Post-processing SCUBA-2 data with PICARD

Processing raw SCUBA-2 data is done with SMURF or the pipeline (ORAC-DR). What happens after that depends on the user and their level of familiarity with particular software packages. Fortunately the SCUBA-2 software team is here to help out and come up with a series of standardized tools for performing a number of basic post-processing tasks.

Introduction to PICARD

Our tool of choice is PICARD which makes use of the existing ORAC-DR infrastructure as well as our existing knowledge of writing primitives and recipes for the SCUBA-2 pipeline. PICARD is run from the command line as follows (I'll use % as the prompt):

% picard [options] [RECIPE_NAME] [list of files to process]

For example,

% picard -log sf -recpars mypar.lis CROP_JCMT_IMAGES myfiles*.sdf

The most commonly used options are -log and -recpars (the full list of available options can be seen by running picard -h). Both of these options take additional arguments.

The "-log" option controls where the messages from PICARD are printed: "-log sf" will write messages to the terminal window and to a file called .picard_PID.log (where PID is the process ID for picard) in the output directory. To avoid creating the .picard_PID.log files, just specify "-log s".

The "-recpars" option allows the user to pass in a text file containing parameters which can be used in the given recipe. The permitted parameters are listed with the various recipes below. The format of this text file is a list of `parameter = value' entries, with the recipe name given in square brackets:

[RECIPE_NAME]
PARAM1 = VALUE1
PARAM2 = VALUE2

PICARD writes its output files to the current directory (unless the environment variable ORAC_DATA_OUT is defined in which case that location will be used).

There are currently four recipes which may be of interest:

• MOSAIC_JCMT_IMAGES
• CROP_JCMT_IMAGES
• REMOVE_BACKGROUND
• SCUBA2_MATCHED_FILTER

These recipes and their parameters are described in more detail below. More recipes will be added as the need arises and as we gain more experience in analyzing SCUBA-2 data. Interested users should update their Starlink installations to get access to these recipes.

MOSAIC_JCMT_IMAGES

Coadd the given files into a single map, taking into account the EXP_TIME and WEIGHTS NDF components. The images are combined using variance weighting and the output variance is derived from the input variances. Currently the recipe uses the KAPPA wcsmosaic task for coadding the images.

The same pixel-spreading method (and any associated parameters) is used for the data and the EXP_TIME and WEIGHTS.

Creates a single output file based on the name of the last file in the list, and with a suffix "_mos" (e.g. mylastfile_mos.sdf).

Available recipe parameters:
[MOSAIC_JCMT_IMAGES]
WCSMOSAIC_METHOD = wcsmosaic pixel-spreading method: see wcsmosaic documentation for available options (default is "nearest")
WCSMOSAIC_PARAMS = additional parameters which may be required for the chosen method

CROP_JCMT_IMAGES

Crop images to the map size in the data header (as specified in the Observing Tool), though this size can be overridden using the recipe parameters below.

Creates an output file for each input file, with the suffix "_crop".

Available recipe parameters:
[CROP_JCMT_IMAGES]
MAP_WIDTH = map width in arcsec
MAP_HEIGHT = map height in arcsec

REMOVE_BACKGROUND

Fit and remove large-scale background variations from images using either KAPPA fitsurface or CUPID findback. See the Starlink documentation on both tasks for more information on the parameters shown below. The option exists to mask out a circular region centred on the source before removing the background.

Be aware that the subtraction of the background will add noise proportional to the RMS deviation between the image and the background fit.

Creates an output file for each input file with the suffix "_back".

Available recipe parameters:
[REMOVE_BACKGROUND]
MASK_SOURCE = flag to mask out a circular region on the source before fitting a background (1 = mask out source; 0 = do not mask out source - the default)
APERTURE_RADIUS = radius of aperture (in arcsec) for masking out source (otherwise 30 arcsec)
BACKGROUND_FITMETHOD = the method for fitting the background, either fitsurface (default) or findback
FITSURFACE_FITTYPE = fittype parameter for fitsurface: polynomial (default) or spline
FITSURFACE_FITPAR = parameters for fit, up to 2 numbers corresponding to NXPAR/NYPAR for fitsurface or KNOTS for spline fit
FINDBACK_BOX = size of box in pixels used by findback for smoothing the image

SCUBA2_MATCHED_FILTER

Apply a matched filter to the data to improve point-source detectability. The images and PSFs are smoothed with a broad Gaussian (default is 30 arcsec but can be varied using the recipe parameter below) and subtracted from the originals. The images are convolved with the modified PSFs. The PSF created by the recipe is a Gaussian with FWHM equal to the JCMT beamsize at the appropriate wavelength (i.e. 7.5 or 14 arcsec).

Creates an output file for each input file with the suffix "_mf", and a PSF file "_psf" if the PSF was not specified as a recipe parameter.

Available recipe parameters:
[SCUBA2_MATCHED_FILTER]
PSF_MATCHFILTER = name of a PSF file (NDF format, will be used for all images)
PSF_NORM = switch to determine whether a PSF is normalized to a peak of unity ("peak" - the default) or a sum of unity ("sum")
SMOOTH_FWHM = FWHM in arcsec of Gaussian to smooth image (and PSF)