1 | //#--------------------------------------------------------------------------- |
---|
2 | //# SDLineFinder.cc: 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: |
---|
30 | //#--------------------------------------------------------------------------- |
---|
31 | |
---|
32 | |
---|
33 | // ASAP |
---|
34 | #include "SDLineFinder.h" |
---|
35 | |
---|
36 | // STL |
---|
37 | #include <iostream> |
---|
38 | |
---|
39 | using namespace asap; |
---|
40 | using namespace casa; |
---|
41 | using namespace std; |
---|
42 | using namespace boost::python; |
---|
43 | |
---|
44 | // SDLineFinder - a class for automated spectral line search |
---|
45 | |
---|
46 | SDLineFinder::SDLineFinder() throw() : edge(0,0) |
---|
47 | { |
---|
48 | // detection threshold - the minimal signal to noise ratio |
---|
49 | threshold=3.; // 3 sigma is a default |
---|
50 | box_size=1./16.; // default box size for running mean calculations is |
---|
51 | // 1/16 of the whole spectrum |
---|
52 | // A minimum number of consequtive channels, which should satisfy |
---|
53 | // the detection criterion, to be a detection |
---|
54 | min_nchan=3; // default is 3 channels |
---|
55 | } |
---|
56 | |
---|
57 | SDLineFinder::~SDLineFinder() throw(AipsError) {} |
---|
58 | |
---|
59 | // set scan to work with (in_scan parameter), associated mask (in_mask |
---|
60 | // parameter) and the edge channel rejection (in_edge parameter) |
---|
61 | // if in_edge has zero length, all channels chosen by mask will be used |
---|
62 | // if in_edge has one element only, it represents the number of |
---|
63 | // channels to drop from both sides of the spectrum |
---|
64 | // in_edge is introduced for convinience, although all functionality |
---|
65 | // can be achieved using a spectrum mask only |
---|
66 | void SDLineFinder::setScan(const SDMemTableWrapper &in_scan, |
---|
67 | const std::vector<bool> &in_mask, |
---|
68 | const boost::python::tuple &in_edge) throw(AipsError) |
---|
69 | { |
---|
70 | try { |
---|
71 | scan=in_scan.getCP(); |
---|
72 | AlwaysAssert(!scan.null(),AipsError); |
---|
73 | if (scan->nRow()!=1) |
---|
74 | throw AipsError("SDLineFinder::setScan - in_scan contains more than 1 row." |
---|
75 | "Choose one first."); |
---|
76 | mask=in_mask; |
---|
77 | if (mask.nelements()!=scan->nChan()) |
---|
78 | throw AipsError("SDLineFinder::setScan - in_scan and in_mask have different" |
---|
79 | "number of spectral channels."); |
---|
80 | |
---|
81 | // number of elements in the in_edge tuple |
---|
82 | int n=extract<int>(in_edge.attr("__len__")()); |
---|
83 | if (n>2 || n<0) |
---|
84 | throw AipsError("SDLineFinder::setScan - the length of the in_edge parameter" |
---|
85 | "should not exceed 2"); |
---|
86 | if (!n) { |
---|
87 | // all spectrum, no rejection |
---|
88 | edge.first=0; |
---|
89 | edge.second=scan->nChan(); |
---|
90 | } else { |
---|
91 | edge.first=extract<int>(in_edge.attr("__getitem__")(0)); |
---|
92 | if (edge.first<0) |
---|
93 | throw AipsError("SDLineFinder::setScan - the in_edge parameter has a negative" |
---|
94 | "number of channels to drop"); |
---|
95 | if (edge.first>=scan->nChan()) |
---|
96 | throw AipsError("SDLineFinder::setScan - all channels are rejected by the in_edge parameter"); |
---|
97 | if (n==2) { |
---|
98 | edge.second=extract<int>(in_edge.attr("__getitem__")(1)); |
---|
99 | if (edge.second<0) |
---|
100 | throw AipsError("SDLineFinder::setScan - the in_edge parameter has a negative" |
---|
