image_line

Process visibilities for spectral line work and create line cubes and images.

enable

bool

Execute segment image_line.

label

str, optional, default = corr

Label of names of MS data sets to be used. MS data set names will always start with the data set id, followed by a hyphen, followed by desc.

line_name

str, optional, default = HI

Line name string to be used for output file names.

restfreq

str, optional, default = 1.420405752GHz

Rest frequency default value for this worker.

subtractmodelcol

Replace the column CORRECTED_DATA with the difference CORRECTED_DATA - MODEL_DATA. This is useful for continuum subtraction as it enables the subtraction of the most recent continuum clean model.

enable

bool, optional, default = True

Execute segment subtractmodelcol.

mstransform

Perform UVLIN continuum subtraction and/or doppler tracking corrections

enable

bool, optional, default = True

Execute segment doppler correction.

telescope

{“meerkat”, “vla”, “gmrt”, “wsrt”, “atca”, “askap”}, optional, default = meerkat

The name of the telescope from which observations were made. Default is the ‘meerkat’ telescope. Current options are gmrt, vla, wsrt, atca.

doppler

bool, optional, default = True

Transform channel labels and visibilities to a different spectral reference frame.

mode

{“frequency”}, optional, default = frequency

Regridding mode (channel/velocity/frequency/channel_b). IMPORTANT - Currently only frequency mode is supported.

outframe

{“”, “topo”, “geo”, “lsrk”, “lsrd”, “bary”, “galacto”, “lgroup”, “cmb”, “source”}, optional, default = bary

Output reference frame, options ‘’, ‘topo’, ‘geo’, ‘lsrk’, ‘lsrd’, ‘bary’, ‘galacto’, ‘lgroup’, ‘cmb’, ‘source’

veltype

str, optional, default = radio

Definition of velocity (as used in mode), radio or optical.

outchangrid

str, optional, default = auto

Output channel grid for Doppler correction. Default is ‘auto’, and the pipeline will calculate the appropriate channel grid. If not ‘auto’ it must be in the format ‘nchan,chan0,chanw’ where nchan is an integer, and chan0 and chanw must include units appropriate for the chosen mode (see parameter ‘mode’ above)

uvlin

bool, optional, default = True

Perform continuum subtraction as in task uvcontsub whilst regridding within mstransform.

fitspw

str, optional, default = ‘ ‘

Spectral window channel selection for fitting the continuumSelection of line-free channels using CASA syntax (e.g. ‘0:0~100;150:300’). If set to null, a fit to all unflagges visibilities will be performed.

fitorder

int, optional, default = 1

Polynomial order for the continuum fits

column

str, optional, default = corrected

Data column to use.

obsinfo

bool, optional, default = True

Create obsinfo.txt and obsinfo.json of MS file created by mstransform.

sunblocker

Use sunblocker to remove solar RFI. See description of sunblocker on github repository gigjozsa/sunblocker in method phazer of module sunblocker.py.

enable

bool, optional, default = False

Execute segment sunblocker.

use_mstransform

bool, optional, default = True

Execute sunblocker on continuum-subtracted data (otherwise use non-continuum-subtracted data).

imsize

int, optional, default = 900

Image size (use the same as in wsclean_image or casa_image).

cell

float, optional, default = 2.

Cell size in arcsec (use the same as in wsclean_image or casa_image).

threshold

float, optional, default = 4.

Distance from average beyond which data are flagged in units of sigma.

vampirisms

bool, optional, default = False

Apply only to data taken during day time.

uvmax

float, optional, default = 2000

Maximum uvdistance in wavelength to be analysed.

uvmin

float, optional, default = 0.

Minimum uvdistance in wavelength to be analysed.

make_cube

Make a line cube with either WSclean + SoFiA (for clean masks) or Casa.

enable

bool, optional, default = True

Execute segment make_cube.

image_with

{“wsclean”, “casa”}, optional, default = wsclean

Choose whether to image with WSclean + SoFiA (“wsclean”) or with Casa (“casa”).

use_mstransform

bool, optional, default = True

Image the .MS file(s) made by CASA MSTRANSFORM (continuum-subtracted and/or Doppler corrected).

pol

str, optional, default = I

Polarizations in output cube (I,Q,U,V,XX,YY,XY,YX,RR,LL,RL,LR and combinations).

spwid

int, optional, default = 0

Spectral window to use.

nchans

int, optional, default = 0

Number of channels of HI cube, 0 means all channels.

firstchan

int, optional, default = 0

First channel of HI cube.

binchans

int, optional, default = 1

Integer binning of channels.

npix

seq, optional, default = 900 , 900

Image size in pixels. List of integers (width and height) or a single integer for square images.

cell

float, optional, default = 2

Scale of a pixel. Default unit is arcsec, but can be specificied, e.g. ‘scale 20asec’.

padding

float, optional, default = 1.2

Images have initial size padding*npix, and are later trimmed to npix.

weight

str, optional, default = briggs

Weightmode can be natural, uniform, briggs. When using Briggs weighting, the Robustness parameter robust has to be specified in addition.

robust

float, optional, default = 0

Robust parameter in case of Briggs weighting.

taper

float, optional, default = 0

Gaussian taper FWHM in arcsec. Zero means no tapering.

niter

int, optional, default = 1000000

Maximum number of clean iterations to perform.

gain

float, optional, default = 0.1

Fraction of the peak that will be cleaned in each minor iteration.

