VLA Data Combination-CASA5.0.0: Difference between revisions

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cl.addcomponent(flux=0.712, fluxunit='Jy',shape='point', dir='J2000 17:45:40.038543 -')

Revision as of 12:19, 31 July 2017

'This tutorial was created and tested using CASA 5.0.0


A perfect image requires measurement of all spatial scales, which is equivalent to filling in the complete uv plane. Unfortunately, this can never be achieved with an aperture synthesis interferometer although a large number of baselines, long integration times, and multi-frequency-synthesis are all good approaches to increase the uv-coverage. One method to obtain more baselines is to observe in different array configurations and to combine the data afterwards. Deconvolution algorithms are then given good starting conditions to interpolate over the gaps in the uv-plane to achieve an improved image - an image that combines the surface brightness sensitivity of the compact baselines with the spatial resolution of the extended baselines.

The VLA can be configured into four principal array configurations, A, B, C, and D. A is the most extended and D is the most compact configuration. Consequently, A configuration data exhibits the highest spatial resolution whereas D configuration delivers the best surface brightness sensitivity and also images the largest scales of the sky brightness distribution.

In this tutorial, we will combine data from three VLA configurations (A & B & C) that were obtained in a monitoring campaign of Sgr A*, the central supermassive black hole of our Milky Way.

Typical Observing Times

When an object is being observed by the VLA in different array configurations, on-source integration times are ideally matched to reach a common surface brightness sensitivity for all scales. Adjacent VLA configurations result in synthesized beams that differ in linear size by approximately a factor of 3. The beam areas therefore change by factors of ~10 and the more extended configuration would ideally need to have 10 times more integration time than the next compact one. This, however, is frequently not very practical and it turns out that integration times that differ by factors of ~3 are delivering data that can be combined satisfactorily as it matches the sensitivity of overlapping VLA visibilities when data are convolved to the same scales.

This rule, however, is only a guidance and any data that are being obtained from any configuration can be combined although overlapping uv-coverages are strongly recommended. Weighting will be primarily achieved during imaging by the "Briggs" scheme that allows one to adjust imaging weights between the "natural" and "uniform" extremes, i.e., between weighting by the number of visibilities that are gridded in each cell and weighting by the cells themselves.

In addition, each visibility exhibits weights that should only depend on correlator integration time, bandwidth, and system temperature (Tsys). The VLA, however, currently does apply Tsys in the online system. Visibility weights between different observations will therefore need to be adjusted as described below before they can be combined.

The Data

In the following we will combine three different datasets from the NRAO Monitoring of the Galactic Center/G2 Cloud Encounter. We will combine S-band A, B, and C configuration data. The data were all calibrated and the science target split out.

The calibrated measurement sets can be downloaded here: 
https://casa.nrao.edu/Data/EVLA/SgrA/VLA-combination-SgrA-files.tar.gz (1.4GB)

As a first step, let's download the files, then untar:

# In Terminal
tar -xzvf VLA-combination-SgrA-files.tar.gz

This will unpack three MeasurementSets, one for each array configuration:




Initial Imaging

We will inspect the data and create separate images to better understand the image parameters such as on-source integration time, resolution, and rms.

Start CASA as usual via

# In Terminal

As a first step, let's have a look at the listobs output for the different MeasurementSets. For example, the A-configuration MS has the following structure:

