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AKARI IRC Data User Manual

1. redbox greenbox bluebox irc tool 5 13 Working on the output Users will receive both the original raw data and processed data up to but not including the co add stage for the toolkit The data is is basic processed with the default parameters of the 74 IRC Data User Manual toolkit and users are advised to re process using the latest version of the IRC toolkit Note the co add products are not initially distributed since the co add often fails especially for the MIR L images Users may therefore use the additional coaddLusingS toolkit feature or other independent methods 5 14 Limitations of the functionalities in the current version of the imaging toolkit 5 14 1 Instrumental characteristics and artefacts in the data First frame effect The first frame of the dark current prior to the pointing observation shows larger values than others particularly for MIR S and MIR L detectors This effect could be related to the detector temperature Increase of hot pixels As shown in Figure 4 1 1 the number of hot pixels is increasing along the mission They should be corrected when coadding individual images or correcting the image by its own dark image Memory effects No noticeable effects have been reported Dark Level The dark level is not stable during the pointing observations The NIR dark level shows no corre
2. 103 6 8 Error messages when running the pipeline and Troubleshooting 106 Chapter 1 Introduction 1 1 Purpose of this document This document is intended to provide a comprehensive guide to data from the Infrared Camera IRC onboard AKARI for observers to get started quickly It includes a brief summary of the instrumentation a summary of the data products and the pipeline software overview together with the calibration of the instrument Part of the data and information given here will be updated as the data reduction and calibration will get improved The latest information may be posted on the web till the revised version will be prepared A comprehensive overview of the instrumentation and operation is described in the ASTRO F Observers Manual and will be given in the AKARI first result volume 2 IRC Data User Manual 1 2 Relevant information AKARI Observer s Web The ISAS Web page contains the most up to date information URL Attp wwuw ir isas jaxa jp A K A RI Observation The ESAC page also includes up to date information URL Attp akari esac esa int observers Helpdesk Any questions and comments on AKARI observations and user support are addressed to the AKARI Helpdesks iris help ir isas jaxa jp http akari esac esa int esupport Version 1 4 May 30 2008 Chapter 2 Instrument overview The Infrared Camera IRC onboard AKARI was originally designed to make wide field deep imaging and low re
3. 2 The whole area is used e det sig real min 1 0 max 1000 0 default 4 0 Source detection threshold in sigmas e sig rej real min 0 0 max 100 0 default 3 0 Rejection unit in sigmas e max itr int min 1 max 10 default 10 Maximum number of iterations in statistical process e obslog string default irclog NEVER CHANGE THIS Output filename of redbox mkirclog e cosmicr boolean yes or no default no Detect and replace cosmic rays in MIR images Cosmic ray events in each image are detected and replaced by the average of the four nearest neighbors Type help cosmicrays inside IRAF s shell for details e wcs boolean yes or no default no Try to match the 2MASS sources to calculate wcs To use this function you should have internet connection to automatically download 2mass catalog from the internet This process will not be executed as default Note although the toolkit was checked on Solaris machines also Solaris does not have curl in the original applications You need to install it to run WCS e selfdar boolean yes or no default no Use an alternative dark to the super dark provided e coaddsh boolean yes or no default no Coadd short exposure frames as well as long ones e interac boolean yes or no default no option to run pipeline interactively With this option selected the pipeline can be run step by step e g as Greenbox anomalous pix Greenbox dark etc or alternatively b
4. After the flat fielding process a f will be added such that ms1CcnDwaF23342 8004 fits becomes fms1lCcnDwaF23342_S004 fits Aspect ratio resampling greenbox aspect_ratio This is a distortion correction The module the corrects aspect ratios of pixels to be square i e Aspect ratio is corrected to 1 to 1 by resampling the image Thus the toolkit corrects the linear distortion only Non linear distortion is not corrected for at present since it is assumed to be negligible After the resampling a e will be added such that fmslCcnDwaF23342 8004 fits be comes efmslCcnDwaF23342 5004 fits prefix before the original filename i e F23342_S004 fits gt gt gt efmslCcnDwaF 23342 S004 fits The resulting data is the basic processed data with individual frames not pointings corrected for detector and instrumental effects 68 IRC Data User Manual 5 10 The pipeline processor Blue Box bluebox coadd wrap per Module 5 10 1 The Blue Box Co Add Wrapper It has not yet been decided whether an additional post pipeline processing module will be released to the users The pre requisite for the IRC data reduction team is at present solely to deliver basic science grade processed data to the users It is not the responsibility of the team to provide modules to produce mosaiced images or to provide tools for photometry etc The output of the green box produces the basic processed data for individual frames Ad ditional processing i
5. IRC Data User Manual IRC SPECTROSCOPY LIMITTING FLUX LEVEL 3 4 5 6 7 8 9 10 12 14 16 18 20 222426 Wavelength um Figure 2 3 7 IRC spectroscopy sensitivity as a function of A Version 1 4 May 30 2008 System Throughput 13 IRC SPECTROSCOPY SYSTEM THROUGHPUT 0 5 NP NG x SGI eX SG2 x LG2 x x 0 1 x E ft o i i x x x 0 05 r x H x 4 x i x x b o3 MEE X x x ME x Took x ANN i x x x aME T i x i T x x 4 0 01 ih l I l boop o l L dq o1 p d 2 3 4 5 6 7 8 9 10 12 14 16 18 20222426 Wavelength um Figure 2 3 8 IRC spectroscopy throughput as a function of A Chapter 3 Distributed Data Products Two levels of data products are delivered to the users raw data and processed data The raw data are intended to be used to run the pipelines described in Chapters 5 and 6 to get interactively the best science out of them The quick look data are merely a rough approximation of what the user will get from his observations They are the result of running the pipeline automatically and with a default setting An interactive and fine tuned run of the pipeline is recommended in order to improve the quality of the results The quick look data header contain the version of the pipeline used Since it is continously evolving it could be different from the version made available to the users 3 1 IRC FITS file naming rule
6. e Pair Files The pair files collect together and list all long and short frames that point the same area of sky Taking the N3 band as an example the following files may be seen pair0001N3 list pair0001 N3 list short pair0001 N3 list long pair0001 N3 list long shift pair0001 N3 list long shift O The pair0001 N3 1ist file lists all long and short frames that point at the same area of sky The contents of the file are the original frame names e g F23343_N001 IRC channel and the coordinates The files pair0001 N3 list short amp pair0001 N3 list long are extracted and segregated from F23343 N001 on the basis of the exposure time long or short exposure frames The file pair0001 N3 1ist long shift lists the result of the coordinate matching before coadding Each line entry in the file consists of a filename x shift pix y shift pix rotation deg and the number of stars used for the shift amp rotation angle calculation For example 72 IRC Data User Manual fdmslnDwaF01001_N003 fits coo 1 0 0 0 0 0 0 0 fdmslnDwaF01007_N003 fits coo 1 19 25942609 0 00474931 359 99288567 126 The values are calcualted relative to the first frame listed in the file such that the first entry is always filename 0 0 0 0 0 0 O There may also be an additional pair file pair0001 N3 1ist long shift O which is almost the same as the pair0001_N3 list_long shift but it also contains detector information as filename detectorID x shift pix y sh
7. task irc pkg irc irc cl DO NOT FORGET THE BEFORE THE IRC PKG DO NOT FORGET THE LAST SLASH the toolkit is now installed and is ready to be run 5 5 How to UPGRADE the version of IRC imaging toolkit Upgrades to the IRC imaging toolkit is a progressive and ongoing process and new versions of the toolkit will be available to users throughout the course of the mission On receiving a new version of toolkit package e g ircY YMMDD tgz the following commands are required to be input e mv ircYYMMDD tgz where you installed previous version e cd where you installed previous version e tar xvzf ircYYMMDD tgz These commands will OVERWRITE any old files directories Then follow the original proce dure described in 5 4 5 and 5 4 7 Finally please type following commands when you use a new version of the toolkit for the first time e launch IRAF e load the ircpackage by typing irc e type unlearn_all e load the irc_tool package by typing irc_tool e type unlearn coaddLusingS 5 6 Setting up your toolkit environment and running the pipeline The steps to reduce the raw data are outlined below 5 6 1 Creating the directory structure The toolkit assumes the following directory structure see Fig 5 6 1 anyname rawdata must be this name anyname your working directory e g data rawdata data working The toolkit should be run in the working directory Thus you ma
8. 99 825 110 E 50 445 120 339 050 29 088 130 120 115 18 531 140 51 864 12 748 150 i 26 407 9 316 160 15 397 7 143 170 B 10 012 5 694 180 i 1 092 4 686 190 5 367 3 959 200 549 483 4 275 3 418 210 264 183 3 041 3 006 220 136 893 3 025 2 685 230 75 855 2 647 2 430 240 44 673 2 361 2 224 250 27 825 2 140 2 055 300 5 291 1 528 1 541 300 2 329 1 268 1 293 400 1 566 1 135 1 154 450 1 270 1 061 1 068 500 1 125 1 017 1 012 600 0 996 0 976 0 946 700 0 949 0 963 0 910 800 0 935 0 962 0 889 900 0 936 0 968 0 876 1000 0 945 0 975 0 868 1500 1 019 1 016 0 855 2000 1 084 1 047 0 855 2500 1 132 1 068 0 857 3000 1 166 1 084 0 860 3500 1 192 1 095 0 862 4000 1 212 1 103 0 864 4500 1 227 1 110 0 866 5000 1 239 1 115 0 867 6000 1 258 1 123 0 869 7000 1 271 1 129 0 871 8000 1 281 1 133 0 873 9000 1 288 1 137 0 874 10000 1 294 1 139 0 874 20000 1 320 1 151 0 879 30000 1 329 1 155 0 880 40000 1 333 1 157 0 881 50000 1 335 1 158 0 881 60000 1 337 1 159 0 881 Values are calculated for Ay 2 4um Ao 3 2m Aa 4 1m Version 1 4 May 30 2008 39 Table 4 8 11 Color Correction factors for MIR channel Black Body a 0 Intrinsic MIR 5 57 MIR S S9W MIR S SI1 MIR L L15 MIR L L20W MIR L L24 Temperature K K 7 0um K 9 0um K 11 0um K 15 0um K 18 0um K 24 0um 40 lt 204 598 14 514 14 825 0 942 50 373 308 21 615 5 989 5 661 0 882 60 31 533 6 632 3 516 3 178 0 870 70 9 722 3 371 2 492 2 198 0 875
9. IRCO3 Observation AOT AOTPARAM 8 0 5 70 AOT Parameter INSTMODE TBD Instrument operation mode TIMESYS UTC Explicit time scale specification 16 DATE OBS DATE END DATE REF AFTM OBS AFTM END AFTM REF PIMTIOBS PIMTIEND PIMTIREF EQUINOX RA DEC ROLL AA SOL AA EAR AA LUN TM SAA SAT POSX SAT POSY SAT POSZ DAYNIGHT STTA NUM STTB NUM STTA MOD STTB MOD COMMENT HISTORY END YYYY MM DDTHH MM SS YYYY MM DDTHH MM SS YYYY MM DDTHH MM SS double double double UxXXXXX UxXXXXX UxXXXXX 2000 0000 320 5533 23 3325 30 553 90 0021 180 2083 210 6821 1829 2903 5528 1704 3092 1968 4286 DAY 4 4 TREK TREK The header keywords are sorted as follows e FITS basic information data size information SIMPLE refers to the standard FITS format TOC IRC Data User Manual Observation start date time Observation end date time Reference time in the Observation DATE OBS in ASTRO F Time DATE END in ASTRO F Time DATE REF in ASTRO F Time DATE OBS in PIM TI 36 bits DHUTI DATE END in PIM TI 36 bits DHUTI DATE REF in PIM TI 36 bits DHUTI Epoch of Coordinate degree Target position at DATE REF degree Target position at DATE REF degree Roll Angle at DATE REF degree Solar avoidance Angle at DATE REF degree Earth avoidance Angle at DATE REF degree Lunar avoidance Angle at DATE REF sec Duration since last SAA at DATE REF km Satellite position a
10. To display these images manually issue show_aperture_on_ds9 lt image gt source_table imag where image could be refimage_ff 1 or specimage_bg etc on the IDL command line When imag option is set the image is shown on the right side of the ds9 with region marks for reference image The default no option is for spectroscopy image See appendix for more on array name conventions 6 5 2 Displaying the extracted images on ATV ATV is a general purpose interactive array image displaying tool The array should be in 2D See ATV web page http www physics uci edu barth atv for more information on the program Command line syntax atv array block Here are some ATV tips e To display whole images issue atv lt array gt 1 1 means long exposure frame and 0 for short Here lt array gt should be something like refimage_bg or specimage_bg Items in parentheses are optional 3In some systems block option may be required for interactive operation on the ATV The conditions for which block requirement seems to depend on local Linux or X11 system settings The author does not have any good ideas on the correct usage of this option 98 IRC Data User Manual e To display extracted images of your desired source id use atv lt array gt source_id Here lt array gt should be something like specimage_n_bg To check mask area use atv lt array gt source_id mask source_id e When co
11. low order polynomial surface fitting is performed for each sub frame and is subtracted off from the flat fielded images For SG2 and LG2 background suffers from straylight from the Earth shine contamination and the flat fielded images are much more structured To make good sky subtraction a median running box filter is applied to estimate the local sky and is subtracted off from the stray light covered background Such background should be removed from indi vidual sub frames since the contribution of the Earthshine depends on the telescope pointing angle from the earth direction and the amount of straylight changes within a single pointing maneuver or within a single AOT operation In the first pass of the processing within the pipeline source masking will not be applied in determining the background because no source position information is available at the stage In the second pass after processing through section 6 1 9 once the background is measured again while considering the source masks The image obtained after background subtraction has the following expression obs obj X x Fo z y A x R A Fi 2 y x spectral_feature x y 6 1 3 6 1 5 Image screening Some sub frames may be severely damaged by cosmic ray shower a satellite passing in front of the telescope etc If this is the case one can interactively set the flag by using ds9 for any sub frames to be discarded in the following processes 6 1 6 Image reg
12. source positions with local Gaussian fitting around the user specified source locations when the toolkit is run with user specified source table use_short_refimage a flag to use short reference image rather than long reference image for source detection This is good for bright saturated sources no slit flat a flag to disable flat field correction for slit spectroscopy data for Np spec Ns spec Nh spec Lc spec Use of this switch is recommended for slit spectroscopy with the current version of the toolkit calibration database nir columnpulldown correction a switch to enable correction for column pull down effect for Np spectra savefile an ascii variable that store the file name of the IDL save file that records the irc specred output e Displaying whole image products Usage Show aperture on ds9 specimage bg source table or show aperture on ds9 refimage bg source table imag options nsum width of source extraction apertures in units of pixel corresponding to the width of red rectangles shown on ds9 Version 1 4 May 30 2008 105 space_shift number of pixels by which to shift the source extraction apertures along spatial direction imag a flag to display reference images Without this flag the procedure assumes that the data to be displayed are spectroscopy images e Plot spectra Usage plot spec with image wave array specimage n wc mask specimage n source_table lt sour
13. 0 980 1 315 1 340 0 937 1 094 1 379 1500 0 999 1 404 1 394 0 948 1 120 1 439 2000 1 009 1 450 1 421 0 953 1 135 1 483 2500 1 015 1 478 1 436 0 957 1 144 1 514 3000 1 019 1 496 1 447 0 959 1 151 1 538 3500 1 022 1 509 1 454 0 961 1 155 1 557 4000 1 025 1 519 1 460 0 963 1 159 1 571 4500 1 026 1 526 1 464 0 964 1 162 1 583 5000 1 028 1 532 1 468 0 964 1 164 1 593 6000 1 030 1 541 1 473 0 966 1 167 1 608 7000 1 031 1 548 1 476 0 967 1 170 1 620 8000 1 032 1 552 1 479 0 967 1 172 1 628 9000 1 033 1 556 1 481 0 968 1 173 1 635 10000 1 034 1 559 1 483 0 968 1 174 1 641 20000 1 037 1 572 1 490 0 970 1 180 1 667 30000 1 038 1 576 1 493 0 971 1 182 1 676 40000 1 038 1 578 1 494 0 971 1 183 1 681 50000 1 039 1 580 1 495 0 971 1 183 1 683 60000 1 039 1 581 1 495 0 972 1 183 1 685 Values are calculated for A4 7 0um As 9 0um Ag 11 0um Ay 15 0um Ag 18 0um Ag 24 0um 42 IRC Data User Manual 4 9 Distortion Because of geometric distortion in the IRC images the original detector pixel solid angle varies over the field of view We observed globular clusters and Galactic center with the IRC where many stars are expected to be detected Then we matched their 2M ASS corrdinates with the detector xy coordinates by fitting polynomials In the fitting we fixed the pixel field of view to be 1 46 2 38 and 2 40 arcsec pix for the NIR MIR S and MIR L respectively The deviation from an ideal grid square are up to 2 0 6 and 16 pixels at the
14. 4 May 30 2008 f diio e ta geo a 5Omm 3 KE a J S folding mirror unit NIR is P d el MIR S Vb detector unit 7 MIR S Figure 2 0 1 Bird s eye view of the IRC camera used with this aperture The rightmost outer part Nh has a 3 arcsec width and is used for the highest resolution spectroscopy of diffuse radiation with the NG grism e The MIR S has a slit of 5 arcsec width for diffuse light As this slit overlaps with the innermost slit of the NIR camera it is also referred to as Ns We assume that the point source density in the mid infrared range is low enough to avoid serious confusion such that spectroscopy of point sources can be made in the imaging field e The MIR L has a 7 arcsec slit for diffuse light similar to that of the MIR S camera This position is referred to as Ls 6 IRC Data User Manual Slit MIR L 7 x0 4 Scan Direction i Telescope Axis pmm 25 0 9 3 0 7 for N2 9 5 0 5 for N3 amp N4 9 1 for MIR S all bands Figure 2 0 2 Field of view location of the three channels of the IRC The vertical arrow indicates the scan direction in t
15. 91 e ext source table An ascii list describing source position X Y in pixel or the target table Example myobjects tbl cat myobjects tbl 100 0 100 0 200 5 200 5 150 0 150 5 This will extract spectra of sources located at 100 0 100 0 200 5 200 5 and 300 0 300 5 in pixel on the reference image If ext source table is set to for automatic source detection null string then the pipeline activates its sub program There are some important tips in preparing the source table Coordinates counts from 1 not 0 i e coordinates of the lower left corner of the image is 1 1 not 0 0 For NIR the toolkit interprets by default the pixel coordinates as measured in the raw image before the image rotation When one measures the source positions in the processed images after the image rotation set the rotated NIR source table option at the pipeline command line For MIR L one can use Y range of either 257 512 for images before detaching MIR S L or 1 256 for images after detaching MIR S L to set Y position of the targets The pipeline subtracts 256 from the Y input if Y 256 e refimage list An ascii file listing FITS file names of reference image Example N3 1st cat N3 1st F000001 N fits A default list is provided with the data distribution and is found in rawdata directory e specimage list an ascii file listing FITS file names of spectroscopy images Example NP 1st
16. Ag and A are effective wavelength for broad band filters Therefore the color term in equation 6 1 3 is expressed as F z y 42 F z y Fy z y eem OA Fea a Therefore the color term correction is calculated by two broad band super flats and one spec troscopy super flat Note that the product PFj x y x spectral feature r y always appears together i e we do not have to separate spectral_feature term from the super flat After the color term correction the image is as follows obs obj X x R X 6 1 6 For the NG spectra with the point source aperture Np flat fielding will be made in a similar way to the slit spectroscopy of diffuse sources since the aperture size is much smaller than the size of dispersed spectroscopy images For spectroscopy with NG at Np and other slit spectroscopy data calibration the super flat is normalized to be unity at each wavelength or Y pixel and there are no spectral features in the flats On the other hand NG spectra at Nc will be reduced in the same way as for other slit less spectroscopy 6 1 13 local Background subtraction from extracted 2D spectra Although the background has been subtracted and it should be close to zero at this stage any remaining background on the extracted 2D spectroscopy images is subtracted at this stage Here we consider source masks for better determination of the local background The background is measured and subtracted off assuming a constant v
17. F40813_L003 NGC104 256 L18W 5 293348 72 44307 IRCO3 3 5020012 F40813_L004 NGC104 256 L18W 5 293348 72 44307 IRCO3 4 5020012 F40813 8001 NGC104 256 87 5 293348 72 44307 IRCO3 1 5020012 1 F40813 8002 NGC104 256 87 5 293348 72 44307 IRCO3 2 5020012 1 F40813 8003 NGC104 256 87 5 293348 72 44307 IRCO3 3 5020012 1 F40813 8004 NGC104 256 87 5 293348 72 44307 IRCO3 4 5020012 1 PPP PR In this case using pair0002_S7 list_long for the reference the coaddLusingS function will make the L18W_long image e coaddLusingS function parameter list In a similar manner to the general pipeline the parameters for the coaddLusingS function may be set via the epar iraf command Please note that in some instances some of the parameters may not be set as desired On executing the function you will be asked to confirm the parameters and users should check at run time that indeed the parameters have the required values and edit them if neces sary In addition note that the option to subtract median filtered sky is not included in the parameter list i e cannot be set using epar but appears during the parameter 78 IRC Data User Manual confirmation at run time e coaddLusingS function coadd failure log Please note that running the the irc tool coaddLusingS function will overwrite any previous coadd failure file in the working di rectory i e if you have an coadd failure from MIR S NIR image processing then this log may
18. IRCDISTPAR LG2 dat e IRC_SPECRED_CALIBDIR APCOR contains the spectral aperture correction tables APCOR APCOR_NP dat APCOR APCOR NG dat APCOR APCOR SG1 dat APCOR APCOR SG2 dat APCOR APCOR LG2 dat 90 IRC Data User Manual 6 4 Running the pipeline 6 4 1 Data reduction order The pipeline has to be run more than once for NP AOT0a or NG AOTOb first then SG1 and SG2 and finally LG2 We need to start processing the shorter wavelength cameras NIR and MIR S where larger number of brighter sources are expected to be observed within the FOV as position reference sources The information derived there will be used for registering the longer wavelength cameras MIR S and MIR L e to measure relative X and Y shift among spectroscopy sub frames of NP NG for registering spectroscopy sub frames of NP NG SG1 SG2 LG2 e to measure relative X and Y shift among reference sub frames of S9W with larger number of brighter sources for registering imaging sub frames of S9W and L18W e to measure relative X and Y shift of the spectroscopy image with respect to the reference image of NP or NG for registering reference and spectroscopy images of NP NG SG1 SG2 LG2 Therefore the data reduction order should be as follows e First run run the pipeline for NP AOT04a or NG AOT04b without a target table for enabling automatic target detection sub program For NG data with point source aperture Np one needs to run the pipel
19. Np Ns Nh at near infrared where the natural background light is faintest the S N of the NG slit flat image is rather poor and this often limits the quality of the processed spectra There is an option to disable the slit flat correction no_slit_flat option of irc_specred We recommend processing the same data with default and without with the option flat correction for comparison If one finds little noticeable differences in spectral features except for quality of the spectra as we expect one may accept the spectra processed without flat correction as a final calibrated data See also section 6 4 3 6 6 2 Tackling narrow spikes seen in NIR spectra especially in slit spectra Even if one is interested in the slit area any anonymous bright stars that happened to be within the big aperture may cause the column pull down effect of the array damaging even the slit spectroscopy data To check this possibility examine not only the 1D extracted spectra but also the entire 2D images even outside of the slit area so as to locate damaged columns or raws since NIR images are rotated during the toolkit processing With the toolkit version 2 new option nir_column_pulldown_correction was introduced and the pulled down columns will be masked out See also section 6 4 3 102 IRC Data User Manual 6 6 3 Examining strange fake features in NP spectra especially around 2 4 3 5 um Sometimes an error in wavelength calibration leads to
20. Retrying automatic source detection with modified detection parameters If you use au tomatic source detection sub program within the pipeline you can retry source detection after tweaking the detection parameters You will see the reference image on the ds9 with detected sources marked and you are asked to answer if the detection is satisfactory or not If the answer is no then another dialog with several detection parameter entries pops up You can edit the parameters and press OK to re find the sources You can repeat this detection process as many times as you like until you get satisfactory source list The sub program uses daofind algorithm with the following parameters threshold Threshold intensity for a point source should generally be 3 or 4 sigma above background fwhm FWHM to be used in the convolve filter sharplim 2 element vector giving low and high cutoff for the sharpness statistic Default 0 2 1 0 Change this default only if the stars have significantly larger or smaller concentration than a Gaussian roundlim 2 element vector giving low and high cutoff for the roundness statistic Default 1 0 1 0 Change this default only if the stars are significantly elongated By default threshold is three times the measured background noise When too much or too less sources are found threshold change would give better results and it is not necessary to take care of sharpness roundness parameters in
21. Since the wavelength for a given pixel in the observed spectrum is slightly different from that in the response table simple interpolation will be performed to match the wavelength of the observed wavelength calibrated spectrum with that in the response table The spectral response function used in the pipeline was defined at the centre of the field of view and checked at the periphery of the field for consistency 6 1 16 Notes on slit spectroscopy The same pipeline can be used for both slit less and slit spectroscopy data reduction Although the reduction of the slit spectroscopy data can be made in a similar way as for the slit less spectroscopy data there are some differences in some processing steps between the two Here we summarize these differences e The slit spectroscopy flat fielding consists of a normalized feature less flat image Therefore no color term correction is necessary e Background subtraction is made on extracted 2D spectra in the case of point sources slit spectroscopy Np after stacking sub frames If dealing with slit spectroscopy for diffuse sources the background subtraction is not performed since entire slit is expected to be filled with the object that is diffuse and there is no pure background area in the image e Shift and add feature of sub frames will be disabled Therefore any spectral change along the slit could not be related to a real change in the spatial dimensions of the extended source in case of l
22. along wavelength direction can be applied for higher S N spectra shifting aperture positions along spatial direction X axis can be made aperture correction Command line syntax a command in a single line plot spec with image wave array specimage n wc mask specimage n source table source id and for short exposures plot spec with image wave array specimage n wc short mask specimage n source table source id short with the following options e nsum Number of pixels along X axis combined for plotting Default is 3 For slitless spectroscopy larger nsum wider aperture collects more photons from the object but this also collects more background noise Therefore the best nsum for highest S N is typically 2 or 3 for point sources corresponding typical full width of image PSF In the case of slit spectroscopy the range to plot the spectrum is NP NG up to the edge of the extracted region SG1 nsum lt 10 G2 nsum lt 8 LG2 nsum lt 8 If space_shift 0 see below then the range should be smaller in order to prevent from extracting the spectrum out of the slit area smooth Boxcar smoothing width in pixel along wavelength direction Default is smooth 0 no smoothing For spectra with higher S N without loosing spectral resolution smooth should be 3 corresponding typical full width of image PSF Larger boxcar smoothing win dow will loose the spectral resolution Note that when even number
23. by default bluebox coadd to form a co added image source extract Perform source extraction calcshift Calculate shift amp rotation between images adjust sky adjust sky level before stacking x irc stack stack individual frames to form a co added image The pipeline can be run automatically or interactively step by step 5 3 Expected Data Processing Rate minimum expectation e NIR 412 512 pixels 16 bit pixel 8 bit byte 412 Kbyte frame 1 NIR fits 412 Kbyte frame 2 frame fits 824 Kbyte fits file e MIR 256 512 pixels 16 bit pixel 8 bit byte 256 Kbyte frame 1 MIR fits 256 Kbyte frame 4 frame fits 1024 Kbyte fits file e AOTO2 6 exposure cycles pointing 1 NIR fits 1 MIR fits exposure cycle 10 8 Mbyte pointing e AOTO3 6 exposure cycles pointing 1 NIR fits 1 MIR fits exposure cycle 10 8 Mbyte pointing e AOTO05 9 exposure cycles pointing 1 NIR fits 1 MIR fits exposure cycle 16 2 Mbyte pointing The toolkit requires 3 or 4 times of disk space compared to the data Version 1 4 May 30 2008 51 5 4 How to install the IRC imaging Toolkit 5 4 1 Requirements The toolkit is developed in a Linux PC environment and has also been successfully run in the OSX Unix environment The toolkit requires the following environment for its full function e unix Solaris MacOS X Linux BSD e IRAF 2 12 2 or later gcc 3 2 or later e perl e
24. curl for WCS calculation on Solaris machines 5 4 2 Install IRAF e http iraf noao edu 5 4 3 Download IRC imaging data reduction software package The latest version of the toolkit with installation and operating instructions can be obtained from the AKARI Observer s web site see section 1 2 5 4 4 Unpack irc tgz e mv ircYYMMDD tgz where you want to install e cd where you want to install e tar xvzf ircYYMMDD tgz 5 4 5 Make irc binaries e cd where you want to install irc sre e make This will create binary files in where you want to install irc bin 5 4 6 Run setpath pl e cd where you want to install irc lib e perl setpath pl This will rewrite the setpath dat Please check the following line in setpath dat is the following format set irchome where you want to install irc This line should indicate the location where you installed the irc package 52 IRC Data User Manual 5 4 7 Perl path Typing which perl in the unix environment indicates where the perl is installed in your system The toolkit assumes that the perl is installed in usr local bin perl Therefore those who have the perl binary elsewhere should do as follows e If you know the root password please create a symbolic link in usr local bin by typing cd usr local bin In s which perl perl It will create a symbolic link perl in usr local bin e If you don t know the root password please modi
25. det KK KK KR EET TIFF TTT et Kure lt a m e pem 7 id Pp 44 SOK amp KA amp kA TTTTTTTT T Preces KGL ERS DD Sa cx Elin El RS A ue oce is a a Yormom Pi A TRO OT RESTA KKKRERAAFE PTT Kaede LAs gt 5 iP secet c K XX uS KAA dhof vf T UT Y um 7 100 200 300 400 50 100 150 200 250 X pixel Figure 4 9 11 Distortion from ideal grid square for N2 S7 and L24 from left to right respec tively For clearity the length of distortion vectors are multiplied by 20 4 10 Memory effects caused by bright source observations MIR S and MIR L channels show an anomalous sign after they observe bright sources An exam ple is shown in Figure 4 10 12 It seems to be a decrease of the sensitivity Although the amount is less than 196 it could severely affect detection of faint sources because of high background in the MIR We recognize that the effect last for hours The threshold level to produce this is not yet clearly known but IR AS 12um sources definitely produce it At this stage no recipe for the Version 1 4 May 30 2008 43 correction is available If your data show this pattern it should come from previous observa tions A list of potentially affected observations is available If you would like to check whether or not your observations are possibly affected please contact us at iris_help ir isas jaxa jp or http akari esac esa int esupport Figure 4 10 12 Transients effects seen in MIR S after a bright source obser
26. dispersion elements per photon 28 IRC Data User Manual Relative Response o o o A oO co o no o 8 12 16 20 Wavelength um Figure 4 5 7 The Relative Spectral Response Function for Fy of the IRC MIR S Camera Relative Response o O N T Oo co o T l Wavelength um Figure 4 5 8 The Relative Spectral Response Function of the IRC MIR S dispersion elements per photon Version 1 4 May 30 2008 29 o o o P oO 0 Relative Response o N o 10 1 5 20 E 25 B 30 Wavelength um Figure 4 5 9 The Relative Spectral Response Function of the IRC MIR L Camera for F5 Relative Response O O O o amp o N o 20 24 28 Wavelength um m Oo Figure 4 5 10 The Relative Spectral Response Function of the IRC MIR L dispersion elements per photon LG1 will not be used for astronomical observations due to degradation Data shown here is 2nd order light subtracted 30 IRC Data User Manual 4 6 Flux calibration for point sources 4 6 1 Observed standards and data processing The standard stars for the absolute flux calibration were selected in the North and South Ecliptic Pole NEP and SEP regions which were established by M Cohen originally for the calibration of the IRAC onboard Spitzer We list the observed NEP and SEP standards in Table 4 6 2 The observations of these standards were carried out with IRC AOT03 which pe
27. errors in the spectral response calibration creating funny fake spectral features in NP In this case the features resemble the response curve or more exactly its change per pixel along wavelength Because of lowest spectral resolution and rather structured response curve shape this effect is most clearly seen in NP spectra Note that even small wavelength offset say a mere 0 5 pixel would produce noticeable pseudo spectral features especially around 2 4 3 5 um We recommend to check the spectra of nearby field stars as well as your object to see if the funny features are common to all objects If they look similar the features are likely to be fake To see how the features change with wavelength offset try the procedure described in sec tion 6 5 3 Although there are no zero th order light images available for NP the command change wave offset works even for NP for testing how the spectral features change with the offset Note that for NP there are no guidelines such as zero th order light to find the best wavelength zero point in general Therefore the user should justify the amount of offset entered with this command Remember that nominal error of the wavelength zero point calculation is 1 0 pixel or less 6 6 4 Examining flux level in consistency among different disperser data Sometimes one may find jumps in flux level between SG1 and SG2 spectra or other pairs of adjacent wavelength for a single source There are possible re
28. in grism spectroscopy images This is caused by the zero th order light of the grisms Since the zero th order light image forms at an offset position from the reference image only about a half of the FOV suffers from its contamination This jump of the background flux level in ADU is about 2 396 of the total background for SG1 SG2 and LG2 e Satellite attitude stability instability Position shifts among sub frames are frequently observed due to the satellite attitude drift in the pointing attitude control mode The drift is as large as several pixels in the worst cases To correct the drift one needs to 48 IRC Data User Manual register images among spectroscopy sub frames and between spectroscopy and reference images The second correction is very important to determine the wavelength reference point Note that it takes about 30 sec to switch the spectroscopy mode to from the imaging mode for the filter wheel rotation Thus the time interval between the last spectroscopy sub frame and the first imaging sub frame is longer by this period than the interval between taking spectroscopy sub frames To measure the image drift among spectroscopy images we use cross correlation image matching technique To measure the image drift between spectroscopy and reference images we could use the same cross correlation technique In this cross correlation we use a template spectrum that was extracted from the data with negligible drifts Then by comparing the
29. most of the cases 6 4 6 Warning messages of the pipeline Some common and frequently appearing warning messages are listed below e Warning irc_specred Wrong number of arguments Check the command line ar guments and try again e Warning No lt gt was found set Stop Some files that should be provided for the pipeline seem missing Check if list files are properly set in the command line This warning will also appear if you run SG1 SG2 LG2 data reduction before performing NP or NG data processing and some mandatory database files e g describing relative image shifts are missing e Warning Offset search box is too small When the telescope drifts too much the image matching sub program fails to find the best shift values among sub frames Normally the sub program resumes searching the shift with larger search box Normally this message is not so serious 96 IRC Data User Manual e Warning No data are available for measurement Returning 0 or Warning Data seems too noisy sigma lt sigma gt Returning 0 These messages will ap pear if e g detected sources are too faint and their positions could not be measured with good enough accuracy Check the source detection parameters for better source detections This message is not so serious in most of the cases Warning sigma of specbox Y shift measurement seems too large This warn ing appears when the toolkit fails to measure the relative Y shift of NP
30. on the fly flux calibration after considering various plotting conditions options Since the default FC images does not care these we strongly recommend to use our plotting tool to review the spectra In _wc_indiv fits and _fc_indiv fits files wavelength information is set in the FITS headers with header keywords CRVAL CDELT CRPIX and CD matrix Users can plot the spectra with e g the standard spectral plotting tool SPLOT on IRAF Note however that there are no such FITS header information for prism NP spectra because of their non linear wavelength solution Here is an example to plot the SG1 spectra with IRAF SPLOT task splot xxxxxxx 1 S9WSG1 specimage_fc_indiv fits Image line aperture to plot 0 1 10 Image band to plot 1 1 2 In this example the plot shows flux calibrated spectrum of the 2nd object along X space 10 pixel Note that 2nd object means source ID 1 on the IRC_SPECRED 94 IRC Data User Manual since IDL counts from zero while IRAF does from one Note also that no aperture correction can be applied for the spectral plot with the SPLOT task These images are in 3D being the third Z dimension for source id NaN Not a Number represents the masked pixel area e Others Target information table a table of target information such as positions after source position tuning flux and size Gaussian FWHM lt targetid gt lt targetsubid gt lt filter_spec gt target_table tbl Its format is th
31. order polynomial that will convert xy to RA and DEC The module attempts to find the best fitting solution by increasing the order of plynomial from 2 to 4 Usually the best result should be 2nd order as long as the image has been corrected for distortion e if matched put wes in the header Note that it is possible to shorten the time to download the relevant 2MASS catalog by changing the download mirror in the toolkit file irc perl get2mass pl Find the line that determines the data server where the 2MASS catalog will be downloaded The default is Tokyo Japan To choose the nearest server un comment the relevant URL and comment out TokyoJapan Note for multiple pointings and deep imaging data many pointings of data may have to be co added In such cases all the images must be rotated and the toolkit will have to take care of this before co adding The final result is the basic science grade images see Figure 5 10 14 5 10 2 Log files produced from the toolkit In addition there are various log files produced by the toolkit which are described below e coo Files The coo files e g SfdmslnDwaF23343_N002 fits coo 1 are the results for robust source extraction that extracts x and y coordinates amp robust photometry One coo file is created for each individual exposure frame These files can then be used to calculate the shift and rotation of frames that are being co added by matching bright stars in the extracted source lists
32. quick look products are distributed in the archive for both imaging and spectroscopy IRC observations These files are not intended for science and the users are strongly encouraged to run the correponding pipelines in order to obtain the best out of the raw data 3 3 1 IRC imaging IRCO5 IRCO02 and IRCO03 As explained in the README file distributed with the data in the archive the irc ql subdirectory contains together with a set of log files a main quick look fits image per detector with the following naming convention Its name is fdmslnDwaFV V Vxxxxxx NSL yyy fits The firts prefixes refer to the performed steps during the processing DARK correction D linearity In distortion correction d and flatfiedling f NSL refer to each detector The irclog file contains a brief description of each file from the data reduction pipeline 3 3 2 IRC spectroscopy IRC04 The quick look products distributed in the case of spectroscopy observations IRC04 are the following e TARGETID SUBID FILTER_DISPERSER refimage_bg fits dark linearity and flatfiled corrected reference image e TARGETID SUBID FILTER DISPERSER specimage bg fits dark linearity and flatfield corrected spectroscopy image This quick look image is usable only for slit less spec troscopy For slit spectroscopy further processing with the spectroscopy pipeline is needed Auxiliary files are described in the README file distributed in the archive 20 IRC Data User
33. ress necem rst rete oper ets M A paier dic eye sia es 2 22 IRO02 24x fe ee RR ek ae BOX x XUL EG 2 2 97 ARCS se ny hU qu UR Phe eek eS Ns eue Eus ue Bae EbNIau 2 220 ARCO Llc ESAMI DR Rut EE eut hux d p Ee S 2 2 5 RECOS a nies terio uet rra ted on tm eer vri ph dte d 2 2 6 IRGIEL e 42 ACERBA Oe eb US Gee eae ER ROO 220 MID S esu soos RIA do SERLO EUR atado ue he dob Ue 2 89 In orbit sensitivity eee Sere 3 Distributed Data Products 3 1 IRC FITS file naming rule ss 3 2 Raw data description 2 22s 3 21 Raw data naming convention 4 2s 3 2 2 AKARI FITS Primary HDU common information rawdata header 3 2 3 Raw data dimensions i6 ae PoP eB Sie Soke Ye OR de bee CORO 3 9 Quick look data ous es wi le uem ae oe eke Be ee ee pee A Elide 3 3 1 IRC imaging IRC05 IRCO2 and IRCOS 3 3 2 IRC spectroscopy IRC04 aoaaa 3 4 IRC04 image orientation and dispersion direction 4 IRC Calibration and Accuracy 4l Darkimage sorora og moane a xc a eha BS He Ere Rom a ee Rob Eg ALD sBlatheld rs mx 6 he gs BOA ed hind SO eo Esa qd dns d 4 2 91 Flatfileds for imaging data les 4 2 0 Flats for spectroscopy images ln 4 3 Instrument linearity aoaaa 4 4 Instrument Point Spread Function ls ASS RSRE eue eise ee mec de ob eee mpm d CER E B b xe rise dms 4 6 Flux calibration for point sources 2e N m 000000148 10 10 10 11 11 11 11 Vers
34. rotation value between image frames bluebox adjust sky Adjusts sky level between individual frames bluebox irc_stack Stacks the IRC images e bluebox putwcs To add WCS information to an image FITS file by matching 2MASS catalog coordinates The present configuration of the Blue Box co add wrapper module is shown in Fig 5 10 13 The starting point for the Blue Box Co Add wrapper are the files created from the final step in the Green Box pipeline Processor efmsiCcnDwaF23342 9004 fits The Co Add module then performs the following tasks 1 Extract bright reference sources bluebox source extract This module extracts individual bright sources from individual frames Before extraction original 412x512 256x256 NIR MIR images are paseted to larger 1024x1024 512x512 images to prepare for the xy shift and rotation During source extraction a S will be added such that fdmslnDwaF23342 8004 fits becomes SfdmslnDwaF23342 8004 fits For each MIR image a median box car filtered image will be made which is then subtracted before source extraction for efficient source extraction in the case of variable background within an image Furthermore a simple cosmic ray detection and rejection process will be applied to the MIR images Then bright sources stars are extracted from each frame as source lists Version 1 4 May 30 2008 69 BLUE BOX Co Add Wrapper bluebox source extract extract reference sources b
35. short and long exposures The short exposure is intended to increase the dynamic range by about 8 to 10 times The clock pattern of one frame is the same for all AOTs except for IRC05 whose frame is twice the period of other AOTs see next section Except for IRC05 one frame is about 63 sec in which NIR has one short and one long exposures and MIR S and MIR L have one short and three long exposures The short exposure is made with the Fowler 1 sampling scheme and the long exposure is made with the Fowler 4 sampling For the IRC05 the clock of the MIR S and MIR L is the same as for other AOTs but repeated twice in a frame The short exposure of the NIR in IRCO5 is taken once and the exposure scheme is the same for other AOTs The long exposure of the NIR in IRCO05 is made with the Fowler 16 sampling scheme and is taken once in a frame 2 2 Instrument AOTs In a pointed observation the filter and dithering combinations for IRC have been fixed to a few patterns which are called Astronomical Observation Template AOT The duration of a pointed observation and the frame time are well determined Each AOT consists of a combination of frames of the IRC operation with dithering and filter wheel rotation operations which is well fixed in a pointed observation Figure 2 2 6 shows an illustration of the pre fixed sequences in each AOT In all the AOTs except for AOT11 a dark frame is carried out before and after the observation pre dark and post dark o
36. template with spectra extracted from the spectroscopy data in question we estimate the relative drift Since all the channels operate simultaneously any image drifts along the X and Y directions found in NIR or MIR S should be seen in MIR L with the different pixel scale For spectra of diffuse sources at the narrow slits Nh Ns and Ls we do not have to take account of the satellite attitude stability if the size of the drift is much smaller than that of the objects e Ghosts in Np observations Ghosts relating the Np slit have also been recognized Left panel of Fig 4 13 16 shows an example of the imaging data There are sources seen on the slit mask region which must be ghosts from the sources in the Np slit Right panel of Fig 4 13 16 shows the corresponding spectral data in which ghost spectra overlap with the source spectrum A similar ghost is also reported for SG2 in which the effect of the ghost should not be significant since the ghost spectrum appears at much shorther wavelengths lower part of the image and does not overlap the source spectrum No definite origin for these ghosts have been elucidated and thus no clear recipe has been prepared to correct for them Figure 4 13 16 Ghosts generated in Np observations Left panel Imaging data Right panel spectroscopic data Chapter 5 Imaging toolkit cookbook 5 1 Introduction The IRC imaging data reduction toolkit is developed to address and correct any IRC Instru
37. the beginning and the end of the operation for both the NIR and MIR channels i e an extra 2 FITS files for both NIR and MIR Therefore as shown in Fifure 2 2 6 for AOT IRCO2 for a single pointing the maximum number of raw data files will comprise of 1 NIR 1 MIR FITS EC x 7 EC 4 Dark 18 FITS files for one pointing Consequently for AOT IRC03 for a single pointing the raw data files will comprise of 1 NIR 1 MIR FITS EC x 8 EC 4 Dark 20 FITS files for one pointing In addition to the raw FITS files a text file is also included giving details of the original target list for the observation The redbox ircslice module slices each raw FITS file into the individual frames separates all individual IRC frames for one Exposure Cycle Thus for every NIR raw FITS file including the Dark redbox ircslice will create 2 FITS files corresponding to the short and long exposure For every MIR raw FITS file including the Dark redbox ircslice will create 8 FITS files corresponding to single short and three long exposures for both the MIR S and MIR L channels Therefore after running redbox ircslice on a single pointing for AOT IRCOS3 you can expect as many as 100 individual FITS files The filename format takes the original format with an extension defining the channel N S L and frame number 001 004 For example an original raw FITS file for the MIR channel F23340_M fits is sliced into 8 separate fits files F23340 L001 fits
38. 0 946 0 917 1 080 220 1 174 0 948 0 922 0 940 0 918 1 088 230 1 143 0 939 0 928 0 935 0 919 1 094 240 1 116 0 933 0 935 0 931 0 921 1 101 250 1 094 0 928 0 942 0 927 0 923 1 107 300 1 023 0 927 0 979 0 917 0 934 1 131 350 0 988 0 944 1 014 0 913 0 946 1 150 400 0 969 0 967 1 045 0 911 0 956 1 164 450 0 960 0 992 1 072 0 911 0 965 1 176 500 0 955 1 016 1 095 0 912 0 973 1 185 600 0 953 1 059 1 132 0 913 0 985 1 200 700 0 955 1 094 1 160 0 915 0 995 1 211 800 0 958 1 124 1 181 0 917 1 002 1 220 900 0 961 1 148 1 198 0 919 1 008 1 227 1000 0 964 1 168 1 212 0 920 1 013 1 233 1500 0 975 1 232 1 253 0 924 1 027 1 254 2000 0 982 1 264 1 273 0 927 1 035 1 267 2500 0 986 1 284 1 285 0 929 1 040 1 275 3000 0 988 1 297 1 293 0 930 1 043 1 281 3500 0 990 1 306 1 298 0 931 1 046 1 285 4000 0 992 1 313 1 303 0 931 1 047 1 288 4500 0 993 1 318 1 306 0 932 1 049 1 291 5000 0 994 1 322 1 308 0 932 1 050 1 293 6000 0 995 1 328 1 312 0 933 1 051 1 297 7000 0 996 1 333 1 315 0 933 1 053 1 299 8000 0 997 1 336 1 317 0 933 1 053 1 301 9000 0 997 1 339 1 318 0 934 1 054 1 302 10000 0 998 1 341 1 320 0 934 1 055 1 303 20000 1 000 1 350 1 325 0 935 1 057 1 309 30000 1 001 1 353 1 327 0 935 1 058 1 311 40000 1 001 1 355 1 328 0 935 1 058 1 312 50000 1 001 1 356 1 329 0 935 1 059 1 312 60000 1 001 1 356 1 329 0 935 1 059 1 313 Values are calculated for A4 7 0um As 9 0um Ag 11 0um Ay 15 0um Ag 18 04m Ag 24 0um Version 1 4 May 30 2008 41 T
39. 07 04 15 00 24 01 KFOIT4 3 2007 06 01 00 37 25 KFO1T5 18040388 6655437 KIII 11 072 2006 06 24 19 55 00 KFO1T5 2 2007 04 15 00 24 01 KFOIT5 3 2007 06 01 00 37 25 for MIR L HD42525 06060937 6602227 AOV 5 751 2006 04 22 02 03 59 NPM1p65_0451 16533704 6538175 K2III 6 524 2006 12 20 01 36 45 HD158485 172604844 5839069 A3V 6 145 2006 08 22 17 47 59 Bp66_1060 17560018 6655430 K2III 6 720 2006 11 07 16 16 54 NPM1p67_0536 17585466 6747368 K2III 6 409 2006 04 24 14 43 03 HD165459 18023073 5837381 A1V 6 584 2007 03 22 01 44 58 Bp66_1073 18030959 6628119 KIIII 7 544 2006 06 28 19 41 30 KFOIT4 18040314 6654459 K1 5III 8 067 2006 06 24 23 13 10 HD166780 18083882 5758468 KAII 3 963 2006 09 29 19 43 33 Version 1 4 May 30 2008 Star HD34461 HD34555 HD34943 HD35094 HD35094 2 HD35183 HD35323 HD35461 HD35461 2 HD35665 HD35905 HD36207 HD37122 HD269704 HD269704 2 HD269757 HD37722 HD37762 HD269788 HD269820 HD269820 2 HD38861 HD38993 HD39980 HD270186 HD34461 HD34461 2 HD34489 HD34943 HD35323 HD35323 2 HD269352 HD35461 HD35665 HD35905 HD36207 HD37122 HD269704 HD37722 HD37722 2 HD37762 HD269788 HD269820 Table 4 6 3 SAGE standard stars 2MASS ID for N3 S7 S11 05121801 6705415 05125331 6744362 05153759 6804070 05164382 6811142 05172303 6828190 05183268 6732320 05194979 6626353 05205607 6759034 05223623 6721285 05244398 6753507 05300077 6958319 05315890 6909392 05335125 6946468 05344387 6928
40. 0um Az 15 0um Ag 18 0um Ag 24 0um 36 IRC Data User Manual Table 4 8 8 Color Correction factors for NIR channel Black Body a 0 Intrinsic NIR N2 NIR N3 NIR N4 Temperature K K 2 4um K 3 2um K 4 1um 40 50 60 70 80 90 396 131 100 164 506 110 z 81 786 120 873 058 46 429 130 297 140 29 139 140 121 814 19 760 150 58 297 14 242 160 31 767 10 776 170 S 19 291 8 482 180 12 811 6 895 190 9 149 5 756 200 S 6 928 4 914 210 5 496 4 275 220 582 603 4 526 3 778 230 316 052 3 839 3 385 240 181 324 3 336 3 069 250 109 374 2 955 2 810 300 16 057 1 952 2 024 350 5 065 1 543 1 643 400 2 631 1 333 1 428 450 1 818 1 212 1 294 500 1 463 1 136 1 204 600 1 167 1 052 1 095 700 1 051 1 012 1 033 800 0 997 0 992 0 994 900 0 970 0 982 0 969 1000 0 957 0 977 0 951 1500 0 963 0 981 0 910 2000 0 990 0 992 0 896 2500 1 013 1 001 0 890 3000 1 031 1 008 0 886 3500 1 045 1 013 0 884 4000 1 056 1 017 0 883 4500 1 064 1 020 0 882 5000 1 071 1 022 0 881 6000 1 081 1 026 0 880 7000 1 088 1 029 0 880 8000 1 094 1 031 0 879 9000 1 098 1 032 0 879 10000 1 101 1 034 0 879 20000 1 116 1 039 0 878 30000 1 121 1 041 0 877 40000 1 123 1 042 0 877 50000 1 125 1 043 0 877 60000 1 126 1 043 0 877 Values are calculated for Ay 2 4um Ao 3 2um Aa 4 1 um Version 1 4 May 30 2008 Table 4 8 9 Color Correction factors for NIR channel Gray Body a 1 I
41. 1 180 1 191 0 924 0 990 1 174 7000 0 977 1 184 1 193 0 924 0 990 1 175 8000 0 977 1 186 1 195 0 924 0 991 1 175 9000 0 977 1 188 1 196 0 924 0 991 1 176 10000 0 978 1 189 1 197 0 924 0 991 1 176 20000 0 979 1 196 1 201 0 924 0 993 1 178 30000 0 979 1 198 1 202 0 924 0 993 1 179 40000 0 979 1 199 1 203 0 924 0 993 1 179 50000 0 979 1 199 1 204 0 925 0 994 1 180 60000 0 980 1 200 1 204 0 925 0 994 1 180 Values are calculated for A4 7 0um As 9 0um Ag 11 0um Ay 15 0um Ag 18 0um Ag 24 0um 40 IRC Data User Manual Table 4 8 12 Color Correction factors for MIR channel Gray Body a 1 Intrinsic MIR 5 57 MIR S S9W MIR S SI1 MIR L L15 MIR L L20W MIR L L24 Temperature K K 7 0um K 9 0um K 11 0um K 15 0um K 18 0um K 24 0um 40 126 883 11 699 11 085 0 913 50 175 833 15 078 4 943 4 371 0 870 60 19 630 5 044 2 961 2 528 0 869 70 7 299 2 712 2 135 1 798 0 883 80 239 889 4 200 1 855 1 715 1 443 0 902 90 44 874 2 906 1 452 1 472 1 247 0 922 100 13 402 2 228 1 235 1 320 1 130 0 942 110 5 953 1 826 1 107 1 218 1 056 0 960 120 3 563 1 568 1 029 1 147 1 008 0 977 130 2 580 1 393 0 979 1 096 0 976 0 993 140 2 088 1 270 0 947 1 057 0 954 1 007 150 1 801 1 181 0 928 1 028 0 940 1 021 160 1 615 1 115 0 916 1 006 0 930 1 033 170 1 485 1 065 0 910 0 988 0 924 1 044 180 1 389 1 027 0 908 0 974 0 920 1 054 190 1 316 0 999 0 909 0 963 0 918 1 063 200 1 258 0 977 0 912 0 954 0 917 1 072 210 1 212 0 960 0 916
