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various work on the Sparse module:

Browse Source 
* added some glue to Eigen/Core (SparseBit, ei_eval, Matrix)
* add two new sparse matrix types:
   HashMatrix: based on std::map (for random writes)
   LinkedVectorMatrix: array of linked vectors
   (for outer coherent writes, e.g. to transpose a matrix)
* add a SparseSetter class to easily set/update any kind of matrices, e.g.:
   { SparseSetter<MatrixType,RandomAccessPattern> wrapper(mymatrix);
     for (...) wrapper->coeffRef(rand(),rand()) = rand(); }
* automatic shallow copy for RValue
* and a lot of mess !
plus:
* remove the remaining ArrayBit related stuff
* don't use alloca in product for very large memory allocation
This commit is contained in:
Gael Guennebaud
2008-06-26 23:22:26 +00:00
parent c5bd1703cb
commit e5d301dc96
17 changed files with 1226 additions and 169 deletions
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41
Eigen/src/Sparse/CoreIterators.h
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@@ -25,30 +25,47 @@
#ifndef EIGEN_COREITERATORS_H
#define EIGEN_COREITERATORS_H
/* This file contains the respective InnerIterator definition of the expressions defined in Eigen/Core
*/
template<typename Derived>
class MatrixBase<Derived>::InnerIterator
{
typedef typename Derived::Scalar Scalar;
public:
InnerIterator(const Derived& mat, int col)
: m_matrix(mat), m_row(0), m_col(col), m_end(mat.rows())
InnerIterator(const Derived& mat, int outer)
: m_matrix(mat), m_inner(0), m_outer(outer), m_end(mat.rows())
{}
Scalar value() { return m_matrix.coeff(m_row, m_col); }
Scalar value()
{
return (Derived::Flags&RowMajorBit) ? m_matrix.coeff(m_outer, m_inner)
: m_matrix.coeff(m_inner, m_outer);
}
InnerIterator& operator++() { m_row++; return *this; }
InnerIterator& operator++() { m_inner++; return *this; }
int index() const { return m_row; }
int index() const { return m_inner; }
operator bool() const { return m_row < m_end && m_row>=0; }
operator bool() const { return m_inner < m_end && m_inner>=0; }
protected:
const Derived& m_matrix;
int m_row;
const int m_col;
int m_inner;
const int m_outer;
const int m_end;
};
template<typename MatrixType>
class Transpose<MatrixType>::InnerIterator : public MatrixType::InnerIterator
{
public:
InnerIterator(const Transpose& trans, int outer)
: MatrixType::InnerIterator(trans.m_matrix, outer)
{}
};
template<typename UnaryOp, typename MatrixType>
class CwiseUnaryOp<UnaryOp,MatrixType>::InnerIterator
{
@@ -57,8 +74,8 @@ class CwiseUnaryOp<UnaryOp,MatrixType>::InnerIterator
typedef typename _MatrixTypeNested::InnerIterator MatrixTypeIterator;
public:
InnerIterator(const CwiseUnaryOp& unaryOp, int col)
: m_iter(unaryOp.m_matrix,col), m_functor(unaryOp.m_functor), m_id(-1)
InnerIterator(const CwiseUnaryOp& unaryOp, int outer)
: m_iter(unaryOp.m_matrix,outer), m_functor(unaryOp.m_functor), m_id(-1)
{
this->operator++();
}
@@ -101,8 +118,8 @@ class CwiseBinaryOp<BinaryOp,Lhs,Rhs>::InnerIterator
typedef typename _RhsNested::InnerIterator RhsIterator;
public:
InnerIterator(const CwiseBinaryOp& binOp, int col)
: m_lhsIter(binOp.m_lhs,col), m_rhsIter(binOp.m_rhs,col), m_functor(binOp.m_functor), m_id(-1)
InnerIterator(const CwiseBinaryOp& binOp, int outer)
: m_lhsIter(binOp.m_lhs,outer), m_rhsIter(binOp.m_rhs,outer), m_functor(binOp.m_functor), m_id(-1)
{
this->operator++();
}

165
Eigen/src/Sparse/HashMatrix.h Normal file
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@@ -0,0 +1,165 @@
// This file is part of Eigen, a lightweight C++ template library
// for linear algebra. Eigen itself is part of the KDE project.
//
// Copyright (C) 2008 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_HASHMATRIX_H
#define EIGEN_HASHMATRIX_H
template<typename _Scalar, int _Flags>
struct ei_traits<HashMatrix<_Scalar, _Flags> >
{
typedef _Scalar Scalar;
enum {
RowsAtCompileTime = Dynamic,
ColsAtCompileTime = Dynamic,
MaxRowsAtCompileTime = Dynamic,
MaxColsAtCompileTime = Dynamic,
Flags = _Flags,
CoeffReadCost = NumTraits<Scalar>::ReadCost,
SupportedAccessPatterns = RandomAccessPattern
};
};
// TODO reimplement this class using custom linked lists
template<typename _Scalar, int _Flags>
class HashMatrix : public SparseMatrixBase<HashMatrix<_Scalar, _Flags> >
{
public:
EIGEN_GENERIC_PUBLIC_INTERFACE(HashMatrix)
class InnerIterator;
protected:
typedef typename std::map<int, Scalar>::iterator MapIterator;
typedef typename std::map<int, Scalar>::const_iterator ConstMapIterator;
public:
inline int rows() const { return m_innerSize; }
inline int cols() const { return m_data.size(); }
inline const Scalar& coeff(int row, int col) const
{
const MapIterator it = m_data[col].find(row);
if (it!=m_data[col].end())
return Scalar(0);
return it->second;
}
inline Scalar& coeffRef(int row, int col)
{
return m_data[col][row];
}
public:
inline void startFill(int reserveSize = 1000) {}
inline Scalar& fill(int row, int col) { return coeffRef(row, col); }
inline void endFill() {}
~HashMatrix()
{}
inline void shallowCopy(const HashMatrix& other)
{
EIGEN_DBG_SPARSE(std::cout << "HashMatrix:: shallowCopy\n");
// FIXME implement a true shallow copy !!
resize(other.rows(), other.cols());
for (int j=0; j<this->outerSize(); ++j)
m_data[j] = other.m_data[j];
}
void resize(int _rows, int _cols)
{
if (cols() != _cols)
{
m_data.resize(_cols);
}
m_innerSize = _rows;
}
inline HashMatrix(int rows, int cols)
: m_innerSize(0)
{
resize(rows, cols);
}
template<typename OtherDerived>
inline HashMatrix(const MatrixBase<OtherDerived>& other)
: m_innerSize(0)
{
*this = other.derived();
}
inline HashMatrix& operator=(const HashMatrix& other)
{
if (other.isRValue())
{
shallowCopy(other);
}
else
{
resize(other.rows(), other.cols());
for (int col=0; col<cols(); ++col)
m_data[col] = other.m_data[col];
}
return *this;
}
template<typename OtherDerived>
inline HashMatrix& operator=(const MatrixBase<OtherDerived>& other)
{
return SparseMatrixBase<HashMatrix>::operator=(other);
}
protected:
std::vector<std::map<int, Scalar> > m_data;
int m_innerSize;
};
template<typename Scalar, int _Flags>
class HashMatrix<Scalar,_Flags>::InnerIterator
{
public:
InnerIterator(const HashMatrix& mat, int col)
: m_matrix(mat), m_it(mat.m_data[col].begin()), m_end(mat.m_data[col].end())
{}
InnerIterator& operator++() { m_it++; return *this; }
Scalar value() { return m_it->second; }
int index() const { return m_it->first; }
operator bool() const { return m_it!=m_end; }
protected:
const HashMatrix& m_matrix;
typename HashMatrix::ConstMapIterator m_it;
typename HashMatrix::ConstMapIterator m_end;
};
#endif // EIGEN_HASHMATRIX_H

288
Eigen/src/Sparse/LinkedVectorMatrix.h Normal file
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@@ -0,0 +1,288 @@
// This file is part of Eigen, a lightweight C++ template library
// for linear algebra. Eigen itself is part of the KDE project.
//
// Copyright (C) 2008 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_LINKEDVECTORMATRIX_H
#define EIGEN_LINKEDVECTORMATRIX_H
template<typename _Scalar, int _Flags>
struct ei_traits<LinkedVectorMatrix<_Scalar,_Flags> >
{
typedef _Scalar Scalar;
enum {
RowsAtCompileTime = Dynamic,
ColsAtCompileTime = Dynamic,
MaxRowsAtCompileTime = Dynamic,
MaxColsAtCompileTime = Dynamic,
Flags = _Flags,
CoeffReadCost = NumTraits<Scalar>::ReadCost,
SupportedAccessPatterns = InnerCoherentAccessPattern
};
};
template<typename Element, int BlockSize = 8>
struct LinkedVector
{
LinkedVector() : size(0), next(0), prev(0) {}
Element data[BlockSize];
LinkedVector* next;
LinkedVector* prev;
int size;
bool isFull() const { return size==BlockSize; }
};
template<typename _Scalar, int _Flags>
class LinkedVectorMatrix : public SparseMatrixBase<LinkedVectorMatrix<_Scalar,_Flags> >
{
public:
EIGEN_GENERIC_PUBLIC_INTERFACE(LinkedVectorMatrix)
class InnerIterator;
protected:
enum {
RowMajor = Flags&RowMajorBit ? 1 : 0
};
struct ValueIndex
{
ValueIndex() : value(0), index(0) {}
ValueIndex(Scalar v, int i) : value(v), index(i) {}
Scalar value;
int index;
};
typedef LinkedVector<ValueIndex,8> LinkedVectorBlock;
inline int find(LinkedVectorBlock** _el, int id)
{
LinkedVectorBlock* el = *_el;
while (el && el->data[el->size-1].index<id)
el = el->next;
*_el = el;
if (el)
{
// binary search
int maxI = el->size-1;
int minI = 0;
int i = el->size/2;
const ValueIndex* data = el->data;
while (data[i].index!=id)
{
if (data[i].index<id)
{
minI = i+1;
i = (maxI + minI)+2;
}
else
{
maxI = i-1;
i = (maxI + minI)+2;
}
if (minI>=maxI)
return -1;
}
if (data[i].index==id)
return i;
}
return -1;
}
public:
inline int rows() const { return RowMajor ? m_data.size() : m_innerSize; }
inline int cols() const { return RowMajor ? m_innerSize : m_data.size(); }
inline const Scalar& coeff(int row, int col) const
{
const int outer = RowMajor ? row : col;
const int inner = RowMajor ? col : row;
LinkedVectorBlock* el = m_data[outer];
int id = find(&el, inner);
if (id<0)
return Scalar(0);
return el->data[id].value;
}
inline Scalar& coeffRef(int row, int col)
{
const int outer = RowMajor ? row : col;
const int inner = RowMajor ? col : row;
LinkedVectorBlock* el = m_data[outer];
int id = find(&el, inner);
ei_assert(id>=0);
// if (id<0)
// return Scalar(0);
return el->data[id].value;
}
public:
inline void startFill(int reserveSize = 1000)
{
clear();
for (int i=0; i<m_data.size(); ++i)
m_ends[i] = m_data[i] = 0;
}
inline Scalar& fill(int row, int col)
{
const int outer = RowMajor ? row : col;
const int inner = RowMajor ? col : row;
if (m_ends[outer]==0)
{
m_data[outer] = m_ends[outer] = new LinkedVectorBlock();
}
else
{
ei_assert(m_ends[outer]->data[m_ends[outer]->size-1].index < inner);
if (m_ends[outer]->isFull())
{
LinkedVectorBlock* el = new LinkedVectorBlock();
m_ends[outer]->next = el;
el->prev = m_ends[outer];
m_ends[outer] = el;
}
}
m_ends[outer]->data[m_ends[outer]->size].index = inner;
return m_ends[outer]->data[m_ends[outer]->size++].value;
}
inline void endFill()
{
}
~LinkedVectorMatrix()
{
if (this->isNotShared())
clear();
}
void clear()
{
for (int i=0; i<m_data.size(); ++i)
{
LinkedVectorBlock* el = m_data[i];
while (el)
{
LinkedVectorBlock* tmp = el;
el = el->next;
delete tmp;
}
}
}
void resize(int rows, int cols)
{
const int outers = RowMajor ? rows : cols;
const int inners = RowMajor ? cols : rows;
if (this->outerSize() != outers)
{
clear();
m_data.resize(outers);
m_ends.resize(outers);
for (int i=0; i<m_data.size(); ++i)
m_ends[i] = m_data[i] = 0;
}
m_innerSize = inners;
}
inline LinkedVectorMatrix(int rows, int cols)
: m_innerSize(0)
{
resize(rows, cols);
}
template<typename OtherDerived>
inline LinkedVectorMatrix(const MatrixBase<OtherDerived>& other)
: m_innerSize(0)
{
*this = other.derived();
}
inline void shallowCopy(const LinkedVectorMatrix& other)
{
EIGEN_DBG_SPARSE(std::cout << "LinkedVectorMatrix:: shallowCopy\n");
resize(other.rows(), other.cols());
for (int j=0; j<this->outerSize(); ++j)
{
m_data[j] = other.m_data[j];
m_ends[j] = other.m_ends[j];
}
other.markAsCopied();
}
inline LinkedVectorMatrix& operator=(const LinkedVectorMatrix& other)
{
if (other.isRValue())
{
shallowCopy(other);
return *this;
}
else
{
// TODO implement a specialized deep copy here
return operator=<LinkedVectorMatrix>(other);
}
}
template<typename OtherDerived>
inline LinkedVectorMatrix& operator=(const MatrixBase<OtherDerived>& other)
{
return SparseMatrixBase<LinkedVectorMatrix>::operator=(other.derived());
}
protected:
std::vector<LinkedVectorBlock*> m_data;
std::vector<LinkedVectorBlock*> m_ends;
int m_innerSize;
};
template<typename Scalar, int _Flags>
class LinkedVectorMatrix<Scalar,_Flags>::InnerIterator
{
public:
InnerIterator(const LinkedVectorMatrix& mat, int col)
: m_matrix(mat), m_el(mat.m_data[col]), m_it(0)
{}
InnerIterator& operator++() { if (m_it<m_el->size) m_it++; else {m_el = m_el->next; m_it=0;}; return *this; }
Scalar value() { return m_el->data[m_it].value; }
int index() const { return m_el->data[m_it].index; }
operator bool() const { return m_el && (m_el->next || m_it<m_el->size); }
protected:
const LinkedVectorMatrix& m_matrix;
LinkedVectorBlock* m_el;
int m_it;
};
#endif // EIGEN_LINKEDVECTORMATRIX_H

32
Eigen/src/Sparse/SparseArray.h
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@@ -32,11 +32,11 @@ template<typename Scalar> class SparseArray
{
public:
SparseArray()
: m_values(0), m_indices(0), m_size(0), m_allocatedSize(0)
: m_values(0), m_indices(0), m_size(0), m_allocatedSize(0), m_isShared(0)
{}
SparseArray(int size)
: m_values(0), m_indices(0), m_size(0), m_allocatedSize(0)
: m_values(0), m_indices(0), m_size(0), m_allocatedSize(0), m_isShared(0)
{
resize(size);
}
@@ -51,6 +51,28 @@ template<typename Scalar> class SparseArray
resize(other.size());
memcpy(m_values, other.m_values, m_size * sizeof(Scalar));
memcpy(m_indices, other.m_indices, m_size * sizeof(int));
m_isShared = 0;
}
void shallowCopy(const SparseArray& other)
{
delete[] m_values;
delete[] m_indices;
m_values = other.m_values;
m_indices = other.m_indices;
m_size = other.m_size;
m_allocatedSize = other.m_allocatedSize;
m_isShared = false;
other.m_isShared = true;
}
~SparseArray()
{
if (!m_isShared)
{
delete[] m_values;
delete[] m_indices;
}
}
void reserve(int size)
@@ -117,7 +139,11 @@ template<typename Scalar> class SparseArray
Scalar* m_values;
int* m_indices;
int m_size;
int m_allocatedSize;
struct {
int m_allocatedSize:31;
mutable int m_isShared:1;
};
};
#endif // EIGEN_SPARSE_ARRAY_H

198
Eigen/src/Sparse/SparseMatrix.h
View File

@@ -25,8 +25,6 @@
#ifndef EIGEN_SPARSEMATRIX_H
#define EIGEN_SPARSEMATRIX_H
template<typename _Scalar> class SparseMatrix;
/** \class SparseMatrix
*
* \brief Sparse matrix
@@ -36,8 +34,8 @@ template<typename _Scalar> class SparseMatrix;
* See http://www.netlib.org/linalg/html_templates/node91.html for details on the storage scheme.
*
*/
template<typename _Scalar>
struct ei_traits<SparseMatrix<_Scalar> >
template<typename _Scalar, int _Flags>
struct ei_traits<SparseMatrix<_Scalar, _Flags> >
{
typedef _Scalar Scalar;
enum {
@@ -45,13 +43,16 @@ struct ei_traits<SparseMatrix<_Scalar> >
ColsAtCompileTime = Dynamic,
MaxRowsAtCompileTime = Dynamic,
MaxColsAtCompileTime = Dynamic,
Flags = 0,
CoeffReadCost = NumTraits<Scalar>::ReadCost
Flags = _Flags,
CoeffReadCost = NumTraits<Scalar>::ReadCost,
SupportedAccessPatterns = FullyCoherentAccessPattern
};
};
template<typename _Scalar>
class SparseMatrix : public MatrixBase<SparseMatrix<_Scalar> >
template<typename _Scalar, int _Flags>
class SparseMatrix : public SparseMatrixBase<SparseMatrix<_Scalar, _Flags> >
{
public:
EIGEN_GENERIC_PUBLIC_INTERFACE(SparseMatrix)
@@ -63,6 +64,8 @@ class SparseMatrix : public MatrixBase<SparseMatrix<_Scalar> >
int m_rows;
int m_cols;
public:
inline int rows() const { return m_rows; }
inline int cols() const { return m_cols; }
@@ -81,8 +84,8 @@ class SparseMatrix : public MatrixBase<SparseMatrix<_Scalar> >
inline Scalar& coeffRef(int row, int col)
{
int id = m_colPtrs[cols];
int end = m_colPtrs[cols+1];
int id = m_colPtrs[col];
int end = m_colPtrs[col+1];
while (id<end && m_data.index(id)!=row)
{
++id;
@@ -95,21 +98,9 @@ class SparseMatrix : public MatrixBase<SparseMatrix<_Scalar> >
class InnerIterator;
inline int rows() const { return rows(); }
inline int cols() const { return cols(); }
/** \returns the number of non zero coefficients */
inline int nonZeros() const { return m_data.size(); }
inline const Scalar& operator() (int row, int col) const
{
return coeff(row, col);
}
inline Scalar& operator() (int row, int col)
{
return coeffRef(row, col);
}
inline void startFill(int reserveSize = 1000)
{
m_data.clear();
@@ -170,143 +161,80 @@ class SparseMatrix : public MatrixBase<SparseMatrix<_Scalar> >
resize(rows, cols);
}
inline void shallowCopy(const SparseMatrix& other)
{
EIGEN_DBG_SPARSE(std::cout << "SparseMatrix:: shallowCopy\n");
delete[] m_colPtrs;
m_colPtrs = 0;
m_rows = other.rows();
m_cols = other.cols();
m_colPtrs = other.m_colPtrs;
m_data.shallowCopy(other.m_data);
other.markAsCopied();
