sequenzo 0.1.17__cp312-cp312-macosx_10_13_universal2.whl → 0.1.19__cp312-cp312-macosx_10_13_universal2.whl

sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR.h

@@ -1,434 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2008-2010 Gael Guennebaud <gael.guennebaud@inria.fr>
-// Copyright (C) 2009 Benoit Jacob <jacob.benoit.1@gmail.com>
-// Copyright (C) 2010 Vincent Lejeune
-//
-// 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_QR_H
-#define EIGEN_QR_H
-
-namespace Eigen { 
-
-namespace internal {
-template<typename _MatrixType> struct traits<HouseholderQR<_MatrixType> >
- : traits<_MatrixType>
-{
-  typedef MatrixXpr XprKind;
-  typedef SolverStorage StorageKind;
-  typedef int StorageIndex;
-  enum { Flags = 0 };
-};
-
-} // end namespace internal
-
-/** \ingroup QR_Module
-  *
-  *
-  * \class HouseholderQR
-  *
-  * \brief Householder QR decomposition of a matrix
-  *
-  * \tparam _MatrixType the type of the matrix of which we are computing the QR decomposition
-  *
-  * This class performs a QR decomposition of a matrix \b A into matrices \b Q and \b R
-  * such that 
-  * \f[
-  *  \mathbf{A} = \mathbf{Q} \, \mathbf{R}
-  * \f]
-  * by using Householder transformations. Here, \b Q a unitary matrix and \b R an upper triangular matrix.
-  * The result is stored in a compact way compatible with LAPACK.
-  *
-  * Note that no pivoting is performed. This is \b not a rank-revealing decomposition.
-  * If you want that feature, use FullPivHouseholderQR or ColPivHouseholderQR instead.
-  *
-  * This Householder QR decomposition is faster, but less numerically stable and less feature-full than
-  * FullPivHouseholderQR or ColPivHouseholderQR.
-  *
-  * This class supports the \link InplaceDecomposition inplace decomposition \endlink mechanism.
-  *
-  * \sa MatrixBase::householderQr()
-  */
-template<typename _MatrixType> class HouseholderQR
-        : public SolverBase<HouseholderQR<_MatrixType> >
-{
-  public:
-
-    typedef _MatrixType MatrixType;
-    typedef SolverBase<HouseholderQR> Base;
-    friend class SolverBase<HouseholderQR>;
-
-    EIGEN_GENERIC_PUBLIC_INTERFACE(HouseholderQR)
-    enum {
-      MaxRowsAtCompileTime = MatrixType::MaxRowsAtCompileTime,
-      MaxColsAtCompileTime = MatrixType::MaxColsAtCompileTime
-    };
-    typedef Matrix<Scalar, RowsAtCompileTime, RowsAtCompileTime, (MatrixType::Flags&RowMajorBit) ? RowMajor : ColMajor, MaxRowsAtCompileTime, MaxRowsAtCompileTime> MatrixQType;
-    typedef typename internal::plain_diag_type<MatrixType>::type HCoeffsType;
-    typedef typename internal::plain_row_type<MatrixType>::type RowVectorType;
-    typedef HouseholderSequence<MatrixType,typename internal::remove_all<typename HCoeffsType::ConjugateReturnType>::type> HouseholderSequenceType;
-
-    /**
-      * \brief Default Constructor.
-      *
-      * The default constructor is useful in cases in which the user intends to
-      * perform decompositions via HouseholderQR::compute(const MatrixType&).
-      */
-    HouseholderQR() : m_qr(), m_hCoeffs(), m_temp(), m_isInitialized(false) {}
-
-    /** \brief Default Constructor with memory preallocation
-      *
-      * Like the default constructor but with preallocation of the internal data
-      * according to the specified problem \a size.
