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AKARI IRC Data User Manual for Post

1. Telescope axis 50mm Figure 2 1 3 Side view of the NIR channel 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 7 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 6 IRC Data User Manual for Post Helium Mission Phase 3 Table 2 0 1 IRC Filters and Dispersion Elements 1 2 3 4 Channel Name Aref Wavelength Dispersion um um um pix N2 2 4 3 3 2 N NIR N4 4 1 NP 0 06 3 5 um NG 0 0097 12 6 19 4 13 9 25 6 20 3 26 0 ET 0 29 f 4 Reference wavelength 5 Defined as where the responsivity for a given energy is larger than 1 e of the peak 6 Isophotal wavelength of the filter band 7 Effective bandwidth 8 Dispersion power of NP depends on wavelength The quoted value corresponds to 3 5um Renamed from L20W No change of the wavelength profile itself Table 2 0 2 General characteristics of the IRC focal plane arrays Dark current e s 0 2 26 same as MI
2. 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 the previous results You can recall the record even if you rename the save file name by issuing restore lt renamed_save_file gt 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 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 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 tool Note that the wavelength for a given pixel is different from pointing to point
3. 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 noisemapn 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 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 78 IRC Data User Manual for Post Helium Mission Phase 3 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 tool e source masks can be considered see also no_mask option e error bars statistical plus systematical ones can be plotted e simple image filters for removing isolated spike pixels can be applied e aperture stacking along spatial direction and smoothing along wavelength direction can be applied for higher S N spectra e shifting aperture positions along spatial direction X axis can be made e 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 lt source_id gt and for short exposures plot_spec_with_imag
4. 1704 3092 SAT POSZ 1968 4286 DAYNIGHT DAY STTA NUM 4 STTB NUM 4 STTA MOD TRE STTB MOD TRK COMMENT HISTORY END The header keywords are sorted as follows e FITS basic information data size information SIMPLE refers to the standard FITS format AS MA 5 5 5 AA AA A 13 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 TT 36 bits DHUTI Epoch of Coordinate degree Solar avoidance Angle at DATE REF Earth avoidance Angle at DATE REF degree Lunar avoidance Angle at DATE REF sec Duration since last SAA at DATE REF km Satellite position at 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 DATE 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 i
5. Increase of hot pixels 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 correlation with temperature 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 originating from the beam splitter are recognized 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 a few 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 Fig 5 13 14 at different pointings see Fig 5 13 15 and in differernt seasons strongest in
6. Phase 3 This will create the login cl file in your home directory Then edit login cl and add 2 lines reset irc_p3 where you install irc_p3 task irc_p3 pkg irc_p3 irc_p3 cl DO NOT FORGET THE BEFORE THE IRC_P3 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_P3 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 irczp3YYMMDD tgz the following commands are required to be input e mv irc p3YYMMDD tgz where you installed previous version e cd where you installed previous version e tar xvzf irc_p3sYYMMDD tgz These commands will OVERWRITE any old files directories Then follow the original procedure 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 irc_p3package by typing irc_p3 e type unlearn_all e load the irc_tool package by typing irc_tool 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 th
7. cold pixels etc Masked area are marked by NaN Not a Number in the mask images MASK SLITMASK NIR lst MASK SLITMASK MIRS lst MASK SLITMASK MIRL lst MASK OUTLIERMASK NIR lst MASK OUTLIERMASK MIRS lst MASK OUTLIERMASK MIRL lst 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 wavelength calibration tables For grisms NG SG1 SG2 LG2 the wavelength um is expressed by a 1st order polynomial linear equation and parameters are 1 dispersion dA dY 2 wavelength at origin Ap 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 T herefore only dispersion and wavelength at the origin are set in the calibration database files The parameters can be applied for all IRC Data User Manual for Post Helium Mission Phase 3 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 sens
8. 2C135 412 DARK 82 75252 65 88891 IRCZ2 1 1900359 1 F011131801 N002 LMC P3 2C135 412 DARK 82 75252 65 88891 IRCZ2 2 1900359 1 F011131802_NO001 LMC P3 2C135 412 NP 82 75252 65 88891 IRCZ2 1 1900359 1 F011131802_N002 LMC P3 2C135 412 NP 82 75252 65 88891 IRCZ2 2 1900359 1 F011131803_N001 LMC P3 2C135 412 N3 82 75252 65 88891 IRCZ2 1 1900359 1 F011131803 N002 LMC P3 2C135 412 N3 82 75252 65 88891 IRCZ2 2 1900359 1 F011131804 N001 LMC P3 2C135 412 N3 82 75364 65 8848 IRCZ2 IL 1900359 1 F011131804_N002 LMC P3 2C135 412 N3 82 75364 65 8848 IRCZ2 2 1900359 1 F011131805 N001 LMC P3 2C135 412 NP 82 75364 65 8848 IRCZ2 1 1900359 ul F011131805_N002 LMC P3 2C135 412 NP 82 75364 65 8848 IRCZ2 2 1900359 il F011131806 N001 LMC P3 2C135 412 NP 82 74459 65 88335 IRCZ2 1 1900359 1 F011131806 N002 LMC P3 2C135 412 NP 82 74459 65 88335 IRCZ2 2 1900359 1 F011131807 N001 LMC P3 2C135 412 N3 82 74459 65 88335 IRCZ2 1 1900359 1 F011131807_N002 LMC P3 2C135 412 N3 82 74459 65 88335 IRCZ2 2 1900359 1 F011131808 N001 LMC P3 2C135 412 N3 82 73914 65 88638 IRCZ2 1 1900359 1 F011131808 N002 LMC P3 2C135 412 N3 82 73914 65 88638 IRCZ2 2 1900359 1 F011131809 N001 LMC P3 2C135 412 NP 82 73914 65 88638 IRCZ2 1 1900359 1 F011131809 N002 LMC P3 2C135 412 NP 82 73914 65 88638 IRCZ2 2 1900359 1 F011131810 N001 LMC P3 2C135 412 DARK 39 74704 48 87008 IR
9. 6 9 7 Known problems Some of the problems described below should hold also for phase 2 data e As describe above the absolute flux calibration for short exposure frames is still under investigation It is different from that can be expected from the difference in the integration time from long exposure data At present the cause is not yet fully understood e New flats for spectroscopic image data of phase 3 are not yet ready New flats will be provided in the future For slit observations Ns and Nh it is still recommended to use the option no_slit_flat which give better S N spectra in most cases e Although we confirmed the spectral performance dispersion is not changed in phase 3 and no change has been applied in the relative spectral response the calibration of NP data shorter than 2 5 um may be changed with a large uncertainty because of the worse PSF of the telescope in phase 3 Users should use NP spectra shorter than 3 um with special caution e The wavelength calibration for the shortest end of NG 2 5 2 6 ym has a systematic error of a pixel 0 05 um For longer wavelengths no systematic deviation is seen so far This problem is under investigation e The calibration of NG for wavelengths longer than 4 9 ym has an error due to the overlap of the second order light In the present calibration the data of blue standard stars are used Therefore it is underestimated and red sources often show a decline at the end of th
10. Aaneorteeced ii ea 9 1 Fowler number PRA detected Where the bitshi ft represents the number of bit shifts emloyed After the normalization process a n will be added such that DwaF23342_N004 fits becomes nDwaF23342_N004 fits nDaF23342_S004 fits becomes cnDaF23342_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 CnDaF23342_N004 fits be comes 1CnDaF23342_N004 fits Saturation greenbox saturation Any pixels that are marked as saturated are masked Physical detector saturation occurs around 2000 ADU after ircnorm for the NIR detector in the phase 3 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 2 Sshort exposure in ADU S physical saturation in ADU Eo ie ea xposure Timejong 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 1CnDaF23342_N004 fits becomes s1CnDaF23342_N004 fits Version 1 1 August 28 2009 49 Table 5 9 2 Prefixe
11. Figure 2 3 6 50 detection limits for diffuse sources with NP or NG in IRCZ4 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 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 AKARI_IRC_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 extract
12. Ns and Nh slit observations a shit of 4 arcsec in the X direction is executed in multi pointing observations 6 9 2 Spectroscopic performance The telescope image quality is degraded in phase 3 by 10 Onaka et al 2008 This leads to a degradation in the spectral resolution of the slit less including Np spectroscopy as well as the revision of the aperture correction In most case the degradation in the resolution is not significant except for the region shorter than 2 5 ym with NP where the calibration becomes more difficult However no change in the spectral response and spectral dispersion is noticed According to the change of the point spread function a new aperture correction table is provided for phase 3 6 9 3 Dark current linearity and hot pixels In phase 3 the dark current is increased and the number of hot pixels is also increased signif icantly To accommodate these changes the array operation was adjusted which reduces the saturation level significantly see the Imaging cookbook A new linearity correction which is the same as for imaging observations is applied to phase 3 data The decrease of the saturation level makes observations at Nc with NP at high background regions low ecliptic latitude regions very difficult The background level becomes very close to the saturation and only a small amount of the dynamic range for point sources is left Because of the increase of hot pixels dark images created from th
13. at present since it is assumed to be negligible After the resampling a e will be added such that fms1CnDaF23342_N004 fits becomes efms1CnDaF23342_N004 fits Therefore at the end of the Green Box correctly processed frame files should have aefmslCcnDwa prefix before the original filename i e F23342_N004 fits gt gt gt efmslCcnDwak23842_N004 fits The resulting data is the basic processed data with individual frames not per pointing corrected for detector and instrumental effects 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 is required to produce the basic science grade processed data There exists 50 IRC Data User Manual for Post Helium Mission Phase 3 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
