function [N,NN,NC]=neighbors(C, center_positions, neighbor_region)
%Extracts the Nearest Neighbors, 'N', Next Nearest Neighbors, 'NN', and the
%number of common vertices shared amongst cells, NC, in a cellular array
%'C'. Shared vertices and Neighbors are computed for cells whose 'center_positions' are within a
%distance 'neighbor_region' of each other.
%
% N - (number of cells) x (number of cells) matrix, with 1 where i^th cell
% is nearest neighbour of j^th cell
% N - (number of cells) x (number of cells) matrix, with 1 where i^th cell
% is nearest neighbour of j^th cell
% NC - (number of cells) x (number of cells) matrix, with number of common vertices between i^th cell
% and j^th cell in the (i,j) position, for nearest neighbor cells.
% C - cell array referring to list of vertices comprising individual cells
% center_positions - Positions of centers of individual cells
% neighbor_region - distance between individual cells to be considered
% neighbors
%
%For bugs, comments, etc. please contact Kapil Krishan :
%kkrishan@uci.edu
%www.physics.uci.edu/~foams
%version: I



x=center_positions(:,1);y=center_positions(:,2);
%'NC' is a matrix indicating the number of common vertices between
%cells
NC=zeros(size(C,1),size(C,1));
for cell_no=1:size(C,1)
    cell_nbhd1=find(abs(x(cell_no)-x)<neighbor_region);
    cell_nbhd2=find(abs(y(cell_no)-y)<neighbor_region);
    for ic=intersect(cell_nbhd1,cell_nbhd2)'
        NC(cell_no,ic)=length(intersect(C{ic},C{cell_no}));
    end
end

%finds the neighbors, 'N' and next-nearest neighbors, 'NN' of cells
N=zeros(size(NC));
NN=zeros(size(NC));
for n_0=1:size(NC,1)
    n_1=find(NC(n_0,:)==2);
    N(n_0,n_1)=1;
    mtx=NC(n_1,:);
    n_2=find(sum(spones(mtx))==2);
    NN(n_0,n_2)=1;
end