umappp 0.1.2

data/vendor/Eigen/src/SparseCore/SparseColEtree.h

@@ -0,0 +1,206 @@
+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// Copyright (C) 2012 Désiré Nuentsa-Wakam <desire.nuentsa_wakam@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/.
+
+
+/* 
+ 
+ * NOTE: This file is the modified version of sp_coletree.c file in SuperLU 
+ 
+ * -- SuperLU routine (version 3.1) --
+ * Univ. of California Berkeley, Xerox Palo Alto Research Center,
+ * and Lawrence Berkeley National Lab.
+ * August 1, 2008
+ *
+ * Copyright (c) 1994 by Xerox Corporation.  All rights reserved.
+ *
+ * THIS MATERIAL IS PROVIDED AS IS, WITH ABSOLUTELY NO WARRANTY
+ * EXPRESSED OR IMPLIED.  ANY USE IS AT YOUR OWN RISK.
+ *
+ * Permission is hereby granted to use or copy this program for any
+ * purpose, provided the above notices are retained on all copies.
+ * Permission to modify the code and to distribute modified code is
+ * granted, provided the above notices are retained, and a notice that
+ * the code was modified is included with the above copyright notice.
+ */
+#ifndef SPARSE_COLETREE_H
+#define SPARSE_COLETREE_H
+
+namespace Eigen {
+
+namespace internal {
+
+/** Find the root of the tree/set containing the vertex i : Use Path halving */ 
+template<typename Index, typename IndexVector>
+Index etree_find (Index i, IndexVector& pp)
+{
+  Index p = pp(i); // Parent 
+  Index gp = pp(p); // Grand parent 
+  while (gp != p) 
+  {
+    pp(i) = gp; // Parent pointer on find path is changed to former grand parent
+    i = gp; 
+    p = pp(i);
+    gp = pp(p);
+  }
+  return p; 
+}
+
+/** Compute the column elimination tree of a sparse matrix
+  * \param mat The matrix in column-major format. 
+  * \param parent The elimination tree
+  * \param firstRowElt The column index of the first element in each row
+  * \param perm The permutation to apply to the column of \b mat
+  */
+template <typename MatrixType, typename IndexVector>
+int coletree(const MatrixType& mat, IndexVector& parent, IndexVector& firstRowElt, typename MatrixType::StorageIndex *perm=0)
+{
+  typedef typename MatrixType::StorageIndex StorageIndex;
+  StorageIndex nc = convert_index<StorageIndex>(mat.cols()); // Number of columns
+  StorageIndex m = convert_index<StorageIndex>(mat.rows());
+  StorageIndex diagSize = (std::min)(nc,m);
+  IndexVector root(nc); // root of subtree of etree 
+  root.setZero();
+  IndexVector pp(nc); // disjoint sets 
+  pp.setZero(); // Initialize disjoint sets 
+  parent.resize(mat.cols());
+  //Compute first nonzero column in each row 
+  firstRowElt.resize(m);
+  firstRowElt.setConstant(nc);
+  firstRowElt.segment(0, diagSize).setLinSpaced(diagSize, 0, diagSize-1);
+  bool found_diag;
+  for (StorageIndex col = 0; col < nc; col++)
+  {
+    StorageIndex pcol = col;
+    if(perm) pcol  = perm[col];
+    for (typename MatrixType::InnerIterator it(mat, pcol); it; ++it)
+    { 
+      Index row = it.row();
+      firstRowElt(row) = (std::min)(firstRowElt(row), col);
+    }
+  }
+  /* Compute etree by Liu's algorithm for symmetric matrices,
+          except use (firstRowElt[r],c) in place of an edge (r,c) of A.
+    Thus each row clique in A'*A is replaced by a star
+    centered at its first vertex, which has the same fill. */
+  StorageIndex rset, cset, rroot;
+  for (StorageIndex col = 0; col < nc; col++) 
+  {
+    found_diag = col>=m;
+    pp(col) = col; 
+    cset = col; 
+    root(cset) = col; 
+    parent(col) = nc; 
+    /* The diagonal element is treated here even if it does not exist in the matrix
+     * hence the loop is executed once more */ 
+    StorageIndex pcol = col;
+    if(perm) pcol  = perm[col];
+    for (typename MatrixType::InnerIterator it(mat, pcol); it||!found_diag; ++it)
+    { //  A sequence of interleaved find and union is performed 
+      Index i = col;
+      if(it) i = it.index();
+      if (i == col) found_diag = true;
+      
+      StorageIndex row = firstRowElt(i);
+      if (row >= col) continue; 
+      rset = internal::etree_find(row, pp); // Find the name of the set containing row
+      rroot = root(rset);
+      if (rroot != col) 
+      {
+        parent(rroot) = col; 
+        pp(cset) = rset; 
+        cset = rset; 
+        root(cset) = col; 
+      }
+    }
+  }
+  return 0;  
+}
+
+/** 
+  * Depth-first search from vertex n.  No recursion.