14. cae kee eee ee ewe eh eee eee Ee eE EB EE He eee 2 3 I n orbit sensitivity 2 4 6 Ge w wow Rook eR JR a oe dw ew we ee wr 4 Distributed Data Products 3 1 IRC FITS file naming Tule ee ras ros A ee Be 52 Raw data CeSCRIDLION ae sasas saad a A A Sw eo we dw ask 2 2 1 Raw data naming convention 6 46 6 as 6 oe eee Bae Ge ee es 3 2 2 AKARI FITS Primary HDU common information rawdata header 3 2 3 Raw data dimensions 4 64 deb oS Go RESO ess zo Ouk look 00 ee erkasi nrar AA 3 3 1 IRC imaging IRCZO0 IRCZ2 and IRCZ3 oaaao 52 IRC spectroscopy IRCZ4 ccoo riores dids 3 4 IRCZ4 image orientation and dispersion direction 2 8 IRC Calibration and Accuracy AE Det 26 ee ae oe ER eRe EPR AEE AAA AD Pinel u m w sea ada wata oe o whe ee ae Ge eee ee ae 42 1 Flatfleds for imaging datas s lt s s aa ssaa oa wm a ow em di A 4 2 2 Flats for spectroscopy images e 40 Instrument nearly ses esise 48 eeteeeeee he eeaedeueeu cede 4 4 Instrument Point Spread Function LL o AO BRE lt gt reo ease error nados 4 6 Flux calibration for point sources ee a 4 6 1 Estimation of the in band flux 4 6 2 Absolute calibration ew 44 MO ew ew eee mod woda 400 Stability of the sensitivity amp 44 44 6a oe wo Be Se wh ew a 4 7 Flux calibration for extended sources 2 o de Color correci n s ses pa aa e e a bbe hs ee PORE E Roa pa 00 00 CONN Z KW 11
15. care of this before co adding The final result is the basic science grade images see Figure 5 10 13 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 Sfdms1CnDaF23342 N004 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 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 pair0001 N3 list pair0001 N3 list_short pair0001 N3 list_long pair0001 N3 list_long shift pair0001 N3 list_long shift 0 The pair0001 N3 list 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 6 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 list_long shift lists the result of the coordinate matching before coadding Each line entry in the file consists of a filename x sh
16. 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 NIR camera provide different spectral resolutions over a similar wavelength range 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 IRC04 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 gal
17. 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 specimage noisemap_indiv f its Note that our spectral plotting tool see below uses _WC image as an input not the FC image since the tool does 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 t
18. 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 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
19. is automatically done by prepipeline In general bad frames may cause 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 5 dark frames are taken at the beginning and the end of the operation in the phase 3 In the phase 3 data reduction the self dark created from these dark frames is always used to estimate the dark current Table 5 8 1 Sample of the irclog file FRAME OBJECT NAXIS1 FILTER RA SET DEC SET AOT EXPID IDNUM SUBID F011131797_NOO1 LMC P3 2C135 412 DARK 82 75252 65 88891 IRCZ2 1 1900359 il F011131797 N002 LMC P3 2C135 412 DARK 82 75252 65 88891 IRCZ2 2 1900359 1 F011131798_NO001 LMC P3 2C135 412 DARK 82 75252 65 88891 IRCZ2 1 1900359 1 F011131798 N002 LMC P3 2C135 412 DARK 82 75252 65 88891 IRCZ2 2 1900359 il F011131799 N001 LMC P3 2C135 412 DARK 82 75252 65 88891 IRCZ2 1 1900359 1 F011131799 N002 LMC_P3 2C135 412 DARK 82 75252 65 88891 IRCZ2 2 1900359 1 F011131800 N001 LMC P3 2C135 412 DARK 82 75252 65 88891 IRCZ2 1 1900359 1 F011131800 N002 LMC P3 2C135 412 DARK 82 75252 65 88891 IRCZ2 2 1900359 1 F011131801 N001 LMC P3
20. 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 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 respectively 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
21. 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 value across the images for all dispersers Version 1 1 August 28 2009 65 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
22. 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 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 IRCZO IRCZ2 and IRCZ3 As explained in the README file distributed with the data in the archive the irc_ql subdirec tory contains together with a set of log files a main quick look fits image per detector with the following naming convention Its name is efmslCnDaFV VVxxxxxx_ N yyy fits The fits pre fixes refer to the performed steps during the processing DARK correction D linearity In distortion correction d and flatfiedling f NSL refer to each detector Under the directory of stacked_IM a stacked image of TARGENAME_FILTER_EXPOSURE fits is also provided The irclog file contains a brief description of each file from the data reduction pipeline Please consult the READM
23. selfdark data created from these dark frames are always used because of the increase of the dark current and the number of hot pixels 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 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 aF23342_N004 fits becomes DaF23342_N004 fits Version 1 1 August 28 2009 GREEN BOx Pipeline Processor Figure 5 9 10 Present configuration of the Green Box pipeline modules 47 48 IRC Data User Manual for Post Helium Mission Phase 3 Figure 5 9 11 Mask file Outlier pixels have a value of O white and others 1 black Any outlier pixels will be masked out by mutipling the mask file to images of concern 3 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
24. 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 IRC Data User Manual for Post Helium Mission Phase 3 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 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 source_id gt options previously lt source_id gt a number that specify the source to be plotted You can find the number by looking at the ds9 wind
25. spectrum of each object Version 1 1 August 28 2009 29 Figure 4 11 5 Banding in NIR array 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 lst 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
26. symbolic link perl in usr local bin e If you do not know the root password please modify 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 1 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_P3 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_p3 where you install irc_p3 task irc_p3 pkg irc_p3 irc_p3 cl DO NOT FORGET THE BEFORE THE IRC_P3 PKG DO NOT FORGET THE LAST SLASH e If you do not know the root password then you should launch iraf from your home directory every time you want to use the irc_p3 package cd change directory to your home directory mkiraf only when using IRAF for the very first time 36 IRC Data User Manual for Post Helium Mission
27. 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 1st DARK DARK MIRS_long lst 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 blank sky images Tn the following contents within the parentheses lt something gt should be changed according to user s interests Version 1 1 August 28 2009 67 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 lst For reference images and color term correction of the flats FLAT IMAG2DFLAT_N3 1st FLAT IMAG2DFLAT_N4 1st FLAT IMAG2DFLAT_S7 1st FLAT IMAG2DFLAT_S9W lst FLAT IMAG2DFLAT S11 lst FLAT IMAG2DFLAT L15 lst FLAT IMAG2DFLAT L18W lst FLAT IMAG2DFLAT L24 lst e IRC_SPECRED_CALIBDIR MASK contains images of known bad pixels hot pixels
28. 0 957 0 971 0 934 900 0 945 0 968 0 915 1000 0 943 0 970 0 902 1500 0 932 0 992 0 875 2000 LO27 1 012 0 868 2500 1 061 1 027 0 866 3000 1 087 1 037 0 865 3900 1 106 1 045 0 865 A000 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 3000 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 1 215 1 089 0 868 50000 1 215 1 089 0 868 60000 1 216 1 090 0 868 a Values are calculated for Ay 2 4um Ag 3 2um Az 4 1um Version 1 1 August 28 2009 Table 4 8 7 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 r0 30 719 020 90 236 320 100 99 825 110 50 445 120 339 050 29 088 130 120 115 18 531 140 51 864 12 748 150 26 407 9 316 160 15 397 7 143 170 10 012 5 694 180 1 092 4 686 190 9 307 3 959 200 949 483 4 275 3 418 210 264 183 3 541 3 006 220 136 893 3 025 2 685 230 15 899 2 647 2 430 240 44 673 2 361 2 224 250 27 825 2 140 2 059 300 5 291 1 528 1 541 350 2 020 1 268 1 293 400 1 566 1 135 1 154 450 1 270 1 061 1 068 500 1 125 1 017 L012 600 0 996 0 976 0 946 700 0 949 0 963 0 910 300 0 935 0 962 0 839 900 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
29. 00 9 065 1 543 1 643 400 2 631 1 333 1 428 450 1 818 1212 1 294 500 1 465 1 156 1 204 600 1 167 1 052 1 095 700 1 051 1 012 1 033 300 0 997 0 992 0 994 900 0 970 0 932 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 0 836 3900 1 045 1 013 0 884 A000 1 056 1 017 0 833 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 3000 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 LET 1 041 0 877 40000 1 125 1 042 0 877 50000 1 125 1 043 0 877 60000 1 126 1 043 0 877 a Values are calculated for Ay 2 4m Ag 3 2um Az 4 1m 26 IRC Data User Manual for Post Helium Mission Phase 3 Table 4 8 6 Color Correction factors for NIR channel Gray Body a 1 Intrinsic NIR N2 NIR N3 NIR N4 Temperature K K 2 4um K 3 2um K 4 1um 40 50 60 r0 30 938 233 90 305 576 100 127 958 110 64 122 120 941 920 36 679 130 187 774 23 187 140 78 796 15 834 150 38 794 11 488 160 21 822 8 749 170 13 696 6 929 180 9 390 9 665 190 6 906 4 757 200 9 307 4 083 210 546 949 4 356 3 071 220 280 566 3 657 3 172 230 153 521 3 154 2 896 240 89 003 1 2 601 250 04 374 2 492 2 393 300 8 881 trio LIST 300 3 276 1 390 1 449 400 1 952 1 223 1 270 450 1 477 142r 1 168 500 1 257 1 069 1 097 600 1 064 1 007 1 011 700 0 989 0 981 0 963 300
30. 11 11 15 16 16 16 17 IRC Data User Manual for Post Helium Mission Phase 3 AO Pare Cee wees wee ee eee Ree a ee ee 28 Al AMON gga EEO See date EER EERE AAA AAA 28 4 1 Arrays anomalies y s csa i bow aa eee a Se ewe 28 4 12 General concerns on slit less spectroscopy data aa aaa aaa 1 28 Imaging toolkit cookbook 32 Oot IMGrOGNGUION a oda aa AA AAA 32 5 2 General overview of the toolkit processing 000008 32 5 3 Expected Data Processing Rate minimum expectation 33 5 4 How to install the IRC imaging Toolkit aaa 34 5 4 1 Requirements ce a a A 34 D42 stall IRAF esperoo ra iaa eee U 34 5 4 3 Download IRC imaging data reduction software package 34 oda Unpack OPZ serenite r rN ai owi EW reee 34 54 5 Make ire binaries s s sss ss sro RK ra wrew ratta ria d 34 D40 Ran selData pl sr dore rra aaa cd eed 34 47 FP 3 sisi tra das ds 30 JAS QA JRACS cutre to IAE a ee ee ee om Awa ee ee WA WEG 35 5 5 How to UPGRADE the version of IRC_P3 imaging toolkit 36 5 6 Setting up your toolkit environment and running the pipeline 36 5 6 1 Creating the directory structure LL ao ee eee eee 36 S02 Launch IRAP srs sesers eee echt AAA OF 500 Load the IRC P3 package 248 8645 2 eb G aa we RAE EES SS oF 5 7 The pre pipeline processor Red Box i i 1 126461011 39 Dita CONHSMEAION a Acta ade bh eRe EER ee eR ee eG ee 3
