Eigen/src/Sparse/SparseMatrix.h - mirror - Git at Google

 // This file is part of Eigen, a lightweight C++ template library
 // for linear algebra.
 //
 // Copyright (C) 2008-2009 Gael Guennebaud <g.gael@free.fr>
 //
 // Eigen is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
 // version 3 of the License, or (at your option) any later version.
 //
 // Alternatively, you can redistribute it and/or
 // modify it under the terms of the GNU General Public License as
 // published by the Free Software Foundation; either version 2 of
 // the License, or (at your option) any later version.
 //
 // Eigen is distributed in the hope that it will be useful, but WITHOUT ANY
 // WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
 // FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License or the
 // GNU General Public License for more details.
 //
 // You should have received a copy of the GNU Lesser General Public
 // License and a copy of the GNU General Public License along with
 // Eigen. If not, see <http://www.gnu.org/licenses/>.

 #ifndef EIGEN_SPARSEMATRIX_H
 #define EIGEN_SPARSEMATRIX_H

 /** \ingroup Sparse_Module
   *
   * \class SparseMatrix
   *
   * \brief The main sparse matrix class
   *
   * This class implements a sparse matrix using the very common compressed row/column storage
   * scheme.
   *
   * \param _Scalar the scalar type, i.e. the type of the coefficients
   * \param _Options Union of bit flags controlling the storage scheme. Currently the only possibility
   *                 is RowMajor. The default is 0 which means column-major.
   *
   * See http://www.netlib.org/linalg/html_templates/node91.html for details on the storage scheme.
   *
   */
 template<typename _Scalar, int _Options>
 struct ei_traits<SparseMatrix<_Scalar, _Options> >
 {
   typedef _Scalar Scalar;
   typedef Sparse StorageKind;
   typedef MatrixXpr XprKind;
   enum {
     RowsAtCompileTime = Dynamic,
     ColsAtCompileTime = Dynamic,
     MaxRowsAtCompileTime = Dynamic,
     MaxColsAtCompileTime = Dynamic,
     Flags = _Options | NestByRefBit,
     CoeffReadCost = NumTraits<Scalar>::ReadCost,
     SupportedAccessPatterns = InnerRandomAccessPattern
   };
 };

 template<typename _Scalar, int _Options>
 class SparseMatrix
   : public SparseMatrixBase<SparseMatrix<_Scalar, _Options> >
 {
   public:
     EIGEN_SPARSE_GENERIC_PUBLIC_INTERFACE(SparseMatrix)
     EIGEN_SPARSE_INHERIT_ASSIGNMENT_OPERATOR(SparseMatrix, +=)
     EIGEN_SPARSE_INHERIT_ASSIGNMENT_OPERATOR(SparseMatrix, -=)
     // FIXME: why are these operator already alvailable ???
     // EIGEN_SPARSE_INHERIT_SCALAR_ASSIGNMENT_OPERATOR(SparseMatrix, *=)
     // EIGEN_SPARSE_INHERIT_SCALAR_ASSIGNMENT_OPERATOR(SparseMatrix, /=)

     typedef MappedSparseMatrix<Scalar,Flags> Map;
     using Base::IsRowMajor;

   protected:

     typedef SparseMatrix<Scalar,(Flags&~RowMajorBit)|(IsRowMajor?RowMajorBit:0)> TransposedSparseMatrix;

     Index m_outerSize;
     Index m_innerSize;
     Index* m_outerIndex;
     CompressedStorage<Scalar> m_data;

   public:

     inline Index rows() const { return IsRowMajor ? m_outerSize : m_innerSize; }
     inline Index cols() const { return IsRowMajor ? m_innerSize : m_outerSize; }

     inline Index innerSize() const { return m_innerSize; }
     inline Index outerSize() const { return m_outerSize; }
     inline Index innerNonZeros(Index j) const { return m_outerIndex[j+1]-m_outerIndex[j]; }

     inline const Scalar* _valuePtr() const { return &m_data.value(0); }
     inline Scalar* _valuePtr() { return &m_data.value(0); }

     inline const Index* _innerIndexPtr() const { return &m_data.index(0); }
     inline Index* _innerIndexPtr() { return &m_data.index(0); }

     inline const Index* _outerIndexPtr() const { return m_outerIndex; }
     inline Index* _outerIndexPtr() { return m_outerIndex; }

     inline Scalar coeff(Index row, Index col) const
     {
       const Index outer = IsRowMajor ? row : col;
       const Index inner = IsRowMajor ? col : row;
       return m_data.atInRange(m_outerIndex[outer], m_outerIndex[outer+1], inner);
     }

     inline Scalar& coeffRef(Index row, Index col)
     {
       const Index outer = IsRowMajor ? row : col;
       const Index inner = IsRowMajor ? col : row;

       Index start = m_outerIndex[outer];
       Index end = m_outerIndex[outer+1];
       ei_assert(end>=start && "you probably called coeffRef on a non finalized matrix");
       ei_assert(end>start && "coeffRef cannot be called on a zero coefficient");
       const Index id = m_data.searchLowerIndex(start,end-1,inner);
       ei_assert((id<end) && (m_data.index(id)==inner) && "coeffRef cannot be called on a zero coefficient");
       return m_data.value(id);
     }

   public:

     class InnerIterator;

