The S -Tools User's Guide - lerma / ens
Contents
1. 22 34 Globalisky Model o ote sud Eres ale A as tee Pe e gw ere oe sh wx 23 9 0 Noises uv EE SUE uw A eo ee eo ee ah hs tu wed 25 4 Querying the S3 databases 26 AT Databasestructtire le leen a a o ea be eked wy ee eek d 26 4 2 Performing online queries 26 4 241 SOE query fokEms koto dd e da a RUE REDE 26 4 2 2 Mandatory attributes for mapping using the Tools 27 4 3 Structure of query result files 28 5 The S3Map GUI 29 5 1 The S3Map GUI and underlying scripts soo oa 29 5 2 83Map Options de ie es Bl a 3 QUE X hok ot ah ee Ole de de a ja vue 29 Did Query TIES 2 se ala Mgr Qe d io rrj Aa tens and 12 vas Te aces Ge ad reete qu dm drea 32 6 Non interactive scripts 6 1 Generalsynt x ow obedece Rue QA OA EN SET ME S E QR Rd 6 2 Arguments and keywords to SEX map script py 0 21 Argubnents ies doe 4 BD ect de dn a y RUP OR RM p SIS PS He vg 6 2 2 Keywords ooo m Re eh ADR ee yk oe Rh a ae toy A 6 3 Arguments and keywords to SAX map script py 68 1 Arguments ana na Ee a dew deer ee gro qu be deemed ex Aeg Gh end 0 3 2 J Keywords i5 A doe eL ute vae te doter er atom qr qx 6 4 RUNN d scrpU su wae sacs Rue ed Ee a vag 6 4 1 Typical script commands 6 4 2 Terminal output while running A script 7 Lower level rout2. e Inclination Possible inclinations range from 0 face on to 90 edge on in steps of 2 We thus recover the expected number of templates as 1150 46 x 5 x 5 2 6 3 Global Sky Model Installation The Global Sky Model de Oliveira Costa et al 2008 data and routines can be downloaded from the GSM website at https www cfa harvard edu adeolive gsm The direct download link is wget http xte mit edu angelica gsm gsm tar gz This archive weighs 109 MB 351 MB uncompressed and contains the following hierarchy rw r r 1 levrier levrier 122683392 Mar 17 2008 component maps 23klocked dat rw r r 1 levrier levrier 122683392 Mar 17 2008 component maps 4081ocked dat TLWCE TIC 1 levrier levrier 122683392 Mar 17 2008 component maps 5deg dat rw r r 1 levrier levrier 1045 Mar 17 2008 components dat rW r r 1 levrier levrier 5413 Mar 17 2008 gsm f After untarring the archive the gsm f F77 file in the distribution must be replaced with a non interactive one available from wget http www lra ens fr levrier Recherche S3 gsm f Compile that file into a gsm executable e g 1877 gsm f o gsm The last step is to edit the Config Path py file so that GSM DIR be set to the directory containing the above hierarchy Now in order for the S Tools to be able to use the GSM the WCS Tools must also be installed see below and 2 6 4 9 This central channel corresponds to v 0 in the galaxy s rest frame
3. After untarring the archive the Config Path py file needs to be edited so that KAPTEYN_TEMPLATES_DIR is set to the directory containing the above hierarchy see 2 4 About the templates The emission cubes all have the same pixel size 4 and are assumed to be at a redshift of z 0 0045 so that the physical size of a pixel is about 0 36 kpc The third dimension of the cubes is velocity and channels are 5 km s wide but the number of channels varies from one template to the next to save space although it is always odd to have a central channel The right ascension and declination axes also have an odd number of pixels 127 to have a central pixel All template galaxies have a null position angle major axis along the vertical The filenames reflect the galaxy s type asymptotical rotation velocity and inclination e Type There are 5 galaxy types S0 Sab Sb Sbc Sc Scd Sd and Sdm dwarf galaxies This is important for the diameter as all large galaxies S0 Sab to Sd are generated to have a 22 kpc diameter measured at X 1 Ma pc but some extend much further because of the faint tail in the radial Hi profile The template dwarf galaxies Sdm have a 16 kpc diameter e Asymptotical rotation velocity Five mass and luminosity ranges are defined using the asymptotical rotation velocity Va which can take the values 100 150 200 250 or 300 km s for S0 Sab to Sd galaxies and 50 75 100 125 or 150 km s for Sdm galaxies
4. Set this option to map CO 10 9 line emission fregaxis Optional Set this option to have a third axis in units of frequency Hz This is the default veloaxis Optional Set this option to have a third axis in units of velocity km s This is only possible when one and only one of hi co 1 0 co 2 1 co 3 2 co 4 3 co 5 4 co 6 5 co 7 6 co 8 7 co 9 8 or co 10 9 is set e gsm Optional Set this option to include the Global Sky Model emission see 2 6 3 e reversera Optional Set this option to have a right ascension axis increasing from left to right e separate maps Optional Set this option to make separate maps for the S data and non S data CMB Global Sky Model LM eu NE NE NF CT NOE 35 e userefpos Optional Set this option to effectively use the map center direction specfied via the rarefpos and decrefpos arguments e nocmb Optional Set this option to skip the inclusion of the CMB emission see 3 3 in the output cube This is an option as the default is to always include it 6 4 Running a script 6 4 1 Typical script commands 6 4 2 Terminal output while running a script What the SEX_map_script py and SAX_map_script py scripts actually do is to first look up the input This means a result file with the right name i e that specified by the in argument s value in the right directory specified by the dir argument s value If one is found the corresponding sql file must be ther
5. Tools that also means that the Config Path py will be missing a couple lines which need to be manually inserted These are Directory where reference files are located and basic functionality tests are run TESTS DIR S3TOOLS PATH Tests Directory where the shell script jobs are placed for parallel computing JOBS_DIR S3TOOLS_PATH Jobs 2 4 Manual installation If the user opted out of automatic configuration when prompted by install py the Config Path py file found under the Config subdirectory needs to be edited manually For simplicity we shall assume that the S Tools were installed in S3Tools that is there is a S3Tools directory under the home folder with subdirectories C Config Doc Jobs Output Routines Tests and Tmp The variables to edit in Config Path py are the following S3TOOLS PATH Should be set to the full path to the S Tools distribution In our example this would be S3TOOLS PATH Users levrier S3Tools python Should be set to the python executable to use Default is python but users with various versions of python may want to use a specific one PDFViewer Should be set to a command used to open PDF files from the terminal It will be called to display this guide from the S3Map GUI when clicking the Help button SAX TEMPLATES DIR Should be set to the full path of the directory under which to find the H1 and CO templates for SAX made by Danail Obreschkow University of Oxfo
6. 0 02 and 0 02 and Components declination between 0 02 and 0 02 idquery result contains a first line listing the attributes retrieved followed by the comma separated list of query results proper For instance component structure right_ascension declination position_angle major_axis minor_axis 53878311 1 0 00213 0 0182 0 0 0 53878312 2 0 00215 0 01942 0 016 8 748 1 917 53878313 2 0 00211 0 01699 0 016 8 748 1 917 28 Chapter 5 The S3Map GUI 5 1 The S3Map GUI and underlying scripts For most users making maps from query results may be done via S3Map a graphical user interface GUI written in python which is run from within the Routines subdirectory cd Routines python S3Map py A window similar to the one presented in Fig 5 1 should appear after a few moments It is through this interface that users specify which maps to make To be more specific the state of the GUI is passed as arguments to a python script command either SEX map script py or SAX_map_script py It is this command that is in charge of actually building the maps using lower level routines The actual command that would be run in the current state of the GUI can be displayed in the terminal by clicking on the Show button Users can then copy paste this command into a terminal window and perform the same mapping non interactively This is a useful feature for building batch jobs or debugging purposes See chapter 6 for more details on these scripts and chapte
7. A string of the form x y z giving the source type indices eligible values are 1 to 5 to include in the map Default is to include all source types that are present in the input tarball e window Optional A string of the form min x max x min y max y giving the spatial window to map Values are to be given in arcseconds and the default is to use the query window from the input tarball query file see 5 3 in which case a conversion from degrees to arcseconds is performed internally e freginfo A string of the form min freq delta freq nchans giving the center frequency of the first channel in GHz the width of each channel in GHz and the number of channels 33 e bmaj Optional Full width at half maximum FWHM of the major axis of the assumed Gaussian beam in arcseconds Default is zero which implies no beam convolution e bmin Optional Full width at half maximum FWHM of the minor axis of the assumed Gaussian beam in arcseconds Default is zero which implies no beam convolution e bpa Optional Position angle of the beam counted positively east from north in radians Default is Zero e noise Optional Level of the Gaussian noise to add in nJy The value specified is the standard deviation of a Gaussian distributed random map with zero mean The noise map is thereafter convolved by the same beam as the noise free map Default is zero no noise e pixelsize Size of a pixel s side in arcseconds Pixels are cons
