[301] | 1 | // ----------------------------------------------------------------------- |
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| 2 | // Statistics.cc: Member functions for the templated StatsContainer |
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| 3 | // class. |
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| 4 | // ----------------------------------------------------------------------- |
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| 5 | // Copyright (C) 2006, Matthew Whiting, 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 |
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| 9 | // Free Software Foundation; either version 2 of the License, or (at your |
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| 10 | // option) any later version. |
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| 11 | // |
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| 12 | // Duchamp is distributed in the hope that it will be useful, but WITHOUT |
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| 13 | // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or |
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| 14 | // FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License |
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| 15 | // 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 |
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| 18 | // along with Duchamp; if not, write to the Free Software Foundation, |
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| 19 | // Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA |
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| 20 | // |
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| 21 | // Correspondence concerning Duchamp may be directed to: |
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| 22 | // Internet email: Matthew.Whiting [at] atnf.csiro.au |
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| 23 | // Postal address: Dr. Matthew Whiting |
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| 24 | // Australia Telescope National Facility, CSIRO |
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| 25 | // PO Box 76 |
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| 26 | // Epping NSW 1710 |
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| 27 | // AUSTRALIA |
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| 28 | // ----------------------------------------------------------------------- |
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[201] | 29 | #include <iostream> |
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[1146] | 30 | #include <fstream> |
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[393] | 31 | #include <duchamp/Utils/Statistics.hh> |
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| 32 | #include <duchamp/Utils/utils.hh> |
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[190] | 33 | |
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[201] | 34 | namespace Statistics |
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[190] | 35 | { |
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[266] | 36 | |
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[271] | 37 | template <class T> |
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| 38 | float madfmToSigma(T madfm){ |
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[266] | 39 | return float(madfm)/correctionFactor; |
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[282] | 40 | } |
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[266] | 41 | template float madfmToSigma<int>(int madfm); |
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| 42 | template float madfmToSigma<long>(long madfm); |
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| 43 | template float madfmToSigma<float>(float madfm); |
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| 44 | template float madfmToSigma<double>(double madfm); |
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| 45 | |
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[222] | 46 | //-------------------------------------------------------------------- |
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[282] | 47 | float sigmaToMADFM(float sigma){ |
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[275] | 48 | return float(sigma)*correctionFactor; |
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[282] | 49 | } |
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[222] | 50 | //-------------------------------------------------------------------- |
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[275] | 51 | //-------------------------------------------------------------------- |
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[222] | 52 | |
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[1152] | 53 | template <class Type> |
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| 54 | StatsContainer<Type>::StatsContainer() |
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| 55 | { |
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| 56 | defined = false; |
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| 57 | mean=Type(0); |
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| 58 | stddev=Type(0); |
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| 59 | median=Type(0); |
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| 60 | madfm=Type(0); |
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| 61 | threshold=Type(0); |
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| 62 | pThreshold=Type(0); |
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| 63 | useRobust=true; |
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| 64 | useFDR=false; |
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| 65 | commentString=""; |
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| 66 | } |
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| 67 | template StatsContainer<int>::StatsContainer(); |
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| 68 | template StatsContainer<long>::StatsContainer(); |
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| 69 | template StatsContainer<float>::StatsContainer(); |
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| 70 | template StatsContainer<double>::StatsContainer(); |
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| 71 | //-------------------------------------------------------------------- |
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| 72 | |
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| 73 | |
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[222] | 74 | template <class Type> |
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| 75 | StatsContainer<Type>::StatsContainer(const StatsContainer<Type>& s) |
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[201] | 76 | { |
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[528] | 77 | /// @details |
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| 78 | /// The copy constructor for the StatsContainer class. Just uses |
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| 79 | /// the assignment operator. |
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| 80 | |
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[365] | 81 | operator=(s); |
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[201] | 82 | } |
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| 83 | template StatsContainer<int>::StatsContainer(const StatsContainer<int>& s); |
