AIPS HELP file for VLBARUN in 31DEC18
As of Mon Sep 24 13:40:00 2018
VLBARUN: Applies amplitude and phase calibration to VLBA data !
To run this procedure you MUST type RUN VLBAUTIL and
RUN VLBARUN first to define the procedures in AIPS.
-- Load the data from disk --
DATAIN Disk file name
DOUVCOMP Compress data? Use -1, 0 or 1
OUTNAME File name (name)
OUTDISK Working disk with ample space
-- OR existing file --
INNAME Input file name
INCLASS Input file class
INSEQ Input file sequence number
INDISK Disk number for input file
OPTYPE For CONT, PSEU or SPEC (LINE)
CLINT CL table interval in minutes.
CHREFANT Reference antenna NAME
TIMERANG A good bandpass scan, or use
scan# in TIMERANG(1)+rest=0
INVER -1.0 46655.0 PC table to use
-1 => don't use Pulse cals
do manual phase cal
CALSOUR List ALL Fring fit & CAL sour
FIRST is bandpass calib
SOURCES ONLY FOR PHASE REFERENCING:
Source *PAIRS* to calibrate
START each pair with phase
referencing calibrator, if
2nd='*': all non-CALSOUR
are phase-referenced to 1st
INFILE Set to DELZN correction file
SOLINT Time interval for fringe-fit
IMSIZE Image size for target SOURCES
=-1 for no images
FACTOR CALSOUR IMSIZE (FACTORx128)
Hint: when setting directory and e-mail lower-case
letters can be retained by NOT using the close quote.
DOPLOT <= 0 no plots;=1 some plots
>1 huge number of plots
OUTFILE DIRECTORY FOR HTML AND PLOT
FILES: if you want an html
file with plots please set
the dir where the html and
plot files can be put.
OUTTEXT E-MAIL ADDRESS: if you want
an e-mail when the script
is complete, set the
BADDISK Disks to avoid for scratch
Use: VLBARUN is the procedure that uses the VLBA calibration procedures
(VLBAUTIL) to calibrate VLBA data. See the explain file for a detailed
description of the procedure.
Simple visibility flagging, bandpass calibration, and
ionospheric (total electron content) corrections are applied before
fringe fitting and averaging. It may attempt to self-cal the
calibrators and will image the targets.
NOTE: currently this procedure is intended for simple experiments!
Type RUN VLBAUTIL and RUN VLBARUN to define the VLBARUN procedures.
The procedure is run by typing : VLBARUN
The procedure will check the inputs (as far as it can) to avoid later
interruptions, and then proceed directly, if the data is already on
CLEAN STARTING CONDITIONS
It is best to use one project per user number, as otherwise you may get
into trouble if different projects use the same source names.
It is not recommended to run two pipelines with the same user number
simultaneously, nor overlapping at any time during the processes.
Clean up all files resulting from previous attempts of running the
procedure, except for the original UVDATA and perhaps, when restarting
a specific frequency-ID, also not the F(X)POL files. When restarting
from disk, make sure the UV data has no extra SN, CL, FG etc tables.
Use the procedure P_RESTART (which is defined in VLBARUN) to do this.
If you wish to flag some additional data (because the procedure did
not flag all the bad data automatically), make sure you put the flags
in FG table number 1.
If you have any antennas that do not have Tsys or Gain curves missing
from the data, please load them with ANTAB into TY and GC tables #1.
It is a VERY good idea to run TASAV before you do this to keep the
original TY, GC, BL and also FG tables number 1 in case of disasters.
Make sure there is enough disk space available on OUTDISK, about 4 to
5 times the expected compressed UVDATA set. For spectral line probably
you need much more because it will make spectral line image cubes.
DATAIN......48-character name of the disk file from which to read a
FITS file. It must be in the form
where is the remote computer name, is the
environment variable (logical name) for the disk area in
which the file named is stored. is
usually omitted when the file is local to the current
computer. If DATAIN is not found, the task will try
DATAIN with the character 1 appended.
