LITTLE THINGS AIPS Reduction of DDO165, D config.: VLA Obs. of 31st of July 2008 ===================================================================== calibration recipe v. 2.0: mrupen 10oct08 calibration recipe v. 2.1: mrupen 13oct08 calibration recipe v. 2.1.update: Dana Ficut Vicas 29 Oct 08 (new adverbs in Aips) calibration recipe v. 2.2: Dana Ficut Vicas 11Dec 08(tiny bits) calibration recipe v. 2.3: Dana Ficut Vicas 11 Feb 09(UVCOP ambiguities) calibration recipe v. 2.4: Dana Ficut Vicas 3 Mar 09(team raised issues) calibration recipe v. 2.5: Dana Ficut Vicas 23 September 2009 (no smoothing with WIPER on the source data) Latest update: 3rd March 2009 Data reduced by Dana Ficut Vicas, Hertfordshire 2nd of July 2010 Suggestion: STARTING with D ARRAY and then working through C array and B array is recommended. D array data will allow you to have a look at the whole field ( the strong continuum sources that might give problems will be obvious here), is more stable and will give you the best feel for the data. The recipe lists the B-array reduction, but obviously the same steps apply to all configurations. 0. Basic stuff B configuration From observing log (available online at http://www.vla.nrao.edu/cgi-bin/oplogs.cgi): * Wind/API rms phase/clouds: yy:yy 2.3-4.8 m/s 3.1-16.7d 90% mixed clouds clouds * ant.1 2 4 5 11 13 14 16 17 18 19 21 23 24 25 26 EVLA antenas included in the project * ant. 2 7 13 18 20 27updated baseline parameters * ant. 3 moved recently * ant. 25 L band receiver removed for repairs * ant. 18 fringe amplitudes very weak 1. FILLM executed on 2nd of July 2010 a. Request archive data: copy public project data : AH927 from this archive file : /home/archive_VLA6/files/2008-03/vla2008-03-23.dat    to this output file : /home/e2earchive/AH927_AM080323.xp1 copy public project data : AH927 from this archive file : /home/archive_VLA6/files/2008-04/vla2008-04-14.dat    to this output file : /home/e2earchive/AH927_AU080414.xp1 copy public project data : AH927 from this archive file : vla2008-07-07.dat to this output file : /home/e2earchive/AH927_BF080707.xp2 copy public project data : AH927 from this archive file : vla2008-07-31.dat to this output file : /home/e2earchive/AH927_BS080731.xp1 copy public project data : AH927 from this archive file : /home/archive_VLA6/files/2008-07/vla2008-07-31.dat    to this output file : /home/e2earchive/AH927_BS080731.xp1 b. FILLM -> DDO165-D1.CH 0.1, DDO165-D1.LINE.1 default FILLM datain 'ARCHIVE:DDO165/Archive/AH927_BS080731.xp band 'l';vlaobs 'AH927'; doall -1 ; qual 3 $ restricts FILLM to the galaxy+calibrators of interest nfiles 0; ncount 1 $ read one filetget fillm, outna 'ddo165-D1' outdisk 1; outseq 0 douvcomp= -1 $ allow channel/IF-dependent weights doweight 10 $ use memo 108 weights (i.e., put weights in 1/Jy^2) bparm= -1,-1 $ avoid opacity & gain corrections cparm 0 cparm(4)=25.1 $ one needs to explicitly flag shadowed antennas $ since the ModComps were retired on 27 June 2007 $ this requires FILLM in 31DEC08 after 18Nov08 MNJ cparm(7)= 0 $ assigns new FREQID if frequency changes by more than $ the max. Doppler shift between sources 180 degrees $ apart. Setting this to -1 forces all data to have same $ FREQID. doconcat=-1 $ Change this to DOCONCAT=1 to add data to an existing file ***N.B. FILLM's channel 0 will ONLY be used for initial flagging. We're quite paranoid here. 2. TASAV -> LINSAV.1 executed on 2nd of July 2010 ***We TASAV right away, because VLANT changes the AN table. Did I mention we're paranoid? default TASAV outna 'D165-1BeTaD outcla 'LINSAV' outdi 2 $ Ideally set this to a different disk from indisk, $ in case of disk crashes getn *.LINE 3. UVCOP -> LINCOP.1 executed on 2nd of July 2010 ***Discard the first and last channels: 1st and last 10 channels if 127 channels total 1st and last 20 channels if 255 channels total ***We discard these Evil Channels because (1) they're pretty much useless; (2) they seem to confuse BPASS (which takes the solution from channel N as the initial guess for channel N+1); (3) their noise characteristics are quite different from the rest of the channels, which can be confusing e.g. in clipping and imaging. default UVCOP outcla 'LINCOP' bchan 11; echan 127-10 $ Use bchan 21 ; echan 255-20 if 255 channels total uvcopprm 0 uvcopprm(4) 1 $ report progress getn *.LINE ***From now on we operate on LINCOP data unless otherwise specified. 4. LISTR/SCAN --> DDO165-D1.listr ***We do this before VLANT because we need to know FREQIDs for VLANT default LISTR optype 'SCAN' docrt 132 getn *.LINCOP --> uhppc51 LISTR(31DEC08) 524 02-JUL-2010 12:26:33 Page 1 File = DDO165-D1 .LINCOP. 1 Vol = 3 Userid = 524 Freq = 1.423248930 GHz Ncor = 2 No. vis = 73644 Scan summary listing Scan Source Qual Calcode Sub Timerange FrqID START VIS END VIS 1 1331+305 : 0003 A 1 0/03:38:45 - 0/03:42:25 1 1 1786 2 1331+305 : 0003 A 1 0/03:42:45 - 0/03:46:25 2 1787 7605 3 1313+675 : 0003 C 1 0/03:47:55 - 0/03:51:25 3 7606 13054 4 DDO165 : 0003 1 0/03:51:45 - 0/04:04:25 3 13055 32535 5 1313+675 : 0003 C 1 0/04:04:45 - 0/04:08:25 3 32536 38354 6 DDO165 : 0003 1 0/04:08:45 - 0/04:21:25 3 38355 57835 7 1313+675 : 0003 C 1 0/04:21:45 - 0/04:25:25 3 57836 63654 8 1331+305 : 0003 A 1 0/04:26:45 - 0/04:31:25 1 63655 69717 9 1331+305 : 0003 A 1 0/04:31:45 - 0/04:34:25 2 69718 73644 Source summary Velocity type = ' ' Definition = ' ' ID Source Qual Calcode RA(2000.0) Dec(2000.0) IFlux QFlux UFlux VFlux No. vis 1 1331+305 : 0003 A 13:31:08.2879 30:30:32.958 0.000 0.000 0.000 0.000 17595 2 1313+675 : 0003 C 13:13:27.9848 67:35:50.376 0.000 0.000 0.000 0.000 17087 3 DDO165 : 0003 13:06:24.8000 67:42:25.000 0.000 0.000 0.000 0.000 38962 ID Source Freq(GHz) Velocity(Km/s) Rest freq (GHz) 1 All Sources 1.4232 0.0000 0.0000 Frequency Table summary FQID IF# Freq(GHz) BW(kHz) Ch.Sep(kHz) Sideband 1 1 1.42324893 1312.2560 6.1035 1 2 1 1.41724893 1312.2560 6.1035 1 3 1 1.42024893 1312.2560 6.1035 1 AIPS 1: Resumes 5. VLANT -> AN/1, CL/2 executed on 2nd of July 2010 ***Note that VLANT can be run only for data observed from 1992 onwards. Data earlier than 1991 produce the following error message: VLANT1: Task VLANT (release of 31DEC07) begins VLANT1: ANT DATA UNAVAILABLE FOR YEAR 1991 DATA START WITH 1992 VLANT1: Purports to die of UNNATURAL causes For earlier data we skip baseline corrections entirely, and hope for the best. If there are clear and systematic phase gradients with time, consult the baseline corrections at http://www.vla.nrao.edu/astro/archive/baselines/ and apply corrections via CLCOR (which is basically what VLANT does). ***10oct08: Currently VLANT works on only one FREQID at a time. We therefore have to run VLANT multiple times for data with multiple FREQIDs. Unfortunately VLANT (1) produces a new CL table every time, and (2) updates the AN table positions every time as well. : CL tables: I'd like to maintain the convention that CL/1 is the original CL table and CL/2 has all the corrections that should have been applied on-line but weren't -- mainly, antenna position corrections. For multiple FREQIDs therefore this recipe calls for deleting the intermediate CL tables created by VLANT, using the rather clumsy mechanism of TASAVing to a temporary file, deleting the original CL tables, and copying the latest one back from the TASAV'd data set. Blah. : AN table: For now, this recipe resets to the original AN table just before running VLANT the last time. This means that only one run of VLANT updates the AN entries, leading to a correct AN table as needed for (e.g.) UVFIX. I've e-mailed DAIP to see about fixing all this, by allowing FREQID= -1 to mean "calculate corrections for all FREQIDs" (currently FREQID= -1 is reset to FREQID= 1). We'll see what Eric says. #####VLANT no longer has freqid as a parameter. 