HI 21cm (1.4 GHz) spectral line data reduction: LEDA 44055

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This tutorial describes the data reduction of the HI spectral line observed of the nearby (4.8 Mpc), gas-rich dwarf galaxy LEDA44055 (Figure 1: grab HST image). For its gas-rich nature, LEDA44055 is quiescent and is an Hα non-detection. Observations by the HST show a weak blue plume structure, and further inspection of GALEX archival images show some faint emission in the optical body, which taken together suggest that LEDA44055 may be in a "post-starburst" phase.

In this 1.4 GHz observation, a 16 MHz wide subband (spectral window, abbreviated as spw in CASA) using 4096 channels was observed, each channel providing ~ 1700 km/s of velocity coverage that results in a channel width of 3.906 kHz per channel. The second IF subband is used to acquire 1-2 GHz continuum imaging of the field; if LEDA44055 is in post-starbust phase, then it may display significant synchotron emission.

The TDEM0025 observation at the VLA was done during C-configuration and spanned 2 hours on the instrument from 31 July 2017 at 12:39 UT to 1 August 2017 at 14:39 UT. Information about the observation can be found on the corresponding VLA Observing Log and the continuation log (the observing log was split at the monthly boundary). This observing log is a record of events that transpired during the observation of the project, including weather conditions and any loss of antenna(s) and/or components that could affect the outcome of the observation.

This observation of LEDA44055 was taken as part of the Observing for University Classes program. The project code for this VLA observation is TDEM0025. This paper by Cannon et. al is the result of the observation.

How to use this CASA guide

Please use CASA 5.4.0 for this tutorial (typing casa -ls in a linux window shows the available versions and the current version; to explicitly change the current version type, e.g., casa -r 5.4.0-68)

There are at least three different ways to interact with CASA, described in more detail in Getting Started in CASA. In this guide we provide the pseudo-interactive method for every step and the interactive method for some of the steps. Since it is possible to use both methods, take care not to run the same task with identical parameters twice using both methods.

  • Interactively examining task inputs. In this mode, one types taskname to load the task, inp to examine the inputs (see Figure 2), 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. Summaries 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. To reset a task to its default settings type, default taskname.
# Interactive CASA
<default|tget> taskname
parameter1 = value1
parameter2 = value2
inp   (Always double check the input parameters before running the task.)  
  • 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.
# Pseudo-interactive CASA
taskname('input parameters')
  • 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 within 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).

Step 1: Obtain the Dataset

From the NRAO Data Archive enter TDEM0025 in the Project Code field and select the data set TDEM0025.sb34039638.eb34043648.57965.965492013886. (This should be the only dataset for the project). The dataset on the archive is around 85 GB in size.

You will download the dataset as an SDM file, either as a .tar file or as an uncompressed file. Under the Jansky VLA datasets options, check the "SDM-BDF dataset (all files)" button and, if you want the dataset downloaded as a .tar file, check the "Create tar file" box.

Once you have your dataset, copy it into a directory where you can launch CASA to begin the data reduction steps below. If you downloaded the dataset as a .tar file, you need to perform the following extra step to extract the dataset before beginning the data reduction steps.

#In a terminal outside of CASA:
tar -xzf TDEM0025.sb34039638.eb34043648.57965.965492013886.tar.gz

Step 2: Import the Dataset into CASA

In earlier versions of CASA, you would import your data using the CASA command importevla. With CASA 5.4.0 and higher this task has been deprecated and, while it is still functional, there will be no further support for this task and you should instead use the CASA task importasdm to import your dataset into CASA. In order to make importasdm duplicate the task importevla, several parameters will need to be set from their default values.

# Interactive CASA
default importasdm
# Psuedo-interactive CASA
    inp                    # lists the inputs available for this task
    adsm='SDM-BDF File ID' # this is the filename of the SDM-BDF to use
    vis='filename.ms'      # this is the name of the output measurement set created (.ms)
    ocorr_mode='co'        # the VLA is a cross-correlator
    savecmds=True          # write the online flagging commands to an output file
    outfile='filename.txt' # name of the file containing the online flags
    applyflags=True        # apply the online flags during creation of the MS
    go                     # executes the task with the given inputs

Next we will use flagcmd to look at the table of online flags. This plot will show a graphical view of the online flags, which are antenna and/or time based flags.

