NNGraph MSConnectivityScore::pick_graph(EdgeSet const &picked) const {
  EdgeSet::const_iterator p;
  std::map<unsigned int, int> idx_to_vtx;
  int n_vert = 0;
  for (p = picked.begin(); p != picked.end(); ++p) {
    std::map<unsigned int, int>::iterator q = idx_to_vtx.find(p->first);
    if (q == idx_to_vtx.end()) idx_to_vtx[p->first] = n_vert++;
    q = idx_to_vtx.find(p->second);
    if (q == idx_to_vtx.end()) idx_to_vtx[p->second] = n_vert++;
  }
  NNGraph ng(n_vert);
  boost::property_map<NNGraph, boost::vertex_name_t>::type vertex_id =
      boost::get(boost::vertex_name, ng);
  boost::property_map<NNGraph, boost::edge_weight_t>::type dist =
      boost::get(boost::edge_weight, ng);
  for (std::map<unsigned int, int>::iterator q = idx_to_vtx.begin();
       q != idx_to_vtx.end(); ++q) {
    boost::put(vertex_id, q->second, q->first);
  }
  for (p = picked.begin(); p != picked.end(); ++p) {
    NNGraph::edge_descriptor e =
        boost::add_edge(idx_to_vtx[p->first], idx_to_vtx[p->second], ng).first;
    double d = restraint_.particle_matrix_.get_distance(p->first, p->second);
    boost::put(dist, e, d);
  }
  return ng;
}
Example #2
0
Triangulation::~Triangulation()
{
	TriangleSet outTriangles;
	triangles(&outTriangles);
	for(auto it = outTriangles.begin(); it != outTriangles.end(); it++)
		delete *it;
	mTlist->clear();

	EdgeSet outEdges;
	edges(&outEdges);
	for(auto it = outEdges.begin(); it != outEdges.end(); it++)
		delete *it;

	VertexSet outVertices;
	vertices(&outVertices);
	for(auto it = outEdges.begin(); it != outEdges.end(); it++)
		delete *it;

	mV2VMap->clear();
}
ParticlePairsTemp MSConnectivityRestraint::get_connected_pairs() const {
  IMP_CHECK_OBJECT(ps_.get());
  tree_.finalize();
  MSConnectivityScore mcs(tree_, ps_.get(), eps_,
                          *const_cast<MSConnectivityRestraint *>(this));
  EdgeSet edges = mcs.get_connected_pairs();
  ParticlePairsTemp ret(edges.size());
  unsigned index = 0;
  for (EdgeSet::iterator p = edges.begin(); p != edges.end(); ++p) {
    ret[index++] = ParticlePair(mcs.get_particle(p->first),
                                        mcs.get_particle(p->second));
  }
  return ret;
}
double MSConnectivityScore::score(DerivativeAccumulator *accum) const {
  EdgeSet edges = get_connected_pairs();
  double sc = 0;
  for (EdgeSet::iterator p = edges.begin(); p != edges.end(); ++p) {
    if (accum) {
      sc += my_evaluate(
          ps_,
          restraint_.particle_matrix_.get_particle(p->first).get_particle(),
          restraint_.particle_matrix_.get_particle(p->second).get_particle(),
          accum);
    } else {
      sc += restraint_.particle_matrix_.get_distance(p->first, p->second);
    }
  }
  return sc;
}
void MSConnectivityScore::add_edges_to_set(NNGraph &G,
                                           EdgeSet &edge_set) const {
  boost::property_map<NNGraph, boost::vertex_name_t>::type vertex_id =
      boost::get(boost::vertex_name, G);
  NNGraph ng(num_vertices(G));
  Ints vertex_id_to_n(restraint_.particle_matrix_.size(), -1);
  for (unsigned int i = 0; i < num_vertices(ng); ++i) {
    unsigned int id = boost::get(vertex_id, i);
    vertex_id_to_n[id] = i;
  }
  for (EdgeSet::iterator p = edge_set.begin(); p != edge_set.end(); ++p) {
    unsigned int i_from = vertex_id_to_n[(*p).first];
    unsigned int i_to = vertex_id_to_n[(*p).second];
    add_edge(i_from, i_to, ng);
  }
  Ints components(num_vertices(ng));
  int ncomp = boost::connected_components(ng, &components[0]);
  if (ncomp == 1) return;
  Vector<std::pair<unsigned int, unsigned int> > candidates;
  NNGraph::edge_iterator e, end;
  for (boost::tie(e, end) = edges(G); e != end; ++e) {
    unsigned int src = boost::get(vertex_id, source(*e, G));
    unsigned int dst = boost::get(vertex_id, target(*e, G));
    if (src > dst) std::swap(src, dst);
    std::pair<unsigned int, unsigned int> candidate = std::make_pair(src, dst);
    if (edge_set.find(candidate) == edge_set.end())
      candidates.push_back(candidate);
  }
  std::sort(candidates.begin(), candidates.end(),
            EdgeScoreComparator(restraint_));
  unsigned int idx = 0;
  while (ncomp > 1 && idx < candidates.size()) {
    unsigned int i_from = vertex_id_to_n[candidates[idx].first];
    unsigned int i_to = vertex_id_to_n[candidates[idx].second];
    if (components[i_from] != components[i_to]) {
      int old_comp = components[i_to];
      for (unsigned int i = 0; i < components.size(); ++i)
        if (components[i] == old_comp) components[i] = components[i_from];
      --ncomp;
      edge_set.insert(candidates[idx]);
    }
    ++idx;
  }
  BOOST_ASSERT(ncomp == 1);
}
Example #6
0
void Network::clearEdges() {
    GraphMap::iterator neit = _node_to_edges.begin();
    EdgeSet edges;
    for(neit = _node_to_edges.begin();
        neit != _node_to_edges.end();
        neit++) {
      edges.insert( neit->second.begin(), neit->second.end() );
      //Clear this set of edges:
      neit->second.clear();
    }
    //Now actually remove the edges:
    EdgeSet::iterator eit;
    for( eit = edges.begin();
         eit != edges.end();
         eit++ ) {
      decrementRefCount(*eit);
    }
}
	void Delaunay::Triangulate(const VertexSet& vertices, TriangleSet& output)
	{
		if (vertices.size() < 3)
		{
			return;
		}

		cVertexIterator iterVertex = vertices.begin();

		double xMin = iterVertex->GetX();
		double yMin = iterVertex->GetY();
		double xMax = xMin;
		double yMax = yMin;

		++iterVertex;

		for (; iterVertex != vertices.end(); ++iterVertex)
		{
			xMax = iterVertex->GetX();
			double y = iterVertex->GetY();

			if (y < yMin)
			{
				yMin = y;
			}
			if (y > yMax)
			{
				yMax = y;
			}
		}

		double dx = xMax - xMin;
		double dy = yMax - yMin;

		double ddx = dx * 0.01;
		double ddy = dy * 0.01;

		xMin -= ddx;
		xMax += ddx;
		dx += 2 * ddx;

		yMin -= ddy;
		yMax += ddy;
		dy += 2 * ddy;

		Vertex vSuper[3];
		vSuper[0] = Vertex(xMin - dy * sqrt3 / 3.0, yMin);
		vSuper[1] = Vertex(xMax + dy * sqrt3 / 3.0, yMin);
		vSuper[2] = Vertex((xMin + xMax) * 0.5, yMax + dx * sqrt3 * 0.5);

		TriangleSet workset;
		workset.insert(Triangle(vSuper));

		for (iterVertex = vertices.begin(); iterVertex != vertices.end(); ++iterVertex)
		{
			TriangleIsCompleted pred1(iterVertex, output, vSuper);
			TriangleSet::iterator iter = workset.begin();

			while (iter != workset.end())
			{
				if (pred1(*iter))
				{
					iter = workset.erase(iter);
				}
				else
				{
					++iter;
				}
			}

			EdgeSet edges;

			VertexIsInCircumstanceCircle pred2(iterVertex, edges);
			iter = workset.begin();

			while (iter != workset.end())
			{
				if (pred2(*iter))
				{
					iter = workset.erase(iter);
				}
				else
				{
					++iter;
				}
			}

			for (EdgeIterator edgeIter = edges.begin(); edgeIter != edges.end(); ++edgeIter)
			{
				workset.insert(Triangle(edgeIter->m_pv0, edgeIter->m_pv1, &(*iterVertex)));
			}
		}

		TriangleIterator where = output.begin();
		TriangleHasVertex pred(vSuper);
		for (auto t : workset)
		{
			if (!pred(t))
			{
				output.insert(output.begin(), t);
			}
		}
	}
Example #8
0
SEXP attribute_hidden
do_provenance_graph(SEXP call, SEXP op, SEXP args, SEXP rho)
{
#ifndef PROVENANCE_TRACKING
    Rf_error(_("provenance tracking not implemented in this build"));
    return 0;
#else
    int nargs = length(args);
    if (nargs != 1)
	Rf_error(_("%d arguments passed to 'provenance.graph' which requires 1"),
		 nargs);
    SEXP arg1 = CAR(args);
    if (!arg1 || arg1->sexptype() != STRSXP)
	    Rf_error(_("invalid 'names' argument"));

