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casa::AgentFlagger Class Reference

AgentFlagger: high-performance automated flagging. More...

#include <AgentFlagger.h>

Public Member Functions

 AgentFlagger ()
 default constructor More...
 
 ~AgentFlagger ()
 destructor More...
 
void done ()
 reset everything More...
 
bool open (casacore::String msname, casacore::Double ntime)
 configure the tool, open the MS More...
 
bool selectData (casacore::Record selrec)
 parse the data selection More...
 
bool selectData (casacore::String field, casacore::String spw, casacore::String array, casacore::String feed, casacore::String scan, casacore::String antenna, casacore::String uvrange, casacore::String timerange, casacore::String correlation, casacore::String intent, casacore::String observation="")
 
bool parseAgentParameters (casacore::Record agent_params)
 parse the parameters of the agent More...
 
casacore::String getExpressionFunction (casacore::String expression)
 
bool isExpressionPolarizationAll (casacore::String expression)
 
bool initAgents ()
 initialize the agents list More...
 
casacore::Record run (casacore::Bool writeflags, casacore::Bool sequential=true)
 Run the tool and write the flags to the MS. More...
 
bool printFlagSelections ()
 Flag backup methods. More...
 
bool saveFlagVersion (casacore::String versionname, casacore::String comment, casacore::String merge)
 
bool restoreFlagVersion (casacore::Vector< casacore::String > versionname, casacore::String merge)
 
bool deleteFlagVersion (casacore::Vector< casacore::String > versionname)
 
bool getFlagVersionList (casacore::Vector< casacore::String > &verlist)
 
bool parseManualParameters (casacore::String field, casacore::String spw, casacore::String array, casacore::String feed, casacore::String scan, casacore::String antenna, casacore::String uvrange, casacore::String timerange, casacore::String correlation, casacore::String intent, casacore::String observation, casacore::Bool autocorr, casacore::Bool apply)
 Agent's specific parsing methods (for convenience only) Parse parameters for manual. More...
 
bool parseClipParameters (casacore::String field, casacore::String spw, casacore::String array, casacore::String feed, casacore::String scan, casacore::String antenna, casacore::String uvrange, casacore::String timerange, casacore::String correlation, casacore::String intent, casacore::String observation, casacore::String datacolumn, casacore::Vector< casacore::Double > clipminmax, casacore::Bool clipoutside, casacore::Bool channelavg, casac::variant chanbin, casacore::Bool timeavg, casacore::String timebin, casacore::Bool clipzeros, casacore::Bool apply)
 Parse parameters for clip. More...
 
bool parseQuackParameters (casacore::String field, casacore::String spw, casacore::String array, casacore::String feed, casacore::String scan, casacore::String antenna, casacore::String uvrange, casacore::String timerange, casacore::String correlation, casacore::String intent, casacore::String observation, casacore::String quackmode, casacore::Double quackinterval, casacore::Bool quackincrement, casacore::Bool apply)
 Parse parameters for quack. More...
 
bool parseElevationParameters (casacore::String field, casacore::String spw, casacore::String array, casacore::String feed, casacore::String scan, casacore::String antenna, casacore::String uvrange, casacore::String timerange, casacore::String correlation, casacore::String intent, casacore::String observation, casacore::Double lowerlimit, casacore::Double upperlimit, casacore::Bool apply)
 Parse parameters for elevation. More...
 
bool parseTfcropParameters (casacore::String field, casacore::String spw, casacore::String array, casacore::String feed, casacore::String scan, casacore::String antenna, casacore::String uvrange, casacore::String timerange, casacore::String correlation, casacore::String intent, casacore::String observation, casacore::Double ntime, casacore::Bool combinescans, casacore::String datacolumn, casacore::Double timecutoff, casacore::Double freqcutoff, casacore::String timefit, casacore::String freqfit, casacore::Int maxnpieces, casacore::String flagdimension, casacore::String usewindowstats, casacore::Int halfwin, casacore::Bool extendflags, casacore::Bool apply, casacore::Bool channelavg, casac::variant chanbin, casacore::Bool timeavg, casacore::String timebin)
 Parse parameters for tfcrop. More...
 