     /** Removes all non zeros */
     inline void setZero()
     {
       m_data.clear();
       memset(m_outerIndex, 0, (m_outerSize+1)*sizeof(Index));
     }

     /** \returns the number of non zero coefficients */
     inline Index nonZeros() const  { return static_cast<Index>(m_data.size()); }

     /** \deprecated use setZero() and reserve()
       * Initializes the filling process of \c *this.
       * \param reserveSize approximate number of nonzeros
       * Note that the matrix \c *this is zero-ed.
       */
     EIGEN_DEPRECATED void startFill(Index reserveSize = 1000)
     {
       setZero();
       m_data.reserve(reserveSize);
     }

     /** Preallocates \a reserveSize non zeros */
     inline void reserve(Index reserveSize)
     {
       m_data.reserve(reserveSize);
     }

     /** \deprecated use insert()
       */
     EIGEN_DEPRECATED Scalar& fill(Index row, Index col)
     {
       const Index outer = IsRowMajor ? row : col;
       const Index inner = IsRowMajor ? col : row;

       if (m_outerIndex[outer+1]==0)
       {
         // we start a new inner vector
         Index i = outer;
         while (i>=0 && m_outerIndex[i]==0)
         {
           m_outerIndex[i] = m_data.size();
           --i;
         }
         m_outerIndex[outer+1] = m_outerIndex[outer];
       }
       else
       {
         ei_assert(m_data.index(m_data.size()-1)<inner && "wrong sorted insertion");
       }
 //       std::cerr << size_t(m_outerIndex[outer+1]) << " == " << m_data.size() << "\n";
       assert(size_t(m_outerIndex[outer+1]) == m_data.size());
       Index id = m_outerIndex[outer+1];
       ++m_outerIndex[outer+1];

       m_data.append(0, inner);
       return m_data.value(id);
     }

     //--- low level purely coherent filling ---

     inline Scalar& insertBack(Index outer, Index inner)
     {
       ei_assert(size_t(m_outerIndex[outer+1]) == m_data.size() && "wrong sorted insertion");
       ei_assert( (m_outerIndex[outer+1]-m_outerIndex[outer]==0 || m_data.index(m_data.size()-1)<inner) && "wrong sorted insertion");
       Index id = m_outerIndex[outer+1];
       ++m_outerIndex[outer+1];
       m_data.append(0, inner);
       return m_data.value(id);
     }

     inline Scalar& insertBackNoCheck(Index outer, Index inner)
     {
       Index id = m_outerIndex[outer+1];
       ++m_outerIndex[outer+1];
       m_data.append(0, inner);
       return m_data.value(id);
     }

     inline void startVec(Index outer)
     {
       ei_assert(m_outerIndex[outer]==int(m_data.size()) && "you must call startVec on each inner vec");
       ei_assert(m_outerIndex[outer+1]==0 && "you must call startVec on each inner vec");
       m_outerIndex[outer+1] = m_outerIndex[outer];
     }

     //---

     /** \deprecated use insert()
       * Like fill() but with random inner coordinates.
       */
     EIGEN_DEPRECATED Scalar& fillrand(Index row, Index col)
     {
       return insert(row,col);
     }

     /** \returns a reference to a novel non zero coefficient with coordinates \a row x \a col.
       * The non zero coefficient must \b not already exist.
       *
       * \warning This function can be extremely slow if the non zero coefficients
       * are not inserted in a coherent order.
       *
       * After an insertion session, you should call the finalize() function.
       */
     EIGEN_DONT_INLINE Scalar& insert(Index row, Index col)
     {
       const Index outer = IsRowMajor ? row : col;
       const Index inner = IsRowMajor ? col : row;

       Index previousOuter = outer;
       if (m_outerIndex[outer+1]==0)
       {
         // we start a new inner vector
         while (previousOuter>=0 && m_outerIndex[previousOuter]==0)
         {
           m_outerIndex[previousOuter] = static_cast<Index>(m_data.size());
           --previousOuter;
         }
         m_outerIndex[outer+1] = m_outerIndex[outer];
       }

       // here we have to handle the tricky case where the outerIndex array
       // starts with: [ 0 0 0 0 0 1 ...] and we are inserting in, e.g.,
       // the 2nd inner vector...
       bool isLastVec = (!(previousOuter==-1 && m_data.size()!=0))
                     && (size_t(m_outerIndex[outer+1]) == m_data.size());

       size_t startId = m_outerIndex[outer];
       // FIXME let's make sure sizeof(long int) == sizeof(size_t)
       size_t id = m_outerIndex[outer+1];
       ++m_outerIndex[outer+1];

