A flag agent that implements the 'rflag' flagdata mode. More...

#include <FlagAgentRFlag.h>

Inheritance diagram for casa::FlagAgentRFlag:

Public Member Functions
	FlagAgentRFlag (FlagDataHandler *dh, casacore::Record config, casacore::Bool writePrivateFlagCube=false, casacore::Bool flag=true)

	~FlagAgentRFlag ()

Public Member Functions inherited from casa::FlagAgentBase
	FlagAgentBase (FlagDataHandler *dh, casacore::Record config, casacore::uShort iterationApproach, casacore::Bool writePrivateFlagCube=false, casacore::Bool flag=true)

virtual	~FlagAgentBase ()

void	start ()

void	terminate ()

void	queueProcess ()

void	chunkSummary ()

void	tableSummary ()

void	completeProcess ()

void *	run ()

void	setProfiling (bool enable)
	Set function to activate profiling. More...

void	setCheckMode (bool enable)
	Set function to activate check mode. More...

Public Member Functions inherited from casa::async::Thread
	Thread ()

virtual	~Thread ()

pthread_t	getId () const

pid_t	gettid () const

bool	isTerminationRequested () const

void *	join ()

void	startThread ()

Protected Member Functions
void	setAgentParameters (casacore::Record config)
	Parse configuration parameters. More...

bool	computeAntennaPairFlags (const vi::VisBuffer2 &visBuffer, VisMapper &visibilities, FlagMapper &flags, casacore::Int antenna1, casacore::Int antenna2, std::vector< casacore::uInt > &rows)
	Compute flags for a given (time,freq) map. More...

void	passIntermediate (const vi::VisBuffer2 &visBuffer)
	Extract automatically computed thresholds to use them in the next pass. More...

void	passFinal (const vi::VisBuffer2 &visBuffer)
	Remove automatically computed thresholds for the following scans. More...

casacore::Double	mean (std::vector< casacore::Double > &data, std::vector< casacore::Double > &counts)
	Convenience function to get simple averages. More...

casacore::Double	median (std::vector< casacore::Double > &data)
	Convenience function to compute median. More...

void	noiseVsRef (std::vector< casacore::Double > &data, casacore::Double ref)

casacore::Double	computeThreshold (std::vector< casacore::Double > &data, std::vector< casacore::Double > &dataSquared, std::vector< casacore::Double > &counts)
	Convenience function to get simple averages. More...

void	computeAntennaPairFlagsCore (std::pair< casacore::Int, casacore::Int > spw_field, casacore::Double noise, casacore::Double scutoff, casacore::uInt timeStart, casacore::uInt timeStop, casacore::uInt centralTime, VisMapper &visibilities, FlagMapper &flags)
	casacore::Function to be called for each timestep/channel More...

void	robustMean (casacore::uInt timestep_i, casacore::uInt pol_k, casacore::uInt nChannels, casacore::Double &AverageReal, casacore::Double &AverageImag, casacore::Double &StdReal, casacore::Double &StdImag, casacore::Double &SumWeightReal, casacore::Double &SumWeightImag, VisMapper &visibilities, FlagMapper &flags)

void	simpleMedian (casacore::uInt timestep_i, casacore::uInt pol_k, casacore::uInt nChannels, casacore::Double &AverageReal, casacore::Double &AverageImag, casacore::Double &StdReal, casacore::Double &StdImag, casacore::Double &SumWeightReal, casacore::Double &SumWeightImag, VisMapper &visibilities, FlagMapper &flags)

FlagReport	getReport ()
	casacore::Function to return histograms More...

FlagReport	getReportCore (map< std::pair< casacore::Int, casacore::Int >, std::vector< casacore::Double > > &data, map< std::pair< casacore::Int, casacore::Int >, std::vector< casacore::Double > > &dataSquared, map< std::pair< casacore::Int, casacore::Int >, std::vector< casacore::Double > > &counts, map< std::pair< casacore::Int, casacore::Int >, casacore::Double > &threshold, FlagReport &totalReport, string label, casacore::Double scale)
	casacore::Function to return histograms More...

void	generateThresholds (map< std::pair< casacore::Int, casacore::Int >, std::vector< casacore::Double > > &data, map< std::pair< casacore::Int, casacore::Int >, std::vector< casacore::Double > > &dataSquared, map< std::pair< casacore::Int, casacore::Int >, std::vector< casacore::Double > > &counts, map< std::pair< casacore::Int, casacore::Int >, casacore::Double > &threshold, string label)
	Dedicated method to generate threshold values. More...