##### Begin Task: listobs            #####
           MeasurementSet Name:  /lustre/aoc/sciops/jott/casa/topicalguide/combination/test/VLA-SgrA-Sband-Aconfig.ms      MS Version 2
   Observer: lorant sjouwerman     Project: uid://evla/pdb/11434214  
Observation: EVLA
Data records: 528000       Total elapsed time = 360 seconds
   Observed from   31-May-2014/09:07:57.0   to   31-May-2014/09:13:57.0 (UTC)
Compute subscan properties
   ObservationID = 0         ArrayID = 0
  Date        Timerange (UTC)          Scan  FldId FieldName             nRows     SpwIds   Average Interval(s)    ScanIntent
  31-May-2014/09:07:57.0 - 09:13:57.0    63      0 J1745-2900              528000  [0,3,4,5,6,7,8,9,10,11,12,13,14,15]  [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] [OBSERVE_TARGET#UNSPECIFIED]
           (nRows = Total number of rows per scan) 
Fields: 1
  ID   Code Name                RA               Decl           Epoch   SrcId      nRows
  0    NONE J1745-2900          17:45:40.038300 - J2000   0         528000
Spectral Windows:  (14 unique spectral windows and 1 unique polarization setups)
  SpwID  Name           #Chans   Frame   Ch0(MHz)  ChanWid(kHz)  TotBW(kHz) CtrFreq(MHz) BBC Num  Corrs  
  0      EVLA_S#A0C0#80     64   TOPO    1988.000      2000.000    128000.0   2051.0000       12  RR  LL
  3      EVLA_S#A0C0#83     64   TOPO    2372.000      2000.000    128000.0   2435.0000       12  RR  LL
  4      EVLA_S#A0C0#84     64   TOPO    2500.000      2000.000    128000.0   2563.0000       12  RR  LL
  5      EVLA_S#A0C0#85     64   TOPO    2628.000      2000.000    128000.0   2691.0000       12  RR  LL
  6      EVLA_S#A0C0#86     64   TOPO    2756.000      2000.000    128000.0   2819.0000       12  RR  LL
  7      EVLA_S#A0C0#87     64   TOPO    2884.000      2000.000    128000.0   2947.0000       12  RR  LL
  8      EVLA_S#B0D0#88     64   TOPO    2988.000      2000.000    128000.0   3051.0000       15  RR  LL
  9      EVLA_S#B0D0#89     64   TOPO    3116.000      2000.000    128000.0   3179.0000       15  RR  LL
  10     EVLA_S#B0D0#90     64   TOPO    3244.000      2000.000    128000.0   3307.0000       15  RR  LL
  11     EVLA_S#B0D0#91     64   TOPO    3372.000      2000.000    128000.0   3435.0000       15  RR  LL
  12     EVLA_S#B0D0#92     64   TOPO    3500.000      2000.000    128000.0   3563.0000       15  RR  LL
  13     EVLA_S#B0D0#93     64   TOPO    3628.000      2000.000    128000.0   3691.0000       15  RR  LL
  14     EVLA_S#B0D0#94     64   TOPO    3756.000      2000.000    128000.0   3819.0000       15  RR  LL
  15     EVLA_S#B0D0#95     64   TOPO    3884.000      2000.000    128000.0   3947.0000       15  RR  LL
Sources: 16
  ID   Name                SpwId RestFreq(MHz)  SysVel(km/s) 
  0    J1745-2900          0     -              -            
  0    J1745-2900          1     -              -            
  0    J1745-2900          2     -              -            
  0    J1745-2900          3     -              -            
  0    J1745-2900          4     -              -            
  0    J1745-2900          5     -              -            
  0    J1745-2900          6     -              -            
  0    J1745-2900          7     -              -            
  0    J1745-2900          8     -              -            
  0    J1745-2900          9     -              -            
  0    J1745-2900          10    -              -            
  0    J1745-2900          11    -              -            
  0    J1745-2900          12    -              -            
  0    J1745-2900          13    -              -            
  0    J1745-2900          14    -              -            
  0    J1745-2900          15    -              -            
