moose-core/basecode/SparseMatrix.h at master · BhallaLab/moose-core · GitHub

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/**********************************************************************

** This program is part of 'MOOSE', the

** Messaging Object Oriented Simulation Environment,

** also known as GENESIS 3 base code.

** It is made available under the terms of the

** GNU Lesser General Public License version 2.1

** See the file COPYING.LIB for the full notice.

**********************************************************************/

#ifndef _SPARSE_MATRIX_H

#define _SPARSE_MATRIX_H

#include <vector>

using namespace std;

/**

* Template for specialized SparseMatrix. Used both for the Kinetic

* solver and for handling certain kinds of messages. Speciality is that

* it can extract entire rows efficiently, for marching through a

* specified row for a matrix multiplication or for traversing messages.

* Requires that type T have an equality operator ==

extern const unsigned int SM_MAX_ROWS;

extern const unsigned int SM_MAX_COLUMNS;

extern const unsigned int SM_RESERVE;

template< class T > class Triplet

{

public:

Triplet()

{

;

}

Triplet( T a, unsigned int b, unsigned int c )

: a_( a ), b_( b ), c_( c )

{

;

}

bool operator< ( const Triplet< T >& other ) const

{

return ( c_ < other.c_ );

}

static bool cmp( const Triplet< T >& p, const Triplet< T >& q )

{

if ( p.b_ == q.b_ )

return ( p.c_ < q.c_ );

else if ( p.b_ < q.b_ )

return true;

return false;

}

T a_;

unsigned int b_; // row

unsigned int c_; // col

};

typedef std::vector< class T >::const_iterator constTypeIter;

template < class T > class SparseMatrix

{

public:

//////////////////////////////////////////////////////////////////

// Constructors

//////////////////////////////////////////////////////////////////

SparseMatrix()

: nrows_( 0 ), ncolumns_( 0 ), rowStart_( 1, 0 )

{

N_.resize( 0 );

N_.reserve( SM_RESERVE );

colIndex_.resize( 0 );

colIndex_.reserve( SM_RESERVE );

}

SparseMatrix( unsigned int nrows, unsigned int ncolumns )

{

setSize( nrows, ncolumns );

}

//////////////////////////////////////////////////////////////////

// Information operations.

//////////////////////////////////////////////////////////////////

unsigned int nRows() const

{

return nrows_;

}

unsigned int nColumns() const

{

return ncolumns_;

}

unsigned int nEntries() const

{

return N_.size();

}

bool operator==()( const SparseMatrix& other ) {

if (

nrows_ == other.nrows_ &&

ncolumns_ == other.ncolumns_ &&

&& N_.size() == other.N_.size() &&

rowStart_ == other.rowStart_ &&

colIndex_ == other.colIndex_ ) {

for ( unsigned int i = 0; i < N_.size(); ++i )

if ( !doubleEq( N_[i], other.N_[i] ) )

return false;

return true;

}

return false;

}

//////////////////////////////////////////////////////////////////

// Individual entry Access operations.

//////////////////////////////////////////////////////////////////

/**

* Should be called only at the start. Subsequent resizing destroys

* the contents.

void setSize( unsigned int nrows, unsigned int ncolumns )

{

if ( nrows == 0 || ncolumns == 0 )

{

N_.clear();

rowStart_.resize( 1 );

rowStart_[0] = 0;

colIndex_.clear();

nrows_ = 0;

ncolumns_ = 0;

return;

}

if ( nrows < SM_MAX_ROWS && ncolumns < SM_MAX_COLUMNS )

{

N_.clear();

N_.reserve( 2 * nrows );

nrows_ = nrows;

ncolumns_ = ncolumns;

rowStart_.clear();

rowStart_.resize( nrows + 1, 0 );

colIndex_.clear();

colIndex_.reserve( 2 * nrows );

}

else

{

cerr << "Error: SparseMatrix::setSize( " <<

nrows << ", " << ncolumns << ") out of range: ( " <<

SM_MAX_ROWS << ", " << SM_MAX_COLUMNS << ")\n";

}

/**

* Assigns and if necessary adds an entry in the matrix.

* This variant does NOT remove any existing entry.

void set( unsigned int row, unsigned int column, T value )

{

if ( nrows_ == 0 || ncolumns_ == 0 )

return;

vector< unsigned int >::iterator i;

vector< unsigned int >::iterator begin =

colIndex_.begin() + rowStart_[ row ];

vector< unsigned int >::iterator end =

colIndex_.begin() + rowStart_[ row + 1 ];

if ( begin == end ) // Entire row was empty.

{

unsigned long offset = begin - colIndex_.begin();

colIndex_.insert( colIndex_.begin() + offset, column );

N_.insert( N_.begin() + offset, value );

for ( unsigned int j = row + 1; j <= nrows_; j++ )

rowStart_[ j ]++;

return;

}

if ( column > *( end - 1 ) ) // add entry at end of row.

{

unsigned long offset = end - colIndex_.begin();

colIndex_.insert( colIndex_.begin() + offset, column );

N_.insert( N_.begin() + offset, value );

for ( unsigned int j = row + 1; j <= nrows_; j++ )

rowStart_[ j ]++;

return;

}

for ( i = begin; i != end; i++ )

{

if ( *i == column ) // Found desired entry. By defn it is nonzero.

{

N_[ i - colIndex_.begin()] = value;

return;

}

else if ( *i > column ) // Desired entry is blank.

{

unsigned long offset = i - colIndex_.begin();

colIndex_.insert( colIndex_.begin() + offset, column );

N_.insert( N_.begin() + offset, value );

for ( unsigned int j = row + 1; j <= nrows_; j++ )

rowStart_[ j ]++;

return;

}

/**

* Removes specified entry.

void unset( unsigned int row, unsigned int column )

{

if ( nrows_ == 0 || ncolumns_ == 0 )

return;

vector< unsigned int >::iterator i;

vector< unsigned int >::iterator begin =

colIndex_.begin() + rowStart_[ row ];

vector< unsigned int >::iterator end =

colIndex_.begin() + rowStart_[ row + 1 ];

if ( begin == end ) // Entire row was empty. Ignore

{

return;

}

if ( column > *( end - 1 ) ) // End of row. Ignore

{

return;

}

for ( i = begin; i != end; i++ )

{

if ( *i == column ) // Found desired entry. Zap it.

{

unsigned long offset = i - colIndex_.begin();

colIndex_.erase( i );

N_.erase( N_.begin() + offset );

for ( unsigned int j = row + 1; j <= nrows_; j++ )

rowStart_[ j ]--;

return;

}

else if ( *i > column ) //Desired entry is blank. Ignore

{

return;

}

/**

* Returns the entry identified by row, column. Returns T(0)

* if not found

T get( unsigned int row, unsigned int column ) const

{

if ( nrows_ == 0 || ncolumns_ == 0 )

return 0;

assert( row < nrows_ && column < ncolumns_ );

vector< unsigned int >::const_iterator i;

vector< unsigned int >::const_iterator begin =

colIndex_.begin() + rowStart_[ row ];

vector< unsigned int >::const_iterator end =

colIndex_.begin() + rowStart_[ row + 1 ];

i = find( begin, end, column );

if ( i == end ) // most common situation for a sparse Stoich matrix.

{

return 0;

}

else

{

return N_[ rowStart_[row] + (i - begin) ];

}

//////////////////////////////////////////////////////////////////

// Row/Column Access operations.

//////////////////////////////////////////////////////////////////

/**

* Used to get an entire row of entries.

* Returns # entries.

* Passes back iterators for the row and for the column index.

* Ideally I should provide a forall type function so that the

* user passes in their operation as a functor, and it is

* applied to the entire row.

unsigned int getRow( unsigned int row,

const T** entry, const unsigned int** colIndex ) const

{

if ( row >= nrows_ || ncolumns_ == 0 )

{

entry = 0;

colIndex = 0;

return 0;

}

unsigned int rs = rowStart_[row];

if ( rs >= N_.size() )

{

entry = 0;

colIndex = 0;

return 0;

}

*entry = &( N_[ rs ] );

*colIndex = &( colIndex_[rs] );

return rowStart_[row + 1] - rs;

}

/**

* getRow: vector version.

* Used to get an entire row of entries.

* Returns # entries.

unsigned int getRow( unsigned int row,

vector< T >& e, vector< unsigned int >& c ) const

{

e.clear();

c.clear();

if ( row >= nrows_ || ncolumns_ == 0 )

{

return 0;

}

unsigned int rs = rowStart_[row];

if ( rs >= N_.size() )

{

return 0;

}

unsigned int ret = rowStart_[row + 1] - rs;

e.insert( e.begin(),

N_.begin() + rs, N_.begin() + rs + ret );

c.insert( c.begin(),

colIndex_.begin() + rs, colIndex_.begin() + rs + ret );

return ret;

}

/**

* This is an unnatural lookup here, across the grain of the

* sparse matrix.

* Ideally should use copy_if, but the C++ chaps forgot it.

unsigned int getColumn( unsigned int col,

vector< T >& entry,

vector< unsigned int >& rowIndex ) const

{

entry.resize( 0 );

rowIndex.resize( 0 );

unsigned int row = 0;

for ( unsigned int i = 0; i < N_.size(); ++i )

{

if ( col == colIndex_[i] )

{

entry.push_back( N_[i] );

while ( rowStart_[ row + 1 ] <= i )

row++;

rowIndex.push_back( row );

}

return entry.size();

}

#if 0

void rowOperation( unsigned int row, unary_function< T, void>& f )

{

assert( row < nrows_ );

constTypeIter i;

// vector< T >::const_iterator i;

unsigned int rs = rowStart_[row];

vector< unsigned int >::const_iterator j = colIndex_.begin() + rs;

// vector< T >::const_iterator end =

constTypeIter end =

N_.begin() + rowStart_[ row + 1 ];

// for_each

for ( i = N_.begin() + rs; i != end; ++i )

f( *i );

}

#endif

/**

* Adds a row to the sparse matrix, must go strictly in row order.

* This is dangerous as there is a test for an empty entry ~0.

* For many types, ~0 may actually be a perfectly legal entry.

void addRow( unsigned int rowNum, const vector< T >& row )

{

assert( rowNum < nrows_ );

assert( rowStart_.size() == (nrows_ + 1 ) );

assert( N_.size() == colIndex_.size() );

if ( ncolumns_ == 0 )

return;

for ( unsigned int i = 0; i < ncolumns_; ++i )

{

if ( row[i] != T( ~0 ) )

{

N_.push_back( row[i] );

colIndex_.push_back( i );

}

rowStart_[rowNum + 1] = N_.size();

}

/**

* Used to set an entire row of entries, already in sparse form.

* Assumes that the SparseMatrix has been suitably allocated.

* rowNum must be done in increasing order in successive calls.

void addRow( unsigned int rowNum,

const vector < T >& entry,

const vector< unsigned int >& colIndexArg )

{

assert( rowNum < nrows_ );

assert( rowStart_.size() == (nrows_ + 1 ) );

assert( rowStart_[ rowNum ] == N_.size() );

assert( entry.size() == colIndexArg.size() );

assert( N_.size() == colIndex_.size() );

if ( ncolumns_ == 0 )

return;

N_.insert( N_.end(), entry.begin(), entry.end() );

colIndex_.insert( colIndex_.end(),

colIndexArg.begin(), colIndexArg.end() );

rowStart_[rowNum + 1] = N_.size();

}

/// Here we expose the sparse matrix for MOOSE use.

const vector< T >& matrixEntry() const

{

return N_;

}

const vector< unsigned int >& colIndex() const

{

return colIndex_;

}

const vector< unsigned int >& rowStart() const

{

return rowStart_;

}

//////////////////////////////////////////////////////////////////

// Operations on entire matrix.

//////////////////////////////////////////////////////////////////

void clear()

{

N_.resize( 0 );

colIndex_.resize( 0 );

assert( rowStart_.size() == (nrows_ + 1) );

rowStart_.assign( nrows_ + 1, 0 );

}

/**

* Does a transpose, using as workspace a vector of size 3 N_

* 0257 -> 0011122

void transpose()

{

vector< Triplet< T > > t;

unsigned int rowIndex = 0;

if ( rowStart_.size() < 2 )

return;

for ( unsigned int i = 0; i < rowStart_.size(); ++i )

cout << rowStart_[i] << " ";

cout << endl;

// cout << "rowNum = ";

unsigned int rs = rowStart_[0];

for ( unsigned int i = 0; i < N_.size(); ++i )

{

while( rs == rowStart_[ rowIndex + 1 ] )

{

rowIndex++;

}

rs++;

if ( i == rowStart_[j] ) {

rowNum++;

j++;

}

// cout << rowNum << " ";

// The rowNum is going to be the new colIndex.

Triplet< T > x( N_[i], rowIndex, colIndex_[i] );

t.push_back( x );

}

// cout << endl;

// cout << "before sort\n"; printTriplet( t );

stable_sort( t.begin(), t.end() );

// cout << "after sort\n"; printTriplet( t );

unsigned int j = ~0;

rowStart_.resize( 0 );

rowStart_.push_back( 0 );

unsigned int ci = 0;

for ( unsigned int i = 0; i < N_.size(); ++i )

{

N_[i] = t[i].a_;

colIndex_[i] = t[i].b_;

while ( ci != t[i].c_ )

{

rowStart_.push_back( i );

ci++;

}

if ( t[i].c_ != j ) {

j = t[i].c_;

rowStart_.push_back( i );

}

for ( j = ci; j < ncolumns_; ++j )

rowStart_.push_back( N_.size() );

// rowStart_.push_back( N_.size() );

j = nrows_;

nrows_ = ncolumns_;

ncolumns_ = j;

assert( rowStart_.size() == nrows_ + 1 );

}

/**

* Reorder columns from the matrix based on a map of old to new

* column indices.

* newCols contains the indices of columns from the old matrix

* that are to be retained, in the order that they will occupy

* in the new

* matrix. It can have fewer or more indices than the original.

void reorderColumns( const vector< unsigned int >& colMap )

{

unsigned int numNewColumns = colMap.size();;

SparseMatrix< T > old = *this;

setSize( nrows_, numNewColumns );

if ( numNewColumns == 0 )

return;

for ( unsigned int i = 0; i < old.nrows_; ++i )

{

const T* entry;

const unsigned int* colIndex;

unsigned int n = old.getRow( i, &entry, &colIndex );

// Make the full-length vectors of the new row.

vector< T > newEntry( numNewColumns );

vector< bool > isNewEntry( numNewColumns, false );

unsigned int numOccupiedEntries = 0;

for ( unsigned int j = 0; j < n; ++j )

{

assert( colIndex[j] < old.ncolumns_ );

for ( unsigned int q = 0; q < colMap.size(); ++q )

{

if ( colMap[q] == colIndex[j] )

{

isNewEntry[q] = true;

newEntry[q] = entry[j];

++numOccupiedEntries;

}

// Compress the full-length vector into the sparse form

vector< T > sparseEntry;

vector< unsigned int > sparseCols;

sparseEntry.reserve( numOccupiedEntries );

sparseCols.reserve( numOccupiedEntries );

for ( unsigned int q = 0; q < numNewColumns; ++q )

{

if ( isNewEntry[q] )

{

sparseEntry.push_back( newEntry[q] );

sparseCols.push_back( q );

}

addRow( i, sparseEntry, sparseCols );

}

//////////////////////////////////////////////////////////////////

// Utility operations.

//////////////////////////////////////////////////////////////////

void tripletFill( const vector< unsigned int >& row,

const vector< unsigned int >& col,

const vector< T >& z, bool retainSize = false )

{

unsigned int len = row.size();

if ( len > col.size() ) len = col.size();

if ( len > z.size() ) len = z.size();

vector< Triplet< T > > trip( len );

for ( unsigned int i = 0; i < len; ++i )

trip[i]= Triplet< T >(z[i], row[i], col[i] );

sort( trip.begin(), trip.end(), Triplet< T >::cmp );

unsigned int nr = nrows_;

unsigned int nc = ncolumns_;

if ( !retainSize ) {

nr = trip.back().b_ + 1;

nc = 0;

for ( typename vector< Triplet< T > >::iterator i =

trip.begin(); i != trip.end(); ++i )

{

if ( nc < i->c_ )

nc = i->c_;

}

nc++;

}

setSize( nr, nc );

vector< unsigned int > colIndex( nc );

vector< T > entry( nc );

typename vector< Triplet< T > >::iterator j = trip.begin();

for ( unsigned int i = 0; i < nr; ++i )

{

colIndex.clear();

entry.clear();

while( j != trip.end() && j->b_ == i )

{

colIndex.push_back( j->c_ );

entry.push_back( j->a_ );

j++;

}

addRow( i, entry, colIndex );

}

void pairFill( const vector< unsigned int >& row,

const vector< unsigned int >& col, T value )

{

vector< T > z( row.size(), value );

tripletFill( row, col, z );

}

//////////////////////////////////////////////////////////////////

// Printing operations.

//////////////////////////////////////////////////////////////////

void printTriplet( const vector< Triplet< T > >& t )

{

for ( unsigned int i = 0; i < t.size(); ++i )

{

cout << i << " " << t[i].a_ << " " << t[i].b_ <<

" " << t[i].c_ << endl;

}

/**

* Prints out the contents in matrix form

void print() const

{

for ( unsigned int i = 0; i < nrows_; ++i )

{

unsigned int k = rowStart_[i];

unsigned int end = rowStart_[i + 1];

unsigned int nextColIndex = colIndex_[k];

for ( unsigned int j = 0; j < ncolumns_; ++j )

{

if ( j < nextColIndex )

{

cout << "0 ";

}

else if ( k < end )

{

cout << N_[k] << " ";

++k;

nextColIndex = colIndex_[k];

}

else

{

cout << "0 ";

}

cout << endl;

}

/**

* Prints out the contents in internal form

void printInternal() const

{

unsigned int max = (nrows_ < N_.size() ) ? N_.size() : nrows_+1;

cout << "# ";

for ( unsigned int i = 0; i < max; ++i )

cout << i << " ";

cout << "\nrs ";

for ( unsigned int i = 0; i < rowStart_.size(); ++i )

cout << rowStart_[i] << " ";

cout << "\ncol ";

for ( unsigned int i = 0; i < N_.size(); ++i )

cout << colIndex_[i] << " ";

cout << "\nN ";

for ( unsigned int i = 0; i < N_.size(); ++i )

cout << N_[i] << " ";

cout << endl;

}

protected:

unsigned int nrows_;

unsigned int ncolumns_;

vector< T > N_; /// Non-zero entries in the SparseMatrix.

* Column index of each non-zero entry.

* This matches up entry-by entry with the N_ vector.

vector< unsigned int > colIndex_;

/// Start index in the N_ and colIndex_ vectors, of each row.

vector< unsigned int > rowStart_;

};

#endif // _SPARSE_MATRIX_H

moose-core/basecode/SparseMatrix.h at master · BhallaLab/moose-core · GitHub

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