Preparing heterodyne observation files (MSBs)
Preparing Heterodyne observations
Experienced as well as novice observers should make sure to read
manual section: the DRRecipe
Component. Also, you are advised to read the manual
secion on 'Heterodyne MSBs'. A detailed and technical discussion 'Heterodyne
Obsmodes' is also available.
Contents A Guided Tour of an Example MSB (Beam-Switched
The Heterodyne MSB library
Guided Tour of an Example MSB (Beam-Switched Sample)
Go to the JCMT root window, and open the ACSIS library by clicking on :
A window will pop up containing a list of folders. The little switch
on the left of the folder icons is an open/close toggle switch. Push
open the folder titled "Samples" and then select the MSB labeled
"Beam-switch sample(1X) " and click "Copy" on the toolbar.
Now go back to your Science Program window, and click on "Paste". The
MSB will be dropped into your science program. Congratulations! You're
now well underway. Now is a good time to save your progress, so use
the File->Save option in your Science Program window and carry
Really Important Aside - or is it Inside?
Do you see how the icon for the MSB is not directly below the icon for the
Science Program but indented to the right? That's because the MSB is
inside the Science Program. This is a classic way of representing
a hierarchical structure, and many of you will be familiar with it from
other applications, such as the "Manage Bookmarks" screen in the Netscape
and Mozilla browsers.
Editing the MSB component
Click on the title of the MSB. This will activate the MSB
editor panel on the right section of your window.
The properties of an MSB are very simple:
There is also a display of the OT's estimate of how long the MSB will
- It has a title, at the moment "Beam-switch sample". When
preparing your own MSB, this title should be changed to something
meaningful describing the observation, usually with target
name. Examples might be "B/SW observation of OMC1" or "3 point grid of
M83". Please take the time to do this - it really
helps the person doing the observing.
- A pull down menu with a repeat counter. Leave that to 1 for the
- The priority of the MSB. Note that this only affects the internal
priority of your MSBs - not the priority allocated to your entire
project by your TAG. So if you had two different MSBs that rose to the
top of the scheduling queue and one had priority "1" and the other
"99", the one marked "1" will normally get done first. If all your
MSBs are of equal interest to you, just don't bother changing the
Small print: Bear in mind though that MSB selection is an operational
decision - marking your MSBs with priorities 1, 2, 3 etc is no
guarantee that they will be done in precisely that particular
order. For example, your lower-priority MSBs could be done because
they are observable at a time of day where there is not much else in
the queue, whereas your high-priority MSBs could be competing against
the top-ranked project. Also, the observer/TSS may sometimes select a
lower priority MSB because it is the most efficient choice at the
time, because of its duration or azimuth.
Elements of an MSB
Click on the push lever to open up your MSB. Inside you will find a
Het Setup component, a Target Info. component, a Site Quality
component, and an observation component which is labelled
Components, Iterators And All That
are individually schedulable blocks and
contain one or more fully specified science
observation and any calibrations. For heterodyne observations,
calibrations will be described in a show-to-observer note.
are observations of a single astronomical
target and contain components and a sequence.
are configurators for the JCMT systems such as
the instrument (het setup component), the telescope (Target
component) and the scheduler (Site Quality component).
are potentially multiple actions and
contain other iterators and one or more
are actions that results in the actual taking
of data - a single data file per eye to be precise.
are a repository of useful information and can
We'll now go through these individually.
The Het Setup component
If you click on the "Het Setup" component you will see the window
below. The purpose of this component is to enable the configuration of
the required heterodyne instrument (the Front End) and ACSIS (the
'back end') prior to an observation.
Four boxes are displayed in the editor panel.
Front End Configuration
- The first item in the Het Setup component enables the user to
choose the required receiver or Front End. The tuning/frequency
range over which the selected receiver can be tuned is displayed in
the Front End Summary box in the top-right corner.
- The Sp.(ectral) regions box allows the selection of
multiple spectral windows. Multiple spectral regions are especially
useful if you wish to observe simultaneously two to four spectral
lines which lie within the same 1.8GHz passband, e.g. H2D+ at 372.4GHz
and N2H+ at 372.67GHz. Commonly used line combinations and
configurations are listed in the Special Config(uration)s
pull-down menu to the right, and are described here. If the configuration you wish
is not in the list, you can create your own using the Frequency Editor described below. The Frequency Editor tool is shown and
hidden using the buttons further down the window. Also, please send a
message to your Friend of the
Project" so we can perhaps add this configuration to the list in
- The Bandwidths menu item allows the selection of the
required bandwidth (in MHz) for each Spectral Region. The resulting
spectral resolution (in kHz) is shown automatically updated in the
"res" entry in the Frequency Configuration table at the bottom of the
Het Setup menu.
- The Mode box allows a choice between double sideband (dsb)
and single sideband (ssb) operation. Note that only receiver W allows
to choose between ssb and dsb: receiver A is a dsb receiver and HARP
a ssb receiver.
- The Sideband menu allows the choice of sideband. Sideband
suppression is not absolute in the SSB receivers, so the user should
avoid, if possible, the situation where the unwanted sideband
corresponds to a frequency where the zenith opacity or receiver noise
is high. In most cases, however, you could simply select "Best".
Tuning of the receiver requires a rest frequency and a velocity. If
the aim is to observe a specific molecular transition the user may use
the pull-down lists of molecules and transitions to
generate the frequency. (If the particular line/transition you are
interested in is not in the list, please send an email to firstname.lastname@example.org so
that the line can be added for the next release.) The example above
shows a special configuration
(HARP_H2DN2H_250X2) with the H2D+ 1(1 0 0)-1(1 1 0) transition at
272.4GHz, and the N2H+ 4-3 transition at 272.7GHz, both using the
250MHz bandwidth mode, observed simultaneously. Alternately, the
tuning frequency may be specified explicitly in GHz. The frequency
will appear in RED until the
Accept button is clicked. This is essential to ensure
acceptance of the input. This method will also result in the
phrase 'No line' appearing in the molecule and transition fields, even
if the frequency does in fact correspond to a known
transition. (Look-up occurs from molecule/transition to frequency only
- no look-up is done in the opposite direction).
The velocity of the target may be entered either here or in the Target Information component; this second option
is activated by ticking the box marked Default tuning velocity to
target velocity. If entering the velocity here you must also
specify the Velocity Definition and Velocity Frame from
the two pull-down menus, and click the "Accept" button (to the right
of the frequency field). (Note that the velocity will appear in RED until you click on the Accept button.
Failure to click on the Accept button will mean the velocity you
entered will be lost.)
- If your source has a very large radial velocity, you should:
- Select the receiver within whose tuning range the (redshifted)
line will fall. For example, at a redshift of 2.0, the neutral
carbon [CI] J=2-1 line, whose rest frequency is 809 GHz, will fall
into the tuning range of RxA.
- Specify the radial velocity of the source, as above, either in
the Het. Setup velocity field, or in the Target Info.
velocity field. (If you choose the latter, make sure the Target
Info. component is on the same level as the Het. Setup component,
and not embedded in the observation sequence.) If you enter the
velocity in the Het. Setup component, be sure to click the
Accept button before proceeding.