Antennas: 26:
  ID   Name  Station   Diam.    Long.         Lat.                Offset from array center (m)                ITRF Geocentric coordinates (m)        
                                                                     East         North     Elevation               x               y               z
  0    ea01  N32       25.0 m   -  +       -441.7442     4689.9683      -16.9356 -1600781.062100 -5039347.430600  3558761.526300
  1    ea02  N64       25.0 m   -  +      -1382.3632    15410.1417      -40.6233 -1599855.668100 -5033332.388100  3567636.626500
  2    ea03  E64       25.0 m   -  +      15507.5911    -7263.7210       67.2006 -1587600.203200 -5050575.869700  3548885.404900
  3    ea04  E24       25.0 m   -  +       2858.1804    -1349.1324       13.7306 -1598663.094300 -5043581.396100  3553767.023200
  4    ea05  W08       25.0 m   -  +       -432.1181     -272.1470       -1.5057 -1601614.092200 -5042001.651900  3554652.509800
  5    ea06  N56       25.0 m   -  +      -1105.2076    12254.3155      -34.2423 -1600128.382500 -5035104.142000  3565024.679400
  6    ea07  N48       25.0 m   -  +       -855.2644     9405.9610      -25.9303 -1600374.875000 -5036704.207500  3562667.885900
  7    ea08  N16       25.0 m   -  +       -155.8517     1426.6442       -9.3792 -1601061.957400 -5041175.883000  3556058.040000
  8    ea09  W64       25.0 m   -  +     -14240.7638    -9606.2696       17.1066 -1616361.587500 -5042770.516600  3546911.446900
  9    ea10  E40       25.0 m   -  +       6908.8305    -3240.7192       39.0202 -1595124.923100 -5045829.467200  3552210.703600
  10   ea11  W24       25.0 m   -  +      -2673.3552    -1784.5888       10.4757 -1604008.749300 -5042135.808900  3553403.716000
  11   ea12  N09       25.0 m   -  +        -77.4204      530.6453       -5.5755 -1601139.471200 -5041679.039700  3555316.553900
  12   ea13  W56       25.0 m   -  +     -11333.2004    -7637.6771       15.3707 -1613255.393400 -5042613.099800  3548545.915000
  13   ea14  E08       25.0 m   -  +        407.8298     -206.0320       -3.2196 -1600801.931000 -5042219.386500  3554706.431200
  14   ea15  E56       25.0 m   -  +      12327.6313    -5774.7469       42.6153 -1590380.611000 -5048810.243300  3550108.432300
  15   ea17  E32       25.0 m   -  +       4701.6413    -2209.7152       25.2066 -1597053.135800 -5044604.681200  3553058.995000
  16   ea18  E72       25.0 m   -  +      19041.8717    -8769.2047        4.7262 -1584460.871200 -5052385.599800  3547600.000100
  17   ea19  W16       25.0 m   -  +      -1348.7109     -890.6216        1.3005 -1602592.853600 -5042054.996800  3554140.704800
  18   ea20  N40       25.0 m   -  +       -633.6074     6878.6018      -20.7693 -1600592.756000 -5038121.357300  3560574.853200
  19   ea21  E48       25.0 m   -  +       9456.6097    -4431.6564       37.9341 -1592894.077600 -5047229.138200  3551221.206000
  20   ea22  N24       25.0 m   -  +       -290.3752     2961.8594      -12.2389 -1600930.087800 -5040316.396400  3557330.387200
  21   ea23  W72       25.0 m   -  +     -17419.4740   -11760.2758       14.9538 -1619757.312900 -5042937.664400  3545120.392300
  22   ea24  W48       25.0 m   -  +      -8707.9403    -5861.7877       15.5282 -1610451.925800 -5042471.125800  3550021.055800
  23   ea25  W32       25.0 m   -  +      -4359.4392    -2923.1244       11.7721 -1605808.634900 -5042230.089000  3552459.209500
  24   ea26  W40       25.0 m   -  +      -6377.9880    -4286.7769        8.2038 -1607962.463800 -5042338.190100  3551324.947500
  25   ea28  E16       25.0 m   -  +       1410.0378     -673.4764       -0.7821 -1599926.107500 -5042772.979700  3554319.790400
##### End Task: listobs              #####