42. 18 39 20 2006 06 03 06 16 38 2006 06 04 05 23 26 2006 05 24 06 54 23 2006 05 21 06 16 33 2006 12 04 17 29 51 2006 12 07 11 40 07 2006 11 29 13 25 55 2006 12 31 13 05 43 2006 11 28 15 55 38 2006 12 06 15 48 56 2006 11 27 18 25 19 2007 04 21 07 56 30 2006 11 07 20 25 50 2006 11 02 19 42 32 2006 11 03 05 37 54 2007 04 12 06 57 26 2006 11 08 22 53 20 2006 11 02 19 42 32 31 32 IRC Data User Manual HD38861 05423256 7022555 KOI 6 780 2007 04 02 06 48 19 HD38993 05431866 7027254 K1 5III 5 478 2007 04 02 05 08 54 HD39980 05495921 6941060 K2III 5 409 2006 10 16 22 35 50 HD270186 05501123 6934296 KOIII 7 774 2006 10 18 19 14 15 The raw data were reduced with the IRC imaging pipeline The pipeline produces one coadded image for each band exposure configuration using median as the combine mode Each configuration image corresponds to the exposure unit listed in Table 4 6 4 The actual exposure time is the unit number x the unit exposure time tunit which is approximately 0 5844 s Table 4 6 4 Exposure time of each band exposure configuration Band Exposure unit number NIR short 8 NIR long 76 112 IRC05 MIR short 1 MIR long 28 One unit time corresponds to about 0 5844 s An aperture photometry IRAF phot was performed for each standard star The radius of the aperture adopted is 10 pixels for NIR band and 7 5 pixels for MIR S and MIR L band respectively We determined the sky value in an annulus outside the aperture
43. 187 05344709 7010197 05345367 6846395 05355068 6929178 05423256 7022555 05431866 7027254 05495921 6941060 05501123 6934296 Sp KIIII A3V MOIII A3V A3V MOIII Kill K1 5II KIIII Kill K2III K2III Kill AAV KOIII KAIII KIIII KOIII K1 5III K2III KOIII for L15 L24 05121801 6705415 05122388 6756520 05153759 6804070 05183268 6732320 05193283 6752441 05194979 6626353 05205607 6759034 05223623 6721285 05244398 6753507 05300077 6958319 05315890 6909392 05344387 6928187 05344709 7010197 05345367 6846395 05355068 6929178 KIIII K2III MOIII MOIII Koll KIIII KI1 5III Kill KIIII K2III K2III AAV KOIII KAIII Kill K 6 927 9 288 3 970 8 554 8 754 5 524 5 683 5 887 6 800 6 451 5 128 6 760 8 187 8 640 5 565 6 331 7 185 6 780 5 478 5 409 7 774 6 927 6 169 3 970 5 524 6 014 5 683 5 887 6 800 6 451 5 128 6 760 8 640 5 565 6 331 7 185 Obs Date 2006 06 08 18 21 09 2006 05 31 05 38 19 2006 05 26 06 46 47 2006 05 23 07 47 52 2006 05 25 06 01 07 2006 05 20 23 40 20 2006 11 29 13 25 55 2006 12 20 04 04 52 2006 12 18 23 57 17 2006 11 24 15 59 18 2006 12 01 05 07 47 2006 11 23 05 15 04 2007 04 25 09 40 22 2006 11 03 18 51 36 2006 11 03 22 10 04 2007 04 22 07 07 59 2007 04 25 03 03 00 2007 04 18 07 03 34 2007 05 02 05 40 40 2006 10 29 19 47 54 2006 10 30 18 56 54 2007 04 08 06 53 36 2007 04 06 05 12 23 2006 10 09 18 39 20 2006 10 09
44. 218 1 F004160561_N002 LMC FIELD218 412 UNDEF 80 53135 68 17282 IRCO2 2 2210218 1 F004160562_L001 LMC FIELD218 256 DARK 359 7475 59 3225 IRCO2 1 2210218 1 F004160562_L002 LMC FIELD218 256 DARK 359 7475 59 3225 IRCO2 2 2210218 1 F004160562_L003 LMC FIELD218 256 DARK 359 7475 59 3225 IRCO2 3 2210218 1 7 F004160562 L004 LMC FIELD218 256 DARK 359 7475 59 3225 IRCO2 4 2210218 1 F004160562_S001 LMC FIELD218 256 DARK 359 7475 59 3225 IRCO2 1 2210218 1 F004160562_S002 LMC FIELD218 256 DARK 359 7475 59 3225 IRCO2 2 2210218 1 3 F004160562 8003 LMC FIELD218 256 DARK 359 7475 59 3225 IRCO2 3 2210218 1 F004160562_S004 LMC FIELD218 256 DARK 359 7475 59 3225 IRCO2 4 2210218 1 F004160563 N001 LMC FIELD218 412 DARK 359 7475 59 3225 IRC02 1 2210218 1 F004160563_N002 LMC FIELD218 412 DARK 359 7475 59 3225 IRCO2 2 2210218 1 60 IRC Data User Manual 5 9 The pipeline processor Green Box 5 9 1 Configuration Before running the pipeline you can configure the parameters for the pipeline by typing epar pipeline O000 X XGterm IRAF v 2 12 1 NFS Darwin IRAF Image Reduction and Analysis Facility PACKAGE irc TASK pipeline irccons J constants database IRC constants database file name com_mod median combine mode average median com_are 2 stack area 1tcommon area 2twhole area sky_are 2 sky matching areat 1 common area 2 whole area det sig 4 Threshold in
45. 2210218 1 F004160558_L002 LMC FIELD218 256 L24 80 53135 68 17282 IRCO2 2 2210218 1 F004160558_L003 LMC FIELD218 256 L24 80 53135 68 17282 IRCO2 3 2210218 1 F004160558_L004 LMC FIELD218 256 L24 80 53135 68 17282 IRCO2 4 2210218 1 F004160558_S001 LMC FIELD218 256 S11 80 53135 68 17282 IRCO2 1 2210218 1 F004160558_S002 LMC FIELD218 256 S11 80 53135 68 17282 IRC02 2 2210218 1 F004160558_S003 LMC FIELD218 256 S11 80 53135 68 17282 IRCO2 3 2210218 1 F004160558_S004 LMC FIELD218 256 S11 80 53135 68 17282 IRCO2 4 2210218 1 F004160559 NO01 LMC FIELD218 412 N3 80 53135 68 17282 IRCO2 1 2210218 1 F004160559_N002 LMC FIELD218 412 N3 80 53135 68 17282 IRCO2 2 2210218 1 F004160560_L001 LMC FIELD218 256 UNDEF 80 53135 68 17282 IRCO2 1 2210218 1 F004160560_L002 LMC FIELD218 256 UNDEF 80 53135 68 17282 IRCO2 2 2210218 1 F004160560_L003 LMC FIELD218 256 UNDEF 80 53135 68 17282 IRCO2 3 2210218 1 7 F004160560 L004 LMC FIELD218 256 UNDEF 80 53135 68 17282 IRCO2 4 2210218 1 F004160560_S001 LMC FIELD218 256 UNDEF 80 53135 68 17282 IRCO2 1 2210218 1 F004160560_S002 LMC FIELD218 256 UNDEF 80 53135 68 17282 IRCO2 2 2210218 1 F004160560_S003 LMC FIELD218 256 UNDEF 80 53135 68 17282 IRCO2 3 2210218 1 F004160560_S004 LMC FIELD218 256 UNDEF 80 53135 68 17282 IRCO2 4 2210218 1 F004160561_N001 LMC FIELD218 412 UNDEF 80 53135 68 17282 IRCO2 1 2210
46. 500 33000 and 33000 ADU after ircnorm for NIR MIR S and MIR L respectively No reports have been given against its reliability Observations of very bright standard stars seem to be compatible with those of medium brightness 4 4 Instrument Point Spread Function Table 4 4 1 shows the FWHM of the in flight PSF in the imaging mode based on observations of standard stars performed in May and September 2006 They are partly affected by th attitude control stability and indicate the worst cases Table 4 4 1 In orbit PSF in pixels The PSF are not spherical Therefore the users are recommended to average individual images in the coadding process if photometric accuracy is concerned In some cases mainly in deep survey the median filtered image will lose some signal if the images are rotated with respect to each other To avoid this problem users should use average instead of median filter when combining individual images The PSF in the spectroscopic mode is worse by one or two pixels compared to imaging data No significant wavelength dependence is seen along dispersers Version 1 4 May 30 2008 25 m IDL o o x n DLO km Joxs MIRL linearity Figure 4 3 3 Raw signal versus fit signal expected if detectors were to behave linearly The white line shows Raw signals equals to fit and the red line shows the calculated correction equations Note that the physical detector saturat
47. 6 The IRC toolkit does not run on the new Intel Mac machines due to differences in the IRAF build in the intel binaries Replacing the intel binaries with the original binaries causes iraf to run under emulation but solves the problem IR AF 2 13 has been successfully run on the intel machines 7 The coaddition process or the coaddLusingS function can cause the crash of the toolkit with the error ERROR on line 128 Attempt to access undefined local variable filter This error will occur if the pre pipeline is attempted to run twice on a given data set As a check the files and their counterpart corresponding MIR L images listed in the pair file e g pair0001_S7 list_long should be examined to see if they have the appropriate FILTER keywords in their header 8 The Matching failed error message that could appear in the putwcs process is not an intrinsic pipeline error It is due to the fact that the 2MASS data format changes from time to time Appropriate updates or patches are made to the pipeline The updates will be recorded in the Observer s page Chapter 6 Spectroscopy pipeline cookbook The spectroscopy pipeline is being developed and maintained by the IRC spectroscopy data reduction team It is mostly written in IDL and uses the IDL ASTRO library maintained at the GSFC among others Although it is developed under Linux environment it may be portable to other platforms after some modifications though we have no pl
48. 68 17107 IRCO2 3 2210218 1 F004160544_L004 LMC FIELD218 256 DARK 80 54688 68 17107 IRCO2 4 2210218 1 F004160544_S001 LMC FIELD218 256 DARK 80 54688 68 17107 IRCO2 1 2210218 1 F004160544_S002 LMC FIELD218 256 DARK 80 54688 68 17107 IRCO2 2 2210218 1 3 F004160544 8003 LMC FIELD218 256 DARK 80 54688 68 17107 IRCO2 3 2210218 1 F004160544_S004 LMC FIELD218 256 DARK 80 54688 68 17107 IRCO2 4 2210218 1 F004160545_N001 LMC FIELD218 412 DARK 80 54688 68 17107 IRCO2 1 2210218 1 F004160545_N002 LMC FIELD218 412 DARK 80 54688 68 17107 IRCO2 2 2210218 1 F004160546_L001 LMC FIELD218 256 L15 80 54688 68 17107 IRCO2 1 2210218 1 F004160546_L002 LMC FIELD218 256 L15 80 54688 68 17107 IRCO2 2 2210218 1 F004160546_L003 LMC FIELD218 256 L15 80 54688 68 17107 IRCO2 3 2210218 1 F004160546_L004 LMC FIELD218 256 L15 80 54688 68 17107 IRCO2 4 2210218 1 F004160546_S001 LMC FIELD218 256 S7 80 54688 68 17107 IRC02 1 2210218 1 F004160546_S002 LMC FIELD218 256 S7 80 54688 68 17107 IRC02 2 2210218 1 F004160546_S003 LMC FIELD218 256 S7 80 54688 68 17107 IRCO2 3 2210218 1 F004160546_S004 LMC FIELD218 256 S7 80 54688 68 17107 IRC02 4 2210218 1 F004160547_NO001 LMC FIELD218 412 NP 80 54688 68 17107 IRCO2 1 2210218 1 7 F004160547 N002 LMC FIELD218 412 NP 80 54688 68 17107 IRCO2 2 2210218 1 F004160558 L001 LMC FIELD218 256 L24 80 53135 68 17282 IRCO2 1
49. 80 619 872 5 209 2 217 1 971 1 720 0 887 90 110 313 3 493 1 685 1 670 1 454 0 902 100 29 730 2 629 1 399 1 480 1 292 0 917 110 11 350 2 124 1 230 1 352 1 187 0 931 120 5 796 1 803 1 123 1 262 1 116 0 945 130 3 691 1 585 1 053 1 196 1 066 0 958 140 2 731 1 430 1 006 1 147 1 031 0 969 150 2 221 1 318 0 973 1 109 1 005 0 980 160 1 917 1 233 0 952 1 079 0 986 0 990 170 1 717 1 168 0 937 1 055 0 972 0 999 180 1 577 1 118 0 927 1 035 0 961 1 007 190 1 474 1 078 0 921 1 019 0 953 1 015 200 1 395 1 047 0 918 1 006 0 947 1 022 210 1 332 1 022 0 917 0 995 0 942 1 029 220 1 282 1 002 0 918 0 986 0 939 1 035 230 1 240 0 986 0 919 0 978 0 937 1 040 240 1 206 0 974 0 922 0 972 0 935 1 046 250 1 176 0 964 0 925 0 966 0 934 1 050 300 1 081 0 939 0 947 0 947 0 933 1 070 350 1 032 0 938 0 970 0 937 0 936 1 085 400 1 004 0 946 0 992 0 931 0 940 1 096 450 0 987 0 958 1 011 0 928 0 944 1 104 500 0 977 0 972 1 028 0 925 0 947 1 111 600 0 967 0 998 1 056 0 923 0 954 1 122 700 0 963 1 021 1 076 0 922 0 959 1 130 800 0 961 1 040 1 092 0 922 0 963 1 135 900 0 961 1 057 1 105 0 921 0 966 1 140 1000 0 962 1 070 1 115 0 921 0 969 1 144 1500 0 966 1 113 1 146 0 922 0 977 1 155 2000 0 969 1 136 1 162 0 922 0 981 1 161 2500 0 971 1 149 1 171 0 923 0 984 1 165 3000 0 972 1 158 1 177 0 923 0 985 1 167 3000 0 973 1 165 1 181 0 923 0 987 1 169 4000 0 974 1 169 1 184 0 923 0 987 1 170 4500 0 975 1 173 1 186 0 924 0 988 1 172 5000 0 975 1 176 1 188 0 924 0 989 1 172 6000 0 976
50. AKARI IRC Data User Manual Version 1 4 Rosario Lorente Takashi Onaka Yoshifusa Ita Youichi Ohyama Toshihiko Tanab and Chris Pearson with contributions from Martin Cohen Daisuke Ishihara Hideo Matsuhara Itsuki Sakon Takehiko Wada Issei Yamamura European Space Astronomy Centre ESAC ESA Tokyo University Japan 3Institute of Space and Astronautical Science ISAS JAXA University of California Berkeley National Astronomical Observatory Japan NAOJ 9Rutherford Appleton Laboratory RAL May 30 2008 Version 1 4 May 30 2008 i Date Comments 07 March 2007 Release of version 1 0 21 March 2007 Updated Table 4 6 7 photometric conversion factors 18 June 2007 Updated Sections 4 6 3 4 10 4 13 5 13 2 5 14 6 1 06 September 2007 Version 1 3 Updated Chapter 4 5 and 6 Included ghosts in Np observations section 4 13 28 May 2008 Chapter 6 updated according to spectroscopy pipeline 20080528 Contents 1 Introduction 1 1 1 2 Purpose of this document 2 22s Relevant information 4 lle es 2 Instrument overview 2d Focal plane arrays 4n X e teinana Rex X WE XGE Bue y oer 2 1 4 Near InfraRed Camera NIR a 2 1 2 Short wavelength Mid InfraRed Camera MIR S 2 1 8 Long wavelength Mid InfraRed Camera MIR L 2 1 4 Arrays operation oaoa rss 2 2 Instrument AQXES 3 nuce RR uec A RUE Ce eet de MEQUE RO REESE ELS 2 24 MRO OOM
51. BS is the DATE OBS in ASTRO F Time AFTM END is the DATE END in ASTRO F Time AFTM REF is the DATE REF in ASTRO F Time PIMTIOBS is the DATE OBS in PIM TI 36 bits DHUTI format OxXXXXX PIMTIEND is the DATE END in PIM TI 36 bits DHUTI same format than above 18 IRC Data User Manual PIMTIREF is the DATE REF in PIM TI 36 bits DHUTI same format than above 7 OBS and END are identical with REF for convenience REF is Reference time from TI sampled during each exposure cycle This is due to the fact that IRC only sample time information once per exposure cycle Note PIMTI is the primary information directly from telemetry AFTI and DATE are from the timing correction based on PIMTI e attitude information 3 2 3 EQUINOX is the Epoch of Coordinate RA is the Target position at DATE REF in degrees DEC is the Target position at DATE REF in degrees ROLL is the Roll Angle at DATE OBS AA SOL is the Solar avoidance Angle at DATE REF in degrees AA EAR is the Earth avoidance Angle at DATE REF in degrees AA LUN is the Lunar avoidance Angle at DATE REF in degrees TM SAA is the duration in seconds since last SAA at DATE REF Definition of SAA is different for different detectors SAA region is defined by the glitch rate map observed by the Star Tracker with arbitrary threshold level IRC follows this threshold Shifts of 30 and 60 seconds are applied to FIS SW and LW r
52. C array operation It is not stationary since the scan mode clock is running for most of the time during the survey mode and the imaging clock is running just around pointing observations Therefore the temperature conditions of the array could be a function of both time and pixel positions since only a part of the entire array is used while in the survey mode The effect can be clearly seen in the pre dark image where series of columns of higher dark current are found around the center of the Y axis in MIR S L and the excess of the dark current decreases with time and is essentially invisible in post dark images taken after 20 min from the start of the imaging mode clock operation In the case of spectroscopy observations the post dark image is taken just after finishing imaging exposures and the image shows a memory pattern of the bright background within the slit less area Therefore it can not be used as the dark image to subtract from other images 4 2 Flatfield 4 2 1 Flatfileds for imaging data The IRC super flats for the MIR bands were derived by observing the high surface brightness zodiacal background For NIR we used hundreds of pointing data from the North Ecliptic Pole survey because the observing chances near ecliptic plane are limitted and we could not erase the stellar contribution from the flat images with only a few pointings of data Unfortunately stray 21 22 IRC Data User Manual Figure 4 1 1 Dark images take
53. F23340 L002 fits F23340_L003 fits F23340 L004 fits F23340_S001 fits F23340_S002 fits F23340_S003 fits F23340_S004 fits Fig 5 7 7 shows the images of IRC raw data for the NIR and MIR bands The orientation of the images are such that the NIR is rotated by 90 degrees relative to MIR S L Please note the dark areas in each images These areas are reserved for slit spectroscopy and they are supposed not to receive any light Therefore these regions are useful to monitor the dark level Hereafter we refer to this this dark area as the slit area and the other as the imaging area 2 redbox mkirclog The redbox mkirclog creates the observing log file irclog This is a text file with content shown in Table 5 8 1 The contents of the irclog file summarize the nature of the processed files in the working directory The table entries correspond e FRAME The filename corresponding to the sliced frame e g following the format such as F23340_L001 fits as described above e OBJECT Target name taken from the original target list e NAXIS Number of pixels in cross scan direction 256 for MIR and 412 for NIR e FILTER Filter name i e N2 N3 N4 S7 L24 or DARK e RA SET Right ascension coordinates e DEC SET Declination coordinates 58 IRC Data User Manual e AOT AOT type e g IRC02 IRC03 etc item EXPID Sequential frame number during an exposure cycle e g 1 or 2 for NIR and 1 2 3 or 4 for MIR S and MIR L images e
54. Fig 5 14 16 at different pointings see Fig 5 14 17 and in differernt seasons strongest in solstices Earthshine in imaging observations Data taken in May June and July may suffer from the Earthshine problem The following recipe should be used Check the drift of the background level during a pointing and comment out any high background MIR L frames from irclog and run the pipeline again If the CoaddLus ingS tool is used the frames with the same frame number must be also commented e e if F0000001 L002 is commented F0000001 8S002 must be also commented use rej sky yes option in order to ignore the bad frames cl gt pipeline rej sky yes Version 1 4 May 30 2008 75 use submedsky option to remove the diffuse background cl gt pipeline submedsky yes use for point sources only adjust the median kernel size in the submedsky option bluebox gt epar adjust_sky x_box 20 If submedsky yes x box car size y box 20 If submedsky yes y box car size e Problem with short exposure frames with IRC A problem exists with the con tiguous short exposure frames of the MIR S and MIR L data taken in IRC00 IRC04 and IRCO5 At present the cause is uncertain however it is advised not to use short exposure frame data for scientific purpose They may be used to check the saturation in long exposure frame data Specifically the IRC MIR pointing is composed of several exposure cycles filter changes and dith
55. H have to be modified by substi tuting somewhere lt anotherwhere gt and lt IDL system path according to your local system settings 6 2 1 Data preparation As explained in Chapter 3 when de packing the data from the archive under IRC SPECRED DATADIR the raw data will be stored in IRC_SPECRED_DATADIR lt targetid gt lt targetsubid gt rawdata IRC SPECRED DATADIR lt targetid gt and lt targetsubid gt will be used in the command line of the pipeline command All the reduced data and related information will be stored in a separate directory called root dir targetid targetsubid irc specred out When the directory is missing the toolkit will create it 6 3 Calibration data When de packing the toolkit the following calibration directories are created 6 3 1 Calibration files e IRC_SPECRED_CALIBDIR DARK contains dark images with high S N combined with pre compiled dark images which can be applied for all the observations after performing a small correction in the count offset There are several super darks for NIR MIR S MIR L as specified in the following list files DARK DARK_NIR_long 1st DARK DARK NIR short lst DARK DARK_MIRS_long 1st DARK DARK MIRS short lst DARK DARK MIRL long lst DARK DARK MIRL short lst e IRC_SPECRED_CALIBDIR FLAT contains two types of flats super flats for spectroscopy and reference images These super flats are made by combining a large number of
56. IDNUM Pointing ID e SUBID sub Pointing ID greater than 1 for multi pointing observations 1 NIR fits image 1 MIR fits image NI SI LI S4 LA N1 short exposure frame NIR S1 short exposure frame MIR S L1 short exposure frame MIR L N2 long exposure frame NIR 2 long exposure frame MIR S L2 long exposure frame MIR L S3 long exposure frame MIR S L3 long exposure frame MIR L S4 long exposure frame MIR S L4 long exposure frame MIR L Figure 5 7 6 IRC raw FITS file data structure for NIR and MIR images Figure 5 7 7 Image of IRC raw data NIR and MIR bands The NIR raw FITS file left is 2 frames deep corresponding to 1 short and 1 long exposure The MIR raw FITS file right is 2 frames wide and 4 frames deep corresponding to 1 short and 3 long exposures each for MIR S and MIR L 5 8 Before runnning the pipeline processor After runnning prepipeline you will get 2 text files namely irclog and darklist before e irclog The irclog file is used to select the data to be reduced and any unnecessary entries should Version 1 4 May 30 2008 59 be removed from the irclog file editing it by hand Alternatively entries and unnecessary lines can be commented out by adding to the head of the entries NOTE the DARK frames and any grism prism images need to be removed commented out before running the Green Box pipeline This is automatically done by prepipeline In general bad frames may cause
57. Manual 3 4 IRCOA image orientation and dispersion direction Since raw NIR images are rotated for technical reasons of data handling in the IRC electronics onboard the satellite NIR images NP NG and N3 will be rotated by 90 deg counterclockwise at the very first stage of the data reduction for convenience in the spectroscopy pipeline This is the original orientation in raw images without rotation for NIR e NP longer wavelength comes at right side toward positive X e NG longer wavelength comes at left side toward negative X G1 2 longer wavelength comes at higher toward positive Y e LG2 longer wavelength comes at lower toward positive Y The IRC04 data reduction pipeline makes the rotation of the NIR images at the first step Af ter the NIR rotation the dispersion directions are the same for all the dispersers in spectroscopy images Note however that NP SG1 and SG2 show positive dispersions longer wavelength comes at higher Y and NG and LG2 show negative dispersions longer wavelength comes at lower Y At the same stage the orientation of all NIR MIR S and MIR L images is also set right i e the image is neither flipped nor mirrored T hus one can match the IRC images with other WCS correct images such as 2MASS images only by shifting and or rotating the images Since the satellite is designed to scan the sky along the ecliptic latitude on the sky and the X axis of the IRC array is aligned perpendicular to t
58. Pointed observation data are distributed to the users as a tar gz package format hearafter data package per observation A data package contains FITS format observation data and a Readme file describing the contents etc During the prioritized data use period data packages are encrypted and compressed by gpg GnuPG program The naming convention for the IRC package is AKARLIRC TargetID SubID tar gpg where TargetID is a 7 digits number and SubID is a 3 digits number given by the observation database Combination of TargetID and SubID give a unique identification of the observation When extracting an IRC data package a directory named AKARLIRC TargetID SubID is created Two subdirectories rawdata and irc_ql contain the raw FITS data files and the processed result files respectively 3 2 Raw data description 3 2 1 Raw data naming convention The naming convention for the IRC raw data files is common for all the IRC AOT ans it is the following FVVxxxxxx N M fits where e F is a fixed character e VVVxxxxxx Extended frame counter decimal degits This is a unique identifier of the exposure 14 Version 1 4 May 30 2008 15 e xxxxxx frame conter in the telemetry file e VVV maintained by the FITS creation program Incremented when xxxxxx is reset to 0 N M NIR MIR Scan mode data may have extra characters to this NIR data is in a separate file while MIR S and MIR L are stored in the same FITS f
59. R arrays e vertical stripes as shown in Figure 4 12 15 e short exposure frame data There is a problem in the short exposure frame data taken with IRCO00 IRC04 and IRC05 The phenomena is only seen in the short frames immediately following the frames without any operations such as filter wheel operation and dithering Therefore the very first short frame in all modes and the short frame after the image frame in IRC04 should be fine since they follow the filter operation These short exposure frames can be used for checking the saturation but should not be used for scientific purpose Figure 4 12 15 MIR array vertical stripes 4 13 General concerns on slit less spectroscopy data This section is dealing mainly with problems related to the slit less spectroscopy data Issues for the slit spectroscopy matters are described separately e Wavelength reference point In the slit less spectroscopy mode the wavelength reference point depends on the location of objects within the FOV Therefore the determination of the source posistions on the reference image is very important Errors in the source positions leads to errors in the asigned wavelengths and hence the flux calibration Version 1 4 May 30 2008 47 e Contamination by nearby sources Spectra of more than two objects aligned along with the Y axis could overlap on the same pixels with different wavelengths It is impossible to separate the spectral overlap on the observed image w
60. R camera provide different spectral resolutions over a similar wavelength range In the MIR S and MIR L each dispersion element covers about half of the camera s wavelength range However unfortunately one of the elements of MIR L LG1 was degradated during the ground tests Thus only LG2 will be used for observations resulting in a gap in the wavelength range corresponding to the LG1 element The slits are primarily designed for extended sources and it should not be assumed that they can be used to guide a point source into the slit except for the NIR camera which has an aperture for point sources The current design is the following e The slit for the NIR camera consists of three parts of different widths The left most closest to the imaging area has a 5 arcsec width and will be mainly used for simultaneous observations of diffuse light with the MIR S camera This slit position is labeled as Ns for IRCO4 AOT observation parameter Both the NP low resolution prism and NG high resolution grism will be used with this slit The middle 1 x 1 square part referred to as Np is for spectroscopy of point sources The aperture is large compared to the absolute pointing accuracy of the satellite designed to be better than 30 arcsec to ensure that the target can be accurately guided into the area Note that for observations of faint sources confusion due to galaxies may be a serious problem The NG grism is assumed to be Version 1
61. a User Manual Folding mirror Detector module Si NO Telescope axis 50mm Figure 2 1 3 Side view of the NIR channel Detector module Filter wheel Beam splitter Ge i i y a Telescope axis 5Omm N Figure 2 1 4 Side view of the MIR S channel The beam splitter that splits the light into NIR and MIR S channels acts as a folding mirror for the MIR S 2 1 3 Long wavelength Mid InfraRed Camera MIR L The MIR L channel consists of 5 lenses of CsI and KRS 5 Fig 2 1 5 It also has a small slit for spectroscopy of diffuse emission Fig 2 0 2 Unfocused ghost images are
62. a es 87 6 4 Running the pipeline 2 22 ee 90 6 4 1 Data reduction order 2 222 eh 90 6 4 2 Running the pipeline lle 90 62L3 Optlonsse uni oP Bak aE aE AE Ee Gee SP ee ee Aii 92 GAA CUPU se Se wus bape od a ma tr on de ASTE dhe ee Bo ae es 92 6 4 5 Summary of interactive operations within the pipeline 95 6 4 06 Warning messages of the pipeline llle 95 6 5 Working on the pipeline output 2 a a a 97 6 5 1 Displaying the whole images on ds9 97 6 5 2 Displaying the extracted images on ATV 97 6 5 3 Checking for wavelength zero reference point with the zero th order light WMA GC Sy dct A A AO eke od ert n ta e se go Mese 98 6 5 4 Spectral plotting tool 2 0 ee 98 6 5 5 Working on saved data oaoa aa ee 101 6 6 Hopefully Useful Tips veces athe Eck EY aoa ww lew ieee eee Bes 101 6 6 1 Getting best S N spectra in slit Ns Nh or Np spectroscopy data 101 6 6 2 Tackling narrow spikes seen in NIR spectra especially in slit spectra 101 6 6 3 Examining strange fake features in NP spectra especially around 2 4 3 5 FUE Se ca SS se eco tig E ed ES INTER Blea cioe d tenes BR tale Reece al Neg 102 6 6 4 Examining flux level in consistency among different disperser data 102 620 Appendix 2 25x ate hoes Bk hee a RS ee Ses WS ae eee ens 103 6 7 1 Variable name conventions 2e 103 6 7 2 Summary of Commands and their Options
63. a failure in the pipeline at a later stage downstream the best strategy may be an iterative run where if a crash occurs the individual frames can be examined and the culprits excluded from future runs of the Green Box The data frame taken during the maneuver can be also automatically discarded so you need not examine each frame and edit irclog e darklist before In a pointing observation a dark frame is taken at the beginning and the end of the operation for both the NIR and MIR channels This file contains the names of the dark frames taken at the beginning of the operation Dark frames taken at the end of the operation may be affected by latent so they are excluded from the list Those who want to use this pre dark images insted of super dark images should turn the selfdark parameter on described later in pipeline section then the pipeline prpcessor willl read the darklist before file and will instead make a dark image by averaging over 3 images of MIR S and MIR L long exposure dark frames However super dark will be used for all short frames and NIR long frames even if selfdark is on Table 5 8 1 Sample of the irclog file ZFRAME OBJECT NAXISI FILTER RA SET DEC SET AOT EXPID TIDNUM SUBID _ F004160544 L00I LMC FIELD218 250 DARK 80 546088 68 17107 IRCO 1 2210218 X 1 7 F004160544 L002 LMC FIELD218 256 DARK 80 54688 68 17107 IRCO2 2 2210218 1 7 F004160544 L003 LMC FIELD218 256 DARK 80 54688
64. able 4 8 13 Color Correction factors for MIR channel Gray Body a 2 Intrinsic MIR 5 57 MIR S S9W MIR S SI1 MIR L L15 MIR L L20W MIR L L24 Temperature K K 7 0um K 9 0um K 11 0um K 15 0um K 18 0um K 24 0um 40 80 578 9 482 8 362 0 890 50 88 714 10 821 4 108 3 417 0 864 60 13 417 3 932 2 513 2 044 0 875 70 866 347 5 731 2 228 1 847 1 500 0 897 80 95 149 3 460 1 582 1 508 1 238 0 923 90 19 552 2 451 1 275 1 313 1 097 0 949 100 6 900 1 909 1 110 1 192 1 015 0 974 110 3 696 1 586 1 016 1 112 0 966 0 996 120 2 559 1 379 0 961 1 057 0 936 1 017 130 2 034 1 240 0 928 1 017 0 919 1 037 140 1 740 1 142 0 910 0 989 0 909 1 054 150 1 553 1 073 0 901 0 968 0 904 1 070 160 1 424 1 023 0 899 0 952 0 903 1 085 170 1 330 0 987 0 901 0 939 0 903 1 099 180 1 258 0 961 0 907 0 930 0 906 1 111 190 1 202 0 942 0 914 0 923 0 909 1 123 200 1 158 0 929 0 923 0 917 0 913 1 133 210 1 122 0 921 0 933 0 913 0 918 1 143 220 1 093 0 915 0 943 0 910 0 923 1 152 230 1 068 0 913 0 954 0 907 0 928 1 161 240 1 048 0 913 0 965 0 905 0 933 1 169 250 1 032 0 914 0 976 0 904 0 938 1 177 300 0 980 0 939 1 031 0 902 0 962 1 208 350 0 957 0 976 1 079 0 904 0 983 1 233 400 0 948 1 016 1 121 0 907 1 000 1 253 450 0 946 1 055 1 157 0 910 1 015 1 269 500 0 947 1 092 1 187 0 914 1 028 1 284 600 0 953 1 156 1 235 0 920 1 048 1 309 700 0 960 1 209 1 272 0 926 1 063 1 329 800 0 967 1 251 1 300 0 930 1 076 1 348 900 0 974 1 286 1 322 0 934 1 086 1 364 1000
65. able NOADS Attitude information not available STTINI STT did not work properly More status may be added as analysis progresses Data other than GOOD may not be in the archive at the first stage e instrument information ORIGIN is the organization creating FITS file TELESCOP is the AKARI mission Satellite Name INSTRUME is the Identifier of the instrument DETECTOR is the detector name either NIR or MIR e observation details OBSERVER is the PI Name Observer s ID PROPOSAL is the Proposal ID OBS CAT is Observation Category either LS MP OT DT CAL or ENG PNTNG ID is the Pointing ID Usually it is identical with the Target ID but is different for parallel mode observations TARGETID is the Target ID SUBID is the Target Sub ID OBJECT is the Object name OBJ RA is the RA Target position in degrees recorded in the database double pre cision OBJ DEC is the DEC Target position in degrees recorded in the database double precision AOT is the Observation AOT AOTPARAM is the AOT Parameters set INSTMODE is the Instrument operation mode Contents TBD TIMESYS is the Time system used in this file DATE OBS is the Observation start date time with format YYYY MM DDTHH MM SS DATE END is the Observation end date time Same format than above DATE REF is the Reference time in the Observation Same format than above AFTM O
66. akeircbinaries e ees 2222s 5 4 6 Run setpath p 22e SAT Perl paths 274 e 2 uos Lm e RS auti Sus At at aede a 5 4 8 Add IRC entry to IRAF aaa How to UPGRADE the version of IRC imaging toolkit Setting up your toolkit environment and running the pipeline 5 6 1 Creating the directory structure les 5 0 2 Daunch IRAE pour idw ke ee Es Gt Ek Red Yum ee RS 5 6 3 Load the IRC package 2e The pre pipeline processor Red Box less 5 751 Configuration 204 243 Re PR ox Paha Wo wo X RR XU SE 5 7 2 Running the prepipeline processor lees Before runnning the pipeline processor 22e The pipeline processor Green Box 22e 5 9 L Configuration o z 2o was eq e bee Gee e EP H dq bo Be eas 5 9 2 Running Green Box pipeline module 2 4 The pipeline processor Blue Box bluebox coadd wrapper Module 5 10 1 The Blue Box Co Add Wrapper es 5 10 2 Log files produced from the toolkit 2l ln The IRC TOOL GBesbonl koe uem a uela eatis us de BAM eMe Ur cba os Toolkit SUructUre uu ee pt ete un ee A CER re Vie ngo E et ee e 4 Worl ng on thevotitputs siae eges rose det IgE ae RR P ee RR D HOD eas Limitations of the functionalities in the current version of the imaging toolkit 5 14 1 Instrumental characteristics and artefacts in the data 5 14 2 Toolkit Limitations and Caveats cnn Error
67. alue across the images for all dispersers 6 1 14 Spectral tilt correction Although we do not reform the image shape along the wavelength direction during the course of wavelength calibration because of simple linear grism dispersion we do reform along X or space direction to correct spectral tilt The tilt occurs due to misalignment of grism insertion direction with respect to chip orientation The tilt is notably seen in NG images in which a pixel shift as large as AX 2 is observed over the longer dispersed image length AY 250 pixel Similar tilt is also observed for other prism grisms NP SG1 SG2 and LG2 although the tilt looks very small due to short dispersed image length However a tilt correction will be made for spectra of all types of dispersers 6 1 15 Spectral response calibration The spectral response calibration R X depends exclusively on the wavelength Therefore the response calibration table is a 1D vector lambda vs ADU s mJy This means that response variations of individual pixels have been removed beforehand by flat fielding processes Being 86 IRC Data User Manual different from the spatial flat correction the spectral response varies significantly with wave length due to change in quantum efficiency of chip and change in optical transmission along the camera optical trains including the disperser The observed wavelength calibrated 1D spectrum in ADU is just divided by the spectral response table
68. an to increase the exportable platforms by ourselves The toolkit also uses the ds9 FITS viewer and the xpa package for communication between the ds9 and the IDL main program The spectroscopy data reduction requires a calibration database FITS images and ascii tables distributed and updated by the IRC spectroscopy data reduction team The database is based on observations of calibration objects and calibration frames taken during PV D T phase observations as well as pre launch calibration experiments in our laboratory Therefore observers do not have to make their own calibration observations 6 1 General overview of the pipeline processing The main pipeline processing consists of several well defined steps which are explained in the following sections In general terms the IRC slitless spectroscopy differs from more standard slit spectroscopy in that in the latter case the pixel position and the wavelength are closely correlated The IRC spectroscopy does not follow this relation and needs to be applied in three steps e Many spectroscopic flats have been combined to form a super flat which can be used to remove the pixel to pixel variation of the monochromatic response of the detector e After subtracting the background extracting the sources and performing the wavelength calibration the wavelength flat can be used The wavelength dependency of the flats is due to the same mechanism to that of imaging mode and is corrected by interp
69. and is typically 0 6 or larger for real data with noise but peak of 0 3 is still good When this warning appears check the quality of the registered and stacked images So far registration of the short exposure frame can not be made with good enough accuracy and one should ignore this warning for short exposure frames This message is not so serious in most of the cases Warning ROB MAPFIT Too few points This message comes from the fitting routine ROB MAPFIT called from some of the toolkit programs The routine tries to fit the image region robustly e g excluding outliers iteratively etc but it sometimes fails when the fitting area is heavily masked out for some reason However it somehow return the result even if the results are not reliable in terms of statistics Users may ignore the messages Warning strange spec file list Stop The irc specred reads list of FITS files to be processed NP Ist NG lst SG1 Ist SG2 1st LG2 lst When something wrong happens during data acquisition i g too much time before stabilizing the telescope point ing telemetry downlink e g loss of telemetry and or data handling at ground e g disk storage failure the listed available FITS files are not in a proper order Observers may notice that the list misses one or more FITS files due to some of these reasons The toolkit analyze the file list before actually processing the data and warns the uses if it detects something strange Upon th
70. are stored in ircroot lib anomalous pix They are shown in Fig 5 9 11 After masking bad hot pix els an a will be added as a prefix to the original filename such that F23342 8004 fits becomes aF23342 8004 fits 2 Wraparound Correction greenbox wraparound Due to data volume constraints the IRC compresses the data when it is transmitted to the ground by discarding the data sign bit This will cause obvious ambiguities in the corresponding flux values Since the IRC data structure uses the 2 s complement method to represent negative numbers discarding the sign bit most significant bit will result 64 IRC Data User Manual GREEN BOX Pipeline Processor Figure 5 9 10 Present configuration of the Green Box pipeline modules Figure 5 9 11 Mask files for NIR MIR S and MIR L from left to right Outlier pixels have value of 0 white and others 1 black so any outlier pixels will be masked out by mutipling these mask files to images of concern Version 1 4 May 30 2008 65 in apparently extremely large positive numbers for negative values thus pixels suffering from this effect may appear as hot or dead in the image plane However these values are designed to be smaller than the saturation limit of the detectors such that values higher than the maximum saturation levels must in fact be wrapped negative numbers This correction is made by Acorrected Auncorrected 2 5 9 1 for any pixels that have a pixe
71. arge telescope jitter motion is observed To measure such motion run the pipeline for slit less mode without any slit processing option in the pipeline command e In the wavelength calibration measurement of the reference image positions will not be made and pre defined slit positions will be used as a wavelength zero reference point 6 2 How to install and to set up the IRC spectroscopy pipeline The package has been tested in a Linux environment It seems to run on the MAC OS X environment though it is not officially supported e Ask you local computer administrator for the IDL installation There are no special re quests in the IDL installation e Ask you local computer administrator for the ds9 xpa installation There are no special requests in the ds9 xpa installation e Get the irc_specred package from the AKARI Observer s web site see section 1 2 Extract and store it under your favorite directory e Set the following environment variables in your command line shell Below is an example for csh setenv IRC_SPECRED_ROOT somewhere setenv IRC_SPECRED_LIB IRC_SPECRED_ROOT LIB setenv IRC SPECRED HOME IRC_SPECRED_ROOT ASTRO F Version 1 4 May 30 2008 87 setenv IRC_SPECRED_CALIBDIR IRC SPECRED HOME IRC SPECRED CALIBDIR setenv IRC SPECRED DATADIR lt anotherwhere gt setenv IDL PATH lt IDL system path gt IRC_SPECRED_HOME IRC SPECRED LIB IRC SPECRED ROOT IRC SPECRED DATADIR and IDL PAT
72. as for other AOTs for both short and long exposures whereas that for the long exposure of NIR is longer than others and is made with the Fowler 16 sampling scheme instead of the Fowler 4 sampling 2 2 6 IRCI11 The IRC11 was designed for wide area observations or slow scan observations with the IRC Only the MIR S and MIR L channels can be used in the IRC11 The arrays are operated in the same manner as in the all sky survey mode making binning of 4 pixels in the cross scan direction On the orbit the data downlink capacity was found to be sufficient to transmit the full resolution data in the IRC slow scan The unbinning mode is now designated as IRC51 and all the IRC slow scan observations from 2007 January are executed with the IRC51 mode 2 2 7 IRCS51 This is the same slow scan mode as the IRC11 except that the IRC51 provides the full spatial resolution without binning in the cross scan direction All the IRC slow scan observations after 2007 January are executed with IRC51 2 3 In orbit sensitivity Optical thougputs of all IRC channels are confirmed to be as expected by observations of stan dard stars The sensitivity values for the imaging AOTs are collected in Table 2 3 3 The IRC05 numbers are preliminary In the case of IRC04 Figures 2 3 7 and 2 3 8 show the sensitivity lo noise with 2 x 2 binning and the trhoughput of the system respectively as a function of A 12 1 o Noise Equivalent Flux mJy 0 1 0 01
73. asons for the jump and tips to solve the problem e Source contamination Degree of contamination changes with wavelength and hence with dispersers causing flux change across the dispersers User needs to check the reference image as well as spectroscopy images to find possible contaminating sources There are no good recipes to remove the contamination e Aperture centering Check the aperture position along X or space to see if the aperture is really at the peak of the dispersed images The toolkit tries to put it at the right position by tracking the telescope jittering motion but it is not always perfect Use space shift option of the plotting tool along with with image option to find the best position See section 6 5 4 for actual operation e Aperture correction uncertainties Aperture correction is not always perfect because one needs to adopt rather narrow aperture nsum 3 or so for achieving the best S N If this is the case even a small shift of the aperture position on sky even at a scale of sub pixel although space shift should be given in an integer pixel unit gives rather large uncertainties in the flux aperture correction Note that spectroscopy data relies on 1D spatial PSF of the source and the pixel scale is not high enough to sample the PSF at good enough accuracy So with these limitations in mind one needs to check the flux level by changing the nsum and or space shift parameters for your own source and its brig
74. ause the color term correction actually cancel out the spectral feature correction For flat fielding slit spectra including NG with the point source aperture Np the super flats are typical for conventional slit spectroscopy These flats are also made by combining a large number of blank sky spectra At present there are only two slit flats for NG at Np and Np at Ns The others NG at Nh SG1 2 at Ns and LG2 at Ls are in preparation 4 3 Instrument linearity Detector linearity was measured in the laboratory before launch and later in flight Measure ments wre made with a calibration lamp that illuminates the detector and an increasing range of integration times At first it was assumed that the detecter behaves linearly below 5000ADU and was fitted with a linear curve by a least squares method Fig 4 3 3 shows the raw signal in ADU versus the fit in ADU signal expected if the detectors were to behave linearly The deviation of the raw signal from the linear expectation was then calculated and correction equa tions by fitting polynomials up to 7th order were applied The red lines in Fig 4 3 3 represent the calculated correction equations Fig 4 3 4 shows how the calculated correction equations work After the correction the error from the ideal linear curve is better than 5 at 12000 20000 and 20000 ADU after ircnorm for NIR MIR S and MIR L respectively Note that from Fig 4 3 3 the physical detector saturation occurs around 12
75. be lost Therefore any previous coadd failure log should be renamed prior to running the coaddLusingS function e coaddition of multiple pointing observations In principle the IRC toolkit will attempt to process and coadd all the frames from any number of pointings in the working directory It should be noted however that no such functionality is available within the coaddLusingS function and only frames corresponding to a specific pointed observation may be coadded at any one time This facility may be included in later versions of the toolkit Figure 5 14 18 Difference in flats for MIR S S11 band for epochs prior to left and after right 2007 01 07 5 15 Error messages when running the pipeline and Troubleshoot ing 1 The pre pipeline stage sometimes give an error message such as 1s rawdata No such file or directoryorcat slice tmpO0 No such file or directory etc al though the pre pipeline seems to run correctly Typing unlearn all should clear these error messages 2 The distortion processing green box processing can give the following error message causing the pipeline crash 4 DISTORTION 4 454 Making the input file list Correcting distortion This may take a while ERROR on line 56 Cannot open file Version 1 4 May 30 2008 79 iraf irc lib distortion DARK_distortion_database dat distortion ircconst constants database logfile irclog prefixs mslnDwa verbose no pipeline This is be
76. blank sky images For slit less spectroscopy FLAT SPEC2DFLAT NP 1st FLAT SPEC2DFLAT_NG 1st FLAT SPEC2DFLAT SG1 1st FLAT SPEC2DFLAT SG2 1st FLAT SPEC2DFLAT LG2 1st For slit spectroscopy FLAT SPEC2DFLAT_NP_slit 1st In the following contents within the parentheses something should be changed according to user s interests IRC Data User Manual For reference images and color term correction of the flats FLAT IMAG2DFLAT N3 1st FLAT IMAG2DFLAT_N4 1st FLAT IMAG2DFLAT S7 1st FLAT IMAG2DFLAT_SOW 1st FLAT IMAG2DFLAT_S11 1st FLAT IMAG2DFLAT_L15 1st FLAT IMAG2DFLAT_L18W 1st FLAT IMAG2DFLAT_L24 1st e IRC_SPECRED_CALIBDIR MASK contains images of known bad pixels hot pixels cold pixels etc Masked area are marked by NaN Not a Number in the mask images MASK SLITMASK_NIR 1st MASK SLITMASK_MIRS 1st MASK SLITMASK_MIRL 1st MASK OUTLIERMASK_ NIR 1st MASK OUTLIERMASK MIRS 1st MASK OUTLIERMASK MIRL 1st e IRC_SPECRED_CALIBDIR COORDOFFSET contains a table of coordinate offsets in pixels dX dY used to extract spectroscopy images for each object based on target positions on the reference image for all dispersers The table also includes sizes of source extraction boxes AX AY on reference and spectroscopy images and offsets dX dY for zero th order light image position COORDOFFSET IRCCOORDOFFSETPAR dat e IRC_SPECRED_CALIBDIR WAVEPAR contains the wavel
77. bservations In a pointed staring observation the IRC observation is started once it receives the notifi cation of the stabilization of the attitude from the attitude and orbital controlling system The IRC observation continues till the angle between the telescope axis and the earth rim becomes 10 IRC Data User Manual less than a certain value Thus the last image in a pointed observation may be taken during the maneuver and cannot be used for astronomical observations This will be correctly treated in the pipeline software Manuever z Figure 2 2 6 Observation sequences of the AOT IRCOO 02 03 04 and 05 Yellow boxes labeled as Exposure cycle indicate exposure frames Orange boxes with M are Micro Scan operations including stabilization and light blue boxes with W are Filter Wheel rotations Dead time for a Filter Wheel change depends on the relative position of the elements The Green area on the right side is the extra observation time which is not guaranteed 2 2 1 IRCO0O0 The IRC00 mode was designed for deep imaging observations After performance investigation in orbit it has been replaced by IRCO05 and is not in use 2 2 2 IRCO02 The IRC02 mode was designed for general purpose imaging observations that take images with two fixed fil
78. c_tool package there is additional independent software the coaddLusingS function that performs the calcula tion of the shift and rotation of each frame using the information from the MIR S channel to coadd the MIR L images In the working directory typing irc tool at the IRAF prompt will enter the irc_tool environment and the coaddLusingS function should be visible in the iraf terminal To use this software type coaddLusingS at the IRAF prompt and it will ask for the name of a reference MIR S list name e g pair0002_S7 list_ long from an already successfully coadded MIR S image to perform the coadding Other additional parameters may be requested but the default will be sufficient for most users After the parameters have been set coaddLusingS will coadd the corresponding MIR L images automatically and move them to the stacked IM directory Note One needs to make sure that the correct corresponding MIR S file is used with the desired MIR L file As an example In the irclog the appropriate corresponding filter pair can be selected using the the same file number F40813 As raw data all these files are packed into a single fits file Pre pipeline slices the MIR fits file into the 8 4MIRS 4MIRL files Version 1 4 May 30 2008 TT ell halk BOD f Figure 5 14 17 Background levels F40813_L001 NGC104 256 L18W 5 293348 72 44307 IRCO3 1 5020012 F40813 L002 NGC104 256 L18W 5 293348 72 44307 IRCO3 2 5020012
79. cat NP 1st F000002 N fits F000004 N fits F000006 N fits A default list is provided with the data distribution and is found in rawdata directory Even if you find some images being damaged severely and you do not want them to be included in the pipeline processing you must list all the images in the input list Then you should specify the sub frames to be removed on ds9 within the pipeline This is because the file names and their order in the list are used to relate FITS files to the exposure timing along the AOT operation sequence e filter spec a string specifying a disperser for the processing Set one of the following N3 NP N3 NG S9W SG1 S9W SG2 L18W_LG2 92 IRC Data User Manual 6 4 3 Options root dir a string specifying a directory in which a set of data is located If set this overrides the setting found in the environment variable IRC SPECRED DATADIR Example root dir DATA ASTRO F IRC SPEC Nh spec Ns spec Ls spec flags for slit spectroscopy data reduction Np spec a flag for Np spectroscopy data reduction See section 6 1 16 for more information of slit spectroscopy data reduction no tune sourcepos a flag for disabling source position tuning subprogram within the pipeline By default irc specred tries to measure accurate source positions by searching Gaussian peak around the coordinates set in the target table This flag disables this functionality use short refimage use a short expo
80. cause the DARK entries should be removed from the irc log file 3 The coadd stage can result in the following error Hitt COADD jh Making the input file list Extracting sources Calculating XY shift Adjusting sky level Coadding images ERROR on line 148 parameter direction not found This problem may be caused when using versions of RAF earlier than IRAF 2 12 2 The problem is with georytran task eparimages immatch geoxytran can be typed in the IRAF shell to see if the parameter exists Even after installing the newer version of IRAF it is necessary to type unlearn geoxytran before the toolkit runs correctly 4 The pre pipeline run can apparently miss some perl scripts and end with an empty or non existing irclog file HHH MKIRCLOG 44454 Making the file list Reading header This may take a while tcsh iraf irc perl formatlog pl Command not found tcsh iraf irc perl checkname pl Command not found 444 MKIRCLOG finished Primarily it has to be checked that the toolkit is being run from the working directory and not for example in iraf If the problem persists then it may be because perl is in the wrong place Perl should be in usr 1ocal bin perl therefore a symbolic link should be set up from the perl library to usr 1ocal bin perl type whichperl to find out where perl is currently hiding 5 If a new version of the toolkit crashes as a first fix unlearn_all should be typed within irc
81. ce IRC 3D images into usual 2D ones e redbox mkirclog making the observing log file irclog The prepipeline processor is run by entering prepipeline at the IRAF command prompt Alternatively the individual Red Box modules can be run by entering redbox at the IRAF command prompt The present configuration of the pre pipeline modules is shown in Fig 5 7 5 Figure 5 7 5 Present configuration of the Red Box pre pipeline modules 1 redbox ircslice The number of FITS files produced for any given single pointing will depend on the AOT Each AOT comprises of a combination of exposure cycles EC Filter Wheel changes W Version 1 4 May 30 2008 57 and Dither Maneuvers M see Fig 2 2 6 The IRC FITS data is not a usual 2D one A raw data FITS file is created for each Exposure Cycle during a pointing for the NIR and combined MIR S MIR L channels i e 1 NIR FITS file and 1 MIR FIT file 2 FITS files per Exposure Cycle The filename format is given as F _N fits or F M fits where is a distinct incremental reference number A NIR raw fits data file is a data cube containing 2 frames within it corresponding to one short and one long exposure Each MIR raw FITS file contains 4 frames within it one short and three long exposures for both the MIR S and MIR L channels respectively making a total of 8 frames per MIR FITS file per Exposure Cycle see Fig 5 7 6 In addition to the Exposure Cycles a Dark frame is taken at
82. ce_id gt options lt source_id gt a number that specify the source to be plotted You can find the number by looking at the ds9 window that displays whole image products short a flag to display short exposure spectra One needs to set specimage_wc_short instead of specimagen_n_wc in the plot spec with image command nsum number of pixels along X axis combined for plotting This nsum parameter also works for diffuse option smooth boxcar smoothing width in pixel along wavelength direction sigma filter a flag to enable sigma filter operation at 3 sigma significance level over 2D spectra to remove spatially isolated high or low count pixels space_shift shift of the plot extracting box along X spatial axis in pixel no_mask a flag to disable masking functionality i e plotting spectra regardless of the possible source overlapping ps root filename of the PS graphical output lt ps gt ps of the spectral plot png root filename of the PNG graphical output lt png gt png of the spectral plot ascii root filename of the ASCII numerical output lt ascii gt spc of the spectra with image a flag to display 2D image below the spectral plot diffuse a flag to convert flux scale to MJy str for slit spectra no aperture correction a flag to disable aperture correction factor in plotting the spectra xrange yrange parameters to specify plot range
83. ct and replace cosmic rays in MIR images e greenbox linearity Correct linearity of the detector response e greenbox saturation Mask saturated pixels e greenbox slit mask Masks the slit area of IRC field of view e greenbox flat Flatten the pixels e greenbox aspect ratio Distortion Correction Aspect ratio resampling Alternatively the individual Green Box modules can be run interactively by 3 possible meth ods 1 By setting the interac parameter in the parameter list 2 By running the pipeline with the command pipeline interactive yes 3 By running the pipeline with the command pipeline interactive When running the pipeline interactively individual steps may be entered as Greenbox anomalous pix Greenbox dark etc or alternatively by typing Greenbox then running from inside the Green Box as anomalous pix dark etc When running interactively there are options to perform skip stop each process The present configuration of the Green Box pipeline modules are shown in Fig 5 9 10 Starting from the original input FITS file e g F23342 S004 fits At each step of the Green Box pipeline processing a qualifier is added as a prefix to the original filename note the original FITS files are preserved These prefixes build up over each processing step The prefixes are summarized in Table 5 9 2 1 Mask bad or dead pixels greenbox anomalous pix Bad or dead pixels were identified by using pre flight laboratory data Mask files
84. cted is about 5 pixels from the left edge and 40 pixels from the bottom and right edges No scattered light is appreciated in the top edge This can be explained by the fabrication of the aperture mask The correction for the scattered light is being investigated and will be included in the nex versions of the pipelines 3 MIR L The flat pattern of the MIR L in orbit is different from that in the laboratory It shows a large scale gradient over the array Part of it may come from the scattering of light in the MIR L camera but we have not been able to identify the cause yet The investigation is ongoing For the time being observers should take care of diffuse structures in the MIR L data as they could be spurious In the worst cases overlapping MIR L observations can show 1096 difference corresponding to the flatfield inaccuracy in the corners 24 IRC Data User Manual 4 2 2 Flats for spectroscopy images The spectroscopy flatfields are images made by a large number of blank sky spectroscopy images combined and normalized so that any faint object spectra are removed by clipping averaging techniques There are five super flats corresponding to NP NG SG1 SG2 and LG2 As will be described at the end of this chapter these flats show spectral features which are not due to the sensitivity variation Therefore object spectra should not follow the flat pattern However this super flat with spectral features is used in the data reduction bec
85. d source masks are created for better background subtraction from individual sub frames section 6 1 4 in the second pass of the pipeline processing 6 1 10 Extracting 2D spectra By using the reference image positions and pre defined coordinates offsets in the calibration database rectangle areas around the source spectra are extracted on the spectroscopy images For NP spectral distortion see below is taken into account along the dispersion direction to find best Y offset when extracting 2D spectra X offset adjustment in spectroscopy image extraction In real data one need to further adjust the offset of the source extraction boxes One may some times find 2D spectra slightly away from the expected position at the center of the extraction box along X axis This kind of shift cannot be corrected in the previous image registration processes and the correction is made at this stage The center position of the 2D spectra is measured for each extracted 2D spectra and the mean X offset from the center of the extraction box is calculated If the pipeline successfully finds the shift value the shift will be applied in extracting the 2D spectra However for some cases where only very faint objects were detected calculating this additional shift may fail and no further shift is applied Measuring the X offset and making good source masks as explained in the previous section are closely related to each other during the pipeline processing I
86. default yes de activate if you do not want to try to coadd images This option is useful for users who have their own coaddition strategy and software default boolean yes or no default yes This parameter defines which flat is used in the toolkit De activate if you want to use your own flat images instead of using the toolkit default flats In that case you have to prepare flat images for nine filters N2 N3 N4 S7 S9W S11 L15 L18W and L24 and put them in where you installed irc lib flat user Their file names should be named as those of the flat images in where you installed irc lib flat soramame ari verbose boolean yes or no default no activate if you want to print verbose progress messages Figure 5 9 9 Area utilized for the Co added images depends upon the parameter com area The 2 options are common area red region and whole area within green dashed region 5 9 2 Running Green Box pipeline module The Green Box pipeline processor can be run by entering pipeline at the IRAF command prompt The Green Box pipeline produces the basic calibrated data and currently consists of the following steps Version 1 4 May 30 2008 63 e greenbox anomalous pix Mask Bad Dead pixels e greenbox wraparound Corrects for wraparound e greenbox dark Subtract dark current e greenbox ircnorm Normalization for sampling and data compression e greenbox scatt light Subtract scattered light pattern e greenbox cosmic ray Dete
87. e no mask by default plots are shown after applying spectral overlapping masks by nearby sources The no_mask option disables this masking functionality and plot spectra regard less of the possible source overlapping Since masks are created without examining the source brightness and or spectral shape e g line emitters continuum emitters with break etc one may often find the situation where no significant change in plots is found when comparing plots with and without the masking If this is the case you can just disable the masking by setting no mask option This option is especially relevant when the source of interest is much brighter that the overlapping ones ps png ascii Plots will be recorded on the files not on the IDL plot window ps lt filename gt creates a postscript file filename ps of the plot in the working output directory under irc specred out png lt filename gt creates a png image filename png of the plot in the working output directory ascii filename creates an ascii file A vs flux and flux errors filename spc of the plot in the working output directory This file can be used for further analysis for example using gnuplot program with the command of plot filename spc with yerrorbar with image tvbottom lt tvbottom gt tvtop tvtop The 2D image will be shown on TV an IDL graphic window below the spectrum plot Extraction box for plotting 1D spectrum is ov
88. e X axis If set explicitly in the plotting tool command line the default settings will be overridden yrange plot range along the Y flux axis By default plots are shown in auto scale mode along Y One can limit fix the plot range by setting yrange xlog ylog plotting in log scale along x or y 6 5 5 Working on saved data All the processed data are saved as an IDL save file as well as FITS output files The IDL save file is actually a dump record of the IDL memory image at the end of the data process ing Therefore one can recall the pipeline results by simply issuing the following command restore lt savefile gt Here the lt savefile gt is a string of the save file name To recall other save file image issue reset session first to clear the current IDL memory contents and then issue another restore command with another save file name See IDL manual to know more on the IDL save file restore and reset session commands After restoring the IDL memory one can use for example the following irc specred com mands to review the results e show aperture on ds9 specimage bg source table e show aperture on ds9 refimage bg source table imag e plot spec with image wave array specimage n wc mask specimage n source_table lt source_id gt 6 6 Hopefully Useful Tips 6 6 1 Getting best S N spectra in slit Ns Nh or Np spectroscopy data Due to the higher dispersion of NG spectra through narrower slit area
89. e following ID image_x image y image_mask_dx image_mask_dy spec_x spec y spec_mask_dx spec_mask_dy flux image_ FWHM spec bgnoise ADU spec_x_pos spec_x_FWHM bad sourcepos flag Target table If the source detection sub program is used within the pipeline a target table will be written The file format is similar to the input target table When source position tuning option is on this file contains the updated source coordinates lt targetid gt lt targetsubid gt lt filter_spec gt source_table tbl IDL save file The output of the pipeline will also be stored in the IDL save file which is basically a dump file of the IDL memory image at the end of the pipeline processing See also 6 5 5 to see how to work on the save file lt targetid gt lt targetsubid gt lt filter_spec gt IRC_SPECRED_OUT sav Log of the toolkit processing a copy of the irc_specred logger is saved as an ascii file lt targetid gt lt targetsubid gt lt filter_spec gt log DS9 region files DS9 region files that have been used to locate targets on reference and spectroscopy images on ds9 lt targetid gt lt targetsubid gt lt filter_spec gt refimage reg lt targetid gt lt targetsubid gt lt filter_spec gt specimage reg The region files and saved FITS images of the whole image products can be used to review the targets on ds9 manually e Pipeline work files The following files will be created by the pipeline The files will be overwritten wi
90. e wavelength array and spectral response curve both of which should show rather smooth change along Y or wavelength axis and not perform sub pixel shifting of the images As a result since object positions change slightly among different pointing observations the wavelength at the same Y pixel of the extracted 2D spectra or the wavelength array also changes with different pointing observations 6 1 12 Flat color term correction The presence of significant color variation in the flat images can be found in the ratio images of the broad band flats e g S7 flat S15 flat Therefore although monochromatic flat fielding can flat the background the object spectrum is affected by the color term of the sensitivity The correction for this could be done after extracting the 2D spectra for each target and applying the wavelength calibration However since we have only two broad band filters for MIR S MIR L S7 and 15 for MIR S and L15 and L24 for MIR L and three for NIR N2 N3 and N4 we Version 1 4 May 30 2008 85 can derive only global trends of wavelength dependence of the flats Note that the wide band filters S9W and L18W are not suitable for deriving the color dependence of the flat within the spectral coverage of the channel Two broad band flat images are interpolated to estimate the flats for a given wavelength in the following way F x y F x y A2 n F a y 1 22 a A1 x A z A1 F x y M 6 1 4 where
91. ebox irc stack Once every frame pointing at the same area of sky in the irclog list has been correctly matched and the sky brightness adjusted every frame is stacked to produce the final co added image The FITS images and files created from the stacking process can be found within a new directory stacked IM The stacking process creates 3 files for any given filter position on the sky e A co added image file e g 1757132 N2 long fits e A noise map e g sigma1757132 N2 long fits e Summary File e g p11757132 N2 long fits pl Figure 5 10 14 Example of final science grade data produced by the Green Box and Blue Box Co Add Wrapper left is the stacked image map right is the corresponding noise map 5 Convert to WCS coordinates bluebox putwcs After the Co add wrapper has been completed the module bluebox putwes adds WCS information to the FITS images by matching with 2MASS catalog coordinates using the following procedure a source extraction of stars from the IRC image b download 2MASS catalog for the observed area c convert 2MASS RA DEC to the x y image coodinates Version 1 4 May 30 2008 71 d match 2MASS x y coordinates with image xy coordinates At this point there will be a list for extracted IRC stars corresponding to stari x1 y2 rail deci x1 y2 star2 x2 y3 ra2 dec2 x2 y2 starN xN yN raN decN xN yN for the matched stars The module then calculates a transformation matrix Nth
92. ed to the estimated flux density vs the normalized ADU ADU t1 The slope of the fitted lines provides the conversion factors fo ADU toh Jy which are tabulated in Table 4 6 6 Using these factors we calculated conversion factors f ADU to Jy for short exposure data and fj ADU to Jy for long exposure data which are tabulated in Table 4 6 7 Table 4 6 6 Conversion factor ADU to unit to Jy Band fo error 76 Nstar N2 3 300 x 10 3 2 84 19 N3 2 580 x 10 5 2 54 16 N4 1 964 x 10 5 3 30 17 S7 2 86 x 10 5 2 30 31 S9W 1 596 x 10 5 97 11 S11 2 165 x 10 5 2 36 25 L15 4 735 x 107 2 82 33 LI8W 3 210 x 107 4 56 13 L24 1 370 x 10 4 4 72 20 Number of standard stars used 34 IRC Data User Manual Table 4 6 7 Conversion factor ADU exposure to Jy calculated from fo Band short exposure long exposure long exposure IRCO5 error 96 fs fi fi N2 4125 x 10 8 4 342 x 107 2 946 x 107 2 84 N3 3225x109 3 394 x 107 2 303 x 107 2 54 N4 2 455 x 10 8 2 584 x 107 1 753 x 107 3 35 S7 2 861 x 10 1 022 x 10 9 2 30 S9W 1 596 x 10 5 700 x 107 5 97 S11 2 165 x 10 5 7 732 x 107 2 36 L15 4 735 10 9 1 691 x 10 9 2 82 LISW 3 10 x 10 5 1 146 x 10 9 4 56 L24 1 370 x 1077 4 892 x 10 9 4 72 Long exposure for IRC05 4 6 4 Overall accuracy of the flux calibration The absolute accuracy for point sources based on observations of standard stars is less than 5 for all the bands The stability of the instruments are being monit
93. edge for NIR MIR S and MIR L respectively There is little difference with filters Fig 4 9 11 shows the distortion vector for N2 S7 and L24 respectively Table 4 9 14 shows the accuracy of the distortion correction L15 distortion database dat L18W distortion database dat L24 distortion database dat N2 distortion database dat N3 distortion database dat NA distortion database dat S11 distortion database dat ST distortion database dat S9W distortion database dat Table 4 9 14 Accuracy of the distortion correction in units of pixels In summary except for L24 the accuracy is about 0 1 pixel N4 may be slightly worse The bad value of L24 comes mostly from scarcity of good bright sources and the matter of statistics With the accumulation of the data it could be improved distortion vectors x20 distortion vectors x20 ere paer 250 T T r r q a 2223127 Bp ph hb bee YAYAAL OOD PPP PELE eS gt beh bbe ker V VYAALS OOD pb bs TEE drca t Wok o bob dod Y ES X x dew 400 Pres LLLA RO 20A A 4 L kEkkkY YA MILLAS E ae a a RR XxLXXx TAS LRL MAR a a a oa E lt Ld date 300 2222 IIT wok ALLL LAAN RA a ex fee oo Fh 4 LL 4 4 EYNMR gt D gt gt er LT 12Z112E 2222223 B hse sc sss Yaa po yy rrr amp xxt a e lt cc lt lt gt gt gt gt gt ee LLL LAND pore Or OTD 200 YS Pte OL a a k a y yTTTTTT X KS gt gt e 24113333 44 a o a OOO TTT XA p pr die d
94. ength calibration tables For grisms NG SG1 SG2 LG2 the wavelength jum is expressed by a 1st order polynomial linear equation and parameters are 1 dispersion dA dY 2 wavelength at origin Ao and 3 position of the origin Yo In the toolkit the position of the origin is fixed at the center of the extracted spectroscopy image Therefore only dispersion and wavelength at the origin are set in the calibration database files The parameters can be applied for all the spectra within the FOV i e the parameters are constant across the FOV Effective wavelength ranges for each disperser are also set in the table there are two kinds of range definitions sensitive and reliable ranges For NP the pixel position for a given A is expressed in a 2nd order polynomial equation defined through three parameters Oth 1st and 2nd order coefficients Note that for data analysis convenience the equation is in pixel function A form being in inverse form for the grisms Effective wavelength ranges are also set in the table Only for NP significant spectroscopy distortion exists i e reference positions on the spec troscopy images cannot be represented by a constant pixel shift dX dY from reference image positions The deviation of pixel shift along wavelength axis or Y axis from the case of constant pixel shift is expressed in 3rd order polynomial equation of reference posi tion dYaistortion function Xref Yref Polyn
95. enough by averaging the offsets measured for many stars Once the offset is measured extraction of the 2D spectra is made again after considering the Y offset as well as X offset as explained earlier The zero reference point is much difficult to be found in NG spectra due to lack of no table spectral features before applying the flux calibration Therefore although the toolkit can estimate the reference point by examining the observed spectroscopy images it is strongly recommended to check the zero th order light images for more accurate wavelength calibration The chance of detecting zero th order light image at significant level for SG1 SG2 and LG2 is not so large Therefore the drift of the wavelength zero reference point is calculated by using the drift measured in NP or NG for MIR S L grisms after correcting the pixel scale difference Another issue related to measuring the wavelength zero reference point is the finite pixel resolution Although the source positions can be measured with an accuracy of less than one pixel size unit on the reference image the extraction of 2D spectroscopy images can only be made on integer pixel number to avoid erroneous image interpolation This means that a pixel error as large as 0 5 could be introduced in the wavelength calibration process if not corrected and is not so small comparing with the full length of the dispersed spectroscopy images 50 pixel As a first order correction we shift both th
96. erlaid The default is with image O0 i e no TV display The top and bottom ADU counts for displaying image can be specified with tvtop and tvbottom These options are active only when with image is set diffuse For slit spectroscopy data spectra will be shown in units of MJy str rather than mJy with this option The diffuse flux calibration is not yet fully established Before this flux scale conversion both nsum and space shift parameters are taken into account to specify the spectral extraction aperture to create the spectrum for plotting no aperture correction Aperture correction for point like sources will be applied au tomatically within the plotting tool The aperture size set by nsum is taken into account to find the correction factor When the no aperture correction option is set the cor rection will be disabled To perform good aperture correction the aperture is centered on the source and nsum should be 3 or more Note that the aperture can be shifted by Space shift parameter Other generic plot options useful in the plotting tool The plotting tool accepts any kind of IDL generic plot options for spectral plotting See plot manual in the IDL documents for full information Version 1 4 May 30 2008 101 Following are some frequently used options xrange plot range along the X wavelength axis By default plots are shown within the wavelength range set in the wavelength calibration database file along th
97. ers Each exposure cycle is made up of 1 short and 3 long frames For AOT IRCO02 IRC03 exposures are always separated by dithers etc and the problem does not arise however for IRC05 IRC00 IRC04 they are not necessarily sepa rated The problem is occurring on contiguous exposure cycles i e nothing in between For example short1 long1 long1 long1 short2 long2 long2 long2 The bad frames are the short2 frames i e those following a previous contiguous exposure cycle This effect extends to the short frame of the final dark even This problem may be critical for spectroscopy of bright sources with IRC04 however for IRC00 amp IRC05 users the effect may not prove critical since users may disregard the short frame since these AOTs are intended for deep imaging the processing of the short frames may be disabled from the Green Box pipeline parameter list 5 14 2 Toolkit Limitations and Caveats e MIR S flat changed As informed via the the AKARI user support web page the flat of MIR S changed early this year 2007 In response new flat data for MIR S has been made available and should be used in preference to the old flat data for observations after 2007 01 07 02 49 00 In particular the pattern in the lower right corner of the MIR S has disappeared after this epoch see Figure 5 14 18 We are planning to include the flat data in each observation but at this stage the flats may be replaced by either 1 replacing the fits files in i
98. es Dark subtraction flat fielding and background sub traction are made lt targetid gt lt targetsubid gt lt filter_spec gt specimage_bg fits lt targetid gt lt targetsubid gt lt filter_spec gt specimage mask fits lt targetid gt lt targetsubid gt lt filter_spec gt residual_specimage_bg fits These images are in 3D being the third Z dimension for the short Z 0 and long Z 1 exposure frames NaN Not a Number represents masked pixel area e Extracted image products Extracted reference images for individual targets lt targetid gt lt targetsubid gt lt filter_spec gt refimage_bg_indiv fits Extracted spectroscopy images for individual targets and corresponding mask im ages There are two kinds of images One is wavelength calibrated _WC image for which flat color term correction and wavelength calibration were applied The other are flux calibrated _FC images for which flux calibration was applied as well as flat color term correction and wavelength calibration lt targetid gt lt targetsubid gt lt filter_spec gt specimage_wc_indiv fits lt targetid gt lt targetsubid gt lt filter_spec gt specimage_mask_indiv fits lt targetid gt lt targetsubid gt lt filter_spec gt specimage_fc_indiv fits lt targetid gt lt targetsubid gt lt filter_spec gt specimagenoisemap_indiv fits Note that our spectral plotting tool see below uses _WC image as an input not the FC image since the tool does
99. espectively SAT POSX is the Satellite position at DATE REF in km SAT POSY is the Satellite position at DATE REF in km SAT POSZ is the Satellite position at DATE REF in km DAYNIGHT is the Day night status at DATE REF These fields are updated as pointing analysis goes on from On board AOCS to G ADS Pointing reconstruction for Survey mode STTA NUM is the number of tracked stars in STT A at DATE REF STTB NUM is the number of tracked stars in STT B at DATE REF STTA MOD is the STT A Mode status at DATE REF either TRK ACQ STB INL R or ININ STTB MOD is the STT B Mode status at DATE REF same as above COMMENT Any strings HISTORY Any strings Raw data dimensions FITS dimension of the NIR frames is 412 x x 512 y x 2 short long exposure sub frames FITS dimension of the MIR S and MIR L frames is 256 x x 256 y x 4 1 short 3 long exposure sub frames Note that for convenience of data handling in the electronics onboard the satellite MIR S and MIR L frames are attached to each other along Y axis and form a single FITS of 256x512x4 dimensions The lower half portion of the 256x512 pixel images is for MIR S and the upper half portion is for MIR L With the AOT04 one will obtain 11 or 12 sets NIR and MIR S MIR L of frames e 1 set of pre dark frame e 8 or 9 sets of spectroscopy exposure frames Version 1 4 May 30 2008 19 e 1 set of reference imaging exposure fra
100. f the features are seen not only in your target object but also in nearby field stars See section 6 6 3 for more information e There are several kinds of difficulties in matching the flux level of the same source across the dispersers especially in slit less spectroscopy mode and jumps in flux level can be found between spectra from different dispersers in the same source See section 6 6 4 for more details e If unexpected narrow emission line objects are found it could be due to zero th order light images of nearby brighter stars See the ds9 window carefully since it shows the expected location of such features with yellow circles
101. flat along Y or the wavelength axis i e there are several spectral features on the super flats due to e g contributions of zero th or higher order light in cases of grism spectroscopy images Although the features should be removed to correct for the pixel to pixel variation of the response we first divide the dark subtracted images by the super flat with the spectral features As shown below in equation 6 1 1 this process makes the background flat facilitating the sky subtraction Assume that the dark subtracted images are represented by the following equation obs sky x Fi z y x spectral f eature x y obj A x Folz y A x R X 6 1 1 where Fj x y is the flat in which the background spectral features are not present Fi z y x spectral_feature x y is the super flat F5 x y A is the wavelength sensitive flat see below for color term correction and R A is the spectral response Since the super flat is only a function of the position in the detector this step is called monochromatic flat fielding If we divide the observation by the super flat we obtain obs sky obj A x Fo z g A x R A Fi a y x spectral f eature z y 6 1 2 6 1 4 Background subtraction from individual sub frames After monochromatic flat fielding the background should be flat over the aperture However in real data this is not occurring in most of the cases For NP NG and SG1 outlier tolerant 82 IRC Data User Manual
102. fy the first line of every perl script file in where you want to install irc perl For example if you have perl in usr bin perl please modify it as usr local bin perl gt usr bin perl As long as you have perl in usr bin perl you can also achieve the same result by runnig a script e cd where you want to install irc perl e perlpath sh which will create a directory temp containing perl files whose first lines are modified as above Then you can overwrite these new perl files by typing e mv temp pl Those who do not have perl in usr bin perl please modify perlpath sh and indicate the location of your perl 5 4 8 Add IRC entry to IRAF e If you know root password and you installed IRAF package into for example iraf cd iraf iraf unix hlib edit the file extern pkg Please add the following 2 lines to A iraf iraf unix hlib extern pkg reset irc where you want to install irc task irc pkg irc irc cl DO NOT FORGET THE BEFORE THE IRC PKG DO NOT FORGET THE LAST SLASH e If you don t know root password then you should launch iraf from your home directory everytime you want to use irc package cd change directory to your home directory mkiraf only when using IRAF for the very first time Version 1 4 May 30 2008 53 This will create the login cl file in your home directory Then edit login cl and add 2 lines reset irc where you want to install irc
103. greenbox flat Flat Fielding e greenbox aspect ratio Aspect Ratio Resampling Slit Mask greenbox slit mask The slit mask processing masks the slit area in the IRC Field of View After the slit mask processing a m will be added such that s1CcnDwaF23342 8004 fits becomes ms1CcnDwaF23342_S004 fits Flat Fielding greenbox flat The flat fielding is made using the imaging super flats described in section 4 2 Note that there was a noticeable pattern in the lower right corner of MIR S flat images A similar pattern also appeared in NIR flat images However these patterns suddenly dissapeared on the 8th January 2007 Thus the pipeline now incorporates two sets of super flats one for the data taken before 8th January 2007 and the other for the data taken after the 8th January 2007 By default the toolkit automatically selects flat images appro priate for the observation data by reading the observation dates in the FITS header However it was noticed that the pattern also slightly changes with time and in some cases the pipeline default flats can not wipe out the pattern completely In this case the data may require flat images made by using the AKARI NEP survey data taken close to the observing date In the near future we plan to attach the most suitable flat im ages to every distributed data set These flats can then be selected by putting them in where you installed irc lib flat user and deactivating the default_flat parameter
104. he scan direction the Y axis is aligned closely with the ecliptic latitude while the X axis is aligned with the ecliptic longitude Chapter 4 IRC Calibration and Accuracy This chapter offers an overview of the main issues related to the IRC calibration and in orbir performance The instrument calibration is addressed in an standard way dark level flat fields linearity point spread function absolute flux calibration and distortion correction Spectroscopy and imaging are addressed at the same time Specific topics for each of them are explicitely indicated Caveats and general concerns are also discussed 4 1 Dark image Superdark is made from the pre dark measurements of LMC observations It is used by default during the automatic processing both for imaging and spectroscopic data after shifting its level by checking the slit area in each image Since the number of hot pixels is increasing along the mission as shown in Figure 4 1 1 the superdark does not correct for them Coadding media filter different images IRC03 05 different observations or IRC02 different images will filter out non corrected hot pixels As an alternative dark current data taken before pointed observations can be used and can provide with better results since it corrects for hot pixels Its SNR is lower than in the superdark one especially in NIR since each observation has only one pre dark frame Another problem related to the dark current arises from the IR
105. he survey mode The NIR and MIR S share the same field of view by means of a beam splitter See text for the usage of the slits 2 1 Focal plane arrays The IRC comprises three channels Fig 2 0 1 The near infrared NIR channel operates in 2 5 um the mid infrared short MIR S channel covers 5 12 um and the mid infrared long MIR L channel works in 12 26 wm The NIR uses 512 x 412 format InSb array and MIR S and MIR L both employ 256 x 256 format Si As impurity band conduction arrays The three channels have a field of view of about 10 x 10 and the NIR and MIR S share the same field of view by the beam splitter whereas the MIR L observes a sky about 25 away from the NIR MIR S sky Figure 2 0 2 2 1 1 Near InfraRed Camera NIR Figure 2 1 3 shows the side view of the NIR channel The light from the telescope is split by a germanium beam splitter see Figure 2 1 4 and the near infrared radiation is introduced to the NIR channel The NIR consists of silicon and germanium lenses There are color aberrations among N2 N3 and N4 and the telescope focus is adjusted in between them Faint ghosts of bright sources are also present which come from internal reflections in the beam splitter The brightness is about 0 796 of the true source and the position is well determined and in a good agreement with the ray tracing simulation There are also ghosts that seem to come from the internal scattering in the NIR optics Details are under investigati
106. hter neighbours to find the accuracy of the absolute flux calibration See section 6 5 4 for actual operation e Wavelength offset error Because of the very low spectral resolution the spectral response curves show rather sharp change near the band edge If the wavelength offset is not properly set a systematic error in the flux level is expected near the band edge due to wrong wavelength assignment in the spectral flux calibration process If this happens the spectrum looks brighter and fainter or fainter and brighter at the shortest and longest Version 1 4 May 30 2008 103 wavelength coverage of the disperser in a systematic manner The way the shape change depends on the sign of error in wavelength offset plus or minus See section 6 5 3 for checking the wavelength offset error 6 7 Appendix 6 7 1 Variable name conventions As a general rule the extension of the IDL variables _ff bg wc fc indicates the finally processed calibration status Examples e ff means that the data is processed all the way to flat fielding e _bg means that the data is processed all the way to background subtraction i e flat fielded and background subtracted e _wc means that the data is processed all the way to wavelength calibration i e flat fielded background subtracted and wavelength calibrated e fc means that the data is processed all the way to flux calibration i e flat fielded background subtracted color term corrected
107. ift pix rotation deg and the number of stars used for the shift amp rotation angle calculation i e fdmslnDwaF01001 NO03 fits coo 1 1 0 0 0 0 0 0 0 fdmslnDwaF01007 NO03 fits coo 1 1 19 25942609 0 00474931 359 99288567 126 exp input files These files contain a list of all the pair files for all filters pointing at one position on the sky There may be files for both the long long_exp input and short Short exp inputexposure frames Skypair Files These log file can be found inside the separate directory logs This log file is produced during the adjustment of the sky level between frames bluebox adjust sky with a name skypair0002 N2 1ist long or similar This file lists the frames looking at a given area on the sky with the corresponding mean median and mode sky brightness and lo standard deviation calcshift log This log file can be found inside the separate directory logs The calcshift log file is the log file for the calculation of shift and rotation in the bluebox calshift process Relative to the first frame in the pair file described above the log file gives the number of stars matched between 2 coo files and the corresponding x amp y offset for these frames The calcshift 1log file will also record any matching failures darklist before 5 11 The IRC TOOL irc_tool It is beyond the original idea of the IRC data reduction software to provide tools for co adding or source extraction within the package as such processing ca
108. ile The README file describes e file list in the data package e observation summary extracted from the FITS file e comments specific for the observation 3 2 2 AKARI FITS Primary HDU common information rawdata header The contents of the AKARI FITS Primary HDU of all raw data both IRC and FIS is as follows SIMPLE ES T Standard FITS format BITPIX 16 number of bits per data pixel NAXIS 3 Number of axes NAXIS1 412 Image dimension NAXIS2 512 Image dimension NAXIS3 2 Image frame EXTEND T Extension may be present FMTTYPE ASTRO F IMAGE IRC Type of File Format in FITS file FTYPEVER 4 Version of FMTTYPE CNTTYPE IRC_NIR Type of data content DATE 2006 09 25T09 45 24 File Creation Date CREATOR TBD Data generator program name CRTRVER 1 0 Version of CREATOR PIPELINE 5 ircpl ver 1 0 Data Processing Pipeline name DATASTAT GOOD Data status ORIGIN ISAS JAXA Organization creating FITS file TELESCOP AKARI AKARI mission INSTRUME IRC Identifier of the instrument DETECTOR NIR Detector name OBSERVER PI Name PI Name Observer s ID PROPOSAL PRPID Proposal ID OBS CAT OT Observation Category PNTNG ID 1234567 Pointing ID TARGETID 1234567 Target ID SUBID 1 SubID OBJECT target Object name OBJ RA 320 5533 degree Target position OBJ DEC 23 3325 degree Target position AOT
109. ine first without Np spec option For other types of slit spectroscopy one may skip this run because shift and add feature is disabled for this observing mode e Second run run the pipeline for your desired targets Make target tables for N3 S9W and L18W on the raw images at this stage only N3 image has been processed Run the pipeline again for NP NG SG1 8G2 LG2 with target lists Image shift database created previously with NP NG will be used for the 2nd run If your target is compact and bright enough to be detected by the source detection sub program you do not have to perform this 2nd run For the 2nd run begin processing for NP NG first then SG1 and finally LG2 e Third run run the pipeline again if you want to revise the target table This is optional Now you got processed reference images for revising the target tables Run the pipeline again with the updated target tables to see final results 6 4 2 Running the pipeline Type the following in the IDL command line a command in a single line irc specred lt targetid gt lt targetsubid gt lt ext_source_table gt refimage list specimage list lt filter_spec gt Mandatory arguments e targetid ID of the pointing observation The information will be provided with the data distribution Example 1331048 e targetsubid Sub ID of the pointing observation The information will be provided with the data distribution Example 1 Version 1 4 May 30 2008
110. ion 060529 Copyright C 2005 Institute of Space and fistronautical Science Japan Aerospace Exploration Agency For help send email to yita ir isas jaxa jp 4 bluebox irc tool prepipeline unlearn all greenbox pipeline redbox ir gt Figure 5 6 3 Start up screen for the IRC package showing the available modules and tools The start up splash screen gives the current version of the toolkit and current versions of flat dark linearity distortion files etc 56 IRC Data User Manual 5 7 The pre pipeline processor Red Box Note that prepipeline processor is a one time only process Do not run prepipeline twice 5 7 1 Configuration Before running prepipeline you can configure the parameter for prepipeline by typing epar prepipeline This displays the parameter screen shown in Figure 5 7 4 Image Reduction and Analysis Facility PACKAGE irc TASK prepipeline verbose B no Print verbose progress messages mode al Hete EE for HELP Figure 5 7 4 parameter screen for the Red Box showing the available parameters Please do not change the parameter irccons Prepipeline has only one changeable param eter verbose If you want to see verbose progress messages change it to yes The default is no 5 7 2 Running the prepipeline processor The prepipeline processor consists of two functions e redbox ircslice sli
111. ion 1 4 May 30 2008 4 7 4 8 4 9 4 10 4 11 4 12 4 13 5 1 5 2 5 3 5 4 5 5 5 6 5 7 5 8 5 9 5 10 5 11 5 12 5 13 5 14 5 15 4 6 1 Observed standards and data processing 0200 4 6 2 Estimation of the in band flux 4 6 5 Absolute calibration 2 2 ee 4 6 4 Overall accuracy of the flux calibration 0040 Flux calibration for extended sources ee a Color COPFECHION ioo uocem AAS eb ue b bidau um DS Wet Distortion Ssa 2 eb ea Se Romo cum beue wee a E OL NOS ee ae Ge eps Memory effects caused by bright source observations 00 4 ASUFOInebbyw opot RA WE Spee Hee eek ee hea Ean he Si ae RA SE eg Arrays anomalies zem ke ge a le Ge ese alle Foe Rae ae e AND NIR array see ea at A te ERR RENEUS Wg See gels eg 4 12 2 MIR Arrays d ve a al X et da an a a a A es General concerns on slit less spectroscopy data Imaging toolkit cookbook Introductions iuacsvexenePecsecectbstneR t ae ake WO ees Wh P General overview of the toolkit processing a Expected Data Processing Rate minimum expectation How to install the IRC imaging Toolkit nn 54k R quimements use eR S IUE ce Te ex bes pA Istal IE XB odo eB ER ges dey Soe a x e UE ORAS 5 4 3 Download IRC imaging data reduction software package JAA Unpackdredga c dasensme ce eek ae Yhkewo ek aad WO TT ESKO RR PR 5 45 M
112. ion occurs around 12500 33000 and 33000 ADU after irenorm for NIR MIR S and MIR L respectively 26 IRC Data User Manual NIR linearity i before correction 5 after correction x or 4 E sL J c 2 5 gt o a 10 4 15 L J 20 1 1 1 1 1 1 0 2000 4000 6000 8000 10000 12000 RAW ADU MIRS linearity T X c 8 5 gt o a 80 Ll 1 fi L fi 1 0 5000 10000 15000 20000 25000 30000 35000 RAW ADU MIRL linearity 20 T oL 4 20 p 4 L4 c Sg 5 gt o a aor 4 60 4 80 1 fi fi 1 1 fi 0 5000 10000 15000 20000 25000 30000 35000 RAW ADU Figure 4 3 4 Raw signal versus deviation from linear curve A negative deviation means the raw signals in ADU is lower than that expected if the detector were linear Red marks show before applying linearity correction and the green marks represents after applying the correction Version 1 4 May 30 2008 af 4 5 RSRFE Figures 4 5 5 to 4 5 10 show the Relative Spectral Response functions for the different filters and dispersion elements o o o A Oo oco T T T Relative Response o N o T 1 2 3 4 5 6 Wavelength um Figure 4 5 5 The Relative Spectral Response Function of the IRC NIR Camera for Fy o co T L NP NG Relative Response O O T o o N T L o T fi 2 3 4 5 6 Wavelength um n Figure 4 5 6 The Relative Spectral Response Function of the IRC NIR
113. is set in the smooth e g smooth 2 the actual smoothing box size would be smooth t1 e g smooth 3 sigma filter This option enables sigma filter operation at 3 sigma significance level over 2D spectra to remove spatially isolated high or low count pixels Default is off If you find too narrow emitting absorbing features in your plots try this option to see if this is a real feature or not Note that if there is a cosmic ray hit at the position in one of the sub frames such count should be removed as an outlier while combining sub frames with sigma clipping averaging method However if there are temporal hot pixels or weaker hot cold pixels that are not shown in the hot pixel mask database you will find outliers hot or cold pixels even after sub frame combination Users should take care not to remove real narrow features 100 IRC Data User Manual Space shift shift of the plot extracting box along X spatial axis in pixel Default is zero Although the pipeline adjusts the X coordinates of spectrum extraction box by measuring positions of spectra one may find remaining X offset in some cases Change this offset to find peak position of the flux If one changes nsum and space shift issue the display command to see the modified spectrum extraction boxes graphically on the spectroscopy images over the ds9 show aperture on ds9 specimage bg source table Space shift space shift nsum nsum a command in a single lin
114. is warning messages users are requested to check the input file lists or contents of distributed FITS files and report any problems to the AKARI IRC Helpdesk for more support Although the irc_specred skips this list check ing routine if a flag no_database_check is set to the toolkit use of this option without noting problems is dangerous and usually is not recommended Version 1 4 May 30 2008 97 6 5 Working on the pipeline output 6 5 1 Displaying the whole images on ds9 Here we explain the region marks on the ds9 that are shown in the processed whole image products e g spectroscopy and reference images before source extraction In the spectroscopy image side left e The blue rectangle shows spectroscopy image extraction area e The green rectangle shows area reserved for the object or masked area for other objects e The red rectangle shows plotting area as defined by the spectral plotting tool e The yellow circle shows the expected positions of the zero th order light In the reference image side right marked circles correspond to source positions with diameter of the source FWHM e Green circles show sources with good position measurements e Red circles show sources with less accurate position measurements Source identification numbers are also indicated by the region marks For clear view of the image under complicated region marks check out the region gt show regions check box in the ds9 pull down menu
115. istration among sub frames Relative image shift due to satellite attitude drift among spectroscopy sub frames is measured by means of cross correlation technique This can be made only with NP and NG due to the number of spectra present in NIR images For SG1 SG2 and LG2 pixel offsets measured with NP NG are used for matching rather than measuring their own shifts since all cameras take images simultaneously Similar shift and add technique is also needed for the reference sub frames except for N3 where there is only a single reference sub frame To find the shift values for L18W we first detect point sources in S9W measure their positions and calculate the shift by using the list of target coordinates and shift both S9W and L18W images 6 1 7 Imaging stacking After registering all the sub frames all the selected screened sub frames are combined to make higher S N stacked images For spectroscopy images a three sigma clipping averaging method is used For reference images a simple median averaging is used due to the small number of sub frames Some sub frames are removed due to satellite maneuver When the toolkit recognizes that the last exposure frame cycle was taken during this maneuvering period the frame is automatically removed from the stacking list Note that although the observing manual says that 8 sub frames will be taken for spectroscopy in AOT04 operation it turned out that one additional frame 9th frame can of
116. ithout knowing the spectrum of each object e Contamination by zero th 2nd order light For the grisms images of the zero th and the 2nd order light can be seen as well as the 1st order image our prime target for data reduction although the efficiency for the zero th and the 2nd order light is very low All these images contaminate other spectra aligned along with the columns of pixels where the objects exit These contaminations can be ignored in most cases and cautions are needed actually only around very bright sources For the NG spectroscopy with point source aperture Np there is little chance for this kind of contamination to occur since the aperture size is much smaller than the size of the dispersed spectroscopy image along the Y or the dispersion direction e Spectral smearing for extended sources In the slit less spectroscopy mode the spectral resolution is determined by the size of the sources or the PSF structure plus satellite attitude drift Thus the spectral resolution is lower for extended objects If an extended object shows resolved structures the interpretation of the 2D spectra becomes very difficult because of the convolution of the spectrum over the object spatial structure e Background spectral features Although the background sky is essentially flat in the imaging mode it is not true for spectroscopy images Note that these features would not be observed with the point source aperture Np and other narrow s
117. ked as saturated are masked Physical detector saturation occurs around 12500 33000 and 33000 ADU after irenorm for NIR MIR S and MIR L re spectively Therefore any pixels with values greater than the scaled values in the short exposure frame are picked out and the corresponding pixels in the long exposure frames will be masked out to be 0 The scaled values in the exposure frames are calculated by Exposure Time short frame 5 9 3 Sshort exposure in ADU Sphysical saturation in ADU Dome EL tee xposure Imejong frame This is done because the IRC uses Correlated Double Sampling and with the current IRC operating clock we cannot tell which pixels are saturated by long exposure frames alone After masking saturated pixels a s will be added such that 1CcnDwaF23342 8004 fits becomes slCcnDwaF23342_S004 fits Version 1 4 May 30 2008 67 9 10 11 Therefore at the end of the Green Box correctly processed frame files should have aefmslCcnDwa Table 5 9 2 Prefixes added during Green Box Pipeline Processing Prefix module action a greenbox anomalous pix Mask Bad or Dead Pixels w greenbox wraparound Wraparound Correction D greenbox dark Dark Subtraction n greenbox norm Normalization c greenbox scat light Subtract Scattered Light Pattern C greenbox cosmic ray Detect and Replace Cosmic Rays l greenbox linearity Linearity Correction S greenbox saturation Mask Saturated Pixels m greenbox slit mask Slit Mask f
118. known to exist for very bright sources whose location depends on the position of the true source in the field of view The origin of the ghost is not yet clearly identified but it is most likely to come from the scattering by the optical elements of the MIR L channel internal scattering Version 1 4 May 30 2008 9 KRS 5 Filter wheel CsI KRS 5 CsI CsI L A N l ete 6417 Hr aE aE l Detector module t eil Es L Cylindrical mirror Telescope axis Figure 2 1 5 Side view of the MIR L The folding mirror is cylindrical to correct the astigmatism Thus the pixel scale of the MIR L channel is not the same for the X and Y directions 2 1 4 Arrays operation The focal plane arrays are operated in a synchronized manner The MIR S and MIR L arrays are operated in the same clock pattern The array operation is made in a unit frame which consists of
119. ky survey obser vations in MIR S L This effect corresponds to the belt like pattern in the horizontal direction b It does not accommodate the increasing number of hot pixels It may be better to use the pre and or post dark frames The super dark is used to get a high S N Due to various reasons 1st frame effect and so on the dark level may vary during a pointing Therefore we monitor the slit area as a reference of the dark level and we shift the super dark and or self dark by adding subtraction a constant to them and then subtracting this from each image to account for the changes in the dark level After the dark subtraction a D will be added such that waF23342_S004 fits becomes DwaF23342 8004 fits 4 Normalization greenbox ircnorm To reduce the readout noise of the detectors the IRC data is read with the Fowler sampling method non destructively reading and summing the array multiple times determined by the Fowler number then dividing this resulting sum by the Fowler number However when the data is transmitted to the ground for the purpose of data compression the least significant bit is dropped The normalization process accounts for this bit loss by correcting the data value by Auncorrected gbitehift Fowler number 5 9 2 Acorrected Where the bitshift represents the number of bit shifts emloyed 66 IRC Data User Manual After the normalization process a n will be added such that DwaF23342 8004 fi
120. l value smaller than 11953 After the wraparound processing is completed a 4 will be added as a prefix to the processed filename such that aF23342 8004 fits becomes waF23342 8004 fits 3 Dark Subtraction greenbox dark In a pointing observation a dark frame is taken at the beginning pre dark and the end of the operation for both the NIR and MIR channels Those who want to use these pre dark images in preference to the super dark images should turn on the self dark parameter and the pipeline processor will make dark images by averaging over the 3 images of MIR S and MIR L long exposure dark frames Hereafter we refer to this dark images as the selfdark image However the super dark will still be used for all short exposure frames and also the NIR long exposure frames even if the selfdark parameter is on Although the S N of the self dark images may be lower than that of the super dark image since the MIR images are usually sky noise limited so the S N of the dark should not significantly change the results unless dealing with very faint objects the self dark may be able to remove hot pixels more efficiently than using the super dark especially for the MIR S and MIR L because the number of hotpixels is increasing since the launch as mentioned in section 4 1 and shown in Figure 4 1 1 There are at least two known flaws in the current super dark a It does not correct for the increased dark signal due to the IRC all s
121. l variation of the flux or some nar row as narrow as one pixel size spike features meanwhile spectra processed without the flat fielding could look better in terms of S N However it seems a good idea to compare the results processed with and without the flat fielding If you find that this is also the case for your data you may adopt the data processed with the option no slit flat nir column pulldown correction a flag for enabling masking column pulled down re gions in NIR images With this option set irc specred searches for any pulled down columns in each sub frame by examining dark area pattern at Nh slit area where back ground is minimum and the pipeline masks out the columns Furthermore the pipeline also masks the same region in the next sub frames in which damage by the column pull down is still visible for deepest pulled down columns 6 4 4 Outputs Whole image products Version 1 4 May 30 2008 93 Processed and stacked reference image and corresponding mask and residual refer ence image x mask images Dark subtraction flat fielding and background sub traction are made lt targetid gt lt targetsubid gt lt filter_spec gt refimage_bg fits lt targetid gt lt targetsubid gt lt filter_spec gt refimagemask fits lt targetid gt lt targetsubid gt lt filter_spec gt residual_refimage_bg fits Processed and stacked spectroscopy image and corresponding mask and residual spectroscopy x mask imag
122. lation with temperature The MIR detector dark level show a weak correlation with temperature The Dark level is also very high after passing SAA Effects of high energy particle hits The toolkit does not perform any deglitching Glitches should disappear when coadding individual images median filter Even so their effect on the responsivity are not yet well investigated Future versions of the toolkit will involve a more careful treatment of cosmic ray hits Ghosts Ghosts appear in all three bands NIR and MIR S ghosts originate from the beam splitter while those in the MIR L arise from the lenses The positions which depend on the real source positions are well determined for all detectors and also depends on the filter The intensity of the ghosts is well determined for NIR a few and MIR S 4 of the parent source for S11 1 for the rest of the filters In the cases where ghosts are detected in MIR L the parent source is saturated therefore there is no quantification of the relative intensity of the ghost in this case Background Level The background level changes during the pointing observations in all bands It is due to the Earth shine reflection therefore it depends on the angle between satellite and Earth and the epoch of the observation The effect from the Earthshine is worse at northern ecliptic latitudes during June July amp August The Background level is different at the begining and at the end of the observation see
123. lits since the aperture size is much smaller than the size of the dispersed spectroscopy image along the Y or the dispersion direction e Faint background areas near the Y 0 or Y Y max edge of FOV For the slit area the background is dominated by the zodiacal light The spectral response curve shows a simple pattern with the decreasing sensitivity at the highest and lowest wavelength ends of the disperser s spectral coverage Thus one will see a background pattern which becomes faint at the top and bottom of the image in untis of ADU For the slit less area both the wavelength and the spatial axis Y go along with the same direction Y and thus the observed background image is a spatially convolved background spectrum Since the length of the spectrum along Y 50 70 pix is much smaller than the aperture size 256 or 412 pix the resultant background spectrum is almost constant across Y after being convolved spatially by the large aperture The regions around Y 0 and Y Yyax are exceptions where the edge of the aperture prevents full convolution of the background spectrum along the Y direction and hence the background signal becomes faint near Y 0 and Y Y max is seen Note that this kind of pattern at the very Y edge of the FOV does occur only for the background light but not for object spectra e Jump of the background ridge near the center of FOV Another background feature is a ridge seen near the Y center stretching along the X axis seen
124. lor table looks abnormal type set_color at the IDL prompt before launching the atv 6 5 3 Checking for wavelength zero reference point with the zero th order light image The toolkit calculates the wavelength zero reference point based primary on positions of the objects on the reference image It also takes into account a wavelength zero point drift due to satellite attitude drift as well as coordinate rounding effect when extracting 2D spectra In most cases these methods work well to estimate the wavelength zero reference point with accuracy of 0 5 pixel or less Since positions of the zero th order light image are also calculated in the same way as for the wavelength zero reference point one may check the wavelength zero reference point accuracy by comparing positions of expected zero th order light image and actually observed ones Unfortunately this check can be made only when bright sources with measurable zero th order light images are observed at some part of the FOV by chance When a shift is found the change wave offset command can correct for the estimated wavelength shift in pixel The shift is calculated from the current position This command changes the internal variable that records the wavelength offset updates an offset database on disk and re draws the images on ds9 with updated zero th order light marks This command can be used as many times as needed until getting satisfactory result Then one can use the spectral plot to
125. luebox calshift Calculate shift amp rotation between image frames bluebox adjust_sky Adjusts sky level between individual frames bluebox irc stack Stacks the IRC images bluebox putwcs Add WCS information to an image Figure 5 10 13 Present configuration of the Blue Box co add wrapper module 2 Calculate Shift amp Rotation to match frames bluebox calshift The bright reference star source lists are used to calculate the relative shift and rotation values between individual image frames looking at a particular field of view on the sky us ing the first frame as a reference After this shift and rotation process the original frame file names will receive additional R prefixes such that Sfdms1nDwaF23342 8004 fits be comes RSfdmslnDwaF23342 8004 fits There is a parameter minmatch that determines the minimum number of stars required for matching between 2 frames If there are not enough stars then a warning will be given and a log file coadd failure created containing the names of the processed frames that could not be combined A log file calcshift log is also produced listing the number of stars matched between and the corresponding x amp y offset for included frames Not that especially for the long wavelength channels MIR L there may be occasions when there are not enough guide stars for matching An alterna tive procedure can then be used which utilizes the MIR S shift amp rotation for the MIR L chan
126. me e 1 set of post dark frame The dark frames will be taken during pre and post satellite maneuvering period with the shutter closed the filter wheel at so called CAL position The spectroscopy frames are taken with dispersers inserted along the optical path by rotating the filter wheel The direct imaging frame is taken with the same ways as for the normal imaging observations with AOTOO 02 and 03 The image taken during the spectroscopy mode AOTO04 is called as the reference image The N3 S9W and L18W wide band filters will be used as the reference images of NIR MIR S and MIR L spectroscopy respectively Other combinations of the broad band filters and dispersers are not available The satellite starts to maneuver back to the survey mode according to the timer irrespective of the IRC operation The last exposure should be discarded since part of the exposure could be made during the maneuver The present FITS header does not record the status of the satellite attitude control In the imaging data pipeline the removal of the last exposure is made automatically by checking the source intensity Such an automatic procedure is not included in the current spectroscopy data reduction software users need to do it by themselves see Chapter 6 Note however that the automatic removal is not always perfect and users may have to do it manually in some cases even for the imaging data 3 3 Quick look data Together with the rawdata
127. ment features such as linearity flat fielding distortion etc and converts the raw ADU signal to physically meaningful units i e flux However in the current version the data number of resultant image is ADU per frame and they should be multiplied by a certain constant to convert it to a physical unit such as Jy We will provide a table of the conversion of ADU s to Jy for point sources in addition to the integration time for each frame The in orbit calibration is made based on aperture photometry with an aperture radius of 10 pixels for the NIR and 7 5 pixels for the MIR S L For other aperture sizes observers have to make an aperture correction which is currently not known owing to the unknown PSF not stable and not well defined Similar to the Spitzer IRAC arrays reflection of the light within the arrays exists also for the IRC arrays The calibration for the diffuse light is currently not available The toolkit including the entire source code will be released and be progressively updated reflecting the user s feedback The user will receive the raw data plus automatic toolkit to make basic science data The user may customize the toolkit at his her own risk However we will provide the super dark and super flat They will be updated periodically and will be given the version number e g Super flat Y YMMDD fits Super darkY YMMDD fits The goal for the toolkit is to achieve an absolute flux accuracy of better than 3096 25 a
128. messages when running the pipeline and Troubleshooting ii 30 32 33 34 34 34 42 42 43 43 43 46 46 iv IRC Data User Manual 6 Spectroscopy pipeline cookbook 80 6 1 General overview of the pipeline processing lens 80 6 Ll Dark s btfPAactlonm uses qi ee ea ee ep ae ce LE es 80 6 1 2 Linearity correction Saturation Masking 81 6 1 3 monochromatic Flat Belding o uc xe Rees 81 6 1 4 Background subtraction from individual sub frames 81 6 1 5 lmapgescreenmnge sarase pyte a G Ex ACER eq PECES 82 6 1 6 Image registration among sub frames len 82 617 Imagine stacking ia dup Dec oe ee ee pie eR Gy Ron EUR dE TR E 82 6 1 8 Target detection position measurement s 82 6 1 9 Background subtraction from stacked image lien 83 6 1 10 Extracting 2D spectra aoaaa 83 6 1 11 Wavelength calibration 22e 84 6 1 12 Flat color term correction 2 es 84 6 1 13 local Background subtraction from extracted 2D spectra 85 6 1 14 Spectral tilt correction les 85 6 1 15 Spectral response calibration ee 85 6 1 16 Notes on slit spectroscopy lh 86 6 2 How to install and to set up the IRC spectroscopy pipeline 86 6 24 1 Data preparation 2222s 8T 6 3 Calibration daba 9 9 et nie ee ar de S E eT ente Su See Tiere te Rp NS 87 6 3 1 Calibration files a ss ers oce sese coan ook a
129. n be done with the softwares commonly distributed The IRC TOOL is however prepared for co addition of MIR L channel that often has few reference stars in the field of view The present configuration of the IRC TOOL is shown in Fig 5 11 15 irc_tool coaddLusingS Use the MIR S image to Co add the MIR L frames Figure 5 11 15 Present configuration of the Blue Box post Pipeline Processor e irc_tool coaddLusingS is an alternative procedure which uses the MIR S shift amp rotation for the MIR L channel This function is especially useful when bluebox calcshift fails to calculate the xy shift and rotation angle for the MIR L channel because there are Version 1 4 May 30 2008 73 few reference stars detected The coaddLusingS has several parameters but they are identical to those in the pipeline except the s list string which is the name of MIR S pair list for which the calcshit has successfully matched frames Its default value is pair0005_S9W list_long 5 12 Toolkit structure rc IRC imaging data reduction pipeline anomalous pix outlier fits dark Hongfits sshortfits aot05 Hongfits short fits distortion distortion database dat flat fits slit mask slit mask fits constants database setenv dat setpath dat setpathpl welcomeorg perl
130. n for expressing the wavelength is assumed Therefore once the 2D spectra extraction is made with sufficient accuracy it is straightforward to make a wavelength calibration For prism NP spectra since the dispersion equation is highly non linear one especially at shorter wavelength end it is better not to transform images to avoid introducing extra uncertain ties in the image interpolating extrapolating processes Rather a separate array whose length is equal to the Y length of the extracted 2D spectra will be created to store the wavelength values for each Y pixel One wavelength array is applicable for all the extracted spectra within the FOV This kind of wavelength array is also used for grism spectra NG SG1 SG2 LG2 Finding wavelength zero reference point Some problems arise for accurate wavelength determination One is the satellite attitude stability problem If the satellite pointing moves between reference and spectroscopy images the reference image does not provide good wavelength zero reference point any more The NP spectrum before flux calibration shows a notable peak around 2 4 um and there are lots of fairly bright stars with almost identical spectra regardless of the type of stars within a single FOV Therefore it is possible to find the best offset of the wavelength zero reference point by measuring the NP peak positions with respect to the spectral template that was taken when the satellite attitude stability was good
131. n in April 2006 above and in August 2006 below of NIR MIR S and MIR L from left to right respectively Cleary the number of hot pixels are incleasing Version 1 4 May 30 2008 23 Figure 4 2 2 Representative Flatfields for each of the channels N3 S7 and L15 light is present in all detectors and an unexpected high background is seen This is probably due to external Earth light which is uniform over the Field of View Therefore observations of the diffuse background may be severely affected The S N of the superflat is estimated to be 5 N2 N3 10 N4 to 100 MIR S L and will limit the signal to noise ratio of the brightest stars There are at least the following problems 1 NIR We notice that there is stray light scattered off the telescope baffle This owes to the short baffle design and was not unexpected The amount depends on the direction and season of the observation worst at the ecliptic poles at the solstices and the wavelength A preliminary report is available in Japanese It cannot be ruled out that the current super flat may include a contribution from the stray light particularly for NIR 2 MIR S There is a noticeable pattern in the lower right quarter A similar pattern may appear even after flat fielding in some cases mostly for non dithering observations which are obviously artifacts The periphery of the MIR S images is affected by scattered light and should be discarded The portion affe
132. n the first pass of the source detection the automatic source detection sub program works even if the target table is supplied in the pipeline command line The X offset is measured with the tentatively detected sources at this stage In the second pass measured X offset as well as Y offset found in adjusting the wavelength zero reference point see the next section between spectroscopy and reference images is taken into account in extracting the 2D spectra Only the sources specified in the source table or sources detected with the sub program will be processed extracted in the second pass This two stage process ensures good source masking for better sky subtraction and good offset measurement with brighter and larger number of sources even for the cases in which the observer is only interested in small number of faint sources Measurement of the center position of the 2D spectra can be made easily for NP NG and SG1 spectra for which larger number of brighter sources can be detected even in blank sky regions Therefore the toolkit measures the X offset at NP and NG for correcting both NP and NG and at SG1 for correcting SG1 SG2 and LG2 Therefore the user must start pipeline processing for NP NG first then SG1 and finally SG2 and LG2 See section 6 4 1 for more explanations 84 IRC Data User Manual 6 1 11 Wavelength calibration In the case of grism spectra the dispersion equation is almost linear theoretically and a linear equatio
133. nd 2596 at the 5 sigma detection limit for NIR MIR S and MIR L channels respectively However these goals are at present the optimal values and we do not guarantee the numbers 5 2 General overview of the toolkit processing The toolkit runs on IRAF and it consists of two main steps plus an optional step At present the toolkit concept consists of 3 boxes currently in a state of development e pre pipeline processor Red Boz e pipeline processor Green Boz e post pipeline processor Blue Boz e Pre pipeline Processor Red Box Produces Basic Data 49 50 IRC Data User Manual redbox ircslice header formatting slice IRC 3D images into usual 2D ones redbox mkirclog making the observing log file irclog e Pipeline Green Box Produces Basic Science Calibrated Data greenbox anomalous pix mask Bad Dead pixels greenbox wraparound wrap around correction greenbox dark subtract dark current greenbox ircnorm Normalize sampling and compression bit shift greenbox scatt light Subtract scattered light pattern greenbox cosmic ray remove cosmic rays greenbox linearity correct linearity of the detector response greenbox saturation mask saturated pixels greenbox slit mask mask slit area on detector greenbox flat flatten the pixels greenbox aspect ratio Distortion Correction Aspect ratio resampling e Post Pipeline Processor Blue Box This is a separated package but called from pipeline processor
134. nel See irc tool section 3 Adjust Sky Level bluebox adjust sky The bluebox adjust sky module collects all frames looking at a given area on the sky and calculates the median sky from each image Each calculated median value is then subtracted from each individual corresponding frame From these median values an average sky brightness is calculated that is then re added to all the frames A log file is produced during this process with a name skypair0002 N2 1ist long or similar This file lists the frames looking at a given area on the sky with the corresponding mean median and mode sky brightness and lo standard deviation Those who want to subtract median box car filtered image instead of adjusting sky level should configure the following parametes by typing epar adjust sky before running pipeline e submeds boolean yes or no default no Subtract median filtered sky e rmmedsk boolean yes or no default yes 70 IRC Data User Manual Remove median filtered image Those who want to check box car median filterd image set this parameter no e x_box integer min 1 max 100 default 21 x box car size e y box integer min 1 max 100 default 21 y box car size The parameters x box and y_box change the size of the median kernel After adjusting the sky level the R prefix is removed and an A is added such that RSfdmslnDwaF23342 8004 fits becomes ASfdmslnDwaF23342 8004 fits 4 Image Stacking Co adding blu
135. ntrinsic NIR N2 NIR N3 NIR N4 Temperature K K 2 4um K 3 2um K 4 1um 40 50 60 70 80 938 233 90 305 576 100 127 958 110 E 64 122 120 541 920 36 679 130 z 187 774 23 187 140 78 796 15 834 150 i 38 794 11 488 160 5 21 822 8 749 170 S 13 696 6 929 180 9 390 5 665 190 E 6 906 4 757 200 xa 5 367 4 083 210 546 949 4 356 3 571 220 280 566 3 657 3 172 230 153 521 3 154 2 856 240 89 003 2 779 2 601 250 54 374 2 492 2 393 300 8 881 1 715 1 757 390 3 276 1 390 1 449 400 1 952 1 223 1 276 450 1 477 1 127 1 168 500 1 257 1 069 1 097 600 1 064 1 007 1 011 700 0 989 0 981 0 963 800 0 957 0 971 0 934 900 0 945 0 968 0 915 1000 0 943 0 970 0 902 1500 0 982 0 992 0 875 2000 1 027 1 012 0 868 2500 1 061 1 027 0 866 3000 1 087 1 037 0 865 3500 1 106 1 045 0 865 4000 1 121 1 051 0 865 4500 1 132 1 056 0 865 5000 1 142 1 059 0 865 6000 1 156 1 065 0 866 7000 1 166 1 069 0 866 8000 1 173 1 072 0 866 9000 1 179 1 074 0 866 10000 1 183 1 076 0 867 20000 1 203 1 084 0 868 30000 1 210 1 087 0 868 40000 1 213 1 089 0 868 50000 1 215 1 089 0 868 60000 1 216 1 090 0 868 Values are calculated for Ay 2 4um Ao 3 2um Aa 4 1m 38 IRC Data User Manual Table 4 8 10 Color Correction factors for NIR channel Gray Body a 2 Intrinsic NIR N2 NIR N3 NIR N4 Temperature K K 2 4um K 3 2um K 4 1um 40 50 60 70 80 119 020 90 236 320 100
136. ol Note that the wavelength for a given pixel is different from pointing to pointing for slit less spectroscopy data even if the same target was observed with the same pointing coordinates One may need to rebin the spectra for a common grid for proper stacking e There are no good tools for plotting spectra for a given source taken with different dispersers at once One needs to dump the spectra with the ASCII option when plotting the individual spectra and then use your favorite plotting software for plotting multiple spectra once e If the spacecraft attitude shifts after the reference frames have been taken the effect will be apparent in the wavelength calibration A shift of more than 1 2 pixels can happen For NP only the signal at the peak of the RSF is used to correct the wavelength reference by default The result will be inserted into the log file which will be further used to correct the drift in 8G1 2 and LG2 Therefore the NIR data should be processed first Similarly for NG in the point source aperture Np the NG slitless spectroscopy field should be processed first The actual correction is made by shifting the wavelength array rather than the image array e Strange features found in the NG spectra taken at Np aperture can be due either to flat field problem or column pull down See section 6 6 1 or 6 6 2 e Strange features in the NP spectra taken with the big aperture for Nc pointing will be due to wrong calibration only i
137. ol for reviewing spectra with updated wavelength and spectral response calibration See below for the plotting tools Command line syntax a command in a single line change wave offset wave offset source table Space profile spec profile wave array specimage fc 1d refimage bg specimage bg refimage n bg refimage n bg short Specimage n sff specimage n sff short Specimage n wc specimage n wc short Specimage n fc specimage n fc short res refimage bg res specimage bg mask refimage mask specimage mask specimage n imagheader specheader imagheader extract specheader extract noisemap noisemap n noisemap short n noise mask dir IRC SPECRED DIR workdir savefile savefile write indiv spec where lt wave_offset gt is a pixel number e g 1 0 0 5 0 5 to be shifted 4 6 5 4 Spectral plotting tool The toolkit s spectral plotting tool can handle many IRC spectroscopy specific features and we recommend to use it for creating spectral plots These are some of the functionalities of the Since this is a very long command it seems better to copy the command that is written in the IRC SPECRED HOME IRC SPECRED irc specred pro program Version 1 4 May 30 2008 99 tool source masks can be considered see also no mask option error bars statistical plus systematical ones can be plotted simple image filters for removing isolated spike pixels can be applied aperture stacking along spatial direction and smoothing
138. olat ing extrapolating the imaging super flat taken with two different filters for every pixel and the wavelength colour correction e Finally the spectral response specific to the spectroscopic mode observation is corrected by the spectral response function obtained from the observations of standard stars More detailed explanations can be found in following subsections 6 1 1 Dark subtraction Scaled super dark images are subtracted from the raw data For the scaling dark count offset is calculated within the pipeline by comparing average counts at the slit mask covered portion of the pre dark image and the corresponding area on the super dark image 80 Version 1 4 May 30 2008 81 Additionally the average dark counts of the mask covered portion of each observed sub frame is measured except for LG2 for which there is no good dark area on the spectroscopy images for measuring the dark level The averaged offset is added to or subtracted from the super dark to make the scaled super dark 6 1 2 Linearity correction Saturation Masking Linearity correction is made following the method adopted for imaging data reduction The saturation masking is also performed as in the imaging pipeline the toolkit first checks the short exposure images and find regions where expected counts in longer exposure frame exceeds the saturation limit based on the exposure time ratio of short long exposure frames see table 4 6 4 Then the regions a
139. omial coefficients are tabulated in a separate Version 1 4 May 30 2008 89 ascii table and are stored under the same directory Note that spectroscopy distortion along X dXgistortion is not so significant and constant pixel shift works rather well for NP as in the same way for NG SG1 SG2 LG2 WAVEPAR IRCWAVEPAR COMMON dat WAVEPAR IRCWAVEPAR NP dat WAVEPAR IRCWAVEPAR NG dat WAVEPAR IRCWAVEPAR SG1 dat WAVEPAR IRCWAVEPAR SG2 dat WAVEPAR IRCWAVEPAR LG2 dat IRCSPECBOXDYPAR NP dat e IRC_SPECRED_CALIBDIR RESPONSE contains ascii files tabulating A vs ADU long expo sure time in seconds mJy for each disperser There are five such tables NP NG SG1 8G2 LG2 The spectral response is measured by observing flux standard stars with known flux energy distribution This directory also contains a NP template spectrum wavelength calibrated spectrum before calibrating spectral response that will be used to find relative image shift along dispersion direction or Y between spectroscopy and reference images RESPONSE RESPONSE NP 1st RESPONSE RESPONSE_NG 1st RESPONSE RESPONSE SG1 1st RESPOUNSE RESPONSE SG2 1st RESPONSE RESPONSE_LG2 1st e IRC_SPECRED_CALIBDIR DISTPAR contains ascii tables containing spectral tilt informa tion of the grism insertion angle DISTPAR IRCDISTPAR NP dat DISTPAR IRCDISTPAR_NG dat DISTPAR IRCDISTPAR SG1 dat DISTPAR IRCDISTPAR_SG2 dat DISTPAR
140. on 2 1 2 Short wavelength Mid InfraRed Camera MIR S The light reflected by the beam splitter is lead to the MIR S It consists of two aspherical germanium lenses Figure 2 1 4 shows the side view of the MIR S channel Part of the narrow slit used for the NIR channel Fig 2 0 2 will also be shared by MIR S for spectroscopy for diffuse emission The MIR S also has ghost images of bright sources due to the internal reflections in Version 1 4 May 30 2008 Y 1 Channel NIR Table 2 0 1 IRC Filters and Dispersion Elements 3 4 Name Aret Wavelength Dispersion um um um pix 2 4 3 2 2 N2 N3 N4 4 1 NP 0 06 3 5 pm NG 0 0097 S7 SOW MIR S S11 SG1 SG2 12 6 19 4 13 9 25 6 MIR L 20 3 26 5 17 5 25 7 4 Reference wavelength 5 Defined as where the responsivity for a given energy is larger than 1 e of the peak Isophotal wavelength of the filter band Effective bandwidth Dispersion power of NP depends on wavelength The quoted value corresponds to 3 5m Renamed from L20W No change of the wavelength profile itself SOO Nara NEA 6 7 8 Table 2 0 2 General characteristics of the IRC focal plane arrays j Dark current e s 0 2 26 same as MIR S a Estimated by Fowler 1 sampling b Estimated by Fowler 4 sampling c Pre launch performance the beam splitter The brightness of the ghost is about 0 8 of the true source for S7 and S9W and 3 8 for S11 band 8 IRC Dat
141. ored by observations of the same stars Observations show no indications of any change in the reponsivity within 5 96 for all the three channels over more than a year 4 7 Flux calibration for extended sources A correction factor should be applied to convert the point sources flux calibration into extended sources flux This calibration will be done using the all sky survey data and the MSX data 10jum The 204m bands calibration will be more difficult because of no good reference data at these wavelengths The absolute calibration is still being in progress with new observations and will be updated 4 8 Color correction s mentioned in previous section the quoted values of the IRC flux calibration assume fy x A For cases of other incident spetra the color correction is required The quoted value at a reference frequency is given by footed x d od Jey where R is the response in units of electron per photon The correction factor K is calculated as fl ay 5959 fil ae Note om a A is actual __ hv V v vi iE K X actual i 7 i TO 6588 C Hm Version 1 4 May 30 2008 35 Thus K is given by We calculate the correction factors for the following incident spetrum cases f A To 2 5 aa 4 8 3 with a 0 1 2 The results are shown in the following tables The reference wavelengths are fixed as A 2 4um Ag 3 2um Aa 4 1m A4 7 0um Ag 9 0um Ag 11
142. rc lib flat directory or 2 changing the entries of flat in constants database in irc lib The new flat data is avalable from http www ir isas jaxa jp ASTRO F Observation DataReduction IRC e Super or Self dark and coadding data The Super dark images were obtained from more than 100 pointings of data of pre dark images taken at an early stage in the mission and should provide superior single to noise However it is known that the number of hot pixels in the detector arrays are gradually increasing throughout the mission and the Super dark image now contains incomplete information on their number and position This can have a severe effect on the coaddition of MIR L frames in certain cases In this scenario it is possible that a coaddition may indeed appear successful but in fact what has happened is that hot pixels may have been included in the coaddition process resulting in a meaningless final image In this case the self dark option should be selected from the toolkit parameter list to ensure valid coaddition e Coadd failure of the MIR L images The coaddLusingS function Often the coadd images procedure fails for MIR L images due to the lack of a sufficient number of 76 IRC Data User Manual NEP 2006 5 17 5 F S 5 3 a 2 4 B B 10 Time in one pointed observation min Figure 5 14 16 Change in the background level in a pointing observation bright stars in the FOV of a MIR L image In response within the ir
143. re masked in the longer exposure frames The user should check the masking in the edges of the saturated regions due to the drift between short and long exposures pointing 6 1 3 monochromatic Flat fielding In the case of the slit less spectroscopy the entire FOV is the aperture for the background sky but the object image itself is the aperture for the object This aperture size difference makes difficulties in flat fielding the slit less spectroscopy images since unlike a conventional long slit spectrograph a given pixel can be illuminated by background photons with a range of wavelengths within the disperser s passband and the mixing fraction of photons of different wavelengths depending on the spatial distributions and spectra of sources We need 3D flat information X Y along space plus Z along the wavelength for full flat calibration However it is impossible to obtain such a detailed flat since there are no good monochromatic flat light nor a series of narrow band filters covering the passband of the disperser Because of these difficulties we will make a flat calibration in two steps starting with the monochromatic correction To correct for the pixel to pixel variation of the monochromatic response response or flat that does not depend on wavelength the whole image is divided by the super flat The super flats are made by combining a larger number of background spectroscopy images Note that the background sky image is not
144. rforms either imagings of all the NIR and MIR S bands or all the MIR L bands In addition to these standards we have included standard stars in the Large Magellanic Cloud A fairly large area in the LMC have been surveyed by one of the AKARI s Large Area Survey programs LSLMC The standard stars in the LMC the so called SAGE standards were also established by M Cohen for the Spizter SAGE program We list observed SAGE standards in Table 4 6 3 This survey was done with IRC AOT02 and only N3 S7 S11 L15 and L24 images are available Table 4 6 2 Observed NEP and SEP standard stars Star 2MASS ID Sp K Obs Date for NIR MIR S HD42525 06060937 6602227 A0V 5 751 2006 04 22 04 08 28 NPM1p60_0581 17245227 6025508 A1V 9 645 2007 02 13 23 48 41 1757132 17571324 6703409 A3V 11 155 2006 04 26 22 49 47 KFO3T1 17574394 6626553 KOLI 9 923 2006 08 03 19 30 00 KF03T2 17575147 6631034 K1 5III 8 963 2006 08 03 19 30 00 KFO6T1 17575849 6652293 K1 5III 10 872 2006 04 26 19 31 48 KFO6T2 17583798 6646522 KI1 5III 11 149 2006 04 26 19 31 48 KFO06T3 17585021 6649406 KIII 10 348 2006 04 26 19 31 48 KFO6T3 2 2006 07 06 19 15 10 KF03T3 175901144 6633262 K1 5III 10 925 2006 08 11 19 08 13 KFO3T4 17590395 6630593 KIIII 10 091 2006 08 11 19 08 13 KFO9T1 17592304 6602561 KOIII 8 114 2007 04 15 02 03 34 KFO9T1 2 2007 06 02 01 28 46 KFO6T4 17592606 6654581 KOIII 11 240 2006 07 06 19 15 10 KFOIT4 18040314 6654459 K1 5III 8 067 2006 06 24 19 55 00 KFO1T4 2 20
