;--------------------------------------------------------------- ;! calibrating amplitude and phase, and imaging VLA data ;# RUN POPS VLA UTILITY CALIBRATION IMAGING ;--------------------------------------------------------------- ;; Copyright (C) 2010-2012 ;; Associated Universities, Inc. Washington DC, USA. ;; ;; This program is free software; you can redistribute it and/or ;; modify it under the terms of the GNU General Public License as ;; published by the Free Software Foundation; either version 2 of ;; the License, or (at your option) any later version. ;; ;; This program is distributed in the hope that it will be useful, ;; but WITHOUT ANY WARRANTY; without even the implied warranty of ;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ;; GNU General Public License for more details. ;; ;; You should have received a copy of the GNU General Public ;; License along with this program; if not, write to the Free ;; Software Foundation, Inc., 675 Massachusetts Ave, Cambridge, ;; MA 02139, USA. ;; ;; Correspondence concerning AIPS should be addressed as follows: ;; Internet email: aipsmail@nrao.edu. ;; Postal address: AIPS Project Office ;; National Radio Astronomy Observatory ;; 520 Edgemont Road ;; Charlottesville, VA 22903-2475 USA ;--------------------------------------------------------------- DOOSRO LLLLLLLLLLLLUUUUUUUUUUUU CCCCCCCCCCCCCCCCCCCCCCCCCCCCC DOOSRO : Applies amplitude, phase calibration to EVLA OSRO data ** Type RUN DOOSRO to load this procedure ** WORKDISK Working disk, thus in/outdisk CATNUM Catalog number of the UV-file INNAME Input UV file name (CATNUM<1) INCLASS Input UV file class(CATNUM<1) INSEQ Input UV file seq. (CATNUM<1) TINT Re-average visibilities (sec) or corr.avg. time if known FASTSW > 0 Correct fast-sw source names AUTOFLAG Level of automatic flags used < 0: no automatic flagging. = 0: default FLAGR = 1: flag beginning of scans PHAINT phase solution interval (min) AMPINT ampl. solution interval (min) REFANT Reference antenna number DOMODEL > 0 Use standard flux calibrator models Note that most standard flux calibrators have models but the absence of a model will make DOOSRO CRASH. (see HELP) UVRANGE UV range for flux calibrator (may be used if no model) ** use next 2 lines if flux calib. is NOT standard ** AMPCAL Alternative flux calib. name FLUX Flux calib. total flux dens. PHACAL Phase calibrators '*' = any CALCODE (continuum) All others are your targets BNDCAL Bandpass calibrators (max 5) NOPAUSE > 0 no pause after GETJY AUTOPLOT > 0 make diagnostic plots ** the following lines are for auto-imaging ** DOIMAGES > 0 apply calibration and image IMGTYPE 'CONT', 'PSEU', or 'LINE' for continuum (single image), pseudo cont (image per IF) or line (full image cube) ARRYSIZE Max baseline in kilometers = 0 let procedure find array IMSIZE Square size of image (pixels) NITER Max number of iterations/chan = 0 recommended for LINE CUTOFF Clean threshold (Jy) ALLIMG > 0 also image continuum calibrators > 1 line calibrators too DOEVAUV Only for IMGTYPE='PSEU' and if > 0 then run 'EVAUV' too ** interactive self calibration mode -- not recommended for beginners ** SLFCAL > 0 do interactive selfcal ABS(SLFCAL) the number of iterations See HELP DOOSRO and EXPLAIN SCIMG BADDISK Disks to avoid for scratch QCREATE See help/explain file! ---------------------------------------------------------------- DOOSRO Type: Procedure Use: DOOSRO is a procedure that does quick and dirty VLA calibration and imaging of line and continuum data, including high frequency data. Full polarization calibration is not included. NOTE: This DOOSRO code originates as a modified version of VLARUN To load the procedure into AIPS type: (this is only required once per AIPS session) > RESTORE 0 (recommended, not required) > RUN DOOSRO > COMPRESS To review inputs type: > TASK'DOOSRO';INPUTS To execute it type: > DOOSRO Adverbs: CATNUM, or all of INNAME, INCLASS, INSEQ (and WORKDISK for both): The catalog number of the file to calibrate; for EVLA data loaded with BDF2AIPS this would be UVEVLA for a yet unprocessed file. Add flagging info on missing receivers, etc., already here in FG1. DOOSRO converts this into a SPLAT0/SPLATL pair to keep the data in spectral window form but also using a channel 0 for speed. If a fisrt instance of DOOSRO has run, the 'SPLAT0' should be chosen. If INNAME etc are used, then set CATNUM to a non-positive value (<=0) i.e. CATNUM=0;GETNAME Do not use both CATNUM and