31. 860 3900 1 192 1 095 0 862 A000 1 212 1 103 0 864 4500 L227 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 3000 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 a Values are calculated for Ay 2 4um Ag 3 2um Az 4 1m 28 IRC Data User Manual for Post Helium Mission Phase 3 4 9 Pixel scale The pixel scale of the NIR image is determined based on observations of globular clusters and Galactic center with the IRC In these images we matched the 2MASS corrdinates of detected stars with the detector xy coordinates by fitting polynomials and determined the pixel scale The pipeline software regrids the image with the pixel scale of 1 46 The deviation from an ideal grid square are up to 2 pixels at the edge No appreciable change is noticed from phase 2 Refer to the IRC Data Users s manual for details of the distorion In summary the accuracy is about 0 1 pixel N4 may be slightly worse 4 10 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 As
32. 9 5 7 2 Running the prepipeline processor 0 0 00 eee eee 39 5 8 Before runnning the pipeline processor 0 0000 ee eee nee 42 5 9 The pipeline processor Green Box 0 0 0000 ee eee eee 43 DL ORASUANO ae s aa oe ee oe ee Oe dd ata wi dE mok AW oe i 43 5 9 2 Running Green Box pipeline module 008 45 5 10 The pipeline processor Blue Box bluebox coadd wrapper Module 49 5 10 1 The Blue Box Co Add Wrapper 0 0 000040 2 eee 49 5 10 2 Log files produced from the toolkit 0 53 5 11 Toolkit Stricture ss s se ea so s esoe d a ee ee a e a dw wod a 54 D12 Working Om the OMPI ss se sars ee em ARA AA we we eS A 55 5 13 Limitations of the functionalities in the current version of the imaging toolkit 55 5 13 1 Instrumental characteristics and artefacts in the data 55 5 13 2 Toolkit Limitations and Caveats 0 0 000 eee eee 56 5 14 Error messages when running the pipeline and Troubleshooting 56 Spectroscopy pipeline cookbook 59 6 1 General overview of the pipeline processing 2 005004 59 Oelel DRESDEN 3 2 ba aros ee ee ee do w ba a ia a 60 6 1 2 Linearity correction Saturation Masking a i 4 2 60 6 1 3 monochromatic Flat fielding Lae 00 60 6 1 4 Background subtraction from individual sub frames 61 ob Mago SECC ses eee PEER SOR ECHRER Ee WAR EEE EE G 61 6 1 6 Image registr
33. 9 75 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 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 e 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 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 e 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 tim
34. AKARI IRC Data User Manual for Post Helium Phase 3 Mission Version 1 1 Takashi Onaka Rosario Lorente Yoshifusa Ita Youichi Ohyama Toshihiko Tanab and Chris Pearson with contributions from Martin Cohen Daisuke Ishihara Itsuki Sakon Takehiko Wada Issei Yamamura and Hideo Matsuhara The University of Tokyo Japan European Space Astronomy Centre ESAC ESA National Astronomical Observatory Japan NAOJ 4 Academia Sinica Institute of Astronomy amp Astrophysics Taiwan ASIAA Rutherford Appleton Laboratory RAL U K University of California Berkeley U S A Institute of Space and Astronautical Science ISAS JAXA Japan August 28 2009 30 January 2009 copy from IDUM 1 4 Y March 2009 Revisions completed 24 August 2009 Table 4 6 4 corrected Date Revision Comments Contents Introduction 1 1 Purpose of this document sa she 44 Oe Gwe ss Be L2 Relevant i i rmalo sa ss ss lt 6 e864 6 24 dd asi wada w GR oo HS Instrument overview gt a ol S sersant ereere iee eee ed 4 eae oe ee AA 2 1 1 Near Intraked Camera NIR s 42 oe eee eee dee ae bo ee dA 212 Arrays ODELII W 4 4 4 4 4ak bee Re AAA 22 IMstcument AOTS 6 245 464 226 5446545 658 46 WAG oo 4 EE x Doe ICA ss ae eee ee taae ee ees eeu eaneeeees sees eu ee 222 ARCZO eee eee ee eee ee eee eee ee eee eet ee eee eee ae 225 MRO ee eee ee ee eee BER eee ee eee hee ee eee ah 2 228 MACH
35. CZ2 1 1900359 1 F011131810 N002 LMC P3 2C135 412 DARK 39 74704 48 87008 IRCZ2 2 1900359 1 F011131811 N001 LMC P3 2C135 412 DARK 34 73183 43 88028 IRCZ2 1 1900359 1 F011131811_N002 LMC P3 2C135 412 DARK 34 73183 43 88028 IRCZ2 2 1900359 1 F011131812_NO001 LMC P3 2C135 412 DARK 31 62331 40 16951 IRCZ2 1 1900359 1 37F011131812 N002 LMC P3 2C135 412 DARK 31 62331 40 16951 IRCZ2 2 1900359 1 F011131813 N001 LMC P3 2C135 412 DARK 28 98775 36 5962 IRCZ2 1 1900359 1 F011131813_N002 LMC P3 2C135 412 DARK 28 98775 36 5962 IRCZ2 2 1900359 ul F011131814_NO001 LMC P3 2C135 412 DARK 26 45258 32 7553 IRCZ2 1 1900359 1 F011131814 N002 LMCUP3 2C135 412 DARK 26 45258 32 7553 IRCZ2 2 1900359 1 F011131815_NO001 LMC P3 2C135 412 DARK 24 12861 28 86755 IRCZ2 1 1900359 1 F011131815 N002 LMC P3 2C135 412 DARK 24 12861 28 86755 IRCZ2 2 1900359 1 Version 1 1 August 28 2009 43 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 y PACKAGE TASK Image Reduction and Analysis Facility Ea pipeline IRC constants database Tile name combine mode average median sky matching area 1 common area whole area Threshold in sigma for source detection Rejection unit in sigmas Maximum number of iterations output of the mkirelog Detect and replace co
36. E file in the delivery package for more information 3 3 2 IRC spectroscopy IRCZ4 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 Version 1 1 August 28 2009 17 3 4 IRCZ4 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 The IRCZ4 data reduction pipeline makes the rotation of the NIR images at the first step After the NIR rotation the dispersion directions are the same for all the dispersers in spec troscopy images Note however that NP shows positive dispers
37. G2 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 lst RESPONSE RESPONSE_NG lst RESPONSE RESPONSE_SG1 lst RESPONSE RESPONSE _SG2 lst 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 IRCDISTPAR_LG2 dat e IRC_SPECRED_CALIBDIR APCOR contains the spectral aperture correction tables Version 1 1 August 28 2009 69 6 4 APCOR APCOR_NP dat APCOR APCOR_NG dat APCOR APCOR_SG1 dat APCOR APCOR_SG2 dat APCOR APCOR_LG2 dat 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 MI
38. 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 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 Sub ID OBJECT target Object name OBJ RA 320 5533 degree Target position OBJ DEC 23 3325 degree Target position AOT IRCO3 Observation AOT AOTPARAM 8 0 5 70 AOT Parameter INSTMODE TBD Instrument operation mode TIMESYS UTC Explicit time scale specification Version 1 1 August 28 2009 DATE OBS YYYY MM DDTHH MM 5SS DATE END YYYY MM DDTHH MM SS DATE REF YYYY MM DDTHH MM S5 AFTM OBS double AFTM END double AFTM REF double PIMTIOBS OxXXXXX PIMTIEND OxXXXXX PIMTIREF OxXXXXX EQUINOX 2000 0000 RA 320 5933 DEC 23 3325 ROLL 30 553 AA SOL 90 0021 AA EAR 180 2083 AA LUN 210 6821 TM SAA 1829 SAT POSX 2903 5528 SAT POSY
39. Mission Phase 3 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 often 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 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 i
40. 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 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 Version 1 1 August 28 2009 5 Scan Direction l Telescope Axis 5 0 7 09 50 r Slit NIR 3 x1 A Slit NIR 1 x1 3195 Slit NIR MIR S 5 x0 8 x 25 0 de 9 3 0 7 for N2 9 5 0 5 for N3 4 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 the 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 Folding mirror Detector module Si
41. R 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 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 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 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 pipeline 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 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 SG2 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 Third run ru
42. R S a Estimated by Fowler 1 sampling b Estimated by Fowler 4 sampling c Pre launch performance the NIR optics Details are under investigation NIR and MIR S channels acts as a folding mirror for the MIR S astigmatism Thus the pixel scale of the MIR L channel is not the same for the X and Y directions Version 1 1 August 28 2009 7 2 1 2 Arrays operation The focal plane arrays are operated in a synchronized manner The array operation is made in a unit frame which consists of short and long exposures The short exposure is intended to increase the dynamic range by about 8 to 10 times However data taken in the short exposure indicate anomalous behavior and at present the short exposure data are not able to be calibrated The clock pattern of one frame is the same for all AOTs One frame is about 63 sec in which NIR has one short and one long exposures The short exposure is made with the Fowler 1 sampling scheme 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 AO T 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 The AOTs in phase 3 are designated by AOTZ Figure 2 2 4 shows an illustration of the pre f
43. REF either TRK ACQ STB INIR or ININ STTB MOD is the STT B Mode status at DATE REF same as above COMMENT Any strings HISTORY Any strings 3 2 3 Raw data dimensions FITS dimension of the NIR frames is 412 x x 512 y x 2 short long exposure sub frames With the AOTZ4 one will obtain 11 or 12 sets of frames e 5 sets of pre dark frame e 5 or 9 sets of spectroscopy exposure frames e set of reference imaging exposure frame e 5 sets set of post dark frame 16 IRC Data User Manual for Post Helium Mission Phase 3 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 AOTZO Z2 and Z3 The image taken during the spectroscopy mode AOTZ4 is called as the reference image The N3 wide band filters will be used as the reference images of NIR 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
44. 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 6 1 11 Wavelength calibration In the case of grism spectra the dispersion equation is almost linear theoretically and a linear equation 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 spectroscop
45. SHIFT_Y dat for shifting the wavelength zero reference points of NG SG1 SG2 LG2 in AOT04b 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 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
46. See section 6 6 3 for more information 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 Version 1 1 August 28 2009 87 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 6 9 Tips for the Phase 3 data reduction The evaluation of the phase 3 data is ongoing Here we summarize the caveats and tips of the phase 3 data reduction In the phase 3 data reduction special options are prepared to deal with the saturation of the reference image 6 9 1 AOT IRCZ4 In phase 3 5 dark frames are taken before and after the observations of your target The observation sequence is the same as in phase 2 4 spectroscopic observations one reference imaging with N3 and 4 spectroscopic observations In phase 3 the number of hot pixels increases significantly To secure redundancy auto matic dithering scheme is implemented for multi pointing observations both for slit less and slit observations For Np observations the pointing position is shifted by 3 arcsec in the X or Y direction whereas 6 arcsec shift is executed for Nc For
47. TV 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 Items in parentheses are optional In 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 Version 1 1 August 28 2009 BR 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 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 color 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 e
