; AVLAPIPE - Lorant Sjouwerman, NRAO - 27 Oct 2005 ; Ver 1.0 : Copy of private Ver 3.0 of VLARUN (public version is 2.3): ; was 3.0 : Corrections/additions to go with VLARUN Ver 3.0 ;--------------------------------------------------------------- ;! calibrating amplitude and phase, and imaging VLA data ;# RUN POPS VLA UTILITY CALIBRATION IMAGING ;--------------------------------------------------------------- ;; Copyright (C) 2002-2005 ;; 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 ;--------------------------------------------------------------- AVLAPIPE LLLLLLLLLLLLUUUUUUUUUUUU CCCCCCCCCCCCCCCCCCCCCCCCCCCCC AVLAPIPE : Applies amplitude and phase calibration to VLA data This procedure does quick and dirty VLA calibration and imaging of line and continuum data, including high frequency data, but without full polarization calibra- tion. The assumptions made in this procedure may not be the best - but it is a great help for lazy people. To run this procedure you MUST type > RESTORE 0 (recommended!) > RUN AVLAPIPE > COMPRESS to define the procedure (only once) in AIPS, and then > TASK'AVLAPIPE';INPUTS > AVLAPIPE to actually execute it (after reviewing the inputs!) Do FILLM and visibility FLAGGING before AVLAPIPE (and also split the data into single-frequency files). You can also use the autoflagging feature (FLAG >=0), but you may want to skip this for fast-switching obs. Compile all flagging in the continuum (CH 0) flag table #1 - also add line flags here (in CH 0)! Flag tables with higher numbers get deleted at restarts. If there is an FG-table, autoflagging is switched off! This is the input dialog to the quick VLA pipeline There are NO DEFAULTS! It assumes you have observed 3C286 or another VLA amplitude calibrator (see HELP) for absolute amplitude calibration. It will use up to 5 sources (may be 3C286 etc) for bandpass in LINE, and can use up to 20 possible phase calibrator names. Bandpass calibrators defined by CALSOUR can be any (but maximum 5) sources in your data. It is ONLY USED for line data sets, using an average of the 5 sources. When you run AVLAPIPE with DOCONT<1 the procedure will STOP once (very soon after starting) in the beginning, after GETJY so you can check your calibrator fluxes. When you run AVLAPIPE with DOALL>0 the procedure will do the imaging for you using IMSIZE, NITER, CUTOFF and DOARRAY (which is the longest baseline cq resolution). AIPS can also determine these parameters (see help!). When you run AVLAPIPE with PLVER>0 the procedure will also makes plot files at critical calibration stages and save with TASAV. View plots on the original multi- source files (also LINE) with: getn [catno]; allplot ----------------------------- BADDISK Disks to avoid for scratch INDISK Working disk, thus in/outdisk DOCAT Catalog number of the UV-file must be 'CH 0' for line data (or use getname/inname etc) INNAME Name etc, of UV-file; if used INCLASS specify them all and set the INSEQ DOCAT variable less than 1! DOALIGN Correct fast-sw source names? FLAGVER Level of automatic flags used < 0 : no automatic flagging. 0: default FLAGR (multi src) 1: QUACK on beginning (<20s) SOLINT CALIB phase solution interval FACTOR FACTOR*SOLINT for amplitude solution intervals (in min) REFANT Good reference antenna number (AIPS will choose if left 0) DOMODEL Use standard models in CALIB? Type CALDIR to see if they exist for your source in 3C names (see the EXPLAIN file) and in your frequency band. Utilize UVRANGE if not there or accept default point src KEYSTRNG Alternative calibrator name & FLUX use this total flux density UVRANGE UV range for flux calibrator SOURCES Phase calibrators (max 20, or '*' = any calcode CONTINUUM) All others are your targets! CALSOUR Bandpass calibrators (max 5) >CALSOUR only used for LINE< dopol SOURCES' source number to use as polarization calibrator, bpa & Polarization position angle DOCONT Continue after GETJY, no stop PLVER Make diagnostic plots if > 0. -- See EXPLAIN AVLAPIPE -- DOALL Also do a split and imaging? -- ONLY USED IF DOALL > 0 -- i.e., only for imaging DOARRAY Max baseline in kilometers: A=35.4, B=10.8, C=3.3, D=1 Pixelsize=17.5/(GHz*doarray) =0 -> let it find the array. <0 -> SETFC determines pixels IMSIZE Square size of image (pixels) <0 -> SETFC determines IMSIZE <-9 then also for calibrators NITER Max number of iterations/chan Zero means zero! (dirty img) (wise to leave 0 for line..) CUTOFF Min flux to consider in clean DOCAL Also image the calibrators ? >0 do continuum, >1 line too - INTERACTIVE SELF_CAL MODE - DORESID Instead of IMAGR, do SCIMG on targets if set. ABS(DORESID) is the number of iterations. DORESID<0 limits the TV use. All this may not be useful; it only applies to continuum data of any target source... ---------------------------------------------------------------- AVLAPIPE Type: Procedure Use: AVLAPIPE is the procedure that blindly applies VLA calibration $---------------------------------------------------------------------------- Type RUN AVLAPIPE to define the AVLAPIPE procedure (once would be enough) CLEAN STARTING CONDITIONS Make sure only one frequency-ID is present (otherwise use UVCOP to split them apart and INDXR to