OpenMS  3.0.0
Scoring.h
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31 // $Maintainer: Hannes Roest$
32 // $Authors: Hannes Roest$
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34 
35 #pragma once
36 
37 #include <numeric>
38 #include <map>
39 #include <vector>
40 
41 #include <OpenMS/OPENSWATHALGO/OpenSwathAlgoConfig.h>
42 
43 namespace OpenSwath
44 {
45 
51  namespace Scoring
52  {
57  typedef std::pair<unsigned int, unsigned int> pos2D;
59  struct pair_hash
60  {
61  template <class T1, class T2>
62  std::size_t operator () (const std::pair<T1,T2> &p) const {
63  auto h1 = std::hash<T1>{}(p.first);
64  auto h2 = std::hash<T2>{}(p.second);
65  return h1 ^ h2;
66  }
67  };
68 
70  typedef std::pair<int, double> XCorrEntry;
72  {
73 public:
74  std::vector<XCorrEntry> data;
75 
76  // Access functions
77  typedef std::vector<XCorrEntry>::iterator iterator;
78  typedef std::vector<XCorrEntry>::const_iterator const_iterator;
79 
80  iterator begin() {return data.begin();}
81  const_iterator begin() const {return data.begin();}
82  iterator end() {return data.end();}
83  const_iterator end() const {return data.end();}
84  };
86 
100  OPENSWATHALGO_DLLAPI double NormalizedManhattanDist(double x[], double y[], int n);
101 
110  OPENSWATHALGO_DLLAPI double RootMeanSquareDeviation(double x[], double y[], int n);
111 
120  OPENSWATHALGO_DLLAPI double SpectralAngle(double x[], double y[], int n);
121 
124  OPENSWATHALGO_DLLAPI XCorrArrayType calcxcorr_legacy_mquest_(std::vector<double>& data1,
125  std::vector<double>& data2, bool normalize);
126 
129  OPENSWATHALGO_DLLAPI XCorrArrayType normalizedCrossCorrelation(std::vector<double>& data1,
130  std::vector<double>& data2, const int maxdelay, const int lag);
131 
133  OPENSWATHALGO_DLLAPI XCorrArrayType normalizedCrossCorrelationPost(std::vector<double>& normalized_data1,
134  std::vector<double>& normalized_data2, const int maxdelay, const int lag);
135 
137  OPENSWATHALGO_DLLAPI XCorrArrayType calculateCrossCorrelation(const std::vector<double>& data1,
138  const std::vector<double>& data2, const int maxdelay, const int lag);
139 
141  OPENSWATHALGO_DLLAPI XCorrArrayType::const_iterator xcorrArrayGetMaxPeak(const XCorrArrayType & array);
142 
144  OPENSWATHALGO_DLLAPI void standardize_data(std::vector<double>& data);
145 
147  OPENSWATHALGO_DLLAPI void normalize_sum(double x[], unsigned int n);
148 
149  // Compute rank of vector elements, append it to @p ranks and return the highest rank
150  OPENSWATHALGO_DLLAPI unsigned int computeAndAppendRank(const std::vector<double>& v, std::vector<unsigned int>& ranks);
151 
152  // Compute rank of vector elements and its highest rank for each row in a 2D array
153  OPENSWATHALGO_DLLAPI std::vector<unsigned int> computeRankVector(const std::vector<std::vector<double>>& intensity, std::vector<std::vector<unsigned int>>& ranks);
154 
155  // Estimate mutual information between two vectors of ranks
156  OPENSWATHALGO_DLLAPI double rankedMutualInformation(std::vector<unsigned int>& ranked_data1, std::vector<unsigned int>& ranked_data2, const unsigned int max_rank1, const unsigned int max_rank2);
157 
159 
160  }
161 }
162 
OpenSwath::Scoring::XCorrArrayType::data
std::vector< XCorrEntry > data
Definition: Scoring.h:74
OpenSwath::Scoring::XCorrArrayType::begin
const_iterator begin() const
Definition: Scoring.h:81
OpenSwath
Definition: Scoring.h:43
OpenSwath::Scoring::computeAndAppendRank
OPENSWATHALGO_DLLAPI unsigned int computeAndAppendRank(const std::vector< double > &v, std::vector< unsigned int > &ranks)
OpenSwath::Scoring::XCorrArrayType::end
const_iterator end() const
Definition: Scoring.h:83
OpenSwath::Scoring::RootMeanSquareDeviation
OPENSWATHALGO_DLLAPI double RootMeanSquareDeviation(double x[], double y[], int n)
Calculate the RMSD (root means square deviation)
OpenSwath::Scoring::XCorrArrayType::end
iterator end()
Definition: Scoring.h:82
OpenSwath::Scoring::rankedMutualInformation
OPENSWATHALGO_DLLAPI double rankedMutualInformation(std::vector< unsigned int > &ranked_data1, std::vector< unsigned int > &ranked_data2, const unsigned int max_rank1, const unsigned int max_rank2)
OpenSwath::Scoring::normalize_sum
OPENSWATHALGO_DLLAPI void normalize_sum(double x[], unsigned int n)
Divide each element of x by the sum of the vector.
