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imager.clean - Function

	Package	synthesis
	Module	imager
	Tool	imager

Calculate a deconvolved image with selected clean algorithm

Synopsis
clean(algorithm, niter, gain, threshold, displayprogress, model, fixed, complist, mask, image, residual, interactive, npercycle, masktemplate, async)

Description
Makes a clean image using either the Hogbom, Clark, multi-scale or multi-field algorithms. The Clark algorithm is the default. The clean is performed on the residual image calculated from the visibility data currently selected. Hence the first step performed in clean is to transform the current model or models (optionally including a componentlist) to fill in the MODEL_DATA column, and then inverse transform the residual visibilities to get a residual image. This residual image is then cleaned using the corresponding point spread function. This means that the initial model is used as the starting point for the deconvolution. Thus if you want to restart a clean, simply set the model to the model that was previously produced by clean.

Rather than explicit CLEAN boxes, mask images are used to constrain the region that is to be deconvolved. To make mask images, use either boxmask (to define a mask via the corner locations blc and trc) or mask (to define a mask via thresholding an existing image) or regionmask (to make masks via regions using the regionmanager or interactively through the viewer) . The default mask is the inner quarter of the image.

The CLEAN deconvolution is joint in whatever Stokes parameters are present. Thus it searchs for peaks in either I or I + | V| or I + $\sqrt{Q^2 + U^2 + V^2}$, the rationale for the latter two forms being to be biased towards finding strongly polarized pixels first (these forms are also the maximum eigenvalue of the coherency matrix). The PSF is constrained to be the same in all polarizations (a feature of this implementation, not of the Hamaker-Bregman-Sault formalism).

The clean algorithms possible are:

Hogbom

The classic algorithm: points are found iteratively by searching for the peak. Each point is subtracted from the full residual image using the shifted and scaled point spread function.

Multiscale

An experimental multi-scale clean algorithm is invoked. The algorithm is fully described in deconvolver.

Clark

The faster algorithm: the cleaning is split into minor and major cycles. In the minor cycles only the brightest points are cleaned, using a subset of the point spread function. In the major cycle, the points thus found are subtracted correctly by using an FFT-based convolution.

Multi-field

Cleaning is split into minor and major cycles. For each field, a Clark-style minor cycle is performed. In the major cycle, the points thus found are subtracted either from the original visibilities (for multiple fields) or using a convolution (for only one field). The latter is much faster. Multi-field imaging has been implemented for Clark, Hogbom, and Multi-scale deconvolution algorithms.

Cotton-Schwab

Cleaning is split into minor and major cycles. For each field, a Clark-style minor cycle is performed. In the major cycle, the points thus found are subtracted from the original visibilities. A fast variant does a convolution using a FFT. This will be faster for large numbers of visibilities. Double the image size from that used for Cotton-Schwab and set a mask to clean only the inner quarter.

Wide-field

The user will need to use a wide-field algorithm to deconvolve if the array is not coplanar over the field of view being imaged . The technique used is to break the field being imaged into smaller pieces (facets), over each of which the array appear planar. We implement a rectangular facetting scheme. If the number of facets specified in setimage is greater than one, Either wfhogbom or wfclark algorithm has to be selected here to perform a wide-field decovolution. The function advise can be used to calculate or check if you need to use a wide-field deconvolution. Note that aliasing can be reduced by using the padding argument in setoptions. In practice the previous sentence means that if you notice the clean to diverge at the edges of the facets then you need to use a larger amount of padding for the FT; the default being 1.2. Wide-field imaging has been implemented for Clark and Hogbom algorithms.

The multi-field clean should be used if either of two conditions hold:

1.

Multiple fields are to be cleaned simultaneously OR

2.

Primary beam correction is enabled. In this case, a mosaiced clean is performed.

Note that for the single pointing algorithms, only a quarter of the image may be cleaned. If no mask is set, then the cleaned region defaults to the inner quarter. If a mask larger than a quarter of the image is set, then only the inner quarter part of that mask is used. However, for the wide-field and multi-field imaging (including the Cotton-Schwab algorithm), the entire field may be imaged because the major cycles either do an exact subtraction from the visibilities or because PSF extent is more than twice the extent of the primary beam support.

Before clean can be run, you must run setdata and setimage. Before clean can be run with a multi-field algorithm, you should run setvp. You may want to run setmfcontrol before running clean with a multi-field or wide-field algorithm, though the default control values may be acceptable. Before clean can be run with a multi-scale algorithm, setscales must be run.

