9.3 Loading, fixing and inspecting data

In theory, AIPS can process data from multiple frequency bands (FQ numbers in AIPS parlance) coexisting within the same data set. However, it is recommended that the data be separated into different frequency bands as soon as possible after loading the data and process each FQ number separately. If you wish to do this, you should do it immediately after performing the relevant steps in 9.3. The VLBAUTIL procedures VLBAFQS and VLBAFIX do this automatically (VLBAFIX is recommended and does other “fixing” tasks like fixing subarrays etc.). If you want to do this by hand use the task UVCOP.

9.3.1 Loading data from the VLBA correlator

9.3.1.1 Running FITLD

The information below applies to data from the VLBA Correlator in what the VLBA archive calls “raw” format, more formally known as FITS-IDI format. The archive now also contains data called “calibrated” which have been run through a few of the simplest VLBA procedures but which are nowhere near calibrated. These files are recommended under normal circumstances. They may also be loaded with FITLD, but the DOCONCAT option does not work with the FITS table format used in the archive.

Data generated by the VLBA correlator are loaded from DAT (or Exabyte) tape (or from disk files) into AIPS using FITLD. First, physically load your tape and MOUNT it (3.9), then run FITLD. Often the data on your tape will be divided into a number of separate files (corresponding to separate “correlator jobs”). In this case, run FITLD with NCOUNT set equal to the number of files on the tape (or a suitably large number), as listed on the paper index which comes with the tape. The adverb ANTNAME allows the user to control the antenna numbering if desired. Also set DOCONCAT = 1  C R to ensure that all tape files with the same structure are concatenated into a single AIPS file. Note that standard tape handling tasks (e.g.PRTTP and TPHEAD) can be used to inspect the tape contents.

Note that antennas, sources, frequency IDs, and other things may be numbered differently in different correlator jobs. FITLD fixes all this for you, but only if you set DOCONCAT = 1 and, better still, load as many files as possible in each execution of FITLD. FITLD can load VLBA correlator data from multiple disk files so long as they have the same name plus a consecutive post-pended number beginning with 1. If you forget to put all the related data together with FITLD you can use MATCH to align the antenna numbers followed by DBCON later.

Typical inputs to FITLD would be:

> TASK FITLD’ ; INP  C R

to review the inputs.

> INTAPE n C R

to specify the input tape number.

> NFILES 0  C R

to skip no files on tape.

> DATAIN ’ ’  C R

to load from tape, not from disk.

> OUTNAME ’TEST’ ; OUTCL FITLD  C R

to specify the name of the output file.

> OUTSEQ  0; OUTDI  1  C R

to specify the sequence number and disk of the output.

> OPTY ’ ’  C R

to load any type of file found.

> NCOUNT 20  C R

to load 20 tape files.

> DOUVCOMP 1  C R

to save disk space by writing compressed data.

> DOCONCAT 1  C R

to concatenate files with same data structure into one disk file.

> CLINT t  C R

set CL table interval to t minutes (see discussion below).

> DIGICOR 1  C R

to request digital corrections (usually VLBA correlator only).

> DELCORR 1  C R

to request delay decorrelation corrections (VLBA correlator only).

> WTTHRESH 0.65  C R

flag incoming visibilities with correlator weights less than 0.65.

> SOURCES ’ ’; QUAL 0 C R

to accept all sources found.

> TIMERANG 0  C R

to accept data from all times.

> BCHAN 0; ECHAN 0; BIF 1; EIF 0  C R

to accept all channels in all IFs.

> SELBAND 0  C R

bandwidth to select (kHz).

> SELFREQ 0; FQTOL 0 C R

frequency to select with tolerance of 10 kHz.

> OPCODE ’ ’ C R

to not copy the tape statistics table (’VT’ table).

> GO  C R

to run the program.

This may seem a bit formidable. For straightforward VLBI observations, there is a collection of procedures to simplify matters including the loading of data. Enter

> RUN VLBAUTIL  C R

to acquire the procedures; this need be done only once since they will be remembered.

> INTAPE n C R

to specify the input tape number.

> NCOUNT 20  C R

to load 20 tape files.

> OUTNAME ’TEST’ ; OUTDI 1  C R

to specify the name and disk of the output file.

> DOUVCOMP 1  C R

to save disk space by writing compressed data.

> CLINT t  C R

to set the CL table interval to t minutes (see discussion below).

> INP VLBALOAD  C R

to review the inputs.

> VLBALOAD  C R

to run the procedure.

Because the data files tend to be very large, you will usually write compressed data (DOUVCOMP=1). These files take about 1/3 of the space of ‘uncompressed’ data sets, but cause information about the weights of individual polarizations, spectral channels, and IFs to be lost. There is some loss in dynamic range and sensitivity when the weight information is (partially) compromised. (See Appendix F for an expanded discussion of when to and when not to write ‘compressed’ data sets.) If your observation has more than one DAT or Exabyte tape, simply run FITLD for each tape. Setting DOCONCAT 1 and setting the output file name completely will ensure that the data from separate tapes with compatible observing band/data structure will be appended to existing AIPS files. Generally, after loading all of your data, you will have one file for each such observing band and/or observing mode. However, observations which require multiple passes through the correlator (including MkIII Modes A, B, and C observations) will have one file per observing mode per correlation pass. Data from separate correlator passes can be concatenated using task VBGLU and/or merged with task VBMRG.

Adverb CLINT, which specifies the CL table time sampling interval, must be short compared to the anticipated coherence time. CLINT should be set such that the shortest anticipated fringe-fit interval is spanned by a few CL entries. Time sampling in the CL table that is too coarse can lead to calibration interpolation errors when applying the fringe-fit solutions at later stages of the data reduction. If the interval is made unnecessarily short the CL table may become unmanageably large.