wscl_mgain

float, optional, default = 1.0

WSclean gain for major iterations, i.e., maximum fraction of peak that will be cleaned in each major iteration.

wscl_sofia_niter

int, optional, default = 2

Maximum number of WSclean + SoFiA iterations. The initial cleaning is done with WSclean automasking or with a user clean mask. Subsequent iterations use a SoFiA clean mask. A value of 1 means that WSclean is only executed once and SoFiA is not used.

wscl_sofia_converge

float, optional, default = 1.1

Stop the WSclean + SoFiA iterations if the cube RMS has dropped by a factor < wscl_sofia_converge when comparing the last two iterations. If set to 0 then the maximum number of iterations is performed regardless of the noise change.

wscl_keep_final_products_only

bool, optional, default = False

If set to true it deletes WSclean + Sofia intermediate cubes from the output directory, if set to false it keeps all the cubes of the WSclean + SoFiA iterations.

wscl_user_clean_mask

str, optional, default = ‘ ‘

WSclean user clean mask for first WSclean + SoFiA iteration (give filename, to be located in the output/masking folder).

wscl_auto_mask

float, optional, default = 10

WSclean option. Construct a mask from found components and when a threshold of sigma is reached, continue cleaning with the mask down to the normal threshold.

wscl_auto_threshold

float, optional, default = 0.5

WSclean option. Auto clean threshold.

wscl_make_cube

bool, optional, default = True

If set to true the output of WSclean is a data cube, if set to false the output is one fits file per spectral channel.

wscl_no_update_mod

bool, optional, default = True

If set to true, WSclean will not store the line clean model in MODEL_DATA.

wscl_multi_scale

bool, optional, default = False

Switch on WSclean multiscale cleaning.

wscl_multi_scale_scales

list of int, optional, default = 0, 10, 20, 30

List of scales of WSclean multiscale in units of pixels. Only used is wscl_multi_scale is set to True.

wscl_multi_scale_bias

float, optional, default = 0.6

Parameter to set the bias towards larger scales during multi-scale cleaning. A lower bias will give preference to larger scales.

casa_threshold

str, optional, default = 10mJy

Flux level to stop CASA cleaning, must include units, e.g. ‘1.0mJy’.

casa_port2fits

bool, optional, default = False

Port CASA output to fits files.

remove_stokes_axis

Remove Stokes axis from HI cube

enable

bool, optional, default = False

Execute this segment.

pb_cube

Make primary beam cube

enable

bool, optional, default = False

Execute this segment.

apply_pb

bool, optional, default = False

Whether to apply the primary beam correction to the image cube.

freq_to_vel

Convert the spectral axis’ header keys of the HI cube from frequency to velocity in the radio definition, v=c(1-obsfreq/restfreq). No change of spectra reference frame is performed.

enable

bool, optional, default = False

Execute conversion.

reverse

bool, optional, default = False

Perform the inverse transformation and change the cube 3rd axis from radio velocity to frequency.

sofia

Run SoFiA source finder to produce a source mask and a Moment-0 map

enable

bool, optional, default = True

Execute segment sofia?

rmsMode

str, optional, default = mad

Method to determine rms (‘mad’ for using median absolute deviation, ‘std’ for using standard deviation, ‘negative’ for using Gaussian fit to negative voxels).

threshold

float, optional, default = 4.0

SoFiA source finding threshold.

flag

bool, optional, default = False

Use flag regions?

flagregion

list of int, optional, default = 10, 10

Pixel/channel range(s) to be flagged prior to source finding. Format is [[x1, x2, y1, y2, z1, z2], …].

merge

bool, optional, default = False

Use method to de-select and merge emission islands detected by any of SoFiA source finding algorithms. If turned on, pixels with a separation of less than mergeX pixels in x direction and less than mergeY pixels in y-direction and less than z pixels in z-direction will be merged and identified as a single object in the mask. Detections whose extent in x-direction is smaller than minSizeX, in y direction is smaller than minSizeY, and in z-direction is smaller than minSizeZ will be removed from the mask. Parameter merge determines if the merging should be applied.

mergeX

int, optional, default = 2

Merge-‘radius’ in x-direction.

mergeY

int, optional, default = 2

Merge-‘radius’ in y-direction.

mergeZ

int, optional, default = 3

Merge-‘radius’ in z-direction (velocity direction).

minSizeX

int, optional, default = 3

Minimum size in x-direction.

minSizeY

int, optional, default = 3

Minimum size in y-direction.

minSizeZ

int, optional, default = 3

Minimum size in y-direction.

do_cubelets

bool, optional, default = True

Create cubelets of HI sources.

do_mom0

bool, optional, default = True

Create moment 0 map.

do_mom1

bool, optional, default = True

Create moment 1 map.

sharpener

Run sharpener to extract spectrum of all continuum sources against the lines of sight. The spectra are then plotted.

enable

bool, optional, default = False

Execute sharpener?

catalog

{“NVSS”, “PYBDSF”}, optional, default = PYBDSF

Type of catalog to use (PYBDSF/NVSS).

channels_per_plot

int, optional, default = 50

Number of channels to plot per detail plot.

thresh

float, optional, default = 20

Threshold to select sources in online catalogs (mJy).

width

str, optional, default = 1.0d

Field of view of output catalog (degrees).

label

str, optional, default = ‘ ‘

Prefix label of plot names and titles.