Home

Aperture Photometry Tool - NITARP - California Institute of Technology

1. 750 LAHER ET AL TABLE 1 OUTPUT FILES CREATED BY APT Filename APT piel cisecnseecnccesstevuteten ASPTABL sajcsisentit teconeecenceqoambeancene SHA siege eormsianieanesseaeess apertureSliceX dat 65 apertureSliceY dat 24 SkyScattendat vc sc ciccssswesievsses sourceScatter dat 0065 curveOfGrowth dat radialProfile dat 005 radialProfileDataFitCurve dat radialProfileDataFitModel dat Scatter dat xiGicasvndecibectatidoewias sourceListByAPT dat directory from which a source list file was read by the source list tool see 7 8 or if this is not available the scratch direc tory there is also the user option on the source list creation panel of selecting the location and filename of choice for the newly generated source list see 7 9 7 4 Aperture Photometry Table APT generates a table of accumulated results during the course of its normal operation This is not automatic however the user must deliberately mouse click on the Save Results but ton after each aperture photometry calculation in order to write a row of results to the table Users can save the table to the disk location and filename of their choice The default location is the invisible subdirectory AperturePhotometryTool in the user s home directory and the default filename is APT tbl Table 2 defines the columns of the table along with applicable d
2. 2012 by the California Institute of Technology REFERENCES Bertin E 2006a ASP Conf Ser 351 Astronomical Data Analysis Laher R R Rebull L M Gorjian V Masci F J Fowler J W Software and Systems XV San Francisco ASP 112 Helou G amp Kulkarni S R et al 2012 PASP 124 2006b SExtractor User s Manual Ver 2 5 Paris IAP Rebull L M Gorjian V Squires G amp Team NITARP2011 BAAS gt Bertin E amp Arnouts S 1996 A amp AS 117 393 43 248 11 Da Costa G S 1992 ASP Conf Ser 23 Astronomical CCD Obser Rebull L M Johnson C H Hoette V Kim J S Laine S Foster ving and Reduction Techniques San Francisco ASP 90 M Laher R Legassie M 2011 AJ 142 25 Daou D Pompea S amp Thaller M 2004 BAAS 36 1500 Shupe D L Moshir M Li J Makovoz D Narron R amp Hook R Holwerda B W 2005 Source Extractor for Dummies Baltimore N 2005 in ASP Conf Ser 347 Astronomical Data Analysis Soft STScI ware and Systems XIV San Francisco ASP 491 Howell S B 1992 ASP Conf Ser 23 Astronomical CCD Observing Tody D 1986 Proc SPIE 627 733 and Reduction Techniques San Francisco ASP 105 1993 in ASP Conf Ser 52 Astronomical Data Analysis Soft Joye W A amp Mandel E 2003 ASP Conf Ser 295 Astronomical ware and Systems II San Francisco ASP 173 Data Analysis Software and Systems XII San Francisco Wells D C Greisen E
3. Adjust stretch max percentile of set range image Comparator 32 q 0 20 40 60 80 100 0 20 40 60 80 100 ia Dynamic range x100 3O gt Stretch Type Toggle Centroid radius pix 5 Inner sky radius pix 9 29 gt Aperture attributes 8 8 0 gt Alter Outer sky radius pix 1s Aperture Slice Source Scatter Sky Scatter Hide Aperture 28 Curve of Growth Radial Profile Sky Histogram Color Table Toggle Magnify Image 1 27 emer i 371 R A Dec N A N A Pixel value 1 2278e 01 Mjy sr 26 PRIMARY IMAGE PHOTOMETRY RESULTS Aperture X Y 130 371 PO conoid 129146 37070 pl Snap 24 Photometry units MJy sr Source_intensity sky subtracted 8 707e 01 Source_unc 5 148e 00 23 Magnitude 22 5957 Magnitude_unc 0 0642 Sky_median Sky_average 9 774e 02 9 740e 02 Sky_scale Sky_sigma 1 879e 02 1 943e 02 22 More Settings Recompute Photometry Blink Refresh 1 Refresh 2 Save Results List Results Piot Results se i 21 20 19 18 7 16 f 14 Sx 10x 20x 12 Fic 1 APT s main GUI panel The numbers with arrows highlight the components that are described in 3 figures shown in this article were taken on an Apple computer running OS X Lion and will have slightly different appearances under other operating systems When running the software hovering the mouse cursor over a widget in the GUI will cause a short pop up explanatory note o
4. Compt Matc uting Tue Mar 27 10 41 h radius arcseconds Number of unfiltered matches 301 Flag Expo Zero Medi Stan Robu Outl to normalize by exposure time 1 sure time seconds 120 000000 gt Results after Ist iteration point magnitude 22 209312 an zero point magnitude 22 212156 dard deviation of zero point magnitude 0 112873 st zero point dispersion magnitude 0 038155 gt Results after 2nd iteration ier rejection filter threshold magnitude 0 300000 Number of filtered matches 294 zero Medi Stan Robu Magnitude difference point magnitude 22 218719 an zero point magnitude 22 212972 dard deviation of zero point magnitude 0 048869 st zero point dispersion magnitude 0 037042 Magnitude Difference Plot 0 25 0 00 0 25 14 15 1 17 1 19 20 21 Matching source brightness mag Fic 17 APT s simple photometric calibration tool data statistics are outputted to guide the user in setting up repeat calculations to refine the result These include the numbers of sources in each list the match radius arcseconds the expo sure time normalization flag the numbers of unfiltered and filtered matches the outlier rejection filter threshold for the magnitude difference magnitude and the first and second pass mean and median zero points standard deviation and afore mentioned robust data dispersion all in units of magnitu
5. and this is reflected immediately by the software displaying the resulting data fit curve in the radial profile graph The text field to the left of the Reset Sigma button can be filled in with an initial guess The Reset Sigma button causes the data fit to be done with the value of in the text field The slider control below it causes data fits to be done with values in the neighborhood of the text field value of Clicking on the Reset Sigma button after vary ing the slider will revert o of the data fit to the initial guess and center the slider The Set Slider button centers the slider on the current value of o and puts that value in the text field as the current initial guess The Recompute Fit button performs the same operations plus does the data fit one more time for good measure Typically the best fit is obtained when x is mini mized that is the goal of the linear regression as implemented in APT Hint A not so good fit can sometimes be made better by reducing the aperture size and sky annulus major radii When a new fit is done the scale and offset parameters are reset to 1 0 and 0 0 respectively more details about these model exogenous parameters are given below 4 Once the user has obtained an acceptable fit the model parameters can be saved by mouse clicking on the Save button The model parameters are written to a file in the scratch direc tory called radialProfileDataFitModel dat Only the data fit model that has
6. In addition to the aforementioned outlier rejection there is yet another outlier rejection method that is applied The median and standard deviation are computed and all data values that lie greater than 3 standard deviations from the median are rejected Currently this number of standard deviations is hard coded and cannot be changed by the user The pixel zap functionality of the pick zap tool can also be used to temporarily eliminate pixels from the background cal culation More details about the pick zap tool are given in 7 7 The median and average of the remaining image data in the sky annulus after the outlier rejection have been applied are computed as possible background estimators The median or average times the number of pixels in the aperture form a pro duct that is the sky contribution optionally subtracted from the integrated image data of the source to get the background subtracted source intensity These quantities are labeled Sky_ median pix and Sky_average pix respectively in the output aperture photometry table see 7 4 The standard deviation is computed for the Sky_sigma column in the aperture photom etry table Likewise the root mean squared rms value is com puted for the Sky_RMS pix column The Sky_scale column a robust estimator of the data dispersion is computed as one half of the difference between the 84 and 16 data percentiles 6 APERTURE PHOTOMETRY IMPLEMENTATION The aperture photometry calcu
7. VAROUJAN GORJIAN LuisA M REBULL FRANK J Masct JOHN W FOWLER GEORGE HELOU SHRINIVAS R KULKARNI AND NICHOLAS M Law Received 2010 March 29 accepted 2012 May 24 published 2012 July 10 ABSTRACT Aperture Photometry Tool APT is software for astronomers and students interested in manually exploring the photometric qualities of astronomical images It is a graphical user interface GUI designed to allow the image data associated with aperture photometry calculations for point and extended sources to be visualized and therefore more effectively analyzed 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 Simply mouse clicking on a source in the displayed image will instantly draw a circular or elliptical aperture and sky annulus around the source and will compute the source intensity and its uncertainty along with several commonly used measures of the local sky background and its variability The results are displayed and can be optionally saved to an aperture photometry table file and plotted on graphs in various ways using functions available in the software 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 convenient source list tool that enables calculations for a
8. ignored if the user wants photometric results for an aperture that is dislocated from the centroid position in which case centroid ing should be turned off The source intensity uncertainty calculation requires the detector gain electrons per D N the conversion factor from image data units to D N and the depth of coverage The default value for these quantities is 1 0 When a primary image is loaded the software attempts to read the GAIN FITS keyword and if found automatically overrides the default gain value For image data that are already in units of D N the value of 1 0 is appropriate for the image data units to D N conversion factor A depth of coverage of 1 0 is correct for a single observation These quantities can be subsequently overridden on the More Settings panel after an image has been loaded The default gain value used in the absence of the GAIN FITS keyword can be changed via the Set Default Image Data Gain option in the Pref erences menu APT computes the source intensity uncertainty Csc using Hs K Age Osk a Ogre gu Age a Y 3 depth ky Asky where Fre is the sky background subtracted source flux density or source intensity G is the detector gain N aep is the depth of coverage 7 is the conversion factor from image data units to D N Age is the aperture area in pixels Osky 18 the sky back ground standard deviation per pixel is a factor that depends on the optional background
9. 124 737 763 processed by APT s source list tool without displaying the GUI APT csh image fits source 1lst This noninteractive batch mode command is handy for gen erating an aperture photometry table file for the source list from a script Control is returned to the user s command shell after APT terminates The image file must be specified before the source list file The parameters that control how the source list is processed by the source list tool are specified by running APT beforehand and saving the parameters as user preferences in the default location which is loaded automatically upon APT startup 7 13 Internationalization We implemented a simple workaround for the sticky problem of commas used in place of decimal points on computers in some non US countries The APT startup scripts APT csh and APT bat force English as the user s language and the United States as the user s geographical region when invoking the JVM This is done using the following JVM options Duser language en Duser region US The net effect is to require the American usage for input floating point numbers e g in FITS headers and to ensure the same for any output floating point numbers e g written to the aperture photometry table file regardless of the language selected when a computer s operating system was installed The workaround was verified for an APT installation on a German Windows machine 762 LAHER ET AL 8 SOFTW
10. 16 APT s source list creation tool panel or they can keep the default location and filename see 7 3 There are three options for controlling the source list genera tion The Source List Creation Tool panel has text fields for three input parameters source detection threshold and minimum and maximum numbers of contiguous pixels allowed for a source The source detection threshold is specified in number of data distribution half widths It is used to calculate the image data threshold at each image pixel position The image data threshold is defined as the local background median plus the source detection threshold times the global dispersion of the image data The dispersion is computed by taking one half of the difference between the 84 and 16 percentiles The two remaining parameters control the size range the user allows for detected sources The source minimum number of pixels is a parameter used to exclude sources with an insufficient number of detected pixels above the image data threshold The parameter for the source maximum number of pixels is useful for excluding very large sources that may lie outside of the user s sphere of interest A source detection threshold of at least 1 0 is recommended Either setting the threshold too low or not narrowing the source size range enough may result in more detections than the soft ware can handle in which case the software will warn the user and recommend another try with a higher
11. 3594e 03 DN R A Dec 104 9727 16 8501 degrees Hide Grid RA degrees pink 104 834 104 935 105 036 Fic 3 APT s primary image thumbnail 2012 PASP 124 737 763 744 LAHER ET AL when the BUNIT keyword is absent from the image s FITS header and can be set via the Set Default Image Data Units op tion in the Preferences menu 28 The six buttons on the left of the button group Aperture Slice Curve of Growth Source Scatter Radial Profile Sky Scatter and Sky Histogram pop up various graphs associated with the current calculation see 7 5 On the right the Hide Aperture button temporarily hides the aperture overlay and sub sequently transforms into the Show Aperture button and the Color Table Toggle button that successively switches to the available presequenced color table options see item 11 above 29 The Alter button next to the aperture attributes label pops up a panel that allows changes to the elliptical aperture s major and minor radii and rotation angle see Fig 4 and the button s label indicates the values of these parameters The text fields in the group allow changes to values of the centroid inner sky and outer sky major radii in integer pixels The default aperture shape is circular in fact and the default settings for the centroid aperture inner sky and outer sky radii are 5 5 8 and 15 pixels respectively These defaults can be changed via the Prefer ences menu 30 The
