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<casaxml xsi:schemaLocation="http://casa.nrao.edu/schema/casa.xsd file:///opt/casa/code/xmlcasa/xml/casa.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://casa.nrao.edu/schema/psetTypes.html">
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<task category="simulation" name="simanalyze" type="function">
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<shortdescription>image and analyze measurement sets created with simobserve</shortdescription>
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<description>
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This task is for imaging and analyzing measurement sets (MSs) simulated
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with simobserve or simalma.
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</description>
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<example>
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* "project" needs to be the directory of results generated by running
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simobserve or simalma. In particular $project/$project.skymodel
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will be required in order to compare output and input images.
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-------------------------------
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mode image=True:
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* One should input one or more simulated MSs using the "vis" parameter.
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These can include a total power MS.
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Simanalyze will grid any total power MS,
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clean (invert and deconvolve) any interferometric MSs,
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and feather the results.
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* the "vis" parameter:
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- example: single MS: vis="mysim.alma.out03.ms"
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- example: multiple MSs: vis="mysim.alma.out03.ms,mysim.aca.tp.ms"
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- one can use "$project" and let the task automatically replace it with
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the project name, e.g., vis="$project.noisy.ms,$project.noisy.sd.ms".
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However, note that if you created measurement set(s) using simobserve,
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MS names will include the configuration, e.g.
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"$project.alma_out20.noisy.ms"
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- setting "vis" to "default" will find and attempt to image
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all measurement sets (interferometric and single dish) in the
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project directory
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* Sometimes it is preferable to grid the single dish MS using the
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sdimaging task for more control. In that case one can input
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the resulting single dish imaging under "featherimage", only
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put interferometric MSs in "vis", and simanalyze will clean the
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interferometric and feather with your "featherimage".
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* Sometimes it is preferable to use a low resolution (single dish or
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synthesis) image as a prior model during clean deconvolution
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of a higher resolution interferometric MS. That is accomplished
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by putting the low-resolution image in "modelimage" and the MS
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to be deconvolved in "vis". NOTE: This is not the original skymodel
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that was used in simobserve or simalma. It is recommended to
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leave this blank unless the user is familiar with using a prior
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in clean deconvolution. (see casaguides) NOTE 2: modelimage will
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not be used if the MS to be imaged is total power.
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* uses Cotton-Schwab clean for single fields and Mosaic gridding
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for multiple fields (with Clark PSF calculation in minor cycles).
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* interactive clean or use of more parameters than the subset
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visible here are available by simply running the clean task directly,
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then using simanalyze in the mode image=False (see below).
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* if graphics are turned on, this step will display the clean image
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and residual image
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* the "mask" parameter:
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Specification of cleanbox(es), mask image(s), primary beam
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coverage level, and/or region(s) to be used for cleaning.
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clean tends to perform better, and is less likely to diverge, if
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the clean component placement is limited by a mask to where real
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emission is expected to be. e.g. pixel ranges mask=[110,110,150,145],
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filename of mask image mask='myimage.mask', or a file with mask
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regions -- see help for the clean task for more information.
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* NOTE: simanalyze was designed to be used after one or more runs of
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simobserve, and as such it assumes it will be able to find a
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sky model image called $project/$project.skymodel, .newmodel, or
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.compskymodel in the $project/ subdirectory. If the simulated
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MS has been created by means other than simply calling simobserve,
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the user may have to copy their sky model image into the $project
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subdirectory and call it "$project.skymodel"
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-------------------------------
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mode image=False:
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* Sometimes the user has created a synthesized image themselves,
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most likely using the clean task, perhaps along with
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sdimaging and feather, or a previous call to simanalyze with image=True
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* The user should input that simulated image as "imagename".
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It will have suffix .image if created by clean, simanalyze, or simalma
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* simanalyze will attempt to find an appropriate skymodel image -
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this is the *.skymodel image created by simobserve or simalma,
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the (optionally rescaled) original sky model, which was used
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to create the measurement set.
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simanalyze will look in the project directory, but if there are
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multuple skymodels present it may not find the right one, so the
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"skymodel" parameter allows explicit specification.
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-------------------------------
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mode analyze=True is used to create an image of the difference between
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the input skymodel and the simulated output image (whether that output
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image is being generated in the same call to simanalyze, with
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image=True, or has already been generated, and simanalyze is being
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called with image=False).
