Otsu Thresholding using graythresh

Question

Gucci 2022-2-24

1
链接

此问题的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/1657935-otsu-thresholding-using-graythresh

评论： Image Analyst 2022-3-20

Hello, I have a mat file of roughly 1000 images, uint16 format, which I convert to double format to then threshold each image and subsequently find the center of mass of each image.

Currently, I have to manually look at some images and determine a suitable Threshold value myself to then input into the loop and determine the center of mass, however I need to find a way to perform an automated way of obtaining this 'Th' value, for example using the function 'graythresh' as seen commented below following the file load statement.

When I use this, however it always returns a Th value of 0 with no errors present. Please help in how to properly implement 'graythresh'

clc;
clear;
close all;
load('C:\Users\Mitre\Desktop\trappedbeaddata\new_data\2022_02_17\30pc_laser.mat');
%% Global image threshold using Otsu's method (graythresh)
Th = graythresh(ims);
ImsThresholded = double(ims).*(ims>(Th*max(ims,[],'all')));
%% Simple threshold input
% Th=input('Threshold limit: ');
%% Center Container
center=zeros(2,size(ims,3));   % zeros array
%% Image loop
for x=1:1000
    A=ims(:,:,x);           % suppress output with semicolon
    AA = double(A);         % Convert to double 
%% Size of Matrix A
[r,c]=size(AA);
%% Compare each element of matrix with threshold value
for i=1:r
    for j=1:c
        if AA(i,j)<Th
           AA(i,j)=0;        % suppress output with semicolon
        else
         %  AA(i,j)>Th;      % Remove for textured center
         %  AA(i,j)=1;       % Remove for textured center % suppress output with semicolon
            AA(i,j)=AA(i,j)-Th;   % Value - Threshold value = More complex threshold
        end
    end
end
%% Center of mass method 1: using mean
% https://uk.mathworks.com/matlabcentral/answers/363181-center-of-mass-and-total-mass-of-a-matrix
tot_mass = sum(AA(:));
[ii,jj] = ndgrid(1:size(AA,1),1:size(AA,2));
R = sum(ii(:).*AA(:))/tot_mass;
C = sum(jj(:).*AA(:))/tot_mass;
%% display / store values of x, (C,R) and FrameTime
% display 'x'
%disp("x=" + num2str(x));
% Columns = x-axis // Rows = y-axis
center(:,x) = [C;R];          
end

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Answer 1

Image Analyst 2022-2-24

1
链接

此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/1657935-otsu-thresholding-using-graythresh#answer_903960

在 MATLAB Online 中打开

How many blobs do you expect in the image?

You don't need to convert to double before thresholding.

To compute the center of mass for each blob you can do

props = regionprops(ImsThresholded, ims, 'WeightedCentroid');

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Gucci 2022-3-13

在 MATLAB Online 中打开

Here is the edited code again,

clc;
clear;
close all;
load('30pc_laser.mat');
%% Global image threshold using Otsu's method (graythresh)
Th = graythresh(ims);
ImsThresholded = double(ims).*(ims>(Th*max(ims,[],'all')));
%% Simple threshold input
% Th=input('Threshold limit: ');
%% Center Container
center=zeros(2,size(ims,3));   % zeros array
%% Image loop
for x=1:3
    A=ims(:,:,x);           
    AA = double(A);         % Convert to double 
%% Size of Matrix A
[r,c]=size(AA);
%% Compare each element of matrix with threshold value
for i=1:r
    for j=1:c
        if AA(i,j)<Th
           AA(i,j)=0;        % suppress output with semicolon
        else
         %  AA(i,j)>Th;      % Remove for textured center
         %  AA(i,j)=1;       % Remove for textured center % suppress output with semicolon
            AA(i,j)=AA(i,j)-Th;   % Value - Threshold value = More complex threshold
        end
    end
end
%% Center of mass method 1: using mean
tot_mass = sum(AA(:));
[ii,jj] = ndgrid(1:size(AA,1),1:size(AA,2));
R = sum(ii(:).*AA(:))/tot_mass;
C = sum(jj(:).*AA(:))/tot_mass;
%% display / store values of x, (C,R) and FrameTime
% display 'x'
%disp("x=" + num2str(x));
% Columns = x-axis // Rows = y-axis
center(:,x) = [C;R];          
end

Gucci 2022-3-19

hi @Image Analyst, Im still a bit confused, been trying this graythresh method, but getting no progress

Image Analyst 2022-3-20

在 MATLAB Online 中打开

You can mask your image to erase/blacken pixels below the threshold then if you don't want to use regionprops() you can do it manually like this:

grayImage = imread('moon.tif');
[rows, columns, numberOfColorChannels] = size(grayImage);
imshow(grayImage);
axis('on', 'image');
sumgx = 0;
sumgy = 0;
sumg = 0;
sumg = sum(grayImage(:))
for col = 1 : columns
    for row = 1 : rows
        gl = double(grayImage(row, col));
        sumgx = sumgx + col * gl;
        sumgy = sumgy + row * gl;
    end
end
xCOG = sumgx / sumg
yCOG = sumgy / sumg
hold on
xline(xCOG, 'LineWidth', 2, 'Color','r');
yline(yCOG, 'LineWidth', 2, 'Color','r');
caption = sprintf('Center of Gravity: (%.2f, %.2f)', xCOG, yCOG);
title(caption, 'FontSize', 18)