1 | // Utilisation de SOPHYA pour faciliter les tests ... |
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2 | #include <regex.h> |
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3 | //#include <regexp.h> |
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4 | #include <stdio.h> |
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5 | |
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6 | #include "sopnamsp.h" |
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7 | #include "machdefs.h" |
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8 | |
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9 | #include <stdlib.h> |
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10 | #include <dirent.h> |
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11 | #include <matharr.h> |
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12 | |
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13 | // include standard c/c++ |
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14 | #include <iostream> |
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15 | #include <fstream> |
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16 | #include <string> |
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17 | #include <vector> |
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18 | #include <map> |
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19 | #include <functional> |
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20 | #include <algorithm> |
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21 | #include <numeric> |
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22 | #include <list> |
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23 | #include <exception> |
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24 | |
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25 | // include sophya mesure ressource CPU/memoire ... |
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26 | #include "resusage.h" |
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27 | #include "ctimer.h" |
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28 | #include "timing.h" |
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29 | #include "timestamp.h" |
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30 | #include "strutilxx.h" |
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31 | #include "ntuple.h" |
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32 | #include "fioarr.h" |
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33 | #include "tarrinit.h" |
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34 | #include "histinit.h" |
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35 | #include "fitsioserver.h" |
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36 | #include "fiosinit.h" |
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37 | #include "ppersist.h" |
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38 | |
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39 | //----------------------------------------------- |
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40 | const sa_size_t NUMBER_OF_CHANNELS = 2; |
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41 | const sa_size_t NUMBER_OF_FREQ = 8192; |
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42 | const sa_size_t TOTAL_NUM_CYCLES = 10000; |
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43 | const r_4 LOWER_FREQUENCY = 1250.0; //MHz |
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44 | const r_4 TOTAL_BANDWIDTH = 250.0; //MHz |
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45 | //----------------------------------------------- |
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46 | //Input parameters |
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47 | struct Param { |
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48 | int debuglev_; //debug |
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49 | string inPath_; //root directory of the input files |
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50 | string outPath_; //output files are located here |
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51 | string sourceName_; //source name & subdirectory of the input files |
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52 | string ppfFile_; //generic name of the input files |
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53 | int nSliceInFreq_; //used by reduceSpectra() fnc |
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54 | } para; |
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55 | //-------------------------------------------------------------- |
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56 | //Utility functions |
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57 | |
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58 | class median_of_empty_list_exception:public std::exception{ |
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59 | virtual const char* what() const throw() { |
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60 | return "Attempt to take the median of an empty list of numbers. " |
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61 | "The median of an empty list is undefined."; |
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62 | } |
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63 | }; |
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64 | template<class RandAccessIter> |
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65 | double median(RandAccessIter begin, RandAccessIter end) |
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66 | throw(median_of_empty_list_exception){ |
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67 | if(begin == end){ throw median_of_empty_list_exception(); } |
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68 | std::size_t size = end - begin; |
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69 | std::size_t middleIdx = size/2; |
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70 | RandAccessIter target = begin + middleIdx; |
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71 | std::nth_element(begin, target, end); |
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72 | |
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73 | if(size % 2 != 0){ //Odd number of elements |
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74 | return *target; |
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75 | }else{ //Even number of elements |
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76 | double a = *target; |
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77 | RandAccessIter targetNeighbor= target-1; |
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78 | std::nth_element(begin, targetNeighbor, end); |
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79 | return (a+*targetNeighbor)/2.0; |
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80 | } |
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81 | } |
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82 | |