- The OT now corrects its lookup table of transitions for the
entered velocity. Select a molecule and transition from the
pull-down menu, or enter the rest frequency of the spectral
line (and click the Accept button). Beware, however, that if you
enter a value manually into the frequency field, the OT will not
check to see if the redshifted line is in the tuning range of the
receiver you selected.
Clicking on the Frequency Editor button will show you something like
The frequency editor tool is particular useful when trying to configure the
backend for multiple lines, multiple resolution windows, or for receivers
operating in double sideband mode, where two differing sky frequencies end
up with the same IF frequency. In each of these cases finding the correct
values for the setup of each window is tricky and the visual presentation
from the frequency editor is indispensable, if only to verify the setup.
The tool now handles multi-spectral window selection and can be used
interactively in choosing observing frequencies and bandwidths for each
window or in combination with
special ACSIS configurations,
or simply to check the atmospheric opacity at the observed (or sideband)
frequency. Before clicking the 'Show Frequency Editor' button, please make
sure to select the desired number of spectral windows under 'Sp. Regions'
(See above). Once inside the frequency editor, the frequencies and bandwidths
can be selected or adjusted.
Working roughly from top to bottom, left to right, in the example above
showing only one Spectral Subsystem (USB) with two spectral windows,
- the observing and image side-bands, marked as LSB and
- their locations within the respective LO2 ranges and their widths
- the identification of the selected emission line associated with a
window, marked Line
- the IF (Intermediate Frequency), sometimes in Hz sometimes GHz
- the bandwidth, in MHz
- the Resolution that the selected bandwidth produces, in kHz
- the molecular transitions in this vicinity, marked by vertical bars,
on a line labelled Emission Lines
- the frequency scale immediately below Emission Lines is the frequency
in the rest frame of the source i.e. the emission lines show at their
nominal laboratory frequency regardless of the doppler shift.
- the line selected is shown in red
- the receiver temperature (TRx) is plotted as
the red line (although there
is no scale currently). It's wise to check this since even a minor
change in radial velocity can shift the observed frequency into a
region of very large atmospheric opacity.
- the FE Frequency scale, shown below the plot of TRx
is the observing frequency in the rest frame of the receiver i.e.
the tuning frequency at the telescope.
You will notice this scale will shift if you enter a non-zero
velocity, and will also shift if you change the velocity
- the Local Oscillator frequency, shown as LO1, located within
the full tuning range of the receiver.
- Note the upper frequency scale, lower frequency scale and LO1 are only
approximate because the correction from the receiver rest frame to the
chosen rest frame requires the Doppler correction for the Earth's
motion, which varies with time.
Among the dynamic functions, we find that
- the positions of the windows can be changed by
clicking on the window sliders and dragging . . . Note how the LO1
and LO2 (ie the IF) both change
- the bandwidth can be changed by clicking on the pull-down menu
- clicking anywhere along the 'Emission lines' level will identify
the nearby lines.
- keeping the mouse button depressed while scrolling
down through the menu makes the line appear in
- The LO1 frequency can be changed by right-clicking on the slider and
dragging. This changes both frequency scales and the line rest frequency.
Moving the LO slider can be a convenient means of choosing a band centre
frequency such that particular spectral lines are included or excluded
from your passband.
The above example shows a setup with three 250 MHz windows and one, lower
resolution, 1000 MHz window for receiver A (for HARP only two windows are
possible). Of the 250 MHz windows, one is centered on a line in the LSB, two
on lines in the USB. The line-id for the top window is 'greyed' because it
corresponds to the observing frequency specified in the main Het. Setup
component and it 'anchors' all windows. Moving the slider of the top window
will also slide all other windows. By contrast the remaining three windows
can be moved independently from one another within the IF band.
To generate such a multi-line, multi-Subsystem configuration:
Note that the movement of the sliders will make for
configurations that may not be easily repeatable and that use of
the 'Special Configurations' is desirable.
If you have a multi-line configuration that you consider
astrophysically important - and which may be useful for either
yourself or others later on - please contact the JCMT staff
and request that it become one of the available 'Special
Configs'. Our (CADC)
database will then be a lot simpler to manage and search if everyone
using this combination of lines uses precisely the same configuration.
- In the Front-End configuration window, select a value of Sp.(ectral)
regions greater than 1.
The Frequency Configuration block at the bottom of the screen will show
the appropriate number of 'Region's, although initially they
are populated with default values.
- Select the first line (for Region 0) as above.
- Press the Frequency Editor button to generate a Frequency Editor
window with the appropriate number of Subsystems. The pre-selected
line is in red.
- Click at the level of 'Emission Lines' in the general vicinity
(frequency space) of the next desired line
- keep the button pressed and scroll down until the line is met,
and shown in green
- click on the 'Line' box appropriate for that subsystem to center the
spectral window and identify it with the selected line.
- Repeat (from Click) for further lines if necessary
- Press the Hide Frequency Editor button to transfer these data to the
Heterodyne Setup window
Note: Please make sure that the window is
anchored on a line if it is intended to be centered on that
line. While the observation will proceed with a 'no line'
label, the line identification is important for archival purpose.
With the rapid data acquisition rates now afforded by HARP and
ACSIS, reducing data by hand has become a very slow and
tedious process. Automatic data reduction pipelines have
become a powerful tool for carrying out these repetitive
tasks. ORACDR has been developed for reducing and combining
JCMT (and UKIRT) data, primarily for producing "preview"
images for assessing data quality at the telescope, but can
also be used for the final reduction. ORACDR uses recipes
to carry out all
the usual reduction steps that were once carried out by
hand. Note that these recipes are still under
development and thus are likely to change and evolve.
The DRRecipe component is used to specify the recipe that is
to be used by ORACDR for reducing the data. The example
shown in the figure above (see Elements
of an MSB) shows the DRRecipe component below
the HetSetup component, although it need not be positioned
exactly here. (Note that the DRRecipe component needs to be
paired with a HetSetup component, however.) Open the
DRRecipe component by clicking on it. The bottom portion of
the window displays a list of the available recipes, with a
very short description of each. (See below for a fuller
description.) Click on the desired recipe, then click the
"Set" button in the top portion of the window corresponding
to the desired observing mode.
Recipe names primarily reflect the method used for fitting a
baseline, since how this step is carried out differs
depending on the line profile(s) expected. Effectively the
recipe chosen tells the fitting routine how to deal with
baseline features. To illustrate this imagine a narrow spike
on a broad profile: this can be a narrow line on a broad
baseline wiggle, a noise spike on a broad line, or a core
plus outflow profile. This process is tricky in this sense:
the baseline fitting can easily remove a feature of interest
from the preview image. Observers should ALWAYS go back and
inspect the raw data carefully to assess the accuracy of the
preview images and pipeline reduction.
Note that for all observations the outer ~5% of channels on either
side typically are too noisy to be useful and are excluded
from the reduction described below. Typically, smoothing and
clump-finding algorithms are used to exclude emission free
regions from the total intensity and intensity weighted
velocity collapses. These moments maps are thus derived
based on the line-widths of each spectrum. The exact methods
differ from recipe to recipe and are still under
investigation and development. Specifically the is aim to
provide the observer with useful preview images that are
representative of their data.
The following standard reduction recipes are currently being
developed for use with the ORACDR pipeline, with an emphasis
on scan-map data. An outline is provided below, but expect
changed and redesigns as we gain experience. The main
purpose of the routines is to
before collapsing the cube into e.g. total intensity and
intensity weighted velocity images.
- a) fit a baseline to the spectra and
- b) select emission from the background
- Intended for nearby galaxies and sources which
have a significant velocity gradient (rotation) across
the field-of-view. Assumes linewidths in excess of
25 channels (~10 km/s @ BW=1000Mhz and ~1 km/s @
BW=250MHz). Baseline regions are determined for each
- Intended for extragalactic and other sources with very wide
lines. Linear baselines are fitted to the outer 1/6 of
the spectral range of the coadded cube (after
truncating the outmost ~5% of the channels on each
end). The integrated intensity and intensity weighted
velocity map are derived from the inner 2/3 of the
- Intended for Galactic sources with not much of a velocity
gradient across the field of view. Baseline regions
are determined from a global average spectrum. This
single set of regions is used to fit the baseline for
all spectra in the cubes.
- Intended for spectral-line surveys, or where multiple
(narrow)spectral lines are expected within the
- Intended for continuum sources, or for absorption
line spectra in front of a continuum source. No
baseline subtraction is done.
The Site Quality component specifies any weather-related scheduling
requirements for an MSB. Click on the Site Quality component to get
the Site Quality panel:
Your TAG normally allocates your program a certain range of tau
(opacity), so you probably don't need to change anything here unless
your program is using multiple receivers and the TAG-allocated tau
range is not sufficiently specific for this MSB. You should specify an
appropriate range of tau to match the demands of the receiver to be
used. But : the resulting range of tau in which
the MSB can be observed is then the intersect of the TAG allocation
and your input: make sure this is not an empty set ! For example, if
the TAG allocation for your project is weather band 4 (tau(225GHz)
between 0.12 and 0.2) and you request a tau range between 0.1 and
0.12, then your project will be picked up for observation ONLY if the
tau is EXACTLY 0.12.
The default value of the sub-millimetre seeing is "Don't Care".
It is useful to set the "τ for noise calculation" value, however,
to the average or expected value of tau during which
your observations are expected to be obtained. (Note that the OT
does not know what τ range was allocated for your project.)
The OT uses the value in this field to calculate the estimated RMS of
the observation specified in the phot/sam etc. "eye"-cons.
The Scheduling Constraints component allows one to restrict or broaden
the time over which an MSB will be selected. To insert this component,
click on the Component button on the left side near the bottom
of the OT window, and select the "Sched. Constraints".
The main reason you might want to insert this component is if your
science targets have a very low or very high declination (i.e. δ
< ~-35o or δ > ~+80o). By default,
MSBs are only selected when the sources are above about 30o
elevation, so low- and high- declination sources may never be selected
unless you specify a lower minimum elevation. Similarly, sources at
~19o declination transit almost directly overhead, and you
may wish to restrict such sources to be selected when they're not at
extremely high elevations.
Another reason to insert this component is if your observations are
time-critical, i.e. they must not be done before a certain date or
after a certain date. This can be specified by changing the Earliest
and/or Latest Schedule Date.
You may also need to use this component if you have a project which
requires periodic observations, for example if you were monitoring a
variable source. In that case, you can specify the repeat time in the
"Reschedule every..." box. The MSB will be reactivated at the
The Observation component
Now click on the Observation component to bring up its panel. If you
recursively open all of the toggle switches, the individual components
will be displayed as a hierarchy, as shown below.
The first element inside the Observation component can be the "Target
information" component. Note, however, that in the templates the
target component is outside the Observation component. This allows one
to construct an MSB to perform multiple observations on a single
target: such MSBs would therefore contain multiple Observation
components. More importantly for heterodyne observations it allows the
Het. Component to access velocity information that may need to be
obtained from the Target Component. Further details on this issue of
component nesting may be found in the section on advanced topics.
Following the Target component in the example is a sequence iterator
which contains a repeat iterator, then (depending upon the observation
type) perhaps a chop iterator or an offset iterator - a
position-switched scan centred on the Target, as in this example,
needs neither - and then, finally, a single (action) "eye". The
sequence iterator doesn't do anything per se, but it is
important to note that it represents the sequence of events at the
telescope. The repeat iterator allows the user to control the number
of repeats carried out for a certain observation. The "eye"-con
represents the observation itself.
The "Flag as calibration" button should be toggled ON if, indeed,
this observation is intended as a calibration for others.
This fact is then made known to the TSS who may decide not to
execute the observation (er . . calibration) if a suitable
calibration has recently been done already.
The target component
Click on the target component to bring up its panel:
In this component you will enter the coordinates and velocity of
the source, and the coordinates of the reference position (for
position-switched observations). The "Target Type" is a pull-down
menu that allows you to select RA/Dec (most common), Orbital Elements
(for comets, etc.), or a Named Planet. The window changes for each
selection. For RA/Dec targets, enter the R.A. and Dec. in the
appropriate boxes, using colons as separators. One of several
different coordinate systems can be selected with another pull-down
menu, such as J2000, B1950, etc.
It is recommended that one specify the radial velocity of the
source in the target component, either as a radio, optical, or
relativistic velocity, or redshift (z). Note that if a velocity is
specified in the Het. Setup component, this
overrides velocities specified in the target component.
To specify a reference position, click on "REFERENCE". The default
is to enter the offset (in arcseconds) from the source position, but
by unchecking the "Offset" button, you can enter an absolute position
for the reference. NOTE: the reference position is required for
position switch observations as the location for the sky reference. If
present in beam-switched observations, the three-load calibration will
be carried out at that location.
Instead of entering the source coordinates manually, you can
download them from the Web. Assuming you have an Internet connection
you can enter the name of your target, select the on-line catalogue to
search (i.e. SIMBAD or NED) from the pull-down menu, and hit "Resolve
Name". After a brief pause the RA and DEC co-ordinate fields should
become populated with the SIMBAD/NED co-ordinates for the source. The
SIMBAD/NED name for the source will also be indicated next to the
"Resolve Name" button.
: Positions of
astronomical objects are often wavelength dependent. For example, the
SIMBAD coordinates for IRAS16293-2224 are many arcminutes different
from the JCMT coordinates. The catalogues you may be using will
have defined the astrometric positions therein on the basis of
optical- or infrared- or radio- observations. You should check that
the positions now showing are valid for your submillimetre studies.
Moving objects (excepting planets and other bodies which are accessible
in the pull down menu in the Target component) are accommodated via
orbital elements. The format of these elements is fairly specific. An
example is given in the figure below.
Orbital elements as found, in
this example, on the
NASA JPL NEO orbit
Elements specified in the
Target Component Elements tab.