Figure 1: Plot from flagcmd.

From this plot (see Figure 1), we can see that ea22 has a subreflector error during the beginning of the observation. We will flag this in a later step.

# Interactive CASA
default flagcmd
flagcmd(vis='TDEM0025.ms', inpmode='table', useapplied=True, action='plot', savepars=True, plotfile='flagcmd-table.png')

Step 3: Flag Antenna Shadowing, Zeros, and Very Bright Values

Next we will use flagdata to flag any antennas that may have been shadowed during the observation. This is a necessary step when observing in D- or C-configuration. Once we set mode='shadow' more parameters become available to edit specific to antenna shadowing, such as tolerance (the amount of shadow allowed (in meters)) and addantenna (file name or dictionary with additional antenna names, positions, and diameters). We will leave those parameters as the default settings of tolerance=0.0 (very conservative) and addantenna (no file or dictionary). Note, if an observation was taken in A- or B-configuration, this step is unnecessary.

# Interactive CASA
default flagdata
# Psuedo-interactive CASA
flagdata(vis='TDEM0025.ms', mode='shadow')

The correlator is known to generate a small number of zeros in the data. We will use flagdata to remove those zeros and to clip the very bright values. Setting mode='clip' in flagdata will reveal new parameters specific to this mode. We will leave most of the parameters as the default settings, however we will set two in particular: correlation='ABS_ALL' will take the absolute value of RR and LL and clip the very bright values and clipzeros=True will clip the zero-value data generated by the correlator.

# Interactive CASA
default flagdata
# Psuedo-interactive CASA
flagdata(vis='TDEM0025.ms', mode='clip', correlation='ABS_ALL', clipzeros=True)

More details regarding the use of flagdata can be found under the importasdm task.

Step 4: Initial Inspection of the Dataset

The next step is to inspect the contents of the MS using listobs. The task listobs provides almost all relevant observational parameters such as correlator setup (frequencies, bandwidths, channel number and widths, polarization products), sources, scans, scan intents, and antenna locations. Setting verbose=True will display all of the contents of the raw data and setting listfile='listobs.txt' will create a text file you can refer to later.

# Interactive CASA
default listobs
# Psuedo-interactive CASA
listobs(vis='TDEM0025.ms', verbose=True, listfile='listobs.txt')

Below is a copy/paste of a portion of the listobs output:

   Observer: Dr. John M. Cannon     Project: uid://evla/pdb/34039543  
Observation: EVLA
Data records: 7480512       Total elapsed time = 7176 seconds
   Observed from   31-Jul-2017/23:10:27.0   to   01-Aug-2017/01:10:03.0 (UTC)

