sequenzo 0.1.18__cp39-cp39-macosx_10_9_universal2.whl → 0.1.20__cp39-cp39-macosx_10_9_universal2.whl

sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LMpar.h

@@ -1,160 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// This code initially comes from MINPACK whose original authors are:
-// Copyright Jorge More - Argonne National Laboratory
-// Copyright Burt Garbow - Argonne National Laboratory
-// Copyright Ken Hillstrom - Argonne National Laboratory
-//
-// This Source Code Form is subject to the terms of the Minpack license
-// (a BSD-like license) described in the campaigned CopyrightMINPACK.txt file.
-
-#ifndef EIGEN_LMPAR_H
-#define EIGEN_LMPAR_H
-
-namespace Eigen {
-
-namespace internal {
-  
-  template <typename QRSolver, typename VectorType>
-    void lmpar2(
-    const QRSolver &qr,
-    const VectorType  &diag,
-    const VectorType  &qtb,
-    typename VectorType::Scalar m_delta,
-    typename VectorType::Scalar &par,
-    VectorType  &x)
-
-  {
-    using std::sqrt;
-    using std::abs;
-    typedef typename QRSolver::MatrixType MatrixType;
-    typedef typename QRSolver::Scalar Scalar;
-//    typedef typename QRSolver::StorageIndex StorageIndex;
-
-    /* Local variables */
-    Index j;
-    Scalar fp;
-    Scalar parc, parl;
-    Index iter;
-    Scalar temp, paru;
-    Scalar gnorm;
-    Scalar dxnorm;
-    
-    // Make a copy of the triangular factor. 
-    // This copy is modified during call the qrsolv
-    MatrixType s;
-    s = qr.matrixR();
-
-    /* Function Body */
-    const Scalar dwarf = (std::numeric_limits<Scalar>::min)();
-    const Index n = qr.matrixR().cols();
-    eigen_assert(n==diag.size());
-    eigen_assert(n==qtb.size());
-
-    VectorType  wa1, wa2;
-
-    /* compute and store in x the gauss-newton direction. if the */
-    /* jacobian is rank-deficient, obtain a least squares solution. */
-
-    //    const Index rank = qr.nonzeroPivots(); // exactly double(0.)
-    const Index rank = qr.rank(); // use a threshold
-    wa1 = qtb;
-    wa1.tail(n-rank).setZero();
-    //FIXME There is no solve in place for sparse triangularView
-    wa1.head(rank) = s.topLeftCorner(rank,rank).template triangularView<Upper>().solve(qtb.head(rank));
-
-    x = qr.colsPermutation()*wa1;
-
-    /* initialize the iteration counter. */
-    /* evaluate the function at the origin, and test */
-    /* for acceptance of the gauss-newton direction. */
-    iter = 0;
-    wa2 = diag.cwiseProduct(x);
-    dxnorm = wa2.blueNorm();
-    fp = dxnorm - m_delta;
-    if (fp <= Scalar(0.1) * m_delta) {
-      par = 0;
-      return;
-    }
-
-    /* if the jacobian is not rank deficient, the newton */
-    /* step provides a lower bound, parl, for the zero of */
-    /* the function. otherwise set this bound to zero. */
-    parl = 0.;
-    if (rank==n) {
-      wa1 = qr.colsPermutation().inverse() *  diag.cwiseProduct(wa2)/dxnorm;
-      s.topLeftCorner(n,n).transpose().template triangularView<Lower>().solveInPlace(wa1);
-      temp = wa1.blueNorm();
-      parl = fp / m_delta / temp / temp;
-    }
-
-    /* calculate an upper bound, paru, for the zero of the function. */
-    for (j = 0; j < n; ++j)
-      wa1[j] = s.col(j).head(j+1).dot(qtb.head(j+1)) / diag[qr.colsPermutation().indices()(j)];
-
-    gnorm = wa1.stableNorm();
-    paru = gnorm / m_delta;
-    if (paru == 0.)
-      paru = dwarf / (std::min)(m_delta,Scalar(0.1));
-
-    /* if the input par lies outside of the interval (parl,paru), */
-    /* set par to the closer endpoint. */
-    par = (std::max)(par,parl);
-    par = (std::min)(par,paru);
-    if (par == 0.)
-      par = gnorm / dxnorm;
-
-    /* beginning of an iteration. */
-    while (true) {
-      ++iter;
-
-      /* evaluate the function at the current value of par. */
-      if (par == 0.)
