As of Mon Nov 29 13:08:54 2021

CLIP: Flags data based on amplitudes/phases out of range


INNAME                             Input UV file name (name)
INCLASS                            Input UV file name (class)
INSEQ             0.0     9999.0   Input UV file name (seq. #)
INDISK            0.0        9.0   Input UV file disk unit #
SOURCES                            Source list
QUAL            -10.0              Source qualifier -1=>all
CALCODE                            Calibrator code '    '=>all
STOKES                             Limit tests to this STOKES
TIMERANG                           Time range to purge
SELBAND                            Bandwidth to select (kHz)
SELFREQ                            Frequency to select (MHz)
FREQID                             Freq. ID to select.
BCHAN             0.0     4096.0   Begin channel number.
ECHAN             0.0     4096.0   End channel number.
BIF               0.0      100.0   Lowest IF number 0=>all
EIF               0.0      100.0   Highest IF number 0=>all
SUBARRAY          0.0     1000.0   Subarray, 0=>all
DOCALIB          -1.0      101.0   > 0 calibrate data & weights
                                   > 99 do NOT calibrate weights
GAINUSE                            CL (or SN) table to apply
DOPOL            -1.0       10.0   If >0 correct polarization.
PDVER                              PD table to apply (DOPOL>0)
BLVER                              BL table to apply.
FLAGVER                            Flag table version: in
OUTFGVER          0.0              Output FG table version
DOBAND           -1.0       10.0   If >0 apply bandpass cal.
                                   Method used depends on value
                                   of DOBAND (see HELP file).
BPVER                              Bandpass table version
SMOOTH                             Smoothing function. See
                                   HELP SMOOTH for details.
ANTENNAS                           Antennas to consider 0=>all
BASELINE                           Baselines with ANTENNAS
UVRANGE                            Range spacings in klambda
PHSLIMIT                           Max allowed parallel phase
DOSCALE          -1.0       3.0    > 0 => scale by SU table
                                   fluxes; = 2 do spectral index
PRTLEV                             =1 -> matrix print of data
                                   and flag fraction, 0 summary
APARM                              Flux range by polarization:
                                   (1) = max. allowed parallel
                                   (2) = max. allowed cross-pol.
                                   (3) = min. allowed parallel
                                   (4) = min. allowed cross-pol.
                                   (5) = min allowed weight
                                   (6) = max allowed weight
                                   (7) Flag channels around bad
                                   (8) > 0 => do not flag cross
                                       because parallel flagged
                                   (9) > 0 => flag all channels
                                       if >= APARM(9) are
                                   (10) > 0 => flag all IFs when
                                       one is bad
BPARM                              (1) > 0 => flag parallel hand
                                       if cross hand is flagged
                                   (2) > 0 flag all Stokes if
                                       any one is flagged (!!)
BADDISK           0.0     9999.0   Disks to avoid for scratch


Task:  This task applies the calibration (optionally) to UV data and
       then examines the amplitudes and weights for data out of range.
       It writes entries in a flag table.  It can handle either
       single- or multi-source data sets but it handles only
       cross-correlations.  Use ACLIP to clip autocorrelations.

       Be aware that a very large number of flag table lines may be
       written.  Setting APARM(9)>0 will reduce this a bit but may
       flag good data.  Task UVCOP may be used to apply the flags and
       is the only task that can handle more than 30000 flags applying
       to a single time.

