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Subsections

• 7.1 Introduction
• 7.2 Manipulating AIPS++ tools
• 7.3 Importing BIMA Data in AIPS++
• 7.4 Inspecting UV data
• 7.5 Editing UV data
• 7.6 Calibration of uv data

7. BIMA Data Reduction

D.M. Mehringer and The LAUGH Group^7.1

7.1 Introduction

David Mehringer, Ray Plante, and Anuj Sarma

This version of the BIMA AIPS++ Cookbook is a much abridged version of the full version which can be found at http://monet.ncsa.uiuc.edu/aips++/forBIMA/cook/cook.html. The abridged version essentially describes only BIMA-specific issues in AIPS++ while the full version has useful chapters on using AIPS++ in general. If you discover errors or have suggestions, please email them to dmehring@astro.uiuc.edu.

7.1.1 Starting AIPS++

To start AIPS++, issue the following commands if you are using c shell:

> source /appl/aips++/stable/aipsinit.sh
> aips++

or, if you are using bash shell:

> . /appl/aips++/stable/aipsinit.sh
> aips++

7.1.2 Exiting AIPS++

There are two ways to exit from AIPS++:

• In the command line interface (Glish window), type after the ``-'' prompt:

       exit
  

  and press return

  
  

• From the Tool Manager GUI,
  select ``File $\Rightarrow$ Exit AIPS++''

7.2 Manipulating AIPS++ tools

Hélène. R. Dickel

7.2.1 How do I create a tool?

The Tool Manager window is used to create tools. Tools and global functions are organized first by Packages and then by Modules, as illustrated by the graphical lists that make up the Tool Manager. The mirfiller tool can be used to import Miriad visibility data into AIPS++.

In the BIMA Data Reduction section of the AIPS++ cookbook, we use a short hand for selecting tools and functions in the Tool Manager. It looks like this:

Package	Module	Tool		Constructor
bima	mirfiller	mirfiller		mirfiller
Don't understand this table? See § 7.2.1

Here's what it means:

1.

Under the Packages list, click on ``bima.''

2.

Under the Modules list, click on ``mirfiller.''

3.

Under the Tools list, click on ``mirfiller.''

4.

Hit the ``Create'' button below the Tools list. This will cause the Tool Manager to morph into a new GUI for constructing a mirfiller tool.

Now that you have the constructor interface up, you need to enter values for its parameters. Here are two most important parameters you need to provide and what they mean:

Constructor: mirfiller
Parameter	Sample Value	What it means
toolname	mymirfiller	The name by which you want to refer to this tool; this is helpful when you want to refer to the tool from the Glish command line or if you have more than one tool of the same type.
mirfile	3c273	The name of the Miriad dataset.

In the BIMA Data Reduction section of the AIPS++ cookbook, a table like the one above is used to summarize the inputs you need to give to a function. Usually, only the most important parameters are listed; all others can be left to their default.

Most likely, the ``toolname'' parameter will already be set to ``mymirfiller;'' however, if you want to change it, move your cursor over the ``toolname'' input, erase its contents and type in the new value.

When all the parameters have been set, you can execute the constructor and create the mirfiller tool by clicking the green button labeled ``Create.''

When the constructor finishes its work, the GUI will morph again to show the interface to the tool's functions.

7.2.2 How do I get rid of a tool?

You can shut down a tool from its function view (where the functions appear in a list on the right; if you do not see this, press the ``mirfiller:mymirfiller" button along the top of the Tool Manager.

Now press the ``Done" button at the bottom, right hand corner of the window. The Tool Manager will morph back into its tool selection view. The ``mirfiller:mymirfiller" button is now gone.

Note that the ``Dismiss" button does not shut down the tool. It simply returns to the tool selection view. The ``mirfiller:mymirfiller" button would remain.

7.3 Importing BIMA Data in AIPS++

Ray Plante

7.3.1 How do I import my Miriad uv-data into AIPS++

Here's a summary of how to import your data it using the GUI:

• Create a mirfiller tool:

  Package	Module	Tool		Constructor
  bima	mirfiller	mirfiller		mirfiller
  Don't understand this table? See § 7.2.1

• Enter the constructor parameters:

  Constructor: mirfiller
  Parameter	Sample Value	What it means
  toolname	mymirfiller	The name by which you want to refer to this tool; this is helpful when you want to refer to the tool from the Glish command line or if you have more than one tool of the same type.
  mirfile	3c273	The name of the Miriad dataset.

