function user_find_tiles_video


addpath /home/wrightc/program/AFMutils

figure(1)

% read data from file
optfile = '/home/wrightc/find/options2';
[inputpath,start,last,outputpath,outputname,conn, a,b,c,d,e,f,g] = ...
    textread( optfile, '%q %u %u %q %q %q %u %u %u %u %u %u %u' );
global OPTIONS;
OPTIONS = [a,b,c,d,e,f,g];

% loop from start to end 
for n = start:last
    str = form(n);
    
    % load image from AFM and flatten
    image = showafm([inputpath{1},'.', str], 0) ;
    image = flatten(image, 1);
    image = scale(image);
    
    image = preprocess( image, (n == start) );  

    image = modify(zeros(size(image)),image);
    
%     distance( image, xave, yave, [outputpath{1}, conn{1}, '.', str])
    
    imwrite( image, [outputpath{1},outputname{1}, '.', str], 'tiff' );
    
    pause;
end

close all;
clear;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function str = form ( in )
% convert in to a 3 digit string
% ex:   5 --> '005' ,   13 --> '013' , 324 --> '324'
if (in < 10)
    str = ['00',int2str(in)];
elseif (in < 100)
    str = ['0',int2str(in)];
else
    str = int2str(in);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function out = preprocess (image, first)

global OPTIONS;
% optional pre-processing
if ( ~isempty(find(OPTIONS == 6)) )
    image = imadjust(image);
end
figure(1)
    imagesc(image)
    colormap gray
    title 'image file'

if ( ~isempty(find(OPTIONS == 1)) )
    h = fspecial('gaussian', 3);
    image = filter2(h, image); 
end
if ( ~isempty(find(OPTIONS == 2)) )
    % option: median filter
    image = medfilt2(image, [3,3]);
end
if ( ~isempty(find(OPTIONS == 3)) )
    global SELECT;
    if (first == true)
        disp( 'mark area to mask' )

        SELECT = roipoly( image );
    end
    image = SELECT .* double(image);
end
out = image;

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function output_image = modify( input_image , raw_image )
[yy,xx] = find(input_image);

output_image = input_image;

figure(4) 
    imagesc(raw_image)
    hold on
    [i,j] = find( input_image );
    plot( j,i , 'b+');
    hold off
    colormap gray
    truesize
    title 'LEFT click = create center, RIGHT click = remove center, CENTER to end'
    
    
    [xmax, ymax] = size(input_image);
    button = 1;
while button ~= 2   
    [x,y,button] = ginput(1);
    x = round(x);
    y = round(y); 
    
    if( x<0 | y<0 | x> xmax | y > ymax)
        break;
    end
    
    if button == 1
        output_image(y,x) = 1;
        xx = [xx;x];
        yy = [yy;y];
        hold on
        plot(x,y,'g+')
        hold off
    elseif button == 3
        n = findclosest(xx,yy, x,y );
        output_image(yy(n),xx(n)) = 0;
        hold on
        plot(xx(n),yy(n),'ro')
        hold off
        yy(n) = 0;
        xx(n) = 0;
     %   ?????????????????? this will cause problems
    end
end    
    hold off
    
    close(4)
    
    
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function n = findclosest( x,y, x1,y1 )

xtemp = x - x1;
xtemp = xtemp .* xtemp;
ytemp = y - y1;
ytemp = ytemp .* ytemp;
temp = xtemp + ytemp;
[minval,n] = min(temp);