User Parameters - Spectral-line Imaging

There are several steps involved in running the spectral-line imaging, with several optional pre-processing steps:

  1. A nominated channel range can optionally be copied to a new MS with mssplit.
  2. The gains solution from the continuum self-calibration can be applied to the spectral-line MS using ccalapply.
  3. The continuum can be subtracted from the spectral-line MS using ccontsubtract The continuum is represented by either the clean model from the continuum imaging, or – as the default – a model image constructed by Cmodel from the component catalogue generated by Selavy. The Selavy parameters used are those described on User Parameters - Continuum Source-finding.

Following this pre-processing, the resulting MS is imaged by either the imager task (the default), or the old simager, creating a set of spectral cubes. Imager provides the ability to image in the barycentric reference frame, and allows (for efficiency purposes) the option of writing out multiple sub-cubes (each having a subset of the full range of channels).

A final task can perform image-based continuum subtraction. There are two choices for this step, made via the SPECTRAL_IMSUB_SCRIPT parameter. The first uses the script in the ACES directory to fit and subtract a low-order polynomial to each spectrum in the cube separately. The second uses the script which uses a Savitzky-Golay filter to find and remove the spectral baseline, again in each spectrum of the cube separately. These tasks are intended as demonstrations of this capability - there will be an ASKAPsoft equivalent to this in a future release. The task assumes that the requested python script is in $ACES/tools - if it is not found, the task will not run.

The variables presented below work in the same manner as those for the continuum imaging, albeit with names that clearly refer to the spectral-imaging.

Whether or not the spectral processing is done is governed by the DO_SPECTRAL_PROCESSING parameter - the default approach of the pipeline is to not do any of the processing above, but if this parameter is set to true then it falls to the individual switches for each task. Each of these default to true, so if DO_SPECTRAL_PROCESSING is turned on then everything will be done.

A note on the imagers and the output formats. The default approach is to use the new imager imager (imager (under test)) to produce the spectral-line cubes. The legacy spectral imager application simager can be used by setting DO_ALT_IMAGER_SPECTRAL or DO_ALT_IMAGER to false. The latter is the switch controlling all types of imaging, but can be overridden by the former, if provided.

The default output format is CASA images, although FITS files can be written directly by setting IMAGETYPE_SPECTRAL to fits (rather than casa). This will only work with the new imager, as simager does not have this functionality. This mode is still in development, so may not be completely reliable. The recommended method for getting images into FITS format is still to use the DO_CONVERT_TO_FITS flag, which makes use of the FITS conversion application. A single FITS file can be produced by setting ALT_IMAGER_SINGLE_FILE=true.

