User Parameters - Spectral-line Source-finding ============================================== It is possible to run source-finding with Selavy on the created spectral-line cubes. Through the pipeline, it is possible to specify either flux or SNR thresholds, apply a variable SNR threshold, and pre-process the cube with smoothing or multi-resolution wavelet reconstruction (to enhance the signal-to-noise of real sources). +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | Variable | Default | Parset equivalent | Description | +==========================================+=================================+==============================================+=============================================================+ | ``DO_SOURCE_FINDING_SPEC`` | ``""`` | none | Whether to do the source-finding with Selavy on the | | | | | final mosaic images. If not given in the config file, it | | | | | takes on the value of ``DO_SPECTRAL_IMAGING``. | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``CATALOGUE_BASE_NAME`` | selavy-%i.txt | Selavy.resultsFile | Base name for source catalogues. The %i wildcard will be | | | | (:doc:`../analysis/selavy`) | resolved into the imageName corresponding to the spectral | | | | | image. You may find this parameter useful to rename new | | | | | catalogues generated from re-processing. | | | | | NB: The same parameter is used for continuum source-finding.| +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``CATALOGUE_ID_BASE`` | SB%s | Selavy.sourceIdBase | Base identifier for catalogue components. The %s wildcard | | | | (:doc:`../analysis/selavy`) | 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 continuum 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_SPEC`` | ``JOB_TIME_DEFAULT`` (24:00:00) | none | Time request for source-finding jobs | | | | | | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``CORES_PER_NODE_SELAVY_SPEC`` | ``""`` | 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_SPEC_NSUBX`` | 6 | nsubx (:doc:`../analysis/selavy`) | Number of divisions in the x-direction that divide the image| | | | | up, allowing parallel processing in the source-detection. | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``SELAVY_SPEC_NSUBY`` | 9 | nsuby (:doc:`../analysis/selavy`) | Number of divisions in the y-direction that divide the image| | | | | up, allowing parallel processing in the source-detection. | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``SELAVY_SPEC_NSUBZ`` | 18 | nsubz (:doc:`../analysis/selavy`) | Number of divisions in the z-direction that divide the image| | | | | up, allowing parallel processing in the source-detection. | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``SELAVY_OVERLAPX`` | 0 | overlapx | The overlap (in pixels) between neighbouring divisions in | | | | (:doc:`../analysis/selavy`) | the x-direction. | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``SELAVY_OVERLAPY`` | 0 | overlapy | The overlap (in pixels) between neighbouring divisions in | | | | (:doc:`../analysis/selavy`) | the y-direction. | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``SELAVY_OVERLAPZ`` | 20 | overlapz | The overlap (in pixels) between neighbouring divisions in | | | | (:doc:`../analysis/selavy`) | the z-direction. | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | **Searching** | | | | | | | | | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``SELAVY_SPEC_SNR_CUT`` | 8.0 | snrcut (:doc:`../analysis/selavy`) | The signal-to-noise ratio threshold to use in the | | | | | source-detection. | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``SELAVY_SPEC_FLAG_GROWTH`` | true | flagGrowth (:doc:`../analysis/selavy`) | A flag indicating whether to grow detections down to a | | | | | lower threshold. | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``SELAVY_SPEC_GROWTH_CUT`` | 3.0 | growthCut (:doc:`../analysis/selavy`) | The secondary signal-to-noise threshold to which detections | | | | | should be grown. | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``SELAVY_SPEC_FLUX_THRESHOLD`` | ``""`` | threshold (:doc:`../analysis/selavy`) | The flux threshold to use in the source-detection. If left | | | | | blank, we use the SNR threshold ``SELAVY_SNR_CUT``. | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``SELAVY_SPEC_GROWTH_THRESHOLD`` | ``""`` | growthCut (:doc:`../analysis/selavy`) | The secondary signal-to-noise threshold to which detections | | | | | should be grown. Only used if ``SELAVY_FLUX_THRESHOLD`` is | | | | | given. | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``SELAVY_SPEC_WEIGHTS_CUTOFF`` | ``""`` | Weights.weightsCutoff | The cutoff level, as a fraction of the peak in the weights | | | | (:doc:`../analysis/thresholds`) | 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 :doc:`ScienceFieldMosaicking`. | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``SELAVY_SPEC_SEARCH_TYPE`` | spatial | searchType (:doc:`../analysis/selavy`) | Type of searching to be performed: either 'spectral' | | | | | (searches are done in each 1D spectrum) or 'spatial' | | | | | (searches are done in each 2D channel image). Anything else | | | | | defaults to spectral. | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``SELAVY_SPEC_VARIABLE_THRESHOLD`` | true | VariableThreshold | A flag indicating whether to determine the signal-to-noise | | | | (:doc:`../analysis/thresholds`) | 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). The dimensions | | | | | of the box are governed by the search type - if 'spectral' | | | | | then it will be a one-dimensional box slid along each | | | | | spectrum, else if 'spatial' it will be a 2D box done on each| | | | | channel image. | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``SELAVY_SPEC_BOX_SIZE`` | 35 | VariableThreshold.boxSize | The half-width of the sliding box used to determine the | | | | (:doc:`../analysis/thresholds`) | local statistics. | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``SELAVY_SPEC_VARIABLE_THRESHOLD_REUSE`` | false | VariableThreshold.reuse | A flag indicating whether to reuse any existing noise maps | | | | (:doc:`../analysis/thresholds`) | created by the variable-threshold algorithm. If false, they | | | | | will be generated each time the job runs. | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``SELAVY_SPEC_MIN_PIX`` | 5 | minPix (:doc:`../analysis/selavy`) | Minimum number of (spatial) pixels allowed in a detection | | | | | | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``SELAVY_SPEC_MIN_CHAN`` | 5 | minChan (:doc:`../analysis/selavy`) | Minimum number of channels allowed in a detection | | | | | | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``SELAVY_SPEC_MAX_CHAN`` | 2592 | maxChan (:doc:`../analysis/selavy`) | Maximum number of channels allowed in a detection | | | | | | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | **Pre-processing** | | | | | | | | | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``SELAVY_SPEC_FLAG_SMOOTH`` | true | flagSmooth | Whether to smooth the input cube prior to searching. | | | | (:doc:`../analysis/preprocessing`) | | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``SELAVY_SPEC_SMOOTH_TYPE`` | spectral | smoothType | Type of smoothing to perform - either 'spectral' or | | | | (:doc:`../analysis/preprocessing`) | 'spatial'. Anything else defaults to spectral. | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``SELAVY_SPEC_HANN_WIDTH`` | 5 | hanningWidth | The width of the Hanning spectral smoothing kernel. | | | | (:doc:`../analysis/preprocessing`) | | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``SELAVY_SPEC_SPATIAL_KERNEL`` | 3 | kernMaj, kernMin, kernPA | The specs for the spatial Gaussian smoothing kernel. Either | | | | (:doc:`../analysis/preprocessing`) | a single number, which is interpreted as a circular Gaussian| | | | | (kernMaj=kernMin, kernPA=0), or a string with three values | | | | | enclosed by square brackets (eg. ``"[4,3,45]"``), | | | | | interpreted as "[kernMaj,kernMin,kernPA]". | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``SELAVY_SPEC_FLAG_WAVELET`` | false | flagAtrous | Whether to use the multi-resolution wavelet reconstruction. | | | | (:doc:`../analysis/preprocessing`) | | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``SELAVY_SPEC_RECON_DIM`` | 1 | reconDim (:doc:`../analysis/preprocessing`) | The number of dimensions in which to perform the | | | | | reconstruction. 1 means reconstruct each spectrum | | | | | separately, 2 means each channel map is done separately, and| | | | | 3 means do the whole cube in one go. | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``SELAVY_SPEC_RECON_SNR`` | 4 | snrRecon (:doc:`../analysis/preprocessing`) | Signal-to-noise threshold applied to wavelet arrays prior to| | | | | reconstruction. | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``SELAVY_SPEC_RECON_SCALE_MIN`` | 1 | scaleMin (:doc:`../analysis/preprocessing`) | Minimum wavelet scale to include in reconstruction. A value | | | | | of 1 means "use all scales”. | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``SELAVY_SPEC_RECON_SCALE_MAX`` | 0 | scaleMax (:doc:`../analysis/preprocessing`) | Maximum wavelet scale to use in the reconstruction. If 0 or | | | | | negative, then the maximum scale is calculated from the size| | | | | of the array. | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | **Pre-processing** | | | | | | | | | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+ | ``SELAVY_SPEC_OPTIMISE_MASK`` | false | optimiseMask | Whether to improve the mask of detected sources prior to | | | | (:doc:`../analysis/postprocessing`) | parameterisation via the mask optimisation technique. | +------------------------------------------+---------------------------------+----------------------------------------------+-------------------------------------------------------------+