Home

Analysis Cookbook - CASA

1. 4 146 4 4 2 Spectral Bandpass Calibration bandpass 146 4 4 2 1 Bandpass Normalization 02000004 147 4 4 2 2 __ B solutio s ses 6G 6 6 oS Se ee eee es ESSE a 148 4 4 2 3 BPOLY solutions amp oe odes ae eon dk Poo AAA 149 4 43 Complex Gain Calibration gaincal 150 4 4 3 1 Polarization dependent Gain G o o 151 4 4 3 2 Polarization independent Gain T 152 4 4 3 3 GSPLINE solutions car A a 153 4 44 Establishing the Flux Density Scale fluxscale 154 4 4 4 1 Using Resolved Calibrators o 156 4 4 5 Instrumental Polarization Calibration D X 157 4 4 5 1 Heuristics and Strategies for Polarization Calibration 158 4 4 5 2 A Polarization Calibration Example 159 4 4 6 Baseline based Calibration blcal 160 4 4 7 EXPERIMENTAL Fringe Fitting fringecal 161 o eee ease eee Se eS 161 4 5 1 Plotting Calibration Solutions ploteal isa 54 i ee28 444485 162 4 5 1 1 Examples for plotcal 163 4 5 2 Listing calibration solutions with listcal 165 4 5 3 Calibration Smoothing smoothcal l o o o oo o 168 4 5 4 Calibration Interpolation and Accumulation accum
2. hd Log Messages sandrock home sandrock3 smyers Testing3 Patch4 N5921 casapy log 5 x File Edit View ia m 153 A Search Message l dto Filter Time gt Y e Time Priority Origin Message ja 2009 05 27 04 42 45 INFO 23220 HHHHHHHHHHHHHHHHAHARRRRRHHHHHHHHHAAR EEE 2009 05 27 04 42 45 INFO ae 2009 05 27 04 42 45 INFO 2009 05 27 04 42 45 INFO 2009 05 27 04 42 45 INFO 2009 05 27 04 42 45 INFO 2009 05 27 04 42 45 INFO home sandrock3 smyers Testing3 Pat 5921 nge5921 demo ms MS Version 2 Observer TEST 2009 05 27 04 42 45 INFO listobs ms Observation VLA 2009 05 27 04 42 45 INFO listobs ms Data records 22653 Total integration time 5280 seconds 2009 05 27 04 42 45 INFO listobs ms Observed from 13 Apr 1995 09 19 00 0 to 13 Apr 1995 10 47 00 0 TAI 2009 05 27 04 42 45 INFO listobs ms 2009 05 27 04 42 45 INFO ObservationIp 0 ArrayID 0 2009 05 27 04 42 45 INFO Date Timerange TAI Scan Fldrd FieldName nVis Int s spwrds 2009 05 27 04 42 45 INFO 13 apr 1995 09 19 00 0 09 24 30 0 1 O 1331 305000 4509 30 101 2003 05 27 04 42 45 INFO 09 27 30 0 2 1 1445 099000 1890 30 10 2009 05 27 04 42 45 INFO 09 33 00 0 3 2 w5921_2 6048 30 10 2003 05 27 04 42 45 INFO 09 50 30 0 4 1 1445 099000 756 30 10 2003 05 27 04 42 45 INFO 10 22 00 0 10 23 00 0 5 1 1445 099000 1134 30 10 200
3. aem lt 5 YEE CASA lt 6 psfmode hogwarts CASA lt 7 inp clean clean Deconvolve an image with selected algorithm vis ngc5921 demo src split ms contsub name of input visibility file imagename demo cleanimg Pre name of output images field o Field Name spw bee Spectral windows channels is all selectdata False Other data selection parameters mode channel Type of selection mfs channel velocity frequency nchan 46 Number of channels planes in output image start 5 first input channel to use width 4 Number of input channels to average interpolation nearest Type of spectral interpolation of visibilities nearest linear cubic niter 6000 Maximum number of iterations gain 0 1 Loop gain for cleaning threshold 3 0 Flux level to stop cleaning Must include units psfmode hogwarts method of PSF calculation to use during minor cycles imagermode a Use csclean or mosaic If use psfmode multiscale set deconvolution scales pixels default multiscale standard CLEAN interactive False use interactive clean with GUI viewer mask 108 108 148 148 cleanbox es mask image s and or region s used in cleaning imsize 256 256 x and y image size in pixels symmetric for single value cell 45 0 15 0 x and y cell size default unit arcsec phasecenter YA Image phase center position or field index restfreq ie rest
4. x iP ee A 4 a 2 Q PY Y A SR hd Data Display Options a a a Y a 8 el 8 24 ngc5921 usecase clean image Display axes Hidden axes Basic Settings g Daana pe Aspect ratio fixed world Px Pixel treatment center ya Y Resampling mode nearest y Iv Y Data range 0 0104926 0 0523443 fe Y Scaling power cycles o fe Y Colormap Hot Metal 1 Px 15 24 007 23700 00 20700 J2000 Position tracking pa Axis labels ax Axis label properties COOOL fonmi E _ Beam Ellipse F A E Blink Rate lt 10 sec Compact Color Wedge Frame Q start End Step Apply Save Restore e E X ngc5921 usecase clean image 1 549e 03 Jy beam 15 23 48 500 04 33 33 633 I 1 603558e 03 km s Dismiss Figure 7 1 The Viewer Display Panel left and Data Display Options right panels that appear when the viewer is called with the image cube from NGC5921 viewer ngc5921 usecase clean image The initial display is of the first channel of the cube The first of these creates an empty Viewer Display Panel 7 2 1 and a Load Data window 7 2 4 The second starts the viewer loaded with a Measurement Set The third example starts the viewer with an image cube see Figure 7 1 Example four brings up a display panel as it was when its state was saved to the given restore f
5. 0 peak area The fit fit_stat cent fwhm nfit peak the parameters dfit input file sdusecase_orions_hc3n asap defaults K specunit channel 2 2 try auto fitting first gt auto Gaussian e auto parameters to their defaults for ept ignore the edge channels 00 a plot while doing this 1 fit output in a file gt sdusecase_orions_hc3n fit and do the fit dfitO ad verbose mode on you probably saw something 0 811 K centre 4091 041 channel FWHM 72 900 channel 62 918 K channel is output in the dictionary 4091 04052734375 0 72398632764816284 72 899894714355469 1 7048574686050415 1 0 81080442667007446 0 016420882195234299 337 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 338 So you can write them out or test them print The line fit parameters were print maximum 6 3f 7 6 3f K fit_stat peak 0 0 fit_stat peak 0 1 print center 6 1f 6 1f channels fit_stat cent 0 0 fit_stat cent 0 1 print FWHM 6 2f 6 2f channels fit_stat fwhm 0 0 fit_stat fwhm 0 1 Which gives The line fit parameters were maximum 0 811 0 016 K center 4091 0 0 7 channels FWHM 72 90 1 70 channels We can do the fit in km s also specunit km s
6. Some examples the default should satisfy even advanced users all INFOx messages all messages including debugging casalog filter INFO casalog filter INF02 casalog filter INF04 casalog filter DEBUG2 HHH WARNING Setting the threshold to DEBUG2 will put lots of messages in the log BETA ALERT We are transitioning to the new Priority Level system and not all tasks and tools obey the guidelines uniformly This will be improved as we progress through the Beta patches Also the casalog tool is the only way to set the threshold currently 1 4 3 Where are my data in CASA Interferometric data are filled into a so called Measurement Set or MS In its logical structure the MS looks like a generalized description of data from any interferometric or single dish telescope Physically the MS consists of several tables in a directory on disk Tables in CASA are actually directories containing files that are the sub tables For example when you create a MS called AM675 ms then the name of the directory where all the tables are stored will CHAPTER 1 INTRODUCTION 63 be called AM675 ms See Chapter 2 for more information on Measurement Set and Data Handling in CASA The data that you originally get from a telescope can be put in any directory that is convenient to you Once you fill the data into a measurement set that can be accessed by CASA it is generally best to keep that MS in
7. 10 00 1400 J2000 Right As 1450 1500 1550 1600 velocity Coordinate world 15 22 07 927 05d01 47 92 velocity z P g O Blink Slol eeo arm Rae Y 10 sec Compact Frame G Star End Step Dismiss ngc5921 ms Measurement Raster Image ngc5921 ms flagversions Directory ngc5921 usecase cleanimage Image ngc5921 usecase clean model Image ngc5921 usecase clean residual Image X ngc5921 usecase clean image Contour Map 2 090e 04 Jy beam 15 22 36 507 04 54 47 181 I 1 546876e 03 km s Vector Map ngc5921 usecase ms Measurement a ngc5921 usecase ms cont Measurement Z X ngc5921 usecase cleanimage contour Marker Map 2 090e 04 Jy beam 15 22 36 507 04 54 47 181 I 1 546876e 03 km s Update R Leave Open Done Figure 7 11 The Image Profile panel that appears if you use the Tools Spectral Profile menu and then use the rectangle or polygon tool to select a region in the image You can also use the crosshair to get the profile at a single position in the image The profile will change to track movements of the region or crosshair if moved by dragging with the mouse Under Region Extent choose whether you want your region to be confined to the viewed plane only or to extend over all channels or all image planes Then trace out your re
8. gt all field 0 2 3C286 selectdata e True More data selection parameters antenna timerange etc antenna 42 antenna baselines gt all antenna 3 VA04 timerange time range gt all timerange 09 14 0709 54 0 correlation a Select data based on correlation scan de scan numbers gt all feed ae multi feed numbers Not yet implemented array gt sub array numbers gt all uvrange na uv range gt all uvrange 0 100klambda default units meters async e False If true the taskname must be started using flagdata The default flagging mode is manualflag See 8 3 5 1 1 more more on this option The mode summary will print out a summary of the current state of flagging into the logger The mode quack will allow dropping of integrations from the beginning of scans See 3 5 1 2 for details The mode shadow option will allow shadowed data to be flagged if it has not already during filling BETA ALERT the mode autoflag option is not currently supported 3 5 1 Flag Antenna Channels The following commands give the results shown in Figure 3 5 CHAPTER 3 DATA EXAMINATION AND EDITING 123 default plotxy plotxy ngc5921 ms channel iteration antenna subplot 311 default flagdata flagdata vis ngc5921 ms antenna 0 spw 0 10715 defau
9. Viewer Display Panel 5 Viewer Display Panel 0 Data Display Panel Tools View Data Display Panel Tools View 24490 8 283424 243492 8 318438424 m r ns a A 3 8 E see 2 als 2 2 8 2 Dx ex iterations cycles threshold Add Displayed Plane Next Action iterations cycles threshold e Add Displayed Plane Next Action 10p 99 0 05 mjy Erase All Channels 57 Ho e 100 99 0 05 my Erase All Channels Oo Ye E J00 Declination OO Declination 21 J ES a Figure 5 3 We continue in our interactive cleaning of Jupiter from where Figure 5 2 1eft off In the first left panel we have cleaned 30 iterations in the region previously marked and are zoomed in again ready to extend the mask to pick up the newly revealed emission Next right we have used the Polygon tool to redraw the mask around the emission and are ready to Continue Cleaning for another 100 iterations For spectral cube images you can use the tapedeck to move through the channels You also use the panel with radio buttons for choosing whether the mask you draw applies to the Diplayed Plane or to A11 Channels See Figure for an example Note that currently the Displayed Plane option is set by default This toggle is unimportant for single channel images or mode mfs Advanced Tip Note that while in interactive clean you are using the viewer Thus you have the ability to open and register other images in o
10. Yes means that saving the edits will flag unflag over the entire MS including fields and possibly spectral windows which are not currently selected for viewing Specifically data within time range s you swept out with the mouse even for unselected fields will be edited In addition if Flag Unflag All boxes were checked such edits will extend throughout the MS Note that only unselected times fields can be edited without checking extent boxes for the edits as well Unselected spectral windows e g will not be edited unless the edit also has Flag Unflag All Spectral Windows checked Warning Beware of checking All Spectral Windows unless you have also checked All Channels or turned Entire MS off channel edits appropriate to the selected spectral windows may not be appropriate to unselected ones Set Use Entire MS to No if your edits need to apply only to the portion of the MS you have selected for viewing Edits can often be saved significantly faster this way as well Also note that checkboxes apply to individual edits and must be checked before making the edit with the mouse Use Entire MS on the other hand applies to all the edits saved at one time and must be set as desired before pressing Save Edits CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 285 e Save Edits MS editing works like a text editor in that you see all of your edits immediately but nothing is
11. 170 4 5 4 1 Interpolation using accum o 171 4 5 4 2 Incremental Calibration using accum 171 Seer te tee ee ee ee 174 4 6 1 Application of Calibration applycal o ooo 175 nk ately e ic a gee aw Se eS 177 4 6 3 Resetting the Applied Calibration using clearcal 179 ose e A 179 4 7 1 Splitting out Calibrated uv data split 179 4 7 1 1 Averaging in split EXPERIMENTAL 180 4 7 2 Hanning smoothing of uv data hanningsmooth 180 4 7 3 Model subtraction from uv data uvsub 181 4 7 4 UV Plane Continuum Subtraction uvcontsub 181 4 7 5 UV Plane Model Fitting uvmodelfit 183 o Ant ere eae e Ee eee a E ae eee 186 5 Synthesis Imaging 188 RE A A A AA a a ES G 188 AAA E eee ee 189 521 Parameter c ll e ssa k a air e dee wa Ge E 189 E ie Seip ts Seng E E de Ge om E oe Hem ENS 190 Loe Sue a OBER ee eRe eee es 190 eb be A ee OS A a 190 2 5 Parameter mod cu ia2cae 2 48 de eee ER ae DR ERS e eid 190 5 2 5 1 Modemtsl o cor pademen paa ee we eS 191 5 2 5 2 Mode channel ss soo s ccosa kp nd RR RR a RE 191 ani Gea Sew teh RO e aad Ges Ge iw a ew A 192 Da eh Pee ew ee oe ad Ee e daa 192 5 2 5 5 Sub parameter interpolation 193 Lada ee ee ee 193 LA a Rae ee he Le eS 193 A ae prt ten tes lt a
12. gt all scan numbers Not yet implemented Optional data selection Specialized but see help The following are the general syntax rules and descriptions of the individual selection parameters of particular interest for the tasks 2 6 1 General selection syntax Most of the selections are effected through the use of selection strings This sub section describes the general rules used in constructing and parsing these strings Note that some selections are done CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 92 though the use of numbers or lists There are also parameter specific rules that are described under each parameter All lists of basic selection specification units are comma separated lists and can be of any length White spaces before and after the commas e g 3C286 3C48 3C84 are ignored while white space within sub strings is treated as part of the sub string e g 3C286 VIRGO A 3C84 All integers can be of any length in terms of characters composed of the characters 0 9 Floating point numbers can be in the standard format DIGIT DIGIT DIGIT or DIGIT or in the mantissa exponent format e g 1 4e9 Places where only integers make sense e g IDs if a floating point number is given only the integer part is used it is truncated Range of numbers integers or real numbers can be given in the format NO N1 For integer ranges it is expanded into a list of integers starting from NO
13. Below this are the eight Mouse Tool buttons Figure 7 4 These allow assignment of each of the three mouse buttons to a different operation on the display area Clicking a mouse tool icon will re Jassign the mouse button that was clicked to that tool The icons show which mouse button is currently assigned to which tool The escape key can be used to cancel any mouse tool operation that was begun but not completed and to erase any tool showing in the display area e Zooming magnifying glass icon To zoom into a selected area press the Zoom tool s mouse button the left button by default on one corner of the desired rectangle and drag to the desired opposite corner Once the button is released the zoom rectangle can still be moved or resized by dragging To complete the zoom double click inside the selected rectangle double clicking outside it will zoom out instead Panning hand icon Press the tool s mouse button on a point you wish to move drag it to the position where you want it moved and release Note The arrow keys Page Up Page Down Home and End keys can also be used to scroll through your data any time you are zoomed in Click on the main display area first to be sure the keyboard is focused there e Stretch shift colormap fiddling crossed arrows This is usually the handiest color adjustment it is assigned to the middle mouse button by default e Brightness contrast colormap fiddling light dark
14. Type of selection mfs channel velocity frequency nchan 1 Number of channels planes in output image start 0 0km s Velocity of first image channel e g 0 0km s width 1km s image channel width in velocity units e g 1 0km s interpolation nearest Type of spectral interpolation of visibilities nearest linear cubic The velocity of the first output channel is given by start and spacing by width Note that the velocity frame is given by the rest frequency in the MS header which can be overridden by the restfreq parameter Averaging is as in mode frequency The interpolation sub parameter 5 2 5 5 sets how channels are gridded into the image cube planes Again using the NGC5921 dataset as an example CHAPTER 5 SYNTHESIS IMAGING 193 mode velocity nchan 21 start 1383 0km s width 10km s Note that in this case the velocity axis runs forward as opposed to the default channelization for channel or frequency BETA ALERT Note that the velocities are expressed in the LSRK frame This is not currently selectable but in the future will be through restfreq 5 2 7 5 2 5 5 Sub parameter interpolation The interpolation sub parameter controls how spectral channels in the MS are gridded into the output image cube This is available in all modes except mfs The options are nearest linear cubic For nearest the chan
15. clean3 clnimage3 imname3 image clnmodel3 imname3 model clnresid3 imname3 residual clnmask3 imname3 clean_interactive mask Selfcal parameters reference antenna 11 11 VLA N1 calrefant 1i1 417 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS Filenames selfcaltabl imprefix selfcali gtable selfcaltab2 imprefix selfcal2 gtable smoothcaltab2 imprefix smoothcal2 gtable Polarization imaging parameters New prefix for polarization imaging output polprefix prefix polimg Set up clean slightly differently polclnalg hogbom polclnmode csclean polimname polprefix clean polimage polimname image polmodel polimname model polresid polimname residual polmask polimname clean_interactive mask Other files ipolimage polimaget I qpolimage polimaget Q upolimage polimaget U poliimage polimage poli polaimage polimaget pola Get to path to the CASA home and stip off the name pathname os environ get CASAPATH split 0 This is where the UVFITS data should be fitsdata pathname data demo jupiter6cm fits Or fitsdata pathname data nrao VLA planets_6cm fits fitsdata home ballista casa devel data nrao VLA planets_6cm fits 418 APPENDIX F APPENDIX AN
16. home basho3 jmcmulli pretest 2 sc captures the output to a variable options are l and v CASA 1 sc x pwd capture output from pwd to the variable x CASA 2 x Out 2 home basho3 jmcmulli pretest CASA 3 sc l x pwd capture the output from pwd to the variable x but split newlines into a list similar to sx command CASA 4 x Out 4 home basho3 jmcmulli pretest CASA 5 sc v x pwd capture output from pwd to a variable x and show what you get verbose mode x nome basho3 jmcmulli pretest CASA 6 x Out 6 home basho3 jmcmulli pretest APPENDIX D APPENDIX PYTHON AND CASA 379 D 7 Logging There are two components to logging within CASA Logging of all command line inputs is done via IPython Upon startup CASA will log all commands to a file called ipython log This file can be changed via the use of the ipythonrc file This log file can be edited and re executed as appropriate using the execfile feature D 11 The following line sets up the logging for CASA There are four options following the specification of the logging file 1 append 2 rotate each session of CASA will create a new log file with a counter incrementing ipython log 1 ipython log 2 etc 3 over overwrite existing file and 4 backup renames existing log file to log name logfile ipython log append The command logstate
17. minimum SNR 3 minsnr 3 saveinputs polcal calprefix polcal saved polcal 433 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 434 List polcal solutions print Listcal PolD listfile caltable list print Listing calibration to file listfile listcal Plot polcal solutions print Plotcal PolD iteration showgui False xaxis antenna 2 2 yaxis amp showgui True figfile plotcal O print These are the amplitudes of D terms versus antenna Pause script if you are running in scriptmode if scriptmode user_check raw_input Return to continue script n Now plot to files showgui False figfile caltable plotcal antamp png print Plotting calibration to file figfile saveinputs plotcal caltablet plotcal antamp saved plotcal xaxis antenna yaxis phase figfile caltable plotcal antphase png print Plotting calibration to file figfile saveinputs plotcal caltable plotcal antphase saved plotcal APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 435 xaxis antenna yaxis snr figfile caltable plotcal antsnr png print Plotting calibration to file figfile saveinputs plotcal caltablet plotcal antsnr saved plotcal xaxis real yaxis imag figfile caltable
18. npts array 3014656 gt quartile array 0 00254881 yms array 0 00202226 gt sigma array 0 0020222 sum array 48 26399646 gt sumsq array 12 32857318 tre array 255 255 O 451 tref 15 19 52 390 05 35 44 246 I 1 41391e 09Hz CASA lt 37 gt mydict2 Out 37 flux 5 4000000000000004 source 0137 331 Thus you can make scripts that save information and use it later like for regressions Note that these examples use Python file handling and IO as well as importing modules such as pickle See your friendly Python reference for more on this kind of stuff Its fairly obvious how it works D 5 Control Flow Conditionals Loops and Exceptions There are a number of ways to control the flow of execution in Python including conditionals if loops for and while and exceptions try We will discuss the first two below D 5 1 Conditionals The standard if block handles conditional execution or branches in Python APPENDIX D APPENDIX PYTHON AND CASA 373 if lt expression gt lt statements gt elif lt expression gt lt statements gt elif lt expression gt lt statements gt else lt statements gt Insert a pass statement if you want no action to be taken for a particular clause The lt expression gt should reduce down to True or False For example if importmode vla Import the data from VLA Export
19. crpix4 0 0 crvali 4 02298392585 rad crval2 0 0884300154344 rad crval3 1 0 crval4 1412808153 26 Hz cdelti 7 27220521664e 05 rad cdelt2 7 27220521664e 05 rad cdelt3 1 0 cdelt4 24414 0625 Hz cuniti rad cunit2 rad cunit3 cunit4 Hz The values for these keywords can be queried using mode get This opens sub parameters mode hditem gt get Options get put summary list stats e header item to get or put Note that the mode get option returns a Python dictionary containing the current value of the hditem This dictionary can be manipulated in Python in the usual manner For example continuing the above example CASA lt 3 gt imagename ngc5921 usecase clean image CASA lt 4 gt mode get CASA lt 5 gt hditem observer CASA lt 6 gt hdvalue imhead EK observer TEST CASA lt 7 gt print hdvalue TEST CHAPTER 6 IMAGE ANALYSIS 234 You can set the values for these keywords using mode put This opens sub parameters mode put Options get put summary list stats hditem z ay header item to get or put hdvalue gt header value to set for mode put Continuing the example further CASA lt 8 gt mode put CASA lt 9 gt hdvalue CASA CASA lt 10 gt imhead CASA lt 11 gt mode list CASA lt 12 gt imhead Available header items to modify General object
20. gt sigma array 0 00201811 sum array 49 1322855 sumsq array 12 27880404 tre array 255 255 0 451 CHAPTER 1 INTRODUCTION 45 tref 15 19 52 390 05 35 44 246 I 1 41391e 09Hz CASA lt 3 gt myrms xstat rms 0 CASA lt 4 gt print 10 0 myrms 0 0201817648485 If you do not catch the return variable it will be lost imstat ngc5921 clean image or default imstat imagename ngc5921 clean image imstat and spewed to terminal Note that go will trap and lose the return value e g default imstat imagename ngc5921 clean image go will not dump the return to the terminal either NOTE You cannot currently catch a return value from a task run asynchronously 3 1 3 4 BETA ALERT Before Patch 2 the return values for tasks like imstat and imhead were put into the global variables xstat and hdvalue respectively This is no longer the case 1 3 4 Running Tasks Asynchronously By default most tasks run synchronously in the foreground Many tasks particularly those that can take a long time to execute have the async parameter This allows the user to send the task to the background for execution BETA ALERT A few tasks such as the exportuvfits and exportfits tasks have async True by default This is a workaround for a known problem where they can trample on other tasks and tools if they use the default global tools underneath
21. newimage image fluxscale_image newimage flux if pbcor if sclt NONE otherwise its already divided ia open newimaget image pixmask fluxscale_image gt str minpb ia calcmask pixmask asdefault True pixels iif fluxscale_imaget gt str minpb result fluxscale_image 0 APPENDIX H APPENDIX WRITING TASKS IN CASA ia calc pixels pixels ia close else people has imaged the fluxed corrected image but want the final image to be non fluxed corrected if sclt NONE ia open newimaget image result newimage image fluxscale_image newimage flux pixels result fluxscale_image ia calc pixels pixels ia close os chdir presdir del imCln except Exception instance print Error instance raise Exception instance 501
22. o o e e 138 G 1 MIRIAD CASA dictionary 20 ee 474 G 2 CLIC CASA dictionary 14 List of Figures 1 1 Screen shot of the default CASA inputs for task clean 53 1 2 The clean inputs after setting values away from their defaults blue text Note that some of the boldface ones have opened up new dependent sub parameters indented and green 54 1 3 The clean inputs where one parameter has been set to an invalid value This is drawn in red to draw attention to the problem This hapless user probably confused ARO 5 T rer 5 1 5 Using the Search facility in the casalogger Here we have specified the string AAA 50 1 6 Using the casalogger Filter facility The log output can be sorted by Priority Time Origin and Message In this example we are filtering by Origin using clean and ANA 6 1 7 CASA Logger Insert facility The log output can be augmented by adding notes Tce Sil ao A EA EE ens 6 AS ote Aa oe tee 65 E N 1 The contents of a Measurement Set These tables compose a Measurement Set named ngc5921 demo ms on disk This display is obtained by using the File Open menu in browsetable and left double clicking on the ngc5921 demo ms directory 77 3 1 The plotxy plotter showing the Jupiter data versus uv distance You can see bad are 1 Mark Region Press this to begin marking regions rather than zooming or panning 2 3 4 Flag Unflag Locate Clic
23. 1 3 4 1 Monitoring Asynchronous Tasks BETA ALERT Currently this is only available with the tm tool We are working on a taskmanager task CHAPTER 1 INTRODUCTION 46 There is a taskmanager tool tm that allows the user to BETA ALERT retrieve the status of and to abort the execution of tasks You should not use the go command running with async True in the background There are eo run a task asynchronously as the two methods of interest for the user tm retrieve and andle will be swallowed by the tm abort Python task wrapper and you will If you run a task with async True then several things will not be able to access it with tm This happen First of all the task returns a handle that is a is also true if you run in a Python number used to identify the process This is printed to the script screen e g CASA lt 5 gt inp mosaic Calculate a multi field deconvolved image with selected clean algorithm async True if True run in the background prompt is freed CASA lt 6 gt mosaic Connecting to controller 127 0 0 1 60775 Out 6 0 where the output value 0 is the handle id You can also catch the return value in a variable e g CASA lt 7 gt handle mosaic CASA lt 8 gt print handle 1 You should also see the usual messages from the task in the logger with some extra lines of information HHEHHHHHHHHHHHHEHHHHHHHHHHEHHHHHHHEHHEHHRHHE REE B
24. 1445 099_avg ms complist gcal cl Plot data versus uv distance plotxy 1445 099_avg ms xaxis uvdist datacolumn corrected Specify green circles for model data overplotted plotxy 1445 099_avg ms xaxis uvdist datacolumn model overplot True plotsymbol go Amplitude of Model Data 0 1 2 3 4 UV Distance klambda Figure 4 10 Use of plotxy to display corrected data red and blue points and uv model fit data green circles 4 8 Examples of Calibration See the scripts provied in Appendix F for examples of calibration In particular we refer the interested user to the demonstrations for CHAPTER 4 SYNTHESIS CALIBRATION e NGC5921 VLA HI a quick demo of basic CASA spectral line calibration F 1 e Jupiter VLA 6cm continuum polarimetry polarization calibration F 2 187 Chapter 5 Synthesis Imaging This chapter describes how to make and deconvolve images starting from calibrated interferometric data possibly sup Inside the Toolkit plemented with single dish data or an image made from The im tool handles synthesis imag single dish data This data must be available in CASA ing operations see 2 on importing data See 4 for information on calibrating synthesis data In the following sections the user will learn how to make various types of images from synthesis data reconstruct images of the sky using the available deconvoluti
25. Flagging Options Blink Basic Settings Figure 7 16 The MS for NGC4826 BIMA observations has been loaded into the viewer We see the first of the spw in the Display Panel and have opened up MS and Visibility Selections in the Data Display Options panel The display panel raster is not full of visibiltiies because spw O is continuum and was only observed for the first few scans This is a case where the different spectral windows have different numbers of channels also This roll up provides choice boxes for Visibility Type Observed Corrected Model Residual and Component Amplitude Phase Real or Imaginary Changes to Visibility Type or Component changing from Phase to Amplitude for example require the data to be retrieved again from the disk into memory which can be a lengthy process When a large MS is first selected for viewing the user must trigger this retrieval manually by pressing the Apply button located below all the options after selecting the data to be viewed see Field IDs and Spectral Windows below Tip Changing visibility type between Observed and Corrected can also be used to assure that data and flags are reloaded from disk You should do this if you re using another flagging tool such as autoflag simultaneously so that the viewer sees the other tool s new edits and doesn t overwrite them with obsolete flags The Apply button alone won t reload unless
26. Hz default current frame frequency frame for spectral axis options str LSRK REST TOPO LSRD BARY GEO GALACTO LGROUP CMB default currently set frame in scantable WARNING frame REST not yet implemented doppler doppler mode options str RADIO OPTICAL Z BETA GAMMA default currently set doppler in scantable scanlist list of scan numbers to process default use all scans example 21 22 23 24 field selection string for selecting scans by name default no name selection example FLS3a this selection is in addition to scanlist iflist and pollist iflist list of IF id numbers to select default use all IFs APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 323 example 15 this selection is in addition to field scanlist and pollist pollist list of polarization id numbers to select default use all pols example 1 this selection is in addition to field scanlist and iflist masklist list of mask regions to INCLUDE in stats default whole spectrum example 4000 4500 for one region 1000 3000 5000 7000 these must be pairs of lo hi boundaries invertmask invert mask EXCLUDE masklist instead options bool True False default false interactive determines interactive masking options bool True False default False example interactive True allo
27. LSRD BARY GEO GALACTO LGROUP CMB default currently set frame in scantable WARNING frame REST not yet implemented doppler doppler mode options str RADIO OPTICAL Z BETA GAMMA APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 314 default currently set doppler in scantable scanlist list of scan numbers to process default use all scans example 21 22 23 24 this selection is in addition to field iflist and pollist field selection string for selecting scans by name default no name selection example FLS3a this selection is in addition to scanlist iflist and pollist iflist list of IF id numbers to select default use all IFs example 15 this selection is in addition to scanlist field and pollist pollist list of polarization id numbers to select default use all polarizations example 1 this selection is in addition to scanlist field and iflist outfile Name of output file default gt lt sdfile gt _cal outform format of output file options ASCII SDFITS MS ASAP default ASAP example the ASAP format is easiest for further sd processing use MS for CASA imaging If ASCII then will append some stuff to the outfile name overwrite overwrite the output file if already exists options bool True False default False WARNING if outform ASCII this
28. Return to continue script n FERRERA RO ROA RO ROA RARA RRHH H HAHAHA RRE RORORORRRA RRHH HORA ERE AAHRPP RRR AAA AAA Statistics on clean image cube print ImStat Clean cube srcstat imstat ngc4826 tutorial 16apr98 src clean image print Found image max tstr srcstat max 0 offbox 106 161 153 200 offstat imstat ngc4826 tutorial 16apr98 src clean image box 106 161 153 200 print Found off source image rms str offstat sigma 0 cenbox 108 108 148 148 offlinechan 0 1 2 3 4 5 30 31 32 33 34 35 offlinestat imstat ngc4826 tutorial 16apr98 src clean image box 108 108 148 148 chans 0 1 2 3 4 5 30 31 32 33 34 35 print Found off line image rms str offlinestat sigma 0 HHHHHHHHHHHE RHEE HHHHHAAAEHA RARER RHEE RAHA H AREER HHA ARR AAA AR Manually correct for mosaic response pattern using image flux images print ImMath PBcor immath outfile ngc4826 tutorial 16apr98 src clean pbcor mode evalexpr expr ngc4826 tutorial 16apr98 src clean image ngc4826 tutorial 16apr98 src clean flux FERRARI AHHH A AHA AA AHR RAR AAR Statistics on PBcor image cube APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 469 print ImStat PBcor cube pbcorstat imstat ngc4826 tutorial 16apr98 src clean pbcor print Found image
29. datacolumn corrected field 1445 width 63 Initial guess is that it s close to the phase center and has a flux of 2 0 a priori we know it s 2 47 uvmodelfit 1445 099_avg ms use averaged data niter 5 Do 5 iterations comptype P P Point source G Gaussian D Disk sourcepar 2 0 1 1 Source parameters for a point source spw 0 outfile gcal cl Output component list file Output looks like There are 19656 3 19653 degrees of freedom iter 0 reduced chi2 0 0418509 I 2 dir 0 1 0 1 arcsec iter 1 reduced chi2 0 003382 I 2 48562 dir 0 020069 0 0268826 arcsec iter 2 reduced chi2 0 00338012 I 2 48614 dir 0 00323428 0 00232235 arcsec iter 3 reduced chi2 0 00338012 I 2 48614 dir 0 00325324 0 00228963 arcsec iter 4 reduced chi2 0 00338012 I 2 48614 dir 0 00325324 0 00228963 arcsec iter 5 reduced chi2 0 00338012 I 2 48614 dir 0 00325324 0 00228963 arcsec If data weights are arbitrarily scaled the following formal errors will be underestimated by at least a factor sqrt reduced chi2 If the fit is systematically poor the errors are much worse I 2 48614 0 0176859 x 0 00325324 0 163019 arcsec y 0 00228963 0 174458 arcsec Writing componentlist to file home sandrock smyers Testing Patch2 N5921 gcal cl CHAPTER 4 SYNTHESIS CALIBRATION 186 Fourier transform the component list into MODEL_DATA column of the MS ft
30. e CORRECTED_DATA used to hold calibrated data for imaging or display e MODEL_DATA holds the Fourier inversion of a particular model image for calibration or imaging e IMAGING WEIGHT holds the gridding weights to be used in imaging The creation and use of the scratch columns is generally done behind the scenes but you should be aware that they are there and when they are used CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 79 Table 2 2 Commonly accessed MAIN Table data related columns Note that the columns ALMA_PHASE_CORR ALMA_NO_PHAS_CORR and ALMA_PHAS_CORR_FLAG_ROW are specific to ALMA data filled using the importasdn filler Column Format Contents DATA Complex N Nf complex visibility data matrix ALMA_PHASE_CORR by default FLAG Bool N Ny cumulative data flags WEIGHT Float N weight for a row WEIGHT SPECTRUM Float N Ny individual weights for a data matrix ALMA _PHASE CORR Complex N Ny on line phase corrected data Not in VLA data ALMA NO PHAS CORR Bool Ne Np data that has not been phase corrected Not in VLA data ALMA PHAS CORR FLAG ROW Bool Ne Nf flag to use phase corrected data or not not in VLA data MODEL DATA Complex Ne Ny Scratch created by calibrater or im ager tools CORRECTED DATA Complex Ne Ny Scratch created by calibrater or im ager tools IMAGING WEIGHT Float N Scratch created by calibrater or im ager tools The most recent s
31. o 0 1 1 7976931348 N5921_2 1 2 0 2 Y a s uw 2 o B v EN a Restore Columns Resize Headers PAGE NAVIGATION First I lt lt ewes gt gt Loading 1000 rows Figure 3 9 browsetable Viewing the SOURCE table of the MS 3 8 MS Plotting and Editing using casaplotms BETA ALERT The casaplotms tool is an experimental standalone plotter application based on Qt It is intended to replace plotxy and will be integrated more fully into CASA in the next release There is no task or toolkit interface to casaplotms from inside casapy You can start the appli cation outside CASA e g by typing casaplotms or from inside the shell using the OS command syntax either casaplotms from IPython or os system casaplotms from IPython or script 3 9 Examples of Data Display and Flagging See the scripts provied in Appendix F for examples of data examination and flagging In particular we refer the interested user to the demonstrations for e NGC5921 VLA HI a quick demo of basic CASA capabilities F 1 e Jupiter VLA 6cm continuum polarimetry more extensive editing F 2 Chapter 4 Synthesis Calibration This chapter explains how to calibrate interferometer data within the CASA task system Calibration is the process Inside the Toolkit of determining the complex correction factors that must be The workhorse for synthesis calibra applied to each visibility i
32. print Calibrate s sd scantable FLS3a_HI asap s set_fluxunit K scanns s getscannos sn list scanns print No scans to be processed len scanns res sd calfs s sn print Save calibrated data res save FLS3a_calfs MS2 print Image data im open FLS3a_calfs im selectvis nchan 901 start 30 step 1 spwid 0 field 0 dir J2000 17 18 29 59 31 23 im defineimage nx 150 cellx 1 5arcmin phasecenter dir mode channel start 30 nchan 901 step 1 im setoptions ftmachine sd cache 1000000000 im setsdoptions convsupport 4 HH HH HH H H OH OF 361 split the data for the field of interest save this scantable to disk asap format free up memory from scantable read in scantable from disk FLS3a set the brightness units to Kelvin get a list of scan numbers convert it to a list calibrate all scans listed using frequency switched calibration method Save the dataset as a MeasurementSet open the data set choose a subset of the data just the key emission channels set map center define image parameters note it assumes symmetry if ny celly aren t specified choose SD gridding use this many pixels to support the gridding function used default prolate spheroidal wave function im makeimage type singledish image FLS3a_HI image make the image APPENDIX A APPENDIX
33. 0 OrionS_ps 01 52 05 1x 08 00 5 0 05 35 13 5 05 24 08 2 0 LSRK 4 5489354e 10 4096 6104 233 Note that our scans are now collapsed timeaverage True but we still have our IF 0 HEHFHHHHHHHHHHHH HEHEHE HESS Plot data HHEHHHHHHHHHHHHHHHEHHE HEHE default sdplot The file we produced after calibration if we hadn t reset defaults it would have been set note that sdplot sdfit sdstat use sdfile as the input file which is the output file of sdcal sdfile sdusecase_orions_hc3n asap 333 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING Lets just go ahead and plot it up as is sdplot Looks ok Plot with x axis in GHz specunit GHz sdplot Note that the rest frequency in the scantable is set correctly to the HCCCN line at 45 490 GHz So you can plot the spectrum in km s specunit km s sdplot Zoom in sprange 100 50 sdplot Lets plot up the lines to be sure We have to go back to GHz for this known deficiency in ASAP specunit GHz sprange 45 48 45 51 linecat all sdplot Too many lines Focus on the HC3N ones linecat HCCCN sdplot Finally we can convert from K to Jy using the aperture efficiencies we have coded into the sdtasks For GBT data do not set telescopeparm fluxunit Jy telescopeparm sdplot Lets save this plot plotfile sdusecase_orions_hc3n eps sdp
34. 2 6 e viewer use the casaviewer to display the MS as a raster image and flag it 101 CHAPTER 3 DATA EXAMINATION AND EDITING 102 3 2 Managing flag versions with flagmanager The flagmanager task will allow you to manage different versions of flags in your data These are stored inside a CASA flagversions table under the name of the MS lt msname gt flagversions For example for the MS jupiter6cm usecase ms there will need to be jupiter6cm usecase ms flagversions on disk This is created on import by importvla or importuvfits or when flagging is first done on an MS without a flagversions e g with plotxy By default when the flagversions is created this directory will contain a flags Original in it containing a copy of the original flags in the MAIN table of the MS so that you have a backup It will also contain a file called FLAG_VERSION_LIST that has the information on the various flag versions there The inputs for flagmanager are vis a Name of input visibility file MS mode list Flag management operation list save restore delete The mode list option will list the available flagversions from the lt msname gt flagversions file For example CASA lt 102 gt default flagmanager CASA lt 103 gt vis jupiter6cm usecase ms CASA lt 104 gt mode list CASA lt 105 gt flagmanager MS home imager b smyers Oct07 jupiter6cm usecase ms main working copy in m
35. 2009 05 27 04 47 13 INFO applycal ca Beginning selectvis MSSelection version a Opening MS ngc5921 demo ms for calibration a Initializing nominal selection to the whole MS 2009 05 27 04 47 13 INFO applycal Ca Performing selection on Measurementset 2009 05 27 04 47 13 INFO applycal ca By selection 22653 rows are reduced to 18144 2009 05 27 04 47 13 INFO applycal ca Frequency selection selecting all channels in all spws 2009 05 27 04 47 13 INFO applycal ca Arranging to APPLY 2009 05 27 04 47 13 INFO applycal ca G Jones table ngc5921 demo fluxscale select FISLD_ID IN 1 interp linear epwmap 0 calwt true 2009 05 27 04 47 13 INFO applycal Ca Arranging to APPLY ia 2009 05 27 04 47 13 INFO applycal Ca B Jones table ngc5921 demo bcal select FIBLD_ID IN 0 1 2 interp nearest spwmap 0 calwt true ig 4 Je Insert Message eje Lock scroll Figure 1 5 Using the Search facility in the casalogger Here we have specified the string plotted and it has highlighted all instances in green and thus should mostly be disregarded on OSX On the Mac you treat this as just another console window and use the usual mouse and hot key actions to do what is needed The CASA logger window for Linux is shown in Figure The main feature is the display area for the log text which is divided into columns The columns are e Time the time that the message was gene
36. 22 1 1 1 What s New in Beta Patch 4 o e 00048 23 1 1 1 1 Previous changes in Patch3 o o 25 1 1 1 2 Previous changes introduced in Patch 2 27 12 CASA Basics Information for First Time Users o a 28 A A 28 1 2 1 1 Environment Variables o a 29 1 2 1 2 Where is CASA e eee 29 pam ae Rk eee Gece oon oe ae Re eee ele Ba tee oe 30 few alk e ew ace ene Ae edge atte Gage ae eae S 30 1 2 4 What happens if something goes wrong 0 0002 0200 30 Rag has Ride of ne nde ane ad deck oh He owe E 31 1 2 6 What happens if CASA crashes 2 20 0 0 0000 eee eee 31 Sk wara Be a eo Boe ae ee ae Se ae aS 32 1 2 7 1 Variables 2 ee 32 1 2 7 2 Lists and Ranges ee 32 127 3 Indexes s os ce ce ee ER Oe ee ORE ee a 33 L24 Indentation sc sgos eaor gok Pe 6A eR he ROR Ee ee 33 1 2 7 5 System shell access ooa ee 33 vie OA oe eee a Ce Ge gk oe 34 ete hiwed hat ba ba aw Ook eee PSO 34 1 2 3 1 TAB key 2a eee eek bbe ee ee ee ee ee ee es 34 1 2 3 2 help lt taskname gt 00 000 0 00 00 35 1 2 8 3 help and PAGER oaaae 37 1 2 8 4 help par lt parameter gt sooo 0 00000 37 1280 Python Help e es 0E or at oes ee ee a Be ee es 37 i honk angie ke Bohl ue BE a Bog deg ae bk age ew ae E 38 13 1 What Tasks are Available o e e e 39 E ee a oe ee 42
37. ATMOPRA DS55 43 CEDUNA HOBART For GBT it fixes default fluxunit to K first then convert to a new fluxunit telescopeparm 104 9 0 43 diameter m ap eff telescopeparm 0 743 gain in Jy K telescopeparm FIX to change default fluxunit see description below specunit units for spectral axis options str channel km s GHz MHz kHz Hz default current example this will be the units for masklist frame frequency frame for spectral axis options str LSRK REST TOPO LSRD BARY GEO GALACTO LGROUP CMB default currently set frame in scantable WARNING frame REST not yet implemented doppler doppler mode options str RADIO OPTICAL Z BETA GAMMA default currently set doppler in scantable calmode calibration mode options ps nod fs fsotf quotient none APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 295 default none example choose mode none if you have already calibrated and want to try averaging scanlist list of scan numbers to process default use all scans example 21 22 23 24 this selection is in addition to field iflist and pollist field selection string for selecting scans by name default no name selection example FLS3a this selection is in addition to scanlist ifl
38. Also split out 0137 331 as a check field calname outputvis calsplitms print Split field data into new ms calsplitms split Force scratch column creation so plotxy will work vis srcsplitms clearcal vis calsplitms clearcal Use Plotxy to look at the split calibrated data print Plotxy default plotxy selectdata True correlation RR LL xaxis uvdist datacolumn data multicolor both iteration selectplot True field JUPITER vis srcsplitms interactive True yaxis amp title field 438 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS Plotxy interactively if desired plotxy O print print print Plotting JUPITER corrected visibilities print Look for outliers Pause script if you are running in scriptmode if scriptmode user_check raw_input Return to continue script n Now go back and plot to files interactive False First the target vis srcsplitms field srcname yaxis amp Use the field name as the title title field figfile vis plotxy amp png print Plotting to file figfile saveinputs plotxy vis plotxy amp saved plotxy O yaxis phase Use the field name as the title figfile vis plotxy phase png print Plotting to file figfile saveinputs plotxy vis p
39. CHAPTER 6 IMAGE ANALYSIS 248 xstat imstat myImage box 2 3 14 15 30 31 42 43 chan 4 5 Select all channels greater the 20 as well as channel 0 and the print the mean and standard deviation xstat imstat myImage chans gt 20 0 print Mean is xstat mean 0 s d xstat sigma 0 Find statistical information for the Q stokes value only then the I stokes values only and print out the statistical values that we are interested in xstat imstat myimage stokes Q si xstat imstat myimage stokes I s2 xstat print MIN MAX MEAN print Q si min 0 si max 1 07 s1 mean 0 print I s2 min 07 s2 max 0 s2 mean 0 6 8 Extracting data from an image imval The imval task will extract the values of the data and mask from a specified region of an image and place in the task return value as a Python dictionary The inputs are imval Get the data value s and or mask value in an image imagename ne Name of the input image region e Image Region Use viewer box q Select one or more box regions chans gt gt Select the channel spectral range stokes ay Stokes params to image 1 IV IQU IQUV async False Area selection using box and region is detailed in and respectively By default box will extract the image informat
40. Position 882590 4 92487e 06 3 94373e 06 Time 01 48 38 Direction 05 35 13 5 05 24 08 2 gt azel 154 696 43 1847 deg Time 01 48 38 Direction 05 35 13 5 05 24 08 2 gt azel 154 696 43 1847 deg Time 01 48 38 Direction 05 35 13 5 05 24 08 2 gt azel 154 696 43 1847 deg Time 01 48 38 Direction 05 35 13 5 05 24 08 2 gt azel 154 696 43 1847 deg Time 01 48 38 Direction 05 35 13 5 05 24 08 2 gt azel 154 696 43 1847 deg APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 350 Once you have the correct Az El you can correct for a known opacity by scans opacity tau 0 09 Opacity from which the correction factor exp tau zenith distance A 3 4 4 Calibration of GBT data Data from the GBT is uncalibrated and comes as sets of integrations representing the different phases within a calibration cycle e g on source calibration on on source calibration off on reference calibration on on reference calibration off Currently there are a number of routines emulating the standard GBT calibration in GBTIDL e calps calibrate position switched data e calfs calibrate frequency switched data e calnod calibration nod beam switch data All these routines calibrate the spectral data to antenna temperature adopting the GBT calibration method as described in the GBTIDL calibration document available at e http wwwlocal gb nrao edu GBT DA gbtidl gbtidl_calibration pdf There are two b
41. Python script casalog origin clean maskimage if mask or mask mask if interactive if mask or mask or mask maskimage imagename mask try af 1 imCln imtool create imset cleanhelper imCln vis if len imagename 0 or imagename isspace raise Exception Cannot proceed with blank imagename casalog origin clean imset defineimages imsize imsize cell cell stokes stokes 498 APPENDIX H APPENDIX WRITING TASKS IN CASA 499 mode mode spw spw nchan nchan start start width width restfreq restfreq field field phasecenter phasecenter imset datselweightfilter field field spw spw timerange timerange uvrange uvrange antenna antenna scan scan wgttype weighting robust robust noise noise npixels npixels mosweight mosweight innertaper innertaper outertaper outertaper if maskimage maskimage imagename mask imset makemaskimage outputmask maskimage imagename imagename maskobject mask define clean alg alg psfmode if multiscale 0 multiscale if type multiscale list and len multiscale gt 0 alg multiscale imCln setscales scalemethod uservector uservector multiscale if imagermode csclean alg mf alg if imagermode mosaic if alg count mf lt 1 alg mf alg imCln setoptions ftmachine ftmachine padding 1
42. The following commands give the results shown in Figure 3 6 plotxy ngc5921 ms uvdist flagdata vis ngc5921 ms clipexpr LL clipminmax 0 0 1 6 clipoutside True plotxy ngc5921 ms uvdist CHAPTER 3 DATA EXAMINATION AND EDITING 124 e Figure 1 Figure 1 Corrected SPWs 0 Pol RR LL Corrected SPWs 0 Pol RR LL Fields 1331 30500002_0 Fields 1331 30500002_0 corrected amp sqrt u 2 v2 m 400 000 Sars sqrt u 2 v 2 m 0 0 ala x 340 y 231 PO lO Hala x 196 y 0 712 Figure 3 6 flagdata Flagging example using the clip facility 3 5 1 2 Flagging the beginning of scans You can use the mode quack option to drop integrations from the beginning of scans as in the AIPS task QUACK mode gt quack Mode manualflag autoflag summary quack autocorr False Flag autocorrelations unflag False Unflag the data specified quackinterval 0 0 Quack n seconds from scan beginning Note that the time is measured from the first integration in the MS for a given scan and this is often already flagged by the online system For example assuming the integration time is 3 3 seconds e g for VLA then mode quack quackinterval 14 0 will flag the first 4 integrations in every scan 3 6 Browse the Data The browsetable task is available for viewing data directly and handles all CASA tables including Measuremen
43. The latest version of this script can be found at http casa nrao edu Doc Scripts ngc4826_tutorial py HHEFHHHHHHHEHHHHEHHEEHHHEHHHEE HEHEHE HREHEHEEHEHHEE HEHEHE HRHEHHEE HEHEHE HRE A ARRE Demo Script for NGC 4826 BIMA line data Converted by STM Updated by CB Updated by STM Updated by CB STM Updated by CB STM Updated by CB STM Updated by CB STM Updated by CB Updated by CB STM Updated by STM Updated by DP Updated by DP Updated by CB HHH HH HHH HH HHH HH OH 2008 05 27 Beta Patch 2 0 new tasking clean cal 2008 05 30 start from raw data 2008 06 01 scriptmode plotting 2008 06 02 improvements 2008 06 03 bigger cube pbcor 2008 06 04 pbcor stuff 2008 06 04 tutorial script 2008 06 05 small tweaks 2008 06 12 final revisions DS 2008 06 14 post school fix 2009 05 05 pre Garching immoments chans 2009 05 05 messages for flagging 2009 05 18 pre Canada spw fix not needed now HE HHH HH HH HHH H HH HH OF 453 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS Updated by CB 2009 05 18 immoments axis spectral Updated by CB 2009 05 19 added restfreq to clean Updated by CB 2009 05 19 removed clearcals N4826 BIMA SONG Data This data is from the BIMA Survey of Nearby Galaxies BIMA SONG Helfer Thornley Regan et al 2003 ApJS 145 259 Many thanks to Michele Thornley for providing the data and description First day of observations only Script Notes o The default commands are not necessary but are
44. atmospheric optical depth default 0 0 no correction blmode mode for baseline fitting options str auto list interact default auto example blmode auto uses expandable parameters in addition to blpoly to run linefinder to determine line free regions USE WITH CARE May need to tweak the parameters thresh avg_limit and edge blmode interact allows adding and deleting mask regions by drawing rectangles on the plot with mouse Draw a rectangle with LEFT mouse to ADD the region to the mask and with RIGHT mouse to DELETE the region gt gt gt blmode expandable parameters thresh S N threshold for linefinder default 5 example a single channel S N ratio above which the channel is considered to be a detection avg_limit channel averaging for broad lines default 4 example a number of consecutive channels not greater than this parameter can be averaged to search for broad lines edge channels to drop at beginning and end of spectrum default 0 example 1000 drops 1000 channels at beginning AND end 1000 500 drops 1000 from beginning and 500 from end Note For bad baselines threshold should be increased and avg_limit decreased or even switched off completely by setting this parameter to 1 to avoid detecting baseline undulations instead of real lines blpoly order of baseline polynomial options int lt 0 turns off baseline fitting default 5 APPENDIX A APPENDIX SIN
45. default single scale interactive False use interactive clean with GUI viewer mask Ml cleanbox es mask image s and or region s imsize 256 256 Image size in pixels nx ny symmetric for single value cell 1 0arcsec 1 0arcsec The image cell size in arcseconds x y phasecenter s Field Identififier or direction of the image phase center restfreq 7 rest frequency to assign to image see help stokes 21 Stokes params to image I IV QU IQUV RR LL XX YY RRLL XXYY weighting natural Weighting to apply to visibilities cyclefactor 1 5 Change the threshold at which the deconvolution cycle will stop degrid and subtract from the visiblities cyclespeedup 1 Cycle threshold doubles in this number of iterations uvtaper False Apply additional uv tapering of visibilities restoringbeam gt gt Output Gaussian restoring beam for CLEAN image async False If true the taskname must be started using widefield Most of the parameters are similar to clean and should be reviewed there Specialized parameters for widefield are as follows The task widefield can be used in two major modes First the w projection mode as chosen with ftmachine deals with the w term the phase associated with the sky array curvature internally Secondly the image can be broken into many facets each small enough so that the w term is not significant These two basic methods can be combined
46. lt description gt Maximum number of iterations lt description gt lt value gt 500 lt value gt lt param gt lt param type double name gain gt lt description gt Loop gain for cleaning lt description gt lt value gt 0 1 lt value gt lt param gt lt param type double name threshold units mJy gt lt description gt Flux level to stop cleaning Must include units lt description gt lt value gt 0 0 lt value gt lt param gt lt Getting rid of this lt param type bool name csclean gt lt description gt Use Cotton Schwab style reconciliation with UV data lt description gt lt value gt False lt value gt lt param gt gt lt param type string name psfmode gt lt description gt method of PSF calculation to use during minor cycles lt description gt lt value gt clark lt value gt lt allowed kind enum gt lt value gt clark lt value gt lt value gt hogbom lt value gt lt allowed gt lt param gt lt param type string name imagermode gt lt description gt Use csclean or mosaic If use psfmode lt description gt APPENDIX H APPENDIX WRITING TASKS IN CASA 483 lt value gt lt value gt lt allowed kind enum gt lt value gt lt value gt lt value gt csclean lt value gt lt value gt mosaic lt value gt lt allowed gt lt param gt lt param type string name ftmachine subparam true gt lt description gt Gridding method for the image l
47. might be meaningful for the dataset in question Note that the order in which multiple spws are given may be important for other parameters For example the mode channel in clean uses the first spw as the origin for the channelization of the resulting image cube 2 6 3 1 Channel selection in the spw parameter Channel selection can be included in the spw string in the form SPWSEL CHANSEL where CHANSEL is the channel se Beta Alert lector In the end the spectral selection within a given Not all options are available yet such spectral window comes down to the selection of specific as percentages or velocities Stay channels We provide a number of shorthand selection op tuned tions for this These CHANSEL options include e Channel ranges START STOP e Frequency ranges FSTART FSTOP e Velocity ranges VSTART VSTOP not yet available e Bandwidth percentages PSTART PSTOP or PWIDTH not yet available Channel striding stepping START STOP STEP or FSTART FSTOP FSTEP The most common selection is via channel ranges START STOP or frequency ranges FSTART FSTOP spw 0 13753 spw 0 channels 13 53 inclusive spw 0 141371414MHz spw 0 1413 1414MHz section only All ranges are inclusive with the channel given by or containing the frequency or velocity given by START and STOP plus all channels between included in the selection You
48. ngc5921 chan21 clean imasked1 go Note that nominally the axes of the mask must be congruent to the axes of the images in expr However one exception is that the image in mask can have fewer axes but not axes that exist but are of the wrong lengths In this case immath will extend the missing axes to cover the range in the images in expr Thus you can apply a mask made from a single channel to a whole cube drop degenerate stokes and freq axes from ngc5921 chan21 clean cleanbox mask ia open ngc5921 chan21 clean cleanbox mask im2 ia subimage outfile ngc5921 chan21 mymask dropdeg True im2 summary im2 close ia close ngc5921 chan21 mymask has only RA and Dec axes Now apply this mask to the whole cube default immath expr ngc5921 clean image mask ngc5921 chan21 mymask gt 0 5 outfile ngc5921 cube imasked go For more on masks as used in LEL see or in above 6 6 Computing the Moments of an Image Cube immoments For spectral line datasets the output of the imaging process is an image cube with a frequency or velocity channel axis in addition to the two sky coordinate axes This can be most easily thought of as a series of image planes stacked along the spectral dimension CHAPTER 6 IMAGE ANALYSIS 242 A useful product to compute is to collapse the cube into a moment image by taking a linear combination of the individual planes N M x yi Y Wm
49. none gt gt gt kernel expandable parameter kwidth width of spectral smoothing kernel options int in channels default 5 example 5 or 10 seem to be popular for boxcar ignored for hanning fixed at 5 chans 0 will turn off gaussian or boxcar blmode mode for baseline fitting options str none auto list interact default none example blmode auto uses expandable parameters in addition to blpoly to run linefinder to determine line free regions USE WITH CARE May need to tweak the parameters thresh avg_limit and edge blmode interact allows adding and deleting mask regions by drawing rectangles on the plot with mouse Draw a rectangle with LEFT mouse to ADD the region to the mask and with RIGHT mouse to DELETE the region gt gt gt blmode expandable parameters thresh S N threshold for linefinder default 5 example a single channel S N ratio above which the channel is considered to be a detection avg_limit channel averaging for broad lines default 4 example a number of consecutive channels not greater than APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 305 this parameter can be averaged to search for broad lines edge channels to drop at beginning and end of spectrum default 0 example 1000 drops 1000 channels at beginning AND end 1000 500 drops 1000 from beginning and 500 from end Note For bad baselines threshold should be increased and avg_limit
50. plotcal reim png print Plotting calibration to file figfile saveinputs plotcal caltable plotcal reim saved plotcal First set the model print Setjy default setjy vis msfile print Use setjy to set IQU fluxes of polxfield field polxfield for spw in usespwlist fluxdensity polxiquv spw saveinputs setjy calprefixt setjy polspw spwt saved setjyQ Polarization X term calibration print PolCal X default polcal print Polarization R L Phase Calibration linear approx vis msfile Start with the G and D tables gaintable gtable ptable use settings from gaincal gaincurve usegaincurve opacity gainopacity APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS HHH HHH HH HHH HH HHH HH HH H HH H OF Output table caltable xtable previously set with setjy field polxfield spw selectdata False Solve for Chi poltype X solint inf combine scan reference antenna refant calrefant minimum SNR 3 minsnr 3 saveinputs polcal calprefix polcal X saved polcal Interpolate the gains onto Jupiter and others print Accum default accum print This will interpolate the gains onto Jupiter vis msfile tablein incrtable ftable calfield 1331 305 0137 331 set the name for the output interpolat
51. print and phase vs time Pause script if you are running in scriptmode user_check raw_input Return to continue script n And you can plot the SNR of the solution plotcal caltable ngc4826 tutorial 16apr98 fcal yaxis snr field You can also plotcal to file figfile ngc4826 tutorial 16apr98 fcal plotcal amp png plotcal caltable ngc4826 tutorial 16apr98 fcal yaxis amp field showgui False figfile figfile figfile ngc4826 tutorial 16apr98 fcal plotcal phase png plotcal caltable ngc4826 tutorial 16apr98 fcal yaxis phase field showgui False figfile figfile HHHHHHHHHHHR REET HHHHHAAAHHA AREER HR RRR H EAHA EERE A RRR AAA AR Correct the calibrater target source data Use new parm spwmap to apply gain solutions derived from spwidi to all other spwids print Applycal default applycal APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 464 print Applying calibration table ngc4826 tutorial i6apr98 fcal to data applycal vis ngc4826 tutorial ms field spw gaincurve False opacity 0 0 gaintable ngc4826 tutorial 16apr98 fcal spwmap 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 FERRARI RRE HARARE HAE AA Raa Check calibrated data print Plotxy default plotxy Here we plot the first of the NGC4826 fields unaveraged versus velocity Notice how the spw fit
52. 02 03 03 03 04 04 04 04 24 48 58 06 27 44 755 07 28 42 58 08 227 42 57 09 26 40 05 05 05 06 06 06 07 07 07 08 08 08 09 09 15 10 23 15 0 26 40 40 10 23 40 13 20 29 33 50 00 23 29 49 03 02 17 12 24 Sone 50 59 03 227 235 249 04 03 18 25 42 56 13 10 13 13 30 20 49 50 20 30 53 00 50 10 49 56 49 50 03 00 36 20 40 13 06 40 20 49 43 30 53 59 09 03 159 233 FOWDOOPOWHODVDWDOAPODOKFADDOWBOAARDGODDWDOWDWBOOFDADWDTIWVDODVDDOWBOrFRKHRDOWBHKHDWON Total integration time 27 to 22 54 20 ArrayID 0 Scan Fldld 23 16 10 0 1 0 23 48 00 0 2 1 23 55 20 0 3 2 00 23 49 9 4 3 00 30 00 1 5 4 00 50 20 0 6 1 00 57 49 9 7 2 01 11 59 9 8 5 01 25 00 1 9 3 01 31 10 0 10 4 01 51 30 0 11 6 02 04 30 0 12 7 02 19 10 0 13 1 02 26 00 0 14 2 02 39 30 0 15 5 02 52 20 1 16 3 03 01 00 0 17 6 03 14 10 0 18 7 03 29 39 9 19 1 03 36 40 0 20 2 03 51 30 1 21 6 04 04 50 0 22 7 04 20 40 0 23 1 04 27 39 9 24 2 04 44 40 0 25 8 04 58 30 1 26 6 05 33 39 9 27 7 05 49 49 9 28 1 06 00 30 0 29 8 06 14 59 9 30 6 06 29 20 0 31 7 06 46 00 0 32 1 06 57 00 0 33 8 07 12 20 0 34 6 07 30 10 1 35 7 07 44 30 0 36 8 08 00 39 9 37 6 08 15 19 9 38 7 08 29
53. 1 3 2 1 Aborting Synchronous Tasks o o 0200 44 vod A EE A ARA ak aie A oS 44 1 34 Running Tasks Asynchronously o 00 eee ee eee 45 1 3 4 1 Monitoring Asynchronous Tasks 1 3 4 2 Aborting Asynchronous Tasks 0 0 2 02005 47 odd oh GH ROE a da Bo BE E 47 1 3 5 1 The scope of parameters in CASA oaoa aaa a 49 1 3 5 2 The default Command 2 a 49 1 3 5 3 The go Commands ias ria es aa 50 1 3 5 4 The inp Command oaaae 51 1 3 5 5 The saveinputs Command o oaa a 53 1 3 5 6 The tget Command 2 000000004 55 E E wa ei Ae ks ee So ee Ge de 56 yai Ae e Gale ee Bate cele BO a Ped hoe Bee eS 57 be p Roe ee Be tee ee ed ae ee dee 57 1 4 1 Your command line history 2 2 0 0 0 ce ee 58 A ote aa te te ee Be Ge eg 58 1 4 2 1 Starup options for the logger o o 60 1 4 2 2 Setting priority levels in the logger 61 1 43 Where are my data in CASA 2 0 0 0 0 00000 ee eee 62 1 4 3 1 How do I get rid of my data in CASA o 63 1 4 4 What s in my data 2 2 ee 64 oe OY Peas ee PCR OE LER RE wee 64 kone ROR ie a s BoP eA AE ct Bata S 64 1 5 1 Loading Data into CASA e eee 65 1 5 1 1 VLA Filling data from VLA archive format 66 1 5 1 2 Filling data from UVFITS format 0 0 66 sb RR A a be a ek ele eo 66 1 5 1 4 Concatenation of m
54. 2003 1 31 08 05 23 applytsys Apply data scaling and weight scaling by nominal sensitivity Tsys default True Strongly recommended autocorr import autocorrelations to ms default gt False no autocorrelations antnamescheme old or new antenna names default gt new gives antnenna names VA04 or EA13 for VLA telescopse 04 and 13 EVLA old gives names 04 or 13 async Run asynchronously default False do not run asychronously Constructor Docstring None 36 BETA ALERT If you type help task without quotes around the task name you will get two copies of the help with alot of extraneous stuff This is a bug introduced in 2 4 0 and will be fixed in later releases You can also get the short help for a CASA tool method by typing help tool method CASA lt 46 gt help ia subimage gt help ia subimage Help on built in function subimage subimage Create a sub image from a region of the image outfile region mask dropdeg false overwrite false list true For a full list of keywords associated with the various tools see the CASA User Reference Manual BETA ALERT The User Reference Manual currently covers only tools not tasks CHAPTER 1 INTRODUCTION 37 1 2 8 3 help and PAGER Your PAGER environment variable determines how help is displayed in the terminal window where you start CASA If you set your bash environment var
55. At str srcstat maxpos 0 str srcstat maxpos 1 Channel str srcstat print srcstat maxposf print print Off Source Rms str im_offrms16 print Signal to Noise ratio str im_srcmax16 im_offrms16 print print Off Line Rms str im_offlinerms16 print Signal to Noise ratio str im_srcmax16 im_offlinerms16 Note previous regression values using this script STM 2008 06 04 were srcmax16 1 45868253708 immax 169 420959473 imrms 14 3375244141 offrms16 0 0438643493782 ttofflinerms16 0 0544108718199 Could print out comparison print print Src image max 16apr98 str im_srcmax16 was str srcmax16 print Off src rms 16apr98 str im_offrms16 was str offrms16 print Off line rms 16apr98 str im_offlinerms16 was str offlinerms16 print Moment 0 max 16apr98 str thistest_immax was str immax print Moment 0 rms 16apr98 str thistest_imrms was str imrms print print Done with NGC4826 Tutorial FERRARI RRA AHA AR AAR Ra Appendix G CASA Dictionaries BETA ALERT These tend to become out of date as we add new tasks or change names G 1 AIPS CASA dictionary Please see e https wikio nrao edu bin view Software CASA AIPSDictionary BETA ALERT This link is out of date and refers mostly to the Toolkit We will update this with
56. CASAPATH split O 0 print pathname BETA ALERT Previous to release 2 4 0 this was called AIPSPATH CHAPTER 1 INTRODUCTION 30 1 2 2 Starting CASA After having run the appropriate casainit script CASA is started by typing casapy on the UNIX command line e g casapy After startup information you should get an Python CASA lt 1 gt command prompt in the xterm window where you started CASA CASA will take approximately 10 seconds to initialize at startup in a new working directory subsequent startups are faster CASA is active when you get a CASA lt 1 gt prompt in the command line interface You will also see a logger GUI appear on your Desktop usually near the upper left Note Under MacOSX the logger will appear in a Console window You also have the option of starting CASA with various logger options see 1 4 2 1 For example if you are running remotely in a terminal window without an X11 connection or if you just do not want to see the logger GUI and want the logger messages to come to your terminal do casapy nologger log2term See for information on the logger in general 1 2 3 Ending CASA You can exit CASA by typing quit This will bring up the query Do you really want to exit y n to give you a chance in case you did not mean to exit You can also quit using exit or CTRL D If you don t want to see the question Do you really want to exit y n then just type Exit or exit and C
57. False Apply internal VLA antenna gain curve correction opacity 0 0 Opacity correction to apply nepers parang False Apply parallactic angle correction async False Data selection is done through the standard field spw and selectdata expandable sub parameters see 2 6 The bulk of the other parameters are the standard solver parameters See above for a description of these The gaintype parameter selects the type of gain solution to compute The choices are T G and GSPLINE The G and T options solve for independent complex gains in each solution interval classic AIPS style with T enforcing a single polarization independent gain for each co polar correlation e g RR and LL or XX and YY and G having independent gains for these See 4 4 3 1 for a more detailed description of G solutions and 4 4 3 2 for more on T The gt GSPLINE fits cubic splines to the gain as a function of time See 4 4 3 3 for more on this option 4 4 3 1 Polarization dependent Gain G Systematic time dependent complex gain errors are almost always the dominant calibration effect and a solution for them is almost always necessary before proceeding with any other calibration Traditionally this calibration type has been a catch all for a variety of similar effects including the relative amplitude and phase gain for each antenna phase and amplitude drifts in the electronics of each antenna
58. Input calibration table caltable ae Output calibration table field de Field name list smoothtype median Smoothing filter to use smoothtime 60 0 Smoothing time sec async False if True run in the background prompt is freed The smoothing will use the smoothtime and smoothtype parameters to determine the new data points which will replace the previous points on the same time sampling grid as for the tablein solutions The currently supported smoothtype options e mean use the mean of the points within the window defined by smoothtime a boxcar average e median use the median of the points within the window defined by smoothtime most useful when many points lie in the interval CHAPTER 4 SYNTHESIS CALIBRATION 169 Note that smoothtime defines the width of the time window that is used for the smoothing BETA ALERT Note that smoothcal currently smooths by field and spw and thus you cannot smooth solutions from different sources or bands together into one solution hd CASA Plotter Mark Regon Pay vag tocate out D0 0 Bla Figure 4 6 The amp of gain solutions for NGC4826 before top and after bottom smoothing with a 7200 sec smoothtime and smoothtype mean Note that the first solution is in a different spw and on a different source and is not smoothed together with the subsequent solutions An example using the smoothcal task to smooth an exist
59. NEW imfit a task to do image plane Gaussian fitting 6 4 The immath task now includes the options to make spectral index linearly polarized intensity and angle images 6 5 e New viewer features The viewer now includes a Region Manager tool that can save the last box or polygon region to a file In addition the pixel coordinates under the cursor are displayed in the Position Tracking panel 7 WARNING Some of these changes will require scripts from Patch 1 or earlier to be changed In some cases you may not get an error but will get noticeably different behavior e g from the solint changes in Calibration CHAPTER 1 INTRODUCTION 28 1 2 CASA Basics Information for First Time Users This section assumes that CASA has been installed on your LINUX or OSX system See Appendix C for instructions on how to obtain and install CASA 1 2 1 Before Starting CASA First you will most likely be starting CASA running from a working directory that has your data in it or at least where you want your output to go It is easiest to start from there rather than changing directories inside casapy BETA ALERT There is at least one task plotxy that fails if the path to your working directory contains spaces in its name e g users smyers MyTest is fine but users smyers My Test is not We will try to bulletproof the file handling better If you have done a default installation under Linux using rpms or on the
60. The off line std deviation 5 3f K off_stat stddev which should give The off line std deviation 0 047 K HHHHHHHHHHHHHHHHHEH HH On line Statistics HHHHHHHHHHHHHHHHHH EHH Now do the line region Continue setting or resetting parameters masklist 3900 4200 line_stat sdstat look at these line_stat which gives eqw 73 335154614280981 max 0 92909121513366699 mean 0 22636228799819946 median 0 10317134857177734 min 0 13283586502075195 rms 0 35585442185401917 stddev 0 27503398060798645 sum 68 135047912597656 of particular interest are the max value print The on line maximum 5 3f K line_stat max which gives The on line maximum 0 929 K and the estimated equivalent width in channels which is the sum max print The estimated equivalent width 5 1f channels line_stat eqw which gives The estimated equivalent width 73 3 channels HHHHHHHHHHHHHHHHHE AHH Line Fitting HHHHHHHHHHHHHHHHHH HHH 336 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING Now we are ready to do some line fitting Default default s Set our sdfile Stick to fluxunit fluxunit specunit We will fitmode A single nfit 1 Leave th now exc edge 10 Lets see plotlevel Save the fitfile Go ahead fit_stat s If you h like
61. amplitude response as a function of elevation gain curve and tropospheric amplitude and phase effects In CASA it is possible to handle many of these effects separately as available information and circumstances warrant but it is still possible to solve for the net effect using calibration type G Generally speaking type G can represent any per spectral window multiplicative polarization and time dependent complex gain effect downstream of the polarizers Polarization independent effects CHAPTER 4 SYNTHESIS CALIBRATION 152 upstream of the polarizers may also be treated with G Multi channel data per spectral window will be averaged in frequency before solving use calibration type B to solve for frequency dependent effects within each spectral window To solve for G on say fields 1 amp 2 on a 90s timescale and apply e g gain curve corrections gaincal data ms caltable cal G Write solutions to disk file cal G field 0 1 Restrict field selection solint 90 0 Solve for phase and amp on a 90s timescale gaincurve True Note gaincurve False by default refant 3 plotcal cal G amp Inspect solutions These G solution will be referenced to antenna 4 Choose a well behaved antenna that is located near the center of the array for the reference antenna For non polarization datasets reference antennas need not be specified although you can if you want If no reference antenna is
62. and are discussed below in 5 4 1 When using widefield the position and image size of each image must be specified This can be done in two ways The first method uses input from a text file outlierfile For example vis wfield ms name of input visibility file imagename w Pre name of output images outlierfile setup txt Text file with image names sizes centers imsize 256 256 Image size in pixels nx ny symmetric for single value cell 1 0arcsec The image cell size in arcseconds x y phasecenter a Field Identififier or direction of the image phase center The cell is identical for all fields and imsize and phasecenter are not used The output image names will be wf main wf outl etc The file outlierfile setup txt is an AIPS style field file used to locate outlier fields For example C main 2048 2048 13 27 20 98 43 26 28 0 Main field with image size and phase center C outi 128 128 13 30 52 158 43 23 08 00 First outlier field specification etc will make a big main image with outliers The C in column 1 must be present although it not presently used The alternative input needing no additional outlier file versus imsize plus phasecenter is CHAPTER 5 SYNTHESIS IMAGING 220 vis wfield ms name of input visibility file imagename w Pre name of output images outlierfile image_setup txt Text file with image names sizes centers imsize 2048 204
63. blc 126 128 O 23 data array 0 00938627 0 01487772 0 00955847 0 01688832 0 00696965 0 01501907 0 00460964 0 01220793 0 00358087 0 00990202 mask array True True True True True True True True True True dtype bool trc 130 129 0 23 unit Jy beam ra mn CASA lt 15 gt print xval data 0 1 0 0148777160794 In this example a rectangular box was extracted and you can see the order in the array and how to address specific elements 6 9 Regridding an Image imregrid It is occasionally necessary to regrid an image onto a new coordinate system The imregrid task will regrid one im age onto the coordinate system of another creating an out put image In this task the user need only specify the names of the input template and output images Inside the Toolkit More complex coordinate system and image regridding operation can be carried out in the toolkit The coordsys cs tool and the ia regrid method are the relevant components CHAPTER 6 IMAGE ANALYSIS 251 If the user needs to do more complex operations such as regridding an image onto an arbitrary but known coor dinate system changing from Equatorial to Galactic coor dinates or precessing Equinoxes the CASA toolkit can be used see sidebox Some of these facilities will eventually be provided in task form The default inputs are imregrid
64. default none Must be supplied example archivefiles AP314_A959519 xp1 example archivefiles AP314_A950519 xp1 AP314_A950519 xp2 vis Name of output visibility file default none Must be supplied example vis NGC7538 ms Will not over write existing ms of same name A backup flag file version Original will be made in vis flagversions See help flagmanager bandname VLA Frequency band default gt all bands example bandname K Options 4 48 96 MHz P 298 345 MHz L 1 15 1 75 GHz C 4 2 5 1 GHz X 6 8 9 6 GHz U 13 5 16 3 GHz K 20 8 25 8 GHz Q 38 51 GHz frequencytol Tolerance in frequency shift in making spectral windows default gt 150000 Hz For Doppler shifted data lt 10000 Hz may CHAPTER 1 INTRODUCTION may produce too many unnecessary spectral windows example frequencytol 1500000 0 units Hz project Project name to import from archive files default gt all projects in file example project AL519 project al519 or AL519 will work Do not include leading zeros project AL0519 will not work starttime Time after which data will be considered for importing default gt all Date must be included syntax starttime 2003 1 31 05 05 23 stoptime Time before which data will be considered for importing default gt all Date must be included syntax stoptime
65. fluxscale The G or T solutions obtained from calibrators for which the flux density was unknown and assumed to be 1 Jansky are correct in a time and antenna relative sense but are mis scaled by a factor equal to the inverse of the square root of the true flux density This scaling can be corrected by enforcing the constraint that mean gain amplitudes determined from calibrators of unknown flux density should be the same as determined from those with known flux densities The fluxscale task exists for this purpose The inputs for fluxscale are fluxscale Bootstrap the flux density scale from standard calibrators vis a Name of input visibility file caltable ix Name of input calibration table fluxtable ad Name of output flux scaled calibration table reference gt Reference field name s transfer flux scale FROM transfer 19 Transfer field name s transfer flux scale TO gt all append False Append solutions refspwmap 1 Scale across spectral window boundaries See help fluxscale async z False If true the taskname must be started using fluxscale Before running fluxscale one must have first run setjy for the reference sources and run a gaincal on both reference and transfer fields After running fluxscale the output fluxtable caltable will have been scaled such that the correct scaling will be applied to the transfer sources For example given a G table e g cal
66. imstat imagename momzeroimage momzerostats imstat imagename momoneimage momonestats imstat fo oooooooooooooooooooooooooooooooooooooooooooooooosooo s Now view the moments if scriptmode print View image Moments viewer momzeroimage print You can add mom 1 image momoneimage print as a contour plot user_check raw_input Return to continue script n fo ooooooooooooooooooooooooooooooooooooosoooosooooosooo Set up an output logfile import datetime datestring datetime datetime isoformat datetime datetime today outfile out prefix datestringt log logfile open outfile w print gt gt logfile Results for prefixt print gt gt logfile Can do some image statistics if you wish Treat this like a regression script 410 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS WARNING currently requires toolkit print NGC5921 results print print gt gt logfile NGC5921 results print gt gt logfile Use the ms tool to get max of the MSs Eventually should be available from a task Pull the max cal amp value out of the MS if you split this ms open calsplitms thistest_cal max ms range amplitude get amplitude ms close oldtest_cal 34 0338668823 diff_cal abs oldtest_cal thistest_cal oldtest_cal p
67. lt description gt lt value gt False lt value gt lt param gt lt param type any name mask gt lt description gt cleanbox es mask image s and or region s used in cleaning lt description gt lt any type variant gt lt value type stringArray gt lt value gt lt param gt lt param type int name nchan subparam true gt lt description gt Number of channels planes in output image lt description gt lt value gt 1 lt value gt lt param gt lt param type any name start subparam true gt lt description gt First channel in input to use lt description gt lt any type variant gt lt value type int gt 0 lt value gt lt param gt lt param type any name width subparam true gt lt description gt Number of input channels to average lt description gt lt any type variant gt lt value type int gt 1 lt value gt lt param gt lt param type intArray name imsize gt lt description gt x and y image size in pixels symmetric for single value lt description gt lt value type vector gt lt value gt 256 lt value gt lt value gt 256 lt value gt lt value gt lt param gt APPENDIX H APPENDIX WRITING TASKS IN CASA 485 lt param type doubleArray name cell units arcsec gt lt description gt x and y cell size default unit arcsec lt description gt lt value type vector gt lt value gt 1 0 lt value gt lt value gt 1 0 lt value gt lt
68. opacity 0 0 Append phase calibrator s solutions no uvrange to the same table gaincal vis ngc7538_XBAND ms caltable cal G field 2 solint 60 0 refant 10 selectdata True uvrange append True gaincurve False opacity 0 0 Fluxscale fluxscale vis ngc7538_XBAND ms caltable cal G reference 0137 331 transfer 2230 697 fluxtable cal Gflx append False while the following illustrates the use of of a model CHAPTER 4 SYNTHESIS CALIBRATION 141 METHOD 2 use a resolved model copied from the data respository for 3C48 and no uvrange NB detailed freq dep flux scaling TBD Copy the model image 3C48_X im to the working directory first setjy vis ngc7538_XBAND ms field 0 modimage 3C48_X im Solutions on both calibrators with no uvrange gaincal vis ngc7538_XBAND ms caltable cal G2 field 0 2 solint 60 0 refant 10 append False gaincurve False opacity 0 0 Fluxscale fluxscale vis ngc7538_XBAND ms caltable cal G2 reference 0137 331 transfer 2230 697 fluxtable cal G2f1x append False Both methods give 2230 flux densities 0 7 Jy in good agreement with AIPS 4 3 5 Other a priori Calibrations and Corrections Other a priori calibrations will be added to the calibrater cb tool in the near future These will include antenna position phase corrections syste
69. over the two coordinate axes in a specified region For example using the NGC5921 image cube with 46 channels immath outfile ngc5921 demo spectrum all mode evalexpr expr rebin ngc5921 demo clean image 256 256 1 1 The resulting image has shape 1 1 1 46 as desired You can view this with the viewer and will see a 1 D spectrum One can also do this with a box immath outfile ngc5921 demo spectrum box mode evalexpr expr rebin ngc5921 demo clean image 256 256 1 1 box 118 118 141 141 BETA ALERT One cannot specify a region without it collapsing the channel axis even when told to use all axes or channels BETA ALERT The following uses the toolkit 6 12 You can make an ascii file containing only the values no other info though ia open ngc5921 demo spectrum all ia toASCII ngc5921 demo spectrum all ascii You can also extract to a record inside Python myspec ia torecord which you can then manipulate in Python CHAPTER 6 IMAGE ANALYSIS 240 6 5 2 Using masks in immath The mask parameter is used inside immath to apply a mask to all the images used in expr before calculations are done if you are curious it uses the ia subimage tool method to make virtual images that are then input in the LEL to the ia imagecalc method For example lets assume that we have made a single channel image using clean for the NGC5921 data see Appendix F 1 default cle
70. panels that appear when the viewer is called with the NGC5921 Measurement Set viewer ngc5921 usecase ms 7 1 1 Running the CASA viewer outside casapy casaviewer is the name of the stand alone viewer application that is available with a CASA installation From the operating system prompt the following commands are equivalent to the casapy task commands given previously casaviewer amp casaviewer ms_filename amp casaviewer image_filename amp casaviewer restore_filename amp CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 259 casaviewer image_filename contour amp casaviewer image_filename 2 lel amp 7 2 The viewer GUI The CASA viewer application consists of a number of graphical user interface GUI windows that respond to mouse and keyboard input Here we describe the Viewer Display Panel and the Load Data window 7 2 4 They are used for both image and MS viewing Several other windows are context specific and are described in the sections on viewing images 8 and Measurement Sets 7 4 7 2 1 The Viewer Display Panel The Viewer Display Panel is the the window that actually displays the image or MS This is shown in the left panels of Figures 7 1 and 7 2 Note that this panel is the same whether an image or MS is being displayed At the top of the Viewer Display Panel are the menus e Data Open choose a data file to load and display Register select de sel
71. passcal none data were observed with online bandpass correction NOTE This data has been filled into MIRIAD line length correction done and then exported as separate files for each source 3c273 was not line length corrected since it was observed for such a short amount of time that it did not need it From miriad source Vlsr 408 delta V is 20 km s HHH HH HHH HH OH FORERO HAA EERE AHR AE HHA EAA RAE Import and concatenate sources HHEHHHHAAHHHAAHHHEAAH HAAR AHH HARA aH HAA aH HAR AHA RHR AR AAR USB spectral windows written separately by miriad for 16apr98 Assumes these are in sub directory called fitsfiles of working directory print Importuvfits 16apr98 default importuvfits print Starting from the uvfits files exported by miriad print The USB spectral windows were written separately by miriad for 16apr98 We could read in each of the individual fits files as example below this works well if you only have one or two files to read but here we have many so instead we use some useful pythonease to simplify the commands importuvfits fitsfile fitsfiles 3c273 fits5 vis ngc4826 tutorial 3c273 5 ms Tutorial Note For the loop to work the high end of range must be 1 number of actual files for i in range 5 9 importuvfits fitsfile fitsfiles 3c273 fits str i vis ngc4826 tutorial 3c273 str i ms for i in range 9 17 i
72. rcParams verbose False or True At the least we should make some of the output less cryptic Strip off leading and trailing whitespace on string parameters 5 SDtasks general issues The SDtasks work off of files saved onto disk in one of the scantable supported formats It might be useful to be able to work off of scantables in memory passing the objects but this would require changes to the tasking system Note that this behavior is consistent throughout the casapy tasks 6 sdaverage and sdcal averageall True is still experimental since test was insufficient because of a lack of test data APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 364 7 sdfit Only way to handle multi IFs is to set fitmode auto linefinder is applied for each spectra and derives initial guesses For fitmode list there are no way to give initial guesses for each IFs by hand 8 sdplot Only handles included JPL line catalog Also see sd plotter issues above Appendix B Simulation BETA ALERT The simulation capabilities are currently under development What we do have is mostly at the Toolkit level We have only a single task almasimmos at the present time Stay tuned For the Beta Release we include this chapter in the Appendix for the use of telescope commissioners and software developers The capability for simulating observations and datasets from the EVLA and ALMA are an important use case for Inside the Toolkit
73. solint 30 0 minsnr 1 0 print Calibrating amplitudes and phases on 30s timescale Do not need to normalize let gains float solnorm False gaincal It is useful to put this up in plotcal print PlotCal default plotcal caltable selfcaltabl multiplot True yaxis amp plotcal O print pr Na a SSSR Sa as print Plotcal print Looking at amplitude in self cal table caltable Pause script if you are running in scriptmode if scriptmode user_check raw_input Return to continue script n yaxis phase plotcal print we print Plotcal 444 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 445 print Looking at phases in self cal table caltable Pause script if you are running in scriptmode if scriptmode user_check raw_input Return to continue scriptin Correct the data no need for interpolation this stage print ApplyCal default applycal vis srcsplitms print Will apply self cal table to over write CORRECTED_DATA in MS gaintable selfcaltabi gaincurve False opacity 0 0 field spw selectdata False calwt True applycal Self cal is now in CORRECTED_DATA column of split ms Use Plotxy to look at the self calibrated data print Plotxy default plotxy vis srcsplitms selectdata True field JUPITER correlation RR LL xaxis uvd
74. the application of the gain curves if gaincurve True is allowed only if the VLA is set as the telescope of observation in the MS otherwise an error will be generated Set gaincurve False if you are not using VLA data A general mechanism for incorporating gaincurve information for other arrays will be made available in future releases Also note that the VLA gain curves are the most recent ones that are also supplied in AIPS Caution should be used in applying these gaincurve corrections to VLA data taken before 2001 as antenna changes were poorly tracked previous to this time We will include gain curves for EVLA antennas when those are measured and become available CHAPTER 4 SYNTHESIS CALIBRATION 136 4 3 3 Atmospheric Optical Depth Correction The troposphere is not completely transparent At high radio frequencies gt 15 GHz water vapor and molecular oxygen begin to have a substantial effect on radio observations According to the physics of radiative transmission the effect is threefold First radio waves from astronomical sources are absorbed and therefore attenuated before reaching the antenna Second since a good absorber is also a good emitter significant noise like power will be added to the overall system noise Finally the optical path length through the troposphere introduces a time dependent phase error In all cases the effects become worse at lower elevations due to the increased air mass through which the antenna is l
75. the auto parentheses feature of IPython can not be used in scripts that is you should make sure all function calls have any opening and closing parentheses file is script py My script to plot the observed visibilities plotxy ngc5921 ms uvdist yaxis defaults to amplitude This can be done by using the execfile command to execute this script execfile will execute the script as though you had typed the lines at the CASA prompt CASA 5 execfile script py gt execfile script py APPENDIX D APPENDIX PYTHON AND CASA 383 D 12 How do I exit from CASA You can exit CASA by using the quit command This will bring up the query Do you really want to exit y n to give you a chance in case you did not mean to exit You can also quit using exit or CTRL D If you don t want to see the question Do you really want to exit y n then just type Exit or exit followed by return and CASA will stop right then and there Appendix E The Measurement Equation and Calibration The visibilities measured by an interferometer must be calibrated before formation of an image This is because the wavefronts received and processed by the observational hardware have been corrupted by a variety of effects These include but are not exclusive to the effects of transmission through the atmosphere the imperfect details amplified electronic digital signal and transmission through the signal processing syste
76. the x surface as a function of the component s relative direction parameters has a shape very much like the inverse of the absolute value of the dirty image of the field Any peak in this image positive or negative corresponds to a local x minimum that could conceivable capture the fit It is the user s responsibility to ensure that the correct minimum does the capturing Currently uvmodelfit relies on the likelihood that the source is very near the phase center within a beamwidth and or the user s savvy in specifying the starting parameters This fairly serious CHAPTER 4 SYNTHESIS CALIBRATION 185 constraint will soon be relieved somewhat by enabling a rudimentary form of uv plane weighting to increase the likelihood that the starting guess is on a slope in the correct x valley Improvements in the works for visibility model fitting include e User specifiable uv plane weighting e Additional component shapes including elliptical disks rings and optically thin spheroids e Optional calibration pre application e Multiple components The handling of more than one component depends mostly on efficient means of managing the list itself not easy in command line options which are currently under development e Combined component and calibration fitting Example see Figure 4 10 Note It s best to channel average the data if many channels before running a modelfit split ngc5921 ms 1445 099_avg ms
77. then the output image names will be ngc5921 usecase moments integrated and ngc5921 usecase moments respectively The axis parameter sets the axis along which the moment is collapsed or calculated Choices are ra dec lat long spectral or stokes A standard moment 0 or moment 1 image of a spectral cube would use the default choice spectral One could make a position velocity map by setting ra or dec The includepix and excludepix parameters are used to set ranges for the inclusion and exclusion of pixels based on values For example includepix 0 05 100 0 will include pixels with values from 50 mJy to 1000 Jy and excludepix 100 0 1000 0 will exclude pixels with values from 100 to 1000 Jy 6 6 1 Hints for using immoments In order to make an unbiased moment 0 image do not put in any thresholding using includepix or excludepix This is so that the presumably zero mean noise fluctuations in off line parts of the image cube will cancel out If you image has large biases like a pronounced clean bowl due to missing large scale flux then your moment 0 image will be biased also It will be difficult to alleviate this with a threshold but you can try To make a usable moment 1 or higher image on the other hand it is critical to set a reasonable threshold to exclude noise from being added to the moment maps Something like a few times the rms noise level in the usable planes
78. thistest_imrms cubestats rms 0 oldtest_imrms 0 0020218724384903908 diff_imrms abs oldtest_imrms thistest_imrms oldtest_imrms print Clean image rms thistest_imrms print Previous rms oldtest_imrms print Difference fractional diff_imrms APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 413 print print gt gt logfile Clean image rms thistest_imrms print gt gt logfile Previous rms oldtest_imrms print gt gt logfile Difference fractional diff_imrms print gt gt logfile Now the moment images thistest_momzeromax momzerostats max 0 oldtest_momzeromax 1 40223777294 diff_momzeromax abs oldtest_momzeromax thistest_momzeromax oldtest_momzeromax print Moment 0 image max thistest_momzeromax print Previous m0 max oldtest_momzeromax print Difference fractional diff_momzeromax print print gt gt logfile Moment O image max thistest_momzeromax print gt gt logfile Previous m0 max oldtest_momzeromax print gt gt logfile Difference fractional diff_momzeromax print gt gt logfile thistest_momoneavg momonestats mean 0 oldtest_momoneavg 1479 77119646 diff_momoneavg abs oldtest_momoneavg thistest_momoneavg oldtest_momoneavg print Moment 1 image mean gt thistest_momoneavg print Previous mi mean oldtest_momoneavg prin
79. time mode channel type of selection channel continuum alg z clark deconvolution algorithm clark hogbom multiscale niter 500 number iterations nchan 1 number of channels to select startfreq gt 89GHz nrequency of first channel chanwidth 10MHz channel width imsize 250 250 Image pixel size x y cell 10arcsec Cell size e g 10arcsec stokes eL Stokes parameters to image weighting natural Weighting of visibilities display T True Plot simulation result images figures This task takes an input model image or list of components plus a list of antennas locations and sizes and simulates a particular observation specifies by mosaic setup and observing cycles and times This is currently very simplistic For example it does not include noise by default or gain errors but see the on line wiki documentation for how to do these The output is a MS suitable for further processing in CASA Its name implies that it is for ALMA but it is mostly general as you can give it any antenna setup it does have the ALMA observatory location hardwired in and sets the telescope name to 7 ALMA but thats about it The task could be easily modified for other instruments BETA ALERT Because of the experimental nature of this task we do not provide extensive documentation in this cookbook For this purpose there is an on line wiki devoted to this task https wikio
80. turned on whether raster or contour so make label adjustments within that tab To add a Contour overlay open the Load Data panel Use the Data menu or click on the Folder icon select the data set and select Contour See Figure for an example using NGC5921 CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER y SS Data Display Options RRR R Data Display Panel Tools View Tat a OGA A a alt o e Normal Compact H e ngc5921 demo moments weighted_coord contour masked Pixel 155 120 0 0 15 21 32 830 05 01 52 605 I 1607 99 km s Contours 1418 5 1455 6 1492 8 1529 9 XX ngc5921 demo moments integrated masked Pixel 155 120 0 0 15 21 32 830 05 01 52 605 I 1607 99 km s ngc5921 demo moments weighted_coord contour ngc5921 demo moments integre Display axes Hidden axes Basic Settings Aspect ratio fixed world IA Pixel treatment edge AY Resampling mode bilinear Ip Relative Contour Levels 0 2 0 4 0 6 0 8 Biv Base Contour Level 13813 F lt Unit Contour Level mee F lt 0 5 FX Line width F lt Dash negative contours true AY Dash positive contours false AY Line color blue AY ex Position tracking Axis labels Axis label properties Beam Ellipse Apply 8 x Dismiss ELA 273 Figure 7 10 The Viewer Display Panel left and Data Display Options panel right after overlaying a Contour Map of velocity on a Raster Image of intensity The image shown is for the mom
81. weighting for polarization average options none var 1 var spec weighted tsys 1 Tsys 2 weighted APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 321 outfile name of output dataset default outform output data format default ASAP Options ASAP MS2 SDFITS ASCIT overwrite overwrite the output file if already exists options bool True False default False WARNING if outform ASCII this parameter is ignored DESCRIPTION Task sdsave writes the single dish data to a disk file in specified format ASAP MS2 SDFITS ASCII It is possible to save the subset of the data by selecting scan numbers IF ids and field names The ASAP scantable format is recommended for further analysis using sd tool For further imaging using imager save the data to the Measurement Set MS2 A 2 1 12 sdscale Keyword arguments sdfile name of input SD dataset factor scaling factor default 1 no scaling scaletsys scaling of associated Tsys default False outfile output file name outfile will write the data to a file named lt sdfile gt _scaled lt factor gt default overwrite overwrite the output file if already exists options bool True False default False DESCRIPTION Task sdscale performs scaling of single dish spectra By setting scaletsys True associated Tsys is also scaled Tsys information are written into the file sdscale
82. 07 J2000 2 N5921_2 15 22 00 00 05 04 00 00 J2000 Thu Jul 5 17 20 55 2007 NORMAL ms summary Spectral Windows 1 unique spectral windows and 1 unique polarization setups SpwID Chans Frame Chi MHz Resoln kHz TotBW kHz Ref MHz Corrs 0 63 LSRK 1412 68608 24 4140625 1550 19688 1413 44902 RR LL Thu Jul 5 17 20 55 2007 NORMAL ms summary Antennas 27 ID 0 3 1 VLA N7 2 VLA W1 3 VLA W2 4 VLA El ID 4 7 5 VLA E3 6 VLA E9 7 VLA E6 8 VLA W8 ID 8 11 9 VLA N5 10 VLA W3 11 VLA N4 12 VLA W5 ID 12 15 13 VLA N3 14 VLA N1 15 VLA N2 16 VLA E7 ID 16 19 17 VLA E8 18 VLA W4 19 VLA E5 20 VLA W9 ID 20 24 21 VLA W6 22 VLA E4 24 VLA E2 25 VLA N6 ID 25 26 26 VLA N9 27 VLA N8 CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 87 Thu Jul 5 17 20 55 2007 NORMAL ms summary Tables rows 1 table absent MAIN 22653 ANTENNA 28 DATA_DESCRIPTION 1 DOPPLER 1 FEED 28 FIELD 3 FLAG_CMD 0 FREQ_OFFSET 1 HISTORY 310 OBSERVATION 1 POINTING 168 POLARIZATION 1 PROCESSOR 0 SOURCE 3 SPECTRAL_WINDOW 1 STATE 0 SYSCAL 1 WEATHER 1 Thu Jul 5 17 20 55 2007 NORMAL ms summary Thu Jul 5 17 20 55 2007 NORMAL ms close Readonly measurement
83. 08 2 LSRK 4 3962126e 10 LSRK 4 264542e 10 4096 4096 6104 6104 6104 6104 6104 6104 6104 6104 6104 6104 6104 6104 6104 6104 6104 6104 233 233 233 233 233 233 233 233 233 233 233 233 233 233 233 233 6104 2336 6104 2336 344 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 14 15 25 OrionS_ps 0 12 13 14 15 05 35 26 OrionS_psr 0 12 13 14 15 05 15 27 OrionS_ps 0 12 13 14 15 05 35 LSRK 4 159498e 10 LSRK 4 3422823e 10 02 04 27 4x 13 5 05 24 08 2 LSRK 4 3962126e 10 LSRK 4 264542e 10 LSRK 4 159498e 10 LSRK 4 3422823e 10 02 07 10 4x 13 5 05 24 08 2 LSRK 4 3962126e 10 LSRK 4 264542e 10 LSRK 4 159498e 10 LSRK 4 3422823e 10 02 09 51 4x 13 5 05 24 08 2 LSRK 4 3962126e 10 LSRK 4 264542e 10 LSRK 4 159498e 10 LSRK 4 3422823e 10 A 3 3 Scantable Manipulation 4096 4096 30 0s 4096 4096 4096 4096 30 0s 4096 4096 4096 4096 30 0s 4096 4096 4096 4096 6104 2336 6104 6104 6104 6104 6104 6104 2336 6104 6104 6104 6104 6104 6104 6104 2336 2336 2336 2336 2336 2336 2336 2336 2336 2336 2336 2336 345 Within ASAP data is stored in a scantable which holds all of the observational information and provides functionality to manipulate the data and information The building block of a scantable is an integration which is a single row of a scantable Each row c
