SAMI/MissingNodes_SrcCode2014/CalcAffinityByCommonNeighbors.m

function [ affinity ] = CalcAffinityByCommonNeighbors( data, actual_graph_size, num_missing_nodes )
%UNTITLED Summary of this function goes here
%   Detailed explanation goes here

%since missing nodes are only connected to one node we will artificially
%connect them to their only neighbor's neighbors, and keep the connection to
%the neighbor itself.
    if nargin > 1
        data = ConnectMissingNodesToNeighborsNeighbors(data, actual_graph_size, num_missing_nodes);
    end
    
    affinity = zeros(size(data,1), size(data,2));
    
    
    for i = 1 : size(data,1)
        num_neighbors_i = sum(data(i,:));
        for j = i : size(data,1)
            num_neighbors_j = sum(data(j,:));
            num_common_neighbors = sum((data(i,:)) > 0 & (data(j,:) > 0));
            if data(i,j) > 0
                num_common_neighbors = num_common_neighbors + 2; %add one for each direction of the link
            end
%             num_common_neighbors = 0;
%             if data(i,j) == 1
%                 num_common_neighbors = 1;
%             end
%             for k = 1 : size(data,1)
%                 if data(i,k) == 1 && data(j,k) == 1
%                     num_common_neighbors = num_common_neighbors + 1;
%                 end        
%             end
            
            %set the lowest affinity to epsilon
            %affinity(i,j) = max(max(num_common_neighbors / num_neighbors_i, num_common_neighbors / num_neighbors_j), eps);
            
            affinity(j,i) = affinity(i,j);
        end
    end
    


end