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showuv -- display uv coverage
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showpsf -- display synthesized (dirty) beam (ignored in single dish simulation)
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showmodel -- display sky model at original resolution
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showconvolved -- display sky model convolved with output beam
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showclean -- display the synthesized image
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showresidual -- display the clean residual image (ignored in single dish simulation)
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showdifference -- display difference between output cleaned image and
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input model sky image convolved with output clean beam
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showfidelity -- display fidelity image
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fidelity = abs(input) / max[ abs(input-output), 0.7*rms(output) ]
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Note that the RMS is calculated in the lower quarter of the image.
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This is likely not the best choice, so you are encouraged to
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measure RMS yourself in an off-source region using the viewer.
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dryrun=True is an advanced technical mode only useful for interferometric
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(not single dish) data.
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This task is for imaging and analyzing MeasurementSets simulated with simobserve or simalma.
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It consists of two main steps, controlled by the image and analyze parameters.
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-------------------------------
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Output produced: (not all will always exist, depending on input parameters)
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To support different runs with different arrays, the names have the
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configuration name from antennalist appended.
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-------------------------------
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project.[cfg].skymodel.flat.regrid.conv = input sky regridded to match
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the output image, and convolved with the output clean beam
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project.[cfg].image = synthesized image
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project.[cfg].flux.pbcoverage = primary beam correction for mosaic image
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project.[cfg].residual = residual image after cleaning
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project.[cfg].clean.last = parameter file of what parameters were used in
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the clean task
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project.[cfg].tclean.last = parameter file of what parameters were used in
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the tclean task call
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project.[cfg].psf = synthesized (dirty) beam calculated from weighted uv
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distribution
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project.[cfg].image.png = diagnostic figure of clean image and residual
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project.[cfg].fidelity = fidelity image
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project.[cfg].analysis.png = diagnostic figure of difference and fidelity
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project.[cfg].simanalyze.last = saved input parameters for simanalyze task
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-------------------------------
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Please see http://casaguides.nrao.edu, and contact the CASA helpdesk
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with questions.
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</example>
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* "project" needs to be the directory of results generated by running
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simobserve or simalma. In particular $project/$project.skymodel
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will be required in order to compare output and input images.
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* NOTE: simanalyze was designed to be used after one or more runs of
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simobserve, and as such it assumes it will be able to find a
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sky model image called $project/$project.skymodel, .newmodel, or
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.compskymodel in the $project/ subdirectory. If the simulated
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MS has been created by means other than simply calling simobserve,
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the user may have to copy their sky model image into the $project
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subdirectory and call it "$project.skymodel".
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* interactive clean or use of more parameters than the subset
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visible here are available by simply running the tclean task directly,
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then using simanalyze in the mode image=False (see below).
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* Sometimes it is preferable to grid the single dish MS using the
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sdimaging task for more control. In that case one can input
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the resulting single dish imaging under "featherimage", only
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put interferometric MSs in "vis", and simanalyze will clean the
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interferometric and feather with your "featherimage".
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* uses Cotton-Schwab clean for single fields and Mosaic gridding
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for multiple fields (with Clark PSF calculation in minor cycles).
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</description>
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<input>
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<param name="project" type="string">
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<shortdescription>root prefix for output file names</shortdescription>
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<description>
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root prefix for input and output file names.
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This must be the directory of results generated by running
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simobserve or simalma. In particular $project/$project.skymodel
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will be required in order to compare output and input images.
