View source for EVLA high frequency Spectral Line Tutorial - CDE

This CASA Guide provides a simplified approach to the editing, calibration, and imaging of a galactic EVLA observation for use in NRAO Community Day Events.  For a complete description of the data reduction process see [[EVLA high frequency Spectral Line tutorial - IRC+10216 part1]] and [[EVLA high frequency Spectral Line tutorial - IRC+10216 part2]].

[[Category:EVLA]][[Category:Calibration]][[Category:Spectral Line]]

== Overview ==
[[Image:irc10216_dust.jpg|thumb|VLT V-band image of IRC+10216 showing dust rings out to a radius of 90" by Le&atilde;o et al. (2006, A&A, 455, 187).]]

This tutorial describes the data reduction for two spectral lines, HC3N and SiS, observed toward the AGB star IRC+10216 by the EVLA in D-configuration.

==Getting the data==

The data for this tutorial can be obtained by anonymous FTP from <tt>ftp://ftp.aoc.nrao.edu/staff/gvanmoor/community_day/</tt>.  Download all 4 TAR files.

For example,

<source lang='bash'>
# In UNIX
wget 'ftp://ftp.aoc.nrao.edu/staff/gvanmoor/community_day/*'
</source>

==Initial Inspection and Flagging==

Get a summary listing of the data set using {{listobs}}.

<source lang="python">
# In CASA
vis = 'day2_TDEM0003_20s_full'
listobs(vis=vis, verbose=True)
</source>

Below we have cut and pasted the most relevant output from the logger.

<pre style="background-color: #fffacd;">
Fields: 4
  ID   Code Name                RA              Decl          Epoch   SrcId nVis
  2    D    J0954+1743          09:54:56.82363 +17.43.31.2224 J2000   2     32726
  3    NONE IRC+10216           09:47:57.38200 +13.16.40.6600 J2000   3     99540
  5    F    J1229+0203          12:29:06.69973 +02.03.08.5982 J2000   5     5436
  7    E    J1331+3030          13:31:08.28798 +30.30.32.9589 J2000   7     2736
   (nVis = Total number of time/baseline visibilities per field)
Spectral Windows:  (2 unique spectral windows and 1 unique polarization setups)
  SpwID  #Chans Frame Ch1(MHz)    ChanWid(kHz)  TotBW(kHz)  Corrs
  0          64 TOPO  36387.2295  125           8000        RR  RL  LR  LL
  1          64 TOPO  36304.542   125           8000        RR  RL  LR  LL
Sources: 10
  ID   Name                SpwId RestFreq(MHz)  SysVel(km/s)
  0    J1008+0730          0     0.03639232     -0.026
  0    J1008+0730          1     0.03639232     -0.026
  2    J0954+1743          0     0.03639232     -0.026
  2    J0954+1743          1     0.03639232     -0.026
  3    IRC+10216           0     0.03639232     -0.026
  3    IRC+10216           1     0.03639232     -0.026
  5    J1229+0203          0     0.03639232     -0.026
  5    J1229+0203          1     0.03639232     -0.026
  7    J1331+3030          0     0.03639232     -0.026
  7    J1331+3030          1     0.03639232     -0.026
Antennas: 19:
  ID   Name  Station   Diam.    Long.         Lat.
  0    ea01  W09       25.0 m   -107.37.25.2  +33.53.51.0
  1    ea02  E02       25.0 m   -107.37.04.4  +33.54.01.1
  2    ea03  E09       25.0 m   -107.36.45.1  +33.53.53.6
  3    ea04  W01       25.0 m   -107.37.05.9  +33.54.00.5
  4    ea05  W08       25.0 m   -107.37.21.6  +33.53.53.0
  5    ea07  N06       25.0 m   -107.37.06.9  +33.54.10.3
  6    ea08  N01       25.0 m   -107.37.06.0  +33.54.01.8
  7    ea09  E06       25.0 m   -107.36.55.6  +33.53.57.7
  8    ea12  E08       25.0 m   -107.36.48.9  +33.53.55.1
  9    ea15  W06       25.0 m   -107.37.15.6  +33.53.56.4
  10   ea19  W04       25.0 m   -107.37.10.8  +33.53.59.1
  11   ea20  N05       25.0 m   -107.37.06.7  +33.54.08.0
  12   ea21  E01       25.0 m   -107.37.05.7  +33.53.59.2
  13   ea22  N04       25.0 m   -107.37.06.5  +33.54.06.1
  14   ea23  E07       25.0 m   -107.36.52.4  +33.53.56.5
  15   ea24  W05       25.0 m   -107.37.13.0  +33.53.57.8
  16   ea25  N02       25.0 m   -107.37.06.2  +33.54.03.5
  17   ea27  E03       25.0 m   -107.37.02.8  +33.54.00.5
  18   ea28  N08       25.0 m   -107.37.07.5  +33.54.15.8
</pre>

We summarize the observing strategy in this table.

