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Today's presentation by A. Remijan on ALMA and the OT: [[ALMA-OT-SISS 2014.pdf]]
Today's presentation by A. Remijan on ALMA and the OT: [[Media:ALMA-OT-SISS 2014.pdf]]

Revision as of 00:31, 15 May 2014

Today's presentation by A. Remijan on ALMA and the OT: Media:ALMA-OT-SISS 2014.pdf

The objective of this tutorial is that you understand the key observation parameters which you would need to define to propose for ALMA observations (spatial resolution, sensitivity, spectral setup), and play extensively with the parameters and options in the OT so that you feel comfortable enough to craft your own proposal for the next Call for Proposals. This worksheet is intended as a step-by-step guide on how to prepare a mock proposal for the last ALMA Call for Proposals, by using the ALMA proposal preparation and submission tool ('Observing Tool' or OT). Please feel free to skip any of the proposed steps which you consider not useful or irrelevant for your own training. Many special modes are not described in this basic tutorial. We recommend the OT User Manual for further reference. Sentences in brackets describe things which you would do in the case of a real proposal, and which are not relevant for this tutorial.

Sources characteristics

Before starting the proposal, you should have handy the sources' characteristics (or at least estimates) which will be necessary to define the proposal. These include (but are not limited to):

  • The coordinates of the source(s), their velocity towards the observer (in km/s or redshift)
  • The extent or size of the emission/absorption regions for your source(s) (in arcseconds "), if they are not point-sources
  • Whether the sources' emits continuum emission in the mm-range, and, if it is possible, an estimation of their continuum emission based on your own models or previous observations (in Jy at a given frequency, or in brightness temperature).
  • What molecular species which can observed by ALMA are present (or expected) in the sources. You can use the Splatalogue to determine which lines of interest are encompassed within the ALMA bands. Be careful to include the sources' redshift/velocity when you do your line search.

If you already have a preferred source (or a set of sources) in mind, please use those for this tutorial. Otherwise, you could consider that you are interested in mapping the mm-wave emission from G0.253+0.016, a galactic molecular cloud. This source has already been observed by at submm-wavelengths with the JCMT (Di Francesco et al., 2008), the MALT90 survey (Foster et al., 2011) and Herschel (Molinari et al., 2011). You can look up the source information in the Longmore et al. 2012 paper. If you want to try and set up an ALMA Proposal based more on your science, try looking up the “Did you Know?” document prepared here: Did you Know?. That document contains specifications on sensitivity, largest angular scale, angular resolution, spectral set-ups, etc…that will help guide you through the proposal preparation process. Or, you can also go ahead and just make up something that is sensible to you.

Measurement goals

Now that you know a little more about your source(s), you should decide what are the scientific goals which you want to achieve, and which are the measurements which allow you to meet your scientific goals. For example, measure the continuum distribution with a spatial resolution of 1.5". Or obtain a 10 sigma detection of HCN in a given region of the source. Or both. The measurements must be achievable within the capabilities offered by ALMA. We will here assume that you are proposing for a Cycle 2 project, for which capabilities are listed here.

You should in particular estimate:

  • The spatial resolution do you want to reach
  • The signal to noise do you want to achieve (on the different line detections, on the continuum detection)
  • The frequency range(s) which you want to observe.
    • For continuum observations, the choice of frequency is usually driven by the optimal compromise between signal to noise and spatial resolution. You can play with the continuum reference frequency in the OT to determine which is the best option depending on your goal.
    • For line observations, this choice is driven by the sky frequencies of the lines would be the most suited for your scientific goal (based on your own models, previous publications, line parameters from Splatalogue)
  • The maximal spatial scale which you want to be able to retrieve

It is very likely that will go back and forth and modify your original goals while preparing the proposal, to satisfy constraints on ALMA observational setups, or optimize the signal to noise.

Starting your proposal in the OT [Lets edit this section a bit tomorrow so we see how to start the OT from the given machines]

Now you can open the OT to prepare your proposal

  • type ./ALMA-OT.sh in your shell in the directory where you have installed the OT. Or if you use the web-based OT, just click on the 'Webstart' button on this page: https://almascience.nrao.edu/proposing/observing-tool
  • select 'Create a new proposal' in the pop-up window. You will see a tree structure on the left panel of the OT display, which describes the structure of the proposal.
  • click on 'Proposal' in the tree structure
  • on the main panel, write some high-level information on the proposal (Title, Abstract, Keywords).
  • [add yourself as a PI and collaborators as co-Is. You can only add people who are registered in the ALMA userbase. You can register at almascience.org ('Register' link at the top-right corner)]
  • [attach a pdf of your scientific justification]

Determine the science goals

An ALMA proposal is composed of one or several science goals (SG). A science goal groups observations which can be obtained in the same observation instance. In practice this means that a SG can include a limited number of sources which are sufficiently nearby in the sky (<10 degrees apart), with a single receiver and correlator setup (central rest frequencies, resolution and width of spectral windows). However, a single science goal can be used with several arrays or configurations (for example, ACA and 12-m array, or extended 12-m and compact 12-m configurations). It is also possible to include sources with (limited) different velocities in a single SG, as long as the spectral setup can be observed within a single ALMA band. [From a scientific goal is produced a scheduling block, which is the set of instructions given to the telescope to perform an observation.]

  • [Determine how many science goals will need to be created based on your sources' characteristics and measurement goals]
  • Create one (or several) scientific goals by clicking on the 'target' button on the task bar of the OT ('New phase 1 science goal')
  • In the project tree, click on the newly created SGs. You will see that each SG is divided in 6 sections (General, Field, Spectral, Calibration, Control, Justification)
  • In the general section of each SG, give a distinctive name to the science goal
  • The next sections will guide you on how to define each SG

Define the sources

  • In the tree structure click on the 'Field Setup' section of a SG
  • In the 'source' panel, define the name, coordinates and velocity (in km/s or z) of one source
  • In the 'expected properties' panel define some expected properties (as far as you know)
  • Note that the expected fluxes densities are defined 'per beam'. This corresponds to the flux encompassed in a resolution unit of the size of your requested angular resolution. For example, if you know that you source is a 4"-wide disk emitting 1 Jy of continuum emission total, the peak flux density per beam of 0.4" will be 10 mJy. You can find more information on how to convert the fluxes from other observations in 'expected flux density per beam' here XX [Gerald's tutorial ?)
  • If you want to add additional sources to the SG, click on 'Add Source' at the bottom of the panel
  • Define each additional source coordinates, velocity and expected properties
  • You can flip through the different defined sources by using the tabs at the top of the panel

Define the receiver and correlator setup

  • In the tree structure on the left panel in the display, click on the 'Spectral Setup' section of a SG
  • On the 'Spectral type' line, you need to define if this is a line project (spectral line or spectral scan) or a continuum project
  • At any time you can have a graphic view of your spectral setup plotted over the atmospheric absorption spectrum in the 'Spectral' tab on the top of the panel.
  • If it is a pure continuum project, you will probably want to maximize the observed bandwidth and use the low resolution-large bandwidth mode of the correlator (Time Domain Mode or TDM). Define the receiver band corresponding to your chosen frequency, and you'll be given a default suggested frequency and a correlator setup (4 2-GHz wide spectral windows). You can change the average sky frequency (the corresponding rest frequency the first defined source is shown below).
  • In the case of a line project, you will need to manually define each of the desired spectral windows within the four basebands. Each baseband encompasses at most 2 continuous GHz of the sky spectrum, and can be split in up to 4 spectral windows. There are several rules restricting how basebands and spectral windows within basebands can be setup with respect to each other.
    • Add spectral windows in each baseband. To do that in a given baseband, you can either:
      • click on the 'add' button below the baseband panel. An additional line appears above, in which you write the desired central frequency directly in either the 'rest' frequency' or 'sky' box
      • click on the 'Select Lines to Observe' button below the baseband panel. A line selection window pops up, showing a selection of lines from the Splatalogue catalogue. You can refine your line search by selecting on the left the desired ALMA band, the range of sky frequencies, or the maximum energy state of the transitions. Once you have identified the line you want, highlight it and click on 'Add to selected transitions'. You can then continue your line search and select up to 4 transitions. When you click on 'ok' (bottom right), a spectral window will be created for each of the selected transition. Any unacceptable selection will be highlighted in red in the 'Spectral Setup Errors' box.
    • Define the spectral resolution/bandwidth and spectral smoothing of each spectral window. This is mainly driven by the expected width of the observed spectral lines, and how well you need to resolve them. Note that all spectral windows within a baseband must shared the same resolution before smoothing. The spectral resolution and smoothing determine
  • Select which one of the spectral windows will define the representative frequency for which parameters such as noise, signal to noise and resolution are calculated.

Define the needed arrays and configurations

Depending on your desired angular resolution and the maximal characteristic scale which you want to image, you may need to combine observation from different arrays or array configurations to reach your measurement goals. An extended configuration of the main array (the 12-m array, composed of 34 12-m antennas) may provide an excellent spatial resolution, but filter out large scales. You may compensate this by adding observations in a more compact configuration of the 12-m array, or observations by the ACA (Atacama Compact Array, composed of 9 7-m antennas). You will find more information to understand the concept of largest recoverable scale here https://science.nrao.edu/science/videos/largest-angular-scale-and-maximum-recoverable-scale.