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</description>
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<value>sim</value>
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</param>
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<!-- IMAGE -->
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<param name="image" type="bool"><shortdescription>(re)image $project.*.ms to $project.image</shortdescription><description>(re)image $project.*.ms to $project.image</description>
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<param name="image" type="bool">
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<shortdescription>(re)image $project.*.ms to $project.image</shortdescription>
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<description>Controls whether tclean is called to image the MeasurementSet data. If true, input one or more simulated MSs using the vis parameter. These can include a total power MS. This task will grid any total power MS, invert and deconvolve any interferometric MS(s) (using the simutil method imtclean), and feather the results. If this parameter is set to False (e.g., if the user has created a synthesized image themselves or simanalyze has previously been run with image=True) the user should provide that image as input to the imagename parameter. This task will then attempt to find an appropriate skymodel image (such as the optionally rescaled *.skymodel produced by simobserve or simalma and used to create the MS).</description>
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<value>True</value>
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</param>
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<param subparam="true" name="imagename" type="string"><shortdescription>simulation output image to analyze (default = first $project/*.image found)</shortdescription><description>simulation output image to analyze (default = first $project/*.image found)</description>
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<!-- if IMAGE==False -->
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<param subparam="true" name="imagename" type="string"><shortdescription>simulation output image to analyze</shortdescription><description>Name of image to image/analyze, expected to be of the same form as those generated by simobserve. Defaults to the first file found with the name $project/*.image</description>
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<value>default</value>
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</param>
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<param subparam="true" name="skymodel" type="string"><shortdescription>skymodel image to analyze (the .skymodel image created by simobserve or simalma and used by one of those tasks to create an MS; if unspecified, will try to find one similar to your specified output image name)</shortdescription><description>skymodel image to analyze (the .skymodel image created by simobserve or simalma and used by one of those tasks to create an MS; if unspecified, will try to find one similar to your specified output image name)</description>
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<param subparam="true" name="skymodel" type="string"><shortdescription>skymodel image to analyze</shortdescription><description>Name of a specific .skymodel image created by simobserve or simalma and used by one of those tasks to create a MS. If unspecified, will try to find one similar to your specified output image name.</description>
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<value/>
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</param>
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<!-- if IMAGE==True -->
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<param subparam="true" name="vis" type="string"><shortdescription>Measurement Set(s) to image</shortdescription><description>Name of the Measurement Set(s) to image, specified as a string or string containing a comma separating the names. If set to "default", will attempt to find and image all MeasurementSets (interferometric and single dish) in the project directory. Note that if you created MeasurementSets using simobserve, the names will include the antenna configuration. Example of a single MS: vis="mysim.alma.out03.ms". Example of multiple MSs: vis="mysim.alma.out03.ms,mysim.aca.tp.ms". Example of using the $project syntax: vis="$project.noisy.ms,$project.noisy.sd.ms".</description>
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<param subparam="true" name="vis" type="string"><shortdescription>Measurement Set(s) to image</shortdescription><description>Measurement Set(s) to image</description>
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<value>default</value>
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</param>
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<param subparam="true" name="modelimage" type="string"><shortdescription>lower resolution prior image to use in clean e.g. existing total power image</shortdescription><description>lower resolution prior image to use in clean e.g. existing total power image</description>
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<value type="string"/>
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<param subparam="true" name="modelimage" type="string"><shortdescription>image to use as clean prior</shortdescription><description>Sometimes it is preferable to use a low resolution (single dish or synthesis) image as a prior model during clean deconvolution of a higher resolution interferometric MS. That is accomplished by specifying the low-resolution image as input to this parameter, and the MS to be deconvolved as input to the vis parameter. This parameter is passed to the startmodel parameter via the simutil method imtclean. Note that this is separate from the functionality controlled by the featherimage parameter. Also note that this is not the original skymodel that was used in simobserve or simalma. It is recommended to leave this blank unless the user is familiar with using a prior in clean deconvolution. Also note that the modelimage will not be used if the MS to be imaged is total power.</description>
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<value type="string"></value>
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</param>
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<param subparam="true" name="imsize" type="intArray"><shortdescription>output image size in pixels (x,y) or 0 to match model</shortdescription><description>output image size in pixels (x,y) or 0 to match model</description>
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<param subparam="true" name="imsize" type="intArray"><shortdescription>output image size in pixel units</shortdescription><description>A list of integers corresponding to the number of pixels in (x,y) dimensions of output image. If 0, will attempt to match model image.</description>
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<value type="intArray"><value>0</value><value>0</value></value>
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</param>
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<param subparam="true" name="imdirection" type="string"><shortdescription>set output image direction, (otherwise center on the model)</shortdescription><description>set output image direction, (otherwise center on the model)</description>
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<value type="string"/>
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<param subparam="true" name="imdirection" type="string"><shortdescription>set output image direction</shortdescription><description>A string corresponding to a direction to adopt as phase center, including epoch, right ascension, and declination. If unset, will adopt center on the model.</description>
