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| '''This page is under development''' | | '''This page is under development''' |
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| | 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]]. |
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| [[Category:EVLA]][[Category:Calibration]][[Category:Spectral Line]] | | [[Category:EVLA]][[Category:Calibration]][[Category:Spectral Line]] |
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| [[Image:irc10216_dust.jpg|thumb|VLT V-band image of IRC+10216 showing dust rings out to a radius of 90" by Leão et al. (2006, A&A, 455, 187).]] | | [[Image:irc10216_dust.jpg|thumb|VLT V-band image of IRC+10216 showing dust rings out to a radius of 90" by Leão et al. (2006, A&A, 455, 187).]] |
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| This tutorial describes the data reduction for two spectral lines observed toward the AGB star IRC+10216. | | 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. |
| In this EVLA OSRO1 mode observation one subband was observed in each of two basebands, the subbands were centered on the HC3N and SiS lines near 36 GHz. The raw data were loaded into CASA with {{importevla}}, where zero and shadowed data were flagged. Then the data were "{{split}}", so we could average from the native 1 second integrations to 10 seconds, select only antennas with Ka-band receivers, and select only spectral windows (called spw in CASA) with Ka-band data. This produces a significantly smaller dataset for processing.
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| IRC+10216 (CW Leo) is the brightest star in the sky at 5 microns but only 16th magnitude visually. It was discovered during the first survey | |
| of the infrared sky, carried out by Bob Leighton and Gerry Neugebauer in 1965. An Asymptotic Giant Branch star, it is a Mira-type variable going through prodigious episodic mass loss. The dust condensed from the atmosphere during the mass loss is responsible for the millimeter emission; the continuum emission seen at radio wavelengths probes the actual stellar photosphere. Molecules form along with the dust, and a steady state chemistry occurs in the dense inner regions (Tsuji 1973 A&A 23, 411). As the density of material drops, the chemistry freezes. But the molecules continue their long coast outward into the Galaxy, and as the shell thins ultraviolet light from the ambient galactic radiation field penetrates and initiates a new chemistry in the gas.
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| SiS, a simple molecule created in the dense inner envelope chemistry is photodissociated as it coasts out into the shell. The result is the
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| centrally condensed emission we see in the present observations. Interestingly, in the next lower transition at 18 GHz, the line shape is
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| much different from what we see here. At the extreme velocities in the profile, very bright narrow emission is seen which has been interpreted
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| as maser emission. The interested student can find EVLA observations of this line in the archive.
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| HC3N, a much more complex species, is created by the photochemistry which becomes active as atoms and pieces of molecules destroyed by
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| ultraviolet radiation undergo the next phase of chemistry in the shell. HC3N has many vibrational modes which may be excited in addition to
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| its rotational modes. Owing to this, it can re-radiate energy absorbed from ultraviolet radiation more effectively than some molecules with a
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| single bond. Eventually it too is destroyed however, but during its brief existence its rise to abundance in the envelope results in a ring of emission, which is what is observed in this image made with the EVLA. A recent model by Cordiner & Millar (2009, ApJ, 697, 68) describes a
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| new chemical model for the shell, which also takes into account the variation of mass loss by the star. They show that in addition to
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| purely chemical effects, local gas and dust density peaks play a role in shaping the observed emission.
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| ==Getting the data== | | ==Getting the data== |
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| The post-split averaged data can be downloaded from http://casa.nrao.edu/Data/EVLA/IRC10216/day2_TDEM0003_10s_norx.tar | | 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. |
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| Once the download is complete, unpack the file:
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| <source lang='bash'>
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| # in a terminal, outside of CASA:
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| tar -xvf day2_TDEM0003_10s_norx.tar
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| </source>
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| == How to Use This casaguide==
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| [[Image:clean.png|thumb|Inputs from one of the clean commands from this tutorial]]
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| There are a number of possible ways to run CASA. Many aspects are described in [[Getting_Started_in_CASA]]. You should review this page if you are new to CASA. In brief you can run CASA interactively by looking at the inputs to tasks with '''inp taskname''' (example: inp clean), setting the parameters one by one (example: selectdata=T) as you desire and then run '''go'''. After setting parameters one by one in a task and then looking at the inputs again, you will notice that the parameters that have been set to something other than their defaults are blue. If you have mistyped any parameters, they will be red and must be fixed for the task to run correctly. You can get more detailed help on any task by typing '''help taskname''' (example: help clean). Once a task is run you can get the same parameters back by running '''tget taskname''' (example: tget clean); subsequent runs will overwrite the previous tget file.
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| The second way to run CASA is to provide task function calls. 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'''. A series of task function calls can be combined together into a script, and run with '''execfile('scriptname.py')'''. It is possible to extract a script containing all the CASA task function calls in this and other casaguides using the method described at the [[Extracting_scripts_from_these_tutorials]] page.
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| If you are a relative novice or just new to CASA it is strongly recommended to work through this tutorial by cutting and pasting the task function calls provided below after you have read all the associated explanations. Work at your own pace, look at the inputs to the tasks to see what other options exist, and read the help files. Later, when you are more comfortable, you might try to extract the script, modify it for your purposes, and begin to reduce other data.
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| | |
| == The Observing Log, Antenna Position Corrections, Opacities, Gaincurves, and other Calibration "Priors"==
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| For all EVLA observations, the operators keep an observing log. You can look at
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| the observing logs at the observing log [[http://www.vla.nrao.edu/cgi-bin/oplogs.cgi website]]. Pertinent information from this observation is repeated below.
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| <pre style="background-color: #E0FFFF;">
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| INFORMATION FROM OBSERVING LOG:
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| Date of the observation: 26-April-2010
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| There are no Ka-band receivers on ea11, ea13, ea14, ea16, ea17, ea18, ea26
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| Antennas ea10, ea06 are out of the array
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| Antenna ea12 is newly back
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| The pointing is often bad on ea15
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| Antennas ea10, ea12, ea22 do not have good baseline positions
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| </pre> | |
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| As mentioned in the log, antennas ea10, ea12, and ea22 do not have good baseline positions.
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| Antenna ea10 was not in the array, but for the other two antennas we need to check for
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| any improved baseline positions that were derived after the observations were taken.
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| In CASA, we need to insert these corrections by hand using '''{{gencal}}'''. The resulting table will need to be supplied as a "prior" calibration to all subsequent calibration steps. The corrections can be ascertained from the [http://www.vla.nrao.edu/astro/archive/baselines/ EVLA/VLA Baseline Corrections page]. Be sure to carefully read to the bottom of that
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| webpage to see how to calculate the additive corrections. The current case is simple as there is only a single correction for each antenna. In the future we will implement an automated lookup of the corrections.
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| <source lang="python">
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| # In CASA
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| gencal(vis='day2_TDEM0003_10s_norx',caltable='antpos.cal',
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| caltype='antpos',
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| antenna='ea12,ea22',
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| parameter=[-0.0072,0.0045,-0.0017, -0.0220,0.0040,-0.0190])
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| </source>
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| '''Please note: '''if you are reducing VLA data taken before March 1, 2010, you need to set caltype='antposvla'.
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| There are two other types of "priors" that we will need to apply at each calibration stage described below:
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| | | For example, |
| (1) Gaincurve -- the gaincurve describes how each antenna behaves as a function of elevation, for each receiver band. Currently only gaincurves for the VLA/EVLA are available (see [[http://www.vla.nrao.edu/astro/guides/vlbivla/current/node18.html]] for the incorporated models). This option should not be used with any other telescopes.
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| (2) Opacity correction -- the opacity of the observation can be computed from a seasonal model and/or weather station information. We are planning to have a task available for this information. At the moment, the [[CASA_EVLA_Scripts]] page hosts a script and a contributed task to display the weather information and to calculate the zenith opacities for each spectral window. After the zenith opacities are derived, they will be recomputed for the correct elevation of the data automatically using <math>e^{[-\csc(el)\tau_z]}</math> in {{gaincal}}, {{applycal}}, {{bandpass}} etc.
