AIPS NRAO AIPS HELP file for FLGIT in 31DEC18



As of Wed Jan 17 4:03:07 2018


FLGIT: Flags data based on the rms of uv-data spectra

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 #
OUTNAME                            Output UV file name (name)
OUTCLASS                           Output UV file name (class)
OUTSEQ           -1.0     9999.0   Output UV file name (seq. #)
OUTDISK           0.0        9.0   Output UV file disk unit #.
OUTFGVER         -1.0              If >=0 write FG table instead
SOURCES                            Source list
QUAL            -10.0              Source qualifier -1=>all
CALCODE                            Calibrator code '    '=>all
TIMERANG                           Time range to purge
SELBAND                            Bandwidth to select (kHz)
SELFREQ                            Frequency to select (MHz)
FREQID                             Freq. ID to select.
BCHAN             0.0     9999.    First channel selected.
ECHAN             0.0     9999.    Last channel selected.
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
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.
OPCODE                             'MWFL' median window
                                   else fit linear function
APARM                              Cutoff parameters: 1. Clip
                                   2. Flag in BL regions
                                   3. Flag in signal regions
                                   4. Flag flux > A(4) * RMS
                                   5. Flag Re/Im > A(5)*RMS
                                   6. VPOL clip level
                                   7. Width of median window
                                   8. Number median pts averaged
                                   9. Flag all samples with
                                       |u| < APARM(9) lambda
                                   10. > 0 => flag cross if
                                      parallel bad
BPARM                              1. Flag BPARM(1) channels
                                      around a bad channel
                                   2. Flag all channels if more
                                      than BPARM(2) are bad
ICHANSEL                           Select channels to fit: NOTE
                                   this is start,end,increment
                                   and IF for each region
ORDER             0.0        1.0   Order of fit line (0 -> DC)
BADDISK           0.0     9999.0   Disks to avoid for scratch

HELP SECTION

FLGIT
Task:  This task applies the calibration to spectral-line data and then
       makes and subtracts a linear fit to the real and imaginary
       spectra using a specified set of the spectral channels or
       subtracts a median window filtered version of the spectrum.  If
       the residual exceeds a noise-based cutoff the channel is
       flagged.  The user specifies the threshold appropriate for a 10
       sec integration and the test is done taking into account the
       weight of the data point.  Different cutoff levels are applied
       to channels specified by BOX and channels not included in BOX.
       Be conservative (i.e. 6 - 8 times the theoretical sigma is a
       good default choice).  Multiple sources may be processed in a
       single run and calibration and editing, if present, should be
       applied, particularly for the linear baseline method.  It is
       important to have a good enough bandpass calibration so that
       the linear fit makes some sense.  A relatively narrow median
       window filter may reduce the need for bandpass calibration.

       You may now choose between writing out the edited data in a new
       data set or writing a flag table.  If a lot of isolated
       channels are flagged, an FG table may actually exceed the size
       of the initial UV data set.
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.
  OUTNAME....Output UV file name (name).     Standard defaults.
  OUTCLASS...Output UV file name (class).    Standard defaults.
  OUTSEQ.....Output UV file name (seq. #).   0 => highest unique
  OUTDISK....Disk drive # of output UV file. 0 => highest w room
  OUTFGVER...< 0 => write a new UV data set
             >= 0 => write a FG table attached to the input file of
             version OUTFGVER.  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.
  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.
  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......First frequency channel selected. 0 => 1.
  ECHAN......Last channel selected. 0 => all
  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 and, if FLGIT generates any flags,
             also written.  > 0 => apply version FLAGVER.
             < 0 or > max => apply none; = 0 apply maximum FG version
  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).
  OPCODE.....'MWFL' => use the median window filter method; otherwise
             use the spectral baseline method.
  APARM......Clipping and flagging parameters:
             APARM(1) Maximum amplitude allowed in the spectrum before
                fitting.  Any channel exceeding this is flagged in
                advance.
             APARM(2) Max. residual flux allowed for channels within the
                baseline fitting regions for unity weight.  This is
                adjusted by the actual weights to account for S/N.
                This should be 6-8 times the rms noise for a single
                channel in a 10 second integration.  Any channel
                exceeding this in amplitude after the spectral baseline
                is subtracted will be flagged on output.
             APARM(3) Max residual allowed in the non-baseline fitting
                regions of the spectrum.  Any channel exceeding this in
                amplitude after the spectral baseline is subtracted will
                be flagged on output.
             APARM(4) Flag all channels having residual flux > APARM(4)
                * RMS.  0 => 6.
             APARM(5) Flag all channels having Real or Imaginary parts >
                APARM(5) * RMS.   0 => 5.
             APARM(6) Maximum amplitude allowed in V polarization; any
                channel exceeding this is flagged in advance of the
                baseline fitting or median filtering.  0 -> infinite
             APARM(7) The width of the median window in channels.
                0 -> 5.  An odd number is recommended,
             APARM(8) The number of channels in the median window which
                are averaged to form the "median".  0 -> 1, an odd
                number < APARM(7) is recommended.
             APARM(9) All samples having abs (u) < APARM(9) will be
                flagged  before fitting.
             APARM(10) > 0 => flag cross-hand polarizations if
                parallel are flagged.
  BPARM......1. Extend the flag of a channel +- BPARM(1) channels
                around the bad channel.  Thus if BPARM(1) = 5 and
                channel 43 is bad, channels 38 through 48 will be
                flagged.
             2. If more than BPARM(2) channels are bad in any
                polarization/IF, flag all channels in that
                polarization/IF.  0 -> a large number of channels.
  ICHANSEL...Select up to 20 groups of channels/IF(s) to fit as sets
             of (Start,end,inc,IF), i.e., ICHANSEL = 6,37,1,0,
             92,123,1,0 for two regions applyingto all IFs.  The first
             group for which ICHANSEL(2,i) <= 0 ends the list.
             Defaults: Any IF having no group assigned to it, gets a
             group including all channels from BCHAN through ECHAN.
             ICHANSEL(1,j) and ICHANSEL(2,j) are restricted to be
             within the range BCHAN through ECHAN
             ICHANSEL(4,j) <= 0 => this group applies to all IFs.
  ORDER......Normally the fit should be done with a first order
             polynomial, namely a DC term and a slope.  If only one box
             is used, the slope may not be adequately defined and a
             simple DC term for the real and for the imaginary parts
             would be more reliable.
  BADDISK....A list of disks on which scratch files are not to be
             placed.