}
inline SparseMatrix& operator=(const SparseMatrix& other)
{
resize(other.rows(), other.cols());
m_colPtrs = other.m_colPtrs;
for (int col=0; col<=cols(); ++col)
m_colPtrs[col] = other.m_colPtrs[col];
m_data = other.m_data;
return *this;
if (other.isRValue())
{
shallowCopy(other);
}
else
{
resize(other.rows(), other.cols());
for (int col=0; col<=cols(); ++col)
m_colPtrs[col] = other.m_colPtrs[col];
m_data = other.m_data;
return *this;
}
}
template<typename OtherDerived>
inline SparseMatrix& operator=(const MatrixBase<OtherDerived>& other)
{
resize(other.rows(), other.cols());
startFill(std::max(m_rows,m_cols)*2);
for (int col=0; col<cols(); ++col)
{
for (typename OtherDerived::InnerIterator it(other.derived(), col); it; ++it)
{
Scalar v = it.value();
if (v!=Scalar(0))
fill(it.index(),col) = v;
}
}
endFill();
return *this;
return SparseMatrixBase<SparseMatrix>::operator=(other);
}
template<typename OtherDerived>
SparseMatrix<Scalar> operator*(const MatrixBase<OtherDerived>& other)
{
SparseMatrix<Scalar> res(rows(), other.cols());
ei_sparse_product<SparseMatrix,OtherDerived>(*this,other.derived(),res);
return res;
}
// old explicit operator+
// template<typename Other>
// SparseMatrix operator+(const Other& other)
// {
// SparseMatrix res(rows(), cols());
// res.startFill(nonZeros()*3);
// for (int col=0; col<cols(); ++col)
// {
// InnerIterator row0(*this,col);
// typename Other::InnerIterator row1(other,col);
// while (row0 && row1)
// {
// if (row0.index()==row1.index())
// {
// std::cout << "both " << col << " " << row0.index() << "\n";
// Scalar v = row0.value() + row1.value();
// if (v!=Scalar(0))
// res.fill(row0.index(),col) = v;
// ++row0;
// ++row1;
// }
// else if (row0.index()<row1.index())
// {
// std::cout << "row0 " << col << " " << row0.index() << "\n";
// Scalar v = row0.value();
// if (v!=Scalar(0))
// res.fill(row0.index(),col) = v;
// ++row0;
// }
// else if (row1)
// {
// std::cout << "row1 " << col << " " << row0.index() << "\n";
// Scalar v = row1.value();
// if (v!=Scalar(0))
// res.fill(row1.index(),col) = v;
// ++row1;
// }
// }
// while (row0)
// {
// std::cout << "row0 " << col << " " << row0.index() << "\n";
// Scalar v = row0.value();
// if (v!=Scalar(0))
// res.fill(row0.index(),col) = v;
// ++row0;
// }
// while (row1)
// {
// std::cout << "row1 " << col << " " << row1.index() << "\n";
// Scalar v = row1.value();
// if (v!=Scalar(0))
// res.fill(row1.index(),col) = v;
// ++row1;
// }
// }
// res.endFill();
// return res;
// // return binaryOp(other, ei_scalar_sum_op<Scalar>());
// }
// WARNING for efficiency reason it currently outputs the transposed matrix
friend std::ostream & operator << (std::ostream & s, const SparseMatrix& m)
{
s << "Nonzero entries:\n";
for (uint 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 (uint i=0; i<m.cols(); ++i)
{
s << m.m_colPtrs[i] << " ";
}
s << std::endl;
s << std::endl;
s << "Matrix (transposed):\n";
for (int j=0; j<m.cols(); j++ )
{
int end = m.m_colPtrs[j+1];
int i=0;
for (int id=m.m_colPtrs[j]; id<end; id++)
EIGEN_DBG_SPARSE(
s << "Nonzero entries:\n";
for (uint i=0; i<m.nonZeros(); ++i)
{
int row = m.m_data.index(id);
// fill with zeros
for (int k=i; k<row; ++k)
s << "0 ";
i = row+1;
s << m.m_data.value(id) << " ";
s << "(" << m.m_data.value(i) << "," << m.m_data.index(i) << ") ";
}
for (int k=i; k<m.rows(); ++k)
s << "0 ";
s << std::endl;
}
s << std::endl;
s << "Column pointers:\n";
for (uint i=0; i<m.cols(); ++i)
{
s << m.m_colPtrs[i] << " ";
}
s << std::endl;
s << std::endl;
);
s << static_cast<const SparseMatrixBase<SparseMatrix>&>(m);
return s;
}
/** Destructor */
inline ~SparseMatrix()
{
delete[] m_colPtrs;
if (this->isNotShared())
delete[] m_colPtrs;
}
};
template<typename Scalar>
class SparseMatrix<Scalar>::InnerIterator
template<typename Scalar, int _Flags>
class SparseMatrix<Scalar,_Flags>::InnerIterator
{
public:
InnerIterator(const SparseMatrix& mat, int col)

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// This file is part of Eigen, a lightweight C++ template library
// for linear algebra. Eigen itself is part of the KDE project.
//
// Copyright (C) 2008 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_SPARSEMATRIXBASE_H
#define EIGEN_SPARSEMATRIXBASE_H
template<typename Derived>
class SparseMatrixBase : public MatrixBase<Derived>
{
public:
typedef MatrixBase<Derived> Base;
typedef typename Base::Scalar Scalar;
enum {
Flags = Base::Flags,
RowMajor = ei_traits<Derived>::Flags&RowMajorBit ? 1 : 0
};
inline const Derived& derived() const { return *static_cast<const Derived*>(this); }
inline Derived& derived() { return *static_cast<Derived*>(this); }
inline Derived& const_cast_derived() const
{ return *static_cast<Derived*>(const_cast<SparseMatrixBase*>(this)); }
SparseMatrixBase()
: m_isRValue(false), m_hasBeenCopied(false)
{}
bool isRValue() const { return m_isRValue; }
Derived& temporary() { m_isRValue = true; return derived(); }
int outerSize() const { return RowMajor ? this->rows() : this->cols(); }
int innerSize() const { return RowMajor ? this->cols() : this->rows(); }
inline Derived& operator=(const Derived& other)
{
if (other.isRValue())
{
m_hasBeenCopied = true;
derived().shallowCopy(other);
}
else
this->operator=<Derived>(other);
return derived();
}
template<typename OtherDerived>
inline Derived& operator=(const MatrixBase<OtherDerived>& other)
{
const bool transpose = (Flags & RowMajorBit) != (OtherDerived::Flags & RowMajorBit);
const int outerSize = (int(OtherDerived::Flags) & RowMajorBit) ? other.rows() : other.cols();
// eval to a temporary and then do a shallow copy
typename ei_meta_if<transpose, LinkedVectorMatrix<Scalar,Flags&RowMajorBit>, Derived>::ret temp(other.rows(), other.cols());
temp.startFill(std::max(this->rows(),this->cols())*2);
// std::cout << other.rows() << " xm " << other.cols() << "\n";
for (int j=0; j<outerSize; ++j)
{
for (typename OtherDerived::InnerIterator it(other.derived(), j); it; ++it)
{
// std::cout << other.rows() << " x " << other.cols() << "\n";
// std::cout << it.m_matrix.rows() << "\n";
Scalar v = it.value();
if (v!=Scalar(0))
if (RowMajor) temp.fill(j,it.index()) = v;
else temp.fill(it.index(),j) = v;
}
}
temp.endFill();
derived() = temp.temporary();
return derived();
}
template<typename OtherDerived>
inline Derived& operator=(const SparseMatrixBase<OtherDerived>& other)
{
const bool transpose = (Flags & RowMajorBit) != (OtherDerived::Flags & RowMajorBit);
const int outerSize = (int(OtherDerived::Flags) & RowMajorBit) ? other.rows() : other.cols();
if ((!transpose) && other.isRValue())
{
// eval without temporary
derived().resize(other.rows(), other.cols());
derived().startFill(std::max(this->rows(),this->cols())*2);
for (int j=0; j<outerSize; ++j)
{
for (typename OtherDerived::InnerIterator it(other.derived(), j); it; ++it)
{
Scalar v = it.value();
if (v!=Scalar(0))
if (RowMajor) derived().fill(j,it.index()) = v;
else derived().fill(it.index(),j) = v;
}
}
derived().endFill();
}
else
this->operator=<OtherDerived>(static_cast<const MatrixBase<OtherDerived>&>(other));
return derived();
}
friend std::ostream & operator << (std::ostream & s, const SparseMatrixBase& m)
{
if (Flags&RowMajorBit)
{
for (int row=0; row<m.rows(); ++row)
{
int col = 0;
for (typename Derived::InnerIterator it(m.derived(), row); it; ++it)
{
for ( ; col<it.index(); ++col)
s << "0 ";
std::cout << it.value() << " ";
}
for ( ; col<m.cols(); ++col)
s << "0 ";
s << std::endl;
}
}
else
{
LinkedVectorMatrix<Scalar, RowMajorBit> trans = m.derived();
s << trans;
}
return s;
}
protected:
bool isNotShared() { return !m_hasBeenCopied; }
void markAsCopied() const { m_hasBeenCopied = true; }
protected:
bool m_isRValue;
mutable bool m_hasBeenCopied;
};
#endif // EIGEN_SPARSEMATRIXBASE_H

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// This file is part of Eigen, a lightweight C++ template library
// for linear algebra. Eigen itself is part of the KDE project.
//
// Copyright (C) 2008 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_SPARSEPRODUCT_H
#define EIGEN_SPARSEPRODUCT_H
#define DENSE_TMP 1
#define MAP_TMP 2
#define LIST_TMP 3
#define TMP_TMP 3
template<typename Scalar>
struct ListEl
{
int next;
int index;
Scalar value;
};
template<typename Lhs, typename Rhs>
static void ei_sparse_product(const Lhs& lhs, const Rhs& rhs, SparseMatrix<typename ei_traits<Lhs>::Scalar>& res)
{
int rows = lhs.rows();
int cols = rhs.rows();
int size = lhs.cols();
float ratio = std::max(float(lhs.nonZeros())/float(lhs.rows()*lhs.cols()), float(rhs.nonZeros())/float(rhs.rows()*rhs.cols()));
std::cout << ratio << "\n";
ei_assert(size == rhs.rows());
typedef typename ei_traits<Lhs>::Scalar Scalar;
#if (TMP_TMP == MAP_TMP)
std::map<int,Scalar> tmp;
#elif (TMP_TMP == LIST_TMP)
std::vector<ListEl<Scalar> > tmp(2*rows);
#else
std::vector<Scalar> tmp(rows);
#endif
res.resize(rows, cols);
res.startFill(2*std::max(rows, cols));
for (int j=0; j<cols; ++j)
{
#if (TMP_TMP == MAP_TMP)
tmp.clear();
#elif (TMP_TMP == LIST_TMP)
int tmp_size = 0;
int tmp_start = -1;
#else
for (int k=0; k<rows; ++k)
tmp[k] = 0;
#endif
for (typename Rhs::InnerIterator rhsIt(rhs, j); rhsIt; ++rhsIt)
{
#if (TMP_TMP == MAP_TMP)
typename std::map<int,Scalar>::iterator hint = tmp.begin();
typename std::map<int,Scalar>::iterator r;
#elif (TMP_TMP == LIST_TMP)
int tmp_el = tmp_start;
#endif
for (typename Lhs::InnerIterator lhsIt(lhs, rhsIt.index()); lhsIt; ++lhsIt)
{
#if (TMP_TMP == MAP_TMP)
r = hint;
Scalar v = lhsIt.value() * rhsIt.value();
int id = lhsIt.index();
while (r!=tmp.end() && r->first < id)
++r;
if (r!=tmp.end() && r->first==id)
{
r->second += v;
hint = r;
}
else
hint = tmp.insert(r, std::pair<int,Scalar>(id, v));
++hint;
#elif (TMP_TMP == LIST_TMP)
Scalar v = lhsIt.value() * rhsIt.value();
int id = lhsIt.index();
if (tmp_size==0)
{
tmp_start = 0;
tmp_el = 0;
tmp_size++;
tmp[0].value = v;
tmp[0].index = id;
tmp[0].next = -1;
}
else if (id<tmp[tmp_start].index)
{
tmp[tmp_size].value = v;
tmp[tmp_size].index = id;
tmp[tmp_size].next = tmp_start;
tmp_start = tmp_size;
tmp_size++;
}
else
{
int nextel = tmp[tmp_el].next;
while (nextel >= 0 && tmp[nextel].index<=id)
{
tmp_el = nextel;
nextel = tmp[nextel].next;
}
if (tmp[tmp_el].index==id)
{
tmp[tmp_el].value += v;
}
else
{
tmp[tmp_size].value = v;
tmp[tmp_size].index = id;
tmp[tmp_size].next = tmp[tmp_el].next;
tmp[tmp_el].next = tmp_size;
tmp_size++;
}
}
#else
tmp[lhsIt.index()] += lhsIt.value() * rhsIt.value();
#endif
//res.coeffRef(lhsIt.index(), j) += lhsIt.value() * rhsIt.value();
}
}
#if (TMP_TMP == MAP_TMP)
for (typename std::map<int,Scalar>::const_iterator k=tmp.begin(); k!=tmp.end(); ++k)
if (k->second!=0)
res.fill(k->first, j) = k->second;
#elif (TMP_TMP == LIST_TMP)
int k = tmp_start;
while (k>=0)
{
if (tmp[k].value!=0)
res.fill(tmp[k].index, j) = tmp[k].value;
k = tmp[k].next;
}
#else
for (int k=0; k<rows; ++k)
if (tmp[k]!=0)
res.fill(k, j) = tmp[k];
#endif
}
res.endFill();
std::cout << " => " << float(res.nonZeros())/float(res.rows()*res.cols()) << "\n";
}
#endif // EIGEN_SPARSEPRODUCT_H

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// This file is part of Eigen, a lightweight C++ template library
// for linear algebra. Eigen itself is part of the KDE project.
//
// Copyright (C) 2008 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_SPARSESETTER_H
#define EIGEN_SPARSESETTER_H
template<typename MatrixType, int AccessPattern,
int IsSupported = ei_support_access_pattern<MatrixType,AccessPattern>::ret>
struct ei_sparse_setter_selector;
template<typename MatrixType,
int AccessPattern,
typename WrapperType = typename ei_sparse_setter_selector<MatrixType,AccessPattern>::type>
class SparseSetter
{
typedef typename ei_unref<WrapperType>::type _WrapperType;
public:
inline SparseSetter(MatrixType& matrix) : m_wrapper(matrix), mp_matrix(&matrix) {}
~SparseSetter()
{ *mp_matrix = m_wrapper; }
inline _WrapperType* operator->() { return &m_wrapper; }
inline _WrapperType& operator*() { return m_wrapper; }
protected:
WrapperType m_wrapper;
MatrixType* mp_matrix;
};
template<typename MatrixType, int AccessPattern>
struct ei_sparse_setter_selector<MatrixType, AccessPattern, AccessPatternSupported>
{
typedef MatrixType& type;
};
// forward each derived of SparseMatrixBase to the generic SparseMatrixBase specializations
template<typename Scalar, int Flags, int AccessPattern>
struct ei_sparse_setter_selector<SparseMatrix<Scalar,Flags>, AccessPattern, AccessPatternNotSupported>
: public ei_sparse_setter_selector<SparseMatrixBase<SparseMatrix<Scalar,Flags> >,AccessPattern, AccessPatternNotSupported>
{};
template<typename Scalar, int Flags, int AccessPattern>
struct ei_sparse_setter_selector<LinkedVectorMatrix<Scalar,Flags>, AccessPattern, AccessPatternNotSupported>
: public ei_sparse_setter_selector<LinkedVectorMatrix<SparseMatrix<Scalar,Flags> >,AccessPattern, AccessPatternNotSupported>
{};
template<typename Scalar, int Flags, int AccessPattern>
struct ei_sparse_setter_selector<HashMatrix<Scalar,Flags>, AccessPattern, AccessPatternNotSupported>
: public ei_sparse_setter_selector<HashMatrix<SparseMatrix<Scalar,Flags> >,AccessPattern, AccessPatternNotSupported>
{};
// generic SparseMatrixBase specializations
template<typename Derived>
struct ei_sparse_setter_selector<SparseMatrixBase<Derived>, RandomAccessPattern, AccessPatternNotSupported>
{
typedef HashMatrix<typename Derived::Scalar, Derived::Flags> type;
};
template<typename Derived>
struct ei_sparse_setter_selector<SparseMatrixBase<Derived>, OuterCoherentAccessPattern, AccessPatternNotSupported>
{
typedef HashMatrix<typename Derived::Scalar, Derived::Flags> type;
};
template<typename Derived>
struct ei_sparse_setter_selector<SparseMatrixBase<Derived>, InnerCoherentAccessPattern, AccessPatternNotSupported>
{
typedef LinkedVectorMatrix<typename Derived::Scalar, Derived::Flags> type;
};
template<typename Derived>
struct ei_sparse_setter_selector<SparseMatrixBase<Derived>, FullyCoherentAccessPattern, AccessPatternNotSupported>
{
typedef SparseMatrix<typename Derived::Scalar, Derived::Flags> type;
};
#endif // EIGEN_SPARSESETTER_H

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Eigen/src/Sparse/SparseUtil.h Normal file
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// This file is part of Eigen, a lightweight C++ template library
// for linear algebra. Eigen itself is part of the KDE project.
//
// Copyright (C) 2008 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_SPARSEUTIL_H
#define EIGEN_SPARSEUTIL_H
#ifdef NDEBUG
#define EIGEN_DBG_SPARSE(X)
#else
#define EIGEN_DBG_SPARSE(X) X
#endif
template<typename _Scalar, int _Flags = 0> class SparseMatrix;
template<typename _Scalar, int _Flags = 0> class HashMatrix;
template<typename _Scalar, int _Flags = 0> class LinkedVectorMatrix;
const int AccessPatternNotSupported = 0x0;
const int AccessPatternSupported = 0x1;
template<typename MatrixType, int AccessPattern> struct ei_support_access_pattern
{
enum { ret = (int(ei_traits<MatrixType>::SupportedAccessPatterns) & AccessPattern) == AccessPattern
? AccessPatternSupported
: AccessPatternNotSupported
};
};
template<typename T> class ei_eval<T,Sparse>
{
typedef typename ei_traits<T>::Scalar _Scalar;
enum {
_Flags = ei_traits<T>::Flags
};
public:
typedef SparseMatrix<_Scalar, _Flags> type;
};
#endif // EIGEN_SPARSEUTIL_H