   ObservationID = 0         ArrayID = 0
  Date        Timerange (UTC)          Scan  FldId FieldName             nRows     SpwIds   Average Interval(s)    ScanIntent
  31-Jul-2017/23:10:27.0 - 23:11:24.0     1      0 1331+305=3C286           60021  [0,1,2,3,4,5,6,7,8]  [3, 3, 3, 3, 3, 3, 3, 3, 3] [SYSTEM_CONFIGURATION#UNSPECIFIED]
              23:11:27.0 - 23:15:54.0     2      0 1331+305=3C286          281151  [0,1,2,3,4,5,6,7,8]  [3, 3, 3, 3, 3, 3, 3, 3, 3] [CALIBRATE_BANDPASS#UNSPECIFIED,CALIBRATE_FLUX#UNSPECIFIED]
              23:15:57.0 - 23:20:21.0     3      0 1331+305=3C286          277992  [0,1,2,3,4,5,6,7,8]  [3, 3, 3, 3, 3, 3, 3, 3, 3] [CALIBRATE_BANDPASS#UNSPECIFIED,CALIBRATE_FLUX#UNSPECIFIED]
              23:20:24.0 - 23:22:21.0     4      1 J1330+2509              123201  [0,1,2,3,4,5,6,7,8]  [3, 3, 3, 3, 3, 3, 3, 3, 3] [CALIBRATE_AMPLI#UNSPECIFIED,CALIBRATE_PHASE#UNSPECIFIED]
              23:22:24.0 - 23:24:21.0     5      1 J1330+2509              123201  [0,1,2,3,4,5,6,7,8]  [3, 3, 3, 3, 3, 3, 3, 3, 3] [CALIBRATE_AMPLI#UNSPECIFIED,CALIBRATE_PHASE#UNSPECIFIED]
              23:24:24.0 - 23:30:45.0     6      2 LEDA44055               401193  [0,1,2,3,4,5,6,7,8]  [3, 3, 3, 3, 3, 3, 3, 3, 3] [OBSERVE_TARGET#UNSPECIFIED]
              23:30:48.0 - 23:37:09.0     7      2 LEDA44055               401193  [0,1,2,3,4,5,6,7,8]  [3, 3, 3, 3, 3, 3, 3, 3, 3] [OBSERVE_TARGET#UNSPECIFIED]
              23:37:12.0 - 23:43:30.0     8      2 LEDA44055               398034  [0,1,2,3,4,5,6,7,8]  [3, 3, 3, 3, 3, 3, 3, 3, 3] [OBSERVE_TARGET#UNSPECIFIED]
              23:43:33.0 - 23:45:30.0     9      1 J1330+2509              123201  [0,1,2,3,4,5,6,7,8]  [3, 3, 3, 3, 3, 3, 3, 3, 3] [CALIBRATE_AMPLI#UNSPECIFIED,CALIBRATE_PHASE#UNSPECIFIED]
              23:45:33.0 - 23:51:54.0    10      2 LEDA44055               401193  [0,1,2,3,4,5,6,7,8]  [3, 3, 3, 3, 3, 3, 3, 3, 3] [OBSERVE_TARGET#UNSPECIFIED]
              23:51:57.0 - 23:58:15.0    11      2 LEDA44055               398034  [0,1,2,3,4,5,6,7,8]  [3, 3, 3, 3, 3, 3, 3, 3, 3] [OBSERVE_TARGET#UNSPECIFIED]
              23:58:18.0 - 00:04:39.0    12      2 LEDA44055               401193  [0,1,2,3,4,5,6,7,8]  [3, 3, 3, 3, 3, 3, 3, 3, 3] [OBSERVE_TARGET#UNSPECIFIED]
  01-Aug-2017/00:04:42.0 - 00:06:39.0    13      1 J1330+2509              123201  [0,1,2,3,4,5,6,7,8]  [3, 3, 3, 3, 3, 3, 3, 3, 3] [CALIBRATE_AMPLI#UNSPECIFIED,CALIBRATE_PHASE#UNSPECIFIED]
              00:06:42.0 - 00:13:03.0    14      2 LEDA44055               401193  [0,1,2,3,4,5,6,7,8]  [3, 3, 3, 3, 3, 3, 3, 3, 3] [OBSERVE_TARGET#UNSPECIFIED]
              00:13:06.0 - 00:19:24.0    15      2 LEDA44055               398034  [0,1,2,3,4,5,6,7,8]  [3, 3, 3, 3, 3, 3, 3, 3, 3] [OBSERVE_TARGET#UNSPECIFIED]
              00:19:27.0 - 00:25:48.0    16      2 LEDA44055               401193  [0,1,2,3,4,5,6,7,8]  [3, 3, 3, 3, 3, 3, 3, 3, 3] [OBSERVE_TARGET#UNSPECIFIED]
              00:25:51.0 - 00:27:48.0    17      1 J1330+2509              123201  [0,1,2,3,4,5,6,7,8]  [3, 3, 3, 3, 3, 3, 3, 3, 3] [CALIBRATE_AMPLI#UNSPECIFIED,CALIBRATE_PHASE#UNSPECIFIED]
              00:27:51.0 - 00:34:09.0    18      2 LEDA44055               398034  [0,1,2,3,4,5,6,7,8]  [3, 3, 3, 3, 3, 3, 3, 3, 3] [OBSERVE_TARGET#UNSPECIFIED]
              00:34:12.0 - 00:40:33.0    19      2 LEDA44055               401193  [0,1,2,3,4,5,6,7,8]  [3, 3, 3, 3, 3, 3, 3, 3, 3] [OBSERVE_TARGET#UNSPECIFIED]
              00:40:36.0 - 00:46:57.0    20      2 LEDA44055               401193  [0,1,2,3,4,5,6,7,8]  [3, 3, 3, 3, 3, 3, 3, 3, 3] [OBSERVE_TARGET#UNSPECIFIED]
              00:47:00.0 - 00:48:57.0    21      1 J1330+2509              123201  [0,1,2,3,4,5,6,7,8]  [3, 3, 3, 3, 3, 3, 3, 3, 3] [CALIBRATE_AMPLI#UNSPECIFIED,CALIBRATE_PHASE#UNSPECIFIED]
              00:49:00.0 - 00:55:18.0    22      2 LEDA44055               398034  [0,1,2,3,4,5,6,7,8]  [3, 3, 3, 3, 3, 3, 3, 3, 3] [OBSERVE_TARGET#UNSPECIFIED]
              00:55:21.0 - 01:01:42.0    23      2 LEDA44055               401193  [0,1,2,3,4,5,6,7,8]  [3, 3, 3, 3, 3, 3, 3, 3, 3] [OBSERVE_TARGET#UNSPECIFIED]
              01:01:45.0 - 01:08:06.0    24      2 LEDA44055               401193  [0,1,2,3,4,5,6,7,8]  [3, 3, 3, 3, 3, 3, 3, 3, 3] [OBSERVE_TARGET#UNSPECIFIED]