101 | "number of channels to drop"); |
---|
102 | edge.second=scan->nChan()-edge.second; |
---|
103 | } else edge.second=scan->nChan()-edge.first; |
---|
104 | if (edge.second<0 || (edge.second+edge.first)>scan->nChan()) |
---|
105 | throw AipsError("SDLineFinder::setScan - all channels are rejected by the in_edge parameter"); |
---|
106 | } |
---|
107 | } |
---|
108 | catch(const AipsError &ae) { |
---|
109 | // setScan is unsuccessfull, reset scan/mask/edge |
---|
110 | scan=CountedConstPtr<SDMemTable>(); // null pointer |
---|
111 | mask.resize(0); |
---|
112 | edge=pair<int,int>(0,0); |
---|
113 | throw; |
---|
114 | } |
---|
115 | } |
---|
116 | |
---|
117 | // search for spectral lines. Number of lines found is returned |
---|
118 | int SDLineFinder::findLines() throw(casa::AipsError) |
---|
119 | { |
---|
120 | const int minboxnchan=4; |
---|
121 | if (scan.null()) |
---|
122 | throw AipsError("SDLineFinder::findLines - a scan should be set first," |
---|
123 | " use set_scan"); |
---|
124 | DebugAssert(mask.nelements()==scan->nChan(), AipsError); |
---|
125 | lines.resize(0); // search from the scratch |
---|
126 | |
---|
127 | max_box_nchan=int(scan->nChan()*box_size); // number of channels in running |
---|
128 | // box |
---|
129 | |
---|
130 | if (max_box_nchan<2) |
---|
131 | throw AipsError("SDLineFinder::findLines - box_size is too small"); |
---|
132 | |
---|
133 | scan->getSpectrum(spectrum); |
---|
134 | |
---|
135 | // fill statistics for initial box |
---|
136 | box_chan_cntr=0; // no channels are currently in the box |
---|
137 | sum=0; // initialize statistics |
---|
138 | sumsq=0; |
---|
139 | int initial_box_ch=edge.first; |
---|
140 | for (;initial_box_ch<edge.second && box_chan_cntr<max_box_nchan; |
---|
141 | ++initial_box_ch) |
---|
142 | advanceRunningBox(initial_box_ch); |
---|
143 | |
---|
144 | if (initial_box_ch==edge.second) |
---|
145 | throw AipsError("SDLineFinder::findLines - too much channels are masked"); |
---|
146 | |
---|
147 | // actual search algorithm |
---|
148 | is_detected_before=False; |
---|
149 | |
---|
150 | if (box_chan_cntr>=minboxnchan) |
---|
151 | // there is a minimum amount of data. We can search in the |
---|
152 | // half of the initial box |
---|
153 | for (int n=edge.first;n<initial_box_ch-max_box_nchan/2;++n) |
---|
154 | processChannel(n); |
---|
155 | |
---|
156 | // now the box can be moved. n+max_box_nchan/2 is a new index which haven't |
---|
157 | // yet been included in the running mean. |
---|
158 | for (int n=initial_box_ch-max_box_nchan/2;n<edge.second;++n) { |
---|
159 | advanceRunningBox(n+max_box_nchan/2); // update running mean & variance |
---|
160 | if (box_chan_cntr>=minboxnchan) // have enough data to process |
---|
161 | processChannel(n); |
---|
162 | else processCurLine(); // just finish what was accumulated before |
---|
163 | } |
---|
164 | return int(lines.size()); |
---|
165 | } |
---|
166 | |
---|
167 | // supplementary function to control running mean calculations. |
---|
168 | // It adds a specified channel to the running mean box and |
---|
169 | // removes (ch-max_box_nchan+1)'th channel from there |
---|
170 | // Channels, for which the mask is false or index is beyond the |
---|
171 | // allowed range, are ignored |
---|
172 | void SDLineFinder::advanceRunningBox(int ch) throw(AipsError) |
---|
173 | { |
---|
174 | if (ch>=edge.first && ch<edge.second) |
---|
175 | if (mask[ch]) { // ch is a valid channel |
---|
176 | ++box_chan_cntr; |
