; OBITMAP ;--------------------------------------------------------------- ;! Simplified access to OBIT task Imager ;# VERB IMAGING ;----------------------------------------------------------------------- ;; Copyright (C) 2011 ;; Associated Universities, Inc. Washington DC, USA. ;; ;; This program is free software; you can redistribute it and/or ;; modify it under the terms of the GNU General Public License as ;; published by the Free Software Foundation; either version 2 of ;; the License, or (at your option) any later version. ;; ;; This program is distributed in the hope that it will be useful, ;; but WITHOUT ANY WARRANTY; without even the implied warranty of ;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ;; GNU General Public License for more details. ;; ;; You should have received a copy of the GNU General Public ;; License along with this program; if not, write to the Free ;; Software Foundation, Inc., 675 Massachusetts Ave, Cambridge, ;; MA 02139, USA. ;; ;; Correspondence concerning AIPS should be addressed as follows: ;; Internet email: aipsmail@nrao.edu. ;; Postal address: AIPS Project Office ;; National Radio Astronomy Observatory ;; 520 Edgemont Road ;; Charlottesville, VA 22903-2475 USA ;----------------------------------------------------------------------- OBITMAP LLLLLLLLLLLLUUUUUUUUUUUU CCCCCCCCCCCCCCCCCCCCCCCCCCCCC 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 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. ---------------------------------------------------------------- OBITMAP 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 Imager. Adverbs: 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. 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% 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 SDIGain If BLFact > 1.0 then the input data will be subjected to a baseline dependent time averaging. Adverbs: 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 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. 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 averaging 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 desired. 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% level as (major, minor axis, position angle) UVRange....(Minimum,Maximum) baseline (kilo-lambda) to process. 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 area. 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 Component. 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 CLEAN. 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 computation. ' ' allows the program to use the fastest method. 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 Peeling 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 results. 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 where 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-iteration/niter)**3 [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: dispURL="http://canis.cv.nrao.edu:8765/RPC2" 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 operations. 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