casacore
MSFlagger.h
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1//# MSFlagger.h: this defines MSFlagger, which implement flagging/editing
2//# Copyright (C) 1997,1998,1999,2000
3//# Associated Universities, Inc. Washington DC, USA.
4//#
5//# This library is free software; you can redistribute it and/or modify it
6//# under the terms of the GNU Library General Public License as published by
7//# the Free Software Foundation; either version 2 of the License, or (at your
8//# option) any later version.
9//#
10//# This library is distributed in the hope that it will be useful, but WITHOUT
11//# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
12//# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Library General Public
13//# License for more details.
14//#
15//# You should have received a copy of the GNU Library General Public License
16//# along with this library; if not, write to the Free Software Foundation,
17//# Inc., 675 Massachusetts Ave, Cambridge, MA 02139, USA.
18//#
19//# Correspondence concerning AIPS++ should be addressed as follows:
20//# Internet email: aips2-request@nrao.edu.
21//# Postal address: AIPS++ Project Office
22//# National Radio Astronomy Observatory
23//# 520 Edgemont Road
24//# Charlottesville, VA 22903-2475 USA
25//#
26//#
27//# $Id$
28
29#ifndef MS_MSFLAGGER_H
30#define MS_MSFLAGGER_H
31
32#include <casacore/casa/aips.h>
33#include <casacore/casa/Arrays/ArrayFwd.h>
34#include <casacore/casa/Containers/Record.h>
35
36namespace casacore { //# NAMESPACE CASACORE - BEGIN
37
38class MSSelector;
39class Table;
40class String;
41
42// <summary>
43// MSFlagger specifies selections on a MeasurementSet
44// </summary>
45
46// <use visibility=export>
47
48// <reviewed reviewer="" date="yyyy/mm/dd" tests="" demos="">
49// </reviewed>
50
51// <prerequisite>
52// <li> MeasurementSet
53// <li> SomeOtherClass
54// <li> some concept
55// </prerequisite>
56//
57// <etymology>
58// MSFlagger is a class that sets flags in an MS
59// </etymology>
60//
61// <synopsis>
62// This class is used to change the flag and flag_history columns in
63// a MeasurementSet. It provides functions for automated flagging based on
64// clipping the data that is too far from the median value.
65// The ms DO uses this class to allow flagging from glish or a GUI.
66//
67// <example> <srcblock>
68// MSFlagger msFlagger(myMS);
69// </srcblock></example>
70// </synopsis>
71//
72// <motivation>
73// Flagging/editing of data is a central requirement in data processing, this
74// class provides some simple flagging algorithms and the code
75// that modifies & creates flag columns in the MS.
76// </motivation>
77//
78// <thrown>
79// <li>
80// <li>
81// </thrown>
82//
83// <todo asof="yyyy/mm/dd">
84// <li> add this feature
85// </todo>
86
88{
89public:
91
92 // construct from an MSSelector object
94
95 // Copy constructor
96 MSFlagger(const MSFlagger& other);
97
98 // Assignment
100
102
103 // Change or Set the MS this MSFlagger refers to.
105
106 // Fill an internal buffer with the data item requested, similar to getData
107 // except that the data is not returned, but kept around for further
108 // processing. Only a single DATA related quantity can be requested, the
109 // corresponding FLAG and FLAG_ROW columns are read automatically.
110 // Reorder the data to 4d with ifr and time axis if ifrAxis is True.
111 Bool fillDataBuffer(const String& item, Bool ifrAxis);
112
113 // Difference the data, subtracting the average over a window of
114 // specified width and taking the absolute value. Complex quantities are
115 // turned into the corresponding amplitude after differencing.
116 // If doMedian==True the median difference is returned for window>2.
117 // For a window width of one, the previous sample is
118 // subtracted, giving a derivative like quantity.
119 // Note that the subtraction is done on row-by-row basis for TIME
120 // differencing, it is up to you to select a single baseline (if
121 // you didn't use ifrAxis=True in fillDataBuffer).
122 // Available directions are: TIME, CHANNEL
123 // Returns statistics over the buffer: median for times and channels,
124 // average absolute deviation over times, channels and all pixels.
125 Record diffDataBuffer(const String& direction, Int window=1,
126 Bool doMedian = False);
127
128 // Return the contents of the internal data buffer, including the flags
129 // as a Record
131 { return buffer_p;}
132
133 // Clip the data buffer at a specified level by setting the corresponding
134 // flags in the buffer. The cliplevel is specified as a multiple of
135 // the average absolute deviations returned by diffDataBuffer.
136 // A value of zero or less will skip the corresponding clip operation.
137 // Clipping will be done repeatedly, recalculating the deviations, until
138 // no more points are clipped.
139 Bool clipDataBuffer(Float pixelLevel, Float timeLevel, Float channelLevel);
140
141 // Replace the flags in the buffer with those in the supplied record.
142 // This allows interactive flagging from glish to be written back to the
143 // buffer for subsequent operations. The record should contain a
144 // flag and flag_row field.
146
147 // Write the flags in the buffer back to the table
149
150 // Clear the internal data buffer, reclaiming memory
152 { buffer_p=Record(); return True;}
153
154 // Create the FLAG_HISTORY column and initialize it from the
155 // FLAG_ROW and FLAG columns. Returns False if FLAG_HISTORY already exists.
