// recursively write clusters and nodes
static void write_ogml_graph(const ClusterGraphAttributes &A, cluster c, int level, ostream &os)
{
if(level > 0) {
GraphIO::indent(os,2+level) << "<node id=\"c" << c->index() << "\">\n";
if (A.has(GraphAttributes::nodeLabel)) {
GraphIO::indent(os,4) << "<label id=\"lc" << c->index() << "\">\n";
GraphIO::indent(os,5) << "<content>" << formatLabel(A.label(c)) << "</content>\n";
GraphIO::indent(os,4) << "</label>\n";
}
}
ListConstIterator<node> itn;
for (itn = c->nBegin(); itn.valid(); ++itn) {
node v = *itn;
GraphIO::indent(os,3+level) << "<node id=\"n" << v->index() << "\">\n";
if (A.has(GraphAttributes::nodeLabel)) {
GraphIO::indent(os,4) << "<label id=\"ln" << v->index() << "\">\n";
GraphIO::indent(os,5) << "<content>" << formatLabel(A.label(v)) << "</content>\n";
GraphIO::indent(os,4) << "</label>\n";
}
GraphIO::indent(os,3+level) << "</node>\n";
}
for (cluster child : c->children) {
write_ogml_graph(child, level+1, os);
}
if(level > 0) {
GraphIO::indent(os,2+level) << "</node>\n";
}
}
// Recursive call for testing c-planarity of the clustered graph
// that is induced by cluster act
bool CconnectClusterPlanar::planarityTest(ClusterGraph &C,
cluster &act,
Graph &G)
{
// Test children first
ListConstIterator<cluster> it;
for (it = act->cBegin(); it.valid();)
{
ListConstIterator<cluster> succ = it.succ();
cluster next = (*it);
if (!planarityTest(C,next,G))
return false;
it = succ;
}
// Get induced subgraph of cluster act and test it for planarity
List<node> subGraphNodes;
ListIterator<node> its;
for (its = act->nBegin(); its.valid(); its++)
subGraphNodes.pushBack(*its);
Graph subGraph;
NodeArray<node> table;
inducedSubGraph(G,subGraphNodes.begin(),subGraph,table);
// Introduce super sink and add edges corresponding
// to outgoing edges of the cluster
node superSink = subGraph.newNode();
EdgeArray<node> outgoingTable(subGraph,0);
for (its = act->nBegin(); its.valid(); its++)
{
node w = (*its);
adjEntry adj = w->firstAdj();
forall_adj(adj,w)
{
edge e = adj->theEdge();
edge cor = 0;
if (table[e->source()] == 0) // edge is connected to a node outside the cluster
{
cor = subGraph.newEdge(table[e->target()],superSink);
outgoingTable[cor] = e->source();
}
else if (table[e->target()] == 0) // dito
{
cor = subGraph.newEdge(table[e->source()],superSink);
outgoingTable[cor] = e->target();
}
// else edge connects two nodes of the cluster
}
}
static void writeCluster(
std::ostream &out, int depth,
const ClusterArray < std::vector<edge> > &edgeMap,
const ClusterGraph &C, const ClusterGraphAttributes *CA, const cluster &c,
int &clusterId)
{
if(C.rootCluster() == c) {
writeHeader(out, depth++, CA);
} else {
GraphIO::indent(out, depth++) << "subgraph cluster" << clusterId
<< " {\n";
}
clusterId++;
bool whitespace; // True if a whitespace should printed (readability).
whitespace = false;
if(CA) {
writeAttributes(out, depth, *CA, c);
whitespace = true;
}
if(whitespace) {
out << "\n";
}
// Recursively export all subclusters.
whitespace = false;
for(ListConstIterator<cluster> cit = c->cBegin(); cit.valid(); ++cit) {
writeCluster(out, depth, edgeMap, C, CA, *cit, clusterId);
whitespace = true;
}
if(whitespace) {
out << "\n";
}
// Then, print all nodes whithout an adjacent edge.
whitespace = false;
for(ListConstIterator<node> nit = c->nBegin(); nit.valid(); ++nit) {
whitespace |= writeNode(out, depth, CA, *nit);
}
if(whitespace) {
out << "\n";
}
// Finally, we print all edges for this cluster (ugly version for now).
const std::vector<edge> &edges = edgeMap[c];
whitespace = false;
for(size_t i = 0; i < edges.size(); i++) {
whitespace |= writeEdge(out, depth, CA, edges[i]);
}
GraphIO::indent(out, --depth) << "}\n";
}
void ClusterGraphCopy::createClusterTree(cluster cOrig)
{
cluster c = m_copy[cOrig];
ListConstIterator<cluster> itC;
for(itC = cOrig->cBegin(); itC.valid(); ++itC) {
cluster child = newCluster(c);
m_copy [*itC] = child;
m_original[child] = *itC;
createClusterTree(*itC);
}
ListConstIterator<node> itV;
for(itV = cOrig->nBegin(); itV.valid(); ++itV) {
reassignNode(m_pH->copy(*itV), c);
}
}
forall_clusters(c,CG) {
if(c != CG.rootCluster()) {
cluster u = c->parent();
newEdge(m_topNode[u], m_topNode[c]);
newEdge(m_bottomNode[c], m_bottomNode[u]);
newEdge(m_topNode[c], m_bottomNode[c]);
}
}
//returns list of all clusters in subtree at c in bottom up order
void MaximumCPlanarSubgraph::getBottomUpClusterList(const cluster c, List< cluster > & theList)
{
ListConstIterator<cluster> it = c->cBegin();
while (it.valid())
{
getBottomUpClusterList((*it), theList);
it++;
}
theList.pushBack(c);
}
/*
* Just a helper method to avoid ugly code in Parser#readEdges method. It just
* populates \a nodes list with either a given \a v node (if not nullptr) or all
* nodes in certain cluster found by performing a lookup with given \a id in
* \a clusterId association.
*/
static inline bool edgeNodes(
node v,
const std::string &id,
const HashArray<std::string, cluster> &clusterId,
List<node> &nodes)
{
if(v) {
nodes.clear();
nodes.pushBack(v);
} else {
const cluster c = clusterId[id];
if(!c) {
return false;
}
c->getClusterNodes(nodes);
}
return true;
}
//in ClusterGraph??
//is not yet recursive!!!
node collapseCluster(ClusterGraph& CG, cluster c, Graph& G)
{
OGDF_ASSERT(c->cCount() == 0)
ListIterator<node> its;
SListPure<node> collaps;
//we should check here if not empty
node robinson = (*(c->nBegin()));
for (its = c->nBegin(); its.valid(); its++)
collaps.pushBack(*its);
CG.collaps(collaps, G);
if (c != CG.rootCluster())
CG.delCluster(c);
return robinson;
}
static void writeCluster(
std::ostream &out, int depth,
const ClusterGraph &C, const ClusterGraphAttributes *CA, cluster c)
{
if(C.rootCluster() != c) {
GraphIO::indent(out, depth) << "<node "
<< "id=\"cluster" << c->index() << "\""
<< ">\n";
} else {
const std::string dir =
(CA && !CA->directed()) ? "undirected" : "directed";
GraphIO::indent(out, depth) << "<graph "
<< "mode=\"static\""
<< "defaultedgetype=\"" << dir << "\""
<< ">\n";
if(CA) {
defineAttributes(out, depth + 1, *CA);
}
}
GraphIO::indent(out, depth + 1) << "<nodes>\n";
for(ListConstIterator<cluster> cit = c->cBegin(); cit.valid(); ++cit) {
writeCluster(out, depth + 2, C, CA, *cit);
}
for(ListConstIterator<node> nit = c->nBegin(); nit.valid(); ++nit) {
writeNode(out, depth + 2, CA, *nit);
}
GraphIO::indent(out, depth + 1) << "</nodes>\n";
if(C.rootCluster() != c) {
GraphIO::indent(out, depth) << "</node>\n";
} else {
writeEdges(out, C.constGraph(), CA);
GraphIO::indent(out, depth) << "</graph>\n";
}
}
void kmedians::calculate_median(cluster & current_cluster, point & median) {
const dataset & data = *m_ptr_data;
const std::size_t dimension = data[0].size();
for (size_t index_dimension = 0; index_dimension < dimension; index_dimension++) {
std::sort(current_cluster.begin(), current_cluster.end(),
[this](std::size_t index_object1, std::size_t index_object2)
{
return (*m_ptr_data)[index_object1] > (*m_ptr_data)[index_object2];
});
std::size_t relative_index_median = (std::size_t) (current_cluster.size() - 1) / 2;
std::size_t index_median = current_cluster[relative_index_median];
if (current_cluster.size() % 2 == 0) {
std::size_t index_median_second = current_cluster[relative_index_median + 1];
median[index_dimension] = (data[index_median][index_dimension] + data[index_median_second][index_dimension]) / 2.0;
