how to calculate the disease severity in percentage.

The severity of a disease depends upon the region being covered by an infection.After identifying the test leaf image sample,percentation of a leaf infection can easily be computed as a ratio of the number of infected pixels is to the number of healthy pixels in the leaf image.

A=(sum of Ai/ AL)*100

Ai is the number of infected image pixels in cluster i(i=1,2,3) and AL represent the total number of pixels lying in the extracted ROI of a leaf image.

upto segmentation code is:

fontSize=10;

location='C:\Users\Keerthi Dev\Desktop\50datasample\original';%folder in which your images exists

ds=imageDatastore(location); %create datastore for all images in your folder

new_folder='C:\Users\Keerthi Dev\Desktop\50datasample\after_resized'; %new folder

k=1;

while hasdata(ds)

img=read(ds); %read image from datastore

scale=imresize(img,[256 256]);

fileName=sprintf('image_%d.jpg',k);

fullFileName=fullfile(new_folder,fileName);

imwrite(scale,fullFileName);

%size(scale)

k=k+1;

%lab conversion

labImage = rgb2lab(scale);

ab = labImage(:,:,2:3);

ab = im2single(ab);

%segmentation

nColors = 3; %repeat the clustering 3 times to avoid local minima

pixel_labels = imsegkmeans(ab,nColors,'NumAttempts',3);

%imshow(pixel_labels,[])

%title('Image labeled by cluster Index');

figure;

subplot(1,4,1)

imshow(scale);

title('leaf image');

mask1 = pixel_labels==1;

cluster1 = scale .* uint8(mask1);

subplot(1,4,2);

imshow(cluster1);

title('objects in cluster1');

mask2 = pixel_labels==2;

cluster2 = scale .* uint8(mask2);

subplot(1,4,3);

imshow(cluster2);

title('objects in cluster2');

mask3 = pixel_labels==3;

cluster3 = scale .* uint8(mask3);

subplot(1,4,4);

imshow(cluster3);

title('objects in cluster3');

end

how to calculate the disease severity?

[Harsh Parikh]

Hi,

I believe the three cluster variables are 'cluster1', 'cluster2' and 'cluster3'.

Depending on the criteria for a pixel to be considered as 'infected' you can use the following piece of code: (I have, as an example, taken the pixel intensity <10, to be considered as an infected pixel.)

cluster1_infected = length(nonzeros(cluster1<10));
cluster2_infected = length(nonzeros(cluster2<10));
cluster3_infected = length(nonzeros(cluster3<10));

disease_severity = ((cluster1_infected+cluster2_infected+cluster3_infected)/(numel(cluster1)+numel(cluster2)+numel(cluster3)))*100

You can change the equations of clusterX_infected according to your need.

[Keerthi D]

When I try this code, healthy leaf also have disease severity. How is it possible?