Guide To Simulating ALMA Data: Difference between revisions

Latest revision as of 21:23, 1 November 2024

Most recently updated for CASA Version 6.6.1 using Python 3.8

Introduction: About this Document

This document describes why and how to use simulated observations to help understand your ALMA data, or to help you plan an ALMA observation. The document covers:

Why you might want to simulate ALMA observations
How simulations can help you plan a proposal
Examples of simulating ALMA data
Running your own simulations with the ALMA Observation Support Tool
Simulating ALMA observations with CASA sim tools

Why Simulate ALMA Observations?

Observations made with radio interferometers can be tricky to interpret and analyze. Interferometers do not sample all spatial frequencies on the sky, so the image you generate from an interferometric observation does not necessarily represent the full sky brightness distribution. Specifically, interferometers are not sensitive to diffuse emission, and depending on a number of factors including the placement of the individual antennas, the length of the observation, and the location of the target source on the sky, an interferometric observation will be insensitive to structure on some angular scales. Observers therefore should use care when analyzing and interpreting interferometric images.

Plots of "uv coverage" are often used to illustrate the range of spatial frequencies measured by a specific interferometric observation. A uv coverage plot can be thought of as a mask that is applied to the Fourier transform of the emission pattern on the sky. More densely sampled uv coverage leads to better images because the observation is more sensitive to a wider range of spatial frequencies on the sky.

Several interferometers, including ALMA and the VLA, offer a number of antenna configurations, amounting to a "zoom lens" capability. To aid in interpreting their data, observers may find it helpful to simulate an interferometric observation using a variety of antenna configurations and different models of the sky brightness distribution. Simulations can also be a powerful tool to help new users understand both the power and the limitations of interferometric observations.

A Note Regarding Use of ALMA Simulations in your Proposal

Simulations of ALMA observations are not required for an ALMA proposal; however, a simulation could bolster an ALMA proposal in some cases. For example, simulations can demonstrate the need for specific configurations, or combinations of configurations, to resolve certain structures or meet specific scientific goals.

In Full Operations, ALMA will include a main array of fifty 12 m antennas, and the ALMA Compact Array (ACA) which comprises twelve 7 m antennas and four 12 m antennas used for "total power" observations. At this time, every ALMA observation employs the 12-m main array. Observations with the 7-m Array and Total Power antennas are optional, used to fill in large-scale structure in mapping experiments. The ALMA OT advises users on whether to use the ACA based on two numbers: the required resolution and the maximum angular scale. If you have some uncertainty in the spatial scales for your ALMA target, you may wish to use simulations to justify inclusion of the ACA.

Background Information for Those New to Interferometry

Those new to interferometric observing can gain some intuition on the use of interferometers by exploring several software tools available on the web. For example, the Virtual Radio Interferometer is an interactive java application that allows one to simulate basic observations with MERLIN, ATCA, or WSRT, or ASKAP. The VRI can demonstrate how antenna arrangement affects uv coverage, the synthesized beam (i.e. the "resolution"), and the range of spatial sensitivities. Users can select from a few sample, idealized sky brightness patterns (e.g. a narrow gaussian) or use real sky images, then fiddle interactively with the placement of antennas and the duration of the observation to see the effects of uv coverage on observations.

Sample Simulations

Before getting to the details of using ALMA simulation tools, it is useful to examine a few example simulations. These examples were generated with the CASA simulation software described later in this document. These simulations demonstrate how observing with different ALMA configurations can affect the final image.

A Collection of Point Sources

This example shows a simulated observation of a model with multiple point sources. The "plus" symbols in the model image represent locations of the point sources. The panels in this example and those that follow show the model image and the simulated observation with an "extended" array on the top row. The bottom row shows an observation with a compact configuration, and then a compact configuration with the ACA included. The ellipse on the bottom left of the simulated data shows the synthesized beam size. The angular size of the image is approximately 6x6 arcsec.

In general, it is preferable to observe closely-spaced compact sources with an extended configuration, as demonstrated in these simulations. Note that the ACA does not contribute significantly to this observation. It's main contribution comes in observing sources with relatively bright, diffuse emission in addition, perhaps, to compact targets.

---

Point Sources and Elliptical Gaussian Brightness Distributions

Expanding on the first example, here we add several elliptical gaussians to the model with the point sources. Again, the "plus" symbols in the model image represent locations of point sources.

In this case, the extended configuration completely misses the emission from the larger Gaussian component. Only the compact configuration recovers the flux from the extended Gaussian components. Including the ACA gives a more complete representation of the source flux. To recover both the conpact and extended structure in this model would require combining data from multiple main-array configurations, plus the ACA.

