wolffd@0: function [engine, loglik] = initialize_engine(engine)
wolffd@0: %initialize
wolffd@0: bnet = bnet_from_engine(engine);
wolffd@0: ns = bnet.node_sizes(:);
wolffd@0: N = length(bnet.dag);
wolffd@0: 
wolffd@0: pot_type = 'scg'
wolffd@0: check_for_cd_arcs([], bnet.cnodes, bnet.dag);
wolffd@0: 
wolffd@0: % Evaluate CPDs with evidence, and convert to potentials  
wolffd@0: pot = cell(1, N);
wolffd@0: C = length(engine.cliques);
wolffd@0: inited = zeros(1, C);
wolffd@0: clpot = cell(1, C);
wolffd@0: evidence = cell(1, N);
wolffd@0: for n=1:N
wolffd@0:   fam = family(bnet.dag, n);
wolffd@0:   e = bnet.equiv_class(n);
wolffd@0:   pot{n} = CPD_to_scgpot(bnet.CPD{e}, fam, ns, bnet.cnodes, evidence);
wolffd@0:   cindex = engine.clq_ass_to_node(n);
wolffd@0:   if inited(cindex)
wolffd@0:       %clpot{cindex} = direct_combine_pots(clpot{cindex}, pot{n});
wolffd@0:       clpot{cindex} = direct_combine_pots(pot{n}, clpot{cindex});
wolffd@0:   else
wolffd@0:       clpot{cindex} = pot{n};
wolffd@0:       inited(cindex) = 1;
wolffd@0:   end
wolffd@0: end
wolffd@0: 
wolffd@0: for i=1:C
wolffd@0:     if inited(i) == 0
wolffd@0:         clpot{i} = scgpot([], [], [], []);
wolffd@0:     end
wolffd@0: end
wolffd@0: 
wolffd@0: seppot = cell(C, C);
wolffd@0: % separators are is not need to initialize
wolffd@0: 
wolffd@0: % collect to root (node to parents)
wolffd@0: for n=engine.postorder(1:end-1)
wolffd@0:   for p=parents(engine.jtree, n)
wolffd@0:       [margpot, comppot] = complement_pot(clpot{n}, engine.separator{p,n});
wolffd@0:       margpot = marginalize_pot(clpot{n}, engine.separator{p,n});
wolffd@0:       clpot{n} = comppot;
wolffd@0:       %seppot{p, n} = margpot;
wolffd@0:       clpot{p} = combine_pots(clpot{p}, margpot);
wolffd@0:       %clpot{p} = combine_pots(margpot, clpot{p});
wolffd@0:   end
wolffd@0: end
wolffd@0: 
wolffd@0: temppot = clpot;
wolffd@0: %temppot = clpot{engine.root};
wolffd@0: for n=engine.preorder
wolffd@0:   for c=children(engine.jtree, n)
wolffd@0:     seppot{n,c} = marginalize_pot(temppot{n}, engine.separator{n,c});
wolffd@0:     %seppot{n,c} = marginalize_pot(clpot{n}, engine.separator{n,c});
wolffd@0:     %clpot{c} = direct_combine_pots(clpot{c}, seppot{n,c});
wolffd@0:     temppot{c} = direct_combine_pots(temppot{c}, seppot{n,c});
wolffd@0:   end
wolffd@0: end
wolffd@0: 
wolffd@0: engine.clpot = clpot;
wolffd@0: engine.seppot = seppot;
wolffd@0: 
wolffd@0: