; COMAP ;--------------------------------------------------------------- ;! Procedure to MAP and Self-Calibrate a UVDATA set ;# Task AP Imaging ;----------------------------------------------------------------------- ;; Copyright (C) 1995, 1997 ;; 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 ;----------------------------------------------------------------------- ;--------------------------------------------------------------- COMAP LLLLLLLLLLLLUUUUUUUUUUUU CCCCCCCCCCCCCCCCCCCCCCCCCCCCC COMAP: Procedure to CLEAN and Self-Calibrate UVDATA INNAME Input UV data (name) INCLASS Input UV data (class) INSEQ Input UV data (seq. #) INDISK Input UV data disk drive # IN2NAME Model for First Self-Cal IN2CLASS Model image (class) IN2SEQ Model image (seq #) IN2DISK Model image disk drive # OUTDISK Output image disk drive # CELLSIZE 0.0 9999.9 (X,Y) size of grid in asec IMSIZE 0.0 4096.0 Image size NITER Number of clean iterations REFANT Reference ant. for Self-cal. SOLINT Min. Solution interval (min) NMAPS Number of Map-Selfcal loops DOPOL >0: Produce Polarization maps DOCENTER >0: Move Source to map center DOALL >0: Do amplitude self-cal CUTOFF Clip Flux Limit. <0: No Clip UVTAPER Taper to apply to UV data UVRANGE Range of UV data to include UVWTFN Weighting function for data GAIN 0.0 2.0 Clean Gain NBOXES 0.0 50.0 Number of boxes for CLEAN CLBOX 0.0 4096.0 Four coordinates for each box BMAJ * FWHM(asec) maj. axis beam BMIN * FWHM(asec) min. axis beam BPA * -360.0 360.0 CLEAN beam position angle BADDISK -1.0 1000.0 Disks to avoid for scratch. ---------------------------------------------------------------- COMAP Type: Procedure Use: COMAP is a procedure which maps and self-calibrates UVDATA. Makes many simplifing assumptions, sets input values for MX and CALIB. Uses UVSUB to divide by the source model before running PHASE to coherence time average the input UV data. TASK SCMAP SELF-CALIBRATES AND IMAGES ALL IN ONE TASK WITH A VARIETY OF INTERACTIVE CLEANING AND EDITING OPTIONS. USE IT RATHER THAN THIS OLD PROCEDURE. Adverbs: 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. IN2NAME....Input Model Image for first self-calibration. if INNAME='POINT', a point source model is used. IN2CLASS...Model Image class IN2SEQ.....Model Image sequence number. IN2DISK....Model Image disk number OUTDISK....The disk drive # of output images. 0 => highest with space (note: map and Beam go on same disk. CELLSIZE...(X,Y) pixel separation in asec. IMSIZE.....(X,Y) The minimum desired size of the fields. NITER......CLEAN iteration limit. 0 => 1000 REFANT.....Reference Antenna for Self-Calibration SOLINT.....Minimum Self-Cal solution interval (min.). 0 => 1 minute NMAPS......Number of Map and Self-Cal Iterations DOPOL......Produce Polarization images. DOCENTER...Shift source peak to center of the map. DOALL......Attempt Amplitude Self-calibration. CUTOFF.....Maximum Flux allowed in UV-Data. UV-data are allowed with brightness between 0 and CUTOFF. <0: No Clipping. =0: Zero spacing flux + Noise UVTAPER....(U,V) gaussian taper (kilolambda) at 30% level UVRANGE....(Minimum,Maximum) baseline (kilolambda) in map. UVWTFN.....Weighting function of (u-v) place. blank=>Uniform; 'NA'=>Natural GAIN.......The CLEAN loop gain. 0 => 0.10. NBOXES.....Number (<=50) of rectangular search boxes To search on the first field; the clean window in all other fields is given by FLDSIZE. 0 => use FLDSIZE to determine windows on field 1. CLBOX......A 4x50 array with the BLC and TRC of each box. 0 => use window specified in FLDSIZE. BMAJ.......The FWHM (asec) major axis of the restoring beam. If 0; value obtained from fitting to the beam. If <0; output will contain the residual image. BMIN.......The FWHM (asec) minor axis of the restoring beam. BPA........The position angle in the unrotated image of BMAJ. 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. ---------------------------------------------------------------- COMAP: Procedure to Map and Self-Calibrate UV data DOCUMENTOR: G. Langston and W. Cotton (NRAO) Also see MX and CALIB documentation. TASKS USED: MX, CALIB, SNPLT, UVPLT, UVPRM, CCFND, TXPL, CLIP and COMB. PURPOSE COMAP combines the functions of Mapping, CLEANing and self-calibrating a UV data set. The UV data must be in AIPS single source format. The COMAP procedure first divides the UV data by the best source model to create "pseudo-point source" UV-data. The AIPS capability unique to COMAP is the use PHASE task which reads in the divided UV data and creates an intermediate "Coherence-Time- Averaged" UV data set. The data in this file are smoothed over the coherence time of each baseline. In this way, short baselines which often have higher signal-to-noise ratio due to more signal as well as lower baseline length dependent effects are more significant in the Self-calibration solution. After the data are smoothed, the data are Self-calibated and the Self-calibaration is applied to the original (unsmoothed) UV data. The Self-Calibrated UV data are then deconvolved and the cycle repeated. ADVERBS PECULIAR TO COMAP Most of the adverbs used by COMAP are duplicates of those used by MX and CALIB. However if the Adverbs are not specified, (such as REFANT or CELLS) value is estimated from the UV data. INNAME, INCLASS, INSEQ, INDISK Input UV-data used by COMAP to creat the self-calibrated UV-data and output Image. COMAP is able to pick a REFerance ANTenna, based on the signal to noise ratio of