Protected Member Functions inherited from casa::FlagAgentBase
void	initialize ()

void	runCore ()
	Convenience function to be shared by parallel/non-parallel mode. More...

void	setDataSelection (casacore::Record config)

casacore::String	sanitizeCorrExpression (casacore::String corrExpression, std::vector< casacore::String > *corrProducts)
	Method to sanitize correlation expression and keep going. More...

void	generateAllIndex ()

void	generateRowsIndex (casacore::uInt nRows)

void	generateChannelIndex (casacore::uInt nChannels)

void	generatePolarizationIndex (casacore::uInt nPolarizations)

std::vector< casacore::uInt > *	generateAntennaPairRowsIndex (casacore::Int antenna1, casacore::Int antenna2)

void	indigen (std::vector< casacore::uInt > &index, casacore::uInt size)
	Generate index for all rows. More...

bool	find (const casacore::Vector< casacore::Int > &validRange, casacore::Int element)
	For checking ids. More...

bool	find (const casacore::Matrix< casacore::Double > &validRange, casacore::Double element)
	For checking ranges. More...

bool	find (const casacore::Matrix< casacore::Int > &validPairs, casacore::Int element1, casacore::Int element2)
	For checking pairs. More...

bool	find (const casacore::Block< int > &columns, int col)
	For checking columns. More...

bool	isNaN (casacore::Double number)
	Check if a given number is nan (for visibilities,gains and Tsys primarily) More...

bool	isNaN (casacore::Float number)

bool	isZero (casacore::Double number)

bool	isZero (casacore::Float number)

bool	isNaNOrZero (casacore::Float number)

bool	isNaNOrZero (casacore::Double number)

bool	checkIfProcessBuffer ()
	Check if buffer has to be processed. More...

virtual void	preProcessBuffer (const vi::VisBuffer2 &visBuffer)
	Common functionality for each visBuffer (don't repeat at the row level) More...

void	iterateRows ()
	Iterate trough list of rows. More...

void	iterateInRows ()
	Iterate trough visibilities mapper. More...

void	iterateAntennaPairs ()
	Iterate trough list of antenna pairs. More...

void	iterateAntennaPairsFlags ()
	Iterate trough list of antenna pairs w/o loading visibilities. More...

void	processAntennaPair (casacore::Int antenna1, casacore::Int antenna2)
	Methods to interactively iterate trough list of antenna pairs. More...

virtual void	iterateAntennaPairsInteractive (antennaPairMap *antennaPairMap_ptr)

void	setVisibilitiesMap (std::vector< casacore::uInt > rows, VisMapper visMap)
	Mapping functions (abs, real, imag, etc.) as requested by Urvashi. More...

void	setFlagsMap (std::vector< casacore::uInt > rows, FlagMapper flagMap)

casacore::Bool	checkVisExpression (polarizationMap *polMap)

virtual bool	computeRowFlags (const vi::VisBuffer2 &visBuffer, FlagMapper &flags, casacore::uInt row)
	Compute flags for a given visibilities point. More...

virtual bool	computeInRowFlags (const vi::VisBuffer2 &visBuffer, VisMapper &visibilities, FlagMapper &flags, casacore::uInt row)
	Compute flags for a given visibilities point. More...

virtual bool	computeAntennaPairFlags (const vi::VisBuffer2 &visBuffer, FlagMapper &flags, casacore::Int antenna1, casacore::Int antenna2, std::vector< casacore::uInt > &rows)
	Compute flags for a given (time,freq) antenna pair map w/o using visibilities. More...

