#include <SparseMsg.h>

Inheritance diagram for SparseMsg:

Collaboration diagram for SparseMsg:

Public Member Functions
void	clear ()

Msg *	copy (Id origSrc, Id newSrc, Id newTgt, FuncId fid, unsigned int b, unsigned int n) const

ObjId	findOtherEnd (ObjId end) const

Eref	firstTgt (const Eref &src) const

vector< unsigned int >	getColIndex () const

vector< unsigned int >	getEntryPairs () const

SparseMatrix< unsigned int > &	getMatrix ()

vector< unsigned int >	getMatrixEntry () const

unsigned int	getNumColumns () const

unsigned int	getNumEntries () const

unsigned int	getNumRows () const

double	getProbability () const

vector< unsigned int >	getRowStart () const

unsigned long	getSeed () const

Id	managerId () const

void	pairFill (vector< unsigned int > src, vector< unsigned int > dest)

unsigned int	randomConnect (double probability)

void	setEntry (unsigned int row, unsigned int column, unsigned int value)

void	setEntryPairs (vector< unsigned int > entries)

void	setMatrix (const SparseMatrix< unsigned int > &m)

void	setProbability (double value)

void	setRandomConnectivity (double probability, long seed)

void	setSeed (unsigned long value)

void	sources (vector< vector< Eref > > &v) const

	SparseMsg (Element e1, Element e2, unsigned int msgIndex)

void	targets (vector< vector< Eref > > &v) const

void	transpose ()

void	tripletFill (vector< unsigned int > src, vector< unsigned int > dest, vector< unsigned int > field)

void	tripletFill1 (vector< unsigned int > entries)

void	unsetEntry (unsigned int row, unsigned int column)

void	updateAfterFill ()

	~SparseMsg ()

Public Member Functions inherited from Msg
Element *	e1 () const

Element *	e2 () const

ObjId	getAdjacent (ObjId) const

vector< string >	getDestFieldsOnE1 () const

vector< string >	getDestFieldsOnE2 () const

Id	getE1 () const

Id	getE2 () const

vector< string >	getSrcFieldsOnE1 () const

vector< string >	getSrcFieldsOnE2 () const

bool	isForward (const Element *src) const

ObjId	mid () const

	Msg (ObjId mid, Element e1, Element e2)
	Constructor. More...

virtual void	sources (vector< vector< Eref > > &v) const =0

virtual void	targets (vector< vector< Eref > > &v) const =0

virtual	~Msg ()
	Destructor. More...

Static Public Member Functions
static const Cinfo *	initCinfo ()

static char *	lookupMsg (unsigned int index)
	Static function for Msg access. More...

static unsigned int	numMsg ()
	Msg lookup functions. More...

Static Public Member Functions inherited from Msg
static void	clearAllMsgs ()

static void	deleteMsg (ObjId mid)

static const Msg *	getMsg (ObjId m)

static const Cinfo *	initCinfo ()

static unsigned int	initMsgManagers ()

static bool	isLastTrump ()
	True when MOOSE has been terminated and is being cleaned up. More...

static const Msg *	lastMsg ()

Private Attributes
moose::MOOSE_UNIFORM_DISTRIBUTION < double >	dist_

SparseMatrix< unsigned int >	matrix_

unsigned int	nrows_

unsigned int	numThreads_

double	p_

moose::MOOSE_RANDOM_DEVICE	rd_

moose::MOOSE_RNG_DEFAULT_ENGINE	rng_

unsigned long	seed_

Static Private Attributes
static Id	managerId_

static vector< SparseMsg * >	msg_

Friends
unsigned int	Msg::initMsgManagers ()

Additional Inherited Members
Protected Attributes inherited from Msg
Element *	e1_
	Index of this Msg on the msg_ vector. More...

Element *	e2_
	Element 1 attached to Msg. More...

ObjId	mid_

Static Protected Attributes inherited from Msg
static bool	lastTrump_ = false
	Flag to indicate termination of program. More...

static Id	msgManagerId_
	Element 2 attached to Msg. More...