84. 1 1 imsize 256 256 stokes I psfmode clark niter 500 imagermode mosaic scaletype SAULT cyclefactor 0 1 Another example of mosaic imaging this time using 3mm BIMA data is given in Appendix F 3 5 3 15 Heterogeneous imaging The clean task and underlying tools can now handle cases where there are multiple dish sizes and thus voltage patterns and primary beams in the array This is effected by using the dish sizes stored in the ANTENNA sub table of the MS Depending on how the data was written and imported into CASA the user may have to manually edit this table to insert the correct dish sizes e g using browsetable or the tb table tool BETA ALERT This feature is new in Patch 3 and has not been extensively tested Currently this works only for an MS where the OBSERVATORY keyword is CARMA ALMA or is unknown You must set imagermode mosaic with ftmachine mosaic even when imaging a single field to use this feature This will be improved and made easier to set and use in future releases 5 3 16 Polarization imaging The clean task handles full and partial Stokes polarization imaging through the setting of the stokes parameter B 2 9 The subsequent deconvolution of the polarization planes of the image and the search for clean components is controlled by the psfmode parameter 5 3 1 If the stokes parameter includes polarization planes other than I then choosing psfmode hogb
85. 1 5 Change depth in between of csclean cycle cyclespeedup 1 Cycle threshold doubles in this number of iterations These options are explained below In the CS mode cleaning is split into minor and major cycles For each field a minor cycle is performed using the PSF algorithm specified in psfmode 5 3 1 At major cycle breakpoints the points thus found are subtracted from the original visibilities A fast variant does a convolution using a FFT This will be faster for large numbers of visibilities If you want to be extra careful double the image size from that used for the Clark clean and set a CHAPTER 5 SYNTHESIS IMAGING 205 mask to clean only the inner quarter or less this is not done by default This is probably the best choice for high fidelity deconvolution of images without lots of large scale structure Note that when using the Cotton Schwab algorithm with a threshold B 3 12 there may be strange behavior when you hit the threshold with a major cycle In particular it may be above threshold again at the start of the next major cycle This is particularly noticeable when cleaning a cube where different channels will hit the threshold at different times BETA ALERT You will see a warning message in the logger similar to this Zero Pixels selected with a Flux limit of 0 000551377 and a maximum Residual of 0 00751239 whenever it find O pixels above the threshold This is normal and not a problem if you ve specifi
86. 1331 305 RR LL for all antennas print Use MarkRegion then draw boxes around points to flag print You can use ESC to drop last drawn box print When happy with boxes hit Flag to flag print You can repeat as necessary print print NOTE These flags will extend to the RL LR cross hands print Because of this the flagging will be slower than otherwise Pause script if you are running in scriptmode if scriptmode user_check raw_input Return to continue script n You can also use flagdata to do this non interactively see below Now look at the cross polar products correlation RL LR extendflag F plotxy O print Print A ee a print Looking at RL LR print Now flag any remaining bad data here Pause script if you are running in scriptmode if scriptmode user_check raw_input Return to continue script n Now do calibrater 0137 331 field 0137 331 correlation RR LL 424 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 425 xaxis uvdist spw 7 iteration antenna As of 2 3 0 Patch 3 you can extend the flags to the cross correlations But this slows things down immensely extendflag T extendcorr all title field plotxy O You 11 see a bunch of bad data along the bottom near zero amp Draw a box around some of it and use Locate Looks like much of it is Antenna 9 ID 8 in spw 1 print Print S
87. 16apr98 1310 323 split ms imagename ngc4826 tutorial 16apr98 cal clean cell 1 1 imsize 256 256 field 0 spw 0 7 threshold 10 mode mfs psfmode clark niter 100 stokes 1 You can look at this in the viewer viewer ngc4826 tutorial 16apr98 cal clean image HHEFHHHHHHHEEHHAEHHHEEHHEHEHEE HEHEHE HEERHEHEHHEE HAH HEHRAEHHHA HERRERA A ARRE IMAGING OF NGC4826 MOSAIC HEFHHHHHHHAEHHHEEHEEHEHHEAEHAEHEHHHAHREEHRHEEHEHHEE HAH HEHRAEHHEAEHRERHRH ARBRE Mosaic field spacing looks like F3 field 3 F2 field 2 F4 field 4 FO field 0 F1 field 1 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 467 F5 field 5 F6 field 6 H 4x64 channels 256 channels Primary Beam should be about 1 6 FWHM 7m dishes 2 7mm wavelength Resolution should be about 5 8 HEFHHHHEHHHHAEAHAHEEREHEAAEHEHAEHRRR AHH A AERA E RHR RR HHH AE RRA H RRR RRR R RS Image the target source mosaic print Clean NGC4826 default clean clean vis ngc4826 tutorial 16apr98 src split ms imagename ngc4826 tutorial 16apr98 src clean field 0 6 spw 073 cell 1 1 imsize 256 256 stokes I mode channel nchan 36 start 35 width 4 psfmode clark imagermode mosaic scaletype SAULT niter 10000 threshold 45mJy restfreq 115 2712GHz interactive F minpb
88. 18 4 33 53 54 8 Thu Jul 5 17 23 55 2007 NORMAL ms summary Tables MAIN 22653 rows ANTENNA 28 rows DATA_DESCRIPTION 1 row DOPPLER lt absent gt CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 89 FEED 28 rows FIELD 3 rows FLAG_CMD lt empty gt FREQ_OFFSET lt absent gt HISTORY 310 rows OBSERVATION 1 row POINTING 168 rows POLARIZATION 1 row PROCESSOR lt empty gt SOURCE 3 rows SPECTRAL_WINDOW 1 row STATE lt empty gt SYSCAL lt absent gt WEATHER lt absent gt Thu Jul 5 17 23 55 2007 NORMAL ms summary Thu Jul 5 17 23 55 2007 NORMAL ms close Readonly measurement set just detaching from file The most useful extra information that verbose True gives is the list of the scans in the dataset 2 4 Listing and manipulating MS metadata vishead BETA ALERT This is still a prototype task The default inputs are vishead List get and put metadata in a measurement set vis a Name of input visibility file mode summary options list summary get put async False For mode list the options are telescope observer project field freq_group_name gt spw_name schedule schedule_type release_date 2 5 Concatenating multiple datasets concat Once you have your data in the form of CASA Measurement Sets you can go ahead and process your data using the editing calibration and imaging tasks In some cases you wil
89. 19688 1413 44902 RR LL Thu Jul 5 17 23 55 2007 NORMAL ms summary Feeds 28 printing first row only Antenna Spectral Window Receptors Polarizations 1 1 2 R L Thu Jul 5 17 23 55 2007 NORMAL ms summary Antennas 27 ID Name Station Diam Long Lat 0 1 VLA N7 25 0 m 107 37 07 2 33 54 12 9 1 2 VLA W1 25 0 m 107 37 05 9 33 54 00 5 2 3 VLA W2 25 0 m 107 37 07 4 33 54 00 9 3 4 VLA El 25 0 m 107 37 05 7 33 53 59 2 4 5 VLA E3 25 0 m 107 37 02 8 33 54 00 5 5 6 VLA E9 25 0 m 107 36 45 1 33 53 53 6 6 7 VLA E6 25 0 m 107 36 55 6 33 53 57 7 7 8 VLA W8 25 0 m 107 37 21 6 33 53 53 0 8 9 VLA N5 25 0 m 107 37 06 7 33 54 08 0 9 10 VLA W3 25 0 m 107 37 08 9 33 54 00 1 10 11 VLA N4 25 0 m 107 37 06 5 33 54 06 1 11 12 VLA W5 25 0 m 107 37 13 0 33 53 57 8 12 13 VLA N3 25 0 m 107 37 06 3 33 54 04 8 13 14 VLA N1 25 0 m 107 37 06 0 33 54 01 8 14 15 VLA N2 25 0 m 107 37 06 2 33 54 03 5 15 16 VLA E7 25 0 m 107 36 52 4 33 53 56 5 16 17 VLA E8 25 0 m 107 36 48 9 33 53 55 1 17 18 VLA W4 25 0 m 107 37 10 8 33 53 59 1 18 19 VLA E5 25 0 m 107 36 58 4 33 53 58 8 19 20 VLA W9 25 0 m 107 37 25 1 33 53 51 0 20 21 VLA W6 25 0 m 107 37 15 6 33 53 56 4 21 22 VLA E4 25 0 m 107 37 00 8 33 53 59 7 23 24 VLA E2 25 0 m 107 37 04 4 33 54 01 1 24 25 VLA N6 25 0 m 107 37 06 9 33 54 10 3 25 26 VLA N9 25 0 m 107 37 07 8 33 54 19 0 26 27 VLA N8 25 0 m 107 37 07 5 33 54 15 8 27 28 VLA W7 25 0 m 107 37
90. 30 0 39 8 08 44 50 0 40 6 08 58 50 0 41 7 09 14 50 1 42 9 09 28 40 0 43 6 09 42 09 9 44 7 85133 2 seconds FieldName 0137 331 0813 482 0542 498 0437 296 VENUS 0813 482 0542 498 0521 166 0437 296 VENUS 1411 522 1331 305 0813 482 0542 498 0521 166 0437 296 1411 522 1331 305 0813 482 0542 498 1411 522 1331 305 0813 482 0542 498 MARS 1411 522 1331 305 0813 482 MARS 1411 522 1331 305 0813 482 MARS 1411 522 1331 305 MARS 1411 522 1331 305 MARS 1411 522 1331 305 NGC7027 1411 522 1331 305 Spwlds 0 1 0 1 0 1 0 1 0 1 0 1 o 1 o 1 0 1 o 1 o 1 0 1 0 1 Lo 1 0 1 0 1 0 1 0 1 o 1 o 1 0 1 o 1 0 1 0 1 0 1 0 1 0 1 0 1 o 1 0 1 o 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 o 1 o 1 o 1 o 1 0 1 420 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 09 56 19 9 09 58 10 0 45 9 NGC7027 10 12 59 9 10 14 50 0 46 8 MARS 10 27 09 9 10 28 50 0 47 6 1411 522 10 40 30 0 10 42 00 0 48 7 1331 305 10 56 10 0 10 57 50 0 49 9 NGC7027 11 28 30 0 11 35 30 0 50 10 NEPTUNE 11 48 20 0 11 50 10 0 51 6 1411 522 12 01 36 7 12 03 10 0 52 7 1331 305 12 35 33 3 12 37 40 0 53 11 URANUS 12 46 30 0 12 48 10 0 54 10 NEPTUNE 13 00 29 9 13 02 10 0 55 6 1411 522 13 15 23 3 13 17 10 1 56 9 NGC7027 13 33 43 3 13 35 40 0 57 11 URA
91. AND EDITING 113 Amplitude of Observed Data 0 10 20 30 40 50 60 Channels X m Figure 3 3 Multi panel display of visibility versus channel top antenna array configuration bottom left and the resulting uv coverage bottom right The commands to make these three panels respectively are 1 plotxy ngc5921 ms xaxis channel datacolumn data field 0 subplot 211 plotcolor plotsymbol go 2 plotxy ngc5921 ms xaxis x field 0 subplot 223 plotsymbol r 3 plotxy ngc5921 ms xaxis u yaxis v field 0 subplot 224 plotsymbol b figfile ngc5921_multiplot png 3 4 4 Averaging in plotxy The averaging parameters and sub parameters are averagemode vector Select averaging type vector scalar timebin 70 length of time in seconds to average default 0 or all crossscans False have time averaging cross over scans crossbls False have averaging cross over baselines CHAPTER 3 DATA EXAMINATION AND EDITING 114 crossarrays False have averaging cross over arrays stackspw e False stack multiple spw on top of each other width 21 number of channels to average default 1 or all allspw The choice of averagemode controls how the amplitudes are calculated in the average The default mode is vector where the complex average is formed by averaging the real and imagin
92. ASAP is also case sensitive with most parameters being upper case such as ASAP for the sd scantable save file format The SDtasks are generally more forgiving APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 291 Also beware Python s sensitivity to indenting A 2 Single Dish Analysis Tasks A set of single dish tasks is available for simplifying basic reduction activities Currently the list includes e sdaverage select calibrate and average SD data e sdsmooth smooth SD spectra e sdbaseline fit remove spectral baselines from SD data e sdcal combined the three tasks above to perform standard single dish processing all at once e sdcoadd merge co add multiple SD data e sdflag channel flagging of SD spectra e sdfit line fitting to SD spectra e sdlist print a summary of a SD dataset e sdmath do simple arithmetic for SD spectra e sdplot plotting of SD spectra including overlay of line catalog data e sdsave save SD data to different format e sdscale scale SD data e sdstat compute statistics of regions of SD spectra e sdtpimaging do a simple calibration and create an image from the total power raster scans All of the SDtasks work from a file on disk rather than from a scantable in memory as the ASAP toolkit does see s A 3 Inside the tasks we invoke a call to sd scantable to read in the data The scantable objects do not persist within CASA after completion of the
93. As an example we first solve for gain solutions for the flux density calibrator 3C286 observed in field 0 using a subset of antennas gaincal vis data ms caltable cal G field 0 selectdata True antenna 077 uvrange 0 15klambda solint 90 write solutions to cal G Select the flux density calibrator Expand other selectors antennas 0 7 limit uvrange to 0 15klambda on 90s timescales write solutions to table called cal G HHHH HH Now solve for other calibrator 0234 285 in field 1 using all antennas implicitly and append these solutions to the same table gaincal vis data ms caltable cal G write solutions to cal G field 1 solint 90 append T Set up to write to the same table Finally run fluxscale to adjust scaling fluxscale vis data ms caltable cal G Input table with unscaled cal solutions fluxtable cal Gflx Write scaled solutions to cal Gflx reference 3C286 Use 3c286 as ref with limited uvrange transfer 0234 285 Transfer scaling to 0234 285 The fluxscale calculation will be performed using only the antennas common to both fields but the result will be applied to all antennas on the transfer field Note that one can nominally get by only with the uvrange selection but you may find that you get strange effects from some antennas only having visibilities to a subset of the baselines and thus causing problems in
94. CASA This not only allows one to get an idea of the ca The simulator methods are in the sm pabilities of these instruments for doing science but also tool Many of the other tools are also provides benchmarks for the performance and utility of the helpful when constructing and ana software for processing realistic datasets To that end lyzing simulations we are developing the simulator sm tool as well as a series of simulation tasks B 1 Simulating ALMA with almasimmos BETA ALERT This is an experimental task that is under development Its functionality and parameters will be changing so check the on line documentation for the latest updates The inputs are almasimmos ALMA Mosaic simulation task Please see the on line documentation for this task project mysim name of simulated project modelimage A image name to derive simulate visibilities complist a8 componentlist table to derive simulated visibilities antennalist ae antenna position ascii file direction J2000 19h00m00 40d00m00 mosaic center direction nmosx 1 number of pointings along x 365 APPENDIX B APPENDIX SIMULATION 366 nmosy 1 number of pointings along y pointingspacing Sarcmin spacing in between beams refdate 2012 05 21 22 05 00 center time date of simulated observation totaltime 72008 total time of observation integration 10s integration sampling
95. Co Lo LO Lo Co o Lo o Lo o Lo Co Lo Lo Co Co Lo Lo o Lo o Lo Lo Co Os Lo Co o Lo Lo Lo o Co Co Lo Lo Lo Lo o Lo Lo Lo o Lo Co Co Lo 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 421 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 422 ID Name Right Ascension Declination Epoch 0 0137 331 01 37 41 30 33 09 35 13 J2000 1 0813 482 08 13 36 05 48 13 02 26 J2000 2 0542 498 05 42 36 14 49 51 07 23 J2000 3 0437 296 04 37 04 17 29 40 15 14 J2000 4 VENUS 04 06 54 11 22 30 35 91 J2000 5 0521 166 05 21 09 89 16 38 22 05 J2000 6 1411 522 14 11 20 65 52 12 09 14 J2000 7 1331 305 13 31 08 29 30 30 32 96 J2000 8 MARS 14 21 41 37 12 21 49 45 J2000 9 NGC7027 21 07 01 59 42 14 10 19 J2000 10 NEPTUNE 20 26 01 14 18 54 54 21 J2000 11 URANUS 21 15 42 83 16 35 05 59 J2000 12 JUPITER 00 55 34 04 04 45 44 71 J2000 Spectral Windows 2 unique spectral windows and 1 unique polarization setups SpwID Chans Frame Chi MHz Resoln kHz TotBW kHz Ref MHz Corrs 0 1 TOPO 4885 1 50000 50000 4885 1 RR RL LR LL 1 1 TOPO 4835 1 50000 50000 4835 1 RR RL LR LL Feeds 28 printing first row only Antenna Spectral Window Receptors Polarizations 1 1 2
96. Figure 7 3 the top row of icons for fast access to some of these menu items e folder Data Open shortcut show the Load Data panel e wrench Data Adjust shortcut show the Data Display Options Adjust panel e panels Data Register shortcut show the menu of loaded data e delete Data Close shortcut closes unloads selected data e new panel Display Panel New Panel e panel wrench Display Panel Panel Options show the Display Panel s options win dow e save save panel state to a restore file e restore restore panel state from a restore file e region save Tools Region Manager save control regions Note some of these newer buttons do not appear in older figures of this document e print Display Panel Print print data e magnifier box Zoom out all the way e magnifier plus Zoom in by a factor of 2 e magnifier minus Zoom out by a factor of 2 CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 261 a OO OR BDENIA Figure 7 3 The display panel s Main Toolbar appears directly below the menus and contains shortcut buttons for most of the frequently used menu items Dies ee a Figure 7 4 The Mouse Tool Bar allows you to assign separate mouse buttons to tools you control with the mouse within the image display area Initially zooming color adjustment and rectangular regions are assigned to the left middle and right mouse buttons respectively
97. For some reason we need to help it along with a mask maskline 50 0 fitfile sdusecase_orions_hc3n_kms fit fit_stat_kms sdfit Should give if in verbose mode 0 peak 0 811 K centre 27 134 km s FWHM 2 933 km s area 2 531 K km s with fit_stat_kms giving cent 27 133651733398438 0 016480101272463799 fwhm 2 93294358253479 0 038807671517133713 nfit 1 peak 0 81080895662307739 0 0092909494414925575 print The line fit parameters were print maximum 6 3f 7 6 3f K YA fit_stat_kms peak 0 0 fit_stat_kms peak 0 1 print center 6 2f 6 2f km s YN fit_stat_kms cent 0 0 fit_stat_kms cent 0 1 print FWHM 7 6 4f 6 4f km s fit_stat_kms fwhm 0 0 fit_stat_kms fwhm 0 1 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 339 The line fit parameters were maximum 0 811 0 009 K center 27 13 0 02 km s FWHM 2 9329 0 0388 km s HHEHHHHHHHHHHHAHHHEHHHHR EH End ORION S Use Case HHEHHHHHHHHHHHAHHHEHHRHHR EH A 2 2 2 Imaging of Total Power Raster Scans This example illustrates the use of sdtpimaging for the total power raster scans of the Moon taken at ATF load single dish module asap_init The data used here uid___X1e1_X3197_X1 ms is the total power raster scans of the Moon taken
98. G containing solutions for a flux density calibrator in this case 3C286 and for one or more gain calibrator sources with unknown flux densities in this example 0234 285 and 0323 022 fluxscale vis data ms caltable cal G Select input table CHAPTER 4 SYNTHESIS CALIBRATION 155 fluxtable cal Gflx Write scaled solutions to cal Gflx reference 3C286 3C286 flux calibrator transfer 0234 258 0323 022 Select calibrators to scale The output table cal Gf1lx contains solutions that are properly scaled for all calibrators Note that the assertion that the gain solutions are independent of the calibrator includes the as sumption that the gain amplitudes are strictly not systematically time dependent While synthesis antennas are designed as much as possible to achieve this goal in practice a number of effects conspire to frustrate it When relevant it is advisable to pre apply gaincurve and opacity cor rections when solving for the G solutions that will be flux scaled see 4 3 and 4 4 1 3 When the G solutions are essentially constant for each calibrator separately the fluxscale operation is likely to be robust The fluxscale task can be executed on either G or T solutions but it should only be used on one of these types if solutions exist for both and one was solved relative to the other use fluxscale only on the first of the two BETA ALERT
99. G solutions In principle any basic calibration type can be accumulated onto itself as long as the result of the accumulation matrix product is of the same type This is true of all the basic types except D Accumulation is currently supported for B G and T and in future F ionospheric Faraday rotation delay rate and perhaps others Accumulation of certain specialized types e g GSPLINE TOPAC etc onto the basic types will be supported in the near future The treatment of various calibration from ancillary data e g system temperatures weather data WVR etc as they become available will also make use of accumulate to achieve the net calibration Note that accumulation only makes sense if treatment of a uniquely incremental solution is required as described above or if a careful interpolation or sampling of a solution is desired In all other cases re solving for the type in question will suffice to form the net calibration of that type For example the product of an existing G solution and an amplitude and phase G self cal solved with the existing solution applied is equivalent to full amplitude and phase G self cal with no prior solution applied as long as the timescale of this solution is at least as short as that of the existing solution One obvious application is to calibrate the amplitudes and phases on different timescales during self calibration Here is a
100. I im expr 3C138_pcal stokes I go outfile Q im expr 3C138_pcal stokes Q go outfile U im expr 3C138_pcal stokes U go outfile V im expr 3C138_pcal stokes V go outfile pol_intensity stokes expr sqrt I im I im Q im Q im U im U im V im V im go 6 5 1 3 Primary beam correction uncorrection In a script using mode evalexpr you might want to assemble the string for expr using string variables that contain the names of files Since you need to include quotes inside the expr string use a different quote outside or escape the string e g For example to do a primary beam correction on the NGC5921 cube imname ngc5921 usecase clean imagename imname clean default immath clnimage imname image pbimage imname flux pbcorimage imname pbcor CHAPTER 6 IMAGE ANALYSIS 239 outfile pbcorimage expr clnimaget pbimaget pbimaget gt 0 1 immath Note that we did not use a minpb when we cleaned so we use the trick above to effectively set a cutoff in the primary beam flux image of 0 1 For more on LEL strings see AIPS Note 223 http aips2 nrao edu docs notes 223 223 html or in above 6 5 1 4 Spectral analysis One can make an integrated 1 d spectrum over the whole image by rebinning integrating
101. Mac with the CASA application then there should be a sh script called casapy in the usr bin area which is in your path This shell will set up its environment and run the version of casapy that it points to If this is how you set up the system then you need to nothing further and can run casapy Depending on your setup there may be other specially built versions available For example at the NRAO AOC the stable build can be started by running casapy test e g usr bin casapy test On some systems particularly if you have multiple versions installed to define environment vari ables and the casapy alias you will need to run one of the casainit shell scripts The location of the startup scripts for CASA will depend upon where you installed CASA on your system For a default installation this will likely be in usr lib casapy For example at the NRAO AOC the current release is executed as usr bin casapy and uses the pathname to usr lib casapy 23 0 6654 001 Sometimes you will have multiple non default versions for example various development versions For example at the NRAO AOC the stable build is in home casa Then to use this version In bash gt home casa casainit sh or for csh gt source home casa casainit csh depending on what shell you are running Bourne or t csh BETA ALERT If you want to run the casabrowser see 3 6 outside of the casapy shell then you will need to put the C
102. RHR ARERR RR An alternative is to mask the pbcor image before calculating moments The following block shows how to do this print Viewer viewer ngc4826 tutorial 16apr98 moments integrated TUTORIAL NOTES After loading change unit contour level in Data Display Options gui to something like 70 select region manager tool from tool drop down menu Then assign the sqiggly Polygon button to a mouse button by clicking on it with a mouse button Then draw a polygon region around galaxy emission avoiding edge regions and double click in the region you created Then in region manager tool select save to file and give file name momOmask rgn HH HH HH APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 471 print ImMoments masked print Creating masked moment 0 image ngc4826 tutorial 1i6apr98 moments integratedmasked immoments imagename ngc4826 tutorial 16apr98 src clean pbcor moments 0 axis spectral chans 7 28 region momOmask rgn outfile ngc4826 tutorial 16apr98 moments integratedmasked print Creating masked moment 1 image ngc4826 tutorial 1i6apr98 moments momimasked immoments imagename ngc4826 tutorial 16apr98 src clean pbcor masked moments 1 axis spectral includepix 0 2 1000 0 chans 7 28 region momOmask rgn outfile ngc4826 tutorial 16apr98 moments momimasked Now view
103. Range thistest_immax thistest_imrms print print Done with I Imaging and Selfcal fo ooooooooooooooooooooooooooooooooooooooooooooooooooooooo o Polarization Imaging fo oooooooooooooooooooooooooooooooooooooooooooooooooooooos o print Clean Polarization default clean print Now clean polarized data vis srcsplitms imagename polimname field spw mode mfs gain 0 1 Polarization stokes IQUV psfmode polclnalg imagermode polclnmode niter clniter threshold clnthreshold imsize clnimsize cell clncell weighting briggs robust 0 5 interactive True npercycle 100 saveinputs clean imagename clean saved clean print Print 2 212 222 2 EE print Clean print Final restored clean image is polimage APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS print Final clean model is polmodel print The clean residual image is polresid print Your final clean mask is polmask Polarization statistics print Final Pol Imstat default imstat imagename polimage on_statistics off_statistics lower right corner of the image clnimsize 288 288 onbox lower right corner of the image clnimsize 288 288 offbox 216 1 287 72 for stokes in I Q U V box onbox on_statisti
104. Rest freque Pointing ce Telescope Observer Date observation Axis Coord ngc5921 usecase clean image PagedImage ity Intensity s None None Jy beam eam eference J2000 eference LSRK ype RADIO ncy 1 42041e 09 Hz nter VLA TEST 1995 04 13 00 00 00 51 5254 arcsec 45 5987 arcsec 14 6417 deg 15 22 00 000000 05 04 00 000000 Coord value at pixel 232 Coord incr Units Type Name Proj Shape Tile Direction Right Ascension SIN 256 Direction Declination SIN 256 Stokes Stokes 1 Spectral Frequency 46 Velocity 64 15 22 00 000 64 05 04 00 000 1 I 8 1 41281e 09 1603 56 128 00 1 500000e 01 arcsec 128 00 1 500000e 01 arcsec 0 00 2 441406e 04 Hz 0 00 5 152860e 00 km s If you choose mode list you get the summary in the logger and a listing of keywords and values to the termi nal CASA lt 2 gt imhead ngc5921 usecase clean image mode list Available header items to modify General Retrieving object N5921_2 telescope VLA observer TEST epoch 1995 04 13 00 00 00 restfrequncy CHAPTER 6 IMAGE ANALYSIS 233 restfrequency 1420405752 0Hz projection SIN bunit Jy beam beam 51 5204238892arcsec 45 598236084arcsec 14 6546726227deg min 0 0104833962396 max 0 0523551553488 axes ctypel Right Ascension ctype2 Declination ctype3 Stokes ctype4 Frequency crpixi 128 0 crpix2 128 0 crpix3 0 0
105. See and for more on area selection Image plane selection is controlled by chans and stokes See for details on plane selction BETA ALERT As of Patch 2 LEL expressions as in expr use 0 based array indices 6 5 1 Examples for immath The following are examples using immath Note that the image names in the expr are assumed to refer to existing image files in the current working directory 6 5 1 1 Simple math Double all values in an image immath expr myimage im 2 outfile double im Take the sine of an image and add it to another CHAPTER 6 IMAGE ANALYSIS 237 immath expr SIN image2 im image1 im outfile newImage im Note that the two input images used in expr need to be the same size Add only the plane associated with the V Stokes value and the first channel together in two images immath expr imagei image2 chans 1 stokes V Select a single plane the 5th channel of the 3 D cube and subtract it from the original image default immath outfile ngc5921 chan5 image expr ngc5921 clean image chans 5 go default immath outfile ngc5921 clean sub5 image expr ngc5921 clean image ngc5921 chan5 image go Note that in this example the 2 D plane gets expanded out and the values are applied to each plane in the 3 D cube Select and save the inner 1 4 of an image for channels 40 42 44 as well as c
106. THE MEASUREMENT EQUATION AND CALIBRATION 386 treatment for similar observations with older arrays in order to reach the advertised dynamic ranges on strong sources In practice it is usually far too difficult to adequately measure most calibration effects absolutely as if in the laboratory for use in calibration The effects are usually far too changeable Instead the calibration is achieved by making observations of calibrator sources on the appropriate timescales for the relevant effects and solving the measurement equation for them using the fact that we have Nant Nant 1 2 measurements and only Nant factors to determine except for M which is only sparingly used Note By partitioning the calibration factors into a series of consecutive effects it might appear that the number of free parameters is some multiple of Nant but the relative algebra and timescales of the different effects as well as the the multiplicity of observed polarizations and channels compensate and it can be shown that the problem remains well determined until perhaps the effects are direction dependent within the field of view Limited solvers for such effects are under study the calibrater tool currently only handles effects which may be assumed constant within the field of view Corrections for the primary beam are handled in the imager tool Once determined these terms are used to correct the visibilities measured for the scientific target This procedure is
107. The GSPLINE option is not yet supported in fluxscale see 4 4 3 3 If the reference and transfer fields were observed in different spectral windows the refspwmap parameter may be used to achieve the scaling calculation across spectral window boundaries The refspwmap parameter functions similarly to the standard spwmap parameter 4 4 1 4 and takes a list of indices indicating the spectral window mapping for the reference fields such that refspwmap i j means that reference field amplitudes from spectral window j will be used for spectral window i Note You should be careful when you have a dataset with spectral windows with different band widths and you have observed the calibrators differently in the different spw The flux scaling will probably be different in windows with different bandwidths For example fluxscale vis data ms caltable cal G fluxtable cal Gflx reference 3C286 transfer 0234 258 0323 022 refspwmap 0 0 0 Select input table Write scaled solutions to cal Gflx 3C286 flux calibrator Select calibrators to scale Use spwid O scaling for spwids 1 amp 2 HH H HF will use spw 0 to scale the others while in fluxscale vis data ms caltable cal G Select input table fluxtable cal Gflx Write scaled solutions to cal Gflx reference 3C286 3C286 flux calibrator transfer 0234 285 0323 022 select calibrators to scale
108. These are currently CASA lt i gt sd scantable set_ lt TAB gt sd scantable set_dirframe sd scantable set_fluxunit sd scantable set_restfreqs sd scantable set_doppler sd scantable set_freqframe sd scantable set_selection sd scantable set_feedtype sd scantable set_instrument sd scantable set_unit For example sd scantable set_fluxunit sets the default units that describe the flux axis scans set_fluxunit K Set the flux unit for data to Kelvin Choices are K or Jy Note the scantable set_fluxunit function only changes the name of the current fluxunit To change fluxunits use scantable convert_flux as described in 4 3 4 2 instead currently you need to do some gymnastics for non AT telescopes Use sd scantable set_unit to set the units to be used on the spectral axis scans set_unit GHz Use GHZ as the spectral axis for plots The choices for the units are km s channel or Hz e g GHz MHz kHz Hz This does the proper conversion using the current frame and Doppler reference as can be seen when the spectrum is plotted You can use sd scantable set_freqframe to set the frame in which the frequency spectral axis is defined CASA lt 2 gt help sd scantable set_freqframe Help on method set_freqframe in module asap scantable set_freqframe self frame None unbound asap scantable scantable method Set the frame type of the Spectral Axis Parameters frame
109. Ve ct es en ea ne ae eS Gee ae 194 DE ge clic hes Ges th it Get Geet Fos Gs a ae BS 194 RE 195 o o fone Gk a ad gee Mee e 195 5 2 11 1 natural welghtidg o e o o 196 5 2 11 2 uniform Wwelghtidg e e e 196 5 2 11 3 superuniform weighting 197 5 2 11 4 radial weighting o 022020004 197 5 2 11 5 briggs weighting o 197 5 2 11 6 briggsabs weighting e e 198 5 212 Parameter vis 2 a dea d rs ra A ee ee h A A 198 Pere badd ee ER Se oe ee ee AA 198 5 3 Deconvolution using CLEAN clean o 0220 ee eee 199 5 3 1 Parameter psfmode 0 000000000000 0004 202 5 3 1 1 The clark algorithm 0 222200 202 5 3 1 2 The hogbom algorithm lt 2 b A e ay oe EES 202 5 3 1 3 The clarkstokes algorithm 202 Sec Helis hate SH os oh ee eas meee Gee ae E 203 chee ier E St Hho es a oe hee Se ae Re Eek ae a eke BS 203 bce Soke Berea oe SS te hee teed AA 204 5 3 4 1 Sub parameter cyclefactor o o 0000 205 5 3 4 2 Sub parameter cyclespeedupl o o 206 5 3 4 3 Sub parameter ftmachine 206 LA oh Rou et oe a do et 207 5 3 4 5 Sub parameter scaletypel o 00000004 207 5 3 4 6 The threshold revisitedl o e 0 222200 207 LA we Rhee
110. Version 2 2 For details on ASAP see the ASAP home page at ATNF e http www atnf csiro au computing software asap You can also download the ASAP User Guide and Reference Manual at this web site There is also a brief tutorial Note that within CASA the ASAP tools are prefaced with sd e g where it says in the ASAP User Guide to use scantable you will use sd scantable in CASA See A 3 for more information on the tools All of the ASAP functionality is available with a CASA installation In the following we outline how to access ASAP functionality within CASA with the tasks and tools and the data flow for standard use cases If you run into trouble be sure to check the list of known issues and features of ASAP and the SDtasks presented in A 5 first A 1 Guidelines for Use of ASAP and SDtasks in CASA A 1 1 Environment Variables There are a number of environment variables that the ASAP tools and thus the SDtasks use to help control their operation These are described in the ASAP User Guide as being in the asapre 288 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 289 file Within CASA these are contained in the Python dictionary sd rcParams and are accessible through its keys and values For SDtask users the most important are the verbose parameter controlling the display of detailed messages from the tools By default sd rcParams verbose True and you get lots of messages Also the scantable storag
111. Wea h a ea amp e a de srta E 208 eS eM hector Re gets okt Yee eevee e Ge ag ds e ewe te A 208 5 3 6 1 Setting clean boxes 2 2 208 5 3 6 2 Using clean box files 2 2 o 209 pa a 209 shoe a A ae wh ee we ae ae eh oS 209 Pepe ko ho Gh eo ea ee ee ee 209 paa kee eB e ee Se YRS 210 ih GRR Soe Se be ea eee eh ae ES ow 210 segs i de ote ets Git BLS Gaia Go Ee e a eS 210 ge She Sy op ce are a oh Hr Sac te Ode ea 210 5 3 12 Parameter threshold 0 0 0 00000 00002 eee eee 211 5 3 13 Interactive Cleaning Example 2 2 004 211 5 3 14 Mosaic imaging 2 e 214 5 3 15 Heterogeneous IMagldgl ea e a 217 5 3 16 Polarization imaging 2 2 e 217 5 4 Wide field imaging and deconvolution widefield 218 5 4 1 ftmachine modes for widefield o e e 220 0 4 1 1 pure w projection s iea sarra e 220 5 4 1 2 faceting only 0 0 0 0 ee ee ee ee 220 5 4 1 3 combination of w projection and faceting 221 5 5 Combined Single Dish and Interferometric Imaging feather 221 5 6 Making Deconvolution Masks makemask 222 5 7 Transforming an Image Model ft 224 5 8 Image plane deconvolution deconvolve o o e 225 PR ak a AA GG A O IR a A 225 5 10 Examples of I
112. When you load data as described above it is first opened and then registered on all existing Display Panels The distinction is subtle An open dataset has been prepared in memory from disk it may be registered enabled for drawing on one Display Panel and not on another All open datasets will have a tab in the Data Options window whether currently registered or not On the other hand only those datasets registered on a particular panel will show in its Tracking area At present it is useful to have more than one image registered on a panel only if you are displaying a contour image over a raster image 7 3 3 or blinking between images see Animator in 7 2 1 In future we also hope to provide transparent overlay of raster images It is the user s responsibility and highly advisable to unregister or close datasets that are no longer in use using the Register or Close toolbutton or menu In future the viewer will attempt to aid in unregistering datasets which are not compatible with a newly loaded one different sky area e g or MS vs image If you close a dataset you must reload it from disk as described above to see it again That can take a little time for MSs especially If you unregister a dataset it is set to draw immediately when you re register it with its options as you have previously set them In general close unneeded datasets but unregister those you ll be working with again 7 3 View
113. With ASAP Toolkit Again the data summary and then the script is given below HHH HHH HH HHH HH HHH HH HH H OH OF Project AGBTO2A_007_01 Observation GBT 1 antennas Telescope Observation Date Observer Project GBT 4 57539e 09 4 5754e 09 Lockman AGBTO2A_007_01 GBT 4 57574e 09 4 57575e 09 Lockman AGBTO2A_007_02 GBT 4 5831e 09 4 58313e 09 Lockman AGBTO2A_031_12 Thu Feb 1 23 15 15 2007 NORMAL ms summary Data records 76860 Total integration time 7 74277e 06 seconds Observed from 22 05 41 to 12 51 56 Thu Feb 1 23 15 15 2007 NORMAL ms summary Fields 2 ID Name Right Ascension Declination Epoch 0 FLS3a 17 18 00 00 59 30 00 00 J2000 1 FLS3b 17 18 00 00 59 30 00 00 J2000 Thu Feb 1 23 15 15 2007 NORMAL ms summary Spectral Windows 2 unique spectral windows and 1 unique polarization setups SpwID Chans Frame Chi MHz Resoln kHz TotBW kHz Ref MHz Corrs 0 1024 LSRK 1421 89269 2 44140625 2500 1420 64269 XX YY 1 1024 LSRK 1419 39269 2 44140625 2500 1418 14269 XX YY FLS3 data calibration this is calibration part of FLS3 data casapath os environ AIPSPATH import asap as sd os environ AIPSPATH casapath print Import s sd scantable FLS3_all_newcal_SP false read in MeasurementSet APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING print Split splitting the data for each field s0 s get_scan FLS3a s0 save FLS3a_HI asap del sO
114. a file The key to making acceptable hardcopies particularly for printing or inclusion in documents is to set the background color and line widths to appropriate values so the plot and labels show up in the limited resolution of the hardcopy Use the Viewer Canvas Manager 7 3 6 to change the Background Color from its default of black to white if you are making plots for printing or inclusion in a document You might also want to change the colormap accordingly Adjust the Line Width of the Axis Label Properties options in the Data Display Options panel so that the labels will be visible when printed Increasing from the default of 1 4 to a value around 2 seems to work well You can choose an output file name in the panel Be sure to make it a new name otherwise it will not overwrite a previous file and will not say anything about it If you will be printing to a postscript printer or to a PS or EPS file dial up the PS Resolution dpi to its maximum of 600 This will increase the size of the PS file somewhat but will make a much better plot Use gzip to compress the PS file if necessary Be sure to choose the desired Output Media and Orientation for PS also CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER Viewer Canvas Manager Margins Number of panels Basic Settings white Save e Display axes Hidden axes Basic Settings Aspectratia fixed word Y 2 Y B
115. a task dictionary G 2 MIRIAD CASA dictionary Table G I provides a list of common Miriad tasks and their equivalent CASA tool or tool function names The two packages differ in both their architecture and calibration and imaging models and there is often not a direct correspondence However this index does provide a scientific user of CASA who is familiar with MIRIAD with a simple translation table to map their existing data reduction knowledge to the new package G 3 CLIC CASA dictionary Table G 2 provides a list of common CLIC tasks and their equivalent CASA tool or tool function names The two packages are very similar since the CASA software to reduce IRAM data is based on the CLIC reduction procedures 473 APPENDIX G APPENDIX CASA DICTIONARIES Table G 1 MIRIAD CASA dictionary MIRIAD Task atlod blflag cgcurs cedisp clean fits gpboot gpcal gpcopy gpplt imcomb imfit impol imstat imsub invert linmos maths mfcal prthd restor selfcal tvclip tvdisp tvflag uvaver uvfit uvflag uvgen uvlist uvmodel uvplt uvsplit Description load ATCA data Interactive baseline based editor flagger Interactive image analysis Image display overlays Clean an image FITS image filler Set flux density scale Polarization leakage and gain calibration copy calibration tables Plot calibration solutions Image combination Image plane component fitter Create polarization images Image statistics E
116. although it does not offer the options for flux rescaling that setjy does Note also that currently setjy will not transform a full Stokes model image such that all polarizations are filled correct You need to use ft for this To limit this operation to certain fields and spectral windows use the field and or spw parameters which take the usual data selection strings 2 6 For example to set the flux density of the first field all spectral windows setjy vis data ms field 0 or to set the flux density of the second field in spectral window 17 setjy vis data ms field 1 spw 17 The full polarization flux density 1 Q U V may also be explicitly provided setjy vis data ms field 1 spw 16 Run setjy on field id 1 spw id 17 fluxdensity 3 5 0 2 0 13 0 0 and set 1 Q U V explicitly Note The setjy or ft operation is different than the antenna gain elevation and atmospheric opacity Prior Calibrations 4 3 3 in that it is applied to and carried with the MS itself rather than via other tables or parameters to the subsequent tasks It is more like the Tsys correction 4 3 1 in this regard CHAPTER 4 SYNTHESIS CALIBRATION 139 4 3 4 1 Using Calibration Models for Resolved Sources If the flux density calibrator is resolved at the observing frequency the point source model generated by setjy will not be appropriate If available a model image of the resolved source
117. and see for yourself HHH H HOH OH TUTORIAL NOTES Moments greater than zero need to have a conservative lower flux cutoff to produce sensible results HH APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 470 immoments imagename ngc4826 tutorial 16apr98 src clean image moments 1 axis spectral includepix 0 2 1000 0 chans 7 28 outfile ngc4826 tutorial 16apr98 moments mom1 Now view the resulting images viewer ngc4826 tutorial 16apr98 moments integrated print Now viewing Moment 0 ngc4826 tutorial i6apr98 moments integrated print Note PBCOR effects at field edge print Change the colorscale to get better image print You can also Open and overlay Contours of Moment 1 ngc4826 tutorial 16apr98 moments mom1i print Close the viewer when done Pause script if you are running in scriptmode user_check raw_input Return to continue script n HHHHHHHHHHHRR HEHEHE HHHHARAEHA AREER R RRR H HAAR RRR AAA AR Statistics on moment images print ImStat Moment images momzerostat imstat ngc4826 tutorial 16apr98 moments integrated print Found moment 0 max str momzerostat max 0 print Found moment 0 rms str momzerostat rms 0 momonestat imstat ngc4826 tutorial 16apr98 moments mom1 print Found moment 1 median str momonestat median 0 HEFHHHHEHHHHEHRAHRAREHEAAEHEE AREER AHH R RHR AR REAR ERR AR
118. and task documentation available online in HTML The CASA home page can be found at http casa nrao edu From there you can find documentation and assistance for the use of the package including the User Documentation You will also find information on how to obtain the latest release and receive user support 1 1 About This Beta Release Currently CASA is in the Beta Release stage This means that much but not all of the eventual functionality Beta Alert is available Furthermore the package is still under devel Boxes like this will bring to your at opment and some features might change in future releases tention some of the features or lack This should be taken into account as users begin to learn thereof in the current Beta release the package We will do our best to point out commands version of CASA tasks and parameters that are likely to change underfoot Unfortunately bugs and crashes also come along with the Beta release territory We will do our best to stamp these out as soon as we find them but sometimes known bugs will persist until we can find the right time to fix them like in a task that we know we want to make a big change to next month See the release notes for the current version for more details In this cookbook we will try to point out known pitfalls and workarounds in the Beta Alert boxes or in BETA ALERT notes in the text Not only is the software in Beta Release but this c
119. anything after the colon will provide you with the last command matching the char acters for example typing op finds reverse i search op im open ngc5921 ms Subsequent hitting of Ctrl r will search for the next command matching the characters D 9 Macros Macros can be made for easy re execution of previous commands For example to store the com mands 13 15 to the macro example CASA 31 macro example 13 16 Macro example created To execute type its name without quotes Macro contents x 1 y 3x x Z x 2 y 2 CASA 32 z Out 32 6 CASA 33 z 10 CASA 34 example Out 34 Executing Macro APPENDIX D APPENDIX PYTHON AND CASA 382 CASA 35 z Out 35 6 CASA 36 D 10 On line editing You can edit files on line in two ways 1 Using the shell access via vi 2 Using the ed function this will edit the file but upon closing it will try to execute the file using the script py example above CASA 13 ed script py this will bring up the file in your chosen editor when you are finished editing the file it will automatically execute it as though you had done a execfile script py Editing done Executing edited code CASA 14 x Out 14 1 CASA 15 y Out 15 3 CASA 16 z Out 16 6 D 11 Executing Python scripts Python scripts are simple text files containing lists of commands as if typed at the keyboard Note
120. array 0 00202226 sigma array 0 0020222 sum array 48 26399646 gt sumsq array 12 32857318 trc array 255 255 O 451 tref 15 19 52 390 05 35 44 246 I 1 41391e 09Hz CASA lt 22 gt mydict Out 22 flux 5 4000000000000004 source 0137 331 CASA lt 23 gt pickfile myxstat pickle CASA lt 24 gt f open pickfile w CASA lt 25 gt p pickle Pickler f CASA lt 26 gt p dump xstat CASA lt 27 gt p dump mydict CASA lt 28 gt f close The dictionaries are now saved in pickle file myxstat pickle in the current directory To retrieve CASA lt 29 gt xstat2 APPENDIX D APPENDIX PYTHON AND CASA 372 CASA lt 30 gt mydict2 CASA lt 31 gt f open pickfile CASA lt 32 gt u pickle Unpickler f CASA lt 33 gt xstat2 u load CASA lt 34 gt mydict2 u load CASA lt 35 gt f close CASA lt 36 gt xstat2 Out 36 blc array 0 0 0 0 plcf 15 24 08 404 04 31 59 181 I 1 41281e 09Hz flux array 4 0795296 max array 0 05235516 maxpos array 134 134 0 381 gt maxposf 15 21 53 976 05 05 29 998 I 1 41374e 09Hz mean array 1 60097857e 05 gt medabsdevmed array 0 00127436 median array 1 17422514e 05 min array 0 0104834 minpos array 160 da 0 307 minposf 15 21 27 899 04 32 14 923 I 1 41354e 09Hz
121. async e False The polcal task uses many of the standard calibration parameters as described above in The key parameter controlling polcal is poltype The choices are D Solve for instrumental polarization leakage D terms using the transform of an IQU model in MODEL_DATA requires no parallactic angle coverage but if the source polarization is non zero the gain calibration must have the correct R L phase registration Note this is unlikely so just use D X to let the position angle registration float This will produce a calibration table of type D D X Solve for instrumental polarization D terms and the polarization position angle cor rection using the transform of an IQU model in MODEL_DATA this mode requires at least 2 distinct parallactic angles to separate the net instrumental polarization and the PA This will produce a calibration table of type D BETA ALERT no table of type X will be produced so you must follow this by a run of polcal with polmode X see below gt D QU Solve for instrumental polarization and source Q iU requires at least 3 distinct parallactic angles to separate the net instrumental polarization from the source Q and U Effectively sets the polarization PA to the value if the R L phase difference were 0 This will produce a calibration table of type D CHAPTER 4 SYNTHESIS CALIBRATION 158 X Solve only for the position angle correction best to us
122. can fit only a single Gaussian component This restriction will be lifted in future patches CHAPTER 6 IMAGE ANALYSIS 236 6 5 Mathematical Operations on an Image immath The inputs are immath Perform math operations on images outfile es File where the output is saved mode evalexpr mode for math operation evalexpr spix pola poli exp dd Mathematical expression using images mask sil Mask to be applied to the images region s File path which contains an Image Region box dl Select one or more box regions in the input images chans gt Select the channel spectral range stokes a Stokes params to image 1 IV IQU IQUV async False If true run asynchronously In all cases outfile must be supplied with the name of the new output file to create The mode parameter selects what immath is to do The default mode evalexpr lets the user specify a mathematical operation to carry out on one or more input images The sub parameter expr contains the Lattice Expression Language LEL string describing the image operations See for more on LEL strings and the expr parameter Mask specification is done using the mask parameter This can optionally contain an on the fly mask expression in LEL or point to an image with a pixel mask See for more on the use of the mask parameter See also for more on LEL strings Region selection is carried out through the region and box parameters
123. chans gt gt Select the channel spectral range string containing channel range immath imstat and imcontsub takes a string listing CHAPTER 6 IMAGE ANALYSIS 229 of channel numbers velocity and or frequency numbers much like the spw paramter Only channel numbers acceptable at this time Default none all Example chans 3 20 chans 0 3 4 8 chans 3 20 50 51 HHH HH H HF The polarization plane s of the image is chosen with the stokes parameter stokes ae Stokes params to image I IV IQU IQUV string containing Stokes selections Stokes parameters to image may or may not be separated by commas but best if you use commas Default none all Example stokes IQUV Example stokes I Q Options I Q U V RR RL LR LL OSA UA Gare To get help on these parameters see the in line help help par chans help par stokes Sometimes as in the immoments task the channel plane selection is generalized to work on more than one axis type In this case the planes parameter is used This behaves like chans in syntax 6 1 3 Lattice Expressions expr Lattice expressions are strings that describe operations on a set of input images to form an output image These strings use the Lattice Expression Language LEL LEL syntax is described in detail in AIPS Note 223 http aips2 nrao edu docs notes 223 223 html BETA ALERT Th
124. clean the entire inner quarter of the primary beam However if you want to limit the region over which you allow the algorithm to find clean components then you can make a deconvolution region or mask To create a deconvolution mask use the makemask task and input that mask as a keyword into the task above CHAPTER 5 SYNTHESIS IMAGING 202 Or you can set up a simple cleanbox region To do this Inside the Toolkit make a first cut at the image and clean the inner quarter The im clean method is used for Then use the viewer to look at the image and get an idea CLEANing data There are a num of where the emission is located You can use the viewer adjustment panel to view the image in pixel coordinates and read out the pixel locations of your cursor ber of methods used to set up the clean including im setoptions Then you can use those pixel read outs you just go to define a clean box region where you specify the bottom left corner blc x amp y and top right corner x amp y locations For example say you have a continuum source near the center of your image between blcx blcy trcx trcy 80 80 120 120 Then to use this region cleanbox 80 80 120 120 Set the deconvolution region as a simple box in the center The following are the clean specific parameters and their allowed values followed by a description of carrying out interactive cleaning 5 3 1 Parameter psfmode The psfmode parameter chooses the
125. clean using the red X button and use our model for self calibration 5 After clean and self calibration using the intensity image we arrive at the final raster is the linear polarization intensity green contours and linear polarization B vectors vectors The color of the contours and the sampling and rotation by 90 degrees of the vectors was set in the Display Options panel A LEL expression was used in the Load Data panel to mask the vectors on the polarized intensity 215 ww N E Aa Lei Pd be Chee e e a OS Ee Gee iia oes 216 6 1 NGC2403 VLA moment zero left and NGC4826 BIMA moment one right images Ge ad as GC a ds e 244 7 3 The display panel s Main Toolbar appears directly below the menus and contains shortcut buttons for most of the frequently used menu items 261 4 The Mouse Tool Bar allows you to assign separate mouse buttons to tools you control with the mouse within the image display area Initially zooming color adjustment and rectangular regions are assigned to the left middle and right mouse buttons respectively 5 The Load Data Viewer panel that appears if you open the viewer without any infile specified or if you use the Data Open menu or Open icon You can see the images and MS available in your current directory and the options for loading them 26 6 The Load Data Viewer panel as it appears if you select an image You can see all options are available to loa
126. committed to disk until you press Save Edits Feel free to experiment with all the other controls nothing but Save Edits will alter your MS on disk As mentioned previously however there is no way to undo your edits once they are saved except by manually entering the reverse edits or restoring a previously saved flag version Also you must save or discard your edits before changing the MS selections If edits are pending the selection change will not be allowed and a warning will appear on the console If you close the MS in the viewer unsaved edits are simply discarded without prior warning It s important therefore to remember to save them yourself You can distinguish unsaved flags when using the Flags In Color option because they are in a lighter shade of blue The program must make a pass through the MS on disk to save the edits This can take a little time progress is shown in the console window 7 4 1 5 MS Options Advanced These settings can help optimize your memory usage especially for large MSs A rule of thumb is that they can be increased until response becomes sluggish when they should be backed down again You can run the unix top program and hit M in it to sort by memory usage in order to examine the effects of these settings Look at the amount of RSS main memory and SWAP used by the X server and casaviewer processes If that sounds familiar and easy then fiddlin
127. currently not for tools by performing the assignment within the CASA shell inside the Toolkit and then inspecting them using the inp command In the current version of CASA you cannot use the task parameter setting features such as the inp default or go commands for the CASA lt 30 gt default bandpass CASA lt 31 gt vis ngc5921 demo ms CASA lt 32 gt caltable ngc5921 demo bcal CASA lt 33 gt field 0 tools CASA lt 34 gt refant 15 CASA lt 35 gt inp bandpass bandpass Calculates a bandpass calibration solution vis ngc5921 demo ms Nome of input visibility file CHAPTER 1 INTRODUCTION 48 caltable gt ngc5921 demo bcal Name of output gain calibration table field 0 Select field using field id s or field name s spw iia Select spectral window channels selectdata False Other data selection parameters solint inf Solution interval combine scan Data axes which to combine for solve scan spw field refant 215 Reference antenna name minblperant 4 Minimum baselines _per antenna_ required for solve solnorm False Normalize average solution amplitudes to 1 0 G T only bandtype B Type of bandpass solution B or BPOLY fillgaps 0 Fill flagged solution channels by interpolation append False Append solutions to the existing table gaintable and Gain calibration table s to apply on the fly gain
128. data Only apply to spectra plottype Some header information of the data are plotted at top Note that colormap and linestyles cannot be controlled at a time The linestyles is ignored if both of them are specified Some plot options like annotation and changing titles legends fonts and the like are not supported in this task You should use sd plotter from the ASAP toolkit directly for this APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 319 This task uses the JPL line catalog as supplied by ASAP If you wish to use a different catalog or have it plot the line IDs from top or bottom rather than alternating then you will need to explore the sd toolkit also See for more information Note that multiple scans and IFs can in principle be handled through stacking and paneling but this is fairly rudimentary at present and you have little control of what happens in individual panels We recommend that you use scanlist field and iflist to give a single selection for each run After plotting you can display a spectral value on a pop up window along with mouse movement Click the LEFT mouse button over a spectrum to select it and drag mouse in the panel to output its value at the x position of mouse cursor The selection is released when you release the mouse button The task sdplot adds an additional toolbar to ASAP plotter which has three buttons spec value statistics and Quit When the
129. data multisource True async True saveinputs exportuvfits prefix exportuvfits saved myhandle exportuvfits print The return value for this exportuvfits async task for tm is str myhandle UV plane continuum subtraction on the target use the split ms this will update the CORRECTED_DATA column print UV Continuum Subtract default uvcontsub vis splitms field N5921 Use channels 4 6 and 50 59 for continuum fitspw 0 476 50759 Output all of spw 0 spw 0 Averaging time none solint 0 0 Fit only a mean level fitorder 0 Do the uv plane subtraction fitmode subtract Let it split out the data automatically for us splitdata True saveinputs uvcontsub prefix uvcontsub saved APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS Pause script if you are running in scriptmode if scriptmode inp user_check raw_input Return to continue scriptin uvcontsub You will see it made two new MS lt vis gt cont lt vis gt contsub srcsplitms splitms contsub Note that ngc5921 demo ms contsub contains the uv subtracted visibilities in its DATA column and ngc5921 demo ms cont the pseudo continuum visibilities as fit The original ngc5921 demo ms now contains the uv continuum subtracted vis in its CORRECTED_DATA column and the continuum in its MODEL_DAT
130. decreased or even switched off completely by setting this parameter to 1 to avoid detecting baseline undulations instead of real lines blpoly order of baseline polynomial options int lt 0 turns off baseline fitting default 5 example typically in range 2 9 higher values seem to be needed for GBT verify verify the results of baseline fitting options bool True False default False WARNING Currently this just asks whether you accept the displayed fit and if not continues without doing any baseline fit masklist list of mask regions to INCLUDE in BASELINE fit default entire spectrum example 1000 3000 5000 7000 if blmode auto then this mask will be applied before fitting outfile Name of output file default lt sdfile gt _cal outform format of output file options ASCIT SDFITS MS ASAP default ASAP example the ASAP format is easiest for further sd processing use MS for CASA imaging If ASCII then will append some stuff to the outfile name overwrite overwrite the output file if already exists options bool True False default False WARNING if outform ASCII this parameter is ignored plotlevel control for plotting of results options int O none l some 2 more lt O hardcopy default O no plotting example plotlevel lt 0 as abs plotlevel e g 1 gt hardcopy of final plot will be named APPENDIX A APPENDIX SINGLE DISH DATA PROCESSI
131. does have the benefit of isolating the overall channel independent gains to the following gaincal stage It is also recommended for the case where you have multiple scans on possibly different bandpass calibrators It may also be preferred when applying the bandpass before doing gaincal and then fluxscale 4 4 4 as significant variation of bandpass among antennas could otherwise enter the gain solution and make probably subtle adjustments to the flux scale We finally note that solnorm False at the bandpass step in the calibration chain will in the end produce the correct results It only means that there will be a part of what we usually think of the gain calibration inside the bandpass solution particularly if bandpass is run as the first step 4 4 2 2 B solutions Calibration type B differs from G only in that it is determined for each channel in each spectral window It is possible to solve for it as a function of time but it is most efficient to keep the B solving timescale as long as possible and use G or T for rapid frequency independent time scale variations The B solutions are limited by the signal to noise ratio available per channel which may be quite small It is therefore important that the data be coherent over the time range of the B solutions As a result B solutions are almost always preceded by an initial G or T solve using gaincal 8 4 4 3 In turn if the B
132. emission print Use rectangle drawing tool to box off source print Double click inside to print statistics print Move box on source and get the max print Calcualte DynRange MAXon RMSoff print I got 1 060 0 004 270 print Still not as good as it can be lets selfcal print Close viewer panel when done If you did not do interactive clean bring up viewer manually viewer clnimagel image Pause script if you are running in scriptmode if scriptmode user_check raw_input Return to continue script n see stuff like this in the terminal jupiter6cm demo clean1 image Jy beam n Std Dev RMS Mean 4712 0 003914 0 003927 0 0003205 Flux Med Dev IntQtlRng Median 0 09417 0 002646 0 005294 0 0001885 On Jupiter n Std Dev RMS Mean 3640 0 1007 0 1027 0 02023 HH HH HHH HH HHH HH HH HH OH OF You can use the right mouse to draw a box in the lower right corner of the image away from emission the double click inside to bring up statistics Use the right mouse to grab this box and move it up over Jupiter and double click again You should Variance Sum 1 532e 05 1 510 Min Max 0 01125 0 01503 Variance Sum 0 01015 73 63 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 443 Flux Med Dev IntQtlRng Median Min Max 4 592 0 003239 0 007120 0 0001329 0 01396 1 060 Estimated dynamic range 1 060 0 003927 270 poor Note that the exact numbers you get will depend on how dee
133. example of this panel is shown in Figure This panel is accessed through the Data Open menu or Open icon of the Viewer Display Panel It also appears if you open the viewer without any infile specified Selecting a file on disk in the Load Data panel will provide options for how to display the data Images can be displayed as 1 Raster Image 2 Contour Map 3 Vector map or 4 Marker Map CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 265 Directory home imager b smyers Oct07 Display As n4826_tjoint2 residual Image ngc5921 ms Measurement Set ngc5921 ms flagversions Directory ngc5921 usecase cal split ms Measurement Set ngc5 921 usecase clean fits FITS Image ngc5921 usecase clean image Image ngc5921 usecase clean model Image ngc5921 usecase clean residual Image LEL Expression Figure 7 5 The Load Data Viewer panel that appears if you open the viewer without any infile specified or if you use the Data Open menu or Open icon You can see the images and MS available in your current directory and the options for loading them You can also enter a Lattice image Expression in the box provided 6 1 3 For example you might enter my clean im my dirty im to display the difference between the two images The images should have the same coordinates and extents A MS can only be displayed as a raster CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 266 7 2 4 1 Registered vs Open Datasets
134. extended name as in the FIELD table summary above it has a VLA seq number appended reference 1331x we want to transfer the flux to our other gain cal source 1445 099 transfer 1445 saveinputs fluxscale prefix fluxscale saved Pause script if you are running in scriptmode if scriptmode inp user_check raw_input Return to continue script n fluxscale In the logger you should see something like Flux density for 1445 09900002_0 in SpW 0 is 2 48576 0 00123122 SNR 2018 94 nAnt 27 If you run plotcal on the tablein ngc5921 demo fluxscale you will see now it has brought the amplitudes in line between the first scan on 1331 305 and the others on 1445 099 Now use plotcal to examine the gain solutions print Plotcal fluxscaled gains default plotcal 399 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 400 caltable ftable field 0 1 Set up 2x1 panels upper panel amp vs time subplot 211 yaxis amp No output file yet wait to plot next panel saveinputs plotcal prefix plotcal gscaled amp saved if scriptmode showgui True else showgui False plotcal Set up 2x1 panels lower panel phase vs time subplot 212 yaxis phase saveinputs plotcal prefix plotcal gscaled phase saved The amp and phase coherence looks good Paus
135. fieldid 0 facets 1 distance 0 0 0 1 mstart Radialvelocity 0 gStep 0 mFreqstart Frequency 0 mage Weighting MS IMAGING _WSIGHT column will be changed mage Briggs weighting sidelobes will be suppressed over full image mage using 256 pixels in the uv plane isse Normal robustness robust 0 5 ean image Sum of weights 191380 JE eje Lock scroll Figure 1 6 Using the casalogger Filter facility The log output can be sorted by Priority Time Origin and Message In this example we are filtering by Origin using clean and it now shows all the log output from the clean task e View show and hide columns Time Priority Origin Message by checking boxes under the View menu pull down You can also change the font here e Insert Message insert additional comments as notes in the log Enter the text into the Insert Message box at the bottom of the logger and click on the Add button or choose to enter a longer message The entered message will appear with a priority of NOTE with the Origin as your username See Figure 1 7 for an example BETA ALERT This message currently will not be inserted into the correct or user controllable order into the log e Copy left click on a row or click drag a range of rows or click at the start and shift click at the end to select Use the Copy button or Edit menu Copy to put the selected rows into the clipboard You can
136. file imagename oe Name of output CASA image whichrep O Which coordinate representation if multiple whichhdu O Which image if multiple zeroblanks True If blanked fill with zeros not NaNs overwrite False Overwrite pre existing imagename async False if True run in the background prompt is freed For example we can read the above image back in importfits ngc5921 usecase image fits ngc5921 usecase image im CHAPTER 6 IMAGE ANALYSIS 253 6 12 Using the CASA Toolkit for Image Analysis Although this cookbook is aimed at general users employ ing the tasks we include here a more detailed description of Inside the Toolkit doing image analysis in the CASA toolkit This is because The image analysis tool ia is there are currently only a few tasks geared towards image the workhorse here It appears in analysis as well as due to the breadth of possible manipu the User Reference Manual as the lations that the toolkit allows that more sophisticated users image tool Other relevant tools will appreciate for analysis and manipulation in To see a list of the ia methods available use the CASA Clude measures me quanta qa help command and coordsys cs CASA lt 1 gt help ia Sassin gt help ia Help on image object class image __builtin__ object image object Methods defined here _init__ X __init__ initializes x see x __class doc__ for signature
137. for 64bit systems 08 Jul 2008 ok on 32bit also spwid setfield 1 int32 tb putcol SPECTRAL_WINDOW_ID spwid tb close For example this is used in the NGC4826 BIMA mosaic script Appendix F 3 2 6 Data Selection Once in MS form subsets of the data can be operated on using the tasks and tools In CASA there are three com Beta Alert mon data selection parameters used in the various tasks Data selection is being changed over field spw and selectdata In addition the selectdata parameter if set to True will open up a number of other ous tasks you may find relics of the sub parameters for selection The selection operation is old way such as fieldid or spwid unified across all the tasks The available selectdata pa to this new unified system In vari rameters may not be the same in all tasks But if present the same parameters mean the same thing and behave in the same manner when used in any task For example field spw selectdata versus field spw selectdata timerange uvrange antenna scan msselect False True gt HH HH H H HF field names or index of calibrators gt all spectral window channels gt all Other data selection parameters field names or index of calibrators gt all spectral window channels gt all Other data selection parameters time range gt all uv range all antenna baselines
138. for prior gaintable s spwmap Spectral window mapping for each gaintable see help This is controlled by the gaintable parameter which takes a string or list of strings giving one or more calibration tables to pre apply For example gaintable ngc5921 bcal ngc5921 gcal specifies two tables in this case bandpass and gain calibration tables respectively The other parameters key off gaintable taking single values or lists with an entry for each table in gaintable The order is given by that in gaintable The gainfield parameter specifies which fields from the respective gaintable to use to apply This is a list with each entry a string or list of strings The default for an entry means to use all in that table For example gaintable ngc5921 bcal ngc5921 gcal gainfield 1331 305 1331 305 1445 099 or using indices CHAPTER 4 SYNTHESIS CALIBRATION 144 gainfield 0 0 1 to specify the field 1331 305 from the table ngc5921 bcal and fields 1331 305 and 1445 099 from the second table ngc5921 gcal We could also have wildcarded the selection e g gainfield 0 gt taking all fields from the second table And of course we could have used the default gainfield 0 gt or even gainfield 0 which is to take all The interp parameter chooses the interpolation scheme to be used wh
139. for the bandpass in channel data before solving for the gain as a function of time However if the gains of the bandpass calibrator observations are fluctuating over the timerange of those observations then it can be helpful to first solve for the gains of that source with gaincal and input these to bandpass via gaintable See more below on this strategy We now describe the issue of bandpass normalization followed by a description of the options bandtype B and bandtype BPOLY 4 4 2 1 Bandpass Normalization The solnorm parameter 4 4 1 6 deserves more explanation in the context of the bandpass Most users are used to seeing a normalized bandpass where the vector sum of the antenna based channel CHAPTER 4 SYNTHESIS CALIBRATION 148 gains sums to unity amplitude and zero phase The toggle solnorm True allows this However the parts of the bandpass solution normalized away will be still left in the data and thus you should not use solnorm True if the bandpass calibration is the end of your calibration sequence e g you have already done all the gain calibration you want to Note that setting solnorm True will NOT rescale any previous calibration tables that the user may have supplied in gaintable You can safely use solnorm True if you do the bandpass first perhaps after a throw away initial gain calibration as we suggest above in 4 2 as later gain calibration stages will deal with this remaining calibration term This
140. frequency This CHAPTER 4 SYNTHESIS CALIBRATION 159 calibration need not have been applied and can be supplied through the gaintable parameters but any cal tables to be used in polcal must agree e g have been derived from the data in the DATA column and the model visibilities in the MODEL_DATA column of the MS Thus for example one would not use the cal table produced by fluxscale as the rescaled amplitudes would no longer agree with the contents of MODEL_DATA Be careful when using resolved calibrators for polarization calibration A particular problem is if the structure in Q and U is offset from that in I Use of a point model or a resolved model for I but point models for Q and U can lead to errors in the X calibration Use of a uvrange will help here The use of a full Stokes model with the correct polarization is the only way to ensure a correct calibration if these offsets are large 4 4 5 2 A Polarization Calibration Example In the following example we do a standard D QU solution on the bright source BLLac 2202 422 which has been tracked through a range in parallactic angle default polcal vis polcal_20080224 cband all ms caltable polcal_20080224 cband all pcal field 2202 422 spw a solint inf combine scan preavg 300 0 refant VA15 minsnr 3 poltype gt D QU gaintable polcal_20080224 cband all gcal gainfield gt gt polcal T
141. further information hitting lt RETURN gt at the help prompt returns you to the CASA prompt CASA lt 2 gt help gt helpQ Welcome to Python 2 5 This is the online help utility If this is your first time using Python you should definitely check out the tutorial on the Internet at http www python org doc tut CHAPTER 1 INTRODUCTION 38 Enter the name of any module keyword or topic to get help on writing Python programs and using Python modules To quit this help utility and return to the interpreter just type quit To get a list of available modules keywords or topics type modules keywords or topics Each module also comes with a one line summary of what it does to list the modules whose summaries contain a given word such as spam type modules spam help gt keywords Here is a list of the Python keywords Enter any keyword to get more help and else import raise assert except in return break exec is try class finally lambda while continue for not yield def from or del global pass elif if print help gt hit lt RETURN gt to return to CASA prompt You are now leaving help and returning to the Python interpreter If you want to ask for help on a particular object directly from the interpreter you can type help object Executing help string has the same effect as typing a particular string at the help gt prompt Further help in working within the Python shell is g
142. g vis ngc5921 ms vis 1 The CASA parameter system will check types when you run a task or tool or more helpfully when you set inputs using inp see below CASA will check and protect the assignments of the global parameters in its namespace Note that Python variable names are case sensitive CASA lt 109 gt Foo bar CASA lt 110 gt foo Bar CASA lt 111 gt foo Out 111 Bar CASA lt 112 gt Foo Out 112 bar so be careful Also note that mis spelling a variable assignment will not be noticed as long as it is a valid Python variable name by the interface For example if you wish to set correlation RR but instead type corellation RR you will find correlation unset and a new corellation variable set Command completion see 1 2 8 1 should help you avoid this 1 2 7 2 Lists and Ranges Sometimes you need to give a task a list of indices If these are consecutive you can use the Python range function to generate this list CASA lt 1 gt iflist range 4 8 CASA lt 2 gt print iflist CHAPTER 1 INTRODUCTION 33 4 5 6 7 CASA lt 3 gt iflist range 4 CASA lt 4 gt print iflist o 1 2 3 See Appendix D 3 for more information 1 2 7 3 Indexes As in C Python indices are 0 based For example the first element in a list antlist would be antlist 0 CASA lt 113 gt antlist range 5 CASA lt 114 gt antlist Out 114 0 1 2 3 4
143. g scanlist range 241 247 giving the same list as above e g CASA lt 1 gt scanlist range 241 247 CASA lt 2 gt print scanlist 241 242 243 244 245 246 Note that range starts from the first limit and goes to one below the second limit Python is 0 based and range is designed to work in loop functions If only a single limit is given the first limit is treated as 0 and the one given is used as the second e g APPENDIX D APPENDIX PYTHON AND CASA 370 CASA lt 3 gt iflist range 4 CASA lt 4 gt print iflist 0 1 2 3 You can also combine multiple ranges by summing lists CASA lt 5 gt scanlist range 241 247 range 251 255 CASA lt 6 gt print scanlist 241 242 243 244 245 246 251 252 253 254 D 4 Dictionaries Python dictionaries are data structures that contain key value pairs sort of like a hash array These are useful to store mini databases of things In CASA the parameter values are kept in a dictionary behind the scenes To initialize a dictionary say we call it mydict for use CASA lt 7 gt mydict To add members 0137 331 CASA lt 8 gt mydict source 5 4 CASA lt 9 gt mydict flux To see its contents CASA lt 10 gt mydict Out 10 flux 5 4000000000000004 source 0137 331 CASA lt 11 gt print mydict source 0137 331 flux 5 4000000000000004 To access a specific entry CASA lt 12 gt pri
144. gt execfile listobs last or CASA lt 19 gt run listobs last Note that the last file in generally not created until the task actually finished successfully so it is often best to manually create a save file beforehand using the saveinputs command if you are running a critical task that you strongly desire to have the inputs saved for CHAPTER 1 INTRODUCTION 57 1 3 6 Tools in CASA The CASA toolkit is the foundation of the functionality in the package and consists of a suite of functions that are callable from Python The tools are used by the tasks and can be used by advanced users to perform operations that are not available through the tasks It is beyond the scope of this Cookbook to describe the toolkit in detail Occasionally examples will be given that utilize the tools e g 6 12 In short tools are always called as functions with any parmeters that are not to be defaulted given as arguments For example ia open ngc5921 chan21 clean cleanbox mask ia calcmask ngc5921 chan21 clean cleanbox mask gt 0 5 mymask ia summary ia close uses the image tool ia to turn a clean mask image into an image mask Tools never use the CASA global parameters To find what tools are available use the toolhelp command CASA lt 1 gt toolhelp Available tools at Juan Pardo ATM library cb Calibration utilities cp Cal solution plotting utilities fg Flagging Flag management u
145. have selected the appropriate tool s on the Mouse Toolbar see above The Rectangle Region drawing tool currently works for the following CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 264 e Region statistics reporting for images e Region spectral profiles for images via the Tools Spectral Profile menu e Flagging of Measurement Sets e Creating and Saving an image region for various types of analysis 7 3 5 e Selecting Clean regions interactively 8 15 3 5 The Polygon Region drawing has the same uses except that polygon region flagging of an MS is not supported The Positioning crosshair tool works for the last two of the above The Spectral Profile display see 7 3 4 when active updates on each change of the rectangle polygon or crosshair Flagging with the crosshair also responds to single click or drag Region statistics are printed in the terminal window not the logger by double clicking the com pleted region The Rectangle Region tool s mouse button must also be double clicked to confirm an MS flagging edit Here is an example of region statistics from the viewer ngc5921 usecase clean image contour Jy beam n Std Dev RMS Mean Variance Sum 52 0 01067 0 02412 0 02168 0 0001139 1 127 Flux Med Dev IntQtlRng Median Min Max 0 09526 0 009185 0 01875 0 02076 0 003584 0 04181 7 2 4 The Load Data Panel You can use the Load Data Viewer GUI to interactively choose images or MS to load into the viewer An
146. ie using gaincurve True and setting the opacity parameter On the other hand if you apply calibration in AIPS by using the SPLIT or SPLAT tasks to apply the CL tables before exporting with FITTP then this calibration will be in the data itself In this case you do not want to re apply these calibrations when processing in CASA 4 3 Preparing for Calibration There are a number of a priori calibration quantities that may need to be applied to the data before further calibration is carried out These include e system temperature correction turn correlation coefficient into correlated flux density necessary for some telescopes e gain curves antenna gain elevation dependence e atmospheric optical depth attenuation of the signal by the atmosphere correcting for its elevation dependence e flux density models establish the flux density scale using standard calibrator sources with models for resolved calibrators These are pre determined effects and should be applied if known before solving for other calibra tion terms If unknown then they will need to be solved for as one of the standard calibration types gain or bandpass We now deal with these in turn 4 3 1 System Temperature Correction Some telescopes including the EVLA and the VLBA record the visibilities in the form of raw correlation coefficient with weights proportional to the number of bits correlated The correlation coefficient is
147. included in case we want to change from function calls to globals o This script has some interactive commands such as with plotxy and the viewer This script will stop and require a carriage return to continue at these points o Sometimes cut and paste of a series of lines from this script into the casapy terminal will get garbled usually a single dropped character In this case try fewer lines like groups of 4 6 HH HH HHH HH HH HHH HHH HH HH FH OH HHHHHHHHHHAR AEH HHHHAAAEHA AREER HORA ERA H AHHH HHA RAR AAA import os Some diagnostic stuff pl ion pl cl Q HEFHHHHHHHEEHHAEEHEEHEHHEHHHAE RHEE HAEHRHEHHEHHEE HARE HEHEHE EHRHA HEHEHE RHEE Clear out previous run results rmtables ngc4826 tutorial os system rm rf ngc4826 tutorial Sets a shorthand for the ms not necessary prefix ngc4826 tutorial msfile prefix 16apr98 ms print Tutorial Script for BIMASONG NGC4826 Mosaic print Will do import flagging calibration imaging print HEFHHHHEHHHHEAHAHEAAEHEAAEHEE ARERR AHH A AERA H RRR AHHH R RRA H RRR E RRR RRR HHFHHHHEHHHHEAHAHRARHHEEAEHER ARERR AHH A EERE R RSE R ERR AE RRA A RRR RRR N4826 BIMA SONG Data CO 1 0 115 2712 GHz 16apr98 454 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 455 source ngc4826 phasecal 1310 323 fluxcal 3c273 Flux 23 Jy on 16apr98
148. interferometric imaging Chapter 5 e image analysis Chapter 6 and e data and image visualization Chapter 7 BETA ALERT For the Beta Release there are also special chapters in the Appendix on e single dish data analysis Chapter A and e simulation Chapter B These are included for users that will be doing EVLA and ALMA telescope commissioning and software development They will become part of the main cookbook in later releases The general appendices provide more details on what s happening under the hood of CASA as well as supplementary material on tasks scripts and relating CASA to other packages These appendices include e obtaining and installing CASA Appendix C e more details about Python and CASA Appendix D e a discussion of the Hamaker Bregman Sault Measurement Equation Appendix E e annotated scripts for typical data reduction cases Appendix F and e CASA dictionaries to AIPS MIRIAD and CLIC Appendix G e Writing your own CASA Task Appendix H The CASA User Documentation includes e CASA Synthesis amp Single Dish Reduction Cookbook this document a task based data analysis walk through and instructions e CASA in line help accessed using help in the casapy interface CHAPTER 1 INTRODUCTION 22 e The CASA Toolkit Reference Manual details on a specific task or tool does and how to use it e The CASA Task Reference Manual the information from the inline help
149. is Yi Vk I xi Yi Vk k 6 1 for pixel and channel k in the cube J There are a number of choices to form the m moment usually approximating some polynomial expansion of the intensity distribution over velocity mean or sum gradient dispersion skew kurtosis etc There are other possibilities other than a weighted sum for calculating the image such as median filtering finding minima or maxima along the spectral axis or absolute mean deviations And the axis along which to do these calculation need not be the spectral axis ie do moments along Dec for a RA Velocity image We will treat all of these as generalized instances of a moment map The immoments task will compute basic moment images from a cube The default inputs are immoments Compute moments of an image cube imagename e des Input image name moments 0 List of moments you would like to compute axis spectral The momement axis ra dec lat long spectral or stokes region cd Image Region Use viewer box e dl Select one or more box regions chans gt Select the channel spectral range stokes 22 Stokes params to image I IV IQU IQUV mask e mask used for selecting the area of the image to calculate the moments on includepix 1 Range of pixel values to include excludepix 1 Range of pixel values to exclude outfile ds Output image file name or root for multiple moments async False If true the tas
150. it fixes default fluxunit to K first then convert to a new fluxunit telescopeparm 104 9 0 43 diameter m ap eff telescopeparm 0 743 gain in Jy K telescopeparm FIX to change default fluxunit see description below specunit units for spectral axis options str channel km s GHz MHz kHz Hz default current example this will be the units for masklist restfreq rest frequency used for specunit km s default use current setting example 4 6e10 float value 46GHz string with unit Allowed units are THz GHz MHz kHz and Hz frame frequency frame for spectral axis options str LSRK REST TOPO LSRD BARY GEO GALACTO LGROUP CMB default currently set frame in scantable WARNING frame REST not yet implemented doppler doppler mode options str RADIO OPTICAL Z BETA GAMMA APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 316 default currently set doppler in scantable scanlist list of scan numbers to process default use all scans example 21 22 23 24 this selection is in addition to field iflist and pollist field selection string for selecting scans by name default no name selection example FLS3a this selection is in addition to scanlist iflist and pollist iflist list of IF id numbers to selec
151. kernel as used in clean The sd option forces gridding as in single dish data For combining single dish and interferometer MS in the imaging the both option will allow clean to choose the ft or sd machines as appropriate for the data The mosaic option the default uses the Fourier trans form of the primary beam the aperture cross correlation Inside the Toolkit function in the uv plane as the gridding kernel This al The im setoptions method sets the lows the data from the multiple fields to be gridded down parameters relevant to mosaic imag to a single uv plane with a significant speed up in per ing such as the ftmachine formance in most non memory limited cases The effect of this extra convolution is an additional multiplication apodization by the primary beam in the image plane This can be corrected for but does result in an image with optimal signal to noise ratio across it The primary beams used in CASA are described in 5 2 13 BETA ALERT Note that making a non square image e g using unequal values in imsize for ftmachine mosaic will grid the data into a uv plane with correspondingly non square cells This has not been extensively tested and may results in undesired image artifacts We recommend that the user make square mosaic images when possible but in principle non square images should work CHAPTER 5 SYNTHESIS IMAGING 207 5 3 4 4 Sub parameter mosweigh
152. known as cross calibration when only phase is considered it is called phase referencing The best calibrators are point sources at the phase center constant visibility amplitude zero phase with sufficient flux density to determine the calibration factors with adequate SNR on the relevant timescale The primary gain calibrator must be sufficiently close to the target on the sky so that its observations sample the same atmospheric effects A bandpass calibrator usually must be sufficiently strong or observed with sufficient duration to provide adequate per channel sensitivity for a useful calibration In practice several calibrators are usually observed each with properties suitable for one or more of the required calibrations Synthesis calibration is inherently a bootstrapping process First the dominant calibration term is determined and then using this result more subtle effects are solved for until the full set of required calibration terms is available for application to the target field The solutions for each successive term are relative to the previous terms Occasionally when the several calibration terms are not sufficiently orthogonal it is useful to re solve for earlier types using the results for later types in effect reducing the effect of the later terms on the solution for earlier ones and thus better isolating them This idea is a generalization of the traditional concept of self calibration where initial imaging of th
153. log as well as they are displayed in the terminal window The infile can be any of ASAP MS SDFITS or RPFITS format If outfile name is given or outfile default the scaled data is written to a new file with the same format as the input data Note in case of the RPFITS format input data it will be written to SDFITS format A 2 1 13 sdstat Keyword arguments APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 322 sdfile name of input SD dataset default none must input file name example mysd asap See sdcal for allowed formats fluxunit units for line flux options str K Jy default keep current fluxunit WARNING For GBT data see description below gt gt gt fluxunit expandable parameter telescopeparm the telescope characteristics options str name or list list of gain info default none set example if telescopeparm it tries to get the telescope name from the data Full antenna parameters diameter ap eff known to ASAP are gt ATPKSMB ATPKSHOH ATMOPRA DSS 43 CEDUNA HOBART For GBT it fixes default fluxunit to K first then convert to a new fluxunit telescopeparm 104 9 0 43 diameter m ap eff telescopeparm 0 743 gain in Jy K telescopeparm FIX to change default fluxunit see description below specunit units for spectral axis options str channel km s GHz MHz kHz
154. lt constraints gt optional A constraints element that lets you constrain params based on the values of other params Attributes None Subelements lt when gt required lt param gt optional The input and output elements consist of param elements Attributes type required allowed values are record variant string int double bool intArray doubleArray boolArray stringArray name required subparam optional allowed values True False Yes or No kind optional mustexist optional allowed values True False Yes or No All param elements require name and type attributes Subelements lt description gt required lt value gt optional lt allowed gt optional lt value gt optional Value returned by the task Attributes type required as specified in lt param gt attributes APPENDIX H APPENDIX WRITING TASKS IN CASA 479 Subelements lt value gt optional lt allowed gt optional Block of allowed values Attributes enum required maybe enum or range If specfied as enum only specific values are allowed If specified as range then the value tags may have min and max attributes Subelements lt value gt optional lt when gt optional When blocks allow value specific handling for parameters Attributes param required Specifies special handling for a lt param gt Subelements lt equals gt optional lt notequals gt optional lt equals gt optional Reset p
155. mentioned field names also correspond to field ID 3 HH H OH field 30 will match only with 3020 2207 in above set However if it is required that the string be matched exclusively as a regular expression it can be supplied within a pair of as delimiters e g BAND A string enclosed within double quotes is used exclusively for pattern matching patterns are a simplified form of regular expressions used in most UNIX commands for string matching Patterns are internally converted to equivalent regular expressions before matching See the Unix command info regex or visit http www regular expressions info for details of regular expressions and patterns Strings can include any character except the following CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 93 re eas 2 1 a NEWLINE since these are part of the selection syntax Strings that do not contain any of the characters used to construct regular expressions or patterns are used for exact matches Although it is highly discouraged to have name in the MS containing the above mentioned reserved characters if one does choose to include the reserved characters as parts of names etc those names can only be matched against quoted strings since regular expression and patterns are a super set of literal strings i e a literal string is also a valid regular expression This leaves or as the lis
156. might have been taken on differ ent days for example The sd average time function takes multiple scantables as input However if taken at significantly different times different days for example then sd scantable freq_align must be used to align the velocity scales to the same time e g CASA lt 65 gt sci sd scantable orions_scan21_if0to3 asap False CASA lt 66 gt sc2 sd scantable orions_scan23_if0to3 asap False CASA lt 67 gt sci freq_align Aligned at reference Epoch 2006 01 19 01 49 23 UTC in frame LSRK CASA lt 68 gt sc2 freq_align reftime 2006 01 19 01 49 23 Aligned at reference Epoch 2006 01 19 01 54 46 UTC in frame LSRK CASA lt 69 gt scav sd average_times scl sc2 A 3 6 Spectral Smoothing Smoothing on data can be done as follows scantable smooth kernel type of smoothing hanning default gaussian boxcar width width in pixls ignored for hanning FWHM for gaussian insitu if False default do smoothing in situ otherwise make new scantable Example spave is an averaged spectrum spave smooth boxcar 5 do a 5 pixel boxcar smooth on the spectrum sd plotter plot spave should see smoothed spectrum A 3 7 Baseline Fitting The function sd scantable poly_baseline carries out a baseline fit given an mask of channels if desired msk scans create_mask 100 400 600 900 scans poly_baseline msk order 1 This will fit a fi
157. missing axes to the image 6 3 1 Examples for imcontsub For example in a cube named cube2403 with 97 spectral line channels it has been determined that channels 0 through 17 and channels 79 through 96 are line free Then default imcontsub imagename cube2403 linefile line2403 contfile cont2403 fitorder 1 chan 0717 79796 stokes 7 imcontsub will fit a first order polynomial to the visibilities in channels 0 through 17 and 79 through 96 subtract that fit from the input cube cube2403 and write the result to the cube line2403 The fitted continuum itself is written to the cube cont2403 and if so desired can be averaged to create a single high signal to noise continuum image 6 4 Image plane Component Fitting imfit The inputs are imfit Fit 2 dimentional Gaussian s on image region s imagename a Name of the input image box 2 Specify one or more box regions for the fit region SS oe Image Region or name Use viewer mask Es Mask to be applied to the image fixed 22 Pparameters to hold fixed not implemented usecleanbeam False Estimate the true source size estfile e 3x3 Initial estimate of parameters Not yet implemented residfile de Residual image removing fit Not yet implemented async False Tf true run asynchronously BETA ALERT This task is new to Patch 2 0 and has not been as extensively tested as the other tasks Currently it
158. nels in the dataset if needed having pre applied the prior calibration Use the bandpass task 8 4 4 2 e Gain Calibration solve for the gain variations of the system as a function of time having pre applied the bandpass if needed and prior calibration Use the gaincal task 8 Polarization Calibration solve for any unknown polarization leakage terms BETA ALERT Polarization Calibration tasks are now available as of Beta Release Patch 1 84 4 5 e Establish Flux Density Scale if only some of the calibrators have known flux densi ties then rescale gain solutions and derive flux densities of secondary calibrators Use the fluxscale task 4 4 4 e Manipulate Accumulate and Iterate if necessary accumulate different calibration solutions tables smooth and interpolate extrapolate onto different sources bands and times Use the accum 4 5 4 and smoothcal 4 5 3 tasks Examine Calibration at any point you can and should use plotcal 4 5 1 and or listcal 4 5 2 to look at the calibration tables that you have created e Apply Calibration to the Data this can be forced explicitly by using the applycal task 4 6 1 and can be undone using clearcal 4 6 3 Post Calibration Activities this includes the determination and subtraction of contin uum signal from line data the splitting of data sets into subsets usually single source and other operations such as model fi
159. nrao edu bin view ALMA SimulatorCookbook Here you can find what documentation we do have along with example files that are needed to specify antenna locations and a FAQ Appendix C Obtaining and Installing CASA C 1 Installation Script Currently you must be able to log into your system as the root user or an administrator user to install CASA The easiest way to install CASA on a RedHat Enterprise Linux or compatible system is to use our installation script load casapy This script will ftp the CASA RPMs and install them To use it first use the link above to download it to your hard disk Next make sure execute permission is set for the file Install CASA into usr by logging in as root and running load casapy root This option will install CASA into usr but it can only be run by the root user Alternatively you can visit our FTP server download the rpms and install them by hand Note you must be root administrater to install CASA in this manner See the following for more details https wikio nrao edu bin view Software ObtainingCASA C 2 Startup This section assumes that CASA has been installed on your LINUX or OSX system For NRAO AOC testers you should do the following on an AOC RHEZ machine gt home casa casainit sh or gt source home casa casainit csh 367 Appendix D Python and CASA CASA uses Python Python and matplotlib within the package Python is an enhanced inter active
160. out of the gain table for transfer use all of the bandpass table CHAPTER 4 SYNTHESIS CALIBRATION 177 gainfield 1 interpolation using linear for gain nearest for bandpass interp linear nearest only one spw do not need mapping spwmap all channels no other selection spw 7 selectdata False no prior calibration gaincurve False opacity 0 0 select the fields for 1445 099 and N5921 fields 1 and 2 field 1 2 applycal Now for completeness apply 1331 305 field 0 to itself field 0 gainfield 0 applycal The CORRECTED_DATA column now contains the calibrated visibilities In another example we apply the final cumulative self calibration of the Jupiter continuum data obtained in the example of 4 5 4 2 applycal vis jupiter6cm usecase split ms gaintable jupiter6cm usecase selfcall selectdata False Again it is important to remember the relative nature of each calibration term A term solved for in the presence of others is in effect residual to the others and so must be used in combination with them or new versions of them in subsequent processing At the same time it is important to avoid isolating the same calibration effects in more than one term e g by solving for both G and T separately without applying the other and then using them together It is always a good idea to examine
161. param mosaicmode gt lt equals type bool value False gt lt equals type bool value True gt lt default param mosweight gt lt value gt False lt value gt lt default gt lt default param ftmachine gt lt value type string gt mosaic lt value gt lt default gt lt default param scaletype gt lt value type string gt SAULT lt value gt lt default gt lt equals gt lt when gt gt lt constraints gt lt input gt lt returns type void gt lt example gt The main clean deconvolution task It contains many functions 1 Make dirty image and dirty beam psf 2 Multi frequency continuum images or spectral channel imaging 3 Full Stokes imaging 4 Mosaicking of several pointings 5 Multi scale cleaning 6 Interactive clean boxing 7 Initial starting model vis Name of input visibility file default none example vis ngc5921 ms imagename Pre name of output images default none example imagename m2 output images are m2 image cleaned and restored image With or without primary beam correction APPENDIX H APPENDIX WRITING TASKS IN CASA 491 m2 psf point spread function dirty beam m2 flux relative sky sensitivity over field m2 model image of clean components m2 residual image of residuals m2 interactive mask image containing clean regions field Select fields in mosaic Use field id s or field name s go listobs to obtain the list id s
162. refspwmap 0 0 1 1 select spwids for scaling the reference amplitudes from spectral window 0 will be used for spectral windows 0 and 1 and reference amplitudes from spectral window 2 will be used for spectral windows 2 and 3 CHAPTER 4 SYNTHESIS CALIBRATION 156 4 4 4 1 Using Resolved Calibrators If the flux density calibrator is resolved the assumption that it is a point source will cause solutions on outlying antennas to be biased in amplitude In turn the fluxscale step will be biased on these antennas as well In general it is best to use model for the calibrator but if such a model is not available it is important to limit the solution on the flux density calibrator to only the subset of antennas that have baselines short enough that the point source assumption is valid This can be done by using antenna and uvrange selection when solving for the flux density calibrator For example if antennas 1 through 8 are the antennas among which the baselines are short enough that the point source assumption is valid and we want to be sure to limit the solutions to the use of baselines shorter than 15000 wavelengths then we can assemble properly scaled solutions for the other calibrator as follows note specifying both an antenna and a uvrange constraint prevents inclusion of antennas with only a small number of baselines within the specified uvrange from being included in the solution such antennas will have poorly constrained solutions
163. regions look just like regions of no data With the default color option flags are shown in shades of blue darker blue for flags already saved to disk lighter blue for new flags not yet saved regions with no data will be shown in black Flag or Unflag This setting determines whether selected regions will be flagged or unflagged This does not affect previous edits it only determines the effect which later edits will have Both flagging and unflagging edits can be accumulated and then saved in one pass through the MS Flag Unflag All These flagging extent checkboxes allow you to extend your edit over any of the five data axes For example to flag all the data in a given time range you would check all the axes except Time and then select the desired time range with the Rectangle Region mouse tool Such edits will extend along the corresponding axes over the entire selected MS whether loaded into memory or not and optionally over unselected portions of the MS as well Use Entire CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 284 MS below Use care in selecting edit extents to assure that you re editing all the data you wish to edit e Flag Unflag Entire Antenna This control can be used to extend subsequent edits to all baselines which include the desired antenna s For example if you set this item to Yes and then click the crosshair on a visibility point with baseline 3 19 the edit would extend over baselines 0 3