Beginning 2003-Oct-16 FITLD can read more than one disk
file at a time. In that case, they must all have the
same name except that the last letter(s) are the
sequence number 1 through NCOUNT with no leading zeros.
DATAIN must give the base name only, omitting the
sequence number. Then either
DATAIN = 'MYDATA:file_
DATAIN = 'MYDATA:file_1
can access files in $MYDATA named file_1, file_2,
file_3, etc. Note that this is similar to the pieces of
a FITS pieced UV-table data set, but only one UV-table
data set may be read at a time.
DOUVCOMP....If true (> 0.5) then output data will be
compressed which saves disk space at the expense
of losing some weighting information.
OUTNAME.....The name for the output files. The output files
will all be given the class UVDATA and assigned
distinct sequence numbers as needed.
OUTDISK.....The disk drive number for the output data if loading from
disk. Choose a disk with a large amount of space. If
data is already loaded into AIPS (i.e. you are using
INNAME, INCLASS etc) then OUTDISK is ignored and INDISK
INNAME......Input UV file name (name) that is already loaded.
Note that you CANNOT use both DATAIN/OUTNAME/OUTDISK
INCLASS.....Input UV file name (class) that is already loaded.
INSEQ.......Input UV file name (seq. #) that is already loaded.
INDISK......Disk drive # of input UV file. NOTE: this is also
used as OUTDISK.
OPTYPE......The type of observation and requested output files:
'' = 'CONT' for channels < 65; 'SPEC' otherwise
'CONT' = Plain continuum observations, uses pulse cals
unless INVER = -1
'PSEU' = Pseudo-continuum observations, uses pulse cals
unless INVER = -1. The data is NOT averaged
over channels, but the resulting images are
continuum images - used for large FOVs
'SPEC' = Spectral line observations. Manual pulse-cal is
performed. Data is unaveraged and images are
spectral line cubes of the phase referenced target
'LINE' = Same as 'SPEC'.
CLINT.......Calibration table interval in minutes. This should
normally be in the range 0.25 to 1.0. If <=0 then
0.25 is assumed.
CHREFANT....Name of reference antenna. If not set, a sensible antenna in
the southwest will be tried (FD, PT, LA or KP).
TIMERANG....Time range on which ALL antennas have good data on the bandpass
calibrator (see below, CALSOUR(1)). Used for instrumental
phase calibration by either the pulse-cals or manually by
running FRING on this scan.
If you know the scan number, you can use the scan number
e.g., set TIMERANGE=66,0 to get the time range associated with
If all 0, then VLBARUN will try to find a good scan by running
BSCAN on the bandpass calibrator.
INVER.......PC table to use, if -1 do manual phase cal
CALSOUR.....All the calibrators should be listed here. All these sources
will be FRING fit. IMPORTANT: the FIRST source is the source
used for instrumental phase and bandpass calibration. If
TIMERANGE was set, it must be a scan on CALSOUR(1).
If you want all sources fringe fitted then you may use
CALSOUR(2)='*' but remember to also specify CALSOUR(1).
These sources will be imaged in (pseudo) continuum mode.
SOURCES.....For phase referencing. List PAIRS of phase-referencing/target
sources. The phase calibrator should be the first in the pair,
i.e., with the odd index. Each target should be the second in
the pair, i.e., have an even index. All the phase calibrators
must be in the CALSOUR list as well. If your are not
phase-referencing any source, then leave SOURCES blank. If
SOURCES = 'PRCAL', '*' then all non-calibrators are phase
referenced to 'PRCAL'.
There is a maximum of 15 pairs, a total of 30 source fields.
SOLINT......The solution interval (min.) for FRING fit. 0 => 1 minute
If SOLINT > Scan/2 (in Multisource) SOLINT = Scan.
INFILE......If you want to apply a DELZN corrections file, set INFILE to
the filename. See CLCOR explain file for more details, the
file format is the OPCODE='ATMO' format (which is the same
as DELZN produces).