  • In the tree structure on the left panel in the display, click on the 'Control and Performance' section of a SG
  • Enter the desired angular resolution and largest angular structure (LAS)
  • Click on 'Suggest' to see whether the use of ACA is suggested to reach your goals. It may be the case that achieving both the requested angular resolution and LAS is not possible.
  • Depending on the suggestion, click 'yes' or 'no' on the 'Request complementary ACA observations' line.

Define the source pointing pattern

Now that you know the frequency range at which you will observe and the arrays which you will request, you are able to determine if the mapping of your source requires several pointings.

  • In the tree structure on the left panel in the display, click on the 'Field Setup' section of a SG
  • if your source size extends beyond half of the primary beam of the telescope, or if it is composed of several regions of interest which are more than half of the primary beam away from each other, you will need to observe multiple pointings within your source. Estimate if you need one or several pointings.
  • If multiple pointings are needed:
    • you may prefer to define yourself the coordinate of each pointing. Select 'individual pointings' on the 'target type' line. Add as many pointings as desired by clicking on 'Add' at the bottom of the 'Field Center coordinates' panel. You can define the coordinates of each pointing in RA/Dec or offsets from the coordinates defined above.
    • you may prefer to set up regular pattern of pointings so as to ideally cover a given area around the source center. Select 'Rectangular field' on the 'target type' line. You will need to define the size of the area in two directions (p and q), and the spacing between pointings. The OT will suggest a number of pointings with the 12-m array, and - if necessary- a number of pointings with the 7m array.
  • In the 'Spatial' tab (top of the panel), you can obtain a graphic view of the chosen pointing pattern. You will need to upload a fits file of the source or make an image query.

How much time will you need ?

You have now defined most of your observational setup. To verify if all parameters are set in a correct way, run a proposal validation (check mark icon on the main task bar). This will indicate if there are some errors in the proposal and parameters need to be changed.

The signal to noise which you want to achieve drives the required sensitivity, which necessitates a certain amount of observing time to be reached. In Cycle 2, up to 100h per proposal could be allocated, and the typical proposal lasted ~ 8h. Determining the necessary sensitivity is (pretty) simple. You have an idea of the signal to noise you want on your detection (S/N ratio). You have an estimate of the flux density (signal) of the source per beam: for a continuum detection this is the peak continuum flux density. For a line detection, this is the peak flux density averaged over the lowest spectral resolution unit on which you want to achieve a detection (usually, the expected FWHM of the line). The sensitivity (noise) hence corresponds to the flux density per beam divided by the S/N ratio. If the SG combines different lines and continuum detections, each leading to different desired sensitivities, the desired sensitivity for the SG will be defined as the most stringent of these sensitivities.

  • In the tree structure on the left panel in the display, click on the 'Control and Performance' section of a SG
  • Write down your desired sensitivity (in Jy)
  • Write the corresponding bandwidth. For a continuum project, this is the aggregate bandwidth over all spectral windows. For a line project, this is the lowest spectral resolution unit on which you want to achieve the detection.
  • Click on 'Time Estimate'. You will obtain a breakdown of the estimated time to be spent on source and on calibrators. The time estimate will also tell you if your requested spatial resolution is achievable (otherwise, change it).

If you think that your time request is too high with respect to what you could hope being awarded, there are many ways to drive it down. Remember that the observing time varies as the square of the sensitivity, so a small change in requested sensitivity can significantly change the time request.

  • Increase the requested angular resolution. With a larger synthesized beam, the sources' expected flux per beam needs to be increased accordingly. For a constant desired S/N ratio, the corresponding desired sensitivity will be increased.
  • Decrease the size of the area to be mapped - hence decreasing the number of necessary pointings.
  • Increase the spectral resolution unit for line detection.
  • If possible, change the frequency for a frequency offering a better S/N ratio (often at the expense of spatial resolution)
  • Eliminate scientific objectives which are too time-expensive

You may need several iterations to hone the most optimal observation parameters. It is also a good idea to regularly run a proposal validation, to verify if all parameters are still consistent and valid.


  • generate a pdf file of your proposal. In the Tool section at the top of the window, click on 'Generate a pdf'
  • [Submit it: In the File section at the top of the window, click on 'Submit' ]

If you used the G0.253+0.016 example, you can compare your setup with the ALMA observations of the same source which were performed in Cycle 0: http://fr.arxiv.org/abs/1403.4734 (Higuchi et al., 2014)