-      * \sa HouseholderQR()
-      */
-    HouseholderQR(Index rows, Index cols)
-      : m_qr(rows, cols),
-        m_hCoeffs((std::min)(rows,cols)),
-        m_temp(cols),
-        m_isInitialized(false) {}
-
-    /** \brief Constructs a QR factorization from a given matrix
-      *
-      * This constructor computes the QR factorization of the matrix \a matrix by calling
-      * the method compute(). It is a short cut for:
-      * 
-      * \code
-      * HouseholderQR<MatrixType> qr(matrix.rows(), matrix.cols());
-      * qr.compute(matrix);
-      * \endcode
-      * 
-      * \sa compute()
-      */
-    template<typename InputType>
-    explicit HouseholderQR(const EigenBase<InputType>& matrix)
-      : m_qr(matrix.rows(), matrix.cols()),
-        m_hCoeffs((std::min)(matrix.rows(),matrix.cols())),
-        m_temp(matrix.cols()),
-        m_isInitialized(false)
-    {
-      compute(matrix.derived());
-    }
-
-
-    /** \brief Constructs a QR factorization from a given matrix
-      *
-      * This overloaded constructor is provided for \link InplaceDecomposition inplace decomposition \endlink when
-      * \c MatrixType is a Eigen::Ref.
-      *
-      * \sa HouseholderQR(const EigenBase&)
-      */
-    template<typename InputType>
-    explicit HouseholderQR(EigenBase<InputType>& matrix)
-      : m_qr(matrix.derived()),
-        m_hCoeffs((std::min)(matrix.rows(),matrix.cols())),
-        m_temp(matrix.cols()),
-        m_isInitialized(false)
-    {
-      computeInPlace();
-    }
-
-    #ifdef EIGEN_PARSED_BY_DOXYGEN
-    /** This method finds a solution x to the equation Ax=b, where A is the matrix of which
-      * *this is the QR decomposition, if any exists.
-      *
-      * \param b the right-hand-side of the equation to solve.
-      *
-      * \returns a solution.
-      *
-      * \note_about_checking_solutions
-      *
-      * \note_about_arbitrary_choice_of_solution
-      *
-      * Example: \include HouseholderQR_solve.cpp
-      * Output: \verbinclude HouseholderQR_solve.out
-      */
-    template<typename Rhs>
-    inline const Solve<HouseholderQR, Rhs>
-    solve(const MatrixBase<Rhs>& b) const;
-    #endif
-
-    /** This method returns an expression of the unitary matrix Q as a sequence of Householder transformations.
-      *
-      * The returned expression can directly be used to perform matrix products. It can also be assigned to a dense Matrix object.
-      * Here is an example showing how to recover the full or thin matrix Q, as well as how to perform matrix products using operator*:
-      *
-      * Example: \include HouseholderQR_householderQ.cpp
-      * Output: \verbinclude HouseholderQR_householderQ.out
-      */
-    HouseholderSequenceType householderQ() const
-    {
-      eigen_assert(m_isInitialized && "HouseholderQR is not initialized.");
-      return HouseholderSequenceType(m_qr, m_hCoeffs.conjugate());
-    }
-
-    /** \returns a reference to the matrix where the Householder QR decomposition is stored
-      * in a LAPACK-compatible way.
-      */
-    const MatrixType& matrixQR() const
-    {
-        eigen_assert(m_isInitialized && "HouseholderQR is not initialized.");
-        return m_qr;
-    }
-
-    template<typename InputType>
-    HouseholderQR& compute(const EigenBase<InputType>& matrix) {
-      m_qr = matrix.derived();
-      computeInPlace();
-      return *this;
-    }
-
-    /** \returns the absolute value of the determinant of the matrix of which
-      * *this is the QR decomposition. It has only linear complexity
-      * (that is, O(n) where n is the dimension of the square matrix)
-      * as the QR decomposition has already been computed.
-      *
-      * \note This is only for square matrices.
-      *
-      * \warning a determinant can be very big or small, so for matrices
-      * of large enough dimension, there is a risk of overflow/underflow.
-      * One way to work around that is to use logAbsDeterminant() instead.
-      *
-      * \sa logAbsDeterminant(), MatrixBase::determinant()
-      */
-    typename MatrixType::RealScalar absDeterminant() const;
-
-    /** \returns the natural log of the absolute value of the determinant of the matrix of which
-      * *this is the QR decomposition. It has only linear complexity
-      * (that is, O(n) where n is the dimension of the square matrix)
-      * as the QR decomposition has already been computed.
-      *
-      * \note This is only for square matrices.
-      *
-      * \note This method is useful to work around the risk of overflow/underflow that's inherent
-      * to determinant computation.
-      *
-      * \sa absDeterminant(), MatrixBase::determinant()
-      */
-    typename MatrixType::RealScalar logAbsDeterminant() const;
-
-    inline Index rows() const { return m_qr.rows(); }
-    inline Index cols() const { return m_qr.cols(); }
-
-    /** \returns a const reference to the vector of Householder coefficients used to represent the factor \c Q.
-      * 
-      * For advanced uses only.
-      */
-    const HCoeffsType& hCoeffs() const { return m_hCoeffs; }
-
-    #ifndef EIGEN_PARSED_BY_DOXYGEN
-    template<typename RhsType, typename DstType>
-    void _solve_impl(const RhsType &rhs, DstType &dst) const;
-
-    template<bool Conjugate, typename RhsType, typename DstType>
-    void _solve_impl_transposed(const RhsType &rhs, DstType &dst) const;
-    #endif
-
-  protected:
-
-    static void check_template_parameters()
-    {
-      EIGEN_STATIC_ASSERT_NON_INTEGER(Scalar);
-    }
-
-    void computeInPlace();
-
-    MatrixType m_qr;
-    HCoeffsType m_hCoeffs;
-    RowVectorType m_temp;
-    bool m_isInitialized;
-};
-
-template<typename MatrixType>
-typename MatrixType::RealScalar HouseholderQR<MatrixType>::absDeterminant() const
-{
-  using std::abs;
-  eigen_assert(m_isInitialized && "HouseholderQR is not initialized.");
-  eigen_assert(m_qr.rows() == m_qr.cols() && "You can't take the determinant of a non-square matrix!");
-  return abs(m_qr.diagonal().prod());
-}
-
-template<typename MatrixType>
-typename MatrixType::RealScalar HouseholderQR<MatrixType>::logAbsDeterminant() const
-{
-  eigen_assert(m_isInitialized && "HouseholderQR is not initialized.");
-  eigen_assert(m_qr.rows() == m_qr.cols() && "You can't take the determinant of a non-square matrix!");
-  return m_qr.diagonal().cwiseAbs().array().log().sum();
-}
-
-namespace internal {
-
-/** \internal */
-template<typename MatrixQR, typename HCoeffs>
-void householder_qr_inplace_unblocked(MatrixQR& mat, HCoeffs& hCoeffs, typename MatrixQR::Scalar* tempData = 0)
-{
-  typedef typename MatrixQR::Scalar Scalar;
-  typedef typename MatrixQR::RealScalar RealScalar;
-  Index rows = mat.rows();
-  Index cols = mat.cols();
-  Index size = (std::min)(rows,cols);
-
-  eigen_assert(hCoeffs.size() == size);
-
-  typedef Matrix<Scalar,MatrixQR::ColsAtCompileTime,1> TempType;
-  TempType tempVector;
-  if(tempData==0)
-  {
-    tempVector.resize(cols);
-    tempData = tempVector.data();
-  }
-
-  for(Index k = 0; k < size; ++k)
-  {
-    Index remainingRows = rows - k;
-    Index remainingCols = cols - k - 1;
-
-    RealScalar beta;
-    mat.col(k).tail(remainingRows).makeHouseholderInPlace(hCoeffs.coeffRef(k), beta);
-    mat.coeffRef(k,k) = beta;
-
-    // apply H to remaining part of m_qr from the left
-    mat.bottomRightCorner(remainingRows, remainingCols)
-        .applyHouseholderOnTheLeft(mat.col(k).tail(remainingRows-1), hCoeffs.coeffRef(k), tempData+k+1);
-  }
-}
-
-/** \internal */
-template<typename MatrixQR, typename HCoeffs,
-  typename MatrixQRScalar = typename MatrixQR::Scalar,
-  bool InnerStrideIsOne = (MatrixQR::InnerStrideAtCompileTime == 1 && HCoeffs::InnerStrideAtCompileTime == 1)>
-struct householder_qr_inplace_blocked
-{
-  // This is specialized for LAPACK-supported Scalar types in HouseholderQR_LAPACKE.h
-  static void run(MatrixQR& mat, HCoeffs& hCoeffs, Index maxBlockSize=32,
-      typename MatrixQR::Scalar* tempData = 0)
-  {
-    typedef typename MatrixQR::Scalar Scalar;
-    typedef Block<MatrixQR,Dynamic,Dynamic> BlockType;
-
-    Index rows = mat.rows();
-    Index cols = mat.cols();
-    Index size = (std::min)(rows, cols);
-
-    typedef Matrix<Scalar,Dynamic,1,ColMajor,MatrixQR::MaxColsAtCompileTime,1> TempType;
-    TempType tempVector;
-    if(tempData==0)
-    {
-      tempVector.resize(cols);
-      tempData = tempVector.data();
-    }
-
-    Index blockSize = (std::min)(maxBlockSize,size);
-
-    Index k = 0;
-    for (k = 0; k < size; k += blockSize)
-    {
-      Index bs = (std::min)(size-k,blockSize);  // actual size of the block
-      Index tcols = cols - k - bs;              // trailing columns
-      Index brows = rows-k;                     // rows of the block
-
-      // partition the matrix:
-      //        A00 | A01 | A02
-      // mat  = A10 | A11 | A12
-      //        A20 | A21 | A22
-      // and performs the qr dec of [A11^T A12^T]^T
-      // and update [A21^T A22^T]^T using level 3 operations.
-      // Finally, the algorithm continue on A22
-
-      BlockType A11_21 = mat.block(k,k,brows,bs);
-      Block<HCoeffs,Dynamic,1> hCoeffsSegment = hCoeffs.segment(k,bs);
-
-      householder_qr_inplace_unblocked(A11_21, hCoeffsSegment, tempData);
-
-      if(tcols)
-      {
-        BlockType A21_22 = mat.block(k,k+bs,brows,tcols);
-        apply_block_householder_on_the_left(A21_22,A11_21,hCoeffsSegment, false); // false == backward
-      }
-    }
-  }
-};
-
-} // end namespace internal
-
-#ifndef EIGEN_PARSED_BY_DOXYGEN
-template<typename _MatrixType>
-template<typename RhsType, typename DstType>
-void HouseholderQR<_MatrixType>::_solve_impl(const RhsType &rhs, DstType &dst) const
-{
-  const Index rank = (std::min)(rows(), cols());
-
-  typename RhsType::PlainObject c(rhs);
-
-  c.applyOnTheLeft(householderQ().setLength(rank).adjoint() );
-
-  m_qr.topLeftCorner(rank, rank)
-      .template triangularView<Upper>()
-      .solveInPlace(c.topRows(rank));
-
-  dst.topRows(rank) = c.topRows(rank);
-  dst.bottomRows(cols()-rank).setZero();
-}
-
-template<typename _MatrixType>
-template<bool Conjugate, typename RhsType, typename DstType>
-void HouseholderQR<_MatrixType>::_solve_impl_transposed(const RhsType &rhs, DstType &dst) const
-{
-  const Index rank = (std::min)(rows(), cols());
-
-  typename RhsType::PlainObject c(rhs);
-
-  m_qr.topLeftCorner(rank, rank)
-      .template triangularView<Upper>()
-      .transpose().template conjugateIf<Conjugate>()
-      .solveInPlace(c.topRows(rank));
-
-  dst.topRows(rank) = c.topRows(rank);
-  dst.bottomRows(rows()-rank).setZero();
-
-  dst.applyOnTheLeft(householderQ().setLength(rank).template conjugateIf<!Conjugate>() );
-}
-#endif
-
-/** Performs the QR factorization of the given matrix \a matrix. The result of
-  * the factorization is stored into \c *this, and a reference to \c *this
-  * is returned.