It is recommended that corrections for digital representation of the correlated signals be performed in FITLD under control of adverb DIGICOR, but only for data from the VLBA correlator. DIGICOR should be set to one for all continuum and nearly all spectral line experiments. Set DIGICOR to 3 or 4 if the digital corrections are desired for a non-VLBA correlator, e.g., some versions of the DiFX correlator. In the special case of spectra with very strong narrow features, the absence of correlator zero-padding may limit the accuracy of the quantization corrections. See the FITLD help file for further information. The details of digital correction for FX correlators can be found in Radio Science 33, 5, 1289–1296, “Correction functions for digital correlators with two and four quantization levels”, by L. Kogan.

Adverb DELCORR enables amplitude corrections for known delay decorrelation losses in the VLBA correlator, as described in AIPS Memo 90 (1995, “Delay decorrelation corrections for VLBA data within AIPS” by A. J. Kemball). Setting DELCORR=1 will create a correlator parameter frequency (CQ) table for each file written by FITLD. Do this for the VLBA correlator only. The presence of this table enables the delay decorrelation correction once the residual delays have been determined in fringe-fitting. These corrections will not be applied if the data were not correlated at the VLBA correlator or if the CQ table is missing. For older FITLD files the CQ table can be generated using task FXVLB and this must be done before any changes in the frequency structure of the file are made. The CQ table is used for rate and delay amplitude decorrelation corrections after residual delay and rate errors have been determined by fringe-fitting, and are being applied to the data. The CQ table has no immediate effect on the data written by FITLD but is essential for later processing.

The WTTHRESH adverb can be applied to drop incoming data with playback weights less than the specified limit. Note that data flagged in this way are unrecoverable except by re-running FITLD. The data weights are normalized to unity so good data usually have weights close to 1.0. You should examine your data carefully if you use WTTHRESH to make sure that you have not discarded too much data at this stage. Typically 0.8 or higher is good for the VLBA, but for non-VLBA stations a lower value such as 0.6 or 0.7 may be appropriate.

Calibration data have been transferred from the correlator with your data if your data include VLBA antennas and were correlated after 1 April 1999 and before late 2009, when the DiFX correlator came on line and your IMHEADER listing shows the presence of GC, TY, WX, PC and FG tables, as in the example below. If you loaded more than one tape file, you must merge the calibration tables. VLBALOAD does the merging for you. See 9.3.1.2 for additional details. Note that, as this example shows, it is possible your data have calibration transfer tables even though they were correlated before 1 April 1999. If your IMHEADER does not show GC and TY tables, you do not have calibration transfer and must manually load calibration information in from text files. Also, even if you have calibration transfer, you may still have to manually load calibration information for some non-VLBA antennas (see http://www.vlba.nrao.edu/astro/obscor/cal-transfer/ for some information in this regard).

The output files produced by FITLD are in standard multi-source format (as described in 4.1) and contain data from all the target and calibrator observations in your observation. FITLD also writes a large number of extension tables including an index (NX) table, and many tables containing calibration information. A description of the VLBA correlator table types is given in 9.8. If you are missing the CORR-ID random axis, your AIPS release is stale (pre-15APR97) and you are strongly encouraged to upgrade to the latest release; much of the information presented in this chapter will not be usable with pre15APR97 releases of AIPS. Your catalog header should be similar to the one, obtained using verb IMHEADER, given below. If you have GC, TY, FG, WX, and PC tables as in this example data header, your data were processed with calibration transfer - see 9.3.1.2 for more details.

 Image=MULTI     (UV)         Filename=329         .OVLB  .   1  
 Telescope=VLBA               Receiver=VLBA  
 Observer=TM008               User #=   44  
 Observ. date=23-SEP-1998     Map date=06-JAN-1999  
 # visibilities      6567     Sort order  **  
 Rand axes: UU-L  VV-L  WW-L  TIME1  BASELINE  SOURCE  FREQSEL  
            INTTIM  CORR-ID  WEIGHT  SCALE  
 ----------------------------------------------------------------  
 Type    Pixels   Coord value     at Pixel     Coord incr   Rotat  
 COMPLEX      1   1.0000000E+00       1.00  1.0000000E+00     .00  
 STOKES       1  -2.0000000E+00       1.00 -1.0000000E+00     .00  
 FREQ        16   4.9714900E+09        .53  5.0000000E+05     .00  
 IF           8   1.0000000E+00       1.00  1.0000000E+00     .00  
 RA           1    00 00 0 .000       1.00        .000000     .00  
 DEC          1    00 00 0 .000       1.00        .000000     .00  
 ----------------------------------------------------------------  
 Coordinate equinox 2000.00  
 Maximum version number of extension files of type HI is   1  
 Maximum version number of extension files of type CQ is   1  
 Maximum version number of extension files of type AT is   1  
 Maximum version number of extension files of type IM is   1  
 Maximum version number of extension files of type CT is   1  
 Maximum version number of extension files of type GC is   1  
 Maximum version number of extension files of type TY is   1  
 Maximum version number of extension files of type FG is   1  
 Maximum version number of extension files of type PC is   1  
 Maximum version number of extension files of type MC is   1  
 Maximum version number of extension files of type OB is   1  
 Maximum version number of extension files of type AN is   1  
 Maximum version number of extension files of type WX is   1  
 Maximum version number of extension files of type FQ is   1  
 Maximum version number of extension files of type SU is   1  
 Keyword = ’OLDRFQ  ’  value =  4.97149000D+09

Note that the sort order of the output data set is listed as ** rather than TB and that there are no attached CL and NX tables. This happens when FITLD detects what might be a sub-array condition (two frequency IDs or two sources observed at the same time) on reading the data. In clear cases, the actual simultaneous frequency IDs and sources will be reported. In this case, FITLD detected the use of multiple integration times on different baselines in the data set; this is common for SVLBI data. The message reported by FITLD in this case takes the form:

**********************************************  
FITLD5:  Subarray or multiple dump-rate condition found.  
FITLD5:  NX/CL tables deleted.  
FITLD5:  Use USUBA to set up subarrays.  
FITLD5:  Rerun INDXR using CPARM(3) and (4)  
FITLD5: *******************************************

Unless any of the following criteria are met, the data written by FITLD are immediately ready for further processing.

