tracking_generateLeafInformation.m

function  [EP, LP, TP, leafID, Area, S0] = tracking_generateLeafInformation(testIm, Template, TemplateTip, AllMasks, last_leafID, newS, smallLeaf)


nLeaf = numel(last_leafID);
LP = zeros(nLeaf, 8);
EP = cell(nLeaf, 1);
TP = zeros(nLeaf, 4);
leafID = last_leafID;
Area = zeros(nLeaf, 1);
S0 = newS;

[distanceMap, edgePixelPositionMap] = bwdist(testIm);
edgePixelPositionMap = double(edgePixelPositionMap);
[m, n] = size(testIm);

threshold = 0.1; % distance of tips are 10% larger than the leaf length

combinedMask = zeros(size(testIm));
for i = 1 : nLeaf
    if last_leafID(i)~=0
        combinedMask = combinedMask + AllMasks{i};
    end
end

combinedMask0 = combinedMask;
combinedMask0(combinedMask0>1) = 1;
for i = 1 : nLeaf
    if last_leafID(i)~=0
        mask0 = AllMasks{i};
        residue = combinedMask - mask0;
        overlap1 = 1 - sum(sum(combinedMask0.*mask0))/sum(mask0(:));   % overlap with background
        overlap2 = sum(sum(combinedMask0.*mask0.*residue))/sum(mask0(:)); % overlap with other leaves
        if overlap1 + overlap2 > 0.5 || sum(mask0(:)) < smallLeaf^2 
            leafID(i) = 0;
            S0(i, :) = 0;
        end
    end
end


for i = 1 : nLeaf
    if leafID(i)~=0
        temp = Template{i};
        tempTip = TemplateTip(i, :);

        theta = S0(i, 1);
        r = S0(i, 2);
        tx = S0(i, 3);
        ty = S0(i, 4);

        x0 = temp(:,1) - mean(temp(:,1));
        y0 = temp(:,2) - mean(temp(:,2));

        newTemp = [cos(theta), -sin(theta); sin(theta), cos(theta)]*[x0';y0']*r + repmat([tx+mean(temp(:,1));ty+mean(temp(:,2))], 1, numel(x0));
        x1 = round(newTemp(1, :))';
        y1 = round(newTemp(2, :))';
        index1 = find(x1<1);
        index2 = find(y1<1);
        index3 = find(x1>m);
        index4 = find(y1>n);
        index = unique([index1(:); index2(:); index3(:); index4(:)]);
        x1(index) = [];
        y1(index) = [];
        EP{i} = [x1, y1];
        
        mask = AllMasks{i};
        Area(i) = sum(mask(:));
        
        [xx1, yy1] = ind2sub(size(testIm), edgePixelPositionMap(sub2ind(size(testIm), x1, y1)));

        start_x = min(xx1);
        start_y = min(yy1);
        height = max(xx1) - min(xx1);
        width = max(yy1) - min(yy1);
        score = sum(sum(distanceMap(sub2ind(size(testIm), x1, y1))))/numel(x1);
        LP(i, 4:8) = [start_x, start_y, height, width, score]; 

        newTempTip = [cos(theta), -sin(theta); sin(theta), cos(theta)]*[tempTip(1:2:end)- mean(temp(:,1)); tempTip(2:2:end)- mean(temp(:,2))]*r + repmat([tx + mean(temp(:,1));ty + mean(temp(:,2))], 1, 2);
        tip = round(newTempTip);
        [tip_x, tip_y] = data_adjustWithinImage(testIm, tip(1,:), tip(2,:));
        [tip_x, tip_y] = ind2sub(size(testIm), edgePixelPositionMap(sub2ind(size(testIm), tip_x, tip_y)));
        tip1 = [tip_x; tip_y];
        TP(i, :) = tip1(:)';

        leafLength = sqrt((TP(i,1)-TP(i,3)).^2 + (TP(i,2)-TP(i,4)).^2);
        
        if distanceMap(TP(i,3), TP(i,4)) > threshold*leafLength
            TP(i, 3:4) = [tip(1,2), tip(2,2)];
        end 
    end
end