[297] | 1 | //#--------------------------------------------------------------------------- |
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| 2 | //# SDLineFinder.cc: A class for automated spectral line search |
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| 3 | //#-------------------------------------------------------------------------- |
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| 4 | //# Copyright (C) 2004 |
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| 5 | //# ATNF |
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| 6 | //# |
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| 7 | //# This program is free software; you can redistribute it and/or modify it |
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| 8 | //# under the terms of the GNU General Public License as published by the Free |
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| 9 | //# Software Foundation; either version 2 of the License, or (at your option) |
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| 10 | //# any later version. |
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| 11 | //# |
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| 12 | //# This program is distributed in the hope that it will be useful, but |
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| 13 | //# WITHOUT ANY WARRANTY; without even the implied warranty of |
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| 14 | //# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General |
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| 15 | //# Public License for more details. |
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| 16 | //# |
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| 17 | //# You should have received a copy of the GNU General Public License along |
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| 18 | //# with this program; if not, write to the Free Software Foundation, Inc., |
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| 19 | //# 675 Massachusetts Ave, Cambridge, MA 02139, USA. |
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| 20 | //# |
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| 21 | //# Correspondence concerning this software should be addressed as follows: |
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| 22 | //# Internet email: Malte.Marquarding@csiro.au |
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| 23 | //# Postal address: Malte Marquarding, |
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| 24 | //# Australia Telescope National Facility, |
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| 25 | //# P.O. Box 76, |
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| 26 | //# Epping, NSW, 2121, |
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| 27 | //# AUSTRALIA |
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| 28 | //# |
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| 29 | //# $Id: |
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| 30 | //#--------------------------------------------------------------------------- |
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| 31 | |
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| 32 | |
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| 33 | // ASAP |
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| 34 | #include "SDLineFinder.h" |
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| 35 | |
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| 36 | // STL |
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| 37 | #include <iostream> |
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| 38 | |
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| 39 | using namespace asap; |
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| 40 | using namespace casa; |
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| 41 | using namespace std; |
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| 42 | using namespace boost::python; |
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| 43 | |
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[331] | 44 | namespace asap { |
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[297] | 45 | |
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[331] | 46 | // An auxiliary class implementing one pass of the line search algorithm, |
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| 47 | // which uses a running mean. We define this class here because it is |
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| 48 | // used in SDLineFinder only. The incapsulation of this code into a separate |
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| 49 | // class will provide a possibility to add new algorithms with minor changes |
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| 50 | class LFRunningMean { |
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| 51 | // The input data to work with. Use reference symantics to avoid |
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| 52 | // an unnecessary copying |
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| 53 | const casa::Vector<casa::Float> &spectrum; // a buffer for the spectrum |
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| 54 | const casa::Vector<casa::Bool> &mask; // associated mask |
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| 55 | const std::pair<int,int> &edge; // start and stop+1 channels |
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| 56 | // to work with |
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| 57 | |
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| 58 | // statistics for running mean filtering |
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| 59 | casa::Float sum; // sum of fluxes |
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| 60 | casa::Float sumsq; // sum of squares of fluxes |
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| 61 | int box_chan_cntr; // actual number of channels in the box |
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| 62 | int max_box_nchan; // maximum allowed number of channels in the box |
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| 63 | // (calculated from boxsize and actual spectrum size) |
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[297] | 64 | |
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[331] | 65 | // temporary line edge channels and flag, which is True if the line |
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| 66 | // was detected in the previous channels. |
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| 67 | std::pair<int,int> cur_line; |
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| 68 | casa::Bool is_detected_before; |
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| 69 | int min_nchan; // A minimum number of consequtive |
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| 70 | // channels, which should satisfy |
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| 71 | // the detection criterion, to be |
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| 72 | // a detection |
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| 73 | casa::Float threshold; // detection threshold - the |
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| 74 | // minimal signal to noise ratio |
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| 75 | public: |
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| 76 | // set up the object with the references to actual data |
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| 77 | // as well as the detection criterion (min_nchan and threshold, see above) |
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| 78 | // and the number of channels in the running box |
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| 79 | LFRunningMean(const casa::Vector<casa::Float> &in_spectrum, |
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| 80 | const casa::Vector<casa::Bool> &in_mask, |
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| 81 | const std::pair<int,int> &in_edge, |
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| 82 | int in_max_box_nchan, |
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| 83 | int in_min_nchan = 3, |
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| 84 | casa::Float in_threshold = 5); |
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| 85 | |
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| 86 | // replace the detection criterion |
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| 87 | void setCriterion(int in_min_nchan, casa::Float in_threshold) throw(); |
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[297] | 88 | |
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[331] | 89 | // find spectral lines and add them into list |
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| 90 | void findLines(std::list<pair<int,int> > &lines) throw(casa::AipsError); |
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| 91 | |
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| 92 | protected: |
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| 93 | // supplementary function to control running mean calculations. |
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| 94 | // It adds a specified channel to the running mean box and |
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| 95 | // removes (ch-maxboxnchan+1)'th channel from there |
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| 96 | // Channels, for which the mask is false or index is beyond the |
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| 97 | // allowed range, are ignored |
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| 98 | void advanceRunningBox(int ch) throw(casa::AipsError); |
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| 99 | |
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[297] | 100 | |
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[331] | 101 | // test a channel against current running mean & rms |
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| 102 | // if channel specified is masked out or beyond the allowed indexes, |
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| 103 | // false is returned |
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| 104 | casa::Bool testChannel(int ch) const |
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| 105 | throw(std::exception, casa::AipsError); |
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[297] | 106 | |
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[331] | 107 | // process a channel: update curline and is_detected before and |
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| 108 | // add a new line to the list, if necessary using processCurLine() |
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| 109 | void processChannel(std::list<pair<int,int> > &lines, |
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| 110 | int ch) throw(casa::AipsError); |
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[297] | 111 | |
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[331] | 112 | // process the interval of channels stored in curline |
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| 113 | // if it satisfies the criterion, add this interval as a new line |
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| 114 | void processCurLine(std::list<pair<int,int> > &lines) throw(casa::AipsError); |
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[297] | 115 | |
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[331] | 116 | }; |
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| 117 | } // namespace asap |
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[297] | 118 | |
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[331] | 119 | /////////////////////////////////////////////////////////////////////////////// |
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| 120 | // |
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| 121 | // LFRunningMean - a running mean algorithm for line detection |
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| 122 | // |
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| 123 | // |
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[297] | 124 | |
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[331] | 125 | // set up the object with the references to actual data |
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| 126 | // as well as the detection criterion (min_nchan and threshold, see above) |
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| 127 | // and the number of channels in the running box |
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| 128 | LFRunningMean::LFRunningMean(const casa::Vector<casa::Float> &in_spectrum, |
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| 129 | const casa::Vector<casa::Bool> &in_mask, |
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| 130 | const std::pair<int,int> &in_edge, |
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| 131 | int in_max_box_nchan, |
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| 132 | int in_min_nchan, casa::Float in_threshold) : |
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| 133 | spectrum(in_spectrum), mask(in_mask), edge(in_edge), |
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| 134 | max_box_nchan(in_max_box_nchan), |
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| 135 | min_nchan(in_min_nchan),threshold(in_threshold) {} |
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| 136 | |
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| 137 | // replace the detection criterion |
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| 138 | void LFRunningMean::setCriterion(int in_min_nchan, casa::Float in_threshold) |
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| 139 | throw() |
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| 140 | { |
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| 141 | min_nchan=in_min_nchan; |
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| 142 | threshold=in_threshold; |
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[297] | 143 | } |
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| 144 | |
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[331] | 145 | |
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[297] | 146 | // supplementary function to control running mean calculations. |
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| 147 | // It adds a specified channel to the running mean box and |
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| 148 | // removes (ch-max_box_nchan+1)'th channel from there |
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| 149 | // Channels, for which the mask is false or index is beyond the |
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| 150 | // allowed range, are ignored |
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[331] | 151 | void LFRunningMean::advanceRunningBox(int ch) throw(AipsError) |
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[297] | 152 | { |
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| 153 | if (ch>=edge.first && ch<edge.second) |
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| 154 | if (mask[ch]) { // ch is a valid channel |
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| 155 | ++box_chan_cntr; |
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| 156 | sum+=spectrum[ch]; |
