sequenzo 0.1.17__cp311-cp311-macosx_10_9_universal2.whl → 0.1.19__cp311-cp311-macosx_10_9_universal2.whl

sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/PolynomialSolver.h

@@ -1,428 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2010 Manuel Yguel <manuel.yguel@gmail.com>
-//
-// 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_POLYNOMIAL_SOLVER_H
-#define EIGEN_POLYNOMIAL_SOLVER_H
-
-namespace Eigen { 
-
-/** \ingroup Polynomials_Module
- *  \class PolynomialSolverBase.
- *
- * \brief Defined to be inherited by polynomial solvers: it provides
- * convenient methods such as
- *  - real roots,
- *  - greatest, smallest complex roots,
- *  - real roots with greatest, smallest absolute real value,
- *  - greatest, smallest real roots.
- *
- * It stores the set of roots as a vector of complexes.
- *
- */
-template< typename _Scalar, int _Deg >
-class PolynomialSolverBase
-{
-  public:
-    EIGEN_MAKE_ALIGNED_OPERATOR_NEW_IF_VECTORIZABLE_FIXED_SIZE(_Scalar,_Deg==Dynamic ? Dynamic : _Deg)
-
-    typedef _Scalar                             Scalar;
-    typedef typename NumTraits<Scalar>::Real    RealScalar;
-    typedef std::complex<RealScalar>            RootType;
-    typedef Matrix<RootType,_Deg,1>             RootsType;
-
-    typedef DenseIndex Index;
-
-  protected:
-    template< typename OtherPolynomial >
-    inline void setPolynomial( const OtherPolynomial& poly ){
-      m_roots.resize(poly.size()-1); }
-
-  public:
-    template< typename OtherPolynomial >
-    inline PolynomialSolverBase( const OtherPolynomial& poly ){
-      setPolynomial( poly() ); }
-
-    inline PolynomialSolverBase(){}
-
-  public:
-    /** \returns the complex roots of the polynomial */
-    inline const RootsType& roots() const { return m_roots; }
-
-  public:
-    /** Clear and fills the back insertion sequence with the real roots of the polynomial
-     * i.e. the real part of the complex roots that have an imaginary part which
-     * absolute value is smaller than absImaginaryThreshold.
-     * absImaginaryThreshold takes the dummy_precision associated
-     * with the _Scalar template parameter of the PolynomialSolver class as the default value.
-     *
-     * \param[out] bi_seq : the back insertion sequence (stl concept)
-     * \param[in]  absImaginaryThreshold : the maximum bound of the imaginary part of a complex
-     *  number that is considered as real.
-     * */
-    template<typename Stl_back_insertion_sequence>
-    inline void realRoots( Stl_back_insertion_sequence& bi_seq,
-        const RealScalar& absImaginaryThreshold = NumTraits<Scalar>::dummy_precision() ) const
-    {
-      using std::abs;
-      bi_seq.clear();
-      for(Index i=0; i<m_roots.size(); ++i )
-      {
-        if( abs( m_roots[i].imag() ) < absImaginaryThreshold ){
-          bi_seq.push_back( m_roots[i].real() ); }
-      }
-    }
-
-  protected:
-    template<typename squaredNormBinaryPredicate>
-    inline const RootType& selectComplexRoot_withRespectToNorm( squaredNormBinaryPredicate& pred ) const
-    {
-      Index res=0;
-      RealScalar norm2 = numext::abs2( m_roots[0] );
-      for( Index i=1; i<m_roots.size(); ++i )
-      {
-        const RealScalar currNorm2 = numext::abs2( m_roots[i] );
-        if( pred( currNorm2, norm2 ) ){
-          res=i; norm2=currNorm2; }
-      }
-      return m_roots[res];
-    }
-
-  public:
-    /**
-     * \returns the complex root with greatest norm.
-     */
-    inline const RootType& greatestRoot() const
-    {
-      std::greater<RealScalar> greater;
-      return selectComplexRoot_withRespectToNorm( greater );
-    }
-
-    /**
-     * \returns the complex root with smallest norm.