Note the different format for Epoch and Time of Perihelion Passage, in
The OT can use the Horizons database to resolve a given minor planet's
name into elements. An example is given below.
|Name resolution for moving objects: When
"Orbital elements" is the selected Target Type, the "Resolve name"
button queries the Horizons database for elements.
Note that the name format is somewhat picky and you may have to use
trial and error to get something that works for a particular target.
Also note that the OT uses a resource at JPL which is intended for
human reading, not computer processing. As such the output format is
subject to arbitrary changes, so there is no guarantee that this search
feature will work or that the results are accurate; for example it is
possible that elements may end up in the wrong field or omitted
double check the returned values.
Allowing for Proper Motion
Entries for the RA and Declination proper motion rates (in
milliarcseconds per year) can be made in your target component.
motion entered as milliarcseconds per year in the target
component. These values are taken into account when slewing the
But wait - that's not all.
The position editor
You can skip this section if you want because
you don't have to do anything, but it's kind of cool and can be very
useful in picking a good chop position. Click on the plot button at
the bottom left of the target panel:
A whole new window will pop up - this is the position editor. Looks a
bit boring at the moment though, with just a small green crosshair in
the middle. Let's make it a bit more interesting - go to Catalog menu
and into the Image Servers item and chose a Digital Sky Survey near
It's now full of stars. The display application, by the way, is is
based on JSky, for those familiar with it.
If you're having problems with the position editor, the most likely
explanation is that your version(s) of JRE, JAI and/or java may not be
sufficiently up-to-date; check the download
page for more information. If you are behind a firewall, you may
need to check your proxy server
The DSS may not be the most useful survey for planning sub-millimetre
observations, but you can read in any FITS image with an appropriate
WCS header using Open under the File menu. You can also fetch a FITS
image over the Web. The screenshot below shows the SCUBA commissioning
scan map of W48 (image courtesy Tim Jenness). If you have an
Internet connection, go to the File menu, select "Open URL...:" and
type in the following URL:
or download the image by clicking on the link and and use
File->Open to read it in. Notice that the RA/DEC position fields of
the target component must be set reasonably near to the world
co-ordinate of the FITS file otherwise the image may not load
You will then see the DSS image replaced with the sub-millimetre
A short technical note if you are planning on generating your own
image for import: if you want to import a SCUBA map in NDF format,
convert it to FITS by using the
convert utility with the following arguments:
ndf2fits encoding=FITS-IRAF bitpix=32 comp=D
If you have difficulty despite doing this, let us know.
As was mentioned before, the green cross-hair is the position of your
science co-ordinates. Click on the button on the left side of the
position editor entitled "Sci Area". The circle that is drawn is the
HPBW of the chosen heterodyne receiver.
Now for the useful thing mentioned earlier: While leaving the position
editor window open, go back to your science program window and click
on your chop iterator that is inside your science observation. Now
look at the position editor. The chop beams and the area in which they
will rotate during integration are drawn. Well, that's no good - we're
chopping onto bright stuff!
This is where the position editor comes into its own. We are going to
use it to specify where exactly we would like to chop. In the chop
iterator, use the drop down menu to change the chopping co-ordinate
frame from AZEL to TRACKING (i.e. RA/DEC). You will notice that in the
position editor the uncertainty circles have disappeared, since we
will always chop in the same position in the sky:
Now back in the position editor, click on the Drag button on the upper
left side of the window. Then click on the centre of one of the chop
beams in the display and drag it away from the emission:
You will note that the values in the chop iterator have automatically
changed to reflect the new chop throw and angle values. Neat, eh?
Remember that by default, any calibrations for your observations will
be performed with the same chop as the science observation.
You can also click on the target component and use Drag to change your
science co-ordinates if you wish.
The chop iterator
Click on the chop iterator:
The chop iterator has a list of chop configurations (in this example
only one 60 arcsecond chop). Each chop needs to be specified by a
throw, an angle, and co-ordinate frame of the angle. In this example
the frame is AZEL (Azimuth Elevation) but other common options are
TRACKING (RA & Dec) or FPLANE (Focal Plane). A 60 arcsecond chop with
an angle of 90 degrees AZEL (i.e. 60 arcsec in the azimuth direction)
is typical for beamswitched observations of compact sources. If the
source is extended, one might want to increase the chop throw, or if
the source was elongated in one direction on the sky, chop in a
rotated direction relative to the RA/DEC frame. The maximum
recommended chop throw is 180 arcsec. There is a software limit of
240 arcsec. Chopping with large throws is less efficient than using
small throws and also there will be a slight distortion of the beam
due to observing off-axis. Clicking on Add one can add chop
configurations. Each configuration will result in a separate
observation (and data file).
The offset iterator
It's often very useful to be able to specify a position with the Target component, but to take an observation at a
position offset from that specified. That can be done with the
"offset" iterator. In addition, with Grid
maps, a whole series of offsets can be specified in either a
regular or irregular spacing.
If an offset iterator is not already specified in the MSB, one can
insert it below the Sequence iterator , usually just above the
stare "eye"-con . Click
on the iterator below which the offset iterator is to be inserted (the
'chop' iterator in the image above), then click on the iterator menu
on the left-hand panel of the OT window and select the offset
iterator. Be sure to "drag" the stare eye-con to the right, so
that it is indented with respect to the offset iterator (see figure
The offset is specified in arcseconds in the 'p' and 'q' boxes. Note
the orientation of these axes to the left of the 'Title' box. In an
unrotated frame, 'p' is in the positive r.a. direction (i.e. east)
while 'q' is in the declination direction (i.e. north). If a rotated
frame is required, enter the position angle (measured east of north)
in the 'PA' box. If you then click on the 'Display Derotated Offsets'
button, the specified offsets in the unrotated frame will be briefly
displayed in the table above.
To add more offsets, click the 'New' button, and enter the offset in
the 'p' and 'q' boxes as above. Repeat for as many positions as
A regular grid can also be specified using the 'Grid Pattern' section
of the window. See the section on Grid
Maps for a description. Note that all offsets at the JCMT are
defined in the Gnomonic (TAN) projection.
The stare eye
The science observation itself is represented within the MSB by the
stare eye. Click on it to display the details of the
observation. The pull down menu near the top of the right hand frame
allows the user to choose from beam switching or position switching.
In this example we are beam-switching, and the chop throw was set with
the chop iterator. In the "Secs per offset
sample" box, enter the total on-source integration time per
sample position in seconds. (Note this is different from how it's been
done in the past when we specified the on+off time.) The estimated RMS
noise per channel is shown in the "Noise" box. Typical recommended
on-source integration times per sample are 5 to 10 minutes. We advise
to use no observing times >15 minutes, at the risk of loosing
observations when something goes wrong.
