#include <FlagAgentTimeFreqCrop.h>

Inheritance diagram for casa::FlagAgentTimeFreqCrop:

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

	~FlagAgentTimeFreqCrop ()

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...

virtual FlagReport	getReport ()
	Get a report casacore::Record from the agent, at the end of the run The report returned by getReport() can be of multiple types – a single report of type "none" : FlagReport("none",agentName_p) – a single report of type "plot" : FlagReport("plot",agentName_p) – a list of reports : FlagReport repList("list"); repList.addReport(FlagReport("plot",agentName_p)); repList.addReport(FlagReport("plot",agentName_p));. 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
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	setAgentParameters (casacore::Record config)
	Parse configuration parameters. 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)

virtual void	passIntermediate (const vi::VisBuffer2 &visBuffer)
	Iter-passes method. More...

virtual void	passFinal (const vi::VisBuffer2 &visBuffer)

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 Member Functions
void	fitBaseAndFlag (casacore::String fittype, casacore::String direction, VisMapper &visibilities, FlagMapper &flags)
	Read original flags or not. More...

casacore::Float	calcMean (casacore::Vector< casacore::Float > &vect, casacore::Vector< casacore::Bool > &flag)
	Calculate Mean, Variance, Stddev while accounting for flags. More...

casacore::Float	calcVar (casacore::Vector< casacore::Float > &vect, casacore::Vector< casacore::Bool > &flag, casacore::Vector< casacore::Float > &fit)

casacore::Float	calcStd (casacore::Vector< casacore::Float > &vect, casacore::Vector< casacore::Bool > &flag, casacore::Vector< casacore::Float > &fit)

casacore::Float	calcStd (casacore::Vector< casacore::Float > &vect, casacore::Vector< casacore::Bool > &flag, casacore::Float mean)

void	fitPiecewisePoly (casacore::Vector< casacore::Float > &data, casacore::Vector< casacore::Bool > &flag, casacore::Vector< casacore::Float > &fit, casacore::uInt maxnpieces, casacore::uInt maxdeg)
	Fit a piece-wise polynomial according to the supplied specs. More...

void	polyFit (casacore::Vector< casacore::Float > &data, casacore::Vector< casacore::Bool > &flag, casacore::Vector< casacore::Float > &fit, casacore::uInt lim1, casacore::uInt lim2, casacore::uInt deg)
	Fit a polynomial of specified degree to a range of data points. More...

void	lineFit (casacore::Vector< casacore::Float > &data, casacore::Vector< casacore::Bool > &flag, casacore::Vector< casacore::Float > &fit, casacore::uInt lim1, casacore::uInt lim2)
	Fit a line to a range of data points. More...

Private Attributes
casacore::Double	time_cutoff_p
	casacore::Input parameters /// More...

casacore::Double	freq_cutoff_p
	Flag threshold in frequency. More...

casacore::Int	maxNPieces_p
	Maximum number of pieces to allow in the piecewise-polynomial fits (1-9) More...

casacore::String	timeFitType_p
	Fitting function for the time direction ('line' or 'poly') More...

casacore::String	freqFitType_p
	Fitting function for the frequency direction ('line' or 'poly') More...

casacore::String	flagDimension_p
	Choose the directions along which to perform flagging ('time', 'freq', 'timefreq', 'freqtime') More...

casacore::Int	halfWin_p
	Half width of sliding window to use with 'usewindowstats' (1,2,3 for 3-point, 5-point or 7-point window sizes) More...

casacore::String	winStats_p
	Use sliding-window statistics to find additional flags ('none', 'sum', 'std', 'both') More...

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

Definition at line 30 of file FlagAgentTimeFreqCrop.h.

Constructor & Destructor Documentation

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

casa::FlagAgentTimeFreqCrop::~FlagAgentTimeFreqCrop ( )

Member Function Documentation

casacore::Float casa::FlagAgentTimeFreqCrop::calcMean	(	casacore::Vector< casacore::Float > &	vect,
		casacore::Vector< casacore::Bool > &	flag
	)

private

Calculate Mean, Variance, Stddev while accounting for flags.

