Basic Information on mirflag

Task: mirflag
Purpose: Automated flagging of a UV data set.
Categories: calibration, uv-data

      MIRFLAG is a MIRIAD task which allows automated
      flagging of a UV data set. The task scans UV data
      on a baseline-dependent and channel-dependent basis
      to find bad data and flag them accordingly.

      Four flagging modes may be specified via options amp,
      rms, short and long.

      Amplitude-based flagging is performed when the "amp"
      option is supplied. On a per-baseline basis the median
      amplitude for a designated "good" channel is determined
      over the course of the observation, this is the
      channel-median. An effective noise measure for the "good"
      channel is made by taking the median of the absolute
      difference between channel-median and the channel
      amplitude throughout the course of the observation, this
      is the channel-diff-median. The "badness" of an amplitude
      measure in another channel is determined by how far it
      deviates from the channel-median with respect to the
      channel-diff-median and a user defined "cutoff" scaling.
      This provides a number of threshold points:

           -2*thresh    -thresh    Median    +thresh   +2*thresh
      <---------+----------+----------+----------+----------+--------->
       Probably | Possibly | Probably | Probably | Possibly | Probably 
         Bad    |   Bad    |    OK    |    OK    |   Bad    |   Bad

      Where the threshold is defined as cutoff * channel-diff-median.
      Visibilities marked as "Probably Bad" will be flagged
      immediately. NOTE: To apply amplitude-based flagging
      on small clusters visibilities marked as "Possibly Bad"
      the "short" option must also be provided.

      RMS-based flagging is performed when the "rms" option
      is supplied. In this task the amplitude RMS is measured on a
      per-baseline and per-scan basis for a designated "good" channel
      (Note: a scan will be split up if the length of the scan
      exceeds the value specified by the "gap" parameter). The median
      of these RMS values is taken as a reference. If the RMS of
      another channel (for a particular scan/baseline) exceeds the
      reference RMS by more than a factor of "rmscut" then the entire
      scan is flagged. 

      Short cluster flagging, as specified with the short option,
      flags short (+/- 60 s) sections around bad points.

      Large cluster flagging, as specified with the long option,
      searches for and flags larger clusters of bad points using
      a running sum window with length specified by the "int"
      parameter. The flagging threshold is specified with the
      "thres" option.


Key: vis
      The name of the input UV data set.  A visibility file name
      must be supplied.  Only one file may be edited at a time.


Key: stokes
      Specifies which stokes parameter/polarization to read and
      analyse (first value) and which polarizations to flag
      (subsequent values). For example, one can read and analyse
      rr and use the results to flag both rr and ll by specifying
      stokes rr,rr,ll. Defaults to read Stokes I and to flag all
      available polarizations.


Key: gap
      Used in conjunction with the "rms" option.
      Time in seconds which defines a scan gap (source changes
      also define scans). Defaults to 150 s.


Key: rmscut
      Used in conjunction with the "rms" option.
      Factor by which the RFI-free channel's scan-by-scan rms is
      to be multiplied and above which data is considered bad.
      Defaults to 3.


Key: goodch
      Number of a good (relatively RFI-free) channel to which the
      other channels are to be compared. By default, mirflag will
      attempt to find the channel with the lowest median noise.


Key: cutoff
      Used in conjunction with the "amp" option.
      Multiples of median of difference to median in data, above
      which data are suspicious. Will be multiplied by two to
      obtain a threshold above which data are certainly bad.
      Defaults to 7.


Key: int
      Used in conjunction with the "long" option.
      Width of running sum window in seconds in which to
      calculate fraction of flagged visibilities.
      1200 is reasonable for weak sources, 600 for calibrator
      observations. Defaults to 1200.


Key: thres
      Used in conjunction with the "long" option.
      Fraction of maximum of running sum, defines threshold above
      which data are deemed bad in search for large clusters of
      bad points. Defaults to 0.15.


Key: options
      Extra processing options. Several can be given, separated by
      commas. Possible values are:
        ignore  Ignore existing flags in data set, default is to
                read them.
        replace Replace existing flags in the data set with new
                ones, default is to add to existing flags.
        noapply Run only the analysis and provide a summary of the
                flagging but do not flag the data.
        amp     Switch on amplitude-based flagging (used in
                combination with the short option).
        rms     Switch on rms-based flagging.
        short   Flag short (+/- 60 s) sections around bad points.
                Without this option amplitude-based flagging is
                effectively turned off because amplitude-
                based flagging does not generate flags directly.
        long    Search for larger clusters of points.
        medsed  Subtract channel median to remove effects of a
                residual SED or poor bandpass calibration.
        medtcal Subtract bandpass median at each time-stamp to
                remove effects of poor secondary calibration.

Revision: mirflag version 0.1.2