EXPLAIN SECTION

FLGIT: Task which subtracts continuum from channels in UV-plane to
       determine entries in a flag table from scatter of residuals.

Documenter:  Juan M. Uson (juson@nrao.edu)

			PURPOSE

FLGIT fits and removes the continuum emission in the UV-plane.  FLGIT
fits to the real and imaginary parts of the visibility.  The residuals
are checked in order to generate flags if the scatter is excessive.
This is done in order to clean-up the data prior to the generation of
BP tables to be used for calibration.  The fit is performed using the
specified channels.

FLAGGING of the data on the basis on discrepancy in the fit is performed
using FLUX: the maximum error allowed (Jy).  This is very useful for
removing narrow band interference.  The number specified is the limit
per unit weight.  This is adjusted by 1/sqrt[visibility weight] to
correct for integration time differences.  If FILLM has been run so that
the weight of the data does NOT take into account the system temperature,
this weight is normally (tint/10 sec).  FLGIT will assume this to be the
case.  If not, you might have to adjust FLUX accordingly although in
the case of the VLA, the Tsys values are only OK as relative values for
any given antenna over the course of the run and are not absolutely
calibrated (they can be off by factors of up to three depending on the
actual frequency used).

Channel selection for fitting and flagging is done with NBOXES pairs of
channel numbers given in BOX e.g.:
     NBOXES=3  ;  BOX=2, 6, 9, 12, 14, 14
specifies that channels 2, 3, 4, 5, 6, 9, 10, 11, 12, and 14 are used
for the fit and then examined for the rms of the residual.  Note that the
flagging is applied to all channels of the visibility point being examined
(e.g., baseline 7 with 8, Stokes LL, all channels for a given time stamp).
This is done in order to obey the assumptions underlying the calibration
of the data.

Notes on STRATEGY:  FLGIT should be used to clean-up RFI from the multi-
source data prior to generating the BP tables which will be used for the
calibration.  However, running the task efficiently requires an initial
BP table as otherwise the bandpass shape will determine the residuals to
the fit to a large extent.  This initial BP table can be generated with
SOLINT=-1 (in BPASS).  If RFI is pervasive, even this initial table can
be so contaminated that it will induce large residuals in most visibility
points.  In that case, start with a high value for FLUX in order to
eliminate the worst part of the data, generate a new BP table and iterate
as needed.

FLGIT will report to the message file on visibilities present as well as
on the percentage that it flags.  It also reports on how many times any
given channel triggered a flag.  Notice that any one visibility might be
flagged on triggers by several channels.  Use the output to decide on
threshold level and trigger channels as discussed in the next paragraph.

If a channel suffers heavily from RFI, it might cause a great number of
flags.  If you need that channel to do the science, you might have to
accept the flagging of a large number of visibilities in order to
generate an interference-free bandpass table.  However, if that
particular frequency is not needed for the research, it might be best to
exclude it from the fit and flagging.  As long as the data have been
Hanning-smoothed (on-line or off-line), the RFI should not spread its
effect to neighboring channels and all that will be lost will be that
particular one, which will have to be ignored in the spectral cube.
Other tasks can be used to help with a contaminated, but needed, channel.
(See for example UVNOU).

FLGIT will work on single-source data but it is best to use UVLIN on
such data.

			REFERENCES

See Cornwell, Uson and Haddad (Astron. Astrophys. 258, 583; 1992) for a
detailed discussion of UVLIN, which includes estimates of errors.


AIPS