Protected Member Functions inherited from casa::async::Thread
bool	isStarted () const

Private Types
enum	optype { MEAN, ROBUST_MEAN, MEDIAN, ROBUST_MEDIAN }

Private Attributes
casacore::Bool	doflag_p
	General parameters. More...

casacore::Bool	doplot_p

casacore::uInt	nTimeSteps_p

casacore::Double	noiseScale_p
	flagdata task param timedevscale More...

casacore::Double	scutoffScale_p
	flagdata task param freqdevscale More...

casacore::uInt	nIterationsRobust_p
	Spectral Robust fit. More...

std::vector< casacore::Double >	thresholdRobust_p

casacore::Double	spectralmin_p

casacore::Double	spectralmax_p

casacore::uInt	optype_p

void(casa::FlagAgentRFlag::*	spectralAnalysis_p )(casacore::uInt, casacore::uInt, casacore::uInt, casacore::Double &, casacore::Double &, casacore::Double &, casacore::Double &, casacore::Double &, casacore::Double &, VisMapper &, FlagMapper &)

map< std::pair< casacore::Int, casacore::Int >, std::vector < casacore::Double > >	field_spw_frequency_p
	Store frequency to be used in Reports. More...

map< std::pair< casacore::Int, casacore::Int > , casacore::Double >	field_spw_frequencies_p

casacore::Double	noise_p
	casacore::Time-direction analysis More...

map< std::pair< casacore::Int, casacore::Int > , casacore::Double >	field_spw_noise_map_p
	holds the timedev thresholds for every field-SPW pair More...

map< std::pair< casacore::Int, casacore::Int > , casacore::Bool >	user_field_spw_noise_map_p

map< std::pair< casacore::Int, casacore::Int >, std::vector < casacore::Double > >	field_spw_noise_histogram_sum_p

map< std::pair< casacore::Int, casacore::Int >, std::vector < casacore::Double > >	field_spw_noise_histogram_sum_squares_p

map< std::pair< casacore::Int, casacore::Int >, std::vector < casacore::Double > >	field_spw_noise_histogram_counts_p

casacore::Double	scutoff_p
	Spectral analysis. More...

map< std::pair< casacore::Int, casacore::Int > , casacore::Double >	field_spw_scutoff_map_p
	holds the freqdev thresholds for every field-SPW pair More...

map< std::pair< casacore::Int, casacore::Int > , casacore::Bool >	user_field_spw_scutoff_map_p

map< std::pair< casacore::Int, casacore::Int >, std::vector < casacore::Double > >	field_spw_scutoff_histogram_sum_p

map< std::pair< casacore::Int, casacore::Int >, std::vector < casacore::Double > >	field_spw_scutoff_histogram_sum_squares_p

map< std::pair< casacore::Int, casacore::Int >, std::vector < casacore::Double > >	field_spw_scutoff_histogram_counts_p

Additional Inherited Members
Public Types inherited from casa::FlagAgentBase
enum	datacolumn { DATA, CORRECTED, MODEL, RESIDUAL, RESIDUAL_DATA, FPARAM, CPARAM, PARAMERR, SNR, WEIGHT_SPECTRUM, FLOAT_DATA }

enum	iteration { ROWS, ROWS_PREPROCESS_BUFFER, IN_ROWS, IN_ROWS_PREPROCESS_BUFFER, ANTENNA_PAIRS, ANTENNA_PAIRS_FLAGS, ANTENNA_PAIRS_INTERACTIVE, ANTENNA_PAIRS_PREPROCESS_BUFFER }

Public Types inherited from casa::async::Thread
typedef void (	ThreadFunction )(void *)

Static Public Member Functions inherited from casa::FlagAgentBase
static FlagAgentBase *	create (FlagDataHandler *dh, casacore::Record config)

Public Attributes inherited from casa::FlagAgentBase
casacore::Bool	backgroundMode_p
	Externally visible configuration. More...

casacore::LogIO::Command	logLevel_p

casacore::Bool	apply_p

casacore::Bool	flag_p

Static Protected Member Functions inherited from casa::async::Thread
static void *	threadFunction (void *)

Protected Attributes inherited from casa::FlagAgentBase
FlagDataHandler *	flagDataHandler_p
	Common used members that must be accessible to derived classes. More...

std::unique_ptr< casacore::LogIO >	logger_p

casacore::String	agentName_p

casacore::String	summaryName_p

casacore::String	mode_p

casacore::uInt64	chunkFlags_p
	Flag counters. More...

