[297] | 1 | //#--------------------------------------------------------------------------- |
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| 2 | //# SDLineFinder.h: 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 | #ifndef SDLINEFINDER_H |
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| 32 | #define SDLINEFINDER_H |
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| 33 | |
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| 34 | // STL |
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| 35 | #include <vector> |
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| 36 | #include <list> |
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| 37 | #include <utility> |
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| 38 | #include <exception> |
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| 39 | |
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| 40 | // boost |
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| 41 | #include <boost/python.hpp> |
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| 42 | |
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| 43 | // AIPS++ |
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| 44 | #include <casa/aips.h> |
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| 45 | #include <casa/Exceptions/Error.h> |
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| 46 | #include <casa/Arrays/Vector.h> |
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| 47 | #include <casa/Utilities/Assert.h> |
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| 48 | #include <casa/Utilities/CountedPtr.h> |
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| 49 | |
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| 50 | // ASAP |
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| 51 | #include "SDMemTableWrapper.h" |
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| 52 | #include "SDMemTable.h" |
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| 53 | |
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| 54 | namespace asap { |
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| 55 | |
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| 56 | // SDLineFinder - a class for automated spectral line search |
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| 57 | struct SDLineFinder { |
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| 58 | SDLineFinder() throw(); |
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| 59 | virtual ~SDLineFinder() throw(casa::AipsError); |
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| 60 | |
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| 61 | // set the scan to work with (in_scan parameter), associated mask (in_mask |
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| 62 | // parameter) and the edge channel rejection (in_edge parameter) |
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| 63 | // if in_edge has zero length, all channels chosen by mask will be used |
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| 64 | // if in_edge has one element only, it represents the number of |
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| 65 | // channels to drop from both sides of the spectrum |
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| 66 | // in_edge is introduced for convinience, although all functionality |
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| 67 | // can be achieved using a spectrum mask only |
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| 68 | void setScan(const SDMemTableWrapper &in_scan, |
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| 69 | const std::vector<bool> &in_mask, |
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| 70 | const boost::python::tuple &in_edge) throw(casa::AipsError); |
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| 71 | |
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| 72 | // search for spectral lines. Number of lines found is returned |
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| 73 | int findLines() throw(casa::AipsError); |
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| 74 | |
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| 75 | // get the mask to mask out all lines that have been found (default) |
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| 76 | // if invert=true, only channels belong to lines will be unmasked |
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| 77 | // Note: all channels originally masked by the input mask (in_mask |
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| 78 | // in setScan) or dropped out by the edge parameter (in_edge |
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| 79 | // in setScan) are still excluded regardless on the invert option |
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| 80 | std::vector<bool> getMask(bool invert=false) const throw(casa::AipsError); |
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| 81 | |
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| 82 | // get range for all lines found. If defunits is true (default), the |
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| 83 | // same units as used in the scan will be returned (e.g. velocity |
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| 84 | // instead of channels). If defunits is false, channels will be returned |
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| 85 | std::vector<int> getLineRanges(bool defunits=true) |
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| 86 | const throw(casa::AipsError); |
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| 87 | protected: |
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[331] | 88 | // concatenate two lists preserving the order. If two lines appear to |
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[343] | 89 | // be adjacent or have a non-void intersection, they are joined into |
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| 90 | // the new line |
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[344] | 91 | static void addNewSearchResult(const std::list<std::pair<int, int> > |
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| 92 | &newlines, std::list<std::pair<int, int> > &lines_list) |
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[331] | 93 | throw(casa::AipsError); |
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[344] | 94 | |
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| 95 | // extend all line ranges to the point where a value stored in the |
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| 96 | // specified vector changes (e.g. value-mean change its sign) |
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| 97 | // This operation is necessary to include line wings, which are below |
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| 98 | // the detection threshold. If lines becomes adjacent, they are |
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| 99 | // merged together. Any masked channel stops the extension |
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| 100 | void searchForWings(std::list<std::pair<int, int> > &newlines, |
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| 101 | const casa::Vector<casa::Int> &signs) |
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| 102 | throw(casa::AipsError); |
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[343] | 103 | |
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| 104 | // An auxiliary object function to test whether two lines have a non-void |
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| 105 | // intersection |
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| 106 | class IntersectsWith : public std::unary_function<pair<int,int>, bool> { |
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| 107 | std::pair<int,int> line1; // range of the first line |
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| 108 | // start channel and stop+1 |
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| 109 | public: |
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| 110 | IntersectsWith(const std::pair<int,int> &in_line1); |
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| 111 | // return true if line2 intersects with line1 with at least one |
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| 112 | // common channel, and false otherwise |
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| 113 | bool operator()(const std::pair<int,int> &line2) const throw(); |
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| 114 | }; |
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| 115 | |
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| 116 | // An auxiliary object function to build a union of several lines |
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| 117 | // to account for a possibility of merging the nearby lines |
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| 118 | class BuildUnion { |
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| 119 | std::pair<int,int> temp_line; // range of the first line |
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| 120 | // start channel and stop+1 |
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| 121 | public: |
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| 122 | BuildUnion(const std::pair<int,int> &line1); |
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| 123 | // update temp_line with a union of temp_line and new_line |
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| 124 | // provided there is no gap between the lines |
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| 125 | void operator()(const std::pair<int,int> &new_line) throw(); |
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| 126 | // return the result (temp_line) |
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| 127 | const std::pair<int,int>& result() const throw(); |
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| 128 | }; |
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| 129 | |
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| 130 | // An auxiliary object function to test whether a specified line |
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| 131 | // is at lower spectral channels (to preserve the order in the line list) |
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| 132 | class LaterThan : public std::unary_function<pair<int,int>, bool> { |
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| 133 | std::pair<int,int> line1; // range of the first line |
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| 134 | // start channel and stop+1 |
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| 135 | public: |
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| 136 | LaterThan(const std::pair<int,int> &in_line1); |
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| 137 | |
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| 138 | // return true if line2 should be placed later than line1 |
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| 139 | // in the ordered list (so, it is at greater channel numbers) |
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| 140 | bool operator()(const std::pair<int,int> &line2) const throw(); |
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| 141 | }; |
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| 142 | |
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[297] | 143 | private: |
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| 144 | casa::CountedConstPtr<SDMemTable> scan; // the scan to work with |
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| 145 | casa::Vector<casa::Bool> mask; // associated mask |
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| 146 | std::pair<int,int> edge; // start and stop+1 channels |
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| 147 | // to work with |
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| 148 | casa::Float threshold; // detection threshold - the |
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| 149 | // minimal signal to noise ratio |
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| 150 | casa::Double box_size; // size of the box for running |
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| 151 | // mean calculations, specified as |
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| 152 | // a fraction of the whole spectrum |
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| 153 | int min_nchan; // A minimum number of consequtive |
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| 154 | // channels, which should satisfy |
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| 155 | // the detection criterion, to be |
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| 156 | // a detection |
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| 157 | std::list<std::pair<int, int> > lines; // container of start and stop+1 |
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| 158 | // channels of the spectral lines |
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| 159 | // a buffer for the spectrum |
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| 160 | mutable casa::Vector<casa::Float> spectrum; |
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| 161 | |
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| 162 | }; |
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| 163 | } // namespace asap |
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| 164 | #endif // #ifndef SDLINEFINDER_H |
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