SAMI Manual
Contents
1. 0 01 0 01 0 01 V R 0 11 0 01 X 10 r R 0 79 0 01 0 03 0 01 V R 0 04 0 01 X 11 i I 0 16 0 01 0 07 0 01 R T 0 02 0 01 X 12 where B V R and I are the magnitudes in the standard system b v r and 7 are the instrumental magnitudes corrected to the exposure time of 1s using a zero point of 25 0 mag and X is the air mass at the time of the observations The r m s deviations from the fits were 0 013 0 013 0 010 and 0 018 mag in B V R and I respectively 5 4 Quick astrometry tool L Fraga created a python script samiqastrometry py to determine offset and angle of SAMI images by referencing to star catalogs It is based on the autoastrometry py by D Perley which compares blindly stellar configurations in the image with the catalog and finds the orientation and offset It starts by running the sextractor to create a list of stars with pixel coordinates and magnitudes The sextractor and python packages numpy pyfits have to be installed to use this tool It is called from the command line as samiastrometry py mzfsoar20121203 026 fits px 0 0455 c tmc if the 2MASS catalog is used Astrometric information is encoded in the FITS header in the form of RA TAN and DEC TAN WCS keywords linear transformation from pixels to RA DEC The image with modified header is saved in the separate file with the a prefix At the end of the header the rms differ2. 10 the sky coordinates degrees not in pixels Therefore the coefficients will depend on the position angle They can be pre calculated for the 4 standard position angles 6 Known problems Problems with SAMI or its data that were encountered during its short lifetime are listed without specific order The SAMI GUI freezes no reaction to commands Dirty exit and re start normally help Filters do not move or do not reach position Try to send the Move command again If the wheel still does not move it may be really stuck Balancing the filters avoid several open positions on one side might help During VNC connection to SAMI the screen freezes and the cursor is replaced by a cross This usually happens after moving windows Wait for 30s the normal cursor comes back again SAMI gets no light Check that SOAR is opened and configured for SAM M3 position and M4 in the ISB that the SAM environmental shutter is open and that the SAM output selector mirror is in the SAMI position A point light source in the SAM guide probe can be placed at center and imaged for a test Deep images in the B filter show a dark cross in the middle and increased background This is the scattered laser light at 355 nm that leaks through SAM dichroic and B filter Nothing can be done about it now Deep images in the V filter show a gradient of the background This is caused by a light source in the SOAR ISB Eventually this will be e
3. point between half max FWHM A and maximum transmission Tmax of the SAMI BV RI filters The last column gives the relative efficiency of SAM SAMI in comparison with the SOAR Optical Imager SOI as measured by L Fraga on the sky In all bands except B SAMI records more photons than SOI per unit time photons or ADU The red SAMI filters transmit more light than the SOI filters the SAM s internal transmission at 633 nm is 0 900 06 R Tighe 100 Transmission percent 300 400 500 600 700 800 900 Wavelength nm Figure 1 Transmission curves of SAMI BV RI filters measurements by D H lck on August 25 2010 Table 1 SAMI filters and efficiency Filt Xo A Tmax SAMI SOI B 4342 984 58 3 0 71 V 5371 892 72 5 1 01 R 6441 1536 76 9 1 58 I 8103 1429 93 8 1 16 Note that the UV laser light at 355nm leaks slightly in the B filter This is seen as extra sky background with a dark cross at the center 2 Detector and electronics The CCD is housed in a liquid nitrogen dewar fabricated at CTIO The hold time is more than 24h The window in front of the ccd is made of fused silica has 9mm thickness and is AR coated with MgF gt 2 The CCD surface is at 4mm behind the window The SDSU controller of SAMI is located close to the dewar Fig 2 It works without cover to prevent over heating Therefore the glycol cooling does not extract the heat generated by the controller as well as b