}
else {
median[index_dimension] = data[index_median][index_dimension];
}
}
}
void agglomerative::calculate_center(const cluster & cluster, point & center) {
const std::vector<point> & data = *m_ptr_data;
const size_t dimension = data[0].size();
center.resize(dimension, 0.0);
for (auto index_point : cluster) {
for (size_t index_dimension = 0; index_dimension < dimension; index_dimension++) {
center[index_dimension] += data[index_point][index_dimension];
}
}
for (size_t index_dimension = 0; index_dimension < dimension; index_dimension++) {
center[index_dimension] /= cluster.size();
}
}
// recursively write clusters and nodes
static void write_ogml_graph(cluster c, int level, ostream &os)
{
if(level > 0) {
GraphIO::indent(os,2+level) << "<node id=\"c" << c->index() << "\">\n";
}
for (node v : c->nodes) {
GraphIO::indent(os,3+level) << "<node id=\"n" << v->index() << "\">\n";
GraphIO::indent(os,3+level) << "</node>\n";
}
for (cluster child : c->children) {
write_ogml_graph(child, level+1, os);
}
if(level > 0) {
GraphIO::indent(os,2+level) << "</node>\n";
}
}
double kmeans::update_center(const cluster & p_cluster, point & p_center) {
point total(p_center.size(), 0.0);
/* for each object in cluster */
for (auto object_index : p_cluster) {
/* for each dimension */
for (size_t dimension = 0; dimension < total.size(); dimension++) {
total[dimension] += (*m_ptr_data)[object_index][dimension];
}
}
/* average for each dimension */
for (size_t dimension = 0; dimension < total.size(); dimension++) {
total[dimension] = total[dimension] / p_cluster.size();
}
const double change = m_metric(p_center, total);
p_center = std::move(total);
return change;
}
//todo: is called only once, but could be sped up the same way as the co-conn check
void MaxCPlanarMaster::clusterConnection(cluster c, GraphCopy &gc, double &upperBoundC) {
// For better performance, a node array is used to indicate which nodes are contained
// in the currently considered cluster.
NodeArray<bool> vInC(gc,false);
// First check, if the current cluster \a c is a leaf cluster.
// If so, compute the number of edges that have at least to be added
// to make the cluster induced graph connected.
if (c->cCount()==0) { //cluster \a c is a leaf cluster
GraphCopy *inducedC = new GraphCopy((const Graph&)gc);
List<node> clusterNodes;
c->getClusterNodes(clusterNodes); // \a clusterNodes now contains all (original) nodes of cluster \a c.
for (node w : clusterNodes) {
vInC[gc.copy(w)] = true;
}
// Delete all nodes from \a inducedC that do not belong to the cluster,
// in order to obtain the cluster induced graph.
node v = inducedC->firstNode();
while (v!=nullptr) {
node w = v->succ();
if (!vInC[inducedC->original(v)]) inducedC->delNode(v);
v = w;
}
// Determine number of connected components of cluster induced graph.
//Todo: check could be skipped
if (!isConnected(*inducedC)) {
NodeArray<int> conC(*inducedC);
int nCC = connectedComponents(*inducedC,conC);
//at least #connected components - 1 edges have to be added.
upperBoundC -= (nCC-1)*m_largestConnectionCoeff;
}
delete inducedC;
// Cluster \a c is an "inner" cluster. Process all child clusters first.
} else { //c->cCount is != 0, process all child clusters first
for (cluster ci : c->children) {
clusterConnection(ci, gc, upperBoundC);
}
// Create cluster induced graph.
GraphCopy *inducedC = new GraphCopy((const Graph&)gc);
List<node> clusterNodes;
c->getClusterNodes(clusterNodes); //\a clusterNodes now contains all (original) nodes of cluster \a c.
for (node w : clusterNodes) {
vInC[gc.copy(w)] = true;
}
node v = inducedC->firstNode();
while (v!=nullptr) {
node w = v->succ();
if (!vInC[inducedC->original(v)]) inducedC->delNode(v);
v = w;
}
// Now collapse each child cluster to one node and determine #connected components of \a inducedC.