casacore::Float casa::FlagAgentTimeFreqCrop::calcStd	(	casacore::Vector< casacore::Float > &	vect,
		casacore::Vector< casacore::Bool > &	flag,
		casacore::Vector< casacore::Float > &	fit
	)

private

casacore::Float casa::FlagAgentTimeFreqCrop::calcStd	(	casacore::Vector< casacore::Float > &	vect,
		casacore::Vector< casacore::Bool > &	flag,
		casacore::Float	mean
	)

private

casacore::Float casa::FlagAgentTimeFreqCrop::calcVar	(	casacore::Vector< casacore::Float > &	vect,
		casacore::Vector< casacore::Bool > &	flag,
		casacore::Vector< casacore::Float > &	fit
	)

private

bool casa::FlagAgentTimeFreqCrop::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::FlagAgentTimeFreqCrop::fitBaseAndFlag	(	casacore::String	fittype,
		casacore::String	direction,
		VisMapper &	visibilities,
		FlagMapper &	flags
	)

private

Read original flags or not.

Note : original flags are those in the casacore::MS (and not those generated by agents) true/false casacore::Bool usePreFlags_p;

/// TFCROP functions

Average the data, fit a piecewise polynomial, divide it out, flag outliers.

void casa::FlagAgentTimeFreqCrop::fitPiecewisePoly	(	casacore::Vector< casacore::Float > &	data,
		casacore::Vector< casacore::Bool > &	flag,
		casacore::Vector< casacore::Float > &	fit,
		casacore::uInt	maxnpieces,
		casacore::uInt	maxdeg
	)

private

Fit a piece-wise polynomial according to the supplied specs.

void casa::FlagAgentTimeFreqCrop::lineFit	(	casacore::Vector< casacore::Float > &	data,
		casacore::Vector< casacore::Bool > &	flag,
		casacore::Vector< casacore::Float > &	fit,
		casacore::uInt	lim1,
		casacore::uInt	lim2
	)

private

Fit a line to a range of data points.

void casa::FlagAgentTimeFreqCrop::polyFit	(	casacore::Vector< casacore::Float > &	data,
		casacore::Vector< casacore::Bool > &	flag,
		casacore::Vector< casacore::Float > &	fit,
		casacore::uInt	lim1,
		casacore::uInt	lim2,
		casacore::uInt	deg
	)

private

Fit a polynomial of specified degree to a range of data points.

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

protectedvirtual

Parse configuration parameters.

Reimplemented from casa::FlagAgentBase.

Member Data Documentation

casacore::String casa::FlagAgentTimeFreqCrop::flagDimension_p

private

Choose the directions along which to perform flagging ('time', 'freq', 'timefreq', 'freqtime')

Definition at line 63 of file FlagAgentTimeFreqCrop.h.

casacore::Double casa::FlagAgentTimeFreqCrop::freq_cutoff_p

private

Flag threshold in frequency.

(flag all data-points further than N-stddev from the fit).

Definition at line 54 of file FlagAgentTimeFreqCrop.h.

casacore::String casa::FlagAgentTimeFreqCrop::freqFitType_p

private

Fitting function for the frequency direction ('line' or 'poly')

Definition at line 60 of file FlagAgentTimeFreqCrop.h.

casacore::Int casa::FlagAgentTimeFreqCrop::halfWin_p

private

Half width of sliding window to use with 'usewindowstats' (1,2,3 for 3-point, 5-point or 7-point window sizes)

Definition at line 66 of file FlagAgentTimeFreqCrop.h.

casacore::Int casa::FlagAgentTimeFreqCrop::maxNPieces_p

private

Maximum number of pieces to allow in the piecewise-polynomial fits (1-9)

Definition at line 56 of file FlagAgentTimeFreqCrop.h.

casacore::Double casa::FlagAgentTimeFreqCrop::time_cutoff_p

private

casacore::Input parameters ///

Flag threshold in time. (flag all data-points further than N-stddev from the fit).

Definition at line 51 of file FlagAgentTimeFreqCrop.h.

casacore::String casa::FlagAgentTimeFreqCrop::timeFitType_p

private

Fitting function for the time direction ('line' or 'poly')

Definition at line 58 of file FlagAgentTimeFreqCrop.h.

casacore::String casa::FlagAgentTimeFreqCrop::winStats_p

private

Use sliding-window statistics to find additional flags ('none', 'sum', 'std', 'both')

Definition at line 69 of file FlagAgentTimeFreqCrop.h.

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

casa/code/flagging/Flagging/FlagAgentTimeFreqCrop.h

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation