2 Wavelength at the end of detector 2 microns INS WLEN END3 Wavelength at the end of detector 3 microns INS WLEN END4 Wavelength at the end of detector 4 microns INS WLEN MIN Minimum wavelength of the unvignetted spectral range microns INS WLEN MAX Maximum wavelength of the unvignetted spectral range microns INS GRAT ORDER Grating order INS LAMP1 ST Halogen lamp status INS LAMP2 ST IR Emitter lamp status INS LAMP3 ST NeKr lamp status INS LAMP4 ST Thorium Argon lamp status INS DROT MODE Derotator mode e g SKY or ELEV DET DIT Detector Integration Time seconds DET NDIT Number of averaged DITs AOS RTC LOOP STATE Adaptive optics loop state closed or open Observation Block Keywords OBS PROG ID Program ID OBS NAME Name of the OB as prepared with P2PP OBS TARG NAME Target package name as prepared with P2PP CRIRES data reduction cookbook VLT MAN ESO 14200 4032 7 2 7 Template Keywords 2 7 1 Keywords common to all templates
21. Inspection of log messages for wavecal reduction in Fig 36 that show the wavelength calibration failed crires spec wavecal v20103 Figure 38 File Help Current Queued Executing Parameters Name Default crire crires spec wavecal display crire crires_spec_wavecal wl_samples crire crires_spec_wavecal wl_starty crire crires spec wavecal wl stopy crire crires spec wavecal degree crire crires spec wavecal wl err crire crires spec wavecal wl xclimit crire crires spec wavecal waves crire crires spec wavecal wl log crire crires spec wavecal wl nolimit crire crires spec wavecal wl clean Include Filename Classification CRIRE 2010 10 20T13 59 48 752 fits CRIRE 2010 10 20T14 01 20 131 fits CRIRE 2010 10 20T14 02 47 227 fits bpm 1087p3 fits master dark 3p0s fits master flat 1087p3 fits lines thar fits model conf fits Locate Display Locate Display Locate Display Locate Display Locate Display Locate Display Locate Display Locte Display j Product Naming Product Root Directory home jsmoker CRIRES Reduced Browse Naming Scheme Successful detector 3 wavelength calibration using gasgano changing the crire cr
22. Let s add the other nodding position Selected Files To Recipe crires_spec_jitter_v20103 This will then appear in the Input Frames sub window We now have a full A B pair so let s try again to run the recipe Hit Execute and wait for a while until we see SUCCESS Fig 21 The reduced files are visible in red see Fig 22 Note that one can use the recipe with only one nodding position but the input parameters have to be changed e g see Sect 7 3 CRIRES data reduction cookbook VLT MAN ESO 14200 4032 File Selected files Tools Help GASGANO Version 2 4 0 jsmoker Linux 38 cg Display Serine oreson Defauttorouning v expand ria ene a i To Redpe Request Fool g GUCCI arenes DPR TECH DPR TYPE INS GRAT ORDER INS WLEN REF DET DIT DET NDIT DET NCORRS NAME 3 Report kd crires model wlmap Move UNKNOWN crires_spec_astro Copy lion crires_spec_dark q Tar t Xi2Cet JHKI crires spec flat Run T03 21 52 7 SPECTRUM NODDING OTHER STD 52 1087 300 2 FowlerNsamp CRIRE 2010 10 20T03 22 23 8 crires_spec wavecal SPECTRUM NODDING OTHER STD 52 1087 300 S FowlerNsamp Ej cRIRE 2010 10 20T03 2 7 7 crires util combine SPECTRUM NOD
23. Smoker Logout Slane Request 27 577 by Jonathan Smoker Data EU SAF HD 49331 two wavelength download for cookbook example Select All J Unselect All Download Selected Requested Datasets UNIX Linux Shell script if you prefer command line download of complete request downloadRequest27577seript sh Files 1 94 of 94 Select Dataset File Category Access H El Y SAF CRIRE 2011 01 15T04 4656 780 n CRIRE 2011 01 15T04 46 56 780 fits Z OBS NOD 40MB CRIRE 2011 01 15T04 47 50 972 fits Z BS NOD 40MB CRIRE 2011 01 15704 45 54 946 fits Z ACQUISITION 14MB CRIRE 2011 01 15T10 03 52 997 fits Z CAL FLAT 56MB CRIRE 2011 01 15T12 33 25 959 fits Z CAL FLAT 59MB CRIRE 2011 01 15T12 34 45 558 fits Z CAL_FLAT 59MB CRIRE 2011 01 15T12 36 09 493 fits Z CAL_FLAT 59MB CRIRE 2011 01 15713 48 41 291 fits Z CAL DARK 61MB CRIRE 2011 01 15T14 05 22 521 fits Z CAL_DARK 6 0MB CRIRE 2011 01 15722 59 15 665 fits Z CAL_DARK 45MB CRIRE 2011 01 15723 04 21 902 fits CAL DARK 45MB M CRIRES 2008 06 17T16 47 59 528 fits CALPRO_HITRAN_CATALOG 86MB M CRIRES 2008 06 17T16 48 16 005 fits CALPRO OH CATALOG 272 8KB M CRIRES 2008 06 17T16 48 31 605 fits CALPRO MODEL CONFIG 112KB M CRIRES 2010 09 21T17 04 57 320 fits DETLIN_A 81MB M CRIRES 2010 09 21T17 05 07 420 fits DETLIN_B 81MB M CRIRES 2010 09 21T17 05 13 214 fits DETLIN C 81MB CRIRE 2011 01 15T04 46 56 780 NL txt NIGHTLOG INFO 666B v x v x v v v
24. T T 0 500 1000 Value 0 0 Equinox Min 273 75 Max 3578 Bitpix 32 Low 0 High 20 Auto Set Cut Levels Z 2 Sl 1 CRIRE 2010 02 04T12 3 923 fits 1 File View Graphics Go Data Servers Pixel Values E Zoom Object CRIRE 2010 0 Equinox Min 3122969 Max 79163 Bitpix 32 Low High foo Auto Set Cut Levels Scale ziz Sizinu Value 53 330730438232 Print Cose Figure 3 Top image A 1 s dark detector 3 range 0 to 20 ADU Bottom image A 600 s dark detector 3 range 0 to 100 ADU Note the strong detector glow present and is visible on all four detectors The cut is taken at y 10 pixels CRIRES data reduction cookbook VLT MAN ESO 14200 4032 13 Rta Real t Cuts 1 View Graphics Real time Pixel Values object CRIRES_SPEC_FL xmo oO Mi 533513 low 533813 1 Scale 1 2x zi X 266 Value 4806 5249023437 pss i Graph plot image pixel values along line zoom restore Figure 4 Science detector image of a flatfield on detector 3 at A 5050 4 nm The diagonal black line is caused by bad pixels The absorption lines in the spectrum are due to water vapour in the instrument between the calibration lamp and the vessel entrance window CRIRES data reduction cookbook VLT MAN ESO 14
25. TYPH INS CR NS LE DET DIT DET NDIT DET NC File Selected files Tools Help Default grouping expand Find entry find so CLASSIFICATION PRO CATG D D TES sd e d C Displaying 8 files Unfiltered Unknown Program Unknown Observation B ines hitran fits Bl ines model fits B ines n2o fits B ines oh fits B ines thar fits Bl model conf fits Bl model conf 04 10 11 2010 fits B stdstars fits CALPRO HITRAN CATALOG CALPRO MODEL WAVEEG CALPRO N20 CATALOG CALPRO OH CATALOG CALPRO THAR CATALOG CALPRO MODEL CONFIG CALPRO MODEL CONFIG CALPRO STD PHOTOFLUX CALPRO HITRAN CATALOG CALPRO MODEL WAVEEG CALPRO N20 CATALOG CALPRO OH CATALOG CALPRO THAR CATALOG CALPRO MODEL CONFIG CALPRO MODEL CONFIG CALPRO STD PHOTOFLUX Figure 17 Top panel Initial opening screen for gasgano Middle panel Before increasing the column width Bottom panel Column width in gasgano increased CRIRES data reduction cookbook VLT MAN ESO 14200 4032 35 File CLASSIFICATION C Displaying 8 files Unfiltered pid Unknown Program Edit directory set Data Directories and Files home2 jsmoker Instruments CRIRES Pipeline crire kit 2 1 3 ci home2 jsmoker Instruments CRIRES Pipeline Data Raw home jsmoker Instruments CRIRES Pipeline Data Reduced 4 Add File Remove Selected Files
26. amongst others 4 cat OBS EXTRACT WL TAB WithAllCals 120s AO1 ascii Extracted RECT D 425 16g Extracted OPT D 425 16g Error RECT D 425 16g Error OPT D 425 16g Weight Norm RECT D 25 16g Weight_Norm_OPT D A25 16g Background noise D 425 16g Wavelength D A25 16g Wavelength model D A25 16g HIERARCH t ESO QC FWHM DIFF 23 4195905544356 HIERARCH t ESO QC FWHM DIFF 23 4195905544356 4738 449440002442 4738 449616523445 2 381331792048803 2 381331880760329 41 34259 43634033203 0 4034 38590909091 all on one line 417132 57120513916 4732 571381441183 2 379854258206329 2 379854346862813 41 34259 43634033203 0 4034 405363636364 all on one line 4744 603256225586 4744 603432975838 2 382877806448656 2 382877895217775 41 34259 43634033203 0 4034 424818181818 all on one line snip If one wanted to select just the wavelength and optimally extracted columns one could then do cat OBS EXTRACT WL TAB WithAllCals 120s AO1 ascii grep iv e printf 20 5f 20 5f n 8 gt OBS EXTRACT WL TAB WithAllCals 120s AO1 Wlen ExtOPT Err ascii all one line Thanks to Ronald Mennickent Cid for the above information 00o
27. fits path master_dark_3p0s fits path master_flat_1087p3 fits CAL_WLLAMP CAL_WLLAMP CAL_WLLAMP CALPRO_DARK CALPRO_FLAT CRIRES data reduction cookbook VLT MAN ESO 14200 4032 68 File Help Current Queued Executing crire crires spec wavecal display crire crires spec wavecal wl samples crire crires spec wavecal wl starty crire crires spec wavecal wl stopy crire crires spec wavecal degree crire crires spec wavecal wl err crire crires spec wavecal wl xclimit crire crires spec wavecal waves crire crires spec wavecal wl log crire crires spec wavecal wl nolimit crire crires spec wavecal wl clean Include Filename Classification CRIRE 2010 10 20T13 59 48 752 fits bpm 1087p3 fits master dark 3p0s fits master flat 1087p3 fits lines_thar fits model_conf_04_to_11_2010 fits Locate Display Locate Display Locate Display Locate Display Locate Display Locate Display Locate Displav Locate Display Product Naming Product Root Directory home ismoker CRIRES Reduced Browse Naming Scheme Execute Selected Filename Classification crires_spec_wavecal_ima_0016 fits xl crires spec wavecal tab 0016 fits CALPRO WAVE 22 10 02 INFO Save the product Product frames home jsmo
28. head ch2 mrdfits datafileTEMP 2 head ch3 mrdfits datafileTEMP 3 head ch4 mrdfits datafileTEMP 4 head repeat begin printf lun chi jl wavelength chi jl extracted opt format f22 5 f22 5 je gH endrep until j eq 1022 free lun lun i i 1 print Counter i equals i endrep until i eq 34 i 0 repeat begin j 2 print Reading in CH2 data datafileIN i openw lun datafileOUT 2 i get lun datafileTEMP datafileIN i header headfits datafileTEMP chi mrdfits datafileTEMP 1 head ch2 mrdfits datafileTEMP 2 head ch3 mrdfits datafileTEMP 3 head ch4 mrdfits datafileTEMP 4 head repeat begin printf lun ch2 jl wavelength ch2 jl extracted opt format f22 5 f22 5 jm ge endrep until j eq 1022 CRIRES data reduction cookbook VLT MAN ESO 14200 4032 free_lun lun i i 1 endrep until i eq 34 i 0 repeat begin j 2 print Reading in CH3 data datafileIN i openw lun datafileOUT 3 i get lun datafileTEMP datafileIN i header headfits datafileTEMP chi mrdfits datafileTEMP 1 head ch2 mrdfits datafileTEMP 2 head ch3 mrdfits datafileTEMP 3 head ch4 mrdfits datafileTEMP 4 head repeat begin printf lun ch3 jl wavelength ch3 jl extracted opt format f22 5 f22 5 jc ge endrep until j eq 1022 free lun lun i i 1 endrep until i eq 34 i 0 repeat begin j 2 print Reading in CH4 data datafileIN i openw lun datafileOUT 4 i get lun datafileTEMP datafileIN i hea
29. home2 jsmoker Instruments CRIRES Pipeline Data Reduced crires spec flat set01 0001 fits 3 h ome2 jsmoker Instruments CRIRES Pipeline Data Reduced crires_spec_flat_set01_bpm_0001 fits Completion status SUCCESS X Figure 31 Use of gasgano to produce a master flatfield CRIRES data reduction cookbook VLT MAN ESO 14200 4032 57 8 4 2 Reduction of flatfields within esorex For observations for pipeline versions later than April 2011 using V2 1 x or later of the pipeline then one uses the following sof file which contains non linearity coefficients COEFFS_CUBE as well as the master dark with the same DIT as the flats that we prepared earlier cat Flatfields_1087p3_A sof CRIRE 2011 XX 20T10 00 53 435 fits CAL_FLAT CRIRE 2011 XX 20T10 02 18 593 fits CAL_FLAT CRIRE 2011 XX 20T10 03 43 485 fits CAL_FLAT home2 jsmoker snip Data Reduced crires_spec_dark_for_flat_0000 fits CALPRO_DARK home2 jsmoker snip Data Reduced detlin_coeffs_cube fits COEFFS_CUBE For observations earlier than April 2011 as in this example then the following sof file should be use that contains non linearity coefficients DETLIN A DETLIN B and DETLIN_C cat Flatfields 1087p3 B sof CRIRE 2010 10 20T10 00 53 435 fits CAL FLAT CRIRE 2010 10 20T10 02 18 593 fits CAL FLAT CRIRE 2010 10 20T10 03 43 485 fits CAL FLAT home2 jsmoker snip Data Reduced crires spec dark 0000 fits CALPRO DARK M CRIRES 2010 09 21T17 04 57 320 fits DETLIN A M C
30. of CRIRES Infrared spectra 3 4 1 Glow The 4 detectors show glow over areas close to the amplifiers as clearly visible in Fig 3 It is stable so can be subtracted by using exposures taken with the same DIT Therefore in order to correct for this detector defect it is recommended that observations at any wavelength setting should include at least one nodding cycle CRIRES data reduction cookbook VLT MAN ESO 14200 4032 16 3 4 2 Optical ghosts Occasionally especially when using the CRIRES Echelle grating in high order a quasi white light ghost is visible on the data It results from a retro reflection from the detector onto the grating which is redirected onto the detector in a different order and with reduced dispersion Ghosts are canceled out by nodding as sky emission lines do An example of ghost is shown in Fig 9 3 4 3 Odd even column effect and detector non linearity Images obtained with the science detector show a pattern aligned with the reading direction parallel to the rows of detector 2 and 3 and to the columns of detector 1 and 4 This pattern called odd even effect consists of alternating rows or columns of larger and smaller intensities than the mean value and it depends on the signal level This effect cannot be removed by simply flat fielding and it is still present after nodding However if during your observations you managed to keep the total signal source sky dark below 10 000 ADUs 80 000e and
31. of the more difficult steps in CRIRES data reduction and the user must be sure to inspect the messages created by gasgano and look at the QC results created by the pipeline in order to ensure that the results look reasonable The top panel of Fig 35 shows detector 3 for the 1087 3 nm ThAr calibrations For best results you should measure by hand the Y positions of the ThAr fibres Bottom panel of Fig 35 which are used as pipeline inputs y_pos_cl y_pos_c2 y_pos_c3 and y pos c4 from v2 3 1 of the pipeline and starty stopy up until v2 1 3 If you do not measure the y positions then the pipeline will use fixed values You must check that there are at least two or three lines on each detector well separated in wavelength otherwise it is likely that the wavelength calibration solution will be poor 8 6 1 Reduction of ThAr frames using gasgano As a first attempt Figure 36 shows the results of a failed attempt at wavelength calibration using the recipe crires spec wavecal and v2 1 3 of the pipeline The calibration failed for two reasons 1 The detectors had the wrong boundaries and 2 The model configuration file was incorrect For the second attempt then we 1 click the crires spec wavecal wl nolimit box to avoid the check of the boundaries and 2 use another model configuration file We Execute the recipe again and although the recipe completes successfully again if we look at the log messages we see the following mes
32. out 0000 fits CALPRO MODEL CONFIG fixed fits e We can now use this amended model file as input to the crires model wlmap to create the 2D wavelength map or use the amended model as input to the crires spec jitter recipe as follows cat CRIRES SpecJitter 1087p3 Model sof CRIRE 2010 10 20T03 21 52 798 fits CAL NOD CRIRE 2010 10 20T03 22 23 810 fits CAL NOD path Reduced bpm 1087p3 fits CALPRO_BPM path Reduced master_dark_esorex_5p0s fits CALPRO_DARK path Reduced master_flat_1087p3 fits CALPRO_FLAT CALPRO_MODEL_CONFIG_fixed fits CALPRO_MODEL_CONFIG M CRIRES 2010 09 21T17 04 57 320 fits DETLIN A M CRIRES 2010 09 21T17 05 07 420 fits DETLIN B M CRIRES 2010 09 21T17 05 13 214 fits DETLIN C path crire 2 1 3 cal stdstars fits CALPRO STD PHOTOFLUX esorex recipe dir Path crire 2 3 0 recipes libs output dir path CRIRES Raw crires spec jitter display 3 CRIRES SpecJitter 1087p3 Model sof Xxx ESO Recipe Execution Tool version 3 9 6 kk x CRIRES data reduction cookbook VL T MAN ESO 14200 4032 INFO INFO INFO INFO INFO INFO INFO lt snip gt m eh ae ERROR INFO INFO INFO INFO ERROR INFO See 073 73 713 INFO INFO INFO A ro lt snip gt INFO INFO INFO mv 4 mv 4 mv 4 mv 4 mv LII C LI LC LL LI out O001 fits out 0002 fits out O003 fits out 0004 fits out 0005 fits crires spec jitter crires spec jitter crires spec jitter crires spec jitter c
33. showing detector 3 only in the two nodding positions for 1087 3 nm obser vations The counts in the two nodding positions are similar Note that the Y position of the traces on the four detectors is different CRIRES data reduction cookbook VLT MAN ESO 14200 4032 81 8 7 1 Reduction of nodding frames using gasgano Figure 44 shows the reduction of a single AB pair using the crires_spec_jitter recipe within gasgano In the example shown we just use the default values which produce a reduced spectrum 8 7 2 Reduction of nodding frames using esorex For a basic reduction one needs a sof file that looks like the following with the individual entries on one line each here linebreaks included for clarity cat CRIRES_SpecJitter_1087p3 sof CRIRE 2010 10 20T03 21 52 798 fits CAL_NOD CRIRE 2010 10 20T03 22 23 810 fits CAL_NOD home2 jsmoker Instruments CRIRES Pipeline Data Reduced bpm_1087p3 fits CALPRO_BPM home2 jsmoker Instruments CRIRES Pipeline Data Reduced master_dark_esorex_5p0s fits CALPRO_DARK home2 jsmoker Instruments CRIRES Pipeline Data Reduced master_flat_1087p3 fits CALPRO_FLAT home2 jsmoker Instruments CRIRES Pipeline Data Reduced ThAr_CALPRO_WAVE_1083p3 fits CALPRO_WAVE M CRIRES 2010 09 21T17 04 57 320 fits DETLIN_A M CRIRES 2010 09 21T17 05 07 420 fits DETLIN_B M CRIRES 2010 09 21T17 05 13 214 fits DETLIN_C home2 jsmoker Instruments CRIRES Pipeline crire kit 2 1 3 calib crire 2 1 3 cal stdstars fits CALPRO_S
34. the fit CRIRES data reduction cookbook VLT MAN ESO 14200 4032 64 r1 ri ri ri ri ri e e e e e e un r wn n M m E B T ari br y e y e n n Ri amp Ri amp amp amp 1083 80 1090 4 chip2 1090 4 chip3 1090 48 1083 78 1090 46 g 1083 76 c bw 1090 44 a 6 1083 74 m B 1090 42 2 1083 72 1090 40 1083 70 1090 38 1083 68 56050 56100 56050 56100 MJD OBS MjD OBS ri ri A mi Du ri e e e e e ex wn w un 9 r e e e o e o e E a gt e gt o gt amp 5 amp amp 5 amp amp amp 5 4045 50 4092 9 chipl i i 4070 50 4092 9 chip2 E D i E 4070 00 r3 4045 00 ra ft Qu zi Si S8 4044 50 g 406950 5 5 2 aadi 5 4069 00 6 56050 56100 o 56050 56100 4092 9 chip3 4054 00 g 4116 50 E E c E E 4093 50 t 4116 00 Y e o m devveemuoss secemeodocetewanenssciscthbemseete v vi vi li m 3 4093 00 8 4558 4092 50 4115 00 56050 56100 56050 56100 MJD OBS MJD OBS Figure 34 Central wavelength against time derived from ThAr calibrations taken daily at 1090 4 nm and N20 gas cell wavelength calibration at 4092 9 nm The scatter on the mea surements is due to the limited reproducability of the grating and prism mechanisms CRIRES data reduction cookbook VLT MAN ESO 14200 4032 65 8 6 Wavelength calibration examples For wavelength calibration of up to 2 5 microns ThAr spectra are typically used Examples of such spectra are shown in Fig 6 Wavelength calibration is one
