sequenzo 0.1.17__cp310-cp310-macosx_10_9_universal2.whl → 0.1.19__cp310-cp310-macosx_10_9_universal2.whl

sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h

@@ -1,444 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2011-2014 Gael Guennebaud <gael.guennebaud@inria.fr>
-//
-// This Source Code Form is subject to the terms of the Mozilla
-// Public License v. 2.0. If a copy of the MPL was not distributed
-// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
-
-#ifndef EIGEN_ITERATIVE_SOLVER_BASE_H
-#define EIGEN_ITERATIVE_SOLVER_BASE_H
-
-namespace Eigen {
-
-namespace internal {
-
-template<typename MatrixType>
-struct is_ref_compatible_impl
-{
-private:
-  template <typename T0>
-  struct any_conversion
-  {
-    template <typename T> any_conversion(const volatile T&);
-    template <typename T> any_conversion(T&);
-  };
-  struct yes {int a[1];};
-  struct no  {int a[2];};
-
-  template<typename T>
-  static yes test(const Ref<const T>&, int);
-  template<typename T>
-  static no  test(any_conversion<T>, ...);
-
-public:
-  static MatrixType ms_from;
-  enum { value = sizeof(test<MatrixType>(ms_from, 0))==sizeof(yes) };
-};
-
-template<typename MatrixType>
-struct is_ref_compatible
-{
-  enum { value = is_ref_compatible_impl<typename remove_all<MatrixType>::type>::value };
-};
-
-template<typename MatrixType, bool MatrixFree = !internal::is_ref_compatible<MatrixType>::value>
-class generic_matrix_wrapper;
-
-// We have an explicit matrix at hand, compatible with Ref<>
-template<typename MatrixType>
-class generic_matrix_wrapper<MatrixType,false>
-{
-public:
-  typedef Ref<const MatrixType> ActualMatrixType;
-  template<int UpLo> struct ConstSelfAdjointViewReturnType {
-    typedef typename ActualMatrixType::template ConstSelfAdjointViewReturnType<UpLo>::Type Type;
-  };
-
-  enum {
-    MatrixFree = false
-  };
-
-  generic_matrix_wrapper()
-    : m_dummy(0,0), m_matrix(m_dummy)
-  {}
-
-  template<typename InputType>
-  generic_matrix_wrapper(const InputType &mat)
-    : m_matrix(mat)
-  {}
-
-  const ActualMatrixType& matrix() const
-  {
-    return m_matrix;
-  }
-
-  template<typename MatrixDerived>
-  void grab(const EigenBase<MatrixDerived> &mat)
-  {
-    m_matrix.~Ref<const MatrixType>();
-    ::new (&m_matrix) Ref<const MatrixType>(mat.derived());
-  }
-
-  void grab(const Ref<const MatrixType> &mat)
-  {
-    if(&(mat.derived()) != &m_matrix)
-    {
-      m_matrix.~Ref<const MatrixType>();
-      ::new (&m_matrix) Ref<const MatrixType>(mat);
-    }
-  }
-
-protected:
-  MatrixType m_dummy; // used to default initialize the Ref<> object
-  ActualMatrixType m_matrix;
-};
-
-// MatrixType is not compatible with Ref<> -> matrix-free wrapper
-template<typename MatrixType>
-class generic_matrix_wrapper<MatrixType,true>
-{
-public:
-  typedef MatrixType ActualMatrixType;
-  template<int UpLo> struct ConstSelfAdjointViewReturnType
-  {
-    typedef ActualMatrixType Type;
-  };
-
-  enum {
-    MatrixFree = true
-  };
-
-  generic_matrix_wrapper()
-    : mp_matrix(0)
-  {}
-
-  generic_matrix_wrapper(const MatrixType &mat)
-    : mp_matrix(&mat)
-  {}
-
-  const ActualMatrixType& matrix() const
-  {
-    return *mp_matrix;
-  }
-
-  void grab(const MatrixType &mat)
-  {
-    mp_matrix = &mat;
-  }
-
-protected:
-  const ActualMatrixType *mp_matrix;
-};
-
-}
-
-/** \ingroup IterativeLinearSolvers_Module
-  * \brief Base class for linear iterative solvers
-  *
-  * \sa class SimplicialCholesky, DiagonalPreconditioner, IdentityPreconditioner
-  */
-template< typename Derived>
-class IterativeSolverBase : public SparseSolverBase<Derived>
-{
-protected:
-  typedef SparseSolverBase<Derived> Base;
-  using Base::m_isInitialized;
-
-public:
-  typedef typename internal::traits<Derived>::MatrixType MatrixType;
-  typedef typename internal::traits<Derived>::Preconditioner Preconditioner;
-  typedef typename MatrixType::Scalar Scalar;
-  typedef typename MatrixType::StorageIndex StorageIndex;
-  typedef typename MatrixType::RealScalar RealScalar;
-
-  enum {
-    ColsAtCompileTime = MatrixType::ColsAtCompileTime,
-    MaxColsAtCompileTime = MatrixType::MaxColsAtCompileTime
-  };
-
-public:
-
-  using Base::derived;
-
-  /** Default constructor. */
-  IterativeSolverBase()
-  {
-    init();
-  }
-
-  /** Initialize the solver with matrix \a A for further \c Ax=b solving.
-    *
-    * This constructor is a shortcut for the default constructor followed
-    * by a call to compute().
-    *
-    * \warning this class stores a reference to the matrix A as well as some
-    * precomputed values that depend on it. Therefore, if \a A is changed
-    * this class becomes invalid. Call compute() to update it with the new
-    * matrix A, or modify a copy of A.
-    */
-  template<typename MatrixDerived>
-  explicit IterativeSolverBase(const EigenBase<MatrixDerived>& A)
-    : m_matrixWrapper(A.derived())
-  {
-    init();
-    compute(matrix());
-  }
-
-  ~IterativeSolverBase() {}
-
-  /** Initializes the iterative solver for the sparsity pattern of the matrix \a A for further solving \c Ax=b problems.
-    *
-    * Currently, this function mostly calls analyzePattern on the preconditioner. In the future
-    * we might, for instance, implement column reordering for faster matrix vector products.
-    */
-  template<typename MatrixDerived>
-  Derived& analyzePattern(const EigenBase<MatrixDerived>& A)
-  {
-    grab(A.derived());
-    m_preconditioner.analyzePattern(matrix());
-    m_isInitialized = true;
-    m_analysisIsOk = true;
-    m_info = m_preconditioner.info();
-    return derived();
-  }
-
-  /** Initializes the iterative solver with the numerical values of the matrix \a A for further solving \c Ax=b problems.
-    *
-    * Currently, this function mostly calls factorize on the preconditioner.
-    *
-    * \warning this class stores a reference to the matrix A as well as some
-    * precomputed values that depend on it. Therefore, if \a A is changed
-    * this class becomes invalid. Call compute() to update it with the new
-    * matrix A, or modify a copy of A.
-    */
-  template<typename MatrixDerived>
-  Derived& factorize(const EigenBase<MatrixDerived>& A)
-  {
-    eigen_assert(m_analysisIsOk && "You must first call analyzePattern()");
-    grab(A.derived());
-    m_preconditioner.factorize(matrix());
-    m_factorizationIsOk = true;
-    m_info = m_preconditioner.info();
-    return derived();
-  }
-
-  /** Initializes the iterative solver with the matrix \a A for further solving \c Ax=b problems.
-    *
-    * Currently, this function mostly initializes/computes the preconditioner. In the future
-    * we might, for instance, implement column reordering for faster matrix vector products.
-    *
-    * \warning this class stores a reference to the matrix A as well as some
-    * precomputed values that depend on it. Therefore, if \a A is changed
-    * this class becomes invalid. Call compute() to update it with the new
-    * matrix A, or modify a copy of A.
