From 7a8d0d8bc2572707c9d35006f30ea835c86954b0 Mon Sep 17 00:00:00 2001
From: sotech117 <michael_foiani@brown.edu>
Date: Tue, 9 Apr 2024 03:14:17 -0400
Subject: first draft to generate waves

---
 Eigen/src/Core/PermutationMatrix.h | 605 +++++++++++++++++++++++++++++++++++++
 1 file changed, 605 insertions(+)
 create mode 100644 Eigen/src/Core/PermutationMatrix.h

(limited to 'Eigen/src/Core/PermutationMatrix.h')

diff --git a/Eigen/src/Core/PermutationMatrix.h b/Eigen/src/Core/PermutationMatrix.h
new file mode 100644
index 0000000..69401bf
--- /dev/null
+++ b/Eigen/src/Core/PermutationMatrix.h
@@ -0,0 +1,605 @@
+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// Copyright (C) 2009 Benoit Jacob <jacob.benoit.1@gmail.com>
+// Copyright (C) 2009-2015 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_PERMUTATIONMATRIX_H
+#define EIGEN_PERMUTATIONMATRIX_H
+
+namespace Eigen { 
+
+namespace internal {
+
+enum PermPermProduct_t {PermPermProduct};
+
+} // end namespace internal
+
+/** \class PermutationBase
+  * \ingroup Core_Module
+  *
+  * \brief Base class for permutations
+  *
+  * \tparam Derived the derived class
+  *
+  * This class is the base class for all expressions representing a permutation matrix,
+  * internally stored as a vector of integers.
+  * The convention followed here is that if \f$ \sigma \f$ is a permutation, the corresponding permutation matrix
+  * \f$ P_\sigma \f$ is such that if \f$ (e_1,\ldots,e_p) \f$ is the canonical basis, we have:
+  *  \f[ P_\sigma(e_i) = e_{\sigma(i)}. \f]
+  * This convention ensures that for any two permutations \f$ \sigma, \tau \f$, we have:
+  *  \f[ P_{\sigma\circ\tau} = P_\sigma P_\tau. \f]
+  *
+  * Permutation matrices are square and invertible.
+  *
+  * Notice that in addition to the member functions and operators listed here, there also are non-member
+  * operator* to multiply any kind of permutation object with any kind of matrix expression (MatrixBase)
+  * on either side.
+  *
+  * \sa class PermutationMatrix, class PermutationWrapper
+  */
+template<typename Derived>
+class PermutationBase : public EigenBase<Derived>
+{
+    typedef internal::traits<Derived> Traits;
+    typedef EigenBase<Derived> Base;
+  public:
+
+    #ifndef EIGEN_PARSED_BY_DOXYGEN
+    typedef typename Traits::IndicesType IndicesType;
+    enum {
+      Flags = Traits::Flags,
+      RowsAtCompileTime = Traits::RowsAtCompileTime,
+      ColsAtCompileTime = Traits::ColsAtCompileTime,
+      MaxRowsAtCompileTime = Traits::MaxRowsAtCompileTime,
+      MaxColsAtCompileTime = Traits::MaxColsAtCompileTime
+    };
+    typedef typename Traits::StorageIndex StorageIndex;
+    typedef Matrix<StorageIndex,RowsAtCompileTime,ColsAtCompileTime,0,MaxRowsAtCompileTime,MaxColsAtCompileTime>
+            DenseMatrixType;
+    typedef PermutationMatrix<IndicesType::SizeAtCompileTime,IndicesType::MaxSizeAtCompileTime,StorageIndex>
+            PlainPermutationType;
+    typedef PlainPermutationType PlainObject;
+    using Base::derived;
+    typedef Inverse<Derived> InverseReturnType;
+    typedef void Scalar;
+    #endif
+
+    /** Copies the other permutation into *this */
+    template<typename OtherDerived>
+    Derived& operator=(const PermutationBase<OtherDerived>& other)
+    {
+      indices() = other.indices();
+      return derived();
+    }
+
+    /** Assignment from the Transpositions \a tr */
+    template<typename OtherDerived>
+    Derived& operator=(const TranspositionsBase<OtherDerived>& tr)
+    {
+      setIdentity(tr.size());
+      for(Index k=size()-1; k>=0; --k)
+        applyTranspositionOnTheRight(k,tr.coeff(k));
+      return derived();
+    }
+
+    /** \returns the number of rows */
+    inline EIGEN_DEVICE_FUNC Index rows() const { return Index(indices().size()); }
+
+    /** \returns the number of columns */
+    inline EIGEN_DEVICE_FUNC Index cols() const { return Index(indices().size()); }
+
+    /** \returns the size of a side of the respective square matrix, i.e., the number of indices */
+    inline EIGEN_DEVICE_FUNC Index size() const { return Index(indices().size()); }
+
+    #ifndef EIGEN_PARSED_BY_DOXYGEN
+    template<typename DenseDerived>
+    void evalTo(MatrixBase<DenseDerived>& other) const
+    {
+      other.setZero();
+      for (Index i=0; i<rows(); ++i)
+        other.coeffRef(indices().coeff(i),i) = typename DenseDerived::Scalar(1);
+    }
+    #endif
+
+    /** \returns a Matrix object initialized from this permutation matrix. Notice that it
+      * is inefficient to return this Matrix object by value. For efficiency, favor using
+      * the Matrix constructor taking EigenBase objects.
+      */
+    DenseMatrixType toDenseMatrix() const
+    {
+      return derived();
+    }
+
+    /** const version of indices(). */
+    const IndicesType& indices() const { return derived().indices(); }
+    /** \returns a reference to the stored array representing the permutation. */
+    IndicesType& indices() { return derived().indices(); }
+
+    /** Resizes to given size.
+      */
+    inline void resize(Index newSize)
+    {
+      indices().resize(newSize);
+    }
+
+    /** Sets *this to be the identity permutation matrix */
+    void setIdentity()
+    {
+      StorageIndex n = StorageIndex(size());
+      for(StorageIndex i = 0; i < n; ++i)
+        indices().coeffRef(i) = i;
+    }
+
+    /** Sets *this to be the identity permutation matrix of given size.
+      */
+    void setIdentity(Index newSize)
+    {
+      resize(newSize);
+      setIdentity();
+    }
+
+    /** Multiplies *this by the transposition \f$(ij)\f$ on the left.
+      *
+      * \returns a reference to *this.
+      *
+      * \warning This is much slower than applyTranspositionOnTheRight(Index,Index):
+      * this has linear complexity and requires a lot of branching.
+      *
+      * \sa applyTranspositionOnTheRight(Index,Index)
+      */
+    Derived& applyTranspositionOnTheLeft(Index i, Index j)
+    {
+      eigen_assert(i>=0 && j>=0 && i<size() && j<size());
+      for(Index k = 0; k < size(); ++k)
+      {
+        if(indices().coeff(k) == i) indices().coeffRef(k) = StorageIndex(j);
+        else if(indices().coeff(k) == j) indices().coeffRef(k) = StorageIndex(i);
+      }
+      return derived();
+    }
+
+    /** Multiplies *this by the transposition \f$(ij)\f$ on the right.
+      *
+      * \returns a reference to *this.
+      *
+      * This is a fast operation, it only consists in swapping two indices.
+      *
+      * \sa applyTranspositionOnTheLeft(Index,Index)
+      */
+    Derived& applyTranspositionOnTheRight(Index i, Index j)
+    {
+      eigen_assert(i>=0 && j>=0 && i<size() && j<size());
+      std::swap(indices().coeffRef(i), indices().coeffRef(j));
+      return derived();
+    }
+
+    /** \returns the inverse permutation matrix.
+      *
+      * \note \blank \note_try_to_help_rvo
+      */
+    inline InverseReturnType inverse() const
+    { return InverseReturnType(derived()); }
+    /** \returns the tranpose permutation matrix.
+      *
+      * \note \blank \note_try_to_help_rvo
+      */
+    inline InverseReturnType transpose() const
+    { return InverseReturnType(derived()); }
+
+    /**** multiplication helpers to hopefully get RVO ****/
+
+  
+#ifndef EIGEN_PARSED_BY_DOXYGEN
+  protected:
+    template<typename OtherDerived>
+    void assignTranspose(const PermutationBase<OtherDerived>& other)
+    {
+      for (Index i=0; i<rows();++i) indices().coeffRef(other.indices().coeff(i)) = i;
+    }
+    template<typename Lhs,typename Rhs>
+    void assignProduct(const Lhs& lhs, const Rhs& rhs)
+    {
+      eigen_assert(lhs.cols() == rhs.rows());
+      for (Index i=0; i<rows();++i) indices().coeffRef(i) = lhs.indices().coeff(rhs.indices().coeff(i));
+    }
+#endif
+
+  public:
+
+    /** \returns the product permutation matrix.
+      *
+      * \note \blank \note_try_to_help_rvo
+      */
+    template<typename Other>
+    inline PlainPermutationType operator*(const PermutationBase<Other>& other) const
+    { return PlainPermutationType(internal::PermPermProduct, derived(), other.derived()); }
+
+    /** \returns the product of a permutation with another inverse permutation.
+      *
+      * \note \blank \note_try_to_help_rvo
+      */
+    template<typename Other>
+    inline PlainPermutationType operator*(const InverseImpl<Other,PermutationStorage>& other) const
+    { return PlainPermutationType(internal::PermPermProduct, *this, other.eval()); }
+
+    /** \returns the product of an inverse permutation with another permutation.
+      *
+      * \note \blank \note_try_to_help_rvo
+      */
+    template<typename Other> friend
+    inline PlainPermutationType operator*(const InverseImpl<Other, PermutationStorage>& other, const PermutationBase& perm)
+    { return PlainPermutationType(internal::PermPermProduct, other.eval(), perm); }
+    
+    /** \returns the determinant of the permutation matrix, which is either 1 or -1 depending on the parity of the permutation.
+      *
+      * This function is O(\c n) procedure allocating a buffer of \c n booleans.
+      */
+    Index determinant() const
+    {
+      Index res = 1;
+      Index n = size();
+      Matrix<bool,RowsAtCompileTime,1,0,MaxRowsAtCompileTime> mask(n);
+      mask.fill(false);
+      Index r = 0;
+      while(r < n)
+      {
+        // search for the next seed
+        while(r<n && mask[r]) r++;
+        if(r>=n)
+          break;
+        // we got one, let's follow it until we are back to the seed
+        Index k0 = r++;
+        mask.coeffRef(k0) = true;
+        for(Index k=indices().coeff(k0); k!=k0; k=indices().coeff(k))
+        {
+          mask.coeffRef(k) = true;
+          res = -res;
+        }
+      }
+      return res;
+    }
+
+  protected:
+
+};
+
+namespace internal {
+template<int SizeAtCompileTime, int MaxSizeAtCompileTime, typename _StorageIndex>
+struct traits<PermutationMatrix<SizeAtCompileTime, MaxSizeAtCompileTime, _StorageIndex> >
+ : traits<Matrix<_StorageIndex,SizeAtCompileTime,SizeAtCompileTime,0,MaxSizeAtCompileTime,MaxSizeAtCompileTime> >
+{
+  typedef PermutationStorage StorageKind;
+  typedef Matrix<_StorageIndex, SizeAtCompileTime, 1, 0, MaxSizeAtCompileTime, 1> IndicesType;
+  typedef _StorageIndex StorageIndex;
+  typedef void Scalar;
+};
+}
+
+/** \class PermutationMatrix
+  * \ingroup Core_Module
+  *
+  * \brief Permutation matrix
+  *
+  * \tparam SizeAtCompileTime the number of rows/cols, or Dynamic
+  * \tparam MaxSizeAtCompileTime the maximum number of rows/cols, or Dynamic. This optional parameter defaults to SizeAtCompileTime. Most of the time, you should not have to specify it.
+  * \tparam _StorageIndex the integer type of the indices
+  *
+  * This class represents a permutation matrix, internally stored as a vector of integers.
+  *
+  * \sa class PermutationBase, class PermutationWrapper, class DiagonalMatrix
+  */
+template<int SizeAtCompileTime, int MaxSizeAtCompileTime, typename _StorageIndex>
+class PermutationMatrix : public PermutationBase<PermutationMatrix<SizeAtCompileTime, MaxSizeAtCompileTime, _StorageIndex> >
+{
+    typedef PermutationBase<PermutationMatrix> Base;
+    typedef internal::traits<PermutationMatrix> Traits;
+  public:
+
+    typedef const PermutationMatrix& Nested;
+
+    #ifndef EIGEN_PARSED_BY_DOXYGEN
+    typedef typename Traits::IndicesType IndicesType;
+    typedef typename Traits::StorageIndex StorageIndex;
+    #endif
+
+    inline PermutationMatrix()
+    {}
+
+    /** Constructs an uninitialized permutation matrix of given size.
+      */
+    explicit inline PermutationMatrix(Index size) : m_indices(size)
+    {
+      eigen_internal_assert(size <= NumTraits<StorageIndex>::highest());
+    }
+
+    /** Copy constructor. */
+    template<typename OtherDerived>
+    inline PermutationMatrix(const PermutationBase<OtherDerived>& other)
+      : m_indices(other.indices()) {}
+
+    /** Generic constructor from expression of the indices. The indices
+      * array has the meaning that the permutations sends each integer i to indices[i].
+      *
+      * \warning It is your responsibility to check that the indices array that you passes actually
+      * describes a permutation, i.e., each value between 0 and n-1 occurs exactly once, where n is the
+      * array's size.
+      */
+    template<typename Other>
+    explicit inline PermutationMatrix(const MatrixBase<Other>& indices) : m_indices(indices)
+    {}
+
+    /** Convert the Transpositions \a tr to a permutation matrix */
+    template<typename Other>
+    explicit PermutationMatrix(const TranspositionsBase<Other>& tr)
+      : m_indices(tr.size())
+    {
+      *this = tr;
+    }
+
+    /** Copies the other permutation into *this */
+    template<typename Other>
+    PermutationMatrix& operator=(const PermutationBase<Other>& other)
+    {
+      m_indices = other.indices();
+      return *this;
+    }
+
+    /** Assignment from the Transpositions \a tr */
+    template<typename Other>
+    PermutationMatrix& operator=(const TranspositionsBase<Other>& tr)
+    {
+      return Base::operator=(tr.derived());
+    }
+
+    /** const version of indices(). */
+    const IndicesType& indices() const { return m_indices; }
+    /** \returns a reference to the stored array representing the permutation. */
+    IndicesType& indices() { return m_indices; }
+
+
+    /**** multiplication helpers to hopefully get RVO ****/
+
+#ifndef EIGEN_PARSED_BY_DOXYGEN
+    template<typename Other>
+    PermutationMatrix(const InverseImpl<Other,PermutationStorage>& other)
+      : m_indices(other.derived().nestedExpression().size())
+    {
+      eigen_internal_assert(m_indices.size() <= NumTraits<StorageIndex>::highest());
+      StorageIndex end = StorageIndex(m_indices.size());
+      for (StorageIndex i=0; i<end;++i)
+        m_indices.coeffRef(other.derived().nestedExpression().indices().coeff(i)) = i;
+    }
+    template<typename Lhs,typename Rhs>
+    PermutationMatrix(internal::PermPermProduct_t, const Lhs& lhs, const Rhs& rhs)
+      : m_indices(lhs.indices().size())
+    {
+      Base::assignProduct(lhs,rhs);
+    }
+#endif
+
+  protected:
+
+    IndicesType m_indices;
+};
+
+
+namespace internal {
+template<int SizeAtCompileTime, int MaxSizeAtCompileTime, typename _StorageIndex, int _PacketAccess>
+struct traits<Map<PermutationMatrix<SizeAtCompileTime, MaxSizeAtCompileTime, _StorageIndex>,_PacketAccess> >
+ : traits<Matrix<_StorageIndex,SizeAtCompileTime,SizeAtCompileTime,0,MaxSizeAtCompileTime,MaxSizeAtCompileTime> >
+{