Interactive cleaning/masking: If the user wants to see what the clean image looks like after npercycle iteration and mask or modify the mask each time, he/she should set interactive=T and give npercycle to a fraction of niter. A viewer with the last residual image along with an overlayed mask appear after every npercycle iteration. The user can add or delete regions (by clicking on the appropriate button) to the mask using the region button and drawing regions and double clicking inside the region. Use 'refresh mask' to review the recent changes in the mask. When satisfied and ready to continue cleaning press 'DONE with masking' (if the user want to terminate the cleaning process use the 'STOP' button). The button 'No more mask changes' should be used if the user want clean to proceed without any further interruption. PLEASE be patient and wait for the viewer to load both the image and mask before clicking on the buttons or drawing regions. If impatient please use interactive=F. Even if interactive=F, and if the parameter 'mask' is non-empty, it is still used in limiting the search area for clean components. If the parameter 'masktemplate' is not empty this means that the user want to use a prior image to make the mask the first time (e.g a previously cleaned image)

Arguments

algorithm	in	Algorithm to use
		Allowed:	String:'clark'|'hogbom'|'multiscale'|'mfclark'|'csclean'|'csfast'| 'mfhogbom'|'mfmultiscale'|'wfclark'|'wfhogbom'
		Default:	'clark'
niter	in	Number of Iterations, set to zero for no CLEANing
		Allowed:	Int
		Default:	1000
gain	in	Loop Gain for CLEANing
		Allowed:	Float
		Default:	0.1
threshold	in	Flux level at which to stop CLEANing
		Allowed:	Quantity
		Default:	'0Jy'
displayprogress	in	Display the progress of the cleaning?
		Allowed:	Bool
		Default:	F
model	in	Names of clean model images
		Allowed:	Vector of strings
		Default:	None
fixed	in	Keep one or more models fixed
		Allowed:	Vector of booleans
		Default:	F
complist	in	Name of component list
		Allowed:	String
mask	in	Names of mask images used for CLEANing
		Allowed:	Vector of strings
image	in	Names of restored images
		Allowed:	Vector of strings or unset
		Default:	model name concatenated with '.restored'
residual	in	Names of residual images
		Allowed:	Vector of strings or unset
		Default:	model name concatenated with '.residual'
interactive	in	whether to stop clean and interactively mask
		Allowed:	Boolean
		Default:	F
npercycle	in	If interactive is 'T', then no of iter of clean before stopping, usually a fraction of niter
		Allowed:	Int
		Default:	100
masktemplate	in	If non empty then will use this image to make the mask the first time
		Allowed:	String
		Default:	''
async	in	Run asynchronously in the background?
		Allowed:	Bool
		Default:	!dowait

Returns
Bool

Example

imgr.clean(model='3C273XC1.clean.model',
mask='3C283XC1.mask', niter=1000, gain=0.25, threshold='0.03Jy')

A few points should be noted in this example:

• When the mask parameter is specified, the number of mask images listed should be equal to the number of model images. They should also have the same coordinate system as their corresponding model images.
• If one or more model images are listed in the model parameter but the image and residual parameters are empty, the restored and residual images are automatically named as the model names appended with '.restored' and '.residual', respectively.
• No restored or residual image is made if the respective image string is explicitly unset.

include 'imager.g';
msfile := 'vlac125K.ms';
imgr:=imager(msfile);
npix := 500; cell:='5arcsec';
#
# CS on 500 by 500
#
imgr.setimage(nx=npix, ny=npix, cellx=cell, celly=cell, stokes='I',
	      spwid=[1,2]);i
imgr.setoptions(padding=1.0);
imgr.setdata(spwid=[1,2]);
imgr.clean('cs', model='vlac125K.cs', image='vlac125K.cs.restored',
	   niter=1000, gain=0.1);
#
# CSF on 1000 by 1000, cleaning inner quarter
#
include 'regionmanager.g';
imgr.setimage(nx=2*npix, ny=2*npix, cellx=cell, celly=cell, stokes='I',
	      spwid=[1,2]);
imgr.regionmask('vlac125K.mask', region=drm.quarter());
imgr.clean('csf', model='vlac125K.csf', image='vlac125K.csf.restored',
	   mask='vlac125K.mask', niter=1000, gain=0.1);

#
# CS on 1000 by 1000, cleaning entire image
#
include 'regionmanager.g';
imgr.setimage(nx=2*npix, ny=2*npix, cellx=cell, celly=cell, stokes='I',
	      spwid=[1,2]);
imgr.clean('cs', model='vlac125K.csl', image='vlac125K.csl.restored',
	   mask='vlac125K.mask', niter=1000, gain=0.1);

imgr.done();