sequenzo 0.1.18__cp310-cp310-macosx_10_9_universal2.whl → 0.1.19__cp310-cp310-macosx_10_9_universal2.whl

sequenzo/dissimilarity_measures/src/eigen/unsupported/Eigen/src/SparseExtra/BlockSparseMatrix.h

@@ -1,1079 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2013 Desire Nuentsa <desire.nuentsa_wakam@inria.fr>
-// Copyright (C) 2013 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_SPARSEBLOCKMATRIX_H
-#define EIGEN_SPARSEBLOCKMATRIX_H
-
-namespace Eigen { 
-/** \ingroup SparseCore_Module
-  *
-  * \class BlockSparseMatrix
-  *
-  * \brief A versatile sparse matrix representation where each element is a block
-  *
-  * This class provides routines to manipulate block sparse matrices stored in a
-  * BSR-like representation. There are two main types :
-  *
-  * 1. All blocks have the same number of rows and columns, called block size
-  * in the following. In this case, if this block size is known at compile time,
-  * it can be given as a template parameter like
-  * \code
-  * BlockSparseMatrix<Scalar, 3, ColMajor> bmat(b_rows, b_cols);
-  * \endcode
-  * Here, bmat is a b_rows x b_cols block sparse matrix
-  * where each coefficient is a 3x3 dense matrix.
-  * If the block size is fixed but will be given at runtime,
-  * \code
-  * BlockSparseMatrix<Scalar, Dynamic, ColMajor> bmat(b_rows, b_cols);
-  * bmat.setBlockSize(block_size);
-  * \endcode
-  *
-  * 2. The second case is for variable-block sparse matrices.
-  * Here each block has its own dimensions. The only restriction is that all the blocks
-  * in a row (resp. a column) should have the same number of rows (resp. of columns).
-  * It is thus required in this case to describe the layout of the matrix by calling
-  * setBlockLayout(rowBlocks, colBlocks).
-  *
-  * In any of the previous case, the matrix can be filled by calling setFromTriplets().
-  * A regular sparse matrix can be converted to a block sparse matrix and vice versa.
-  * It is obviously required to describe the block layout beforehand by calling either
-  * setBlockSize() for fixed-size blocks or setBlockLayout for variable-size blocks.
-  *
-  * \tparam _Scalar The Scalar type
-  * \tparam _BlockAtCompileTime The block layout option. It takes the following values
-  * Dynamic : block size known at runtime
-  * a numeric number : fixed-size block known at compile time
-  */
-template<typename _Scalar, int _BlockAtCompileTime=Dynamic, int _Options=ColMajor, typename _StorageIndex=int> class BlockSparseMatrix;
-
-template<typename BlockSparseMatrixT> class BlockSparseMatrixView;
-
-namespace internal {
-template<typename _Scalar, int _BlockAtCompileTime, int _Options, typename _Index>
-struct traits<BlockSparseMatrix<_Scalar,_BlockAtCompileTime,_Options, _Index> >
-{
-  typedef _Scalar Scalar;
-  typedef _Index Index;
-  typedef Sparse StorageKind; // FIXME Where is it used ??
-  typedef MatrixXpr XprKind;
-  enum {
-    RowsAtCompileTime = Dynamic,
-    ColsAtCompileTime = Dynamic,
-    MaxRowsAtCompileTime = Dynamic,
-    MaxColsAtCompileTime = Dynamic,
-    BlockSize = _BlockAtCompileTime,
-    Flags = _Options | NestByRefBit | LvalueBit,
-    CoeffReadCost = NumTraits<Scalar>::ReadCost,
-    SupportedAccessPatterns = InnerRandomAccessPattern
-  };
-};
-template<typename BlockSparseMatrixT>
-struct traits<BlockSparseMatrixView<BlockSparseMatrixT> >
-{
-  typedef Ref<Matrix<typename BlockSparseMatrixT::Scalar, BlockSparseMatrixT::BlockSize, BlockSparseMatrixT::BlockSize> > Scalar;
-  typedef Ref<Matrix<typename BlockSparseMatrixT::RealScalar, BlockSparseMatrixT::BlockSize, BlockSparseMatrixT::BlockSize> > RealScalar;
-
-};
-
-// Function object to sort a triplet list
-template<typename Iterator, bool IsColMajor>
-struct TripletComp
-{
-  typedef typename Iterator::value_type Triplet;
-  bool operator()(const Triplet& a, const Triplet& b)
-  { if(IsColMajor)
-      return ((a.col() == b.col() && a.row() < b.row()) || (a.col() < b.col()));
-    else
-      return ((a.row() == b.row() && a.col() < b.col()) || (a.row() < b.row()));
-  }
-};
-} // end namespace internal
-
-
-/* Proxy to view the block sparse matrix as a regular sparse matrix */
-template<typename BlockSparseMatrixT>
-class BlockSparseMatrixView : public SparseMatrixBase<BlockSparseMatrixT>
-{
-  public:
-    typedef Ref<typename BlockSparseMatrixT::BlockScalar> Scalar;
-    typedef Ref<typename BlockSparseMatrixT::BlockRealScalar> RealScalar;
-    typedef typename BlockSparseMatrixT::Index Index;
-    typedef  BlockSparseMatrixT Nested;
-    enum {
-      Flags = BlockSparseMatrixT::Options,
-      Options = BlockSparseMatrixT::Options,
-      RowsAtCompileTime = BlockSparseMatrixT::RowsAtCompileTime,
-      ColsAtCompileTime = BlockSparseMatrixT::ColsAtCompileTime,
-      MaxColsAtCompileTime = BlockSparseMatrixT::MaxColsAtCompileTime,
-      MaxRowsAtCompileTime = BlockSparseMatrixT::MaxRowsAtCompileTime
-    };
-  public:
-    BlockSparseMatrixView(const BlockSparseMatrixT& spblockmat)
-     : m_spblockmat(spblockmat)
-    {}
-
-    Index outerSize() const
-    {
-      return (Flags&RowMajorBit) == 1 ? this->rows() : this->cols();
-    }
-    Index cols() const
-    {
-      return m_spblockmat.blockCols();
-    }
-    Index rows() const
-    {
-      return m_spblockmat.blockRows();
-    }
-    Scalar coeff(Index row, Index col)
-    {
-      return m_spblockmat.coeff(row, col);
-    }
-    Scalar coeffRef(Index row, Index col)
-    {
-      return m_spblockmat.coeffRef(row, col);
-    }
-    // Wrapper to iterate over all blocks
-    class InnerIterator : public BlockSparseMatrixT::BlockInnerIterator
-    {
-      public:
-      InnerIterator(const BlockSparseMatrixView& mat, Index outer)
-          : BlockSparseMatrixT::BlockInnerIterator(mat.m_spblockmat, outer)
-      {}
-
-    };
-
-  protected:
-    const BlockSparseMatrixT& m_spblockmat;
-};
-
-// Proxy to view a regular vector as a block vector
-template<typename BlockSparseMatrixT, typename VectorType>
-class BlockVectorView
-{
-  public:
-    enum {
-      BlockSize = BlockSparseMatrixT::BlockSize,
-      ColsAtCompileTime = VectorType::ColsAtCompileTime,
-      RowsAtCompileTime = VectorType::RowsAtCompileTime,
-      Flags = VectorType::Flags
-    };
-    typedef Ref<const Matrix<typename BlockSparseMatrixT::Scalar, (RowsAtCompileTime==1)? 1 : BlockSize, (ColsAtCompileTime==1)? 1 : BlockSize> >Scalar;
-    typedef typename BlockSparseMatrixT::Index Index;
-  public:
-    BlockVectorView(const BlockSparseMatrixT& spblockmat, const VectorType& vec)
-    : m_spblockmat(spblockmat),m_vec(vec)
-    { }
-    inline Index cols() const
-    {
-      return m_vec.cols();
-    }
-    inline Index size() const
-    {
-      return m_spblockmat.blockRows();
-    }
-    inline Scalar coeff(Index bi) const
-    {
-      Index startRow = m_spblockmat.blockRowsIndex(bi);
-      Index rowSize = m_spblockmat.blockRowsIndex(bi+1) - startRow;
-      return m_vec.middleRows(startRow, rowSize);
-    }
-    inline Scalar coeff(Index bi, Index j) const
-    {
-      Index startRow = m_spblockmat.blockRowsIndex(bi);
-      Index rowSize = m_spblockmat.blockRowsIndex(bi+1) - startRow;
-      return m_vec.block(startRow, j, rowSize, 1);
-    }
-  protected:
-    const BlockSparseMatrixT& m_spblockmat;
-    const VectorType& m_vec;
-};
-
-template<typename VectorType, typename Index> class BlockVectorReturn;
-
-
-// Proxy to view a regular vector as a block vector
-template<typename BlockSparseMatrixT, typename VectorType>
-class BlockVectorReturn
-{
-  public:
-    enum {
-      ColsAtCompileTime = VectorType::ColsAtCompileTime,
-      RowsAtCompileTime = VectorType::RowsAtCompileTime,
-      Flags = VectorType::Flags
-    };
-    typedef Ref<Matrix<typename VectorType::Scalar, RowsAtCompileTime, ColsAtCompileTime> > Scalar;
-    typedef typename BlockSparseMatrixT::Index Index;
-  public:
-    BlockVectorReturn(const BlockSparseMatrixT& spblockmat, VectorType& vec)
-    : m_spblockmat(spblockmat),m_vec(vec)
-    { }
-    inline Index size() const
-    {
-      return m_spblockmat.blockRows();
-    }
-    inline Scalar coeffRef(Index bi)
-    {
-      Index startRow = m_spblockmat.blockRowsIndex(bi);
-      Index rowSize = m_spblockmat.blockRowsIndex(bi+1) - startRow;
-      return m_vec.middleRows(startRow, rowSize);
-    }
-    inline Scalar coeffRef(Index bi, Index j)
-    {
-      Index startRow = m_spblockmat.blockRowsIndex(bi);
-      Index rowSize = m_spblockmat.blockRowsIndex(bi+1) - startRow;
-      return m_vec.block(startRow, j, rowSize, 1);
-    }
-
-  protected:
-    const BlockSparseMatrixT& m_spblockmat;
-    VectorType& m_vec;
-};
-
-// Block version of the sparse dense product
-template<typename Lhs, typename Rhs>
-class BlockSparseTimeDenseProduct;
-
-namespace internal {
-
-template<typename BlockSparseMatrixT, typename VecType>
-struct traits<BlockSparseTimeDenseProduct<BlockSparseMatrixT, VecType> >
-{
-  typedef Dense StorageKind;
-  typedef MatrixXpr XprKind;
-  typedef typename BlockSparseMatrixT::Scalar Scalar;
-  typedef typename BlockSparseMatrixT::Index Index;
-  enum {
-    RowsAtCompileTime = Dynamic,
-    ColsAtCompileTime = Dynamic,
-    MaxRowsAtCompileTime = Dynamic,
-    MaxColsAtCompileTime = Dynamic,
-    Flags = 0,
-    CoeffReadCost = internal::traits<BlockSparseMatrixT>::CoeffReadCost
-  };
-};
-} // end namespace internal
-
-template<typename Lhs, typename Rhs>
-class BlockSparseTimeDenseProduct
-  : public ProductBase<BlockSparseTimeDenseProduct<Lhs,Rhs>, Lhs, Rhs>
-{
-  public:
-    EIGEN_PRODUCT_PUBLIC_INTERFACE(BlockSparseTimeDenseProduct)
-
-    BlockSparseTimeDenseProduct(const Lhs& lhs, const Rhs& rhs) : Base(lhs,rhs)
-    {}
-
-    template<typename Dest> void scaleAndAddTo(Dest& dest, const typename Rhs::Scalar& alpha) const
-    {
-      BlockVectorReturn<Lhs,Dest> tmpDest(m_lhs, dest);
