As of Sat Jun 22 16:53:58 2024

OBITMAP: Make/Clean images with OBIT task Imager


DOWAIT           -1.0        3.0   > wait for and display output
DOCRT            -4.0      132.0   > 0 display output on
                                   terminal, else message file
OBITVERS          0.0              =2 for python2, else 3
INNAME                             Input UV data (name)
INCLASS                            Input UV data (class)
INSEQ                              Input UV data (seq. #)
INDISK                             Input UV data disk drive #
STOKES                             Desired Stokes: I, Q, U, or V
BCHAN            0.0     8192.0    Low freq. channel 0 for cont.
ECHAN            0.0     8192.0    Highest freq channel
NCHAV                              Number of chan. to average.
CHINC                              Channel incr. between maps.
BIF                                First IF in average.
EIF                                Last IF in average.
OUTNAME                            end of output image name
OUTSEQ          -1.0     9999.0    Output seq. no.
OUTDISK                            Output image disk drive #
FOV           1.E-6                Radius of the desired field
                                   of view (in degrees)
CELLSIZE         0.0               (X,Y) size of grid in asec
UVTAPER         0.                 (U,V) Gaussian taper
                                     units are kilo-lambda
ROBUST                             Robustness power: -5 -> pure
                                   uniform weights, 5 => natural
NITER              0.0             Maximum # of Clean components
FLUX                               Stop Clean when max residual
                                   < FLUX
IM2PARM                            (1) > 0 => automatically find
                                       Clean boxes - do this!
PRTLEV            -1.0         5.0 Amount of messages desired:
                                   0 -> 2.
DOTV              -1.0       512.0 Display residuals on OBIT TV
NTHREAD            1.0             Maximum number threads to use
BADDISK           -1.0      1000.0 Disks to avoid for scratch.


Type:  "Verb"
 Use:  The OBIT package of astronomy software written by Bill Cotton
       of NRAO Charlottesville is available at some institutions.  If
       it is available and in your $PATH, then you may use this verb
       to run a simplified version of the OBIT imaging task Imager.
       It does not offer multi-scale, SDI, peeling, self-cal,
       re-centering or other complicated options of Imager.  It does a
       multi-facet, DO3DIM false image, followed by a FLATN.  The
       Clean components are retained with the flattened image and may
       be used for self-cal.  It limits Imager to using pre-calibrated,
       single-source data.

       The log and run file for each execution of OBITMAP will appear
       in your $HOME area.  The UV work file will appear on OUTDISK,
       named with the source name, a class of 'Imager', and a new
       higher sequence number.

       The input adverbs are saved with a TPUT equivalent when this
       verb is invoked.

       The Explain file attached contains the full help file for
  DOWAIT.....A log file is written into your $HOME area from the obit
             task.  If DOWAIT <= 0.0, AIPS does not wait for the OBIT
             task Imager and you will need to look at the log file
             with more, less, cat, or an editor.  If 0 < DOWAIT < 2,
             the messages from Imager will appear as the OBIT task
             generates them.  If DOWAIT >= 2, AIPS will wait for
             Imager to finish and then echo the log file under control
             of DOCRT.
  DOCRT......>  0  Use the terminal, the full length of the log file
                   lines will appear so widen it at least a little.
             <= 0  Write log file to message file at level 0 (no echo
                   to the terminal).  Some messages may get truncated.
             DOCRT is not used when DOWAIT < 2.
  OBITVERS...OBIT now is designed to run on python 3 or 2.7.  If you
             have a newer version of OBIT (post 01-Apr-2021) then you
             may want the python3 version which is now the default.
             If you need the older version, set OBITVERS=2.
  INNAME.....Input UV data file (name).       Standard defaults.
  INCLASS....Input UV data file (class).      Standard defaults.
  INSEQ......Input UV data file (seq. #).     0 => highest.
  INDISK.....Input UV data file disk drive #. 0 => any.
  BCHAN......First channel number to image, 0=>1.  Channel numbers are 1
             relative as defined in the input data file.
  ECHAN......Highest channel number to to include in image,
             0 => max   The actual # of output channels will be
                  (BCHAN-ECHAN+1-NCHAV)/CHINC + 1
             Thus, ECHAN is the highest channel in the input averaged
             into the output and is the highest output channel only if
             NCHAV and CHINC are 1.
  NCHAV......NCHAV is the number of channels to be averaged together
             in in the gridding process.  0 => 1.  If this value is less
             than the total number of channels, then a multi-channel
             image will result.
  CHINC......Number of input channels to skip between images. 0 => 1
  BIF........The lowest numbered IF to include.  Multiple IFs can be
             included in a bandwidth synthesis average.   0 => 1.
  EIF........The highest numbered IF to include. 0 =>highest.
             Note: not all data sets will have IFs.
  OUTNAME....The output image name will be the source name + Stokes +
             the contents of OUTNAME in that order.
  OUTSEQ.....Output sequence number. 0 => highest to produce unique maps
             and beam.  Note that this will produce, potentially, maps
             and beams with a variety of sequence numbers depending on
             what files are already on disk.  If OUTSEQ > 0, all images
             and beams for all fields are assigned that sequence number
             and pre-existing files are reused.  An error will occur if
             the pre-exsitng files are of different sizes than the ones
             currently being requested.
  OUTDISK....The disk drive # of output images.  0 => highest with space
             Image and Beam go on same disk.  Note:  OUTCLASS='xCLnnn'
             where x=Stokes, nnn=field number and 'xBMnnn' is the beam
             CLASS.  If NITER=0, OUTCLASS='xIMnnn'
  FOV........Radius of the field-of-view to be imaged in degrees.
             NO DEFAULT.
  CELLSIZE...(X,Y) pixel separation in asec.  0,0 => let Imager
             choose which is a reasonable option.  Imager will choose
             the IMSIZE for you in any case.
  UVTAPER....(U,V) Gaussian taper (kilo-lambda) at 30 percent level
             0,0 => no taper.
  ROBUST.....Briggs' "robustness" parameter.  "Uniform" weights are
             tempered by a constant being added to the local density of
             weights.  ROBUST = -4 is nearly pure uniform weighting,
             ROBUST = +4 is nearly pure natural weighting.  Use of this
             option requires a second array in the "AP" memory and may
             therefore force the data to be sorted.  The option is
             turned off if ROBUST < -7 and uniform weighting is turned
             off is ROBUST > 7.  See HELP ROBUST - the AIPS ROBUST
             differs numerically from that of Briggs.
  NITER......Clean iteration limit. 0 => no Cleaning.
  FLUX.......Stop Clean when abs(resid. image max) < FLUX (Jy)  If FLUX
             < 0 then Clean stops at first negative Clean Component.
  IM2PARM....(1) > 0 => automatically find Clean boxes - Bill Cotton
                        recommends this option highly.
                 <= 0 => Clean the full inscribed circle.
  PRTLEV.....Level of messages desired.  0 -> 2 which is the usual
             IMAGR level of messages.  Use 1 for a modest set of
             messages and 3 for more than you would normally want.
  DOTV.......> 0 => try to use ObitView to view and interact with the
                    imaging process.  ObitView needs to be running for
                    this to work probably.
             <= 0 => don't try.
  NTHREAD....Use this number of threads when executing Imager.  0 ->
             1.  Imager will make excellent use of multi-threading.
  BADDISK....This array contains the numbers of disks on which it is
             desired that scratch files not be located.  BADDISK has no
             effect on input and output maps.


        Note that most of these capablities are not offered by
        the OBITMAP verb.  The full Imager help file follows:

Imager Imaging task for radio interferometry data
Type:  Task
 Use:  Batch processing of radio interferometry data

   The products of this task are a CLEAN image.
Unless otherwise specified, a fly's eye pattern of
fields with circular CLEAN boxes will be used to cover the specified
field of view (FOV).  When processing is finished, the CLEAN images
are "flattened" onto a single image.
   If multiple sources are being processed, some failures are allowed.
In this case, the error messages will be displayed and the Status in
the PS table set to "Failed  " rather than "Done    ".
   Greisen variant of Steer-Dewdney-Ito CLEAN implemented via
   If BLFact > 1.0 then the input data will be subjected to a
baseline dependent time averaging.