The Continuum Mode box can be checked if you need an accurate
measurement of the continuum level. Typically this only makes sense
when doing a BMSW observation, because the switching time for PSSW
observations are too long for a reliable determination of the
continuum. For BMSW observations, the effect of checking 'Continuum
mode' is to run the chopper much faster. This will result in higher
overheads which can significantly increase the time it takes for the
observation to complete. Hence, this mode should only be used when
really needed. As a concrete example: the maximum time between chops
typically allows for the completion of a full 9x9 jiggle with 0.1sec
step, i.e. 8.1 secs. The chopper will then spend ~3 secs in the
off-position, resulting in an 11-sec cycle plus some overhead. In
continuum mode the chopper will move to the reference every 0.1secs
and spend equal times in the 'on' and 'ref' position. A 9x9 jiggle will
thus take 16.2 secs plus significantly more overheads due to transit
times of the chopper. Limited testing so far suggests that the typical
penalty for using continuum mode is an increase of the observing time
by a factor of 1.7.
The repeat iterator and integration time in general
Back to your Science Program window now. Click on the Repeat
iterator. It's only property is a repeat counter:
The repeat iterator acts on things that are inside
the repeat iterator (i.e. indented under it) in turn. So if you set it
to 2, your science observation consist of two spectral line samples;
i.e you will end up with precisely two spectral line observations. If
you require a long integration of a source, it makes sense to break
the observation down into shorter integrations of around ten minutes
or so, so that data quality can be assessed as the observation
progresses. In practice, you set up the integration time required per
spectral line observation using the stare eye and then use the
repeat iterator to define a sufficient number of repeats to give the
total required integration time.
Now you can see how your time usage builds up. Working our way inside
out (and bottom to top):
- The stare
eye is set to an on-source integration time (and shows you the
estimated RMS noise) which will end up in a single file.
- The Repeat
iterator multiplies the number of times the sample is carried
out. If you increase it from the default of 1, don't forget to
take that into account when calculating how deep you will go.
- The observation
component shows you the estimated time of the sequence it
- The MSB component will give
you the estimated time of the observations inside it. For the
heterodyne OT, you only need to define MSBs for your science
observations. Obviously, before the observation, the TSS will tune the
receiver (when necessary), focus the telescope, and do a pointing
observation. Specific calibration instructions, for example, the
observation of a spectral line standard and/or a planet should be
described in the note attached to the MSB. Be sure to remember to
click the show-to-observer tick box for the note. In conclusion, the
estimated time for an MSB only includes observations of the science
target - one should remember there will be instrument set up and
calibration overheads on top of this when planning your observing
- The Science Program will
give you the estimated time of all MSBs inside it including the number
of repeats. So if you have a 1hr MSB (as in this example) and you set
the MSB counter to 2, your MSB estimated time will be 1hr and your
Science Program time will show 2hrs. Remember that different MSBs may
be observed on different nights, whereas observations within a single
MSB will be observed within a aingle night.
Adding information in "Note" elements
By default, the heterodyne library MSBs contain two note element at
the beginning of the MSB. The notes can be combined into a single one
- A note for general remarks concerning the program
- A calibration note for specific instructions for the calibration
observations. In the future we hope to be able to replace this
note with better methods for including calibration observations.
The note component consists of a text window where you can include
textual information, with the option of showing the note to the
observer and TSS at the time the observation is made. If you click on
the note icon, the right hand panel allows you to enter the name of
the note and the main text body of the note. The "Show to observer"
check-box should be checked if you want the note to be visible for the
observer/TSS at the time of observation. It is strongly
recommended that each of your MSBs contains at least one "Show to
observer" note. All of the information about the observation not
covered by other elements of the MSB should be included in "show to
observer" notes. This would be much of the material which would have
previously gone into the "Overall Strategy" and "Observing Cookbook"
sections of heterodyne observing templates. It is important to note
that calibration details are not yet explicitly included in heterodyne
MSBs, so the observer should spell out the required calibration
observations in a "Calibration" note.
Setting the "Show to observer" tick box brings up a "Completion
Parameter" and "binning" field. These should contain information which
help the observer and TSS to decide when to consider your observation
to be complete. By default, your program will be executed with exactly
the number of integration and number of repeats as specified. However,
where possible, an attempt will be made to optimize the process using
the specified Completion Parameters. The detailed logistics of the
scheduling may prevent this, but when possible this may save time for your
project or guarantee the results. For instance you may want to
allow for more time than the MSBs nominally take to allow for the
addition of extra repeats in order to ensure the requested
rms. Setting a S/N target may save unnecassary repeats, etc.
The "Completion Parameter" should include a value for the total
expired time, and/or a required signals-to-noise, and/or RMS noise
value. Best is to provide all three and whichever one is reached first
determines the completion. The assumed bin size, either in km/s or
MHz, should be entered in the "Binning" field. The above screenshot
shows an example of a possible "Show to observer" for an extragalactic
spectral line observation. Be aware, however, that ultimately it is
up to YOU, the PI, to determine when the data have sufficient
S/N, by downloading and analyzing your data soon after they are
acquired and updating your MSBs as required.
Additional notes can be inserted at any point in the MSB from the icon
menu and you may have more than one "show to observer" notes in an
MSB. For example, you could choose to insert a "show to observer" note
above the "chop" element to clarify the use of an unusual chopping
Finally, there is no need to repeat information in notes that is
already included in other components of the MSB. This might include
receiver tunings, chop throws, offset positions and science
targets. All of these should be set up in the appropriate MSB
components. If they are reproduced in notes, there is a risk that
changes made to main body of the MSB will not be reflected in the
notes, leading to conflicts between the notes and the MSB components
resulting in confusion at the telescope.
Summary: Making your heterodyne MSB
So far, the various elements of the MSB have been described. We now
summarise the general procedure for making your own.
- Choose the corresponding MSB template from the heterodyne library and
copy/paste it to your science program. Each of these is described
- Fill out the het setup component with the frontend/backend details
for your observation.
- Set up the site quality component, normally this means simply leaving
the "allocated" button checked.
- Enter the target information for your target. This step can be as
simple as entering the RA/DEC and epoch. Don't forget there are
the useful tools of the Name resolver and the position editor to
help you out here.
- Set up the chop iterator. Again this can simply mean entering the
chop throw angle and reference frame, or this iterator can be set up
via the position editor.
- Set up the stare eye. Remember to enter the total
on-source integration time per sample.
- Set up the repeat counter to give the number of repeats of the
time set up in the stare eye to get your total required
integration time. If you want a total integration of 30 minutes
on-source, you should set up an integration time of 5 minutes in
the stare eye and set the repeat counter to 6. When
observing, you can then monitor the observation by inspecting the
data file produced every ~13 minutes, and co-add the spectra as
you go along. In general, if you want to build up long
integrations, you will want the duration of the basic observation
to be of the order 10-15 minutes ("on+off+overheads").
- Add at least one "show to observer" note. This should contain
additional information on the overall aims of your science
program, details of required calibrations and any other special
notices you want the observer and TSS to act upon when the
observation is made.
- Click on the outermost level of the MSB. In the right hand panel
you should give the MSB a meaningful name. Be aware that
observers and operator typically will see only the start of that
line in the browsing tool, hence put the most significant
information at the start. E.g.
