wolffd@0: function [intra, inter, Qnodes, Fnodes, Onode] = mk_hhmm_topo_F1(D, all_Q_to_Qs, Ops)
wolffd@0: % MK_HHMM_TOPO Make Hierarchical HMM topology assuming level 1 can finish 
wolffd@0: % function [intra, inter, Qnodes, Fnodes, Onode] = mk_hhmm_topo(D, all_Q_to_Qs, Ops, F1)
wolffd@0: %
wolffd@0: % D is the depth of the hierarchy
wolffd@0: % If all_Q_to_Qs = 1, level i connects to all levels below, else just to i+1 [0]
wolffd@0: % Ops are the Q parents of the observed node [Qnodes(end)]
wolffd@0: % If F1=1, level 1 can finish (restart), else there is no F1->Q1 arc [0]
wolffd@0: 
wolffd@0: Qnodes = 1:D;
wolffd@0: 
wolffd@0: if nargin < 2, all_Q_to_Qs = 1; end
wolffd@0: if nargin < 3, Ops = Qnodes(D); end
wolffd@0: if nargin < 4, F1 = 0; end
wolffd@0: 
wolffd@0: if F1
wolffd@0:   Fnodes = 2*D:-1:D+1; % must number from bottom to top
wolffd@0:   Onode = 2*D+1;
wolffd@0:   ss = 2*D+1;
wolffd@0: else
wolffd@0:   Fnodes = (2*D)-1:-1:D+1;
wolffd@0:   Onode = 2*D;
wolffd@0:   ss = 2*D;
wolffd@0: end
wolffd@0: 
wolffd@0: intra = zeros(ss);
wolffd@0: intra(Ops, Onode) = 1;
wolffd@0: for d=1:D-1
wolffd@0:   if all_Q_to_Qs
wolffd@0:     intra(Qnodes(d), Qnodes(d+1:end)) = 1;
wolffd@0:   else
wolffd@0:     intra(Qnodes(d), Qnodes(d+1)) = 1;
wolffd@0:   end
wolffd@0: end
wolffd@0: for d=D:-1:3
wolffd@0:   intra(Fnodes(d), Fnodes(d-1)) = 1;
wolffd@0: end
wolffd@0: if F1
wolffd@0:   intra(Fnodes(2), Fnodes(1)) = 1;
wolffd@0: end
wolffd@0: if all_Q_to_Qs
wolffd@0:   for d=1:D
wolffd@0:     intra(Qnodes(d), Fnodes(d:end)) = 1;
wolffd@0:   end
wolffd@0: else
wolffd@0:   for d=1:D
wolffd@0:     if d < D
wolffd@0:       intra(Qnodes(d), Fnodes([d d+1])) = 1;
wolffd@0:     else
wolffd@0:       intra(Qnodes(d), Fnodes(d)) = 1;
wolffd@0:     end
wolffd@0:   end
wolffd@0: end
wolffd@0: 
wolffd@0: inter = zeros(ss);
wolffd@0: for d=1:D
wolffd@0:   inter(Qnodes(d), Qnodes(d)) = 1;
wolffd@0: end
wolffd@0: for d=1:D
wolffd@0:   if d==1
wolffd@0:     inter(Fnodes(d), Qnodes(d)) = 1;
wolffd@0:   else
wolffd@0:     inter(Fnodes(d), Qnodes([d-1 d])) = 1;
wolffd@0:   end
wolffd@0: end