select a pixel on the grayscale image to get a mask

I would need to understand how to select the pixel from the figure on the left (e.g., with the ginput command) in order to get the figure on the right.

I am currently using this demo by Image Analyst, but I would like to select the region of interest when the original grayscale image appears.

% Demo by Image Analyst
clc;    % Clear the command window.
close all;  % Close all figures (except those of imtool.)
clear;  % Erase all existing variables. Or clearvars if you want.
workspace;  % Make sure the workspace panel is showing.
format long g;
format compact;
fontSize = 16;
markerSize = 40;
%--------------------------------------------------------------------------------------------------------
%    READ IN TEST IMAGE
folder = [];
baseFileName = 'example_my.jpg';
fullFileName = fullfile(folder, baseFileName);
% Check if file exists.
if ~exist(fullFileName, 'file')
    % The file doesn't exist -- didn't find it there in that folder.
    % Check the entire search path (other folders) for the file by stripping off the folder.
    fullFileNameOnSearchPath = baseFileName; % No path this time.
    if ~exist(fullFileNameOnSearchPath, 'file')
        % Still didn't find it.  Alert user.
        errorMessage = sprintf('Error: %s does not exist in the search path folders.', fullFileName);
        uiwait(warndlg(errorMessage));
        return;
    end
end
grayImage = imread(fullFileName);
% Get the dimensions of the image.
% numberOfColorChannels should be = 1 for a gray scale image, and 3 for an RGB color image.
[rows, columns, numberOfColorChannels] = size(grayImage);
if numberOfColorChannels > 1
    % It's not really gray scale like we expected - it's color.
    fprintf('It is not really gray scale like we expected - it is color\n');
    % Extract the blue channel.
    grayImage = rgb2gray(grayImage);
end
% Display the image.
% subplot(2, 2, 1);
figure
imshow(grayImage, []);
impixelinfo;
axis('on', 'image');
title('Original Gray Scale Image', 'FontSize', fontSize, 'Interpreter', 'None');
% Update the dimensions of the image.
% numberOfColorChannels should be = 1 for a gray scale image, and 3 for an RGB color image.
[rows, columns, numberOfColorChannels] = size(grayImage);
% Maximize window.
g = gcf;
g.WindowState = 'maximized';
drawnow;


%--------------------------------------------------------------------------------------------------------
% Threshold to create mask
lowThreshold = 31;
highThreshold = 255;
% Interactively and visually set a threshold on a gray scale image.
% https://www.mathworks.com/matlabcentral/fileexchange/29372-thresholding-an-image?s_tid=srchtitle
% [lowThreshold, highThreshold] = threshold(lowThreshold, highThreshold, grayImage);
mask = grayImage >= lowThreshold & grayImage <= highThreshold;
% xline(lowThreshold, 'Color', 'r', 'LineWidth', 2)
% Get rid of blobs touching the border.
% mask = imclearborder(mask);
% Take 2 largest blobs.
mask = bwareafilt(mask, 2);
% Ask user to click on the blob they want to keep.
% % uiwait(helpdlg('Click on the blob you want to keep'));
% Extract only the blob they clicked on.
mask = bwselect(mask, 8);
% Fill the blobs.
mask = imfill(mask, 'holes');
% subplot(2, 2, 3);
figure
imshow(mask);
impixelinfo;
axis('on', 'image');
title('Mask Image', 'FontSize', fontSize, 'Interpreter', 'None');
g = gcf;
g.WindowState = 'maximized';
drawnow;

Answer 1

[Abhishek]

Hi Alberto,

I understand that you want to interactively select pixels in figures for certain masking application. The code you posted require two coordinate values: one for low threshold and another for high threshold.

You can achieve it through ‘ginput’ function with argument n=2 for high and low threshold. Note that first point you select will correspond to high threshold. Refer to the code below: -

%--------------------------------------------------------------------------------------------------------
% Threshold to create mask
%lowThreshold = 31;
%highThreshold = 255;

[threshold_x, threshold_y] = ginput(2);
highThreshold = grayImage(uint8(threshold_x(1)), uint8(threshold_y(1))); %lighter area
lowThreshold = grayImage(uint8(threshold_x(2)), uint8(threshold_y(2))); %darker area

Using the code, I'm getting following result.

For more information on ginput, you can refer to this documentation page: Identify axes coordinates - MATLAB ginput (mathworks.com)