-     */
-    inline const RootType& smallestRoot() const
-    {
-      std::less<RealScalar> less;
-      return selectComplexRoot_withRespectToNorm( less );
-    }
-
-  protected:
-    template<typename squaredRealPartBinaryPredicate>
-    inline const RealScalar& selectRealRoot_withRespectToAbsRealPart(
-        squaredRealPartBinaryPredicate& pred,
-        bool& hasArealRoot,
-        const RealScalar& absImaginaryThreshold = NumTraits<Scalar>::dummy_precision() ) const
-    {
-      using std::abs;
-      hasArealRoot = false;
-      Index res=0;
-      RealScalar abs2(0);
-
-      for( Index i=0; i<m_roots.size(); ++i )
-      {
-        if( abs( m_roots[i].imag() ) <= absImaginaryThreshold )
-        {
-          if( !hasArealRoot )
-          {
-            hasArealRoot = true;
-            res = i;
-            abs2 = m_roots[i].real() * m_roots[i].real();
-          }
-          else
-          {
-            const RealScalar currAbs2 = m_roots[i].real() * m_roots[i].real();
-            if( pred( currAbs2, abs2 ) )
-            {
-              abs2 = currAbs2;
-              res = i;
-            }
-          }
-        }
-        else if(!hasArealRoot)
-        {
-          if( abs( m_roots[i].imag() ) < abs( m_roots[res].imag() ) ){
-            res = i;}
-        }
-      }
-      return numext::real_ref(m_roots[res]);
-    }
-
-
-    template<typename RealPartBinaryPredicate>
-    inline const RealScalar& selectRealRoot_withRespectToRealPart(
-        RealPartBinaryPredicate& pred,
-        bool& hasArealRoot,
-        const RealScalar& absImaginaryThreshold = NumTraits<Scalar>::dummy_precision() ) const
-    {
-      using std::abs;
-      hasArealRoot = false;
-      Index res=0;
-      RealScalar val(0);
-
-      for( Index i=0; i<m_roots.size(); ++i )
-      {
-        if( abs( m_roots[i].imag() ) <= absImaginaryThreshold )
-        {
-          if( !hasArealRoot )
-          {
-            hasArealRoot = true;
-            res = i;
-            val = m_roots[i].real();
-          }
-          else
-          {
-            const RealScalar curr = m_roots[i].real();
-            if( pred( curr, val ) )
-            {
-              val = curr;
-              res = i;
-            }
-          }
-        }
-        else
-        {
-          if( abs( m_roots[i].imag() ) < abs( m_roots[res].imag() ) ){
-            res = i; }
-        }
-      }
-      return numext::real_ref(m_roots[res]);
-    }
-
-  public:
-    /**
-     * \returns a real root with greatest absolute magnitude.
-     * A real root is defined as the real part of a complex root with absolute imaginary
-     * part smallest than absImaginaryThreshold.
-     * absImaginaryThreshold takes the dummy_precision associated
-     * with the _Scalar template parameter of the PolynomialSolver class as the default value.
-     * If no real root is found the boolean hasArealRoot is set to false and the real part of
-     * the root with smallest absolute imaginary part is returned instead.
-     *
-     * \param[out] hasArealRoot : boolean true if a real root is found according to the
-     *  absImaginaryThreshold criterion, false otherwise.
-     * \param[in] absImaginaryThreshold : threshold on the absolute imaginary part to decide
-     *  whether or not a root is real.
-     */
-    inline const RealScalar& absGreatestRealRoot(
-        bool& hasArealRoot,
-        const RealScalar& absImaginaryThreshold = NumTraits<Scalar>::dummy_precision() ) const
-    {
-      std::greater<RealScalar> greater;
-      return selectRealRoot_withRespectToAbsRealPart( greater, hasArealRoot, absImaginaryThreshold );
-    }
-
-
-    /**
-     * \returns a real root with smallest absolute magnitude.
-     * A real root is defined as the real part of a complex root with absolute imaginary
-     * part smallest than absImaginaryThreshold.
-     * absImaginaryThreshold takes the dummy_precision associated
-     * with the _Scalar template parameter of the PolynomialSolver class as the default value.
-     * If no real root is found the boolean hasArealRoot is set to false and the real part of
-     * the root with smallest absolute imaginary part is returned instead.
-     *
-     * \param[out] hasArealRoot : boolean true if a real root is found according to the
-     *  absImaginaryThreshold criterion, false otherwise.
-     * \param[in] absImaginaryThreshold : threshold on the absolute imaginary part to decide
-     *  whether or not a root is real.
-     */
-    inline const RealScalar& absSmallestRealRoot(
-        bool& hasArealRoot,
-        const RealScalar& absImaginaryThreshold = NumTraits<Scalar>::dummy_precision() ) const
-    {
-      std::less<RealScalar> less;
-      return selectRealRoot_withRespectToAbsRealPart( less, hasArealRoot, absImaginaryThreshold );
-    }
-
-
-    /**
-     * \returns the real root with greatest value.
-     * A real root is defined as the real part of a complex root with absolute imaginary
-     * part smallest than absImaginaryThreshold.