We see that A-configuration contains only the central source, "J1745-2900", which is just a different name for Sgr A*. The on-source integration time amounts to only six minutes and the 16 spectral windows span a frequency range from 1.988 to 4.012GHz. Inspection of the other array configuration files show almost identical setups. Although the integration times between the different array configurations do not follow the 1:3:9 ratios that we discussed in the previous section, we can still combine the data without any problems. In the end, having better signal to noise on the shorter baselines can only improve the overall, combined image.

To better understand the data, let's check the uv-coverage of each of the three datasets:

# A-config: 
# B-config
# C-config:

The uv-coverage plots are shown in Fig. 1. The u:v aspect ratio of each uv-coverage is high as Sgr A* is a very southern source. We also see that the longest baseline in each array differs by about a factor of 3 between the three configurations, as expected from the VLA A, B, and C configurations.

Figure 1a:
UV-coverage of the A-configuration data.
Figure 1b:
UV-coverage of the B-configuration data.
Figure 1c:
UV-coverage of the C-configuration data.

The next step is to determine the image quality, the synthesized beam, and the rms of each image. To do so, the images do not have to be perfectly deconvolved as we only would like to see how the combination will improve over the individual arrays.

To keep things simple, we will use common cell sizes of 0.1 arcsec, images of 1280 pixels on each side, and we will clean 1000 iterations (see the VLA CASA imaging guide for more sophisticated imaging parameter choices):

# A-config: 
clean(vis='VLA-SgrA-Sband-Aconfig.ms', imagename='SgrA-Aonly',field='J1745-2900',
# B-config
clean(vis='VLA-SgrA-Sband-Bconfig.ms', imagename='SgrA-Bonly',field='J1745-2900',
# C-config:
clean(vis='VLA-SgrA-Sband-Cconfig.ms', imagename='SgrA-Conly',field='J1745-2900',

The clean images, shown in Fig. 2, give a first impression of the data. Note that when combining the images, we will improve on the uv-coverage and will therefore not only combine high resolution with high surface brightness sensitivity on large scales, but also expect a higher image fidelity, i.e. fewer artifacts due to better deconvolution.

Figure 2a:
Simple image of the A-configuration data.
Figure 2b:
Simple image of the B-configuration data.
Figure 2c:
Simple image of the C-configuration data.

The basic parameters of the individual images can be checked through imhead for the spatial resolution, and by determining the rms in the viewer when checking the statistics of empty areas. The central point source, Sgr A*, is variable and we see this reflected in the flux density values from the images taken in the three different configurations, which were separated in observing time by several months:

A-configuration: synthesized beam  1.44" x 0.40"; rms ~0.8mJy; peak flux density of Sgr A* 0.712 Jy/beam
B-configuration: synthesized beam  4.33" x 1.34"; rms ~0.7mJy; peak flux density of Sgr A* 0.691 Jy/beam
C-configuration: synthesized beam 11.02" x 4.20"; rms ~0.6mJy; peak flux density of Sgr A* 1.35 Jy/beam

Check and Adjust the Visibility Weights

VLA weights are currently only based on channel width and correlator integration time. In the future, the VLA may use the switched power measurements to derive absolute calibrated weights. At the moment, however, the VLA weights need to be taken as being relative to each other. The relative sensitivity within an observation is measured by the gain, so weights of single, continuous observation are self-consistent. It is important, however, to adjust the weights between separate observations as they will be on different scales.

Let's have a look at the weights of the different datasets. We will plot the weights as a function of uv-distance, average over all channels in one spectral window, and will colorize by antenna:

# A-config: 
# B-config
# C-config:

Fig. 3 shows that there are some differences. Data from configurations A and B have weights that are reasonably consistent, C-configuration data, however, seems to have consistently lower values.

Figure 3a:
A-config original weights.
Figure 3b:
B-config original weights.
Figure 3c:
C-config original weights.

The task statwt in CASA will recalculate the visibility weights based on their rms. statwt is part of the VLA pipeline, which was used to calibrate the original data. This explains the similarity of the A and B configuration weights in Fig. 3. But we nevertheless will run statwt once more on all files in order to ensure proper compatibility of the data (older versions of CASA may have been used for the pipeline, and CASA underwent major changes in its definition of data weights).

statwt needs to be executed on each MS. The default setting calculates the weight based on the rms of each scan and spectral window. This setting works quite well for continuum observations. We would like to note though that for spectral line data the fitspw parameter should be set to exclude the line from the calculations. Otherwise, strong lines will be down-weighted.