35. 0 33 08 Mar 2012 Last modified Thu 02 28 55 19 Apr 2012 Pixel file Crires_sv_ngc6253_068_0001 fits ok EXTEND T FITS Extension may be present ORIGIN ESO Paranal Source of the file DATE 2012 03 08T09 40 32 7467 Date the file was written TELESCOP ESO VLT U1 Telescope name INSTRUME CRIRES Instrument name OBJECT TEST Content description RA 254 775705 16 59 06 1 RA J2000 pointing deg DEC 52 71581 52 42 56 9 DEC J2000 pointing deg EQUINOX 2000 Standard FK5 years RADECSYS FK5 Coordinate reference frame EXPTIME 10 0000000 Integration time MJD OBS 55994 40302817 Obs start 2012 03 08T09 40 21 634 lt snip gt Additionally some reduced calibration frames can be displayed and manipulated cl display OBS_WL_MAP_IMA_WithoutCals_100s_A fits 1 frame to be written into 1 16 1 z1 4034 347 z2 4054 035 cl imstat SpecJit 1087p4 PipeDefaults STD BGD MAP IMA fits 1 IMAGE NPIX MEAN STDDEV MIN MAX SpecJit_1087p4_PipeDefaults_STD_BGD_MAP_IMA fits 1 524288 0 6774 0 4675 cl imarith SpecJit_1087p4_PipeDefaults_STD_BGD_MAP_IMA fits 1 100 0 SpecJit 1087p4 PipeDefaults STD BGD MAP IMA Times 100 Detectori fits Problems can occur when plotting the final reduced spectra on splot SpecJit 1087p4 PipeDefaults STD EXTRACT SENS TAB fits ERROR MWCS dimension mismatch mw open CRIRES data reduction cookbook VLT MAN ESO 14200 4032 93 One so
36. 059022839282 HIERARCH ESO QC XCORR 0 208174330229398 dfits x 0 crires_spec_wavecal_ima fits grep RESOL HIERARCH ESO QC RESOL MED 239922 774365529 HIERARCH ESO QC RESOL MED 140029 604526438 HIERARCH ESO QC RESOL MED 221013 021706264 HIERARCH ESO QC RESOL MED 188169 29772676 8 7 Combining nodding spectra We combine nodding spectra such as Fig 43 using the recipe crires spec jitter As input this needs a set of nodding positions plus optionally the bad pixel map master dark and flatfield wavelength solution and detector linearity coefficients In the case of a standard star observation the fits file containing the flux against wavelength may also be included One can also perform the extraction of the individual nodding positions in order to retain full resolution and also it is possible to run the recipe on only one spectrum in OBS DIR mode see 7 3 Note that from version 2 3 1 of the pipeline preferred the wavelength calibration is applied at the different Y positions and ThAr pinhole data are fully supported First have a look at the raw spectra and check that e The counts do not exceed 10 000 ADU on any of the four detectors including sky If they do exceed this quantity the non linearity correction will not be so good and pipeline results should be treated with caution e The counts in the two nods are similar Figure 43 shows the counts in two nodding positions for detector 3 only CRIRES data reduct
37. 14200 4032 1 1 Introduction 1 1 Purpose The document is intended for astronomers who want to reduce CRIRES data It describes the various data formats delivered by CRIRES observational scenarios and reduction procedures The document also describes the algorithms implemented in the CRIRES pipeline data re duction package Though the CRIRES pipeline is described in detail in the CRIRES pipeline User Manual see http www eso org pipelines here we will list and present some of the CRIRES pipeline routines The current document is aimed at describing the algorithmic concepts present in the recipes and provide help for users who want to analyze data from CRIRES The pipeline does produce reduced data however this is not meant to replace more general reduction packages such as IRAF MIDAS or IDL This document does not describe the CRIRES instrument its mode of operations how to acquire data the offered templates or the various issues attached to Phase II Observing Preparation The reader is assumed to have read the CRIRES User s Manual beforehand and have a basic knowledge of infrared data reduction in spectroscopy 1 2 Reference documents 1 CRIRES User Manual 2 CRIRES Pipeline User Manual The latest version of the CRIRES pipeline should always be used this is available at http www eso org projects dfs dfs shared web vlt vlt instrument pipelines htm The latest version of the user manual is available here http ww
38. 200 4032 i Object CRIRE 2010 0 Pixel Values Bitpix 32 Low 2o00 High 4000 Auto Set Gut Levels Scale a Ziz Si zin Figure 5 Science detector image of a flatfield at 1561 nm that shows strong ghosts CRIRES data reduction cookbook VLT MAN ESO 14200 4032 15 3 3 3 ThAr wavelength calibration ThAr wavelength calibration is typically performed using the crires spec cal wave tem plate and using a 0 2 arcsec slit Because of problems with scattered light this calibration is now performed using fibres Note that ThAr calibration is only performed for wavelengths shorter than 2400 nm The DIT and NDIT are calculated automatically from table cmm cfgMaxFluxThAr dat which contains ThAr intensities every twenty pixels This aims at avoiding remnance caused by very bright ThAr lines An example of a ThAr calibration on the science detector is shown in Fig 6 Note that as well as the six ThAr fibres there are also metrology fibres at the top and bottom of the science detector These fibres do not go through the same optical path as the six ThAr fibres hence are not aligned in wavelength with the main fibres The fibres at the top pass through the grating only those at the bottom through the prism and the grating ThAr calibrations are taken daily by the observatory for each wavelength setting used the previous night for A lt 2400 nm In future the frequency of these c
39. 6 ThAr fibres and entering their y coordinates in y pos cN The recipe will collapse 10 rows from the input image at positions 59 158 476 on detectorl 77 158 472 on detector2 63 142 459 on detector3 and 57 136 453 on detector 4 and all the successful calibrations are used to generate a 2D wavelength map per detector CRIRES data reduction cookbook VLT MAN ESO 14200 4032 71 path bpm_1087p3 fits CALPRO_BPM path crire calib 2 1 3 cal lines_thar fits CALPRO_THAR_CATALOG M CRIRES 2010 09 21T17 04 57 320 fits DETLIN A M CRIRES 2010 09 21T17 05 07 420 fits DETLIN B M CRIRES 2010 09 21T17 05 13 214 fits DETLIN C esorex output dir path Reduced crires spec wavecal wl starty 217 wl stopy 227 display 3 wl log true wl nolimit true ThAr 1087p3 sof This will produce output like the following Xxxx ESO Recipe Execution Tool version 3 9 0 seeek INFO crires_spec_wavecal KKK KK KK K KK K K K K K K K K K KK K K KK K K K K KK K K INFO crires_spec_wavecal Detector 1 Y 1 gt Y 512 pixels INFO crires_spec_wavecal Detector 2 Y 1 gt Y 512 pixels INFO crires_spec_wavecal Detector 3 Y 1 gt Y 512 pixels INFO crires_spec_wavecal Detector 4 Y 1 gt Y 512 pixels INFO crires spec wavecal KKK KK KK K KK K K ok K K K ok ok ok ok ok ok ok ok OK K K K KKK K K INFO crires_spec_wavecal Apply the Wavelength Calibration INFO crires_spec_wavecal Get the calibration from the thar lamp
40. 8 47 742 fits DARK 2308 000 3 0000000 CALIB CRIRE 2010 10 20T13 56 57 981 fits DARK 5219 100 5 0000000 CALIB CRIRE 2010 10 20T13 57 24 036 fits DARK 5219 100 5 0000000 CALIB CRIRE 2010 10 20T13 57 52 040 fits DARK 5219 100 5 0000000 CALIB Finally we want to download the following three files that contain the non linearity coefficients dfits M fits fitsort OBJECT INS WLEN REF DET DIT DPR CATG DPR TYPE PRO CATG M CRIRES 2010 09 21T17 04 57 320 fits FLAT LAMP DETCHECK 4007 1 M CRIRES 2010 09 21T17 05 07 420 fits FLAT LAMP DETCHECK 4007 1 M CRIRES 2010 09 21T17 05 13 214 fits FLAT LAMP DETCHECK 4007 1 Note that the coefficients change with time so you should check the following webpage for the correct version corresponding to the date of your observation http www eso org observing dfo quality CRIRES pipeline pipe calib html Finally note that post April 2011 instead of DETLIN A B and C the pipeline uses a single file with category COEFFS CUBE for the non linearity correction 8 2 Master dark creation The first step in the creation of the darks is to find out what the DIT is of your science standard and flatfield frames In this case we are lucky because the standard star at 1087 3 nm has the same DIT as the flatfield i e 5 seconds Hence we can use the same master dark for both images However the DIT used for the ThAr images is 3 seconds so a separate dark must be used for their reduction dfits CRIRE fits fitso
41. 9 y_pos_c4 57 136 215 295 374 453 y_width 10 display 3 wl_log true wl nolimit true ThAr_1087p3 sof 8 6 4 Reduction of OH line frames using esorex Figure 40 shows an example of a sky frame taken at a wavelength of 1111 7 nm detector 3 only We can use the OH lines present in the image for wavelength calibration The method gives variable results due to the sparsity and weakness of OH features indeed the setting selected does not give a good solution so you must always check that there are enough strong lines present before proceeding Below 1 8 microns the OH line catalogue is used redwards of this the HITRAN model is used The following sof file shows an example of how you would go about performing this cali bration Note that in the case that one uses a science observation with classification such as a CAL_NOD for OH wavelength calibration then one would 1 use y values of the detector free CRIRES data reduction cookbook VLT MAN ESO 14200 4032 73 from the object spectra and 2 fool the pipeline into thinking it is a wavelength calibration by changing CAL NOD to CAL WLSKY in the sof file or gasgano input cat OH Pipeline OHcat 1111p7 sof CRIRE 2011 07 11T22 49 11 821 fits CAL WLSKY path crire kit 2 3 0 calib crire 2 3 0 cal lines_oh fits CALPRO OH CATALOG The following esorex command should be run in order to perform the reduction In this case we collapse 30 lines at two positions on each of the detect
42. 9 shows an example of the use of the CRIRES flatfield with the gas cell inserted for DIT 100 s NDIT 1 and DIT 2 s NDIT 50 These data can be used to check the efficacy of the non linearity correction by looking at the depth of the absorption lines in the spectra More information can be obtained by contacting criresQeso org Figure 49 Raw CRIRES images with DIT 2 s NDIT 50 top plot and DIT 100 s NDIT 1 bottom plot CRIRES data reduction cookbook VLT MAN ESO 14200 4032 95 Filename DIT s NDIT Count Det 3 ADU CRIRE 2012 04 17T03 31 14 065 fits 1 100 80 CRIRE 2012 04 17T04 23 18 166 fits 2 50 190 CRIRE 2012 04 17T04 20 52 616 fits 3 34 300 CRIRE 2012 04 17T04 11 57 389 fits 4 25 400 CRIRE 2012 04 17T04 14 18 624 fits 5 20 500 CRIRE 2012 04 17T04 16 33 561 fits 10 10 1000 CRIRE 2012 04 17T04 18 44 152 fits 20 5 1900 CRIRE 2012 04 17T04 20 52 616 fits 40 3 3800 CRIRE 2012 04 17T04 23 18 166 fits 50 2 4800 CRIRE 2012 04 17T04 25 20 496 fits 67 1 6200 CRIRE 2012 04 17T04 26 47 827 fits 100 1 9000 CRIRE 2012 04 17T04 28 48 799 fits 120 1 11000 Table 3 DIT and NDIT combinations for test of the CRIRES non linearity correction 10 5 Problems in running gasgano Following are a handful of problems that users may encounter when running gasgano and how to avoid them e Gasgano will not start with CPL initialisation failed gasgano jsmoker localhost gasgano amp 1 19723 gasgan
43. AMPLES as shown in the CRIRES webpages These values are different depending on the readout mode used and are shown in Table 1 3 3 2 Flatfields For flatfields the Halogen lamp or infrared emitter is used The S N ratio of the flatfields can be found here There may be large gradients from detector 1 to detector 4 due to the position of the centre of the order and or the presence of absorption lines caused by water vapour in the path between the lamp and the entrance window and or vignetting by the intermediate slit A flatfield with reference wavelength of 5050 4 nm is shown in Fig 4 Note that many flats such as the one displayed show absorption due to water vapour in the instrument between the calibration lamp and the vessel entrance window Flatfields are taken with a 0 2 arcsec slit Some flats show ghosts for example visible in Fig 5 Until now flatfields have been taken daily by the observatory for each wavelength setting used although it is possible that this calibration frequency may decrease in the future CRIRES data reduction cookbook VLT MAN ESO 14200 4032 12 ee Figure 2 Example of windowed mode Note that only detectors 2 and 3 are read out and there is no flux on detectors 1 or 4 WY Skycat version 3 0 1 CRIRE 2010 02 05T11 54 27 759 fits 1 File View Graphics Go Data Servers Pixel Values E Zoom Object CRIRE 2010 0 x 5730 Y 19 0
44. ARKSTDEV 0 127293764968731 HIERARCH ESO QC RON1 4 54955875147938 HIERARCH ESO QC RON2 3 53587998287295 HIERARCH ESO QC DARKMED 2 6111110051473 HIERARCH ESO QC DARKSTDEV 4 75389685389413 HIERARCH ESO QC RON1 5 70574272668766 HIERARCH ESO QC RON2 5 67308598788528 HIERARCH ESO QC DARKMED 2 19444437821706 HIERARCH ESO QC DARKSTDEV 0 240562589220506 HIERARCH ESO QC RON1 6 8746721627819 HIERARCH ESO QC RON2 6 77970798213789 HIERARCH ESO QC DARKMED 2 94444449742635 HIERARCH ESO QC DARKSTDEV 0 647287800699611 The fact that we have four readout noises dark levels and standard deviations is due to the fact that we have four detectors In our case the values are reasonable so we can proceed to the next step CRIRES data reduction cookbook VLT MAN ESO 14200 4032 53 EU _________ LE Figure 29 Master dark frame created by the ESO CRIRES pipeline The DIT was 5 s so the glow is weak compared to the a 600 s dark image for example shown in the bottom panel of Fig CRIRES data reduction cookbook VLT MAN ESO 14200 4032 54 8 3 Linearity correction using detmon_ir_lg At the moment there is not the possibility to produce the fits files used to correct for non linearity In the near future the detmon package should be used which is the same recipe used across all of the ESO infrared instruments Until then the linearity correction files should be downloaded either from the archive or from here htt
45. BE depending on the date of the raw image 9 1 2 crires util extract This recipe can be used providing the files in the command line esorex output dir outdir crires util extract combinedimage fits contributionmap fits This recipe to extract spectra has been tested with a SOF containing combinedimage fits COMMAND LINE contributionmap fits COMMAND LINE This recipe can also be used without a SOF however for some purposes using a SOF is more convenient 9 1 3 crires util wlcalib This recipe can be used providing the files in the command line esorex output dir outdir crires util wlcalib extractedspectrum fits referencelinecatalog fits fits This wavelength calibration recipe has been tested with a SOF containing extractedspectrum fits COMMAND LINE referencelinecatalog fits COMMAND LINE 9 1 4 crires util wlassign This recipe can be used providing the files in the command line esorex output dir outdir crires util wlassign extractedspectrum fits wlcalib fits It can as well be used with a SOF providing the files and using the COMMAND LINE tag but make sure that the order is as shown in the help file 9 1 5 crires util genlines This recipe is used to create a reference line catalogue It is not clear to be confirmed if the recipe works through the command line Using a SOF only one entry is needed asciilinetable txt CATALOG CRIRES data reduction cookbook VLT MAN ESO 14200 4032 91 10 Limitations and pro
46. DING OTHER STD 38 1504 800 2 FowlerNsamp Ei CRIRE 2010 10 20T03 24 32 3 cres util conversion SPECTRUM NODDING OTHER STD 38 1504 800 2 FowlerNsamp El CRIRE 2010 10 20T03 26 00 1 aires util convert SPECTRUM NODDING OTHER STD 26 2205 000 2 FowlerNsamp E El CRIRE 2010 10 20T03 26 34 7 crires util extract SPECTRUM NODDING OTHER STD 26 2205 000 22 FowlerNsamp El CRIRE2010 10 20T03 28 13 9 cires util genconfig SPECTRUM NODDING OTHER STD 16 3611 000 2 FowlerNsamp El CRIRE 2010 10 20T03 28 48 4 cries util genlines SPECTRUM NODDING OTHER STD 16 3611 000 2 FowlerNsamp El CRIRE 2010 10 20703 31 23 9 qires util genstd SPECTRUM NODDING OTHER STD 11 5050 400 6 FowlerNsamp El CRIRE 2010 10 20703 32 22 8 crires util plot SPECTRUM NODDING OTHER STD 1 5050 400 6 FowlerNsamp arre cires uul pranie D CRIRES_ACQ_SKY264_0004 fits es uui sensitivity i E IMAGE SKY 34 1646 800 GuideMode RstRdRd T D cRIRES_ACQ_SLIT264_0006 fit CI S utilLwlassign je IMAGE OBJECT 34 1646 800 GuideMode RstRdRd Ej CRIRES_SPEC_OBS264_0100 fitg Tives uUiwicalib L SPECTRUM NODDING OTHER OBJECT 34 1646 800 FowlerNsampGRstWin chines soc rita diokhd crires util wlinit L SPECTRUM NODDING OTHER OBJECT 34 1646 800 FowlerNsampGRstWin E 200220569 2MASS J0159 4019 r Cires win dark Bid Unknown Program crires win flat L amp m Unknown Ohcenation Clires win jitter lt home2 jsmoker Instruments CRIRES Pipeline Data Raw CRIRE 2010 10 20T03 28 13 918 fits CRIRES S
47. ES data reduction cookbook VLT MAN ESO 14200 4032 32 Using these aliases defined above we setup the paths and run gasgano crires_cpl crires_pipe gasgano At this point gasgano should fire up and if you click on the small tabs within it you should see a window as shown in Fig 17 with lines in red such as lines_hitran fits lines model fits and so on These are calibration files that may be used in the data reduction Note that to see the headers better for example CLASSIFT then move the mouse to the right hand side of the column in question until the left right arrow appears then left mouse click and drag the column heading to the right to increase its size Now we want to make it possible for gasgano to see the raw data e File Add Remove file Add file in this case home jsmoker Instruments CRIRES Pipeline Data Raw and Reduced then OK see Fig 18 At this point the CRIRES raw files are visible in blue With the raw files selected we are now ready to perform data reduction using the pipeline 6 2 The ESO CRIRES pipeline under MacOS The ESO CRIRES pipeline does not support MAC OS and the quality of the results produced has not been verified There may be subtle effects in the pipeline output that are not immediately obvious The author uses linux so has not been able to check the following so the information is given as is To compile the pipeline using 64 bits 10 6 8 java 1 6 then using csh on