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| In the following we will download the contributed task, and bring it into CASA. Download these two files:
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| [[File:Task_plotWX.py]] and [[File:PlotWX.xml]]. The first file contains the actual python code and the second the interface and inline help for CASA. Download the files and note that for obscure reasons the wiki will always capitalize the uploaded files abut we need to change this. In a regular terminal:
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| <source lang='bash'> | | <source lang='bash'> |
| # in a terminal, outside of CASA: | | # In UNIX |
| wget http://casaguides.nrao.edu/images/e/e4/PlotWX.xml | | wget 'ftp://ftp.aoc.nrao.edu/staff/gvanmoor/community_day/*' |
| mv PlotWX.xml plotWX.xml
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| wget http://casaguides.nrao.edu/images/2/24/Task_plotWX.py
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| mv Task_plotWX.py task_plotWX.py
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| </source> | | </source> |
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|
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| Now, we go back to CASA and build the task itself with '''buildmytask''' (it is a shell command and not a CASA command, but we will run it from within CASA; it will create a few *.pyc and *cli files as well as mytasks.py). And then add it into your CASA session by running '''mytasks.py''':
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|
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| <source lang="python">
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| # In CASA
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| !buildmytasks
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| execfile('mytasks.py')
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| </source>
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|
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| Now your brand-new '''plotWX''' task is available:
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|
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| <pre style="background-color: #fffacd;">
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| CASA <7>: inp plotWX
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| --------> inp(plotWX)
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| # plotWX :: Plot elements of the weather table for a given MS
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| vis = '' # MS name
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| seasonal_weight = 0.5 # weight of the seasonal model
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| doPlot = True # set this to True to create a plot
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| async = False # If true the taskname must be started using plotWX(...)
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| </pre>
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|
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| '''seasonal_weight''' is a parameter that combines global seasonal weather conditions (measured over many years) with the weather information from the weather station obtained during the observations. 0.5 will combine both with equal weight.
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|
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| [[Image:day2_TDEM0003_10s_norx.plotWX.png|200px|thumb|right|plotWX weather table figure]]
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|
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| We will be running plotWX in a way that will assign the opacity list (one entry for each spw in ascending order) to the variable myTau:
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|
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| <source lang="python">
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| # In CASA
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| myTau=plotWX(vis='day2_TDEM0003_10s_norx', doPlot=T)
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| </source>
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|
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| With this imput, the the task returns the opacity values to the logger:
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|
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| <pre style="background-color: #fffacd;">
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| wrote weather figure: day2_TDEM0003_10s_norx.plotWX.png
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| SPW : Frequency (GHz) : Zenith opacity (nepers)
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| 0 : 36.387 : 0.041
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| 1 : 36.305 : 0.041
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| </pre>
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|
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|
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| creates a file '''"day2_TDEM0003_10s_norx.plotWX.png"''' with the elevation of the sun, the wind speed and direction, the temperature, precipitable water vapor (PWV) as functions of time over the observation (view this file wiht your preferred image viewer like xv or Preview),
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|
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| and assigns the myTau variable to the list of opacities per spectral window:
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|
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| <source lang="python">
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| # In CASA
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| print myTau
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| [0.041019209411983566, 0.040779609355637569]
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| </source>
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|
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| The calibration task opacity parameters can now take either the variable directly '''opacity=myTau''' or the list of opacities like '''opacity=[0.0410, 0.0408]''' or, if a single value is good enough to correct for all spectral windows, one can simple use '''opacity=0.041'''.
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| ==Initial Inspection and Flagging== | | ==Initial Inspection and Flagging== |
|
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| {{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: | | GEt a summary listing of the data set using {{listobs}}. |
|
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| <source lang="python"> | | <source lang="python"> |
| # In CASA | | # In CASA |
| listobs(vis='day2_TDEM0003_10s_norx') | | vis = 'day2_TDEM0003_20s_full' |
| | listobs(vis=vis, verbose=True) |
| </source> | | </source> |
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| <pre style="background-color: #fffacd;"> | | <pre style="background-color: #fffacd;"> |
| Fields: 4 | | Fields: 4 |
| ID Code Name RA Decl Epoch SrcId nVis | | ID Code Name RA Decl Epoch SrcId nVis |
| 2 D J0954+1743 09:54:56.8236 +17.43.31.2224 J2000 2 65326 | | 2 D J0954+1743 09:54:56.82363 +17.43.31.2224 J2000 2 32726 |
| 3 NONE IRC+10216 09:47:57.3820 +13.16.40.6600 J2000 3 208242 | | 3 NONE IRC+10216 09:47:57.38200 +13.16.40.6600 J2000 3 99540 |
| 5 F J1229+0203 12:29:06.6997 +02.03.08.5982 J2000 5 10836 | | 5 F J1229+0203 12:29:06.69973 +02.03.08.5982 J2000 5 5436 |
| 7 E J1331+3030 13:31:08.2880 +30.30.32.9589 J2000 7 5814 | | 7 E J1331+3030 13:31:08.28798 +30.30.32.9589 J2000 7 2736 |
| (nVis = Total number of time/baseline visibilities per field) | | (nVis = Total number of time/baseline visibilities per field) |
| Spectral Windows: (2 unique spectral windows and 1 unique polarization setups) | | Spectral Windows: (2 unique spectral windows and 1 unique polarization setups) |
| SpwID #Chans Frame Ch1(MHz) ChanWid(kHz)TotBW(kHz) Ref(MHz) Corrs | | SpwID #Chans Frame Ch1(MHz) ChanWid(kHz) TotBW(kHz) Corrs |
| 0 64 TOPO 36387.2295 125 8000 36387.2295 RR RL LR LL | | 0 64 TOPO 36387.2295 125 8000 RR RL LR LL |
| 1 64 TOPO 36304.542 125 8000 36304.542 RR RL LR LL | | 1 64 TOPO 36304.542 125 8000 RR RL LR LL |
| Sources: 10 | | Sources: 10 |
| ID Name SpwId RestFreq(MHz) SysVel(km/s) | | ID Name SpwId RestFreq(MHz) SysVel(km/s) |
| 0 J1008+0730 0 0.03639232 -0.026 | | 0 J1008+0730 0 0.03639232 -0.026 |
| 0 J1008+0730 1 0.03639232 -0.026 | | 0 J1008+0730 1 0.03639232 -0.026 |
| 2 J0954+1743 0 0.03639232 -0.026 | | 2 J0954+1743 0 0.03639232 -0.026 |
| 2 J0954+1743 1 0.03639232 -0.026 | | 2 J0954+1743 1 0.03639232 -0.026 |
| 3 IRC+10216 0 0.03639232 -0.026 | | 3 IRC+10216 0 0.03639232 -0.026 |
| 3 IRC+10216 1 0.03639232 -0.026 | | 3 IRC+10216 1 0.03639232 -0.026 |
| 5 J1229+0203 0 0.03639232 -0.026 | | 5 J1229+0203 0 0.03639232 -0.026 |
| 5 J1229+0203 1 0.03639232 -0.026 | | 5 J1229+0203 1 0.03639232 -0.026 |
| 7 J1331+3030 0 0.03639232 -0.026 | | 7 J1331+3030 0 0.03639232 -0.026 |
| 7 J1331+3030 1 0.03639232 -0.026 | | 7 J1331+3030 1 0.03639232 -0.026 |
| Antennas: 19: | | Antennas: 19: |
| ID Name Station Diam. Long. Lat. | | ID Name Station Diam. Long. Lat. |
| 0 ea01 W09 25.0 m -107.37.25.2 +33.53.51.0 | | 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 | | 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 | | 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 | | 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 | | 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 | | 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 | | 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 | | 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 | | 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 | | 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 | | 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 | | 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 | | 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 | | 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 | | 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 | | 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 | | 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 | | 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 | | 18 ea28 N08 25.0 m -107.37.07.5 +33.54.15.8 |
| </pre> | | </pre> |
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|
| In addition to source names, antenna names, etc. CASA indexes each of these parameters staring from 0. When, say a field is specified, one can use the index or the name, both is accepted.
| | We summarize the observing strategy in this table. |
|
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|
| | | {| border="1" align="center" cellpadding="10" cellspacing="0" |
| Note that the Rest Frequency and Systemic Velocity are wrong in the listobs log by a factor 10^6 and 1000, respectively, given the quoted units (MHz) and (km/s). This was due to a temporary error in the EVLA Observing Tool that has subsequently been fixed. Because the sky frequencies are correct, and we set the rest frequency explicitly later in the deconvolution stage, this does not present a problem for the data reductions.
| | ! Gain calibrator |
| | | | J0954+1743 |
| <pre style="background-color: #E0FFFF;">
| | | field id = 2 |
| Summary of Observing Strategy
| | |- |
| Gain Calibrator: J0954+1743 field id=2
| | ! Bandpass calibrator |
| Bandpass Calibrator: J1229+0203 field id=5 | | | J1229+0203 |
| Flux Calibrator: J1331+3030 (3C286) field id=7 | | | field id = 5 |
| Target: IRC+10216 field id=3
| | |- |
| Ka-band spws = 0,1
| | ! Flux calibrator |
| </pre>
| | | J1331+3030 (3C286) |
| | | field id = 7 |
| | |- |
| | ! Science target |
| | | IRC+10216 |
| | | field id = 3 |
| | |} |
|
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|
| [[Image:Ant_locations.png|thumb|Antenna locations from running plotants ]] | | [[Image:Ant_locations.png|thumb|Antenna locations from running plotants ]] |
| Look at a graphical plot of the antenna locations and save hardcopy
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| in case you want it later. This will be useful for picking a reference antenna --
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| typically a good choice is an antenna close to the center of the array. Unless it
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| shows problems after inspection of the data, we provisionally chose ea02.
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|
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|
| [[Image:elevationvstime.png|thumb|Elevation as a function of time (after selecting colorize by field).]]
| | Create a plot of antenna positions using {{plotants}}. |
| <source lang="python">
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| # In CASA
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| plotants(vis='day2_TDEM0003_10s_norx',figfile='ant_locations.png') | |
| </source>
| |
| | |
| Next, let's look at the elevation as a function of time for all sources. It's not the case for these data, but if the elevation is very low (usually at start or end of track) you may want to flag. Also, how near in elevation your flux calibrator is to your target will impact your ultimate absolute flux calibration accuracy. Unfortunately, the target and flux calibrator are not particularly well-matched for this observation, as you can show by plotting the elevation for each source (each sources has a different colors). We will be using data in spectral window 0, channels 4 to 60 for this plot as given by the '''spw='0:4~60'''' parameter, the general CASA selection syntax is described in the [http://www.aoc.nrao.edu/~sbhatnag/misc/msselection/msselection.html Measurement Selection Syntax Document]:
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|
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|
| <source lang="python"> | | <source lang="python"> |
| # In CASA | | # In CASA |
| plotms(vis='day2_TDEM0003_10s_norx',
| | plotants(vis=vis) |
| xaxis='time',yaxis='elevation',correlation='RR,LL',
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| avgchannel='64',spw='0:4~60', coloraxis='field')
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| </source> | | </source> |
|
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| Thus we are strongly dependent on the opacity and gaincurve corrections to get the flux scale right for these data. (This is something to keep in mind when planning observations!)
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|
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|
| [[Image:plotallfields.png|thumb|Result of plotms]] | | [[Image:plotallfields.png|thumb|Result of plotms]] |
| [[Image:Zoom1_mark.png|thumb|Zooming in and marking region (hatched box)]] | | [[Image:Zoom1_mark.png|thumb|Zooming in and marking region (hatched box)]] |
|
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|
| Next, let's look at all the source amplitudes as a function of time. | | Next, let's look at all the source amplitudes as a function of time using {{plotms}}. |
| | |
| <source lang="python"> | | <source lang="python"> |
| # In CASA | | # In CASA |
| plotms(vis='day2_TDEM0003_10s_norx', | | plotms(vis=vis, xaxis='time', yaxis='amp', correlation='RR,LL', |
| xaxis='time',yaxis='amp',correlation='RR,LL',
| | avgchannel='64', spw='0:4~60', coloraxis='field') |
| avgchannel='64',spw='0:4~60', coloraxis='field') | |
| </source> | | </source> |
|
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| |
|
| Now zoom in on the region very near zero amplitude for sources J0954+1743 and IRC+10216. To zoom, select the | | 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. | | 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 is be shown in the logger. Since all the "located" baselines include ea12, this is the responsible antenna. | | 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. |
| | |
| <pre style="background-color: #98FB98;">
| |
| IMPORTANT NOTES ON PLOTMS:
| |
| | |
| * When using the locate button it is important to have only selected a modest number
| |
| of points with the mark region tool (see example of marked region in the thumnail),
| |
| otherwise the response will be very slow and possibly hang the tool
| |
| (all of the information will be output to your terminal window, not the logger).
| |
| | |
| * Throughout the tutorial, when you are done marking/locate use the Clear Regions
| |
| tool to get rid of the marked box before plotting other things.
| |
| | |
| * After flagdata command flagging, you have to force a complete reload of the cache
| |
| to look at the same plot again with the new flags applied. To do this change anything
| |
| in the plotms GUI (the colorize parameter, antenna, spw, anything) and hit the
| |
| plot button.
| |
| | |
| * If the plotms tool does get hung during a plot try clicking the cancel button on the
| |
| load progress GUI, and/or if you see a "table locked" message try typing
| |
| clearstat on the CASA command line.
| |
| | |
| * Occasionally plotms will get into a strange state that you cannot clear from inside.
| |
| We are working on these issues, but for now, when all else fails, exit from casapy and
| |
| restart.
| |
| | |
| </pre>
| |
|
| |
|
| 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. | | 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. |
Line 297: |
Line 133: |
| 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). | | 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 set up a flagging command to get both bad antennas for the | | We can flag the bad data using {{flagdata}}. |
| appropriate time and spw:
| |
|
| |
|
| <source lang="python"> | | <source lang="python"> |
| # In CASA | | # In CASA |
| flagdata(vis='day2_TDEM0003_10s_norx', | | flagdata(vis=vis, |
| field=['2,3','2,3'], | | field=['2,3','2,3'], |
| spw=['','1'], | | spw=['','1'], |
Line 314: |
Line 149: |
| needed; however, flagdata will run fastest if you put as many constraints as possible. | | needed; however, flagdata will run fastest if you put as many constraints as possible. |
|
| |
|
| Now remove the !ea07 from antenna and replot both spw, zooming in to
| | ==Set Up the Model for the Flux Calibrator== |
| be sure that all obviously low points are gone. Also zoom in and
| |
| check 3C286 (J1229+0203 is already obvious because it is so bright!).
| |
| | |
| [[Image:IRC10216_uvdist1.png|thumb|Amplitude vs. uv-distance for IRC+10216, both spw]]
| |
| | |
| Lets look more closely at IRC+10216:
| |
| | |
| <source lang="python">
| |
| # In CASA
| |
| plotms(vis='day2_TDEM0003_10s_norx',field='3',
| |
| xaxis='time',yaxis='amp',correlation='RR,LL',
| |
| avgchannel='64',spw='0~1:4~60', coloraxis='spw')
| |
| </source>
| |
|
| |
|
| You can see a
| | We set the model for the flux calibrator using {{setjy}}. First, check the availability of calibration models. |
| that there are some noisy high points. But now try
| |
|
| |
|
| <source lang="python"> | | <source lang="python"> |
| # In CASA | | # In CASA |
| plotms(vis='day2_TDEM0003_10s_norx',field='3',
| | setjy(vis=vis,listmodimages=T) |
| xaxis='uvdist',yaxis='amp',correlation='RR,LL',
| |
| avgchannel='64',spw='0~1:4~60', coloraxis='spw')
| |
| </source> | | </source> |
|
| |
|
| Most of the high points on IRC+10216 are due to large scale emission on short baselines, but there is still some noisy stuff -- for a target like this with extended emission it's best to wait until later to decide what to do about it. We will not be able to get adequate calibration for antennas that are truly bad (even if they don't stand out here) so these will be obvious later.