-    */
-  template<typename MatrixDerived>
-  Derived& compute(const EigenBase<MatrixDerived>& A)
-  {
-    grab(A.derived());
-    m_preconditioner.compute(matrix());
-    m_isInitialized = true;
-    m_analysisIsOk = true;
-    m_factorizationIsOk = true;
-    m_info = m_preconditioner.info();
-    return derived();
-  }
-
-  /** \internal */
-  EIGEN_CONSTEXPR Index rows() const EIGEN_NOEXCEPT { return matrix().rows(); }
-
-  /** \internal */
-  EIGEN_CONSTEXPR Index cols() const EIGEN_NOEXCEPT { return matrix().cols(); }
-
-  /** \returns the tolerance threshold used by the stopping criteria.
-    * \sa setTolerance()
-    */
-  RealScalar tolerance() const { return m_tolerance; }
-
-  /** Sets the tolerance threshold used by the stopping criteria.
-    *
-    * This value is used as an upper bound to the relative residual error: |Ax-b|/|b|.
-    * The default value is the machine precision given by NumTraits<Scalar>::epsilon()
-    */
-  Derived& setTolerance(const RealScalar& tolerance)
-  {
-    m_tolerance = tolerance;
-    return derived();
-  }
-
-  /** \returns a read-write reference to the preconditioner for custom configuration. */
-  Preconditioner& preconditioner() { return m_preconditioner; }
-
-  /** \returns a read-only reference to the preconditioner. */
-  const Preconditioner& preconditioner() const { return m_preconditioner; }
-
-  /** \returns the max number of iterations.
-    * It is either the value set by setMaxIterations or, by default,
-    * twice the number of columns of the matrix.
-    */
-  Index maxIterations() const
-  {
-    return (m_maxIterations<0) ? 2*matrix().cols() : m_maxIterations;
-  }
-
-  /** Sets the max number of iterations.
-    * Default is twice the number of columns of the matrix.
-    */
-  Derived& setMaxIterations(Index maxIters)
-  {
-    m_maxIterations = maxIters;
-    return derived();
-  }
-
-  /** \returns the number of iterations performed during the last solve */
-  Index iterations() const
-  {
-    eigen_assert(m_isInitialized && "ConjugateGradient is not initialized.");
-    return m_iterations;
-  }
-
-  /** \returns the tolerance error reached during the last solve.
-    * It is a close approximation of the true relative residual error |Ax-b|/|b|.
-    */
-  RealScalar error() const
-  {
-    eigen_assert(m_isInitialized && "ConjugateGradient is not initialized.");
-    return m_error;
-  }
-
-  /** \returns the solution x of \f$ A x = b \f$ using the current decomposition of A
-    * and \a x0 as an initial solution.
-    *
-    * \sa solve(), compute()
-    */
-  template<typename Rhs,typename Guess>
-  inline const SolveWithGuess<Derived, Rhs, Guess>
-  solveWithGuess(const MatrixBase<Rhs>& b, const Guess& x0) const
-  {
-    eigen_assert(m_isInitialized && "Solver is not initialized.");
-    eigen_assert(derived().rows()==b.rows() && "solve(): invalid number of rows of the right hand side matrix b");
-    return SolveWithGuess<Derived, Rhs, Guess>(derived(), b.derived(), x0);
-  }
-
-  /** \returns Success if the iterations converged, and NoConvergence otherwise. */
-  ComputationInfo info() const
-  {
-    eigen_assert(m_isInitialized && "IterativeSolverBase is not initialized.");
-    return m_info;
-  }
-
-  /** \internal */
-  template<typename Rhs, typename DestDerived>
-  void _solve_with_guess_impl(const Rhs& b, SparseMatrixBase<DestDerived> &aDest) const
-  {
-    eigen_assert(rows()==b.rows());
-
-    Index rhsCols = b.cols();
-    Index size = b.rows();
-    DestDerived& dest(aDest.derived());
-    typedef typename DestDerived::Scalar DestScalar;
-    Eigen::Matrix<DestScalar,Dynamic,1> tb(size);
-    Eigen::Matrix<DestScalar,Dynamic,1> tx(cols());
-    // We do not directly fill dest because sparse expressions have to be free of aliasing issue.