       float reallocRatio = 1;
       if (m_data.allocatedSize()<=m_data.size())
       {
         // if there is no preallocated memory, let's reserve a minimum of 32 elements
         if (m_data.size()==0)
         {
           m_data.reserve(32);
         }
         else
         {
           // we need to reallocate the data, to reduce multiple reallocations
           // we use a smart resize algorithm based on the current filling ratio
           // in addition, we use float to avoid integers overflows
           float nnzEstimate = float(m_outerIndex[outer])*float(m_outerSize)/float(outer+1);
           reallocRatio = (nnzEstimate-float(m_data.size()))/float(m_data.size());
           // furthermore we bound the realloc ratio to:
           //   1) reduce multiple minor realloc when the matrix is almost filled
           //   2) avoid to allocate too much memory when the matrix is almost empty
           reallocRatio = std::min(std::max(reallocRatio,1.5f),8.f);
         }
       }
       m_data.resize(m_data.size()+1,reallocRatio);

       if (!isLastVec)
       {
         if (previousOuter==-1)
         {
           // oops wrong guess.
           // let's correct the outer offsets
           for (Index k=0; k<=(outer+1); ++k)
             m_outerIndex[k] = 0;
           Index k=outer+1;
           while(m_outerIndex[k]==0)
             m_outerIndex[k++] = 1;
           while (k<=m_outerSize && m_outerIndex[k]!=0)
             m_outerIndex[k++]++;
           id = 0;
           --k;
           k = m_outerIndex[k]-1;
           while (k>0)
           {
             m_data.index(k) = m_data.index(k-1);
             m_data.value(k) = m_data.value(k-1);
             k--;
           }
         }
         else
         {
           // we are not inserting into the last inner vec
           // update outer indices:
           Index j = outer+2;
           while (j<=m_outerSize && m_outerIndex[j]!=0)
             m_outerIndex[j++]++;
           --j;
           // shift data of last vecs:
           Index k = m_outerIndex[j]-1;
           while (k>=Index(id))
           {
             m_data.index(k) = m_data.index(k-1);
             m_data.value(k) = m_data.value(k-1);
             k--;
           }
         }
       }

       while ( (id > startId) && (m_data.index(id-1) > inner) )
       {
         m_data.index(id) = m_data.index(id-1);
         m_data.value(id) = m_data.value(id-1);
         --id;
       }

       m_data.index(id) = inner;
       return (m_data.value(id) = 0);
     }

     EIGEN_DEPRECATED void endFill() { finalize(); }

     /** Must be called after inserting a set of non zero entries.
       */
     inline void finalize()
     {
       Index size = static_cast<Index>(m_data.size());
       Index i = m_outerSize;
       // find the last filled column
       while (i>=0 && m_outerIndex[i]==0)
         --i;
       ++i;
       while (i<=m_outerSize)
       {
         m_outerIndex[i] = size;
         ++i;
       }
     }

     void prune(Scalar reference, RealScalar epsilon = NumTraits<RealScalar>::dummy_precision())
     {
       Index k = 0;
       for (Index j=0; j<m_outerSize; ++j)
       {
         Index previousStart = m_outerIndex[j];
         m_outerIndex[j] = k;
         Index end = m_outerIndex[j+1];
         for (Index i=previousStart; i<end; ++i)
         {
           if (!ei_isMuchSmallerThan(m_data.value(i), reference, epsilon))
           {
             m_data.value(k) = m_data.value(i);
             m_data.index(k) = m_data.index(i);
             ++k;
           }
         }
       }
       m_outerIndex[m_outerSize] = k;
       m_data.resize(k,0);
     }

     /** Resizes the matrix to a \a rows x \a cols matrix and initializes it to zero
       * \sa resizeNonZeros(Index), reserve(), setZero()
       */
     void resize(Index rows, Index cols)
     {
       const Index outerSize = IsRowMajor ? rows : cols;
       m_innerSize = IsRowMajor ? cols : rows;
       m_data.clear();
       if (m_outerSize != outerSize || m_outerSize==0)
       {
         delete[] m_outerIndex;
         m_outerIndex = new Index [outerSize+1];
         m_outerSize = outerSize;
       }
       memset(m_outerIndex, 0, (m_outerSize+1)*sizeof(Index));
     }
     void resizeNonZeros(Index size)
     {
       m_data.resize(size);
     }

     inline SparseMatrix()
       : m_outerSize(-1), m_innerSize(0), m_outerIndex(0)
     {
       resize(0, 0);
     }

     inline SparseMatrix(Index rows, Index cols)
       : m_outerSize(0), m_innerSize(0), m_outerIndex(0)
     {
       resize(rows, cols);
     }

     template<typename OtherDerived>
     inline SparseMatrix(const SparseMatrixBase<OtherDerived>& other)
       : m_outerSize(0), m_innerSize(0), m_outerIndex(0)
     {
       *this = other.derived();
     }

     inline SparseMatrix(const SparseMatrix& other)
       : Base(), m_outerSize(0), m_innerSize(0), m_outerIndex(0)
     {
       *this = other.derived();
     }

     inline void swap(SparseMatrix& other)
     {
       //EIGEN_DBG_SPARSE(std::cout << "SparseMatrix:: swap\n");
       std::swap(m_outerIndex, other.m_outerIndex);
       std::swap(m_innerSize, other.m_innerSize);
       std::swap(m_outerSize, other.m_outerSize);
       m_data.swap(other.m_data);
     }

