User Parameters - Continuum Source-finding

Source-finding is run in two ways within these scripts. It can be run after each individual beam is imaged, and then again after the mosaicking has completed.

The source-finding applies a spatially-varying signal-to-noise threshold, and fits 2D Gaussians to detected islands to create a component catalogue.

When the source-finding operates on the mosaicked image, it uses the weights image to apply a weights cutoff (as described at Thresholds in Selavy), so that the searching is only done on the imaged region.

The RM Synthesis capabilities of Selavy have been made available. Full control over this mode is provided through the pipeilne configuration, so that RM Synthesis can be performed on the full-Stokes spectra of continuum components. This is designed to work with the continuum cube imaging (User Parameters - Continuum imaging), and checks are made for the existence of the required cubes at run-time for this mode to be switched on.

Additionally, Selavy can extract spectra from the continuum-subtracted cube (or the restored cube if image-based continuum subtraction is not being used) at the location of each bright continuum component. Both source and noise spectra will be extracted. The flux limit can be set via SELAVY_EXTRACT_FLUX_LIMIT, given in mJy (since that is how fluxes are recorded in the Selavy catalogues).

Following completion of the source-finding, a validation script is run that cross-matches the Selavy catalogue with those of SUMSS and NVSS, comparing positions and fluxes with those catalogues to obtain measures of the quality of the imaging. A full report is provided in HTML format, with interactive plots, along with a summary table listing a small number of metrics that have associated quality flags (essentially “good”, “uncertain”, “bad”). These metrics are presented within CASDA to assist with the validation of data. (See doc:validation for details.)

This validation can be performed on the individual beam images, although the default is to just do it on the mosaicked images (and it is only the latter that are passsed to CASDA).

Variable	Default	Parset equivalent	Description
DO_SOURCE_FINDING_CONT	""	none	Whether to do the source-finding with Selavy on the final mosaic continuum images. If not given in the config file, it takes on the value of DO_CONT_IMAGING.
CATALOGUE_BASE_NAME	selavy-%i.txt	Selavy.resultsFile (Selavy Basics)	Base name for source catalogues. The %i wildcard will be resolved into the imageName corresponding to the continuum image. You may find this parameter useful to rename new catalogues generated from re-processing. NB: The same parameter is used for spectral source-finding.
CATALOGUE_ID_BASE	SB%s	Selavy.sourceIdBase (Selavy Basics)	Base identifier for catalogue components. The %s wildcard will be resolved into the SBID of the observation. You may find this parameter useful to rename new catalogue components generated from re-processing. NB: The same parameter is used for spectral source-finding.
DO_SOURCE_FINDING_BEAMWISE	false	none	If true, the source-finding will be run on the individual beam images as well.
DO_SOURCE_FINDING_FIELD_MOSAICS	false	none	If true, the source-finding will be run on the individual field mosaics. Will be set to false if the number of fields is one.
JOB_TIME_SOURCEFINDING	JOB_TIME_DEFAULT (24:00:00)	none	Time request for source-finding jobs.
DO_CONTINUUM_VALIDATION	true	none	Run the continuum validation script following source finding. This cross-matches the catalogue with publshed radio calaogues from NVSS and SUMSS, and compares fluxes and positions. A number of metrics are obtained that describe the quality of the image and catalogue, and these, along with a more detailed HTML-based report, are sent to CASDA.
Basic sourcefinding
CORES_PER_NODE_SELAVY	10	none	Number of cores used on each node. If not provided, it will be the lower of the number of cores requested or the maximum number of cores available per node.
SELAVY_NSUBX	6	nsubx (Selavy Basics)	Number of divisions in the x-direction that divide the image up, allowing parallel processing in the source-detection.
SELAVY_NSUBY	6	nsuby (Selavy Basics)	Number of divisions in the y-direction that divide the image up, allowing parallel processing in the source-detection.
SELAVY_OVERLAPX	0	overlapx (Selavy Basics)	The overlap (in pixels) between neighbouring divisions in the x-direction.
SELAVY_OVERLAPY	0	overlapy (Selavy Basics)	The overlap (in pixels) between neighbouring divisions in the y-direction.
SELAVY_SNR_CUT	5	snrcut (Selavy Basics)	The signal-to-noise ratio threshold to use in the source-detection.
SELAVY_FLAG_GROWTH	true	flagGrowth (Selavy Basics)	A flag indicating whether to grow detections down to a lower threshold.
SELAVY_GROWTH_CUT	3	growthCut (Selavy Basics)	The secondary signal-to-noise threshold to which detections should be grown.
SELAVY_FLUX_THRESHOLD	""	threshold (Selavy Basics)	The flux threshold to use in the source-detection. If left blank, we use the SNR threshold SELAVY_SNR_CUT.
SELAVY_GROWTH_THRESHOLD	""	growthCut (Selavy Basics)	The secondary signal-to-noise threshold to which detections should be grown. Only used if SELAVY_FLUX_THRESHOLD is given.
SELAVY_WEIGHTS_CUTOFF	""	Weights.weightsCutoff (Thresholds in Selavy)	The cutoff level, as a fraction of the peak in the weights image, used in the source-finding. Only applies if the image being searched has a corresponding weights image. If not given, the value used is the square of LINMOS_CUTOFF from User Parameters - Mosaicking.
SELAVY_VARIABLE_THRESHOLD	true	VariableThreshold (Thresholds in Selavy)	A flag indicating whether to determine the signal-to-noise threshold on a pixel-by-pixel basis based on local statistics (that is, the statistics within a relatively small box centred on the pixel in question).
SELAVY_BOX_SIZE	50	VariableThreshold.boxSize (Thresholds in Selavy)	The half-width of the sliding box used to determine the local statistics.
SELAVY_VARIABLE_THRESHOLD_REUSE	false	VariableThreshold.reuse (Thresholds in Selavy)	A flag indicating whether to reuse any existing noise maps created by the variable-threshold algorithm. If false, they will be generated each time the job runs.
SELAVY_FLAG_ADJACENT	true	flagAdjacent (Selavy Basics)	Whether to enforce pixels in islands to be contiguous.
SELAVY_SPATIAL_THRESHOLD	5	threshSpatial (Selavy Basics)	If SELAVY_FLAG_ADJACENT=false, this is the threshold in pixels within which islands are joined.
SELAVY_WRITE_DUCHAMP_FILES	false	none	If true, the standard Duchamp catalogue files are written in addition to the Selavy ones (island, component, etc)
SELAVY_INCLUDE_GALACTIC_COORDS	false	catalogueHasGalacticCoords (Selavy Basics)	Whether to include Galactic coordinates in the output catalogues (components & islands). If the input image is GALACTIC (via LINMOS_DIRECTION_TYPE=GALACTIC) this will be set to true automatically.
Spectral indices
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 SELAVY_SPECTRAL_INDEX_THRESHOLD_SNR.
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.
USE_CONTCUBE_FOR_SPECTRAL_INDEX	false	none	When true, the spectral indices in the component catalogue are measured from the Stokes-I continuum cube. When false (the default), the Taylor-term images are used. See Post-processing of detections for information about each method.
SELAVY_NUM_SPECTRAL_TERMS	3	spectralTerms.nterms (Post-processing of detections)	The number of terms to be fitted to the spectrum when using the continuum cube to find the spectral index & curvature.
RM Synthesis
DO_RM_SYNTHESIS	false	none	Whether to perform RM Synthesis after continuum source-finding.
SELAVY_POL_OUTPUT_BASE	pol	Forms part of RMSynthesis.outputBase (Post-processing of detections)	Base part of the filenames of extracted spectra and Faraday Dispersion function. All files will go in a directory PolData within the Selavy directory, and will be called “<outputBase>_<imageBase>_spec” or similar.
SELAVY_POL_WRITE_SPECTRA	true	RMSynthesis.writeSpectra (Post-processing of detections)	Whether to write the extracted Stokes spectra to individual files.
SELAVY_POL_WRITE_COMPLEX_FDF	false	RMSynthesis.writeComplexFDF (Post-processing of detections)	Whether to write the Faraday Dispersion Function for each source as a single complex-valued spectrum (true) or as a pair of real-valued spectra containing amplitude & phase (false).
USE_FITS_TABLE_FOR_EXTRACTED_SPECTRA	false	RMSynthesis.usefitstable (Post-processing of detections)	Whether to write the extracted spectra to a single FITS binary table (if true), rather than individual FITS files. The binary table option is only available from askapsoft/1.14 onwards.
SELAVY_POL_BOX_WIDTH	5	RMSynthesis.boxWidth (Post-processing of detections)	The width (N) of the NxN box to be applied in the extraction of Stokes spectra.
SELAVY_POL_NOISE_AREA	50	RMSynthesis.noiseArea (Post-processing of detections)	The number of beam areas over which to measure the noise in each channel.
SELAVY_POL_ROBUST_STATS	true	RMSynthesis.robust (Post-processing of detections)	Whether to use robust statistics in the calculation of the noise spectra.
SELAVY_POL_WEIGHT_TYPE	variance	RMSynthesis.weightType (Post-processing of detections)	The type of weighting to be used in the RM Synthesis - either “variance” or “uniform”.
SELAVY_POL_MODEL_TYPE	taylor	RMSynthesis.modelType (Post-processing of detections)	The type of Stokes-I model to use. Either “taylor” (Taylor-term decomposition from the MFS imaging), or “poly” (polynomial fit to the Stokes-I spectrum).
SELAVY_POL_MODEL_ORDER	3	RMSynthesis.modelPolyOrder (Post-processing of detections)	When SELAVY_POL_MODEL_TYPE=poly, this gives the order of the polynomial that is fit to the Stokes-I spectrum.
SELAVY_POL_SNR_THRESHOLD	8	RMSynthesis.polThresholdSNR (Post-processing of detections)	Signal-to-noise threshold (in the FDF) for a valid detection. Only sources above this threshold have their spectra written to disk.
SELAVY_POL_SNR_THRESHOLD_BEAMWISE	0	RMSynthesis.polThresholdSNR (Post-processing of detections)	As for SELAVY_POL_SNR_THRESHOLD, but applied to the beam-wise source-finding (ie. source-finding on the individual beam images - when DO_SOURCE_FINDING_BEAMWISE=true)
SELAVY_POL_DEBIAS_THRESHOLD	5	RMSynthesis.polThresholdDebias (Post-processing of detections)	Signal-to-noise threshold (in the FDF) above which to perform debiasing.
SELAVY_POL_NUM_PHI_CHAN	30	RMSynthesis.numPhiChan (Post-processing of detections)	Number of Faraday Depth channels used in RM Synthesis.
SELAVY_POL_DELTA_PHI	5	RMSynthesis.deltaPhi (Post-processing of detections)	Spacing between the Faraday depth channels [rad/m2].
SELAVY_POL_PHI_ZERO	0	RMSynthesis.phiZero (Post-processing of detections)	Faraday depth [rad/m2] of the central channel of the FDF.
Spectral extraction
DO_EXTRACT_COMPONENT_SPECTRA	false	none	Whether to extract spectra for each bright continuum component. When true, both source and noise spectra are extracted. The cube used will be the contsub cube (if made - else the regular restored cube). If the cube doesn’t exist, this mode is turned off.
USE_FITS_TABLE_FOR_EXTRACTED_SPECTRA	false	Components.extractSpectra.usefitstable Components.extractNoiseSpectra.usefitstable (Post-processing of detections)	Whether to write the extracted spectra to a single FITS binary table (if true), rather than individual FITS files. The binary table option is only available from askapsoft/1.14 onwards.
SELAVY_EXTRACT_FLUX_LIMIT		Components.extractSpectra.fluxLimit Components.extractNoiseSpectra.fluxLimit (Post-processing of detections)	The flux limit to apply when extracting. The value should be given in mJy, and is applied to the integrated flux of the component. The same flux limit is applied for both source and nosie spectra.
SELAVY_EXTRACT_BOX_WIDTH	5	Components.extractSpectra.spectralBoxWidth (Post-processing of detections) (Extraction of Spectra, Images and Cubelets)	The width (N) of the NxN box to be applied in the spectral extraction.
SELAVY_EXTRACT_NOISE_AREA	50	Components.extractNoiseSpectra.noiseArea (Post-processing of detections) (Extraction of Spectra, Images and Cubelets)	The number of beam areas over which to measure the noise in each channel.
PURGE_SPECTRA_AFTER_TAR	false	none	If set, the spectra extracted either from DO_EXTRACT_COMPONENT_SPECTRA=true or DO_RM_SYNTHESIS=true are removed immediately after they are tarred up into tar files for archiving.