visablities. IN2NAME, IN2CLASS, IN2SEQ, IN2DISK First model image used to self-calibrate the input UV-data. The clean components for the image specified by IN2NAME, IN2CLASS, IN2SEQ and IN2DISK are selected in the same manner as subsequent self-calibrations. If no image NAME is specified, the first self-calibration follows the first deconvolution. If IN2NAME is "POINT" then a point source model used used as the starting point of self-calibraton. IMSIZE The minimum desired size for all of the fields. The limits are 32x32 to 4096x4096 and must be a power of 2. The adverb FLDSIZE define the region over which clean components are searched for. NBOXES, CLBOX For the first field, up to 50 CLEAN windows can be specified via CLBOX as an alternate to FLDSIZE. This allows more flexibility than a single window centered on the phase center. If NBOXES is greater than 0 then the contents of CLBOX is used to specify the input window. Since these values are in pixels care should be taken that they are determined from an image made with the same cellsize and shift. NOTE: the values containes in CLBOX are not used to determine the size of the image for field 1. IMSIZE and/or FLDSIZE must be used for this. In the case that CLBOX and NBOXES are used, this is the only use made of FLDSIZE for field 1. Its use for higher numbered fields is unaffected. If CLBOX is 0's then the value of FLDSIZE (or its default) is used for CLBOX. NBOXES and CLBOX specify the size and location of the rectangular boxes comprising the "CLEAN Window" area A. You make the best use of prior knowledge about the source to help COMAP do its job when you restrict A as closely as possible to the true boundaries of its emission. Recall that CLEAN attempts to optimize F(n) as a representation of the sky, with zeroes everywhere else. The more information you provide about where the "real" emission is, the more likely COMAP is to converge on a unique, credible solution. UVWTFN When using COMAP to make several small maps over a large field of view, use Natural weighting rather than Uniform weighting in order to obtain the signal to noise and resolution which are comparable to that obtained from one large map over the field of view. For mapsizes of 256 or less, the loss of signal to noise using Uniform weighting can be a factor of two or three. OUTDISK : If OUTDISK = 0, the map and beam will be put on the same disk. The Q and U maps may be put on another disk. It is best to specify OUTDISK. FLDSIZE,IMSIZE,CELLSIZE : For effective CLEANing of the maps, the number of pixels per beam should be such that the pixel value immediately north or east of the beam center is no less than about 50% of the peak. However, if tapering is used, the outlying (u,v) points may not have any significant weight in the map. Strong aliased sources should be CLEANed in separate fields unless they are close to the object of interest. COMAP will make maps which have a power of two pixels on a side; between 32 and 4096 on the X-axis and between 32 and 4096 on the Y-axis. FLDSIZE defines the region to be searched for CLEAN components. If for some reason it is desirable to map a region much larger than the region being CLEANed, IMSIZE can specify the minimum size of a map. Components will be CLEANed from the region specified by FLDSIZE but the output image size will be as specified by IMSIZE. Values in IMSIZE must be powers of 2. STOKES : If you do not expect your source to show significant circular polarization, as is normally the case with galactic and extragalactic continuum sources, making a V map can be a useful diagnostic for calibration problems, correlator offsets, etc. The V map should be a pure noise map close to the theoretical sensitivity if your data base is well calibrated and edited. UVWTFN : The default uniform weighting option gives higher resolution than natural weighting. However, uniform weighting gives a lower signal to noise ratio. Natural weighting is therefore preferable for detection experiments. With uniform weighting the dirty beam size decreases slightly with larger maps, other parameters remaining unchanged. GAIN and NITER : The depth to which CLEAN carries out its deconvolution is approximately measured by the product NITER*GAIN. The first CC extension file version corresponds to the first output frequency channel. The value of NITER and the execution time needed to reach a given CLEANing depth are minimized by setting GAIN = 1.0, but setting GAIN > 0.5 is recommended only when removing the sidelobes of a single bright unresolved component from surrounding fainter structure. BMAJ, BMIN, BPA : The default values of 0 for these parameters invoke an algorithm whereby the central portion of the dirty beam B is fitted with an elliptical Gaussian function whose parameters are then used to specify the Clean Beam H. The algorithm can be "fooled" by positive or negative sidelobes near the main lobe of B, and has been known to prescribe unsatisfactory forms for H, particularly for snapshot maps. BATCH : Mapit can be used in BATCH mode. Below is a sample AIPS session which sets up the BATCH queue and runs COMAP: >INPUT COMAP >INPUT COMAP_MX >INPUT COMAP_DO ... if mapit inputs look ok >SAVE MYCOMAPINPUTS >BATCH ... create a list of batch commands SUBMIT Hidden ADVERBS There are several hidden ADVERBS to COMAP which are not usually changed by the user. In an attempt to keep the inputs to COMAP simple, these ADVERBS are not in the ADVERB list