List<node> oChildClusterNodes;
List<node> cChildClusterNodes;
for (cluster ci : c->children) {
ci->getClusterNodes(oChildClusterNodes);
// Compute corresponding nodes of graph \a inducedC.
for (node u : oChildClusterNodes) {
node copy = inducedC->copy(gc.copy(u));
cChildClusterNodes.pushBack(copy);
}
inducedC->collapse(cChildClusterNodes);
oChildClusterNodes.clear();
cChildClusterNodes.clear();
}
// Now, check \a inducedC for connectivity.
if (!isConnected(*inducedC)) {
NodeArray<int> conC(*inducedC);
int nCC = connectedComponents(*inducedC,conC);
//at least #connected components - 1 edges have to added.
upperBoundC -= (nCC-1)*m_largestConnectionCoeff;
}
delete inducedC;
}
}//clusterConnection
forall_clusters(workc, cGraph)
{
resultCluster[workc] = workc; //will be set to copy if non-c-planar
orCluster[workc] = workc;
originalClId[workc] = workc->index();
}
// Recursive call for testing c-planarity of the clustered graph
// that is induced by cluster act
bool CconnectClusterPlanar::planarityTest(
ClusterGraph &C,
cluster &act,
Graph &G)
{
// Test children first
ListConstIterator<cluster> it;
for (it = act->cBegin(); it.valid();)
{
ListConstIterator<cluster> succ = it.succ();
cluster next = (*it);
if (!planarityTest(C,next,G))
return false;
it = succ;
}
// Get induced subgraph of cluster act and test it for planarity
List<node> subGraphNodes;
for (node s : act->nodes)
subGraphNodes.pushBack(s);
Graph subGraph;
NodeArray<node> table;
inducedSubGraph(G,subGraphNodes.begin(),subGraph,table);
// Introduce super sink and add edges corresponding
// to outgoing edges of the cluster
node superSink = subGraph.newNode();
EdgeArray<node> outgoingTable(subGraph,nullptr);
for (node w : act->nodes)
{
//adjEntry adj = w->firstAdj();
for(adjEntry adj : w->adjEntries)
{
edge e = adj->theEdge();
edge cor = nullptr;
if (table[e->source()] == nullptr) // edge is connected to a node outside the cluster
{
cor = subGraph.newEdge(table[e->target()],superSink);
outgoingTable[cor] = e->source();
}
else if (table[e->target()] == nullptr) // dito
{
cor = subGraph.newEdge(table[e->source()],superSink);
outgoingTable[cor] = e->target();
}
// else edge connects two nodes of the cluster
}
}
if (superSink->degree() == 0) // root cluster is not connected to outside clusters
{
subGraph.delNode(superSink);
superSink = nullptr;
}
bool cPlanar = preparation(subGraph,act,superSink);
if (cPlanar && act != C.rootCluster())
{
// Remove induced subgraph and the cluster act.
// Replace it by a wheel graph
while (!subGraphNodes.empty())
{
node w = subGraphNodes.popFrontRet();
// C.unassignNode(w);
G.delNode(w);
}
cluster parent = act->parent();
if (superSink && m_clusterPQTree[act])
constructWheelGraph(C,G,parent,m_clusterPQTree[act],outgoingTable);
C.delCluster(act);
if (m_clusterPQTree[act] != nullptr) // if query necessary for clusters with just one child
{
m_clusterPQTree[act]->emptyAllPertinentNodes();
delete m_clusterPQTree[act];
}
}
else if (!cPlanar)
{
m_errorCode = nonCPlanar;
}//if not cplanar
return cPlanar;
}
//compute bag affiliation for all vertices
//store result in m_bagindex
void ClusterAnalysis::computeBags() {
const Graph &G = m_C->constGraph();
// Storage structure for results
m_bagindex.init(G);
// We use Union-Find for chunks and bags
DisjointSets<> uf;
NodeArray<int> setid(G); // Index mapping for union-find
#if 0
node* nn = new node[G.numberOfNodes()]; // dito
#endif
// Every cluster gets its index
ClusterArray<int> cind(*m_C);
// We store the lists of cluster vertices
List<node>* clists = new List<node>[m_C->numberOfClusters()];
int i = 0;
// Store index and detect the current leaf clusters
List<cluster> ccleafs;
ClusterArray<int> unprocessedChildren(*m_C); //processing below: compute bags
for(cluster c : m_C->clusters)
{
cind[c] = i++;
if (c->cCount() == 0) ccleafs.pushBack(c);
unprocessedChildren[c] = c->cCount();
}
// Now we run through all vertices, storing them in the parent lists,
// at the same time, we initialize m_bagindex
for(node v : G.nodes)
{
// setid is constant in the following
setid[v] = uf.makeSet();
// Each vertex v gets its own ClusterArray that stores v's bag index per cluster.
