Aperture Photometry Tool
Contents
1. 50 60 Sky noise data number 45 50 55 60 65 70 75 80 Sky scale data number FIG 16 Comparison of source noise computed by APT vs SExtractor for cases 1 left and 2 right The top panels are scatter plots of the relative percentage error between SExtractor and APT versus source intensity The middle panels are scatter plots of the relative percentage error between SExtractor and APT versus sky noise The bottom panels are scatter plots of the relative percentage error between SExtractor and APT versus sky scale2. is as follows Section II gives basic APT usage instructions for users wanting a quick start Section III explains how APT does sky background estimation and the available options for controlling it Get Image FITS Header 5 C Source List About amp Help Exit Lower boundof stretch Mjy sr 2 4598e 01 Upper bound of stretch Mjy sr 2 5623e 01 Stretch to Bounds C Stretch to Min Max 4 Image Histogram p i image Comparator Adjust stretch min percentile of set range Adjust stretch max percentile of set range 0 20 40 60 80 100 0 20 40 60 80 100 Log Stretch Enabled tt YY Dynamic range x 100 l Enable Linear Stretch 0 100 200 300 400 500 Centroid radius pix 5 Inner sky radius pix 8 Aperture radius pix L gt o a gt Aperture Slice Source Scatter Sky Scatter C Hide Show Aperture p Curve of Growth ye Radial Profile 3 z Sky Histogram Y L Color Table Toggle B wore eee ee nee REAL TIME RESULTS Cursor X Y 282 2932 Blink Refresh C Refresh2 R A Dec 14h28m20 7s 35d24m17 4s Image 1 Magnify O sx Pixel value 2 5349e 01 Miy sr Aperture X Y A 2 932 fa Centroid X Y 281 59 2935 40 Snap Photometry data units Mjy sr Source_intensity sky subtracted 5 770e 01 Source_noise 3 449e 00 Sky_median Sky_average 2 467 01 2 469e 01 Sky_scale Sky_moise 6 055e 02 1 15le 0
3. line along the obvious lower range leading edge of the data points the slope of the line formed by the data in the bottom panel is the same as the lower range lead ing edge of the data in the corresponding middle panel which is not readily seen because the horizontal axes have different scales Thus it can now be easily seen that the discrepancy in source noise estimates between APT and SExtractor increases with increasing sky scale It is unclear whether this effect can be attributed to the un certainty in background estimation rather than to the background estimation itself The devil is in the details but further investigation is beyond the scope of this pa per XVII CONCLUSION We have introduced important new software for the astronomical community that facilitates the visualiza tion of aperture photometry APT is appropriate useful and convenient for professional work and it is also now playing a vital role in educating the next generation of astronomers in the United States It has been success fully utilized in the past Spitzer Teachers program and will be the centerpiece of the newly formed NASA IPAC Archive Teacher Research Project NITARP There are indubitably many reasons that give APT a purpose in today s world and chief among them are its graphical 1 E Bertin and S Arnouts Astronomy and Astrophysics Supp Ser 117 393 1996 2 D C Wells E W Greisen and R H Harten Astronomy and Astrophysics
4. 1 More Settings p C Recompute Photometry Save Photometry Data Show Photometry File 10x 20x ENEN REAL TIME RESULTS Cursor X Y 266 2945 Pixel value 2 4604 01 Mjy sr Erro 247440901 FIG 1 Main GUI panel of APT Section IV provides details on how APT does aperture photometry calculations and what options are available for refining it Section V by way furnishing indispensi ble non patent information relates crucial miscellaneous APT features and behaviors Subsequent sections discuss APT s salient components functions and functionality user preferences output files columns in output photom etry table graphs radial profile interpolation zoom pick tool source list tool image comparator and blink capa bility software limitations and troubleshooting and bug reporting The paper crescendoes with a quantitative comparison of similar calculational results from SExtrac tor and APT and finally resolves with a concluding section II BASIC USAGE INSTRUCTIONS APT is simple to use Basically you display a FITS image and then mouse click on a source or astronom ical object in the image to overlay a circular aperture on it The latter action causes the software to automat ically compute source centroid position source intensity source noise sky background level and sky background noise The default sky algorithm is no sky background subtraction f
