source: trunk/src/STLineFinder.h@ 3123

Last change on this file since 3123 was 3106, checked in by Takeshi Nakazato, 8 years ago

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Check-in asap modifications from Jim regarding casacore namespace conversion.

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File size: 12.5 KB
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1//#---------------------------------------------------------------------------
2//# STLineFinder.h: A class for automated spectral line search
3//#---------------------------------------------------------------------------
4//# Copyright (C) 2004
5//# ATNF
6//#
7//# This program is free software; you can redistribute it and/or modify it
8//# under the terms of the GNU General Public License as published by the Free
9//# Software Foundation; either version 2 of the License, or (at your option)
10//# any later version.
11//#
12//# This program is distributed in the hope that it will be useful, but
13//# WITHOUT ANY WARRANTY; without even the implied warranty of
14//# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
15//# Public License for more details.
16//#
17//# You should have received a copy of the GNU General Public License along
18//# with this program; if not, write to the Free Software Foundation, Inc.,
19//# 675 Massachusetts Ave, Cambridge, MA 02139, USA.
20//#
21//# Correspondence concerning this software should be addressed as follows:
22//# Internet email: Malte.Marquarding@csiro.au
23//# Postal address: Malte Marquarding,
24//# Australia Telescope National Facility,
25//# P.O. Box 76,
26//# Epping, NSW, 2121,
27//# AUSTRALIA
28//#
29//# $Id: STLineFinder.h 3106 2016-10-04 07:20:50Z TakeshiNakazato $
30//#---------------------------------------------------------------------------
31#ifndef STLINEFINDER_H
32#define STLINEFINDER_H
33
34// ASAP
35#include "ScantableWrapper.h"
36#include "Scantable.h"
37
38// STL
39#include <vector>
40#include <list>
41#include <utility>
42#include <exception>
43
44// AIPS++
45#include <casa/aips.h>
46#include <casa/Exceptions/Error.h>
47#include <casa/Arrays/Vector.h>
48#include <casa/Utilities/Assert.h>
49#include <casa/Utilities/CountedPtr.h>
50
51namespace asap {
52
53///////////////////////////////////////////////////////////////////////////////
54//
55// LFLineListOperations - a class incapsulating operations with line lists
56// The LF prefix stands for Line Finder
57//
58
59struct LFLineListOperations {
60 // concatenate two lists preserving the order. If two lines appear to
61 // be adjacent or have a non-void intersection, they are joined into
62 // the new line
63 static void addNewSearchResult(const std::list<std::pair<int, int> >
64 &newlines, std::list<std::pair<int, int> > &lines_list);
65
66 // extend all line ranges to the point where a value stored in the
67 // specified vector changes (e.g. value-mean change its sign)
68 // This operation is necessary to include line wings, which are below
69 // the detection threshold. If lines becomes adjacent, they are
70 // merged together. Any masked channel stops the extension
71 static void searchForWings(std::list<std::pair<int, int> > &newlines,
72 const casacore::Vector<casacore::Int> &signs,
73 const casacore::Vector<casacore::Bool> &mask,
74 const std::pair<int,int> &edge);
75protected:
76
77 // An auxiliary object function to test whether two lines have a non-void
78 // intersection
79 class IntersectsWith : public std::unary_function<pair<int,int>, bool> {
80 std::pair<int,int> line1; // range of the first line
81 // start channel and stop+1
82 public:
83 explicit IntersectsWith(const std::pair<int,int> &in_line1);
84 // return true if line2 intersects with line1 with at least one
85 // common channel, and false otherwise
86 bool operator()(const std::pair<int,int> &line2) const;
87 };
88
89 // An auxiliary object function to build a union of several lines
90 // to account for a possibility of merging the nearby lines
91 class BuildUnion {
92 std::pair<int,int> temp_line; // range of the first line
93 // start channel and stop+1
94 public:
95 explicit BuildUnion(const std::pair<int,int> &line1);
96 // update temp_line with a union of temp_line and new_line
97 // provided there is no gap between the lines
98 void operator()(const std::pair<int,int> &new_line);
99 // return the result (temp_line)
100 const std::pair<int,int>& result() const;
101 };
102
103 // An auxiliary object function to test whether a specified line
104 // is at lower spectral channels (to preserve the order in the line list)
105 class LaterThan : public std::unary_function<pair<int,int>, bool> {
106 std::pair<int,int> line1; // range of the first line
107 // start channel and stop+1
108 public:
109 explicit LaterThan(const std::pair<int,int> &in_line1);
110
111 // return true if line2 should be placed later than line1
112 // in the ordered list (so, it is at greater channel numbers)
113 bool operator()(const std::pair<int,int> &line2) const;
114 };
115
116
117};
118
119//
120///////////////////////////////////////////////////////////////////////////////
121
122///////////////////////////////////////////////////////////////////////////////
123//
124// STLineFinder - a class for automated spectral line search
125//
126//
127
128struct STLineFinder : protected LFLineListOperations {
129 STLineFinder();
130 virtual ~STLineFinder();
131
132 // set the parameters controlling algorithm
133 // in_threshold a single channel threshold default is sqrt(3), which
134 // means together with 3 minimum channels at least 3 sigma
135 // detection criterion
136 // For bad baseline shape, in_threshold may need to be
137 // increased
138 // in_min_nchan minimum number of channels above the threshold to report
139 // a detection, default is 3
140 // in_avg_limit perform the averaging of no more than in_avg_limit
141 // adjacent channels to search for broad lines
142 // Default is 8, but for a bad baseline shape this
143 // parameter should be decreased (may be even down to a
144 // minimum of 1 to disable this option) to avoid
145 // confusing of baseline undulations with a real line.
146 // Setting a very large value doesn't usually provide
147 // valid detections.
