cflag (Flagging Utility)

The cflag pipeline task is responsible for both selection based and dynamic flagging of visibilities. It takes as input a configuration file which specifies both the dataset (Measurement Set) to be transformed, the flaggers to use and parameters for these flaggers. Current supported strategies are:

• Selection (i.e. manual selection)
• Elevation thresholding
• Stokes-V thresholding
• Amplitude thresholding

These flaggers are described in more detail below, along with the description of parameters.

Running the program

It can be run with the following command, where “config.in” is a file containing the configuration parameters described in the next section.

$ cflag -c config.in

The cflag program is not parallel/distributed, it runs in a single process operating on a single input measurement set.

Configuration Parameters

An example configuration parameter set is provided in the Configuration Example section.

Parameter	Default	Example	Description
Cflag.dataset	None	fornax.ms	The measurement set (uv-dataset) to be flagged. This file has flagging applied in place (i.e. it is modified)
Cflag.dryrun	false	true	If set to true, the dataset will not be modified. The flaggers will still report flagging information so the user can see what flagging would have taken place if “dryrun” was set to false.
Cflag.summary	true	false	If “true” then a summary of the measurement set is displayed before flagging. This contains information such as previous flagging. However, an extra pass over the data is done, so for very large measurement sets this can be avoided by setting this parameter to “false”

Selection Base Flagging

A selection based flagging flagger. This allows flagging based on: - Baseline (i.e. an antenna or a pair of antennas) - Field index number - Time range - Scan index number - Feed/beam index number - UVRange - Autocorrelations only - Spectral Window (e.g. channel index number or frequency)

Parameter	Default	Example	Description
Cflag.selection_flagger.rules	None	[rule1, rule2]	The list of rules for selection based flagging. If this parameter is not specified, the selection based flagger is not used.
Cflag.selection_flagger.<rule>.field	None	See below URL	Flag based on field index number
Cflag.selection_flagger.<rule>.spw	None	See below URL	Flag based on spectral window
Cflag.selection_flagger.<rule>.antenna	None	See below URL	Flag based on an antenna or antenna pair
Cflag.selection_flagger.<rule>.timerange	None	See below URL	Flag based on a time range
Cflag.selection_flagger.<rule>.correlation	None	See below URL	Flag specific correlation products
Cflag.selection_flagger.<rule>.scan	None	See below URL	Flag all rows in a given scan, based on scan index number
Cflag.selection_flagger.<rule>.feed	None	[0, 1]	An array of beam index numbers to flag.
Cflag.selection_flagger.<rule>.uvrange	None	See below URL	Flag all baselines for a given UV distance range
Cflag.selection_flagger.<rule>.autocorr	false	true	Flag auto correlations

Selection syntax is described here: http://www.aoc.nrao.edu/~sbhatnag/misc/msselection/msselection.html

Elevation Thresholding

This flagger will flag any visibilities where one or both of the antennas have an elevation either lower than the “low” threshold or higher than the “high” threshold. This allows flagging when the antennas are pointed either near the horizon or the zenith.

Parameter	Default	Example	Description
Cflag.elevation_flagger.enable	false	true	Enable the elevation thresholding based flagging
Cflag.elevation_flagger.low	0.0	10.0	Defines the lower threshold (in degrees). All visibilities for which the elevation was lowever than this threshold will be flagged.
Cflag.elevation_flagger.high	90.0	89.5	Defines the upper threshold (in degrees). All visibilities for which the elevation was higher than this threshold will be flagged.

Stokes-V Thresholding

Performs flagging based on Stokes-V thresholding. For each row the mean and standard deviation for all Stokes-V correlations (i.e. all channels within a given row) are calculated. Then, where the Stokes-V correlation exceeds the average plus (stddev * threshold) all correlations for that channel in that row will be flagged.

Parameter	Default	Example	Description
Cflag.stokesv_flagger.enable	false	true	Enable the Stokes-V dynamic flagging
Cflag.stokesv_flagger.threshold	5.0	5.0	The threshold at which visibilities will be flagged. Where the amplitude of a correlation exceeds the (average + (stddev * threshold)) all correlations for that spectral channel in the row will be flagged.
Cflag.stokesv_flagger.useRobustStatistics	false	true	Use the median and interquartile range to estimate average and stddev (see below).
Cflag.stokesv_flagger.integrateSpectra	false	true	Integrate the spectra in time and flag any channels outside bounds, set using the robust statistics described below. Uses scalar averaging. Spectra for different baselines, beams, fields and polarisation are kept separate. Requires a second pass over the data.
Cflag.stokesv_flagger.integrateSpectra.threshold	5.0	4.0	The threshold factor used to bound integrated spectra.
Cflag.stokesv_flagger.integrateTimes	false	true	Integrate across spectra and flag any time samples outside bounds, set using the robust statistics described below. Uses scalar averaging. Series for different baselines, beams, fields and polarisation are kept separate. Requires a second pass over the data.
Cflag.stokesv_flagger.integrateTimes.threshold	5.0	4.0	The threshold factor used to bound integrated spectra.