8. gt 3 CO 7 6 D Bal 5 5 CO 6 5 3 LL 2 L CO 5 4 1l CO 4 3 CO 3 2 CO 2 1 A CO 1 0 0 20 40 60 80 100 120 140 v GHz Figure 3 8 Spatially integrated spectrum from the cube containing emission from all H1 and CO lines The Hi line is too faint see text to be apparent on this plot 1e 10 T o Flux density Jy HG N N Ww w in o in o in E o T e ul T 0 03 131 132 133 134 135 136 137 v MHz Figure 3 9 Spatially integrated HI emission spectra for the single source within single sax tar gz using University of Oxford templates for various spectral coverages full spectral line solid blue line lower frequency band blue circles central frequency band green circles and upper frequency band red circles The spectral resolution used is 60 kHz for all four data cubes 19 140r 7 140r 5 1351 7 135r 130r 1 130r 215 210 205 200 215 210 205 200 Figure 3 10 Spatially unresolved frequency integrated HI emission for the single source within single sax tar gz using Kapteyn Institute templates with right and without left Gaussian beam smearing The pixel size is 0 5 for a source with a 0 15 major axis and the map size is 40x40 pixels The circular Gaussian beam used on the right has a 1 full width at half maximum FWHM The red reticule shows the position of the source s center 1 622710 1 4 1 2F 1 0 0 8r 0 6r
9. 10This is because by default the executable resulting from the compilation of gsm f prompts the user for a frequency at which to make a map and a name for the output file Both of these things must be dealt with by the S map making routines without user intervention thus requiring that the gsm executable be non interactive 10 About the GSM The Global Sky Model uses Principal Component Analysis PCA CITE of 11 publically available large scale radio surveys from 10 MHz to 94 GHz to allow the building of Galactic emission maps at any intermediate frequency via interpolation The output maps are in Galactic coordinates using the HEALPIX scheme CITE with Nside 512 As the cubes built from S data are in equatorial coordinates conversion is performed by the WCSTools which therefore need to be installed see 2 6 4 Assuming this is the case and that the user has requested a spectral data cube be made with p frequency channels 14 vo Vp p GSM maps need to be built This is done internally using routines that can be found in GSM routines py 2 6 4 WCSTools The WCS Tools are required for the correct inclusion of the Global Sky Model in S data cubes They can be downloaded from http tdc www harvard edu wcstools After untarring the wcstools xxx tar gz archive into a directory compilation of the one program that is required xy2sky is done under UNIX in that directory by typing make xy2sky The resulting xy2sky executabl
10. Flux density Jy 0 4f 0 2r 0 0 LA d aililid l PA 5 3 0410 115 120 125 130 135 140 145 150 155 v MHz Figure 3 11 Spatially integrated HI emission spectra for the single source within single sax tar gz using Kapteyn Institute templates for various spectral resolutions 6 kHz solid blue line 60 kHz blue circles 600 kHz red bars 2 MHz green bars 10 MHz blue bars and 40 MHz magenta bars 20 1 388e2 1 388e2 T 0 45 T 0 4f 0 40 0 35 0 3 0 30 Z 0 25 0 2F 0 20 0 15 0 1 0 101 0 40 0 35 0 30 0 25 0 20 0 15 0 10 0 05 0 40 0 35 0 30 0 25 0 20 0 15 0 10 0 05 al 2 084e2 al 2 084e2 1 388e2 1 388e2 0 45F T 0 45F T 0 40 J 0 40 0 35 0 35 0 30 0 30 0 25 0 25 m 0 20 0 20 0 15 0 15 0 10 0 10 0 40 0 35 0 30 0 25 0 20 0 15 0 10 0 05 0 40 0 35 0 30 0 25 0 20 0 15 0 10 0 05 2 084e2 2 084e2 p al Figure 3 12 Spatially resolved frequency integrated HI emission for the single source within single sax tar gz using Kapteyn Institute templates The pixel sizes are 15 milliarcseconds top left 5 milliarcseconds top right 1 milliarcsecond bottom left and 0 3 milliarcsecond bottom right The source has a 0 15 major axis and a 0 0228 minor axis with a 4 position angle and is represented by the thin black ellipse The red reticule shows the position of the source s cent
11. a Components table which lists the properties of the several components that may make up a single galaxy such as cores and radio lobes e For S SAX a galaxies line table containing the apparent position and emission line properties of the galaxies and a galaxies delu table containing the intrinsic properties of the galaxies as in the catalog from de Lucia et al 2006 For more information on the structure of the database and the attributes held in the various tables please refer to the appropriate sections of the S website 4 2 Performing online queries 4 2 1 SQL query forms The databases can be queried via SQL forms on the dedicated S SEX and S SAX sections of the S website More specifically the query forms may be found at e http s cubed physics ox ac uk queries new sim s3 sex for S SEX e http s cubed physics ox ac uk queries new sim s3 sax for S SAX In both cases queries should be written in the SQL format which is quite straightforward to understand and implement at least in this simple case For instance with S SEX select from Galaxies Components where Galaxies galaxy Components galaxy and Galaxies right ascension between 0 02 and 0 02 and Galaxies declination between 0 02 and 0 02 will select all properties that s what the wildcard stands for from both Galaxies and Components tables where the center of the galaxy falls within the central 0 04 x0 04 of the simulation and after identificatio
12. d __ From Query Y From 01 0 0 0 d From Query To 01 0 0 0 d __ From Query Minimum Frequency 1420 405751 1H units Frequency Resolution 62 5 H units _ PA Setup 1 channels for Line 5 with zin 00 O0 Beam Major FWHM 2 0 units FA Beam Minor FWHM 2 0 Units Beam Position Angle 0 0 units PA Pixel size 1 0 units FA Noise level 0 0 Force Source List Source Types HJ GPS E Reset J Continuum line CO lines _ EoR signal Global Sky Mode Image accuracy Y Map Center R A Dec About 1 Q U V 20 Z axis HJ _ Reverse R A 12 01 0 0 h m s 0 0 0 0 d Help Show Run Quit Figure 5 1 The S3Map graphical user interface 30 e From Query checkboxes If set the adjacent entry field one of X From X To Y From and Y To is updated with the value read from the WINDOW keyword in the input query file see 5 3 e Minimum Frequency entry field Specifies the frequency of the center of the first spectral channel to consider Units can be changed by using the Units drop down menu e Frequency Resolution entry field Specifies the width dv of each spectral channel Channels are assumed to be perfect bandpass filters Units can be changed by using the Units drop down menu e Number of Channels entry field Specifies the number of spectral channels to be considered e Setup button Uses the value of the Num
13. e sftype Star formation type None 0 Quiescent 1 Starburst 2 e agntype AGN type None 0 Radio Quiet 1 FRI 2 FRII 3 GPS 4 e m hi Mass of HI gas in Mo Only necessary if HI mapping is requested In the Components table e galaxy Object identifier This is the same for all components of a single galaxy e right ascension Right ascension of the component s center in degrees declination Declination of the component s center in degrees position angle Position angle of the component in radians counted positively east from north major_axis Major axis of the component in arcseconds minor axis Minor axis of the component in arcseconds i 151 Base 10 logarithm log 1151 of the component s flux density at 151 MHz in Jy i 610 Base 10 logarithm log Z610 of the component s flux density at 610 MHz in Jy i 1400 Base 10 logarithm log 11400 of the component s flux density at 1 4 GHz in Jy 4860 Base 10 logarithm log Z4860 of the component s flux density at 4 86 GHz in Jy i 18000 Base 10 logarithm log 1 8000 of the component s flux density at 18 GHz in Jy S SAX In the galaxies line table only e ra Right ascension of the galaxy s center in degrees e decl Declination of the galaxy s center in degrees e zapparent Apparent redshift including peculiar velocities e diskpositionangle Position angle of the galaxy in radians counted positively east from north e d
14. o o Figure 3 3 Spatially unresolved frequency integrated HI emission for the single source within single sax tar gz using University of Oxford templates with right and without left Gaussian beam smearing The pixel size is 0 5 for a source with a 0 15 major axis and the map size is 40x40 pixels The circular Gaussian beam used on the right has a 1 full width at half maximum FWHM The red reticule shows the position of the source s center cd Routines sh run SAX Oxford tests sh sh run SAX Kapteyn tests sh These scripts perform a series of python SAX map script py commands with varying arguments see chapter 6 to test the making of H1 and CO emission data cubes with various spatial and spectral res olutions The difference between the two being the set of templates used either those made by Danail Obreschkow University of Oxford which can be used for both HI and CO or those made by Rense Boomsma Kapteyn Institute for H1 only Obviously for the scripts to work the corresponding tem plates need to be installed and the Config Path py file configured so the scripts can find them see 2 6 1 and 2 6 2 The tests performed by run SAX Oxford tests sh are the following e Spatially unresolved HI emission with varying spectral resolution channel widths 6 60 600 kHz and 2 10 and 40 MHz both with and without Gaussian beam smearing see Figs 3 3 and 3 4 e Spatially resolved H1 emission at varying spatial resolut
15. png Fig 3 14 3 4 Global Sky Model To check that the Global Sky Model plugin for the S Tools works the following shell script may be run Ash run GSM tests sh This script builds 10 single pixel single frequency images at 10 20 50 300 MHz and 1 2 20 30 40 and 50 GHz named gsm 6am 10MHz fits togsm 6am 50GHz fits centered on galactic coordinates 11 3 and b 89 6 chosen to match those from Fig 3 in de Oliveira Costa et al 2008 and which are devoid of any signal from the single S SAX test source The spectrum derived from these in brightness temperature K as a function of frequency GHz see chapter 7 is saved into gsm spectrum png which can be directly compared to the aforementioned figure see the left panel of Fig 3 15 Also built is a large scale 30 on a side emission map from the GSM at 1 GHz This is saved into gsm 30deg 1GHz fits 23 6 TIK 10 107 10 10 102 205 200 195 190 185 180 v GHz al Figure 3 15 Flux density of the Global Sky Model emission at Galactic coordinates 1 b 11 3 89 6 left and Global Sky Model emission at v 1 GHz on a 30 x 30 sky area right 5 o w w o in M in E in Probability Distribution Function N o o o in o o 6 4 2 0 2 Pixel value Jy Figure 3 16 Example 10 nJy noise only map over a square degree with a 5 pixel size left Also shown right is the histog
16. test script run SEX tests sh is available under Routines To run it from the command line users should type sh run SEX tests sh This script performs a series of python SEX map script py commands with varying arguments see chap ter 6 to test the making of continuum emission data cubes e Emission with varying spatial resolution both with and without Gaussian beam smearing see Fig 3 1 e Emission spectra from both lobes and central core of the single test source see Fig 3 2 e Spatial window splitting Using spatially resolved 0 1 pixels continuum emission four maps are made corresponding to the four quadrants of the source This is to test that we can split a map in different patches without affecting pixel values The four submaps are shown on the left panel of Fig 3 13 and should be compared with the full map at the same resolution which is the top left panel of Fig 3 1 3 2 S SAX To test making maps out of S SAX query results two test scripts are available To run these from the command line the user should type 12 75 75 70 70 Z e5f Z est o o eo eo 55b 55b T A 50 A i 15 10 5 0 5 10 15 10 5 0 5 10 ji ii a a 90 90 sob s0 70 J 70 as o o eo eo 50 50 aot 40 30 20 10 10 20 30 20 10 10 20 ii ii a a 200r 1 200r 100r 1 100r 100r 20
17. under which to find the HI templates for SAX made by Rense Boomsma Path To Kapteyn Templates Give full path to directory under which to find the WCS binaries Path To WCS bin Give full path to directory under which to find Global Sky Model Path To GSM Give full path to directory under which to find the IQU continuum templates for SAX made by Tigran Arshakian Path To MPIFR Templates Give full path to directory under which to find the EoR signal templates made by Mario Santos Path To IST Templates These are used to automatically edit the configuration file Config Config Path py the original file being moved to Config Path py bak This configuration can be done manually as explained in 2 4 The installation script then proceeds with making the already mentioned symbolic links in Jobs and finally reminds the user of a final mandatory step which is explained in 2 5 For the S3Tools to work you need to compile the file S3 c under Routines into a lib83 so shared object library Please refer to the README file 2 3 2 Upgrade As already mentioned the install py script can also upgrade an existing installation Although users may want to do a backup of the Routines subdirectory it is not necessary as the script will always make copies of the existing python files and shell scripts with a bak extension In any case it is not advised to do a full backup of the entire installation especially if the Output subdirectory
18. x min y max y giving the spatial window to map Values are to be given in arcseconds and the default is to use the query window from the input tarball query file see 5 3 in which case a conversion from degrees to arcseconds is performed internally e freginfo A string of the form min freq delta freq nchans giving the center frequency of the first channel in GHz the width of each channel in GHz and the number of channels e bmaj Optional Full width at half maximum FWHM of the major axis of the assumed Gaussian beam in arcseconds Default is zero which implies no beam convolution e bmin Optional Full width at half maximum FWHM of the minor axis of the assumed Gaussian beam in arcseconds Default is zero which implies no beam convolution e bpa Optional Position angle of the beam counted positively east from north in radians Default is Zero e noise Optional Level of the Gaussian noise to add in nJy The value specified is the standard deviation of a Gaussian distributed random map with zero mean The noise map is thereafter convolved by the same beam as the noise free map Default is zero no noise e pixelsize Size of a pixel s side in arcseconds Pixels are considered square e dir Optional Full path to the directory where the input tarball should be found and the output cube should be put The default is to use the directory specified by the OUTPUT DIR variable in Config Path py e hi Optional Set
19. 0f 300r 200 100 0 100 200 300 a 100r 200f 300r 200 100 0 100 200 300 a Figure 3 1 Continuum emission for the single source within single sex tar gz which is made up of two 8 7 x1 9 lobes and a central pointlike core at varying spatial resolutions pixel sizes are 0 1 top row 3 middle row and 40 bottom row In each row the left figure shows the spatially resolved emission without Gaussian beam smearing while the figure on the left includes the effect of a circular Gaussian beam with FWHM twice the size of the pixel On each figure two thin black ellipses represent the lobes and a red reticule shows the position of the core 13 Flux density y 10 F 101 10 10 v MHZ Figure 3 2 Spectral energy distribution SED over the full S SEX frequency range 151 MHz 18 GHz for the single source within single sex tar gz Represented are the flux densities for the entire field blue line the expected values at the reference frequencies for the lobes blue squares and the core red diamonds as well as the expected total intensities colored circles Also represented is the flux density for the pixel containing the sole core red curve as computed by the S routines over the full frequency range see chapter 7 14 145 d 145 140 d 140 Sl ot 130r 1 130r 215 210 205 200 215 210 205 200
20. 930132 Example of a S SEX query file DB S3SEX N_OBJECTS 1 CLUSTER_ITEMS GALAXY ITEMS galaxy cluster sftype agntype distance modified redshift WINDOW 0 00211 0 00215 0 01699 0 01942 REDSHIFT 1 970476 1 970476 TYPES FRI GPS NO 32 Chapter 6 Non interactive scripts 6 1 General syntax The S3Map GUI is actually a front end to two python scripts called SEX_map_script py for S SEX data and SAX map script py for S SAX data whose arguments are derived from the state of the GUI Consequently it is possible to run map making jobs from the command line without using S3Map The arguments to SEX map script py and SAX map script py are described below in 6 4 2 and also in the corresponding help files which can be printed out by issuing the following python command at the prompt python SEX map script py help Or python SAX map script py help The general syntax for these scripts is python XXX map script py argument value keyword where the arguments and keywords depend on which script is run 6 2 Arguments and keywords to SEX map script py 6 2 1 Arguments The following lists the possible arguments to SEX map script py and gives an explanation of the ex pected values for each e in ID of the query results tarball to use as input This is the filename minus the tar gz extension e out Name of the FITS file to write the results to This is to be given without the fits extension e types Optional
21. The S Tools User s Guide Frangois Levrier University of Oxford LERMA Ecole Normale Sup rieure de Paris April 2011 Contents 1 Introduction 2 1 1 The SKA Simulated Skies 9 104 apo eet da la a Fred Rp 2 T 2 Th A O eae des so ael al a dar a ae thd 2 1 3 Using this User s Guide 3 L3 Organization 4 o ae DA ses a ARA AA dee a 3 1 3 2 Conventions used in this document 3 2 Installation 4 21 Prerequisites A A d a a eee ee ae REGS etn cer to te lat LC e d 4 2 2 Cotimethes S TODIS Gets a Late RE O e EUR Bed Se e 4 2 3 Automatic installation using install py 5 279 1 Bulb installation zie wed s des a R dons Poe htm up euet de bre oa 5 2 3 2 Upgrade ss uere it aia RA E EE ee ee erre 6 2 4 Manual installations e aele 2 4 4 ooh Rode A a UR ES du ud T 2 5 C components of the STO e a dan de Eb de rU y due ds he T 2 6 External data and tools 2 o m sra osos e ds A da RA 8 2 6 1 Hi and CO templates University of Oxford 8 2 6 2 Hr templates Kapteyn Institute 9 2 6 3 Global Sky Model 4 sara ee as le 4e mis de ga lg 10 2 64 WESTO S v de es AR AN EEE Eust A A LE de ee RS 11 3 Standard tests 12 0 ESEX Na aes faced de ten iS hy Been TM ee ae tata ales Ste UNE 12 SA AP BTN NT EE TNS a D E RA oe Sete tas mia a Me amas pa 12 3 3 Cosmic Microwave Background