  INNAME.....Input UV file name (name).      Standard defaults.
  INCLASS....Input UV file name (class).     Standard defaults.
  INSEQ......Input UV file name (seq. #).    0 => highest.
  INDISK.....Disk drive # of input UV file.  0 => any.
  SOURCES....Source list.  The task loops over all sources specified.
             '*' = all; a "-" before a source name means all except ANY
             source named.
  QUAL.......Only sources with a source qualifier number in the SU table
             matching QUAL will be used if QUAL is not -1.
  CALCODE....Sources may be selected on the basis of the calibrator code
             given in the SU table.
                  '    ' => any calibrator code selected
                  '*   ' => any non blank code (cal. only)
                  '-CAL' => blank codes only (no calibrators)
                  anything else = calibrator code to select.
             NB: The CALCODE test is applied in addition to the other
             tests, i.e. SOURCES and QUAL, in the selection of sources
             to process.
  STOKES.....Specifies which STOKES parameters are examined for flux
             out of range:  ' ' => 'FULL'
               'I','Q','U','V', 'IV', 'IQU', 'IQUV'
               'RR','LL', 'RL', 'LR', 'RRLL', 'RLLR', 'RLRL'
               'XX','YY', 'XY', 'YX', 'XXYY', 'XYYX', 'XYXY'
             'HALF', 'CROS', and 'FULL' have sensible interpretations
             depending on the Stokes present in the data.  The last in
             each of the 3 rows above == 'FULL'.
  TIMERANG...Time range of the data to be copied. In order: Start day,
             hour, min. sec,  day, hour, min. sec. Days relative to
             reference date.
  SELBAND....Bandwidth of data to be selected. If more than one IF is
             present SELBAND is the width of the first IF required.
             Units = kHz. For data which contain multiple
             bandwidths/frequencies the task will insist that some form
             of selection be made by frequency or bandwidth.
  SELFREQ....Frequency of data to be selected. If more than one IF is
             present SELFREQ is the frequency of the first IF required.
             Units = MHz.
  FREQID.....Frequency identifier to select (you may determine which is
             applicable from the OPTYPE='SCAN' listing produced by
             LISTR). If either SELBAND or SELFREQ are set, their values
             override that of FREQID. However, setting SELBAND and
             SELFREQ may result in an ambiguity.  In that case, the task
             will request that you use FREQID.
  BCHAN......Begin (line) channel number.    0 => 1.
  ECHAN......End (line) channel number.      0 => highest.
             All channels are processed by only BCHAN-ECHAN are examined
             for setting flags.
  BIF........First IF to copy. 0=>all.
  EIF........Highest IF to copy. 0=>all higher than BIF
  SUBARRAY...Subarray number to copy. 0=>all.
  DOCALIB....If true (>0), calibrate the data using information in the
             specified Cal (CL) table for multi-source or SN table for
             single-source data.  Also calibrate the weights unless
             DOCALIB > 99 (use this for old non-physical weights).
  GAINUSE....version number of the CL table to apply to multi-source
             files or the SN table for single-source files.
             0 => highest.
  DOPOL......If > 0 then correct data for instrumental polarization as
             represented in the AN or PD table.  This correction is
             only useful if PCAL has been run or feed polarization
             parameters have been otherwise obtained.  See HELP DOPOL
             for available correction modes: 1 is normal, 2 and 3 are
             for VLBI.  1-3 use a PD table if available; 6, 7, 8 are
             the same but use the AN (continuum solution) even if a PD
             table is present.
  PDVER......PD table to apply if PCAL was run with SPECTRAL true and
             0 < DOPOL < 6.  <= 0 => highest.
  BLVER......Version number of the baseline based calibration
             (BL) table to appply. <0 => apply no BL table,
             0 => highest.
  FLAGVER....specifies the version of the flagging table to be applied
             to the data on input.     0 -> highest, -1 -> none.
  OUTFGVER...Flag table version to be used on output for both single-
             and multi-source data sets.  If OUTFGVER is <= 0 or
             greater than FGmax (the previously highest FG version
             number), then a new FG table will be created for the new
             flags with version FGmax+1.  This new table will also
             contain the flags applied on input (if any) from FG
             version FLAGVER.  If OUTFGVER specifies a pre-existing FG
             version, then the input flags are not copied even if
             OUTFGVER and FLAGVER are not equal.
  DOBAND.....If true (>0) then correct the data for the shape of the
             antenna bandpasses using the BP table specified by BPVER.
             The correction has five modes:
             (a) if DOBAND=1 all entries for an antenna in the table
             are averaged together before correcting the data.
             (b) if DOBAND=2 the entry nearest in time (including
             solution weights) is used to correct the data.