164. resulting image is determined by the channelization in the first MS of vis of the first spw specified the reference spw The actual channels to be gridded and used in the clean are selected via the spw parameter as usual The resulting image cube will have nchan channels spaced evenly in frequency The first output channel will be located at the frequency of channel start in the first reference spw If width gt 1 then input MS channels with centers within a frequency range given by width 1 2 times the reference spw spacing will be gridded together as in mode mfs above into the channels of the output image cube The output channel spacing is thus given by width channels in the reference spw of the MS The interpolation sub parameter sets how channels are gridded into the image cube planes For nearest the channels in spw beyond the first are mapped into the nearest output image channel within half a channel if any Otherwise the chosen interpolation scheme will be used Image channels that lie outside the MS frequency range or have no data mapped to them will be blank in the output image but will be in the cube See the example in F 1 for using the channel mode to image a spectral line cube In this case we use mode channel nchan 46 start 5 width 1 which will produce a 46 channel cube starting with channel 5 of the MS with the same channel width as the MS CHAPTER 5 SYNTHESIS IMA
165. scale factor for absolute flux density calibration and may include phase and amplitude corrections due to changes in the atmosphere in lieu of T These gains are polarization dependent e Bij Bandpass frequency dependent response such as that introduced by spectral filters in the electronic transmission system e Mi Baseline based correlator non closing errors By definition these are not factorable into antenna based parts Note that the terms are listed in the order in which they affect the incoming wavefront G and B represent an arbitrary sequence of such terms depending upon the details of the particular electronic system Note that M differs from all of the rest in that it is not antenna based and thus not factorable into terms for each antenna As written above the measurement equation is very general not all observations will require treatment of all effects depending upon the desired dynamic range E g bandpass need only be considered for continuum observations if observed in a channelized mode and very high dynamic range is desired Similarly instrumental polarization calibration can usually be omitted when observing only total intensity using circular feeds Ultimately however each of these effects occurs at some level and a complete treatment will yield the most accurate calibration Modern high sensitivity instruments such as ALMA and EVLA will likely require a more general calibration APPENDIX E APPENDIX
166. seems to work put into includepix or excludepix as needed Also use chans to ignore channels with bad data 6 6 2 Examples using immoments For example using the NGC5921 example F 1 default immoments imagename ngc5921 demo cleanimg image Do first and second moments moments 0 1 Need to mask out noisy pixels currently done using hard global limits CHAPTER 6 IMAGE ANALYSIS 244 excludepix 100 0 009 Include all channels chans Output root name outfile ngc5921 demo moments immoments It will have made the images ngc5921 demo moments integrated ngc5921 demo moments weighted_coord Other examples of NGC2403 a moment zero image of a VLA line dataset and NGC4826 a moment one image of a BIMA CO line dataset are shown in Figure 6 1 52 PT 7 45 F d 48 F 30 F J 44 F g o 8 E gmk 4100 p 7 E 36 2 45 F J o aar gt 3 o Sagi A 5 id 24 F a O grong bee J 21 40 00 F E E l i l J ii eaaa a a o 12 56 48 46 44 425 405 o7 39 30 38 00 36 30 35 00 i J2000 Right Ascension J2000 Right Ascension Figure 6 1 NGC2403 VLA moment zero left and NGC4826 BIMA moment one right images as shown in the viewer BETA ALERT We are working on improving the thresholding of planes beyond the global cutoffs in includepix and excludepix 6 7 Computing image statistics imstat The imstat task
167. something within the viewer itself requires it in the future a button will be provided to reload flags from the disk unconditionally You can also choose to view the difference from a running mean or the local RMS deviation of either Phase or Amplitude There is a slider for choosing the nominal number of time slots in the local neighborhood for these displays CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 281 Note Insufficient Data is shown in the tracking area during these displays when there is no other unflagged data in the local neighborhood to compare to the point in question The moving time windows will not extend across changes in either field ID or scan number boundaries so you may see this message if your scan numbers change with every time stamp An option will be added later to ignore scan boundaries e Field IDs e Spectral Windows You can retrieve and edit a selected portion of the MS data by entering the desired Spectral Window and Field ID numbers into these boxes Important Especially with large MSs often the first thing you ll want to do is to select spectral windows which all have the same number of channels and the same polarization setup It also makes sense to edit only a few fields at a time Doing this will also greatly reduce data retrieval times and memory requirements You can separate the ID numbers with spaces or commas you do not need to enter enclosing brackets Changes to either entry box will cau
168. sources As usual blocks are closed by blank lines of the previous indentation level You can use the range D 3 Python function to generate a numerical loop vis polcal_20080224 cband all ms for i in range 0 6 fld str i plotxy vis field fld xaxis uvdist yaxis amp Done with fields 0 1 2 3 4 5 There is also a while loop construct while lt expression gt lt statements gt which executes the statement block while the lt expression gt is True The while loop can also take an else block For example APPENDIX D APPENDIX PYTHON AND CASA 375 Do an explicit set of clean iterations down to a limit prevrms 1 e10 while rms gt 0 001 clean vis splitms field src spw spwid imagename imname stokes IQUV psfmode hogbom imagermode csclean imsize 288 288 cel1 0 4 0 4 niter 200 threshold 1 3 mask 134 134 154 154 offstat imstat imname residual box 224 224 284 284 rms offstat sigma 0 if rms gt prevrms break the rms has increased stop prevrms rms Clean until the off source rms residual reaches 0 001 Jy Note that you can exit a loop using the break statement as we have here when the rms increases D 6 System shell access For scripts the os system methods are the preferred way to access system shell commands see D51 In interactive mode any input line beginning with a character is passed verb
169. specified an effective phase reference that is an average over the data will be calculated and used For data that requires polarization calibration you must choose a reference antenna that has a constant phase difference between the right and left polarizations e g no phase jumps or drifts If no reference antenna or a poor one is specified the phase reference may have jumps in the R L phase and the resulting polarization angle response will vary during the observation thus corrupting the polarization imaging To apply this solution to the calibrators and the target source field 2 say applycal data ms field 0 1 2 Restrict field selection cals src opacity 0 0 Don t apply opacity correction gaintable cal G Apply G solutions and correct data written to the CORRECTED_DATA column Note calwt True by default plotxy data ms xaxis channel datacolum data subplot 211 plotxy data ms xaxis channel datacolumn corrected subplot 212 4 4 3 2 Polarization independent Gain T At high frequencies it is often the case that the most rapid time dependent gain errors are intro duced by the troposphere and are polarization independent It is therefore unnecessary to solve for separate time dependent solutions for both polarizations as is the case for G Calibration type T is available to calibrate such tropospheric effects differing from G only i
170. spectrum without launching sdstat A 2 1 11 sdsave Keyword arguments sdfile name of input SD dataset APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 320 scanlist list of to process default use all scans example 21 22 23 24 this selection is in addition to field iflist and pollist field selection string for selecting scans by name default no name selection example FLS3a this selection is in addition to scanlist iflist and pollist iflist list of IF id numbers to select default use all IFs example 15 this selection is in addition to scanlist field and pollist pollist list of polarization id numbers to select default use all polarizations example 1 this selection is in addition to scanlist field and iflist scanaverage average integrations within scans options bool True False default False example if True average integrations before it is saved timeaverage average times for multiple scan cycles options bool True False default False gt gt gt timeaverage expandable parameter tweight weighting for time average options none var 1 var spec weighted tsys 1 Tsys 2 weighted tint integration time weighted tintsys Tint Tsys 2 median median averaging default none polaverage average polarizations options bool True False default False gt gt gt polaverage expandable parameter pweight
171. the antennas in the solution its more or less like setting the weighted sum of the antenna phases to zero It is usually prudent to select an antenna in the center of the array that is known to be particularly stable as any gain jumps or wanders in the refant will be transferred to the other antenna solutions Although rarely needed setting a preavg time will let you average data over periods shorter than the solution interval first before solving on longer timescales The minimum signal to noise ratio allowed for an acceptable solution is specified in the minsnr parameter BETA ALERT Not all calibration tasks have this parameter The minblperant parameter sets the minimum number of baselines to other antennas that must be preset for a given antenna to get a solution 4 4 1 6 Action append and solnorm The following parameters control some things that happen after solutions are obtained solnorm False Normalize solution amplitudes post solve append False Append solutions to existing table False will overwrite The solnorm parameter toggles on the option to normalize the solution amplitudes after the solu tions are obtained The exact effect of this depends upon the type of solution Not all tasks include this parameter One should be aware when using solnorm that if this is done in the last stage of a chain of calibration then the part of the calibration that is normalized away will be lost It is best to use this in
172. the corrected data after calibration using plotxy to compare the raw data and corrected corrected visibilities as we describe next 4 6 2 Examine the Calibrated Data Once the source data is calibrated using applycal you should examine the uv data and flag anything that looks bad If you find source data that has not been flanked by calibration scans CHAPTER 4 SYNTHESIS CALIBRATION 178 delete it it will not be calibrated For example to look at the calibrated Jupiter data in the last example given in the previous section plotxy jupiter6cm usecase split ms uvdist amp corrected selectdata True correlation RR LL fontsize 14 0 will show the CORRECTED_DATA column See Figure CASA Plotter pas pa E ES Es 58 0 O gt Ba Zoom to rect mode x 6 115 y 0 185 Figure 4 9 The final amp versus uvdist plot of the self calibrated Jupiter data as shown in plotxy The RR LL correlations are selected No outliers that need flagging are seen See 3 4 for a description of how to display and edit data using plotxy and 7 4 for use of the viewer to visualize and edit a Measurement Set CHAPTER 4 SYNTHESIS CALIBRATION 179 4 6 3 Resetting the Applied Calibration using clearcal The applycal task will set the CORRECTED DATA column The clearcal task will reset it to be the same as the DATA column This may or may not be what you really want to
173. the fraction of the total signal that is correlated and thus multiplication by the system temperature and the antenna gain in Jy K will produce visibilities with units of correlated flux density Note that the old VLA system did this initial calibration on line and ALMA will also provide some level of on line calibration TBD BETA ALERT There is as yet no mechanism available in importvla or in the calibration tasks to use the system temperature information provided by the VLA EVLA on line system to calibrate EVLA or VLBA data in raw form This includes VLA data taken after the Modcomp turn over CHAPTER 4 SYNTHESIS CALIBRATION 135 in late June 2007 You may pass the data through AIPS first You can also just forge ahead with standard calibration The drawback to this is that short term changes in Tsys which are not tracked by calibrator observations or self calibration will remain in the data 4 3 2 Antenna Gain Elevation Curve Calibration Large antennas such as the 25 meter antennas used in the VLA and VLBA have a forward gain and efficiency that changes with elevation Gain curve calibration involves compensating for the effects of elevation on the amplitude of the received signals at each antenna Antennas are not absolutely rigid and so their effective collecting area and net surface accuracy vary with elevation as gravity deforms the surface This calibration is especially important at higher frequencies where the deformations repres
174. the iteration parameter BETA ALERT Note that plotcal cannot currently display delay or delayrate solutions from fringecal 4 5 2 Listing calibration solutions with listcal The listcal task will list the solutions in a specified calibration table The inputs are listcal List data set summary in the logger CHAPTER 4 SYNTHESIS CALIBRATION 166 CASA Plotter Mar Rogen Fg vna tocata 10 0 D0 0 Bla Zoom to rect mode x 26 126 y 23 651 Figure 4 4 Display of the amplitude upper phase middle and signal to noise ratio lower of the bandpass B solutions for antenna 0 and both polarizations for ngc5921 Note the falloff of the SNR at the band edges in the lower panel vis a caltable at field dd antenna dd spw 23 listfile a pagerows 0 async e False An example listing is HH HH HF Name of input visibility file MS Input calibration table to list Select data based on field name or index Select data based on antenna name or index Spectral window channel to list Disk file to write else to terminal Rows listed per page Listing CalTable jupiter6cm usecase split ms smoothcal2 G Jones CHAPTER 4 SYNTHESIS CALIBRATION 167 CASA Plotter Mark Regon Reg vna tocate wont D0 0 Bla Figure 4 5 Display of the amplitude of the bandpass B solutions Iteration over antennas was turned on using iteration antenna The
175. the number of correlations voltage products formed by the correlator for an array Table 2 1 lists the non data columns of the MAIN table that are most important during a typical data reduction session Table 2 2 lists the key data columns of the MAIN table of an interferome ter MS The MS produced by fillers for specific instruments may insert special columns such as ALMA PHASE_CORR ALMA_NO_PHAS_CORR and ALMA PHAS_CORR_FLAG_ROW for ALMA data filled using the importasdm filler 2 2 3 These columns are visible in browsetable and are accessible from the toolkit in the ms tool e g the ms getdata method and from the tb table tool e g using tb getcol Note that when you examine table entries for IDs such as FIELD_ID or DATA_DESC_ID you will see 0 based numbers Table 2 1 Common columns in the MAIN table of the MS Parameter Contents ANTENNA1 First antenna in baseline ANTENNA2 Second antenna in baseline FIELD ID Field source no identification DATA_DESC_ID Spectral window number polarization identifier pair IF no ARRAY_ID Subarray number OBSERVATION ID Observation identification POLARIZATION_ID Polarization identification SCAN_NUMBER Scan number TIME Integration midpoint time UVW UVW coordinates The MS can contain a number of scratch columns which are used to hold useful versions of other columns such as the data or weights for further processing The most common scratch columns are
176. the plotter Multi panel plotting is poor Currently you can only add things like lines text etc to the first panel Also sd plotter set_range sets the same range for multiple panels while we would like it to be able to set the range for each independently including the default ranges The appearance of the plots need to be made a lot better In principle matplotlib can make publication quality figures but in practice you have to do a lot of work to make it do that and our plots are not good The sd plotter object remembers things throughout the session and thus can easily get con fused For example you have to reset the range sd plotter set_range if you have ever APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 363 set it manually This is not always the expected behavior but is a consequence of having sd plotter be its own object that you feed data and commands to There are known bugs if you try to switch between the task based plotting with sdplot and the tool based plotting the sdplot adds extra control buttons and this is not implemented in the sd toolkit so no spec value statistics nor Quit button for the plotter display with sd plotter plot Once statistics button on sdplot is used and deleted sdplot display with Quit button you can still use mouse buttons to select region to get statistics with the plotter displayed with sd plotter plot But spectral values won t be displayed
177. the resulting images viewer ngc4826 tutorial 16apr98 moments integratedmasked print Now viewing masked Moment 0 ngc4826 tutorial 16apr98 moments integratedmasked print You can Open and overlay Contours of Moment 1 ngc4826 tutorial 16apr98 moments momimasked Pause script if you are running in scriptmode user_check raw_input Return to continue script n Finally can compute and print statistics print ImStat masked moments maskedmomzerostat imstat ngc4826 tutorial 16apr98 moments integratedmasked print Found masked moment 0 max str maskedmomzerostat max 0 print Found masked moment 0 rms str maskedmomzerostat rms 0 maskedmomonestat imstat ngc4826 tutorial 16apr98 moments momimasked print Found masked moment 1 median str maskedmomonestat median 0 HEHHHHHHHHHEHRAHEHHEHEEHEHHEHAH HEHEHE HEHE HEHEHE HEHEHE HAH HEHEHE EHH Now show how to print out results print Results 16apr98 print Currently using non PBcor values im_srcmax16 srcstat max 0 im_offrms16 offstat sigma 0 im_offlinerms16 offlinestat sigma 0 thistest_immax momzerostat max 0 thistest_imrms momzerostat rms 0 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 472 Report a few key stats print NGC4826 Image Cube Max str im_srcmax16 print
178. the same directory where you started CASA so you can get access to it easily rather than constantly having to specify a full path name When you generate calibration solutions or images again these are in table format these will also be written to disk It is a good idea to keep them in the directory in which you started CASA 1 4 3 1 How do I get rid of my data in CASA Note that when you delete a measurement set calibration table or image which are in fact direc tories you must delete this and all underlying directories and files If you are not running casapy this is most simply done by using the file delete method of the operating system you started CASA from For example when running CASA on a Linux system in order to delete the measurement set named AM675 ms type CASA lt 5 gt rm r AM675 ms from within CASA The tells CASA that a system command follows see 1 2 7 5 and the r makes sure that all subdirectories are deleted recursively It is convenient to prefix all MS calibration tables and output files produced in a run with a common string For example one might prefix all files from VLA project AM675 with AM675 e g AM675 ms AM675 cal AM675 clean Then CASA lt 6 gt rm r AM675 will clean up all of these In scripts the escape to the OS will not work Instead use the os system function Ap pendix D 6 1 to do the same thing os system rm r AM675 If you are within casapy
179. then the CASA system is keeping a cache of tables that you have been using and using the OS to delete them will confuse things For example running a script that contains rm commands multiple times will often not run or crash the second time as the cache gets confused The clean way of removing CASA tables MS caltables images inside casapy is to use the rmtables task rmtables AM675 ms and this can also be wildcarded rmtables AM675x CHAPTER 1 INTRODUCTION 64 though you may get warnings if it tries to delete files or directories that fit the name wildcard that are not CASA tables BETA ALERT Some CASA processes lock the file and forget to give it up when they are done plotxy is usually the culprit You will get WARNING messages from rmtables and your script will probably crash second time around as the file isnt removed The safest thing is still to exit casapy and start a new session for multiple runs 1 4 4 What s in my data The actual data is in a large MAIN table that is organized in such a way that you can access different parts of the data easily This table contains a number of rows which are effectively a single timestamp for a single spectral window like an IF from the VLA and a single baseline for an interferometer There are a number of columns in the MS the most important of which for our purposes is the DATA column this contains the original visibility data from when the MS was create
180. to MS default importvla print Use importvla to read VLA Export and make an MS archivefiles datafile vis msfile bandname exportband autocorr False antnamescheme new project exportproject importvla elif importmode fits Import the data from VLA Export to MS default importuvfits print Use importuvfits to read UVFITS and make an MS fitsfile datafile vis msfile async False importuvfits else Copy from msfile print Copying datafile to msfile os system cp r t datafilet msfile vis msfile chooses branches based on the value of the importmode Python variable set previously in script APPENDIX D APPENDIX PYTHON AND CASA 374 D 5 2 Loops The for loop for iter in seq lt statements gt iterates over elements of a sequence seq assigning each in turn to iter The sequence is usually a list of values For example splitms polcal_20080224 cband all split ms srclist 0137 331 2136 006 2202 422 2253 161 0319 415 0359 509 spwlist 0 17 for src in srclist for spwid in spwlist imname splitms src spwid clean clean vis splitms field src spw spwid imagename imname stokes IQUV psfmode hogbom imagermode csclean imsize 288 288 cell 0 4 0 4 niter 1000 threshold 1 3 mask 134 134 154 154 Done with spw Done with
181. to allow frame information is hardwired into LSRK For example restfreq 115 2712GHz will set the rest frequency to that of the CO 1 0 line BETA ALERT Setting restfreq explicitly here in clean is good practice and may be necessary if your MS has been concatenated from different files for different spectral windows 2 5 5 2 8 Parameter spw The spw parameter selects the spectral windows that will be used to form the image and possibly a subset of channels within these windows The spw parameter is a string with an integer list of integers or a range e g spw 1 select spw 1 spw 0 1 2 3 select spw 0 1 2 3 spw 073 same thing using ranges You can select channels in the same string with a separator for example spw 1 10730 select channels 10 30 of spw 1 spw 0 5755 3 5 6 7 chans 5 55 of spw O and 5 6 7 of spw 3 This uses the standard syntax for spw selection is given in See that section for more options Note that the order in which multiple spws are given is important for mode channel as this defines the origin for the channelization of the resulting image 5 2 9 Parameter stokes The stokes parameter specifies the Stokes parameters for the resulting images Note that forming Stokes Q and U images requires the presence of cross hand polarizations e g RL and LR for circularly polarized systems such as the VLA in the data Stokes V requires both parallel han
182. to define regions to fit for lines with nfit in each auto will use the linefinder to fit for lines using the following parameters gt gt gt fitmode expandable parameters thresh S N threshold for linefinder default 5 example a single channel S N ratio above which the channel is considered to be a detection min_nchan minimum number of consecutive channels for linefinder default 3 example minimum number of consecutive channels required to pass threshold APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 311 avg_limit channel averaging for broad lines default 4 example a number of consecutive channels not greater than this parameter can be averaged to search for broad lines box_size running mean box size default 0 2 example a running mean box size specified as a fraction of the total spectrum length edge channels to drop at beginning and end of spectrum default 0 example 1000 drops 1000 channels at beginning AND end 1000 500 drops 1000 from beginning and 500 from end Note For bad baselines threshold should be increased and avg_limit decreased or even switched off completely by setting this parameter to 1 to avoid detecting baseline undulations instead of real lines maskline list of mask regions to INCLUDE in LINE fitting default all example maskline 3900 4300 for a single region or maskline 3900 4300 5000 5400 for two etc invertmask invert mask EXCLUDE masklist instead
183. together Interactive plotxy print Will plot all the NGC4826 calibrated data unaveraged this will take a while plotxy vis ngc4826 tutorial ms xaxis velocity yaxis amp field 278 spw 12 15 averagemode vector datacolumn corrected selectplot True newplot False title Field 278 SPW 12715 print print Look for outliers flag them if there are any bad ones print Pause script if you are running in scriptmode user_check raw_input Return to continue script n You can also plot all the N4826 fields 2 through 8 for example using a loop for fld in range 2 9 field str fld plotxy vis ngc4826 tutorial ms xaxis velocity yaxis amp field field spw 11715 averagemode vector datacolumn corrected selectplot True newplot False title Field field SPW 11715 user_check raw_input Return to continue script n Now here we time average the data plotting versus velocity plotxy vis ngc4826 tutorial ms xaxis velocity yaxis amp field field spw spw averagemode vector datacolumn corrected timebin 1e7 crossscans True plotcolor blue selectplot True newplot False title Field field SPW spw print print Final Spectrum field field spw spwt TimeAverage Corrected Data APPENDIX F APPENDIX ANNOTA
184. using the go command either explicitly CASA lt 44 gt go listobs gt go listobs Executing listobs CHAPTER 1 INTRODUCTION 51 or implicitly if taskname is defined e g by previous use of default or inp CASA lt 45 gt taskname clean CASA lt 46 gt go Executing clean You can also execute a task simply by typing the taskname CASA lt 46 gt clean Executing clean The go command can also be used to launch a different task without changing the current taskname without disrupting the inp process on the current task you are working on For example default gaincal set current task to gaincal and default vis n5921 ms set the working ms seats set some more parameters go listobs launch listobs w o chaning current task inp see the inputs for gaincal not listobs BETA ALERT Doing go listobs vis foo ms will currently change the taskname and will change vis which might not be what is desired 1 3 5 4 The inp Command You can set the values for the parameters for tasks but currently not for tools by performing the as signment within the CASA shell and then inspecting them using the inp command This command can be invoked in any of three ways via function call inp lt taskname gt or inp lt taskname gt without parentheses inp lt taskname gt or inp lt taskname gt or using the current taskname vari able setting with inp For example C
185. uv cell size 0 gt field of view uvtaper False Apply additional uv tapering of visibilities modelimage es Name of model image s to initialize cleaning restoringbeam EXE Dutput Gaussian restoring beam for CLEAN image pbcor False Output primary beam corrected image minpb 0 4 Minimum PB level to use async False If true the taskname must be started using clean CASA lt 6 gt E Figure 1 2 The clean inputs after setting values away from their defaults blue text Note that some of the boldface ones have opened up new dependent sub parameters indented and green The first is the usual taskname parameter The second is the name for the output Python file If there is no second argument for example saveinputs clean a file with name lt taskname gt saved in this case clean saved will be created or overwritten if extant If invoked with no arguments e g saveinputs it will use the current values of the taskname variable as set using inp lt taskname gt or default lt taskname gt You can also use the taskname global parameter explicitly saveinputs taskname taskname _1 save For example starting from default values CASA lt 1 gt default listobs CASA lt 2 gt vis ngc5921 demo ms CASA lt 3 gt saveinputs CASA lt 4 gt more listobs saved IPython system call more listobs saved taskname listobs CHAPTER 1 INTRODUCTION 55
186. weighting The weighting radial mode is a seldom used option that increases the weight by the radius in the uv plane ie Wi 0 fu 5 3 Technically I would call that an inverse uv taper since it depends on uv coordinates and not on the data per se Its effect is to reduce the rms sidelobes for an east west synthesis array This option has limited utility 5 2 11 5 briggs weighting The weighting briggs mode is an implementation of the flexible weighting scheme developed by Dan Briggs in his PhD thesis See http www aoc nrao edu dissertations dbriggs This choice brings up the sub parameters weighting briggs Weighting to apply to visibilities robust 0 0 Briggs robustness parameter npixels O number of pixels to determine uv cell size 0 gt field of view The actual weighting scheme used is Wi TE 5 4 Ki 1 Wg f2 where W is defined as in uniform and superuniform weighting and 5 x 1078 f 6x107 5 5 AL ui and R is the robust parameter The key parameter is the robust parameter which sets R in the Briggs equations The scaling of Ris such that R 0 gives a good trade off between resolution and sensitivity The robust R takes value between 2 0 close to uniform weighting to 2 0 close to natural Superuniform weighting can be combined with Briggs weighting using the npixels sub parameter This works as in superuniform weighting 5 2 11 3 CH
187. will calculate statistics on a region of an image and return the results as a return value in a Python dictionary CHAPTER 6 IMAGE ANALYSIS 245 The inputs are imstat Displays statistical information on an image or image region imagename ds Name of the input image region dd Image Region or name Use Viewer box aN Select one or more box regions chans gt Select the channel spectral range stokes ay Stokes params to image I IV IQU IQUV async False Area selection using box and region is detailed in and respectively Plane selection is controlled by chans and stokes See for details on plane selction BETA ALERT As with imcontsub if the image is missing one or more of the stokes and spectral axes then imstat will fail See the discussion of the workaround for this in 6 3 6 7 1 Using the task return value The contents of the return value of imstat are in a Python dictionary of key value sets For example xstat imstat will assign this to the Python variable xstat BETA ALERT The return of the statistics as a return value and not a global variable is new to Patch 2 0 The keys for xstat are then KEYS ble absolute PIXEL coordinate of the bottom left corner of the bounding box surrounding the selected region blcf Same as blc but uses WORLD coordinates instead of pixels tre the absolute PIXEL coordinate of the top right corner of the bounding box surrounding the se
188. will open the usual set of sub parameters for these methods 5 9 Self Calibration Once you have a model image or set of model components reconstructed from your data using one of the deconvolution techniques described above you can use it to refine your calibration This is called self calibration as it uses the data to determine its own calibration rather than observations of special calibration sources In principle self calibration is no different than the calibration process we described earlier 4 In effect you alternate between calibration and imaging cycles refining the calibration and the model as you go The trick is you have to be careful as defects in early stages of the calibration can get into the model and thus prevent the calibration from improving In practice it is best to not clean very deeply early on so that the CLEAN model contains correct components only One important thing to keep in mind is that the self calibration relies upon having the most recent Fourier transform of the model in the MODEL_DATA column of the MS This is indeed the case if you follow the imaging using clean directly by the self calibration If you have done something strange in between and have lost or overwritten the MODEL_DATA column for example done some extra cleaning that you do not want to keep then use the ft task see 5 7 above which fills the MODEL_DATA column with the Fourier transform of the specified model or model imag
189. 0 20arcsec First scale should always be O point we suggest second on the order of synthesized beam third 3 5 times synthesized beam etc For example if synthesized beam is 10 and cell 2 try multscale 0 5 15 Note multiscale is currently a bit slow default multiscale standard CLEAN using psfmode algorithm no multi scale Example multscale 0 5 15 amp gt amp gt amp gt multiscale expandable parameter s negcomponent Stop APPENDIX H APPENDIX WRITING TASKS IN CASA 495 component search when the largest scale has found this number of negative components 1 means continue component search even if the largest component is negative default 1 example negcomponent 50 imsize Image pixel size x y default 256 256 example imsize 350 350 imsize 500 is equivalent to 500 500 cell Cell size x y default 1 0arcsec example cell 0 5arcsec 0 5arcsec or cell larcmin 1larcmin cell larcsec is equivalent to 1arcsec 1larcsec NOTE cell 2 0 amp gt 2arcsec 2arcsec phasecenter direction measure or fieldid for the mosaic center default gt first field selected example phasecenter 6 or phasecenter J2000 19h30m00 40d00m00 restfreq Specify rest frequency to use for output image default Occasionally it is necessary to set this for example some VLA spectral line data For example for NH_3 1 1 put restfreq 23 6
190. 0 imCln setvp dovp True PBCOR or not sclt SAULT if scaletype PBCOR or scaletype pbcor sclt NONE imCln setvp dovp True else if imagermode mosaic make a pb for flux scale imCln setvp dovp True imCln makeimage type pb image imagename flux APPENDIX H APPENDIX WRITING TASKS IN CASA 500 imCln setvp dovp False restoring imset setrestoringbeam restoringbeam model image imset convertmodelimage modelimages modelimage outputmodel imagename model after all the mask shenanigans make sure to use the 1last mask maskimage imset outputmask if imagermode mosaic imCln setmfcontrol stoplargenegatives negcomponent scaletype sclt minpb minpb cyclefactor cyclefactor cyclespeedup cyclespeedup fluxscale imagename flux else imCln setmfcontrol stoplargenegatives negcomponent cyclefactor cyclefactor cyclespeedup cyclespeedup imCln clean algorithm alg niter niter gain gain threshold qa quantity threshold mJy model imagename model residual imagename residual image imagename image psfimage imagename psf mask maskimage interactive interactive npercycle npercycle imCln close presdir os path realpath newimage imagename if imagename count gt 0 newimage os path basename imagename os chdir os path dirname imagename result MX
191. 0 3 pbcor False NOTE Sault weighting implies a uniform noise mosaic NOTE that niter is set to large number so that stopping point is controlled by threshold NOTE with pbcor False the final image is not flux correct instead the image has constant noise despite roll off in power as you move out from the phase center s Though this format makes it look nicest for all flux density measurements and to get an accurate integrated intensity image one needs to divide the srcimage image srcimage flux in order to correct for the mosaic response pattern One could also achieve this by setting pbcor True in clean Try running clean adding the parameter interactive True This parameter will periodically bring up the viewer to allow interactive clean boxing For poor uv coverage deep negative bowls from missing short spacings this can be very important to get correct integrated flux densities H OH OH HEFHHHHEHHHHEAHHHEARHHAEAAE HARARE R RHEE R RHR AE RRA R ERR AR RRA A RRA RRR Do interactive viewing of clean image print Viewer viewer ngc4826 tutorial 16apr98 src clean image APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 468 print print This is the non pbcorrected cube of NGC4826 print Use tape deck to move through channels print Close the viewer when done print Pause script if you are running in scriptmode user_check raw_input
192. 000 6000 7000 8000 Channel Brightness Temperature K a LL s a 01600 2000 3000 4000 5000 6000 7000 8000 1000 2000 2000 4000 5000 6000 7000 8000 Channel Channel 0 0 ea Figure A 3 Multi panel display of the scantable There are two plots per scan indicating the _psr reference position data and the _ps source data s summary summary info s set_fluxunit K make K default unit scal sd calps s 20 21 22 23 Calibrate HC3N scans scal recalc_azel recalculate az el to scal opacity 0 09 do opacity correction sel sd selector Prepare a selection sel set_ifs 0 select HC3N IF scal set_selection sel get this IF stave sd average_time scal weight tintsys average in time spave stave average_pol weight tsys average polarizations Tsys weighted 1 Tsys 2 average sd plotter plot spave plot spave smooth boxcar 5 boxcar 5 spave auto_poly_baseline order 2 baseline fit order 2 sd plotter plot spave plot spave set_unit GHz sd plotter plot spave sd plotter set_histogram hist True draw spectrum using histogram sd plotter axhline color r linewidth 2 zline sd plotter save orions_hc3n_reduced eps save postscript spectrum APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 358 60e IXI ASAP Plotter Tk OrionS_ps OrionS_ps Brightness Temperature K n n 1 n n n n n n n
193. 05 were in spw 1 The use of spwmap was necessary to transfer the interpolation correctly onto the NGC4826 scans type and incremental relative to the first is required and it is not possible or convenient to recover the cumulative solution by a single solve Much of the time it is in fact possible to recover the cumulative solution This is because the equation describing the solution for the incremental solution using the original solution and that describing the solution for their product are fundamentally the same equation the cumulative solution if unique must always be the same no matter what initial solution is One circumstance where an incremental solution is necessary is the case of phase only self calibration relative to a full amplitude and phase calibration already obtained from a different field For example a phase only G self calibration on a target source may be desired to tweak the full amplitude and phase G calibration already obtained from a calibrator The initial calibration from the calibrator contains amplitude information and so must be carried forward yet the CHAPTER 4 SYNTHESIS CALIBRATION 173 phase only solution itself cannot by definition recover this information as a full amplitude and phase self calibration would In this case the initial solution must be applied while solving for the phase only solution then the two solutions combined to form a cumulative calibration embodyi
194. 1 Solve for G on the bandpass calibrator using T opacity and F gain curve solutions already derived 2 Solve for B on the bandpass calibrator using G T opacity and E gain curve solutions 3 Solve for G on primary gain near target and flux density calibrators using B T opacity and E gain curve solutions 4 Scale G solutions for the primary gain calibrator according to the flux density calibrator solutions 5 Apply T opacity E gain curve G and B solutions to the target data 6 Image the calibrated target data For continuum polarimetry the typical pattern is 1 Solve for G on the polarization calibrator using analytical P solutions 2 Solve for D on the polarization calibrator using P and G solutions Solve for G on primary gain and flux density calibrators using P and D solutions gt Ww Scale G solutions for the primary gain calibrator according to the flux density calibrator solutions al Apply P D and G solutions to target data 6 Image the calibrated target data For a spectro polarimetry observation these two examples would be folded together In all cases the calibrator model must be adequate at each solve step At high dynamic range and or high resolution many calibrators which are nominally assumed to be point sources become slightly resolved If this has biased the calibration solutions the offending calibrator may be imaged at any point in the process and the resultin
195. 1 1 Manual flagging and clipping in flagdata 123 3 5 1 2 Flagging the beginning of scans 2 124 ra an Oh ce ROW om eg HU Be RR ee AOR Be a Oe 124 3 7 Plotting antenna positions plotants 00000000004 126 art Sg Gee a Ba A Re eee de eS 127 3 9 Examples of Data Display and Flagging ooa aaa 127 128 4 1 Calibration Tasks ooa aaa ee 128 4 2 The Calibration Process Outline and Philosophy 129 a Reheat bEe Ge Ghee a 131 iit Bd Ge ha Ba A he eee eed oS 132 Eats a ep ce Aoi Ge ee A 133 vee a Re ks bee a eee we be ea eh ee a es 134 pais We ake Sook ae ees Ge eins we ae ee een ese 134 sds ge Hoss dodo oak eg be 135 ek nea tee ee eek Ge Bw os ee S 136 4 3 3 1 Determining opacity corrections for VLA data 136 4 3 4 Setting the Flux Density Scale using setjy 137 4 3 4 1 Using Calibration Models for Resolved Sources 139 Pe at AA 141 ee rd 141 4 4 1 Common Calibration Solver Parameters 141 4 4 1 1 Parameters for Specification vis and caltable 142 4 4 1 2 Selection field spw and selectdata 142 4 4 1 3 Prior Calibration and Correction parang gaincurve and opacity 143 4 4 1 4 Previous Calibration gaintable gainfield interp and spwmap 143 4 4 1 5 Solving solint combine preavg refant minblperant minsnr 145 4 4 1 6 Action append and solnorm
196. 1 3 2 3 3 3 3 4 3 nAntennas 1 Note that the second antenna of the selection 19 is irrelevant here you can click anywhere within the Antenna 3 block i e where the first antenna number is 3 to select all baselines which include antenna 3 This item controls the edit extent only along the baseline axis If you wish to flag all the data for a given antenna you must still check the boxes to flag all Times Channels Polarizations and Spectral Windows There would be no point however in activating both this item and the Flag All Baselines checkbox You can flag an antenna in a limited range of times etc by using the appropriate checkboxes and selecting a rectangular region of visibilities with the mouse Note You do not need to include the entire antenna block in your rectangle and you may stray into the next antenna if you try Anywhere within the block will work To flag higher numbered antennas it often helps to zoom in e Undo Last Edit e Undo All Edits The Undo buttons do the expected thing completely undo the effect of the last edit or all unsaved edits Please note however that only unsaved edits can be undone here there is no ability to revert to the flagging state at the start of the session once flags have been saved to disk unless you have previously saved a flag version The flag version tool is not available through the viewer directly e Use Entire MS When Saving Edits
197. 1 var spec weighted gt tsys 1 Tsys 2 weighted default none tau atmospheric optical depth default 0 0 no correction outfile Name of output file default lt sdfile gt _cal outform format of output file options ASCII SDFITS MS ASAP default ASAP example the ASAP format is easiest for further sd processing use MS for CASA imaging If ASCII then will append some stuff to the outfile name overwrite overwrite the output file if already exists options bool True False default False WARNING if outform ASCII this parameter is ignored plotlevel control for plotting of results options int O none l some 2 more lt O hardcopy default O no plotting example plotlevel lt 0 as abs plotlevel e g 1 gt hardcopy of final plot will be named lt outfile gt _calspec eps WARNING be careful plotting in fsotf mode DESCRIPTION 296 Task sdaverage performs data selection calibration for single dish spectra By setting calmode none one can run sdaverage on already calibrated data for further selection averaging and atmospheric optical depth correction APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 297 If you give multiple IFs in iflist then your scantable will have multiple IFs This can be handled but there can be funny interactions later on We recommend you split each IF out into separate files by re running sdaverage with e
198. 2stre Ges x __str__ lt gt str x adddegaxes Add degenerate axes of the specified type to the image outfile direction false spectral false stokes linear false tabular false overwrite false addnoise unlock Release any lock on the image Data and other attributes defined here CHAPTER 6 IMAGE ANALYSIS or for a compact listing use lt TAB gt completion on ia e g CASA lt 2 gt ia Display all 101 possibilities ia __class__ ia ia __delattr__ ia ia __doc__ ia ia __getattribute__ ia ia __hash__ ia ia __init__ ia ia __new__ ia ia __reduce__ ia ia __reduce_ex__ ia ia __repr__ ia ia __setattr__ ia ia __str__ ia ia adddegaxes ia ia addnoise ia ia boundingbox ia ia brightnessunit ia ia calc ia ia calcmask ia ia close ia ia continuumsub ia ia convertflux ia ia convolve ia ia convolve2d ia ia coordmeasures ia ia coordsys ia ia decompose ia ia deconvolvecomponentlist ia ia done ia ia echo ia ia fft ia ia findsources ia ia fitallprofiles ia ia fitpolynomial ia ia fitprofile ia A common use of the ia tool is to do region statistics on an image new__ T __new__ S lt built in method __new y or n fitsky fromarray fromascii fromfits Tromforeign fromimage fromshape getchunk getregion getslice hanning haslock histograms history imagecalc image
199. 3 33 33 33 33 33 33 33 33 33 33 33 33 33 53 54 54 54 53 53 53 53 53 53 53 54 54 54 54 53 57 04 01 03 56 55 59 58 51 56 59 01 10 19 15 54 ANNOTATED EXAMPLE SCRIPTS 0 0OuUVRJ OORR AH 00 00 00 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS Set the fluxes of the primary calibrator s print Setjy default setjy vis msfile 1331 305 3C286 is our primary calibrator Use the wildcard on the end of the source name since the field names in the MS have inherited the AIPS qualifiers field 1331 305 This is 1 4GHz D config and 1331 305 is sufficiently unresolved that we dont need a model image For higher frequencies particularly in A and B config you would want to use one modimage Setjy knows about this source so we dont need anything more saveinputs setjy prefix setjy saved Pause script if you are running in scriptmode if scriptmode inp user_check raw_input Return to continue script n setjyO You should see something like this in the logger and casapy log file 1331 30500002_0 spwid 0 I 14 76 Q 0 U 0 V 0 Jy Perley Taylor 99 So its using 14 76Jy as the flux of 1331 305 in the single Spectral Window in this MS fosoooooooooooooooooooooooooooooooooooooooooooooooooooooos Bandpass
200. 3 05 27 04 42 45 INFO 10 26 00 0 10 43 00 0 6 2 w5921_2 6804 30 10 E lt Ey Insert Message Il JE lle Lock scroll Figure 1 4 The CASA Logger GUI window under Linux Note that under MacOSX a stripped down logger will instead appear as a Console The output contained in casapy log is also displayed in a separate window using the casalogger Generally the logger window will be brought up when casapy is started If you do not want the logger GUI to appear then start casapy using the nologger option casapy nologger which will run CASA in the terminal window See 8 1 4 2 1 for more startup options BETA ALERT Due to problems with Qt under MacOSX we had to replace the GUI qtcasalogger with a special stripped down one that uses the Mac Console This still has the important capabil ties such as showing the messages and cut paste The following description is for the Linux version CHAPTER 1 INTRODUCTION 59 hd Log Messages sandrock home sandrock3 smyers Testing3 Patch4 N5921 casapy log Uj Uy a x File Edit View B y Search Message apply Filter Time M Y e Time Priority Origin Message al 2009 05 27 04 47 11 INFO plotcal c HHHH HHHH HHH HHHH HHHH HHHH HHHH HEHHEHE HEHEHEHEHE 2009 05 27 04 47 13 INFO applycal 2009 05 27 04 47 13 INFO applycal HHHHHHHHHHHHHHHHHHHHHHHHAHHHHHHH AHHH HAHHEH 2009 05 27 04 47 13 INFO 2009 05 27 04 47 13 INFO 2009 05 27 04 47 13 INFO
201. 3 54 00 1 10 11 VLA N4 25 0 m 107 37 06 5 33 54 06 1 393 APPENDIX F APPENDIX 11 12 VLA W5 12 13 VLA N3 13 14 VLA N1 14 15 VLA N2 15 16 VLA E7 16 17 VLA E8 17 18 VLA W4 18 19 VLA E5 19 20 VLA W9 20 21 VLA W6 21 22 VLA E4 23 24 VLA E2 24 25 VLA N6 25 26 VLA N9 26 27 VLA N8 27 28 VLA W7 Tables MAIN ANTENNA DATA_DESCRIPTION DOPPLER FEED FIELD FLAG_CMD FREQ_OFFSET HISTORY OBSERVATION POINTING POLARIZATION PROCESSOR SOURCE SPECTRAL_WINDOW STATE SYSCAL WEATHER 25 0 m 25 0 m 25 0 m 25 0 m 25 0 m 25 0 m 25 0 m 25 0 m 25 0 m 25 0 m 25 0 m 25 0 m 25 0 m 25 0 m 25 0 m 25 0 m 22653 28 1 lt absent gt 28 3 lt empty gt lt absent gt 273 1 168 1 lt empty gt 3 1 lt empty gt lt absent gt lt absent gt Get rid of the autocorrelations print Flagautocorr Don t default this one either there is only one parameter vis flagautocorr 107 107 107 107 107 107 107 107 107 107 107 107 107 107 107 107 rows rows row rows rows rows row rows row rows row from the MS 37 37 37 37 36 36 37 36 37 37 37 37 37 37 37 37 13 06 06 06 52 48 10 58 25 15 00 04 06 07 07 18 FPOwWDOFAMDFAAWADANOWO 33 33 3
202. 3 6 Adjusting Canvas Parameters Multi panel displays The display area can also be manipulated with the following controls in the Panel Options or Viewer Canvas Manager window Use the wrench icon with a P or the Display Panel menu to show this window e Margins specify the spacing for the left right top and bottom margins e Number of panels specify the number of panels in x and y and the spacing between those panels e Background Color white or black more choices to come CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 276 7 W Viewer Display Panel Data Display Panel Tools View a QO Els Gi QRA Dm e i 4o on 20 28 00 4g 20 9 Declination 27 00 40 20 4726 00 407 1327158 54 59 50 48 46 81950 Right Ascension x m5 1 fits 439 Pixel 235 264 13 27 48 552 47 27 20 367 Figure 7 13 Selecting an image region with the polygon tool CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 277 7 3 6 1 Setting up multi panel displays Figure illustrates a multi panel display along with the Viewer Canvas Manager settings which created it bud Viewer Display Panel ddd ddd dd o x Data DisplayPanel Tools View rX BEAR BARRAS cs ee a o 2 Y Viewer Canvas Manager 1499 78 km s 1494 63 km s Margins Left margin space PG chars Bottom margin space PG chars Right margin space PG chars To
203. 44 0 11 11 0 o 0 0 0 2 63 Boolean 0 0 0 Boolean 23814 23814 0 0514344 0 17 17 0 0 o o 0 0 2 63 Boolean 0 0 0 Boolean 23814 23814 0 0514344 0 9 9 0 0 3 o 0 0 2 63 Boolean 0 0 0 Boolean 23814 23814 0 0514344 0 19 19 0 0 0 0 0 2 63 Boolean 0 0 0 Boolean 23814 23814 0 0514344 0 20 20 0 o 0 0 0 2 63 Boolean 0 0 0 Boolean 23814 23814 0 0514344 0 18 18 0 o Jr Restore Columns Resize Headers PAGE NAVIGATION First lt lt t1 23 gt gt Last 1 Go Loading 1000 rows Figure 3 7 browsetable The browser displays the main table within a frame You can scroll through the data x columns of the MAIN table and y the rows or select a specific page or row as desired By default 1000 rows of the table are loaded at a time but you can step through the MS in batches Note that one useful feature is that you can Edit the table and its contents Use the Edit table choice from the Edit menu or click on the Edit button Be careful with this and make a backup copy of the table before editing Use the Close Tables and Exit option from the Files menu to quit the casabrowser CHAPTER 3 DATA EXAMINATION AND EDITING 126 Y Table Browser File Edit View Tools Export Help wx 22 OR ar Ex ngc5921 ms Extra Information Float 2 table data ANTENNA Table home sandrock smyers Testing 2 008 03 ngc5
204. 44442865 b eda G hd da aD SG 248 6 9 Regridding an Image imregrid o o eee ee ee 250 6 10 Image Convolution imsmooth 4444 60 e44o eh 4d ae wwe ed oe ew a4 251 6 11 Image Import Export to FITS 47 incidencia rr e 251 6 11 1 FITS Image Export exportfits c ccccoomor corr eee 252 6 11 2 FITS Image Import import its 252 A A an ngs aw la 253 S be aea a A a a a 255 256 a a EIN A A A a de eee 256 7 1 1 Running the CASA viewer outside casapyl 258 12 Theviever GUI e soxor a RI RR we aa Oe g 259 7 2 1 The Viewer Display Panel o e o 259 acabas aces 263 7 2 3 Region Selection and Positioning e e 263 7 2 4 The Load Data Panell 2 2 20 0 02 02 0200 a 264 7 2 4 1 Registered vs Open Datasets o 02005 266 ah ese Gee eden ee a GS ee ee ee ee ee T 266 7 3 1 Viewing a Taster Map o 24 206 db ek eke GR ee Ree Bowe 266 7 3 1 1 Raster Image Basic Settings 204 268 7 3 1 2 Raster Image Other Settings 20 270 7 3 2 Viewing a contour Map 271 7 3 3 Overlay contours on a raster map ooo a 0002 eee ee eee 272 7 3 4 Spectral Profile Plotting 02 020 00 20220004 273 Deg Fae Pe a ke Gd a a PE ee a 273 TAS 275 7 3 6 1 Setting up multi panel displays 277 7 3 6 2 Background Color a 277 a a RR A A E 277
205. 4m00 17d02m00 AZEL 123d48m29 15d41m41 ephemsrcname ephemeris source name to proper shifting to center on the moving source for imaging default if the source name in the data matches one of the known solar objects by the system this task automatically set the source name example moon plotlevel control for plotting of results options int O none 1 some 2 more lt O hardcopy default O no plotting example plotlevel lt 0 as abs plotlevel e g 1 hardcopy plot will be named lt sdfile gt _scans eps 1 plot raw data calibrated data for calmode baseline APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 326 plot raw or if exist calibrated data for calmode none 2 plot raw data progressively display baseline fitting for each scan and final calibrated data for calmode baseline DESCRIPTION Task sdtpimaging performs data selection calibration and imaging for single dish totalpower raster scan data This is a still experimental task made to work for the data taken at the ALMA Testing Facility ATF and OSF Currently this task directly accesses the Measurement Set data because of the data access efficiency So it differs from other single dish tasks that mostly operate on the ASAP scantable data format By setting calmode none one can run sdtpimaging to plot the data raw or calibrated if exists and further imaging by setting createimage True The calibration availab
206. 5 gt taskhelp Available tasks accum almasimmos applycal bandpass blcal browsetable clean clearcal clearplot clearstat concat deconvolve exportfits exportuvfits feather find flagautocorr flagdata flagmanager fluxscale fringecal ft gaincal hanningsmooth imcontsub imfit imhead immath immoments importasdm importfits importuvfits Accumulate incremental calibration solutions into a calibration table ALMA mosaic simulation task prototype Apply calibrations solutions s to data Calculates a bandpass calibration solution Calculate a baseline based calibration solution gain or bandpass Browse a table MS calibration table image Deconvolve an image with selected algorithm Re initializes the calibration for a visibility data set Clear the matplotlib plotter and all layers Clear all read write locks Concatenate two visibility data sets Image based deconvolver Convert a CASA image to a FITS file Convert a CASA visibility data set to a UVFITS file Feathering Combine two images using the Fourier Addition Find string in tasks task names parameter names Flag autocorrelations A11 purpose flagging task based on selections Enable list save restore and delete flag version files Bootstrap the flux density scale from standard calibrators Calculate a baseline based fringe fitting solution phase delay delay rate Note ct Insert a source model into the MODEL_DATA column o
207. 6 2 Directory Navigation e D 6 3 Shell Command and Capture 020002 ee ee eee D 7 Logging D 8 History and Searching Gotan Geek ke ve Tees D 10 On line editing D 11 Executing Python scripts ee D 12 How do l exit from CASA 2 ee E Appendix The Measurement Equation and Calibration E 1 The HBS Measurement Equation 0 0 a E 2 General Calibrater Mechanics 2 2 0 0 0 00 eee ee ee F Appendix Annotated Example Scripts F 1 NGC 5921 VLA red shifted HI emission 0 00 005 F 2 Jupiter VLA continuum polarization o o e e F 3 BIMA Mosaic Spectral Imaglidgl e G Appendix CASA Dictionaries G 1 AIPS CASA dictionary G 2 MIRIAD CASA dictionary 2 2 2 e G 3 CLIC CASA dictionary H Appendix Writing Tasks in CASA H 1 The XML filel H 2 The task_yourtask py file 00 0000 0020000000000 H 3 Example The clean task e eee eee H 3 1 File clean xml 365 365 367 367 367 368 368 369 369 370 370 372 372 374 375 375 377 377 379 379 381 382 382 383 384 384 388 389 389 414 453 473 473 473 473 H 3 2 File task_clean py List of Tables 2 1 Common MS Columns 2 0 0 00 2 78 2 2 Commonly accessed MAIN Table columns aooaa aa 00052408 79 4 1 Recognized Flux Density Calibrators
208. 6cm demo Clean up old files os system rm rf prefixt This is the output MS file name msfile prefix ms Calibration variables Use same prefix as rest of script calprefix prefix spectral windows to process usespw usespwlist 0 17 prior calibration to apply usegaincurve True gainopacity 0 0 reference antenna 11 11 VLA N1 calrefant 1i1 gtable calprefix gcal ftable calprefix fluxscale atable calprefix accum Polarization calibration setup APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS dopolcal True ptable calprefix pcal xtable calprefix polx Pol leakage calibrator poldfield 0137 331 Pol angle calibrator polxfield 1331 305 At Cband the fractional polarization of this source is 0 112 and the R L PhaseDiff 66deg EVPA 33deg polxfpol 0 112 polxrlpd_deg 66 0 Dictionary of IPOL in the spw polxipol 0 7 462 21 7 510 Make Stokes lists for setjy polxiquv for spw in 0 1 ipol polxipol spw fpol polxfpol ppol ipol fpol rlpd polxrlpd_deg pi 180 0 qpol ppol cos rlpd upol ppol sin rlpd polxiquv spw ipol qpol upol 0 0 Split output setup srcname JUPITER srcsplitms calprefix srcname split ms calname 0137 331 calsplitms calprefix cal
209. 7 4 1 Data Display Options Panel for Measurement Sets 278 D es Po da a ees 279 eyo orerrr 279 Spre be Raa K Gwe ary de eR a 281 La eae Oe wae Ee 282 7 4 1 5 MS Options Advanced 00005002 eee 285 7 4 1 6 MS Options Apply Button 286 Sea ee ee Re ge BL Re Pee ek ee Be A E 286 288 naar Dewi hep ee wh Sg 288 bg beige fob ent Roe Gu eos ee a Ge ay ne 288 Paa tates A a a ae ee ee oe ee ee 289 Gaia fo ee ee Se as Be a es ee eee es ee 289 lee ue St Be ea Bate cal ee a ee ed oe Bee ee E 290 bi ae ae oh ese Bk geet Sve eke Cte A ee ee ee dee YG 290 See Martek Gea oe cea aaa a en ete 291 BOETE oe eh ek Hh ee we eo ee a a So Gee e 294 Del SAAVEDRA wa a ha ta aide aa a AAA AA 294 A212 sdsmooth sao ao pras RRR e ee A 297 Pee eee E te ee meee eee A 298 ALZA LA gdcall s ss 5 8 ao be Ge Ae eB Boke Oe eb ee amp GA ee S 302 A 2 1 50 SdCoadd o 3248 h 2544008 oe een eee EME ER ES dd 2 306 A216 sdflag o copin iaoe e G ai a p eee oh eee ea ee es 308 AZL SOP AE E 309 A 21 8 SOTA errorea 4A oR Bw Re Se eS ew ae BLES 312 A 2 1 9 sdmath nsss serar reroror eepe ee 313 ner a a esse E ee eee ee 315 A a a a ee ep ee te See E 319 Aa a Pee a eye O a a ee eee ee eee eee 321 O oe xt eed oa Beko ee Sone dee edie at ee eee E tt 321 be erpne amp A ete A Bee ee SX Se le a 324 eer ee 326 EE 326 a as 339 ro AN 340 A ET 342 Mok Books RRR SE Lae wn AAA as 343 bbe W
210. 7 8 9 10 11 32 chans print field 2 8 NGC4826 spwids 12 13 14 15 64 chans print print See listobs summary in logger PERRA RARO RORA RO ROA RARO ROOR ARO ROIRA RARO RARA HOR ORORR RO R AERA E RHA R ERR AR RRA H RRA R RRR Plotting and Flagging HEFHHHHEHHHHEAEAHEAREHAAAEHER ARERR AERA A RHR AR RE RA AHHH AR RRA H RRR R The plotxy task is the interactive x y display and flagging GUI print Plotxy default plotxy Here we will suggest things to plot and actually only do a few near the end of this task block If you like you can uncomment these when you run this script First look at amplitude as a funciton of uv distance using an average over all channels for each source Interactive plotxy plotxy vis ngc4826 tutorial ms xaxis uvdist yaxis amp field 0 spw 073 averagemode vector width 1000 selectplot True title Field 0 SPW 073 Pause script if you are running in scriptmode user_check raw_input Return to continue script n NOTE width here needs to be larger than combination of all channels selected with spw and or field Since field and spw are unique in this case both don t need to be specified however plotting is much faster if you help it by selecting both Now average over all times across scans but not over channel and plot versus channel There are four 64 channel spws set end to end by plotxy You
211. 7 showing the use of the Display Axes controls to change the axes on the animation and sliders 7 4 1 4 MS Options Flagging Options These options allow you to edit flag or unflag MS data The Crosshair and Rectangle Region Mouse Tools 7 2 3 are used on the display to select the area to edit When using the Rectangle Region tool double click inside the selected rectangle to confirm the edit The options below determine how edits will be applied e Show Flagged Regions CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 283 iv Data Display Options n4826_16apr ms Advanced MS and Visibility Selection Display Axes X Axis Baseline Y Axis Time Animation Axis Spectral Window 2000 3000 4000 5000 6000 5000 Baseline Channel x 0 BN Polarization Soo s Normal Flagging Options Blink J 10 fsec Compact Basic Settings Start Ena Star Figure 7 18 The MS for NGC4826 continuing from Figure We have now put spectral window on the Animation Axis and used the tapedeck to step to spw 2 where we see the data from the rest of the scans Now channels is on a Display Axes slider which has been dragged to show Channel 33 You have the option to display flagged regions in the background color as in TVFLG or to highlight them with color In the former case flagged
212. 8 These are not discussed in this walk through see the indicated sections for details See Chapter 5 for more on synthesis imaging 1 5 4 1 Cleaning a single field image or a mosaic The CLEAN algorithm is the most popular and widely studied method for reconstructing a model image based on interferometer data It iteratively removes at each step a fraction of the flux in the brightest pixel in a defined region of the current dirty image and places this in the model image The clean task implements the CLEAN algorithm for single field data The user can choose from a number of options for the particular flavor of CLEAN to use CHAPTER 1 INTRODUCTION 72 Often the first step in imaging is to make a simple gridded Fourier inversion of the calibrated data to make a dirty image This can then be examined to look for the presence of noticeable emission above the noise and to assess the quality of the calibration by searching for artifacts in the image This is done using clean with niter 0 The clean task can jointly deconvolve mosaics as well as single fields See 5 3 for an in depth discussion of the clean task 1 5 4 2 Feathering in a Single Dish image If you have a single dish image of the large scale emission in the field this can be feathered in to the image obtained from the interferometer data This is carried out using the feather tasks as the weighted sum in the uv plane of the gridded transforms of the
213. 8 128 128 Image size in pixels nx ny cell 1 0arcsec The image cell size in arcseconds x y phasecenter J2000 13h27m20 98 43d26m28 0 J2000 13h30m52 158 43d23m08 00 The other parameters are described in clean and multi scale cleaning in available Mosaicing and MEM is not yet included in widefield 5 4 1 ftmachine modes for widefield The crucial part of widefield is the parameters under ftmachine The three types of use are 1 w projection only 2 facets only 3 w projection with facets 5 4 1 1 pure w projection The pure w projection mode is invoked using ftmachine wproject ftmachine wproject Gridding method for the image wproject ft wprojplanes 64 Number of planes to use in wprojection convolutiuon function facets 1 Number of facets along each axis in main image only A reasonable value for wprojplanes is equal to Mw Bmaz ink x imagewidth inarcmin 600 with a minimum value of nuy 16 The w projection algorithm is much faster than using faceting but it does consume a lot of memory On most 32 bit machines with 1 or 2 Mbytes of memory images larger than about 4000 x 4000 cannot be made 5 4 1 2 faceting only Faceting only mode will break the image into many small parts This is invoked using ftmachine ft ftmachine ft Gridding method for the image wproject ft 7 Number of facets along each axis in main image only facets In this examp
214. 8 2 12 LSRK 4 3962126e 10 4096 6104 2336 13 LSRK 4 264542e 10 4096 6104 2336 14 LSRK 4 159498e 10 4096 6104 2336 15 LSRK 4 3422823e 10 4096 6104 2336 27 OrionS_ps 02 09 51 4x 30 0s 0 05 35 13 5 05 24 08 2 12 LSRK 4 3962126e 10 4096 6104 2336 13 LSRK 4 264542e 10 4096 6104 2336 14 LSRK 4 159498e 10 4096 6104 2336 15 LSRK 4 3422823e 10 4096 6104 2336 The HC3N and CH30H lines are in IFs O and 2 respectively of scans 20 21 22 23 We will pull these out in our calibration HHHHHHHHHHHHHHHHHHHHHHHH HS Calibrate data HHHHHHHHHHHHHHHHHHHHHHEH HS We will use the sdcal task to calibrate the data Set the defaults default sdcal You can see the inputs with inp Set our sdfile which would have been set from our run of sdlist if we were not cautious and reset defaults sdfile OrionS_rawACSmod fluxunit K Lets leave the spectral axis in channels for now specunit channel This is position switched data so we tell sdcal this APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 331 calmode ps For GBT data it is safest to not have scantable pre average integrations within scans average True scanaverage False We do want sdcal to average up scans and polarization after calibration however The averaging of scans are weighted by integration time and Tsys and the averaging of polarization by Tsys timeaverage True tweight t
215. 9 30 0 2 1 1445 09900002_0 0 09 33 00 0 09 48 00 0 3 2 N5921_2 0 09 50 30 0 09 51 00 0 4 1 1445 09900002_0 0 10 22 00 0 10 23 00 0 5 1 1445 09900002_0 0 10 26 00 0 10 43 00 0 6 2 N5921_2 0 10 45 30 0 10 47 00 0 7 1 1445 09900002_0 0 Fields 3 ID Code Name Right Ascension Declination Epoch 0 C 1331 30500002_013 31 08 29 30 30 32 96 J2000 1 A 1445 09900002_014 45 16 47 09 58 36 07 J2000 2 N5921_2 15 22 00 00 05 04 00 00 J2000 Spectral Windows 1 unique spectral windows and 1 unique polarization setups SpwID Chans Frame Chi MHz Resoln kHz TotBW kHz Ref MHz Corrs 0 63 LSRK 1412 68608 24 4140625 1550 19688 1413 44902 RR LL Feeds 28 printing first row only Antenna Spectral Window Receptors Polarizations 1 1 2 R L Antennas 27 E E SE SE SE SE SEE SEE SE SE SE SE SE SE SE SE SE SE SE SE SE SE SE SE SE SE SE SE SE SE SE SE SE SE SE SE SE SE SE SE HHH H HH HH OH OF ID Name Station Diam Long Lat 0 1 VLA N7 25 0 m 107 37 07 2 33 54 12 9 1 2 VLA W1 25 0 m 107 37 05 9 33 54 00 5 2 3 VLA W2 25 0 m 107 37 07 4 33 54 00 9 3 4 VLA E1 25 0 m 107 37 05 7 33 53 59 2 4 5 VLA E3 25 0 m 107 37 02 8 33 54 00 5 5 6 VLA E9 25 0 m 107 36 45 1 33 53 53 6 6 7 VLA E6 25 0 m 107 36 55 6 33 53 57 7 7 8 VLA W8 25 0 m 107 37 21 6 33 53 53 0 8 9 VLA N5 25 0 m 107 37 06 7 33 54 08 0 9 10 VLA W3 25 0 m 107 37 08 9 3
216. 92 1_regression ngc5921 ms ANTENNA Subtable has 28 rows DATA_DESCRIPTION Table home sandrock smyers Testing 2 008 03 ngc5 921_regression ngc5921 ms DATA_D Subtable has 1 rows FEED Table home sandrock smyers Testing 2 008 03 ngc5 92 1_regression ngc5 92 1 ms FEED Subtable has 28 rows FLAG_CMD Table home sandrock smyers Testing 2 008 03 ngc5 92 1_regression ngc5921 ms FLAG_C Subtable has no rows table keywords FIELD Table nome sandrock smyers Testing 2 008 03 ngc5 92 1_regression ngc5 921 ms FIELD Subtable has 3 rows HISTORY Table home sandrock smyers Testing 2 008 03 ngc5921_regression ngc5921 ms HISTORY Subtable has 379 rows OBSERVATION Table home sandrock smyers Testing 2 008 03 ngc5 92 1_regression ngc5921 ms OBSER Subtable has 1 rows POINTING Table home sandrock smyers Testing 2 008 03 ngc5 921_regression ngc5921 ms POINTING Subtable has no rows field keywords POLARIZATION Table nome sandrock smyers Testing 2 008 03 ngc5 92 1_regression ngc5921 ms POLARI Subtable has 1 rows PROCESSOR Table home sandrock smyers Testing 2 008 03 ngc5 921_regression ngc5921 ms PROCE Subtable has no rows SPECTRAL_WINDOW Table home sandrock smyers Testing 2 008 03 ngc5 92 1_regression ngc5921 ms SPECTR Subtable has 1 rows STATE Table nome sandrock smyers Testing 2 008 03 ngc5 92 1_regression ngc5 92 1 ms STATE Subtable has no rows SOURCE Table home sandrock smyers Testing 2 008 03 ngc5 92 1_regression n
217. 924 max array 0 02945151 maxpos array 124 131 0 211 gt maxposf 15 22 04 016 05 04 44 999 I 1 41332e 09Hz mean array 0 00078684 gt medabsdevmed array 0 00152346 median array 0 00013726 min array 0 00612453 minpos array 142 110 0 21 minposf 15 21 45 947 04 59 29 990 I 1 41332e 09Hz npts array 1681 gt quartile array 0 00305395 yms array 0 00411418 gt sigma array 0 00403944 sum array 1 3226716 sumsq array 0 02845345 trc array 148 148 0 211 tref 15 21 39 919 05 08 59 981 I 1 41332e 09Hz BETA ALERT The return dictionary currently includes NumPy array values which have to be accessed by an array index to get the array value To access these dictionary elements use the standard Python dictionary syntax e g xstat lt key string gt lt array index gt For example to extract the standard deviation as a number mystddev xstat sigma 0 6 7 2 Examples using imstat We give a few examples of the use of imstat in particular to extact the information from the return value Select a two box region box 1 bottom left coord is 2 3 and top right coord is 14 15 box 2 bottom left coord is 30 31 and top right coord is 42 43 xstat imstat myImage box 2 3 14 15 30 31 42 43 Select the same two box regions but only channels 4 and 5
218. 94496GHz stokes Stokes parameters to image default I example stokes IQUV Options I IV QU IQUV RR LL XX YY RRLL XXYY niter Maximum number iterations if niter 0 then no CLEANing is done invert only default 500 example niter 5000 gain Loop gain for CLEANing default 0 1 example gain 0 5 threshold Flux level at which to stop CLEANing default 0 0OmJy example threshold 2 3mJy always include units threshold 0 0023Jy threshold 0 0023Jy beam okay also interactive use interactive clean with GUI viewer default interactive False example interactive True interactive clean allows the user to build the cleaning mask interactively using the viewer The viewer will appear every npercycle interation but modify as needed The final interactive maks is saved in the file imagename_interactive mask The initial masks use the union of mask and cleanbox see below amp gt amp gt amp gt interactive True expandable parameter npercycle this is the number of iterations between each clean to update mask interactively Set to about niter 5 but can also be APPENDIX H APPENDIX WRITING TASKS IN CASA 496 changed interactively mask Specification of cleanbox es mask image s and or region s to be used for CLEANing As long as the image has the same shape size mask images from a previous interactive session can be us
219. A lt 2 gt sd rcParams Out 2 insitu True plotter colours plotter decimate False plotter ganged True plotter gui True plotter histogram False plotter linestyles plotter panelling s plotter papertype A4 plotter stacking p gt scantable autoaverage True gt scantable freqframe LSRK scantable save ASAP scantable storage memory gt scantable verbosesummary False useplotter True gt verbose True The use of these parameters is described in detail in the ASAP Users Guide You can also change these parameters through the sd rc function The use of this is described in help sd rc CASA lt 3 gt help sd rc Help on function rc in module asap rc group kwargs Set the current rc params Group is the grouping for the rc eg for scantable save the group is scantable for plotter stacking the group is plotter and so on kwargs is a list of attribute APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 343 name value pairs eg rc scantable save SDFITS sets the current rc params and is equivalent to rcParams scantable save SDFITS Use rcdefaults to restore the default rc params after changes A 3 2 Import Data can be loaded into ASAP by using the scantable function which will read a variety of recognized formats RPFITS varieties of SDFITS t
220. A column as per the fitmode subtract Done with calibration Here is how to make a dirty image cube print Clean dirty image default clean Pick up our split source continuum subtracted data vis srcsplitms dirtyname prefix dirtyimg imagename dirtyname mode channel nchan 46 start 5 width 1 field 0 spw imsize 256 256 cell 15 15 weighting briggs robust 0 5 No cleaning niter 0 saveinputs clean prefixt invert saved 405 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS Pause script if you are running in scriptmode if scriptmode inpO user_check raw_input Return to continue script n clean dirtyimage dirtyname image Get the dirty image cube statistics dirtystats imstat dirtyimage See ee as Now clean an image cube of N5921 print Clean clean default clean Pick up our split source continuum subtracted data vis srcsplitms Make an image root file name imname prefix cleanimg imagename imname Set up the output image cube mode channel nchan 46 start 5 width 1 This is a single source MS with one spw field 0 spw Standard gain factor 0 1 gain 0 1 Set the output image size and cell size arcsec imsize 256 256 Do a simple Cl
221. AN image bmaj bmin bpa elliptical Gaussian restoring beam default units are in arc seconds for bmaj bmin degrees for bpa default restoringbeam Use PSF calculated from dirty bean example restoringbeam 10arcsec circular Gaussian FWHM 10 example restoringbeam 10 0 5 0 45 0deg 10 x5 at 45 degrees pbcor Output primary beam corrected image default pbcor False output un corrected image example pbcor True output pb corrected image masked outside minpb Note if you set pbcor False you can later recover the pbcor image by dividing by the flux image e g using immath minpb Minimum PB level to use default 0 1 example minpb 0 01 Note this minpb is always in effect regardless of pbcor True False async Run asynchronously default False do not run asychronously lt example gt APPENDIX H APPENDIX WRITING TASKS IN CASA lt task gt lt casaxml gt H 3 2 File task_clean py Task clean implementation file import os from taskinit import from cleanhelper import def clean vis imagename field spw selectdata timerange uvrange antenna scan mode niter gain threshold psfmode imagermode ftmachine mosweight scaletype multiscale negcomponent interactive mask nchan start width imsize cell phasecenter restfreq stokes weighting robust uvtaper outertaper innertaper modelimage restoringbeam pbcor minpb noise npixels npercycle cyclefactor cyclespeedup
222. APTER 5 SYNTHESIS IMAGING 198 5 2 11 6 briggsabs weighting For weighting briggsabs a slightly different Briggs weighting is used with Wi A AA 9 6 W R 20 Wi where R is the robust parameter and op is the noise parameter This choice brings up the sub parameters weighting briggsabs Weighting to apply to visibilities robust 0 0 Briggs robustness parameter noise 0 0Jy noise parameter for briggs weighting when rmode abs npixels 0 number of pixels to determine uv cell size 0 gt field of view Otherwise this works as weighting briggs above 5 2 11 5 5 2 12 Parameter vis The value of the vis parameter is either the name of a sin gle MS or a list of strings containing the names of multiple Beta Alert MSs that should be processed to produce the image The Multi MS handling is not percolated MS referred to by the first name in the list if more than to the tasks yet as we are still work one is used to determine properties of the image such as ing on this Use single MS only channelization and rest frequency For example vis ngc5921 ms set a single input MS while vis ngc5921_day1 ms ngc5921_day2 ms ngc5921_day3 ms points to three separate measurement sets that will be gridded together to form the image This means that you do not have to concatenate datasets for example from different configurations bef
223. ASA lt 1 gt inp clean CASA lt 2 gt inp clean Sone aS gt inp clean CASA lt 3 gt inp clean CASA lt 4 gt inp clean Babe Se gt inp clean CASA lt 5 gt taskname clean CHAPTER 1 INTRODUCTION 52 all do the same thing When you invoke the task inputs via inp you see a list of the parameters their current values and a short description of what that parameters does For example starting from the default values CASA lt 18 gt inp clean clean Deconvolve an image with selected algorithm vis ae name of input visibility file imagename 22 Pre name of output images field z 2 Field Name spw ad Spectral windows channels is all selectdata False Other data selection parameters mode mfs Type of selection mfs channel velocity frequency niter 500 Maximum number of iterations gain 0 1 Loop gain for cleaning threshold E 0 0mJy Flux level to stop cleaning Must include units psfmode clark method of PSF calculation to use during minor cycles imagermode de Use csclean or mosaic If use psfmode multiscale multi scale deconvolution scales pixels interactive False use interactive clean with GUI viewer mask cleanbox es mask image s and or region s imsize 256 256 x and y image size in pixels cell 1 0arcsec 1 0arcsec x and y cell size default unit arcsec phasec
224. ASA root in your path using one of the above mechanisms CHAPTER 1 INTRODUCTION 29 1 2 1 1 Environment Variables Before starting up casapy you should set or reset any environment variables needed as CASA will adopt these on startup For example the PAGER environment variable determines how help is displayed in the CASA terminal window see 1 2 8 3 The choices are less more and cat In bash pick one of PAGER less PAGER more PAGER cat followed by export PAGER In csh or tcsh pick one of setenv PAGER less setenv PAGER more setenv PAGER cat The actions of these are as if you were using the equivalent Unix shell command to view the help material See 1 2 8 3 for more information on these choices We recommend using the cat option for most users as this works smoothly both interactively and in scripts BETA ALERT There is currently no way within CASA to change these environment variables 1 2 1 2 Where is CASA Note that the path to the CASA installation which contains the scripts and data repository will also depend upon the installation With a default installation under Linux this will probably be in usr lib casapy while in a Mac OSX default install it will likely be an application in the Applications folder with the data repository in opt casa You can find the location after initialized by looking at the CASAPATH environment variable You can find it within casapy by pathname 0s environ get
225. ASA will stop right then and there 1 2 4 What happens if something goes wrong BETA ALERT This is a Beta Release and there are still ways to cause CASA to crash Please check the CASA Home Page for Beta Release information including a list of known problems If you think you have encountered an unknown problem please consult the CASA HelpDesk contact information on the CASA Home Page See also the caveats to this Beta Release 1 1 for pointers to our policy on User Support First always check that your inputs are correct use the CHAPTER 1 INTRODUCTION 31 help lt taskname gt L259 or help par lt parameter name gt 1 2 8 4 to review the inputs output 1 2 5 Aborting CASA execution If something has gone wrong and you want to stop what is executing then typing CNTL C Control and C keys simultaneously will usually cleanly abort the application This will work if you are running a task synchronously If this does not work on your system or you are running a task asynchronously then try CNTL Z to put the task or shell in the background and then follow up with a kill 9 lt PID gt where you have found the relevant casapy process ID PID using ps see 1 2 6 below See for more information on running tasks If the problem causes CASA to crash see the next sub section 1 2 6 What happens if CASA crashes Usually restarting casapy is sufficient to get you going again after a crash takes you o
226. ASAP example the ASAP format is easiest for further sd processing use MS for CASA imaging If ASCII then will append some stuff to the outfile name overwrite overwrite the output file if already exists options bool True False default False WARNING if outform ASCII this parameter is ignored plotlevel control for plotting of results options int O none l some 2 more lt O hardcopy default O no plotting example plotlevel lt 0 as abs plotlevel e g 1 gt hardcopy of final plot will be named lt outfile gt _smspec eps DESCRIPTION Task sdsmooth performs smoothing of the single dish spectra Set plotlevel lt 1 to plot spec trum before and after smoothing A 2 1 3 sdbaseline Keyword arguments APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 299 sdfile name of input SD dataset fluxunit units for line flux options K Jy default keep current fluxunit WARNING For GBT data see description below gt gt gt fluxunit expandable parameter telescopeparm the telescope characteristics options str name or list list of gain info default none set example if telescopeparm it tries to get the telescope name from the data Full antenna parameters diameter ap eff known to ASAP are gt ATPKSMB ATPKSHOH ATMOPRA DSS 43 gt CEDUNA HOBART For GBT it fixes default fluxunit to K first then convert to
227. ATA_DESCRIPTION 2 rows DOPPLER lt absent gt FEED 28 rows FIELD 13 rows FLAG_CMD lt empty gt FREQ_OFFSET lt absent gt HISTORY 7058 rows OBSERVATION 1 row POINTING 2604 rows POLARIZATION 1 row PROCESSOR lt empty gt SOURCE lt empty gt see FIELD SPECTRAL_WINDOW 2 rows STATE lt empty gt SYSCAL lt absent gt WEATHER lt absent gt fosooooooooooooooooooooooooooooooooooooooooooooooooooooooo Data Examination and Flagging fosoooooooooooooooooooooooooooooooooooooooooooooooooooooos Use Plotxy to interactively flag the data print Plotxy default plotxy print Now we use plotxy to examine and interactively flag data vis msfile The fields we are interested in 1331 305 JUPITER 0137 331 selectdata True First we do the primary calibrator field 1331 305 Plot only the RR and LL for now correlation RR LL As of 2 3 0 Patch 3 you can extend the flags to the cross correlations But this slows things down immensely extendflag T extendcorr all 423 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS Plot amplitude vs uvdist xaxis uvdist yaxis amp multicolor both Use the field name as the title selectplot True title field iteration plotxy O print Print HH SS Sse SSeS SSeS Ree SS SRS SSS A 9229 RSS print Plotxy print Showing
228. AY vlev 0 0189144 1 06089 2 Y Pixel treatment edge Resampling mode nearest Data range Scaling power cycles A Y Hoama yw Colormap Hot Metal 1 Position tracking Axis labels Beam Ellipse L Axis label properties Color Wedge Apply Save I Restore L eel R jupiter6cm demo clean1 image g Viewer Print Manager x Y Viewer Display Panel Working Directory home sandrock smyers Testing Patch2 Jupiter Data DisplayPanel Tools View Current Canvas Size 721 x 703 pixels 12 OR as lt u Pe 3 g E 22 E 25 Ourputfile outjupiter demo ps elv PS PDF Output media Lerrer y m PS PDF Orientation portrait 2 if PS PDF Resolution dpi oe Y 30 in z Image Output size pixels a BEAC 48 00 F mage Output size multiplicative factor 1 00 SF Y 30 F es Save Print Dismiss 47 00 F 7 30 F 7 46 00 F 7 30 F 7 45 00 F 7 30 P a o L al 4 44 00 O 30 E i L ql heeMy cs s s s s s s 00557457 39 367 337 30 27 24 J2000 Right Ascension a x 0 00794789 Jy beam Pixel 103 162 0 0 00 55 44 900 04 46 56 419 I 12 443 km s 287 Figure 7 19 Setting up to print to a file The background color has been set to white the line width to 2 and the print resolution to 600 dpi for an postscript plot To make the plot use the Save button on t
229. CASA lt 115 gt antlist 0 Out 115 O CASA lt 116 gt antlist 4 Out 116 4 CASA also uses 0 based indexing internally for elements in the Measurement Set MS the basic construct that contains visibility and or single dish data see Chapter 2 Thus we will often talk about Field or Antenna ID s which will be start at 0 For example the first field in an MS would have FIELD_ID 0 in the MSselect syntax and can be addressed as be indexed as field 0 in most tasks as well as by name field 0137 331 assuming thats the name of the first field You will see these indices in the MS summary from the task listobs 1 2 7 4 Indentation Python pays attention to the indentation of lines as it uses indentation to determine the level of nesting in loops Be careful when cutting and pasting if you get the wrong indentation then unpredictable things can happen usually it just gives an error See Appendix D 2 for more information 1 2 7 5 System shell access If you want to access system commands from a script use the os system command Appendix D 6 1 In interactive mode any input line beginning with a character is passed verbatim minus the of course to the underlying operating system Also several common commands 1s pwd less may be executed with or without the although the cp command must use and cd must be executed without the For example CASA lt 5 gt rm r m
230. CASA Synthesis amp Single Dish Reduction Cookbook Beta Release Edition Patch 4 Version 2 4 0 NGC4826 CO J 1 O Moment 1 36 550 g 24 500 2 or E 450 gt 21 41 00 8 o ae a 48 400 O aa 36 S 350 gQ em 300 eh O i i t t E 250 12 56 48 465 44 425 40 395 J2000 Right Ascension e IX Viewer Display Panel 000 X Image Profile FLS3a_HI image A BAsa 72s 9 age es ADAG AAA e fe el e mi a roe M E 9000 e f53a Hlimage Coordinate world LJ 171741 633 6043458 594 SSO e a e tn cine ETE Version June 29 2009 CASA Synthesis amp Single Dish Reduction Cookbook Beta Release Edition Chef Editor Steven T Myers CASA Project Scientist Sous Chef Joe McMullin CASA Project Manager CASA SYNTHESIS amp SINGLE DISH REDUCTION COOKBOOK BETA RELEASE EDITION Version June 29 2009 2007 National Radio Astronomy Observatory The National Radio Astronomy Observatory is a facility of the National Science Foundation operated under cooperative agreement by Associated Universities Inc This tome was scribed by The CASA Developers and the NRAO Applications User Group NAUG Do you dare to enter CASA Stadium and join battle with the Ironic Chefs Let us see whose cuisine reigns supreme Contents 1 Introduction 20 1 1 About This Beta Release e
231. CASA document system Most selection can be carried out using the other selection parameters However these are merely shortcuts to the underlying TaQL selection For example field and spectral window selection can be done using msselect rather than through field or spw msselect FIELD_ID 0 Field id O only msselect FIELD_ID lt 1 Field id O and 1 msselect FIFLD_ID IN 1 2 Field id 1 and 2 msselect FIELD_ID 0 amp amp DATA_DESC_ID 3 Field id O in spw id 3 only BETA ALERT The msselect style parameters will be phased out of the tasks TaQL selection will still be available in the Toolkit Chapter 3 Data Examination and Editing 3 1 Plotting and Flagging Visibility Data in CASA The tasks available for plotting and flagging of data are e flagmanager manage versions of data flags 3 2 e flagautocorr non interactive flagging of auto correlations 3 3 e plotxy create X Y plots of data in MS flag data 3 4 e flagdata non interactive flagging of data 3 5 browsetable browse data in any CASA table including a MS e plotants create simple plots of antenna positions 3 7 casaplotms prototype next generation X Y MS plotter experimental 3 8 The following sections describe the use of these tasks Information on other related operations can be found in e listobs list what s in a MS 8 2 3 e selectdata general data selection syntax
232. Displaying pol I now You should overlay pola vectors APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 452 print Bring up the Load Data panel print print Use LEL for POLA VECTOR with cut above 6 mysigma in POLI str 6 mysigma print For example print polaimage poliimage gt 0 0048 print print In the Data Display Options for the vector plot print Set the x y increments to 2 default is 3 print Use an extra rotation this 90deg to get B field print Note the lengths are all equal You can fiddle these print print You can also load the poli image as contours Pause script if you are running in scriptmode if scriptmode user_check raw_input Return to continue script n NOTE the LEL will be something like jupiter6cm demo polimg clean image pola jupiter6cm demo polimg clean image poli gt 0 005 NOTE The viewer can take complex images to make Vector plots although the image analysis tasks and ia tool cannot yet handle these But we can use the imagepol tool which is not imported by default to make a complex image of the linear polarized intensity for display See CASA User Reference Manual http casa nrao edu docs casaref imagepol Tool html Make an imagepol tool and open the clean image potool casac homefinder find_home_by_name imagepolHome po potool create po open polimage Use complexlinpol to make a Q i
233. E SOURCE MS AND THEN IMAGE THE CALIBRATOR HHHHHHHHHHHEE EHH HHHHHHAAEHA AREER RRR R AREA ARH HHH RRA AAA AR Split out calibrated target source and calibrater data print Split default split print Splitting 3C273 data to ngc4826 tutorial 16apr98 3C273 split ms split vis ngc4826 tutorial ms outputvis ngc4826 tutorial 16apr98 3C273 split ms APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 466 field 0 spw 073 0763 datacolumn corrected print Splitting 1310 323 data to ngc4826 tutorial 16apr98 1310 323 split ms split vis ngc4826 tutorial ms outputvis ngc4826 tutorial 16apr98 1310 323 split ms field 1 spw 4 11 0731 datacolumn corrected print Splitting NGC4826 data to ngc4826 tutorial i6apr98 src split ms split vis ngc4826 tutorial ms outputvis ngc4826 tutorial 16apr98 src split ms field 278 spw 12715 0763 datacolumn corrected HHHHHHHHHHHER HEE HHHHHAAAEHAA ERE HORA EERE HARE R RRR AAA AAA If you want to use plotxy before cleaning to look at the split ms plotxy vis ngc4826 tutorial 16apr98 src split ms xaxis time yaxis amp HHHHHHHHHHAA RHEE HHHHRAAEHA AAR HHR RRR E HAAR RRR ARR AAA AAA You might image the calibrater data print Clean 1310 323 default clean clean vis ngc4826 tutorial
234. EXT day timerange 09 44 00 pick data within one integration of time timerange amp gt 10 24 00 data after this time uvrange Select data within uvrange default units meters default all example APPENDIX H APPENDIX WRITING TASKS IN CASA 492 uvrange 0 1000klambda uvrange from 0 1000 kilo lambda uvrange amp gt 4klambda uvranges greater than 4 kilo lambda antenna Select data based on antenna baseline default all If antenna string is a non negative integer it is assumed to be an antenna index otherwise it is considered an antenna name antenna 5kamp 6 baseline between antenna index 5 and index 6 antenna VA05 amp amp VA06 baseline between VLA antenna 5 and 6 antenna 5kamp 6 7kamp 8 baselines 5 6 and 7 8 antenna 5 all baselines with antenna index 5 antenna 05 all baselines with antenna number 05 VLA old name antenna 5 6 9 all baselines with antennas 5 6 9 index numbers scan Scan number range default all example scan 1 5 Check go listobs to insure the scan numbers are in order mode Frequency Specification NOTE See examples below default mfs mode mfs means produce one image from all specified data mode channel Use with nchan start width to specify output image cube See examples below mode velocity means channels are specified in velocity mode frequency me
235. F Frame RefVal RefPix Sa a ae a a 2 SS Se eS a a ee SS a SS Se 20 OrionS_psr 01 45 58 4x 30 0s 0 05 15 13 5 05 24 08 2 0 LSRK 4 5489354e 10 4096 6104 233 1 LSRK 4 5300785e 10 4096 6104 233 2 LSRK 4 4074929e 10 4096 6104 233 3 LSRK 4 4166215e 10 4096 6104 233 21 OrionS_ps 01 48 38 4x 30 08 0 05 35 13 5 05 24 08 2 0 LSRK 4 5489354e 10 4096 6104 233 1 LSRK 4 5300785e 10 4096 6104 233 2 LSRK 4 4074929e 10 4096 6104 233 3 LSRK 4 4166215e 10 4096 6104 233 22 OrionS_psr 01 51 21 4x 30 0s 0 05 15 13 5 05 24 08 2 0 LSRK 4 5489354e 10 4096 6104 233 1 LSRK 4 5300785e 10 4096 6104 233 2 LSRK 4 4074929e 10 4096 6104 233 3 LSRK 4 4166215e 10 4096 6104 233 23 OrionS_ps 01 54 01 4x 30 08 0 05 35 13 5 05 24 08 2 0 LSRK 4 5489354e 10 4096 6104 233 1 LSRK 4 5300785e 10 4096 6104 233 2 LSRK 4 4074929e 10 4096 6104 233 3 LSRK 4 4166215e 10 4096 6104 233 24 OrionS_psr 02 01 47 4x 30 0s 0 05 15 13 5 05 24 08 2 12 LSRK 4 3962126e 10 4096 6104 2336 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 330 13 LSRK 4 264542e 10 4096 6104 2336 14 LSRK 4 159498e 10 4096 6104 2336 15 LSRK 4 3422823e 10 4096 6104 2336 25 OrionS_ps 02 04 27 4x 30 08 0 05 35 13 5 05 24 08 2 12 LSRK 4 3962126e 10 4096 6104 2336 13 LSRK 4 264542e 10 4096 6104 2336 14 LSRK 4 159498e 10 4096 6104 2336 15 LSRK 4 3422823e 10 4096 6104 2336 26 OrionS_psr 02 07 10 4x 30 08 0 05 15 13 5 05 24 0
236. FITS The sdsave task is available exclusively for exporting with data selection options The sdcoadd task is available to merge data in separate data files into one You can get a brief summary of the data in a file using the sdlist task Plotting of spectra is handled in the sdplot task It also offers some selection averaging and smoothing options in case you are working from a dataset that has not been split or averaged Note that there is some rudimentary plotting capability in many of SD tasks controlled through the plotlevel parameter to aid in the assessment of the performance of these tasks Scaling of the spectra and Tsys is available in the sdscale For arithmetic operations of spectra in separate scantables a new task sdmath is added Calculation of statistics on spectral regions is available in the sdstat task Results are passed in a Python dictionary return variable Basic Gaussian line fitting is handled by the sdfit task It can deal with the simpler cases and offers some automation as well as interactive selection of fitting region but more complicated fitting is best accomplished through the toolkit sd fitter Basic non interactive channel flagging is available in the sdflag task By default or by specifying outfile parameter a new file is created containing dataset with the flag information To update flags in the input data outfile none must be set Limited total power data analysis functionality is availab
237. False It is still experimental and limited to the data obtained with the two element synthesis data e Importing of Nobeyama Radio Observatory NRO OTF data is now available However it is still experimental and only tested to work from toolkit level Use the summary function to examine the data and get basic information APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING CASA lt 8 gt scans summary IFs Polarisations Channels Observer Obs Date Project Obs Type Antenna Name Flux Unit Rest Freqs Abcissa Selection Scan Source 26 2 8192 linear Joseph McMullin 2006 01 19 01 45 58 AGBTO6A_018_01 Off0n PSWITCHOFF TPWCAL GBT Jy 4 5490258e 10 Hz Channel none Time Integration Beam Position J2000 20 OrionS_psr 0 05 0 1 2 3 21 OrionS_ps 0 05 0 1 2 3 22 OrionS_psr 0 05 0 1 2 3 23 OrionS_ps 0 05 0 1 2 3 24 OrionS_psr 0 05 12 13 35 15 35 15 Frame RefVal 01 45 58 4x 713 5 05 24 08 2 LSRK 4 5489354e 10 LSRK 4 5300785e 10 LSRK 4 4074929e 10 LSRK 4 4166215e 10 01 48 38 4x 13 5 05 24 08 2 LSRK 4 5489354e 10 LSRK 4 5300785e 10 LSRK 4 4074929e 10 LSRK 4 4166215e 10 01 51 21 4x 13 5 05 24 08 2 LSRK 4 5489354e 10 LSRK 4 5300785e 10 LSRK 4 4074929e 10 LSRK 4 4166215e 10 01 54 01 4x 13 5 05 24 08 2 LSRK 4 5489354e 10 LSRK 4 5300785e 10 LSRK 4 4074929e 10 LSRK 4 4166215e 10 02 01 47 4x 13 5 05 24
238. GING 192 5 2 5 3 Mode frequency For mode frequency an output image cube is created with nchan channels spaced evenly in frequency mode frequency Type of selection mfs channel velocity frequency nchan 1 Number of channels planes in output image start 1 4GHz Frequency of first image channel e q 1 4GHz width 10kHz Image channel width in frequency units e g 1 0kHz interpolation nearest Type of spectral interpolation of visibilities nearest linear cubic The frequency of the first output channel is given by start and spacing by width The sign of width determines whether the output channels ascend or descend in frequency Output channels have a width also given by width Data from the input MS with centers that lie within one half an input channel overlap of the frequency range of width 2 centered on the output channels are gridded together The interpolation sub parameter 5 2 5 5 sets how channels are gridded into the image cube planes Using the NGC5921 dataset as an example mode frequency nchan 21 start 1412 830MHz width 50kHz would produce a 21 channel output cube with 50 kHz wide channels rather than the default chan nelization of the MS 24 4 kHz 5 2 5 4 Mode velocity If mode velocity is chosen then an output image cube with nchan channels will be created with channels spaced evenly in velocity Parameters are mode velocity
239. GLE DISH DATA PROCESSING 301 example typically in range 2 9 higher values seem to be needed for GBT verify verify the results of baseline fitting options bool True False default False WARNING Currently this just asks whether you accept the displayed fit and if not continues without doing any baseline fit masklist list of mask regions to INCLUDE in BASELINE fit default entire spectrum example 1000 3000 5000 7000 if blmode auto then this mask will be applied before fitting outfile Name of output file default lt sdfile gt _bs outform format of output file options ASCII SDFITS MS ASAP default ASAP example the ASAP format is easiest for further sd processing use MS for CASA imaging If ASCII then will append some stuff to the outfile name overwrite overwrite the output file if already exists options bool True False default False WARNING if outform ASCII this parameter is ignored plotlevel control for plotting of results options int O none l some 2 more lt O hardcopy default O no plotting example plotlevel lt 0 as abs plotlevel e g 1 gt hardcopy of final plot will be named lt outfile gt _bspec eps WARNING be careful plotting in fsotf mode DESCRIPTION Task sdbaseline performs baseline fitting removal for single dish spectra The fit parameters terms and rms of base line are saved to an ASCII file lt outfile
240. HERA RR RARA HARE Updated Updated Updated Updated Updated Updated HE HHH HHH HH HHH HH HH H OH OH STM STM STM STM STM STM 2008 05 15 2008 06 11 2008 06 12 2008 06 13 2008 12 24 2009 05 29 Beta Beta Beta Beta Beta Beta Use Case Script for Jupiter 6cm VLA Trimmed down from Use Case jupiter6cm_usecase py Patch Patch Patch Patch Patch Patch PONNNN 0 0 0 0 0 0 for summer school demo make a bit faster extendflags for mcmaster tutorial This is a VLA 6cm dataset that was observed in 1999 to set the flux scale for calibration of the VLA were observations of the planets including Jupiter Included in the program This is D configuration data with resolution of around 14 Includes polarization imaging and analysis HH HH HHH HH HHH HHH H HOH OF HHEFHHHHHHHHEHHHEHHEAEHHAEHEHEEHHHAEHEHEEHRREEHHEEHEHRHHERHA EHR RRR RARA ARE import time import os print Jupiter 6cm Interactive Tutorial Demo Script print Version 2009 05 29 Version 2 4 0 Patch 4 0 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 415 This script has some interactive commands scriptmode True if you are running it and want it to stop during interactive parts scriptmode True Set up some useful variables these will be set during the script also but if you want to restart the script in the middle here they are in one place This will prefix all output file names prefix jupiter
241. HOH ATMOPRA DSS 43 gt CEDUNA HOBART For GBT it fixes default fluxunit to K first then convert to a new fluxunit telescopeparm 104 9 0 43 diameter m ap eff APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 310 telescopeparm 0 743 gain in Jy K telescopeparm FIX to change default fluxunit see description below specunit units for spectral axis options str channel km s GHz MHz kHz Hz default current frame frequency frame for spectral axis options str LSRK REST TOPO LSRD BARY GEO GALACTO LGROUP CMB default currently set frame in scantable WARNING frame REST not yet implemented doppler doppler mode options str RADIO OPTICAL Z BETA GAMMA default currently set doppler in scantable scanlist list of scan numbers to process default use all scans example 21 22 23 24 field selection string for selecting scans by name default no name selection example FLS3a this selection is in addition to scanlist and iflist iflist list of IF id numbers to select default use all IFs example 15 pollist list of polarization id numbers to select default use all polarizations example 1 fitmode mode for fitting options str list auto default auto example list will use maskline
242. If p is the positive value chosen The data value is scaled linearly to lie between 0 and p and 10 is raised to this power yielding a value in the range 1 10 Finally that value is scaled linearly to the number of available colors CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 271 7 3 2 Viewing a contour map Viewing a contour image is similar to the process above A contour map shows lines of equal data value e g flux density for the selected plane of gridded data Figure 7 9 Contour maps are particularly useful for overlaying on raster images so that two different measurements of the same part of the sky can be shown simultaneously 7 3 3 Several Basic Settings options control the contour levels used The contours themselves are specified by a list in the RelativeContourLevels box These are defined relative to the two other parameters the BaseContourLevel which sets what 0 in the relative contour list corresponds to in the image and the UnitContourLevel which sets what 1 in the relative contour list corresponds to in the image Note that negative contours are usually dashed BETA ALERT This scheme was adopted in 2 4 0 and is slightly different to that used in previous versions Data Display Panel Tools View ngc5921 demo cleanimg image contour a a Y o n E a dd 8 O EA SS Display axes Qi Slt 108 Y Hidden axes Basic Settings Aspect ratio fixed world AY Pixel treatment edge Ki Resampling mode bilin
243. NG 306 lt outfile gt _calspec eps WARNING be careful plotting in fsotf mode DESCRIPTION Task sdcal performs data selection calibration and or spectral baseline fitting for single dish spectra This task internally calls the tasks sdaverage sdsmooth and sdbaseline and it can be used to run all the three steps in one task execution By setting calmode none one can run sdcal on already calibrated data for further selection averaging and atmospheric optical depth correction See the sdaverage description for information on fluxunit conversion and the telescopeparm parameter To save the output spectra in a certain range of channels you set the range in channelrange Averaging of multi resolution spectra can be achieved by setting the sub parameter of average averageall to True It generally handles multi IFs by selecting overlaps in IFs and assigning new IFs in the output spectra Beta Patch 4 New Features 1 Interactive mask selection for baseline fitting is enabled with blmode interact 2 The parameter interactive is renamed as verify A 2 1 5 sdcoadd Keyword arguments sdfilelist list of names of input SD dataset fluxunit units for line flux options K Jy default keep current fluxunit WARNING For GBT data see description below gt gt gt fluxunit expandable parameter telescopeparm the telescope characteristics options str name or list list of gain info defau
244. NOTATED EXAMPLE SCRIPTS Can also be found online at http casa nrao edu Data VLA Planets6cm planets_6cm fits Use version in current directory fitsdata planets_6cm fits Import the data from FITS to MS print Import Safest to start from task defaults default importuvfits print Use importuvfits to read UVFITS and make an MS Set up the MS filename and save as new global variable msfile prefix ms print MS will be called msfile Use task importuvfits fitsfile fitsdata vis msfile importuvfits List a summary of the MS print Listobs Don t default this one and make use of the previous setting of vis Remember the variables are GLOBAL print Use listobs to print verbose summary to logger You may wish to see more detailed information in this case use the verbose True option verbose True listobs You should get in your logger window and in the casapy log file something like Observer FLUX99 Project 419 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS Observation VLA Data records 2021424 Observed from ObservationID Date Timerange 15 Apr 1999 23 38 53 22 28 48 56 01 23 23 16 Apr 1999 00 00 00 00 01 01 01 02 02 02 02
245. NTRODUCTION 73 e viewer there are useful region statistics and image cube plotting capabilities in the viewer 817 1 5 6 1 What s in an image The imhead task will print out a summary of image header keywords and values This task can also be used to retrieve and change the header values See for more 1 5 6 2 Image statistics The imstat task will print image statistics There are options to restrict this to a box region and to specified channels and Stokes of the cube This task will return the statistics in a Python dictionary return variable See for more 1 5 6 3 Moments of an Image Cube The immoments task will compute a moments image of an input image cube A number of options are available from the traditional true moments zero first second and variations thereof to other images such as median minimum or maximum along the moment axis See for details 1 5 6 4 Image math The immath task will allow you to form a new image by mathematical combinations of other images or parts of images This is a powerful but tricky task to use See for more 1 5 6 5 Regridding an Image It is occasionally necessary to regrid an image onto a new coordinate system The imregrid task can be used to regrid an input image onto the coordinate system of an existing template image creating a new output image See 6 9 for a description of this task CHAPTER 1 INTRODUCTION 74 1 5 6 6 Display
246. NUS 13 44 30 0 13 46 10 0 58 10 NEPTUNE 14 00 46 7 14 01 39 9 59 O 0137 331 14 10 40 0 14 12 09 9 60 12 JUPITER 14 24 06 6 14 25 40 1 61 11 URANUS 14 34 30 0 14 36 10 1 62 10 NEPTUNE 14 59 13 4 15 00 00 0 63 O 0137 331 15 09 03 3 15 10 40 1 64 12 JUPITER 15 24 30 0 15 26 20 1 65 9 NGC7027 15 40 10 0 15 45 00 0 66 11 URANUS 15 53 50 0 15 55 20 0 67 10 NEPTUNE 16 18 53 4 16 19 49 9 68 O 0137 331 16 29 10 1 16 30 49 9 69 12 JUPITER 16 42 53 4 16 44 30 0 70 11 URANUS 16 54 53 4 16 56 40 0 71 9 NGC7027 17 23 06 6 17 30 40 0 72 2 0542 498 17 41 50 0 17 43 20 0 73 3 0437 296 17 55 36 7 17 57 39 9 74 4 VENUS 18 19 23 3 18 20 09 9 75 O 0137 331 18 30 23 3 18 32 00 0 76 12 JUPITER 18 44 49 9 18 46 30 0 77 9 NGC7027 18 59 13 3 19 00 59 9 78 2 0542 498 19 19 10 0 19 21 20 1 79 5 0521 166 19 32 50 1 19 34 29 9 80 3 0437 296 19 39 03 3 19 40 40 1 81 4 VENUS 20 08 06 7 20 08 59 9 82 O 0137 331 20 18 10 0 20 19 50 0 83 12 JUPITER 20 33 53 3 20 35 40 1 84 1 0813 482 20 40 59 9 20 42 40 0 85 2 0542 498 21 00 16 6 21 02 20 1 86 5 0521 166 21 13 53 4 21 15 29 9 87 3 0437 296 21 20 43 4 21 22 30 0 88 4 VENUS 21 47 26 7 21 48 20 1 89 O 0137 331 21 57 30 0 21 59 10 0 90 12 JUPITER 22 12 13 3 22 14 00 1 91 2 0542 498 22 28 33 3 22 30 19 9 92 4 VENUS 22 53 33 3 22 54 19 9 93 O 0137 331 Fields 13 o Lo
247. O O data array 8 45717848e 04 1 93370355e 03 1 53750915e 03 2 88399984e 03 2 38683447e 03 2 89159478e 04 3 16268904e 03 9 93389636e 03 1 88773088e 02 3 01138610e 02 3 14478502e 02 4 03211266e 02 3 82498614e 02 3 06552909e 02 2 80734301e 02 1 72479432e 02 1 20884273e 02 6 13593217e 03 9 04005766e 03 1 71429547e 03 5 22095338e 03 2 49114982e 03 5 30831399e 04 4 80734324e 03 1 19265869e 05 1 29435991e 03 3 75700940e 04 2 34788167e 03 2 72604497e 03 1 78467855e 03 9 74952069e 04 2 24676146e 03 1 82263291e 04 1 98463408e 06 2 02975096e 03 9 65532148e 04 1 68218743e 03 2 92119570e 03 1 29359076e 03 5 11484570e 04 1 54162932e 03 4 68662125e 04 8 50282842e 04 7 91683051e 05 2 95954203e 04 CHAPTER 6 IMAGE ANALYSIS 1 30133145e 031 250 mask array True True True True True True True True True True True True True True True True True True True True True True True True True True True True True True True True True True True True True trc 125 125 O 45 unit Jy beam To extract a region from the plane of a cube True True True True True True True True True dtype bool CASA lt 13 gt xval imval ngc5921 demo clean image box 126 128 130 129 chans 23 CASA lt 14 gt xval Out 14 axes 0 Right Ascension 1 Declination 3 Frequency 2 Stokes
248. PENDIX SINGLE DISH DATA PROCESSING import os NOTE you should have already run asap_init to import the ASAP tools as sd lt tool gt and the SDtasks This is the environment variable pointing to the head of the CASA tree that you are running casapath os environ AIPSPATH This bit removes old versions of the output files os system rm rf sdusecase_orions This is the path to the OrionS GBT ms in the data repository datapath casapath data regression ATST5 OrionS OrionS_rawACSmod The following will remove old versions of the data and copy the data from the repository to your current directory Comment this out if you already have it and don t want to recopy os system rm rf OrionS_rawACSmod copystring cp r datapath os system copystring Now is the time to set some of the more useful ASAP environment parameters the ones that the ASAP User Manual claims are in the asaprc file These are in the Python dictionary sd rcParams You can see whats in it by typing sd rcParams One of them is the verbose parameter which tells ASAP whether to spew lots of verbiage during processing or to keep quiet The default is sd rcParams verbose True You can make ASAP run quietly with only task output with sd rcParams verbose False Another key one is to tell ASAP to save memory by going off the d
249. R L Antennas 27 ID Name Station Diam Long Lat 0 1 VLA W9 25 0 m 107 37 25 1 33 53 51 0 1 2 VLA N9 25 0 m 107 37 07 8 33 54 19 0 2 3 VLA N3 25 0 m 107 37 06 3 33 54 04 8 3 4 VLA N5 25 0 m 107 37 06 7 33 54 08 0 4 5 VLA N2 25 0 m 107 37 06 2 33 54 03 5 5 6 VLA El 25 0 m 107 37 05 7 33 53 59 2 6 7 VLA E2 25 0 m 107 37 04 4 33 54 01 1 7 8 VLA N8 25 0 m 107 37 07 5 33 54 15 8 8 9 VLA E8 25 0 m 107 36 48 9 33 53 55 1 9 10 VLA W3 25 0 m 107 37 08 9 33 54 00 1 10 11 VLA N1 25 0 m 107 37 06 0 33 54 01 8 11 12 VLA E6 25 0 m 107 36 55 6 33 53 57 7 12 13 VLA W7 25 0 m 107 37 18 4 33 53 54 8 13 14 VLA E4 25 0 m 107 37 00 8 33 53 59 7 14 15 VLA N7 25 0 m 107 37 07 2 33 54 12 9 15 16 VLA W4 25 0 m 107 37 10 8 33 53 59 1 16 17 VLA W5 25 0 m 107 37 13 0 33 53 57 8 17 18 VLA N6 25 0 m 107 37 06 9 33 54 10 3 18 19 VLA E7 25 0 m 107 36 52 4 33 53 56 5 19 20 VLA E9 25 0 m 107 36 45 1 33 53 53 6 21 22 VLA W8 25 0 m 107 37 21 6 33 53 53 0 22 23 VLA W6 25 0 m 107 37 15 6 33 53 56 4 23 24 VLA W1 25 0 m 107 37 05 9 33 54 00 5 24 25 VLA W2 25 0 m 107 37 07 4 33 54 00 9 25 26 VLA E5 25 0 m 107 36 58 4 33 53 58 8 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 26 27 VLA N4 25 0 m 107 37 06 5 33 54 06 1 27 28 VLA E3 25 0 m 107 37 02 8 33 54 00 5 Tables MAIN 2021424 rows ANTENNA 28 rows D
250. RHE4 Fedora 6 located in usr lib casapy data nrao VLA CalModels e MAC OSX dmg located in opt casa data nrao VLA CalModels e NRAO AOC stable home casa data nrao VLA CalModels e NRAO AOC daily home ballista casa daily data nrao VLA CalModels e g these are found in the data nrao VLA CalModels sub directory of the CASA installation For example just point to the repository copy e g modimage usr lib casapy data nrao VLA CalModels 3C48_C im or if you like you can copy the ones you wish to use to your working directory The models available are 3C138_C im 3C147_C im 3C286_C im 3C48_C im 3C138_K im 3C147_K im 3C286_K im 3C48_K im 3C138_L im 3C286_L im 3C48_L im 3C138_Q im 3C147_Q im 3C286_Q im 3C48_Q im 3C138_U im 3C147_U im 3C286_U im 3C48_U im 3C138_X im 3C147_X im 3C286_X im 3C48_X im CHAPTER 4 SYNTHESIS CALIBRATION 140 These are all un reconvolved images of AIPS CC lists properly scaled to the Perley Taylor 1999 flux density for the frequencies at which they were observed It is important that the model image not be one convolved with a finite beam it must have units of Jy pixel not Jy beam Note that setjy will rescale the flux in the models for known sources e g those in Table to match those it would have calculated It will thus extrapolated the flux out of the frequency band of the model image to whatever spectral windows in the MS are specified but will use the structure of the source in the mode
251. S see se SS a SS e print Plotting 0137 331 RR LL all antennas print You see bad data along bottom print Mark a box around a bit of it and hit Locate print Look in logger to see what it is print You see much is Antenna 9 ID 8 in spw 1 Pause script if you are running in scriptmode if scriptmode user_check raw_input Return to continue scriptin xaxis time spw 1 correlation extendflag F Note that the strings like antenna 9 first try to match the NAME which we see in listobs was the number 9 for ID 8 So be careful here why naming antennas as numbers is bad antenna 9 plotxy O YES the last 4 scans are bad Box em and flag print e o pl print Plotting vs time antenna 9 and spw 1 print Box up last 4 scans which are bad and Flag Pause script if you are running in scriptmode if scriptmode APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 426 user_check raw_input Return to continue script n Go back and clean up xaxis uvdist spw antenna correlation RR LL Note that RL LR are too weak to clip on As of 2 3 0 Patch 3 you can extend the flags to the cross correlations But this slows things down immensely extendflag T extendcorr all plotxy O Box up the bad low points basically a clip below 0 52 and flag print Print SSSR essa SS A SS SS SS print Back to al
252. SINGLE DISH DATA PROCESSING ooo X Viewer Display Panel 0O00 X Image Profile FLS3a_Hl image B400 20 9 AUDE Flu Dersity my GIO OO ao OI 901 i BE 10 sec Compact y Blink Frame J san J Oo is J 300 Sey J i 0 200 400 600 800 1000 piel siames Cak poa o ooo id MATO EA anal 362 Figure A 6 FLS3a HI emission The display illustrates the visualization of the data cube left and the profile display of the cube at the cursor location right the Tools menu of the Viewer Display Panel has a Spectral Profile button which brings up this display By default it grabs the left mouse button Pressing down the button and moving in the display will show the profile variations A 5 Known Issues Problems Deficiencies and Features The Single Dish calibration and analysis package within CASA is still very much under develop ment Not surprisingly there are a number of issues with ASAP and the SDtasks that are known and are under repair Some of these are non obvious features of the way ASAP or sd is imple mented or limitations of the current Python tasking environment Some are functions that have yet to be implemented These currently include 1 sd plotter Currently you can get hardcopy only after making a viewed plot Ideally ASAP should allow you to choose the device for plotting when you set up
253. TED EXAMPLE SCRIPTS 465 Pause script if you are running in scriptmode user_check raw_input Return to continue script n Here we overplot 3C273 the Time Chan averaged calibrated and uncalibrated data First the corrected column in blue field 0 spw 073 plotxy vis ngc4826 tutorial ms xaxis uvdist yaxis amp field field spw spw averagemode vector width 1000 datacolumn corrected timebin 1e7 crossscans True plotcolor blue selectplot True newplot False title Field field SPW spw print print Plotting field field spw spwt TimeChanAverage Corrected Data in blue Now the original data column in red plotxy vis ngc4826 tutorial ms xaxis uvdist yaxis amp field field spw spw averagemode vector width 1000 datacolumn data timebin 1e7 crossscans True plotcolor red overplot True selectplot True newplot False title Field field SPW spw print OverPlotting field field spw spwt TimeChanAverage Original Data in red Pause script if you are running in scriptmode user_check raw_input Return to continue script n Can repeat for field 1 spw 4711 print Done calibration and plotting HHHHHHHHHHHR RHEE HHHHAAAAHA AREER H HERR RH HAAR HHH RRA RAR AAA AAA SPLIT THE DATA INTO SINGL
254. TION 65 An end to end workflow diagram for CASA data reduction for interferometry data is shown in Figure This might help you chart your course through the package In the following sub sections we will chart a rough course through this process with the later chapters filling in the individual boxes Input Data Process Output Data Input dataset Data Import Data Examination and Flagging Flagging Table Calibrated UV Data Calibrator Model Calibration Table Self Cal Model Image Restored Image Residual Image Image Analysis Figure 1 8 Flow chart of the data processing operations that a general user will carry out in an end to end CASA reduction session Note that single dish data reduction for example with the ALMA single dish system follows a similar course This is detailed in Chapter A 1 5 1 Loading Data into CASA The key data and image import tasks are CHAPTER 1 INTRODUCTION 66 e importuvfits import visibility data in UVFITS format 2 2 1 e importvla import data from VLA that is in export format 2 2 2 e importasdm import data in ALMA ASDM format P 2 3 e importfits import a FITS image into a CASA image format table 8 6 11 These are used to bring in your interferometer data to be stored as a CASA Measurement set MS and any previously made images or models to be stored as CASA image tables The data import tasks will create a MS with a path and n
255. The uvrange Parameter o a e 2 6 4 5 The msselect Parameter Data Examination and Editing 3 1 Plotting and Flagging Visibility Data in CASA 3 2 Managing flag versions with flagmanager 2 2 0 4 3 3 Flagging auto correlations with flagautocorr o 3 4 X Y Plotting and Editing of the Data o e e e 3 4 1 GUI Plot Conmtroll e 3 4 2 The selectplot Parameters 00 00 0000 22 ees 108 3 4 3 Plot Control Parameters 2 0 0 000 ee ee ee ee 109 3 4 3 1 iteration e copus ee hE a we ew awe A 109 3 4 3 2 overplot 6 en 109 3 4 3 9 plotrange euros sea bee es ee es 110 3 4 3 4 plotsymbol je se sssrds adaa 20 e 02 49 111 A A a A ae he ae a Les 112 JA30 SUBPLOT a a a ct a a a n a a Gl a oe 112 9 4 4 Averaging in plot Y occ soc A Oe ERA a a aa 113 3 4 5 Interactive Flagging in plotxy e a 114 3 4 6 Flag extension in plotxy e 115 3 4 7 Setting rest frequencies in plotxy 0020000000048 116 3 4 8 Printing from plotxy 2 117 3 4 9 Exiting plotxy cai se e p poa p He ek ce ee nk Sl ew Gee i a 118 3 4 10 Example session using plotxy 2 0 000002 eee eee 118 generic tA ge Swen SRG GMa Grokeds CpG Gis foe oe PRES 121 soe ele eves Gp ate eee eee Goce Bp eee a ee F 122 3 9
256. U image complexlinpolimage polimname cmplxlinpol po complexlinpol complexlinpolimage po close You can now display this in the viewer in particular overlay this over the intensity raster with the poli contours The vector lengths will be proportional to the polarized intensity You can play with the Data Display Options panel for vector spacing and length You will want to have this masked like the pola image above on the polarized intensity When you load the image use the LEL jupiter6cm demo polimg clean cmplxlinpol jupiter6cm demo polimg clean image poli gt 0 005 fosooooooooooooooooooooooooooooooooooooooooooooooooooooooo Print results print wee print Jupiter polarization results APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS print print Polarization Stokes stokest mymax on_statistics stokes max 0 mymin on_statistics stokes min 0 myrms off_statistics stokes rms 0 absmax max mymax mymin mydra absmax myrms print Clean image ON SRC max mymax print Clean image ON SRC min mymin print Clean image OFF SRC rms myrms print Clean image dynamic rng mydra print Done fo ooooooooooooooooooooooooooooooooooooooooooooooooooooos F 3 BIMA Mosaic Spectral Imaging This script analyzes a BIMA SONG mosaic of the galaxy NGC 4826 at 3mm
257. X ANNOTATED EXAMPLE SCRIPTS 431 spw a priori calibration application gaincurve usegaincurve opacity gainopacity scan based G solutions for both amplitude and phase gaintype G calmode ap one solution per scan solint inf combine do not apply parallactic angle correction yet parang False reference antenna refant calrefant minimum SNR 3 minsnr 3 gaincal Bootstrap flux scale print Fluxscale default fluxscale print Use fluxscale to rescale gain table to make new one vis msfile set the name for the output rescaled caltable fluxtable ftable print Output scaled gain cal table is ftable point to our first gain cal table caltable gtable we will be using 1331 305 the source we did setjy on as our flux standard reference reference 1331 305 we want to transfer the flux to our other gain cal source 0137 331 to bring its gain amplitues in line with the absolute scale APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 432 transfer 0137 331 fluxscale You should see in the logger something like Flux density for 0137 331 in SpW 0 is 5 42575 0 00285011 SNR 1903 7 nAnt 27 Flux density for 0137 331 in SpW 1 is 5 46569 0 00301326 SNR 1813 88 nAnt 27 Plot calibration print PlotCal default plotcal showgui True caltable ftable mu
258. YS values while Modcomp era data had this applied online In all cases CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 83 importvla will do the correct thing to data and weights based on an internal flag in the VLA Archive file either scaling it or unscaling based on your choice for applytys If applytsys True and you see strange behavior in data amplitudes it may be due to erroneous TSYS values from the online system You might want to then fill with applytsys False and look at the correlation coefficients to see if the behavior is as expected 2 2 2 2 Parameter bandname The bandname indicates the VLA Frequency band s to load using the traditional bandname codes These are e 4 48 96 MHz e P 298 345 MHz e L 1 15 1 75 GHz e C 4 2 5 1 GHz e X 6 8 9 6 GHz e U 13 5 16 3 GHz e K 20 8 25 8 GHz e Q 38 51 GHz e gt all bands default Note that as the transition from the VLA to EVLA progresses the actual frequency ranges covered by the bands will expand and additional bands will be added namely S from 1 2 GHz and A from 26 4 40 GHz 2 2 2 3 Parameter frequencytol The frequencytol parameter specifies the frequency separation tolerated when assigning data to spectral windows The default is frequencytol 150000 Hz For Doppler tracked data where the sky frequency changes with time a frequencytol lt 10000 Hz may may produce too many unnecessary sp
259. __hash__ os EX_OSFILE os __init__ os EX_PROTOCOL os __name__ os EX_SOFTWARE os __new__ os EX_TEMPFAIL os __reduce__ os EX_UNAVAILABLE os __reduce_ex__ os EX_USAGE os __repr__ os F_OK os __setattr__ os NGROUPS_MAX os __str__ os O_APPEND os _copy_reg os O_CREAT os _execvpe os O_DIRECT os _exists os O_DIRECTORY os _exit os O_DSYNC os _get_exports_list os O_EXCL os _make_stat_result os O_LARGEFILE os _make_statvfs_result os O_NDELAY os _pickle_stat_result os O_NOCTTY os _pickle_statvfs_result os D_NOFOLLOW os _spawnvef os O_NONBLOCK os abort os O_RDONLY os access os O_RDWR os altsep os O_RSYNC os chdir os O_SYNC os chmod os O_TRUNC os chown os O_WRONLY os chroot os P_NOWAIT os close os P_NOWAITO os confstr os P_WAIT os confstr_names os R_OK os ctermid os SEEK_CUR os curdir os SEEK_END os defpath os 376 see these by using tab completion datasync dopen fork forkpty fpathconf stat Istatv s fsync ftruncate getcwd getcwdu getegid getenv geteuid getgid getgroups getloadavg getlogin getpgid getpgrp getpid getppid getsid getuid isatty kill killpg lchown Linesep link listdir 1seek 1stat major makedev makedirs minor mkdir mkfifo mknod name os os os os os os os os os os os os os os os os os os os os os os os os os os os os os os os os os os
260. a new fluxunit telescopeparm 104 9 0 43 diameter m ap eff telescopeparm 0 743 gain in Jy K telescopeparm FIX to change default fluxunit see description below specunit units for spectral axis options str channel km s GHz MHz kHz Hz default current example this will be the units for masklist frame frequency frame for spectral axis options str LSRK REST TOPO LSRD BARY GEO GALACTO LGROUP CMB default currently set frame in scantable WARNING frame REST not yet implemented doppler doppler mode options str RADIO OPTICAL Z BETA GAMMA default currently set doppler in scantable scanlist list of scan numbers to process default use all scans example 21 22 23 24 this selection is in addition to field iflist and pollist field selection string for selecting scans by name default no name selection example FLS3a this selection is in addition to scanlist iflist and pollist iflist list of IF id numbers to select default use all IFs APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 300 example 15 this selection is in addition to scanlist field and pollist pollist list of polarization id numbers to select default use all polarizations example 1 this selection is in addition to scanlist field and iflist tau
261. ach IF in turn unless you want to averaging of multi resolution spectra see below To save the output spectra in a certain range of channels you set the range in channelrange Averaging of multi resolution spectra can be achieved by setting the sub parameter in timeaverage averageall to True It generally handles multi IFs by selecting overlaps in IFs and assigning new IFs in the output spectra ASAP recognizes the data of the AT telescopes but currently does not know about the GBT or any other telescope This task does know about GBT Telescope name is obtained from the data If you wish to change the fluxunit see below by leaving the sub parameter telescopeparm unset telescopeparm it will use internal telescope parameters for flux conversion for the data from AT telescopes and it will use an approximate aperture efficiency conversion for the GBT data If you give telescopeparm a list then if the list has a single float it is assumed to be the gain in Jy K if two or more elements they are assumed to be telescope diameter m and aperture efficiency respectively Note that sdaverage assumes that the fluxunit is set correctly in the data already If not then set telescopeparm FIX and it will set the default units to fluxunit without conversion NOTE If the data in sdfile is an ms from GBT and the default flux unit is missing this task automatically fixes the default fluxunit to K before the conversion A 2 1 2 s
262. active production of hardcopy plots See 8 for more details on saving plots to disk The iteration overplot plotrange plotsymbol showflags and subplot parameters deserve extra explanation and are described in below For example plotxy vis jupiter6cm ms xaxis uvdist jupiter 6cm dataset plot uv distance on x axis yaxis amp plot amplitude on y axis field JUPITER plot only JUPITER selectdata True open data selection correlation RR LL plot RR and LL correlations selectplot True open plot controls title Jupiter 6cm uncalibrated give it a title CHAPTER 3 DATA EXAMINATION AND EDITING 107 The plotter resulting from these settings is shown in figure BETA ALERT The plotxy task still has a number of issues The averaging has been greatly speeded up in this release but there are cases where the plots will be made incorrectly In particular there are problems plotting multiple spw at the same time There are sometimes also cases where data that you have flagged in plotxy from averaged data is done so incorrectly This task is under active developement for the next cycle to fix these remaining problems so users should be aware of this BETA ALERT Another know problem with plotxy is that it fails if the path to your working directory contains spaces in its name e g users smyers MyTest is fine but users smyers My Test is not 3 4 1 GUI Plot Control You can
263. agic hist more temp py Note shell commands are designated in this way __IP system more temp py quickhelp im open ngc5921 ms im summary ipmagic pdoc im setdata 10 11 12 13 14 15 16 17 18 19 20 21 im close quickhelp ipmagic logstate x 1 y 3x x Zz x 2 y 2 x y Zz Out 16 _17 Note autoparenthesis are added in the history The history can be saved as a script or used as a macro for further use CASA 24 save script py 13 16 File script py exists Overwrite y N1 y The following commands were written to file script py x 1 y 3x x Z x 2 y 2 APPENDIX D APPENDIX PYTHON AND CASA 381 CASA 25 more script py x 1 y 3x x Z X 24yx 2 Note that the history commands will be saved up to but not including the last value i e history commands 13 16 saves commands 13 14 and 15 There are two mechanisms for searching command history 1 Previous Next use Ctrl p previous up and Ctrl n next down to search through only the history items that match what you have typed so far min match completion If you use Ctrl p or Ctrl n at a blank prompt they behave just like the normal arrow keys 2 Search Ctrl r opens a search prompt Begin typing and the system searches your history for lines that contain what you ve typed so far completing what it can For example CASA 37 lt Cntl r gt reverse i search Typing
264. ain table Original Original flags at import into CASA flagautocorr flagged autocorr xyflags Plotxy flags The mode parameter expands the options For example if you wish to save the current flagging state of vis lt msname gt mode gt save Flag management operation list save restore delete versionname en Name of flag version no spaces comment on Short description of flag version merge replace Merge option replace and or with the output version name specified by versionname For example the above xyflags version was written using default flagmanager vis jupiter6cm usecase ms mode save versionname xyflags comment Plotxy flags flagmanager CHAPTER 3 DATA EXAMINATION AND EDITING 103 and you can see that there is now a sub table in the flagversions directory CASA lt 106 gt ls jupiter6cm usecase ms flagversions IPython system call ls F jupiter6cm usecase ms flagversions flags flagautocorr flags Original flags xyflags FLAG_VERSION_LIST It is recommended that you use this facility regularly to save versions during flagging You can restore a previously saved set of flags using the mode restore option mode restore Flag management operation list save restore delete versionname gt g Name of flag version no spaces merge replace Merge option replace and or The merge sub parameter will control the a
265. ajor cycle break and reconciliation occurs cycle threshold cyclefactor max sidelobe max residual CHAPTER 5 SYNTHESIS IMAGING 206 If your uv coverage results in a poor PSF then you should reconcile often a cyclefactor of 4 or 5 For reasonable PSFs use cyclefactor in the range 1 5 to 2 0 For good PSFs or for faster cleaning at the expense of some fidelity we recommend trying a lower value e g cyclefactor 0 25 which at least in some of our mosaicing tests led to a speedup of around a factor of two with little change in residuals 5 3 4 2 Sub parameter cyclespeedup This sub parameter is activated for imagermode csclean and mosaic The cyclespeedup parameter allows the user to let clean to raise the threshold at which a major cycle is forced if it is not converging to that threshold To do this set cyclespeedup to an integer number of iterations at which if the threshold is not reached the threshold will be doubled See cyclefactor above for more details By default this is turned off cyclespeedup 1 In our tests a value like cyclespeedup 50 has been used successfully 5 3 4 3 Sub parameter ftmachine This sub parameter is activated for imagermode mosaic The ftmachine parameter controls the gridding method and kernel to be used to make the image A string value type is expected Choices are ft sd both or mosaic the default The ft option uses the standard gridding
266. algorithm that will be used to calculate the synthesized beam for use during the minor cycles in the image plane The value types are strings Allowed choices are clark default and hogbom 5 3 1 1 The clark algorithm In the clark algorithm the cleaning is split into minor and major cycles In the minor cycles only the brightest points are cleaned using a subset of the point spread function In the major cycle the points thus found are subtracted correctly by using an FFT based convolution This algorithm is reasonably fast Also for polarization imaging Clark searches for the peak in J Q U 4 V 5 3 1 2 The hogbom algorithm The hogbom algorithm is the Classic image plane CLEAN where model pixels are found itera tively by searching for the peak Each point is subtracted from the full residual image using the shifted and scaled point spread function In general this is not a good choice for most imaging problems clark or csclean are preferred as it does not calculate the residuals accurately But in some cases with poor uv coverage and or a PSF with bad sidelobes the Hogbom algorithm will do better as it uses a smaller beam patch For polarization cleaning Hogbom searches for clean peak in J Q U and V independently 5 3 1 3 The clarkstokes algorithm In the clarkstokes algorithm the Clark psf 5 3 1 1 is used but for polarization imaging the Stokes planes are cleaned sequentially for compon
267. ame specified by the vis parameter See 8 for more information on MS in CASA The measurement set is the internal data format used by CASA and conversion from any other native format is necessary for most of the data reduction tasks Once data is imported there are other operations you can use to manipulate the datasets e concat concatenate a second MS into a given MS 2 5 Data import export concatenation and selection detailed in Chapter 2 1 5 1 1 VLA Filling data from VLA archive format VLA data in archive format are read into CASA from disk using the importvla task see 2 2 2 This filler supports the new naming conventions of EVLA antennas when incorporated into the old VLA system Note that future data from the EVLA in ASDM format will use a different filler This will be made available in a later release 1 5 1 2 Filling data from UVFITS format For UVFITS format use the importuvfits task A subset of popular flavors of UVFITS in particular UVFITS as written by AIPS is supported by the CASA filler See for details 1 5 1 3 Loading FITS images For FITS format images such as those to be used as calibration models use the importfits task Most though not all types of FITS images written by astronomical software packages can be read in See for more information CHAPTER 1 INTRODUCTION 67 1 5 1 4 Concatenation of multiple MS Once you have loaded data into measurement sets on disk you ca
268. ameters These are detailed in the common imaging task parameters section 5 2 A typical setup for clean on the NGC5921 dataset after setting parameter values might look like vis ngc5921 usecase ms contsub Name of input visibility file imagename ngc5921 usecase clean Pre name of output images field e 20 Field Name spw Spectral windows channels is all selectdata False Other data selection parameters mode channel Type of selection mfs channel velocity frequency CHAPTER 5 SYNTHESIS IMAGING nchan start width interpolation niter gain threshold psfmode imagermode multiscale interactive mask imsize cell phasecenter restfreq stokes weighting robust npixels uvtaper modelimage restoringbeam pbcor minpb async 201 46 Number of channels planes in output image 5 first input channel to use 1 Number of input channels to average nearest Spectral interpolation nearest linear cubic 6000 Maximum number of iterations 0 1 Loop gain for cleaning 8 0 Flux level to stop cleaning Must include units gt clark method of PSF calculation to use during minor cycles gt Use csclean or mosaic or image plane only if set deconvolution scales pixels False use interactive clean with GUI viewer 108 108 148 148 cleanbox es mask image s and or region s 256 256 x and y image size in pixels 15 0 15 0 x and
269. an vis ngc5921 ms contsub imagename ngc5921 chan21 clean mode channel nchan 1 start 21 step 1 field 0 spw imsize 256 256 cell 15 15 alg clark gain 0 1 niter 6000 threshold 8 0 weighting briggs rmode norm robust 0 5 mask cleanbox 108 108 148 148 clean There is now a file ngc5921 chan21 clean cleanbox mask that is an image with values 1 0 inside the cleanbox region and 0 0 outside We can use this to mask the clean image default immath expr ngc5921 chan21 clean image mask ngc5921 chan21 clean cleanbox mask gt 0 5 outfile ngc5921 chan21 clean imasked go Note that there are also pixel masks that can be contained in each image These are Boolean masks and are implicitly used in the calculation for each image in expr If you want to use the mask in a different image not in expr try it in mask CHAPTER 6 IMAGE ANALYSIS 241 First make a pixel mask inside ngc5921 chan21 clean cleanbox mask ia open ngc5921 chan21 clean cleanbox mask ia calcmask ngc5921 chan21 clean cleanbox mask gt 0 5 ia summary ia close There is now a maskO mask in this image as reported by the summary Now apply this pixel mask in immath default immath expr ngc5921 chan21 clean image mask mask ngc5921 chan21 clean cleanbox mask outfile
270. an optional frame type default LSRK Valid frames are REST TOPO LSRD LSRK BARY gt GEO GALACTO LGROUP CMB Examples scan set_freqframe BARY APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 347 The most useful choices here are frame LSRK the default for the function and frame gt TOPO what the GBT actually observes in Note that the REST option is not yet available The Doppler frame is set with sd scantable set_doppler CASA lt 3 gt help sd scantable set_doppler Help on method set_doppler in module asap scantable set_doppler self doppler RADIO unbound asap scantable scantable method Set the doppler for all following operations on this scantable Parameters doppler One of RADIO OPTICAL Z BETA GAMMA Finally there are a number of functions to query the state of the scantable These can be found in the usual way CASA lt 4 gt sd scantable get lt TAB gt sd scantable get_abcissa sd scantable get_restfreqs sd scantable getbeamnos sd scantable get_azimuth sd scantable get_scan sd scantable getcycle sd scantable get_column_names sd scantable get_selection sd scantable getif sd scantable get_direction sd scantable get_sourcename sd scantable getifnos sd scantable get_elevation sd scantable get_time sd scantable getpol sd scantable get_fit sd scantable get_tsys sd scantable getpolnos sd scantable get_fl
271. and image interferometric and single dish radio astro nomical data using the CASA Common Astronomy Software Application package CASA is a suite of astronomical data reduction tools and tasks that can be run via the Python interface to Python CASA is being developed in order to fulfill the data post processing requirements of the ALMA and EVLA projects but also provides basic and advanced capabilities useful for the analysis of data from other radio millimeter and submillimeter telescopes You have in your hands the Beta Release of CASA This means that there are a number of caveats and limitations for the use of this package See 1 1 below for more information and pay heed to the numerous BETA ALERTS placed throughout this cookbook You can expect regular updates and patches as well as increasing functionality But you can also expect interface changes The goals of this Beta Release are to get the package out into the hands of real users so you can take it for a spin Please knock it about a bit but remember it is not a polished finished product Beware This cookbook is a task based walk through of interfero metric data reduction and analysis In CASA tasks rep Inside the Toolkit resent the more streamlined operations that a typical user Throughout this Cookbook we will would carry out The idea for having tasks is that they occasionally intersperse boxed off are simple to use provide a more familiar interface and pointer
272. anged the buttons that control add erase the application of mask to channels and whether to stop complete or RE 20 In the initial stage left the window pops up and you can see it dominated by a bright source in the center Next right we zoom in and draw a box around this emission We have also at this stage dismissed the tape deck and Position Tracking parts of the display 7 2 1 as they are not used here We have also changed the iterations to 30 for this boxed clean We will now hit the Next Action Continue Cleaning button the green clockwise arrow to start cleaning 21 5 3 We continue in our interactive cleaning of Jupiter from where Figure 5 2 left off In the first left panel we have cleaned 30 iterations in the region previously marked and are zoomed in again ready to extend the mask to pick up the newly revealed emission Next right we have used the Polygon tool to redraw the mask around the emission and are ready to Continue Cleaning for another 100 iterations 21 5 1 We continue in our interactive cleaning of Jupiter from where Figure 4 left off In the first left panel it has cleaned deeper and we come back and zoom in to see that our current mask is good and we should clean further We change npercycle to 500 from 100 in the box at upper right of the window In the final panel right we see the results after this clean The residuals are such that we should terminate the
273. animg mask ngc5921 demo cleanimg model HHH 407 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 408 ngc5921 demo cleanimg psf ngc5921 demo cleanimg residual clnimage imname image Done with imaging Now view the image cube of N5921 if scriptmode print View image print Use Spectral Profile Tool to get line profile in box in center viewer clnimage image user_check raw_input Return to continue scriptin fo oooooooooooooooooooooooooooooooooooooosooooosoooosooo Here is how to export the Final CLEAN Image as FITS Run asynchronously so as not to interfere with other tasks BETA also avoids crash on next importfits print Final Export CLEAN FITS default exportfits clnfits prefix cleanimg fits imagename clnimage fitsimage clnfits async True saveinputs exportfits prefix exportfits saved myhandle2 exportfits print The return value for this exportfits async task for tm is str myhandle2 Se Ee Print the image header print Imhead default imhead imagename clnimage mode summary imhead A summary of the cube will be seen in the logger APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS f Get the cube statistics print Imstat cube def
274. ans channels are specified in frequency amp gt amp gt amp gt mode expandable parameters for modes other than mfs Start width are given in units of channels frequency or velocity as indicated by mode but only channel is complete nchan Number of channels planes in output image default 1 example nchan 3 start Start input channel relative 0 default 0 example start 5 width Output channel width in units of the input channel width amp gt 1 indicates channel averaging default 1 example width 4 examples APPENDIX H APPENDIX WRITING TASKS IN CASA 493 spw 70 1 mode mfs will produce one image made from all channels in spw O and 1 spw 0 572872 mode mfs will produce one image made with channels 5 7 9 25 27 spw 0 mode channel nchan 3 start 5 width 4 will produce an image with 3 output planes plane 1 contains data from channels 5 6 7 8 plane 2 contains data from channels 9 10 11 12 plane 3 contains data from channels 13 14 15 16 spw 0 0 6373 mode channel nchan 21 start 0 width 1 will produce an image with 20 output planes Plane 1 contains data from channel 0 Plane 2 contains date from channel 2 Plane 21 contains data from channel 61 spw 0 0 4072 mode channel nchan 3 start 5 width 4 will produce an image with three output planes plane 1 contains channels 5 7 plane 2 contains channels 13 15 plane 3 contains cha
275. arameters if equal to the specified value Attributes value required the value of the parameter Subelements lt default gt required lt notequals gt optional Reset specified parameters if not equal to the specified value Attributes value required The value of the parameter Subelements lt default gt optional lt default gt optional Resets default values for specified parameters Attributes param required Name of the lt param gt to be reset Subelements lt value gt required the revised value of the lt param gt lt example gt optional An example block typically in python Attributes lang optional specifies the language of the example defaults to python Subelements None APPENDIX H APPENDIX WRITING TASKS IN CASA 480 H 2 The task yourtask py file You must write the python code that does the actual work The task_ py file function call sequence must be the same as specified in the XML file We may relax the requirement that the function call sequence exactly match the sequence in the XML file in a future release H 3 Example The clean task H 3 1 File clean xml Clean xml gives a fairly comprehensive example of how to construct the XML file lt xml version 1 0 encoding UTF 8 gt lt xml stylesheet type text xsl gt lt casaxml xmlns http casa nrao edu schema psetTypes html xmlns xsi http www w3 org 2001 XMLSchema instance xsi schemaLocation http casa nrao e
276. archive data files AP314_A95019 xp to your working directory and started casapy Then default importvla archivefiles AP314_A950519 xp1 AP314_A950519 xp2 AP314_A950519 xp3 vis ngc7538 ms bandname K frequencytol 10e6 importvla If the data is located in a different directory on disk then use the full path name to specify each archive file e g archivefiles home rohir2 jmcmul1i ALMATST1 Data N7538 AP314_A950519 xp1 gt home rohir2 jmcmulli ALMATST1 Data N7538 AP314_A950519 xp2 X gt home rohir2 jmcmulli ALMATST1 Data N7538 AP314_A950519 xp3 Important Note importvla will import the on line flags from the VLA system along with the data These will be put in the MAIN table and thus available to subsequent tasks and tools If you wish to revert to unflagged data use flagmanager to save the flags if you wish and then use flagdata with mode manualflag and unflag True to toggle off the flags The other parameters are 2 2 2 1 Parameter applytsys The applytys parameter controls whether the nominal sensitivity scaling based on the measured TSYS with the weights scaled accordingly using the integration time is applied to the visibility amplitudes or not If True then it will be scaled so as to be the same as AIPS FILLM ie approx imately in deciJanskys Note that post Modcomp data is in raw correlation coefficient and will be scaled using the TS
277. ark clean psfmode clark No Cotton Schwab iterations csclean False If desired you can do a Cotton Schwab clean but will have only marginal improvement for this data csclean True Twice as big for Cotton Schwab cleans inner quarter 406 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS imsize 512 512 Pixel size 15 arcsec for this data 1 3 of 45 beam VLA D config L band cell 15 15 Fix maximum number of iterations niter 6000 Also set flux residual threshold in mJy threshold 8 0 Set up the weighting Use Briggs weighting a moderate value on the uniform side weighting briggs robust 0 5 Set a cleanbox 20 pixels around the center 128 128 mask 108 108 148 148 But if you had a cleanbox saved in a file e g regionfile txt you could use it mask regionfile txt If you don t want any clean boxes or masks then mask If you want interactive clean set to True interactive True interactive False saveinputs clean prefix clean saved Pause script if you are running in scriptmode if scriptmode inp user_check raw_input Return to continue scriptin clean Should find stuff in the logger like Fitted beam used in restoration 51 5643 by 45 6021 arcsec at pa 14 5411 deg HH H H EA It will have made the images ngc5921 demo cleanimg flux ngc5921 demo cleanimg image ngc5921 demo cle
278. ary parts of the relevant visibilities If scalar is chosen then the amplitude of the average is formed by a scalar average of the individual visibility amplitudes Time averaging is effected by setting the timebin parameter to a value larger than the integration time Currently timebin takes a string containing the averaging time in seconds e g timebin 60 0 to plot one minute averages Channel averaging is invoked by setting width to a value greater than 1 Currently the averaging width is given as a number of channels By default the averaging will not cross scan boundaries as set in the import process However if crossscans True then averaging will cross scans Note that data taken in different sub arrays are never averaged together Likewise there is no way to plot data averaged over field 3 4 5 Interactive Flagging in plotxy Interactive flagging on the principle of see it flag it is possible on the X Y display of the data plotted by plotxy Hint The user can use the cursor to mark one or more regions pn the plotting environments such as and then flag unflag or list the data that falls in these p1otxy the ESC key can be used to zones of the display remove the last region box drawn There is a row of buttons below the plot in the window You can punch the Mark Region button which will appear to depress then mark a region by left clicking and dragging the mouse each cl
279. aseline dependent non closing errors WARNING this is in general a very dangerous thing to do since baseline dependent errors once introduced are difficult to remove You must be sure you have an excellent model for the source better than the magnitude of the baseline dependent errors The inputs are blcal vis caltable field spw selectdata solint combine freqdep calmode solnorm gaintable gainfield interp spwmap gaincurve opacity parang async Calculate a baseline based calibration solution gain or bandpass 23 HHH HHH HHH H HOH HOH OA Nome of input visibility file Name of output gain calibration table Select field using field id s or field name s Select spectral window channels Other data selection parameters Solution interval Data axes which to combine for solve scan spw and or field Solve for frequency dependent solutions Type of solution ap p a Normalize average solution amplitudes to 1 0 Gain calibration table s to apply on the fly Select a subset of calibrators from gaintable s Interpolation mode in time to use for each gaintable Spectral windows combinations to form for gaintables s Apply internal VLA antenna gain curve correction Opacity correction to apply nepers Apply parallactic angle correction If true the taskname must be started using blcal CHAPTER 4 SYNTHESIS CALIBRATION 161 The freqdep parameter controls whether blcal solves fo
280. asic steps First determine system temperature using a noise tube calibrator sd dototalpower For each integration the system temperature is calculated from CAL noise on off data as lt refealof f gt Teal Tsys cal X lt refealon Tefealof f gt 2 ref refers to reference data and the spectral data are averaged across the bandpass Note that the central 80 of the spectra are used for the calculation Second determine antenna temperature sd dosigref The antenna temperature for each channel is calculated as Ta v Tsys x O where sig 3 Sigcalon Sigcaloff ref E sigcalon Si gcalof f Each calibration routine may be used as scans sd scantable inputdata False create a scantable called scans calibrated_scans sd calps scans scanlist calibrate scantable with position switched scheme Note For calps and calnod the scanlist must be scan pairs in correct order as these routines only do minimal checking APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 301 A 3 5 Averaging One can average polarizations in a scantable using the sd scantable average_pol function averaged_scan scans average_pol mask weight where Parameters mask An optional mask defining the region where the averaging will be applied The output will have all specified points masked weight Weighting scheme none default var 1 var spec weighted or tsys 1 Tsys 2 weigh
281. asily CASA lt 29 gt cat gt cleanboxes txt IPython system call cat gt cleanboxes txt 1 80 80 120 120 2 20 40 24 38 3 70 42 75 66 lt CNTL D gt CASA lt 30 gt cat cleanboxes txt IPython system call cat cleanboxes txt 1 80 80 120 120 2 20 40 24 38 3 70 42 75 66 Then in CASA makemask vis source ms imagename source mask cleanbox cleanboxes txt mode mfs make a multi frequency synthesis map combine channels imsize 200 200 Set image size 200x200 pixels cell 0 1 0 1 Using 0 1 arcsec pixels spw 0 1 2 Combine channels from 3 spectral windows field 0 Use the first field in this split dataset stokes I Image stokes I polarization This task will then create a mask image that has the 3 cleanboxes specified in the cleanboxes txt file You can also specify the cleanbox as a list of lists of blc tre pairs 4 veritices e g cleanbox 80 80 120 120 20 40 24 38 70 42 75 66 is equivalent to the cleanboxes txt given above Likewise CHAPTER 5 SYNTHESIS IMAGING 224 cleanbox 80 80 120 120 puts in a single cleanbox Note that you must specify a visibility dataset and create the image properties so the mask image will have the same dimensions as the image you want to actually clean BETA ALERT Eventually we will add functionality to deal with the creation of non rectangular regions and with multi plane masks There is also
282. asks This is a convenient alternative to using the Python execfile command see above CHAPTER 1 INTRODUCTION 56 Typing tget without a taskname will recover the saved values of the inputs for the current task as given in the current value of the taskname parameter Adding a task name e g tget lt taskname gt will recover values for the specified task This is done by searching for 1 a lt taskname gt last file see 1 3 5 7 below then for 2 a lt taskname gt saved file see 1 3 5 5 above and then executing the Python in these files For example default gaincal set current task to gaincal and default tget read saved inputs from gaincal last or gaincal saved inp see these inputs tget bandpass now get from bandpass last or bandpass saved inp task is now bandpass with recovered inputs 1 3 5 7 The last file Whenever you successfully execute a CASA task a Python script file called lt taskname gt last will be written or over written into the current working directory For example if you ran the listobs task as detailed above then CASA lt 14 gt vis ngc5921 ms CASA lt 15 gt verbose True CASA lt 16 gt listobs CASA lt 17 gt more listobs last IPython system call more listobs last taskname listobs vis ngc5921 ms verbose True listobs vis ngc5921 ms verbose False You can restore the parameter values from the save file using CASA lt 18
283. at ATF with both antennas It is in MS format which was converted from the ASDM format Do data plotting only default sdtpimaging inp plotlevel 2 select antenna 1 Vertex antenna antenna 1 sdfile uid X1e1_X3197_X1 ms sdtpimaging Now rerun sdtpimaging to do actual data reduction applying baseline subtraction from each scan and then do imaging Do baseline subtraction calmode baseline masklist 30 use 30 data points from each end of scan for fitting Do imaging createimage True imagename moon im imagesize 200 200 cell 0 2 in arcmin phasecenter AZEL 187d54m22s 41d03m0s APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 340 x Figure 1 Jolx uid__Xlel_X3197_X1 ms Ant DVO1 odd scan no CORRECTED_DATA 20000 40000 60000 80000 100000 120000 140000 160000 MooH row Figure A 2 Total power data display using sdtpimaging with calmode baseline The top panel shows uncalibrated data versus row numbers The middle panel shows baseline fitting of each scan only shown here the last scan The bottom panel shows the calibrated baseline subtracted data ephemsrcname moon specify ephemeris source name can be omitted plotlevel 1 plotlevel 2 to see progress of each fitting sdtpimaging A 3 Using The ASAP Toolkit Within CASA ASAP is included with the CASA installation build It is not loaded upon star
284. at the observing frequency may be used to generate the appropriate visibilities using the modimage parameter or in older versions explicitly with the ft task To use this provide modimage with the path to the model image Remember if you just give the file name it will assume that it is in the current working directory Note also that setjy using a model image will only operate on that single source thus you would run it multiple times with different field settings for different sources Otherwise you may need to use the uvrange selection in the calibration solving tasks to exclude the baselines where the resolution effect is significant There is not hard and fast rule for this though you should consider this if your calibrator is shows a drop of more than 10 on the longest baselines use plotxy 3 4 to look at this You may need to do antenna selection also if it is heavily resolved and there are few good baselines to the outer antennas Note that uvrange may also be needed to exclude the short baselines on some calibrators that have extended flux not accounted for in the model Note the calibrator guides for the specific telescopes usually indicate appropriate min and max for uvrange For example see the VLA Calibration Manual at http www vla nrao edu astro calib manual for details on the use of standard calibrators for the VLA Model images for some flux density calibrators are provided with CASA e Red Hat Linux RPMs
285. ata in the CORRECTED_DATA column of the MS For example to split out 46 channels 5 50 from spw 1 of our NGC5921 calibrated dataset split vis ngc5921 usecase ms outputvis ngc5921 split ms field 2 Output NGC5921 data field 2 spw 0 5 50 Select 46 chans from spw 0 datacolumn corrected Take the calibrated data column CHAPTER 4 SYNTHESIS CALIBRATION 180 4 7 1 1 Averaging in split EXPERIMENTAL BETA ALERT The averaging in split is still problematic In some known cases the time averaging produces incorrect results Channel averaging seems to work but needs more testing User beware Time and channel averaging are now available using the timebin and width parameters The timebin parameter give the averaging time It takes a quantity e g timebin 30s The width parameter defines the number of channels to average to form a given output channel This can be specified globally for all spw e g width 5 or specified per spw e g width 2 3 to average 2 channels of 1st spectral window selected and 3 in the second one BETA ALERT The ability to average channels in both time and channel simultaneously is not yet available Also if you average time and channel through sequential runs of split you must average in time first 4 7 2 Hanning smoothing of uv data hanningsmooth The hanningsmooth task will apply Hanning smoothing to a spectral line uv data set It will be applied t
286. ata values to colormap cells The color for a data value is determined as follows first the value is clipped to lie within the data range specified above then mapped to an index into the available colors as described in the next paragraph The color corresponding to this index is determined finally by the current colormap and its fiddling shift slope and brightness contrast settings see Mouse Toolbar above Adding a Color Wedge to your image can help clarify the effect of the various color controls The Scaling power cycles option controls the mapping of clipped data values to colormap indices Set to zero the default a straight linear relation is used For negative scaling values a logarithmic mapping assigns an larger fraction of the available colors to lower data values this is usually what you want Setting dataMin to something around the noise level is often useful appropriate in conjunction with a negative Power cycles setting For positive values an larger fraction of the colormap is used for the high data values The actual functions are computed as follows CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 270 See Figure 7 8 for sample curves y 2 S 1 A A E ae saseecar es b x lt 8 o E Lo 5 i i Z scaling power lt 0 o Es scaling power 0 2 Ss 8 4 m scaling power gt 0 Input data value Data minimum Data maximum Figure 7 8 Example curves for scaling p
287. atically swap axes maintaining different axes on each control Changing axes or slider animator positions does not normally require pressing Apply the new slice is shown immediately However the display may be partially or completely grey in areas if the required data is not currently in memory either because no data has been loaded yet or because not all the selected data will fit into the allowed memory CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER A Daa Display Options tdddddddddddddddddddddddddddddddddddddd dd d n4826_16apr ms Advanced MS and Visibility Selection X Axis Y Axis Animation Axis Spectral Window Display Axes Baseline Time Channel lt A 3000 4000 5000 6000 6000 Baseline 282 Polarization Flagging Options Basic Settings Figure 7 17 The MS for NGC4826 from Figure 7 16 now with the Display Axes open in the Data Display Options panel By default channels are on the Animation Axis and thus in the tapedeck while spectral window and polarization are on the Display Axes sliders Press the Apply button in this case to load the data see 7 4 1 6 and Max Visibility Memory at the end of 7 4 1 5 Within the Display Axes rollup you may also select whether to order the baseline axis by antennal antenna2 the default or by unprojected baseline length See Figures 7 1
288. atim minus the to the underlying operating system Several common commands 1s pwd less may be executed with or without the Note that the cd command must be executed without the and the cp command must use as there is a conflict with the cp tool in casapy For example CASA 1 pwd export home corsair vml jmcmulli data CASA 2 ls n ngc5921 ms ngc5921 py CASA 3 cp r test py D 6 1 Using the os system methods To use this you need the os package This should be loaded by default by casapy but if not you can use import os in your script For example in our scripts we use this to clean up any existing output files APPENDIX D APPENDIX PYTHON AND CASA The prefix to use for all output files prefix ngc5921 usecase Clean up old files os system rm rf prefixt Note that the os package has many useful methods You can CASA lt 2 gt os lt tab gt Display all 223 possibilities y or n os os os os os os os os os os os os os os os os os os os os os os os os os os os os os os os os os os os os os os os os os EX_CANTCREAT os X_OK os EX_CONFIG os _Environ os EX_DATAERR os __all__ os EX_IOERR os __class__ os EX_NOHOST os __delattr__ os EX_NOINPUT os __dict__ os EX_NOPERM os __doc__ os EX_NOUSER os __file__ os EX_OK os __getattribute__ os EX_OSERR os
289. atistics2 imstat Now do stats in the lower right corner of the image remember clnimsize 288 288 box 216 1 287 72 off_statistics2 imstat Pull the max and rms from the clean image thistest_immax on_statistics2 max 0 print Found Max in image thistest_immax thistest_imrms off_statistics2 rms 0 print Found rms in image thistest_imrms print Clean image Dynamic Range thistest_immax thistest_imrms print fosoooooooooooooooooooooooooooooooooooooooooooooooooooooos Print results and regression versus previous runs print print Final Jupiter results print print Pull the max and rms from the clean image thistest_immax on_statistics2 max 0 oldtest_immax 1 07732224464 print Clean image ON SRC max thistest_immax print Previously found to be oldtest_immax diff_immax abs oldtest_immax thistest_immax oldtest_immax print Difference fractional diff_immax print thistest_imrms off_statistics2 rms 0 oldtest_imrms 0 0010449 print Clean image OFF SRC rms thistest_imrms print Previously found to be oldtest_imrms diff_imrms abs oldtest_imrms thistest_imrms oldtest_imrms 448 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 449 print Difference fractional diff_imrms print print Final Clean image Dynamic
290. ault imstat imagename clnimage Do whole image box or you could stick to the cleanbox box 108 108 148 148 cubestats imstat Statistics will printed to the terminal and the output parameter will contain a dictionary of the statistics f sooooooooooooooooooooooooooooooooooooooooooooooooooooooo Get some image moments print ImMoments default immoments imagename clnimage Do first and second moments moments 0 1 Need to mask out noisy pixels currently done using hard global limits excludepix 100 0 009 Collapse along the spectral channel axis axis spectral Include all planes chans Output root name momfile prefix moments outfile momfile saveinputs immoments prefix immoments saved Pause script if you are running in scriptmode if scriptmode inp user_check raw_input Return to continue script n 409 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS immoments momzeroimage momfile integrated momoneimage momfile weighted_coord It will have made the images ae a a a SS SR SS SS Ss 2 ngc5921 demo moments integrated ngc5921 demo moments weighted_coord f Get some statistics of the moment images print Imstat moments default
291. ble to load the image as a Raster Image Contour Map Vector Map or Marker Map In this example clicking on the Raster Image button would bring up the displays shown in Figure 7 1 Starting the casaviewer with an image as a raster map will look something like the example in Figure 7 1 You will see the GUI which consists of two main windows entitled Viewer Display Panel and Load Data In the Load Data panel you will see all of the viewable files in the current working directory along with their type Image Measurement Set etc After selecting a file you are presented with the available display types raster contour vector marker for these data Clicking on the button Raster Map will create a display as above The data display can be adjusted by the user as needed This is done through the Data Display Options panel This window appears when you choose the Data Adjust menu or use the wrench icon from the Main Toolbar This also comes up by default along with the Viewer Display Panel when the data is loaded The Data Display Options window is shown in the right panel of Figure 7 1 It consists of a tab for each image or MS loaded under which are a cascading series of expandable categories For an CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 268 image these are e Display axes e Hidden axes e Basic Settings e Position tracking e Axis labels e Axis label properties e Beam Ellipse e Color Wedge Th
292. calibration print Bandpass default bandpass We can first do the bandpass on the single 5min scan on 1331 305 At 1 4GHz phase stablility should be sufficient to do this without a first rough gain calibration This will give us the relative antenna gain as a function of frequency vis msfile 395 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 396 set the name for the output bandpass caltable btable prefix bcal caltable btable No gain tables yet gaintable eu gainfield interp 23 Use flux calibrator 1331 305 3C286 FIELD_ID 0 as bandpass calibrator field 0 all channels spw No other selection selectdata False In this band we do not need a priori corrections for antenna gain elevation curve or atmospheric opacity at 8GHz and above you would want these gaincurve False opacity 0 0 Choose bandpass solution type Pick standard time binned B rather than BPOLY bandtype B set solution interval arbitrarily long get single bpass solint inf combine scan reference antenna Name 15 15 VLA N2 Id 14 refant 15 saveinputs bandpass prefix bandpass saved Pause script if you are running in scriptmode if scriptmode inp user_check raw_input Return to continue script n bandpass Use plotcal to examine the bandpass solutions print Plotca
293. can also select the spectral window via frequency ranges FSTART FSTOP as described above spw 1413 1414MHz 1413 1414MHz channels falling within 1413 1414MHz spw 141371414MHz does the same thing You can also specify multiple spectral window or channel ranges e g spw 2 16 3 32734 spw 2 channel 16 plus spw 3 channels 32 34 spw 2 173 57763 spw 2 channels 1 3 and 57 63 spw 173 10720 spw 1 3 channels 10 20 spw 4756 all spw channels 4 56 CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 96 Note the use of the wildcard in the last example A step can be also be included using STEP as a postfix spw 0 10710072 chans 10 12 14 100 of spw 0 spw 7 74 chans 0 4 8 of all spw spw 1007 150GHz 10GHz closest chans to 100 110 150GHz A step in frequency or velocity will pick the channel in which that frequency or velocity falls or the nearest channel 2 6 4 The selectdata Parameters The selectdata parameter if set to True will expand the inputs to include a number of sub parameters given below and in the individual task descriptions if different If selectdata False then the sub parameters are treated as blank for selection by the task The default for selectdata is False The common selectdata expanded sub parameters are 2 6 4 1 The antenna Parameter The antenna selection string is a semi colon separated list
294. ccumulator only a single calibration type e g B G can be smoothed or all types are then input to applycal as shown in Figure 11 3 Display of the amplitude upper and phase lower gain solutions for all antennas 4 4 Display of the amplitude upper phase middle and signal to noise ratio lower Lee ee RES 166 turned on using iteration antenna The first page is shown The user would ATT 167 4 6 The amp of gain solutions for NGC4826 before top and after bottom smoothing with a 7200 sec smoothtime and smoothtype mean Note that the first solution eet eed eae eee en eter eee 169 4 7 The phase of gain solutions for NGC4826 before top and after bottom linear interpolation onto a 20 sec accumtime grid The first scan was 3C273 in spw 0 while the calibrator scans on 1331 305 were in spw 1 The use of spwmap was necessary to transfer the interpolation correctly onto the NGC4826 scans 172 4 8 The final amp top and phase bottom of the self calibration gain solutions for bee poe Boge Ae oe eee Sone ee ee ee ee ee 175 4 9 The final amp versus uvdist plot of the self calibrated Jupiter data as shown in plotxy The RR LL correlations are selected No outliers that need flagging are E PA AIN 5 1 Close up of the top of the interactive clean window Note the boxes at the left where the iterations cycles and threshold can be ch
295. cease when this number of negative components are found at the largest scale If negcomponent 1 then component search will continue even if the largest component is negative The CASA multi scale algorithm uses Multi scale CLEAN to deconvolve using delta functions and circular Gaussians as the basis functions for the model instead of just delta functions or pixels as in the other clean algorithms This algorithm is still in the experimental stage mostly because we are working on better algorithms for setting the scales for the Gaussians The sizes of the Gaussians are set using the scales sub parameter We are working on defining a better algorithm for scale setting In the toolkit there is an nscale argument which sets scales l Oi Ormin OO 5 7 where N nscales and Opmin is the fitted FWHM of the minor axis of the CLEAN beam 5 3 3 Parameter gain The gain parameter sets the fraction of the flux density in the residual image that is removed and placed into the clean model at each minor cycle iteration The default value is gain 0 1 and is suitable for a wide range of imaging problems Setting it to a smaller gain per cycle such as gain 0 05 can sometimes help when cleaning images with lots of diffuse emission Larger values up to gain 1 are probably too aggressive and are not recommended CHAPTER 5 SYNTHESIS IMAGING 204 Data Display Panel Tools View AER ICE di eme 2 Qu Xx Next Action o gt e AS Fig
296. ces of data fields to apply calibration gt all spw gt spectral window channels gt all CHAPTER 4 SYNTHESIS CALIBRATION 176 selectdata False Other data selection parameters gaintable gt gt List of calibration table s to apply gainfield a Field selection for each gaintable interp me Interpolation mode in time for each gaintable spwmap Spectral window mapping for each gaintable see help gaincurve SS False Apply VLA antenna gain curve correction opacity 0 0 Opacity correction to apply nepers parang False Apply the parallactic angle correction calwt True Apply calibration also to the WEIGHTS async False if True run in the background prompt is freed As in other tasks setting selectdata True will open up the other selection sub parameters see 2 6 Many of the other parameters are the common calibration parameters that are described in ay The single non standard parameter is the calwt option to toggle the ability to scale the visibility weights by the inverse of the products of the scale factors applied to the amplitude of the antenna gains for the pair of antennas of a given visibility This should in almost all cases be set to its default True The weights should reflect the inverse noise variance of the visibility and errors in amplitude are usually also in the weights For applycal the list of final cumulative tables is given in gaintable In this cas
297. concat insert isopen ispersistent lock makearray makecomplex maketestimage maskhandler maxfit miscinfo modify moments name newimage newimagefromarray newimagefromfile newimagefromfits newimagefromimage ia ia ia ia ia ia ia ia replacemaskedpixels ia ia ia ia ia ia ia ia ia ia ia ia ia ia ia ia ia ia toworld ia ia ia ia mode stats to do this quickly over the entire image cube planes or sub regions For example in the Jupiter 6cm example script F 2 the ia tool is used to get on source and off source statistics for regression The variable clnimage points to the clean image name 254 of type object at 0x55d0f20 gt gt a new object with type S a subtype of T newimagefromshape ia ia open outputvariant pixelvalue putchunk ia putregion rebin regrid remove removefile rename restoringbeam rotate sepconvolve set setboxregion setbrightnessunit setcoordsys sethistory setmiscinfo setrestoringbeam shape statistics subimage summary toASCII tofits topixel twopointcorrelation type unlock The imhead task has The tool can do this on specific CHAPTER 6 IMAGE ANALYSIS 255 Pull the max and rms from the clean image ia open clnimage on_statistics ia statistics thistest_immax on_statistics max 0 oldtest_immax 1 07732224464 print Clean image ON SRC ma
298. cs stokes imstat box offbox off_statistics stokes imstat Peel off some Q and U planes print Immath default immath mode evalexpr stokes I outfile ipolimage expr polimaget immath O print Created I image outfile stokes Q outfile qpolimage expr polimaget immath O print Created Q image outfile 450 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 451 stokes U outfile upolimage expr polimaget immath O print Created U image outfile Now make POLI and POLA images stokes outfile poliimage mode poli imagename qpolimage upolimage Use our rms above for debiasing mysigma 0 5 off_statistics Q rms 0 off_statistics U rms 0 sigma str mysigma Jy beam This does not work well yet sigma 0 0Jy beam immath O print Created POLI image outfile outfile polaimage mode pola immath O print Created POLA image outfile Save statistics of these images default imstat imagename poliimage stokes box onbox on_statistics POLI imstat box offbox off_statistics POLI imstat Display clean I image in viewer but with polarization vectors If you did not do interactive clean bring up viewer manually viewer polimage image print
299. ction For merge replace the flags in versionname will replace those in the MAIN table of the MS For merge and only data that is flagged in BOTH the current MAIN table and in versionname will be flagged For merge or data flagged in EITHER the MAIN or in versionname will be flagged The mode delete option can be used to remove versionname from the flagversions mode delete Flag management operation list save restore delete versionname 22 Name of flag version no spaces 3 3 Flagging auto correlations with flagautocorr The flagautocorr task can be used if all you want to do is to flag the auto correlations out of the MS Nominally this can be done upon filling from the VLA for example but you may be working from a dataset that still has them This task has a single input the MS file name vis a Name of input visibility file MS To use it just set and go CASA lt 90 gt vis jupiter6cm usecase ms CASA lt 91 gt flagautocorr Note that the auto correlations can also be flagged using flagdata 3 5 but the flagautocorr task is an handy shortcut for this common operation 3 4 X Y Plotting and Editing of the Data BETA ALERT The plotxy code is fragile and slow and is being replaced by the casaplotms tool 3 8 A prototype version of that application is available in Version 2 4 0 CHAPTER 3 DATA EXAMINATION AND EDITING 104 The principal way to get X Y plots of visibili
300. ctive Cleaning Example If interactive True is set then an interactive window will appear at various cycle stages while you clean so you can set and change mask regions These breakpoints are controlled by the npercycle sub parameter which sets the number of iterations of clean before stopping The window controls are fairly self explanatory It is basically a form of the viewer A close up of the controls are shown in Figure and an example can be found in Figures You assign one of the drawing functions rectangle or polygon default is rectangle to the right mouse button usually then use it to mark out regions on the image Zoom in if necessary standard with the left mouse button assignment Double click inside the marked region to add it to the mask If you want to reduce the mask click the Erase radio button rather than Add then mark and select as normal When finished setting or changing your mask click the green clockwise arrow Continue Cleaning Next Action button If you want to finish your clean with no more changes to the mask hit the blue right arrow Apply mask edits and proceed with non interactive clean button If you want to terminate the clean click the red X Stop deconvolving now button While stopped in an interactive step you can change a number of control parameters in the boxes provided at the left of the menu bar The main use of this is to control how many iterations before the next breakpoin
301. d or filled There are other helpful scratch columns which hold useful versions of the data or weights for fur ther processing the CORRECTED_DATA column which is used to hold calibrated data the MODEL_DATA column which holds the Fourier inversion of a particular model image and the IMAGING_WEIGHT column which can hold the weights to be used in imaging The creation and use of the scratch columns is generally done behind the scenes but you should be aware that they are there and when they are used We will occasionally refer to the rows and columns in the MS More on the contents of the MS can be found in 2 1 1 4 5 Data Selection in CASA We have tried to make the CASA task interface as uniform as possible If a given parameter appears in multiple tasks it should as far as is possible mean the same thing and be used in the same way in each There are groups of parameters that appear in a number of tasks to do the same thing such as for data selection The parameters field spw and selectdata which if True expands to a number of sub parameters are commonly used in tasks to select data on which to work These common data selection param eters are described in 2 6 1 5 From Loading Data to Images The subsections below provide a brief overview of the steps you will need to load data into CASA and obtain a final calibrated image Each subject is covered in more detail in Chapters 2 through 6 CHAPTER 1 INTRODUC
302. d the image as a Raster Image Contour Map Vector Map or Marker Map In this example clicking on the Raster Image button would bring up the displays shown in Figure 7 1 oo 1 The Basic Settings category of the Data Display Options panel as it appears if you load the image as a Raster Image This is a zoom in for the data displayed TPIS el RA RA IR GB RO ER FRE he ee 8 Example curves for scaling power Cycles 2 0 ee ee ee 27 9 The Viewer Display Panel left and Data Display Options panel right after choosing Contour Map from the Load Data panel The image shown is for channel 11 of the NGC5921 cube selected using the Animator tape deck and zoomed in using the tool bar icon Note the different options in the open Basic Settings category of the Data Display Options panel 27 10 The Viewer Display Panel left and Data Display Options panel right after overlaying a Contour Map of velocity on a Raster Image of intensity The image shown is for the moments of the NGC5921 cube zoomed in using the tool bar icon The tab for the contour plot is open in the Data Display Options panel 27 11 The Image Profile panel that appears if you use the Tools Spectral Profile menu and then use the rectangle or polygon tool to select a region in the image You can also use the crosshair to get the profile at a single position in the image The profile will change to track movements of the regio
303. dard parameter bold black grey none expandable parameter plain green none yes sub parameter Values plain black none none default value plain blue none none non default value plain red none none invalid value Figure 1 2 shows what happens when you set some of the clean parameters to non default values Some have opened up sub parameters which can now be seen and set Figure shows what happens when you set a parameter in this case vis and mode to an invalid value now appears in red Reasons for invalidation include incorrect type an invalid menu choice or a filename that does not exist For example since vis expects a filename it will be invalidated red if it is set to a non string value or a string that is not the name of a file that can be found The mode happy is invalid because its not a supported choice mfs channel velocity or frequency 1 3 5 5 The saveinputs Command Its value The saveinputs command will save the current values of a given task parameters to a Python plain ascii file It can take up to two arguments e g saveinputs taskname outfile CHAPTER 1 INTRODUCTION 54 xterm lt 5 YY CASA lt 4 gt tget clean Restored parameters from file clean last CASA lt 5 gt inp clean clean Deconvolve an image with selected algorithm vis ngc5921 demo src split ms contsub name of input visibility file imagename 921 demo cleanimg P
304. do nominally you will rerun applycal to get new calibration if you have changed the tables or want to apply them differently There is only a single input to clearcal clearcal Re initializes calibration for an ms vis ee Name of input visibility file Note clearcal also resets the MODEL_DATA column to 1 0 for all fields and spectral windows 4 7 Other Calibration and UV Plane Analysis Options 4 7 1 Splitting out Calibrated uv data split The split task will apply calibration and output a new sub MS containing a specified list of sources usually a single source The inputs are split Create a visibility subset from an existing visibility set vis qe Name of input measurement set outputvis i Name of output measurement set datacolumn corrected Which data column to split out field gt Select field using field id s or field name s spw e di Select spectral window channels width 1 Number of channels to average to form one output channel antenna ae Select data based on antenna baseline timebin 0s Value for timeaveraging timerange dl Select data based on time range scan a select data based on scan numbers uvrange z ve select data based on uv distance range async False If true the taskname must be started using split Usually you will run split with datacolumn corrected as previous operations e g applycal will have placed the calibrated d
305. ds RR and LL for circularly polarized systems or the cross hands XY and YX for linearly polarized systems such as ALMA and ATCA This parameter is specified as a string of up to four letters IQUV For example stokes I Intensity only stokes IQU Intensity and linear polarization stokes IV Intensity and circular polarization stokes IQUV All Stokes imaging CHAPTER 5 SYNTHESIS IMAGING 195 are common choices The output image will have planes along the polarization axis corre sponding to the chosen Stokes parameters If as input to deconvolution tasks such as clean the stokes parameter includes polarization planes other than I then choosing psfmode hogbom 3 5 3 1 2 or psfmode clarkstokes 5 3 1 3 5 3 1 1 will will clean search for components each plane sequentially while psfmode clark deconvolve jointly 5 2 10 Parameter uvtaper This controls the radial weighting of visibilities in the uv plane see 5 2 11 below through the multiplication of the visibilities by the Fourier transform of an elliptical Gaussian This is itself a Gaussian and thus the visibilities are tapered with weights decreasing as a function of uv radius The uvtaper parameter expands the menu upon setting uvtaper True to reveal the following sub parameters uvtaper True Apply additional uv tapering of visibilities outertaper uv taper on outer baseline
306. dsmooth Keyword arguments sdfile name of input SD dataset scanaverage average integrations within scans options bool True False default False example if True this happens in read in For GBT set False scanlist list of scan numbers to process default use all scans example 21 22 23 24 this selection is in addition to field iflist and pollist field selection string for selecting scans by name default no name selection example FLS3a this selection is in addition to scanlist iflist pollist iflist list of IF id numbers to select default use all IFs example 15 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 298 this selection is in addition to scanlist field and pollist pollist list of polarization id numbers to select default use all polarizations example 1 this selection is in addition to scanlist field and iflist kernel type of spectral smoothing options hanning gaussian boxcar default hanning gt gt gt kernel expandable parameter kwidth width of spectral smoothing kernel options int in channels default 5 example 5 or 10 seem to be popular for boxcar ignored for hanning fixed at 5 chans 0 will turn off gaussian or boxcar outfile Name of output ASAP format scantable file default lt sdfile gt _sm outform format of output file options ASCII SDFITS MS ASAP default
307. du schema casa xsd file opt casa code xmlcasa xml casa xsd gt lt This is the param set for clean gt lt This does the equivalent of gt lt imgr imager anyfile ms gt lt imgr setdata mode channel nchan 100 start 1 step 1 fieldid 1 gt lt imgr setimage nx 512 ny cellx larcsec celly tarcsec stokes I gt lt mode channel start 35 step 1 nchan 40 gt lt fieldid 1 gt lt imgr weight natural gt lt imgr clean algorithm csclean niter 500 model field1 gt lt task type function name clean gt lt shortdescription gt Deconvolve an image with selected algorithm lt shortdescription gt lt description gt Form images from visibilities Handles continuum and spectral line cubes lt description gt lt input gt lt param type string name vis kind ms mustexist true gt lt description gt name of input visibility file lt description gt APPENDIX H APPENDIX WRITING TASKS IN CASA 481 lt value gt lt value gt lt param gt lt param type string name imagename gt lt description gt Pre name of output images lt description gt lt value gt lt value gt lt param gt lt param type string name field gt lt description gt Field Name lt description gt lt value gt lt value gt lt param gt lt param type any name spw gt lt description gt Spect
308. dual True plot residual get_parameters retrieve fit parameters f O peak 0 786 K centre 4091 236 channel FWHM 70 586 channel area 59 473 K channel f store_fit orions_hc3n_fit txt store fit Save the spectrum spave save orions_hc3n_reduced ASCII True save the spectrum A 4 Single Dish Imaging Single dish imaging is supported within CASA using standard tasks and tools The data must be in the Measurement Set format Once there you can use the im imager tool to create images Tool example scans save outputms MS2 Save your data from ASAP into an MS im open outputms im selectvis nchan 901 start 30 step 1 spwid 0 field 0 dir J2000 17 18 29 59 31 23 im defineimage nx 150 cellx 1 5arcmin open the data set choose a subset of the data just the key emission channels set map center define image parameters HHHH APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 360 phasecenter dir mode channel start 30 note it assumes symmetry if ny celly nchan 901 step 1 aren t specified im setoptions ftmachine sd cache 1000000000 im setsdoptions convsupport 4 choose SD gridding use this many pixels to support the gridding function used default prolate spheroidal wave function make the image HH H HF im makeimage type singledish image FLS3a_HI image A 4 1 Single Dish Imaging Use Case
309. e Likewise during self calibration once you have a new calibration solution the imaging part relies upon having the CORRECTED_DATA column contain the self calibrated data This is done with the applycal task 4 6 1 CHAPTER 5 SYNTHESIS IMAGING 226 The clearcal command can be used during the self calibration if you need to clear the CORRECTED DATA column and revert to the original DATA If you need to restore the CORRECTED_DATA to any previous stage in the self calibration use applycal again with the appropriate calibration tables BETA ALERT In later patches we will change the tasks so that users need not worry what is contained in the MS scratch columns and how to fill them CASA will handle that underneath for you For now we refer the user back to the calibration chapter for a reminder on how to run the calibration tasks See the example of cleaning and self calibrating the Jupiter 6cm continuum data given below in Appendix 5 10 Examples of Imaging See the scripts provied in Appendix F for examples of imaging In particular we refer the interested user to the demonstrations for e NGC5921 VLA HI a quick demo of basic CASA spectral line cube imaging and analysis F 1 e Jupiter VLA 6cm continuum polarimetry polarization imaging and analysis F 2 e NGC4826 BIMA 3mm CO mosaic imaging of spectral line data F 3 Chapter 6 Image Analysis Once data has been calibrated and imaged in the case
310. e Basic Settings category is expanded by default To expand a category to show its options click on it with the left mouse button 7 3 1 1 Raster Image Basic Settings This roll up is open by default It has some commonly used parameters that alter the way the image is displayed three of these affect the colors used An example of this part of the panel is shown in Figure Basic Settings Aspect ratio fixed world TKR Pixel treatment center gt FP Y Resampling mode nearest v 4 Y Data range 0 0104926 0 0523443 4 Y 0 Scaling power cycles 4 Y Colormap Hot Metal 1 v of Figure 7 7 The Basic Settings category of the Data Display Options panel as it appears if you load the image as a Raster Image This is a zoom in for the data displayed in Figure 7 1 The options available are CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 269 e Basic Settings Aspect ratio This option controls the horizontal vertical size ratio of data pixels on screen Fixed world the default means that the aspect ratio of the pixels is set according to the coordinate system of the image i e true to the projected sky Fixed lattice means that data pixels will always be square on the screen Selecting flexible allows the map to stretch independently in each direction to fill as much of the display area as possible e Basic Settings Pixel treatment This option cont
311. e applied to all sources not just the one used to determine the bandpass gaintable btable gainfield Use nearest there is only one bandpass entry interp nearest Gain calibrators are 1331 305 and 1445 099 FIELD_ID O and 1 field 0 1 We have only a single spectral window SPW 0 Choose 51 channels 6 56 out of the 63 to avoid end effects Channel selection is done inside spw spw 0 6756 No other selection selectdata False In this band we do not need a priori corrections for antenna gain elevation curve or atmospheric opacity at 8GHz and above you would want these gaincurve False opacity 0 0 scan based G solutions for both amplitude and phase gaintype G solint inf combine calmode ap minimum SNR allowed minsnr 1 0 reference antenna 15 15 VLA N2 refant 15 saveinputs gaincal prefix gaincal saved if scriptmode inp user_check raw_input Return to continue scriptin 398 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS gaincal Bootstrap flux scale print Fluxscale default fluxscale vis msfile set the name for the output rescaled caltable ftable prefix fluxscale fluxtable ftable point to our first gain cal table caltable gtable we will be using 1331 305 the source we did setjy on as our flux standard reference note its
312. e of input VLA archive file s vis dl Name of output visibility file bandname a VLA frequency band name gt obtain all bands in archive files frequencytol 150000 0 Frequency shift to define a unique spectral window Hz project g Project name gt all projects in file starttime dd start time to search for data stoptime a end time to search for data applytsys True apply nominal sensitivity scaling to data amp weights autocorr False import autocorrelations to ms if set to True antnamescheme new old or new VA04 or 4 for ant 4 keepblanks False Fill scans with empty source names e g tipping scans async False The main parameters are archivefiles to specify the input VLA Archive format file names and vis to specify the output MS name CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 82 BETA ALERT The scaling of VLA data both before and after the June 2007 Modcomp turnoff is fully supported based on the value of applytsys The NRAO Archive is located at e https archive nrao edu Note that archivefiles takes a string or list of strings as there are often multiple files for a project in the archive For example archivefiles AP314_A950519 xp1 AP314_A950519 xp2 vis NGC7538 ms The importvla task allows selection on the frequency band Suppose that you have 1 3cm line observations in K band and you have copied the
313. e parameter controlling whether scant able operations are done in memory or on disk The default sd rcParams scantable storage memory does it in memory best choice if you have enough while to force the scantables to disk use sd rcParams scantable storage disk which might be necessary to allow processing of large datasets See for more details on the ASAP environment variables A 1 2 Assignment Some ASAP methods and function require you to assign that method to a variable which you can then manipulate This includes sd scantable and sd selector which make objects For example s sd scantable OrionS_rawACSmod average False A 1 3 Lists For lists of scans or IFs such as in scanlist and iflist in the SDtasks the tasks and functions want a comma separated Python list e g scanlist 241 242 243 244 245 246 You can use the Python range function to generate a list of consecutive numbers e g scanlist range 241 247 giving the same list as above e g CASA lt 3 gt scanlist range 241 247 CASA lt 4 gt print scanlist 241 242 243 244 245 246 You can also combine multiple ranges by summing lists APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 290 CASA lt 5 gt scanlist range 241 247 range 251 255 CASA lt 6 gt print scanlist 241 242 243 244 245 246 251 252 253 254 Note that in the future the sd tools and SDtasks will use the same select
314. e script if you are running in scriptmode if scriptmode If you want to do this interactively and iterate over antenna set iteration antenna showgui True plotcal user_check raw_input Return to continue script n else No GUI for this script showgui False Now send final plot to file in PNG format via png suffix figfile caltable plotcal png plotcal Apply our calibration solutions to the data This will put calibrated data into the CORRECTED_DATA column print ApplyCal default applycal vis msfile APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS We want to correct the calibrators using themselves and transfer from 1445 099 to itself and the target N5921 Start with the fluxscale gain and bandpass tables gaintable ftable btable pick the 1445 099 out of the gain table for transfer use all of the bandpass table gainfield 1 interpolation using linear for gain nearest for bandpass interp linear nearest only one spw do not need mapping spwmap all channels spw selectdata False as before gaincurve False opacity 0 0 select the fields for 1445 099 and N5921 field 71 2 applycal Now for completeness apply 1331 305 to itself field 0 gainfield 0 The CORRECTED_DATA column now contains the calibrated visibilities saveinputs applycal pre
315. e target source supplies the visibility model for a re solve of the gain calibration G or T Iteration tends toward convergence to a statistically optimal image In general the quality of each calibration and of the source model are mutually dependent In principle as long as the solution for any calibration component or the source model itself is likely to improve substantially through the use of new information provided by other improved solutions it is worthwhile to continue this process In practice these concepts motivate certain patterns of calibration for different types of observation and the calibrater tool in CASA is designed to accommodate these patterns in a general and flexible manner For a spectral line total intensity observation the pattern is usually 1 Solve for G on the bandpass calibrator 2 Solve for B on the bandpass calibrator using G APPENDIX E APPENDIX THE MEASUREMENT EQUATION AND CALIBRATION 387 3 Solve for G on the primary gain near target and flux density calibrators using B solutions just obtained 4 Scale G solutions for the primary gain calibrator according to the flux density calibrator solutions 5 Apply G and B solutions to the target data 6 Image the calibrated target data If opacity and gain curve information are relevant and available these types are incorporated in each of the steps in future an actual solve for opacity from appropriate data may be folded into this process
316. e this after getting the D terms from one of the above modes Requires the observation of a calibrator with known Q iU or at least known U Q This will produce a calibration table of type X There are channelized solution modes for the above options For example substitute Df for D in the Dx modes described above to get a channelized D term solution BETA ALERT X solutions are currently always frequency independent BETA ALERT polcal will obtain a separate D term solution for each field supplied to it This limitation will be relaxed in the future enabling more sensitive solutions as well as flexibilities like solving for D X using a single scan each of two or more position angle calibrators 4 4 5 1 Heuristics and Strategies for Polarization Calibration Fundamentally with good ordinary gain and bandpass if relevant calibration already in hand good polarization calibration must deliver both the instrumental polarization and position angle calibration An unpolarized source can deliver only the first of these but does not require paral lactic angle coverage A polarized source can only deliver the position angle calibration also if its polarization is known a priori Sources that are polarized but with unknown polarization must always be observed with sufficient parallactic angle coverage where sufficient is determined by SNR and the details of the solving mode These principles are stated assumi
317. e you will have run accum if you have done incremental calibration for any of the types such as G You can also feed gaintable the full sets and rely on use of gainfield interp and spwmap to do the correct interpolation and transfer It is often more convenient to go through accumulation of each type with accum as described above see 4 5 4 2 as this makes it easier to keep track of the sequence of incremental calibration as it is solved and applied You can also do any required smoothing of tables using smoothcal 4 5 3 as this is not yet available in accum or applycal If you are not doing polarization calibration or imaging then you can set parang False to make the calculations faster If you are applying polarization calibration or wish to make polarization images then set parang True so that the parallactic angle rotation is applied to the appropriate correlations Currently you must do this in applycal as this cannot be done on the fly in clean or mosaic See 4 4 1 3 for more on parang For example to apply the final bandpass and flux scaled gain calibration tables solutions to the NGC5921 data default applycal vis ngc5921 usecase ms We want to correct the calibrators using themselves and transfer from 1445 099 to itself and the target N5921 Start with the fluxscale gain and bandpass tables gaintable ngc5921 usecase fluxscale ngc5921 usecase bcal pick the 1445 099 field 1
318. ear Kv Relative Contour Levels 0 2 0 4 0 6 0 8 Bit Base Contour Level Ma F lt Unit Contour Level rc PAY Line width 05 Biv Dash negative contours true Ki Dash positive contours false Kv Line color foreground vB Position tracking Axis labels Axis label properties Q Q Q O O 11 46 Normal Beam Ellipse Rate 10 sec Compact B Apply Frame ngc5921 demo cleanimg image contour 0 00135671 Jy beam Pixel 106 142 0 11 15 22 21 800 05 07 24 193 1 1551 31 km s Contours 0 0105 0 021 0 0314 0 0419 Dismiss Figure 7 9 The Viewer Display Panel left and Data Display Options panel right after choosing Contour Map from the Load Data panel The image shown is for channel 11 of the NGC5921 cube selected using the Animator tape deck and zoomed in using the tool bar icon Note the different options in the open Basic Settings category of the Data Display Options panel For example it is relatively straightforward to set fractional contours e g percent levels e g CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 272 RelativeContourLevels 0 2 0 4 0 6 0 8 BaseContourLevel 0 0 UnitContourLevel lt image max gt This maps the maximum to 1 and thus our contours are fractions of the peak Another example shows how to set absolute values so that the contours are given in flux density units Jy RelativeContourLevels 0 010 0 0 020 0 040 0 080 0 160 0 320 BaseContou
319. early stages for example in a first bandpass calibration so that later stages such as final gain calibration can absorb the lost normalization scaling It is not strictly necessary to use solnorm True at all but is sometimes helpful if you want to have a normalized bandpass for example The append parameter if set to True will append the solutions from this run to existing solutions in caltable Of course this only matters if the table already exists If append False and caltable exists it will overwrite 4 4 2 Spectral Bandpass Calibration bandpass For channelized data it is often desirable to solve for the gain variations in frequency as well as in time Variation in frequency arises as a result of non uniform filter passbands or other dispersive effects in signal transmission It is usually the case that these frequency dependent effects vary CHAPTER 4 SYNTHESIS CALIBRATION 147 on timescales much longer than the time dependent effects handled by the gain types G and T Thus it makes sense to solve for them as a separate term B using the bandpass task The inputs to bandpass are bandpass Calculate a bandpass solution vis xa Nome of input visibility file caltable we Name of output gain calibration table field 22 Select field using field id s or field name s spw a a Select spectral window channels selectdata False Other data selection parameters solint inf Solution interval c
320. easurement set This can then be used in later calibration tasks Currently setjy knows the flux density as a function of frequency for several standard VLA flux calibrators and the value of the flux density can be manually inserted for any other source If the source is not well modeled as a point source then a model image of that source structure can be used with the total flux density scaled by the values given or calculated above for the flux density Models are provided for the standard VLA calibrators Antenna gain elevation curves e g for the VLA antennas and atmospheric optical depth cor rections applied as an elevation dependent function may be pre applied before solving for the bandpass and gains This is currently done by setting the gaincurve and opacity parameters in the various calibration solving tasks See 4 3 for more details 1 5 3 2 Bandpass Calibration The bandpass task calculates a bandpass calibration solution that is it solves for gain variations in frequency as well as in time Since the bandpass relative gain as a function of frequency generally varies much more slowly than the changes in overall mean gain solved for by gaincal one generally uses a long time scale when solving for the bandpass The default B solution mode solves for the gains in frequency slots consisting of channels or averages of channels A polynomial fit for the solution solution type BPOLY may be carried out instead o
321. econvolution If the units of the image are Jy pixel then this is treated as a model image If the units of the image are Jy beam or Jy per solid angle then this is treated as a single dish image and rescaled by the resolution in the beam image header keyword Inclusion of the SD image here is superior to feathering it in later See 5 5 for more information on feathering 5 3 9 Parameter niter The niter parameter sets the maximum total number of minor cycle CLEAN iterations to be performed during this run of clean If restarting from a previous state it will carry on from where it was Note that the threshold parameter can cause the CLEAN to be terminated before the requested number of iterations is reached 5 3 10 Parameter pbcor The pbcor parameter controls whether the final image is scaled to correct for the Primary Beam of the array or not If pbcor False the default then no such scaling is done and the image is in whatever raw scaling used by the imagermode algorithm underneath For single field cleaning with imagermode or gt csclean this is the standard constant noise image If imagermode mosaic then this is the SAULT scaled image regardless of what scaletype is set to If pbcor True the at the end of deconvolution and imaging the raw image is rescaled by dividing by the noise and PB correction image This is what is output by clean as the flux image Note that regardl
322. ect the previously loaded data file s which should display right now menu expands to the right showing all loaded data Close close unload selected data file menu expands to the right Adjust open the Data Display Options Adjust panel Print print the displayed image Save Panel State to a restore file xml format Restore Panel State from a restore file Close Panel close the Viewer Display Panel will exit if this is the last display panel open Quit Viewer close all display panels and exit e Display Panel New Panel create another Viewer Display Panel cleared Panel Options open the Display Panel s options window Save Panel State Restore Panel State Print print displayed image CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 260 Close Panel close the Viewer Display Panel will exit if this is the last display panel open e Tools Annotations not yet available greyed out Spectral Profile plot frequency velocity profile of point or region of image Region Manager save regions and control their extent e View Main Toolbar show hide top row of icons Mouse Toolbar show hide second row of mouse button action selection icons Animator show hide tapedeck control panel Position Tracking show hide bottom position tracking report box Below this is the Main Toolbar
323. ection general data selection syntax 2 6 e viewer image display including region statistics and image cube slice and profile capabil ities 5 2 Common Imaging Task Parameters We now describe some parameters are are common to the imaging tasks These should behave the same way in any Inside the Toolkit imaging task that they are found in These are in alpha The im setimage method is used to betical order set many of the common image pa BETA ALERT There are still a subset of data selection TRALEE s usk ARASA field spw timerange In a later patch we will use the starrlArd hedef Herben gese ey oP for imaging 5 2 1 Parameter cell The cell parameter defines the pixel size in the x and y axes for the output image If given as floats or integers this is the cell size in arc seconds e g cell 0 5 0 5 make 0 5 pixels You can also give the cell size in quantities e g cell 1arcmin 1arcmin If a single value is given then square pixels of that size are assumed CHAPTER 5 SYNTHESIS IMAGING 190 5 2 2 Parameter field The field parameter selects the field indexes or names to be used in imaging Unless you are making a mosaic this is usually a single index or name field 0 First field index 0 field 1331 305 3c286 field all fields in dataset The syntax for field selection is given in 5 2 3 Parameter imagename The value of the i
324. ectral windows 2 2 2 4 Parameter project You can specify a specific project name to import from archive files The default gt will import data from all projects in file s archivefiles For example for VLA Project AL519 CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 84 project AL519 this will work project al519 this will also work while project AL0519 will NOT work even though that is what queries to the VLA Archive will print it as sorry 2 2 2 5 Parameters starttime and stoptime You can specify start and stop times for the data e g starttime 1970 1 31 00 00 00 stoptime 2199 1 31 23 59 59 Note that the blank defaults will load all data fitting other criteria 2 2 2 6 Parameter autocorr Note that autocorrelations are filled into the data set if autocorr True Generally for the VLA autocorrelation data is not useful and furthermore the imaging routine will try to image the autocorrelation data it assumes it is single dish data which will swamp any real signal Thus if you do fill the autocorrelations you will have to flag them before imaging 2 2 2 7 Parameter antnamescheme The antnamescheme parameter controls whether importvla will try to use a naming scheme where EVLA antennas are prefixed with EA e g EA16 and old VLA antennas have names prefixed with VA e g VA11 Our method to detect whether an antenna is EVLA is not yet perfected and thus
325. ed a non zero threshold On the other hand if you get this warning with the threshold set to the default of 0Jy then you should look carefully at your inputs or your data since this usually means that the masking is bad The option imagermode mosaic is for multi field mosaics This choice opens up the sub parameters imagermode mosaic Use csclean or mosaic If use psfmode mosweight False Individually weight the fields of the mosaic ftmachine mosaic Gridding method for the image scaletype gt SAULT Controls scaling of pixels in the image plane cyclefactor 1 5 change depth in between of csclean cycle cyclespeedup 1 Cycle threshold doubles in this number of iteration These options are explained below 5 3 4 1 Sub parameter cyclefactor This sub parameter is activated for imagermode csclean and mosaic Inside the Toolkit The im setmfcontrol method sets the parameters that control the cy cles and primary beam used in mo salcing The cyclefactor parameter allows the user to change the threshold at which the deconvolution cycle will stop and then degrid and subtract the model from the visibilities to form the residual This is with respect to the breaks between minor and major cycles that the clean part would normally force Larger values force a major cycle more often This parameter in effect controls the threshold used by CLEAN to test whether a m
326. ed caltable caltable atable print Output cumulative gain table will be atable linear interpolation interp linear make 10s entries accumtime 10 0 436 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS accum NOTE bypassing this during testing atable ftable Correct the data This will put calibrated data into the CORRECTED_DATA column print ApplyCal default applycal print This will apply the calibration to the DATA print Fills CORRECTED_DATA vis msfile Start with the interpolated fluxscale gain table gaintable atable ptable xtable use settings from gaincal gaincurve usegaincurve opacity gainopacity select the fields field 1331 305 0137 331 JUPITER spw selectdata False IMPORTANT set parang True for polarization parang True do not need to select subset since we did accum note that correct only does nearest interp gainfield applycal Now split the Jupiter target data print Split Jupiter default split vis msfile Now we write out the corrected data to a new MS 437 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS Select the Jupiter field field srcname spw pick off the CORRECTED_DATA column datacolumn corrected Make an output vis file outputvis srcsplitms print Split field data into new ms srcsplitms split
327. ed for a new execution NOTE the initial clean mask actually used is the union of what is specified in mask and amp lt imagename amp gt mask default no masking Possible pecification types a Explicit cleanbox pixel ranges example mask 110 110 150 145 clean region with blc 110 100 trc 150 145 pixel values b Filename with cleanbox pixel values with ascii format example mask mycleanbox txt amp 1t fieldid blc x blc y trc x trc y gt on each line 1 45 66 123 124 2 23 100 300 340 c Filename for image mask example mask myimage mask d Filename for region specification e g from viewer example mask myregion rgn e Combinations of any of the above example mask 110 110 150 145 mycleanbox txt myimage mask myregion rgn uvtaper Apply additional uv tapering of the visibilities default uvtaper False example uvtaper True amp gt amp gt amp gt uvtaper True expandable parameters outertaper uv taper on outer baselines in uv plane bmaj bmin bpa taper Gaussian scale in uv or angular units NOTE uv taper in klambda is roughly on sky FWHM arcsec 200 default outertaper no outer taper applied example outertaper 5klambda circular taper FWHM 5 kilo lambda outertaper 5klambda 3klambda 45 0deg outertaper 10arcsec on sky FWHM 10 outertaper 300 0 default units are meters in aperture plane innertaper uv taper in center of uv pla
328. ed in Patch 2 These were changes made in July 2008 with Beta Release Patch 2 0 2 2 e New interface changes Global parameters variables are not changed in task calls 1 3 5 1 Global parameters variables are not used if a task is called as a function with one or more arguments specified e g task argl val1 Non specified parameters are defaulted to the task specific default values 1 3 2 Return values from tasks are used instead of output variables 1 3 3 e New data handling features The concat task now takes multiple input MS and will combine into a possibly new output MS 2 5 e New synthesis calibration features The calibration tasks now include a combine which allows control of the scope of solutions GELIS The behavior of the solint parameter has changed with solint 0 now giving per integration solutions instead of per scan This is used in conjunction with combine to control solution scope 4 4 1 5 e New synthesis imaging features The clean task now incorporates the features of old tasks invert and mosaic with added capabilities B 3 e New image analysis features Lattice Expression Language LEL in the image analysis tasks and tools is now fully 0 based while previously it was partly 1 based This is most noticeable in the immoments task with the planes parameter and in using the INDEXIN LEL function in the ia tool methods 6 1 3
329. ed myflags flagmanager vis ngc4826 tutorial ms mode save versionname myflags comment My flags merge replace Can also use Flagmanager to list all saved versions ttflagmanager vis ngc4826 tutorial ms mode list HEFHHHHHHHHEHHEEHEHEEHEHHEAHHAE HEHEHE HAEHRHREHEHHEE AEH HRAEHHAA HERE HRH ARE E APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 462 CALIBRATION HHHHHHHHHHHH ERE HHHHHAAAEHA AREER HR RRR HE HARRAH Bandpasses are very flat because of observing mode used online bandpass correction so bandpass calibration is unecessary for these data HHHHHHHHHHARR EHH HHHHHHAAEHA AREER HHRERRH HAHAHA AAR Derive gain calibration solutions We will use VLA like G per scan calibration HHHHHHHHHHHE REET HHHHHAAAEHA AREER HERR H HARE RARE ARA Set the flux density of 3C273 to 23 Jy print Setjy 3C273 default setjy setjy vis ngc4826 tutorial ms field 0 fluxdensity 23 0 0 0 0 spw 073 Not really necessary to set spw but you get lots of warning messages if you don t HHHHHHHHHHHH ERE HHHHAAAEAA AARP HORA RRR HH HARE R RAR AAA AAA Gain calibration print Gaincal default gaincal This should be combining all spw for the two calibrators for single scan based solutions print Gain calibration for fields 0 1 and spw 0711 print Using solint inf combin
330. ee faint emission Use rectangle drawing tool to box off source Double click inside to print statistics Move box on source and get the max Calculate DynRange MAXon RMSoff This time I got 1 050 0 001 1050 better Still not as good as it can be you can try selfcal again We will stop here Close viewer panel when done clnimage2 image Pause script if you are running in scriptmode if scriptmode user_check raw_input Return to continue script n print 447 jupiter6cm demo clean2 image Jy beam n Std Dev RMS Mean Variance Sum 5236 0 001389 0 001390 3 244e 05 1 930e 06 0 1699 Flux Med Dev IntQtlRng Median Min Max 0 01060 0 0009064 0 001823 1 884e 05 0 004015 0 004892 On Jupiter n Std Dev RMS Mean Variance Sum 5304 0 08512 0 08629 0 01418 0 007245 75 21 Flux Med Dev IntQtlRng Median Min Max 4 695 0 0008142 0 001657 0 0001557 0 004526 1 076 Estimated dynamic range 1 076 0 001389 775 better Note that the exact numbers you get will depend on how deep you take the interactive clean and how you draw the box for the stats APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS print After this script is done you can continue on with print more self cal or try different cleaning options Can do some image statistics if you wish print Imstat Cycle 2 default imstat imagename clnimage2 on_st
331. egin Task mosaic Tue Oct 2 17 58 16 2007 NORMAL mosaic Use tm abort return_value to abort the asynchronous task tm retrieve return_value to retrieve the status usual messages here End Task mosaic HHEHHHHHHHHHHHHEHHHHHHHHHHEHHHHHEHEHEHEAHEHEEEH for the example above To show the current state of an asynchronous task use the tm retrieve method using the handle id as the argument For example CHAPTER 1 INTRODUCTION 47 CASA lt 9 gt tm retrieve handle Out 9 result None state pending or CASA lt 10 gt tm retrieve 1 Out 10 result None state pending which means its still running You should be seeing output in the logger also while the task is running When a task is finished you will see CASA lt 11 gt tm retrieve 1 Out 11 result None state done which indicates completion 1 3 4 2 Aborting Asynchronous Tasks To abort a task while it is running in the background use the tm abort method again with the task handle id as the argument For example CASA lt 12 gt handle mosaic CASA lt 13 gt tm abort handle will abort the task if it is running If this does not work try CNTL Z followed by a kill 9 lt PID gt for the appropriate process ID See 8 for more on these methods to abort CASA execution 1 3 5 Setting Parameters and Invoking Tasks One can set parameters for tasks but
332. ek Be hed iy owns ptes 345 Oe kok Gb we be ae oe a ee SA mio 345 ih beh ae Sg awd oe hae Paes eae G 346 by dl kp hb Se une a BS ee RETR Ape ce ney amp ce ER eh 347 SS SU O E E 348 bin eS ye ee Snes ee es ee e 348 Sn oe rs eee Seen ws ee ee eee tg 348 A a Oe ON ee ere a ee ee re 349 eee eg Dee eae Beg a A ee ee al Meee cee 349 aaa 349 340 AAA 350 as fs St Ses a ee Ce ee NE A A A A fee ees 351 A ri eA ares eh ap a ee SAY Ce Gk SelB ake 352 yams bee A op Sere ae eee es ee a ee 352 a Been ay Ge oy Saray ay ay Aten ere ie E Grae a ea ee 353 Mie Bak toe Gms ee a ee AAA Be ee ee a 354 aa hed iy own E gee 354 peta ea eee ae Re eae ee ARA 354 beh Ede Aen AA ae oka 355 patios 356 Cate he dada a ee a ee Oe Seo 359 peewee were se 360 A 5 Known Issues Problems Deficiencies and Features 2 00084 362 B Appendix Simulation B 1 Simulating ALMA with almasimmos 0 000000 2b eee C Appendix Obtaining and Installing CASA C 1 Installation Script C 2 Startup D Appendix Python and CASA D 1 Automatic parentheses D 2 Indentation D 3 Lists and Ranges D 4 Dictionaries D 4 1 Saving and Reading Dictionaries 0 200020005 2 ae D 5 Control Flow Conditionals Loops and Exceptions 2 D 5 1 Conditionals D 5 2 Loops D 6 System shell access D 6 1 Using the os system methods e e D
333. emo polimg clean image pi 4 Display axes Fl Hidden axes Basic Settings lect ratio fixed world AY treatment edge y Aly litude scale factor os Aly crement 2 hy rement 2 BY fa rotation 90 Biv w arrow heads false AY KID 03 Dismiss 00 55 40 38 Directory home sandrock3 smyers Testing3 Patch3 Jupiter Type m i Display As cm demo ms flagversions Directory Raster Image cm demo polimg clean flux Image e 0 O O O O O Lo 4 Normal cm demo polimg clean image image ONGS A 5 aime cm demo polimg clean image Image Rate 10 sec Compact cm demo polimg clean image Q Image Vector Map sr cm demo polimg clean image U Image Frame cm demo polimg clean image pola Image Marker Map em demo polima clean image poli Image cm demo polimg clean model Image cm demo polimg clean modelmask Image cm demo polimg clean psf Image E IO TS cm demo polimg clean residual Image iI 0 000632453 sy beam Pixel 117 127 0 0 ae TG 00 55 41 143 04 44 38 554 I 12 443 km s jupiter cm dem 0 0048 vector r LEL Expression masked Pixel 117 127 0 0 r x 0 0048 00 55 41 143 04 44 38 554 Pangle 12 443 km s jupiter6cm demo polimg clean image poli contour Update X Leave Open Done 0 000483434 gy beam Pixel 117 127 0 0 00 55 41 143 04 44 38 554 Plinear 12 443 km s Figure 5 5 After clean and self calibration using
334. en pre applying the solution in the tables This interpolation is currently only in time The choices are currently nearest linear and aipslin e nearest just picks the entry nearest in time to the visibility in question e linear interpolation calibrates each datum with calibration phases and amplitudes linearly interpolated from neighboring time values In the case of phase this mode will assume that phase jumps greater than 180 between neighboring points indicate a cycle slip and the interpolated value will follow this change in cycle accordingly e aipslin emulates the classic AIPS interpolation mode with linearly interpolated ampli tudes and phases derived from interpolation of the complex calibration values While this method avoids having to track cycle slips which is unstable for solutions with very low SNR it will yield a phase interpolation which becomes increasingly non linear as the spanned phase difference increases The non linearity mimics the behavior of interp nearest as the spanned phase difference approaches 180 the phase of the interpolated complex calibration value initially changes very slowly then rapidly jumps to the second value at the midpoint of the interval If the uncalibrated phase is changing rapidly a nearest interpolation is not desirable Usually interp linear is the best choice For example interp nearest linear uses nearest int
335. enough characters to make the command unique lt TAB gt will complete it CHAPTER 1 INTRODUCTION 35 CASA lt 15 gt cle lt TAB gt clean clean_description clearcal_check_params clearplot clearstat clean_check_params clear clearcal_defaults clearplot_defaults clearstat_defaults clean_defaults clearcal clearcal_description clearplot_description clearstat_description 1 2 8 2 help lt taskname gt Basic information on an application including the parameters used and their defaults can be obtained by typing pdoc task help task or task The pdoc task currently gives the cleanest documentation format with the smallest amount of object oriented programmer output This inline help provides a one line description of the task and then lists all parameters a brief description of the parameter the parameter default an example setting the parameter and any options if there are limited allowed values for the parameter For example CASA lt 10 gt pdoc importvla Class Docstring Import VLA archive file s to a measurement set Imports an arbitrary number of VLA archive format data sets into a casa measurement set If more than one band is present they will be put in the same measurement set but in a separate spectral window The task will handle old style and new style VLA after July 2007 archive data and apply the tsys to the data and to the weights Keyword arguments archivefiles Name of input VLA archive file s
336. ent a greater fraction of the observing wavelength By design this effect is usually minimized i e gain maximized for elevations between 45 and 60 degrees with the gain decreasing at higher and lower elevations Gain curves are most often described as 2nd or 3rd order polynomials in zenith angle Gain curve calibration has been implemented in CASA for the VLA only with gain curve polyno mial coefficients available directly from the CASA data repository To make gain curve corrections for VLA data set gaincurve True for any of the calibration tasks BETA ALERT The gaincurve parameter must be supplied to any calibration task that allows pre application of the prior calibration e g bandpass gaincal applycal This should be done consistently through the calibration process In future updates we will likely move to a separate task to calibrate the gain curve For example to pre apply the gaincurve during gain calibration gaincal data ms cal GO gaincuve True solint 0 refant 11 NOTE Set gaincurve False if you are not using VLA data The gain curve will be calculated per timestamp Upon execution of a calibration task e g gaincal bandpass applycal etc the gain curve data appropriate to the observing frequencies will be automatically retrieved from the data repository and applied BETA ALERT Currently gain curves for VLA are built into the CASA system and this is what is applied when gaincurve True Therefore
337. enter ee Image phase center position or field index restfreq dl rest frequency to assign to image see help stokes T Stokes params to image eg I IV QU IQUV weighting natural Weighting of uv natural uniform briggs uvtaper False Apply additional uv tapering of visibilities modelimage a Name of model image s to initialize cleaning restoringbeam a gt gt Output Gaussian restoring beam for CLEAN image pbcor False Output primary beam corrected image minpb 0 1 Minimum PB level to use async False If true the taskname must be started using clean Figure 1 1 shows how this will look to you on your terminal Note that some parameters are in boldface with a gray background This means that some values for this parameter will cause it to expand revealing new sub parameters to be set CASA uses color and font to indicate different properties of parameters and their values Parameter and Values in CASA inp CHAPTER 1 INTRODUCTION 53 AAA Az EEE CASA lt 2 gt default clean CASA lt 3 gt inp clean clean Deconvolve an image with selected algorithm vis name of input visibility file imagename Pre name of output images field Field Name spw sh Spectral windows channels is all selectdata False Other data selection parameters mode mfs Type of selection mfs channel velocity frequency niter 500 Maximum number of iterati
338. ents instead of jointly as in clark This means CHAPTER 5 SYNTHESIS IMAGING 203 that this is the same as clark for Stokes I imaging only This option can also be combined with imagermode csclean 5 3 4 5 3 2 The multiscale parameter BETA ALERT The multiscale option is currently under development and should be used with caution and be considered as an experimental algorithm The multi scale CLEAN method is known to need careful tuning in order to properly converge However currently the only control for multiscale in the clean task is the setting of the scales To activate multi scale mode specify a non blank list of scales in the multiscale parameter e g Inside the Toolkit multiscale 0 3 10 30 Four scales including pp tite sHaRe cates method sets the multi scale Gaussian widths In ad These are given in numbers of pixels and specify FWHM _ dition to choosing a list of sizes in of the Gaussians used to compute the filtered images pixels you can just pick a number of Setting the multiscale parameter to a non empty list Scales AT Be ONES Benes OF opens up the sub parameter oe multiscale 0 3 10 30 set deconvolution scales pixels negcomponent 1 Stop if largest scale finds this many neg components The negcomponent sub parameter is here to set the point at which the clean terminates because of negative com ponents For negcomponent gt 0 component search will
339. ents of the NGC5921 cube zoomed in using the tool bar icon The tab for the contour plot is open in the Data Display Options panel 7 3 4 Spectral Profile Plotting From the Tools menu the Spectral Profile plotting tool can be selected This will pop up a new Image Profile window containing an x y plot of the intensity versus spectral axis usually velocity You can then select a region with the Rectangle or Polygon Region drawing tools or pinpoint a position using the Crosshair tool The profile for the region or position selected will then appear in the Image Profile window This profile will update in real time to track changes to the region or crosshair which can be moved by click dragging the mouse See Figure 7 3 5 Managing and Saving Regions To save a region of an image you have on display first open the Region Manager window the Tools Region Manager menu item or the corresponding toolbutton A window will appear as in Figure CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 274 Viewer Display Panel Xh Display Options Data Display Panel Jools View 240800 ASA BE Be 2 S921 usecase clean image ngc5921 usecase cleanimage contour Display axes Hidden axes Basic Settings iv Image Profile ngc5921 usecase clean image Rectangle Region Profile Flux Density muy Maia y e em e e e ve Sagaqaaaqagqaaa
340. er mode see help for options Examples of transitions include restfreq 1420405751 786Hz 21cm HI frequency restfreq HI 21cm HI transition name restfreq 115 2712GHz CO 1 0 line frequency For a list of known lines in the CASA measures system use the toolkit command me linelist For example CASA lt 14 gt me linelist Dut 14 C109A CI CII166A DI H107A H110A H138B H166A H240A H272A H2CO HE110A HE138B HI 0H1612 OH1665 CHAPTER 3 DATA EXAMINATION AND EDITING 117 BETA ALERT The list of known lines in CASA is currently very restricted and will be increased in upcoming releases to include lines in ALMA bands for example You can use the me spectralline tool method to turn transition names into frequencies CASA lt 16 gt me spectralline HI Out 17 m0 unit Hz value 1420405751 786 refer REST gt type frequency not necessary for this task but possibly useful The frame sub parameter sets the frequency frame The allowed options can be listed using the me listcodes method on the me frequency method e g CASA lt 17 gt me listcodes me frequency Out 17 extra array dtype S1 normal array REST LSRK LSRD BARY GEO TOPO GALACTO LGROUP CMB dtype S8 The doppler sub parameter likewise sets the Doppler system The allowed codes can be
341. er of unique sub parameters bandtype BPOLY Type of bandpass solution B or BPOLY degamp 3 Polynomial degree for BPOLY amplitude solution degphase 3 Polynomial degree for BPOLY phase solution visnorm False Normalize data prior to BPOLY solution maskcenter O Number of channels in BPOLY to avoid in center of band maskedge O Percent of channels in BPOLY to avoid at each band edge CHAPTER 4 SYNTHESIS CALIBRATION 150 The degamp and degphase parameters indicate the polynomial degree desired for the amplitude and phase solutions The maskcenter parameter is used to indicate the number of channels in the center of the band to avoid passing to the solution e g to avoid Gibbs ringing in central channels for PdBI data The maskedge drops beginning and end channels The visnorm parameter turns on normalization before the solution is obtained rather than after for solnorm The combine parameter 4 4 1 5 can be used to combine data across spectral windows scans and fields Note that bandpass will allow you to use multiple fields and can determine a single solution for all specified fields using combine field If you want to use more than one field in the solution it is prudent to use an initial gaincal using proper flux densities for all sources not just 1Jy and use this table as an input to bandpass because in general the phase towards two widely separated sources will not be sufficiently similar to combine the
342. er6cm usecase selfcali amp antenna 1 subplot 211 plotcal jupiter6cm usecase selfcall phase antenna 1 subplot 212 The final plot is shown in Figure BETA ALERT Only interpolation is offered in accum no smoothing as in smoothcal 4 6 Application of Calibration to the Data After the calibration solutions are computed and written to one or more calibration tables one then needs to apply them to the data CHAPTER 4 SYNTHESIS CALIBRATION 175 hd CASA Plotter Mar Regon Reg vna tocate 1 ou D0 0 Bj Figure 4 8 The final amp top and phase bottom of the self calibration gain solutions for Jupiter An initial phase calibration on 10s solint was followed by an incremental gain solution on each scan These were accumulated into the cumulative solution shown here 4 6 1 Application of Calibration applycal After all relevant calibration types have been determined they must be applied to the target source s before splitting off to a new MS or before imaging This is currently done by explicitly taking the data in the DATA column in the MAIN table of the MS applying the relevant calibration tables and creating the CORRECTED_DATA scratch column The original DATA column is untouched The applycal task does this The inputs are applycal Apply calibration solution s to data vis gt Name of input visibility file field ee Names or indi
343. erpolation on the first table and linear on the second The spwmap parameter sets the spectral window combinations to form for the gaintable s This is a list or a list of lists of integers giving the spw IDs to map There is one list for each table in gaintable with an entry for each ID in the MS For example CHAPTER 4 SYNTHESIS CALIBRATION 145 spwmap 0 0 1 1 apply from spw 0 to 0 1 and 1 to 2 3 for an MS with spw 0 1 2 3 For multiple gaintable use lists of lists e g spwmap 0 0 1 1 0 1 0 1 2nd table spw 0 to 0 2 and 1 to 1 3 BETA ALERT This scheme for mapping the pre apply tables is not particularly elegant partic ularly for spwmap This may change in the future 4 4 1 5 Solving solint combine preavg refant minblperant minsnr The parameters controlling common aspects of the solution are solint inf Solution interval egs inf 60s see help combine des Data axes which to combine for solve scan spw and or field preavg 1 0 Pre averaging interval sec rarely needed refant q Reference antenna name no explicit reference minblperant 4 Minimum baselines _per antenna_ required for solve minsnr 0 0 Reject solutions below this SNR 0 gt no rejection The solution interval is given by solint If given a number without a unit this is in seconds The special values inf and 1 specify an infinite solution interval encompassing the entire dataset
344. ers 0 4 4100 200 component 0 For multiple components set initial guesses for each e g set two gaussian components set initial guesses for Gaussian for first component 0 set initial guesses for Gaussian for second component 1 f set_function gauss 2 f set_gauss_parameters 0 4 4100 200 component 0 f set_gauss_parameters 0 1 4200 100 component 1 A 3 9 Plotting A 3 9 1 ASAP plotter The ASAP plotter uses the same Python matplotlib library as in CASA for x y plots It is accessed via the sd plotter lt TAB gt see all functions omitted here sd plotter plot scans the workhorse function sd plotter set lt TAB gt sd plotter set_abcissa sd plotter set_legend sd plotter set_range sd plotter set_colors sd plotter set_linestyles sd plotter set_selection sd plotter set_colours sd plotter set_mask sd plotter set_stacking sd plotter set_font sd plotter set_mode sd plotter set_title sd plotter set_histogram sd plotter set_ordinate sd plotter set_layout sd plotter set_panelling Spectra can be plotted at any time and it will attempt to do the correct layout depending on whether it is a set of scans or a single scan The details of the plotter display matplotlib are detailed in the earlier section A 3 9 2 Line Catalog ASAP allows to load a custom line catalog in ASCII format The ASCII text file must have at least 4 columns with Molecule name frequency in MH
345. es A range of frequencies are used to select all spectral windows which contain channels within the given range Frequencies can be specified with an optional unit the default unit being Hz Other common choices for radio and mm sub mm data are kHz MHz and GHz You will get the entire spectral windows not just the channels in the specified range You will need to do channel selection see below to do that The spw can also be selected via comparison for integer IDs For example gt ID will select all spectral windows with ID greater than the specified value while lt ID will select those with ID lesser than the specified value BETA ALERT In the current Beta Release lt ID and gt ID are inclusive with the ID specified included in the selection e g spw lt 2 is equivalent to spw 0 1 2 and not spw 0 1 as was intended This will be fixed in an upcoming release Spectral window selection using strings follows the standard rules spw 1 SPWID 1 spw 1 3 5 SPWID 1 3 5 spw 073 SPWID 0 1 2 3 spw 073 5 SPWID 0 1 2 3 and 5 spw lt 3 5 SPWID 0 1 2 3 and 5 spw All spectral windows spw 1412 1415MHz Spectral windows containing 1412 1415MHz In some cases the spectral windows may allow specification by name For example CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 95 spw 3mmUSB 3mmLSB choose by names if available
346. ess of what you set pbcor to you can recover the other option using immath 6 5 to either multiply or divide by the flux image 5 3 11 Parameter restoringbeam The restoringbeam parameter allows the user to set a specific Gaussian restoring beam to make the final restored image from the final model and residuals If restoringbeam the default then the restoring beam is calculated by fitting to the PSF e g the psf image For a mosaic this is at the center of the field closest to the phasecenter To specify a restoring beam provide restoringbeam a list of bmaj bmin bpa which are the pa rameters of an elliptical Gaussian The default units are in arc seconds for bmaj bmin components and degrees for the bpa component CHAPTER 5 SYNTHESIS IMAGING 211 For example restoringbeam 10arcsec circular Gaussian FWHM 10 restoringbeam 10 0 5 0 45 0deg 10 x5 at PA 45 degrees 5 3 12 Parameter threshold The threshold parameter instructs clean to terminate when the maximum absolute residual reaches this level or below Note that it may not reach this residual level due to the value of the niter parameter which may cause it to terminate early If threshold is given a floating point number then this is the threshold in milli Jansky You can also supply a flux density quanta to threshold e g threshold 8 0mJy threshold 0 008Jy these do the same thing 5 3 13 Intera
347. evious max oldtest_dirtymax print Difference fractional diff_dirtymax print print gt gt logfile Dirty Image max thistest_dirtymax print gt gt logfile Previous max oldtest_dirtymax print gt gt logfile Difference fractional diff_dirtymax print gt gt logfile thistest_dirtyrms dirtystats rms 0 oldtest_dirtyrms 0 00243866862729 diff_dirtyrms abs oldtest_dirtyrms thistest_dirtyrms oldtest_dirtyrms print Dirty image rms thistest_dirtyrms print Previous rms oldtest_dirtyrms print Difference fractional diff_dirtyrms print print gt gt logfile Dirty Image rms thistest_dirtyrms print gt gt logfile Previous rms oldtest_dirtyrms print gt gt logfile Difference fractional diff_dirtyrms print gt gt logfile Now the clean image thistest_immax cubestats max 0 oldtest_immax 0 052414759993553162 diff_immax abs oldtest_immax thistest_immax oldtest_immax print Clean image max gt thistest_immax print Previous max oldtest_immax print Difference fractional diff_immax print print gt gt logfile Clean Image max thistest_immax print gt gt logfile Previous max oldtest_immax print gt gt logfile Difference fractional diff_immax print gt gt logfile
348. f a visibility set Determine temporal gains from calibrator observations Hanning smooth frequency channel data to remove Gibbs ringing Subtracts specified continuum channels from a spectral line data set Fit One Elliptical Gaussian Component on an image region s List get and put image header parameters Perform math operations on images Compute moments from an image Convert an ALMA Science Data Model observation into a CASA visibility file Convert an image FITS file into a CASA image Convert a UVFITS file to a CASA visibility data set CHAPTER 1 importvla imregrid imstat imval invert listcal listhistory listobs listvis makemask mosaic newclean newflagdata oldclean plotants plotcal plotxy polcal sdaverage sdbaseline sdcal sdcoadd sdfit sdflag sdlist sdplot sdsave sdscale sdsmooth sdstat sdtpimaging setjy smoothcal specfit split uvcontsub uvmodelfit uvsub viewer widefield INTRODUCTION 41 Import VLA archive file s to a measurement set regrid an image onto a template image Displays statistical information from an image or image region Get the data value s and or mask value in an image Calculate the dirty image and dirty beam from a visibility set List calibrated antenna gain solutions List the processing history of a dataset List data set summary in the logger List measurement set visibilities Derive a mask image from a cleanbox blc trc regions Create a multi fie
349. f input CASA image fitsimage ds Name of output image FITS file velocity e False tt Use velocity rather than frequency as spectral axis optical False Use the optical rather than radio velocity convention bitpix 32 Bits per pixel minpix O Minimum pixel value maxpix O Maximum pixel value overwrite False Overwrite pre existing imagename dropstokes False Drop the Stokes axis stokeslast True Put Stokes axis last in header async True If true the taskname must be started using exportfits The dropstokes or stokeslast parameter may be needed to make the FITS image compatible with an external application For example exportfits ngc5921 usecase clean image ngc5921 usecase image fits BETA ALERT Setting async True is recommended because there is a flaw in the Beta version of the FITS classes that will cause subsequent FITS import importfits or importuvfits after an export to fail Using asynchronous export will circumvent this by forcing the creation and use of a new tool object rather than using default one 6 11 2 FITS Image Import importfits You can also use the importfits task to import a FITS image into CASA image table format Note the CASA viewer can read fits images so you don t need to do this if you just want to look a the image The inputs for importfits are importfits Convert an image FITS file into a CASA image fitsimage pe Name of input image FITS
350. f plot options spectra totalpower pointing azel default spectra stack code for stacking on single plot for spectral plotting options p b 1i t s or pol beam if time scan default p example maximum of 25 stacked spectra stack by pol beam if time scan panel code for splitting into multiple panels for spectral plotting options p b 1i t s or gt pol beam if time scan default i example maximum of 25 panels panel by pol beam if time scan flrange range for flux axis of plot for spectral plotting options list min max default full range example flrange 0 1 2 0 if K assumes current fluxunit sprange range for spectral axis of plot options list min max default full range example sprange 42 1 42 5 if GHz assumes current specunit linecat control for line catalog plotting for spectral plotting options str all none or by molecule default none no lines plotted example linecat Si0 for Si0 lines linecat 0H for alcohols uses sprange to limit catalog WARNING specunit must be in frequency Hz to plot from the line catalog and must be GHz or MHz to use sprange to limit catalog APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 318 linedop doppler offset for line cata
351. f the default frequency slot based B solutions This single solution will span combine multiple spectral windows Bandpass calibration is discussed in detail in If the gains of the system are changing over the time that the bandpass calibrator is observed then you may need to do an initial gain calibration see next step 1 5 3 3 Gain Calibration The gaincal task determines solutions for the time based complex antenna gains for each spectral window from the specified calibration sources A solution interval may be specified The default G solution mode solved for gains in specified time solution invervals A spline fit for the solution solution type GSPLINE may be carried out instead of the default time slot based G solutions This single solution will span combine multiple spectral windows See for more on gain calibration CHAPTER 1 INTRODUCTION 70 1 5 3 4 Polarization Calibration The polcal task will solve for any unknown polarization leakage and cross hand phase terms D and X solutions The D leakage solutions will work on sources with no polarization sources with known and supplied polarization and sources with unknown polarization tracked through a range in parallactic angle on the sky The solution for the unknown cross hand polarization phase difference X term requires a polarized source with known linear polarization Q U See for more on polarization ca
352. field S Select a subset of calibrators from gaintable s interp a Interpolation mode in time to use for each gaintable spwmap Spectral windows combinations to form for gaintables s gaincurve False Apply internal VLA antenna gain curve correction opacity e 0 0 Opacity correction to apply nepers parang False Apply parallactic angle correction async False See 1 3 5 4 below for more details on the use of the inputs command All task parameters have global scope within CASA the parameter values are common to all tasks and also at the CASA command line This allows the convenience of not changing parameters that are shared between tasks but does require care when chaining together sequences of task invocations to ensure proper values are provided If you want to reset the input keywords for a single task use the default command 1 3 5 2 For example to set the defaults for the bandpass task type CASA lt 30 gt default bandpass as we did above To inspect a single parameter value just type it at the command line Continuing the above example CASA lt 36 gt combine Out 14 scan CASA parameters are just Python variables Parameters for a given task can be saved by using the saveinputs command see 1 3 5 5 and restored using the execfile lt filename gt command Note that if the task is successfully exe cuted then a lt taskname gt last file is created in t
353. first page is shown The user would use the Next button to advance to the next set of antennas Spwld 0 channel 0 Time Field Ant Amp Phase Amp Phase 1999 04 16 14 10 43 5 JUPITER 1 1 016 11 5 1 016 9 22 127 1 013 5 3 0 993 3 1 73 0 993 0 8 0 990 5 1 24 0 997 10 7 0 999 8 3 5 0 985 2 7 0 988 4 0 6 1 005 8 4 1 009 5 3 Ea 0 894 8 7 0 897 6 8 18 1 001 0 1 0 992 0 7 29 0 989 12 4 0 992 13 5 2402 1 000F 4 2F 1 000F 3 2F le 0 896 0 0 0 890 0 0 CHAPTER 4 SYNTHESIS CALIBRATION 168 212 0 996 10 6 0 996 4 2 213 1 009 8 4 1 011 6 1 214 0 993 17 6 0 994 16 1 215 1 002 0 8 1 002 ziei 16 1 010 9 9 1 012 8 6 ABR 1 014 8 0 1 017 id 18 0 998 3 0 1 005 1 0 x19 0 997 39 1 0 994 38 9 220 0 984 5 7 0 986 3 0 21 1 000F 4 2F 1 000F 3 2F 22 1 003 11 8 1 004 10 4 223 1 007 13 8 1 009 11 7 224 1 000F 4 2F 1 000F 3 2F 225 1 000F 4 2F 1 000F 3 2F 226 0 992 3 7 1 000 0 2 227 0 994 5 6 0 991 4 3 28 0 993 10 7 0 997 3 8 BETA ALERT It is likely that the format of this listing will change to better present it to the user 4 5 3 Calibration Smoothing smoothcal The smoothcal task will smooth calibration solutions most usefully G or T over a longer time interval to reduce noise and outliers The inputs are smoothcal Smooth calibration solution s derived from one or more sources vis q Name of input visibility file tablein oe
354. first try to match the NAME which we see in listobs was the number 9 for ID 8 So be careful here why naming antennas as numbers is bad antenna 9 plotxy O YES the last 4 scans are bad Box em and flag Go back and clean up xaxis uvdist spw antenna correlation RR LL plotxy O Box up the bad low points basically a clip below 0 52 and flag Note that RL LR are too weak to clip on Finally do JUPITER field JUPITER correlation iteration xaxis time plotxy O Here you will see that the final scan at 22 00 00 UT is bad Draw a box around it and flag it Now look at whats left correlation RR LL xaxis uvdist spw 71 antenna iteration antenna plotxy O As you step through you will see that Antenna 9 ID 8 is often bad in this spw If you box and do Locate or remember from 0137 331 its probably a bad time CHAPTER 3 DATA EXAMINATION AND EDITING 121 The easiset way to kill it antenna 9 iteration xaxis time correlation plotxy O Draw a box around all points in the last bad scans and flag em Now clean up the rest xaxis uvdist correlation RR LL antenna spw You will be drawing many tiny boxes so remember you can use the ESC key to get rid of the most recent box if you make a mistake plotxy O N
355. fit outfile a Optional output component list table async False if True run in the background prompt is freed BETA ALERT This task currently only fits a single component The user specifies the number of non linear solution iterations niter the component type comptype an initial guess for the component parameters sourcepar and optionally a vector of Booleans se lecting which component parameters should be allowed to vary fixpar and a filename in which to store a CASA componentlist for use in other applications file Allowed comptypes are currently point P or Gaussian G The function returns a vector containing the resulting parameter list This vector can be edited at the command line and specified as input sourcepar for another round of fitting The sourcepar parameter is currently the only way to specify the starting parameters for the fit For points there are three parameters I total flux density and relative direction RA Dec offsets in arcsec from the observation s phase center For Gaussians there are three additional parameters the Gaussian s semi major axis width arcsec the aspect ratio and position angle degrees It should be understood that the quality of the result is very sensitive to the starting parameters provided by the user If this first guess is not sufficiently close to the global y mini mum the algorithm will happily converge to an incorrect local minimum In fact
356. fix applycal saved Pause script if you are running in scriptmode if scriptmode inp user_check raw_input Return to continue script n applycal Now use plotxy to plot the calibrated target data before contsub print Plotxy NGC5921 401 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS default plotxy vis msfile field 2 Edge channels are bad spw 0 4759 Time average across scans timebin 86000 crossscans True Set up 2x1 panels upper panel amp vs channel subplot 211 xaxis channel yaxis amp datacolumn corrected No output file yet wait to plot next panel saveinputs plotxy prefixt plotxy final amp saved print Amp averaged across time and baseline upper figfile if scriptmode interactive True else interactive False plotxy O Set up 2x1 panels lower panel phase vs time subplot 212 yaxis phase datacolumn corrected Time average across scans and baselines timebin 86000 crossscans True crossbls True saveinputs plotxy prefix plotxy final phase saved print Phase averaged across time and baseline lower print Final calibrated data Pause script if you are running in scriptmode if scriptmode interactive True figfile plotxy 402 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS user_check raw_
357. fixed in 2 4 0 release 2 The keepblanks parameter is defaulted to False so tipping scans will not be in cluded in the measurement set Setting this to True will include the tipping scans 3 Data edited as having zero weight are now flagged instead of simply being carried around with a weight of 0 This fixes an issue in the viewer where existing flags were ignored while performing additional flagging 4 VLA antennas are now sorted into numerical name order and the station naming has been enhanced to include the VLA EVLA distinction 5 Duplicate field names for different source positions in the archive a rare occurence are resolved with an appended digit to permit selecting such fields uniquely in sub sequent processing The task importuvfits has a new parameter antnamescheme as in importvla which when set to new and you are importing VLA data then it will prepend either VA or EV to the antenna name 8 2 2 1 1 Data can be compressed in importasdm by setting compression True 2 2 3 The concat task now has a timesort parameter to trigger time based resorting of the output MS 2 5 A number of changes to listobs output including reporting of rest frequency and velocity information integration time source identification time frame 2 3 There is a prototype vishead task that allows the user to manipulate some common metadata items in a measurement set e g to list get and put va
358. frequency to assign to image see help stokes T Stokes params to image eg 1 1Y QU IQUV weighting briggs Weighting of uv natural uniform briggs robust Ong Briggs robustness parameter npixels 0 number of pixels to determine uv cell size 0 gt field of view uvtaper False Apply additional uv tapering of visibilities modelimage ol Name of model image s to initialize cleaning restoringbeam Output Gaussian restoring beam for CLEAN image pbcor False Output primary beam corrected image minpb O54 Minimum PB level to use async False If true the taskname must be started using clean CASA lt 8 gt E Figure 1 3 The clean inputs where one parameter has been set to an invalid value This is drawn in red to draw attention to the problem This hapless user probably confused the hogbom clean algorithm with Harry Potter vis ngc5921 demo ms verbose True listobs vis ngc5921 ms verbose False To read these back in use the Python execfile command For example CASA lt 5 gt execfile listobs saved and we are back An example save to a custom named file CASA lt 6 gt saveinputs listobs ngc5921_listobs par You can also use the CASA tget command see 1 3 5 6 below instead of the Python execfile to restore your inputs 1 3 5 6 The tget Command The tget command will recover saved values of the inputs of t
359. ft off In the first left panel it has cleaned deeper and we come back and zoom in to see that our current mask is good and we should clean further We change npercycle to 500 from 100 in the box at upper right of the window In the final panel right we see the results after this clean The residuals are such that we should terminate the clean using the red X button and use our model for self calibration more convenient for the user to treat the channels in order cleaning each in turn before moving on This will be implemented in an upcoming update 5 3 14 Mosaic imaging The clean task contains the capability to image multiple pointing centers together into a single mosaic image This ability is controlled by setting imagermode mosaic 5 3 4 The key parameter that controls how clean produces the mosaic is the ftmachine sub parameter 8 B 3 4 3 For ftmachine ft clean will perform a weighted combination of the images pro duced by transforming each mosaic pointing separately This can be slow as the individual sub images must be recombined in the image plane NOTE this option is preferred for data taken with sub optimal mosaic sampling e g fields too far apart on a sparse irregular pattern etc CHAPTER 5 SYNTHESIS IMAGING 215 v Viewer Display Panel 5 x OX Data Display Panel Tools View 24305000 xa32A3ga x a 38le 2 e eje 2 fer6cm dem 0 0048 vector jupiter cm d
360. g model used to improve the calibration Finally if sufficiently strong the target may be self calibrated as well APPENDIX E APPENDIX THE MEASUREMENT EQUATION AND CALIBRATION 388 E 2 General Calibrater Mechanics The calibrater tasks tool are designed to solve and apply solutions for all of the solution types listed above and more are in the works This leads to a single basic sequence of execution for all solves regardless of type 1 Set the calibrator model visibilities 2 Select the visibility data which will be used to solve for a calibration type 3 Arrange to apply any already known calibration types the first time through none may yet be available 4 Arrange to solve for a specific calibration type including specification of the solution timescale and other specifics 5 Execute the solve process 6 Repeat 1 4 for all required types using each result as it becomes available in step 2 and perhaps repeating for some types to improve the solutions By itself this sequence doesn t guarantee success the data provided for the solve must have suffi cient SNR on the appropriate timescale and must provide sufficient leverage for the solution e g D solutions require data taken over a sufficient range of parallactic angle in order to separate the source polarization contribution from the instrumental polarization Appendix F Annotated Example Scripts Note These data sets are available with the full CASA rpm di
361. g the antenna names in double quotes ANT E g the string antenna 107 15 21 VA22 will expand into an antenna ID list 10 11 12 13 14 15 21 22 assuming the index of the antenna named VA22 is 22 If the antenna with ID index 50 is named 21 the string antenna 10715 21 VA22 will expand into an antenna ID list of 10 11 12 13 14 15 50 22 Read elsewhere e g info regex under Unix for details of regular expression and patterns CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 98 2 6 4 2 The scan Parameter The scan parameter selects the scan ID numbers of the data There is currently no naming convention for scans The scan ID is filled into the MS depending on how the data was obtained so use this with care Examples scan 3 scan number 3 scan 7178 scan numbers 1 through 8 inclusive scan 1 2 4 6 scans 1 2 4 6 scan lt 9 scans lt 9 1 8 NOTE ALMA and VLA EVLA number scans starting with 1 and not 0 You can see what the numbering is in your MS using the listobs task with verbose True see 2 3 2 6 4 3 The timerange Parameter The time strings in the following TO T1 and dT can be specified as YYYY MM DD HH MM SS FF The time fields i e YYYY MM DD HH MM SS and FF starting from left to right may be omitted and they will be replaced by context sensitive defaults as explained below Some examples 1 timerange TO T1 Select all time sta
362. g with these settings is for you Otherwise the default settings should provide reasonable performance in most cases e Cache size The value of this option specifies the maximum number of different views of the data to save so that they can be redrawn quickly If you run an animation or scroll around zoomed data you will notice that the data displays noticeably faster the second time through because of this feature Often setting this value to the number of animation frames is ideal Note however that on multi panel displays each panel counts as one cached image Large images naturally take more room than small ones The memory used for these images will show up in the X server process If you need more Visibility Memory below for a really large ms it is usually better to forgo caching a large number of views e Max Visibility Memory This option specifies how many megabytes of memory may be used to store visibility data from the measurement set internally Even if you do not adjust this entry it is useful to look at it to see how many megabytes are required to store your entire selected MS in memory If the slider setting is above this the whole selected MS will fit into the memory buffer Otherwise some data planes will be greyed out see Apply Button below and the selected data will have to be viewed one buffer at a time which is somewhat less convenient In most cases this means you should select fewer fields or spect
363. gc5921 ms SOURCE Subtable has 3 rows Figure 3 8 browsetable You can use the tab for Table Keywords to look at other tables within an MS You can then double click on a table to view its contents There are alot of features in the casabrowser that are not fully documented here Feel free to explore the capabilities such as plotting and sorting BETA ALERT You are likely to find that the casabrowser needs to get a table lock before proceeding Use the clearstat command to clear the lock status in this case 3 7 Plotting antenna positions plotants This task is a simple plotting interface to the plotxy functionality to produce plots of the antenna positions taken from the ANTENNA sub table of the MS The inputs to plotants are plotants Plot the antenna distribution in the local reference frame vis gt Name of input visibility file MS figfile an Save the plotted figure to this file async False CHAPTER 3 DATA EXAMINATION AND EDITING 127 Y Table Browser F File Edit View Tools Export Help 7 a F AL aw Y e B ar yx ngc5921 ms SOURCE l x DIRECTION ROPER_MOTIOI IBRATION_GRC CODE INTERVAL NAME NUM_LINES SOURCE_ID cTRAL_w 0 2 74393 05 o 0 E 1 7976931348 1331 305000 1 0 0 2 f2 42085 02 o 0 1 1 7976931348 1445 099000 1 1 0 n p 2 122602 0 08
364. gion on the display panel using the rectangle or polygon region mouse tools 7 2 11 and confirm by double clicking inside the region Figure shows an image region selected with the polygon tool Note The extent of the region is determined by the extent button in effect when the region is defined not when it is saved Therefore it is important to select the extent before double clicking the region with the mouse If you neglected to do this you can just double click again within the region after you select the extent and before saving Make any desired adjustments to the offered pathname and press Save Last region to save the region to a file The example Casa commands below illustrate usage of such files CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 275 e Displayed Plane Only gt All Channels Save Region As home stn data wkg m5 1 fits rgn x Leave Open Save Last Region Figure 7 12 The Region Manager panel that appears if you select the Tools Region Manager menu item reg rg fromfiletorecord my im rgn ia open my im ia statistics region reg BETA ALERT Visual region management is incomplete Very soon the region will be placed in side the image file rather than stored separately Compound regions with iterative additions deletions and better visual feedback will also be provided Note that the current Region Extent choice also affects the image points used in computing statistics 23 7
365. gt lt value gt lt default gt APPENDIX H APPENDIX WRITING TASKS IN CASA 488 lt default param antenna gt lt value type string gt lt value gt lt default gt lt default param scan gt lt value type string gt lt value gt lt default gt lt equals gt lt when gt lt when param multiscale gt lt notequals type vector value gt lt default param negcomponent gt lt value gt 1 lt value gt lt default gt lt notequals gt lt when gt lt when param mode gt lt equals value mfs gt lt equals value channel gt lt default param nchan gt lt value gt 1 lt value gt lt default gt lt default param start gt lt value gt 0 lt value gt lt description gt first input channel to use lt description gt lt default gt lt default param width gt lt value gt 1 lt value gt lt default gt lt equals gt lt equals value velocity gt lt default param nchan gt lt value gt 1 lt value gt lt default gt lt default param start gt lt value type string gt 0 0km s lt value gt lt description gt Velocity of first image channel e g 0 0km s lt description gt lt default gt lt default param width gt lt value type string gt 1km s lt value gt lt description gt image channel width in velocity units e g 1 0km s lt description gt lt default gt lt equals gt lt equals value frequency gt lt default param nchan gt lt value gt 1 lt value g
366. gt lt stxDd234nhd Plot color The range of data to be plotted see help Plot in different colors Options none both chan corr Select additional plotting options e g fontsize title etc Overplot on current plot if possible Show flagged data Show plot on gui no plot hardcopy otherwise supply name If true the taskname must be started using plotxy The plotxy task expects all of the scratch columns to be present in the MS even if it is not asked to plot the contents If you get an error to the effect Invalid Table operation cannot add a column then use clearcal to force these columns to be made in the MS Note that this will clear anything in all scratch columns in case some were actually there and being used Setting selectdata True opens up the selection sub parameters selectdata antenna timerange correlation scan feed array uvrange True 12 22 23 ad HH HH H OH OF Other data selection parameters antenna baselines gt all antenna 3 VA04 time range gt all correlations default scan numbers Not yet implemented multi feed numbers Not yet implemented array numbers Not yet implemented uv range gt all uvrange 0 100k1 default unit meters CHAPTER 3 DATA EXAMINATION AND EDITING 106 These are described in 2 6 Averaging is controlled with the set of parameters averagemode vector Select averaging t
367. gt _blparam txt Also see the notes on fluxunit and telescopeparm in the section for sdaverage See the sdaverage description for information on fluxunit conversion and the telescopeparm param eter By setting blmode interact you can set unset mask regions interactively using mouse buttons Current mask regions will be shown in yellow shade in the plot Baseline fit parameters and rms of fitted spectra are automatically saved to an ASCII file lt outfile gt _blparam txt APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 302 Beta Patch 4 New Features The parameter interactive is renamed to verify A 2 1 4 sdcal Keyword arguments sdfile name of input SD dataset fluxunit units for line flux options K Jy default keep current fluxunit WARNING For GBT data see description below gt gt gt fluxunit expandable parameter telescopeparm the telescope characteristics options str name or list list of gain info default none set example if telescopeparm it tries to get the telescope name from the data Full antenna parameters diameter ap eff known to ASAP are gt ATPKSMB ATPKSHOH ATMOPRA DSS 43 CEDUNA HOBART For GBT it fixes default fluxunit to K first then convert to a new fluxunit telescopeparm 104 9 0 43 diameter m ap eff telescopeparm 0 743 gain in Jy K telescopeparm FIX to change default fluxunit see descrip
368. hannels 10 and below default immath expr ngc5921 clean image box 64 64 192 192 chans lt 10 40 42 44 outfile ngc5921 clean inner go BETA ALERT Note that if chan selects more than one channel then the output image has a number of channels given by the span from the lowest and highest channel selected in chan In the example above it will have 45 channels The ones not selected will be masked in the output cube If we had set chans 40 42 44 then there would be 5 output channels corresponding to channels 40 41 42 43 44 of the MS with 41 43 masked Also the chans lt 10 selects channels 0 9 Note that the chans syntax allows the operators lt lt gt gt For example chans lt 17 gt 79 chans lt 16 gt 80 CHAPTER 6 IMAGE ANALYSIS 238 do the same thing Divide an image by another making sure we are not dividing by zero default immath expr orion image iif my image 0 1 0 my image outfile my_orion image go Note that this will put 1 0 in the output image where the divisor image is zero You can also just mask below a certain level in the divisor image e g default immath expr orion image my image my image gt 0 1 outfile my_orion image go 6 5 1 2 Polarization manipulation Create a polarized intensity image from a IQUV image default immath outfile
369. hat same CORRECTED_DATA column The reverse operation is achieved by specifying reverse True in that case uvsub will add the value in the MODEL column to that in the CORRECTED_DATA column in the input MS and store the result in that same CORRECTED DATA column The inputs are uvsub Subtract add model from to the corrected visibility data vis gt Name of input visibility file MS reverse False reverse the operation add rather than subtract async e False For example uvsub ngc5921 split ms BETA ALERT Currently uvsub operates on the scratch columns in the MS vis Eventually we will provide the option to handle these columns behind the scenes and to write out a new MS 4 7 4 UV Plane Continuum Subtraction uvcontsub At this point consider whether you are likely to need continuum subtraction If there is significant continuum emission present in what is intended as a spectral line observation continuum subtrac tion may be desirable You can estimate and subtract continuum emission in the uv plane prior to imaging or wait and subtract an estimate of it in the image plane Note that neither method is ideal and the choice depends primarily upon the distribution and strength of the continuum emis sion Subtraction in the uv plane is desirable if continuum emission dominates the source since deconvolution of the line emission will be more robust if not subject to errors in deconvolution of the brighter continu
370. hat this generally produces images with the poorest angular resolution since the density of visibilities falls radially in the uv plane 5 2 11 2 uniform weighting For weighting uniform the data weights are calculated as in natural weighting The data is then gridded to a number of cells in the uv plane and after all data is gridded the uv cells are re weighted to have uniform imaging weights This pumps up the influence on the image of data with low weights they are multiplied up to be the same as for the highest weighted data which sharpens resolution and reduces the sidelobe level in the field of view but increases the rms image noise No sub parameters are linked to this mode choice For uniform weighting we first grid the inverse variance w for all selected data onto a grid with uv cell size given by 2 FOV where FOV is the specified field of view defaults to the image field of view This forms the gridded weights W The weight of the i th sample is then Wi We 5 2 wi CHAPTER 5 SYNTHESIS IMAGING 197 5 2 11 3 superuniform weighting The weighting superuniform mode is similar to the uniform weighting mode but there is now an additional npixels sub parameter that specifies a change to the number of cells on a side with respect to uniform weighting to define a uv plane patch for the weighting renormalization If npixels 0 you get uniform weighting 5 2 11 4 radial
371. he CASA Measurement Set and NRO OTF data format For example CASA lt 1 gt scans sd scantable OrionS_rawACSmod average False Importing OrionS_rawACSmod The following are some cautions when using this import feature It is important to use the average False parameter setting as the calibration routines sup porting GBT data require all of the individual times and phases e GBT data may need some pre processing prior to using ASAP In particular the program which converts GBT raw data into CASA Measurement Sets tends to proliferate the number of spectral windows due to shifts in the tracking frequency this is being worked on by GBT staff In addition GBT SDFITS is currently not readable by ASAP in progress e The Measurement Set to scantable conversion is able to deduce the reference and source data and assigns an _r to the reference data to comply with the ASAP conventions e GBT observing modes are identifiable in scantable in the name assignment position switched _ps Nod _nod and frequency switched _fs These are combined with the reference data assignment For example the reference data taken in position switched mode observa tion are assigned as _psr It is possible to read the ATF interferometric data as a single dish data to further examine it using ASAP Toolkit and the SD tasks The usage is the same as importing single dish data e g s sd scantable your_ATF_synthesis_ms
372. he Viewer Print Manager panel positioned in the figure in the upper right and select a format with the drop down or use the Print button to send directly to a printer BETA ALERT The postscript printing capabilities of the casaviewer are currently limited due to some issues with the way we use Qt and do axis labels Significant improvements have been made in Patch 3 This will be further upgraded in the future but for now you will need to follow the suggestions above to get a useable plot Note that ghostview may show a poorer version of the PS than you will get when you print Appendix A Single Dish Data Processing BETA ALERT The single dish analysis package within CASA is still experimental It is included in the Beta release for the use of the ALMA computing and commissioning groups and is not intended for general users Therefore this is included in this Cookbook as an appendix For single dish spectral calibration and analysis CASA uses the ATNF Spectral Analysis Package ASAP This is imported as the sd tool and forms the basis for a series of tasks the SDtasks that encapsulate the functionality within the standard CASA task framework ASAP was developed to support the Australian telescopes such as Mopra Parkes and Tidbinbilla and we have adapted it for use within CASA for GBT and eventually ALMA data also Note some support for the ALMA data are now available For Patch 4 ASAP included in CASA was updated to
373. he interested user to the demonstrations for e NGC5921 VLA HI a quick demo of basic CASA spectral line analyis F 1 e Jupiter VLA 6cm continuum polarimetry polarization image analysis F 2 Chapter 7 Visualization With The CASA Viewer This chapter describes how to display data with the casaviewer either as a stand alone or through the viewer task You can display both images and Measurement Sets 7 1 Starting the viewer Within the casapy environment the viewer task can be used to display an image or MS The inputs are viewer infile displaytype View an image or visibility data set 29 raster H HHHH Examples of starting the viewer CASA lt 1 gt CASA lt 2 gt CASA lt 3 gt CASA lt 4 gt CASA lt 5 gt CASA lt 6 gt viewer viewer ngc5921 usecase viewer ngc5921 usecase viewer ngc5921 usecase viewer ngc5921 usecase Optional Name of file to visualize Optional Type of visual rendering raster contour vector or marker lel for infile advanced if an lel expression is given ms clean image clean image rstr clean image contour viewer ngc5921 usecase clean image 2 lel 256 CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 257 Y Viewer Display Panel Ox Data DisplayPanel Tools View
374. he working directory containing the parameter values see 1 3 5 7 We now describe the individual CASA task parameter interface commands and features in more detail CHAPTER 1 INTRODUCTION 1 3 5 1 The scope of parameters in CASA All task parameters have global scope within CASA the 49 parameter values are common to all tasks and also at the Advanced Tip CASA command line This allows the convenience of not By default the scope of CASA changing parameters that are shared between tasks but parameters is global as stated does require care when chaining together sequences of task here However if you call a invocations to ensure proper values are provided Tasks task as a function with one or DO NOT change the values of the global parameters nor more arguments specified e g does the invocation of tasks using the functional call with task argl val1 then arguments change the globals non specified parameters will be This does mean that unless you do an explict default of defaulted and no globals used the task 8 1 3 5 2 previously set values may be unex This makes scripting more robust pectedly used if you do not inspect the inp carefully For Tasks DO NOT change the value of example good practice is globals default imhead imagename ngc5921 demo cleanimg image mode list imhead If you supply the task call with arguments then these will be used for the va
375. hi MHz Resoln kHz TotBW kHz Ref MHz Corrs 0 8192 LSRK 45464 3506 6 10423298 50005 8766 45489 3536 RR LL HC3N 1 8192 LSRK 45275 7825 6 10423298 50005 8766 45300 7854 RR LL HN15C0 2 8192 LSRK 44049 9264 6 10423298 50005 8766 44074 9293 RR LL CH30H 3 8192 LSRK 44141 2121 6 10423298 50005 8766 44166 2151 RR LL HCCC1i5N 12 8192 LSRK 43937 1232 6 10423356 50005 8813 43962 1261 RR LL HNCO 13 8192 LSRK 42620 4173 6 10423356 50005 8813 42645 4203 RR LL H15NCO 14 8192 LSRK 41569 9768 6 10423356 50005 8813 41594 9797 RR LL HNC180 15 8192 LSRK 43397 8198 6 10423356 50005 8813 43422 8227 RR LL Si0 Scans 21 24 Setup 1 HC3N et al Scans 25 28 Setup 2 Si0 et al casapath os environ AIPSPATH ASAP script COMMENTS AS SS a a ee M ae oa a a ee a i import asap as sd import ASAP package into CASA Orion S SiO line reduction only Notes scan numbers zero based as compared to GBTIDL changes made to get to OrionS_rawACSmod modifications to label sig ref positions os environ AIPSPATH casapath set this environment variable back ASAP changes it s sd scantable OrionS_rawACSmod False load the data without averaging APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 357 ene X ASAP Plotter Tk OrionS_psr OrionS_ps OnonS_par T T T T T M EJ Y Brightness Temperature K o_u Brightness Temperature K e 1000 2000 3000 4000 5
376. his assumes setjy and gaincal have already been run Note that the original gain calibration table is used in gaintable so that what is in the MODEL_DATA column is in agreement with what is in the gaintable rather than using the table resulting from fluxscale A bit later on we need to set the R L phase using a scan on 3C48 0137 331 default polcal vis polcal_20080224 cband all ms caltable polcal_20080224 cband all polx field 0137 331 refant VA15 minsnr 3 poltype X gaintable polcal_20080224 cband all gcal polcal_20080224 cband all pcal polcal CHAPTER 4 SYNTHESIS CALIBRATION 160 If on the other hand we had a scan on an unpolarized bright source for example 3C84 0319 415 we could use this to calibrate the leakages default polcal vis caltable field refant poltype gaintable polcal polcal_20080224 cband all ms polcal_20080224 cband all_3c84 pcal 0319 415 gt VA15 2D polcal_20080224 cband all gcal We would then do the X calibration as before but using this D table in gaintable A full processing example for continuum polarimetry can be found in F 2 4 4 6 Baseline based Calibration blcal BETA ALERT The blcal task has not had extensive testing and is included as part of our support for the ALMA and EVLA commissioning efforts You can use the blcal task to solve for b
377. his selection is in addition to scanlist field and iflist channelrange channel range selection default use all channel example 0 5000 Note that specified values are recognized as channel regardless of the value of specunit average averaging on spectral data options bool True False default False gt gt gt average expandable parameter scanaverage average integrations within scans options bool True False default False example if True this happens in read in For GBT set False timeaverage average times for multiple scan cycles options bool True False default False example if True this happens after calibration tweight weighting for time average options none var 1 var spec weighted tsys 1 Tsys 2 weighted tint integration time weighted tintsys Tint Tsys 2 median median averaging APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 304 default none averageall average multi resolution spectra spectra are averaged by referring their frequency coverage default False polaverage average polarizations options bool True False default False pweight weighting for polarization average options none var 1 var spec weighted tsys 1 Tsys 2 weighted tau atmospheric optical depth default 0 0 no correction kernel type of spectral smoothing options none hanning gaussian boxcar default
378. his suggestion This restriction will be lifted in the future when we migrate to a better FFTW engine 5 2 5 Parameter mode The mode parameter defines how the frequency channels in the synthesis MS are mapped onto the image The allowed values are mfs channel velocity frequency The mode parameter is expandable with some options uncovering a number of sub parameters depending upon its value CHAPTER 5 SYNTHESIS IMAGING 191 5 2 5 1 Mode mfs The default mode mfs emulates multi frequency synthesis in that each visibility channel datum k with baseline vector By at wavelength Az is gridded into the uv plane at ug By Ax The result is a single image plane regardless of how many channels are in the input dataset This image plane is at the frequency given by the midpoint between the highest and lowest frequency channels in the input spw s Currently there is no way to choose the center frequency of the output image plane independently 5 2 5 2 Mode channel If mode channel is chosen then an image cube will be created This is an expandable parameter with dependent parameters mode channel Type of selection mfs channel velocity frequency nchan 1 Number of channels planes in output image start O first input channel to use width 1 Number of input channels to average interpolation nearest Type of spectral interpolation of visibilities nearest linear cubi The channelization of the
379. hon will display the interpretation of the line 368 APPENDIX D APPENDIX PYTHON AND CASA 369 beneath the one typed as indicated by the gt Default behavior in CASA is to have automatic parenthesis enabled D 2 Indentation Python pays attention to indentation of lines in scripts or when you enter them interactively It uses indentation to determine the level of nesting in loops Be careful when cutting and pasting if you get the wrong indentation then unpredictable things can happen usually it just gives an error A blank line can be used to return the indentation to a previous level For example expanded pa rameters in tasks cause indentation in subsequent lines in the interface For example the following snippet of inputs from clean can be cut and pasted without error due to the blank line after the indented parameters mode channel Type of selection nchan 1 Number of channels to select start 0 Start channel step 1 Increment between channels velocity width 1 Channel width alg gt clark Algorithm to use If the blank line were not there an error would result if you pasted this at the casapy prompt D 3 Lists and Ranges Sometimes you need to give a task a list of indices For example some tasks and tools expect a comma separated Python list e g scanlist 241 242 243 244 245 246 You can use the Python range function to generate a list of consecutive numbers e
380. iable PAGER less setenv PAGER less in csh then typing help lt taskname gt will show you the help but the text will vanish and return you to the command line when you are done viewing it Setting PAGER more setenv PAGER more will scroll the help onto your command window and then return you to your prompt but leaving it on display Setting PAGER cat setenv PAGER cat will give you the more equivalent without some extra formatting baggage and is the recommended choice If you have set PAGER more or PAGER less the help display will be fine but the display of taskname will often have confusing formatting content at the beginning lots of ESC surrounding the text This can be remedied by exiting casapy and doing an unset PAGER unsetenv PAGER in t csh at the Unix command line You can see the current value of the PAGER environment variable with CASA by typing lecho PAGER note the double This will show what command paging is pointed to 1 2 8 4 help par lt parameter gt Typing help par lt parameter gt provides a brief description of a given parameter lt parameter gt CASA lt 46 gt help par robust Help on function robust in module parameter_dictionary robust Brigg s robustness parameter Options 2 0 close to uniform to 2 0 close to natural 1 2 8 5 Python help Typing help at the casapy prompt with no arguments will bring up the native Python help facility and give you the help gt prompt for
381. iation In this case it is desirable to solve for a best fit functional form for each antenna using the GSPLINE solver This fits a time series of cubic B splines to the phase and or amplitude of the calibrator visibilities The combine parameter 4 4 1 5 can be used to combine data across spectral windows scans and fields Note that if you want to use combine field then all fields used to obtain a GSPLINE amplitude solution must have models with accurate relative flux densities Use of incorrect relative flux densities will introduce spurious variations in the GSPLINE amplitude solution The GSPLINE solver requires a number of unique additional parameters compared to ordinary G and T solving The sub parameters are gaintype GSPLINE Type of solution G T or GSPLINE splinetime 3600 0 Spline smooth timescale sec default 1 hours npointaver 3 Points to average for phase wrap okay phasewrap 180 Wrap phase when greater than this okay The duration of each spline segment is controlled by splinetime The actual splinetime will be adjusted such that an integral number of equal length spline segments will fit within the overall range of data Phase splines require that cycle ambiguities be resolved prior to the fit this operation is controlled by npointaver and phasewrap The npointaver parameter controls how many contiguous points in the time series are used to predict the cyc
382. ible to do simple mathematics directly on scantables from the CASA command line using the operators as well as their cousins CASA lt 10 gt scan2 scan1 2 0 add 2 0 to data CASA lt 11 gt scan 1 05 scale spectrum by 1 05 NOTE mathematics between two scantables is not currently available in ASAP A 3 3 6 Scantable Save and Export ASAP can save scantables in a variety of formats suitable for reading into other packages The formats are e ASAP This is the internal format used for ASAP It is the only format that allows the user to restore the data fits etc without loosing any information As mentioned before the ASAP scantable is a CASA Table memory based table This function just converts it to a disk based table You can access this with the CASA browsetable task or any other CASA table tasks e SDFITS The Single Dish FITS format This format was designed for interchange between packages but few packages can actually read it e ASCII A simple text based format suitable for the user to process using Python or other means e Measurement Set V2 CASA format Saves the data in a Measurement Set All CASA tasks which use an MS should work on this scans save output_filename format e g CASA lt 19 gt scans save FLS3a_calfs MS2 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 349 A 3 4 Calibration For some observatories the calibra
383. ick and drag will mark an additional region You can get rid of all your regions by clicking again on the Mark Region button which will appear to un depress or you can use the ESC key to remove the last box you drew Once regions are marked you can then click on one of the other buttons to take action 1 Flag flag the points in the region s 2 Unflag unflag flagged points in the region s 3 Locate spew out a list of the points in the region s to the logger Warning this could be a long list CHAPTER 3 DATA EXAMINATION AND EDITING 115 EJ CASA Plotter 0 EDITA SGI ry T Y o Y 2 3 2 E UV Distance klambda UV Distance klambda Mark Region Flag Unflag Locate Quit Mark Region Flag Unflag Locate Quit 0101 01 ABa uan m O OJ 1 B baas negon mnte Figure 3 4 Plot of amplitude versus uv distance before left and after right flagging two marked regions The call was plotxy vis ngc5921 ms xaxis uvdist field 1445 Whenever you click on a button that action occurs without forcing a disk write unlike previous versions If you quit plotxy and re enter you will see your previous edits A table with the name lt msname gt flagversions where vis lt msname gt will be created in the same directory if it does not exist already It is recommended that you save important flagg
384. ies similar to those for a raster image 7 3 1 1 Together with the brightness contrast and colormap adjustment icons on the Mouse Toolbar of the Display Panel they are especially important for adjusting the color display of your MS The available Basic options are e Data minimum maximum This has the same usage as for raster images Lowering the data maximum will help brighten weaker data values Scaling power cycles This has exactly the same usage as for raster images see 7 3 1 1 Again lowering this value often helps make weaker data visible If you want to view several fields with very different amplitudes simultaneously this is typically one of the best adjustments to make early together with the Colormap fiddling mouse tool which is on the middle mouse button by default e Colormap Greyscale or Hot Metal colormaps are generally good choices for MS data 7 4 1 2 MS Options MS and Visibility Selections e Visibility Type e Visibility Component e Moving Average Size CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 280 2 Lye 2 an a Data Display Options n4826_16apr ms Advanced MS and Visibility Selection Visibility Type Observed Visibility Component Amplitude 3 Moving Average Size m a A 4000 5000 6000 6000 Field IDs 0 1 2 3 4 5 6 7 8 in Spectral Windows 0 1 2 3 4 5 Display Axes Normal Too 10 sec Compact
385. ile ngc5921 usecase clean image rstr This includes the data displayed as well as options and viewer settings See 7 2 2 Saving and Restoring Viewer State Examples five and six are less common cases which make use of the second parameter displaytype Example five displays the image in contour form Example six uses Lattice Image Expression Language to display the square of the image data NOTE the viewer task now determines file types images MSs restore files automatically It is no longer necessary to specify filetype ms explicitly CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 258 Y Viewer Display Panel Data Display Panel Tools View BOAR GDGAAG 2G Be 2 bata Display Options BE ngc5921 usecase ms Advanced MS and Visibility Selection Flagging Options Display Axes Basic Settings Data minimum o Pad Y Data maximum 1 82385 Big Scaling power cycles o yA Y 5000 Baseline Colormap Hot Metal 1 gt Pid e O OO 9 QG 31 63 e Normal r 0 Blink Rate 10 sec Compact Axis Drawing and Labels Color Wedge Apply 1 tor Px Frame tart End X ngc5921 usecase ms 1 407 Jy 13 Apr 1995 09 19 30 t 1 scan 1 1331 30500002_0 Field 0 2 26 b 81 SP Win 0 s 0 1 413443 GHz ch 31 RR p 0 Dismiss Figure 7 2 The Viewer Display Panel left and Data Display Options right
386. in such case Also if you try to go back sdplot after using sd plotter plot you may encounter an error and the plotter window won t be displayed In that case you can reset the window state by deleting the plotter window opened by sd plotter plot with the command sd plotter _plotter unmap Eventually we would like the capability to interactively set things using the plots like select frequency ranges identify lines start fitting 2 sd selector The selector object only allows one selection of each type It would be nice to be able to make a union of selections without resorting to query for the set_name note that the others like scans and IFs work off lists which is fine Should make set_name work off lists of names 3 sd scantable There is no useful inline help on the scantable constructor when you do help sd scantable nor in help sd The inline help for scantable summary claims that there is a verbose parameter but there is not The scantable verbosesummary asaprc parameter e g in sd rcParams does nothing GBT data has undefined fluxunit should be K incorrect freqframe LSRK is really gt TOPO and reference frequency set to that of the first IF only The sd scantable freq_align does not yet work correctly 4 sd general issues There should be a sdhelp equivalent of toolhelp and tasklist for the sd tools and tasks The current output of ASAP is verbose and is controlled by setting sd
387. inclusive to N1 inclusive For real numbers it is used to select all values present for the appropriate parameter in the Measurement Set between NO and N1 including the boundaries Note that the character is used rather than the more obvious in order to accommodate hyphens in strings and minus signs in numbers Wherever appropriate units can be specified The units are used to convert the values given to the units used in the Measurement Set For ranges the unit is specified only once at the end and applies to both the range boundaries 2 6 1 1 String Matching String matching can be done in three ways Any component of a comma separated list that cannot be parsed as a number a number range or a physical quantity is treated as a regular expression or a literal string If the string does not contain the characters or it is treated as a literal string and used for exact matching If any of the above mentioned characters are part of the string they are used as a regular expression As a result for most cases the user does not need to supply any special delimiters for literal strings and or regular expressions For example field 237 match field ID 3 and not select field named 3C286 field 3x used as a pattern and matched against field names If names like 3C84 3C286 3020 2207 are found all will match Field ID 3 will not be selected unless of course one of the above
388. ine data and the MODEL_DATA column with the continuum model You can use fitmode replace to replace the CORRECTED_DATA column with the continuum model however it is probably better to use fitmode subtract and then use split to select the MODEL_DATA and form a dataset appropriate for forming an image of the estimated continuum Note that a continuum image formed from this model will only be strictly correct near the phase center for the reasons described above The splitdata parameter can be used to have uvcontsub write out split MS for both the continuum subtracted data and the continuum It will leave the input MS in the state as if fitmode subtract was used Note that the entire channel range of the MS will be written out not just the channels specified in spw that have had the subtraction so follow up with a split if you want to further restrict the output channel range If splitdata True then uvcontsub will make two output MS CHAPTER 4 SYNTHESIS CALIBRATION 183 with names lt input msname gt contsub and lt input msname gt cont BETA ALERT be sure to run with fitmode subtract if setting splitdata True Note that it is currently the case that uvcontsub will overwrite the CORRECTED_DATA column Therefore it is desirable to first split the relevant corrected data into a new Measurement Set If you run uvcontsub on the original dataset you will have to re apply the calibration as described in the previous chapte
389. ing bandpass from the frequency channels by solving for the bandpass see above Thus the bandpass calibration table would be input to gaincal via the gaintable parameter see below The gaincal task has the following inputs gaincal Determine temporal gains from calibrator observations CHAPTER 4 SYNTHESIS CALIBRATION 151 vis Nome of input visibility file caltable aa Name of output gain calibration table field 22 Select field using field id s or field name s spw ae Select spectral window channels selectdata False Other data selection parameters solint inf Solution interval see help combine dd Data axes which to combine for solve scan spw and or field preavg 1 0 Pre averaging interval sec refant de Reference antenna name minblperant 4 Minimum baselines _per antenna_ required for solve minsnr 0 0 Reject solutions below this SNR solnorm False Normalize average solution amplitudes to 1 0 G T only gaintype gt G Type of gain solution G T or GSPLINE calmode ap Type of solution ap p a append e False Append solutions to the existing table gaintable Gain calibration table s to apply on the fly gainfield Select a subset of calibrators from gaintable s interp Interpolation mode in time to use for each gaintable spwmap Spectral windows combinations to form for gaintables s gaincurve
390. ing Images To display an image use the viewer task The viewer will display images in raster contour or vector form Blinking and movies are available for spectral line image cubes To start the viewer type viewer Executing the viewer task will bring up two windows a viewer screen showing the data or image and a file catalog list Click on an image or ms from the file catalog list choose the proper display and the image should pop up on the screen Clicking on the wrench tool second from left on upper left will obtain the data display options Most functions are self documenting The viewer can be run outside of casapy by typing casaviewer See 7 for more on viewing images 1 5 7 Getting data and images out of CASA The key data and image export tasks are e exportuvfits export a CASA MS in UVFITS format 2 2 1 e exportfits export a CASA image table as FITS 6 11 These tasks can be used to export a CASA MS or image to UVFITS or FITS respectively See the individual sections referred to above for more on each Chapter 2 Visibility Data Import Export and Selection To use CASA to process your data you first will need to get it into a form that is understood by the package These are measurement sets for synthesis and single dish data and image tables for images There are a number of tasks used to fill telescope specific data to import export standard formats to list data conte
391. ing Images You have several options for viewing an image These are seen at the right of the Load Data Viewer panel described in and shown in Figure 7 6 when an image is selected They are e Raster Image a greyscale or color image e Contour Map contours of intensity as a line plot e Vector Map vectors as in polarization as a line plot e Marker Map a line plot with symbols to mark positions The Raster Image is the default image display and is what you get if you invoke the viewer from casapy with an image file name In this case you will need to use the Open menu to bring up the Load Data panel to choose a different display 7 3 1 Viewing a raster map A raster map of an image shows pixel intensities in a two dimensional cross section of gridded data with colors selected from a finite set of normally smooth and continuous colors i e a colormap CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 267 Load Data Viewer Directory homefimager b smyers Sep07 Display As ngc1333_both ms Measurement Raster Image ngc5921 ms Measurement ngc5921 ms flagversions Directory Contour Map ngc5921 usecase clean image Image Vector Map ngc5 92 1 usecase clean model Image ngc5921 usecase clean residual Image i Marker Map p ngc5921 usecase ms Measurement Figure 7 6 The Load Data Viewer panel as it appears if you select an image You can see all options are availa
392. ing over spw print Output table ngc4826 tutorial 16apr98 gcal gaincal vis ngc4826 tutorial ms caltable ngc4826 tutorial 16apr98 gcal field 0 1 spw 0711 gaintype G minsnr 2 0 refant ANT5 gaincurve False opacity 0 0 solint inf combine spw FORRADO RIERA ROA AAR Transfer the flux density scale print Fluxscale default fluxscale APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 463 print print Transferring flux of 3C273 to sources 1310 323 print Output table ngc4826 tutorial 16apr98 fcal fluxscale vis ngc4826 tutorial ms caltable ngc4826 tutorial 16apr98 gcal fluxtable ngc4826 tutorial i6apr98 fcal reference 3C273 transfer 1310 323 Flux density for 1310 323 is 1 48 0 016 SNR 90 6 nAnt 8 HEHHHHHHHHHEHHAHEHHEHEEHEHHEHAA HEHEHE HEHE HEHEHE HEH HEHEHE HAHA HHHRA HEHEHE Plot calibration print Plotcal fluxscale default plotcal Interactive plotcal plotcal caltable ngc4826 tutorial 16apr98 fcal yaxis amp field print print Plotting final scaled gain calibration table print First amp vs time for all fields Pause script if you are running in scriptmode user_check raw_input Return to continue script n plotcal caltable ngc4826 tutorial 16apr98 fcal yaxis phase field print
393. ing stages using the flagmanager task 3 2 3 4 6 Flag extension in plotxy Flag extension is controlled using extendflag T and its sub parameters extendflag True Have flagging extend to other data points extendcorr a flagging correlation extension type extendchan Pe flagging channel extension type extendspw we flagging spectral window extension type extendant Ms flagging antenna extension type extendtime at flagging time extension type The use of extendflag enables the user to plot a subset of the data and extend the flagging to a wider set BETA ALERT Using the extendflag options will greatly slow down the flagging in plotxy You will see a long delay after hitting the Flag button with lots of logger messages as it goes through each flag Fixing this requires a refactoring of plotxy which is underway starting in Patch 4 development CHAPTER 3 DATA EXAMINATION AND EDITING 116 Setting extendchan a11 will extend the flagging to other channels in the same spw as the dis played point For example if spw 0 0 and channel 0 is displayed then flagging will extend to all channels in spw 0 The extendcorr sub parameter will extend the flagging beyond the correlations displayed If extendcorr al1 then all correlations will be flagged e g with RR displayed RR RL LR LL will be flagged If extendcorr half then the extension will be to those correlations in common with that show e g with RR d
394. ing table smoothcal n4826_16apr ms tablein n4826_16apr gcal caltable n4826_16apr smoothcal smoothtime 7200 smoothtype mean Plot up before and after tables plotcal n4826_16apr gcal amp antenna 1 subplot 211 CHAPTER 4 SYNTHESIS CALIBRATION 170 plotcal n4826_16apr smoothcal amp antenna 1 subplot 212 This example uses 2 hours 7200 sec for the smoothing time and smoothtype mean The plotcal results are shown in Figure 4 5 4 Calibration Interpolation and Accumulation accum The accum task is used to interpolate calibration solutions onto a different time grid and to accumulate incremental calibrations into a cumulative calibration table Its inputs are accum Accumulate incremental calibration solutions vis a Name of input visibility file tablein ae Input cumulative calibration table use on first run accumtime 1 0 Timescale on which to create cumulative table incrtable ne Input incremental calibration table to add caltable gt Output cumulative calibration table field id List of field names to process from tablein calfield qn List of field names to use from incrtable interp linear Interpolation mode to use for resampling incrtable solutions spwmap 1 Spectral window combinations to apply The mapping implied here is tablein incrtable gt caltable mathematica
395. ing the name of a mask image to be used for CLEAN to search for components You can use the makemask task to construct this mask or use one made using interactive True 5 3 5 5 3 6 4 Using region files You can give the mask parameter a string pointing to a file that describes a region This region file can be generated in the viewer 7 5 3 7 Parameter minpb The minpb parameter sets the level down to which the primary beam or more correctly the voltage patterns in the array can go and have a given pixel included in the image This is important as it defines where the edge of the visible image or mosaic is The default is 0 1 or equivalent to the 10 response level If there is alot of emission near the edge then set this lower if you want to be able to clean it out NOTE The minpb parameter is the level in the primary beam PB at which the cut is made If you are using ftmachine mosaic 5 3 4 3 this will show up in the flux pbcoverage image new in version 2 4 0 See the discussion of threshold 5 3 4 6 for related issues CHAPTER 5 SYNTHESIS IMAGING 210 5 3 8 Parameter modelimage The modelimage parameter specifies the name s of one or more input starting image s to use to calculate the first residual before cleaning These are used in addition to any image with a name defaulting from the imagename root e g on a restart The output model will contain this model plus clean components found during d
396. ining column of the MS see 2 1 1 is to be written out to the UV FITS file Choices are data corrected and model There are a number of special parameters that control what is written out These are mostly here for compatibility with AIPS The writesyscal parameter toggles whether GC and TY extension tables are written These are important for VLBA data and for EVLA data BETA ALERT Not yet available The multisource parameter determines whether the UV FITS file is a multi source file or a single source file if you have a single source MS or choose only a single source Note the difference between a single source and multi source UVFITS file here is whether it has a source SU table and the source ID in the random parameters If you select more than one source in fields then the multisource parameter will be overridden to be True regardless The combinespw parameter allows combination of all spectral windows at one time If True then all spectral windows must have the same shape For AIPS to read an exported file then set combinespw True The writestation parameter toggles the writing of the station name instead of antenna name 2 2 2 VLA Filling data from archive format importvla VLA data in archive format i e as downloaded from the VLA data archive are read into CASA from disk using the importvla task The inputs are importvla import VLA archive file s to a measurement set archivefiles gt Nam
397. input Return to continue script n else interactive False Now send final plot to file in PNG format via png suffix figfile vis plotxy png plotxy O Split the sources out pick off the CORRECTED_DATA column Split NGC5921 data before continuum subtraction print Split NGC5921 Data default split vis msfile splitms prefix src split ms outputvis splitms field N5921 spw datacolumn corrected saveinputs split prefix split n5921 saved split O print Created splitms If you want split out the calibrater 1445 099 field all chans print Split 1445 099 Data calsplitms prefix cal split ms outputvis calsplitms field 1445x saveinputs split prefix split 1445 saved Here is how to export the NGC5921 data as UVFITS Start with the split file Since this is a split dataset the calibrated data is in the DATA column already Write as a multisource UVFITS with SU table even though it will have only one field in it Run asynchronously so as not to interfere with other tasks HHH H HH H OH 403 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 404 BETA also avoids crash on next importuvfits print Export UVFITS default exportuvfits srcuvfits prefix split uvfits vis splitms fitsfile srcuvfits datacolumn
398. interferometer image is multiplied by 1 FTSDB u v This basically down weights the shorter spacing data from the interferometer image 4 The Fourier transform of the single dish image is scaled by the volume ratio of the interfer ometer restoring beam to the single dish beam 5 The results from 3 and 4 are added and Fourier transformed back to the image plane The term feathering derives from the tapering or down weighting of the data in this technique the overlapping Other Packages shorter spacing data from the deconvolved interferometer The feather task is analogous image is weighted down compared to the single dish im to the AIPS IMERG task and the age while the overlapping longer spacing data from the MIRIAD immerge task with option single dish are weighted down compared to the interferom gt feather eter image The tapering uses the transform of the low resolution point spread function This can be specified as an input image or the appropriate telescope beam for the single dish The point spread function for a single dish image may also be calculated using clean CHAPTER 5 SYNTHESIS IMAGING 222 Advice Note that if you are feathering large images be advised to have the number of pixels along the X and Y axes to be composite numbers and definitely not prime numbers In general FFTs work much faster on even and composite numbers You may use subimage function of the image tool to trim the number of
399. intsys polaverage True pweight tsys Do an atmospheric optical depth attenuation correction Input the zenith optical depth at 43 GHz tau 0 09 Select our scans and IFs for HC3N scanlist 20 21 22 23 iflist 0 We do not require selection by field name they are all the same except for on and off field We will do some spectral smoothing For this demo we will use boxcar smoothing rather than the default kernel hanning We will set the width of the kernel to 5 channels kernel boxcar kwidth 5 We wish to fit out a baseline from the spectrum The GBT has particularly nasty baselines We will let ASAP use auto_poly_baseline mode but tell it to drop the 1000 edge channels from the beginning and end of the spectrum A 2nd order polynomial will suffice for this test You might try higher orders for fun blmode auto blpoly 2 edge 1000 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING We will not give it regions as an input mask though you could with something like masklist 1000 3000 5000 7000 masklist By default we will not get plots in sdcal but can make them using sdplot plotlevel 0 But if you wish to see a final spectrum set plotlevel 1 or even plotlevel 2 to see intermediate plots and baselining output Now we give the name for the output file outfile sdusecase_ori
400. ion 2 1 CASA Measurement Sets ooa aa 2 1 1 Under the Hood Structure of the Measurement Set 2 2 Data Import and Export soaa aaa ee 2 2 1 UVFITS Import and Export o e 2 2 1 1 Import using importuv its 2 2 1 2 Export using exportuv litSs 2 2 2 VLA Filling data from archive format importvla 2 2 2 1 Parameter applytsyS 2 2 2 2 Parameter bandname 2 2 2 3 Parameter frequencytol o 2 2 2 4 Parameter projectl o o e 2 2 2 5 Parameters starttime and stoptime EA RA G NETA 2 2 3 ALMA Filling ALMA Science Data Model ASDM observations 2 3 Summarizing your MS listobs iaa rar E ARA A 2 4 Listing and manipulating MS metadata vishead 2 5 Concatenating multiple datasets concat o o A A gk Ok dee DE ede eet et GG ew eS 8 46 be Ruk oe bee AES OTe S HKG ES 2 6 1 1 String Matching 022000000222 ee 2 6 2 The field Parameter 2 2 0 00 e al ARANA AA AAA AA 2 6 3 1 Channel selection in the spw parameter 2 6 4 The selectdata Parameters a 2 6 4 1 The antenna Parameterl o e 0020200048 2 6 4 2 The scan Parameter gt gt ios scs sop ecce woi ee ee nee 2 6 4 3 The timerange Parameter o 2 6 4 4
401. ion at the reference pixel on the direction axes Plane selection is controlled by chans and stokes See for details on plane selction By default chans and stokes will extract the image information in all channels and Stokes planes For instance xval imval myimage box 144 144 stokes I will extract the Stokes I value or spectrum at pixel 144 144 while CHAPTER 6 IMAGE ANALYSIS 249 xval imval myimage box 134 134 154 154 stokes I will extract a 21 by 21 pixel region Extractions are returned in NumPy arrays in the return value dicionary plus some extra elements describing the axes and selection CASA lt 2 gt xval imval ngc5921 demo moments integrated CASA lt 3 gt xval Out 3 axes 0 Right Ascension 1 Declination 3 Frequency 2 Stokes blc 128 128 0 O data array 0 89667124 mask array True dtype bool tre 128 128 0 O unit Jy beam km s extracts the reference pixel value in this 1 plane image Note that the data and mask elements are NumPy arrays not Python lists To extract a spectrum from a cube CASA lt 8 gt xval imval ngc5921 demo clean image box 125 125 CASA lt 9 gt xval Out 9 axes 0 Right Ascension 1 Declination 3 Frequency 2 Stokes blc 125 125
402. ion language as in the synthesis part of the package Spectral regions such as those for setting masks are pairs of min and max values for whatever spectral axis unit is currently chosen These are fed into the tasks and tools as a list of lists with each list element a list with the min max for that sub region e g masklist 1000 3000 5000 7000 A 1 4 Dictionaries Currently the SDtasks return the Python dictionary for the results of line fitting in sdfit and region statistics in sdstat If you invoke these tasks by assigning variable for the return you can then access the elements of these through the keywords e g CASA lt 10 gt line_stat sdstat Current fluxunit K No need to convert fluxunits Using current frequency frame Using current doppler convention CASA lt 11 gt line_stat Out 11 eqw 70 861755476162784 max 1 2750182151794434 gt mean 0 35996028780937195 gt median 0 23074722290039062 min 0 20840644836425781 rms 0 53090775012969971 gt stddev 0 39102539420127869 gt sum 90 350028991699219 You can then use these values in scripts by accessing this dictionary e g CASA lt 12 gt print Line max 5 3f K line_stat max Line max 1 275 K for example A 1 5 Line Formatting The SDtasks trap leading and trailing whitespace on string parameters such as infile and sdfile but ASAP does not so be careful with setting string parameters
403. is document was written in the context of glish based AIPS and is not yet updated to CASA syntax see below The expr string contains the LEL expression expr on Mathematical expression using images string containing LEL expression CHAPTER 6 IMAGE ANALYSIS 230 A mathematical expression with image file names image file names must be enclosed in double quotes Default none Example expr min image2 im 2 max imagel im Available functions in the expr and mask paramters PIO EQ SINO SINH Q ASINO COSO COSH TAN TANH ATAN EXPO LOGO LOG10 POWO SQRT COMPLEX CONJO REAL IMAGO ABSO ARG PHASE AMPLITUDE MINO MAX ROUND ISGN FLOOR CEIL REBIN SPECTRALINDEX PAO IIF INDEXIN REPLACE HH HHH H HH HOF For examples using LEL expr see below BETA ALERT As of Patch 2 LEL expressions use 0 based indices 6 1 4 Masks mask The mask string contains a LEL expression see above This string can be an on the fly OTF mask expression or refer to an image pixel mask mask ae Mask to be applied to the images string containing LEL expression Name of mask applied to each image in the calculation Default means no mask Example mask ngc5921 clean cleanbox mask gt 0 5 mask mask ngc5921 clean cleanbox mask Note that the mask file supplied in the mask parameter must have the same shape same number of a
