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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.

Following this pre-processing, the resulting MS is imaged by the
simager task, creating a set of spectral cubes. At this point, no
mosaicking of these is done, but this will be added in a future
version of the pipeline.

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.


+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| Variable | Default | Parset equivalent | Description |
+===============================================+===============================+====================================+===================================================================+
| ``DO_SPECTRAL_IMAGING`` | false | none | Whether to do the spectral-line imaging |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| **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. |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``CHAN_RANGE_SL_SCIENCE`` | "1-``NUM_CHAN_SCIENCE``" | channel (:doc:`../calim/mssplit`) | The range of channels to copy from the original dataset (1-based).|
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``TILENCHAN_SL`` | 1 | stman.tilenchan | The number of channels in the tile size used for the new MS. The |
| | | (:doc:`../calim/mssplit`) | tile size defines the minimum amount read at a time. Since the |
| | | | simager will process single channels, making this 1 (the default) |
| | | | means the simager workers only read what they need to . |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``DO_APPLY_CAL_SL`` | false | none | Whether to apply the gains calibration determined from the |
| | | | continuum self-calibration (see ``GAINS_CAL_TABLE`` in |
| | | | :doc:`ScienceFieldSelfCalibration`). |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``DO_CONT_SUB_SL`` | false | 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. |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| **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 |
| | | | (:doc:`../calim/cmodel`) from a continuum components catalogue |
| | | | generated by Selavy (:doc:`../analysis/selavy`); **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 (:doc:`../analysis/selavy`) | Division of image in x-direction for source-finding |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``CONTSUB_SELAVY_NSUBY`` | 3 | nsuby (:doc:`../analysis/selavy`) | Division of image in y-direction for source-finding |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``CONTSUB_SELAVY_THRESHOLD`` | 6 | snrCut (:doc:`../analysis/selavy`) | SNR threshold for detection with Selavy in determining components |
| | | | to go into the continuum model. |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``CONTSUB_MODEL_FLUX_LIMIT`` | 0mJy | flux_limit (:doc:`../calim/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. Default (0mJy) implies |
| | | | *all* compoennts are used. |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| **Basic variables for imaging** | | | |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``NUM_CPUS_SPECIMG_SCI`` | 2000 | none | The total number of processors allocated to the spectral-imaging |
| | | | job. One will be the master, while the rest will be devoted to |
| | | | imaging individual channels. |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``CPUS_PER_CORE_SPEC_IMAGING`` | 20 | none | The number of processors per node to use (max 20). |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``IMAGE_BASE_SPECTRAL`` | i.cube | Helps form | The base name for image cubes: if ``IMAGE_BASE_SPECTRAL=i.blah`` |
| | | Images.name | then we'll get image.i.blah, image.i.blah.restored, psf.i.blah etc|
| | | (:doc:`../calim/simager`) | |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``DIRECTION_SCI`` | none | Images.direction | The direction parameter for the image cubes, i.e. the central |
| | | (:doc:`../calim/simager`) | 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`` | 2048 | Images.shape | The number of spatial pixels along the side for the image cubes. |
| | | (:doc:`../calim/simager`) | Needs to be specified (unlike the continuum imaging case). |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``CELLSIZE_SPECTRAL`` | 10 | Images.cellsize | The spatial pixel size for the image cubes. Must be specified. |
| | | (:doc:`../calim/simager`) | |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``REST_FREQUENCY_SPECTRAL`` | HI | Images.restFrequency | The rest frequency for the cube. Can be a quantity string (eg. |
| | | (:doc:`../calim/simager`) | 1234.567MHz), or the special string 'HI' (which is 1420.405751786 |
| | | | MHz). If blank, no rest frequency will be written to the cube. |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| **Gridding** | | | |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``GRIDDER_SPECTRAL_SNAPSHOT_IMAGING`` | true | snapshotimaging | Whether to use snapshot imaging when gridding. |
| | | (:doc:`../calim/gridder`) | |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``GRIDDER_SPECTRAL_SNAPSHOT_WTOL`` | 2600 | snapshotimaging.wtolerance | The wtolerance parameter controlling how frequently to snapshot. |
| | | (:doc:`../calim/gridder`) | |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``GRIDDER_SPECTRAL_WMAX`` | 2600 | WProject.wmax | The wmax parameter for the gridder. |
| | | (:doc:`../calim/gridder`) | |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``GRIDDER_SPECTRAL_NWPLANES`` | 99 | WProject.nwplanes | The nwplanes parameter for the gridder. |
| | | (:doc:`../calim/gridder`) | |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``GRIDDER_SPECTRAL_OVERSAMPLE`` | 4 | WProject.oversample | The oversampling factor for the gridder. |
| | | (:doc:`../calim/gridder`) | |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``GRIDDER_SPECTRAL_MAXSUPPORT`` | 512 | WProject.maxsupport | The maxsupport parameter for the gridder. |
| | | (:doc:`../calim/gridder`) | |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| **Cleaning** | | | |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``SOLVER_SPECTRAL`` | Clean | solver | Which solver to use. You will mostly want to leave this as |
| | | (:doc:`../calim/solver`) | 'Clean', but there is a 'Dirty' solver available. |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``CLEAN_SPECTRAL_ALGORITHM`` | Basisfunction | Clean.algorithm | The name of the clean algorithm to use. Note that the default has |
| | | (:doc:`../calim/solver`) | changed to 'Basisfunction', as we don't need the multi-frequency |
| | | | capabilities of 'BasisfunctionMFS'. |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``CLEAN_SPECTRAL_MINORCYCLE_NITER`` | 500 | Clean.niter | The number of iterations for the minor cycle clean. |
| | | (:doc:`../calim/solver`) | |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``CLEAN_SPECTRAL_GAIN`` | 0.5 | Clean.gain | The loop gain (fraction of peak subtracted per minor cycle). |
| | | (:doc:`../calim/solver`) | |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``CLEAN_SPECTRAL_SCALES`` | "[0,3,10]" | Clean.scales | Set of scales (in pixels) to use with the multi-scale clean. |
| | | (:doc:`../calim/solver`) | |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``CLEAN_SPECTRAL_THRESHOLD_MINORCYCLE`` | "[30%, 0.9mJy]" | threshold.minorcycle | Threshold for the minor cycle loop. |
| | | (:doc:`../calim/solver`) | |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``CLEAN_SPECTRAL_THRESHOLD_MAJORCYCLE`` | 1mJy | threshold.majorcycle | The target peak residual. Major cycles stop if this is reached. A |
| | | (:doc:`../calim/solver`) | negative number ensures all major cycles requested are done. |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``CLEAN_SPECTRAL_NUM_MAJORCYCLES`` | 0 | ncycles | Number of major cycles. |
| | | (:doc:`../calim/solver`) | |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``CLEAN_WRITE_AT_MAJOR_CYCLE`` | false | Images.writeAtMajorCycle | If true, the intermediate images will be written (with a .cycle |
| | | (:doc:`../calim/simager`) | suffix) after the end of each major cycle. |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| **Preconditioning** | | | |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``PRECONDITIONER_LIST_SPECTRAL`` | "[Wiener, GaussianTaper]" | preconditioner.Names | List of preconditioners to apply. |
| | | (:doc:`../calim/solver`) | |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``PRECONDITIONER_SPECTRAL_GAUSS_TAPER`` | "[50arcsec, 50arcsec, 0deg]" | preconditioner.GaussianTaper | Size of the Gaussian taper - either single value (for circular |
| | | (:doc:`../calim/solver`) | taper) or 3 values giving an elliptical size. |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``PRECONDITIONER_SPECTRAL_WIENER_ROBUSTNESS`` | 0.5 | preconditioner.Wiener.robustness | Robustness value for the Wiener filter. |
| | | (:doc:`../calim/solver`) | |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``PRECONDITIONER_SPECTRAL_WIENER_TAPER`` | "" | preconditioner.Wiener.taper | Size of gaussian taper applied in image domain to Wiener filter. |
| | | (:doc:`../calim/solver`) | Ignored if blank (ie. тАЬтАЭ). |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| **Restoring** | | | |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``RESTORE_SPECTRAL`` | true | restore | Whether to restore the image cubes. |
| | | (:doc:`../calim/simager`) | |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``RESTORING_BEAM_SPECTRAL`` | fit | restore.beam | Restoring beam to use: 'fit' will fit the PSF in each channel |
| | | (:doc:`../calim/simager`) | separately to determine the appropriate beam for that channel, |
| | | | else give a size (such as 30arcsec, or |
| | | | тАЬ[30arcsec, 30arcsec, 0deg]тАЭ). |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``RESTORING_BEAM_REFERENCE`` | mid | restore.beamReference | Which channel to use as the reference when writing the restoring |
| | | (:doc:`../calim/simager`) | 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'|
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+
| ``RESTORING_BEAM_LOG`` | beamLog.IMAGE.txt (with IMAGE | restore.beamLog | The ASCII text file to which will be written the restoring beam |
| | from ``IMAGE_BASE_SPECTRAL``) | (:doc:`../calim/simager`) | for each channel. If blank, no such file will be written. |
+-----------------------------------------------+-------------------------------+------------------------------------+-------------------------------------------------------------------+