12. Stretch Type Toggle button cycles the image display stretch from linear to logarithmic to histogram equalization and then back to linear 31 The dynamic range slide control allows the dynamic range of the logarithmic image display stretch to vary from 0 eoo Elliptical Aperture Attributes 196 B 893 l Check box to the left for circular aperture Center X Y Major radius pixels om 1 ERE E BA E E E G 17 0 20 40 60 80 100 120 140 160 180 200 Minor radius pixels CE z cr Trreperepeerpernge i E 7 0 20 40 60 80 100 120 140 160 180 200 Rotation angle degrees F Le hs ne perge i SEEE 37 90 75 60 45 30 I5 0 15 30 45 60 75 90 Fic 4 APT s panel for setting the elliptical aperture attributes equivalent to a linear stretch to 5 orders of magnitude which visually differentiates the smallest image data values that are above the lower bound of the stretch The default setting is one order of magnitude The slide control is disabled for non logarithmic types of stretches 32 The stretch minimum and stretch maximum slide con trols allow the lower and upper limits of the image display stretch respectively to be varied from their current settings The new stretch is instantiated only after the Stretch to Bounds button is pressed see next item 33 The Stretch to Bounds button sets the limits of the image display stretch to the two values in the lower bound and upper bound te
13. a panel that lists the FITS header of the primary image In the case of a multiextension FITS file the headers of all extensions are listed The top of the panel has functionality for case sensitive searches which is useful for finding particular keywords values and comments in the FITS header listing 3 The pull down menu with the default label 1 99 has several options for setting the limits of the image display stretch which is the mapping of pixel intensities to values in the 0 255 range for 8 bit graphics The options include the image data minimum and maximum as well as various combi nations of image data percentiles As the default label indicates the default setting for stretch is the selection with the 1 and 99 percentiles Located above this pull down menu on the main GUI panel are text fields that display the lower and upper bounds of the stretch corresponding to the menu selection made see item 34 below FITS stands for Flexible Image Transport System see http fits gsfc nasa gov and Wells et al 1981 2012 PASP 124 737 763 4 The Source List button pops up a panel for performing a large number of aperture photometry calculations at source positions that are read from a source list see 7 8 From this panel additional functionality for generating a source list auto matically is available see 7 9 5 The Image Histogram button pops up a panel with a his togram plot for the entire primary image
14. cause the calculation to revert to centering the aperture on the integer pixel coordinates of the selected aperture position Note that although centroiding moves the center position of the aperture with subpixel resolution the center position of the sky annulus is incremented only with integer pixel resolution The Snap button in the lower left main GUI panel is available to nudge the aperture onto the computed source centroid loca tion After moving the aperture it automatically recomputes the photometric results just like the Recompute Photometry but ton If centroiding is turned on and the aperture is already fairly close to the centroid the recomputation may give the same non background subtracted source intensity as before with slight changes possible to the source intensity uncertainty sky back ground and sky background dispersion and the main differ ence will be that the aperture will appear to be better centered on the centroid position and the data points plotted 748 LAHER ET AL in most of the APT graphs will be shifted accordingly If cen troiding is turned off the user will obtain a new result at the new aperture position which after snapping the aperture will be the centroid position represented by integer image coordinates The Snap button text will turn the color yellow to remind the user to mouse click on this button to fully center the aperture on the centroid location This color reminder can and should be
15. is thus suitable for the classroom but not only that it is also an effective analysis tool for astronomical research This article gives many details about how to use the software and how it works The objective of the software is to make aperture photometry easy more accurate and even fun through an intuitive graphical user inter face GUI The software enables aperture photometry to be per formed interactively and gives visual feedback in various ways to facilitate learning and calculational refinement According to Howell 1992 We are all students in the astronomy game and in the context and spirit of that remark APT was developed to provide a better understanding of aperture photometry and its computed results 7 See http sha ipac caltech edu Our initial goal was to create a GUJI based aperture photometry software application that is instructive on how to perform aperture photometry but over time the fruits of our labor evolved into software that works well enough for profes sional use in research APT has been used in the setting of in volving teachers and students in original astronomical research as part of the Spitzer Space Telescope Research Program for Teachers and Students Daou et al 2005 Rebull et al 2011 and is now being used in that program s successor the NASA IPAC Archive Teacher Research Project NITARP Moreover the research has led to new scientific discoveries Rebull et al 2011 G
16. large number of detections in a given image The source list tool can be run either in automatic mode to generate an aperture photometry table quickly or in manual mode to permit inspection and adjustment of the calculation for each individual detection APT displays a variety of useful graphs with just the push of a button including image histogram x and y aperture slices source scatter plot sky scatter plot sky histogram radial profile curve of growth and aperture photometry table scatter plots and histograms APT has many functions for customizing the 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 source intensity from pixels with missing data and can be especially beneficial in crowded fields 1 INTRODUCTION Aperture photometry in astronomical image data analysis is a basic technique for measuring the brightness of an astronom ical object such as a star or galaxy It is the calculation of source intensity by summing the measured counts from a subimage containing the source or possibly sources and subtracting the sky background contribution estimated from a nearby im aged region that excludes the source of interest Da Costa 1992 The subimage containing the source brightness or so called aperture is a bounding region for the calculation
17. such as the stretch or color table 15 The Pick Zap button pops up a panel with the pick zap tool see 7 7 16 The Blink button is for image blinking the primary image and up to three comparator images see 7 11 17 The Thumbnail button pops up a panel that is capable of displaying the entire primary image rather than just the portion of it that may be currently displayed in the main image viewing panel At the top of the thumbnail panel are a Show Grid button and a display of real time mouse cursor position in both image and equatorial coordinates as well as a display of the real time pixel data value at the cursor position The Show Grid button will overlay a grid labeled with equatorial coordinates and then subsequently transform into a Hide Grid button If a world coordinate system WCS is not available in the image s FITS header then the grid overlay will be disabled The thumbnail image can be made to fit on the user s computer screen using the Set Maximum Thumbnail Size option in the Preferences menu If it is set to larger than the user s screen then the panel will be automatically scaled to fit and scroll bars will appear Figure 3 shows an example primary image thumbnail with a coordinates grid overlay 18 The Recompute Photometry button repeats the aperture photometry calculation after changes to its setup have been made such as different aperture geometrical parameters Such changes which affect the results c
18. the aperture photometry table file and then overlay an aperture onto the image for the next source in the source list The marker Manual Source List Processing will be written to the file prior to saving the results record for the first source The above steps are repeated for each successive source in the source list After the source list has been exhausted the message Done with source list will be displayed To reset manual processing and start again perhaps after another selection of aperture photometry settings have been made simply press the Manually Process Source List but ton once more 7 9 Source List Generation The Create Source List button on the source list tool panel pops up another panel with functionality to generate a source list by extracting sources from the current primary image see Fig 16 and to then write the source list to a file The source list is generated with image pixel coordinates Users can either save the source list to the disk location and filename of their choice using the Reset Source List Filename button on the 2012 PASP 124 737 763 APERTURE PHOTOMETRY TOOL 759 Source List Creation Tool Create Source List in Image Pixel Coordinates Source list filename Users laher sourceListByAPT dat Reset Source List Filename Source detection threshold Source minimum number of pixels Source maximum number of pixels Create Source List 2 000000 19 299 Close Window Fic
19. the main image viewing panel The subimage is changed in real time as the mouse cursor is moved The magnification options of the image magnifier panel are 5x 10x the default setting and 20x 13 The Refresh 2 button repaints the image for both visible and nonvisible portions of the image in the main image viewing panel This is useful after image display characteristics such as the stretch or color table have been changed After the short amount of time required for this operation to complete the main image viewing panel s scroll bars can be used to quickly scroll about the entire image which will be thereafter displayed with the same image viewing characteristics until such time that image viewing changes are made again 14 The Refresh 1 button repaints the visible portion of the image in the main image viewing panel plus the relatively small nonvisible portion that lies within the bounding box graphics see item 9 This option is faster than the repainting of the entire image done by the Refresh 2 button and is mainly useful for re drawing the bounding box graphics and eliminating any residual bounding box graphics in the visible portion of the displayed image The latter can occur after the scroll bar positions of the main image viewing panel have been moved or after the main GUI panel has been enlarged For the most part the visible portion of the image is repainted automatically after changes to image viewing characteristics
20. threshold Up to 100 000 segmented detections are currently allowed by the soft ware where the segments consist of 100 pixels each The algorithm for computing the local background median is given as follows The primary image is divided up into 2012 PASP 124 737 763 N x N pixel cells where N is an odd number that varies with the size of the image is chosen to have at least 10 cells across the shortest image dimension and is allowed to be no smaller than 33 pixels The median of the image data in each cell is computed and bilinear interpolation over the cells is then used to estimate the spatially varying local background median Spe cial handling of the calculation is done at the far image edges to avoid extrapolation Source detections occur for image data pixels that are both greater than or equal to the spatially varying image data thresh old and greater than zero A source is defined by a set of con tiguous detections where contiguous pixels are joined either at pixel sides or corners The centroid of each source defines its position in the image and the centroid image coordinates are written to the specified source list file 7 10 Simple Photometric Calibration Tool The software includes a user friendly tool to provide the capability of performing simple photometric calibration see Fig 17 The tool matches two source lists and computes a single parameter the photometric zero point via sum of squared error minimizati
21. usage image display user pref erences output files columns in the output aperture photometry table graphs radial profile interpolation pick zap tool source list processing source list generation simple photometric cali bration image comparator and blink capability batch mode and internationalization Section 8 covers software limitations and future upgrade plans A summary is provided in the concluding section See http nitarp ipac caltech edu 10 APT can be downloaded from http www aperturephotometry org This Web site has also has information on using APT including installation instruc tions for Mac OS X Linux Windows and Solaris machines 8 APT requires the following packages JFreeChart www jfree org JRegEx jregex sourceforge net and Jama math nist gov javanumerics jama plus a handful of the Spitzer Science Center Spot Leopard Java classes for the astro metric calculations These come packaged with APT and so the user need not install them separately 2012 PASP 124 737 763 A companion article in the same issue of the PASP that this article appears gives a quantitative comparison of calculational results from SExtractor and APT with identical inputs for the case of noncrowded sources Laher et al 2012 The article shows that both software programs give results that are gener ally in excellent agreement especially for bright sources and seeks to find explanations for the discrepancies that o