casacore::uInt64	chunkNaNs_p

casacore::uInt64	tableFlags_p

casacore::uInt64	tableNaNs_p

casacore::uInt64	visBufferFlags_p

bool	flagRow_p

casacore::Bool	multiThreading_p
	Multithreading configuration and agent id. More...

casacore::Int	nThreads_p

casacore::Int	threadId_p

casacore::Bool	prepass_p
	Running configuration. More...

std::vector< casacore::uInt >	rowsIndex_p
	Lists of elements to process jagonzal (CAS-4312): We need channelIndex_p available for the Rflag agent, in order to take into account channel selection for the frequency mapping. More...

std::vector< casacore::uInt >	channelIndex_p

std::vector< casacore::uInt >	polarizationIndex_p

casacore::String	dataColumn_p
	Needed to be protected for timeavg in clip. More...

casacore::Bool	timeavg_p
	Pre-averaging parameters. More...

casacore::Double	timebin_p

casacore::Bool	channelavg_p

casacore::Vector< casacore::Int >	chanbin_p

Detailed Description

A flag agent that implements the 'rflag' flagdata mode.

Uses the FlagAgentBase::ANTENNA_PAIRS iteration approach.

Note that the user interface provided by flagdata is complex/misleading in trying to replicate the use patterns of RFlag in AIPS. This produces a potentially confusing pattern when implementing the virtuals of FlagAgentBase. The per-channel RMS/variance values are calculated in computeAntennaPairFlagsCore(). Then, the overall thresholds (timedev, freqdev) are calculated in getReport(). The different display modes are essentially implemented in getReportCore().

This implementation takes as reference implementation the AIPS task RFlag by Erich Greisen, see The AIPS Cookbook Appendix E : Special Considerations for EVLA data calibration and imaging in AIPS E.5 Detailed Flagging http://www.aips.nrao.edu/cook.html#CEE

Definition at line 54 of file FlagAgentRFlag.h.

Member Enumeration Documentation

enum casa::FlagAgentRFlag::optype

private

Enumerator
MEAN
ROBUST_MEAN
MEDIAN
ROBUST_MEDIAN

Definition at line 56 of file FlagAgentRFlag.h.

Constructor & Destructor Documentation

casa::FlagAgentRFlag::FlagAgentRFlag	(	FlagDataHandler *	dh,
		casacore::Record	config,
		casacore::Bool	writePrivateFlagCube = `false`,
		casacore::Bool	flag = `true`
	)

casa::FlagAgentRFlag::~FlagAgentRFlag ( )

Member Function Documentation

bool casa::FlagAgentRFlag::computeAntennaPairFlags	(	const vi::VisBuffer2 &	visBuffer,
		VisMapper &	visibilities,
		FlagMapper &	flags,
		casacore::Int	antenna1,
		casacore::Int	antenna2,
		std::vector< casacore::uInt > &	rows
	)

protectedvirtual

Compute flags for a given (time,freq) map.

Reimplemented from casa::FlagAgentBase.

void casa::FlagAgentRFlag::computeAntennaPairFlagsCore	(	std::pair< casacore::Int, casacore::Int >	spw_field,
		casacore::Double	noise,
		casacore::Double	scutoff,
		casacore::uInt	timeStart,
		casacore::uInt	timeStop,
		casacore::uInt	centralTime,
		VisMapper &	visibilities,
		FlagMapper &	flags
	)

protected

casacore::Function to be called for each timestep/channel

casacore::Double casa::FlagAgentRFlag::computeThreshold	(	std::vector< casacore::Double > &	data,
		std::vector< casacore::Double > &	dataSquared,
		std::vector< casacore::Double > &	counts
	)

protected

Convenience function to get simple averages.

void casa::FlagAgentRFlag::generateThresholds	(	map< std::pair< casacore::Int, casacore::Int >, std::vector< casacore::Double > > &	data,
		map< std::pair< casacore::Int, casacore::Int >, std::vector< casacore::Double > > &	dataSquared,
		map< std::pair< casacore::Int, casacore::Int >, std::vector< casacore::Double > > &	counts,
		map< std::pair< casacore::Int, casacore::Int >, casacore::Double > &	threshold,
		string	label
	)

protected

Dedicated method to generate threshold values.