// See comment on use of ClusterArrays above
m_bagindex[v] = new ClusterArray<int>(*m_C,DefaultIndex, m_C->maxClusterIndex()+1);//m_C->numberOfClusters());
cluster c = m_C->clusterOf(v);
// Push vertices in parent list
clists[cind[c]].pushBack(v);
}
// Now each clist contains the direct vertex descendants
// We process the clusters bottom-up, compute the chunks
// of the leafs first. At each level, for a cluster the
// vertex lists of all children are concatenated
// (could improve this by having an array of size(#leafs)
// and concatenating only at child1), then the bags are
// updated as follows: chunks may be linked by exactly
// the edges with lca(c) ie the ones in m_lcaEdges[c],
// and bags may be built by direct child clusters that join chunks.
// While concatenating the vertex lists, we can check
// for the vertices in each child if the uf number is the same
// as the one of a first initial vertex, otherwise we join.
// First, lowest level clusters are processed: All chunks are bags
OGDF_ASSERT(!ccleafs.empty());
while (!ccleafs.empty()){
const cluster c = ccleafs.popFrontRet();
Skiplist<int*> cbags; //Stores bag indexes ocurring in c
auto storeResult = [&] {
for (node v : clists[cind[c]]) {
int theid = uf.find(setid[v]);
(*m_bagindex[v])[c] = theid;
if (!cbags.isElement(&theid)) {
cbags.add(new int(theid));
}
// push into list of outer active vertices
if (m_storeoalists && isOuterActive(v, c)) {
(*m_oalists)[c].pushBack(v);
}
}
(*m_bags)[c] = cbags.size(); // store number of bags of c
};
if (m_storeoalists){
//no outeractive vertices detected so far
(*m_oalists)[c].clear();
}
//process leafs separately
if (c->cCount() == 0) {
//Todo could use lcaEdges list here too, see below
for (node u : c->nodes)
{
for(adjEntry adj : u->adjEntries) {
node w = adj->twinNode();
if (m_C->clusterOf(w) == c)
{
uf.link(uf.find(setid[u]),uf.find(setid[w]));
}
}
}
// Now all chunks in the leaf cluster are computed
// update for parent is done in the else case
storeResult();
}
else {
// ?We construct the vertex list by concatenating
// ?the lists of the children to the current list.
// We need the lists for storing the results efficiently.
// (Should be slightly faster than to call clusterNodes each time)
// Bags are either links of chunks by edges with lca==c
// or links of chunk by child clusters.
// Edge links
for(edge e : (*m_lcaEdges)[c]) {
uf.link(uf.find(setid[e->source()]),uf.find(setid[e->target()]));
}
// Cluster links
for(cluster cc : c->children)
{
//Initial id per child cluster cc: Use value of first
//vertex, each time we encounter a different value in cc,
//we link the chunks
//add (*itcc)'s vertices to c's list
ListConstIterator<node> itvc = clists[cind[cc]].begin();
int inid;
if (itvc.valid()) inid = uf.find(setid[*itvc]);
while (itvc.valid())
{
int theid = uf.find(setid[*itvc]);
if (theid != inid)
uf.link(inid,theid);
clists[cind[c]].pushBack(*itvc);
++itvc;
}
}
storeResult();
}
// Now we update the status of the parent cluster and,
// in case all its children are processed, add it to
// the process queue.
if (c != m_C->rootCluster())
{
OGDF_ASSERT(unprocessedChildren[c->parent()] > 0);
unprocessedChildren[c->parent()]--;
if (unprocessedChildren[c->parent()] == 0) ccleafs.pushBack(c->parent());
}
}
// clean up
delete[] clists;
}