bool parseAntIntParameters (casacore::String field, casacore::String spw, casacore::String array, casacore::String feed, casacore::String scan, casacore::String antenna, casacore::String uvrange, casacore::String timerange, casacore::String correlation, casacore::String intent, casacore::String observation, casacore::String antint_ref_antenna, casacore::Double minchanfrac, casacore::Bool verbose, casacore::Bool apply)
 Parse parameters for the 'antint' mode (antenna integrations) More...
 
bool parseExtendParameters (casacore::String field="", casacore::String spw="", casacore::String array="", casacore::String feed="", casacore::String scan="", casacore::String antenna="", casacore::String uvrange="", casacore::String timerange="", casacore::String correlation="", casacore::String intent="", casacore::String observation="", casacore::Double ntime=0.0, casacore::Bool combinescans=false, casacore::Bool extendpols=true, casacore::Double growtime=50.0, casacore::Double growfreq=50.0, casacore::Bool growaround=false, casacore::Bool flagneartime=false, casacore::Bool flagnearfreq=false, casacore::Bool apply=true)
 Parse parameters for extend. More...
 
bool parseSummaryParameters (casacore::String field, casacore::String spw, casacore::String array, casacore::String feed, casacore::String scan, casacore::String antenna, casacore::String uvrange, casacore::String timerange, casacore::String correlation, casacore::String intent, casacore::String observation, casacore::Bool spwchan, casacore::Bool spwcorr, casacore::Bool basecnt, casacore::Bool fieldcnt, casacore::String name)
 Parse parameters for summary. More...
 

Protected Attributes

casacore::String msname_p
 variables used to initialize the FlagDataHandler More...
 
casacore::uShort iterationApproach_p
 
casacore::Double timeInterval_p
 
casacore::Bool isMS_p
 
casacore::String spw_p
 members to parse to selectData More...
 
casacore::String scan_p
 
casacore::String field_p
 
casacore::String antenna_p
 
casacore::String timerange_p
 
casacore::String correlation_p
 
casacore::String intent_p
 
casacore::String feed_p
 
casacore::String array_p
 
casacore::String uvrange_p
 
casacore::String observation_p
 
casacore::Record dataselection_p
 
casacore::String mode_p
 agent's members More...
 
casacore::Record agentParams_p
 
FlagAgentSummarysummaryAgent_p
 
casacore::Bool combinescans_p
 
casacore::Bool extendflags_p
 
casacore::Bool mixed_p
 true if there are apply and unapply parameters in the list More...
 
casa::FlagAgentDisplaydisplayAgent_p
 Display agent parameters. More...
 
FlagDataHandlerfdh_p
 variables for initAgents More...
 
std::vector< casacore::Recordagents_config_list_p
 
std::vector< casacore::Recordagents_config_list_copy_p
 
FlagAgentList agents_list_p
 

Static Protected Attributes

static casacore::LogIO os
 

Private Member Functions

 AgentFlagger (const AgentFlagger &)
 
AgentFlaggeroperator= (const AgentFlagger &)
 
void getMax (casacore::Double value)
 Maximum between two numbers. More...
 
bool isModeValid (casacore::String mode)
 Check if mode is valid against a list of known modes. More...
 
casacore::Bool validateDataColumn (casacore::String datacol)
 

Private Attributes

casacore::LogSink logSink_p
 Sink used to store history. More...
 
casacore::Double max_p
 Store the temporary maximum value. More...
 
casacore::Bool timeset_p
 Helper members. More...
 
casacore::Bool iterset_p
 
casacore::Bool timeAvg_p
 casacore::Time average parameter in clip mode More...
 

Static Private Attributes

static const bool dbg
 Debug message flag. More...
 

Detailed Description

AgentFlagger: high-performance automated flagging.

Intended use:

Prerequisite

Etymology

Synopsis

AgentFlagger performs automated flagging operations on a measurement set or calibration table. The class is constructed from an casacore::MS or cal table. After that, the run method may be used to run any number of flagging agents.

Example

// The following is a typical way of using this class and its methods to perform flagging.
// Open the casacore::MS or a calibration file and attach it to the tool. This will create an object of the
// FlagDataHandler (fdh) type. The constructor of the fdh takes three arguments,
// the casacore::MS or CAL table, the iteration approach to use and the time interval. Only the MS
// is mandatory to use. By default it will use the FlagDataHandler::SUB_INTEGRATION iteration
// approach and 0.0 seconds as the time interval.
af->open('my.ms')
// Select the data where to flag. If left blank, the whole casacore::MS will be selected. This step
// will use the casacore::MS Selection class. There are two methods to perform the selection. One takes
// a casacore::Record of the parameters, the other takes the individual parameters as arguments.
// 1) First method:
casacore::String spw = "0:1~10";
casacore::String scan = "1";
selection.define("spw", spw);
selection.define("scan", scan);
af->selectData(selection);
// 2) Second method:
af->selectData(spw=spw, scan=scan);
// Now it is time to build a list of the agents that we want to run to process the data. This
// step will create a list of all the agents that will be executed to flag/unflag the data.
// This method can be called multiple times. Every call should contain the desired parameters of
// the agent and optionally data selection parameters. When data selection parameters are present,
// the agent will loop through only that portion of the data.
// This method will check if the requested agent (mode) is known from the following list
// (manual, clip, quack, shadow, elevation, tfcrop, rflag, extend, unflag, summary, and antint). If
// empty or unknown, it will give a warning and return.
// If any tfcrop, rflag or extend mode is present, this method will calculate the maximum value
// of time interval (ntime) from these agents. The maximum value will be used for all agents in
// the list.
// A similar situation will happen with the combinescans parameter. If any of the combinescans is
// true, it will be taken as true to all agents.
// Async I/O will be activated if any of the modes clip, tfcrop or rflag is requested. Also for
// these three modes, there will be a call to a function that will validate the requested
// datacolumn parameter. It will detect if the input is an casacore::MS or a cal table and validate the
// column. The default is the DATA column. If the input is a cal table, the function will
// first check if FPARAM is available, then CPARAM. If none of them is available it will return
// false and the agent will not be created.
// Only for the tfcrop agent, if a correlation ALL is requested, this method will create one
// agent for each available polarization in the MS. For example, if the casacore::MS contains polarizations
// XX and YY and the parameter is correlation="ABS_ALL", then there will be two tfcrop agents,
// one with correlation="ABS_XX" and the other with correlation="ABS_YY". The apply parameter
// is set by default to true to apply the flags.
agent_pars.define("mode", "clip");
agent_pars.define("clipzeros", true);
agent_pars.define("apply", true);
af->parseAgentParameters(agent_pars);
agent_pars.define("mode", "manual");
agent_pars.define("autocorr", true);
af->parseAgentParameters(agent_pars);
agent_pars.define("mode", "summary");
agent_pars.define("basecnt", true);
af->parseAgentParameters(agent_pars);
// There are convenience functions to parse the agent's parameters, one specific for each agent.
// The above calls can also be done using these functions instead.
af->parseClipParameters(clipzeros=true, apply=true);
af->parseManualParameters(autocorr=true);
af->parseSummaryParameters(basecnt=true);
// In either one of the cases, three agents will be created.
//
// NOTE: it is possible to add multiple summary agents to the list and gather a list of summary
// reports when executing the tool.
// We need to initialize the agents, which
// will call the constructor of each one of them and set the parameters that were given in the previous
// calls. Some basic checks will be performed at this stage for types and values of the parameters.
// If any tfcrop, rflag, extend or display agent is in the list, the iteration approach will be
// set to a different value depending on whether combinescans is true or not. When true, the
// iteration approach will be set to FlagDataHandler::COMBINE_SCANS_MAP_ANTENNA_PAIRS_ONLY, otherwise
// to FlagDataHandler::COMPLETE_SCAN_MAP_ANTENNA_PAIRS_ONLY.
// This method will create agents and add them to a FlagAgentList. If for any reason, the call to
// FlagAgentBase::create(fdh_p, agent_rec) fails, an error message will be displayed. Any agents previously
// added to the FlagAgentList will remain there. A subsequent call to this method can be done to add
// more agents to the same FlagAgentList.
af->initAgents();
// Before next step which will write the new flags, it is advisable to create a backup of
// the current flags in the MS.
af.saveflagversion(versionname='backup_before_manual_1',
comment='Backup of flags before running manual',merge='replace')
// The next step in the chain is to actually process the flags and write them or
// not to the MS. The run method takes two parameters, writeflags and sequential.
// The parameter writeflags controls whether to write the flags or not to the MS.
// By default it is set to true. Setting writeflags to false is useful when one
// wants to run the tool together with the display agent to see what is going to be
// flagged before deciding to write or not to the MS. The sequential parameter
// controls if the order of the agent's list needs to be preserved or not. If set to false,
// the order will not be preserved and the framework may execute the agent's list in parallel.
// By default sequential is set to true.
// The run method gathers several reports, depending on which agents are run. The display and summary agents
// produce reports that can be retrieved from calling the run method. The reports are returned via a Record
// that may contain multiple reports at the same time.
casacore::Record myReports;
myReports = af->run();
// To destroy the tool, call a method to execute the destructor.
af->done();