22. ar gz using University of Oxford templates for various spectral resolutions 6 kHz solid blue line 60 kHz blue circles 600 kHz red bars 2 MHz green bars 10 MHz blue bars and 40 MHz magenta bars CO 4 3 0 000131 Jy km s when expected integrated flux is 0 000131 Jy km s CO 5 4 0 000201 Jy km s when expected integrated flux is 0 000201 Jy km s CO 6 5 0 000284 Jy km s when expected integrated flux is 0 000284 Jy km s CO 7 6 0 000376999999999 Jy km s when expected integrated flux is 0 000377 Jy km s C0 8 7 0 000478999999999 Jy km s when expected integrated flux is 0 000479 Jy km s CO 9 8 0 000547999999998 Jy km s when expected integrated flux is 0 000548 Jy km s CO 10 9 0 000441999999999 Jy km s when expected integrated flux is 0 000442 Jy km s e Channel splitting Using spatially unresolved HI emission with 60 kHz spectral resolution and 6 MHz bandwidth three cubes are built corresponding to the lower 2 4 MHz of the band the central 1 2 MHz and the upper 2 4 MHz This is done to check that we recover the same emission as the one we get when building the whole 6 MHz cube in one go This is essential for the correct working of the parallel map making jobs described in chapter 8 see Fig 3 9 e Spatial window splitting Using spatially resolved 1 mas pixels H1 emission at 120 kHz spectral resolution four maps are made corresponding to the four quadrants of the sour
23. ber of Channels entry field and the range in redshifts specified by the with z in entry fields along with the selection from the Line drop down menu to compute frequency coverage and update the Minimum Frequency and Frequency Resolution entry fields see chapter 7 e Beam Major FWHM entry field Specifies the full width at half maximum FWHM of the assumed elliptical Gaussian beam to use along its major axis Units can be changed by using the Units drop down menu e Beam Minor FWHM entry field Specifies the full width at half maximum FWHM of the assumed elliptical Gaussian beam to use along its minor axis Units can be changed by using the Units drop down menu e Beam Position Angle entry field Specifies the position angle of the beam s major axis counted positively east from north Units can be changed by using the Units drop down menu e Pixel size entry field Specifies the size of a pixel s side Pixels are considered square Units can be changed by using the Units drop down menu e Noise level entry field Specifies the amount of Gaussian noise to be added to the map in nJy This value is the standard deviation of a zero mean Gaussian random map which is then convolved by the same beam as the noise free map e Source Types drop down menu Allows the user to select the types of sources Radio quiet AGN FRI radio loud AGN FRII radio loud AGN quiescent star forming galaxies and starburst galaxies that should be mapped Of co
24. ce This is to test that we can split a map in different patches without losing sources and that pixel values are not affected by the process The four submaps are shown on the right panel of Fig 3 13 and should be compared with the full map at the same resolution which is the bottom left panel of Fig 3 5 The tests performed by run SAX Kapteyn tests sh are the following e Spatially unresolved H1 emission with varying spectral resolution channel widths 6 60 600 kHz and 2 10 and 40 MHz both with and without Gaussian beam smearing see Figs 3 10 and 3 11 e Spatially resolved H1 emission at varying spatial resolutions and constant 120 kHz spectral resolution both with and without Gaussian beam smearing see Fig 3 12 These scripts use as an input the single sax tar gz archive which contains full data for a single galaxy from the S SAX database Some scripts take longer to complete than others but the data cubes should 16 1 388e2 0 4 0 3 ot 0 2 Oir 1 388e2 0 40 0 35 0 30 025 a 0 20 0 15 0 10 0 05 2 084e2 0 45 0 40f 0 35f 0 30 0 40 0 35 0 30 0 25 0 20 0 15 0 10 0 05 a 2 084e2 ot 0 45 0 357 0 30 0 20 0 15 0 25 0 20 1 388e2 0 40 0 35 0 30 0 25 0 20 0 15 0 10 0 05 a 2 084e2 1 389e2 0 15F 0 10 0 20 0 15 0 10 0 05 o 2 085e2 Figure 3 5 Spatiall
25. conds as mapping window Using query redshift 1 96970937 1 96970937 as mapping redshift range Also in the query file is the number of objects inside the full results which is printed to the screen File contains 1 objects 36 If the beam size specified by the values of the bmin and bmaj arguments is not greater than the requested pixel size specified by pixelsize then no convolution will be done Beam size too small with respect to pixel size I will not be performing convolution Computation of the image size is performed so the user knows what to expect and may abort the run if the output map size is too big see chapter 7 Will build 720 x 720 x 1 image Then the actual map making proceeds via the SEX build map and SAX build map routines which are described extensively in chapter 7 Actually making S3 map takes 0 118352890015 seconds Finally the S data cube is written out to a FITS file whose name is specified by the value of the out argument and placed in the same directory as the input Writing to FITS takes 0 172261953354 seconds If some additional data is to be considered Cosmic Microwave Background Global Sky Model it is treated as a post processing step For instance Making CMB signal Added CMB signal to my map fits Making GSM map s outfile 1420 405751 already exists No need to rebuild it Added GSM signal to my map fits For more details on these see chapter 7 37 Cha
26. d SAX map script py scripts as explained in chapter 6 Also displayed are the size of the would be output map or cube both in number of pixels and in estimated memory usage e Run button Runs the map making command with the current configuration of the GUI e Quit button Exits the S3Map GUI 5 3 Query files During the develoment of the S Tools it appeared that some form of a summary for the result files returned by database queries was necessary e g to deactivate buttons on the GUI which are irrelevant for a certain set of results or to initialize some fields with relevant values such as spatial or redshift extents These summaries are called query files and given the suffix query They are built by two dedicated routines SEX create query file and SAX create query file Example of a S SAX query file DB S3SAX N_OBJECTS 1 CLUSTER_ITEMS GALAXY ITEMS id galaxyid box ra decl distance WINDOW 0 057951 0 057951 0 038626 0 038626 REDSHIFT 9 66001 9 66001 HI_RANGE 0 130232090735 0 136195883628 C0 1 0 RANGE 10 4982261246 11 1199930132 C0 2 1 RANGE 20 9964522492 22 2399860263 CO_3_2_RANGE 31 4946783739 33 3599790395 CO_4_3_RANGE 41 9929044985 44 4799720527 C0 5 4 RANGE 52 4911306231 55 5999650659 CO_6_5_RANGE 62 9893567477 66 719958079 CO_7_6_RANGE 73 4875828723 77 8399510922 CO_8_7_RANGE 83 985808997 88 9599441054 CO_9_8_RANGE 94 4840351216 100 079937119 CO_10_9_RANGE 104 982261246 111 199
27. e are required as well as the WOS Tools See 2 6 3 and 2 6 4 for details 2 6 1 Hi and CO templates University of Oxford Installation The templates can be downloaded as an archive SAX templates tgz from the LRA ftp server Shttp www cmake org That may change in the future when infrared emission is taken into account as spectral energy distribution SED templates may have to be used in this frequency domain 8 Also dubbed S GAL on the 5 website wget ftp ftp lra ens fr outgoing levrier SAX templates tgz The user should be aware that the archive weighs over 2 GB and 11 6 GB when uncompressed It contains four files and four directories drwxr xr x 398 levrier levrier 13532 Feb 15 20 09 FITS drwxr xr x 8282 levrier levrier 281588 May 8 2009 ascii drwxr xr x 8282 levrier levrier 281588 May 11 2009 line_profiles IW I I 1 levrier levrier 157500 May 11 2009 line widths CO txt SENTE 1 levrier levrier 157500 May 11 2009 line_widths_HI txt drwxr xr x 8282 levrier levrier 281588 May 11 2009 major_axis_profiles TIW I I 1 levrier levrier 144900 May 11 2009 spatial widths CO txt rw r r 1 levrier levrier 144900 May 11 2009 spatial_widths_HI txt After untarring the archive the Config Path py file needs to be edited so that SAX TEMPLATES DIR is set to the directory containing the above hierarchy see 2 4 Note for users of S Tools predating March 2011 Older predating March 2011 installations of these temp
28. e is located in the bin subdirectory and it is this one that the WCS DIR variable in Config Path py should be set to To compile all programs in the WCSTools the above command should be replaced by make all Troubleshooting regarding installation of the WCS Tools should be dealt with according to instructions on the WCSTools website ll where xxx refers to the version of the software 11 Chapter 3 Standard tests The S Tools installation contains in the Routines subdirectory a few shell scripts that can be run to test the correct working of the S Tools more precisely of SAX map script py and SEX map script py see chapter 6 These scripts basically build some data cubes which then need to be compared to refer ence files Consequently to use these scripts user should download an archive containing these reference files from the LRA ftp server dwget ftp ftp lra ens fr outgoing levrier Tests tgz Uncompressed in the Tests subdirectory of the installation target directory it reveals a couple input files Tests single sax tar gz and Tests single sex tar gz as well as a Tests Reference hierarchy containing a number of fits png and log files which are to be used as references The source in single sax tar gz is a single galaxy and the one in single sex tar gz is a radio source which is made up of two 8 7 x1 9 lobes and a central pointlike core 3 1 S SEX To test making cubes out of S SEX query results a