re-index the files). It can process both continuum and line data, but the line files must have inclass 'CH 0' and 'LINE'. If any, flags must be made in the highest numbered FG table on the continuum or 'CH 0' files, so if you flag the 'LINE' data you have to copy the line flags/flag-table to the 'CH 0' file. Restarting is straightforward - fluxes are reset and tables are deleted although naming back fast-switching sources is irreverisble (DOALIGN>0). ADVICE ! When using AVLAPIPE for the first time on a data set (or on line data) do not do any cleaning, nor self-cal (very fragile!) - it will go much faster and will tell you right away if you should expect problems. If you switch on autoflagging (but see below), you'll see where extra flags are needed and whether it did what you expected and intended (typo's in the input, can you do self-cal, better reference antenna, solint, etc). Maybe also wait with the imaging at this stage and make plots (PLVER>0). ** Set NITER low or CUTOFF high on a first image try, also set IMSIZE>0. DOCAT, or all of INNAME, INCLASS, INSEQ (and INDISK): The catalog number of the file to calibrate (the continuum, or the 'CH 0'-file for spectral line data). If INNAME etc are used, then set DOCAT to a non-positive value (<=0) -> DOCAT=0;GETNAME DOALIGN: Sometimes, with fast-switching, calibrator source names are messed up, in particular you may have more than one name for the same source. Set DOALIGN positive to do a check on position (better than 3 mas in R.A. and in DEC.), qualifier and calcode. If two sources are the same it will keep the shortest name and save you ending up with multiple images of the same source. Up to 100 source names can be modified. FLAGVER: A negative value means to do no automated flagging. NOTE: if an FG table is detected, it will NOT DO any form of automated flagging on the data. You may want to NOT do autoflagging when you have very short scans (i.e. in fast-switching mode) - flag by hand in higest FG-table (always kept). 0 -> Only perform FLAGR, OPTYPE'TIME' on the raw multisource data set An integration time is guessed and three samples make up SOLINT. 1 -> Include also QUACK, OPCODE'BEG', APARM(2)=MIN(20 SEC, 3 samples) Again, you may not want to do this if you have short scans (~30s). .... 2 -> Nothing yet (but probably flag the single source calibrated data) SOLINT, FACTOR: SOLINT is the solution interval in minutes used in CALIB (and SCIMG) for phase calibration - typically the scan length on your phase calibrator, but much shorter (0.2-0.5) for high-frequency data. FACTOR scales SOLINT to a new value for amplitude calibration; probably best between 1-10. AVLAPIPE first calibrates the phases, then the amplitudes (including phase), i.e., the second SN table should have phases very close to 0! REFANT: Well behaving antenna (number) to be used as reference antenna. Usually one in the center of the array. AIPS will make a choice if left zero. DOMODEL: If set positive, CALIB will use a (standard) model for any of the five standard flux density calibrators (3C48, 3C138, 3C147, 3C286, 3C295, or their standardized IAU names - see KEYSTRNG below) that are in your data set, assuming they exist. Currently they exist for the higher frequencies (5 GHz and up), but more are added when they become available. For the latest available models type 'CALDIR' and/or 'EXPLAIN CALRD'. Note that if you select this mode, AVLAPIPE will crash if no model is available! For lower frequencies, and for smaller arrays, it is usually sufficient to use a non-positive DOMODEL, i.e., to use a point source model for the standard flux density calibrators. KEYSTRNG and FLUX: If none of the standard flux calibrators is observed (see below), then enter the name and flux density of an alternative source here. NOTE: if specified it will be used by force even if a standard calibrator is present! So you can force your own flux scale if desired. List of all names recognized as a VLA amplitude calibrator in SETJY: - 3C48 is also known as: 0134+329, 0137+331, or J0137+3309 - 3C138 is also known as: 0518+165, 0521+166, or J0521+1638 - 3C147 is also known as: 0538+498, 0542+498, or J0542+4951 - 3C286 is also known as: 1328+307, 1331+305, or J1331+3030 - 3C295 is also known as: 1409+524, 1411+522, or J1411+5212 At least one of these names (3C or other) must be in the data set for the flux calibration. If a different source is used, then you have to specify this other source using KEYSTRNG and FLUX (and maybe UVRANGE). UVRANGE: UVRANGE to go with the standard or alternative flux calibrator. Leave zero if you are using a standard calibrator source model (DOMODEL>0), or want a point source model approximation for the one in KEYSTRNG. SOURCES: Specify your continuum phase calibrators. Limited to 20 in total, and if there are more, use '*' in the FIRST argument to select sources with any calcode. Also include your flux and/or bandpass calibrators if you want them to be calibrated. Any source not appearing in SOURCES are "targets". Use SOURCES='*','' if all your phase calibrators have calcodes. CALSOUR: Specify up to five bandpass calibrator sources. Only used for line data. ....dopol SOURCES' source