4. For SAMI the correct relations are DECPANGL PA 1 RAPANGL PA 90 2 The keywords in the SAMI headers actually correspond to these relations For example the image mzfsoar20121203 028 fits has http iraf noao edu projects ccdmosaic imagedef fitsdic html RAPANGL 270 Position angle of RA axis deg DECPANGL 180 Position angle of DEC axis deg which corresponds to PA 180 In this case RAPANGL 90 would be also correct The actual orientation of SAM frames on the sky can differ by as much as 0 5 from the nominal orientation This was determined by linear astrometric solutions with quickastrometry Depending on the density of stars the North direction relative to the SAMI Y axis On orn is determined with standard errors between 0 2 and 0 3 The accuracy increases to 0 1 when SAMI image is corrected for distortion see below The SAM guider Y axis is rotated w r t SAMI Y axis by Osamr 0 12 as determined by imaging the fiber light source in SAMI at various positions 4 2 Pixel scale The pixel scale of SAMI is 45 5 0 05 mas as determined by quickastrometry With 15 um pixels this corresponds to the effective telescope focal length of 68 00 m The pixel scale corresponds to CDELT of 1 2639E 5 degrees per pixel However this keyword is not used by FITS nowadays being replaced by the matrix CD that transforms pixels to degrees on the sky Combining the scale and orientation the ele
5. distortion are discussed in Sect 5 5 below 5 Data reduction 5 1 Image display The images are written as multi extension FITS files To display those data in DS9 use Open Other Open Mosaic IRAF in the File menu Alternatively display the images in IRAF Run IRAF in the xgterm window and load the packages gt iraf gt ecl gt mscred to work with mosaic images Also do not forget the command gt set imt 4096 at the beginning Go to the image directory and use the following typical commands mscdisplay soar20130225 0037 fits zs zr z1 0 z2 40000 mscexam Note that star coordinates and FWHM are reported by IRAF in un binned pixels even for images with binning To show image in standard orientation matching the GMAP display in SAM North up East left flip the X axis in DS9 in the Zoom menu 5 2 Basic reductions bias and flat field L Fraga has set up a reduction pipeline at the soarpd1 computer SAMI data are transferred to this computer The pipeline works in pyraf See the description at http www ctio noao edu fraga pysoar tasks sami doc cookbook html The instructions are as follows e Go to the data directory e g cd home observer data 2012 03 01 Suggestion create a RED directory and copy all your data to it Go to the RED directory Important The calibration frames biases and flat fields and the science frames must be in the same directory If you already have the master bias and master flats just copy both to
6. the same directory e Run the pipeline with the command line soipipe py When the script is finished you are going to reduced files with the following nomenclature The script will create lists of images as below OSAMIList_Zerolx1 List of biases with binning 1x1 1SAMIList_Flat1x1B List of dome flat fields with binning 1x1 and filter B 2SAMIList_SFlat1x1B List of sky flat fields with binning 1x1 and filter B 3SAMIList_Dark1x1 List of dark frames with binning 1x1 ASAMIList_OBJ1x1B List of science images with binning 1x1 and filter B For a raw science frame like image 001 fits the reduced frame will be like mzfimage 001 fits The prefix z means zero subtract f means flat field divided and m means that the file has been converted from multi extesion FITS to single continuous image 5 3 Photometric system Calibration of the SAMI BV RI system against standards was done by L Fraga in 2012 2 Here we give an extract from his paper Fraga L et al 2013 AJ submitted In order to transform instrumental magnitudes and colors into the standard system calibration images were obtained with SAMI in open loop under photometric conditions during the night of 2012 June 6 The zeropoint color terms and extinction were determined using the IRAF package photcal through a uniformly weighted fit of the following transformation equations b B 0 06 0 03 0 21 0 01 B V 0 18 0 02 X 9 v V 0 48
7. S catalog The pixel coordinates corresponding to the catalogued stars are calculated from the information in the FITS header 3 The following steps are executed in IRAF Load the packages digiphot and appphot Display the image mark the stars by gt tvmark coord image xy label mark circle 4 Find centroids of the stars by the IRAF command gt center aimage fits coords image xy cbox 25 output image1 xy If the files imagel xy and image2 xy already exist from previous iterations they must be deleted first 5 Transform the IRAF output into a 2 column file by the command gt txdump image1 xy xcent ycent yes gt image2 xy 6 Combine the RA DEC and x y in a 5 column text file by the python script side by side py image radec image2 xy gt ccdmap dat 7 Determine the distortion correction by gt ccmap aimage fits The parameters of this procedure should be set to take long lat from columns 1 2 and x y from columns 4 5 of the input file ccmap dat The result is written in the FITS header of the image 8 Iterate by re computing the centroids in a smaller box repeat from step 4 with a smaller cbox Application of this procedure results in the rms residuals from 0 04 1 pixel to 0 07 In principle it is possible to provide a first order distortion correction in the raw images by pre calculating the polynomials in WATj_nnn The difficulty is that these transformations are defined in 3http iraf noao edu projects ccdmosaic tnx html