Variable Default Parset equivalent Description
DO_SPECTRAL_PROCESSING false none Whether to do the spectral-line processing.
JOB_TIME_SPECTRAL_IMAGE JOB_TIME_DEFAULT (24:00:00) none Time request for imaging the spectral-line data
IMAGETYPE_SPECTRAL fits imagetype (imager (under test)) Image format to use - can be either ‘casa’ or ‘fits’, although ‘fits’ can only be given in conjunction with DO_ALT_IMAGER_SPECTRAL=true.
Preparation of spectral dataset      
DO_COPY_SL false none Whether to copy a channel range of the original full-spectral-resolution measurement set into a new MS. If the original MS is, this will create
JOB_TIME_SPECTRAL_SPLIT JOB_TIME_DEFAULT (24:00:00) none Time request for splitting out a subset of the spectral data
CHAN_RANGE_SL_SCIENCE “1-NUM_CHAN_SCIENCE channel (mssplit (Measurement Splitting/Averaging Utility)) The range of channels to copy from the original dataset (1-based).
TILENCHAN_SL 1 stman.tilenchan (mssplit (Measurement Splitting/Averaging Utility)) The number of channels in the tile size used for the new MS. The tile size defines the minimum amount read at a time.
DO_APPLY_CAL_SL true none Whether to apply the gains calibration determined from the continuum self-calibration (see GAINS_CAL_TABLE in User Parameters - Continuum imaging).
JOB_TIME_SPECTRAL_APPLYCAL JOB_TIME_DEFAULT (24:00:00) none Time request for applying the gains calibration to the spectral data
DO_CONT_SUB_SL true none Whether to subtract a continuum model from the spectral-line dataset. If true, the clean model from the continuum imaging will be used to represent the continuum, and this will be subtracted from the spectral-line dataset (either the original full-spectral-resolution one, or the reduced-channel-range copy), which gets overwritten.
JOB_TIME_SPECTRAL_CONTSUB JOB_TIME_DEFAULT (24:00:00) none Time request for subtracting the continuum from the spectral data
Continuum subtraction      
CONTSUB_METHOD Cmodel none This defines which method is used to determine the continuum that is to be subtracted. It can take one of three values: Cmodel (the default), which uses a model image constructed by Cmodel (cmodel (Model Image Generator)) from a continuum components catalogue generated by Selavy (Selavy Basics); Components, which uses the Selavy catalogue directly by in the form of components; or CleanModel, in which case the clean model from the continuum imaging will be used.
CONTSUB_SELAVY_NSUBX 6 nsubx (Selavy Basics) Division of image in x-direction for source-finding
CONTSUB_SELAVY_NSUBY 3 nsuby (Selavy Basics) Division of image in y-direction for source-finding
CONTSUB_SELAVY_THRESHOLD 6 snrCut (Selavy Basics) SNR threshold for detection with Selavy in determining components to go into the continuum model.
CONTSUB_MODEL_FLUX_LIMIT 10uJy flux_limit (cmodel (Model Image Generator)) Flux limit applied to component catalogue - only components brighter than this will be included in the model image. Parameter takes the form of a number+units string.
CONTSUB_SELAVY_FLAG_ADJACENT true flagAdjacent (Selavy Basics) Whether to enforce pixels in islands to be contiguous.
CONTSUB_SELAVY_SPATIAL_THRESHOLD 5 threshSpatial (Selavy Basics) If CONTSUB_SELAVY_FLAG_ADJACENT=false, this is the threshold in pixels within which islands are joined.
Basic variables for imaging      
DO_SPECTRAL_IMAGING true none Whether to do the spectral imaging
NUM_CPUS_SPECIMG_SCI 200 none The total number of cores allocated to the spectral-imaging job. One will be the master, while the rest will be devoted to imaging individual channels. This is not used when DO_ALT_IMAGER_SPECTRAL=true - instead, it is set to NCHAN / NCHAN_PER_CORE_SL + 1. If NCHAN_PER_CORE_SL does not evenly divide into NCHAN, then an error is raised and no jobs are submitted.
CPUS_PER_CORE_SPEC_IMAGING 20 none The number of cores per node to use (max 20).
IMAGE_BASE_SPECTRAL i.SB%s.cube Helps form (simager) The base name for image cubes: if IMAGE_BASE_SPECTRAL=i.blah then we’ll get image.i.blah, image.i.blah.restored, psf.i.blah etc. The %s wildcard will be resolved into the scheduling block ID.
DIRECTION_SCI none Images.direction (simager) The direction parameter for the image cubes, i.e. the central position. Can be left out, in which case it will be determined from the measurement set by mslist. This is the same input parameter as that used for the continuum imaging.