48. ES pipeline Full data reduction of CRIRES nodding images The full data cascade of CRIRES is described in Sect 8 of the pipeline manual and is followed here for the nodding case Note that in the majority of cases the output from one recipe e g crires_spec_dark is used by the next recipe in the chain e g crires_spec_flat e Dark creation CAL_DARK crires_spec_dark e Linearity ON RAW amp OFF RAW detmon ir lg Available soon At the time of writing users should download data from http www eso org observing dfo quality CRIRES pipeline pipe calib html e Flatfielding CAL FLAT crires_spec_flat e Wavelength calibration CAL WLSKY CAL WLLAMP CAL WLABS crires spec wavecal e Wavelength refinement MODEL REFINE RAW crires model refine e Final reduction OBS DIR or DIR JIT OBS NOD or NOD JIT CAL DIR or DIR JIT CAL NOD or NOD JIT OBS OBJECT or SKY OBS GENERIC OFFSET or SKY crires spec jitter We will concentrate on two cases a standard star with a reference wavelength at 1087 3 nm and the same bright standard at 3611 0 nm 8 1 Look at the raw data and calibrations One should use dfits to see what data are available and then use programmes such as rtd or ds9 and assess their quality In the current case we have standard star observations flats and ThAr wavelength calibrations taken at 1087 3 nm and standard star and flatfields only available for the 3611 0 nm remember that no ThAr exposures are taken redwar
49. ESO QC NBBAD 15863 HIERARCH ESO QC FLAT MEAN 719 548624674479 HIERARCH ESO QC FLAT STDEV 2 00897466141822 HIERARCH ESO QC FLAT FLUX 143 909724934896 HIERARCH ESO QC FLAT MASTER RMS 0 485489309666914 HIERARCH ESO QC NBBAD 3487 HIERARCH ESO QC FLAT MEAN 4984 8427734375 HIERARCH ESO QC FLAT STDEV 8 01957517557057 HIERARCH ESO QC FLAT FLUX 996 9685546875 HIERARCH ESO QC FLAT MASTER RMS 0 188135783694171 HIERARCH ESO QC NBBAD 1053 HIERARCH ESO QC FLAT MEAN 6063 73388671875 HIERARCH ESO QC FLAT STDEV 7 62383087763282 HIERARCH ESO QC FLAT FLUX 1212 74677734375 HIERARCH ESO QC FLAT MASTER RMS 0 0843839718156275 HIERARCH ESO QC NBBAD 86285 HIERARCH ESO QC FLAT MEAN 2641 94441731771 CRIRES data reduction cookbook VLT MAN ESO 14200 4032 HIERARCH ESO QC FLAT STDEV 0 281828109551431 HIERARCH ESO QC FLAT FLUX 528 388883463542 HIERARCH ESO QC FLAT MASTER RMS 0 722128724207729 59 CRIRES data reduction cookbook VLT MAN ESO 14200 4032 60 Detector 1 Detector 1 Detector 2 L 500 Detector 3 0 9 Detector 3 o4 Detector 4 a Rm ET 0 500 Figure 32 Master flatfield at 1087 3 nm Detectors 1 and 4 cannot be well flatfielded as they are affected by necessary vignetting by the interemediate slit CRIRES data reduction cookbook VLT MAN ESO 14200 4032 61 8 5 Strategies for wavelength calibration Depending on the wavelength region used and type of wavelen
50. 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 CRIRES data reduction cookbook Doc No VLT MAN ESO 14200 4032 Issue 91 0 Date 05 11 2012 J Smoker E Valenti D Asmus P Birstow A Smette M Hilker B Wolff Y Jung Prepared essere ee sh Ge Gy A Bu aaga ae aAa Date Signature A Kaufer Approved naoa ink o3 99 oP OP Lane EIE I UOCE oh ee ae Date Signature C Dumas Released os Shue 4 oe Se cde od oe OE a Date Signature CRIRES data reduction cookbook VLT MAN ESO 14200 4032 This page was intentionally left blank CRIRES data reduction cookbook VL T MAN ESO 14200 4032 ill Change Record Issue Rev Date Section Parag affected Reason Initiation Documents Remarks 80 0 11 10 2007 all cookbook creation and first archiving 88 0 01 10 2011 all major updates 89 0 27 04 2012 all comments requested 89 1 20 06 2012 all major updates 89 2 13 07 2012 all major updates 89 3 18 09 2012 all updates 89 4 24 09 2012 all updates 90 0 20 10 2012 all final updates 91 0 05 11 2012 all document released CRIRES data reduction cookbook VLT MAN ESO 14200 4032 iv Acknowled
51. ILE CRIRES SPEC FLAT363 0001 fits Aladdin3 IR Figure 1 Gasgano main window CRIRES products e ORIGFILE contains the name of the file on the instrument workstation e ARCFILE is the archive file name 2 4 Telescope Keywords Here is a non exhaustive list of telescope keywords e RA Right ascension J2000 in degrees Notice that the comment field indicates the value in hh mm ss s format e DEC Declination J2000 in degrees Notice that the comment field indicates the value in hh mm ss s format e INS1 DROT POSANG Position angle on sky as measured from North to East degrees e TEL AIRM START Airmass at start e TEL AIRM END Airmass at end e TEL AMBI FWHM START Astronomical Site Monitor seeing at start Note that this value might differ significantly from the CRIRES image quality which is usually better e TEL AMBI FWHM END Astronomical Site Monitor seeing at end Note that this value might differ significantly from the CRIRES image quality which is usually better e TEL IA FWHMLIN Delivered seeing on Image Analysis detector at 550 nm e TEL IA FWHMLINOBS Delivered seeing on Image Analysis detector at 550 nm CRIRES data reduction cookbook VLT MAN ESO 14200 4032 6 2 5 TEL AMBI IWV START Average of the Integrated Water Vapor measurements towards zenith over the previous 2min at start of exposure Implemented soon This can be compared with the requested value ESO OBS WATERVAPOUR TEL AMBI
52. INFO crires_spec_flat Correct for the dark INFO crires_spec_flat Normalise with the median INFO crires spec flat Save the products INFO crires spec f1at Writing FITS propertylist product CALPRO_FLAT crires_spec_flat_set01 fits INFO crires spec flat Writing FITS propertylist product CALPRO_BPM crires spec flat setO1 bpm fits INFO esorex Created product home2 jsmoker Reduced out_0000 fits INFO esorex Created product home2 jsmoker Reduced out_0001 fits INFO esorex 2 products created T 70 3 mv home2 jsmoker Instruments CRIRES Pipeline Data Reduced out_0000 fits home2 jsmoker Instruments CRIRES Pipeline Data Reduced master flat 1087p3 fits mv home2 jsmoker Instruments CRIRES Pipeline Data Reduced out_0001 fits home2 jsmoker Instruments CRIRES Pipeline Data Reduced bpm 1087p3 fits The first file produced is the flatfield ideally normalised to unity but in practice not always with the second being a bad pixel map 8 4 3 Inspection of pipeline results for master flatfield and QC parameters Figure 32 shows the master flatfield produced by the ESO pipeline In this case detectors 1 and 4 clearly are not near to unity so the flatfielding in these chips will be very poor One looks at the Quality Control QC parameters using the following dfits command dfits x 0 home2 jsmoker Instruments CRIRES Pipeline Data Reduced master flat 1087p3 fits grep QC all on one line HIERARCH
53. IRE 2012 02 02T09 42 29 718 4036 14 6 12 6 det gt 15 total 1 det 5 total CRIRE 2012 02 02T09 47 09 343 4539 12 7 10 0 l det lt 5 total 1 det lt 5 total Table 2 Residuals obtained using the CRIRES physical model and header keywords at dif ferent wavelength ranges 8 5 4 Science frame with no gas cell or ThAr wavelength calibration and no OH or sky absorption lines One has two possibilities here either use the physical model or use the header keywords Table 2 shows the results of tests to determine the absolute and relative accuracy of the physical model and header The absolute calibration offered by the automatic header wavelength is usually not bad however the residual varies significantly across the detector and from detector to detector since a linear interpolation is applied to the detector start and end wavelengths The Physical Model PM on the other hand typically has larger absolute residuals but the relative calibration is good to 1 2 pixels across a detector 5 pixels across the array Hence if one knows the absolute wavelength of a stellar or interstellar feature then one can well calibrate the whole array a posteriori CRIRES data reduction cookbook VLT MAN ESO 14200 4032 63 y 151 cf 0 99 Figure 33 Well calibrated ThAr spectrum in flux against wavelength with reference wave length of 1111 7 nm The figure shows the inner 3 fibres and Detector 3 only A second order polynomial was used for
54. IRES data reduction cookbook VLT MAN ESO 14200 4032 34 GASGANO Version 2 4 0 jsmoker Linux File Selected files Tools Help Default grouping w expand Find entry find File CLASSIFI PRO CA DPR TE DPR TYPE INS GR INS WLE DET DIT DET NDIT DET NC C Displaying 8 files Unfiltered 9 Bi Unknown Program Unknown Observation Bl ines hitran fits CALPR CALPR B lines_model fits CALPR CALPR B ines n2o fits CALPR CALPR B lines_oh fits CALPR CALPR B ines thar fits CALPR CALPR Bl model conf fits CALPR CALPR G model conf 04 to 11 2010 fits CALPR CALPR B stdstars fits CALPR CALPR File Selected files Tools Help GASGANO Version 2 4 0 jsmoker Linux C Displaying 8 files Unfiltered pid Unknown Program Unknown Observation Bl ines hitran fits Bl ines model fits Bl ines n2o fits Bl ines oh fits Bl ines thar fits Bl model_conf fits Bl model conf 04 t0 11 2010 fits B stdstars fits CALPR CALPR CALPR CALPR CALPR CALPR CALPR CALPR CALPR CALPR CALPR CALPR CALPR CALPR CALPR CALPR GASGANO Version 2 4 0 jsmoker Linux de 5 E Default grouping w expand Find entry find File CLASSIF RO CA DPR TE DPF
55. Implicit in this statement is that the same flat was used for both the target and the standard and that the target and the standard were observed at roughly the same place on the array If neither of these things are true then flux calibration relative and absolute will be less accurate The described procedure can be also done by using some IRAF s tasks such as flatcombine under the the mscred environment 5 3 Wavelength calibration The wavelength calibration of CRIRES spectra is the most critical step in the whole data reduction procedure mainly because of the small number of known and or suitable lines The wavelength scale can be calibrated with either arc frames or the OH lines that are im printed on each spectrum Normally the advantage of the arc is that there are lines covering the entire wavelength range although given the high resolution of CRIRES the density of the known lines is quite small The disadvantage is that the arcs are taken separately and in most cases this means that the grating has moved between the time when the target was observed and the arcs were taken One can use the OH lines if present to cross check and correct the zero point of the wavelength calibration The advantage of the OH lines is that above 2 2m they are numerous and that they may lead to a slightly more accurate wavelength calibration The disadvantage is that below 2 2m they are often too faint to allow a good fit In general for an accuracy c
56. NTRIBUTION IMA Model fits SpecJit 1087p4 PipeDefaults STD PROFILE IMA Model fits SpecJit 1087p4 PipeDefaults STD WL MAP IMA Model fits SpecJit 1087p4 PipeDefaults STD EXTRACT SENS TAB Model fits 8 6 6 Inspection of the pipeline results produced by crires spec wave to check on the wavelength calibration solution As written in the CRIRES Pipeline Users Manual the recipe produces a 4 extensions file with tables containing the polynomial coefficients giving the relation wavelength F pixel CALPRO_WAVE It also produces 2 wavelength maps the one obtained by cross correlation WL_MAP_IMA and the one computed by the model WL MAP MODEL IMA Figure 42 shows plots produced by the pipeline of the extraction for detector 3 One should check that e The detected lines correspond to actual ThAr fibres on the spectra e The computed initial solution difference wavelength does not show large values typically they should be 0 1 nm e The initial computed and solution fits are similar CRIRES data reduction cookbook VLT MAN ESO 14200 4032 78 One should also look at the headers to check the cross correlation Small numbers lt 0 5 mean that likely the solution is bad In this case the Detector 3 cross correlation result was 0 83 so the fit is good and wavelength solution can be trusted dfits x 0 crires_spec_wavecal_ima fits grep XCORR HIERARCH ESO QC XCORR i HIERARCH ESO QC XCORR i HIERARCH ESO QC XCORR 0 834
57. O CRIRES pipeline under MacOS lll 32 6 3 The ESO CRIRES pipeline reflex environment 33 7 The ESO CRIRES pipeline Quick look data reduction of CRIRES nodding and stare images using the recipe crires spec jitter 36 7 1 Data reduction of nodding spectra using gasgano 36 7 2 Quick data reduction of nodding spectra using esorex 42 7 3 Quick reduction of stare frames using esorex lll sn 42 7 4 Plotting the reduced spectra uou e eoo Rex eR eme e Y dE ere o ME Ss 44 8 The ESO CRIRES pipeline Full data reduction of CRIRES nodding images 48 Bl look at the raw date and calibrations e s s ooo see o ee eae Poe bee A 48 Bd Master datk creation os noe bed ORR Ow EROR REPRE ho RHEE 49 8 2 1 Reduction of darks within gasgano 2 22299 o dw 49 8 2 2 Reduction of darks within esorex for flats and science frames 51 8 2 8 Inspection of pipeline results for master dark and QC parameters 51 8 3 Linearity correction using detmonirlg s 54 B4 Master fatheld creation os iaces sedea ie 3 9 R93 x3 y xoxo 54 8 4 1 Reduction of Datbelds within gasgano 2 46044 o y oem E XA 54 8 4 2 Reduction of flatfields within esorex 2l ll 57 8 4 3 Inspection of pipeline results for master flatfield and QC parameters 58 8 5 Strategies for wavelength calibration c r 61 8 5 1 Wavelength less than 2 4 microns with more than two or three we
58. Observation Block name CRIRES data reduction cookbook OBS TARG NAME ORIGFILE PIPEFILE PRO PRO PRO PRO PRO PRO PRO PRO PRO RA SEQ SEQ SEQ SEQ SEQ TEL TEL TEL TEL TPL TPL TPL CATG DATANCOM DATE DID RECi ID RECi DRS ID REDLEVEL STATUS TYPE CUMOFFSETX CUMOFFSETY CUMOFFSETA CUMOFFSETD POISSON AIRM START AIRM END AMBI FWHM START AMBI FWHM END ID NEXP EXPNO Target package name File name given during acquisition File name as attributed by the pipeline Data product category Number of frames combined into this product Pipeline reduction date Dictionary version for PRO keywords Applied recipe ID Data Reduction System ID Data product reduction level Data product reduction status Data product type Right ascension J2000 in degrees Cumulative offset in X in pixels Copulated offset in Y in pixels Emulated offset in alpha in arcseconds Accumulated offset in delta in arcseconds Poisson homogeneity in jitter throw Airmass at start of exposure Airmass at end of exposure ASM seeing at start ASM seeing at end Template ID Number of exposures expected in the template Exposure rank in the template VL T MAN ESO 14200 4032 CRIRES data reduction cookbook VLT MAN ESO 14200 4032 10 DIT s NDSAMPLES 1 to 9 2 10 15 4 20 6 30 8 45 10 60 14 90 20 120 28 180 40 300 66 600 900 128 Table 1 NDSAMPLES per DIT for CRIRES 3 C
59. PEC STD293 0009 fits CAL NOD Exten HEADER Find in header find Load Filter C Filter q gt Keyword Value SIMPLE T A BITPIX B NAXIS 0 EXTEND ORIGIN ESO Paranal DATE 2010 11 14T18 09 45 754 TELESCOP ES0 VLT U1 INSTRUME CRIRES OBJECT STD RA 02 28 09 5 DEC 08 27 39 82 EQUINOX 2000 RADECSYS FKS EXPTIME 5 0000 MJD OBS 55489 14460553 z Figure 19 Preparing the reduction of nodding observations in gasgano using the recipe CRIRES SPEC JITTER CRIRES data reduction cookbook VLT MAN ESO 14200 4032 39 Executing Default m crire crires spec jitter display dd to pool crire crires spec jitter hor size crire crires spec jitter spec hsize IV crire crires spec jitter closing hs crire crires spec jitter wl samples laesa aU a crire crires spec jitter wl starty Input Frames Include Filename Classification CRIRE 2010 10 20T03 28 13 918 fits Locate Display Product Naming l R Product Root Directory home jsmoker Instruments CRIRES Pip Naming Scheme IV Execute Selected Filename Classification Log Messages ERROR 11 57 39 ERROR Cannot combine the images ERROR 11 57 39 ERROR Cannot combine chip 1 ERROR 11 57 39 ERROR Cannot combine the images ERROR 11 57 39 ERROR Dumping all 1 error s ERROR 11 57 39 ERROR 1 1 Illegal input 14 at crires spec jitter crires spe
60. RIRES 2010 09 21T17 05 07 420 fits DETLIN B M CRIRES 2010 09 21T17 05 13 214 fits DETLIN C And then run esorex using the following command esorex output dir home2 jsmoker Instruments CRIRES Pipeline Data Reduced crires spec flat Flatfields_1087p3_B sof Xxxx ESO Recipe Execution Tool version 3 9 0 seek INFO crires spec flat bbo ooo oook kkk kkk kkk INFO crires spec flat Detector 1 Y 1 gt Y 512 pixels INFO crires spec flat Detector 2 Y 1 gt Y 512 pixels INFO crires spec flat Detector 3 Y 1 gt Y 512 pixels INFO crires spec flat Detector 4 Y 1 gt Y 512 pixels INFO crires spec flat eR SARC CSSA CK I AAA INFO crires_spec_flat Reduce data set 1 1 INFO crires spec flat DIT value 5 sec INFO crires spec flat Verify the dark DIT INFO crires spec flat Compute the MASTER FLAT for chip nb 1 INFO crires spec flat Correct for the dark INFO crires spec flat Normalise with the median INFO crires spec flat Compute the MASTER FLAT for chip nb 2 INFO crires spec flat Correct for the dark INFO crires spec flat Normalise with the median INFO crires spec flat Compute the MASTER FLAT for chip nb 3 INFO crires spec flat Correct for the dark CRIRES data reduction cookbook VLT MAN ESO 14200 4032 58 INFO crires_spec_flat Normalise with the median INFO crires spec flat Compute the MASTER FLAT for chip nb 4
61. RIRES data and calibrations CRIRES uses a science detector which is a 4x1 mosaic of four Raytheon 1024x1024 pixel InSb Aladdin III detectors When reducing data you should keep in mind the following points e The arrays are read out simultaneously e Only the bottom half of each detector is illuminated by the slit so the useful mosaic actually consists of 4x1024x512 pixels The reading out is executed parallel to the mosaic for detector 2 and 3 and perpendicular to it for detectors 1 and 4 e There is no shutter so the array is continuously exposed to light 3 1 Readout modes The CRIRES IRACE controller and the associated DCS software control the readout of the array Currently two read out modes are supported Fowler Sampling FNS and Fowler Sampling with Global Reset and Window FowlerNsampGRstWin In FNS mode the detector is first reset then each pixel is non destructively read NDSAMPLE 2 times at the start of the exposure then again NDSAMPLE 2 at the end of the exposure time DIT The slope of the relation provides the intensity of the given pixel NDSAMPLE varies with the DIT 2 for DIT 10 sec 4 for 10 sec lt DIT lt 20 sec etc up to 128 In case of very bright targets the FowlerNsampGRst Win mode can be used This mode only reads detector 2 and 3 It executes a global reset of the detector before applying the Fowler Sampling on two small stripes that fully cover detector 2 and 8 in the spectral direction but only a us
62. S Xx REESE a Ja Nom ease mo re BA He Se ed BEE 3 Y Wor Aw POR ee 3 ee og eos ee ra te ee ae ge ee ee BE ee aa eoa oe OO o Se eee ek OS Se OE Re E ee ee 8 5 0 ThAr wavelength calipration o 6s deo eh 9 x9 S y XO BO 3 3 4 Gas cell wavelength calibrations llle 4 9 5 Detector linearity images 262 ee de o RR RR RR 3 4 General Features of CRIRES Infrared spectra rn SA RO es Se Se A re ee ed He Ba ws oe Be a E A 34 2 Optical ON ok ec e RAE we Be eR A bE BES Boe e 9 a 3 4 8 Odd even column effect and detector non linearity 344A Remnants trom bright SOHEOBS oe de we eee ee gem ES Sud I nod X ae OMe YE eo De eee ee ee ee Jn oft eS Downloading CRIRES raw data and calibrations 5 Reducing the science data aul Ins supe unu B ud b RE RISE RUE PEDE A dO b HSE NO BO NO on oL LH O 1 1 10 O0 OU 4 amp 0 Q CRIRES data reduction cookbook VLT MAN ESO 14200 4032 vi oc Flat ee oe bce he pogue ee DRS ESS ee ee eee ek we ES 26 o Wavelength cablbislbiOl ua ao doe 4 9 9 3 3 9 3X 9 o 9e ELE Fs Rw oos 27 Oe COMPIA Ed Sees cee se A eB ee ee ee emo D ee m ORC 27 59 Extraction inn ee Dad ee X ko wee EES OEE EORURCEOR Bee Veo 28 5 6 Removing telluric lines 2 4 2 642 oa Peed eee AR ORO RO 28 or Pe calibrati 2 4 2 ei ee RRR Ea ERROR ERASE OA EES EE KES s 29 6 The ESO CRIRES pipeline installation 30 6 1 Opening gasgano resizing columns and selecting data for reduction 31 6 2 The ES
63. T03 23 57 755 fits CAL_NOD SPECTRUM NODDI STD 38 1504 800 5 00 2 FowlerNsamp i CRIRE 2010 10 20T03 24 32 399 fits CAL NOD SPECTRUM NODDI STD 38 1504 800 5 00 2 FowlerNsamp F i CRIRE 2010 10 20T03 26 00 136 fits CAL_NOD SPECTRUM NODDI STD 26 2205 000 5 00 2 FowlerNsamp fi CRIRE 2010 10 20T03 26 34 717 fits CAL NOD SPECTRUM NODDI STD 26 2205 000 5 00 2 FowlerNsamp i CRIRE 2010 10 20T03 28 13 918 fits CAL NOD SPECTRUM NODDI STD 16 3611 000 5 00 2 FowlerNsamp i CRIRE 2010 10 20T03 28 48 488 fits CAL_NOD SPECTRUM NODDI STD 16 3611 000 5 00 2 FowlerNsamp CRIRE 2010 10 20T03 31 23 984 fits CAL NOD SPECTRUM NODDI STD 11 5050 400 5 00 6 FowlerNsamp i CRIRE 2010 10 20T03 32 22 834 fits CAL NOD SPECTRUM NODDI STD 11 5050 400 5 00 6 FowlerNsamp U crires spec iitter bamap fits STD BGD MAP IMA STD_BGD_MAP_IMA 16 3611 5 2 FowlerNsamp crires_spec_jitter_comb fits STD_COMBINED_IMA STD_COMBINED_IMA 16 3611 5 2 FowlerNsamp crires_spec_jitter_contrib fits STD CONTRIBUTION IMA STD_CONTRIBUTION_IMA 16 3611 5 2 FowlerNsamp U crires_spec_jitter_extracted fits STD_EXTRACT_WL_TAB E D EXTRACT WL TAB 16 3611 ae 2 FowlerNsamp U crires spec iitter prof fits STD PROFILE IMA STD_PROFILE_IMA 16 3611 5 2 FowlerNsamp crires_spec_jitter_wlmap fits STD_WL_MAP_IMA STD_WL_MAP_IMA 16 3611 5 2 FowlerNsamp B 60 A 9800 CRIRES UNKNOWN 200220568 2MASS J0159 4019 FowlerNsampGRs ACO FRAME IMAGE KY 34 1646 800 730 1
64. TD_PHOTOFLUX And then run the esorex using the following command esorex output dir home2 jsmoker Instruments CRIRES Pipeline Data Reduced crires spec jitter display 3 CRIRES_SpecJitter_1087p3 sof Xxx ESO Recipe Execution Tool version 3 9 0 seek INFO crires spec jitter bbb oook kkk kkk kkk kk INFO crires spec jitter Detector 1 Y 1 gt Y 512 pixels INFO crires spec jitter Detector 2 Y 1 gt Y 512 pixels INFO crires spec jitter Detector 3 Y 1 gt Y 512 pixels INFO crires spec jitter Detector 4 Y 1 gt Y 512 pixels INFO crires spec jitter bobb kkk kkk kkk kk INFO crires spec jitter Images combination INFO crires spec jitter Load the chip number 1 INFO crires spec jitter Correct the bad pixels INFO crires spec jitter Correct for the dark INFO crires spec jitter Correct for the flat field lt snip gt CRIRES data reduction cookbook VLT MAN ESO 14200 4032 82 INFO crires_spec_jitter Throughput computation INFO crires spec jitter Exposure time 20 sec INFO crires spec jitter Sensitivity computation INFO crires spec jitter Save the product INFO crires spec jitter Writing FITS propertylist product STD COMBINED IMA crires spec jitter comb fitspectrums INFO crires spec jitter Writing FITS propertylist product STD CONTRIBUTION IMA crires spec jitter contrib fits INFO crires spec jitter Writing FITS pr
65. WL MAP IMA 1083p3 fits mv home2 jsmoker Instruments CRIRES Pipeline Data Reduced out_0001 fits home2 jsmoker Instruments CRIRES Pipeline Data Reduced ThAr CALPRO WAVE 1083p3 fits 8 6 3 Reduction of ThAr frames using pipeline 2 3 1 or later and esorex This is the preferred method as it will collapse 10 rows from the input image at positions given by y pos cN and apply the cross correlation for each of the six fibre positions e g around Y 63 142 221 301 380 and 459 in the case of detector 3 If no values of y pos cN are input then the pipeline will used fixed values however as the Y position of the fibres can slightly shift it is recommended to measure them yourself and use these values in the recipe All the successful calibrations are then used to generate a 2D wavelength map per detector cat ThAr 1087p3 sof CRIRE 2010 10 20T13 59 48 752 fits CAL_WLLAMP CRIRE 2010 10 20T14 01 20 131 fits CAL_WLLAMP CRIRE 2010 10 20T14 02 47 227 fits CAL WLLAMP path master dark 3pO0s fits CALPRO DARK path master flat 1087p3 fits CALPRO FLAT path bpm 1087p3 fits CALPRO_BPM path crire calib 2 1 3 cal lines_thar fits CALPRO_THAR_CATALOG M CRIRES 2010 09 21T17 04 57 320 fits DETLIN_A M CRIRES 2010 09 21T17 05 07 420 fits DETLIN_B M CRIRES 2010 09 21T17 05 13 214 fits DETLIN_C esorex output dir path Reduced crires_spec_wavecal y pos ci 79 158 237 317 396 476 y pos c2 77 158 235 314 396 472 y pos c3 2 63 142 221 301 380 45
66. a Applet that is used to retrieve the science frames and associated calibrations and put them on your computer For Unix Linux users a shell script is also created that can be downloaded and run in order to easily fetch all of the data e Once the download is complete you are ready to inspect the science and calibration data and reduce your data CRIRES data reduction cookbook VLT MAN ESO 14200 4032 18 1473 1 1475 0 Figure 6 Science detector images whilst a ThAr image is being taken Light blue green circles examples of ThAr lines for each of the six fibres Green circles Metrology fibres Yellow circles Metrology fibres Note that the metrology fibres do not go through the same optical path as the six ThAr fibres hence are not aligned in wavelength Vertical red lines stray light generated by strong spectral features falling close to the intermediate slit border Ble View Graphics Real time lt lt lt Pixel Values Object CRIRES_SPEC_W x 255 0 oO Min 256 45 j Low zdoo Scale dx C Value 3442 8999023437 Gose Figure 7 Science detector image on detector 4 of a flatfield with the N20 gas cell inserted This produces a sharp lined absorption line spectrum that can be used for wavelength calibration CRIRES data reduction cookbook VLT MAN ESO 14200 4032 19 CRIRE 2011 04 10T01 44 12
67. a are uncalibrated 7 3 Quick reduction of stare frames using esorex One can reduce staring frames using the pipeline with the use of the blind parameter within the crires spec jitter recipe For example if we have a single stellar observation as shown in Fig 25 we create a simple sof file like cat QuickReduceNoCals HD29085 OBS DIR NoNod sof GasCell HD29085 1579p137 272 0009 fits OBS DIR and reduce it in esorex using the following command esorex recipe dir path crire kit 2 3 0 crire 2 3 0 recipes libs output dir path Projects NoNod crires spec jitter y pos ci 290 y pos c2 289 y pos c3 274 y_pos_c4 264 y width 30 blind true display 3 QuickReduceNoCals HD29085 OBS DIR NoNod sof Note that one can also extract non stellar spectra in the same way for example gas cell flatfields etc although sometimes the OPTimal extractions will fail on detector two as there is no profile to optimally extract In this case just inspect the RECTangular extractions In the example shown below both OPT and RECT extraction worked on the raw data shown in Fig 24 with sof file Gas Cell No Star RawData sof cat Gas Cell No Star RawData sof Gas Cell No Star RawData fits OBS DIR CRIRES data reduction cookbook VLT MAN ESO 14200 4032 43 Anio eo mI mE m TTL dere o ee AD ODCE Rer AE NS PT T UE EN mS IRI AS B oum DDR 40000 TAREE DELLI AREA SEREEN RN Deas BUE Sede e
68. aded from the ESO archive at http archive eso org wdb wdb eso crires form Figures 11 to 13 show the different steps in the download process e Figure 11 shows the initial search One can search one or several parameters including but not limited to programme ID target name night or range of nights coordinates CRIRES data reduction cookbook VLT MAN ESO 14200 4032 17 in RA Dec or Galactic systems with or without search box and or proposal title A list of targets can also be used as input By default no sorting is performed on the output although it may be convenient to sort by observation time or type One can also increase the number of rows returned from the default value of 200 e Figure 12 shows the result of the search If the check boxes on the left are green then the spectra can be downloaded if red then they are still within their proprietary period typically 1 year and can only be accessed by the P I or in the future possibly Cols given permission by the P I Mark the spectra that you would like to download e Figure 13 shows the result of the request At this point one should normally click the Cal selector and Add IRAF keywords boxes The former searches the ESO archive for calibrations close in time to the science frames The latter adds IRAF keywords to the headers e Figures 14 and 15 show the results of the request but now with the associated calibra tions e Finally figure 16 shows the jav
69. alibrations may be reduced Any such change will be announced in the CRIRES news pages Note that due to bad pixels and the scratch on detector 2 and other detector features false lines may be detected in the wavelength solution that cause a decrease in the correlation Such features can be removed by masking before doing the wavelength calibration We note at present this is not possible within the CRIRES pipeline although may be rectified in a future release 3 3 4 Gas cell wavelength calibrations Wavelength calibration can also be performed by taking a flatfield but with the gas cell in serted This produces an absorption line spectrum in the flatfield as shown in Fig 7 An N20 line list is provided that can be used for wavelength calibration using cires spec wavecal Gas cell calibrations are taken daily by the observatory for each wavelength setting used the previous night 3 3 5 Detector linearity images Typically every 1 2 months flatfield calibrations are taken with the IR emitter at 4007 0 nm at a variety of DIT settings 1 2 3 4 5 6 7 8 9 10 20 30 80 90 100 s in order to determine the non linearity coefficients of the detector so called Detector monitoring Fig 8 shows an example of such flatfields taken with 2 0 s and 100 0 s DITs These non linearity images are processed in Quality Control Garching and are available here http www eso org observing dfo quality CRIRES pipeline pipe calib html 3 4 General Features
70. annot find recipe files Sometimes you may have several versions of the CRIRES pipeline on your computer To select a particular set of recipes just add the following to your esorex command esorex recipe dir path crire kit 2 3 0 crire 2 3 0 recipes libs To check which recipes gasgano is looking at go to File Preferences Recipe Configuration from the gasgano main panel 10 7 Problems in running esorex A list of frequently asked questions is available here http www eso org sci software cpl faq html CRIRES data reduction cookbook VLT MAN ESO 14200 4032 97 A Example IDL script to read in reduced data and pro duce ascii format output files If we have IDL and an input file called Reduced wl map filelist ascii which contains a list of the spectra with product category CRIRES OBS_EXTRACT_WL_TAB reduced files produced by the pipeline combined with output names for each of the 4 detectors cat Reduced wl map filelist ascii OBS EXTRACT WL TAB WithAllCals OO1s A fits OBS EXTRACT WL TAB WithAllCals O01s A ch ascii OBS EXTRACT WL TAB WithAllCals O01s A ch2 ascii OBS EXTRACT WL TAB WithAllCals O01s A ch3 ascii OBS EXTRACT WL TAB WithAllCals OO01s A ch4 ascii all on one line OBS EXTRACT WL TAB WithAllCals 002s A fits OBS EXTRACT WL TAB WithAllCals 002s A ch ascii OBS EXTRACT WL TAB WithAllCals 002s A ch2 ascii OBS EXTRACT WL TAB WithAllCals O02s A ch3 ascii OBS EXTRACT WL TAB WithAllCals 002s A ch4 ascii all on on
71. arent due to the fact that the wavelength calibration in v2 1 3 of the pipeline did not take into account slight differences in the solution on different Y parts of the detectors This issue was fixed in v2 3 1 of the pipeline which can apply the derived solution at different Y positions on the detectors see Fig 39 and Sect 8 6 3 CRIRES data reduction cookbook VLT MAN ESO 14200 4032 87 8 8 Telluric line correction At present telluric line correction is not possible within the CRIRES pipeline One should either use a telluric standard star taken close in time and airmass or an atmospheric model such as the one provided by ESO available at www eso org observing etc skycalc skycalc htm Note that the exposure time calculator http www eso org observing etc also includes an atmospheric model and should be consulted before your observations to check the position of telluric lines compared with stellar or interstellar features of interest See Fig 48 for an example 8 9 Importing reduced data into IDL or IRAF 8 9 1 IDL To read in CRIRES reduced data to IDL then one uses the mrdfits command Example scripts are shown in Appendix A 8 9 2 IRAF To read in CRIRES reduced data to IRAF then one uses STRFITS within STSDAS followed by TXDUMP to write out an ascii format file See Appendix B 8 10 Plotting reduced spectra To plot the reduced spectra within the CRIRES pipeline then follow the procedure explained in Sect 7 4 using the
72. at requires some care and possibly some experimentation The aim is to remove the large number of telluric lines that appear in IR spectra This is done by dividing the object spectrum with that of a telluric standard or a model spectrum of the sky as created by for example www eso org observing etc skycalc skycalc htm Since this is a division of one spectrum by another it is important that the strength shape and centroid of the telluric lines match First and foremost the telluric standard and the object have to be observed with the same instrument setup with roughly the same airmass and if possible consecutively Secondly the object and science data should be reduced in the same way and with the same calibration frames For the best results one may have to modify the spectrum of the telluric standard so that the center and strength of the telluric lines match those of the object spectrum The next step is to remove spectral features that have been imprinted onto the object spectrum from the telluric standard itself Telluric standards are either hot stars or solar type dwarfs Both types contain spectral features that should be removed For solar type stars one can use the observed solar spectrum to remove the features Hot stars usually contain helium and hydrogen lines If the spectral regions around these lines are of interest then one should think carefully about using these type of stars However one can still try to remove these lines
73. ation is present in the ESO dictionaries available from the ESO archive Web site here http archive eso org cms tools documentation eso data interface control html The following section only tries to summarise the most important information 2 1 Extracting FITS Information There are many tools to extract and parse FITS headers One convenient way of extracting FITS information and displaying it on a terminal or re directing it to a text file is to use two stand alone programs called dfits and fitsort which are both included in the scisoft package and also available here http archive eso org saft dfits dumps a FITS header to stdout You can use it to dump the FITS headers of many files to allow the parsing of the output For example jsmoker pc015042 src dfits usage dfits x xtnum lt list of FITS files gt usage dfits x xtnum The former version expects file names The latter expects data coming in from stdin x xtnum specifies the extension header to print x 0 specifies main header all extensions or in action dfits fits grep TPL ID Usually you want to get the value of a list of given FITS keywords in a list of FITS files fitsort reads the output from dfits classifies the keywords into columns and prints out in a readable format the keyword values and file names An example follows dfits fits fitsort NAXIS1 NAXIS2 BITPIX fitsort also understands the shortFITS notation where e g
74. blems The CRIRES pipeline and the calibration data on which it works suffers from a number of limitations some of which are noted below 10 1 Wavelength calibration issues 10 1 1 Limited accuracy in the ThAr and OH line catalogues Until the release of CRIRES pipeline 2 3 1 the ThAr and OH catalogues used by the CRIRES pipeline fits and ascii tables only had an accuracy of two decimal places for example 1265 27 This was fixed in version 2 3 1 of the pipeline 10 1 2 Too few ThAr lines In order to obtain a good wavelength solution with CRIRES you should have at least two or three ThAr lines visible on each detector preferably well spaced at least for a 2nd order polynomial Otherwise the results of the solution will likely not be trustworthy Obviously this is not a problem of the pipeline but with the wavelength calibration source itself In the future it is hoped to include a UNe lamp in CRIRES that will solve a lot of the current issues at a stroke due to the high density of lines and large wavelength coverage 10 1 3 False identification of ThAr line features The scratch on detector number 2 plus other features in the raw frames are often misinterpreted by the pipeline as being ThAr features Masking of these may be performed before the wavelength calibration is performed otherwise a degraded solution could result One should check the output of the crires spec wave recipe to check that detected lines actually match up with kno