-     * absImaginaryThreshold takes the dummy_precision associated
-     * with the _Scalar template parameter of the PolynomialSolver class as the default value.
-     * If no real root is found the boolean hasArealRoot is set to false and the real part of
-     * the root with smallest absolute imaginary part is returned instead.
-     *
-     * \param[out] hasArealRoot : boolean true if a real root is found according to the
-     *  absImaginaryThreshold criterion, false otherwise.
-     * \param[in] absImaginaryThreshold : threshold on the absolute imaginary part to decide
-     *  whether or not a root is real.
-     */
-    inline const RealScalar& greatestRealRoot(
-        bool& hasArealRoot,
-        const RealScalar& absImaginaryThreshold = NumTraits<Scalar>::dummy_precision() ) const
-    {
-      std::greater<RealScalar> greater;
-      return selectRealRoot_withRespectToRealPart( greater, hasArealRoot, absImaginaryThreshold );
-    }
-
-
-    /**
-     * \returns the real root with smallest value.
-     * A real root is defined as the real part of a complex root with absolute imaginary
-     * part smallest than absImaginaryThreshold.
-     * absImaginaryThreshold takes the dummy_precision associated
-     * with the _Scalar template parameter of the PolynomialSolver class as the default value.
-     * If no real root is found the boolean hasArealRoot is set to false and the real part of
-     * the root with smallest absolute imaginary part is returned instead.
-     *
-     * \param[out] hasArealRoot : boolean true if a real root is found according to the
-     *  absImaginaryThreshold criterion, false otherwise.
-     * \param[in] absImaginaryThreshold : threshold on the absolute imaginary part to decide
-     *  whether or not a root is real.
-     */
-    inline const RealScalar& smallestRealRoot(
-        bool& hasArealRoot,
-        const RealScalar& absImaginaryThreshold = NumTraits<Scalar>::dummy_precision() ) const
-    {
-      std::less<RealScalar> less;
-      return selectRealRoot_withRespectToRealPart( less, hasArealRoot, absImaginaryThreshold );
-    }
-
-  protected:
-    RootsType               m_roots;
-};
-
-#define EIGEN_POLYNOMIAL_SOLVER_BASE_INHERITED_TYPES( BASE )  \
-  typedef typename BASE::Scalar                 Scalar;       \
-  typedef typename BASE::RealScalar             RealScalar;   \
-  typedef typename BASE::RootType               RootType;     \
-  typedef typename BASE::RootsType              RootsType;
-
-
-
-/** \ingroup Polynomials_Module
-  *
-  * \class PolynomialSolver
-  *
-  * \brief A polynomial solver
-  *
-  * Computes the complex roots of a real polynomial.
-  *
-  * \param _Scalar the scalar type, i.e., the type of the polynomial coefficients
-  * \param _Deg the degree of the polynomial, can be a compile time value or Dynamic.
-  *             Notice that the number of polynomial coefficients is _Deg+1.
-  *
-  * This class implements a polynomial solver and provides convenient methods such as
-  * - real roots,
-  * - greatest, smallest complex roots,
-  * - real roots with greatest, smallest absolute real value.
-  * - greatest, smallest real roots.
-  *
-  * WARNING: this polynomial solver is experimental, part of the unsupported Eigen modules.
-  *
-  *
-  * Currently a QR algorithm is used to compute the eigenvalues of the companion matrix of
-  * the polynomial to compute its roots.
-  * This supposes that the complex moduli of the roots are all distinct: e.g. there should
-  * be no multiple roots or conjugate roots for instance.
-  * With 32bit (float) floating types this problem shows up frequently.
-  * However, almost always, correct accuracy is reached even in these cases for 64bit
-  * (double) floating types and small polynomial degree (<20).
-  */
-template<typename _Scalar, int _Deg>
-class PolynomialSolver : public PolynomialSolverBase<_Scalar,_Deg>
-{
-  public:
-    EIGEN_MAKE_ALIGNED_OPERATOR_NEW_IF_VECTORIZABLE_FIXED_SIZE(_Scalar,_Deg==Dynamic ? Dynamic : _Deg)
-
-    typedef PolynomialSolverBase<_Scalar,_Deg>    PS_Base;
-    EIGEN_POLYNOMIAL_SOLVER_BASE_INHERITED_TYPES( PS_Base )
-
-    typedef Matrix<Scalar,_Deg,_Deg>                 CompanionMatrixType;
-    typedef typename internal::conditional<NumTraits<Scalar>::IsComplex,
-                                          ComplexEigenSolver<CompanionMatrixType>,
-                                          EigenSolver<CompanionMatrixType> >::type EigenSolverType;
-    typedef typename internal::conditional<NumTraits<Scalar>::IsComplex, Scalar, std::complex<Scalar> >::type ComplexScalar;
-
-  public:
-    /** Computes the complex roots of a new polynomial. */
-    template< typename OtherPolynomial >
-    void compute( const OtherPolynomial& poly )
-    {
-      eigen_assert( Scalar(0) != poly[poly.size()-1] );
-      eigen_assert( poly.size() > 1 );
-      if(poly.size() >  2 )
-      {
-        internal::companion<Scalar,_Deg> companion( poly );
-        companion.balance();
-        m_eigenSolver.compute( companion.denseMatrix() );
-        m_roots = m_eigenSolver.eigenvalues();
-        // cleanup noise in imaginary part of real roots:
-        // if the imaginary part is rather small compared to the real part
-        // and that cancelling the imaginary part yield a smaller evaluation,
-        // then it's safe to keep the real part only.