Detailed Description

This is a parallelized sparse message. It is a general message type optimized for sparse matrix like projection patterns. For each source object[DataId] there can be a target object[DataId]. For parallel/multithreaded use, we need to guarantee that all requests to the same target object (and all its synapses) are on the same queue. So it builds up a separate SparseMatrix for each thread.

It has a function to do the node/thread decomposition to generate an equivalent of the original sparse matrix, but using only the appropriate RNG seed.

A typical case is from an array of IntFire objects to an array of Synapses, which are array fields of IntFire objects. The sparse connectivity maps between the source IntFire and target Synapses.

The location of the entry in the sparse matrix provides the index of the target IntFire. The data value in the sparse matrix provides the index of the Synapse at that specific connection. This assumes that only one Synapse mediates a given connection between any two IntFire objects.

It is optimized for input coming on Element e1, and going to Element e2. If you expect any significant backward data flow, please use BiSparseMsg. It can be modified after creation to add or remove message entries.

Definition at line 46 of file SparseMsg.h.

Constructor & Destructor Documentation

SparseMsg::SparseMsg	(	Element *	e1,
		Element *	e2,
		unsigned int	msgIndex
	)

Definition at line 389 of file SparseMsg.cpp.

References matrix_, msg_, Element::numData(), rd_, rng_, seed_, and SparseMatrix< T >::setSize().

Referenced by copy().

     : Msg( ObjId( managerId_, (msgIndex != 0) ? msgIndex: msg_.size() ),
            e1, e2 ),
       numThreads_( 1 ),
       nrows_( 0 ),
       p_( 0.0 ), seed_( 0 )
 {
     unsigned int nrows = 0;
     unsigned int ncolumns = 0;
     nrows = e1->numData();
     ncolumns = e2->numData();
     matrix_.setSize( nrows, ncolumns );
     if ( msgIndex == 0 )
     {
         msg_.push_back( this );
     }
     else
     {
         if ( msg_.size() <= msgIndex )
             msg_.resize( msgIndex + 1 );
         msg_[ msgIndex ] = this;
     }
 
     // cout << Shell::myNode() << ": SparseMsg constructor between " << e1->getName() << " and " << e2->getName() << endl;
 
     // Init rng with random device.
     if( seed_ == 0 )
         rng_.seed( rd_() );
 }

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SparseMsg::~SparseMsg ( )

Definition at line 419 of file SparseMsg.cpp.

References ObjId::dataIndex, Msg::mid_, and msg_.

 {
     assert( mid_.dataIndex < msg_.size() );
     msg_[ mid_.dataIndex ] = 0; // ensure deleted ptr isn't reused.
 }

Member Function Documentation

void SparseMsg::clear ( )

Definition at line 289 of file SparseMsg.cpp.

References SparseMatrix< T >::clear(), and matrix_.

Referenced by initCinfo().

 {
     matrix_.clear();
 }

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Msg * SparseMsg::copy	(	Id	origSrc,
		Id	newSrc,
		Id	newTgt,
		FuncId	fid,
		unsigned int	b,
		unsigned int	n
	)		const

virtual

Make a copy of this Msg. The original msg was on origSrc. The new Msg should go from newSrc to newTgt, and have the function fid, on bindIndex b. The copy may have to be a higher-order Msg type to handle arrays if n > 1. Note that n is not the number of msgs, but the multiplier by which numData will be scaled.

Implements Msg.

Definition at line 570 of file SparseMsg.cpp.

References Element::addMsgAndFunc(), Msg::e1(), Msg::e2(), Id::element(), matrix_, Msg::mid(), nrows_, setMatrix(), and SparseMsg().