75. c jitter c 5 10 Completion status FAILURE Execution error Execution failed with code 14 Figure 20 Failed reduction because only one spectrum was used in the recipe crires spec jitter with the default parameters CRIRES data reduction cookbook VLT MAN ESO 14200 4032 40 crires spec jitter v20103 File Help Current Queued Executing Parameters Default crire crires_spec_jitter onlyA crire crires_spec_jitter onlyB crire crires spec jitter blind IU crire crires spec jitter wl log crire crires spec jitter wl nolimit crire crires spec jitter wl clean Request Pool Input Frames Include Filename Classification CRIRE 2010 10 20T03 28 13 918 fits locate CRIRE 2010 10 20T03 28 48 488 fits Locate Display Product Naming Product Root Directory home jsmoker Instruments CRIRES Pip Browse Naming Scheme Iv Execute Selected Filename Classification crires spec jitter comb fits STD COMBINED IMA crires spec jitter contrib fits STD OTRE A crires spec jitter prof fits STD PROFILE IMA crires spec jitter bgmap fits E NE crires spec jitter wImap fits STD_WL_MAP_IMA crires spec jitter extracted fits ISTD EXTRACT WL TAB Log Messages home jsmoker Instruments CRIRES Pipeline Data Rawj crires spec jitter comb fits home jsmoker Instruments
76. der headfits datafileTEMP chi mrdfits datafileTEMP 1 head ch2 mrdfits datafileTEMP 2 head ch3 mrdfits datafileTEMP 3 head ch4 mrdfits datafileTEMP 4 head repeat begin printf lun ch4 j wavelength ch4 j extracted_opt format 22 5 22 5 Jijel endrep until j eq 1022 free_lun lun i i 1 endrep until i eq 34 end 99 CRIRES data reduction cookbook VLT MAN ESO 14200 4032 100 B Example IRAF script to read in reduced data and produce ascii format output files If we have IRAF and wish to read in a CRIRES reduced spectrum with category CRIRES OBS_EXTRACT_WL_TAB produced by the pipeline we need to use strfits and tdump in the following way cl NOAO IRAF PC IRAF Revision 2 15 1a EXPORT Mon Feb 21 18 54 16 MST 2011 This is the EXPORT version of IRAF V2 15 1a supporting PC systems stsdas 4 Space Telescope Science Data Analysis System STSDAS Version 3 14 4 analysis describe fitsio hst_calib problems toolbox contrib examples graphics playpen sobsolete 4 epar strfits change the paramaters lpar strfits Image Reduction and Analysis Facility PACKAGE fitsio TASK strfits fits fil OBS EXTRACT WL TAB WithAllCals 120s A fits FITS data source file lis File list iraf fil OBS EXTRACT IRAF IRAF filename templat none template filename long_he no Pr
77. display still show the old wl starty wl stopy parameters that were updated in v2 3 1 of the pipeline e Examples of the pipeline extraction at low S N ratios e Examples of how well the linearity correction works at low and high S N ratios e Residuals obtained using the CRIRES model at wavelengths shorter than 3 5 microns The next version will include these topics 1 6 Suggestions for improvements to the cookbook If you have suggestions for improvements to the cookbook or find mistakes in it please email criresQeso org This account is read by the Paranal Instrument Scientist who is currently the author of the cookbook Questions about the pipeline itself should be sent to usd help eso org or better by using the Ask for help link within the ESO user portal here http www eso org UserPortal Note that many of the examples in this cookbook refer to version 2 1 3 of the pipeline however the newest version should always be used which at the time of writing is 2 3 1 Updates to the cookbook will be announced in the CRIRES news pages CRIRES data reduction cookbook VLT MAN ESO 14200 4032 3 2 CRIRES FITS Information Ancillary data attached to CRIRES files are all written into FITS headers The following chapter lists the most important keywords and describes commands on how to retrieve them For ease of reading keywords are shortened from HIERARCH ESO A B C to A B C shortFITS notation Notice that all of this inform
78. ds of 2400 nm dfits CRI fits fitsort OBJECT INS WLEN REF DET DIT DPR CATG DPR TYPE grep 1087 CRIRE 2010 10 20T03 21 52 798 fits STD 1087 300 5 0000000 CALIB CRIRE 2010 10 20T03 22 23 810 fits STD 1087 300 5 0000000 CALIB CRIRE 2010 10 20T10 00 53 435 fits FLAT 1087 300 5 0000000 CALIB CRIRE 2010 10 20T10 02 18 593 fits FLAT 1087 300 5 0000000 CALIB CRIRE 2010 10 20T10 03 43 485 fits FLAT 1087 300 5 0000000 CALIB CRIRE 2010 10 20T13 59 48 752 fits WAVE LAMP 1087 300 3 0000000 CALIB CRIRE 2010 10 20T14 01 20 131 fits WAVE LAMP 1087 300 3 0000000 CALIB CRIRE 2010 10 20T14 02 47 227 fits WAVE LAMP 1087 300 3 0000000 CALIB dfits CRI fits fitsort OBJECT INS WLEN REF DET DIT DPR CATG DPR TYPE grep 3611 CRIRE 2010 10 20T03 28 13 918 fits STD 3611 000 5 0000000 CALIB CRIRE 2010 10 20T03 28 48 488 fits STD 3611 000 5 0000000 CALIB CRIRE 2010 10 20T10 45 49 238 fits FLAT 3611 000 5 0000000 CALIB CRIRE 2010 10 20T10 47 14 067 fits FLAT 3611 000 5 0000000 CALIB CRIRE 2010 10 20T10 48 34 697 fits FLAT 3611 000 5 0000000 CALIB CRIRES data reduction cookbook VLT MAN ESO 14200 4032 49 Additionally we want to use darks taken with a 5 0 s DIT to reduce the flatfields and with a 3 0 s DIT to reduce the arcs dfits CRI fits fitsort OBJECT INS WLEN REF DET DIT DPR CATG DPR TYPE grep DARK CRIRE 2010 10 19T15 38 05 389 fits DARK 2308 000 3 0000000 CALIB CRIRE 2010 10 19T15 38 25 378 fits DARK 2308 000 3 0000000 CALIB CRIRE 2010 10 19T15 3
79. e 5 sec INFO crires spec dark NDIT value 3 INFO crires spec dark Dark computation INFO crires spec dark Load chip number 1 lt snip gt INFO crires_spec_dark Collapse images for chip number 4 INFO crires spec dark Division by DIT INFO crires spec dark Save the product INFO crires spec dark Writing FITS propertylist product CALPRO DARK crires spec dark fits INFO esorex Created product home2 jsmoker Instruments CRIRES Pipeline Data Reduced out 0000 fits INFO esorex 1 product created Note that the output file is by default called out 0000 fits so within your esorex script you also have to have a line like the following mv home2 jsmoker Instruments CRIRES Pipeline Data Reduced out 0000 fits home2 jsmoker Instruments CRIRES Pipeline Data Reduced master dark esorex b5pOs fits 8 2 3 Inspection of pipeline results for master dark and QC parameters Figure 29 shows the master dark created by the CRIRES pipeline One should check that the count level looks reasonable and that the readout noise is as expected check the CRIRES ETC CRIRES data reduction cookbook VLT MAN ESO 14200 4032 52 or manual Look at the fits header information created by the pipeline in the QC Quality Control parameters dfits x 0 master_dark_esorex fits grep QC HIERARCH ESO QC RON1 3 45630348085064 HIERARCH ESO QC RON2 3 44496225098102 HIERARCH ESO QC DARKMED 1 27777775128682 HIERARCH ESO QC D
80. e line OBS EXTRACT WL TAB WithAllCals O004s A fits OBS EXTRACT WL TAB WithAllCals O004s A ch ascii OBS EXTRACT WL TAB WithAllCals 004s A ch2 ascii OBS EXTRACT WL TAB WithAllCals O04s A ch3 ascii OBS EXTRACT WL TAB WithAllCals 004s A ch4 ascii all on one line OBS EXTRACT WL TAB WithAllCals O05s A fits OBS EXTRACT WL TAB WithAllCals O05s A ch ascii OBS EXTRACT WL TAB WithAllCals O05s A ch2 ascii OBS EXTRACT WL TAB WithAllCals O05s A ch3 ascii OBS EXTRACT WL TAB WithAllCals O05s A ch4 ascii all on one line OBS EXTRACT WL TAB WithAllCals 010s A fits OBS EXTRACT WL TAB WithAllCals 010s A ch ascii OBS EXTRACT WL TAB WithAllCals 010s A ch2 ascii OBS EXTRACT WL TAB WithAllCals O10s A ch3 ascii OBS EXTRACT WL TAB WithAllCals 010s A ch4 ascii all on one line Then we can read in the fits files and write out the individual output files by doing the following jsmoker pc015042 ReducedData idl IDL Version 8 1 linux x86_64 m64 c 2011 ITT Visual Information Solutions IDL gt r CRIRES_Convert_Fits_To_Ascii pro Compiled module CRIRES_CONVERT_FITS_TO_ASCII IDL gt CRIRES_Convert_Fits_To_Ascii This will produce output files called ch1 ascii ch2 ascii ch3 ascii and ch4 ascii The CRIRES_Convert_Fits_To_As is listed below The code is very simple but works pro CRIRES_Convert_Fits_To_Ascii Basic code that reads in reduced OBS_EXTRACT_WL_TAB fits files produced by the CRIRES pipeline and produces ascii format files
81. e may try bash export JAVA HOME System Library Frameworks JavaVM framework Versions CurrentJDK Home install pipeline follow the instructions at the end of the installation to set properly the gasgano esorex paths and the environment variables setenv in csh export in bash The information above was taken from http www sc eso org epompei mac html If one tries to launch gasgano after having installed the pipeline on a MAC gasgano will fail because there are some definitions in the gasgano script which do not work in particular the path for the CPLdir is incorrect In order to correct this the user should first install the pipeline as described in the web pages then before launching gasgano the file called gasgano which is under home gasgano bin needs to be edited as follows e Comment out the following lines DYLIB LIBRARY PATH CPLDIR lib BASE lib DYLIB LIBRARY PATH export DYLIB LIBRARY PATH optjre optjre Djava library path DYLIB LIBRARY PATH CRIRES data reduction cookbook VLT MAN ESO 14200 4032 33 e Replace them with the following DYLD LIBRARY PATH CPLDIR lib BASE lib DYLD LIBRARY PATH export DYLD LIBRARY PATH optjre optjre Djava library path DYLD LIBRARY PATH 6 3 The ESO CRIRES pipeline reflex environment In a future release it is hoped that data reduction of CRIRES data will be possible using the reflex environment which allows more hands on interaction with the reduction process CR
82. ecifies the number of raw frames that were combined to generate the product Its exact meaning depends on the recipe see each recipe documentation to learn what it refers to 2 9 Summary Table The following table summarises all keywords introduced in this chapter in alphabetical order FITS keyword Meaning ARCFILE Archive file name DEC Declination J2000 in degrees DET DIT Detector Integration Time DET NDIT Number of averaged DITs DPR CATG Data product category DPR TYPE Data product type DPR TECH Data product acquisition technique INS DROT MODE Derotator mode e g SKY or ELEV INS1 DROT POSANG Position angle on sky degrees INS GRAT ORDER Grating order INS LAMP1 ST Status of the Halogen lamp INS LAMP2 ST Status of the IR emitter lamp INS LAMP3 ST Status of the NeKr lamp INS LAMPA ST Status of the Thorium Argon lamp INS SLIT1 WID Entrance slit width since Oct 2011 set to 0 2 or 0 4 arcseconds INS WLEN REF Reference wavelength microns INS WLEN CWLEN Central wavelength microns INS WLEN END1 Wavelength at the end of detector 1 microns INS WLEN END2 Wavelength at the end of detector 2 microns INS WLEN END3 Wavelength at the end of detector 3 microns INS WLEN END4 Wavelength at the end of detector 4 microns INS WLEN MIN Minimum wavelength of the unvignetted spectral range microns INS WLEN MAX Maximum wavelength of the unvignetted spectral range microns OBS PROG ID Program ID OBS NAME
83. ector then you should enter their y coordinates in y pos cN A wavelength solution is then obtained at each position and a 2D map of the wavelength solution is produced 23 26 13 INFO Calibrate chip number 3 23 26 13 INFO Wavelength range 1084 7 1089 91 23 26 13 INFO Correct the bad pixels 23 26 13 INFO Correct for the dark 23 26 13 INFO Correct for the flat field 23 26 13 INFO Wavelength error 60 pix 0 305572 nm 23 26 13 INFO Sub Catalog extraction lt snip gt 23 26 15 INFO Refine the degree 2 polynomial 23 26 15 INFO Wl error 0 0122229 nm 2 4 pix 23 26 15 INFO Nb of samples 10 23 26 15 INFO J Nb of candidates 1000 23 26 15 INFO Cross Correlation factor 0 492632 lt Much lt snip gt 8 6 2 Reduction of ThAr frames using pipeline 2 1 3 or earlier and esorex To reduce ThAr wavelength calibration frames using esorex we use the crires spec wavecal recipe In order to improve the correlation coefficient c f Fig 35 we only use y value of the data from 217 to 227 which means that the derived wavelength solution will be good only for detector 3 in this case the position of the fibres being different on the other detectors Note that the master dark used was taken with a 3 second DIT which corresponds to that used for the ThAr exposure cat ThAr 1087p3 sof improved CRIRE 2010 10 20T13 59 48 752 fits CRIRE 2010 10 20T14 01 20 131 fits CRIRE 2010 10 20T14 02 47 227
84. ee Intensity OPT ADU sec 2900019 2 86 TUUS UTE DU E NU UU rus EEE E E ed Ae uem m nen eee n 34000 Se 1579 1580 1581 1582 1583 Wavelength nm 1576 1577 1578 Figure 23 Example of a CRIRES stare observation and quick look reduction using crires spec jitter and the blind true option Detector 3 only is shown DOW run esorex esorex recipe dir path crire kit 2 3 0 crire 2 3 0 recipes libs output dir path Projects NoNod crires spec jitter y pos ci 290 y pos c2 289 y pos c3 274 y pos c4 264 y width 30 blind true display 3 Gas Cell No Star RawData sof o produce the following output Xxx ESO Recipe Execution Tool version 3 9 6 seek INFO crires spec jitter tid2000 eR CRC gt k xk xk k k 3k k k k KK 2K k K 2K K K INFO crires_spec_jitter tid 000 Detector 1 Y 1 gt Y 512 pixels INFO crires_spec_jitter tid 000 Detector 2 Y 1 gt Y 512 pixels INFO crires_spec_jitter tid 000 Detector 3 Y 1 gt Y 512 pixels INFO crires_spec_jitter tid 000 Detector 4 Y 1 gt Y 512 pixels INFO crires_spec_jitter tid2000 kkk gt k gt k k k kkk k ke kk KK ke oko 2K k KK K K lt snip gt CRIRES data reduction cookbook VLT MAN ESO 14200 4032 44 WARNING crires_spec_jitter tid 000 The spectrum positions in chip 2 and chip 3 are too different 220 gt 189 WARNING crires_spec_jitter tid 000 The spectrum po
85. er selected number of pixels 64 128 or 256 in the spatial direction As only a small fraction of the detector is read shorter DITs can be used On the other hand for comparable DITSs this mode allows to reduce the read out noise by a factor 2 compared to the FNS mode hence observations of faint targets are less affected by the read out noise Table 1 shows the NDSAMPLES value for each DIT The information is also present on the following webpage http www eso org sci facilities paranal instruments crires doc DIT NDSAMPLE html CRIRES data reduction cookbook VLT MAN ESO 14200 4032 11 Fig 2 shows an example of windowed mode FowlerNsampGRstWin only strips of Detectors 2 and 3 are read out with Fig 6 showing an example of normal readout mode Fowler Sampling 3 2 EXPTIME NDIT and DIT Up until March 2000 the ESO EXPTIME keyword was defined as NDIT x DIT This caused some confusion as the frames are the average and not the sum of NDIT exposures After March 2000 the EXPTIME keyword is set to the DIT 3 3 Calibrations 3 3 1 Darks Figure 3 shows dark images taken with a 1 s and 600 s exposure time Long darks show detector glow as is very obvious from this figure The calibration plan specifies 3 darks taken per DIT setting Visitors should be reminded to avoid very long DITs of slightly different value e g 600 s 650 s 700 s due to the extra calibration load this imposes Note that any DIT is comprised of a number of NDS
86. ers an automatic data classification only by applying an instrument specific rule A view on a set of CRIRES data is shown in Fig 2 1 as an example where the keywords FILE TPL ID and DPR TYPE have been specified in the appropriate Preferences fields More information about a single file can be obtained by clicking on its name the corresponding FITS file header will be displayed on the bottom panel where specific keywords can be opportunely filtered and searched See the Gasgano User s Manual for a complete description of the Gasgano interface It is available at http www eso org sci software gasgano Sections 6 1 and 10 5 also provide some information on the use of gasgano 2 2 Visualising FITS Tables Similarly a FITS table can be visualised on the command line without the need to call a full fledged FITS capable package The dtfits command has been written for precisely that purpose You will find it useful for spectroscopic data reduction if you need to check out the results of the pipeline recipes that produce FITS tables dfits and fitsort will help you classify tables and see ancillary data attached to them but dtfits will display all information contained in the table itself in ASCII format on the command line There are various options to help make the output readable on a terminal or by a spreadsheet program See the dtfits manual page to get more information 2 3 File Names e PIPEFILE if set contains the name of the pr
87. gment The layout of this cookbook was initially based on the ISAAC data reduction guide written by J G Cuby P Amico N Devillard and C Lidman We thank Ronald Mennickent Cid for details of importing reduced CRIRES spectra into IRAF CRIRES data reduction cookbook VLT MAN ESO 14200 4032 Contents 1 Introduction LE TED aa iio oe ie Be ee EE et ee X 1 2 Reference documents 2 22 hk ee eRe Ry ee Oe eR ee Ee 1 3 Abbreviations and acronyms 2 5 ooo OREM AREER GE L4 Stylistic conventions cuu kb eR NOE Xue d Xv OSE e HEE Ce HGR a s 1 5 Topics not covered by the cookbook llle 1 6 Suggestions for improvements to the cookbook lll 2 CRIRES FITS Information 21 Extracting FITS Information s soe o saian e ORR RR Ewe REE E oec Eos 22 Vieualiene FITS Tables o hv don oed don Ro om eh eR eR eS 29 File DUANE soe ea coreg apos EX ee Ge EGO b kA GE OA RAO RS Ee REL 24 Telescope Keywords c ces reete sekeut ea ERROR ROO Ron 20 Instrument Keywords lt e s gue ox 84 E X OR 3 ne 0o E e RR og e 2 6 Observation Block Keywords 4454444 442 be eee Ee EGO 2 7 Template Keywords uw ee RE ewe eee RR OEY RR eS ES 2 7 1 Keywords common to all templates 258 Pipelne CBS aucem deat eRe aE SEDER ee Redd eed BS DEO uy Tec uus xo Ae ES eS CR CR eee ee AN 3 CRIRES data and calibrations Al Readout modes se e priset eG REE EERE PEASE RS RO RO OA B RU EH ox PAP TM NDIT and DIT ua ae ah Oa ERE ORE