     inline SparseMatrix& operator=(const SparseMatrix& other)
     {
 //       std::cout << "SparseMatrix& operator=(const SparseMatrix& other)\n";
       if (other.isRValue())
       {
         swap(other.const_cast_derived());
       }
       else
       {
         resize(other.rows(), other.cols());
         memcpy(m_outerIndex, other.m_outerIndex, (m_outerSize+1)*sizeof(Index));
         m_data = other.m_data;
       }
       return *this;
     }

     template<typename Lhs, typename Rhs>
     inline SparseMatrix& operator=(const SparseProduct<Lhs,Rhs>& product)
     {
       return Base::operator=(product);
     }

     template<typename OtherDerived>
     EIGEN_DONT_INLINE SparseMatrix& operator=(const SparseMatrixBase<OtherDerived>& other)
     {
       const bool needToTranspose = (Flags & RowMajorBit) != (OtherDerived::Flags & RowMajorBit);
       if (needToTranspose)
       {
         // two passes algorithm:
         //  1 - compute the number of coeffs per dest inner vector
         //  2 - do the actual copy/eval
         // Since each coeff of the rhs has to be evaluated twice, let's evaluate it if needed
         typedef typename ei_nested<OtherDerived,2>::type OtherCopy;
         typedef typename ei_cleantype<OtherCopy>::type _OtherCopy;
         OtherCopy otherCopy(other.derived());

         resize(other.rows(), other.cols());
         Eigen::Map<Matrix<Index, Dynamic, 1> > (m_outerIndex,outerSize()).setZero();
         // pass 1
         // FIXME the above copy could be merged with that pass
         for (Index j=0; j<otherCopy.outerSize(); ++j)
           for (typename _OtherCopy::InnerIterator it(otherCopy, j); it; ++it)
             ++m_outerIndex[it.index()];

         // prefix sum
         Index count = 0;
         VectorXi positions(outerSize());
         for (Index j=0; j<outerSize(); ++j)
         {
           Index tmp = m_outerIndex[j];
           m_outerIndex[j] = count;
           positions[j] = count;
           count += tmp;
         }
         m_outerIndex[outerSize()] = count;
         // alloc
         m_data.resize(count);
         // pass 2
         for (Index j=0; j<otherCopy.outerSize(); ++j)
         {
           for (typename _OtherCopy::InnerIterator it(otherCopy, j); it; ++it)
           {
             Index pos = positions[it.index()]++;
             m_data.index(pos) = j;
             m_data.value(pos) = it.value();
           }
         }
         return *this;
       }
       else
       {
         // there is no special optimization
         return SparseMatrixBase<SparseMatrix>::operator=(other.derived());
       }
     }

     friend std::ostream & operator << (std::ostream & s, const SparseMatrix& m)
     {
       EIGEN_DBG_SPARSE(
         s << "Nonzero entries:\n";
         for (Index i=0; i<m.nonZeros(); ++i)
         {
           s << "(" << m.m_data.value(i) << "," << m.m_data.index(i) << ") ";
         }
         s << std::endl;
         s << std::endl;
         s << "Column pointers:\n";
         for (Index i=0; i<m.outerSize(); ++i)
         {
           s << m.m_outerIndex[i] << " ";
         }
         s << " $" << std::endl;
         s << std::endl;
       );
       s << static_cast<const SparseMatrixBase<SparseMatrix>&>(m);
       return s;
     }

     /** Destructor */
     inline ~SparseMatrix()
     {
       delete[] m_outerIndex;
     }

     /** Overloaded for performance */
     Scalar sum() const;
 };

 template<typename Scalar, int _Options>
 class SparseMatrix<Scalar,_Options>::InnerIterator
 {
   public:
     InnerIterator(const SparseMatrix& mat, Index outer)
       : m_matrix(mat), m_outer(outer), m_id(mat.m_outerIndex[outer]), m_start(m_id), m_end(mat.m_outerIndex[outer+1])
     {}

     template<unsigned int Added, unsigned int Removed>
     InnerIterator(const Flagged<SparseMatrix,Added,Removed>& mat, Index outer)
       : m_matrix(mat._expression()), m_outer(outer), m_id(m_matrix.m_outerIndex[outer]),
         m_start(m_id), m_end(m_matrix.m_outerIndex[outer+1])
     {}

     inline InnerIterator& operator++() { m_id++; return *this; }

     inline Scalar value() const { return m_matrix.m_data.value(m_id); }
     inline Scalar& valueRef() { return const_cast<Scalar&>(m_matrix.m_data.value(m_id)); }

     inline Index index() const { return m_matrix.m_data.index(m_id); }
     inline Index outer() const { return m_outer; }
     inline Index row() const { return IsRowMajor ? m_outer : index(); }
     inline Index col() const { return IsRowMajor ? index() : m_outer; }

     inline operator bool() const { return (m_id < m_end) && (m_id>=m_start); }

   protected:
     const SparseMatrix& m_matrix;
     const Index m_outer;
     Index m_id;
     const Index m_start;
     const Index m_end;
 };