-      internal::sparse_time_dense_product( BlockSparseMatrixView<Lhs>(m_lhs),  BlockVectorView<Lhs, Rhs>(m_lhs, m_rhs), tmpDest, alpha);
-    }
-
-  private:
-    BlockSparseTimeDenseProduct& operator=(const BlockSparseTimeDenseProduct&);
-};
-
-template<typename _Scalar, int _BlockAtCompileTime, int _Options, typename _StorageIndex>
-class BlockSparseMatrix : public SparseMatrixBase<BlockSparseMatrix<_Scalar,_BlockAtCompileTime, _Options,_StorageIndex> >
-{
-  public:
-    typedef _Scalar Scalar;
-    typedef typename NumTraits<Scalar>::Real RealScalar;
-    typedef _StorageIndex StorageIndex;
-    typedef typename internal::ref_selector<BlockSparseMatrix<_Scalar, _BlockAtCompileTime, _Options, _StorageIndex> >::type Nested;
-
-    enum {
-      Options = _Options,
-      Flags = Options,
-      BlockSize=_BlockAtCompileTime,
-      RowsAtCompileTime = Dynamic,
-      ColsAtCompileTime = Dynamic,
-      MaxRowsAtCompileTime = Dynamic,
-      MaxColsAtCompileTime = Dynamic,
-      IsVectorAtCompileTime = 0,
-      IsColMajor = Flags&RowMajorBit ? 0 : 1
-    };
-    typedef Matrix<Scalar, _BlockAtCompileTime, _BlockAtCompileTime,IsColMajor ? ColMajor : RowMajor> BlockScalar;
-    typedef Matrix<RealScalar, _BlockAtCompileTime, _BlockAtCompileTime,IsColMajor ? ColMajor : RowMajor> BlockRealScalar;
-    typedef typename internal::conditional<_BlockAtCompileTime==Dynamic, Scalar, BlockScalar>::type BlockScalarReturnType;
-    typedef BlockSparseMatrix<Scalar, BlockSize, IsColMajor ? ColMajor : RowMajor, StorageIndex> PlainObject;
-  public:
-    // Default constructor
-    BlockSparseMatrix()
-    : m_innerBSize(0),m_outerBSize(0),m_innerOffset(0),m_outerOffset(0),
-      m_nonzerosblocks(0),m_values(0),m_blockPtr(0),m_indices(0),
-      m_outerIndex(0),m_blockSize(BlockSize)
-    { }
-
-
-    /**
-     * \brief Construct and resize
-     *
-     */
-    BlockSparseMatrix(Index brow, Index bcol)
-      : m_innerBSize(IsColMajor ? brow : bcol),
-        m_outerBSize(IsColMajor ? bcol : brow),
-        m_innerOffset(0),m_outerOffset(0),m_nonzerosblocks(0),
-        m_values(0),m_blockPtr(0),m_indices(0),
-        m_outerIndex(0),m_blockSize(BlockSize)
-    { }
-
-    /**
-     * \brief Copy-constructor
-     */
-    BlockSparseMatrix(const BlockSparseMatrix& other)
-      : m_innerBSize(other.m_innerBSize),m_outerBSize(other.m_outerBSize),
-        m_nonzerosblocks(other.m_nonzerosblocks),m_nonzeros(other.m_nonzeros),
-        m_blockPtr(0),m_blockSize(other.m_blockSize)
-    {
-      // should we allow copying between variable-size blocks and fixed-size blocks ??
-      eigen_assert(m_blockSize == BlockSize && " CAN NOT COPY BETWEEN FIXED-SIZE AND VARIABLE-SIZE BLOCKS");
-
-      std::copy(other.m_innerOffset, other.m_innerOffset+m_innerBSize+1, m_innerOffset);
-      std::copy(other.m_outerOffset, other.m_outerOffset+m_outerBSize+1, m_outerOffset);
-      std::copy(other.m_values, other.m_values+m_nonzeros, m_values);
-
-      if(m_blockSize != Dynamic)
-        std::copy(other.m_blockPtr, other.m_blockPtr+m_nonzerosblocks, m_blockPtr);
-
-      std::copy(other.m_indices, other.m_indices+m_nonzerosblocks, m_indices);
-      std::copy(other.m_outerIndex, other.m_outerIndex+m_outerBSize, m_outerIndex);
-    }
-
-    friend void swap(BlockSparseMatrix& first, BlockSparseMatrix& second)
-    {
-      std::swap(first.m_innerBSize, second.m_innerBSize);
-      std::swap(first.m_outerBSize, second.m_outerBSize);
-      std::swap(first.m_innerOffset, second.m_innerOffset);
-      std::swap(first.m_outerOffset, second.m_outerOffset);
-      std::swap(first.m_nonzerosblocks, second.m_nonzerosblocks);
-      std::swap(first.m_nonzeros, second.m_nonzeros);
-      std::swap(first.m_values, second.m_values);
-      std::swap(first.m_blockPtr, second.m_blockPtr);
-      std::swap(first.m_indices, second.m_indices);
-      std::swap(first.m_outerIndex, second.m_outerIndex);
-      std::swap(first.m_BlockSize, second.m_blockSize);
-    }
-
-    BlockSparseMatrix& operator=(BlockSparseMatrix other)
-    {
-      //Copy-and-swap paradigm ... avoid leaked data if thrown
-      swap(*this, other);
-      return *this;
-    }
-
-    // Destructor
-    ~BlockSparseMatrix()
-    {
-      delete[] m_outerIndex;
-      delete[] m_innerOffset;
-      delete[] m_outerOffset;
-      delete[] m_indices;
-      delete[] m_blockPtr;
-      delete[] m_values;
-    }
-
-
-    /**
-      * \brief Constructor from a sparse matrix
-      *
-      */
-    template<typename MatrixType>
-    inline BlockSparseMatrix(const MatrixType& spmat) : m_blockSize(BlockSize)
-    {
-      EIGEN_STATIC_ASSERT((m_blockSize != Dynamic), THIS_METHOD_IS_ONLY_FOR_FIXED_SIZE);
-
-      *this = spmat;
-    }
-
-    /**
-      * \brief Assignment from a sparse matrix with the same storage order
-      *
-      * Convert from a sparse matrix to block sparse matrix.