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<value type="string"></value>
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</param>
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<param subparam="true" name="cell" type="string"><shortdescription>cell size with units e.g. "10arcsec" or "" to equal model</shortdescription><description>cell size with units e.g. "10arcsec" or "" to equal model</description>
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<value type="string"/>
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<param subparam="true" name="cell" type="string"><shortdescription>cell size with units</shortdescription><description>Specify the cell size with units, e.g., "10arcsec". If left unset (an empty string), the model cell size will be used. This is the default setting.</description>
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<value type="string"></value>
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</param>
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<param subparam="true" name="interactive" type="bool"><shortdescription>interactive clean? (make sure to set niter>0 also)</shortdescription><description>interactive clean? (make sure to set niter>0 also)</description>
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<param subparam="true" name="interactive" type="bool"><shortdescription>call tclean in interactive mode</shortdescription><description>Controls how the simutil method imtclean will call the tclean task. If this parameter is set to True, make sure to set the parameter niter to a value >0.</description>
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<value type="bool">False</value>
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</param>
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<!-- force the same channelization as the ms -->
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<!--
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<param subparam="true" name="start" type="string"><shortdescription>frequency of first channel (default=ms)</shortdescription><description>frequency of first channel (default=ms)</description>
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<value>89GHz</value>
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</param>
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<param type="string" name="width" subparam="true"><shortdescription>channel width (default=ms)</shortdescription><description>channel width (default=ms)</description>
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<value>10MHz</value>
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</param>
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<param type="int" name="nchan" subparam="true"><shortdescription>number of channels or -1 for full range</shortdescription><description>number of channels or -1 for full range</description>
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<value>-1</value>
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</param>
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-->
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<param subparam="true" name="niter" type="int"><shortdescription>maximum number of iterations</shortdescription><description>Controls the value of the niter parameter in tclean call, and thus the maximum number of iterations per minor cycle. Set to 0 to produce a dirty image. Can also be modified through the viewer GUI via the interactive parameter.</description>
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<param subparam="true" name="niter" type="int"><shortdescription>maximum number of iterations (0 for dirty image)</shortdescription><description>maximum number of iterations (0 for dirty image)</description>
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<value>0</value>
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</param>
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<param subparam="true" name="threshold" type="string"><shortdescription>flux level (+units) to stop cleaning</shortdescription><description>flux level (+units) to stop cleaning</description>
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<param subparam="true" name="threshold" type="string"><shortdescription>target flux level and units</shortdescription><description>Set the quantity corresponding to the target flux level at which to stop cleaning. This value is passed to tclean via the simutil method imtclean.</description>
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<value>0.1mJy</value>
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</param>
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<param subparam="true" name="weighting" type="string"><shortdescription>weighting to apply to visibilities. briggs will use robust=0.5</shortdescription><description>weighting to apply to visibilities. briggs will use robust=0.5</description>
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<param subparam="true" name="weighting" type="string"><shortdescription>control image weighting method</shortdescription><description>Set the weighting scheme to apply to visibilities during image reconstruction. If set to briggs, will use the tclean default robust parameter (0.5)</description>
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<value>natural</value>
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<allowed kind="enum">
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<value>natural</value>
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<value>uniform</value>
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<value>briggs</value>
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</allowed>
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</param>
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<param subparam="true" name="mask" type="any"><shortdescription>Cleanbox(es), mask image(s), region(s), or a level</shortdescription><description>Cleanbox(es), mask image(s), region(s), or a level</description>
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<param subparam="true" name="mask" type="any"><shortdescription>Cleanbox(es), mask image(s), region(s), or a level</shortdescription><description>Accepts a list of cleanbox(es), mask image file name(s), region(s), and/or a primary beam coverage level. Input to this parameter will specify areas to be searched for clean components. tclean tends to perform better and is less likely to diverge if the component placement is limited by a mask to where real emission is expected. See the tclean task documentation for more information about masking. Example of a pixel range mask: mask=[110,110,150,145]</description>
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<any type="variant"/>
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<value type="intArray"/>
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</param>
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<param subparam="true" name="outertaper" type="stringArray"><shortdescription>uv-taper on outer baselines in uv-plane</shortdescription><description>uv-taper on outer baselines in uv-plane</description>
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<param subparam="true" name="outertaper" type="stringArray"><shortdescription>uv-taper on outer baselines in uv-plane</shortdescription><description>Accepts a list of strings in the form of a quantity that sets an other threshold on baselines in the uv-plane. Usually used to achieve a lower effective angular resolution and recover more extended emission in reconstructed image. If left unset via empty list (the default) no outer taper will be applied.</description>
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<value/>
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</param>
