source: branches/newfiller/src/STLineFinder.h@ 2591

Last change on this file since 2591 was 1757, checked in by Kana Sugimoto, 14 years ago

New Development: Yes

JIRA Issue: Yes (CAS-2211)

Ready for Test: Yes

Interface Changes: Yes

What Interface Changed: ASAP 3.0.0 interface changes

Test Programs:

Put in Release Notes: Yes

Module(s): all the CASA sd tools and tasks are affected.

Description: Merged ATNF-ASAP 3.0.0 developments to CASA (alma) branch.

Note you also need to update casa/code/atnf.


  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 12.2 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 1757 2010-06-09 09:03:06Z KanaSugimoto $
30//#---------------------------------------------------------------------------
31#ifndef STLINEFINDER_H
32#define STLINEFINDER_H
33
34// STL
35#include <vector>
36#include <list>
37#include <utility>
38#include <exception>
39
40// AIPS++
41#include <casa/aips.h>
42#include <casa/Exceptions/Error.h>
43#include <casa/Arrays/Vector.h>
44#include <casa/Utilities/Assert.h>
45#include <casa/Utilities/CountedPtr.h>
46
47// ASAP
48#include "ScantableWrapper.h"
49#include "Scantable.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 throw(casa::AipsError);
66
67 // extend all line ranges to the point where a value stored in the
68 // specified vector changes (e.g. value-mean change its sign)
69 // This operation is necessary to include line wings, which are below
70 // the detection threshold. If lines becomes adjacent, they are
71 // merged together. Any masked channel stops the extension
72 static void searchForWings(std::list<std::pair<int, int> > &newlines,
73 const casa::Vector<casa::Int> &signs,
74 const casa::Vector<casa::Bool> &mask,
75 const std::pair<int,int> &edge)
76 throw(casa::AipsError);
77protected:
78
79 // An auxiliary object function to test whether two lines have a non-void
80 // intersection
81 class IntersectsWith : public std::unary_function<pair<int,int>, bool> {
82 std::pair<int,int> line1; // range of the first line
83 // start channel and stop+1
84 public:
85 explicit IntersectsWith(const std::pair<int,int> &in_line1);
86 // return true if line2 intersects with line1 with at least one
87 // common channel, and false otherwise
88 bool operator()(const std::pair<int,int> &line2) const throw();
89 };
90
91 // An auxiliary object function to build a union of several lines
92 // to account for a possibility of merging the nearby lines
93 class BuildUnion {
94 std::pair<int,int> temp_line; // range of the first line
95 // start channel and stop+1
96 public:
97 explicit BuildUnion(const std::pair<int,int> &line1);
98 // update temp_line with a union of temp_line and new_line
99 // provided there is no gap between the lines
100 void operator()(const std::pair<int,int> &new_line) throw();
101 // return the result (temp_line)
102 const std::pair<int,int>& result() const throw();
103 };
104
105 // An auxiliary object function to test whether a specified line
106 // is at lower spectral channels (to preserve the order in the line list)
107 class LaterThan : public std::unary_function<pair<int,int>, bool> {
108 std::pair<int,int> line1; // range of the first line
109 // start channel and stop+1
110 public:
111 explicit LaterThan(const std::pair<int,int> &in_line1);
112
113 // return true if line2 should be placed later than line1
114 // in the ordered list (so, it is at greater channel numbers)
115 bool operator()(const std::pair<int,int> &line2) const throw();
116 };
117
118
119};
120
121//
122///////////////////////////////////////////////////////////////////////////////
123
124///////////////////////////////////////////////////////////////////////////////
125//
126// STLineFinder - a class for automated spectral line search
127//
128//
129
130struct STLineFinder : protected LFLineListOperations {
131 STLineFinder() throw();
132 virtual ~STLineFinder() throw(casa::AipsError);
133
134 // set the parameters controlling algorithm
135 // in_threshold a single channel threshold default is sqrt(3), which
136 // means together with 3 minimum channels at least 3 sigma
137 // detection criterion
138 // For bad baseline shape, in_threshold may need to be
139 // increased
140 // in_min_nchan minimum number of channels above the threshold to report
141 // a detection, default is 3
142 // in_avg_limit perform the averaging of no more than in_avg_limit
143 // adjacent channels to search for broad lines
144 // Default is 8, but for a bad baseline shape this
145 // parameter should be decreased (may be even down to a
146 // minimum of 1 to disable this option) to avoid
147 // confusing of baseline undulations with a real line.
148 // Setting a very large value doesn't usually provide
149 // valid detections.
150 // in_box_size the box size for running mean calculation. Default is
151 // 1./5. of the whole spectrum size
152 // in_noise_box the box size for off-line noise estimation (if working with
153 // local noise. Negative value means use global noise estimate
154 // Default is -1 (i.e. estimate using the whole spectrum)
155 // in_median true if median statistics is used as opposed to average of
156 // the lowest 80% of deviations (default)
157 void setOptions(const casa::Float &in_threshold=sqrt(3.),
158 const casa::Int &in_min_nchan=3,
159 const casa::Int &in_avg_limit=8,
160 const casa::Float &in_box_size=0.2,
161 const casa::Float &in_noise_box=-1.,
162 const casa::Bool &in_median = casa::False) throw();
163
164 // set the scan to work with (in_scan parameter)
165 void setScan(const ScantableWrapper &in_scan) throw(casa::AipsError);
166
167 // search for spectral lines in a row specified by whichRow
168 // in_mask and in_edge parameters control channel rejection
169 // if in_edge has zero length, all channels chosen by mask will be used
170 // if in_edge has one element only, it represents the number of
171 // channels to drop from both sides of the spectrum
172 // in_edge is introduced for convinience, although all functionality
173 // can be achieved using a spectrum mask only
174 // Number of lines found is returned
175 int findLines(const std::vector<bool> &in_mask,
176 const std::vector<int> &in_edge = std::vector<int>(),
177 const casa::uInt &whichRow = 0) throw(casa::AipsError);
178
179 // get the mask to mask out all lines that have been found (default)
180 // if invert=true, only channels belong to lines will be unmasked
181 // Note: all channels originally masked by the input mask (in_mask
182 // in setScan) or dropped out by the edge parameter (in_edge
183 // in setScan) are still excluded regardless on the invert option
184 std::vector<bool> getMask(bool invert=false) const throw(casa::AipsError);
185
186 // get range for all lines found. The same units as used in the scan
187 // will be returned (e.g. velocity instead of channels).
188 std::vector<double> getLineRanges() const throw(casa::AipsError);
189 // The same as getLineRanges, but channels are always used to specify
190 // the range
191 std::vector<int> getLineRangesInChannels() const throw(casa::AipsError);
192protected:
193 // auxiliary function to average adjacent channels and update the mask
194 // if at least one channel involved in summation is masked, all
195 // output channels will be masked. This function works with the
196 // spectrum and edge fields of this class, but updates the mask
197 // array specified, rather than the field of this class
198 // boxsize - a number of adjacent channels to average
199 void averageAdjacentChannels(casa::Vector<casa::Bool> &mask2update,
200 const casa::Int &boxsize)
201 throw(casa::AipsError);
202
203 // auxiliary function to fit and subtract a polynomial from the current
204 // spectrum. It uses the Fitter class. This action is required before
205 // reducing the spectral resolution if the baseline shape is bad
206 void subtractBaseline(const casa::Vector<casa::Bool> &temp_mask,
207 const casa::Int &order) throw(casa::AipsError);
208
209 // an auxiliary function to remove all lines from the list, except the
210 // strongest one (by absolute value). If the lines removed are real,
211 // they will be find again at the next iteration. This approach
212 // increases the number of iterations required, but is able to remove
213 // the sidelobes likely to occur near strong lines.
214 // Later a better criterion may be implemented, e.g.
215 // taking into consideration the brightness of different lines. Now
216 // use the simplest solution
217 // temp_mask - mask to work with (may be different from original mask as
218 // the lines previously found may be masked)
219 // lines2update - a list of lines to work with
220 // nothing will be done if it is empty
221 // max_box_nchan - channels in the running box for baseline filtering
222 void keepStrongestOnly(const casa::Vector<casa::Bool> &temp_mask,
223 std::list<std::pair<int, int> > &lines2update,
224 int max_box_nchan)
225 throw (casa::AipsError);
226private:
227 casa::CountedConstPtr<Scantable> scan; // the scan to work with
228 casa::Vector<casa::Bool> mask; // associated mask
229 std::pair<int,int> edge; // start and stop+1 channels
230 // to work with
231 casa::Float threshold; // detection threshold - the
232 // minimal signal to noise ratio
233 casa::Double box_size; // size of the box for running
234 // mean calculations, specified as
235 // a fraction of the whole spectrum
236 int min_nchan; // A minimum number of consequtive
237 // channels, which should satisfy
238 // the detection criterion, to be
239 // a detection
240 casa::Int avg_limit; // perform the averaging of no
241 // more than in_avg_limit
242 // adjacent channels to search
243 // for broad lines. see setOptions
244 casa::uInt last_row_used; // the Row number specified
245 // during the last findLines call
246 std::list<std::pair<int, int> > lines; // container of start and stop+1
247 // channels of the spectral lines
248 // a buffer for the spectrum
249 mutable casa::Vector<casa::Float> spectrum;
250
251 // the box size for off-line noise estimation (if working with
252 // local noise. Negative value means use global noise estimate
253 // Default is -1 (i.e. estimate using the whole spectrum)
254 casa::Float itsNoiseBox;
255
256 // true if median statistics is used as opposed to average of
257 // the lowest 80% of deviations (default)
258 casa::Bool itsUseMedian;
259};
260
261//
262///////////////////////////////////////////////////////////////////////////////
263
264} // namespace asap
265#endif // #ifndef STLINEFINDER_H
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