+  * This routine was contributed by Cédric Doucet, CEDRAT Group, Meylan, France.
+*/
+template <typename IndexVector>
+void nr_etdfs (typename IndexVector::Scalar n, IndexVector& parent, IndexVector& first_kid, IndexVector& next_kid, IndexVector& post, typename IndexVector::Scalar postnum)
+{
+  typedef typename IndexVector::Scalar StorageIndex;
+  StorageIndex current = n, first, next;
+  while (postnum != n) 
+  {
+    // No kid for the current node
+    first = first_kid(current);
+    
+    // no kid for the current node
+    if (first == -1) 
+    {
+      // Numbering this node because it has no kid 
+      post(current) = postnum++;
+      
+      // looking for the next kid 
+      next = next_kid(current); 
+      while (next == -1) 
+      {
+        // No more kids : back to the parent node
+        current = parent(current); 
+        // numbering the parent node 
+        post(current) = postnum++;
+        
+        // Get the next kid 
+        next = next_kid(current); 
+      }
+      // stopping criterion 
+      if (postnum == n+1) return; 
+      
+      // Updating current node 
+      current = next; 
+    }
+    else 
+    {
+      current = first; 
+    }
+  }
+}
+
+
+/**
+  * \brief Post order a tree 
+  * \param n the number of nodes
+  * \param parent Input tree
+  * \param post postordered tree
+  */
+template <typename IndexVector>
+void treePostorder(typename IndexVector::Scalar n, IndexVector& parent, IndexVector& post)
+{
+  typedef typename IndexVector::Scalar StorageIndex;
+  IndexVector first_kid, next_kid; // Linked list of children 
+  StorageIndex postnum; 
+  // Allocate storage for working arrays and results 
+  first_kid.resize(n+1); 
+  next_kid.setZero(n+1);
+  post.setZero(n+1);
+  
+  // Set up structure describing children
+  first_kid.setConstant(-1); 
+  for (StorageIndex v = n-1; v >= 0; v--) 
+  {
+    StorageIndex dad = parent(v);
+    next_kid(v) = first_kid(dad); 
+    first_kid(dad) = v; 
+  }
+  
+  // Depth-first search from dummy root vertex #n
+  postnum = 0; 
+  internal::nr_etdfs(n, parent, first_kid, next_kid, post, postnum);
+}
+
+} // end namespace internal
+
+} // end namespace Eigen
+
+#endif // SPARSE_COLETREE_H

data/vendor/Eigen/src/SparseCore/SparseCompressedBase.h

@@ -0,0 +1,370 @@
+// 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_SPARSE_COMPRESSED_BASE_H
+#define EIGEN_SPARSE_COMPRESSED_BASE_H
+
+namespace Eigen { 
+
+template<typename Derived> class SparseCompressedBase;
+  
+namespace internal {
+
+template<typename Derived>
+struct traits<SparseCompressedBase<Derived> > : traits<Derived>
+{};
+
+} // end namespace internal
+
+/** \ingroup SparseCore_Module
+  * \class SparseCompressedBase
+  * \brief Common base class for sparse [compressed]-{row|column}-storage format.
+  *
+  * This class defines the common interface for all derived classes implementing the compressed sparse storage format, such as:
+  *  - SparseMatrix
+  *  - Ref<SparseMatrixType,Options>
+  *  - Map<SparseMatrixType>
+  *
+  */
+template<typename Derived>
+class SparseCompressedBase
+  : public SparseMatrixBase<Derived>
+{
+  public:
+    typedef SparseMatrixBase<Derived> Base;
+    EIGEN_SPARSE_PUBLIC_INTERFACE(SparseCompressedBase)
+    using Base::operator=;
+    using Base::IsRowMajor;
+    
+    class InnerIterator;
+    class ReverseInnerIterator;
+    
+  protected:
+    typedef typename Base::IndexVector IndexVector;
+    Eigen::Map<IndexVector> innerNonZeros() { return Eigen::Map<IndexVector>(innerNonZeroPtr(), isCompressed()?0:derived().outerSize()); }
+    const  Eigen::Map<const IndexVector> innerNonZeros() const { return Eigen::Map<const IndexVector>(innerNonZeroPtr(), isCompressed()?0:derived().outerSize()); }
+        
+  public:
+    
+    /** \returns the number of non zero coefficients */
+    inline Index nonZeros() const
+    {
+      if(Derived::IsVectorAtCompileTime && outerIndexPtr()==0)
+        return derived().nonZeros();
+      else if(isCompressed())
+        return outerIndexPtr()[derived().outerSize()]-outerIndexPtr()[0];
+      else if(derived().outerSize()==0)
+        return 0;
+      else
+        return innerNonZeros().sum();
+    }
+    
+    /** \returns a const pointer to the array of values.
