1 | //#--------------------------------------------------------------------------- |
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2 | //# SDLineFinder.cc: A class for automated spectral line search |
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3 | //#-------------------------------------------------------------------------- |
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4 | //# Copyright (C) 2004 |
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5 | //# ATNF |
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6 | //# |
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7 | //# This program is free software; you can redistribute it and/or modify it |
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8 | //# under the terms of the GNU General Public License as published by the Free |
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9 | //# Software Foundation; either version 2 of the License, or (at your option) |
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10 | //# any later version. |
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11 | //# |
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12 | //# This program is distributed in the hope that it will be useful, but |
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13 | //# WITHOUT ANY WARRANTY; without even the implied warranty of |
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14 | //# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General |
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15 | //# Public License for more details. |
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16 | //# |
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17 | //# You should have received a copy of the GNU General Public License along |
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18 | //# with this program; if not, write to the Free Software Foundation, Inc., |
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19 | //# 675 Massachusetts Ave, Cambridge, MA 02139, USA. |
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20 | //# |
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21 | //# Correspondence concerning this software should be addressed as follows: |
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22 | //# Internet email: Malte.Marquarding@csiro.au |
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23 | //# Postal address: Malte Marquarding, |
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24 | //# Australia Telescope National Facility, |
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25 | //# P.O. Box 76, |
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26 | //# Epping, NSW, 2121, |
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27 | //# AUSTRALIA |
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28 | //# |
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29 | //# $Id: |
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30 | //#--------------------------------------------------------------------------- |
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31 | |
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32 | |
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33 | // ASAP |
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34 | #include "SDLineFinder.h" |
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35 | |
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36 | // STL |
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37 | #include <functional> |
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38 | #include <algorithm> |
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39 | #include <iostream> |
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40 | |
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41 | using namespace asap; |
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42 | using namespace casa; |
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43 | using namespace std; |
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44 | using namespace boost::python; |
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45 | |
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46 | namespace asap { |
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47 | |
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48 | /////////////////////////////////////////////////////////////////////////////// |
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49 | // |
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50 | // IStatHolder - an abstract class to collect statistics from the running |
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51 | // mean calculator, if necessary. |
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52 | // We define it here, because it is used in LFRunningMean and |
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53 | // SDLineFinder only |
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54 | // |
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55 | |
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56 | struct IStatHolder { |
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57 | // This function is called for each spectral channel processed by |
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58 | // the running mean calculator. The order of channel numbers may be |
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59 | // arbitrary |
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60 | // ch - a number of channel, corresponding to (approximately) the centre |
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61 | // of the running box |
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62 | // box_nchan - number of channels in the box |
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63 | // |
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64 | virtual void accumulate(int ch, Float sum, Float sum2, int box_nchan) |
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65 | throw(AipsError) = 0; |
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66 | }; |
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67 | |
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68 | // |
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69 | /////////////////////////////////////////////////////////////////////////////// |
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70 | |
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71 | /////////////////////////////////////////////////////////////////////////////// |
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72 | // |
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73 | // SignAccumulator - a simple class to deal with running mean statistics: |
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74 | // it stores the sign of the value-mean only |
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75 | // |
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76 | class SignAccumulator : public IStatHolder { |
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77 | Vector<Int> sign; // either +1, -1 or 0 |
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78 | const Vector<Float> &spectrum; // a reference to the spectrum |
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79 | // to calculate the sign |