29. e too Looking for a result file A result file was found Looking for a sql file A sql file was found If no relevant result file can be found the scripts look for a tar or tar gz file of the same name also in the same directory This is typically the case when using database query results directly In that case the files in the tarball which should include the result and sql files are extracted Looking for a result file No result file found Looking for a tar ball Tar ball found Processing it If not even a tarball can be found the script exits cleanly and warns the user Looking for a result file No result file found Looking for a tar ball No tar ball found Check your inputs especially the dir and in arguments Assuming proper input was found the scripts then look up a corresponding i e with the same name query file see 5 3 Looking for a query file A query file was found If no such file can be found one is built automatically via the already mentioned routines SEX_create query file and SAX create query file which are described in chapter 7 Looking for a query file No query file found Building one The scripts use these to read in the spatial and redshift extents covered by the data to use as default values if the window or zrange arguments are missing In that case the user is notified Using query window 7 596 7 74 61 164 69 912 arcse
30. er 21 1 39e2 1 39e2 0 25 0 25 78 78 76 76 0 20 3 74f 74 p 0 15 vn 72 70 70 68 68 9 10 66L 66b i f 18 16 14 12 10 8 5 0 5 10 0 20 0 15 0 10 0 05 0 20 0 15 0 10 0 05 1 388e2 2 086e2 1 388e2 2 084e2 0 25 0 25 64 64 er a 0 20 0 20 60 60 si 58 58 0 15 0 15 o 56 56 541 54 0 10 0 10 52 52 50 50 18 16 141210 8 5 0 5 10 0 20 015 010 005 020 015 010 005 n n 117 2 086e 1 2 084e a a a a Figure 3 13 Demonstration of spatial window splitting on resolved continuum emission for the single source within single sex tar gz left and on resolved Hi frequency integrated emission for the single source within single sax tar gz using University of Oxford templates right The four subplots show the four quadrants of the sources The pixel size is 100 milliarcsecond in the S SEX case and 1 milliarcsecond in the S SAX case Figures should be compared respectively with the top left panel of Fig 3 1 and the bottom left panel of Fig 3 5 all be done in a few minutes They are put in the Tests subdirectory and then automatically compared via UNIX diff commands to the corresponding files in the Tests Reference subdirectory If all goes well there should not be any difference found However it is possible that small differences could be present for instance due to different rounding schemes in floating point operations Therefore the scripts also build plo
31. idered square e dir Optional Full path to the directory where the input tarball should be found and the output cube should be put The default is to use the directory specified by the OUTPUT DIR variable in Config Path py e continuum Optional A comma separated list of Stokes parameters I Q U V to specify which type of continuum is to be mapped Currently only continuum I is possible e imageaccuracy Optional Minimum half size in pixels of all single source images Default is 20 e rarefpos Optional Value of the right ascension at the image center in degrees Default is 180 that is 12 hours e decrefpos Optional Value of the declination at the image center in degrees Default is 0 e zrange Optional A string of the form z min z max specifying which range of redshift should be mapped Default is to use the query range from the input tarball query file see 5 3 e ztype Optional Can be either redshift or modified redshift depending on whether the redshift to be used is the Hubble flow one or the apparent one Default is to use the latter e flux limit Optional Allows to specify a flux limit in nJy so that any source whose fluxes at the reference frequencies are all below that cutoff are not mapped Currently inactive 6 2 2 Keywords The following lists the possible keywords to SEX map script py and gives an explanation of their effects when set e hi Optional Set this option to map HI line em
32. ines 8 Parallel extensions i Acknowledgements I started working on the SKA Simulated Skies and what were to become the S Tools as a SKADS postdoc with the subdepartment of Astrophysics of the University of Oxford I therefore wish to heartily thank Steve Rawlings who was head of the subdepartment at the time for his constant enthusiasm and support I also wish to thank those Ian Heywood and Hans Rainer Kl ckner mostly who helped debugging the code kept asking for new functionalities and never failed to say thanks when I replied to their calls for help Thanks also to Richard Wilman and Danail Obreschkow for providing the S databases that this work builds upon and to Rense Boomsma for his HI templates As far as optimization and parallelization are concerned I am deeply indebted to Mihai C Duta Matteo Turilli and Fred Dulwich from the Oxford e Research Center OeRC Chapter 1 Introduction 1 1 The SKA Simulated Skies 5 The SKA Simulated Skies project S aims at building mock radio skies suitable for planning science with the SKA and the pathfinder experiments such as the South African MeerKAT and the Asutralian ASKAP The S project comprises a number of simulations of which essentially two are relevant for the present guide e S SEX Semi Empirical eXtragalactic a large scale simulation of the extragalactic radio continuum sky covering a sky area of 20 x 20 out to redshift z 20 and down to 10 nJy wi
33. ions and constant 120 kHz spectral resolution both with and without Gaussian beam smearing see Fig 3 5 e Spatially unresolved CO emission in the J 1 0 to J 10 gt 9 lines with spectral resolution varying in proportion to rest frequency without Gaussian beam smearing see Fig 3 6 e Spatially resolved 1 milliarcsecond pixels CO emission in the J 1 0 to J 10 gt 9 lines with spectral resolution varying in proportion to rest frequency without Gaussian beam smearing Fig 3 6 e Spatially integrated CO 1 0 emission spectra at varying spectral resolutions see Fig 3 7 e Spatially unresolved H1 and CO emission in all lines with a 10 MHz 200 GHz frequency coverage see Fig 3 8 The script also computes the integrated flux over the ranges in frequency correspondign to the various lines for comparison with expected values HI 2 38999999998e 08 Jy km s when expected integrated flux is 2 39e 08 Jy km s CO 1 0 8 43e 06 Jy km s when expected integrated flux is 8 43e 06 Jy km s CO 2 1 3 34999999999e 05 Jy km s when expected integrated flux is 3 35e 05 Jy km s CO 3 2 7 47999999997e 05 Jy km s when expected integrated flux is 7 48e 05 Jy km s 15 1e 10 4 5 4 0 3 5 3 0 2 5 2 0 Flux density Jy 1 5 1 0 0 5 0 115 120 125 130 135 140 145 150 155 v MHz Figure 3 4 Spatially integrated HI emission spectra for the single source within single sax t
34. is swollen When upgrading the script looks through the py and sh files inside the Routines subdirectory of the distribution source and seeks a file of the same name in the existing installation Upgrading S3Tools in Users levrier Desktop S3try If no such file can be found the file is copied to the target directory for instance Adding ipol py to your distribution If a corresponding file is found a diff command is performed on these If a difference is found the existing file is backed up with a bak extension and the new one is installed in its place e g ipol py needs upgrading For the sake of users of earlier versions of the S Tools the script also looks to see if you already have the C Tests and Jobs subdirectories which are new additions as of March 2011 If not it creates them and fills them with the relevant files i e C related files into C and symbolic links to the python files in Routines into Jobs The Tests subdirectory is created empty as in the case of a full installation Be warned however that any existing py bak file e g from a previous upgrade will be lost in the process Note for users of S Tools predating March 2011 It is important to note that when upgrading an existing installation the script will not alter any of the files inside the Config subdirectory so as to avoid breaking working configurations However for users of an older predating March 2011 installation of the S
35. is the repository for both input and output files e Routines contains all routines both low and high level e Tests contains files for test runs of the S Tools see 3 e Tmp is where input tarballs are uncompressed to access query results Users may create subdirectories under Tmp to hold single source cubes for parallel jobs see chapter 8 2 3 Automatic installation using install py Installation can be performed easily via a dedicated python script Type python install py at the command line prompt and follow the instructions The script first checks for necessary modules Running tests for Python modules os ok ss matplotlib ok It then inquires whether a former installation of the S Tools exists or not Is there an existing installation of the S3Tools Y N then prompts for the existing or desired installation directory Give full path to existing desired installation directory Depending on the answer to the first question the script will either fully install the S Tools in the specified directory or upgrade the existing installation towards which it is pointed 2 3 1 Full installation In that case all files within the archive are copied to the target directory and the user is prompted as to whether the script should proceed with configuration Installing S3Tools in Users levrier Desktop S3try Do you want to proceed with path configuration now Y N If the answer is no then the script
