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CASA Synthesis & Single Dish Reduction Cookbook

1. ree tas a00 see fa t 200 400 600 800 1000 phoi x FLS3a_HL image Coordinate world 17 17 41 633 60434 58 594 pixel T 00 e TT 030 5 anal Figure A 5 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 375 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 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 t
2. Get rid of the autocorrelations from the MS print Flagautocorr Don t default this one either there is only one parameter vis flagautocorr 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 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 99 194 CHAPTER 4 SYNTHESIS CALIBRATION 195 So its using 14 76Jy as the flux of 1331 305 in the single Spectral Window in this MS Bandpass 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 set the name for
3. Vector Ma E 195000760109 Eee ngc5921 usecase clean residual Image 2 gt ngc5921 usecase ms Measurement X ngc5921 usecase clean image contour g fal Marker Map ngc5921 usecase ms cont Measurement gt 2 090e 04 Jy bean 15 22 36 507 04 54 47 181 bd I 1 546876e 03 km s Update K Leave Open Done Figure 7 9 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 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 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 CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 298 Region Extent Display
4. 185 4 7 5 UV Plane Model Fitting uvmodelfit cocos percal 5 187 ose eee eR e Cee a E e DA eek a te ek 190 4 8 1 Spectral Line Calibration for NGC5921 2 2 2 2 190 Ce 6 iG oa ees Be EE ee 203 5 Synthesis Imaging 208 eta oh eek Goon Ue EEDA Gage Se nee em Ae ee ee Te 208 Ae ie eck A Gd ee eae ys Be de arg F 209 Sch ek ae e Ba a ps DA ed a a i 209 Las A AA ee eee eS Ae eS 209 oh eee eee be oe ee oe ee ee ee eS 210 IED ARA ek ee A ek i a 210 pte hte AAA 210 525 Modems vs a Ge agas AA 210 5 2 5 2 Mode chammel 211 a A e E O Ge Geom de oe E 211 pde sk AAA AA 212 UA AA ea 212 5 2 7 Parameter restfreq a 213 D 2 9 Parameter SpW oss sle s a aon a ee A kee RR we ee e 213 hie RRE a A O RR a eG 213 Lui e how Awe wae eked ds A we S 214 mi Sh oh ds Ree ee eee ko Aa ee Ae Sd 214 5 2 11 1 natural welghting o e 022020004 215 5 2 11 2 uniform welghtidg o e o o 215 5 2 11 3 superuniform weighting 216 5 2 11 4 radial weighting o e e e 216 5 2 11 5 briggs weighting e 0000000000 216 5 2 11 6 briggsabs weighting o e 217 AA EA 217 5 3 Deconvolution using CLEAN clean o 000000048 217 5 3 1 Parameter psfalg e 220 5 3 1 1 The clark algorithm o e
5. 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 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 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS Don t need a priori cals 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 solint 30 0 minsnr 1 0 print Calibrating amplitudes and phases on 30s timescale
6. shows blank autocorr pages antenna amp does not show the autocorrs antenna amp amp show both auto and cross cor default antenna kk 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 enclosing the antenna names in double quotes ANT gt E g the string antenna 10715 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 2 5 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 CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 92
7. You should get in your logger window and in the casapy log file something like Observer FLUX99 Project Observation VLA Data records 2021424 Total integration time 85133 2 seconds Observed from 23 15 27 to 22 54 20 ObservationID 0 ArrayID 0 Date Timerange Scan Fldld FieldName Spwlds CHAPTER 3 DATA EXAMINATION AND EDITING 23 23 16 Apr 1999 00 00 00 00 01 01 01 02 02 02 02 02 03 03 03 05 05 05 06 06 06 07 07 07 08 08 08 09 09 09 10 10 10 11 11 HHH HHH HH HHH HHHHH HH HH HHH HH HHHH HHH HH HHH HH HH HH HHH HH HOH OF 15 Apr 1999 23 238 253 222 228 248 756 01 23 29 49 03 iT 24 237 50 59 03 227 235 249 03 18 02 04 04 04 04 04 24 48 58 13 22 244 256 07 28 42 58 13 2273 42 57 13 26 40 56 10 06 08 09 15 10 12 25 42 56 10 12 227 40 56 28 48 26 40 40 10 23 40 13 20 29 33 50 00 30 20 49 50 20 30 53 00 250 10 49 56 49 50 03 00 36 20 40 13 06 40 20 49 43 30 53 59 09 03 59 33 19 59 09 30 10 30 20 GD COOOMOMOOFR on O OPOOOOOoOrOrROOYOOoOoOOoSOOoOoOOoOoyYyOOoOROOOOoOoyYO0oORPpPOYROoOOo N 23 23 23 00 00 00 00 01 01 01 01 02 02 02 02 02 03 03 03 03 03
8. e 220 5 3 1 2 The hogbom algorithm 30 a A eee o 220 E he meg ee ee are te ee cee a 220 ee ee oes a ree ee eo Gree pegs ee e 221 b gout St Ore ai A Ge gree a a a A 221 5 3 4 1 Sub parameter cyclefactor o o 0000 223 ee ee re E 223 5 3 5 1 Sub parameter ftmachine e 223 5 3 5 2 Sub parameter mosweight o 224 5 3 5 3 Sub parameter scaletypel oo o 224 5 3 5 4 The threshold revisitedl o e 02 02 0004 225 a ia edo ene ee as ani dub E 225 O aR Ge ae ene ee oe eas a kh gS 226 5 3 7 1 Setting clean boxes o e e 226 5 3 7 2 Using clean box files s s scs sos sop oe o ee 226 eye he td ee 226 bie iaa ov cee ae ee tas ee Se A 227 be a hve Oe AN ne Aegon este od ese esd E eqs owe oh ek we 227 A g geg Goa OR Beal s Bd Aiea AAA S 227 a ai ra Boas la a ge Sse nee So Gera al a 227 oe he Ges Bees Se ee ee eee E 227 a ea er E a a ee ee ee ee 228 ee ee ee eee ee 228 5 3 14 Example Interactive Cleaning 2 02 00 0004 228 5 3 15 Example Mosaicing 2 0 0 ee 231 5 4 Combined Single Dish and Interferometric Imaging feather 233 5 5 Making Deconvolution Masks makemask o o 234 5 6 Transforming an Image Model t o 236 5 7 Image plane deconvolution deconvolve o a 237 A TA a So
9. preavg 300 0 refant a gt VA15 minsnr 3 poltype gt D QU gaintable polcal_20080224 cband all gcal gainfield gt polcal This 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 gt VA15 minsnr 3 poltype X gaintable polcal_20080224 cband all gcal polcal_20080224 cband all pcal polcal CHAPTER 4 SYNTHESIS CALIBRATION 164 Tf 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 polcal_20080224 cband all ms caltable polcal_20080224 cband all_3c84 pcal field 0319 415 refant 7 gt VA15 poltype D gaintable polcal_20080224 cband all gcal polcal 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 3 4 4 6 Baseline based Calibration blcal BETA ALERT The blcal task has not had e
10. 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 5 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 5 4 1 The antenna Parameter The antenna selection string is a semi colon separated list 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 amp is an abbreviation for 7ANTI 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 ANT1 amp amp amp Select only autocorrelations specified by the selector ANT1
11. 53 54 54 54 54 53 54 54 53 54 54 53 53 53 54 53 53 54 53 53 53 53 54 54 53 54 54 51 19 04 08 03 59 01 15 55 00 01 57 54 59 12 59 57 10 56 53 53 56 00 00 58 06 00 OrWoNOonPPODATAWBArFON ON WDFRRFRArRFRFNNTNOAWACO R L RR RL LR LL RR RL LR LL 121 CHAPTER 3 DATA EXAMINATION AND EDITING 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 f Data Examination and Flagging f Get rid of the autocorrelations from the MS print Flagautocorr print Use flagautocorr to zap auto correlations print Not strictly necessary but here for completeness Don t default this one either flagautocorr Use Flagmanager to save a copy of the flags print Flagmanager default flagmanager print Use flagmanager to save these new flags print These go in the flagversions sub dir vis msfile Save a copy o
12. 6104 6104 6104 6104 6104 6104 6104 6104 6104 6104 6104 6104 233 233 233 233 233 233 233 233 233 233 2336 2336 2336 2336 2336 2336 2336 2336 2336 2336 2336 2336 2336 2336 2336 2336 358 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 contains 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 359 CASA lt 5 gt scan27 scans get_scan 27 Get the 27th scan CASA lt 6 gt scans20to24 scans get_scan range 20 25 Get scans 20 24 CASA lt 7 gt scans_on scans get_scan _ps Get ps scans on source CASA lt 8 gt scansOrion scans get_scan Ori Get all Orion scans To copy a scantable do CASA lt 15 gt ss scans copy A 3 3 1 Data Selection 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
13. 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 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 5 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 CHAPTER 3 DATA EXAMINATION AND EDITING 104 The overplot parameter interacts with the newplot sub parameter see 3 4 2 See 813 4 3 5 for an example using overplot 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 3 4 3 4 plotsymbol The plotsymbol parameter defines both the line or symbol for the data being drawn a
14. 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 331 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
15. Sly Spectral Windows fo 1 2 3 4 5 Ex Display Axes Flagging Options re gt 10 sec Compact Basic Settings Figure 7 14 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 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 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 w
16. 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 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 match 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 CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 91 antenna 1738 46 10 11 will select baselines between antennas 1 2 3 and 4 5 6 1 amp 4 185 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
17. 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 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 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 ma
18. 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 utilities 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 53 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
19. import asap as sd os environ AIPSPATH casapath print Import s sd scantable FLS3_all_newcal_SP false print Split splitting the data for each field s0 s get_scan FLS3a s0 save FLS3a_HI asap del sO 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 HH HH 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 5 Vil 1024 LSRK 1419 39269 2 44140625 2500 1418 14269 XX YY read in MeasurementSet split the data for t
20. importuvfits saved importuvfits Note that there will be a ngc5921 usecase 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 listobs You should get in your logger window and in the casapy log file something like MeasurementSet Name home sandrock2 smyers Testing2 Sep07 ngc5921 usecase 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 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 Fields 3 ID Code Name Right Ascension Declination Epoch 0 C 1331 30500002_013 31 08 29 30 30 32 96 J2000 HHH HHH HHH HH HH HHH HH HHH HH H H OH 1 A 1445 09900002_014 45 16 47 09 58 36 07 J2000 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 405
21. 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 CHAPTER 1 INTRODUCTION 43 1 3 5 Setting Parameters and Invoking Tasks One can set parameters for tasks but currently not for tools by performing the assignment within the CASA shell and then inspecting them using the inp command CASA lt 30 gt default plotxy CASA lt 31 gt vis ngc5921 ms CASA lt 32 gt xaxis channel CASA lt 33 gt yaxis amp CASA lt 34 gt datacolumn data CASA lt 35 gt inp plotxy vis ngc5921 ms xaxis channel yaxis gt amp datacolumn data field q spw a selectdata False average aie subplot 111 overplot False showflags False iteration oe plotsymbol ae plotcolor darkcya
22. the time that the message was generated Note that this will be in local computer time usually UT for casapy generated messages and may be different for user generated messages e 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 59 Y Log Messages imager b home imager b smyers Nov07 casapy log 50X File Edit View Basa B P search Message A Fiter origin y clean MW Time Priority Message Tue Nov 6 18 09 53 2007 INFO HSRAARARRKAAARARRRARAASR RAR AAR RAR R AAAS RTA Tue Nov 6 18 09 53 2007 INFO Begin Task clean Tue Nov 6 18 09 5
23. 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 TT 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 0 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 0 0137 331 o Lo Co Co Os Lo C
24. 7 462 119 2574510 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 calname split ms f soooooooooooooooooooooooooooooooooooooooooooooooooooooos 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 557 428 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS Synthesized beam FWHM 14 RMS in 10min 600s 0 06 mJy thats now but close enough 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
25. ASCII this parameter is ignored APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 319 plotlevel control for plotting of results options int O none l some 2 more lt 0O 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 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 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 each IF in turn 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 ga
26. 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 number 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 153 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 PABI data The maskedge drops beginning and end channels The visnorm parameter turns on normalization before the solution is obtained rather than after for solnorm BETA ALERT Note that currently BPOLY solutions cannot be solved for in a time dependent manner Furthermore bandpass will allow you to use multiple fields but will determine a single solution for all specified fields If you want to use more than one field in the solution it is prudent to use an initial gaincal and use this table a
27. 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 print print 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 O print we 455 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 456 print Plotcal 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 script n 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 7 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 uvdist yaxis amp datacolumn corrected multicolor both Use the fie
28. 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 20137 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 print 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 383 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 g
29. VLA red shifted HI emission 002000004 F 1 1 NGC 5921 data summary ooo F 2 Jupiter VLA continuum polarization 202000004 F 3 VLA Polarization Calibration 0 020002 ee ee G Appendix CASA Dictionaries G 1 AIPS CASA dictionary G 2 MIRIAD CASA dictionary 2 2 2 a G 3 CLIC CASA dictionary 396 396 400 401 401 424 426 464 List of Tables 2 1 Common MS Columns 2 0 00 00 0 73 2 2 Commonly accessed MAIN Table columns aooaa 00052004 74 4 1 Recognized Flux Density Calibrators 0 0 0 0 2 200000 ee eee 141 G 1 MIRIAD CASA dictionary 2 2 2 0 a 495 G 2 CLIC CASA dictionary 13 List of Figures 1 1 Screen shot of the default CASA inputs for task clean 48 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 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 RAIN 50 e aa 53 1 5 Using the Search facility in the casalogger Here we have specified the string AAA Z 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 SAA 5 CASA Logger
30. 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 an optional frame type default LSRK Valid frames are REST TOPO LSRD LSRK BARY gt GEO GALACTO LGROUP CMB Examples scan set_freqframe BARY 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 CA
31. e viewer the CASA viewer can display as a raster image MS data with some editing capabilities 7 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 Amplitudes 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 8 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 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
32. gt a new object with type S a subtype of T newimagefromshape open outputvariant pixelvalue ia putchunk putregion rebin regrid ia remove removefile rename replacemaskedpixels restoringbeam ia rotate sepconvolve set setboxregion setbrightnessunit setcoordsys 275 CHAPTER 6 IMAGE ANALYSIS 276 ia continuumsub ia lock ia sethistory ia convertflux ia makearray ia setmiscinfo ia convolve ia makecomplex ia setrestoringbeam ia convolve2d ia maketestimage ia shape ia coordmeasures ia maskhandler ia statistics ia coordsys ia maxfit ia subimage ia decompose ia miscinfo ia summary ia deconvolvecomponentlist ia modify ia toASCII ia done ia moments ia tofits ia echo ia name ia topixel ia fft ia newimage ia toworld ia findsources ia newimagefromarray ia twopointcorrelation ia fitallprofiles ia newimagefromfile ia type ia fitpolynomial ia newimagefromfits ia unlock ia fitprofile ia newimagefromimage A common use of the ia tool is to do region statistics on an image 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 The imhead task has The tool can do this on specific to get on source and off source statistics for regression The variable clnimage points to the clean image name Pull the max and rms from the clean image ia open clnimage on_statistics ia statistics thistest_imm
33. interactive mode for baseline fitting options bool True False APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 323 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 Also see the notes on fluxunit and telescopeparm in the section for sdaverage See the sdaverage description for information on fluxunit
34. lt prefix gt ms contsub lt prefix gt clean image lt prefix gt clean model lt prefix gt clean residual HHH H HHH H HHH HH HHH HH HHH HH HH HHHH HHH HH HHH HH HH HH HHH HH HOH OF 402 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS exportfits gt lt prefix gt clean 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 H HHH HH HHH HH OF HHEFHHHHHHHEEHHAEEHEEHEHHEHHHREH HEHE HHEEHEHREHEHHEE HARE HEHRAEHHHA HERRERA A ARRE import time import os Set up some useful variables Get to path to the CASA home and stip off the name pathname os environ get AIPSPATH split 0 This is where the NGC5921 UVFITS data will be fitsdata pathnamet data demo NGC5921 fits Or use data in current directory fitsdata NGC5921 fits The prefix to use for all output files prefix ngc5921 usecase Clean up old 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 403 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 404 saveinputs importuv its prefix
35. 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 339 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 11 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 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
36. save postscript spectrum spave set_unit channel APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 371 006 XI ASAP Plotter Tk OrionS_ps Brightness Temperature K 45 47 4548 45 45 155 4551 LSRK Frequency GHz Al ol ol ral al a x 45 477 y 3 09 Figure A 4 Calibrated spectrum with a line at zero using histograms 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 H Se a a a Se es ee 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 fit fit f plot residual True plot residual APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 372 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 Save the
37. scan 37 scan number 3 scan 2178 scan numbers 1 through 8 inclusive scan 21 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 5 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 stamps 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 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 rigoro
38. 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 BETA ALERT The B solutions will allow you to use multiple fields but in this case bandpass will produce different solutions for each source i e you cannot average in time across different fields Note that this currently provides a safety net of sorts because you should not average across fields unless the phase has already been corrected e g in an initial gaincal In the future it will be possible to do this but then BPOLY caveat below will then hold for B solutions obtained using this option as well in the multiple field case 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
39. 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 Wp The weight of the i th sample is then 5 2 CHAPTER 5 SYNTHESIS IMAGING 216 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 weighting The weighting radial mode is a seldom used option that increases the weight by the radius Wi wi fu 02 5 3 Technically I would call that an inverse uv taper si
40. 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 5DE In interactive mode any input line beginning with a character is passed verbatim 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
41. 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 0 ee ee 5 8 Different message priority levels as seen in the casalogger window These can also be Filtered Upa 2 0 ee 5 9 Flow chart of the data processing operations that a general user will carry out in an end to end CASA reduction session 2 oa e 60 E al O E 00 1 The contents of a Measurement Set These tables compose a Measurement Set named ngc5921 demo ms on disk is display is obtained by using the File Open menu N aj A H e ie in browsetable and left double clicking on the ngc5921 demo ms directory 72 14 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 y 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 98 iteration antenna Each time you press the Next button you get the next series OL Plots s ou aca oe ia a a a BS 103 3 3 Multi panel display of visibility versus channel top antenna array configuration bott
42. Names or indices of data fields to apply calibration gt all spw on spectral window channels gt all selectdata False Other data selection parameters gaintable gt List of calibration table s to apply gainfield e 2a Field selection for each gaintable interp gt Interpolation mode in time for each gaintable CHAPTER 4 SYNTHESIS CALIBRATION 180 spwmap Spectral window mapping for each gaintable see help gaincurve 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 5 Many of the other parameters are the common calibration parameters that are described in 4 4 1 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 gaintab
43. Rate lt 10 sec Compact Color Wedge Frame Q start End Step Apply Save Restore Bid 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 7 1 1 Starting the casaviewer outside of casapy The casaviewer is the name of the stand alone application that is available with a CASA instal lation From outside casapy you can call this command from the command line in the following ways Start the casaviewer with no default image MS loaded it will pop up the Load Data frame 7 2 3 and a blank standard Viewer Display Panel 7 2 1 gt casaviewer amp Start the casaviewer with the selected image the image will be displayed in the Viewer Display Panel If the image is a cube more than one plane for frequency or polarization then it will be one the first plane of the cube CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER Data Display Panel Tools View BORRAGAARA flees efele y Baseline Rate GA 10 sec Compact Frame tart End X ngc5921 usecase ms 1 407 Jy 13 Apr 1995 09 19 30 t 1 scan 1 1331 30500002_0
44. 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 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 available at this time Soon they will be obtained at the ALMA Test Facility ATF right now some simulated data exist Thus this filler is in a development stage Also currently there are no options for filling selected data you get the whole data set For example CASA lt 1 gt importasdm home basho3 jmcmulli ASDM ExecBlock3 ii gt importasdm home basho3 jmcmulli ASDM ExecBlock3 Parameter asdm is home basho3 jmcmulli ASDM ExecBlock3 and has type lt type str gt CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 80 Taking the dataset home basho3 jmcmulli ASDM ExecBlock3 as input Time spent parsing the XML medata 1 16 s The measurement set will be filled with complex data About to create a new measurement set home basho3 jmcmulli ASDM ExecBlock3 ms The dataset has 4 antennas successfully copied them into the measurement set The dataset has 33
45. True applycal Self cal is now in CORRECTED_DATA column of split ms print Clean 2 default clean vis srcsplitms imname2 prefix clean2 imagename imname2 field spw 7 mode mfs gain 0 1 niter 10000 245 CHAPTER 5 SYNTHESIS IMAGING threshold 0 04 psfalg clnalg imagermode clnmode imsize clnimsize cell clncell weighting briggs robust 0 5 cleanbox interactive npercycle 100 clean Set up variables clnimage2 imname2 image clnmodel2 imname2 model clnresid2 imname2 residual clnmask2 imname2 clean_interactive mask T SSN i ass ss SN ek as a a a it a Ss SS Look at this in viewer viewer clnimage2 image jupiter6cm usecase clean2 image Jy beam n Std Dev RMS Mean 5236 0 001389 0 001390 3 244e 05 Flux Med Dev IntQtlRng Median 0 01060 0 0009064 0 001823 1 884e 05 On Jupiter n Std Dev RMS Mean 5304 0 08512 0 08629 0 01418 Flux Med Dev IntQtlRng Median 4 695 0 0008142 0 001657 0 0001557 HHH HHH HHH HH HHH HH HH H HH OF Variance 1 930e 06 Min 0 004015 Variance 0 007245 Min 0 004526 Estimated dynamic range 1 076 0 001389 775 better Sum 0 1699 Max 0 004892 Sum 75 21 Max 1 076 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
46. Tue Nov 6 18 23 15 2007 DEBUG1 plotxy TPPL Entered Function endPlot panel Tue Nov 6 18 23 16 2007 DEBUG2 plotxy TPPL Plotter timing Allocation 0 sec Filling 0 sec Resizing 0 sec Plot to Python 0 04 sec Tue Nov 6 18 23 16 2007 DEBUG1 plotxy MsPl Eniting Function plotxy Tue Nov 6 18 23 16 2007 INFO Tue Nov 6 18 23 16 2007 INFO Tue Nov 6 18 23 16 2007 INFO End Task plotxy AOARAARA NARA NARARDARA NAL ARA CAD ARA RARA NACERDORA penaa EAEE EEEE EEEE EREEREER EEE EREEREER EEEE Begin Task plotxy Number of selected rows is x Preparing data Plotting from the Main Measrument Set 3 Tue Nov 6 18 25 26 2007 INFO Tue Nov 6 18 25 26 2007 INFO2 MsPlot TaQL for Table 0 CROSS 180 PI PHASEC SUMS IIF FLAG 1 1 1 1 2 1 0 0 DATA 1 1 1 1 2 1 2 CROSS 180 PI PHASEC SUMS IIF FLAG 1 1 1 3 4 1 0 0 DATA 1 1 1 3 4 1 2 SUMSC IIF FLAG 1 1 1 3 AT O A 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
47. and GBT 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 fluxunit units for line flux options K Jy default keep current fluxunit of the first data in the sdfilelist 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 average 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
48. chans gt Select the channel spectral range string containing channel range immath imstat and imcontsub takes a string listing 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 3720 chans 0 3 4 8 chans 3 20 50 51 HH HH HH H OF CHAPTER 6 IMAGE ANALYSIS 254 The polarization plane s of the image is chosen with the stokes parameter stokes de Stokes params to image 1 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 XK ED O ES ERA A A 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
49. 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 e 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 20713753 spw 0 channels 13 53 inclusive 0 141371414MHz spw 0 1413 1414MHz section only spw spw 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 can also select the spectral window via frequency ranges FSTART FSTOP as described above 141371414MHz 1413 1414MHz channels falling within 1413 1414MHz 2 141371414MHz does the same thing spw spw 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 Note the use of the wildcard in the last example A step can be also be included using STEP as a postfix CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 90 spw 0 10710072 chans 10 12 14 100 of spw 0 spw 7 74 chans 0 4 8 of all spw spw
50. 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 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 e The CASA User Reference Manual details on a specific task or tool does and how to use it BETA ALERT Currently the Reference Manual describes only tools not tasks CHAPTER 1 INTRODUCTION 22 The CASA home page can be found at http casa nrao edu From there you can find documentation and assistance for th
51. fluxcalfield spw usespw If we need a model or fluxdensities then put those here modimage fluxcaldir fluxcalmodel saveinputs setjy prefix setjy saved setjyO You should see something like this in the logger and casapy log file 0137 331 spwid 0 I 5 405 Q 0 U 0 V 0 Jy Perley Taylor 99 0137 331 spwid 1 I 5 458 Q 0 U 0 V 0 Jy Perley Taylor 99 cf AIPS SETJY 0137 331 gt IF 1 FLUX 5 4054 Jy calcd SETJY 0137 331 gt IF 2 FLUX 5 4585 Jy calcd print Look in logger for the fluxes should be 5 405 and 5 458 Jy default gaincal print Solve for antenna gains on sources gaincalfield print We have 2 single channel continuum spw vis msfile set the name for the output gain caltable 475 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS print Output gain table name is gtable caltable gtable All fields are calibrators We have 2 IFs SPW 0 1 with one channel each Assemble field string from gaincalfield list field fieldgain print Calibrating using fields field Calibrate these spw spw usespw a priori calibration application gaincurve usegaincurve opacity gainopacity do not apply parallactic angle correction parang False G solutions for both amplitude and phase using gainsolint gaintype G solint gainsolint calmode ap reference antenna refant calrefant minimum S
52. gt all scan 3 scan numbers Not yet implemented msselect gi 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 contains extended flux not accounted for in the model e g 4 3 4 1 See 2 5 for more on the selection parameters CHAPTER 4 SYNTHESIS CALIBRATION 146 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 correctio
53. pixel 1 iflx ipix value value spwref I iflx Stokes Q qpix ia pixelvalue xref yref 1 0 qflx qpix value value spwref Q qflx Stokes U upix ia pixelvalue xref yref 2 0 uflx upix value value APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 489 spwref U uflx Stokes V vpix ia pixelvalue xref yref 3 0 v lx vpix value value spwref V vflx Polarization quantities pflx sqrt qflx 2 uflx 2 fflx pflx iflx xflx atan2 uflx qf1x 180 0 pi spwref P pflx spwref F fflx spwref X xflx spwref xref xref spwref yref yref Now the values at the maximum of I spwmax Pull the maxpos of I xref spwstats I maxpos 0 yref spwstats I maxpos 1 Stokes I iflx spwstats 1 max 0 spwmax I iflx Stokes Q qpix ia pixelvalue xref yref 1 0 qflx qpix value value spwmax Q gqflx Stokes U upix ia pixelvalue xref yref 2 0 uflx upix value value spwmax U uflx Stokes V vpix ia pixelvalue xref yref 3 0 v lx vpix value value spwmax V vflx spwmax xref xref spwmax yref yref Done with ia tool ia close spwmodel refval spwmodel maxval
54. plotcal See Figure 4 5 for this example This uses 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 vis 2 Name of input visibility file MS caltable ii Input calibration table to list CHAPTER 4 SYNTHESIS CALIBRATION 170 fxd CASA Plotter Pr a rial Jd 05508 Not 0H IO O Ba 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 field a Select data based on field name or index antenna aa Select data based on antenna name or index spw a Spectral window channel to list listfile a Disk file to write else to terminal pagerows O Rows listed per page async False An example listing is Listing CalTable jupiter6cm usecase split ms smoothcal2 G Jones Spwld 0 channel 0 Time Field Ant Amp Phase Amp Phase CHAPTER 4 SYNTHESIS CALIBRATION 171 CASA Plotter Mark Rogon Pay ung teste nest Moot Sa Figure 4 5 Display of the amplitude of t
55. 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 347 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 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_orion
56. 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 atmospheric optical depth default 0 0 no correction blmode mode for baseline fitting options str auto list 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 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 example typically in range 2 9 higher values seem to be needed for GBT interactive
57. something like 431 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 432 Observer FLUX99 Project Observation VLA Data records 2021424 Total integration time 85133 2 seconds Observed from 23 15 27 to 22 54 20 ObservationID 0 ArrayID 0 Date Timerange Scan FldId FieldName Spwlds 15 Apr 1999 23 15 26 7 23 16 10 0 1 O 0137 331 o 1 23 38 40 0 23 48 00 0 2 1 0813 482 o 1 23 53 40 0 23 55 20 0 3 2 0542 498 o 1 16 Apr 1999 00 22 10 1 00 23 49 9 4 3 0437 296 o 1 00 28 23 3 00 30 00 1 5 4 VENUS o 1 00 48 40 0 00 50 20 0 6 1 0813 482 o 1 00 56 13 4 00 57 49 9 7 2 0542 498 o 1 01 10 20 1 01 11 59 9 8 5 0521 166 o 1 01 23 29 9 01 25 00 1 9 3 0437 296 o 1 01 29 33 3 01 31 10 0 10 4 VENUS o 1 01 49 50 0 01 51 30 0 11 6 1411 522 o 1 02 03 00 0 02 04 30 0 12 7 1331 305 o 1 02 17 30 0 02 19 10 0 13 1 0813 482 o 1 02 24 20 0 02 26 00 0 14 2 0542 498 o 1 02 37 49 9 02 39 30 0 15 5 0521 166 o 1 02 50 50 1 02 52 20 1 16 3 0437 296 o 1 02 59 20 0 03 01 00 0 17 6 1411 522 o 1 03 12 30 0 03 14 10 0 18 7 1331 305 o 1 03 27 53 3 03 29 39 9 19 1 0813 482 o 1 03 35 00 0 03 36 40 0 20 2 0542 498 o 1 03 49 50 0 03 51 30 1 21 6 1411 522 o 1 04 03 10 0 04 04 50 0 22 7 1331 305 o 1 04 18 49 9 04 20 40 0 23 1 0813 482 o 1 04 25 56 6 04 27 39 9 24 2 0542 498 o 1 04 4
58. vis msfile field 2 Edge channels are bad spw 0 4759 Time average across scans timebin 86000 crossscans True No GUI for this script interactive False 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 plotxy O Set up 2x1 panels lower panel phase vs time subplot 212 yaxis phase datacolumn corrected Now send final plot to file in PNG format via png suffix figfile vis plotxy png plotxy O Split the gain calibrater data then the target print Split 1445 099 Data default split vis msfile We first want to write out the corrected data for the calibrator CHAPTER 4 SYNTHESIS CALIBRATION Make an output vis file calsplitms prefix cal split ms outputvis calsplitms Select the 1445 099 field all chans field 1445x spw pick off the CORRECTED_DATA column datacolumn corrected split Now split NGC5921 data before continuum subtraction print Split NGC5921 Data splitms prefix src split ms outputvis splitms Pick off N5921 field N5921 Export the NGC5921 data as UVFITS Start with the split file print Export UVFITS default exportuvfits srcuvfits prefix spli
59. 020202004 160 4 4 5 Instrumental Polarization Calibration D X 00 161 4 4 5 1 Heuristics and Strategies for Polarization Calibration 162 4 4 5 2 A Polarization Calibration Example 163 4 4 6 Baseline based Calibration blcal 164 4 4 7 EXPERIMENTAL Fringe Fitting fringecal 165 se ig bk he ee eee OD os Se ee A 165 4 5 1 Plotting Calibration Solutions ploteal sv 2s lt 4 44 a eee 4 165 4 5 1 1 Examples for plotcal 0 000 4 167 4 5 2 Listing calibration solutions with listcal 169 4 5 3 Calibration Smoothing smoothcal ooo o 172 4 5 4 Calibration Interpolation and Accumulation accum 174 4 5 4 1 Interpolation using accum o 175 4 5 4 2 Incremental Calibration using accum 175 A EE de a E eee y 178 4 6 1 Application of Calibration applycal 178 lt i eo AR Ree eo AR W i 181 4 6 3 Resetting the Applied Calibration using clearcal 182 OA 183 4 7 1 Splitting out Calibrated uv data split 183 4 7 1 1 Averaging in split EXPERIMENTAD 183 4 7 2 Hanning smoothing of uv data hanningsmooth 184 4 7 3 Model subtraction from uv data uvsub 185 4 7 4 UV Plane Continuum Subtraction uvcontsub
60. 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 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 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
61. 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 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 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 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
62. 52 50 648 46 81950 Right Ascension x m5 1 fits 439 Pixel 235 264 13 27 48 552 47 27 20 367 Figure 7 11 Selecting an image region with the polygon tool inclusion in documents CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 300 hd Viewer Display Panel O x Data DisplayPanel Tools View A IP y QQ AQ Ea LCBO EAR BARRA x q DIR 4 gale ee 2 Viewer Canvas Manager X 1499 78 km s Margins 12 Left margin space PG chars P Pad Y 9 a Bottom margin space PG chars Fit 4 Right margin space PG chars Fd Y 4 Top margin space PG chars Fit Number of panels 2 Number of panels in x eee a AY e 2 Number of panels in y i FS aes Er Bix P 0 FA f X Spacing of Panels py GIOIO O 01010 lo noma 0 o Blink Y Spacing of Panels Bi Rate 10 sec Compact Basic Settings Frame end 4 x Background Color black Rv ES E X ngc5921 demo clean image r 0 00358195 Jy beam pixel 81 119 0 22 Apply pave a OP Fly 15 22 47 684 05 01 41 878 I 1494 63 km s Figure 7 12 A multi panel display set up through the Viewer Canvas Manager 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 Warning Only one MS should be regist
63. Field 0 2 26 b 81 pee Win 0 s 0 1 413443 GHz ch 31 RR p 0 e O OO 9 QG 31 63 e Normal Blink Y Viewer Display Panel hd Data Display Options 7 ngc5921 usecase ms 283 Advanced MS and Visibility Selection Display Axes Flagging Options Basic Settings Data minimum Data maximum Scaling power cycles Colormap Apply o Av ms a p F lv Hot Metal 1 gt Pid Axis Drawing and Labels Color Wedge Dismiss Figure 7 2 panels that appear when the viewer viewer ngc5921 usecase ms ms The Viewer Display Panel left and Data Display Options right is called with the NGC5921 Measurement Set gt casaviewer image_filename amp Start the casaviewer with the selected Measurement Set note the additional parameter indicating that it is an ms the default is image gt casaviewer ms_filename ms amp 7 2 The viewer GUI The CASA viewer application consists of a number of graphical user interfaces GUIs that are mouse cursor and button controlled There are a number of panels to this GUI CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 284 We describe the Viewer Display Panel 7 2 1 and the Load Data Viewer 7 2 3 below as these are common to whether you are viewing and image or MS The other panels are context specific and described in the following sections on viewing i
64. Have to split all spw to preserve numbering spw pick off the CORRECTED_DATA column datacolumn corrected print Split CORRECTED_DATA into DATA in new ms srcsplitms saveinputs split prefix split saved split O 484 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 485 Plot up the visibilities for the main calibrators print Plotxy default plotxy vis srcsplitms field fluxcalfield spw selectdata True xaxis uvdist interactive False correlation RR LL yaxis amp figfile prefixt split field uvplot amp png saveinputs plotxy prefixt plotxy field amp saved plotxy O correlation RL LR yaxis phase figfile prefixt split field uvplot rlphase png saveinputs plotxy prefixt plotxy field rlphase saved plotxy O if polcalfield fluxcalfield Now the poln calibrator field polcalfield correlation RR LL yaxis amp figfile prefixt split field uvplot amp png saveinputs plotxy prefixt plotxy field amp saved plotxy O correlation RL LR yaxis phase figfile prefixt split field uvplot rlphase png saveinputs plotxy prefixt plotxy field rlphase saved plotxy O APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS Loop over sources and spw
65. No way to input guesses 8 sdplot Only handles included JPL line catalog Also see sd plotter issues above 9 sdstat Cannot return the location channel frequency or velocity of the maximum or minimum 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 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 d
66. Normal Dash negative contours true a Y ra 10 jec al O Blink Dash positive contours false E Y Line color foreground z Fad Y Frame St End Ster Position tracking Axis labels X ngc5921 usecase clean image contour Axis label properties I 1 546876e 03 km s 1 786e 03 Jy beam 15 21 34 929 05 10 18 429 Beam Ellipse X ngc5921 usecase clean image I 1 546876e 03 km s Dismiss 1 786e 03 Jy beam 15 21 34 929 05 10 18 429 Figure 7 8 The Viewer Display Panel left and Data Display Options panel right after overlaying a Contour Map on a Raster Image from the same image cube 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 The tab for the contour plot is open in the Data Display Options panel 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 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 region on the display panel using the rectangle or polygon region mouse tools 7 2 11 7 2 2 and confirm by double clicking insid
67. 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 5 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 amplitude response as a function of elevation gain curve and
68. Set up 2x1 panels lower panel phase vs time subplot 212 yaxis phase CHAPTER 4 SYNTHESIS CALIBRATION Now send final plot to file in PNG format via png suffix figfile caltable plotcal png plotcal O The amp and phase coherence looks good Apply our calibration solutions to the data This will put calibrated data into the CORRECTED_DATA column print ApplyCal default applycal vis msfile 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 1 2 applycal Now for completeness apply 1331 305 to itself field 0 gainfield 0 The CORRECTED_DATA column now contains the calibrated visibilities 199 CHAPTER 4 SYNTHESIS CALIBRATION 200 applycal Now use plotxy to plot the calibrated target data before contsub print Plotxy NGC5921 default plotxy
69. Set up for new clean in patch 2 for src in srclist srcmodel for spwid in usespwlist print Clean srct spw spwid default clean field src spw spwid Pick up our split source data vis srcsplitms Make an image root file name imnamel prefix src spwid clean imagename imnamel print Output images will be prefixed with imnamel Set up the output continuum image single plane mfs mode mfs All polarizations stokes IQUV Use chose clean style psfmode clnalg csclean usecsclean imsize clnimsize clnimsize cell clncell clncell1 Standard gain factor 0 1 gain 0 1 niter clniter threshold clthreshold Set up the weighting Use Briggs weighting a moderate value on the uniform side weighting briggs 486 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 487 robust 0 5 Use natural weighting weighting natural Use the cleanbox mask myclnbox saveinputs clean prefixt clean src spwidt saved clean Set up variables clnimagel imname1 image clnmodeli imnameit model clnresidi imnameit residual clnmaski imnameit mask clnpsf1 imnamel psf clnfluxi imnameit flux Ho Get some statistics of the clean image
70. 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 5u 6 7 8 9 __IP system vi temp py ipmagic run i temp py Note magic commands are designated in this way ipmagic hist more temp py Note shell commands are designated in this way __IP system more temp py quickhelp im open ngc5921 ms im summary 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 ipmagic pdoc im setdata 10 11 12 13 14 15 16 17 18 19 20 21 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 N y The following commands were written to file script py x 1 y 3 x Z x 2 y 2 APPENDIX D APPENDIX PYTHON AND CASA 393 CASA 25 more script py x 1 y 3x x Z X 24yx 2 Note that th