| | There is no Ka-band model of 3C286. We will use the K-band model instead. |
| | |
| ==Set Up the Model for the Flux Calibrator==
| |
| | |
| Next, we set the model for the flux calibrator. Depending on your observing frequency and angular resolution you can do this several ways. In the past, one typically used a point source (constant flux) model for
| |
| the flux calibrator, possibly with a uvrange cutoff if necessary. More recently for the VLA/EVLA, model images for the most common flux calibrators have been made available for use in cases where the sources are somewhat resolved. This is most likely to be true at higher frequencies and at higher resolutions (more extended arrays).
| |
| | |
| Currently, CASA contains models for the most common calibrators at the most common frequencies but not yet the new EVLA frequency bands S, Ku, and Ka. These will be added as son as they become available. One may check the availability of calibration models in {{setjy}}:
| |
| | |
|
| |
|
| <source lang="python"> | | <source lang="python"> |
| # In CASA | | # In CASA |
| setjy(vis='day2_TDEM0003_10s_norx',listmodimages=T) | | setjy(vis=vis,field='7',spw='0~1', |
| | modimage='3C286_K.im') |
| </source> | | </source> |
|
| |
|
| The terminal will now show the available models, e.g. 3C286_C.im, 3C48_K.im etc. ({{setjy}} will search in the working directory for images that may contain models, as well as in a CASA directory where known calibrator models are stored)
| | {{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. |
| | |
| As mentioned above, the Ka band does not yet have a model incorporated at this time as the full configuration cycle has not ended yet (the A-configuration data has not yet obtained as of Aug 2011). However, models of Ka band that are good for D, C, and B configurations are available from the [https://science.nrao.edu/facilities/evla/data-processing/flux-calibrator-models-for-new-evla-bands EVLA calibrator model webpage for the new frequency bands].
| |
| | |
| From this page, please download the file 36.68 GHz CASA image of 3C286, this is the [http://www.aoc.nrao.edu/evlacal/3C286_36.68G.model.tgz direct link.] To do so, you may run
| |
| | |
| | |
| <source lang='bash'>
| |
| # in a terminal, outside of CASA:
| |
| wget http://www.aoc.nrao.edu/evlacal/3C286_36.68G.model.tgz
| |
| tar xzvf 3C286_36.68G.model.tgz
| |
| </source>
| |
| | |
| to create the model '''3C286_36.68G.model''' on disk.
| |
| | |
| {{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 -- it is a good idea to save this information for your records. | |
| | |
| | |
| <source lang="python">
| |
| # In CASA
| |
| setjy(vis='day2_TDEM0003_10s_norx',field='7',spw='0~1',
| |
| modimage='3C286_36.68G.model')
| |
| </source>
| |
|
| |
|
| <pre style="background-color: #fffacd;"> | | <pre style="background-color: #fffacd;"> |
| The logger output for each spw is: | | The logger output for each spw is: |
| J1331+3030 rawspwid= 0 [I=1.776, Q=0, U=0, V=0] Jy, (Perley-Butler 2010) | | J1331+3030 (fld ind 7) spw 0 [I=1.7762, Q=0, U=0, V=0] Jy, (Perley-Butler 2010) |
| J1331+3030 rawspwid= 1 [I=1.779, 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> | | </pre> |
|
| |
|
| The absolute fluxes for the frequencies have now been determined and one can proceed to the bandpass and complex gain calibrations. | | The absolute fluxes for the frequencies have now been determined and one can proceed to the bandpass and complex gain calibrations. |
|
| |
|
| ==Bandpass== | | ==Bandpass Calibration== |
| | |
| Before determining the bandpass solution, we need to inspect phase and amplitude
| |
| variations with time and frequency on the bandpass calibrator to
| |
| decide how best to proceed. We limit the number of antennas to make
| |
| the plot easier to see. We chose ea02 as it seems like a good
| |
| candidate for the reference antenna.
| |
|
| |
|
| <source lang="python">
| | Correct the phase variations with time before solving for the bandpass to |
| # In CASA
| |
| plotms(vis='day2_TDEM0003_10s_norx',field='5',
| |
| xaxis='channel',yaxis='phase',correlation='RR',
| |
| avgtime='1e8',spw='0:4~60',antenna='ea02&ea23')
| |
| </source>
| |
| [[Image:Nobandpass_phase.png|thumb|Phase as a function of channel for ea02 (after Custom and upping "Style" to 3.)]]
| |
| The phase variation is modest ~10 degrees. Now expand to all baselines that include ea02, then hit the "Plot" button.
| |
| | |
| <source lang="python">
| |
| # In CASA
| |
| plotms(vis='day2_TDEM0003_10s_norx',field='5',
| |
| xaxis='channel',yaxis='phase',correlation='RR',
| |
| avgtime='1e8',spw='0:4~60',antenna='ea02', coloraxis='antenna2')
| |
| </source>
| |
| [[Image:Nobandpass_phasetime.png|thumb|Phase as a function of time for all baselines with antenna ea02 (after Custom and upping "Style" to 3.)]]
| |
| From this
| |
| you can see that the phase variation across the bandpass is
| |
| modest. Next check LL, and spw=1, both correlations. Also check
| |
| other antennas if you like.
| |
| | |
| Now look at the phase as a function of time.
| |
| | |
| <source lang="python">
| |
| # In CASA
| |
| plotms(vis='day2_TDEM0003_10s_norx',field='5',
| |
| xaxis='time',yaxis='phase',correlation='RR',
| |
| avgchannel='64',spw='0:4~60',antenna='ea02&ea23')
| |
| </source>
| |
| | |
| | |
| Expand to all antennas with ea02
| |
| | |
| <source lang="python">
| |
| # In CASA
| |
| plotms(vis='day2_TDEM0003_10s_norx',field='5',
| |
| xaxis='time',yaxis='phase',correlation='RR',
| |
| avgchannel='64',spw='0:4~60',antenna='ea02', coloraxis='antenna2')
| |
| </source>
| |
| | |
| You may want to select "Custom" under "unflagged points symbol" and then change Style from "2" to "3" under the "Display" tab, "Unflagged Points Symbol" .
| |
| | |
| You can see that the phase variations are smooth, but do vary
| |
| significantly over the 5 minutes of observation -- in most cases by
| |
| a few 10s of degrees. Zoom in to see this better if you want.
| |
| | |
| The conclusion from this investigation is that you need to correct
| |
| the phase variations with time before solving for the bandpass to | |
| prevent decorrelation of the vector averaged bandpass | | prevent decorrelation of the vector averaged bandpass |
| solution. Since the phase variation as a function of channel is | | solution. |
| modest, you can average over several channels to increase the signal
| |
| to noise of the phase vs. time solution. If the phase variation as a
| |
| function of channel is larger you may need to use only a few
| |
| channels to prevent introducing delay-based closure errors as can happen from averaging over
| |
| non-bandpass corrected channels with large phase variations.
| |
|
| |
|
| | [[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.]] |
|
| |
|
| Since the bandpass calibrator is quite strong we do the phase-only
| |
| solution on the integration time of 10 seconds (solint='int').
| |
|
| |
| Remember that previously we determined the '''myTau''' variable as a list of opacities. It's repeated here but may still be in your CASA session.
| |
|
| |
| [[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"> | | <source lang="python"> |
| # In CASA | | # In CASA |
| myTau=[0.041019209411983566, 0.040779609355637569]
| | gaincal(vis=vis, caltable='bpphase.gcal', field='5', spw='0~1:20~40', |
| gaincal(vis='day2_TDEM0003_10s_norx',caltable='bpphase.gcal', | | refant='ea02', gaintype='G', calmode='p',solint='int', |
| field='5',spw='0~1:20~40',
| | gaincurve=T) |
| refant='ea02',calmode='p',solint='int',minsnr=2.0, | |
| gaintable=['antpos.cal'],
| |
| opacity=myTau,gaincurve=T) | |
| </source> | | </source> |
|
| |
|
| Plot the solutions | | Plot the solutions using {{plotcal}}. |
|
| |
|
| <source lang="python"> | | <source lang="python"> |
Line 474: |
Line 198: |
| iteration='antenna',subplot=331,plotrange=[0,0,-180,180]) | | iteration='antenna',subplot=331,plotrange=[0,0,-180,180]) |
| </source> | | </source> |
|
| |
| These solutions will appear in the CASA plotter gui. If you closed it after plotting the antennas above, it should reopen. If it is still open from before, the new plots should just appear. After you are done looking at the first set of plots, push the "Next" button on the GUI to see the next set of antennas.