-        RealScalar coarse_prec = RealScalar(std::pow(4,poly.size()+1))*NumTraits<RealScalar>::epsilon();
-        for(Index i = 0; i<m_roots.size(); ++i)
-        {
-          if( internal::isMuchSmallerThan(numext::abs(numext::imag(m_roots[i])),
-                                          numext::abs(numext::real(m_roots[i])),
-                                          coarse_prec) )
-          {
-            ComplexScalar as_real_root = ComplexScalar(numext::real(m_roots[i]));
-            if(    numext::abs(poly_eval(poly, as_real_root))
-                <= numext::abs(poly_eval(poly, m_roots[i])))
-            {
-              m_roots[i] = as_real_root;
-            }
-          }
-        }
-      }
-      else if(poly.size () == 2)
-      {
-        m_roots.resize(1);
-        m_roots[0] = -poly[0]/poly[1];
-      }
-    }
-
-  public:
-    template< typename OtherPolynomial >
-    inline PolynomialSolver( const OtherPolynomial& poly ){
-      compute( poly ); }
-
-    inline PolynomialSolver(){}
-
-  protected:
-    using                   PS_Base::m_roots;
-    EigenSolverType         m_eigenSolver;
-};
-
-
-template< typename _Scalar >
-class PolynomialSolver<_Scalar,1> : public PolynomialSolverBase<_Scalar,1>
-{
-  public:
-    typedef PolynomialSolverBase<_Scalar,1>    PS_Base;
-    EIGEN_POLYNOMIAL_SOLVER_BASE_INHERITED_TYPES( PS_Base )
-
-  public:
-    /** Computes the complex roots of a new polynomial. */
-    template< typename OtherPolynomial >
-    void compute( const OtherPolynomial& poly )
-    {
-      eigen_assert( poly.size() == 2 );
-      eigen_assert( Scalar(0) != poly[1] );
-      m_roots[0] = -poly[0]/poly[1];
-    }
-
-  public:
-    template< typename OtherPolynomial >
-    inline PolynomialSolver( const OtherPolynomial& poly ){
-      compute( poly ); }
-
-    inline PolynomialSolver(){}
-
-  protected:
-    using                   PS_Base::m_roots;
-};
-
-} // end namespace Eigen
-
-#endif // EIGEN_POLYNOMIAL_SOLVER_H

sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/Polynomials/PolynomialUtils.h

@@ -1,143 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2010 Manuel Yguel <manuel.yguel@gmail.com>
-//
-// 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_POLYNOMIAL_UTILS_H
-#define EIGEN_POLYNOMIAL_UTILS_H
-
-namespace Eigen { 
-
-/** \ingroup Polynomials_Module
- * \returns the evaluation of the polynomial at x using Horner algorithm.
- *
- * \param[in] poly : the vector of coefficients of the polynomial ordered
- *  by degrees i.e. poly[i] is the coefficient of degree i of the polynomial
- *  e.g. \f$ 1 + 3x^2 \f$ is stored as a vector \f$ [ 1, 0, 3 ] \f$.
- * \param[in] x : the value to evaluate the polynomial at.
- *
- * \note for stability:
- *   \f$ |x| \le 1 \f$
- */
-template <typename Polynomials, typename T>
-inline
-T poly_eval_horner( const Polynomials& poly, const T& x )
-{
-  T val=poly[poly.size()-1];
-  for(DenseIndex i=poly.size()-2; i>=0; --i ){
-    val = val*x + poly[i]; }
-  return val;
-}
-
-/** \ingroup Polynomials_Module
- * \returns the evaluation of the polynomial at x using stabilized Horner algorithm.
