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createNetwork.cpp
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#include "createNetwork.h"
//#include "specialNodes.h"
#include "pulseCoupledPhaseOscillator.h"
#include "nodeImplement.h"
#include "statisticsNetwork.h"
#include <cmath>
#include "ioNode.h"
namespace conedy {
static bool cmp2d ( pair< int, int > a, pair< int, int > b )
{
return ( a.first * a.first + a.second * a.second ) < ( b.first * b.first + b.second * b.second );
}
nodeDescriptor createNetwork::lattice ( int sizex, int sizey, double c, nodeBlueprint *n, edgeBlueprint *l )
{
int i,j;
int a, b;
c=c*c;
if (sizex == 0 || sizey == 0)
return -1;
unsigned int firstNodeNumber= addNode ( n );
// bool passedCircle = false;
for ( i = 1 ; i < sizex*sizey; i++ )
{
addNode ( n );
}
for ( i = 0; i < sizex; i++ )
for ( j = 0; j < sizey; j++ )
for ( a= 0 ; a < sizex ; a++ )
{
if ( ( a-i ) * ( a-i ) > c )
continue;
for ( b = 0 ; b < sizey ; b++ )
{
if ( ( a - i ) * ( a - i ) + ( b-j ) * ( b-j ) <= c && ( a - i ) * ( a - i ) + ( b-j ) * ( b-j ) > 0 )
{
network::link (firstNodeNumber+ i + sizey * j ,firstNodeNumber+ a + sizey * b, l );
}
}
}
return firstNodeNumber;
}
nodeDescriptor createNetwork::torusNearestNeighbors ( int sizex, int sizey, double k, nodeBlueprint *n, edgeBlueprint *l )
{
vector< pair< int, int > > distVector;
vector< pair< int, int > > toAddForAllNodes;
vector< pair< int, int > > toSelectRandomlyFrom;
vector< pair<int, int > >::iterator it;
// bool cmp (pair< int, int > a, pair< int, int > b);
for ( unsigned int i = 1; i < 50; i++ )
for ( unsigned int j = 0; j <= i; j++ )
distVector.push_back ( make_pair<int,int> ( i,j ) );
sort ( distVector.begin(), distVector.end(), &cmp2d );
// distVector.sort(&cmp);
int i,j;
it = distVector.begin();
for ( ; it != distVector.end(); ++it )
{
if ( it->first == it->second )
{
if ( k < 4 )
{
toSelectRandomlyFrom.push_back ( make_pair<int,int> ( it->first, it->second ) );
toSelectRandomlyFrom.push_back ( make_pair<int,int> ( -it->first, it->second ) );
toSelectRandomlyFrom.push_back ( make_pair<int,int> ( it->first, -it->second ) );
toSelectRandomlyFrom.push_back ( make_pair<int,int> ( -it->first, -it->second ) );
break;
}
else
{
k = k - 4;
toAddForAllNodes.push_back ( make_pair<int,int> ( it->first, it->second ) );
toAddForAllNodes.push_back ( make_pair<int,int> ( -it->first, it->second ) );
toAddForAllNodes.push_back ( make_pair<int,int> ( it->first, -it->second ) );
toAddForAllNodes.push_back ( make_pair<int,int> ( -it->first, -it->second ) );
}
}
else if ( it->second == 0 )
{
if ( k < 4 )
{
toSelectRandomlyFrom.push_back ( make_pair<int,int> ( it->first, 0 ) );
toSelectRandomlyFrom.push_back ( make_pair<int,int> ( -it->first, 0 ) );
toSelectRandomlyFrom.push_back ( make_pair<int,int> ( 0, it->first ) );
toSelectRandomlyFrom.push_back ( make_pair<int,int> ( 0, -it->first ) );
break;
}
else
{
k = k - 4;
toAddForAllNodes.push_back ( make_pair<int,int> ( it->first, 0 ) );
toAddForAllNodes.push_back ( make_pair<int,int> ( -it->first, 0 ) );
toAddForAllNodes.push_back ( make_pair<int,int> ( 0, it->first ) );
toAddForAllNodes.push_back ( make_pair<int,int> ( 0, -it->first ) );
}
}
else
{
if ( k < 8 )
{
toSelectRandomlyFrom.push_back ( make_pair<int,int> ( it->first, it->second ) );
