how to find diameter of multiple shapes in one image? i get the error message index exceeds area bounds

obj = imread('venn.png');

imshow(obj)

%%Segmenting image

%% Divide image "obj" into its respective RGB intenstites

red = obj(:,:,1);

green = obj(:,:,2);

blue = obj(:,:,3);

figure(1)

subplot(2,2,1); imshow(obj); title('Original Image');

subplot(2,2,2); imshow(red); title('Red Plane');

subplot(2,2,3); imshow(green); title('Green Plane');

subplot(2,2,4); imshow(blue); title('Blue Plane');

%Threshold the blue plane

figure(2)

level = 0.37;

bw2 = imbinarize(blue,level);

subplot(2,2,1);imshow(bw2); title('Blue plane threshold')

%%Remove Noise

%%Fill any holes

fill = imfill(bw2, 'holes');

subplot(2,2,2); imshow(fill); title('Holes Filled');

%%Remove any blobs on the border of the image

clear = imclearborder(fill);

subplot(2,2,3); imshow(clear); title('Remove blobs on border');

%%Remove blobs that are smaller than 7 pixels across

se = strel('disk',7);

open = imopen(fill,se);

subplot(2,2,4); imshow(clear); title('Remove small blobs')

%% Measure Object Diameter

diameter = regionprops(open,'MajorAxisLength');

%%Show result

figure(3)

imshow(obj)

d = imdistline; %%Include a line to physically measure the ball

so this in this code, i am able to find pixel diameters of the images which have one circle or one square in them but when i try to use images with two shapes in them, such as a venn diagram or just three random shapes in the image, i get this "Index in position 3 exceeds array bounds (must not exceed 1)"

please help asap

Answer 1

[Image Analyst]

You're opening a gray scale image so when you do

green = obj(:,:,2);

it throws an error because there is no second color channel. Before that do this

if ndims(obj) == 1
    message = 'Error because this image is gray scale not color.';
    uiwait(warndlg(message));
    return;
end

Also you could also compute diameters like this:

props = regionprops(open,'EquivDiameter');
allDiameters = 2 * [props.EquivDiameter]

This is the diameter of a circle with the same area as your blob, so it essentially fits a circle to it. MajorAxisLength fits an ellipse to it.

[Madhav Natarajan]

thankyou for replying! the diameter optimisation works great!

but now i tried using a colour image and still the problem persists. i have attached a screenshot for your reference...

please note this happens only when there is more than one shape in the image, the original code works fine where there is one shape , colour or BW, which makes me puzzled. bottom left corner reference image

[Image Analyst]

Looks like your mask is all black meaning your threshold was not chosen correctly. You should put in a check to see that the max of the mask image is 1, not zero

if max(open(:)) == 0
    message = 'Error because no mask was found.';
    uiwait(warndlg(message));
    return;
end

Not sure why you're doing an opening. That's used when you want to clip off little tendrils from your blobs. But if your blobs are really thin it can make them, or parts of them, disappear.

I also wouldn't use "open" as the name of your variable since it's a built-in function. Call it openedImage instead of open.