148 // in_box_size the box size for running mean calculation. Default is
149 // 1./5. of the whole spectrum size
150 // in_noise_box the box size for off-line noise estimation (if working with
151 // local noise. Negative value means use global noise estimate
152 // Default is -1 (i.e. estimate using the whole spectrum)
153 // in_median true if median statistics is used as opposed to average of
154 // the lowest 80% of deviations (default)
155 void setOptions(const casacore::Float &in_threshold=sqrt(3.),
156 const casacore::Int &in_min_nchan=3,
157 const casacore::Int &in_avg_limit=8,
158 const casacore::Float &in_box_size=0.2,
159 const casacore::Float &in_noise_box=-1.,
160 const casacore::Bool &in_median = casacore::False);
161
162 void setDetailedOptions( const casacore::Int &order=9 ) ;
163
164 // set the scan to work with (in_scan parameter)
165 void setScan(const ScantableWrapper &in_scan);
166
167 // set spectrum data to work with. this is a method to allow linefinder work
168 // without setting scantable for the purpose of using linefinder inside some
169 // method in scantable class. (Dec. 22, 2010 by W.Kawasaki)
170 void setData(const std::vector<float> &in_spectrum);
171
172 // search for spectral lines in a row specified by whichRow
173 // in_mask and in_edge parameters control channel rejection
174 // if in_edge has zero length, all channels chosen by mask will be used
175 // if in_edge has one element only, it represents the number of
176 // channels to drop from both sides of the spectrum
177 // in_edge is introduced for convinience, although all functionality
178 // can be achieved using a spectrum mask only
179 // Number of lines found is returned
180 int findLines(const std::vector<bool> &in_mask,
181 const std::vector<int> &in_edge = std::vector<int>(),
182 const casacore::uInt &whichRow = 0);
183
184 // get the mask to mask out all lines that have been found (default)
185 // if invert=true, only channels belong to lines will be unmasked
186 // Note: all channels originally masked by the input mask (in_mask
187 // in setScan) or dropped out by the edge parameter (in_edge
188 // in setScan) are still excluded regardless on the invert option
189 std::vector<bool> getMask(bool invert=false) const;
190
191 // get range for all lines found. The same units as used in the scan
192 // will be returned (e.g. velocity instead of channels).
193 std::vector<double> getLineRanges() const;
194 // The same as getLineRanges, but channels are always used to specify
195 // the range
196 std::vector<int> getLineRangesInChannels() const;
197protected:
198 // auxiliary function to average adjacent channels and update the mask
199 // if at least one channel involved in summation is masked, all
200 // output channels will be masked. This function works with the
201 // spectrum and edge fields of this class, but updates the mask
202 // array specified, rather than the field of this class
203 // boxsize - a number of adjacent channels to average
204 void averageAdjacentChannels(casacore::Vector<casacore::Bool> &mask2update,
205 const casacore::Int &boxsize);
206
207 // auxiliary function to fit and subtract a polynomial from the current
208 // spectrum. It uses the Fitter class. This action is required before
209 // reducing the spectral resolution if the baseline shape is bad
210 void subtractBaseline(const casacore::Vector<casacore::Bool> &temp_mask,
211 const casacore::Int &order);
212
213 // an auxiliary function to remove all lines from the list, except the
214 // strongest one (by absolute value). If the lines removed are real,
215 // they will be find again at the next iteration. This approach
216 // increases the number of iterations required, but is able to remove
217 // the sidelobes likely to occur near strong lines.
218 // Later a better criterion may be implemented, e.g.
219 // taking into consideration the brightness of different lines. Now
220 // use the simplest solution
221 // temp_mask - mask to work with (may be different from original mask as
222 // the lines previously found may be masked)
223 // lines2update - a list of lines to work with
224 // nothing will be done if it is empty
225 // max_box_nchan - channels in the running box for baseline filtering
226 void keepStrongestOnly(const casacore::Vector<casacore::Bool> &temp_mask,
227 std::list<std::pair<int, int> > &lines2update,
228 int max_box_nchan);
229private:
230 casacore::CountedPtr<Scantable> scan; // the scan to work with
231 casacore::Vector<casacore::Bool> mask; // associated mask
232 std::pair<int,int> edge; // start and stop+1 channels
233 // to work with
234 casacore::Float threshold; // detection threshold - the
235 // minimal signal to noise ratio
236 casacore::Double box_size; // size of the box for running
237 // mean calculations, specified as
238 // a fraction of the whole spectrum
239 int min_nchan; // A minimum number of consequtive
240 // channels, which should satisfy
241 // the detection criterion, to be
242 // a detection
243 casacore::Int avg_limit; // perform the averaging of no
244 // more than in_avg_limit
245 // adjacent channels to search
246 // for broad lines. see setOptions
247 casacore::uInt last_row_used; // the Row number specified
248 // during the last findLines call
249 std::list<std::pair<int, int> > lines; // container of start and stop+1
250 // channels of the spectral lines
251 // a buffer for the spectrum
252 mutable casacore::Vector<casacore::Float> spectrum;
253
254 // the box size for off-line noise estimation (if working with
255 // local noise. Negative value means use global noise estimate
256 // Default is -1 (i.e. estimate using the whole spectrum)
257 casacore::Float itsNoiseBox;
258
259 // true if median statistics is used as opposed to average of
260 // the lowest 80% of deviations (default)
261 casacore::Bool itsUseMedian;
262
263 // true if spectra and mask data should be provided from
264 // scantable (default = true)
265 bool useScantable;
266
267 // shared object for nominal throw
268 casacore::AipsError err ;
269};
270
271//
272///////////////////////////////////////////////////////////////////////////////
273
274} // namespace asap
275#endif // #ifndef STLINEFINDER_H
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