48. although the treatment of dark frames and the linearity correction are different 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 Box e pipeline processor Green Box e post pipeline processor Blue Boz 32 Version 1 1 August 28 2009 33 e Pre pipeline Processor Red Box Produces Basic Data redbox ircslice header formatting slice IRC 3D images into usual 2D ones c 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 by default bluebox coa
49. ame 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 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 We provide super flats which will be updated periodically with the version number e g Super dark Y YMMDD fits The toolkit for phase 3 data reduction is released separately from that for phase 2 data reduction The user interface is basically the same but users should not use it for phase 2 data reduction It can be installed simultaneously with that for the phase 2 data reduction toolkit as described below For users who are familiar with the phase 2 data reduction the usage of the toolkit is completely the same
50. an error message such as ls rawdata No such file or directoryorcat slice_tmp0 No such file or directory etc al though the pre pipeline seems to run correctly Typing unlearn_all should clear these error messages Version 1 1 August 28 2009 57 Figure 5 13 15 Background levels 2 The distortion processing green box processing can give the following error message causing the pipeline crash HHH DISTORTION 444 Making the input file list Correcting distortion This may take a while ERROR on line 56 Cannot open file iraf irc lib distortion DARK_distortion_database dat distortion ircconst constants database logfile irclog prefixs mslnDwa verbose no pipeline This is because the DARK entries should be removed from the irc log file 3 The coadd stage can result in the following error Hitt COADD FFF Making the input file list Extracting sources Calculating XY shift Adjusting sky level Coadding images 58 IRC Data User Manual for Post Helium Mission Phase 3 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 georytran 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 The pre pipeline run can app
51. arently miss some perl scripts and end with an empty or non existing 2rclog file HHH MKIRCLOG 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 4 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 local bin perl therefore a symbolic link should be set up from the perl library to usr local bin perl type whichperl to find out where perl is currently hiding If a new version of the toolkit crashes as a first fix unlearn_all should be typed within Irc 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 IRAF 2 13 has been successfully run on the intel machines 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 listed in the pair file should be examined to see if they have the appropri
52. ate FILTER keywords in their header 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 plan 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 DT phase observations as well as pre launch calibration experiments in our laboratory Therefore observers do not have to make their own calibration observations The reduction of the data of phase 3 observations requires special care and tips The new pipeline software IRC_SPEC_TOOLKIT_P3
53. ation among sub frames o ao e a a a 61 Os Imagine stacking s s s spss ow eee eee eae nd daw deo R 61 6 1 8 Target detection position measurement 4 62 Version 1 1 August 28 2009 iii 6 2 6 3 6 4 6 5 6 6 6 7 6 8 6 9 6 1 9 Background subtraction from stacked image ooo 1 1 1 1 2 11 62 0 1 10 Egtractmg 2D spectra ec iso or ener A 62 61 11 Wavelength calibration ea aer ers desen ae A 63 6 1 12 Flat color term correction 2s aooo dowd 64 6 1 13 local Background subtraction from extracted 2D spectra 64 6 1 14 Spectral tilt correction twa np eR ee EOG W w 6 a we eS 65 6 1 15 Spectral response calibration 65 6 1 16 Notes on slit spectroscopy 1 a 4 1 65 How to install and to set up the IRC spectroscopy pipeline 65 02 1 Data preparation s s a sa dvwvebeebavbeeean eae eb wees 66 Colpranlon Gata oo das ise ee ee ee wee ee Se 66 Oe Calibration He be eee eee eRe eS SS 66 Running the pipeline poso sons era ads 69 B4AL Data red ction order crisis es esa 69 6 4 2 Running the pipeline ee a 0 1 69 G45 ODU sekere saene renren 71 04A OMD aso eu dee he rasa heeds ea ee 12 6 4 5 Summary of interactive operations within the pipeline 14 6 4 6 Warning messages of the pipeline LL a e a 74 Working on the pipeline output Lao a 0 1 76 6 5 1 Displaying the whole ima
54. avelength zero point manually Usage change_wave_offset lt wave_offset gt source_table space_profile spec_profile wave_array specimage_fc_ld Version 1 1 August 28 2009 85 6 8 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 noisemapn 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 SG1 1st SG2 1st SOWSG 1 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 quotation marks should be given For example irc _specred SG1 lst SG2 lst S9W_5G1 will give an error messa
55. axies may be a serious problem The NG grism is assumed to be 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 4 IRC Data User Manual for Post Helium Mission Phase 3 5Omm oS folding mirror NIR 7 unit NIR filter unit MIR S MIR S detector unit MIR S Figure 2 0 1 Bird s eye view of the IRC camera 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 um 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
56. be observed with the point source aperture Np and other narrow slits 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 30 IRC Data User Manual for Post Helium Mission Phase 3 4 FR e TTE eS LN gt e E im FEE i Figure 4 11 6 NIR array anomalies Muxbleed Muxstripes and column pulldown 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 Y max 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 1s seen Note that this
57. ble meth ods 1 2 3 By setting the interac parameter in the parameter list By running the pipeline with the command pipeline interactive yes 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_N004 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 L Mask bad or dead pixels greenbox anomalous_pix Bad or dead pixels were identified by using pre flight laboratory data Mask files 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_S004 fits becomes aF23342_N004 fits Dark Subtraction greenbox dark In a pointing observation 5 dark frames are taken at the beginning pre dark and the end of the operation In phase 3 data reduction the
58. co add wrapper module is shown in Fig 5 10 12 BLUE BOX Co Add Wrapper bluebox source_extract extract reference sources bluebox calshitt Calculate shift amp rotation between image frames bluebox adjust_sky Adjusts sky level between individual frames blue box irc_stack Stacks the IRC images bluebox putwes Add WCS information to an image Figure 5 10 12 Present configuration of the Blue Box co add wrapper module The starting point for the Blue Box Co Add wrapper are the files created from the final step in the Green Box pipeline Processor efms1CcnDwaF23342_S004 fits The Co Add module then performs the following tasks Version 1 1 August 28 2009 51 1 Extract bright reference sources bluebox source_extract This module extracts individual bright sources from individual frames Before extrac tion original 412x512 NIR images are paseted to larger 1024x1024 images to prepare for the xy shift and rotation During source extraction a S will be added such that fdms1CnDaF23342_N004 fits becomes SfdmslCnDaF23342_N004 fits Bright sources stars are extracted from each frame as source lists 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 rota
59. completely different from the phase 2 observations where the superdark is used instead of the self dark for the NIR channel 4 2 Flatfield 4 2 1 Flatfileds for imaging data Figure 4 2 1 Flatfields for N2 N3 and N4 The IRC super flats for the NIR bands were derived from all the imaging observations so far taken during the phase 3 Unfortunately stray light is present and an unexpected high background is seen This is due to Earth rim light which is uniform over the Field of View Therefore observations of the diffuse background may be severely affected 19 20 IRC Data User Manual for Post Helium Mission Phase 3 The S N of the superflat is estimated to be 100 for N2 and N3 and about 400 for N4 The superflats will be updated in future 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 Super flats are prepared for NP and NG As will be described at the end of this chapter these flats show spectral features which are not due to the sensitivity variation T here fore object spectra should not follow the flat pattern However this super flat with spectral features is used in the data reduction because the color term correction actually cancel out the spectral feature correction For flat fielding slit spectra including NG with
60. ctra 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 In the first pass of the source detection the automatic source detection sub program works even if the target table is supplied Version 1 1 August 28 2009 63 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
61. ctroscopy 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 large 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 66 IRC Data User Manual for Post Helium Mission Phase 3 Ask you local computer administrator for the IDL installation There are no special re quests in the IDL installation Ask you local computer administrator for the ds9 xpa
62. d of using the toolkit default flats In that case you have to prepare flat images for three filters N2 N3 and N4 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 soramam ari e 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 e greenbox anomalous_pix Mask Bad Dead pixels e greenbox dark Subtract dark current e greenbox ircnorm Normalization for sampling and data compression 46 IRC Data User Manual for Post Helium Mission Phase 3 greenbox cosmic_ray Detect and replace cosmic rays in MIR images greenbox linearity Correct linearity of the detector response greenbox saturation Mask saturated pixels greenbox slit_mask Masks the slit area of IRC field of view greenbox flat Flatten the pixels greenbox aspect_ratio Distortion Correction Aspect ratio resampling Alternatively the individual Green Box modules can be run interactively by 3 possi
63. d 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 along with the current flat dark distortion and linearization versions e g 40 IRC Data User Manual for Post Helium Mission Phase 3 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 and Dither Maneuvers M see Fig 2 2 4 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 channel The filename format is given as F _N 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 In addition to the Exposure Cycles 5 Dark frames are taken at the beginning and the end of the operation i e extra 10 FITS files Therefore as shown in Figure 2 2 4 for AOT IRCZ2 for a single pointing the maximum number of raw data files will comprise of 1 NIR EC x 7 EC 10 Dark 17 FITS files for one pointing Consequently for AOT IRCZ3 for a single pointing the raw data files will comprise of 1 NIR EC x 8 EC 10 Dark 18 FITS file
