VLBA Basic Spectral Line Tutorial DRAFT

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This CASA Guide is for Version 6.6.3 of CASA. If you are using a later version of CASA and this is the most recent available guide, then you should be able to use most, if not all, of this tutorial.

Overview

This CASA Guide describes the procedure for calibrating a phase-referenced VLBA observation of methanol masers in W3OH. The data were taken specifically for this tutorial. The observation made use of the DDC observing personality, using dual polarization with one spectral windows in each polarization. The spectral window has a bandwidth of 32 MHz divided into 256 spectral channels centered at 6668 MHz for the methanol maser line.

This tutorial will focus on calibrating the data and creating a continuum (Stokes I) image of the phase reference calibrator and images of the masers in the W3OH.

Please note that CASA should be used with caution when calibrating VLBA data. At the current time, CASA should only be used to calibrate relatively simple VLBA observations (basic continuum, simple phase-referenced, etc.). In particular, CASA is currently not recommended for calibrating the following types of VLBA observations:

  • Polarimetric — Calibration of resolved polarized sources is not yet available in CASA.
  • Astrometric — Earth orientation parameter (EOP) and pulse-cal tone corrections are not yet available in CASA.
  • Spectral line projects requiring fringe-rate mapping — Fringe-rate mapping is not yet available in CASA.
  • Low Frequency (<4 GHz) — Total electron content (TEC) corrections have not yet been verified to work correctly for VLBI observations in CASA. Also, note that many C-band (4 to 8 GHz) VLBA observations will benefit from TEC corrections.
  • VLBA+Y27 or other VLBA+ arrays that require the use of antab files — CASA does not currently support the use of antab files for ingesting calibration data (system temperatures, gain curves, etc.)
  • VLBA data correlated prior to December 2009 — CASA cannot load data correlated with the old VLBA hardware correlator. Your data must have been correlated with the DiFX correlator.

If your observation involves any of the above, you should use AIPS to calibrate your data.

A note on VLBA+Y1 observations: It is currently possible to calibrate VLBA+Y1 (VLBA and single VLA antenna) in CASA. Any data taken after 2022 July 06 should work with minimal extra steps (namely, checking that the Y1 antenna diameter is correct). VLBA+Y1 data observed prior to 2022 July 06 may not include the system temperature and/or gain curve values need for calibration. For these data sets, refer to VLBA Scientific Memo 39 for details on how to prepare the data for calibration in either CASA or AIPS.

How to Use This CASA Guide

There are a number of possible ways to run CASA, described in more detail in Getting Started in CASA. In brief, there are at least three different ways to use CASA:

  • Interactively examining task inputs. In this mode, one types taskname to load the task, inp to examine the inputs, and go once those inputs have been set to your satisfaction. Allowed inputs are shown in blue and bad inputs are colored red. The input parameters themselves are changed one by one, e.g., selectdata=True. Screenshots of the inputs to various tasks used in the data reduction below are provided, to illustrate which parameters need to be set. More detailed help can be obtained on any task by typing help taskname. Once a task is run, the set of inputs are stored and can be retrieved via tget taskname; subsequent runs will overwrite the previous tget file.
  • Pseudo-interactively via task function calls. In this case, all of the desired inputs to a task are provided at once on the CASA command line. This tutorial is made up of such calls, which were developed by looking at the inputs for each task and deciding what needed to be changed from default values. For task function calls, only parameters that you want to be different from their defaults need to be set.
  • Non-interactively via a script. A series of task function calls can be combined together into a script, and run from within CASA via execfile('scriptname.py'). This and other CASA Tutorial Guides have been designed to be extracted into a script via the script extractor by using the method described at the Extracting_scripts_from_these_tutorials page. Should you use the script generated by the script extractor for this CASA Guide, be aware that it will require some small amount of interaction related to the plotting, occasionally suggesting that you close the graphics window and hitting return in the terminal to proceed. It is in fact unnecessary to close the graphics windows (it is suggested that you do so purely to keep your desktop uncluttered).

