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| function roi = multiROI(img, nroi)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% 1) Goal: Draw & process multiple ROIs interactively on an image. %
%% %
%% 2) Usage: multiROI(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. %
%% You may used img = imread(...) to read an image into your WorkSpace, show it %
%% by imshow(img), then use multiROI(img, nroi) to process it; %
%% Alternatively, if there is no image in your WorkSpace, you MUST use square %
%% brackets to occupy the argument space for img, for example, multiROI([],nroi) %
%% let you open a new image and process correspondingly. %
%% %
%% 3) Results: ROI statistics are displayed on screen or output to file (optional). %
%% %
%% 4) Notes: Since ROI was drawn by Spline interpolation, it is desirable to have %
%% more data points at around the sharp corner region; The line/label color was %
%% 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 process. %
%% %
%% Shanrong Zhang %
%% Department of Radiology %
%% University of washington %
%% 02/05/2004 %
%% %
%% email: zhangs@u.washington.edu %
%% %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if nargin == 2
% get current image handle
fighandle = findobj(0, 'Type', 'Figure');
imhandle = findobj(0, 'Type', 'Image');
oldpathname = pwd;
% if no image opened, open a new one
if isempty(imhandle)
if length(img) == 0
[filename pathname] = uigetfile('*.*','Please select an image file');
if filename ~= 0
% cd(pathname);
img = imread([pathname filename]);
imhandle = imshow(img);
cd(oldpathname);
else
disp('Cancel by user!')
return
end
else
imhandle = imshow(img);
end
end
axishandle = gca;
[nrows, ncols, ncolors] = size(img);
% Save ROIs to a file (optional)
[outfilename, outpathname] = uiputfile('*', 'Select an output file');
if outfilename == 0
disp('ROI results were not saved!');
else
fid = fopen([outpathname outfilename], 'w+');
fprintf(fid, '%20s\t %-50s\n', 'Date\time = ', datestr(now));
end
% generate a colormap according to number of ROIS
cmap = jet(nroi);
rndp = randperm(nroi);
croi = 1;
% loop untill total number of ROIs been processed
while croi <= nroi
x = [];
y = [];
color = cmap(rndp(croi), :);
if (~isempty(x) & ~isempty(y))
nx = length(x);
ny = length(y);
if (nx<3) | (ny<3)
disp(' ROI size is too small !')
return
x = x(1 : min(nx, ny));
y = y(1 : min(nx, ny));
x( x < 0.5 ) = 0.5;
x( x > ncols+0.5 ) = ncols + 0.5;
y( y < 0.5 ) = 0.5;
y( y > nrows+0.5 ) = nrows + 0.5;
hold on;
linehandle = plot(x, y, 'Color', color);
end
else
% Get the ROI interactively
[x , y, linehandle] = getpoints(axishandle, color);
end;
%Calculate ROI area
n = length(x);
diffx = [diff(x) (x(1) - x(n))];
diffy = [diff(y) (y(1) - y(n))];
avector = y .* diffx + diffx .* diffy ./2;
% Copy area, vectors and linehandle to roi stucture
roi.label = croi;
roi.apix = abs(sum(avector));
roi.x = x;
roi.y = y;
roi.linehandle = linehandle;
% Change the pointer to something that is familiar to Microsoft users...