             (c) if DOBAND=3 the table entries are interpolated in
             time (using solution weights) and the data are then
             (d) if DOBAND=4 the entry nearest in time (ignoring
             solution weights) is used to correct the data.
             (e) if DOBAND=5 the table entries are interpolated in
             time (ignoring solution weights) and the data are then
  BPVER......Specifies the version of the BP table to be applied
             0 => highest numbered table.
             <0 => no bandpass correction to be applied.
  SMOOTH.....Specifies the type of spectral smoothing to be applied to
             a uv database . The default is not to apply any smoothing.
             The elements of SMOOTH are as follows:
             SMOOTH(1) = type of smoothing to apply: 0 => no smoothing
               To smooth before applying bandpass calibration
                 1 => Hanning, 2 => Gaussian, 3 => Boxcar, 4 => Sinc
               To smooth after applying bandpass calibration
                 5 => Hanning, 6 => Gaussian, 7 => Boxcar, 8 => Sinc
             SMOOTH(2) = the "diameter" of the function, i.e. width
               between first nulls of Hanning triangle and sinc
               function, FWHM of Gaussian, width of Boxcar. Defaults
               (if < 0.1) are 4, 2, 2 and 3 channels for SMOOTH(1) =
               1 - 4 and 5 - 8, resp.
             SMOOTH(3) = the diameter over which the convolving
               function has value - in channels.  Defaults: 1,3,1,4
               times SMOOTH(2) used when input SMOOTH(3) < net
  ANTENNAS...A list of the antennas to be examined.  All 0 => all.
             If any number is negative then all antennas listed are NOT
             to be copied and all others are.
  BASELINE...If any elements of BASELINE are non zero then all baselines
             between antennas named in ANTENNAS and those named in
             BASELINE are specified.  If ANTENNAS contains a negative
             value then all baselines NOT specified are selected.
  UVRANGE....Range of baselines in kilolambda.
  PHSLIMIT...Maximum allowed absolute value of phase in degrees for
             parallel-hand polarizations.  0 => 180.
  DOSCALE....> 0 => scale the visibilities by the fluxes found for the
                    source in the SU table.  If there are no fluxes,
                    the source is ignored.
             = 2 => scale the visibilities as above, but also
                    determine a spectral index from the SU table
                    fluxes and apply that as well.
             = 3 => scale the visibilities as above, but also
                    determine a flux at 1 GHz, spectral index, and
                    curvature from the SU table fluxes and apply them
                    as well.
             <= 0 => Examine visibilities as they come out of the
                    calibration routines - i.e. in Jy.
  PRTLEV.....<= 0 -> print summary only of flags generated
             > 0.5 -> also print matrix of fraction of data present
                     and fraction of data flagged for each IF and
  APARM......Sets an allowable range in amplitudes (Jy or normalized)
                APARM(1) = max. parallel-hand amplitude.
                           (IPOL, RR, or LL) 0 => 1.e6
                APARM(2) = max. cross-amplitude. 0 -> 1e6.
                           (QPOL, UPOL, VPOL, RL, or LR)
                APARM(3) = min. parallel-hand amplitude. 0 -> -1.e6
                APARM(4) = min. cross-hand amplitude.
                Note that sign is significant for autocorrelation data
                such as single-dish data.
             APARM(5) = min allowed weight (after calibration and
                        Stokes conversion are applied).  With
                        proper calibration, weight = 1/sigma**2 in
             APARM(6) = max allowed weight.  0 -> very large.
             APARM(7) > 0 -> extend the flag +- APARM(7) spectral
                        channels surrounding a high channel
                        Thus if APARM(7) = 5 and channel 43 is bad,
                        channels 38 through 48 will be flagged.
                        This option is allowed to extend beyond the
                        BCHAN throughh ECHAN range.
             APARM(8) > 0 => do not flag cross-polarization
                        correlators when the corresponding
                        parallel-hand ones are flagged.
             APARM(9) > 0 => Flag all spectral channels of a data
                        sample (1 baseline, 1 time, 1 IF, 1 Stokes)
                        if >= APARM(9) of the spectral channels in
                        that 1 baseline, 1 time, 1 IF, and 1 Stokes
                        are clipped.  Note - this means all
                        channels 1 through max, not just BCHAN
                        through ECHAN.
             APARM(10) > 0 => Flag all IFs rather than a single IF
                        whenever a new flag is written.
  BPARM.....(1) > 0 => flag parallel-hand polarizations if one of the
                       cross-hand polarizations is flagged
            (2) > 0 => flag all polarizations if any one is flagged.
                       **** BE CAREFUL ****
  BADDISK....A list of disks on which scratch files are not to be


CLIP:   Task to flag data whose amplitude is out of range.


     CLIP is a task which will flag all visibilities whose amplitudes
are larger than a specified limit or are smaller than a specified
limit.  Some interaction between the flagging of correlators is
     The task is the most convenient method for flagging large,
spurious visibility values.  Before serious imaging it is worthwhile
to run UVPLT in order to display the visibility amplitude as a
function of UV projected spacing.  The plot should show a relatively
smooth decline of amplitude versus spacing; the details of which
depend of the angular extent of the source and the signal to noise.
Large amplitude spikes are generally very obvious and these
visibilities can be flagged by using CLIP over all or some the
visibility spacing range.  Task WIPER may also be used to flag the
bad data seen in a UVPLT by interactive means.
     NOTE: UVPLT is normally run to display Stokes I - the vector
average of RR and LL.  This vector average can appear ok with bad,
high amplitude RR and LL of different phase or can appear low (and
bad) with ok amplitude RR and LL of different phase.  CLIP will flag
the former, but not the latter in its normal mode.  However, the
STOKES adverb allows the conversion to Stokes in CLIP before testing
the amplitudes.  For normal VLA data, if IPOL or VPOL is bad, RR and
LL will be flagged (and RL and LR depending on APARM(6)) and, if QPOL
or UPOL is bad, RL and LR will be flagged.
     For a bright radio source where the correlated flux density in
the source obscures possible amplitude spikes, the following scheme is
advised.  After getting a reasonably CLEAN image, subtract the clean
components from the visibility data using UVSUB.  The data will now be
more dominated by noise since the majority of flux density from the
source has been removed, and the subsequent use of UVPLT and CLIP can
flag bad data.  Do not forget to add back in the clean components
using UVSUB in the opposite sign in order to get back to the original
visibility data.
     After execution CLIP will report on the number of visibilities
which have been flagged.  The correlator order (1,2,3,4) corresponds
to (RR,LL,RL,LR).


     Set the uv-spacing range (in klambda) appropriately for sources
which are dominated by large and small-scale structure.

  (1)  Clip any parallel hand vis. amplitude greater than this value.
       0 => no upper limit. (10**6)
  (2)  Clip any crossed-hand vis. amplitude greater than this value.
       0 => no upper limit. (10**6)
  (3)  Clip any parallel hand vis. amplitude less than this value.
       0=>no lower limit.        (-10**6)
  (4)  Clip any crossed-hand vis. amplitude less than this value.
       0=>no lower limit.        (-10**6)
  Sign is significant - autocorrelation data may have either sign while
  cross-correlation data always has positive amplitude.
  (5)  Clip any data with weights below this value. 0 => no lower
       limit  (-10**12)
  (6)  Clip any data with weights above this value. 0 => no upper
       limit  (+10**12)
  (8)  <= 0 => Flag crossed-hand correlators if parallel hand
       correlator(s) are flagged.
       > 0  => Do not flag crossed-hand correlators if parallel hand
       correlator(s) are flagged.
  (9)  > 0  => Flag all spectral channels of a given IF and Stokes if
       APARM(8) or more of them exceed the clip limit (within a single
       sample - i.e. 1 baseline, 1 time)
       <= 0 => Flag spectral channels individually.
  (10) > 0  => Flag all IFs when one is bad - likely to be excessive
               in multi-channel synthesis
       <= 0 => Flag only the specific IF that apperas to be bad

Use UVFND before CLIP if you wish to see which data will be flagged.