+      * This function is aimed at interoperability with other libraries.
+      * \sa innerIndexPtr(), outerIndexPtr() */
+    inline const Scalar* valuePtr() const { return derived().valuePtr(); }
+    /** \returns a non-const pointer to the array of values.
+      * This function is aimed at interoperability with other libraries.
+      * \sa innerIndexPtr(), outerIndexPtr() */
+    inline Scalar* valuePtr() { return derived().valuePtr(); }
+
+    /** \returns a const pointer to the array of inner indices.
+      * This function is aimed at interoperability with other libraries.
+      * \sa valuePtr(), outerIndexPtr() */
+    inline const StorageIndex* innerIndexPtr() const { return derived().innerIndexPtr(); }
+    /** \returns a non-const pointer to the array of inner indices.
+      * This function is aimed at interoperability with other libraries.
+      * \sa valuePtr(), outerIndexPtr() */
+    inline StorageIndex* innerIndexPtr() { return derived().innerIndexPtr(); }
+
+    /** \returns a const pointer to the array of the starting positions of the inner vectors.
+      * This function is aimed at interoperability with other libraries.
+      * \warning it returns the null pointer 0 for SparseVector
+      * \sa valuePtr(), innerIndexPtr() */
+    inline const StorageIndex* outerIndexPtr() const { return derived().outerIndexPtr(); }
+    /** \returns a non-const pointer to the array of the starting positions of the inner vectors.
+      * This function is aimed at interoperability with other libraries.
+      * \warning it returns the null pointer 0 for SparseVector
+      * \sa valuePtr(), innerIndexPtr() */
+    inline StorageIndex* outerIndexPtr() { return derived().outerIndexPtr(); }
+
+    /** \returns a const pointer to the array of the number of non zeros of the inner vectors.
+      * This function is aimed at interoperability with other libraries.
+      * \warning it returns the null pointer 0 in compressed mode */
+    inline const StorageIndex* innerNonZeroPtr() const { return derived().innerNonZeroPtr(); }
+    /** \returns a non-const pointer to the array of the number of non zeros of the inner vectors.
+      * This function is aimed at interoperability with other libraries.
+      * \warning it returns the null pointer 0 in compressed mode */
+    inline StorageIndex* innerNonZeroPtr() { return derived().innerNonZeroPtr(); }
+    
+    /** \returns whether \c *this is in compressed form. */
+    inline bool isCompressed() const { return innerNonZeroPtr()==0; }
+
+    /** \returns a read-only view of the stored coefficients as a 1D array expression.
+      *
+      * \warning this method is for \b compressed \b storage \b only, and it will trigger an assertion otherwise.
+      *
+      * \sa valuePtr(), isCompressed() */
+    const Map<const Array<Scalar,Dynamic,1> > coeffs() const { eigen_assert(isCompressed()); return Array<Scalar,Dynamic,1>::Map(valuePtr(),nonZeros()); }
+
+    /** \returns a read-write view of the stored coefficients as a 1D array expression
+      *
+      * \warning this method is for \b compressed \b storage \b only, and it will trigger an assertion otherwise.
+      *
+      * Here is an example:
+      * \include SparseMatrix_coeffs.cpp
+      * and the output is:
+      * \include SparseMatrix_coeffs.out
+      *
+      * \sa valuePtr(), isCompressed() */
+    Map<Array<Scalar,Dynamic,1> > coeffs() { eigen_assert(isCompressed()); return Array<Scalar,Dynamic,1>::Map(valuePtr(),nonZeros()); }
+
+  protected:
+    /** Default constructor. Do nothing. */
+    SparseCompressedBase() {}
+
+    /** \internal return the index of the coeff at (row,col) or just before if it does not exist.
+      * This is an analogue of std::lower_bound.