88. gth calibration available one may try different strategies 8 5 1 Wavelength less than 2 4 microns with more than two or three well spaced ThAr lines available per detector This is the easiest case to calibrate well One should use the crires_spec_wavecal or crires util wlcalib and crires util wlassign recipes A good fit is shown in Fig 33 Note that because of the limited reproducability of the grating and prism mechanism unless the ThAr spectrum is taken directly after the science exposure then there may be an offset between the science and ThAr wavelength calibration solutions that is impossible to verify See Fig 34 for an example of the typical scatter in the derived central wavelengths for two settings taken daily before the introduction of metrology 8 5 2 Wavelength less than 2 4 microns with less than two ThAr fibres available per detector Accurate calibration is more difficult in this case One has several options e Calibrate as above Sect 8 5 1 using the crires_spec_wavecal or crires util wlcalib and crires util wlassign recipes Because with two points I can fit an elephant the two points being two ThAr features the interpolation may lead to inaccurate results e Use the crires model refine recipe to improve the model This recipe applies a de tection of the Thorium Argon emission lines from a calibration lamp exposures and uses a cross check of the detected lines with the lines catalogue to perform an optimisation
89. gz crire 2 1 3 tar gz with the following pipeline calibration file s crire calib 2 1 3 tar gz The software installation will be organised in bin lib include and crire 2 1 3 directories while the calibration files will be installed in a calib directory Oops I cannot proceed with the gasgano installation gasgano must be installed in home jsmoker gasgano You appear to already have gasgano installed there I intended to rename your existing gasgano installation to home jsmoker gasgano old but home jsmoker gasgano old already exists You can either let me D Delete the current home jsmoker gasgano before I install gasgano there R Replace home jsmoker gasgano old with your current home jsmoker gasgano or 8 Stop so you can backup both home jsmoker gasgano and home jsmoker gasgano old and then restart the installation D Delete R Replace 8 Stop d R s R Where should I install the software packages home jsmoker home jsmoker Instruments CRIRES Pipeline crire kit 2 1 3 CRIRES data reduction cookbook VLT MAN ESO 14200 4032 31 Where should I install the pipeline calibration files home jsmoker Instruments CRIRES Pipeline crire kit 2 1 3 lt smip gt Updating home jsmoker gasgano config CRIRE prefs Updating home jsmoker gasganorc In order to use the recipes from gasgano you need to set the environment variable CPLDIR to home jsmoker Instruments CRIRES Pipeline Dependi
90. ing cat CRIRES model fix 1087p3 sof CRIRE 2010 10 20T13 59 48 752 fits MODEL FIX RAW 000 Model Fix File ThAr Test txt CALPRO MODEL FIX TAB model conf 11 2010 to 04 2011 fits CALPRO MODEL CONFIG Note that the headers of the MODEL FIX RAW and CALPRO MODEL CONFIG are checked by the recipe to make sure that the correct model file is used 5o in the example shown the model file used is correct even though the filename of the CAL PRO MODEL CONFIG indicates that the date is not valid One needs to tell the recipe the position of a line or preferably of lines that are measured by the user The file needs to contain the x and y coordinates detector number and wavelength of the line in nm cat 000 Model Fix File ThAr Test txt 513 6 222 4 3 1087 294870 CRIRES data reduction cookbook VLT MAN ESO 14200 4032 74 Wavelength nm Figure 40 Example of a science frame for detector 2 with reference wavelength of 1111 7 nm CRIRES data reduction cookbook VLT MAN ESO 14200 4032 75 Area of image to be examined Image Statistics Image X 51 3 6 Image Y 222 44 LL n Equinox Peak above bg e0e8 2o 26 Background level FWHM X Y en ze Angle of X axis 42 5 Pixels in x y 20 0 Pick Object Cancel Close Figure 41 Example of a ThAr image for detector 3 with reference wavelength at 1087 3 nm The cyan circle is a pick object using the programme rtd of a ThAr li
91. int FITS header cards short_h yes Print short header datatyp default IRAF data type blank 0 Blank value scale yes Scale the data xdimtog yes Transform xdim FITS to multigroup oldiraf no Use old IRAF name in place of iraf file force yes Force conversion from fits offset 0 Tape file offset Version 2 Aug 2000 Strfits version mode q1 4 epar starfits go Fits file IRAFNAME Dimensions BP DATE OBJECT OBS_EXTRACT_WL_T OBS_EXTRACT_WL_TAB 16 2012 08 13 AB WithAllCals 1 _WithAl1Cals_120s_A 20s A fits hhh OBS EXTRACT WL TAB 72 1024 Ncols OBS EXTRACT WL TAB 72 1024 Ncols OBS EXTRACT WL TAB 72 1024 Ncols OBS EXTRACT WL TAB 72 1024 Ncols ow oO oO CRIRES data reduction cookbook VLT MAN ESO 14200 4032 101 1s OBS_EXTRACT_WL_TAB_WithA11Cals_120s_A hhh OBS_EXTRACT_WL_TAB_WithA11Cals_120s_A01 tab OBS_EXTRACT_WL_TAB_WithA11Cals_120s_A02 tab OBS EXTRACT WL TAB WithAllCals 120s AO3 tab OBS EXTRACT WL TAB WithAllCals 120s AO04 tab The above creates a file called hhh and tab note the force yes to force conversion from fits files and oldiraf no Now we need to write this out in ascii format using the ttools package cl tdump OBS EXTRACT WL TAB WithAllCals 120s AO1 tab gt OBS EXTRACT WL TAB WithAllCals 120s AO 1 ascii all on one line This produces an ascii file with nine columns including the wavelength and extracted counts for optical and rectangular
92. ion cookbook VLT MAN ESO 14200 4032 79 0 005 8 1 i Computed Initial wavelenth XC 1 Initial catalog 2 Corrected catalog 3 Observed Vector rums sap bee ear escas cctconamened ENR SENN i escis Sette AGE SEEN ABSA E R Ls A TELE Mare o is TRIES bal ree bersorstones 0 025 0 03 Wavelength difference 0 035 0 04 0 045 0 05 0 200 600 Position pixels 1087 1090 Wavelength nm xe 534 138 y 0 0449202 7 4 5 1090 1 Initial 2 Computed 3 S lution AF 1088 i Y abeeeesede Beepeee Redeeeeseepbpeeeieeeeee 1088 E Qe beau E AEE atit nin ors nce neris rei EEE E ues nmt 8 1087 i 7 Mem E EPP PERE IUD Age E E ER ON E S EI i 1 AAD Lese snnt bere eepe ee leespepeeeifeeedee 1086 D UL cessas Noam ete ano c a ose eei etia rao i 1085 1 ds pics mn em eed o ee e o oci tm ota 0 1084 1084 1085 1086 1087 1088 1089 1090 0 200 400 600 800 1000 1200 Wavelength nm Position pixels ie 1083 88 u 4 50552 xz 87 4587 y 1084 8 Figure 42 Results of the CRIRES pipeline wavelength calibration fit for Detector 3 1087 3 nm These plots are produced directly from the pipeline using the display N option with N being the detector number 1 4 CRIRES data reduction cookbook VLT MAN ESO 14200 4032 80 Lar unn I Figure 43 Figure
93. ires spec wavecal wlstarty and stopy pipeline version 2 1 3 Detectors 1 2 and 4 would need to be reduced separately CRIRES data reduction cookbook VLT MAN ESO 14200 4032 70 isl e crires spec wavecal v20300 Yo Q9 File Help Current Queued Executing Parameters Name Default crire crires spec wavecal display Add to pool crire crires_spec_wavecal wl samples crire crires spec wavecal y width crire crires spec wavecal degree crire crires spec wavecal wl err 5 Request Pool crire crires spec wavecal wl xclimit crire crires spec wavecal y pos c1 crire crires spec wavecal y pos c2 crire crires spec wavecal y pos c3 crire crires spec wavecal y pos c4 crire crires spec wavecal waves Solo a il LT Filename CRIRE 2010 10 20T13 59 48 752 fits C locate Display CRIRE 2010 10 20T14 01 20 131 fits WLLAN Locae Display CRIRE 2010 10 20T 14 02 47 227 fits WLLAMF Locate Display master dark 3p0s fits master flat 1087p3 fits jlines_thar fits model_conf_04_to_11_2010 fits Product Naming Product Root Directory diska home jsmoker CRIRES Reduced Browse Naming Scheme 1L Execute Selected Mene EE o Figure 39 Wavelength calibration using gasgano using v2 3 0 of the pipeline using the mea sured positions of the
94. itter offsets are generated using a Poisson distribution SEQ POISSON refers to the num ber of Poisson numbers which have been generated at the start of the jitter sequence See the eclipse web page http www eso org projects dfs papers jitter99 for more information about this factor 2 8 Pipeline Products To allow identification of pipeline products some keywords are inserted in the output FITS headers e PIPEFILE is a standard 8 char FITS keyword which contains the name of the file as set by the pipeline when creating the product it is useful as a label to identify the file e PRO DID contains the version number of the dictionary used for all product keywords l Templates might have been aborted so it is possible to have fewer frames than TPL NEXP in a batch CRIRES data reduction cookbook VLT MAN ESO 14200 4032 8 e PRO SCIENCE contains a boolean to identify SCIENCE products e PRO TYPE contains the type of the data products as one of COMBINED DARK SPEC PIX SPEC WL etc replaces e PRO TYPE contains the type of the data products as one of TEMPORARY PREPRO CESSED REDUCED or QCPARAM e PRO DATE gives the date and time of the pipeline execution for the frame creation e PRO REC1 ID identifies the recipe that generated the file with a unique name e PRO REC1 DRS ID identifies the Data Reduction System that was used to produce the file CRIRES pipeline for all CRIRES recipes e PRO DATANCOM sp
95. kbook VLT MAN ESO 14200 4032 89 The files listed in the Set Of Frames sof file must be tagged raw file fits OBS_DIR or raw file fits OBS_DIR_JIT or raw file fits CAL_DIR or raw file fits CAL_DIR_JIT or raw file fits OBS_OBJECT or raw file fits OBS_SKY or raw file fits OBS_GENERIC_OBJECT or raw file fits OBS_GENERIC_SKY or raw file fits OBS_NOD or raw file fits OBS_NOD_JIT or raw file fits CAL_NOD or raw file fits CAL_NOD_JIT or flat file fits CALPRO_FLAT or bpm file fits CALPRO_BPM or dark file fits CALPRO DARK or detlin file fits COEFFS CUBE or snip esorex man page crires util extract Xxx ESO Recipe Execution Tool version 3 9 0 seek NAME crires util extract Spectrum extraction routine SYNOPSIS esorex esorex options crires util extract crires util extract options sof DESCRIPTION This recipe accepts 1 parameter optionally a 2nd one First parameter the combined image PRO TYPE COMBINED Second parameter optional the contribution map PRO TYPE CONTRIB snip 9 1 Examples of the use of the utilities Some examples of utility usage is described below 9 1 1 crires util combine This recipe to combine spectra has been tested with a SOF containing CRIRES data reduction cookbook VLT MAN ESO 14200 4032 90 raw_image fits OBS_DIR masterflat fits CALPRO_FLAT badpixmap fits CALPRO PBM masterdark fits CALPRO DARK nonlinearity fits either DETLIN A to _C 3 frames or COEFFS CU
96. ker CRIRES Reduced crires spec wavecal ima 0016 fits home jsmoker CRIRES Reduced crires spec wavecal tab 0016 fits Completion status SUCCESS 22 10 02 INFO Writing FITS propertyist product WL_MAP_IMA crires_spec_wavecal_ima fits 22 10 02 INFO Writing FITS table product CALPRO_WAVE crires_spec_wavecal_tab fits Figure 36 Apparently successful wavelength calibration using gasgano the pipeline but in fact it Failed see Fig 37 and version 2 1 3 of CRIRES data reduction cookbook VLT MAN ESO 14200 4032 69 22 09 57 INFO 22 09 57 WARNING ERROR 22 09 57 ERROR ERROR 22 09 57 ERROR 22 09 57 INFO 22 09 57 INFO 22 09 57 INFO ERROR 22 10 02 ERROR 22 10 02 INFO 22 10 02 INFO 22 10 02 INFO Product frames Wavelength error 60 pix 0 332845 nm Start on pixel 1133 Wrong boundaries 1133 pix 1024 pix Cannot compute the wavelength calibration Calibrate chip number 2 Wavelength range 1077 81 1083 26 Correct the bad pixels The cfg file home2 jsmoker Instruments CRIRES Pipeline crire kit 2 1 3 calib crire 2 1 3 cal model conf 04 to 11 2010 fits is not compatible with the science file home jsmoker CRIRES Raw CRIRE 2010 10 20T13 59 48 752 fits Save the product Writing FITS propertyist product WL MAP IM A crires_spec_wavecal_ima fits Writing FITS table product CALPRO WAVE crires spec wavecal tab fits Figure 37
97. l 2011 First one should visually check the normally three flatfields to see if the data quality looks OK in particular that the count levels do not exceed 10 000 ADU and that there is flux on all four detectors and exposures Some settings particularly in the blue suffer from vignetting on detectors 1 and 4 Fig 31 which is necessary to avoid contamination by adjacent orders One should thus look at the keywords INS WLEN MIN MAX to see where the usable range lies Note that flatfields especially at long wavelengths may be affected by water vapour between the calibration lamp and the vessel entrance window Fig 4 and or ghosts Fig 5 8 4 1 Reduction of flatfields within gasgano Figure 31 shows the creation of flatfields using gasgano CRIRES data reduction cookbook VLT MAN ESO 14200 4032 55 Figure 30 CRIRES nodding The integrated flux in the two nodding positions typically should be the same as long as the atmosphere was stable between the two observations CRIRES data reduction cookbook VLT MAN ESO 14200 4032 56 crires spec flat v20103 File Help Current Queued Executing rParameters Add to pool Request Pool Name Value Default Range crire crires spec flat starty 1 crire crires spec flat stopy 1 crire crires spec flat kappa sigclip 3 0 crire crires_spec_flat lines_ratio 0 5 crire crires spec flat thresholds 0 5 2 0 crire crires spec fla
98. ll spaced ThAr lines available per detector 61 8 5 2 Wavelength less than 2 4 microns with less than two ThAr fibres avail able per detector uus o hoo uo dex R9 Ra OES Pee ees 61 8 5 3 Wavelength more than 2 4 microns with gas cell spectra available 61 8 5 4 Science frame with no gas cell or ThAr wavelength calibration and no OH or sky absorption lines 24 22 93 ox o9 oRX X x3 62 8 6 Wavelength calibration examples 65 8 6 1 Reduction of ThAr frames using gasgano 4 65 8 6 2 Reduction of ThAr frames using pipeline 2 1 3 or earlier and esorex 67 8 6 3 Reduction of ThAr frames using pipeline 2 3 1 or later and esorex 72 CRIRES data reduction cookbook VLT MAN ESO 14200 4032 vii 8 6 4 Reduction of OH line frames using esorex 72 8 6 5 Use of the physical model and esorex to improve the wavelength solution 73 8 6 6 Inspection of the pipeline results produced by crires spec wave to check on the wavelength calibration solution ry B Combining nodding speclt amp so sos se oaos moes RE OE OE 9 OR Rs 78 8 7 1 Reduction of nodding frames using gasgano 81 8 7 2 Reduction of nodding frames using esorex 81 8 7 38 Inspection of pipeline results produced by crires_spec_jitter 82 8 8 Telluric line correction 2 gd eee ox Rok hoc ee X o De eR eG 87 8 9 Importing reduced data into IDL or IRAF
99. lot pmin crire crires util plot pmax crire crires util plot model crire crires util plot adjust 1100 Input Frames Include Filename Classification L crires spec jitter extracted 0000 fits crires spec jitter extracted 0001 fits 1050 Intensity OPT ADU sec 1000 950 Eur Naming Product Root Directory home jsmoker Instruments CRIRES Pipeline Data Raw 300 i i i l i ue mm D 1084 1085 1086 1087 1088 1089 1090 ay Wavelength nm x 1083 76 u 974 18 Output Frames Filename Classification R Extracted Spectrum OPT Intensity OPT ADU sec Parameters crire crires util plot display2 3 crire crires util plot pmin 1 crire crires util plot pomax 1 crire crires util plot model false crire crires util plot adjust false Input Frames home2 jsmoker Instruments CRIRES Pipeline Data Raw crires spec jitter extracte Completion status SUCCESS 20 3502 3504 3606 3608 3610 3612 3614 3616 3618 3620 Wavelength nm 4 x 3615 49 y 158 779 Figure 26 Plot of reduced spectra detector 3 using with the crires util plot recipe The recipe was run twice to display the two different wavelength ranges for the two quick reductions at 1087 3 and 3711 0 nm CRIRES data reduction cookbook VLT MAN ESO 14200 4032 48 8 The ESO CRIR
100. lution to this is to read in the data into a table format as explained in Appendix 1 The following iraf related issues that the ESO pipelines have was taken from http www eso org observing dfo quality CRIRES ServiceMode ServiceMode html which should be considered the main reference e Filename Length To display or manipulate the FITS files with older versions of IRAF before 2 11 you can copy these FITS files to your hard disk and rename them with filenames lt 32 characters in length create symbolic links with filenames lt 32 characters in length to your DVD files e Header Interpretation ESO FITS files use the ESO HIERARCH FITS keyword ex tensions standard to all ESO telescopes Note that IRAF treats all ESO HIERARCH header lines as COMMENT lines i e IRAF and IDL cannot automatically interpret the information provided in ESO HIERARCH header lines The problem may be solved us ing the tool hierarch28 Find information about this tool at http archive eso org saft hierarch28 g jsmoker gt hierarch28 SpecJit 1087p4 PipeDefaults STD EXTRACT SENS TAB fits xxx hierarch28 searching SpecJit 1087p4 PipeDefaults STD EXTRACT SENS TAB fits and replacing the following keywords UTC gt UT LST gt ST RA gt RA DEC gt DEC HIERARCH ESO TEL AIRM START gt AIRMASS HIERARCH ESO DPR TYPE gt IMAGETYP HIERARCH ESO INS FILT1 NAME gt FILTER1 HIERARCH ESO INS SLIT2 NAME g
101. name of FITS file e g CRIRE 2010 03 13T00 00 00 500 f 1 Figure 11 Initial steps in downloading data from the ESO archive searching for CRIRES observations of HD 49331 between 1st Jan 2011 and 1st June 2011 CRIRES data reduction cookbook VLT MAN ESO 14200 4032 File Edit View History Bookmarks Tools Help 4 HADS NAPOD amp NEWS BAstroPH 4Goog SIM oY ESO FLA BiFLAINT FLA QC NJVS Sch BPSO EPSO Int Remedy BICRIRES BiCRIRES Int BiResorting Query MESO Paranal Ins ESO PSO home 6 http archive eso org wdb wdb eso crires query g g g ae 22 AES M 0 I ESO Science Arc x ECRIRES SCIOPS ESO Science Archive CRIRES Query Results v To request datasets please mark the datasets then press either the Instant download button or the FTP or media delivery button You will be prompted for your ESO User Portal username and password If you do not yet have an ESO User Portal account please fill out the registration form Datasets for which the proprietary period is over are highlighted in green and are publicly available Datasets that are still under the proprietary period are highlighted in red and can only be downloaded by the corresponding PI Any comments or suggestions for improvement of this form can be sent to archive eso org Define new query Status of Requests SIMBAD coordinates for HD 49331 06 47 37 2 08 59 54 6