As statwt will overwrite the WEIGHT column, we first create copies of our MSs in case we will have to revert to the original data:

# In a Terminal
cp -r VLA-SgrA-Sband-Aconfig.ms VLA-SgrA-Sband-Aconfig-statwt.ms
cp -r VLA-SgrA-Sband-Bconfig.ms VLA-SgrA-Sband-Bconfig-statwt.ms
cp -r VLA-SgrA-Sband-Cconfig.ms VLA-SgrA-Sband-Cconfig-statwt.ms

Now, we execute statwt on the new datasets:

# A-config: 
# B-config
# C-config:

CASA will come up with a message that the CORRECTED column is not found and that DATA is being used. This is fine as indeed the MS only contains a DATA column as CORRECTED was split out after calibration, which then populated the DATA column in the new MS.

Let's have a look at the weight values again to see if statwt has adjusted the weights properly:

# A-config: 
# B-config
# C-config:

In Fig. 4 we plot the new, recalculated weights. The absolute scaling has indeed changed, likely due to a different weight definition that was used in earlier versions of CASA when the data were calibrated. The relative weights between A and B configurations still appear to be similar to the original, relative numbers. The C-configuration weights, however, appear to be slightly elevated relative to A and B.

Figure 4a:
A-config recalculated weights.
Figure 4b:
B-config recalculated weights.
Figure 4c:
C-config recalculated weights.

Removal of the variable Sgr A* point source

This step is only necessary for our case which includes a variable source. In most cases, one can skip this step.

As we have seen in the initial images, Sgr A* is a variable source. Unfortunately, this also introduces some problems for data combination as the visibilities of the different sessions will reflect this difference. Cleaning will be difficult in such a situation as flux levels at different uv points (times and baselines) are not consistent in their portion for the central point source. We therefore will remove the unresolved Sgr A* in each dataset. To recover Sgr A* we will insert a new point source with a consistent, nominal flux value. However, it is perfectly fine and to image without the artificial source.

To start with, we create a component list for each dataset that includes only a point source at the position of Sgr A*. To do so, we fit a point source model to the A-configuration data using imfit:


(J2000 RA=17:45:40.038543, DEC=-29:00:28.051472). The component list will be inserted as a model column into the respective MS via ft. uvsub will then subtract the point source model from the CORRECTED data column. Since there's no CORRECTED column to start with, uvsub will initially copy the DATA column to the CORRECTED column. Note that an implication of this procedures is that running uvsub twice will oversubtract. So we recommend to once more create backup copies of the previous datasets before subtracting Sgr A*:

# In a Terminal
cp -r VLA-SgrA-Sband-Aconfig-statwt.ms VLA-SgrA-Sband-Aconfig-statwt-sub.ms
cp -r VLA-SgrA-Sband-Bconfig-statwt.ms VLA-SgrA-Sband-Bconfig-statwt-sub.ms
cp -r VLA-SgrA-Sband-Cconfig-statwt.ms VLA-SgrA-Sband-Cconfig-statwt-sub.ms

Let's start with the A-configuration data and create a component list of a point sources with a flux of 0.712 Jy at a position of (J2000) RA=17h45m40.03599s DEC=-29d00m28.1699s (more examples are provided in a different CASA guide):

cl.addcomponent(flux=0.712, fluxunit='Jy',shape='point', dir='J2000 17:45:40.038543 -')

The component list is now stored in 'component-SgrA-A.cl' and we will use it to populate the MODEL column via ft:

ft(vis='VLA-SgrA-Sband-Aconfig-statwt-sub.ms', complist='component-SgrA-A.cl', usescratch=True)

Finally we will subtract the MODEL from the DATA/CORRECTED DATA with uvsub:


Note that to revert back to the original state, one could use clearcal to reset the MODEL column and to set CORRECTED to be identical with DATA (thus undoing the source subtraction).