| |
|
| |
|
| Next we can apply this phase solution on the fly while determining | | 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'). | | the bandpass solutions on the timescale of the bandpass calibrator scan (solint='inf'). |
|
| |
| We also use the opacity list now instead of myTau - but both options will work.
| |
|
| |
|
| |
|
| <source lang="python"> | | <source lang="python"> |
| # In CASA | | # In CASA |
| bandpass(vis='day2_TDEM0003_10s_norx',caltable='bandpass.bcal',field='5', | | bandpass(vis=vis, caltable='bandpass.bcal', field='5', refant='ea02', |
| refant='ea02',solint='inf',solnorm=T,
| | solint='inf', solnorm=T, gaintable='bpphase.gcal', |
| gaintable=['antpos.cal','bpphase.gcal'],
| | gaincurve=T) |
| opacity=[0.041, 0.0408],gaincurve=T)
| |
| </source> | | </source> |
|
| |
| '''A few words about solint and combine:'''
| |
|
| |
| The use of solint='inf' in {{bandpass}} will derive one bandpass
| |
| solution for the whole J1229+0203 scan. Note that if there had been two observations of the bandpass calibrator (for example), this command would have combined the data from both scans to form one bandpass solution, because the default of the combine parameter '''for {{bandpass}}''' is combine='scan'. To solve for one bandpass for each bandpass calibrator scan you would also need to include combine='''' '''' in the bandpass call. In all calibration tasks, regardless of solint, scan boundaries are only crossed when combine='scan'. Likewise, field (spw) boundaries are only crossed if combine='field' (combine='spw'), the latter two are not generally good ideas for bandpass solutions.
| |
|
| |
|
| Plot the solutions, amplitude and phase: | | Plot the solutions, amplitude and phase: |
Line 513: |
Line 226: |
| </source> | | </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. |
|
| |
|
| Note that phases on ea12 look noiser than on other antennas. This
| | 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. |
| jitter could indicate bad pointing; note that ea12 had just come back in
| |
| the array. | |
|
| |
|
| This step isn't necessary from a calibration perspective, but if you | | This tutorial picks up where [[ EVLA high frequency spectral line tutorial - IRC+10216 - calibration]] leaves off. |
| want to go ahead and check the bandpass calibration on the bandpass
| |
| calibrator you can run {{applycal}} here. In future we hope to plot
| |
| corrected data on-the-fly without this {{applycal}} step. Later applycals
| |
| will overwrite this one, so no need to worry.
| |
|
| |
|
| [[Image:Applybandpass_phase.png|thumb|Phase as a function of channel, plotting the corrected data (after Custom and upping "Style" to 3.)]]
| | ==Imaging== |
|
| |
|
| <source lang="python">
| | [[Image:irc10216_uvspec.png|thumb|UV-plot of the spectral line signal in both spw for IRC+10216.]] |
| applycal(vis='day2_TDEM0003_10s_norx',field='5',
| |
| gaintable=['antpos.cal','bandpass.bcal'],
| |
| gainfield=['','5'],
| |
| opacity=[0.0410, 0.0408],gaincurve=T,calwt=F)
| |
| </source>
| |
|
| |
|
| Similar to {{flagdata}}, {{applycal}} works like a matrix. The first entries in the lists are to be used together, so are the second entries etc. (except for the opacity list, which is referring to spws). All will be applied to the 'field' selection. In the above example, 'antpos.cal' from any field is applied to source '5', and the 'bandpass.cal' that was obtained for field '5' (the bandpass observation) is also applied to field '2'. Again, lists within the lists are fine.
| | The continuum-subtracted spectral line data is contained in <tt>IRC10216_spls.ms</tt>. Use {{plotms}} to plot the lines. |
|
| |
|
| <source lang="python"> | | <source lang="python"> |
| plotms(vis='day2_TDEM0003_10s_norx',field='5', | | plotms(vis='IRC10216_spls.ms', xaxis='channel', yaxis='amp', |
| xaxis='channel',yaxis='phase',ydatacolumn='corrected',
| | avgtime='1e8', avgscan=T, coloraxis='spw') |
| correlation='RR',
| |
| avgtime='1e8',spw='0:4~60',antenna='ea02', coloraxis='antenna2') | |
| </source> | | </source> |
|
| |
|
| <source lang="python">
| | Now it is time to image the visibility data using {{clean}}. For illustration, we will clean channel 22 of the SiS line. |
| plotms(vis='day2_TDEM0003_10s_norx',field='5',
| |
| xaxis='channel',yaxis='amp',ydatacolumn='corrected',
| |
| correlation='RR',
| |
| avgtime='1e8',spw='0:4~60',antenna='ea02', coloraxis='antenna2')
| |
| </source>
| |
| | |
| Note that the phase and amplitude as a function of channel are very flat now.
| |
| | |
| ==Gain Calibration==
| |
| | |
| Now that we have a bandpass solution to apply we can solve for the antenna-based phase and amplitude gain calibration. Since the phase changes on a much shorter timescale than the amplitude, we will solve for them separately. In particular, if the phase changes significantly over a scan time, the amplitude would be decorrelated, if the un-corrected phase were averaged over this timescale. Note that we re-solve for the gain solutions of the bandpass calibrator, so we can derive new solutions that are corrected for the bandpass shape. Since the bandpass calibrator will not be used again, this is not strictly necessary, but is useful to check its calibrated flux density for example. We use a minimum signal-to-noise of 2 here as it seems to be a good compromise for using good data without rejecting too many solutions (minsnr=2). | |
|
| |
|
| <source lang="python"> | | <source lang="python"> |
| # In CASA | | # In CASA |
| gaincal(vis='day2_TDEM0003_10s_norx',caltable='intphase.gcal',
| | os.system('rm -rf ch22.*') # remove previously generated image, if it exists |
| field='2,5,7',spw='0~1:4~60',
| | clean(vis='IRC10216_spls.ms', imagename='ch22', spw='1:22~22', |
| refant='ea02',calmode='p',solint='int',minsnr=2.0,
| | mode='channel', nchan=1, start='', width=1, niter=100000, |
| gaintable=['antpos.cal','bandpass.bcal'],
| | gain=0.1, threshold='3.0mJy', psfmode='clark', imagermode='csclean', |
| opacity=[0.0410, 0.0408],gaincurve=T)
| | interactive=T, npercycle=100, imsize=300, cell=['0.4arcsec', '0.4arcsec'], |
| | stokes='I', weighting='briggs', robust=0.5) |
| </source> | | </source> |
| [[Image:allcal_phaseint2.png|thumb|Plot of phase solutions on an integration time.]]
| |
|
| |
|
| Here solint='int' coupled with calmode='p' will derive a single phase solution for each 10 second integration. Note that the bandpass table is applied on-the-fly before solving for the phase solutions, however the bandpass is NOT applied to the data permanently until applycal is run later on.
| | 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. |
|
| |
|
| Note that quite a few solutions are rejected due to SNR<2 (printed to terminal). For the most part it
| | Open the resulting image using the {{viewer}}. |
| is only one or two solutions out of >30 so this isn't too worrying. Take note if you see large numbers of rejected solutions per integration. This is likely an indication that solint is too short for the S/N of the data.
| |
| | |
| Now look at the phase solution, and note the obvious scatter within a scan time.