-    // For non square least-square problems, b and dest might not have the same size whereas they might alias each-other.
-    typename DestDerived::PlainObject tmp(cols(),rhsCols);
-    ComputationInfo global_info = Success;
-    for(Index k=0; k<rhsCols; ++k)
-    {
-      tb = b.col(k);
-      tx = dest.col(k);
-      derived()._solve_vector_with_guess_impl(tb,tx);
-      tmp.col(k) = tx.sparseView(0);
-
-      // The call to _solve_vector_with_guess_impl updates m_info, so if it failed for a previous column
-      // we need to restore it to the worst value.
-      if(m_info==NumericalIssue)
-        global_info = NumericalIssue;
-      else if(m_info==NoConvergence)
-        global_info = NoConvergence;
-    }
-    m_info = global_info;
-    dest.swap(tmp);
-  }
-
-  template<typename Rhs, typename DestDerived>
-  typename internal::enable_if<Rhs::ColsAtCompileTime!=1 && DestDerived::ColsAtCompileTime!=1>::type
-  _solve_with_guess_impl(const Rhs& b, MatrixBase<DestDerived> &aDest) const
-  {
-    eigen_assert(rows()==b.rows());
-
-    Index rhsCols = b.cols();
-    DestDerived& dest(aDest.derived());
-    ComputationInfo global_info = Success;
-    for(Index k=0; k<rhsCols; ++k)
-    {
-      typename DestDerived::ColXpr xk(dest,k);
-      typename Rhs::ConstColXpr bk(b,k);
-      derived()._solve_vector_with_guess_impl(bk,xk);
-
-      // The call to _solve_vector_with_guess updates m_info, so if it failed for a previous column
-      // we need to restore it to the worst value.
-      if(m_info==NumericalIssue)
-        global_info = NumericalIssue;
-      else if(m_info==NoConvergence)
-        global_info = NoConvergence;
-    }
-    m_info = global_info;
-  }
-
-  template<typename Rhs, typename DestDerived>
-  typename internal::enable_if<Rhs::ColsAtCompileTime==1 || DestDerived::ColsAtCompileTime==1>::type
-  _solve_with_guess_impl(const Rhs& b, MatrixBase<DestDerived> &dest) const
-  {
-    derived()._solve_vector_with_guess_impl(b,dest.derived());
-  }
-
-  /** \internal default initial guess = 0 */
-  template<typename Rhs,typename Dest>
-  void _solve_impl(const Rhs& b, Dest& x) const
-  {
-    x.setZero();
-    derived()._solve_with_guess_impl(b,x);
-  }
-
-protected:
-  void init()
-  {
-    m_isInitialized = false;
-    m_analysisIsOk = false;
-    m_factorizationIsOk = false;
-    m_maxIterations = -1;
-    m_tolerance = NumTraits<Scalar>::epsilon();
-  }
-
-  typedef internal::generic_matrix_wrapper<MatrixType> MatrixWrapper;
-  typedef typename MatrixWrapper::ActualMatrixType ActualMatrixType;
-
-  const ActualMatrixType& matrix() const
-  {
-    return m_matrixWrapper.matrix();
-  }
-
-  template<typename InputType>
-  void grab(const InputType &A)
-  {
-    m_matrixWrapper.grab(A);
-  }
-
-  MatrixWrapper m_matrixWrapper;
-  Preconditioner m_preconditioner;
-
-  Index m_maxIterations;
-  RealScalar m_tolerance;
-
-  mutable RealScalar m_error;
-  mutable Index m_iterations;
-  mutable ComputationInfo m_info;
-  mutable bool m_analysisIsOk, m_factorizationIsOk;
-};
-
-} // end namespace Eigen
-
-#endif // EIGEN_ITERATIVE_SOLVER_BASE_H

sequenzo/dissimilarity_measures/src/eigen/Eigen/src/IterativeLinearSolvers/LeastSquareConjugateGradient.h

@@ -1,198 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2015 Gael Guennebaud <gael.guennebaud@inria.fr>
-//
-// This Source Code Form is subject to the terms of the Mozilla
-// Public License v. 2.0. If a copy of the MPL was not distributed
-// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
-
-#ifndef EIGEN_LEAST_SQUARE_CONJUGATE_GRADIENT_H
-#define EIGEN_LEAST_SQUARE_CONJUGATE_GRADIENT_H
-
-namespace Eigen { 
-
-namespace internal {
-
-/** \internal Low-level conjugate gradient algorithm for least-square problems
-  * \param mat The matrix A
-  * \param rhs The right hand side vector b
-  * \param x On input and initial solution, on output the computed solution.
