Simdata CASA 3.1

mosaic simulation task:
mosaic simulation task (prototype):     

    This task simulates interfermetric observations (currently 
    only ALMA can be done easily).  New functionality is actively 
    being added, so if you have changed versions of CASA, check 
    the inputs carefully.
    Please contact CASA experts with any questions, especially 
    about features noted below as *experimental*    
    -------------------------------
    project -- root filename for all output files.
    -------------------------------
    modifymodel -- change the coordinate system of the model sky image?
       * if graphics selected, display the rescaled model image
    skymodel -- if modifymodel=False, use this as the sky model. 
       * if modifyimage=True, use this as the starting point, modify it 
         write the output to a different image (default $project.skymodel)
         and use that new image as the sky model
    inbright -- peak brightness in Jy/pixel, or "" for unchanged
       * NOTE: "unchanged" will take the numerical values in your image 
         and assume they are in Jy/pixel, even if it says some other unit 
         in the header. 
    indirection -- central direction, or "" for unchanged
    incell -- spatial pixel size, or "" for unchanged
    incenter -- frequency of center channel e.g. "89GHz", or "" for unchanged
    inwidth -- width of channels, or "" for unchanged - this should be a 
         string representing a quantity with units e.g. "10MHz"
       * NOTE: only works reliably with frequencies, not velocities
       * NOTE: it is not possible to change the number of spectral planes
         of the sky model, only to relabel them with different frequencies
         That kind of regridding can be accomplished with the CASA toolkit.
    -------------------------------
    setpointings -- calculate a map of pointings, or if false, provide ptgfile
       * if graphics selected, display the pointings shown on the model image
    ptgfile -- a text file specifying directions in the same 
         format as the example, and optional integration times, e.g.
         #Epoch     RA          DEC      TIME(optional)
         J2000 23h59m28.10 -019d52m12.35 10.0
       * if the time column is not present in the file, it will use
         "integration" for all pointings.
       * NOTE: at this time the file should contain only science pointings:
         simdata will observe these, then optionally the calibrator, 
         then the list of science pointings again, etc, until totaltime
         is used up. 
    integration --- Time interval for each integration e.g '10s'
       * NOTE: to simulate a "scan" longer than one integration, use 
         setpointings to generate a pointing file, and then edit the 
         file to repeat each pointing several times before moving to the 
         next point.
    direction -- mosaic center direction e.g 'J2000 19h00m00 -40d00m00'
       * can optionally be a list of pointings
       * otherwise simdata will pack mapsize according to maptype
    mapsize -- angular size of map 
       * set to "" to span the model image
    maptype -- hexagonal or linear 
    pointingspacing -- spacing in between beams e.g '1arcsec'    
    -------------------------------
    predict -- calculate visibilities from skymodel (which may have been 
         modified above, (optionally) complist, and $ptgfile (which 
         may have been generated above)
       * if graphics selected, display the array (like plotants), the uv 
         coverage, the synthesized (dirty) beam, and ephemeris information
    refdate -- central time of simulated observation eg: '2012/05/21/22:05:00'
       * NOTE: observations are currently centered at the nearest transit *
    totaltime --- total time of observation e.g '7200s'
    antennalist -- ascii file containing antenna positions.
         each row has x y z coordinates and antenna diameter; 
         header lines are required to specify the observatory name
         and coordinate system e.g. 
           # observatory=ALMA
           # coordsys=UTM
           # datum=WGS84
           # zone=19
       * standard arrays are found in your CASA data repository, 
         os.getenv("CASAPATH").split()[0]+"/data/alma/simmos/"        
       * if "", will not not produce an interferometric MS
       * NEW: a string of the form "alma;0.5arcsec" will be parsed into a full 12m ALMA
         configuration.  This only works for full ALMA and may fail to find the 
         standard configuration files on some systems - see casaguides.nrao.edu
    caldirection -- *NEW* an unresolved calibrator can be observed 
         interleaved with the science pointings.  This feature is 
         experimental, so please contact us with any questions.
       * The calibrator is implemented as a point source clean component 
         with this direction and flux=calflux
    sdantlist -- antenna position file with antennas to be used for 
         single dish or total power simulation 
       * if "", will not produce a total power MS
    sdant -- the index of the antenna in the list to use for total 
         power.  defaults to the first antenna on the list. 
    -------------------------------
    thermalnoise -- add thermal noise 
       * NOTE: both the interferometric and single-dish MS will be 
         corrupted if they've been created above.
       * currently only knows correct temps for ALMA and EVLA receivers
       * this parameter takes two possible values:
       tsys-atm: J. Pardo's ATM library will be used to construct an
         atmospheric profile for the ALMA site and user_pwv. 
         noise is calculated from the specified ground temperature, 
         internally tabulated antenna spillover parameters, the sky brightness
         temperature returned by ATM, and internally tabulated receiver 
         temperatures
       tsys-manual: instead of using the ATM model, specify the zenith 
         sky brightness and opacity manually.  Noise is added and then
         the visibility flux scale is referenced above the atmosphere. 
    t_ground -- ground/spillover temperature in K 
    user_pwv -- precipitable water vapor if constructing an atmospheric model
    t_sky -- atmospheric temperature in K [for tsys-manual]
    tau0 -- zenith opacity at observing frequency [for tsys-manual]
       * see casaguides.nrao.edu for more information on noise, 
         in particular how to add a phase screen using the toolkit
    -------------------------------
    leakage -- add cross polarization corruption of this fractional magnitude
    -------------------------------
    image -- invert and deconvolve the measurement set(s)
       * NOTE: interactive clean or more parameters than the subset visible
         here are available by simply running the clean task directly, 
         then returning to simdata to run "analyze" if desired.
       * NOTE: the channelization of the output image cube will be the 
         same as that in the simulated Measurement Set.
       * if graphics selected, display the clean image and residual image
       * uses Cotton-Schwab clean for single fields and Mosaic gridding
         for multiple fields (with Clark PSF calculation in minor cycles).
    ms -- the simulated interferometric MS, or total-power one, or both
    modelimage -- prior (e.g. SD) image to be used in clean
    cell -- cell size e.g '10arcsec'.  "" defaults to the skymodel cell
    imsize -- image size in spatial pixels (x,y)
       0 or -1 will use the model image size; example: imsize=[500,500]
    niter -- mumber of clean/deconvolution iterations, 0 for no cleaning
    threshold -- flux level to stop cleaning
    weighting -- weighting to apply to visibilities
       options: 'natural','uniform','briggs' (robust=0.5)
    outertaper -- apply additional uv outer taper of visibilities
    stokes -- Stokes parameters to image; 'I','IV','IQU','IQUV'
    -------------------------------
    analyze -- compute and display difference between model and output, 
         fidelity, etc. 
       * it is recommended to have graphics turned on for this subtask
    showarray -- like plotants
    showuv -- display uv coverage
    showpsf -- display synthesized (dirty) beam
    showmodel -- display sky model at original resolution
    showconvolved -- display sky model convolved with output beam 
    showclean -- display the synthesized image
    showresidual -- display the clean residual image
    showdifference -- display difference image 
    showfidelity -- display fidelity image
    



    -------------------------------
    How to specify a model image:
    -------------------------------
    * simdata requires a CASA or fits image. If you merely have a grid of 
      numbers, you will need to write them out as fits or write a CASA script to
      read them in and use the ia tool to create an image and insert the data.
    
    * simdata does NOT require a coordinate system in the header. If the
      coordinate information is incomplete, missing, or you would like to
      override it, set "modifymodel=True".  simdata will then assume that the
      axes of your input correspond to RA, Dec, and (optionally) frequency and
      (optionally) Stokes parameter.  

    * If you have a proper Coordinate System, simdata will so its best to
      generate visibilities from that, and then create a synthesis image
      according to the specified user parameters.  Regridding the
      spectral dimension may not have complete flexibility yet.

    * You can manipulate an image header with the "imhead" task, or you can
      delve deeper with the ia and cs tools.  If you use the tools, you should
      be aware that a CoordinateSystem in CASA can exist independently of an
      Image.  Once the CoordinateSystem is detached from the image, it is the
      users responsibility to do any manipulation e.g. axis reordering on
      both. Example:
        ia.open("myimage_filename")
        ia.summary() # see header as attached to the image
        csys=ia.coordsys() # detach the CoordinateSystem
        csys.summary() # examine it
        csys.setreferencepixel([100,100]) 
        arr=ia.getchunk() # get the data from the Image
        ia.done()
        csys.reorder([0,2,1])  # reorder the CoordinateSystem
    -------------------------------
    How to specify a model image:
    -------------------------------
    * simdata requires a CASA or fits image. If you merely have a grid of 
      numbers, you will need to write them out as fits or write a CASA script to
      read them in and use the ia tool to create an image and insert the data.
    
    * simdata does NOT require a coordinate system in the header. If the
      coordinate information is incomplete, missing, or you would like to
      override it, set "modifymodel=True".  simdata will then assume that the
      axes of your input correspond to RA, Dec, and (optionally) frequency and
      (optionally) Stokes parameter.  

    * If you have a proper Coordinate System, simdata will so its best to
      generate visibilities from that, and then create a synthesis image
      according to the specified user parameters.  Regridding the
      spectral dimension may not have complete flexibility yet.

    * You can manipulate an image header with the "imhead" task, or you can
      delve deeper with the ia and cs tools.  If you use the tools, you should
      be aware that a CoordinateSystem in CASA can exist independently of an
      Image.  Once the CoordinateSystem is detached from the image, it is the
      users responsibility to do any manipulation e.g. axis reordering on
      both. Example:
        ia.open("myimage_filename")
        ia.summary() # see header as attached to the image
        csys=ia.coordsys() # detach the CoordinateSystem
        csys.summary() # examine it
        csys.setreferencepixel([100,100]) 
        arr=ia.getchunk() # get the data from the Image
        ia.done()
        csys.reorder([0,2,1])  # reorder the CoordinateSystem
        arr=arr.reorder([0,2,1])  # reorder the data         
        ia.fromshape(outfile="mynewimage_file",shape=[32,32,256],csys=csys.torecord(),overwrite=True)
            # make a new image, with the right shape and CoordinateSystem
        ia.putchunk(arr)   # put the data into the new image.
        csys.done()
        ia.done()

    -------------------------------
    Output produced:
    -------------------------------
    Needs rewriting...