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| 84 | template StatsContainer<long>::StatsContainer(const StatsContainer<long>& s); |
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| 85 | template StatsContainer<float>::StatsContainer(const StatsContainer<float>& s); |
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| 86 | template StatsContainer<double>::StatsContainer(const StatsContainer<double>& s); |
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| 87 | //-------------------------------------------------------------------- |
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[192] | 88 | |
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[222] | 89 | template <class Type> |
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[271] | 90 | StatsContainer<Type>& |
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| 91 | StatsContainer<Type>::operator= (const StatsContainer<Type>& s) |
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[201] | 92 | { |
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[528] | 93 | /// The assignment operator for the StatsContainer class. |
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[271] | 94 | |
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[270] | 95 | if(this == &s) return *this; |
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[201] | 96 | this->defined = s.defined; |
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| 97 | this->mean = s.mean; |
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| 98 | this->stddev = s.stddev; |
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| 99 | this->median = s.median; |
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| 100 | this->madfm = s.madfm; |
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| 101 | this->threshold = s.threshold; |
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| 102 | this->pThreshold = s.pThreshold; |
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| 103 | this->useRobust = s.useRobust; |
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| 104 | this->useFDR = s.useFDR; |
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[1137] | 105 | this->commentString = s.commentString; |
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[270] | 106 | return *this; |
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[201] | 107 | } |
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| 108 | template StatsContainer<int>& StatsContainer<int>::operator= (const StatsContainer<int>& s); |
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| 109 | template StatsContainer<long>& StatsContainer<long>::operator= (const StatsContainer<long>& s); |
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| 110 | template StatsContainer<float>& StatsContainer<float>::operator= (const StatsContainer<float>& s); |
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| 111 | template StatsContainer<double>& StatsContainer<double>::operator= (const StatsContainer<double>& s); |
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| 112 | //-------------------------------------------------------------------- |
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[192] | 113 | |
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[222] | 114 | template <class Type> |
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[271] | 115 | float StatsContainer<Type>::getThresholdSNR() |
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| 116 | { |
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[528] | 117 | /// @details |
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| 118 | /// The SNR is defined in terms of excess over the middle estimator |
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| 119 | /// in units of the spread estimator. |
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[271] | 120 | return (threshold - this->getMiddle())/this->getSpread(); |
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| 121 | } |
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| 122 | template float StatsContainer<int>::getThresholdSNR(); |
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| 123 | template float StatsContainer<long>::getThresholdSNR(); |
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| 124 | template float StatsContainer<float>::getThresholdSNR(); |
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| 125 | template float StatsContainer<double>::getThresholdSNR(); |
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| 126 | //-------------------------------------------------------------------- |
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| 127 | |
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| 128 | template <class Type> |
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| 129 | void StatsContainer<Type>::setThresholdSNR(float snr) |
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| 130 | { |
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[528] | 131 | /// @details |
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| 132 | /// The SNR is defined in terms of excess over the middle estimator |
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| 133 | /// in units of the spread estimator. |
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[1152] | 134 | if(this->defined) |
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[1170] | 135 | this->threshold=this->getMiddle() + snr*this->getSpread(); |
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[271] | 136 | } |
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| 137 | template void StatsContainer<int>::setThresholdSNR(float snr); |
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| 138 | template void StatsContainer<long>::setThresholdSNR(float snr); |
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| 139 | template void StatsContainer<float>::setThresholdSNR(float snr); |
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| 140 | template void StatsContainer<double>::setThresholdSNR(float snr); |
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| 141 | //-------------------------------------------------------------------- |
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| 142 | |
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| 143 | template <class Type> |
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[481] | 144 | float StatsContainer<Type>::valueToSNR(float value) |
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[271] | 145 | { |
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[528] | 146 | /// @details |
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| 147 | /// The SNR is defined in terms of excess over the middle estimator |
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| 148 | /// in units of the spread estimator. |
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[1152] | 149 | if(this->defined) |
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| 150 | return (value - this->getMiddle())/this->getSpread(); |
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| 151 | else |
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| 152 | return Type(0); |
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[271] | 153 | } |
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[481] | 154 | template float StatsContainer<int>::valueToSNR(float value); |
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| 155 | template float StatsContainer<long>::valueToSNR(float value); |