| |
| | |
| <source lang="python">
| |
| # In CASA
| |
| plotcal(caltable='intphase.gcal',xaxis='time',yaxis='phase',
| |
| iteration='antenna',subplot=331,plotrange=[0,0,-180,180])
| |
| </source>
| |
|
| |
|
| Although solint='int' (i.e. the integration time of 10 seconds) is the best choice to apply before for solving for the amplitude solutions, it is not a good idea to use this to apply to the target. This is because the phase-scatter within a scan can dominate the interpolation between calibrator scans. Instead, we also solve for the phase on the scan time, solint='inf' (but combine='''' '''', since we want one solution per scan) for application to the target later on. '''Unlike the bandpass task,''' for gaincal, the default of the combine parameter is combine='''' ''''.
| |
| [[Image:allcal_phaseinf2.png|thumb|Plot of phase solutions on a scan time.]]
| |
| <source lang="python"> | | <source lang="python"> |
| # In CASA | | # In CASA |
| gaincal(vis='day2_TDEM0003_10s_norx',caltable='scanphase.gcal',
| | viewer("ch22.image") |
| field='2,5,7',spw='0~1:4~60',
| |
| refant='ea02',calmode='p',solint='inf',minsnr=2.0,
| |
| gaintable=['antpos.cal','bandpass.bcal'],
| |
| opacity=[0.0410, 0.0408],gaincurve=T)
| |
| </source> | | </source> |
|
| |
|
| <source lang="python">
| | In the viewer, make a region and click inside it to get statistics about the portion of the image in the region. |
| # In CASA
| |
| plotcal(caltable='scanphase.gcal',xaxis='time',yaxis='phase',
| |
| iteration='antenna',subplot=331,plotrange=[0,0,-180,180])
| |
| </source>
| |
|
| |
|
| Note that there are no failed solutions here because of the added S/N afforded by the longer solint.
| | ==Analyze the Image Cubes== |
| Alternatively, instead of making a separate phase solution for application to the target, one can also run {{smoothcal}} to smooth the solutions derived on the integration time.
| |
|
| |
|
| Next we apply the bandpass and solint='int' phase-only calibration solutions on-the-fly to derive amplitude solutions.
| | Open the HC3N image cube in the {{viewer}}. |
| Here the use of solint='inf', but combine='''' '''' will result in one solution per scan interval.
| |
|
| |
|
| <source lang="python"> | | <source lang="python"> |
| # In CASA | | # In CASA |
| gaincal(vis='day2_TDEM0003_10s_norx',caltable='amp.gcal',
| | viewer("IRC10216_HC3N.image") |
| field='2,5,7',spw='0~1:4~60',
| |
| refant='ea02',calmode='ap',solint='inf',minsnr=2.0,
| |
| gaintable=['antpos.cal','bandpass.bcal','intphase.gcal'],
| |
| opacity=[0.0410, 0.0408],gaincurve=T)
| |
| </source> | | </source> |
| [[Image:allcal_ampphase.png|thumb|Plot of residual phase solutions on a scan time]]
| |
|
| |
|
| Now let's look at the resulting phase solutions. Since we have taken out the phase as best we can by applying the solint='int' phase-only solution, this plot will give a good idea of the residual phase error. If you see scatter of more than a few degrees here, you should consider going back and looking for more data to flag, particularly bad timeranges etc.
| | 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. |
|
| |
|
| <source lang="python">
| | Open the SiS image cube in the viewer. |
| # In CASA
| |
| plotcal(caltable='amp.gcal',xaxis='time',yaxis='phase',
| |
| iteration='antenna',subplot=331)
| |
| </source>
| |
|
| |
|
| Indeed, both antenna ea12 (all times) and ea23 (first 1/3 of observation) show particularly large residual phase noise.
| |
| [[Image:allcal_amp.png|thumb|Plot of amplitude solutions on a scan time]]
| |
| <source lang="python"> | | <source lang="python"> |
| # In CASA | | # In CASA |
| plotcal(caltable='amp.gcal',xaxis='time',yaxis='amp',
| | viewer("IRC10216_SiS.image") |
| iteration='antenna',subplot=331)
| |
| </source> | | </source> |
|
| |
|
| Note that the amplitude solutions for ea12 are very low; this is another indication that this antenna is dubious.
| | Determine what channels in the cube have emission. Then make moment maps using {{immoments}}. |
| | |
| Next we use the flux calibrator (whose flux density was set in {{setjy}} above) to derive the flux of the other calibrators. Note that the flux table REPLACES the amp.gcal in terms of future application of the calibration to the data, i.e. the flux table contains both the amp.gcal and flux scaling. Unlike the gain calibration steps, this is not an incremental table.
| |
| | |
| <source lang="python">
| |
| # In CASA
| |
| fluxscale(vis='day2_TDEM0003_10s_norx',caltable='amp.gcal',
| |
| fluxtable='flux.cal',reference='7')
| |
| </source>
| |
| | |
| [[Image:allcal_flux.png|thumb|Plot of flux corrected amplitude solutions.]]
| |
| It is a good idea to note down for your records the derived flux densities:
| |
| | |
| <pre style="background-color: #fffacd;">
| |
| Flux density for J0954+1743 in SpW=0 is: 0.237135 +/- 0.000858511 (SNR = 276.216, nAnt= 19)
| |
| Flux density for J0954+1743 in SpW=1 is: 0.247597 +/- 0.00063498 (SNR = 389.928, nAnt= 19)
| |
| Flux density for J1229+0203 in SpW=0 is: 26.508 +/- 0 (SNR = inf, nAnt= 19)
| |
| Flux density for J1229+0203 in SpW=1 is: 26.2517 +/- 0 (SNR = inf, nAnt= 19)
| |
| | |
| </pre>
| |
| | |
| Obviously, the signal-to-noise for J1229+0203 can't be infinity! This is just an indication that there is only one scan for this source, and we derived a scan based amplitude solution, so there is no variation to calculate.
| |
| | |
| Next, check that the flux.cal table looks as expected.
| |
| | |
| <source lang="python">
| |
| # In CASA
| |
| plotcal(caltable='flux.cal',xaxis='time',yaxis='amp',
| |
| iteration='antenna',subplot=331)
| |
| </source>
| |
| | |
| ==Applycal and Inspect==
| |
| | |
| Now we apply the calibration to each source, according to which tables are appropriate, and which source should be used to do that particular calibration. For the calibrators, all bandpass solutions come from the bandpass calibrator (id=5), and the phase and amplitude calibration comes from their own solutions.
| |
| | |
| '''Note:''' In applycal we set calwt=F. It is very important to turn off this parameter which determines if the weights are calibrated along with the data. Data from antennas with better receiver performance and/or longer integration times should have higher weights, and it can be advantageous to factor this information into the calibration. During the VLA era, meaningful weights were available for each visibility. However, EVLA is not yet recording the information necessary to calculate meaningful weights. Since these data weights are used at the imaging stage you can get strange results from having calwt=T when the input weights are themselves not meaningful, especially for self-calibration on resolved sources (your flux calibrator and target for example). In a few months EVLA data will again have meaningful weights and the default calwt=T will likely again be the best option.