-  * \param precond A preconditioner being able to efficiently solve for an
-  *                approximation of A'Ax=b (regardless of b)
-  * \param iters On input the max number of iteration, on output the number of performed iterations.
-  * \param tol_error On input the tolerance error, on output an estimation of the relative error.
-  */
-template<typename MatrixType, typename Rhs, typename Dest, typename Preconditioner>
-EIGEN_DONT_INLINE
-void least_square_conjugate_gradient(const MatrixType& mat, const Rhs& rhs, Dest& x,
-                                     const Preconditioner& precond, Index& iters,
-                                     typename Dest::RealScalar& tol_error)
-{
-  using std::sqrt;
-  using std::abs;
-  typedef typename Dest::RealScalar RealScalar;
-  typedef typename Dest::Scalar Scalar;
-  typedef Matrix<Scalar,Dynamic,1> VectorType;
-  
-  RealScalar tol = tol_error;
-  Index maxIters = iters;
-  
-  Index m = mat.rows(), n = mat.cols();
-
-  VectorType residual        = rhs - mat * x;
-  VectorType normal_residual = mat.adjoint() * residual;
-
-  RealScalar rhsNorm2 = (mat.adjoint()*rhs).squaredNorm();
-  if(rhsNorm2 == 0) 
-  {
-    x.setZero();
-    iters = 0;
-    tol_error = 0;
-    return;
-  }
-  RealScalar threshold = tol*tol*rhsNorm2;
-  RealScalar residualNorm2 = normal_residual.squaredNorm();
-  if (residualNorm2 < threshold)
-  {
-    iters = 0;
-    tol_error = sqrt(residualNorm2 / rhsNorm2);
-    return;
-  }
-  
-  VectorType p(n);
-  p = precond.solve(normal_residual);                         // initial search direction
-
-  VectorType z(n), tmp(m);
-  RealScalar absNew = numext::real(normal_residual.dot(p));  // the square of the absolute value of r scaled by invM
-  Index i = 0;
-  while(i < maxIters)
-  {
-    tmp.noalias() = mat * p;
-
-    Scalar alpha = absNew / tmp.squaredNorm();      // the amount we travel on dir
-    x += alpha * p;                                 // update solution
-    residual -= alpha * tmp;                        // update residual
-    normal_residual = mat.adjoint() * residual;     // update residual of the normal equation
-    
-    residualNorm2 = normal_residual.squaredNorm();
-    if(residualNorm2 < threshold)
-      break;
-    
-    z = precond.solve(normal_residual);             // approximately solve for "A'A z = normal_residual"
-
-    RealScalar absOld = absNew;
-    absNew = numext::real(normal_residual.dot(z));  // update the absolute value of r
-    RealScalar beta = absNew / absOld;              // calculate the Gram-Schmidt value used to create the new search direction
-    p = z + beta * p;                               // update search direction
-    i++;
-  }
-  tol_error = sqrt(residualNorm2 / rhsNorm2);
-  iters = i;
-}
-
-}
-
-template< typename _MatrixType,
-          typename _Preconditioner = LeastSquareDiagonalPreconditioner<typename _MatrixType::Scalar> >
-class LeastSquaresConjugateGradient;
-
-namespace internal {
-
-template< typename _MatrixType, typename _Preconditioner>
-struct traits<LeastSquaresConjugateGradient<_MatrixType,_Preconditioner> >
-{
-  typedef _MatrixType MatrixType;
-  typedef _Preconditioner Preconditioner;
-};
-
-}
-
-/** \ingroup IterativeLinearSolvers_Module
-  * \brief A conjugate gradient solver for sparse (or dense) least-square problems
-  *
-  * This class allows to solve for A x = b linear problems using an iterative conjugate gradient algorithm.