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| 156 | template float StatsContainer<float>::valueToSNR(float value); |
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| 157 | template float StatsContainer<double>::valueToSNR(float value); |
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[271] | 158 | //-------------------------------------------------------------------- |
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[481] | 159 | |
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| 160 | template <class Type> |
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| 161 | float StatsContainer<Type>::snrToValue(float snr) |
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| 162 | { |
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[528] | 163 | /// @details |
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| 164 | /// The SNR is defined in terms of excess over the middle estimator |
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| 165 | /// in units of the spread estimator. |
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[481] | 166 | return snr * this->getSpread() + this->getMiddle(); |
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| 167 | } |
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| 168 | template float StatsContainer<int>::snrToValue(float value); |
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| 169 | template float StatsContainer<long>::snrToValue(float value); |
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| 170 | template float StatsContainer<float>::snrToValue(float value); |
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| 171 | template float StatsContainer<double>::snrToValue(float value); |
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| 172 | //-------------------------------------------------------------------- |
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[271] | 173 | |
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| 174 | template <class Type> |
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[475] | 175 | void StatsContainer<Type>::setMiddle(float middle) |
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| 176 | { |
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[528] | 177 | /// @details |
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| 178 | /// The middle value is determined by the StatsContainer::useRobust |
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| 179 | /// flag -- it will be either the median (if true), or the mean (if |
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| 180 | /// false). |
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[475] | 181 | if(useRobust) this->median = Type(middle); |
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| 182 | else this->mean = middle; |
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| 183 | } |
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| 184 | template void StatsContainer<int>::setMiddle(float middle); |
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| 185 | template void StatsContainer<long>::setMiddle(float middle); |
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| 186 | template void StatsContainer<float>::setMiddle(float middle); |
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| 187 | template void StatsContainer<double>::setMiddle(float middle); |
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| 188 | //-------------------------------------------------------------------- |
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| 189 | |
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| 190 | template <class Type> |
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[271] | 191 | float StatsContainer<Type>::getMiddle() |
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| 192 | { |
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[528] | 193 | /// @details |
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| 194 | /// The middle value is determined by the StatsContainer::useRobust |
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| 195 | /// flag -- it will be either the median (if true), or the mean (if |
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| 196 | /// false). |
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[385] | 197 | if(useRobust) return float(this->median); |
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| 198 | else return this->mean; |
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[271] | 199 | } |
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| 200 | template float StatsContainer<int>::getMiddle(); |
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| 201 | template float StatsContainer<long>::getMiddle(); |
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| 202 | template float StatsContainer<float>::getMiddle(); |
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| 203 | template float StatsContainer<double>::getMiddle(); |
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| 204 | //-------------------------------------------------------------------- |
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| 205 | |
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| 206 | template <class Type> |
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[528] | 207 | void StatsContainer<Type>::setSpread(float spread) |
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| 208 | { |
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| 209 | /// @details |
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| 210 | /// The spread value is set according to the |
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| 211 | /// StatsContainer::useRobust flag -- it will be either the madfm |
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| 212 | /// (if true), or the rms (if false). If robust, the spread value will be |
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| 213 | /// converted to a madfm from an equivalent rms under the assumption of |
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| 214 | /// Gaussianity, using the Statistics::sigmaToMADFM function. |
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[475] | 215 | if(useRobust) this->madfm = Type(sigmaToMADFM(spread)); |
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| 216 | else this->stddev = spread; |
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| 217 | } |
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| 218 | template void StatsContainer<int>::setSpread(float spread); |
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| 219 | template void StatsContainer<long>::setSpread(float spread); |
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| 220 | template void StatsContainer<float>::setSpread(float spread); |
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| 221 | template void StatsContainer<double>::setSpread(float spread); |
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| 222 | //-------------------------------------------------------------------- |
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| 223 | |
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| 224 | template <class Type> |
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[528] | 225 | float StatsContainer<Type>::getSpread() |
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| 226 | { |
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| 227 | /// @details |
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| 228 | /// The spread value returned is determined by the |
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| 229 | /// StatsContainer::useRobust flag -- it will be either the madfm |
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| 230 | /// (if true), or the rms (if false). If robust, the madfm will be |
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| 231 | /// converted to an equivalent rms under the assumption of |
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| 232 | /// Gaussianity, using the Statistics::madfmToSigma function. |
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[385] | 233 | if(useRobust) return madfmToSigma(this->madfm); |
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| 234 | else return this->stddev; |
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[271] | 235 | } |
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| 236 | template float StatsContainer<int>::getSpread(); |
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| 237 | template float StatsContainer<long>::getSpread(); |
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| 238 | template float StatsContainer<float>::getSpread(); |
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| 239 | template float StatsContainer<double>::getSpread(); |
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| 240 | //-------------------------------------------------------------------- |
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| 241 | |
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| 242 | template <class Type> |
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[275] | 243 | void StatsContainer<Type>::scaleNoise(float scale) |
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| 244 | { |
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[528] | 245 | /// @details |
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| 246 | /// Multiply the noise parameters (stddev & madfm) by a given |
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| 247 | /// factor, and adjust the threshold. |
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[275] | 248 | float snr = (threshold - this->getMiddle())/this->getSpread(); |
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| 249 | this->madfm = Type(this->madfm*scale); |
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| 250 | this->stddev *= scale; |
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| 251 | this->threshold = this->getMiddle() + snr*this->getSpread(); |
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| 252 | } |
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| 253 | template void StatsContainer<int>::scaleNoise(float scale); |
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| 254 | template void StatsContainer<long>::scaleNoise(float scale); |
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| 255 | template void StatsContainer<float>::scaleNoise(float scale); |
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| 256 | template void StatsContainer<double>::scaleNoise(float scale); |
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| 257 | //-------------------------------------------------------------------- |
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| 258 | |
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| 259 | template <class Type> |
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[271] | 260 | float StatsContainer<Type>::getPValue(float value) |
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| 261 | { |
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[528] | 262 | /// @details |
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| 263 | /// Get the "probability", under the assumption of normality, of a |
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| 264 | /// value occuring. |
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| 265 | /// |
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| 266 | /// It is defined by \f$0.5 \operatorname{erfc}(z/\sqrt{2})\f$, where |
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| 267 | /// \f$z=(x-\mu)/\sigma\f$. We need the factor of 0.5 here, as we are |
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| 268 | /// only considering the positive tail of the distribution -- we |
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| 269 | /// don't care about negative detections. |
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[271] | 270 | |
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| 271 | float zStat = (value - this->getMiddle()) / this->getSpread(); |
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| 272 | return 0.5 * erfc( zStat / M_SQRT2 ); |
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| 273 | } |
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| 274 | template float StatsContainer<int>::getPValue(float value); |
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| 275 | template float StatsContainer<long>::getPValue(float value); |
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| 276 | template float StatsContainer<float>::getPValue(float value); |
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| 277 | template float StatsContainer<double>::getPValue(float value); |
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| 278 | //-------------------------------------------------------------------- |
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| 279 | |
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| 280 | template <class Type> |
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[528] | 281 | bool StatsContainer<Type>::isDetection(float value) |
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| 282 | { |
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| 283 | /// @details |
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| 284 | /// Compares the value given to the correct threshold, depending on |
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| 285 | /// the value of the StatsContainer::useFDR flag. |
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[271] | 286 | if(useFDR) return (this->getPValue(value) < this->pThreshold); |
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| 287 | else return (value > this->threshold); |
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| 288 | } |
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| 289 | template bool StatsContainer<int>::isDetection(float value); |
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| 290 | template bool StatsContainer<long>::isDetection(float value); |
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| 291 | template bool StatsContainer<float>::isDetection(float value); |
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| 292 | template bool StatsContainer<double>::isDetection(float value); |
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| 293 | //-------------------------------------------------------------------- |
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| 294 | |
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| 295 | template <class Type> |
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[1170] | 296 | void StatsContainer<Type>::define(float mean, Type median, float stddev, Type madfm) |
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| 297 | { |
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| 298 | /// @details |
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| 299 | /// Set all four statistics directly |
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| 300 | /// |
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| 301 | this->mean = mean; |
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| 302 | this->median = median; |
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| 303 | this->stddev = stddev; |
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| 304 | this->madfm = madfm; |
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| 305 | this->defined = true; |
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| 306 | } |
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| 307 | template void StatsContainer<int>::define(float mean, int median, float stddev, int madfm); |
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| 308 | template void StatsContainer<long>::define(float mean, long median, float stddev, long madfm); |
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| 309 | template void StatsContainer<float>::define(float mean, float median, float stddev, float madfm); |
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| 310 | template void StatsContainer<double>::define(float mean, double median, float stddev, double madfm); |
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| 311 | //-------------------------------------------------------------------- |
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| 312 | |
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| 313 | template <class Type> |
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[222] | 314 | void StatsContainer<Type>::calculate(Type *array, long size) |
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[201] | 315 | { |
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[528] | 316 | /// @details |
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| 317 | /// Calculate all four statistics for all elements of a given |
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| 318 | /// array. |
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| 319 | /// |
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| 320 | /// \param array The input data array. |
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| 321 | /// \param size The length of the input array |
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[275] | 322 | // findNormalStats(array, size, this->mean, this->stddev); |
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| 323 | // findMedianStats(array, size, this->median, this->madfm); |
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| 324 | findAllStats(array,size,this->mean,this->stddev,this->median,this->madfm); |
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[201] | 325 | this->defined = true; |
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| 326 | } |
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[222] | 327 | template void StatsContainer<int>::calculate(int *array, long size); |
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| 328 | template void StatsContainer<long>::calculate(long *array, long size); |
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| 329 | template void StatsContainer<float>::calculate(float *array, long size); |
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| 330 | template void StatsContainer<double>::calculate(double *array, long size); |
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[201] | 331 | //-------------------------------------------------------------------- |
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[190] | 332 | |
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[222] | 333 | template <class Type> |
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[1413] | 334 | void StatsContainer<Type>::calculate(Type *array, long size, std::vector<bool> mask) |
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[201] | 335 | { |
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[528] | 336 | /// @details |
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| 337 | /// Calculate all four statistics for a subset of a given |
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| 338 | /// array. The subset is defined by an array of bool |
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| 339 | /// variables. |
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| 340 | /// |
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| 341 | /// \param array The input data array. |
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| 342 | /// \param size The length of the input array |
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| 343 | /// \param mask An array of the same length that says whether to |
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| 344 | /// include each member of the array in the calculations. Use a |
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| 345 | /// value if mask=true. |
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[275] | 346 | // findNormalStats(array, size, mask, this->mean, this->stddev); |
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| 347 | // findMedianStats(array, size, mask, this->median, this->madfm); |
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| 348 | findAllStats(array, size, mask, |
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| 349 | this->mean, this->stddev, this->median, this->madfm); |
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[201] | 350 | this->defined = true; |
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| 351 | } |
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[1413] | 352 | template void StatsContainer<int>::calculate(int *array, long size, std::vector<bool> mask); |
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| 353 | template void StatsContainer<long>::calculate(long *array, long size, std::vector<bool> mask); |
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| 354 | template void StatsContainer<float>::calculate(float *array, long size, std::vector<bool> mask); |
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| 355 | template void StatsContainer<double>::calculate(double *array, long size, std::vector<bool> mask); |
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[201] | 356 | //-------------------------------------------------------------------- |
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[190] | 357 | |
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[222] | 358 | template <class Type> |
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| 359 | std::ostream& operator<< (std::ostream& theStream, StatsContainer<Type> &s) |
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[201] | 360 | { |
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[528] | 361 | /// Prints out the four key statistics to the requested stream. |
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[1137] | 362 | theStream << s.commentString << " " |
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| 363 | << "Mean = " << s.mean << "\t" |
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[201] | 364 | << "Std.Dev. = " << s.stddev << "\n" |
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[1137] | 365 | << s.commentString << " " |
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[201] | 366 | << "Median = " << s.median << "\t" |
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[519] | 367 | << "MADFM = " << s.madfm << " (= " << madfmToSigma(s.madfm) << " as std.dev.)\n"; |
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[270] | 368 | return theStream; |
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[201] | 369 | } |
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| 370 | template std::ostream& operator<<<int> (std::ostream& theStream, StatsContainer<int> &s); |
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| 371 | template std::ostream& operator<<<long> (std::ostream& theStream, StatsContainer<long> &s); |
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| 372 | template std::ostream& operator<<<float> (std::ostream& theStream, StatsContainer<float> &s); |
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| 373 | template std::ostream& operator<<<double> (std::ostream& theStream, StatsContainer<double> &s); |
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| 374 | |
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[1146] | 375 | //-------------------------------------------------------------------- |
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[201] | 376 | |
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[1146] | 377 | template <class Type> |
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| 378 | void StatsContainer<Type>::writeToBinaryFile(std::string filename) |
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| 379 | { |
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| 380 | std::ofstream outfile(filename.c_str(), std::ios::out | std::ios::binary | std::ios::app); |
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| 381 | outfile.write(reinterpret_cast<const char*>(&this->defined), sizeof this->defined); |
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| 382 | outfile.write(reinterpret_cast<const char*>(&this->mean), sizeof this->mean); |
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| 383 | outfile.write(reinterpret_cast<const char*>(&this->stddev), sizeof this->stddev); |
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| 384 | outfile.write(reinterpret_cast<const char*>(&this->median), sizeof this->median); |
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| 385 | outfile.write(reinterpret_cast<const char*>(&this->madfm), sizeof this->madfm); |
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| 386 | outfile.write(reinterpret_cast<const char*>(&this->threshold), sizeof this->threshold); |
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| 387 | outfile.write(reinterpret_cast<const char*>(&this->pThreshold), sizeof this->pThreshold); |
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| 388 | outfile.write(reinterpret_cast<const char*>(&this->useRobust), sizeof this->useRobust); |
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| 389 | outfile.write(reinterpret_cast<const char*>(&this->useFDR), sizeof this->useFDR); |
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| 390 | writeStringToBinaryFile(outfile,this->commentString); |
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| 391 | outfile.close(); |
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| 392 | } |
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| 393 | template void StatsContainer<int>::writeToBinaryFile(std::string filename); |
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| 394 | template void StatsContainer<long>::writeToBinaryFile(std::string filename); |
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| 395 | template void StatsContainer<float>::writeToBinaryFile(std::string filename); |
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| 396 | template void StatsContainer<double>::writeToBinaryFile(std::string filename); |
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[201] | 397 | |
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[1146] | 398 | //-------------------------------------------------------------------- |
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| 399 | |
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| 400 | template <class Type> |
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| 401 | std::streampos StatsContainer<Type>::readFromBinaryFile(std::string filename, std::streampos loc) |
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| 402 | { |
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| 403 | std::ifstream infile(filename.c_str(), std::ios::in | std::ios::binary); |
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| 404 | if(!infile.is_open()){ |
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| 405 | // DUCHAMPERROR("read binary stats","Could not open binary catalogue \""<<filename <<"\""); |
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| 406 | std::cerr << "Read binary stats : Could not open binary catalogue \"" << filename << "\"\n"; |
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| 407 | return -1; |
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| 408 | } |
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| 409 | infile.seekg(loc); |
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| 410 | infile.read(reinterpret_cast<char*>(&this->defined), sizeof this->defined); |
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| 411 | infile.read(reinterpret_cast<char*>(&this->mean), sizeof this->mean); |
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| 412 | infile.read(reinterpret_cast<char*>(&this->stddev), sizeof this->stddev); |
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| 413 | infile.read(reinterpret_cast<char*>(&this->median), sizeof this->median); |
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| 414 | infile.read(reinterpret_cast<char*>(&this->madfm), sizeof this->madfm); |
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| 415 | infile.read(reinterpret_cast<char*>(&this->threshold), sizeof this->threshold); |
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| 416 | infile.read(reinterpret_cast<char*>(&this->pThreshold), sizeof this->pThreshold); |
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| 417 | infile.read(reinterpret_cast<char*>(&this->useRobust), sizeof this->useRobust); |
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| 418 | infile.read(reinterpret_cast<char*>(&this->useFDR), sizeof this->useFDR); |
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| 419 | this->commentString=readStringFromBinaryFile(infile); |
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| 420 | std::streampos newloc = infile.tellg(); |
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| 421 | infile.close(); |
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| 422 | return newloc; |
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| 423 | } |
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| 424 | template std::streampos StatsContainer<int>::readFromBinaryFile(std::string filename, std::streampos loc); |
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| 425 | template std::streampos StatsContainer<long>::readFromBinaryFile(std::string filename, std::streampos loc); |
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| 426 | template std::streampos StatsContainer<float>::readFromBinaryFile(std::string filename, std::streampos loc); |
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| 427 | template std::streampos StatsContainer<double>::readFromBinaryFile(std::string filename, std::streampos loc); |
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| 428 | |
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| 429 | |
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| 430 | |
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[201] | 431 | } // matches: namespace Statistics { |
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