If you are a relative novice or just new to CASA, it is strongly recommended to work through this tutorial by cutting and pasting the task function calls provided below after you have read all the associated explanations. Work at your own pace, look at the inputs to the tasks to see what other options exist, and read the help files. Later, when you are more comfortable, you might try to extract the script, modify it for your purposes, and begin to reduce other data.

NOTE: It is not recommended to use scripts to generate "science-ready" VLBA data products. Nearly all VLBA observations will require some amount of hands-on calibration. Calibration and imaging scripts should only be used as "first pass" attempts at calibration, which can be useful to determine if the observation resulted in a detection and to identify problems in the data.

Obtaining the Data

This Guide is intended to cover the entire process one would follow for calibrating their own VLBA observation. Therefore, we will start with a FITS-IDI file rather than a Measurement Set. The FITS-IDI file for this Guide is: TL016B.idifits (right-click and select "Save Link As..."; file size: 1.8 GB). Additionally, you will need to download the zoom band file containing the high spectral resolution data for the masers.

Alternatively, you may download the data from the NRAO Archive. In the archive search inputs, enter "TL016" in the Project Code field. Expand the results for TL016B and look for the file VLBA_TL016B_tl016b_BIN0_SRC0_1_220307T210851.idifits. Select the file, click "Download", and follow the instructions. Once you have downloaded the FITS-IDI file from the archive, it will be helpful to change the filename to "TL016G.idifits".

The Observing Log

Before diving into the calibration, it is always a good idea to look over the observing log to check for notes from the operators that can inform us about potential issues with the data (missing stations, bad weather, etc.). These logs are always emailed to the PI's of an observation, but you can also access them later from the NRAO's vlbiobs fileserver. To locate an observing log, first find the directory for observing month and the last two digits of the year (for the observation used in this Guide, that directory is jan24 for January 2024). Once inside the proper month+year directory, look for the project code (in this case, tl016d). Look for a file named <project code>log.vbla (tl016dlog.vlba).

The observing log for this particular observation looked like this: 

VERY LONG BASELINE ARRAY OBSERVING LOG
--------------------------------------
Project:        TL016G
Observer:       Linford, Justin
Project type:   TEST
Obs filename:   tl016d.vex
Date/Day:       2024JAN07/007
Ants Scheduled: SC HN NL FD LA PT KP OV BR MK

=UT-Time===Comment===============================================MF#===%AD==AMD=
           Operator: Trevor Seddon                                              
     2359  Begin                                                                
2359-0416 *BR out, FRM stuck in SX position wo-19696             FRM    100  257
2359-0416 *KP out, elevation up limit and brake interlock fault  WEA    100  257
           that are likely caused by ice tripping the switches                  
2359-0112 *HN out to avoid snow                                  WEA    100   73
     0000  Date is 2024JAN08/008.                                               
     0030 %OV windy                                                             
     0228  New Operator: Paul Padilla                                           
     0416  End.                                                                 


Downtime Summary:
	Total downtime : 587 min
	Percentage downtime of observing: 22.8%
	Average downtime per hour : 13.7 min

    Total scheduled observing time (# Antennas): 2570 min (10)

Notes:
    * = Entries where data was affected.
    % = Entries where data may have been affected.
    & = Entries where the site tech was called out.
  WEA = Weather entries.
  MF# = Maintenance form or major downtime category associated with a problem.
  %AD = The percentage of an antenna affected by a problem.
  AMD = Total antenna-minutes downtime for a problem.
 Tsys = System Temperature (TP/SP x Tcal/2)
  ACU = Antenna Control Unit
  FRM = Focus/Rotation Mount
  RFI = Radio Frequency Interference
   CB = Circuit Breaker

Creating the Measurement Set

Before beginning our data reduction, we must start CASA. If you have not used CASA before, some helpful tips are available on the Getting Started in CASA page. Remember to start CASA in the directory containing the observation data.

Once you have CASA up and running, it is time to get the data into a format that CASA can use. Unlike VLA data, a VLBA observation is only available as a FITS-IDI file and cannot be downloaded as a CASA Measurement Set. So, the first step in calibrating a VLBA observation with CASA is to create a Measurement Set from the FITS-IDI file. To do this, we will use the task importfitsidi: 

# In CASA
importfitsidi(fitsidifile='TL016G.idifits', vis='tl016g.ms', constobsid=True, scanreindexgap_s=6)

The scanreindexgap_s parameter is used to reconstruct scan boundaries in those cases where sources do not change between scans. In general, it is good to set scanreindexgap_s to some non-zero number to help CASA properly organize the scan list. The recommended value is 15 seconds, but shorter values may work as well (although you probably don't want to go much shorter than about 5 seconds). If you find that the resulting MS contains too few scans, run importfitsidi again with scanreindexgap_s set to a smaller number. If your MS has too many scans, especially multiple scans on the same source when you think it should just be one scan, run importfitsidi again with scanreindexgap_s set to a larger number.

NOTE: You may see warnings in the CASA window like "Table not yet implemented" and "Keyword has wrong data type". This is normal behavior for VLBA data and due to the fact that CASA does not yet handle the pulse-cal tone data in the FTIS-IDI file. Just ignore them. However, do not ignore any SEVERE warnings, as these can indicate there are serious problems with the data.

The Observation Summary

It will be useful later to have the basic information about the observation. The task listobs will return a list of all the scans, the sources observed, which stations were used, and the frequency setup. It is possible to run listobs in two ways: printing information in the CASA logger, or saving the information to a file.

To simply display the information in the CASA logger: 

#In CASA
listobs(vis='tl016g.ms')

You should see the listobs output in the CASA logger window: 

OUTPUT TO FILL IN LATER

NOTE: You can also assign the listobs output to a python dictionary (e.g., "obs_dict") by typing "obs_dict = listobs(vis='tl016g.ms')".

It is usually useful to have a copy of the listobs output in a file that you can refer to later. To save the listobs output to a file named "tl016b_listobs.txt", run listobs again with listfile='tl016b_listobs.txt'. 

#In CASA
listobs(vis='tl016g.ms', listfile='tl016g_listobs.txt')

A few things that are useful to note from the listobs output:

  • While the antenna number, field number, and spw number all start at 0, the scan number starts at 1.
  • The fringe finder and bandpass calibrator is J0102+5824, with 4 scans of about 4 minutes each.
  • There is also a back-up fringe finder and bandpass calibrator, J0217+7349.
  • The phase reference calibrator is J0306+6243. Each phase reference scan is about 1 minute long.

Identifying a Good Reference Antenna

VLBA calibration makes use of a reference antenna: one antenna that all other antennas can be referenced to when generating solutions. Usually, you will want to use one of the more central stations: FD, KP, LA, or PT.

To determine which is the best to use as the reference antenna, use plotms to plot phase vs frequency for a single scan on a bright source (usually the fringe finder or bandpass calibrator). For this observation, use the second scan on J0102+5824, which is scan ?? from the listobs output. Inspect each of the 4 central antennas and use the one which has the most well-behaved phases. We start with scan ?? because it is near the middle of our observation, so J0102+5824 should be at relatively high elevations at all stations during that scan. 

#In CASA
plotms(vis='tl016g.ms', xaxis='frequency', yaxis='phase', field='J0102+5824', scan='??', correlation='rr,ll', antenna='FD,KP,LA,PT', iteraxis='baseline', coloraxis='corr')

Use the GUI to step though the baselines. Our observation does not include the cross-hand polarizations (lr and rl), and you usually won't worry about inspecting them anyway since they will usually be too low to see anything useful.

We should also look at our back-up fringe finder, J0217+7349, to see how it compares to J0102+5824. In the GUI, change the "Field" parameter to J0217+7349, and change the scan number to ?? (the second scan on J0217+7349).

In the GUI, go to the "Axes" tab and change the "Data" axis to "Amp" (this is equivalent to setting yaxis='amplitude') to inspect the shapes of the bandpasses and look for RFI. If an antenna has strong RFI, you should not use it as the reference antenna. Also look at the bandpass shapes for J0217+7349.

Should see that J0102 is the better calibration target

For spectral line observations, it is often a good idea to also inspect the autocorreltion data for signs of strong RFI at each site. You can plot the autocorrelations by setting the antenna parameter to *&&&. 

#In CASA
plotms(vis='tl016g.ms', xaxis='frequency', yaxis='amp', field='J0102+5824', scan='??', correlation='rr,ll', antenna='*&&&', iteraxis='antenna', coloraxis='corr')

WILL WANT AN IMAGE HERE OF THE PT AUTOCORRELATIONS SHOWING THAT NASTY CRUD

For this observation, we will use Fort Davis (FD) as the reference antenna. Its phases are fairly smooth, it is free of RFI, and the bandpasses look pretty clean.

Identifying a Good Time Range for the Instrumental Delay Calibration

Next, we will look for a good time interval (about 1 minute long) for the instrumental delay calibration. This will be done using the fringe finder (J0102+5824), so we should inspect each scan on it: ??1, ??2, ??3, and ??4. We will want to plot amplitude vs time for each of these scans. To save time, we will just plot the baselines to the reference antenna, FD. Start by plotting scan 1. 

#In CASA
plotms(vis='tl016b.ms', xaxis='frequency', yaxis='amp', field='J0102+5824', antenna='FD', scan='1', correlation='rr,ll', iteraxis='baseline', coloraxis='corr')

Use the GUI to step through each baseline for the scan. Then, use the "scan" field in the GUI to look at the other scans on J0102+5824 (scans ??, ??, ??, and ??). Look for outliers in the amplitude data. We want to use a time range with no RFI and with all antennas on source.

Scan ?? is close to the middle of the observation, and looks mostly clean. Use the plotms GUI to set the "scan" to "??" (in the "Data" tab) and the "X Axis" to "Time" (in the "Axes" tab) and step through the baselines again. Notice that some baselines have some higher amplitude points early on in this scan. We will want to avoid these early times. The time range TIME1 to TIME2 looks nice for each baseline to the reference antenna, so we will use that for our instrumental delay calibration later.

Looking for Spectral Line

This is a spectral line dataset, so we should take a minute to check that we the maser lines on the science target.

Again, use plotms to plot the data. 

#In CASA
plotms(vis='tl016b.ms', xaxis='frequency', yaxis='amp', field='W3OH', antenna='FD', scan='??', correlation='rr,ll', iteraxis='baseline', coloraxis='corr')

Stepping through the baselines, you should see that there is indeed a large amplitude spike near the expected maser frequency of 6668.519 MHz on all baselines.

Flagging Data

Should not need to quack these data

Flagging Problem Antennas

We know from our inspection of the fringe finders that PT has some major RFI near the maser line. Therefore, we should not include PT in our calibration.

Flag the PT antenna for the entire observation by using the flagdata command 

#In CASA
flagdata(vis='tl016g.ms', mode='manual', antenna='PT')

Automated Flagging

The the flagdata task includes a useful automated flagging mode known as "TFCrop". For more details on using the automated TFcrop mode, see the VLA CASA Flagging topical tutorial. Because this is a spectral line data set, we want to limit the automatic flagging to only the time domain.

To begin, you just want to get a feel for what TFCrop will do to the data, which means you should set action='calculate' . 

#In CASA
flagdata(vis='tl016g.ms', mode='tfcrop', datacolumn='data', timecutoff=4.0, flagdimension='time', action='calculate', display='both')

This will open a new window with a GUI. The top row of the GUI will display the data as it currently is. The bottom row shows what the data will look like after the flags are applied (blue regions are flagged). Step through the antennas by clicking "Next Baseline". Step through the spectral windows by clicking "Next SPW". Step through at least a few scans by clicking "Next Scan". With timecutoff=4.0, it should really only flag those data points that are 4-times the standard deviation in the time dimension. This should be sufficient to remove the worst of the time-dependent RFI in our observation.

To generate the flags, we will need to run flagdata again with action='apply' . 

#In CASA
flagdata(vis='tl016g.ms', mode='tfcrop', datacolumn='data', timecutoff=4.0, flagdimension='time', action='apply', display='both')

You should double check that the automatic flagging will behave as you expect. Once you are satisfied that the flagging will do what you want, click "Stop Display". The program will then look through the entire observation and apply the flags.

NOTE: You can always exit the TFCrop mode without applying any flags by clicking "Quit", even when you set action='apply' .

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