FITLD can also be used to load archived AIPS data previously written to tape using either FITTP or FITAB, as described in 5.1.2. In this case the VLBA correlator-specific adverbs, such as those enabling digital and delay corrections, are not active.

9.3.1.2 Calibration transfer

Beginning on 1 April 1999, the VLBA correlator attaches calibration information for VLBA and some non-VLBA antennas directly to the output FITS files. If your IMHEADER listing shows GC, TY, WX, FG, and PC tables, then the correlator has provided calibration information; this service is called calibration transfer. Note that projects correlated at slightly earlier dates may also have calibration transfer information. You must have 15APR99 or later version of AIPS to take advantage of calibration transfer. Not all antennas provide all the information needed for calibration transfer to the VLBA correlator, see

http : ∕∕library.nrao.edu∕public∕memos ∕vlba∕ops∕V LBAO x34.pdf
for the latest information on this subject. For those antennas for which calibration information was not transferred by the VLBA correlator, you must process the log files in the traditional way as outlined in 9.5.2. Calibration for the VLA and the GBT began to be transferred with the FITS files in November 2003.

Between April 1999 and late 2009 the information processed by the correlator was somewhat redundant so that the calibration tables, the GC table in particular, must be merged using TAMRG, a very general and hence complicated task. There are a couple procedures to do this for you in the VLBAUTIL package, VLBAFIX and VLBAMCAL, if you have previously run VLBAFIX your tables have been merged:

> RUN VLBAUTIL  C R

to acquire the procedures; this should be done only once since they will be remembered.

> INDISK n ; GETN ctn  C R

to specify the input file.

> INP VLBAFIX  C R

to review the inputs.

> VLBAFIX  C R

to run the procedure.

X

You should use VLBAFIX after you have finished loading the data from tape, but before you either change the polarization structure of the data with FXPOL, load any calibration data for non-VLBA telescopes, or apply the calibration data.

At this point it is a good idea to save the tables that were loaded with your data with TASAV. This protects you from having to reload the uv data from scratch if one of the original tables is damaged in some way. If you need to copy a table from the TASAV’ed file use TACOP.

9.3.1.3 Repairing VLBA data after FITLD

As listed above, there are a variety of reasons why VLBA data may need some repair after FITLD has been run. They may need to be sorted into strict time order, to have the subarray nomenclature corrected, to be split into different frequencies, to have the polarization structure fixed, and/or to have the original index (NX) table and calibration ((CL) recreated. These repairs can all be done by the procedure VLBAFIX, which will examine the data and perform any of the necessary fixes. If the data contain subarrays then the procedure must be told to split the data into multiple subarrays (SUBARRAY=2), otherwise it will assume no subarrays and force all the data into one subarray.VLBAFIX is intended to replace VLBASUBS, VLBAFQS, VLBAMCAL and VLBAFPOL, all of which can be run individually instead. Also we have recommended in the last few sections that VLBAFIX be run, if you have already run it, it does not need to be run again.

> RUN VLBAUTIL  C R

to acquire the procedures; this should be done only once since they will be remembered.

> INDISK n ; GETN ctn  C R

to specify the input file.

> CLINT t  C R

to set the CL table interval to t minutes (see discussion above in 9.3.1.1).

> OUTDISK m  C R

to specify the output disk when needed.

> INP VLBAFIX  C R

to review the inputs.

> VLBAFIX  C R

to run the procedure.

Remember that all of the VLBAUTIL procedures have HELP files with good discussions about when to use the simple procedures and when to use the tasks directly.

9.3.1.4 Sorting and indexing VLBA correlator data

If multiple integration times are used on different baselines, the VLBA correlator will write data that are not in strict time-baseline (TB) sort order. VLBAFIX (9.3.1.3) will sort your data if needed, if you want to do the sorting by hand do the following. In general, task UVSRT can be used to sort randomly ordered uv data files in AIPS, but has significant disk space requirements through the use of intermediate scratch files. A special task, MSORT, has been written which uses a direct memory sort with sufficiently large buffers to accommodate the scale over which the data deviate from true time-baseline sort order. No intermediate scratch files are used and it can be significantly faster than UVSRT for this special case. MSORT competes with UVSRT in performance even in other cases, particularly when the individual visibility records are large due to many spectral channels and/or IFs. The inputs to MSORT are similar to those required by UVSRT and take the form:

> TASK MSORT’ ; INP  C R

to review the inputs.

> INDISK n ; GETN ctn  C R

to specify the input file.

> OUTDISK n ; OUTNAM ’ ’, OUTCLA ’ ’

to specify the output file.

> SORT    C R

to select default sort order (’TB’ or time-baseline).

> GO  C R

to run the program.

Note that if the input and output file names are identical, the input file is sorted in place. In-place sorting is dangerous, but may be necessary if there is insufficient disk space for a second copy of the data set or for the intermediate scratch files required by UVSRT. Never abort an in-place sort in progress because you will destroy the integrity of your data set.

