[540] | 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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[542] | 40 | const sa_size_t NUMBER_OF_CHANNELS = 2; |
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[544] | 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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[542] | 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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[544] | 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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[540] | 58 | char *regexp (const char *string, const char *patrn, int *begin, int *end) { |
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| 59 | int i, w=0, len; |
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| 60 | char *word = NULL; |
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| 61 | regex_t rgT; |
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| 62 | regmatch_t match; |
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| 63 | regcomp(&rgT,patrn,REG_EXTENDED); |
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| 64 | if ((regexec(&rgT,string,1,&match,0)) == 0) { |
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| 65 | *begin = (int)match.rm_so; |
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| 66 | *end = (int)match.rm_eo; |
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| 67 | len = *end-*begin; |
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| 68 | word=(char*)malloc(len+1); |
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| 69 | for (i=*begin; i<*end; i++) { |
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| 70 | word[w] = string[i]; |
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| 71 | w++; } |
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| 72 | word[w]=0; |
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| 73 | } |
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| 74 | regfree(&rgT); |
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| 75 | return word; |
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| 76 | } |
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[544] | 77 | //------- |
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[540] | 78 | sa_size_t round_sa(r_4 r) { |
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| 79 | return static_cast<sa_size_t>((r > 0.0) ? (r + 0.5) : (r - 0.5)); |
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| 80 | } |
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| 81 | //----- |
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| 82 | string StringToLower(string strToConvert){ |
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| 83 | //change each element of the string to lower case |
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| 84 | for(unsigned int i=0;i<strToConvert.length();i++) { |
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| 85 | strToConvert[i] = tolower(strToConvert[i]); |
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| 86 | } |
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| 87 | return strToConvert;//return the converted string |
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| 88 | } |
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| 89 | //----- |
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| 90 | bool stringCompare( const string &left, const string &right ){ |
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| 91 | if( left.size() < right.size() ) |
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| 92 | return true; |
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| 93 | for( string::const_iterator lit = left.begin(), rit = right.begin(); lit != left.end() && rit != right.end(); ++lit, ++rit ) |
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| 94 | if( tolower( *lit ) < tolower( *rit ) ) |
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| 95 | return true; |
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| 96 | else if( tolower( *lit ) > tolower( *rit ) ) |
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| 97 | return false; |
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| 98 | return false; |
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| 99 | } |
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| 100 | //----- |
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| 101 | list<string> ListOfFileInDir(string dir, string filePettern) throw(string) { |
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| 102 | list<string> theList; |
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| 103 | |
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| 104 | |
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| 105 | DIR *dip; |
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| 106 | struct dirent *dit; |
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| 107 | string msg; string fileName; |
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| 108 | string fullFileName; |
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| 109 | size_t found; |
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| 110 | |
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| 111 | if ((dip=opendir(dir.c_str())) == NULL ) { |
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| 112 | msg = "opendir failed on directory "+dir; |
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| 113 | throw msg; |
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| 114 | } |
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| 115 | while ( (dit = readdir(dip)) != NULL ) { |
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| 116 | fileName = dit->d_name; |
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| 117 | found=fileName.find(filePettern); |
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| 118 | if (found != string::npos) { |
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| 119 | fullFileName = dir + "/"; |
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| 120 | fullFileName += fileName; |
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| 121 | theList.push_back(fullFileName); |
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| 122 | } |
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| 123 | }//eo while |
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| 124 | if (closedir(dip) == -1) { |
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| 125 | msg = "closedir failed on directory "+dir; |
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| 126 | throw msg; |
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| 127 | } |
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| 128 | |
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| 129 | theList.sort(stringCompare); |
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| 130 | |
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| 131 | return theList; |
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| 132 | |
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| 133 | } |
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| 134 | // |
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| 135 | class StringMatch : public unary_function<string,bool> { |
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| 136 | public: |
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| 137 | StringMatch(const string& pattern): pattern_(pattern){} |
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| 138 | bool operator()(const string& aStr) const { |
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| 139 | |
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| 140 | |
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| 141 | int b,e; |
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| 142 | regexp(aStr.c_str(),pattern_.c_str(),&b,&e); |
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| 143 | |
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[541] | 144 | // cout << "investigate " << aStr << " to find " << pattern_ |
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| 145 | // << "[" <<b<<","<<e<<"]" |
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| 146 | // << endl; |
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[540] | 147 | |
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| 148 | |
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| 149 | if (b != 0) return false; |
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[544] | 150 | if (e != (int)aStr.size()) return false; |
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[540] | 151 | return true; |
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| 152 | |
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| 153 | } |
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| 154 | private: |
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| 155 | string pattern_; |
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| 156 | }; |
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| 157 | //------------------------------------------------------- |
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[544] | 158 | //Rebin in frequence + compute mean and sigma |
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| 159 | void reduceSpectra(const TMatrix<r_4>& specMtxInPut, |
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| 160 | TMatrix<r_4>& meanMtx, |
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| 161 | TMatrix<r_4>& sigmaMtx) { |
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| 162 | sa_size_t nSliceFreq = para.nSliceInFreq_; |
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| 163 | sa_size_t deltaFreq = NUMBER_OF_FREQ/nSliceFreq; |
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| 164 | for (sa_size_t iSlice=0; iSlice<nSliceFreq; iSlice++){ |
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| 165 | sa_size_t freqLow= iSlice*deltaFreq; |
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| 166 | sa_size_t freqHigh= freqLow + deltaFreq -1; |
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| 167 | for (sa_size_t iCh=0; iCh<NUMBER_OF_CHANNELS; ++iCh){ |
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| 168 | TVector<r_4> reducedRow; |
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| 169 | reducedRow = specMtxInPut.SubMatrix(Range(iCh),Range(freqLow,freqHigh)).CompactAllDimensions(); |
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| 170 | double mean; |
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| 171 | double sigma; |
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| 172 | MeanSigma(reducedRow,mean,sigma); |
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| 173 | meanMtx(iCh,iSlice) = mean; |
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| 174 | sigmaMtx(iCh,iSlice) = sigma; |
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| 175 | }//eo loop on channels |
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| 176 | }//eo loop on slices |
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| 177 | } |
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[541] | 178 | //------------------------------------------------------- |
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[544] | 179 | //Compute the mean of Raw spectra and also the mean/sigma of rebinned spectra |
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| 180 | //Used like: |
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| 181 | // |
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[540] | 182 | void meanOnCycles() throw(string) { |
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| 183 | list<string> listOfFiles; |
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| 184 | string directoryName; |
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| 185 | directoryName = para.inPath_ + "/" + para.sourceName_; |
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| 186 | |
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[542] | 187 | //Make the listing of the directory |
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[541] | 188 | listOfFiles = ListOfFileInDir(directoryName,para.ppfFile_); |
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[540] | 189 | |
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[541] | 190 | list<string>::const_iterator iFile, iFileEnd, iSpec, iSpecEnd; |
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[540] | 191 | iFileEnd = listOfFiles.end(); |
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| 192 | |
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[542] | 193 | StringMatch match("specONOFFRaw[0-9]+"); //Tag of the PPF objects |
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[544] | 194 | TMatrix<r_4> meanOfSpectra(NUMBER_OF_CHANNELS,NUMBER_OF_FREQ); |
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[542] | 195 | uint_4 nSpectra=0; |
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| 196 | //Loop on files |
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[540] | 197 | for (iFile = listOfFiles.begin(); iFile != iFileEnd; ++iFile) { |
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[542] | 198 | if (para.debuglev_>90){ |
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| 199 | cout << "load file <" << *iFile << ">" << endl; |
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| 200 | } |
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[540] | 201 | PInPersist fin(*iFile); |
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| 202 | vector<string> vec = fin.GetNameTags(); |
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[541] | 203 | list<string> listOfSpectra; |
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[542] | 204 | //Keep only required PPF objects |
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[540] | 205 | std::remove_copy_if( |
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| 206 | vec.begin(), vec.end(), back_inserter(listOfSpectra), |
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| 207 | not1(match) |
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| 208 | ); |
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| 209 | |
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[541] | 210 | iSpecEnd = listOfSpectra.end(); |
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| 211 | listOfSpectra.sort(stringCompare); |
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[542] | 212 | //Loop of spectra matrix |
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[541] | 213 | for (iSpec = listOfSpectra.begin(); iSpec !=iSpecEnd; ++iSpec){ |
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[542] | 214 | if (para.debuglev_>90){ |
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| 215 | cout << " spactra <" << *iSpec << ">" << endl; |
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| 216 | } |
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| 217 | TMatrix<r_4> aSpec(NUMBER_OF_CHANNELS,NUMBER_OF_FREQ); |
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| 218 | fin.GetObject(aSpec,*iSpec); |
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| 219 | //How to see if the GetObject is ok?? Ask Reza |
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| 220 | nSpectra++; |
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[544] | 221 | meanOfSpectra+=aSpec; |
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[542] | 222 | }//eo loop on spectra in a file |
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| 223 | }//eo loop on files |
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| 224 | |
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| 225 | //Normalisation |
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[544] | 226 | if(nSpectra>0)meanOfSpectra/=(r_4)(nSpectra); |
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[541] | 227 | |
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[544] | 228 | //Compute the reduced version of the mean and sigma |
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| 229 | TMatrix<r_4> meanRedMtx(NUMBER_OF_CHANNELS,para.nSliceInFreq_); |
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| 230 | TMatrix<r_4> sigmaRedMtx(NUMBER_OF_CHANNELS,para.nSliceInFreq_); |
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| 231 | reduceSpectra(meanOfSpectra,meanRedMtx,sigmaRedMtx); |
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| 232 | |
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[542] | 233 | {//Save the result |
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| 234 | stringstream tmp; |
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| 235 | tmp << nSpectra; |
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| 236 | string fileName = para.outPath_+"/meanDiffOnOffRaw_"+StringToLower(para.sourceName_)+"-"+tmp.str()+"Cycles.ppf"; |
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| 237 | cout << "Save mean based on " << nSpectra << " cycles " << endl; |
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[544] | 238 | POutPersist fos(fileName); |
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| 239 | |
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[542] | 240 | string tag = "mean"; |
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[544] | 241 | fos << PPFNameTag(tag) << meanOfSpectra; |
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| 242 | tag = "meanred"; |
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| 243 | fos << PPFNameTag(tag) << meanRedMtx; |
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| 244 | tag = "sigmared"; |
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| 245 | fos << PPFNameTag(tag) << sigmaRedMtx; |
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| 246 | } |
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| 247 | } |
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| 248 | //------------------------------------------------------- |
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| 249 | //Compute the median of Raw spectra and also the mean/sigma of rebinned spectra |
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| 250 | //Used like: |
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| 251 | // |
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| 252 | void medianOnCycles() throw(string) { |
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| 253 | list<string> listOfFiles; |
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| 254 | string directoryName; |
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| 255 | directoryName = para.inPath_ + "/" + para.sourceName_; |
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| 256 | |
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| 257 | //Make the listing of the directory |
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| 258 | listOfFiles = ListOfFileInDir(directoryName,para.ppfFile_); |
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| 259 | |
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| 260 | list<string>::const_iterator iFile, iFileEnd, iSpec, iSpecEnd; |
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| 261 | iFileEnd = listOfFiles.end(); |
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| 262 | |
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| 263 | |
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| 264 | TArray<r_4> tableOfSpectra(NUMBER_OF_FREQ,NUMBER_OF_CHANNELS,TOTAL_NUM_CYCLES); //TOTAL_NUM_CYCLES should be large enough... |
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| 265 | |
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| 266 | StringMatch match("specONOFFRaw[0-9]+"); //Tag of the PPF objects |
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| 267 | uint_4 nSpectra=0; |
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| 268 | //Loop on files |
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| 269 | for (iFile = listOfFiles.begin(); iFile != iFileEnd; ++iFile) { |
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| 270 | if (para.debuglev_>90){ |
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| 271 | cout << "load file <" << *iFile << ">" << endl; |
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| 272 | } |
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| 273 | PInPersist fin(*iFile); |
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| 274 | vector<string> vec = fin.GetNameTags(); |
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| 275 | list<string> listOfSpectra; |
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| 276 | //Keep only required PPF objects |
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| 277 | std::remove_copy_if( |
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| 278 | vec.begin(), vec.end(), back_inserter(listOfSpectra), |
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| 279 | not1(match) |
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| 280 | ); |
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| 281 | |
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| 282 | iSpecEnd = listOfSpectra.end(); |
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| 283 | listOfSpectra.sort(stringCompare); |
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| 284 | //Loop of spectra matrix |
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| 285 | for (iSpec = listOfSpectra.begin(); iSpec !=iSpecEnd; ++iSpec){ |
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| 286 | if (para.debuglev_>90){ |
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| 287 | cout << " spactra <" << *iSpec << ">" << endl; |
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| 288 | } |
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| 289 | TMatrix<r_4> aSpec(NUMBER_OF_CHANNELS,NUMBER_OF_FREQ); |
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| 290 | fin.GetObject(aSpec,*iSpec); |
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| 291 | |
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| 292 | if ((sa_size_t)nSpectra < TOTAL_NUM_CYCLES ) { |
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| 293 | //STORE THE spectra |
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| 294 | // tableOfSpectra(Range::all(),Range::all(),Range(nSpectra)).Show(); |
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| 295 | // aSpec.Show(); |
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| 296 | tableOfSpectra(Range::all(),Range::all(),Range(nSpectra)) = aSpec; |
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| 297 | // aSpec.Show(); |
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| 298 | // cout << "deb 1" << endl; |
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| 299 | // tmp = aSpec; |
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| 300 | // cout << "deb 2" << endl; |
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| 301 | } else { |
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| 302 | stringstream tmp; |
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| 303 | tmp<<nSpectra; |
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| 304 | throw "FATAL: SIZE ERROR: too many cycles:"+tmp.str(); |
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| 305 | } |
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| 306 | nSpectra++; |
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| 307 | }//eo loop on spectra in a file |
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| 308 | }//eo loop on files |
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| 309 | |
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| 310 | //Resize |
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| 311 | |
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| 312 | nSpectra--;//For further selection in Range |
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| 313 | if (para.debuglev_>90){ |
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| 314 | cout << "Cycles < 0," << nSpectra << ">" << endl; |
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| 315 | } |
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| 316 | |
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| 317 | |
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| 318 | TMatrix<r_4> medianOfSpectra(NUMBER_OF_CHANNELS,NUMBER_OF_FREQ); |
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| 319 | //Compute the median for each freq. and Channel |
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| 320 | for (sa_size_t iCh=0; iCh<NUMBER_OF_CHANNELS; iCh++){ |
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| 321 | for (sa_size_t freq =0; freq<NUMBER_OF_FREQ; freq++){ |
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| 322 | TVector<r_4> tmp0(tableOfSpectra(Range(freq),Range(iCh),Range(0,nSpectra)).CompactAllDimensions()); |
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| 323 | vector<r_4> tmp; |
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| 324 | tmp0.FillTo(tmp); |
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| 325 | nth_element(tmp.begin(),tmp.begin()+tmp.size()/2,tmp.end()); |
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| 326 | medianOfSpectra(iCh,freq) = *(tmp.begin()+tmp.size()/2); |
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| 327 | } |
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| 328 | } |
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| 329 | |
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| 330 | |
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| 331 | //Compute the reduced version of the mean and sigma |
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| 332 | TMatrix<r_4> meanRedMtx(NUMBER_OF_CHANNELS,para.nSliceInFreq_); |
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| 333 | TMatrix<r_4> sigmaRedMtx(NUMBER_OF_CHANNELS,para.nSliceInFreq_); |
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| 334 | reduceSpectra(medianOfSpectra,meanRedMtx,sigmaRedMtx); |
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| 335 | |
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| 336 | {//Save the result |
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| 337 | stringstream tmp; |
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| 338 | tmp << nSpectra; |
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| 339 | string fileName = para.outPath_+"/medianDiffOnOffRaw_"+StringToLower(para.sourceName_)+"-"+tmp.str()+"Cycles.ppf"; |
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| 340 | cout << "Save median based on " << (nSpectra+1) << " cycles " << endl; |
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[542] | 341 | POutPersist fos(fileName); |
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[544] | 342 | |
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| 343 | string tag = "median"; |
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| 344 | fos << PPFNameTag(tag) << medianOfSpectra; |
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| 345 | tag = "meanmedred"; |
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| 346 | fos << PPFNameTag(tag) << meanRedMtx; |
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| 347 | tag = "sigmamedred"; |
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| 348 | fos << PPFNameTag(tag) << sigmaRedMtx; |
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[540] | 349 | } |
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| 350 | } |
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[544] | 351 | |
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[540] | 352 | //------------------------------------------------------- |
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[544] | 353 | int main(int narg, char* arg[]) { |
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[540] | 354 | |
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| 355 | int rc = 0; //return code |
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| 356 | string msg; //message used in Exceptions |
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| 357 | |
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| 358 | |
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[544] | 359 | |
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| 360 | //default value for initial parameters (see Para structure on top of the file) |
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[540] | 361 | string debuglev = "0"; |
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[544] | 362 | string action = "meanDiffOnOff"; |
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[540] | 363 | string inputPath = "."; |
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| 364 | string outputPath = "."; |
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| 365 | string sourceName = "Abell85"; |
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[541] | 366 | string ppfFile; |
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[544] | 367 | string nSliceInFreq = "32"; |
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[540] | 368 | |
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| 369 | |
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| 370 | // bool okarg=false; |
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| 371 | int ka=1; |
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| 372 | while (ka<(narg-1)) { |
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| 373 | if (strcmp(arg[ka],"-debug")==0) { |
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| 374 | debuglev=arg[ka+1]; |
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| 375 | ka+=2; |
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| 376 | } |
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| 377 | else if (strcmp(arg[ka],"-act")==0) { |
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| 378 | action=arg[ka+1]; |
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| 379 | ka+=2; |
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| 380 | } |
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| 381 | else if (strcmp(arg[ka],"-inPath")==0) { |
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| 382 | inputPath=arg[ka+1]; |
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| 383 | ka+=2; |
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| 384 | } |
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| 385 | else if (strcmp(arg[ka],"-outPath")==0) { |
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| 386 | outputPath=arg[ka+1]; |
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| 387 | ka+=2; |
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| 388 | } |
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[541] | 389 | else if (strcmp(arg[ka],"-src")==0) { |
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[540] | 390 | sourceName=arg[ka+1]; |
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| 391 | ka+=2; |
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| 392 | } |
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[541] | 393 | else if (strcmp(arg[ka],"-ppfFile")==0) { |
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| 394 | ppfFile=arg[ka+1]; |
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[540] | 395 | ka+=2; |
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| 396 | } |
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[544] | 397 | else if (strcmp(arg[ka],"-nSliceInFreq")==0) { |
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| 398 | nSliceInFreq=arg[ka+1]; |
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| 399 | ka+=2; |
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| 400 | } |
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[540] | 401 | else ka++; |
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| 402 | }//eo while |
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| 403 | |
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[544] | 404 | para.debuglev_ = atoi(debuglev.c_str()); |
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| 405 | para.inPath_ = inputPath; |
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| 406 | para.outPath_ = outputPath; |
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[540] | 407 | para.sourceName_ = sourceName; |
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[544] | 408 | para.ppfFile_ = ppfFile; |
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| 409 | para.nSliceInFreq_ = atoi(nSliceInFreq.c_str()); |
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[540] | 410 | |
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| 411 | cout << "Dump Initial parameters ............" << endl; |
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| 412 | cout << " action = " << action << "\n" |
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[544] | 413 | << " inputPath = " << para.inPath_ << "\n" |
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| 414 | << " outputPath = " << para.outPath_ << "\n" |
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| 415 | << " sourceName = " << para.sourceName_ << "\n" |
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| 416 | << " ppfFile = " << para.ppfFile_ << "\n" |
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| 417 | << " nSliceInFreq = " << para.nSliceInFreq_ << "\n" |
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| 418 | << " debuglev = " << para.debuglev_ << "\n"; |
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[540] | 419 | cout << "...................................." << endl; |
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| 420 | |
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[541] | 421 | if ( "" == ppfFile ) { |
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| 422 | cerr << "mergeRawOnOff.cc: you have forgotten ppfFile option" |
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| 423 | << endl; |
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| 424 | return 999; |
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| 425 | } |
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| 426 | |
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| 427 | |
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[540] | 428 | try { |
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| 429 | |
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[542] | 430 | // int b,e; |
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| 431 | // char *match=regexp("truc0machin","[a-z]+[0-9]*",&b,&e); |
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| 432 | // printf("->%s<-\n(b=%d e=%d)\n",match,b,e); |
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[540] | 433 | |
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[544] | 434 | if ( action == "meanDiffOnOff" ) { |
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[540] | 435 | meanOnCycles(); |
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[544] | 436 | } else if (action == "medianDiffOnOff") { |
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| 437 | medianOnCycles(); |
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| 438 | } else { |
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| 439 | msg = "Unknown action " + action; |
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| 440 | throw msg; |
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[540] | 441 | } |
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| 442 | |
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[544] | 443 | |
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[540] | 444 | } catch (std::exception& sex) { |
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| 445 | cerr << "mergeRawOnOff.cc std::exception :" << (string)typeid(sex).name() |
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| 446 | << "\n msg= " << sex.what() << endl; |
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| 447 | rc = 78; |
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| 448 | } |
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| 449 | catch ( string str ) { |
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| 450 | cerr << "mergeRawOnOff.cc Exception raised: " << str << endl; |
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| 451 | } |
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| 452 | catch (...) { |
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| 453 | cerr << "mergeRawOnOff.cc catched unknown (...) exception " << endl; |
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| 454 | rc = 79; |
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| 455 | } |
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| 456 | |
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| 457 | return 0; |
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| 458 | |
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| 459 | } |
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