AIPS HELP file for CLIP in 31DEC24
As of Sun Apr 28 22:21:43 2024
CLIP: Flags data based on amplitudes/phases out of range
INPUTS
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
'PDIF' special value for
RR-LL, VV-HH
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
DOREAL -1.0 1.0 > 0 => below ranges apply to
abs(real), abs(imaginary)
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
clipped
(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 (!!)
Flag on average BCHAN-ECHAN :
(3) = max. allowed parallel
(4) = max. allowed cross-pol.
(5) = min. allowed parallel
(6) = min. allowed cross-pol.
(7) phase limit parallel
BADDISK 0.0 9999.0 Disks to avoid for scratch
HELP SECTION
CLIP
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.
Adverbs:
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'
'VV','HH', 'VH', 'HV', 'VVHH', 'VHHV', 'VHVH'
'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'.
'PDIF' is a special value to test APARM(1) and (3) on
(RR - LL) / 2 or (VV - HH) / 2.
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
corrected.
(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
corrected.
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
SMOOTH(2).
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
polarization
DOREAL.....> 0 => APARM(1), APARM(2), BPARM(3), BPARM(4) apply to
abs(real part), abs(imaginary part) of the vis
rather than amplitude. In this case APARM(3),
APARM(4), BPARM(5), BPARM(6) are set to -1.E6
and PHSLIMIT is set to 180.
<= 0 => clipping is on amplitude.
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
1/Jy**2.
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 ****
...... Set an allowable range in amplitudes (Jy or normalized) of
the vector average of BCHAN-ECHAN
BPARM(3) = max. parallel-hand amplitude.
(IPOL, RR, or LL) 0 => 1.e6
BPARM(4) = max. cross-amplitude. 0 -> 1e6.
(QPOL, UPOL, VPOL, RL, or LR)
BPARM(5) = min. parallel-hand amplitude. 0 -> -1.e6
BPARM(6) = min. cross-hand amplitude.
Note that sign is significant for autocorrelation data
such as single-dish data.
BPARM(7) = max allowed phase of parallel hands (deg)
0 -> 1000
BADDISK....A list of disks on which scratch files are not to be
placed.
EXPLAIN SECTION
CLIP: Task to flag data whose amplitude is out of range.
Related Programs: PRTUV, UVFLG, UVSUB, UVPLT, WIPER
PURPOSE
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
possible.
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).
COMMENTS
UVRANGE
Set the uv-spacing range (in klambda) appropriately for sources
which are dominated by large and small-scale structure.
APARM
(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.