---

An M51-like Galaxy

Here we simulate an observation of a galaxy similar in structure to M51, but smaller in angular scale. The extended array observation gives a reasonably good representation of the model image, because most of the apparent emission is on small angular scales. The compact array observation shows a negative "bowl" of emission between the spiral arms because of the missing short-spacing data. By adding the ACA to the compact array observation, the short spacings are recovered and the final flux densities recorded are truer to the model image.

---

ALMA Simulation Tools

ALMA observers have two powerful simulation tools available: the CASA tasks (simalma, simobserve, and simanalyze), and the Observation Support Tool (OST). Both of these simulators are built on the CASA sm toolkit, and both are available from links on the ALMA Science Portal.

Note that significant differences may be seen between the noise predicted by the ALMA Sensitivity Calculator and the measured RMS in simulated images. These differences are primarily a result of the RMS measured in an image depending sensitively on the details of how the image is deconvolved. Noise values determined from CASA simulations or the OST should not be used in a proposal. Only values from the ALMA sensitivity calculator should be used to calculate exposure times for ALMA Science Goals, as it is the ALMA sensitivity calculator that will be used in the technical assessment of ALMA proposals. However, the results of simulations may be helpful to support a request for more observing time than is required by the sensitivity calculator, in order to obtain better uv-plane coverage. Therefore, if using the results from the simulators in a Technical Justification of an observing proposal, users should discuss any significant discrepancies between the RMS in the simulated image and that determined by the sensitivity calculator.

In addition, users should note that the simulator currently underestimates both the surface brightness and the total flux in single dish maps by as much as 20% because of uncertainties in the primary beam shape. Any simulation that uses the TP array will be affected by this calibration issue.

The OST

The OST is a web-based interface hosted by the EU ARC at the University of Manchester. Users who do not have experience with CASA, and who do not need full control of the simulation and imaging process will usually find the OST a good choice for generating simulated images. The GUI works in a straightforward top-down approach. Full documentation for the OST is available.

The OST determines atmospheric opacity in a slightly different way than the CASA simulation tasks, and so it may return slightly different results from the CASA simulation tasks. The differences are most noticeable for simulations in Bands 9 and 10.

CASA simulation tools

CASA provides a powerful capability to simulate interferometric observations with ALMA, as well as other telescopes. The main CASA tasks for simulation are simobserve and simanalyze. The task simobserve generates a data set with simulated visibilities based on an input model image. The task simanalyze produces a cleaned image based on the simulated visibilities, and it generates some diagnostic images.

CASA also provides the task simalma. This task simplifies the steps needed to simulate ALMA observations that combine data from multiple arrays or multiple configurations. For example, users can simulate observations that combine data from the main 12 m array with data from the ALMA Compact Array using simalma.

These tasks are described here: Simulating Observations in CASA. Usage of simalma is described in the final simulation tutorial on that page.

Guide To Simulating ALMA Data: Difference between revisions

Latest revision as of 21:23, 1 November 2024

Contents

Introduction: About this Document

Why Simulate ALMA Observations?