9.3.1.5 Subarraying VLBA correlator data

If the project was observed without using subarrays (defined as times at which separate antennas are simultaneously observing different sources or at different frequencies), this step involving USUBA is not necessary and should be skipped.

If the observations have been scheduled in separate subarrays, defined either by source or frequency selection, the subarrays should be labeled in AIPS before proceeding any further. The VLBA correlator does not conserve subarray information, which in any event often has no unique characterization. This is specified in AIPS using task USUBA which allows subarrays to be defined through either the input adverbs, an external KEYIN text file, or through the use of an automatic algorithm to identify and label subarrays found in the data. The automatic algorithm is recommended, but its results should be checked closely. Note that ANTAB tables do not know about subarrays that will be assigned by USUBA, so you must run all ANTABs before running USUBA.

If you have subarrays, they need to be sorted, have the subarray nomenclature corrected, and/or have the index (NX) table and calibration (CL) version 1 table rebuilt. In this case, there is a simplified procedure to combine the three repair operation, VLBASUBS. Only use this procedure if you know you have subarrays.

> RUN VLBAUTIL  C R

to acquire the procedures; this should be done only once since they will be remembered.

> INDISK n ; GETN ctn  C R

to specify the input file.

> CLINT t  C R

to set the CL table interval to t minutes.

> INP VLBASUBS  C R

to review the inputs.

> VLBASUBS  C R

to run the procedure.

The only user-controllable input is the CL table interval; see discussion above. VLBAFIX will perform this operation if requested (9.3.1.3).

For automatic subarray labeling by USUBA, representative input parameters would be:

> TASK USUBA’ ; INP  C R

to review the inputs.

> INDISK n ; GETN ctn  C R

to specify the input file.

> OPCODE ’AUTO’  C R

to identify subarrays automatically.

> TIMERANG 0  C R

to include all times.

> ANTENNAS 0 ; SOURCES ’ ’  C R

to include all antennas and sources.

> FREQID -1 ; SUBA 0  C R

to include all frequency IDs and subarrays.

> INFILE    C R

to use no external file for subarray identifications.

> GO  C R

to run the program.

Sometimes FITLD erroneously identifies a subarray condition, usually because of spurious total-power data points. In such cases, you can set OPCODE = ’ ’ ; SUBARRAY = 1 to force all data into the first subarray.

In circumstances requiring USUBA, one often wants the calibration in one subarray to apply to other subarrays. USUBA will make the subarray column have value 0 which means all. Other tasks may not be so obliging so you may need to use TABED or verb TABPUT to change tables from subarray-specific to subarray-general.

9.3.1.6 Indexing VLBA correlator data

If FITLD had not written NX or CL tables or it was necessary to sort the data as described in 9.3.1.4, you must run task INDXR. If VLBAFIX (9.3.1.3) was run this is done automatically. INDXR will generate an NX table and, if need be, a CL table. Typical parameters for INDXR are:

> TASK INDXR’ ; INP  C R

to review the inputs.

> INDISK n ; GETN ctn  C R

to specify the input file.

> PRTLEV 0 C R

to print minimal details of progress.

> CPARM 0, 0 , t , 1  C R

to set the CL interval to t and recalculate the model.

> GO  C R

to run the program.

Note that CPARM(4) can be set to zero unless the correlator model is required in later reduction (e.g., in astrometry or geodesy observations) The CL table sampling interval t should be chosen subject to the same considerations given regarding adverb CLINT in the discussion of FITLD in 9.3.1.1. VLBAFIX will perform this operation if needed (9.3.1.3).

9.3.1.7 Concatenating VLBA correlator data

Sometimes an observation is correlated using multiple passes through the VLBA correlator. In this context, multiple pass means different IFs/pass; this is due to data rate limitations in the correlator. Be careful to have FITLD load each pass into a separate disk file; otherwise a very confused data set will be produced. If it is desired to join together the IFs correlated on each pass, the task VBGLU should be used. VBGLU can only join data sets which are identical except in the frequencies covered. Task MATCH may be used to make the antenna, source, and frequency ID numbers in one data set the same as those in another data set so that they may be used as inputs to VBGLU.

The inputs to VBGLU are rather simple. Each of the input files to be glued together is specified via INNAMEIN4NAME, and an output file is specified via OUTNAME. The choice of input file 1 is no longer important. No data are lost in the revised version of this task.

> TASK VBGLU’ ; INP  C R

to review the inputs.

> INDISK n ; GETN ctn  C R

to specify the input file.

> IN2DISK n ; GET2N ctn  C R

to specify the 2nd input file.

> IN3DISK n ; GET3N ctn  C R

to specify the 3rd input file.

> IN4DISK n ; GET4N ctn  C R

to specify the 4th input file.

> OUTDISK n  C R

to specify the output disk.

> GO  C R

to run the program.

With the changes in recording technology, it is also possible that a correlator will not have enough playback units for all antennas in an experiment. In this case, multiple correlations will also have to be done in order to correlate every possible baseline. But, inevitably, certain baselines will appear more than once in these correlations. FITLD will load all passes into a single data set (if DOCONCAT=1) or separate disk files which may be concatenated, after MATCH, with DBCON. Sort the data set into ’BT’ order with UVSRT. Then task VBMRG may be used to discard any duplicate data. In 31DEC14, task DBAPP may be used to avoid the 2n proliferation of files, but only if the files are fairly similar in antennas, subarrays, and frequency IDs.