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83 | //-------------------------------------------------------------- |
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84 | char *regexp (const char *string, const char *patrn, int *begin, int *end) { |
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85 | int i, w=0, len; |
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86 | char *word = NULL; |
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87 | regex_t rgT; |
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88 | regmatch_t match; |
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89 | regcomp(&rgT,patrn,REG_EXTENDED); |
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90 | if ((regexec(&rgT,string,1,&match,0)) == 0) { |
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91 | *begin = (int)match.rm_so; |
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92 | *end = (int)match.rm_eo; |
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93 | len = *end-*begin; |
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94 | word=(char*)malloc(len+1); |
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95 | for (i=*begin; i<*end; i++) { |
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96 | word[w] = string[i]; |
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97 | w++; } |
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98 | word[w]=0; |
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99 | } |
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100 | regfree(&rgT); |
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101 | return word; |
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102 | } |
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103 | //------- |
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104 | sa_size_t round_sa(r_4 r) { |
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105 | return static_cast<sa_size_t>((r > 0.0) ? (r + 0.5) : (r - 0.5)); |
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106 | } |
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107 | //----- |
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108 | string StringToLower(string strToConvert){ |
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109 | //change each element of the string to lower case |
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110 | for(unsigned int i=0;i<strToConvert.length();i++) { |
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111 | strToConvert[i] = tolower(strToConvert[i]); |
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112 | } |
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113 | return strToConvert;//return the converted string |
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114 | } |
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115 | //----- |
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116 | bool stringCompare( const string &left, const string &right ){ |
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117 | if( left.size() < right.size() ) |
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118 | return true; |
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119 | for( string::const_iterator lit = left.begin(), rit = right.begin(); lit != left.end() && rit != right.end(); ++lit, ++rit ) |
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120 | if( tolower( *lit ) < tolower( *rit ) ) |
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121 | return true; |
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122 | else if( tolower( *lit ) > tolower( *rit ) ) |
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123 | return false; |
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124 | return false; |
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125 | } |
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126 | //----- |
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127 | list<string> ListOfFileInDir(string dir, string filePettern) throw(string) { |
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128 | list<string> theList; |
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129 | |
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130 | |
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131 | DIR *dip; |
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132 | struct dirent *dit; |
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133 | string msg; string fileName; |
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134 | string fullFileName; |
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135 | size_t found; |
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136 | |
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137 | if ((dip=opendir(dir.c_str())) == NULL ) { |
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138 | msg = "opendir failed on directory "+dir; |
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139 | throw msg; |
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140 | } |
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141 | while ( (dit = readdir(dip)) != NULL ) { |
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142 | fileName = dit->d_name; |
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143 | found=fileName.find(filePettern); |
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144 | if (found != string::npos) { |
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145 | fullFileName = dir + "/"; |
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146 | fullFileName += fileName; |
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147 | theList.push_back(fullFileName); |
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148 | } |
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149 | }//eo while |
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150 | if (closedir(dip) == -1) { |
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151 | msg = "closedir failed on directory "+dir; |
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152 | throw msg; |
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153 | } |
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154 | |
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155 | theList.sort(stringCompare); |
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156 | |
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157 | return theList; |
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158 | |
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159 | } |
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160 | // |
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161 | class StringMatch : public unary_function<string,bool> { |
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162 | public: |
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163 | StringMatch(const string& pattern): pattern_(pattern){} |
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164 | bool operator()(const string& aStr) const { |
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165 | |
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166 | |
