tree_as_swc_array_from_tree_as_struct.m

function tree_as_swc_array = tree_as_swc_array_from_tree_as_struct(tree_as_struct)
    % Get data out of tree_as_struct
    dA_raw = tree_as_struct.dA ;  % the directed adjacency matrix for the tree: dA_raw(i,j)==1 means an edge points from i to j
    xyz_raw = [tree_as_struct.X,tree_as_struct.Y,tree_as_struct.Z] ;  % must be in um
    r_raw = tree_as_struct.R;
    d_raw = tree_as_struct.D;

    % This will be useful
    node_count = size(dA_raw,1) ;

    % Convert to an undirected adjacency matrix
    A_raw = max(dA_raw, dA_raw') ;
    
    % Traverse the graph in depth-first order from the root, allowing us to order
    % the nodes topologically.
    disc = graphtraverse(A_raw,1,'Method','DFS');
    
    % Reorder everything so things are in topological order 
    A = A_raw ;
    A(1:end,:) = A(disc,:) ;
    A(:,1:end) = A(:,disc) ;
    xyz = xyz_raw(disc,:) ;
    r = r_raw(disc,:) ;
    d = d_raw(disc,:) ;
        
    % Get the predecessor (parent) of each node
    %[~,~,pred_slow_as_row] = graphshortestpath(A,1,'DIRECTED',false);
    %pred_slow = pred_slow_as_row(:) ;
    dA = tril(A) ;  % the directed adjacency graph of A
    [is,js] = ind2sub(size(dA), find(dA)) ;
    pred = zeros(node_count, 1) ;
    pred(is) = js ;
    %assert(all(pred==pred_slow)) ;
    
    % Package things as an swc array
    tree_as_swc_array = [(1:node_count)' d xyz r pred] ;
    if node_count>=1 ,
        tree_as_swc_array(1,7) = -1 ;  % the swc convention is that the root parent is -1
    end
end