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