IN<*> TINT: Some EVLA data sets have unnecessary short (i.e., 1 sec) visibility integrations. Set this to a larger value (>=1, typically an integer multiple of the original correlator integration interval) to decrease the data size by this factor. Leave zero to do no averaging, though if the correlator averaging time is known, setting it to that interval (in sec) will take out the guess work in finding a value from the data. FASTSW: Sometimes, with fast-switching, single calibrator may have more than one name. Set FASTSW positive to check the positions (closer than 3 mas in R.A. and DEC.), qualifier and calcode. If sources have the same position, DOOSRO will rename them all with the shortest name. This will prevent multiple images of the same source. Up to 100 source names can be modified. AUTOFLAG: < 0 -> no automated flagging. NOTE: if an FG table is detected, it WILL NOT DO any form of automated flagging on the data. You may not want to do autoflagging when you have very short scans (i.e. in fast-switching mode) and flag by hand. The highest FG-table is always kept. 0 -> Perform FLAGR (OPTYPE'TIME') on the raw multi-source data set DOOSRO estimates the integration time and SOLINT, in FLAGR, is set to 3 times the integration time. 1 -> Also flag beginning of scans (usually necessary). Uses QUACK (OPCODE'BEG'; APARM(2)=MIN(20 SEC, 3 int. times). Again, you may not want to do this if you have short scans (~30s). PHAINT, AMPINT: PHAINT is the solution interval in minutes for phase calibration - typically the scan length on your phase calibrator, but much shorter (0.2-0.5) for high-frequency data. AMPINT is the solution interval for amplitude calibration - probably best between 1-10 times the value of PHAINT. DOOSRO first calibrates the phases, then the amplitudes (including phase), i.e., the second SN table should have phases very close to 0. REFANT: # of antenna to be used as reference antenna, should be well behaving antenna towards to middle of array. AIPS will make a choice if left zero. DOMODEL: > 0 -> CALIB will use a standard model for any of the five standard flux density calibrators (3C48, 3C138, 3C147, 3C286, 3C295, or their standardized IAU names - see EXPLAIN DOOSRO), assuming they exist. Currently they exist for most calibrators and bands, and more are added all the time. For the latest available models type 'CALDIR' and/or 'EXPLAIN CALRD'. For lower frequencies, and for smaller arrays, it is usually sufficient to use a non-positive DOMODEL, i.e., to use a point source model for the standard flux density calibrators. !! NOTE THAT IF YOU SELECT THIS MODE, DOOSRO WILL CRASH IF NO MODEL !! !! IS AVAILABLE FOR YOUR PARTICULAR CALIBRATOR. Check this with !! !! 'CALDIR' and/or 'EXPLAIN CALRD'. !! AMPCAL: If none of the standard flux calibrators is observed (see EXPLAIN DOOSRO), then enter the name of an alternative source here. NOTE: if specified it will be used by force even if a standard calibrator is present! So you can force your own flux scale if desired. FLUX: Total flux density of amplitude calibrator specified in AMPCAL. UVRANGE: UV range for which flux calibrator (standard or not) is a point source. Leave zero if you are using a flux calibrator model (DOMODEL>0), or want a point source model approximation for the one in AMPCAL. PHACAL: Specify your continuum phase calibrators. Limited to a total of 20. If there are more, use '*' in the FIRST argument to select sources with any calcode. Include your flux and/or bandpass calibrators if you want them to be calibrated. Any source not appearing in PHACAL are considered targets. BNDCAL: Specify up to five bandpass calibrator sources. Bandpass calibrators defined here can be any (but maximum 5) sources in your data. If multiple sources are specified then an average of the sources is used. NOPAUSE: < 0 then DOOSRO will pause after GETJY calculated the fluxes for the secondary calibrators. This allows you to check the flux densities (specifically their errors) of your secondary calibrators, which is a good diagnostic of the calibration up to this point. Simply press to continue. AUTOPLOT: Make diagnostic plots: < 0 -> No plots 1 -> Only make plot files of SN tables 2 -> Also include plots of CL tables 3 -> (LINE data) add plots of the BP table 4 -> (LINE data) also plot BP calibrators with CL and BP table applied DOIMAGES: > 0 -> continue with imaging. < 0 -> do not image. You may check the calibration (in a different window) and continue with imaging by typing: "IMAPIPE(1,,)" in the DOOSRO window directly after the calibration part has finished. The '1' in the first argument of IMAPIPE means to start with SPLIT, but if you have SPLIT the data already in the other window, use a 'zero' instead. IMGTYPE: Choice of 'CONT', 'PSEU', or 'LINE' (no default). For a single image averaged over all channels and IFs (spectral windows) use 'CONT'. For spectral line applications, 'LINE' will make separate cubes retaining all channels for each IF/spectral window (producing one cube per IF). Note that 'CONT' is a proper on-the-fly averaging of the visibilities. The 'PSEU' will make so-called pseudo continuum or reference images; a channel averaged continuum image for each IF/spectral window, combined in an image cube. For example, an 8 IF visibility data set with 256 channels per IF will result in 8 pseudo-continuum images, each averaged over the inner 240 (256*30/32) channels. 1/32 of each edge is skipped for cubes of more than 128 channels, 1/16 of each edge for fewer. ARRYSIZE (if DOIMAGES>0): Maximum baseline length in kilometers; this sets the resolution. The pixel size will be 17.5/freq(GHz)/ARRYSIZE. For the VLA arrays use 35.4 (A-array), 10.8 (B), 3.3 (C), 1 (D), or 73 (PT-link) kilometer. If =0, DOOSRO will guess the maximum unprojected baseline from the antenna file and set ARRYSIZE to about the above values. If <0, SETFC will be used to figure out the best cell size. IMSIZE (if DOIMAGES>0): Target image size in pixels, with a minimum of 128. For calibrators the default is 256. < 0, AIPS will try to image the full primary beam (using SETFC). < -9, then this also applies to calibrator sources. NITER (if DOIMAGES>0): The number of clean components to be used in the imaging. Because spectral line data can take a very long time to image you may want to use zero or a low number of iterations and check that there is no bad data or a faulty calibration. Then you can re-imaging with more iterations. If ALLIMG >0 (i.e., image calibrators), 500 iterations is used as there should be no need for deep cleans for calibration check images. However if IMSIZE<-9, then the number of iterations=NITER, for all sources. If negative, NITER=6e6, effectively using CUTOFF as the only criterion of when to stop. Note that NITER=0 means zero iterations, i.e., make the dirty image (and ignore CUTOFF). CUTOFF (if DOIMAGES>0): Stop cleaning when this level (in Jy) is reached in the residual image. < 0 and NITER >>> 0, then it will stop cleaning after the first negative clean component. Same for calibrators and targets, but also competes with NITER, i.e., whichever is reached first will determine when clean stops. < 0 and NITER < 0 then DOOSRO will estimate a conservative value for the noise level from the visibility data header, and stop at three times this noise level. NOTE that for strong sources the dynamic range limitation may prevent it from reaching this limit - it is VERY wise to set either NITER or CUTOFF (or both) on a first trial of using the pipeline on a particular data set. ALLIMG (if DOIMAGES>0): > 0 -> image calibrators also. > 0 ALLIMG >= 1 -> only image continuum calibrators in spectral line dataset. > 1 -> image both continuum and line calibrators. Set IMSIZE to <-9 if you want larger images than 256 pixels squared and deeper cleans than 500 iterations for the calibrators. DOEVAUV (if DOIMAGES>0): Only used when IMGTYPE='PSEU'. If > 0 then after the imaging, compare the pseudo continuum image with the SPLAT0 continuum UV data set. That is, per IF run task 'EVAUV' and dump the statistics/results to the terminal. If > 1 or if AUTOPLOT > 0 then make histograms. SLFCAL (if DOIMAGES>0): <> 0 -> do self-calibration for targets only in continuum data (SLFCAL is ignored for spectral line data). > 0 -> you wish to interact with the image using the AIPS TV, this includes UV data editing options. < 0 -> only display at the end of each clean. ABS(SLFCAL) specifies how many cycles of self-cal to do. This option should be used with EXTREME care. Care should be taken that there is enough flux in the field for self-cal to work. Note that the input PHAINT is taken as the solution interval, which in most cases will be an invalid assumption !! USE OF SLFCAL BY NOVICES IS HIGHLY DISCOURAGED. !! BADDISK Disk not to use for scratch files. Usually only used if there is a read-only or 100% full disk. QCREATE Only use if you understand its implications! Set > 0 to speed up output file creation. If set > 0, it will crash the pipeline if not enough disk space on the working disk is available. Suppose the original data set is X GB in size; another X is needed for TYAPL (if not skipped, see hint 6 below), as well as X/Tavg for SPLATL, plus X/Tavg for SPLITs (where Tavg is the amount of averaging of visibilities). That is, X+2X/Tavg more than the original. This still excludes the disk space needed for imaging, so only use QCREATE if you know the original data sise and have made sure more than the expected disk space is available on the working disk. But of course this disk space requirement also applies for QCREATE <= 0 ... --------------------------------------------------------------------------- DOOSRO : Procedure to calibrate VLA data blindly. Documenter: Lorant Sjouwerman, Amy Mioduszewski Related Programs: VLA calibration, imaging and plotting routines Type RUN DOOSRO to define the DOOSRO procedure (once is enough) BEFORE RUNNING DOOSRO: 1) Load data with BDF2AIPS (using Obit) or FITLD/UVLOD 2) Flag the known bad data and add the flags into FG table 1. If a run of DOOSRO has produced a SPLAT0/SPLATL pair these inital flags will be applied. For additional flagging, add to FG 1 attached to the SPLAT0 file; if there is a flag table then AUTOFLAGing is disallowed. 3) If preprocessed data, compile all flagging in the continuum (SPLAT0) flag table #1. Also add line flags here to the first flag table attached to the SPLAT0 dataset. 4) Check for long (>12 char) source names - typically in mozaics and for eg. full IRAS or CXO names. DOOSRO expects names to be <= 12 characters, so they need to be changed if longer than 12 char. If you don't care about the exact names you can get approximate/reversed short names by running the predefined procedure 'shortnames' on the data file (note, if EVLA data then run it both on SPLAT0 and SPLATL). 5) Check and rename the dummy sources in the SU table with TABPUT/TABED (ie, source enties that appear twice: rename the one without calcode). 6) If you want to speed things up at the start, opt to skip applying the SysPower corrections and thus skip to recompute all visibilities by deleting (after TASAV) the SY table. 7) If you want to speed things up at the imaging stage, opt to average the data more than you'd notmally do, using TINT. Note that flag tables with numbers higher than 1 get deleted at restarts. CLEAN STARTING CONDITIONS Make sure only one frequency-ID is present (otherwise use UVCOP to split them apart and INDXR to re-index the files). It can process both continuum and line data, but the line files must have inclass 'SPLAT0' and 'SPLATL'. If any, flags must be made in FG table number 1 on the continuum or 'SPLAT0' files, so if you flag the 'SPLATL' data you have to copy the line flags/flag-table to the 'SPLAT0' file. Restarting is straightforward - fluxes are reset and tables are deleted although naming back fast-switching sources is irreversible (FASTSW>0). OTHER NOTES: - There are NO DEFAULTS! - Assumes you have observed 3C286 or other standard VLA amplitude calibrator (see below) for absolute amplitude calibration. - Will use up to 5 sources (maybe 3C286 etc) for bandpass in SPLATL, - Will use up to 20 possible phase calibrators (or more if '*'). PRIMARY FLUX CALIBRATORS: List of all names recognized as a VLA amplitude calibrator in SETJY: - 3C48 is also known as: 0134+329, 0137+331, or J0137+3309 - 3C138 is also known as: 0518+165, 0521+166, or J0521+1638 - 3C147 is also known as: 0538+498, 0542+498, or J0542+4951 - 3C286 is also known as: 1328+307, 1331+305, or J1331+3030 - 3C295 is also known as: 1409+524, 1411+522, or J1411+5212 At least one of these names (3C or other) must be in the data set for the flux calibration. If a different source is used, then you have to specify this other source using AMPCAL and FLUX (and maybe UVRANGE). ADVICE! When using DOOSRO for the first time on a data set (or on line data) do not do any cleaning (NITER=0), or self-cal (very fragile!). It will go much faster and tell you right away if you should expect problems. If you switch on autoflagging, you'll see where extra flags are needed and whether it did what you expected and intended (i.e., if there are any typo's in the input; if you can you do self-cal; if you should find better reference antenna, PHAINT, etc). ----------------------------------------------------------------------------