[297] | 1 | //#---------------------------------------------------------------------------
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[881] | 2 | //# STLineFinder.h: A class for automated spectral line search
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[297] | 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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[890] | 29 | //# $Id: STLineFinder.h 3106 2016-10-04 07:20:50Z TakeshiNakazato $
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[297] | 30 | //#---------------------------------------------------------------------------
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[881] | 31 | #ifndef STLINEFINDER_H
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| 32 | #define STLINEFINDER_H
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[297] | 33 |
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[3085] | 34 | // ASAP
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| 35 | #include "ScantableWrapper.h"
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| 36 | #include "Scantable.h"
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| 37 |
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[297] | 38 | // STL
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| 39 | #include <vector>
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| 40 | #include <list>
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| 41 | #include <utility>
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| 42 | #include <exception>
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| 43 |
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| 44 | // AIPS++
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| 45 | #include <casa/aips.h>
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| 46 | #include <casa/Exceptions/Error.h>
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| 47 | #include <casa/Arrays/Vector.h>
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| 48 | #include <casa/Utilities/Assert.h>
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| 49 | #include <casa/Utilities/CountedPtr.h>
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| 50 |
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| 51 | namespace asap {
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| 52 |
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[352] | 53 | ///////////////////////////////////////////////////////////////////////////////
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| 54 | //
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| 55 | // LFLineListOperations - a class incapsulating operations with line lists
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| 56 | // The LF prefix stands for Line Finder
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| 57 | //
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[297] | 58 |
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[881] | 59 | struct LFLineListOperations {
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[331] | 60 | // concatenate two lists preserving the order. If two lines appear to
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[881] | 61 | // be adjacent or have a non-void intersection, they are joined into
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[343] | 62 | // the new line
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[344] | 63 | static void addNewSearchResult(const std::list<std::pair<int, int> >
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[3029] | 64 | &newlines, std::list<std::pair<int, int> > &lines_list);
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[344] | 65 |
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| 66 | // extend all line ranges to the point where a value stored in the
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| 67 | // specified vector changes (e.g. value-mean change its sign)
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| 68 | // This operation is necessary to include line wings, which are below
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| 69 | // the detection threshold. If lines becomes adjacent, they are
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| 70 | // merged together. Any masked channel stops the extension
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[352] | 71 | static void searchForWings(std::list<std::pair<int, int> > &newlines,
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[3106] | 72 | const casacore::Vector<casacore::Int> &signs,
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| 73 | const casacore::Vector<casacore::Bool> &mask,
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[3029] | 74 | const std::pair<int,int> &edge);
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[352] | 75 | protected:
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[881] | 76 |
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[343] | 77 | // An auxiliary object function to test whether two lines have a non-void
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| 78 | // intersection
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| 79 | class IntersectsWith : public std::unary_function<pair<int,int>, bool> {
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| 80 | std::pair<int,int> line1; // range of the first line
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| 81 | // start channel and stop+1
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| 82 | public:
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[1353] | 83 | explicit IntersectsWith(const std::pair<int,int> &in_line1);
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[343] | 84 | // return true if line2 intersects with line1 with at least one
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| 85 | // common channel, and false otherwise
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[3029] | 86 | bool operator()(const std::pair<int,int> &line2) const;
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[343] | 87 | };
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| 88 |
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| 89 | // An auxiliary object function to build a union of several lines
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| 90 | // to account for a possibility of merging the nearby lines
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| 91 | class BuildUnion {
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| 92 | std::pair<int,int> temp_line; // range of the first line
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| 93 | // start channel and stop+1
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| 94 | public:
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[1353] | 95 | explicit BuildUnion(const std::pair<int,int> &line1);
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[343] | 96 | // update temp_line with a union of temp_line and new_line
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| 97 | // provided there is no gap between the lines
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[3029] | 98 | void operator()(const std::pair<int,int> &new_line);
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[343] | 99 | // return the result (temp_line)
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[3029] | 100 | const std::pair<int,int>& result() const;
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[343] | 101 | };
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[881] | 102 |
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[343] | 103 | // An auxiliary object function to test whether a specified line
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| 104 | // is at lower spectral channels (to preserve the order in the line list)
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| 105 | class LaterThan : public std::unary_function<pair<int,int>, bool> {
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| 106 | std::pair<int,int> line1; // range of the first line
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| 107 | // start channel and stop+1
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| 108 | public:
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[1353] | 109 | explicit LaterThan(const std::pair<int,int> &in_line1);
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[343] | 110 |
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| 111 | // return true if line2 should be placed later than line1