156 // The first flagging bit is filled with the flags as found in the MS,
157 // subsequent bits can be used for user generated flags.
159
160 // Apply the flags in the FLAG_HISTORY column to the FLAG and FLAG_ROW
161 // columns. Returns False if FLAG_HISTORY doesn't exist.
162 // The default argument will apply the currently active flag level
163 // (as specified by the FLAG_LEVEL column keyword).
164 // Sets the current level to the flag level restored.
166
167 // Save the current flags to the FLAG_HISTORY. Save to the currently
168 // active level or (newLevel=True) the next highest level (if available).
169 // Will reset the current level to the level saved to.
170 Bool saveFlags(Bool newLevel);
171
172 // Return the current flaglevel (value of FLAG_LEVEL keyword)
174
175protected:
176 // fill the FLAG_HISTORY column from the FLAG and FLAG_ROW column
177 void fillFlagHist(Int nHis, Int numCorr, Int numChan, Table& tab);
178
179 // find the HypercubeId column for a tiled column (if any)
180 Bool findHypercubeId(String& hyperCubeId, const String& column,
181 const Table& tab);
182
183 // copy the flags to the flag history
184 void saveToFlagHist(Int level, Table& tab);
185
186 // copy the flag history back to the flags
187 void applyFlagHist(Int level, Table& tab);
188
189 // get buffer statistics - med=median, ad=average absolute deviation,
190 // T=Time, F=Frequency.
191 void getStats(Array<Float>& medTF, Array<Float>& adTF,
192 Array<Float>& medT, Array<Float>& medFmedT,
193 Array<Float>& adT, Array<Float>& medF,
194 Array<Float>& medTmedF, Array<Float>& adF,
195 const Array<Float>& diff, const Array<Bool>& flag,
196 const Array<Bool>& flagRow);
197
198 // add the statistics to a buffer
199 void addStats(Record& buf, const Array<Bool>& flag,
200 const Array<Bool> flagRow, const Array<Float>& data);
201
202 // reorder from 2d to 1d (removing ifr axis)
204
205 // collapse array "in" (with absolute differences)
206 // along specified axis by taking medians by profile taking into account
207 // the flags.
208 void diffMedian(Array<Float>& out, const Array<Float>& in,
209 Int axis, const Array<Bool>& flag);
210
211 // apply the row flags to the data flags and v.v.
212 void applyRowFlags(Array<Bool>& flag, Array<Bool>& flagRow);
213
214 // check if we are attached to an MSSelector
216
217private:
220};
221
222
223} //# NAMESPACE CASACORE - END
224
225#endif
226
227
228
229
230
231
232
void setMSSelector(MSSelector &msSel)
Change or Set the MS this MSFlagger refers to.
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 ...
Bool saveFlags(Bool newLevel)
Save the current flags to the FLAG_HISTORY.
Bool restoreFlags(Int level=-1)
Apply the flags in the FLAG_HISTORY column to the FLAG and FLAG_ROW columns.
MSSelector * msSel_p
Definition: MSFlagger.h:218
Bool writeDataBufferFlags()
Write the flags in the buffer back to the table.
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 tak...
MSFlagger & operator=(const MSFlagger &other)
Assignment.
Bool findHypercubeId(String &hyperCubeId, const String &column, const Table &tab)
find the HypercubeId column for a tiled column (if any)
void applyRowFlags(Array< Bool > &flag, Array< Bool > &flagRow)
apply the row flags to the data flags and v.v.
Bool createFlagHistory(Int nHis=2)
Create the FLAG_HISTORY column and initialize it from the FLAG_ROW and FLAG columns.
void addStats(Record &buf, const Array< Bool > &flag, const Array< Bool > flagRow, const Array< Float > &data)
add the statistics to a buffer
void fillFlagHist(Int nHis, Int numCorr, Int numChan, Table &tab)
fill the FLAG_HISTORY column from the FLAG and FLAG_ROW column
Bool check()
check if we are attached to an MSSelector
void saveToFlagHist(Int level, Table &tab)
copy the flags to the flag history
MSFlagger(const MSFlagger &other)
Copy constructor.
MSFlagger(MSSelector &msSel)
construct from an MSSelector object
Bool clearDataBuffer()
Clear the internal data buffer, reclaiming memory.
Definition: MSFlagger.h:151
void applyFlagHist(Int level, Table &tab)
copy the flag history back to the flags
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...
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.
Int flagLevel()
Return the current flaglevel (value of FLAG_LEVEL keyword)
void reorderFlagRow(Array< Bool > &flagRow)
reorder from 2d to 1d (removing ifr axis)
Record getDataBuffer()
Return the contents of the internal data buffer, including the flags as a Record.
Definition: MSFlagger.h:130
Bool clipDataBuffer(Float pixelLevel, Float timeLevel, Float channelLevel)
Clip the data buffer at a specified level by setting the corresponding flags in the buffer.
Bool setDataBufferFlags(const Record &flags)
Replace the flags in the buffer with those in the supplied record.
String: the storage and methods of handling collections of characters.
Definition: String.h:225
this file contains all the compiler specific defines
Definition: mainpage.dox:28
const Bool False
Definition: aipstype.h:44
float Float
Definition: aipstype.h:54
int Int
Definition: aipstype.h:50
bool Bool
Define the standard types used by Casacore.
Definition: aipstype.h:42
const Bool True
Definition: aipstype.h:43