- *
- * \param[in] poly : the vector of coefficients of the polynomial ordered
- *  by degrees i.e. poly[i] is the coefficient of degree i of the polynomial
- *  e.g. \f$ 1 + 3x^2 \f$ is stored as a vector \f$ [ 1, 0, 3 ] \f$.
- * \param[in] x : the value to evaluate the polynomial at.
- */
-template <typename Polynomials, typename T>
-inline
-T poly_eval( const Polynomials& poly, const T& x )
-{
-  typedef typename NumTraits<T>::Real Real;
-
-  if( numext::abs2( x ) <= Real(1) ){
-    return poly_eval_horner( poly, x ); }
-  else
-  {
-    T val=poly[0];
-    T inv_x = T(1)/x;
-    for( DenseIndex i=1; i<poly.size(); ++i ){
-      val = val*inv_x + poly[i]; }
-
-    return numext::pow(x,(T)(poly.size()-1)) * val;
-  }
-}
-
-/** \ingroup Polynomials_Module
- * \returns a maximum bound for the absolute value of any root of the polynomial.
- *
- * \param[in] poly : the vector of coefficients of the polynomial ordered
- *  by degrees i.e. poly[i] is the coefficient of degree i of the polynomial
- *  e.g. \f$ 1 + 3x^2 \f$ is stored as a vector \f$ [ 1, 0, 3 ] \f$.
- *
- *  \pre
- *   the leading coefficient of the input polynomial poly must be non zero
- */
-template <typename Polynomial>
-inline
-typename NumTraits<typename Polynomial::Scalar>::Real cauchy_max_bound( const Polynomial& poly )
-{
-  using std::abs;
-  typedef typename Polynomial::Scalar Scalar;
-  typedef typename NumTraits<Scalar>::Real Real;
-
-  eigen_assert( Scalar(0) != poly[poly.size()-1] );
-  const Scalar inv_leading_coeff = Scalar(1)/poly[poly.size()-1];
-  Real cb(0);
-
-  for( DenseIndex i=0; i<poly.size()-1; ++i ){
-    cb += abs(poly[i]*inv_leading_coeff); }
-  return cb + Real(1);
-}
-
-/** \ingroup Polynomials_Module
- * \returns a minimum bound for the absolute value of any non zero root of the polynomial.
- * \param[in] poly : the vector of coefficients of the polynomial ordered
- *  by degrees i.e. poly[i] is the coefficient of degree i of the polynomial
- *  e.g. \f$ 1 + 3x^2 \f$ is stored as a vector \f$ [ 1, 0, 3 ] \f$.
- */
-template <typename Polynomial>
-inline
-typename NumTraits<typename Polynomial::Scalar>::Real cauchy_min_bound( const Polynomial& poly )
-{
-  using std::abs;
-  typedef typename Polynomial::Scalar Scalar;
-  typedef typename NumTraits<Scalar>::Real Real;
-
-  DenseIndex i=0;
-  while( i<poly.size()-1 && Scalar(0) == poly(i) ){ ++i; }
-  if( poly.size()-1 == i ){
-    return Real(1); }
-
-  const Scalar inv_min_coeff = Scalar(1)/poly[i];
-  Real cb(1);
-  for( DenseIndex j=i+1; j<poly.size(); ++j ){
-    cb += abs(poly[j]*inv_min_coeff); }
-  return Real(1)/cb;
-}
-
-/** \ingroup Polynomials_Module
- * Given the roots of a polynomial compute the coefficients in the
- * monomial basis of the monic polynomial with same roots and minimal degree.
- * If RootVector is a vector of complexes, Polynomial should also be a vector
- * of complexes.
- * \param[in] rv : a vector containing the roots of a polynomial.
- * \param[out] poly : the vector of coefficients of the polynomial ordered
- *  by degrees i.e. poly[i] is the coefficient of degree i of the polynomial
- *  e.g. \f$ 3 + x^2 \f$ is stored as a vector \f$ [ 3, 0, 1 ] \f$.
- */
-template <typename RootVector, typename Polynomial>
-void roots_to_monicPolynomial( const RootVector& rv, Polynomial& poly )
-{
-
-  typedef typename Polynomial::Scalar Scalar;
-
-  poly.setZero( rv.size()+1 );
-  poly[0] = -rv[0]; poly[1] = Scalar(1);
-  for( DenseIndex i=1; i< rv.size(); ++i )
-  {
-    for( DenseIndex j=i+1; j>0; --j ){ poly[j] = poly[j-1] - rv[i]*poly[j]; }
-    poly[0] = -rv[i]*poly[0];
-  }
-}
-
-} // end namespace Eigen
-
-#endif // EIGEN_POLYNOMIAL_UTILS_H