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| 157 | sumsq+=square(spectrum[ch]); |
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| 158 | } |
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| 159 | int ch2remove=ch-max_box_nchan; |
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| 160 | if (ch2remove>=edge.first && ch2remove<edge.second) |
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| 161 | if (mask[ch2remove]) { // ch2remove is a valid channel |
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| 162 | --box_chan_cntr; |
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| 163 | sum-=spectrum[ch2remove]; |
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| 164 | sumsq-=square(spectrum[ch2remove]); |
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| 165 | } |
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| 166 | } |
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| 167 | |
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| 168 | // test a channel against current running mean & rms |
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| 169 | // if channel specified is masked out or beyond the allowed indexes, |
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| 170 | // false is returned |
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[331] | 171 | Bool LFRunningMean::testChannel(int ch) const throw(exception, AipsError) |
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[297] | 172 | { |
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| 173 | if (ch<edge.first || ch>=edge.second) return False; |
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| 174 | if (!mask[ch]) return False; |
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| 175 | DebugAssert(box_chan_cntr, AipsError); |
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| 176 | Float mean=sum/Float(box_chan_cntr); |
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| 177 | Float variance=sqrt(sumsq/Float(box_chan_cntr)-square(mean)); |
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| 178 | /* |
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| 179 | if (ch>3900 && ch<4100) |
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| 180 | cout<<"Tested "<<ch<<" mean="<<mean<<" variance="<<variance<<" sp-mean="<<spectrum[ch]-mean<<endl; |
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| 181 | */ |
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| 182 | return fabs(spectrum[ch]-mean)>=threshold*variance; |
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| 183 | } |
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| 184 | |
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| 185 | // process a channel: update cur_line and is_detected before and |
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| 186 | // add a new line to the list, if necessary |
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[331] | 187 | void LFRunningMean::processChannel(std::list<pair<int,int> > &lines, |
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| 188 | int ch) throw(casa::AipsError) |
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[297] | 189 | { |
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| 190 | try { |
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| 191 | if (testChannel(ch)) { |
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| 192 | if (is_detected_before) |
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| 193 | cur_line.second=ch+1; |
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| 194 | else { |
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| 195 | is_detected_before=True; |
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| 196 | cur_line.first=ch; |
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| 197 | cur_line.second=ch+1; |
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| 198 | } |
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[331] | 199 | } else processCurLine(lines); |
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[297] | 200 | } |
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| 201 | catch (const AipsError &ae) { |
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| 202 | throw; |
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| 203 | } |
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| 204 | catch (const exception &ex) { |
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| 205 | throw AipsError(String("SDLineFinder::processChannel - STL error: ")+ex.what()); |
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| 206 | } |
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| 207 | } |
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| 208 | |
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| 209 | // process the interval of channels stored in cur_line |
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| 210 | // if it satisfies the criterion, add this interval as a new line |
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[331] | 211 | void LFRunningMean::processCurLine(std::list<pair<int,int> > &lines) |
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| 212 | throw(casa::AipsError) |
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[297] | 213 | { |
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| 214 | try { |
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| 215 | if (is_detected_before) { |
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| 216 | if (cur_line.second-cur_line.first>min_nchan) { |
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| 217 | // it was a detection. We need to change the list |
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| 218 | Bool add_new_line=False; |
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| 219 | if (lines.size()) { |
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| 220 | for (int i=lines.back().second;i<cur_line.first;++i) |
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| 221 | if (mask[i]) { // one valid channel in between |
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| 222 | // means that we deal with a separate line |
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| 223 | add_new_line=True; |
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| 224 | break; |
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| 225 | } |
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| 226 | } else add_new_line=True; |
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| 227 | if (add_new_line) |
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| 228 | lines.push_back(cur_line); |
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| 229 | else lines.back().second=cur_line.second; |
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| 230 | } |
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| 231 | is_detected_before=False; |
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| 232 | } |
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| 233 | } |
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| 234 | catch (const AipsError &ae) { |
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| 235 | throw; |
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| 236 | } |
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| 237 | catch (const exception &ex) { |
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| 238 | throw AipsError(String("SDLineFinder::processCurLine - STL error: ")+ex.what()); |
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| 239 | } |
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| 240 | } |
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| 241 | |
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[331] | 242 | // find spectral lines and add them into list |
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| 243 | void LFRunningMean::findLines(std::list<pair<int,int> > &lines) |
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| 244 | throw(casa::AipsError) |
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| 245 | { |
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| 246 | const int minboxnchan=4; |
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| 247 | |
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| 248 | // fill statistics for initial box |
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| 249 | box_chan_cntr=0; // no channels are currently in the box |
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| 250 | sum=0; // initialize statistics |
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| 251 | sumsq=0; |
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| 252 | int initial_box_ch=edge.first; |
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| 253 | for (;initial_box_ch<edge.second && box_chan_cntr<max_box_nchan; |
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| 254 | ++initial_box_ch) |
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| 255 | advanceRunningBox(initial_box_ch); |
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| 256 | |
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| 257 | if (initial_box_ch==edge.second) |
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| 258 | throw AipsError("LFRunningMean::findLines - too much channels are masked"); |
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| 259 | |
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| 260 | // actual search algorithm |
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| 261 | is_detected_before=False; |
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| 262 | |
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| 263 | if (box_chan_cntr>=minboxnchan) |
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| 264 | // there is a minimum amount of data. We can search in the |
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| 265 | // half of the initial box |
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| 266 | for (int n=edge.first;n<initial_box_ch-max_box_nchan/2;++n) |
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| 267 | processChannel(lines,n); |
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| 268 | |
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| 269 | // now the box can be moved. n+max_box_nchan/2 is a new index which haven't |
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| 270 | // yet been included in the running mean. |
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| 271 | for (int n=initial_box_ch-max_box_nchan/2;n<edge.second;++n) { |
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| 272 | advanceRunningBox(n+max_box_nchan/2); // update running mean & variance |
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| 273 | if (box_chan_cntr>=minboxnchan) // have enough data to process |
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| 274 | processChannel(lines,n); |
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| 275 | else processCurLine(lines); // just finish what was accumulated before |
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| 276 | } |
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| 277 | } |
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| 278 | |
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| 279 | // |
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| 280 | /////////////////////////////////////////////////////////////////////////////// |
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| 281 | |
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| 282 | |
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| 283 | // SDLineFinder - a class for automated spectral line search |
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| 284 | |
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| 285 | SDLineFinder::SDLineFinder() throw() : edge(0,0) |
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| 286 | { |
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| 287 | // detection threshold - the minimal signal to noise ratio |
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| 288 | threshold=3.; // 3 sigma is a default |
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| 289 | box_size=1./16.; // default box size for running mean calculations is |
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| 290 | // 1/16 of the whole spectrum |
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| 291 | // A minimum number of consequtive channels, which should satisfy |
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| 292 | // the detection criterion, to be a detection |
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| 293 | min_nchan=3; // default is 3 channels |
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| 294 | } |
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| 295 | |
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| 296 | SDLineFinder::~SDLineFinder() throw(AipsError) {} |
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| 297 | |
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| 298 | // set scan to work with (in_scan parameter), associated mask (in_mask |
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| 299 | // parameter) and the edge channel rejection (in_edge parameter) |
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| 300 | // if in_edge has zero length, all channels chosen by mask will be used |
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| 301 | // if in_edge has one element only, it represents the number of |
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| 302 | // channels to drop from both sides of the spectrum |
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| 303 | // in_edge is introduced for convinience, although all functionality |
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| 304 | // can be achieved using a spectrum mask only |
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| 305 | void SDLineFinder::setScan(const SDMemTableWrapper &in_scan, |
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| 306 | const std::vector<bool> &in_mask, |
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| 307 | const boost::python::tuple &in_edge) throw(AipsError) |
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| 308 | { |
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| 309 | try { |
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| 310 | scan=in_scan.getCP(); |
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| 311 | AlwaysAssert(!scan.null(),AipsError); |
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| 312 | if (scan->nRow()!=1) |
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| 313 | throw AipsError("SDLineFinder::setScan - in_scan contains more than 1 row." |
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| 314 | "Choose one first."); |
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| 315 | mask=in_mask; |
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| 316 | if (mask.nelements()!=scan->nChan()) |
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| 317 | throw AipsError("SDLineFinder::setScan - in_scan and in_mask have different" |
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| 318 | "number of spectral channels."); |
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| 319 | |
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| 320 | // number of elements in the in_edge tuple |
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| 321 | int n=extract<int>(in_edge.attr("__len__")()); |
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| 322 | if (n>2 || n<0) |
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| 323 | throw AipsError("SDLineFinder::setScan - the length of the in_edge parameter" |
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| 324 | "should not exceed 2"); |
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| 325 | if (!n) { |
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| 326 | // all spectrum, no rejection |
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| 327 | edge.first=0; |
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| 328 | edge.second=scan->nChan(); |
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| 329 | } else { |
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| 330 | edge.first=extract<int>(in_edge.attr("__getitem__")(0)); |
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| 331 | if (edge.first<0) |
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| 332 | throw AipsError("SDLineFinder::setScan - the in_edge parameter has a negative" |
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| 333 | "number of channels to drop"); |
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| 334 | if (edge.first>=scan->nChan()) |
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| 335 | throw AipsError("SDLineFinder::setScan - all channels are rejected by the in_edge parameter"); |
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| 336 | if (n==2) { |
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| 337 | edge.second=extract<int>(in_edge.attr("__getitem__")(1)); |
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| 338 | if (edge.second<0) |
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| 339 | throw AipsError("SDLineFinder::setScan - the in_edge parameter has a negative" |
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| 340 | "number of channels to drop"); |
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| 341 | edge.second=scan->nChan()-edge.second; |
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| 342 | } else edge.second=scan->nChan()-edge.first; |
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| 343 | if (edge.second<0 || (edge.second+edge.first)>scan->nChan()) |
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| 344 | throw AipsError("SDLineFinder::setScan - all channels are rejected by the in_edge parameter"); |
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| 345 | } |
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| 346 | } |
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| 347 | catch(const AipsError &ae) { |
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| 348 | // setScan is unsuccessfull, reset scan/mask/edge |
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| 349 | scan=CountedConstPtr<SDMemTable>(); // null pointer |
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| 350 | mask.resize(0); |
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| 351 | edge=pair<int,int>(0,0); |
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| 352 | throw; |
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| 353 | } |
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| 354 | } |
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| 355 | |
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| 356 | // search for spectral lines. Number of lines found is returned |
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| 357 | int SDLineFinder::findLines() throw(casa::AipsError) |
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| 358 | { |
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| 359 | const int minboxnchan=4; |
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| 360 | if (scan.null()) |
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| 361 | throw AipsError("SDLineFinder::findLines - a scan should be set first," |
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| 362 | " use set_scan"); |
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| 363 | DebugAssert(mask.nelements()==scan->nChan(), AipsError); |
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| 364 | int max_box_nchan=int(scan->nChan()*box_size); // number of channels in running |
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| 365 | // box |
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| 366 | if (max_box_nchan<2) |
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| 367 | throw AipsError("SDLineFinder::findLines - box_size is too small"); |
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| 368 | |
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| 369 | scan->getSpectrum(spectrum); |
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| 370 | |
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| 371 | lines.resize(0); // search from the scratch |
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| 372 | Vector<Bool> temp_mask(mask); |
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| 373 | size_t cursz; |
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| 374 | do { |
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| 375 | cursz=lines.size(); |
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| 376 | // line find algorithm |
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| 377 | LFRunningMean lfalg(spectrum,temp_mask,edge,max_box_nchan,min_nchan,threshold); |
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| 378 | lfalg.findLines(lines); |
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| 379 | temp_mask=getMask(); |
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| 380 | } while (cursz!=lines.size()); |
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| 381 | return int(lines.size()); |
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| 382 | } |
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| 383 | |
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| 384 | |
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[297] | 385 | // get the mask to mask out all lines that have been found (default) |
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| 386 | // if invert=true, only channels belong to lines will be unmasked |
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| 387 | // Note: all channels originally masked by the input mask (in_mask |
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| 388 | // in setScan) or dropped out by the edge parameter (in_edge |
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| 389 | // in setScan) are still excluded regardless on the invert option |
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| 390 | std::vector<bool> SDLineFinder::getMask(bool invert) |
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| 391 | const throw(casa::AipsError) |
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| 392 | { |
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| 393 | try { |
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| 394 | if (scan.null()) |
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| 395 | throw AipsError("SDLineFinder::getMask - a scan should be set first," |
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| 396 | " use set_scan followed by find_lines"); |
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| 397 | DebugAssert(mask.nelements()==scan->nChan(), AipsError); |
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| 398 | /* |
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| 399 | if (!lines.size()) |
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| 400 | throw AipsError("SDLineFinder::getMask - one have to search for " |
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| 401 | "lines first, use find_lines"); |
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| 402 | */ |
