Difference between revisions of "HI 21cm (1.4 GHz) spectral line data reduction: LEDA 44055"

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(Step 3: Flag Antenna Shadowing and Zeros)
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<source lang="python">
 
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# Psuedo-interactive CASA
 
# Psuedo-interactive CASA
importasdm(asdm='TDEM0025.sb34039638.eb34043648.57965.965492013886',vis='TDEM0025.ms',ocorr_mode='co',savecmds=True,outfile='TDEM0025_onlineflags.txt',applyflags=False)
+
importasdm(asdm='TDEM0025.sb34039638.eb34043648.57965.965492013886',vis='TDEM0025.ms',ocorr_mode='co',savecmds=True,outfile='TDEM0025_onlineflags.txt',applyflags=True)
 
</source>
 
</source>
  

Revision as of 17:03, 14 March 2019

Overview

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
inp 
parameter1 = value1
parameter2 = value2
(etc) 
inp   (Always double check the input parameters before running the task.)  
go
  • 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
inp
asdm='TDEM0025.sb34039638.eb34043648.57965.965492013886'
vis='TDEM0025.ms'
ocorr_mode='co'
savecmds=True
outfile='TDEM0025_onlineflags.txt'
applyflags=True
inp
go
# Psuedo-interactive CASA
importasdm(asdm='TDEM0025.sb34039638.eb34043648.57965.965492013886',vis='TDEM0025.ms',ocorr_mode='co',savecmds=True,outfile='TDEM0025_onlineflags.txt',applyflags=True)
Where:
    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
vis='TDEM0025.ms'
inpmode='table'
useapplied=True
action='plot'
savepars=True
plotfile='flagcmd-table.png'
inp
go
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
inp
vis='TDEM0025.ms'
mode='shadow'
inp
go
# 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
inp
vis='TDEM0025.ms'
mode='clip'
correlation='ABS_ALL'
clipzeros=True
inp
go
# 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
inp
vis='TDEM0025.ms'
verbose=True
listfile='listobs.txt'
inp
go
# 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 +30.30.32.95886 J2000   0         619164
  1    NONE J1330+2509          13:30:37.689201 +25.09.10.97800 J2000   1         859248
  2    NONE LEDA44055           12:55:41.000000 +19.12.33.00000 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   -107.37.37.4  +33.53.44.2       -835.3760     -544.2316        0.5650 -1602044.902600 -5042025.803400  3554427.822700
  1    ea02  W04       25.0 m   -107.37.10.8  +33.53.59.1       -152.8711      -83.7955       -2.4675 -1601315.900500 -5041985.306670  3554808.309400
  2    ea03  W10       25.0 m   -107.37.28.9  +33.53.48.9       -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
inp
vis='TDEM0025.ms'
outputvis='TDEM0025_HI.ms'
spw=0
datacolumn='data'
inp
go
# Psuedo-interactive CASA
split(vis='TDEM0025.ms', output='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: For Angie to Edit