+  typedef PermutationStorage StorageKind;
+  typedef Map<const Matrix<_StorageIndex, SizeAtCompileTime, 1, 0, MaxSizeAtCompileTime, 1>, _PacketAccess> IndicesType;
+  typedef _StorageIndex StorageIndex;
+  typedef void Scalar;
+};
+}
+
+template<int SizeAtCompileTime, int MaxSizeAtCompileTime, typename _StorageIndex, int _PacketAccess>
+class Map<PermutationMatrix<SizeAtCompileTime, MaxSizeAtCompileTime, _StorageIndex>,_PacketAccess>
+  : public PermutationBase<Map<PermutationMatrix<SizeAtCompileTime, MaxSizeAtCompileTime, _StorageIndex>,_PacketAccess> >
+{
+    typedef PermutationBase<Map> Base;
+    typedef internal::traits<Map> Traits;
+  public:
+
+    #ifndef EIGEN_PARSED_BY_DOXYGEN
+    typedef typename Traits::IndicesType IndicesType;
+    typedef typename IndicesType::Scalar StorageIndex;
+    #endif
+
+    inline Map(const StorageIndex* indicesPtr)
+      : m_indices(indicesPtr)
+    {}
+
+    inline Map(const StorageIndex* indicesPtr, Index size)
+      : m_indices(indicesPtr,size)
+    {}
+
+    /** Copies the other permutation into *this */
+    template<typename Other>
+    Map& operator=(const PermutationBase<Other>& other)
+    { return Base::operator=(other.derived()); }
+
+    /** Assignment from the Transpositions \a tr */
+    template<typename Other>
+    Map& operator=(const TranspositionsBase<Other>& tr)
+    { return Base::operator=(tr.derived()); }
+
+    #ifndef EIGEN_PARSED_BY_DOXYGEN
+    /** This is a special case of the templated operator=. Its purpose is to
+      * prevent a default operator= from hiding the templated operator=.
+      */
+    Map& operator=(const Map& other)
+    {
+      m_indices = other.m_indices;
+      return *this;
+    }
+    #endif
+
+    /** const version of indices(). */
+    const IndicesType& indices() const { return m_indices; }
+    /** \returns a reference to the stored array representing the permutation. */
+    IndicesType& indices() { return m_indices; }
+
+  protected:
+
+    IndicesType m_indices;
+};
+
+template<typename _IndicesType> class TranspositionsWrapper;
+namespace internal {
+template<typename _IndicesType>
+struct traits<PermutationWrapper<_IndicesType> >
+{
+  typedef PermutationStorage StorageKind;
+  typedef void Scalar;
+  typedef typename _IndicesType::Scalar StorageIndex;
+  typedef _IndicesType IndicesType;
+  enum {
+    RowsAtCompileTime = _IndicesType::SizeAtCompileTime,
+    ColsAtCompileTime = _IndicesType::SizeAtCompileTime,
+    MaxRowsAtCompileTime = IndicesType::MaxSizeAtCompileTime,
+    MaxColsAtCompileTime = IndicesType::MaxSizeAtCompileTime,
+    Flags = 0
+  };
+};
+}
+
+/** \class PermutationWrapper
+  * \ingroup Core_Module
+  *
+  * \brief Class to view a vector of integers as a permutation matrix
+  *
+  * \tparam _IndicesType the type of the vector of integer (can be any compatible expression)
+  *
+  * This class allows to view any vector expression of integers as a permutation matrix.
+  *
+  * \sa class PermutationBase, class PermutationMatrix
+  */
+template<typename _IndicesType>
+class PermutationWrapper : public PermutationBase<PermutationWrapper<_IndicesType> >
+{
+    typedef PermutationBase<PermutationWrapper> Base;
+    typedef internal::traits<PermutationWrapper> Traits;
+  public:
+
+    #ifndef EIGEN_PARSED_BY_DOXYGEN
+    typedef typename Traits::IndicesType IndicesType;
+    #endif
+
+    inline PermutationWrapper(const IndicesType& indices)
+      : m_indices(indices)
+    {}
+
+    /** const version of indices(). */
+    const typename internal::remove_all<typename IndicesType::Nested>::type&
+    indices() const { return m_indices; }
+
+  protected:
+
+    typename IndicesType::Nested m_indices;
+};
+
+
+/** \returns the matrix with the permutation applied to the columns.
+  */
+template<typename MatrixDerived, typename PermutationDerived>
+EIGEN_DEVICE_FUNC
+const Product<MatrixDerived, PermutationDerived, AliasFreeProduct>
+operator*(const MatrixBase<MatrixDerived> &matrix,
+          const PermutationBase<PermutationDerived>& permutation)
+{
+  return Product<MatrixDerived, PermutationDerived, AliasFreeProduct>
+            (matrix.derived(), permutation.derived());
+}
+
+/** \returns the matrix with the permutation applied to the rows.
+  */
+template<typename PermutationDerived, typename MatrixDerived>
+EIGEN_DEVICE_FUNC
+const Product<PermutationDerived, MatrixDerived, AliasFreeProduct>
+operator*(const PermutationBase<PermutationDerived> &permutation,
+          const MatrixBase<MatrixDerived>& matrix)
+{
+  return Product<PermutationDerived, MatrixDerived, AliasFreeProduct>
+            (permutation.derived(), matrix.derived());
+}
+
+
+template<typename PermutationType>
+class InverseImpl<PermutationType, PermutationStorage>
+  : public EigenBase<Inverse<PermutationType> >
+{
+    typedef typename PermutationType::PlainPermutationType PlainPermutationType;
+    typedef internal::traits<PermutationType> PermTraits;
+  protected:
+    InverseImpl() {}
+  public:
+    typedef Inverse<PermutationType> InverseType;
+    using EigenBase<Inverse<PermutationType> >::derived;
+
+    #ifndef EIGEN_PARSED_BY_DOXYGEN
+    typedef typename PermutationType::DenseMatrixType DenseMatrixType;
+    enum {
+      RowsAtCompileTime = PermTraits::RowsAtCompileTime,
+      ColsAtCompileTime = PermTraits::ColsAtCompileTime,
+      MaxRowsAtCompileTime = PermTraits::MaxRowsAtCompileTime,
+      MaxColsAtCompileTime = PermTraits::MaxColsAtCompileTime
+    };
+    #endif
+
+    #ifndef EIGEN_PARSED_BY_DOXYGEN
+    template<typename DenseDerived>
+    void evalTo(MatrixBase<DenseDerived>& other) const
+    {
+      other.setZero();
+      for (Index i=0; i<derived().rows();++i)
+        other.coeffRef(i, derived().nestedExpression().indices().coeff(i)) = typename DenseDerived::Scalar(1);
+    }
+    #endif
+
+    /** \return the equivalent permutation matrix */
+    PlainPermutationType eval() const { return derived(); }
+
+    DenseMatrixType toDenseMatrix() const { return derived(); }
+
+    /** \returns the matrix with the inverse permutation applied to the columns.
+      */
+    template<typename OtherDerived> friend
+    const Product<OtherDerived, InverseType, AliasFreeProduct>
+    operator*(const MatrixBase<OtherDerived>& matrix, const InverseType& trPerm)
+    {
+      return Product<OtherDerived, InverseType, AliasFreeProduct>(matrix.derived(), trPerm.derived());
+    }
+
+    /** \returns the matrix with the inverse permutation applied to the rows.
+      */
+    template<typename OtherDerived>
+    const Product<InverseType, OtherDerived, AliasFreeProduct>
+    operator*(const MatrixBase<OtherDerived>& matrix) const
+    {
+      return Product<InverseType, OtherDerived, AliasFreeProduct>(derived(), matrix.derived());
+    }
+};
+
+template<typename Derived>
+const PermutationWrapper<const Derived> MatrixBase<Derived>::asPermutation() const
+{
+  return derived();
+}
+
+namespace internal {
+
+template<> struct AssignmentKind<DenseShape,PermutationShape> { typedef EigenBase2EigenBase Kind; };
+
+} // end namespace internal
+
+} // end namespace Eigen
+
+#endif // EIGEN_PERMUTATIONMATRIX_H
-- 
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