  When you have filled in the above-mentioned values,
  press Create.

  
  

  
  
  

• Run the fill function to copy the data to an AIPS++ measurement set:

  Function: fill
  Parameter	Sample Value	What it means
  msfile	3c273.ms	The name of the output measurement set to fill.
  verbose	True	Setting this to true will send messages on mirfiller's progress to the logger window.

  After filling in the above values,
  press Go.

• Delete the tool when the filling is done.

7.3.1.1 How do I do the same thing in Glish?

If you have the scripter running, you can just look the scripter window. You'll see exactly what was run by the GUI.

Note that AIPS++ will usually write Glish commands to the scripter in their most verbose form. Here's a more compact form:

  include 'mirfiller.g'
  mymirfiller := mirfiller("3c273");
  mymirfiller.fill("3c273.ms", verbose=T);
  mymirfiller.done();

Parameters left to their default values do not have to be included. Plus, if you give the parameter values in the order that they appear in the GUI (or the documentation), you don't have to give the parameter names.

7.3.2 How do I import my FITS uv-data into AIPS++

Loading of FITS uv-data into AIPS++ can be done using the ms tool via its fitstoms constructor. Here a summary of how to import FITS data using the GUI:

• Create an ms tool by selecting the following in the Tool Manager window.

  Package	Module	Tool		Constructor
  general	ms	ms		fitstoms
  Don't understand this table? See § 7.2.1

• Choose the fitstoms constructor. To do this, click on fitstoms on the left hand side of the ms tool under `ms all constructors.'
  Now fill in the values for the parameters that appear on the right hand side. Sample values are given in the table below.

  
  

  Constructor: fitstoms
  Parameter	Sample Value	What it means
  toolname	myms	The name by which you want to refer to this tool.
  msfile	3c273	Name of the output AIPS++ measurement set to be created.
  fitsfile	3C273.FITS	Name of your input UVFITS file.

  When you are done filling in the above inputs,
  press Create.

  
  

• Delete the tool when you are done.

  
  

  
  
  

The glish equivalent of the above procedure is the following:

   include 'ms.g';
   myms := fitstoms(msfile="3c273.ms", fitsfile="3C273.FITS");
   myms.done();

7.4 Inspecting UV data

David Fong

7.4.1 Overview

This section describes how one can inspect UV data by means of the following questions:

7.4.2

How do I plot the uv-data using the imager tool?

7.4.3

How do I examine the uv-data using msplot?

7.4.3

How do I list the spectral parameters of the uv-data?

7.4.2 How do I plot the uv-data using the imager tool?

The imager tool contains the functions for imaging. If you wish to have a quick look at the uv-data before imaging, then follow these steps. If you wish examine the uv-data in greater detail, then use msplot (see § 7.4.3).

• Create an imager tool
  In the Tool Manager window, select the following:

  Package	Module	Tool		Constructor
  synthesis	imager	imager		imager
  Don't understand this table? See § 7.2.1

  
  

• Enter the constructor parameters:

  Constructor: Imager
  Parameter	Sample Value	What it means
  toolname	myimager	The name by which you want to refer to this tool; this is helpful when you want to refer to the tool from the Glish command line or if you have more than one tool of the same type.
  filename	cloud.ms	Name of the AIPS++ measurement set.

  When you are done filling in the above inputs,
  press Create.

  When the constructor is finished, the GUI will morph into the imager tool window.

  
  

  
  
  

• Make the plots.

  1.

  If you wish to plot the uv-coverage:

  • select $\Rightarrow$ plotting (under the ``Function group'' menu)

    
    

    
    

    
    
    

    
    

  • select $\Rightarrow$ plotuv (below plotting functions)

  • press Go -- after a while, a new pgplot screen will pop up and display the uv-coverage plot.

  
  

  2.

  If you wish to plot amplitude vs. uv-distance:

  • select $\Rightarrow$ plotvis (below plotting functions)

  • press Go

7.4.3 How do I examine the uv-data using msplot?

msplotprovides more selection options for plotting uv-data. The GUI-based tool can make plots, displays or listings of various parts of an MS (see Reference manual: general.ms.msplot for a full description).

• Create an msplottool
  In the Tool Manager window, select the following:

  Package	Module	Tool		Constructor
  general	ms	msplot		msplot
  Don't understand this table? See § 7.2.1

• Enter the constructor parameters:

  Constructor: msplot
  Parameter	Sample Value	What it means
  toolname	mymsplot	The name by which you want to refer to this tool.
  msfile	cloud.ms	Name of the measurement set.
  edit	False	False option only allows inspection of the uv-data.
  		True option allows interactive flagging of the uv-data.

  When you are done entering the above parameters,
  press Create.

  When the constructor is finished, a new msplot GUI window will start up.

Example 1: A common plot to make is X vs Y, where the X and Y axes can be time, UV-distance, amplitude, phase, etc.

• select $\Rightarrow$ `Plot X vs Y'
  (default option for the menu bar the on the first row, next to `Show')

  For `Plot X vs Y', the X and Y axes to be plotted are chosen by selecting the options found under the menu bars on the second row labeled `X Axis' and `Y Axis'.

• select $\Rightarrow$ uvdist (under X axis menu)
• select $\Rightarrow$ amplitude
  (first under `Y axis' menu, next under `data' submenu, and then under `value' subsubmenu)

• use the buttons in the third row, namely, `X, Y plot limits,' `Data selection,' `Spectral selection,' and `Polarization selection' to specify the data you want to plot. Selecting one of these buttons will open a panel below the button -- this panel has additional input parameters to control data selection

• press Go

  
  

  
  
  

Example 2: Another common plot to create is the UV-coverage.

• select $\Rightarrow$ `Plot UV Coverage' (under the menu bar the on the first row, next to `Show')

• press Go
  

To individually plot the UV-coverage for each baseline:

• select $\Rightarrow$ `Antenna 1' and `Antenna2' (under `Iteration selection' menu on the first row)

  
  

  
  
  

• press Go

7.4.3.1 How do I list the spectral parameters of the uv-data?

• select $\Rightarrow$ `Summarize MS in logger'
  (found under the menu bar on the first row, next to `Show')

• press Go

  The spectral parameters will be listed in the Logger window.

7.5 Editing UV data

Anuj Sarma

7.5.1 Overview

This section will describe how to flag/edit your uv-data.

7.5.2

How do I flag uv-data?

7.5.3

How do I carry out all the above steps to flag uv-data using glish?

7.5.4

How do I re-generate the wideband data after flagging?

7.5.2 How do I flag uv-data?

Flagging and editing of the uv-data can be done using the autoflag tool.

To use autoflag, go to the `Manager' view in the Tool Manager GUI and make the following selections:

• Create an autoflag tool:

  Package	Module	Tool		Constructor
  synthesis	autoflag	autoflag		autoflag
  Don't understand this table? See § 7.2.1

  
  

  
  
  

• Enter the constructor parameters:

  Constructor: autoflag
  Parameter	Sample Value	What it means
  toolname	myautoflag	The name by which you want to refer to this tool; this is helpful when you want to refer to the tool from the Glish command line or if you have more than one tool of the same type.
  msname	bllac.ms	Name of the AIPS++ measurement set that you wish to flag.

  When you are done entering the above constructor parameters,
  press Create.

  
  

  
  

  
  
  

  
  The GUI will morph into the autoflag tool window when the constructor is done.

  
  
  

  
  
  

  
  

• In the list under `all functions' on the left of the autoflag tool, click on setselect. On the right, you will get a list of options. You can choose to flag based on one or more of these options. For a detailed description of each of these options, see the User Reference Manual for autoflag.setselect.

  
  

  
  

  
  
  

  
  

  When you are done filling in all the desired options in setselect,
  press Go.

  
  

• Having made the selections on which you wish to flag, the next step is to run autoflag and apply the flags to the data.
  Look in the list on the left under `all functions' again, and this time
  click on run.

  
  

  You will get the following view, go ahead and make the selections shown in the Sample Values:

  Function: run
  Parameter	Sample Value	What it means
  globparm	[=]	Record of global method parameters. Leave at default.
  plotscr	F	Number of plots per window in flagging report. `F' means ``do not print this report.'' Default is to print report.
  plotdev	F	Number of plots per page in hardcopy flagging report. `F' means ``do not generate this report.''
  devfile		Name of hardcopy report. Leave blank if you don't want hardcopy. (Default is flagreport.ps/ps.)
  reset	False	Reset pre-existing flags. Pull-down menu.

  When you are done making the above selections for run,
  press Go.

The data for `bllac.ms' are now flagged.

7.5.3 How do I carry out all the above steps to flag uv-data using glish?

All the steps described in the last section can be done in glish.

Follow the steps below to flag your data using glish. The procedure followed is identical to that in the last section.

• First, include the autoflag script

    include 'autoflag.g'
  

• Then, create the autoflag tool. To do this, attach the tool to the dataset you wish to flag. In this example, we have named the dataset `bllac.ms.'

    af:=autoflag('bllac.ms')
  

• The next step is to select the data to be flagged. You can choose to flag based on a variety of criteria, all of which are listed in the User Reference Manual for autoflag.setselect. Below, we choose to flag all data for antenna 3, and clip all data that are outside the amplitude range (0,25).

    af.setselect(ant=2, clip=[expr='ABS YY', min=0, max=25]);
  

  
  

  
  
  

  
  

  Once you have run the above by hitting return, you should get the following list. Anything other than an `F' signifies that you chose to flag based on that criterion, and the value you used to determine how to flag (except for `dtime,' which is related to `timeslot' and has the value dtime=10 as default). For example, ant=2 because you set that in setselect above; similarly for clip.

     spwid       = F
     field       = F
     fq          = F
     chan        = F
     corr        = F
    *ant         = 2
     baseline    = F
     timerng     = F
     autocorr    = F
     timeslot    = F
     dtime       = 10
     quack       = F
    *clip        = [expr=ABS YY, min=0, max=25]
     flagrange   = F
     unflag      = F
  

• Finally, run the autoflagger.

   
    af.run(plotscr=F, plotdev=F);
  

  
  

  
  
  

Two cautionary notes: Do not flag the target source data until after the calibration has been done on the phase calibrator and the calibration tables have been copied over to the target source (see Chapter 7.6 on page ). Otherwise, the bimacalibrator tool will exit with an error. This is due to a bug in the AIPS++ code for heterogenous spectral windows, and is under investigation.

If you are flagging a calibrator, make sure you run the reavg routine in bimams before you calibrate, so that the wideband data for the calibrator are recalculated after the flags have been applied. This procedure is described in § 7.5.4 below.

7.5.4 How do I re-generate the wideband data after flagging?

After flagging the calibrator data, you will have to re-generate the wideband data, in order to carry over the flags to the sideband averages. To do this, use the reavg routine in the bimams tool.

To use reavg go to the 'Manager' view in the Tool Manager GUI and make the following selections:

• Create a bimams tool:

  Package	Module	Tool		Constructor
  bima	bimams	bimams		bimams
  Don't understand this table? See § 7.2.1

  
  

  
  
  

  
  

• Enter the constructor parameters:

  Constructor: bimams
  Parameter	Sample Value	What it means
  toolname	mybimams	The name by which you want to refer to this tool; this is helpful when you want to refer to the tool from the Glish command line or if you have more than one tool of the same type.
  msname	bllac.ms	Name of the flagged AIPS++ phase calibrator measurement set for which you want to re-generate the wideband data.

  When you are done entering the above constructor parameters,
  press Create.

  
  The GUI will morph into the bimams tool window when the constructor is finished.

  
  
  

  
  
  

  
  

• Click on the `Function group' button on the left of the bimams tool GUI. From the drop-down list, select `spectral window'. A list of spectral window functions will appear below the button.

• Click on reavg in the list of `spectral window functions' below the `Function group' button.

• Enter values for the function parameters:

  Function: reavg
  Parameter	Sample Value	What it means
  out		Output dataset -- Leave blank. If left blank, it will modify the input dataset.
  dosort	True	Sort data when doing subqueries. Pull-down menu. Default is True. Best bet is to leave at default. Set to False only if sure that data is already in order required by reavg.

  When you are done entering the above function parameters,
  press Go.

The above procedure will re-generate the wideband data. You are now ready to calibrate the data.