A Note Regarding Use of ALMA Simulations in your Proposal

Background Information for Those New to Interferometry

Sample Simulations

ALMA Simulation Tools

The OST

CASA simulation tools

Navigation menu

Page actions

Page actions

Personal tools

Search

Tools

@@ Line 1: / Line 1: @@
+{{checked_6.6.1}}
 [[Category: Simulations]] [[Category: ALMA]]
-'''THIS PAGE IS UNDER CONSTRUCTION, IN PREPARATION FOR THE ALMA CYCLE 2 CALL FOR PROPOSALS'''
+== Introduction: About this Document ==
-'''This document describes simulations of ALMA observations.  It is applicable to CASA version 4.1.'''
+This document describes why and how to use simulated observations to help understand your ALMA data, or to help you plan an ALMA observation.  The document covers:
+* Why you might want to simulate ALMA observations
+* How simulations can help you plan a proposal
+* Examples of simulating ALMA data
+* Running your own simulations with the ALMA Observation Support Tool
+* Simulating ALMA observations with CASA sim tools
-== Introduction: Why Simulate ALMA Observations? ==
+== Why Simulate ALMA Observations? ==
-Observations made with radio interferometers can be tricky to interpret and analyze.  Interferometers, by their nature, do not sample all spatial frequencies on the sky.  Specifically, they are not sensitive to diffuse emission, and depending on a number of factors including the placement of the individual antennas, the length of the observation, and the location of the target source on the sky, an interferometric observation will be insensitive to some spatial structure in the sky brightness distribution.  Observers therefore should use caution when analyzing and interpreting interferometric images.
+Observations made with radio interferometers can be tricky to interpret and analyze.  Interferometers do not sample all spatial frequencies on the sky, so the image you generate from an interferometric observation does not necessarily represent the full sky brightness distribution.  Specifically, interferometers are not sensitive to diffuse emission, and depending on a number of factors including the placement of the individual antennas, the length of the observation, and the location of the target source on the sky, an interferometric observation will be insensitive to structure on some angular scales.  Observers therefore should use care when analyzing and interpreting interferometric images.
-Plots of "uv coverage" are often used to illustrate the range of spatial frequencies measured by a specific interferometric observation.  The uv coverage plot can be thought of as a mask that is applied to the Fourier transform of the emission pattern on the sky.  More densely sampled uv coverage leads to better images because the observation is more sensitive to a wider range of spatial frequencies on the sky.
+Plots of "uv coverage" are often used to illustrate the range of spatial frequencies measured by a specific interferometric observation.  A uv coverage plot can be thought of as a mask that is applied to the Fourier transform of the emission pattern on the sky.  More densely sampled uv coverage leads to better images because the observation is more sensitive to a wider range of spatial frequencies on the sky.
-To aid in interpreting their data, observers may find it helpful to simulate an interferometric observation using a variety of antenna configurations and different models of the sky brightness distribution.  Simulations can also be a powerful tool to help new users understand both the power and the limitations of interferometric observations.
+Several interferometers, including ALMA and the VLA, offer a number of antenna configurations, amounting to a "zoom lens" capability.  To aid in interpreting their data, observers may find it helpful to simulate an interferometric observation using a variety of antenna configurations and different models of the sky brightness distribution.  Simulations can also be a powerful tool to help new users understand both the power and the limitations of interferometric observations.
-=== When to Use ALMA Simulations in your Proposal ===
+=== A Note Regarding Use of ALMA Simulations in your Proposal ===
-Simulations of ALMA observations are not required for an ALMA proposal; however, in some cases, an ALMA simulation could bolster a proposal.  For example, simulations can demonstrate the need for specific configurations, or combinations of configurations, to resolve certain structures or meet specific scientific goals.
+Simulations of ALMA observations are not required for an ALMA proposal; however, a simulation could bolster an ALMA proposal in some cases.  For example, simulations can demonstrate the need for specific configurations, or combinations of configurations, to resolve certain structures or meet specific scientific goals.
-At this time, every ALMA observation employs the 12-m main array.  The ACA and Total Power arrays are optional.  The ALMA OT advises users on whether to use the ACA based on two numbers: the required resolution and the maximum angular scale.  If you have some uncertainty in the spatial scales for your ALMA target, you may wish to use simulations to justify inclusion of the ACA.
