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DIAlign
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DIAlign
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Similarity matrix namespace. More...
Classes | |
| struct | square |
| Calculates sum of previous result and square of current element (useful for sum of squares). More... | |
Functions | |
| double | meanVecOfVec (const std::vector< std::vector< double > > &vov) |
| double | eucLenVecOfVec (const std::vector< std::vector< double > > &vov) |
| std::vector< double > | perSampleEucLenVecOfVec (const std::vector< std::vector< double > > &vov) |
| std::vector< double > | perSampleSqrSumVecOfVec (const std::vector< std::vector< double > > &vov) |
| std::vector< double > | perSampleMeanVecOfVec (const std::vector< std::vector< double > > &vov) |
| std::vector< double > | perSampleSumVecOfVec (const std::vector< std::vector< double > > &vov) |
| void | distToSim (SimMatrix &s, double offset, double Numerator) |
| Calculates distance as Distance = Numerator/(Similarity score + offset). | |
| void | clamp (std::vector< double > &vec, double minValue, double maxValue) |
| Limits values between minValue and maxValue. | |
| std::vector< std::vector< double > > | meanNormalizeVecOfVec (const std::vector< std::vector< double >> &d) |
| Returns a vector of vector with values divided by the output of meanVecOfVec(). | |
| std::vector< std::vector< double > > | L2NormalizeVecOfVec (const std::vector< std::vector< double >> &d) |
| Returns a vector of vector with values divided by the output of eucLenVecOfVec(). | |
| std::vector< std::vector< double > > | divideVecOfVec (const std::vector< std::vector< double >> &vov, double num) |
| Returns a vector of vector with values divided by num. | |
| void | ElemWiseSumOuterProd (const std::vector< double > &d1, const std::vector< double > &d2, SimMatrix &s) |
| Adds outer prodict of d1 and d2 in similarity matrix s. | |
| void | ElemWiseSumOuterProdMeanSub (const std::vector< double > &d1, const std::vector< double > &d2, SimMatrix &s, const std::vector< double > &mean1, const std::vector< double > &mean2) |
| Adds outer prodict of (d1-mean1) and (d2-mean2) in similarity matrix s. | |
| void | ElemWiseSumOuterEucl (const std::vector< double > &d1, const std::vector< double > &d2, SimMatrix &s) |
| Adds outer prodict of (d1-d2)*(d1-d2) in similarity matrix s. | |
| void | ElemWiseOuterCosine (const std::vector< double > &d1, const std::vector< double > &d2, const std::vector< double > &d1_mag, const std::vector< double > &d2_mag, SimMatrix &s) |
| Adds outer prodict of cosAng(d1,d2) in similarity matrix s. | |
| void | SumOuterProd (const std::vector< std::vector< double >> &d1, const std::vector< std::vector< double >> &d2, const std::string Normalization, SimMatrix &s) |
| Given Normalization modifies d1 and d2, and subsequently sums ElemWiseSumOuterProd() of d1 vectors with d2 vectors (d1 and d2 must be of same length). | |
| void | SumOuterCov (const std::vector< std::vector< double >> &d1, const std::vector< std::vector< double >> &d2, const std::string Normalization, SimMatrix &s) |
| Given Normalization modifies d1 and d2, and subsequently sums ElemWiseSumOuterProdMeanSub() of d1 vectors with d2 vectors (d1 and d2 must be of same length). | |
| void | SumOuterCorr (const std::vector< std::vector< double >> &d1, const std::vector< std::vector< double >> &d2, const std::string Normalization, SimMatrix &s) |
| Given Normalization modifies d1 and d2, and subsequently sums correlation coefficient of d1 vectors with d2 vectors (d1 and d2 must be of same length). | |
| void | SumOuterEucl (const std::vector< std::vector< double >> &d1, const std::vector< std::vector< double >> &d2, const std::string Normalization, SimMatrix &s) |
| Given Normalization modifies d1 and d2, and subsequently sums ElemWiseSumOuterEucl() of d1 vectors with d2 vectors (d1 and d2 must be of same length). | |
| void | SumOuterCosine (const std::vector< std::vector< double >> &d1, const std::vector< std::vector< double >> &d2, const std::string Normalization, SimMatrix &s) |
| Given Normalization modifies d1 and d2, and subsequently sums ElemWiseOuterCosine() of d1 vectors with d2 vectors (d1 and d2 must be of same length). | |
| SimMatrix | getSimilarityMatrix (const std::vector< std::vector< double >> &d1, const std::vector< std::vector< double >> &d2, const std::string Normalization, const std::string SimType, double cosAngleThresh, double dotProdThresh) |
| Returns a similarity matrix between d1 and d2 vector of vectors. More... | |
| double | meanVecOfVec (const std::vector< std::vector< double >> &vov) |
| Returns the average value of vector of vectors. | |
| double | eucLenVecOfVec (const std::vector< std::vector< double >> &vov) |
| Returns the sum of squares of all elemets of vector of vectors. | |
| std::vector< double > | perSampleEucLenVecOfVec (const std::vector< std::vector< double >> &vec) |
| Returns Eucledian length of the vector at each index projected by vectors in VoV. More... | |
| std::vector< double > | perSampleSqrSumVecOfVec (const std::vector< std::vector< double >> &vec) |
| Returns the sum of squares of vector intensities at each index (All vectors must be of the same length). | |
| std::vector< double > | perSampleMeanVecOfVec (const std::vector< std::vector< double >> &vec) |
| Returns the mean of vector intensities at each index (All vectors must be of the same length). | |
| std::vector< double > | perSampleSumVecOfVec (const std::vector< std::vector< double >> &vec) |
| Returns the sum of vector intensities at each index (All vectors must be of the same length). | |
Similarity matrix namespace.
| SimMatrix DIAlign::SimilarityMatrix::getSimilarityMatrix | ( | const std::vector< std::vector< double >> & | d1, |
| const std::vector< std::vector< double >> & | d2, | ||
| const std::string | Normalization, | ||
| const std::string | SimType, | ||
| double | cosAngleThresh, | ||
| double | dotProdThresh | ||
| ) |
Returns a similarity matrix between d1 and d2 vector of vectors.
First d1 and d2 are normalized, subsequently, similarity matrix is calculated with appropriate SimType. For SimType = dotProductMasked, matrix is further modified with cosAngleThresh and dotProdThresh parameters. For SimType == "cosine2Angle", matrix is constrained between -1.0 and 1.0.
| d1 | corresponds to signal A. Must be of same size of d2. |
| d2 | corresponds to signal B. Must be of same size of d1. |
| Normalization | Must be from "mean", "L2", "None". |
| SimType | Must be from "dotProductMasked", "dotProduct", "cosineAngle", "cosine2Angle", "euclideanDist", "covariance", "correlation". |
| std::vector<double> DIAlign::SimilarityMatrix::perSampleEucLenVecOfVec | ( | const std::vector< std::vector< double >> & | vec | ) |
Returns Eucledian length of the vector at each index projected by vectors in VoV.
Eucledian length is calculated as the square-root of sum of squares of vector intensities at an index. All vectors must be of the same length.
1.8.11 