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| 403 | std::vector<bool> res_mask(mask.nelements()); |
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| 404 | // iterator through lines |
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| 405 | std::list<std::pair<int,int> >::const_iterator cli=lines.begin(); |
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| 406 | for (int ch=0;ch<res_mask.size();++ch) |
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| 407 | if (ch<edge.first || ch>=edge.second) res_mask[ch]=false; |
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| 408 | else if (!mask[ch]) res_mask[ch]=false; |
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| 409 | else { |
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| 410 | res_mask[ch]=!invert; // no line by default |
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| 411 | if (cli==lines.end()) continue; |
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| 412 | if (ch>=cli->first && ch<cli->second) |
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| 413 | res_mask[ch]=invert; // this is a line |
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| 414 | if (ch>=cli->second) |
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| 415 | ++cli; // next line in the list |
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| 416 | } |
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| 417 | |
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| 418 | return res_mask; |
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| 419 | } |
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| 420 | catch (const AipsError &ae) { |
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| 421 | throw; |
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| 422 | } |
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| 423 | catch (const exception &ex) { |
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| 424 | throw AipsError(String("SDLineFinder::getMask - STL error: ")+ex.what()); |
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| 425 | } |
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| 426 | } |
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| 427 | |
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| 428 | // get range for all lines found. If defunits is true (default), the |
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| 429 | // same units as used in the scan will be returned (e.g. velocity |
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| 430 | // instead of channels). If defunits is false, channels will be returned |
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| 431 | std::vector<int> SDLineFinder::getLineRanges(bool defunits) |
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| 432 | const throw(casa::AipsError) |
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| 433 | { |
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| 434 | try { |
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| 435 | if (scan.null()) |
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| 436 | throw AipsError("SDLineFinder::getLineRanges - a scan should be set first," |
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| 437 | " use set_scan followed by find_lines"); |
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| 438 | DebugAssert(mask.nelements()==scan->nChan(), AipsError); |
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| 439 | |
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| 440 | if (!lines.size()) |
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| 441 | throw AipsError("SDLineFinder::getLineRanges - one have to search for " |
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| 442 | "lines first, use find_lines"); |
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| 443 | |
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| 444 | // temporary |
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| 445 | if (defunits) |
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| 446 | throw AipsError("SDLineFinder::getLineRanges - sorry, defunits=true have not " |
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| 447 | "yet been implemented"); |
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| 448 | // |
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| 449 | std::vector<int> res(2*lines.size()); |
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| 450 | // iterator through lines & result |
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| 451 | std::list<std::pair<int,int> >::const_iterator cli=lines.begin(); |
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| 452 | std::vector<int>::iterator ri=res.begin(); |
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| 453 | for (;cli!=lines.end() && ri!=res.end();++cli,++ri) { |
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| 454 | *ri=cli->first; |
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| 455 | if (++ri!=res.end()) |
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| 456 | *ri=cli->second-1; |
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| 457 | } |
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| 458 | return res; |
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| 459 | } |
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| 460 | catch (const AipsError &ae) { |
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| 461 | throw; |
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| 462 | } |
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| 463 | catch (const exception &ex) { |
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| 464 | throw AipsError(String("SDLineFinder::getLineRanges - STL error: ")+ex.what()); |
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| 465 | } |
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| 466 | } |
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[331] | 467 | |
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| 468 | // concatenate two lists preserving the order. If two lines appear to |
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| 469 | // be adjacent, they are joined into the new one |
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| 470 | void SDLineFinder::addNewSearchResult(const std::list<pair<int, int> > &newlines) |
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| 471 | throw(AipsError) |
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| 472 | { |
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| 473 | try { |
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| 474 | for (std::list<pair<int,int> >::const_iterator cli=newlines.begin(); |
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| 475 | cli!=newlines.end();++cli) { |
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| 476 | // search for a right place for the new line |
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| 477 | //TODO |
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| 478 | } |
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| 479 | } |
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| 480 | catch (const AipsError &ae) { |
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| 481 | throw; |
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| 482 | } |
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| 483 | catch (const exception &ex) { |
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| 484 | throw AipsError(String("SDLineFinder::addNewSearchResult - STL error: ")+ex.what()); |
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| 485 | } |
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| 486 | |
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| 487 | } |
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