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80 | public: |
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81 | // all channels >=nchan are ignored |
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82 | SignAccumulator(uInt nchan, const Vector<Float> &in_spectrum); |
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83 | |
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84 | // This function is called for each spectral channel processed by |
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85 | // the running mean calculator. The order of channel numbers may be |
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86 | // arbitrary |
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87 | // ch - a number of channel, corresponding to (approximately) the centre |
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88 | // of the running box |
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89 | // box_nchan - number of channels in the box |
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90 | // |
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91 | virtual void accumulate(int ch, Float sum, Float, int box_nchan) |
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92 | throw(AipsError); |
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93 | |
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94 | // access to the sign |
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95 | const Vector<Int>& getSigns() const throw(); |
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96 | }; |
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97 | |
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98 | // |
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99 | /////////////////////////////////////////////////////////////////////////////// |
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100 | |
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101 | /////////////////////////////////////////////////////////////////////////////// |
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102 | // |
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103 | // LFRunningMean - a running mean algorithm for line detection |
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104 | // |
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105 | // |
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106 | |
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107 | // An auxiliary class implementing one pass of the line search algorithm, |
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108 | // which uses a running mean. We define this class here because it is |
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109 | // used in SDLineFinder only. The incapsulation of this code into a separate |
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110 | // class will provide a possibility to add new algorithms with minor changes |
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111 | class LFRunningMean { |
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112 | // The input data to work with. Use reference symantics to avoid |
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113 | // an unnecessary copying |
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114 | const casa::Vector<casa::Float> &spectrum; // a buffer for the spectrum |
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115 | const casa::Vector<casa::Bool> &mask; // associated mask |
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116 | const std::pair<int,int> &edge; // start and stop+1 channels |
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117 | // to work with |
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118 | |
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119 | // statistics for running mean filtering |
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120 | casa::Float sum; // sum of fluxes |
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121 | casa::Float sumsq; // sum of squares of fluxes |
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122 | int box_chan_cntr; // actual number of channels in the box |
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123 | int max_box_nchan; // maximum allowed number of channels in the box |
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124 | // (calculated from boxsize and actual spectrum size) |
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125 | |
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126 | // temporary line edge channels and flag, which is True if the line |
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127 | // was detected in the previous channels. |
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128 | std::pair<int,int> cur_line; |
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129 | casa::Bool is_detected_before; |
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130 | int min_nchan; // A minimum number of consequtive |
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131 | // channels, which should satisfy |
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132 | // the detection criterion, to be |
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133 | // a detection |
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134 | casa::Float threshold; // detection threshold - the |
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135 | // minimal signal to noise ratio |
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136 | public: |
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137 | // set up the object with the references to actual data |
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138 | // as well as the detection criterion (min_nchan and threshold, see above) |
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139 | // and the number of channels in the running box |
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140 | LFRunningMean(const casa::Vector<casa::Float> &in_spectrum, |
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141 | const casa::Vector<casa::Bool> &in_mask, |
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142 | const std::pair<int,int> &in_edge, |
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143 | int in_max_box_nchan, |
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144 | int in_min_nchan = 3, |
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145 | casa::Float in_threshold = 5); |
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146 | |
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147 | // replace the detection criterion |
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148 | void setCriterion(int in_min_nchan, casa::Float in_threshold) throw(); |
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149 | |
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150 | // find spectral lines and add them into list |
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151 | // if statholder is not NULL, the accumulate function of it will be |
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152 | // called for each channel to save statistics |
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153 | void findLines(std::list<pair<int,int> > &lines, |
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154 | IStatHolder* statholder = NULL) throw(casa::AipsError); |