toSelectRandomlyFrom.push_back ( make_pair<int,int> ( -it->first, it->second ) );
toSelectRandomlyFrom.push_back ( make_pair<int,int> ( it->first, -it->second ) );
toSelectRandomlyFrom.push_back ( make_pair<int,int> ( -it->first, -it->second ) );
toSelectRandomlyFrom.push_back ( make_pair<int,int> ( it->second, it->first ) );
toSelectRandomlyFrom.push_back ( make_pair<int,int> ( -it->second, it->first ) );
toSelectRandomlyFrom.push_back ( make_pair<int,int> ( it->second, -it->first ) );
toSelectRandomlyFrom.push_back ( make_pair<int,int> ( -it->second, -it->first ) );
break;
}
else
{
k = k - 8;
toAddForAllNodes.push_back ( make_pair<int,int> ( it->first, it->second ) );
toAddForAllNodes.push_back ( make_pair<int,int> ( -it->first, it->second ) );
toAddForAllNodes.push_back ( make_pair<int,int> ( it->first, -it->second ) );
toAddForAllNodes.push_back ( make_pair<int,int> ( -it->first, -it->second ) );
toAddForAllNodes.push_back ( make_pair<int,int> ( it->second, it->first ) );
toAddForAllNodes.push_back ( make_pair<int,int> ( -it->second, it->first ) );
toAddForAllNodes.push_back ( make_pair<int,int> ( it->second, -it->first ) );
toAddForAllNodes.push_back ( make_pair<int,int> ( -it->second, -it->first ) );
}
}
}
nodeDescriptor smallest = addNode(n);
for ( i = 1 ; i < sizex*sizey ; i++ )
{
addNode ( n );
}
// nodeDescriptor largest = addNode(n); unused, daher auskommentiert und die for-Schleife verlängert
int targetX;
int targetY;
for ( i = 0; i < sizex; i++ )
for ( j = 0; j < sizey; j++ )
{
for (it = toAddForAllNodes.begin(); it != toAddForAllNodes.end(); ++it)
{
targetX = it->first + i;
targetY = it->second + j;
while (targetX < 0) targetX+= sizex;
while (targetY < 0) targetY+= sizey;
targetX = targetX % sizex;
targetY = targetY % sizey;
network::link (smallest + i + sizex * j , smallest + targetX + sizex*targetY, l );
}
int targetVector;
for (unsigned int ij = 0; ij < k ; ij++)
{
do
{
targetVector = network::noise.getUniformInt( 0, toSelectRandomlyFrom.size() -1);
targetX = toSelectRandomlyFrom[targetVector].first + i;
targetY = toSelectRandomlyFrom[targetVector].second + j;
while (targetX < 0) targetX+= sizex;
while (targetY < 0) targetY+= sizey;
targetX = targetX % sizex;
targetY = targetY % sizey;
} while ( network::isLinked(smallest + i+sizex*j,smallest + targetX + sizex*targetY));
network::link ( smallest + i + sizex * j , smallest + targetX + sizex*targetY, l );
}
}
return smallest;
}
nodeDescriptor createNetwork::torus ( int sizex, int sizey, double c, nodeBlueprint *n, edgeBlueprint *l )
{
int i,j;
int a, b;
int distx, disty;
c = c * c;
if (sizex == 0 || sizey ==0)
return -1;
unsigned int firstNodeNumber = addNode(n);
for ( i = 1 ; i < sizex*sizey; i++ )
{
addNode ( n );
}
for ( i = 0; i < sizex; i++ )
for ( j = 0; j < sizey; j++ )
for ( a= 0 ; a < sizex ; a++ )
{
if ( abs ( a-i ) > abs ( abs ( a-i ) - sizex ) )
distx = abs ( abs ( a-i )-sizex );
else
distx = abs ( a-i );
if ( distx*distx > c )
continue;
for ( b = 0 ; b < sizey ; b++ )
{
if ( abs ( b-j ) > abs ( abs ( b-j ) - sizex ) )
disty = abs ( abs ( b-j )-sizex );
else
disty = abs ( b-j );
if ( distx * distx + disty * disty <= c && distx*distx + disty*disty > 0 )
{
network::link (firstNodeNumber + i + sizey * j ,firstNodeNumber + a + sizey * b, l );
}
}
}
// cout << "HIERRAUS" << endl;