5. 997 CCDID 8 The right panel is a histogram of the relative percentage errors for all case 1 filtered sources Relative error 10 SRE LL LL tt n 1 0E 04 1 0E 05 Source Intensity data number 1 0E 06 Relative error 0 50 100 150 200 250 300 350 400 Number of sources FIG 15 Comparison of source intensity computed by APT vs SExtractor for case 2 The left panel is a scatter plot of the relative percentage error between SExtractor and APT as a function of source intensity for the 2 653 filtered sources from PTF image PTF200912015481_2_0_2116 CCDID 8 The right panel is a histogram of the relative percentage errors for all case 2 filtered sources filtered sources of cases 1 and 2 are shown The top panels are scatter plots of the source noise relative per centage error between SExtractor and APT as a function of source intensity which have median values of 2 73 for case 1 and 2 48 for case 2 As might be ex pected the larger discrepancy occurs for case 1 which has the higher background of the two cases The nega tive values indicate that APT overestimates the source noise relative to SExtractor which may not be a sur prising result because APT includes the uncertainty of the background estimation whereas SExtractor does not according to 3 Moreover a comparable plot of SEx tractor s FLUXERR versus FLUX results in a locus of data points that fairly sm
6. Aperture Photometry Tool Russ R Laher and Luisa M Rebull Spitzer Science Center California Institute of Technology M S 314 6 Pasadena CA 91125 Varoujan Gorjian Frank J Masci John W Fowler and George X Helou Infrared Processing and Analysis Center California Institute of Technology M S 100 22 Pasadena CA 91125 Shrinivas R Kulkarni Caltech Optical Observatories California Institute of Technology M S 249 17 Pasadena CA 91125 Nicholas M Law Dunlap Institute for Astronomy and Astrophysics University of Toronto 50 St George St Rm 101 Toronto ON Canada M5S 3H4 Dated January 4 2010 Aperture Photometry Tool APT is software for astronomers interested in manually exploring the photometric qualities of astronomical images It is a graphical user interface GUI designed to allow aperture photometry calculations to be visualized The finely tuned layout of the GUI along with judicious use of color coding and alerting is intended to give maximal user utility and convenience and minimal chance of blunders Simply clicking on a source in the displayed image will instantly compute and print out source intensity and noise along with both non robust and robust measures of the sky background and noise APT is geared toward processing sources in a small number of images and is not suitable for bulk processing a large number of images unlike other aperture photometry packages e g SExtractor However APT does have a conve
7. Supp Ser 44 363 1981 3 E Bertin SEzstractor v 2 5 User s Manual Institut dAstrophysique amp Observatoire de Paris 2006 4 F Masci and R R Laher PASP manuscript in prepa ration 2010 20 user interface and feedback machine independence ease of installation and use and accuracy The latter was clearly demonstrated here by comparing similar results between SExtractor and APT It is expected that APT will be upgraded over time to shake out any remaining bugs and augment the software with new functionality and capabilities Acknowledgments APT requires the following packages JFreeChart www jfree org JRegEx jregex sourceforge net and Jama math nist gov javanumerics jama plus a hand ful of the Spitzer Spot Leopard Java classes for astrom etry These come packaged with APT and so the user need not install them separately We wish to thank the beta testers In particular Drs Tom Jarrett Seppo Laine Robert Lupton Alberto Crespo Noriega Bill Reach Nancy Silbermann and Jeonghee Rho made numerous helpful suggestions We are also grateful to Xiuqin Wu Trey Roby Loi Ly and Booth Hartley for generous expert Java programming help and the use of their Spitzer SPOT Leopard Java classes This research made use of Montage funded by the National Aeronautics and Space Administration s Earth Science Technology Office Computation Technologies Project under Cooperative Agreement Number NCC5 626 bet
8. graphical user interface GUI as shown in Fig ure 13 The software enables aperture photometry to be performed interactively and gives visual feedback in various ways to facilitate calculational refinement APT is meant to complement rather than supplant popular non interactive batch mode aperture photometry soft ware such as the increasingly popular SExtractor 1 The initial beta version of APT was released in Novem ber of 2007 and since that time there have been many releases of the package to add new capabilities and fix bugs APT is available free of charge to anyone from Electronic address laher ipac caltech edu http spider ipac caltech edu staff laher apt This URL has download installation instructions for a variety of computer operating systems including but not limited to Mac OS X Linux Windows and Solaris APT is an all Java software implementation There are no software dependencies on other astronomical packages or libraries However you will need to have a recent version of the Java Runtime Environment JRE installed on your machine Version 1 0 0 of APT was compiled with javac 1 5 0_16 APT s minimum memory requirement is probably around 4 MBytes APT can be used on machines with relatively small memories to analyze portions of very large images which is effected by setting the maximum image size under APT s Preferences menu to as little as 500 pixels on a side The layout of this paper
9. l more on this in Section IV be low The inner and outer radii of the sky annulus in integer pixels only can be specified on the main GUI panel On the control panel that pops up after clicking on the More Settings button the user can select from one of four available sky algorithms 1 No background subtraction 2 Sky median subtraction 3 Custom sky subtraction or 4 Sky mean subtraction Only sky median subtraction is insensitive to other sources that may fall within the sky annulus which might otherwise cause the background to be overestimated Ac cording to Bertin and Arnouts 1 strictly speaking the background includes everything but the source in the ret icle of the aperture As a practical matter we estimate the background in the aperture from the sky annulus that surrounds it An intense source in the sky annulus con tributes to the background in the aperture and its effect is not necessarily something that is to be completely ig nored or filtered out which is why APT has a variety of sky models from which to choose The More Settings panel also has text fields where the user can optionally specify lower and upper thresh olds for rejection of outlier pixels in the sky annulus from the background calculation The default values for the lower and upper thresholds are the largest possible nega tive and positive double precision numbers respectively so that by default no pixels are rejected Val
10. lt sub pixel size is 0 01 pixels which can cause the computations to take several sec onds for very large centroid aperture and or sky annulus radii The sub pixel size can be changed via the Prefer ences menu By default the aperture photometry calculation is per formed with the aperture centered on the calculated cen troid to the resolution given by the sub pixel size The Centroid X Y label on the lower left of the main GUI panel is displayed in a green color to indicate that centroiding is enabled Un checking the Use centroid in photometry calculation check box on the More Set tings panel will cause the photometry calculation to re vert to centering the aperture on the integer pixel co ordinates of the selected aperture position and be per formed on whole pixels only The More Settings panel 10 8 4 Saat a a eg a Aperture radius 5 pixels oe Barks ee om 44 OPE SOLO ak A E 24 Ne p e 5 Je 5 0 v E 2 v a 64 8 74 10 AAA er 1 0E 03 1 0E 04 1 0E 05 1 0E 06 Source intensity data number 19 Relative error 10 T t T T T 0 50 100 150 200 250 300 Number of sources FIG 14 Comparison of source intensity computed by APT vs SExtractor for case 1 The left panel is a scatter plot of the relative percentage error between SExtractor and APT as a function of source intensity for the 2 069 filtered sources from PTF image PTF200912018278_2_0_1
11. ngs as needed Redraw overlay new aperture by either clicking on Recompute Photometry button OR clicking on Snap button for nudging the aperture toward the integer pixel coordinates of the source centroid lo cation OR placing mouse cursor on image and click ing If necessary increment decrement aperture posi tion using the spinner controls for fine tuning the aperture s position Click on Recompute Photometry button to re draw overlay new aperture Show study the various graphs again 12 13 IIT Optionally click on Save Photometry Data but ton to save append the results to APT s output photometry table file e g APT tbl Repeat above steps for each source of interest SKY BACKGROUND ESTIMATION APT uses fairly straightforward methods for estimat ing the sky background in the region local to the source of interest and there are a few options available for con trolling how it is done Only image pixels in a sky annu lus centered on a selected center position are used in the background calculation The center position for purposes of background estimation is specified in integer pixels only tion There are three ways to specify the center posi Mouse clicking on the image displayed in upper right image viewing panel Adjusting the spinner controls in the lower left main GUI panel or 3 Clicking on the Snap button in the lower left main GUI pane