The above procedure to re-generate the wideband data can be carried out in glish using the following:

  include 'bimams.g';
  mybimams:=bimams('bllac.ms');
  mybimams.reavg();
  mybimams.done();

7.6 Calibration of uv data

Anuj Sarma

7.6.1 Overview

This section will answer the following questions concerning the calibration of your uv data:

7.6.2

How do I calibrate the data?

7.6.3

How do I carry out the above steps to calibrate the data using glish?

[A work in progress. Future updates will include interactive editing of gain tables, self-calibration, and bandpass correction.]

7.6.2 How do I calibrate the data?

Calibration of BIMA data is done using the bimacalibrater tool. Before using this tool, make sure that the following steps have been completed.

• First, apply the linelength correction to the data in miriad. A procedure to apply the linelength correction is under development in AIPS++. Watch this space for updates!

• Load the data into AIPS++ using the mirfiller tool (see § 7.3.1).

• The data may be edited and flagged using autoflag (§ 7.5.2). Flag only the calibrator data at this stage. Do not flag the target source data; due to a bug in AIPS++, the calibration routines will not work if you flag the target source data before the calibration. (The target source data should be flagged after the calibration routines below have been run.)

• After flagging the calibrator data, use the reavg routine in the bimams tool to recalculate the wideband data for the calibrator. This is described in § 7.5.4.

Now, you are ready to start calibrating the data. Below, we describe the steps to calibrate BIMA data based on observations of a phase calibrator. In the example below, the phase calibrator is named ``bllac'' (hence the AIPS++ measurement set is bllac.ms) and the target source is named ``cepa.''

Go the the `Manager' view in the Tool Manager and make the following selections.

• Create a bimacalibrater tool:

  Package	Module	Tool		Constructor
  bima	bimacalibrater	bimacalibrater		bimacalibrater
  Don't understand this table? See § 7.2.1

  
  

  
  

  
  
  

  
  

• Enter the constructor parameters:

  
  

  Constructor: bimacalibrater
  Parameter	Sample Value	What it means
  toolname	mybimacalibrater	The name by which you want to refer to this tool; this is helpful when you want to refer to the tool from the Glish command line or if you have more than one tool of the same type.
  targets	cepa.ms	The name of the target source dataset.
  phcals	bllac.ms	The name of the phase calibrator dataset.
  pbcals		The name of the passband calibrator -- leave blank.
  fcals		The name of the flux calibrator -- leave blank.
  targetnames	narrow	Your nickname for the target source.
  phcalnames	wide	Your nickname for the phase calibrator.

  
  

  When you are done entering the above parameters,
  press Create.

  
  The GUI will morph into the bimacalibrater tool window when the constructor is done.

  
  

  
  

  
  
  

  
  

• In the list under `all functions' on the left of the bimacalibrater tool, click on setjy. On the right, you will get a list of parameters that need to be set. An example is given below.

  
  

  Function: setjy
  Parameter	Sample Value	What it means
  sources	wide	Phase calibrator nickname.
  fluxdensity	[1,0,0,0]	Flux density for the phase calibrator in Jy. For now, you have to fill in this value by yourself, e.g., we have filled in a value of 1.0 for the I-flux. A routine to get this value automatically from a calibrator table is under development.

  When you are done filling in all the desired options in setjy,
  press Go.

  
  

  
  
  

  
  

• Now, you have to set the parameters to solve for the gains. Again, in the list under `all functions' on the left hand side, click on setsolve. Enter the values for the parameters on the right hand side. Sample values are given below.

  
  

  Function: setsolve
  Parameter	Sample Value	What it means
  sources	wide	Phase calibrator nickname.
  type	G	Component type = G-Jones. This is a pull-down menu.
  t	600	Solution interval in seconds.
  phaseonly	True	Only solve for phases. Pull-down menu.
  refant	2	Reference antenna. Note bimacalibrater has 1-based numbering, so antenna 2 means antenna 2, not antenna 3.
  table	gcal	Output calibration table name.

  When you are done filling in all the desired options in setsolve,
  press Go.

  
  

• Solve for the selected calibration components that you set above. In the list under `all functions' click on solve.