FlagReport casa::FlagAgentRFlag::getReport ( )

protectedvirtual

casacore::Function to return histograms

Reimplemented from casa::FlagAgentBase.

FlagReport casa::FlagAgentRFlag::getReportCore	(	map< std::pair< casacore::Int, casacore::Int >, std::vector< casacore::Double > > &	data,
		map< std::pair< casacore::Int, casacore::Int >, std::vector< casacore::Double > > &	dataSquared,
		map< std::pair< casacore::Int, casacore::Int >, std::vector< casacore::Double > > &	counts,
		map< std::pair< casacore::Int, casacore::Int >, casacore::Double > &	threshold,
		FlagReport &	totalReport,
		string	label,
		casacore::Double	scale
	)

protected

casacore::Function to return histograms

casacore::Double casa::FlagAgentRFlag::mean	(	std::vector< casacore::Double > &	data,
		std::vector< casacore::Double > &	counts
	)

protected

Convenience function to get simple averages.

casacore::Double casa::FlagAgentRFlag::median ( std::vector< casacore::Double > & data )

protected

Convenience function to compute median.

void casa::FlagAgentRFlag::noiseVsRef	(	std::vector< casacore::Double > &	data,
		casacore::Double	ref
	)

protected

void casa::FlagAgentRFlag::passFinal ( const vi::VisBuffer2 & visBuffer )

protectedvirtual

Remove automatically computed thresholds for the following scans.

Reimplemented from casa::FlagAgentBase.

void casa::FlagAgentRFlag::passIntermediate ( const vi::VisBuffer2 & visBuffer )

protectedvirtual

Extract automatically computed thresholds to use them in the next pass.

Reimplemented from casa::FlagAgentBase.

void casa::FlagAgentRFlag::robustMean	(	casacore::uInt	timestep_i,
		casacore::uInt	pol_k,
		casacore::uInt	nChannels,
		casacore::Double &	AverageReal,
		casacore::Double &	AverageImag,
		casacore::Double &	StdReal,
		casacore::Double &	StdImag,
		casacore::Double &	SumWeightReal,
		casacore::Double &	SumWeightImag,
		VisMapper &	visibilities,
		FlagMapper &	flags
	)

protected

void casa::FlagAgentRFlag::setAgentParameters ( casacore::Record config )

protectedvirtual

Parse configuration parameters.

Reimplemented from casa::FlagAgentBase.

void casa::FlagAgentRFlag::simpleMedian	(	casacore::uInt	timestep_i,
		casacore::uInt	pol_k,
		casacore::uInt	nChannels,
		casacore::Double &	AverageReal,
		casacore::Double &	AverageImag,
		casacore::Double &	StdReal,
		casacore::Double &	StdImag,
		casacore::Double &	SumWeightReal,
		casacore::Double &	SumWeightImag,
		VisMapper &	visibilities,
		FlagMapper &	flags
	)

protected

Member Data Documentation

casacore::Bool casa::FlagAgentRFlag::doflag_p

private

General parameters.

Definition at line 151 of file FlagAgentRFlag.h.

casacore::Bool casa::FlagAgentRFlag::doplot_p

private

Definition at line 152 of file FlagAgentRFlag.h.

map< std::pair<casacore::Int,casacore::Int>,casacore::Double > casa::FlagAgentRFlag::field_spw_frequencies_p

private

Definition at line 169 of file FlagAgentRFlag.h.

map< std::pair<casacore::Int,casacore::Int>,std::vector<casacore::Double> > casa::FlagAgentRFlag::field_spw_frequency_p

private

Store frequency to be used in Reports.

