User Parameters - Spectral-line Imaging

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

1. The mssplit (Measurement Splitting/Averaging Utility) tool may be used to copy a nominated channel range, and/or average a nominated number of channels together, to form a new spectral-line MS.

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, the component catalogue generated by Selavy, or a model image constructed by Cmodel from that catalogue. The Selavy parameters used are those described on User Parameters - Continuum Source-finding.

4. The continuum (or residual continuum after the previous subtraction) can also be fitted and subtracted by the uvlin feature of ccontsubtract which allows visibility-based modeling and subtraction method using basis functions comprising of polynomials and harmonics. This implements some of the functionality of the previous (separate) tool to do this:

5. The tool remUVcont allows removal of both continuum as well as instrument-induced non-idealities. As the name suggests this is a visibility-based modeling and subtraction method using basis functions comprising of polynomials and harmonics with useful frills suitable for dealing with instrumental systematics.

These preprocessing steps, other than continuum subtraction, may be done in a single slurm job if SINGLE_JOB_PREIMAGING=true (which is the case by default).

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).

The output spectral fram can be specified by the FREQ_FRAME_SL parameter, which can be one of “topo”, “bary”, “lsrk”. For the latter two, the direction used for the frame conversion is taken from the DOPPLER_TRACKING_DIRECTION parameter. This can take one of two special values: “beam” (the default) means use the centre direction of the current beam (and so each beam will get a slightly different correction), and “target” means use the pointing centre (if there is more than one interleave position, the first is used). Alternatively, a direction specification of the form “[ra, dec, equinox]” can be provided.

The point at which the Doppler correction is done is chosen by the parameter DOPPLER_CORRECTION_IN_IMAGER. If true, the correction will be done at the start of the imager job, when the data is read in. If false, it will be done in the mssplit job that runs prior to imaging. This is the job that makes a copy of the data (with an optional channel-range cut), triggered by DO_COPY_SL.

In the latter case, the frame correction can make use of interpolation to improve the accuracy, with the type of interpolation given by DOPPLER_CORRECTION_INTERPOLATION.

When the mssplit option is used, it is advisable to not use the UV continuum subtraction option DO_CONT_SUB_SL, since the continuum subtraction is done after the splitting, and the doppler correction will change the location of topocentric features such as beamforming regions. A check is in place to prevent inadvertent use in this scenario, although an override parameter OVERRIDE_CONTSUB_MSSPLIT_DOPPLER_CHECK exists to avoid the check.

Following imaging, the cube statistics are calculated, using a distributed task within the same slurm job as the spectral imaging. This produces a file listing a series of statistics for each channel, as well as a plot of the statistics. See Validation and Diagnostics for examples. These statistics are then used to identify problematic channels (for example, due to divergence in the imaging caused by RFI) that are then masked. Blank channels (those not imaged, e.g. due to barycentric correction or missing data) are also masked. The statistics file is then regenerated.

A final task can perform image-based continuum subtraction. The default tool is the imcontsub tool. This fits and subtracts a low-order polynomial to each spectrum in the cube separately. It is able to fit independently in blocks of channels, which allows it to take into account potential discontinuities at the edges of beam-forming intervals.

Alternatively, there are two python tools available for this step, selected by setting IMCONTSUB_USE_PYTHON=true, and choosing the script via the SPECTRAL_IMSUB_SCRIPT parameter. These were originally developed as demonstration tools, which led to the development of the imcontsub tool. The first option uses the robust_contsub_mpi.py script in the ACES directory, which has a similar behaviour to the imcontsub tool. The second uses the contsub_im.py script which uses a Savitzky-Golay filter to find and remove the spectral baseline, again in each spectrum of the cube separately. The requested python script is assumed to be in $ACES/tools - if it is not found, the task will not run. The former script is MPI-enabled, allowing it to run on multiple cores (defined by NUM_CORES_IMCONTSUB). The latter is still a serial task, so will take considerably longer.

The image-based continuum subtraction can take into account the potential discontinuities at the edges of beam-forming intervals. This is assumes the intervals are a constant size (given by SPECTRAL_IMSUB_BLOCKSIZE), and with some offset relative to the start of the spectrum (given by SPECTRAL_IMSUB_SHIFT, where it takes the value of the number of channels from the start of the first interval to the start of the spectrum). By default, these parameters are derived from the edge frequencies recorded in the SB obs variables, but this may be over-ridden by specifying one or both of these parameters (if only one is given, the other defaults to zero). Providing these parameters will be necessary for SBs older than 26120. Note also that contsub_im.py does not provide this functionality.

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) 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.

Optional Image products

Imager allows users to specify whether or not to write optional output products such as the residual, weights, natural psf, preconditioned psf etc. images. These are aimed at minimising disk I/O and occupancy where possible.

Note that information on weights is required by the linear mosaicking applications: linmos and linmos-mpi. For non A-Projection gridders like WProject, where the weights value across the image extent is constant, imager can write out the weight value into an ascii text file that linmos can make use of. This can be specified using WRITE_WEIGHTS_LOG_SPECTRAL parameter for the spectral line imaging case.

For A-project gridders, or when snapshot imaging is turned on, one will have to necessarily write out the weights images for use in linmos. An exception will be thrown by processASKAP.sh if this condition is violated.

The imager can also optionally output the gridded visibility cubes. This can be requested by setting WRITE_UVGRIDS_SPECTRAL=true.

More details on writing these optional image products are discussed in the sections below. See also User Parameters - Continuum imaging and User Parameters - Mosaicking.

In addition, cube statistics and plots thereof (see Validation and Diagnostics for examples) will be generated for each cube, and copied to a directory within the diagnostics directory. This will be avaiable for download from CASDA within the calibration-metadata-processing-logs evalution tar file.

Spectral Imaging Parameters

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)	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 original.ms, this will create original_SL.ms.
DO_AVERAGE_SL	false	none	Whether to average channels of the spectral dataset when creating the spectral (“_SL.ms”) measurement set
NUM_CHAN_SL_AVERAGE	2	width (mssplit (Measurement Splitting/Averaging Utility))	How many channels to average together when DO_AVERAGE_SL=true. If this doesn’t evenly divide the number of channels, and error is raised and the pipeline exits prior to submitting any jobs.
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	CleanModel	none	This defines which method is used to determine the continuum that is to be subtracted. It can take one of four values: Cmodel, which uses a model image constructed by Cmodel (cmodel) from a continuum components catalogue generated by Selavy (Selavy Basics); Components, which uses the Selavy catalogue directly by in the form of components; CleanModel, in which case the clean model from the continuum imaging will be used; or remUVcont, that models each visibility spectrum using basis functions comprising of a combination of polynomials (equivalent to miriad UVLIN) and harmonics to remove continuum as well instrumental artifacts.
CMODEL_NEAREST_CONTSUB	true	Cmodel.nearest (cmodel)	For CONTSUB_METHOD=Cmodel whether to use nearest neighbour interpolation for point sources. If set to false, Lanczos5 interpolation will be used.
CONTSUB_UVLIN	false	CContSubtract.doUVlin	Whether to subtract a fitted continuum model. If subtraction of an image or component based model is also requested, the fitting will be done on the residual visibilities.
CONTSUB_UVLIN_POLY_ORDER	1	CContSubtract.uvlin.order	Order of the polynomial function used in fitting
CONTSUB_UVLIN_HARM_ORDER	0	CContSubtract.uvlin.harmonic	Order of the harmonic function used in fitting. Each order adds an additional sine and cosine term
CONTSUB_UVLIN_WIDTH	0	CContSubtract.uvlin.width	The data will be divided into bins of ‘width’ channels that are then fitted independently.
CONTSUB_UVLIN_OFFSET	0	CContSubtract.uvlin.offset	When fitting in bins, shift the bins left by ‘offset’ channels to match beam forming intervals
CONTSUB_UVLIN_THRESHOLD	2.5	CContSubtract.uvlin.threshold	Exclude outliers from the continuum fit. This first determines a robust estimate of rms and then rejects channels more than threshold*rms from the model. Set to zero to skip thresholding.
CONTSUB_UVLIN_DIRECTION	None	CContSubtract.uvlin.direction	Specify direction to rotate visibilities to before doing the fit to each spectrum. After the fit/subtract the visibilities are rotated back. A general Direction Measure is supported, e.g., [12h34m56.7,-23.34.45.6,J2000] or SUN
REMUVCONT_POLY_ORDER	“”	none	Order of the polynomial function used in fitting
REMUVCONT_HARM_ORDER	“”	none	Order of the harmonic function used in fitting
REMUVCONT_N_WIN	“”	none	The data will be divided into nWin windows and a moving fit is done to derive a smooth model
REMUVCONT_N_TAPER	“”	none	Gaussian Taper width in number of channels to be used in an intermediate step where the spectrum is passed through a low pass filter to interpolate across flagged channels. The good data are not altered. This helps make the fitting robust.
REMUVCONT_N_ITER	“”	none	The intermediate los pass filter is an iterative method based on FFT. This parameter specifies the number of iterations. Usually a few tens of iterations suffices. To avoid the low-pass filter step, use 0
REMUVCONT_F54	“”	none	Set this to an integer value N such that 54 x N = beam-forming width in units of number of channels. If this parameter is set, the fitting will be done only within beam-forming intervals. This is necessary to be robust against any discontinuities at the beam-forming and/or ODC update intervals. Note1: When this option is turned ON REMUVCONT_N_WIN is computed internally. Note2: For small windows, choose REMUVCONT_POLY_ORDER and REMUVCONT_HARM_ORDER carefully. Use low orders.
GRIDDER_CONTSUB	“”	gridder (Gridders)	Specify griddder to use: WProject or MPIWProject. Defaults to the value of GRIDDER (ie. the continuum imaging one). MPIWProject can save memory and time when using multiple ranks
GRIDDER_CONTSUB_CFRANK	16	MPIWProject.cfrank (Gridders)	Number of ranks per node to use to speed up convolution
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)	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.
CONTSUB_SELAVY_SPECTRAL_INDEX_THRESHOLD	“”	spectralTerms.threshold (Post-processing of detections)	Threshold applied to component peak fluxes in determining which have a spectral index (and curvature) value reported in the component catalogue. Not used if left blank. Takes precedence over CONTSUB_SELAVY_SPECTRAL_INDEX_THRESHOLD_SNR.
CONTSUB_SELAVY_SPECTRAL_INDEX_THRESHOLD_SNR		spectralTerms.thresholdSNR (Post-processing of detections)	Threshold applied to component peak signal-to-noise values in determining which have a spectral index (and curvature) value reported in the component catalogue. Not used if left blank.
GRIDDER_CONTSUB	“”	CContSubtract.gridder (ccontsubtract)	Gridder to use in the continuum subtraction. If left blank, it will use the value of GRIDDER.
GRIDDER_CONTSUB_CFRANK	16	gridder.cfrank (Gridders)	The number of ranks used to distribute the convolution functions in the gridding for the continuum subtraction. Only used when GRIDDER_CONTSUB=MPIWProject.
Basic variables for imaging
DO_SPECTRAL_IMAGING	true	none	Whether to do the spectral imaging
NUM_CORES_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.
CORES_PER_NODE_SPEC_IMAGING	20	none	The number of cores per node to use (max 20).
IMAGE_BASE_SPECTRAL	i.%t.SB%s.cube	Helps form Images.name (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, and the %t will be resolved into the “target”, or scheduling block alias.
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.
DO_MASK_BAD_CHANNELS	true	none	Whether to mask out bad or blank channels from the spectral cube.
MASK_CHANS_USE_SIG	false	none	Whether to use the “signifcance”, or the ratio of the 1-percent statistic to the MADFM, to determine the bad channels.
MASK_CHANS_SIG_THRESHOLD		none	The significance level at which to reject channels.
MASK_CHANS_USE_NOISE	true	none	Whether to mask out bad channels on the basis of the MADFM value alone.
MASK_CHANS_NOISE_THRESHOLD		none	The value of MADFM (in mJy/beam), above which a channel is deemed bad.
MASK_CHANS_BLANK	true	none	Whether to mask out blank channels from the continuum cube.
Gridding
GRIDDER_SPECTRAL	WProject	gridder (Gridders)	Specify griddder to use: WProject or MPIWProject. MPIWProject can save memory and time when using multiple ranks
DO_NYQUIST_GRIDDING_SPECTRAL	false	Images.nyquistgridding (imager)	Whether to turn on Nyquist gridding.
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.
GRIDDER_SPECTRAL_CFRANK	16	MPIWProject.cfrank (Gridders)	Number of ranks per node to use to speed up convolution function calculation. Useful range: ~4 to #ranks/node.
Cleaning
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	MAXBASE	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.
CLEAN_SPECTRAL_DETECT_DIVERGENCE	true	Clean.detectdivergence (Solvers)	Whether to detect that the deconvolution is starting to diverge (in which case it is stopped).
Preconditioning
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_GAUSS_TAPER_IS_PSF	"false"	preconditioner.GaussianTaper.isPsfSize (Solvers)	Decide if rather than applying the specified taper, the taper should be adjusted to ensure that the output image planes have the specified resolution.
PRECONDITIONER_SPECTRAL_GAUSS_TAPER_TOL	0.005	preconditioner.GaussianTaper.tolerance (Solvers)	Fractional tolerance for the fitted beam size when PRECONDITIONER_SPECTRAL_GAUSS_TAPER_IS_PSF = true The default is set to 0.5%
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. "").
Restoring
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]”). NB: If PRECONDITIONER_SPECTRAL_GAUSS_TAPER_IS_PSF=true the restoring beam will be derived such that the output image planes have the fixed specified resolution.
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)	The number of channels each core will process.
USE_TMPFS	false	usetmpfs (imager)	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)	Location of the shared memory.
NUM_SPECTRAL_WRITERS	""	nwriters (imager)	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. If left blank, the number of writers will be the number of worker nodes in the imaging job.
ALT_IMAGER_SINGLE_FILE	true	singleoutputfile (imager)	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)	The reference frame in which to write the spectral cube - one of topo, bary, lsrk. Anything else (or an unset value) default to bary. The frame conversion is done assuming a fixed direction (using the dopplertracking.direction parameter on imager). This direection is governed by the DOPPLER_TRACKING_DIRECTION parameter.
DOPPLER_TRACKING_DIRECTION	beam	dopplertracking.direction (imager)	The specific direction to use for doppler tracking (when FREQ_FRAME_SL is bary or lsrk. Can be “beam”, “target”, or a direction string “[ra,dec,equinox]”.
DOPPLER_CORRECTION_IN_IMAGER	true	dopplertracking (imager) dopplercorrection (mssplit (Measurement Splitting/Averaging Utility))	If true, the doppler correction is done by imager, else it is done by mssplit in the preparation of the spectral MS.
DOPPLER_CORRECTION_INTERPOLATION	cubic	interpolation (mssplit (Measurement Splitting/Averaging Utility))	Form of interpolation to use in the Doppler correction when the mssplit option is used. Does not apply if DOPPLER_CORRECTION_IN_IMAGER=true.
OVERRIDE_CONTSUB_MSSPLIT_DOPPLER_CHECK	false	none	If true, the usual check to ensure we don’t combine mssplit doppler correction and UV continuum subtraction is not applied.
OUTPUT_CHANNELS_SL	""	Frequencies (imager)	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.
Optional outputs
WRITE_RESIDUAL_SPECTRAL	true	write.residualimage (imager)	Whether to write the residual image cube
WRITE_PSF_RAW_SPECTRAL	false	write.psfrawimage (imager)	Whether to write the naturally weighted psf image cube
WRITE_PSF_IMAGE_SPECTRAL	false	write.psfimage (imager)	Whether to write the preconditioned psf image cube
WRITE_WEIGHTS_IMAGE_SPECTRAL	false	write.weightsimage (imager)	Whether to write the weights image cube
WRITE_WEIGHTS_LOG_SPECTRAL	true	write.weightslog (imager)	Option to write the weight spectra into an ascii text file Note 1: Should not be used with A-project gridders. The ASKAPpipeline in any case supports WProject only. Note 2: For snapshot imaging, this option is internally forced to “false” by the pipeline scripts. Set WRITE_WEIGHTS_IMAGE_CONT=true in this case.
WRITE_MODEL_IMAGE_SPECTRAL	true	write.modelimage (imager)	Whether to write the model image cube Note: The pipeline ensures that intermediate model images get generated if required by selfcal jobs.
WRITE_UVGRIDS_SPECTRAL	false	write.grids (imager)	Whether to write the UV-grids (cubes only)
UVGRID_EXPORT_WHEN_IMAGING	false	none	Whether to write the UV-grids from within the spectral imaging job. If false (the default), it will write them (when WRITE_UVGRIDS_SPECTRAL=true) in a separate task, that is parameterised by the parameters below. If true, it is done only as part of the spectral imaging job, and so takes on the same parameters as for imaging.
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
IMCONTSUB_USE_PYTHON	false	none	Whether to use one of the python tools (see next item), instead of the default tool imcontsub (imcontsub).
SPECTRAL_IMSUB_IMAGEACCESS	individual (collective when run on galaxy)	imcontsub.imageaccess (imcontsub)	The type of image access method used within the imcontsub tool: this can be ‘collective’ or ‘individual’.
SPECTRAL_IMSUB_SCRIPT	"robust_contsub_mpi.py"	none	The name of the script from the ACES repository to use for image-based continuum subtraction. The only two accepted values are “robust_contsub_mpi.py” and “contsub_im.py”. Anything else reverts to the default.
NUM_CORES_IMCONTSUB	256	none	Number of cores to use for the robust_contsub_mpi.py script. Ignored if contsub_im.py is used. Must divide evenly into the number of spatial pixels in the spectral cube.
SPECTRAL_IMSUB_VERBOSE	true	none	Whether to use verbose output in the logging for the image-based continuum subtraction.
SPECTRAL_IMSUB_THRESHOLD	2.0	imcontsub.threshold (imcontsub) or ‘threshold’ parameter in robust_contsub_mpi.py	Threshold [sigma] to mask outliers prior to fitting the continuum baseline.
SPECTRAL_IMSUB_FIT_ORDER	2	imcontsub.order (imcontsub) or ‘fit_order’ parameter in robust_contsub_mpi.py	Order of the polynomial to fit to the continuum baseline.
SPECTRAL_IMSUB_CHAN_SAMPLING	1	none (‘n_every’ parameter in robust_contsub_mpi.py)	If set to n, we use only every nth channel in the polynomial fit (1 uses every channel). Only for “robust_contsub_mpi.py”
SPECTRAL_IMSUB_BLOCKSIZE	“”	imcontsub.blocksize (imcontsub) or ‘blocksize’ parameter in robust_contsub_mpi.py	Do the fitting and subtracting in blocks of n channels. A value of 0 will result in all channels being used at once. By default, the value for this will be determined from the weights information in the SB obsvariables.
SPECTRAL_IMSUB_SHIFT .	“”	imcontsub.shift (imcontsub) or ‘shift’ parameter in robust_contub_mpi.py	Shift the edges of the blocks to the left by this many channels. By default, the value for this will be determined from the weights information in the SB obsvariables.
SPECTRAL_IMSUB_INTERLEAVE	false	imcontsub.interleave (imcontsub) or ‘interleave’ parameter in robust_contsub_mpi.py	Interleave the blocks by a half, but only take the middle of each interleave. This reduces edge effects
SPECTRAL_IMSUB_LOG_SAMPLING	1	none (‘log_every’ parameter in robust_contsub_mpi.py)	How frequently the log messages from “robust_contsub_mpi.py” should be written (1 means every channel).
SPECTRAL_IMSUB_SG_FILTERWIDTH	200	none (‘filterwidth’ parameter in contsub_im.py)	The half-width of the Savitzky-Golay filter for baseline smoothing in the “contsub_im.py” script.
SPECTRAL_IMSUB_SG_BINWIDTH	4	none (‘binwidth’ parameter in contsub_im.py)	The bin width used for binning the spectrum before continuum subtraction (“contsub_im.py” only).

