When your data comes out of the map-maker it is in units of picowatts (pW). A flux conversion factor, or FCF, needs to be applied to scale your data from units of pW to janskys (Jy). For more information on calibrating SCUBA-2 data see Dempsey et al. (2013) .
Below are our default FCFs.
|450 m||850 m||450 m||850 m|
|4.71 0.5||2.34 0.08||491 67||537 24|
To get the flux density of extended sources with aperture photometry you should apply the . You can then sum the emission in an aperture. was determined using a 60-arcsec diameter aperture. If your aperture differs from this you should scale your flux accordingly—the scaling factor can be read off the curve of growth (see Appendix F). This graph gives the ratio of aperture flux to total flux for a range of aperture diameters.
is determined using 1-arcsec pixels. For different pixel sizes you will also need to multiply by the pixelsize squared.
If you want to read off the peak flux from your map, you should apply the (also known as the peak FCF). When you open your map in Gaia the value of the brightest pixel will be the peak flux of your source. (If your source is point-like, the peak value in the map is the total flux density). Applying will result in a map with units of Jy/beam. For point-like or compact sources smaller than the beam (with a Gaussian profile), this peak value will be the flux density of your source.
Calibration observations are taken at various points throughout the night and we recommend you compare the FCF calculated from your nearest calibrator to the standard FCF. You can use this FCF to scale the the standard value accordingly. You should chose the calibrator nearest in time to your science observations, unless the weather has changed significantly.
dimmconfig_bright_compact.lisas the configuration file.
This will produce a log file (
log.checkcal) which records the both
Check that these values closely approximate the standard FCF values given above.
You can apply the FCF using the Picard recipe
CALIBRATE_SCUBA2_DATA. By default this will multiply your map by
obtained from the start of Section 8.1. This produces a calibrated map with units of mJy/beam.
You can supply a parameter file if you wish to use a different value for the FCF or use
recipe will write out the calibrated file with an
_cal suffix and will change the units in the map
Note that the recipe will also take account of the pixel size when applying .
The nature of the scan patterns results in SCUBA-2 maps significantly larger than the requested size. The high noise towards the outer edges is a consequence of the scanning pattern. Although this excess data are down-weighted during reduction by the map-maker, you may wish to remove it before either combining maps (see Section 8.3) or publishing your map.
You can crop your map to the map-size set in the data header or to any requested size of box or circle using the
CROP_SCUBA2_IMAGES. The centre of the cropping area will always be the centre of your
The example above includes a parameter file specifying the radius of the circle to be extracted (in arcsecs). The format for the parameter file is shown below.
If this parameter file is omitted it will default to a box of sides equal to the map size in the header (as requested in the
MSB). The output from
CROP_SCUBA2_IMAGES is a file with the suffix
_crop. Full details of this recipe can be found in the
You may have multiple maps of the same source which you would like to co-add. Picard has a recipe called
MOSAIC_JCMT_IMAGES that co-adds maps while correctly dealing with the exposure time and weights NDF
extensions. The images are combined using inverse-variance weighting and the output variance is derived from
the input variances.
This creates a single output file based on the name of the last file in the list, and with a suffix
There are a number of options associated with
MOSAIC_JCMT_IMAGES (see the Picard manual for a full
description). However, the main one is choosing between wcsmosaic (default) and the Ccdpack option
makemos for the combination method. For more information on makemos and advice on choosing the best
method see SUN/139.
The example parameter file below chooses makemos using a 3- clipping threshold.
Currently there is no advantage in terms of data quality to reducing all observations simultaneously or separately. However, the latter does allow the option of assessing the individual maps before co-adding.
cat. Remember to include the back quotes. For example,
% picard MOSAIC_JCMT_IMAGES `cat myfiles.txt`.
You can register a series of SCUBA-2 maps to a common reference position using the Picard recipe
SCUBA2_REGISTER_IMAGES. This is only possible if a there is a common, known source that is present in all of the
input maps. This should be done before combining your maps.
Here the parameter file contains the equatorial position of the reference source as in the example below. See SUN/265 for more details.
REGISTER_Y may also be galactic longitude and latitude respectively, both measured in decimal
You can use the Picard recipe
SCUBA2_MAPSTATS get the noise. This recipe estimates the RMS from both
the map, the NEP, and the RMS predicted by the Integration Time Calculator. It then writes out a
series of results in a log file called
log.mapstats. The parameters written to this file are listed in
This recipe will report the noise in the same input units provided.
SCUBA2_MAPSTATS is only designed to work on reductions of a single observations. On coadded
observations it could produce misleading results, or even fail completely to work.
If multiple files are run through
SCUBA2_MAPSTATS, either in a single call of PICARD or by repeatedly running
PICARD in the same terminal on different files, the results will be appended to the existing log.mapstats file.
The final columns — project, recipe and filename — are given to ensure it is clear to users which line of the
logfile corresponds to which input file.
After applying any necessary FCF,
SCUBA2_MAPSTATS simply executes the following steps to get the map
The Kappa commands histat and stats are very similar and both return a range of statistics describing any
NDF. In addition to the main data array they can be passed the error (
comp=err), variance (
comp=var) or quality
comp=qua) arrays (if available).
The reported statistics include the pixel maximum and minimum, standard deviation, number of pixels used
and omitted, along with pixel mode, and mean. If you supply the
order keyword, the median is also
Note: the standard deviation of the data array will give a similar result to the mean/median of the error array except with additional contamination from sources.
You can view a histogram of the error array with the Kappa command histogram. Again
comp=err must be
The output is shown in the Figure 8.1. For more information on the options for histogram see SUN/95.
It is also useful to view the error map itself. Open your reduced map in Gaia, then select the Error button on the Select NDF in container file window—see Figure 8.2. You will need to adjust the scaling to view the error map properly.
To assess the noise using Gaia, go to the toolbar on the main window and click on Image-AnalysisImage regions. Next select the region shape you would like to check and draw it on your map by clicking and dragging the mouse. Click the Stats selected button in the Image regions window to get a report of the statistics in the selected region.
% ndfcopy map comp=err map_err
To change the pixel size use the Kappa command compave. The following example increases the pixel size from 4 arcsec to 8 arcsec by using a compression factor of 2.
SCUBA-2 maps created using “
AST-masking” (see Section 3.5) will contain a
Quality array indicating the
background pixels that were masked (i.e. forced to zero). In itself this is fairly simple - background pixels have a
non-zero Quality value and source pixels have a Quality value of zero. However, it is also possible to have
independent masks for the
COM models, in addition to the
AST mask. For instance, maps created using
dimmconfig_jsa_generic will have
Quality arrays that contain
FLT and an
AST mask, and so some care needs to be used when interpreting the
Each value in the
Quality array is restricted to taking integer values between 0 and 255, and so can
be thought of as 8 separate bits. Each “bit plane” within the
Quality array holds a single mask -
COM. The showqual command can be used to find out which mask is held by which bit
This means that the
AST mask is stored in bit 1 (the least significant bit), the
FLT mask is stored in bit 2, and there
COM mask. Note, if a map was produced using
FLT masking but no
AST masking, then the
FLT mask would
be stored in bit 1.
The decimal integer value of any element of the
Quality array is equal to the binary value formed from the bits
listed by showqual. So in the above case the maximum
Quality value is 3 (the decimal equivalent of binary “11”
— both bits set). Remembering that a bit is set (i.e. is 1) for background pixels and cleared (i.e. is 0)
for source pixels, it follows that the four possible decimal
Quality values in the above case (0-3)
FLTmask (a source pixel).
ASTmask but inside the
FLTmask (a border-line pixel).
ASTmask but outside the
FLTmask (a border-line pixel).
Figure 8.3 shows a simple map of the
Quality array values — the black areas have value zero and are thus
inside both masks, the dark brown areas have value 2 and are thus inside the
AST mask but outside the
FLT mask. The light brown areas have value 3 and are inside neither mask. In this particular case,
there are no areas with a quality value of 1, so the
FLT mask is contained entirely within the
To produce a plot like this, first open your map in Gaia. Select the top level NDF from list in the pop-up window then click the Quality button. You will need to rescale the map to bring out the masks–see Figure 8.4 for another example showing the full Gaia window (using rather brighter colours this time!).
