%% bubbles_annotator
%{
Version: v6
Description: 
This script provides a user interface to manually draw bubble contours on a 
sequence of images. It allows the user to define regions of interest (ROIs) 
interactively. The contour data for all processed images is then aggregated 
and can be exported to a single, structured JSON file.

Instructions:
1. Run this script in MATLAB.
2. A dialog will appear. Select the folder containing your images.
3. For each image, a figure window will open.
   - Left-click to place the vertices of a polygon around a bubble.
   - Keyboard backspace to undo a click point.
   - Double-click to finalize the shape. The bubble will be drawn in red.
4. After each bubble, a dialog will ask for your next action.
   - 'Define more': Draw another bubble on the same image.
   - 'Redefine last bubble': Erase the last bubble you just drew.
   - 'Reset all': Clear all bubbles on the current image and start over.
   - 'Next image': Move to the next image in the folder.
   - 'Stop defining': End the annotation session.
5. At the end, you will be prompted to save all collected data to a JSON file.

Last modified: 2025/10/08
Author: Lige Zhang
Reference: International Journal of Heat and Mass Transfer 255 (2026): 127894.
%}
%% ------------------- Setup -------------------
clear, clc
close all
format long
%% --------------------- SCRIPT INITIALIZATION ---------------------
% Let the user interactively select the folder containing the images
imageFolderDIR = uigetdir('', 'Select the folder containing your SOURCE images');
if imageFolderDIR == 0
    disp('Source folder selection cancelled. Script terminated.');
    return;
end

% --- Automatically create a subfolder for the images results ---
outputFolderDIR = fullfile(imageFolderDIR, 'annotated_results');
if ~exist(outputFolderDIR, 'dir')
    mkdir(outputFolderDIR);
end

% User-configurable settings
img_type = '.jpg';
output_json_filename = 'bubble_labeled_data.json';

% Get a list of all image files of the specified type in the folder
im_files = dir(fullfile(imageFolderDIR, ['*' img_type]));
if isempty(im_files)
    disp(['No images of type "' img_type '" found in the source folder.']);
    return;
end

% Initialize a master struct to store data for all images
allFramesData = struct;
disp(['Found ' num2str(length(im_files)) ' images to process.']);

%% --------------------- MAIN PROCESSING LOOP ---------------------
for j = 1:length(im_files)
    
    imageFileName = im_files(j).name;
    
    % Create a custom, MATLAB-compatible struct field name
    imageName = strrep(imageFileName, img_type, '');
    imageName = strrep(imageName, '.', 'd');
    imageName = strrep(imageName, '-', '');
    if isstrprop(imageName(1), 'digit')
        imageName = ['Image' imageName];
    end
    
    % Call the interactive drawing function for the current image
    [stop_processing, imageBubblesData] = drawROI(imageFolderDIR, imageFileName); 
    
    % Store the data for the current image in the master struct
    allFramesData.(imageName) = imageBubblesData;
    
    % --- NEW: Save the annotated image ---
    if ~isempty(fieldnames(imageBubblesData.Bubbles))
        % Load the original image again
        I = imread(fullfile(imageFolderDIR, imageFileName));
        % Create a new figure, but keep it invisible
        fig_to_save = figure('Visible', 'off');
        imshow(I);
        hold on;
        
        % Get the names of the bubbles to draw
        bubble_names = fieldnames(imageBubblesData.Bubbles);
        for i = 1:length(bubble_names)
            bubble_data = imageBubblesData.Bubbles.(bubble_names{i});
            plot(bubble_data.x_coordinate, bubble_data.y_coordinate, 'r--', 'LineWidth', 2);
        end
        hold off;
        
        % Save the figure to the selected output directory
        output_image_path = fullfile(outputFolderDIR, imageFileName);
        saveas(fig_to_save, output_image_path);
        close(fig_to_save); % Close the invisible figure
    end
    
    % Display progress to the user
    remaining = length(im_files) - j;
    disp(['Number of images remaining to process: ' num2str(remaining)])
    
    if stop_processing
        disp('User stopped the process.');
        break
    end
end