---|
177 | sum+=spectrum[ch]; |
---|
178 | sumsq+=square(spectrum[ch]); |
---|
179 | } |
---|
180 | int ch2remove=ch-max_box_nchan; |
---|
181 | if (ch2remove>=edge.first && ch2remove<edge.second) |
---|
182 | if (mask[ch2remove]) { // ch2remove is a valid channel |
---|
183 | --box_chan_cntr; |
---|
184 | sum-=spectrum[ch2remove]; |
---|
185 | sumsq-=square(spectrum[ch2remove]); |
---|
186 | } |
---|
187 | } |
---|
188 | |
---|
189 | // test a channel against current running mean & rms |
---|
190 | // if channel specified is masked out or beyond the allowed indexes, |
---|
191 | // false is returned |
---|
192 | Bool SDLineFinder::testChannel(int ch) throw(exception, AipsError) |
---|
193 | { |
---|
194 | if (ch<edge.first || ch>=edge.second) return False; |
---|
195 | if (!mask[ch]) return False; |
---|
196 | DebugAssert(box_chan_cntr, AipsError); |
---|
197 | Float mean=sum/Float(box_chan_cntr); |
---|
198 | Float variance=sqrt(sumsq/Float(box_chan_cntr)-square(mean)); |
---|
199 | /* |
---|
200 | if (ch>3900 && ch<4100) |
---|
201 | cout<<"Tested "<<ch<<" mean="<<mean<<" variance="<<variance<<" sp-mean="<<spectrum[ch]-mean<<endl; |
---|
202 | */ |
---|
203 | return fabs(spectrum[ch]-mean)>=threshold*variance; |
---|
204 | } |
---|
205 | |
---|
206 | // process a channel: update cur_line and is_detected before and |
---|
207 | // add a new line to the list, if necessary |
---|
208 | void SDLineFinder::processChannel(int ch) throw(casa::AipsError) |
---|
209 | { |
---|
210 | try { |
---|
211 | if (testChannel(ch)) { |
---|
212 | if (is_detected_before) |
---|
213 | cur_line.second=ch+1; |
---|
214 | else { |
---|
215 | is_detected_before=True; |
---|
216 | cur_line.first=ch; |
---|
217 | cur_line.second=ch+1; |
---|
218 | } |
---|
219 | } else processCurLine(); |
---|
220 | } |
---|
221 | catch (const AipsError &ae) { |
---|
222 | throw; |
---|
223 | } |
---|
224 | catch (const exception &ex) { |
---|
225 | throw AipsError(String("SDLineFinder::processChannel - STL error: ")+ex.what()); |
---|
226 | } |
---|
227 | } |
---|
228 | |
---|
229 | // process the interval of channels stored in cur_line |
---|
230 | // if it satisfies the criterion, add this interval as a new line |
---|
231 | void SDLineFinder::processCurLine() throw(casa::AipsError) |
---|
232 | { |
---|
233 | try { |
---|
234 | if (is_detected_before) { |
---|
235 | if (cur_line.second-cur_line.first>min_nchan) { |
---|
236 | // it was a detection. We need to change the list |
---|
237 | Bool add_new_line=False; |
---|
238 | if (lines.size()) { |
---|
239 | for (int i=lines.back().second;i<cur_line.first;++i) |
---|
240 | if (mask[i]) { // one valid channel in between |
---|
241 | // means that we deal with a separate line |
---|
242 | add_new_line=True; |
---|
243 | break; |
---|
244 | } |
---|
245 | } else add_new_line=True; |
---|
246 | if (add_new_line) |
---|
247 | lines.push_back(cur_line); |
---|
248 | else lines.back().second=cur_line.second; |
---|
249 | } |
---|
250 | is_detected_before=False; |
---|
251 | } |
---|
252 | } |
---|
253 | catch (const AipsError &ae) { |
---|
254 | throw; |
---|
255 | } |
---|
256 | catch (const exception &ex) { |
---|
257 | throw AipsError(String("SDLineFinder::processCurLine - STL error: ")+ex.what()); |
---|
258 | } |
---|
259 | } |
---|
260 | |
---|
261 | // get the mask to mask out all lines that have been found (default) |
---|
262 | // if invert=true, only channels belong to lines will be unmasked |
---|