return firstNodeNumber;
}
nodeDescriptor createNetwork::beeWeb ( int x, int y, nodeBlueprint *n, edgeBlueprint *l )
{
int i, a_x,a_y,b_x,b_y;
int dist_x, dist_y;
if (x == 0 || y == 0)
return -1;
nodeDescriptor firstNodeNumber = addNode(n);
for ( i = 1; i < x*y; i++ )
addNode ( n );
for ( b_x = 0; b_x < x;b_x++ )
for ( b_y = 0; b_y < y;b_y++ )
{
for ( a_x = 0; a_x < x;a_x++ )
for ( a_y = 0; a_y < y;a_y++ )
{
dist_x = ( a_x - b_x ) % ( x );
dist_y = ( a_y - b_y ) % ( y );
if ( sqrt ( (baseType) dist_x*dist_x+dist_y*dist_y+dist_x*dist_y ) <=1 )
network::link ( a_x * x + a_y, b_x*x + b_y, l );
}
}
return firstNodeNumber;
}
void createNetwork::addRandomEdgesUndirected ( double meanOutDeg, edgeBlueprint *l )
{
int source, target;
baseType meanOut = ( ( statisticsNetwork* ) this )->meanDegree() ;
int toDo = ( int ) ( ( meanOutDeg - meanOut ) * network::numberVertices() / 2 );
if ( toDo > 0 )
{
for ( int i = 0; i < toDo; i++ )
{
do
{
source = network::randomNode();
target = network::randomNode();
}
while ( source == target || network::isLinked ( source,target ) );
network::link ( source,target,l );
network::link ( target,source,l );
}
}
}
void createNetwork::removeRandomEdgesUndirected ( double prop, edgeBlueprint * l)
{
network::edgeList allLinks;
network::edgeList toChange;
network::edgeIterator it;
network::edgesMatching (allLinks, l->getEdgeInfo().theEdgeType);
for (it = allLinks.begin(); it != allLinks.end();++it)
if (getTarget(*it) > getSource(*it))
toChange.push_back(*it);
for ( it = toChange.begin(); it != toChange.end(); ++it )
{
if ( network::noise.getUniform() > prop )
continue;
nodeDescriptor source;
nodeDescriptor target;
source = it->first ;
target = getTarget ( *it);
network::unlink ( source, target );
network::unlink ( target, source );
}
network::clean();
}
void createNetwork::removeRandomEdgesDirected ( double prop, edgeBlueprint * l)
{
network::edgeList toChange;
network::edgeIterator it;
network::edgesMatching (toChange, l->getEdgeInfo().theEdgeType);
for ( it = toChange.begin(); it != toChange.end(); ++it )
{
if ( network::noise.getUniform() > prop )
continue;
nodeDescriptor source;
nodeDescriptor target;
source = it->first ;
target = getTarget ( *it);
network::unlink ( source, target );
}
network::clean();
}
void createNetwork::addRandomEdgesDirected ( double meanOutDeg, edgeBlueprint *l )
{
int source, target;
baseType meanOut = ( ( statisticsNetwork* ) this )->meanDegree() ;
int toDo = ( int ) ( ( meanOutDeg - meanOut ) * network::numberVertices() );
if ( toDo > 0 )
{
for ( int i = 0; i < toDo; i++ )
{
do
{
source = network::randomNode();
target = network::randomNode();
}
while ( source == target || network::isLinked ( source,target ) );
network::link ( source,target,l );
}
}
}
// template < typename RANDOM>
//void createNetwork::randomOutDegreeDistribution ( int number, RANDOM &r, nodeBlueprint *n )
//{
// int i, j;
// int deg;
// int rnd;
// network::clear();
// for ( i = 0; i < number; i++ )
// addNode ( n );
// uniformInt randomNode ( 0,number-1 );
// for ( i = 0; i < number; i++ )
// {
// deg = ( int ) r();
// if ( deg > number - 1 )
// deg = number - 1;
//
//
// for ( j = 0; j < deg; j++ )
// {
// do { rnd = randomNode(); }
// while ( ( rnd == i ) || network::isLinked ( i,rnd ) );
// network::link ( i,rnd );
// }
// }
//}
//
//
//
// template < typename RANDOM>
//void createNetwork::randomInDegreeDistribution ( int number, RANDOM &r, nodeBlueprint *n )
//{
// int i, j;
// int deg;
// int rnd;
// network::clear();
// for ( i = 0; i < number; i++ )
// addNode ( n );
// uniformInt randomNode ( 0,number-1 );
// for ( i = 0; i < number; i++ )
// {
// deg = ( int ) r();
// if ( deg > number - 1 )
// deg = number - 1;
//
//
// for ( j = 0; j < deg; j++ )
// {
// do { rnd = randomNode(); }
// while ( ( rnd == i ) || network::isLinked ( i,rnd ) );
// network::link ( rnd,i );
// }
// }
//}
//
//
void createNetwork::addRandomEdgesDegreeDistributionUndirected ( function <double () > r , edgeBlueprint *l)
{
nodeList vl;
verticesMatching (vl,_dynNode_);
nodeIterator it;
vector <nodeDescriptor> nodeStubs;
unsigned int numberLinks;
double randomNumber;
for (it = vl.begin(); it != vl.end(); ++it)
{
randomNumber = r();
if (randomNumber >= 0)
numberLinks = randomNumber;
else
numberLinks = 0;
for (unsigned int i = 0; i < numberLinks ; i++)
nodeStubs.push_back(*it);
}
// shuffle the stub-list with Fisher-Yates
unsigned int j;
nodeDescriptor swap;
for (unsigned int i = nodeStubs.size()-1; i > 1 ; i = i - 1)
{
j = gslNoise::getUniformInt (0, i);
swap = nodeStubs [j];
nodeStubs [j] = nodeStubs[i];
nodeStubs [i] = swap;
}
for (unsigned int i = 0 ; i < nodeStubs.size() / 2; i++ )
{
link ( nodeStubs[2 * i], nodeStubs [ 2 * i + 1], l);
link ( nodeStubs[2 * i + 1], nodeStubs [ 2 * i], l);
}
}
void createNetwork::addRandomEdgesDegreeDistributionDirected ( function <double () > r , edgeBlueprint *l)
{
nodeList vl;
verticesMatching (vl,_dynNode_);
nodeIterator it;
vector <nodeDescriptor> nodeStubs;
unsigned int numberLinks;
for (it = vl.begin(); it != vl.end(); ++it)
{
numberLinks = r();
for (unsigned int i = 0; i < numberLinks ; i++)
nodeStubs.push_back(*it);
}
// shuffle the stub-list with Fisher-Yates
unsigned int j;
nodeDescriptor swap;
for (unsigned int i = nodeStubs.size()-1; i > 1 ; i = i - 1)
{
j = gslNoise::getUniformInt (0, i);
swap = nodeStubs [j];
nodeStubs [j] = nodeStubs[i];
nodeStubs [i] = swap;
}
for (unsigned int i = 0 ; i < nodeStubs.size() / 2; i++ )
link ( nodeStubs[2 * i], nodeStubs [ 2 * i + 1], l);
}
nodeDescriptor createNetwork::streamInLattice ( int sizex, int sizey,string s )
{
nodeBlueprint *n = new streamInNode( s );
nodeDescriptor ret = lattice ( sizex,sizey,1,n, stdEdge );
delete n;
return ret;
}
nodeDescriptor createNetwork::createFromAdjacencyList(string fileName, nodeBlueprint * n, edgeBlueprint *l)
{
ifstream in (fileName.c_str());
if (!in.is_open())
throw (fileName + " nicht gefunden!").c_str();
unsigned int size;
in >> size;
unsigned int smallest = addNode(n);
for (unsigned int i = 1; i < size; i++)
addNode(n);
int source, target;
baseType weight;
while (in.peek() != -1)
{
in >> source;
in >> target;
in >> weight;
if (in.eof())
break;
// if (weight == 0.0)
// continue;
if (weight != 1.0)
((edgeVirtual*)l)->setWeight(weight);
network::link(source +smallest, target +smallest, l);
}
return smallest;
}
nodeDescriptor createNetwork::completeNetwork ( int number, nodeBlueprint *n, edgeBlueprint *l )
{
int i, j;
//network::clear();
if (number == 0)
return -1;
nodeDescriptor firstNodeNumber = addNode(n);
for ( i = 1; i < number; i++ )
{
addNode ( n );