  DataType..'FITS' or 'AIPS'  type of input
  inFile.....FITS input uvdata if Type=='FITS'
  inName.....Input multisource UV data file
  inClass....Input UV data file (class).      Standard defaults.
  inSeq......Input UV data file (seq. #).     0 => highest.
  inDisk.....Input UV data file disk drive #. 0 => any.

       Data selection
  doPS.......If true, the PS (Processing Summary) table,
             if it exists, is searched and fields already processed,
             present and Status 'Done' will not be reprocessed.
  Sources....List of sources (pointings) to be processed.
             '*' or blank = 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.  Qual affects the selection of both the list of
             sources and the list of calibrators.
  souCode....Calibrators 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 souCode test is applied in addition to the
             other tests, i.e. Sources and Qual, in the
             selection of sources to process.
  timeRange..Time range of the data to be processed. In order:
             Start and end times in days relative to ref. date.
             Use  dhms2day to convert from human readable form
  Stokes.....Stokes parameters to process.
             'I' = Stokes I only, 'IQU' = also Q, U
             'RR', 'LL' also.
             '    ' => I, Q, U,
             'F'=> formal I (both orthogonal Stokes needed)
  FreqID.....Frequency identifier to select , <=0=>any
  BChan......First channel number to image, 0=>1.  Channel numbers are 1
             relative as defined in the input data file.
  EChan......Highest channel number to to include in image,
             0 => max
  RChan......Channel number to restart CLEAN
             0 => BChan
  chInc......Increment between channels to image in spectral cube.
             This is after averaging due to BLchAvg
  chAvg......Number of channels to average, 0=> all
             This is after averaging due to BLchAvg
  BIF........First IF to process. 0=>1
  EIF........Highest IF to process 0=> do BIF to highest.
             Note: not all data sets will have IFs.
  subA.......Sub-array number to use. 0=>all.
  doCalib....If true, apply SN or CL table
  gainUse....CL/SN table version number to apply. 0=> highest.
  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
             Imager uses doBand as the nearest integer; 0.1 is therefore
             no correction.
  BPVer......Specifies the version of the AIPS BP table to be applied
                0 => highest numbered table.
               <0 => no bandpass correction to be applied.
  flagVer....AIPS FG table to use for editing. 0 => highest.
  doPol......>=1 apply polarization calibration
  Alpha......If != 0.0 then correct data by spectral index Alpha before
             imaging and self calibration.
             -0.7 is typical for synchrotron.
  BLFact.....Baseline dependent time averaging factor.
             If BLFact>1.00 then the input data is time averaged in
             a baseline dependent fashion and written to the output
             data for further processing.
             Use the following parameters:
               BLFact = Maximum allowable amplitude loss due to time
               BLFOV = Field of view over which the amplitude distortion
                  is not to exceed BLFact.
               The lesser of solPInt and solAInt is used for the
                  maximum averaging time.
                  If both are zero, 1 min. is used
             This option can substantially reduce the data volume and
             reduce processing time.
             A value between 1.004 and 1.01 give a good tradeoff between
             dynamic range and data reduction.
  BLFOV......The radius of the field of view over which baseline
             dependent averaging is not to distort amplitudes by more
             than BLFact. Defaults to FOV.
  BLchAvg....If doing baseline dependent averaging then also average
             selected channels by no more than will give bandwidth
             smearing of BLFact.
  doFull.....If True make full field (flattened) image