263 | // Note: all channels originally masked by the input mask (in_mask |
---|
264 | // in setScan) or dropped out by the edge parameter (in_edge |
---|
265 | // in setScan) are still excluded regardless on the invert option |
---|
266 | std::vector<bool> SDLineFinder::getMask(bool invert) |
---|
267 | const throw(casa::AipsError) |
---|
268 | { |
---|
269 | try { |
---|
270 | if (scan.null()) |
---|
271 | throw AipsError("SDLineFinder::getMask - a scan should be set first," |
---|
272 | " use set_scan followed by find_lines"); |
---|
273 | DebugAssert(mask.nelements()==scan->nChan(), AipsError); |
---|
274 | /* |
---|
275 | if (!lines.size()) |
---|
276 | throw AipsError("SDLineFinder::getMask - one have to search for " |
---|
277 | "lines first, use find_lines"); |
---|
278 | */ |
---|
279 | std::vector<bool> res_mask(mask.nelements()); |
---|
280 | // iterator through lines |
---|
281 | std::list<std::pair<int,int> >::const_iterator cli=lines.begin(); |
---|
282 | for (int ch=0;ch<res_mask.size();++ch) |
---|
283 | if (ch<edge.first || ch>=edge.second) res_mask[ch]=false; |
---|
284 | else if (!mask[ch]) res_mask[ch]=false; |
---|
285 | else { |
---|
286 | res_mask[ch]=!invert; // no line by default |
---|
287 | if (cli==lines.end()) continue; |
---|
288 | if (ch>=cli->first && ch<cli->second) |
---|
289 | res_mask[ch]=invert; // this is a line |
---|
290 | if (ch>=cli->second) |
---|
291 | ++cli; // next line in the list |
---|
292 | } |
---|
293 | |
---|
294 | return res_mask; |
---|
295 | } |
---|
296 | catch (const AipsError &ae) { |
---|
297 | throw; |
---|
298 | } |
---|
299 | catch (const exception &ex) { |
---|
300 | throw AipsError(String("SDLineFinder::getMask - STL error: ")+ex.what()); |
---|
301 | } |
---|
302 | } |
---|
303 | |
---|
304 | // get range for all lines found. If defunits is true (default), the |
---|
305 | // same units as used in the scan will be returned (e.g. velocity |
---|
306 | // instead of channels). If defunits is false, channels will be returned |
---|
307 | std::vector<int> SDLineFinder::getLineRanges(bool defunits) |
---|
308 | const throw(casa::AipsError) |
---|
309 | { |
---|
310 | try { |
---|
311 | if (scan.null()) |
---|
312 | throw AipsError("SDLineFinder::getLineRanges - a scan should be set first," |
---|
313 | " use set_scan followed by find_lines"); |
---|
314 | DebugAssert(mask.nelements()==scan->nChan(), AipsError); |
---|
315 | |
---|
316 | if (!lines.size()) |
---|
317 | throw AipsError("SDLineFinder::getLineRanges - one have to search for " |
---|
318 | "lines first, use find_lines"); |
---|
319 | |
---|
320 | // temporary |
---|
321 | if (defunits) |
---|
322 | throw AipsError("SDLineFinder::getLineRanges - sorry, defunits=true have not " |
---|
323 | "yet been implemented"); |
---|
324 | // |
---|
325 | std::vector<int> res(2*lines.size()); |
---|
326 | // iterator through lines & result |
---|
327 | std::list<std::pair<int,int> >::const_iterator cli=lines.begin(); |
---|
328 | std::vector<int>::iterator ri=res.begin(); |
---|
329 | for (;cli!=lines.end() && ri!=res.end();++cli,++ri) { |
---|
330 | *ri=cli->first; |
---|
331 | if (++ri!=res.end()) |
---|
332 | *ri=cli->second-1; |
---|
333 | } |
---|
334 | return res; |
---|
335 | } |
---|
336 | catch (const AipsError &ae) { |
---|
337 | throw; |
---|
338 | } |
---|
339 | catch (const exception &ex) { |
---|
340 | throw AipsError(String("SDLineFinder::getLineRanges - STL error: ")+ex.what()); |
---|
341 | } |
---|
342 | } |
---|