 #endif // EIGEN_SPARSEMATRIX_H
	// This file is part of Eigen, a lightweight C++ template library
	// for linear algebra.
	//
	// Copyright (C) 2008-2009 Gael Guennebaud <g.gael@free.fr>
	//
	// Eigen is free software; you can redistribute it and/or
	// modify it under the terms of the GNU Lesser General Public
	// License as published by the Free Software Foundation; either
	// version 3 of the License, or (at your option) any later version.
	//
	// Alternatively, you can redistribute it and/or
	// modify it under the terms of the GNU General Public License as
	// published by the Free Software Foundation; either version 2 of
	// the License, or (at your option) any later version.
	//
	// Eigen is distributed in the hope that it will be useful, but WITHOUT ANY
	// WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
	// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License or the
	// GNU General Public License for more details.
	//
	// You should have received a copy of the GNU Lesser General Public
	// License and a copy of the GNU General Public License along with
	// Eigen. If not, see <http://www.gnu.org/licenses/>.

	#ifndef EIGEN_SPARSEMATRIX_H
	#define EIGEN_SPARSEMATRIX_H

	/** \ingroup Sparse_Module
	*
	* \class SparseMatrix
	*
	* \brief The main sparse matrix class
	*
	* This class implements a sparse matrix using the very common compressed row/column storage
	* scheme.
	*
	* \param _Scalar the scalar type, i.e. the type of the coefficients
	* \param _Options Union of bit flags controlling the storage scheme. Currently the only possibility
	* is RowMajor. The default is 0 which means column-major.
	*
	* See http://www.netlib.org/linalg/html_templates/node91.html for details on the storage scheme.
	*
	*/
	template<typename _Scalar, int _Options>
	struct ei_traits<SparseMatrix<_Scalar, _Options> >
	{
	typedef _Scalar Scalar;
	typedef Sparse StorageKind;
	typedef MatrixXpr XprKind;
	enum {
	RowsAtCompileTime = Dynamic,
	ColsAtCompileTime = Dynamic,
	MaxRowsAtCompileTime = Dynamic,
	MaxColsAtCompileTime = Dynamic,
	Flags = _Options \| NestByRefBit,
	CoeffReadCost = NumTraits<Scalar>::ReadCost,
	SupportedAccessPatterns = InnerRandomAccessPattern
	};
	};

	template<typename _Scalar, int _Options>
	class SparseMatrix
	: public SparseMatrixBase<SparseMatrix<_Scalar, _Options> >
	{
	public:
	EIGEN_SPARSE_GENERIC_PUBLIC_INTERFACE(SparseMatrix)
	EIGEN_SPARSE_INHERIT_ASSIGNMENT_OPERATOR(SparseMatrix, +=)
	EIGEN_SPARSE_INHERIT_ASSIGNMENT_OPERATOR(SparseMatrix, -=)
	// FIXME: why are these operator already alvailable ???
	// EIGEN_SPARSE_INHERIT_SCALAR_ASSIGNMENT_OPERATOR(SparseMatrix, *=)
	// EIGEN_SPARSE_INHERIT_SCALAR_ASSIGNMENT_OPERATOR(SparseMatrix, /=)

	typedef MappedSparseMatrix<Scalar,Flags> Map;
	using Base::IsRowMajor;

	protected:

	typedef SparseMatrix<Scalar,(Flags&~RowMajorBit)\|(IsRowMajor?RowMajorBit:0)> TransposedSparseMatrix;

	Index m_outerSize;
	Index m_innerSize;
	Index* m_outerIndex;
	CompressedStorage<Scalar> m_data;

	public:

	inline Index rows() const { return IsRowMajor ? m_outerSize : m_innerSize; }
	inline Index cols() const { return IsRowMajor ? m_innerSize : m_outerSize; }

	inline Index innerSize() const { return m_innerSize; }
	inline Index outerSize() const { return m_outerSize; }
	inline Index innerNonZeros(Index j) const { return m_outerIndex[j+1]-m_outerIndex[j]; }

	inline const Scalar* _valuePtr() const { return &m_data.value(0); }
	inline Scalar* _valuePtr() { return &m_data.value(0); }

	inline const Index* _innerIndexPtr() const { return &m_data.index(0); }
	inline Index* _innerIndexPtr() { return &m_data.index(0); }

	inline const Index* _outerIndexPtr() const { return m_outerIndex; }
	inline Index* _outerIndexPtr() { return m_outerIndex; }

	inline Scalar coeff(Index row, Index col) const
	{
	const Index outer = IsRowMajor ? row : col;
	const Index inner = IsRowMajor ? col : row;
	return m_data.atInRange(m_outerIndex[outer], m_outerIndex[outer+1], inner);
	}

	inline Scalar& coeffRef(Index row, Index col)
	{
	const Index outer = IsRowMajor ? row : col;
	const Index inner = IsRowMajor ? col : row;

	Index start = m_outerIndex[outer];
	Index end = m_outerIndex[outer+1];
	ei_assert(end>=start && "you probably called coeffRef on a non finalized matrix");
	ei_assert(end>start && "coeffRef cannot be called on a zero coefficient");
	const Index id = m_data.searchLowerIndex(start,end-1,inner);
	ei_assert((id<end) && (m_data.index(id)==inner) && "coeffRef cannot be called on a zero coefficient");
	return m_data.value(id);
	}

	public:

	class InnerIterator;

	/** Removes all non zeros */
	inline void setZero()
	{
	m_data.clear();
	memset(m_outerIndex, 0, (m_outerSize+1)*sizeof(Index));
	}

	/** \returns the number of non zero coefficients */
	inline Index nonZeros() const { return static_cast<Index>(m_data.size()); }

	/** \deprecated use setZero() and reserve()
	* Initializes the filling process of \c *this.
	* \param reserveSize approximate number of nonzeros
	* Note that the matrix \c *this is zero-ed.
	*/
	EIGEN_DEPRECATED void startFill(Index reserveSize = 1000)
	{
	setZero();
	m_data.reserve(reserveSize);
	}

	/** Preallocates \a reserveSize non zeros */
	inline void reserve(Index reserveSize)
	{
	m_data.reserve(reserveSize);
	}

	/** \deprecated use insert()
	*/
	EIGEN_DEPRECATED Scalar& fill(Index row, Index col)
	{
	const Index outer = IsRowMajor ? row : col;
	const Index inner = IsRowMajor ? col : row;

	if (m_outerIndex[outer+1]==0)
	{
	// we start a new inner vector
	Index i = outer;
	while (i>=0 && m_outerIndex[i]==0)
	{
	m_outerIndex[i] = m_data.size();
	--i;
	}
	m_outerIndex[outer+1] = m_outerIndex[outer];
	}
	else
	{
	ei_assert(m_data.index(m_data.size()-1)<inner && "wrong sorted insertion");
	}
	// std::cerr << size_t(m_outerIndex[outer+1]) << " == " << m_data.size() << "\n";
	assert(size_t(m_outerIndex[outer+1]) == m_data.size());
	Index id = m_outerIndex[outer+1];
	++m_outerIndex[outer+1];

	m_data.append(0, inner);
	return m_data.value(id);
	}

	//--- low level purely coherent filling ---

	inline Scalar& insertBack(Index outer, Index inner)
	{
	ei_assert(size_t(m_outerIndex[outer+1]) == m_data.size() && "wrong sorted insertion");
	ei_assert( (m_outerIndex[outer+1]-m_outerIndex[outer]==0 \|\| m_data.index(m_data.size()-1)<inner) && "wrong sorted insertion");
	Index id = m_outerIndex[outer+1];
	++m_outerIndex[outer+1];
	m_data.append(0, inner);
	return m_data.value(id);
	}

	inline Scalar& insertBackNoCheck(Index outer, Index inner)
	{
	Index id = m_outerIndex[outer+1];
	++m_outerIndex[outer+1];
	m_data.append(0, inner);
	return m_data.value(id);
	}

	inline void startVec(Index outer)
	{
	ei_assert(m_outerIndex[outer]==int(m_data.size()) && "you must call startVec on each inner vec");
	ei_assert(m_outerIndex[outer+1]==0 && "you must call startVec on each inner vec");
	m_outerIndex[outer+1] = m_outerIndex[outer];
	}

	//---

	/** \deprecated use insert()
	* Like fill() but with random inner coordinates.
	*/
	EIGEN_DEPRECATED Scalar& fillrand(Index row, Index col)
	{
	return insert(row,col);
	}

	/** \returns a reference to a novel non zero coefficient with coordinates \a row x \a col.
	* The non zero coefficient must \b not already exist.
	*
	* \warning This function can be extremely slow if the non zero coefficients
	* are not inserted in a coherent order.
	*
	* After an insertion session, you should call the finalize() function.
	*/
	EIGEN_DONT_INLINE Scalar& insert(Index row, Index col)
	{
	const Index outer = IsRowMajor ? row : col;
	const Index inner = IsRowMajor ? col : row;

	Index previousOuter = outer;
	if (m_outerIndex[outer+1]==0)
	{
	// we start a new inner vector
	while (previousOuter>=0 && m_outerIndex[previousOuter]==0)
	{
	m_outerIndex[previousOuter] = static_cast<Index>(m_data.size());
	--previousOuter;
	}
	m_outerIndex[outer+1] = m_outerIndex[outer];
	}

	// here we have to handle the tricky case where the outerIndex array
	// starts with: [ 0 0 0 0 0 1 ...] and we are inserting in, e.g.,
	// the 2nd inner vector...
	bool isLastVec = (!(previousOuter==-1 && m_data.size()!=0))
	&& (size_t(m_outerIndex[outer+1]) == m_data.size());

	size_t startId = m_outerIndex[outer];
	// FIXME let's make sure sizeof(long int) == sizeof(size_t)
	size_t id = m_outerIndex[outer+1];
	++m_outerIndex[outer+1];