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| 112 | // in the ordered list (so, it is at greater channel numbers)
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[3029] | 113 | bool operator()(const std::pair<int,int> &line2) const;
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[881] | 114 | };
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| 115 |
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| 116 |
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[352] | 117 | };
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| 118 |
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| 119 | //
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| 120 | ///////////////////////////////////////////////////////////////////////////////
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| 121 |
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| 122 | ///////////////////////////////////////////////////////////////////////////////
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| 123 | //
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[881] | 124 | // STLineFinder - a class for automated spectral line search
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[352] | 125 | //
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| 126 | //
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| 127 |
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[881] | 128 | struct STLineFinder : protected LFLineListOperations {
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[3029] | 129 | STLineFinder();
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| 130 | virtual ~STLineFinder();
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[352] | 131 |
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[369] | 132 | // set the parameters controlling algorithm
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| 133 | // in_threshold a single channel threshold default is sqrt(3), which
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| 134 | // means together with 3 minimum channels at least 3 sigma
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| 135 | // detection criterion
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| 136 | // For bad baseline shape, in_threshold may need to be
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| 137 | // increased
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| 138 | // in_min_nchan minimum number of channels above the threshold to report
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| 139 | // a detection, default is 3
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| 140 | // in_avg_limit perform the averaging of no more than in_avg_limit
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| 141 | // adjacent channels to search for broad lines
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[881] | 142 | // Default is 8, but for a bad baseline shape this
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[369] | 143 | // parameter should be decreased (may be even down to a
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| 144 | // minimum of 1 to disable this option) to avoid
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| 145 | // confusing of baseline undulations with a real line.
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[881] | 146 | // Setting a very large value doesn't usually provide
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| 147 | // valid detections.
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[369] | 148 | // in_box_size the box size for running mean calculation. Default is
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| 149 | // 1./5. of the whole spectrum size
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[1644] | 150 | // in_noise_box the box size for off-line noise estimation (if working with
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| 151 | // local noise. Negative value means use global noise estimate
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| 152 | // Default is -1 (i.e. estimate using the whole spectrum)
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| 153 | // in_median true if median statistics is used as opposed to average of
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| 154 | // the lowest 80% of deviations (default)
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[3106] | 155 | void setOptions(const casacore::Float &in_threshold=sqrt(3.),
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| 156 | const casacore::Int &in_min_nchan=3,
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| 157 | const casacore::Int &in_avg_limit=8,
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| 158 | const casacore::Float &in_box_size=0.2,
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| 159 | const casacore::Float &in_noise_box=-1.,
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| 160 | const casacore::Bool &in_median = casacore::False);
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[369] | 161 |
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[3106] | 162 | void setDetailedOptions( const casacore::Int &order=9 ) ;
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[2580] | 163 |
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[907] | 164 | // set the scan to work with (in_scan parameter)
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[3029] | 165 | void setScan(const ScantableWrapper &in_scan);
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[907] | 166 |
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[2012] | 167 | // set spectrum data to work with. this is a method to allow linefinder work
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| 168 | // without setting scantable for the purpose of using linefinder inside some
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| 169 | // method in scantable class. (Dec. 22, 2010 by W.Kawasaki)
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| 170 | void setData(const std::vector<float> &in_spectrum);
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| 171 |
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[907] | 172 | // search for spectral lines in a row specified by whichRow
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| 173 | // in_mask and in_edge parameters control channel rejection
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| 174 | // if in_edge has zero length, all channels chosen by mask will be used
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[352] | 175 | // if in_edge has one element only, it represents the number of
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| 176 | // channels to drop from both sides of the spectrum
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| 177 | // in_edge is introduced for convinience, although all functionality
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[881] | 178 | // can be achieved using a spectrum mask only
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| 179 | // Number of lines found is returned
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[907] | 180 | int findLines(const std::vector<bool> &in_mask,
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| 181 | const std::vector<int> &in_edge = std::vector<int>(),
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[3106] | 182 | const casacore::uInt &whichRow = 0);
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[352] | 183 |
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| 184 | // get the mask to mask out all lines that have been found (default)
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| 185 | // if invert=true, only channels belong to lines will be unmasked
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| 186 | // Note: all channels originally masked by the input mask (in_mask
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| 187 | // in setScan) or dropped out by the edge parameter (in_edge
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| 188 | // in setScan) are still excluded regardless on the invert option
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[3029] | 189 | std::vector<bool> getMask(bool invert=false) const;
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[352] | 190 |
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[370] | 191 | // get range for all lines found. The same units as used in the scan
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[881] | 192 | // will be returned (e.g. velocity instead of channels).