36. iskinclination Inclination of the galaxy s disc on the line of sight in radians 0 means face on 7 2 means edge on e distance Comoving distance in Mpc To these users should add the following for mapping the HI line e hiintflux Velocity integrated line flux of the HI line in Jy km s 27 e himajoraxis_10max Radius at which the surface brightness in the line Nyy is at least 10 of its maximum value in arcseconds e hiwidth50 Width of the line at 50 of the peak luminosity in km s e hiwidth20 Width of the line at 20 of the peak luminosity in km s e rmolc H5 HI surface density ratio at the disk center Only necessary when using the University of Oxford templates see 2 6 1 e hubbletype Numerical Hubble type along the RC2 sequence 6 10 Only necessary when using the Kapteyn Institute templates see 2 6 2 For mapping the CO J J 1 line users will obviously require the corresponding attributes e cointflux 1 Velocity integrated line flux of the CO 1 0 line in Jy km s e cointflux 2 Velocity integrated line flux of the CO 2 1 line in Jy km s e cointflux 3 Velocity integrated line flux of the CO 3 2 line in Jy km s e cointflux 4 Velocity integrated line flux of the CO 4 3 line in Jy km s e cointflux 5 Velocity integrated line flux of the CO 5 4 line in Jy km s e cointflux 6 Velocity integrated line flux of the CO 6 5 line in Jy km s e cointflux 7 Vel
37. ission e freqaxis Optional Set this option to have a third axis in units of frequency Hz This is the default e veloaxis Optional Set this option to have a third axis in units of velocity km s This is only possible in conjunction with the hi keyword e gsm Optional Set this option to include the Global Sky Model emission see 2 6 3 e reversera Optional Set this option to have a right ascension axis increasing from left to right Default is the customary convention in astronomical images right acension increases from right to left e separate maps Optional Set this option to make separate cubes for the different source types and non 5 data CMB Global Sky Model e userefpos Optional Set this option to effectively use the map center direction specified via the rarefpos and decrefpos arguments e nocmb Optional Set this option to skip the inclusion of the CMB emission see 3 3 in the output cube This is an option as the default is to always include it 6 3 Arguments and keywords to SAX map script py 6 3 1 Arguments The following lists the possible arguments to SAX map script py and gives an explanation of the ex pected values for each e in ID of the query results tarball to use as input This is the filename minus the tar gz extension 34 e out Name of the FITS file to write the results to This is to be given without the fits extension e window Optional A string of the form min x max
38. lates did not include the FITS subdirectory into which FITS files for the templates are placed The original template files are ascii under ascii but they take a while to load into arrays much longer than when read from FITS files Consequently when making SAX cubes the script first looks for a FITS file and uses that if it can find it Otherwise it uses the ascii file and takes the opportunity to convert it to FITS and save it under FITS for future use The downside of that is that FITS files take up a much bigger disk space typically 8 to 9 times larger than ascii files so storage issues may occur About the templates TO BE COMPLETED 2 6 2 Hi templates Kapteyn Institute Installation The templates can be downloaded as an archive KI templates tgz from the LRA ftp server dwget ftp ftp lra ens fr outgoing levrier KI templates tgz This archive weighs 265 MB but almost 2 7 GB after decompression It contains a Profiles subdirec tory 3 txt files and 1150 FITS files of the form template type vasymp_inclination fits drwXrWXrWX 1177 levrier levrier 40018 May 7 2008 Profiles rw r r 1 levrier levrier 46026 Jun 20 2008 hi_widths_0 2 txt S SiO A eia ae 1 levrier levrier 45968 Jun 20 2008 hi_widths_0 5 txt IWS rs 1 levrier levrier 46337 Feb 1 2010 spatial widths txt rWXr Xr x 1 levrier levrier 812160 Jan 22 2008 template_S0 Sab_100_0 fits buts rwxr Xr x 1 levrier levrier 1713600 Jan 22 2008 template_Sdm_75_90 fits
39. n of the object via the galaxy index which is common to the Galaxies and Components tables Similarly for SAX a typical query line would be I These are called attributes in SQL speak 26 select from galaxies_line where galaxies_line ra between 0 02 and 0 02 and galaxies_line decl between 0 02 and 0 02 which would also select all properties from objects in the galaxies_line table which fall within the central 0 04 x 0 04 of the simulation In both of these queries the wildcard after the select command means that all attributes will be returned It can be replaced by a comma separated list of attributes keeping in mind that to make maps from these simulations it is mandatory that some properties be included in the query as the mapping algorithms require them The next paragraph lists these mandatory attributes For more complicated queries users may refer to the S website or the MySQL documentation at http www mysql com 4 2 2 Mandatory attributes for mapping using the 5 Tools S SEX In the Galaxies table e galaxy Object identifier This is the same index as the galaxy attribute in the Components table e redshift Hubble flow redshift At least one of redshift or modified redshift is required e modified redshift Apparent redshift including peculiar velocities At least one of redshift or modi fied redshift is required e distance Comoving distance in Mpc Only necessary if H1 mapping is requested
40. n the test phase e Global Sky Model checkbox If set the output cube will include the Global Sky Model signal see 2 6 3 e Image Accuracy entry field Specifies the image accuracy parameter Only applies to S SEX data e Z Axis drop down menu Allows to select the third axis units the choice being velocity or frequency e Reverse R A Axis checkbox If set the output cube s right ascension axis will increase from left to right instead of increasing from right to left which is customary in astronomical images e Map Center Right Ascension and Map Center Declination entry fields Allow to specify the parameters of the desired map center Right ascension is entered in hours minutes and seconds declination in degrees 2For a channel centered on vo the bandpass is one for frequencies v such that v vo lt v 2 and 0 otherwise 31 arcminutes and arcseconds recalling that 1 second in right ascension corresponds to 15 arcseconds Be careful not to skip the sign entry fields See for more details e About button Displays information about the S Tools in a separate window e Help button Launches the PDF viewer specified by the PDFViewer variable in Config Path py see 2 4 and opens this User s guide e Show button Displays in the terminal the full python command that will be issued should the user press the Run button with the current configuration of the GUI This python command is based on the SEX map script py an
41. ocity integrated line flux of the CO 7 6 line in Jy km s e cointflux 8 Velocity integrated line flux of the CO 7 7 line in Jy km s e cointflux 9 Velocity integrated line flux of the CO 9 8 line in Jy km s e cointflux 10 Velocity integrated line flux of the CO 10 9 line in Jy km s e h2majoraxis_10max Radius at which the surface brightness in the molecular lines Xp is at least 10 of its maximum value in arcseconds Needed for any J e cowidth50 Width of the molecular lines at 50 of the peak luminosity in km s Needed for any J e cowidth20 Width of the molecular lines at 20 of the peak luminosity in km s Needed for any J e rmolc H2 Hi surface density ratio at the disk center Needed for any J Finally when parallel jobs are required one should also add the id attribute to the list see chapter 8 4 3 Structure of query result files When a query is completed users are e mailed with a link to download the results These are saved in a gzipped tarball idquery tar gz where idquery is a hash given by the S database server at submission time The tarball contains two plain text files idquery sql and idquery result In idquery sql the original SQL formatted query is recalled for instance select component structure right ascension declination position angle major axis minor axis from Galaxies Components where Galaxies galaxy Components galaxy and Components right ascension between
42. pter 7 Lower level routines TO BE COMPLETED 38 Chapter 8 Parallel extensions TO BE COMPLETED 39 References de Lucia et al 2006 de Lucia G Springel V White S D M Croton D Kauffmann G 2006 MNRAS 366 499 de Oliveira Costa et al 2008 de Oliveira Costa A Tegmark M Gaensler B M Jonas J Lan decker T L Reich P 2008 MNRAS 388 247 Levrier et al 2009 Levrier F Wilman R J Obreschkow D Kl ckner H R Heywood L Rawl ings S 2009 in Widefield Science and Technology for the SKA SKADS Conference 2009 edited by S A Torchinsky A vanArdenne T van den Brink Havinga A van Es A J Faulkner Obreschkow et al 2009 Obreschkow D Kl ckner H R Heywood I Levrier F Rawlings S 2009 ApJ 703 1890 Springel et al 2005 Springel V White S D M Jenkins A Frenk C S Yoshida N Gao L Navarro J Thacker R Croton D Helly J Peacock J A Cole S Thomas P Couchman H Evrard A Colberg J Pearce F 2005 Nature 435 629 Wilman et al 2008 Wilman R J Miller L Jarvis M L Mauch T Levrier F Abdalla F B Rawlings S Kl ckner H R Obreschkow D Olteanu D Young S 2008 MNRAS 388 1335 Wilman et al 2010 Wilman R J Jarvis M L Mauch T Rawlings S Hickey S 2010 MNRAS 405 447 40