+In Full Operations, ALMA will include a main array of fifty 12 m antennas, and the ALMA Compact Array (ACA) which comprises twelve 7 m antennas and four 12 m antennas used for "total power" observations.  At this time, every ALMA observation employs the 12-m main array.  Observations with the 7-m Array and Total Power antennas are optional, used to fill in large-scale structure in mapping experiments.  The ALMA OT advises users on whether to use the ACA based on two numbers: the required resolution and the maximum angular scale.  If you have some uncertainty in the spatial scales for your ALMA target, you may wish to use simulations to justify inclusion of the ACA.
-=== Web Tools for Those New to Interferometry ===
+=== Background Information for Those New to Interferometry ===
-There are several tools available on the web to help observers understand interferometric data and simulate observations.  For example, those new to interferometry can get a basic understanding of how antenna placement affects uv coverage, the synthesized beam (i.e. the "resolution"), and the range of spatial sensitivities by exploring the [http://www.narrabri.atnf.csiro.au/astronomy/vri.html Virtual Radio Interferometer].  This is an interactive java application that allows one to simulate basic observations with MERLIN, ATCA, or WSRT, or ASKAP.  The user can select from a few sample, idealized sky brightness patterns (e.g. a narrow gaussian) or use real sky brightness patterns, then fiddle interactively with the placement of antennas and the duration of the observation to see the effects of uv coverage on observations.
+Those new to interferometric observing can gain some intuition on the use of interferometers by exploring several software tools available on the web.  For example, the [http://www.narrabri.atnf.csiro.au/astronomy/vri.html Virtual Radio Interferometer] is an interactive java application that allows one to simulate basic observations with MERLIN, ATCA, or WSRT, or ASKAP.  The VRI can demonstrate how antenna arrangement affects uv coverage, the synthesized beam (i.e. the "resolution"), and the range of spatial sensitivities.  Users can select from a few sample, idealized sky brightness patterns (e.g. a narrow gaussian) or use real sky images, then fiddle interactively with the placement of antennas and the duration of the observation to see the effects of uv coverage on observations.
-=== Sample Simulations ===
+== Sample Simulations ==
-Here we include several sample simulations of ALMA observations to demonstrate the capabilities of different array configurations.  These simulations were generated with the CASA simulation tools, which are described below.
+Before getting to the details of using ALMA simulation tools, it is useful to examine a few example simulations.  These examples were generated with the CASA simulation software described later in this document.  These simulations demonstrate how observing with different ALMA configurations can affect the final image.
 {| style="width: 100%; valign: top; background-color:#E0E0E0; border:1px solid #3366FF; text-align: left; cellpadding=0"
-| rowspan=2; stype="border-bottom:1px solid black;" | [[File:points-panels.png | 200px]]
+| rowspan=2; stype="border-bottom:1px solid black;" | [[File:Points-panels-hf.png | 200px]]
+! A Collection of Point Sources
 |-
-| style="border-bottom:1px solid black;" | This example shows a simulated observation of a model with multiple point sources.  The "plus" symbols in the model image represent locations of the point sources.  The panels in this example and those that follow show the model image and the simulated observation with an "extended" array on the top row.  The bottom row shows an observation with a compact configuration, and then a compact configuration with the ACA included.  The ellipse on the bottom left of the simulated data shows the synthesized beam size.  The angular size of the image is XX" by XX" (get this from Juergen).
+| style="border-bottom:1px solid black;" | This example shows a simulated observation of a model with multiple point sources.  The "plus" symbols in the model image represent locations of the point sources.  The panels in this example and those that follow show the model image and the simulated observation with an "extended" array on the top row.  The bottom row shows an observation with a compact configuration, and then a compact configuration with the ACA included.  The ellipse on the bottom left of the simulated data shows the synthesized beam size.  The angular size of the image is approximately 6x6 arcsec.
+In general, it is preferable to observe closely-spaced compact sources with an extended configuration, as demonstrated in these simulations.  Note that the ACA does not contribute significantly to this observation.  It's main contribution comes in observing sources with relatively bright, diffuse emission in addition, perhaps, to compact targets.
 |-
 |}
@@ Line 36: / Line 45: @@
 {| style="width: 100%; valign: top; background-color:#E0E0E0; border:1px solid #3366FF; text-align: left; cellpadding=0"
-| rowspan=2; stype="border-bottom:1px solid black;" | [[File:gaussians-panels.png | 200px]]
+| rowspan=2; stype="border-bottom:1px solid black;" | [[File:Gaussians-panels-hf.png | 200px]]
+! Point Sources and Elliptical Gaussian Brightness Distributions
 |-
-| style="border-bottom:1px solid black;" | Expanding on the first example, here we expand the model by adding several elliptical gaussians to the point sources.  Again, the "plus" symbols in the model image represent locations of point sources.
+| style="border-bottom:1px solid black;" | Expanding on the first example, here we add several elliptical gaussians to the model with the point sources.  Again, the "plus" symbols in the model image represent locations of point sources.
+In this case, the extended configuration completely misses the emission from the larger Gaussian component.  Only the compact configuration recovers the flux from the extended Gaussian components.  Including the ACA gives a more complete representation of the source flux.  To recover both the conpact and extended structure in this model would require combining data from multiple main-array configurations, plus the ACA.
 |-
 |}
@@ Line 45: / Line 57: @@
 {| style="width: 100%; valign: top; background-color:#E0E0E0; border:1px solid #3366FF; text-align: left; cellpadding=0"
-| rowspan=2; stype="border-bottom:1px solid black;" | [[File:m51-panels.png | 200px]]
+| rowspan=2; stype="border-bottom:1px solid black;" | [[File:M51-panels-hf.png | 200px]]
+! An M51-like Galaxy
 |-
-| style="border-bottom:1px solid black;" | Here we simulate an observation of a galaxy.  The angular scale is XX" by XX".
+| style="border-bottom:1px solid black;" | Here we simulate an observation of a galaxy similar in structure to M51, but smaller in angular scale.  The extended array observation gives a reasonably good representation of the model image, because most of the apparent emission is on small angular scales.  The compact array observation shows a negative "bowl" of emission between the spiral arms because of the missing short-spacing data.  By adding the ACA to the compact array observation, the short spacings are recovered and the final flux densities recorded are truer to the model image.
 |-
 |}
 ---
+<!--
 {| style="width: 100%; valign: top; background-color:#E0E0E0; border:1px solid #3366FF; text-align: left; cellpadding=0"
-| rowspan=2; stype="border-bottom:1px solid black;" | [[File:proto-panels.png | 200px]]
+| rowspan=2; stype="border-bottom:1px solid black;" | [[File:Proto-panels-hf.png | 200px]]
+! A Simplified Model of a Proto-planetary Disk
 |-
-| style="border-bottom:1px solid black;" | This simulation shows a ring plus a compact target.
+| style="border-bottom:1px solid black;" | This simulation shows an observation of a model image representing a ring plus a planet.  With most of the emission on small angular scales, the extended array observation is best at picking out the structures.  The compact configuration + ACA appears shows some minor deformities because of the manner in which the data were deconvolved.  Observations that combine data from multiple arrays or array configurations should be deconvolved ("cleaned") with care to maximize image fidelity.
 |-
 |}
+-->
 == ALMA Simulation Tools ==
-ALMA observers have two powerful simulation tools available: the CASA sim_observe/sim_analyze tasks, and the [http://almaost.jb.man.ac.uk/ Observation Support Tool (OST)].  Both of these simulators are built on the CASA sm toolkit, and both are available from links on the [https://almascience.nrao.edu/ ALMA Science Portal].
+ALMA observers have two powerful simulation tools available: the CASA tasks ({{simalma_6.6.1}}, {{simobserve_6.6.1}}, and {{simanalyze_6.6.1}}), and the [http://almaost.jb.man.ac.uk/ Observation Support Tool (OST)].  Both of these simulators are built on the CASA sm toolkit, and both are available from links on the [https://almascience.org/ ALMA Science Portal].
+Note that significant differences may be seen between the noise predicted by the [https://almascience.org/proposing/sensitivity-calculator/ ALMA Sensitivity Calculator] and the measured RMS in simulated images. These differences are primarily a result of the RMS measured in an image depending sensitively on the details of how the image is deconvolved.  Noise values determined from CASA simulations or the OST should not be used in a proposal.  Only values from the ALMA sensitivity calculator should be used to calculate exposure times for ALMA Science Goals, as it is the ALMA sensitivity calculator that will be used in the technical assessment of ALMA proposals.  However, the results of simulations may be helpful to support a request for more observing time than is required by the sensitivity calculator, in order to obtain better uv-plane coverage.   Therefore, if using the results from the simulators in a Technical Justification of an observing proposal, users should discuss any significant discrepancies between the RMS in the simulated image and that determined by the sensitivity calculator.
-Note that significant differences may be seen between the noise predicted by the ALMA Sensitivity Calculator and the measured RMS in simulated images. These differences are primarily a result of the RMS measured in an image depending sensitively on the details of how the image is deconvolved. The ALMA sensitivity calculator is the primary tool used for time estimates during the technical assessment of ALMA proposals.  Therefore, if using the results from the simulators in a Technical Justification of an observing proposal, users should discuss or reconcile any significant discrepancies between the RMS in the simulated image and that determined by the sensitivity calculator.
+In addition, users should note that the simulator currently underestimates both the surface brightness and the total flux in single dish maps by as much as 20% because of uncertainties in the primary beam shape.  Any simulation that uses the TP array will be affected by this calibration issue.
 == The OST ==
-The OST is a web-based interface hosted by the EU ARC at the University of Manchester.   Users who do not have experience with CASA, and who do not need full control of the simulation and imaging process will usually find the OST a good choice for generating simulated images.  The GUI works in a straightforward top-down approach.  Full documentation for the OST is available [http://almaost.jb.man.ac.uk/help/ here].
+The [http://almaost.jb.man.ac.uk/ OST] is a web-based interface hosted by the EU ARC at the University of Manchester.   Users who do not have experience with CASA, and who do not need full control of the simulation and imaging process will usually find the OST a good choice for generating simulated images.  The GUI works in a straightforward top-down approach.  [http://almaost.jb.man.ac.uk/help/ Full documentation for the OST] is available.
-The OST determines atmospheric opacity in a slightly different way than the CASA sim tasks, and so it may return slightly results from the CASA sin tasks.  The differences are most noticeable for simulations in Bands 9 and 10.
+The OST determines atmospheric opacity in a slightly different way than the CASA simulation tasks, and so it may return slightly different results from the CASA simulation tasks.  The differences are most noticeable for simulations in Bands 9 and 10.
 == CASA simulation tools ==
-Simulating ALMA observations in CASA proceeds in the following steps:
+CASA provides a powerful capability to simulate interferometric observations with ALMA, as well as other telescopes.  The main CASA tasks for simulation are {{simobserve_6.6.1}} and {{simanalyze_6.6.1}}.  The task {{simobserve_6.6.1}} generates a data set with simulated visibilities based on an input model image.  The task {{simanalyze_6.6.1}} produces a cleaned image based on the simulated visibilities, and it generates some diagnostic images.
-# Make a model image.  The model image is a representation of the sky brightness distribution that you would like to simulate observing, stored initially as a FITS file.  There are several paths to making the FITS file, discussed below.
-# Generate uv data with the <tt>simobserve</tt> task.
-# Image the simulated observation with the <tt>simanalyze</tt> task.
-The [http://casa.nrao.edu/stable/docs/TaskRef/simobserve-task.html <tt>simobserve</tt>] task generates the visibilities that would be measured by observing the specified input model of sky brightness.  The user needs to specify a telescope to use for the observation.  CASA includes a set of configuration files for ALMA, the VLA, CARMA, the SMA, ATCA, and the Plateau de Bure interferometers.  The specific configuration files shipped with a CASA installation are available [http://casaguides.nrao.edu/index.php?title=Antenna_Configurations_Models_in_CASA here].  The <tt>simobserve</tt> task can add thermal noise to the visibilities.  The <tt>simobserve</tt> task uses the [http://www.mrao.cam.ac.uk/~bn204/alma/atmomodel.html aatm] atmospheric model (based on Juan Pardo's [http://damir.iem.csic.es/PARDO/class_atm.html ATM] library) to simulate real observing conditions and introduce atmospheric "corruption", i.e. noise and phase delay.
-Next, the [http://casa.nrao.edu/stable/docs/TaskRef/simanalyze-task.html <tt>simanalyze</tt>] task is used to produce a cleaned image based on the generated visibilities.  It can compare the simulated image with your input (convolved with the output clean beam) and then calculate a "fidelity image" that indicates how well the simulated output matches the convolved input image.
-=== Generating a Model Image ===
-A "model image" is a FITS file that contains a representation of the sky brightness distribution, and it represents the object to be "observed" in the simulation.  The FITS file must contain a realistic set of spatial axes, and a realistic flux density.  There are several ways to generate a model image.
-* '''An existing FITS image'''
-The simplest option is to begin with an existing FITS image of a millimeter or submillimeter observation.  The FITS image can be either a single plane (i.e. one observed frequency channel) or a cube.  A common simulation exercise is to begin with a FITS file representing an observation of a target, then scale the spatial axes and the flux to shift the data to what would be observed for a similar target at a different distance.  The <tt>simobserve</tt> task has parameters to set the peak flux density, coordinates on the sky, pixel size, frequency of the center channel, and channel width.  See the discussion below.
-* '''A component list'''
-It may be useful to simulate observations of an idealized model image consisting, for example, of point sources and Gaussians.  The CASA component list tool (<tt>cl</tt>) allows the user to create a FITS file by specifying a set of point sources, Gaussians, disks, and limb-darkened disks.  Each of these is a "component" in the FITS image.  [http://casaguides.nrao.edu/index.php?title=Simulation_Guide_Component_Lists_%28CASA_4.1%29 This CASA guide] provides an example of creating a FITS file from a component list.
-* '''A GIF or JPG image'''
-A user may wish to convert a GIF or JPG image to a FITS file for simulation in CASA.  The image should be converted to a 16-bit FITS image for use with the CASA sim tools.  See [http://casaguides.nrao.edu/index.php?title=Convert_jpg_to_fits this page] for an example of using <tt>gimp</tt> to convert a JPG image to a FITS file.  Alternatively, you could use ImageMagik, like so:
- convert myfile.jpg myfile.fits
-Then proceed to trim and convert the file in CASA like so:
- importfits(fitsimage='myfile.fits',imagename='testimage',overwrite=T)
- default 'immath'
- imagename = 'testimage'
- expr = 'IM0'
- box = '0,0,299,299'
- outfile = 'testimage2'
- immath()
- exportfits(imagename ='testimage2',fitsimage ='myfile_16bit.fits',bitpix=16,overwrite=T)
-You could also use the parameters in the <tt>simobserve</tt> task to modify the peak flux density, coordinates on the sky, pixel size, frequency of the center channel, and channel width.  See the discussion below.
-=== Generating visibilities with '''simobserve''' ===
-The task [http://casa.nrao.edu/stable/docs/TaskRef/simobserve-task.html <tt>simobserve</tt>] takes several steps to generate observed visibilities.  The major steps are:
-* Modify Model.  If desired, you can modify the header parameters in your data model to mimic different observing targets.  For example, if you start with a model of M100 you might wish to scale the axes to simulate an observation of an M100-like galaxy that is 4X more distant.  The settable parameters include:
-** '''inbright''': Scaling the model flux densities by setting the peak flux density of the brightest pixel, e.g. "1.2Jy/pixel"
-** '''indirection''': Set the center target coordinates, e.g. "J2000 19h00m00 -40d00m00"
-** '''incell''': Set the angular size of each pixel, e.g. "0.1arcsec"
-** '''incenter''': Set the observed sky frequency.  If the model is a spectral cube, this parameter applies to the center channel.
-** '''inwidth''': Set the channel width, e.g. "10MHz"
-* Set Pointings. If the angular size of your model image is comparable or larger than the 12-m primary beam, you can simulate observing the target as a mosaic.  In this step, the individual pointings are determined and saved in a text file.  You can also generate such a text file yourself.
-* Generate visibilities.  The visibilities are determined based on the telescope and configuration specified, and the length in time of the observation.
-* Add noise.  Finally, noise is added to the visibilities.
-=== Transforming to images with '''simanalyze''' ===
-The task [http://casa.nrao.edu/stable/docs/TaskRef/simanalyze-task.html <tt>simanalyze</tt>] then images the visibility data using CASA's [http://casa.nrao.edu/stable/docs/TaskRef/clean-task.html <tt>clean</tt>] task.  It also calculates and displays the difference between the simulates observation and the original model data, and it generates a "fidelity image".  Fidelity is defined as I/| I-T |, where I is the observed image intensity and T is the true image intensity, given in this case by the sky model.
-## Image - Image the visibility data with CASA's [http://casa.nrao.edu/stable/docs/TaskRef/clean-task.html <tt>clean</tt>] task.
-## Analyze - Calculate and display the difference between output and input, and the fidelity image.
-The [http://casaguides.nrao.edu/index.php?title=Simulation_Guide_for_New_Users_CASA_4.1 Simulation Guide for New Users] tutorial introduces and explains the individual steps in detail.  It is possible to run the steps independently and optionally, as long as you follow the <tt>simobserve</tt> and <tt>simanalyze</tt> conventions about filenames.
-<u>Taskname History</u>
-The simulation tasks have been under significant revision and development.
-* In CASA 3.3 <tt>simobserve</tt> and <tt>simanalyze</tt> were named <tt>sim_observe</tt> and <tt>sim_analyze</tt>, respectively.
-* In CASA 3.4 and earlier, the functionality of both tasks was contained in task simdata, which is now obsolete.
-* In CASA 4.1, a new experimental task [http://casa.nrao.edu/stable/docs/TaskRef/simalma-task.html <tt>simalma</tt>] has been introduced, which simplifies simulation of 12m interferometric + 7m interferometric + total power ALMA observations.  Please report any issue with <tt>simalma</tt>, and check back here for an upcoming <tt>simalma</tt> casaguide.
-'''Values from <tt>simobserve</tt> or the OST should not be used to calculate exposure times for ALMA Science Goals.  Only values from the ALMA sensitivity calculator should be used for this purpose, as it is the ALMA sensitivity calculator that will be used in the technical assessment of ALMA proposals.  However, the results of simulations may be helpful to support a request for more observing time than is required by the sensitivity calculator, in order to obtain better uv-plane coverage.'''
-== Tutorials ==
-{| style="width: 100%; valign: top; background-color:#E0FFFF; border:1px solid #3366FF; text-align: center; cellpadding=0"
-! [[Simulation Guide for New Users (CASA 4.1)]]
-| rowspan=2 style="border-bottom:1px solid black;" | [[File:30Dor_ES.png|100px]]
-|-
-| style="border-bottom:1px solid black;" | A fully annotated tutorial that uses a Spitzer SAGE 8 micron continuum image of 30 Doradus and scales it to greater distance.  A good place for new users to start.
-|-
-! [[Protoplanetary Disk Simulation (CASA 4.1)]]
-| rowspan=2; stype="border-bottom:1px solid black;" | [[File:Psimthumb.png|100px]]
-|-
-| style="border-bottom:1px solid black;" | A sky model with a lightly annotated script that simulates a protoplanetary disk.  Uses a theoretical model of dust continuum from Sebastian Wolff, scaled to the distance of a nearby star.   This is another fairly generic simulation - if you're short on time, you probably don't need to go through this one and the New Users guide, but it can be useful to go through multiple examples.
