All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Properties Friends Macros Modules Pages
StatsHelpers.h
Go to the documentation of this file.
1 // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Timo Sachsenberg $
6 // $Authors: Witold Wolski $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
11 #include <OpenMS/OPENSWATHALGO/OpenSwathAlgoConfig.h>
12 #include <algorithm>
13 #include <cmath>
14 #include <complex>
15 #include <numeric>
16 #include <vector>
17 #include <cstddef>
18 
19 namespace OpenSwath
20 {
21 
25  OPENSWATHALGO_DLLAPI void normalize(const std::vector<double>& intensities, double normalization_factor, std::vector<double>& normalized_intensities);
26 
30  template <typename T>
31  double norm(T beg, T end)
32  {
33  double res = 0.0;
34  for (; beg != end; ++beg)
35  {
36  double tmp = *beg;
37  res += tmp * tmp;
38  }
39  return sqrt(res);
40  }
41 
45  template <typename Texp, typename Ttheo>
46  double dotProd(Texp intExpBeg, Texp intExpEnd, Ttheo intTheo);
47 
49 
50  // Explicit template instantiation declarations (tell the compiler these exist)
51  extern template double dotProd<std::vector<double>::const_iterator, std::vector<double>::const_iterator>(
52  std::vector<double>::const_iterator, std::vector<double>::const_iterator, std::vector<double>::const_iterator);
53 
54  extern template double dotProd<std::vector<float>::const_iterator, std::vector<float>::const_iterator>(
55  std::vector<float>::const_iterator, std::vector<float>::const_iterator, std::vector<float>::const_iterator);
56 
57  extern template double dotProd<std::vector<int>::const_iterator, std::vector<int>::const_iterator>(
58  std::vector<int>::const_iterator, std::vector<int>::const_iterator, std::vector<int>::const_iterator);
59 
61 
69  OPENSWATHALGO_DLLAPI double dotprodScoring(std::vector<double> intExp, std::vector<double> theorint);
70 
74  template <typename Texp, typename Ttheo>
75  double manhattanDist(Texp itExpBeg, Texp itExpEnd, Ttheo itTheo)
76  {
77  double sum = 0.0;
78  for (; itExpBeg < itExpEnd; ++itExpBeg, ++itTheo)
79  {
80  sum += fabs(*itExpBeg - *itTheo);
81  }
82  return sum;
83  }
84 
92  OPENSWATHALGO_DLLAPI double manhattanScoring(std::vector<double> intExp, std::vector<double> theorint);
93 
94 
98  template <typename TInputIterator, typename TInputIteratorY>
99  typename std::iterator_traits<TInputIterator>::value_type cor_pearson(
100  TInputIterator xBeg,
101  TInputIterator xEnd,
102  TInputIteratorY yBeg
103  )
104  {
105  typedef typename std::iterator_traits<TInputIterator>::value_type value_type;
106  value_type m1, m2;
107  value_type s1, s2;
108  value_type corr;
109  m1 = m2 = s1 = s2 = 0.0;
110  corr = 0.0;
111  ptrdiff_t n = std::distance(xBeg, xEnd);
112  value_type nd = static_cast<value_type>(n);
113  for (; xBeg != xEnd; ++xBeg, ++yBeg)
114  {
115  corr += *xBeg * *yBeg;
116  m1 += *xBeg;
117  m2 += *yBeg;
118  s1 += *xBeg * *xBeg;
119  s2 += *yBeg * *yBeg;
120  }
121  m1 /= nd;
122  m2 /= nd;
123  s1 -= m1 * m1 * nd;
124  s2 -= m2 * m2 * nd;
125 
126  if (s1 < 1.0e-12 || s2 < 1.0e-12)
127  return 0.0;
128  else
129  {
130  corr -= m1 * m2 * (double)n;
131  corr /= sqrt(s1 * s2);
132  return corr;
133  }
134  }
135 
139  class OPENSWATHALGO_DLLAPI mean_and_stddev
140  {
141  double m_, q_;
142  unsigned long c_;
143 public:
144  typedef double argument_type, result_type;
146  m_(0.0), q_(0.0), c_(0u)
147  {
148  }
149 
150  void operator()(double sample)
151  {
152  double const delta = sample - m_;
153  m_ += delta / ++c_;
154  q_ += delta * (sample - m_);
155  }
156 
157  double sample_variance() const
158  {
159  return (c_ > 1u) ? (q_ / (c_ - 1)) : 0;
160  }
161 
162  double standard_variance() const
163  {
164  return (c_ > 1u) ? (q_ / c_) : 0;
165  }
166 
167  double sample_stddev() const
168  {
169  return std::sqrt(sample_variance());
170  }
171 
172  double standard_stddev() const
173  {
174  return std::sqrt(standard_variance());
175  }
176 
177  double mean() const
178  {
179  return m_;
180  }
181 
182  unsigned long count() const
183  {
184  return c_;
185  }
186 
187  double variance() const
188  {
189  return sample_variance();
190  }
191 
192  double stddev() const
193  {
194  return sample_stddev();
195  }
196 
197  double operator()() const
198  {
199  return stddev();
200  }
201 
202  };
203 
204 } //end namespace OpenSwath
205 
functor to compute the mean and stddev of sequence using the std::foreach algorithm
Definition: StatsHelpers.h:140
double result_type
Definition: StatsHelpers.h:144
mean_and_stddev()
Definition: StatsHelpers.h:145
double standard_stddev() const
Definition: StatsHelpers.h:172
unsigned long c_
Definition: StatsHelpers.h:142
double sample_stddev() const
Definition: StatsHelpers.h:167
double mean() const
Definition: StatsHelpers.h:177
double stddev() const
Definition: StatsHelpers.h:192
double argument_type
Definition: StatsHelpers.h:144
double variance() const
Definition: StatsHelpers.h:187
unsigned long count() const
Definition: StatsHelpers.h:182
double standard_variance() const
Definition: StatsHelpers.h:162
void operator()(double sample)
Definition: StatsHelpers.h:150
double m_
Definition: StatsHelpers.h:141
double operator()() const
Definition: StatsHelpers.h:197
double sample_variance() const
Definition: StatsHelpers.h:157
static double sum(IteratorType begin, IteratorType end)
Calculates the sum of a range of values.
Definition: StatisticFunctions.h:81
Definition: Scoring.h:18
double manhattanDist(Texp itExpBeg, Texp itExpEnd, Ttheo itTheo)
compute manhattan distance between Exp and Theo
Definition: StatsHelpers.h:75
OPENSWATHALGO_DLLAPI double dotprodScoring(std::vector< double > intExp, std::vector< double > theorint)
the dot product scoring
OPENSWATHALGO_DLLAPI void normalize(const std::vector< double > &intensities, double normalization_factor, std::vector< double > &normalized_intensities)
Normalize intensities in vector by normalization_factor.
double dotProd(Texp intExpBeg, Texp intExpEnd, Ttheo intTheo)
compute dotprod of vectors
OPENSWATHALGO_DLLAPI double manhattanScoring(std::vector< double > intExp, std::vector< double > theorint)
manhattan scoring
double norm(T beg, T end)
compute the Euclidean norm of the vector
Definition: StatsHelpers.h:31
std::iterator_traits< TInputIterator >::value_type cor_pearson(TInputIterator xBeg, TInputIterator xEnd, TInputIteratorY yBeg)
compute pearson correlation of vector x and y
Definition: StatsHelpers.h:99