Definition at line 168 of file FlagAgentRFlag.h.

map< std::pair<casacore::Int,casacore::Int>,std::vector<casacore::Double> > casa::FlagAgentRFlag::field_spw_noise_histogram_counts_p

private

Definition at line 178 of file FlagAgentRFlag.h.

map< std::pair<casacore::Int,casacore::Int>,std::vector<casacore::Double> > casa::FlagAgentRFlag::field_spw_noise_histogram_sum_p

private

Definition at line 176 of file FlagAgentRFlag.h.

map< std::pair<casacore::Int,casacore::Int>,std::vector<casacore::Double> > casa::FlagAgentRFlag::field_spw_noise_histogram_sum_squares_p

private

Definition at line 177 of file FlagAgentRFlag.h.

map< std::pair<casacore::Int,casacore::Int>,casacore::Double > casa::FlagAgentRFlag::field_spw_noise_map_p

private

holds the timedev thresholds for every field-SPW pair

Definition at line 174 of file FlagAgentRFlag.h.

map< std::pair<casacore::Int,casacore::Int>,std::vector<casacore::Double> > casa::FlagAgentRFlag::field_spw_scutoff_histogram_counts_p

private

Definition at line 187 of file FlagAgentRFlag.h.

map< std::pair<casacore::Int,casacore::Int>,std::vector<casacore::Double> > casa::FlagAgentRFlag::field_spw_scutoff_histogram_sum_p

private

Definition at line 185 of file FlagAgentRFlag.h.

map< std::pair<casacore::Int,casacore::Int>,std::vector<casacore::Double> > casa::FlagAgentRFlag::field_spw_scutoff_histogram_sum_squares_p

private

Definition at line 186 of file FlagAgentRFlag.h.

map< std::pair<casacore::Int,casacore::Int>,casacore::Double > casa::FlagAgentRFlag::field_spw_scutoff_map_p

private

holds the freqdev thresholds for every field-SPW pair

Definition at line 183 of file FlagAgentRFlag.h.

casacore::uInt casa::FlagAgentRFlag::nIterationsRobust_p

private

Spectral Robust fit.

Definition at line 160 of file FlagAgentRFlag.h.

casacore::Double casa::FlagAgentRFlag::noise_p

private

casacore::Time-direction analysis

Definition at line 172 of file FlagAgentRFlag.h.

casacore::Double casa::FlagAgentRFlag::noiseScale_p

private

flagdata task param timedevscale

Definition at line 155 of file FlagAgentRFlag.h.

casacore::uInt casa::FlagAgentRFlag::nTimeSteps_p

private

Definition at line 153 of file FlagAgentRFlag.h.

casacore::uInt casa::FlagAgentRFlag::optype_p

private

Definition at line 164 of file FlagAgentRFlag.h.

casacore::Double casa::FlagAgentRFlag::scutoff_p

private

Spectral analysis.

Definition at line 181 of file FlagAgentRFlag.h.

casacore::Double casa::FlagAgentRFlag::scutoffScale_p

private

flagdata task param freqdevscale

Definition at line 157 of file FlagAgentRFlag.h.

void(casa::FlagAgentRFlag::* casa::FlagAgentRFlag::spectralAnalysis_p)(casacore::uInt, casacore::uInt, casacore::uInt, casacore::Double &, casacore::Double &, casacore::Double &, casacore::Double &, casacore::Double &, casacore::Double &, VisMapper &, FlagMapper &)

private

Definition at line 165 of file FlagAgentRFlag.h.

casacore::Double casa::FlagAgentRFlag::spectralmax_p

private

Definition at line 163 of file FlagAgentRFlag.h.

casacore::Double casa::FlagAgentRFlag::spectralmin_p

private

Definition at line 162 of file FlagAgentRFlag.h.

std::vector<casacore::Double> casa::FlagAgentRFlag::thresholdRobust_p

private

Definition at line 161 of file FlagAgentRFlag.h.

map< std::pair<casacore::Int,casacore::Int>,casacore::Bool > casa::FlagAgentRFlag::user_field_spw_noise_map_p

private

Definition at line 175 of file FlagAgentRFlag.h.

map< std::pair<casacore::Int,casacore::Int>,casacore::Bool > casa::FlagAgentRFlag::user_field_spw_scutoff_map_p

private

Definition at line 184 of file FlagAgentRFlag.h.

The documentation for this class was generated from the following file:

casa/code/flagging/Flagging/FlagAgentRFlag.h

Public Member Functions

Protected Member Functions

Private Types

Private Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation