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casacore::MSFlagger Class Reference

MSFlagger specifies selections on a MeasurementSet. More...

#include <MSFlagger.h>

Public Member Functions

 MSFlagger ()
 
 MSFlagger (MSSelector &msSel)
 construct from an MSSelector object More...
 
 MSFlagger (const MSFlagger &other)
 Copy constructor. More...
 
MSFlaggeroperator= (const MSFlagger &other)
 Assignment. More...
 
 ~MSFlagger ()
 
void setMSSelector (MSSelector &msSel)
 Change or Set the MS this MSFlagger refers to. More...
 
Bool fillDataBuffer (const String &item, Bool ifrAxis)
 Fill an internal buffer with the data item requested, similar to getData except that the data is not returned, but kept around for further processing. More...
 
Record diffDataBuffer (const String &direction, Int window=1, Bool doMedian=False)
 Difference the data, subtracting the average over a window of specified width and taking the absolute value. More...
 
Record getDataBuffer ()
 Return the contents of the internal data buffer, including the flags as a Record. More...
 
Bool clipDataBuffer (Float pixelLevel, Float timeLevel, Float channelLevel)
 Clip the data buffer at a specified level by setting the corresponding flags in the buffer. More...
 
Bool setDataBufferFlags (const Record &flags)
 Replace the flags in the buffer with those in the supplied record. More...
 
Bool writeDataBufferFlags ()
 Write the flags in the buffer back to the table. More...
 
Bool clearDataBuffer ()
 Clear the internal data buffer, reclaiming memory. More...
 
Bool createFlagHistory (Int nHis=2)
 Create the FLAG_HISTORY column and initialize it from the FLAG_ROW and FLAG columns. More...
 
Bool restoreFlags (Int level=-1)
 Apply the flags in the FLAG_HISTORY column to the FLAG and FLAG_ROW columns. More...
 
Bool saveFlags (Bool newLevel)
 Save the current flags to the FLAG_HISTORY. More...
 
Int flagLevel ()
 Return the current flaglevel (value of FLAG_LEVEL keyword) More...
 

Protected Member Functions

void fillFlagHist (Int nHis, Int numCorr, Int numChan, Table &tab)
 fill the FLAG_HISTORY column from the FLAG and FLAG_ROW column More...
 
Bool findHypercubeId (String &hyperCubeId, const String &column, const Table &tab)
 find the HypercubeId column for a tiled column (if any) More...
 
void saveToFlagHist (Int level, Table &tab)
 copy the flags to the flag history More...
 
void applyFlagHist (Int level, Table &tab)
 copy the flag history back to the flags More...
 
void getStats (Array< Float > &medTF, Array< Float > &adTF, Array< Float > &medT, Array< Float > &medFmedT, Array< Float > &adT, Array< Float > &medF, Array< Float > &medTmedF, Array< Float > &adF, const Array< Float > &diff, const Array< Bool > &flag, const Array< Bool > &flagRow)
 get buffer statistics - med=median, ad=average absolute deviation, T=Time, F=Frequency. More...
 
void addStats (Record &buf, const Array< Bool > &flag, const Array< Bool > flagRow, const Array< Float > &data)
 add the statistics to a buffer More...
 
void reorderFlagRow (Array< Bool > &flagRow)
 reorder from 2d to 1d (removing ifr axis) More...
 
void diffMedian (Array< Float > &out, const Array< Float > &in, Int axis, const Array< Bool > &flag)
 collapse array "in" (with absolute differences) along specified axis by taking medians by profile taking into account the flags. More...
 
void applyRowFlags (Array< Bool > &flag, Array< Bool > &flagRow)
 apply the row flags to the data flags and v.v. More...
 
Bool check ()
 check if we are attached to an MSSelector More...
 

Private Attributes

MSSelectormsSel_p
 
Record buffer_p
 

Detailed Description

MSFlagger specifies selections on a MeasurementSet.

Intended use:

Public interface

Review Status

Date Reviewed:
yyyy/mm/dd

Prerequisite

Etymology

MSFlagger is a class that sets flags in an MS

Synopsis

This class is used to change the flag and flag_history columns in a MeasurementSet. It provides functions for automated flagging based on clipping the data that is too far from the median value. The ms DO uses this class to allow flagging from glish or a GUI.

Example

MSFlagger msFlagger(myMS);

Motivation

Flagging/editing of data is a central requirement in data processing, this class provides some simple flagging algorithms and the code that modifies & creates flag columns in the MS.

Thrown Exceptions

To Do

Definition at line 87 of file MSFlagger.h.

Constructor & Destructor Documentation

casacore::MSFlagger::MSFlagger ( )
casacore::MSFlagger::MSFlagger ( MSSelector msSel)

construct from an MSSelector object

casacore::MSFlagger::MSFlagger ( const MSFlagger other)

Copy constructor.

casacore::MSFlagger::~MSFlagger ( )

Member Function Documentation

void casacore::MSFlagger::addStats ( Record buf,
const Array< Bool > &  flag,
const Array< Bool flagRow,
const Array< Float > &  data 
)
protected

add the statistics to a buffer

void casacore::MSFlagger::applyFlagHist ( Int  level,
Table tab 
)
protected

copy the flag history back to the flags

void casacore::MSFlagger::applyRowFlags ( Array< Bool > &  flag,
Array< Bool > &  flagRow 
)
protected

apply the row flags to the data flags and v.v.