102. ne at 513 6 222 4 with wavelength 1087 294870 nm CRIRES data reduction cookbook VLT MAN ESO 14200 4032 76 The recipe is run as follows esorex recipe dir path crire kit 2 3 0 crire 2 3 0 recipes libs output dir diska home jsmoker CRIRES Raw crires model fix CRIRES model fix 1087p3 sof which produces output such as the following Xxx ESO Recipe Execution Tool version 3 9 6 kk INFO crires model fix tid 000 Parse the passed TXT file INFO crires model fix tid 000 Compute the new configuration file INFO crires model fix tid 000 Get the shape of the spectra INFO crires model fix tid 000 slit position 0 817091mm check 0 1087 294870 0 0 817091 2 2 515 193469 222 403017 513 600000 222 402359 1 593469 0 000659 52 43670 191670 0 854000 INFO crires model fix tid 000 Iterations 66 Mean x residual 95 756981 INFO crires model fix tid 000 Iterations 68 Mean x residual 37 199280 INFO crires model fix tid 000 Iterations 70 Mean x residual 16 787411 lt snip gt INFO crires_model_fix tid 000 Iterations 22458 Mean x residual 0 000001 INFO crires model fix tid 000 Save the new configuration file INFO crires model fix tid 000 Writing FITS table product CALPRO MODEL CONFIG crires model fix fits INFO esorex tid 000 Created product diska home jsmoker CRIRES Raw out 0000 fits INFO esorex tid 000 1 product created rara mv
103. ng on your type of shell a possible command for doing this may be export CPLDIR home jsmoker Instruments CRIRES Pipeline Warning Your PATH does not point to your newly installed home jsmoker Instruments CRIRES Pipeline bin esorex and home jsmoker gasgano bin gasgano To ensure execution of the newly installed software you should modify your PATH Depending on your type of shell a possible command for doing this may be export PATH home jsmoker starlink star new hawaiki star java jre bin scisoft bin home jsmoker gasgano bin home jsmoker Instruments CRIRES Pipeline bin In the above case I use tcsh so define the following aliases in my tcshrc before using the pipeline alias crires cpl setenv CPLDIR home jsmoker Instruments CRIRES Pipeline crire kit 2 1 3 alias crires pipe setenv PATH home jsmoker Instruments CRIRES Pipeline crire kit 2 1 3 bin home jsmoker gasgano bin home jsmoker java jdk 16 jdk1 6 0 16 bin home jsmoker Instruments CRIRES Pipeline crire kit 2 1 3 crire 2 1 3 recipes libs PATH setenv LD_LIBRARY_PATH LD_LIBRARY_PATH home2 jsmoker Instruments CRIRES Pipeline crire kit 2 1 3 lib 6 1 Opening gasgano resizing columns and selecting data for re duction Remember that a full description of gasgano can be found here http www eso org sci software gasgano First we want to make sure that we are looking in the correct place for the pipeline java version and gasgano CRIR
104. o_227 gasgano_230 gasgano_253 gasgano_260 jsmoker localhost Lost output message 10 52 04 WARNING CPL messaging initialization failed Lost error message 10 52 04 ERROR Dumping all 1 error s 1 1 File cannot be created Lost error message 10 52 04 ERROR 8 at cpl_msg_set_log_level cpl_msg c 874 Solution Likely you do not have write access for the current directory Change directory to somewhere where you can create files Gasgano hangs when adding new files Solution You may have fits gz files in the tree Either move them somewhere else or gunzip them Recipe fails because frames not classified Occasionally you may see an UNDEF in the Classification column of gasgano recipe window e g Fig 44 This either means that there is a problem with the FITS headers DPR CATG DPR TECH and or DPR TYPE or that the rules file used to classify the frames is not loaded and or is faulty You can still force gasgano to do a reduction by entering the classification by hand for example click on UNDEF and change to CALPRO FLAT if you are sure that image is a master flatfield e Telescope keywords not present in reduced files CRIRES data reduction cookbook VLT MAN ESO 14200 4032 96 Solution Make sure that the first file in your sof file is a science file If it is a calibration then the TEL keywords will not be present in the output file because they are not present in the calibration 10 6 C
105. oduct using the official naming scheme for OPEN line OPEN line CLOSED line CLOSED line CRIRES data reduction cookbook VLT MAN ESO 14200 4032 5 GASGANO Version 2 2 7 evalenti Mac OS X File Selected files Tools Help de a Default grouping m File C3 Displaying 6 files Unfiltered v pid 60 A 9051 A CRIRES CRIRES Operation Team Y EB 200163466 Calibration CRIRE 2007 12 29T10 14 04 115 fits Vl CRIRE 2007 12 29T10 15 12 599 fits El CRIRE 2007 12 29T10 16 20 880 fits El CRIRE 2007 12 29T10 20 50 893 fits El CRIRE 2007 12 29T10 21 59 008 fits CRIRE 2007 12 29T10 23 07 576 fits expand Users evalenti PARANAL CRIRES work CRIRE 2007 12 29T10 14 04 115 fits Find entry M C fina 1 TPL ID DPR TYPE DET DIT CRIRES spec cal LampFlats RAT 10 0000000 CRIRES_spec_cal_LampFlats FLAT 10 0000000 CRIRES_spec_cal_LampFlats FLAT 10 0000000 CRIRES_spec_cal_LampFlats FLAT 10 0000000 CRIRES_spec_cal_LampFlats FLAT 10 0000000 CRIRES_spec_cal_LampFlats FLAT 10 0000000 CRIRES_SPEC_FLAT363_0001 fits UNCLASSIFIED Find in header DET CHIP NAME DFT CHIP TYPF Extension F find Load Filter C Filter O Auto Display Keyword Value BE 7 BITPIX 8 NAXIS 0 EXTEND T ORIGIN ESO Paranal DATE 2007 12 29T10 15 06 7598 INSTRUME CRIRES OBJECT FLAT EXPTIME 10 0000000 MJD OBS 54463 42643652 DATE OBS 2007 12 29T10 14 04 1153 PI COI CRIRES Operation Team ORIGF
106. of various model parameters because the physical model is fit simultaneously across the spectral range of the observation it is less sensitive to the number of lines on each detector and typically requires in total only 1 4 as many lines as crires spec wavecal or crires util wlcalib to get an equivalent fit After those parameters are optimised they are saved in a new model configuration file that can be used to calibrate subsequent science observations e Use the crires model fix recipe after the initial wavelength calibration has been per formed This recipe refines the model configuration file using any CRIRES file for its header a TXT file with of user specified pixel position wavelength associations and a first guess model configuration file 8 5 3 Wavelength more than 2 4 microns with gas cell spectra available Because the crires model refine recipe only works with ThAr emission line exposures which consist of emission lines with a given x y position we have to use the crires model fix recipe This entails interactively identifying x y coordinates of known calibration features along the slit and using them in combination with a first guess model configuration file CRIRES data reduction cookbook VL T MAN ESO 14200 4032 62 Filename Ac O Mean offset pix Variation pix nm Header PM Header PM CRIRE 2012 02 02T09 54 30 443 3456 16 25 40 15 1 5 det 1 det 5 total CR
107. on cookbook VLT MAN ESO 14200 4032 84 1200 Extracted Spectrum RECT Vector 2 1150 1100 1050 Intensity RECT ADU sec 1000 350 900 1085 1085 5 1086 1086 5 1087 1087 5 1088 Wavelength nm xz 1083 03 y 1027 13 1200 Extracted Spectrum OPT Vector 2 1150 1100 1050 1000 Intensity OPT ADU sec 350 300 850 L 1085 1085 5 1086 1086 5 1087 1087 5 1088 Wavelength nm x 1082 83 y 1205 81 Figure 45 Comparison of output from crires_spec_jitter for uncalibrated observations green and after full reduction red both for rectangular and optimal extraction detector 3 only The improvement in S N ratio is apparent CRIRES data reduction cookbook VLT MAN ESO 14200 4032 85 1200 1200 i F 1 Extracted Spectrum OPT Extracted Spectrum RECT 1000 F 3900 M sisse iioii A 80 eee e IIIS Moraine por eee fxh enl h 800 3 E 1 3 i m 2 2 5 B00 E ii GENS CEU Sereno MIRAE ATEM Soto LOSS RUBUS j E EE k g 600 2 2 i 3 E 3 ae a Cee eee re Bees h 40 Pr SFR Ga re i SO EEDEN EDIE PE A9 ecce V NNNM MN hoa CMM SENEE 1084 1085 1086 1087 1088 1089 1090 1084 1085 1086 1087 1088 1089 1090 Wavelength nm Wavelength nm x 1080 38 y 175 737 70 BI icis sspe rip 50 a 3 i 3 40 2 A z 5 B c 5 30 f 3 a 20 0 1084 1085 1086
108. opertylist product STD PROFILE IMA crires spec jitter prof fits INFO crires spec jitter Writing FITS propertylist product STD BGD MAP IMA crires spec jitter bgmap fits INFO crires spec jitter Writing FITS propertylist product STD WL MAP IMA crires spec jitter wlmap fits INFO crires spec jitter Writing FITS table product STD EXTRACT SENS TAB crires spec jitter extracted fits INFO esorex Created product home2 jsmoker snip Data Reduced out 0000 fits INFO esorex Created product home2 jsmoker snip Data Reduced out 0001 fits INFO esorex Created product home2 jsmoker snip Data Reduced out 0002 fits INFO esorex Created product home2 jsmoker snip Data Reduced out 0003 fits INFO esorex Created product home2 jsmoker snip Data Reduced out 0004 fits INFO esorex Created product home2 jsmoker snip Data Reduced out 0005 fits mv home2 jsmoker snip Data Reduced out 0000 fits home2 jsmoker snip Data Reduced SpecJit 1087p4 PipeDefaults STD COMBINED IMA fits mv home2 jsmoker snip Reduced out_0001 fits home2 jsmoker snip Reduced SpecJit 1087p4 PipeDefaults STD CONTRIBUTION IMA fits mv home2 jsmoker snip Reduced out_0002 fits home2 jsmoker snip Reduced SpecJit 1087p4 PipeDefaults STD PROFILE IMA fits mv home2 jsmoker snip Reduced out_0003 fits home2 jsmoker snip Reduced SpecJit 1087p4 PipeDefaults STD BGD MAP IMA fits mv home2 jsmoker snip Reduced out_0004 fit
109. opriate scaling by convolving the spectrum with the filter curve CRIRES standard star observations typically are done with a 0 4 arcsecond slit hence slit losses are an issue even when using adaptive optics In the case the telluric has been observed with the same slit width it is possible to estimate the slit losses by taking a cross cut across the spatial axis for both science and telluric spectra Alternatively if the seeing did not change too drastically while the target and the standard were observed slit losses can be ignored Very accurate flux calibration is difficult with CRIRES CRIRES data reduction cookbook VLT MAN ESO 14200 4032 30 6 The ESO CRIRES pipeline installation The ESO CRIRES pipeline can be downloaded at http www eso org sci software pipelines where you will find the release file including CPL Gasgano EsoRex and calibration data plus the excellent pipeline manual Note that many of the examples in this cookbook refer to version 2 1 3 of the pipeline however the newest version should always be used which at the time of the release of this document is 2 3 1 Once downloaded you simply have to proceed as follows pwd home2 jsmoker Instruments CRIRES Pipeline gunzip crire kit 2 1 3 tar gz tar xvf crire kit 2 1 3 tar cd crire kit 2 1 3 sh install pipeline I am about to install the following software packages gasgano 2 4 0 tar gz cfitsio3090 tar gz cpl 5 3 1 tar gz esorex 3 9 0 tar
110. or corresponding to a 10 arcsecond nodding position for the particular observations in question One should look at the raw data for example shown in Fig 43 in order to work out which range of y values to extract per detector esorex recipe dir path crire kit 2 3 0 crire 2 3 0 recipes libs output dir path Reduced crires spec wavecal y pos c 1 238 353 y pos c2 238 352 y pos c3 223 337 y pos c4 214 328 y_width 30 display 3 OH Pipeline 0Hcat 1111p7 sof The esorex command above will produce plots showing the extraction overlaid on the OH lines from the catalogue You should compare your actual data with the catalogue as shown in Fig 40 to check the number of lines present In the current case there are indeed too few lines for even a reasonable wavelength calibration 8 6 5 Use of the physical model and esorex to improve the wavelength solution Figure 41 shows an example of a ThAr wavelength exposure with reference wavelength of 1087 3 nm As explained in Sect 8 6 2 for this particular wavelength region there are sufficient lines on detector 3 for a good wavelength calibration However for the purposes of this explanation let s assume that we just had ONE ThAr feature on detector 3 with x y position of 513 6 222 4 and no other features on the other detectors In this case we can choose to use the physical model of the instrument to obtain a wavelength solution The sof file needs to be like the follow
111. org rh confirmationAuthenticated 1d82b662 5839 4a02 9e8c amp J a di HADS MAPOD amp NEWS BlAstroPH Goog SIM e Y MESO WFLA EFLA INT WFLA QC MJVS Sch MPSO EPSO Int Remedy WCRIRES BiCRIRES Int Resorting Query WESO Paranallns NESO PSOhome la Eso Request Han X IBi CRIRES SCIOPS T ESO Archive Requests Jonathan Smoker Logout rSubmit Request Request Description HD 49331 two wavelength download for cookbook example Options M Cal selector Paranal instruments data acquired since June 2009 4 Add IRAF keywords has an impact on download duration FAQ Requested Datasets CRIRE 2011 01 15T04 46 56 780 CRIRE 2011 01 15T04 47 50 972 CRIRE 2011 01 18T05 05 20 631 CRIRE 2011 01 18T05 05 53 843 NGRH 41 4 10 ESO Data Flow infrastructure Send us your comments Subscribe to Newsleter Privacy Statement Figure 13 Intermediate steps in downloading data from the ESO archive Clicking the calS elector tab will query the archive for calibrations needed to reduce the science data 9 File Edit View History Bookmarks Tools Help e http dataportal eso org rh requests JSMOKER 27577 4g Google Uk a d HADS APOD SNEWS BlAstroPH Goog SIM oY MESO WFLA EFLA INT WFLA QC MJVS_Sch WPSO PSO Int is Remedy WICRIRES EICRIRES Int AResorting Query BESO Paranal Ins BESO PSO home Eso Request Han WiCRIRES SCIOPS ESO Archive Requests
112. orresponding to 3 pixels the start and end wavelength and the derived dispersion assumed to be linear for each detector is sufficient in particular for the CRIRES standard settings It is worth mentioning that in case the wavelength calibration is done by using ThAr lamp frame and the CRIRES pipeline with the crires_spec_wave recipe in order to improve the cross correlation one should run the recipe by using not only the lamp and master flat frames but also a master dark frame taken with the same DIT as the lamp flat An alternative is the use of the crires_util_wlcalib recipe In order to perform the wavelength calibration procedure with IRAF one can use the task identify under the onedspec environment 5 4 Combining 2d spectra For the classical ABBA technique one multiplies each image by 1 and adds it back to itself after a suitable shift This method of combining data is often called double sky subtraction as it effectively removes any residual sky that remains after the first subtraction It results in an image that has one positive spectrum and two negative spectra either side of the positive spectrum In the more complex cases one combines the individual spectra after suitable shifts have been applied To combine 2d spectra one can either use the CRIRES pipeline crires_util_combine recipe or with IRAF by using the task mscarith under mscred environment CRIRES data reduction cookbook VLT MAN ESO 14200 4032 28 5 5 Ex
113. p www eso org observing dfo quality CRIRES pipeline pipe calib html Note that for V2 1 x and later of the pipeline one must use a single non linearity image with category COEFFS_CUBE and for earlier versions of the pipeline use three files with categories DETLIN_A DETLIN_B and DETLIN_C There are several different versions of these files depending on the date of observation be sure to use the one indicated on the webpage or use the provided when you run calSelector during the download process see Sect 4 In our case we need to download the following files valid between 18th July 2010 and April 2011 viz CR_PDLA_100727A_ALL fits DETLIN_A CR_PDLB_100727A_ALL fits DETLIN_B CR_PDLC_100727A_ALL fits DETLIN_C These files are used by many recipes such as crires_spec_flat and crires_spec_jitter Section 10 4 describes the limitations of non linearity correction for low and high count CRIRES observations 8 4 Master flatfield creation Typically three flatfields classification CAL_FLAT are taken in the day following any CRIRES science or standard observation with the same reference wavelength Three darks with the same DIT as the flats are also taken that should be used to create a master dark with classifi cation CALPRO_DARK according to Sect 8 2 Finally the recipe accepts three non linearity files with classification DETLIN A DETLIN B and DETLIN_C for pre April 2011 data or one with classification COEFFS_CUBE post Apri
114. recipe crires util plot 9 Utilities recipes The CRIRES pipeline has a number of utilities recipes that allow reduction of spectra Note that when using the utility recipes great care has to be taken when tagging the files In partic ular use of the utility recipes with TAGGED inputs in a sof file is depreciated although see below Typically the input FITS files should be passed on the command line for example es orex crires util wlcalib a fits lines fits The support of COMMAND LINE tag is a workaround for gasgano The order of the expected input parameters is IMPORTANT and always documented in the man pages for example esorex man page crires util combine NAME crires util combine Images Combination tool SYNOPSIS esorex esorex options crires util combine crires util combine options sof DESCRIPTION crires util combine Images Combination tool CRIRES data reduction cookbook VLT MAN ESO 14200 4032 88 Extracted Speckrum DP ntes pg OPT PR pec end rong 150r at La 19x IET ma 158 Marea Leng rea 1500 1000 1808 1504 1508 1508 Figure 48 Output of the CRIRES exposure time calculator for a B3 star compared with actual observations of Eta Hy Many telluric features caused by atmospheric absorption are visible in the spectra The observations were taken with a water vapour column of around 2 5 mm which was the value used by the exposure time calculator ETC CRIRES data reduction coo
115. rires spec jitter crires spec jitter crires spec jitter crires spec jitter crires spec jitter crires spec jitter crires spec jitter crires spec jitter crires spec jitter crires spec jitter crires spec jitter crires spec jitter crires spec jitter tid 000 tid 000 tid 000 tid 000 tid 000 tid 000 tid 000 tid 000 tid 000 tid 000 tid 000 tid 000 tid 000 tid 000 tid 000 tid 000 tid 000 BER kk kk kkk kk I kkk kkk k k Y 1 gt Y 512 pixels Y 1 gt Y 512 pixels Y 1 gt Y 512 pixels Detector 1 Detector 2 Detector 3 Detector 4 FRI IO kk kkk kk kkk a 2 2k kk kk Y 1 gt Y 512 pixels Images combination The catalogs are missing No computed No computed No computed No computed Missing CFG solution solution solution solution IDENT in available available available available TT uniform Map uniform Map uniform Map uniform Map CALPRO_MODEL_CONFIG_fixed fit Call the model to get the wavelengths slit position 0 446678mm Sensitivity Conversion Throughput computation Search a star around RA 37 0396 DEC 8 46107 in the catalog esorex tid 000 Created product diska home jsmoker CRIRES Raw out 0004 fits esorex tid 000 Created product diska home jsmoker CRIRES Raw out 0005 fits esorex tid 000 6 products created SpecJit 1087p4 PipeDefaults STD COMBINED IMA Model fits SpecJit 1087p4 PipeDefaults STD CO