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155 | |
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156 | protected: |
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157 | // supplementary function to control running mean calculations. |
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158 | // It adds a specified channel to the running mean box and |
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159 | // removes (ch-maxboxnchan+1)'th channel from there |
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160 | // Channels, for which the mask is false or index is beyond the |
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161 | // allowed range, are ignored |
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162 | void advanceRunningBox(int ch) throw(casa::AipsError); |
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163 | |
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164 | |
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165 | // test a channel against current running mean & rms |
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166 | // if channel specified is masked out or beyond the allowed indexes, |
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167 | // false is returned |
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168 | casa::Bool testChannel(int ch) const |
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169 | throw(std::exception, casa::AipsError); |
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170 | |
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171 | // process a channel: update curline and is_detected before and |
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172 | // add a new line to the list, if necessary using processCurLine() |
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173 | void processChannel(std::list<pair<int,int> > &lines, |
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174 | int ch) throw(casa::AipsError); |
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175 | |
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176 | // process the interval of channels stored in curline |
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177 | // if it satisfies the criterion, add this interval as a new line |
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178 | void processCurLine(std::list<pair<int,int> > &lines) throw(casa::AipsError); |
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179 | |
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180 | }; |
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181 | |
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182 | // |
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183 | /////////////////////////////////////////////////////////////////////////////// |
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184 | } // namespace asap |
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185 | |
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186 | /////////////////////////////////////////////////////////////////////////////// |
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187 | // |
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188 | // SignAccumulator - a simple class to deal with running mean statistics: |
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189 | // it stores the sign of the value-mean only |
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190 | // |
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191 | |
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192 | // all channels >=nchan are ignored |
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193 | SignAccumulator::SignAccumulator(uInt nchan, |
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194 | const Vector<Float> &in_spectrum) : sign(nchan,0), |
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195 | spectrum(in_spectrum) {} |
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196 | |
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197 | |
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198 | // This function is called for each spectral channel processed by |
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199 | // the running mean calculator. The order of channel numbers may be |
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200 | // arbitrary |
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201 | // ch - a number of channel, corresponding to (approximately) the centre |
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202 | // of the running box |
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203 | // box_nchan - number of channels in the box |
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204 | // |
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205 | void SignAccumulator::accumulate(int ch, Float sum, Float, int box_nchan) |
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206 | throw(AipsError) |
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207 | { |
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208 | if (ch>=sign.nelements()) return; |
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209 | DebugAssert(ch>=0,AipsError); |
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210 | DebugAssert(ch<=spectrum.nelements(), AipsError); |
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211 | if (box_nchan) { |
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212 | Float buf=spectrum[ch]-sum/Float(box_nchan); |
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213 | if (buf>0) sign[ch]=1; |
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214 | else if (buf<0) sign[ch]=-1; |
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215 | else sign[ch]=0; |
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216 | } else sign[ch]=0; |
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217 | } |
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218 | |
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219 | // access to the sign |
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220 | const Vector<Int>& SignAccumulator::getSigns() const throw() |
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221 | { |
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222 | return sign; |
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223 | } |
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224 | |
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225 | |
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226 | // |
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227 | /////////////////////////////////////////////////////////////////////////////// |
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228 | |
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229 | |
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230 | /////////////////////////////////////////////////////////////////////////////// |
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231 | // |
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232 | // LFRunningMean - a running mean algorithm for line detection |
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233 | // |
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234 | // |
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235 | |
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236 | // set up the object with the references to actual data |
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237 | // as well as the detection criterion (min_nchan and threshold, see above) |
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238 | // and the number of channels in the running box |
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239 | LFRunningMean::LFRunningMean(const casa::Vector<casa::Float> &in_spectrum, |
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240 | const casa::Vector<casa::Bool> &in_mask, |
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241 | const std::pair<int,int> &in_edge, |
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242 | int in_max_box_nchan, |
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243 | int in_min_nchan, casa::Float in_threshold) : |
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244 | spectrum(in_spectrum), mask(in_mask), edge(in_edge), |
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245 | max_box_nchan(in_max_box_nchan), |
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246 | min_nchan(in_min_nchan),threshold(in_threshold) {} |
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247 | |
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248 | // replace the detection criterion |
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249 | void LFRunningMean::setCriterion(int in_min_nchan, casa::Float in_threshold) |
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250 | throw() |
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251 | { |
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252 | min_nchan=in_min_nchan; |
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253 | threshold=in_threshold; |
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254 | } |
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255 | |
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256 | |
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257 | // supplementary function to control running mean calculations. |
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258 | // It adds a specified channel to the running mean box and |
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259 | // removes (ch-max_box_nchan+1)'th channel from there |
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260 | // Channels, for which the mask is false or index is beyond the |
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261 | // allowed range, are ignored |
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262 | void LFRunningMean::advanceRunningBox(int ch) throw(AipsError) |
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263 | { |
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264 | if (ch>=edge.first && ch<edge.second) |
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265 | if (mask[ch]) { // ch is a valid channel |
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266 | ++box_chan_cntr; |
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267 | sum+=spectrum[ch]; |
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268 | sumsq+=square(spectrum[ch]); |
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269 | } |
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270 | int ch2remove=ch-max_box_nchan; |
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271 | if (ch2remove>=edge.first && ch2remove<edge.second) |
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272 | if (mask[ch2remove]) { // ch2remove is a valid channel |
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273 | --box_chan_cntr; |
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274 | sum-=spectrum[ch2remove]; |
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275 | sumsq-=square(spectrum[ch2remove]); |
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276 | } |
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277 | } |
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278 | |
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279 | // test a channel against current running mean & rms |
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280 | // if channel specified is masked out or beyond the allowed indexes, |
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281 | // false is returned |
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282 | Bool LFRunningMean::testChannel(int ch) const throw(exception, AipsError) |
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283 | { |
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284 | if (ch<edge.first || ch>=edge.second) return False; |
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285 | if (!mask[ch]) return False; |
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286 | DebugAssert(box_chan_cntr, AipsError); |
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287 | Float mean=sum/Float(box_chan_cntr); |
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288 | Float variance=sqrt(sumsq/Float(box_chan_cntr)-square(mean)); |
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289 | /* |
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290 | if (ch>3900 && ch<4100) |
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291 | cout<<"Tested "<<ch<<" mean="<<mean<<" variance="<<variance<<" sp-mean="<<spectrum[ch]-mean<<endl; |
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292 | */ |
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293 | return fabs(spectrum[ch]-mean)>=threshold*variance; |
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294 | } |
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295 | |
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296 | // process a channel: update cur_line and is_detected before and |
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297 | // add a new line to the list, if necessary |
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298 | void LFRunningMean::processChannel(std::list<pair<int,int> > &lines, |
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299 | int ch) throw(casa::AipsError) |
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300 | { |
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301 | try { |
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302 | if (testChannel(ch)) { |
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303 | if (is_detected_before) |
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304 | cur_line.second=ch+1; |
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305 | else { |
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306 | is_detected_before=True; |
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307 | cur_line.first=ch; |
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308 | cur_line.second=ch+1; |
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309 | } |
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310 | } else processCurLine(lines); |
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311 | } |
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312 | catch (const AipsError &ae) { |
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313 | throw; |
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314 | } |
