function ROI(img, nroi)
% 1) Goal: Draw & process multiple ROIs interactively within an image.
%
% 2) Usage: ROI(img, nroi), where 'img' is your image, and 'nroi' is a
% total number to ROIs to be processed. The opened image will be processed
% BY DEFAULT. A prefered procedure is as follows: a) img = imread(...); b)
% imh = imshow(img) and c) ROI(img, nroi).
% Alternatively, if there is no image in your WorkSpace, you MUST use
% square brackets to occupy the argument space for img, such as, ROI([],5),
% will let you open a new image and process with 5 ROIs.
%
% 3) Since getline('closed') is used to get the polygon interactively,
% please click left mouse button to select, and right button to finish up a
% ROI (Backspace to delete the lastest click). You may repeat this process
% till all ROIs were processed. For more infos, please may see help
% getline.
%
% 4) Results: ROI statistics are displayed on screen or output to a text
% file (optional).
%
% 5) The colors of line/text label are generated by 'jet' colormap,
% therefore, certain color may be too close to tell, especially when you
% select too many ROIs. In that case, you may need to edit the color after
% ROI processing. For more infos, please see help jet.
%
% 6) For your convenience, you may use the following m-scripts to clear
% your enviroments: 'dt', 'dl' and 'df' to delete all text characters,
% lines and figures, respectively.
%
% 7) This package includes 5 m-files: 'ROI.m', 'MultiROI', 'df.m', 'dl.m' and 'dt.m'.
% MultiROI is similar to ROI. The only difference is that it uses spline
% interprate to smooth the ROI edge.
%
% Shanrong Zhang
% Department of Radiology
% University of Washington
% 02/09/2004
%
% email: zhangs@u.washington.edu
if nargin == 2
imh = findobj(0, 'Type', 'Image');
% if no image opened, open a new one
if isempty(imh)
if length(img) == 0
[infn inpn] = uigetfile('*.*','Please select an image file');
if infn ~= 0
img = imread([inpn infn]);
imh = imshow(img);
axis image; axis off;
else
disp('Cancel by user!')
return
end
else
imh = imshow(img);
end
end
[nrows, ncols, ncolors] = size(img);
% Save ROIs to a file (optional)
SaveIt = questdlg('Do you want to save ROI outputs ?');
switch SaveIt
case 'Yes'
[outfn, outpn] = uiputfile('*', 'Select an output file');
if outfn == 0
disp('Cancel by user !');
else
fid = fopen([outpn outfn], 'w+');
fprintf(fid, '%20s\t %-50s\n', 'Date\time = ', datestr(now));
end
otherwise
outfn = 0;
end
% generate a jet colormap according to nroi
cmap = jet(nroi);
rndp = randperm(nroi);
hold on;
croi = 1;
while croi <= nroi
[x,y] =getline('closed');
XData = get(imh, 'XData');
YData = get(imh, 'YData');
xmingrid = max( XData(1), floor(min(x)) );
xmaxgrid = min( XData(2), ceil(max(x)) );
ymingrid = max( YData(1), floor(min(y)) );
ymaxgrid = min( YData(2), ceil(max(y)) );
xgrid = xmingrid : xmaxgrid;
ygrid = ymingrid : ymaxgrid;
[X, Y] = meshgrid(xgrid, ygrid);
k_inside = inpolygon(X, Y, x, y);
Xin = X(k_inside);
Yin = Y(k_inside);
cdata = get(imh, 'CData');
smallcdata = double(cdata(ygrid, xgrid, :));
roi.index = croi;
roi.area = polyarea(x,y);
roi.center = [mean(Xin(:)), mean(Yin(:))];
for i=1:ncolors
roicidata = smallcdata(:, :, i);
roi.mean(i) = mean(roicidata(k_inside));
roi.std(i) = std(roicidata(k_inside));
roi.min(i) = min(roicidata(k_inside));
roi.max(i) = max(roicidata(k_inside));
roi.median(i) = median(roicidata(k_inside));
end;
plot(x,y,'Color',cmap(rndp(croi), :));
text(roi.center(1), roi.center(2), num2str(croi), 'Color', cmap(rndp(croi), :), 'FontWeight','Bold');
% write ROI statistics into file if necessary
if outfn ~= 0
fprintf(fid, '\n');
fprintf(fid, '%20s\t %10.0f\n', 'ROI Index = ', roi.index);
fprintf(fid, '%20s\t ', 'area = ');
fprintf(fid, '%10.2f\t', roi.area);
fprintf(fid, '\n');
fprintf(fid, '%20s\t ', 'mean = ');
fprintf(fid, '%10.2f\t', roi.mean);
fprintf(fid, '\n');
fprintf(fid, '%20s\t ', 'std = ');
fprintf(fid, '%10.2f\t', roi.std);
fprintf(fid, '\n');
fprintf(fid, '%20s\t ', 'min = ');
fprintf(fid, '%10.2f\t', roi.min);
fprintf(fid, '\n');
fprintf(fid, '%20s\t ', 'max = ');
fprintf(fid, '%10.2f\t', roi.max);
fprintf(fid, '\n');
fprintf(fid, '%20s\t ', 'median = ');
fprintf(fid, '%10.2f\t', roi.median);
fprintf(fid, '\n');
fprintf(fid, '%20s\t ', 'roicenter = ');
fprintf(fid, '%10.2f\t', roi.center);
fprintf(fid, '\n');
end
disp(' ');
disp(sprintf('%20s\t %10.0f', 'ROI index = ', roi.index));
disp(sprintf('%20s\t %10.2f', 'area = ', roi.area));
disp(sprintf('%20s\t %10.2f\t %10.2f\t %10.2f', 'mean = ', roi.mean) );
disp(sprintf('%20s\t %10.2f\t %10.2f\t %10.2f', 'std = ', roi.std) );
disp(sprintf('%20s\t %10.2f\t %10.2f\t %10.2f', 'min = ', roi.min) );
disp(sprintf('%20s\t %10.2f\t %10.2f\t %10.2f', 'max = ', roi.max) );
disp(sprintf('%20s\t %10.2f\t %10.2f\t %10.2f', 'median = ', roi.median) );
disp(sprintf('%20s\t %10.2f\t %10.2f\t', 'roicenter [x,y] = ', roi.center));
disp(' ');
croi = croi + 1;
end
if outfn == 0
disp('Done, but ROI statistics were not saved !!!');
disp(' ' );
else
disp(['Done, ROI statistics been output to ', outfn]);
disp('But the image with ROI lines/labels was not saved yet !!!');
fclose(fid);
end
else
disp(' ')
disp(' Number of arguments is incorrect !!!')
disp(' ')
help ROI
end
% end of code