number to use .... as polarization calibrator, ....bpa & Polarization position angle ....implement RLDIF DOCONT: If set positive, then AVLAPIPE will pause after GETJY, until you press . This allows you to check the flux densities (with their errors) of your secondary calibrators, which is a good practice and diagnostic. PLVER: Make diagnostic plots; a positive value means to make these plot files: 1 -> Only make plot files of SN tables 2 -> Also include plots of CL tables 3 -> (LINE data) add plots of the BP table 4 -> (LINE data) also plot BP calibrators with CL and BP table applied DOALL: If set positive, then AVLAPIPE will continue with the imaging part. If set non-positive (<=0, to avoid imaging if you're not sure about the results), open another AIPS window to look at the diagnostic plots (make sure you set PLVER, preferably as high as possible), and if satisfied you can continue with imaging if you type "IMAPIPE(1,,)" in the AVLAPIPE window directly after the calibration part has finished. The '1' in the first argument of IMAPIPE means to start with SPLIT, but if you have splitted the data already in the other window, use a 'zero' instead. DOARRAY (if DOALL>0): Sets the resolution; use the maximum baseline length in kilometers. The pixel size will be 17.5 divided by the product of the frequency (in GHz, read from the UV file header) and the value you set for DOARRAY. For the VLA arrays use, e.g., for A-array 35.4, B 10.8, C 3.3, and D 1 kilometer, and set it to 73 kilometer if Pie Town was used. If set to 0, AVLAPIPE will guess the maximum unprojected baseline from the antenna file and fix values to 36, 11, 3.5, 1, or 75 respectively. If negative, SETFC will be used to figure out the best cell size. IMSIZE (if DOALL>0): The image size in pixels, with a minimum of 128. For calibrators it is assumed that 256 is large enough in all cases, so this applies to targets. If negative, AIPS will try to image the full primary beam (using SETFC); if large negative (<-9), then this also applies to calibrator sources. NITER (if DOALL>0): The number of clean components to be used in the imaging. Maybe it would be wise to use zero or a low number for spectral line data and re-image with a larger value after AVLAPIPE has finished and you're convinced that there is no bad data (or a faulty calibration) that would mess things up. For calibrators, if DOCAL set positive (>0), a maximum of 500 is used as there should be no need for deep cleans for calibration check images, .... unless the full primary beam is imaged (IMSIZE<-9); then NITER=NITER. If negative, AIPS will set it to a huge number (6e6) and instead thus effectively use CUTOFF below to determine when to stop. Note that NITER=0 means zero iterations, i.e., make the dirty image (and ignore CUTOFF). CUTOFF (if DOALL>0): Stop cleaning when this level (in Jy) is reached in the residual image. If CUTOFF is negative and NITER (large!) positive, then it will stop cleaning after the first negative clean component. Same for calibrators and targets, but also competes with NITER, i.e., whichever is reached first will determine when clean stops. If both NITER and CUTOFF are negative, AIPS will estimate a conservative value for the noise level from the visibility data header, and stop at three times this noise level. This also applies to calibrators if both NITER and CUTOFF are negative. NOTE that for strong sources the dynamic range limitation may prevent it from reaching this limit - it is VERY wise to set either NITER or CUTOFF (or both) on a first trial of using the pipeline on a particular data set. DOCAL (if DOALL>0): Set positive to have the calibrators imaged too for checking purposes or if you're interested in the source. A positive DOCAL up to one will limit the imaging of calibrators to the continuum data of spectral line sets, larger than one will also image the line data of the calibrators. Set IMSIZE and NITER (and CUTOFF) negative if you want larger images than 256 pixels squared and deeper cleans than 500 iterations for the calibrators. DORESID (if DOALL>0): Continuum data only (spectral line data ignores DORESID and uses IMAGR). This option should be used with EXTREME care. It allows one to use SCIMG instead of IMAGR, i.e., to perform self-cal hybrid mapping on the target sources only. Care should be taken that there is enough flux in the field for self-cal to work. Also note that the input SOLINT is taken, which in most cases will be an invalid assumption. Be safe and leave zero to use IMAGR. Otherwise the absolute value of DORESID determines the number of cycles (NMAPS in SCIMG). The sign of DORESID determines the level of interactive TV use: if negative, the only display is at the end of each clean; if positive then also interact with that image including UV data editing options. Use of DORESID other than zero is highly discouraged. $--------------------------------------------------------------------------- AVLAPIPE : Procedure to calibrate VLA data blindly. Documenter: Lorant Sjouwerman, lsjouwerman@nrao.edu Related Programs: VLA calibration, imaging and plotting routines ----------------------------------------------------------------------------