      Output files
  outDType..'FITS' or 'AIPS'  type of output
             Defaults to DataType.
  outFile....Ending of output FITS image file name
             filename = source_name+Stokes+outFile
  outName....Ending of output AIPS Image Name,
             Name = source_name+Stokes+outName
  outClass...Output image class.  Default = 'ICLEAN'
             Only the last 5 characters given are used and the
             first is replaced with the Stokes.
             Output image name = pointing name (SOURCES)
             The output CLEAN image will be used during
             execution as the residual image.
  outSeq.....Output image sequence number.
  outDisk....The disk drive # of output images.  0 => highest
             with space (note: map and Beam go on same disk.
  CCVer......CC table version number for continuum data only.
             For line data the channel number is used for the
             version number.
  out2File...Ending of output FITS UV data file name
             filename = source_name+Stokes+out2File
             Defaults to 'UV'
             This file will contain the last selected data
             with any calibration tables.
  out2Name...Ending of output AIPS UV data Name,
             Name = source_name+Stokes+out2Name
             Defaults to 'UV'
             This file will contain the last selected data
             with any calibration tables.
  out2Class..Output uv data class.  Default = 'IMAGER'
  out2Seq....Output AIPS uv data sequence number.
  out2Disk...The disk drive # of output uv date.  0 => highest
             with space. default  = outDisk

   The following control imaging:
  FOV........Radius of the desired field of view in deg..
  NField.....Optional parameter to specify fields and overrides
             the FOV parameter.  Up to 64 may be specified as
             parameters; you should have a good reason for doing
             this as the default behavior is usually what is
  xCells     [optional] Image cell spacing in X in asec.
             If left 0 then the program will compute the value
             from the data.  All fields use the same value.
  yCells     [optional] Image cell spacing in Y in asec.
             If left 0 then the program will compute the value
             from the data.  All fields use the same value.
  nx.........[optional] Number of x pixels in each field specified.
  ny.........[optional] Number of y pixels in each field specified.
  RAShift....[optional] RA shift (asec) per field
  DecShift...[optional] Dec shift (asec) per field
  Catalog....Name of FITS file containing outlier catalog
             Default  NVSSVZ.FIT
             This must be in the form of an "AIPS VZ" table.
             'None' =. Use no outliers
  OutlierDist..max. distance from pointing to include (deg)
               default = 10
  OutlierFlux..min. estimated flux density (Jy)
                 default = 0.05
  OutlierSI....Spectral index to use,   default = -0.7
  OutlierSize.. Size in pixels of confusing fields, default 50
                NB: This should not be so large as to cause the
                outlying fields to be larger than the fields tiling
                the FOV or the program may die.
  UVTaper....(U,V) Gaussian taper (kilo-lambda) at 30 percent level
             as (major, minor axis, position angle)
  UVRange....(Minimum,Maximum) baseline (kilo-lambda) to
  Robust.....Briggs' "robustness" parameter.  "Uniform" weights are
             tempered by a constant being added to the local density of
             weights.  Robust = -4 is nearly pure uniform weighting,
             Robust = +4 is nearly pure natural weighting.  Use of this
             option requires a second array in the memory and may
             therefore force the data to be sorted.  The option is
             turned off if Robust < -7 and uniform weighting is turned
             off is Robust > 7.
  WtBox......(U,V) box size for weighting.  This is the support radius
             over which a sample is counted.  I.e., the sample or its
             weight is counted over an area 2*WtBox+1 cells on each side
             in the UV plane, where the UV cell size is (after
             correcting units) given by 1 / (UVSIZE(i) * Cellsize).
  WtFunc.....If WtBox > 0, WtFunc controls how the samples are counted
             as a function of u and v (WtFunc < 0) or of radius (WtFunc
             > 0).  In the latter case, the function is 0 for radius >
             WtBox.  Functions are pill box, linear, exponential, and
             Gaussian for abs(WtFunc) = 1-4, resp.  0 -> 1.
  doFull.....Make full field (flattened) image?
             Otherwise only make facets and leave them.
  doRestore..Restore CCs to images?
  do3D.......If True, make the reference pixel in each facet tangent
             to the celestial sphere, else on single tangent plane.
             If False, CLEAN components are left on flattened image.