8. SAMI Manual Full frame image of planetary nebula NGC 2440 in Ha filter taken with SAMI on February 26 2013 Exposure time 60s FWHM resolution 0 32 binning 2x2 Prepared by A Tokovinin Version 1 Date March 13 2013 File soar SAMI doc sami manual tex Contents 1 Overview SAMI at a glance 2 2 Detector and electronics 3 3 Image acquisition 5 4 Geometry 5 Al Orientation on the sky 14 esta 2a en ge oe Ag se ie Ph gO 5 42 Pixel Scalea ag se se gti band hd Be eee Gl fo End hE Bley fae ate en ae fetes a 7 ds DIStOPUON we fst ah a GEA Mesa ects amp eb We kee the ck SE A he we ee ai 7 5 Data reduction 8 5 Imaperdisplay ics Oe alter shed ee Nk A Bl ce A ie gs oe aes hh ad Ig a Eo 8 5 2 Basic reductions bias and flat field 2 2 20 2 0 0 0 0 0 200008 8 53 Photome tric system fx 6 ee aida 8 cee ee a Gp ane a es e 8 5 4 Quick astrom try tol sias ecg ae og RO cee Be Ea we YA ete 9 dD Distortion COrechiOnes lt 6 a ek ed Re ae AE ad A i a t 9 6 Known problems 11 1 Overview SAMI at a glance SAMI is the CCD imager used together with the SOAR Adaptive Module SAM A brief overview of SAMI given in this Section should be sufficient for writing proposals while more details are found in the rest of this document The CCD detector has a format of 4096 H x4112 V pixels continuous not a mosaic The physical pixel size is 15x15 wm or image area 61 4x61 4mm The chip is CCD231 84 from E2V It is bac
9. e properties of the resulting image when the signal is combined from several adjacent pixels the noise is reduced while in the pixels that are displaced by a near integer number the noise is not affected If a list of star positions in pixels is created by some star finding routine such as sextractor it can be passed through a filter that would produce the undistorted list Such filter can be written in any language e g in pyraf It is recommendable to use such filter before running quickastrometry Non linear relation between the CCD coordinates in pixels and the WCS in degrees on the sky can be encoded in the FITS header Unfortunately there is no universally accepted FITS standard for non linear WCS transformations One such convention the RA TNX and DEC TNX WCS system is recognized by IRAF The linear part of the transformation from pixels to degrees is encoded in the CD matrix as in the TNG tangential WCS system Then polynomial corrections are added defined by the WATj_nnn keywords Polynomials of order 3 with half cross terms are recommended The procedure for SAMI astrometric calibration is as follows 1 In a terminal run the samiqastrometry py on the image fits to get first order astrometry in aimage fits 2 In the same terminal run the python script scat py to create lists of catalog coordinates and corresponding pixel coordinates in image radec and image xy respectively The script requires astLib It queries the 2MAS
10. ecommended for easing the load on TCS connections while SAMI is not used If this does not work e g when the SAMI GUI hangs kill the window Then open the terminal check for Labview processes with the command ps ax and kill the Labview process corresponding to SAMI to finish the dirty exit 4 Geometry 4 1 Orientation on the sky The position angle of the Nasmyth rotator is not written in the FITS headers of the SAMI images Instead they contain the keywords RAPANGL and DECPANGL According to the mosaic FITS perate Tools Window Help 7 SAMI Miter Control SOAR Adaptive ra a Ro r Vaccum SOAR Telescope Module Imager White Spot Leach Controller X Y 2098 2056 Box size x Y a00 faao W Roi Enable Universal Time Rotator 1 22 31 51 077 15 44 08 9 0 0000 ua E Pr Binning 22 Mount Dec E 30 17 19 402 oo 0 0000 mm Display image Write Proc PEA iam Grid eee mm imm Controller State pe Mode NORMAL ae Time ADC 22 26 58 7 E e000 SAM_ADC mome2 images 20130303 Zero Object Dak Drar Sfat Fitr Observation Tille tia Wi Exp ExpTime sec aq Inso Obs Editor Fitter Editor Geometry Gria Toot script Toot Grange Par oftset Engineering Figure 3 GUI of the SAMI data taking software convention these keywords indicate the position angle of the RA and DEC axes relative to the Y axis of the CCD counting positive CCW
