iGalFit: An Interactive Tool for GalFit
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1. Secondly if the identification software fails to de blend a neighboring object which presumably should be either simultaneously modeled or masked from the fitting then the results are not to be trusted Both rryanQstsci edu Physics Department University of California Davis CA 95616 ba Space Telescope Science Institute Baltimore MD 21218 of these issues and many others can be mitigated by human intervention or supervision throughout the pro cess which is the primary motivation for this work In this article we present our software iGalFit which is a graphical user interface GUI for running GalFit The software is inspired by the successful image dis play tool as and its predecessors produced and maintained by the Chandra X ray Science Center In iGalFit the Users is expected to place circular ellip tical and rectangular regions on the image to indicate the function to be fit and the initial guesses of the pa rameters In this way the User has complete control over the critical identification step while abdicating the assembly line power of a pipeline This article should be treated as somewhat of a User s Manual and a reference point for the package The ar ticle is organized as follows in Section P we describe the basics of the code in Section B we briefly describe a second package to integrate SExtractor with GalFit in Section 4 we discuss potential ancillary uses and in Sec tion 52. based on the current state of the morphology pulldown menu in the primary toolbar see Figure I If on a valid region then this will select the region allowing the user to translate or delete the region and initiate the region handles The handles can be selected to adjust the size left click and rotate left click while holding the SHIFT key Middle click Recenter on the current mouse po sition Right click and drag Adjust the stretch of the color map vertical and horizontal move ments adjust the bias and contrast respec tively Left double click If on a region then the Re gion Information sub GUI will open Keyboard Commands When the cursor is in the main display window there are several actions which can be run by keyboard actions We briefly describe the valid functions in Table B iGalFit User s Manual 000 X iGalFit v1 0 File Display Scale Zoom Regions F Bad Pixel Mask F I Make BPX Bel erste GJ Sa A E m Ala core sex File 1 0 Constraints Ranges Image Prop Sky Add File Input Output B Output Image F Inspect Fic 1 Screenshot of iGalFit We show iGalFit in its initial state no image regions or sub GUIs present As discussed in 2 2 many of the fields can be set programmatically from the IDL prompt or the command line via our Perl script Toolbar Functions Immediately above the main dis 1 In principle iG
3. we mention several upgrades for future versions 2 INTERACTIVE GalFit iGalFit 2 1 Installing iGalFit The entire package is written in the Interactive Data Languag hereafter IDL therefore having IDL in stalled is an obvious prerequisite With IDL installed the installation is relatively straightforward 1 Obtain the IDL routines for iGalFit from http dls physics ucdavis edu rer or by email ing the author 2 Create an environment variable in your start up file named igalfit and set it equal to the full path of the IDL routines 3 http hea www harvard edu RD ds9 j http www ittvis com language en us productsservices idl aspx 2 Ryan Jr TABLE 1 IGALFIT OPTIONAL INPUTS IDL Perl Function LOADSETTINGS load Load an iGalFit save file SCIFILE sci Load the science image UNCFILE unc Load the uncertainty image PSFFILE psf Load the PSF image BPXFILE bpx Load the bad pixel image IMGFILE img Load the output image MAGZERO zero Set the magnitude zeropoint While IDL is not case sensitive we follow the convention that optional keywords are in all caps 3 Amend the IDL_PATH variable to include this newly set variable Obviously the variable should be set ABOVE the IDL_PATH setting 4 For the Mac OS X platform configure the Ap ple Key for the keyboard accelerators used by iGalFit a In the User s home directory there may be a file called Xdmodmap if not create one an
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5. DRAFT VERSION OCTOBER 7 2011 Preprint typeset using ATEX style emulateapj v 5 25 10 iGalFit AN INTERACTIVE TOOL FOR GALFIT R E RYAN JR Draft version October 7 2011 ABSTRACT We present a suite of IDL routines to interactively run GalFit whereby the various surface brightness profiles and their associated parameters are represented by regions which the User is expected to place The regions may be saved and or loaded from the ASCII format used by ds9 or in the Hierarchical Data Format version 5 The software has been tested to run stably on Mac OS X and Linux with IDL 7 0 4 In addition to its primary purpose of modeling galaxy images with GalFit this package has several ancillary uses including a flexible image display routines several basic photometry functions and qualitatively assessing SExtractor We distribute the package freely and without any implicit or explicit warranties guarantees or assurance of any kind We kindly ask users to report any bugs errors or suggestions to us directly as opposed to fixing them themselves to ensure version control and uniformity Subject headings methods data analysis techniques image processing galaxies structure galaxies fundamental parameters 1110 1090v1 astro ph IM 5 Oct 2011 iV arX 1 INTRODUCTION The shape size and structure of distant galaxies can provide invaluable insight to their formation history Consequently many there have been many tec