There are several commands within Kappa that manipulate
Quality arrays in various ways. For instance, the
setbb command allows pixel data values to be set bad if the associated
Quality value has a specified collection
of set bits. Thus:
will set all pixels bad in
fred.sdf except for those inside the
AST mask. Likewise,
will set all pixels bad except for those inside the
FLT mask. Note, the change made by setbb is temporary - it can
be undone by doing:
To display the
fred.sdf map and then overlay the
AST mask in blue and the
FLT mask in red, do:
The resulting plot is shown in Figure 8.5.
Alternatively, Gaia can be used to contour the
Quality array over an image, but you cannot then distinguish
AST mask from the
FLT mask. First you will need to copy out the QUALITY component of the data to a
separate file using ndfcopy:
Then open your map in Gaia and contour the mask NDF on top. Select Contouring... from the Image-Analysis menu, and supply the name of the mask NDF either by entering its name in the Other image: box, or selecting with Choose file... file browser. See Figure 8.6.
For more information on the use of masks by makemap and the parameters that affect them see sectyion 3.5.
This effectively fits a single Gaussian point spread function (PSF), centered over every pixel in the map, and applies a background suppression filter to remove any residual large-scale noise.
Cosmology maps usually contain very faint sources that often need extra help extracting. The Picard recipe
SCUBA2_MATCHED_FILTER can be used to improve point-source detectability.
The matched filter works by smoothing the map and PSF with a broad Gaussian, and then subtracting from the originals. The images are then convolved with the modified PSF. The output map should be used primarily for source detection only. Although the output is normalised to preserve peak flux density, the accuracy of this depends on how closely the real PSF matches the telescope beam size. In the case of nearby sources, each ends up contributing flux to both peaks.
As in the example parameter file below we have requested the background should be estimated by first smoothing the map and PSF with a 15-arcsec Gaussian.
This is a fairly common technique used throughout the extra-galactic sub-millimetre community to identify potential sources. A full description of the matched filter principle is given in Appendix D, while the Picard manual gives full details of all the available parameters.
The Cupid application findclumps can be used to generate a clump catalogue. It identifies clumps of emission in one-, two- or three-dimensional NDFs. You can select from the clump-finding algorithms “FellWalker”, “Gaussclumps”, “ClumpFind” or “Reinhold” and must supply a configuration file specific to each method. See the Cupid manual for descriptions of the various algorithms.
The result is returned as a catalogue in a text file and as a NDF pixel mask showing the clump boundaries.
The shape option allows findclumps to create an STC-S description (polygonal or elliptical) for each clump. These are added as extra columns to the output catalogue.
|Polygon||Each polygon will have, at most, 15 vertices. For two-dimensional data the polygon is a fit to the clump’s outer boundary (the region containing all good data values). For three-dimensional data the spatial footprint of each clump is determined by rejecting the least significant 10% of spatial pixels, where "significance" is measured by the number of spectral channels that contribute to the spatial pixel. The polygon is then a fit to the outer boundary of the remaining spatial pixels.|
|Ellipse||All data values in the clump are projected onto the spatial plane and "size" of the collapsed clump at four different position angles—all separated by 45—is found. The ellipse that generates the same sizes at the four position angles is then found and used as the clump shape.|
You may want to check a reduced file to determine which raw files went into it and what configuration parameters were used with the map-maker. There are a number of useful Kappa commands to help you with this:
The output of provshow can be very long. If you merely want to know what were the original file, the ones with no parents, select the root ancestors.
diffuse, and are searched for in that order. The follow example illustrates two ways to run configmeld:
Another useful command is the Kappa command configecho. This is very versatile and will display the name and value of one or all configuration parameters either from a configuration file or from the history of an NDF.
The first example below will return the value of
numiter from the map
850map.sdf. The second example
will display the values of all the parameters in
850map.sdf and will prefix them with a ‘+’ if they differ
from the the default parameter values defined in