 {
     const Element* orig = origSrc.element();
     if ( n <= 1 )
     {
         SparseMsg* ret = 0;
         if ( orig == e1() )
         {
             ret = new SparseMsg( newSrc.element(), newTgt.element(), 0 );
             ret->e1()->addMsgAndFunc( ret->mid(), fid, b );
         }
         else if ( orig == e2() )
         {
             ret = new SparseMsg( newTgt.element(), newSrc.element(), 0 );
             ret->e2()->addMsgAndFunc( ret->mid(), fid, b );
         }
         else
         {
             assert( 0 );
         }
         ret->setMatrix( matrix_ );
         ret->nrows_ = nrows_;
         return ret;
     }
     else
     {
         // Here we need a SliceMsg which goes from one 2-d array to another.
         cout << "Error: SparseMsg::copy: SparseSliceMsg not yet implemented\n";
         return 0;
     }
 }

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ObjId SparseMsg::findOtherEnd ( ObjId ) const

virtual

Find the other end of this Msg. In most cases this is a straightforward return of e1 or e2, plus perhaps a DataId. But in some complex msgs we need to figure out DataIds that match with the target. In many-to-one cases we just return the first entry. If no Element match, return ObjId( Id(), DataId::bad() ) If Element e matches but not DataId, return ObjId( e.id(), DataId::bad() )

Implements Msg.

Definition at line 544 of file SparseMsg.cpp.

References BADINDEX, ObjId::dataIndex, Msg::e1(), Msg::e2(), ObjId::element(), SparseMatrix< T >::getColumn(), SparseMatrix< T >::getRow(), matrix_, and rowIndex().

 {
     if ( f.element() == e1() )
     {
         const unsigned int* entry;
         const unsigned int* colIndex;
         unsigned int num = matrix_.getRow( f.dataIndex, &entry, &colIndex );
         if ( num > 0 )   // Return the first matching entry.
         {
             return ObjId( e2()->id(), colIndex[0] );
         }
         return ObjId( 0, BADINDEX );
     }
     else if ( f.element() == e2() )     // Bad! Slow! Avoid!
     {
         vector< unsigned int > entry;
         vector< unsigned int > rowIndex;
         unsigned int num = matrix_.getColumn( f.dataIndex, entry, rowIndex );
         if ( num > 0 )   // Return the first matching entry.
         {
             return ObjId( e1()->id(), DataId( rowIndex[0] ) );
         }
     }
     return ObjId( 0, BADINDEX );
 }

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Eref SparseMsg::firstTgt ( const Eref & src ) const

virtual

Obtain the first target Eref for the specified Src Eref It is really meant only to work with messages with a single target ObjId for each given src, typically OneToOne.

Implements Msg.

Definition at line 433 of file SparseMsg.cpp.

References Eref::dataIndex(), Msg::e1_, Msg::e2_, Eref::element(), SparseMatrix< T >::getRow(), matrix_, and SparseMatrix< T >::nEntries().

 {
     if ( matrix_.nEntries() == 0 )
         return Eref( 0, 0 );
 
     if ( src.element() == e1_ )
     {
         const unsigned int* fieldIndex;
         const unsigned int* colIndex;
         unsigned int n = matrix_.getRow( src.dataIndex(),
                                          &fieldIndex, &colIndex );
         if ( n != 0 )
         {
             return Eref( e2_, colIndex[0], fieldIndex[0] );
         }
     }
     else if ( src.element() == e2_ )
     {
         return Eref( e1_, 0 );
     }
     return Eref( 0, 0 );
 }

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vector< unsigned int > SparseMsg::getColIndex ( ) const

Definition at line 234 of file SparseMsg.cpp.

References SparseMatrix< T >::colIndex(), and matrix_.

Referenced by initCinfo().

 {
     return matrix_.colIndex();
 }

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vector< unsigned int > SparseMsg::getEntryPairs ( ) const

Definition at line 251 of file SparseMsg.cpp.

References SparseMatrix< T >::colIndex(), matrix_, SparseMatrix< T >::nRows(), and SparseMatrix< T >::rowStart().

Referenced by initCinfo().

 {
     vector< unsigned int > cols = matrix_.colIndex();
     vector< unsigned int > y;
     for ( unsigned int row = 0; row < matrix_.nRows(); ++row )
     {
         unsigned int begin = matrix_.rowStart()[row];
         unsigned int end = matrix_.rowStart()[row+1];
         for ( unsigned int j = begin; j < end; ++j )
             y.push_back( row );
     }
     assert( cols.size() == y.size() );
     y.insert( y.end(), cols.begin(), cols.end() );
     return y;
 }

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SparseMatrix< unsigned int > & SparseMsg::getMatrix ( )

Returns the connection matrix

Definition at line 539 of file SparseMsg.cpp.

References matrix_.

 {
     return matrix_;
 }

vector< unsigned int > SparseMsg::getMatrixEntry ( ) const

Definition at line 229 of file SparseMsg.cpp.

References matrix_, and SparseMatrix< T >::matrixEntry().

Referenced by initCinfo().

 {
     return matrix_.matrixEntry();
 }

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unsigned int SparseMsg::getNumColumns ( ) const

Definition at line 219 of file SparseMsg.cpp.

References matrix_, and SparseMatrix< T >::nColumns().

Referenced by initCinfo().

 {
     return matrix_.nColumns();
 }

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unsigned int SparseMsg::getNumEntries ( ) const

Definition at line 224 of file SparseMsg.cpp.

References matrix_, and SparseMatrix< T >::nEntries().

Referenced by initCinfo().

 {
     return matrix_.nEntries();
 }

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unsigned int SparseMsg::getNumRows ( ) const

Definition at line 214 of file SparseMsg.cpp.

References matrix_, and SparseMatrix< T >::nRows().

Referenced by initCinfo().

 {
     return matrix_.nRows();
 }

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double SparseMsg::getProbability ( ) const

Definition at line 193 of file SparseMsg.cpp.

References p_.

Referenced by initCinfo().

 {
     return p_;
 }

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vector< unsigned int > SparseMsg::getRowStart ( ) const

Definition at line 239 of file SparseMsg.cpp.

References matrix_, and SparseMatrix< T >::rowStart().

Referenced by initCinfo().

 {
     return matrix_.rowStart();
 }

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unsigned long SparseMsg::getSeed ( ) const

Definition at line 209 of file SparseMsg.cpp.

References seed_.

Referenced by initCinfo().

 {
     return seed_;
 }

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const Cinfo * SparseMsg::initCinfo ( )

static

Connection matrix entries to manipulate in Python.

connection matrix column indices to manipulate in Python.

connection matrix rowStart to manipulate in Python.

Definition at line 24 of file SparseMsg.cpp.

References clear(), getColIndex(), getEntryPairs(), getMatrixEntry(), getNumColumns(), getNumEntries(), getNumRows(), getProbability(), getRowStart(), getSeed(), Msg::initCinfo(), numEntries, pairFill(), setEntry(), setEntryPairs(), setProbability(), setRandomConnectivity(), setSeed(), sparseMsgCinfo, transpose(), tripletFill(), tripletFill1(), and unsetEntry().

Referenced by Msg::initMsgManagers().

 {
     // Field definitions.
     static ReadOnlyValueFinfo< SparseMsg, unsigned int > numRows(
         "numRows",
         "Number of rows in matrix.",
         &SparseMsg::getNumRows
     );
     static ReadOnlyValueFinfo< SparseMsg, unsigned int > numColumns(
         "numColumns",
         "Number of columns in matrix.",
         &SparseMsg::getNumColumns
     );
     static ReadOnlyValueFinfo< SparseMsg, unsigned int > numEntries(
         "numEntries",
         "Number of Entries in matrix.",
         &SparseMsg::getNumEntries
     );
 
     static ValueFinfo< SparseMsg, vector< unsigned int > > connectionList(
         "connectionList",
         "Pairwise specification of connection matrix where each x,y value "
         "represents a connection from src[x] to dest[y]. "
         "The (x,y) entries are ordered in a single vector as \n"
         "(x0, x1,... x_n-1, y0, y1,... y_n-1)\n",
         &SparseMsg::setEntryPairs,
         &SparseMsg::getEntryPairs
     );
 
     static ReadOnlyValueFinfo< SparseMsg, vector< unsigned int > >
     matrixEntry(
         "matrixEntry",
         "The non-zero matrix entries in the sparse matrix. Their"
         "column indices are in a separate vector and the row"
         "informatino in a third",
         &SparseMsg::getMatrixEntry
     );
     static ReadOnlyValueFinfo< SparseMsg, vector< unsigned int > >
     columnIndex(
         "columnIndex",
         "Column Index of each matrix entry",
         &SparseMsg::getColIndex
     );
     static ReadOnlyValueFinfo< SparseMsg, vector< unsigned int > >
     rowStart(
         "rowStart",
         "Row start for each block of entries and column indices",
         &SparseMsg::getRowStart
     );
 
     static ValueFinfo< SparseMsg, double > probability(
         "probability",
         "connection probability for random connectivity.",
         &SparseMsg::setProbability,
         &SparseMsg::getProbability
     );
 
     static ValueFinfo< SparseMsg, unsigned long > seed(
         "seed",
         "Random number seed for generating probabilistic connectivity.",
         &SparseMsg::setSeed,
         &SparseMsg::getSeed
     );
 
 // DestFinfos
 
     static DestFinfo setRandomConnectivity( "setRandomConnectivity",
                                             "Assigns connectivity with specified probability and seed",
                                             new OpFunc2< SparseMsg, double, long >(
                                                     &SparseMsg::setRandomConnectivity ) );
 
     static DestFinfo setEntry( "setEntry",
                                "Assigns single row,column value",
                                new OpFunc3< SparseMsg, unsigned int, unsigned int, unsigned int >(
                                    &SparseMsg::setEntry ) );
 
     static DestFinfo unsetEntry( "unsetEntry",
                                  "Clears single row,column entry",
                                  new OpFunc2< SparseMsg, unsigned int, unsigned int >(
                                      &SparseMsg::unsetEntry ) );
 
     static DestFinfo clear( "clear",
                             "Clears out the entire matrix",
                             new OpFunc0< SparseMsg >(
                                 &SparseMsg::clear ) );
 
     static DestFinfo transpose( "transpose",
                                 "Transposes the sparse matrix",
                                 new OpFunc0< SparseMsg >(
                                     &SparseMsg::transpose ) );
 
     static DestFinfo pairFill( "pairFill",
                                "Fills entire matrix using pairs of (x,y) indices to indicate "
                                "presence of a connection. If the target is a FieldElement it"
                                "automagically assigns FieldIndices.",
                                new OpFunc2< SparseMsg,
                                vector< unsigned int >, vector< unsigned int> >(
                                    &SparseMsg::pairFill ) );
 
     static DestFinfo tripletFill( "tripletFill",
                                   "Fills entire matrix using triplets of (x,y,fieldIndex) to fully "
                                   "specify every connection in the sparse matrix.",
                                   new OpFunc3< SparseMsg,
                                   vector< unsigned int >, vector< unsigned int>,
                                   vector< unsigned int >    >(
                                       &SparseMsg::tripletFill ) );
 
     static DestFinfo tripletFill1( "tripletFill1",
                                    "Single contiguous array to fill entire connection matrix using "
                                    "triplets of (x,y, fieldindex) ordered as \n"
                                    "(x0, x1,... xn-1, y0, y1,... yn-1, fi0, fi1,... fi_n-1)\n",
                                    new OpFunc1< SparseMsg, vector< unsigned int > >(
                                        &SparseMsg::tripletFill1 ) );
 
 // Assemble it all.
 
     static Finfo* sparseMsgFinfos[] =
     {
         &numRows,           // readonly value
         &numColumns,        // readonly value
         &numEntries,        // readonly value
         &connectionList,    // value
         &matrixEntry,       // ReadOnlyValue
         &columnIndex,       // ReadOnlyValue
         &rowStart,      // ReadOnlyValue
         &probability,       // value
         &seed,              // value
         &setRandomConnectivity, // dest
         &setEntry,          // dest
         &unsetEntry,        //dest
         &clear,             //dest
         &transpose,         //dest
         &pairFill,          //dest
         &tripletFill,       //dest
         &tripletFill1,      //dest
     };
 
     static Dinfo< short > dinfo;
     static Cinfo sparseMsgCinfo (
         "SparseMsg",                    // name
         Msg::initCinfo(),           // base class
         sparseMsgFinfos,
         sizeof( sparseMsgFinfos ) / sizeof( Finfo* ),   // num Fields
         &dinfo
     );
 
     return &sparseMsgCinfo;
 }

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char * SparseMsg::lookupMsg ( unsigned int index )

static

Static function for Msg access.

Definition at line 643 of file SparseMsg.cpp.

References msg_.

Referenced by Msg::clearAllMsgs(), and Msg::initMsgManagers().

 {
     assert( index < msg_.size() );
     return reinterpret_cast< char* >( msg_[index] );
 }

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Id SparseMsg::managerId ( ) const

Definition at line 529 of file SparseMsg.cpp.

References managerId_.

 {
     return SparseMsg::managerId_;
 }

unsigned int SparseMsg::numMsg ( )

static

Msg lookup functions.

Static function for Msg access.

Definition at line 637 of file SparseMsg.cpp.

References msg_.

Referenced by Msg::clearAllMsgs(), and Msg::initMsgManagers().

 {
     return msg_.size();
 }

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void SparseMsg::pairFill	(	vector< unsigned int >	src,
		vector< unsigned int >	dest
	)

Fills up the entire message based on pairs of src,dest (i.e., row,column) values. All filled entries are set to zero.

We set retainSize flag to true since the # of src/dest objects doesn't change. We can explicitly assign it elsewhere if needed.

Definition at line 323 of file SparseMsg.cpp.

References Msg::e1(), Msg::e2(), matrix_, Element::numData(), SparseMatrix< T >::tripletFill(), and updateAfterFill().

Referenced by initCinfo(), and setEntryPairs().

 {
     // Sanity check
     vector< unsigned int >::const_iterator i;
     for ( i = src.begin(); i != src.end(); ++i )
     {
         if (*i >= e1()->numData() )
         {
             cout << "Warning: SparseMsg::pairFill: Src index " << *i <<
                  " exceeds Src array size " << e1()->numData() <<
                  ". Aborting\n";
             return;
         }
     }
     for ( i = dest.begin(); i != dest.end(); ++i )
     {
         if (*i >= e2()->numData() )
         {
             cout << "Warning: SparseMsg::pairFill: Dest index " << *i <<
                  " exceeds Dest array size " << e2()->numData() <<
                  ". Aborting\n";
             return;
         }
     }
 
     vector< unsigned int > numAtDest( dest.size(), 0 );
     vector< unsigned int > fieldIndex( dest.size(), 0 );
     for ( unsigned int i = 0; i < dest.size(); ++i )
     {
         fieldIndex[i] = numAtDest[ dest[i] ];
         // Could do on previous line, but clarity
         ++numAtDest[ dest[i] ];
     }
 
     matrix_.tripletFill( src, dest, fieldIndex, true );
     updateAfterFill();
 }

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unsigned int SparseMsg::randomConnect ( double probability )

Returns number of synapses formed. Fills it in transpose form, because we need to count and index the number of synapses on the target, so we need to iterate over the sources in the inner loop. Once full, does the transpose. Should really have a seed argument for the random number. Later need a way to fast-forward mtrand to just the entries we need to fill.

Definition at line 465 of file SparseMsg.cpp.

References SparseMatrix< T >::addRow(), SparseMatrix< T >::clear(), dist_, Msg::e1(), Msg::e2(), Msg::e2_, Element::localDataStart(), Element::markRewired(), matrix_, SparseMatrix< T >::nColumns(), SparseMatrix< T >::nRows(), Element::numData(), Element::numLocalData(), Element::resizeField(), rng_, and SparseMatrix< T >::transpose().

Referenced by setProbability(), setRandomConnectivity(), setSeed(), and testSparseMsg().

 {
     unsigned int nRows = matrix_.nRows(); // Sources
     unsigned int nCols = matrix_.nColumns();    // Destinations
     matrix_.clear();
     unsigned int totalSynapses = 0;
     vector< unsigned int > sizes( nCols, 0 );
     unsigned int totSynNum = 0;
     Element* syn = e2_;
     unsigned int startData = syn->localDataStart();
     unsigned int endData = startData + syn->numLocalData();
 
     assert( nCols == syn->numData() );
 
     matrix_.transpose();
     for ( unsigned int i = 0; i < nCols; ++i )
     {
         vector< unsigned int > synIndex;
         // This needs to be obtained from current size of syn array.
         // unsigned int synNum = sizes[ i ];
         unsigned int synNum = 0;
         for ( unsigned int j = 0; j < nRows; ++j )
         {
             double r = dist_( rng_ ); // Want to ensure it is called each time round the loop.
             if ( r < probability )
             {
                 synIndex.push_back( synNum );
                 ++synNum;
                 ++totSynNum;
             }
             else
             {
                 synIndex.push_back( ~0 );
             }
         }
 
         if ( i >= startData && i < endData )
         {
             e2_->resizeField( i - startData, synNum );
         }
         totalSynapses += synNum;
         matrix_.addRow( i, synIndex );
         /*
          * This is the correct form, but I need to implement something
          * to check up for target nodes in order to use this.
         if ( i >= startData && i < endData ) {
             e2_->resizeField( i - startData, synNum );
             totalSynapses += synNum;
             matrix_.addRow( i, synIndex );
         } else {
             synIndex.resize( 0 );
             synIndex.assign( nRows, ~0 );
             matrix_.addRow( i, synIndex );
         }
         */
     }
 
     matrix_.transpose();
     // cout << Shell::myNode() << ": sizes.size() = " << sizes.size() << ", ncols = " << nCols << ", startSynapse = " << startSynapse << endl;
     e1()->markRewired();
     e2()->markRewired();
     return totalSynapses;
 }

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void SparseMsg::setEntry	(	unsigned int	row,
		unsigned int	column,
		unsigned int	value
	)

Definition at line 278 of file SparseMsg.cpp.

References matrix_, and SparseMatrix< T >::set().

Referenced by initCinfo().

 {
     matrix_.set( row, column, value );
 }

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void SparseMsg::setEntryPairs ( vector< unsigned int > entries )

Definition at line 244 of file SparseMsg.cpp.

References pairFill().

Referenced by initCinfo().

 {
     vector< unsigned int > src( v.begin(), v.begin() + v.size()/2 );
     vector< unsigned int > dest( v.begin() + v.size()/2, v.end() );
     pairFill( src, dest );
 }

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void SparseMsg::setMatrix ( const SparseMatrix< unsigned int > & m )

Assigns the whole connection matrix

Definition at line 534 of file SparseMsg.cpp.

References matrix_.

Referenced by copy().

 {
     matrix_ = m;
 }

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void SparseMsg::setProbability ( double value )

Definition at line 187 of file SparseMsg.cpp.

References p_, and randomConnect().

Referenced by initCinfo().

 {
     p_ = probability;
     randomConnect( probability );
 }

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void SparseMsg::setRandomConnectivity	(	double	probability,
		long	seed
	)

Definition at line 271 of file SparseMsg.cpp.

References p_, randomConnect(), and rng_.

Referenced by initCinfo().

 {
     p_ = probability;
     rng_.seed( seed );
     randomConnect( probability );
 }

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void SparseMsg::setSeed ( unsigned long value )

Definition at line 198 of file SparseMsg.cpp.

References p_, randomConnect(), rd_, rng_, and seed_.

Referenced by initCinfo().

 {
     if( seed > 0 )
         seed_ = seed;
         else
               seed_ = rd_();
 
         rng_.seed( seed_ );
     randomConnect( p_ );
 }

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void SparseMsg::sources ( vector< vector< Eref > > & v ) const

Definition at line 624 of file SparseMsg.cpp.

References Msg::e1_, Msg::e2_, fillErefsFromMatrix(), matrix_, and SparseMatrix< T >::transpose().

 {
     SparseMatrix< unsigned int > temp( matrix_ );
     temp.transpose();
     fillErefsFromMatrix( temp, v, e2_, e1_ );
 }

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void SparseMsg::targets ( vector< vector< Eref > > & v ) const

Definition at line 631 of file SparseMsg.cpp.

References Msg::e1_, Msg::e2_, fillErefsFromMatrix(), and matrix_.

 {
     fillErefsFromMatrix( matrix_, v, e1_, e2_ );
 }

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void SparseMsg::transpose ( )

Definition at line 294 of file SparseMsg.cpp.

References Msg::e1(), Msg::e2(), Element::markRewired(), matrix_, and SparseMatrix< T >::transpose().

Referenced by initCinfo().

 {
     matrix_.transpose();
     e1()->markRewired();
     e2()->markRewired();
 }

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void SparseMsg::tripletFill	(	vector< unsigned int >	src,
		vector< unsigned int >	dest,
		vector< unsigned int >	field
	)

Fills up the entire message based on triplets of src,destDataIndex,destFieldIndex

Definition at line 366 of file SparseMsg.cpp.

References matrix_, SparseMatrix< T >::tripletFill(), and updateAfterFill().

Referenced by initCinfo(), and tripletFill1().

 {
     // We set retainSize flag to true
     matrix_.tripletFill( src, destDataIndex, destFieldIndex, true );
     updateAfterFill();
 }

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void SparseMsg::tripletFill1 ( vector< unsigned int > entries )

Fills up the entire message based on triplets of src,destDataIndex,destFieldIndex, but catenates them all into a single long vector since PyMoose doesn't know how to handle multiple vectors.

Definition at line 375 of file SparseMsg.cpp.

References tripletFill().

Referenced by initCinfo().

 {
     unsigned int s3 = v.size() / 3;
     vector< unsigned int > src( v.begin(), v.begin() + s3 );
     vector< unsigned int > dest( v.begin() + s3, v.begin() + 2 * s3 );
     vector< unsigned int > fieldIndex( v.begin() + 2 * s3, v.end() );
     tripletFill( src, dest, fieldIndex );
 }

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void SparseMsg::unsetEntry	(	unsigned int	row,
		unsigned int	column
	)

Definition at line 284 of file SparseMsg.cpp.

References matrix_, and SparseMatrix< T >::unset().

Referenced by initCinfo().

 {
     matrix_.unset( row, column );
 }

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void SparseMsg::updateAfterFill ( )

Utility function to update all sorts of values after we've rebuilt the matrix.

Definition at line 301 of file SparseMsg.cpp.

References Msg::e1(), Msg::e2(), Msg::e2_, SparseMatrix< T >::getRow(), Element::localDataStart(), Element::markRewired(), matrix_, SparseMatrix< T >::nRows(), Element::numLocalData(), Element::resizeField(), and SparseMatrix< T >::transpose().

Referenced by pairFill(), and tripletFill().

 {
     unsigned int startData = e2_->localDataStart();
     unsigned int endData = startData + e2_->numLocalData();
     SparseMatrix< unsigned int > temp( matrix_);
     temp.transpose();
     for ( unsigned int i = 0; i < temp.nRows(); ++ i )
     {
         const unsigned int* colIndex;
         const unsigned int* entry;
         unsigned int num = temp.getRow( i, &entry, &colIndex );
         if ( i >= startData && i < endData )
         {
             // Inefficient. Better to do it in one pass after getting
             // the max num
             e2_->resizeField( i - startData, num + 1 );
         }
     }
     e1()->markRewired();
     e2()->markRewired();
 }