oldpointershape = get(fighandle, 'Pointer');
set(fighandle, 'Pointer', 'watch');
%Calculate the ROI area in square point units
XData = get(imhandle, 'XData');
YData = get(imhandle, 'YData');
pixarea = (diff(XData) + 1) * (diff(YData) + 1);
% Create the smallest rectangular grid around the ROI
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);
mask = zeros(nrows, ncols);
mask(ygrid, xgrid) = 1;
cdata = get(imhandle, 'CData');
smallcdata = double(cdata(ygrid, xgrid, :));
[m, n, ncolors] = size(smallcdata);
% Analyze only the points in the polygon
k_inside = inpolygon(X, Y, x, y);
Xin = X(k_inside);
Yin = Y(k_inside);
clear X Y
% Determine the center of the polygon and label ROI
roi.center = [mean(Xin(:)), mean(Yin(:))];
text(roi.center(1), roi.center(2), num2str(croi), 'Color', color, 'FontWeight', 'Bold');
clear Xin Yin
% Calculate the mean, SD, etc... and as fields add to roi structure for each color
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;
% Add the date and time for future reference (in files)
roi.timestamp = datestr(now);
% Reset pointer shape
set(fighandle, 'Pointer', oldpointershape);
% write ROI statistics into file if necessary
if outfilename ~= 0
fprintf(fid, '\n');
fprintf(fid, '%20s\t %10.0f\n', 'ROI label = ', roi.label);
fprintf(fid, '%20s\t %10.2f\n', 'pix area = ', roi.apix);
fprintf(fid, '%20s\t ', 'roicenter = ');
fprintf(fid, '%10.2f\t', roi.center);
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');
end
% dispplay each ROI statistics on screen
disp(' ');
disp(fprintf('%20s\t %10.0f', 'ROI label = ', roi.label) );
disp(fprintf('%20s\t %10.2f', 'pix area = ', roi.apix) );
disp(sprintf('%20s\t %10.2f\t %10.2f\t', 'roicenter [x,y] = ', roi.center));
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(' ');
croi = croi + 1;
end
if outfilename ~= 0
disp(['ROI statistics saved into file ', outfilename]);
disp('But the image with ROIs was not !!!');
fclose(fid);
end
else
disp(' ')
disp(' Number of arguments is incorrect!')
disp(' ')
help multiROI
end
%
% LOCAL FUNCTION GETPOINTS
%
function [xs, ys, linehandle] = getpoints(axishandle, color)
% Find parent figure for the argument axishandle
axes(axishandle);
figure(get(axishandle, 'Parent'));
% Change pointer shape
oldpointershape = get(gcf, 'Pointer');
ptrc = ones(16) + 1;
ptrc( 1, :) = 1;
ptrc(16, :) = 1;
ptrc(: , 1) = 1;
ptrc(: ,16) = 1;
ptrc(1:4,8:9) = 1;
ptrc(8:9,1:4) = 1;
ptrc(13:16, 8:9 ) = 1;
ptrc( 8:9 ,13:16) = 1;
ptrc(5:12, 5:12) = NaN;
set(gcf,'Pointer', 'custom',...
'PointerShapeCData', ptrc,...
'PointerShapeHotSpot', [8 8]);
% Prepare for interactive collection of ROI boundary points
hold on
pointhandles = [];
xpts = [];
ypts = [];
splinehandle = [];
n = 0;
but = 1;
BUTN = 0;
KEYB = 1;
done = 0;
% Loop until right hand mouse button or keayboard is pressed
while ~done;
% Analyze each buttonpressed event
keyb_or_butn = waitforbuttonpress;
if keyb_or_butn == BUTN;
currpt = get(axishandle, 'CurrentPoint');
seltype = get(gcf, 'SelectionType');
switch seltype
case 'normal',
but = 1;
case 'alt',
but = 2;
otherwise,
but = 2;
end;
elseif keyb_or_butn == KEYB
but = 2;
end;
% Get coordinates of the last buttonpressed event
xi = currpt(2, 1);
yi = currpt(2, 2);
% Start a spline throught the points or
% update the line through the points with a new spline
if but == 1
if ~isempty(splinehandle)
delete(splinehandle);
end;
pointhandles(n+1) = plot(xi, yi, 'Color', color, 'Marker', 'o');
n = n + 1;
xpts(n, 1) = xi;
ypts(n, 1) = yi;
% Draw a spline line through the points
if n > 1
t = 1:n;
ts = 1: 0.1 : n;
xs = spline(t, xpts, ts);
ys = spline(t, ypts, ts);
splinehandle = plot(xs, ys, 'Color', color);
end;
elseif but > 1
% Exit for right hand mouse button or keyboard input
done = 1;
end;
end;
% Add first point to the end of the vector for spline
xpts(n+1, 1) = xpts(1, 1);
ypts(n+1, 1) = ypts(1, 1);
% (re)draw the final spline
if ~ isempty(splinehandle)
delete(splinehandle);
end;
t = 1:n+1;
ts = 1: 0.25 : n+1;
xs = spline(t, xpts, ts);
ys = spline(t, ypts, ts);
linehandle = plot(xs, ys, 'Color', color);
drawnow;
% Delete the point markers
if ~isempty(pointhandles)
delete(pointhandles)
end;
% Reset pointershape
set(gcf, 'Pointer', oldpointershape);
% END OF LOCAL FUNCTION GETPOINTS
% |
image juste avec des ROI
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