	float reallocRatio = 1;
	if (m_data.allocatedSize()<=m_data.size())
	{
	// if there is no preallocated memory, let's reserve a minimum of 32 elements
	if (m_data.size()==0)
	{
	m_data.reserve(32);
	}
	else
	{
	// we need to reallocate the data, to reduce multiple reallocations
	// we use a smart resize algorithm based on the current filling ratio
	// in addition, we use float to avoid integers overflows
	float nnzEstimate = float(m_outerIndex[outer])*float(m_outerSize)/float(outer+1);
	reallocRatio = (nnzEstimate-float(m_data.size()))/float(m_data.size());
	// furthermore we bound the realloc ratio to:
	// 1) reduce multiple minor realloc when the matrix is almost filled
	// 2) avoid to allocate too much memory when the matrix is almost empty
	reallocRatio = std::min(std::max(reallocRatio,1.5f),8.f);
	}
	}
	m_data.resize(m_data.size()+1,reallocRatio);

	if (!isLastVec)
	{
	if (previousOuter==-1)
	{
	// oops wrong guess.
	// let's correct the outer offsets
	for (Index k=0; k<=(outer+1); ++k)
	m_outerIndex[k] = 0;
	Index k=outer+1;
	while(m_outerIndex[k]==0)
	m_outerIndex[k++] = 1;
	while (k<=m_outerSize && m_outerIndex[k]!=0)
	m_outerIndex[k++]++;
	id = 0;
	--k;
	k = m_outerIndex[k]-1;
	while (k>0)
	{
	m_data.index(k) = m_data.index(k-1);
	m_data.value(k) = m_data.value(k-1);
	k--;
	}
	}
	else
	{
	// we are not inserting into the last inner vec
	// update outer indices:
	Index j = outer+2;
	while (j<=m_outerSize && m_outerIndex[j]!=0)
	m_outerIndex[j++]++;
	--j;
	// shift data of last vecs:
	Index k = m_outerIndex[j]-1;
	while (k>=Index(id))
	{
	m_data.index(k) = m_data.index(k-1);
	m_data.value(k) = m_data.value(k-1);
	k--;
	}
	}
	}

	while ( (id > startId) && (m_data.index(id-1) > inner) )
	{
	m_data.index(id) = m_data.index(id-1);
	m_data.value(id) = m_data.value(id-1);
	--id;
	}

	m_data.index(id) = inner;
	return (m_data.value(id) = 0);
	}

	EIGEN_DEPRECATED void endFill() { finalize(); }

	/** Must be called after inserting a set of non zero entries.
	*/
	inline void finalize()
	{
	Index size = static_cast<Index>(m_data.size());
	Index i = m_outerSize;
	// find the last filled column
	while (i>=0 && m_outerIndex[i]==0)
	--i;
	++i;
	while (i<=m_outerSize)
	{
	m_outerIndex[i] = size;
	++i;
	}
	}

	void prune(Scalar reference, RealScalar epsilon = NumTraits<RealScalar>::dummy_precision())
	{
	Index k = 0;
	for (Index j=0; j<m_outerSize; ++j)
	{
	Index previousStart = m_outerIndex[j];
	m_outerIndex[j] = k;
	Index end = m_outerIndex[j+1];
	for (Index i=previousStart; i<end; ++i)
	{
	if (!ei_isMuchSmallerThan(m_data.value(i), reference, epsilon))
	{
	m_data.value(k) = m_data.value(i);
	m_data.index(k) = m_data.index(i);
	++k;
	}
	}
	}
	m_outerIndex[m_outerSize] = k;
	m_data.resize(k,0);
	}

	/** Resizes the matrix to a \a rows x \a cols matrix and initializes it to zero
	* \sa resizeNonZeros(Index), reserve(), setZero()
	*/
	void resize(Index rows, Index cols)
	{
	const Index outerSize = IsRowMajor ? rows : cols;
	m_innerSize = IsRowMajor ? cols : rows;
	m_data.clear();
	if (m_outerSize != outerSize \|\| m_outerSize==0)
	{
	delete[] m_outerIndex;
	m_outerIndex = new Index [outerSize+1];
	m_outerSize = outerSize;
	}
	memset(m_outerIndex, 0, (m_outerSize+1)*sizeof(Index));
	}
	void resizeNonZeros(Index size)
	{
	m_data.resize(size);
	}

	inline SparseMatrix()
	: m_outerSize(-1), m_innerSize(0), m_outerIndex(0)
	{
	resize(0, 0);
	}

	inline SparseMatrix(Index rows, Index cols)
	: m_outerSize(0), m_innerSize(0), m_outerIndex(0)
	{
	resize(rows, cols);
	}

	template<typename OtherDerived>
	inline SparseMatrix(const SparseMatrixBase<OtherDerived>& other)
	: m_outerSize(0), m_innerSize(0), m_outerIndex(0)
	{
	*this = other.derived();
	}

	inline SparseMatrix(const SparseMatrix& other)
	: Base(), m_outerSize(0), m_innerSize(0), m_outerIndex(0)
	{
	*this = other.derived();
	}

	inline void swap(SparseMatrix& other)
	{
	//EIGEN_DBG_SPARSE(std::cout << "SparseMatrix:: swap\n");
	std::swap(m_outerIndex, other.m_outerIndex);
	std::swap(m_innerSize, other.m_innerSize);
	std::swap(m_outerSize, other.m_outerSize);
	m_data.swap(other.m_data);
	}