12. nient source list tool that enables aperture photometry calculations for a large number of detections in a given image The source list tool can be run either in automatic mode to quickly generate a photometry table or in manual mode to permit inspection and adjustment of the aperture photometry calculation for each individual detection APT displays a variety of useful plots with just the push of a button including image histogram aperture slice source scatter sky scatter sky histogram radial profile and curve of growth APT has many functions for customizing aperture photometry calculations including outlier rejection pixel picking and zapping and a selection of source and sky models The radial profile interpolation source model which is accessed via the radial profile plot panel allows recovery of flux density in pixels with missing data and can be especially beneficial in crowded fields APT s results are in excellent agreement with similar output from SExtractor Keywords Data analysis Aperture photometry Aperture Photometry Tool APT Astronomical software Source intensity Source noise Sky background Graphical user interface SExtractor Palomar Transient Factory PTF I INTRODUCTION This paper introduces new software called Aperture Photometry Tool APT and gives many details about how to use it and how it works The intent of the software is to make aperture photometry easy and fun through an intuitive
13. ntroid radius calculation of the source s centroid position can involve fewer or more pixels than in the aperture photometry calculation and a selected center position instructions for doing this are given in Section III above The aperture and centroid radii in integer pixels only can be specified on the main GUI panel The More Settings panel has text fields where the user can optionally specify lower and upper thresholds for rejection of spurious aperture pixels in the aperture photometry calculation The default values for the lower and upper thresholds are the largest possible negative and positive double precision numbers respectively so that by default no pixels are rejected Again values for outlier rejection thresholds must be given in image data units The pixel zap functionality of the zoom pick tool can also be used to temporarily eliminate pixels from the aperture photometry calculation More details about the zoom pick tool are given in Section XI below The More Settings panel also has radio buttons for the user to select from one of three available source algo rithms 1 No aperture interpolation 2 Aperture interpolation only for NaN or Inf pixels including zapped pixels or 3 Interpolation only for all aperture pixels Note that NaN stands for not a number and Inf stands for infinity The aperture photometry calculation is done with sub pixel resolution The defau
14. oothly follows the lower edge of the scattered APT data points which is in conformance with the statement that SExtractor s source noise esti mate can only be regarded as a lower limit 3 Our crude simulations of folding the uncertainty of the background estimation into SExtractor s source noise values improve the aformentioned median values of the source noise rel ative percentage error to about 1 for both cases The middle panels are scatter plots of the source noise relative percentage error between SExtractor and APT as a func tion of sky noise As defined in Section VIII the sky noise is the standard deviation of samples in the sky annulus after the sky outliers have been rejected there were none rejected in cases 1 and 2 since APT s source list tool was run in automated mode and APT has no No outlier rejection capability yet APT only has outlier rejection whose lower and upper thresholds must be explicitly set One can start to see a dependence of source noise relative percentage error on sky noise This is even more appar ent in the bottom panels which are scatter plots of the source noise relative percentage error between SExtrac tor and APT as a function of sky scale The sky scale also defined in Section VIII is a robust estimator of the sky noise and comparing the middle and bottom pan els demonstrates how the sky scale is a representation of source noise that is mostly collapsed horizontally onto a