6. alFit is capable of displaying large play window is a row of buttons which control sev eral commonly used functions see Figure I We briefly describe the function of each button in Ta ble 2 4 Modeling Galaxy Profiles The primary motivation for developing iGalFit was to interactively create the input files for GalFit e g bad pixel masks constraint files galfit feedme and uncer tainty maps In this section we describe the typical order of operations to interactively model galaxy pro files roughly 10 kx 10 k pixels However manipulating a large number of pixels is computationally expen sive and is generally unnecessary or ill advised for running GalFit Therefore we recommend op erating on images sized for each object roughly 1 kx1 k pixels While GalFit is capable of running without a PSF and uncertainty map these images are essential for robust estimates of the galaxy profiles Further more GalFit is more reliable when operating on images which are in the units of counts cts Peng priv comm despite the more common convention to process images in count rate cts s Therefore the user should set the appropriate exposure time and unit in the Image Properties tab Finally for 4 TABLE 3 IGALFIT TOOLBAR Icon Function Load an iGalFit save file Save an iGalFit save file m Inspect an iGalFit save file a Zoom in on center of window Q Zoom out on center of window x Delete currently select
7. cessing of SExtractor 5 FUTURE IMPROVEMENTS As with most software iGalFit is a work in progress and there are several additions or improvements we would like to include Asymmetry Parameters In the latest version of 6 http www physics uci edu barth atv T http mips as arizona edu MIPS IDP3 GalFit there are a bevy of asymmetry parameters e g boxiness bending modes fourier components truncation radii to model azimuthally asymmetric structures like bars spiral arms or tidal tails By including these parameters the user can create far more complex and perhaps realistic models Additional Morphological Programs While this project was conceived to provide a user friendly interface to GalFit there are additional modeling programs which can be included as well for example GALPHAT shapelet decompositions e g 2005 and model independent estimators e g iGalFit User s Manual T Law et al 2007 Special thanks to J Bosch and M Mechtley for advice and suggestions We would also like to thank our beta Improved Memory Efficiency and Image Display testers M Rutkowski S Cohen P Thorman L Al We mentioned in the rendering of large corn and M Jee Support for this work was provided images can be very computationally expensive and by NASA through grant numbers 11772 from the Space dramatically slow down even the most powerful Telescope Science Institute which is operated by AURA wo
8. d add the following lines e clear mod1 e clear mod2 e add mod1 Meta_L b Start the X11 server and open the Preferences tab Under the Input dialog make the the following items are UNCHECKED e Follow system keyboard layout e Enable key equivalents under X11 5 To install the optional Perl script which can call iGalFit from the command line simply include the path to the Perl executable in your start up file 6 Restart the X11 server 2 2 Starting iGalFit Since the code is primarily written in IDL the simplest way to start iGalFitis to issue the command igalfit at the IDL prompt IDL gt igalfit OPTIONS options This of course requires that IDL is running which can be a nuisance Therefore we include a brief Perl script which will initialize IDL and run iGalFit and can be run from the command line in the usual way There are several optional keywords which can be set in either the IDL or Perl to pre set various items A complete list ing can be given by typing igalfit help in IDL igalfit help at the command line or are given in Table I 2 3 Controls The controls to iGalFit are largely modeled after those of ds9 and so users should be able to seamlessly move between programs However we will describe the control system for completeness TABLE 2 IGALFIT KEYBOARD COMMANDS Key Function Zoom in on the center of the display Zoom out on the center of the display q Clos
