1 | //#--------------------------------------------------------------------------- |
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2 | //# STLineFinder.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: STLineFinder.h 2580 2012-06-28 04:22:10Z ShinnosukeKawakami $ |
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30 | //#--------------------------------------------------------------------------- |
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31 | #ifndef STLINEFINDER_H |
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32 | #define STLINEFINDER_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 | // AIPS++ |
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41 | #include <casa/aips.h> |
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42 | #include <casa/Exceptions/Error.h> |
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43 | #include <casa/Arrays/Vector.h> |
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44 | #include <casa/Utilities/Assert.h> |
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45 | #include <casa/Utilities/CountedPtr.h> |
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46 | |
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47 | // ASAP |
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48 | #include "ScantableWrapper.h" |
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49 | #include "Scantable.h" |
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50 | #include "STFitter.h" |
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51 | |
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52 | namespace asap { |
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53 | |
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54 | /////////////////////////////////////////////////////////////////////////////// |
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55 | // |
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56 | // LFLineListOperations - a class incapsulating operations with line lists |
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57 | // The LF prefix stands for Line Finder |
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58 | // |
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59 | |
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60 | struct LFLineListOperations { |
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61 | // concatenate two lists preserving the order. If two lines appear to |
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62 | // be adjacent or have a non-void intersection, they are joined into |
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63 | // the new line |
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64 | static void addNewSearchResult(const std::list<std::pair<int, int> > |
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65 | &newlines, std::list<std::pair<int, int> > &lines_list) |
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66 | throw(casa::AipsError); |
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67 | |
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68 | // extend all line ranges to the point where a value stored in the |
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69 | // specified vector changes (e.g. value-mean change its sign) |
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70 | // This operation is necessary to include line wings, which are below |
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71 | // the detection threshold. If lines becomes adjacent, they are |
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72 | // merged together. Any masked channel stops the extension |
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73 | static void searchForWings(std::list<std::pair<int, int> > &newlines, |
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74 | const casa::Vector<casa::Int> &signs, |
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75 | const casa::Vector<casa::Bool> &mask, |
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76 | const std::pair<int,int> &edge) |
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77 | throw(casa::AipsError); |
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78 | protected: |
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79 | |
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80 | // An auxiliary object function to test whether two lines have a non-void |
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81 | // intersection |
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82 | class IntersectsWith : public std::unary_function<pair<int,int>, bool> { |
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83 | std::pair<int,int> line1; // range of the first line |
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84 | // start channel and stop+1 |
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85 | public: |
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86 | explicit IntersectsWith(const std::pair<int,int> &in_line1); |
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87 | // return true if line2 intersects with line1 with at least one |
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88 | // common channel, and false otherwise |
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89 | bool operator()(const std::pair<int,int> &line2) const throw(); |
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90 | }; |
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91 | |
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92 | // An auxiliary object function to build a union of several lines |
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93 | // to account for a possibility of merging the nearby lines |
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94 | class BuildUnion { |
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95 | std::pair<int,int> temp_line; // range of the first line |
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96 | // start channel and stop+1 |
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97 | public: |
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98 | explicit BuildUnion(const std::pair<int,int> &line1); |
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99 | // update temp_line with a union of temp_line and new_line |
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100 | // provided there is no gap between the lines |
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101 | void operator()(const std::pair<int,int> &new_line) throw(); |
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102 | // return the result (temp_line) |
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103 | const std::pair<int,int>& result() const throw(); |
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104 | }; |
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105 | |
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106 | // An auxiliary object function to test whether a specified line |
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107 | // is at lower spectral channels (to preserve the order in the line list) |
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108 | class LaterThan : public std::unary_function<pair<int,int>, bool> { |
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109 | std::pair<int,int> line1; // range of the first line |
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110 | // start channel and stop+1 |
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111 | public: |
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112 | explicit LaterThan(const std::pair<int,int> &in_line1); |
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113 | |
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114 | // return true if line2 should be placed later than line1 |
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115 | // in the ordered list (so, it is at greater channel numbers) |
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116 | bool operator()(const std::pair<int,int> &line2) const throw(); |
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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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124 | |