//<baseType>::addNode < nodeBlueprint< baseType > > ();
for ( j = 0; j < i; j++ )
{
network::link (firstNodeNumber + i, firstNodeNumber + j,l );
network::link (firstNodeNumber + j, firstNodeNumber + i,l );
}
}
return firstNodeNumber;
}
void createNetwork::normalizeOutputs (baseType r)
{
nodeIterator it;
nodeList dynNodes;
verticesMatching(dynNodes, _dynNode_);
unsigned int degree;
for (it = dynNodes.begin(); it != dynNodes.end(); ++it)
{
degree = dynNode::lookUp(*it)->degree();
for (unsigned int i = 0 ; i < dynNode::lookUp(*it)->degree(); i ++)
{
dynNode::lookUp(*it)->setWeight (i, r / degree);
}
}
}
void createNetwork::normalizeInputs (baseType r)
{
nodeIterator it;
nodeList dynNodes;
verticesMatching(dynNodes, _dynNode_);
for (it = dynNodes.begin(); it != dynNodes.end(); ++it)
dynNode::lookUp(*it)->normalizeInWeightSum(r);
network::clean();
}
nodeDescriptor createNetwork::cycle ( int number, int a,nodeBlueprint *n, edgeBlueprint *l )
{
if (number == 0)
return - 1;
else if (number == 1)
return addNode(n);
unsigned int smallest = addNode(n);
for (unsigned int i = 1 ; i < number ; i++ )
addNode ( n );
for (unsigned int j = 0; j < number; j++ )
for (unsigned int i = 1; i <= a ; i++ )
{
link ( smallest + j, smallest + ( ( number + j - i ) % number) ,l );
link ( smallest + j, smallest + ( ( number + j + i ) % number) ,l );
}
return smallest;
}
//void createNetwork::cycle ( int number, int a,nodeBlueprint *n )
//{
// cycle (number, a, n, stdEdge);
//}
nodeDescriptor createNetwork::line ( unsigned int number, unsigned int a,nodeBlueprint *n, edgeBlueprint *l )
{
unsigned int i, j;
nodeDescriptor smallest = addNode(n);
for ( i = 1 ; i < number - 1; i++ )
addNode ( n );
nodeDescriptor largest = addNode(n);
for ( j = smallest; j <= largest; j++ )
for ( i = 1; i <= a ; i++ )
{
// cout << "VON:"<< j<< "NACH:" << ((number + j - i) % number)<< endl;
if (j + i <= largest)
network::link ( j, j + i ,l );
if (j >= smallest + i)
network::link ( j, j - i ,l );
}
return smallest;
}
nodeDescriptor createNetwork::cycleCluster (int number1, nodeBlueprint *n1, int number2, nodeBlueprint *n2, int a)
{
network::clear();
int number = number1 + number2;
int i1, i2, i, j;
nodeDescriptor smallest = addNode(n1);
for ( i1 = 1 ; i1 < number1; i1++ )
addNode ( n1 );
for ( i2 = 0 ; i2 < number2; i2++ )
addNode ( n2 );
for ( j = 0; j < number; j++ )
{
for ( i = 1; i <= a ; i++ )
{
network::link ( j, ( ( number + ( j ) - i ) % number ) , stdEdge );
network::link ( j, ( ( number + ( j ) + i ) % number ) , stdEdge );
}
}
return smallest;
}
void createNetwork::rewireTargetDirected ( double prop, nodeKind theNodeKind )
{
network::edgeList toChange;
network::edgeIterator it;
network::edgesBetween ( toChange,theNodeKind,theNodeKind );
nodeList vl;
network::verticesMatching(vl, theNodeKind);
getRandomNode r (vl);
for ( it = toChange.begin() ; it != toChange.end(); ++it )
if (( network::noise.getUniform() <= prop ) )
dynNode::lookUp(it->first)->getEdgeBlueprint(it->second)->targetNumber = r();
}
void createNetwork::rewireWeights ( double prop ,boost::function<double () > r,nodeKind theNodeKind )
{
network::edgeList toChange;
network::edgeIterator it;
// unsigned int i;
network::edgesBetween ( toChange, theNodeKind, theNodeKind );
nodeList vl;
network::verticesMatching(vl, theNodeKind);
