AIPS HELP file for VLARUN in 31DEC22
As of Sun Feb 5 20:03:39 2023
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
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
BADDISK Disks to avoid for scratch
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
To review inputs type:
To execute it type:
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.
!! NOTE THAT IF YOU SELECT THIS MODE, VLARUN WILL CRASH IF NO MODEL !!
!! IS AVAILABLE FOR YOUR PARTICULAR CALIBRATOR. Check this with !!
!! '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
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.
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, 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.
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 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.
ALLIMG (if DOIMAGES>0):
> 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.
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. !!
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)
BEFORE RUNNING VLARUN:
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
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 '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.
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).
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).