'IRC+10216 spectral line
survey, CO molecule, transition 230.538'
line survey, CO molecule, transition 220.399'
similar without expanding the name field in the
'IRC+10216 230.538, spectral line survey, CO
'IRC+10216 220.399, spectral line survey, CO
would be a better compromise.
Below the name field, there is pull down menu labeled
"Observe". This counter allows you to control how many times you
want the whole MSB observed. If you want it done just once, leave
this as (1x). You can set the relative priority of the MSB within
your science program using the "Priority" pull down menu. Set
this between 1 and 99, with 1 signifying the highest
That's pretty much all you need to know to start preparing your
MSB. The remainder of this primer covers the Heterodyne MSB library.
The Heterodyne MSB library
The heterodyne library groups the MSB templates according to whether
the observation is to be a Sample, a Grid, a Jiggle-Chop, or a
- Single-position Samples: this is
the most fundamental of the observing modes, in being a single spectrum
observed toward at a single position. The sample can either use a
position switch (Sample-PSSW) or a beam switch
(Sample-BMSW). PSSW observations typically spend of order 30
secs on the source before going to the reference position for 30 secs,
but they can accommodate large switches exceeding several degrees.
BMSW observations by contrast offer a better sky cancellation by
switching much faster between the source and reference (up to several
Hertz in 'continuum mode'), but are restricted to a switch of 180" at
the most. Also, the telescope will nod: half the time will be
spent chopping to one side of the source, half to the other side,
requiring both sky positions to be free of emission.
The offset iterator can be used to observe at a position offset from
the one specified in the Target Component. If
you specify multiple offsets these modes will be equivalent to a
Grid-PSSW or a Jiggle-Chop, although the detailed execution will be
different in case of the latter (see below).
- Grids: these observations are
Samples carried out at multiple offsets, either in a regular grid or
as a series of explicit offsets. The observations from each grid point
end up in a single cube, sharing calibrations and possibly offs. The
observations at each position can be either position-switched or
beam-switched. Position switched patterns are executed as
OFF-ON(s)-ON(s)-OFF-OFF-... Grid maps are used where relatively
small, sparse maps are required with longish integration times per
(Note: it is possible to do a grid of jiggle-maps by putting a
"Jiggle-Eye" inside an "Offset" iterator. However, in this
case the jiggles will be executed as fully independent observations at
each grid point, resulting in independent cubes.)
- Jiggles: this mode makes a small map
by "jiggling" the secondary mirror rapidly over all the points in the
map and is similar to Sample-BMSW/Sample-PSSW observations on a
regular, pre-defined grid, such as a 4x4 pattern. There is an
important distinction: rather than fully completing each position
before going to the next, Jiggles will combine sequences of short
integrations at all positions and possibly cover the whole jiggle
pattern many times to build up the integration time at each
point. Thus, it will typically observe multiple source positions
before going to the reference position for a relatively longer time,
although this is configurable through the Separate offs
Jiggles are new to heterodyne observing at the JCMT, and specifically
designed for HARP although useful for single receptor receivers as
- Scan-PSSW: This mode is useful
for making large maps rapidly. The telescope continuously takes data
while scanning across the source in e.g. a back-and-forth pattern. It
will typically go to the reference between rows and an interpolation
of the references on either side of the row will be used for each of
the samples in the row. This mode is much more efficient to map large
regions than Grid maps.
A detailed description of the various observing modes, rms noise, and
durations is available as a document Heterodyne Obsmodes. Even though the information is not required in order to
set up a science program, experienced as well as novice JCMT observers
are encouraged to read the document as a general
background. The discussion below concentrates on the
mode-specific components in the JCMT OT.
Centering the observations
RxA and RxW at any time observe only a single position on the sky and
by default the target-position will be centered on the receptor:
they are receptor-centered.
For HARP the situation is more complicated. Firstly, it has 16
receptors, each of which in principle can be aligned with the target
position for receptor-centered observations. But, secondly, and
more to the point, the 4x4 receptor array does not have a center
receptor. For regular grids or jiggles this results in maps
with even dimensions, such as 16x16. The center of the map will thus
fall between the center four pixels. Since the output pixels are the
locations observed by the receptors, this also means that
center-position of such a map will not have been observed precisely by
any receptor. For fully sampled maps the consequences should not be
significant, but for user-defined sparse grids they can be disastrous
since possibly no receptor may come even close to the target position.
Consequently, for HARP there are three possible alignments:
- receptor-centered: the target position is placed on
one of the center-four receptors. Since these receptors are offset
(15",15") from the array center, this will result in strongly
asymmetric maps with the target position displaced 21" towards one of
the four corners. Which corner will depend on the elevation of the
observations, since it depends on which of 4 possible angles,
differing by 90 degrees, the k-mirror will select. Combining
receptor-centered observations from different elevations
may thus result in a wind-mill pattern with spectra from only
9 of the 16 receptors overlapping in all observations (see figure
below). For compact targets smaller than the area mapped by a single
receptor this may still be the observing mode of choice, since the
whole source will be mapped by a single receptor. Which of the
center-four receptors will be the "tracking receptor" is set in a
telescope configuration file and is in principle not user
configurable. All patterns with names like NxN (3x3, 4x4 etc.) are
- array-centered: the target position is placed in the
center of the array between the center-four receptors. The
resulting map will be symmetric around the target position and
independent of the K-mirror orientation. However, none of the
receptors will align exactly with the target position, which
may not be an issue for an extended source, but will probably be a
serious problem for a sparse grid of a source with a point-like core.
In case of a fully sampled observation using one of the special HARP
jiggle patterns this mode is referred to as map-centered since
the target position will be between the center-four pixels in the
output map which will be either 7.5" or 6" apart depending on the
pattern selected. The map-centered harp jiggle patterns are
named harp4_mc and harp5_mc in the JCMTOT.
- pixel-centered: the target position is placed on one
of the center-four pixels of a jiggle map, slightly offset by half a
pixel in each direction from the center of the map. This mode is only
available when using one of the special HARP jiggle patterns and is
the counter-part to the map-centered observations above. As is
the case for the receptor-centered map, discussed above, the
map will be asymmetric around the target but only by one map
pixel. A wind-mill pattern resulting from the K-mirror flipping
by 90 degress will only affect a 7.5" or 6" rim along the edges of the
map. The pixel-centered harp jiggle patterns are named
harp4 and harp5 in the JCMTOT.
The figure below illustrates the pixel-centered and
map-centered centering for the HARP jiggles: the cross shows
the location of the target position in the output map. Note that the
HARP4 and HARP5 pattern, shown here offset to the top-left corner, can
be offset to any other corner depending on the elevation of the
observation. For receptor-centered grids the cross would be at
the same location as the middle of the dark-blue poststamp in the
center of the HARP5 images. Another discussion of the HARP jiggle
patterns can be found
Shared or Separate offs
The concept of shared or separate offs almost
exclusively applies to jiggle and scan maps. Offs will also be
shared for position-switched grids with very short integration times
(≤ 15s), but that choice is not user configurable. Shared
offs are also required for scan-maps. However, Jiggles can be
configured either with shared or separate offs.
