function distance(filepath, ext)
% if ~(isempty(filepath))
%     centers = imread(filepath, ext);
% % else
% centers = imread ('/home/wrightc/program/images/center1', 'tiff');
% centers = imread ('/home/wrightc/program/images/image6center', 'tiff');
% centers = imread('/home/wrightc/matlab/dimages/error2010_2', 'tiff');
centers = imread('/home/wrightc/program/images/im4tf','tiff');
% end
[imax, jmax] = size(centers);

figure(1)
imagesc(centers);
colormap gray

% assumes only one points per center.
N = floor(bwarea(centers));

% number of sections in histogram.
ratio = 1.5;
x = sqrt( N / ratio );            % 1.5 is assumption about rows vs columns
NUM = ceil( 4 * x );
NUM2 = ceil( 4 * ratio * x );

% finding y distance ------------------------------------------------------
XY = zeros (ceil (N*N / 2), 1);
[y,x] = find(centers);
n = 1;
for i = 1:N
    yi = y(i);
    for j = 1: (i-1)
        XY(n) = abs( yi - y(j) );
        n = n+1;
    end
end
yhist = hist( XY, NUM );

% find max points of histogram
high = zeros(5,1);
j = 1;
for i= 2:NUM
    if ( yhist(i-1) < yhist(i) & yhist(i) > yhist(i+1) )
        high(j) = i;
        j = j + 1;
        if j == 6
            break
        end
    end
end

% compute average distance 
yave = 0;
for i = 1:4
    yave = yave + high(i+1) - high(i);
end
yave = yave/4;
yave = yave * imax / NUM


% finding x distance ------------------------------------------------------
% if a point is within a certain y range, computer its distance to the
% other points.
% reuse = X vector
range = yave / 3;
n = 1;
for i = 1:N
    xi = x(i);
    yi = y(i);
    for j = 1:i-1
        if ( abs(yi - y(j)) < range )
            XY(n) = abs( xi - x(j) );
            n = n+1;  
        end
    end
end
xhist = hist( XY(1:n) , NUM2 );

% find max points of histogram
high = zeros(5,1);
j = 1;
for i= 2:NUM2
    if ( xhist(i-1) < xhist(i) & xhist(i) > xhist(i+1) )
        high(j) = i;
        j = j + 1;
        if j == 6
            break
        end
    end
end

% compute average distance 
xave = 0;
for i = 1:4
    xave = xave + high(i+1) - high(i);
end
xave = xave/4;
xave = xave * jmax / NUM2


% Find connections --------------------------------------------------------
% method: look in range of anticipated connection 

figure(1)
hold on
plot(x,y,'g.')

yshift = floor(yave);
xshift = floor(xave);
yrange = floor(2*yave/5);
xrange = floor(2*xave/5);
conn = zeros(N, 6);
for n = 1:N
    
    % find points horizontal to the right ---------------------------------
    lookhere(1) = x(n) + xshift;
    lookhere(2) = y(n);
    t = find( x < lookhere(1) + xrange & x > lookhere(1) - xrange );
    t2 = find( y(t(:)) < lookhere(2) + yrange & y(t(:)) > lookhere(2) - yrange, 1, 'last');
    
    if ( ~isempty(t2) )
        %horizontal and to the right connections
        hr = t(t2);
        conn(n, 1) = hr;
        conn(hr, 4) = n;
        plot( [x(n),x(hr)],[y(n), y(hr)],'b-' )
    end
    t = [];
    t2 = [];
    
    % find points to the lower right --------------------------------------
    lookhere(1) = x(n) + xshift/2;
    lookhere(2) = y(n) + yshift;
    t = find( x < lookhere(1) + xrange & x > lookhere(1) - xrange );
    t2 = find( y(t(:)) < lookhere(2) + yrange & y(t(:)) > lookhere(2) - yrange, 1, 'last');
   
    if ( ~isempty(t2) )
        % down and to the right connections
        lr = t(t2);
        conn(n, 2) = lr;
        conn(lr, 5) = n;
        plot( [x(n),x(lr)],[y(n), y(lr)],'c-' )
    end
    t = [];
    t2 = [];
    
    % find points to the lower left ---------------------------------------
    lookhere(1) = x(n) - xshift/2;
    lookhere(2) = y(n) + yshift;
    t = find( x < lookhere(1) + xrange & x > lookhere(1) - xrange );
    t2 = find( y(t(:)) < lookhere(2) + yrange & y(t(:)) > lookhere(2) - yrange, 1, 'last');
   
    if ( ~isempty(t2) )
        %horizontal and to the right connections
        ll = t(t2);
        conn(n, 3) = ll;
        conn(ll, 6) = n;
        plot( [x(n),x(ll)],[y(n), y(ll)],'c-' )
    end
    t = [];
    t2 = [];
    
    % stores connections
    % stores index of points and its 6 connections in a row
    % 1 2 6 should be larger than the row number
    % 3 4 5 should be smaller than the row number.
    % all connections stored twice, will reduce speed of processing when
    % walking through image.
end

% add / remove connections ------------------------------------------------
title 'LEFT click = add connection, RIGHT click = remove connection, CENTER = exit'
disp( 'click on two tiles, then enter the direction of connection')
disp( '[1] right' )
disp( '[2] lower right' )
disp( '[3] lower left' )
disp( '[4] left' )
disp( '[5] upper left' )
disp( '[6] upper right' )

figure(1)
hold on
    button = 1;
while button ~= 2   
    % first point
    [x1,y1,button] = ginput(1);
    if ( button == 2 )
        break;
    end
    [y1,x1] = findclosest(centers, floor(y1), floor(x1));
    temp = find( x == x1 );
    temp2 = find ( y(temp) == y1);
    n1 = temp(temp2)
    plot(x1,y1,'go')

    type = input( 'choose connection type [1-6]: ');
    % add connection
    if button == 1      
        % second point
        [x2,y2] = ginput(1);
        x2 = round(x2);
        y2 = round(y2);
        [y2, x2] = findclosest(centers, y2, x2);
        temp = find( x == x2 );
        temp2 = find ( y(temp) == y2);
        n2 = temp(temp2)
        plot(x2,y2,'go')
    
        if type > 3
            temp = n1;      n1 = n2;     n2 = temp;
            type = type - 3;
        end
    
        conn(n1, type) = n2;
        conn(n2, type+3) = n1;
        
        plot( [x(n1),x(n2)],[y(n1), y(n2)],'g-' )
    % remove connection
    elseif button == 3
        n2 = conn(n1,type);
        if n2 == 0
            disp( 'there was no connection to break')
        else
            conn(n1,type) = 0;
            if type < 4
                conn(n2, type+3) = 0;
            else
                conn(n2, type-3) = 0;
            end

            plot( [x(n1),x(n2)],[y(n1), y(n2)],'r-' )
        end
    end
end
hold off

figure(2)
imagesc (centers)
plotconn( 2,x,y,conn, N )

pause;
close all
clear
pack

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

function plotconn( fig, x,y,conn, N )

figure(fig)
hold on
plot(x,y,'g.')

for n = 1:N
    for i = 1:3
        if conn(n,i) ~= 0
            plot( [x(n), x(conn(n,i))], [y(n), y(conn(n,i))], 'c-');
        end
    end
end
hold off

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

function [i2,j2] = findclosest( input_image, i , j )

if (input_image(i,j))
    i2=i;
    j2=j;
    return;
end

%create image with only selected point in it
point = zeros( size(input_image) );
point(i,j) = 1;
% find distance from that point for all points
point = bwdist( point ); 
% multiply by orig bw image so that only points already in image are counted
point = point .* double(input_image);
% find the point with the minimum distance from selected point
indicies = find(point);
[c,I] = min( point(indicies) );
I= indicies(I);
[i2,j2] = ind2sub(size(point), I);

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%