First Look at Self Calibration 4.4

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This script steps you through continuum imaging and self calibration of the science data for our science target, TW Hydra.

You should have downloaded the data package as part of the previous imaging tutorial. If you haven't done that yet, check the First Look At Imaging Guide for instructions.

In that first tutorial you made a first continuum image in the previous imaging lesson. We start here by repeating that step and then we iteratively self-calibrate the data, focusing on short-timescale phase corrections.

First, copy the calibrated and flagged data from the working directory. Remember that this is our best version of the data.

# In CASA
os.system("rm -rf sis14_twhya_calibrated_flagged.ms")
os.system("cp -r ../working_data/sis14_twhya_calibrated_flagged.ms .")

Run a quick listobs to get oriented:

# In CASA
listobs("sis14_twhya_calibrated_flagged.ms")

Now, use clean to make a continuum image of TW Hydra (field 5). This call is interactive, but the automated approach that we used in the last lesson would also work. See the last lesson for details. Clean until the residuals near TW HYdra are comparable to those in the rest of the image. For example, you might place your clean mask over the central feature, only, and clean with for two main cycles. That is, use the green arrow twice, and then click the red X to finish the clean.

# In CASA
os.system('rm -rf first_image.*')
clean(vis='sis14_twhya_calibrated_flagged.ms',
imagename='first_image',
field='5',
spw='',
mode='mfs',
nterms=1,
imsize=[250,250],
cell=['0.08arcsec'],
weighting='natural',
threshold='0mJy',
interactive=True,
usescratch=True)
Figure 1: Residuals from the first clean after 2 main cycles of cleaning.

In addition to creating an image, CLEAN saves the cleaned "model" of the science target with the measurement set (the parameter "usescratch" tells clean to save the model as a discrete data column in the MS). This model is required for later self-calibration steps. Note, in the previous lessons we only had models for the calibrators, not the science target itself. Of course this model for our science target is not perfect, only as good as the first clean, but it's a good starting point.

With a model in place, we are in a position to calibrate the science target directly. We use gaincal, which is the task used both for general gain calibration using an external calibrator, and for self-calibration. We will focus here on phase corrections - generally good practice for self calibration - because amplitude self calibration has a larger potential to change the source characteristics (i.e. introduce artifacts). Figuring out the best averaging parameters is often the key to good self-calibration. You would like the solution interval to be short enough so that it tracks changes in the atmospheric phase with high accuracy, but long enough so that you measure phases with good signal-to-noise. Also, ideally you'd like to keep solutions separate for difference spw's and polarizations, but for faint sources when you need to boost SNR, it may be necessary to average over these parameters to achieve good solutions. Using 30 seconds for the solution interval is a good choice for TW Hydra.

# In CASA
os.system("rm -rf phase.cal")
gaincal(vis="sis14_twhya_calibrated_flagged.ms",
caltable="phase.cal",
field="5",
solint="30s",
calmode="p",
refant="DV22",
gaintype="G")

Try playing around with different solution intervals or averaging options. Bear in mind that you want the shortest possible interval while also retaining separate SPW and polarizations. However, none of this helps you if you don't get good solutions. So you generally will experiment with the following options: (1) combine="scan" or "spw" to allow solutions to cross SPW/scan boundaries, or you can do both using combine="scan,spw"; (2) increase solint to set the solution interval; and (3) toggling gaintype between "G" and "T" (the former generates solutions independently for each polarization, and the latter averages two polarizations before determining the solutions).

Plot the resulting solutions. We are finding nontrivial, though not enormous, solutions (a few 10s of degrees) with the two correlations tracking one another pretty well. If the data were already perfectly calibrated, these values would solve to be zero.

# In CASA
plotcal(caltable="phase.cal",
xaxis="time",
yaxis="phase",
subplot=331,
iteration="antenna",
plotrange=[0,0,-30,30],
markersize=5,
fontsize=10.0,
figfile="sis14_selfcal_phase_scan.png",
showgui = True)
Figure 2: Phase solutions after the first round of self calibration.

We are happy with this solution. So let's apply it to the data using applycal. We only care about field 5 (the science target).

# In CASA
applycal(vis="sis14_twhya_calibrated_flagged.ms",
field="5",
gaintable=["phase.cal"],
interp="linear")

At this point the self-calibrated data are stored in the MS in the "corrected data" column. Because we will want to try more rounds of self calibration, it's often useful (though not strictly necessary) at this point to split out the corrected data into a new data set.

# In CASA
os.system("rm -rf sis14_twhya_selfcal.ms")
split(vis="sis14_twhya_calibrated_flagged.ms",
outputvis="sis14_twhya_selfcal.ms",
datacolumn="corrected"
)

Now clean the self-calibrated data. Again, clean until the residuals on TW Hydra resemble those in the surrounding image.

