Simulation Guide for New Users (CASA 3.3)

↵ Simulating Observations in CASA

This guide is applicable to CASA version 3.3. For simulation instructions for older versions of CASA see Simdata New Users Guide (CASA 3.2).

To create a script of the Python code on this page see Extracting scripts from these tutorials.

Explanation of the guide

When planning an interferometric observation it is useful to simulate the output of the instrument under a variety of conditions. In CASA, interferometric observations can be simulated using task sim_observe and quickly analyzed using task sim_analyze. This guide will demonstrate how to simulate an ALMA observation using these tasks. (Task sim_observe can also be used to simulate observations with other interferometers, but this currently requires advanced techniques not covered here.)

We begin with an image similar to something that might be observed with ALMA. We show how to rescale the image and specify the ALMA antenna configuration. We produce a simulated set of visibility measurements and then produce an image from the visibility data. In the process, we also generate useful figures to help us analyze the simulated output.

We will assume throughout only a general knowledge of interferometry and no specific knowledge of CASA.

Getting Started

The two things you need to get started are

1. The image we will work with, and
2. CASA version 3.3.

We will use the Spitzer IRAC 8 micron image of 30 Doradus, which you can download from the Simulation Inputs CASA Guide page.

To install CASA, follow the instructions given on the Obtaining CASA page.

CASA Basics

CASA is the post-processing package for ALMA and EVLA and can handle both interferometric and single dish data. Because sim_observe and sim_analyze are tasks within CASA, we start here with a brief introduction to some CASA basics. To learn much more about CASA, go to the CASA homepage. Walk-throughs of CASA data reduction for a variety of data sets can be found on the CASA Guides website.

Starting CASA

Once you have installed CASA, you can launch it by typing "casapy" at the prompt or by double-clicking on the icon, depending on your system and preferences.

Running CASA Tasks

Screen shot of "inp simdata". Note that "chicken" is not a valid value for "setpointings", so it is shown in red. "tsys-atm" is a valid, but not the default, value for "thermalnoise" so it is displayed in blue. The parameter "thermalnoise", in grey, has been expanded based on the value "tsys-atm".

To see a list of all available CASA tasks, at the CASA prompt type

> tasklist

To look at the inputs for an available task, use "inp". For instance

> inp sim_observe

Any parameter with a grey background is expandable. Red text shows an invalid value. Blue text shows a valid, but not default, value.

To get help on a given task, use "help" (to exit from help, hit the "q" key). For instance

> help sim_observe

To reset a task to its default values, use "default". For instance

> default sim_observe

To run a task using the current global values of its input parameters, just type its name at the CASA prompt. For instance

> sim_observe

It's a good idea to double-check these values (i.e., re-run "inp sim_observe") immediately before running a task.

Using sim_observe

Getting Your Input Image Into Simdata

Now we'll tell sim_observe where to find the model (input) image and how to scale it appropriately for our purposes. Just to be safe, we'll first restore the default values of sim_observe and then set the 30 Doradus image as the skymodel (Note: you might need to include the path to your data set, if you are not currently in the working directory where the data set is).

#Initialize sim_observe
default sim_observe
skymodel = '30dor.fits'

We are using a Spitzer 8 micron image of 30 Doradus in this example, and we are going to ask sim_observe to modify this image in angular scale, observed wavelength, and brightness scale.

Angular Scale

If you open the fits image of 30 Doradus in your favorite viewer (e.g. viewer in CASA), you will see that it covers quite a large footprint on the sky, about 10' on a side. We are going to tell sim_observe to rescale the pixels to shrink the image by roughly a factor of 15 (from 2.3" to 0.15" pixels through the incell parameter) so that the model is approximately 40" on a side. This rescaled model will fit within a small mosaic of 6 pointings. Although we do this primarily for convenience in this example, a scientific motivation for this type of rescaling would be to approximate what a super-giant HII region like 30 Doradus would look like if moved from the Large Magellanic Cloud to the distance of M33 or M31. For the sake of demonstration, we will also change the coordinates of the center of the map (using the indirection parameter). Units are case sensitive, please take care to enter them in verbatim, CASA will throw an error otherwise.

incell = '0.15arcsec'
indirection = 'J2000 10h00m00 -40d00m00'