9. e iGalFit DELETE Delete the selected region r Display a radial profile of object closest to cursor position m Display image statistics for a small area around the cursor position l Display a line plot for some region around the cursor posi tion c Display a column plot for some region around the cursor position h Display a pixel histogram for some region around the cursor position e Display a contour plot for some region around the cursor position File Input Output While many of the individual files needed to run GalFit can be saved loaded at any time users may find it convenient to save load a file which encodes the complete state of iGalFit This facilitates an easy recall or programmatically assigning a state of iGalFit These files are writ ten in the Hierarchical Data Format version 5 HDF5 though by default named igalfit_save hd These files can be saved loaded by buttons on the toolbar or the File pulldown menu or with the command line options see Table I Region Input Output The regions for iGalFit in dicate the positions sizes and morphologies of the objects to be fit regions to be masked and al lowable fitting regions discussed in more detail in 2 4 Users can save load regions from the Re gions pulldown menu and are meant to be directly compatible with ds9 Mouse Functions The mouse controls many aspects of iGalFit Left click and drag If on a blank region of the image then a new region
10. e of parameters which govern the operations however we re strict control to only the few which are most commonly modified The SExtractor GUI employs two sub GUIs to set the measurements i e the param file and build a convolu tion filter i e the conv files The parameters needed for iGalFit are set by default The convolution routine allows for several common filters Gaussian Mexican hat top hat delta function and a user defined function of a single parameter As of the time preparing this doc ument SExtractor version 2 5 0 2009 09 30 did not permit any filters larger than 32 pixels however iSEx will not warn the use of this potential issue 4 ANCILLARY USES While the primary purpose of iGalFit is to model the two dimensional light distributions of various objects we suggest other applications which users may find valuable 4 1 Interactively Assessing SEctractor Settings SExtractor has become the de facto standard for de tecting and measuring a number of properties of faint objects particularly for deep field surveys Not sur prisingly there are a host of tunable parameters to be set by the user which govern the detection deblending measurement memory usage and outputting There fore a typical session involving SExtractor begins with a trial and error period of tweaking various parameters until the output catalog satisfies some qualitative prop erty often times the detection deblending of the faintest
11. e user is expected to indicate the initial conditions for GalFit by drawing regions which represent the model that should be fit In Table 4 we list the currently supported regions and their functions There are three ways a user may draw regions in iGalFit Manual The primary advantage of iGalFit is the ability to interactively place the model profiles In this way the fitting can be done iteratively by modifying properties of the re gions such as the color see Table 4 position adding removing additional regions or mask ing objects Automated Despite the obvious advantages with interactively placing regions this can be very tedious and daunting for large images with many objects Therefore we include a second package which will call SExtractor to identify objects and draw the appropriate re gions discussed in more detail in B To de termine which fitting function to assume see Table 4 we have a crude star galaxy separa tion algorithm of ISOAREA_IMAGE lt Acrit PSF R 2 Rerit 2 ISOAREA_IMAGE lt Acrit ae Mask 3 where we define R vrab and a b are the semi major minor axes respectively We consider objects which are considerably smaller in area and extent than the PSF to be likely image defects or unrejected cosmic rays and in which case should be masked in the GalFit calculations All remaining ob jects are considered to be extended and are assigned a single fitting function The tu
12. ed region eat View pixel histogram and set pixel min max for display View a pixel values under cursor the size of the table can be set in the Preferences menu oO Manually adjust the display settings minimum maximum bias and contrast A Manually edit the GalFit input file ps Inspect and modify the properties of the loaded regions GalFit Run GalFit with the current state SEx Launch the SExtractor sub GUI TABLE 4 IGALFIT REGIONS Shape Color Rotate Purpose ellipse green Y Fit S rsic function blue Y Fit ExpDisk function red Y Fit DeVauc function skyblue Y Fit Nuker function cyan Y Fit Edge on Disk function seagreen Y Fit King function orange Y Fit Gaussian function maroon Fit Moffat function black N Mask section circle magenta N Fit emprical PSF black N Mask section rectangle yellow N Define a fitting section black Y Mask section Ryan Jr a meaningful estimate of the y and parameter un certainties the uncertainty image should represent all sources of uncertainty Often times particularl with data from MultiDrizzle 2002 the weight uncertainty maps do not include any shot noise from the objects If this is the case then the user should set this flag and iGalFit will modify the uncertainty image U j according to Hig gt U2 Siz 1 where S is the science image both the science and uncertainty images have units of counts After loading a science image and PSF and uncer tainty maps th