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[3029] | 193 | std::vector<double> getLineRanges() const;
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[370] | 194 | // The same as getLineRanges, but channels are always used to specify
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| 195 | // the range
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[3029] | 196 | std::vector<int> getLineRangesInChannels() const;
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[368] | 197 | protected:
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| 198 | // auxiliary function to average adjacent channels and update the mask
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| 199 | // if at least one channel involved in summation is masked, all
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| 200 | // output channels will be masked. This function works with the
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| 201 | // spectrum and edge fields of this class, but updates the mask
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| 202 | // array specified, rather than the field of this class
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| 203 | // boxsize - a number of adjacent channels to average
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[3106] | 204 | void averageAdjacentChannels(casacore::Vector<casacore::Bool> &mask2update,
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| 205 | const casacore::Int &boxsize);
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[369] | 206 |
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| 207 | // auxiliary function to fit and subtract a polynomial from the current
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[890] | 208 | // spectrum. It uses the Fitter class. This action is required before
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[369] | 209 | // reducing the spectral resolution if the baseline shape is bad
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[3106] | 210 | void subtractBaseline(const casacore::Vector<casacore::Bool> &temp_mask,
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| 211 | const casacore::Int &order);
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[881] | 212 |
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[368] | 213 | // an auxiliary function to remove all lines from the list, except the
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| 214 | // strongest one (by absolute value). If the lines removed are real,
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[881] | 215 | // they will be find again at the next iteration. This approach
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| 216 | // increases the number of iterations required, but is able to remove
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[368] | 217 | // the sidelobes likely to occur near strong lines.
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| 218 | // Later a better criterion may be implemented, e.g.
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| 219 | // taking into consideration the brightness of different lines. Now
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[881] | 220 | // use the simplest solution
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[368] | 221 | // temp_mask - mask to work with (may be different from original mask as
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| 222 | // the lines previously found may be masked)
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| 223 | // lines2update - a list of lines to work with
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| 224 | // nothing will be done if it is empty
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| 225 | // max_box_nchan - channels in the running box for baseline filtering
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[3106] | 226 | void keepStrongestOnly(const casacore::Vector<casacore::Bool> &temp_mask,
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[368] | 227 | std::list<std::pair<int, int> > &lines2update,
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[3029] | 228 | int max_box_nchan);
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[297] | 229 | private:
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[3106] | 230 | casacore::CountedPtr<Scantable> scan; // the scan to work with
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| 231 | casacore::Vector<casacore::Bool> mask; // associated mask
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[297] | 232 | std::pair<int,int> edge; // start and stop+1 channels
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| 233 | // to work with
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[3106] | 234 | casacore::Float threshold; // detection threshold - the
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[297] | 235 | // minimal signal to noise ratio
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[3106] | 236 | casacore::Double box_size; // size of the box for running
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[297] | 237 | // mean calculations, specified as
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| 238 | // a fraction of the whole spectrum
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| 239 | int min_nchan; // A minimum number of consequtive
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| 240 | // channels, which should satisfy
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| 241 | // the detection criterion, to be
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| 242 | // a detection
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[3106] | 243 | casacore::Int avg_limit; // perform the averaging of no
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[369] | 244 | // more than in_avg_limit
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| 245 | // adjacent channels to search
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| 246 | // for broad lines. see setOptions
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[3106] | 247 | casacore::uInt last_row_used; // the Row number specified
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[370] | 248 | // during the last findLines call
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[297] | 249 | std::list<std::pair<int, int> > lines; // container of start and stop+1
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| 250 | // channels of the spectral lines
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| 251 | // a buffer for the spectrum
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[3106] | 252 | mutable casacore::Vector<casacore::Float> spectrum;
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[1644] | 253 |
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| 254 | // the box size for off-line noise estimation (if working with
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| 255 | // local noise. Negative value means use global noise estimate
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| 256 | // Default is -1 (i.e. estimate using the whole spectrum)
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[3106] | 257 | casacore::Float itsNoiseBox;
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[1644] | 258 |
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| 259 | // true if median statistics is used as opposed to average of
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| 260 | // the lowest 80% of deviations (default)
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[3106] | 261 | casacore::Bool itsUseMedian;
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[2012] | 262 |
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| 263 | // true if spectra and mask data should be provided from
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| 264 | // scantable (default = true)
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| 265 | bool useScantable;
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[2580] | 266 |
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| 267 | // shared object for nominal throw
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[3106] | 268 | casacore::AipsError err ;
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[352] | 269 | };
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[297] | 270 |
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[352] | 271 | //
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| 272 | ///////////////////////////////////////////////////////////////////////////////
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| 273 |
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[297] | 274 | } // namespace asap
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[881] | 275 | #endif // #ifndef STLINEFINDER_H
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