116. rt DET DIT DET NDIT DPR CATG DPR TYPE see Sect 8 1 for details The master dark is a simple recipe to run that just needs as input three raw darks taken with the same DIT as the science Note that in ESOs calibration plan the NDIT may be different to the science observations As noted above darks may also be used as input to reduce flatfield frames 8 2 1 Reduction of darks within gasgano Figures 27 and 28 show how gasgano is used to create the master dark image and the resulting output image Check that it has similar counts but reduced noise to the individual dark frames The quality control parameters are listed in the reduced image and have names like QC e g QC RONI QC DARKMED etc CRIRES data reduction cookbook VLT MAN ESO 14200 4032 File Help Current Queued if Executin Parameters Name crire crires spec dark nsamples crire crires spec dark hsize Default Filename CRIRE 2010 10 19T15 16 07 776 fits CRIRE 2010 10 19T15 16 35 681 fits CRIRE 2010 10 19T15 17 03 820 fits Classification Locate Locate Locate Request Pool Execute Selected Filename Classification crires_spec_dark_0000 fits CALPRO DARK Log Messages 19 03 29 INFO Collapse images for chip number 4 19 03 29 INFO Division by DIT 19 03 29 INFO Save the product 19 03 29 INFO
117. s home2 jsmoker snip Reduced SpecJit 1087p4 PipeDefaults STD WL MAP IMA fits mv home2 jsmoker snip Reduced out_0005 fits home2 jsmoker snip Reduced SpecJit 1087p4 PipeDefaults STD EXTRACT SENS TAB fits 8 7 3 Inspection of pipeline results produced by crires spec jitter The results for such an extraction are shown in Fig 45 with the same reduction without any calibration applied also being displayed Note that these spectra are the combination of the two nodding positions Figure 46 shows results of optimal and rectangular extraction Finally Fig 47 shows the results of the extraction using crires spec jitter comb used NODA NODB or COMP Note that this figure and the wavelength calibration was created using version 2 1 3 of the pipeline that did not apply the different wavelength solutions at different Y positions on the detectors Versions 2 3 1 and above take this correction into account CRIRES data reduction cookbook VLT MAN ESO 14200 4032 83 crires spec jitter v20103 File Help Current Queued Executing Parameters Name Default crire crires_spec_jitter display crire crires_spec_jitter hor_size crire crires spec jitter spec hsize crire crires spec jitter closing hs crire crires spec jitter wl samples crire crires spec jitter wl starty crire crires spec jitter wl stopy crire crires spec jitter degree crire crires spec jitter kappa crire crires spec jitter clean rate
118. s Z Queued gt 22 44 32 Downloading Retry failed Pause all Speed 119 9KB s Completed O of 88 files failed O 1 2MB of 300 5MB Conc Downloads 1 5 fa E Applet started a Figure 16 Final download to the users computer using the java applet The shell script highlighted in Fig 15 can also be used CRIRES data reduction cookbook VLT MAN ESO 14200 4032 26 5 Reducing the science data The most basic way of taking IR spectra is to observe the target along two slit positions i e nodding along the slit The sky is then removed by a process which is sometimes called double sky subtraction The basic steps of how to reduce these type of data are 1 First subtraction Ghost and Glow Removal 2 Flat fielding 3 Wavelength calibration 4 Combining 2d spectra 5 Extraction 6 Telluric line correction 7 Flux calibration 5 1 First subtraction There are two techniques observers use in taking IR spectra i the classic sequence where one observes the object at two slit positions i e ABBA AutoNodOnSlit template and ii the more complex case where one has observed the target along several slit positions i e GenericOffset template In case i one simply subtracts frames taken at different slit positions So one needs to form A B B A couples and then combine them together This simple step removes the dark and results in an image with 3 spectra one positive and 2 negative Moreover as mentioned in section 3 4 also the glo
119. sages 23 13 18 INFO Calibrate chip number 3 23 13 18 INFO Wavelength range 1084 7 1089 91 23 13 18 INFO Correct the bad pixels 23 13 18 INFO Correct for the dark 23 13 18 INFO Correct for the flat field 23 13 18 INFO Wavelength error 60 pix 0 305572 nm 23 13 18 INFO Sub Catalog extraction 23 13 18 INFO Find the best linear solution 23 13 18 INFO Wl error 0 305572 nm 60 pix 23 13 18 INFO 1 Nb of samples 100 23 13 18 INFO J Nb of candidates 10000 23 13 19 INFO Cross Correlation factor 0 135488 23 13 19 INFO Find the best degree 2 polynomial 23 13 19 INFO Wl error 0 0611144 nm 12 pix 23 13 19 INFO Nb of samples 10 23 13 19 INFO J Nb of candidates 1000 23 13 20 INFO Cross Correlation factor 0 14317 23 13 20 INFO Refine the degree 2 polynomial 23 13 20 INFO Wl error 0 0122229 nm 2 4 pix 23 13 20 INFO Nb of samples 10 23 13 20 INFO J Nb of candidates 1000 23 13 20 INFO Cross Correlation factor 0 147038 CRIRES data reduction cookbook VLT MAN ESO 14200 4032 66 Area of image to be examined Image Statistics Image X 513 6 Image Y 2224 S a j Equinox Peak above bg 202 6 Background level 1 3 FWHMXY 20 22 Angle of X axis 42 5 Pixels in x y 20 0 Area of image to be examined Image Statistics
120. sitions in chip 3 and chip 4 are too different 189 gt 328 lt snip gt INFO crires_spec_jitter tid 000 Save the product INFO crires_spec_jitter tid 000 Writing FITS propertylist product OBS_COMBINED_IMA crires_spec_jitter_comb fits INFO crires spec jitter tid 000 Writing FITS propertylist product OBS_CONTRIBUTION_IMA crires_spec_jitter_contrib fits INFO crires spec jitter tid 000 Writing FITS propertylist product OBS_PROFILE_IMA crires_spec_jitter_prof fits INFO crires spec jitter tid 000 Writing FITS propertylist product OBS BGD MAP IMA crires spec jitter bgmap fits INFO crires spec jitter tid 000 Writing FITS propertylist product OBS WL MAP IMA crires spec jitter wlmap fits INFO crires spec jitter tid 000 Writing FITS table product OBS EXTRACT WL TAB crires spec jitter extracted fits INFO esorex tid 000 Created product diska home jsmoker CRIRES Projects NoNod out_0000 fits INFO esorex tid 000 Created product diska home jsmoker CRIRES Projects NoNod out_0001 fits INFO esorex tid 000 Created product diska home jsmoker CRIRES Projects NoNod out_0002 fits INFO esorex tid 000 Created product diska home jsmoker CRIRES Projects NoNod out_0003 fits INFO esorex tid 000 Created product diska home jsmoker CRIRES Projects NoNod out_0004 fits INFO esorex tid 000 Created product diska home jsmoker CRIRES Projects NoNod out_0005 fi
121. t SLIT HIERARCH ESO INS GRIS1 NAME gt GRISM HIERARCH ESO INS GRAT NAME gt GRAT HIERARCH ESO INS GRAT1 NAME gt GRAT1 HIERARCH ESO INS GRAT2 NAME gt GRAT2 HIERARCH ESO INS GRAT WLEN gt WLEN HIERARCH ESO INS GRAT1 WLEN gt WLEN1 HIERARCH ESO INS GRAT2 WLEN gt WLEN2 HIERARCH ESO INS GRAT ORDER gt 0RDER One can also use the following idl code provided by Alain Smette asmette 2010 03 21 v1 0 function get_hierarch h keyword keyname HIERARCH ESO Strput keyname keyword 13 CRIRES data reduction cookbook VLT MAN ESO 14200 4032 94 keyname strtrim keyname res strpos h keyname pos where res eq 0 if pos 0 eq 1 then begin return 1 endif line h pos pos strpos line if pos 0 gt 0 then begin pos strpos line 32 value strmid line 32 pos 0 32 endif else begin pos strpos line poseq strpos line 1 value float strmid line 0 poseq 0 pos 0 poseq 0 endelse return value 0 end e RA DEC Please note that the RA and DEC keywords are recorded in degrees To translate these keywords so that they can be used by IRAF you have to use the asthedit task in the noao astutil package The help file for this task gives an example of how to translate the ESO format to the IRAF format 10 4 Correcting for non linearity The non linearity correction for CRIRES has its limitations in great part due to the detector itself Figure 4
122. t coll meth sig crire crires spec flat replace icrire crires sner flat clean flat Filename Classification CRIRE 2011 01 15T12 33 25 959 fits Locate Displa CRIRE 2011 01 15T12 34 45 559 fits Locate Display CRIRE 2011 01 15T12 36 09 493 fits Locate Display crires_spec_dark_0001 fits Locate Display M CRIRES 2010 09 2 1T17 04 57 320 fits Locate Display M CRIRES 2010 09 2 1T17 05 07 420 fits Locate M CRIRES 2010 09 2 1T17 05 13 214 fits ate Display pProduct Naming Product Root home2 jsmoker Instruments CRIRES Pipeline Data Reduced Browse Naming Schem IL Execute Selected o Execute ar p Output Frames Clear Filename Classification crires spec flat setO1 0001 fits CALPRO_FLAT crires_spec_flat_setO1_bpm_0001L fits CALPRO_BPM k rLog Messages Save Clear a Compute the MASTER FLAT for chip nb 4 i 4 20 Correct for the dark 01 20 19 INFO Normalise with the median 01 20 19 INFO Save the products 01 20 19 INFO Writing FITS propertMist product CALPRO FLAT crires spec flat setO1 fits 01 20 19 INFO Writing FITS propertyist product CALPRO BPM crires spec flat setO01 bpm fits Product frames
123. t if there is a problem with the classification or you want to fool the system you can edit this field e Product naming By default the products are placed in your home directory It is advis able to change this to somewhere else in this case home2 jsmoker Instruments CRIRES Pipeline Data Reduced to prevent large number of files being present in your home area Note that the Naming Scheme can be set to Numeric or Overwrite In the first case whenever you run a reduction it will be named sequentially which can be useful when comparing reductions done with different parameters Alternatively with Overwrite only the latest reduction will be saved e Output frames e Log Messages These are also saved in ASCII files in the products directory with names such as crires spec jitter 2011 09 29 10 41 55 1og OK now it is time to run the first reduction Hit the Execute button and look at Fig 20 for the output It failed Why Well if we look in the error log we see the following message lt snip gt ERROR 11 57 39 ERROR Only one offset in the list abort ERROR 11 57 39 ERROR Cannot classify the data CRIRES data reduction cookbook VLT MAN ESO 14200 4032 37 ERROR 11 57 39 ERROR 1 1 Illegal input 14 at crires_spec_jitter crires_spec_jitter c 510 Completion status FAILURE Execution error Execution failed with code 14 So the recipe had problems because we only gave it one nodding position
124. traction For the classical ABBA technique one should extract the spectrum without fitting the sky Fitting the sky only adds noise For more complex cases a low order fit to the sky may be required As for all the steps listed above the extraction procedure can be done with several differ ent tools such as IRAF MIDAS or of course by using the CRIRES pipeline In the latter case running the recipe crires_spec_jitter will allow simultaneously to correct the science data for non linear effects flat fielding wavelength calibration and finally extract the spec trum An alternative is the use of the recipe crires_util_extract Note that in v2 3 of the pipeline the starty and stopy parameters have been replaced by y pos c1 2 3 4 and y_width options For example in place of start_y 100 start_y 200 one would use recipe parameters y pos cN 150 and y_width 100 In case one is dealing with science frames showing more than one spectrum e g because there are more than one source on the slit the CRIRES pipeline by default will ex tract only the brightest spectrum Therefore to extract the fainter one you should run the crires spec jitter recipe with suitable values of starty and stopy which define the region in pixel where the spectrum is If one is using IRAF the extraction of the spectra can be done with the task apall under the twodspec apextract environment 5 6 Removing telluric lines This is a critical step th
125. ts INFO esorex tid 000 6 products created jsmoker pc015042 NoNod The reduced spectra for this uncalibrated detector 3 only extraction are shown in Fig 25 7 4 Plotting the reduced spectra We see that the reduced products are now visible in gasgano in RED Fig 22 with names crires spec jitter fits To display them we select as input STD EXTRACT WL TAB and send them to the recipe crires_util_plot By default 8 plots will be produced In order to remove unwanted plots from the screen hit q Figure 26 shows the last window plotted which shows the final extracted spectrum obtained using optimal extraction CRIRES data reduction cookbook VLT MAN ESO 14200 4032 45 Figure 24 Raw detector 2 and 3 only images of a gas cell 46 VLT MAN ESO 14200 4032 CRIRES data reduction cookbook S5 h pztBoTh TI b 0 o QrTt b TIT P BoIP 9 EFE E RE ae i ANA cg 340jdnug S dou 6 lt p gt jojdnus Taada pa3993x3 y 3ojdnuoS OM SAAR lt gt jojdnug A X Mo 0 lt S gt jo dnus y li n 0 lt g gt 3ojdnus 3 X i9 mo Figure 25 Reduced OPTimal and RECTangular extraction of all four detectors for the gas cell data shown in Fig 24 CRIRES data reduction cookbook VLT MAN ESO 14200 4032 AT r l g File Help 1200 Extracted Spectrum OPT Current I Queued Executing Parameters Name Value crire crires util plot display crire crires util p
126. w and ghost defects are canceled out In case ti one could build a sky frame from several spectra as one does when building the sky frame in imaging This results in an image with only one positive spectrum In this case you will might not be able to correct for ghost and glow since the obtained sky would result from the median of your spectra so it will not contain the same glow and ghost features as your science frames 5 2 Flat fielding For each wavelength setting three lamp flat images are taken The CRIRES pipeline recipe crires spec flat provides a master flat obtained as follows e normalise each single flat to the median value of its central part not affected by vi gnetting In case the vignetting region is actually different from the one expected one can change the value of the starty and stopy parameter to opportunely set the zone where to compute the median used to normalise the single flat lamps e divide each frame by a 2nd degree polynomial whose coefficients are part of the static calibration files specifically obtained to correct for non linearity effects and available at http www eso org observing dfo quality CRIRES pipeline pipe_calib html CRIRES data reduction cookbook VLT MAN ESO 14200 4032 27 e average the resulting three flats The recipe does not remove the wavelength dependence of the lamp from the flat field This is removed when the telluric standard is divided into the spectrum of the science target
127. w eso org sci facilities paranal instruments crires doc 1 3 Abbreviations and acronyms The following abbreviations and acronyms are used in this document DCS Detector Control System DIT Detector Integration Time DPR Data Products FITS identifier SciOps 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 Right Ascension UT Unit Telescope VLT Very Large Telescope CRIRES data reduction cookbook VLT MAN ESO 14200 4032 2 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 1 5 Topics not covered by the cookbook The following topics are either not covered or incompletely covered by the current version of the cookbook e Reduction of generic offset observations A full explanation of 2D wavelength calibration From version 2 3 1 of the pipeline the ThAr pinhole data are now properly supported The wavelength calibration is applied at the different Y positions Some figures containing gasgano screenshots
128. with columns for the wavelength and extracted optimal extraction The directory dir home jsmoker CRIRES Projects Linearity ReducedData should be changed in most cases The input file Reduced wl map filelist ascii contains lines that look like the following OBS EXTRACT WL TAB WithAllCals OO1s A fits OBS EXTRACT WL TAB WithAllCals O01s A ch ascii OBS EXTRACT WL TAB WithAllCals OO1s A ch2 ascii OBS EXTRACT WL TAB WithAllCals O01s A ch3 asci OBS EXTRACT WL TAB WithAllCals O01s A ch4 ascii all one line CRIRES data reduction cookbook VLT MAN ESO 14200 4032 98 OBS EXTRACT WL TAB WithAllCals 0028 A ch ascii OBS_EXTRACT_WL_TAB_WithA11Cals_002s_A_ch2 asci OBS EXTRACT WL TAB WithAllCals 0028 A ch3 ascii OBS EXTRACT WL TAB WithAllCals 002s A ch4 asci all on one line To see the structure of the file with column names do the following help chi structure read in input and output files from a list the following directory should be changed dir home jsmoker CRIRES Projects Linearity ReducedData fname Reduced_wl_map_filelist ascii readcol dir fname datafileIN datafileOUT 1 datafileOUT 2 datafileOUT_3 datafileOUT_4 format A A A A A A comment silent i 0 repeat begin j 2 print Reading in CH1 data datafileIN i openw lun datafileOUT 1 i get lun datafileTEMP datafileIN i header headfits datafileTEMP chi mrdfits datafileTEMP 1
129. wn features 10 2 Problems in tracing If the Signal to Noise ratio is low or if the spectrum just contains emission lines with no continuum the extraction of the spectra will likely fail 10 3 IRAF issues Raw CRIRES slit viewer images and spectra can be displayed and analysed using iraf and ds9 for example the first four iraf commands will estimate the statistics of the four detectors for a dark frame with the fifth and sixth used to display and show the fits header of a CRIRES slit viewer image cl imstat CRIRES SPEC DARK108 0077 fits 1 IMAGE NPIX MEAN STDDEV MIN MAX CRIRES_SPEC_DARK108_0077 fits 1 524288 1 711 34 88 575 2 7111 cl imstat CRIRES SPEC DARK108 0077 fits 2 IMAGE NPIX MEAN STDDEV MIN MAX CRIRES data reduction cookbook VLT MAN ESO 14200 4032 92 CRIRES_SPEC_DARK108_0077 fits 2 524288 0 6321 62 17 416 4 8514 cl imstat CRIRES_SPEC_DARK108_0077 fits 3 IMAGE NPIX MEAN STDDEV MIN MAX CRIRES_SPEC_DARK108_0077 fits 3 524288 0 5176 29 52 376 3 6682 cl imstat CRIRES SPEC DARK108 0077 its 4 IMAGE NPIX MEAN STDDEV MIN MAX CRIRES_SPEC_DARK108_0077 fits 4 524288 3 9 182 1948 16182 cl gt display Crires_sv_ngc6253_068_0001 fits 1 fi z1 45 z2 1833 705 cl gt imhead Crires_sv_ngc6253_068_0001 fits lo Crires_sv_ngc6253_068_0001 fits 1024 1024 real TEST No bad pixels min 0 max 0 old Line storage mode physdim 1024 1024 length of user area 21668 s u Created Thu 06 4

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