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/SPQRSupport/SuiteSparseQRSupport.h

@@ -1,335 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2012 Desire Nuentsa <desire.nuentsa_wakam@inria.fr>
-// Copyright (C) 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_SUITESPARSEQRSUPPORT_H
-#define EIGEN_SUITESPARSEQRSUPPORT_H
-
-namespace Eigen {
-  
-  template<typename MatrixType> class SPQR; 
-  template<typename SPQRType> struct SPQRMatrixQReturnType; 
-  template<typename SPQRType> struct SPQRMatrixQTransposeReturnType; 
-  template <typename SPQRType, typename Derived> struct SPQR_QProduct;
-  namespace internal {
-    template <typename SPQRType> struct traits<SPQRMatrixQReturnType<SPQRType> >
-    {
-      typedef typename SPQRType::MatrixType ReturnType;
-    };
-    template <typename SPQRType> struct traits<SPQRMatrixQTransposeReturnType<SPQRType> >
-    {
-      typedef typename SPQRType::MatrixType ReturnType;
-    };
-    template <typename SPQRType, typename Derived> struct traits<SPQR_QProduct<SPQRType, Derived> >
-    {
-      typedef typename Derived::PlainObject ReturnType;
-    };
-  } // End namespace internal
-  
-/**
-  * \ingroup SPQRSupport_Module
-  * \class SPQR
-  * \brief Sparse QR factorization based on SuiteSparseQR library
-  *
-  * This class is used to perform a multithreaded and multifrontal rank-revealing QR decomposition
-  * of sparse matrices. The result is then used to solve linear leasts_square systems.
-  * Clearly, a QR factorization is returned such that A*P = Q*R where :
-  *
-  * P is the column permutation. Use colsPermutation() to get it.
-  *
-  * Q is the orthogonal matrix represented as Householder reflectors.
-  * Use matrixQ() to get an expression and matrixQ().transpose() to get the transpose.
-  * You can then apply it to a vector.
-  *
-  * R is the sparse triangular factor. Use matrixQR() to get it as SparseMatrix.
-  * NOTE : The Index type of R is always SuiteSparse_long. You can get it with SPQR::Index
-  *
-  * \tparam _MatrixType The type of the sparse matrix A, must be a column-major SparseMatrix<>
-  *
-  * \implsparsesolverconcept
-  *
-  *
-  */
-template<typename _MatrixType>
-class SPQR : public SparseSolverBase<SPQR<_MatrixType> >
-{
-  protected:
-    typedef SparseSolverBase<SPQR<_MatrixType> > Base;
-    using Base::m_isInitialized;
-  public:
-    typedef typename _MatrixType::Scalar Scalar;
-    typedef typename _MatrixType::RealScalar RealScalar;
-    typedef SuiteSparse_long StorageIndex ;
-    typedef SparseMatrix<Scalar, ColMajor, StorageIndex> MatrixType;
-    typedef Map<PermutationMatrix<Dynamic, Dynamic, StorageIndex> > PermutationType;
-    enum {
-      ColsAtCompileTime = Dynamic,
-      MaxColsAtCompileTime = Dynamic
-    };
-  public:
-    SPQR() 
-      : m_analysisIsOk(false),
-        m_factorizationIsOk(false),
-        m_isRUpToDate(false),
-        m_ordering(SPQR_ORDERING_DEFAULT),
-        m_allow_tol(SPQR_DEFAULT_TOL),
-        m_tolerance (NumTraits<Scalar>::epsilon()),
-        m_cR(0),
-        m_E(0),
-        m_H(0),
-        m_HPinv(0),
-        m_HTau(0),
-        m_useDefaultThreshold(true)
-    { 
-      cholmod_l_start(&m_cc);
-    }
-    
-    explicit SPQR(const _MatrixType& matrix)
-      : m_analysisIsOk(false),
-        m_factorizationIsOk(false),
-        m_isRUpToDate(false),
-        m_ordering(SPQR_ORDERING_DEFAULT),
-        m_allow_tol(SPQR_DEFAULT_TOL),
-        m_tolerance (NumTraits<Scalar>::epsilon()),
-        m_cR(0),
-        m_E(0),
-        m_H(0),
-        m_HPinv(0),
-        m_HTau(0),
-        m_useDefaultThreshold(true)
-    {
-      cholmod_l_start(&m_cc);
-      compute(matrix);
-    }
-    
-    ~SPQR()
-    {
-      SPQR_free();
-      cholmod_l_finish(&m_cc);
-    }
-    void SPQR_free()
-    {
-      cholmod_l_free_sparse(&m_H, &m_cc);
-      cholmod_l_free_sparse(&m_cR, &m_cc);
-      cholmod_l_free_dense(&m_HTau, &m_cc);
-      std::free(m_E);
-      std::free(m_HPinv);
-    }
-
-    void compute(const _MatrixType& matrix)
-    {
-      if(m_isInitialized) SPQR_free();
-
-      MatrixType mat(matrix);
-      
-      /* Compute the default threshold as in MatLab, see:
-       * Tim Davis, "Algorithm 915, SuiteSparseQR: Multifrontal Multithreaded Rank-Revealing
-       * Sparse QR Factorization, ACM Trans. on Math. Soft. 38(1), 2011, Page 8:3 
-       */
-      RealScalar pivotThreshold = m_tolerance;
-      if(m_useDefaultThreshold) 
-      {
-        RealScalar max2Norm = 0.0;
-        for (int j = 0; j < mat.cols(); j++) max2Norm = numext::maxi(max2Norm, mat.col(j).norm());
-        if(max2Norm==RealScalar(0))
-          max2Norm = RealScalar(1);
-        pivotThreshold = 20 * (mat.rows() + mat.cols()) * max2Norm * NumTraits<RealScalar>::epsilon();
-      }
-      cholmod_sparse A; 
-      A = viewAsCholmod(mat);
-      m_rows = matrix.rows();
-      Index col = matrix.cols();
-      m_rank = SuiteSparseQR<Scalar>(m_ordering, pivotThreshold, col, &A, 
-                             &m_cR, &m_E, &m_H, &m_HPinv, &m_HTau, &m_cc);
-
-      if (!m_cR)
-      {
-        m_info = NumericalIssue;
-        m_isInitialized = false;
-        return;
-      }
-      m_info = Success;
-      m_isInitialized = true;
-      m_isRUpToDate = false;
-    }
-    /** 
-     * Get the number of rows of the input matrix and the Q matrix
-     */
-    inline Index rows() const {return m_rows; }
-    
-    /** 
-     * Get the number of columns of the input matrix. 
-     */
-    inline Index cols() const { return m_cR->ncol; }
-    
-    template<typename Rhs, typename Dest>
-    void _solve_impl(const MatrixBase<Rhs> &b, MatrixBase<Dest> &dest) const
-    {
-      eigen_assert(m_isInitialized && " The QR factorization should be computed first, call compute()");
-      eigen_assert(b.cols()==1 && "This method is for vectors only");
-
-      //Compute Q^T * b
-      typename Dest::PlainObject y, y2;
-      y = matrixQ().transpose() * b;
-      
-      // Solves with the triangular matrix R
-      Index rk = this->rank();
-      y2 = y;
-      y.resize((std::max)(cols(),Index(y.rows())),y.cols());
-      y.topRows(rk) = this->matrixR().topLeftCorner(rk, rk).template triangularView<Upper>().solve(y2.topRows(rk));
-
-      // Apply the column permutation 
-      // colsPermutation() performs a copy of the permutation,
-      // so let's apply it manually:
-      for(Index i = 0; i < rk; ++i) dest.row(m_E[i]) = y.row(i);
-      for(Index i = rk; i < cols(); ++i) dest.row(m_E[i]).setZero();
-      
-//       y.bottomRows(y.rows()-rk).setZero();
-//       dest = colsPermutation() * y.topRows(cols());
-      
-      m_info = Success;
-    }
-    
-    /** \returns the sparse triangular factor R. It is a sparse matrix
-     */
-    const MatrixType matrixR() const
-    {
-      eigen_assert(m_isInitialized && " The QR factorization should be computed first, call compute()");
-      if(!m_isRUpToDate) {
-        m_R = viewAsEigen<Scalar,ColMajor, typename MatrixType::StorageIndex>(*m_cR);
-        m_isRUpToDate = true;
-      }
-      return m_R;
-    }
-    /// Get an expression of the matrix Q
-    SPQRMatrixQReturnType<SPQR> matrixQ() const
-    {
-      return SPQRMatrixQReturnType<SPQR>(*this);
-    }
-    /// Get the permutation that was applied to columns of A
-    PermutationType colsPermutation() const
-    { 
-      eigen_assert(m_isInitialized && "Decomposition is not initialized.");
-      return PermutationType(m_E, m_cR->ncol);
-    }
-    /**
-     * Gets the rank of the matrix. 
-     * It should be equal to matrixQR().cols if the matrix is full-rank
-     */
-    Index rank() const
-    {
-      eigen_assert(m_isInitialized && "Decomposition is not initialized.");
-      return m_cc.SPQR_istat[4];
-    }
-    /// Set the fill-reducing ordering method to be used
-    void setSPQROrdering(int ord) { m_ordering = ord;}
-    /// Set the tolerance tol to treat columns with 2-norm < =tol as zero
-    void setPivotThreshold(const RealScalar& tol)
-    {
-      m_useDefaultThreshold = false;
-      m_tolerance = tol;
-    }
-    
-    /** \returns a pointer to the SPQR workspace */
-    cholmod_common *cholmodCommon() const { return &m_cc; }
-    
-    
-    /** \brief Reports whether previous computation was successful.
-      *
-      * \returns \c Success if computation was successful,
-      *          \c NumericalIssue if the sparse QR can not be computed
-      */
-    ComputationInfo info() const
-    {
-      eigen_assert(m_isInitialized && "Decomposition is not initialized.");
-      return m_info;
-    }
-  protected:
-    bool m_analysisIsOk;
-    bool m_factorizationIsOk;
-    mutable bool m_isRUpToDate;
-    mutable ComputationInfo m_info;
-    int m_ordering; // Ordering method to use, see SPQR's manual
-    int m_allow_tol; // Allow to use some tolerance during numerical factorization.
-    RealScalar m_tolerance; // treat columns with 2-norm below this tolerance as zero
-    mutable cholmod_sparse *m_cR; // The sparse R factor in cholmod format
-    mutable MatrixType m_R; // The sparse matrix R in Eigen format
-    mutable StorageIndex *m_E; // The permutation applied to columns
-    mutable cholmod_sparse *m_H;  //The householder vectors
-    mutable StorageIndex *m_HPinv; // The row permutation of H
-    mutable cholmod_dense *m_HTau; // The Householder coefficients
-    mutable Index m_rank; // The rank of the matrix
-    mutable cholmod_common m_cc; // Workspace and parameters
-    bool m_useDefaultThreshold;     // Use default threshold
-    Index m_rows;
-    template<typename ,typename > friend struct SPQR_QProduct;
-};
-
-template <typename SPQRType, typename Derived>
-struct SPQR_QProduct : ReturnByValue<SPQR_QProduct<SPQRType,Derived> >
-{
-  typedef typename SPQRType::Scalar Scalar;
-  typedef typename SPQRType::StorageIndex StorageIndex;
-  //Define the constructor to get reference to argument types
-  SPQR_QProduct(const SPQRType& spqr, const Derived& other, bool transpose) : m_spqr(spqr),m_other(other),m_transpose(transpose) {}
-  
-  inline Index rows() const { return m_transpose ? m_spqr.rows() : m_spqr.cols(); }
-  inline Index cols() const { return m_other.cols(); }
-  // Assign to a vector
-  template<typename ResType>
-  void evalTo(ResType& res) const
-  {
-    cholmod_dense y_cd;
-    cholmod_dense *x_cd; 
-    int method = m_transpose ? SPQR_QTX : SPQR_QX; 
-    cholmod_common *cc = m_spqr.cholmodCommon();
-    y_cd = viewAsCholmod(m_other.const_cast_derived());
-    x_cd = SuiteSparseQR_qmult<Scalar>(method, m_spqr.m_H, m_spqr.m_HTau, m_spqr.m_HPinv, &y_cd, cc);
-    res = Matrix<Scalar,ResType::RowsAtCompileTime,ResType::ColsAtCompileTime>::Map(reinterpret_cast<Scalar*>(x_cd->x), x_cd->nrow, x_cd->ncol);
-    cholmod_l_free_dense(&x_cd, cc);
-  }
-  const SPQRType& m_spqr; 
-  const Derived& m_other; 
-  bool m_transpose; 
-  
-};
-template<typename SPQRType>
-struct SPQRMatrixQReturnType{
-  
-  SPQRMatrixQReturnType(const SPQRType& spqr) : m_spqr(spqr) {}
-  template<typename Derived>
-  SPQR_QProduct<SPQRType, Derived> operator*(const MatrixBase<Derived>& other)
-  {
-    return SPQR_QProduct<SPQRType,Derived>(m_spqr,other.derived(),false);
-  }
-  SPQRMatrixQTransposeReturnType<SPQRType> adjoint() const
-  {
-    return SPQRMatrixQTransposeReturnType<SPQRType>(m_spqr);
-  }
-  // To use for operations with the transpose of Q
-  SPQRMatrixQTransposeReturnType<SPQRType> transpose() const
-  {
-    return SPQRMatrixQTransposeReturnType<SPQRType>(m_spqr);
-  }
-  const SPQRType& m_spqr;
-};
-
-template<typename SPQRType>
-struct SPQRMatrixQTransposeReturnType{
-  SPQRMatrixQTransposeReturnType(const SPQRType& spqr) : m_spqr(spqr) {}
-  template<typename Derived>
-  SPQR_QProduct<SPQRType,Derived> operator*(const MatrixBase<Derived>& other)
-  {
-    return SPQR_QProduct<SPQRType,Derived>(m_spqr,other.derived(), true);
-  }
-  const SPQRType& m_spqr;
-};
-
-}// End namespace Eigen
-#endif