getRandomNode rn (vl);
for ( it = toChange.begin(); it != toChange.end(); ++it )
{
if ( network::noise.getUniform() > prop )
continue;
nodeDescriptor newSource;
nodeDescriptor newTarget;
nodeDescriptor oldSource = it->first ;
nodeDescriptor oldTarget = getTarget(*it);
do
{
newSource = rn();
newTarget = rn();
}
while ( newSource == newTarget || dynNode::lookUp(newSource)->isLinked ( newTarget ) ); // keine Selbst- und Doppelverbindungen
// if ((network::theNodes[newSource] == (*it)->source) && (network::theNodes[newTarget] == (*it)->target))
// continue;
getEdgeBlueprint(*it)->setWeight( r() );
network::link ( newSource,newTarget, dynNode::lookUp(it->first)-> getEdgeBlueprint(it->second));
network::unlink( oldSource, oldTarget);
}
network::clean();
}
void createNetwork::rewireDirected ( double prop, nodeBlueprint *n )
{
network::edgeList toChange;
network::edgeIterator it;
network::edgesBetween ( toChange, n,n);
nodeList vl;
network::verticesMatching(vl, n);
getRandomNode r (vl);
for ( it = toChange.begin(); it != toChange.end(); ++it )
{
if ( network::noise.getUniform() > prop )
continue;
nodeDescriptor newSource, oldSource;
nodeDescriptor newTarget, oldTarget;
oldSource = getSource ( *it);
oldTarget = getTarget ( *it);
do
{
newSource = r();
newTarget = r();
}
while ( newSource == newTarget || dynNode::lookUp(newSource)->isLinked ( newTarget ) ); // keine Selbst- und Doppelverbindungen
if ( ( newSource == oldSource ) && ( newTarget == oldTarget ) )
continue;
network::link ( newSource,newTarget, getEdgeBlueprint(*it));
network::remove (*it);
}
network::clean(); // removes holes in the edge arrays of nodes which were created by removing of edges.
}
void createNetwork::replaceEdges ( double prop, edgeBlueprint * l, nodeBlueprint *n )
{
if (!directed)
throw "replaceEdges for undirected networks not implemented at the moment.";
network::edgeList toChange;
network::edgeIterator it;
network::edgesBetween ( toChange, n,n);
nodeList vl;
network::verticesMatching(vl, n);
getRandomNode r (vl);
for ( it = toChange.begin(); it != toChange.end(); ++it )
{
if ( network::noise.getUniform() > prop )
continue;
nodeDescriptor newSource, oldSource;
nodeDescriptor newTarget, oldTarget;
oldSource = it->first ;
oldTarget = getTarget(*it);
do
{
newSource = r();
newTarget = r();
}
while ( newSource == newTarget || dynNode::lookUp(newSource)->isLinked ( newTarget ) ); // keine Selbst- und Doppelverbindungen
if ( ( newSource == oldSource ) && ( newTarget == oldTarget ) )
continue;
network::link ( newSource,newTarget, l );
dynNode::lookUp(oldSource)->unlink ( oldTarget );
}
clean();
}
void createNetwork::rewireUndirected ( double prop, nodeBlueprint * n ) // rewire für ungerichtete Netzwerke die danach immer noch ungerichtetet sein sollen
{
network::edgeList allLinks, toChange;
network::edgeIterator it;
network::edgesBetween ( allLinks, n,n);
nodeList vl;
network::verticesMatching(vl, n);
getRandomNode r (vl);
for (it = allLinks.begin(); it != allLinks.end();++it)
if (getTarget(*it) > getSource(*it))
toChange.push_back(*it);
for ( it = toChange.begin(); it != toChange.end(); ++it )
{
if ( network::noise.getUniform() > prop )
continue;
nodeDescriptor newSource, oldSource;
nodeDescriptor newTarget, oldTarget;
oldSource = it->first ;
oldTarget = getTarget (*it);