-      * \warning Before calling this function, tt is necessary to call
-      * either setBlockLayout() (matrices with variable-size blocks)
-      * or setBlockSize() (for fixed-size blocks).
-      */
-    template<typename MatrixType>
-    inline BlockSparseMatrix& operator=(const MatrixType& spmat)
-    {
-      eigen_assert((m_innerBSize != 0 && m_outerBSize != 0)
-                   && "Trying to assign to a zero-size matrix, call resize() first");
-      eigen_assert(((MatrixType::Options&RowMajorBit) != IsColMajor) && "Wrong storage order");
-      typedef SparseMatrix<bool,MatrixType::Options,typename MatrixType::Index> MatrixPatternType;
-      MatrixPatternType  blockPattern(blockRows(), blockCols());
-      m_nonzeros = 0;
-
-      // First, compute the number of nonzero blocks and their locations
-      for(StorageIndex bj = 0; bj < m_outerBSize; ++bj)
-      {
-        // Browse each outer block and compute the structure
-        std::vector<bool> nzblocksFlag(m_innerBSize,false);  // Record the existing blocks
-        blockPattern.startVec(bj);
-        for(StorageIndex j = blockOuterIndex(bj); j < blockOuterIndex(bj+1); ++j)
-        {
-          typename MatrixType::InnerIterator it_spmat(spmat, j);
-          for(; it_spmat; ++it_spmat)
-          {
-            StorageIndex bi = innerToBlock(it_spmat.index()); // Index of the current nonzero block
-            if(!nzblocksFlag[bi])
-            {
-              // Save the index of this nonzero block
-              nzblocksFlag[bi] = true;
-              blockPattern.insertBackByOuterInnerUnordered(bj, bi) = true;
-              // Compute the total number of nonzeros (including explicit zeros in blocks)
-              m_nonzeros += blockOuterSize(bj) * blockInnerSize(bi);
-            }
-          }
-        } // end current outer block
-      }
-      blockPattern.finalize();
-
-      // Allocate the internal arrays
-      setBlockStructure(blockPattern);
-
-      for(StorageIndex nz = 0; nz < m_nonzeros; ++nz) m_values[nz] = Scalar(0);
-      for(StorageIndex bj = 0; bj < m_outerBSize; ++bj)
-      {
-        // Now copy the values
-        for(StorageIndex j = blockOuterIndex(bj); j < blockOuterIndex(bj+1); ++j)
-        {
-          // Browse the outer block column by column (for column-major matrices)
-          typename MatrixType::InnerIterator it_spmat(spmat, j);
-          for(; it_spmat; ++it_spmat)
-          {
-            StorageIndex idx = 0; // Position of this block in the column block
-            StorageIndex bi = innerToBlock(it_spmat.index()); // Index of the current nonzero block
-            // Go to the inner block where this element belongs to
-            while(bi > m_indices[m_outerIndex[bj]+idx]) ++idx; // Not expensive for ordered blocks
-            StorageIndex idxVal;// Get the right position in the array of values for this element
-            if(m_blockSize == Dynamic)
-            {
-              // Offset from all blocks before ...
-              idxVal =  m_blockPtr[m_outerIndex[bj]+idx];
-              // ... and offset inside the block
-              idxVal += (j - blockOuterIndex(bj)) * blockOuterSize(bj) + it_spmat.index() - m_innerOffset[bi];
-            }
-            else
-            {
-              // All blocks before
-              idxVal = (m_outerIndex[bj] + idx) * m_blockSize * m_blockSize;
-              // inside the block
-              idxVal += (j - blockOuterIndex(bj)) * m_blockSize + (it_spmat.index()%m_blockSize);
-            }
-            // Insert the value
-            m_values[idxVal] = it_spmat.value();
-          } // end of this column
-        } // end of this block
-      } // end of this outer block
-
-      return *this;
-    }
-
-    /**
-      * \brief Set the nonzero block pattern of the matrix
-      *
-      * Given a sparse matrix describing the nonzero block pattern,
-      * this function prepares the internal pointers for values.
-      * After calling this function, any *nonzero* block (bi, bj) can be set
-      * with a simple call to coeffRef(bi,bj).
-      *
-      *
-      * \warning Before calling this function, tt is necessary to call
-      * either setBlockLayout() (matrices with variable-size blocks)
-      * or setBlockSize() (for fixed-size blocks).
-      *
-      * \param blockPattern Sparse matrix of boolean elements describing the block structure
-      *
-      * \sa setBlockLayout() \sa setBlockSize()
-      */
-    template<typename MatrixType>
-    void setBlockStructure(const MatrixType& blockPattern)
-    {
-      resize(blockPattern.rows(), blockPattern.cols());
-      reserve(blockPattern.nonZeros());
-
-      // Browse the block pattern and set up the various pointers
-      m_outerIndex[0] = 0;
-      if(m_blockSize == Dynamic) m_blockPtr[0] = 0;
-      for(StorageIndex nz = 0; nz < m_nonzeros; ++nz) m_values[nz] = Scalar(0);
-      for(StorageIndex bj = 0; bj < m_outerBSize; ++bj)
-      {
-        //Browse each outer block
-
-        //First, copy and save the indices of nonzero blocks
-        //FIXME : find a way to avoid this ...
-        std::vector<int> nzBlockIdx;
-        typename MatrixType::InnerIterator it(blockPattern, bj);
-        for(; it; ++it)
-        {
-          nzBlockIdx.push_back(it.index());
-        }
-        std::sort(nzBlockIdx.begin(), nzBlockIdx.end());
-
-        // Now, fill block indices and (eventually) pointers to blocks
-        for(StorageIndex idx = 0; idx < nzBlockIdx.size(); ++idx)
-        {
-          StorageIndex offset = m_outerIndex[bj]+idx; // offset in m_indices
-          m_indices[offset] = nzBlockIdx[idx];
-          if(m_blockSize == Dynamic)
-            m_blockPtr[offset] = m_blockPtr[offset-1] + blockInnerSize(nzBlockIdx[idx]) * blockOuterSize(bj);
-          // There is no blockPtr for fixed-size blocks... not needed !???
-        }
-        // Save the pointer to the next outer block
-        m_outerIndex[bj+1] = m_outerIndex[bj] + nzBlockIdx.size();
-      }
-    }
-
-    /**
-      * \brief Set the number of rows and columns blocks
-      */
-    inline void resize(Index brow, Index bcol)
-    {
-      m_innerBSize = IsColMajor ? brow : bcol;
-      m_outerBSize = IsColMajor ? bcol : brow;
-    }
-
-    /**
-      * \brief set the block size at runtime for fixed-size block layout
-      *
-      * Call this only for fixed-size blocks
-      */
-    inline void setBlockSize(Index blockSize)
-    {
-      m_blockSize = blockSize;
-    }
-
-    /**
-      * \brief Set the row and column block layouts,
-      *
-      * This function set the size of each row and column block.
-      * So this function should be used only for blocks with variable size.
-      * \param rowBlocks : Number of rows per row block
-      * \param colBlocks : Number of columns per column block
-      * \sa resize(), setBlockSize()
-      */
-    inline void setBlockLayout(const VectorXi& rowBlocks, const VectorXi& colBlocks)
-    {
-      const VectorXi& innerBlocks = IsColMajor ? rowBlocks : colBlocks;
-      const VectorXi& outerBlocks = IsColMajor ? colBlocks : rowBlocks;
-      eigen_assert(m_innerBSize == innerBlocks.size() && "CHECK THE NUMBER OF ROW OR COLUMN BLOCKS");
-      eigen_assert(m_outerBSize == outerBlocks.size() && "CHECK THE NUMBER OF ROW OR COLUMN BLOCKS");
-      m_outerBSize = outerBlocks.size();
-      //  starting index of blocks... cumulative sums
-      m_innerOffset = new StorageIndex[m_innerBSize+1];
-      m_outerOffset = new StorageIndex[m_outerBSize+1];
-      m_innerOffset[0] = 0;
-      m_outerOffset[0] = 0;
-      std::partial_sum(&innerBlocks[0], &innerBlocks[m_innerBSize-1]+1, &m_innerOffset[1]);
-      std::partial_sum(&outerBlocks[0], &outerBlocks[m_outerBSize-1]+1, &m_outerOffset[1]);
-
-      // Compute the total number of nonzeros
-      m_nonzeros = 0;
-      for(StorageIndex bj = 0; bj < m_outerBSize; ++bj)
-        for(StorageIndex bi = 0; bi < m_innerBSize; ++bi)
-          m_nonzeros += outerBlocks[bj] * innerBlocks[bi];
-
-    }
-
-    /**
-      * \brief Allocate the internal array of pointers to blocks and their inner indices
-      *
-      * \note For fixed-size blocks, call setBlockSize() to set the block.
-      * And For variable-size blocks, call setBlockLayout() before using this function
-      *
-      * \param nonzerosblocks Number of nonzero blocks. The total number of nonzeros is
-      * is computed in setBlockLayout() for variable-size blocks
-      * \sa setBlockSize()
-      */
-    inline void reserve(const Index nonzerosblocks)
-    {
-      eigen_assert((m_innerBSize != 0 && m_outerBSize != 0) &&
-          "TRYING TO RESERVE ZERO-SIZE MATRICES, CALL resize() first");
-
-      //FIXME Should free if already allocated
-      m_outerIndex = new StorageIndex[m_outerBSize+1];
-
-      m_nonzerosblocks = nonzerosblocks;
-      if(m_blockSize != Dynamic)
-      {
-        m_nonzeros = nonzerosblocks * (m_blockSize * m_blockSize);
-        m_blockPtr = 0;
-      }
-      else
-      {
-        // m_nonzeros  is already computed in setBlockLayout()
-        m_blockPtr = new StorageIndex[m_nonzerosblocks+1];
-      }
-      m_indices = new StorageIndex[m_nonzerosblocks+1];
-      m_values = new Scalar[m_nonzeros];
-    }
-
-
-    /**
-      * \brief Fill values in a matrix  from a triplet list.
-      *
-      * Each triplet item has a block stored in an Eigen dense matrix.
-      * The InputIterator class should provide the functions row(), col() and value()
-      *
-      * \note For fixed-size blocks, call setBlockSize() before this function.
-      *
-      * FIXME Do not accept duplicates
-      */
-    template<typename InputIterator>
-    void setFromTriplets(const InputIterator& begin, const InputIterator& end)
-    {
-      eigen_assert((m_innerBSize!=0 && m_outerBSize !=0) && "ZERO BLOCKS, PLEASE CALL resize() before");
-
-      /* First, sort the triplet list
-        * FIXME This can be unnecessarily expensive since only the inner indices have to be sorted
-        * The best approach is like in SparseMatrix::setFromTriplets()
-        */
-      internal::TripletComp<InputIterator, IsColMajor> tripletcomp;
-      std::sort(begin, end, tripletcomp);
-
-      /* Count the number of rows and column blocks,
-       * and the number of nonzero blocks per outer dimension
-       */
-      VectorXi rowBlocks(m_innerBSize); // Size of each block row
-      VectorXi colBlocks(m_outerBSize); // Size of each block column
-      rowBlocks.setZero(); colBlocks.setZero();
-      VectorXi nzblock_outer(m_outerBSize); // Number of nz blocks per outer vector
-      VectorXi nz_outer(m_outerBSize); // Number of nz per outer vector...for variable-size blocks
-      nzblock_outer.setZero();
-      nz_outer.setZero();
-      for(InputIterator it(begin); it !=end; ++it)
-      {
-        eigen_assert(it->row() >= 0 && it->row() < this->blockRows() && it->col() >= 0 && it->col() < this->blockCols());
-        eigen_assert((it->value().rows() == it->value().cols() && (it->value().rows() == m_blockSize))
-                     || (m_blockSize == Dynamic));
-
-        if(m_blockSize == Dynamic)
-        {
-          eigen_assert((rowBlocks[it->row()] == 0 || rowBlocks[it->row()] == it->value().rows()) &&
-              "NON CORRESPONDING SIZES FOR ROW BLOCKS");
-          eigen_assert((colBlocks[it->col()] == 0 || colBlocks[it->col()] == it->value().cols()) &&
-              "NON CORRESPONDING SIZES FOR COLUMN BLOCKS");
-          rowBlocks[it->row()] =it->value().rows();
-          colBlocks[it->col()] = it->value().cols();
-        }
-        nz_outer(IsColMajor ? it->col() : it->row()) += it->value().rows() * it->value().cols();
-        nzblock_outer(IsColMajor ? it->col() : it->row())++;
-      }
-      // Allocate member arrays
-      if(m_blockSize == Dynamic) setBlockLayout(rowBlocks, colBlocks);
-      StorageIndex nzblocks = nzblock_outer.sum();
-      reserve(nzblocks);
-
-       // Temporary markers
-      VectorXi block_id(m_outerBSize); // To be used as a block marker during insertion
-
-      // Setup outer index pointers and markers
-      m_outerIndex[0] = 0;
-      if (m_blockSize == Dynamic)  m_blockPtr[0] =  0;
-      for(StorageIndex bj = 0; bj < m_outerBSize; ++bj)
-      {
-        m_outerIndex[bj+1] = m_outerIndex[bj] + nzblock_outer(bj);
-        block_id(bj) = m_outerIndex[bj];
-        if(m_blockSize==Dynamic)
-        {
-          m_blockPtr[m_outerIndex[bj+1]] = m_blockPtr[m_outerIndex[bj]] + nz_outer(bj);
-        }
-      }
-
-      // Fill the matrix
-      for(InputIterator it(begin); it!=end; ++it)
-      {
-        StorageIndex outer = IsColMajor ? it->col() : it->row();
-        StorageIndex inner = IsColMajor ? it->row() : it->col();
-        m_indices[block_id(outer)] = inner;
-        StorageIndex block_size = it->value().rows()*it->value().cols();
-        StorageIndex nz_marker = blockPtr(block_id[outer]);
-        memcpy(&(m_values[nz_marker]), it->value().data(), block_size * sizeof(Scalar));
-        if(m_blockSize == Dynamic)
-        {
-          m_blockPtr[block_id(outer)+1] = m_blockPtr[block_id(outer)] + block_size;
-        }
-        block_id(outer)++;
-      }
-
-      // An alternative when the outer indices are sorted...no need to use an array of markers
-//      for(Index bcol = 0; bcol < m_outerBSize; ++bcol)
-//      {
-//      Index id = 0, id_nz = 0, id_nzblock = 0;
-//      for(InputIterator it(begin); it!=end; ++it)
-//      {
-//        while (id<bcol) // one pass should do the job unless there are empty columns
-//        {
-//          id++;
-//          m_outerIndex[id+1]=m_outerIndex[id];
-//        }
-//        m_outerIndex[id+1] += 1;
-//        m_indices[id_nzblock]=brow;
-//        Index block_size = it->value().rows()*it->value().cols();
-//        m_blockPtr[id_nzblock+1] = m_blockPtr[id_nzblock] + block_size;
-//        id_nzblock++;
-//        memcpy(&(m_values[id_nz]),it->value().data(), block_size*sizeof(Scalar));
-//        id_nz += block_size;
-//      }
-//      while(id < m_outerBSize-1) // Empty columns at the end
-//      {
-//        id++;
-//        m_outerIndex[id+1]=m_outerIndex[id];
-//      }
-//      }
-    }
-
-
-    /**
-      * \returns the number of rows
-      */
-    inline Index rows() const
-    {
-//      return blockRows();
-      return (IsColMajor ? innerSize() : outerSize());
-    }
-
-    /**
-      * \returns the number of cols
-      */
-    inline Index cols() const
-    {
-//      return blockCols();
-      return (IsColMajor ? outerSize() : innerSize());
-    }
-
-    inline Index innerSize() const
-    {
-      if(m_blockSize == Dynamic) return m_innerOffset[m_innerBSize];
-      else return  (m_innerBSize * m_blockSize) ;
-    }
-
-    inline Index outerSize() const
-    {
-      if(m_blockSize == Dynamic) return m_outerOffset[m_outerBSize];
-      else return  (m_outerBSize * m_blockSize) ;
-    }
-    /** \returns the number of rows grouped by blocks */
-    inline Index blockRows() const
-    {
-      return (IsColMajor ? m_innerBSize : m_outerBSize);
-    }
-    /** \returns the number of columns grouped by blocks */
-    inline Index blockCols() const
-    {
-      return (IsColMajor ? m_outerBSize : m_innerBSize);
-    }
-
-    inline Index outerBlocks() const { return m_outerBSize; }
-    inline Index innerBlocks() const { return m_innerBSize; }
-
-    /** \returns the block index where outer belongs to */
-    inline Index outerToBlock(Index outer) const
-    {
-      eigen_assert(outer < outerSize() && "OUTER INDEX OUT OF BOUNDS");
-
-      if(m_blockSize != Dynamic)
-        return (outer / m_blockSize); // Integer division
-
-      StorageIndex b_outer = 0;
-      while(m_outerOffset[b_outer] <= outer) ++b_outer;
-      return b_outer - 1;
-    }
-    /** \returns  the block index where inner belongs to */
-    inline Index innerToBlock(Index inner) const
-    {
-      eigen_assert(inner < innerSize() && "OUTER INDEX OUT OF BOUNDS");
-
-      if(m_blockSize != Dynamic)
-        return (inner / m_blockSize); // Integer division
-
-      StorageIndex b_inner = 0;
-      while(m_innerOffset[b_inner] <= inner) ++b_inner;
-      return b_inner - 1;
-    }
-
-    /**
-      *\returns a reference to the (i,j) block as an Eigen Dense Matrix
-      */
-    Ref<BlockScalar> coeffRef(Index brow, Index bcol)
-    {
-      eigen_assert(brow < blockRows() && "BLOCK ROW INDEX OUT OF BOUNDS");
-      eigen_assert(bcol < blockCols() && "BLOCK nzblocksFlagCOLUMN OUT OF BOUNDS");
-
-      StorageIndex rsize = IsColMajor ? blockInnerSize(brow): blockOuterSize(bcol);
-      StorageIndex csize = IsColMajor ? blockOuterSize(bcol) : blockInnerSize(brow);
-      StorageIndex inner = IsColMajor ? brow : bcol;
-      StorageIndex outer = IsColMajor ? bcol : brow;
-      StorageIndex offset = m_outerIndex[outer];
-      while(offset < m_outerIndex[outer+1] && m_indices[offset] != inner)
-        offset++;
-      if(m_indices[offset] == inner)
-      {
-        return Map<BlockScalar>(&(m_values[blockPtr(offset)]), rsize, csize);
-      }
-      else
-      {
-        //FIXME the block does not exist, Insert it !!!!!!!!!
-        eigen_assert("DYNAMIC INSERTION IS NOT YET SUPPORTED");
-      }
-    }
-
-    /**
-      * \returns the value of the (i,j) block as an Eigen Dense Matrix
-      */
-    Map<const BlockScalar> coeff(Index brow, Index bcol) const
-    {
-      eigen_assert(brow < blockRows() && "BLOCK ROW INDEX OUT OF BOUNDS");
-      eigen_assert(bcol < blockCols() && "BLOCK COLUMN OUT OF BOUNDS");
-
-      StorageIndex rsize = IsColMajor ? blockInnerSize(brow): blockOuterSize(bcol);
-      StorageIndex csize = IsColMajor ? blockOuterSize(bcol) : blockInnerSize(brow);
-      StorageIndex inner = IsColMajor ? brow : bcol;
-      StorageIndex outer = IsColMajor ? bcol : brow;
-      StorageIndex offset = m_outerIndex[outer];
-      while(offset < m_outerIndex[outer+1] && m_indices[offset] != inner) offset++;
-      if(m_indices[offset] == inner)
-      {
-        return Map<const BlockScalar> (&(m_values[blockPtr(offset)]), rsize, csize);
-      }
-      else
-//        return BlockScalar::Zero(rsize, csize);
-        eigen_assert("NOT YET SUPPORTED");
-    }
-
-    // Block Matrix times vector product
-    template<typename VecType>
-    BlockSparseTimeDenseProduct<BlockSparseMatrix, VecType> operator*(const VecType& lhs) const
-    {
-      return BlockSparseTimeDenseProduct<BlockSparseMatrix, VecType>(*this, lhs);
-    }
-
-    /** \returns the number of nonzero blocks */
-    inline Index nonZerosBlocks() const { return m_nonzerosblocks; }
-    /** \returns the total number of nonzero elements, including eventual explicit zeros in blocks */
-    inline Index nonZeros() const { return m_nonzeros; }
-
-    inline BlockScalarReturnType *valuePtr() {return static_cast<BlockScalarReturnType *>(m_values);}
-//    inline Scalar *valuePtr(){ return m_values; }
-    inline StorageIndex *innerIndexPtr() {return m_indices; }
-    inline const StorageIndex *innerIndexPtr() const {return m_indices; }
-    inline StorageIndex *outerIndexPtr() {return m_outerIndex; }
-    inline const StorageIndex* outerIndexPtr() const {return m_outerIndex; }
-
-    /** \brief for compatibility purposes with the SparseMatrix class */
-    inline bool isCompressed() const {return true;}
-    /**
-      * \returns the starting index of the bi row block
-      */
-    inline Index blockRowsIndex(Index bi) const
-    {
-      return IsColMajor ? blockInnerIndex(bi) : blockOuterIndex(bi);
-    }
-
-    /**
-      * \returns the starting index of the bj col block
-      */
-    inline Index blockColsIndex(Index bj) const
-    {
-      return IsColMajor ? blockOuterIndex(bj) : blockInnerIndex(bj);
-    }
-
-    inline Index blockOuterIndex(Index bj) const
-    {
-      return (m_blockSize == Dynamic) ? m_outerOffset[bj] : (bj * m_blockSize);
-    }
-    inline Index blockInnerIndex(Index bi) const
-    {
-      return (m_blockSize == Dynamic) ? m_innerOffset[bi] : (bi * m_blockSize);
-    }
-
-    // Not needed ???