  
  

  Function: solve
  Parameter	Sample Value	What it means
  sources	wide	Phase calibrator nickname.

  press Go.

• To look at the solutions, click on plotcal under `all functions' and enter values for sources (wide) and tablename (gcal), and choose the plottype (AMP or PHASE) in the list of parameters that comes up on the right. Pressing Go will give you the desired plot.

• Transfer the calibration components to a new table. To do this, click on transfer under `all functions' on the left hand side of the bimacalibrater tool.

  
  

  
  

  
  
  

  
  

  Function: transfer
  Parameter	Sample Value	What it means
  outtable	gcal.xfer	Output table in which to write calibration solutions.
  intable	gcal	Input table generated by solve step.
  spwmap	[ ]	Array describing the spectral window mapping from input window to output window. Should be able to leave at default. The function is intelligent enough to figure out how spectral windows need to be mapped from input to output.
  calibratees	narrow	Nicknames of sources to which the solutions will be applied, e.g., if you have more than one source, you can include them all here with their given nicknames (or roles, e.g., targets). If you specify more than one source here, then all must have the same spectral window configuration, otherwise run transfer multiple times.

  When you are done setting the above inputs,
  press Go.

  
  

• Next, set up how the calibration components will be applied to the target source. On the left hand side under `all functions' click on setapply. Sample inputs are given below.

  
  

  Function: setapply
  Parameter	Sample Value	What it means
  sources	narrow	Target source nickname.
  type	G	Component type = G-Jones; pull-down menu.
  t	0.0	Interpolation interval in seconds. Leave at default (0.0).
  table	gcal.xfer	Input calibration table. Should be the output table given by transfer.
  select		Leave at default, which is blank.

  When you are done setting the above inputs,
  press Go.

• Finally, apply the calibration to the target source. Click on correct under `all functions' on the left hand side, and fill in the inputs on the right hand side, like the sample below.

  
  

  Function: correct
  Parameter	Sample Value	What it means
  sources	narrow	Nicknames of target source(s) where calibration components are to be applied.

  press Go.

The calibration is now done. Remember, you must flag the target source data after calibration and before imaging (meaning now, see Chapter 7.5) -- this will continue to be the procedure until the bug in AIPS++ is removed.

7.6.3 How do I carry out the above steps to calibrate the uv-data using glish?

All the steps described in the last section can be done in glish. First, make sure you are in the glish environment (which is started by typing ``glish'' at the command line prompt) and that you have loaded the data into AIPS++, flagged only the phase calibrator data, and regenerated the wideband data for the flagged phase calibrator, as described in the last section.

• Before using the bimacalibrater tool, define the following two quantities. Such a pre-definition is given here as an example; it will allow you to ignore the code and make changes at the top of the file when using glish scripts.

    RefAnt := 2; 
    IntTime := 600;
  

  
  

  
  
  

• Now, include the bimacalibrater script:

    include 'bimacalibrater.g';
  

• Create the bimacalibrater tool. To do this, specify the target source name and the name of the phase calibrator. You can also specify aliases for the target and calibrator, using ``targetnames'' and ``phcalnames.''

    bc := bimacalibrater(targets='cepa.ms',targetnames='narrow',
                            phcals='bllac.ms', phcalnames='wide');
  

• As mentioned before, you have to manually set the flux density for the calibrator for now. An automatic way to do this is under development.

    bc.setjy(fluxdensity=[1.0,0,0,0]);
  

• Set the parameters to solve for the gains. The solutions will be written into a table named ``gcal.'' You have to specify the reference antenna and the integration time; in this example, we have set these quantities in the pre-definition above, so we just call these quantities below.

    bc.setsolve(type='G',refant=RefAnt,table='gcal',t=IntTime,phaseonly=T);
  

• Now solve for the selected calibration components above.

    bc.solve();
  

• You may now examine the ``gcal'' table using bc.plotcal. If things look OK, transfer the calibration components from one table to another. As mentioned before, this is required because a BIMA target source may have a different number of spectral windows from the calibrator.

    bc.transfer(outtable='gcal.xfer',intable='gcal');
  

• Set up how the calibration components will be applied to the target source.

    bc.setapply();
  

• Apply the calibration to the target source:

    bc.correct();
  

• The calibration is now complete. Close the tool.

    bc.done();