5a. default VLANT getn *.LINCOP 6. PRTAN AN/1 default PRTAN docrt 132 getn *.LINCOP Location Of VLA Antennas N9 ( 7) N8 ( 9) N7 (13)* N6 (26)* N5 (27) N4 (12) N3 (18)* N2 (25)* N1 (20) *( 1) W1 E1 (15) (22) W2 E2 (21)* *(24) W3 E3 (11)* *(19) W4 E4 ( 5)* *(17) W5 E5 ( 2)* *(16) W6 ( ) ( 8) W7 E7 (14)* ( 6) W8 E8 (10) *( 4) W9 E9 (23)* VLA:_OUT ( 3) VLA:_OUT (28) VPT:_OUT (29) * => EVLA ANTENNA ***To choose the reference antenna the following algorithm should be followed: 1. should be present throughout the run 2. should be on an "inner" pad, but NOT N1/E1/W1 (to avoid shadowing) 3. NOT on the master pad (since those are always weird) 4. NOT an EVLA antenna (since those are often weird) 5. try to avoid the north arm in the smaller configurations (to avoid shadowing) 6. NOT listed in any interesting way in the log file (to avoid problems with the reference antenna) 7. preferably consistent with other recent runs 8. should be a fairly stable antenna (can't tell until TVFLG/CALIB of course...) ===> Refant: 22 $ W2 7. Calibrators ***Check out the calibrators in the on-line calibrator manual: http://www.vla.nrao.edu/astro/calib/manual/index.shtml ***Max baseline at 21 cm in B array is 54.3 klambda C array is 16.2 klambda D array is 4.9 klambda primary (flux/bandpass) calibrators: 1331+305=3C286 ***You can ignore the uv-ranges for these, since there are now models for the most important ones. secondary (gain) calibrator: 1313+675 1313+675 J2000 C 13h13m27.9848s 67d35'50.376" 1311+678 B1950 C 13h11m45.0360s 67d51'42.310" ----------------------------------------------------- BAND A B C D FLUX(Jy) UVMIN(kL) UVMAX(kL) ===================================================== 20cm L P P P P 2.40 ===> secondary cal --- NO restrictions 7b. SETJY -> SU/1 executed on 2nd of July 2010 ***Set aparm(2) to corespond to date of observation. If date <1990 aparm(2)=3 If 19921998 aparm(2)=0 ***We need to enter a flux density for each primary (flux) calibrator. ***If we have more than one FREQID, we assume that the frequency offsets used are small, so that the flux densities of the flux calibrators are nearly the same for each FREQID. Typical frequency offsets are of order the bandwidth, +/-3 MHz; at 1420 MHz, for a worst-case spectral index of -1, this leads to an error of 2*3 MHz/1420 MHz= 0.4% -- not worth worrying about. So, we use any FREQID which covers all primary flux calibrators. If flux calibrator A is observed only with FREQID 1, while flux calibrator B is observed only with FREQID 2, we have to run SETJY twice: default SETJY sources '1331+305','' $ primary (flux) calibrator A optype 'CALC'; freqid=1 $ FREQID for A aparm 0,0 $ data taken after 1998 getn *.LINCOP; / Flux calculated using known spectrum uhppc5> SETJY1: BIF = 1 EIF = 1 /Range of IFs uhppc5> SETJY1: '1331+305 ' IF = 1 FLUX =14.7122 (Jy calcd) uhppc5> SETJY1: / Using (1999.2) VLA or Reynolds (1934-638) coefficients default SETJY sources '1331+305','' $ primary (flux) calibrator B optype 'CALC'; freqid=2 $ FREQID for B aparm 0,0 $ data taken after 1998 getn *.LINCOP; / Flux calculated using known spectrum uhppc5> SETJY1: BIF = 1 EIF = 1 /Range of IFs uhppc5> SETJY1: '1331+305 ' IF = 1 FLUX =14.7418 (Jy calcd) uhppc5> SETJY1: / Using (1999.2) VLA or Reynolds (1934-638) coefficients 7c. CALRD executed on 2 July 2010 ***Read in models of flux density calibrators: default CALRD object '3c286';band 'L'; ***Note: These models are in J2000 coordinates. If your data are in B1950, change the model images to B1950 with EPOSWTCH. We will later use UVFIX to fix the uv-data. Both in J2000!!! 8. PRTUV (used to find integration times on calibrators & sources) default PRTUV cparm 0; cparm(9)=103 $ Pick a baseline -- here, baseline 1-3 docrt 132 getn *.LINCOP --> calib: 10s source: 10s 9. UVFLG -> FG/1 executed on 2 July 2010 ***We toss the EVLA-EVLA baselines, to avoid dealing with aliasing. There should still be plenty of VLA-EVLA baselines to allow antenna-based solutions for the EVLA...but keep an eye out for oddities (e.g., in BPASS)! default UVFLG outfgver 1;opcode 'flag';reason 'EVLA' getn *.CH0 $ Note that we use FILLM's CH0 for initial flags -- we'll $ TACOP later. antenna=EVLA;baseline=EVLA; ***NOTE!!! do NOT run UVFLG if EVLA=0 (try PRINT EVLA to check) -- otherwise you'll delete ALL of your data. 10. TVFLG -> FG/1 executed on 2 July 2010 ***Again, we *only* use the original CH 0 from FILLM for initial flagging. Here we flag calibrators only, to remove any gross, obvious problems. - Check the first scan carefully -- often the system isn't "organized" on this first scan - On-line flagging isn't as reliable as in the old days, so there are plenty of hot pixels and hiccups. - We are NOT quacking, because (1) FILLM's NX table isn't correct; (2) QUACK flags data from the beginning-of-scan, whereas we want to flag data from antennas-on-source. default TVFLG calcode '*' $ calibrators only docat -1 $ avoid saving temporary files dohist -1 $ avoid creation of history entries Freqid 1 $ must step through all FREQIDs! docalib -1 flagver 1;outfgver 1 $ keep all flags in FG/1 dparm 0 dparm(3) 1 $ show baselines twice, to treat all antennas identically -- $ this displays baseline 27-1 as well as 1-27 dparm(6)=10 $ time resolution: should be set to the calibrators' integration $ time, in seconds getn *.CH0 $ note this is the ONLY time we use FILLM's Channel 0! ***Within TVFLG: - Set useful defaults: SMOOTH=1 to avoid averaging date before displays SCAN= 20 to use a long time for median filters (AMP/PH DIFF) FLAG ALL CHANNELS FLAG STOKES FULL (usually -- sometimes you'll want NORR or NOLL) ***If individual Stokes need to be flagged, make sure you set the STOKES FLAG to correspond to the polarization that is displayed on the TV SWITCH SOURCE FLAG to ONE-SOURCE to avoid inadvertantly flagging your galaxy (though sometimes you'll want to of course) - Be sure to inspect BOTH polarizations! ***We suggest the following steps: - Set the above defaults - Flag first integration in every scan (manual QUACK) -- this should be the first integration AFTER most antennas are on-source, which is why we can't use the usual QUACK. - Inspect the following: AMPLITUDE to check for missing records or antennas AMP DIFF to check for variable gains PHS DIFF to check for variable atmosphere/gains - If your data set is in D array(if your source is southern than also check for this problem in the C array) than keep an open eye for solar interference. It will be obvious if in TVFLG you choose a SORT BY BASELINE display, showing you how the short baselines behave,the ones affected by solar interference.If solar interference is affecting your data than in CALIB you should use a UVRANGE. ***Note: occasionally, flagging using UVFLG can be more straightforward (e.g., deleting an antenna). 