Amplitude Thresholding

The “amplitude thresholding” flagger is a simple flagger used to flag visibilities which fall outside some amplitude bounds. This was designed for ASKAP commissioning to potentially work around some correlator problems, but has been extended to dynamically estimate flagging thresholds and to look for interference peaks in averaged data.

Parameter	Default	Example	Description
Cflag.amplitude_flagger.enable	false	true	Enable amplitude threshold flagging
Cflag.amplitude_flagger.low	None	1e-17	The lower bound for valid visibilities. Any visibility with a lower amplitude will be flagged. If this parameter is not present in the parset, then no lower bound will be enforced.
Cflag.amplitude_flagger.high	None	12345.0	The upper bound for valid visibilities. Any visibility with a higher amplitude will be flagged. If this parameter is not present in the parset, then no upper bound will be enforced.
Cflag.amplitude_flagger.stokes	None	[XX, YY]	Specifies which correlation products are to be subject to flagging. If this parameter is not specified then all products will be subject to flagging. To just flag XX, then specify “[XX]”. For XX & YY, “[XX, YY]”, and so on. No stokes conversion is done, so only the products contained in the measurement set should be specified.
Cflag.amplitude_flagger.dynamicBounds	false	true	If true, automatically generate low and high amplitude bounds for each spectrum using the statistics described below. Both Cflag.amplitude_flagger.low and Cflag.amplitude_flagger.high have preference over the dynamic bounds.
Cflag.amplitude_flagger.threshold	5.0	4.0	The threshold factor used in the statistics described below.
Cflag.amplitude_flagger.integrateSpectra	false	true	Integrate the spectra in time and flag any channels outside bounds, also set using the robust statistics described below. Uses scalar averaging. Spectra for different baselines, beams, fields and polarisation are kept separate. Requires a second pass over the data.
Cflag.amplitude_flagger.integrateSpectra.threshold	5.0	4.0	The threshold factor used to bound integrated spectra.
Cflag.amplitude_flagger.integrateTimes	false	true	Integrate across spectra and flag any time samples outside bounds, also set using the robust statistics described below. Uses scalar averaging. Series for different baselines, beams, fields and polarisation are kept separate. Requires a second pass over the data.
Cflag.amplitude_flagger.integrateTimes.threshold	5.0	4.0	The threshold factor used to bound integrated spectra.
Cflag.amplitude_flagger.aveAll	false	true	Do not separate spectra based on baseline, etc., when integrating spectra or time series. Average everything together.
Cflag.amplitude_flagger.aveAll.noPol	false	true	Do separate spectra for different polarisations.
Cflag.amplitude_flagger.aveAll.noBeam	false	true	Do separate spectra for different beams.

Robust Statistics

To avoid additional passes over data containing RFI spikes when generating statistics, the median and interquartile range are used in place of the mean and standard deviation used in many thresholding algorithms. These are more robust to a modest number of outliers. If Gaussian noise dominates most of the frequency channels, then ~50% of the samples will lie within 0.674 sigma of the mean, such that sigma ~ 1.349*IQL (IQL = the interquartile range). Samples outside [median - threshold*sigma, median + threshold*sigma] are flagged.

Configuration Example

Example 1

This example demonstrates configuration of the Stokes-V (dynamic) flagger and the selection based flagger with two rules specified:

# The path/filename for the measurement set
Cflag.dataset                           = target.ms

# Enable Stokes V flagging flagger with a 5-sigma threshold
Cflag.stokesv_flagger.enable            = true
Cflag.stokesv_flagger.threshold         = 5.0

# Enable selection based flagging with two rules
Cflag.selection_flagger.rules           = [rule1, rule2]

# Selection Rule 1: Beams 0 and 1 on antenna "ak01"
Cflag.selection_flagger.rule1.antenna   = ak01
Cflag.selection_flagger.rule1.feed      = [0, 1]

# Selection Rule 2: Spectral Channels 0 to 16 (inclusive) on spectral window 0
Cflag.selection_flagger.rule2.spw       = 0:0~16

Example 2

This example demonstrates configuration of the elevation flagger and the amplitude based flagger with both a low and high threshold:

# The path/filename for the measurement set
Cflag.dataset                           = target.ms

# Elevation based flagging
Cflag.elevation_flagger.enable          = true
Cflag.elevation_flagger.low             = 12.0
Cflag.elevation_flagger.high            = 89.0

# Amplitude based flagging
Cflag.amplitude_flagger.enable          = true
Cflag.amplitude_flagger.high            = 10.25
Cflag.amplitude_flagger.low             = 1e-3

Example 3

This example demonstrates configuration of the amplitude based flagger with dynamic thresholding:

# The path/filename for the measurement set
Cflag.dataset                                         = target.ms
# Amplitude based flagging
Cflag.amplitude_flagger.enable                        = true
# Threshold using the median and IQR of each spectrum
Cflag.amplitude_flagger.dynamicBounds                 = true
# Threshold again after averaging spectra in time
Cflag.amplitude_flagger.integrateSpectra              = true
Cflag.amplitude_flagger.integrateSpectra.threshold    = 4.0
Cflag.amplitude_flagger.integrateTimes                = true