{| border="1" align="center" cellpadding="10" cellspacing="0"
 ! Gain calibrator
 | J0954+1743
 | field id = 2
 |-
 ! Bandpass calibrator
 | J1229+0203
 | field id = 5
 |-
 ! Flux calibrator
 | J1331+3030 (3C286)
 | field id = 7
 |-
 ! Science target
 | IRC+10216
 | field id = 3
 |}

[[Image:Ant_locations.png|thumb|Antenna locations from running plotants ]]

Create a plot of antenna positions using {{plotants}}.

<source lang="python">
# In CASA
plotants(vis=vis)
</source>

[[Image:plotallfields.png|thumb|Result of plotms]]
[[Image:Zoom1_mark.png|thumb|Zooming in and marking region (hatched box)]]

Next, let's look at all the source amplitudes as a function of time using {{plotms}}.

<source lang="python">
# In CASA
plotms(vis=vis, xaxis='time', yaxis='amp', correlation='RR,LL',
       avgchannel='64', spw='0:4~60', coloraxis='field')
</source>

Now zoom in on the region very near zero amplitude for sources J0954+1743 and IRC+10216. To zoom, select the 
Zoom tool in lower left corner of  the {{plotms}} GUI, then you can left click to draw a box. 
Look for the low values (you may want to zoom a few times to really see the suspect points clearly). Now use the Mark Region and Locate buttons (located along the bottom of the GUI) to see which antenna is causing problems. The output will be shown in the logger. Since all the "located" baselines include ea12, this is the responsible antenna.

Now click the clear region button, and then go back to the zoom button to zoom in further to note exactly what the time range is: 03:41:00~04:10:00.

Check the other sideband by changing spw to 1:4~60. You will have to
rezoom. If you have trouble, click on the Mark icon and then back to
zoom.  In spw=1, ea07 is bad from the beginning until after next
pointing run: 03:21:40~04:10:00.  To see this, compare the amplitudes when antenna is set to 'ea07' and when it is set to one of the other antennas, such as 'ea08'.

If you set antenna to 'ea12' and zoom in on this intial timerange, you can also see that ea12 is bad during the same time range as for spw 0.  You can also see this by entering '!ea07' for antenna, which removes ea07 from the plot (in CASA selection, ! deselects). 

We can flag the bad data using {{flagdata}}.

<source lang="python">
# In CASA
flagdata(vis=vis,
         field=['2,3','2,3'],
         spw=['','1'],
         antenna=['ea12','ea07'],
         timerange=['03:41:00~04:10:00','03:21:40~04:10:00'])
</source>

{{flagdata}} works by spanning up a matrix. The first entries in each list must be taken as one flagging command, as well as the second entries etc. Lists within lists are fine. In the above example, the first flagging command is issued for fields 2 and 3 for all spws and within the 03:41:00~04:10:00 timerange. A second command is again for the fields 2 and 3 but for spw 1 only and for the second timerange in the list '03:21:40~04:10:00'. 

Note that because  the chosen timerange is limited to fields 2 and 3, the field parameter is not really
needed; however, flagdata will run fastest if you put as many constraints as possible.

==Set Up the Model for the Flux Calibrator==

We set the model for the flux calibrator using {{setjy}}.  First, check the availability of calibration models.

<source lang="python">
# In CASA
setjy(vis=vis,listmodimages=T)
</source>

There is no Ka-band model of 3C286.  We will use the K-band model instead.

<source lang="python">
# In CASA
setjy(vis=vis,field='7',spw='0~1',
      modimage='3C286_K.im')
</source>

{{setjy}} scales the total flux in the model image to that appropriate for your individual spectral window frequencies according to the calibrator's flux and reports this number to the logger.

<pre style="background-color: #fffacd;">
The logger output for each spw is:
J1331+3030 (fld ind 7) spw 0  [I=1.7762, Q=0, U=0, V=0] Jy, (Perley-Butler 2010)
J1331+3030 (fld ind 7) spw 1  [I=1.7794, Q=0, U=0, V=0] Jy, (Perley-Butler 2010)
</pre>

The absolute fluxes for the frequencies have now been determined and one can proceed to the bandpass and complex gain calibrations.

==Bandpass Calibration==

Correct the phase variations with time before solving for the bandpass to
prevent decorrelation of the vector averaged bandpass
solution. 

[[Image:Prebp_phasecal2.png|thumb|Phase only calibration before bandpass. The 4 lines are both polarizations in both spw, unfortunately two of them get the same color green at the moment.]]

<source lang="python">
# In CASA
gaincal(vis=vis, caltable='bpphase.gcal', field='5', spw='0~1:20~40',
        refant='ea02', gaintype='G', calmode='p',solint='int',
        gaincurve=T)
</source>

Plot the solutions using {{plotcal}}.