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<param subparam="true" name="pbcor" type="bool"><shortdescription>correct the output of synthesis images for primary beam response?</shortdescription><description>correct the output of synthesis images for primary beam response?</description>
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<param subparam="true" name="pbcor" type="bool"><shortdescription>correct synthesis images for primary beam response?</shortdescription><description>Controls whether primary beam correction is applied in the call to task tclean.</description>
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<value type="bool">True</value>
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</param>
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<param subparam="true" name="stokes" type="string"><shortdescription>Stokes params to image</shortdescription><description>Stokes params to image</description>
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<param subparam="true" name="stokes" type="string"><shortdescription>Stokes parameterss to image</shortdescription><description>Stokes parameters to include in the call to tclean via the simutil method imtclean. Note that forming Stokes Q and U images requires the presence of cross-hand polarizations (e.g., RL and LR for circularly polarized systems such as the VLA) in the input data. Stokes V requires both parallel hands (RR and LL) for circularly-polarized systems or the cross-hands (XY and YX) for linearly polarized systems such as ALMA and ATCA.</description>
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<value>I</value>
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<allowed kind="enum">
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<value>I</value>
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<value>IV</value>
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<value>QU</value>
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<value>IQUV</value>
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<value>RR</value>
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<value>LL</value>
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<value>RRLL</value>
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<value>XX</value>
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<value>YY</value>
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<value>XXYY</value>
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</allowed>
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</param>
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<param subparam="true" name="featherimage" type="string"><shortdescription>image (e.g. total power) to feather with new image</shortdescription><description>image (e.g. total power) to feather with new image</description>
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<param subparam="true" name="featherimage" type="string"><shortdescription>image to feather with new image</shortdescription><description>String corresponding to the name of an image (e.g., total power data) to feather with the interferometric synthesis image. Sometimes it is preferable to grid the single dish MS using the sdimaging task for more control. In that case, the user can input the resulting single dish imaging under featherimage, only pass interferometric data as input to the vis parameter, and this task will clean the interferometric and feather with the featherimage.</description>
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<value/>
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</param>
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<!-- ANALYZE -->
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<param name="analyze" type="bool"><shortdescription>create analytical images</shortdescription><description>Used to create an image of the difference between the input skymodel and the simulated output image (whether that output image is being generated in the same call to simanalyze, with image=True, or has already been generated, and simanalyze is being called with image=False). If True, only the first 6 selected subparameter outputs will be displayed.</description>
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<param name="analyze" type="bool"><shortdescription>(only first 6 selected outputs will be displayed)</shortdescription><description>(only first 6 selected outputs will be displayed)</description>
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<value>False</value>
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</param>
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<!--
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<param subparam="true" name="sim_image" type="string"><shortdescription>simulated image, created by this task or manually</shortdescription><description>simulated image, created by this task or manually</description>
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<value>$project/$project.image</value>
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</param>
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-->
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<param subparam="true" name="showuv" type="bool"><shortdescription>display uv coverage</shortdescription><description>Displays a plot of the simulated uv coverage</description>
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<param subparam="true" name="showuv" type="bool"><shortdescription>display uv coverage</shortdescription><description>display uv coverage</description>
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<value>True</value>
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</param>
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<param subparam="true" name="showpsf" type="bool"><shortdescription>display synthesized (dirty) beam (ignored in single dish simulation)</shortdescription><description>display synthesized (dirty) beam (ignored in single dish simulation)</description>
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<param subparam="true" name="showpsf" type="bool"><shortdescription>display synthesized beam</shortdescription><description>Displays synthesized (dirty) beam. Ignored in single dish simulation.</description>
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<value>True</value>
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</param>
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<param subparam="true" name="showmodel" type="bool"><shortdescription>display sky model at original resolution</shortdescription><description>display sky model at original resolution</description>
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<param subparam="true" name="showmodel" type="bool"><shortdescription>display sky model at original resolution</shortdescription><description>Displays the sky model at original resolution of input image.</description>
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<value>True</value>
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</param>
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<param subparam="true" name="showconvolved" type="bool"><shortdescription>display sky model convolved with output clean beam</shortdescription><description>display sky model convolved with output clean beam</description>
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<param subparam="true" name="showconvolved" type="bool"><shortdescription>display sky model convolved with output clean beam</shortdescription><description>Displays the sky model convolved with output clean beam.</description>
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<value>False</value>
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</param>
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<param subparam="true" name="showclean" type="bool"><shortdescription>display the synthesized image</shortdescription><description>display the synthesized image</description>