-        par = (std::max)(dwarf,Scalar(.001) * paru); /* Computing MAX */
-      wa1 = sqrt(par)* diag;
-
-      VectorType sdiag(n);
-      lmqrsolv(s, qr.colsPermutation(), wa1, qtb, x, sdiag);
-
-      wa2 = diag.cwiseProduct(x);
-      dxnorm = wa2.blueNorm();
-      temp = fp;
-      fp = dxnorm - m_delta;
-
-      /* if the function is small enough, accept the current value */
-      /* of par. also test for the exceptional cases where parl */
-      /* is zero or the number of iterations has reached 10. */
-      if (abs(fp) <= Scalar(0.1) * m_delta || (parl == 0. && fp <= temp && temp < 0.) || iter == 10)
-        break;
-
-      /* compute the newton correction. */
-      wa1 = qr.colsPermutation().inverse() * diag.cwiseProduct(wa2/dxnorm);
-      // we could almost use this here, but the diagonal is outside qr, in sdiag[]
-      for (j = 0; j < n; ++j) {
-        wa1[j] /= sdiag[j];
-        temp = wa1[j];
-        for (Index i = j+1; i < n; ++i)
-          wa1[i] -= s.coeff(i,j) * temp;
-      }
-      temp = wa1.blueNorm();
-      parc = fp / m_delta / temp / temp;
-
-      /* depending on the sign of the function, update parl or paru. */
-      if (fp > 0.)
-        parl = (std::max)(parl,par);
-      if (fp < 0.)
-        paru = (std::min)(paru,par);
-
-      /* compute an improved estimate for par. */
-      par = (std::max)(parl,par+parc);
-    }
-    if (iter == 0)
-      par = 0.;
-    return;
-  }
-} // end namespace internal
-
-} // end namespace Eigen
-
-#endif // EIGEN_LMPAR_H

sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/LevenbergMarquardt/LMqrsolv.h

@@ -1,188 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2009 Thomas Capricelli <orzel@freehackers.org>
-// Copyright (C) 2012 Desire Nuentsa <desire.nuentsa_wakam@inria.fr>
-//
-// This code initially comes from MINPACK whose original authors are:
-// Copyright Jorge More - Argonne National Laboratory
-// Copyright Burt Garbow - Argonne National Laboratory
-// Copyright Ken Hillstrom - Argonne National Laboratory
-//
-// This Source Code Form is subject to the terms of the Minpack license
-// (a BSD-like license) described in the campaigned CopyrightMINPACK.txt file.
-
-#ifndef EIGEN_LMQRSOLV_H
-#define EIGEN_LMQRSOLV_H
-
-namespace Eigen { 
-
-namespace internal {
-
-template <typename Scalar,int Rows, int Cols, typename PermIndex>
-void lmqrsolv(
-  Matrix<Scalar,Rows,Cols> &s,
-  const PermutationMatrix<Dynamic,Dynamic,PermIndex> &iPerm,
-  const Matrix<Scalar,Dynamic,1> &diag,
-  const Matrix<Scalar,Dynamic,1> &qtb,
-  Matrix<Scalar,Dynamic,1> &x,
-  Matrix<Scalar,Dynamic,1> &sdiag)
-{
-    /* Local variables */
-    Index i, j, k;
-    Scalar temp;
-    Index n = s.cols();
-    Matrix<Scalar,Dynamic,1>  wa(n);
-    JacobiRotation<Scalar> givens;
-
-    /* Function Body */
-    // the following will only change the lower triangular part of s, including
-    // the diagonal, though the diagonal is restored afterward
-
-    /*     copy r and (q transpose)*b to preserve input and initialize s. */
-    /*     in particular, save the diagonal elements of r in x. */
-    x = s.diagonal();
-    wa = qtb;
-    
-   
-    s.topLeftCorner(n,n).template triangularView<StrictlyLower>() = s.topLeftCorner(n,n).transpose();
-    /*     eliminate the diagonal matrix d using a givens rotation. */
-    for (j = 0; j < n; ++j) {
-
-        /*        prepare the row of d to be eliminated, locating the */
-        /*        diagonal element using p from the qr factorization. */
-        const PermIndex l = iPerm.indices()(j);
-        if (diag[l] == 0.)
-            break;
-        sdiag.tail(n-j).setZero();
-        sdiag[j] = diag[l];
-
-        /*        the transformations to eliminate the row of d */
-        /*        modify only a single element of (q transpose)*b */
-        /*        beyond the first n, which is initially zero. */
-        Scalar qtbpj = 0.;
-        for (k = j; k < n; ++k) {
-            /*           determine a givens rotation which eliminates the */
-            /*           appropriate element in the current row of d. */
-            givens.makeGivens(-s(k,k), sdiag[k]);
-
-            /*           compute the modified diagonal element of r and */
-            /*           the modified element of ((q transpose)*b,0). */
-            s(k,k) = givens.c() * s(k,k) + givens.s() * sdiag[k];
-            temp = givens.c() * wa[k] + givens.s() * qtbpj;
-            qtbpj = -givens.s() * wa[k] + givens.c() * qtbpj;
-            wa[k] = temp;
-
-            /*           accumulate the transformation in the row of s. */
-            for (i = k+1; i<n; ++i) {
-                temp = givens.c() * s(i,k) + givens.s() * sdiag[i];
-                sdiag[i] = -givens.s() * s(i,k) + givens.c() * sdiag[i];
-                s(i,k) = temp;
-            }
-        }
-    }
-  
-    /*     solve the triangular system for z. if the system is */
-    /*     singular, then obtain a least squares solution. */
-    Index nsing;
-    for(nsing=0; nsing<n && sdiag[nsing]!=0; nsing++) {}
-
-    wa.tail(n-nsing).setZero();
-    s.topLeftCorner(nsing, nsing).transpose().template triangularView<Upper>().solveInPlace(wa.head(nsing));
-  
-    // restore
-    sdiag = s.diagonal();
-    s.diagonal() = x;
-
-    /* permute the components of z back to components of x. */
-    x = iPerm * wa; 
-}
-
-template <typename Scalar, int _Options, typename Index>
-void lmqrsolv(
-  SparseMatrix<Scalar,_Options,Index> &s,
-  const PermutationMatrix<Dynamic,Dynamic> &iPerm,
-  const Matrix<Scalar,Dynamic,1> &diag,
-  const Matrix<Scalar,Dynamic,1> &qtb,
-  Matrix<Scalar,Dynamic,1> &x,
-  Matrix<Scalar,Dynamic,1> &sdiag)
-{
-  /* Local variables */
-  typedef SparseMatrix<Scalar,RowMajor,Index> FactorType;
-    Index i, j, k, l;
-    Scalar temp;
-    Index n = s.cols();
-    Matrix<Scalar,Dynamic,1>  wa(n);
-    JacobiRotation<Scalar> givens;
-
-    /* Function Body */
-    // the following will only change the lower triangular part of s, including
-    // the diagonal, though the diagonal is restored afterward
-
-    /*     copy r and (q transpose)*b to preserve input and initialize R. */
-    wa = qtb;
-    FactorType R(s);
-    // Eliminate the diagonal matrix d using a givens rotation
-    for (j = 0; j < n; ++j)
-    {
-      // Prepare the row of d to be eliminated, locating the 
-      // diagonal element using p from the qr factorization
-      l = iPerm.indices()(j);
-      if (diag(l) == Scalar(0)) 
-        break; 
-      sdiag.tail(n-j).setZero();
-      sdiag[j] = diag[l];
-      // the transformations to eliminate the row of d
-      // modify only a single element of (q transpose)*b
-      // beyond the first n, which is initially zero. 
-      
-      Scalar qtbpj = 0; 
-      // Browse the nonzero elements of row j of the upper triangular s
-      for (k = j; k < n; ++k)
-      {
-        typename FactorType::InnerIterator itk(R,k);
-        for (; itk; ++itk){
-          if (itk.index() < k) continue;
-          else break;
-        }
-        //At this point, we have the diagonal element R(k,k)
-        // Determine a givens rotation which eliminates 
-        // the appropriate element in the current row of d
-        givens.makeGivens(-itk.value(), sdiag(k));
-        
-        // Compute the modified diagonal element of r and 
-        // the modified element of ((q transpose)*b,0).
-        itk.valueRef() = givens.c() * itk.value() + givens.s() * sdiag(k);
-        temp = givens.c() * wa(k) + givens.s() * qtbpj; 
-        qtbpj = -givens.s() * wa(k) + givens.c() * qtbpj;
-        wa(k) = temp;
-        
-        // Accumulate the transformation in the remaining k row/column of R
-        for (++itk; itk; ++itk)
-        {
-          i = itk.index();
-          temp = givens.c() *  itk.value() + givens.s() * sdiag(i);
-          sdiag(i) = -givens.s() * itk.value() + givens.c() * sdiag(i);
-          itk.valueRef() = temp;
-        }
-      }
-    }
-    
-    // Solve the triangular system for z. If the system is 
-    // singular, then obtain a least squares solution
-    Index nsing;
-    for(nsing = 0; nsing<n && sdiag(nsing) !=0; nsing++) {}
-    
-    wa.tail(n-nsing).setZero();
-//     x = wa; 
-    wa.head(nsing) = R.topLeftCorner(nsing,nsing).template triangularView<Upper>().solve/*InPlace*/(wa.head(nsing));
-    
-    sdiag = R.diagonal();
-    // Permute the components of z back to components of x
-    x = iPerm * wa; 
-}
-} // end namespace internal
-
-} // end namespace Eigen
-
-#endif // EIGEN_LMQRSOLV_H