404. is performed on a constant signal to noise image This is equivalent to a dirty mosaic that is formed by coadding dirty images made from the individual fields after apodizing each by the PB function Thus compared to the true sky this has a factor of the PB in it You will thus preferentially find components in the centers of the mosaic fields even more so than in the ft mosaics Both these cases should have the same flux scale in the centers of the lowest noise pointings in the mosaic This is where the threshold units match those in the image being used in the minor cycle BETA ALERT This is fairly complicated and we are working on explaining this better and possibly making this more straightforward to specify 5 3 5 Parameter interactive If interactive True is set then an interactive window will appear at various cycle stages while you clean so you can set and change mask regions These breakpoints are controlled by the npercycle sub parameter which sets the number of iterations of clean before stopping interactive True use interactive clean with GUI viewer mpercycle 100 Number of iterations before interactive prompt BETA ALERT npercycle is currently the only way to control the breakpoints in interactive clean See the example of interactive cleaning in 5 3 13 5 3 6 Parameter mask The mask parameter takes a list of elements each of which can be a list of coordinates specifying a box or a string pointi
405. isk instead The default is sd rcParams scantable storage memory but if you are on a machine with small memory do 327 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING sd rcParams scantable storage disk You can reset back to defaults with sd rcdefaults HHHHHHHHHHHHHHHHHEHHHHEEEH ORION S HC3N Position Switched data HHEFHHHHHHHHHHHHHHHHEHEEEHE startTime time time startProc time clock HHFHHHHHHHEHEHHHHHEHEHE HEH List data HHEHHHHHHHEHEHHHHHEHEHEHEH List the contents of the dataset First reset parameter defaults safe default sdlist You can see its inputs with inp sdlist or just inp now that the defaults sdlist set the taskname sdlist Set the name of the GBT ms file sdfile OrionS_rawACSmod Set an output file in case we want to refer back to it listfile sdusecase_orions_summary txt sdlist You could also just type go You should see something like 328 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING Increment 329 IFs 26 Polarisations 2 linear Channels 8192 Observer Joseph McMullin 0bs Date 2006 01 19 01 45 58 Project AGBTO6A_018_01 0bs Type Off0n PSWITCHOFF TPWCAL Antenna Name GBT Flux Unit Jy Rest Freqs 4 5490258e 10 Hz Abcissa Channel Selection none Scan Source Time Integration Beam Position J2000 I
406. isplayed then RR RL LR will be flagged Setting extendspw a11 will extend the flagging to all other spw for the selection Using the same example as above with spw 0 0 displayed then channel 0 in ALL spw will be flagged Note that use of extendspw could result in unintended behavior if the spw have different numbers of channels or if it is used in conjunction with extendchan WARNING use of the following options particularly in conjunction with other flag extensions may lead to deletion of much more data than desired Be careful Setting extendant a11 will extend the flagging to all baselines that have antennas in common with those displayed and marked For example if antenna 1 amp 2 is shown then ALL baselines to BOTH antennas 1 and 2 will be flagged Currently there is no option to extend the flag to ONLY baselines to the first or second antenna in a displayed pair so it is better to use flagdata to remove specific antennas Setting extendtime all will extend the flagging to all times matching the other selection or extension for the data in the marked region 3 4 7 Setting rest frequencies in plotxy The restfreq parameter can be set to a transition or frequency and expands to allow setting of frame information For example restfreq HI a frequency quanta or transition name see help for options frame LSRK frequency frame for spectral axis see help for options doppler RADIO doppl
407. ist yaxis amp datacolumn corrected multicolor both selectplot True title field iteration APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS plotxy O print print A o so print Plotting JUPITER self corrected visibilities print Look for outliers and you can flag them Pause script if you are running in scriptmode if scriptmode user_check raw_input Return to continue script n print Clean 2 default clean print Now clean on self calibrated data vis srcsplitms imagename imname2 field spw mode mfs gain 0 1 Imaging mode params psfmode clnalg imagermode clnmode imsize clnimsize cell clncell niter clniter threshold clnthreshold weighting briggs robust 0 5 mask interactive True npercycle 100 saveinputs clean imagenamet clean saved clean print we 446 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS print print print print print print print print print print print print print print print print If you did not do interactive clean bring up viewer manually viewer Clean Final clean model is clnmodel2 Final restored clean image is clnimage2 The clean residual image is clnresid2 Your final clean mask is clnmask2 This is the final restored clean image in the viewer Zoom in and set levels to s
408. ist and pollist iflist list of IF id numbers to select default use all IFs example 15 this selection is in addition to scanlist field and pollist pollist list of polarization id numbers to select default use all polarizations example 1 this selection is in addition to scanlist field and iflist channelrange channel range selection default use all channel example 0 5000 Note that specified values are recognized as channel regardless of the value of specunit scanaverage average integrations within scans options bool True False default False example if True this happens in read in For GBT set False timeaverage average times for multiple scan cycles options bool True False default False example if True this happens after calibration gt gt gt timeaverage expandable parameter tweight weighting for time average options none var 1 var spec weighted tsys 1 Tsys 2 weighted tint integration time weighted tintsys Tint Tsys 2 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING median median averaging default none averageall average multi resolution spectra spectra are averaged by referring their frequency coverage default False polaverage average polarizations options bool True False default False gt gt gt polaverage expandable parameter pweight weighting for polarization average options none var
409. ith the CLEAN algorithm use the clean task This task will work for single field data or for multi field mosaics 5 3 14 BETA ALERT There is now an experimental feature to image data taken with heterogeneous arrays with non identical dish sizes 5 3 15 The clean task uses many of the common imaging parameters These are described above in 5 2 There are also a number of parameters specific to clean These are listed and described below The default inputs to clean are clean Calculates a deconvolved image with a selected clean algorithm vis 22 name of input visibility file MS imagename ae Pre name of output images field sad Field Name CHAPTER 5 SYNTHESIS IMAGING 200 spw sd Spectral windows channels is all selectdata False Other data selection parameters mode mfs Type of selection mfs channel velocity frequency niter 500 Maximum number of iterations gain 0 1 Loop gain for cleaning threshold 0 0mJy Flux level to stop cleaning Must include units psfmode gt clark method of PSF calculation to use during minor cycles imagermode di Use csclean or mosaic If use psfmode multiscale set deconvolution scales pixels interactive False use interactive clean with GUI viewer mask O cleanbox es mask image s and or region s imsize 256 256 x and y image size in pixels cell 1 0arcsec 1 0arcsec x a
410. ity writing the CORRECTED_DATA column which can then be plotted e g in plotxy split out as the DATA column of a new MS or imaged e g using clean Any existing corrected data are overwritten CHAPTER 1 INTRODUCTION 71 See for details 1 5 3 9 Splitting the Data After a suitable calibration is achieved it may be desirable to create one or more new measurement sets containing the data for selected sources This can be done using the split task 4 7 1 Further imaging and calibration e g self calibration can be carried out on these split Measurement Sets 1 5 4 Synthesis Imaging The key synthesis imaging tasks are e clean Calculates a deconvolved image based on the visibility data using one of several clean algorithms 5 3 e feather Combines a single dish and synthesis image in the Fourier plane 5 5 Most of these tasks are used to take calibrated interferometer data with the possible addition of a single dish image and reconstruct a model image of the sky There are several other utility imaging tasks of interest e makemask Makes a mask image from a cleanbox a file or list specifying sets of pairs of box corners 5 6 e ft Fourier transforms the specified model or component list and inserts this into the MODEL_DATA column of the MS 5 7 e deconvolve Deconvolve an input image from a provided PSF using one of several image plane deconvolution algorithms 5
411. iven in Appendix D 1 3 Tasks and Tools in CASA Originally CASA consisted of a collection of tools combined in the so called toolkit Since the majority of prospective users is far more familiar with the concept of tasks an effort is underway to replace most if not all toolkit functionality by tasks While running CASA you will have access to and be interacting with tasks either indirectly by providing parameters to a task or directly by running a task Each task has a well defined purpose and a number of associated parameters the values of which are to be supplied by the user Technically speaking tasks are built on top of tools when you are running a task you are running tools in the toolkit though this should be transparent As more tasks are being written and the functionality of each task is enhanced there will be less CHAPTER 1 INTRODUCTION 39 and less reason to run tools in the toolkit We are working toward a system in which direct access to the underlying toolkit is unnecessary for all standard data processing 1 3 1 What Tasks are Available As mentioned in the introduction tasks in CASA are python interfaces to the more basic toolkit Tasks are executed to perform a single job such as loading plotting flagging calibrating and imaging the data Basic information on tasks including the parameters used and their defaults can be obtained by typing help lt taskname gt or lt taskname gt at the CASA pr
412. k image from a cleanbox and set of imaging parameters cleanbox Clean box file or regions vis gt gt Name of input visibility file if no input image imagename e Name of output mask images mode mfs Type of selection mfs channel velocity imsize 256 256 Image size in spatial pixels x y cell 1 1 Cell size in arcseconds phasecenter Es Field identifier or direction of the phase center stokes 12 Stokes parameter to image I IV IQU IQUV field 20 Field ids list to use in mosaic spw 20 Spectral window identifier 0 based CHAPTER 5 SYNTHESIS IMAGING 223 The majority of the parameters are the standard imaging parameters 5 2 The cleanbox parameter uses the syntax for cleanboxes as in the clean parameter mask see 5 3 6 with the option for interactive also The imagename parameter specifies the name for the output mask image You can use the viewer to figure out the cleanbox ble trc x y settings make the mask image and then bring it into the viewer as a contour image over your deconvolved image to compare exactly where your mask regions are relative to the actual emission In this example create a mask from many cleanbox regions specified in a file on disk cleanboxes txt containing 1 80 80 120 120 2 20 40 24 38 3 70 42 75 66 where each line specifies the field index and the blc x y and trc x y positions of that cleanbox For example in casapy you can do this e
413. k on these to flag unflag or list the data within the marked regions 5 Next Click to move to the next in a series of iterated plots Finally the cursor readout is on the bottom right 104 15 3 2 The plotxy iteration plot The first set of plots from the example m 8 4 3 with iteration antenna Each time you press the Next button you get the next fe eee ae ee Oe Gee Sh hee Pee ee oe eee ee ee 110 bottom left and the resulting uv coverage bottom right The commands to make these three panels respectively are 1 plotxy ngc5921 ms xaxis channel datacolumn data field 0 subplot 211 plotcolor plotsymbol go 2 plotxy ngc5921 ms xaxis x field 0 subplot 223 plotsymbol r 3 plotxy ngc5921 ms xaxis u yaxis v field 0 subplot 224 plotsymbol b fig 3 5 flagdata Example showing before and after displays using a selection of one an tenna and a range of channels Note that each invocation of the flagdata task repre sents a cumulative selection i e running antenna 0 will flag all data with antenna 123 AAN 124 through the data x columns of the MAIN table and y the rows or select a specific Aa ide 125 AP 126 3 9 browsetable Viewing the SOURCE table of the MS 127 lation and plotting tasks accum plotcal and smoothcal sec Figure i 2 130 the a
414. ke labels larger markersize 10 0 Make dots bigger caltable ngc5921 usecase fluxscale yaxis amp subplot 211 plotcal O yaxis phase subplot 212 plotcal The results are shown in Figure This makes use of the subplot option to make multi panel displays hd CASA Plotter Mark Regon Pay vas tocate gt out D0 0 Blu Figure 4 3 Display of the amplitude upper and phase lower gain solutions for all antennas and polarizations in the ngc5921 post fluxscale table CHAPTER 4 SYNTHESIS CALIBRATION 165 Similarly to plot amplitude or phase as a function of channel for B solutions for NGC5921 default plotcal fontsize 14 0 Make labels larger markersize 10 0 Make dots bigger caltable ngc5921 usecase bcal antenna 1 yaxis amp subplot 311 plotcal yaxis phase subplot 312 plotcal yaxis snr subplot 313 plotcal The results are shown in Figure This stacks three panels with amplitude phase and signal to noise ratio We have picked antenna 1 to show For example to show 6 plots per page of B amplitudes on a 3 x 2 grid default plotcal fontsize 12 0 Make labels just large enough markersize 10 0 Make dots bigger caltable ngc5921 usecase bcal yaxis amp subplot 231 iteration antenna plotcal See Figure 4 5 for this example This uses
415. kname must be started using immoments This task will operate on the input file given by imagename and produce a new image or set of images based on the name given in outfile The moments parameter chooses which moments are calculated The choices for the operation mode are moments 1 mean value of the spectrum moments 0 integrated value of the spectrum moments 1 intensity weighted coordinate traditionally used to get velocity fields intensity weighted dispersion of the coordinate traditionally used to get velocity dispersion moments 2 moments 3 median of I moments 4 median coordinate moments 5 standard deviation about the mean of the spectrum moments 6 root mean square of the spectrum moments 7 absolute mean deviation of the spectrum moments 8 maximum value of the spectrum moments 9 coordinate of the maximum value of the spectrum moments 10 minimum value of the spectrum moments 11 coordinate of the minimum value of the spectrum CHAPTER 6 IMAGE ANALYSIS 243 The meaning of these is described in the CASA Reference Manual http casa nrao edu docs casaref image moments html If a single moment is chosen the outfile specifies the exact name of the output image If multiple moments are chosen then outfile will be used as the root of the output filenames which will get dif ferent suffixes for each moment For example if moments 0 1 and outfile ngc5921 usecase moments
416. l bandpass default plotcal APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS caltable btable field 0 Set up 2x1 panels upper panel amp vs channel subplot 211 yaxis amp No output file yet wait to plot next panel saveinputs plotcal prefixt plotcal b amp saved if scriptmode showgui True else showgui False plotcal Set up 2x1 panels lower panel phase vs channel subplot 212 yaxis phase saveinputs plotcal prefixt plotcal b phase saved Note the rolloff in the start and end channels Looks like channels 6 56 out of 0 62 are the best Pause script if you are running in scriptmode if scriptmode If you want to do this interactively and iterate over antenna set iteration antenna showgui True plotcal user_check raw_input Return to continue script n else No GUI for this script showgui False Now send final plot to file in PNG format via png suffix figfile caltable plotcal png plotcal Gain calibration print Gaincal default gaincal Armed with the bandpass we now solve for the time dependent antenna gains 397 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS vis msfile set the name for the output gain caltable gtable prefix gcal caltable gtable Use our previously determined bandpass Note this will automatically b
417. l data print Clean up remaining bad points print print NOTE These flags will extend to the RL LR cross hands print Because of this the flagging will be slower than otherwise Pause script if you are running in scriptmode if scriptmode user_check raw_input Return to continue script n Finally do JUPITER field JUPITER correlation RR LL iteration xaxis uvdist title field plotxy O Here you will see that the final scan at 22 00 00 UT is bad Draw a box around it and flag it print printi aS print Now plot JUPITER versus uvdist print Lots of bad stuff near bottom print Lets go and find it try Locate print Looks like lots of different antennas but at same time APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 427 Pause script if you are running in scriptmode if scriptmode user_check raw_input Return to continue script n correlation extendflag F xaxis time plotxy O Here you will see that the final scan at 22 00 00 UT is bad Draw a box around it and flag it print Pring 1 222 3232 2 55 7222229595209 SSS SSeS P a print Now plotting vs time print See bad scan at end flag it Pause script if you are running in scriptmode if scriptmode user_check raw_input Return to continue script n Now look at whats left correlation RR LL As of 2 3 0 Patch 3 you can extend the flags to
418. l image BETA ALERT The reference position in the modimage is currently used by setjy when it does the Fourier transform thus differences from the positions for the calibrator in the MS will show up as phase gradients in the uv plane If your model image position is significantly different but you don t want this to affect your calibration then you can doctor either the image header using imhead or in the MS using the ms tool as appropriate In an upcoming Beta patch we will put in a toggle to use or ignore the position of the modimage Note that this will not affect the flux scaling only put in erroneous model phases in any event small position differences such as those arising by changing epoch from B1950 to J2000 using regridimage 6 9 will be inconsegential to the calibration This illustrates the use of uvrange for a slightly resolved calibrator Import the data importvla archivefiles AS776_A031015 xp2 vis ngc7538_XBAND ms freqtol 10000000 0 bandname X Flag the ACs flagautocorr ngc7538_XBAND ms METHOD 1 Use point source model for 3C48 plus uvrange in solve Use point source model for 3C48 setjy vis ngc7538_XBAND ms field 0 Limit 3C48 fieldid 0 solutions to uvrange 0 40 klambda gaincal vis ngc7538_XBAND ms caltable cal G field 0 solint 60 0 refant 10 selectdata True uvrange 0 40klambda append False gaincurve False
419. l most efficiently operate on single MS for a particular session such as calibration Other tasks will eventually take multiple Measurement Sets as input For others it is easiest to combine your multiple data files into one If you need to combine multiple datasets you can use the concat task The default inputs are CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 90 concat Concatenate two or more visibility data sets vis gt gt Name of input visibility files to be concatenated concatvis ar Name of output visibility file freqtol de Frequency tolerance for considering data as the same spwid dirtol ae Direction tolerance for considering data as the same field timesort False If true sort by TIME in ascending order async False If true the taskname must be started using concat The vis parameter will take a list of one or more MS Usually this will contain all the MS to combine The concatvis parameter contains the name of the output MS If this points to an existing file on disk then the MS in vis will appended to it otherwise a new MS file is created to contain the concatenated data Be careful here The parameters freqtol and dirtol control how close together in frequency and angle on the sky spectral windows or field locations need to be before calling them the same BETA ALERT Note that if multiple frequencies or pointings are combined using freqtol or dirtol then the data are no
420. l parameters are common calibration parameters as described in BETA ALERT This task has not been updated to use the new standard solint and combine syntax Also note that plotcal cannot currently display delay or delayrate solutions from fringecal 4 5 Plotting and Manipulating Calibration Tables At some point the user should examine plotting or listing the calibration solutions Calibra tion tables can also be manipulated in various ways such as by interpolating between times and sources smoothing of solutions and accumulating various separate calibrations into a single table CHAPTER 4 SYNTHESIS CALIBRATION 162 4 5 1 Plotting Calibration Solutions plotcal The plotcal task is available for examining solutions of all of the basic solvable types G T B D M MF K The inputs are plotcal caltable xaxis yaxis poln field antenna spw timerange subplot overplot clearpanel iteration plotrange showflags plotsymbol plotcolor markersize fontsize showgui figfile An all purpose plotter for calibration results HH HH HH HH HH HH HH HO HH H Name of input calibration table Value to plot along x axis time chan amp phase real imag snr Value to plot along y axis amp phase real imag snr Polarization to plot RL R L XY X Y Field names or index all 3C286 P1321x Antenna selection E g antenna 37 5 Spectral window all 0 1 means spw O and 1 Time selec
421. ld deconvolved image with selected algorithm Deconvolve an image with selected algorithm Flag Clip data based on selections Deconvolve an image with selected algorithm Plot the antenna distribution in the local reference frame An all purpose plotter for calibration results An X Y plotter interactive flagger for visibility data Determine instrumental polarization calibrations ASAP SD task do data selection calibration and averaging ASAP SD task fit remove a spectral baseline ASAP SD task do sdaverage sdsmooth and sdbaseline in one task ASAP SD task coadd multiple scantables into one ASAP SD task fit a spectral line ASAP SD spectral flagging task ASAP SD task list summary of single dish data ASAP SD plotting task ASAP SD task save the sd spectra in various format ASAP SD task scale the sd spectra ASAP SD task do smoothing of spectra ASAP SD task list statistics of spectral region SD task do a simple calibration and imaging for total power data Smooth calibration solution s derived from one or more sources Fit 1 dimentional profile s or polynomial s to an image or image region Continuum fitting and subtraction in the uv plane Fit a single component source model to the uv data Subtract add model from to the corrected visibility data View an image or visibility data set Wide field imaging and deconvolution with selected algorithm Typing startup will pro
422. le See for more on accumulation and interpolation Figure 4 2 graphs the flow of these tables through the sequence solve gt smooth gt accumulate Note that this sequence applied to separate types of tables e g B G although tables of other types can be previous calibration input to the solver The final set of cumulative calibration tables is what is applied to the data using applycal You will have to keep track of which tables are the intermediate incremental tables and which are cumulative and which were previous to certain steps so that they can also be previous to later steps until accumulation This can be a confusing business and it will help if you adopt a consistent table naming scheme see F igure 4 2 for an example naming scheme CHAPTER 4 SYNTHESIS CALIBRATION 133 Previous Calibration Calibrator Model s Tables point source fluxes model images self cal models Input dataset e g from gaincal Incremental Calibration Table eg lt ms gt bcal lt ms gt gcal Prior Calibration Calibration Solver Information eg Antenna Gain Curves bandpass Atmospheric Models gaincal Smoothed Calibration no smoothing Caltable Smoothing i Table i smoothcal j eg lt ms gt gcals tablein Cumulative Calibration Table eg lt ms gt gcalx Caltable Accumulation accum Figure 4 2 Chart of the table flow during calibration The parameter names for input or output of the tasks a
423. le ambiguity of the next point in the time series and phasewrap sets the threshold phase jump in degrees that would indicate a cycle slip Large values of npointaver improve the SNR of the cycle estimate but tend to frustrate ambiguity detection if the phase rates are large The phasewrap parameter may be adjusted to influence when cycles are detected Generally speaking large values gt 180 are useful when SNR is high and phase rates are low Smaller values for phasewrap can force cycle slip detection when low SNR conspires to CHAPTER 4 SYNTHESIS CALIBRATION 154 obscure the jump but the algorithm becomes significantly less robust More robust algorithms for phase tracking are under development including fringe fitting For example to solve for GSPLINE phase and amplitudes with splines of duration 600 seconds gaincal data ms caltable cal spline ap gaintype GSPLINE Solve for GSPLINE calmode ap Solve for amp amp phase field 0 1 Restrict data selection to calibrators splinetime 600 Set spline timescale to 10min BETA ALERT The GSPLINE solutions can not yet be used in fluxscale You should do at least some G amplitude solutions to establish the flux scale then do GSPLINE in phase before or after to fix up the short timescale variations Note that the phase tracking algorithm in gt GSPLINE needs some improvement 4 4 4 Establishing the Flux Density Scale
424. le at this moment is just a simple baseline subtraction for each scan The fitted regions set by masklist are the common for all the scans Selection of the antennas can be made by setting antenna ID s or antenna name s in string e g 0 0 1 DVO1 etc For baseline subtraction it currently works properly for a single antenna selection So a separate sdtpimaging task needs to be run for each antenna It currently assumes that the data has a single spw 0 and fieldid 0 By setting flaglist one can set flag by scan numbers to be excluded from imaging Note scan numbers are determined from state id and related to SUB_SCAN column in STATE subtable and they are typically different from SCAN_NUMBER in MS Beta Patch 4 New Feature The parameter stokes is added for selecting polarization A 2 2 Single Dish Analysis Use Cases With SDTasks A 2 2 1 GBT Position Switched Data Analysis As an example the following illustrates the use of the SDtasks for the Orion data set which contains the HCCCN line in one of its IFs This walk through contains comments about setting parameter values and some options during processing HHEHHHHHHHHHHHEHHHEHHHHEEHHRHHRR RES HH ORION S SDtasks Use Case Position Switched data Version TT 2008 10 14 updated Version STM 2007 03 04 This is a detailed walk through for using the SDtasks on a test dataset HH HH HH H HOH OF HHHHHHHHHHHEHH HE R ARA ARAAAAA import time APPENDIX A AP
425. le the image is broken into 49 7 x 7 facets A reasonable value of facets is such that the image width of each facet does not need the w term correction The computation method with pure faceting is slow so that wprojection is recom mended CHAPTER 5 SYNTHESIS IMAGING 221 5 4 1 3 combination of w projection and faceting You can also use a combination of wprojection and faceting with ftmachine wproject ftmachine wproject Gridding method for the image wproject ft wprojplanes 32 Number of planes to use in wprojection convolutiuon function facets Z 3 Number of facets along each axis in main image only This hybrid method allows for a smaller number of wprojplanes in order to try to conserve memory if the image size approached the memory limit of the computer However there is a large penalty in execution time 5 5 Combined Single Dish and Interferometric Imaging feather The term feathering is used in radio imaging to describe how to combine or feather two images together by forming a weighted sum of their Fourier transforms in the gridded uv plane Intermediate size scales are down weighted to give interferometer resolution while preserving single dish total flux density The feathering technique does the following 1 The single dish and interferometer images are Fourier transformed 2 The beam from the single dish image is Fourier transformed FT SDB u v 3 The Fourier transform of the
426. le through the task sdtpimaging This task directly access the Measurement Set without converting it to scantable format APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 293 Data Process Parameters infile scanaverage Input dataset fluxunit set freaframe set doppler optical depth calibrate average_time timeaverage baseline cate Figure A 1 Wiring diagram for the SDtask sdcal The stages of processing within the task are shown along with the parameters that control them APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 294 A 2 1 SDtask Summaries The following are the list of parameters and brief descriptions of each of the SDtasks These descriptions are also contained in the information produced by help lt taskname gt once asap_init has been invoked Note that you can use inp lt taskname gt on these as for other tasks A 2 1 1 sdaverage Keyword arguments sdfile name of input SD dataset fluxunit units for line flux options K Jy default keep current fluxunit WARNING For GBT data see description below gt gt gt fluxunit expandable parameter telescopeparm the telescope characteristics options str name or list list of gain info default none set example if telescopeparm it tries to get the telescope name from the data Full antenna parameters diameter ap eff known to ASAP are gt ATPKSMB ATPKSHOH
427. lean fits v imhead gt casapy log v imstat gt xstat parameter v immoments gt lt prefix gt moments integrated lt prefix gt moments weighted_coord v HH HHH HHH HHH HH H HOF HHEFHHHHHHHEEHHEEHHAEEHHEAHHAE HEHEHE HAEHEHEEHEHREE PORRA PERRERA RARA HEHEHE HRH A ARRE print Demo Script for NGC5921 VLA HI observation print Version for Beta Patch 4 2 4 0 1 June 2009 print import time import os scriptmode True The prefix to use for all output files prefix ngc5921 demo Set up some useful variables these will also be set later on msfile prefix ms btable prefix bcal gtable prefix gcal ftable prefix fluxscale splitms prefix src split ms imname prefix cleanimg Get to path to the CASA home and stip off the name pathname os environ get CASAPATH split 0 This is where the NGC5921 UVFITS data will be fitsdata pathname data demo NGC5921 fits Or uncomment the following to use data in current directory fitsdata NGC5921 fits Clean up old files Use rmtables on ms and cal tables to clear cache not working on multiple runs for 2 4 0 release 391 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS rmtables msfile rmtables btable rmtables gtable rmtables ftable rmtables ftable rmtables splitms rmtab
428. lear About to getData About to new VMSData Exit from getDataCols ASDM Main table row 1 transformed into 40 MS Main table rows ASDM Main table row 71 transformed into 40 MS Main table rows successfully copied them into the measurement set About to flush and close the measurement set Overall time spent in ASDM methods to read process the ASDM Main table cpu 5 31 s Overall time spent in AIPS methods to fill the MS Main table cpu 1 3 CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 86 2 3 Summarizing your MS listobs Once you import your data into a CASA Measurement Set you can get a summary of the MS contents with the listobs task The inputs are vis 5 Name of input visibility file MS verbose True Extended summary list of data set in logger The summary will be written to the logger and to the casapy log file For example using verbose False listobs n5921 ms False results in the logger messages Thu Jul 5 17 20 55 2007 NORMAL ms summary MeasurementSet Name home scamper CASA N5921 n5921 ms MS Version 2 Observer TEST Project Observation VLA 28 antennas Thu Jul 5 17 20 55 2007 NORMAL ms summary Data records 22653 Total integration time 5280 seconds Observed from 09 19 00 to 10 47 00 Thu Jul 5 17 20 55 2007 NORMAL ms summary Fields 3 ID Name Right Ascension Declination Epoch 0 1331 30500002_013 31 08 29 30 30 32 96 J2000 1 1445 09900002_014 45 16 47 09 58 36
429. lected region trcf Same as trc but uses WORLD coordinates instead of pixels flux the integrated flux density if the beam is defined and the if brightness units are Jy beam npts the number of unmasked points used max the maximum pixel value min minimum pixel value maxpos absolute PIXEL coordinate of maximum pixel value maxposf Same as maxpos but uses WORLD coordinates instead of pixels minpos absolute pixel coordinate of minimum pixel value minposf Same as minpos but uses WORLD coordinates instead of pixels sum the sum of the pixel values sum 1_i sumsq the sum of the squares of the pixel values sum 1_i72 mean the mean of pixel values ar I sum I_i n CHAPTER 6 IMAGE ANALYSIS 246 sigma the standard deviation about the mean sigma 2 sum I_i ar I 2 n 1 rms the root mean square sqrt sum I_i 2 n median the median pixel value if robust T medabsdevmed the median of the absolute deviations from the median if robust T quartile the inter quartile range if robust T Find the points which are 25 largest and 75 largest the median is 50 largest find their difference and divide that difference by 2 For example an imstat call might be default imstat imagename ngc5921 usecase clean image The NGC5921 image cube box 108 108 148 148 20 pixels around the center chans 21 channel 21 xstat imstat In the terminal window imsta
430. les imnamet rmtables prefixt moments Final clean up of auxiliary files os system rm rf prefixt Import the data from FITS to MS print Import Safest to start from task defaults default importuvfits Set up the MS filename and save as new global variable msfile prefix ms Use task importuvfits fitsfile fitsdata vis msfile saveinputs importuvfits prefix importuvfits saved importuvfits Note that there will be a ngc5921 demo ms flagversions there containing the initial flags as backup for the main ms flags List a summary of the MS print Listobs Don t default this one and make use of the previous setting of vis Remember the variables are GLOBAL You may wish to see more detailed information like the scans In this case use the verbose True option verbose True 392 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS listobs You should get in your logger window and in the casapy log file something like MeasurementSet Name home sandrock2 smyers Testing2 Sep07 ngc5921 demo ms MS Version 2 Observer TEST Project Observation VLA Data records 22653 Total integration time 5280 seconds Observed from 09 19 00 to 10 47 00 ObservationID 0 ArrayID 0 Date Timerange Scan FldId FieldName Spwlds 13 Apr 1995 09 19 00 0 09 24 30 0 1 O 1331 30500002_0 0 09 27 30 0 09 2
431. less and you have set the verbose ASAP environment variable to True the default then the screen version of the summary will page You can disable this for sdlist by setting sd rcParams verbose False before running sdlist Set it back afterward if you want lots of information A 2 1 9 sdmath Keyword arguments expr Mathematical expression using scantables fluxunit units for line flux options K Jy default keep current fluxunit WARNING For GBT data see description below gt gt gt fluxunit expandable parameter telescopeparm the telescope characteristics options str name or list list of gain info default none set example if telescopeparm it tries to get the telescope name from the data Full antenna parameters diameter ap eff known to ASAP are ATPKSMB ATPKSHOH ATMOPRA DSS 43 CEDUNA HOBART For GBT it fixes default fluxunit to K first then convert to a new fluxunit telescopeparm 104 9 0 43 diameter m ap eff telescopeparm 0 743 gain in Jy K telescopeparm FIX to change default fluxunit see description below specunit units for spectral axis options str channel km s GHz MHz kHz Hz default current example this will be the units for masklist frame frequency frame for spectral axis options str LSRK REST TOPO
432. libration 1 5 3 5 Examining Calibration Solutions The plotcal task will plot the solutions in a calibration table The xaxis choices include time for gaincal solutions and channel e g for bandpass calibration The plotcal interface and plotting surface is similar to that in plotxy Eventually plotcal will allow you to flag and unflag calibration solutions in the same way that data can be edited in plotxy The listcal task 4 5 2 will print out the calibration solutions in a specified table 1 5 3 6 Bootstrapping Flux Calibration The fluxscale task bootstraps the flux density scale from primary standard calibrators to the secondary calibration sources Note that the flux density scale must have been previously established on the primary calibrator s typically using setjy and of course a calibration table containing valid solutions for all calibrators must be available See for more 1 5 3 7 Calibration Accumulation The accum task applies an incremental solution of a given type from a table to a previous calibra tion table of the same type and writes out a cumulative solution table Different interpolation schemes may be selected A description of this process is given in 1 5 3 8 Correcting the Data The final step in the calibration process applycal may be used to apply several calibration tables e g from gaincal or bandpass The corrections are applied to the DATA column of the visibil
433. listed using the me listcodes method on the me doppler method CASA lt 18 gt me listcodes me doppler Out 18 extra array dtype S1 normal array RADIO Z RATIO BETA GAMMA gt OPTICAL TRUE RELATIVISTIC dtype S13 For most cases the RADIO Doppler system is appropriate but be aware of differences For more information on frequency frames and spectral coordinate systems see the paper by Greisen et al A amp A 446 747 2006 3 4 8 Printing from plotxy There are two ways to get hardcopy plots in plotxy The first is to use the disk save icon from the interactive plot GUI to print the current plot This will bring up a sub menu GUI that will allow you to choose the filename and format The allowed formats are png PNG eps EPS and svg SVG If you give the filename with a suffix png Also at http www aoc nrao edu egreisen scs ps CHAPTER 3 DATA EXAMINATION AND EDITING 118 eps or svg it will make a plot of that type Otherwise it will put a suffix on depending on the format chosen from the menu BETA ALERT The plot files produced by the EPS option can be large and the SVG files can be very large The PNG is the smallest The second is to specify a figfile You probably want to disable the GUI using interactive False in this case The type of plot file that is made will depend upon the filename suffix The allowed choice
434. ll Fourier transform the model image and insert the resulting model in the MODEL_DATA column of the rows of the MS corresponding to the source 1328 307 Note that after clean the transform of the final model is left in the MODEL_DATA column so you can go directly to a self calibration step without explicitly using ft CHAPTER 5 SYNTHESIS IMAGING 225 5 8 Image plane deconvolution deconvolve If you have only an image obtained from some telescope and an image of its point spread function then you can attempt a simple image plane deconvolution Note that for interferometer data full uv plane deconvolution using clean or similar algorithm is superior The default inputs for deconvolve are deconvolve Deconvoving a point spread function from an image imagename gt Name of image to decolvolve model e gt Name of output image to which deconvolved components are stored psf gt Name of psf or gaussian parameters if psf is assumed gaussian alg clark Deconvolution alorithm to use niter 10 number of iteration to use in deconvolution process gain 0 1 CLEAN gain parameter threshold 0 0Jy level below which sources will not be deconvolved mask gt Name of image that has mask to limit region of deconvolution async False if True run in the background prompt is freed The algorithm alg options are clark hogbom multiscale or mem The multiscale and mem options
435. lly the cal solutions are multiplied as complex numbers as per the Measurement Equation The tablein is optional see below You must specify an incrtable and a caltable The tablein parameter is used to specify the existing cumulative calibration table to which an incremental table is to be applied Initially no such table exists and if tablein then accu mulate will generate one from scratch on the fly using the timescale in seconds specified by the sub parameter accumtime These nominal solutions will be unit amplitude zero phase calibra tion ready to be adjusted by accumulation according to the settings of other parameters When accumtime is negative the default the table name specified in tablein must exist and will be used If tablein is specified then the entries in that table will be used The incrtable parameter is used to specify the incremental table that should be applied to tablein The calibration type of incrtable sets the type assumed in the operation so tablein if specified must be of the same type If it is not accum will exit with an error message Certain combinations of types and subtypes will be supported by accum in the future The caltable parameter is used to specify the name of the output table to write If un specified gt gt then tablein will be overwritten Use this feature with care since an error here will require building up the cumulative table from the most recent distinct version if an
436. log plotting spectral plotting options float doppler velocity km s default 0 0 example linedop 30 0 colormap the colours to be used for plot lines default None example colormap green red black cyan magenta html standard colormap g r k c m abbreviation colormap 008000 00FFFF FF0090 RGB tuple The plotter will cycle through these colours when lines are overlaid stacking mode linestyles the linestyles to be used for plot lines default None example linestyles line dashed dotted dashdot dashdotdot dashdashdot The plotter will cycle through these linestyles when lines are overlaid stacking mode WARNING Linestyles can be specified only one color has been set linewidth width of plotted lines default None example linewidth 1 integer linewidth 0 75 double histogram plot histogram options bool True False default False plotfile file name for hardcopy output options str filename eps ps png default no hardcopy example specplot eps specplot png Note this autodetects the format from the suffix eps ps png overwrite overwrite the output file if already exists options bool True False default False DESCRIPTION Task sdplot displays single dish spectra It assumes that the spectra have been calibrated in sdcal It does allow selection of scans IFs polarizations and some time and channel averaging smoothing options also but does not write out this
437. lot HHHHHHHHHHHHHHHHHHHHHHHHHH Off line Statistics HHHHHHHHHHHHHHHHHHHHHHHHHH 334 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING Now do some region statistics First the line free region Set parameters default sdstat sdfile sdusecase_orions_hc3n asap Keep the default spectrum and flux units K and channel fluxunit specunit Pick out a line free region You can bring up a default sdplot again to check this masklist 5000 7000 This is a line free region so we don t need to invert the mask invertmask False You can check with inp sdstat returns some results in the Python dictionary You can assign this to a variable off_stat sdstat and look at it off_stat which should give eqw 38 563105620704945 max 0 15543246269226074 gt mean 0 0030361821409314871 median 0 0032975673675537109 min 0 15754437446594238 rms 0 047580458223819733 gt stddev 0 047495327889919281 sum 6 0754003524780273 HE HHHH H You see it has some keywords for the various stats We want the standard deviation about the mean or stddev print The off line std deviation off_stat stddev 335 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING which should give The off line std deviation 0 0474953278899 or better formatted using Python I O formatting print
438. lots will be cycled through for each timestamp in turn Note that iteration can take more than one iteration choice as a single string containing a comma separated list of the options BETA ALERT the iteration order is fixed independent of the order specified in the iteration string for example iteration antenna time field iteration time antenna field will both iterate over each field fastest then time next and antenna slowest The order is iteration antenna time field spw from the slowest outer loop to fastest inner loop The markersize and fontsize parameters are especially helpful in making the dot and label sizes appropriate for the plot being made The screen shots in this section used this feature to make the plots more readable in the cookbook Adjusting the fontsize can be tricky on multi panel plots as the labels can run together if too large You can also help yourself by manually resizing the Plotter window to get better aspect ratios on the plots BETA ALERT Unfortunately plotcal has many of the same problems that plotxy does as they use similar code underneath An overhaul is underway so stay tuned 4 5 1 1 Examples for plotcal For example to plot amplitude or phase as a function of time for G solutions after rescaling by fluxscale for the NGC5921 demo data see Appendix F 1 CHAPTER 4 SYNTHESIS CALIBRATION 164 default plotcal fontsize 14 0 Ma
439. lotxy phase saved plotxy O Now the calibrator vis calsplitms field calname yaxis amp Use the field name as the title title field figfile vis plotxy amp png print Plotting to file figfile saveinputs plotxy vis plotxy amp saved plotxy O 439 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 440 yaxis phase figfile vis plotxy phase png print Plotting to file figfile saveinputs plotxy vis plotxy phase saved plotxy O print Calibration completed Make the scratch columns in the split ms print Clearcal default clearcal vis srcsplitms clearcal print Created scratch columns for MS vis print wee Now clean an image of Jupiter NOTE this uses the new combined invert clean mosaic task Patch 2 print Clean 1 default clean Pick up our split source data vis srcsplitms Make an image root file name imagename imnamel print Output images will be prefixed with imnamel Set up the output continuum image single plane mfs mode mfs stokes I print Will be a single MFS continuum image APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS NOTE current version field doesnt work field Combine all spw spw Imaging mode params psfmode clnalg imagermode clnmode Imsize and cell imsize cl
440. low diagram for CASA calibration of interferometry data is shown in Figure This should help you chart your course through the complex set of calibration steps In the following sections we will detail the steps themselves and explain how to run the necessary tasks and tools This can be broken down into a number of discrete phases CHAPTER 4 SYNTHESIS CALIBRATION 130 Input Data Tables amp Information Process Output Data Tables amp Information Input dataset Flux Calibrator Model s Prior Calibration Prior Calibration Antenna Gain Curves e g setjy Information Atmospheric Models Bandpass Calibrator a Bandpass Model s Calibration Table Gain Calibrator aincal Model s 9 fluxscale i Gain Calibration Table i Scaled Gain Table i polcal coming soon applycal Calibrated Data Figure 4 1 Flow chart of synthesis calibration operations Not shown are use of table manipulation and plotting tasks accum plotcal and smoothcal see Figure 4 2 CHAPTER 4 SYNTHESIS CALIBRATION 131 Prior Calibration set up previously known calibration quantities that need to be pre applied such as the flux density of calibrators antenna gain elevation curves and atmospheric models Use the setjy task 4 3 4 and set the gaincurve 4 3 2 and opacity 4 3 3 parameters in subsequent tasks e Bandpass Calibration solve for the relative gain of the system over the frequency chan
441. lt none set example if telescopeparm it tries to get the telescope name from the data Full antenna parameters diameter ap eff known to ASAP are gt ATPKSMB ATPKSHOH ATMOPRA DSS 43 CEDUNA HOBART For GBT it fixes default fluxunit to K first then convert to a new fluxunit telescopeparm 104 9 0 43 diameter m ap eff telescopeparm 0 743 gain in Jy K telescopeparm FIX to change default fluxunit see description below APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 307 specunit units for spectral axis options str channel km s GHz MHz kHz Hz default current example this will be the units for masklist frame frequency frame for spectral axis options str LSRK REST TOPO LSRD BARY GEO GALACTO LGROUP CMB default currently set frame in scantable WARNING frame REST not yet implemented doppler doppler mode options str RADIO OPTICAL Z BETA GAMMA default currently set doppler in scantable scanaverage average integrations within scans options bool True False default False example if True this happens in read in For GBT set False timeaverage average times for multiple scan cycles options bool True False default False example if True this happens after calibration polaverage ave
442. lt plotxy plotxy ngc5921 ms channel iteration antenna subplot 311 Figure 1 corrected vs Channel ANTENNA1 1 Figure 1 corrected vs Channel ANTENNA1 1 i i go E a i corrected amp POSO corrected amp or 3 30 40 50 50 Channel corrected vs Channel ANTENNAI 2 corrected amp a Sho ea corrected amp 30 Channel corrected vs Channel ANTENNAI 3 corrected vs Channel ANTENNA1 3 ele ek D gi eu Boer 808 30 0 800 Bo 10 EJ 30 a 50 oo Channel Channel O9 0 E MO 0 5 Figure 3 5 flagdata Example showing before and after displays using a selection of one antenna and a range of channels Note that each invocation of the flagdata task represents a cumulative se lection i e running antenna 0 will flag all data with antenna 0 while antenna 0 spw 0 10 15 will flag only those channels on antenna 0 3 5 1 1 Manual flagging and clipping in flagdata For mode manualflag manual flagging and clipping is controlled by the sub parameters mode manualflag Mode manualflag autoflag summary quack autocorr False Flag autocorrelations unflag False Unflag the data specified clipexpr gt ABS RR Expression to clip on clipminmax Range to use for clipping clipcolumn DATA Data column to use for clipping clipoutside True Clip outside the range or within it
443. ltiplot True yaxis amp showgui True plotcal print Print HssssSsesss ss ssse sae sae print Plotcal print Looking at amplitude in cal table caltable Pause script if you are running in scriptmode if scriptmode user_check raw_input Return to continue scriptin Now go back and plot to file showgui False yaxis amp figfile caltable plotcal amp png print Plotting calibration to file figfile saveinputs plotcal caltable plotcal amp saved plotcal yaxis phase figfile caltable plotcal phase png APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS print Plotting calibration to file figfile saveinputs plotcal caltable plotcal phase saved plotcal if dopolcal print Polcal D default polcal print Solve for polarization leakage on 0137 331 print Pretend it has unknown polarization vis msfile Start with the un fluxscaled gain table gaintable gtable use settings from gaincal gaincurve usegaincurve opacity gainopacity Output table caltable ptable Use a 3C48 tracked through a range of PA field 0137 331 spw No need for further selection selectdata False Polcal mode D QU unknown pol for D poltype D QU One solution for entire dataset solint inf combine scan reference antenna refant calrefant
444. lues 2 4 A new task called rmtables has been created to cleanly remove tables This helps if the user is trying to process data e g an image from scratch and not continue from a previous session It will not remove things that have open handles 1 4 3 1 e New plotting and flagging features A number of changes were made to flagdata 3 5 CHAPTER 1 INTRODUCTION 24 1 The task now has the feature where some parameters can take lists so only one invocation of the task can apply any number of flagging specification 2 The task now uses the standard selectdata parameters 3 The correlation sub parameter now takes more options e g RR LL RR LL etc 4 The mode parameter now has a shadow option The task plotants now has the capability to save a plot as a file parameter figfile GEJ There is a new prototype MS plotting application casaplotms This is experimental and under active development and is not yet integrated into casapy 3 8 e New synthesis calibration features There are models for 3C147 at C and X band now available in setjy 4 3 4 In the calibration tasks there is now a minblperant parameter which enables the user to control the minimum number of baselines required for an antenna to be solved for 4 4 1 5 The task split can now go directly from a multi SPW measurement set to a time averaged one with the same set of SPWs and or spli
445. lues of those parameters see above However if some but not all arguments are supplied then those parameters not given as arguments will default and NOT use the current global values Thus imhead ngc5921 demo cleanimg image mode list will reproduce the above 1 3 5 2 The default Command Each task has a special set of default parameters defined for its parameters You can use the default command to reset the parameters for a specified task or the current task as defined by the taskname variable to their default Important Note The default command resets the values of the task parameters to a set of defaults as specified in the task code Some defaults are blank strings or empty lists 01 others are specific numerical values strings or lists It is important to understand that just setting a string parameter to an empty string is not setting it to its default Some parameters do not have a blank as an allowed value See the help for a particular task to find out its default If gt is the default or an allowed value it will say so explicitly For example suppose we have been running CASA on a particular dataset e g CHAPTER 1 INTRODUCTION 50 CASA lt 40 gt inp clean sob bed tats gt inp clean clean Deconvolve an image with selected algorithm vis ngc5921 demo src split ms contsub name of input visibility file imagename ngc5921 demo cleanimg Pre name of ou
446. luxscale gaincal split 475 Appendix H Writing Tasks BETA ALERT This prescription for writing and incorporating tasks in CASA is for the power user This procedure is also likely to change in future releases It is possible to write your own task and have it appear in casapy You must create two files yourtask xml and a task_yourtask py The xml file is use to describe the interface to the task and the task_yourtask py does the actual work The argument names must be the same in both the yourtask xml and task_yourtask py file The yourtask xml file is used to generated all the interface files so yourtask will appear in the casapy system Synopsis e buildmytasks yourtask e execfile PATH_TO_YOURTASK yourtask py from inside casapy H 1 The XML file The key to getting your task into casapy is constructing a task interface description XML file Some XML basics an xml element begins with lt element gt and ends with lt element gt If an XML element contains no other XML element you may specify it via lt element gt An XML element may have zero or more attributes which are specified by attribute attribute value You must put the attribute value in quotes i e lt element myattribute attribute value gt All task xml files must start with this header information lt xml version 1 0 encoding UTF 8 gt lt xml stylesheet type text xsl gt lt casaxml xmlns http casa nrao edu schema
447. ly 1000 2000 3000 4000 5000 5000 7000 8000 1000 2000 3000 4000 5000 5000 7000 8000 Channel Channel ootd eS rst Figure A 4 Two panel plot of the calibrated spectra The GBT data has a separate scan for the SOURCE and REFERENCE positions so scans 20 21 22 and 23 result in these two spectra 0006 IX ASAP Plotter Tk OrionS_ps Brightness Temperature K 45 47 15 48 45 49 155 45 51 LSRK Frequency GHz Al O Aaa 4 45 47 y 3 09 Figure A 5 Calibrated spectrum with a line at zero using histograms APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 359 spave set_unit channel rmsmask spave create_mask 5000 7000 get rms of line free regions rms spave stats stat rms mask rmsmask rms Scan 0 OrionS_ps Time 2006 01 19 01 52 05 IF O 0 048 So Sa SS SS a a a ee oS a a ee eee LINE linemask spave create_mask 3900 4200 max spave stats max linemask IF O 0 918 sum spave stats sum linemask IF O 64 994 median spave stats median linemask IF 0 0 091 mean spave stats mean linemask IF O 0 210 Fitting spave set_unit channel set units to channel sd plotter plot spave plot spectrum f sd fitter msk spave create_mask 3928 4255 create region around line f set_function gauss 1 set a single gaussian component f set_scan spave msk set the data and region for the fitter f fitQ fit f plot resi
448. m and the effects of formation of the cross power spectra by a correlator Calibration is the process of reversing these effects to arrive at corrected visibilities which resemble as closely as possible the visibilities that would have been measured in vacuum by a perfect system The subject of this chapter is the determination of these effects by using the visibility data itself E 1 The HBS Measurement Equation The relationship between the observed and ideal desired visibilities on the baseline between an tennas i and j may be expressed by the Hamaker Bregman Sault Measurement Equation Fo gt IDEAL Vig Jij Vij where Vi represents the observed visibility ye represents the corresponding ideal visibilities and Jij represents the accumulation of all corruptions affecting baseline ij The visibilities are indicated as vectors spanning the four correlation combinations which can be formed from dual polarization signals These four correlations are related directly to the Stokes parameters which fully describe the radiation The J term is therefore a 4x4 matrix Most of the effects contained in J indeed the most important of them are antenna based i e they arise from measurable physical properties of or above individual antenna elements in a synthesis array Thus adequate calibration of an array of Nant antennas forming Nant Nant 1 2 baseline visibilities is usually achieved through the determination of only Nant factors s
449. m and you want the same amplitude scale If you do not include amplitude in the initial gaincal you probably want to set visnorm True also to take out the amplitude normalization change Note also in the case of multiple fields that the BPOLY solution will be labeled with the field ID of the first field used in the BPOLY solution so if for example you point plotcal at the name or ID of one of the other fields used in the solution plotcal does not plot For example to solve for a BPOLY 5th order in amplitude 7th order in phase using data from field 2 with G corrections pre applied gaintable cal G refant 14 Pre apply gain solutions derived previously bandpass vis data ms input data set caltable cal BPOLY spw 0 2756 Use channels 3 57 avoid end channels field 0 Select bandpass calibrater field 0 bandtype BPOLY Select bandpass polynomials degamp 5 5th order amp degphase 7 7th order phase 4 4 3 Complex Gain Calibration gaincal The fundamental calibration to be done on your interferometer data is to calibrate the antenna based gains as a function of time in the various frequency channels and polarizations Some of these calibrations are known beforehand a priori and others must be determined from observations of calibrators or from observations of the target itself self calibration It is best to have removed a slowly vary
450. m fit timescale fitorder O Polynomial order for the fit fitmode subtract Use of continuum fit subtract replace model splitdata False Split out continuum continuum subtracted data async False For each baseline and over the timescale specified in solint uvcontsub will provide a simple linear fit to the real and imaginary parts of the continuum only channels specified in fitspw using the standard spw selection syntax and then subtract this model from all channels specified in spw or from all channels in spectral windows of fitspw if spw BETA ALERT The fits are currently done independently in the spectral windows specified in fitspw and thus overlapping channels in different spw will be corrected only with the fits from their respective fitspw Usually one would set solint int which does no averaging and fits each integration However if the continuum emission comes from a small region around the phase center then you can set solint larger as long as it is shorter than the timescale for changes in the visibility function of the continuum If your scans are short enough you can also use scan averaging solint inf Be warned setting solint too large will introduce time smearing in the estimated continuum and thus not properly subtracting emission not at the phase center Running uvcontsub with fitmode subtract will replace the CORRECTED_DATA column in the MS with continuum subtracted l
451. m temperature normalization amplitude corrections tropospheric phase corrections derived from Water Vapor Radiometry WVR mea surements instrumental line length corrections etc Where appropriate solving capabilities for these effects will also be added 4 4 Solving for Calibration Bandpass Gain Polarization These tasks actually solve for the unknown calibration parameters placing the results in a cal ibration table They take as input an MS and a number of parameters that specify any prior calibration or previous calibration tables to pre apply before computing the solution These are placed in the proper sequence of the Measurement Equation automatically We first discuss the parameters that are in common between many of the calibration tasks Then we describe each solver in turn 4 4 1 Common Calibration Solver Parameters There are a number of parameters that are in common between the calibration solver tasks These also appear in some of the other calibration manipulation and application tasks CHAPTER 4 SYNTHESIS CALIBRATION 142 4 4 1 1 Parameters for Specification vis and caltable The input measurement set and output table are controlled by the following parameters vis Name of input visibility file caltable des Name of output calibration table The MS name is input in vis If it is highlighted red in the inputs 1 3 5 4 then it does not exist and the task will not execute Check the name and pa
452. magename parameter is used as the root name of the output image Depending on the particular task and the options chosen one or more images with names built from that root will be created For example the clean task run with imagename ngc5921 a series of output images will be created with the names ngc5921 clean ngc5921 residual ngc5921 model etc If an image with that name already exists it will in general be overwritten Beware using names of existing images however If the clean is run using an imagename where lt imagename gt residual and lt imagename gt model already exist then clean will continue starting from these effectively restarting from the end of the previous clean Thus if multiple runs of clean are run consecutively with the same imagename then the cleaning is incremental as in the difmap package 5 2 4 Parameter imsize The image size in numbers of pixels on the x and y axes is set by imsize For example imsize 288 288 makes a square image 288 pixels on a side If a single value is given then a square image of that dimension is made This need not be a power of two but for optimal performance should be a composite number divisible only by 2 and also 3 and or 5 Note that in the example above 288 25 37 BETA ALERT You will be warned if you give a non composite imsize and it will suggest the nearest appropriate value But it will continue cleaning so you may have to abort if you want to make use of t
453. magidgl 2 226 227 ee ee ee land ee ee S 228 6 1 1 Region Selection box o a 228 6 1 2 Plane Selection chans Stokes o o 228 6 1 8 Lattice Expressions expr 2 si as Ge lt lt e 229 6 1 4 Masks mask os cos ese fo BS RAS RECA Sa OE AS eww ow 230 6 1 5 Regions ESPLO ea so a Re he Ree Oe A eS 230 6 2 Image Header Manipulation imhead 231 6 2 1 Examples for imhead a 232 6 3 Continuum Subtraction on an Image Cube imcontsub 234 6 3 1 Examples for imcontsub 42 2 024 eee a 235 6 4 Image plane Component Fitting imfit a aaa 0 20000 eee 235 6 5 Mathematical Operations on an Image immath a 236 6 5 1 Examples for immath a 236 6 5 1 1 Simple math o oaaae 236 6 5 1 2 Polarization manipulation aa e e 238 o eE ere 238 bas moi tr a Be ae bs Bek oa Y 239 6 5 2 Using masks in immath lt sos so sace acs aokoe e Wa i e a poe e e e 240 6 6 Computing the Moments of an Image Cube immoments 241 6 6 1 Hints for using immoments ooa a a 243 6 6 2 Examples using immoments 243 6 7 Computing image statistics imstat occiso 244 6 7 1 Using the task return value 2 2 eee 245 6 7 2 Examples using imstat 2 0 ee ee 247 6 8 Extracting data from an image imval 0
454. max str pbcorstat max 0 pbcoroffstat imstat ngc4826 tutorial 16apr98 src clean pbcor box 106 161 153 200 print Found off source image rms str pbcoroffstat sigma 0 pbcorofflinestat imstat ngc4826 tutorial 16apr98 src clean pbcor box 108 108 148 148 chans 0 1 2 3 4 5 30 31 32 33 34 35 print Found off line image rms t str pbcorofflinestat sigma 0 HHHHHHHHHHHE RHEE HHHHRAAAHA AAR HHHR EERE H HAAR HH RRR R ARR AAA AAA Do zeroth and first moments NGC4826 LSR velocity is 408 km s delta is 20 km s print ImMoments default immoments momfile ngc4826 tutorial 16apr98 moments momzeroimage ngc4826 tutorial 16apr98 moments integrated momoneimage ngc4826 tutorial 16apr98 moments mom1 print Calculating Moments 0 1 for PBcor image immoments imagename ngc4826 tutorial 16apr98 src clean pbcor moments 0 axis spectral chans 7 28 outfile ngc4826 tutorial 16apr98 moments integrated TUTORIAL NOTES For moment O we use the image corrected for the mosaic response to get correct integrated flux densities However in real signal regions the value of moment 1 does not dependent on the flux being correct so the non pb corrected SAULT image can be used this avoids having lots of junk show up at the edges of your moment 1 image due to the primary beam correction Try it both ways
455. me robust subparam true gt lt description gt Briggs robustness parameter lt description gt lt value gt 0 0 lt value gt lt allowed kind range gt lt value range min gt 2 0 lt value gt lt value range max gt 2 0 lt value gt lt allowed gt lt param gt lt param type bool name uvtaper gt lt description gt Apply additional uv tapering of visibilities lt description gt lt value gt False lt value gt lt param gt lt param type stringArray name outertaper subparam true gt lt description gt uv taper on outer baselines in uv plane lt description gt lt value type vector gt lt value gt lt value gt lt value gt lt param gt lt param type stringArray name innertaper subparam true gt lt description gt uv taper in center of uv plane lt description gt lt value gt 1 0 lt value gt lt param gt lt param type string name modelimage gt lt description gt Name of model image s to initialize cleaning lt description gt lt value gt lt value gt lt param gt lt param type stringArray name restoringbeam gt lt description gt Output Gaussian restoring beam for CLEAN image lt description gt lt value gt lt value gt lt param gt lt param type bool name pbcor gt lt description gt Output primary beam corrected image lt description gt lt value gt False lt value gt lt param gt APPENDIX H APPENDIX WRITING TASKS IN CASA 487 lt pa
456. meter and sub parameters that allow the setting of a rest frequency or transition name as well as frame info 3 4 7 synthesis calibration features The bandtype BPOLY option now has the capability of getting solutions in different sets of spectral windows 4 4 2 3 synthesis imaging features NEW widefield a prototype task to make wide field e g low frequency images using w projection and or faceting Includes the ability to image multiple flanking fields set up using a box file B 4 The clean task now handles multiple dish sizes for heterogeneous imaging 5 3 15 The clean task has been improved in its handling of mosaics 5 3 14 image analysis features NEW imval a task that will return the data values in an image at a given pixel or in a specified region 6 8 The imfit task has improved reporting of fit results 6 4 The task regrid has been renamed imregrid This task will regrid an image onto a template image 6 9 viewer features The viewer now includes the ability to Save and Restore the GUI settings via a Data menu item 7 2 2 There is now improved control and appearance of Printing from the viewer 7 5 documentation features There is now an appendix on how to write and include your own CASA tasks intended for the power user H There is now an online CASA Task Reference Manual CHAPTER 1 INTRODUCTION 27 1 1 1 2 Previous changes introduc
457. mportuvfits fitsfile fitsfiles 1310 323 11 fits str i vis ngc4826 tutorial 1310 323 11 str i ms for i in range 5 9 importuvfits fitsfile fitsfiles ngc4826 11 fits str i vis ngc4826 tutorial ngc4826 11 str i ms HHHHHHHHHHHEHHAHEHHEHEEHEHHEHAAHHHEA HEHE HEA HEHE HEHEHE RARA HEHEHE EHH print Concat default concat APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS concat vis ngc4826 tutorial 3c273 5 ms gt ngc4826 tutorial 3c273 6 ms ngc4826 tutorial 3c273 7 ms gt ngc4826 tutorial 3c273 8 ms ngc4826 tutorial 1310 323 11 9 ms gt ngc4826 tutorial 1310 323 11 10 ms gt ngc4826 tutorial 1310 323 11 11 ms ngc4826 tutorial 1310 323 11 12 ms gt ngc4826 tutorial 1310 323 11 13 ms gt ngc4826 tutorial 1310 323 11 14 ms gt ngc4826 tutorial 1310 323 11 15 ms ngc4826 tutorial 1310 323 11 16 ms gt ngc4826 tutorial ngc4826 11 5 ms ngc4826 tutorial ngc4826 11 6 ms ngc4826 tutorial ngc4826 11 7 ms gt ngc4826 tutorial ngc4826 11 8 ms concatvis ngc4826 tutorial ms fregtol dirtol larcsec async False HHEEHHHHHHHAEHHAEHEHEAHEHHEAHHEEHEHHHHHHEEHRHREHEHHEE PORRA RARE RARO RRRO RO RERR RARA A ARRE HH HH HH HH HHH HH HHH HH HHH HH HH H HH FH OH TUTORIAL NOTES You can invoke tasks in two ways 1 2 As function calls with arguments as shown above for concat and used extensively i
458. mps from TO to T1 For example timerange 2007 10 09 00 40 00 2007 10 09 03 30 00 Note that fields missing in TO are replaced by the fields in the time stamp of the first valid row in the MS For example timerange 09 00 40 00 09 03 30 00 where the YY MM part of the selection has been defaulted to the start of the MS Fields missing in T1 such as the date part of the string are replaced by the corresponding fields of TO after its defaults are set For example timerange 2007 10 09 22 40 00 03 30 00 does the same thing as above 2 timerange TO Select all time stamps that are within an integration time of TO For example timerange 2007 10 09 23 41 00 Integration time is determined from the first valid row more rigorously an average integration time should be computed Default settings for the missing fields of TO are as in 1 CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 99 3 timerange TO dT Select all time stamps starting from TO and ending with time stamp TO dT For example timerange 23 41 00 01 00 00 picks an hour long chunk of time Defaults of TO are set as usual Defaults for dT are set from the time corresponding to MJD 0 Thus dT is a specification of length of time from the assumed nominal start of time 4 timerange gt TO Select all times greater than TO For example timerange gt 2007 10 09 23 41 00 Default set
459. n example using the Jupiter VLA 6m continuum imaging example see Appendix Put clean model into MODEL_DATA column ft vis jupiter6cm usecase split ms model jupiter6cm usecase cleani model CHAPTER 4 SYNTHESIS CALIBRATION 174 Phase only self cal on 10s timescales gaincal vis jupiter6cm usecase split ms caltable jupiter6cm usecase phasecali gaintype G calmode p refant 6 solint 10 0 minsnr 1 0 Plot up solution phase and SNR plotcal jupiter6cm usecase phasecal1 phase antenna 1 subplot 211 plotcal jupiter6cm usecase phasecal1 snr antenna 1 subplot 212 Amplitude and phase self cal on scans gaincal vis jupiter6cm usecase split ms caltable jupiter6cm usecase scancali gaintable jupiter6cm usecase phasecali gaintype G calmode ap refant 6 solint inf minsnr 1 0 Plot up solution amp and SNR plotcal jupiter6cm usecase scancalil amp antenna 1 subplot 211 plotcal jupiter6cm usecase scancalil snr antenna 1 subplot 212 Now accumulate these they will be on the 10s grid accum vis jupiter6cm usecase split ms tablein jupiter6cm usecase phasecal1l incrtable jupiter6cm usecase scancall caltable jupiter6cm usecase selfcall interp linear Plot this up plotcal jupit
460. n or crosshair if moved by dragging with the Mouse 2 2 ee ee 27 bo O ES al N a a N D 00 E N 99 IS 7 12 The Region Manager panel that appears if you select the Tools Region Manager ee RRE RR aE R A 275 7 13 Selecting an image region with the polygon tool 0 276 7 14 A multi panel display set up through the Viewer Canvas Manager 277 15 The Load Data Viewer panel as it appears if you select an MS The only option available is to load this as a Raster Image In this example clicking on the Raster image button would bring up the displays shown m Figure fA 278 16 The MS for NGC4826 BIMA observations has been loaded into the viewer We see the first of the spw in the Display Panel and have opened up MS and Visibility Selections in the Data Display Options panel The display panel raster is not full of visibiltiies because spw 0 is continuum and was only observed for the first few scans This is a case where the different spectral windows have different numbers of channels alse c soa sate ee ee a 28 17 17 The MS for NGC4826 from Figure 10 now with the Display Axes open in the Data Display Options panel By default channels are on the Animation Axis and thus in the tapedeck while spectral window and polarization are on the Display Axes sliders o e e 28 718 The MS for NGC4820 continuing from Figure 7 17 We have now put
461. n order to make them as close as tion is the cb tool possible to what an idealized interferometer would measure such that when the data is imaged an accurate picture of the sky is obtained This is not an arbitrary process and there is a philosophy behind the CASA calibration methodology see 4 2 1 for more on this For the most part calibration in CASA using the tasks is not too different than calibration in other packages such as AIPS or Miriad so the user should not be alarmed by cosmetic differences such as task and parameter names 4 1 Calibration Tasks The standard set of calibration tasks are e accum Accumulate incremental calibration solutions into a cumulative cal table 4 5 4 e applycal Apply calculated calibration solutions 4 6 1 e bandpass B calibration solving supports pre apply of other calibrations 4 4 2 e clearcal Re initialize visibility data set calibration data 4 6 3 fluxscale Bootstrap the flux density scale from standard calibration sources 4 4 4 e gaincal G calibration solving supports pre apply of other calibrations 4 4 3 e listcal list calibration solutions s e plotcal Plot calibration solutions 14 5 1 polcal polarization calibration 4 4 5 128 CHAPTER 4 SYNTHESIS CALIBRATION 129 e setjy Compute the model visibility for a specified source flux density 4 3 4 e smoothcal Smooth calibrati
462. n other sd tasks as there are no controls for these Note that you can use sdsave to do selection writing out a new scantable Note that multiple scans and IFs can in principle be handled but we recommend that you use scanlist field and iflist to give a single selection for each fit For complicated spectra sdfit does not do a good job of auto guessing the starting model for the fit We recommend you use sd fitter in the toolkit which has more options such as fixing components in the fit and supplying starting guesses by hand See the sdaverage description for information on fluxunit conversion and the telescopeparm parameter Beta Patch 4 New Features The parameter overwirte is added to allow overwirte of output fitfile A 2 1 8 sdlist Keyword arguments sdfile name of input SD dataset scanaverage average integrations within scans options bool True False default False example if True this happens in read in For GBT set False listfile Name of output file for summary list default no output file example mysd_summary txt overwrite overwrite the output file if already exists options bool True False default False APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 313 DESCRIPTION Task sdlist lists the scan summary of the dataset after importing as a scantable into ASAP It will optionally output this summary as file Note that if your PAGER environment variable is set to
463. n that a single com mon solution for both polarizations is determined In cases where only one polarization is observed type T is adequate to describe the time dependent complex multiplicative gain calibration In the following example we assume we have a G solution obtained on a longish timescale longer than a few minutes say and we want a residual T solution to track the polarization independent variations on a very short timescale CHAPTER 4 SYNTHESIS CALIBRATION 153 gaincal data ms Visibility dataset caltable cal T Specify output table name gaintype T Solve for T field 0 1 Restrict data selection to calibrators solint 3 0 Obtain solutions on a 3s timescale gaintable cal120 G Pre apply prior G solution For dual polarization observations it will always be necessary to obtain a G solution to account for differences and drifts between the polarizations which traverse different electronics but solutions for rapidly varying polarization independent effects such as those introduced by the troposphere will be optimized by using T Note that T can be used in this way for self calibration purposes too 4 4 3 3 GSPLINE solutions At high radio frequencies where tropospheric phase fluctuates rapidly it is often the case that there is insufficient signal to noise ratio to obtain robust G or T solutions on timescales short enough to track the var
464. n this script e g task pari val1 par2 val2 with parameters set as arguments in the call Note that in this case the global parameter values are NOT used or changed and any task parameters that are not specified as arguments to the call will be defaulted to the task specific default values see the help task description By setting the values of the global parameters and then using the go command if taskname is set or calling the task with no arguments For example default task pari vall par2 val2 inp task In this case the default command sets the parmeters to their task defaults and sets the taskname paramter to the task to be run The inp command displays the current values for the task 456 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS parameters Then the call with no arguments runs with the globals Warning go does not work inside scripts See Cookbook Using the concat call above as an example we would do default concat vis ngc4826 tutorial 3c273 5 ms gt ngc4826 tutorial 3c273 6 ms gt ngc4826 tutorial 3c273 7 ms gt ngc4826 tutorial 3c273 8 ms ngc4826 tutorial 1310 323 11 9 ms ngc4826 tutorial 1310 323 11 10 ms gt ngc4826 tutorial 1310 323 11 11 ms ngc4826 tutorial 1310 323 11 12 ms ngc4826 tutorial 1310 323 11 13 ms ngc4826 tutorial 1310 323 11 14 ms
465. n use the concat task to combine them Currently concat will add a second MS to an existing MS not producing a new one This would be run multiple times if you had more than two sets to combine See for details 1 5 2 Data Examination Editing and Flagging The main data examination and flagging tasks are e listobs summarize the contents of a MS 2 3 e flagmanager save and manage versions of the flagging entries in the measurement set 8 2 e flagautocorr non interactive flagging of auto correlations 8 3 3 e plotxy interactive X Y plotting and flagging of visibility data 8 3 4 e flagdata non interactive flagging and unflagging of specified data 8 3 5 e viewer the CASA viewer can display as a raster image MS data with some editing capabilities 7 e casaplotms a prototype experimental next generation interactive MS X Y plotting and flagging tool that will eventually replace plotxy new in Version 2 4 0 3 8 These tasks allow you to list plot and or flag data in a CASA MS There will eventually be tasks for automatic flagging to data based upon statistical criteria Stay tuned Examination and editing of synthesis data is described in Chapter Visualization and editing of an MS using the casaviewer is described in Chapter 1 5 2 1 Interactive X Y Plotting and Flagging The principal tool for making X Y plots of visibility data is plotxy see 3 4 Ampli
466. name split ms f sooooooooooooooooooooooooooooooooooooooooooooooooooooooo Intensity imaging parameters Same prefix for this imaging demo output imprefix prefix This is D config VLA 6cm 4 85GHz obs Check the observational status summary Primary beam FWHM 45 f_GHz 557 Synthesized beam FWHM 14 RMS in 10min 600s 0 06 mJy thats now but close enough 416 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS Set the output image size and cell size arcsec 4 will give 3 5x oversampling clncell 4 4 280 pix will cover to 2xPrimaryBeam clean will say to use 288 a composite integer for efficiency clnalg clark clnmode For Cotton Schwab use clnmode csclean clnimsize 288 288 iterations clniter 10000 Also set flux residual threshold 0 04 mJy From our listobs Total integration time 85133 2 seconds With rms of 0 06 mJy in 600s gt rms 0 005 mJy Set to 10x thermal rms clnthreshold 0 05 Filenames imnamel imprefix clean1 clnimagel imname1 image clnmodeli imname1 model clnresid1 imnamei residual clnmaski imnamei clean_interactive mask imname2 imprefix clean2 clnimage2 imname2 image clnmodel2 imname2 model clnresid2 imname2 residual clnmask2 imname2 clean_interactive mask imname3 imprefix
467. name regular expression pattern fails to match any field name the given name regular expression pattern are matched against the field code If still no field is selected an exception is thrown Field specifications can also be given by their integer IDs IDs can be a single or a range of IDs Field ID selection can also be done as a boolean expression For a field specification of the form gt ID all field IDs greater than ID are selected Similarly for lt ID all field IDs less than the ID are selected For example if the MS has the following observations CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 94 FIELDID SPWID NChan Pol NRows Source Name 0 0 127 RR 10260 0530 135 1 0 127 RR 779139 05582 16320 2 0 127 RR 296190 05309 13319 3 0 127 RR 58266 0319 415 4 0 127 RR 32994 1331 305 5 1 1 RR RL LL RR 23166 KTIP one might select field 072 KTIP FIELDID 0 1 2 and field name KTIP field 0530 135 field 0530 135 field 05 fields 0530 135 05582 16320 05309 13319 2 6 3 The spw Parameter The spw parameter is a string that indicates the specific spectral windows and the channels within them to be used in subsequent processing Spectral window selection SPWSEL can be given as a spectral window integer ID a list of integer IDs a spectral window name specified as a literal string for exact match or a regular expression or pattern The specification can be via frequency ranges or by index
468. ncluding derivation from weather information and solving directly from the visibility data capabilities will be made available in the future If you do not have an externally supplied value for opacity for example from a VLA tip procedure then you should either use an average value for the telescope or leave it at zero and hope that your gain calibration compensates e g that your calibrator is at the same elevation as your target at approximately the same time As noted above there are no facilities yet to estimate this from the data e g by plotting TANT vs elevation Below we give instructions for determining opacity for VLA observations where tip curve data is available It is beyond the scope of this cookbook to provide information for other telescopes 4 3 3 1 Determining opacity corrections for VLA data For VLA data zenith opacity can be measured at the frequency and during the time observations are made using a VLA tipping scan in the observe file Historical tipping data are available at CHAPTER 4 SYNTHESIS CALIBRATION 137 http www vla nrao edu astro calib tipper Choose a year and click Go to get a list of all tipping scans that have been made for that year If a tipping scan was made for your observation then select the appropriate file Go to the bottom of the page and click on the button that says Press here to continue The results of the tipping scan will be displayed Go to the section called Overall Fit S
469. nd y cell size default unit arcsec phasecenter ae Image phase center position or field index restfreq me rest frequency to assign to image see help stokes E Stokes params to image eg I IV QU IQUV weighting natural Weighting to apply to visibilities uvtaper False Apply additional uv tapering of visibilities modelimage ad Name of model image s to initialize cleaning restoringbeam gt gt Output Gaussian restoring beam for CLEAN image pbcor False Output primary beam corrected image minpb 0 1 Minimum PB level to use async False The clean task will produce a number of output images based on the root name given in imagename These include lt imagename gt clean image lt imagename gt clean flux lt imagename gt clean flux pbcoverage lt imagename gt clean model lt imagename gt clean residual lt imagename gt clean psf the restored image the effective response e g for pbcor the PB coverage ftmachine mosaic only the model image the residual image the synthesized dirty beam HH H H FH BETA ALERT The lt imagename gt clean flux pbcoverage image is new in Patch 4 version 2 4 0 and reflects the unweighted primary beam coverage without weighting or gridding kernel factors used for the minpb cutoff B 3 7 This is produced only for imagermode mosaic with ftmachine mosaic The mode psfmode imagermode and weighting parameters open up other sub par
470. ne bmaj bmin bpa Gaussian scale at which taper falls to zero at uv 0 default innertaper no inner taper applied NOT YET IMPLEMENTED modelimage Name of model image s to initialize cleaning If multiple images then these will be added together to form initial staring model NOTE these are in addition to any initial model in the amp lt imagename amp gt model image file default none example modelimage orion model modelimage orion model sdorion image Note if the APPENDIX H APPENDIX WRITING TASKS IN CASA 497 units in the image are Jy beam as in a single dish image then it will be converted to Jy pixel as ina model image using the restoring beam in the image header weighting Weighting to apply to visibilities default natural example weighting uniform Options natural uniform briggs gt superuniform briggsabs radial amp gt amp gt amp gt Weighting expandable parameters For weighting briggs and briggsabs robust Brigg s robustness parameter default 0 0 example robust 0 5 Options 2 0 to 2 0 2 uniform 2 natural For weighting briggsabs noise noise parameter to use for Briggs abs weighting example noise 1 0mJy For superuniform briggs briggsabs weighting npixels number of pixels to determine uv cell size for weight calculation example npixels 7 restoringbeam Output Gaussian restoring beam for CLE
471. nels in spw beyond the first are mapped into the nearest output image channel within half a channel if any For linear the channels are gridded into the planes using weights given by a linear function of the frequency of the MS channel versus the plane Each input channel will be mapped to 1 or 2 output planes For most users this is the best choice For cubic the channels are gridded using a cubic interpolation function 5 2 6 Parameter phasecenter The phasecenter parameter indicates which of the field IDs should be used to define the phase center of the mosaic image or what that phase center is in RA and Dec The default action is to use the first one given in the field list For example phasecenter 5 field 5 in multi src ms phasecenter J2000 19h30m00 40d00m00 specify position Note that the format for angles prefers to use hm for RA time units and dm for Dec Angle units as separators The colon separator is interpreted as RA time even if its used for the Dec so be careful not to copy paste from other sources 5 2 7 Parameter restfreq The value of the restfreq parameter if set will over ride the rest frequency in the header of the first input MS to define the velocity frame of the output image CHAPTER 5 SYNTHESIS IMAGING 194 BETA ALERT The restfreq parameter takes the options of transitions and frequencies as in the corresponding plotxy parameter 3 4 7 but does not currently expand
472. ng the net effect of both In terms of the Measurement Equation the net calibration is the product of the initial and incremental solutions Cumulative calibration tables also provide a means of generating carefully interpolated calibration on variable user defined timescales that can be examined prior to application to the data with applycal The solutions for different fields and or spectral windows can be interpolated in different ways with all solutions stored in the same table The only difference between incremental and cumulative calibration tables is that incremental tables are gener Other Packages ated directly from the calibration solving tasks gaincal The analog of accum in classic AIPS bandpass etc and cumulative tables are generated from lis the use of CLCAL to combine a se other cumulative and incremental tables via accum In all ries of incremental SN calibration other respects internal format application to data with tables to form successive cumula applycal plotting with plotcal etc they are the same tive CL calibration tables AIPS and therefore interchangeable Thus accumulate and cu sn CL tables are the analog of G mulative calibration tables need only be used when circum tables in CASA stances require it The accum task represents a generalization on the classic AIPS CLCAL see sidebox model of cumulative calibration in that its application is not limited to accumulation of
473. ng plotted The poln RL plots both R and L polarizations on the same plot The respective XY options do equivalent things The poln option plots amplitude ratios or phase differences between whatever polarizations are in the MS R and L or X and Y The field spw and antenna selection parameters are available to obtain plots of subsets of solutions The syntax for selection is given in 2 6 The subplot parameter is particularly helpful in making multi panel plots The format is subplot yxn where yxn is an integer with digit y representing the number of plots in the y axis digit x the num ber of panels along the x axis and digit n giving the location of the plot in the panel array where n 1 xy in order upper left to right then down See for more details on this option The iteration parameter allows you to select an identifier to iterate over when producing multi panel plots The choices for iteration are antenna time spw field For example if per antenna solution plots are desired use iteration antenna You can then use subplot to specify the number of plots to appear on each page In this case set the n to 1 for subplot yxn Use the Next button on the plotcal window to advance to the next set of plots Note that if there is more than one timestamp in a B table the user will be queried to interactively advance the plot to each timestamp or if multiplot True the antennas p
474. ng the instrumental polarization solution is solved using the linear approximation where cross terms in more than a single product of the instrumental or source polarizations are ignored in the Measurement Equation see E A general non linearized solution with sufficient SNR may enable some relaxation of the requirements indicated here For instrumental polarization calibration there are 3 types of calibrator choice CASA Polarization Calibration Modes Cal Polarization Parallactic Angles MODEL_DATA polmode Result unpolarized any set Q U 0 D or Df D terms only known non zero 2 scans set Q U 2D X or D X D terms and PA unknown 3 scans ignored D QU or Df QU D terms and source Note that the parallactic angle ranges spanned by the scans in the modes that require this should be large enough to give good separation between the components of the solution In practice 60 is a good target Each of these solutions should be followed with a X solution on a source with known polarization position angle and correct Q iU in MODEL_DATA BETA ALERT polmode D X will soon deliver this automatically The polcal task will solve for the D or X terms using the model visibilities that are in the MODEL_DATA column of the MS Calibration of the parallel hands must have already been carried out using gaincal and or bandpass in order to align the phases over time and
475. ng to the name of a cleanbox file mask image or region file These are used by CLEAN to define a region to search for components Note that for imagermode 5 3 4 the default with mask is to restrict clean to the inner quarter of the image 5 3 6 1 Setting clean boxes If mask is given a list these are taken to be pixel coordinates for the blc and tre bottom left and top right corners of one or more rectangular boxes Each box is a four element list For example mask 110 110 150 145 180 70 190 80 defines two boxes CHAPTER 5 SYNTHESIS IMAGING 209 5 3 6 2 Using clean box files You can provide mask a string with the name of an ASCII file containing the BLC TRC of the boxes with one box per line Each line should contain five numbers lt fieldindex gt lt blc x gt lt blc y gt lt trc x gt lt trc y gt with whitespace separators Currently the lt fieldindex gt is ignored Here is an example cleanbox file CASA lt 21 gt cat mycleanbox txt IPython system call cat mycleanbox txt 1 108 108 148 148 2 160 160 180 180 NOTE In future patches we will include options for the specification of circular and polygonal regions in the cleanbox file as well as the use of world coordinates not just pixel and control of plane ranges for the boxes For now use the mask mechanism for more complicated CLEAN regions 5 3 6 3 Using clean mask images You can give the mask parameter a string contain
476. ng with this data and again we will flag the edge channels non interactively later for consistency Normally if there were obviously bad data you would flag it here before calibration To do this hit the Mark Region button then draw a box around some of the moderately high outliers and then Flag But this data is relatively clean and flagging will not improve results Interactive plotxy plotxy vis ngc4826 tutorial ms xaxis velocity yaxis amp field 2 spw 12715 averagemode vector timebin 1le7 crossscans True selectplot True newplot False title Field 2 SPW 12715 print You could Mark Region around outliers and Flag Pause script if you are running in scriptmode user_check raw_input Return to continue script n You could set up a Python loop to do all the N4826 fields like this APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 460 for fld in range 2 9 field str fld plotxy vis ngc4826 tutorial ms xaxis velocity yaxis amp field field spw spw averagemode vector timebin 1e7 crossscans True selectplot True newplot False title Field field SPW spw print Nominally Mark Region around outliers and Flag Pause script if you are running in scriptmode user_check raw_input Return to continue script n Back to first field You can also ha
477. ngc4826 tutorial 1310 323 11 15 ms ngc4826 tutorial 1310 323 11 16 ms gt ngc4826 tutorial ngc4826 11 5 ms gt ngc4826 tutorial ngc4826 11 6 ms gt ngc4826 tutorial ngc4826 11 7 ms ngc4826 tutorial ngc4826 11 8 ms concatvis ngc4826 tutorial ms freqtol dirtol larcsec async False concat HEHHHHHEEHERHEAHHATHA THREE REA RODAR ORAR ARREARS RAHA EHR RRR RRR Fix up the MS This ensures that the rest freq will be found for all spws NOTE STILL NECESSARY IN 2 4 print Fixing up spw rest frequencies in MS vis ngc4826 tutorial ms tb open vist SOURCE nomodify false spwid tb getcol SPECTRAL_WINDOW_ID spwid setfield 1 int Had to do this for 64bit systems 08 Jul 2008 spwid setfield 1 int32 tb putcol SPECTRAL_WINDOW_ID spwid tb close HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHEHHHEE HEHEHE HHH AER HRE R A 16 APR Calibration 457 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 458 HHEFHHHHHEHHAEHHHEEHHEHEHHEHHEHEEHEHHHAHEHEHRHEHHEHREE HAH PARAR RARA ROH RERR AHHH AHR REE List contents of MS print Listobs listobs vis ngc4826 tutorial ms Should see the listing included at the end of this script print There are 3 fields observed in a total of 16 spectral windows print field 0 3c273 spwids 0 1 2 3 64 chans print field 1 1310 323 spwids 4 5 6
478. nimsize cell clncell NOTE will eventually have an imadvise task to give you this information Standard gain factor 0 1 gain 0 1 Fix maximum number of iterations and threshold niter clniter threshold clnthreshold Note we can change niter and threshold interactively during clean Set up the weighting Use Briggs weighting a moderate value on the uniform side weighting briggs robust 0 5 No clean mask or box mask Use interactive clean mode interactive True Moderate number of iter per interactive cycle npercycle 100 saveinputs clean imagename clean saved clean When the interactive clean window comes up use the right mouse to draw rectangles around obvious emission double right clicking inside them to add to the flag region You can also assign the right mouse to polygon region drawing by right clicking on the polygon drawing icon in the toolbar When you are happy with the region click Done Flagging and it will go and clean another HH 4 H OF 441 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 442 100 iterations When done click Stop print Final clean model is clnmodeli print Final restored clean image is clnimagel print The clean residual image is clnresid1 print Your final clean mask is clnmask1i print This is the final restored clean image in the viewer print Zoom in and set levels to see faint
479. nnels 21 23 psfmode method of PSF calculation to use during minor cycles default clark Options clark hogbom gt clark use smaller beam faster usually good enough hogbom full width of image slower better for poor uv coverage Note psfmode will be used to clean is imagermode imagermode Advanced imaging e g mosaic or Cotton Schwab clean default imagermode Options csclean mosaic default gt psfmode cleaning algorithm used amp gt amp gt amp gt imagermode mosaic expandable parameter s Image as a mosaic of the different pointings uses csclean style too mosweight Individually weight the fields of the mosaic default False example mosweight True This can be useful if some of your fields are more sensitive than others i e due to time spent on source this parameter will give more weight to higher sensitivity fields in the overlap regions ftmachine Gridding method for the image Options ft standard interferometric gridding sd standard single dish both ft and sd as appropriate mosaic gridding use PB as convolution function APPENDIX H APPENDIX WRITING TASKS IN CASA 494 default mosaic example ftmachine ft scaletype Controls scaling of pixels in the image plane Not fully implemented for now only controls what is seen if interactive True but in the future will control the image on which clean components a
480. no cleanbox interactive version currently available You have to run clean with cleanbox interactive to generate a mask graphically 5 7 Transforming an Image Model ft The ft task will Fourier transform an image and insert the resulting model into the MODEL_DATA column of a Measure Inside the Toolkit ment Set You can also convert a CLEAN component list The im t method does what the ft to a model and insert that into the MODEL_DATA column task does Its main use is setting The MS MODEL_DATA column is used for example to hold he MODEL DATA column in the MS so the model for calibration purposes in the tasks and toolkit that the cb tool can use it for subse This is especially useful if you have a resolved calibrator quent calibration and you want to start with a model of the source before you derive accurate gain solutions This is also helpful for self calibration see 5 9 below The inputs for ft are vis 22 Name of input visibility file fieldid e O Field index identifier field aed Field name list model e ae Name of input model image complist xa Name of component list incremental False Add to the existing MODEL_DATA column An example of how to do this ft vis n75 ms Start with the visibility dataset n75 ms field 1328 Select field name 1328 307 minimum match model 1328 model image Name of the model image you have already This task wi
481. nt mydict flux 5 4 D 4 1 Saving and Reading Dictionaries To save a simple dictionary to a file CASA lt 13 gt dictfile open mydictfile py w CASA lt 14 gt print gt gt dictfile mydict mydict CASA lt 15 gt dictfile close CASA lt 16 gt cat mydictfile py APPENDIX D APPENDIX PYTHON AND CASA 371 IPython system call cat mydictfile py mydict source 0137 331 flux 5 4000000000000004 CASA lt 17 gt mydict CASA lt 18 gt run mydictfile py CASA lt 19 gt mydict Out 19 flux 5 4000000000000004 source 0137 331 More complex dictionaries like those produced by imstat that contain NumPy arrays require a different approach to save The pickle module lets you save general data structures from Python For example CASA lt 20 gt import pickle CASA lt 21 gt xstat Out 21 blc array 0 0 0 0 blcf 15 24 08 404 04 31 59 181 I 1 41281e 09Hz flux array 4 0795296 max array 0 05235516 maxpos array 134 134 0 381 maxposf 15 21 53 976 05 05 29 998 I 1 41374e 09Hz mean array 1 60097857e 05 gt medabsdevmed array 0 00127436 median array 1 17422514e 05 min array 0 0104834 minpos array 160 dis 0 307 gt minposf 15 21 27 899 04 32 14 923 I 1 41354e 09Hz npts array 3014656 gt quartile array 0 00254881 yms
482. nt to draw into For example subplot 212 would draw into the lower of two panels stacked vertically in the figure An example use of subplot capability is shown in Fig 3 3 These were drawn with the commands for the top bottom left and bottom right panels respectively plotxy n5921 ms channel plot channels for the n5921 ms data set field 0 plot only first field datacolumn corrected plot corrected data plotcolor over ride default plot color plotsymbol go subplot 211 plotxy n5921 ms x field 0 datacolumn corrected subplot 223 plotcolor plotsymbol r plotxy n5921 ms u v field 0 datacolumn corrected subplot 224 plotcolor plotsymbol b use green circles plot to the top of two panels plot antennas for n5921 ms data set plot only first field plot corrected data plot to 3rd panel lower left in 2x2 grid over ride default plot color red dots plot uv coverage for n5921 ms data set plot only first field plot corrected data plot to the lower right in a 2x2 grid over ride default plot color blue somewhat larger dots NOTE You can change the gridding and panel size by manipulating the ny x nx grid HHH HH H OF See also 3 4 3 1 above and Figure 3 2 for an example of channel averaging using iteration and subplot CHAPTER 3 DATA EXAMINATION
483. nterpolate an existing table onto a new time grid accum vis n4826_16apr ms tablein accumtime 20 0 incrtable n4826_16apr gcal caltable n4826_16apr 20s gcal interp linear spwmap 0 1 1 1 1 1 plotcal n4826_16apr gcal phase antenna 1 subplot 211 plotcal n4826_16apr 20s gcal phase antenna 1 subplot 212 See Figure 4 7 for the plotcal results The data used in this example is BIMA data single polar ization YY where the calibrators were observed in single continuum spectral windows spw 0 1 and the target NGC4826 was observed in 64 channel line windows spw 2 3 4 5 Thus it is necessary to use spwmap 0 1 1 1 1 1 to map the bandpass calibrator in spw 0 onto itself and the phase calibrator in spw 1 onto the target source in spw 2 3 4 5 4 5 4 2 Incremental Calibration using accum It is occasionally desirable to solve for and apply calibration incrementally This is the case when a calibration table of a certain type already exists from a previous solve a solution of the same CHAPTER 4 SYNTHESIS CALIBRATION 172 hd CASA Plotter Mark Regon Pay vas tocate out D0 0 Bla Figure 4 7 The phase of gain solutions for NGC4826 before top and after bottom linear interpolation onto a 20 sec accumtime grid The first scan was 3C273 in spw 0 while the calibrator scans on 1331 3