43. r 7 for lower level routines 5 2 S3Map options The various buttons on the S3Map GUI have the following functions e Input Tarball entry field Allows the user to specify the name of the tarball to use which can be either a tar ora tar gz file This is the name without extension and by default the file is looked for in the directory given by the OUTPUT DIR variable in Config Path py unless the input tarball is selected by the Browse button see below e Browse button Allows the user to select the input tarball via a file selction popup window The filename without extension is then reproduced in the Input Tarball entry field and the directory is retained to use for the output e Output Name entry field Allows the user to specify the name of the output file s This is the name without any extension as these are automatically added only fits for FITS files at the moment The file is put in the same directory as the input tarball e X From X To Y From and Y To entry fields Allow to specify the parameters of the rectangular area to map Values are entered in degrees arcminutes and arcseconds Be careful not to skip the sign entry field for each parameter 1Be careful that right ascension is in degrees arcminutes and arcseconds and not hours minutes seconds 29 ODO S3Map Input Tarball _ Browse Output Tarball Refresh X From 01 0 0 0 d __ From Query To 0 0 0 0
44. ram in blue of the pixel values for that noise map overlaid with a Gaussian PDF with 10 nJy red line 24 and a figure of it is saved into gsm 30deg png see the right panel of Fig 3 15 The png files can be built separately once the FITS files are present under Tests by running python plot GSM tests py which is actually run automatically at the end of run GSM tests sh 3 5 Noise Noise can be added to cubes made via the S Tools This functionality can be tested with the following shell script Ash run noise tests sh This script uses single sax tar gz as an input and build two maps each covering the same square degree field outside the source with a 10 nJy level noise see chapter 7 for details Both maps are 720x720 pixels the pixel size being 5 and one is convolved with a 30 FWHM circular Gaussian beam The maps are saved in map noise fits and map noise smeared fits On Fig 3 16 are shown the unconvolved map and the histogram of its values overlaid with a Gaussian PDF with o 10 nJy These plots are built by the python script plot noise tests py at the end of run noise tests sh 25 Chapter 4 Querying the S3 databases 4 1 Database structure The S SEX and S SAX databases have similar structures and consist of the following tables e For S SEX a Clusters table holding cluster properties a Galaxies table holding galaxy properties possibly including the cluster index to which they belong and
45. rd see 2 6 1 KAPTEYN TEMPLATES DIR Should be set to the full path of the directory under which to find the HI templates for SAX made by Rense Boomsma Kapteyn Institute see 2 6 2 GSM DIR Should be set to the full path to the Global Sky Model distribution see 2 6 3 WCS DIR Should be set to the full path to the WCSTools binaries see 2 6 4 IST EOR TEMPLATES DIR Should be set to the full path of the directory under which to find the EoR sig nal templates from Mario Santos Instituto Superior T cnico Lisbon This is currently in the test phase MPIFR_TEMPLATES_DIR Should be set to the full path of the directory under which to find the IQU templates for SAX made by Tigran Arshakian Max Planck Institut fur Radioastronomie This is not implemented yet 2 5 C components of the S Tools The S Tools now include a tiny bit of C to speed up some computations The single C file is S3 c located under the C subdirectory and it needs to be compiled into a shared object library file called 5To be precise the single C function is used to perform spatial resolution degrading of emission template cubes see libS3 so To do so a typical UNIX command would be gcc Wall 02 fPIC c S3 c amp amp gcc shared Wl soname lib83 so o libS3 so 83 o Mac OS X users may need to install the free cross platform make CMake and do a little more work Instead of the one liner above the following steps should yield the desi
46. red shared library object cd C mkdir build cd build cmake make If all goes well a 1ibS3 so should appear under C build This file must then be copied over to Routines and a symbolic link to it created in Jobs In the gcc case that would be done like this cp libS3 so Routines cd Jobs fin s Routines libS3 so and in the CMake case cp libS3 so Routines hcd Jobs win s Routines libS3 so 2 6 External data and tools By themselves the S Tools can only make data cubes from S SEX query results as the sources for that simulation are either pointlike or ellipses which can be built on the fly and require no emission template For other functionalities the user needs to download and install other elements e To make S SAX data cubes a set of position position velocity PPV emission templates is required For HI emission there are two sets available one by Danail Obreschkow University of Oxford and one by Rense Boomsma Kapteyn Institute These are described in 2 6 1 and 2 6 2 respectively For emission in the rotational lines of CO J 1 0 to J 10 gt 9 users will require the set of Oxford templates e The S Tools include the possibility to add diffuse Galactic emission from 10 MHz to 100 GHz via the Global Sky Model de Oliveira Costa et al 2008 which is derived from a number of publically available large area radio surveys To use it the GSM data and softwar
47. s S SAX is concerned a set of templates The next chapter describes the installation procedure in detail The S Tools were designed to meet the following requirements Thttp www skatelescope org 2http www ska ac za Shttp www atnf csiro au SKA http www skads eu org e Versatile and reliable mapping of S sources both line and continuum over a certain area of the sky and a certain range in frequency at a given resolution e Positioning of the output maps and cubes at a user specified position in the sky so as to be observable by a given array for instance e Possible addition of ancillary signals such as Cosmic Microwave Background CMB emission diffuse Galactic emission signal from the Epoch of Reionization EoR e Inclusion of noise and Gaussian beam smearing e Batch mode with a hint of parallel computing for heavy map making jobs To achieve these goals while keeping a user friendly approach Graphical User Interfaces GUI are used serving as frontends to scripts which handle the actual work Thus the S Map GUI is the way users will specify which maps to make out of a set of S sources To be more specific the state of the GUI is passed as arguments to a python script command either SEX map script py or SAX map script py It is this command that actually builds the maps using lower level routines 1 3 Using this User s Guide 1 3 1 Organization This guide is organized as follows e Chapter 2 deal
48. s with the installation of the S Tools and additional data required to make maps e Chapter 3 explains the standard tests that can be performed to check the S Tools work correctly e Chapter 4 explains how to query the S databases so as to obtain query results that hold the necessary information for the S Tools to work e Chapter 5 details the practical steps involved to make images and cubes from S query results using the S3Map GUI e Chapter 6 goes one step deeper and focuses on the non interactive scripts SEX map script py and SAX map script py e Chapter 7 delves into all the gory details about the algorithms used in the lower level routines e Chapter 8 describes the solutions devised to split up large map making jobs into smaller sub jobs so the S Tools can be run on a cluster or on cloud computing resources 1 3 2 Conventions used in this document Throughout this document different fonts are used for different types of items e File and directory names terminal output command line input e Graphical User Interfaces buttons menus and entry fields Chapter 2 Installation 2 1 Prerequisites In order to use the 9 Tools a number of python modules are required os sys getopt math numpy scipy pyfits time random types ctypes stat Image Tkinter tkFileDialog tkFont matplotlib The install script install py contained in the distribution and described below first looks for the necessary packages and warns the u
49. ser if some cannot be found Depending on which package is missing the limitations could go from not being able to build the plots when running tests to downright not being able to make maps at all so a missing package is not to be taken lightly For Mac OS X users the necessary packages should all be included in the SciSoft package version 2008 3 1 onwards 2 2 Getting the S Tools Although they should find a permanent home on the S website in the future the S Tools are currently hosted on an external website at http www lra ens fr levrier Recherche S3 To get them di rectly the following command may be used wget http www lra ens fr levrier Recherche S3 S3Tools tgz Once the archive is retrieved it should be uncompressed in a temporary directory tar zxvf S3Tools tgz The archive contains the following e Two files README which is a shortened version of this chapter of the User s Guide and install py which is the installation script described in 2 3 e Eight subdirectories C Config Doc Jobs Output Routines Tests Tmp Each subdirectory serves a specific purpose e C contains the C components of the S Tools see 2 5 e Conf ig contains configuration files such as Config Path py which is discussed in 2 4 and Config Map py which is mentioned in chapter 7 e Doc contains documentation and help files e Jobs is dedicated to holding shell scripts e g to run batch jobs see chapter 8 e Dutput