IMSIZE......Output target image sizes. Minimum IMSIZE of 512 up to
8192 pixels. Sources listed in CALSOUR are automatically
imaged with a size of 128 by 128 unless FACTOR is set.
Pixel size is automatically set by frequency:
IMSIZE=-1 do not make images.
FACTOR......scaled image size of CALSOURs. Image size of sources listed
in CALSOUR is FACTOR*128. The maximum FACTOR is 64.
DOPLOT......Make diagnostic plots to judge quality of procedure results.
<=0 => no plots
1 => some plots
2 => lots of plots (could be hundreds)
OUTFILE.....Directory of html and plots files. If you want the diagnostic
plots written to disk and an html file created to make the
plots easier to examine please set directory here. This is
limited to 37 characters (including final /). Environmental
variables are allowed and must end with a ':'. Mixed
environmental and regular are not allowed, e.g.,
IT IS STRONGLY RECOMMENDED THAT THE DIRECTORY GIVEN IS EMPTY.
OUTTEXT.....E-mail address for notifications when script is done or
BADDISK.....A list of disk numbers to be avoided when creating scratch
VLBARUN: Procedure that attempts to calibrate VLBI data blindly.
Documentor: Amy Mioduszewski, email@example.com.
Related Programs: All VLBAUTIL procs, BPASS, SPLIT, IMAGR,..
POSSM, VPLOT and many many more
VLBARUN applies VLBAUTIL procedures to simple VLBI experiments. VLBARUN
attempts to make sensible choices if inputs are left to default. The only
inputs that must be set are:
DATAIN or INNAME (INCLASS, INSEQ and INDISK) -> so the dataset is defined
CALSOUR(1) -> so VLBARUN knows what calibrator to use as the bandpass/
instrumental phase calibrator
SOURCES -> if the experiment is phase referenced
More detail about defaults
VLBARUN tries to pick sensible defaults if inputs are left blank. Below
describes how it makes these decisions.
OPTYPE='' -> VLBARUN checks the total number of channels and decides from
that whether dataset is continuum (64 or less) or spectral
CLINT=0 -> set to 0.25 minutes
CHREFANT='' -> Chooses the first antenna present from the southwest VLBA
antennas in the order of FD, PT, LA and KP.
TIMERANGE=0 -> Runs the task BSCAN on CALSOUR(1) to select scan with the
highest signal to noise with all the antennas present. If
INVER>=0 then BSCAN also checks if there are PC table
entries for that scan.
VLBARUN offers the option to create diagnostic plots. If DOPLOT is set
to 0 no plots are made. For 0<DOPLOT<1.5 (i.e. DOPLOT=1) the following plots
-POSSM plot of bandpass solution
-SNPLT of amplitudes in CL table after ACSCL
-SNPLT of amplitudes in CL table after APCAL
-POSSM plots of amp and phase after instrumental phase calibration
-SNPLT of phase, delay, rate and SNR in CL table after FRING
-VPLOT of phase of data for phase reference sources with all calibration
-KNTR (contour) plots of the images produced, if images are requested
For DOPLOT>1.5, IN ADDITION to the above plots the following are produced
-SNPLT of amplitudes in SN table after ACSCL
-SNPLT of amplitudes in SN table after ACCOR
-SNPLT of amplitudes in CL table after ACCOR
-SNPLT of amplitudes in SN table after APCAL
-SNPLT of phase, delay, rate and SNR in SN table after FRING
-SNPLT of amplitude in CL table after FRING
Output of plots to disk, creation of html file and e-mail message
VLBARUN will create .gif files on disk in the directory defined by OUTFILE of
the plots that are requested. It then makes a vlbarun.html file that includes
headings for the plots and at the bottom a list of the CL tables and what
calibration is added to each. This vlbarun.html file is intended to make
examination of the diagnostic plots easier, so the user can quickly judge whether
the pipeline worked.