11. ence between catalog and star centroids and the rotation are listed as ASTR_UNC 0 09891016893935835 Astrometric scatter vs catalog arcsec ASTR_SPA 0 09456702004780501 Measured uncertainty in PA degrees ASTR_DPA 180 749724946754 Change in PA degrees The ASTR_DPA angle is counted from the Y axis CCW same at DECPANGL The procedure does not change the pixel scale in the FITS header We note that the SAMI data in December 2012 had PA offset of 0 8 while this offset was 0 2 in March and May 2012 The SOAR TCS therefore does not maintain a very accurate alignment of the Nasmyth rotator with celestial coordinates 5 5 Distortion correction The ways to deal with distortion in SAMI depend on the goals Distortion prevents simple co addition of dithered images or mosaicing In this case images must be re binned into undistorted pixels before recombination If on the other hand we just want to do astrometry correcting the world coordinate system WCS in the FITS header is the best way to proceed For image un wrapping the IDL program samiwrap pro was written It uses the standard IDL procedure poly_2d and implements the equations 8 where the polynomial coefficients were determined by samipoly pro We use bi linear interpolation to make this transformation as local as possible the cubic interpolation uses a larger patch of the image and spreads the cosmic ray events over several pixels The interpolation affects nois
12. k illuminated with astro broad band AR coating and quantum efficiency around 90 between 500 nm and 700 nm manufacturer s data The CCD is read out through 4 amplifiers using the SDSU III Leach controller The image is written in a multi extension FITS file The readout time of the full frame without binning is about 8s the gain is 2 1 electrons per ADU and the readout noise is 1 83 ADU or 3 8el Pattern noise is absent The response is linear to 0 5 up to the digital saturation at 65536 ADU 16 bit unsigned integer The blade shutter of SAMI can realize exposures as short as 0 1s The sky is projected onto the CCD through SAM without changing the effective focal length of the SOAR telescope 68 0m This gives a pixel scale of 45 5mas and the square field of view of 186 3 1 With nominal SAM position angle of 0 the X axis increasing pixel count along the line points East Y axis increasing line count points North The angle between Y and North is typically within 0 5 from zero depending on the SOAR Nasmyth rotator setting The optics of SAM introduces quadratic distortion reaching 42 pixels in the corners of the CCD see below SAMI has one filter wheel with 7 positions for 3 square filters The Bessell BV RI filters are installed permanently the remaining 3 positions are occupied by narrow band filters for now Ha only Filter transmission curves are plotted in Fig 1 Table 1 lists the central wavelength Xo mid
13. liminated The star images have cometary tails on one side or several fainter rays These defects are caused by the SAM AO system they are reduced by proper tuning of the SAM AO loop Stars have bright long tails This is caused by divergence of the SAM tip tilt guiding loop due to wrong information received from the TCS Discard those images 11
14. ments of this matrix should be set for SAMI to CD11 1 2639E 5 x cos CD22 1 2639E 5 x cos CD12 1 2639E 5 x sin 0 CD21 1 2639E 5 x sind e E e gt Ae w aD SSF Ney Se NE where 0 DECPANGL PA for SAMI The non diagonal terms CD1_2 and CD2_1 become leading when the position angle is 90 or 270 4 3 Distortion The re imaging system of SAM has substantial distortion reaching 42 pixels 1 93 on the sky in the corners of the image It was studied in the SDN 2325 by measuring pixel coordinates of point light sources on the guide probes that were placed at different positions in the field using the XY stages these measures were repeated on March 4 2013 and confirmed the previous result The distortion is well described by quadratic terms in X and Y Ay Cele x Coy y yo 7 Ay Cyg ro Cyy Y yo 8 where Ax and Ay are the corrections to the star position in pixels to be added for removing the distortion x and y are the measured star coordinates xo 2048 and yo 2056 are the CCD centers All coordinates here are determined in original un binned pixels The coefficients are determined to be Cry 2 00E 6 Cry 2 15 6 Cyr 4 24E 6 Cyy 4 37E 6 Unlike classical radial distortion in optical instruments the distortion in SAMI moves stars in the same direction down and to the right in all corners of the field Ways to account for the
