/usr/include/casacore/ms/MSOper/MSFlagger.h is in casacore-dev 2.2.0-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 | //# MSFlagger.h: this defines MSFlagger, which implement flagging/editing
//# Copyright (C) 1997,1998,1999,2000
//# Associated Universities, Inc. Washington DC, USA.
//#
//# This library is free software; you can redistribute it and/or modify it
//# under the terms of the GNU Library General Public License as published by
//# the Free Software Foundation; either version 2 of the License, or (at your
//# option) any later version.
//#
//# This library is distributed in the hope that it will be useful, but WITHOUT
//# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
//# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Library General Public
//# License for more details.
//#
//# You should have received a copy of the GNU Library General Public License
//# along with this library; if not, write to the Free Software Foundation,
//# Inc., 675 Massachusetts Ave, Cambridge, MA 02139, USA.
//#
//# Correspondence concerning AIPS++ should be addressed as follows:
//# Internet email: aips2-request@nrao.edu.
//# Postal address: AIPS++ Project Office
//# National Radio Astronomy Observatory
//# 520 Edgemont Road
//# Charlottesville, VA 22903-2475 USA
//#
//#
//# $Id$
#ifndef MS_MSFLAGGER_H
#define MS_MSFLAGGER_H
#include <casacore/casa/aips.h>
#include <casacore/casa/Containers/Record.h>
namespace casacore { //# NAMESPACE CASACORE - BEGIN
template <class T> class Array;
class MSSelector;
class Table;
class String;
// <summary>
// MSFlagger specifies selections on a MeasurementSet
// </summary>
// <use visibility=export>
// <reviewed reviewer="" date="yyyy/mm/dd" tests="" demos="">
// </reviewed>
// <prerequisite>
// <li> MeasurementSet
// <li> SomeOtherClass
// <li> some concept
// </prerequisite>
//
// <etymology>
// MSFlagger is a class that sets flags in an MS
// </etymology>
//
// <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> <srcblock>
// MSFlagger msFlagger(myMS);
// </srcblock></example>
// </synopsis>
//
// <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.
// </motivation>
//
// <thrown>
// <li>
// <li>
// </thrown>
//
// <todo asof="yyyy/mm/dd">
// <li> add this feature
// </todo>
class MSFlagger
{
public:
MSFlagger();
// construct from an MSSelector object
MSFlagger(MSSelector& msSel);
// Copy constructor
MSFlagger(const MSFlagger& other);
// Assignment
MSFlagger& operator=(const MSFlagger& other);
~MSFlagger();
// Change or Set the MS this MSFlagger refers to.
void setMSSelector(MSSelector& msSel);
// 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.
Bool fillDataBuffer(const String& item, Bool ifrAxis);
// 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.
Record diffDataBuffer(const String& direction, Int window=1,
Bool doMedian = False);
// Return the contents of the internal data buffer, including the flags
// as a Record
Record getDataBuffer()
{ return buffer_p;}
// 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 clipDataBuffer(Float pixelLevel, Float timeLevel, Float channelLevel);
// 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.
Bool setDataBufferFlags(const Record& flags);
// Write the flags in the buffer back to the table
Bool writeDataBufferFlags();
// Clear the internal data buffer, reclaiming memory
Bool clearDataBuffer()
{ buffer_p=Record(); return True;}
// 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.
Bool createFlagHistory(Int nHis = 2);
// 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 restoreFlags(Int level=-1);
// 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.
Bool saveFlags(Bool newLevel);
// Return the current flaglevel (value of FLAG_LEVEL keyword)
Int flagLevel();
protected:
// fill the FLAG_HISTORY column from the FLAG and FLAG_ROW column
void fillFlagHist(Int nHis, Int numCorr, Int numChan, Table& tab);
// find the HypercubeId column for a tiled column (if any)
Bool findHypercubeId(String& hyperCubeId, const String& column,
const Table& tab);
// copy the flags to the flag history
void saveToFlagHist(Int level, Table& tab);
// copy the flag history back to the flags
void applyFlagHist(Int level, Table& tab);
// get buffer statistics - med=median, ad=average absolute deviation,
// T=Time, F=Frequency.
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);
// add the statistics to a buffer
void addStats(Record& buf, const Array<Bool>& flag,
const Array<Bool> flagRow, const Array<Float>& data);
// reorder from 2d to 1d (removing ifr axis)
void reorderFlagRow(Array<Bool>& flagRow);
// collapse array "in" (with absolute differences)
// along specified axis by taking medians by profile taking into account
// the flags.
void diffMedian(Array<Float>& out, const Array<Float>& in,
Int axis, const Array<Bool>& flag);
// apply the row flags to the data flags and v.v.
void applyRowFlags(Array<Bool>& flag, Array<Bool>& flagRow);
// check if we are attached to an MSSelector
Bool check();
private:
MSSelector* msSel_p;
Record buffer_p;
};
} //# NAMESPACE CASACORE - END
#endif
|