It is STRONGLY recommended that the directory defined by OUTFILE be an empty
directory. VLBARUN creates and deletes files in this directory so it is safer
if there aren't any files for VLBARUN to potentially clobber or delete.
VLBARUN checks if there is an existing vlbarun.html file and will not run if
It is also recommended that if OUTFILE is used then an e-mail address be
provided in OUTTEXT.
The e-mail will state whether VLBARUN is done (subject: VLBARUN DONE) or failed
(subject: VLBARUN FAILED). The FAILED message only catches failure do to a
problem with how VLBARUN was set up, if the pipeline fails because a task fails
that is not captured and no e-mail message is sent. If OUTFILE is set, the DONE
message includes the URI to the vlbarun.html file assuming that the machine
you are viewing it on is the "localhost". So if you are on that machine, you
can copy that URI ("file:///etc") into your web browser and look at the plots.
If you are not on the machine where the plots were created then just copying
the file:///... URI will not work.
CONSIDERATIONS FOR MAC OS X AND OTHER OS THAT MIGHT NOT INCLUDE COMMON LINUX
COMMAND-LINE TOOLS -- the output of plots to display using .gif and
html files requires the command-line command "convert". If you do not
have "convert" then you cannot use the OUTFILE input. There are packages you
can install on your machine that will give you access to linux command-
line tools like convert.
What does VLBARUN do?
Below are the basic calibration steps that VLBARUN performs. This does not
include all the plotting etc..
1) checks that the inputs are correct as well as it can, sets some defaults.
2) run VLBATECR - corrects ionosphere if the observing frequency is less than
12 GHz. This procedure uses Global Positioning System (GPS)
models of the electron content in the ionosphere to correct
the dispersive delays caused by the ionosphere. This
correction is particularly important for phase referencing
experiments at low frequency.
3) run VLBAEOPS - corrects Earth Orientation Parameters (EOP) used in correlation.
VLBI correlators must use measurements of the EOPs while
correlating. These change slowly with time and therefore the
EOPs used by the correlator must be continually updated. Even
though the EOPs that a correlator uses are the the most accurate
at the time of correlation, frequently after the correlation the
EOPs are improved. This procedure inserts a correction for the
difference between the EOPs used in correlation and the current
best calculation of the EOPs. This is particularly important
for phase referencing.
4) run VLBACCOR - sampler corrections. This procedure corrects the amplitudes
in cross- correlation spectra due to errors in sampler
thresholds using measurements of auto-correlation spectra
5) run VLBAPCOR or VLBAMPCL - correct instrumental delays if there is more than one
IF. These delays or "instrumental single-band delays" are caused
by the passage of the signal through the electronics of the
baseband converters and can be corrected with either the pulse
cals (VLBAPCOR) or by running FRING on one scan (VLBAMPCL).
6) run VLBABPSS - Runs BPASS to calibrate the bandpass response functions for
7) run VLBAAMP - Runs ACSCL which applies the BP table and previous calibration
tables and corrects the cross-correlation spectra using auto-
correlations. For more information see VLBA Scientific Memo #37
(Craig Walker). Then preforms a-priori amplitude gain calibration
using the gain curves and system temperatures.
8) run VLBAPANG - correct paralactic angle. The RCP and LCP feeds on alt-az
antennas will rotate in position angle with respect to the
source during the course of the observation (all VLBA and
VLA antennas are alt-az). Since this rotation is a simple
geometric effect, it can be corrected by adjusting the phases
without looking at the data. You must do this correction for
polarization and phase referencing experiments.
9) run CLCOR - OPTIONAL, if INFILE is not blank will run CLCOR with OPCODE='ATMO'
in order to apply a DELZN output file specified in INFILE.
8) run FRING - final fringe fit of the data. This step removes the global frequency-
and time-dependent phase errors.
9) run SPLIT - applies final calibration and splits into single source files. If
OPTYPE 'CONT' then frequencies are averaged.
10) run IMAGR - OPTIONAL, if IMSIZE > 0 then produce images of all the sources
using the IMAGR autoboxing feature.