              01:08:09.0 - 01:10:03.0    25      1 J1330+2509              120042  [0,1,2,3,4,5,6,7,8]  [3, 3, 3, 3, 3, 3, 3, 3, 3] [CALIBRATE_AMPLI#UNSPECIFIED,CALIBRATE_PHASE#UNSPECIFIED]
           (nRows = Total number of rows per scan) 
Fields: 3
  ID   Code Name                RA               Decl           Epoch   SrcId      nRows
  0    NONE 1331+305=3C286      13:31:08.287984 + J2000   0         619164
  1    NONE J1330+2509          13:30:37.689201 + J2000   1         859248
  2    NONE LEDA44055           12:55:41.000000 + J2000   2        6002100
Spectral Windows:  (9 unique spectral windows and 2 unique polarization setups)
  SpwID  Name          #Chans   Frame   Ch0(MHz)  ChanWid(kHz)  TotBW(kHz) CtrFreq(MHz) BBC Num  Corrs  
  0      EVLA_L#A0C0#0   4096   TOPO    1410.330         3.906     16000.0   1418.3276       12  RR  LL
  1      EVLA_L#B0D0#1    128   TOPO     988.000      1000.000    128000.0   1051.5000       15  RR  RL  LR  LL
  2      EVLA_L#B0D0#2    128   TOPO    1116.000      1000.000    128000.0   1179.5000       15  RR  RL  LR  LL
  3      EVLA_L#B0D0#3    128   TOPO    1244.000      1000.000    128000.0   1307.5000       15  RR  RL  LR  LL
  4      EVLA_L#B0D0#4    128   TOPO    1372.000      1000.000    128000.0   1435.5000       15  RR  RL  LR  LL
  5      EVLA_L#B0D0#5    128   TOPO    1500.000      1000.000    128000.0   1563.5000       15  RR  RL  LR  LL
  6      EVLA_L#B0D0#6    128   TOPO    1628.000      1000.000    128000.0   1691.5000       15  RR  RL  LR  LL
  7      EVLA_L#B0D0#7    128   TOPO    1756.000      1000.000    128000.0   1819.5000       15  RR  RL  LR  LL
  8      EVLA_L#B0D0#8    128   TOPO    1884.000      1000.000    128000.0   1947.5000       15  RR  RL  LR  LL
Sources: 27
  ID   Name                SpwId RestFreq(MHz)  SysVel(km/s) 
  0    1331+305=3C286      0     1420.405752    419          
  0    1331+305=3C286      1     1420.405752    419          
  0    1331+305=3C286      2     1420.405752    419          
  0    1331+305=3C286      3     1420.405752    419          
  0    1331+305=3C286      4     1420.405752    419          
  0    1331+305=3C286      5     1420.405752    419          
  0    1331+305=3C286      6     1420.405752    419          
  0    1331+305=3C286      7     1420.405752    419          
  0    1331+305=3C286      8     1420.405752    419          
  1    J1330+2509          0     1420.405752    419          
  1    J1330+2509          1     1420.405752    419          
  1    J1330+2509          2     1420.405752    419          
  1    J1330+2509          3     1420.405752    419          
  1    J1330+2509          4     1420.405752    419          
  1    J1330+2509          5     1420.405752    419          
  1    J1330+2509          6     1420.405752    419          
  1    J1330+2509          7     1420.405752    419          
  1    J1330+2509          8     1420.405752    419          
  2    LEDA44055           0     1420.405752    419          
  2    LEDA44055           1     1420.405752    419          
  2    LEDA44055           2     1420.405752    419          
  2    LEDA44055           3     1420.405752    419          
  2    LEDA44055           4     1420.405752    419          
  2    LEDA44055           5     1420.405752    419          
  2    LEDA44055           6     1420.405752    419          
  2    LEDA44055           7     1420.405752    419          
  2    LEDA44055           8     1420.405752    419          
Antennas: 27:
  ID   Name  Station   Diam.    Long.         Lat.                Offset from array center (m)                ITRF Geocentric coordinates (m)        
                                                                     East         North     Elevation               x               y               z
  0    ea01  W12       25.0 m   -  +       -835.3760     -544.2316        0.5650 -1602044.902600 -5042025.803400  3554427.822700
  1    ea02  W04       25.0 m   -  +       -152.8711      -83.7955       -2.4675 -1601315.900500 -5041985.306670  3554808.309400
  2    ea03  W10       25.0 m   -  +       -619.2934     -398.4403       -0.5229 -1601814.060900 -5042012.886450  3554548.229820