9.3.1.8 Labeling VLBA correlator polarization data

The VLBA correlator does not preserve polarization information unless it is operating in full polarization mode. This results in polarizations not being labeled correctly when both RR and LL polarizations are observed without RL and LR. Each VLBA correlator band is loaded into AIPS as a separate IF and is assigned the same polarization. FXPOL takes a data set from the VLBA correlator and produces a new data set that has the correct IF and polarization assignments. Unfortunately, there is no reliable way to determine the polarization of each IF from the input data set and you must specify the polarization assignments using the BANDPOL adverb.

Most VLBA setups assign odd-numbered bands to RCP and even-numbered bands to LCP. In this case BANDPOL should be set to ’*(RL) ’ (the default) and FXPOL will generate a new data set that is of equal size to the input data set, but has two polarizations and half the number of IFs. This case normally applies if LISTR shows pairs of IFs with the same frequency and QHEADER shows one pixel on the STOKES axis with coordinate value RR, but there may be exceptions to this rule when non-VLBA antennas are used.

Most MkIII and MkIV VLBI setups reverse the polarizations and assign odd-numbered bands to LCP and even-numbered bands to RCP. In this case BANDPOL should be set to ’*(LR) ’ and the output data set will again be of equal size to the input data with two polarizations and half the number of IFs. This case normally applies if LISTR shows pairs of IFs with the same frequency and QHEADER shows one pixel on the STOKES axis with coordinate value LL, but there may be exceptions to this rule when non-VLBA antennas are used.

There is a procedure for use with VLBA-only data that attempts to determine which of the above cases applies and then runs FXPOL for you, if you ran VLBAFIX (9.3.1.3) this has already been done:

> RUN VLBAUTIL  C R

to acquire the procedures; this should be done only once since they will be remembered.

> INDISK n ; GETN ctn  C R

to specify the input file.

> INP VLBAFPOL  C R

to review the inputs.

> VLBAFPOL  C R

to run the procedure.

Use VLBAFPOL to check whether you need to relabel the polarizations in your data after loading the data, looking for subarrays, and merging redundant calibration data, but before reading any calibration data from non-VLBA stations. VLBAFPOL assumes that all of your FREQIDs have similar polarization setups. For this reason, you should normally run VLBAFPOL after copying each frequency ID to a separate file using VLBAFQS (9.5). This strategy also reduces the amount of disk space needed for VLBAFPOL.

To use FXPOL directly, typical inputs are:

> TASK FXPOL’ ; INP  C R

to review the inputs.

> INDISK n ; GETN ctn  C R

to specify the input file.

> BANDPOL ’*(RL)’  C R

to specify the normal VLBA polarization structure.

> GO  C R

to run the program.

Consult HELP FXPOL for further information about more complicated cases. Note that FXPOL has to write a new output file since the structure of the data is being changed. All standard extension files are also converted, but it is still a good idea to run FXPOL before running the calibration tasks.

In single-polarization observations, LL data may simply be mis-labeled as RR or vice-versa. This does not need to be corrected within AIPS but the user needs to take this into account when selecting or calibrating the data, particularly in specifying the polarization in the amplitude calibration text file (9.5.2). The Stokes axis can however be modified. Before running PUTHEAD, you should run IMHEAD to check which axis is the Stokes axis in the catalog header.

> INP PUTHEAD C R

to review the inputs.

> INDISK n ; GETN ctn  C R

to specify the input file.

> KEYWORD ’CRVALm  C R

to select the Stokes or mth axis in the header.

> KEYVALUE = -2  C R

to set the Stokes value to ’LL’ (or -1 for ’RR’).

> PUTHEAD  C R

to set the coordinate value.

9.3.1.9 Ionospheric corrections

At low frequencies (2 GHz and lower) the ionosphere can cause large unmodeled dispersive delays, seen as rapid phase wrapping. This can be of particular importance in phase referencing observations, where phases must be interpolated over weak sources. Even at high frequencies (e.g., 8 GHz) the ionosphere can be important, depending on the experiment and the condition of the atmosphere during the observation. One way to remove at least some of the ionospheric phase offsets is by applying a global ionospheric model derived from GPS measurements. The AIPS task TECOR processes such ionospheric models that are in standard format known as the IONEX format. These models are available from the Crustal Dynamics Data Information System (CDDIS) archive. There is a procedure which is part of VLBAUTIL, called VLBATECR that automatically downloads the needed IONEX files from CDDIS and runs TECOR. It will examine the header and the NX table and figure out which dates need to be downloaded, so the observation date in the header must be correct and an NX table must exist. See EXPLAIN VLBATECR for other requirements.

> RUN VLBAUTIL  C R

to acquire the procedures; this should be done only once since they will be remembered.

> INDISK n ; GETN ctn  C R

to specify the input file.

> INP VLBATECR  C R

to review the inputs.

> VLBATECR  C R

to run the procedure.

You can also download the files manually from the CDDIS archive through anonymous ftp and run TECOR, see EXPLAIN TECOR for detailed instructions on how to retrieve the models. TECOR interpolates between the maps of electron content in the ionosphere; therefore IONEX files must be retrieved to cover the entire experiment. Presently, each IONEX file contains maps every 2 hours from hours 00:00 to 24:00. Before November 2002, they contained maps every 2 hours from hours 1:00 through 23:00. Therefore, for example, if an experiment prior to November 2002 started at 0:00 then files must be retrieved for the day of the experiment and the previous day so the times between 0:00 and 0:59 can be interpolated. More recent experiments require two or more files only if they occurred in two or more days.

Typical inputs to TECOR are:

> TASK TECOR’ ; INP  C R

to review the inputs.

> INDISK n ; GETN ctn  C R

to specify the input file.