NUM_PIXELS_SPECTRAL 1024 Images.shape (simager) The number of spatial pixels along the side for the image cubes. Needs to be specified (unlike the continuum imaging case).
CELLSIZE_SPECTRAL 8 Images.cellsize (simager) The spatial pixel size for the image cubes. Must be specified.
REST_FREQUENCY_SPECTRAL HI Images.restFrequency (simager) The rest frequency for the cube. Can be a quantity string (eg. 1234.567MHz), or the special string ‘HI’ (which is 1420.405751786 MHz). If blank, no rest frequency will be written to the cube.
SPECTRAL_IMAGE_MAXUV 2000 MaxUV (Data Selection) A maximum UV distance (in metres) to apply in the data selection step. Only used if a positive value is applied.
SPECTRAL_IMAGE_MINUV 0 MinUV (Data Selection) A minimum UV distance (in metres) to apply in the data selection step. Only used if a positive value is applied.
GRIDDER_SPECTRAL_SNAPSHOT_IMAGING false snapshotimaging (Gridders) Whether to use snapshot imaging when gridding.
GRIDDER_SPECTRAL_SNAPSHOT_WTOL 2600 snapshotimaging.wtolerance (Gridders) The wtolerance parameter controlling how frequently to snapshot.
GRIDDER_SPECTRAL_SNAPSHOT_LONGTRACK true snapshotimaging.longtrack (Gridders) The longtrack parameter controlling how the best-fit W plane is determined when using snapshots.
GRIDDER_SPECTRAL_SNAPSHOT_CLIPPING 0.01 snapshotimaging.clipping (Gridders) If greater than zero, this fraction of the full image width is set to zero. Useful when imaging at high declination as the edges can generate artefacts.
GRIDDER_SPECTRAL_WMAX 2600 (GRIDDER_SNAPSHOT_IMAGING=true) or 35000 (GRIDDER_SNAPSHOT_IMAGING=false) WProject.wmax (Gridders) The wmax parameter for the gridder. The default for this depends on whether snapshot imaging is invoked or not (GRIDDER_SNAPSHOT_IMAGING).
GRIDDER_SPECTRAL_NWPLANES 257 WProject.nwplanes (Gridders) The nwplanes parameter for the gridder.
GRIDDER_SPECTRAL_OVERSAMPLE 4 WProject.oversample (Gridders) The oversampling factor for the gridder.
GRIDDER_SPECTRAL_MAXSUPPORT 512 (GRIDDER_SNAPSHOT_IMAGING=true) or 1024 (GRIDDER_SNAPSHOT_IMAGING=false) WProject.maxsupport (Gridders) The maxsupport parameter for the gridder. The default for this depends on whether snapshot imaging is invoked or not (GRIDDER_SNAPSHOT_IMAGING).
GRIDDER_SPECTRAL_SHARECF true WProject.sharecf (Gridders) Whether to use a (static) cache for the convolution functions in the WProject gridder.
SOLVER_SPECTRAL Clean solver (Solvers) Which solver to use. You will mostly want to leave this as ‘Clean’, but there is a ‘Dirty’ solver available.
CLEAN_SPECTRAL_ALGORITHM BasisfunctionMFS Clean.algorithm (Solvers) The name of the clean algorithm to use.
CLEAN_SPECTRAL_MINORCYCLE_NITER 800 Clean.niter (Solvers) The number of iterations for the minor cycle clean.
CLEAN_SPECTRAL_GAIN 0.2 Clean.gain (Solvers) The loop gain (fraction of peak subtracted per minor cycle).
CLEAN_SPECTRAL_PSFWIDTH 256 Clean.psfwidth (Solvers) The width of the psf patch used in the minor cycle.
CLEAN_SPECTRAL_SCALES "[0,3,10,30]" Clean.scales (Solvers) Set of scales (in pixels) to use with the multi-scale clean.
CLEAN_SPECTRAL_THRESHOLD_MINORCYCLE "[45%, 3.5mJy, 0.5mJy]" threshold.minorcycle (Solvers) Threshold for the minor cycle loop.
CLEAN_SPECTRAL_THRESHOLD_MAJORCYCLE 0.5mJy threshold.majorcycle (Solvers) The target peak residual. Major cycles stop if this is reached. A negative number ensures all major cycles requested are done.
CLEAN_SPECTRAL_NUM_MAJORCYCLES 3 ncycles (Solvers) Number of major cycles.
CLEAN_WRITE_AT_MAJOR_CYCLE false Images.writeAtMajorCycle (simager) If true, the intermediate images will be written (with a .cycle suffix) after the end of each major cycle.
CLEAN_SPECTRAL_SOLUTIONTYPE MAXCHISQ Clean.solutiontype (see discussion at Multi-Scale and/or Multi-Frequency deconvolution) The type of peak finding algorithm to use in the deconvolution. Choices are MAXCHISQ, MAXTERM0, or MAXBASE.
PRECONDITIONER_LIST_SPECTRAL "[Wiener, GaussianTaper]" preconditioner.Names (Solvers) List of preconditioners to apply.
PRECONDITIONER_SPECTRAL_GAUSS_TAPER "[20arcsec, 20arcsec, 0deg]" preconditioner.GaussianTaper (Solvers) Size of the Gaussian taper - either single value (for circular taper) or 3 values giving an elliptical size.
PRECONDITIONER_SPECTRAL_WIENER_ROBUSTNESS 0.5 preconditioner.Wiener.robustness (Solvers) Robustness value for the Wiener filter.
