AIPS HELP file for VLARUN in 31DEC25
As of Sat Feb 15 21:59:15 2025
VLARUN: Applies amplitude and phase calibration to VLA data
INPUTS
** 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
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 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
image
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
** interactive self calibration mode
-- not recommended for beginners **
SLFCAL > 0 do interactive selfcal
ABS(SLFCAL) the number of
iterations
See HELP VLARUN and
EXPLAIN SCIMG
BADDISK Disks to avoid for scratch
HELP SECTION
VLARUN
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:
> TASK'VLARUN';INPUTS
To execute it type:
> VLARUN
Adverbs:
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
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, 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.
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
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, 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.
VLARUN 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 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'. !!
AMPCAL:
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.
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. 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.
NOPAUSE:
< 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.
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 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
negativeclean 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 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.
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.
EXPLAIN SECTION
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
disallowed.
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
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 '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).
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 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).
ADVICE!
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).