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<param subparam="true" name="showclean" type="bool"><shortdescription>display the synthesized image</shortdescription><description>Displays the synthesized image produced by the call to task tclean.</description>
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<value>True</value>
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</param>
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<param subparam="true" name="showresidual" type="bool"><shortdescription>display the clean residual image (ignored in single dish simulation)</shortdescription><description>display the clean residual image (ignored in single dish simulation)</description>
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<param subparam="true" name="showresidual" type="bool"><shortdescription>display the clean residual image</shortdescription><description>Displays the residual image produced by the call to task tclean. Ignored in single dish simulations.</description>
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<value>False</value>
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</param>
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<param subparam="true" name="showdifference" type="bool"><shortdescription>display difference between output cleaned image and input model sky image convolved with output clean beam</shortdescription><description>display difference between output cleaned image and input model sky image convolved with output clean beam</description>
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<param subparam="true" name="showdifference" type="bool"><shortdescription>display difference between cleaned output and convolved model input</shortdescription><description>Displays a difference image between cleaned image output by the tclean call, and input model sky image convolved with synthesized beam determined by output of tclean call.</description>
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<value>True</value>
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</param>
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<param subparam="true" name="showfidelity" type="bool"><shortdescription>display fidelity (see help)</shortdescription><description>display fidelity (see help)</description>
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<param subparam="true" name="showfidelity" type="bool"><shortdescription>display fidelity image</shortdescription><description>Display a fidelity image. Note that the RMS is calculated in the lower quarter of the image. This is likely not the best choice, so you are encouraged to measure RMS yourself in an off-source region. Fidelity = abs(input) / max[ abs(input-output), 0.7*rms(output) ]</description>
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<value>True</value>
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</param>
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<param name="graphics" type="string"><shortdescription>where to display graphics at each stage</shortdescription><description>Controls where graphics are displayed. Options are screen, file, both, or none.</description>
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<param name="graphics" type="string"><shortdescription>display graphics at each stage to [screen|file|both|none]</shortdescription><description>display graphics at each stage to [screen|file|both|none]</description>
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<value type="string">both</value>
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<allowed kind="enum">
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<value>screen</value>
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<value>file</value>
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<value>both</value>
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<value>none</value>
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<value/>
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</allowed>
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</param>
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<param name="verbose" type="bool"><shortdescription></shortdescription><description/>
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<param name="verbose" type="bool"><shortdescription>report task activity</shortdescription><description>Controls task activity is reported in the log.</description>
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<value>False</value>
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</param>
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<param name="overwrite" type="bool"><shortdescription>overwrite files starting with $project</shortdescription><description>overwrite files starting with $project</description>
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<param name="overwrite" type="bool"><shortdescription>overwrite files starting with $project</shortdescription><description>Controls whether the task will overwrite existing files starting with $project name.</description>
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<value>True</value>
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</param>
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<param visibility="hidden" name="dryrun" type="bool"><shortdescription>only print information [experimental; only for interfermetric data]</shortdescription><description>only print information [experimental; only for interfermetric data]</description>
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<param visibility="hidden" name="dryrun" type="bool"><shortdescription>only print information</shortdescription><description>Experimental feature for interfermetric data only. Controls whether information pertaining to the tclean call and analysis will be recorded and written to files for inspection and adaption.</description>
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<value>False</value>
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</param>
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<param name="logfile" type="string"><shortdescription></shortdescription><description/>
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<param name="logfile" type="string"><shortdescription>user-defined log file</shortdescription><description>Allows for a user-defined log file naming convention if the verbose parameter is set to True.</description>
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<value/>
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</param>
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<constraints>
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<default param="showdifference"><value type="bool">True</value></default>
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<default param="showfidelity"><value type="bool">True</value></default>
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</equals>
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</when>
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</constraints>
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</input>
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<returns type="void"/>
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<example>
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For more information, see the task pages of simobserve in CASA Docs:
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https://casa.nrao.edu/casadocs/
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Please see http://casaguides.nrao.edu, and contact the CASA helpdesk
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with questions.
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</example>
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</task>
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</casaxml>
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</casaxml>