| |
|
| |
|
| <source lang="python"> | | <source lang="python"> |
| # In CASA | | # In CASA |
| # for the gain/phase calibrator (field '2'):
| | os.system('rm -rf IRC10216_Sis.mom0') # remove previously generated map, if it exists |
| applycal(vis='day2_TDEM0003_10s_norx',field='2',
| | immoments(imagename="IRC10216_SiS.image", moments=[0], axis="spectral", |
| gaintable=['antpos.cal','bandpass.bcal','intphase.gcal','flux.cal'],
| | chans="12~40", outfile="IRC10216_Sis.mom0") |
| gainfield=['','5','2','2'],
| |
| opacity=[0.0410, 0.0408],gaincurve=T,calwt=F)
| |
| </source> | | </source> |
|
| |
|
| <source lang="python">
| | Open the moment map in the viewer. |
| # In CASA
| |
| # for the bandpass calibrator (field '5'):
| |
| applycal(vis='day2_TDEM0003_10s_norx',field='5',
| |
| gaintable=['antpos.cal','bandpass.bcal','intphase.gcal','flux.cal'],
| |
| gainfield=['','5','5','5'],
| |
| opacity=[0.0410, 0.0408],gaincurve=T,calwt=F)
| |
| </source>
| |
|
| |
|
| <source lang="python"> | | <source lang="python"> |
| # In CASA | | # In CASA |
| # for the flux calibrator (field '7'):
| | viewer("IRC10216_Sis.mom0") |
| applycal(vis='day2_TDEM0003_10s_norx',field='7',
| |
| gaintable=['antpos.cal','bandpass.bcal','intphase.gcal','flux.cal'],
| |
| gainfield=['','5','7','7'],
| |
| opacity=[0.0410, 0.0408],gaincurve=T,calwt=F)
| |
| </source> | | </source> |
|
| |
|
| For the target we apply the bandpass from id=5, and the calibration from the gain calibrator (id=2):
| | Overlay contours by selecting '''Data --> Open''' from the pull down menu, selecting the moment-0 map, and clicking 'contour map'. |
| | |
| <source lang="python">
| |
| # In CASA
| |
| # for the target source IRC10216 (field '3'):
| |
| applycal(vis='day2_TDEM0003_10s_norx',field='3',
| |
| gaintable=['antpos.cal','bandpass.bcal','scanphase.gcal','flux.cal'],
| |
| gainfield=['','5','2','2'],
| |
| opacity=[0.0410, 0.0408],gaincurve=T,calwt=F)
| |
| </source>
| |
| | |
| Now inspect the corrected data:
| |
| [[Image:applycal_inspect.png|thumb|Plot of calibrated amplitudes over time.]]
| |
| <source lang="python">
| |
| # In CASA
| |
| plotms(vis='day2_TDEM0003_10s_norx',field='5',ydatacolumn='corrected',
| |
| xaxis='time',yaxis='amp',correlation='RR,LL',
| |
| avgchannel='64',spw='0:4~60',antenna='', coloraxis='antenna1')
| |
| </source>
| |
| | |
| This plot shows some data deviating from the average amplitudes. Use methods described above to
| |
| mark a region for a small number of deviant data points, and click "Locate". You will find that ea12 is responsible.
| |
| | |
| <source lang="python">
| |
| # In CASA
| |
| plotms(vis='day2_TDEM0003_10s_norx',field='2',ydatacolumn='corrected',
| |
| xaxis='time',yaxis='amp',correlation='RR,LL',
| |
| avgchannel='64',spw='0:4~60',antenna='', coloraxis='antenna2')
| |
| </source>
| |
| | |
| Here we see some problems, with high points. Mark some regions
| |
| and locate in {{plotms}} to find out which antennas and in which spws. Pay special
| |
| attention to antennas that have been called out already as showing some dubious behavior.
| |
| | |
| What you find is that ea07 which we flagged spw=1 above, is also bad for the same timerange in spw=0. This was not obvious in the raw data, because spw=0 was adjusted in the on-line system by a gain attenuator, while spw=1 wasn't. So a lack of power on this antenna can look like very low (and obvious) amplitudes in spw=1 but not for spw=0. Looking carefully you'll see that ea07 is actually pretty noisy throughout.
| |
| [[Image:ea12.png|thumb|Plot of antenna ea12 by itself]]
| |
| [[Image:ea23.png|thumb|Plot of antenna ea23 by itself]]
| |
| | |
| From the locate we also find that ea12 and ea23 show some high points; to see this, replot baselines using each of them alone:
| |
| | |
| <source lang="python">
| |
| plotms(vis='day2_TDEM0003_10s_norx',field='2',ydatacolumn='corrected',
| |
| xaxis='time',yaxis='amp',correlation='RR,LL',
| |
| avgchannel='64',spw='0:4~60',antenna='ea12', coloraxis='antenna2')
| |
| </source>
| |
| | |
| <source lang="python">
| |
| plotms(vis='day2_TDEM0003_10s_norx',field='2',ydatacolumn='corrected',
| |
| xaxis='time',yaxis='amp',correlation='RR,LL',
| |
| avgchannel='64',spw='0:4~60',antenna='ea23', coloraxis='antenna2')
| |
| </source>
| |
| | |
| it may be a a good idea to flag ea12 completely - it's just a bit noisy all around and ea23 is pretty noisy during the first scans between initial and second pointing. Recall that these are antennas we became suspicious of while inspecting the calibration solutions.
| |
| | |
| [[Image:target_uvdist.png|thumb|IRC+10216 as a function of uv-distance.]]
| |
| Now lets see how the target looks. Because the target has resolved structure, its best to look at it as
| |
| a function of uvdistance. We'll go ahead and exclude the three antennas we already know have problems.
| |
| | |
| <source lang="python">
| |
| # In CASA
| |
| plotms(vis='day2_TDEM0003_10s_norx',field='3',ydatacolumn='corrected',
| |
| xaxis='uvdist',yaxis='amp',correlation='RR,LL',
| |
| avgchannel='64',spw='0:4~60',antenna='!ea07;!ea12;!ea23', coloraxis='antenna2')
| |
| </source>
| |
| | |
| you can see that the spikes
| |
| are caused by a single antenna. Use, zoom, mark, and locate to see which one.
| |
| Also look at spw=1.
| |
| | |
| Turns out to be ea28; to confirm, replot with antenna=!ea28, and
| |
| | |
| <source lang="python">
| |
| # In CASA
| |
| plotms(vis='day2_TDEM0003_10s_norx',field='3',ydatacolumn='corrected',
| |
| xaxis='uvdist',yaxis='amp',correlation='RR,LL',
| |
| avgchannel='64',spw='0:4~60',antenna='!ea07;!ea12;!ea23;!ea28', coloraxis='antenna2')
| |
| </source>
| |
| | |
| To see if it's restricted to a certain time
| |
| | |
| <source lang="python">
| |
| # In CASA
| |
| plotms(vis='day2_TDEM0003_10s_norx',field='3',ydatacolumn='corrected',
| |
| xaxis='time',yaxis='amp',correlation='RR,LL',
| |
| avgchannel='64',spw='0:4~60',antenna='ea28', coloraxis='antenna1')
| |
| </source>
| |
| | |
| | |
| Baselines with ea28 clearly show issues until about two-thirds of the way through the observation.
| |
| Plot another distant antenna to compare. We will go ahead and flag it all, since its hanging far out on the north
| |
| arm by itself.
| |
| | |
| The additional data we've identified as bad need to be flagged, and then all the calibration steps will need to be run
| |
| again.
| |
| | |
| <source lang="python">
| |
| # In CASA
| |
| flagdata(vis='day2_TDEM0003_10s_norx',
| |
| field=['',''],
| |
| spw=['',''],
| |
| antenna=['ea07,ea12,ea28','ea07,ea23'],
| |
| timerange=['','03:21:40~04:10:00'])
| |
| </source>
| |
| | |
| ==Redo Calibration after more Flagging==
| |
| | |
| After flagging, you'll need to repeat the calibration steps above. Here, we append _redo to the table names to distinguish them from the first round, in case we want to compare with previous versions.