above. However, there are situations where these other ADVERBS might prove useful to the advanced user. These adverbs are listed via INPUT or HELP COMAP_DO and COMAP_MX. DOINT: SCALAR, default FALSE (-1) DO INTeractive COMAP; if true, before deconvolution the user is requested to input clean boxes, marking the locations were the image will be searched for clean components. This option allows spurious source components to be rejected allowing MX to clean only in user specified regions. This interactive mode also alls the user to stop cleaning when satisfied with the output. This mode was inspired by the Jodrel Bank OLAF package software. DOZAP: SCALAR, default TRUE (1) If DOZAP is true, then all intermediate images and self- calibration solutions are deleted. This step is necessary to conserve disk space. If the user wishes to study COMAP progress setting DOZAP false leaves all intermediate images and UV-data around for examination. RMSFACT: SCALAR, default 1.2 RMS FACtor is the rms noise factor used to stop bad self-calibrations and deconvolutions within COMAP. COMAP continues the cycle of self-calibration and deconvolution until the requested number of iterations are performed OR the noise in the image produce by the current deconvolution is worse than the previous deconvolution. Setting RMSFAC greater than one allows the solution to get worse, in the hope that as the COMAP parameters change, the solution will improve. Note that the default allows the solution to get 20 % worse before quiting. Experience has found that the transition from PHASE to AMP+PHASE self-calibration causes significant changes to the RMS noise level IN EITHER DIRECTION. Few errors have snuck past the 20 % level and failed to improve. If AMP solution is bad it is usually EXTREAMLY bad and is detected. CLIMIT: SCALAR, default 0.04 Jy Clip LIMIT: the lowest source flux level which may be cliped in the CLIP step. Because of the current performace of the VLA receivers, clipping at a lower level is certainly cliping the NOISE due to the receiver temperature. The function of CLIP is to remove NON-GAUSIAN distributed noise (ie interference). CCFACT: SCALAR, default 2 CC FACTor is used to determine the number of clean components to use in the next self-calibration cycle. It is assumed that all negative CCs are spurious. If negative CCs are spurious, then probably a few faint positive CCs are sperious as well. CCFACT is used to determine the positive clean component limit. All CCs brighter than CCFACT times the absolute value of the brightness of the first negative CC are used in the Self-cal model. SOLFAC: SCALAR ARRAY, defaults 1, 3/4, 2/3, 1/2, 1/3, 1/4, 1/5, 1/6, 1/8, 1/10 SOLution interval FACtors, is an array of values used to scale the input self-calibration solution interval. Self-calibration is most successful if the time over which the data is averaged is just longer than the time over which ionosphere (atmosphere) changes the phase of the data. However the longer the averaging time, the better the model is. The SOLFAC array is used to scale SOLINT from long to short as a function of self-calibration loop. The first two self-cals use the input interval, the third self- cal uses 2/3 SOLINT, the fourth, a half SOLINT, etc. SCTYPE: STRING*2, default ' ' (least square fit) Self-Calibration solution TYPE, SCTYPE, is the type of fit used by CALIB to calculate the antenna gains which minimize the difference between UV-data and the source model. The least linear fit (SCTYPE='L1' is less sensitive to a few spurious data than the least squares (SCTYPE='') fit. The least squares fit is better if the data has errors which are gaussian distributed. The least linear fit is better if interference is present. NOLDUV: SCALAR, default 2 NOLDUV is number of self-calibration cycles using the original UV-data as input. After NOLDUV self-cals, the previous self-cal output is used as input to the next self-cal executions. By default, the first two self-cals use the original UV-data. Notest on Snapshot imaging A number of interesting observations have been made concerning imaging VLA snapshots during the testing of COMAP. One is the use of the MX adverb FACTOR to determine when the MX minor cycle clean should stop. (Also See MX HELP) In brief, MX, performs a minor cycle clean by reading in a large number of bright pixels of an image. MX finds the maximum pixel in the input image and subtracts the beam from the entire image, until the brightest residual is fainter than the Beam's brightest sidelobe. In this way no BEAM features are confused with real sources. The point to note is that the VLA BEAM model assumes perfect phase calibration, however for snap-shots, the phase calibration is usually rare and the BEAM side-lobes are usually large. This causes sidelobe in the image to be brighter than expected and can be turned into sperious features due to self-calibration. Fortunately there is an easy way to avoid this problem, using the MX adverb FACTOR. By setting FACTOR to -1, the minor cycle clean stops after each clean component is found, but is very slow. The MX default is FACTOR equals 0. For FACTOR = 1, the Minor Cycle does not stop until all NITERations are complete. A reasonable value for FACTOR for snapshots is between -0.4 and -0.1, so that cleaning stops before side-lobes are confused with sources. See HELP COMAP_DO and HELP COMAP_MX for further COMAP inputs. ----------------------------------------------------------------