Shared offs means that the observations at a number of
positions in the map, i.e. ons, share the sky reference, the
off. This concept originates from traditional scan-map
observations where the telescope scans across an extended source
before going to a sky reference. By necessity all positions observed
along the scan will share the same sky reference or off.
Since 50% of the noise observed in a spectrum (i.e. on-off)
results from the off this would lead to severe 'striping' of
successive rows unless the integration time in the off position
is sufficiently increased to drop its noise significantly below the
noise of the on measurements. Calculations show that the
integration time in the off needs to be multiplied with
sqrt(np), where np is the number of on positions
in the row. Of course, there is nothing special about scan-maps: the
same applies for any observations where a number of points share the
sky reference, as is the case for HARP jiggle-maps where the full 4x4
or 5x5 jiggle pattern is observed before going to the off.
Observations benefit from shared offs in two ways and the more
so the more points between the offs (the larger the
scan-map). To illustrate, consider 1s observations of 16 positions
(which would be a very small scan map). Separate offs would
require 32s on the sky equally split between ons and
offs. Using shared offs the observation needs only
16+4=20s. But also for each point individually the noise is
reduced because of the longer observation of the
off. Expressed in a time required to reach a particular rms the
combined effect makes shared off observations 4 times
faster than separate observations in the limit of many points. More
precisely, the factor is ~4/(1+2/sqrt(np)) or ~2.7 for the relatively
small HARP jiggle patterns and ignoring fixed overheads (which reduce
the factor to closer to ~2). Nevertheless, one night instead of two
nights is a huge gain, which is why shared offs are the default
for JCHOP observations.
The figure below shows the benefits in terms of the duration of the
HARP4 jiggle observation, including realistic overheads, needed to
reach a certain rms (assumed Tsys = 250 K and frequency channels of 1
MHz). Note that shared/separate offs are only relevant within a
single observation, which typically take 10-20 minutes. The figure
shows that e.g. a 15min observation using shared offs (blue line) will have the same rms noise as a 33min
observation using separate offs (red
line). Note that coadding successive observations will
decrease the noise with the usual sqrt(nr spectra) factor,
irrespective of the shared mode chosen.
Of course, the above gain comes at a price: all 16 or 25
jiggle-positions from each receptor are correlated because they have
the same sky reference (off). As long as the pixels are kept
separate this is not an issue because noise remains dominated by the
on measurement and the points can be regarded to be only weakly
correlated. However, any operation in which pixels are combined will
'suffer' from this correlation in the sense that it will combine
pixels that are not fully independent and the noise will hence not
drop with the customary sqrt(np) factor. Note that this both applies
to operations that use a spatial convolution (smoothing)
as well as total flux measurements that sum or average
over pixels such as aperture photometry. In the extreme, when
averaging data over the whole footprint of a harp4 observation, the
noise will be 1/4th (16 independent receptors) instead of 1/16th (196
pixels) of the noise per pixel. Finally: note that JCHOP continuum
mode observations always will have separate offs, because
the secondary will chop to the off position faster than it moves
around the jiggle pattern.
In conclusion: if imaging or velocity/frequency data are the
primary aim of the observations, shared offs are hugely
beneficial and recommended; if accurate flux measurements over
extended regions are the primary aim or the final maps will be
spatially smoothed significantly, separate offs are
A sample denotes an observation consisting of one pointing per science
target. It can be beam switched (BMSW) or position switched (PSSW).
If you open up the PSSW sample MSB in the heterodyne library, you will
see that it contains the same elements as the BMSW MSB, with the
exception of the "chop" component. Opening the "Target Component"
component, however, reveals two rows in the bottom right hand window,
a SCIENCE and a REFERENCE row. Clicking on one of them allows the user
to specify the co-ordinates of either the SCIENCE, or "on" position,
or the REFERENCE or "off" position. The REFERENCE position can either
be specified as a co-ordinate offset from the SCIENCE position, by
checking the "offset" tick-box, or as an absolute co-ordinate, by
leaving the "offset" tick-box unchecked.
Important: If you put or leave a REFERENCE position in the
Target Component of a chopped observation (Sample-BMSW, Jiggle-Chop)
that position will be used when doing a three-load calibration
For all sample modes, the total "on" integration time per
sample is indicated in the "Stare" eye.
that integration time no longer is the "on+off" time, only the "on"
Observations of a single science target at multiple positions are
generically referred to as Grid observations. Note that the user can
define any list of positions and that there is no requirement that the
pointings form a regularly shaped grid. Opening the various grid MSBs
in the heterodyne library shows they are similar to the Sample-PSSW or
Sample-BMSW MSBs except for the addition of an Offset Iterator. This iterator enables the user
to specify the required pointings for the observation.
Suppose the user requires three pointings along the long axis of a
galaxy, at a half beam width spacing of 10 arcseconds. Let us assume
the long axis of the galaxy has a position angle of 30 degrees on the
sky. First enter the position angle in the "P.A." field. The rotated
frame has axes labeled p and q, so in order to obtain the required
pointings along our galaxy we require (p,q) offsets of (0,-10), (0,0)
and (0,10). One adds a new pointing by clicking on the "New"
button. One then modifies the offsets via the p and q boxes directly
above the "New" button. The highlighted pointing can be removed using
the "Remove" button. The "Rm. all" button removes all of the
user-added pointings. The arrow buttons to the right of the box
displaying the pointings allow the pointings to be re-ordered. The
highlight pointing can be advanced one position up or down the
pointing list, or to the top or bottom of the list by clicking on
these arrow buttons. For our example, the completed Offset Iterator
will appear as shown below.
If you want to see what the offsets are in the sky frame (which will
be the co-ordinate frame specified in the "target information"
element), click and hold the "Display Derotated Offsets" button.
The Offset Iterator has the ability to automatically generate
regularly spaced grids without the need to enter each pointing
individually. The "Grid Pattern" section of the "Offset iterator"
allows the user to specify the offset of the top-left corner of the
grid (i.e. most positive 'p' and 'q'), the grid point spacing, and the
dimensions of the grid, in grid points. To create a 3x3 grid, with a
ten arcsecond spacing, one would fill in the fields of the grid
pattern section as illustrated below, and then click on either
"Create/Centre on Base" button, or the "Create" i.e. on corner
button. The pointings generated then appear in the pointing list box
Notice that "Create/Centre on Base" chooses the the geometrical centre
of the grid for the (0,0) position, and ignores the contents of the
"initial offset" fields. The "Create" (on corner) button, on the other
hand, will place the top left pixel at the offset specified in the
"initial offset" fields. For example, if you want a 2x2 grid with 10
arcsecond spacing at offsets (0,0),(-10",0),(-10",-10"),(0,-10"), then
set the initial offsets to p=0,q=0, spacing p=10",q=10", and
dimensions 2x2, and click the "Create" button.
