autoflag - Module autoflag

2.1 autoflag - Module autoflag

Module for automatic flagging of synthesis data
include autoflag.g

Description The autoflag module provides automatic synthesis flagging capabilities within CASA. The primary purpose of this module is to flag data inside a MeasurementSet using a number of different algorithms and heuristics.

The facilities of the autoflag module are made available in Glish by including the following script:

- include ’autoflag.g’
T

where a hyphen precedes user input. The Glish response is indicated without the prompt.

An autoflag tool is created and attached to a specified measurement set as indicated in the following example:

- af:=autoflag(’3C273XC1.MS’)

A variety of algorithms (called methods in this context) can be applied for any given autoflag tool. A setdata method allows a user to apply setmethods to the whole measurement set with default parameters or to a subset of the measurement set by specifying parameters. Individual methods are set up in advance by calling Glish functions of the tool, i.e.: af.setmethod(parameters). Afterwards, a call to af.run(options) actually applies all the specified methods simultaneously. Here is an example:

- af:=autoflag(’3C273XC1.MS’)
- af.setdata()
- af.settimemed(thr=6,hw=5)
Added method 1: timemed (TimeMedian)
   *thr         = 6
   *hw          = 5
    rowthr      = 10
    rowhw       = 6
    column      = DATA
    expr        = ABS I
    debug       = F
    fignore     = F
T
- af.setuvbin(nbins=100,thr=.01)
Added method 2: uvbin (UVBinner)
   *thr         = 0.01
   *nbins       = 100
    plotchan    = F
    econoplot   = T
    column      = DATA
    expr        = ABS I
    fignore     = F
T
- af.settimemed(thr=5,hw=5,expr="- ABS XX YY")
Added method 3: timemed (TimeMedian)
    thr         = 5
   *hw          = 5
    rowthr      = 10
    rowhw       = 6
    column      = DATA
   *expr        = - ABS XX YY
    debug       = F
    fignore     = F
T
- af.run(trial=T)
   lots of interesting messages
-

Here, three methods -- a UV binner and two time-median filters -- are set up and executed. Note the following crucial points:

The setmethod() functions respond with a summary of the parameters with which the method will be run. All parameter have reasonable defaults. Parameters for which you have specified an explicit non-default value are marked with an ‘‘*’’ symbol.
You may set up multiple instances of a method, using different parameters for each instance. In the above example, two timemed methods are set up. The first one is applied to |I| , the second one -- to |XX|-|Y Y |.
Most methods perform flagging based on some real value derived from a set of complex correlations, e.g. |I|, or |XX| - |Y Y |. You can specify how the value is derived by using the expr parameter. This parameter is either a string or an array of strings. A single string will be automatically split at whitespace, so "ABS XX" and ’ABS XX’ are fully equivalent. Currently, the following types of expressions are recognized:
func CC
  --- real function of a complex correlation. E.g. "ABS XX" for |XX|.
+/- func C1 C2
  --- sum/difference of functions of two correlations. E.g. "- ABS RR LL" for |RR|-|LL|.
func +/- C1 C2
  --- function of a sum/difference of two correlations. E.g. "ARG - XX YY" for arg(XX - Y Y ).
func I
  --- I is used to specify Stokes I. Depending on polarization frame, it is equivalent to either XX + Y Y or RR + LL. |I| ("ABS I") is in fact the default expression for all methods.

The following functions are currently recognized: ABS, ARG, RE, IM, NORM. Any correlations present in the measurement set are recognized.
The column parameter specifies which measurement set column to use. Possible values are DATA, MODEL or CORR for corrected data.
All methods by default honor pre-existing flags (as determined by the FLAG and FLAGROW columns), in the sense that flagged values are omitted from all calculations. Methods may be asked to ignore existing flags via the fignore parameter. The reset option to autoflag.run clears all pre-existing flags prior to a flagging run.
For each flagging run, autoflag will automatically produce a graphical flagging report, consisting of a summary and several plots showing the distribution of flags by baseline, antenna, frequency, time, etc. By default, this report is written in PostScript format to a file named flagreport.ps. However, the devfile parameter of autoflag.run() can be used to redirect this output to a different file or a different PGPlot device.
If your measurement set contains different fields and/or spectral windows (or, more generally, different data description IDs), autoflag will automatically treat it as a set of disjoint chunks. Flagging is performed independently within each chunk (i.e. independently for each spectral window, field, etc.)
autoflag will attempt to manage its memory consumption to stay roughly within the meximum physical memory specified in your .aipsrc file. If you find your system swapping to disk when running autoflag, you can improve performance by using a reduced memory setting. Conversely, if a lot of memory remains free during an autoflag run, performance may be improced by increasing the setting.

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