22. 012 Close 0 1 2 3 4 5 6 Source Aperture Inner sky 7 8 9 10 11 12 13 Distance from aperture center pixels Outer sky Sky level median Zero level Fic 7 Sample curve of growth plot generated by APT 2012 PASP 124 737 763 eoo APERTURE PHOTOMETRY TOOL 753 Source Scatter Plot Source Scatter 15 000 12 500 10 000 7 500 5 000 2 500 at tm Sky subtracted surface brightness DN Wed Mar 28 06 46 26 PDT 2012 Close 0 1 2 3 4 5 6 8 9 10 11 12 13 Distance from aperture center pixels Source Aperture Inner sky Outer sky Sky level median Zero level Fic 8 Sample source scatter plot generated by APT away click on the More Settings button on the lower left side of the main GUI panel to bring up the outlier rejection controls Each time a graph generation button is mouse clicked a new graph is displayed and previously displayed graphs are not de stroyed We deliberately made the choice of allowing users to display an arbitrary number of graphs on their computer screens to enhance APT s function as an educational tool This software behavior allows users to create and compare graphs from different APT settings Users must exercise some discipline in closing graph windows themselves in order to prevent the 75 8 0 8 5 9 0 9 5 10 0 proliferation of graph panels on their computer screens The date and time label on each graph is helpful for di
23. 11 The image display graphic shows the currently selected display type and color table The available types are grayscale inverted grayscale false color and inverted false color There are two false color tables available one is called contour be cause it seeks to differentiate adjacent colors in the color table Image Histogram Plot Image Histogram 90 000 80 000 70 000 5 60 000 A 50 000 3 Z 40 000 30 000 20 000 10 000 CH 5 00E 2 1 00E 1 L50E 1 2 00E 1 Wed Mar 28 06 20 59 PDT 2012 4 00E 1 3 50E 1 2 50E 1 3 00E 1 Surface brightness MJy sr E Image pixels Image data statistics MJy sr min amp max 4 163332e 00 4 529429e 02 mean amp sigma 1 426465e 01 1 565410e 00 median amp scale 1 069381e 01 1 amp 99 percentiles 3 442749e 02 samples NaNs ints 4862326 2 743290e 02 4 125885e 01 1630646 Fic 2 Sample image histogram plot generated by APT 2012 PASP 124 737 763 742 LAHER ET AL and the other eponymous color table has a gradation of rain bow colors There are 24 levels of grayscale or 24 hues in the color tables The display type and color table can be set via op tions in the Preferences menu See item 28 below for related information on the Color Table Toggle button 12 The image magnifier panel displays a subimage of the image currently shown in the main image viewing panel The subimage is centered at the mouse cursor position in
24. ARE LIMITATIONS Some of the functionality described above is admittedly not well integrated into the main functionality and these areas could use more work For example the Simple Photometric Calibration Tool could be upgraded to allow APT s output aperture photometry table as an input see 7 10 Below is a list of items that could or will be addressed in later software versions in no particular order Future software status and updates will be posted on the APT World Wide Web site 1 Handle accompanying image data masks and uncertainty images 2 Account for sky background variation across the aperture in the calculation 3 Change the number of standard deviations used in outlier rejection for sky background estimation from a hard coded value into a user specifiable parameter 4 Inflate the sky background standard deviation after reject ing outliers in order to account for the clipping of the distribu tion s tails 5 Include pixel to pixel noise correlations and spatially varying co add coverage depth in the calculation of source intensity uncertainties 6 Implement bit flags to indicate potential problems related to the calculation e g source saturation source located near edge source in crowded field etc Cf SExtractor Bertin amp Arnouts 1996 7 Upgrade the image comparator to have independent stretch controls and automatic image registration using the images WCS solutions 8 Add functionality t
25. Photometry Size Parameters option under the Preferences menu On the APT control panel that pops up after clicking on the More Settings button the user can select from one of four avail able sky models Model A No sky background subtraction Model B Sky median subtraction Model C Custom sky subtraction Model D Sky average subtraction Sky median subtraction is less sensitive than sky average subtraction to other bright sources that may fall within the sky annulus which might otherwise cause the background to be overestimated If model C is specified then the custom value to be used must be specified in the text field labeled Custom sky value on the More Settings panel The More Settings panel has text fields where the user can optionally specify lower and upper thresholds for the rejection of outlier pixels in the sky annulus from the background calcu lation The default values for the lower and upper thresholds are the largest possible negative and positive double precision num bers respectively so that by default no pixels are rejected The values for the outlier rejection thresholds must be given in the data units of the image s FITS file It is best to study the various aperture photometry graphs provided by APT in order to figure out the best thresholds and then set these thresholds before optionally converting the image data units into the desired source intensity units see 7 5 for how to do the latter
26. W amp Harten R H 1981 A amp AS 44 ASP 489 363 2012 PASP 124 737 763
27. a Spitzer Science Center California Institute of Technology Mail Stop 314 6 Pasadena CA 91125 laher ipac caltech edu Jet Propulsion Laboratory California Institute of Technology Mail Stop 169 506 Pasadena CA 91109 Spitzer Science Center California Institute of Technology Mail Stop 220 6 Pasadena CA 91125 Infrared Processing and Analysis Center California Institute of Technology Mail Stop 100 22 Pasadena CA 91125 Caltech Optical Observatories California Institute of Technology Mail Stop 249 17 Pasadena CA 91125 Dunlap Institute for Astronomy and Astrophysics University of Toronto Room 101 Toronto ON Canada M5S 3H4 737 two dimensional area used to define just the portion of a photo graph or digital image of the nighttime sky that contains most if not nearly all of the observed radiance of the astronomical ob ject under investigation Conventionally the aperture is centered on the source of interest although the calculation is usually in sensitive to exact aperture placement and in some cases it is desirable to offset the aperture slightly from the source s center to possibly omit the effect of a neighboring source The shape of the aperture is circular in its simplest form Often the shape of an astronomical object such as a spiral galaxy viewed at an ob lique angle will determine the aperture shape that is optimal for its scientific study e g elliptical In addition to geometr
28. a significant number of blank pixels in the aperture Model 1 was designed to remedy this but it requires that the user set up a radial profile model for the interpolation and APT has a tool that makes it easy as discussed in 7 6 Model 2 uses the radial profile model to compute data values for all pixels in the aperture and generally gives a result that is within a few percent or better of model 0 if the radial profile model was set up on the same source Model 2 is most useful in cases where the source of interest has missing aperture pixels and the radial profile model was set up on a different source that has no missing pix els which is facilitated by the built in automatic scaling and offsetting of the radial profile The aperture photometry calculation is done with subpixel resolution The default subpixel size is 0 01 pixels The small value can cause the computations to take several seconds for very large aperture ellipses The subpixel size can be changed via the Set Calculation Step Size option in the Preferences menu By default the calculation is performed with the aperture centered on the calculated source centroid The Centroid X Y label on the lower left side of the main GUI panel is displayed in the color green to indicate that centroiding is enabled and in the color black to indicate that it is disabled Unchecking the Use centroid in photometry calculation check box on the More Settings panel will do the disabling and
29. al flow of the work progresses from the buttons and controls in the upper left region of the main GUI panel to the middle left region and then lower left region of the same Here are the basic instructions 1 Take a moment to review the default settings by selecting List Preferences from the Preferences menu More informa tion on user preferences and how to change them is given in 7 2 2 Choose a primary image to display by mouse clicking on the Get Image button in the upper left corner of the GUI panel The primary image as defined here is the first image displayed in the main image viewing panel after the primary image is loaded a subsequent mouse click on the Get Image button will 2012 PASP 124 737 763 Select source algorithm Select sky algorithm Custom sky value MJy sr Use centroid in photometry calculation Reject source values MJy sr less than Reject source values MJy sr greater than Reject sky values MJy sr less than Reject sky values MJy sr greater than BUNIT Default image data title Gain electrons per D N Image data to D N conversion factor Aperture correction Magnitude zero point Depth of coverage Perform new image data conversion see settings below New image data conversion factor Image data units after new conversion Image data title after new conversion APERTURE PHOTOMETRY TOOL 745 More Settings Model 0 No aperture interpolation _ Model 1 Interpolat
30. amiliar measure of the distribution s half width This model was deliberately chosen to be relatively simple and yet have enough degrees of freedom to work well on images with a point spread function PSF that is by and large radially symmetric Optimizing the data fit involves manually choosing the value of o that minimizes the least squared error goodness of fit measure y In order to build a model for the image of interest the user must adhere to the following instructions precisely 1 On the More Settings panel accessed via the More Set tings button on the lower left part of the main GUI panel select the Model 0 source algorithm and the Model A sky algorithm Also the check box labeled Perform new image data conversion on the More Settings panel should be unchecked A picture of the More Settings panel is shown in Figure 5 Warnings will be given when the model is saved with these conditions not met 2 Select a source from which to create the radial profile mod el and overlay an aperture onto it in the main image viewing panel For a model that is to be representative of the sources in the image it is best to select a moderately bright unsaturated source which will be photon noise dominated and have a rela tively lower percentage of noise versus signal 3 Fit the radial profile data by operating the controls on the right hand side of the radial profile plot panel A new fit will be done when the user changes the value of
31. aperture onto the source cen troid location or placing the mouse cursor on the image and clicking 9 If necessary increment or decrement the spinner controls for fine tuning the aperture s position 10 Click on the Recompute Photometry button to redraw overlay a new aperture 11 Show and study the various graphs again 12 Optionally click on the Save Results button located in the lower left corner of the main GUI panel in order to save append the results to APT s output photometry table file e g APT tbl The adjacent List Results and Plot Results buttons can be used to list and plot the saved results 13 Repeat the above steps for each source of interest 746 LAHER ET AL 5 SKY BACKGROUND ESTIMATION Strictly speaking the background should be the best estimate of the true underlying background emission excluding contam ination from the source flux being measured and not biased by any other neighboring sources or outliers As a practical matter we estimate the background in the aperture from an elliptical sky annulus surrounding it and this method does not account for gradients in the sky background caused by sources in the annulus A bright source in the sky annulus contributes to the background in the aperture and its effect is not necessarily something that is to be completely ignored or filtered out which is why APT has a variety of sky models from which to choose APT has fairly straightforward methods for
32. ase will not be done until the Recompute Photometry button has been utilized Clicking on the frame around the main image viewing window when the mouse cursor is shown in the crosshair style will cause the overlaid aperture and displayed subimage to be removed as well as the picks and zaps 7 8 Source List Tool After an image for aperture photometry calculations has been selected the user can access the source list tool via the Source List button near the upper left corner of the main GUI panel Figure 15 shows the tool s user interface The tool does automatic or manual processing of a source list associated with the chosen image An input source list file is required for the tool and the file can be created in a variety of ways It can be created by parsing the output of popular source extraction software such as SExtractor with a user provided script It is possible to create a source list by hand editing or parsing with a script APT s out put aperture photometry table file from an earlier session after copying it to another filename In these cases the Choose 2012 PASP 124 737 763 Source List button is utilized to read in an existing source list file Alternatively APT has functionality for fast automatic source list creation by extracting sources from the current pri mary image directly and then generating a source list file The Create Source List button is utilized for this purpose see 7 9 The format of the s
33. ata units in the order the columns appear in the table The table can be listed by mouse clicking on the List Results button lo cated in the lower left corner of the main GUI panel The table s data are stored in a plain text file which can be easily parsed with a user supplied script 7 5 Graphs APT produces three different general categories of graphs One is simply the aforementioned image histogram which does not fit into the two remaining categories see item 5 in 3 and Fig 2 Another is a set of different graphs that pertain to the current aperture photometry calculation category A The other is the capability of making scatter plots and histograms of user selected columns in the output aperture photometry table cate gory B Category A graphs are most useful for analyzing and refining the current calculation and category B graphs are for visualizing a set of calculations such as might cover a large number of sources extracted from a given image There are six different category A graphs and these are eas ily displayed by mouse clicking on the associated main GUI Definition Default filename of customizable user preferences see 7 2 Default filename of output aperture photometry table see 7 4 Listing of the FITS header Image data corresponding to a horizontal slice across the aperture Image data corresponding to a vertical slice across the aperture Data shown in the sky scatter graph Data sho
34. ause the Recompute Photom etry button text to change from the color black to the color red as a reminder to the user that the calculation needs to be updated More details about how this button works and is used are given in 4 6 7 7 and 7 8 19 The Plot Results button pops up a panel that allows the setting up of scatter plots of one data column in the output aper ture photometry table versus another Histograms of data col umns can also be plotted Section 7 5 describes the available functionality in more detail 20 The List Results button pops up a spreadsheet style list ing of the output aperture photometry table The data columns in the table are fully described in 7 4 21 The Save Results button stores a record of the latest aper ture photometry calculation as a single row in the output aperture photometry table file A calculation may be manually repeated many times with different settings but it is not saved in the file until this button is utilized and then only the last result is saved 22 The More Settings button pops up panel that enables parametric changes to the aperture photometry calculation in cluding the specification of source and sky models The options and controls on this panel are fundamental to utilizing APT to its fullest and are described in 4 5 and 6 as well as mentioned throughout the remainder of this article 23 The main results of the latest aperture photometry calcu lation are disp
35. been written to this file will be sub sequently used in APT calculations involving interpolation After the radial profile model parameters have been saved as described in the above steps the model can be subsequently used on any source in the image for interpolation with any 2012 PASP 124 737 763 eoo Plot Photometry Data X plot size pixels 900 Y plot size pixels 700 Plot title from Aperture Photometry Tool X axis title Source intensity D N Y axis title arce intensity uncertainty D N X axis data Source_intensity s Y axis data Source_unc X axis minimum 0 X axis maximum 500000 Y axis minimum 200 Y axis maximum 1200 X axis number format 0 0E0 Y axis number format 0 X axis type O Linear _ Logarithmic Y axis type Linear Logarithmic Invert plot Number of histogram bins 50 Histogram Plot Close Window Fic 11 APT s control panel for plotting results of the appropriate source models available and any of the avail able sky models this of course assumes that the image data are sufficiently sampled in the case of data undersampling one cannot reconstruct a radial profile with goodenough accuracy The models can be selected on the aforementioned More Settings panel The source models that involve interpolation are described as follows The model source model is used for interpolating across aperture pixels with NaN values or Inf values in order to fill in the missing source intens
36. ccur for faint sources Users who want to begin using APT right away may down load and install the software and then skip directly to the tu torial in 4 2 DESIGN CONSIDERATIONS APT is meant to complement rather than supplant pre vailing noninteractive batch mode aperture photometry soft ware programs e g the aforementioned SExtractor APT was modeled after the popular DS9 FITS viewer Joye and Mandel 2003 in some ways but with a focus on advanced aper ture photometry capabilities There are other interactive soft ware programs that do aperture photometry such as IRAF which is a well established workhorse in the astronomical com munity but these can be difficult to install and less than straight forward to use especially for nonspecialists There are also commercial aperture photometry software packages that are popular with astronomers e g the Interactive Data Language and associated IDL Astronomy User s Library which are available at some cost APT was designed to address these points and also to have unique features and functions not found in other aperture photometry programs Why is it desirable to visualize the data and interact with the aperture photometry calculations There are many answers to this question and the problems associated with aperture pho tometry are not easily realized until one looks at the data For example an astronomer may not be aware that an astronomical source of inte
37. d is located at pix el x yj and ae is the smallest data value in the centroid ellipse The data values included in the summing must be great er than dei not NaN or Inf and less than or equal to the upper outlier rejection threshold for the calculation The centroid ellipse is allowed to move with each iteration so it is necessary to recompute dec each time The centroid calculation is done with subpixel resolution but the step size is currently limited to no less than 0 05 pixels for computational speed The method generally converges for isolated sources but not always and the user is cautioned to check that the resulting source centroid is a reasonable one The source centroid calculation does not always 2012 PASP 124 737 763 APERTURE PHOTOMETRY TOOL 747 give the best aperture position for the source of interest espe cially if there are other sources nearby that fall within the centroid ellipse One can use visual feedback from the aper ture slice and source scatter graphs for improved manual aper ture positioning See 7 5 for more information about the available APT graphs The More Settings panel has radio buttons for the user to select one of three available source models Model 0 No aperture interpolation Model I Apertture interpolation only for NaN and Inf pix els including zapped pixels Model 2 Interpolation for all aperture pixels Model 0 will underestimate the source intensity if there are
38. de The required inputs are two space delimited source lists in plain text files The software assumes that one of the source lists is calibrated and the other is not The calibrated source list must have only the three following columns right ascension decli nation and absolute magnitude The uncalibrated source list must have only the three following columns right ascension declination and instrumental magnitude The equatorial coordi nates must be in decimal degrees Each source list file may in clude a header line containing three space separated single word column titles e g RA Dec Mag The software will read in up to 100 000 sources from each source list The source lists are by default expected to be located in the source list directory specified in the APT user preferences but the user can navigate elsewhere if necessary There are optional inputs to control the computation The match radius gives the maximum tolerable distance between sources for a match and its default value is 1 The double sided outlier rejection threshold in magnitude allows outliers to be defined and excluded from the computation and its default value is 0 3 The faint source rejection threshold in magnitude assures that only matches of sufficient brightness will be in cluded in the computation and its default value is 21 The tool will optionally normalize the zero point by an input exposure time and the default exposure time is 1 s wh
39. de Show Aperture APERTURE PHOTOMETRY TOOL 757 Pick Zap Tool Cursor X Y 465 1374 Pixel value 1 3222e 03 Photometry units DN Pick Zap mask 1x1 pixels 3x3 pixels 5x5 pixels 7x7 pixels Pick 428 1413 1 3425e 03 429 1419 1 3424e 03 429 1418 1 3819e 03 429 1417 1 3368e 03 429 1416 1 3650e 03 429 1415 1 3750e 03 429 1414 1 3049e 03 429 1413 1 3367e 03 430 1419 1 3455er03 430 1418 1 3357e 03 430 1417 1 3283e 03 430 1416 1 3714e 03 430 1415 1 3504e 03 430 1414 1 3952e 03 430 1413 1 3645e 03 427 1416 1 2949e 03 Zap plus existing NaNs Infs 459 1378 1 4187e 03 gt NaN 460 1384 1 4425e 03 gt NaN 460 1383 1 4940e t03 gt NaN 460 1382 1 6534e 03 gt NaN 460 1381 1 7698e t03 gt NaN 460 1380 1 5806e 03 gt NaN 460 1379 1 4683e 03 gt NaN 460 1378 1 4091e t03 gt NaN 461 1384 1 3554e 03 gt NaN 461 1383 1 3734e 03 gt NaN 461 1382 1 4050e 03 gt NaN 461 1381 1 4483e 03 gt NaN 461 1380 1 4408e 03 gt NaN 461 1379 1 4017e 03 gt NaN 461 1378 1 3469e 03 gt NaN 458 1381 9 3609et03 gt NaN Close Window Fic 14 APT s pick zap tool The picks in a 7 x 7 block of pixels are shown in magenta The zaps in a block of the same size are shown in blue move the aperture to the centroid position Adjusting the aperture position spinner controls will also clear the picks and zaps although the aperture movement itself in this c
40. e crowding The annulus is commonly either circular or elliptical and the annular hole is as large as the aperture or larger in order to exclude a significant amount of signal from the source of interest for ac curate sky background estimation The inner and outer major and minor radii of an elliptical annulus are the geometrical parameters that determine the number of data samples involved in the background estimation The outer annular dimensions should be small enough to keep the calculation local to the source but large enough to contain enough samples to suffi ciently minimize the statistical uncertainty Aperture photometry therefore has its complexities It is often practical more instructive and sometimes more accurate to perform aperture photometry manually on individual sources rather than to rely on results from automated software programs such as SExtractor Bertin amp Arnouts 1996 Holwerda 2005 The intended audience for this article is anyone who is interested in aperture photometry including professional and amateur astronomers and astronomy students We introduce free interactive software called Aperture Photometry Tool APT that performs aperture photometry calculations and digital image analysis in a highly demonstrative manner The software is designed to be used with astronomical science images which are freely available from a variety of public data archives e g the Spitzer Heritage Archive The software
41. earing the picks and zaps The same goes for changes made within the More Settings panel After these sorts of changes in which the aperture may be resized but may not be moved either the Recompute Photometry button text will change from the color black to the color red to indicate that the calculation needs to be updated or it will be automati cally recalculated in the case of major radii changes where the user hits the Enter key after the change Clicking on the Recompute Photometry button will nevertheless use the new settings to update the calculation Finally any adjustment that changes the aperture s position will cause the picks and temporary zaps to be cleared and the image data values will revert to those in the original image The software behaves this way to inculcate the understanding that the zaps are temporary The picks and zaps are cleared when the aperture is moved because it is presumed that the user is done with the calculation and ready to do another We also made this design choice to prevent the frustration of a subsequent proximate calculation Note that NaN values in the original image will of course be preserved The aperture can be moved by mouse clicking on either another source in the main image viewing window or the Snap button which will automatically 2012 PASP 124 737 763 200 Overlay aperture on image in main panel and then click on sub image below Recompute photometry after zapping pixels Hi
42. ected by configuring APT s maximum image size to as little as 500 pixels on a side APT can also be set up with a compact sized GUI that fits on some computer screens that are smaller than normal in size such as those on the smaller laptops APT has relatively simple installation instructions some APT users have reported that APT is much easier to install than IRAF We have eliminated all high level software dependen cies by putting it in a single package to simplify the process Additionally we have refined the installation process down to just a handful of steps APT is especially easy to install on a Mac Finally the software can be downloaded via the Internet and used free of charge for research and education in astronomy and astrophysics satisfying the last criterion in our list of classroom suitability attributes 3 MAIN GUI PANEL This section summarizes the prominent features of APT s main GUI panel with more details given later in 7 The layout of APT s main GUI panel is shown in Figure 1 and the enumeration below in this section refers to the numbered items in the figure The computer screen shots in Figure 1 and other 740 LAHER ET AL eoo Aperture Photometry Tool 34 Get l Header d List amp Help Exit NA Lower bound of stretch MJy sr 6 4326e 02 Upper bound of stretch Mjy sr 2 0553e 01 33 gt _Stretch to Bounds 4 98 image Histogram Adjust stretch min percentile of set range
43. ed to an image with a s exposure time The case that applies should be documented and therefore known If the latter is the case then the magnitude zero point for a 1 s exposure must be corrected for the image s exposure time before inputting to APT in order to yield accurate results as APT does not do this automatically This correction is done by adding 2 5 logig Texp to the time normalized magnitude zero point where T exp is the exposure time in seconds In the event adjustments are made to the GUI controls that affect any of APT s calculational results the Recompute Pho tometry button text will change from the color black to the color red as a reminder to the user that the calculation needs to be updated This visual device aims to reduce user errors resulting from incorrect associations made between mutually inconsistent inputs and outputs BUNIT is a keyword defined by the FITS standard for spec ifying the physical units of the image data If this keyword is missing or its setting is null in the image FITS header then for clarity in various GUI panel labels the software will assume the setting of the default image data units This can be changed via the Set Default Image Data Units option in the Preferences menu and it is initially D N 2012 PASP 124 737 763 7 SUPPLEMENTARY SOFTWARE FUNCTIONALITY 7 1 Image Data Display In the main image viewing panel which is located in the upper right corner of the main GUI pa
44. enerally APT users report a positive ex perience with the software and many find it easy to install on their computers themselves The initial beta version of APT was released in 2007 Novem ber and since that time there have been many releases of the package to add new capabilities and fix bugs APT is an object oriented all Java software implementation and as such the same source code is built to generate software packages for Java capable computers Currently four different packages are available to facilitate installation on various types of computers There are no software dependencies on other as tronomical packages or libraries However a recently installed version of the Java Runtime Environment JRE is required Version 2 1 5 of APT is available at the time of completion of this writing and it was compiled with JDK 1 6 0_31 The structure of this article is as follows Section 2 discusses the design considerations that went into creating APT Section 3 tours the layout of APT s main GUI panel Section 4 gives basic APT usage instructions for users wanting a quick start Section 5 explains how APT does sky background estimation and the available options for controlling it Section 6 provides details on how APT does aperture photometry calculations and what options are available for refining the calculations Section 7 con tains several subsections that discuss APT s salient components functionality applicability and
45. estimating the sky background in the region local to the source of interest and there are a few options available for controlling how it is done Only image pixels in an elliptical sky annulus centered on a user selected center position are considered for the back ground calculation The pixels with NaN or Inf are rejected outright The center position for purposes of background esti mation is specified in integer pixels only There are three dif ferent ways of specifying the center position in APT 1 Mouse clicking on the image displayed in the main image viewing panel 2 Changing the values in the spinner controllable text fields for the aperture position which are located near the lower left corner of the main GUI panel 3 Clicking on the Snap button in the lower left corner of the main GUI panel more on this in 6 The inner and outer major radii of the sky annulus in integer pixels only can be specified on the main GUI panel These major radii are used to scale the ellipse specified for the aper ture The inner radius of the sky annulus must be greater than or equal to the radius of the elliptical aperture along any direction from the center of the ellipse No limitation is placed on the outer radius of the sky annulus except that it must be greater than the inner radius The default values that specify the size and shape of the aperture and sky annulus which are loaded when APT is launched can be specified via the Set
46. estimation type or sky model em ployed in the computation see below and Ay is the area of the sky annulus in pixels Equation 3 has three terms under the square root sign The first two terms are well known e g see Bertin 2006b The third term accounts for the uncertainty in the background estimation which SExtractor omits Equa tion 3 does not account for possible pixel to pixel noise cor relations which are present in co added images The derivation of this formula is beyond the scope of this article and may be found in Masci and Laher 2012 in preparation Equation 3 allows that the image the user has in hand is not necessarily as observed with the detector s gain factor but rather the combination of some number of images as in a co added image or mosaic The depth of coverage can vary with source position and so this must be adjusted for each individual source The depth of coverage Naepn can be specified on the More Settings panel Depending on whether the APT optional sky average sky median or custom sky value is used in the sky background sub traction the value of in equation 3 is equal to either 1 0 7 2 or 0 0 respectively In the first two cases APT uses the sky scale which is defined in 7 4 as a robust estimator of the sky background standard deviation 7 in the latter case Osky 18 taken to be zero In this article robust refers to methods that are generally somewhat less optimal tha
47. fferentiating the on screen graphs 7 6 Radial Profile Interpolation APT s radial profile graph panel has extra controls for fitting a parameterized radial profile model to the data associated with the currently selected source see Fig 13 The radial profile model is a smooth continuous curve that is designed for a ra dially symmetric source Sky Scatter Plot Sky Scatter Wed Mar 28 06 52 16 PDT 2012 Close 10 5 11 0 11 5 12 0 12 5 13 0 Distance from aperture center pixels Sky Inner sky Outer sky Sky level median Fic 9 Sample sky scatter plot generated by APT 2012 PASP 124 737 763 754 LAHER ET AL Sky Histogram Plot Sky Histogram Number Wed Mar 28 06 54 32 PDT 2012 Milal 705 710 715 720 725 730 735 740 745 750 755 Surface brightness DN E Sky pixels in sky annulus 760 765 770 775 780 785 790 795 800 805 810 Fic 10 Sample sky histogram plot generated by APT pe S r A Br Cr Dr Ert Fexp 4 Oo where S r is the pixel intensity or surface brightness as a function of radial distance from the aperture center r in pixels which is constrained by r gt 0 the data fit coefficients A through F are determined via linear regression and is a fixed parameter that can be manually adjusted to optimize the data fit The right most term containing the exponential function is a scaled Gaus sian distribution and therefore is the f
48. g representation of the graph image data title for the converted image data e g flux density The latter if the check box is enabled will override the default image data title Figure 6 shows an Aperture Slice plot generated by APT The blue and pink curves correspond to slices through the aperture center along horizontal and vertical image axes respectively The slices extend across both aperture and sky annulus Along with the plotted curves are colored lines that visually convey the size and shape of the aperture and sky annulus All vertical colored lines in the plot map directly to the colors used in the overlay symbol representing the aperture and sky annulus on the image Figures 7 10 give random examples of the other category A graphs available The Curve of Growth graph is useful for determining the best aperture and sky annulus major and minor radii assuming the rotation angle of the elliptical aperture is set correctly The Source Scatter Sky Scatter and Sky Histo gram graphs are useful in setting efficacious outlier rejection 2012 PASP 124 737 763 APERTURE PHOTOMETRY TOOL 751 TABLE 2 COLUMNS IN APERTURE PHOTOMETRY TABLE GENERATED BY APT Definition Sky coordinates of the aperture center decimal degrees or sexagesimal representation as set via the Preferences menu Sky coordinates of the source centroid decimal degrees or sexagesimal representation as set via the Preferences menu Column s RA Dec ccsi
49. h many built in features for altering the 752 LAHER ET AL e020 Aperture Slice Plot Aperture Slice 17 500 15 000 12 500 10 000 7 500 5 000 Surface brightness DN 2 500 Wed Mar 28 06 34 06 PDT 2012 Close 13 12 11 10 9 8 7 6 5 4 3 2 1 t 2348S 67F sev WR SB Position relative to aperture center pixels X Slice Y Slice Aperture Inner sky Outer sky Sky level median Fic 6 Sample aperture slice plot generated by APT graph s appearance The user can drag the mouse cursor across the graph to narrow the range of the plotted data The user can also right button mouse click on the graph to zoom in and out change the foreground and background colors save the graph as a PNG formatted image etc Mac users will need a mighty mouse and will also have to configure the mouse under the System Preferences menu to set up right click as a secondary button The graphing software cannot handle very large or very small numbers and sometimes responds by creating a graph with no numbers on the affected graph axis If this is encountered adjust the outlier rejection range as needed until the problem goes Curve Of Growth Plot Curve Of Growth 120 000 140 200 100 000 4 90 000 80 000 70 000 60 000 50 000 40 000 4 30 000 20 000 10 000 Cumulative sky subtracted surface brightness DN ee O S S S Ieee Wed Mar 28 06 39 04 POT 2
50. ical considerations photometric criteria can govern the aperture s shape e g a set of contiguous pixels in a digital image with data values greater than some threshold A multiplier greater than one called an aperture correction is employed to correct for source intensity outside of the aperture which is needed for cases where source crowding effects warrant using a smaller aperture In theory an aperture correction is always needed because of limited bandwidth considerations but in practice no aperture correction is made for sufficiently large apertures As the size of an aperture is increased the signal from the source 738 LAHER ET AL becomes more fully contained and the noise encompassed by the aperture is increased and the signal to noise ratio S N of the aperture photometry result is therefore decreased these considerations mainly influence the size of the aperture chosen for a study Aperture photometry calculations as mentioned above also normally involve subtracting the contributions to the image data that do not originate from the source of interest which is gen erally referred to as the sky background An annulus centered on the source may define a region containing the image data pixels used to locally estimate the background under the as sumption that the background is constant across the aperture This assumption is violated to varying degrees in the case of crowded fields depending on the level of th
51. ich is equivalent to not normalizing by the exposure time The tool generates and displays a plot of magnitude differ ence versus magnitude There are options to customize the plot on the tool s main panel The user can also right click on the plot to expose additional plotting options One of these options allows the user to save the plot as a PNG image 7 11 Image Comparator and Blink APT comes with a pop up tool called the Image Compara tor for comparing images side by side The image comparator is basically a panel containing a series of up to four magnifier tools 2012 PASP 124 737 763 APERTURE PHOTOMETRY TOOL 761 e090 image Comparator image offsets relative to primary image on left Magnification 3c78 3 6um fits 1 1 3c78 4 5um fits 1 1 Cursor X Y 257 237 Cursor X Y 260 237 Pixel value 4 3336e 01 Pixel value 3 4248e 01 Offset X Y Offset X Y 3 oO 3c78 5 8um fits 1 1 Cursor X Y 257 237 Pixel value 2 9811e 01 Offset X Y oll Oo sx 10x 20x 3c78 8 0um fits 1 1 Cursor X Y 260 237 Pixel value 3 6021e 01 Offset X Y 3 ol Fic 18 APT s Image Comparator showing Spitzer IRAC images in the 3 6 4 5 5 8 and 8 0 um bands The primary image is on the left that enable simultaneous comparison of the primary image with up to three different comparator images see Fig 18 This functionality is accessed via the Image Compa
52. in and without the Preferences menu are the instantaneous user s preferences for the session albeit not necessarily saved to disk This can be verified by mouse clicking on the List Preferences function un der the Preferences Menu One exception is the setting of the aperture geometrical parameters and the centroid and sky annu lus inner and outer major radii whose preferred values should be set via the Set Aperture Size Shape and Angle and Set Photometry Size Parameters options in the Preferences menu these values may be changed to other values directly on the main GUI panel as needed for experimentation without affect ing the preferences Therefore the Save Preferences option will for the most part capture the current state of the user s session 7 3 Output Files During the operation of the software several output files are created at various stages see Table 1 With the exceptions noted below all output files are created in the scratch directory with fixed filenames The output aperture photometry table disk location and filename the location of the scratch directory and the user preferences location and filename can be changed via options available in the Preferences menu The filename sourceListByAPT dat is by default generated in the last 15 Note that the environment variable APT_HOME must be set to the location where APT is installed and this location is not to be confused with the user s home directory
