C.5 VLBA Pipeline

VLBARUN is a procedure which uses the VLBA calibration procedures (from VLBAUTIL) and some logic to calibrate and image VLBA data. VLBARUN attempts to make intelligent decisions on defaults, so it can be run fairly automatically if the names of the sources are known. If desired, VLBARUN will produce diagnostic plot files and write them to disk, creating an HTML file to ease examination of these files. Images will be produced, but no self-cal is done, so the images should be considered diagnostic in nature.

VLBARUN does all the calibration steps described in C.1 and the next few sections. It does not do polarization calibration. In 31DEC19 it offers options to use CLIP and/or RFLAG to do flagging. It also offers options to flag data at low elevations and to try to clean up bad values in the system temperature table. Although VLBARUN is intended for simple VLBI observations, the addition of non-VLBA antennas should work if all the non-VLBA system temperature and gain curve information are loaded into the first TY and GC tables.

Sample inputs for procedure VLBARUN are:

> RUN VLBAUTIL  C R

to acquire the procedures used by VLBARUN.

> RUN VLBARUN  C R

to acquire VLBARUN.

> INDISK n ; GETN ctn  C R

to specify the input data file.

> OPTYPE ’CONT’  C R

to say this is a continuum data set.

> CLINT 0  C R

to use default.

> CHREFANT ’FD’  C R

to set reference antenna to Fort Davis.

> CHINC -1  C R

to have the procedure determine an appropriate channel increment for FRING.

> TIMERANG 0  C R

to have VLBARUN determine a good instrumental delay calibration scan.

> INVER 0  C R

PC table to use, -1 if you want to force manual phase cal.

> CALSOUR ’CAL-BAND’, ’CAL-PHASE’, ’CAL-AMP’  C R

to list calibrators, bandpass calibrator must be first.

> SOURCES ’CAL-PHASE’, ’TARGET’,  C R

to list phase referencing and target pairs.

> INFILE   C R

set if you want to apply a zenith delay file produced by DELZN.

> SOLINT 0  C R

to use default.

> IMSIZE 512  C R

to make images and specify size of target images.

> FACTOR 0  C R

to make calibrator images 128x128.

> DOCLIP fp,fc  C R

to run CLIP to flag a sample when the parallel-hand flux is above |fp| or the cross-hand flux is above |fc|. If fp is positive, the clip is done after amplitude calibration; if negative, it is done before the bandpass and amplitude calibration. The appropriate values for fp and fc are different in these two cases.

> DOFLAG 1  C R

to run RFLAG on each source individually.

> TYSMOLEV 100 C R

to clip system temperatures above 100 K with median-window filtering at 10 K and replacing the clipped values with nearby good ones.

> ELEVLIM 15  C R

to flag out all data for which the elevation is < 15 degrees.

> BPASS5 -2  C R

to normalize bandpass scans before the fit. Default is +1 to normalize the bandpass functions themselves without normalization of the data.

> CALTASK ’CALIBS’  C R

to use FRING for the initial time series calibration but use CALIB for any self-cal. Other choices are CALIBand FRING (the default) to use the specified task for all time series calibrations.

> DOPLOT 1  C R

to make some diagnostic plots. Use level 2 only if there are serious issues; it generates a lot of plots.

> OUTFILE /directory/name  C R

to specify directory for output plots. If this is set, plots are written out from AIPS and organized in an HTML file for easy viewing. The plots, HTML file, and message file contents are put in a dated subdirectory below the specified directory.

> OUTTEXT email@somewhere.edu  C R

to specify an e-mail address if the user wants to be notified when the pipeline is done.

> BADDISK 0  C R

to specify which disks to avoid for scratch.

> VLBARUN  C R

to run the procedure.

It is a good idea to examine your TY table with SNPLT before running VLBARUN; this will tell you what a reasonble upper limit to Tsys will be and whether there are bad values in need of correction. SNRMS provides a summary of the statistics of tables such as the TY table. It’s maxima and rmses will make problems with the table very clear. Note that editing with CLIP is always a good idea. RFLAG appears to work well at low frequencies but to be overly enthusiastic at C-band and above. Note that the flagging is done after all calibration steps, so you may examine your data with and without the new flags to determine their correctness. RFLAG is run using baseline-dependent clip levels and so should work with arrays containing high-sensitivity telescopes as well as the VLBA. You may wish to use VLBARUN without RFLAG (or to discard the flags produced by RFLAG) and then run SPFLG to flag the visibility data interactively. Then use VLBARUN over again applying the manually produced flags.

VLBARUN will then run and produce the requested number of diagnostic plots. For details on the plots produced for each level of DOPLOT see EXPLAIN VLBARUN. If an e-mail address is specified then a VLBARUN DONE or VLBARUN FAILED message will be sent. However, the VLBARUN FAILED message will only be sent if VLBARUN failed because of problems with the inputs, if VLBARUN failed because a task it was running failed this message is not sent. It is highly recommended that the user read the explain file for VLBARUN.

A similar RUN file named VLBAMPHC is available in 31DEC19 to calibrate, flag, and image data sets for secondary phase stopping centers when DiFX has been used to correlate multiple centers from a single pointing. A pipeline called VLBARFI appeared in 31DEC21. It calibrates a data set concentrating on the autocorrelation data on which it performs a statistical analysis.