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125 | /////////////////////////////////////////////////////////////////////////////// |
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126 | // |
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127 | // STLineFinder - a class for automated spectral line search |
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128 | // |
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129 | // |
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130 | |
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131 | struct STLineFinder : protected LFLineListOperations { |
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132 | STLineFinder() throw(); |
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133 | virtual ~STLineFinder() throw(casa::AipsError); |
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134 | |
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135 | // set the parameters controlling algorithm |
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136 | // in_threshold a single channel threshold default is sqrt(3), which |
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137 | // means together with 3 minimum channels at least 3 sigma |
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138 | // detection criterion |
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139 | // For bad baseline shape, in_threshold may need to be |
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140 | // increased |
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141 | // in_min_nchan minimum number of channels above the threshold to report |
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142 | // a detection, default is 3 |
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143 | // in_avg_limit perform the averaging of no more than in_avg_limit |
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144 | // adjacent channels to search for broad lines |
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145 | // Default is 8, but for a bad baseline shape this |
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146 | // parameter should be decreased (may be even down to a |
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147 | // minimum of 1 to disable this option) to avoid |
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148 | // confusing of baseline undulations with a real line. |
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149 | // Setting a very large value doesn't usually provide |
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150 | // valid detections. |
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151 | // in_box_size the box size for running mean calculation. Default is |
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152 | // 1./5. of the whole spectrum size |
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153 | // in_noise_box the box size for off-line noise estimation (if working with |
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154 | // local noise. Negative value means use global noise estimate |
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155 | // Default is -1 (i.e. estimate using the whole spectrum) |
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156 | // in_median true if median statistics is used as opposed to average of |
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157 | // the lowest 80% of deviations (default) |
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158 | void setOptions(const casa::Float &in_threshold=sqrt(3.), |
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159 | const casa::Int &in_min_nchan=3, |
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160 | const casa::Int &in_avg_limit=8, |
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161 | const casa::Float &in_box_size=0.2, |
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162 | const casa::Float &in_noise_box=-1., |
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163 | const casa::Bool &in_median = casa::False) throw(); |
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164 | |
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165 | void setDetailedOptions( const casa::Int &order=9 ) ; |
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166 | |
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167 | // set the scan to work with (in_scan parameter) |
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168 | void setScan(const ScantableWrapper &in_scan) throw(casa::AipsError); |
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169 | |
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170 | // set spectrum data to work with. this is a method to allow linefinder work |
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171 | // without setting scantable for the purpose of using linefinder inside some |
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172 | // method in scantable class. (Dec. 22, 2010 by W.Kawasaki) |
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173 | void setData(const std::vector<float> &in_spectrum); |
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174 | |
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175 | // search for spectral lines in a row specified by whichRow |
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176 | // in_mask and in_edge parameters control channel rejection |
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177 | // if in_edge has zero length, all channels chosen by mask will be used |
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178 | // if in_edge has one element only, it represents the number of |
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179 | // channels to drop from both sides of the spectrum |
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180 | // in_edge is introduced for convinience, although all functionality |
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181 | // can be achieved using a spectrum mask only |
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182 | // Number of lines found is returned |
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183 | int findLines(const std::vector<bool> &in_mask, |
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184 | const std::vector<int> &in_edge = std::vector<int>(), |
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185 | const casa::uInt &whichRow = 0) throw(casa::AipsError); |
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186 | |
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187 | // get the mask to mask out all lines that have been found (default) |
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188 | // if invert=true, only channels belong to lines will be unmasked |
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189 | // Note: all channels originally masked by the input mask (in_mask |
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190 | // in setScan) or dropped out by the edge parameter (in_edge |
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191 | // in setScan) are still excluded regardless on the invert option |
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192 | std::vector<bool> getMask(bool invert=false) const throw(casa::AipsError); |
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193 | |
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194 | // get range for all lines found. The same units as used in the scan |
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195 | // will be returned (e.g. velocity instead of channels). |
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196 | std::vector<double> getLineRanges() const throw(casa::AipsError); |
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197 | // The same as getLineRanges, but channels are always used to specify |
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198 | // the range |
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199 | std::vector<int> getLineRangesInChannels() const throw(casa::AipsError); |
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200 | protected: |