53. inates type is available on the source list tool panel The user has the option of selecting the button labeled Auto matically Process Source List in which case calculations will be performed for all sources in the source list for the current aper ture photometry settings Thus it is important that the user select the desired settings before mouse clicking on this button Once this option has been selected identical calculations will be done for all sources in the source list and a record will be auto matically saved for each source in the aperture photometry table file The marker Automatic Source List Processing will be written to the aperture photometry table file prior to saving the aperture photometry records Another option available to the user is the Manually Process Source List button in which case an aperture will be overlaid onto the image for the first source in the source list and the message Ready to process source number 1 will be displayed The user can at this time manually adjust any or all of the aper ture photometry settings for that particular source on the main GUI panel and via the More Settings button and then press the Recompute Photometry button and view the graphs to make sure that the settings are just right After the user is satisfied with the settings for that particular source the Step Through Source List button can be pressed which will redo the calcula tion save a record of the results to
54. ion only for NaN Iinf outlier pixels Model 2 Interpolation for all aperture pixels C Model A No sky background subtraction Model B Sky median subtraction _ Model C Custom sky subtraction below Model D Sky average subtraction 0 00000e 00 4 1 79769e 308 1 79769e 308 1 79769e 308 1 79769e 308 Mjy sr Surface brightness 3 3000000e 00 1 0000000e 00 1 0000 27 4454 1 0000 g 1 0153700e 01 Jy Flux density Apply Settings Close Window Fic 5 APT s More Settings panel allow the user to load either a different primary image or com parator images 3 Adjust the image display stretch for best viewing As an aid click on the Image Histogram button to see the stretch range spanned by the image 4 Select centroid and sky annulus major radii integer values only and click on the Alter button beside the aperture attributes label to select the elliptical aperture attributes as appropriate for the source of interest 5 Place the mouse cursor over the source of interest in the image displayed in the main image viewing panel and click to overlay an aperture 6 Show and study the various graphs instructions are given in 7 5 7 Select the desired new radii as appropriate and or change other settings as needed 2012 PASP 124 737 763 8 Redraw or overlay a new aperture by either clicking on the Recompute Photometry button or clicking on the Snap button for nudging the
55. ise in the image data However for saturated sources with missing data at small r and especially at r 0 extrapolation of the radial profile model essentially occurs through the compu tation of the scale and offset and this can lead to potentially large errors in the results for such cases The radial profile graph panel has also been equipped with controls for manually scaling and offsetting the radial profile model which are located at the bottom of the panel The cur rent purpose of these controls is mainly to allow the user to ex periment with the scale and offset parameters and to instantly visualize the effects on the plotted model curve 7 7 Pick Zap Tool The pick zap tool which is accessed via the Pick Zap button in the bottom middle portion of the main GUI panel see Fig 14 has a few useful functions for probing and fine tuning aperture photometry calculations After an aperture has been overlaid onto the primary image source an enlarged subimage centered on the aperture is displayed in the pick zap tool s work area Moving the mouse cursor over the subimage causes the passed over pixel positions and associated image data values to be rapidly displayed When the Pick radio button is selected and the subimage is displayed the user can mouse click on the subimage to pick out specific pixels Picked pixels are highlighted in the sub image by an outline around the pixel in the current pick color The picked locations a
56. ity contributions It also replaces the missing source intensity associated with rejected outliers in the aperture provided that the interpolated result falls within the lower and upper limits set for source outlier rejection Tem porarily zapped pixels are also interpolated see 7 7 The model 2 source model is used for interpolating source intensities in all aperture pixels even for those pixels with good data This model will thus yield a smoothed data result When either of the source models involving interpolation is selected a two parameter linear regression is automatically per formed for each calculation to scale and offset the radial profile model which is treated as a fixed model here in order to best fit the model to the data for the sources of interest Thus the 2012 PASP 124 737 763 APERTURE PHOTOMETRY TOOL 755 Results from Aperture Photometry Tool 1200 y 1100 z Q 1000 900 8s o 800 z z a e ead er i J 600 g 500 S 5 400 a 300 200 0 0E0 1 0E5 2 0E5 3 0E5 4 0E5 5 0E5 Source intensity D N Fic 12 Sample scatter plot of results generated by APT radial profile model can be derived from one source and applied to other sources This model is particularly useful when the image data have a radially symmetrical PSF and the PSF is invariant over the image The results that are computed with radial profile interpolation will be less sensitive to the effects of no
57. lation primarily yields the source intensity and its uncertainty The former involves sum ming pixel values within the aperture to get the total intensity then subtracting the product of the aperture area in pixels and the per pixel sky background in order to get the source inten sity The latter also requires the aperture and sky annulus geom etry as well as extra information including the detector gain the conversion factor from image data units to D N if image is not already in units of D N the background estimation method and the sky background standard deviation APT works under the assumption that the background is constant across the aperture APT performs its calculations with an elliptical aperture which the user specifies with major and minor radii and a rota tion angle These quantities are recorded in the MajR_aper MinR_aper and Rot_aper columns respectively in the output 2012 PASP 124 737 763 aperture photometry table see 7 4 Of course APT also allows circular apertures as a circle is a special case of an ellipse with its major radius equal to its minor radius The basic inputs for the calculation are the elliptical aperture geometrical parameters the source centroid major radius and position coordinates of the aperture center the instructions for selecting these quantities are given in 5 The calculation of the source s centroid position which shares the same center position as the apertu
58. layed near the lower left corner of the main GUI panel under the heading PRIMARY IMAGE PHOTOMETRY RESULTS Section 7 4 defines the displayed quantities which are among the quantities written to the output aperture pho tometry table when the user mouse clicks on the Save Results button 24 The Snap button nudges the aperture onto the computed centroid of the source of interest see 6 for more details in cluding the color coding 25 The source s centroid position in floating point pixels is displayed just to the left of the Snap button see 6 26 The aperture s position in integer pixels is displayed in spinner controllable text fields and can be changed here via ei ther text field editing or mouse clicking on the tiny increment decrement buttons located just to the right of the corresponding text field 27 The real time pixel coordinates the corresponding equa torial coordinates and the image data value at the position of the mouse cursor in the main image viewing window are displayed under the heading REAL TIME RESULTS The representation of the sky coordinates can be changed to either sexagesimal or decimal degrees via theSet Celestial Coordinates Units option in the Preferences menu The image data units are given along side the image data value The default image data units are used 2012 PASP 124 737 763 APERTURE PHOTOMETRY TOOL 743 e090 Primary Image Thumbnail Cursor X Y 1483 4087 Pixel value 1
59. ma Y CHICAGO JOURNALS Aperture Photometry Tool Author s Russ R Laher Varoujan Gorjian Luisa M Rebull Frank J Masci John W Fowler George Helou Shrinivas R Kulkarni and Nicholas M Law Reviewed work s Source Publications of the Astronomical Society of the Pacific Vol 124 No 917 July 2012 pp 737 763 Published by The University of Chicago Press on behalf of the Astronomical Society of the Pacific Stable URL http www jstor org stable 10 1086 666883 Accessed 09 08 2012 11 48 Your use of the JSTOR archive indicates your acceptance of the Terms amp Conditions of Use available at http www jstor org page info about policies terms jsp JSTOR is a not for profit service that helps scholars researchers and students discover use and build upon a wide range of content in a trusted digital archive We use information technology and tools to increase productivity and facilitate new forms of scholarship For more information about JSTOR please contact support jstor org The University of Chicago Press and Astronomical Society of the Pacific are collaborating with JSTOR to digitize preserve and extend access to Publications of the Astronomical Society of the Pacific http www jstor org PUBLICATIONS OF THE ASTRONOMICAL SOCIETY OF THE PACIFIC 124 737 763 2012 July 2012 The Astronomical Society of the Pacific All rights reserved Printed in U S A Aperture Photometry Tool Russ R LAHER
60. n data units given by the Data_units column above Standard deviation of the data in the sky annulus after the sky outliers have been rejected in data units given by the Data_units column above calculated using the unbiased or 1 N 1 method This result has not been inflated to account for the data clipping of the Robust estimator of the sky background data dispersion in data units given by the Data_units column above It is given by the difference between the 84 and 16 percentiles of the sky data distribution which corresponds to approximately 1 standard Major radius of the elliptical region for computing the source centroid position pixels Rotation angle of the elliptical aperture degrees This angle is with respect to the image s horizontal axis and a positive angle rotates Number of pixels in the aperture after the source outliers have been rejected see N_rej column below It is the data associated with these pixels that are summed to yield the integrated image data in the aperture This quantity has a fractional component because the Number of source outliers rejected The rejects represent potential losses of integrated image data which as an option can be filled in Sky sigma distribution s tails Skyzscale sursessiisan deviation in a Gaussian distribution divided by 2 R COE suiran ar Maj R Aper aruiiisrsis Major radius of the elliptical aperture pixels MinR_aper Minor radiu
61. n done if radial profile interpolation has been done only for NaN Inf pixels in the aperture or 2 if radial profile interpolation has been done for all aperture pixels Sky model sacccecsss A if the background sky contribution has not been subtracted from the Source_intensity see above B if the median sky has been subtracted C if the custom sky has been subtracted or D if the average sky has been subtracted Sky_median pix Per pixel median of the data in the sky annulus after the sky outliers have been rejected in data units given by the Data_units column above This value which is a robust estimator of the sky level times the number of pixels in the aperture form a product that is the sky contribution optionally subtracted from the integrated image data of the source Sky_average pix Per pixel average of the data in the sky annulus after the sky outliers have been rejected in data units given by the Data_units column above A disparity between the average and the median is an indicator of skewness in the data distribution Sky_RMS pix Per pixel rms value of the data in the sky annulus after the sky outliers have been rejected in data units given by the Data_units column above This value is slightly larger than the average and will be equal to the population standard deviation in the special case of zero mean data Sky_custom pix Per pixel custom sky value specified by the user i
62. n methods appli cable to well characterized noise but more stable against outliers For example the sample median is a robust estimate of the population mean when the sample is contaminated but the sample mean is most optimal when the noise is well behaved In the artificial case of no sky background subtrac tion an APT option that is useful in radial profile interpolation as discussed in 7 6 only the first term under the square root sign in equation 3 determines the source intensity uncer tainty The More Settings panel allows the user to specify two ad ditional quantities related to the calculation It provides for set ting an aperture correction a multiplicative factor greater than 1 0 that when multiplied by the result for source intensity ac counts for the missing source intensity that becomes a problem when the aperture is too small for the source This is useful when it is impractical to make the aperture as large as is needed such as in dense fields The user can also set a magnitude zero point so that photometrically calibrated source magnitudes will be computed The magnitude zero point if available for the im age at hand comes from prior photometric calibration against reference stars either in the same image or in images acquired by the telescope in the same night and for the same camera filter used When the magnitude zero point is determined it can either be done for the image s exposure time or normaliz
63. nd associated image data values are listed 756 LAHER ET AL Radial Profile Plot Radial Profile 17 500 49 15 0004 12 500 10 000 Surface brightness DN vo oN gt 8 8 N u t o 2 500 Distance from aperture center pixels Source sky Aperture Inner sky Outer sky Sky level median Zero level Data fit Create Data Fit Model Radial profile data fit model Si A Br CrA2 DrA3 E r 4 F exp rA2 2 sigma 2 A 2 428e 03 B 5 330e 02 C 5 081e 01 D 8 972e 01 E 5 170e 02 F 1 445e 04 sigma 9 315e 01 Optimize parameter sigma 9 315e 01 Reset Sigma Vary sigma to minimize ChiA2 Scale and Offset the Model for Application to Any Source by Minimizing Chi 2 scale 1 000e 00 1 000e 00 Reset Scale i offset 0 000e 00 0 000e 00 Reset Offset l Chi2 1 048e 03 ee j 30 lt 6 Chi2 1 048e 03 50 30 10 10 30 50 Set Sliders E Set Slider i Ci Auto Minimize 30 50 Recompute Fit Fic 13 APT s radial profile panel The example data fit shown has been optimized in the adjacent uneditable text area The pick color can be changed via the Set Image Display Attributes Pick Color op tion in the Preferences menu With the Zap radio button the user can temporarily set spe cific pixel values to NaN by mouse clicking on the pixels of interest NaN values are excluded from the calculations but this happens only af
64. nel the stretch and color table controls work automatically only for the visible portion of the displayed image plus some margin around the visible image s edges This design feature allows the software to run faster and be more responsive The positions of the panel s scroll bars determine which portion of the image is visible and actively updated when the image viewing settings are changed Moving the scroll bars for large images will reveal the once active portion of the image inside a visually obvious bounding box The image outside of the bounding box will be displayed with a different stretch and or color table which was set earlier in the APT session To remove the unsightly remnants of the bounding box and refresh the displayed image two re fresh options are available The Refresh 1 button quickly re freshes just the visible portion of the image to save time The Refresh 2 button refreshes the entire image by launching multiple processor threads for refreshing the unseen portion of the image so that immediate GUI control is returned to the user and additional computer CPU cores if available on the user s machine are utilized to finish the job faster For very large images however the threads take some time to complete and may still be running even though the user is allowed to con tinue normal work with the GUI To avoid queueing up too many threads the user is advised to not mouse click on the Re fresh 2 button more than
65. o compute a suite of statistics for a given column of data in the aperture photometry table 9 Add zoom in out capability for the main image viewing panel 10 Add a button that rotates an image so that north is up based on the WCS in the FITS headers 11 Add functionality to allow manual override of the cur rently built in automatic scaling and offsetting of the radial profile model when used for interpolation 12 Add an option to exclude saturated pixels when extract ing sources from an image 13 Add a tool that measures distances on the dis played image 14 Add basic parameter settings as differentiating labels on the graphs 15 Add a new Keep Zaps button and eponymous function ality for the pick zap tool The default maximum image size is 5000 x 5000 pixels which has been tested on a computer equipped with 2 Gbytes of random access memory The maximum image size setting under the Preferences menu can be increased to accommodate larger images assuming the user s machine has sufficient mem ory and in conjunction with this increase the user may have to start up APT with a larger heap space setting Currently java mx1024M APT is executed in APT csh which is the APT C shell startup script for UNIX based platforms and in APT bat which is the batch file for starting up APT on Windows machines Mac users running APT as a double click ap plication can similarly edit this specification in the Contents Info plist s
66. on At least one match is required but no more than 100 000 matches are allowed in the computation The algorithm makes two passes through the data The first pass computes ro bust data statistics namely the median and the data dispersion given by one half of the difference between the 84 1 and 15 9 percentiles The second pass applies outlier rejection and faint source rejection to filter the data A sufficient variety of 760 LAHER ET AL Simple Photometric Calibration Tool Simple Photometric Calibration Choose Calibrated Source List Choose Uncalibrated Source List Match radius arcsec 1 000000 Outlier rejection threshold mag 0 300000 Faint source rejection threshold mag 21 000000 Normalize by exposure time vw Exposure time seconds 120 Match Source Lists amp Compute Zero Point Main title of plot Magnitude Difference Plot X axis title on plot Matching source brightness mag Y axis title on plot Magnitude difference X axis minimum on plot 14 X axis maximum on plot 21 Y axis minimum on plot 0 3 Y axis maximum on plot 0 3 Close Phot Read Calil in R ometric Calibration Calculation and Results ing in new calibrated source list brated source list Users laher rlaher NITARP SRC27 PhotometricCalibr txt Number of sources 412 Read Unca ing in new uncalibrated source list librated source list Users laher rlaher NITARP BRC27 apt APT 42 inst Number of sources 1032
67. once in a reasonable time interval at least a few seconds When needed the Refresh 2 button text will change from the color black to the color yellow to remind the user to click on this button before scrolling about the image It is not mandatory for the user to click on the Refresh 2 button when its text turns yellow the user can defer doing this until after the scroll bars are subsequently moved For purposes of image display only all image data values outside the interval specified by the stretch extrema are set to the corresponding extreme value Image data values that are set to NaN or Inf are displayed with the blank color set by the user the color blue is the default Inf values are handled the same as NaN values and almost no distinction is made be tween these two bad data types The blank color can be changed using the blank color picker accessible via the Set Image Display Attributes option in the Preferences menu The user can specify the maximum image size that the soft ware will load into memory This is done using the Set Maximum Image Size option in the Preferences menu The de fault maximum image size is 5000 pixels on an image side and this preference can be reset to as many as 100 000 pixels For images larger than the preferred value the user will be prompted to specify the desired portion of the image after its filename has been selected 2012 PASP 124 737 763 APERTURE PHOTOMETRY TOOL 749 7 2 User Preference
68. ource list file is plain text and consists of one set of source coordinates per line in the file where the coordinates are delimited only by one or more spaces Either image pixel coordinates or equatorial coordinates are permitted Equatorial coordinates if given must be converted into decimal degrees Here is a short example source list file that gives the pixel positions of source centroids 7232 279 0 729 4 145 45 622 195 205 857 595 9 318 4 731 11 195 54 674 84 140 09 643 2 153 1 735 0 161 6 A file improperly formatted error will be issued if the file format is incorrect e g comma separated values are not 758 LAHER ET AL Select source list type Source List Tool Aperture Photometry Calculations at Listed Source Positions _ Image pixel coordinates Equatorial coordinates decimal degrees Source list file Users laher sourcelist dat Number of sources 3 Choose Source List Create Source List _Automatically Process Source List Above button starts automatic processing Manually Process Source List Above button starts manual processing Source list coordinates pixels Step Through Source List N A N A Fic 15 APT s source list tool for performing aperture photometry calculations from a source list allowed The maximum number of sources per source list file allowed by APT is 100 000 A set of radio buttons for the user to indicate the source list coord
69. parator images on the right for a side by side comparison see 7 11 9 The main image viewing panel displays either the primary image or a comparator image see item 16 below If the image is bigger than the viewing window then the scroll bars on the window can be used to view the desired image portion the user may have to mouse click on the image to make the scroll bars appear Bounding box graphics are overlaid onto the image just outside the visible portion of the image in order to visually define the region updated by the Refresh 1 button see item 14 below The example image in Figure 1 is a Spitzer Space Tele scope mosaic with pixels having missing data represented by the blank color blue The left middle side of the image contain ing data has an aperture and sky annulus overlay which is drawn by the software when the user mouse clicks on a source in the displayed image 10 The filename label indicates the image currently dis played in the main image viewing panel see previous item The label is embedded with additional useful information The number enclosed in the first set of square brackets indicates whether the currently displayed image is the primary image value is 1 or a comparator image value is greater than 1 The two numbers separated by a colon and enclosed within the sec ond set of square brackets indicate the image extension number and the image data plane number within the image extension respectively
70. r tool tip to be displayed Not shown in Figure 1 are the Preferences File and Tools pull down menus which are located at the top of the computer screen in the case of Macs or in the main GUI panel s upper left corner in the case of non Mac machines Section 7 2 gives more information about the Preferences menu Currently the File menu only has one option which is to clear the contents of the output aperture photometry table file Section 7 10 dis cusses the tool menu option of performing simple photometric calibration of astronomical sources extracted from an image The remainder of this section gives descriptions for the num bered items called out in Figure 1 1 The Get Image button is used to load an image and display it in the GUI The actions associated with this button have func tionality to load either a primary image or a comparator image The primary image is by definition the first image loaded and the subsequently loaded images are called comparator images whose purpose is visual comparison with the primary image see 7 11 Up to three comparator images are permitted Aperture photometry calculations are done only for the primary image APT can read only FITS formatted images This includes single extension FITS files FITS files with multiple image data planes in a single image extension and FITS files with multiple image extensions but not those with binary table extensions 2 The FITS header button pops up
71. rator button located in the upper middle portion of the main GUI panel The comparator images can be offset in x and y relative to the primary image using the available spinner adjustments if neces sary Separate control over the stretch of each comparator image is currently not implemented For comparing images with dras tically different stretches judicious use of the primary image logarithmic stretch capability can compensate somewhat for this tool s deficiency Closely related to the functionality of the Image Comparator is APT s image blink capability Repeatedly mouse clicking on the Blink button located in the lower middle portion of the main GUI panel will quickly cycle the image display from the pri mary image to the first comparator image in the sequence sub sequently advancing to the next comparator image if available and then eventually back again to the primary image This capa bility is good for spotting image pixels with variable stars or affected by cosmic rays 7 12 Batch Mode There are two different options available for running APT in batch mode The first is that APT can be executed with an image specified on the command line in which case that image will be loaded and displayed in the GUI APT csh image fits The second option is that APT can be executed with both an image and source list specified on the command line in which case the image and source list will be loaded by the software and 2012 PASP
72. re can involve a different number of pixels than used in the calculation The source centroid ellipse is its major radius scaled to the ellipse specified for the aperture The aperture geometrical parameters and centroid major radius 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 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 pick zap tool can also be used to temporarily eliminate pixels from the calculation More details about the pick zap tool are given in 7 7 The method that computes the source centroid position is iterative and runs for 100 iterations The first iteration is boot strapped from the user selected aperture position The k 1th iteration computes the following x and y image coordinates of the source centroid gt z a Te a dij dk k 1 1 i jES k tat T De roid y dij _ dk d i jesS k and RG T YEentroia dij E d in k 1 o LJEle asa eer 2 X dig drin ijeS k where the sums are over pixels in the centroid ellipse S k that meet criteria given below image data value
73. rest is in the crust of a mosaicked image which has a lower depth of coverage and ipso facto implications of higher measurement uncertainty Or one may not realize that a source has a significant number of blank or missing pixels i e pixels set to NaN not a number or Inf infinity even though SExtractor may have yielded FLAGS 0 for that source The accuracy of the background estimation can have a substan tial effect on the results especially for large apertures and rela tively faint sources In many cases one will want to look at the contents of the image region used for background estimation as a sanity check and possibly make adjustments With the above considerations in mind the classroom suitability criteria that we adopted for APT are listed as follows See http www astromatic net software sextractor TRAF stands for Image Reduction and Analysis Facility see http Airaf noao edu and Tody 1986 1993 See http idlastro gsfc nasa gov 2012 PASP 124 737 763 APERTURE PHOTOMETRY TOOL 739 visualization of inputs and outputs user interaction ease of use ability to run on a variety of machines and operating systems ease of installation and zero acquisition cost Data visualization pertains to graphical and statistical repre sentations of not only the aperture photometry results but also the input data We found that showing an overlay of the aperture and sky annulus on the input image was impor
74. riety of ways APT is appropriate useful and conve nient for professional work It is also playing a vital role in educating the next generation of astronomers in the United States and abroad There are indubitably many reasons that give APT a purpose in today s world and chief among them are its graphical user interface and the critical user feedback it pro vides its rich medley of tools machine independence ease of installation and intuitive use Validation of APT has been done by comparing several large statistical samples of similar results from SExtractor and APT which is documented in a companion article appearing in this issue of the PASP Laher et al 2012 It is expected that APT will continue to be upgraded over time both to remove any remaining bugs and to augment the software with new functionality and capabilities We thank the beta testers In particular Tom Jarrett Seppo Laine Alberto Crespo Noriega Bill Reach Jeonghee Rho and 2012 PASP 124 737 763 APERTURE PHOTOMETRY TOOL 763 Nancy Silbermann made numerous helpful suggestions Inga of some of their Java classes We also thank Benne W Holwerda Saathoff conducted invaluable beta testing in Germany We for his insightful suggestions and manuscript corrections Aper are also grateful to Xiugin Wu Trey Roby Loi Ly and Booth ture Photometry Tool s motto Inviso notitia and logo are copy Hartley for generous expert Java programming help and the use right
75. s Various options in the Preferences menu allow users to change the default settings and then save them to disk for a later APT session When APT is launched it automatically loads the preferences from a special file called APT pref that is located in the invisible subdirectory called AperturePhotometryTool in the user s home directory Users also have the option of later manually loading in another preferences file from a different disk location and filename If the special preferences file does not exist then factory default preferences are loaded into the user s session but are not automatically saved the user must explicitly save them via the Save Preferences option in the Pref erences menu if that is what the user wants to do Within a given APT session whenever a new primary image is read in the preferences are restored from the special preferences file Selecting the Reset Default Preferences option in the Prefer ences menu will restore the factory default settings to the user s session but will not save them again the user must manually select the option to do this If the Save Preferences option is selected then the current settings of the user s session will be written to a user selected location and filename and if that file already exists then all prior custom settings in that file will be overwritten At any time during a user s session most of the current settings as set by the various GUI controls with
76. s of the elliptical aperture pixels Rotaper css ences the ellipse counterclockwise RA sk gt sacadeteeteade Major radius of the inner sky annulus pixels R OSKY zarmena Major radius of the outer sky annulus pixels Nape asssorseiirsiai calculation is done with subpixel resolution NGIEJ danbesadamanseiate via APT s radial profile interpolation NUSKY aesae diosidas Number of data points in the sky annulus after the sky outliers have been rejected Image risi hdsendaads thresholds The example Radial Profile graph is discussed in more detail in 7 6 Regarding category B graphs selected columns in the aper ture photometry table can be plotted via the Plot Results button located in the lower left corner of the main GUI panel This but ton brings up a plot panel that allows the user to customize the graph see Fig 11 Both scatter and histogram plots are 2012 PASP 124 737 763 Path and filename of the associated image Experimental For Spitzer IRAC images MJD_OBS DATE_OBS pseudo FILTER settings are appended after the image filename available Most of the columns in the aperture photometry table can be plotted against one another in a scatter plot by selecting the desired columns from the pull down menus The plot panel controls give flexibility in creating a variety of graphs A sample scatter plot to illustrate this is given in Figure 12 JFreeChart the Java package used by APT to generate graphs comes wit
77. see Fig 2 The lower and upper limits of the graph s horizontal axis are set by the image display stretch bounds This histogram is of course use ful for determining the best stretch There is an inset table of global image data statistics on the graph minimum maximum mean sigma standard deviation median scale a robust mea sure of the data dispersion given by one half the difference between the 84 1 and 15 9 percentiles which is equivalent to 1 standard deviation in the case of Gaussian distributed data 1 and 99 percentiles number of data values used in computing the statistics and number of pixels set to either NaN or Inf in the image data The intent of the displayed statistics is to make the user aware of the image data contents Except for the number counts the data units of the image statistics are given by the image s BUNIT FITS header keyword or if BUNIT is not available the default is D N digital or data number The default setting can be changed via the Set Default Image Data Units option in the Preferences menu 6 The About amp Help button pops up a panel showing the software version number and the built in documentation 7 The Exit button terminates the software program in a user friendly way one more chance is given to cancel the termination 8 The Image Comparator button pops up a panel displaying the primary image on the left side of the panel and up to three APERTURE PHOTOMETRY TOOL 741 com
78. tant in giving the user important visual information for setting up the aperture photometry calculation in relation to the astronomical source of interest and its environs APT s GUI has many controls that promote user interaction such as changing the size of the aper ture and sky annulus and then immediately seeing the resulting overlay The feedback provided by APT s various graphs allows the user to make intelligent choices in modifying the input parameters The overall effect of equipping APT with a rich palette of controls and capabilities is to engage the user so that the user will want to spend time running the software At least this is our aim It is important to us that the software is able to be executed on a variety of machines particularly Mac Windows and Linux computers which are the most popular today It is for this reason that we chose to implement APT in the Java programming lan guage In fact any computing platform that runs the Java Virtual Machine JVM can run APT We also programmed APT with special functionality to enable it to run on computers with smaller memories and with smaller screens APT s minimum memory requirement is by design very modest only around 300 Mbytes with a 2048 x 4096 pixel image loaded This is small enough to accommodate older machines often found in the classroom APT can be easily used on machines with relatively small memo ries to analyze portions of very large images This is eff
79. ter the Recompute Photometry button has been clicked to update the calculation The pixel zapping function ality is useful for example for eliminating sources from the sky annulus that adversely affect the sky background calcula tion Zapped pixels are displayed in the subimage with the blank color and their locations and associated image data values are listed in the adjacent text area The blank color can be changed via the Set Image Display Attributes Blank Color option in the Preferences menu The Hide Show Aperture button is a toggle that alternately hides and shows the overlaid aperture It is included as a con venience for more clearly showing the subimage When the aperture is not hidden all aperture pixels are outlined in the color red on the subimage except for the aperture center pixel which is outlined in the color cyan to indicate the aperture cen ter The sky annulus pixels are outlined in the color green The outlined aperture pixels are complete pixels and do not reflect that the aperture photometry is computed at subpixel resolution The picks and temporary zaps are kept on the subimage and in the text areas when the Hide Show Aperture button is pressed This is also true when any of the image display controls are adjusted including stretch linear logarithmic scaling color table and pick and blank colors The aperture geometrical pa rameters and the centroid and sky annulus major radii can also be changed without cl
80. ubdirectory of the APT package before installing the package in the Mac Applications directory Finally some of the Spitzer Science Center Spot Leopard Java classes for conversion from pixel to celestial coordinates have been incorporated into APT However the user is cau tioned that only the gnomonic tangent orthographic Carte sian and Aitoff for FITS viewing only projections are implemented Only equatorial coordinates are computed no Galactic coordinates Geometric image distortion up to the ninth polynomial order is handled by the gnomonic projection only for cases where RA TAN SIP CTYPE E2 DEC TAN STIP CTYPE is specified in the image s FITS header see Shupe et al 2005 for a description of the SIP convention In the absence of the SIP suffix in the CTYPE and CTYPE2 settings for the gnomonic projection APT will attempt to read and apply the PV _ distortion keywords generated by SCAMP for the image s astrometrical calibration Bertin 2006a which is up to seventh polynomial order identical to the SExtractor imple mentation Other types of projections and geometric distortion representations in the astrometric calculations may be imple mented as the need arises 9 CONCLUSION In this article we have introduced important new software to the astronomical community called Aperture Photometry Tool or APT which facilitates the visualization of aperture photome try in a va
81. wn in the source scatter graph Data shown in the curve of growth graph Data shown in the radial profile graph Data fit curve shown in the radial profile graph Data fit model for aperture interpolation see 7 6 Scatter plot data from user selected columns in the aperture photometry table Source list file generated by APT s extraction of image sources see 7 9 panel buttons located in the middle of the main GUI panel see item 28 in 3 The choices are Aperture Slice Curve of Growth Source Scatter Sky Scatter Sky Histogram and Radial Profile All of these graphs require that an aperture be overlaid onto the primary image as described above The graphs may be selected in any order although the order listed above is a good one for adjusting APT settings systematically for a given source There is a text field near the middle of the More Settings panel labeled Default image data title for the user to specify the graph s image data title e g Surface brightness At the bottom of the More Settings panel there are options that control the data plotted in the category A graphs There is a check box labeled Perform image data conversion that enables the conver sion of the image data from the image data units of the FITS file to any desired source intensity units In addition there are as sociated text fields for specifying the conversion factor a string representation of the physical units e g MJy sr and a strin
82. wsecscaee RA_cen Dec_cen DY a Van s Gavnaistacintants Nearest integer image coordinates of the aperture center pixels r F E A E E Image coordinates of the source centroid pixels C orroit Centroiding flag equal to 1 when the option to perform the calculation with the aperture centered on the source centroid has been selected and zero otherwise This option is accessible on the control panel via the More Settings button in the lower left corner of the main GUI panel Source_intensity Integrated intensity of the source in the aperture in data units given by the Data_units column see below Also known as flux density or surface brightness Can either include the sky contribution or not depending upon the setting of the Sky_model column Uncertainty associated with the source intensity in data units given by the Data_units column see below This calculation uses Sky_scale as a robust estimator of the sky background standard deviation see below Source_unc Data_units Sky_scale columns Magnitude Map Une asccisesncings Uncertainty associated with the magnitude Source_model Data units of the Source_intensity Source_unc Sky_median pix Sky_average pix Sky_RMS pix Sky_custom pix Sky_sigma and Magnitude associated with the source intensity after the aperture correction and magnitude zero point have been applied 0 if no radial profile interpolation has bee
83. xt fields see next item 34 The lower and upper limits of the current image display stretch can be manually changed by typing new values into the lower bound and upper bound text fields respectively The user must either press Enter on the keyboard or mouse click on the Stretch to Bounds to apply changes made directly to these text fields 4 BASIC USAGE INSTRUCTIONS APT is intended to be simple to use Basically one displays a FITS image and then mouse clicks on a source i e an astro nomical object shown in the main image viewing panel to over lay an elliptical aperture onto it The latter action causes the software to automatically perform an aperture photometry cal culation The computed quantities include among others source centroid position source intensity source intensity un certainty sky background level and sky background dispersion width The default sky algorithm is no sky background sub traction from the source intensity and the reason for this is to facilitate proper use of APT s radial profile interpolation capability More often than not however the user will require the sky background to be subtracted from the source intensity in which case this sky model can be selected from the control panel that pops up after mouse clicking on the More Settings button located in the lower left corner of the main GUI panel see also item 22 in 3 See Figure 5 for a depiction of the More Settings panel The gener

Aperture Photometry Tool - NITARP - California Institute of Technology

Contents

Download Pdf Manuals

Related Search

Related Contents