PRECONDITIONER_SPECTRAL_WIENER_TAPER "" preconditioner.Wiener.taper (Solvers) Size of gaussian taper applied in image domain to Wiener filter. Ignored if blank (ie. "").
RESTORE_SPECTRAL true restore (simager) Whether to restore the image cubes.
RESTORING_BEAM_SPECTRAL fit restore.beam (simager) Restoring beam to use: ‘fit’ will fit the PSF in each channel separately to determine the appropriate beam for that channel, else give a size (such as “[30arcsec, 30arcsec, 0deg]”).
RESTORING_BEAM_CUTOFF_SPECTRAL 0.5 restore.beam.cutoff (simager) Cutoff value used in determining the support for the fitting (ie. the rectangular area given to the fitting routine). Value is a fraction of the peak.
RESTORING_BEAM_REFERENCE mid restore.beamReference (simager) Which channel to use as the reference when writing the restoring beam to the image cube. Can be an integer as the channel number (0-based), or one of ‘mid’ (the middle channel), ‘first’ or ‘last’
New imager parameters      
DO_ALT_IMAGER_SPECTRAL "" none If true, the spectral-line imaging is done by imager (doc:../calim/imager). If false, it is done by simager (simager). When true, the following parameters are used. If left blank (the default), the value is given by the overall parameter DO_ALT_IMAGER (see User Parameters - Pipeline & job control).
NCHAN_PER_CORE_SL 64 nchanpercore (imager (under test)) The number of channels each core will process.
USE_TMPFS false usetmpfs (imager (under test)) Whether to store the visibilities in shared memory. This will give a performance boost at the expense of memory usage. Better used for processing continuum data.
TMPFS /dev/shm tmpfs (imager (under test)) Location of the shared memory.
NUM_SPECTRAL_WRITERS 16 nwriters (imager (under test)) The number of writers used by imager. Unless ALT_IMAGER_SINGLE_FILE=true, this will equate to the number of distinct spectral cubes produced. In the case of multiple cubes, each will be a sub-band of the full bandwidth. No combination of the sub-cubes is currently done. The number of writers will be reduced to the number of workers in the job if necessary.
ALT_IMAGER_SINGLE_FILE true singleoutputfile (imager (under test)) Whether to write a single cube, even with multiple writers (ie. NUM_SPECTRAL_WRITERS>1). Only works when IMAGETYPE_SPECTRAL=fits
FREQ_FRAME_SL bary freqframe (imager (under test)) The reference frame in which to write the spectral cube - one of topo, bary, lsrk. Anything else (or an unset value) default to bary.
OUTPUT_CHANNELS_SL "" Frequencies (imager (under test)) The output channels for the spectral cube. Should be of the form [number,start,width], with the start and width parameters are in Hz. If not given, the behaviour is to use the same frequency values as the input MS, albeit in the requested frequency frame.
Image-based continuum subtraction      
DO_SPECTRAL_IMSUB true none Whether to run an image-based continuum-subtraction task on the spectral cube after creation.
JOB_TIME_SPECTRAL_IMCONTSUB JOB_TIME_DEFAULT (24:00:00) none Time request for image-based continuum subtraction
SPECTRAL_IMSUB_SCRIPT "" none The name of the script from the ACES repository to use for image-based continuum subtraction. The only two accepted values are “” and “”. Anything else reverts to the default.
SPECTRAL_IMSUB_VERBOSE true none Whether to use verbose output in the logging for the image-based continuum subtraction.
SPECTRAL_IMSUB_THRESHOLD 2.0 none (‘threshold’ parameter in Threshold [sigma] to mask outliers prior to fitting the continuum baseline in the “” version of the image-based continuum-subtraction.
SPECTRAL_IMSUB_FIT_ORDER 2 none (‘fit_order’ parameter in Order of the polynomial to fit to the continuum baseline in the “” version of the image-based continuum subtraction.
SPECTRAL_IMSUB_CHAN_SAMPLING 1 none (‘n_every’ parameter in If set to n, we use only every nth channel in the polynomial fit (1 uses every channel). Only for “”
SPECTRAL_IMSUB_LOG_SAMPLING 1 none (‘log_every’ parameter in How frequently the log messages from “” should be written (1 means every channel).
SPECTRAL_IMSUB_SG_FILTERWIDTH 200 none (‘filterwidth’ parameter in The half-width of the Savitzky-Golay filter for baseline smoothing in the “” script.
SPECTRAL_IMSUB_SG_BINWIDTH 4 none (‘binwidth’ parameter in The bin width used for binning the spectrum before continuum subtraction (“” only).

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