Bool casacore::MSFlagger::check ( )
protected

check if we are attached to an MSSelector

Bool casacore::MSFlagger::clearDataBuffer ( )
inline

Clear the internal data buffer, reclaiming memory.

Definition at line 151 of file MSFlagger.h.

References buffer_p, and casacore::True.

Bool casacore::MSFlagger::clipDataBuffer ( Float  pixelLevel,
Float  timeLevel,
Float  channelLevel 
)

Clip the data buffer at a specified level by setting the corresponding flags in the buffer.

The cliplevel is specified as a multiple of the average absolute deviations returned by diffDataBuffer. A value of zero or less will skip the corresponding clip operation. Clipping will be done repeatedly, recalculating the deviations, until no more points are clipped.

Bool casacore::MSFlagger::createFlagHistory ( Int  nHis = 2)

Create the FLAG_HISTORY column and initialize it from the FLAG_ROW and FLAG columns.

Returns False if FLAG_HISTORY already exists. The first flagging bit is filled with the flags as found in the MS, subsequent bits can be used for user generated flags.

Record casacore::MSFlagger::diffDataBuffer ( const String direction,
Int  window = 1,
Bool  doMedian = False 
)

Difference the data, subtracting the average over a window of specified width and taking the absolute value.

Complex quantities are turned into the corresponding amplitude after differencing. If doMedian==True the median difference is returned for window>2. For a window width of one, the previous sample is subtracted, giving a derivative like quantity. Note that the subtraction is done on row-by-row basis for TIME differencing, it is up to you to select a single baseline (if you didn't use ifrAxis=True in fillDataBuffer). Available directions are: TIME, CHANNEL Returns statistics over the buffer: median for times and channels, average absolute deviation over times, channels and all pixels.

void casacore::MSFlagger::diffMedian ( Array< Float > &  out,
const Array< Float > &  in,
Int  axis,
const Array< Bool > &  flag 
)
protected

collapse array "in" (with absolute differences) along specified axis by taking medians by profile taking into account the flags.

Bool casacore::MSFlagger::fillDataBuffer ( const String item,
Bool  ifrAxis 
)

Fill an internal buffer with the data item requested, similar to getData except that the data is not returned, but kept around for further processing.

Only a single DATA related quantity can be requested, the corresponding FLAG and FLAG_ROW columns are read automatically. Reorder the data to 4d with ifr and time axis if ifrAxis is True.

void casacore::MSFlagger::fillFlagHist ( Int  nHis,
Int  numCorr,
Int  numChan,
Table tab 
)
protected

fill the FLAG_HISTORY column from the FLAG and FLAG_ROW column

Bool casacore::MSFlagger::findHypercubeId ( String hyperCubeId,
const String column,
const Table tab 
)
protected

find the HypercubeId column for a tiled column (if any)

Int casacore::MSFlagger::flagLevel ( )

Return the current flaglevel (value of FLAG_LEVEL keyword)

Record casacore::MSFlagger::getDataBuffer ( )
inline

Return the contents of the internal data buffer, including the flags as a Record.

Definition at line 130 of file MSFlagger.h.

References buffer_p.

void casacore::MSFlagger::getStats ( Array< Float > &  medTF,
Array< Float > &  adTF,
Array< Float > &  medT,
Array< Float > &  medFmedT,
Array< Float > &  adT,
Array< Float > &  medF,
Array< Float > &  medTmedF,
Array< Float > &  adF,
const Array< Float > &  diff,
const Array< Bool > &  flag,
const Array< Bool > &  flagRow 
)
protected

get buffer statistics - med=median, ad=average absolute deviation, T=Time, F=Frequency.

MSFlagger& casacore::MSFlagger::operator= ( const MSFlagger other)

Assignment.

void casacore::MSFlagger::reorderFlagRow ( Array< Bool > &  flagRow)
protected

reorder from 2d to 1d (removing ifr axis)

Bool casacore::MSFlagger::restoreFlags ( Int  level = -1)

Apply the flags in the FLAG_HISTORY column to the FLAG and FLAG_ROW columns.

Returns False if FLAG_HISTORY doesn't exist. The default argument will apply the currently active flag level (as specified by the FLAG_LEVEL column keyword). Sets the current level to the flag level restored.

Bool casacore::MSFlagger::saveFlags ( Bool  newLevel)

Save the current flags to the FLAG_HISTORY.

Save to the currently active level or (newLevel=True) the next highest level (if available). Will reset the current level to the level saved to.

void casacore::MSFlagger::saveToFlagHist ( Int  level,
Table tab 
)
protected

copy the flags to the flag history

Bool casacore::MSFlagger::setDataBufferFlags ( const Record flags)

Replace the flags in the buffer with those in the supplied record.

This allows interactive flagging from glish to be written back to the buffer for subsequent operations. The record should contain a flag and flag_row field.

void casacore::MSFlagger::setMSSelector ( MSSelector msSel)

Change or Set the MS this MSFlagger refers to.

Bool casacore::MSFlagger::writeDataBufferFlags ( )

Write the flags in the buffer back to the table.

Member Data Documentation

Record casacore::MSFlagger::buffer_p
private

Definition at line 219 of file MSFlagger.h.

Referenced by clearDataBuffer(), and getDataBuffer().

MSSelector* casacore::MSFlagger::msSel_p
private

Definition at line 218 of file MSFlagger.h.


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