Let's repeat the steps for B-configuration, now using a flux of 0.691 Jy:

cl.addcomponent(flux=0.691, fluxunit='Jy',shape='point', dir='J2000 17:45:40.038543 -')
ft(vis='VLA-SgrA-Sband-Bconfig-statwt-sub.ms', complist='component-SgrA-B.cl', usescratch=True)

And for C-configuration with 1.35 Jy:

cl.addcomponent(flux=1.35, fluxunit='Jy',shape='point', dir='J2000 17:45:40.038543 -')
ft(vis='VLA-SgrA-Sband-Cconfig-statwt-sub.ms', complist='component-SgrA-C.cl', usescratch=True)

Let's pause and briefly look at images with Sgr A* removed. We will run clean but since the point source is removed, we only do 500 iterations for A and B configurations, and 200 iterations of the C configuration data:

# A-config: 
clean(vis='VLA-SgrA-Sband-Aconfig-statwt-sub.ms', imagename='SgrA-Aonly-noPNT',field='J1745-2900',
# B-config
clean(vis='VLA-SgrA-Sband-Bconfig-statwt-sub.ms', imagename='SgrA-Bonly-noPNT',field='J1745-2900',
# C-config:
clean(vis='VLA-SgrA-Sband-Cconfig-statwt-sub.ms', imagename='SgrA-Conly-noPNT',field='J1745-2900',

Finally, we will add in a point source with a canonical flux density of 1 Jy to bring back Sgr A*. reverse=True will add instead of subtract the MODEL to DATA/CORRECTED in uvsub. This step can be skipped when Sgr A* is not required. When the data is going to be self-calibrated, we actually recommend not to introduce an artificial source. But for now we introduce the new Sgr A* 1Jy point source:

cl.addcomponent(flux=1, fluxunit='Jy',shape='point', dir='J2000 17:45:40.038543 -')
# A-config
ft(vis='VLA-SgrA-Sband-Aconfig-statwt-sub.ms', complist='component-SgrA.cl', usescratch=True)
# B-config
ft(vis='VLA-SgrA-Sband-Bconfig-statwt-sub.ms', complist='component-SgrA.cl', usescratch=True)
# C-config
ft(vis='VLA-SgrA-Sband-Cconfig-statwt-sub.ms', complist='component-SgrA.cl', usescratch=True)

Image Combined Data

We will now create a combined image of all three re-weighted datasets.

First, let's check the new uv-coverage. To do so, we need to concatenate the data with concat:


Fig. 5 shows the combined uv-coverage, which extends to A-configuration baselines but with a much higher density at the intermediate and shorter baselines contributed from B and C configurations.

Figure 5:
Combined uv-coverage.

Although concat merges all three MSs into a single one, it is actually not a required step before imaging. clean will take care of the combination when all datasets are specified as a list. By default, clean will image the data in the CORRECTED column, i.e. it will use the portion of the MS which exhibits the replaced Sgr A* point source (if CORRECTED is not present, it will image the visibilities stored in the DATA column). Clean will also perform the spectral regridding of all datasets on the fly, when mode="velocity" or mode="frequency". There's no need to cvel the MSs beforehand.

We will now create a combined image in clean. The threshold parameter was derived by a previous run of clean in which we determined the rough rms noise. For our threshold, we will use the rms noise multiplied by a factor of ~2.5:


The resulting image has a beam size of 1.58" x 0.50" (Fig. 6), very similar to the resolution of A-configuration only. This is what we want to achieve. The rms is with ~2mJy better than A-only and there are clearly many more extended spatial scales in the image. This is a pretty good combination product.

Figure 6:
Combined image.

The image can still be improved. For simplicity, we did not use any interactive cleaning in the above, but we highly recommend it for producing the final images. Improvements can also be obtained, e.g., by adjusting the image weights via the Briggs robust parameter, adding a taper, or weighting the different datasets against each other (using visweightscale in concat). Wide-band imaging and multi-scale imaging will also lead to better results. We refer to the VLA CASA Imaging Guide for more details and examples.

Tips for Selfcal

If the source has a bright nucleus [or bright unresolved emission generally], start with the A array data, selfcal, then add B array, selfcal again, and so on. If the source is mostly diffuse, then there is not much signal in the A array data, so start with the D array, selfcal, then add C array, selfcal, and so on. Each selfcal step should be phase only first with maybe two or more iterations. At the end of each selfcal step, a phase+amplitude selfcal can be attempted, before merging in the next array configuration data. After each merge the selfcal steps can be repeated.

Last checked on CASA Version 4.6.0