Observed Wavelength

The model image of 30 Doradus shows 8 micron continuum emission. ALMA does not observe at wavelengths this short, so we will tell sim_observe that this is actually a 230 GHz (1.3 mm) continuum map. We will also tell sim_observe that the observations were taken with a 2-GHz bandwidth. Although for this particular example the channel width is not a critical number, it would be very important if we were modifying a spectral cube instead of a continuum image.

incenter = '230GHz'
inwidth = '2GHz'

Brightness Scale

The 8 micron emission is probably not a great approximation for the millimeter emission from 30 Doradus. For a true science case, one would want to calculate what the expected 230 GHz emission would be from an object like this at the distance of about 750 kiloparsec. For the sake of simplicity, we will rescale the image so that the brightest pixel in the map has a flux density of 0.06 mJy. This number is chosen such that the extended emission is a factor of a few brighter than the expected noise in a 2 hour observation. The ALMA sensitivity calculator can be used to determine the expected noise for an observation.

inbright = '0.06mJy/pixel'

After entering the above commands the first part of the sim_observe inputs (inp) will be,

#  sim_observe :: mosaic simulation task:
project             =      'sim'        #  root prefix for output file names
skymodel            = '30dor.fits'      #  model image to observe
     inbright       = '0.06mJy/pixel'   #  scale surface brightness of brightest
                                        #   pixel e.g. "1.2Jy/pixel"
     indirection    = 'J2000 10h00m00 -40d00m00' #  set new direction e.g. "J2000
                                        #   19h00m00 -40d00m00"
     incell         = '0.15arcsec'      #  set new cell/pixel size e.g.
                                        #   "0.1arcsec"
     incenter       =   '230GHz'        #  set new frequency of center channel
                                        #   e.g. "89GHz" (required even for 2D
                                        #   model)
     inwidth        =     '2GHz'        #  set new channel width e.g. "10MHz"
                                        #   (required even for 2D model)

Defining the Mock Observations

Screen shot of input parameters for "setpointings" and "predict"

Now that sim_observe knows how to interpret the input image, the next step is to define the simulated observations.

Pointings and Scan Time

We will first change the parameters within "setpointings"

• integration
• direction
• mapsize
• maptype
• pointingspacing

The default value for "integration", 10 seconds, might be appropriate to simulate real observations. However, sim_observe will run much faster if the value for "integration" is increased, reducing the number of data points to be generated. In this demonstration we will set it to 600 seconds. When simdata is used for scientific purposes it may be best to set "integration" to a large value at first to make sure that sim_observe runs as expected, and then decrease "integration" to a more realistic time for the final run. You will get a more accurate simulation with 10 second integrations than with 600 second integrations, especially in Early Science observations with a limited number of baselines.

integration = '600s'

Note that the integration time is different than the total (on-source) time of the observations. The integration time, set here, is the averaging time for each data point. The total time spent on-source is set below. Each pair of antennas will generate a number of data points equal to the total observing time divided by the integration time.

We will keep "direction" at the default (blank) value to center the observations on the model coordinates, as given in "indirection" above.

We will keep "mapsize" at the default value so that the mosaic will automatically cover the entire image. In our case, this will require a mosaic of 6 pointings (as we will see later on). One could also set an exact output image size via mapsize = ['10arcmin','10arcmin'] for example.

The default mosaic pattern, maptype = 'ALMA', tells sim_observe to use the same hexagonal algorithm as the ALMA OT. We will leave this unchanged.

Finally, we will also leave "pointingspacing" to its default value (blank), which automatically sets the pointings to be half a primary beam apart, corresponding to Nyquist sampling.

Antenna Positions and Total Observation Time

We will now consider the subparameters available when observe = True. We will keep the default values for every parameter (including totaltime = 7200s) except antennalist, which tells sim_observe the locations and sizes of each antenna in the array. We will simulate an Early Science observation, so we will first find the location where CASA has stored the ALMA configuration files. Then we will tell sim_observe to use the configuration file designed for Early Science.

#Set the path where CASA has stored the ALMA configuration files 
repodir = os.getenv("CASAPATH").split(' ')[0]
antennalist =  repodir+"/data/alma/simmos/alma.cycle0.compact.cfg"

The first line, run within CASA, uses a Linux command to determine the path for CASA. The second line sets the antennalist parameter to the Early Science configuration. Other .cfg files in the same directory exist for various ALMA Full Science array configurations as well as the configuration files for other radio interferometers.

Most of the other parameters are not relevant for this simulation as we are not using a component list to describe the sky emission, we do not want to simulate observations of a calibrator, and we do not want to simulate single dish observations. Note that at this stage of simulation development, the time portion of the refdate parameter is ignored and all observations are instead centered around transit on the date specified.

Thermal Noise

For this simple simulation, we will not include any thermal noise in the observations, so we can leave thermalnoise at its default (blank) value.

sim_observe Execution and Output

With all the input parameters set, we are ready to execute the task:

#In CASA
sim_observe

All sim_observe output will be written to a directory whose name was given by the project parameter, in our case, project = 'sim'. Inside this directory, you will find

1. The simulated measurement set (sim.ms),
2. a CASA image of the point spread function (sim.quick.psf),
3. a CASA image of the input sky model rescaled according to the skymodel sub-parameters (sim.skymodel),
4. a flattened CASA image of the input sky model rescaled (sim.skymodel.flat),
5. a flattened PNG image of the input sky model rescaled and overlaid with the mosaic pattern specified by the setpointings sub-parameters (sim.skymodel.png),
6. a 2x2 PNG plot showing,
   1. source elevation vs. time,
   2. antenna position,
   3. uv coverage,
   4. and the point spread function,
7. and an ASCII text listing of mosaic pointings.

When sim_observe is executed, the 2x2 PNG plot will be displayed in the CASA plotter.

Using sim_analyze

Screen shot of input parameters for "image" and "analyze"

Now that sim_observe has created a simulated set of visibility measurements, we are ready to image the visibilities and analyze the result. sim_analyze can perform the imaging and display the image data in a convenient format. We begin by resetting the sim_analyze inputs to their default values.

#In CASA
default sim_analyze

We next setup the imaging and analysis input parameters.

Image

We would like to make a deconvolved output image, but we don't want to spend too much time optimizing the cleaning. So, all we need to do is make sure the "image" parameter is set to True (which it is by default) and leave all of its sub-parameters at their default values. Other data reduction guides describe the process of cleaning in greater detail.

For simulations intended for a proposal or scientific analysis, one would almost certainly want to choose a more appropriate cleaning threshold and define the region to be cleaned. Instructions for how to define the region to be cleaned with the "mask" parameter can be found by typing

> help clean

or by looking at the Clean CASA Guide page.

Analyze

To specify how sim_analyze displays the imaged data, set the parameter "analyze" to True and then pick your favorite output formats. If the graphics parameter is set to 'screen' or 'both', up to six output formats will be displayed in the CASA plotter. More than six outputs can be written to disk (graphics = 'file' or 'both'), but only six can be displayed in the plotter. In this example we will look at,

1. uv coverage in the 2 hour observation
2. Synthesized beam (point spread function)
3. Original sky model (as defined in "modifymodel")
4. Convolved model (sky model convolved with the synthesized beam)
5. Clean image (the sky as observed with the interferometer after deconvolution)
6. and the difference between the clean image and the convolved model.

To make these choices, use the following lines in CASA

#In CASA
analyze = True
showconvolved = True
showfidelity = False

sim_analyze Execution and Output

Execute sim_analyze by typing,

#In CASA
sim_analyze

The six outputs we selected will be displayed in the CASA plotter and written to disk in the sim directory.

All CASA images written to disk can be opened later using the CASA viewer. Just type

> viewer

at the CASA prompt to start the viewer tool. Navigate to the appropriate directory, in our case sim. To display the simulated observations, first click on sim.image, then click the "raster image" button and then click "done". The image will be shown in the viewer, and clicking on the picture of the wrench in the upper left corner will allow you to alter the image in many ways, such as changing the color scale, changing the coordinate scale, and axis labels. The image to the right was created by:

1. Changing "basic settings -> color map" from Rainbow 2 to Hot Metal 1
2. Changing "beam ellipse -> beam style" from outline to filled
3. Changing "color wedge -> display color wedge" from No to Yes

You can learn much more about the functionality of the CASA viewer by watching this instructional video.

↵ Simulating Observations in CASA