+      */
+    internal::LowerBoundIndex lower_bound(Index row, Index col) const
+    {
+      eigen_internal_assert(row>=0 && row<this->rows() && col>=0 && col<this->cols());
+
+      const Index outer = Derived::IsRowMajor ? row : col;
+      const Index inner = Derived::IsRowMajor ? col : row;
+
+      Index start = this->outerIndexPtr()[outer];
+      Index end = this->isCompressed() ? this->outerIndexPtr()[outer+1] : this->outerIndexPtr()[outer] + this->innerNonZeroPtr()[outer];
+      eigen_assert(end>=start && "you are using a non finalized sparse matrix or written coefficient does not exist");
+      internal::LowerBoundIndex p;
+      p.value = std::lower_bound(this->innerIndexPtr()+start, this->innerIndexPtr()+end,inner) - this->innerIndexPtr();
+      p.found = (p.value<end) && (this->innerIndexPtr()[p.value]==inner);
+      return p;
+    }
+
+    friend struct internal::evaluator<SparseCompressedBase<Derived> >;
+
+  private:
+    template<typename OtherDerived> explicit SparseCompressedBase(const SparseCompressedBase<OtherDerived>&);
+};
+
+template<typename Derived>
+class SparseCompressedBase<Derived>::InnerIterator
+{
+  public:
+    InnerIterator()
+      : m_values(0), m_indices(0), m_outer(0), m_id(0), m_end(0)
+    {}
+
+    InnerIterator(const InnerIterator& other)
+      : m_values(other.m_values), m_indices(other.m_indices), m_outer(other.m_outer), m_id(other.m_id), m_end(other.m_end)
+    {}
+
+    InnerIterator& operator=(const InnerIterator& other)
+    {
+      m_values = other.m_values;
+      m_indices = other.m_indices;
+      const_cast<OuterType&>(m_outer).setValue(other.m_outer.value());
+      m_id = other.m_id;
+      m_end = other.m_end;
+      return *this;
+    }
+
+    InnerIterator(const SparseCompressedBase& mat, Index outer)
+      : m_values(mat.valuePtr()), m_indices(mat.innerIndexPtr()), m_outer(outer)
+    {
+      if(Derived::IsVectorAtCompileTime && mat.outerIndexPtr()==0)
+      {
+        m_id = 0;
+        m_end = mat.nonZeros();
+      }
+      else
+      {
+        m_id = mat.outerIndexPtr()[outer];
+        if(mat.isCompressed())
+          m_end = mat.outerIndexPtr()[outer+1];
+        else
+          m_end = m_id + mat.innerNonZeroPtr()[outer];
+      }
+    }
+
+    explicit InnerIterator(const SparseCompressedBase& mat)
+      : m_values(mat.valuePtr()), m_indices(mat.innerIndexPtr()), m_outer(0), m_id(0), m_end(mat.nonZeros())
+    {
+      EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived);
+    }
+
+    explicit InnerIterator(const internal::CompressedStorage<Scalar,StorageIndex>& data)
+      : m_values(data.valuePtr()), m_indices(data.indexPtr()), m_outer(0), m_id(0), m_end(data.size())
+    {
+      EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived);
+    }
+
+    inline InnerIterator& operator++() { m_id++; return *this; }
+    inline InnerIterator& operator+=(Index i) { m_id += i ; return *this; }
+
+    inline InnerIterator operator+(Index i) 
+    { 
+        InnerIterator result = *this;
+        result += i;
+        return result;
+    }
+
+    inline const Scalar& value() const { return m_values[m_id]; }
+    inline Scalar& valueRef() { return const_cast<Scalar&>(m_values[m_id]); }
+
+    inline StorageIndex index() const { return m_indices[m_id]; }
+    inline Index outer() const { return m_outer.value(); }
+    inline Index row() const { return IsRowMajor ? m_outer.value() : index(); }
+    inline Index col() const { return IsRowMajor ? index() : m_outer.value(); }
+
+    inline operator bool() const { return (m_id < m_end); }
+
+  protected:
+    const Scalar* m_values;
+    const StorageIndex* m_indices;
+    typedef internal::variable_if_dynamic<Index,Derived::IsVectorAtCompileTime?0:Dynamic> OuterType;
+    const OuterType m_outer;
+    Index m_id;
+    Index m_end;
+  private:
+    // If you get here, then you're not using the right InnerIterator type, e.g.:
+    //   SparseMatrix<double,RowMajor> A;
+    //   SparseMatrix<double>::InnerIterator it(A,0);
+    template<typename T> InnerIterator(const SparseMatrixBase<T>&, Index outer);
+};
+
+template<typename Derived>
+class SparseCompressedBase<Derived>::ReverseInnerIterator
+{
+  public:
+    ReverseInnerIterator(const SparseCompressedBase& mat, Index outer)
+      : m_values(mat.valuePtr()), m_indices(mat.innerIndexPtr()), m_outer(outer)
+    {
+      if(Derived::IsVectorAtCompileTime && mat.outerIndexPtr()==0)
+      {
+        m_start = 0;
+        m_id = mat.nonZeros();
+      }
+      else
+      {
+        m_start = mat.outerIndexPtr()[outer];
+        if(mat.isCompressed())
+          m_id = mat.outerIndexPtr()[outer+1];
+        else
+          m_id = m_start + mat.innerNonZeroPtr()[outer];
+      }
+    }
+
+    explicit ReverseInnerIterator(const SparseCompressedBase& mat)
+      : m_values(mat.valuePtr()), m_indices(mat.innerIndexPtr()), m_outer(0), m_start(0), m_id(mat.nonZeros())
+    {
+      EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived);
+    }
+
+    explicit ReverseInnerIterator(const internal::CompressedStorage<Scalar,StorageIndex>& data)
+      : m_values(data.valuePtr()), m_indices(data.indexPtr()), m_outer(0), m_start(0), m_id(data.size())
+    {
+      EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived);
+    }
+
+    inline ReverseInnerIterator& operator--() { --m_id; return *this; }
+    inline ReverseInnerIterator& operator-=(Index i) { m_id -= i; return *this; }
+
+    inline ReverseInnerIterator operator-(Index i) 
+    {
+        ReverseInnerIterator result = *this;
+        result -= i;
+        return result;
+    }
+
+    inline const Scalar& value() const { return m_values[m_id-1]; }
+    inline Scalar& valueRef() { return const_cast<Scalar&>(m_values[m_id-1]); }
+
+    inline StorageIndex index() const { return m_indices[m_id-1]; }
+    inline Index outer() const { return m_outer.value(); }
+    inline Index row() const { return IsRowMajor ? m_outer.value() : index(); }
+    inline Index col() const { return IsRowMajor ? index() : m_outer.value(); }
+
+    inline operator bool() const { return (m_id > m_start); }
+
+  protected:
+    const Scalar* m_values;
+    const StorageIndex* m_indices;
+    typedef internal::variable_if_dynamic<Index,Derived::IsVectorAtCompileTime?0:Dynamic> OuterType;
+    const OuterType m_outer;
+    Index m_start;
+    Index m_id;
+};
+
+namespace internal {
+
+template<typename Derived>
+struct evaluator<SparseCompressedBase<Derived> >
+  : evaluator_base<Derived>
+{
+  typedef typename Derived::Scalar Scalar;
+  typedef typename Derived::InnerIterator InnerIterator;
+  
+  enum {
+    CoeffReadCost = NumTraits<Scalar>::ReadCost,
+    Flags = Derived::Flags
+  };
+  
+  evaluator() : m_matrix(0), m_zero(0)
+  {
+    EIGEN_INTERNAL_CHECK_COST_VALUE(CoeffReadCost);
+  }
+  explicit evaluator(const Derived &mat) : m_matrix(&mat), m_zero(0)
+  {
+    EIGEN_INTERNAL_CHECK_COST_VALUE(CoeffReadCost);
+  }
+  
+  inline Index nonZerosEstimate() const {
+    return m_matrix->nonZeros();
+  }
+  
+  operator Derived&() { return m_matrix->const_cast_derived(); }
+  operator const Derived&() const { return *m_matrix; }
+  
+  typedef typename DenseCoeffsBase<Derived,ReadOnlyAccessors>::CoeffReturnType CoeffReturnType;
+  const Scalar& coeff(Index row, Index col) const
+  {
+    Index p = find(row,col);
+
+    if(p==Dynamic)
+      return m_zero;
+    else
+      return m_matrix->const_cast_derived().valuePtr()[p];
+  }
+
+  Scalar& coeffRef(Index row, Index col)
+  {
+    Index p = find(row,col);
+    eigen_assert(p!=Dynamic && "written coefficient does not exist");
+    return m_matrix->const_cast_derived().valuePtr()[p];
+  }
+
+protected:
+
+  Index find(Index row, Index col) const
+  {
+    internal::LowerBoundIndex p = m_matrix->lower_bound(row,col);
+    return p.found ? p.value : Dynamic;
+  }
+
+  const Derived *m_matrix;
+  const Scalar m_zero;
+};
+
+}
+
+} // end namespace Eigen
+
+#endif // EIGEN_SPARSE_COMPRESSED_BASE_H