-  *
-  * \sa class HouseholderQR, HouseholderQR(const MatrixType&)
-  */
-template<typename MatrixType>
-void HouseholderQR<MatrixType>::computeInPlace()
-{
-  check_template_parameters();
-  
-  Index rows = m_qr.rows();
-  Index cols = m_qr.cols();
-  Index size = (std::min)(rows,cols);
-
-  m_hCoeffs.resize(size);
-
-  m_temp.resize(cols);
-
-  internal::householder_qr_inplace_blocked<MatrixType, HCoeffsType>::run(m_qr, m_hCoeffs, 48, m_temp.data());
-
-  m_isInitialized = true;
-}
-
-/** \return the Householder QR decomposition of \c *this.
-  *
-  * \sa class HouseholderQR
-  */
-template<typename Derived>
-const HouseholderQR<typename MatrixBase<Derived>::PlainObject>
-MatrixBase<Derived>::householderQr() const
-{
-  return HouseholderQR<PlainObject>(eval());
-}
-
-} // end namespace Eigen
-
-#endif // EIGEN_QR_H

sequenzo/dissimilarity_measures/src/eigen/Eigen/src/QR/HouseholderQR_LAPACKE.h

@@ -1,68 +0,0 @@
-/*
- Copyright (c) 2011, Intel Corporation. All rights reserved.
-
- Redistribution and use in source and binary forms, with or without modification,
- are permitted provided that the following conditions are met:
-
- * Redistributions of source code must retain the above copyright notice, this
-   list of conditions and the following disclaimer.
- * Redistributions in binary form must reproduce the above copyright notice,
-   this list of conditions and the following disclaimer in the documentation
-   and/or other materials provided with the distribution.
- * Neither the name of Intel Corporation nor the names of its contributors may
-   be used to endorse or promote products derived from this software without
-   specific prior written permission.
-
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
- ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
- WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
- DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
- ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
- ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
- ********************************************************************************
- *   Content : Eigen bindings to LAPACKe
- *    Householder QR decomposition of a matrix w/o pivoting based on
- *    LAPACKE_?geqrf function.
- ********************************************************************************
-*/
-
-#ifndef EIGEN_QR_LAPACKE_H
-#define EIGEN_QR_LAPACKE_H
-
-namespace Eigen { 
-
-namespace internal {
-
-/** \internal Specialization for the data types supported by LAPACKe */
-
-#define EIGEN_LAPACKE_QR_NOPIV(EIGTYPE, LAPACKE_TYPE, LAPACKE_PREFIX) \
-template<typename MatrixQR, typename HCoeffs> \
-struct householder_qr_inplace_blocked<MatrixQR, HCoeffs, EIGTYPE, true> \
-{ \
-  static void run(MatrixQR& mat, HCoeffs& hCoeffs, Index = 32, \
-      typename MatrixQR::Scalar* = 0) \
-  { \
-    lapack_int m = (lapack_int) mat.rows(); \
-    lapack_int n = (lapack_int) mat.cols(); \
-    lapack_int lda = (lapack_int) mat.outerStride(); \
-    lapack_int matrix_order = (MatrixQR::IsRowMajor) ? LAPACK_ROW_MAJOR : LAPACK_COL_MAJOR; \
-    LAPACKE_##LAPACKE_PREFIX##geqrf( matrix_order, m, n, (LAPACKE_TYPE*)mat.data(), lda, (LAPACKE_TYPE*)hCoeffs.data()); \
-    hCoeffs.adjointInPlace(); \
-  } \
-};
-
-EIGEN_LAPACKE_QR_NOPIV(double, double, d)
-EIGEN_LAPACKE_QR_NOPIV(float, float, s)
-EIGEN_LAPACKE_QR_NOPIV(dcomplex, lapack_complex_double, z)
-EIGEN_LAPACKE_QR_NOPIV(scomplex, lapack_complex_float, c)
-
-} // end namespace internal
-
-} // end namespace Eigen
-
-#endif // EIGEN_QR_LAPACKE_H