OpenSwath::Scoring::XCorrArrayType::iterator
std::vector< XCorrEntry >::iterator iterator
Definition: Scoring.h:77
OpenSwath::Scoring::pos2D
std::pair< unsigned int, unsigned int > pos2D
Definition: Scoring.h:57
OpenSwath::Scoring::normalizedCrossCorrelationPost
OPENSWATHALGO_DLLAPI XCorrArrayType normalizedCrossCorrelationPost(std::vector< double > &normalized_data1, std::vector< double > &normalized_data2, const int maxdelay, const int lag)
Calculate crosscorrelation on std::vector data that is already normalized.
OpenSwath::Scoring::calcxcorr_legacy_mquest_
OPENSWATHALGO_DLLAPI XCorrArrayType calcxcorr_legacy_mquest_(std::vector< double > &data1, std::vector< double > &data2, bool normalize)
OpenSwath::Scoring::XCorrArrayType::begin
iterator begin()
Definition: Scoring.h:80
OpenSwath::Scoring::pair_hash
Simple hash function for Scoring::pos2D.
Definition: Scoring.h:59
OpenSwath::Scoring::pair_hash::operator()
std::size_t operator()(const std::pair< T1, T2 > &p) const
Definition: Scoring.h:62
OpenSwath::Scoring::calculateCrossCorrelation
OPENSWATHALGO_DLLAPI XCorrArrayType calculateCrossCorrelation(const std::vector< double > &data1, const std::vector< double > &data2, const int maxdelay, const int lag)
Calculate crosscorrelation on std::vector data without normalization.
OpenSwath::Scoring::normalizedCrossCorrelation
OPENSWATHALGO_DLLAPI XCorrArrayType normalizedCrossCorrelation(std::vector< double > &data1, std::vector< double > &data2, const int maxdelay, const int lag)
OpenSwath::Scoring::XCorrArrayType::const_iterator
std::vector< XCorrEntry >::const_iterator const_iterator
Definition: Scoring.h:78
OpenSwath::Scoring::NormalizedManhattanDist
OPENSWATHALGO_DLLAPI double NormalizedManhattanDist(double x[], double y[], int n)
Calculate the normalized Manhattan distance between two arrays.
OpenSwath::Scoring::standardize_data
OPENSWATHALGO_DLLAPI void standardize_data(std::vector< double > &data)
Standardize a vector (subtract mean, divide by standard deviation)
OpenSwath::Scoring::SpectralAngle
OPENSWATHALGO_DLLAPI double SpectralAngle(double x[], double y[], int n)
Calculate the Spectral angle (acosine of the normalized dotproduct)
OpenSwath::Scoring::xcorrArrayGetMaxPeak
OPENSWATHALGO_DLLAPI XCorrArrayType::const_iterator xcorrArrayGetMaxPeak(const XCorrArrayType &array)
Find best peak in an cross-correlation (highest apex)
OpenSwath::Scoring::XCorrEntry
std::pair< int, double > XCorrEntry
Cross Correlation array contains (lag,correlation) pairs.
Definition: Scoring.h:70
OpenSwath::normalize
OPENSWATHALGO_DLLAPI void normalize(const std::vector< double > &intensities, double normalization_factor, std::vector< double > &normalized_intensities)
Normalize intensities in vector by normalization_factor.
OpenSwath::Scoring::XCorrArrayType
Definition: Scoring.h:71
OpenSwath::Scoring::computeRankVector
OPENSWATHALGO_DLLAPI std::vector< unsigned int > computeRankVector(const std::vector< std::vector< double >> &intensity, std::vector< std::vector< unsigned int >> &ranks)