# In CASA
os.system('rm -rf second_image.*')
clean(vis='sis14_twhya_selfcal.ms',
imagename='second_image',
field='5',
spw='',
mode='mfs',
nterms=1,
imsize=[250,250],
cell=['0.1arcsec'],
weighting='natural',
threshold='0mJy',
interactive=True,
niter=5000)
Figure 3: Residuals from the second clean after 2 main cycles of cleaning.

The residuals do look better this time around. Run the viewer and compare the first and second images. You should see a noticeable improvement in the noise and some improvement in the signal, so that the overall signal-to-noise (dynamic range) is much improved.

This second clean also produces a model, hopefully a mildly better one this time.

Now we will run a second round of phase-only self calibration using the improved model.

# In CASA
os.system("rm -rf phase_2.cal")
gaincal(vis="sis14_twhya_selfcal.ms",
caltable="phase_2.cal",
field="5",
solint="30s",
calmode="p",
refant="DV22",
gaintype="G")

Let's plot the calibration table again. At this point, we see much smaller phase scatter relative to the model, so we don't expect more phase-only self calibration to do much.

# In CASA
plotcal(caltable="phase_2.cal",
xaxis="time",
yaxis="phase",
subplot=331,
iteration="antenna",
plotrange=[0,0,-30,30],
markersize=5,
fontsize=10.0,
figfile="sis14_selfcal_phase_scan_2.png", 
showgui = True)
Figure 4: Phase solutions after the second round of self calibration.

Apply the solutions again:

# In CASA
applycal(vis="sis14_twhya_selfcal.ms",
field="5",
gaintable=["phase_2.cal"],
interp="linear")

Split the data off again. Here you can see the work flow for heavily iterative self-calibration. We progressively calibrate, split.

# In CASA
os.system("rm -rf sis14_twhya_selfcal_2.ms")
split(vis="sis14_twhya_selfcal.ms",
outputvis="sis14_twhya_selfcal_2.ms",
datacolumn="corrected"
)

Clean a third time.

# In CASA
os.system('rm -rf third_image.*')
clean(vis='sis14_twhya_selfcal_2.ms',
imagename='third_image',
field='5',
spw='',
mode='mfs',
nterms=1,
imsize=[250,250],
cell=['0.1arcsec'],
weighting='natural',
threshold='0mJy',
interactive=True,
niter=5000)
Figure 5: Residuals from the third clean after 2 main cycles of cleaning.

The improvement is really marginal at this point. Confident that we have done what we can on the phase, we can experiment with amplitude self calibration. This is potentially dangerous as it has much more potential to change the characteristics of the source than phase self-calibration. We mitigate this somewhat by setting solnorm=True, so that the solutions are normalized.

# In CASA
os.system("rm -rf amp.cal")
gaincal(vis="sis14_twhya_selfcal_2.ms",
caltable="amp.cal",
field="5",
solint="30s",
calmode="ap",
refant="DV22",
gaintype="G",
solnorm=True)

# Plot the amplitude solutions.
plotcal(caltable="amp.cal",
xaxis="time",
yaxis="amp",
subplot=331,
iteration="antenna",
plotrange=[0,0,0,0],
markersize=5,
fontsize=10.0, 
showgui = True)
Figure 6: Amplitude solutions after the third round of self calibration.

We see a good deal of scatter and some offsets between correlations. It is at least worth looking at what the effects of applying this will be. So let's apply these solutions on an interim basis.

# In CASA
applycal(vis="sis14_twhya_selfcal_2.ms",
field="5",
gaintable=["amp.cal"],
interp="linear")

At this point the self-calibrated data live in the corrected column. Because we will want to try more rounds of self calibration, it's very useful (though not strictly necessary) at this point to split out the corrected data into a new data set.

# In CASA
os.system("rm -rf sis14_twhya_selfcal_3.ms")
split(vis="sis14_twhya_selfcal_2.ms",
outputvis="sis14_twhya_selfcal_3.ms",
datacolumn="corrected"
)

Clean a fourth time.

# In CASA
os.system('rm -rf fourth_image.*')
clean(vis='sis14_twhya_selfcal_3.ms',
imagename='fourth_image',
field='5',
spw='',
mode='mfs',
nterms=1,
imsize=[250,250],
cell=['0.1arcsec'],
weighting='natural',
threshold='0mJy',
interactive=True,
niter=5000)
Figure 7: Residuals from the fourth clean after 5 main cycles of cleaning.

This time, notice from the residuals that you can clean more deeply. After 5 main cycles, the background residuals look very random on the scale of the beam size. This is good!

Compare the third and fourth images. The noise level is dramatically better, while the flux has not changed markedly (this is very good, it's what we worry about with amplitude self calibration). By assuming that the previous cleans represent good models we have managed to improve the signal-to-noise on the data by almost an order of magnitude. Not bad!

This fourth image is our best continuum image. We can use the data set (sis14_twhya_selfcal_3.ms) to proceed with later work. In the next lesson we'll do UV continuum subtraction and line imaging.

(ASIDE: Note that you would need to do the primary beam correction on this data in the same way as you corrected the previous continuum image before making science measurements).