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201 | // auxiliary function to average adjacent channels and update the mask |
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202 | // if at least one channel involved in summation is masked, all |
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203 | // output channels will be masked. This function works with the |
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204 | // spectrum and edge fields of this class, but updates the mask |
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205 | // array specified, rather than the field of this class |
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206 | // boxsize - a number of adjacent channels to average |
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207 | void averageAdjacentChannels(casa::Vector<casa::Bool> &mask2update, |
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208 | const casa::Int &boxsize) |
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209 | throw(casa::AipsError); |
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210 | |
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211 | // auxiliary function to fit and subtract a polynomial from the current |
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212 | // spectrum. It uses the Fitter class. This action is required before |
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213 | // reducing the spectral resolution if the baseline shape is bad |
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214 | void subtractBaseline(const casa::Vector<casa::Bool> &temp_mask, |
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215 | const casa::Int &order) throw(casa::AipsError); |
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216 | |
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217 | // an auxiliary function to remove all lines from the list, except the |
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218 | // strongest one (by absolute value). If the lines removed are real, |
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219 | // they will be find again at the next iteration. This approach |
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220 | // increases the number of iterations required, but is able to remove |
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221 | // the sidelobes likely to occur near strong lines. |
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222 | // Later a better criterion may be implemented, e.g. |
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223 | // taking into consideration the brightness of different lines. Now |
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224 | // use the simplest solution |
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225 | // temp_mask - mask to work with (may be different from original mask as |
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226 | // the lines previously found may be masked) |
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227 | // lines2update - a list of lines to work with |
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228 | // nothing will be done if it is empty |
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229 | // max_box_nchan - channels in the running box for baseline filtering |
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230 | void keepStrongestOnly(const casa::Vector<casa::Bool> &temp_mask, |
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231 | std::list<std::pair<int, int> > &lines2update, |
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232 | int max_box_nchan) |
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233 | throw (casa::AipsError); |
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234 | private: |
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235 | casa::CountedConstPtr<Scantable> scan; // the scan to work with |
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236 | casa::Vector<casa::Bool> mask; // associated mask |
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237 | std::pair<int,int> edge; // start and stop+1 channels |
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238 | // to work with |
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239 | casa::Float threshold; // detection threshold - the |
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240 | // minimal signal to noise ratio |
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241 | casa::Double box_size; // size of the box for running |
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242 | // mean calculations, specified as |
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243 | // a fraction of the whole spectrum |
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244 | int min_nchan; // A minimum number of consequtive |
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245 | // channels, which should satisfy |
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246 | // the detection criterion, to be |
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247 | // a detection |
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248 | casa::Int avg_limit; // perform the averaging of no |
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249 | // more than in_avg_limit |
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250 | // adjacent channels to search |
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251 | // for broad lines. see setOptions |
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252 | casa::uInt last_row_used; // the Row number specified |
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253 | // during the last findLines call |
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254 | std::list<std::pair<int, int> > lines; // container of start and stop+1 |
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255 | // channels of the spectral lines |
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256 | // a buffer for the spectrum |
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257 | mutable casa::Vector<casa::Float> spectrum; |
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258 | |
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259 | // the box size for off-line noise estimation (if working with |
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260 | // local noise. Negative value means use global noise estimate |
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261 | // Default is -1 (i.e. estimate using the whole spectrum) |
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262 | casa::Float itsNoiseBox; |
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263 | |
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264 | // true if median statistics is used as opposed to average of |
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265 | // the lowest 80% of deviations (default) |
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266 | casa::Bool itsUseMedian; |
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267 | |
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268 | // true if spectra and mask data should be provided from |
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269 | // scantable (default = true) |
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270 | bool useScantable; |
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271 | |
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272 | // shared object for nominal throw |
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273 | casa::AipsError err ; |
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274 | }; |
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275 | |
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276 | // |
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277 | /////////////////////////////////////////////////////////////////////////////// |
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278 | |
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279 | } // namespace asap |
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280 | #endif // #ifndef STLINEFINDER_H |
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