-|-
-<!--
-! [[M51 at z = 0.1 and z = 0.3 (CASA 4.1)]]
-| rowspan=2; style="border-bottom:1px solid black;" | [[File:M51thumb.png|100px]]
-|-
-| style="border-bottom:1px solid black;" | A fully annotated tutorial that uses a BIMA-SONG cube of a nearby galaxy and scales it to greater distance.
-|- -->
-! [[Simulation Guide Component Lists (CASA 4.1)]]
-| rowspan=2; style="border-bottom:1px solid black;" | [[File:Analyze_fits_list.jpg|100px]]
-|-
-| style="border-bottom:1px solid black;" | Tutorial for simulating data based on multiple sources (using both a FITS image and a component list).  If you are interested in simulating from a list of simple sources (point, Gaussian, disk), rather than or in addition to a sky model image, then read the considerations here.
-|-
-<!--
-! [[N891 simdata (CASA 3.4)]]
-| rowspan=2; style="border-bottom:1px solid black;" | [[File:N891thumb.png|100px]]
-|-
-| style="border-bottom:1px solid black;" | A sky model, script, and discussion that simulates a nearby edge-on spiral galaxy. Uses a galactic CO cube from the Galactic Ring Survey and places it at 10Mpc. The data are similar to what NGC891 would look like if it were observable from the southern hemisphere.
-|- -->
-! [[Einstein-Face (CASA 4.1)]]
-| rowspan=2; style="border-bottom:1px solid black;" | [[File:einstein_fs_cfg8_1hr.gif|100px]]
-|-
-| style="border-bottom:1px solid black;" | A sky model and lightly annotated script that simulates the face of Einstein as seen by ALMA.  This simulation is particularly useful for those who wish to better understand spatial filtering by an interferometer, but doesn't demonstrate new capabilities of the simulation tasks beyond those described above.
-|-
-! [[ACA Simulation (CASA 4.1)]]
-| rowspan=2; style="border-bottom:1px solid black;" | [[File:M51c.ALMA 0.5arcsec.skymodel.png|100px]]
-|-
-| style="border-bottom:1px solid black;" | A tutorial for simulating ALMA observations that use multiple configurations or use the 12-meter array in combination with the ALMA Compact Array.  This tutorial demonstrates combining data from each ALMA component "by hand".  This guide is of particular interest to those wishing to explore using the 12-m array in combination with the ACA, and those interested in combining data from multiple 12-m array configurations.
-|-
-! [http://casaguides.nrao.edu/index.php?title=Simalma_v2 simalma]
-| rowspan=2; style="border-bottom:1px solid black;" | [[File:M51c.ALMA 0.5arcsec.skymodel.png|100px]]
-|-
-| style="border-bottom:1px solid black;" | This tutorial demonstrates how to use '''simalma''', a task that simplifies simulations that include the main 12-m array plus the ACA.  Like the previous guide, this one is of particular interest to those wishing to explore multi-component ALMA observations.
-|}
-=== Example Input Images ===
-Several examples of input model images are showcased here: [[Sim Inputs]].  These may be useful for running your own simulation tests, beyond what are presented in the above tutorials.
-== Advanced CASA Simulation ==
-=== Under the Hood: The sm Tool ===
-<tt>simobserve</tt> calls methods in the '''sm''' (simulation) tool.  For advanced CASA users, the <tt>sm </tt> tool has methods that can add to simulated data: phase delay variations, gain fluctuations and drift, cross-polarization, and (coming soon) bandpass and pointing errors.  <tt>sm </tt> also has more flexibility than <tt>simobserve</tt> in adding thermal noise.  The tutorials linked from this page describe the simulation of data using the task interface only.  To learn more about the <tt>sm</tt> tool, see the [http://casa.nrao.edu/docs/CasaRef/CasaRef.html CASA Toolkit Reference Manual].
-The <tt>sm </tt> tool can be used to corrupt your measurement set with thermal noise, phase noise, cross-polarization, etc., in a more advanced way than is done in <tt>simobserve</tt>.  To learn advanced techniques for corrupting a simulated measurement set, see [[Corrupt]].
-=== Ephemeris and Geodesy ===
-Generic ephemeris and geodesy calculations can be done using CASA Python module [[simutil.py]].
-== Warning: CLEAN Bias ==
-As is the case for real images, cleaning images produced by <tt>simobserve</tt> can lead to a spurious decrease in object fluxes and noise on the image (an effect known as "clean bias"). This is particularly true for observations with poor coverage of the uv-plane, i.e. using telescopes with small numbers of antennas, such as the ALMA Early Science configurations, and/or in short "snapshot" observations. Users should always clean images with care, using a small number of iterations and/or a conservative (3-5sigma) threshold and boxing bright sources.
-== User Feedback ==
+CASA also provides the task {{simalma_6.6.1}}.  This task simplifies the steps needed to simulate ALMA observations that combine data from multiple arrays or multiple configurations.  For example, users can simulate observations that combine data from the main 12 m array with data from the ALMA Compact Array using {{simalma_6.6.1}}.
-We welcome input on developing the CASA simulator.  Contact "rindebet at nrao.edu" if you would like to volunteer your input.
+These tasks are described here: [[Simulating Observations in CASA]].  Usage of {{simalma_6.6.1}} is described in the final simulation tutorial on that page.