Jiggle observations, like Grids, map a region around a source. This
mode is primarily intended for array instruments with widely spaced
receptors for which 'jiggling' is needed in order to achieve a Nyquist
sampling. Nevertheless it is available for single-pixels receivers as
well. As opposed to Grids, the chopping secondary is used to move
over the points in the pattern. This allows for a fast switching of
the position and makes it possible to observe e.g. the whole jiggle
pattern before going to the reference position. (In "continuum mode",
however, where the chop frequency is much higher, half the time is
spent at the reference position.) Jiggle-chops are beam-switched
observations, and hence the distance to the sky reference can be no
more than 180". Jiggle-PSSW use a jiggle to maps the source, but a
position-switch to move to the reference.
Opening the various chop MSBs in the heterodyne library shows they are
similar to the Sample-BMSW example above except that there is a
"jiggle eye" instead of the "stare eye". It offers various
jiggle patterns: 3x3 through 11x11 plus HARP-specific jiggles (such as
HARP4 and HARP5).
Since any spacing can be specified using the NxN patterns, in order to
guarantee that the target falls on one of the pixels in the
output map (as opposed to between e.g. widely spaced pixels), these
patterns are receptor-centered. Four special patterns are also
available for making fully sampled maps with the HARP array receiver.
HARP4 & HARP4_mc are 4x4 patterns with 7.5" pixels
designed to fill in the footprint, but slightly under Nyquist sampled,
and HARP5 & HARP5_mc are 5x5 pattern with 6" pixels,
i.e. slightly better than Nyquist sampled.
- HARP4 and HARP5 are pixel-centered: these will give you
fully-sampled maps with the target position on one of the center 4
pixels of the output map. The resulting map will be slightly
asymmetric and maps observed at different time may have a different
orientation. However, the affected area will only be a single-pixel
wide rim along two or more edges of the map.
- HARP4_mc and HARP5_mc are map-centered: these will give
you fully-sampled maps with the target position in the exact center of
the output map, between the 4 central pixels. The resulting
map will be symmetric around this position.
For a more extensive discussion see Centering the observations and the figures there.
For the NxN patterns the "Jiggle Spacing" needs to be defined by the
user: typically 0.5 or 1 beam-spacing in arcsecs. The PA and System
should be left at "0.0" and "Tracking" for the typical user. Finally,
the integration time for each jiggle position can be specified as
"secs/jig posn". (Note that this is the total "on-source" time per
position.) As for the "stare" eye, the estimated RMS noise per
channel is shown in the "Noise" box.
"Continuum mode" can be selected as is explained for the
"stare eye". Due to the resulting
increase of the time needed to complete the observation, by a factor
of approximately 1.7, only check this if you really need the
measurement of the continuum level.
Important: If you put or leave a REFERENCE position in the
Target Component of a chopped observation (Sample-BMSW, Jiggle-Chop)
that position will be used when doing a three-load calibration
The format of the position switched scan MSB is similar to the
sample MSB, except that the "stare" eye is replaced by the
"scan" eye. The fields in the "Area" panel allow you control
the size and sampling of the scan map. The resulting Nr. of
samples/pixels and Nr. of scans/pixels in each dimension is shown. The
total required on-source integration time per sample point can be specified in
the "Sample time" box. The system will automatically break up the
observations into multiple passes over the map.
Setting up scan maps is significantly different when using a non-array receiver (i.e. RxA or RxW), or
an array receiver (i.e. HARP). Read
the example below for setting up MSBs for an RxA/RxW Scan Map, and for a HARP Scan Map.
Making a Scan Map With a Non-Array Receiver (RxA/RxW)
When using a single-pixel receiver such as RxA or RxW, the "sample
spacing" will be the pixel-size along scan direction of the
telescope. The "scan spacing" will be the pixel-size in the cross-scan
direction i.e. between the scanned rows. Be aware that there will be a
pixel centered on the base position only if the number of pixels in
each direction is odd. The size of the map must be a multiple
of the pixel-size in each direction, and is defined as the distance
between the centers of the outmost pixels!
Suppose, for example, that you want to use RxA to make a 238"x28"
map. A sample spacing of 7" and scan spacing of 7" will result in a
pixel map of 35x5. Note that it is customary to oversample the
scan-direction to counter-act smearing, although this often requires a
regridding of the final map to recover the intended rms/pixel.
The sample time box allows the user to set the amount of time data is
taken for for each map "point" as the receiver is scanned across the
sky. The RMS noise per channel of the final co-added map is also
indicated, as is the estimated time to complete each row and the
It is possible to set the scanning direction, but for most purposes
this should be left to the default values.
Making a Scan map With an Array Receiver (i.e. HARP).
HARP is a 4x4 square array of receptors, which are separated by 30".
To make a scan map, the telescope scans continuously along (by
default) the longest axis of the map (defined by the width
and height of the map). The array is rotated by 14.04º
to the direction of the scan. This results in a fully sampled map,
with 7.3" pixels. Thus the HARP sample spacing is set by the
OT to 7.2761". At the end of a scan, the array is shifted up by the
scan spacing and the telescope makes another scan across the
area to be mapped. A pull-down menu allows one to set the scan
spacing, so that one can step by the full array (i.e. no overlap
of pixels during subsequent scans), by 3/4 array, 1/2 array, 1/4
array, 1/8 array or by a single pixel (i.e. a shift of 7.28").
Effectively the largest single map one can make is one square degree.
Larger maps can be made, but they should be broken up into smaller
pieces, one piece per MSB, with an offset iterator for each piece.
Note that mosaicing such large maps will likely tax most computing
systems beyond their capacities.
In the lower left panel of the SCAN window, one can
specify the direction and orientation of the scan, using two pull-down
menues, PA and System. For all but very special
applications, the System should be left in its default,
TRACKING coordinates (e.g. R.A./Dec.). If PA is
left in its default state (automatic), then the telescope
will scan along the longest axis of the scan box defined by
width, height, and PA specified in the
Area panel. One can, however, set the scan direction to any
arbitrary value, by selecting user def from the PA
pull-down menu, and typing in the required scan direction in degrees,
where PA=0 is north and PA=90 is east.
If the scan map is to be repeated, a useful technique is to "basket
weave" the scans, i.e. make a scan map by scanning along one axis of
the map, and then repeat by scanning along the other axis. This
minimizes striping in the resultant map. One way to do this is to edit
a science observation for a scan map, set the parameters as
required, then copy the entire science observation and paste the copy
below the original. In the original scan "eye"-con, set the
SCAN PA (lower left panel) to Along Width. Do the same in the
copy scan "eye"-con, but set the SCAN PA to Along Height.
Sample Time: The sample time is the total
integration time per pixel in the completed map. The minimum
time depends on the setup of the backend. It is about 0.3 seconds with
8192 channels (e.g. single 250 MHz band), but can be as low as 0.1
second with 2048 channels. There is no physical limit for the maximum
sample time. However, it should be noted that the telescope does not
check the reference position until at least one row is completed.
Thus one should make sure that the total time per row is less than
about 60 seconds (or 120 seconds under stable weather conditions), and
the total time for the MSB is no more than 1.5 to 2 hours at most.
For large maps the integration time per pixel (sample time)
should be set to a small value, e.g. 0.3 seconds per pixel, and then
repeat the MSB to build up integration time.