64. d 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 99 60 IRC Data User Manual for Post Helium Mission Phase 3 is due to the same mechanism to that of imaging mode and is corrected by interpolat 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 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 Saturati
65. d with the savefile savefile option and issue restore savefile command 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 pixel 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 grou
66. dd to form a co added image source_extract Perform source extraction x calcshift Calculate shift zrotation between images adjust_sky adjust sky level before stacking 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 NIR 412 512 pixels 16 bit pixel 8 bit byte 412 Kbyte frame e 1 NIR fits 412 Kbyte frame 2 frame fits 824 Kbyte fits file e AOTZO 6 exposure cycles pointing 1 NIR fits exposure cycle 10 8 Mbyte pointing e AOTZ2 6 exposure cycles pointing 1 NIR fits exposure cycle 10 8 Mbyte pointing e AOTZ3 6 exposure cycles pointing 1 NIR fits exposure cycle 10 8 Mbyte pointing The toolkit requires 3 or 4 times of disk space compared to the data 34 IRC Data User Manual for Post Helium Mission Phase 3 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 2a or later e gcc 3 0 or later e perl e curl for WCS calculation on Solaris machines We notice that the toolkit does not work properly under IRAF 2 14 and it is not fully tested with later versions of IRAF 2 14 5 4 2 Install IRAF e http i
67. dsk boolean yes or no default yes 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 RSfdmslCnDaF23342 N004 fits becomes ARSfdms1CnDaF23342 N004 fits 4 Image Stacking Co adding bluebox 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 52 IRC Data User Manual for Post Helium Mission Phase 3 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 pl1757132 N2_long fits pl Figure 5 10 13 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 putwcs adds WCS info
68. e 10 dark observations before and after the target observations in the same pointing is applied in the phase 3 data reduction The toolkit for phase 3 have several options to deal with this situation see sec tion 6 9 5 such as the usage of short exposure frames to detect point sources in the slit less modes Nc and Np 6 9 4 Response No change is noticed in the relative spectral response in phase 3 However the absolute sensi tivity is estimated to be 70 of the phase 2 based on observations of the standard stars This 88 IRC Data User Manual for Post Helium Mission Phase 3 is compatible with the result of imaging observations The 0 7 factor is included in the phase 3 toolkit On the other hand there is a problem unclear at present in the absolute calibration in short exposure frame data Therefore short exposure data cannot be used to estimate the flux accurately 6 9 5 New options for the phase 3 data reduction In irc_specred we have the following new options e use_short_refimage This option allows the program to use the short exposure image for the detection of point sources when they are saturated in the long exposure image e no_long_saturation mask This option dismisses the saturation mask for long exposure frames This option is useful for high background observations where the frame to frame shift measurement fails with the mask Try this option if you found unrealistic values in the X or Y shifts betw
69. e NG spectrum This is not a true feature Since this is a problem originating from the second order light there will be no recipe to correct for it for objects that have different colors from standard stars
70. e 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 template with spectra extracted from the spectroscopy data in question we estimate the relative drift For spectra of diffuse sources at the narrow slits Nh and Ns 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 12 7 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 12 7 shows the corresponding spectral data in which ghost spectra overlap with the source spectrum No definite origin for these ghosts has been elucidated and thus no clear recipe has been prepared to correct for them at present Figure 4 12 7 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 Instrument 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 fr
71. e 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_directory where to_your_working_directory should follow the rules explained in Section 5 6 1 5 6 3 Load the IRC_P3 package The irc_p3 package can be loaded by typing irc_p3 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 38 IRC Data User Manual for Post Helium Mission Phase 3 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 EA A OA datalo IFE NIET alot stsdas utilities dbms Wenas NDAD EN anes system xqd 1 MSLIM images language obsolete softools tables el GE BE O O O ARARI IRC imaging data reduction pipeline pipeline version G809274P3 Flat version O80925P3 linearity version 080924P3 aj CE 2005 Institute of Space and Astronautical Science Japan Aerospace Exploration Agency This version is only for Phase 3 datassk For help send emails to ijiris_help ir isas jaxa jp Jp SS SS O O O O O O SS O O SS SS O SS RR bluebax WE toal prepipeline Unlearn_al greenbox pipeline redb
72. e 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 Version 1 1 August 28 2009 83 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 that should be encompassed with single quotations e Running the pipeline Usage irc_specred lt targetid gt lt targetsubid gt lt ext_source_table gt lt refimage_list gt lt specimag
73. e wave_array specimage_n_wc_short mask_specimage_n source_table lt source_id gt 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 SGl nsum lt 10 SG2 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 e 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 is set in the smooth e g smooth 2 the actual smoothing box size would be smooth 1 e g smooth 3 e 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 opt
74. e_list gt lt filter_spec gt Options lt targetid gt pointing id of your observation Typically 1254567 Check your data distribution lt targetsubid gt pointing sub id of your observation Typically 1 Check your data distribution lt ext_source_table gt 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 lt refimage_list gt an ascii file that specifies the FITS file names of the reference images to be processed Typically either N3 1st S9W 1st or L18W 1st lt specimage_list gt an ascii file that specifies the FITS file names of the spec troscopy images to be processed Typically either NP 1st NG 1lst SG1 1st 54Z 1St or LG2 15G 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 L18W_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 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
75. ed frame e g following the format such as F23340 N001 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 or DARK e RA SET Right ascension coordinates e DEC SET Declination coordinates e AOT AOT type e g IRCZ2 IRCZ3 etc item EXPID Sequential frame number during an exposure cycle 1 or 2 e IDNUM Pointing ID e SUBID sub Pointing ID greater than 1 for multi pointing observations Version 1 1 August 28 2009 41 1 NIR FITS image Ll Ll N1 NIR short exposure frame N2 NIR long exposure frame Figure 5 7 6 IRC NIR raw FITS file data structure Figure 5 7 7 Image of NIR raw data The NIR raw FITS file is 2 frame deep corresponding to 1 short and 1 long exposure 42 IRC Data User Manual for Post Helium Mission Phase 3 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 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
76. een frames e use_short_for_wave_offset This option allows the program to determine the zero point of the wavelength in the short exposure frame This option works in a similar way for the spectroscopic images to use_short_refimage for the reference image data Try this option if the software cannot measure the zero point of the wavelength e short_saturation_mask With this option the saturation mask of short exposure frames of spectroscopy data is used to calculate the wavelength offset This is applied only for the spectroscopic data For the phase 2 toolkit the saturation mask is applied only for long exposure frames Similar saturation masks cannot be applied to the short exposure reference image because saturated pixels are treated as hot pixels and corrected by interpolation In the present software there is only one mask data which include hot pixels and saturated pixels e use_short_for_calc_x_shift This option allows the software to determine the shift between the spectroscopic images and the reference images from the short exposure frames With too many hot pixels it becomes difficult to determine the shift and this option may be useful For plot_spec_with_image we have the following option for the phase 3 data reduction e median 3 Whereas the shift and add process reduces the number of masked pixels in slit less observations the reduction of masked pixels is not expected for slit observations Ns and Nh a
77. es 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 e 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 e 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 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 e Warning ROB_MAPFIT Too few points This message comes from the fitting routine ROB_MAPFIT called from some of the toolkit programs T
78. g 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 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 recom
79. ge 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 SG2 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 86 IRC Data User Manual for Post Helium Mission Phase 3 The filename where the toolkit saves the information is always lt targetid gt
80. ge obtained after background subtraction has the following expression obs obj A x Fo x y A x R A Fi 2 y x spectral_feature z 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 registration 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 62 IRC Data User Manual for Post Helium
81. ges onds9 0 0008 76 6 5 2 Displaying the extracted images on ATV 76 6 5 3 Checking for wavelength zero reference point with the zero th order light IMM BO a AR A ee ee ss rg 694 Spe tralplotiine Ool eese cra riia aaea 4 wre a 78 6 5 5 Working on saved data 64 65 49 oe eo daw o oe id w bowie h ke os 80 Hopefully Useful Tips vw ae we 5 eee wt eo Ge arado 80 6 6 1 Getting best S N spectra in slit Ns Nh or Np spectroscopy data 80 6 6 2 Tackling narrow spikes seen in NIR spectra especially in slit spectra 80 6 6 3 Examining strange fake features in NP spectra especially around 2 4 3 5 PMs zene nasa ol 6 6 4 Examining flux level in consistency among different disperser data 81 APO ada esas are 82 6 1 Variable name conventions s raas ter inad erra ZA ES A 82 6 7 2 Summary of Commands and their Options 83 Error messages when running the pipeline and Troubleshooting 85 Tips for the Phase 3 data reduction 2 4i 4622668 486be s ue 4s 87 BOR ROVING san raros Poeun ERE GRE MEE GG 87 6 9 2 Spectroscopic performance 2 0 eee ee a 2 1 87 6 9 3 Dark current linearity and hot pixels 0 4 87 6 9 4 Response wena Sew eee eee ee ee ee ee ee Re A 87 6 9 5 New options for the phase 3 data reduction 88 6 9 6 Installation and usage of the toolkit for phase 3 1 1 1 1 1 88 6 9 7 Known problem
82. hape 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 reasons 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 f
83. has been developed for the phase 3 data re duction which is designed to work also for the phase 2 data However at the present the verification of IRC_SPEC_TOOLKIT_P3 has not yet been completed It is recommended that IRC_SPEC_TOOLKIT_P3 should be used exclusively for phase 3 data whereas for phase 2 data the previous IRC_SPEC_TOOLKIT be employed It should also be noted that the basic usage of IRC_SPEC_TOOLKIT_P3 is exatly the same as IRC_SPEC_TOOLKIT We provide special commands in IRC_SPEC_TOOLKIT_P3 to work with phase 3 data Therefore in the followings the chapters for the phase 2 data reduction remain which include those not relevant to the phase 3 data reduction such as MIR S and MIR L data reduction Users who are interested only in the phase 3 data can skip those descriptions In addition a chapter special for the phase 3 data reduction is added at the end section 6 9 Users who work on the phase 3 spectroscopic data should read this chapter carefully 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 combine
84. he 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 without 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 SOW_SHIFT_XY dat for registering S9W and L18W sub frames NP_SPECBOX_SHIFT_X dat for shifting SG2 LG2 along X in AOT 04a 14 IRC Data User Manual for Post Helium Mission Phase 3 NP_SPECBOX_SHIFT_Y dat for shifting the wavelength zero reference point for NP SG1 SG2 LG2 in AOT04a NG_SPECBOX_SHIFT_X dat for shifting SG2 LG2 along X in AOT04b NG_SPECBOX_
85. he 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 e Warning strange spec file list Stop The irc_specred reads list of FITS files to be processed NP lst NG lst SG1 lst SG2 lst 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 76 IRC Data User Manual for Post Helium Mission Phase 3 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 this 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 6 5 Working on the pipeline output 6 5 1 Displaying the whole i
86. ics to adjust sky level before coadding frames 44 IRC Data User Manual for Post Helium Mission Phase 3 1 Only the common area is used 2 The whole area is used det_sig real min 1 0 max 1000 0 default 4 0 Source detection threshold in sigmas sig_rej real min 0 0 max 100 0 default 3 0 Rejection unit in sigmas max_itr int min 1 max 10 default 10 Maximum number of iterations in statistical process obslog string default irclog NEVER CHANGE THIS Output filename of redbox mkirclog 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 selfdar boolean yes or no default no Use an alternative dark to the super dark provided coaddsh boolean yes or no default no Coadd short exposure frames as well as long ones 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 by typing Greenbox then running from inside the Green Box as anomalous_pix dark etc deltemp boolean yes or
87. ift pix y shift pix rotation deg and the number of stars used for the shift amp rotation angle calculation For example fdmslnDwaF01001_N003 fits coo 1 0 0 0 0 0 0 O fdmslnDwaF01007_NOO3 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 0 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 shift pix rotation deg and the number of stars used for the shift amp rotation angle calculation i e fdmslnDwaF01001 N003 fits coo 1 1 0 0 0 0 0 0 0 fdmslnDwaF01007_N003 fits coo 1 1 19 25942609 0 00474931 359 99288567 126 e 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 e 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 54 IRC Data User Manual for Post Helium Mission Phase 3 with a name skypair0002 N2 1list_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 s
88. ind 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 brighter neighbours to find the accuracy of the absolute flux calibration See section 6 5 4 for actual operation 82 IRC Data User Manual for Post Helium Mission Phase 3 e Wavelength offset error Because of the very low spectral resolution the spectral response c
89. ing an IRC data package a directory named AKARI_IRC_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 AOTs 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 11 13 IRC Data User Manual for Post Helium Mission Phase 3 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 file 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 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
90. ing 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 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 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 SG1 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 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 Strange features in the NP spectra taken with the big aperture for Nc pointing will be due to wrong calibration only if the features are seen not only in your target object but also in nearby field stars
91. installation There are no special requests in the ds9 xpa installation Get the irc_specred package from the AKARI Observer s web site see section 1 2 Extract and store it under your favorite directory Set the following environment variables in your command line shell Below is an example for csh setenv IRC_SPECRED_ROOT lt somewhere gt setenv IRC_SPECRED_LIB IRC_SPECRED_ROOT LIB setenv IRC_SPECRED_HOME IRC_SPECRED_ROOT ASTRO F 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_PATH have to be modified by substi tuting lt somewhere gt lt anotherwhere gt and lt IDL system path gt 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 lt root_dir gt lt targetid gt lt targetsubid gt irc_specred_out When the directory is missing the toolkit will create it 6 3 Calibration data When de packing the
92. int esupport IRC Data User Manual for Post Helium Mission Phase 3 Chapter 2 Instrument overview The Infrared Camera IRC onboard AKARI was originally designed to make wide field deep imaging and low resolution 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 In the phase 3 mission only the NIR camera is working and the MIR cameras are turned off In the followings however some description of the MIR cameras is also given 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
93. 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 gt 256 e refimage_list An ascii file listing FITS file names of reference image Example N3 1st cat N3 lst 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 lst cat NP lst 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 Version 1 1 August 28 2009 71 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 filter_spec a string specifying a disperser for the processing Set one of
94. ion 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 e 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 80 IRC Data User Manual for Post Helium Mission Phase 3 e 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 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 the 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 plottin
95. ion 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 Version 1 1 August 28 2009 79 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 e 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 lt space_shift gt nsum lt nsum gt a command in a single line 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 conti
96. ions longer wavelength comes at higher Y whereas NG shows negative dispersions longer wavelength comes at lower Y At the same stage the orientation of all NIR images is also set right i e the image is neither flipped nor mirrored Thus 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 the scan direction the Y axis is aligned closely with the ecliptic latitude while the X axis is aligned with the ecliptic longitude 18 IRC Data User Manual for Post Helium Mission Phase 3 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 Please be aware that the calibration for the phase 3 period has not been completed and the followings are preliminary results 4 1 Dark image Five dark images are taken before and after the target observation in a pointing observation for phase 3 The self dark image is created from these 10 dark frames This is
97. 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 OBS 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 DHU TT same format than above Version 1 1 August 28 2009 15 PIMTIREF is the DATE REF in PIM TI 36 bits DHUTI same format than above 177 _OBS and _END are identical with _ REF for convenience _ REF is Reference time from TI sampled during each exposure cycle This
98. is name anyname your working directory e g data rawdata data working The toolkit should be run in the working directory Thus you may create sets of these directory structures for different sets of IRC data Version 1 1 August 28 2009 37 polaireryita pud fhomeyita s tar xzf sample_data tgz e cd sample_data e mkdir yita 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_p3 package in the list of the IRAF packages If you install both the toolkits for phase 2 and phase3 both irc and irc_p3 should appear in the list of the IRAF packages see Fig 5 6 2 tem E E MOAQ PC IRAF Revision 2 12 2a EXPORT Wed Jul 14 20 45 34 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 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 news to find out what is new in the version of the system you are using The following commands or packages are currently defined dataia IFC lasts plata stsdas Utilities dems Ire Aaa noao a system d1msLum E images 1 angua ME obsolete spftools tables lee Here Figure 5 6 2 Start up screen for IRAF showing the IRC package visibl
99. itive 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 dY distortion function Xye Yref Polynomial coefficients are tabulated in a separate 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 SG2 L
100. ixed 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 observations 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 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 Maneuver 0 O Figure 2 2 4 Observation sequences of the AOT IRCZO Z2 Z3 and Z4 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 8 IRC Data User Manual for Post Helium Mission Phase 3 Table 2 3 3 IRC sensitivity and image quality N2 N3 N4 5 0 sensitivity uJy AOTZO 18 18 18 AOTZ2 Sl 21 AOTZ3 39 39 38 2 2 1 IRCZO The IRCZO mode was designed for deep imaging observations 2 2 2 IRCZ2 The IRCO02 mode was designed for general purp
101. k 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 11 Arrays anomalies NIR anomalies are shown in Figures 4 11 5 and 4 11 6 Most of them also affects the Spitzer IRAC instrument e Muxbleed e Muxstripes e Column pulldown e Banding 4 12 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 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 without knowing the