13. f iGalFit was inspired by ds9 it has a many flexible quick look tools built in The images can be scaled and stretched zoomed panned and separate frames al though this would be implemented by loading additional images into the PSF and Uncertainty fields for easy dis play and comparisons At present rotations are not sup ported but this will likely be included in subsequent ver sions As mentioned in 2 4 the display and processing of large images 10k x 10k pixels is ill advised 4 3 Quick Look Photometry One question that invariably arises in nearly all forms of observational astronomy What is the brightness of that object Therefore many astronomical display routines give the user tools to answer this question 6 Ryan Jr AAA X GalFit Results Chi nu y Nfree Y Emid Ndof i Nfix Sky0 dS dx dS dy Fic 3 Screenshot of the GUI to inspect the GalFit results All of the information displayed here is taken from the GalFit output file i e the imgblock fits This GUI has many of the same controls and mouse functionality as iGalFit e g ImExamine in IRAF atv prdf idp3 prd Stobid and iGalFit is no different However a major advantage to iGalFit is the photometry routines are in tegrated into an image display tool which combines the flexibility of ds9 with the computational power of IDL and the image pro
14. hniques and codes developed to make these measurements GIM2D and GALPHAT Yoon Weinberg amp Katz 2011 While this is in no way meant to be an exhaustive list it merely highlights the interest in and emphasis placed on ro bustly measuring the properties of the two dimensional light distributions of galaxies As astronomical surveys have grown ever wider sam ples of galaxies have become larger and accordingly these detailed modeling techniques have also evolved Turn ing toward a pipeline approach whereby many so phisticated programs are called in concert to stream line the measurements on large samples e g GALAPAGOS H u ler et all 2011 many authors sacrifice detailed fit ting for bulk properties Naturally such a paradigm will invariably generate a series of tunable parameters to be set by the User many of which can significantly alter the success or reliability of the pipeline While appro priate settings are likely obvious or easily ascertained they are often tailored to a particular sample and as the sample changes so must the settings For example Users often need to provide the shape modeling codes a source list since rarely do these codes also identify ob jects Obviously this places the utmost importance on the identification scheme for multiple reasons First and most obviously if the object of interest is failed to be cataloged then clearly the power of the pipeline is for not
15. nable parameters Acrit Rerit and default extended source function can be set in the Preferences menu in iGalFit We caution that these clas sifications are only meant to guide the user in placing the regions and should not be trusted as a robust morphological indicator File Regions can be loaded from a standard ds9 regions file In Appendix A we give an exam ple regions file to illustrate the format 3 With the fitting regions indicating the initial condi tions of GalFit set the user should consider setting two ancillary regions First any pixel which is seri ously corrupted by non object flux such as cosmic rays image defects diffraction spikes bleeds etc should be masked If bad pixels are left unmasked then they will bias the estimate of the sky bright ness by GalFit which will adversely affect other parameters notably the radius and or give incor rect results for the objects directly such as posi tion total magnitude or radius Second users should consider setting a Fitting Section region which restricts the GalFit calculation to the in terior pixels If the fitting section is not set then iGalFit will fit the entire image Once the fitting regions have been placed the user should consider defining any possible constraints While the use of constraints are discouraged they do have some utility particularly when fitting 5 The sky pixels will be modeled by the sky function and there fo
16. name psf_f125w fits global color green dashlist 8 3 width 1 font helvetica 10 normal select 1 highlite 1 dash 0 fixed 0 edit 1 move 1 delete 1 include 1 source 1 image circle 593 586 44 019807 color magenta ellipse 456 543 75 28 338 58853 color green ellipse 679 458 40 20 35 134193 color red ellipse 528 476 40 20 330 01836 color blue box 587 5 547 5 369 313 0 color yellow box 537 5 605 5 37 59 0 color black box 713 607 80 40 0 color black B BASIC SExtractor CATALOG As discussed in 3 iGalFit can call SExtractor to identify objects for later use but can also take a catalog derived by other means However to properly interpret the columns the file should be in the ASCII_HEAD format here we give an example of a catalog which contains the mandatory fields additional columns may be present 1 NUMBER Running object number 2 ISOAREA_IMAGE Isophotal area above Analysis threshold pixel 2 3 X_IMAGE Object position along x pixel 4 Y_IMAGE Object position along y pixel 5 MAG_AUTO Kron like elliptical aperture magnitude mag 6 MAGERR_AUTO RMS error for AUTO magnitude mag 7 A_IMAGE Profile RMS along major axis pixel 8 B_IMAGE Profile RMS along minor axis pixel 9 THETA_IMAGE Position angle CCW x deg 10 FLAGS Extraction flags 1 17 55 004 12 177 8 3319 0 0490 1 120 0 930 21 7 0 2 118 46 653 48 326 10 8804 0 0100 2 262 2 078 17 9 0 3 T 22 492 47 101 7 7120
17. re should not be masked iGalFit User s Manual 5 composite functions such as bulge and disk Ob viously any parameter which is found by GalFit to be fixed on a constraint border is dubious and the user should relax the constraint In most cases if a constraint can be avoided it is safest to do so 5 At any point in the process the user can inspect the GalFit input file e g galfit feedme and make any manual modifications We caution there are no safe guards to verify that these files do not contain any errors 6 If GalFit successfully runs to completion the de fault behavior is to load the output file e g img block fits into a sub GUI to display the results see Figure 3 This sub GUI will display the science model and residual images on the same stretch the best fit results and global properties e g de grees of freedom x sky properties etc The various output images can also be displayed in the main GUI 3 SOURCE EXTRACTOR Since GalFit does not identify objects the user is re quired to indicate approximate positions of all sources whether to be fit or masked In many deep galaxy im ages the number of objects may be overwhelming to mark every source Therefore we include a separate GUI to run Source Extractor hereafter SExtractor Bertin amp Arnouts 1996 While this package can be run independently of iGalFit the main features are only accessible through iGalFit There are a multitud
18. rkstations In future versions we plan to Inc under NASA contract NAS 5 26555 employ additional advanced graphics capabilities in IDL to improve the real time image display REFERENCES Berin E amp Arnouts S 1996 A amp AS 117 393 Marleau F R amp Simard L 1998 507 585 Conselice C J Bershady M A Dickinson M amp Papovich C Massey R amp Refregier A 2005 MNRAS 3636 197 2003 AJ 126 1183 Peng C Y Ho L C Impey C D amp Rix H W 2002 AJ Koekemoer A Fruchter A S Hook R N amp Hack W 2002 124 266 HST Calib Workshop 337 Peng C Y Ho L C Impey C D amp Rix H W 2010 AJ HauBler B Barden M Bamford S P amp Rojas A 2011 139 2097 ASPC 442 155 Pignatelli E Fasano G amp Cassata P 2006 A amp A 446 373 Law D Steidel C C Erb D K Pettini M Reddy N A Refregier A 2003 MNRAS 338 35 Shapley A E Adelberger K L amp Simenc D J 2007 ApJ E Stobie 2006 ASPC 351 540 656 1 Yoon I Weinberg M D amp Katz N 2011 MNRAS 414 1625 Lotz J M Madau P Giavalisco M amp Primack J 2004 ApJ 613 262 APPENDIX A EXAMPLE REGIONS FILE iGalFit will read and write regions files in the same format as ds9 allowing users to employ existing tasks to define regions For completeness we give an example regions file as written by iGalFit Region file made by iGalFit on Mon Aug 1 00 31 43 2011 File
19. sources Despite the various manuals Source Extractor for Dummies B Holwerda SExtractor User s Manual X SExtractor 7 File Help Background Check Images Memory Miscellaneous Catalog Primary Inputs measurement image i measurement weight F NONE T detection image i detection weight F NONE 4 Configuration File ex config Inputs Extraction Photometry SEx executable bex Run SExtractor Fic 2 A screenshot of the SExtractor GUI Each stanza of the default configuration file is represented as a separate tab Ad ditional sub GUIs are included to create convolution filters i e the conv files and select parameters to be measured i e the param files While this GUI can be run independently of iGalFit it is most useful when used in conjunction with iGalFit The SExtractor GUI initializes with the parameters necessary to inter face with iGalFit and the user is discouraged from changing the CATALOG_TYPE or removing any measurement parameters though adding parameters is acceptable E Bertin there can be a great deal of confusion on the role of a given parameter and how it can be affected by other parameters particularly for novice users Since iGalFit can directly control SExtractor using a sep arate interface users are able to experiment with any combination of SExtractor settings and their effects 4 2 Inspect Images Since the controls and image display aspects o
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