Motivation

To flag data using different algorithms.

Definition at line 212 of file AgentFlagger.h.

Constructor & Destructor Documentation

casa::AgentFlagger::AgentFlagger ( )

default constructor

casa::AgentFlagger::~AgentFlagger ( )

destructor

casa::AgentFlagger::AgentFlagger ( const AgentFlagger )
inlineprivate

Definition at line 357 of file AgentFlagger.h.

Member Function Documentation

bool casa::AgentFlagger::deleteFlagVersion ( casacore::Vector< casacore::String versionname)
void casa::AgentFlagger::done ( )

reset everything

casacore::String casa::AgentFlagger::getExpressionFunction ( casacore::String  expression)
bool casa::AgentFlagger::getFlagVersionList ( casacore::Vector< casacore::String > &  verlist)
void casa::AgentFlagger::getMax ( casacore::Double  value)
private

Maximum between two numbers.

bool casa::AgentFlagger::initAgents ( )

initialize the agents list

bool casa::AgentFlagger::isExpressionPolarizationAll ( casacore::String  expression)
bool casa::AgentFlagger::isModeValid ( casacore::String  mode)
private

Check if mode is valid against a list of known modes.

bool casa::AgentFlagger::open ( casacore::String  msname,
casacore::Double  ntime 
)

configure the tool, open the MS

AgentFlagger& casa::AgentFlagger::operator= ( const AgentFlagger )
inlineprivate

Definition at line 359 of file AgentFlagger.h.

bool casa::AgentFlagger::parseAgentParameters ( casacore::Record  agent_params)

parse the parameters of the agent

bool casa::AgentFlagger::parseAntIntParameters ( casacore::String  field,
casacore::String  spw,
casacore::String  array,
casacore::String  feed,
casacore::String  scan,
casacore::String  antenna,
casacore::String  uvrange,
casacore::String  timerange,
casacore::String  correlation,
casacore::String  intent,
casacore::String  observation,
casacore::String  antint_ref_antenna,
casacore::Double  minchanfrac,
casacore::Bool  verbose,
casacore::Bool  apply 
)

Parse parameters for the 'antint' mode (antenna integrations)

bool casa::AgentFlagger::parseClipParameters ( casacore::String  field,
casacore::String  spw,
casacore::String  array,
casacore::String  feed,
casacore::String  scan,
casacore::String  antenna,
casacore::String  uvrange,
casacore::String  timerange,
casacore::String  correlation,
casacore::String  intent,
casacore::String  observation,
casacore::String  datacolumn,
casacore::Vector< casacore::Double clipminmax,
casacore::Bool  clipoutside,
casacore::Bool  channelavg,
casac::variant  chanbin,
casacore::Bool  timeavg,
casacore::String  timebin,
casacore::Bool  clipzeros,
casacore::Bool  apply 
)

Parse parameters for clip.

bool casa::AgentFlagger::parseElevationParameters ( casacore::String  field,
casacore::String  spw,
casacore::String  array,
casacore::String  feed,
casacore::String  scan,
casacore::String  antenna,
casacore::String  uvrange,
casacore::String  timerange,
casacore::String  correlation,
casacore::String  intent,
casacore::String  observation,
casacore::Double  lowerlimit,
casacore::Double  upperlimit,
casacore::Bool  apply 
)

Parse parameters for elevation.