15. rom the source intensity and the reason for this is to facilitate proper use of APT s radial profile in terpolation capability More often than not however the user will require the sky background to be subtracted from the source intensity in which case this can be se lected from the control panel that pops up after clicking on the More Settings button located at the bottom left corner of the main GUI panel See Figure 2 for a depiction of the More Settings panel The general flow of the work progresses from the but tons and controls at the top left corner of the main GUI panel to the middle left region and then bottom left re gion of the same Here are the basic instructions 1 Take a moment to review the default settings by se lecting List Preferences from the Preferences menu More information on user preferences is given in Section VI 2 Choose a primary image to display by mouse clicking on the Get Image button in the upper left corner of the GUI panel APT only reads in FITS formatted images the image format com monly adopted by astronomers 2 A primary im age is by definition the first image displayed in the upper right image viewing panel 3 Adjust image stretch for best viewing As an aid click on the Image Histogram button to see the stretch range spanned by the image 4 Select centroiding aperture and sky annulus radii integer values only as appropriate for
16. the source of interest 10 11 Select source algorithm Select sky algorithm Custom sky value D N Use centroid in photometry calculation Reject source values D N less than Reject source values D N greater than Reject sky values D N less than Reject sky values D N greater than BUNIT Default image data title Gain electrons per D N Image data to D N conversion factor Perform new image data conversion see settings below New image data conversion factor O Model 0 No aperture interpolation O Model 1 Interpolation only for NaN Inf pixels O Model 2 Interpolation for all aperture pixels Model A No sky subtraction O Model B Sky median subtraction O Model C Custom sky subtraction below O Model D Sky average subtraction 0 00000e 00 m 1 79769e 308 1 79769e 308 1 79769e 308 1 79769e 308 N A Surface brightness 1 5000000e 00 1 0000000e 00 m 1 0153728e 01 Image data units after new conversion Jy Image data title after new conversion Flux density 4 Apply Settings 7 Close Window p FIG 2 More Settings panel of APT Place mouse cursor over source of interest in image displayed in upper right image viewing panel and click to overlay an aperture Show study the various graphs instructions are given in Section IX below Select desired new radii and or change other set ti
17. ues for outlier rejection thresholds must be given in image data units It is best to show study the various graphs and set these thresholds before converting image data units to desired source intensity units via Perform image data conversion checkbox on the More Settings panel more on this in Section IX below The pixel zap functionality of the zoom pick tool can also be used to temporarily eliminate pixels from the background calculation More details about the zoom pick tool are given in Section XI below IV APERTURE PHOTOMETRY The aperture photometry calculation primarily results in source intensity and source noise The former involves summing of pixel values within the aperture to get the total intensity and subtracting off the product of the aperture area and per pixel sky background The lat ter requires extra information including detector gain aperture geometry sky annulus geometry background estimation method and sky noise APT works under the assumption that the background is constant across the aperture Version 1 0 0 of APT only performs aperture photometry calculations with circular apertures It is not inconceivable that later versions of APT will have options for other types of aperture photometry calcula tions e g SExtractor s isophotal and Petrosian like and Kron like eliptical aperture options Basic inputs for the aperture photometry calculation are aperture radius source ce
18. ween NASA and the California Institute of Tech nology Montage is maintained by the NASA IPAC In frared Science Archive This work is based in part on archival data ob tained with the Spitzer Space Telescope which is op erated by the Jet Propulsion Laboratory California In stitute of Technology under a contract with NASA Sup port for this work was provided by an award issued by JPL Caltech 5 M Law S R Kulkarni R G Dekany E O Ofek M Quimby P E Nugent J Surace C C Grillmair S Bloom M M Kasliwal et al PASP 121 1395 2009 6 B W Holwerda Source Extractor for Dummies Space Telescope Science Institute 2005 5th ed N R J Relative error h uw Source Noise Comparison Sextractor vs APT Case 1 1 0E 03 1 0E 04 1 0E 05 10 15 20 Relative error 25 30 35 Source intensity data number 1 0E 06 1 0E 01 1 0E 02 1 0E 03 1 0E 04 Relative error nN wm Sky noise data number Aperture radius 5 pixels 55 60 65 70 75 80 Sky scale data number Relative error Relative error Relative error 60 21 Source Noise Comparison Sextractor vs APT Case 2 T rrr T reri T a 1 0E 03 1 0E 04 1 0E 05 1 0E 06 10 10 20 30 60 Source intensity data number 1 0E 01 1 0E 02 1 0E 03 1 0E 04 10 10 20 30
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