From the listobs output, note the field ID for each of the sources and scan intent(s) (or source type). This information will be used for future calibration tasks and when splitting the data.

Field ID   Source       Scan Intent
   0       3C286        flux density scale and bandpass calibrator
   1       J1330+2509   complex gain (amplitude and phase) calibrator
   2       LEDA44055    observe target

Since the goal of this tutorial is to find the HI (1.420405752 GHz rest frequency) spectral line in LEDA 44055, note the spw ID containing the spectral line setup. From this particular instrument configuration, the spectral line setup is spw ID 0, while spw ID's 1-8 are continuum. Make note of the spectral line setup for spw 0. This information will be used later.

spw 0
4096 channels
TOPO frame indicates Barycentric Optical Doppler setting
3.906 kHz channel width indicates the resolution
16 MHz bandwidth indicates the full width of the spw
1418.3276 MHz center frequency of the spw

Step 5: Split Out the HI Line

Before we begin calibration or flagging of misbehaving antennas or RFI, we will run split to create a new smaller MS containing only the HI line (spw 0).

# Interactive CASA
default split
# Psuedo-interactive CASA
split(vis='TDEM0025.ms', outputvis='TDEM0025_HI.ms', spw=0, datacolumn='data')

Now if we run listobs on this new MS, we can see the output shows everything but the continuum spw's 1-8.

# Psuedo-interactive CASA
listobs(vis='TDEM0025_HI.ms', verbose=True, listfile='listobs_HI.txt')

Step 6: Initial Flux Density Scaling

Using setjy, we will list available models and set the model for the flux calibrator. By setting listmodels=True, setjy will show all available models for specific calibrators with specific bands in the Perley-Butler 2017 standard. setjy will look within the directory in which CASA was run for *.im *.mod files for user-defined models or images. If none are found, setjy will confirm this, for this particular dataset we will use a model in CalModels instead.

# Interactive CASA
default setjy

# Psuedo-interactive CASA
#terminal output
No candidate modimages matching '*.im* *.mod*' found in .  # The single period here refers to the current working directory. 

Candidate modimages (*) in /home/casa/data/distro/nrao/VLA/CalModels:
3C138_A.im  3C138_L.im  3C138_U.im  3C147_C.im  3C147_Q.im  3C147_X.im  3C286_K.im  3C286_S.im  3C48_A.im  3C48_L.im  3C48_U.im
3C138_C.im  3C138_Q.im  3C138_X.im  3C147_K.im  3C147_S.im  3C286_A.im  3C286_L.im  3C286_U.im  3C48_C.im  3C48_Q.im  3C48_X.im
3C138_K.im  3C138_S.im  3C147_A.im  3C147_L.im  3C147_U.im  3C286_C.im  3C286_Q.im  3C286_X.im  3C48_K.im  3C48_S.im  README

Using setjy, we will set the model for the flux calibrator 3C286 (field='0') which was observed in L band.

# Interactive CASA
default setjy
standard='Perley-Butler 2017'
# Psuedo-interactive CASA
setjy(vis='TDEM0025_HI.ms',listmodels=False,field='0',spw='0',scalebychan=True,fluxdensity=-1,standard='Perley-Butler 2017',model='3C286_L.im',usescratch=True)
    vis='TDEM0025_HI.ms'          # the split HI ms.
    listmodels='False'            # do not list the available models for VLA calibrators. 
    field='0'                     # set the model for 3C286, the flux density calibrator for this observation.
    spw='0'                       # calculate the model for one spw. 
    scalebychan=True              # set as default, the model is calculated per channel. 
    fluxdensity=-1                # uses the flux density standard for recognized sources, and [1,0,0,0] for unrecognized.
    standard='Perley-Butler 2017' # Flux density standard used as the default.
    model='3C286_L.im'            # Use the L band model for 3C286.
    usescratch=True               # create a MODEL_DATA column containing model data

Within the casalogger, setjy outputs the flux in Janskys for Stokes I for a specific frequency.

2019-03-26 17:32:38 INFO imager	Using channel dependent flux densities
2019-03-26 17:32:38 INFO imager	Selected 68796 out of 831168 rows.
2019-03-26 17:32:38 INFO imager	1331+305=3C286 (fld ind 0) spw 0  [I=15.028, Q=0, U=0, V=0] Jy @ 1.4103e+09Hz, (Perley-Butler 2017)
2019-03-26 17:32:58 INFO imager	Using model image /home/casa/data/distro/nrao/VLA/CalModels/3C286_L.im
2019-03-26 17:32:58 INFO imager	Scaling spw(s) [0]'s model image by channel to  I = 15.0281, 14.9855, 14.9431 Jy @(1.41037e+09, 1.41838e+09, 1.42638e+09)Hz (LSRK) for visibility prediction (a few representative values are shown).
2019-03-26 17:32:58 INFO imager	The model image's reference pixel is 0.000254726 arcsec from 1331+305=3C286's phase center.
2019-03-26 17:32:58 INFO imager	Will clear any existing model with matching field=1331+305=3C286 and spw=*
2019-03-26 17:32:58 INFO  	Clearing model records in MS header for selected fields.
2019-03-26 17:32:58 INFO  	 1331+305=3C286 (id = 0) not found.
2019-03-26 17:32:58 INFO imager	Selected 68796 out of 831168 rows.
2019-03-26 17:32:58 INFO setjy	##### End Task: setjy                #####
2019-03-26 17:32:58 INFO setjy	##########################################

Step 7: Prior Calibration

In this step, we will look at the antenna layout, weather conditions during the observation, generate antenna gain curve corrections, and antenna position corrections. We will summarize opacity corrections, ionospheric TEC corrections, and requantizer gain corrections and why they may not benefit this dataset. Then we'll do an initial assessment of the amplitude versus time to see any RFI, or bad antennas before the calibration stage.

Antenna configuration

Using plotants, we'll look at the overall antenna layout and chose the best reference antenna based on certain criteria. We will want to choose a reference antenna that is closer to the center of the array, so any atmospheric changes are similar for all antennas. For D and C configuration, low declination sources are subject to antenna shadowing and antennas will collect less radiation, causing lower sensitivity which may not be the best choice for the reference antenna. For this guide, we will use ea10 as the reference antenna.

Figure 2: Plot from plotants.
# Interactive CASA
default plotants
# Psuedo-interactive CASA

Usually, the array will take a few seconds to stabilize at the start of a scan. Using flagdata with mode quack, we will flag the first 5 seconds at the beginning of each scan.

# Interactive CASA
default flagdata
# Psuedo-interactive CASA
    vis='TDEM0025_HI.ms'   # the split HI ms.
    mode='quack'           # specific flagging mode, flag data at the beginning or end of a scan.
    quackinterval=5.0      # time in seconds.
    quackmode='beg'        # flag the first n seconds for each scan designated in the parameter scan.
    scan=''                # flag data for all scans in vis.

Using plotms, we'll create an elevation versus time plot for all sources. Criteria for the complex gain (amplitude and phase) calibrator should be closer to the source to obtain a similar environment regarding changes in amplitude and phase which will be applied to the source.

Figure 4: Elevation versus time for TDEM0025.
# Interactive CASA
default plotms
# Psuedo-interactive CASA
    vis='TDEM0025_HI.ms'         # the split HI ms.
    xaxis='time'                 # plot time along the x axis.
    yaxis='elevation'            # plot elevation along the y axis.
    correlation='RR,LL'          # plot the two parallel hand polarizations, Right and Left polarizations. 
    avgchannel='64'              # average data every 64 channels.
    coloraxis='field'            # colorize data points by field.
    plotfile='elevstime.png'     # automatically save this plot to a file titled elevstime.png.

Antenna gain-elevation curve calibration

With elevation, the effective collecting area and surface accuracy of antennas varies as gravity tugs at the surface of the non-rigid antenna. Using gencal, we will write the gain curve solutions to a calibration table.

# Interactive CASA
default gencal
# Psuedo-interactive CASA
    vis='TDEM0025_HI.ms'   # the split HI ms.
    caltable='antgain.cal' # name of output calibration table where values are stored.
    caltype='gc'           # gain curve calculated per spw.

Opacities and weather conditions

Figure 3: Plot from plotweather.

Using plotweather, we'll look at weather conditions throughout the observation that may affect the data. plotweather provides an estimate of the opacity on a per spw basis with units in nepers. The seasonal weight parameter calculates the opacities based on the weather data, seasonal model, or a combination of two. When the seasonal_weight is set to 1 the opacity corrections are derived using only the seasonal data and when set to 0 the opacity corrections are derived from only the weather data.

Atmospheric opacity attenuates incoming radiation and observations at different elevations affect the flux density scale of sources. For lower frequency observation (Ku and lower), this attenuation is small and opacity corrections are usually skipped. Luckily for L band, weather conditions do not significantly affect (unless it’s snow, rain, or strong winds) the data, therefore we can save the weather plots for reference and skip opacity corrections.

# Interactive CASA
default plotweather
# Psuedo-interactive CASA
    vis='TDEM0025_HI.ms'                         # the split HI ms.
    seasonal_weight=0.5                          # calculate opacities using both the seasonal model and weather data.
    plotName='TDEM0025weathercond.png'           # name of the generated plot 
    doPlot=True                                  # create plot. If set to false, do not create plot and output only the calculated opacities. 

Requantizer gains calibration

Requantizer gain corrections account for gain changes that occur when resetting the quantizer gains as the correlator changes to a new 3-bit configuration. Requantizer gains need to be redetermined after a change of tuning. To create a calibration table containing corrections for the requantizer gains one would use gencal with caltype=’rq’. However, since this observation uses 8-bit setup this step can be skipped. For information on 8 bit, 3 bit setup observations, and requantizer setup scans here is a link to 8/3-Bit Attenuator and Requantizer Gain Setup Scans

Ionopsheric TEC(total electron content) calibration

The Total Electron Content (TEC) is the total number of electrons present along a path between a radio source and receiver. Ionospheric corrections are important for frequencies below 1GHz or for polarimetry. For this guide, we will not derive or apply TEC corrections.

Applying antenna position corrections

We will apply antenna position corrections using gencal which queries the VLA Archive: Baseline Corrections.

# Interactive CASA
default gencal
# Psuedo-interactive CASA
    vis='TDEM0025_HI.ms'   # the split HI ms
    caltype='antpos'       # the type of calibration to solve for, where antpos gathers the ITRF antenna position offsets
    caltable='antpos.cal'  # create a calibration table titled antpos.cal where the antenna position offsets can be stored
    antenna=''             # search for all antennas

gencal will report into the casalogger, if there are any antenna position corrections found. In this case, there are position corrections for antenna ea25 that are saved into the calibration table antpos.cal and will be applied in later stages using applycal and gaincal.

  • Please note gencal will also report to the logger if there are no antenna position corrections for the observation. This simply means all antenna position corrections were applied by the VLA Operator before the science observation was made.
2019-03-25 21:52:22	INFO	gencal::::+	##########################################
2019-03-25 21:52:22	INFO	gencal::::+	##### Begin Task: gencal             #####
2019-03-25 21:52:22	INFO	gencal::::	gencal(vis="TDEM0025_HI.ms",caltable="antpos.cal",caltype="antpos",infile="",spw="",
2019-03-25 21:52:22	INFO	gencal::::+	        antenna="",pol="",parameter=[],uniform=True)
2019-03-25 21:52:22	INFO	calibrater::open	****Using NEW VI2-driven calibrater tool****
2019-03-25 21:52:22	INFO	calibrater::open	Opening MS: TDEM0025_HI.ms for calibration.
2019-03-25 21:52:22	INFO	Calibrater::	Initializing nominal selection to the whole MS.
2019-03-25 21:52:22	INFO	gencal::::	 Determine antenna position offsets from the baseline correction database
2019-03-25 21:52:22	INFO	gencal::::	offsets for antenna ea25 : -0.00200   0.00000  -0.00120
2019-03-25 21:52:22	INFO	calibrater::specifycal	Beginning specifycal-----------------------
2019-03-25 21:52:22	INFO		Creating KAntPos Jones table from specified parameters.
2019-03-25 21:52:22	INFO		Writing solutions to table: antpos.cal
2019-03-25 21:52:22	INFO	gencal::::	##### End Task: gencal               #####

Initial inspection of amplitude versus time.

Figure 4: Amplitude vs time for all fields colorized by baselines

Let's look at amplitude variations with respect to time for each field. We will want to flag significant variations in amplitude and keep track of recurring antennas/timeframes/frequencies/sudden spikes(RFI) in amplitude so these may be flagged as a collection of an issue.

By setting colors per baseline, we notice that one antenna is pretty noisy. Within the plotms GUI, click on the Mark Regions icon, select a few points of the widely varying amplitude, use the Locate icon (the magnifying glass) to output information on the data, and assess common details of the data. We notice that ea24 causes significant noise seen in Figure 4, where the purple data is ea24.

  • Please keep in mind when using the flag icon in plotms, which is close to the locate icon, an automatic flagbackup is not set when interactively flagging.

Within the Data tab exclude ea24 by typing !ea24 in the antenna selection. Re-plotting, we can see the overall amplitude is less variable as seen in Figure 5.

# Interactive CASA
default plotms
Figure 5: Amplitude vs time for all fields colorized by baselines excluding ea24
# Psuedo-interactive CASA

    vis='TDEM0025_HI.ms'       # the split HI ms
    xaxis='time'               # plot time along the x axis  
    yaxis='amp'                # plot amplitude along the y axis
    correlation='RR,LL'        # plot the two parallel hand polarizations, Right and Left polarizations
    selectdata=True            # expand the parameters to choose from. 
    avgchannel='64'            # average data every 64 channels 
    coloraxis='baseline'       # colorize data points by baseline

We can also iterate per baseline to the reference antenna ea10 and the suspected antenna ea24. by using the green arrow icon within plotms Here we notice that all baselines associated to ea24 vary in amplitude significantly. Figure 6 shows one baseline with ea16&ea24, and iterating through baselines with ea24 all show varying amplitudes.

Figure 6: Amplitude vs time for ea16&ea24 baseline
# Interactive CASA
default plotms
# Psuedo-interactive CASA

    vis='TDEM0025_HI.ms'       # the split HI ms.
    xaxis='time'               # plot time along the x axis.  
    yaxis='amp'                # plot amplitude along the y axis.
    antenna='ea10,ea24'        # includ antennas ea10 and ea24 only.
    correlation='RR,LL'        # plot the two parallel hand polarizations, Right and Left polarizations.
    selectdata=True            # expand the parameters to choose from. 
    avgchannel='64'            # average data every 64 channels.
    coloraxis='antenna1'       # colorize by the first antenna. 
    iteraxis='baseline'        # create a plot for each baseline to ea10 and ea24.

Now that we've narrowed down the noisy antenna, we will flag ea24 using flagdata which will also output to the casalogger the flagbackup version name.

# Interactive CASA
default flagdata
# Psuedo-interactive CASA

    vis='TDEM0025_HI.ms'   # the split HI ms
    mode='manual'          # flag data based on parameters specified.
    antenna='ea24'         # flag antennas and 24.
    action='apply'         # apply the flags to the split HI ms.
    flagbackup=True        # automatically save flags into a predesignated flagversion name.

Now that we have completed initial assessment of the data and flagged bad antennas we will proceed to bandpass calibration.

Step 8: Delay, Bandpass, and Gain Calibration