-  * The matrix A can be non symmetric and rectangular, but the matrix A' A should be positive-definite to guaranty stability.
-  * Otherwise, the SparseLU or SparseQR classes might be preferable.
-  * The matrix A and the vectors x and b can be either dense or sparse.
-  *
-  * \tparam _MatrixType the type of the matrix A, can be a dense or a sparse matrix.
-  * \tparam _Preconditioner the type of the preconditioner. Default is LeastSquareDiagonalPreconditioner
-  *
-  * \implsparsesolverconcept
-  * 
-  * The maximal number of iterations and tolerance value can be controlled via the setMaxIterations()
-  * and setTolerance() methods. The defaults are the size of the problem for the maximal number of iterations
-  * and NumTraits<Scalar>::epsilon() for the tolerance.
-  * 
-  * This class can be used as the direct solver classes. Here is a typical usage example:
-    \code
-    int m=1000000, n = 10000;
-    VectorXd x(n), b(m);
-    SparseMatrix<double> A(m,n);
-    // fill A and b
-    LeastSquaresConjugateGradient<SparseMatrix<double> > lscg;
-    lscg.compute(A);
-    x = lscg.solve(b);
-    std::cout << "#iterations:     " << lscg.iterations() << std::endl;
-    std::cout << "estimated error: " << lscg.error()      << std::endl;
-    // update b, and solve again
-    x = lscg.solve(b);
-    \endcode
-  * 
-  * By default the iterations start with x=0 as an initial guess of the solution.
-  * One can control the start using the solveWithGuess() method.
-  * 
-  * \sa class ConjugateGradient, SparseLU, SparseQR
-  */
-template< typename _MatrixType, typename _Preconditioner>
-class LeastSquaresConjugateGradient : public IterativeSolverBase<LeastSquaresConjugateGradient<_MatrixType,_Preconditioner> >
-{
-  typedef IterativeSolverBase<LeastSquaresConjugateGradient> Base;
-  using Base::matrix;
-  using Base::m_error;
-  using Base::m_iterations;
-  using Base::m_info;
-  using Base::m_isInitialized;
-public:
-  typedef _MatrixType MatrixType;
-  typedef typename MatrixType::Scalar Scalar;
-  typedef typename MatrixType::RealScalar RealScalar;
-  typedef _Preconditioner Preconditioner;
-
-public:
-
-  /** Default constructor. */
-  LeastSquaresConjugateGradient() : Base() {}
-
-  /** Initialize the solver with matrix \a A for further \c Ax=b solving.
-    * 
-    * This constructor is a shortcut for the default constructor followed
-    * by a call to compute().
-    * 
-    * \warning this class stores a reference to the matrix A as well as some
-    * precomputed values that depend on it. Therefore, if \a A is changed
-    * this class becomes invalid. Call compute() to update it with the new
-    * matrix A, or modify a copy of A.
-    */
-  template<typename MatrixDerived>
-  explicit LeastSquaresConjugateGradient(const EigenBase<MatrixDerived>& A) : Base(A.derived()) {}
-
-  ~LeastSquaresConjugateGradient() {}
-
-  /** \internal */
-  template<typename Rhs,typename Dest>
-  void _solve_vector_with_guess_impl(const Rhs& b, Dest& x) const
-  {
-    m_iterations = Base::maxIterations();
-    m_error = Base::m_tolerance;
-
-    internal::least_square_conjugate_gradient(matrix(), b, x, Base::m_preconditioner, m_iterations, m_error);
-    m_info = m_error <= Base::m_tolerance ? Success : NoConvergence;
-  }
-
-};
-
-} // end namespace Eigen
-
-#endif // EIGEN_LEAST_SQUARE_CONJUGATE_GRADIENT_H