Visibility handling: UV-grid export and MS cutouts & copies

The pipeline allows for the export of the UV grids that would be used in the spectral imaging, along with their inclusion in the deposit into CASDA. By default this is done through an additional job that runs imager - it is a separate job to the spectral imaging, to allow for different cellsizes or UV ranges to be applied. It can, however, be done from within the spectral imaging job itself, by setting UVGRID_EXPORT_WHEN_IMAGING=true. If the separate job is used, there are a set of specific parameters available to fine-tune the export.

The default approach is to save the complex grids as separate real & imaginary FITS files (FITS does not allow for complex-valued image arrays) - on pair each for image types “visgrid”, “psfgrid”, and “pcfgrid”. These files will be written into a directory with the same name as the spectral MS, save for replacing the “.ms” extension with “.uvgrid”. The FITS headers for the files are extracted to .hdr text files, and the FITS files are then compressed with gzip (the .hdr files are just to allow ease of examination without unzipping the images). The gzip process will compress the files noticeably, due to the large amount of zero-valued pixels in them. This directory will be included for deposit into CASDA, where it will be tarred and made available alongside the measurement sets.

Copies of the measurementsets themselves can be made in a couple of ways. If a set of known positions & velocities is provided, cutouts of the relevant beam MSs can be made for archiving into CASDA. These will be of a predefined width (in channels), and are identified from a provided catalogue within a certain angular offset from the pointing centre. The catalogue name can either be a CSV file (contact Operations for details about format, as this is being developed in conjunction with WALLABY), or the special word ‘HIPASS’, which will query the HIPASS catalogues (the main HICAT, the northern version NHICAT, and the bright galaxy catalogue BGC).

In addition, the full spectral MSs can be copied to a nominated location on disk at Pawsey. This can be either the MS imaged to form the spectral cubes, or the MS prior to continuum subtraction. The destination needs to be appropriate in terms of permissions, and the data policies still apply if this option is utilised (ie. anything published must come from data released on CASDA).

Variable	Default	Parset equivalent	Description
UV-grid export
NUM_PIXELS_SPECTRAL_UVGRID	2560	Images.shape (../calim/imager)	Size of the image & uv pixel grids.
CELLSIZE_SPECTRAL_UVGRID	3.5	Images.cellsize (../calim/imager)	Cellsize in the image plane (in arcsec) of the images that would be created. This determines the angular size of the cell
SPECTRAL_UVGRID_MAXUV	0	MaxUV (Data Selection)	Maximum UV to be read from the dataset. If 0, no maximum UV distance is applied.
SPECTRAL_UVGRID_MINUV	0	MinUV (Data Selection)	Minimum UV to be read from the dataset. If 0, no minimum UV distance is applied.
SPECTRAL_UVGRID_USE_UVCOORD	false	write.grids.uvcoord (imager)	Whether the axes in the exported UVgrid FITS file should be labelled with the UV coordinates, rather than the image plane RA/Dec coordinates.
CORES_PER_NODE_SPECTRAL_UVGRID	10	none	Number of cores per node to be used for the uvgrid export imager job.
NCHAN_PER_CORE_SPECTRAL_UVGRID	“”	nchanpercore (imager)	Number of channels per rank for the UVgrid export job. If blank (the default), it will take the value of NCHAN_PER_CORE_SL.
MS cutouts
DO_SPECTRAL_MS_CUT	false	none	Whether to cut out a spectral range from certain beam MSs corresponding to identified sources from a catalogue.
MS_CUTOUT_CATALOGUE	HIPASS	none	The catalogue to search for sources from. The can be either “HIPASS”, which results in a query from static (downloaded) catalogues of HICAT, NHICAT and BGC, or the name of a local CSV file.
MS_CUTOUT_CATDIR	$PIPELINEDIR/data	none	Directory in which the HIPASS catalogues are located.
MS_CUTOUT_WIDTH	6	none	Maximum search radius [deg] from the field centre for extraction of sources from the catalogue.
MS_CUTOUT_MAXSEP	1.5	none	Maximum allowed separation [deg] between the source and a beam centre.
MS_CUTOUT_NUM_CHAN	250	none	Number of channels around the source’s central velocity to extract (this is the full width)
MS copying
COPY_SPECTRAL_MS	false	none	Whether to copy the full spectral MS to a location on disk.
SPECTRAL_MS_DESTINATION	“”	none	The location on disk to which the spectral MSs should be copied.
SPECTRAL_MS_TPYE_TO_COPY	pre	none	Which type of MS to copy. Possible values are pre, meaning the pre-continuum-subtracted data, or post, meaning the data after continuum-subtraction (ie the MS that is imaged).

Spectral polarisation imaging & leakage calibration

This table shows the parameters relevant to the jobs that apply the leakages to the full-spectral-resolution measurement sets (see also User Parameters - Continuum imaging for the continuum-resolution equivalent). The leakages are applied after the application of the gains derived from self-calibration. Parameters for the creation of the leakage tables can be found at User Parameters - Bandpass Calibration.

Additionally, instrumental leakage of Stokes-I into other Stokes parameters in off-axis regions of the beams can be corrected during mosaicking. For more details, see the pipeline documentation on linear mosaicking at User Parameters - Mosaicking and code documentation at linmos (Linear Mosaic Applicator).

The Stokes parameters given by SPECTRAL_POLARISATIONS are iterated over in the imaging (and mosaicking) to create a separate spectral cube for each. The default is just to do Stokes I.

Variable	Default	Parset equivalent	Description
JOB_TIME_APPLY_LEAKAGE	JOB_TIME_DEFAULT (24:00:00)	none	Time request for applying the leakage calibration
DO_APPLY_LEAKAGE_SPEC	false	none	Whether to apply the leakage calibration to the fully-calibrated spectral-line dataset, using the table derived using DO_LEAKAGE_CAL_SPEC=true
SPECTRAL_POLARISATIONS	"I"	ImageName.polarisation (imager)	List of polarisations to create cubes for. This should be a comma-separated list of (upper-case) polarisations. Separate jobs will be launched for each polarisation given.

Joint imaging

ASKAPsoft offers the possibility of imaging multiple beams jointly - this can help recover signal at the largest scales, comparable to the beam scale. Within the pipeline, this is possible just (for now) fro the spectral-line data, to meet the requirements of the GASKAP-HI Survey Science Project.

When used, this has a slightly different workflow, whereby each beam is processed in the usual way up to the continuum subtraction, and then all (across all fields, if more than one is present) are combined in a single imaging job. No linmos of the spectral cubes is done (as that is part of the joint imaging), although image-based continuum subtraction can be.

Variable	Default	Parset equivalent	Description
JOB_TIME_JOINT_IMAGING_SPECTRAL	JOB_TIME_DEFAULT (24:00:00)	none	Time request for the joint imaging job
DO_JOINT_IMAGING_SPECTRAL	false	none	Whether to run joint imaging
NUM_PIXELS_SUBSHAPE_SPECTRAL	1024	…
GRIDDER_JOINT_SPECTRAL	AProjectWStack	gridder (imager)	Gridder to use for joint imaging. SHould be AWProject or AProjectWStack.
GRIDDER_JOINT_SPECTRAL_WMAX	18000	wmax (Gridders)	The wmax parameter for the joint gridder.
GRIDDER_JOINT_SPECTRAL_NWPLANES	9	nwplanes (Gridders)	The nwplanes parameter for the joint gridder.
GRIDDER_JOINT_SPECTRAL_OVERSAMPLE	8	oversample (Gridders)	The oversample parameter for the joint gridder
GRIDDER_JOINT_SPECTRAL_MAXFEEDS	36	maxfeeds (Gridders)
GRIDDER_JOINT_SPECTRAL_MAXFIELDS	4	maxfields (Gridders)
GRIDDER_JOINT_SPECTRAL_DIAMETER	12m	diameter (Gridders)
GRIDDER_JOINT_SPECTRAL_BLOCKAGE	2m	blockage (Gridders)
GRIDDER_JOINT_SPECTRAL_MAXSUPPORT	2048	maxsupport (Gridders)
GRIDDER_JOINT_SPECTRAL_SHARECF	false	sharecf (Gridders)
GRIDDER_JOINT_SPECTRAL_SPHEROIDALTAPER	true	spheroidaltaper (Gridders)
GRIDDER_JOINT_SPECTRAL_SPHEROIDAL_CUTOFF	0.01	spheroidalweightscutoff (Gridders)
GRIDDER_JOINT_SPECTRAL_ROBUSTNESS	0	gridder.robustness (Gridders)
CLEAN_SPECTRAL_TOLERANCE	0.1	tolerance (Solvers)
CLEAN_SPECTRAL_WEIGHTCUTOFF	zero	weightcutoff (Solvers)