<source lang="python">
# In CASA
plotcal(caltable='bpphase.gcal',xaxis='time',yaxis='phase',
        iteration='antenna',subplot=331,plotrange=[0,0,-180,180])
</source>

Next we can apply this phase solution on the fly while determining
the bandpass solutions on the timescale of the bandpass calibrator scan (solint='inf'). 

<source lang="python">
# In CASA
bandpass(vis=vis, caltable='bandpass.bcal', field='5', refant='ea02',
         solint='inf', solnorm=T, gaintable='bpphase.gcal',
         gaincurve=T)
</source>

Plot the solutions, amplitude and phase:
[[Image:Bandpass_amp.png|thumb|Amplitude Bandpass solutions]]
[[Image:Bandpass_phase1.png|thumb|Phase Bandpass solutions]]

<source lang="python">
# In CASA
plotcal(caltable='bandpass.bcal',xaxis='chan',yaxis='amp',
        iteration='antenna',subplot=331)
</source>


<source lang="python">
# In CASA
plotcal(caltable='bandpass.bcal',xaxis='chan',yaxis='phase',
        iteration='antenna',subplot=331)
</source>

==Remaining Calibration==

In this Community Day Event guide, we will skip over the remaining calibration steps.  However, you can refer to [[EVLA high frequency Spectral Line tutorial - IRC+10216 part1]] for full details.  To summarize the missing steps, you bootstrap the flux densities of the secondary calibrators by

# doing a phase only calibration on all calibrators using {{gaincal}},
# doing amplitude only calibration on all calibrators while applying the phase-only solutions, and
# deriving the flux density of the secondary calibrators while applying the previously obtained solutions.

Then, you can calibrate the target source using the phase and amplitude solutions you have obtained.  Apply the target source calibration solutions using {{applycal}}.  Use {{plotms}} to examine the calibrated data.  If more flagging is required, redo all calibration steps.  When the data look good, {{split}} the target source into a separate measurement set.  Subtract the continuum flux using {{uvcontsub}}.  Make Doppler corrections using {{cvel}}, or let {{clean}} do the Doppler corrections on the fly.

This tutorial picks up where [[ EVLA high frequency spectral line tutorial - IRC+10216 - calibration]] leaves off. 

==Imaging==

[[Image:irc10216_uvspec.png|thumb|UV-plot of the spectral line signal in both spw for IRC+10216.]]

The continuum-subtracted spectral line data is contained in <tt>IRC10216_spls.ms</tt>.  Use {{plotms}} to plot the lines.

<source lang="python">
plotms(vis='IRC10216_spls.ms', xaxis='channel', yaxis='amp',
       avgtime='1e8', avgscan=T, coloraxis='spw')
</source>

Now it is time to image the visibility data using {{clean}}.  For illustration, we will clean channel 22 of the SiS line.

<source lang="python">
# In CASA
os.system('rm -rf ch22.*') # remove previously generated image, if it exists
clean(vis='IRC10216_spls.ms', imagename='ch22', spw='1:22~22',
      mode='channel', nchan=1, start='', width=1, niter=100000, 
      gain=0.1, threshold='3.0mJy', psfmode='clark', imagermode='csclean',
      interactive=T, npercycle=100, imsize=300, cell=['0.4arcsec', '0.4arcsec'],
      stokes='I', weighting='briggs', robust=0.5) 
</source>

After running the above command, make a region in the CASA viewer.  Double-click inside the region and clean by clicking the green circular arrow.  After each cycle, click the green circular arrow again if the flux inside the region is brighter than the flux peaks outside the region.  When you are finished cleaning, click the red 'STOP' button. 

[[File:IRC10216 cleaned.png|thumb|Image of SiS channel 22 after cleaning.]]

Open the resulting image using the {{viewer}}.

<source lang="python">
# In CASA
viewer("ch22.image")
</source>

In the viewer, make a region and click inside it to get statistics about the portion of the image in the region.

==Analyze the Image Cubes==

Open the HC3N image cube in the {{viewer}}.

<source lang="python">
# In CASA
viewer("IRC10216_HC3N.image")
</source>

Click the 'Play' button to view all channels in the cube.  Select '''Tool --> Spectral profile...''' from the pull down menu.  Create a region on the image to view the spectrum within the region.

Open the SiS image cube in the viewer.

<source lang="python">
# In CASA
viewer("IRC10216_SiS.image")
</source>

[[File:IRC10216 SiS mom0.png|thumb|SiS moment-0 map]]

Determine what channels in the cube have emission.  Then make moment maps using {{immoments}}.

<source lang="python">
# In CASA
os.system('rm -rf IRC10216_Sis.mom0') # remove previously generated map, if it exists
immoments(imagename="IRC10216_SiS.image", moments=[0], axis="spectral",
          chans="12~40", outfile="IRC10216_Sis.mom0") 
</source>

Open the moment map in the viewer.

<source lang="python">
# In CASA
viewer("IRC10216_Sis.mom0")
</source>

Overlay contours by selecting '''Data --> Open''' from the pull down menu, selecting the moment-0 map, and clicking 'contour map'.

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