15. rhrc computer IP 139 229 15 163 It is accessed by VNC connection to soarhre 9 To launch the SAMI GUI use the icon in the desktop menu in the lower right corner The SAMI software was cloned from SOI it is nearly identical Figure 3 is a screen shot of the SAMI GUI the instrument was switched off when it was taken The GUI is self explanatory Its upper part shows information on temperatures information from the TCS progress of current exposure and readout and current detector geometry binning and ROI Just below we enter the data directory like home2 images 20130225 and base file name like soar20130225 The lower left part greyed out in the figure is used to set the object name exposure duration and the number of exposures The lower right panel changes the filters select the new filter then press Move and verify that it actually changed The buttons in the bottom part of the GUI activate respective plug ins opening additional win dows See the future document on SAMI software for details Each acquired image can be immediately displayed if the DS9 program is running and if the real time display is enabled in the Misc plug in of SAMI GUI Note however that this display has some problems and that the pixel coordinates shown by this display are different from the true coordinates We recommend to disable the real time display and to examine the images using IRAF Use the button Exit in the upper right to exit the software this is r
16. variance There is some additional low frequency noise in the quadrants amplifiers 1 and 2 but only white noise in quadrants 3 and 4 Table 3 reports noise in each CCD quadrant calculated from bias images in 3 different ways on the bias section on the image section and by considering only the white noise floor These noise characteristics were achieved with the small power supply a larger power supply used originally caused increased pattern noise The filter wheel and shutter mechanisms of SAMI are controlled by electronic modules in SAM Table 3 Noise in SAMI ADU rms per quadrant normal mode Condition Ql Q2 Q3 Q4 Bias section 1 85 1 99 2 13 1 42 Image 2 54 2 84 2 12 2 05 Noise floor 1 78 1 84 1 50 1 97 When SAM electronics is powered off SAMI cannot be used The filter wheel of SAMI is designed to be interchangeable with the wheel of SOI which has 5 positions with 4 square filters Such wheel swap has not been tested yet To remove the filter wheel disconnect its motor and free the holding screw on the left side of the wheel Be careful not to damage the cables that obstruct access to the wheel Fig 2 It is a good idea to select empty filter before removing the wheel thus protecting the filters from occasional damage After each filter wheel manipulation the dust on the filters changes and new flat field calibrations must be taken 3 Image acquisition The SAMI data acquisition software runs on the soa
17. y its power supply and it degrades the environment in the SOAR dome Preliminary results of CCD tests in the laboratory prior to the installation on SAM are reported by R Schmidt file SAMI_acceptancel xls and reproduced below in Table 2 n a stands for non available Dewar Power supply Leach controller Filter wheel Figure 2 View of SAMI Table 2 Characteristics of the SAMI detector in the lab measured by R Schmidt Parameter Slow Normal Fast Gain el ADU 0 66 2 1 4 85 Noise ADU 3 71 1 83 1 27 Full well el n a n a gt 200kel Non linearity n a n a lt 0 5 Charge transfer efficiency n a gt 0 9999927 n a Pixel time ps 5 20 2 320 1 60 Dwell time ns 2120 680 320 The detector has several hot pixels the most prominent are at 1961 1962 707 1553 911 696 and 744 402 The average dark current at the nominal CCD temperature of 120 C is lt 2 el pixel hour It was found that the CCD temperature rises by 5 when the chip is not clocked e g during long exposures Otherwise the long term stability of the temperature control is 1 or better No pattern noise in the bias images was noticed in the initial lab tests However Fourier spectrum of the signal in each CCD line reveals periodic components with periods of 5 and 2 5 pixels As these frequencies are exact multiples of the pixel time their origin is most likely in the controller This periodic noise does not dominate the overall
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