484. nts and to concatenate multiple datasets These are e importuvfits import visibility data in UVFITS format e importvla import data from VLA that is in export format e importasdm import data in ALMA ASDM format e exportuvfits export a CASA MS in UVFITS format 8 e listobs summarize the contents of a MS e concat concatenate two or more MS into a new MS 8 e vishead list and change the metadata contents of a MS In CASA there is a standard syntax for selection of data that is employed by multiple tasks This is described in 2 6 There are also tasks for the import and export of image data using FITS e importfits import a FITS image into a CASA image format table 6 11 e exportfits export a CASA image table as FITS 6 11 75 CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 76 2 1 CASA Measurement Sets Data is handled in CASA via the table system In particular visibility data are stored ina CASA table known as a Measurement Set MS Details of the physical and logical MS structure are given below but for our purposes here an MS is just a construct that contains the data An MS can also store single dish data essentially a set of auto correlations of a 1 element interferometer though there are also data formats more suitable for single dish spectra see A Note that images are handled through special image tables although standard FITS I O is also su
485. o catch this value you need to assign it to a Python variable Using the functional call method myvalue imhead ngc5921 clean image mode get hditem beam Using globals default imhead imagename ngc5921 clean image mode get hditem beam myvalue imhead See for more on return values BETA ALERT This has changed in Patch 2 0 In previous versions hdvalue was an output variable for mode get The mode put allows the user to replace the current value for a given keyword hditem with that specified in hdvalue There are two sub parameters that are opened by this option mode put imhead options get put summary and list hditem r Header item to get or set hdvalue gt Value to set Header Item hditem to WARNING Be careful when using mode put This task does no checking on whether the values you specify e g for the axes types are valid and you can render your image invalid Make sure you know what you are doing when using this option CHAPTER 6 2 1 Ex 6 IMAGE ANALYSIS amples for imhead For example CASA lt 1 gt imhead ngc5921 usecase clean image summary Summary inf ormation is listed in logger prints in the logger Opened image ngc5921 usecase clean image Image name Object name Image type Image quant Pixel mask Region s Image units Restoring B Direction r Spectral r Velocity t
486. o the data in the DATA column of the input MS and it writes the Hanning smoothed data into the CORRECTED DATA column of that same MS Hanning smoothing replaces the contents of channel with a weighted sum of the contents of a number of channels surrounding channel i In its current form only channels i 1 i and i 1 participate with weights 0 25 0 50 and 0 25 respectively but we intend to extend the kernel size in future releases A typical use for Hanning smoothing is to remove Gibbs ringing The inputs are hanningsmooth Hanning smooth frequency channel data vis ngc5921 split ms Name of input visibility file MS async False In many cases the data to be smoothed are in the CORRECTED_DATA column of the MS in that case run split first to copy the contents of the CORRECTED_DATA column of the input MS to the DATA column of the output MS Then run hanningsmooth on the newly created MS CHAPTER 4 SYNTHESIS CALIBRATION 181 After hanning smoothing the contents of the first and last channel of each visibility are undefined hanningsmooth will therefore flag the first and last channel BETA ALERT We intend to make the kernel size a user supplied parameter In the longer term we intend to offer other varieties of spectral smoothing as well 4 7 3 Model subtraction from uv data uvsub The uvsub task will subtract the value in the MODEL column from that in the CORRECTED_DATA column in the input MS and store the result in t
487. of synthesis data the resulting image or image cube must be displayed or analyzed in order to extract quantitative infor mation such as statistics or moment images In addition there need to be facilities for the coordinate conversion of images for direct comparison We have assembled a skele ton of image analysis tasks for this release Many more are still under development The image analysis tasks are Inside the Toolkit Image analysis is handled in the ia tool Many options exist there in cluding region statistics and image math See 6 12 below for more in formation e imhead summarize and manipulate the header information in a CASA image 6 2 e imcontsub perform continuum subtraction on a spectral line image cube 6 3 e imfit image plane Gaussian component fitting 6 4 e immath perform mathematical operations on or between images 6 5 e immoments compute the moments of an image cube e imstat calculate statistics on an image or part of an image 6 7 e imval extract the data and mask values from a pixel or region of an image e imregrid regrid an image onto the coordinate system of another image e imsmooth smooth images in the spectral and angular directions 6 10 e importfits import a FITS image into a CASA image format table 6 11 2 e exportfits write out an image in FITS format 6 11 1 There are othe
488. of baseline specifications A baseline specification is of the form e ANT1 Select all baselines including the antenna s specified by the selector ANT1 e ANT1 amp Select only baselines between the antennas specified by the selector ANT1 gt ANT1 amp ANT2 Select only the cross correlation baselines between the antennas specified by selector ANT1 and antennas specified by selector ANT2 Thus ANT1 is an abbreviation for ANT1 amp ANT1 ANT1 amp amp ANT2 Select only auto correlation and cross correlation baselines between anten nas specified by the selectors ANT1 and ANT2 Note that this is what the default antenna gives you gt ANT1 amp amp amp Select only autocorrelations specified by the selector ANT1 The selectors ANT1 and ANT2 are comma separated lists of antenna integer IDs or literal antenna names patterns or regular expressions The ANT strings are parsed and converted to a list of antenna integer IDs or IDs of antennas whose name match the given names pattern regular ex pression Baselines corresponding to all combinations of the elements in lists on either side of ampersand are selected CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 97 Integer IDs can be specified as single values or a range of integers When items of the list are parsed as literal strings or regular expressions or patterns see for more details on strings All antenna names that ma
489. om or psfmode clarkstokes 5 3 1 3 will clean search for components each plane sequentially 5 3 1 1 while psfmode clark 8 will deconvolve jointly The interactive clean example given above 8 5 3 13 shows a case of polarization imaging You can also find the script for this example in Appendix F 2 CHAPTER 5 SYNTHESIS IMAGING 218 5 4 Wide field imaging and deconvolution widefield When imaging sufficiently large angular regions the sky can no longer be treated as a two dimensional plane and the use of the standard clean task will produce distortions around sources that become increasingly severe with increasing distance from the phase center In this case one must use a wide field imaging algorithm such as w projection or faceting When is wide field imaging needed It depends on the expected dynamic range the image In order to keep the phase error associated with the sky array curvature less than about 5 good to about 500 1 dynamic range use the following table suitably scaled for guidance Maximum Radius of Image Before widefield is Needed Assuming 5 deg phase error and 35 km Baseline Wavelength Radius of image 6 cm 1 4 arcmin 20 cm 2 6 arcmin 90 cm 5 3 arcmin Radius of image SQRT Wavelength phase error Maximum baseline arcmin cm deg km If a relatively small image is being made but there are outliers sources beyond the above limits then widefield should also be u
490. ombine scan Data axes which to combine for solve scan spw and or field refant 9 Reference antenna name minblperant 4 Minimum baselines _per antenna_ required for solve solnorm False Normalize average solution amplitudes to 1 0 bandtype 7B Type of bandpass solution B or BPOLY fillgaps O Fill flagged solution channels by interpolation append SS False Append solutions to the existing table gaintable Gain calibration table s to apply on the fly gainfield Select a subset of calibrators from gaintable s interp Interpolation mode in time to use for each gaintable spwmap Spectral windows combinations to form for gaintables s gaincurve False Apply internal VLA antenna gain curve correction opacity 0 0 Opacity correction to apply nepers parang False Apply parallactic angle correction async False if True run in the background prompt is freed Many of these parameters are in common with the other calibration tasks and are described above in The bandtype parameter selects the type of solution used for the bandpass The choices are B and BPOLY The former solves for a complex gain in each channel in the selected part of the MS See for more on B The latter uses a polynomial as a function of channel to fit the bandpass and expands further to reveal a number of sub parameters See 4 4 2 3 for more on gt BPOLY It is usually best to solve
491. ompt where lt taskname gt is the name of a given task As described above in 1 2 8 2 help lt taskname gt provides a description of the task and then lists all parameters a brief description of the parameter the parameter default an example setting the parameter and any options if there are limited allowed values for the parameter To see what tasks are available in CASA use tasklist e g CASA lt 4 gt tasklist Available tasks Import Export Information Data Editing Display Plot importvla listcal flagautocorr clearplot importasdm listhistory flagdata plotants importfits listobs flagmanager plotcal importuvfits listvis plotxy plotxy exportfits imhead viewer exportuvfits imstat vishead Calibration Imaging Modelling Utility accum clean setjy help task applycal deconvolve uvcontsub help par parameter bandpass feather uvmodelfit taskhelp blcal ft tasklist gaincal invert browsetable fluxscale makemask clearplot fringecal mosaic clearstat clearcal concat listcal filecatalog smoothcal startup polcal split hanningsmooth fixvis Image Analysis Simulation Single Dish imcontsub simdata sdaverage CHAPTER 1 imhead immath immoments imregrid imstat imval specfit INTRODUCTION 40 sdbaseline sdcal sdcoadd sdfit sd lag sdlist sdplot sdsave sdscale sdsmooth sdstat The tasks with name in parentheses are experimental Typing taskhelp provides a one line description of all available tasks CASA lt
492. on solutions derived from one or more sources 4 5 3 e split Write out new MS containing calibrated data from a subset of the original MS GETI There are some development versions of calibration and utility tasks that are recently added to the Beta Release suite e hanningsmooth apply a Hanning smoothing filter to spectral line uv data 14 7 2 e uvcontsub uv plane continuum fitting and subtraction 4 7 4 e uvsub subtract the transform of a model image from the uv data 14 7 3 These are not yet full featured and may have only rudimentary controls and options Finally there are also more advanced and experimental calibration tasks available in this release e blcal baseline based gain or bandpass calibration supports pre apply of other calibrations 3 e fringecal Experimental baseline based fringe fitting calibration solving supports pre apply of other calibrations 4 4 7 e uvmodelfit fit a component source model to the uv data 8 4 7 5 The following sections outline the use of these tasks in standard calibration processes Information on other useful tasks and parameter setting can be found in e listobs list what is in a MS 2 3 e plotxy X Y plotting and editing 8 4 e flagdata non interactive data flagging 3 5 e data selection general data selection syntax 2 6 4 2 The Calibration Process Outline and Philosophy A work f
493. on techniques include single dish information in the imaging process and to prepare to use the results of imaging for improvement of the calibration process sel calibration 5 1 Imaging Tasks Overview The current imaging and deconvolution tasks are e clean calculate a deconvolved image with a selected clean algorithm including mosaicing or make a dirty image 5 3 e feather combine a single dish and synthesis image in the Fourier plane 5 5 e deconvolve image plane only deconvolution based on the dirty image and beam using one of several algorithms 5 8 e widefield a prototype task to create and deconvolve a wide field image using w projection and or faceting There are also tasks that help you set up the imaging or interface imaging with calibration e makemask create cleanbox deconvolution regions 5 6 188 CHAPTER 5 SYNTHESIS IMAGING 189 e ft Fourier transform the specified model or component list and insert the source model into the MODEL column of a visibility set 5 7 The full tool kit that allows expert level imaging must still be used if you do not find enough functionality within the tasks above Information on other useful tasks and parameter setting can be found in e listobs list whats in a MS 2 3 e split Write out new MS containing calibrated data from a subset of the original MS section cal split e data sel
494. ond one may call tasks and tools by name with parameters set on the same line Parameters may be set either as explicit lt parameter gt lt value gt arguments or as a series of comma delimited lt value gt s in the correct order for that task or tool Note that missing parameters will use the default values for that task For example the following are equivalent Specify parameter names for each keyword input plotxy vis ngc5921 ms xaxis channel yaxis amp datacolumn data when specifying the parameter name order doesn t matter e g plotxy xaxis channel vis ngc5921 ms datacolumn data yaxis amp use parameter order for invoking tasks plotxy ngc5921 ms channel amp data This non use of globals when calling as a function is so that robust scripts can be written One need only cut and paste the calls and need not worry about the state of the global variables or what has been run previously It is also more like the standard behavior of function calls in Python and other languages Tools can only be called in this second manner by name with arguments 1 3 6 Tools never use the global parameters and the related mechanisms of inp and go CHAPTER 1 INTRODUCTION 44 1 3 2 1 Aborting Synchronous Tasks If you are running CASA tasks synchronously then you can usually use CNTL C to abort execution of the task If this does not work try CNTL Z foll
495. onfusion Unregister or close the others At the bottom of the Display Panel is the Position Tracking panel As the mouse moves over the main display this panel shows information such as flux density position e g RA and Dec Stokes CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 263 and frequency or velocity for the point currently under the cursor Each registered image MS displays its own tracking information Tracking can be frozen and unfrozen again with the space bar Click on the main display area first to be sure the keyboard is focused there The Animator or Tracking panels can be hidden or detached and later re attached by using the boxes at upper right of the panels this is useful for increasing the size of the display area Use the View menu to show a hidden panel again The individual tracking areas one for each registered image can be hidden using the checkbox at upper left of each area 7 2 2 Saving and Restoring Display Panel State It is straightforward to save a display panel s current state what data is on display along with data and panel settings Select Save the unadorned floppy toolbutton and confirm the filename It is usually advisable but not required to retain the file s rstr extension Press Restore the button to the right of Save to choose a previously created restore file You can also select restore files from the Load Data window It is possible to res
496. ons gain 0 1 Loop gain for cleaning threshold 0 OmJy Flux level to stop cleaning Must include units psfmode clark method of PSF calculation to use during minor cycles imagermode 7 Use csclean or mosaic If use psfmode multiscale 4 set deconvolution scales pixels default multiscale standard CLEAN interactive 3 False use interactive clean with GUI viewer mask cleanbox es mask image s and or region s used in cleaning imsize 256 256 x and y image size in pixels symmetric for single value cell 1 0arcsec arcsec x and y cell size default unit arcsec phasecenter gi Image phase center position or field index restfreq rest frequency to assign to image see help stokes cr Stokes params to image eg I IV QU IQUY weighting natural Weighting of uv natural uniform briggs uvtaper False Apply additional uv tapering of visibilities modelimage ay Name of model image s to initialize cleaning restoringbeam Eta Dutput Gaussian restoring beam for CLEAN image pbcor False Qutput primary beam corrected image minpb 0 1 Minimum PB level to use async False If true the taskname must be started using clean casa lt 4 gt E Figure 1 1 Screen shot of the default CASA inputs for task clean Text Font Text Color Highlight Indentation Meaning Parameters plain black none none stan
497. ons medabsdevmed 53 7114 2009 05 27 04 48 05 INFO Quartile quartile 107 913 2009 05 27 04 48 05 INFO 2009 05 27 04 48 05 INFO H44H Bnd Task imstat HHHH 2009 05 27 04 48 05 INFO 2009 05 27 04 48 05 INFO 2009 05 27 04 48 05 INFO HEEE HE EHE BE EHE HEHEHE EHHE HE E HE HEHEHE EEHEHE HEHHEE HEHEHE EEHEEHE EEEH HEHEHE HEHEHEHE HEBE HE HEEE BE EHE HH HE HEHEHE HE H HH PE EHE PEE HE HEHH BE E HE HE B HE HEBE HE EHHE EEHEEHE HEHE 2009 05 27 04 48 05 INFO HHH Begin Task viewer HHHHH 2009 05 27 04 48 05 INFO 2009 05 27 04 48 05 INFO a 2009 05 27 04 48 05 INFO a HHHH End Task viewer ane a Tue May 26 23 01 0 NOTS snyers STM test of demo script 4 py insert Message J E e JE tock scron Figure 1 7 CASA Logger Insert facility The log output can be augmented by adding notes or comments during the reduction The file should then be saved to disk to retain these changes casapy lt logger option gt These options are log2term logging message go to terminal nologfile no casapy log logfile is produced logfile lt filename gt use specified name for logfile instead of casapy log nologger do not bring up GUI logger see above nolog is deprecated use nologger For example to not bring up a GUI but send the message to your terminal do casapy nologger log2term while casapy logfile mynewlogfile log will start casapy with logger mes
498. ons_hc3n asap We will write it out in ASAP scantable format outform asap You can look at the inputs with inp Before running lets save the inputs in case we want to come back and re run the calibration saveinputs sdcal sdcal orions save These can be recovered by execfile sdcal orions save We are ready to calibrate sdcal Note that after the task ran it produced a file sdcal last which contains the inputs from the last run of the task all tasks do this You can recover this anytime before sdcal is run again with execfile sdcal last HHEHHHHHHHHHHHHEHHHHHHHHH HS List data HHHHHHHHHHHHHHHHHHHHHHHH HS List the contents of the calibrated dataset Set the input to the just created file sdfile outfile 332 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING listfile sdlist You should see eae a ae Sii a a ee a a Si is Scan Table Summary A EN ca a EEE a Se a a a a NN at a EEEE EEE a a a a le Beams 1 tlFs 26 Polarisations 1 linear Channels 8192 Observer Joseph McMullin 0bs Date 2006 01 19 01 45 58 Project AGBTO6A_018_01 0bs Type OffOn PSWITCHOFF TPWCAL Antenna Name GBT Flux Unit K Rest Freqs 4 5490258e 10 Hz Abcissa Channel Selection none Scan Source Time Integration Beam Position J2000 IF Frame RefVal RefPix Increment eee oleae a a A E E a ee ee a
499. ontains just one spectrum for each beam IF and polarization Once you have a scantable in ASAP you can select a subset of the data based on scan numbers sources or types of scan note that each of these selections returns a new scantable with all of the underlying functionality CASA lt 5 gt CASA lt 6 gt CASA lt 7 gt CASA lt 8 gt scan27 scans get_scan 27 scans20to24 scans get_scan range 20 25 scans_on scans get_scan _ps scansOrion scans get_scan Ori To copy a scantable do CASA lt 15 gt ss scans copy A 3 3 1 Data Selection Get the 27th scan Get scans 20 24 Get ps scans on source Get all Orion scans In addition to the basic data selection above data can be selected based on IF beam polarization scan number as well as values such as Tsys To make a selection you create a selector object which you then define with various selection functions e g APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 346 sel sd selector initialize a selector object sel lt TAB gt will list all options sel set_ifs 0 select only the first IF of the data scans set_selection sel apply the selection to the data print scans shows just the first IF A 3 3 2 State Information Some properties of a scantable apply to all of the data such as example spectral units frequency frame or Doppler type This information can be set using the scantable _set_xxxx_ methods
500. ookbook is also a living document You can expect this document as well as other on line and in line user support guides to be updated regularly Also feel free to send us comments and suggestions on the contents of our documentation Please check the CASA Home page http casa nrao edu regularly to look for updates to the release and to the documentation and to check the list of known problems You can find the contact information for feedback here also We also note here that we are also in the process of commissioning our User Support system for CASA Thus we can only support a limited number of official Beta Release Users at this time See the CASA Home Page for more information on the policies and conditions on obtaining and getting support for this Beta Release CHAPTER 1 INTRODUCTION 23 1 1 1 What s New in Beta Patch 4 This Cookbook is for CASA Beta Release Patch 4 version Versions 2 4 0 This patch differs from previous versions of CASA in a number of ways e New interface changes The AIPSPATH environment variable is now the CASAPATH variable If you type help task without quotes around the task name you will get two copies of the help with alot of extraneous stuff This is a bug introduced in 2 4 0 and will be fixed in later releases e New data handling features A number of importvla improvements were made 1 In previous releases importvla did not provide a valid DOPPLER subtable This has been
501. ooking In CASA the opacity correction described here compensates only for the first of these effects tropospheric attenuation using a plane parallel approximation for the troposphere to estimate the elevation dependence Opacity corrections are a component of calibration type T To make opacity corrections in CASA an estimate of the zenith opacity is required see observatory specific chapters for how to measure zenith opacity This is then supplied to the opacity parameter in the calibration tasks BETA ALERT The opacity parameter must be supplied to any calibration task that allows pre application of the prior calibration e g bandpass gaincal applycal This should be done consistently through the calibration process In future updates we will likely move to a separate task to calibrate the atmospheric optical depth For example if the zenith optical depth is 0 1 nepers then use the following parameters gaincal data ms cal GO solint 0 refant 11 opacity 0 1 The calibration task in this example will apply an elevation dependent opacity correction scaled to 0 1 nepers at the zenith for all antennas for this example calculated at each scan solint 0 Set solint 1 instead to get a solution every timestamp BETA ALERT Currently you can only supply a single value of opacity which will then be pre applied to whatever calibration task that you set it in Generalizations to antenna and time dependent opacities i
502. options bool True False default False example invertmask True then will make one region that is the exclusion of the maskline regions nfit list of number of gaussian lines to fit in in maskline region default O no fitting example nfit 1 for single line in single region nfit 2 for two lines in single region nfit 1 1 for single lines in each of two regions etc fitfile name of output file for fit results default no output fit file example mysd fit overwrite overwrite the fitfile if already exists options bool True False default False plotlevel control for plotting of results options int O none 1 some 2 more default O no plotting example plotlevel 1 plots fit plotlevel 2 plots fit and residual APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 312 no hardcopy available for fitter WARNING be careful plotting OTF data with lots of fields Returns a Python dictionary of line statistics keys gt peak cent fwhm nfit example each value is a list of lists with one list of 2 entries fitvalue error per component e g xstat peak 234 9 4 8 234 2 5 3 for 2 components DESCRIPTION Task sdfit is a basic line fitter for single dish spectra It assumes that the spectra have been calibrated in sdaverage or sdcal Furthermore it assumes that any selection of scans IFs polarizations and time and channel averaging smoothing has also already been done i
503. or names default all fields If field string is a non negative integer it is assumed to be a field index otherwise it is assumed to be a field name field 0 2 field ids 0 1 2 field 0 4 5 7 field ids 0 4 5 6 7 field 3C286 3C295 field named 3C286 and 3C295 field 3 4Cx field id 3 all names starting with 4C spw Select spectral window channels NOTE This selects the data passed as the INPUT to mode default all spectral windows and channels spw 072 4 spectral windows 0 1 2 4 all channels spw 0 5 61 spw 0 channels 5 to 61 spw amp 1t 2 spectral windows less than 2 i e 0 1 spw 0 10 3 3 45 spw 0 10 all channels spw 3 channels 3 to 45 spw 0 2 2 6 spw 0 1 2 with channels 2 through 6 in each spw 0 0710 15 60 spectral window 0 with channels 0 10 15 60 spw 0 0710 1 20 30 2 1 2 3 spw 0 channels 0 10 spw 1 channels 20 30 and spw 2 channels 1 2 and 3 selectdata Other data selection parameters default True amp gt amp gt amp gt selectdata True expandable parameters See help par selectdata for more on these timerange Select data based on time range default all examples timerange gt YYYY MM DD hh mm ss YYYY MM DD hh mm ss Note if YYYY MM DD is missing date defaults to first day in data set timerange 09 14 0709 54 0 picks 40 min on first day timerange 25 00 00727 30 00 picks 1 hr to 3 hr 30min on N
504. ore imaging 5 2 13 Primary beams in imaging The CASA imaging task and tools use primary beams based on models for each observatory s antenna types In addition to different antenna diameters different functions may be used The voltage patterns are based on the following antenna primary beams based on the TELESCOPE _NAME keyword in the OBSERVATION table CHAPTER 5 SYNTHESIS IMAGING 199 VLA Airy disk fitted to measurement Note that a R L beam squint is also included with feed dependent angle ALMA Airy disk for 12m dish with a blockage of 1m ATA Airy disk for 6m dish ATCA polynomial fitted to measurement of main lobe BIMA HATCREEK Gaussian with halfwidth of A 2D CARMA Airy patterns for the BIMA or OVRO dish sizes as appropriate GBT polynomial fitted to measurement of main lobe GMRT VLA Airy disk scaled to 45 0m IRAMPDB Airy disk for dish of 15m with a blockage of 1m NRAO12M VLA beam scaled to 12m OVRO VLA Airy disk scaled to 10 4m SMA Spheroidal function fit to FWHM WSRT polynomial fitted to measurement of main lobe If the telescope name is unknown or is CARMA or ALMA then the DISH_DIAMETER in the ANTENNA table is used with a scaled VLA pattern Note that for the purposes of mosaicing in clean the primary beams that are Airy or spheroidal are best behaved see 8 5 3 14 5 3 Deconvolution using CLEAN clean To create an image and then deconvolve it w
505. ote that the end result is we ve flagged lots of points in RR and LL We will rely upon imager to ignore the RL LR for points with RR LL flagged 3 5 Non Interactive Flagging using flagdata Task flagdata will flag the visibility data set based on the specified data selections most of the information coming from a run of the listobs task with without verbose True Currently you can select based on any combination of e antennas antenna e baselines antenna e spectral windows and channels spw e correlation types correlation e field ids or names field e uv ranges uvrange e times timerange or scan numbers scan CHAPTER 3 DATA EXAMINATION AND EDITING 122 e antenna arrays array and choose to flag unflag clip setclip and sub parameters and remove the first part of each scan setquack and or the autocorrelations autocorr The inputs to flagdata are flagdata Flag Clip data based on selections vis r2 Name of input visibility file mode manualflag Mode manualflag quack shadow autoflag summary autocorr e False Flag autocorrelations unflag False Unflag the data specified clipexpr ABS RR Expression to clip on clipminmax Range to use for clipping clipcolumn DATA Data column to use for clipping clipoutside True Clip outside the range or within it spw gt spectral window frequency channel field 1 Field names or field index numbers
506. ototalpower fitter interactivemask is_ipython linecatalog linefinder list_files sd sd list_scans sd sd sd sd sd sd sd sd sd sd sd sd mask_and mask_not mask_or merge os plf plotter print_log quotient rc rcParams rcParamsDefault rc_params sd sd sd sd sd sd sd sd sd sd sd rcdefaults reader revinfo scantable selector simple_math sys unique version welcome xyplotter In particular the following are essential for most reduction sessions e sd scantable the data structure for ASAP and the core methods for manipulating the data allows importing data making data selections basic operations averaging baselines etc and setting data characteristics e g frequencies etc e sd selector selects a subset of data for subsequent operations e sd fitter fit data APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 342 e sd plotter plotting facilities uses matplotlib The scantable functions are used most often and can be applied to both the initial scantable and to any spectrum from that scan table Type sd scantable lt TAB gt using TAB completion to see the full list A 3 1 Environment Variables The asapre environment variables are stored in the Python dictionary sd rcParams in CASA This contains a number of parameters that control how ASAP runs for both tools and tasks You can see what these are set to by typing at the CASA prompt CAS
507. owed by a kill See for more on these methods to abort CASA execution You may have to quit and restart CASA after an abort as the internal state can get mixed up 1 3 3 Getting Return Values Some tasks and tools return a record usually a Python dictionary to the interface For example the imstat task 6 7 returns a dictionary with the image statistics in it To catch these return values into a Python variable you MUST assign that variable to the task call e g xstat imstat ngc5921 clean image or default imstat imagename ngc5921 clean image xstat imstat Note that tools that return values work in the same way 1 3 6 You can print or use the return value in Python for controlling scripts For example CASA lt 1 gt xstat imstat ngc5921 clean image CASA lt 2 gt xstat Out 2 blc array 0 0 0 0 plcf 15 24 08 404 04 31 59 181 I 1 41281e 09Hz flux array 4 15292207 max array 0 05240594 maxpos array 134 134 0 381 gt maxposf 15 21 53 976 05 05 29 998 I 1 41374e 09Hz mean array 1 62978083e 05 gt medabsdevmed array 0 00127287 gt median array 1 10467618e 05 min array 0 0105249 minpos array 160 1 0 301 minposf 15 21 27 899 04 32 14 923 I 1 41354e 09Hz npts array 3014656 gt quartile array 0 00254587 rms array 0 00201818
508. ower cycles e Basic settings Colormap You can select from a variety of colormaps here Hot Metal Rainbow and Greyscale col ormaps are the ones most commonly used 7 3 1 2 Raster Image Other Settings Many of the other settings on the Data Options panel for raster images are self explanatory such as those which affect Beam ellipse drawing only available if your image provides beam data or the form of the Axis labeling and Position tracking information You can also give your image a Color wedge a key to the current mapping from data values to colors You can control which of your image s axes are on the vertical and horizontal display axes and which on the animation or movie axis within the Display axes drop down You must set the X Y and Z animation axes so that each shows a different image axis in order for your choice to take effect If your image has a fourth axis typically Stokes it can be controlled by a slider within the Hidden axes drop down For negative scaling values say p the data is scaled linearly from the range dataMin dataMax to the range 1 10 Then the program takes the log base 10 of that value arriving at a number from 0 to p and scales that linearly to the number of available colors Thus the data is treated as if it had p decades of range with an equal number of colors assigned to each decade For positive scaling values the inverse exponential functions are used
509. p margin space PG chars Number of panels in x Number of panels iny ax X Spacing of Panels alo O O 165 olo mc Res Y Spacing of Panels a aa o Compact Blink Frame End 4 Basic Settings Background Color black pl XX ngc5921 demo clean image 0 00358195 Jy beam Pixel 81 119 0 22 15 22 47 684 05 01 41 878 I 1494 63 km s Apply Figure 7 14 A multi panel display set up through the Viewer Canvas Manager 7 3 6 2 Background Color The Background Color selection can be used to change the background color from its default of black Currently the only other choice is white which is more appropriate for printing or inclusion in documents 7 4 Viewing Measurement Sets Visibility data can also be displayed and flagged directly from the viewer For Measurement Set files the only option for display is Raster similar to AIPS task TVFLG An example of MS display is shown in Figure loading of an MS is shown in Figure CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 278 Load Data Viewer Directory homefimager b smyers Sep07 Display As i ngc5 921 usecase clean image Image Raster Image ngc5 92 1 usecase clean model Image ngc5921 usecase clean residual Image ngc5921 usecase ms Measurement j ngc5921 usecase ms cont Measurement ngc5921 usecase ms contsub Measurement i ngc5921 usecase ms flagversions Directory Figure 7 15 The Load Data Viewer
510. p to 8 are reasonable Most users of this method should find the default value sufficient plot plot the fit and the residual In this each individual fit has to be approved by typing y or n insitu if False a new scantable is returned Otherwise the scaling is done in situ The default is taken from asaprc False Example scans auto_poly_baseline order 2 threshold 5 A 3 8 Line Fitting Multi component Gaussian fitting is available This is done by creating a fitting object specifying fit parameters and finally fitting the data Fitting can be done on a scantable selection or an entire scantable using the auto_fit function spave is an averaged spectrum f sd fitter Q msk spave create_mask 3928 4255 f set_function gauss 1 f set_scan spave msk create fitter object create mask region around line set a single gaussian component set the scantable and region Automatically guess start values fit plot residual f fit f plot residual True HH H HO H HF OF APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 304 f get_parameters retrieve fit parameters O peak 0 786 K centre 4091 236 channel FWHM 70 586 channel area 59 473 K channel f store_fit orions_hc3n_fit txt store fit To specify initial guess set a single gaussian component set initial guesses for Gaussian for first component 0 peak center fwhm Fh set_function gauss 1 f set_gauss_paramet
511. p you take the interactive clean and how you draw the box for the stats Se Es Do some non interactive image statistics print Imstat default imstat imagename clnimagel on_statisticsl imstat Now do stats in the lower right corner of the image remember clnimsize 288 288 box 216 1 287 72 off_statistics1 imstat Pull the max and rms from the clean image thistest_immax on_statistics1 max 0 print Found Max in image thistest_immax thistest_imrms off_statistics1 rms 0 print Found rms in image thistest_imrms print Clean image Dynamic Range thistest_immax thistest_imrms print A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A A Self cal using clean model Note clean will have left FT of model in the MODEL_DATA column If you ve done something in between can use the ft task to do this manually print SelfCal 1 default gaincal vis srcsplitms print Will self cal using MODEL_DATA left in MS by clean New gain table caltable selfcaltabl print Will write gain table selfcaltabl Don t need a priori cals APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS selectdata False gaincurve False opacity 0 0 This choice seemed to work refant calrefant Do amp and phase gaintype G calmode ap Do 30s solutions with SNR gt 1
512. panel as it appears if you select an MS The only option available is to load this as a Raster Image In this example clicking on the Raster Image button would bring up the displays shown in Figure Warning Only one MS should be registered at a time on a Display Panel Only one MS can be shown in any case You do not have to close other images MSs but you should at least unregister them from the Display Panel used for viewing the MS If you wish to see other images or MSs at the same time create multiple Display Panel windows 7 4 1 Data Display Options Panel for Measurement Sets The Data Display Options panel provides adjustments for MSs similar to those for images and also includes flagging options As with images this window appears when you choose the Data Adjust menu or use the wrench icon from the Main Toolbar It is also shown by default when an MS is loaded The right panel of Figure 7 2 shows a Data Options window It has a tab for each open MS containing a set of categories The options within each category can be either rolled up or expanded by clicking the category label For a Measurement Set the categories are CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 279 e Advanced e MS and Visibility Selection e Display Axes e Flagging Options e Basic Settings e Axis Drawing and Labels e Color Wedge 7 4 1 1 MS Options Basic Settings The Basic Settings roll up is expanded by default It contains entr
513. parameter is ignored DESCRIPTION Task sdmath execute a mathematical expression for single dish spectra The spectral data file can be any of the formats supported by ASAP scantable MS rpfits and SDFITS In the expression these file names should be put inside of single or double quotes The fluxunit specunit and frame can be set otherwise the current settings of the first spectral data in the expression are used Other selections e g scan No IF Pol also apply to all the spectral data in the expression so if any of the data does not contains selection the task will produce no output Example APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 315 do on off off calculation expr orion_on_data asap orion_off_data asap orion_off_data asap outfile orion_cal asap sdmath A 2 1 10 sdplot Keyword arguments sdfile name of input SD dataset fluxunit units for line flux options K Jy default keep current fluxunit WARNING For GBT data see description below gt gt gt fluxunit expandable parameter telescopeparm the telescope characteristics options str name or list list of gain info default none set example if telescopeparm it tries to get the telescope name from the data Full antenna parameters diameter ap eff known to ASAP are gt ATPKSMB ATPKSHOH ATMOPRA DSS 43 gt CEDUNA HOBART For GBT
514. pecification for the MS is Aips MeasurementSet definition version 2 0 http casa nrao edu Memos 229 html 2 2 Data Import and Export There are a number of tasks available to bring data in various forms into CASA as a Measurement Set e UVFITS format can be imported into and exported from CASA importuvfits and exportuvfits e VLA Archive format data can be imported into CASA importvla e ALMA and EVLA Science Data Model format data can be imported into CASA importasdm 2 2 1 UVFITS Import and Export The UVFITS format is not exactly a standard but is a popular archive and transport format nonetheless CASA supports UVFITS files written by the AIPS FITTP task and others UVFITS is supported for both import and export CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 80 2 2 1 1 Import using importuvfits To import UVFITS format data into CASA use the importuvfits task CASA lt 1 gt inp importuvfits fitsfile gt Name of input UVFITS file vis gt Name of output visibility file MS antnamescheme old For VLA only new or old VA04 or 04 for VLA ant 4 async False if True run in the background prompt is freed This is straightforward since all it does is read in a UVFITS file and convert it as best it can into a MS For example importuvfits fitsfile NGC5921 fits vis ngc5921 ms BETA ALERT We cannot currently fill CARMA data exported via Mi
515. pixels to something desirable The inputs for feather are imagename a Name of output feathered image highres 22 Name of high resolution synthesis image lowres d Name of low resolution single dish image async False If true the taskname must be started using feather Note that the only inputs are for images Note that feather does not do any deconvolution but combines presumably deconvolved images after the fact Starting with a cleaned synthesis image and a low resolution image from a single dish telescope the following example shows how they can be feathered feather imagename feather im Create an image called feather im highres synth im The synthesis image is called synth im owres single_dish im The SD image is called single_dish im Note that the single dish image must have a well defined beam shape and the correct flux units for a model image Jy beam instead of Jy pixel so use the tasks imhead and immath first to convert if needed 5 6 Making Deconvolution Masks makemask For most careful imaging you will want to restrict the region over which you allow CLEAN com ponents to be found To do this you can create a deconvolution region or mask image using the makemask task This is useful if you have a complicated region over which you want to clean and it will take many clean boxes to specify The parameter inputs for makemask are makemask Derive a mas
516. plotting nd or imaging gt gt gt calmode baseline expandable parameters masklist mask in numbers of rows from each edge of each scan to be included for baseline fitting default none example 30 30 or 30 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 325 used first 30 rows and last 30 rows of each scan for the baseline blpoly polynomial order for the baseline fit default 1 flaglist list of scan numbers to flag ranges can be accepted default use all scans example 0 3 80 flag the scan range 0 3 0 1 2 3 and scan 80 antenna select data based on antenna name s or id s in string default use all antennas example 0 1 DVO1 WARNING currently baseline subtraction properly only one of the antennas stokes select data based on stokes or polarization type default use all polarizations example XX createimage do imaging default False gt gt gt createimage True expandable parameters imagename output image name default none example mySDimage im imsize x and y image size in pixels symmetric for single value default 256 256 example imsize 200 equivalent to 200 200 cell x and y cell size default unit arcmin default 1 0arcmin example cell 0 2arcmin 0 2arcmin cell 0 2arcmin equivalent to example above phasecenter image phase center direction measure or fieldid default 0 example J2000 13h4
517. plotxy task The inputs are plotxy vis xaxis yaxis datacolumn selectdata spw field averagemode timebin crossscans crossbls crossarrays stackspw width restfreq extendflag subplot plotsymbol plotcolor plotrange multicolor selectplot overplot showflags interactive figfile async BETA ALERT Table plotter interactive flagger for visibility data time amp data False 23 2 vector 20 False False False False 21 22 False 111 2 2 darkcyn 1 a corr False False False True 23 False HHHH HHH H H HH H A HHH HHH HH H OF Name of input visibility X axis def time see help for options Y axis def amp see help for options data raw corrected model residual corrected model Other data selection parameters spectral window channels gt all spw 1 5757 field names or index of calibrators gt all Select averaging type vector scalar Length of time interval in seconds to average Have time averaging cross scan boundaries have averaging cross over baselines have averaging cross over arrays stack multiple spw on top of each other Number of channels to average a frequency quanta or transition name see help for options Have flagging extend to other data points Panel number on display screen yxn Options include gt o 7v
518. pported Images and Inside the Toolkit image data are described in a separate chapter Measurement sets are handled in the ms tool Import and export methods include ms fromfits and ms tofits Unless your data was previously processed by CASA or software based upon its predecessor aips you will need to import it into CASA as an MS Supported formats in clude some standard flavors of UVFITS the VLA Ex port archive format and most recently the ALMA Science Data Model ASDM format These are described below in 2 2 Once in Measurement Set form your data can be accessed through various tools and tasks with a common interface The most important of these is the data selection interface 2 6 which allows you to specify the subset of the data on which the tasks and tools will operate 2 1 1 Under the Hood Structure of the Measurement Set It is not necessary that a casual CASA user know the spe cific details on how the data in the MS is stored and the Inside the Toolkit contents of all the sub tables However we will occasion Generic CASA tables are handled in ally refer to specific columns of the MS when describing the tb tool You have direct access the actions of various tasks and thus we provide the fol to keywords rows and columns of the lowing synopsis to familiarize the user with the necessary tables with the methods of this tool nomenclature You may skip ahead to subsequent section
519. psetTypes html xmlns xsi http www w3 org 2001 XMLSchema instance xsi schemaLocation http casa nrao edu schema casa xsd 476 APPENDIX H APPENDIX WRITING TASKS IN CASA 477 file opt casa code xmlcasa xml casa xsd gt and the file must have the end tag lt casaxml gt Inside a lt task gt tags you will need to specify the following elements lt task gt Attributes type required allowed value is function name required Subelements shortdescription required description required input optional output optional returns optional constraints optional lt shortdescription gt required by lt task gt A short one line description describing your task Attributes None Subelements None lt description gt required by lt task gt Also used by lt param gt a A longer description describing your task with multiple lines Attributes None Subelements None lt input gt optional element used by lt task gt An input block specifies which parameters are used for input Attributes None Subelements APPENDIX H APPENDIX WRITING TASKS IN CASA 478 lt param gt optional lt output gt optional An output element that contains a list of parameters that are returned by the task Attributes None Subelements lt param gt optional lt returns gt optional Value returned by the task Attributes type optional as specfied in lt param gt Subelements lt description gt optional
520. r So the recommended procedure is as follows Finish calibration as described in the previous chapter e Use split to form a separate dataset Use the invert or clean task on the split result to form an exploratory image that is useful for determining the line free channels e Use uvcontsub with mode subtract to subtract the continuum from the CORRECTED_DATA in the MS and write the continuum model in the MODEL_DATA column Set splitdata True to have it automatically split out continuum subtracted and continuum datasets else do this manually Image the line only emission with the clean task e If an image of the estimated continuum is desired and you did not use splitdata True then run split again on the uvcontsub d dataset and select the MODEL_DATA then run clean to image it For example we perform uv plane continuum subtraction on our NGC5921 dataset Want to use channels 4 6 and 50 59 for continuum uvcontsub vis ngc5921 usecase ms field N5921 spw fitspw 0 4 7 50759 solint inf fitorder 0 fitmode subtract splitdata True all spw only O in this data channels 4 6 and 50 59 scans are short enough mean only uv plane subtraction split the data for us HHHH OF You will see it made two new MS ngc5921 usecase ms cont ngc5921 usecase ms contsub 4 7 5 UV Plane Model Fitting uvmodelfit It is often desirable to fit simple analytic source componen
521. r gain freqdep True or bandpass freqdep False style calibration Other parameters are the same as in other calibration tasks These common calibration parameters are described in 4 4 7 EXPERIMENTAL Fringe Fitting fringecal BETA ALERT The fringecal task has not had extensive testing and is included as part of our support for the ALMA commissioning effort The fringecal task provides the capability for solving for baseline based phase phase delay and delay rate terms in the gains G type This is not full antenna based fringe fitting as is commonly used in VLBI The main use is to calibrate ALMA or EVLA commissioning data where the delays may be improperly set and to test fringe solutions as a way for dealing with non dispersive atmospheric terms The inputs are fringecal BL based fringe fitting solution vis 22 Name of input visibility file MS caltable ane Name of output bandpass calibration table field oe Select data based on field name or index spw ae Select data based on spectral window selectdata False Activate data selection details gaincurve a False Apply VLA antenna gain curve correction opacity 0 0 Opacity correction to apply nepers gaintable a Gain calibration solutions to apply gainfield a solint 0 0 Solution interval sec refant a Reference antenna async False if True run in the background prompt is freed All of the fringeca
522. r an example using overplot CHAPTER 3 DATA EXAMINATION AND EDITING 110 CASA Plotter E al EA ES E ES 4 0 O Bla Figure 3 2 The plotxy iteration plot The first set of plots from the example in 3 4 3 1 with iteration antenna Each time you press the Next button you get the next series of plots 3 4 3 3 plotrange The plotrange parameter can be used to specify the size of the plot The format is xmin xmax ymin ymax The units are those on the plot For example plotrange 20 100 15 30 Note that if xmin xmax and or ymin ymax then the values will be ignored and a best guess will be made to auto range that axis BETA ALERT Unfortunately the units for the time axis must be in Julian Days which are the plotted values CHAPTER 3 DATA EXAMINATION AND EDITING 111 3 4 3 4 plotsymbol The plotsymbol parameter defines both the line or symbol for the data being drawn as well as the color from the matplotlib online documentation e g type pl plot for help The following line styles are supported solid line S dashed line Fa dash dot line dotted line points pixels circle symbols o triangle up symbols triangle down symbols triangle left symbols triangle right symbols square symbols plus symbols cross symbols diamond symbols thin diamond symbols tripod down symbols tripod up symbols tripod left symbols tripod right symbols hexagon
523. r tasks which are useful during image analysis These include 227 CHAPTER 6 IMAGE ANALYSIS 228 e viewer there are useful region statistics and image cube slice and profile capabilities in the viewer We also give some examples of using the CASA Toolkit to aid in image analysis 6 12 6 1 Common Image Analysis Task Parameters We now describe some sets of parameters are are common to the image analysis These should behave the same way in any of the tasks described in this section that they are found in 6 1 1 Region Selection box Area selection in the image analysis tasks is controlled by the box parameter or through the regions parameter 6 1 5 The box parameter selects rectangular areas box dl Select one or more box regions string containing blcx blcy trcx trcy A box selection in the directional portion of an image The directional portion of an image are the axes for right ascension and declination for example Boxes are specified by there bottom left corner blc and top right corner trc as follows blcx blcy trcx trcy ONLY pixel values acceptable at this time Default none all Example box 0 0 50 50 Example box 10 20 30 40 100 100 150 150 H HH HHH HOH OF To get help on box see the in line help help par box 6 1 2 Plane Selection chans stokes The channel frequency or velocity plane s of the image is chosen using the chans parameter
524. rLevel 0 0 UnitContourLevel 1 0 Here we have contours starting at 1OmJy and doubling every contour We can also set contours in multiples of the image rms sigma RelativeContourLevels 3 3 5 10 15 20 BaseContourLevel 0 0 UnitContourLevel lt image rms gt Here we have first contours at negative and positive 3 sigma You can get the image rms using the imstat task 6 7 or using the Viewer statistics tool on a region of the image 7 2 3 As a final example not all images are of intensity for example a moment 1 image ga has units of velocity In this case absolute contours will work fine but by default the viewer will set fractional contours but referred to the min and max velocity RelativeContourLevels 0 2 0 4 0 6 0 8 BaseContourLevel lt image min gt UnitContourLevel lt image max gt Here we have contours spaced evenly from min to max and this is what you get by default if you load a non intensity image like the moment 1 image See Figure for an example of this 7 3 3 Overlay contours on a raster map Contours of either a second data set or the same data set can be used for comparison or to enhance visualization of the data The Data Options Panel will have multiple tabs which allow adjusting each overlay individually Note tabs along the top Beware it s easy to forget which tab is active Also note that axis labeling is controlled by the first registered image overlay that has labeling
525. r_data bookmark data gt home ballista jmcmulli other_data 6 3 Shell Command and Capture See also D 8 for the use of the command history 1 sx shell command shell_ccommand this captures the output to a list CASA 1 sx pwd stores output of pwd in a list Out 1 home basho3 jmcmulli pretest CASA 2 pwd is a shortcut for sx Out 2 home basho3 jmcmulli pretest CASA 3 sx ls v stores output of pwd in a list Out 3 vla_calplot jpg gt vla_calplot png vla_msplot_cals jpg os os os os os os os os os os os os os os 377 tmpnam ttyname umask uname unlink unsetenv urandom utime wait wait3 wait4 waitpid walk write access to APPENDIX D APPENDIX PYTHON AND CASA 378 gt vla_msplot_cals png gt vla_plotcal_bpass jpg gt vla_plotcal_bpass png gt vla_plotcal_fcal jpg gt vla_plotcal_fcal png gt vla_plotvis jpg gt vla_plotvis png CASA 4 x _ remember _ is a shortcut for the output from the last command CASA 5 x Out 5 vla_calplot jpg vla_calplot png vla_msplot_cals jpg vla_msplot_cals png vla_plotcal_bpass jpg gt vla_plotcal_bpass png vla_plotcal_fcal jpg gt vla_plotcal_fcal png vla_plotvis jpg gt vla_plotvis png CASA 6 y 0ut 2 or just refer to the enumerated output CASA 7 y Out 7
526. rage polarizations options bool True False default False outfile Name of output file default scantable example outform format of output file options ASCIT SDFITS MS ASAP default ASAP example the ASAP format is easiest for further sd processing use MS for CASA imaging If ASCII then will append some stuff to the outfile name overwrite overwrite the output file if already exists options bool True False default False WARNING if outform ASCII this parameter is ignored DESCRIPTION Task sdcoadd merges multiple single dish spectral data given by a list of spectral data file names in any of the following formats ASAP MS2 and SDFITS The units of line flux the units of spectral axis frame and doppler are assumed to be those of the first one in the sdfilelist if not specified The timaverage and polaverage are used to perform time and polarization averaging over scans on the merged scantable to obtained co added spectra before saving to a file on disk APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 308 A 2 1 6 sdflag Keyword arguments sdfile name of input SD dataset scanlist list of scan numbers to process default use all scans example 21 22 23 24 this selection is in addition to field and iflist field selection string for selecting scans by name default no name selection example FLS3a this selection is in addition
527. ral windows see 7 4 1 2 CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 286 The casaviewer process contains this buffer memory it contains the entire viewer but the memory buffer can take most of the space 7 4 1 6 MS Options Apply Button When viewing large MSs the display may be partially or completely grey in areas where the required data is not currently in memory either because no data has been loaded yet or because not all the selected data will fit into the allowed memory see Max Visibility Memory above When the cursor is over such an area the following message shows in the position tracking area press Apply on Adjust panel to load data Pressing the Apply button which lies below all the options will reload the memory buffer so that it includes the slice you are trying to view The message No Data has a different meaning in that case there simply s no data in the selected MS at the indicated position For large measurement sets loading visibility data into memory is the most time consuming step Progress feedback is provided in the console window Again careful selection of the data to be viewed can greatly speed up retrieval 7 5 Printing from the Viewer You can use the Data Print menu or the Print button to bring up the Viewer Print Manager From this panel you can print a hardcopy of what is in the Display Panel or save it in a variety of formats Figure shows an example of printing to
528. ral windows channels is all lt description gt lt any type variant gt lt value type string gt lt value gt lt param gt lt param type bool name selectdata gt lt description gt Other data selection parameters lt description gt lt value gt False lt value gt lt param gt lt param type string name timerange subparam true gt lt description gt Range of time to select from data lt description gt lt value gt lt value gt lt param gt lt param type string name uvrange subparam true gt lt description gt Select data within uvrange lt description gt lt value gt lt value gt lt param gt lt param type string name antenna subparam true gt lt description gt Select data based on antenna baseline lt description gt lt value gt lt value gt lt param gt lt param type string name scan subparam true gt lt description gt scan number range lt description gt lt value gt lt value gt lt param gt lt param type string name mode gt lt description gt Type of selection mfs channel velocity frequency lt description gt APPENDIX H APPENDIX WRITING TASKS IN CASA 482 lt value gt mfs lt value gt lt allowed kind enum gt lt value gt mfs lt value gt lt value gt channel lt value gt lt value gt velocity lt value gt lt value gt frequency lt value gt lt allowed gt lt param gt lt param type int name niter gt
529. ram type double name minpb gt lt description gt Minimum PB level to use lt description gt lt value gt 0 1 lt value gt lt param gt lt param type any name noise subparam true gt lt description gt noise parameter for briggs abs mode weighting lt description gt lt any type variant gt lt value type string gt 1 0Jy lt value gt lt param gt lt param type int name npixels subparam true gt lt description gt number of pixels for superuniform or briggs weighting lt description gt lt value gt 0 lt value gt lt param gt lt param type int name npercycle subparam true gt lt description gt Number of iterations before interactive prompt lt description gt lt value gt 100 lt value gt lt param gt lt param type double name cyclefactor subparam true gt lt description gt change depth in between of csclean cycle lt description gt lt value gt 1 5 lt value gt lt param gt lt param type int name cyclespeedup subparam true gt lt description gt Cycle threshold doubles in this number of iteration lt description gt lt value gt 1 lt value gt lt param gt lt constraints gt lt when param selectdata gt lt equals type bool value False gt lt equals type bool value True gt lt default param timerange gt lt value type string gt lt value gt lt default gt lt default param uvrange gt lt value type string
530. rated Note that this will be in local computer time usually UT for casapy generated messages and may be different for user generated messages Priority the Priority Level see below of the message e Origin where within CASA the message came from This is in the format Task Tool Method one or more of the fields may be missing depending upon the message e Message the actual text The casalogger GUI has a range of features which include e Search search messages by entering text in the Search window and clicking the search icon The search currently just matches the exact text you type anywhere in the message See Figure 1 5 for an example e Filter a filter to sort by message priority time task tool of origin and message contents Enter text in the Filter window and click the filter icon to the right of the window Use the pull down at the left of the Filter window to choose what to filter The matching is for the exact text currently no regular expressions See Figure 1 6 for an example CHAPTER 1 INTRODUCTION 60 hd Log Messages sandrock home sandrock3 smyers Testing3 Patch4 N5921 casapy log File Edit View Filter Origin y clean ca HREH HEHHEHE H H H HE HEH HE EHE HE BEHE HHH HE HEHE HE H HE HEHEHE HEHEHEHEHE HEHE Begin Task clean HHH jeasurementset ies nx 256 ny 256 cellx l5arcsec celly 15arcsec stokes I mode CHANNEL nchan 46 start 5 step 1 spwids 1
531. ration 4 4 5 e accum Accumulates incremental calibration solutions into a cumulative calibration table 8 4 5 4 e smoothcal Smooths calibration solutions derived from one or more sources 5 3 applycal Applies calculated calibration solutions 4 6 1 e clearcal Re initializes calibrated visibility data in a given measurement set 4 6 3 e listcal Lists calibration solutions 4 5 2 e plotcal Plots and optionally flags calibration solutions 8 4 5 1 e uvcontsub carry out uv plane continuum subtraction for spectral line data 4 7 4 e split write out a new calibrated MS for specified sources 4 7 1 During the course of calibration the user will specify a set of calibrations to pre apply before solving for a particular type of effect for example gain or bandpass or polarization The solutions are stored in a calibration table subdirectory which is specified by the user not by the task care must be taken in naming the table for future use The user then has the option as the calibration process proceeds to accumulate the current state of calibration in a new cumulative table Finally the calibration can be applied to the dataset Synthesis data calibration is described in detail in Chapter 4 CHAPTER 1 INTRODUCTION 69 1 5 3 1 Prior Calibration The setjy task places the Fourier transform of a standard calibration source model in the MODEL_DATA column of the m
532. rder to help you set up the clean mask For example if you have a previously cleaned image of a complex source or mosaic that you wish to use to guide the placement of boxes or polygons just use the Open button or menu item to bring in that image which will be visible and registered on top of your dirty residual image that you are cleaning on You can then draw masks as usual which will be stored in the mask layer as before Note you can blink between the new and dirty image change the colormap and or contrast and carry out other standard viewer operations See 7 for more on the use of the viewer BETA ALERT Currently interactive spectral line cleaning is done globally over the cube with halts for interaction after searching all channels for the requested npercycle total iterations It is CHAPTER 5 SYNTHESIS IMAGING 214 Rd Viewer Display TT 7 iewer Display Panel RS Data Display Panel Tools View Data Display Panel Tools View 4430900 2RA3ILAA 430490 A3ISAS 318 12 918 2 jala e 2 8 a ax EJES iterations cycles threshold spo 98 0 05 my Next Action Oo gt O Next Action Oo gt Add Displayed Plane All Channels iterations cycles threshold 500 97 0 05 mjy Add Displayed Plane All Channels Erase Erase S p o oO o a a 38 oo 5s 48 L Figure 5 4 We continue in our interactive cleaning of Jupiter from where Figure 5 3 le
533. re name of output images field 9 Field Name spw a Spectral windows channels is all selectdata False Other data selection parameters mode channel Type of selection mfs channel velocity frequency nchan 46 Number of channels planes in output image start 5 first input channel to use width 4 Number of input channels to average interpolation nearest Type of spectral interpolation of visibilities nearest linear cubic niter 6000 Maximum number of iterations gain 0 1 Loop gain for cleaning threshold 3 0 Flux level to stop cleaning Must include units psfmode hogbom method of PSF calculation to use during minor cycles imagermode is Use csclean or mosaic If use psfmode multiscale 7 set deconvolution scales pixels default multiscale standard CLEAN interactive False use interactive clean with GUI viewer mask 108 108 148 148 cleanbox es mask image s and or region s used in cleaning imsize 256 256 x and y image size in pixels symmetric for single value cell 19 0 15 01 x and y cell size default unit arcsec phasecenter i Image phase center position or field index restfreq ee rest frequency to assign to image see help stokes OE Stokes params to image eg 1 IV QU IQUY weighting briggs Weighting of uv natural uniform briggs robust 0 5 Briggs robustness parameter npixels 0 number of pixels to determine
534. re searched default SAULT example scaletype PBCOR Options PBCOR SAULT SAULT when interactive True shows the residual with constant noise across the mosaic If pbcor False the final output image is NOT corrected for the PB pattern and therefore is not flux correct Division of SAULT amp lt imagename amp gt image by the amp lt imagename amp gt flux image will produce a flux correct image can also be acheived by setting pbcor True gt PBCOR uses the SAULT scaling scheme for deconvolution but if interactive True shows the primary beam corrected image the final PBCOR image is flux correct if pbcor True amp gt amp gt amp gt imagermode csclean expandable parameter s Image using the Cotton Schwab algorithm in between major cycles cyclefactor Change the threshold at which the deconvolution cycle will stop degrid and subtract from the visibilities For poor PSFs reconcile often cyclefactor 4 or 5 For good PSFs use cyclefactor 1 5 to 2 0 Note threshold cyclefactor max sidelobe max residual default 1 5 example cyclefactor 4 cyclespeedup Cycle threshold doubles in this number of iterations default 1 example cyclespeedup 3 try cyclespeedup 50 to speed up cleaning multiscale set of scales to use in deconvolution If set cleans with several resolutions using hobgom clean The scale sizes are in units of cellsize So if cell 2arcsec a multiscale scale 1
535. re shown on the connectors Note that from the output solver through the accumulator only a single calibration type e g B G can be smoothed interpolated or accumulated at a time The final set of cumulative calibration tables of all types are then input to applycal as shown in Figure 4 2 3 The Calibration of VLA data in CASA CASA supports the calibration of VLA data that is imported from the Archive through the importvla task See for more information BETA ALERT Data taken both before and after the Modcomp turn off in late June 2007 will be handled automatically by importvla You do not need to set special parameters to do so and it will obey the scaling specified by applytsys You can also import VLA data in UVFITS format with the importuvfits task 2 2 1 1 However in this case you must be careful during calibration in that some prior or previous calibrations see below may or may not have been done in AIPS and applied or not before export CHAPTER 4 SYNTHESIS CALIBRATION 134 For example the default settings of AIPS FILLM will apply VLA gaincurve and approximate weather based atmospheric optical depth corrections when it generates the extension table CL 1 If the data is exported immediately using FITTP then this table is included in the UVFITS file However CASA is not able to read or use the AIPS SN or CL tables so that prior calibration information is lost and must be applied during calibration here
536. readlink remove removedirs rename renames rmdir os sep setegid seteuid setgid setgroups setpgid os setpgrp setregid os setreuid setsid setuid spawnl spawnle spawnlp Spawnlpe os spawnv Spawnve os spawnvp spawnvpe stat stat_float_times stat_result os statvfs_result os statvfs strerror symlink sys sysconf sysconf_names system tcgetpgrp tcsetpgrp tempnam times tmpfile APPENDIX D APPENDIX PYTHON AND CASA os os os os os os os os os os os os os os os D In SEEK_SET os devnull os nice TMP_MAX os dup os open UserDict os dup2 os openpty WCONTINUED os environ os pardir WCOREDUMP os error os path WEXITSTATUS os execl os pathconf WIFCONTINUED os execle os pathconf_names WIFEXITED os execlp os pathsep WIFSIGNALED os execlpe os pipe WIFSTOPPED OS execv os popen WNOHANG os execve os popen2 WSTOPSIG os execvp os popen3 WTERMSIG os execvpe os popen4 WUNTRACED os extsep os putenv W_OK os fchdir os read 6 2 Directory Navigation addition filesystem navigation is aided through the use of bookmarks to simplify frequently used directories D CASA 4 cd home ballista jmcmulli other_data CASA 4 pwd home ballista jmcmulli other_data CASA 5 bookmark other_data CASA 6 cd export home corsair vml jmcmulli data CASA 7 pwd export home corsair vml jmcmulli data CASA 8 cd b othe
537. regrid an image onto a template image imagename eae Name of input image template qa Name of reference image output es Name of output regridded image async False The output image will have the data in imagename regridded onto the coordinate system of template image BETA ALERT The imregrid task is currently under test againt similar AIPS tasks and we are looking to improve its performance Future releases will enable regridding without the need for a template image 6 10 Image Convolution imsmooth The default inputs are imsmooth Smooth an image or portion of an image imagename ae Name of the input image kernel boxcar Type of kernel to use gaussian or boxcar region RZ Image Region or name Use viewer box oe Select one or more box regions chans gt Select the channel spectral range stokes es Stokes params to image 1 IV IQU IQUV mask ee mask used for selecting the area of the image to smooth outfile 22 Output smoothed image file name async False 6 11 Image Import Export to FITS These tasks will allow you to write your CASA image to a FITS file that other packages can read and to import existing FITS files into CASA as an image CHAPTER 6 IMAGE ANALYSIS 252 6 11 1 FITS Image Export exportfits To export your images to fits format use the exportfits task The inputs are exportfits Convert a CASA image to a FITS file imagename dd Name o
538. retrieve current rest frequencies 0 45490258000 0 All the rest frequencies currently set to the data are listed in python dictionary for each MOLECULE ID To set multiple rest frequencies to spectra for a particular IF for example Select IFs then set rest frequencies sel sd selector sel setifs 0 scans set_selection sel scans set_restfreqs 45490258000 0 45590258000 0 45690258000 0 NOTE there is no functionality yet to select a specific rest frequency to apply to a specific line etc Currently the first one in the list of the rest frequencies is used for such calculation APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 356 A 3 11 Single Dish Spectral Analysis Use Case With ASAP Toolkit Below is a script that illustrates how to reduce single dish data using ASAP within CASA First a summary of the dataset is given and then the script MeasurementSet Name home rohir3 jocular SD OrionS_rawACSmod MS Version 2 Project AGBTO6A_018_01 Observation GBT 1 antennas Data records 256 Total integration time 1523 13 seconds Observed from 01 45 58 to 02 11 21 Fields 4 ID Name Right Ascension Declination Epoch 0 Orions 05 15 13 45 05 24 08 20 J2000 1 Orions 05 35 13 45 05 24 08 20 J2000 2 Orions 05 15 13 45 05 24 08 20 J2000 3 Orions 05 35 13 45 05 24 08 20 J2000 Spectral Windows 8 unique spectral windows and 1 unique polarization setups SpwID Chans Frame C
539. riad UVFITS 2 2 1 2 Export using exportuvfits The exportuvfits task will take a MS and write it out in UVFITS format The defaults are exportuvfits Convert a CASA visibility data set MS to a UVFITS file vis a Name of input visibility file fitsfile q Name of output UVFITS file datacolumn corrected which data to write data corrected model field ant Field name list spw F me Spectral window and channel selection antenna Re antenna list to select time za time range selection nchan St Number of channels to select start 0 Start channel width 1 Channel averaging width value gt 1 indicates averaging writesyscal False Write GC and TY tables multisource True Write in multi source format combinespw True Combine spectral windows True for AIPS writestation True Write station name instead of antenna name async False if True run in the background prompt is freed For example exportuvfits vis ngc5921 split ms fitsfile NGC5921 split fits multisource False CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 81 The MS selection parameters field spw antenna and timerange follow the standard selection syntax described in 2 6 BETA ALERT The nchan start and width parameters will be superseded by channel selection in spw Currently there is a time parameter rather than timerange The datacolumn parameter chooses which data conta
540. rint Calibrator data ampl max gt thistest_cal print Previous cal data max oldtest_cal print Difference fractional diff_cal print print gt gt logfile Calibrator data ampl max thistest_cal print gt gt logfile Previous cal data max oldtest_cal print gt gt logfile Difference fractional diff_cal print gt gt logfile Pull the max src amp value out of the MS ms open srcsplitms thistest_src max ms range amplitude get amplitude ms close oldtest_src 46 2060050964 now in all chans diff_src abs oldtest_src thistest_src oldtest_src print Target Src data ampl max thistest_src print Previous src data max oldtest_src print Difference fractional diff_src print print gt gt logfile Target Src data ampl max thistest_src print gt gt logfile Previous src data max oldtest_src print gt gt logfile Difference fractional diff_src print gt gt logfile Now use the stats produced by imstat above DIRTY IMAGE MAX amp RMS IF YOU MADE A DIRTY IMAGE 411 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 412 thistest_dirtymax dirtystats max 0 oldtest_dirtymax 0 0515365377069 diff_dirtymax abs oldtest_dirtymax thistest_dirtymax oldtest_dirtymax print Dirty image max gt thistest_dirtymax print Pr
541. rint we print Flagging edge channels in all spw print 0 3 071 627 63 4711 071 30731 12 15 071 62763 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 461 print we flagdata vis ngc4826 tutorial ms mode manualflag spw 073 0 1 62 63 4711 0 1 30 31 12715 0 1 62 63 Flag correlator glitch print print Flagging bad correlator field 8 antenna 3 amp 9 spw 15 all channels print timerange 1998 04 16 06 19 00 0 1998 04 16 06 20 00 0 print flagdata vis ngc4826 tutorial ms mode manualflag field 8 spw 15 antenna 3 9 timerange 1998 04 16 06 19 00 071998 04 16 06 20 00 0 HHHHHHHHHHHER HHH HHHHAAAEHA AREER HHR RRR H HARE HHH RRR RRR ARA AAA Some example clean up editing Slightly high almost edge channel in field 1 spw 4 channel 2 can be flagged interactively with plotxy plotxy vis ngc4826 tutorial ms xaxis channel yaxis amp field 1 spw 4 averagemode vector timebin 1le7 crossscans True selectplot True newplot False title Field 1 SPW 4 print Completed pre calibration flagging HEHHHHHHEEHARHHAHHATHA TRAE REAR HRA HAHAHA R RRR RA RAHA HARARE RRR Use Flagmanager to save a copy of the flags so far print Flagmanager default flagmanager print Now will use flagmanager to save a copy of the flags we just made print These are nam
542. rison operators When specified in the format gt UVDIST all visibilities with uv distances greater than the given UVDIST are selected Likewise when specified in the format lt UVDIST all rows with uv distances less than the given UVDIST are selected Any number of above mentioned uv distance specifications can be given as a comma separated list Examples uvrange 100km uvrange 100klambda baselines of length 100km uv radius 100 kilolambda uvrange 100 200km an annulus in physical baseline length uvrange 24 35Mlambda 40 45Mlambda two annuli in units of mega wavelengths uvrange lt 45klambda less than 45 kilolambda uvrange gt Olambda greater than zero length no auto corrs 2 6 4 5 The msselect Parameter More complicated selections within the MS structure are possible using the Table Query Language TaQL This is accessed through the msselect parameter Note that the TaQL syntax does not follow the rules given in 2 6 1 for our other selection strings TaQL is explained in more detail in Aips NOTE 199 Table Query Language aips2 nrao edu docs notes 199 199 html This will eventually become a CASA document The specific columns of the MS are given in the most recent MS specification document Aips NOTE 229 MeasurementSet definition version 2 0 http aips2 nrao edu docs notes 229 229 htm1 This documentation will eventually be updated to the
543. rols the precise alignment of the edge of the current zoom window with the data lattice edge the default means that whole data pixels are always drawn even on the edges of the display For most purposes edge is recommended center means that data pixels on the edge of the display are drawn only from their centers inwards Note that a data pixel s center is considered its definitive position and corresponds to a whole number in data pixel or lattice coordinates e Basic Settings Resampling mode This setting controls how the data are resampled to the resolution of the screen nearest the default means that screen pixels are colored according to the intensity of the nearest data point so that each data pixel is shown in a single color bilinear applies a bilinear interpo lation between data pixels to produce smoother looking images when data pixels are large on the screen bicubic applies an even higher order and somewhat slower interpolation e Basic Settings Data Range You can use the entry box provided to set the minimum and maximum data values mapped to the available range of colors as a list min max For very high dynamic range images you will probably want to enter a max less than the data maximum in order to see detail in lower brightness level pixels The next setting also helps very much with high dynamic range data e Basic settings Scaling power cycles This option allows logarithmic scaling of d
544. rows parameter if set to an integer n greater than 1 will allow only every nth point to be plotted It does this as the name suggests by skipping over whole rows of the MS so beware channels are all within the same row for e g plotxy a given spw Be careful flagging on data where you have skipped points Note that you can also reduce the number of points plotted via averaging 8 or channel striding in the spw specification P 6 3 The newplot toggle lets you choose whether or not the last layer plotted is replaced when overplot True or whether a new layer is added The clearpanel parameter turns on off the clearing of plot panels that lie under the current panel layer being plotted The options are none clear nothing auto automatically clear the plotting area current clear the current plot area only and a11 clear the whole plot panel The title xlabels and ylabels parameters can be used to change the plot title and axes labels CHAPTER 3 DATA EXAMINATION AND EDITING 109 The fontsize parameter is useful in order to enlarge the label fonts so as to be visible when making plots for screen capture or just to improve legibility Shrinking can help if you have lots of panels on the plot also The windowsize parameter is supposed to allow adjustments on the window size BETA ALERT This currently does nothing unless you set it below 1 0 in which case it will produce an error 3 4 3 Plo
545. rst order polynomial to the selected channels and subtract this polynomial from the full spectrum The auto_poly_baseline function can be used to automatically baseline your data without having to specify channel ranges for the line free data It automatically figures out the line free emission and fits a polynomial baseline to that data The user can use masks to fix the range of channels or velocity range for the fit as well as mark the band edge as invalid APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 353 scans auto_poly_baseline mask edge order threshold chan_avg_limit plot insitu Parameters mask an optional mask retrieved from scantable edge an optional number of channel to drop at the edge of spectrum If only one value is specified the same number will be dropped from both sides of the spectrum Default is to keep all channels Nested tuples represent individual edge selection for different IFs a number of spectral channels can be different order the order of the polynomial default is 0 threshold the threshold used by line finder It is better to keep it large as only strong lines affect the baseline solution chan_avg_limit a maximum number of consecutive spectral channels to average during the search of weak and broad lines The default is no averaging and no search for weak lines If such lines can affect the fitted baseline e g a high order polynomial is fitted increase this parameter usually values u
546. s if you like All CASA data files including Measurement Sets are written into the current working directory by default with each CASA table represented as a separate sub directory MS names therefore need only comply with UNIX file or directory naming conventions and can be referred to from within CASA directly or via full path names An MS consists of a MAIN table containing the visibility data and associated sub tables containing auxiliary or secondary information The tables are logical constructs with contents located in the physical table files on disk The MAIN table consists of the table files in the main directory of the ms file itself and the other tables are in the respective subdirectories The various MS tables and sub tables can be seen by listing the contents of the MS directory itself e g using Unix 1s or via the browsetable task 3 6 See Fig 2 1 for an example of the contents of a MS directory Or from the casapy prompt CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION TT CASA lt 1 gt ls ngc5921 ms IPython system call 1s F ngc5921 ms ANTENNA POLARIZATION table f1 table f3_TSM1 table f8 DATA_DESCRIPTION PROCESSOR table f10 table f4 table f8_TSM1 FEED SORTED_TABLE table f10_TSM1 table f5 table f9 FIELD SOURCE table f11 table f5_TSM1 table f9_TSM1 FLAG_CMD SPECTRAL_WINDOW table f11_TSM1 table f6 table info HISTORY STATE table f2 table f6_TSMO table lock OBSERVATION table dat
547. s a list only if flagmode is set to restore Note that the restore mode refers scanlist iflist and pollist DESCRIPTION Task sdflag performs simple channel based flagging on spectra The flag regions in channels can be specified in maskflag This is not interactive flagging If plotlevel gt 1 the task asks you if you really apply the flags before it is actually written to the data with a plot indicating flagged regions The flags are not written to the current input datasets unless outfile none Flagged regions or values of flag masks already applied of the input data can be listed by setting flagmode restore It will print out a summary on the screen and returns maskflag values for each spectrum as a list Please note that this task is still experimental A 2 1 7 sdfit Keyword arguments sdfile name of input SD dataset default none must input file name example mysd asap See sdcal for allowed formats fluxunit units for line flux options str K Jy default keep current fluxunit WARNING For GBT data see description below gt gt gt fluxunit expandable parameter telescopeparm the telescope characteristics options str name or list list of gain info default none set example if telescopeparm it tries to get the telescope name from the data Full antenna parameters diameter ap eff known to ASAP are gt ATPKSMB ATPKS
548. s are png PNG eps EPS and svg SVG This latter option is most useful from scripts For example default plotxy vis ngc5921 ms field 2 spw 7 xaxis uvdist yaxis amp interactive False figfile ngc5921 uvplot amp png plotxy O will plot amplitude versus uv distance in PNG format No plotxy GUI will appear BETA ALERT if you use this option to print to figfile with an iteration set you will only get the first plot 3 4 9 Exiting plotxy You can use the Quit button to clear the plot from the window and detach from the MS You can also dismiss the window by killing it with the X on the frame which will also detach the MS You can also just leave it alone The plotter pretty much keeps running in the background even when it looks like it s done You can keep doing stuff in the plotter window which is where the overplot parameter comes in Note that the plotcal task will use the same window and can also overplot on the same panel If you leave plotxy running beware of for instance deleting or writing over the MS without stopping It may work from a memory version of the MS or crash 3 4 10 Example session using plotxy The following is an example of interactive plotting and flagging using plotxy on the Jupiter 6cm continuum VLA dataset This is extracted from the script jupiter6cm_usecase py available in the script area This assumes that the MS jupiter6cm usecase m
549. s in uv plane innertaper uv taper in center of uv plane not implemented The sub parameters specify the size and optionally shape and orientation of this Gaussian in the uv plane or optionally the sky plane The outertaper refers to a Gaussian centered on the origin of the uv plane Some examples outertaper outertaper 5klambda outertaper 5klambda 3klambda 45 0deg outertaper 10arcsec outertaper 300 07 no outer taper applied circular uv taper FWHM 5 kilo lambda elliptical Gaussian on sky FWHM 10 300m in aperture plane HH H FF Note that if no units are given on the taper then the default units are assumed to be meters in aperture plane BETA ALERT The innertaper option is not yet implemented 5 2 11 Parameter weighting In order to image your data we must have a map from the visibilities to the image Part of that map which is Inside the Toolkit effectively a convolution is the weights by which each vis The im weight method has more ibility is multiplied before gridding The first factor in the weighting options than available in weighting is the noise in that visibility represented by the imaging tasks See the User the data weights in the MS which is calibrated along with Reference Manual for more infor mation on imaging weights CHAPTER 5 SYNTHESIS IMAGING 196 the visibility data The weighting function can also de pend
550. s is on disk with flagautocorr already run BETA ALERT Exact syntax may be slightly different in your version as the Beta Release progress CHAPTER 3 DATA EXAMINATION AND EDITING default plotxy vis jupiter6cm usecase ms The fields we are interested in 1331 305 JUPITER 0137 331 selectdata True First we do the primary calibrator field 1331 305 Plot only the RR and LL for now correlation RR LL Plot amplitude vs uvdist xaxis uvdist yaxis amp multicolor both The easiest thing is to iterate over antennas iteration antenna plotxy O You 11 see lots of low points as you step through RR LL RL LR A basic clip at 0 75 for RR LL and 0 055 for RL LR will work If you want to do this interactively set iteration plotxy O You can also use flagdata to do this non interactively see below Now look at the cross polar products correlation RL LR plotxy O Now do calibrater 0137 331 field 0137 331 correlation RR LL xaxis uvdist spw 7 iteration antenna plotxy O You 11 see a bunch of bad data along the bottom near zero amp Draw a box around some of it and use Locate 119 CHAPTER 3 DATA EXAMINATION AND EDITING 120 Looks like much of it is Antenna 9 ID 8 in spw 1 xaxis time spw 71 correlation Note that the strings like antenna 9
551. s to parts of the toolkit that are easy to learn for most astronomers who are familiar power users might want to explore with radio interferometric data reduction and hopefully for novice users as well In CASA the tools provide the full capability of the package and are the atomic functions that form the basis of data reduction These tools augment the tasks or fill in gaps left by tasks that are under development but not yet available See the CASA User Reference Manual for more details on the tools Note that in most cases the tasks are Python interface scripts to the tools but with specific limited access to them and a standardized interface for parameter setting The tasks and tools can be used together to carry out more advanced data reduction operations For the moment the audience is assumed to have some basic grasp of the fundamentals of synthesis imaging so details of how a radio interferometer or telescope works and why the data needs to 20 CHAPTER 1 INTRODUCTION 21 undergo calibration in order to make synthesis images are left to other documentation a good place to start might be Synthesis Imaging in Radio Astronomy II 1999 ASP Conference Series Vol 180 eds Taylor Carilli amp Perley This cookbook is broken down by the main phases of data analysis e data import export and selection Chapter 2 e examination and flagging of data Chapter 3 interferometric calibration Chapter 4
552. sages going to the file mynewlogfile log 1 4 2 2 Setting priority levels in the logger Logger messages are assigned a Priority Level when generated within CASA The current levels of Priority are 1 SEVERE errors CHAPTER 1 INTRODUCTION 62 2 WARN warnings 3 INFO basic information every user should be aware of or has requested 4 INFO1 information possibly helpful to the user 5 INFO2 details the power user might want to see 6 INFO3 even more details 7 INFO4 lowest level of non debugging information 8 DEBUGGING most important debugging messages 9 DEBUG1 more details 10 DEBUG2 lowest level of debugging messages The debugging levels are intended for the developers use There is a threshold for which these messages are writ ten to the casapy log file and are thus visible in the Inside the Toolkit logger By default only messages at level INFO and The casalog tool can be used to con above are logged The user can change the threshold using trol the logging In particular the the casalog filter method This takes a single string casalog filter method sets the argument of the level for the threshold The level sets priority threshold This tool can also the lowest priority that will be generated and all messages be used to change the output log file of this level or higher will go into the casapy 1log file and to post messages into the logger
553. se the selected MS data to be reloaded from disk If you select say spectral windows 7 8 23 and 24 the animator slice position sliders and axis labeling will show these as 0 1 2 and 3 the slice positions or pixel coordinates of the chosen spectral windows Looking at the position tracking display is the best way to avoid confusion in such cases It will show something like Sp Win 23 s 2 when you are viewing spectral window 23 plane 2 of the selected spectral windows Changes to MS selections will not be allowed until you have saved or discarded any previous edits you have made see Flagging Options Save Edits below A warning is printed on the console not the logger Initially all fields and spectral windows are selected To revert to this unselected state choose Original under the wrench icons next to the entry boxes See Figure for an example showing the use of the MS and Visibility Selections controls when viewing an MS 7 4 1 3 MS Options Display Axes This roll up is very similar to that for images it allows the user to choose which axes from Time Baseline Polarization Channel and Spectral Window are are on the display and the animator There are also sliders here for choosing positions on the remaining axes It s useful to note that the data is actually stored internally in memory as an array with these five axes For MSs changing the choice of axis on one control will autom
554. se two images While not as accurate as a true joint reconstruction of an image from the synthesis and single dish data together it is sufficient for most purposes See 5 5 for details on the use of the feather task 1 5 5 Self Calibration Once a calibrated dataset is obtained and a first deconvolved model image is computed a self calibration loop can be performed Effectively the model not restored image is passed back to another calibration process on the target data This refines the calibration of the target source which up to this point has had usually only external calibration applied This process follows the regular calibration procedure outlined above Any number of self calibration loops can be performed As long as the images are improving it is usually prudent to continue the self calibration iterations This process is described in 5 9 1 5 6 Data and Image Analysis The key data and image analysis tasks are e imhead summarize and manipulate the header information in a CASA image 8 6 2 e imcontsub perform continuum subtraction on a spectral line image cube 6 3 e immath perform mathematical operations on or between images 6 5 e immoments compute the moments of an image cube 6 6 e imstat calculate statistics on an image or part of an image 6 7 e imregrid regrid an image onto the coordinate system of another image 6 9 CHAPTER 1 I
555. sed The task widefield has been introduced for this purpose This is currently a prototype task that can be used to make and deconvolve a wide field image e g from low frequency data It contains most but not all of the flexibility of clean The w term is handled using a combination of w projection and faceting Besides making large area undistorted images widefield can be used to outlying fields to image isolated regions e g containing bright confusing sources distant from the field center The inputs for widefield are widefield Wide field imaging and deconvolution with selected algorithm vis name of input visibility file imagename Pre name of output images outlierfile Zi Text file with image names sizes centers field a Field Name spw de Spectral windows channels is all selectdata False Other data selection parameters mode mfs Type of selection mfs channel velocity frequency niter 500 Maximum number of iterations gain 0 1 Loop gain for cleaning threshold 0 0Jy Flux level to stop cleaning Must include units psfmode clark Algorithm to use clark hogbom ftmachine wproject Gridding method for the image wproject ft wprojplanes 256 Number of planes to use in w convolution function facets 1 Number of facets along each axis in main image only CHAPTER 5 SYNTHESIS IMAGING 219 multiscale set deconvolution scales pixels
556. set just detaching from file If you choose the default verbose True option there will be more information For example listobs n5921 ms True will result in the logger messages Thu Jul 5 17 23 55 2007 NORMAL ms summary MeasurementSet Name home scamper CASA N5921 n5921 ms MS Version 2 Observer TEST Project Observation VLA Thu Jul 5 17 23 55 2007 NORMAL ms summary Data records 22653 Total integration time 5280 seconds Observed from 09 19 00 to 10 47 00 Thu Jul 5 17 23 55 2007 NORMAL ms summary ObservationID 0 ArrayID 0 Date Timerange Scan FldId FieldName Spwlds 13 Apr 1995 09 19 00 0 09 24 30 0 1 O 1331 30500002_0 0 09 27 30 0 09 29 30 0 2 1 1445 09900002_0 0 09 33 00 0 09 48 00 0 3 2 N5921_2 0 09 50 30 0 09 51 00 0 4 1 1445 09900002_0 0 10 22 00 0 10 23 00 0 5 1 1445 09900002_0 0 10 26 00 0 10 43 00 0 6 2 N5921_2 0 10 45 30 0 10 47 00 0 7 1 1445 09900002_0 0 Thu Jul 5 17 23 55 2007 NORMAL ms summary Fields 3 ID Name Right Ascension Declination Epoch 0 1331 30500002_013 31 08 29 30 30 32 96 J2000 1 1445 09900002_014 45 16 47 09 58 36 07 J2000 CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 2 N5921_2 15 22 00 00 05 04 00 00 J2000 Thu Jul 5 17 23 55 2007 NORMAL ms summary Spectral Windows 1 unique spectral windows and 1 unique polarization setups SpwID Chans Frame Chi MHz Resoln kHz TotBW kHz Ref MHz Corrs 0 63 LSRK 1412 68608 24 4140625 1550
557. shell to Python which provides many features for efficient command line interaction while matplotlib is a Python 2 D plotting library for publication quality figures in different hardcopy formats From www python org Python is an interpreted interactive object oriented programming lan guage Python is used as the underlying command line interface scripting language to CASA Thus CASA inherits the features and the annoyances of Python For example since Python is inherently 0 based in its indexing of arrays vectors etc CASA is also 0 based any Index inputs e g start for start channel fieldIndex antennalD etc will start with 0 Another example is that indenting of lines means something to Python of which users will have to be aware Some key links are e http python org Main Python page o tp python org doc 2 4 2 ref reE Hal Python Reference tp python org a0e72 4 2 eut Eat hem Python Tutorial netp ipython scipy org Python page netp aakplotlib sourceforge net matplotlib page Each of the features of these components behave in the standard way within CASA In the following sections we outline the key elements for analysis interactions see the Python references and the IPython page for the full suite of functionality D 1 Automatic parentheses Automatic parenthesis is enabled for calling functions with argument lists this feature is intended to allow less typing for common situations Pyt
558. should see bad edge channels in each spw segment We will flag these non interactively later HHH H HH HH H OF APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 459 Interactive plotxy plotxy vis ngc4826 tutorial ms xaxis channel yaxis amp field 0 spw 073 averagemode vector timebin 1le7 crossscans True selectplot True newplot False title Field 0 SPW 073 Pause script if you are running in scriptmode user_check raw_input Return to continue script n You can also plot versus velocity by setting xaxis velocity You might do this for all the other spw field combos You can also non interactively plotxy to a file note this works only if iteration is not set Also see how we use Python variables to make this easier field 0 spw 073 figfile ngc4826 tutorial ms plotxy field spectrum raw png plotxy vis ngc4826 tutorial ms xaxis velocity yaxis amp field field spw spw averagemode vector timebin 1e7 crossscans True selectplot True newplot False title Field field SPW spw interactive False figfile figfile Now lets look at the target source the first of the NGC4826 mosaic fields which are 278 in this MS Since we are plotting versus velocity we can clearly see the bad edge channels and the overlap between spw There is nothing terribly wro
559. solution improves the frequency domain coherence significantly a G or T solution following it will be better than the original For example to solve for a B bandpass using a single short scan on the calibrator then default bandpass vis n5921 ms caltable n5921 bcal gaintable No gain tables yet gainfield interp field 0 Calibrator 1331 305 3C286 FIELD_ID 0 spw all channels selectdata False No other selection gaincurve False No gaincurve at L band opacity 0 0 bandtype B solint inf No troposphere standard time binned B rather than BPOLY set solution interval arbitrarily long HH H HH FH OF CHAPTER 4 SYNTHESIS CALIBRATION 149 refant 15 ref antenna 15 VLA N2 ID 14 bandpass On the other hand we might have a number of scans on the bandpass calibrator spread over time but we want a single bandpass solution In this case we could solve for and then pre apply an initial gain calibration and let the bandpass solution cross scans gaintable n5921 init gcal Our previously determined G table gainfield 0 interp linear Do linear interpolation solint inf One interval over dataset combine scan Solution crosses scans Note that we obtained a bandpass solution for all channels in the MS If explicit channel selection is desired for example some channels are
560. spec value button is pressed and activated you can display a spectral value on the toolbar along with mouse movement Click the LEFT mouse button over a spectrum to select it and drag mouse in the panel to output its value at the x position of mouse cursor The selection is released when you release the mouse button When statistic button is pressed and activated you can get statistic values of a channel region selected by mouse Select a rectangle region with LEFT RIGHT mouse to SELECT EXCLUDE the channel region to calculate statistics for the all spectra plotted The results are printed on the casapy console Press Quit button to close the plotter other plottype options plottype totalpower is used to plot the total power data and only plot option is amplitude versus data row number plottype azel plots azimuth and elevation tracks of the source plottype pointing plots antenna pointing Currently most of the plotting parameters are ignored these modes See the sdaverage description for information on fluxunit conversion and the telescopeparm parameter WARNING be careful plotting OTF on the fly mosaic data with lots of fields Beta Patch 4 New Features e The parameter restfreq is added to set rest frequency when specunit km s is chosen e Improvement on spectral value display feature is made e Now you can specify the region interactively on the plot to get statistics of the region of the
561. spectral window on the Animation Axis and used the tapedeck to step to spw 2 where we see the data from the rest of the scans Now channels is on a Display Axes slider which has been dragged to show Channel BB o a 28 7 19 Setting up to print to a file The background color has been set to white the line width to 2 and the print resolution to 600 dpi for an postscript plot To make the plot use the Save button on the Viewer Print Manager panel positioned in the figure in the upper right and select a format with the drop down or use the Print button to send directly to a printer o e 287 ANT 293 fitting of each scan only shown here the last scan The bottom panel shows the calibrated baseline subtracted data psr reference position data and the ps source data 00 357 aaa oa E Re ee ee ee A 358 A 5 Calibrated spectrum with a line at zero using histograms A 6 FLS3a HI emission The display illustrates the visualization of the data cube left and the profile display of the cube at the cursor location right the Tools menu of the Viewer Display Panel has a Spectral Profile button which brings up this display By default it grabs the left mouse button Pressing down the button and moving in the display will show the profile variations 2 0 0 0 0 0 0 0022 eae 362 j bo ww Chapter 1 Introduction This document describes how to calibrate
562. stribution Other data sets can be made available upon request The scripts are intended to illustrate the types of commands needed for different types of reduction astronomical observations BETA ALERT During the Beta Release period we will be occasionally updating the syntax of the tasks which may break older versions of the scripts You can find the latest versions of these and other scripts at http casa nrao edu Doc Scripts F 1 NGC 5921 VLA red shifted HI emission This script demonstates basic spectral calibration and imaging but does not include any self calibration steps The latest version of this script can be found at http casa nrao edu Doc Scripts ngc5921_demo py HHETHHHHHHHAEHHAEHHEEHEHHEHHHEEEHEHHHREEHEHEEEHREE HAHAHA RARA RO RARA RARA A ARRE Use Case Script for NGC 5921 Converted by STM 2007 05 26 Updated STM 2007 06 15 Alpha Patch 1 Updated STM 2007 09 05 Alpha Patch 2 Updated STM 2007 09 18 Alpha Patch 2 Updated STM 2007 09 18 Pre Beta add immoments Updated STM 2007 10 04 Beta update Updated STM 2007 10 10 Beta add export Updated STM 2007 11 08 Beta Patch 0 5 add RRusk stuff 389 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS Updated Updated Updated Updated Updated Updated Updated HHH HHH HH HHH HH HHH HH HH HHH HH HHHH HHH HH HHH HH HH HH HHH HH HOH OF Input Data D array STM STM STM STM STM STM STM Fea