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315 | catch (const exception &ex) { |
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316 | throw AipsError(String("SDLineFinder::processChannel - STL error: ")+ex.what()); |
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317 | } |
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318 | } |
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319 | |
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320 | // process the interval of channels stored in cur_line |
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321 | // if it satisfies the criterion, add this interval as a new line |
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322 | void LFRunningMean::processCurLine(std::list<pair<int,int> > &lines) |
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323 | throw(casa::AipsError) |
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324 | { |
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325 | try { |
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326 | if (is_detected_before) { |
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327 | if (cur_line.second-cur_line.first>min_nchan) { |
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328 | // it was a detection. We need to change the list |
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329 | Bool add_new_line=False; |
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330 | if (lines.size()) { |
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331 | for (int i=lines.back().second;i<cur_line.first;++i) |
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332 | if (mask[i]) { // one valid channel in between |
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333 | // means that we deal with a separate line |
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334 | add_new_line=True; |
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335 | break; |
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336 | } |
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337 | } else add_new_line=True; |
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338 | if (add_new_line) |
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339 | lines.push_back(cur_line); |
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340 | else lines.back().second=cur_line.second; |
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341 | } |
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342 | is_detected_before=False; |
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343 | } |
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344 | } |
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345 | catch (const AipsError &ae) { |
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346 | throw; |
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347 | } |
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348 | catch (const exception &ex) { |
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349 | throw AipsError(String("SDLineFinder::processCurLine - STL error: ")+ex.what()); |
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350 | } |
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351 | } |
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352 | |
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353 | // find spectral lines and add them into list |
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354 | void LFRunningMean::findLines(std::list<pair<int,int> > &lines, |
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355 | IStatHolder* statholder) |
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356 | throw(casa::AipsError) |
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357 | { |
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358 | const int minboxnchan=4; |
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359 | |
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360 | // fill statistics for initial box |
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361 | box_chan_cntr=0; // no channels are currently in the box |
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362 | sum=0; // initialize statistics |
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363 | sumsq=0; |
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364 | int initial_box_ch=edge.first; |
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365 | for (;initial_box_ch<edge.second && box_chan_cntr<max_box_nchan; |
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366 | ++initial_box_ch) |
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367 | advanceRunningBox(initial_box_ch); |
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368 | |
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369 | if (initial_box_ch==edge.second) |
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370 | throw AipsError("LFRunningMean::findLines - too much channels are masked"); |
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371 | |
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372 | // actual search algorithm |
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373 | is_detected_before=False; |
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374 | |
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375 | if (statholder!=NULL) |
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376 | for (int n=0;n<initial_box_ch-max_box_nchan/2;++n) |
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377 | statholder->accumulate(n,sum,sumsq,box_chan_cntr); |
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378 | |
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379 | if (box_chan_cntr>=minboxnchan) |
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380 | // there is a minimum amount of data. We can search in the |
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381 | // half of the initial box |
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382 | for (int n=edge.first;n<initial_box_ch-max_box_nchan/2;++n) |
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383 | processChannel(lines,n); |
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384 | |
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385 | // now the box can be moved. n+max_box_nchan/2 is a new index which haven't |
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386 | // yet been included in the running mean. |
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387 | for (int n=initial_box_ch-max_box_nchan/2;n<edge.second;++n) { |
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388 | advanceRunningBox(n+max_box_nchan/2); // update running mean & variance |
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389 | if (statholder!=NULL) |
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390 | statholder->accumulate(n,sum,sumsq,box_chan_cntr); |
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391 | if (box_chan_cntr>=minboxnchan) // have enough data to process |
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392 | processChannel(lines,n); |
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393 | else processCurLine(lines); // just finish what was accumulated before |
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394 | } |
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395 | if (statholder!=NULL) |
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396 | for (int n=edge.second;n<spectrum.nelements();++n) |
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397 | statholder->accumulate(n,sum,sumsq,box_chan_cntr); |
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398 | } |
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399 | |
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400 | // |
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401 | /////////////////////////////////////////////////////////////////////////////// |
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402 | |
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403 | /////////////////////////////////////////////////////////////////////////////// |
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404 | // |
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405 | // SDLineFinder::IntersectsWith - An auxiliary object function to test |
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406 | // whether two lines have a non-void intersection |
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407 | // |
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408 | |
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409 | |
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410 | // line1 - range of the first line: start channel and stop+1 |
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411 | SDLineFinder::IntersectsWith::IntersectsWith(const std::pair<int,int> &in_line1) : |
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412 | line1(in_line1) {} |
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413 | |
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414 | |
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415 | // return true if line2 intersects with line1 with at least one |
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416 | // common channel, and false otherwise |
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417 | // line2 - range of the second line: start channel and stop+1 |
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418 | bool SDLineFinder::IntersectsWith::operator()(const std::pair<int,int> &line2) |
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419 | const throw() |
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420 | { |
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421 | if (line2.second<line1.first) return false; // line2 is at lower channels |
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422 | if (line2.first>line1.second) return false; // line2 is at upper channels |
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423 | return true; // line2 has an intersection or is adjacent to line1 |
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424 | } |
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425 | |
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426 | // |
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427 | /////////////////////////////////////////////////////////////////////////////// |
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428 | |
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429 | /////////////////////////////////////////////////////////////////////////////// |
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430 | // |
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431 | // SDLineFinder::BuildUnion - An auxiliary object function to build a union |
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432 | // of several lines to account for a possibility of merging the nearby lines |
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433 | // |
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434 | |
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435 | // set an initial line (can be a first line in the sequence) |
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436 | SDLineFinder::BuildUnion::BuildUnion(const std::pair<int,int> &line1) : |
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437 | temp_line(line1) {} |
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438 | |
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439 | // update temp_line with a union of temp_line and new_line |
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440 | // provided there is no gap between the lines |
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441 | void SDLineFinder::BuildUnion::operator()(const std::pair<int,int> &new_line) |
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442 | throw() |
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443 | { |
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444 | if (new_line.first<temp_line.first) temp_line.first=new_line.first; |
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445 | if (new_line.second>temp_line.second) temp_line.second=new_line.second; |
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446 | } |
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447 | |
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448 | // return the result (temp_line) |
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449 | const std::pair<int,int>& SDLineFinder::BuildUnion::result() const throw() |
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450 | { |
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451 | return temp_line; |
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452 | } |
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453 | |
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454 | // |
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455 | /////////////////////////////////////////////////////////////////////////////// |
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456 | |
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457 | /////////////////////////////////////////////////////////////////////////////// |
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458 | // |
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459 | // SDLineFinder::LaterThan - An auxiliary object function to test whether a |
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460 | // specified line is at lower spectral channels (to preserve the order in |
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461 | // the line list) |
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462 | // |
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463 | |
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464 | // setup the line to compare with |
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465 | SDLineFinder::LaterThan::LaterThan(const std::pair<int,int> &in_line1) : |
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466 | line1(in_line1) {} |
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467 | |
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468 | // return true if line2 should be placed later than line1 |
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469 | // in the ordered list (so, it is at greater channel numbers) |
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470 | bool SDLineFinder::LaterThan::operator()(const std::pair<int,int> &line2) |
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471 | const throw() |
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472 | { |
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473 | if (line2.second<line1.first) return false; // line2 is at lower channels |
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474 | if (line2.first>line1.second) return true; // line2 is at upper channels |
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475 | |
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476 | // line2 intersects with line1. We should have no such situation in |
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477 | // practice |
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478 | return line2.first>line1.first; |
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479 | } |
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480 | |
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481 | // |
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482 | /////////////////////////////////////////////////////////////////////////////// |
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483 | |
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484 | |
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485 | /////////////////////////////////////////////////////////////////////////////// |
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486 | // |
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487 | // SDLineFinder - a class for automated spectral line search |
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488 | // |
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489 | // |
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490 | |
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491 | SDLineFinder::SDLineFinder() throw() : edge(0,0) |
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492 | { |
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493 | // detection threshold - the minimal signal to noise ratio |
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494 | threshold=3.; // 3 sigma is a default |
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495 | box_size=1./16.; // default box size for running mean calculations is |
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496 | // 1/16 of the whole spectrum |
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497 | // A minimum number of consequtive channels, which should satisfy |
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498 | // the detection criterion, to be a detection |
---|
499 | min_nchan=3; // default is 3 channels |
---|
500 | } |
---|
501 | |
---|
502 | SDLineFinder::~SDLineFinder() throw(AipsError) {} |
---|
503 | |
---|
504 | // set scan to work with (in_scan parameter), associated mask (in_mask |
---|
505 | // parameter) and the edge channel rejection (in_edge parameter) |
---|
506 | // if in_edge has zero length, all channels chosen by mask will be used |
---|
507 | // if in_edge has one element only, it represents the number of |
---|
508 | // channels to drop from both sides of the spectrum |
---|
509 | // in_edge is introduced for convinience, although all functionality |
---|
510 | // can be achieved using a spectrum mask only |
---|
511 | void SDLineFinder::setScan(const SDMemTableWrapper &in_scan, |
---|
512 | const std::vector<bool> &in_mask, |
---|
513 | const boost::python::tuple &in_edge) throw(AipsError) |
---|
514 | { |
---|
515 | try { |
---|
516 | scan=in_scan.getCP(); |
---|
517 | AlwaysAssert(!scan.null(),AipsError); |
---|
518 | if (scan->nRow()!=1) |
---|
519 | throw AipsError("SDLineFinder::setScan - in_scan contains more than 1 row." |
---|
520 | "Choose one first."); |
---|
521 | mask=in_mask; |
---|
522 | if (mask.nelements()!=scan->nChan()) |
---|
523 | throw AipsError("SDLineFinder::setScan - in_scan and in_mask have different" |
---|
524 | "number of spectral channels."); |
---|
525 | |
---|
526 | // number of elements in the in_edge tuple |
---|
527 | int n=extract<int>(in_edge.attr("__len__")()); |
---|
528 | if (n>2 || n<0) |
---|
529 | throw AipsError("SDLineFinder::setScan - the length of the in_edge parameter" |
---|
530 | "should not exceed 2"); |
---|
531 | if (!n) { |
---|
532 | // all spectrum, no rejection |
---|
533 | edge.first=0; |
---|
534 | edge.second=scan->nChan(); |
---|
535 | } else { |
---|
536 | edge.first=extract<int>(in_edge.attr("__getitem__")(0)); |
---|
537 | if (edge.first<0) |
---|
538 | throw AipsError("SDLineFinder::setScan - the in_edge parameter has a negative" |
---|
539 | "number of channels to drop"); |
---|
540 | if (edge.first>=scan->nChan()) |
---|
541 | throw AipsError("SDLineFinder::setScan - all channels are rejected by the in_edge parameter"); |
---|
542 | if (n==2) { |
---|
543 | edge.second=extract<int>(in_edge.attr("__getitem__")(1)); |
---|
544 | if (edge.second<0) |
---|
545 | throw AipsError("SDLineFinder::setScan - the in_edge parameter has a negative" |
---|
546 | "number of channels to drop"); |
---|
547 | edge.second=scan->nChan()-edge.second; |
---|
548 | } else edge.second=scan->nChan()-edge.first; |
---|
549 | if (edge.second<0 || (edge.second+edge.first)>scan->nChan()) |
---|
550 | throw AipsError("SDLineFinder::setScan - all channels are rejected by the in_edge parameter"); |
---|
551 | } |
---|
552 | } |
---|
553 | catch(const AipsError &ae) { |
---|
554 | // setScan is unsuccessfull, reset scan/mask/edge |
---|
555 | scan=CountedConstPtr<SDMemTable>(); // null pointer |
---|
556 | mask.resize(0); |
---|
557 | edge=pair<int,int>(0,0); |
---|
558 | throw; |
---|
559 | } |
---|
560 | } |
---|
561 | |
---|
562 | // search for spectral lines. Number of lines found is returned |
---|
563 | int SDLineFinder::findLines() throw(casa::AipsError) |
---|
564 | { |
---|
565 | const int minboxnchan=4; |
---|
566 | if (scan.null()) |
---|
567 | throw AipsError("SDLineFinder::findLines - a scan should be set first," |
---|
568 | " use set_scan"); |
---|
569 | DebugAssert(mask.nelements()==scan->nChan(), AipsError); |
---|
570 | int max_box_nchan=int(scan->nChan()*box_size); // number of channels in running |
---|
571 | // box |
---|
572 | if (max_box_nchan<2) |
---|
573 | throw AipsError("SDLineFinder::findLines - box_size is too small"); |
---|
574 | |
---|
575 | scan->getSpectrum(spectrum); |
---|
576 | |
---|
577 | lines.resize(0); // search from the scratch |
---|
578 | Vector<Bool> temp_mask(mask); |
---|
579 | |
---|
580 | while (true) { |
---|
581 | // line find algorithm |
---|
582 | LFRunningMean lfalg(spectrum,temp_mask,edge,max_box_nchan,min_nchan, |
---|
583 | threshold); |
---|
584 | SignAccumulator sacc(spectrum.nelements(),spectrum); |
---|
585 | |
---|
586 | // a buffer for new lines found at this iteration |
---|
587 | std::list<pair<int,int> > new_lines; |
---|
588 | |
---|
589 | lfalg.findLines(new_lines,&sacc); |
---|
590 | if (!new_lines.size()) break; // nothing new |
---|
591 | |
---|
592 | searchForWings(new_lines, sacc.getSigns()); |
---|
593 | |
---|
594 | // update the list (lines) merging intervals, if necessary |
---|
595 | addNewSearchResult(new_lines,lines); |
---|
596 | // get a new mask |
---|
597 | temp_mask=getMask(); |
---|
598 | } |
---|
599 | return int(lines.size()); |
---|
600 | } |
---|
601 | |
---|
602 | |
---|
603 | // get the mask to mask out all lines that have been found (default) |
---|
604 | // if invert=true, only channels belong to lines will be unmasked |
---|
605 | // Note: all channels originally masked by the input mask (in_mask |
---|
606 | // in setScan) or dropped out by the edge parameter (in_edge |
---|
607 | // in setScan) are still excluded regardless on the invert option |
---|
608 | std::vector<bool> SDLineFinder::getMask(bool invert) |
---|
609 | const throw(casa::AipsError) |
---|
610 | { |
---|
611 | try { |
---|
612 | if (scan.null()) |
---|
613 | throw AipsError("SDLineFinder::getMask - a scan should be set first," |
---|
614 | " use set_scan followed by find_lines"); |
---|
615 | DebugAssert(mask.nelements()==scan->nChan(), AipsError); |
---|
616 | /* |
---|
617 | if (!lines.size()) |
---|
618 | throw AipsError("SDLineFinder::getMask - one have to search for " |
---|
619 | "lines first, use find_lines"); |
---|
620 | */ |
---|
621 | std::vector<bool> res_mask(mask.nelements()); |
---|
622 | // iterator through lines |
---|
623 | std::list<std::pair<int,int> >::const_iterator cli=lines.begin(); |
---|
624 | for (int ch=0;ch<res_mask.size();++ch) |
---|
625 | if (ch<edge.first || ch>=edge.second) res_mask[ch]=false; |
---|
626 | else if (!mask[ch]) res_mask[ch]=false; |
---|
627 | else { |
---|
628 | res_mask[ch]=!invert; // no line by default |
---|
629 | if (cli==lines.end()) continue; |
---|
630 | if (ch>=cli->first && ch<cli->second) |
---|
631 | res_mask[ch]=invert; // this is a line |
---|
632 | if (ch>=cli->second) |
---|
633 | ++cli; // next line in the list |
---|
634 | } |
---|
635 | |
---|
636 | return res_mask; |
---|
637 | } |
---|
638 | catch (const AipsError &ae) { |
---|
639 | throw; |
---|
640 | } |
---|
641 | catch (const exception &ex) { |
---|
642 | throw AipsError(String("SDLineFinder::getMask - STL error: ")+ex.what()); |
---|
643 | } |
---|
644 | } |
---|
645 | |
---|
646 | // get range for all lines found. If defunits is true (default), the |
---|
647 | // same units as used in the scan will be returned (e.g. velocity |
---|
648 | // instead of channels). If defunits is false, channels will be returned |
---|
649 | std::vector<int> SDLineFinder::getLineRanges(bool defunits) |
---|
650 | const throw(casa::AipsError) |
---|
651 | { |
---|
652 | try { |
---|
653 | if (scan.null()) |
---|
654 | throw AipsError("SDLineFinder::getLineRanges - a scan should be set first," |
---|
655 | " use set_scan followed by find_lines"); |
---|
656 | DebugAssert(mask.nelements()==scan->nChan(), AipsError); |
---|
657 | |
---|
658 | if (!lines.size()) |
---|
659 | throw AipsError("SDLineFinder::getLineRanges - one have to search for " |
---|
660 | "lines first, use find_lines"); |
---|
661 | |
---|
662 | // temporary |
---|
663 | if (defunits) |
---|
664 | throw AipsError("SDLineFinder::getLineRanges - sorry, defunits=true have not " |
---|
665 | "yet been implemented"); |
---|
666 | // |
---|
667 | std::vector<int> res(2*lines.size()); |
---|
668 | // iterator through lines & result |
---|
669 | std::list<std::pair<int,int> >::const_iterator cli=lines.begin(); |
---|
670 | std::vector<int>::iterator ri=res.begin(); |
---|
671 | for (;cli!=lines.end() && ri!=res.end();++cli,++ri) { |
---|
672 | *ri=cli->first; |
---|
673 | if (++ri!=res.end()) |
---|
674 | *ri=cli->second-1; |
---|
675 | } |
---|
676 | return res; |
---|
677 | } |
---|
678 | catch (const AipsError &ae) { |
---|
679 | throw; |
---|
680 | } |
---|
681 | catch (const exception &ex) { |
---|
682 | throw AipsError(String("SDLineFinder::getLineRanges - STL error: ")+ex.what()); |
---|
683 | } |
---|
684 | } |
---|
685 | |
---|
686 | // concatenate two lists preserving the order. If two lines appear to |
---|
687 | // be adjacent, they are joined into the new one |
---|
688 | void SDLineFinder::addNewSearchResult(const std::list<pair<int, int> > &newlines, |
---|
689 | std::list<std::pair<int, int> > &lines_list) |
---|
690 | throw(AipsError) |
---|
691 | { |
---|
692 | try { |
---|
693 | for (std::list<pair<int,int> >::const_iterator cli=newlines.begin(); |
---|
694 | cli!=newlines.end();++cli) { |
---|
695 | |
---|
696 | // the first item, which has a non-void intersection or touches |
---|
697 | // the new line |
---|
698 | std::list<pair<int,int> >::iterator pos_beg=find_if(lines_list.begin(), |
---|
699 | lines_list.end(), IntersectsWith(*cli)); |
---|
700 | // the last such item |
---|
701 | std::list<pair<int,int> >::iterator pos_end=find_if(pos_beg, |
---|
702 | lines_list.end(), not1(IntersectsWith(*cli))); |
---|
703 | |
---|
704 | // extract all lines which intersect or touch a new one into |
---|
705 | // a temporary buffer. This may invalidate the iterators |
---|
706 | // line_buffer may be empty, if no lines intersects with a new |
---|
707 | // one. |
---|
708 | std::list<pair<int,int> > lines_buffer; |
---|
709 | lines_buffer.splice(lines_buffer.end(),lines_list, pos_beg, pos_end); |
---|
710 | |
---|
711 | // build a union of all intersecting lines |
---|
712 | pair<int,int> union_line=for_each(lines_buffer.begin(), |
---|
713 | lines_buffer.end(),BuildUnion(*cli)).result(); |
---|
714 | |
---|
715 | // search for a right place for the new line (union_line) and add |
---|
716 | std::list<pair<int,int> >::iterator pos2insert=find_if(lines_list.begin(), |
---|
717 | lines_list.end(), LaterThan(union_line)); |
---|
718 | lines_list.insert(pos2insert,union_line); |
---|
719 | } |
---|
720 | } |
---|
721 | catch (const AipsError &ae) { |
---|
722 | throw; |
---|
723 | } |
---|
724 | catch (const exception &ex) { |
---|
725 | throw AipsError(String("SDLineFinder::addNewSearchResult - STL error: ")+ex.what()); |
---|
726 | } |
---|
727 | } |
---|
728 | |
---|
729 | // extend all line ranges to the point where a value stored in the |
---|
730 | // specified vector changes (e.g. value-mean change its sign) |
---|
731 | // This operation is necessary to include line wings, which are below |
---|
732 | // the detection threshold. If lines becomes adjacent, they are |
---|
733 | // merged together. Any masked channel stops the extension |
---|
734 | void SDLineFinder::searchForWings(std::list<std::pair<int, int> > &newlines, |
---|
735 | const casa::Vector<casa::Int> &signs) throw(casa::AipsError) |
---|
736 | { |
---|
737 | try { |
---|
738 | for (std::list<pair<int,int> >::iterator li=newlines.begin(); |
---|
739 | li!=newlines.end();++li) { |
---|
740 | // update the left hand side |
---|
741 | for (int n=li->first-1;n>=edge.first;--n) { |
---|
742 | if (!mask[n]) break; |
---|
743 | if (signs[n]==signs[li->first] && signs[li->first]) |
---|
744 | li->first=n; |
---|
745 | else break; |
---|
746 | } |
---|
747 | // update the right hand side |
---|
748 | for (int n=li->second;n<edge.second;++n) { |
---|
749 | if (!mask[n]) break; |
---|
750 | if (signs[n]==signs[li->second-1] && signs[li->second-1]) |
---|
751 | li->second=n; |
---|
752 | else break; |
---|
753 | } |
---|
754 | } |
---|
755 | // need to search for possible mergers. |
---|
756 | std::list<std::pair<int, int> > result_buffer; |
---|
757 | addNewSearchResult(newlines,result_buffer); |
---|
758 | newlines.clear(); |
---|
759 | newlines.splice(newlines.end(),result_buffer); |
---|
760 | } |
---|
761 | catch (const AipsError &ae) { |
---|
762 | throw; |
---|
763 | } |
---|
764 | catch (const exception &ex) { |
---|
765 | throw AipsError(String("SDLineFinder::extendLines - STL error: ")+ex.what()); |
---|
766 | } |
---|
767 | } |
---|