%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% TP_FN_ellipse Function for getting an evaluation of the quality
% Input:  (1) name of the file generated by your method (see the GT.bmp for how to save your result)
%         (2) (INT default: 12)     the radius for the circle drawn on each point
%         (3) (BOOL default: true) save the result
% Output: (1) TruePositive FalsePositive TrueNegative average_distance_if_TP FalsePositiveRate TruePositiveRate
%
%For Crop_colony radius 6
%For cell 17, radius 6
%For newCell, radius 12
%For Stomate, radius 7
%For Taxi, radius 8
% 25.01.13 Yannick Verdie
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function[] = TP_FN_ellipse(name_image,varargin)

%-----------------------------------parameters
narginchk(1, 3);

numvarargs = length(varargin);
if numvarargs > 3
    error('get_score:TooManyInputs','requires at most 2 optional inputs');
end

% set defaults for optional inputs
optargs = {12 true};
optargs(1:numvarargs) = varargin;
[radius save_txt] = optargs{:};
%-----------------------------------

im = imread(['GT.bmp']);
[m n k] = size(im);
[indy,indx] = find(im(:,:,1) > 128);
fprintf('nb Object GT:%d\n',length(indy));


[xx yy] = meshgrid(1:n,1:m);

[pathstr, name_file, ext] = fileparts(name_image);

is_free = ones(1,length(indy));

imRJ = imread(name_image);
[ind2y,ind2x]  = find(imRJ(:,:,1) > 128);
fprintf('nb Object Method:%d\n',length(ind2y));
 TP = 0;FP = 0;
sum_distance = 0;
for i=1:length(ind2x);%for each object detected
   y = ind2y(i);
   x = ind2x(i);
   %Fim = Fim | (((x-xx).^2+(y-yy).^2)<=radius*radius);
   
  id = find(((x-indx).^2+(y-indy).^2)<=radius*radius);
  if (~isempty(id))
      id2 = find(is_free(id) == 1);
      if (~isempty(id2))
          TP = TP + 1;
          sum_distance = sum_distance + sqrt((x-indx(id(id2(1)))).^2+(y-indy(id(id2(1)))).^2);
          is_free(id(id2(1))) = 0;
      else
          FP = FP + 1;
      end
  else
       FP = FP + 1;
  end
end

FN = sum(is_free);%what is left is missed

 precision = TP/(TP+FP);
 recall = TP/(TP+FN);
data = [TP FP FN sum_distance/TP precision recall]

if (save_txt)
dlmwrite([name_file '_data_object.txt'],data,'delimiter',' ','precision','%10.6g');
end