   The following control CLEANing:
  CLEANBox...A 4x50 array with the specification of a search
             Box(1,i)=-1 indicates a circle of radius Box(2,i)
             pixels centered on (Box(3,i), Box(4,i))
             Box(1,i) >= 0 indicates a rectangular box.
             0 => full and inner fields.
             If a round box is specified with pixel positions<=0 then
             the box will be centered on the center of the image.
             Note: the default boxes are set on the basis of
             the image size, tilling pattern and autoWindow
  autoWindow.If true, automatically set boxes around significant
             emission. (Highly recommended)
  Gain.......The CLEAN loop gain.  0 => 0.10.
  minFlux...Stop Clean when abs(resid. image max) < minFlux (Jy)
            If minFlux < 0 then Clean stops at first negative Clean
  minPatch..Minimum half width of the portion of the beam
            which is used in the minor CLEAN. Default 500
  Niter.....CLEAN iteration limit.  0 => 1500
  ccfLim....Limit CLEAN in each major cycle not to CLEAN below
            ccfLim times the initial residual peak.
            If using SDIGain, set to the maximum value of 0.9.
  SDIGain...Fraction of pixels in the upper half of the pixel
            histogram to trigger SDI mode. <=0 -> no SDI CLEAN.
            If this test is satisfied then all pixels above
            a threshold determined will be the site of a new CLEAN
            component with a value depending on the local density
            of pixels above this threshold.
            This is the Greisen implementation of  Steer-Dewdney-Ito
            A value of 0.1 is a reasonable initial value
  Beam......CLEAN restoring beam major, minor axis size in asec and
            the position angle.  If zeroes, fit beam.
  Reuse.....If >0 then each cycle of self cal after the first will
            begin with all summed components whose abs value exceeds
            Reuse*RMS(Field 1). Default 10
  autoCen...If the sum of the clean components within 1.5 pixels
            of any pixel exceeds autoCen and is not within 0.05 of a cell
            of a pixel then the image is  remade and deconcolved with the
            bright sources (>autoCen, one per facet) on a pixel.
            This is necessary to achieve high dynamic range.
            If the initial dirty image has a pixel brighter than autoCen
            then it presumes that the final image will need centering and
            the initial CLEAN is stopped at minFlux=0.1*autoCen
  Cmethod...This determines the method used to compute the
            model visibility values.
            'DFT' uses the direct Fourier transform, this
               method is the most accurate.
            'GRID' does a gridded-FFT interpolation model
            '    ' allows the program to use the fastest
  PBCor......Apply Frequency dependent primary beam corrections?
  antSize....Diameter of antenna for PBCor (m), default = 25

  CCFilter...Clean component filtering parameters.
             If [0] > 0.0 then for each CLEAN conponent, the
             sum of all components within CCFilter[1] cells
             is determined, and if less than CCFilter[0], the
             component is rejected.
             This is done after all self-calibration, CLEANing is done
             and if necessary the residuals remade.
  maxPixel...The maximum number of pixels that are searched for
             components in each major cycle.  < 3000
             => 20050.  This number affects the cpu usage significantly.
             Too many causes the task to search over many points it will
             never use.  Too few causes the task to do many more small
             major cycles, also at great expense.  Use this with great
             caution, but big wins are possible using larger sizes on
             very large Cleans.

                          Selfcal info
              Either phase only or amplitude and phase or both types of
              Self calibration can be performed.  If both are done, then
              phase calibration is done first and applied to the data before
              Amp & Phase self calibration.  In any case, there will be an
              SN table attached to the output uv data which is needed to
              fully calibrate it.
  maxPSCLoop..Maximum number of phase self calibration loops
  minFluxPSC..Min. peak flux density required for phase self cal (Jy)
  solPInt.....phase SC Solution interval (min)
  solPType....phase SC Solution Type: '  ', 'L1',
  solPMode....phase SC Solution Mode:'A&P', 'P', 'P!A',
  maxASCLoop..Maximum number of A&P self calibration loops
  minFluxASC..Min. peak flux density required for A&P self cal (Jy)
  solAInt.....A&P SC Solution interval (min)
  solAType....A&P SC Solution Type: '  ', 'L1',
  solAMode....A&P SC Solution Mode:'A&P', 'P', 'P!A',
  refAnt......Reference antenna number for selfcal
  WtUV........Weighting (wrt 1) to use outside of basic uv range in SC
  avgPol......Average Polarizations in self calibration?
  avgIF.......Average IFs in self calibration?
  noNeg.......If True, exclude negative summed CLEAN components from the
              self-cal model calculation.  This is useful if the initial
              calibration is poor and there are negative components due
              to phase errors but is harmful if the initial calibration is
              relatively good and the negative components are needed to
              describe a high dynamic range image (say DR>1000:1)
  doMGM.......Apply mean gain modulus to A&P selfcal soln.
  minSNR......Min. allowed SNR in self cal solution
  minNo.......Min. allowed no. antennas in selfcal
  prtLv.......Print level in selfcal, 0=>none

  PeelFlux....Peeling is the procedure of doing a self calibration on
              a single source, removing it and reverting to the
              previous calibration.  This is useful for a very strong
              source whose artifacts disturb the other parts of the
              field.  If the maximum pixel value in any image
              (as defined by the CLEAN components) exceeds PeelFlux,
              then the facet in which the maximum value occured is
              peeled.  This procedure is iterated until no facet has a
              pixel in excess of PeelFlux.
                 NB: peeling of many sources will likely degrade the
                 It is strongly recommended that autoCen be no larger
              than PeelFlux so that the source is properly centered in
              its facet.
  PeelLoop....Maximum number of peeling self calibration loops
  PeelRefAnt..Reference antenna number for Peel selfcal
  PeelSNRMin..Min. allowed SNR in peeling self cal solution
  PeelSolInt..Peel SC Solution interval (min)
  PeelType....Peel SC Solution type '  ', 'L1'
  PeelMode....Peel SC Solution mode:'A&P', 'P', 'P!A',
              "P" is used for all but the last peel which uses PeelMode
  PeelNiter...Max. number of components in Peel CLEAN
  PeelMinFlux.Min. Peel CLEAN flux density
  PeelAvgPol..Average Polarizations in Peel self calibration?
  PeelAvgIF ..Average IFs in Peel self calibration?

                      Multiresolution CLEAN
                 A multiresolution CLEAN is enabled using nTaper>0.
              This allows multiple circular imaging tapers to be
              specified in units of pixels; full resolution is
              generally 3-8 pixels. The full mosaic is reproduced in
              each resolution
                 Each major cycle, which resolution is to be used is
              picked on the basis of image statistics, the weightings
              of which are controled by MResKnob.
              The objective function used to chose the resolution is
              given by:
                fact1 * (maxTaper - Taper)/maxTaper +
                fact2 * (resid_peak/resid_RMS) +
                fact3 * quality
                fact1 is from the reduced MResKnob[0]
                fact2 = MResKnob[1]
                fact3 = MResKnob[2]
                maxTaper is the highest beam taper (lowest res)
                Taper is the beam taper of the given resolution
                resid_peak is the peak residual in the facet
                resid_RMS is the robust RMS of the residual
                quality is the measure used to pick amoung the facets
                   at a given resolution and is a function of peak and
                   average residual.
              The comparison is performed on the facet at each
              resolution with the highest "quality".
  nTaper......Number of resolutions expressed as the number of tapers
              to be applied to the data
  Tapers......List of circular Gaussian tapers in (x) pixels.
  MResKnob....Controls on selecting resolution to be CLEAned next.
              [0] Bias towards higher resolution, 0=>0.2
                  As the CLEAN progresses, this factor is reduced by
              [1] SNR factor,                     0=>0.35
              [2] "Quality" factor,               0=>0.2

                          Interactive display
  dispURL.....The URL of the display server to use. "None"=>none
              "ObitView" =  "http://localhost:8765/RPC2"
              This will display fields being CLEANed and allow
              interactive editing of the CLEAN window.
              If the display is running on a machine on which the
              data is not visible, use "http://myhost:port/RPC2"
              where myhost is the network name and port is the port
              number (usually 8765), Example:
  nThreads....If The Obit libraries are compiled with multiple
              thread operation enabled, this parameter sets the
              number of threads that can be used for parallel
              NB: This only improves performance if there are
              multiple processors and/or cores in the host.
  taskLog.....Log file to write messages to INSTEAD of the terminal
              This is useful in long runs or batch files where
              a bug in the ObitTalk message handling may cause
              tasks to hang.  Path is absolute or relative to where
              the task executes.
  noScrat.....A list of AIPS disk numbers on which you do not
              wish scratch files