-    inline Index blockInnerSize(Index bi) const
-    {
-      return (m_blockSize == Dynamic) ? (m_innerOffset[bi+1] - m_innerOffset[bi]) : m_blockSize;
-    }
-    inline Index blockOuterSize(Index bj) const
-    {
-      return (m_blockSize == Dynamic) ? (m_outerOffset[bj+1]- m_outerOffset[bj]) : m_blockSize;
-    }
-
-    /**
-      * \brief Browse the matrix by outer index
-      */
-    class InnerIterator; // Browse column by column
-
-    /**
-      * \brief Browse the matrix by block outer index
-      */
-    class BlockInnerIterator; // Browse block by block
-
-    friend std::ostream & operator << (std::ostream & s, const BlockSparseMatrix& m)
-    {
-      for (StorageIndex j = 0; j < m.outerBlocks(); ++j)
-      {
-        BlockInnerIterator itb(m, j);
-        for(; itb; ++itb)
-        {
-          s << "("<<itb.row() << ", " << itb.col() << ")\n";
-          s << itb.value() <<"\n";
-        }
-      }
-      s << std::endl;
-      return s;
-    }
-
-    /**
-      * \returns the starting position of the block \p id in the array of values
-      */
-    Index blockPtr(Index id) const
-    {
-      if(m_blockSize == Dynamic) return m_blockPtr[id];
-      else return id * m_blockSize * m_blockSize;
-      //return blockDynIdx(id, typename internal::conditional<(BlockSize==Dynamic), internal::true_type, internal::false_type>::type());
-    }
-
-
-  protected:
-//    inline Index blockDynIdx(Index id, internal::true_type) const
-//    {
-//      return m_blockPtr[id];
-//    }
-//    inline Index blockDynIdx(Index id, internal::false_type) const
-//    {
-//      return id * BlockSize * BlockSize;
-//    }
-
-    // To be implemented
-    // Insert a block at a particular location... need to make a room for that
-    Map<BlockScalar> insert(Index brow, Index bcol);
-
-    Index m_innerBSize; // Number of block rows
-    Index m_outerBSize; // Number of block columns
-    StorageIndex *m_innerOffset; // Starting index of each inner block (size m_innerBSize+1)
-    StorageIndex *m_outerOffset; // Starting index of each outer block (size m_outerBSize+1)
-    Index m_nonzerosblocks; // Total nonzeros blocks (lower than  m_innerBSize x m_outerBSize)
-    Index m_nonzeros; // Total nonzeros elements
-    Scalar *m_values; //Values stored block column after block column (size m_nonzeros)
-    StorageIndex *m_blockPtr; // Pointer to the beginning of each block in m_values, size m_nonzeroblocks ... null for fixed-size blocks
-    StorageIndex *m_indices; //Inner block indices, size m_nonzerosblocks ... OK
-    StorageIndex *m_outerIndex; // Starting pointer of each block column in m_indices (size m_outerBSize)... OK
-    Index m_blockSize; // Size of a block for fixed-size blocks, otherwise -1
-};
-
-template<typename _Scalar, int _BlockAtCompileTime, int _Options, typename _StorageIndex>
-class BlockSparseMatrix<_Scalar, _BlockAtCompileTime, _Options, _StorageIndex>::BlockInnerIterator
-{
-  public:
-
-    enum{
-      Flags = _Options
-    };
-
-    BlockInnerIterator(const BlockSparseMatrix& mat, const Index outer)
-    : m_mat(mat),m_outer(outer),
-      m_id(mat.m_outerIndex[outer]),
-      m_end(mat.m_outerIndex[outer+1])
-    {
-    }
-
-    inline BlockInnerIterator& operator++() {m_id++; return *this; }
-
-    inline const Map<const BlockScalar> value() const
-    {
-      return Map<const BlockScalar>(&(m_mat.m_values[m_mat.blockPtr(m_id)]),
-          rows(),cols());
-    }
-    inline Map<BlockScalar> valueRef()
-    {
-      return Map<BlockScalar>(&(m_mat.m_values[m_mat.blockPtr(m_id)]),
-          rows(),cols());
-    }
-    // Block inner index
-    inline Index index() const {return m_mat.m_indices[m_id]; }
-    inline Index outer() const { return m_outer; }
-    // block row index
-    inline Index row() const  {return index(); }
-    // block column index
-    inline Index col() const {return outer(); }
-    // FIXME Number of rows in the current block
-    inline Index rows() const { return (m_mat.m_blockSize==Dynamic) ? (m_mat.m_innerOffset[index()+1] - m_mat.m_innerOffset[index()]) : m_mat.m_blockSize; }
-    // Number of columns in the current block ...
-    inline Index cols() const { return (m_mat.m_blockSize==Dynamic) ? (m_mat.m_outerOffset[m_outer+1]-m_mat.m_outerOffset[m_outer]) : m_mat.m_blockSize;}
-    inline operator bool() const { return (m_id < m_end); }
-
-  protected:
-    const BlockSparseMatrix<_Scalar, _BlockAtCompileTime, _Options, StorageIndex>& m_mat;
-    const Index m_outer;
-    Index m_id;
-    Index m_end;
-};
-
-template<typename _Scalar, int _BlockAtCompileTime, int _Options, typename _StorageIndex>
-class BlockSparseMatrix<_Scalar, _BlockAtCompileTime, _Options, _StorageIndex>::InnerIterator
-{
-  public:
-    InnerIterator(const BlockSparseMatrix& mat, Index outer)
-    : m_mat(mat),m_outerB(mat.outerToBlock(outer)),m_outer(outer),
-      itb(mat, mat.outerToBlock(outer)),
-      m_offset(outer - mat.blockOuterIndex(m_outerB))
-     {
-        if (itb)
-        {
-          m_id = m_mat.blockInnerIndex(itb.index());
-          m_start = m_id;
-          m_end = m_mat.blockInnerIndex(itb.index()+1);
-        }
-     }
-    inline InnerIterator& operator++()
-    {
-      m_id++;
-      if (m_id >= m_end)
-      {
-        ++itb;
-        if (itb)
-        {
-          m_id = m_mat.blockInnerIndex(itb.index());
-          m_start = m_id;
-          m_end = m_mat.blockInnerIndex(itb.index()+1);
-        }
-      }
-      return *this;
-    }
-    inline const Scalar& value() const
-    {
-      return itb.value().coeff(m_id - m_start, m_offset);
-    }
-    inline Scalar& valueRef()
-    {
-      return itb.valueRef().coeff(m_id - m_start, m_offset);
-    }
-    inline Index index() const { return m_id; }
-    inline Index outer() const {return m_outer; }
-    inline Index col() const {return outer(); }
-    inline Index row() const { return index();}
-    inline operator bool() const
-    {
-      return itb;
-    }
-  protected:
-    const BlockSparseMatrix& m_mat;
-    const Index m_outer;
-    const Index m_outerB;
-    BlockInnerIterator itb; // Iterator through the blocks
-    const Index m_offset; // Position of this column in the block
-    Index m_start; // starting inner index of this block
-    Index m_id; // current inner index in the block
-    Index m_end; // starting inner index of the next block
-
-};
-} // end namespace Eigen
-
-#endif // EIGEN_SPARSEBLOCKMATRIX_H