71. 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 294 2 2 S 4i A A dole tence sateen ies b x lt 8 o Ev 5 i A 5 7 scaling power lt 0 o o eS scaling power 0 o T A 8 scaling power gt 0 Input data value Data minimum Data maximum Figure 7 6 Example curves for scaling power cycles 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 7 3 2 Viewing a contour map Viewing a contour image is similar 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 7 Several Basic Settings options control the contour levels used 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 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 individuall
72. Type of selection mfs channel velocity frequency alg clark Algorithm to use hogbom clark csclean multiscale niter 500 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 using the go command either explicitly CHAPTER 1 INTRODUCTION 46 CASA lt 44 gt go listobs gt go listobs Executing listobs 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 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 ES 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 tasknam
73. 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 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 inputs are imstat Displays statistical information on an image or image region imagename re Name of the input image box a Select one or more box regions chans gt Select the channel spectral range stokes 39 Stokes params to image I IV IQU IQUV async False CHAPTER 6 IMAGE ANALYSIS 269 52 TT T 7 45 F 4 48 30 F 7 44 F 7 S o 8 E zel E 3 4100 F 7 3 36 2 45 F 4 o 32 s S x L J So 28 7 E ag i 5 F 4 24 F 4 O 65 20 L 4 21 40 00 C fi fi fi fi fi fi J a a ee 12 56 48 46 44 428 408 1 L o7 39 30 38 005 36 30 35 008 3 n 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 Region selection is carried out through the box parameter See for more on region selection using this parameter Image 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 workaroun
74. 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 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 t
75. 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 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 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 BETA ALERT there is an Open function in the File menu and an Open button but these are grayed out in the beta Sorry 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 casapy lt logger option gt CHAPTER 1 INTRODUCTION 56 00 X Log Messages casapy log a File Edit ta All Se
76. 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 vis a Nome of input visibility file caltable ox Name of output gain calibration table field gt Select field using field id s or field name s spw dd Select spectral window channels selectdata False Other data selection parameters solint inf Solution interval see help combine neh Data axes which to combine for solve scan spw and or field preavg 1 0 Pre averaging interval sec refant Reference antenna name minsnr 3 0 0 Reject solutions below this SNR solnorm False Normalize average solution amplitudes to 1 0 G T only CHAPTER 4 SYNTHESIS CALIBRATION 155 gaintype gt G Type of gain solution G T or GSPLINE calmode ap Type of solution ap p a append z 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
77. default imstat field src spw spwid Use the clean box mybox str clnblc str clnblc str clntrc str clntrc spwmodel spwstats spwfluxes spwsum spwmod for stokes in I Q U V Use the clean image imagename clnimagel box mybox saveinputs imstat prefix imstat src spwid stokes saved xstat imstat spwstats stokes xstat Peak max or min in box xmax xstat max 0 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 488 xmin xstat min 0 if abs xmin gt abs xmax xpol xmin else xpol xmax spwfluxes stokes xpol Integrated flux in box xsum xstat flux 0 spwsum stokes xsum Use the clean model and no box imagename clnmodell box saveinputs imstat prefix imstat src spwid stokes model saved xstat imstat Integrated flux in image xmod xstat sum 0 spwmod stokes xmod Done with stokes spwmodel stat spwstats spwmodel f1ux spwfluxes spwmodel integ spwsum spwmodel model spwmod Use ia tool for pixel values in the restored image imagename clnimagel Get image values at the reference pixel spwref ia open imagename Stokes I ipix ia pixelvalue Get reference pixel xref ipix pixel 0 yref ipix
78. gt logfile Now the clean image APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 423 Pull the max from the cubestats dictionary created above using imstat thistest_immax cubestats max 0 oldtest_immax 0 052414759993553162 diff_immax abs oldtest_immax thistest_immax oldtest_immax print Clean Image max 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 Pull the rms from the cubestats dictionary thistest_imrms cubestats rms 0 oldtest_imrms 0 0020218724384903908 diff_imrms abs oldtest_imrms thistest_imrms oldtest_imrms print Clean image rms gt thistest_imrms print Previous rms oldtest_imrms print Difference fractional diff_imrms print print gt gt logfile Clean image rms gt 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 Pull the max from the momzerostats dictionary thistest_momzeromax momzerostats max 0 oldtest_momzeromax 1 40223777294 diff_momzeromax abs oldtest_mo
79. home casa casainit csh depending on what shell you are running Bourne or tjcsh BETA ALERT If you want to run the casabrowser see 3 6 outside of the casapy shell then you will need to put the CASA root in your path using one of the above mechanisms 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 1ess PAGER more PAGER cat CHAPTER 1 INTRODUCTION 25 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
80. i e running antenna will flag only those channels on antenna 0 0 will flag all data with antenna 0 while antenna 0 spw 0 10 15 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 autocorr False unflag False clipexpr ABS RR clipminmax Do clipcolumn gt DATA clipoutside True Mode manualflag autoflag summary quack Flag autocorrelations Unflag the data specified Expression to clip on Range to use for clipping Data column to use for clipping Clip outside the range or within it 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 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 CHAPTER 3 DATA EXAMINATION AND EDITING 115 e Figure 1 eee Figure 1 Corrected SPWs 0 Pol RR LL Corrected SPWs 0 Pol RR LL Fields 1331 30500002_0 Fields 1331 30500002_0 20 corrected amp corrected amp 2 o ur E h m if 14 ij sil HA os del 4 yi Sti A 400 600 000 sei a00 EL NES B00 D00 sqrt u 2 v 2 m sqrt u 2
81. 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 __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 O_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 o
82. 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 142 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 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 It is 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 cal
83. print print print Back to all data print Clean up remaining bad points 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 print 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 Pause script if you are running in scriptmode if scriptmode user_check raw_input Return to continue scriptin correlation xaxis time CHAPTER 3 DATA EXAMINATION AND EDITING 127 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 Print 5 2223932523332 ra SSS RSS SSS SSCS SSR SSS SS n 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 xaxis uvdist spw 71 antenna iteration antenna plotxy O As you step through you will see that Antenna 9 ID 8 is often tt bad in this spw If you box and do
84. 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 329 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 coadded spectra before saving to a file on disk 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 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 maskflag list of mask regions to apply flag unflag default entire spectrum exampl
85. 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 Pull the max from the cubestats dictionary created above using imstat thistest_dirtymax dirtystats max 0 oldtest_dirtymax 0 0515365377069 diff_dirtymax abs oldtest_dirtymax thistest_dirtymax oldtest_dirtymax First the dirty image print Dirty Image max thistest_dirtymax print Previous 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 Pull the rms from the cubestats dictionary 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
86. 0 0 Position angle of filter degrees The sub parameters specify the size and orientation of this Gaussian in the image plane in arc seconds Note that since this filter effectively multiplies the intrinsic visibility weights the resulting image will not have a PSF given by the size of the filter but a PSF given by its intrinsic size convolved by the filter Thus you should end up with a synthesized beam of size equal to the quadratic sum of the original beam and the filter BETA ALERT We will soon give the option of specifying the filter taper in uv units e g kilo lambda or meters 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 the visibility data The weighting function can also de mation on imaging weights pend upon the uv locus of that visibility e g a taper to change resolution This is actually controlled by the CHAPTER 5 SYNTHESIS IMAGING 215 uvfilter parameter see 5 2 10 The weighting matrix also include
87. 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 18 4 33 53 54 8 Tables MAIN 22653 rows ANTENNA 28 rows DATA_DESCRIPTION 1 row DOPPLER lt absent gt FEED 28 rows FIELD 3 rows FLAG_CMD lt empty gt FREQ_OFFSET lt absent gt HISTORY 273 rows OBSERVATION 1 row Ca E SE SE E SE SE SE SE SE SE SE SE SE SE SE SE SE SE SE SE E SE SE SE SE SE SE E HHH HH HH HHH HHH HHH HH FH OH OF OF a w APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 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 f Get rid of the autocorrelations from the MS print Flagautocorr Don t default this one either there is only one parameter vis flagautocorr 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 freq
88. 20 40 24 38 3 70 42 75 66 where each line specifies the field index and the ble x y and trc x y positions of that cleanbox For example in casapy you can do this easily 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 cleanbox 80 80 120 120 CHAPTER 5 SYNTHESIS IMAGING 236 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 wan
89. 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 The return value in xstat is CASA lt 152 gt xstat Out 152 blce array 108 108 0 211 bl1cf 15 22 20 076 04 58 59 981 I 1 41332e 09Hz flux array 0 11179924 max array 0 02945151 maxpos array 124 131 0 21 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 0 211 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 gt sumsq array 0 02845345 tre array 148 148 0 211 tref 15 21 39 919 05 08 59 981
90. 427 Includes polarization imaging and analysis HHHHHHHHHHHEEEHHHHHHHHHHAAEHA RARER HH HHA H HAAR import time import os 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 jupiter6cm usecase 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 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS Polarization calibration setup dopolcal True ptable xtable calprefix polx calprefix pcal 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
91. 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 regridimage regrid an image onto the coordinate system of another image 6 8 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 CHAPTER 1 INTRODUCTION 68 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 ax
92. 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 Updated STM 2008 03 25 Beta Patch 1 0 401 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS Updated Updated HHH HHH HHH HH HH HHH HH HHH HH HH HHH HHH HHH HHH HH HHH H HH HH OF Features Tested The script illustrates end to end as depicted in the following flow Filenames will have the lt prefix gt Input Data Process NGC5921 fits gt importuvfits gt 1 4GHz 63 sp chan v D array listobs gt v flagautocorr v setjy v bandpass gt v gaincal gt v fluxscale gt v applycal gt v split gt v split gt v exportuvfits gt v uvcontsub gt STM 2008 05 23 Beta Patch 2 0 new tasking clean cal STM 2008 06 11 Beta Patch 2 0 processing with CASA Chart ngc5921 usecase 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
93. ALERT This 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 a4 Mathematical expression using images string containing LEL expression 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 SINHO ASINO COSO COSHO TANO TANHO ATAN EXPO LOGO LOG10 POWO SQRT COMPLEXO CONJO REAL IMAGO ABSO ARG PHASE AMPLITUDE MINO MAX ROUND ISGN FLOOR CEIL REBIN SPECTRALINDEX PACO IIF INDEXIN REPLACE CHAPTER 6 IMAGE ANALYSIS 255 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 a 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 numb
94. APPENDIX ANNOTATED EXAMPLE SCRIPTS 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 Select the Jupiter field field srcname spw 448 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS pick off the CORRECTED_DATA column datacolumn corrected Make an output vis file outputvis srcsplitms print Split field data into new ms srcsplitms split Also split out 0137 331 as a check field calname outputvis calsplitms print Split field data into new ms calsplitms split O Force scratch column creation so plotxy will work vis srcsplitms clearcal vis calsplitms clearcal
95. CHAPTER 4 SYNTHESIS CALIBRATION 190 3 0 2 8 N mn Amplitude of Model Data N gt 2 2 2 0 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 Here are two examples of calibration BETA ALERT Note that the syntax has been changing recently and these may get out of date quickly 4 8 1 Spectral Line Calibration for NGC5921 The following is an example calibration using the NGC5921 VLA observations as the demonstration This uses the CASA tasks as of the Beta Release This data is available with the CASA release and so you can try this yourself The full NGC5921 example script can be found in Appendix F 1 CHAPTER 4 SYNTHESIS CALIBRATION HHEEHHHHHEHHEEHHAEHEHEEHEHHEAHHEEEHHHAHHEEHRHEHHEHHEE PERRERA RARA HORROR RARA RARA ARRE Calibration Script for NGC 5921 Updated STM 2008 03 25 Beta Patch 1 0 Updated STM 2008 06 11 Beta Patch 2 0 Filenames will have the lt prefix gt ngc5921 usecase Input Data Process Output Data NGC5921 fits gt importuvfits gt lt prefix gt ms 1 4GHz lt prefix gt ms flagversions 63 sp chan v D array listobs gt casapy log v flagautocorr v setjy v bandpass gt lt prefix gt bcal v gaincal gt lt prefi
96. EXAMPLE SCRIPTS 463 viewer polimage image print Displaying pol I now You should overlay pola vectors 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 polaimaget 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 usecase polimg clean image pola jupiter6cm usecase 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
97. 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 134 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 5 4 3 3 parameters in subsequent tasks e Bandpass Calibration solve for the relative gain of the system over the frequency chan 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 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 a
98. 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 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 160 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 uvra
99. IMPORT EXPORT AND SELECTION 76 The MS selection parameters field spw antenna and timerange follow the standard selection syntax described in 2 5 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 containing 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 writestati
100. Locate or remember from 0137 331 its probably a bad time print print 52 2 225592 25922412 2999 9 ae SSeS print Step through antennas with Next print See bad Antenna 9 ID 8 as in 0137 331 Pause script if you are running in scriptmode if scriptmode user_check raw_input Return to continue script n 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 print we print Now plotting vs time antenna 9 spw 1 CHAPTER 3 DATA EXAMINATION AND EDITING 128 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 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 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 25225223 5 ee Se ors SS eR P RARAS k 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
101. 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 e Locate 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 markersize linewidth skipnrows newplot clearpanel title xlabels ylabels fontsize windowsize True 5 0 1 0 1 False auto 1 0 1 2 2 2 0 0 2 2 HHH HH HH HOH OH OF Select additional plotting options e g fontsize title etc Size of plotted marks Width of plotted lines Plot every nth point Replace the last plot or not when overplotting Specify if old plots are cleared or not Plot title above plot Label for x axis La
102. Med Dev IntQtlRng Median Min Max 4 653 0 0006676 0 001383 1 892e 06 0 002842 1 076 Estimated dynamic range 1 076 0 001015 1060 even 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 Greg Taylor got 1600 1 so we still have some ways to go This will probably take several more careful self cal cycles HHH HHH HH HHH HH HHH HHH H HH OH OF Set up final variables clnimage clnimage3 clnmodel clnmodel3 clnresid clnresid3 clnmask clnmask3 f Export the Final CLEAN Image as FITS print Final Export CLEAN FITS default exportfits clnfits prefix clean fits imagename clnimage fitsimage clnfits Run asynchronously so as not to interfere with other tasks BETA also avoids crash on next importfits async True exportfits CHAPTER 5 SYNTHESIS IMAGING Export the Final Self Calibrated Jupiter data as UVFITS print Final Export UVFITS default exportuvfits caluvfits prefix selfcal uvfits vis srcsplitms fitsfile caluvfits The self calibrated data is in the CORRECTED_DATA column datacolumn corrected Write as a multisource UVFITS with SU table even though it will have only one field in it multisource True Run asynchronously so as not to i
103. 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 5 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 htm1 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 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
104. Resoln kHz TotBW kHz Feeds 28 printing first row only Antenna 1 1 Antennas 27 Spectral Window ID Name Station Diam 0 1 VLA N7 25 0 1 2 VLA W1 25 0 2 3 VLA W2 25 0 3 4 VLA El 25 0 4 5 VLA E3 25 0 5 6 VLA E9 25 0 6 7 VLA E6 25 0 7 8 VLA W8 25 0 8 9 VLA N5 25 0 9 10 VLA W3 25 0 10 11 VLA N4 25 0 11 12 VLA W5 25 0 12 13 VLA N3 25 0 13 14 VLA N1 25 0 14 15 VLA N2 25 0 15 16 VLA E7 25 0 16 17 VLA E8 25 0 17 18 VLA W4 25 0 18 19 VLA E5 25 0 19 20 VLA W9 25 0 20 21 VLA W6 25 0 21 22 VLA E4 25 0 23 24 VLA E2 25 0 24 25 VLA N6 25 0 B5B BBEBEBBBBBEBEBBEBSEBBBBBBBBBEBBEBEB Long Lat 107 37 07 2 33 107 37 05 9 33 107 37 07 4 33 107 37 05 7 33 107 37 02 8 33 107 36 45 1 33 107 36 55 6 33 107 37 21 6 33 107 37 06 7 33 107 37 08 9 33 107 37 06 5 33 107 37 13 0 33 107 37 06 3 33 107 37 06 0 33 107 37 06 2 33 107 36 52 4 33 107 36 48 9 33 107 37 10 8 33 107 36 58 4 33 107 37 25 1 33 107 37 15 6 33 107 37 00 8 33 107 37 04 4 33 107 37 06 9 33 54 54 54 53 54 53 53 53 54 54 54 53 54 54 54 53 53 53 53 53 53 53 54 54 12 00 00 59 00 53 57 53 08 00 06 57 04 01 03 56 55 59 58 51 56 59 01 10 1412 68608 24 4140625 1550 19688 Receptors Polarizations 2 WrFNPOWFRPRFRAATUAAAArFRRFROAOAONODANO YN O 1413 44902 RR LL 425 APPEN
105. 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 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 F igure 7 9 CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 296 Y Viewer Display Panel Data DisplayPanel Tools View Ah E 2 Qi Q Ea o Pe 3 E SN N 4 Data Display Options BE a g a e E 8 amp ngc5921 usecase clean image ngc5921 usecase clean image contour Display axes Hidden axes Basic Settings Aspect ratio fixed world gt e Y Pixel treatment center 3 Y Resampling mode nearest MA Ead Y Contour levels yA Y Contour scale factor 0 00942197 yA Y Level type abs X Y ax Line width as P Y R Q O O O 2 46
106. The msselect Parameter 0 0 00 0000 eee 3 Data Examination and Editing A A a Suse eee ae ey ee totes See a O Soe ees aa BA GULP Controls ssa Spe M4 is GOA 2 ee a is A 3 4 3 Plot Control Parameters seca rusa tuera ee 3 4 3 1 Tteration messi de eTe a a e Re a D432 OVErPIOt s s ag y e a a a 3 4 3 3 plotrange ooa a radi ga pea E ea y ee KS 104 3 434 plotsymboll p e 104 34 3 0 showflags oe cac esene mae a e a E 105 3 4 3 6 SUDplotl dead a e 105 3 4 4 Averaging in plotxy ooa ee ee 106 3 4 5 Interactive Flagging in plotxy ooa aaa a 106 3 4 6 Printing from plotxy oaa ee ee 108 3 4 7 Exiting plotxy s aca sa bis ate aoe ae eg a e a DoR a Gee ek 109 3 4 8 Example session using plOtXY e 109 O Bee aat 112 Kag up AO es a E g A ated Ra teed ce 113 3 5 1 1 Manual flagging and clipping in flagdatal 114 3 5 1 2 Flagging the beginning of scans 20 4 114 eR ek Galak Me GANG a Ei ol e as oe ee ae ae aa gl A 115 3 7 Examples of Data Display and Flagging ooa aaa 117 131 Ad Calbration Tasks c cos 4 4 Bw Pos ecw hoe RA ee ew eek eR RE ee od 131 4 2 The Calibration Process Outline and Philosophy 132 sek Hoe ee ee d eA A t 134 eee hb Bo yeh Qe G Bie ak he ae eS 135 By Ged via E 136 Sie ae de Sect gee ee ee dake cee ee Gees Cg Os eer 137 4 3 1 S
107. True run in the background prompt is freed All of the fringecal 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 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 CHAPTER 4 SYNTHESIS CALIBRATION 166 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 HO HH A 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 375 Spectral
108. Type of selection mfs channel velocity frequency nchan Number of channels to select start Start channel step Increment between channels velocity width Channel width value gt 1 indicates channel averaging alg Algorithm to use hogbom clark csclean multiscale niter Number of iterations gain Loop gain for cleaning threshold Flux level to stop cleaning mJy mask Name of mask image used in cleaning cleanbox El clean box regions or file name or interactive imsize 256 256 Image size in pixels nx ny symmetric for single value cell 15 0 15 0 Cell size in arcseconds x y stokes a es Stokes parameter to image I IV IQU IQUV field QO Field name phasecenter Ms Field Identifier or direction of the image phase center spw f spectral window channels gt all weighting briggs Weighting to apply to visibilities rmode norm Robustness mode for Briggs weighting robust 0 5 Briggs robustness parameter noise 0 0Jy noise parameter for briggs weighting when rmode abs npixels number of pixels to determine uv cell size 0 gt field of view uvfilter False Apply additional filtering uv tapering of the visibilities timerange 24 range of time to select from data restfreg A restfrequency to use in image async False if True run in the background prompt is freed ha CASA lt 31 gt E 49 Figure 1 2 The clean inputs
109. Use Plotxy to look at the split calibrated data print Plotxy default plotxy vis srcsplitms selectdata True Plot only the RR and LL for now correlation RR LL Plot amplitude vs uvdist xaxis uvdist datacolumn data multicolor both iteration selectplot True interactive True field yaxis JUPITER amp 449 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS Use the field name as the title title field 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 plotxy 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
110. VA20 VLA E12 25 0 m 107 36 31 7 33 53 48 5 10 VA15 VLA E4 25 0 m 107 37 00 8 33 53 59 7 11 VA28 VLA E6 25 0 m 107 36 55 6 33 53 57 7 12 VA10 VLA E8 25 0 m 107 36 48 9 33 53 55 1 13 EA14 VLA E16 25 0 m 107 36 09 8 33 53 40 0 14 EA11 VLA E10 25 0 m 107 36 40 9 33 53 52 0 15 VAO3 VLA E14 25 0 m 107 36 21 3 33 53 44 5 16 EA23 VLA E18 25 0 m 107 35 57 2 33 53 35 1 17 EA21 VLA E2 25 0 m 107 37 04 4 33 54 01 1 18 VA12 VLA N4 25 0 m 107 37 06 5 33 54 06 1 19 VA0O2 VLA N20 25 0 m 107 37 13 2 33 55 09 5 20 EA13 VLA N16 25 0 m 107 37 10 9 33 54 48 0 21 EA26 VLA N32 25 0 m 107 37 22 0 33 56 33 6 22 EA25 VLA N24 25 0 m 107 37 16 1 33 55 37 7 23 VAO9 VLA N8 25 0 m 107 37 07 5 33 54 15 8 24 EA18 VLA N12 25 0 m 107 37 09 0 33 54 30 0 25 VAO7 VLA N36 25 0 m 107 37 25 6 33 57 07 6 26 VA27 VLA N28 25 0 m 107 37 18 7 33 56 02 5 Tables MAIN 318708 rows ANTENNA 27 rows DATA_DESCRIPTION 2 rows DOPPLER 2 rows FEED 27 rows FIELD 9 rows FLAG_CMD lt empty gt FREQ_OFFSET lt absent gt HISTORY 6 rows OBSERVATION 1 row POINTING lt empty gt POLARIZATION 1 row PROCESSOR lt empty gt SOURCE 9 rows SPECTRAL_WINDOW 2 rows STATE lt empty gt SYSCAL lt absent gt WEATHER lt absent gt E E E SE SOE SOE SE SE SEE SE SE SE SE SE SE SE SE E SE E SE SE SE SE SE SE SE SE SE SE SE SE SE SE SE E SE SE H HH H HOF End Task listobs HHHRHHHHHHH
111. 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 the auto parentheses feature of Python 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 395 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 Y
112. 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 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 measurement 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 CHAPTER 1 INTRODUCTION 64 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 Calib
113. a deconvolved image with a selected clean algorithm Name of input visibility file Pre name of output images Type of selection mfs channel velocity frequency Algorithm to use hogbom clark csclean multiscale Number of iterations Loop gain for cleaning Flux level to stop cleaning mJy Name of mask image used in cleaning clean box regions or file name or interactive Image size in pixels nx ny symmetric for single value Cell size in arcseconds x y Stokes parameter to image I IV IQU IQUV Field name Field Identifier or direction of the image phase center spectral window channels gt all Weighting to apply to visibilities Apply additional filtering uv tapering of the visibilities range of time to select from data restfrequency to use in image if True run in the background prompt is freed 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 48 rw CASA lt 23 gt default clean SESSE Ls SS gt default clean gt CASA lt 24 gt inp zanasaass gt inp clean Calculates a deconvolved image with a selected clean algorithm vis hi Name of inpu
114. a different source and is not smoothed together with the subsequent solutions 2 6k a a 17 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 13314305 were in spw 1 The use of spwmap was EEN 17 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 AAN 179 9 The final amp versus uvdist plot of the self calibrated Jupiter data as shown SCCM A IATA 182 4 10 Use of plotxy to display corrected data red points and uv model fit data blue circles E w aD SARA 222 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 will now hit the Done button to start cleaning ee 22 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 100 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 th
115. antlist would be antlist 0 CHAPTER 1 INTRODUCTION 29 CASA lt 113 gt antlist range 5 CASA lt 114 gt antlist Out 114 0 1 2 3 4 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 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
116. at the center of the highest weighted mosaic field with higher noise regions down scaled accordingly Compared to the true 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 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 6 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 npercyc
117. be scan pairs in correct order as these routines only do minimal checking 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 weighted Example spave stave average_pol weight tsys One can also average scans over time using sd average_time APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 365 sd average_time scantable mask scanav weight align where Parameters one scan or comma separated scans 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
118. 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 looking 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 dep
119. 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 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 CHAPTER 3 DATA EXAMINATION AND EDITING 117 Y Table Browser File Edit View Tools Export Help wx 209 Of arFix Type Extra Information Float 2 table data ANTENNA Table nome sandrock smyers Testing 2 008 03 ngc5 92 1_regression ngc5921 ms ANTENNA Subtable has 28 rows DATA_DESCRIPTION Table nome sandrock smyers Testing 2 008 03 ngc5 92 1_regression ngc5921 ms DATA_D Subtable has 1 rows FEED Table nome sandrock smyers Testing 2 008 03 ngc5 92 1_regression ngc5 921 ms FEED Subtable has 28 rows FLAG_CMD Table nome sandrock smyer
120. ca a a a a a a aca cs ca ce me a a a a 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 HHHHHHHHHHHHHHHHHHHHHHHHHH Plot data HHHHHHHHHHHHHHHHHHHHHHHHHH 348 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 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 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 O 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 telescope GBT fluxunit Jy sdplot 349 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING Lets save thi
121. calibration embodying 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 C 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 t
122. call was plotxy vis ngc5921 ms xaxis uvdist field 1445 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 flagging stages using the flagmanager task 3 2 3 4 6 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 CHAPTER 3 DATA EXAMINATION AND EDITING 109 formats are png PNG eps EPS and svg SVG If you give the filename with a suffix png 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 GUl using interactive False in this case The type of plot file that is made will depend upon the filename suffix The allowed choices 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 xaxis uvdist yaxis amp interactive False figfile ngc
123. caltable mathematically 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 recen
124. 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 fiddling 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 adj
125. 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 452 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 453 polygon drawing icon in the toolbar When you are happy with the region click Done Flagging and it will go and clean another 100 iterations When done click Stop print print 2332 TSR ESS SA SS tse print Clean 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 print This is the final restored clean image in the viewer print Zoom in and set levels to see faint emission print Use rectangle drawing tool to box off source print Double click inside to print statistics print Move box on source and
126. 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 tasks This is a convenient alternative to using the Python execfile command see above 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 CHAPTER 1 INTRODUCTION 51 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 clean set current task to clean and default tget read saved inputs from clean last or clean saved inp see these inputs tget mosaic now get from mosaic last or mosaic saved inp task is now mosaic 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
127. 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 ae Name of the input image linefile a Output line image file name contfile os Output continuum image file name fitorder O Polynomial order for the continuum estimation box d Select one or more box regions chans gt gt Select the channel spectral range stokes ae Stokes params to image 1 IV IQU IQUV async False Region selection using box is detailed in Image cube plane selection using chans and stokes are described in 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 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 0 17 79796 stokes T imcontsub will fit a first order polynomial to the visibilities in channels 0 through 17 and 79 through 96 subtract that fit from the
128. conversion and the telescopeparm parameter 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 324 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 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 O
129. deconvolve image plane only deconvolution based on the dirty image and beam using one of several algorithms 5 7 There are also tasks that help you set up the imaging or interface imaging with calibration e makemask create cleanbox deconvolution regions 5 5 e ft Fourier transform the specified model or component list and insert the source model into the MODEL column of a visibility set 3 5 6 208 CHAPTER 5 SYNTHESIS IMAGING 209 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 selection general data selection syntax 2 5 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 EMBELVESs usk PAAR ie HOS field spw timerange In a later patch we will use the
130. dependent antenna gains vis msfile set the name for the output gain caltable gtable prefix gcal caltable gtable Use our previously determined bandpass Note this will automatically be 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 gaincal 409 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 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 ga
131. 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 enough characters to make the command unique lt TAB gt will complete it 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 ob tained by typing help task pdoc task and task are equivalent commands with some additional programming information returned help task 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 CHAPTER 1 INTRODUCTION 31 CASA lt 45 gt help uvcontsub gt help uvcontsub Help on function uvcontsub in module uvcontsub uvcontsub vis None field None spw None chans None solint None fitorder None fitmode None splitdata None async None Continuum fitting and subtraction in the uv plane A polynomial of the desired order is fit across the specified channels that define the continuum emission The data may be averaged in time
132. 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 messages 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 2 WARN warnings CHAPTER 1 INTRODUCTION 57 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
133. example uses accum to interpolate 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 17 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 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 CHAPTER 4 SYNTHESIS CALIBRATION 176 hd CASA Plotter Mark Regon a unas tocate gt out DO 0 Bla Figure 4 7 The phase of gain solutions for NGC48
134. f plot residual True plot residual 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 f set_function gauss 1 set a single gaussian component f set_gauss_parameters 0 4 4100 200 component 0 set initial guesses for Gaussian for first component 0 peak center fwhm 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 368 A 3 9 Plotting 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 se
135. file figfile saveinputs plotxy vis plotxy amp saved 450 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 451 plotxy O yaxis phase Use the field name as the title 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 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS print Will be a single MFS continuum image NOTE current version field doesnt work field Combine all spw spw Imaging mode params psfmode clnalg imagermode clnmode Imsize and cell imsize clnimsize 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
136. folder with the data repository in opt casa You can find the location after initialized by looking at the AIPSPATH environment variable You can find it within casapy by pathname 0s environ get AIPSPATH split 0 print pathname 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 CHAPTER 1 INTRODUCTION 26 After startup information you should get an IPython 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
137. 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 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 387 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
138. 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 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 Again using the NGC5921 dataset as an example 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 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 CHAPTER 5 SYNTHESIS IMAGING 213 phasecenter 5 field 5 in multi src ms phasecenter J2000 19h30m00 40d00m00 specify position 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 5 2 8 Pa
139. 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 3 4 e flagdata non interactive data flagging 8 3 5 e data selection general data selection syntax 2 5 4 2 The Calibration Process Outline and Philosophy A work flow 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 133 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
140. 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 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 see stuff like this in the terminal jupiter6cm usecase clean1 image Jy beam on Std Dev RMS Mean Variance Sum 4712 0 003914 0 003927 0 0003205 1 532e 05 1 510 Flux Med Dev IntQtlRng Median Min Max 0 09417 0 002646 0 005294 0 0001885 0 01125 0 01503 On Jupiter n Std Dev RMS Mean Variance Sum APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 454 3640 0 1007 0 1027 0 02023 0 01015 73 63 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 deep you take the interactive clean and how you draw the box for the stats fosooooooooooooooooooooooooooooooooooooooooooooooooooooooo
141. 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 mask image from a cleanbox and set of imaging parameters cleanbox Clean box file or regions vis gt Name of input visibility file if no input image imagename et 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 as Field identifier or direction of the phase center stokes 2T Stokes parameter to image I IV IQU IQUV field 20 Field ids list to use in mosaic spw 20 Spectral window identifier 0 based 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 7 with the option for interactive also The imagename parameter specifies the name for the output mask image CHAPTER 5 SYNTHESIS IMAGING 235 You can use the viewer to figure out the cleanbox blc 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
142. implemented multi feed numbers Not yet implemented array numbers Not yet implemented uv range gt all uvrange 0 100k1 default unit meters Select averaging type vector scalar Length of time interval in seconds to average Have time averaging cross scan boundaries 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 CHAPTER 3 DATA EXAMINATION AND EDITING 100 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 interactive 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 plot RR and LL correlations open plot controls give it a title correlation RR LL selectplot True title Jupiter 6cm uncalibrated The plotter resulting from these settings is shown in figure BETA ALERT The plotxy task still has a number of issues T
143. in J Q U and V independently 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 The im setscales method sets the multiscale 0 3 10 30 Four scales including ppin sources z multi scale Gaussian widths In ad dition to choosing a list of sizes in pixels you can just pick a number of scales and get a geometric series of These are given in numbers of pixels and specify FWHM of the Gaussians used to compute the filtered images Setting the multiscale parameter to a non empty list opens up the sub parameter sizes CHAPTER 5 SYNTHESIS IMAGING 221 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 cease when this number of negative components are found at the largest scale If negcomponent 1 then component search wil
144. in the data The scantable objects do not persist within CASA after completion of the 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 writting 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 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 315 Data Process Parameters Input dataset 5 nan El le scanaverage set_fluxunit fluxunit convert_flux telescope set_unit specunit a optical depth timeaverage kernel kwidth baseline m st auto pars output dataset Figure A 1 Wiring diagram for the SDtask sdcal The stages of processing within the task are show
145. 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 CHAPTER 6 IMAGE ANALYSIS 260 6 4 Image plane Component Fitting imfit The inputs are imfit Fit 2 dimentional Gaussian s on image region s imagename ii Name of the input image box at Specify one or more box regions for the fit region 2 Image Region Use viewer mask Ai Mask to be applied to the image fixed 22 Pparameters to hold fixed not implemented usecleanbeam False Estimate the true source size estfile que Initial estimate of parameters Not yet implemented residfile q 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 can fit only a single Gaussian component This restriction will be lifted in future patches 6 5 Mathematical Operations on an Image immath The inputs are immath Perform math operations on images outfile si File where the output is saved mode evalexpr mode for math operation evalexpr spix pola poli exp ae Mathematical expression using images mask 22 Mask to be applied to the images region el File path which contains an Image Region box ed Selec
146. 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 5 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 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 Note that single dish data reduction for example with the ALMA single dish system follows a similar course This is detailed in Chapter A CHAPTER 1 INTRODUCTION 60 Input Data Process Output Data Input dataset Data Import Data Examination and Flagging Flagging Table Calibrated UV Data Calibration Table I a A i Model Image Imaging Restored Image Residual Image Image Analysis Figure 1
147. 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 ask argi 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 elobals default imhead imagename ngc5921 usecase clean image mode list imhead If you supply the task call with arguments then these will be used for the values 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 usecase clean image mode list will reproduce the above CHAPTER 1 INTRODUCTION 45 1 3 5 2 The default Command Each task has a special set of default par
148. 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 psfalg parameter B 3 1 This method is not recommended for high dynamic range or high fidelity imaging applications but can be significantly faster than CS clean The csclean choice specifies the Cotton Schwab algorithm This opens up the sub parameters imagermode csclean Use csclean or mosaic If use psfmode cyclefactor 1 5 Change depth in between of csclean cycle cyclespeedup 1 Cycle threshold doubles in this number of iterations CHAPTER 5 SYNTHESIS IMAGING 222 viewer Display Panel Data DisplayPanel Tools View a ft Te x Clean Regions Channels Masking Clean y Cycle Control j aaa niter cycle 100 a All ncycles 10 O Erase threshold 0 05 mJy Figure 5 1 Close up of the top of the interactive clean window Note the boxes at the right where the npercycle niter and threshold can be changed the buttons that control the masking and whether to continue or stop cleaning and the row of Mouse button tool assignment icons These options are explained below In the CS mode cleaning is split into minor and major cycl
149. max print Calcualte DynRange MAXon RMSoff print This time I got 1 076 0 001389 775 better print Still not as good as it can be lets selfcal again print Close viewer panel when done If you did not do interactive clean bring up viewer manually viewer clnimage2 image Pause script if you are running in scriptmode if scriptmode user_check raw_input Return to continue script n n 5236 Flux 0 01060 On Jupiter n 5304 Flux 4 695 HH HH HHH HH HH HH HHH HH OH OF Std Dev 0 001389 Med Devl 0 0009064 Std Dev 0 08512 Med Devl 0 0008142 Estimated dynamic range jupiter6cm usecase clean2 image RMS 0 001390 IntQt1Rng 0 001823 RMS 0 08629 IntQt1Rng 0 001657 Jy beam Mean 3 244e 05 Median 1 884e 05 Mean 0 01418 Median 0 0001557 Variance 1 930e 06 Min 0 004015 Variance 0 007245 Min 0 004526 1 076 0 001389 775 better Sum 0 1699 Max 0 004892 Sum 75 21 Max 1 076 Note that the exact numbers you get will depend on how deep you APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS take the interactive clean and how you draw the box for the stats print print 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 o
150. 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 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 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 332 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 examp
151. or without the although the cp command must use and cd must be executed without the For example CASA lt 5 gt rm r mydata ms 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 echo 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 CHAPTER 1 INTRODUCTION 30 CASA lt 7 gt execfile myscript py or CASA lt 8 gt execfile myscript py which will invoke the IPython auto parenthesis feature NOTE in some cases you can use the IPython 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 5 7 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
152. 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 data Some plot options like annotation and changing titles legends colors fonts and the like are not supported in this task You should use sd plotter from the ASAP toolkit directly for this 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 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 Currently setting specunit GHz fixes the x axis span of each IF panel to be the same an example of the limitations of ASAP plotting at present 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 A 2 1 10 sdsave Keyword arguments sdfile name of input SD dataset scan
153. polcal_20080224 cband edited ms datafile 20080224C UVF NOTE This file may be obtained from the CASA repository http casa nrao edu Data VLA Polcal POLCA_20080224_1 datafile POLCA_20080224_17 If from export set these exportproject POLCA exportband C Spectral windows to use in ms usually 0 1 usespw usespwlist 0 1 The ms will have this name msfile prefix ms These are names of calibration tables gtable prefix gcal APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS ftable prefix fluxscale ptable prefix pcal xtable prefix polx Flagging myquackinterval 14 0 if gt 0 then quack scan beginnings Flagging these antennas if blank then no flagging NOTE This script uses NEW names so VLA ants are VAxx flagants flagants EA keep only VLA antennas flagants VA keep only EVLA antennas List of sources in ms 0 A 1924 292 19 24 51 06 29 14 30 12 J2000 1 A 1743 038 17 43 58 86 03 50 04 62 J2000 2 A 2202 422 22 02 43 29 42 16 39 98 J2000 3 A 2253 161 22 53 57 75 16 08 53 56 J2000 4 B 2136 006 21 36 38 59 00 41 54 21 J2000 E 5 B 0137 331 01 37 41 30 33 09 35 13 J2000 6 A 2355 498 23 55 09 46 49 50 08 34 J2000 7 B 0319 415 03 19 48 16 41 30 42 10 J2000 8 B 0359 509 03 59 29 75 50 57 50 16 J2000 These sources are the gain c
154. prefix src split ms outputvis splitms Pick off N5921 field N5921 413 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 414 saveinputs split prefix split n5921 saved split Export the NGC5921 data as UVFITS Start with the split file print Export UVFITS default exportuvfits srcuvfits prefix split uvfits vis splitms fitsfile srcuvfits Since this is a split dataset the calibrated data is in the DATA column already datacolumn data Write as a multisource UVFITS with SU table even though it will have only one field in it multisource True Run asynchronously so as not to interfere with other tasks BETA also avoids crash on next importuvfits async True saveinputs exportuvfits prefixt 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 this will update the CORRECTED_DATA column print UV Continuum Subtract default uvcontsub vis msfile Pick off N5921 field N5921 Use channels 4 6 and 50 59 for continuum fitspw 0 476 50759 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 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 fitmod
155. print Q sif min 0 si max 0 s1 mean 0 print I s2 min 07 s2 max 0 s2 mean 0 6 8 Regridding an Image regridimage It is occasionally necessary to regrid an image onto a new coordinate system The regridimage task will regrid one Inside the Toolkit image onto the coordinate system of another creating an More complex coordinate system output image In this task the user need only specify the and image regridding operation can names of the input template and output images be carried out in the toolkit The coordsys cs tool and the ia regrid method are the relevant components 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 CHAPTER 6 IMAGE ANALYSIS 273 used see sidebox Some of these facilities will eventually be provided in task form The default inputs are regridimage Regrid imagename to have template image parameters imagename oe Name of image to be regridded template a image having the parameters that is wanted in regridded image output a es Name of image in which result of regridding is stored async False if True run in the background prompt is freed 6 9 Image Import Export to FITS These tasks will allow you to w
156. 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 something within the viewer itself requires it in the future a button will be provided to reload flags from the disk unconditionally CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 303 5 Se a 2 Ag B w oo w Data Display Options n4826_16apr ms Advanced MS and Visibility Selection Visibility Type Observed Visibility Component Amplitude y 3 Moving Average Size y Y A A 2000 3000 4000 5000 6000 6000 Baseline Field IDs 0 1 2 3 4 5 6 7 8
157. 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 12 sdstat 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 340 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 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 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 gt GEO GALACTO LGROUP CMB default curr
158. selection functions e g 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 These are currently CASA lt 1 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 A 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 360 The choices for the units are km s
159. 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 plotxy X Y plotter interactive flagger for visibility data vis 22 xaxis time yaxis amp datacolumn data Name of input visibility X axis def Y axis def data raw time see help for options amp see help for options corrected model residual corrected model CHAPTER 3 DATA EXAMINATION AND EDITING field spw selectdata averagemode timebin crossscans width subplot overplot showflags iteration plotsymbol plotcolor connect multicolor interactive figfile plotrange selectplot BETA ALERT Table 2 r 2 False vector 20 False 21 111 False False 2 2 2 Fi darkcyan none corr True 2 1 f i 2 False HH HHHH HH HH HH HO H OH OF 1 99 field names or index of calibrators gt all spectral window channels gt all spw 1 5757 Other data selection parameters Select averaging type vector scalar Length of time interval in seconds to average Have time averaging cro
160. 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 sdgrid task or the im imager tool to create images Tool example scans save outputms MS2 Save your data from ASAP into an MS im open outputms open the data set im selectvis nchan 901 start 30 step 1 choose a subset of the dataa spwid 0 field 0 just the key emission channels dir J2000 17 18 29 59 31 23 set map center im defineimage nx 150 cellx 1 5arcmin define image parameters 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 choose SD gridding im setsdoptions convsupport 4 use this many pixels to support the gridding function used default prolate spheroidal wave function im makeimage type singledish make the image image FLS3a_HI image A 4 1 Single Dish Imaging Use Case With ASAP Toolkit Again the data summary and then the script is given below Project AGBTO2A_007_01 Observation GBT 1 antennas APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 373 FLS3 data calibration this is calibration part of FLS3 data casapath os environ AIPSPATH
161. stats 246 CHAPTER 5 SYNTHESIS IMAGING 247 Next self cal cycle print SelfCal 2 default gaincal vis srcsplitms selfcaltab2 srcsplitms selfcal2 caltable selfcaltab2 selectdata False gaincurve False opacity 0 0 refant 11 This time amp phase on 10s timescales SNR gt 1 gaintype G calmode ap solint 10 0 minsnr 1 0 solnorm False gaincal It is useful to put this up in plotcal print PlotCal default plotcal tablein selfcaltab2 multiplot True yaxis amp plotcal Use the Next button to iterate over antennas Pause script if you are running in scriptmode if scriptmode user_check raw_input Return to continue script n yaxis phase plotcal You can see it is not too noisy CHAPTER 5 SYNTHESIS IMAGING Pause script if you are running in scriptmode if scriptmode user_check raw_input Return to continue script n Lets do some smoothing anyway Smooth calibration solutions print Smooth default smoothcal vis srcsplitms tablein selfcaltab2 smoothcaltab2 srcsplitms smoothcal2 caltable smoothcaltab2 Do a 30s boxcar average smoothtype mean smoothtime 30 0 smoothcal If you put into plotcal you 11 see the results For example you can grap the inputs from the last time you ran plotcal set
162. strings field 1331 305 0137 331 spw 7 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 442 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS set the name for the output rescaled caltable fluxtable ftable print Dutput 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 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 ftabl
163. 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 sections 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 pr
164. 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 Y Log Messages imager b home imager b smyers Nov07 casapy log SHG File Edit View JA A A y z Bs fal x 5 iB Search Message es Filter Time a Time Origin Message Tue Nov 6 21 52 44 2007 INFO listobs e 8deeeeeseaseseeeeeeteeeeessssseeeeeeees Tue Nov 6 21 52 44 2007 INFO listobs Begin Task listobs MeasurementSet Name home imager b smyers Nov07 ngc5921 usecase ms MS Version 2 Tue Nov 6 21 52 44 2007 INFO listobs ms A Observer TEST Project Observation VLA E i ti ine Tue Nov 6 21 52 44 2007 ES 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 SpwIds 13 Apr 1995 09 19 00 0 09 24 30 0 2 1331 30500002_0 0 09 27 30 0 09 29 30 0 2 1 1445 09900002_0 0 Tue Nov 6 21 52 44 2007 INFO Listobs ms 09 33 00 0 09 48 00 0 3 2 N5921_2 o 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 o 10 4
165. 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 model 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 8 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 ngc75
166. to increase the signal to noise This fit represents a model of the continuum in all channels For fitmode subtract the fitted continuum spectrum is subtracted from all channels and the result presumably only line emission is stored in the CORRECTED_DATA The continuum fit is stored in the MODEL_DATA For fitmode model the continuum model is stored in the MODEL_DATA but the CORRECTED_DATA is unaffected For fitmode replace the continuum model is stored in the CORRECTED_DATA this is useful to image the continuum model result Keyword arguments vis Name of input visibility file default none example vis ngc5921 ms field Field selection default field means select all fields field 1 will get field_id 1 if you give it an integer it will retrieve the source with that index field 1328 307 specifies source 1328 307 field 13 will retrieve 1328 307 and any other fields beginning with 13 spw Spectral selection default spw means select all spws example spw 1 chans List of channels to fit for the continuum default all example chans range 4 7 range 50 60 solint Averaging time for per baseline fit seconds default 1 0 gt no averaging fit every integration example solint 10 gt average to 10s before fitting fitorder Polynomial order for the fit of the continuum default 0 constant example fitorder 1 fitmode U
167. to make a Q iU 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 usecase polimg clean cmplxlinpol jupiter6cm usecase polimg clean image poli gt 0 005 H HHH HH HF Print results APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS max min rms rng gt stokest gt mymax gt mymin gt myrms gt mydra print print Jupiter polarization results print print for stokes in I Q U V POLI print print print print Polarization Stokes 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 print Clean image ON SRC print Clean image OFF SRC print Clean image dynamic print Done F 3 VLA Polarization Calibration 464 This script analyzes a standard V
168. 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 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 CHAPTER 4 SYNTHESIS CALIBRATION 156 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 specified an effective phase reference that is an average over
169. viewer Must include units CHAPTER 5 SYNTHESIS IMAGING 219 mask 108 108 148 148 cleanbox es mask image s and or region s imsize 256 256 x and y image size in pixels cell 15 0 15 0 x and y cell size default unit arcsec phasecenter dar Image phase center position or field index restfreq ais rest frequency to assign to image see help stokes Ta Stokes params to image eg I IV QU IQUV weighting briggs Weighting to apply to visibilities robust a 0 5 Briggs robustness parameter npixels O uv cell size in pixels 0 gt field of view uvtaper False Apply additional uv tapering of visibilities modelimage oo Name of model image s to initialize cleaning restoringbeam bead Output Gaussian restoring beam for CLEAN image pbcor False Output primary beam corrected image minpb 0 1 Minimum PB level to use async False An example of the clean task to create a continuum image from many channels is given below clean vis ggtau imm split ms Use data in ggtau imm split ms imagename ggtau imm alg clark niter 500 gain 0 1 mode mfs spw 0 2 2757 field 0 stokes I weighting briggs rmode norm robust 0 5 cell 0 1 0 1 imsize 256 256 HHH HH HH H HOH OF Name output images ggtau imm on disk Use the Clark CLEAN algorithm Iterate 500 times using gain of 0 1 multi frequency synthesis combine c
170. vis gt Name of output visibility file MS 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 Miriad 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 R Name of input visibility file fitsfile ane Name of output UVFITS file datacolumn corrected which data to write data corrected model field aa Field name list spw a Spectral window and channel selection antenna F ae antenna list to select time ae time range selection nchan 4 Number of channels to select start e 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
171. we ee Oe ee 39 1 34 Running Tasks Asynchronously o eee ee ee 41 1 3 4 1 Monitoring Asynchronous TasksS o a 41 1 3 4 2 Aborting Asynchronous Tasks o 42 Dejes emis a dd a Ms Gr ene be e ae cee E 43 1 3 5 1 The scope of parameters in CASA 44 1 3 5 2 The default Commaddl o 45 135 3 The go Commadadl e 45 1 3 5 4 The inp Command 0 2 00 0000004 46 1 3 5 5 The saveinputs Command 0004 48 1 3 5 6 The tget Command i282 ee a Re ee eR ae 50 fe ke bb oR Soe eee ee ee ee Ge es 51 ent past Gate eka Aetna ye aces Ge ees E we ae ee eee ee 52 bate ah eth Se A ee Ge 52 1 4 1 Your command line history o e e o 53 pai le Belk ey WO A eed ae Re eee da a 53 1 4 2 1 Starup options for the logger o 55 1 4 2 2 Setting priority levels in the logger 56 1 43 Where are my data in CASA 2 20 0 0 2 0 00 00 eee ee 57 L4 4 What s in my datall e ca ce sssaaa esmau paa aia Re aa 59 E O 59 ia a eee a Sl Ge aa 59 1 5 1 Loading Data into CASA 2 0 0 0 00 0 200 2 ee ee 60 1 5 1 1 VLA Filling data from VLA archive format 61 1 5 1 2 Filling data from UVFITS format 0 61 ood Se ete A Oe ee a 61 1 5 1 4 Concatenation of multiple MS 61 1 5 2 Data Examination Editing and Flagg
172. weighting Use Briggs weighting a moderate value on the uniform side weighting briggs robust 0 5 saveinputs clean prefix invert saved clean Should find stuff in the logger like Fitted beam used in restoration 51 5204 by 45 5982 arcsec at pa 14 6547 deg HHHH A It will have made the images ngc5921 usecase clean image ngc5921 usecase clean model ngc5921 usecase clean residual ngc5921 usecase clean boxclean mask HHHH dirtyimage imname image fo oooooooooooooooooooooooooooooooooooooooooooosoooooooooo o o Get the dirty image cube statistics print Imstat dirty cube default imstat imagename dirtyimage Do whole image 416 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS box dirtystats imstat Statistics will printed to the terminal and the output parameter will contain a dictionary of the statistics fo oooooocoooooooooooooooooooooooooooooosoooooooooosooo o 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 clean 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 facto
173. window all 0 1 means spw O and 1 Time selection 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 IPython 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 The poln parameter determines what polarization or combination o
174. 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 a Name of input image FITS file imagename a 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 6 10 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 Sesa gt help ia Help on image o
175. 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 CHAPTER 6 IMAGE ANALYSIS 268 rms noise level in the usable planes seems to work put into includepix or excludepix as needed Also use planes to ignore channels with bad data 6 6 2 Examples using immoments For example using the NGC5921 example F 1 default immoments imagename ngc5921 usecase clean image Do first and second moments moments 0 1 Need to mask out noisy pixels currently done using hard global limits excludepix 100 0 009 Include all planes planes Output root name outfile ngc5921 usecase moments immoments It will have made the images ngc5921 usecase moments integrated ngc5921 usecase moments weighted_coord Other examples of NGC2403
176. 04 04 04 04 04 05 05 06 06 06 06 06 07 07 07 08 08 08 08 08 09 09 09 09 10 10 10 10 11 11 16 48 55 223 30 50 abia 11 2b 31 51 04 19 26 39 52 01 14 29 36 51 04 20 27 44 58 33 49 00 14 29 46 57 12 30 44 00 15 29 44 58 14 28 42 58 14 28 42 5 3D 50 10 00 20 49 00 20 49 59 00 10 30 30 10 00 30 20 00 10 39 40 30 50 40 39 40 30 39 49 30 59 20 00 00 20 10 30 39 19 30 50 50 50 40 09 10 50 50 00 50 30 10 o0o00DOO0OO0O0O0vwvOorO0oO0o00o00ov 0 O0OO0OO0OO000rOo0ooOoro0ooOorooOo0oOoOoOor0o0wooroooOo oono PUNB 0 0H PP ds ds ds PPP RP WWBWWWWWWWWNONNNNNNNNNRPRPRP RPP RPP RP RP FOWOMOANODOPWNHRFRFRDOANDOATKPWNHRFPDODAANDAARPWNHRPTOWOAN DOAKRWNHrF O O ONDWON DON MDANMADANAMADAWDKENAWKFPENAADANHKFNADNKFPNDWBHONKFPNDPWHONFPBPWBNHF OO m A O 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 NGC7027 MARS 1411 522 1331 305 NGC7027 NEP
177. 1 Under the Hood Structure of the Measurement Set 2 2 Data Import and Export 2 aaa ee 2 2 1 UVFITS Import and Export 0 0 0 2 02202004 2 2 1 1 Import using importuvfits 04 2 2 1 2 Export using exportuvfits 04 2 2 2 VLA Filling data from archive format importvla 2 2 2 1 Parameter applytsys 0 2 2 2 2 2 2 Parameter bandname 20 0000 eee eee 2 2 2 3 Parameter frequencytol o 222 4 Parameter project p ee hin so ete a a ll lt be 2 2 2 5 Parameters starttime and stoptime ee aa ee eee a ee E E e a 2 2 3 ALMA Filling ALMA Science Data Model ASDM observations 2 3 Summarizing your MS listobs i624 4 45 puerros ee ee a 2 4 Concatenating multiple datasets concat o AAA A A ee Ah a pd A o eA ee de A 2 5 1 1 String Matching 20 02 0000 02 ee ee 2 5 2 The field Parameter eee eee ee ees yng wk OK ok ore Bs eee a OS ee eee amp we A we A 2 5 3 1 Channel selection in the spw parameter 2 5 4 The selectdata Parameters 0000000000 ee eee 2 5 4 1 The antenna Parameter ooa 0 000000 2 5 4 2 The scan Parameter 2 2 2 0 2 ee 2 5 4 3 The timerange Parameter o 2 5 4 4 The uvrange Parameter o o 00004 2 5 4 5
178. 10x thermal rms clnthreshold 0 05 Filenames imnamel imprefix clean1 clnimagel imnamei image clnmodeli imnameit model clnresidi imnameit 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 clean3 clnimage3 imname3 image clnmodel3 imname3 model clnresid3 imname3 residual clnmask3 imname3 clean_interactive mask Selfcal parameters reference antenna 11 11 VLA N1 calrefant 11 429 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS Filenames selfcaltab1 imprefix selfcal1 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 polimage I qpolimage polimaget Q upolimage polimaget
179. 15 VLA N2 refant 15 gaincal Bootstrap flux scale print Fluxscale default fluxscale vis msfile CHAPTER 4 SYNTHESIS CALIBRATION 198 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 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 1445x 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 usecase 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 caltable ftable field 0 1 No GUI for this script showgui False If you want to do this interactively and iterate over antenna set iteration antenna showgui True Set up 2x1 panels upper panel amp vs time subplot 211 yaxis amp No output file yet wait to plot next panel plotcal
180. 19 53 31 7 19 54 48 3 12 2 2202 422 o 1 Fields 9 ID Code Name Right Ascension Declination Epoch 0 A 1924 292 19 24 51 06 29 14 30 12 J2000 1 A 1743 038 17 43 58 86 03 50 04 62 J2000 2 A 2202 422 22 02 43 29 42 16 39 98 J2000 3 A 2253 161 22 53 57 75 16 08 53 56 J2000 4 B 2136 006 21 36 38 59 00 41 54 21 J2000 5 B 0137 331 01 37 41 30 33 09 35 13 J2000 6 A 2355 498 23 55 09 46 49 50 08 34 J2000 7 B 0319 415 03 19 48 16 41 30 42 10 J2000 8 B 0359 509 03 59 29 75 50 57 50 16 J2000 Spectral Windows 2 unique spectral windows and 1 unique polarization setups SpwID Chans Frame Chi MHz ChanWid kHz TotBW kHz Ref MHz Corrs HHH HHH HH HHH HH HHH HH HHH HH HH HHH HH HH HH HHH HH HHH HHH H HH OH OF 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 27 printing first row only Antenna Spectral Window Receptors Polarizations 1 a 2 R L Antennas 27 ID Name Station Diam Long Lat 0 EA24 VLA Wi2 25 0 m 107 37 37 4 33 53 44 2 1 EA16 VLA W6 25 0 m 107 37 15 6 33 53 56 4 2 EA01 VLA Wi0 25 0 m 107 37 28 9 33 53 48 9 3 EA19 VLA W4 25 0 m 107 37 10 8 33 53 59 1 4 VAOS VLA Wi6 25 0 m 107 37 57 4 33 53 33 0 5 EA17 VLA Wi4 25 0 m 107 37 46 9 33 53 38 9 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 472 6 VAOG VLA W8 25 0 m 107 37 21 6 33 53 53 0 T VA22 VLA W2 25 0 m 107 37 07 4 33 54 00 9 8 EAO4 UNKNOWN 25 0 m 107 37 41 3 33 53 42 0 9
181. 2 1261 RR LL HNCO 13 8192 LSRK 42620 4173 6 10423356 50005 8813 42645 4203 RR LL H15NCO APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 369 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 SiO Scans 21 24 Setup 1 HC3N et al Scans 25 28 Setup 2 Si0 et al casapath os environ AIPSPATH ASAP script COMMENTS i i a i nn i Sn a i i import asap as sd import ASAP package into CASA Orion S Si0 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 eee X ASAP Plotter Tk OrionS_psr OmanS_ps OrionS_psr pa T T T T T Za 3 EXT ES f 20 3 gos t 1 E 8 10 4 5 55 a OriapS_ps OrianS_par OrionS_ps E gt AAA 225 YY YY Y E a E 505 10 4 5 s s E z nn Or pr OrionS ps A S x y gt 1000 2000 3000 4000 5000 6000 7000 8000 Za YY YY Channel p 20 a Pika 8 10 3 5 55 E Ll A Channel Channel O O 6a Figure A 2 Multi panel display of the scantable There are two plots per scan ind
182. 2 49 9 04 44 40 0 25 8 MARS o 1 04 56 50 0 04 58 30 1 26 6 1411 522 o 1 05 24 03 3 05 33 39 9 27 7 1331 305 o 1 05 48 00 0 05 49 49 9 28 1 0813 482 o 1 05 58 36 6 06 00 30 0 29 8 MARS o 1 06 13 20 1 06 14 59 9 30 6 1411 522 o 1 06 27 40 0 06 29 20 0 31 7 1331 305 o 1 06 44 13 4 06 46 00 0 32 1 0813 482 o 1 06 55 06 6 06 57 00 0 33 8 MARS o 1 07 10 40 0 07 12 20 0 34 6 1411 522 o 1 07 28 20 0 07 30 10 1 35 7 1331 305 o 1 07 42 49 9 07 44 30 0 36 8 MARS o 1 07 58 43 3 08 00 39 9 37 6 1411 522 o 1 08 13 30 0 08 15 19 9 38 7 1331 305 o 1 08 27 53 4 08 29 30 0 39 8 MARS o 1 08 42 59 9 08 44 50 0 40 6 1411 522 o 1 08 57 09 9 08 58 50 0 41 7 1331 305 o 1 09 13 03 3 09 14 50 1 42 9 NGC7027 o 1 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 09 26 59 9 09 28 40 0 43 6 1411 522 09 40 33 4 09 42 09 9 44 7 1331 305 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 URANUS
183. 2 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 HHEHHHHHHHHHHHHHHHHHHHHHH HS Calibrate data HHHHHHHHHHHHHHHHHHHHHHHH 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 infile which would have been set from our run of APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 346 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 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 tintsys
184. 20 55 2007 NORMAL ms summary Antennas 27 ID 0 3 1 VLA N7 2 VLA W1 3 VLA W2 4 VLA E1 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 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 CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 82 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 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
185. 203 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 before imaging 5 3 Deconvolution using CLEAN clean To create an image and then deconvolve it with the CLEAN algorithm use the clean task This task will work for single field d
186. 26 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 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 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 CHAPTER 4 SYNTHESIS CALIBRATION 177 phase only solution then the two solutions combined to form a cumulative
187. 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 5 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 indexes 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 i
188. 3 2007 INFO Tue Nov 6 18 09 53 2007 INFO Tue Nov 6 18 09 53 2007 INFO Tue Nov 6 18 09 53 2007 INFO Use tm abort return_value to abort the asynchronous task tm retrieve return_value to retrieve the status Tue Nov 6 18 09 53 2007 INFO clean Tue Nov 6 18 09 54 2007 INFO clean Image Opening MeasurementSet home imager b smyers NovO7 ngc5921 usecase ms contsub Tue Nov 6 18 09 54 2007 INFO clean VisSe Adding MODEL_DATA CORRECTED_DATA and IMAGING_WEIGHT columns Tue Nov 6 18 09 54 2007 INFO clean VisSe Initializing MODEL_DATA to unity and CORRECTED_DATA to DATA Tue Nov 6 18 09 55 2007 INFO clean Image Initializing natural weights Q clean image Selecting data clean inage Performing selection on MeasurementSet clean image Selecting on field nanes 0 clean image Selection did not drop any rows 56 2007 INFO clean Image Selecting 46 channels starting at visibility channel 5 stepped by 1 for spw 0 Tue Nov 6 18 09 Tue Nov 6 18 09 clean image Defining image properties Tue Nov 6 18 09 56 2007 INFO clean image Weighting MS IMAGING_WEIGHT column will be changed E 3 Briggs weighting sidelobes will be suppressed over full inage 7 ser message u gt O 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
189. 31 305 0137 331 set the name for the output interpolated caltable atable prefix accum caltable atable linear interpolation interp linear make 10s entries accumtime 10 0 accum Correct the data This will put calibrated data into the CORRECTED_DATA column print ApplyCal default applycal CHAPTER 4 SYNTHESIS CALIBRATION vis msfile Start with the interpolated fluxscale gain table bptable gaintable atable Since we did gaincurve True in gaincal we need it here also gaincurve True opacity 0 0 select the fields field 1331 305 0137 331 JUPITER spw 7 selectdata False 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 for the calibrator Make an output vis file srcsplitms prefix split ms outputvis srcsplitms Select the Jupiter field field JUPITER spw 7 pick off the CORRECTED_DATA column datacolumn corrected Export the Jupiter data as UVFITS Start with the split file 206 CHAPTER 4 SYNTHESIS CALIBRATION print Export UVFITS default exportuvfits srcuvfits prefix split uvfits vis srcsplitms fitsfile sr
190. 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 blce array 0 0 0 0 blcf 15 24 08 404 04 31 59 181 I 1 41281e 09Hz gt 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 medabsdevmed array 0 00127436 median array 1 17422514e 05 min array 0 0104834 minpos array 160 i 0 307 minposf 15 21 27 899 04 32 14 923 I 1 41354e 09Hz npts array 3014656 gt quartile array 0 00254881 rms array 0 00202226 gt sigma array 0 0020222 sum array 48 26399646 gt sumsq array 12 32857318 trc array 255 255 0 451 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 ar
191. 38_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 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 144 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 m
192. 4 05 01 12 12 12 13 13 13 13 14 14 14 14 15 15 15 15 15 16 16 16 16 17 17 17 18 18 18 19 19 19 19 20 20 20 20 21 21 21 21 21 22 22 22 Ascension 30 05 36 04 54 89 41 13 42 37 06 21 36 09 03 37 48 02 17 35 46 01 12 25 36 00 10 26 245 255 19 30 44 56 30 43 57 20 32 46 00 21 34 40 08 19 235 242 202 15 22 48 59 14 30 54 14 17 11 10 40 10 10 10 40 10 39 09 40 10 00 40 20 00 20 49 49 30 40 40 20 39 09 00 30 59 20 29 40 59 50 40 40 20 29 30 20 10 00 19 19 0OOrRrO0orOo0ororowuororovoOoOowo owooooOooooOorrorr rowoooroooOo 52 7 53 11 54 10 55 6 56 9 57 11 58 10 59 0 60 12 61 11 62 10 63 0 64 12 65 9 66 11 67 10 68 0 69 12 70 11 71 9 72 2 73 3 74 4 75 0 76 12 77 9 78 2 79 5 80 3 81 4 82 0 83 12 84 1 85 2 86 5 87 3 88 4 89 0 90 12 91 2 92 4 93 0 Declination 33 09 35 13 48 13 02 26 49 51 07 23 29 40 15 14 22 30 35 91 16 38 22 05 1331 305 URANUS NEPTUNE 1411 522 NGC7027 URANUS NEPTUNE 0137 331 JUPITER URANUS NEPTUNE 0137 331 JUPITER NGC7027 URANUS NEPTUNE 0137 331 JUPITER URANUS NGC7027 0542 498 0437 296 VENUS 0137 331 JUPITER NGC7027 0542 498 0521 166 0437 296 VENUS 0137 331 J
193. 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 335 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 timeaverage average times for multiple scan cycles
194. 45 099 field 1 out of the gain table for transfer use all of the bandpass table gainfield 1 x interpolation using linear for gain nearest for bandpass interp linear nearest CHAPTER 4 SYNTHESIS CALIBRATION 181 only one spw do not need mapping spwmap all channels no other selection spw 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 O 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 i
195. 4x 30 0s 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 2 3 22 OrionS_psr 0 05 0 1 2 3 23 OrionS_ps 0 05 Nro 3 24 OrionS_psr 0 05 12 13 14 15 25 OrionS_ps 0 05 12 13 14 15 26 OrionS_psr 0 05 12 13 14 15 27 OrionS_ps 0 05 12 13 14 15 15 35 15 35 15 35 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 08 2 LSRK 4 3962126e 10 LSRK 4 264542e 10 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 30 0s 4096 4096 4096 4096 30 0s 4096 4096 4096 4096 30 0s 4096 4096 4096 4096 6104 6104 6104 6104 6104 6104 6104 6104 6104 6104 6104 6104 6104 6104
196. 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 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 gt 1 4GHz Frequency of first image channel e q 1 4GHz width 10kHz Image channel width in frequency units e g 1 0kHz The frequency of the first output channel is given by start and spacing by step The sign of width determines whether the output channels ascend or descend in frequency Output channels have a CHAPTER 5 SYNTHESIS IMAGING 212 width also given by step Data from the input MS with centers that lie within one half an input channel overlap of the frequency range of step 2 centered on the output channels are gridded together 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 Type of selection mfs channel velocity
197. 5 30 0 10 47 00 0 7 1 1445 09900002_0 0 Fields 3 ID Code Name Right Ascension Declination Epoch insert Message l gt Jl 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 54 Y Log Messages imager b home imager b smyers Nov07 casapy log F x File Edit View o D S Bo de SB LD search message ploned Q Fiter Time gt a Time Priority Origin Message 2 Tue Nov 6 18 23 15 2007 DEBUG1 plotxy TPPL Entered Function plotXY panel layer colour Tue Nov 6 18 23 15 2007 DEBUG1 plotxy TPP1 Entered Function plotXY panel layer colour Tue Nov 6 18 23 15 2007 DEBUG1 plotxy TPPL Entered Function plotXY panel layer colour
198. 5921 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 7 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 8 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 ms is on disk with flagautocorr already run CHAPTER 3 DATA EXAMINATION AND EDITING 110 BETA ALERT Exact syntax may be slightly different in your version as the Beta Release progress default plotxy vis jupiter6cm usecase ms The field
199. 9 Flow chart of the data processing operations that a general user will carry out in an end to end CASA reduction session 1 5 1 Loading Data into CASA The key data and image import tasks are 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 2 2 3 e importfits import a FITS image into a CASA image format table 6 9 CHAPTER 1 INTRODUCTION 61 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 name 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 4 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
200. APTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 73 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 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 DA
201. APTER 6 IMAGE ANALYSIS 264 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 10 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 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 5 9 1 default clean 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 CHAPTER 6 IMAGE ANALYSIS 265 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
202. ASA 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 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 xx 2 yx x 2 CASA 14 x Out 14 1 CASA 15 y Out 15 3 APPENDIX D APPENDIX PYTHON AND CASA 392 CASA 16 z Out 16 10 CASA 17 Out 14 Note Out 17 1 CASA 18 _15 Note Out 18 3 CASA 19 ___ Note Dut 19 10
203. ASA I 5 351 P 0 090 F 0 0168 X 124 92 deg spw 1 CASA I 5 333 P 0 094 F 0 0177 X 128 78 deg f Done logfile close print Results are in outfile Now save stat dictionaries using Pickle pickfile prefix pickle f open pickfile w pickle Pickler f dump clnmode1 dump polmodel close hd 9 O print wee print Dictionaries clnmodel polmodel saved in pickfile print Use Pickle to retrieve print we e g f open pickfile u Unpickler f clnmodel u load polmodel u load f close print nn print Completed Processing 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 a task dictionary G 2 MIRIAD CASA dictionary Table G 1 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 re
204. ASA 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 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 prompt where lt taskname gt is the name of a given task As described above in 1 2 8 2 help l
205. 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 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 ae Name of input visibility file MS CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 81 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 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
206. ATA PROCESSING 313 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 selection 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 gt max 1 2750182151794434 gt mean 0 35996028780937195 gt median 0 23074722290039062 min 0 20840644836425781 rms 0 53090775012969971 gt stddev 0 39102539420127869 gum 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_st
207. BPOLY bandtype B set solution interval arbitrarily long get single bpass solint 86400 0 reference antenna Name 15 15 VLA N2 Id 14 refant 15 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS saveinputs bandpass prefix bandpass saved bandpass Use plotcal to examine the bandpass solutions print Plotcal bandpass default plotcal caltable btable field 0 No GUI for this script showgui False If you want to do this interactively and iterate over antenna set iteration antenna showgui True 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 plotcal O Set up 2x1 panels lower panel phase vs channel subplot 212 yaxis phase Now send final plot to file in PNG format via png suffix figfile caltable plotcal png saveinputs plotcal prefixt plotcal b phase saved plotcal O Note the rolloff in the start and end channels Looks like channels 6 56 out of 0 62 are the best f Gain calibration print Gaincal default gaincal Armed with the bandpass we now solve for the 408 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS time
208. CALIBRATION 145 4 4 1 1 Parameters for Specification vis and caltable The input measurement set and output table are controlled by the following parameters vis a Name of input visibility file caltable sed 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 path 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 ds 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 ae time range gt all uvrange a uv range gt all antenna me antenna baselines
209. CASA Synthesis amp Single Dish Reduction Cookbook Beta Release Edition Beta Patch 2 NGC4826 CO J 1 0 Moment 1 36 550 g 24 500 12 450 gt T 21 41 00 5 D BS A 48 400 y 2 36 3 350 x ad 300 yonk 0 i t i t 250 1275648 46 44 427 40 39 J2000 Right Ascension v0 4 IXI Viewer Display Panel POS XI Image Profile FLS3a_HI image Daia Display Panel Tools As a T s 9 aad da A 0 9 a sama a Pe e phe x FLS3a HI image Coordinate world ff 17 17 41 633 60434 58 594 ih T 17 41 624 60 24 54 595 Version August 21 2008 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 August 21 2008 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 Relea
210. CESSING 333 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 in 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 WARNING sdfit will currently return the fit for the first row in the scantable Does not handle multiple polarizations See the sdaverage description for information on fluxunit conversion and the telescopeparm parameter 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 li
211. Channel S5election none Scan Source Time Integration Beam Position J2000 IF Frame RefVal RefPix SSS SSeS Se SSeS Se eee Se 2222522 0 0 o 0 a o eS 20 OrionS_psr 01 45 58 4x 30 0s 0 05 15 13 5 05 24 08 2 0 LSRK 4 5489354e 10 4096 1 LSRK 4 5300785e 10 4096 2 LSRK 4 4074929e 10 4096 3 LSRK 4 4166215e 10 4096 21 OrionS_ps 01 48 38 4x 30 0s 0 05 35 13 5 05 24 08 2 0 LSRK 4 5489354e 10 4096 1 LSRK 4 5300785e 10 4096 2 LSRK 4 4074929e 10 4096 3 LSRK 4 4166215e 10 4096 22 OrionS_psr 01 51 21 4x 30 08 0 05 15 13 5 05 24 08 2 0 LSRK 4 5489354e 10 4096 1 LSRK 4 5300785e 10 4096 2 LSRK 4 4074929e 10 4096 3 LSRK 4 4166215e 10 4096 23 OrionS_ps 01 54 01 4x 30 0s APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 345 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 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 0s 0 05 15 13 5 05 24 08 2 1
212. D 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 5 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 5 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 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 88 FTELDID 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
213. D 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 other_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 command 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 vla_calplot png vla_msplot_cals jpg os os os os os os os os os os os os os os 389 tmpnam ttyname umask uname unlink Unsetenv urandom utime Wait Wait3 Wait4 waitpid walk write access to AP
214. DATA column First using gaincalfield print ApplyCal default applycal print This will apply the calibration to the DATA print Fills CORRECTED_DATA vis msfile Start with the fluxscaled G table the D table and the X table if dopolx gaintable ftable ptable xtable else gaintable ftable ptable use settings from gaincal gaincurve usegaincurve opacity gainopacity select all the data spw usespw selectdata False IMPORTANT set parang True for polarization APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS parang True use the list of gain calibrators apply to themselves field fieldgain gainselect field print Applying calibration to gain calibrators field saveinputs applycal prefix applycal saved applycal if len targets gt 0 Now with targets if any transfer from gaincalfield Assemble field string from target list field fieldtargets print Applying calibration to targets field saveinputs applycal prefix applycal targets saved applycal O f Now write out the corrected data print Split default split vis msfile Now we write out the corrected data to a new MS Make an output vis file srcsplitms prefix split ms outputvis srcsplitms Select all data field
215. DIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 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 18 4 33 53 54 8 Tables MAIN 22653 rows ANTENNA 28 rows DATA_DESCRIPTION 1 row DOPPLER lt absent gt FEED 28 rows FIELD 3 rows FLAG_CMD lt empty gt FREQ_OFFSET lt absent gt HISTORY 353 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 F 2 Jupiter VLA continuum polarization 426 Note This script includes interactive flagging and cleaning and self calibration loops Polarization calibration and imaging is still missing The latest version of this script can be found at http casa nrao edu Doc Scripts jupiter6cm_usecase py HHEFHHHHHHHEEHHHEEHHEHHHAAHEHEEE HEHEHE HHHRHEHHEE HHH HRAE HERRERA ERE This flux were This HHH HH HH HH H OH OF Use Case Script for Jupiter 6cm VLA Trimmed down from Use Case jupiter6cm_usecase py Updated STM 2008 05 15 Beta Patch 2 0 Updated STM 2008 06 11 Beta Patch 2 0 is a VLA 6cm dataset that was observed in 1999 to set the scale for calibration of the VLA Included in the program observations of the planets including Jupiter is D configuration data with resolution of around 14 HH HH H HH HH HH OH OF APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS
216. Difference fractional 0 00019288621809 Moment O image max should be 1 40223777294 Found Moment O Max 1 40230333805 Difference fractional 4 67574844349e 05 Moment 1 image mean should be 1479 77119646 Found Moment 1 Mean 1479 66974528 Difference fractional 6 85586935973e 05 See eee rs Done logfile close print Results are in outfile F 1 1 NGC 5921 data summary Summary created with listobs ngc5921 usecase ms verbose True This is written to the logger Obs and the casapy log file erver TEST Project Observation VLA Data records 22653 Total integration time 5280 seconds Obs erved from 09 19 00 to 10 47 00 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS FieldName 1331 30500002_0 1445 09900002_0 N5921_2 1445 09900002_0 1445 09900002_0 N5921_2 1445 09900002_0 Epoch 30 30 32 96 J2000 09 58 36 07 J2000 ObservationID 0 ArrayID 0 Date Timerange Scan FldId 13 Apr 1995 09 19 00 0 09 24 30 0 1 0 09 27 30 0 09 29 30 0 2 1 09 33 00 0 09 48 00 0 3 2 09 50 30 0 09 51 00 0 4 1 10 22 00 0 10 23 00 0 5 1 10 26 00 0 10 43 00 0 6 2 10 45 30 0 10 47 00 0 7 1 Fields 3 ID Name Right Ascension Declination 0 1331 30500002_013 31 08 29 1 1445 09900002_014 45 16 47 2 N5921_2 15 22 00 00 05 04 00 00 J2000 Spectral Windows SpwID Chans Frame Ch1 MHz 0 63 LSRK 1 unique spectral windows and 1 unique polarization setups
217. E3 DATA_DESCRIPTION Diam 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 OO OO o E OO OO OO OO OM OO OO ON OO ORO Ooo BBBBBBBBBEBBBBBBBEBBBBBBBB SB BB 65 29 37 59 14 83 04 52 30 12 42 18 16 04 50000 50000 Feeds 28 printing first row only Spectral Window 12 30 21 35 45 Receptors 2 Long 107 107 107 107 107 107 107 107 107 107 107 107 107 107 107 107 107 107 107 107 107 107 107 107 107 107 107 2021424 rows 28 rows 2 rows 37 25 37 07 37 06 37 06 37 06 37 05 37 04 37 07 36 48 37 08 37 06 36 55 37 18 37 00 37 07 37 10 37 13 37 06 36 52 36 45 37 21 37 15 37 05 37 07 36 58 37 06 37 02 0 0M S p0000r q gt soo0Nn00 0000om P JN JJOO 09 32 49 14 54 10 54 05 44 14 96 45 19 21 59 71 50000 50000 J2000 J2000 J2000 J2000 J2000 J2000 J2000 Spectral Windows 2 unique spectral windows and 1 unique SpwID Chans Frame Chi MHz Resoln kHz TotBW kHz polarization setups Ref MHz Corrs 4885 1 4835 1 Polarizations Lat 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
218. ER 1 INTRODUCTION 40 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 gt 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 median array 1 10467618e 05 min array 0 0105249 minpos array 160 1 0 30 minposf 15 21 27 899 04 32 14 923 I 1 41354e 09Hz npts array 3014656 gt quartile array 0 00254587 yms array 0 00201818 gt sigma array 0 00201811 gt sum array 49 1322855 gt sumsq array 12 27880404 trc array 255 255 0 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 ima
219. Examples using imstat 2 2 2 ee ee 6 8 Regridding an Image regridimage 6 9 Image Import Export to FITS 6242s bake eee eA GEER e ARES 6 9 1 FITS Image Export exportfits 6 9 2 FITS Image Import importfits cs 40 okt ew ee ew eee dees 6 10 Using the CASA Toolkit for Image Analysis 20 6 11 Examples of CASA Image Analysis 0 0 0 0 020000 eee ee ee 6 11 1 Spectral Line Image Analysis with NGC5921 2 2 pra ea a p Aa ee eee 7 1 1 Starting the casaviewer outside of casapy T2 Whe viewer GUI ais acsi sa dE ee a Bas es 7 2 1 The Viewer Display Panel 0 0 0 020000022 ee 7 2 2 Region Selection and Positioning 2 2 022004 1 2 3 The Load Data Panell ee ee RR eee Ae ee 7 2 3 1 Registered vs Open Datasets o o 0200 5 Sg Te ee ae Bo oy BE dR ek aes Seah ee ee ee eo ee 7 3 1 Viewing a raster map ee 7 3 1 1 Raster Image Basic Settings 204 7 3 1 2 Raster Image Other Settings 293 7 3 2 Viewing a contour map e 294 7 3 3 Overlay contours on a raster map 2 0 0 0 0 eee ee eee 294 7 3 4 Spectral Profile Plotting 02 2 0 20002220004 295 Oe eee PAG Ree a bb be Bees eG 24 S 296 ten Sosa 298 7 3 6 1 Setting up multi panel displays o o 298 7 3 6 2 Backgr
220. For spectral cube images you can use the tapedeck to move through the channels There is a panel Channels with a radio button A11 which toggles the ability of the mask that will be drawn to apply of the current or all channels See Figure 5 5 for an example Note that the Channels A11 toggle is currently set so masks apply to all channels 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 order to help you set up the clean mask For CHAPTER 5 SYNTHESIS IMAGING 231 v Viewer Display Panel 5 x Viewer Display Panel 0 Data DisplayPanel Tools View Data DisplayPanel Tools View BAR AIRASA X BORrgaanga aig 2 al E 81 ag E 0 DB Y bap bce oo eo od co Clean Regions Chani Masking Cea Cycle Control Clean Regions Channels Masking Cl Cycle Control niter cycle Ee niterieycle 500 7 Al E all neycles 7 threshold a mJy threshold 0 05 mJy Figure 5 4 We continue in our interactive cleaning of Jupiter from where Figure 5 3 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
221. G search Message A QY Filter Message J Time Priority Origin Message Sun Oct 22 02 NORMAL ms summary 2 63 LSRK 23696 1273 118 156877 6151 96961 23699 1586 RR 3 63 LSRK 23724 2709 118 156877 6151 96961 23727 3023 LL Antennas 27 ID 1 5 2 VLA W1 10 VLA W3 8 WLA W8 3 VLA W2 12 VLA WS 18 VLA W4 ID 7 11 28 VLA W7 20 VLA W9 21 VLA W6 17 VLA E8 7 VLA E6 4 VWLA El ID 13 17 16 VLA E7 22 VLA E4 19 VWLA ES 6 VLA E9 24 VLA E2 5 VLA E3 ID 19 23 23 VLA N2 11 VLA N4 27 VLA N8 13 VLA N3 25 VLA N6 14 VLA N1 ID 25 26 1 VLA N7 26 VLA N9 9 VLA NS Tables rows 1 table absent MAIN 8 38404 ANTENNA 27 DATA_DESCRIPTION 4 DOPPLER 4 FEED 27 FIELD FLAG_CMD O FREQLOFFSET 1 HISTORY 45 OBSERVATION 3 POINTING O POLARIZATION 2 PROCESSOR O SOURCE 6 SPECTRAL_WINDOW 4 STATE O SYSCAL 1 WEATHER 1 Sun Oct 22 02 NORMAL ms summary Sun Oct 22 02 NORMAL ms summary Sun Oct 22 02 NORMAL ms summary sat Oct 21 2 NOTE jmemulli Note Antenna 12 looks bad based on amp plot 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 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
222. H HHH HH HHHH HHH HH HHH HH HHH HHH HH HH OH OF 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 E1 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 ES 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 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 435 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 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 DATA_DESCRIPTION 2 rows DOPPLER l
223. HH HHH HH HHH HH HH H HH OF Self cal using clean model HH HH OH do this manually print SelfCal 1 default gaincal vis srcsplitms New gain table selfcaltab1 srcsplitms selfcali caltable selfcaltabl Don t need a priori cals selectdata False gaincurve False opacity 0 0 This choice seemed to work refant 11 Lets do phase only first time around gaintype G calmode p Jy beam Mean 0 0003205 Median 0 0001885 Mean 0 02023 Median 0 0001329 Variance 1 532e 05 Min 0 01125 Variance 0 01015 Min 0 01396 Estimated dynamic range 1 060 0 003927 270 poor 244 Sum 1 510 Max 0 01503 Sum 73 63 Max 1 060 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 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 CHAPTER 5 SYNTHESIS IMAGING Do scan based solutions with SNR gt 3 solint inf combine minsnr 3 0 Do not need to normalize let gains float solnorm False gaincal Correct the data no need for interpolation this stage print ApplyCal default applycal vis srcsplitms gaintable selfcaltabl gaincurve False opacity 0 0 field spw selectdata False calwt
224. HHHHHHHHHHHHHHRHHHHHHHHHHHRHHHHHHHHH Note that the antennas are out of order as loaded by importvla Data Flagging if needed APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 473 if myquackinterval gt 0 0 First quack the data print Flagdata default flagdata print Quacking scan beginnings using interval str myquackinterval vis msfile correlation field antenna spw usespw mode quack quackinterval myquackinterval saveinputs flagdata prefix flagdata quack saved flagdata Use Flagmanager to save a copy of the flags so far default flagmanager print Now will use flagmanager to save the flags vis msfile mode save versionname quack comment Quack str myquackinterval merge replace saveinputs flagmanager prefixt flagmanager quack saved flagmanager if flagants and not flagants isspace print Flagdata default flagdata print Flag all data to AN flagants vis msfile correlation field spw usespw mode manualflag APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS antenna flagants saveinputs flagdata prefix flagdata ants saved flagdata Use Flagmanager to save a copy of the flags so far default flagmanager print Now will use flagmanager
225. HR HRE HRA ERE Display and Flagging Use Case Jupiter 6cm VLA Last Updated STM 2008 03 25 Beta Patch 1 0 HHEFHHHHHHHHEHHAEHHHEEHHHAHEHEEH HAAR HEEH RHEE RO FERRERO PARRA RO RERRO RARA RO RRRR A AAA scriptmode True prefix jupiter6cm usecase msfile prefix ms fo oooooocoooooooooooooooooooosooooooooooooooosooooso List a summary of the MS print Listobs default listobs vis msfile CHAPTER 3 DATA EXAMINATION AND EDITING 118 Y Table Browser File Edit View Tools Export Help wx 22 Of aris ngc5921 ms SOURCE A DIRECTION ROPER_MOTIOI IBRATION_GRC CODE INTERVAL NAME NUM_LINES SOURCE_ID CTRAL_W lo b2 74393 0 5 o 0 1 1 7976931348 1331 305000 1 0 0 1 E2 42085 0 1 0 0 1 1 7976931348 1445 099000 1 1 0 2 2 2602 0 08 0 0 1 1 797693 1348 N5921_2 1 2 0 l field keywords table keywords Restore Columns Resize Headers PAGE NAVIGATION First Il lt lt ETES Loading 1000 rows Figure 3 9 browsetable Viewing the SOURCE table of the MS 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
226. 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 CHAPTER 6 IMAGE ANALYSIS 272 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 xstat return variable 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 xstat imstat myImage box 2 3 14 15 30 31 42 43 chan 475 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
227. IFs SPW 0 1 with one channel each selection is via the field and spw strings field 1331 305 0137 331 spw 7 a priori calibration application atmospheric optical depth turn off gaincurve True opacity 0 0 scan based G solutions for both amplitude and phase gaintype G solint inf combine calmode ap reference antenna 11 11 VLA N1 refant 11 minimum SNR 3 minsnr 3 gaincal Bootstrap flux scale print Fluxscale default fluxscale vis msfile set the name for the output rescaled caltable ftable prefix fluxscale fluxtable ftable 204 CHAPTER 4 SYNTHESIS CALIBRATION 205 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 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 p Interpolate the gains onto Jupiter and others print Accum default accum vis msfile tablein incrtable ftable calfield 13
228. IX A APPENDIX SINGLE DISH DATA PROCESSING 318 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 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 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 default none tau atmospheric optical depth default 0 0 no correction outfile Name of output file default gt 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
229. LA 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 18 4 33 53 54 8 Tables MAIN 22653 rows ANTENNA 28 rows DATA_DESCRIPTION 1 row DOPPLER lt absent gt FEED 28 rows FIELD 3 rows FLAG_CMD lt empty gt FREQ_OFFSET lt absent gt HISTORY 273 rows CHAPTER 4 SYNTHESIS CALIBRATION 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 f
230. LA Project POLCA run This is a polarization calibration and monitoring program run by VLA staff The latest version of this script can be found at http casa nrao edu Doc Scripts run_polcal_20080224_cband_usecase py HHEFHHHHHHHEEHHAEHEHEEHHHEAHHAEHHHHAHEAEHEHEEHRHHEE HEH RO RAR RO RARRRO RO RORR RARA HARE Use Case Script for POLCAL 6cm Data Using POLCA data 20080224 BnC config C band Last Updated STM 2008 05 23 Beta Patch 2 STM 2008 06 11 Beta Patch 2 0 Updated Uses new clean task HHH HH H OF HHEFHHHHHHHHEHHAEHHEEHHHE HEHEHE HHHAHEREHEHHHHRHHAE HEHEHE PERRERA RRA RO RRR RARA A ARRE import time import os APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 465 import pickle This script may have 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 to control subsequent actions pathname os environ get AIPSPATH split 0 This name will prefix all output files prefix polcal_20080224 cband all Clean up old files os system rm rf prefixt Import data from export or use already existing MS Or UVFITS importmode vla vila fits ms This is the name of the datafile used in import or the name of a previously made ms that will be copied NOTE if an ms name must be different than prefix ms datafile
231. 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 For example default concat vis n4826_16apr split ms n4826_22apr split ms concatvis n4826_tboth ms freqtol 50MHz concat CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 85 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 This has changed in Patch 2 Previously only appended a single MS given in concatvis to that in vis somewhat the reverse of what it does now 2 5 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 to this new unified system In vari parameter if set to True will open up a number of other oys tasks you may find relics of the sub parameters for selection The selection operation is old way such as fieldid or spwi
232. NR 3 minsnr 3 saveinputs gaincal prefix gaincal saved gaincal use plotcal to view or listcal to list List gain calibration print Listcal listfile caltable list print Listing calibration to file listfile listcal O 476 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 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 ftable prefix fluxscale fluxtable ftable print Output scaled gain cal table is ftable point to our first gain cal table caltable gtable use the source we did setjy on as our flux standard reference reference fluxcalfield transfer the flux to all our other sources to bring amplitues in line with the absolute scale transfer fieldgain saveinputs fluxscale prefix fluxscale saved fluxscale You should see in the logger something like Found reference field s 0137 331 Storing result in polcal_20080224 cband vla_3c84 fluxscale Flux density for 0359 509 in SpW 1 is 5 10322 0 00990264 SNR Flux density for 1924 292 in SpW 0 is 8 25145 0 00988121 SNR Flux density for 1924 292 in SpW 1 is 8 22457 0 0140951 SNR Flux density for 1743 038 in SpW 0 is 5 31336 0 00603626 SNR Flux density for 1743 038 in
233. ODEL 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 22 Name of input visibility file MS reverse False reverse the operation add rather than subtract async 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 continuum 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 d
234. 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 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 19688 1413 44902 RR LL Thu Jul 5 17 23 55 2007 NORMAL ms summary Feeds 28 printing first row only CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION Antenna Spectral Window Receptors Polarizations 1 z1 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
235. 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 Fourier transform the component list into MODEL_DATA column of the MS ft 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
236. PENDIX D APPENDIX PYTHON AND CASA 390 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 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 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 1 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 391 D 7 Logging There are two components to logging within C
237. PTICAL 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 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 325 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 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 tim
238. Proj Shape Tile Coord value at pixel Coord incr Units 0 0 Direction Right Ascension SIN 256 64 15 22 00 000 128 00 1 500000e 01 arcsec 1 0 Direction Declination SIN 256 64 05 04 00 000 128 00 1 500000e 01 arcsec 2 1 Stokes Stokes 1 1 I 3 2 Spectral Frequency 46 8 1 41281e 09 0 00 2 441406e 04 Hz Velocity 1603 56 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 terminal CASA lt 2 gt imhead ngc5921 usecase clean image mode list Available header items to modify General object N5921_2 telescope VLA observer TEST epoch 1995 04 13 00 00 00 Retrieving restfrequncy 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 crpix4 0 0 crvali 4 02298392585 rad crval2 0 0884300154344 rad crval3 1 0 crval4 1412808153 26 Hz cdelti 7 27220521664e 05 rad CHAPTER 6 IMAGE ANALYSIS 258 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 get Option
239. R 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 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 149 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
240. R 5 SYNTHESIS IMAGING print Final Export CLEAN FITS default exportfits clnfits prefix clean fits imagename clnimage fitsimage clnfits Run asynchronously so as not to interfere with other tasks BETA also avoids crash on next importfits async True exportfits 5 9 2 Continuum Imaging of Jupiter 241 The following is an example use of interactive clean and self calibration on the Jupiter 6cm VLA dataset This assumes you have already flagged calibrated and split out that data and are ready to image as well as having the split calibrated ms file jupiter6cm usecase split ms on disk in your working directory See In this script notice the different self calibrations that were done each cycle and how they gradually improved the image The full Jupiter example script can be found in Appendix F 2 HHEFHHHHHEHHAEHHHEHHEEHHHAEEHEEE HEAR HEEHHRHEHHEEHEHRHEEHAE HERE RARA HARE Imaging Self Calibration Script for Jupiter 6cm VLA Last Updated STM 2008 03 25 Beta Patch 1 0 HH H H HHEFHHHHHEHHHEHHAEEHEEHHHHAHEHEEE HEHEHE EH HER RRA HHH RERERO RO RARR RARA RA AAA Some variables defined prefix jupiter6cm usecase srcsplitms prefix split ms Now clean an image of Jupiter print Clean 1 default clean CHAPTER 5 SYNTHESIS IMAGING 242 Pick up our split source data vis srcsplitms Make an image root file name imname
241. SA 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_fluxunit 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 361 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
242. SpW 1 is 5 3184 0 00480634 SNR Flux density for 2202 422 in SpW 0 is 2 46545 0 00335055 SNR Flux density for 2202 422 in SpW 1 is 2 46072 0 00353799 SNR Flux density for 2253 161 in SpW 0 is 8 74607 0 0142334 SNR Flux density for 2253 161 in SpW 1 is 8 77219 0 0102289 SNR Flux density for 2136 006 in SpW 0 is 9 97863 0 013815 SNR Flux density for 2136 006 in SpW 1 is 9 99001 0 0170089 SNR Flux density for 2355 498 in SpW 0 is 1 29395 0 00181169 SNR Flux density for 2355 498 in SpW 1 is 1 29893 0 00217214 SNR Flux density for 0319 415 in SpW 0 is 13 5742 0 0221722 SNR Flux density for 0319 415 in SpW 1 is 13 5481 0 Flux density for 0359 509 in SpW 0 is 5 13982 0 00906505 SNR 477 Found transfer field s 1924 292 1743 038 2202 422 2253 161 2136 006 2355 498 0319 415 0359 509 835 065 nAnt 13 583 505 nAnt 13 880 239 nAnt 13 1106 54 nAnt 13 735 833 nAnt 13 695 512 nAnt 13 614 474 nAnt 13 857 587 nAnt 13 722 303 nAnt 13 587 339 nAnt 13 714 221 nAnt 13 597 995 nAnt 13 612 218 nAnt 13 0230828 SNR 586 932 nAnt 13 566 993 nAnt 13 515 339 nAnt 13 Writing solutions to table polcal_20080224 cband vla_3c84 fluxscale APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS List fluxscale table print Listcal ftable caltable list caltable lis
243. Stats print print gt gt logfile print gt gt logfile Final Stats print gt gt logfile for src in srclist print Source src print gt gt logfile Source src for spwid in usespwlist field src spw spwid Get fluxes from images ipol clnmodel src spwid flux I qpol clnmodel src spwid flux Q upol clnmodel src spwid flux U vpol clnmodel src spwid flux V Now get polarization results ppol sqrt qpol 2 upol 2 fpol ppol ipol rlpd atan2 upol qpol rlpd_deg rlpd 180 0 pl pi print spw s CASA I 7 3f Q 47 3f U 47 3f V 7 3f gt YA spwid ipol qpol upol vpol print spw 4s CASA I 47 31 P 17 31 F 7 4f X 17 2f deg spwid ipol ppol fpol rlpd_deg print gt gt logfile spw s CASA I 7 3f P 47 3f F 17 4f X 7 2f deg NM spwid ipol ppol fpol rlpd_deg if aipsmodel has_key src iflx aipsmodel src spwid 0 1000 0 fflx aipsmodel src spwid 1 rlaips_deg aipsmodel src spwid 2 rlaips rlaips_deg pl pi 180 0 iflx fflx pflx cos rlaips pflx qflx APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS E E E EEE uflx pflx sin rlaips vflx 0 0 print print gt gt logfile Done with spw print wee print gt gt logfile Should see something like R L phase residual from image of 0137 331 R L Phase Cor
244. TA_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 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 74 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 Np 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 No
245. TUNE 1411 522 o Lo Co Co Os Lo Co o Lo o Lo Lo 0 Co Lo Lo Co Co o Lo Lo Lo o Co Lo Co Os Lo Co o Lo o Lo o Lo Co Lo Co Lo Lo Lo Lo o Lo o Lo Co Co 0 0 Lo 1 1 1 1 1 1 1 11 1 11 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 11 1 11 1 1 1 1 1 1 1 1 119 CHAPTER 3 DATA EXAMINATION AND EDITING 12 12 12 13 13 13 15 15 15 15 16 16 16 17 17 17 18 18 18 19 19 20 20 20 21 21 21 21 22 22 Fields 13 ID Name 0137 331 0813 482 0542 498 0437 296 VENUS 0521 166 HHH HHH HH HHH HHHHH HH HH HHH HH HHHH HHH HH HHH HH HHH HHH HH HH HOF oP WNF OO 16 19 20 21 22 201 235 46 00 13 233 244 14 14 14 14 14 15 00 10 19 30 44 59 19 32 39 08 18 1338 40 00 13 20 147 257 12 28 253 236 233 230 29 23 43 30 46 40 24 34 59 09 24 40 153 18 229 242 254 129 41 755 18 06 30 13 03 30 10 50 53 10 53 53 06 50 36 23 223 49 13 10 50 03 06 10 53 59 16 53 43 26 30 13 33 33 WWWONPRPDOWON WRF OWDOWBWNOWHHKFPRPPDWOWDOWAOWBRODOAONDWDWBWO OWN Right 37 08 05 04 0
246. 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 saicing 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 If your uv coverage results in a poor PSF then you should reconcile often a cyclefactor of 4 or 5 For good PSFs use cyclefactor in the range 1 5 to 2 0 This parameter in effect controls the threshold used by CLEAN to test whether a major cycle break and reconciliation occurs cycle threshold cyclefactor max sidelobe max residual 5 3 5 Parameter cyclespee
247. 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 controls 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 interpolati
248. U poliimage polimage poli polaimage polimaget pola Get to path to the CASA home and stip off the name pathname os environ get AIPSPATH 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 430 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS Can also be found online at http casa nrao edu Data VLA Planets6cm planets_6cm fits fitsdata planets_6cm fits Clean up old files os system rm rf prefixt 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
249. UPITER 0813 482 0542 498 0521 166 0437 296 VENUS 0137 331 JUPITER 0542 498 VENUS 0137 331 Epoch J2000 J2000 J2000 J2000 J2000 J2000 o Lo Co Co Os Lo Co o Lo o Lo Lo 0 Co Lo Lo Co Co o Lo Lo Lo o Co Lo Co Os Lo Co o Lo o Lo Lo Co Co Lo Lo Lo Lo o Lo 1 1 1 1 1 1 1 11 1 11 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 11 1 120 CHAPTER 3 DATA EXAMINATION AND EDITING 6 1411 5 T 1331 3 8 MARS 9 NGC702 10 NEPTUN 11 URANUS 12 JUPITE 0 1 Antenna 1 Antennas 27 ID Name 0 1 1 2 2 3 3 4 4 5 5 6 6 7 T 8 8 9 9 10 10 11 11 12 12 13 13 14 14 15 15 16 16 17 17 18 18 19 19 20 21 22 22 23 23 24 24 25 25 26 26 27 27 28 Tables MAIN ANTENNA 22 05 T E R 14 13 14 21 20 21 00 11 31 21 07 26 15 55 20 08 41 01 01 42 34 1 TOPO 4885 1 1 TOPO 4835 1 1 Station VLA VLA VLA VLA VLA VLA VLA VLA VLA VLA VLA VLA VLA VLA VLA VLA VLA VLA VLA VLA VLA VLA VLA VLA VLA VLA VLA W9 N9 N3 N5 N2 E1 E2 N8 E8 W3 Ni E6 W7 E4 N7 W4 W5 N6 E7 E9 W8 W6 wi W2 ES N4
250. Unknown telecope 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 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 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
251. Working Directory home imager b smyers Nov07 Label Position Auto Ex ax 12 EN PS Output media LETTER MIP ane Character font normal k Av PS Orientation portrait vii 2 2 ES 300 Line width y Fv PS Resolution dpi Biv i 1 World or pixel coordinates world F lt PS Magnification ym aR El 5 Ahsolute or relative ahsolute Li Y 2 jupiter cm u 1 147e 03 Dismiss I 1 244302 save Print Dismiss all 310 Figure 7 17 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 300 dpi for a postscript plot A name has been given in preparation for saving as a PNG raster To make the plot use the Save button on the Viewer Print Manager panel positioned by the user below the display area and select a format with the drop down or use the Print button to send directly to a printer Appendix A Single Dish Data Processing BETA ALERT The single dish analysis package within CASA is still largely toolkit based with a few experimental basic tasks thrown in 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 e
252. a PNG raster To make the plot use the Save button on the Viewer Print Manager panel positioned by the user below the display area and select a format with the drop down or use the Print button to send directly to a printer e A 1 Wiring diagram for the SDtask sdcal The stages of processing within the task are shown along with the parameters that control them A 2 Multi panel display of the scantable There are two plots per scan indicating the psr reference position data and the ps source data 00 A 3 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 SPECTA ice a ee a Be a a e ee a ae we ee oe A 4 Calibrated spectrum with a line at zero using histograms 30 30 30 du al O A 5 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 o ee 374 Chapter 1 Introduction This document describes how to calibrate and image interferometric and single dish radio astro nomical data usin
253. ading 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 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 file dial up the PS Resolution dpi to its maximum of 300 This will increase
254. 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 saveinputs plotxy a file with name lt taskname gt saved in this case plotxy 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 ms CASA lt 3 gt saveinputs CASA lt 4 gt more listobs saved IPython system call more listobs saved taskname listobs vis ngc5921 ms verbose True listobs vis ngc5921 ms verbose False CHAPTER 1 INTRODUCTION 50 arw E CASA lt 31 gt alg hogwarts CASA lt 32 gt inp SEE gt inp clean Calculates a deconvolved image with a selected clean algorithm vis S Name of input visibility file imagename e clean Pre name of output images mode Type of selection mfs channel velocity frequency nchan Number of channels to select start Start channel step Increment between channels velocity width Channel width value gt 1 indicates channel averaging alg A
255. ages 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 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 CHAPTER 4 SYNTHESIS CALIBRATION 150 bandpass Calculate a bandpass solution vis 22 Nome of input visibility file caltable oe Name of output gain calibration table field 22 Select field using field id s or field name s spw e an 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
256. al and fields 1331 305 and 1445 099 from the second table ngc5921 gcal We could also have wildcarded the selection e g gainfield 70 gt J 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 when 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
257. ale 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 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 138 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 calibrati
258. alibrators gaincalfield 0137 331 2202 422 1743 038 1924 292 2136 006 2253 161 2355 498 0319 415 0359 5097 These sources will have calibration transferred from srclist targets Assemble field strings from lists fieldgain if len gaincalfield gt 0 for fn in range len gaincalfield if fn gt 0 fieldgain fieldgain gaincalfield fn fieldtargets if len targets gt 0 for fn in range len targets if fn gt 0 fieldtargets fieldtargets targets fn This list is used for final clean and stats srclist gaincalfield targets 466 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 467 Location of Cal Models e g for MacOSX fluxcaldir opt casa data nrao VLA CalModels or standard distro fluxcaldir pathname data nrao VLA CalModels or in place fluxcaldir Calibration parameters fluxcalfield 0137 331 primary calibrator for setjy fluxcalmodel 3C48_C im if non blank use this model image gaincalfield names of gain calibrators all fields usegaincurve False use a priori antenna gain elevation curve gainopacity 0 0 a priori atmospheric optical depth Tau calrefant VA15 reference antenna name for calibration VA15 EA19 gainsolint 20 0 20s for gaincal solutions polcalfield 2202 422 polariza
259. also quit using 4exit 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 CASA 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 help lt taskname gt 1232 or help par lt parameter name gt 1 2 8 4 to review the inputs output CHAPTER 1 INTRODUCTION 27 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 8 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
260. ameters 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 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 CASA lt 40 gt inp clean AN gt inp clean vis ngc5921 ms Name of input visibility file imagename ngc5921 Pre name of output images mode mfs Type of selection mfs channel velocity frequency alg csclean Algorithm to use hogbom clark csclean multiscale niter 1000 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 REESE gt inp vis 2 Name of input visibility file imagename 22 Pre name of output images mode mfs
261. ant 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 want 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 F ig 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 use green circles subplot 211 plot to the top of two panels plotxy n5921 ms x plot antennas for n5921 ms data set field 0 plot only first field datacolumn corrected plot corrected data CHAPTER 3 DATA EXAMINATION AND EDITING 106 subplot 223 plot to 3rd panel lower left in 2x2 grid plotcolor over ride default plot color plotsymbol r red d
262. 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 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 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 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 early stages for example in a first bandpass calibration so that later st
263. anualflag See 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 BETA ALERT the mode autoflag option is not currently supported 3 5 1 Flag Antenna Channels The following commands give the results shown in F igure 3 5 default plotxy plotxy ngc5921 ms channel iteration antenna subplot 311 default flagdata flagdata vis ngc5921 ms antenna 0 spw 0 10715 default plotxy plotxy ngc5921 ms channel iteration antenna subplot 311 CHAPTER 3 DATA EXAMINATION AND EDITING 114 Figure 1 corrected vs Channel ANTENNA1 1 ia oNbawopas corrected amp 10 20 30 40 50 60 70 corrected amp SOS SiO WO yea 30 20 Channel corrected amp DOLO tt Sd Mo 0 a Figure 1 corrected vs Channel ANTENNA1 1 Feed n 7 a ul coto ACACIA y au I 02 W A Bay 10 20 30 40 30 50 70 Channel i annel ANTENNA1 2 16 te qu 1A E 02 80 10 40 70 30 Channel corrected amp AO SAO 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
264. apper and you will happen First of all the task returns a handle that is a not be able to access it with tm This number used to identify the process This is printed to the is also true if you run in a Python screen e g script 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 O 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 CHAPTER 1 INTRODUCTION 42 HHHHHHHHHHEHHHHHHHHHHEHHHEHHHHHEHEHHHHHHHHEREEH Begin 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 wee usual messages here End Task mosaic HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHE REE 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 CASA lt 9 gt tm retrieve handle Out 9 result None state pending or CASA lt 10 gt tm retrieve 1 Out 10
265. arcsec imsize 256 256 Do a simple Clark clean psfalg clark If desired you can do a Cotton Schwab clean but will have only marginal improvement for this data imagermode csclean imagermode 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 239 CHAPTER 5 SYNTHESIS IMAGING 240 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 If you don t want any clean box then tfmask But if you had a cleanbox saved in a file e g regionfile txt you could use it mask regionfile txt and if you wanted to use interactive clean interactive True clean Should find stuff in the logger like Fitted beam used in restoration 51 5643 by 45 6021 arcsec at pa 14 5411 deg HHHH OF It will have made the images ngc5921 usecase clean image ngc5921 usecase clean model ngc5921 usecase clean residual ngc5921 usecase clean boxclean mask HHH clnimage imname image Done with imaging Now view the image cube of N5921 print View image viewer clnimage image Export the Final CLEAN Image as FITS CHAPTE
266. ards 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 CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 287 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 confusion 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 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 mai
267. are e flagmanager manage versions of data flags e flagautocorr non interactive flagging of auto correlations 3 3 e plotxy create X Y plots of data in MS flag data 8 e flagdata non interactive flagging of data e browsetable browse data in any CASA table including a MS 8 3 6 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 2 3 e selectdata general data selection syntax 2 5 e viewer use the casaviewer to display the MS as a raster image and flag it 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 95 CHAPTER 3 DATA EXAMINATION AND EDITING 96 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 the
268. 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 interferometric imaging Chapter 5 e image analysis Chapter 6 and
269. 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 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 jmcmul1i ALMATST1 Data N7538 AP314_A950519 xp2 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 th
270. arm 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 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 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 APPEND
271. arting 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 256 256 makes a square image 256 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 should not be a prime number 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 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 uz 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 CHAPTER 5 SYNTHESIS IMAGING 211 5 2 5 2 Mode channel If mode channel is chosen then an imag
272. 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 Tuv VU v 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 UVDIST can also be selected via comparison 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 CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 94 2 5 4 5 The msselect
273. as iteration antenna plotxy O print PA O ose print Plotxy print Showing 1331 305 with iteration antenna print Use Next button to step through antennas print You see some low level crud that you want to clip out Pause script if you are running in scriptmode if scriptmode user_check raw_input Return to continue script n 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 print print o sese print Now showing 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 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 plotxy O print Print 2952523222922 SS SS ASAS print Looking at RL LR print Now flag the bad data here Pause script if you are running in scriptmode CHAPTER 3 DATA EXAMINATION AND EDITING 125 if scriptmode user_check raw_input Return to continue script n Now do calibrater 0137 331 field 0137 331 correlation RR LL xaxis u
274. 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 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 52 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 10 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
275. as well Use Entire MS below Use care in selecting edit extents to assure that you re editing all the data you wish to edit 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 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 CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 307 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 Undo Last Edit U
276. asaviewer 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 image these are e Display axes e Hidden axes e Basic Settings e Position tracking CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 291 Load Data Viewer Directory home imager b smyers Sep07 Display As ngc1333_both ms Measurement Raster Image ngc5921 ms Measurement ngc5 921 ms flagversions Directory Contour Map ngc5921 usecase clean image Image Vector Map gt ngc5921 us
277. ase 7 gaintable cal G refant 14 bandpass vis data ms caltable cal BPOLY 1 spw 1 2756 bandtype BPOLY degamp 5 CHAPTER 4 SYNTHESIS CALIBRATION 154 degphase 7 gaintable cal G refant 14 bandpass vis data ms caltable cal BPOLY 2 spw 2 2 56 field 0 bandtype BPOLY degamp 5 degphase 7 gaintable cal G refant 14 Each solution is stored in a separate table As a result subsequent calibration operations may also be undertaken for each spectral window separately or all the tables included in gaintable during later operations BETA ALERT Once you do a separate bandpass run for different fields making separate tables you will need to continue keeping the calibration for these fields separate in gaincal etc as they cannot be currently recombined later Because of this complication we recommend doing bandpass with BPOLY on a single field only at this time 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 varying
278. assumes you have already run that script and have all of the defined variable in your session as well as the split calibrated ms files on disk The full NGC5921 example script can be found in Appendix F 1 HHEHHHHHHHHEEHHHEHHHHHHHAEHEHHEHHHHE AFERRA RO RRERO RE RERRORORARRER PERRERA RARA AEREA EERE RS Imaging Script for NGC 5921 Updated STM 2008 06 11 Beta Patch 2 0 uvcontsub gt lt prefix gt ms cont lt prefix gt ms contsub v clean gt lt prefix gt clean image lt prefix gt clean model lt prefix gt clean residual v exportfits gt lt prefix gt clean fits v HHEHHHHHHHHHEHHEEHHHAAHHAEEHEEEHHEE HEHEHE HHHA HEHEHE HRHA HEHEHE HRHRR ARR EH RS CHAPTER 5 SYNTHESIS IMAGING Set up some useful variables The prefix to use for all output files prefix ngc5921 usecase The split MS filename msfile prefix split ms Done with calibration Now clean an image cube of N5921 print Clean default clean Pick up our split source continuum subtracted data vis srcsplitms Make an image root file name imname prefix clean 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 7 Standard gain factor 0 1 gain 0 1 Set the output image size and cell size
279. ast 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 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 25 Name of input visibility file caltable ne Name of input calibration table fluxtable D Name of output flux scaled calibration table reference Reference field name s transfer flux scale FROM transfer a Transfer field name s transfer flux scale TO gt all append False Append solutions refspwmap 1 Scale across spectral window boundaries See help fluxscale Before running fluxscale one must have first run setjy for the reference sources and run a gaincal on both reference and tran
280. at 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 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 314 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 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 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
281. at 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 scale 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 136 Previous Calibration Calibrator Model
282. at 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 the solving CHAPTER 4 SYNTHESIS CALIBRATION 161 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 gt t Nome of input visibility file caltable 2a Name of output gain calibration table field 22 Select field using field id s or field name s spw de 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 minsnr 0 0 Reject solutions below this SNR poltype gt D QU Type of instrumental polarization solution see help append 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 fo
283. at this stage dismissed the tape deck and Position Tracking parts of the display as they are not used here We will now hit the Done button to start cleaning 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 change Clean Regions to Erase then mark and select as normal When finished changing your mask click the green Masking Done button If you want to finish your clean with no more changes to the mask hit the yellow Masking No More button If you want to terminate the clean click the red Clean Stop button While stopped in an interactive step you can change a number of control parameters in the boxes provided The main use of this is to control how many iterations before the next breakpoint and to change the threshold for ending cleaning Note the boxes at the top right if the interactive panel where the npercycle niter and threshold can be changed Typically the user would start with a relatively small npercycle 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 CHAPTER 5 SYNTHESIS IMAGING 230 and thus it is useful to set niter to a large number to b
284. ata or for multi field mosaics 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 CHAPTER 5 SYNTHESIS IMAGING clean vis imagename field spw selectdata mode niter gain threshold psfmode imagermode multiscale interactive mask imsize cell phasecenter restfreq stokes weighting uvtaper modelimage restoringbeam pbcor minpb async 218 Calculates a deconvolved image with a selected clean algorithm gt name of input visibility file MS dl Pre name of output images de Field Name a Spectral windows channels is all False Other data selection parameters mfs Type of selection mfs channel velocity frequency 500 Maximum number of iterations 0 1 Loop gain for cleaning 0 0mJy Flux level to stop cleaning Must include units gt clark method of PSF calculation to use during minor cycles 22 Use csclean or mosaic If use psfmode set deconvolution scales pixels False use interactive clean with GUI viewer O cleanbox es mask image s and or region s 256 256 x and y image size in pixels 1 0arcsec 1 0arcsec x and y cell size default unit arcsec a Image phase center position or field index 29 rest frequency to assign to image see help T Stokes params t
285. ation 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 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 317 Full antenna parameters diameter ap eff known to ASAP are gt ATPKSMB ATPKSHOH 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 telescopep
286. ave 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 CHAPTER 5 SYNTHESIS IMAGING 225 Note that this scaling as a function of position in the image occurs after the weighting of mosaic fields specified by mosweight and implied by the gridding weights ftmachine and weighting 5 3 5 4 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 5 3 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
287. aved 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 Save Edits MS editing works like a text editor in that you see all of your edits immediately but nothing is 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 CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 308 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
288. ax on_statistics max 0 oldtest_immax 1 07732224464 print Clean image ON SRC max 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 S 2 gt 2 gt 7 ia close CHAPTER 6 IMAGE ANALYSIS 277 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 11 Example
289. before and after the commas e g 3C286 3048 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 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 5 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 regula
290. bel for y axis Font size for labels Window size not yet The markersize parameter will change the size of the plot symbols Increasing it will help legibility when doing screen shots Decreasing it can help in congested plots The linewidth parameter will do similar things to the lines implemented Inside the Toolkit For even more functionality you can 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 e g plotxy CHAPTER 3 DATA EXAMINATION AND EDITING 102 The skipnrows 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 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 3 4 4 or channel striding in the spw specification 2 5 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 all clear the who
291. bject class image __builtin__ object image object Methods defined here __init__ X __init__ initializes x see x __class doc__ for signature Est Cen x __str__ lt gt str x CHAPTER 6 IMAGE ANALYSIS or for a compact listing use lt TAB gt completion on ia e g adddegaxes Add degenerate axes of the specified type to the image outfile direction spectral stokes linear tabular overwrite false false false false false addnoise unlock Release any lock on the image Data and other attributes defined here new__ CASA lt 2 gt ia Display all 101 possibilities ia ia ia ia ia ia ia ia ia ia ia ia ia ia ia ia ia ia ia __getattribute_ __class__ __delattr__ doc __hash__ _init_ __new__ __reduce__ __reduce_ex__ __repr __setattr__ __Str__ adddegaxes addnoise boundingbox brightnessunit calc calcmask close lt built in method __new__ T __new__ S ia ia ia ia ia ia ia ia ia ia ia histograms ia ia ia ia ia ia ia y or n fitsky fromarray fromascii fromfits fromforeign fromimage fromshape getchunk ia getregion getslice hanning haslock history imagecalc imageconcat insert isopen ispersistent ia ia ia ia ia ia ia ia ia ia ia ia ia ia ia ia of type object at 0x55d0f20 gt
292. ble save ASAP gt 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 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 and the CASA Measurement Set For example CASA lt 1 gt scans sd scantable OrionS_rawACSmod average False Importing OrionS_rawACSmod APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 357 NOTE It is important to use the average False parameter setting as the calibration routines supporting GBT data require all of the individual times and phases NOTE GBT data may need some pre processing prior to using ASAP In particular the progra
293. 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 Stop the clean and use our model for self calibration 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 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 15 Example Mosaicing An example of a simple mosaic clean call is shown below CHAPTER 5 SYNTHESIS IMAGING 232 Y Viewer Display Panel Data Display Panel Tools View 2 YSODAIMAA she 2 TRZ Clean Regions Channels Masking Clean Cycle Control niter cycle 100 All sup ncycles 60 threshold 8 mJy 00 Right Ascen
294. c5921 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 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 CHAPTER 4 SYNTHESIS CALIBRATION 184 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 Ist 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 to 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 smoot
295. cal png plotcal O Note the rolloff in the start and end channels Looks like channels 6 56 out of 0 62 are the best f Gain calibration print Gaincal default gaincal Armed with the bandpass we now solve for the time dependent antenna gains vis msfile set the name for the output gain caltable gtable prefix gcal caltable gtable 196 CHAPTER 4 SYNTHESIS CALIBRATION 197 Use our previously determined bandpass Note this will automatically be 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
296. cal task to smooth an existing 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 plotcal n4826_16apr smoothcal amp antenna 1 subplot 212 CHAPTER 4 SYNTHESIS CALIBRATION 174 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 23 Name of input visibility file tablein id Input cumulative calibration table use on first run accumtime 1 0 Timescale on which to create cumulative table incrtable di Input incremental calibration table to add caltable gt Output cumulative calibration table field q List of field names to process from tablein calfield de 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
297. 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 7 3 Using clean mask images You can give the mask parameter a string containing 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 6 CHAPTER 5 SYNTHESIS IMAGING 227 5 3 7 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 8 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 5 3 9 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 deconvolution If t
298. come from 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 CHAPTER 3 DATA EXAMINATION AND EDITING flagmanager You can use Flagdata to explicitly clip the data also print Flagdata default flagdata print As a demonstration show how to clip the data with flagdata print Note we had already flagged many of these interactively vis Set some msfile clipping mode manualflag clipcolumn DATA clipoutside False Clip calibraters field 1331 305 clipexpr clipminmax flagdata clipexpr clipminmax flagdata clipexpr clipminmax flagdata clipexpr clipminmax flagdata ABS RR 0 0 0 ABS LL 0 0 0 ABS RL 0 0 0 ABS LR 0 0 0 field 0137 331 clipexpr clipminmax flagdata Q clipexpr clipminmax flagdata ABS RR 0 0 0 ABS LL 0 0 0 regions 75 75 055 055 55 55 You can also do the antenna edits on 0137 331 and JUPITER wit
299. 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 1 1 1 What s New in Patch 2 This Cookbook version is for Patch 2 June 2008 This patch differs from previous versions of CASA in a number of ways e Tasking interface changes CHAPTER 1 INTRODUCTION 23 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 synthesis calibration features The calibration tasks now include a combine which allows control of the scope of solutions GITA The behavior of the solint parameter has changed with solint 0 now giving per integration solutions ins
300. cuvfits Since this is a split dataset the calibrated data is in the DATA column already datacolumn data Write as a multisource UVFITS with SU table even though it will have only one field in it multisource True Run asynchronously so as not to interfere with other tasks BETA also avoids crash on next importuvfits async True exportuvfits 207 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 deconvolution 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 4 e
301. cytol 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 spectral 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 79 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
302. d unified across all the tasks The available selectdata pa 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 HH HH H OH OF 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 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 5 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 though the use of numbers or lists There are also parameter specific rules that are described under each parameter CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 86 All lists of basic selection specification units are comma separated lists and can be of any length White spaces
303. d for this in 6 3 The xstat parameter is used as a return variable only Its value when calling imstat has no effect on its operation See below for more on xstat and its usage 6 7 1 Using the xstat 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 CHAPTER 6 IMAGE ANALYSIS tre the absolute PIXEL coordinate of the top right corner of the bounding box surrounding the selected 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 valu
304. dea to examine 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 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 CHAPTER 4 SYNTHESIS CALIBRATION 182 plotxy jupiter6cm usecase split ms uvdist amp corrected selectdata True correlation RR LL fontsize 14 0 will show the CORRECTED_DATA column See Figure Ad CASA Plotter BS el E ae ee E Molota Bia 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 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 do nominally you will re
305. duction 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 494 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 Extract 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 So
306. dup 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 5 3 5 1 Sub parameter ftmachine This sub parameter is activated for imagermode mosaic CHAPTER 5 SYNTHESIS IMAGING 224 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 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 signif
307. e disk You can reset back to defaults with sd rcdefaults HHHHHHHHHHHHHHHHHHHHEHHEEHE ORION S HC3N Position Switched data HHHHHHHHHHHHHHHHHHHHEHEEEHE startTime time time startProc time clock HHEHHHHHHHEHHHHHHHEHEHAHEH List data HHHHHHHHHHEHEHHHEHEHEHAHEH 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING go You should see something like Increment 6104 6104 6104 6104 6104 6104 6104 6104 6104 6104 6104 6104 233 233 233 233 233 233 233 233 233 233 233 233 344 A A AA A A ea ee a Se i Se Se Se ee ee eS Se Scan Table Summary 2S 2 ee ee Se ee SS ee ee Se SS a ee a a a ea Se a Se ee eS ee ee eee Se Beams 1 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
308. e thistest_immax thistest_imrms print print Done with I Imaging and Selfcal fosooooooooooooooooooooooooooooooooooooooooooooooooooooooo Polarization Imaging f sooooooooooooooooooooooooooooooooooooooooooooooooooooooo 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 we 460 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS Print 25952 3522922 SS SR SS OA ss ml print Clean print Final restored clean image is polimage 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_
309. e Type of file ms image or vector Examples of starting the viewer CASA lt 4 gt viewer CASA lt 5 gt viewer ngc5921 usecase ms ms CASA lt 6 gt viewer ngc5921 usecase clean image The first of these starts an empty viewer which will bring up an empty Viewer Display Panel 7 2 1 and a Load Data panel 7 2 3 The second starts the viewer loaded with a Measure ment Set The last of these examples starts the viewer with an image cube see Figure 7 1 BETA ALERT the viewer task cannot currently figure out whether a given file is an image or MS so for now you need to specify filetype ms explicitly if you want to view an MS in raster mode 281 CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 282 Y Viewer Display Panel Ox Data DisplayPanel Tools View E 9 Q PG Y AAA E Data Display Options a Y a 8 el 8 24 ngc5921 usecase clean image Display axes Hidden axes Basic Settings Aspect ratio fixed world al Px N Pixel treatment center z ya Y Resampling mode nearest BA F Y Data range 0 0104926 0 0523443 ya Y fo Scaling power cycles FF va Colormap Hot Metal 1 Ex 15 24 007 23700 00 20 00 42000 Position tracking SAR Axis labels ax Axis label properties 1 leoleo O fo norma _ Beam Ellipse F A E Blink
310. e subtract Let it split out the data automatically for us splitdata True saveinputs uvcontsub prefixt uvcontsub saved uvcontsub You will see it made two new MS ngc5921 usecase ms cont ngc5921 usecase ms contsub srcsplitms msfile contsub Note that ngc5921 usecase ms contsub contains the uv subtracted visibilities in its DATA column and ngc5921 usecase ms cont the pseudo continuum visibilities as fit The original ngc5921 usecase ms now contains the uv continuum subtracted vis in its CORRECTED_DATA column and the continuum in its MODEL_DATA column as per the fitmode subtract Done with calibration fo ooooooooooooooooooooooooooooooooooooooooooooosoooooooooo o o Now make a dirty image cube print Clean invert default clean Pick up our split source continuum subtracted data vis srcsplitms Make an image root file name imname prefix dirty imagename imname Set up the output image cube mode channel 415 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS nchan 46 start 5 width 1 This is a single source MS with one spw field 0 spw Set the output image size and cell size arcsec imsize 256 256 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 0 Set up the
311. e e http python org Main Python page o iktp python org doc 2 4 2 ret r6E heal Python Reference tep python org a0e72 4 2 eut Eat he Python Tutorial netp ipython scipy org IPython page etp aatplotlib 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 Python will display the interpretation of the line 380 APPENDIX D APPENDIX PYTHON AND CASA 381 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 cl
312. e 1000 3000 5000 7000 unflag unflag the masked regions default False example True for unflag 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 330 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 _flag eps WARNING be careful plotting in fsotf mode 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 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
313. e double im Take the sine of an image and add it to another 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 image1 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 channels 10 and below CHAPTER 6 IMAGE ANALYSIS 262 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 wo
314. e 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 CASA lt 1 gt inp clean CASA lt 2 gt inp clean ER AS gt inp clean CASA lt 3 gt inp clean CHAPTER 1 INTRODUCTION CASA lt 4 gt inp clean A gt inp clean CASA lt 5 gt taskname clean CASA lt 6 gt inp gt inpO all do the same thing 47 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 vis ee imagename oe mode mfs alg gt clark niter z 500 gain 0 1 threshold 0 0 mask gt gt cleanbox imsize 256 256 cell 1 0arcsec 1 stokes I field 20 phasecenter dd spw ae weighting natural uvfilter False timerange ae restfreq ae async False Oarcsec Calculates
315. e multiplot True yaxis amp showgui True plotcal print Print 3 SS 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 script n 443 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS Now go back and plot to file showgui False yaxis amp figfile caltable plotcal print Plotting calibration to saveinputs plotcal caltable plotcal yaxis phase figfile caltable plotcal print Plotting calibration to saveinputs plotcal caltable plotcal if dopolcal print Polcal D default polcal amp png file figfile plotcal amp saved phase png file figfile plotcal phase saved 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 444 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 445 One solution for entire dataset sol
316. e 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 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 A 2 1 5 sdcoadd Keyword arguments sdfilelist list of names of input SD dataset 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 DS5 43 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 328 gt CEDUNA HOBART
317. e Data Open menu or Open icon You can see the secase clean i all options are available to load the image as a Raster Image Contour Map Vector bring up the displays shown in Figure 7 1 ooo 29 5 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 mn PICU RA RAR A RRA RA he RR 29 a eR ee a e 29 7 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 o o 29 7 8 The Viewer Display Panel left and Data Display Options panel right after overlaying a Contour Map on a Raster Image from the same image cube 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 The tab for the contour plot is open in the Data Display Options panel o e 29 E N E al O 9 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 T
318. e Polygon tool to redraw the mask around the emission and are ready to hit Done to clean another 100 iterations 23 oO 5 4 We continue in our interactive cleaning of Jupiter from where Figure 5 3 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 DAA e A 231 spectral line dataset Note the new box at the top second from left where the Channels A11 toggle can be set unset We have just used the Polygon tool to draw a mask region around the emission in this channel The Channels A11 toggle is unset so the mask will apply to this channel only 232 6 1 NGC2403 VLA moment zero left and NGC4826 BIMA moment one right images a el 269 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 The initial display is of the first channel of the cube 282 7 2 The Viewer Display Panel left and Data Display Options right panels that appear when the viewer is called with the NGC5921 Measurement Set viewer ngc5921 usecase ms m 7 3 The Load Data Viewer panel that appears if you open the viewer without any infile specified or if you use th
319. e 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 385 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 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 386 D 5 2 Loops The for loop
320. e 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 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 none gt gt gt kernel expandable parameter kwidth width of spectral smoothing kernel options int in channels default 5 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 326 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 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 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 numb
321. e 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 The channelization of the 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 Channels in spw beyond the first are mapped into the nearest output image channel within half a channel if any 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 for using the channel mode to image a spectral line cube In this case we use mode channel nchan 46 start
322. e 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 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 3 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 394 CASA 35 z Out 35 6 CASA 36 D 10 On line editing
323. e 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 e 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 0 fitspw 0 4 7 50759 solint inf fitorder 0 spw 0 channels 4 6 and 50 59 scans are short enough mean only fitmode subtract splitdata True uv plane subtraction split the data for us HHHH A 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 component models directly to visibility data Such fitting has its origins in early interferometry especially VLBI where arrays consisted of only a few antennas and the calibration and deconvolution problems were poorly constrained These methods overcame the calibration uncertainties by fitti
324. e 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 cycle 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 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 CHAPTER 4 SYNTHESIS CALIBRATION 158 caltable cal spline ap gaintype GSPLINE calmode ap field 0 1 splinetime 600 Solve for GSPLINE Solve for amp amp phase Restrict data selection to calibrators Set spline timescale to 10min HOH BETA ALERT The GSPLINE solutions can not yet be used in fluxscale You should do at le
325. e 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 2 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 feature 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 backw
326. e 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 s A Note that images are handled through special image tables although standard FITS I O is also supported 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 5 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
327. e 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 CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 297 Y Viewer Display Panel X h Display Options ile Pi PESE we Es l5921 usecase cleanimage ngc5921 usecase cleanimage contour L E QQ l a Ea OORS Display axes a 40 El a 3 m ES op ap S G 32 Hidden axes Basic Settings Isnectratio F lt a Image Profile ngc5921 usecase clean image fiv Rectangle Region Profile Fly Caka Ay Es hy gt E iv 5 3 Fiv i iv hy 15h29m40 o 410 00 Lal Pe 1400 1450 1500 1550 1600 J2000 Right As velocity Coordinate world 15 22 07 927 05d01 47 92 velocity i Lj a CATO s a norma poga O 2 Rate Y 10 sec Compact O Blink i Dismiss Frame D star Enc Step ngc5921 ms Measurement Raster Image Aa er ngc5921 ms Magversions Directory X ngc5921 usecase cleanimage ngc5921 usecase cleanimage Image Contour map ngc5921 usecase clean model Image 2 090e 04 Jy beam 15 22 36 507 04 54 47 181
328. e 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 cookbook 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
329. e 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 TSYS values while Modcomp era data had this applied online In all cases CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 78 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 frequen
330. ean 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 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 382 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
331. ecase clean model Image i ngc5921 usecase clean residual Image i Marker Map ngc5921 usecase ms Measurement Figure 7 4 The Load Data Viewer panel as it appears if you select an image You can see all options are available 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 e Axis labels e Axis label properties e Beam Ellipse e Color Wedge The 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 CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 292 shown in Figure Basic Settings Aspect ratio fixed world AO Pixel treatment center 4 Y Resampling mode nearest v y e Data range 0 0104926 0 0523443 4 Y Scaling power cycles i Y Colormap Hot Metal 1 MO Y Figure 7 5 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 e Basic Settings Aspect ratio
332. ecase 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 The principal way to get X Y plots of visibility data is using the plotxy task This task also provides editing capability Inside the Toolkit CASA uses the matplotlib plotting library to display its Access to matplotlib is also pro plots You can find information on matplotlib at vided through the pl tool See be matplotlib sourceforge net low for a description of the pl tool To bring up this plotter use the plotxy task The inputs functions are CHAPTER 3 DATA EXAMINATION AND EDITING 98 hd CASA Plotter o E o N a jo S 3 Jupiter 6cm uncalibrated 10 UV Distance klambda Mark Reon Pag Untag tacto Out Aoo 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
333. ectangle 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 CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 288 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 3 The Load Data Panel Directory home imager b smyers Oct07 Display As n4826_tjoint2 residual ngc5921 ms Measurement Set ngc5921 ms flagversions Directory ngc5921 usecase cal splitms Measurement Set ngc5 92 1 usecase clean fits FITS Image ngc5921 usecase clean image Image ngc5921 usecase clean model Image c5921 usecase clean residual Imag LEL Expression Figure 7 3 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 use the Load Data Viewer GUI to interactively choose images or MS to load into the viewer An example of this panel is shown in Figure This panel is accessed through the CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 289 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 pan
334. ed 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 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 CHAPTER 4 SYNTHESIS CALIBRATION 157 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 variation In this case it is desirable to solve for a best fit functional f
335. ed Plane Only gt All Channels Save Region As home stn data wkg m5 1 fits rgn x Leave Open Save Last Region Figure 7 10 The Region Manager panel that appears if you select the Tools Region Manager menu item Note that the current Region Extent choice also affects the image points used in computing statistics 623 7 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 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 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 CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 299 r W Viewer Display Panel Data Display Panel Tools View la QO Els MARA ela 2 2 8la 40 2 ya 28 00 4 20 b Declination 2700 40 20 4726 00 40 UT 54
336. egin with you can always terminate the clean interactively when you think it is done E Viewer Display Panel 01 IEEE ex Data Display Panel Tools View Data Display Panel Tools View z i BOTRGAAA r BOTRIGAARA f E sat stele 2 Bats amp Blgsla Clean Regions Channelsy Masking Clean Cycle Control Clean Regions Channelsy Masking Clean Cycle Control I Add pore miterfeyeles 200 Ayr Ce nitereyele 100 All neycles 9 All se neycles 9 threshold 0 05 mJy threshold 0 05 mJy ll Figure 5 3 We continue in our interactive cleaning of Jupiter from where Figure left off In the first left panel we have cleaned 100 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 hit Done to clean another 100 iterations 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 8 The sequence of cleaning starting with the raw externally calibrated data is shown in Figures
337. el 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 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 7 2 3 1 Registered vs Open Datasets 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 attemp
338. eneral 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 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 dis 0 307 minposf 15 21 27 899 04 32 14 923 I 1 41354e 09Hz npts array 3014656 gt quartile array 0 00254881 yms array 0 00202226 sigma array 0 0020222 sum array 48 26399646 gt sumsq array 12 32857318 tre array 255 255 0 451 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 384 CASA lt 30 gt mydict2 CASA lt
339. enna 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 THE MEASUREMENT EQUATION AND CALIBRATION 398 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 m
340. enter clnimsize 2 clnblc clncenter clnimsize 8 clntrc clncenter clnimsize 8 For poor uv coverage use tigher box 6 x SynthBeam 18xcell clnblc clncenter 10 clntrc clncenter 10 centerbox clnblc clnblc clntrc clntrc myclnbox centerbox Can also force interactive cleaning myclnbox interactive aipsmodel Polarization of X angle calibrator 0137 331 If setpolmodel True Set up fluxcalmodel fcalmodel The flux model for 0137 331 C band fcalfield NOTE you must have entries for all spw in usespwlist 1 Q U V fcalfield 0 5 405 0 0 0 fcalfield 1 5 458 0 0 0 fcalmodel 0137 331 fcalfield Put in 2202 422 These values from AIPS http www vla nrao edu astro calib polar 2004 fcalfield fcalfield 0 2 465 0 0 0 fcalfield 1 2 461 0 0 0 fcalmodel 2202 422 fcalfield Set up pcalmodel pcalmodel The polarization model for 0137 331 pcalfield NOTE you must have entries for all spw in usespwlist 468 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS From calibrator manual C band RLPD 148deg P I 0 041 IPOL FPOL RLPHASE pealfield 0 5 405 0 041 148 0 pealfield 1 5 458 0 041 148 0 pcalmodel 0137 331 pcalfield Put in 2202 422 with effective flux of 1 0 before fluxscale These values from AIPS http www vla nrao edu a
341. ently 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 the 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
342. ently 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 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 341 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 Returns a Python dictionary of line statistics keys rms stddev max min sum median mean eqw example xstat sdstat print rms xstat rms these can be used for testing in scripts or for regression eqw is equivalent width sum mag where mag is either max or min dependi
343. er of axes 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 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 au 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 get imhead options get put summary and list hditem on Header item to get or set CHAPTER 6 IMAGE ANALYSIS 256 Note that to 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 value
344. er 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 example typically in range 2 9 higher values seem to be needed for GBT interactive interactive mode for 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 327 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 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 nam
345. ered 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 CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 301 Load Data Viewer Directory home imager b smyers Sep07 Display As ngc5921 usecase clean image Image Raster Image f ngc5921 usecase clean model Image ngc5921 usecase clean residual Image ngc5921 usecase ms Measurement i ngc5921 usecase ms cont Measurement ngc5921 usecase ms contsub Measurement ngc5921 usecase ms flagversions Directory Figure 7 13 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 in Figure for each open MS containing a set of categories The options withi
346. es sum 1_i72 mean the mean of pixel values ar I sum I_i n sigma the standard deviation about the mean sigma 2 sum I_i ar I 72 n 1 rms the root mean square sqrt sum I_i72 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 imstat reports Statistics on ngc5d921 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 0 270 CHAPTER 6 IMAGE ANALYSIS 271 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
347. es For each field a minor cycle is performed using the PSF algorithm specified in psfalg B 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 Double the image size from that used for the Clark clean and set a mask to clean only the inner quarter 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 5 3 13 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 0 pixels above the threshold This is normal and not a problem if you ve specified 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 CHAPTER 5 SYNTHESIS IMAGING 223 The option imagermode mosaic is for multi field mosaics
348. 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 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 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 CH
349. f polarization is being plotted The poln RL plots both R and L polarizations on the same plot The respective XY options CHAPTER 4 SYNTHESIS CALIBRATION 167 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 5 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 p
350. f the MAIN table flags mode save versionname flagautocorr comment flagged autocorr merge replace 122 CHAPTER 3 DATA EXAMINATION AND EDITING 123 flagmanager If you look in the jupiter6cm usecase ms flagversions you 11 see flags flagautocorr there along with the flags Original that importuvfits made for you Or use mode list print Now use flagmanager to list flag versions flagmanager In the logger you will see something like MS home sandrock2 smyers Testing2 Aug07 jupiter6cm usecase ms main working copy in main table Original Original flags at import into CASA flagautocorr flagged autocorr See logger for flag versions for this file He HH HH H OF f 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 Plot amplitude vs uvdist xaxis uvdist yaxis amp multicolor both Use the field name as the title selectplot True CHAPTER 3 DATA EXAMINATION AND EDITING 124 title field The easiest thing is to iterate over antenn
351. f 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 CHAPTER 1 INTRODUCTION 67 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 these 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 4 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 8 1
352. fect 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 CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 306 iv Data Display Options n4826_16apr ms Advanced MS and Visibility Selection Display Axes X Axis Baseline A F lt Y Axis Time AY Animation Axis Spectral Window gt ya Y 2000 3000 4000 5000 6000 6000 Baseline 33 a Channel Fad Y i ax 0 Polarization y 7 na Sooo 10 sec Compact Start Ena crar l Normal Flagging Options O Blink Basic Settings Figure 7 16 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 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
353. g 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 e 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 CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 286 Brightness contrast colormap fiddling light dark sun 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 Rectangle and Polygon region drawing The rectangl
354. g the CASA Common Astronomy Software Application package CASA is a suite of astronomical data reduction tools and tasks that can be run via the IPython 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 LI 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 pointers to parts of the toolkit that are easy to learn for most astronomers who
355. gename 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 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 CHAPTER 1 INTRODUCTION 41 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 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 There is a taskmanager tool tm that allows the user to retrieve the status of and to abort the execution of tasks BETA ALERT running with async True in the background There are You should not use the go command two methods of interest for the user tm retrieve and to run a task asynchronously as the tm abort handle will be swallowed by the If you run a task with async True then several things will Python task wr
356. gression script 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 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 print Calibrator data ampl max 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 421 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 422 ms close oldtest_src 46 2060050964 now in all chans diff_src abs oldtest_src thistest_src oldtest_src rint Target Src data ampl max thistest_src P g P print Previous src data max oldtest_src print Difference fractional diff_src print print gt gt logfile Target Src data ampl max gt
357. h flagdata CHAPTER 3 DATA EXAMINATION AND EDITING 130 Done with flagging Use Flagmanager to list all saved versions print Flagmanager default flagmanager print Now will use flagmanager to list all the versions we saved vis msfile mode list flagmanager 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 in 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
358. hannels 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 This example will 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 Or you can set up a simple cleanbox region To do this make a first cut at the image and clean the inner quarter Then use the viewer to look at the image and get an idea 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 Then you can use those pixel read outs you just go to define a clean box region where you specify the bottom Inside the Toolkit The im clean method is used for CLEANing data There are a num ber of methods used to set up the clean including im setoptions left corner ble 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 CHAPTER 5 SYNTHESIS IMAGING 220 cleanbox 80 80 120 120 Set the deconvolution region as a simp
359. hanningsmooth Hanning smooth frequency channel data to remove Gibbs ringing imhead List set image header properties immath Perform math on images immoments Compute moments from an image see URM for mathematical details importasdm ATF Convert an ALMA Science Data Model directory to a CASA data set MS importfits Convert a FITS image to a CASA image importuvfits Convert a UVFITS file to a CASA visibility data set MS importvla Convert VLA archive file s to a CASA visibility data set MS imstat Displays statistical information on an image or image region invert Calculate a dirty image and dirty beam listcal List calibration solutions to terminal listhistory List the processing history of a data set listobs List the observations in a data set listvis List visibility table makemask Calculate mask from image or visibility data set mosaic Calculate a multi field deconvolved image with selected clean algorithm plotants Plot the antenna distribution in local reference frame plotcal Plot calibration solutions plotxy Plot points for selected X and Y axes regridimage Grid image to same shape and coordinates as template sdaverage ASAP SD task do data selection calibartion and averaging sdbaseline ASAP SD task fit remove a spectral baseline sdcdal ASAP SD task do sdaverage sdsmooth and sdbaseline in one task sdsdcoadd ASAP SD task coadd multiple scantables into one sdfit ASAP SD task f
360. he 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 135 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 P 1 The MS includes a number of columns that can hold calibrated data model information and weights e calibration 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 th
361. he 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 3 4 1 GUI Plot Control You can 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 e 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 Panels The window thingy button second from right brings up a menu to adjust the panel placement in the plot CHAPTER 3 DATA EXAMINATION AND EDITING 101 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
362. he bandpass B solutions Iteration over antennas was turned on using iteration antenna The first page is shown The user would use the Next button to advance to the next set of antennas 1999 04 16 14 10 43 5 JUPITER 1 1 016 11 5 1 016 9 2 2 1 013 5 3 0 993 3 1 AS 0 993 0 8 0 990 5 1 24 0 997 10 7 0 999 8 3 25 0 985 D 0 988 4 0 26 1 005 8 4 1 009 5 3 ae 0 894 8 7 0 897 6 8 28 1 001 0 1 0 992 0 7 29 0 989 12 4 0 992 13 5 1Q 1 000F 4 2F 1 000F 3 2F waa 0 896 0 0 0 890 0 0 212 0 996 10 6 0 996 4 2 213 1 009 8 4 1 011 6 1 CHAPTER 4 SYNTHESIS CALIBRATION 172 214 0 993 17 6 0 994 16 1 15 1 002 0 8 1 002 ee Bee 216 1 010 9 9 1 012 8 6 e172 1 014 8 0 1 017 Ped 18 0 998 3 0 1 005 1 0 19 0 997 39 1 0 994 38 9 20 0 984 5 7 0 986 3 0 24 1 000F 4 2F 1 000F 3 2F 222 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 a Name of i
363. he display to select the area to edit When using the Rectangle Region tool double click inside the selected rectangle to confirm the edit CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 305 e E Display Options 2 n4826_16apr ms Advanced MS and Visibility Selection Display Axes X Axis Baseline Y Axis Time AY Animation Axis Channel v ya Y 3000 4000 5000 6000 6000 j Baseline Spectral Window Polarization o 76 8 Normal Flagging Options 10 Blink Basic Settings Figure 7 15 The MS for NGC4826 from Figure 7 14 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 The options below determine how edits will be applied Show Flagged Regions 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 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 ef
364. he 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 374 res save FLS3a_calfs MS2 Save the dataset as a MeasurementSet 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 open the data set choose a subset of the dataa just the key emission channels set map center define image parameters note it assumes symmetry if ny celly aren t specified HH HH HF OF im setoptions ftmachine sd cache 1000000000 choose SD gridding im setsdoptions convsupport 4 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 000 IXI Viewer Display Panel e200 X Image Profile FLS3a_Hl image Data Display Panel Tools ana 08 y Fluz Dersity indy Ga OG Ol o SY a sana Es EE 10 see Compact Y Blink
365. he 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 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 CHAPTER 4 SYNTHESIS CALIBRATION 189 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 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
366. he help prompt returns you to the CASA prompt CASA lt 2 gt help 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 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 CHAPTER 1 INTRODUCTION 34 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 given in Appendix D 1 3 Tasks and Tools in CASA Originally C
367. he profile will change to track movements of the region or crosshair if moved by dragging with the Mouse ee D 5 e D E Image button would bring up the displays shown in Figure 7 21 14 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 als aa a a a ra ee al A da le kw ee 15 The MS for NGC4826 from Figure 7 14 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 e a 716 The MS for NGCI82 continuing from Figure 714 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 33 000 0005004 7 17 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 300 dpi for a postscript plot A name has been given in preparation for saving as
368. he 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 alot 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 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 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 fluxu
369. he 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 4 for more information on feathering 5 3 10 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 11 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 CHAPTER 5 SYNTHESIS IMAGING 228 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 N
370. her 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 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 HAHAHAHA will use spw 0 to scale the others while in fluxscale vis data ms caltable cal
371. hing 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 2 1 i and 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 Hhanningsmooth Hanning smooth frequency channel data vis ngc5921 split ms Name of input visibility file MS async e 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 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 CHAPTER 4 SYNTHESIS CALIBRATION 185 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 that same CORRECTED_DATA column The reverse operation is achieved by specifying reverse True in that case uvsub will add the value in the M
372. ibrators 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 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 3C138_Q im 3C147_K im 3C286_C im 3C286_Q im 3C48_C im 3C48_Q im 3C138_K im 3C138_U im 3C147_Q im 3C286_K im 3C286_U im 3C48_K im 3C48_U im 3C138_L im 3C138_X im 3C147_U im 3C286_L im 3C286_X im 3C48_L im 3C48_X im CHAPTER 4 SYNTHESIS CALIBRATION 143 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
373. icant 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 5 3 5 2 Sub parameter mosweight 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 5 3 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 mary beam and noise across the im age 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 If scaletype SAULT then the image will be scaled so as to h
374. icating the psr reference position data and the _ps source data s summary summary info s set_fluxunit K make K default unit APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 370 scal sd calps s 20 21 22 23 60e X ASAP Plotter Tk OrionS_ps Brightness Temperature K Calibrate HC3N scans OrionS_ps ly 1000 2000 3000 4000 5000 6000 7000 8000 Channel 1000 2000 3000 4000 5000 6000 7000 8000 Channel io O 18ju x 3759 5 y 5 67 Figure A 3 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 scal recalc_azel scal opacity 0 09 sel sd selector sel set_ifs 0 scal set_selection sel recalculate az el to do opacity correction Prepare a selection select HC3N IF get this IF stave sd average_time scal weight tintsys average in time spave stave average_pol weight tsys sd plotter plot spave spave smooth boxcar 5 spave auto_poly_baseline order 2 sd plotter plot spave spave set_unit GHz sd plotter plot spave sd plotter set_histogram hist True average polarizations Tsys weighted 1 Tsys 2 average plot boxcar 5 baseline fit order 2 plot draw spectrum using histogram sd plotter axhline color r linewidth 2 zline sd plotter save orions_hc3n_reduced eps
375. ient parallactic angle coverage where sufficient is determined by SNR and the details of the solving mode These principles are stated assuming 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 D 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 c
376. ight 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 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 inher
377. 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 density 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 dl Field name list or field ids list spw a Spectral window identifier list modimage f Model image name fluxdensity 1 Specified flux density I Q U V standard Perley Taylor 99 Flux density standard CHAPTER 4 SYNTHESIS CALIBRATION 141 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 defau
378. imary 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 resulting 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 400 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 solutio
379. ime 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 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 Fields 3 ID Code Name Right Ascension Declination Epoch HHH HHH HH HHH HH HHH HH HHH HH OH OF 0 C 1331 30500002_013 31 08 29 30 30 32 96 J2000 CHAPTER 4 SYNTHESIS CALIBRATION 193 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 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 V
380. 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 CHAPTER 1 INTRODUCTION 59 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 TF 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 created 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
381. in cal table caltable gtable we will be using 1331 305 the source we did setjy on as our flux standard reference note its extended name as in the FIELD table summary above it has a VLA seq number appended reference 1331 we want to transfer the flux to our other gain cal source 1445 099 transfer 1445 saveinputs fluxscale prefix fluxscale saved 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 usecase 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 fosoooooooooooooooooooooooooooooooooooooooooooooooooooooos Now use plotcal to examine the gain solutions print Plotcal fluxscaled gains default plotcal caltable ftable field 0 1 No GUI for this script showgui False If you want to do this interactively and iterate over antenna set 410 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 411 iteration antenna showgui True 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 plotcal O Set up 2x1 panels lower panel phase vs
382. in 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 sdsmooth 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 320 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 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 gau
383. ing o 62 1 5 2 1 Interactive X Y Plotting and Flagging o 62 1 5 2 2 Flag the Data Non interactively o o 62 1 5 2 3 Viewing and Flagging the MS o o e 62 ell A eet BO a ee Pek de Be et 63 1 5 3 1 Prior Calbrationl s 40 ee eon oor ee ee we Re ee 63 1 5 3 2 Bandpass Calibration 0 0 e e 64 1533 Gain Calibration 2 2 ee 64 Quek Seah E h peated eek Seg Gok oh Gk we E 64 1 5 3 5 Examining Calibration Solutions 0 65 Spoke Paw Boe aOR Aw a Glew o 65 Br a ay ged a ee Gee ee de ree e 65 1 5 3 8 Correcting the Data 2002000002 eee 65 1 5 3 9 Splitting the Data 2 0 020 002 0200 65 1 5 4 Synthesis Imaging e 66 1 5 4 1 Cleaning a single field image or a mosaic 66 1 5 4 2 Feathering in a Single Dish image o 67 ide e ad a a dE ds ee a 67 LR A a a RA 67 1 5 6 1 What s in animage 0 020000 2 ee ee 67 1 5 6 2 Image statistics ee 68 dbo amp 4 ae ete Samos Bee ees ee we 68 1 5 6 4 Image math ssi sox eee eo pon Oe e Be oe ce 68 1 5 6 5 Regridding an Image e e eee ee 1 5 6 6 Displaying Images e e o 1 5 7 Getting data and images out of CASA 2 02040 2 Visibility Data Import Export and Selection 2 1 CASA Measurement Sets 2 0 a 2 1
384. int Plotxy NGC5921 default plotxy vis msfile field 2 Edge channels are bad spw 0 4759 Time average across scans timebin 86000 crossscans True No GUI for this script interactive False 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 412 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS saveinputs plotxy prefix plotxy final amp saved plotxy O Set up 2x1 panels lower panel phase vs time subplot 212 yaxis phase datacolumn corrected Now send final plot to file in PNG format via png suffix figfile vis plotxy png saveinputs plotxy prefix plotxy final phase saved plotxy O Split the gain calibrater data then the target print Split 1445 099 Data default split vis msfile We first want to write out the corrected data for the calibrator Make an output vis file calsplitms prefix cal split ms outputvis calsplitms Select the 1445 099 field all chans field 1445x spw pick off the CORRECTED_DATA column datacolumn corrected saveinputs split prefix split 1445 saved split O Now split NGC5921 data before continuum subtraction print Split NGC5921 Data splitms
385. int inf combine scan reference antenna refant calrefant minimum SNR 3 minsnr 3 saveinputs polcal calprefixt polcal saved polcal 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 real yaxis imag figfile caltable plotcal reim png print Plotting calibration to file figfile saveinputs plotcal caltable plotcal reim saved plotcal xaxis antenna yaxis amp figfile caltable plotcal antamp png print Plotting calibration to file figfile saveinputs plotcal caltablet plotcal antamp saved plotcal xaxis antenna yaxis phase APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 446 figfile caltable plotcal antphase png print Plotting calibration to file figfile saveinputs plotcal caltable plotcal antphase saved plotcal xaxis antenna yaxis snr figfile caltable plotcal antsnr png print Plotting calibration to file figfile saveinputs plotcal caltablet plotcal antsnr saved plotcal First set the model print Setjy default setjy vis msfile print Use setjy to set IQU fluxes of
386. is 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 regridimage 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 8 for a description of this task 1 5 6 6 Displaying 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 CHAPTER 1 INTRODUCTION 69 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 8 e exportfits export a CASA image table a
387. 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 up to 8 are reasonable Most APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 367 users of this method should find the default value sufficient plot plot the fit and the residual In this each indivual 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 create fitter object msk spave create_mask 3928 4255 create mask region around line f set_function gauss 1 set a single gaussian component f set_scan spave msk set the scantable and region Automatically guess start values f fitO fit
388. 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_scan20t023_if0to3 asap False 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 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 sc1 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 366 scantable smooth kernel type of smoothing hanning default gaussian boxcar width width in pixls ignored for hanning FWHM for gaussian insi
389. 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 399 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 1 Solve for G on the bandpass calibrator using T opacity and E 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 pr
390. isas Bee oe oe a RO eH a Ree a A 3 3 4 Scantable Management 0 0 000000 ee eee A 3 3 5 Scantable Mathematics 0 0000000 eee LO Peralada Beech ee eee oa ee Gea ool A pede Eee ome eke ook eee eae AAA A 3 4 3 Gain Elevation and Atmospheric Optical Depth Corrections A 3 44 Calibration of GBT datal AA a e er a a E e a RA RRA E A a at ee dos A ee eee eee A A bene a ee ig eG eee bs L ae eee Sos ee he Gee SOCO OOE e a es Bee y Heh peo ai Ep a a a edo B Appendix Simulation B 1 Simulating ALMA with almasimmos 02 2000000424 G C Appendix Obtaining and Installing CASA C 1 Installation Script 2 ee PA s bel Oe oe A ee a a ee a ee Se a Y D Appendix Python and CASA D 1 Automatic parentheses 2 0 ee 1 2 Indentation ex 2 06 ia we ae Be ee Ge ee ee ee el ae ee ep eee hace aS ele eh si e ene erecta Fs ek aes es Slabs os eee Ae ee RE een e A O ads esos pares ada eo dia ea be e ee ie den ancla ts e ius ee a Gama eee Eta a incense owen et aged an tdo de cea de debe nee boa eho E Rs Bee eae es oe eee teed bee eee is ee er ee ph HS aS Goh ne ESB As oe oe GREASE o Gren doh Se Ae eds ente or en a 377 377 379 379 379 D 12 How do l exit from CASA E Appendix The Measurement Equation and Calibration E 1 The HBS Measurement Equation 0 a E 2 General Calibrater Mechanics F Appendix Annotated Example Scripts F 1 NGC 5921
391. it Once this is done all of the ASAP functionality is now under the Python sd tool bf 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 __class__ sd _validate_bool sd list_scans sd __date__ sd _validate_int sd mask_and sd __delattr__ sd asapfitter sd mask_not sd __dict__ sd asaplinefind sd mask_or sd __doc__ sd asaplog sd merge sd __file__ sd asaplotbase sd os sd __getattribute__ sd asaplotgui sd plf APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 355 sd __hash__ sd asapmath sd plotter sd __init__ sd asapplotter sd print_log sd __name__ sd asapreader sd quotient sd __new__ sd average_time sd rc sd __path__ sd calfs sd rcParams sd __reduce__ sd calnod sd rcParamsDefault sd __reduce_ex__ sd calps sd rc_params sd __repr__ sd commands sd rcdefaults sd __setattr__ sd defaultParams sd reader sd __str__ sd dosigref sd scantable sd __version__ sd dototalpower sd selector sd _asap sd fitter sd simple_math sd _asap_fname sd is_ipython sd sys sd _asaplog sd linecatalog sd unique sd _is_sequence_or_number sd linefinder sd version sd _n_bools sd list_files sd welcome sd _to_list sd list_rcparameters sd xyplo
392. it a spectral line sdflag ASAP SD spectral flagging task CHAPTER 1 sdplot sdlist sdsave sdscale sdsmooth sdstat setjy smoothcal split tget uvcontsub uvmodelfit viewer INTRODUCTION 37 ASAP ASAP ASAP ASAP ASAP ASAP SD SD SD SD SD SD plotting task task task task task task list summary of single dish data save the sd spectra in various format scale the sd spectra do smoothing of spectra list statistics of spectral region Compute Produce the model visibility for a specified source flux density a smoothed calibration table Create a new data set MS from a subset of an existing data set MS Recover set parameters for a specified task Continuum fitting and subtraction in the uv plane Fit a single component source model to the uv data View an image or visibility data set Typing startup will provide the startup page displayed when entering CASA For example CASA lt 6 gt startup Available tasks accum applycal bandpass browsetable clean clearcal clearplot clearstat concat deconvolve exportfits imhead sdaverage sdfit sdsave exportuvfits immoments plotants feather importfits plotcal filecatalog importuvfits plotxy find importvla regridimage flagautocorr invert setjy flagdata listcal smoothcal flagmanager listhistory split fluxscale listobs tget ft listvis uvcontsub gaincal makemask uvmodelfit hanningsmooth mosaic viewer immath ims
393. ith large MSs often the first thing you ll want to do is to select spectral windows which all have the same number CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 304 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 cause 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 a
394. l prefix cleani imagename imnamel Set up the output continuum image single plane mfs mode mfs stokes I NOTE current version field doesnt work field Combine all spw spw 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 HHHH Set the output image size and cell size arcsec 4 will give 3 5x oversampling 280 pix will cover to 2xPrimaryBeam clean will say to use 288 a composite integer for efficiency clnalg clark if you want CS Clean HHH clnmode csclean clnmode clnimsize 288 288 clncell 4 4 psfalg clnalg imagermode clnmode imsize clnimsize 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 niter 10000 Also set flux residual threshold 0 04 mJy CHAPTER 5 SYNTHESIS IMAGING 243 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 threshold 0 05 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 robus
395. l 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 1067 2 2 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 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
396. ld name as the title APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS selectplot True title field iteration plotxy O print o a Sa SSS See 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 7 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 imagename clean saved 457 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 458 clean print print 0 east sre tases ar res ssa sSse print Clean print Final clean model is clnmodel2 print Final restored clean image is clnimage2 print The clean residual image is clnresid2 print Your final clean mask is print we print This is the final restored clean image in the viewer clnmask2 print Zoom in and set levels to see faint 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
397. le 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 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 plotlevel control for plotting of results options int O none 1 some 2 more default O no plotting example plotlevel 1 plots fit and residual no hardcopy available for fitter WARNING be careful plotting OTF data with lots of fields Retruns a Python dictionary of line statistics keys gt peak cent fwhm example each value is a list of lists with one list of APPENDIX A APPENDIX SINGLE DISH DATA PRO
398. le In this case 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 14
399. le 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 14 CHAPTER 5 SYNTHESIS IMAGING 226 5 3 7 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 pointing 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 The default is to restrict clean to the inner quarter of the image 5 3 7 1 Setting clean boxes If mask is given a list these are taken to be pixel coordinates for the blc and trc bottom left and top right corners of one or more rectangular boxes For example cleanbox 110 110 150 145 180 70 190 80 defines two boxes 5 3 7 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
400. le 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 psfalg The psfalg parameter chooses the 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
401. le plot panel The title xlabels and ylabels parameters can be used to change the plot title and axes labels 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 Plot 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 CHAPTER 3 DATA EXAMINATION AND EDITING 103 KA CASA Plotter Se Sl ES ES E E a O O aja
402. lgorithm to use hogbom clark csclean multiscale niter Number of iterations ain Loop gain for cleaning threshold Flux level to stop cleaning mJy mask Name of mask image used in cleaning cleanbox Ed clean box regions or file name or interactive imsize 256 256 Image size in pixels Enx ny symmetric for single value cell 115 0 15 0 Cell size in arcseconds x yl stokes et ts Stokes parameter to image 1 IY IQU IQUY gt field o Field name phasecenter ih Field Identifier or direction of the image phase center spw By spectral window channels gt all weighting briggs Weighting to apply to visibilities rmode norm Robustness mode for Briggs weighting robust 0 5 Briggs robustness parameter noise 0 0Jy noise parameter for briggs weighting when rmode abs npixels 0 number of pixels to determine uv cell size O gt Field of view uvfilter False Apply additional filtering uv tapering of the visibilities timerange ee range of time to select from data restfreq restfrequency to use in image async False if True run in the background prompt is freed CASA lt 33 gt B 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 To read these back in use the Python execfile
403. linear approx on polcalfield vis msfile Start with the un fluxscaled gain table gaintable gtable use settings from gaincal gaincurve usegaincurve opacity gainopacity Output table ptable prefix pcal caltable ptable Use an unpolarized source or a source tracked through a range of PA field polcalfield spw usespw selectdata True uvrange polduvrange Polcal mode poltype polcalmode Currently 1 day timescale is hardwired solint 86400 reference antenna refant calrefant minimum SNR 3 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS minsnr 3 saveinputs polcal prefix polcal saved polcal You should see something like Fractional polarization solution for 2202 422 spw 0 Q 0 00356182 U 0 0717148 P 0 0718032 X 43 5783 deg Fractional polarization solution for 2202 422 spw 1 Q 0 00561314 U 0 0720833 P 0 0723015 X 47 2263 deg f List polcal solutions print Listcal listfile caltable list print Listing calibration to file listfile listcal Plot polcal solutions print Plotcal iteration showgui False xaxis real yaxis imag figfile caltable plot reim png print Plotting calibration to file figfile saveinputs plotcal prefixt
404. list 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 338 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 polaverge 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
405. ll 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 CHAPTER 1 INTRODUCTION 33 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 further information hitting lt RETURN gt at t
406. lot to each timestamp or if multiplot True the antennas plots 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 usecase data see below and Appendix F 1 default plo
407. lotxy the ESC key can be used to 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 CHAPTER 3 DATA EXAMINATION AND EDITING 108 left clicking and dragging the mouse each click 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 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 EJ CASA Plotter 0 EDITE 01 o T 4 o Y 2 3 UV Distance klambda 7 3 UV Distance klambda Mark Region ag Untag Locate 1 quit Mark Region Flag Untag Locate 1 Quit l0 0 18la uo note O O 188 anc negen to Figure 3 4 Plot of amplitude versus uv distance before left and after right flagging two marked regions The
408. lowing a Es 22 af NEWLINE CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 87 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 x 4 or as the list 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 BANDx will also be used as a string pattern matching any string which has the sub string BAND in it e The string BAN
409. lt 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 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 5 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
410. lt 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 Its 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 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 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 CHAPTER 1 INTRODUCTION grwa CASA lt 29 gt tget clean acia gt tget clean Restored parameters from file clean last CASA lt 30 gt inp ii gt imp clean 3 Calculates a deconvolved image with a selected clean algorithm vis ms contsub Name of input visibility file imagename Pre name of output images mode
411. m 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 NOTE 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 NOTE 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 observation are assigned as _pstr Use the summary function to examine the data and get basic information CASA lt 8 gt scans summary Beams 1 IFs 26 Polarisations 2 linear Channels 8192 Observer Joseph McMullin Obs Date 2006 01 19 01 45 58 Project AGBTO6A_018_01 Obs 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 IF Frame RefVal RefPix Increment 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
412. mages 8 7 3 and Measurement Sets 6 73 7 2 1 The Viewer Display Panel The Viewer Display Panel GUI is the the panel that contains the image or MS display 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 GUI are the menus e Data Open open an image from disk Register register unregister selected image menu expands to the right containing all loaded images Close close selected image menu expands to the right Adjust open the Data Display Options Adjust panel Print print the displayed image 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 a new Viewer Display Panel Panel Options open the Display Panel s options window Print print displayed image 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 exrent e View Main Toolbar show hide top row of icons Mouse Toolbar show hide second row of mouse button action selectio
413. mat 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 A 3 4 Calibration For some observatories the calibration 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 363 scans convert_flux eta 0 48 d 35 Unknown telescope scans convert_flux jypk 15
414. mmos ALMA mosaic simulation task prototype applycal Apply calculated calibration solutions bandpass Calculate a bandpass calibration solution blcal ATF Calculate a baseline based calibration solution prototype browsetable Browse a visibility data set or calibration table casalogger FUNCTION invoke to call up the logger gui clean Calculate a deconvolved image with selected clean algorithm clearcal Re initialize visibility data set calibration data clearplot Clear matplotlib plotter and all layers clearstat Clear all read write locks on tables concat Concatenate two visibility data sets deconvolve Image based deconvolver exportfits Convert a CASA image to a FITS image exportuvfits Export MS to UVFITS file feather Feather together an interferometer and a single dish image in the Fourier plane filecatalog File Catalog GUI find Find a string in the task help flagautocorr Flag autocorrelations typically in a filled VLA data set flagdata Flag data based on time baseline antenna clip etc flagmanager Enable list save restore and delete of flag versions fluxscale Bootstrap the flux density scale from standard calibraters fringecal ATF Calculate a baseline based fringe fitting soln phase delay delay rate ft Fourier transform the specified model or component list gaincal Calculate gain calibration solutions polcal Calculate instrumental polarization calibration solutions
415. msfile APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 482 Start with the G and D tables gaintable gtable ptable use settings from gaincal gaincurve usegaincurve opacity gainopacity Output table xtable prefix polx caltable xtable previously set with setjy field polxfield spw usespw selectdata True uvrange polxuvrange Solve for Chi poltype X solint 86400 reference antenna refant calrefant minimum SNR 3 minsnr 3 saveinputs polcal prefix polcal X saved polcal You should get something like Position angle offset solution for 0137 331 spw 0 72 437 deg Position angle offset solution for 0137 331 spw 1 21 0703 deg List polcal solutions print Listcal listfile caltable list print Listing calibration to file listfile tlistcalO APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 483 Plot polcal solutions print Plotcal xaxis antenna yaxis phase iteration showgui False figfile caltable plot png print Plotting calibration to file figfile saveinputs plotcal prefixt plotcal polcal x antphase saved plotcal else if polxfield and not polxfield isspace print DO NOT HAVE PCALMODEL FOR polxfield print PCALMODEL pcalmodel Correct the data This will put calibrated data into the CORRECTED_
416. mzeromax thistest_momzeromax oldtest_momzeromax print Moment O image max gt thistest_momzeromax print Previous m0 max oldtest_momzeromax print Difference fractional diff_momzeromax print print gt gt logfile Moment 0 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 Pull the mean from the momonestats dictionary thistest_momoneavg momonestats mean 0 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 424 oldtest_momoneavg 1479 77119646 diff_momoneavg abs oldtest_momoneavg thistest_momoneavg oldtest_momoneavg print Moment 1 image mean thistest_momoneavg print Previous mi mean oldtest_momoneavg print 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
417. n markersize e 5 0 linewidth 1 0 connect none plotrange 1 1 1 1 skipnpoints 1 multicolor False replacetopplot False removeoldpanels True title ae xlabels ee ylabels 72 fontsize 10 0 windowsize 1 0 HHH HHH SE HH HHH HHH HH HH HHH HH OH OF Inside the Toolkit In the current version of CASA you cannot use the task parameter setting features such as the inp default or go commands for the tools Name of input visibility azimuth elevation hourangle baseline channel time u v w uvdis azimuth elevation hourangle baseline amp pha u v w uvdist data raw corrected model Select data based on field name or index Select data based on spectral window Select a subset of the data opens selection params Select averaging mode time or channel Panel number on display screen yxn Overplot values on current plot if possible Show flagged data Plot separate panels by field antenna baseline scan feed pylab plot symbol pylab plot color Size of plotted marks Width of plotted lines Specifies which points are connected with lines The range of data to be plotted can be time values Plot every nth point Plot polarizations and channels in different colors Replace the last plot or not when overplotting Turn on of automatic clearing of panels Plot title above plot Label for x axis Label for y axis Font size for labels Window size See 1 3 5 4 below for more details on the u
418. n along with the parameters that control them 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 316 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 FITS The sdsave task is available exclusively for exporting with data selection options The sdcoadd task is available to merge data in seperate 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 Basic 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 autom
419. n 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 dl Input image name moments 0 List of moments to compute axis 3 Axis for moment calculation planes gt Set of planes channels to use for moment e g 3720 21 includepix 1 Range of pixel values to include excludepix 1 Range of pixel values to exclude outfile de Output image file name or root for multiple moments async False if True run in the background prompt is freed 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 CHAPTER 6 IMAGE ANALYSIS 267 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 moments 2 intensity weighted dispersion of the coordinate traditionally used to get velocity dispersion 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 mome
420. n 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 automatically 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 Press the Apply button in this case to load the data see 7 4 1 6 and Max Visibility Memory at the end of 8 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 15 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 2 are used on t
421. n 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 Region Selection and Positioning You can draw regions or select positions on the display with the mouse once you have selected the appropriate tool s on the Mouse Toolbar see above The Rectangle Region drawing tool currently works for the following 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 5 3 6 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 R
422. n each category can be either rolled up or expanded by clicking the category label For a Measurement Set the categories are e Advanced e MS and Visibility Selection e Display Axes e Flagging Options e Basic Settings e Axis Drawing and Labels e Color Wedge CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 302 7 4 1 1 MS Options Basic Settings The Basic Settings roll up is expanded by default It contains entries similar to those for a raster image 8 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 This roll up
423. n icons Animator show hide tapedeck control panel CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 285 Position Tracking show hide bottom position tracking report box Below this is the Main Toolbar the top row of icons for fast access to some of these menu items e folder Data Open shortcut pulls up Load Data panel e wrench Data Adjust shortcut pulls up Data Display Options Adjust panel e panels Data Register shortcut pull up menu of loaded data e delete Data Close shortcut closes unloads selected data e panel Display Panel New Panel e panel wrench Display Panel Panel Options pulls up the Display Panel s options window e region save Tools Region Manager save control regions button not shown in all fig ures 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 Below this are the eight Mouse Tool buttons 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 magnifyin
424. n repeat as necessary 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 plotxy O print PHAN ss A ES ER SSeS n print Looking at RL LR print Now flag the 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 xaxis uvdist spw iteration antenna title field 436 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 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 1 Sasa a 2293222 2222 SS 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 script n xaxis time spw 71 correlation Note that the strings like antenna 9 first try to match the NAME which we see in list
425. n 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 spw 3mmUSB 3mmLSB choose by names if available CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 89 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 5 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
426. n 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 distribution 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 Note This script does not include any self calibration steps The latest version of this script can be found at http casa nrao edu Doc Scripts ngc5921_usecase py HHEHHHHHHHHHEHHEHHHHAEHHAE HHA HHEE HEHEHE HRHE HEHEHE HRHA HEHE HEHEHE RRS RS Use Case Script for NGC
427. n 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 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 147 gainfield 0 0 1 to specify the field 1331 305 from the table ngc5921 bc
428. n_statistics2 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 459 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS print Clean image OFF SRC rms thistest_imrms print Previously found to be oldtest_imrms diff_imrms abs oldtest_imrms thistest_imrms oldtest_imrms print Difference fractional diff_imrms print print Final Clean image Dynamic Rang
429. ncapsulate 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 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 asaprc 311 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 312 file Within CASA these are contained in the Python dictionary sd rcParams and are accessible through its keys and val
430. nce 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 in the uv plane ie 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 0 0 Briggs robustness parameter O number of pixels to determine uv cell size 0 gt field of view robust npixels The actual weighting scheme used is Wi Te 5 4 Ml 1 Wg f where W is defined as in uniform and superuniform weighting and 5 x 1078 f 51074 5 5 2p W 4 i 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 CHAPTER 5 SYNTHESIS IMAGING 217 5 2 11 6 briggsabs weighting For weighting briggsabs a slightly different Briggs weighting is used with Wi a n _ 5 6 W R2
431. nd 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 fitting 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 t
432. ndo 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 Use Entire MS When Saving Edits 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 s
433. negative Power cycles setting For positive values an larger fraction of the colormap is used for the high data values See Figure 7 6 for sample curves 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 The actual functions are computed as follows 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 If p is the positive value chosen
434. ng 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 show in Figure and an example is shown in Figure You assign one of the drawing functions rectangle or polygon default is rectangle to the right mouse button usually CHAPTER 5 SYNTHESIS IMAGING 229 E Viewer Display Panel px PIE SEA Data Display Panel Jools View Data Display Panel Jools View rBOeArRGASQAAG ABORDA alet a o Hel ale a ug E Meee 2 EE 115222 88 Clean Regions Channels Masking Clean Cycle Control Clean Regions Channels Masking Clean Cycle Control a E niter cycle 100 aa CN niter cycle 100 all seo neycles 10 All se neycles 10 threshold 0 05 mJy threshold 0 05 mJy J2000 Declination Figure 5 2 Screen shots 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
435. ng 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 pixels to something desirable CHAPTER 5 SYNTHESIS IMAGING 234 The inputs for feather are imagename of Name of output feathered image highres 2 Name of high resolution synthesis image lowres q Name of low resolution single dish image 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 5 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
436. ng on which has greater magnitude 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 averag ing smoothing has also already been done as there are no controls for these 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 A 2 2 A Single Dish Analysis Use Case With SDTasks 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 HHHFHHHHHHHHEHHHHAHHEHHHHHHHAHHHHHE HH ORION S SDtasks Use Case Position Switched data APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING Version STM 2007 03 04 This is a detailed walk through for using the SDtasks on a test dataset HHHHHHHHHHHHHH AH RA RARA import time 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
437. ng 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 CHAPTER 4 SYNTHESIS CALIBRATION 188 uvmodelfit Fit a single component source model to the uv data vis qa Name of input visibility file field e 2 field name or index spw 2 spectral window selectdata False Activate data selection details niter 5 Number of fitting iterations to execute comptype 5 Pp 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 fit outfile q 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
438. ngc5921 usecase clean boxclean mask HHH clnimage imname image Done with imaging Now view the image cube of N5921 print View image viewer clnimage image 418 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS Export the Final CLEAN Image as FITS print Final Export CLEAN FITS default exportfits clnfits prefix clean fits imagename clnimage fitsimage clnfits Run asynchronously so as not to interfere with other tasks BETA also avoids crash on next importfits async True saveinputs exportfits prefixt exportfits saved myhandle2 exportfits print The return value for this exportfits async task for tm is str myhandle2 fosoooooooooooooooooooooooooooooooooooooooooooooooooooooos Print the image header print Imhead default imhead imagename clnimage mode summary imhead A summary of the cube will be seen in the logger f Get the cube statistics print Imstat cube default imstat imagename clnimage Do whole image box or you could stick to the cleanbox box 108 108 148 148 419 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS cubestats imstat Statistics will printed to the terminal and the output parameter will contain a dicti
439. nge 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 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 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 antenna 077 uvrange 0 15klambda solint 90 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 th
440. ning that you do not want to keep then use the ft task see 5 6 above which fills the MODEL_DATA column with the Fourier transform of the specified model or model image 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 238 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 5 9 2 5 9 Examples of Imaging Here are two examples of imaging BETA ALERT Note that the syntax has been changing recently and these may get out of date quickly 5 9 1 Spectral Line Imaging with NGC5921 The following is an example use of clean on the NGC5921 VLA data that we calibrated in the previous Chapter 4 8 1 This
441. nit should be K incorrect freqframe LSRK is really TOPO and reference frequency set to that of the first IF only The sd scantable freq_align does not yet work correctly Need to add to scantable stats maxord minord the ordinate channel vel freq of the max min 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 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 376 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 Need interactive region selection baseline fitting etc 6 sdcal Can crash if timeaverage True and or polaverage True and you give a list of scans that contain a combination of IFs We need to make the tools smarter about this but in the meantime you should restrict your scanlist and iflist to scans with the same set of IFs 7 sdfit Handles multiple IFs poorly a general problem currently in the package
442. nput visibility file tablein e re Input calibration table caltable a Output calibration table field 2 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 Note that smoothtime defines the width of the time window that is used for the smoothing CHAPTER 4 SYNTHESIS CALIBRATION 173 YU CASA Plotter Mar Regn Pa vna tocate 1 ou Moot Sa 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 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 An example using the smooth
443. ns 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 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 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 CHAPTER 4 SYNTHESIS CALIBRATION 151 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 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 calib
444. nt ImportUVFITS default importuvfits print Use importuvfits to read UVFITS and make an MS fitsfile datafile vis msfile async False saveinputs importuvfits prefix importuvfits saved importuvfits else Copy from msfile print MS Copy print Copying datafile to msfile os system cp r t datafilet msfile vis msfile print Listobs print List summary of MS listobs HHEEHHHHHHHEEHHHEHEHAEHHHEAHHAEHHEHAHRRE RHEE RRR 470 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 471 Begin Task listobs MeasurementSet Name home sandrock smyers Testing 2008 03 polcal_20080224 polcal_20080224 cband raw ms MS Version 2 Observer unavailable Project POLCA Observation VLA Data records 318708 Total integration time 9836 67 seconds Observed from 17 10 52 to 19 54 48 ObservationID 0 ArrayID 0 Date Timerange Scan FldId FieldName Spwlds 24 Feb 2008 17 10 51 7 17 12 08 3 1 O 1924 292 o 1 17 21 01 7 17 22 18 3 2 1 1743 038 o 1 17 34 31 7 17 35 48 3 3 2 2202 422 o 1 17 45 01 7 17 46 18 3 4 3 2253 161 o 1 17 55 11 7 17 56 28 3 5 4 2136 006 o 1 18 08 01 7 18 09 18 3 6 5 0137 331 o 1 18 22 11 7 18 23 58 3 7 6 2355 498 o 1 18 32 51 7 19 07 58 3 8 2 2202 422 o 1 19 20 51 7 19 22 18 3 9 5 0137 331 o 1 19 32 11 7 19 33 48 3 10 7 0319 415 o 1 19 42 01 7 19 43 18 3 11 8 0359 509 o 1
445. nt The off line std deviation 5 3f K off_stat stddev which should give The off line std deviation 0 047 K HHHHHHHHHHHHHHHHHAE EH On line Statistics HHHHHHHHHHHHHHHHHE HH HE 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 gt mean 0 22636228799819946 gt median 0 10317134857177734 min 0 13283586502075195 rms 0 35585442185401917 gt stddev 0 27503398060798645 sum 68 135047912597656 HH HH OF 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 351 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING which is the sum max print The estimated equivalent width 5 1f channels line_stat eqw 1 which gives The estimated equivalent width 73 3 channels PERRA AR ARRRRRRIRRARARARARARAAR Line Fitting HHHHHHHHHHHHHHHHHH HHH Now we are ready to do some line fitting Default the parameters default sdfit Set our input file sdfile sdusecase_orions_hc3n asap Stick to defaults fluxunit K specunit channel fluxunit specunit We will try auto fitting firs
446. nterfere with other tasks BETA also avoids crash on next importuvfits async True exportuvfits 251 Chapter 6 Image Analysis Once data has been calibrated and imaged in the case of synthesis data the resulting image or image cube must be Inside the Toolkit displayed or analyzed in order to extract quantitative infor Image analysis is handled in the ia mation such as statistics or moment images In addition tool Many options exist there in there need to be facilities for the coordinate conversion of cluding region statistics and image images for direct comparison We have assembled a skele math See below for more in ton of image analysis tasks for this release Many more are formation still under development The image analysis tasks are imhead summarize and manipulate the header information in a CASA image 6 2 imcontsub perform continuum subtraction on a spectral line image cube imfit image plane Gaussian component fitting immath perform mathematical operations on or between images 6 5 immoments compute the moments of an image cube 8 imstat calculate statistics on an image or part of an image regridimage regrid an image onto the coordinate system of another image importfits import a FITS image into a CASA image format table exportfits write out an image in FITS format There are other tasks which are useful d
447. nto 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 RHE machine gt home casa casainit sh or gt source home casa casainit csh 379 Appendix D Python and CASA CASA uses Python IPython and matplotlib within the package IPython is an enhanced inter active 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 ar
448. nts 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 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 then the output image names will be ngc5921 usecase moments integrated and ngc5921 usecase moments 1 respectively The axis parameter sets the axis along which the moment is collapsed or calculated This is a 0 based index Usually this is either the third axis 2 or fourth axis 3 axis of the image cube The planes parameter sets the range of image cube planes along the specified axis to include in the moment calculation BETA ALERT As of Patch 2 the planes parameter is now 0 based as per other specifications 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
449. nvoked 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 CHAPTER 3 DATA EXAMINATION AND EDITING 107 Amplitude of Observed Data 0 10 20 30 40 50 60 Channels 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 Interactive flagging on the principle of see it flag it is Hint possible on the X Y display of the data plotted by plotxy The user can use the cursor to mark one or more regions and then flag unflag or list the data that falls in these zones of the display In the plotting environments such as p
450. o o Lo o Lo Lo 0 Co Lo Lo Co Co o Lo Lo Lo o Co Lo Co Os Lo Co o Lo o Lo o Lo Co Lo Co Lo Lo Lo Lo o Lo o Lo Co Co 0 0 Lo 1 1 1 1 1 1 1 11 1 11 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 11 1 11 1 1 1 1 1 1 1 1 433 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 434 Fields 13 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 R L Antennas 27 HHH HHH HH HHH HH HHHHH H
451. o accumulation of 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 calib
452. o image eg I IV QU IQUV natural Weighting to apply to visibilities 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 The mode psfalg imagermode and weighting parameters open up other sub parameters 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 imagename field spw selectdata mode nchan start width niter gain threshold psfmode imagermode multiscale interactive gt ngc5921 usecase ms contsub Name of input visibility file ngc5921 usecase clean Pre name of output images 20 False gt channel 46 6000 0 1 8 0 clark False HHH HHH HHH HH HF Field Name Spectral windows channels is all Other data selection parameters Type of selection mfs channel velocity frequency Number of channels planes in output image first input channel to use Number of input channels to average Maximum number of iterations Loop gain for cleaning Flux level to stop cleaning method of PSF calculation to use during minor cycles Use csclean or mosaic If use psfmode set deconvolution scales pixels use interactive clean with GUI
453. obs 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 print a SS ne SS a 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 user_check raw_input Return to continue scriptin 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 437 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS print pr o A print Back to all data print Clean up remaining bad points 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 print A A A er ara 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 Pause script if you are running in scriptmode if scriptmode user_check raw_inp
454. ocumentation for this task project mysim name of simulated project modelimage mee image name to derive simulate visibilities complist ay componentlist table to derive simulated visibilities antennalist a2 antenna position ascii file direction J2000 19h00m00 40d00m00 mosaic center direction nmosx 1 number of pointings along x 377 APPENDIX B APPENDIX SIMULATION 378 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 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 start req 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 aL 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 currentl
455. 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 e plotcal Plot calibration solutions 4 5 1 polcal polarization calibration 4 4 5 131 CHAPTER 4 SYNTHESIS CALIBRATION 132 e setjy Compute the model visibility for a specified source flux density 4 3 4 e smoothcal Smooth calibration 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 4 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 63 e fringecal Experimental baseline based
456. of the viewer on an MS is detailed in 7 4 CHAPTER 1 INTRODUCTION 63 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 bandpass Solves for frequency dependent bandpass complex gains 4 4 2 e gaincal Solves for time dependent frequency independent complex gains 4 4 3 fluxscale Bootstraps the flux density scale from standard calibrators 4 4 4 e polcal polarization calibration 4 4 5 accum Accumulates incremental calibration solutions into a cumulative calibration table 4 5 4 e smoothcal Smooths calibration solutions derived from one or more sources 4 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
457. 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 364 e http wwwlocal gb nrao edu GBT DA gbtidl gbtidl_calibration pdf There are two basic 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 x sys cal 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 T v Toys x SSP ref v where sig 3 Sigcalon Si gcaloff ref 3 Sigcalon Sigcaloff 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
458. olarization 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 CHAPTER 1 INTRODUCTION 65 See for more on polarization calibration 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 calibrat
459. olumn 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 frequency This CHAPTER 4 SYNTHESIS CALIBRATION 163 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 e ay solint 7 inf combine gt scan
460. om left and the resulting uv coverage bottom right The commands to make these three panels respectively are 1 plotxy ngc5921 ms xaxis channel EAT eee ee ee Re en eee ee eee 108 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 g a warmer 115 through the data x columns of the MAIN table and y the rows or select a specific en Far errr 11 A 117 ee da ia 118 O atom and plotting tasks accum plotcal and snoothcal see Figure 12 E the accumulator only a single calibration type e g B G can be smoothed oral types are then input to applycal as shown in Figure il 13 w aD 4 3 Display of the amplitude upper and phase lower gain solutions for all antennas and polarizations in the ngc5921 post fluxscale table 4 4 Display of the amplitude upper phase middle and signal to noise ratio lower Note the falloff of the SNR at the band edges in the lower panel 170 5 Display of the amplitude of the bandpass B solutions Iteration over antennas was turned on using iteration antenna The first page is shown The user would E AA 171 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
461. ompt CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION CASA lt 1 gt 1s ngc5921 ms IPython system call ls F ngc5921 ms ANTENNA POLARIZATION table f1 table f3_TSM1 table DATA_DESCRIPTION PROCESSOR table f10 table f4 table FEED SORTED_TABLE table f10_TSM1 table f5 table FIELD SOURCE table f11 table f5_TSM1 table FLAG_CMD SPECTRAL_WINDOW table f11_TSM1 table f6 table HISTORY STATE table f2 table f6_TSMO table OBSERVATION table dat table f2_TSM1 table f7 POINTING table f0 table f3 table f7_TSM1 72 8 18_TSM1 9 19_TSM1 info lock 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 YI Data a Computer D A FEED FIELD FLAG_CMD HISTORY OBSERVATION POINTING POLARIZATION PROCESSOR SORTED_TABLE SOURCE SPECTRAL_WINDOW STATE Look in E3 Mome sandrock smyers Testing Patch3 N5921 ngc5921 y Goog E precon Files oftype Directories M 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 CH
462. on CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 293 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 data 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
463. on 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 Name of input VLA archive file s vis Name of output visibility file bandname aie VLA frequency band name gt obtain all bands in archive files frequencytol 150000 0 Frequency shift to define a unique spectral window Hz project ee Project name gt all projects in file starttime dl start time to search for data stoptime zoe 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 VAO4 or 4 for ant 4 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 TT 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
464. 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 7 all channels selectdata False No other selection gaincurve False No gaincurve at L band opacity 0 0 No troposphere bandtype B standard time binned B rather than BPOLY solint inf set solution interval arbitrarily long 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 CHAPTER 4 SYNTHESIS CALIBRATION 152 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 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
465. on 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 represent 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 F
466. onary of the statistics fosooooooooooooooooooooooooooooooooooooooooooooooooooooooo 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 Include all planes planes Output root name momfile prefix moments outfile momfile saveinputs immoments prefix immoments saved immoments momzeroimage momfile integrated momoneimage momfile weighted_coord It will have made the images _ ae a E E E E ngc5921 usecase moments integrated ngc5921 usecase moments weighted_coord f Get some statistics of the moment images print Imstat moments default imstat imagename momzeroimage momzerostats imstat 420 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS imagename momoneimage momonestats imstat 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 re
467. oooooooooooooooooooooooo Print the image header print Imhead default imhead imagename clnimage mode summary imhead A summary of the cube will be seen in the logger f Get the cube statistics print Imstat cube default 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 cubestats will contain a dictionary of the statistics fosooooooooooooooooooooooooooooooooooooooooooooooooooooooo Get some image moments print ImMoments default immoments imagename clnimage Do first and second moments moments 0 1 278 CHAPTER 6 IMAGE ANALYSIS Need to mask out noisy pixels currently done using hard global limits excludepix 100 0 009 Include all planes planes Output root name momfile prefix moments outfile momfile immoments momzeroimage momfile integrated momoneimage momfile weighted_coord It will have made the images ae ee a a O a O A a ngc5921 usecase moments integrated ngc5921 usecase moments weighted_coord f Get some statistics of
468. 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 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 ant
469. 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 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 336 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 of plot options spectra 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 pl
470. or 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 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 139 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
471. or field refant a Reference antenna name solnorm False Normalize average solution amplitudes to 1 0 bandtype 7B Type of bandpass solution B or BPOLY append 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 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 observatio
472. orm 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 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 chapter So the recommended procedure is as follows e Finish calibration as described in the previous chapter CHAPTER 4 SYNTHESIS CALIBRATION 187 e Use split to form a separate dataset e Use the invert or clean task on the split result to form an exploratory image that is useful for determining th
473. orm 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 BETA ALERT Unlike ordinary G a single common GSPLINE solution will be determined from data for all selected spectral windows and fields specified in the MS selection parameters and the resulting solution will be applicable to any field or spectral window in the same Measurement Set This behavior is similar to that of the BPOLY in bandpass If you do want separate spectral window solutions then you will have to do separate runs of gaincal An important consequence of this is that 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 th
474. ors 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 visibility 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 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 CHAPTER 1 INTRODUCTION 66 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 B 4 Most of these tasks are used to
475. ose 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 ox File Edit View Tools Export Help wks 20Pf R arise x 3 UVW FLAG LAG_CATEGOR WEIGHT SIGMA ANTENNAL ANTENNA2 ARRAY_ID DATA 3 0 o 0 0 2 63 Boolean 0 0 0 Boolean 23814 23814 0 0514344 0 1 1 0 0 nm mm o o 0 2 63 Boolean 0 0 0 Boolean 23814 23814 0 0514344 0 27 27 0 0 2 0 0 0 2 63 Boolean 0 0 0 Boolean 23814 23814 0 0514344 0 7 z 0 0 gt lawl o 0 0 2 63 Boolean 0 0 0 Boolean 23814 23814 0 0514344 0 2 2 0 0 El 0 0 0 2 63 Boolean 0 0 0 Boolean 23814 23814 0 0514344 0 11 11 0 0 s 0 0 0 2 63 Boolean 0 0 0 Boolean 23814 23814 0 0514344 0 17 17 0 0 o ik 6 o 0 0 2 63 Boolean 0 0 0 Boolean 23814 23814 0 0514344 0 9 9 0 0 3 al o 0 0 2 63 Boolean 0 0 0 Boolean 23814 23814 0 0514344 0 19 19 0 0 7 dl 0 0 0 2 63 Boolean 0 0 0 Boolean 23814 23814 0 0514344 0 20 20 0 0 pm o 0 0 2 63 Boolean 0 0 0 Boolean 23814 23814 0 0514344 0 18 18 0 0 EL 1 Restore Columns Resize Headers PAGE NAVIGATION IN lt lt Jt 123 gt gt Loading 1000 rows Figure 3 7 browsetable The
476. otal 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 FTSDB u v 3 The Fourier transform of the 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 Advice Note that if you are feathering large images be advised to have the number of pixels alo
477. ote that regardless 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 12 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 For example restoringbeam 10arcsec circular Gaussian FWHM 10 restoringbeam 10 0 5 0 45 0deg 10 x5 at PA 45 degrees 5 3 13 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 14 Example Interactive Cleani
478. ots plotxy n5921 ms u v plot uv coverage for n5921 ms data set P field 0 plot only first field datacolumn corrected plot corrected data subplot 224 plot to the lower right in a 2x2 grid plotcolor over ride default plot color plotsymbol b blue somewhat larger dots NOTE You can change the gridding and panel size by manipulating the ny x nx grid See also 3 4 3 1 above and Figure 3 2 for an example of channel averaging using iteration and subplot 3 4 4 Averaging in plotxy The averaging parameters and sub parameters are averagemode vector Select averaging type vector scalar timebin 20 Length of time interval in seconds to average crossscans e False Have time averaging cross scan boundaries width 21 Number of channels to average 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 imaginary 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 i
479. otting 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 linedop doppler offset for line catalog plotting spectral plotting options float doppler velocity km s default 0 0 example linedop 30 0 histogram plot histogram options bool True False default False APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 337 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
480. ou 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 system 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 Fe IDEAL Vij Jij Vij where Vij represents the observed visibility po eeu represents the corresponding ideal visibilities and Jij represents the accumulation of all corrup
481. ound Color o e e 298 a a A A ee ee Be 300 7 4 1 Data Display Options Panel for Measurement Sets 300 og te ts eb a ee ok tee le 302 i AE a A 302 E ca o de a e 304 LR ae a Ra 304 7 4 1 5 MS Options Advanced 000002002 eee 308 7 4 1 6 MS Options Apply Button 308 mek be Sei an Sra Ses Gee Be es epee eee ee eee 309 311 e tte E 311 pg a A ek ae wk Wa A Ge a ee eS 311 Ada ASSIEME A E lt P ate oe eee ad Bk eS a 312 me Ra gee wea He fe cies sae sas Ge Ee Gh we cee RN 312 age Grace oe nee ei et es Se Stee sree F 313 a a ee ee ee eee ae 313 teh dap 6 ao mau ak nap oes 314 oe Ae es es a e ae yee GO ee 316 bhad amp 32h deck t we a ao dt et bee Gh eS 316 Ad l2 SASMOOtH s ssia eR oe a a ew eea A 319 SERED ERE Ba Seb eda be eae bee RES 321 ADA sdcalls 2 ss 6 4 2 2d oe PR ee ee es Re ee eee ESS 323 IA its a kok doe a a eo ee a Re i aia da Sea 327 AAA 329 AAA A ey ee tee ee ee Poe Bek ee Be cat Y 330 FAA ae ek ae ee ee te A ek ee ee ee 333 A 2 1 9 Sdplot cti Boe oe Ae we ee ee OR S 334 a ae ih a ae GAA Gu al Se ce WS A tae ie es SG A 337 Doh GW he a daly BAG A a HE a ia ra 339 Chee eke SR 8G ee a Be Ne ae PR hee es 339 ee EAE 34 a res ad a y 354 E Ge gee Cede Ge Seve A 355 WOR paai BR RA GAG a ee EE Oe RE we ee we 356 O 358 A331 Data election e 359 A 3 3 2 State Information 0 0 0 00000 ee eee PA 33 3 Maski ca s
482. 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 interpolation 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 148 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 refant and minsnr The parameters controlling common aspects of the solution are solint inf Solution interval combine aa Data axes which to combine for solve scan spw and or field refant 23 Reference antenna name no explicit reference minsnr 0 0 Reject solutions below this SN
483. plotcal polcal d reim saved plotcal O xaxis antenna yaxis amp figfile caltable plot antamp png print Plotting calibration to file figfile saveinputs plotcal prefixt plotcal polcal d antamp saved plotcal xaxis antenna yaxis phase figfile caltable plot antphase png print Plotting calibration to file figfile saveinputs plotcal prefixt plotcal polcal d antphase saved 480 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 481 plotcal O xaxis antenna yaxis snr figfile caltable plot antsnr png print Plotting calibration to file figfile saveinputs plotcal prefixt plotcal polcal d antsnr saved plotcal O dopolx False if pcalmodel has_key polxfield dopolx True if setpolmodel and not polcalmode count X gt 0 Now run setjy if we havent already print Setjy default setjy vis msfile print Use setjy to set IQU fluxes of polxfield field polxfield for spw in usespwlist fluxdensity polmodel field spw flux saveinputs setjy prefixt setjy polspw spwt saved setjyQ o oo eo oo ee o ooo oo e o o o o Polarization X term calibration print PolCal default polcal print Polarization R L Phase Calibration linear approx vis
484. 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 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 followed 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 CHAPT
485. 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 Output table caltable xtable previously set with setjy APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS HH HH HHH HH HHH HH HHH HH HH HH H HH OH OH 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 interpolated caltable caltable atable print Output cumulative gain table will be atable linear interpolation interp linear make 10s entries accumtime 10 0 accum NOTE bypassing this during testing atable ftable 447 APPENDIX F
486. previous calibrations see below may or may not have been done in AIPS and applied or not before export CHAPTER 4 SYNTHESIS CALIBRATION 137 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 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 sc
487. produce a calibration table of type D CHAPTER 4 SYNTHESIS CALIBRATION 162 X Solve only for the position angle correction best to use 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 suffic
488. r 0 1 gain 0 1 Set the output image size and cell size arcsec imsize 256 256 Do a simple Clark 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 imsize 512 512 Pixel size 15 arcsec for this data 1 3 of 45 beam VLA D config L band cell 15 15 417 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 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 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 OF It will have made the images ngc5921 usecase clean image ngc5921 usecase clean model ngc5921 usecase clean residual
489. r 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 3 match field ID 3 and not select field named 3C286 field 3 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 mentioned field names also correspond to field ID 3 HH H 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 fol
490. r 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 g lt H n 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 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
491. rameter 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 spw 1 10730 select channels 10 30 of spw 1 20 5755 3 1D 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 hands 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 pola
492. ration 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 of 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 1 5 3 4 P
493. ration Here is an example using the Jupiter VLA 6m continuum imaging example see 8 below Put clean model into MODEL_DATA column ft vis jupiter6cm usecase split ms model jupiter6cm usecase cleani model Phase only self cal on 10s timescales gaincal vis jupiter6cm usecase split ms caltable jupiter6cm usecase phasecali CHAPTER 4 SYNTHESIS CALIBRATION 178 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 phasecal1 incrtable jupiter6cm usecase scancall caltable jupiter6cm usecase selfcali interp linear Plot this up plo
494. rators 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 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
495. re The inputs for flagmanager are vis 22 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 main table Original Original flags at import into CASA flagautocorr flagged autocorr xy lags 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 save Flag management operation list save restore delete versionname ae Name of flag version no spaces comment 7 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 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 flag
496. rection SPW O R L Phase Correction Final Stats Source 0137 331 spw 0 CASA T 5 spw 1 CASA I 5 Source 2202 422 spw 0 CASA I 2 spw 1 CASA I 2 Source 1743 038 spw 0 CASA T 5 spw 1 CASA I 5 Source 1924 292 spw 0 CASA I 8 spw 1 CASA I 8 Source 2136 006 spw 0 CASA I 10 spw 1 CASA I 10 Source 2253 161 spw 0 CASA I 9 096 spw 1 CASA I 9 Source 2355 498 spw O CASA I 1 spw 1 CASA I 1 Source 0319 415 SPW 320 362 570 571 545 543 243 184 491 521 113 340 355 1 U 229 236 185 188 073 078 058 073 153 145 527 524 003 003 deg deg H Il 0430 0439 0719 0733 0131 0141 0070 0089 0146 0138 0578 0576 0022 0023 gt lt spw s AIPS I 7 3f P 7 3f F spwid iflx pflx fflx rlaips_deg spw 4s AIPS I 7 3f P spwid iflx pflx fflx rlaips_deg 47 3f F 148 148 57 53 12 27 171 160 AS 162 151 7 4f X 50 17 71 43 69 38 19 61 12 42 12 58 08 deg deg deg deg deg deg deg deg deg deg deg deg deg deg 492 7 2 deg 7 4 X 17 2f deg YN APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 493 spw 0 CASA I 14 147 P 0 041 F 0 0029 X 79 67 deg spw 1 CASA I 14 229 P 0 043 F 0 0030 X 130 02 deg Source 0359 509 spw 0 C
497. rite your CASA image to a FITS file that other packages can read and to import existing FITS files into CASA as an image 6 9 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 aa Name of input CASA image fitsimage fa Name of output FITS image velocity False Prefer velocity for spectral axis optical True Prefer optical velocity definition bitpix 32 Bits per pixel 32 floating point 16 integer minpix O Minimum pixel value maxpix z 0 Maximum pixel value overwrite False Overwrite pre existing output file dropdeg False Drop degenerate axes deglast False Put degenerate axes last in header async S True if True run in the background Recommended 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 CHAPTER 6 IMAGE ANALYSIS 274 6 9 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
498. rization stokes IQUV All Stokes imaging CHAPTER 5 SYNTHESIS IMAGING 214 are common choices The output image will have planes along the polarization axis corre sponding to the chosen Stokes parameters Ifthe stokes parameter is being input to deconvolution tasks such as clean then with the exception of alg hogbom see 5 3 1 the chosen Stokes images will be deconvolved jointly rather than sequentially as in AIPS BETA ALERT The stokes QU for linear polarization only is not currently an option There is also no option to make single polarization product e g separate RR and LL or XX and YY images from data with dual polarizations available You currently would have to make stokes I images from data with a single polarization product e g RR or LL split out 5 2 10 Parameter uvfilter 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 uvfilter parameter expands the menu upon setting uvfilter True to reveal the following sub parameters uvfilter True Apply additional filtering uv tapering of the visibilities uvfilterbmaj 1 0 Major axis of filter arcseconds uvfilterbmin 1 0 Minor axis of filter arcseconds uvfilterbpa
499. rm for gaintables s gaincurve False Apply internal VLA antenna gain curve correction opacity 0 0 Opacity correction to apply nepers async 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
500. row PROCESSOR lt empty gt CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 84 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 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 will 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 concat Concatenate two or more visibility data sets vis Name of input visibility files to be concatenated concatvis oe Name of output visibility file freqtol 25 Frequency tolerance for considering data as the same spwid dirtol E E Direction tolerance for considering data as the same field 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
501. rs Nov07 casapy log 0X File Edit View Basa B P search Message Q Fiter Time gt 2g Time Priority Origin Message Tue Nov 6 18 25 26 2007 INFO2 plotxy MsPL May need to read 126720 values from disk Tue Nov 6 18 25 26 2007 INFO2 plotxy Tabl Preparing the plotter Tue Nov 6 18 25 28 2007 INFO2 plotxy TPP1 Number of points being plotted 12256 Tue Nov 6 18 25 28 2007 INFO2 plotxy TPPL Number of points NOT being plotted 13088 Tue Nov 6 18 25 29 2007 INFO Tue Nov 6 18 25 29 2007 INFO Tue Nov 6 18 25 29 2007 INFO End Task plotxy sedeeeseeeaseseeseseeseseneesteeesteeaseseaeeee Tue Nov 6 18 25 55 2007 INFO2 plotxy Tabl Preparing the plotter Tue Nov 6 18 25 56 2007 INFO2 plotxy TPPL Number of points being plotted 9344 Tue Nov 6 18 25 56 2007 INFO2 plotxy TPPL Number of points NOT being plotted 13184 Tue Nov 6 18 26 04 2007 INFO2 plotxy Tabl Preparing the plotter Tue Nov 6 18 26 05 2007 INFO2 plotxy TPP1 Number of points being plotted 9664 Tue Nov 6 18 26 05 2007 INFO2 plotxy TPPL Number of points NOT being plotted Requested JD56069 Tue Nov 6 21 41 43 2007 WARN plotxy Meas Calculations will pr gt No requested dUT1 data available from IERS tables Tue Nov 6 21 41 43 2007 WARN plotxy Meas Proceeding with probably less precision Tue Nov 6 21 41 43 2007 INFO plotxy imag Opened image m51_21 input_model Tue Nov 6 21 41 43 2007 INFO plotxy imag Crea
502. rue run in the background prompt is freed The algorithm alg options are clark hogbom multiscale or mem The multiscale and mem options will open the usual set of sub parameters for these methods 5 8 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 8 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 clea
503. run applycal to get new calibration if you have changed the tables or want to apply them differently CHAPTER 4 SYNTHESIS CALIBRATION 183 There is only a single input to clearcal clearcal Re initializes calibration for an ms vis 47 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 2 Name of input visibility file outputvis 22 Name of output visibility file field fs Field name list spw a Spectral window identifier width 1 number of channel to average to form one output channel antenna Antenna selection timebin tis time averaging of data timerange i time range for subset of data datacolumn corrected which column to split data corrected model async False if True run in the background prompt is freed Usually you will run split with datacolumn corrected as previous operations e g applycal will have placed the calibrated data 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 ng
504. s 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 CHAPTER 3 DATA EXAMINATION AND EDITING 112 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 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 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 3 5 Non Interactive Flagging using flagdata Task flagdata will flag the visibility data
505. s 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 z ae 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 6 2 1 Examples for imhead For example CASA lt 1 gt imhead ngc5921 usecase clean image summary Summary information is listed in logger prints in the logger Opened image ngc5921 usecase clean image Image name ngc5921 usecase clean image Object name Image type PagedImage Image quantity Intensity Pixel mask s None Region s None Image units Jy beam Restoring Beam 51 5254 arcsec 45 5987 arcsec 14 6417 deg Direction reference J2000 CHAPTER 6 IMAGE ANALYSIS 257 Spectral reference LSRK Velocity type RADIO Rest frequency 1 42041e 09 Hz Pointing center 15 22 00 000000 05 04 00 000000 Telescope VLA Observer TEST Date observation 1995 04 13 00 00 00 Axis Coord Type Name
506. s 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 system 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
507. s R_OK os ctermid os SEEK_CUR os curdir os SEEK_END os defpath os 388 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 1chown 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 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 WIFCONTINUE
508. s get put summary list stats oy 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 Ak observer TEST CASA lt 7 gt print hdvalue TEST You can set the values for these keywords using mode put This opens sub parameters mode put Options get put summary list stats hditem ex 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 telescope VLA observer CASA CHAPTER 6 IMAGE ANALYSIS 259 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
509. s FITS 6 9 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 contents 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 8 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 In CASA there is a standard syntax for selection of data that is employed by multiple tasks This is described in 2 5 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 e exportfits export a CASA image table as FITS 70 CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 71 2 1 CASA Measurement Sets Data is handled in CASA via the table system In particular visibility data ar
510. s Tables jinen Input dataset e g from g gaincal self cal models 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 are 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
511. s Testing 2 008 03 ngc5 92 1_regression ngc5 921 ms FLAG_C Subtable has no rows table keywords FIELD Table nome sandrock smyers Testing 2 008 03 ngc5 92 1_regression ngc5 92 1 ms FIELD Subtable has 3 rows HISTORY Table nome sandrock smyers Testing 2 008 03 ngc5 921_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 92 1_regression ngc5921 ms POINTING Subtable has no rows field keywords POLARIZATION Table home 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 92 1_regression ngc5921 ms PROCE Subtable has no rows SPECTRAL_WINDOW Table nome 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 nome sandrock smyers Testing 2 008 03 ngc5 921_regression ngc5921 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 3 7 Examples of Data Display and Flagging HHEFHHHHHEHHAEHHEEHHEAHHHAEHEHEEE HAE HEEHHRHEHHEE HRA HHA E
512. s an input to bandpass because in general the phase towards two widely separated sources will not be sufficiently similar to combine them 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 gt 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 H 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 Note that all available spectral windows will be used to obtain a single solution spanning them all If separate solutions for each spectral window are desired solve for each separately e g if there are 3 spectral windows 0 1 2 bandpass vis data ms caltable cal BPOLY 0 spw 0 2756 field 0 bandtype BPOLY degamp 5 degph
513. s flagautocorr flags Original flags xyflags FLAG_VERSION_LIST CHAPTER 3 DATA EXAMINATION AND EDITING 97 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 we Name of flag version no spaces merge replace Merge option replace and or The merge sub parameter will control the action 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 a 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 2 Name of input visibility file MS To use it just set and go CASA lt 90 gt vis jupiter6cm us
514. s of CASA Image Analysis Here are some examples of image analysis BETA ALERT Note that the syntax has been changing recently and these may get out of date quickly 6 11 1 Spectral Line Image Analysis with NGC5921 The following is an example use of the image analysis tasks on the NGC5921 VLA data that we calibrated and imaged in the previous chapters 4 8 1 5 9 1 This assumes you have already run those and have all of the defined variables in your session as well as the final split calibrated ms files and image cubes on disk The full NGC5921 example script can be found in Appendix F 1 HHEFHHHHHHHEEHHHEHHEEHEHHEEHHEEE RORRERORARRORO RO RERRO RO PERERERO PORRO RARA RO RARER ROA RRR RARA A ARRE Image Analysis Script for NGC 5921 Updated STM 2008 03 25 Beta Patch 1 0 clean gt lt prefix gt clean image lt prefix gt clean model lt prefix gt clean residual v HHEFHHHHHHHEEHHAEHHEAHEHHEHHHREE HEHEHE EHRHREHEHREE HAHAHA RO RORORRO RRA R RARA ARRE Set up some useful variables The prefix to use for all output files prefix ngc5921 usecase The split MS filename msfile prefix split ms Clean will have made the images ngc5921 usecase clean image CHAPTER 6 IMAGE ANALYSIS ngc5921 usecase clean model ngc5921 usecase clean residual ngc5921 usecase clean boxclean mask clnimage imname image fosooooooooooooooooooooooooooooooo
515. s plot plotfile sdusecase_orions_hc3n eps sdplot HHHHHHHHHHHHHHHHHHHHHHHHHH Off line Statistics HHHHHHHHHHHHHHHHHEH EH 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 DR 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 You see that 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 mean 0 0030361821409314871 median 0 0032975673675537109 min 0 15754437446594238 350 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING rms 0 047580458223819733 stddev 0 047495327889919281 sum 6 0754003524780273 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 which should give The off line std deviation 0 0474953278899 or better formatted using Python I O formatting pri
516. s 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 i is given by 5 1 Wi Wi ad gt 7 where the data weight w is determined from o is the rms noise on visibility 7 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 that 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
517. s 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 iteration antenna plotxy O CHAPTER 3 DATA EXAMINATION AND EDITING 111 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 xaxis time spw 71 correlation 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 Go back and clean up xaxi
518. s well as the color from the matplotlib online documentation e g type pl plot for help The following line styles are supported solid line dashed line dash dot line dotted line points pixels circle symbols 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 symbols rotated hexagon symbols pentagon symbols vertical line symbols horizontal line symbols steps use gnuplot style steps kwarg only o gt z0 TyPPWNHNHRAKAOHM H VAS CHAPTER 3 DATA EXAMINATION AND EDITING 105 The following color abbreviations are supported blue green red cyan magenta yellow black w white 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 WHS BAKO Oo 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 w
519. s whether blcal solves for gain freqdep True or bandpass freqdep False style calibration CHAPTER 4 SYNTHESIS CALIBRATION 165 Other parameters are the same as in other calibration tasks These common calibration parameters are described in 8 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 e Name of output bandpass calibration table field nd Select data based on field name or index spw dd Select data based on spectral window selectdata False Activate data selection details gaincurve False Apply VLA antenna gain curve correction opacity 0 0 Opacity correction to apply nepers gaintable z el Gain calibration solutions to apply gainfield ae solint 0 0 Solution interval sec refant se Reference antenna async False if
520. s_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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING Hexecfile sdcal last HHEHHHHHHHHHHHHHHHHHHHHHH HS List data HHEHHHHHHHHHHHHHHHHHHHHHH HS List the contents of the calibrated dataset Set the input to the just created file sdfile outfile listfile sdlist You should see Se ee 22 ee ee ee a ea Ss a a a ee a eee ae a ea a ee a Scan Table Summary i ca ee ac a cs es ac a a a a a a ec aa ca a a em a ee 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 Off0n 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 i sc i a a ce a a
521. 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 antenna spw APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 440 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 33222 E 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 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 Es Use Flagmanager to list all saved
522. scopeparm if GBT or AT telescopes 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 fluxunit units for line flux options K Jy default keep current fluxunit WARNING For GBT data 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 322 example 15 this selection is in addition to scanlist field and pollist
523. se e e ee 22 1 1 1 What s New in Patch 2 e e eo 22 12 CASA Basics Information for First Time Users o 23 k aoma a A ge bee ale be a bbe REE g 24 1 2 1 1 Environment Variables 0 0 00 0020 e 24 1 2 1 2 Whereis CASA o a 25 A ae Be ee toe E a ee ee ee ee 25 ee set ere tee BO ee Pe eee ee ee he a 26 1 2 4 What happens if something goes wrong 0 0 080204 26 sap Rites Gente Vale Bowe age gp ate 8 age dd E 27 1 2 6 What happens if CASA crashes 0 00 00 00000 0 eee eee 27 RAGE ie on 2 a ed ee ee oe oh we 27 L271 Variables s 4 4 24 Sed RRA a ee a ee es 28 1 2 7 2 Lists and Ranges ee 28 WAREZ A 28 1 2 7 4 IndemtatioMl ee 29 1 2 7 5 System shell access 2 2 o e e 29 E Ear EG goad bop Bee E wae aes 29 Mee BRB kone Bk eR ek ee a ee de eee ae 30 1 2 8 TAB key rc a 4 4 Bote be hk heed ee eee a oo ek eS 30 1 2 3 2 help lt taskname gt 00 00 0000 00000 30 1 2 8 3 help and PAGER 0 0 00 eee ee ee 32 1 2 8 4 help par lt parametel gt 00 33 12 8 0 Python Help ss ses ers e ew EO Se oO Rs 33 E chet Pe eee ede Be ee 34 13 1 What Tasks are Available o 0 020002 2 eee ee 34 be Rowe See Eh Age ge eb age ee ee E 38 1 3 2 1 Aborting Synchronous Tasks o o 39 A ele Oo es
524. se Split out continuum continuum subtracted data async False BETA ALERT The spw parameter can currently only be used to specify the Spectral Window not channelization For now we provide the channels parameter see the example below 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 syntax and subtract this model from all channels specified in spw 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 line 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 f
525. se of the continuum fit model default subtract example fitmode replace Options gt subtract store fitted continuum model in MODEL and subtract this continuum from data in CORRECTED to produce line emission in CORRECTED CHAPTER 1 INTRODUCTION 32 gt model store fit continuum model in MODEL but do not change data in CORRECTED gt replace replace CORRECTED with continuum mode fit splitdata Split out continuum and continuum subtracted line data default False example splitdata True The continuum data will be placed in vis cont The continuum subtracted data will be placed in vis contsub async Run task in a separate process return CASA prompt default False example async True You can also get the short help for a CASA tool method by typing help tool method CASA lt 46 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 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 variable PAGER less setenv PAGER less in csh then typing help lt taskname gt wi
526. se 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 CHAPTER 1 INTRODUCTION 44 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 clean task type CASA lt 12 gt default clean To inspect a single parameter value just type it at the command line CASA lt 16 gt alg type alg to see the what the algorithm keyword is set to Out 16 clark CASA tells you it is set to use the Clark algorithm 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 the 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 1 3 5 1 The scope of parameters in CASA All task parameters have global scope within CASA the parameter values are common to all tasks and also at the Advanced Tip CASA command