10b. TABED FG/1 executed on 2 July 2010 ***Here we TABED the CH 0 flags to LINCOP (with FREQID= -1). After this we're done with FILLM's channel 0. default TABED opty 'repl' inext 'fg' inver 1 ; outver 1; bcount 1;ecount 0 ; $until recently there was a parameter called $ncount which is no longer there aparm 0 aparm(1) 3 $ Changing column 3 = FREQID keyval= -1,0 $ ...to FREQID= -1 getn *.CH 0 getona *.LINCOP --> LINCOP FG/1 11. BPASS ***This is a first-order BPASS leading to a new Channel 0. The goal is to avoid closure errors in Channel 0 calibration due to huge delays (phase slopes) on VLA-EVLA baselines. We divide each visibility by the vector average of the inner 3/4 of the band (i.e., an on-the-fly channel 0). Thus we remove source structure (tho' getting the weights wrong) and take care of the amplitude scale. ***There is a split here between the easy case (one FREQID for all sources) and the Galactic HI case (multiple FREQIDs, usually different for the bandpass calibrator and the galaxy (and phase calibrator)). Check LISTR/SCAN to see which you're doing. 11b. BPASS: Multiple FREQIDs -> BP/1,2,3 executed on 2 July 2010 ***The overall plan here is as follows (assuming FREQIDs 1 and 2 refer to the offset [bandpass calibrator] frequencies, and FREQID 3 refers to that of the galaxy & phase calibrator): (1) run BPASS once for FREQID=1 (-> BP/1) and once for FREQID=2 (-> BP/2). (2) check both BP tables with POSSM. They should look virtually identical. (3) If they do appear virtually identical, we concatenate them: (a) write out both tables [TBOUT], (b) concatenate the two [vi/emacs], (c) read them back in [TBIN] as BP/3, (4) If they do NOT appear identical, there is Something Wrong. The case we've come across involves the use of a front-end filter combined with the use of unexpected LOs (see Adrienne's note), so that one FREQID was observed through the edge of the filter. The resulting bandpasses show a strong slope in the amplitude gains for most VLA antennas. So far we've seen this only for central frequencies around 1423 MHz. In this case, simply copy the "good" BP table to BP/3 using TACOP. (5) modify BP/3 to refer to FREQID=3 [TABED]. ***It is a VERY good idea to use POSSM carefully throughout to be sure you're doing what you think you're doing. 11b1. BPASS FREQID 1 -> BP/1 executed on DDmonYY default BPASS calsour '1331+305','' $ Select bandpass calibrators docal 1 ; gainuse 2 $ apply VLANT changes. Probably irrelevant. flagver 1 $ apply initial flags refant 22 $ Change this to your refant Qual -1 solint 0 $ one solution per scan minamper 7 ; minphser 7 $ report closures > 7%/7d smooth 0 $ no smoothing soltype '' ; weightit 0 $ L1, L1R, etc. seem _less_ stable -- weird bpassprm 0 bpassprm(5) 0 $ derive "channel 0" on a record-by-record basis -- $ more biased than averaging first, but avoids $ some subtle pitfalls (see EXPLAIN file) bpassprm(2) 1 $ some closure info is printed bpassprm(6) 2 $ print avg. closure errors > 2% bpassprm(7) 2 $ print avg. closure errors > 2d ichansel 0 $ derive channel 0 from inner 3/4 of the band freqid 1 $ 1st offset FREQID getn *.LINCOP --> BP/1 11b2. BPASS FREQID 2 -> BP/2 executed on DDmonYY ***Same as 11b1, now on FREQID 2 default BPASS calsour '1331+305','' $ Select bandpass calibrators docal 1 ; gainuse 2 $ apply VLANT changes. Probably irrelevant. flagver 1 $ apply initial flags refant 22 $ Change this to your refant Qual -1 solint 0 $ one solution per scan minamper 7 ; minphser 7 $ report closures > 7%/7d smooth 0 $ no smoothing soltype '' ; weightit 0 $ L1, L1R, etc. seem _less_ stable -- weird bpassprm 0 bpassprm(5) 0 $ derive "channel 0" on a record-by-record basis -- $ more biased than averaging first, but avoids $ some subtle pitfalls (see EXPLAIN file) bpassprm(2) 1 $ some closure info is printed bpassprm(6) 2 $ print avg. closure errors > 2% bpassprm(7) 2 $ print avg. closure errors > 2d ichansel 0 $ derive channel 0 from inner 3/4 of the band freqid 2 $ 2nd offset FREQID getn *.LINCOP --> BP/2 11b3. POSSM to compare BP/1 and BP/2 default POSSM $ to check BPASS results flagver 1 aparm 0, 1, 0.7, 1.3, -180, 180, 0, 2, 0, 0 $ Plot BP, with amp/ph ranges source '0137+331','0542+498','1331+305','' $ POSSM doesn't work with $ source '' for some reason! solint -1 $ Separate plots for each scan nplots 9 $ 9 plots per page bparm 0 dotv 1 freqid 1; bpver 1 ; grch 1 freqid 2; bpver 2 ; grch 2 getn *.LINCOP tvinit If worried: try POSSM on secondary calibrator, applying this BPASS (if BPASS stable, secondary should look flat) 11b5. *If* BP/1 and BP/2 are NOT virtually identical, pick the one that best matches the behavior of the phase calibrator (possibly by doing a quickie BPASS on the phase calibrator and comparing the results), and copy that BP table to BP/3: default TACOP inext 'bp' inver 2 $ Set this to the "good" BP table getn *.LINCOP ; getona *.LINCOP --> BP/3 ***You should IGNORE the "bad" FREQID for all subsequent processing. 11b6. TABED BP/3 to set FREQID=-1 (so we can use the same BP table for everyone) --> BP/4 default TABED opty 'repl' inext 'bp' inver 3 ; outver 4 aparm 0 aparm(1) 8 $ Changing column 8 = FREQID keyval= -1,0 $ ...which we change to FREQID= -1 getn *.LINCOP --> BP/4 11c. POSSM to check BP table 11c1. Plot BP table itself default POSSM $ to check BPASS results flagver 1 aparm 0, 1, 0.7, 1.3, -180, 180, 0, 2, 0, 0 $ Plot BP, with amp/ph ranges source '1331+305','' $ POSSM doesn't work with $ source '' for some reason! solint -1 $ Separate plots for each scan nplots 9 $ 9 plots per page bparm 0 docal 1 ; gainuse 2 ; doband 1 dotv 1 freqid 3; bpver 4 $ for multiple-FREQID data sets getn *.LINCOP tvinit 11c2. Apply BP table to 2ndary calibrator & plot individual baselines default POSSM flagver 1 aparm 0 $ Plot data solint -1 $ Separate plots for each scan nplots 9 $ 9 plots per page aparm 0 aparm(1) 1 $ vector average source='1313+675','' $ Secondary (phase) calibrator docal 1 ; gainuse 2 ; doband 1 $ average all BP entries dotv 1 freqid 3; bpver 4 $ for multiple-FREQID data sets getn *.LINCOP tvinit 11c3. Apply BP table to 2ndary calibrator & vector average all data default POSSM flagver 1 aparm 0 $ Plot data solint 0 $ average all time nplots 0 $ average all baselines aparm 0 aparm(1) 1 $ vector average source='1313+675','' $ Secondary (phase) calibrator docal 1 ; gainuse 2 ; doband 1 $ average all BP entries dotv 1 freqid 3; bpver 4 $ for multiple-FREQID data sets getn *.LINCOP tvinit ***This plot should be flat in both amp. and phase as a function of frequency, with no slope.. If some channels are off, note which ones those are and keep an eye out for interference or other bad data. If there are large errors consider running BPASS on the secondary calibrator and using that to correct the galaxy. Note that this will be somewhat painful since AIPS does not allow incremental BP tables -- unlike SN or CL tables. Sigh. 12. AVSPC -> NEWCH0.1 (2,3) executed on 2 July 2010 ***AVSPC must be run once for each FREQID (unfortunately FREQID=-1 purports to work, but creates an empty data set). This entails some nasty bookkeeping for data sets with multiple FREQIDs. Here I assume we have one or three FREQIDs. If BPASS checks above show that one FREQID is useless, you should ignore that one entirely in this and all subsequent processing. ***We will use these NEWCH0 files for (1) further flagging, and (2) time-dependent gain calibration. 12a. FREQID=1 --> NEWCH0.1 default AVSPC docalib -1;gainuse 0; flagver -1 $ do NOT apply flags doband 1 freqid 1; bpver 4 $ for multiple-FREQID data sets getn *.LINCOP outname inna ; outcl 'NEWCH0' --> NEWCH0.1 12b. FREQID=2 (if multiple-FREQID data set) --> NEWCH0.2 ***Skip FREQID=2 if the corresponding BP table looked irrelevant (see 11b5) default AVSPC docalib -1;gainuse 0; flagver -1 $ do NOT apply flags doband 1 freqid 2; bpver 4 $ for multiple-FREQID data sets getn *.LINCOP outname inna ; outcl 'NEWCH0' ; outse= freqid --> NEWCH0.2 12c. FREQID=3 (if multiple-FREQID data set) --> NEWCH0.3 ***Skip FREQID=3 if the corresponding BP table looked irrelevant (see 11b5) default AVSPC docalib -1;gainuse 0; flagver -1 $ do NOT apply flags doband 1 freqid 3; bpver 4 $ for multiple-FREQID data sets getn *.LINCOP outname inna ; outcl 'NEWCH0' ; outse= freqid --> NEWCH0.3 12d. LISTR/SCAN ***It is a VERY good idea to run LISTR/SCAN on each of the NEWCH0 data sets at this point, to be sure each has the data you expect. 13. TABED LINCOP FG/1 -> NEWCH0 FG/1 ***We use TABED to set FREQID to -1 (apply to all FREQIDs) in the FG table, since AVSPC will change all FREQIDs to 1 in the NEWCH0 data sets. 13a. NEWCH0.1 default TABED opty 'repl' inext 'fg' inver 1 ; outver 1 aparm 0 aparm(1) 3 $ Changing column 3 = FREQID keyval= -1,0 $ ...to FREQID= -1 getn *.LINCOP getona *.NEWCH0.1 --> NEWCH0.1, FG/1 13b. If multiple FREQIDs: NEWCH0.2 default TABED opty 'repl' inext 'fg' inver 1 ; outver 1 aparm 0 aparm(1) 3 $ Changing column 3 = FREQID keyval= -1,0 $ ...to FREQID= -1 getn *.LINCOP getona *.NEWCH0.2 --> NEWCH0.2, FG/1 13c. If multiple FREQIDs: NEWCH0.3 default TABED opty 'repl' inext 'fg' inver 1 ; outver 1 aparm 0 aparm(1) 3 $ Changing column 3 = FREQID keyval= -1,0 $ ...to FREQID= -1 getn *.LINCOP getona *.NEWCH0.3 --> NEWCH0.3, FG/1 14. CALIB -> NEWCH0.1(,2,3) SN/1 executed on 2 July 2010 ***If we only have one FREQID, all CALIBs are run on the same NEWCH0.1 . If we have multiple FREQIDs, CALIBs for a given source must be run for all NEWCH0.1,2,3 in which that source appears (probably easiest to check with LISTR/SCAN). ***Note: if 'SN' table must be destroyed: task 'extdest'; inext 'sn'; invers 0 ***If solar interference is affecting your data than in CALIB you should use a UVRANGE. The worst case scenario, baselines up to a distance of 1 kilolambda could be afected, while in the best case scenario baselines are affected only up to 0.5kilolambda distance. We recommend using: UVRANGE 0.7,0 for D array UVRANGE 0.7,0 for C array After calibration, if UVPLT still shows signs of solar interference,it means that not enough short baselines were discarded; therefore the calibration has to be redone and UVRANGE to be reset. Note that the Sun might rise or set, especially during a long B-array run, in which case you might wish to split the calibration by timerange in a set affected and a set without solar interference. 14a. Primary (flux density) calibrators --> SN/1 default CALIB calsour '1331+305','' $ flux density calibrator #1 get2n 3C286_L.MODEL.1 nmap 1 ; ncomp 1e6,0 ; inver 1 ; cmethod 'DFT' freqid -1 docal 1 ; gainuse 2 flagver 1 refant 22 $ Change this to your refant solint 0 aparm 4,0,0,0,0,2; $ min 4 antennas; print closures soltype 'L1'; solmode 'A&P'; weightit 1 $ true L1 minimization solcon 0 minamper 10; minphser 10 $ complain if >10%/10d off cparm 0,0,10,10,1 $ complain if avg > 10%/10d off snver 1 getn *.NEWCH0 $ ***NOTE: must run this for all NEWCH0.1,2 in which $ this calibrator appears! --> SN/1 14b. Secondary (phase) calibrator --> SN/1 ***Check uv restrictions for secondary calibrators carefully. For 0702+445: no restrictions, so uvra= 0,0 . default CALIB calsour '1313+675','' $ phase calibrator uvrange 0,0 wtuv 0.0 $ may have to set wtuv 0.01 if solutions are $ crazy and uvrange is not 0,0 freqid -1 docal 1 ; gainuse 2 flagver 1 refant 22 $ Change this to your refant solint 0 aparm 4,0,0,0,0,2; $ min 4 antennas; print closures soltype 'L1'; solmode 'A&P'; weightit 1 $ true L1 minimization solcon 0 minamper 10; minphser 10 $ complain if >10%/10d off cparm 0,0,10,10,1 $ complain if avg > 10%/10d off snver 1 getn *.NEWCH0 $ ***NOTE: must run this for all NEWCH0.1,2,3 in which $ this calibrator appears! 15a. TABED all SN tables to NEWCH0.1 --> SN/2,3 ***This step is only required if we have more than one FREQID (NEWCH0). We copy everything to NEWCH0.1 to match the FREQID=1 case. ***Skip this step if you only have one FREQID! default TABED opty 'repl' inext 'sn' inver 1 ; outver 0 aparm 0 aparm(1) 6 $ Changing column 3 = FREQID keyval= -1,0 $ ...which we change to FREQID= -1 getn *.NEWCH0.2 getona *.NEWCH0.1 --> NEWCH0.1, SN/2 default TABED opty 'repl' inext 'sn' inver 1 ; outver 0 aparm 0 aparm(1) 6 $ Changing column 3 = FREQID keyval= -1,0 $ ...which we change to FREQID= -1 getn *.NEWCH0.3 getona *.NEWCH0.1 --> NEWCH0.1, SN/3 15b. GETJY SN/1-3, SU/1 executed on 2 July 2010 ***Find flux density of secondary calibrator, and set SN table amplitude gains to reflect a common flux density scale. default GETJY sources '1313+675','' $ Secondary (phase) calibrators) calsour '1331+305','' $ Primary (flux) calibrators freqid -1 snver 0 $ Use all SN tables getn *.NEWCH0.1 Task GETJY (release of 31DEC08) begins uhppc5> GETJY1: Source:Qual CALCODE IF Flux (Jy) uhppc5> GETJY1: 1313+675 : 3 C 1 2.34455 +/- 0.01035 15c. CLCAL/MERG to merge all SN tables -> SN/4 ***This step is only required if we have more than one FREQID (NEWCH0). Skip this step if you only have one FREQID! default CLCAL opcode 'MERG' $ Merge SN tables, for ease of plotting etc. refant 22 $ Change this to your refant getn *.NEWCH0.1 --> SN/4 $ creates a merged SN table -- doesn't change CL tables at all. Must now copy this new SN table to all other NEWCH0: default TACOP inext 'SN';inver 4 getn *.NEWCH0.1 getona *.NEWCH0.2 getona *.NEWCH0.3 16. SN table checks 16a. SNPLT last SN table executed on 2 July 2010 16a1. SNPLT phase: default SNPLT inext 'sn';inver 0 pixrange 0 opcode 'alsi';do3col 1;dotv 1; nplots 9 factor 2; symbol 5 xinc 1; optype 'phas'; getn *.NEWCH0.1 ===> Note any phase jumps (on the phase calibrator) for future flagging. The EVLA antennas, even after applying VLANT, still show quite a bit of phase drift. This is OK so long as a linear interpolation between the phases looks like it will work. 16a2. SNPLT amplitude: default SNPLT inext 'sn';inver 0 pixrange 0 opcode 'alsi';do3col 1;dotv 1; nplots 9 factor 2; symbol 5 xinc 1; optype 'amp'; getn *.NEWCH0.1 ===> Note whether the amp. is roughly constant for a given antenna/pol'n/IF. ***We have seen a couple cases where the first phase cal scan has a significantly different amplitude gain for the EVLA antennas. The reason is not clear but the raw data do show this effect, so CALIB is doing the right thing. This area warrants further tests, to learn whether we should simply flag the EVLA antennas on the first phase calibrator scan. 16b. LISTR/GAIN print SN table executed on 2 July 2010 default LISTR optype 'gain'; Inext 'sn'; inver 0; freqid -1 dparm 5,0; $ Amp & phase factor 0; docrt 132 outprint '' antennas 0; $ may have to list missing antennas explicitly, to avoid $ column overrun. To list missing antennas, use the form $ANTENNAS -3,2,0 to have antennas 3 and 2 left out. getn *.NEWCH0.1 --> check for phase jumps and other inconsistencies. ***We have seen a couple cases where the first phase cal scan has a significantly different amplitude gain for the EVLA antennas. The reason is not clear but the raw data do show this effect, so CALIB is doing the right thing. This area warrants further tests, to learn whether we should simply flag the EVLA antennas on the first phase calibrator scan. uhppc51 LISTR(31DEC08) 524 02-JUL-2010 13:44:34 Page 1 File = DDO165-D1 .NEWCH0. 