As of Sat Mar 17 17:49:23 2018

VLARUN: Applies amplitude and phase calibration to VLA data


          ** Type RUN VLARUN to load this procedure **
WORKDISK                           Working disk, thus in/outdisk
CATNUM                             Catalog number of the UV-file
                                    must be 'CH 0' for line data
INNAME                             Input UV file name (CATNUM<1)
INCLASS                            Input UV file class(CATNUM<1)
INSEQ                              Input UV file seq. (CATNUM<1)
FASTSW                             > 0 Correct fast-sw source
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 VLARUN CRASH. (see HELP)
UVRANGE                            UV range for flux calibrator
                                   (set 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)
                                   *BNDCAL only used for LINE*
NOPAUSE                            > 0 no pause after GETJY
AUTOPLOT                           > 0 make diagnostic plots
          ** the following lines are for auto-imaging **
DOIMAGES                           > 0 apply calibration and
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
                                   > 1 line calibrators too
          ** interactive self calibration mode
                    -- not recommended for beginners **
SLFCAL                             > 0 do interactive selfcal
                                   ABS(SLFCAL) the number of
                                   See HELP VLARUN and
                                   EXPLAIN SCIMG
BADDISK                            Disks to avoid for scratch


Type: Procedure
Use:  VLARUN 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.

      To load the procedure into AIPS type:
             (this is only required once per AIPS session)
          > RESTORE 0 (recommended, not required)
          > RUN VLARUN
          > COMPRESS
      To review inputs type:
      To execute it type:
          > VLARUN

CATNUM, or all of INNAME, INCLASS, INSEQ (and WORKDISK for both):
      The catalog number of the file to calibrate (the continuum, or the
      'CH 0'-file for spectral line data). If INNAME etc are used, then
      set CATNUM to a non-positive value (<=0) -> CATNUM=0;GETNAME 

      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, VLARUN 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.

      < 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
           VLARUN 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 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.
      VLARUN first calibrates the phases, then the amplitudes (including
      phase), i.e., the second SN table should have phases very close to 0.

      # 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

      > 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 VLARUN), 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.

      !! 'CALDIR' and/or 'EXPLAIN CALRD'.                                 !!

      If none of the standard flux calibrators is observed (see EXPLAIN VLARUN),
      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.

      Total flux density of amplitude calibrator specified in AMPCAL.

      UV range for which flux calibrator (standard or not) is a point
      Leave zero if you are using a flux calibrator model (DOMODEL>0),
      or want a point source model approximation for the one in AMPCAL.

      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

      Specify up to five bandpass calibrator sources. Only used for line data.
      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.

      < 0 then VLARUN 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.

      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

     > 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
            VLARUN 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.

     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, VLARUN will guess the maximum unprojected baseline from the
     antenna file and ARRAYSIZE to the above values.
     If <0, SETFC will be used to figure out the best cell size.

     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.

     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).

     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 VLARUN 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.

     > 0 -> image calibrators also.
     > 0 ALLIMG >= 1 -> only image continuum calibrators in spectral line
     > 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.

     <> 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

     Disk not to use for scratch files.  Usually only used if there is a
     read-only or 100 percent full disk.


VLARUN :            Procedure to calibrate VLA data blindly.
Documenter:         Lorant Sjouwerman, Amy Mioduszewski
Related Programs:   VLA calibration, imaging and plotting routines

Type RUN VLARUN to define the VLARUN procedure (once is enough)

    1) Load data with FILLM
    2) Flag, although if there is a flag table then AUTOFLAGing is
    3) If spectral line data, compile all flagging in the continuum (CH 0)
       flag table #1.  Also add line flags here to the first flag table
       attached to the CH 0 dataset.
    4) Check for long (>12 char) source names - typically in mozaics and
       for eg. full IRAS or CXO names. VLARUN 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 spectral data then run it both on CH 0 and LINE).

    Note that flag tables with numbers higher than 1 get deleted at

      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 'CH 0'
      and 'LINE'. If any, flags must be made in FG table number 1 on the
      continuum or 'CH 0' files, so if you flag the 'LINE' data you have to
      copy the line flags/flag-table to the 'CH 0' file.  Restarting is
      straightforward - fluxes are reset and tables are deleted although
      naming back fast-switching sources is irreversible (FASTSW>0).

    - 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 LINE,
    - Will use up to 20 possible phase 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).

      When using VLARUN 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).