50. skips this part and proceeds with making symbolic links in Jobs to the python routines and shell scripts within Routines In that case manual configuration will be needed see 2 4 If the answer is yes on the other hand the user is prompted for a number of installation specific pieces of information e The python executable to use Give python executable python e The PDF viewer that will be used to open this guide from the S3Map GUI I Note that the installation script will not halt if it finds a missing module signalled by a NO It is up to the user to check whether modules are missing and act on it 2This is the command used to launch the python interpreter from the command line This is configurable here so that users may choose between different python versions 3 This is also how the viewer is launched from the command line as the python routines basically spawn a UNIX child process using that command Give PDF viewer command for help files acroread e The paths to external data and tools H1 and CO templates Global Sky Model WCSTools EoR templates see 2 6 If any of these are not installed simply hitting the RETURN key will leave the de fault values indicated and of course the corresponding functionality of the S Tools will not be available Give full path to directory under which to find the HI and CO templates for SAX made by Danail Obreschkow Path To Oxford Templates Give full path to directory
51. th a frequency coverage going from 151 MHz to 18 GHz It also includes H1 gas masses for star forming galaxies For a complete description see Wilman et al 2008 Wilman et al 2010 e S SAX Semi Analytical eXtragalactic a smaller scale simulation of the extragalactic HI and CO line emissions derived from the Millenium simulation Springel et al 2005 which comes in two flavours S SAX Sky is a skyfield simulation giving the apparent properties of galaxies with a field of view that depends on the maximum redshift while S SA X Box is a simulation of a cubic volume giving their intrinsic properties Throughout this guide S SAX shall be understood as meaning S SAX Sky For a complete description see Obreschkow et al 2009 The S set of simulations performed at the University of Oxford in the framework of the European Union s SKADS program are publically available on the S website http s cubed physics ox ac uk and the databases built from these may be queried there The S Tools may then be used on query results to build maps and spectral data cubes 1 2 The Tools The S Tools are a set of Python and C routines whose purpose is to provide user friendly access to the S simulations in particular to build 2 dimensional images and 3 dimensional spectral data cubes that may be used as input for instrument simulators In order to use the S Tools you will need a number of python modules a C compiler and as far a
52. to either Oxford or Kapteyn to specify which set of HI emission templates are to be used Default is not to request H1 mapping which corresponds to hi 0 e rarefpos Optional Value of the right ascension at the image center in degrees Default is 180 that is 12 hours e decrefpos Optional Value of the declination at the image center in degrees Default is 0 e zrange Optional A string of the form z min z max specifying which range of redshift should be mapped Default is to use the query range from the input tarball query file see 5 3 e hash Optional Set to a user chosen string which is meant to identify several map making jobs as part of the same project See chapter 8 for more details 6 3 2 Keywords The following lists the possible keywords to SAX map script py and gives an explanation of their effects when set line emission line emission line emission line emission line emission line emission co 1 0 Optional Set this option to map CO 1 0 co 2 1 Optional Set this option to map CO 2 1 co 3 2 Optional Set this option to map CO 3 2 co_4 3 Optional Set this option to map CO 4 3 co 5 4 Optional Set this option to map CO 5 4 co_6_5 Optional Set this option to map CO 6 5 co 7 6 Optional Set this option to map CO 7 6 line emission co 8 7 Optional Set this option to map CO 8 7 line emission co 9 8 Optional Set this option to map CO 9 8 line emission co 10 9 Optional
53. ts of spectra for the different cubes produced and save these plots as png files in the Tests subdirectory Visual inspection of these plots with respect to the corresponding ones in the Tests Reference subdirectory should make it clear whether there is cause for alarm or not As a matter of fact the figures in this chapter are simply eps versions of these test plots which can be built independently of making the FITS files by running python plot SAX Oxford tests py or python plot SAX Kapteyn tests py Actually the shell scripts run SAX Oxford tests sh and run SAX Kapteyn tests sh simply run these python commands themselves after having built the FITS files 3 3 Cosmic Microwave Background To check that Cosmic Microwave Background CMB emission a simple uniform blackbody emission at T 2 725 K can be correctly included in the output data cubes the following shell script may be run sh run CMB tests sh This script builds a cube of unresolved emission centered on the S SAX source single sax tar gz called hi co cmb fits covering all Hi and CO lines from 100 MHz to 1 THz including the CMB i e the nocmb flag has been removed from the calls to SAX map script py and a cube of the same size called cmb fits centered on a different patch of sky which thus recovers only CMB emission The python script plot CMB tests py which is called at the end of run CMB test sh then builds a difference cube and checks that correct integrated fl
54. urse a source type that was not included in the query cannot be mapped Only active when using S SEX data e GPS drop down menu Allows the user to select whether GPS sources should be included Only active when using S SEX data containing such sources e Continuum checkbox If set the output map or cube will include continuum emission Currently only applies to S SEX data cubes e Q U V drop down menu Allows to select whether the output map or cube will include an extra axis for polarization Currently only total unpolarized continuum intensity is available for S SEX and no continuum is available for SAX e Hi line checkbox If set the output map or cube will include Hi line emission In the case of S SAX the Hi Data drop down menu becomes active allowing the user to choose between Oxford templates see 2 6 1 and Kapteyn templates see 2 6 2 e CO lines checkbox If set the output map or cube will include CO line emission Only active when using S SAX data In that case the Transitions drop down menu becomes active allowing the user to choose which of the ten possible transitions to map Only those present in the input tarball may be ticked on and they are by default The All and None buttons allow to select all CO lines or none of them e EoR signal checkbox If set the output cube will include the Epoch of Reionization signal The data templates to be used can be selected via the EoR Data drop down menu Currently i
55. uxes are recovered for each line 22 1e8 4 0 3 5 3 0 2 5 2 0 1 5 Flux density Jy sr 1 0 0 5 0 0 0 200 400 600 v GHz 800 1000 1200 Figure 3 14 Flux density of the CMB emission computed from the CMB only cube blue circle overlaid with the expected curve solid red HI 2 38999999998e 08 Jy km s when expected integrated flux is 2 39e 08 Jy km s CO 1 0 8 43e 06 Jy km s when expected integrated flux is 8 43e 06 Jy km s CO 2 1 gt 3 34999999999e 05 Jy km s when expected integrated flux is 3 35e 05 Jy km s CO 3 2 7 47999999997e 05 Jy km s when expected integrated flux is 7 48e 05 Jy km s C0 4 3 gt 0 000131 Jy km s when expected integrated flux is 0 000131 Jy km s CO 5 4 0 000201 Jy km s when expected integrated flux is 0 000201 Jy km s C0 6 5 0 000284 Jy km s when expected integrated flux is 0 000284 Jy km s CO 7 6 0 000376999999999 Jy km s when expected integrated flux is 0 000377 Jy km s CO 8 7 0 000478999999999 Jy km s when expected integrated flux is 0 000479 Jy km s C0 9 8 gt 0 000547999999998 Jy km s when expected integrated flux is 0 000548 Jy km s CO 10 9 0 000441999999999 Jy km s when expected integrated flux is 0 000442 Jy km s It also builds a plot of the emission from the CMB only cube in Jy sr see chapter 7 overlaid with the expected curve and saves it under cmb_spectrum
56. y resolved frequency integrated HI emission for the single source within single sax tar gz using University of Oxford templates The pixel sizes are 15 milliarcseconds top left 5 milliarcseconds top right 1 milliarcsecond bottom left and 0 3 milliarcsecond bottom right The source has a 0 15 major axis and a 0 0228 minor axis with a 4 position angle and is represented by the thin black ellipse The red reticule shows the position of the source s center 17 1 389e2 0 25F 145r 0 207 z 0 15F St E o LJ gt 135r 0 10f 130r 215 210 205 200 0 20 0 15 0 10 0 05 al a 2 085e2 Figure 3 6 Spatially unresolved left and resolved right CO 1 0 frequency integrated emission for the single source within single sax tar gz The pixel sizes are respectively 0 5 arcsecond and 1 milliarc second The source has a 33 5 milliarcsecond major axis and a 5 1 milliarcsecond minor axis with a 4 position angle and is represented by the thin black ellipse The red reticule shows the position of the source s center le 8 Flux density Jy 18400 10500 10600 10700 10800 10900 11000 11100 11200 v MHz Figure 3 7 Spatially integrated CO 1 0 emission spectra for the single source within single sax tar gz for various spectral resolutions 7 MHz solid blue line 14 MHz blue circles and 21 MHz red bars 18 CO 9 8 5 L CO 10 9 al CO 8 7
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