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167 | int b,e; |
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168 | regexp(aStr.c_str(),pattern_.c_str(),&b,&e); |
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169 | |
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170 | // cout << "investigate " << aStr << " to find " << pattern_ |
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171 | // << "[" <<b<<","<<e<<"]" |
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172 | // << endl; |
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173 | |
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174 | |
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175 | if (b != 0) return false; |
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176 | if (e != (int)aStr.size()) return false; |
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177 | return true; |
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178 | |
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179 | } |
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180 | private: |
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181 | string pattern_; |
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182 | }; |
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183 | //------------------------------------------------------- |
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184 | //Rebin in frequence + compute mean and sigma |
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185 | void reduceSpectra(const TMatrix<r_4>& specMtxInPut, |
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186 | TMatrix<r_4>& meanMtx, |
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187 | TMatrix<r_4>& sigmaMtx) { |
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188 | sa_size_t nSliceFreq = para.nSliceInFreq_; |
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189 | sa_size_t deltaFreq = NUMBER_OF_FREQ/nSliceFreq; |
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190 | for (sa_size_t iSlice=0; iSlice<nSliceFreq; iSlice++){ |
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191 | sa_size_t freqLow= iSlice*deltaFreq; |
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192 | sa_size_t freqHigh= freqLow + deltaFreq -1; |
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193 | for (sa_size_t iCh=0; iCh<NUMBER_OF_CHANNELS; ++iCh){ |
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194 | TVector<r_4> reducedRow; |
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195 | reducedRow = specMtxInPut.SubMatrix(Range(iCh),Range(freqLow,freqHigh)).CompactAllDimensions(); |
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196 | double mean; |
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197 | double sigma; |
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198 | MeanSigma(reducedRow,mean,sigma); |
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199 | meanMtx(iCh,iSlice) = mean; |
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200 | sigmaMtx(iCh,iSlice) = sigma; |
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201 | }//eo loop on channels |
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202 | }//eo loop on slices |
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203 | } |
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204 | //------------------------------------------------------- |
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205 | //Compute the mean of Raw spectra and also the mean/sigma of rebinned spectra |
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206 | //Used like: |
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207 | // |
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208 | void meanOnCycles() throw(string) { |
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209 | list<string> listOfFiles; |
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210 | string directoryName; |
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211 | directoryName = para.inPath_ + "/" + para.sourceName_; |
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212 | |
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213 | //Make the listing of the directory |
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214 | listOfFiles = ListOfFileInDir(directoryName,para.ppfFile_); |
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215 | |
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216 | list<string>::const_iterator iFile, iFileEnd, iSpec, iSpecEnd; |
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217 | iFileEnd = listOfFiles.end(); |
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218 | |
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219 | StringMatch match("specONOFFRaw[0-9]+"); //Tag of the PPF objects |
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220 | TMatrix<r_4> meanOfSpectra(NUMBER_OF_CHANNELS,NUMBER_OF_FREQ); |
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221 | uint_4 nSpectra=0; |
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222 | //Loop on files |
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223 | for (iFile = listOfFiles.begin(); iFile != iFileEnd; ++iFile) { |
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224 | if (para.debuglev_>90){ |
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225 | cout << "load file <" << *iFile << ">" << endl; |
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226 | } |
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227 | PInPersist fin(*iFile); |
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228 | vector<string> vec = fin.GetNameTags(); |
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229 | list<string> listOfSpectra; |
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230 | //Keep only required PPF objects |
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231 | std::remove_copy_if( |
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232 | vec.begin(), vec.end(), back_inserter(listOfSpectra), |
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233 | not1(match) |
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234 | ); |
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235 | |
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236 | iSpecEnd = listOfSpectra.end(); |
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237 | listOfSpectra.sort(stringCompare); |
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238 | //Loop of spectra matrix |
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239 | for (iSpec = listOfSpectra.begin(); iSpec !=iSpecEnd; ++iSpec){ |
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240 | if (para.debuglev_>90){ |
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241 | cout << " spactra <" << *iSpec << ">" << endl; |
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242 | } |
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243 | TMatrix<r_4> aSpec(NUMBER_OF_CHANNELS,NUMBER_OF_FREQ); |
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244 | fin.GetObject(aSpec,*iSpec); |
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245 | //How to see if the GetObject is ok?? Ask Reza |
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246 | nSpectra++; |
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247 | meanOfSpectra+=aSpec; |
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248 | }//eo loop on spectra in a file |
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249 | }//eo loop on files |
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250 | |
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251 | //Normalisation |
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252 | if(nSpectra>0)meanOfSpectra/=(r_4)(nSpectra); |
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253 | |
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254 | //Compute the reduced version of the mean and sigma |
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255 | TMatrix<r_4> meanRedMtx(NUMBER_OF_CHANNELS,para.nSliceInFreq_); |
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256 | TMatrix<r_4> sigmaRedMtx(NUMBER_OF_CHANNELS,para.nSliceInFreq_); |
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257 | reduceSpectra(meanOfSpectra,meanRedMtx,sigmaRedMtx); |
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258 | |
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259 | {//Save the result |
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260 | stringstream tmp; |
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261 | tmp << nSpectra; |
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262 | string fileName = para.outPath_+"/meanDiffOnOffRaw_"+StringToLower(para.sourceName_)+"-"+tmp.str()+"Cycles.ppf"; |
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263 | cout << "Save mean based on " << nSpectra << " cycles " << endl; |
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264 | POutPersist fos(fileName); |
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265 | |
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266 | string tag = "mean"; |
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267 | fos << PPFNameTag(tag) << meanOfSpectra; |
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268 | tag = "meanred"; |
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269 | fos << PPFNameTag(tag) << meanRedMtx; |
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270 | tag = "sigmared"; |
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271 | fos << PPFNameTag(tag) << sigmaRedMtx; |
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272 | } |
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273 | } |
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274 | //------------------------------------------------------- |
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275 | //Compute the median of Raw spectra and also the mean/sigma of rebinned spectra |
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276 | //Used like: |
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277 | // |
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278 | void medianOnCycles() throw(string) { |
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279 | list<string> listOfFiles; |
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280 | string directoryName; |
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281 | directoryName = para.inPath_ + "/" + para.sourceName_; |
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282 | |
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283 | //Make the listing of the directory |
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284 | listOfFiles = ListOfFileInDir(directoryName,para.ppfFile_); |
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285 | |
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286 | list<string>::const_iterator iFile, iFileEnd, iSpec, iSpecEnd; |
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287 | iFileEnd = listOfFiles.end(); |
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288 | |
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289 | |
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290 | TArray<r_4> tableOfSpectra(NUMBER_OF_FREQ,NUMBER_OF_CHANNELS,TOTAL_NUM_CYCLES); //TOTAL_NUM_CYCLES should be large enough... |
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291 | |
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292 | StringMatch match("specONOFFRaw[0-9]+"); //Tag of the PPF objects |
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293 | uint_4 nSpectra=0; |
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294 | //Loop on files |
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295 | for (iFile = listOfFiles.begin(); iFile != iFileEnd; ++iFile) { |
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296 | if (para.debuglev_>90){ |
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297 | cout << "load file <" << *iFile << ">" << endl; |
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298 | } |
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299 | PInPersist fin(*iFile); |
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300 | vector<string> vec = fin.GetNameTags(); |
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301 | list<string> listOfSpectra; |
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302 | //Keep only required PPF objects |
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303 | std::remove_copy_if( |
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304 | vec.begin(), vec.end(), back_inserter(listOfSpectra), |
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305 | not1(match) |
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306 | ); |
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307 | |
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308 | iSpecEnd = listOfSpectra.end(); |
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309 | listOfSpectra.sort(stringCompare); |
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310 | //Loop of spectra matrix |
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311 | for (iSpec = listOfSpectra.begin(); iSpec !=iSpecEnd; ++iSpec){ |
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312 | if (para.debuglev_>90){ |
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313 | cout << " spactra <" << *iSpec << ">" << endl; |
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314 | } |
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315 | TMatrix<r_4> aSpec(NUMBER_OF_CHANNELS,NUMBER_OF_FREQ); |
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316 | fin.GetObject(aSpec,*iSpec); |
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317 | |
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318 | if ((sa_size_t)nSpectra < TOTAL_NUM_CYCLES ) { |
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319 | tableOfSpectra(Range::all(),Range::all(),Range(nSpectra)) = aSpec; |
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320 | } else { |
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321 | stringstream tmp; |
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322 | tmp<<nSpectra; |
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323 | throw "FATAL: SIZE ERROR: too many cycles:"+tmp.str(); |
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324 | } |
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325 | nSpectra++; |
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326 | }//eo loop on spectra in a file |
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327 | }//eo loop on files |
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328 | |
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329 | //Resize |
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330 | |
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331 | |
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332 | TMatrix<r_4> medianOfSpectra(NUMBER_OF_CHANNELS,NUMBER_OF_FREQ); |
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333 | //Compute the median for each freq. and Channel |
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334 | for (sa_size_t iCh=0; iCh<NUMBER_OF_CHANNELS; iCh++){ |
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335 | for (sa_size_t freq =0; freq<NUMBER_OF_FREQ; freq++){ |
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336 | TVector<r_4> tmp0(tableOfSpectra(Range(freq),Range(iCh),Range(0,nSpectra-1)).CompactAllDimensions()); |
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337 | vector<r_4> tmp; |
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338 | tmp0.FillTo(tmp); |
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339 | medianOfSpectra(iCh,freq) = median(tmp.begin(),tmp.end()); |
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340 | } |
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341 | } |
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342 | |
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343 | |
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344 | //Compute the reduced version of the mean and sigma |
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345 | TMatrix<r_4> meanRedMtx(NUMBER_OF_CHANNELS,para.nSliceInFreq_); |
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346 | TMatrix<r_4> sigmaRedMtx(NUMBER_OF_CHANNELS,para.nSliceInFreq_); |
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347 | reduceSpectra(medianOfSpectra,meanRedMtx,sigmaRedMtx); |
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348 | |
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349 | {//Save the result |
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350 | stringstream tmp; |
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351 | tmp << nSpectra; |
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352 | string fileName = para.outPath_+"/medianDiffOnOffRaw_"+StringToLower(para.sourceName_)+"-"+tmp.str()+"Cycles.ppf"; |
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353 | cout << "Save median based on " << nSpectra << " cycles " << endl; |
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354 | POutPersist fos(fileName); |
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355 | |
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356 | string tag = "median"; |
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357 | fos << PPFNameTag(tag) << medianOfSpectra; |
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358 | tag = "meanmedred"; |
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359 | fos << PPFNameTag(tag) << meanRedMtx; |
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360 | tag = "sigmamedred"; |
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361 | fos << PPFNameTag(tag) << sigmaRedMtx; |
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362 | tag = "cycleVsfreq"; |
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363 | |
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364 | TArray<r_4> tarr(tableOfSpectra(Range::all(),Range::all(),Range(0,nSpectra-1))); |
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365 | fos << PPFNameTag(tag) << tarr; |
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366 | } |
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367 | } |
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368 | |
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369 | //------------------------------------------------------- |
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370 | int main(int narg, char* arg[]) { |
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371 | |
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372 | int rc = 0; //return code |
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373 | string msg; //message used in Exceptions |
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374 | |
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375 | |
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376 | |
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377 | //default value for initial parameters (see Para structure on top of the file) |
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378 | string debuglev = "0"; |
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379 | string action = "meanDiffOnOff"; |
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380 | string inputPath = "."; |
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381 | string outputPath = "."; |
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382 | string sourceName = "Abell85"; |
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383 | string ppfFile; |
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384 | string nSliceInFreq = "32"; |
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385 | |
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386 | |
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387 | // bool okarg=false; |
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388 | int ka=1; |
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389 | while (ka<(narg-1)) { |
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390 | if (strcmp(arg[ka],"-h")==0) { |
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391 | cout << "Usage: -act [meanDiffOnOff]|medianDiffOnOff\n" |
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392 | << " -src [Abell85]\n -inPath [.]|<top_root_dir of the ppf file>\n" |
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393 | << " (ex. /sps/baoradio/AmasNancay/JEC/\n " |
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394 | << " -outPath [.]|<dir of the output> \n" |
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395 | << " -nSliceInFreq [32]|<number of bin in freq. to cumulate>\n" |
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396 | << " -ppfFile <generic name of the input ppf files> (ex. diffOnOffRaw)" |
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397 | << " -debug <level> " |
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398 | << endl; |
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399 | return 0; |
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400 | } |
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401 | else if (strcmp(arg[ka],"-debug")==0) { |
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402 | debuglev=arg[ka+1]; |
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403 | ka+=2; |
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404 | } |
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405 | else if (strcmp(arg[ka],"-act")==0) { |
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406 | action=arg[ka+1]; |
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407 | ka+=2; |
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408 | } |
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409 | else if (strcmp(arg[ka],"-inPath")==0) { |
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410 | inputPath=arg[ka+1]; |
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411 | ka+=2; |
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412 | } |
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413 | else if (strcmp(arg[ka],"-outPath")==0) { |
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414 | outputPath=arg[ka+1]; |
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415 | ka+=2; |
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416 | } |
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417 | else if (strcmp(arg[ka],"-src")==0) { |
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418 | sourceName=arg[ka+1]; |
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419 | ka+=2; |
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420 | } |
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421 | else if (strcmp(arg[ka],"-ppfFile")==0) { |
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422 | ppfFile=arg[ka+1]; |
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423 | ka+=2; |
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424 | } |
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425 | else if (strcmp(arg[ka],"-nSliceInFreq")==0) { |
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426 | nSliceInFreq=arg[ka+1]; |
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427 | ka+=2; |
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428 | } |
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429 | else ka++; |
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430 | }//eo while |
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431 | |
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432 | para.debuglev_ = atoi(debuglev.c_str()); |
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433 | para.inPath_ = inputPath; |
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434 | para.outPath_ = outputPath; |
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435 | para.sourceName_ = sourceName; |
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436 | para.ppfFile_ = ppfFile; |
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437 | para.nSliceInFreq_ = atoi(nSliceInFreq.c_str()); |
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438 | |
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439 | cout << "Dump Initial parameters ............" << endl; |
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440 | cout << " action = " << action << "\n" |
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441 | << " inputPath = " << para.inPath_ << "\n" |
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442 | << " outputPath = " << para.outPath_ << "\n" |
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443 | << " sourceName = " << para.sourceName_ << "\n" |
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444 | << " ppfFile = " << para.ppfFile_ << "\n" |
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445 | << " nSliceInFreq = " << para.nSliceInFreq_ << "\n" |
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446 | << " debuglev = " << para.debuglev_ << "\n"; |
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447 | cout << "...................................." << endl; |
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448 | |
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449 | if ( "" == ppfFile ) { |
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450 | cerr << "mergeRawOnOff.cc: you have forgotten ppfFile option" |
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451 | << endl; |
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452 | return 999; |
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453 | } |
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454 | |
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455 | |
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456 | try { |
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457 | |
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458 | // int b,e; |
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459 | // char *match=regexp("truc0machin","[a-z]+[0-9]*",&b,&e); |
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460 | // printf("->%s<-\n(b=%d e=%d)\n",match,b,e); |
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461 | |
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462 | if ( action == "meanDiffOnOff" ) { |
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463 | meanOnCycles(); |
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464 | } else if (action == "medianDiffOnOff") { |
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465 | medianOnCycles(); |
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466 | } else { |
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467 | msg = "Unknown action " + action; |
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468 | throw msg; |
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469 | } |
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470 | |
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471 | |
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472 | } catch (std::exception& sex) { |
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473 | cerr << "mergeRawOnOff.cc std::exception :" << (string)typeid(sex).name() |
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474 | << "\n msg= " << sex.what() << endl; |
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475 | rc = 78; |
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476 | } |
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477 | catch ( string str ) { |
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478 | cerr << "mergeRawOnOff.cc Exception raised: " << str << endl; |
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479 | } |
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480 | catch (...) { |
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481 | cerr << "mergeRawOnOff.cc catched unknown (...) exception " << endl; |
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482 | rc = 79; |
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483 | } |
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484 | |
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485 | return 0; |
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486 | |
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487 | } |
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