102. kind of pattern at the very Y edge of the FOV does occur only for the background light but not for object spectra 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 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 Version 1 1 August 28 2009 31 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 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 w
103. l 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 64 IRC Data User Manual for Post Helium Mission Phase 3 pixel As a first order correction we shift both the 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 15 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 si
104. led monochromatic flat fielding If we divide the observation by the super flat we obtain obs sky obj A x Fa x y A x R A F x y x spectral_feature 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 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 ima
105. mages 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 To display these images manually issue show_aperture_on_ds9 lt image gt source_table imag 2 where lt image gt could be refimage ff x 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 A
106. mend 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 Version 1 1 August 28 2009 81 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 6 6 3 Examining strange fake features in NP spectra especially around 2 4 3 9 um Sometimes an error in wavelength calibration leads to 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 s
107. n 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 CNTTYPE is the type of data content It can be IRC_NIR or IRC_MIR DATE is the file Creation Date CREATOR is the data generator program name CRTRVER is the version of CREATOR Contents TBD IRC Data User Manual for Post Helium Mission Phase 3 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 available 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
108. n 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 lt refimage_list gt lt specimage_list gt lt filter_spec gt 70 IRC Data User Manual for Post Helium Mission Phase 3 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 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 O i e coordinates of the lower left corner of the image is 1 1 not 0 0 For NIR the toolkit
109. nce we have only two broad band filters for MIR S MIR L S7 and S15 for MIR S and L15 and L24 for MIR L and three for NIR N2 N3 and N4 we 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 Fa x y A F z y A2 F z y A1 X2 A1 x A 11 F 2 y A1 6 1 4 where A and A are effective wavelength for broad band filters Therefore the color term in equation 6 1 3 is expressed as F a y A2 F zy A F x y A mi a ck ia ie bh 6 1 5 spectral_featurela y x Fila y spectral_feature z y x Fi z y 6 1 5 Therefore the color term correction is calculated by two broad band super flats and one spec troscopy super flat Note that the product F x y x spectral_feature x 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 A x R A 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
110. nd hot pixel masked pixels are often seen in the final stacked image With the option median 3 the data are median averaged in the spatial direction to make up the masked pixels This will be useful for observations of extended sources but it is introduced only to make the spectrum look better For scientific purposes users should apply more sophisticated methods 6 9 6 Installation and usage of the toolkit for phase 3 The installation of the toolkit is the same as that for phase 2 except that the software will be installed in the directory irc_spec_toolkit_p3 You should set the path to this directory To start the toolkit it is the same as for phase 2 for the observation of 12345678 1 obsID obs as IDL gt irc_specred 12345678 9 N3 1st NG 1st N3NG root_dir dir Version 1 1 August 28 2009 89 No change is needed also for plot_spec_with_image The toolkit automatically recognizes AOTZ4 data from the FITS headers The software irc_specred should be executed without any new options first and follow the same sequence as for the phase 2 data If your sources are too bright and saturated in long exposure reference image then use the option use_short_ref image If you find that a large fraction of the area is saturated in the long exposure frames of the spectroscopic images try the options use_short_refimage no_long_saturation mask short_saturation mask use_short_for_wave_offset use_short_for_calc_x_shift
111. nd 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 12 IRC Data User Manual for Post Helium Mission Phase 3 6 4 4 Outputs e Whole image products 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 refimage mask 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 images 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
112. ng 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 2 The actual 22 IRC Data User Manual for Post Helium Mission Phase 3 1 W ave NP A 7 0 6 NG Y 204 i y 0 2 0 1 2 3 4 5 6 Wavelength um Figure 4 5 4 The Relative Spectral Response Function of the IRC NIR dispersion elements per photon exposure time is the unit number x the unit exposure time tunit Which is approximately 0 5844 S Table 4 6 2 Exposure time of each band exposure configuration Band Exposure unit number NIR short 8 NIR long 76 One unit time corresponds to about 0 5844 s 4 6 1 Estimation of the in band flux The in band flux density of each band at the nominal wavelength NO was calculated by the following equation Vie R W fu du uoted vi hy i SS 4 6 1 Or O Mm 4 6 2 J R X AdA 3 A where 1 A is the flux density of a standard star Cohen template and R A is the spectral re sponse the transmission of the optics and the response of the detector unit electron photon Version 1 1 August 28 2009 23 of the band i Here f xv or fy x A is assumed The adopted normal wavelengths of each band A are listed in Table 4 6 3 along with the range of the integration Aie Table 4 6 3 The normal wavelength A and the range of integ
113. no default yes delete any temporary created files rejecti string none minmax ecdclip 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 pclip Reject pixels using sigma based on percentiles Version 1 1 August 28 2009 45 e 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 e 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 e coadd boolean yes or no 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 e 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 instea
114. nuum 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 e 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 lt filename gt 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 e with_image tvbottom lt tvbottom gt tvtop lt tvtop gt The 2D image will be shown on TV an IDL graphic window below the spectrum plot Extraction box for plotting 1D spectrum is overlaid The default is with_image 0 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 e diffuse For slit spectroscopy data spectra will be shown in units of MJy str rather than mJy with this opt
115. o plot the SGI spectra with IRAF SPLOT task splot xxxxxxx 1 59WSGl specimage_ fc_indiv fits Version 1 1 August 28 2009 73 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 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 the 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 t
116. on 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 2 Then the regions are 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 the
117. ose imaging observations that take images with two fixed filters in a pointed observation It provides at least three images for a filter with dithering operations 2 2 3 IRCZ3 The IRCZ3 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 IRCZ4 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 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 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 AOT are collected in Table 2 3 3 In the case of IRCZ4 Figures 2 3 5 and 2 3 6 show the 50 sensitivity for point and diffuse sources respectively as a function of A Version 1 1 August 28 2009 9 100 10 5o Detection Limit mJy es 4 5 5 5 9 2 2 5 3 39 4 l Wavelength um Figure 2 3 5 50 detection limits for point sources with NP or NG in IRCZ4 with the Ns slit 10 5o Detection Limit MJy sr IRC Data User Manual for Post Helium Mission Phase 3 2 2 5 3 3 5 4 45 p 5 5 Wavelength um
118. ow 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 1 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 ranges 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 w
119. ox 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 Version 1 1 August 28 2009 39 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 JE xterm EE TRAE Image Reduction and Analysis Facility PACKAGE irc_p3 TASK prepipel ine Circcons constants database IRC constants database file name verbose no Print verbose progress messages al mode listi Here 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 slice 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 comman
120. 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 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 Version 1 1 August 28 200
121. raf noao edu 5 4 3 Download IRC imaging data reduction software package The latest version of the toolkit with installation and operating instructions for the phase 3 data reduction can be obtained from the AKARI Observer s web site see section 1 2 It can be installed simultaneously with that for the phase 2 data reduction toolkit but must be installed in a different directory 5 4 4 Unpack irc_p3 tgz e mv ircYYMMDD tgz where you install irc_p3 e cd where install irc_p3 e tar xvzf ircY YMMDD_p3 tgz 5 4 5 Make irc binaries e cd where you install irc_p3 src 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 install irc_p3 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 install irc_p3 This line should indicate the location where you installed the irc_p3 package Version 1 1 August 28 2009 35 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
122. ration A and A band Ai Ai Ai N2 2 40 1 60 5 770 N3 3 20 1 60 5 770 N4 4 10 1 60 5 770 4 6 2 Absolute calibration The conversion factors for phase 3 imaging observations were derived based on observations of standard stars performed until March 2009 The results are summarized in Table 4 6 4 Note that the ratio of the conversion factors between the long and short exposures in the phase is not the one expected from the exposure time The reason is not known at present The calibration for phase 3 spectroscopy has not been completed We simply apply a factor of 0 7 reduction in the sensitivity in the spectroscopy pipeline toolkit at the present Table 4 6 4 Conversion factors ADU exposure to Jy Band short exposure error long exposure error ie Ji N2 5 50 x 107 1 85 6 60 x 107 2 16 N3 3 89x 107 1 96 4 95 x 107 2 37 N4 2 78 x107 2 13 3 62 x 1077 2 28 4 6 3 Stability of the sensitivity Although the temperature of the IRC is gradually increasing we do not so far see any systematic change in the sensitivity at the time when this document is being prepared Updated information on the stability will be posted on the web 4 7 Flux calibration for extended sources A correction factor should be applied to convert the point sources flux calibration into extended sources flux The absolute calibration for diffuse sources is being planned but is not available at present 24 IRC Data User Manual for Post Heli
123. rmation to the FITS images by matching with 2MASS catalog coordinates using the following procedure source extraction of stars from the IRC image download 2MASS catalog for the observed area convert 2MASS RA DEC to the x y image coodinates a b c d match 2MASS x y coordinates with image xy coordinates At this point there will be a list for extracted IRC stars corresponding to star x1 y2 ral 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 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 Version 1 1 August 28 2009 53 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
124. s ew ae cae ee ee ee kad wie WAWA 89 IRC Data User Manual for Post Helium Mission Phase 3 Chapter 1 Introduction 1 1 Purpose of this document This document is intended to provide a comprehensive guide to data taken during the post Helium hereafter phase 3 mission with the Infrared Camera IRC onboard AKARI for ob servers 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 opera tion is described in the AKARI IRC Data User Manual and is given in the AKARI first result volume Publications of the Japanease Astronomical Society volume 59 No SP2 Also see the AKARI Observer s Manual for the Post Helium Phase 3 Mission 1 2 Relevant information AKARI Observer s Web The ISAS Web page contains the most up to date information URL Attp www ir isas jaxa jp AKARI Observation The ESAC page also includes up to date information URL http 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 1sas jaxa jp http akari esac esa
125. s added during Green Box Pipeline Processing Prefix module action a greenbox anomalous_pix Mask Bad or Dead Pixels D ereenbox dark Dark Subtraction n greenbox norm Normalization C ereenbox cosmic_ray Detect and Replace Cosmic Rays greenbox linearity Linearity Correction S greenbox saturation Mask Saturated Pixels m greenbox slit mask Slit Mask f greenbox flat Flat Fielding e greenbox aspect_ratio Aspect Ratio Resampling 6 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 s1CnDaF23342_S004 fits becomes ms1CnDaF23342_N004 fits 7 Flat Fielding greenbox flat The flat fielding is made using the imaging super flats described in section 4 2 In the near future we plan to attach the most suitable flat images 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 After the flat fielding process a f will be added such that ms1CnDaF23342_N004 fits becomes fmslCnDaF23342_N004 fits 8 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
126. s 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 Therefore after running redbox ircslice on a single pointing for AOT IRCZ3 you can expect as many as 50 individual FITS files The filename format takes the original format with an extension defining the channel N and frame number 001 002 Fig 5 7 7 shows the images of IRC raw data for the NIR bands The orientation of the images are such that the NIR is rotated by 90 degrees 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 redbox mkirclog J 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 slic
127. s 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 detected 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 spe
128. se 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 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 x y x spectral_feature x y obj AX x Falx y A x ROA 6 1 1 Version 1 1 August 28 2009 61 where F x y is the flat in which the background spectral features are not present F x y x spectral_feature x y is the super flat Fa 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 cal
129. smic rays Try to compute wes and write it in the header JESEENES I EEGSTANEE da TAKAEF aia mediano sky_are 13 c det_sig 5 0 sig_rej 3 1 max_itr 105 Tie Log ves yes no no ves avsigelibi ves no ves ves del temp rejecti rej_sky submeds Cee Coadd short exposure frames Run pipeline interactively Delete intermediate files rej in coadd minmax cedcliplcrreject sigcliplavs Remove images with outlier sky level Subtract median filtered sky in adjust_sky Coadd Use pipeline s default flat defaul t More ARA For HELP 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 statist
130. solstices Note that the latter figures are in the MIR but similar variations should be present in the NIR 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 frames from irclog and run the pipeline again use rej sky yes option in order to ignore the bad frames cl gt pipeline rej sky yes 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 56 IRC Data User Manual for Post Helium Mission Phase 3 y box 20 If submedsky yes y box car size e Problem with short exposure frames with IRC At present no reliable estimate of the sensitivity in the short exposure frame data is obtained They can be used to check the saturation in the long exposure frame data but should not be used to derive the flux of bright objects NEP 2006 5 17 5 u s 4 p E Time In one polnted observation min Figure 5 13 14 Change in the background level in a pointing observation 5 13 2 Toolkit Limitations and Caveats 5 14 Error messages when running the pipeline and Troubleshoot ing 1 The pre pipeline stage sometimes give
131. tandard deviation e 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 z amp y offset for these frames The calcshift log file will also record any matching failures e darklist before 5 11 Toolkit structure Ro IRC imaging data reduction pipeline anomalous_pix outlier_ fits dark long fits s hort fits long fits short fits distortion _distortion_database dat flat fits slit mask slit mask_ fits constants database setenv dat setpath dat setpath pl welcome org perl Version 1 1 August 28 2009 55 5 12 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 toolkit and users are advised to re process using the latest version of the IRC toolkit 5 13 Limitations of the functionalities in the current version of the imaging toolkit 5 13 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 This effect could be related to the detector temperature
132. the following N3_NP N3_NG S9W_SG1 S9W_SG2 L18W_LG2 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 exposure 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_specre
133. 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 Preliminary flats are prepared for the Ns and Nh slits They have low S N ratios and they could degrade the data quality when applied Better flats are being prepared 4 3 Instrument linearity The detector operation parameters have been adjusted to accommodate the increase of the dark current in phase 3 This reduced the detector well capacity significantly and the saturation level changed from 12000 ADU in phase 2 to 2000 ADU in phase 3 Accordingly the linearity was changed The data taken with the calibration lamp is used for phase 3 data instead of the laboratory measurement to derive the linearity correction formula The data taken with constant illumination of the calibration lamp are fitted with a polynomial The correction accuracy is estimated to be about 5 for the range up to 2000 ADU Fig 4 3 2 shows the raw signal green and the signal after linearity correction red in ADU 20 Deviation o i i Sek 0 500 1000 1500 2000 2500 FIT ADU Figure 4 3 2 Raw signals green and signals after linearity correction red in units of ADU 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 October 2007 after the telescope focus adjus
134. tion process the original frame file names will receive additional R prefixes such that Sfdms1CnDaF23342_N004 fits be comes RSfdms1CnDaF23342_N004 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 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 list_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 rmme
135. tment It is slightly Version 1 1 August 28 2009 21 degraded from the phase 2 performance due to the degradation of the telescope image quality around 40K Onaka et al 2008 Proc of SPIE 7010 70102X Table 4 4 1 In orbit PSF in pixels The PSFs 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 45 RSRF Figures 4 5 3 and 4 5 4 show the relative spectral response functions for the NIR filters and dispersion elements No change has been recognized from phase 2 and the same RSR data can be used for the phase 3 data reduction N3 Relative Response O O O O N FR O 00 O 1 2 3 5 6 4 Wavelength um Figure 4 5 3 The Relative Spectral Response Function of the IRC NIR Camera for PY 4 6 Flux calibration for point sources Observations of the same standard stars employed in phase 2 are being executed At this stage only tentative absolute calibration results are available The raw data were reduced with the IRC imagi
136. types of dispersers 6 1 15 Spectral response calibration The spectral response calibration R A 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 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 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 spe
137. um Mission Phase 3 4 8 Color correction s mentioned in previous section the quoted values of the IRC flux calibration assume fy x A 1 For cases of other incident spetra the color correction is required The quoted value at a reference frequency is given by 3 MALE 52 iow hv da z ts V where R is the response in units of electron per photon The correction factor K is calculated as Ri v DEA i y EDO Pan dy foroted l z E 7 5 1 a actual E ee OR actual gg Aj factual Thus K is given by a Tx V dv We calculate the correction factors for the following incident spetrum cases HO a Z Sa 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 Aq 3 2um and A3 Alum Version 1 1 August 28 2009 Table 4 8 5 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 r0 30 90 396 131 100 164 506 110 81 786 120 873 058 46 429 130 297 140 29 139 140 121 814 19 760 150 98 297 14 242 160 31 767 10 776 170 19 291 8 482 180 12 811 6 895 190 9 149 5 156 200 6 928 4 914 210 5 496 4 270 220 982 603 4 526 3 178 230 316 052 3 999 3 389 240 181 324 3 336 3 069 250 109 374 2 955 2 810 300 16 057 1 952 2 024 3
138. urves 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 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 1 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 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 Th
139. xtracting 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 tool 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 gt source_table space profile specprofile wave_array specimage fc_ld 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
140. y 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 wm 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 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 pixe

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