%% --------------------- EXPORT TO JSON FILE ---------------------
if ~isempty(fieldnames(allFramesData))
    jsonText = jsonencode(allFramesData, "PrettyPrint", true);
    
    promptMessage = 'Save the collected bubble data to a JSON file?';
    titleBarCaption = 'Export Data';
    button = questdlg(promptMessage, titleBarCaption, 'Save', 'Do Not Save', 'Save');
    
    if strcmpi(button, 'Save')
        % --- CHANGE: Save JSON to the selected output directory ---
        json_output_path = fullfile(outputFolderDIR, output_json_filename);
        fileID = fopen(json_output_path, 'w');
        fprintf(fileID, jsonText);
        fclose(fileID);
        disp(['Data successfully saved to: ' json_output_path]);
    else
        disp('Data not saved.');
    end
end

disp('Annotation process finished.');


%% #################### LOCAL FUNCTION: drawROI (Unchanged) ####################
function [stop_define, imageBubblesData] = drawROI(imageFolderDIR, imageFileName)
    
    stop_define = false;
    ImageFile = fullfile(imageFolderDIR, imageFileName);
    
    I = imread(ImageFile);
    if size(I, 3) == 3
        I = rgb2gray(I);
    end
    
    regionsOfInterests = struct;
    
    fig = figure(1);
    imshow(I);
    title({imageFileName, 'Left-click to draw; Keyboard backspace to undo a click point; Double-click to finish a bubble.'}, 'Interpreter', 'none');
    hold on;
    
    while true
        roi = drawpolygon('Color','g');
        
        xi = round(roi.Position(:,1));
        yi = round(roi.Position(:,2));
        
        plot(xi, yi, 'r--', 'LineWidth', 2);
        
        num_regions = length(fieldnames(regionsOfInterests)) + 1;
        bubble_name = ['b' sprintf('%04d', num_regions)];
        bubble_data = struct('x_coordinate', xi, 'y_coordinate', yi);
        regionsOfInterests.(bubble_name) = bubble_data;

        promptMessage = 'What to do next?';
        titleBarCaption = 'Action';
        choices = {'Define more', 'Redefine last bubble', 'Reset all', 'Next image', 'Stop defining'};
        
        [indx, tf] = listdlg('PromptString', promptMessage, ...
                           'SelectionMode', 'single', ...
                           'ListString', choices, ...
                           'Name', titleBarCaption, ...
                           'ListSize', [250, 120]);
        
        if ~tf
            choice = 'Next image';
        else
            choice = choices{indx};
        end
        
        switch choice
            case 'Define more'
                continue;
                
            case 'Redefine last bubble'
                disp('Removing the last drawn bubble.');
                bubble_names = fieldnames(regionsOfInterests);
                if ~isempty(bubble_names)
                    last_bubble_name = bubble_names{end};
                    regionsOfInterests = rmfield(regionsOfInterests, last_bubble_name);
                    cla;
                    imshow(I);
                    title({imageFileName, 'REDEFINE LAST: Left-click to draw, Double-click to finish.'}, 'Interpreter', 'none');
                    hold on;
                    remaining_bubble_names = fieldnames(regionsOfInterests);
                    for i = 1:length(remaining_bubble_names)
                        bubble_data = regionsOfInterests.(remaining_bubble_names{i});
                        plot(bubble_data.x_coordinate, bubble_data.y_coordinate, 'r--', 'LineWidth', 2);
                    end
                else
                    disp('No bubbles to redefine.');
                end
                continue;

            case 'Reset all'
                disp('Clearing all bubbles for this image. Please start again.');
                regionsOfInterests = struct;
                cla; 
                imshow(I);
                title({imageFileName, 'RESET: Left-click to draw, Double-click to finish.'}, 'Interpreter', 'none');
                continue;
                
            case 'Next image'
                break;
                
            case 'Stop defining'
                stop_define = true;
                break;
        end
    end
    
    close(fig);
    
    imageBubblesData = struct;
    imageBubblesData.FileName = imageFileName;
    imageBubblesData.Bubbles = regionsOfInterests;
end