| |
| | |
| <source lang="python">
| |
| # In CASA
| |
| gaincal(vis='day2_TDEM0003_10s_norx',caltable='bpphase_redo.gcal',
| |
| field='5',spw='0~1:20~40',
| |
| refant='ea02',calmode='p',solint='int',minsnr=2.0,
| |
| gaintable=['antpos.cal'],
| |
| opacity=[0.0410, 0.0408],gaincurve=T)
| |
| </source>
| |
| | |
| <source lang="python">
| |
| # In CASA
| |
| bandpass(vis='day2_TDEM0003_10s_norx',caltable='bandpass_redo.bcal',
| |
| field='5',
| |
| refant='ea02',solint='inf',solnorm=T,
| |
| gaintable=['antpos.cal','bpphase_redo.gcal'],
| |
| opacity=[0.0410, 0.0408],gaincurve=T)
| |
| </source>
| |
| | |
| <source lang="python">
| |
| # In CASA
| |
| gaincal(vis='day2_TDEM0003_10s_norx',caltable='intphase_redo.gcal',
| |
| field='2,5,7',spw='0~1:4~60',
| |
| refant='ea02',calmode='p',solint='int',minsnr=2.0,
| |
| gaintable=['antpos.cal','bandpass_redo.bcal'],
| |
| opacity=[0.0410, 0.0408],gaincurve=T)
| |
| </source>
| |
| | |
| <source lang="python">
| |
| # In CASA
| |
| gaincal(vis='day2_TDEM0003_10s_norx',caltable='scanphase_redo.gcal',
| |
| field='2,5,7',spw='0~1:4~60',
| |
| refant='ea02',calmode='p',solint='inf',minsnr=2.0,
| |
| gaintable=['antpos.cal','bandpass_redo.bcal'],
| |
| opacity=[0.0410, 0.0408],gaincurve=T)
| |
| </source>
| |
| | |
| <source lang="python">
| |
| # In CASA
| |
| gaincal(vis='day2_TDEM0003_10s_norx',caltable='amp_redo.gcal',
| |
| field='2,5,7',spw='0~1:4~60',
| |
| refant='ea02',calmode='ap',solint='inf',minsnr=2.0,
| |
| gaintable=['antpos.cal','bandpass_redo.bcal','intphase_redo.gcal'],
| |
| opacity=[0.0410, 0.0408],gaincurve=T)
| |
| </source>
| |
|
| |
| <source lang="python">
| |
| # In CASA
| |
| fluxscale(vis='day2_TDEM0003_10s_norx',caltable='amp_redo.gcal',
| |
| fluxtable='flux_redo.cal',reference='7')
| |
| </source>
| |
| | |
| <pre style="background-color: #fffacd;">
| |
| Flux density for J0954+1743 in SpW=0 is: 0.235345 +/- 0.000879422
| |
| (SNR = 267.613, nAnt= 16)
| |
| Flux density for J0954+1743 in SpW=1 is: 0.241996 +/- 0.000930228
| |
| (SNR = 260.147, nAnt= 16)
| |
| Flux density for J1229+0203 in SpW=0 is: 25.2479 +/- 0
| |
| (SNR = inf, nAnt= 16)
| |
| Flux density for J1229+0203 in SpW=1 is: 24.9907 +/- 0
| |
| (SNR = inf, nAnt= 16)
| |
| | |
| Flux density for J0954+1743 in SpW=0 is: 0.247052 +/- 0.000946345 (SNR = 261.059, nAnt= 16)
| |
| Flux density for J0954+1743 in SpW=1 is: 0.254038 +/- 0.00097531 (SNR = 260.47, nAnt= 16)
| |
| Flux density for J1229+0203 in SpW=0 is: 26.5079 +/- 0 (SNR = inf, nAnt= 16)
| |
| Flux density for J1229+0203 in SpW=1 is: 26.2335 +/- 0 (SNR = inf, nAnt= 16)
| |
| </pre>
| |
| | |
| Feel free to pause here and remake the calibration solution plots from above, just be sure to put in the revised table names.
| |
| | |
| ==Redo Applycal and Inspect==
| |
| | |
| Now, apply all the new calibrations, which will overwrite the old ones. These commands are identical to those above, with the exception of the _redo part of each calibration filename.
| |
| | |
| <source lang="python">
| |
| # In CASA
| |
| applycal(vis='day2_TDEM0003_10s_norx',field='2',
| |
| gaintable=['antpos.cal','bandpass_redo.bcal','intphase_redo.gcal','flux_redo.cal'],
| |
| gainfield=['','5','2','2'],
| |
| opacity=[0.0410, 0.0408],gaincurve=T,calwt=F)
| |
| </source>
| |
| | |
| <source lang="python">
| |
| # In CASA
| |
| applycal(vis='day2_TDEM0003_10s_norx',field='5',
| |
| gaintable=['antpos.cal','bandpass_redo.bcal','intphase_redo.gcal','flux_redo.cal'],
| |
| gainfield=['','5','5','5'],
| |
| opacity=[0.0410, 0.0408],gaincurve=T,calwt=F)
| |
| </source>
| |
| | |
| <source lang="python">
| |
| # In CASA
| |
| applycal(vis='day2_TDEM0003_10s_norx',field='7',
| |
| gaintable=['antpos.cal','bandpass_redo.bcal','intphase_redo.gcal','flux_redo.cal'],
| |
| gainfield=['','5','7','7'],
| |
| opacity=[0.0410, 0.0408],gaincurve=T,calwt=F)
| |
| </source>
| |
| | |
| [[Image:gaincal_corrflag.png|thumb|Gain calibrator after further flagging and recalibration]]
| |
| [[Image:target_corrflag.png|thumb|IRC+10216 after further flagging and recalibration (after selecting colorize by spw).]]
| |
| | |
| <source lang="python">
| |
| # In CASA
| |
| applycal(vis='day2_TDEM0003_10s_norx',field='3',
| |
| gaintable=['antpos.cal','bandpass_redo.bcal','scanphase_redo.gcal','flux_redo.cal'],
| |
| gainfield=['','5','2','2'],
| |
| opacity=[0.0410, 0.0408],gaincurve=T,calwt=F)
| |
| </source>
| |
| | |
| Now you can inspect the calibrated data again. Except for random scatter things look pretty good.
| |
| | |
| <source lang="python">
| |
| # In CASA
| |
| plotms(vis='day2_TDEM0003_10s_norx',field='2',ydatacolumn='corrected',
| |
| xaxis='time',yaxis='amp',correlation='RR,LL',
| |
| avgchannel='64',spw='0:4~60',antenna='', coloraxis='antenna2')
| |
| </source>
| |
| | |
| You can use the Mark and Locate buttons to assess that the remaining scatter seems random, i.e. no particular antenna or time range appears to be responsible.
| |
| | |
| <source lang="python">
| |
| # In CASA
| |
| plotms(vis='day2_TDEM0003_10s_norx',field='3',ydatacolumn='corrected',
| |
| xaxis='uvdist',yaxis='amp',correlation='RR,LL',
| |
| avgchannel='64',spw='0~1:4~60',antenna='', coloraxis='spw')
| |
| </source>
| |
| | |
| ==Split==
| |
| | |
| Now we split the data into individual files. This is not strictly necessary, as you can select the appropriate fields in later clean stages, but it is safer in case for example you get confused with later processing and want to fall back to this point (this is especially a good idea if you plan to do continuum subtraction or self calibration later on). It also makes smaller individual files in case you want to copy to another machine or colleague.
| |
| | |
| Here, we split off the data for the phase calibrator and the target:
| |
| | |
| <source lang="python">
| |
| # In CASA
| |
| split(vis='day2_TDEM0003_10s_norx',outputvis='J0954',
| |
| field='2')
| |
| </source>
| |
| | |
| <source lang="python">
| |
| # In CASA
| |
| split(vis='day2_TDEM0003_10s_norx',outputvis='IRC10216',
| |
| field='3')
| |
| </source>
| |
| | |
| To reinitialize the scratch columns for use by later tasks, we need to run clearcal for both new datasets
| |
| | |
| <source lang="python">
| |
| # In CASA
| |
| clearcal(vis='J0954')
| |
| </source>
| |
| | |
| <source lang="python">
| |
| # In CASA
| |
| clearcal(vis='IRC10216')
| |
| </source>
| |
| | |
| This concludes the calibration phase of the data reductions. The tutorial continues with continuum subtraction, imaging, and image analysis in
| |
| [[EVLA high frequency Spectral Line tutorial - IRC+10216 part2]].
| |
|
| |
|
| [[Main Page | ↵ '''CASAguides''']] | | [[Main Page | ↵ '''CASAguides''']] |
|
| |
| --[[User:Cbrogan|Crystal Brogan]]
| |
| --additions:[[User:Jott| Juergen Ott]]
| |
|
| |
|
| {{Checked 3.3.0}} | | {{Checked 3.3.0}} |