527. 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 CHAPTER 3 DATA EXAMINATION AND EDITING 113 e times timerange or scan numbers scan 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 ed Name of input visibility file antenna va antenna baseline spw me spectral window frequency channel correlation a Select data based on correlation field md field names or indices uvrange gt gt uv range def meters timerange on time range scan e vs scan number feed a feed number NOT ENABLED array 2 ds array mode manualflag Mode manualflag autoflag summary quack 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 gt DATA Data column to use for clipping clipoutside True Clip outside the range or within it The default flagging mode is m
528. set 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 will 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 237 5 7 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 gt 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 T
529. sfer 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 ca1 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 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 CHAPTER 4 SYNTHESIS CALIBRATION 159 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 eit
530. sion ax cjoe eooo fe nom san 0 na C Bx X ngc5921 usecase clean residual 4 689e 03 Jy beam 15 22 52 063 04 52 20 463 I 1 490195e 03 km s x ngc5921 usecase clean_interactive mask contour 0 000e 00 15 22 52 063 04 52 20 463 I 1 490195e 03 km s Figure 5 5 Screen shot of the interactive clean window during deconvolution of the NGC5921 spectral line dataset Note the new box at the top second from left where the Channels A11 toggle can be set unset We have just used the Polygon tool to draw a mask region around the emission in this channel The Channels A11 toggle is unset so the mask will apply to this channel only 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 CHAPTER 5 SYNTHESIS IMAGING 233 spw 072 field 076 cell 1 1 imsize 256 256 stokes I psfalg clark niter 500 imagermode mosaic scaletype SAULT cyclefactor 0 1 5 4 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 t
531. sk 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 CHAPTER 6 IMAGE ANALYSIS 266 For more on masks as used in LEL see http aips2 nrao edu docs notes 223 223 html 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 A useful product to compute is to collapse the cube into a moment image by taking a linear combination of the individual planes N Malta yi See Es Yi Vk 6 1 k for pixel and channel k in the cube 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 calculatio
532. specified channels The mask is stored in a simple Python variable a list and so may be manipulated using an Python facilities 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 possible 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 362 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 for
533. spectral windows successfully copied them into the measurement set The dataset has 4 polarizations successfully copied them into the measurement set The dataset has 41 data descriptions successfully copied them into the measurement set The dataset has 125 feeds successfully copied them into the measurement set The dataset has 2 fields successfully copied them into the measurement set The dataset has 0 flags The dataset has 0 historys The dataset has 1 execBlock s successfully copied them into the measurement set The dataset has 12 pointings successfully copied them into the measurement set The dataset has 3 processors successfully copied them into the measurement set The dataset has 72 sources successfully copied them into the measurement set The dataset has 3 states The dataset has 132 calDevices The dataset has 72 mains Processing row 0 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 clear 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
534. spwref spwmax APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS srcmodel spwid spwmodel Done with spw clnmodel src srcmodel Done with srcs print Results for prefixt print we 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 if polmodel has_key polxfield Check RL phase offset on X calibrator print R L phase residual from image of polxfield print print gt gt logfile R L phase residual from image of polxfield print gt gt logfile src polxfield rlcor for spwid in usespwlist ipol clnmodel src spwid flux 1 qpol clnmodel src spwid f1ux gt Q upol clnmodel src spwid flux U vpol clnmodel src spwid flux V rlpd atan2 upol qpol rlpdcal polmodel src spwid poln rlpd rlpcor rlpdcal rlpd 2 scor sin rlpcor ccor cos rlpcor rlpcor atan2 scor ccor rlcor spwid rlpcor rlpcor_deg rlpcor 180 0 p1 pi print R L Phase Correction SPW spwid 7 2f deg rlpcor_deg print gt gt logfile R L Phase Correction SPW spwid 7 2f deg rlpcor_deg 490 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 491 Loop over sources and spw print print Final
535. ss scan boundaries Number of channels to average Panel number on display screen yxn Overplot values on current plot if possible Show flagged data Plot separate panels by field antenna baseline scan feed pylab plot symbol pylab plot color Specifies which points are connected with lines Plot in different colors Options none both chan corr Show plot on gui no plot hardcopy otherwise supply name The range of data to be plotted see help for times Select additional plotting options e g fontsize title etc 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 l 2 2 2 These are described in 2 5 Averaging is controlled with the set of parameters averagemode timebin crossscans width i d i 2 vector 20 False 24 HE HH HH H OH OF HH H Other data selection parameters antenna baselines gt all antenna 3 VA04 time range gt all correlations default scan numbers Not yet
536. ssian 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 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 1 some 2 more lt 0 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 321 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 sdfile name of input SD dataset telescopeparm the telescope name or characteristics options str name or list list of gain info default none set example tele
537. st default no output file example mysd_summary txt overwrite overwrite the output file if already exists options bool True False default False 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 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 334 Note that if your PAGER environment variable is set to 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 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 it fixes default fluxunit to K first then convert to a new fluxunit telescopeparm 104 9 0
538. starlata bella bas sea tg ep 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 1larcmin larcmin If a single value is given then square pixels of that size are assumed 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 CHAPTER 5 SYNTHESIS IMAGING 210 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 imagename 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 with names ngc5921 clean ngc5921 residual and ngc5921 model will be created 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 st
539. statistics 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 461 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 462 immath O print Created Q image outfile 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 APPENDIX F APPENDIX ANNOTATED
540. stem See Appendix C for instructions on how to obtain and install CASA CHAPTER 1 INTRODUCTION 24 1 2 1 Before Starting CASA If you have done a default installation under Linux using rpms or on the 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 20 0 4769 002 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
541. stro calib polar 2004 pcalfield pcalfield 0 1 0 0 072 55 00 pealfield 1 1 0 0 072 55 00 pcalmodel 2202 422 pcalfield Set the polmodel from pcalmodel print Setting up Polarization models polmodel for field in pcalmodel keys spwmodel the RLPD is atan2 U Q so Q I P I cos RLPD U I P I sin RLPD for spw in usespwlist ipol pcalmodel field spw 0 fpol pcalmodel field spw 1 rlpd_deg pcalmodel field spw 2 rlpd rlpd_deg pl pi 180 0 ppol ipol fpol qpol ppol cos rlpd upol ppol sin rlpd fluxdensity ipol qpol upol 0 0 pmodel pmodel rlpd_deg rlpd_deg pmodel rlpd rlpd pmodel fpol fpol fmodel fmodel flux fluxdensity fmodel poln pmodel spwmodel spw fmodel polmodel field spwmodel print Created polmodel dictionary print polmodel if importmode vla 469 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS Import the data from VLA Export to MS print ImportVLA default importvla print Use importvla to read VLA Export and make an MS archivefiles datafile vis msfile exportband autocorr False bandname antnamescheme new project exportproject saveinputs importvla prefix importvla saved importvla elif importmode fits Import the data from VLA Export to MS pri
542. 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 out 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 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 CHAPTER 1 INTRODUCTION 28 1 2 7 1 Variables Python variables are set using the lt paramete
543. 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 6 9 for more information 1 5 1 4 Concatenation of multiple MS Once you have loaded data into measurement sets on disk you can 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 CHAPTER 1 INTRODUCTION 62 1 5 2 Data Examination Editing and Flagging The main data examination and flagging tasks are e listobs summarize the contents of a MS 8 2 3 e flagmanager save and manage versions of the flagging entries in the measurement set B 2 e flagautocorr non interactive flagging of auto correlations 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
544. t 0 5 No clean mask or box mask Use interactive clean mode interactive True Moderate number of iter per interactive cycle npercycle 100 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 100 iterations When done click Stop HHH HH FH Set up variables clnimagel imnamei image clnmodeli imnameit model clnresidi imnameit residual clnmaski imnameit clean_interactive mask T cl SN ss ss ss ec a ee os SS Look at this in viewer viewer clnimagel image 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 see stuff like this in the terminal HH H H OF CHAPTER 5 SYNTHESIS IMAGING jupiter6cm usecase cleani image n Std Dev RMS 4712 0 003914 0 003927 Flux Med Dev IntQt1Rng 0 09417 0 002646 0 005294 On Jupiter n Std Dev RMS 3640 0 1007 0 1027 Flux Med Dev IntQt1Rng 4 592 0 003239 0 007120 HHH H
545. t fitmode auto A single Gaussian nfit 1 Leave the auto parameters to their defaults for now except ignore the edge channels edge 1000 Lets see a plot while doing this plotlevel 1 Save the fit output in a file fitfile sdusecase_orions_hc3n fit Go ahead and do the fit fit_stat sdfit If you had verbose mode on you probably saw something like 0 peak 0 811 K centre 4091 041 channel FWHM 72 900 channel area 62 918 K channel 302 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 353 The fit is output in the dictionary fit_stat cent 4091 04052734375 0 72398632764816284 fwhm 72 899894714355469 1 7048574686050415 nfit 1 peak 0 81080442667007446 0 016420882195234299 So you can write them out or test them print The line fit parameters were print maximum 6 3f 7 6 3f K A 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 For some reason we need
546. t 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 CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 290 7 3 Viewing 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 4 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 Starting the c
547. t 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 fo ooooooooooooooooooooooooooooooooooooooooooooooooooooooo Data Examination and Flagging fosooooooooooooooooooooooooooooooooooooooooooooooooooooooo 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 Plot amplitude vs uvdist xaxis uvdist yaxis amp APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS multicolor both Use the field name as the title selectplot True title field iteration plotxy O print Print 3 gt 9 9 2 SSeS aa 221292299449 SS print Plotxy print Showing 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 ca
548. t distinct version if any 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 CHAPTER 4 SYNTHESIS CALIBRATION 175 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
549. t in VLA data ALMA NO PHAS CORR Bool Ne Nf data that has not been phase corrected Not in VLA data ALMA PHAS CORR FLAG ROW Bool Ne Ny 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 specification 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 exportuv its 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 75 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
550. t one or more box regions in the input images chans gt gt Select the channel spectral range stokes dl Stokes params to image I IV IQU IQUV async False Tf 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 CHAPTER 6 IMAGE ANALYSIS 261 Region selection is carried out through the region and box parameters See 8 for more on region 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 outfil
551. t 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 CHAPTER 1 INTRODUCTION 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 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 Image Analysis Simulation Single Dish imhead almasimmos sdaverage immath sdbaseline immoments sdcal imstat sdcoadd regridimage sdfit sdflag sdlist sdplot sdsave sdscale sdsmooth sdsdtat The tasks with name in parentheses are experimental Typing taskhelp provides a one line description of all available tasks CASA lt 5 gt taskhelp Available tasks accum Accumulate calibration solutions into a cumulative table 35 CHAPTER 1 INTRODUCTION 36 almasi
552. t 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 140 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 Summary 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
553. t 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 no cleanbox interactive version currently available You have to run clean with cleanbox interactive to generate a mask graphically 5 6 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 ft 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 8 below The inputs for ft are vis q Name of input visibility file fieldid O Field index identifier field ae Field name list model ae Name of input model image complist ve 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 data
554. t uvfits vis splitms fitsfile srcuvfits Since this is a split dataset the calibrated data is in the DATA column already datacolumn data Write as a multisource UVFITS with SU table even though it will have only one field in it multisource True Run asynchronously so as not to interfere with other tasks BETA also avoids crash on next importuvfits async True 201 CHAPTER 4 SYNTHESIS CALIBRATION exportuvfits UV plane continuum subtraction on the target this will update the CORRECTED_DATA column print UV Continuum Subtract default uvcontsub vis msfile Pick off N5921 field N5921 Use channels 4 6 and 50 59 for continuum fitspw 0 476 50759 Apply to all of spw 0 spw 70 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 uvcontsub You will see it made two new MS ngc5921 usecase ms cont ngc5921 usecase ms contsub srcsplitms msfile contsub Note that ngc5921 usecase ms contsub contains the uv subtracted visibilities in its DATA column and ngc5921 usecase ms cont the pseudo continuum visibilities as fit The original ngc5921 usecase ms now contains the uv continuum subtracted vis in its CORRECTED_DATA column and the continuum in i
555. t visibility file imagename Pre name of output images mode mfs Type of selection mfs channel velocity frequency alg clark Algorithm to use hogbom clark csclean multiscale niter 500 Number of iterations ain 0 1 Loop gain for cleaning threshold 0 0 Flux level to stop cleaning mJy mask E Name of mask image used in cleaning cleanbox CI clean box regions or file name or interactive imsize 256 256 Image size in pixels nx nyl symmetric for single value cell 1 0arcsec 1 0arcsec Cell size in arcseconds x y stokes Tr Stokes parameter to image I IV IQU IQUY field o Field name phasecenter re Field Identifier or direction of the image phase center spw spectral window channels gt all weighting natural Weighting to apply to visibilities uvfilter False Apply additional filtering uv tapering of the visibilities timerange we range of time to select from data restfreq restfrequency to use in image async False if True run in the background prompt is freed CASA lt 25 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 standard 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 defau
556. t_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 10 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 jmcmulli 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 Chi 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 4396
557. 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 5 e ft Fourier transforms the specified model or component list and inserts this into the MODEL DATA column of the MS 8 5 6 e deconvolve Deconvolve an input image from a provided PSF using one of several image plane deconvolution algorithms B 7 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 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 o
558. tat polcal sdbaseline sdcal sdcoadd sdflag sdlist sdplot sdscale sdsmooth sdstat Additional tasks are available for ALMA commissioning use still alpha code as of Beta O release almasimmos 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 CHAPTER 1 INTRODUCTION 38 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 start 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 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 BETA ALERT This is a new behavior in Patch 2 In previous versions global parameters
559. tcal jupiter6cm 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 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 CHAPTER 4 SYNTHESIS CALIBRATION 179 fd CASA Plotter Mar Rogon Reg una tocate 1 out M0 0 Sa 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 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 r2
560. tcal fontsize 14 0 Make labels larger CHAPTER 4 SYNTHESIS CALIBRATION markersize 10 0 Make dots bigger caltable ngc5921 usecase fluxscale yaxis amp subplot 211 plotcal yaxis phase subplot 212 plotcal O 168 The results are shown in Figure This makes use of the subplot option to make multi panel displays LU CASA Plotter Mar Region Reg vna tocate 1 ou Moot Bla Figure 4 3 Display of the amplitude upper and phase lower gain solutions for all antennas and polarizations in the ngc5921 post fluxscale table Similarly to plot amplitude or phase as a function of channel for B solutions for NGC5921 CHAPTER 4 SYNTHESIS CALIBRATION 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 O 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
561. tead 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 5 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 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 Other features The concat task now takes multiple input MS and will combine into a possibly new output MS 2 4 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 1 2 CASA Basics Information for First Time Users This section assumes that CASA has been installed on your LINUX or OSX sy
562. tfile print Listing calibration to file listfile listcal Plot final gain calibration print Plotcal iteration showgui False xaxis time yaxis amp figfile caltable plot amp png print Plotting calibration to file figfile saveinputs plotcal prefixt plotcal fluxscale amp saved plotcal O xaxis time yaxis phase figfile caltable plot phase png print Plotting calibration to file figfile saveinputs plotcal prefixt plotcal fluxscale phase saved plotcal xaxis antenna yaxis amp figfile caltable plot antamp png print Plotting calibration to file figfile saveinputs plotcal prefixt plotcal fluxscale antamp saved plotcal if setpolmodel and polcalmode count X gt 0 Now run setjy to re set model for polxfield print Setjy default setjy 478 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 479 vis msfile print Use setjy to set IQU fluxes of polxfield field polxfield for spw in usespwlist fluxdensity polmodel field spw flux saveinputs setjy prefix setjy polspw spwt saved setjyO f o o o o o oo o Polarization D term calibration print PolCal default polcal print Polarization D term Calibration
563. th 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 including 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 a
564. 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 follwing 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 342 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 343 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 disk instead The default is sd rcParams scantable storage memory but if you are on a machine with small memory do sd rcParams scantable storag
565. 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 in that a single com mon solution for both polarizations is determin
566. the moment images print Imstat moments default imstat imagename momzeroimage momzerostats imstat imagename momoneimage momonestats imstat print 9 ssssss s Now use the stats produced by imstat above print Pull the max from the cubestats dictionary created above using imstat thistest_immax cubestats max 0 print Clean image max thistest_immax print 279 CHAPTER 6 IMAGE ANALYSIS Pull the rms from the cubestats dictionary thistest_imrms cubestats rms 0 print Clean image rms thistest_imrms print Pull the max from the momzerostats dictionary thistest_momzeromax momzerostats max 0 print Moment O image max thistest_momzeromax print Pull the mean from the momonestats dictionary thistest_momoneavg momonestats mean 0 print Moment 1 image mean thistest_momoneavg print print Done 280 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 there is a viewer task which can be used to call up an image The inputs are viewer View an image or visibility data set infile d Name of file to visualize filetype gt imag
567. the new tablename and plot run plotcal last tablein smoothcaltab2 plotcal Correct the data print ApplyCal default applycal vis srcsplitms gaintable smoothcaltab2 gaincurve False opacity 0 0 field spw selectdata False calwt True 248 CHAPTER 5 SYNTHESIS IMAGING applycal print Clean 3 default clean vis srcsplitms imname3 prefix clean3 imagename imname3 field spw mode mfs gain 0 1 niter 10000 threshold 0 04 psfalg clnalg imagermode clnmode imsize clnimsize cell clncell weighting briggs robust 0 5 cleanbox interactive npercycle 100 clean Cleans alot deeper You can change the npercycle to larger numbers like 250 or so as you get deeper also Set up variables clnimage3 imname3 image clnmodel3 imname3 model clnresid3 imname3 residual clnmask3 imname3 clean_interactive mask Look at this in viewer viewer clnimage3 image 249 CHAPTER 5 SYNTHESIS IMAGING 250 jupiter6cm usecase clean3 image Jy beam n Std Dev RMS Mean Variance Sum 5848 0 001015 0 001015 4 036e 06 1 029e 06 0 02360 Flux Med Dev IntQtlRng Median Min Max 0 001470 0 0006728 0 001347 8 245e 06 0 003260 0 003542 On Jupiter n Std Dev RMS Mean Variance Sum 6003 0 08012 0 08107 0 01245 0 006419 74 72 Flux
568. the output bandpass caltable btable prefix bcal caltable btable No gain tables yet gaintable gainfield eat interp Use flux calibrator 1331 305 3C286 FIELD_ID 0 as bandpass calibrator field 0 all channels spw 7 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 CHAPTER 4 SYNTHESIS CALIBRATION bandpass Use plotcal to examine the bandpass solutions print Plotcal bandpass default plotcal caltable btable field 0 No GUI for this script showgui False If you want to do this interactively and iterate over antenna set iteration antenna showgui True Set up 2x1 panels upper panel amp vs channel subplot 211 yaxis amp No output file yet wait to plot next panel plotcal Set up 2x1 panels lower panel phase vs channel subplot 212 yaxis phase Now send final plot to file in PNG format via png suffix figfile caltable plot
569. the size of the PS file unfortunately 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 BETA ALERT The postscript printing capabilities of the casaviewer are currently fairly poor due to some limitations in Qt and the way we do axis labels This will be 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 You may also wish to consider outputting as PNG and then using another program such as convert to turn into PS CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER V Viewer Display Panel ax vi nvas Manager X File f Data DisplayPanel Tools View Margins gt BORaRIDGQAAG Number of panels M d E Time 2 2 2108 Thu Basic Settings Thuj Background Color white par Apply Fly 4700 Y Data Display Options jupiter6cm usecase clean1 image 30 Display axes Fl E 2 Hidden axes ES Q0 o 2 45 00 Basic Settings 3 Position tracking o 30 Axis labels 8 Qq Axis label properties 45 00 Title color foreground PA i X axis label color foreground Ex 30 Y axis label color foreground Ex 44400 X gridftick color foreground PA h m E 00 55742 38 3e 4 32 W 628 Y gridftick color foreground Ex Avi 7 gt Plot border color foreground Biv Viewer Print Manager
570. the threshold The level sets priority threshold This tool can also the lowest priority that will be generated and all messages he used to change the output log file of this level or higher will go into the casapy 1og file and to post messages into the logger 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 58 Y Log Messages imager b home imager b smye
571. time subplot 212 yaxis phase Now send final plot to file in PNG format via png suffix figfile caltable plotcal png saveinputs plotcal prefix plotcal gscaled phase saved plotcal O The amp and phase coherence looks good Apply our calibration solutions to the data This will put calibrated data into the CORRECTED_DATA column print ApplyCal default applycal vis msfile 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 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 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 prefix applycal saved applycal Now use plotxy to plot the calibrated target data before contsub pr
572. ting new statistics storage lattice of shape 8 kmo Figure 1 8 Different message priority levels as seen in the casalogger window These can also be Filtered upon 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 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 Note that when you delete a measurement set calibration table or image you must delete the top level directory and all underlying directories and files 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
573. tion D term calibrator polcalmode D QU polarization D term calibration mode polduvrange gt uvrange for polcal D setpolmodel True if true then use setjy to set pol model polxfield 0137 331 polarization angle X calibrator polxuvrange uvrange for polcal X setjymode set mode for fluxcal setyjy set flux ft This is the name of the split file for corrected data srcsplitms prefix split ms Set up general clean parameters RMS in 10min 600s 0 06 mJy thats now but close enough Set the output image size and cell size arcsec 0 4 will give 3x oversampling at least clean will say to use a composite integer e g 288 for efficiency clnalg clark clnalg hogbom usecsclean False clnimsize 288 clncell 0 4 Fix maximum number of iterations clniter 200 This is BnC config VLA 6cm 4 85GHz obs Check the observational status summary Primary beam FWHM 45 f_GHz 557 Synthesized beam for VLA EVLA at C Band A config FWHM 0 4 B config FWHM 1 2 C config FWHM 3 9 D config FWHM 14 0 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS Also set flux residual threshold 0 04 mJy Our scans are around 120s With rms of 0 06 mJy in 600s gt rms 0 13 mJy Set to 10x thermal rms clthreshold 1 3 Set up a clean box in the center 1 8 of image clnc
574. tions 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 Jj term is therefore a 4x4 matrix Most of the effects contained in Ji 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 such that Hamaker J P Bregman J D amp Sault R J 1996 Astronomy and Astrophysics Supplement v 117 p 137 147 396 APPENDIX E APPENDIX THE MEASUREMENT EQUATION AND CALIBRATION 397 Jij J 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 By Gig Dig Eig Pig Tig VPA where e Ti Polarization independent multiplicative effects introduced by the troposphere such as
575. to help it along with a mask maskline 50 0 fitfile sdusecase_orions_hc3n_kms fit 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 or fit_stat_kms sdfit with fit_stat_kms giving cent 27 133651733398438 0 016480101272463799 fwhm 2 93294358253479 0 038807671517133713 nfit 1 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 304 peak 0 81080895662307739 0 0092909494414925575 J 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 6 4f 6 4f km s fit_stat_kms fwhm 0 0 fit_stat_kms fwhm 0 1 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 HHHHHHHHHHHHHHHHHHHHHHEH HS End ORION S Use Case HHEHHHHHHHHHHHHHHHHHHHHHH HS A 3 Using The ASAP Toolkit Within CASA ASAP is included with the CASA installation build It is not loaded upon start up however and must be imported as a standard Python package A convenience function exists for importing ASAP along with a set of prototype tasks for single dish analysis CASA lt i gt asap_in
576. to save the flags vis msfile mode save versionname antflags comment flag AN flagants merge replace saveinputs flagmanager prefixt flagmanager ants saved flagmanager Calibration Set the fluxes of the primary calibrator s if setjymode flux print Setjy default setjy vis msfile print Use setjy to set flux of fluxcalfield to point model field fluxcalfield spw usespw If we need a model for flux calibrator then put this here modimage fluxcaldir fluxcalmodel Loop over spw for spw in usespwlist fluxdensity fcalmodel fluxcalfield spw print Setting SPW spw to str fluxdensity saveinputs setjy prefixt setjy spwt saved setjyQ elif setjymode ft print FT 474 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS default ft vis msfile field fluxcalfield for spw in usespwlist model fluxcaldir fluxcalmodel _ spwt _IQUV model print Use FT to set model model saveinputs ft prefix ft 0 saved 1t0 else Se Initial gain calibration print Gaincal print Setjy default setjy vis msfile print Use setjy to set flux of fluxcalfield field
577. ts MODEL_DATA column as per the fitmode subtract 202 CHAPTER 4 SYNTHESIS CALIBRATION 203 4 8 2 Continuum Calibration of Jupiter The following is an example of continuum calibration on the Jupiter 6cm VLA dataset This as sumes you have already imported and flagged the data and have the ms file jupiter6cm usecase ms on disk in your working directory See 3 7 The full Jupiter example script can be found in Appendix F 2 FERRARI RRA Calibration Script for Jupiter 6cm VLA Updated STM 2008 03 25 Beta Patch 1 0 Updated STM 2008 06 11 Beta Patch 2 0 FERRARI RRHH AR HH H HA prefix jupiter6cm usecase msfile prefix ms Set the fluxes of the primary calibrator s print Setjy default setjy 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 CHAPTER 4 SYNTHESIS CALIBRATION Initial gain calibration print Gaincal default gaincal vis msfile set the name for the output gain caltable gtable prefix gcal caltable gtable Gain calibrators are 1331 305 and 0137 331 FIELD_ID 7 and 0 We have 2
578. ts ek Bs Boe Sh Ga ee a en Oe wo ed 237 5 9 Examples of Imaging ooo aaa 238 5 9 1 Spectral Line Imaging with NGC5921 o o 238 5 9 2 Continuum Imaging of Jupiter 2 2 20 e e e 6 Image Analysis 6 1 Common Image Analysis Task Parameters o o e 6 1 1 Region Selection box sir pe rr RE A 6 1 2 Plane Selection chans stokes 6 1 3 Lattice Expressions expr Gola Masks m sk s a xke cuida cae ARA 6 2 Image Header Manipulation imhead o 6 2 1 Examples for imhead o 6 3 Continuum Subtraction on an Image Cube imcontsub 6 3 1 Examples for imcontsub o 00 be e eee aes 6 4 Image plane Component Fitting imfit o o o e e 6 5 Mathematical Operations on an Image immath o 6 5 1 Examples for immath o 6 5 1 1 Simple math esos gs siis ee ww a e Re ae e 6 5 1 2 Polarization manipulation 20 4 6 5 1 3 Primary beam correction uncorrection 6 5 1 4 Spectral analysiS o o e o 6 5 2 Using masks in immath e 6 6 Computing the Moments of an Image Cube immoments 6 6 1 Hints for using immoments 6 6 2 Examples using immoments 6 7 Computing image statistics meter las cir gee de ee cee AR 6 7 1 Using the xstat return value 2 2 2 0 0 0220002 ee ee ee 6 7 2
579. tter to see the list of tools 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 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 asaprc 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 CASA lt 2 gt sd rcParams Out 2 APPENDIX A APPENDIX SINGLE DISH DATA PROCESSING 356 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 gt scanta
580. tu 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 first 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 scans auto_poly_baseline mask edge order threshold chan_avg_limit plot insitu Parameters mask an optional mask retreived 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
581. uencies 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 setjyO You should see something like this in the logger and casapy log file 406 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 407 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 Bandpass 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 set the name for the output bandpass caltable btable prefix bcal caltable btable No gain tables yet gaintable gainfield 5 interp 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
582. ues 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 and the scantable storage parameter controlling whether scantable 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 D
583. uld 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 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 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 x U im V im V im go CHAPTER 6 IMAGE ANALYSIS 263 6 5 1 3 Primary beam correction uncorrection In a script using mode evalexpr you might want to assemble the string for
584. uplication 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 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 CHAPTER 4 SYNTHESIS CALIBRATION 186 uvcontsub Continuum fitting and subtraction in the uv plane vis 32 Nome of input visibility file field gt Select field using field id s or field name s fitspw me Spectral window channel selection for fitting the continuum spw e qa Spectral window selection for subtraction export solint int Continuum fit timescale fitorder O Polynomial order for the fit fitmode subtract Use of continuum fit subtract replace model splitdata Fal
585. urce 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 495 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 fluxscale gaincal split 496
586. uring image analysis These include 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 10 252 CHAPTER 6 IMAGE ANALYSIS 253 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 Region selection in the image analysis tasks is controlled by a set of parameters that allow you to specify regions of an image Currently the only available region selection is using the box parameter box E os Select one or more box regions string containing blcx blcy trcx trcy A box region 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 HHH HH H OH OH 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
587. usly an average integration time should be computed Default settings for the missing fields of TO are as in 1 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 CHAPTER 2 VISIBILITY DATA IMPORT EXPORT AND SELECTION 93 4 timerange gt TO Select all times greater than TO For example timerange gt 2007 10 09 23 41 00 Default settings 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 00 2020 12 31 23 59 59 which would choose all possible data 2 5 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
588. ust 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 7 4 1 6 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 spectral windows see 7 4 1 2 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 CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 309 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 lo
589. ut Return to continue script n correlation 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 print SS sr SS A O 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 438 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS 439 Now look at whats left correlation RR LL 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 11 2323222 2225252222259 Ras SSS SS SSS Sas Serer Sse a 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 Pause script if you are running in scriptmode if scriptmode user_check raw_input Return to continue scriptin 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 print wee Pring M2 2322232259222 SSS Rae SRS Ss SSSR SSS SSS See print Now plotting vs time antenna 9 spw 1 print Box up the bad
590. v 2 m 0 0 a x 340 y 231 AOO x 196 y 0 712 Figure 3 6 flagdata Flagging example using the clip facility 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 Measurement 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 browsetable Browse a table MS calibration table image tablename a Name of input table CHAPTER 3 DATA EXAMINATION AND EDITING 116 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 cho
591. vdist spw iteration antenna 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 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 script n xaxis time spw 71 correlation 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 print 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 CHAPTER 3 DATA EXAMINATION AND EDITING 126 if scriptmode user_check raw_input Return to continue script n 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
592. versions print Flagmanager default flagmanager print Now will use flagmanager to list all the versions we saved APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS vis msfile mode list flagmanager Done Flagging print Done with flagging 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 441 APPENDIX F APPENDIX ANNOTATED EXAMPLE SCRIPTS print Do not want bandpass calibration vis msfile set the name for the output gain caltable caltable gtable print Dutput 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
593. were always used no matter how the task was called 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 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 CHAPTER 1 INTRODUCTION 39 yaxis amp datacolumn data plotxy O which will also use the global parameter values Second 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
594. x gt gcal v fluxscale gt lt prefix gt fluxscale v applycal gt lt prefix gt ms v split gt lt prefix gt cal split ms v split gt lt prefix gt src split ms v exportuvfits gt lt prefix gt split uvfits v uvcontsub gt lt prefix gt ms cont lt prefix gt ms contsub v HHHHHHHHHHHHHHHHHHHHHHHHHHHHRHHHHHHHHHRHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Set up some useful variables The prefix to use for all output files 191 CHAPTER 4 SYNTHESIS CALIBRATION 192 prefix ngc5921 usecase The MS filename is assumed to be ngcb921 usecase ms and already imported msfile prefix ms Use task importuvfits to make an ms Note that there will be a ngc5921 usecase ms flagversions in additon to ngc5921 usecase ms with the data 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 listobs You should get in your logger window and in the casapy log file something like MeasurementSet Name home sandrock2 smyers Testing2 Sep07 ngc5921 usecase ms MS Version 2 Observer TEST Project Observation VLA Data records 22653 Total integration t
595. xtensive 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 baseline 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 Calculate a baseline based calibration solution gain or bandpass vis ue Nome of input visibility file caltable e ra Name of output gain calibration table field 22 Select field using field id s or field name s spw z oe 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 freqdep False Solve for frequency dependent solutions 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 T False Apply internal VLA antenna gain curve correction opacity 0 0 Opacity correction to apply nepers parang False Apply parallactic angle correction async False The freqdep parameter control
596. y 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 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 7 8 for an example using NGC5921 CHAPTER 7 VISUALIZATION WITH THE CASA VIEWER 295 Y Viewer Display Panel Data Display Panel Tools View Ea S B Q E PS 3 AARAA age se 2 Y Data Display Options Ox ngc5921 usecase clean image contour Display axes Hidden axes Basic Settings Aspect ratio fixed world ha ya Y Pixel treatment center AY Resampling mode nearest AY Contour levels 1 2 3 4 5 PAY Contour scale factor 0 00942197 FAO Level type abs rf Y amo 107 00 507 407 30 Line width 2 Px J2000 Right Dash negative contours true Sl Fad Y Dash positive contours false nA 4 Y Q Q q O Q 11 46 8 Normal Line color foreground rf Y Blink Rate 10 sec Compact Position tracking Axis labels Frame Axis label properties X ngc5921 usecase clean image contour Beam Ellipse 2 475e 03 Jy beam 15 21 40 502 05 07 28 641 I 1 546876e 03 km s Dismiss Figure 7 7 The Viewer Display Panel left and Data Display Options panel right after choosing Contour Map from the Load Data panel
597. y 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 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 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 i
598. ystem Temperature Correction 2 0 0 0 a ee ee 137 Baf Beh AR Gate es 138 be fe eA Boe A ad A F 139 4 3 3 1 Determining opacity corrections for VLA data 139 4 3 4 Setting the Flux Density Scale using setjy 140 4 3 4 1 Using Calibration Models for Resolved Sources 142 Seeger eee 144 eto kas 144 4 4 1 Common Calibration Solver Parameters 144 4 4 1 1 Parameters for Specification vis and caltable 145 4 4 1 2 Selection field spw and selectdata 145 4 4 1 3 Prior Calibration and Correction parang gaincurve and opacity 146 4 4 1 4 Previous Calibration gaintable gainfield interp and spwmap 146 4 4 1 5 Solving solint combine refant and minsnr 148 E A Re ra BG 149 4 42 Spectral Bandpass Calibration bandpass 149 4 4 2 1 Bandpass Normalization 2 e o 150 MPA s s a acs sa aa Bree ode ke ee ROEM BAS oe Re amp Gm S 151 4 4 2 3 BPOLY SOCIOS e honk Aree bogs eae eR a 152 4 43 Complex Gain Calibration gaincal 154 4 4 3 1 Polarization dependent Gain G 155 4 4 3 2 Polarization independent Gain T 156 4433 GSPLINE solutions 157 4 44 Establishing the Flux Density Scale fluxscale 158 4 4 4 1 Using Resolved Calibrators

CASA Synthesis & Single Dish Reduction Cookbook

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CASA Synthesis &amp; Single Dish Reduction Cookbook

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CASA Synthesis & Single Dish Reduction Cookbook