> INFILE ’FITS:JPLG1230.01I’  C R

to set the name of the IONEX file. If there is more than one file, this name must be a standard format and be the first file. See EXPLAIN TECOR for more details.

> NFILES n  C R

to set number of IONEX files to be read.

> SUBARRAY 0  C R

to process all subarrays. This option allows you to process subarrays used on different dates.

> ANTENNAS 1 2 3 4 6 7 8 9 10  C R

to find corrections for all antennas except antenna 5 in a ten antenna experiment. This is important because if the IONEX models do not cover an antenna and it is not excluded here then all the solutions for that antenna will be undefined and the data flagged when the CL table is applied.

> GAINVER 1  C R

to apply corrections to the first CL table.

> GAINUSE 2  C R

to create CL table 2 with the corrections.

> APARM 1 0  C R

to correct for dispersive delay; otherwise only the ionospheric Faraday rotation will be corrected.

> GO  C R

to run TECOR, correcting for the ionosphere in a new CL table.

The dispersive delays should be checked using SNPLT (options INEXT ’CL’; INVERS 2; OPTY ’DDLY’) and VPLOT (options BPARM 0; APARM 0; DOCAL 1; GAINUSE 2). TECOR is only as good as the models, which at this time are quite rough. Therefore, it is a very good idea to compare the corrected and uncorrected phases using VPLOT.

CLCOR has a OPCODE = ’IONO’ to make delay corrections for the ionosphere, similar to the ’ATMO’ operation which is for the atmosphere (9.5.7.5).

9.3.1.10 Corrections to the Earth Orientation Parameters

This correction is only useful for experiments correlated at the VLBA correlator. VLBI correlators must use measurements of the Earth Orientation Parameters (EOPs) to take them out of the observations. These change slowly with time and therefore the EOPs used by the correlator must be continually updated. From 5-May-2003 to 9-Aug-2005 the VLBA correlator used old predicted EOPs which could be significantly wrong and will effect all phase referencing experiments. Incorrect EOPs can both move the position and possibly smear the target of a phase referencing experiment. Self-calibration can improve the smearing. Even outside the above quoted period of particularly bad EOPs the EOPs can be off so it is recommended that all phase-referencing experiments, particularly astrometry experiments should have their EOPs corrected. CLCOR (OPCODE=’EOPS’) can do this correction. It uses the CT table which is only produced by the VLBA correlator, so at the moment CLCOR can only correct experiments processed at the VLBA correlator. CLCOR also uses a file of measured EOPs, which can be downloaded from NASA (see EXPLAIN CLCOR for details). There is a procedure which is part of VLBAUTIL, called VLBAEOPS, which downloads the file automatically and runs CLCOR. To run the procedure:

> RUN VLBAUTIL  C R

to acquire the procedures; this should be done only once since they will be remembered.

> INDISK n ; GETN ctn  C R

to specify the input file.

> INFILE    C R

to automatically download file.

> INP VLBAEOPS  C R

to review the inputs.

> VLBAEOPS  C R

to run the procedure.

The procedure will correct the highest CL version while copying it to a version one higher.

To run CLCOR manually, download the file using the instructions in CLCOR’s explain file. Sample inputs are as follows:

> TASK CLCOR’ ; INP  C R

to review the inputs.

> INDISK n1 ; GETN ctn  C R

to specify the input file.

> OPCODE ’EOPS’  C R

to select correction of the EOPs.

> GAINVER clin  C R

CL table to read, new default is the current highest version.

> GAINUSE 0  C R

CL table to write; version highest+1 is written unless GAINUSE = GAINVER.

> INFILE ’FITS:usno_finals.erp  C R

to specify file with correct EOPs — note missing close quote to retain lower case letters.

> GO  C R

to run the program.

9.3.1.11 Preparing the OB table for SVLBI data

The spacecraft orbit table (OB) as produced by FITLD contains the spacecraft position (x,y,z) and velocity (vx,vy,vz) as calculated to high accuracy from the JPL reconstructed orbit using the SPICE package (developed at JPL). These quantities are calculated by the correlator on-line software and are passed directly through to AIPS via FITLD by the VLBA correlator. The orbit table is indexed on time and can include information such as the angle between the spacecraft pointing direction and the Sun, the time since the start and end of the last eclipse, and the spacecraft parallactic angle. The latter quantities are not available to the correlator on-line software and, if desired, need to be computed separately for later use in AIPS by task OBTAB. Additionally OBTAB stores orbital elements in the AN table; these are essential for later use in plotting or inspecting spacecraft orbit information. Sample inputs for OBTAB, are as follows:

> TASK OBTAB’ ; INP  C R

to review the inputs.

> INDISK n ; GETN ctn  C R

to specify the input file.

> INVERS 1  C R

to process OB table 1.

> SUBARRAY 1  C R

to select subarray number.

> APARM 1, 0  C R

to update orbital elements in AN table

> GO  C R

to run the program.

Note that APARM(8) can be used to directly specify which antenna is the orbiting antenna (this task assumes there is only one orbiting antenna).

Task OBTAB determines mean orbital elements from the OB table using the spacecraft positions and velocities and updates the AN table under control of APARM(1). The orbital elements can be examined by using PRTAB to review the updated AN table. The mean elements are used to compute uv coordinates for the spacecraft so that model amplitudes AND closure phases and amplitudes can be plotted (by tasks VPLOT, CLPLT, and CAPLT). The orbit table can be plotted using task OBPLT. Alternatively, the task TAPLT can be used to display individual columns. Use PRTAB to determine the names of the columns you wish plotted.