    Environment* env = static_cast<Environment*>(rho);
    Provenance::Set provs;
    StringVector* sv = static_cast<StringVector*>(arg1);
    for (size_t i = 0; i < sv->size(); i++) {
	const char* name = (*sv)[i]->c_str();
	Symbol* sym = Symbol::obtain(name);
	Frame::Binding* bdg = env->findBinding(sym);
	if (!bdg)
	    Rf_error(_("symbol '%s' not found"), name);
	else {
	    Provenance* prov = const_cast<Provenance*>(bdg->provenance());
	    if (!prov)
		Rf_warning(_("'%s' does not have provenance information"),
			   name);
	    else provs.insert(prov);
	    }
	}

    Provenance::Set* ancestors = Provenance::ancestors(provs);

    GCStackRoot<ListVector> ans(CXXR_NEW(ListVector(7)));
    std::map<const Provenance*, unsigned int> ancestor_index;
    std::vector<std::pair<unsigned int, const RObject*> > xenogenous_bdgs;

    // Assemble information on graph nodes:
    {
	size_t n = ancestors->size();
	GCStackRoot<ListVector> symbols(CXXR_NEW(ListVector(n)));
	GCStackRoot<ListVector> commands(CXXR_NEW(ListVector(n)));
	GCStackRoot<RealVector> timestamps(CXXR_NEW(RealVector(n)));
	size_t i = 0;
	for (Provenance::Set::iterator it = ancestors->begin();
	     it != ancestors->end(); ++it) {
	    const Provenance* p = *it;
	    (*symbols)[i] = const_cast<Symbol*>(p->symbol());
	    (*commands)[i] = const_cast<RObject*>(p->command());
	    (*timestamps)[i] = p->timestamp();
	    ++i;
	    ancestor_index[p] = i;
	    if (p->isXenogenous())
		xenogenous_bdgs.push_back(std::make_pair(i, p->value()));
	}

	(*ans)[0] = symbols;
	(*ans)[1] = commands;
	(*ans)[2] = timestamps;
    }

    // Record information on xenogenous bindings:
    {
	size_t xn = xenogenous_bdgs.size();
	GCStackRoot<IntVector> xenogenous(CXXR_NEW(IntVector(xn)));
	GCStackRoot<ListVector> values(CXXR_NEW(ListVector(xn)));
	for (unsigned int i = 0; i < xn; ++i) {
	    std::pair<unsigned int, const RObject*>& pr = xenogenous_bdgs[i];
	    (*xenogenous)[i] = pr.first;
	    (*values)[i] = const_cast<RObject*>(pr.second);
	}
	(*ans)[3] = xenogenous;
	(*ans)[4] = values;
    }

    // Assemble information on graph edges:
    {
	typedef std::set<std::pair<unsigned int, unsigned int> > EdgeSet;
	EdgeSet edges;
	for (Provenance::Set::iterator it = ancestors->begin();
	     it != ancestors->end(); ++it) {
	    const Provenance* child = *it;
	    unsigned int child_idx = ancestor_index[child];
	    std::pair<CommandChronicle::ParentVector::const_iterator,
		      CommandChronicle::ParentVector::const_iterator>
		pr = child->parents();
	    for (CommandChronicle::ParentVector::const_iterator it = pr.first;
		 it != pr.second; ++it) {
		const Provenance* parent = *it;
		unsigned int parent_idx = ancestor_index[parent];
		edges.insert(std::make_pair(parent_idx, child_idx));
	    }
	}

	size_t en = edges.size();
	GCStackRoot<IntVector> parents(CXXR_NEW(IntVector(en)));
	GCStackRoot<IntVector> children(CXXR_NEW(IntVector(en)));
	unsigned int i = 0;
	for (EdgeSet::const_iterator it = edges.begin(); it != edges.end(); ++it) {
	    const std::pair<unsigned int, unsigned int>& edge = *it;
	    (*parents)[i] = edge.first;
	    (*children)[i] = edge.second;
	    ++i;
	}
		
	(*ans)[5] = parents;
	(*ans)[6] = children;
    }
    delete ancestors;
    return ans;
#endif  // PROVENANCE_TRACKING
}
Example #9
0
Network::NeighborIterator::NeighborIterator(Node* n, const EdgeSet& edges) {
  _beg = edges.begin();
  _end = edges.end();
  _neighbors_of = n;
  reset();
}