145. s in X and Y axes respectively xlog ylog a flag to plot spectra in logarithmic scale along X and Y axes re spectively e Tweak wavelength zero point manually Usage change_wave_offset lt wave_offset gt source_table Space profile spec profile wave array specimage fc 1d refimage bg specimage bg refimage n bg refimage n bg short Specimage n sff specimage n sff short Specimage n wc specimage n wc short Specimage n fc specimage n fc short res refimage bg res specimage bg mask refimage mask specimage mask specimage n 106 6 8 IRC Data User Manual imagheader specheader imagheader extract specheader extract noisemap noisemap n noisemap short n noise mask dir IRC SPECRED DIR workdir savefile savefile write indiv spec lt wave_offset gt offset along wavelength direction in pixel units Error messages when running the pipeline and Troubleshoot ing In general double quotation mark can cause problems when calling the toolkit in IDL For example restore 12345678_some_more_information sav or irc_specred 12345678_some_more_information tbl S5G1 1st SG2 1st SOWSG1 give IDL syntax error We suggest to use single quotation mark rather than double quotation mark anytime when you work with the IRC_SPECRED toolkit For more check the IDL manual search quotation When one of the input parameters of the toolkit is a null string no space between single quota
146. s required to produce the basic science grade processed data There exists a jitter between frames in the IRC images causing frames to become unaligned with each other note this is not an intentional dither which is a separate procedure The attitude of these frames must be matched for any shift and rotation in position and stacked This processing is carried out by the modules called from the Blue Box pipeline Note this is not the same as actually running the Blue Box Post Pipeline processor In reality this process occurs automat ically at the end of the Green Box pipeline processor In order to do this bright sources stars are extracted from each frame as source lists These source lists are then used to calculate the shift and rotation for each frame looking at a particular field of view on the sky using the first frame as a reference The processing currently consists of the following steps almost entirely included in the blue box co add wrapper module e Co add individual frames bluebox coadd This module calls further individual modules to coadd the image frames together There is also an alternative module that may be called to coadd the image frames for MIR L using the information from the MIR S channel in the case that there are not enough bright stars for an independent calculation of the shift and rotation of each frame bluebox source extract Extracts bright reference sources bluebox calshift Calculate shift and
147. sigma for source detection sig rej 3 Rejection unit in sigmas max itr 10 Maximum number of iterations obslog irclog output of the mkirclog selfdar no Use selfdark instead of Super Dark coaddsh no Coadd short exposure frames interac no Run pipeline interactivelu deltemp yes Delete intermediate files rejecti sigclip rej in coaddiminmaxlccdcliplerrejectlsigcliplavs verbose no Print verbose progress messages mode al list Figure 5 9 8 Screen for parameter configuration for pipeline The pipeline has several parameters e irccons string default constants database NEVER CHANGE THIS This is the irc constant file name e com mod string average median default median Method of combination of frame images average median e com area int 1 or 2 default 2 Coadded image area of stacked frames used for extraction see Fig 5 9 9 NOTE although strictly speaking a Blue Box process but is run from the Green Box Pipeline script THIS PARAMETER IS NOT SUPPORTED YET AND YOU WILL GET THE WHOLE AREA IMAGE EVEN IF YOU CHOOSE 1 TO GET THE COMMON AREA 1 Only the common area red region is extracted 2 The whole area areas within green dashed line is extracted e sky are int 1 or 2 default 2 Area of sky to be used for statistics to adjust sky level before coadding frames 1 Only the common area is used Version 1 4 May 30 2008 61
148. solution spectroscopic observations in the pointing mode of the AK ARI satel lite Its unique wide field coverage of 10 x 10 arcmin is ideal for survey type observations or multi object spectroscopic programs The capability for the use in the survey mode has later been explored and now is also being used to carry out mid infrared all sky survey observations Each channel has a filter wheel on which medium band filters dispersive elements and a blank window as a shutter are installed Table 2 0 1 summarizes the parameters of the IRC filters and dispersion elements The NIR camera covers three independent wavelength bands that very roughly correspond to the well known K L and M bands Each of the two MIR cameras have two narrow filters which cover the shorter and longer half of the wavelength range of the cameras and a wide filter that overlaps the two narrow filters The S9W and L18W bands are used for the all sky survey observations The pixel scale and the imaging area of the focal plane arrays are summarized in Table 2 0 2 The imaging area is the rectangular area excluding the slit region The dispersion elements of the IRC are set into the filter wheel so that all the light in the FoV is dispersed A spectrum is obtained in the direction parallel to the scan path in scan direction Slits are provided for each camera Figure 2 0 2 in order to avoid contamination by nearby sources diffuse radiation The two dispersion elements of the NI
149. spectra with respect to N3 reference image Check the reference image on ds9 to know if source de tection could be made successfully Sometimes the program might detect only cosmic ray hits not stars if the parameters are not optimized Warning sky level is larger than 1 5 times sky sigma After extracting spec troscopy images remaining sky will be subtracted off locally around the source If every thing works fine the average of the remaining sky should be very small and is typically less than 1 5 times sky rms fluctuation This warning message will appear if sky level is larger than the typical value When this warning appears check the ds9 image to see if there remains large scale sky level variation Presence of such sky often indicates failure in monochromatic flat fielding and or global sky subtraction or any big unexpected debris Note that this warning will not appear for slit spectroscopy including NG at Np Warning Available sky area is too small Due to clouded source masking the remaining sky area is too small for measuring sky Check the source detection parameters for fewer source detection Usually this message is not so serious Warning Cross correlation peak is weak The cross correlation function will be calculated while registering sub frames and or short and long exposure frames The peak value of the cross correlation function is a good measure of the frame registration The value is 1 for ideal image matching
150. sure image to measure source positions By de fault irc specred uses the long exposure frame for measuring source positions in the reference image With this flag set the toolkit uses the short exposure frame for measur ing the source positions Note that the data reduction will be made for both short and long exposure frames even with this flag set This flag could be useful for measuring source positions of bright and saturated objects in the long exposure frame savefile set this option to a named variable that will contain the file name of the IDL save file section 6 5 5 The simplest way to restore the IDL save file is to run irc specred with the savefile savefile option and issue restore savefile conmand after irc specred finished and before e g plotting the spectra no slit flat a flag for disabling flat fielding process for slit spectroscopy at NIR By de fault irc specred performs spectroscopy flat fielding with the super flat image However as the natural background is faint in the NIR the quality of the flat can not be improved so much As a result unfortunately the quality of the processed spectra is limited by the quality of the flat not by the dark current nor photon noise With this option set irc specred skips performing the flat fielding Users are recommended to compare the spectra processed with and without the flat fielding process We expect no big differences among the two spectra except for random pixel to pixe
151. t should be encompassed with single quotations 104 IRC Data User Manual e Running the pipeline Usage irc specred lt targetid gt lt targetsubid gt ext source table refimage list lt specimage_list gt filter spec Options lt targetid gt pointing id of your observation Typically 12345677 Check your data distribution lt targetsubid gt pointing sub id of your observation Typically Check your data distribution ext source table an ascii file that specifies the source coordinates in X and Y in units of pixels If this is set to be null then automatic source detection program will be enabled within the pipeline refimage list an ascii file that specifies the FITS file names of the reference images to be processed Typically either N3 1st S9W lst or L18W lst specimage list an ascii file that specifies the FITS file names of the spec troscopy images to be processed Typically either NP 1st NG 1st SG1 1st SG2 1st or LG2 1st lt filter_spec gt an code to specify the data processing mode or a pair of filter and disperser names for the processing This should be one of the following N3_NP N3_NG S9W SG1 S9W_SG2 or Li8W_LG2 Nh spec Ns spec Np spec Ls spec flags to specify the slit spectroscopy data reduction no tune sourcepos a flag to disable source centering functionality fine tuning of
152. t DATE REF km Satellite position at DATE REF km Satellite position at DATE REF Day night status at DATE REF number of tracked stars in STT A at DATE REF number of tracked stars in STT B at DATE REF STT A Mode status at DATE REF STT B Mode status at DAT E REF Any strings Any strings BITPIX is the number of bits per data pixel and equal to 16 in the case of IRC NAXIS is the number of axes equal to 3 for IRC NAXIS1 and NAXIS2 are the image dimensions NAXIS3 is the number of image frames EXTEND refers to the presence of extensions in the FITS file e Data type creation and processing information FMTTYPE is the type of File Format in FITS file It can be ASTRO F IMAGE IRC or ASTRO F SCAN IRC FTYPEVER is the version of the file format described in FMTTYPE DATE is the file Creation Date CREATOR is the data generator program name CNTTYPE is the type of data content It can be IRC_NIR or IRC_MIR CRIRVER is the version of CREATOR Contents TBD Version 1 4 May 30 2008 17 PIPELINE is the Data Processing Pipeline name and version DATASTAT is the Data status It describes data status mainly from complete ness of telemetry data This does not tell detailed scientific quality of the data All appropriate error status are listed otherwise GOOD is given GOOD No problem INCOMPLETE Scientific data incomplete due to telemetry loss etc NOHK HK Status not avail
153. t saves the information is always lt targetid gt lt targetsubid gt lt filter_spec gt IRC_SPECRED_OUT sav Therefore the savefile is a string variable output that records the save file name not an input to specify the save file name If the pipeline is run more than once with different options the savefile should be renamed before the second run in order to be able to recover Version 1 4 May 30 2008 107 the previous results You can recall the record even if you rename the save file name by issuing restore lt renamed_save_file gt e If you want to see the results of previous toolkit run recalling the save file and you do not remember the ID of your source issue show_aperture_on_ds9 lt image gt source_table imag as instructed at section 6 5 1 This launches a ds9 and displays image and region marks on it Do not forget to include source_table after lt image gt e There are no good ways to run more than two pipeline processes at a same time on a single computer as a single user because more than two toolkit processes share some same dS9 windows Please use other computers or other user account e There are no good tools to coadd data taken over multiple pointings This is be yond the purpose of the toolkit right now The simplest way is to average combine ex tracted 1D spectra after dumping the results on ASCII files with the ASCII option of the plot_spec_with_image command and coadd them with any available to
154. ten be taken without suffering from satellite maneuvering You may add the frame for stacking 6 1 8 Target detection position measurement Target positions can be provided by the user in the form of a source table see below or automatically computed within the toolkit using the daofind method for target detection Even Version 1 4 May 30 2008 83 if the target positions are set by users the toolkit performs re centering of the source positions by means of Gaussian peak search This functionality can be disabled with the command line option This process is coupled with the following step background subtraction 6 1 9 Background subtraction from stacked image Although background subtraction has been already applied before stacking images any remain ing background is removed at this step The background subtraction and target detection position measurement explained in the previous section are made iteratively in the following way First the target is tentatively de tected by the automatic source detection program not based on the user supplied source table and source masks will be created for all detectable sources Then the background is measured while considering the source masks and is subtracted off from the original stacked image The background subtracted image is used for better source detection position measurement and better source masks will be created for better background subtraction When sources are detecte
155. ters in a pointed observation It provides at least three images for a filter with dithering operations 2 2 3 IRCO3 The IRC03 mode was designed for general purpose imaging observations that take images with three filters in a pointed observation For each filter two imaging observations are made with dithering operations 2 2 4 IRC04 The IRC04 mode was designed for general purpose spectroscopic observations This mode does not have dithering operations It has an imaging observation sandwiched by spectroscopic Version 1 4 May 30 2008 11 Table 2 3 3 IRC sensitivity and image quality N2 N3 N4 S7 SOW S11 L15 L18W L24 5 0 sensitivity uJy AOT02 16 16 16 74 76 132 279 273 584 AOT03 20 19 19 91 93 162 341 335 716 AOTO05 5 57 9 43 44 76 161 158 337 The values for N2 N3 and N4 of IRCO05 are tentative observations observations with the dispersive elements of 4 frames The imaging observation will be used to determine the wavelength reference point for slit less spectroscopy 2 2 5 IRCO5 The IRC05 mode was designed for deep imaging observations with a filter in a pointed observa tion This mode has neither dithering operation nor filter change Thus observers are requested to make a number of pointed observations for a give target for the redundancy This mode replaces IRCO00 after confirming its high performance for faint source observations for the NIR channel The exposure times for the MIR S and MIR L are the same
156. thout notice User are asked not to delete any of these files NP_SHIFT_XY dat for registering NP SG1 SG2 LG2 sub frames in AOT04a NG SHIFT XY dat for registering NP SG1 SG2 LG2 sub frames in AOT04b S9W SHIFT XY dat for registering S9W and L18W sub frames NP SPECBOX SHIFT X dat for shifting SG2 LG2 along X in AOT04a NP SPECBOX SHIFT Y dat for shifting the wavelength zero reference point for NP SG1 8G2 LG2 in AOT04a NG SPECBOX SHIFT X dat for shifting SG2 LG2 along X in AOT04b NG SPECBOX SHIFT Y dat for shifting the wavelength zero reference points of NG SG1 SG2 LG2 in AOT04b Version 1 4 May 30 2008 95 6 4 5 Summary of interactive operations within the pipeline Although the pipeline program works as a pipeline i e without interactive operation by users some operations in the irc specred do require interactive operation e Removing one or more sub frames before combining the sub frames In some sub frames one may find severe damage by cosmic ray shower nearby satellite passing in front of the telescope etc To check the sub frames and remove from the sub frame combination list all the dark subtracted flat fielded sky subtracted sub frames will be shown on a ds9 for reviewing To remove some sub frames use the Frame gt show hide frames pull down menu of ds9 to hide the frame s you need to remove The toolkit checks the hidden sub frames and remove them from the internal sub frame combination list e
157. tion marks should be given For example irc_specred SG1 1st SG2 1st S9WSG1 will give an error message because the toolkit tries to find the source table whose name is blank space and it fails The correct syntax is irc_specred SG1 1st 5G2 1st S9WSG1 If IDL complains about some undefined procedures functions probably some thing is wrong in the setting Check cshrc carefully and or After launching the IDL issue print path on the IDL command line This com mand shows all the paths for the IDL to search the libraries See if all the TOOLKIT directories are included in path If after running the pipeline several times successfully it fails with some unknown reasons try resetting the IDL session by issuing reset command at the IDL command line This resets everything stored in the IDL memory including IDL common and environmental variables that are referred updated during the toolkit session Some old settings might cause the trouble We recommend to reset every time the toolkit is restarted after a pipeline processing failure to avoid any confusion regarding old IDL variables Remember however that the reset command will destroy even the main IDL memory contents that contain information for e g plotting the spectra Of course users can restore the IDL save file contents back to the main IDL memory to resume the data analysis The filename where the toolki
158. tory where to your working directory should follow the rules explained in Section 5 6 1 5 6 3 Load the IRC package The irc package can be loaded by typing irc You should then see the IRC pipelin splash screen welcome message and a list of the available IRC packages see Fig 5 6 3 The screen shows the version of toolkit super flat super dark linearity and distortion Please let us know these numbers if you send any email to the help desk iris_help ir isas jaxa jp to inquire any trouble with the toolkit Version 1 4 May 30 2008 55 rane X XGterm IRAF v 2 12 1 NFS Darwin NOAO PC IRAF Revision 2 12 2 EXPORT Sun Jan 25 16 09 03 MST 2004 This is the EXPORT version of PC IRAF V2 12 supporting most PC systems Welcome to IRAF To list the available commands type or To get detailed information about a command type help command To run a command or load a package type its name Type bye to exit a package or logout to get out of the CL Type neus to find out what is new in the version of the system you are using The following commands or packages are currently defined dataio irc noao proto utilities dbms language obsolete softools images lists plot system cl irc 4 AKARI IRC imaging data reduction pipeline Pipeline version 060801 flat version 060626 dark version 060428 linearity version 051130 distortion vers
159. ts becomes nDwaF23342_S004 fits Scattered light pattern rejection greenbox scatt light Due to the scattering of light from the edges of the detectors lattice shaped sky patterns are present in the imaging area The patterns are especially prominent in the MIR S images The intensity of the pattern is proportional to the sky background level Therefore the scattered light pattern has been modeled and template images made for the three MIR S filters They are stored in where you installed irc lib scatt Figure 5 9 12 shows the modeled scattered light template images These template images are multiplied by the mode of the sky background level which is then subtracted from each image to eliminate the pattern After the scatt light process a c will be added such that nDwaF23342 8004 fits becomes cnDwaF23342_5004 fits Figure 5 9 12 The modeled scattered light pattern images from left to right for the S7 S9W and S11 bands 6 Cosmic ray rejection greenbox cosmic_ray Detect and replace cosmic rays in the MIR images After the comic ray rejection a C will be added such that cnDwaF23342 8004 fits becomes CcnDwaF23342 8004 fits linearity correction greenbox linearity The linearity correction is made as explained in section 4 3 After the linearity correction a will be added such that CcnDwaF23342 8004 fits becomes 1CcnDwaF23342 8004 fits Saturation greenbox saturation Any pixels that are mar
160. vation top left The following images correspond to observations taken 2 4 and 5 hours after the first one A deep can be seen where the bright source was located in the first observation 4 11 Astrometry A corrected and final astrometry can be achieved at the end of the pipeline cross correlating with the 2MASS catalogue This option is turned off by default This is because the software to retrieve the 2MASS catalog may be platform dependent To enable this option curl has to be installed in the system The instructions for it are beyond this manual Ask your computer administrator for the installation The current pipeline has a capability to first include the pointing information from the attitude and orbital control system AOCS directly in the WCS format If matching with the 2MASS data is successful then the pointing information will be replaced by the matching data The parameter WCSROOT in the FITS header indicates which information AOCS or 2MASS is used to determine the coordinates 4 12 Arrays anomalies 4 12 1 NIR array NIR anomalies are shown in Figures 4 12 13 and 4 12 14 Most of them also affects the Spitzer IRAC instrument e Muxbleed 44 e Muxstripes e Column pulldown e Banding IRC Data User Manual Figure 4 12 13 Banding in NIR array Version 1 4 May 30 2008 Figure 4 12 14 NIR array anomalies Muxbleed Muxstripes and column pulldown 45 46 IRC Data User Manual 4 12 2 MI
161. wavelength calibrated and flux calibrated Whole image products ff and bg are in 3D format X Y short long ID Short exposure frame is in Z 0 and long exposure frame is in Z 1 Extracted image products n images are in 3D The third dimension is for indicating the source id The following extensions refer to different processing stages e n bg background subtracted on extracted images e n wc wavelength calibrated after color term corrected residual background subtracted e n fc flux calibrated after color term corrected residual background subtracted and wavelength calibrated Finally these are the most frequently referred arrays e refimage bg Flat fielded background subtracted whole reference image in 3D X Y short long ID e specimage bg Flat field background subtracted whole spectroscopy image in 3D X Y short long ID e specimage n wc Wavelength calibrated extracted 2D spectra in 3D X Y source id e specimage n fc flux calibrated extracted 2D spectra in 3D X Y source id 6 7 2 Summary of Commands and their Options This is a broad outline of the main commands related to the pipeline together with their general syntax For arguments encompassed by lt gt and lt gt you need to specify your own processing parameters Options starting with are flags or switches to enable some functionality of the routine For other options you can set your parameters in numerals or ascii characters tha
162. with a width of 5 pixels A simple mean of the measured ADU values is used if the star was observed more than once 4 6 2 Estimation of the in band flux e Estimated flux density The in band flux density of each band at the nominal wavelength este was calcu lated by the following equation Show gBE 4 6 1 NE favored Vj or Ne RO AWA uote ris ee 4 6 2 f 3 RO Ad Ans where fA A is the flux density of a standard star Cohen template and R A is the spectral response the transmission of the optics and the response of the detector unit Version 1 4 May 30 2008 33 electron photon of the band i Here f c v or fy x A is assumed The adopted normal wavelengths of each band A are listed in Table 4 6 5 along with the range of the integration Ais Aie Table 4 6 5 The normal wavelength A and the range of integration A and A band i Ais i N2 2 40 1 60 5 770 N3 3 20 1 60 5 770 N4 4 10 1 60 5 770 S7 7 00 2 50 23 860 SOW 9 00 2 50 23 510 S11 11 00 2 50 24 000 L15 15 00 2 50 23 760 L18W 18 00 2 50 28 720 L24 24 00 2 50 28 720 4 6 3 Absolute calibration e The observed ADUs are converted to ADU toh according to the unit number Table 4 6 4 We assumed that the error of the estimated flux density of the standard star is 5 Observational errors ranging from 5 to 100 were assigned according to their ADU values A straight line was fitt
163. y create sets of these directory structures for different sets of IRC data 54 IRC Data User Manual polairetyita Z pud home yita polairetyita tar xzf sample_data tgz polairetyita cd sample data polairetyita Z mkdir yita polairetyita ls rawdata yita polairetyita 2 B Figure 5 6 1 Example directory structure for IRC toolkit 5 6 2 Launch IRAF Launch IRAF in your home directory and check that you have an entry for the irc package in the list of IRAF packages see Fig 5 6 2 NOAO PC IRAF Revision 2 12 2 EXPDRT Sun Jan 25 16 09 03 MST 2004 This is the EXPORT version of PC IRAF VZ 12 supporting most FC systems Welcome to IRAF To list the available commands type or 77 To get detailed information about a command type help command To run a command or load a package type its name Type bye to exit a package or logout to get out of the CL Type neus to find out what is new in the version of the system you are using The following commands or packages are currently defined color images noan softools utilities ctio irc obsolete southafrica dataio language plot stsdas doms lists proto system finder nmisc sirius tables Here Figure 5 6 2 Start up screen for IRAF showing the IRC package visible in the lsit of IRAF packages Then you can move to your working directory before starting to run the different tools by typing e cd to_your_working_direc
164. y typing Greenbox then running from inside the Green Box as anomalous pix dark etc e deltemp boolean yes or no default yes delete any temporary created files e rejecti string none minmax ccdclip crreject sigclip avsigclip pclip default sigclip Type of rejection operation performed in coadding none No rejection minmax Reject the nlow and nhigh pixels ccdclip Reject pixels using CCD noise parameters crreject Reject only positive pixels using CCD noise parameters sigclip Reject pixels using a sigma clipping algorithm avsigclip Reject pixels using an averaged sigma clipping algorithm 62 IRC Data User Manual pclip Reject pixels using sigma based on percentiles rej sky boolean yes or no default yes activate if you want to reject any images which have outlier sky level from the coaddition process Some frames may be taken during maneuver and the pipeline will detect such frames by watchig their sky level skip_L boolean yes or no default no activate if you want to skip the process of coadding MIR L images It will save you great time and you can use a tool to coadd the L image after the pipeline has finished submeds boolean yes or no default no activate if you want to make a median filtered sky image and subtract it from each image before coadding This option is useful for deep imaging observation where the sky has no structure coadd boolean yes or no

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