9.3.1.12 Loading the time corrections file for SVLBI data

The round-trip residual delay measurements determined by the tracking stations are supplied to the correlator in FITS format. These so-called delta-T tables are not passed to AIPS by the correlator but can be loaded indirectly. This table might be used, for example, to plot the time correction as a function of time. Such information could be useful if a user suspects a loss of coherence due to a poor predicted orbit or a clock jump at the tracking station. The table contains no internal time stamps, so the row number must be used to determine the approximate time of a given entry (there are typically 10 rows per second).

The delta-T tables can be loaded at present using FITLD and attached to a null uv data file, using input parameters as follows:

> TASK FITLD’ ; INP  C R

to review the inputs.

> OUTDISK n  C R

to specify a separate output file.

> OUTNAM ’DUMMY’, OUTCLA ’DT’

> DATAIN ’FITS:3551708.kct.a  C R

to specify the external FITS file.

> GO  C R

to run the program.

The other FITLD adverbs are not relevant in this instance. Note that lower case letters can be used in the DATAIN adverb if the trailing quotation mark is omitted. FITLD will load the external FITS file successfully but will print an error message complaining that no array geometry table was found. This message can be ignored in this case. The delta-T table will appear as an unknown table of type UK, and can be plotted using task TAPLT

9.3.2 Loading data from a MkIII/MkIV correlator

9.3.2.1 Running MK3IN

Data from a MkIII correlator, such as that in Bonn, Germany or Haystack, Massachusetts, can also be read into AIPS. To do this you need to be supplied with the so called “A” tape output, also known as “type 52’s.” These data tapes can be read and translated by the task MK3IN. The process of reading MkIII correlator data into AIPS and preparing it for further processing is more cumbersome than the equivalent process for VLBA correlator data. This simply reflects the manner in which data are generated on a baseline-based correlator with a limited number of playback drives. MkIII data may also appear in the form of a Unix tar file. For such data, use M3TAR and TFILE rather than MK3IN and AFILE, respectively.

Before running MK3IN, run the task MK3TX to extract the text files from the MkIII archive tape. These text files contain information about the correlated scans in the data set. MK3TX will first provide an index of all the text files and then ask you to select files for loading onto disk. It then asks you interactively for the desired destination of the text files. It is important to load and concatenate all the “A” files, i.e., those files having names like Atttt. The meaning of the other text files is described in the MK3TX Explain file. Sometimes the text files are not on the tapes, which means that you cannot select sub-sets of the data using the A-files, but is not otherwise catastrophic.

If the A-files are present and have been loaded onto the disk, use AFILE to sort and edit these files to produce a list of scans to be loaded by MK3IN. Use APARM settings in AFILE to establish criteria for selecting between any duplicate scans which may appear on the archive. If the data set contains data at multiple frequencies, you should edit the resulting output text file so that there is a version for each frequency, containing only those scans at that frequency.

The final step before running MK3IN is to create another text file which provides the commands for the task. This step is necessary since some information that is needed by AIPS is not present on the tape. Ideally, in this text file (as shown below), the parameter STATIONS should be a list of all the stations correlated, with the exact name used at correlation. If you do not have such a list, you can instead specify a list containing STATIONS ‘ANY’, ‘ANY’ Note that there must be at least as many ‘ANY’ entries as there are stations in the data set or some of the stations will not be loaded. The parameters in this text file are:

STOKES=’RR’,’LL’

the Stokes range of the output file. The standard abbreviations are used to select the polarization range. The largest consistent range is used. For example: STOKES=’RR’,’LL’ will cause only RR and LL to be written. STOKES=’LL’ will cause just LL to be written. STOKES=’RR’,’LR’ will cause all four circular polarization combinations to be in the output file, since RR and LR span the range of allowed AIPS Stokes values.

FREQCODE=’R’,’L’,’r’,l’

the polarization codes used by MkIII correlators are anything but standard and they need to be supplied to MK3IN using the parameter FREQCODE. The one character polarization identifiers are expected in the order RR, LL, RL, and LR. The usual correlator convention is ’R’=RR, ’L’=LL, ’r’=RL, ’l’=LR and this is the default assumed by MK3IN. However, other codes are possible. For example FREQCODE = ’A’, ’B’, ’C’, ’D’ will interpret ’A’ as RR, ’B’ as LL and so forth, while FREQCODE = ’R’, ’C’, ’r’, ’l’ will use the default abbreviations except that ’C’=LL. If MK3IN encounters an unidentified polarization code the task will report: AT20XX: Unidentified Stokes parameter: ’X. In this case, modify the FREQCODE parameter to include this polarization identifier. This will ensure that polarizations are not misidentified inadvertently.

NO_POL=2

the number of polarization correlations (e.g., RR, LL, RL and LR), the default is 1.

STATIONS=’NRAO’,’VLA’,’OVRO’,’FDVS’,’MPI’

station names.

/

keyin style delimiter.

Then, from inside AIPS, mount the tape (3.9) and run MK3IN:

> TASK MK3IN’ ; INP  C R

to review the inputs.

> INFILE ’MYVLB:PARAM.LIS’  C R

to define the text control file.

> IN2FILE ’MYVLB:AFILE.LIS  C R

to point to a file containing a list of scans to be loaded as produced by AFILE

> INTAPE 4  C R

to specify the tape drive number.

> NFILES 0 C R

to skip no files on tape.

> OUTNA EXP 86-34’  C R

to select the output file name.

> OUTCL MK3IN  C R

to select the default output class name.

> REFDATE ’12/11/89’  C R

to tell MK3IN the start date of the observations — get this right or you may get negative times.

> SOURCES  C R

to accept all sources found.

> TIMERANG 0 C R

to accept data from all times found.

> DOUVCOMP 1  C R

to write data on disk in compressed format.