bool casa::AgentFlagger::parseExtendParameters ( casacore::String  field = "",
casacore::String  spw = "",
casacore::String  array = "",
casacore::String  feed = "",
casacore::String  scan = "",
casacore::String  antenna = "",
casacore::String  uvrange = "",
casacore::String  timerange = "",
casacore::String  correlation = "",
casacore::String  intent = "",
casacore::String  observation = "",
casacore::Double  ntime = 0.0,
casacore::Bool  combinescans = false,
casacore::Bool  extendpols = true,
casacore::Double  growtime = 50.0,
casacore::Double  growfreq = 50.0,
casacore::Bool  growaround = false,
casacore::Bool  flagneartime = false,
casacore::Bool  flagnearfreq = false,
casacore::Bool  apply = true 
)

Parse parameters for extend.

bool casa::AgentFlagger::parseManualParameters ( casacore::String  field,
casacore::String  spw,
casacore::String  array,
casacore::String  feed,
casacore::String  scan,
casacore::String  antenna,
casacore::String  uvrange,
casacore::String  timerange,
casacore::String  correlation,
casacore::String  intent,
casacore::String  observation,
casacore::Bool  autocorr,
casacore::Bool  apply 
)

Agent's specific parsing methods (for convenience only) Parse parameters for manual.

bool casa::AgentFlagger::parseQuackParameters ( casacore::String  field,
casacore::String  spw,
casacore::String  array,
casacore::String  feed,
casacore::String  scan,
casacore::String  antenna,
casacore::String  uvrange,
casacore::String  timerange,
casacore::String  correlation,
casacore::String  intent,
casacore::String  observation,
casacore::String  quackmode,
casacore::Double  quackinterval,
casacore::Bool  quackincrement,
casacore::Bool  apply 
)

Parse parameters for quack.

bool casa::AgentFlagger::parseSummaryParameters ( casacore::String  field,
casacore::String  spw,
casacore::String  array,
casacore::String  feed,
casacore::String  scan,
casacore::String  antenna,
casacore::String  uvrange,
casacore::String  timerange,
casacore::String  correlation,
casacore::String  intent,
casacore::String  observation,
casacore::Bool  spwchan,
casacore::Bool  spwcorr,
casacore::Bool  basecnt,
casacore::Bool  fieldcnt,
casacore::String  name 
)

Parse parameters for summary.

bool casa::AgentFlagger::parseTfcropParameters ( casacore::String  field,
casacore::String  spw,
casacore::String  array,
casacore::String  feed,
casacore::String  scan,
casacore::String  antenna,
casacore::String  uvrange,
casacore::String  timerange,
casacore::String  correlation,
casacore::String  intent,
casacore::String  observation,
casacore::Double  ntime,
casacore::Bool  combinescans,
casacore::String  datacolumn,
casacore::Double  timecutoff,
casacore::Double  freqcutoff,
casacore::String  timefit,
casacore::String  freqfit,
casacore::Int  maxnpieces,
casacore::String  flagdimension,
casacore::String  usewindowstats,
casacore::Int  halfwin,
casacore::Bool  extendflags,
casacore::Bool  apply,
casacore::Bool  channelavg,
casac::variant  chanbin,
casacore::Bool  timeavg,
casacore::String  timebin 
)

Parse parameters for tfcrop.

bool casa::AgentFlagger::printFlagSelections ( )

Flag backup methods.

bool casa::AgentFlagger::restoreFlagVersion ( casacore::Vector< casacore::String versionname,
casacore::String  merge 
)
casacore::Record casa::AgentFlagger::run ( casacore::Bool  writeflags,
casacore::Bool  sequential = true 
)

Run the tool and write the flags to the MS.

bool casa::AgentFlagger::saveFlagVersion ( casacore::String  versionname,
casacore::String  comment,
casacore::String  merge 
)
bool casa::AgentFlagger::selectData ( casacore::Record  selrec)

parse the data selection

bool casa::AgentFlagger::selectData ( casacore::String  field,
casacore::String  spw,
casacore::String  array,
casacore::String  feed,
casacore::String  scan,
casacore::String  antenna,
casacore::String  uvrange,
casacore::String  timerange,
casacore::String  correlation,
casacore::String  intent,
casacore::String  observation = "" 
)
casacore::Bool casa::AgentFlagger::validateDataColumn ( casacore::String  datacol)
private

Member Data Documentation

casacore::Record casa::AgentFlagger::agentParams_p
protected

Definition at line 241 of file AgentFlagger.h.

std::vector<casacore::Record> casa::AgentFlagger::agents_config_list_copy_p
protected

Definition at line 257 of file AgentFlagger.h.

std::vector<casacore::Record> casa::AgentFlagger::agents_config_list_p
protected

Definition at line 256 of file AgentFlagger.h.

FlagAgentList casa::AgentFlagger::agents_list_p
protected

Definition at line 258 of file AgentFlagger.h.

casacore::String casa::AgentFlagger::antenna_p
protected

Definition at line 229 of file AgentFlagger.h.

casacore::String casa::AgentFlagger::array_p
protected

Definition at line 234 of file AgentFlagger.h.

casacore::Bool casa::AgentFlagger::combinescans_p
protected

Definition at line 243 of file AgentFlagger.h.

casacore::String casa::AgentFlagger::correlation_p
protected

Definition at line 231 of file AgentFlagger.h.

casacore::Record casa::AgentFlagger::dataselection_p
protected

Definition at line 237 of file AgentFlagger.h.

const bool casa::AgentFlagger::dbg
staticprivate

Debug message flag.

Definition at line 373 of file AgentFlagger.h.

casa::FlagAgentDisplay* casa::AgentFlagger::displayAgent_p
protected

Display agent parameters.

Definition at line 251 of file AgentFlagger.h.

casacore::Bool casa::AgentFlagger::extendflags_p
protected

Definition at line 244 of file AgentFlagger.h.

FlagDataHandler* casa::AgentFlagger::fdh_p
protected

variables for initAgents

Definition at line 255 of file AgentFlagger.h.

casacore::String casa::AgentFlagger::feed_p
protected

Definition at line 233 of file AgentFlagger.h.

casacore::String casa::AgentFlagger::field_p
protected

Definition at line 228 of file AgentFlagger.h.

casacore::String casa::AgentFlagger::intent_p
protected

Definition at line 232 of file AgentFlagger.h.

casacore::Bool casa::AgentFlagger::isMS_p
protected

Definition at line 222 of file AgentFlagger.h.

casacore::uShort casa::AgentFlagger::iterationApproach_p
protected

Definition at line 220 of file AgentFlagger.h.

casacore::Bool casa::AgentFlagger::iterset_p
private

Definition at line 380 of file AgentFlagger.h.

casacore::LogSink casa::AgentFlagger::logSink_p
private

Sink used to store history.

Definition at line 370 of file AgentFlagger.h.

casacore::Double casa::AgentFlagger::max_p
private

Store the temporary maximum value.

Definition at line 376 of file AgentFlagger.h.

casacore::Bool casa::AgentFlagger::mixed_p
protected

true if there are apply and unapply parameters in the list

Definition at line 247 of file AgentFlagger.h.

casacore::String casa::AgentFlagger::mode_p
protected

agent's members

Definition at line 240 of file AgentFlagger.h.

casacore::String casa::AgentFlagger::msname_p
protected

variables used to initialize the FlagDataHandler

Definition at line 219 of file AgentFlagger.h.

casacore::String casa::AgentFlagger::observation_p
protected

Definition at line 236 of file AgentFlagger.h.

casacore::LogIO casa::AgentFlagger::os
staticprotected

Definition at line 216 of file AgentFlagger.h.

casacore::String casa::AgentFlagger::scan_p
protected

Definition at line 227 of file AgentFlagger.h.

casacore::String casa::AgentFlagger::spw_p
protected

members to parse to selectData

Definition at line 226 of file AgentFlagger.h.

FlagAgentSummary* casa::AgentFlagger::summaryAgent_p
protected

Definition at line 242 of file AgentFlagger.h.

casacore::Bool casa::AgentFlagger::timeAvg_p
private

casacore::Time average parameter in clip mode

Definition at line 383 of file AgentFlagger.h.

casacore::Double casa::AgentFlagger::timeInterval_p
protected

Definition at line 221 of file AgentFlagger.h.

casacore::String casa::AgentFlagger::timerange_p
protected

Definition at line 230 of file AgentFlagger.h.

casacore::Bool casa::AgentFlagger::timeset_p
private

Helper members.

Definition at line 379 of file AgentFlagger.h.

casacore::String casa::AgentFlagger::uvrange_p
protected

Definition at line 235 of file AgentFlagger.h.


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