AIPS NRAO AIPS HELP file for PIPEAIPS in 31DEC25



As of Wed Apr 23 14:25:48 2025


PIPEAIPS: LLLLLLLLLLLLUUUUUUUUUUUU CCCCCCCCCCCCCCCCCCCCCCCCCCCCC

INPUTS

PIPEAIPS: Amp+phase calibration for conn. elem. interferometers

          ** Type RUN PIPEAIPS 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
FACTOR                             Frequency averaging? 0,2 or 4
FASTSW                             > 0 Correct fast-sw source
                                       names
VLANTCOR                           Run VLANT? Only do once!
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)
BASEBAND                           Data has N equal basebands:
                                    see help and FRING aparm(5)
BBMAXIF                            For unequal IFs/baseband set
                                    BASEBAND=-1 and fill up to 4
                                    indices of max IFs. See help
BPNORM    -2.5        1.5          Bandpass 'divide-by' control
                                    see help, BPASS bpassprm(5)
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 this CRASH. (see HELP)
VLAOBS                             Alternative MODEL frequency,
                                    see explain file for CALRD
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                            'SIMP','CONT','PSEU' & 'LINE'
                                    for continuum (single image)
                                    from "Ch.0" or "line" cube,
                                    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 PIPEAIPS and
                                   EXPLAIN SCIMG
BADDISK                            Disks to avoid for scratch
QCREATE                            See help/explain file!

HELP SECTION

PIPEAIPS
Type: Procedure
Use:  PIPEAIPS 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 PIPEAIPS code originates from earlier VLARUN/DOOSRO versions

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

Adverbs:
CATNUM, or all of INNAME, INCLASS, INSEQ (and WORKDISK for both):
      The catalog number of the file to calibrate; for VLA data loaded
      with BDF2AIPS this would be UVEVLA for a yet unprocessed file.
      Add flagging info on missing receivers, etc., already here in FG1.
      PIPEAIPS 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 first instance of PIPEAIPS 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 (VLA) 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.

FACTOR:
      Reduce data size by averaging the frequency axis by a factor 2 or
      4.  Note that this is done after fringe fitting (i.e., correcting
      delay) when creating the SPLATL file. The TYAPL file remains
      unaveraged.

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, PIPEAIPS 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.

VLANTCOR:
      Skip running VLANT if < 0 or for an input file with class 'UVLANT'
      or for an input file with class 'SPLAT*' (i.e. 'SPLAT0' and
      'SPLATL').  VLANT should be run only once so set negative if you
      know it was run.  If set to 0, the pipeline runs VLANT and will
      change the class of the input file (e.g. 'UVEVLA' or 'UVDATA') to
      'UVLANT' and thus skip it on successive runs of PIPEAIPS.

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

BASEBAND, BBMAXIF:
      In FRING set aparm(5) to make solutions for combinations of  1, 2
      or 4 equal divisions of the IFs. Thus APARM(5) will be set to 1,
      3 or 4.  If left to 0 it will assume default wideband continuum
      and choose two basebands for bands up to K (18 GHz), four for K,
      Ka and Q bands.  If an unequal number of subbands per basebands
      WAS used (eg 11,15,14 and 14) use BASEBAND=-1 (i.e. to set
      aparm(5)=-1) and fill BBMAXIF with the *ending* IF numbers (i.e.,
      to set bparm, see help FRING), in the example:
      BASEBAND=-1; BBMAXIF=11,26,40,54
      (that is: 11,11+15,11+15+14,11+15+14+14).
      BBMAXIF uses up to 4 values, derive them from LISTR, using OPTYPE
      'scan'.

BPNORM:
      The value of BPASSPRM(5) in BPASS for line data; Defaults to zero,
      but some data sets are better off using, e.g, -2. See EXPLAIN
      BPASS

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 PIPEAIPS),
      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, PIPEAIPS WILL CRASH IF !!
      !! NO MODEL IS AVAILABLE FOR YOUR PARTICULAR CALIBRATOR.     !!
      !! Check this with 'CALDIR' and/or 'EXPLAIN CALRD'.          !!

VLAOBS:
      If an alternative model available (with CALRD) is preferred over
      the standard flux calibrator model for the band (the typical L, C,
      K, etc models), provide the string that combines the model with
      the source in VLAOBS. That is, provide the string '2.7' to use
      3C138_2.7.MODEL.

AMPCAL:
      If none of the standard flux calibrators is observed (see EXPLAIN
      PIPEAIPS), then enter the name of an alternative source here.
      NOTE: if specified it will be used by force even if a standard
      calibrator 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 PIPEAIPS 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 PIPEAIPS 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 'SIMP', 'CONT', 'PSEU', or 'LINE' (no default).  For a
     single image averaged over all channels and IFs (spectral windows)
     use 'SIMP' or 'CONT'.  Here 'SIMP' uses the IF-channel averaged
     data set (i.e. "CH 0" or "SPLAT0"), whereas 'CONT' uses all
     (frequency averaged) channels (a.k.a. "LINE"or "SPLATL") data thus
     reducing the potential effects of bandwidth smearing (within an IF
     bandwidth) at the cost of slower operation.  Note that 'CONT' is a
     proper on-the-fly averaging of the visibilities.  For spectral
     line applications, 'LINE' will make separate cubes retaining all
     channels for each IF/spectral window (producing one cube per IF).
     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, PIPEAIPS will guess the maximum unprojected
     baseline from the antenna file and set ARRYSIZE to about the above
     values but this code is fragile. 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 PIPEAIPS will estimate a conservative value
         forthe 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 percent 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 ...

EXPLAIN SECTION

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

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

BEFORE RUNNING PIPEAIPS:
    0) Load data with BDF2AIPS (using Obit) or FITLD/UVLOD
    1) Recommended to use TABPUT to place calibrator codes on your
       calibrators
    2) Flag the known bad data and add the flags into FG table 1.  If a
       run of PIPEAIPS 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. PIPEAIPS 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
       very first one) or flag scans that are typically <1 min at the
       start before a longer one.
    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 normally 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!
      The best results are obtained if flagging of bad data is recorded
      in FG table 1 before starting PIPEAIPS. Use UVFLG for known bad
      antennas or basebands (from the operator log), a semi-automated
      procedure like RFLAG, FGSPW, or manual usage of e.g. WIPER, CLIP,
      TVFLG, SPFLG, etc.  Make sure that these flags end up in FG#1
      (outfgver=1) or they will be lost on reruns. A TASAV before and
      after flagging is good practice!

      When using PIPEAIPS 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 a better
      reference antenna, different PHAINT, etc).


AIPS