> APARM 1, 0  C R

to set the time increment in the CL table entries in minutes.

> APARM(7) 1  C R

to separate sidebands into separate AIPS IFs; the default is to store both USB and LSB in the same IF.

> GO  C R

to run the program.

If the data are contained on more than one Exabyte or DAT tape, load the second tape and re-run MK3IN, setting DOCONCAT = 1  C R so that the data are appended to the previous output file. Before running MK3IN a second time, it is important to set the list of STATIONS in the control file to exactly those found when loading the first tape; use PRTAN on the output file to obtain this list. Also leave additional ‘ANY’ entries after the list for any stations that are on the second tape but which were not on the first tape. The use of DOUVCOMP = 1 is recommended for most data sets, see Appendix F.

9.3.2.2 Sorting MkIII/IV data

The AIPS data files created by MK3IN will be in an arbitrary sort order. Use UVSRT or MSORT to sort them into time-baseline order:

> TASK UVSRT’ ; INP  C R

to review the inputs.

> INDISK n ; GETN ctn  C R

to select the input file.

> OUTNA INNA ; OUTCL ’TBSRT’  C R

to specify the output file.

> SORT ’TB’  C R

to sort to time-baseline order.

> GO  C R

to make the sorted uv file.

9.3.2.3 Concatenating MkIII/IV data

If you did not set DOCONCAT=1 when running MK3IN and as a result several files were loaded from tape for one observation, use DBCON to concatenate them together. In order to have the concatenated data all appear in a single subarray, both input files for DBCON must have the same reference day number and identical antenna numbers. That is, the antennas extension (AN) files with each input uv data file must be the same. MATCH may be used to repair discrepancies.

You may list the contents of AN files using PRTAN. To run DBCON:

> TASK DBCON’ ; INP  C R

to review the inputs.

> INDISK n1 ; GETN ctn1  C R

to select the 1st input file.

> IN2DISK n2 ; GET2N ctn2  C R

to select the 2nd input file.

> OUTNA INNA ; OUTCL DBCON  C R

to specify the output file.

> DOARRAY 1  C R

to force DBCON to mark the output data records as being in the same sub-array. For this to work properly, both of the input files must have the same reference day and have identical antennas files.

> GO  C R

to concatenate the two files.

In 31DEC14, task DBAPP may be used to avoid the 2n proliferation of files, but only if the files are fairly similar in antennas, subarrays, and frequency IDs.

9.3.2.4 Merging MkIII/IV data

MkIII VLBI correlators usually produce redundantly correlated data. You must merge the data using UVAVG:

> TASK UVAVG’ ; INP  C R

to review the inputs.

> INDISK n ; GETN ctn  C R

to specify the input file.

> OUTNA INNA ; OUTCL ’UVMRG’  C R

to specify the output file.

> YINC 4.0  C R

to set the averaging interval of the input data records (in seconds).

> OPCODE MERG  C R

to direct the task to perform the merge operation.

> GO  C R

to run the program.

The CL table should only contain one entry for each antenna at each time stamp. But, due to the merging process described above and the fact that redundant correlations may have been performed, there is one step to follow before you have consolidated your database fully. You must run TAMRG to remove the redundant CL entries:

> TASK TAMRG’ ; INP  C R

to review the inputs.

> INDISK n ; GETN ctn  C R

to specify the input file.

> INEXT ’CL’  C R

to specify the table type to merge.

> INVER 1; OUTVER INVER  C R

to process the input table in place.

> APARM 4, 1, 4, 0, 1, 1, 1, 0  C R

to control the merging: don’t ask why, just do it!

> BPARM 1, 4  C R

to set compared columns — again, don’t ask.

> CPARM 1.157e-5, 0.2  C R

to set degree of equality — ditto.

> GO  C R

to run the program.

9.3.2.5 Correcting MkIII/IV sideband phase offsets

If your observation contains a mixture of VLBA and non-VLBA antennas and you have not stored the sidebands as separate IFs, there will be a phase offset of about 130 between the upper and lower sidebands on baselines from VLBA to non-VLBA antennas. A correction for this offset is achieved using the task SBCOR:

> TASK SBCOR’ ; INP  C R

to review the inputs.

> INDISK n1 ; GETN ctn  C R

to specify the input file.

> OUTNA INNA ; OUTCL SBCOR  C R

to specify the output file.

> BCHAN 1  C R

to specify the lowest channel of lower sideband.

> ECHAN 4  C R

to specify the highest channel of lower sideband.

> APARM(1) 0  C R

to apply the default phase offset (i.e.-130deg.)

> ANTENNAS =  VLBA ; INP  C R

to specify the VLBA antenna numbers; the = sign is required here. The verb VLBA reads the antenna file to find VLBA antennas.

> GO  C R

to run the program.

If you have loaded the VLBAUTIL procedures, then you may use a procedure called ANTNUM to translate a station name into a station number. Thus ANTENNAS = ANTNUM(’BR’), ANTNUM(’FD’), . The verb VLBA in is easier.

9.3.2.6 Indexing MkIII/IV data

Next, you must index your data. The NX table is useful as a summary of the file for you, and is also used by the calibration programs to provide quick access for reading data. Create this file with INDXR:

> TASK INDXR’ ; INP  C R

to review the inputs.

> INDISK n ; GETN ctn  C R

to specify the input file.

> CPARM 0, 30, -1  C R

to allow 10-minute time gaps within scans, to limit scans to 30 minutes, and to not create a new CL table.

> GO  C R

to run the program.

Other than these initial loading and merging steps, the reduction of MkIII and MkIV correlator data is identical to that of VLBA correlator data.