563. sun e Positioning bombsight This tool can place a crosshair marker on the display to select a position It is used to flag Measurement Set data or to select an image position for spectral profiles Click on the desired position with the tool s mouse button to place the crosshair once placed you can drag it to other locations Double click is not needed for this tool See 8 for more detail CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 262 e Rectangle and Polygon region drawing The rectangle region tool is assigned to the right mouse button by default As with the zoom tool a rectangle region is generated by dragging with the assigned mouse button the selection is confirmed by double clicking within the rectangle Polygon regions are created by clicking the assigned mouse button at the desired vertices clicking the final location twice to finish Once created a polygon can be moved by dragging from inside or reshaped by dragging the handles at the vertices Double click inside to confirm region selection See 7 2 3 for the uses of this tool Polyline drawing A polyline can be created by selecting this tool It is manipulated similarly to the polygon region tool create segments by clicking at the desired positions and then double click to finish the line Uses for this tool are still to be implemented The main Display Area lies below the toolbars Underneath the display area is an Animator panel The most prominent feat
564. supported by CASA CASA will read and write standard compliant FITS images FITS image files that are not WCS compliant are accepted by applying a dummy linear coordinate along each axis In FITS images all brightness units complying with the FITS standard v3 0 are recog nized Non recognized units are accepted and treated as non dimensional The unit maps in quanta and the FITS unit add on were extended to cover the FITS standard v3 0 There is a new task called imsmooth that will smooth images in the spectral and XY planes 6 10 All of the image analysis tasks imstat imval etc with the region parameter have been updated to take as input region file name saved by the viewers region manager region name stored with the image given by imagename region in any image with the syntax image_filename region_name e New viewer features The viewer Maximum Contour slider has been replaced with the Unit Contour slider found under basic settings 7 3 2 The region manager on the viewer has changed and you can now save regions with an image file and or on disk 7 3 5 e New single dish processing features The sdfit task now has the capability to plot the whole spectral region to see the entire spectral shape when the fitted result is verified A 2 1 7 In the sdbaseline and sdcal tasks the parameter interactive has been renamed as verify A 2 1 In the sdcal task in
565. sweight and implied by the gridding weights ftmachine and weighting 5 3 4 6 The threshold revisited For mosaics the specification of the threshold is not straightforward as it is in the single field case This is because the different fields can be observed to different depths and get different weights in the mosaic For efficiency clean does its component search on a weighted and scales version of the sky For ftmachine ft the minor cycles of the deconvolution are performed on an image that has been weighted to have constant noise as in SAULT weighting see 5 3 4 5 This is equivalent to making a dirty mosaic by coadding dirty images made from the individual pointings with a sum of the mosaic contributions to a given pixel weighted by so as to give constant noise across the image This means that the flux scale can vary across the mosaic depending on the effective noise higher weighted regions have lower noise and thus will have higher fluxes in the SAULT map Effectively the flux scale that threshold applies to is that at the center of the highest weighted mosaic field with higher noise regions down scaled accordingly Compared to the true CHAPTER 5 SYNTHESIS IMAGING 208 sky this image has a factor of the PB plus a scaling map returned in the flux image You will preferentially find components in the low noise regions near mosaic centers When ftmachine mosaic the underlying deconvolution
566. symbols rotated hexagon symbols pentagon symbols vertical line symbols horizontal line symbols steps use gnuplot style steps kwarg only The following color abbreviations are supported blue green red cyan magenta yellow black w white waryrPPWNRFAKAOUOHMH CHAVA SC AS BaAK OB OO In addition you can specify colors in many weird and wonderful ways including full names green hex strings 008000 RGB or RGBA tuples 0 1 0 1 or grayscale intensities as a string 0 8 Line styles and colors are combined in a single format string as in bo for blue circles CHAPTER 3 DATA EXAMINATION AND EDITING 112 3 4 3 5 showflags The showflags parameter determines whether only unflagged data showflags False or flagged showflags True data is plotted by this execution The default is False and will show only unflagged good data Note that if you want to plot both unflagged and flagged data in different colors then you need to run plotxy twice using overplot see 3 4 3 2 the second time e g gt plotxy vis myfile xaxis uvdist yaxis amp gt plotxy vis myfile xaxis uvdist yaxis amp overplot True showflags True 3 4 3 6 subplot The subplot parameter takes three numbers The first is the number of y panels stacking ver tically the second is the number of xpanels stacking horizontally and the third is the number of the panel you wa
567. t Flagmanager default flagmanager print Now will use flagmanager to list all the versions we saved vis msfile mode list flagmanager Done Flagging print Done with flagging APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS Set the fluxes of the primary calibrator s print Setjy default setjy print Use setjy to set flux of 1331 305 3C286 vis msfile 1331 305 3C286 is our primary calibrator field 1331 305 Setjy knows about this source so we dont need anything more setjyO You should see something like this in the logger and casapy log file 1331 305 spwid 0 I 7 462 Q 0 U 0 V 0 Jy Perley Taylor 99 1331 305 spwid 1 I 7 51 Q 0 U 0 V 0 Jy Perley Taylor 99 print Look in logger for the fluxes should be 7 462 and 7 510 Jy Initial gain calibration print Gaincal default gaincal print Solve for antenna gains on 1331 305 and 0137 331 print We have 2 single channel continuum spw print Do not want bandpass calibration vis msfile set the name for the output gain caltable caltable gtable print Output gain cal table will be gtable Gain calibrators are 1331 305 and 0137 331 FIELD_ID 7 and 0 We have 2 IFs SPW 0 1 with one channel each selection is via the field and spw strings field 1331 305 0137 331 430 APPENDIX F APPENDI
568. t Difference fractional diff_momoneavg print print Done print gt gt logfile Moment 1 image mean thistest_momoneavg print gt gt logfile Previous mi mean oldtest_momoneavg print gt gt logfile Difference fractional diff_momoneavg print gt gt logfile print gt gt logfile Done Should see output like Clean image max should be 0 0524147599936 Found Image Max 0 0523551553488 Difference fractional 0 00113717290288 Clean image rms should be 0 00202187243849 Found Image rms 0 00202226242982 Difference fractional 0 00019288621809 Moment O image max should be 1 40223777294 Found Moment 0 Max 1 40230333805 HHH H HH HH HH H OF APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS Found Done Difference fractional Moment 1 Mean Difference fractional logfile close print Results are in outfile Moment 1 image mean should be 4 67574844349e 05 1479 77119646 1479 66974528 6 85586935973e 05 F 2 Jupiter VLA continuum polarization 414 This script demonstrates continuum polarization calibration and imaging including self calibration There is also extensive interactive flagging and image analysis The latest version of this script can be found at http casa nrao edu Doc Scripts jupiter6cm_demo py HHEEHHHHHHHHEHHAEHHEEAHHAEHEHEEHHHAEHEHEEH PERRERA HEE HRA RHAE
569. t If mosweight True then individual mosaic fields will receive independent weights which will give optimum signal to noise ratio If mosweight False then the data will be weighted so that the signal to noise ratio is as uniform as possible across the mosaic image 5 3 4 5 Sub parameter scaletype The scaletype parameter controls weighting of pixels in the image plane This sub parameter is activated for Inside the Toolkit imagermode mosaic The im setmfcontrol method gives more options for controlling the pri The default scaletype PBCOR scales the image to have the correct flux scale across it out to the beam level cutoff minpb This means that the noise level will vary across the image being increased by the inverse of the weighted primary beam responses that are used to rescale the fluxes This option should be used with care particularly if your data has very different exposure times and hence intrinsic noise levels between the mosaic fields mary beam and noise across the im age If scaletype SAULT then the image will be scaled so as to have constant noise across it This means that the point source response function varies across the image attenuated by the weighted primary beam s However this response is output in the flux image and can be later used to correct this Note that this scaling as a function of position in the image occurs after the weighting of mosaic fields specified by mo
570. t default use all IFs example 15 this selection is in addition to scanlist field and pollist pollist list of polarization id numbers to select default use all polarizations example 1 this selection is in addition to scanlist field and iflist scanaverage average integs within scans options bool True False default False timeaverage average times for multiple scan cycles options bool True False default False example if True this happens after calibration gt gt gt timeaverage expandable parameter tweight weighting for time average options none var 1 var spec weighted tsys 1 Tsys 2 weighted tint integration time weighted tintsys Tint Tsys 2 median median averaging default none polaverage average polarizations options bool True False default False gt gt gt polaverage expandable parameter pweight weighting for polarization average options none var 1 var spec weighted tsys 1 Tsys 2 weighted APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 317 kernel type of spectral smoothing options hanning gaussian boxcar none default none gt gt gt kernel expandable parameter kwidth width of spectral smoothing kernel options int in channels default 5 example 5 or 10 seem to be popular for boxcar ignored for hanning fixed at 5 chans 0 will turn off gaussian or boxcar plottype type o
571. t description gt lt value gt mosaic lt value gt lt allowed kind enum gt lt value gt mosaic lt value gt lt value gt ft lt value gt lt value gt sd lt value gt lt value gt both lt value gt lt allowed gt lt param gt lt param type bool name mosweight subparam true gt lt description gt Individually weight the fields of the mosaic lt description gt lt value gt False lt value gt lt param gt lt param type string name scaletype subparam true gt lt description gt Controls scaling of pixels in the image plane default SAULT example scaletype PBCOR Options PBCOR SAULT lt description gt lt value gt SAULT lt value gt lt allowed kind enum gt lt value gt SAULT lt value gt lt value gt PBCOR lt value gt lt allowed gt lt param gt lt param type intArray name multiscale gt lt description gt set deconvolution scales pixels default multiscale standard CLEAN lt description gt lt value type vector gt lt value gt lt value gt lt value gt lt param gt lt param type int name negcomponent subparam true gt APPENDIX H APPENDIX WRITING TASKS IN CASA 484 lt description gt Stop cleaning if the largest scale finds this number of neg components lt description gt lt value gt 0 lt value gt lt param gt lt param type bool name interactive gt lt description gt use interactive clean with GUI viewer
572. t initially set to npercycle how many cycles before completion initially equal to niter npercycle and to change the threshold for ending cleaning Typically the user would start with a relatively small number of iterations 50 or 100 to clean the bright emission in tight mask regions and then increase this as you get deeper and the masking covers more of the emission region For extended sources you may end up needing to clean a large number of components 10000 or more and thus it is useful to set niter to a large number to begin with you can always terminate the clean interactively when you think it is done Note that if you CHAPTER 5 SYNTHESIS IMAGING 212 J Viewer Display Panel A P0 AAA 7 7 epa Data Display Panel Tools View Data Display Panel Tools View 244000 EASRA 44092 A3ILAA E de e M S y 318122 21016 2 Blis 2 08 2 8 x ex iterations cycles threshold Add Displayed Plane Next Action iterations cycles threshold a Add Displayed Plane Next Action 00 100 0 05 miy Erase All Channels x Pe e 30 100 0 05 miy Erase All Channels a Pe e Declination 121 J Normal 2 6 Blink Compact se jupiter cm demo clean1 residual 0 0911246 Jy bean Pixel 280 90 0 0 00 54 57 663 04 42 08 058 I 12 443 km s X jupiter6cm demo clean1 model mask contour 0 Pixel 00 54 57 663 04 42 08 058 I 12 443 km s Figure 5 2 Screen sho
573. t lt default gt lt default param start gt lt value type string gt 1 4GHz lt value gt lt description gt Frequency of first image channel e q 1 4GHz lt description gt lt default gt lt default param width gt lt value type string gt 10kHz lt value gt lt description gt Image channel width in frequency units e g 1 0kHz lt description gt lt default gt lt equals gt lt when gt APPENDIX H APPENDIX WRITING TASKS IN CASA 489 lt when param weighting gt lt equals value natural gt lt equals value uniform gt lt equals value briggs gt lt default param robust gt lt value gt 0 0 lt value gt lt default gt lt default param npixels gt lt value gt 0 lt value gt lt description gt number of pixels to determine uv cell size O g8t field of view lt description gt lt default gt lt equals gt lt equals value briggsabs gt lt default param robust gt lt value gt 0 0 lt value gt lt default gt lt default param noise gt lt value type string gt 1 0Jy lt value gt lt default gt lt default param npixels gt lt value gt 0 lt value gt lt description gt number of pixels to determine uv cell size O g8t field of view lt description gt lt default gt lt equals gt lt equals value superuniform gt lt default param npixels gt lt value gt 0 lt value gt lt description gt number of pixels to determine uv cell size O amp gt 3pixels lt descrip
574. t Control Parameters The iteration overplot plotrange plotsymbol showflags and subplot parameters deserve extra explanation 3 4 3 1 iteration There are currently four iteration options available field antenna and baseline If one of these options is chosen the data will be split into separate plot displays for each value of the iteration axis e g for the VLA the antenna option will get you 27 displays one for each antenna BETA ALERT There will eventually be scan and feed options also An example use of iteration choose channel averaging every 5 channels plotxy n5921 ms channel subplot 221 iteration antenna width 5 The results of this are shown in Figure Note that this example combines the use of width iteration and subplot NOTE If you use iteration antenna or baseline be aware if you have set antenna selec tion You can also control whether you see auto correlations or not using the appropriate syntax e g antenna amp amp or antenna amp amp amp 2 6 4 1 3 4 3 2 overplot The overplot parameter toggles whether the current plot will be overlaid on the previous plot or subpanel via the subplot setting section edit plot opt subplot or will overwrite it The default is False and the new plot will replace the old The overplot parameter interacts with the newplot sub parameter see 3 4 2 See 813 4 3 5 fo
575. t Sets calibration tables and images This task brings up the CASA Qt casabrowser which is a separate program You can launch this from outside casapy The default inputs are CHAPTER 3 DATA EXAMINATION AND EDITING 125 browsetable Browse a table MS calibration table image tablename re Name of input table Currently its single input is the tablename so an example would be browsetable ngc5921 ms For an MS such as this it will come up with a browser of the MAIN table see Fig 3 7 If you want to look at sub tables use the tab table keywords along the left side to bring up a panel with the sub tables listed Fig 3 8 then choose left click a table and View Details to bring it up Fig 3 9 You can left click on a cell in a table to view the contents Y Table Browser File Edit View Tools Export Help YX 202 OB arise E uvw FLAG Lac_catecor WEIGHT SIGMA ANTENNAL ANTENNA2 ARRAY_ID pari 3 o 0 0 2 63 Boolean 0 0 0 Boolean 23814 23814 0 0514344 0 1 1 0 o al 0 0 0 2 63 Boolean 0 0 0 Boolean 23814 23814 0 0514344 0 27 27 0 o o 0 0 2 63 Boolean 0 0 0 Boolean 23814 23814 0 0514344 0 7 7 0 0 0 0 0 2 63 Boolean 0 0 0 Boolean 23814 23814 0 0514344 0 2 2 0 o El o 0 0 2 63 Boolean 0 0 0 Boolean 23814 23814 0 05143
576. t changed ie not rephased to the single phase center Use of these parameters is intended to be tolerant of small offsets e g planets tracked which move slightly in J2000 over the course of observations or combining epochs observed with slightly different positions For example default concat vis n4826_16apr split ms n4826_22apr split ms concatvis n4826_tboth ms freqtol 50MHz concat combines the two days in n4826_16apr split ms and n4826_22apr split ms into a new output MS called n4826_tboth ms BETA ALERT There are additional issues when concatenating individual MS files with different spectral windows In this case the rest frequencies if set of these windows may be lost in sub sequent operations e g split If this occurs then you can either set the restfreq explicitly in certain tasks plotxy and clean or use the following snippet of code to fix this up after concat has run HEAHHHRAHHHAAHH HHA HAA HHA E AHHH EA EHH EA EHR A HHA A HRA AHA ARR Fix up the MS after concat NOTE STILL NECESSARY IN 2 4 This ensures that the rest freq will be found for all spws print Fixing up spw rest frequencies in MS vis ngc4826 tutorial ms Example vis name put yours here tb open vis SOURCE nomodify false spwid tb getcol SPECTRAL_WINDOW_ID CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 91 The following is
577. t models directly to visibility data Such fitting has its origins in early interferometry especially VLBI where arrays consisted of only a few CHAPTER 4 SYNTHESIS CALIBRATION 184 antennas and the calibration and deconvolution problems were poorly constrained These methods overcame the calibration uncertainties by fitting the models to calibration independent closure quantities and the deconvolution problem by drastically limiting the number of free parameters required to describe the visibilities Today even with larger and better calibrated arrays it is still desirable to use visibility model fitting in order to extract geometric properties such as the positions and sizes of discrete components in radio sources Fits for physically meaningful component shapes such as disks rings and optically thin spheres though idealized enable connecting source geometry directly to the physics of the emission regions Visibility model fitting is carried out by the uvmodelfit task The inputs are uvmodelfit Fit a single component source model to the uv data vis ay Name of input visibility file field Z field name or index spw A spectral window selectdata False Activate data selection details niter 5 Number of fitting iterations to execute comptype P Component type P pt source G ell gauss D ell disk sourcepar 1 0 0 Starting guess flux xoff yoff bmajaxrat bpa varypar Which parameters can vary in
578. t of printable character that cannot be part of a name i e a name containing this character can never be matched in a MSSelection expression These will be treated as pattern matching even inside double double quotes There is currently no escape mechanism e g via a backslash Some examples of strings regular expressions and patterns e The string LBAND will be used as a literal string for exact match It will match only the exact string LBAND e The wildcarded string BAND will be used as a string pattern for matching This will match any string which has the sub string BAND in it e The string BAND will also be used as a string pattern matching any string which has the sub string BAND in it e The string BAND will be used as a regular expression This will also match any string which as the sub string BAND in it the regex operator has the same meaning as the wildcard operator of patterns 2 6 2 The field Parameter The field parameter is a string that specifies which field names or ids will be processed in the task or tool The field selection expression consists of comma separated list of field specifications inside the string Field specifications can be literal field names regular expressions or patterns see 2 6 1 1 Those fields for which the entry in the NAME column of the FIELD MS sub table match the literal field name regular expression pattern are selected If a field
579. t reports Statistics on ngc5921 usecase clean image Region bottom left corner pixel blc 108 108 0 21 top right corner pixel trc 148 148 0 21 bottom left corner world blcf 15 22 20 076 04 58 59 981 I 1 41332e 09Hz top right corner world trcf 15 21 39 919 05 08 59 981 I 1 41332e 09Hz Values flux flux 0 111799236126 number of points npts 1681 0 maximum value max 0 029451508075 minimum value min 0 00612453464419 position of max value pixel maxpos 124 131 0 21 position of min value pixel minpos 142 110 O 21 position of max value world maxposf 15 22 04 016 05 04 44 999 I 1 41332e 09Hz position of min value world minposf 15 21 45 947 04 59 29 990 I 1 41332e 09Hz Sum of pixel values sum 1 32267159822 Sum of squared pixel values sumsq 0 0284534543692 Statistics Mean of the pixel values mean 0 000786836167885 Standard deviation of the Mean sigma 0 00403944306904 Root mean square rms 0 00411418313161 Median of the pixel values median 0 000137259965413 Median of the deviations medabsdevmed 0 00152346317191 Quartile quartile 0 00305395200849 CHAPTER 6 IMAGE ANALYSIS 247 The return value in xstat is CASA lt 152 gt xstat Out 152 blce array 108 108 0 211 plcf 15 22 20 076 04 58 59 981 I 1 41332e 09Hz flux array 0 11179
580. t to a single SPW at the same time GETI The split task can now do frequency averaging then time averaging consecutively with no issues 4 7 1 The split task datacolumn parameter now takes options data corrected model all GETI e New synthesis imaging features A number of clean improvements were made 1 The mode parameter has a new sub parameter interpolation to control how data is gridded onto the spectral cube axis in channel velolcity and frequency modes This has 3 possible values nearest linear and cubic 5 2 5 5 2 There were a number of cosmetic and fuctional changes made to the interactive clean viewer panel B 3 5 3 In clean if you are reducing data from a telescope whose beam is not found in the list of known arrays in CASA the dish diameter found in the antenna table is used to scale an Airy disk pattern beam B 2 13 4 Option stokes IQU is now available 5 The psfmode settings hogbom does sequential cleaning while clark and csclean do joint convolution 6 For imagermode mosaic the minpb parameter now cuts the imaging off at the specified level in the unweighted primary beam coverage as reflected in the new output image lt imagename gt flux pbcoverage B 3 7 e New image analysis features CHAPTER 1 INTRODUCTION 25 l All of the WCS projections for FITS images described in the FITS standard v3 0 are now
581. t up however and must be imported as a standard Python package A convenience function exists for importing APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 341 ASAP along with a set of prototype tasks for single dish analysis CASA lt 1 gt asap_init Once this is done all of the ASAP functionality is now under the Python sd tool Note This means that if you are following the ASAP cookbook or documentation all of the commands should be invoked with a sd before the native ASAP command The ASAP interface is essentially the same as that of the CASA toolkit that is there are groups of functionality aka tools which have the ability to operate on your data Type CASA lt 4 gt sd lt TAB gt sd __builtins__ sd __class__ sd __date__ sd __delattr__ sd __dict__ sd __doc__ sd __file__ sd __getattribute__ sd __hash__ sd __init_ sd __name_ sd __new__ sd __path__ sd __reduce__ sd __reduce_ex__ sd __repr sd __revision__ sd __setattr__ sd __str__ sd __version__ sd _asap sd _asap_fname sd _asaplog sd _is_sequence_or_number sd _n_bools to see the list of tools sd sd sd sd sd sd sd sd sd sd sd sd sd sd sd sd sd sd sd sd sd sd sd sd sd _validate_bool _validate_int asapfitter asaplinefind asaplog asaplotbase asaplotgui asapmath asapplotter asapreader average_time calfs calnod calps casapath commands defaultParams dosigref d
582. table f2_TSM1 table f7 POINTING table f0 table f3 table f7_TSM1 Note that the MAIN table information is contained in the table files in this directory Each of the sub table sub directories contain their own table dat and other files e g CASA lt 2 gt 1s ngc5921 ms SOURCE IPython system call ls F ngc5921 ms SOURCE table dat table f0 table f0i table info table lock v Find Data E Look in E3 Mome sandrock smyers Testing Patch3 N592 1 ngc5921 GO O O K a El computer ANTENNA ed DATA_DESCRIPTION A spaas FEED FIELD FLAG _CMD HISTORY OBSERVATION POINTING POLARIZATION PROCESSOR SORTED_TABLE SOURCE SPECTRAL_WINDOW STATE Directory Files of type Directories Cancel Figure 2 1 The contents of a Measurement Set These tables compose a Measurement Set named ngc5921 demo ms on disk This display is obtained by using the File Open menu in browsetable and left double clicking on the ngc5921 demo ms directory CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 78 Each row in a table contains entries for a number of specified columns For example in the MAIN table of the MS the original visibility data is contained in the DATA column each cell contains a matrix of observed complex visibilities for that row at a single time stamp for a single baseline in a single spectral window The shape of the data matrix is given by the number of channels and
583. tains extended flux not accounted for in the model e g 4 3 4 1 See 2 6 for more on the selection parameters CHAPTER 4 SYNTHESIS CALIBRATION 143 4 4 1 3 Prior Calibration and Correction parang gaincurve and opacity These parameters control the on the fly application of various calibration or effect based corrections prior to the solving process The parang parameter turns on the application of the antenna based parallactic angle correction P in the measurement equation This is necessary for polarization calibration and imaging or for cases where the parallactic angles are different for geographically spaced antennas e g VLBI For dealing with only the parallel hand corrections e g RR LL XX YY for a co located array e g the VLA or ALMA you can set parang False and save some computational effort Otherwise set parang True to apply this correction There are two control parameters for applying Prior Calibration gaincurve False Apply VLA antenna gain curve correction opacity 0 0 Opacity correction to apply nepers See 4 3 for more on Prior Calibration 4 4 1 4 Previous Calibration gaintable gainfield interp and spwmap Calibration tables that have already been determined can also be applied before solving for the new table gaintable 22 Prior gain calibration table s to apply gainfield gt Field selection on prior gaintable s interp gt Interpolation mode in time
584. tart up screen 1 3 2 Running Tasks and Tools Tools are functions linked to the Python interface which must be called by name with arguments Tasks have higher level capabilities than tools Tasks require input pa BETA ALERT This is a new behavior in Patch 2 and later In previous versions global pa rameters were always used no matter how the task was called CHAPTER 1 INTRODUCTION 43 rameters which maybe be specified when you call the task as a function or be set as parameters in the interface A task like a tool is a function under Python and may be written in Python C or C the CASA toolkit is made up of C functions There are two distinct ways to run tasks You can either set the global CASA parameters relevant to the task and tell the task to go or you can call the task as a function with one or more arguments specified These two invocation methods differ in whether the global parameter values are used or not For example default plotxy vis ngc5921 ms xaxis channel yaxis amp datacolumn data go will execute plotxy with the set values for the parameters see 1 3 5 Instead of using go command 8 1 3 5 3 to invoke the task you can also call the task with no arguments e g default plotxy vis ngc5921 ms xaxis channel yaxis amp datacolumn data plotxy O which will also use the global parameter values Sec
585. tasks and are destroyed to free up memory Three tasks sdaverage sdsmooth and sdbaseline are the workhorse for the calibration selection averaging baseline fitting and smoothing The output datasets for each task are written to a file on disk Alternatively one can use the task sdcal to perform all the steps in the three tasks described above in a single task invocation It is comparable to run sdaverage sdsmooth and sdbaseline in that order since sdcal internally calls these three tasks Its operation is controlled by three main mode parameters calmode which selects the type of calibration if any to be applied APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 292 kernel which selects the smoothing and blmode which selects baseline fitting There are also parameters controlling the selection such as scanlist iflist field scanaverage timeaverage and polaverage Note that sdcal can be run with calmode none to allow re selection or writing out of data that is already calibrated There is a wiring diagram of the dataflow and control inputs for sdcal shown in Figure This might help you chart your course through the calibration The SDtasks support the import and export file formats supported by ASAP itself For import this includes ASAP scantables MS CASA measurement set RPFITS and SDFITS For export this includes ASAP scantables MS CASA measurement set ASCII text file SDFITS a flavor of SD
586. tch the given string exact match regular expression pattern are selected The comma is used only as a separator for the list of antenna specifications The list of baselines specifications is a semi colon separated list e g antenna 1738 46 1011 will select baselines between antennas 1 2 3 and 4 5 6 1 amp 4 1825 3 amp 6 plus baseline 210811 The wildcard operator will be the most often used pattern To make it easy to use the wildcard and only this operator can be used without enclosing it in quotes For example the selection antenna VA will match all antenna names which have VA as the first 2 characters in the name irrespective of what follows after these characters Some examples antenna shows blank autocorr pages antenna amp does not show the autocorrs antenna amp amp show both auto and cross cor default antenna amp amp amp shows only autocorrs antenna 5 amp shows non auto baselines with AN 5 antenna 5 6 amp amp amp AN 5 and 6 autocor antenna 5kk amp 6 amp AN 5 autocor plus cross cors to AN 6 Antenna numbers as names Needless to say naming antennas such that the names can also be parsed as a valid token of the syntax is a bad idea Nevertheless antenna names that contain any of the reserved characters and or can be parsed as integers or integer ranges can still be used by enclosin
587. te Print out some information to the logger on points in the marked regions e Next Step to the next plot in an iteration e Quit Exit plotcal clear the window and detach from the MS These buttons are shared with the plotcal tool 3 4 2 The selectplot Parameters These parameters work in concert with the native matplotlib functionality to enable flexible repre sentations of data displays Setting selectplot True will open up a set of plotting control sub parameters selectplot True Select additional plotting options e g fontsize title etc markersize 5 0 Size of plotted marks linewidth 1 0 Width of plotted lines skipnrows 1 Plot every nth point newplot False Replace the last plot or not when overplotting clearpanel Auto Specify if old plots are cleared or not title 22 Plot title above plot xlabels a Label for x axis ylabels a Label for y axis fontsize 10 0 Font size for labels windowsize 5 0 Window size not yet implemented The markersize parameter will change the size of the plot symbols Increasing it will help legibility when doing screen Inside the Toolkit shots Decreasing it can help in congested plots The For even more functionality you can linewidth parameter will do similar things to the lines access the pl tool directly using Py lab functions that allow one to an notate alter or add to any plot displayed in the matplotlib plotter The skipn
588. ted Example spave stave average_pol weight tsys One can also average scans over time using sd average_time sd average_time scantable mask scanav weight align where Parameters one scan or comma separated scans compel if True enable averaging of multi resolution spectra mask an optional mask only used for var and tsys weighting scanav True averages each scan separately False default averages all scans together weight Weighting scheme none mean no weight var 1 var spec weighted tsys 1 Tsys 2 weighted tint integration time weighted tintsys Tint Tsys 2 median median averaging align align the spectra in velocity before averaging lt takes the time of the first spectrum in the first scantable as reference time Example stave sd average_time scans weight tintsys Note that alignment of the velocity frame should be done before averaging if the time spanned by the scantable is long enough This is done through the align True option in sd average time or explicitly through the sd scantable freq_align function e g CASA lt 62 gt sc sd scantable orions_scan20to23_if0to3 asap False APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 302 CASA lt 63 gt sc freq_align Aligned at reference Epoch 2006 01 19 01 49 23 UTC in frame LSRK CASA lt 64 gt av sd average_times sc The time averaging can also be applied to multiple scantables This
589. telescope VLA observer CASA 6 3 Continuum Subtraction on an Image Cube imcontsub One method to separate line and continuum emission in an image cube is to specify a number of line free channels in that cube make a linear fit to the visibilities in those channels and subtract the fit from the whole cube Note that the task uvcontsub serves a similar purpose see 4 7 4 for a synopsis of the pros and cons of either method The imcontsub task will subtract a polynomial baseline fit to the specified channels from an image cube The default inputs are imcontsub Continuum subtraction on images imagename 12 Name of the input image linefile 20 Output line image file name contfile a Output continuum image file name fitorder O Polynomial order for the continuum estimation region d Image region or name to process see viewer box dis Select one or more box regions chans gt gt Select the channel spectral range stokes ae Stokes params to image I IV IQU IQUV async False Area selection using box and region is detailed in and respectively Image cube plane selection using chans and stokes are described in CHAPTER 6 IMAGE ANALYSIS 235 BETA ALERT imcontsub has issues when the image does not contain a spectral or stokes axis Errors are generated when run on an image missing one or both of these axes You will need to use the Toolkit e g the ia adddegaxes method to add degenerate
590. teractive mask selection is enabled with blmode interact GEZI It is now possible in sdplot to get statistics by selecting a region with mouse button on a plot displayed by the task A 2 1 10 There are a number of other changes as this CASA module is under continuous devel opment See the Appendix A for the latest guide e New simulator features The simulator task is now called simdata used to be almasimmos This task has many new features B 1 1 1 1 Previous changes in Patch3 CASA Beta Release Patch 3 version 2 3 0 was released in December 2008 In January 2009 we released an update to Patch 3 as Version 2 3 1 This fixed and updated a small number of issues encountered in the original Patch 3 release version 2 3 0 CHAPTER 1 INTRODUCTION 26 e New e New e New e New e New interface changes The versioning of CASA has changed such that the startup and casalog version now report Version X Y Z where X 2 for the Beta Release Y is the Patch number and Z is the sub patch release For example the December 2008 Patch 3 0 release is Version 2 3 0 data handling features The importasdm task now has better handling of ALMA ATF data 2 2 3 plotting and flagging features The plotxy task now has the extendflag parameter and sub parameters that allow the extension of interactive flagging to data cells beyond those plotted 3 4 6 The plotxy task now has the restfreq para
591. th in this case The output table name is placed in caltable Be sure to give a unique name to the output table or be careful If the table exists then what happens next will depend on the task and the values of other parameters e g 4 4 1 6 The task may not execute giving a warning that the table already exists or will go ahead and overwrite the solutions in that table or append them Be careful 4 4 1 2 Selection field spw and selectdata Selection is controlled by the parameters field d field names or index of calibrators gt all spw ae spectral window channels gt all selectdata False Other data selection parameters Field and spectral window selection are so often used that we have made these standard parameters field and spw respectively The selectdata parameter expands as usual uncovering other selection sub parameters selectdata True Other data selection parameters timerange a time range gt all uvrange a8 uv range gt all antenna oe antenna baselines gt all scan a9 scan numbers Not yet implemented msselect g Optional data selection Specialized but see help Note that if selectdata False these parameters are not used when the task is executed even if set underneath The most common selectdata parameter to use is uvrange which can be used to exclude longer baselines if the calibrator is resolved or short baselines of the calibrator con
592. the XML medata 1 16 s The measurement About to create The The The The The The The The The The The The The The The dataset dataset dataset dataset dataset dataset dataset dataset dataset dataset dataset dataset dataset dataset dataset has has has has has has has has has has has has has has has set will be filled with complex data a new measurement set home basho3 jmcmulli ASDM ExecBlock3 ms 4 antennas successfully copied them into the measurement set 33 spectral windows successfully copied them into the measurement set 4 polarizations successfully copied them into the measurement set 41 data descriptions successfully copied them into the measurement set 125 feeds successfully copied them into the measurement set 2 fields successfully copied them into the measurement set O flags O historys 1 execBlock s successfully copied them into the measurement set 12 pointings successfully copied them into the measurement set 3 processors successfully copied them into the measurement set 72 sources successfully copied them into the measurement set 3 states 132 calDevices 72 mains Processing row O in MainTable Entree ds getDataCols About to clear About to getData About to new VMSData Exit from getDataCols ASDM Main table row 0 transformed into 40 MS Main table rows Processing row 1 in MainTable Entree ds getDataCols About to c
593. the cross correlations But this slows things down immensely extendflag T extendcorr all xaxis uvdist spw 1 antenna iteration antenna plotxy O As you step through you will see that Antenna 9 ID 8 is often bad in this spw If you box and do Locate or remember from 0137 331 its probably a bad time print print S s s SSH passe 9221202 1 ee Reo ai ES m print Looking now at SPW 1 print Now we set iteration to Antenna print Step through antennas with Next print See bad Antenna 9 ID 8 as in 0137 331 print Do not flag yet we will isolate this next Pause script if you are running in scriptmode if scriptmode APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 428 user_check raw_input Return to continue script n The easiset way to kill it antenna 9 iteration xaxis time correlation extendflag F plotxy O Draw a box around all points in the last bad scans and flag em print print 1 2 gt gt sss Sessa sae SSS Sn 222 2 print Now plotting vs time antenna 9 spw 1 print Box up the bad scans and Flag Pause script if you are running in scriptmode if scriptmode user_check raw_input Return to continue script n Now clean up the rest xaxis uvdist correlation RR LL As of 2 3 0 Patch 3 you can extend the flags to the cross correlations But this slows
594. the intensity image we arrive at the final polar ization image of Jupiter Shown in the viewer superimposed on the intensity raster is the linear polarization intensity green contours and linear polarization B vectors vectors The color of the contours and the sampling and rotation by 90 degrees of the vectors was set in the Display Options panel A LEL expression was used in the Load Data panel to mask the vectors on the polarized intensity The primary beams used in CASA are described in 5 2 13 If ftmachine mosaic then the data are gridded onto a single uv plane which is then trans formed to produce the single output image This is accomplished by using a gridding kernel that approximates the transform of the primary beam pattern Note that for this mode the lt imagename gt flux image includes this convolution kernel in its effective weighted response pat tern needed to primary beam correct the output image For this mode only an additional image lt imagename gt flux pbcoverage is produced that is the primary beam coverage only used to compute the minpb cutoff 5 3 7 BETA ALERT In order to avoid aliasing artifacts for ftmachine mosaic in the mosaic image due to the discrete sampling of the mosaic pattern on the sky you should make an image in which CHAPTER 5 SYNTHESIS IMAGING 216 Y Viewer Display Panel Data Display Panel Tools View X BEARS weAaDBDAAG James aff oo do Ne
595. the solving CHAPTER 4 SYNTHESIS CALIBRATION 157 4 4 5 Instrumental Polarization Calibration D X BETA ALERT The polcal task is now available as of Beta Patch 1 It is still undergoing extensive testing and only basic capabilities are currently provided The inputs to polcal are polcal Determine instrumental polarization from calibrator observations vis ae Nome of input visibility file caltable ma Name of output gain calibration table field 22 Select field using field id s or field name s spw ne Select spectral window channels selectdata False Other data selection parameters solint inf Solution interval combine scan Data axes which to combine for solve scan spw and or field preavg 300 0 Pre averaging interval sec refant q Reference antenna name minblperant 4 Minimum baselines _per antenna_ required for solve minsnr 0 0 Reject solutions below this SNR poltype gt D QU Type of instrumental polarization solution see help append e False Append solutions to the existing table gaintable Gain calibration table s to apply gainfield Select a subset of calibrators from gaintable s interp Interpolation mode in time to use for each gaintable spwmap Spectral windows combinations to form for gaintables s gaincurve False Apply internal VLA antenna gain curve correction opacity 0 0 Opacity correction to apply nepers
596. then usually paste this where you wish BETA ALERT this does not work routinely in the current version You are best off going to the casapy log file if you want to grab text e Open There is an Open function in the File menu and an Open button that will allow you to load old casalogger files BETA ALERT You cannot see the old casapy log files with timestamps e g names like casapy log 2009 05 26T22 24 31 currently in the file browser but you can type the name in explicitly and hit lt return gt to view them Other operations are also possible from the menu or buttons Mouse flyover will reveal the operation of buttons for example 1 4 2 1 Starup options for the logger One can specify logger options at the startup of casapy on the command line CHAPTER 1 INTRODUCTION 61 hd Log Messages sandrock home sandrock3 smyers Testing3 Patch4 N5921 casapy log 0 File Edit View a mi B A Search Message dto Filter Time yl Y e Time Priority Origin Message 2009 05 27 04 48 05 INFO imstat 2009 05 27 04 48 05 INFO Statistics 2009 05 27 04 48 05 INFO Mean of the pixel values mean 1484 1 2009 05 27 04 48 05 INFO Variance of the pixel values 3003 86 2009 05 27 04 48 05 INFO Standard deviation of the Mean sigma 54 8075 2009 05 27 04 48 05 INFO Root mean square rms 1485 1 Median of the pixel values median 1479 59 2009 05 27 04 48 05 INFO Median of the deviati
597. things down immensely extendflag T extendcorr all antenna spw 7 You will be drawing many tiny boxes so remember you can use the ESC key to get rid of the most recent box if you make a mistake plotxy O Note that the end result is we ve flagged lots of points in RR and LL We will rely upon imager to ignore the RL LR for points with RR LL flagged print print O SS print Final cleanup of JUPITER data print Back to uvdist plot see remaining bad data print You can draw little boxes around the outliers and Flag print Depends how patient you are in drawing boxes print Could also use Locate to find where they come from APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 429 print wee print NOTE These flags will extend to the RL LR cross hands print Because of this the flagging will be slower than otherwise Pause script if you are running in scriptmode if scriptmode user_check raw_input Return to continue script n print Done with plotxy Use Flagmanager to save a copy of the flags so far print Flagmanager default flagmanager print Now will use flagmanager to save a copy of the flags we just made print These are named xyflags vis msfile mode save versionname xyflags comment Plotxy flags merge replace flagmanager Se Use Flagmanager to list all saved versions prin
598. tilities ia Image analysis utilities im Imaging utilities me Measures utilities ms MeasurementSet MS utilties mp MS plotting data amp phase versus other quantities tb Table utilities selection extraction etc tp Table plotting utilities qa Quanta utilities sm Simulation utilities vp Voltage pattern primary beam utilties pl pylab functions e g pl title etc You can find much more information about the toolkit in the CASA User Reference Manual http casa nrao edu docs casaref CasaRef html 1 4 Getting the most out of CASA There are some other general things you should know about using CASA in order to make things go smoothly during your data reduction CHAPTER 1 INTRODUCTION 58 1 4 1 Your command line history Your command line history is automatically maintained and stored as ipython log in your local di rectory This file can be edited and re executed as appropriate using the execfile lt filename gt feature You can also use the up arrow and down arrow keys for command line recall in the casapy interface If you start typing text and then use up arrow you will navigate back through commands matching what you typed 1 4 2 Logging your session The output from CASA commands is sent to the file casapy log also in your local directory Whenever you start up casapy the previous casapy log is renamed based on the date and time and a new log file is started
599. tings for TO are as above 5 timerange lt T1 Select all times less than T1 For example timerange lt 2007 10 09 23 41 00 Default settings for T1 are as above An ultra conservative selection might be timerange 1960 01 01 00 00 0072020 12 31 23 59 59 which would choose all possible data 2 6 4 4 The uvrange Parameter Rows in the MS can also be selected based on the uv distance or physical baseline length that the visibilities in each row correspond to This uvrange can be specified in various formats The basic building block of uv distance specification is a valid number with optional units in the format N UNIT the unit in square brackets is optional We refer to this basic building block as UVDIST The default unit is meter Units of length such as m and km select physical baseline distances independent of wavelength The other allowed units are in wavelengths such as lambda klambda and Mlambda and are true uv plane radii Tin u 02 2 1 If only a single UVDIST is specified all rows the uv distance of which exactly matches the given UVDIST are selected UVDIST can be specified as a range in the format NO N1 UNIT where NO and N1 are valid numbers All rows corresponding to uv distance between NO and N1 inclusive when converted the specified units are selected CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 100 UVDIST can also be selected via compa
600. tion all Panel number on display screen yxn Overplot solutions on existing display Specify if old plots are cleared or not Iterate on antenna time spw field plot axes ranges xmin xmax ymin ymax If true show flags pylab plot symbol initial plotting color size of plot symbols size of label font Show plot on gui no plot hardcopy otherwise supply name 2073 BETA ALERT Currently plotcal needs to know the MS from which caltable was derived to get indexing information It does this using the name stored inside the table which does not include the full path but assumes the MS is in the cwd Thus if you are using a MS in a directory other than the current one it will not find it You need to change directories using cd in Python or os chdir inside a script to the MS location The controls for the plotcal window are the same as for plotxy see 3 4 1 The xaxis and yaxis plot options available are e amp amplitude e phase phase e real the real part e imag the imaginary part e snr the signal to noise ratio of the calibration solutions that are in the caltable The xaxis choices also include time and channel which will be used as the sensible defaults if xaxis for gain and bandpass solutions respectively CHAPTER 4 SYNTHESIS CALIBRATION 163 The poln parameter determines what polarization or combination of polarization is bei
601. tion below specunit units for spectral axis options str channel km s GHz MHz kHz Hz default current example this will be the units for masklist frame frequency frame for spectral axis options str LSRK REST TOPO LSRD BARY GEO GALACTO LGROUP CMB default currently set frame in scantable WARNING frame REST not yet implemented doppler doppler mode options str RADIO OPTICAL Z BETA GAMMA default currently set doppler in scantable calmode calibration mode options ps nod fs fsotf quotient none default none example choose mode none if you have already calibrated and want to try baselines or averaging APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 303 scanlist list of scan numbers to process default use all scans example 21 22 23 24 this selection is in addition to field iflist and pollist field selection string for selecting scans by name default no name selection example FLS3a this selection is in addition to scanlist iflist and pollist iflist list of IF id numbers to select default use all IFs example 15 this selection is in addition to scanlist field and pollist pollist list of polarization id numbers to select default use all polarizations example 1 t
602. tion gt lt default gt lt equals gt lt when gt lt when param uvtaper gt lt equals type bool value False gt lt equals type bool value True gt lt default param outertaper gt lt value type vector gt lt value gt lt default gt lt default param innertaper gt lt value type vector gt lt value gt lt default gt lt equals gt lt when gt lt when param interactive gt lt equals type bool value False gt lt equals type bool value True gt lt default param npercycle gt lt value gt 100 lt value gt lt default gt lt equals gt lt when gt lt when param imagermode gt lt equals value gt lt equals value csclean gt lt default param cyclefactor gt lt value gt 1 5 lt value gt lt default gt lt default param cyclespeedup gt lt value gt 1 lt value gt lt default gt lt equals gt lt equals value mosaic gt APPENDIX H APPENDIX WRITING TASKS IN CASA 490 lt default param mosweight gt lt value gt False lt value gt lt default gt lt default param ftmachine gt lt value type string gt mosaic lt value gt lt default gt lt default param scaletype gt lt value type string gt SAULT lt value gt lt default gt lt default param cyclefactor gt lt value gt 1 5 lt value gt lt default gt lt default param cyclespeedup gt lt value gt 1 lt value gt lt default gt lt equals gt lt when gt lt Get rid of that soon lt when
603. tion happens transparently as the input data contains the Tsys measurements taken during the observations The nominal Tsys values may be in Kelvin or Jansky The user may wish to apply a Tsys correction or apply gain elevation and opacity corrections A 3 4 1 Tsys scaling If the nominal Tsys measurement at the telescope is wrong due to incorrect calibration the scale function allows it to be corrected scans scale 1 05 tsys True by default only the spectra are scaled and not the corresponding Tsys unless tsys True A 3 4 2 Flux and Temperature Unit Conversion To convert measurements in Kelvin to Jansky and vice versa the convert_flux function may be used This converts and scales the data to the selected units The user may need to supply the aperture efficiency telescope diameter or the Jy K factor scans convert_flux eta 0 48 d 35 Unknown telescope scans convert_flux jypk 15 Unknown telescope alternative scans convert_flux known telescope mostly AT telescopes scans convert_flux eta 0 48 if telescope diameter known A 3 4 3 Gain Elevation and Atmospheric Optical Depth Corrections At higher frequencies it is important to make corrections for atmospheric opacity and gain elevation effects NOTE Currently the MS to scantable conversion does not adequately populate the azimuth and elevation in the scantable As a result one must calculate these via scans recalc_azel Computed azimuth elevation using
604. tion tables these are in the form of standard CASA tables and hold the calibration solutions or parameterizations thereof e task parameters sometimes the calibration information is in the form of CASA task parameters that tell the calibration tasks to turn on or off various features contain important values such as flux densities or list what should be done to the data At its most basic level Calibration in CASA is the process of taking uncalibrated data setting up the operation of calibration tasks using parameters solving for new calibration tables and then applying the calibration tables to form calibrated data Iteration can occur as necessary with the insertion of other non calibration steps e g self calibration via imaging 4 2 2 Keeping Track of Calibration Tables The calibration tables are the currency that is exchanged between the calibration tasks The solver tasks gaincal bandpass blcal fringecal take in the MS which may have a cali bration model in the MODEL_DATA column from setjy or ft and previous calibration tables and will output an incremental calibration table it increments the previous calibration if any This table can then be smoothed using smoothcal if desired You can accumulate the incremental calibration onto previous calibration tables with accum which will then output a cumulative calibration table This task will also interpolate onto a different time sca
605. to scanlist and iflist iflist list of IF id numbers to select default use all IFs example 15 this selection is in addition to scanlist and field pollist list of polarization id numbers to select default use all polarizations example 1 this selection is in addition to scanlist field and iflist maskflag list of mask regions to apply flag unflag default entire spectrum example 1000 3000 5000 7000 flagmode flag mode default flag options flag unflag restore in restore mode a history of flagging is displayed and current flag state is returned outfile Name of output file default lt sdfile gt _f outform format of output file options ASCII SDFITS MS ASAP default ASAP example the ASAP format is easiest for further sd processing use MS for CASA imaging overwrite overwrite the output file if already exists options bool True False default False WARNING if outform ASCII this parameter is ignored plotlevel control for plotting of results options int O none l some 2 more lt 0O hardcopy APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 309 default O no plotting example plotlevel lt 0 as abs plotlevel e g 1 gt hardcopy of final plot will be named lt outfile gt _flag eps WARNING be careful plotting in fsotf mode Returns Current values of maskflag for each spectrum a
606. tore MSs or images multiple layers such as contour over raster and LEL displays You can also the save the panel state with no data loaded to restore preferred initial settings such as overall panel size Animation and zoom state should likewise restore themselves Restore is fairly forgiving about data location and will find files located e in the original location recorded in the restore file e in the current working directory where you started the viewer e in the restore file s directory e in the original location relative to the restore file This means that restore files will generally work if moved together with data files The process is less forgiving if you save the display of an LEL image expression however the files must be in the locations specified in the original LEL expression If a data file is not found restore will attempt to proceed but results will vary Restore files are in ascii xml format and some obvious manual edits are possible However these files are longer and more complex than you might imagine Use caution and back up restore files you want to preserve If you make a mistake the viewer may not recognize the file as a restore file other unexpected results could also occur It is usually easier and safer to make changes on the display panel and then save the restore file again 7 2 3 Region Selection and Positioning You can draw regions or select positions on the display with the mouse once you
607. tput images field 20 Field Name spw Ye Spectral windows channels is all selectdata False Other data selection parameters mode channel Type of selection mfs channel velocity frequency nchan 46 Number of channels planes in output image start 5 first input channel to use width 1 Number of input channels to average interpolation nearest Spectral interpolation nearest linear cubic niter 6000 Maximum number of iterations and now we wish to switch to a different one We can reset the parameter values using default CASA lt 41 gt default gt default CASA lt 42 gt inp sss gt inp clean Deconvolve an image with selected algorithm vis d name of input visibility file imagename ae Pre name of output images field ner Field Name spw es Spectral windows channels is all selectdata False Other data selection parameters mode mfs Type of selection mfs channel velocity frequency niter 500 Maximum number of iterations It is good practice to use default before running a task if you are unsure what state the CASA global variables are in BETA ALERT You currently can only reset ALL of the parameters for a given task to their defaults In an upcoming update we will allow the default command to take a second argument with a specific parameter to default its value 1 3 5 3 The go Command You can execute a task
608. ts of the interactive clean window during deconvolution of the VLA 6m Jupiter dataset We start from the calibrated data but before any self calibration In the initial stage left the window pops up and you can see it dominated by a bright source in the center Next right we zoom in and draw a box around this emission We have also at this stage dismissed the tape deck and Position Tracking parts of the display as they are not used here We have also changed the iterations to 30 for this boxed clean We will now hit the Next Action Continue Cleaning button the green clockwise arrow to start cleaning change iterations you may also want to change cycles or your clean may terminate before you expect it to For strangely shaped emission regions you may find using the polygon region marking tool the second from the right in the button assignment toolbar the most useful See the example of cleaning and self calibrating the Jupiter 6cm continuum data given below in Appendix F 2 The sequence of cleaning starting with the raw externally calibrated data is shown in Figures The final result of all this cleaning for Jupiter is shown in Figure 5 5 The viewer 8 7 was used to overplot the polarized intensity contours and linear polarization vectors calculated using immath 6 5 on the total intensity See the following chapters on how to make the most of your imaging results CHAPTER 5 SYNTHESIS IMAGING 213
609. tting Use the uvcontsub 4 7 4 split 4 7 1 and uvmodelfit 4 7 5 tasks The flow chart and the above list are in a suggested order However the actual order in which you will carry out these operations is somewhat fluid and will be determined by the specific data reduction use cases you are following For example you may need to do an initial Gain Calibration on your bandpass calibrator before moving to the Bandpass Calibration stage Or perhaps the polarization leakage calibration will be known from prior service observations and can be applied as a constituent of Prior Calibration 4 2 1 The Philosophy of Calibration in CASA Calibration is not an arbitrary process and there is a methodology that has been developed to carry out synthesis calibration and an algebra to describe the various corruptions that data might be subject to the Hamaker Bregman Sault Measurement Equation ME described in Appendix E The user need not worry about the details of this mathematics as the CASA software does that for CHAPTER 4 SYNTHESIS CALIBRATION 132 you Anyway its just matrix algebra and your familiar scalar methods of calibration such as in AIPS are encompassed in this more general approach There are a number of physical components to calibration in CASA e data in the form of the Measurement Set 2 1 The MS includes a number of columns that can hold calibrated data model information and weights e calibra
610. tudes and phases among other things can be plotted against several x axis options Interactive flagging i e see it flag it is possible on the plotxy X Y displays of the data 8 3 4 5 Since flags are inserted into the measurement set it is useful to backup or make a copy of the current flags before further flagging is done using flagmanager 3 2 Copies of the flag table can also be restored to the MS in this way CHAPTER 1 INTRODUCTION 68 1 5 2 2 Flag the Data Non interactively The flagdata task 3 5 will flag the visibility data set based on the specified data selections The listobs task 2 3 may be run e g with verbose True to provide some of the information needed to specify the flagging scope 1 5 2 3 Viewing and Flagging the MS The CASA viewer can be used to display the data in the MS as a grayscale or color raster image The MS can also be edited Use of the viewer on an MS is detailed in 7 4 1 5 3 Calibration The major calibration tasks are e setjy Computes the model visibilities for a specified source given a flux density or model image knows about standard calibrator sources 4 3 4 e bandpass Solves for frequency dependent bandpass complex gains 4 4 2 gaincal Solves for time dependent frequency independent complex gains 4 4 3 e fluxscale Bootstraps the flux density scale from standard calibrators 4 4 4 polcal polarization calib
611. tures Tested The script illustrates end to end processing with CASA as depicted in the following flow chart 2008 03 25 2008 05 23 2008 06 11 2008 06 13 2008 06 14 2008 07 06 2009 05 26 Beta Beta Beta Beta Beta Beta Beta Process Vv NGC5921 fits gt importuvfits 1 4GHz 63 sp chan listobs Vv flagautocorr Vv setjy Vv bandpass Vv gaincal Vv fluxscale vV applycal Vv split Vv split Vv exportuvfits Vv uvcontsub gt gt gt gt gt gt gt gt gt Patch Patch Patch Patch Patch Patch Patch PBNNNNNR 0 0 0 0 0 0 0 new tasking clean cal demo version post school update regression version McMaster demo Filenames will have the lt prefix gt ngc5921 demo Output Data lt prefix gt ms lt prefix gt ms flagversions casapy log lt prefix gt bcal lt prefix gt gcal lt prefix gt fluxscale lt prefix gt ms lt prefix gt cal split ms lt prefix gt src split ms lt prefix gt split uvfits lt prefix gt ms cont lt prefix gt ms contsub HHH H HHH H HHH HH HHH HH HH HHH HH HHHH HHH HH HHH HH HHH HHH HH HH HOF 390 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS v clean gt lt prefix gt clean image lt prefix gt clean model lt prefix gt clean residual v exportfits gt lt prefix gt c
612. ty data is using inside the Toolkit the plotxy task This task also provides editing capability Access to matplotlib is also pro CASA uses the matplotlib plotting library to display its videg through the pl tool See be plots You can find information on matplotlib at low for a description of the pl tool matplotlib sourceforge net fmetions hd CASA Plotter Jupiter 6cm uncalibrated o E a jo 5 3 E a 10 UV Distance klambda 0 O Ba Figure 3 1 The plotxy plotter showing the Jupiter data versus uv distance You can see bad data in this plot The bottom set of buttons on the lower left are 1 2 3 Home Back and Forward Click to navigate between previously defined views akin to web navigation 4 Pan Click and drag to pan to a new position 5 Zoom Click to define a rectangular region for zooming 6 Subplot Configuration Click to configure the parameters of the subplot and spaces for the figures 7 Save Click to launch a file save dialog box The upper set of buttons in the lower left are 1 Mark Region Press this to begin marking regions rather than zooming or panning 2 3 4 Flag Unflag Locate Click on these to flag unflag or list the data within the marked regions 5 Next Click to move to the next in a series of iterated plots Finally the cursor readout is on the bottom right CHAPTER 3 DATA EXAMINATION AND EDITING 105 To bring up this plotter use the
613. ty scales or point sources of unit flux density if the flux density is unknown The MODEL_DATA column can also be filled with a model generated from an image of the source e g the Fourier transform of an image generated after initial calibration of the data The inputs for setjy are setjy Place flux density of sources in the measurement set vis axe Name of input visibility file field dd Field name list or field ids list spw Y Spectral window identifier list modimage oo Model image name fluxdensity A Specified flux density 1 Q U V standard Perley Taylor 99 Flux density standard CHAPTER 4 SYNTHESIS CALIBRATION 138 Table 4 1 3C Name B1950 Name J2000 Name 3C286 1328 307 1331 305 3C48 0134 329 0137 331 3C147 0538 498 0542 498 3C138 0518 165 0521 166 1934 638 3C295 1409 524 1411 522 By default the setjy task will cycle through all fields and spectral windows setting the flux density either to 1 Jy unpolarized or if the source is recognized as one of the calibrators in the above table to the flux density assumed unpolarized appropriate to the observing frequency For example to run setjy on a measurement set called data ms setjy vis data ms This will set all fields and spectral windows BETA ALERT At this time all that setjy does is to fill the MODEL_DATA column of the MS with the Fourier transform of a source model The ft task will do the same thing
614. uch that Hamaker J P Bregman J D amp Sault R J 1996 Astronomy and Astrophysics Supplement v 117 p 137 147 384 APPENDIX E APPENDIX THE MEASUREMENT EQUATION AND CALIBRATION 385 Jij Ji Jj For the rest of this chapter we will usually assume that Jj is factorable in this way unless otherwise noted As implied above J may also be factored into the sequence of specific corrupting effects each hav ing their own particular relative importance and physical origin which determines their unique algebra Including the most commonly considered effects the Measurement Equation can be writ ten Vij Mij Bij Gig Dig Eig Pig Tig VPA where e Ti Polarization independent multiplicative effects introduced by the troposphere such as opacity and path length variation e Pi Parallactic angle which describes the orientation of the polarization coordinates on the plane of the sky This term varies according to the type of the antenna mount e Fij Effects introduced by properties of the optical components of the telescopes such as the collecting area s dependence on elevation e Di Instrumental polarization response D terms describe the polarization leakage between feeds e g how much the R polarized feed picked up L polarized emission and vice versa e Gij Electronic gain response due to components in the signal path between the feed and the correlator This complex gain term Gij includes the
615. ultiple MS 67 1 5 2 Data Examination Editing and Flagging 67 1 5 2 1 Interactive X Y Plotting and Flagging 67 1 5 2 2 Flag the Data Non interactively 204 68 1 5 2 3 Viewing and Flagging the MS 0 68 a eRe we eh ee ee Ea oe ae ee es ee Ss ee 68 1 5 3 1 Prior Calibration 2 2 ee 69 1 5 3 2 Bandpass Calibration 0 0 2 0 0 eee eee 69 1 5 3 3 Gain Calibration 2 2 a 69 tet Auta tag ta ds es ee Be RE dea w de rra 70 1 5 3 5 Examining Calibration Solutions 04 70 Dee Ewe Oe ke BE eee we GE 70 epg a BS Gd A ee A Be ee 70 1 5 3 8 Correcting the Data o e 70 1 5 3 9 Splitting the Data o a 71 1 5 4 Synthesis Imaging e 71 1 5 4 1 Cleaning a single field image or a mosaic 71 1 5 4 2 Feathering in a Single Dish image o 72 A A E O a 72 adenda e a ee ee 72 1 5 6 1 What s in animage 0 020002 ee eee 73 1 5 6 2 Image statistics 2 a 1 5 6 3 Moments of an Image Cube o e 02 1 5 6 4 Image math sr x iga r eate map e e o 1 5 6 5 Regridding an Image e e e 1 5 6 6 Displaying Images e e 1 5 7 Getting data and images out of CASAL o e 2 Visibility Data Import Export and Select
616. um There is also a performance benefit since the continuum is probably the same in each channel of the observation and it is desirable to avoid duplication of effort However the main drawback of subtraction in the uv plane is that it is only strictly correct for the phase center since without the Fourier transform the visibilities only describe the phase center Thus uv plane continuum subtraction will be increasingly poor for emission distributed further from the phase center If the continuum emission is relatively weak it is usually adequate to subtract it in CHAPTER 4 SYNTHESIS CALIBRATION 182 the image plane this is described in the Image Analysis section of this cookbook Here we describe how to do continuum subtraction in the uv plane The uv plane continuum subtraction is performed by the uvcontsub task First determine which channels in your data cube do not have line emission perhaps by forming a preliminary image as described in the next chapter This image will also help you decide whether or not you need to come back and do uv plane continuum subtraction at all The inputs to uvcontsub are uvcontsub Continuum fitting and subtraction in the uv plane vis a Nome of input visibility file field gt Select field using field id s or field name s fitspw ap Spectral window channel selection for fitting the continuum spw oa Spectral window selection for subtraction export solint int Continuu
617. ummary to find the fit quality and the fitted zenith opacity in percent If the zenith opacity is reported as 6 then the actual zenith optical depth value is opacity 0 060 for gaincal and other calibration tasks If there were no tipping scans made for your observation then look for others made in the same band around the same time and weather conditions If nothing is available here then at K and Q bands you might consider using an average value e g 6 in reasonable weather See the VLA memo http www vla nrao edu memos test 232 232 pdf for more on the atmospheric optical depth correction at the VLA including plots of the seasonal variations 4 3 4 Setting the Flux Density Scale using setjy When solving for visibility plane calibration CASA calibration applications compare the observed DATA column with the MODEL_DATA column The first time that an imaging or calibration task is executed for a given MS the MODEL_DATA column is created and initialized with unit point source flux density visibilities unpolarized for all sources e g AMP 1 phase 0 The setjy task is then used to set the proper flux density for flux calibrators For sources that are recognized flux calibrators listed in Table 4 1 setjy will calculate the flux densities Fourier transform the data and write the results to the MODEL_DATA column For the VLA the default source models are customarily point sources defined by the Baars or Perley Taylor flux densi
618. unless you require this feature simply use antnamescheme old 2 2 3 ALMA Filling ALMA Science Data Model ASDM observations The importasdm task will fill an ASDM into a CASA visibility data set MS BETA ALERT Note that ASDM data are not generally available at this time except for com missioning at the ALMA Test Facility ATF and the site Thus this filler is in a development stage Also currently there are no options for filling selected data you get the whole data set Current inputs are importasdm Convert an ALMA Science Data Model observation into a CASA visibility file asdm gt Name of input asdm directory on disk corr_mode all gt Correlation mode on input e g ao co ac srt all Spectral resolution type on input e g fr ca bw time_sampling all Time sampling INTEGRATION i and or SUBINTEGRATION si CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 85 ocorr_ mode compression async For example co Output correlation mode AUTO_ONLY ao CROSS_ONLY co or CROSS_AND_AUTO c False Flag for turning on data compression False Run task asynchronously CASA lt 1 gt importasdm home basho3 jmcmulli ASDM ExecBlock3 Parameter asdm is home basho3 jmcmulli ASDM ExecBlock3 and has type lt type str gt Taking the dataset home basho3 jmcmulli ASDM ExecBlock3 as input Time spent parsing
619. upon the uv locus of that visibility e g a taper to change resolution This is actually controlled by the uvtaper parameter see 5 2 10 The weighting matrix also includes the convolution kernel that distributes that visibility onto the uv plane during gridding before Fourier transforming to make the image of the sky This depends upon the density of visibilities in the uv plane e g natural uniform robust weighting The user has control over all of these BETA ALERT You can find a weighting description in the online User Reference Manual at http casa nrao edu docs casaref imager weight html The weighting parameter expands the menu to include various sub parameters depending upon the mode chosen 5 2 11 1 natural weighting For weighting natural visibilities are weighted only by the data weights which are calculated during filling and calibration and should be equal to the inverse noise variance on that visibility Imaging weight w of sample 7 is given by 1 Wi Wi a 5 1 where the data weight w is determined from o is the rms noise on visibility i When data is gridded into the same uv cell for imaging the weights are summed and thus a higher uv density results in higher imaging weights No sub parameters are linked to this mode choice It is the default imaging weight mode and it should produce optimum image with with the lowest noise highest signal to noise ratio Note t
620. ure 5 1 Close up of the top of the interactive clean window Note the boxes at the left where the iterations cycles and threshold can be changed the buttons that control add erase the application of mask to channels and whether to stop complete or continue cleaning and the row of Mouse button tool assignment icons iterations cycles threshold 100 100 0 05 mly e Displayed Plane All Channels e Add Erase 5 3 4 Parameter imagermode This choose the mode of operation of clean either as single field deconvolution using image plane major and minor cycles only imagermode single field deconvolution using Cotton Schwab CS residual visibilities for major cycles imagermode csclean or multi field mosaics using CS major cycles imagermode mosaic In the default mode imagermode the major and minor clean cycles work off of the gridded FFT dirty image with residuals updated using the PSF calculation algorithm set by the psfmode parameter 5 3 1 This method is not recommended for high dynamic range or high fidelity imaging applications but can be significantly faster than CS clean Note that for this option only if mask no mask or box set then it will clean the inner quarter of the image by default The csclean choice specifies the Cotton Schwab algorithm This opens up the sub parameters imagermode csclean Use csclean or mosaic If use psfmode cyclefactor
621. ure is the tape deck which provides movement between image planes along a selected third dimension of an image cube This set of buttons is only enabled when a registered image reports that it has more than one plane along its Z axis In the most common case the animator selects the frequency channel From left to right the tape deck controls allow the user to e rewind to the start of the sequence i e the first plane e step backwards by one plane e play backwards or repetitively step backwards e stop any current play e play forward or repetitively step forward e step forward by one plane e fast forward to the end of the sequence To the right of the tape deck is an editable text box indicating the current frame channel number and a label showing the total number of frames Below that is a slider for controlling the nominal animation speed To the right is a Full Compact toggle In Full mode the default a slider controlling frame number and a Blink mode control are also available Blink mode is useful when more than one raster image is registered In that mode the tapedeck controls which image is displayed at the moment rather than the particular image plane set that in Normal mode first The registered images must cover the same portion of the sky and use the same coordinate projection Note In Normal mode it is advisable to have only ONE raster image registered at a time to avoid c
622. use the various buttons on the plotxy GUI to control its operation in particular to determine flagging and unflagging behaviors There is a standard row of buttons at the bottom These include left to right e Home The house button 1st on left returns to the original zoom level Step The left and right arrow buttons 2nd and 3rd from left step through the zoom settings you ve visited e Pan The four arrow button 4th from left lets you pan in zoomed plot e Zoom The most useful is the magnifying glass 5th from the left which lets you draw a box and zoom in on the plot e Panels The window thingy button second from right brings up a menu to adjust the panel placement in the plot e Save The disk button last on right saves a png copy of the plot to a generically named file on disk In a row above these there are a set of other buttons left to right e Mark Region If depressed lets you draw rectangles to mark points in the panels This is done by left clicking and dragging the mouse You can Mark multiple boxes before doing something Clicking the button again will un depress it and forget the regions ESC will remove the last region marked e Flag Click this to Flag the points in a marked region e Unflag Click this to Unflag any flagged point that would be in that region even if invisible CHAPTER 3 DATA EXAMINATION AND EDITING 108 e Loca
623. useless and can be avoided entirely e g edge channels or those dominated by Gibbs ringing then spw can be set to select only these channels e g spw 0 4759 channels 4 59 of spw 0 This is not so critical for B solutions as for BPOLY as each channel is solved for independently and poor solutions can be dropped If you have multiple time solutions then these will be applied using whatever interpolation scheme is specified in later tasks The combine parameter 4 4 1 5 can be used to combine data across spectral windows scans and fields 4 4 2 3 BPOLY solutions For some observations it may be the case that the SNR per channel is insufficient to obtain a usable per channel B solution In this case it is desirable to solve instead for a best fit functional form for each antenna using the bandtype BPOLY solver The BPOLY solver naturally enough fits Chebychev polynomials to the amplitude and phase of the calibrator visibilities as a function of frequency Unlike ordinary B a single common BPOLY solution will be determined for all spectral windows specified or implicit in the selection As such it is usually most meaningful to select individual spectral windows for BPOLY solves unless groups of adjacent spectral windows are known a priori to share a single continuous bandpass response over their combined frequency range e g PdBI data The BPOLY solver requires a numb
624. ut of the Python interface Note that there may be spawned subprocesses still running such as the casaviewer or the logger These can be dismissed manually in the usual manner After a crash there may also be hidden processes You can find these by listing processes e g in linux ps elf grep casa or on MacOSX or other BSD Unix ps aux grep casa You can then kill these for example using the Unix kill or killall commands This may be necessary if you are running remotely using ssh as you cannot logout until all your background processes are terminated For example killall ipcontroller or killall Python will terminate the most common post crash zombies CHAPTER 1 INTRODUCTION 32 1 2 7 Python Basics for CASA Within CASA you use Python to interact with the system This does not mean an extensive Python course is necessary basic interaction with the system assigning parameters running tasks is straightforward At the same time the full potential of Python is at the more experienced user s disposal Some further details about Python IPython and the interaction between Python and CASA can be found in Appendix D The following are some examples of helpful hints and tricks on making Python work for you in CASA 1 2 7 1 Variables Python variables are set using the lt parameter gt lt value gt syntax Python assigns the type dynamically as you set the value and thus you can easily give it a non sensical value e
625. uxunit sd scantable get_unit sd scantable getscan sd scantable get_parangle sd scantable getbeam sd scantable getscannos These include functions to get the current values of the states mentioned above as well as as meth ods to query the number of scans IFs and polarizations in the scantable and their designations See the inline help for the individual functions for more information A 3 3 3 Masks Several functions fitting baseline subtraction statistics etc may be run on a range of channels or velocity frequency ranges You can create masks of this type using the create_mask function spave an averaged spectrum spave set_unit channel rmsmask spave create_mask 5000 7000 create a region over channels 5000 7000 rms spave stats stat rms mask rmsmask get rms of line free region rmsmask spave create_mask 3000 4000 invert True choose the region excluding the specified channels The mask is stored in a simple Python variable a list and so may be manipulated using an Python facilities APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 348 A 3 3 4 Scantable Management scantables can be listed via CASA lt 33 gt sd list_scans The user created scantables are scans20to24 s scan27 As every scantable will consume memory if you will not use it any longer you can explicitly remove it via del lt scantable name gt A 3 3 5 Scantable Mathematics It is poss
626. value gt lt param gt lt param type any name phasecenter gt lt description gt Image phase center position or field index lt description gt lt any type variant gt lt value type string gt lt value gt lt param gt lt param type string name restfreq gt lt description gt rest frequency to assign to image see help lt description gt lt value gt lt value gt lt param gt lt param type string name stokes gt lt description gt Stokes params to image eg I IV QU IQUV lt description gt lt value gt I lt value gt lt allowed kind enum gt lt value gt I lt value gt lt value gt IV lt value gt lt value gt QU lt value gt lt value gt IQUV lt value gt lt value gt RR lt value gt lt value gt LL lt value gt lt value gt RRLL lt value gt lt value gt XX lt value gt lt value gt YY lt value gt lt value gt XXYY lt value gt lt allowed gt lt param gt lt param type string name weighting gt lt description gt Weighting to apply to visibilities lt description gt lt value gt natural lt value gt lt allowed kind enum gt lt value gt natural lt value gt lt value gt uniform lt value gt lt value gt briggs lt value gt APPENDIX H APPENDIX WRITING TASKS IN CASA 486 lt value gt briggsabs lt value gt lt value gt radial lt value gt lt value gt superuniform lt value gt lt allowed gt lt param gt lt param type double na
627. ve it iterate over baselines using Next to advance Ignore baselines 1 1 2 2 etc as they would correspond to autocorrelations if they were present they are not in this dataset HHHH OF Interactive plotxy plotxy vis ngc4826 tutorial ms xaxis channel yaxis amp field 0 spw 073 averagemode vector timebin 1e7 crossscans True iteration baseline selectplot True newplot False title Field 0 SPW 073 Pause script if you are running in scriptmode user_check raw_input Return to continue script n Finally look for bad data Here we look at field 8 w o averaging plotxy vis ngc4826 tutorial ms xaxis time yaxis amp field 8 spw 12715 selectplot True newplot False title Field 8 SPW 12715 print You can see some bad data here print Mark Region and Locate look in logger print This is a correlator glitch in baseline 3 9 at 06 19 30 print PLEASE DON T FLAG ANYTHING HERE THE SCRIPT WILL DO IT print In a normal session you could Mark Region and Flag print Here we will use flagdata instead Pause script if you are running in scriptmode user_check raw_input Return to continue script n If you change xaxis channel you see its all channels HHHHHHHHHHHRR EHH HHHHHAAAAHA AREER HORA RRR EHR A RAR AAA AR Flag end channels print Flagdata default flagdata p
628. vide the startup page displayed when entering CASA For example CASA lt 6 gt startup Available tasks accum applycal bandpass flagdata invert sdflag flagmanager listcal sdlist fluxscale listhistory sdplot CHAPTER 1 INTRODUCTION browsetable ft listobs clean gaincal listvis clearcal hanningsmooth makemask clearplot imcontsub mosaic clearstat imhead plotants concat immoments plotcal deconvolve importfits plotxy exportfits importuvfits sdaverag exportuvfits importvls sdbaseli feather imregrid sdcal filecatalog imstat sdciadd find imval sdfit e ne 42 sdsave sdscale sdsmooth sdstat setjy smoothcal specfit split tget uvcontsub uvmodelfit viewer Additional tasks available for ALMA commissioning use still alpha code as of release simdata blcal fringecal importasdm Available tools cb calibrater cp cal plot fg flagger ia image analysis im imager me measures mp MS plot ms MS ga quanta sm simulation tb table tp table plot vp voltage patterns pl pylab functions sd ASAP functions run asap_init to import into CASA casalogger Call up the casalogger if it goes away Help help taskname Full help for task help par parametername Full help for parameter name find string Find occurances of string in doc tasklist Task list organized by catagory taskhelp One line summary of available tasks toolhelp One line summary of available tools startup The s
629. w scantable The calculated statistics are written into a file specified by statfile Interactive mask specification is possible with interactive True Integrated intensity will be shown on the screen and will be included in the saved statfile but not yet available in the returned dictionary Note that multiple scans and IFs can in principle be handled but we recommend that you use scanlist field iflist and pollist to give a single selection for each run See the sdcal description for information on fluxunit conversion and the telescopeparm param eter WARNING If you do have multiple scantable rows then xstat values will be lists Beta Patch 4 New Features e The total intensity of spectrum and the abscissa channel frequency or velocity of maximum and minimum intensities are calculated and returned with their units You can refer to the total intensities with key totint in the returned dictionary while the key max_abscissa and min_abscissa refer to the abscissa of maximum and minimum respectively e The equivalent width is also returned with it s unit in returned dictionary e The overwrite is added to allow overwrite of statfile A 2 1 14 sdtpimaging Keyword arguments sdfile name of input SD MS dataset calmode calibration mode currently only baseline subtraction options baseline none default none example choose mode none if you have already calibrated and want to do
630. while int or zero specify a solution every integration aYou can use time quanta in the string e g solint 1m and solint 60s both specify solution intervals of one minute Note that solint interacts with combine to determine whether the solutions cross scan or field boundaries The parameter controlling the scope of the solution is combine For the default combine solutions will break at scan field and spw boundaries Specification of any of these in combine will extend the solutions over the boundaries up to the solint For example combine spw will combine spectral windows together for solving while combine scan will cross scans Thus to do scan based solutions single solution for each scan set solint inf combine while solint inf combine scan will make a single solution for the entire dataset for a given field and spw You can specify multiple choices for combination combine scan spw CHAPTER 4 SYNTHESIS CALIBRATION 146 for example The reference antenna is specified by the refant parameter This useful to lock the solutions with time effectively rotating after solving the phase of the gain solution for the reference antenna to be zero the exact effect depends on the type of solution You can also run without a reference antenna but in this case the solutions will float with time with a phase that rotates around with the relative weights of
631. will provide details on the current logging setup CASA 12 logstate File ipython log Mode append State active Logging can be turned on and off using the logon logoff commands The second component is the output from applications which is directed to the file casapy log See for more on the casalogger D 8 History and Searching Numbered input output history is provided natively within IPython Command history is also maintained on line CASA 11 x 1 CASA 12 y 3 x CASA 13 z x 2 y 2 CASA 14 x Out 14 1 CASA 15 y Out 15 3 APPENDIX D APPENDIX PYTHON AND CASA 380 CASA 16 z Out 16 10 CASA 17 Out 14 Note Out 17 1 CASA 18 _15 Note Out 18 3 CASA 19 ___ tt Note Dut 19 10 The Out vector contains command output The return value can be accessed by _number The last three return values can be accessed as Command history can be accessed via the hist command The history is reset at the beginning of every CASA session that is typing hist when you first start CASA will not provide any commands from the previous session However all of the commands are still available at the command line and can be accessed through the up or down arrow keys and through searching CASA 22 hist 1 2 3 4 Biz 6 7 8 9 __IP system vi temp py ipmagic run i temp py Note magic commands are designated in this way ipm
632. ws adding and deleting mask regions by drawing rectangles on the plot with mouse Draw a rectangle with LEFT mouse to ADD the region to the mask and with RIGHT mouse to DELETE the region statfile name of output file for line statistics default no output statistics file example stat txt overwrite overwrite the statistics file if already exists options bool True False default False Returns a Python dictionary of line statistics keys rms stddev max max_abscissa min min_abscissa sum median mean gt totint eqw example xstat sdstat print rms xstat rms these can be used for testing in scripts or for regression totint is the integrated intensity sum dx where dx is the abscissa interval in specunit eqw is equivalent width totint mag where mag is either max or min depending on which has greater magnitude Note that both totint and eqw are quantities dictionaries with unit and value APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 324 DESCRIPTION Task sdstat computes basic statistics rms mean median sum for single dish spectra It assumes that the spectra have been calibrated Furthermore it assumes that any time and channel aver aging smoothing has also already been done as there are no controls for these Note that you can run sdcal with calmode none and do selection writing out a ne
633. x should be oldtest_immax print Found Max in image thistest_immax diff_immax abs oldtest_immax thistest_immax oldtest_immax print Difference fractional diff_immax print Now do stats in the lower right corner of the image box ia setboxregion 0 75 0 00 1 00 0 25 frac true off_statistics ia statistics region box thistest_imrms off_statistics rms 0 oldtest_imrms 0 0010449 print Clean image OFF SRC rms should be oldtest_imrms print Found rms in image thistest_imrms diff_imrms abs oldtest_imrms thistest_imrms oldtest_imrms print Difference fractional diff_imrms print print Final Clean image Dynamic Range thistest_immax thistest_imrms print print ia close BETA ALERT Bad things can happen if you open some tools like ia in the Python command line on files and forget to close them before running scripts that use the os system rm rf lt filename gt call to clean up We are in the process of cleaning up cases like this where there can be stale handles on files that have been manually deleted but for the meantime be warned that you might get exceptions usually of the SimpleOrderedMap remove flavor or even Segmentation Faults and core dumps 6 13 Examples of CASA Image Analysis See the scripts provied in Appendix F for examples of data and image analysis In particular we refer t
634. xes and same axes length as the images supplied in the expr parameter with one exception The mask may be missing some of the axes if this is the case then the mask will be expanded along these axes to become the same shape For examples using mask see below 6 1 5 Regions region The region parameter points to an ImageRegion file An ImageRegion file can be created with the CASA viewer s region manager 7 3 5 Typically ImageRegion files will have the suffix rgn If a region file is given then the box chans and stokes parameters will be ignored For example region myimage im rgn CHAPTER 6 IMAGE ANALYSIS 231 6 2 Image Header Manipulation imhead To summarize and change keywords and values in the header of your image use the imhead task Its inputs are imhead Lists gets and puts image header parameters imagename a Name of input image file mode summary Options get put summary list stats async False The mode parameter controls the operation of imhead Setting mode summary will print out a summary of the image properties and the header to the logger Setting mode list prints out a list of the header keywords and values to the terminal The mode get allows the user to retrieve the current value for a specified keyword hditem mode gt get imhead options get put summary and list hditem dl Header item to get or set Note that t
635. xt Action Y gt iterations cycles threshold e Displayed Plane 100 60 8 mjy Add Erase All Channels E ca B a a 2 2 a N o 21 Right GO Q O O A 22 46 Normal Blink Rate 10 sec Compact i Frame Start E XX ngc5921 demo interclean residual 0 000135066 Jy beam Pixel 163 131 0 22 15 21 24 650 05 04 43 322 I 1494 63 km s XX ngc5921 demo interclean model mask contour 0 Pixel 163 131 0 22 15 21 24 650 05 04 43 322 I 1494 63 km s Figure 5 6 Screen shot of the interactive clean window during deconvolution of the NGC5921 spectral line dataset Note where we have selected the mask to apply to the Displayed Plane rather than A11 Channels We have just used the Polygon tool to draw a mask region around the emission in this channel which will apply to this channel only the desired unmasked part of the image above minpb lies within the inner quarter In other words make an image twice as big as necessary to encompass the mosaic It is also important to choose an appropriate phasecenter for your output mosaic image sec tion im pars phasecenter An example of a simple mosaic clean call is shown below CHAPTER 5 SYNTHESIS IMAGING 217 clean vis n4826_tboth ms imagename tmosaic mode channel nchan 30 start 46 Make the output cube 30 chan width 4 start with 46 of spw 0 avg by 4 chans spw 072 field 076 cell
636. xtract sub image Synthesis imaging linear mosaic combination of images Calculations involving images Bandpass and gain calibration Print header of image or uvdata Restore a clean component model selfcalibration of visibility data automated flagging based on clip levels Load image to TV display Interactive TB data editing Average select data apply calibration uv plane component fitter Command based flagging Simulator List uv data Source model computation uv data plotting split uv file in sources and spectral windows CASA task tool atcafiller tool mp raster displays viewer viewer clean importfits fluxscale cb with G and D not needed plotcal im tool ia imagefitter ia imagepol ia statistics ia subimage invert im tool mosaic ia imagecalc ia calc bandpass imhead listobs im tool clean gaincal etc flagdata viewer viewer applycal split uvmodelfit flagdata sm tool listvis TBD ft plotxy split 474 APPENDIX G APPENDIX CASA DICTIONARIES Table G 2 CLIC CASA dictionary CLIC Function load print flag phcor rf phase flux ampl table Description Load data Print text summary of data Flag data Atmospheric phase correction Radio frequency bandpass Phase calibration Absolute flux calibration Amplitude calibration Split out calibrated data uv table CASA task tool almatifiller tool listobs plotxy flagdata viewer almatifiller bandpass gaincal setjy f
637. y CHAPTER 4 SYNTHESIS CALIBRATION 171 The field parameter specifies those field names in tablein to which the incremental solution should be applied The solutions for other fields will be passed to caltable unaltered If the cumulative table was created from scratch in this run of accumulate then the solutions for these other fields will be unit amplitude zero phase as described above The calfield parameter is used to specify the fields to select from incrtable to use when applying to tablein Together use of field and calfield permit completely flexible combinations of calibration accumulation with respect to fields Multiple runs of accum can be used to generate a single table with many combinations In future a self mode will be enabled that will simplify the accumulation of field specific solutions The spwmap parameter gives the mapping of the spectral windows in the incrtable onto those in tablein and caltable The syntax is described in 4 4 1 4 The interp parameter controls the method used for interpolation The options are currently nearest linear and aipslin These are described in 4 4 1 4 For most purposes the linear option should suffice We now describe the two uses of accum 4 5 4 1 Interpolation using accum Calibration solutions most notably G or T can be interpolated onto the timestamps of the science target observations using accum The following example uses accum to i
638. y cell size default unit arcsec gt Image phase center position or field index gt rest frequency to assign to image see help gt I Stokes params to image eg I IV QU IQUV briggs Weighting to apply to visibilities 0 5 Briggs robustness parameter O uv cell size in pixels 0 gt field of view False Apply additional uv tapering of visibilities gt Name of model image s to initialize cleaning gt gt Output Gaussian restoring beam for CLEAN image False Output primary beam corrected image 0 1 Minimum PB level to use False An example of the clean task to clean vis ggtau imm split ms imagename ggtau imm psfmode clark imagermode mask niter 500 gain 0 1 mode mfs spw 07 2 2757 field 0 stokes I weighting briggs rmode norm robust 0 5 cell 0 1 0 1 imsize 256 256 create a continuum image from many channels is given below Use data in ggtau imm split ms Name output images ggtau imm on disk Use the Clark CLEAN algorithm Do not mosaic or use csclean Do not use clean box or mask Iterate 500 times using gain of 0 1 multi frequency synthesis combine channels Combine channels from 3 spectral windows Image stokes I polarization Use Briggs robust weighting with robustness parameter of 0 5 Using 0 1 arcsec pixels Set image size 256x256 pixels HE HH HH HH HH HOH HH OF This example will
639. ydata ms CHAPTER 1 INTRODUCTION 34 Note that if you want to access a Unix environment variable you will need to prefix with a double instead of a single for example to print the value of the PAGER variable you would use CASA lt 6 gt lecho PAGER See Appendix D 6 for more information 1 2 7 6 Executing Python scripts You can execute Python scripts ASCII text files containing Python or casapy commands using the execfile command For example to execute the script contained in the file myscript py in the current directory you would type CASA lt 7 gt execfile myscript py or CASA lt 8 gt execfile myscript py which will invoke the Python auto parenthesis feature NOTE in some cases you can use the Python run command instead e g CASA lt 9 gt run myscript py In this case you do not need the quotes around the filename This is most useful for re initializing the task parameters e g CASA lt 10 gt run clean last see 13 577 See Appendix for more information 1 2 8 Getting Help in CASA 1 2 8 1 TAB key At any time hitting the lt TAB gt key will complete any available commands or variable names and show you a list of the possible completions if there s no unambiguous result It will also complete filenames in the current directory if no CASA or Python names match For example it can be used to list the available functionality using minimum match once you have typed
640. ype vector scalar timebin 20 Length of time interval in seconds to average crossscans False Have time averaging cross scan boundaries crossbls False have averaging cross over baselines crossarrays False have averaging cross over arrays stackspw False stack multiple spw on top of each other width A Number of channels to average Note that the timebin crossscans and width sub parameters are always open and available whether averagemode vector or scalar See below for more on averaging You can extend the flagging beyond the data cell plotted extendflag True Have flagging extend to other data points extendcorr a flagging correlation extension type extendchan E a flagging channel extension type extendspw re flagging spectral window extension type extendant as flagging antenna extension type extendtime d flagging time extension type See below for more on flag extension The restfreq parameter can be set to a transition or frequency restfreq HIT a frequency quanta or transition name see help for options frame LSRK frequency frame for spectral axis see help for options doppler RADIO doppler mode see help for options See below for more on setting rest frequencies and frames Setting selectplot True will open up a set of plotting control sub parameters These are described in below The interactive and figfile parameters allow non inter
641. z frequency error and intensity any units If the molecule name contains any spaces they must be wrapped in quotes A sample of the ASCII catalog is shown below APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 355 H2D 3955 2551 228 8818 7 1941 H2D 12104 7712 177 1558 6 0769 H2D 45809 2731 118 3223 3 9494 CH 701 6811 0441 7 1641 CH 724 7709 0456 7 3912 CH 3263 7940 1000 6 3501 CH 3335 4810 1000 6 0304 You can load the ASCII line catalog for example if it is called my_custom_linecat txt by following command mycatlog sd linecatlog my_custom_linecat txt Use sd plotter plot_line to overlay the line catalog on the plot Currently overplotting line catalog works only spectra plotted in frequency scans set_unit GHz sd plotter plot scans sd plotter plot_line mycatlog Following are some useful functions to control the line catalog access See ASAP User Guide for more complete descriptions mycatlog save my_custom_linecat tbl save to the internal table format mycatlog set_frequency_limits 100 115 GHz set a frequency range for line selection mycatlog set_name 0H select all alchols A 3 10 Setting Getting Rest Frequencies The rest frequencies used in the data can be retrieve by sd scantable get_restfreqs and set to new values by sd scantable set_restfreqs The CASA version of ASAP now can store multiple rest frequencies for each IF scans get_restfreqs

Analysis Cookbook - CASA

Contents

Download Pdf Manuals

Related Search

Related Contents