clc;
clear;
img = imread('10.png'); %import the image
Size = size(img);                                %get the size of the image
temp = uint8(ones(Size).*255);                   %create a temp image, same size with original image

%%%%%%%%%%%%%%%%%%%%%%%%%
%The threshold to separate the leaf from the background
%%%%%%%%%%%%%%%%%%%%%%%%%
GreenThreshold = 0;                             %set the green threshold in RGB
HSV2Thresholdmin = 10;                           %Set the minimum threshold of H channel in HSV
HSV2Thresholdmax = 99;                           %Set the maximum threshold of H channel in HSV
VThresholdmin = 46;                              %Set the minimum threshold of V channel in HSV
SThresholdmin = 43;                              %Set the minimum threshold of S channel in HSV

%dissociate RGB values, the green channel value of the leaf will be relatively large, so anything less than the threshold value is not a leaf
for I=1:Size(1)
    for J=1:Size(2)
        if img(I,J,2)>GreenThreshold
            temp(I,J,1) = img(I,J,1);
            temp(I,J,2) = img(I,J,2);
            temp(I,J,3) = img(I,J,3);
        end
    end
end

HSV = rgb2hsv(temp);                           %Convert RGB gamut to HSV gamut
HSV(:,:,1) = HSV(:,:,1).*180;                  %All the values converted by matlab are [0,1], so multiply by the corresponding coefficient to restore the real value
HSV(:,:,2) = HSV(:,:,2).*255;
HSV(:,:,3) = HSV(:,:,3).*255;

LeafArea = 0;                                  %Define variables that whole leaf area
TotalArea = Size(1)*Size(2);                   %The area of the entire image

%%%%%%%%%%%%%%%%%%%%%%%%%%
%On the basis of RGB separation of the leaves, HSV is used to separate them again to ensure the purity of the background and to calculate the size of the leaves
%%%%%%%%%%%%%%%%%%%%%%%%%
for I=1:Size(1)
    for J=1:Size(2)
        if HSV(I,J,1)>HSV2Thresholdmin&&HSV(I,J,1)<HSV2Thresholdmax&&HSV(I,J,2)>SThresholdmin&&HSV(I,J,3)>VThresholdmin %In this range are leaves
            LeafArea = LeafArea+1;
        else  %Otherwise the background will be white
            temp(I,J,1) = 255;
            temp(I,J,2) = 255;
            temp(I,J,3) = 255;
        end
    end
end

TempletSize = round(LeafArea.*0.005);                     %Calculate the area of 10%

imshow(temp);
%%%%%%%%%%%%%%%%%%%%%%%%%
%Mouse position acquisition
%%%%%%%%%%%%%%%%%%%%%%%%%
k = waitforbuttonpress;                                 % Wait for the mouse to press
point1 = get(gca,'CurrentPoint');                       % The mouse was clicked
finalRect = rbbox; 
point2 = get(gca,'CurrentPoint');                       % Loosen the mouse
point1 = point1(1,1:2);                                 % Extract two points
point2 = point2(1,1:2);
p1 = min(floor(point1),floor(point2));                  % Calculate of position
p2 = max(floor(point1),floor(point2));

%%%%%%%%%%%%%%%%%%%%%%%%%%%
%Define 10%
%%%%%%%%%%%%%%%%%%%%%%%%%%%
W = sqrt(TempletSize);                      
H = sqrt(TempletSize);
if abs(p2(2)-p1(2))*abs(p2(1)-p1(1))<TempletSize||abs(p2(2)-p1(2))*abs(p2(1)-p1(1))>TempletSize   %If the area taken from the box is inconsistent with 10%, it shall be adjusted
    p2(2) = round(p2(2)+W-abs(p2(2)-p1(2)));
    p2(1) = round(p2(1)+H-abs(p2(1)-p1(1)));
end

Templet = uint8(ones(abs(p2(2)-p1(2)),abs(p2(1)-p1(1)),3)*255);      %Create template image
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%Saves the area taken from the box to the template image
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
for I=1:abs(p2(2)-p1(2))   
    for J = 1:abs(p2(1)-p1(1))
        Templet(I,J,1) = temp(p1(2)+I-1,p1(1)+J-1,1);
        Templet(I,J,2) = temp(p1(2)+I-1,p1(1)+J-1,2);
        Templet(I,J,3) = temp(p1(2)+I-1,p1(1)+J-1,3);
    end
end

TempletHsv = rgb2hsv(Templet);                          %Convert the template to an HSV gamut
THSize = size(TempletHsv);                              %Calculate the area of the template
THSizeAll = THSize(1)*THSize(2);
SH = (sum(sum(TempletHsv(:,:,1)))/THSizeAll)*180;       %Statistics the average HSV gamut of the template
SS = (sum(sum(TempletHsv(:,:,2)))/THSizeAll)*255;        
SV = (sum(sum(TempletHsv(:,:,3)))/THSizeAll)*255;

GreenHsvThreshold = uint8(SH.*0.8);                     %Set an 80% threshold for average green

HSV = rgb2hsv(temp);                                    %Convert the image to HSV
HSV(:,:,1) = HSV(:,:,1)*180;
out = temp;
YellowTotal = 0; %Create a variable for the yellow area
for I=1:Size(1)
    for J=1:Size(2)
        if HSV(I,J,1)<GreenHsvThreshold&&HSV(I,J,1)>11      %Yellow leaf area calculation and marking
            out(I,J,1) = 255;
            out(I,J,2) = 0;
            out(I,J,3) = 0;
            YellowTotal = YellowTotal+1;
        end
    end
end
imshow(temp);
figure
imshow(out);
W = (YellowTotal/LeafArea)*100;
Text = ['Etiolation rate(W):',num2str(W),'%'];
text(10,10,Text,'horiz','left','color','r') %Mark the Etiolation rate In the Image