1 Vol = 3 Userid = 524 IF = 1 Freq= 1.423248930 GHz Ncor= 2 No. vis= 7849 Polarization = R Subarray = 0 Listing SN table, version 4 SN table has not been applied to a CL table Gain amplitudes, 1000 = 10.000000 Stokes = R IF = 1 Freq = 1.423248930 GHz Time Source -- 1-- 2-- 3-- 4-- 5-- 6-- 7-- 8-- 9--10--11--12--13--14--15--16--17--18--19--20--21--22--23--24--25--26--27 Day # 0 03:41:55 1331+305 208 286 376 281 329 291 244 323 313 357 327 313 315 227 415 288 322 283 329 294 490 306 254 03:44:35 1331+305 201 285 355 269 316 295 237 311 313 335 357 321 331 302 440 286 318 274 352 295 449 324 249 03:49:45 1313+675 206 282 373 273 322 294 240 316 312 349 362 316 336 298 439 290 318 279 353 308 479 323 250 04:06:35 1313+675 203 287 374 273 324 293 242 317 313 350 364 320 331 270 439 291 320 280 352 309 474 322 250 04:23:35 1313+675 205 287 374 274 323 293 242 319 316 351 364 322 332 269 445 287 321 278 359 306 473 319 252 04:29:10 1331+305 212 293 384 281 328 244 323 314 357 383 313 343 284 435 288 325 281 374 316 501 331 254 04:33:20 1331+305 286 368 268 317 295 237 312 313 335 362 321 333 277 446 287 320 274 359 297 449 328 249 File = DDO165-D1 .NEWCH0. 1 Vol = 3 Userid = 524 IF = 1 Freq= 1.423248930 GHz Ncor= 2 No. vis= 7849 Polarization = R Subarray = 0 Listing SN table, version 4 SN table has not been applied to a CL table Type Q to stop, just hit RETURN to continue uhppc51 LISTR(31DEC08) 524 02-JUL-2010 13:44:35 Page 2 File = DDO165-D1 .NEWCH0. 1 Vol = 3 Userid = 524 IF = 1 Freq= 1.423248930 GHz Ncor= 2 No. vis= 7849 Polarization = L Subarray = 0 Listing SN table, version 4 SN table has not been applied to a CL table Gain amplitudes, 1000 = 10.000000 Stokes = L IF = 1 Freq = 1.423248930 GHz Time Source -- 1-- 2-- 3-- 4-- 5-- 6-- 7-- 8-- 9--10--11--12--13--14--15--16--17--18--19--20--21--22--23--24--25--26--27 Day # 0 03:41:55 1331+305 254 277 400 304 321 261 230 325 308 335 341 266 331 221 357 307 362 261 345 346 414 298 252 03:44:35 1331+305 245 275 374 293 317 255 223 320 301 308 328 272 355 218 372 292 359 250 334 344 382 299 243 03:49:45 1313+675 251 278 391 295 313 256 224 316 299 326 339 267 362 218 355 295 357 253 334 353 413 295 244 04:06:35 1313+675 247 278 394 296 319 258 227 317 302 324 339 270 356 218 349 294 358 254 333 352 416 295 243 04:23:35 1313+675 254 278 388 297 316 258 225 318 300 328 337 271 359 216 347 292 359 253 336 354 414 293 247 04:29:10 1331+305 261 284 404 304 323 230 325 307 335 351 266 367 223 362 305 367 261 350 366 430 300 252 04:33:20 1331+305 278 380 293 318 256 222 320 300 309 336 273 359 221 379 292 363 252 338 347 390 301 244 File = DDO165-D1 .NEWCH0. 1 Vol = 3 Userid = 524 IF = 1 Freq= 1.423248930 GHz Ncor= 2 No. vis= 7849 Polarization = L Subarray = 0 Listing SN table, version 4 SN table has not been applied to a CL table Type Q to stop, just hit RETURN to continue uhppc51 LISTR(31DEC08) 524 02-JUL-2010 13:44:36 Page 3 File = DDO165-D1 .NEWCH0. 1 Vol = 3 Userid = 524 IF = 1 Freq= 1.423248930 GHz Ncor= 2 No. vis= 7849 Polarization = R Subarray = 0 Listing SN table, version 4 SN table has not been applied to a CL table Gain phases in degrees Stokes = R IF = 1 Freq = 1.423248930 GHz Time Source -- 1-- 2-- 3-- 4-- 5-- 6-- 7-- 8-- 9--10--11--12--13--14--15--16--17--18--19--20--21--22--23--24--25--26--27 Day # 0 03:41:55 1331+305 -17 -77 -55 -30 153-125 -1 -74 173 -27-108 -76-147 8 -26 104 -41 0-150 44 50 151 108 03:44:35 1331+305 -113 171 29 175 111 140 20 108 74 34-135-102 174 -90 -22 119 -54 0 106 46 2 65 125 03:49:45 1313+675 -18 -86 34 179 121 143 28 131 83 42 -70 -76-119 8 22 129 -1 0-159 94 77 157 131 04:06:35 1313+675 -21 -81 26-177 122 146 30 126 83 40 -73 -77-114 10 21 129 1 0-164 90 77 156 133 04:23:35 1313+675 -20 -85 28 179 121 142 30 133 83 35 -67 -75-115 10 21 129 3 0-157 86 79 157 134 04:29:10 1331+305 33 -25 -2 -32 152 -3 -80 174 20 -56 -76 -89 61 35 106 15 0-104 93 109-157 109 04:33:20 1331+305 -129 83-179 110 145 20 109 74 81 -77-101-120 -30 38 119 5 0 163 97 58 117 125 File = DDO165-D1 .NEWCH0. 1 Vol = 3 Userid = 524 IF = 1 Freq= 1.423248930 GHz Ncor= 2 No. vis= 7849 Polarization = R Subarray = 0 Listing SN table, version 4 SN table has not been applied to a CL table Type Q to stop, just hit RETURN to continue uhppc51 LISTR(31DEC08) 524 02-JUL-2010 13:44:36 Page 4 File = DDO165-D1 .NEWCH0. 1 Vol = 3 Userid = 524 IF = 1 Freq= 1.423248930 GHz Ncor= 2 No. vis= 7849 Polarization = L Subarray = 0 Listing SN table, version 4 SN table has not been applied to a CL table Gain phases in degrees Stokes = L IF = 1 Freq = 1.423248930 GHz Time Source -- 1-- 2-- 3-- 4-- 5-- 6-- 7-- 8-- 9--10--11--12--13--14--15--16--17--18--19--20--21--22--23--24--25--26--27 Day # 0 03:41:55 1331+305 -10 -79 -60 -96 6 151-145 151 63 72 151-158 67 149-148 -22 102 0 38 115 -84-169 91 03:44:35 1331+305 -77 -160 54 109 21 67-120 4 4 163 156 179 59 80-118 9 119 0 -32 144-108 135 123 03:49:45 1313+675 25 -53 63 111 30 71-107 23 10 176-135-158 131-177 -67 20 178 0 65-161 -26-129 132 04:06:35 1313+675 22 -48 55 114 33 74-104 18 11 174-138-158 137-175 -68 18 179 0 61-165 -26-129 134 04:23:35 1313+675 24 -51 58 111 33 72-104 26 11 171-130-155 138-173 -67 21-177 0 69-168 -23-127 136 04:29:10 1331+305 42 -25 -6 -97 7 -145 147 65 121-154-154 128-157 -85 -19 161 0 86 166 -27-115 93 04:33:20 1331+305 -97 110 117 23 75-120 7 5-146-143-177 130 143 -54 12-179 0 27-162 -49-170 125 File = DDO165-D1 .NEWCH0. 1 Vol = 3 Userid = 524 IF = 1 Freq= 1.423248930 GHz Ncor= 2 No. vis= 7849 Polarization = L Subarray = 0 Listing SN table, version 4 SN table has not been applied to a CL table AIPS 1: Resumes 17. UVFLG -> NEWCH0.1 FG/1 executed on DDmonYY ***If the SN table shows a phase jump on the phase calibrator, you should flag the data between the two phase cal scans which show the jump (since those cannot be calibrated). ***Note that we flag NEWCH0.1, *regardless* of whether the galaxy appears in this data set. This is because later on (step 20/TVFLG) we flag the NEWCH0 data in order from inseq 1 through inseq freqid_max, copying the FG table from one file to the next. UVFLG itself doesn't care whether the flags you enter actually do anything -- it just adds entries to the FG table, which are then applied (or ignored if irrelevant) by other tasks. ***This step may of course be skipped if there are no obvious phase jumps. This example deals with a phase jump on antenna 18. default UVFLG antenna 18,0 $ the antenna which "jumped" timer 0 6 33 0 0 6 59 0; $ the source scan between the offending ph.cal scans opcode 'FLAG' reason 'phase jump' outfgver 1 getn *.NEWCH0.1 --> NEWCH0.1 FG/1 18. CLCAL NEWCH0 --> CL/3 executed on 2 July 2010 ***For multi-FREQID data this becomes rather complicated, since we need a new CL table for every NEWCH0 file, to allow detailed checks and second-order flagging. ***Note that there is no need to work around any phase jumps, since the intervening data are flagged (see step 17 above [UVFLG]). 18a. CLCAL for the primary calibrators -> CL/3 default CLCAL sour= '1331+305','' $ Primary (flux) calibrators calsour= sour interpol 'SELF' gainver 2 ; gainuse 3 refant 22 $ Change this to your refant dobtween -1 $ Don't interpolate entries for different sources snver 4 $ if multiple FREQIDs getn *.NEWCH0.1,2 $ do this for all NEWCH0 with primary (flux) $ calibrator data 18b. CLCAL for the phase calibrator and galaxy -> CL/3 default CLCAL sour= '1313+675','DDO165','' $ Secondary (phase) calibrator + galaxy calsour= '1313+675','' $ Secondary (phase) calibrator interpol 'SIMP' gainver 2 ; gainuse 3 refant 22 $ Change this to your refant dobtween -1 $ Don't interpolate entries for different sources cutoff 120 $ Don't extrapolate/interpolate beyond 120 minutes snver 4 $ if multiple FREQIDs ***If your data set used +/- frequency switching for the phase calibrator (our observations did not, but some archival data may), you should use BPARM with SAMPTYPE='BOX' to select a smoothing time which covers both frequency settings. LISTR/SCAN on LINCOP will help you choose this; normally something like 12 minutes should be OK. bparm 12/60 ; samptype='BOX' getn *.NEWCH0.1 $ do this for all NEWCH0 with secondary (phase) $ calibrator or galaxy data ***At this point we have a new CL table for all NEWCH0 files. 19a. ANBPL executed on 2 July 2010 ***We use ANBPL to check the data weights. Data with very high weights (factor 5-10 or more above normal) should be flagged with UVFLG. default ANBPL docalib 1;gainuse 3 flagver 1 bparm 2,17,0 $ Plot antenna-based weight vs. time nplots 9; dotv 1 docrt 132 $ Print as well as plotting weights -- useful for $ finding exact times of bad weights $ Note you can also use outprint to send to a file. opcode 'alsi' $ Plot all IFs together do3col 1 $ ...using different colors getn *.NEWCH0.1 $ Must do this separately for every NEWCH0 file 19b. UVFLG to eliminate very high weights ***Should UVFLG on NEWCH0.1, even if Evil Weights are seen in NEWCH0.2 or NEWCH0.3 -- we'll be copying FG/1 from NEWCH0.1 to NEWCH0.2 for subsequent second-order flagging. 20. TVFLG FG/1 executed on 2 July 2010 20a. TVFLG on calibrators: NEWCH0.1 The calibrators should now have constant amplitude and zero phase...apart from source structure for the primary (flux) calibrators, and any uvrange for the secondary (phase) calibrators. If we see huge problems on the calibrators we may have to re-run CALIB etc. -- let's hope not!! default TVFLG calcode '*' $ calibrators only docat -1 $ avoid saving temporary files dohist -1 $ avoid creation of history entries docalib 1 ; gainuse 3 $ apply the new CL table flagver 1;outfgver 1 $ keep all flags in FG/1 dparm 0 dparm(3) 1 $ show baselines twice, to treat all antennas identically -- $ this displays baseline 27-1 as well as 1-27 dparm(6)=10 $ time resolution: should be set to the calibrators' $ integration time, in seconds getn *.NEWCH0.1 ***Within TVFLG: - Set useful defaults: SMOOTH=1 to avoid averaging date before displays SCAN= 20 to use a long time for median filters (AMP/PH DIFF) FLAG ALL CHANNELS FLAG STOKES FULL (usually -- sometimes you'll want NORR or NOLL) ***If individual Stokes need to be flagged, make sure you set the STOKES FLAG to correspond to the polarization that is displayed on the TV SWITCH SOURCE FLAG to ONE-SOURCE to avoid inadvertantly flagging your galaxy (though sometimes you'll want to of course) - Be sure to inspect BOTH polarizations! ***We suggest the following steps: - Set the above defaults - Check AMPLITUDE, AMP DIFF, PHS DIFF. Be wary of known source structure and uv-range limits!! ***Note: occasionally, flagging using UVFLG can be more straightforward (e.g., deleting an antenna). 20b. If we have multiple NEWCH0s (FREQIDs): (1) Copy the FG table: default TABED opty 'repl' inext 'FG' ; inver 1 ; outver 2 bcount 1;ecount 0; aparm 0 aparm(1) 3 $ Changing column 3 = FREQID keyval= -1,0 $ ...to FREQID= -1 getn *.NEWCH0.1 getona *.NEWCH0.2 Re-run TVFLG with same inputs as above, except: flagver 2 ; outfgver 2 getn *.NEWCH0.2 (2) Assuming there are three FREQIDs, we do this yet again: Copy the FG table: default TABED opty 'repl' inext 'FG' ; inver 2 ;outver 2 bcount 1;ecount 0; aparm 0 aparm(1) 3 $ Changing column 3 = FREQID keyval= -1,0 $ ...to FREQID= -1 getn *.NEWCH0.2 getona *.NEWCH0.3 Re-run TVFLG with same inputs as above, except: flagver 2 ; outfgver 2 getn *.NEWCH0.3 21. Calibration/flagging checks: calibrators 21a. UVPLT executed on 2 July 2010 ***Check the amp & phase vs. uv-distance for all calibrators. Amplitude should match the results of SETJY/GETJY. If there are obvious outliers which are not expected due to source structure, go back and flag those (and possibly re-run CALIB etc.). default UVPLT calco '*' docal 1 ; gainuse 3 flagver 1 $ set this to the latest FG version -- may be >1 if $ there are multiple NEWCH0s (FREQIDs). dotv 1 do3col 1 getn *.NEWCH0.1 $ do this for each NEWCH0 file bparm 0 $ amp. vs. uv-distance bparm 0,2 $ phase vs. uv-distance The primary calibrator looks very odd. 21b. IMAGR executed on DDmonYY [if desired -- this is not really necessary] default IMAGR sources '0702+445','' $ calibrator to image docalib 1; gainuse 3 $ apply latest calibration flagver 1 $ apply latest flags -- set this to the $ highest-numbered FG table outname 'junkcal' $ some obviously cruddy name cellsize 1 $ for B configuration cellsize 3.5 $ for C configuration cellsize 10 $ for D configuration imsize 1024 $for B array imsize 512 $for C and D array niter 1000 nbox 1 ; clbox -1,5,512,513 $ calibrator should be in the center minpa 121 uvwtfn 'NA'; robust 0.5 dotv 1 getn *.NEWCH0.xx $ whichever file has the calibrator you're imaging --> shouldn't see obvious calibration errors or striping. CLEANed flux density should roughly match SETJY/GETJY. Note: If uvwtfn is set to 'NA' it will override any value given to robust. 22. TVFLG on the galaxy: NEWCH0.xx ***This is our first run of flagging on the galaxy. - Check the first scan carefully -- often the system isn't "organized" on this first scan - On-line flagging isn't as reliable as in the old days, so there are plenty of hot pixels and hiccups. - We are NOT quacking, because (1) FILLM's NX table isn't correct; (2) QUACK flags data from the beginning-of-scan, whereas we want to flag data from antennas-on-source. 22b. If there's more than one NEWCH0 (FREQID): ***I assume here that the galaxy is in NEWCH0.3 . If not, you should first TACOP FG/2 from NEWCH0.3 to the file with the galaxy in it. This will now be FG/3 . default TVFLG calcode '-CAL' $ non-calibrators only docat -1 $ avoid saving temporary files dohist -1 $ avoid creation of history entries docalib 1 ; gainuse 3 $ apply the new CL table flagver 2;outfgver 2 $ or flagver 3 ; outfgver 3 if you had to TACOP $ the FG table from another file dparm 0 dparm(3) 1 $ show baselines twice, to treat all antennas identically -- $ this displays baseline 27-1 as well as 1-27 dparm(6)=10 $ time resolution: should be set to the sources' $ integration time, in seconds getn *.NEWCH0.xx $ This should be the file with the galaxy data ***Within TVFLG: - Set useful defaults: SMOOTH=1 to avoid averaging date before displays SCAN= 20 to use a long time for median filters (AMP/PH DIFF) FLAG ALL CHANNELS FLAG STOKES FULL (usually -- sometimes you'll want NORR or NOLL) ***If individual Stokes need to be flagged, make sure you set the STOKES FLAG to correspond to the polarization that is displayed on the TV SWITCH SOURCE FLAG to ONE-SOURCE to avoid inadvertantly flagging your galaxy (though sometimes you'll want to of course) - Be sure to inspect BOTH polarizations! ***We suggest the following steps: - Set the above defaults - Flag first integration in every scan (manual QUACK) -- this should be the first integration AFTER most antennas are on-source, which is why we can't use the usual QUACK. - Check AMPLITUDE (for missing data), AMP DIFF . PHS DIFF may occasionally be useful, but it's likely to be mostly random, unless you have a strong continuum source near your galaxy. ***Note: occasionally, flagging using UVFLG can be more straightforward (e.g., deleting an antenna). 23. Calibration/flagging checks: sources 23a. UVPLT executed on 2 July 2010 ***Check the amp vs. uv-distance for the galaxy. If there are obvious outliers which are not expected due to source structure or RFI (i.e., not mostly on short spacings), go back and flag those. Note any obvious short-spacing horrors, which may be due to solar or terrestrial RFI. default UVPLT docal 1 ; gainuse 3 flagver 2 $ set this to the latest FG version -- may be >1 if $ there are multiple NEWCH0s (FREQIDs). dotv 1 do3col 1 source 'DDO165','' getn *.NEWCH0.1 $ whichever file holds the galaxy bparm 0 $ amp. vs. uv-distance 23b. IMAGR executed on 2 July 2010 default IMAGR sources 'DDO165','' $ the galaxy docalib 1; gainuse 3 $ apply latest calibration flagver 2 $ apply latest flags -- set this to the $ highest-numbered FG table outname 'junk' $ some obviously cruddy name cellsize 10 $ for D configuration imsize 512 $ for C and D configurations niter 1000 nbox 0 minpa 121 uvwtfn 'na'; robust 0.5 dotv -1 getn *.NEWCH0.xx $ whichever file has the source you're imaging --> shouldn't see obvious calibration errors or striping. Note that this "channel 0" includes HI emission, so you may see some odd effects (e.g., very woofly noise in B configuration) -- don't panic! Note: If uvwtfn is set to 'NA' it will override any value given to robust. ### If you find a strong continuum source rippling your map even in a 512x512 imsize D array configuration channel zero image than refer to Elias and Dana for further steps. 24. TASAV -> CH0SAV.1,2,3 executed on 2 July 2010 default TASAV outna 'D165-1MidTaD outcla 'ch0sav' outdi 2 $ Ideally set this to a different disk from indisk, $ in case of disk crashes getn *.NEWCH0 $ loop over NEWCH0 files (= FREQIDs) outse inseq 25. TABED SN, FG tables to LINCOP executed on 2 July 2010 ***Use TABED to ensure FREQID=-1 for all tables (paranoia is your friend...) 25a. NEWCH0.xx FG/yy -> LINCOP FG/2 default TABED opty 'repl' inext 'fg' aparm 0 aparm(1) 3 $ Changing column 3 = FREQID keyval= -1,0 $ ...which we change to FREQID= -1 inver 3 $ if multiple FREQIDs: set this to max. flag table number outver 2 getn *.NEWCH0.3 $ if multiple FREQIDs: set this to file you flagged $ on most recently (usually the file with the $ galaxy in it) getona *.LINCOP --> LINCOP FG/2 25b. NEWCH0.xx SN/yy -> LINCOP SN/1 default TABED opty 'repl' inext 'sn' inver 4 $ if multiple FREQIDs outver 0 aparm 0 aparm(1) 6 $ Changing column 3 = FREQID keyval= -1,0 $ ...which we change to FREQID= -1 getn *.NEWCH0 $ if multiple FREQIDs: all should have same merged SN $ table so you can use whichever NEWCH0 file you want getona *.LINCOP --> LINCOP SN/1 26. CLCAL LINCOP SN/1 --> CL/3 executed on 2 July 2010 ***We do CLCAL directly on LINCOP rather than copying, to avoid (even more) confusion in the multiple-FREQID case. ***Note that there is no need to work around any phase jumps, since the intervening data are flagged (see step 17 above [UVFLG]). 26a. CLCAL for the primary calibrators -> CL/3 default CLCAL sour= '1331+305','' $ Primary (flux) calibrators calsour= sour interpol 'SELF' gainver 2 ; gainuse 3 refant 22 $ Change this to your refant dobtween -1 $ Don't interpolate entries for different sources snver 1 freqid= 1 $ You must run CLCAL once for each FREQID with $ the relevant calibators present getn *.LINCOP 26b. CLCAL for the phase calibrator and galaxy -> CL/3 default CLCAL sour= '1313+675','DDO165','' $ Secondary (phase) calibrator + galaxy calsour= '1313+675','' $ Secondary (phase) calibrator interpol 'SIMP' gainver 2 ; gainuse 3 refant 22 $ Change this to your refant dobtween -1 $ Don't interpolate entries for different sources cutoff 120 $ Don't extrapolate/interpolate beyond 120 minutes snver 1 ***If your data set used +/- frequency switching for the phase calibrator (our observations did not, but some archival data may), you should use BPARM with SAMPTYPE='BOX' to select a smoothing time which covers both frequency settings. LISTR/SCAN on LINCOP will help you choose this; normally something like 12 minutes should be OK. bparm 12/60 ; samptype='BOX' freqid= 1 $ You must run CLCAL once for each FREQID with $ the phase calibrator or galaxy present getn *.LINCOP 27. Calibration/flagging checks: calibrators 27a. WIPER executed on 2 July 2010 ***Check the amp & phase vs. uv-distance for all calibrators. Amplitude should match the results of SETJY/GETJY, and phase should be zero, apart from known structure (reflected in source model for gain calibrators and uvrange for phase calibrators). If there are obvious, unexpected outliers, go back and flag those (and possibly re-run various tasks...). default WIPER calcode '*' docal 1 ; gainuse 3 doband 3; bpver 4 $ for multiple-FREQID data sets freqid 1 $ set this to match the calibrator flagver 2 $ should be the latest FG table smooth 7, 117 $ boxcar average over all channels -- use $ smooth 7, 235 if you started with 255 channels dotv 1 do3col 1 bparm 0 getn *.LINCOP bparm(2) 1 $ amp. vs. uv-distance bparm(2) 2 $ phase vs. uv-distance ###It shows a plot similar to the UVPLT output just quicker.It is also useful for identifying which antennas or baselines have calibration problems. 27b. POSSM executed on 2 July 2010 ***Check vector average of all data for each calibrator. Amplitude should match the results of SETJY/GETJY; phase should be flat, and consistent with zero (corresponding to a point source at the origin)...apart from known source structure and possibly HI absorption. default POSSM calcode '*' docal 1 ; gainuse 3 doband 3; bpver 4 $ for multiple-FREQID data sets freqid 3 $ set this to match the calibrator flagver 2 $ should be the latest FG table aparm 0 $ Plot data solint 0 $ average all time nplots 0 $ average all baselines aparm 0 aparm(1) 1 $ vector average source='1313+675','' $ Secondary (phase) calibrator uvrange= 0,0 $ should be set to eliminate known source structure, $ as in CALIB dotv 1 getn *.LINCOP tvinit 27c. IMAGR executed on DDmonYY [if desired -- this is not really necessary] default IMAGR docal 1 ; gainuse 3 doband 1; bpver 1 $ for single-FREQID data sets doband 3; bpver 4 $ for multiple-FREQID data sets freqid 1 $ set this to match the calibrator flagver 2 $ should be the latest FG table outname 'junk' $ some obviously cruddy name cellsize 1 $ for B configuration cellsize 3.5 $ for C configuration cellsize 10 $ for D configuration imsize 1024 $ for B array imsize 512 $ for C and D array niter 200 $ reasonable for a point source nbox 1 ; clbox -1,5,512,513 $ calibrator should be in the center minpa 121 uvwtfn 'na'; robust 0.5 dotv -1 $ so you can go eat lunch getn *.LINCOP ***You shouldn't see obvious calibration errors or striping. CLEANed flux density should roughly match SETJY/GETJY. If you _do_ have Evil Stuff, UVLSF will likely take care of it, so don't get too worked up. Note: If uvwtfn is set to 'NA' it will override any value given to robust. NOT DONE!!! 28. Calibration/flagging checks: sources 28a.1 WIPER executed on 2 July 2010 ***Check the amp vs. uv-distance for the galaxy. If there are obvious outliers which are not expected due to source structure or RFI (i.e., not mostly on short spacings), go back and flag those. Note any obvious short-spacing horrors, which may be due to solar or terrestrial RFI. default WIPER docal 1 ; gainuse 3 doband 3; bpver 4 $ for multiple-FREQID data sets freqid 3 $ set this to match the galaxy flagver 2 $ should be the latest FG table smooth 0 $do not smooth: smoothing will decrease your noise and $consequently show you a lower flux level than the level $that your data has in fact dotv 1 do3col 1 sources 'DDO165','' bparm 0 getn *.LINCOP bparm(2) 1 $ amp. vs. uv-distance bparm(2) 2 $ phase vs. uv-distance Use bparm(3)=1;bparm(6)=0;bparm(7)=20 if you want to force a range to the Y axis of the WIPER plot. ###It shows a plot similar to the UVPLT output just quicker.It is also useful for identifying which antennas or baselines have calibration problems.If you do find things you want to flag, UVFLG is highly recommended. #####CAREFUL with smoothing when doing WIPER on the source, it should NOT be done at this step.Smoothing will decrease your noise and consequently show you a lower flux level than the level that your data has in fact. #######It is very probable that when doing a WIPER on all the line data, some channels with junk will ruin your WIPER display and you will not be able to really make out what the clipping level should be. If the junk consists of random hot pixels then just run another WIPER in which you force the y axis to a 0-20 range (bparm(3)=1;bparm(6)=0;bparm(7)=20). If the junk comes in a structured manner than further investigations are needed to identify which baselines, in which channels might be missbehaving. Use WIPER only to identify the problematic baselines and channels, and use TVFLG or UVFLG to remove them form the data. defalut UVFLG antennas 10,0;basel 26,0; outfgver 2 opco 'FLAG';reason 'HOT' getn *.LINCOP defalut UVFLG antennas 15,0;basel 20,0; outfgver 2 opco 'FLAG';reason 'HOT' getn *.LINCOP 28a.2 Up to which level most of the values(leaving aside the very hot pixels) comfortably fit in? 12Jy ###This is the value that you will be using in CLIP when combining your data!!! 28b. IMAGR executed on 2 July 2010 default IMAGR docal 1 ; gainuse 3 doband 3; bpver 4 $ for multiple-FREQID data sets freqid 3 $ set this to match the galaxy flagver 2 $ should be the latest FG table outname 'junk_line' $ some obviously cruddy name cellsize 10 $ for D configuration imsize 512 $ for C configuration niter 1000 $ a light clean, just to see what we've got. niter 0 $ would be ok too, esp. if you IMLIN afterwards nbox 0 ; clbox 0 minpa 121 uvwtfn 'NA'; robust 0.5 dotv -1 $ so you can go eat lunch sourc 'ddo165','' getn *.LINCOP ***You shouldn't see obvious calibration errors or striping. You should however see of order 100 mJy of continuum sources in the field, as well as some indication of your galaxy. The latter may be quite confusing for B configuration, which resolves out most of the structure. Don't fret until you've combined all the array configurations. Note: If uvwtfn is set to 'NA' it will override any value given to robust. ### If you find a strong continuum source rippling your map even after trying a 512x512 imsize D array configuration cube than refer to Elias and Dana for further steps. 28c. Noise Estimations: calculated on 7 of July 2010 ##The easiest way to calculate the expected sensitivity is to say 7 S(mJy) = ---------------------------- sqrt{ N (N-1) delta_nu t} where 7 is a constant that depends on the system temperature of the receivers(a quite conservative value) N = number of antennas in the array, delta_nu = channel resolution in MHz, and t = integration time in hours. You need to use for N the number of Antennas which have on average been giving good data during the run. The total time should be the actual time spent on source. No need to be super precise, of course. One simply wants to get a ballpark figure which is good to 10-20%. ###Note that for data which are Hanning smoothed (archive data) the channel spacing is equal to the resolution delta_nu. Without Hanning smoothing, the resolution is ~1.4 x delta_nu (note that after offline Hanning smoothing, if you preserve all channels, the resolution becomes 2 x delta_nu; it reverts to a new "double the old delta_nu" if you delete every other channel). ####Finally, if you want to know the noise in a single visibility, use N=2 and t = 1/360, and probably multiply by sqrt{2} because a visibility is a single polarisation as well. N =26; t=0.5; delta_nu=0.006 The Expected noise level is: 4.97mJy The rms Noise level in a line free channel is: 4.82mJy 29. TASAV -> EndTaB.LINSAV.1 executed on 7th of July 2010 default TASAV outna 'D165-1EndTaD outcla 'linsav' outdi 2 $ Ideally set this to a different disk from indisk, $ in case of disk crashes getn *.LINCOP I AM HERE !!!! 30. FITTP executed on DDmonYY create: DDO210_B_UV_CALIB_NEWCH0.FITS $ one per FREQID DDO210_B_UV_CALIB_LINCOP.FITS DDO210_B-BeginTasav.FITS DDO210_B-MidTasav.FITS $ one per FREQID DDO210_B-EndTasav.FITS 31. Send to DEIDRE DDmonYY See Little THINGS Web site for current instructions. Apart from the FITS data from step 29/FITTP, the following should be archived: * Observing log * This data reduction log * LISTR/SCAN output (if saved to a file) 31. Celebrate your victory with an appropriate beverage! ================================================================================ ================================================================================ Ater the data has been checked by an independent member of the team and changes/corrections have been suggested the log should continue here with the steps that have been reiterated and the values used in the reiteration. If you need to recreate tables it is best at this stage to not delete the already existing ones but rather to give the tables higher version numbers.