	inline SparseMatrix& operator=(const SparseMatrix& other)
	{
	// std::cout << "SparseMatrix& operator=(const SparseMatrix& other)\n";
	if (other.isRValue())
	{
	swap(other.const_cast_derived());
	}
	else
	{
	resize(other.rows(), other.cols());
	memcpy(m_outerIndex, other.m_outerIndex, (m_outerSize+1)*sizeof(Index));
	m_data = other.m_data;
	}
	return *this;
	}

	template<typename Lhs, typename Rhs>
	inline SparseMatrix& operator=(const SparseProduct<Lhs,Rhs>& product)
	{
	return Base::operator=(product);
	}

	template<typename OtherDerived>
	EIGEN_DONT_INLINE SparseMatrix& operator=(const SparseMatrixBase<OtherDerived>& other)
	{
	const bool needToTranspose = (Flags & RowMajorBit) != (OtherDerived::Flags & RowMajorBit);
	if (needToTranspose)
	{
	// two passes algorithm:
	// 1 - compute the number of coeffs per dest inner vector
	// 2 - do the actual copy/eval
	// Since each coeff of the rhs has to be evaluated twice, let's evaluate it if needed
	typedef typename ei_nested<OtherDerived,2>::type OtherCopy;
	typedef typename ei_cleantype<OtherCopy>::type _OtherCopy;
	OtherCopy otherCopy(other.derived());

	resize(other.rows(), other.cols());
	Eigen::Map<Matrix<Index, Dynamic, 1> > (m_outerIndex,outerSize()).setZero();
	// pass 1
	// FIXME the above copy could be merged with that pass
	for (Index j=0; j<otherCopy.outerSize(); ++j)
	for (typename _OtherCopy::InnerIterator it(otherCopy, j); it; ++it)
	++m_outerIndex[it.index()];

	// prefix sum
	Index count = 0;
	VectorXi positions(outerSize());
	for (Index j=0; j<outerSize(); ++j)
	{
	Index tmp = m_outerIndex[j];
	m_outerIndex[j] = count;
	positions[j] = count;
	count += tmp;
	}
	m_outerIndex[outerSize()] = count;
	// alloc
	m_data.resize(count);
	// pass 2
	for (Index j=0; j<otherCopy.outerSize(); ++j)
	{
	for (typename _OtherCopy::InnerIterator it(otherCopy, j); it; ++it)
	{
	Index pos = positions[it.index()]++;
	m_data.index(pos) = j;
	m_data.value(pos) = it.value();
	}
	}
	return *this;
	}
	else
	{
	// there is no special optimization
	return SparseMatrixBase<SparseMatrix>::operator=(other.derived());
	}
	}

	friend std::ostream & operator << (std::ostream & s, const SparseMatrix& m)
	{
	EIGEN_DBG_SPARSE(
	s << "Nonzero entries:\n";
	for (Index i=0; i<m.nonZeros(); ++i)
	{
	s << "(" << m.m_data.value(i) << "," << m.m_data.index(i) << ") ";
	}
	s << std::endl;
	s << std::endl;
	s << "Column pointers:\n";
	for (Index i=0; i<m.outerSize(); ++i)
	{
	s << m.m_outerIndex[i] << " ";
	}
	s << " $" << std::endl;
	s << std::endl;
	);
	s << static_cast<const SparseMatrixBase<SparseMatrix>&>(m);
	return s;
	}

	/** Destructor */
	inline ~SparseMatrix()
	{
	delete[] m_outerIndex;
	}

	/** Overloaded for performance */
	Scalar sum() const;
	};

	template<typename Scalar, int _Options>
	class SparseMatrix<Scalar,_Options>::InnerIterator
	{
	public:
	InnerIterator(const SparseMatrix& mat, Index outer)
	: m_matrix(mat), m_outer(outer), m_id(mat.m_outerIndex[outer]), m_start(m_id), m_end(mat.m_outerIndex[outer+1])
	{}

	template<unsigned int Added, unsigned int Removed>
	InnerIterator(const Flagged<SparseMatrix,Added,Removed>& mat, Index outer)
	: m_matrix(mat._expression()), m_outer(outer), m_id(m_matrix.m_outerIndex[outer]),
	m_start(m_id), m_end(m_matrix.m_outerIndex[outer+1])
	{}

	inline InnerIterator& operator++() { m_id++; return *this; }

	inline Scalar value() const { return m_matrix.m_data.value(m_id); }
	inline Scalar& valueRef() { return const_cast<Scalar&>(m_matrix.m_data.value(m_id)); }

	inline Index index() const { return m_matrix.m_data.index(m_id); }
	inline Index outer() const { return m_outer; }
	inline Index row() const { return IsRowMajor ? m_outer : index(); }
	inline Index col() const { return IsRowMajor ? index() : m_outer; }

	inline operator bool() const { return (m_id < m_end) && (m_id>=m_start); }

	protected:
	const SparseMatrix& m_matrix;
	const Index m_outer;
	Index m_id;
	const Index m_start;
	const Index m_end;
	};

	#endif // EIGEN_SPARSEMATRIX_H