AutomaticSegmentation

% Copyright (c) 2022 Olivier Rukundo
% Enhancing the Innovation Potential by Advancing the Know-How on Biomedical Image Analysis 
% Kuopio Biomedical Image Analysis (KUBIAC)
% A.I. Virtanen Institute for Molecular Sciences, University of Eastern of Finland, Kuopio
% E-mail: olivier.rukundo@uef.fi | orukundo@gmail.com
% Version 1.0  dated 19.06.2022

classdef AutomaticSegmentation < matlab.apps.AppBase

    % Properties that correspond to app components
    properties (Access = public)
        AUTOMATICSEGMENTATIONOFMINITEMIMAGESUIFigure  matlab.ui.Figure
        SELECTIMAGEButton  matlab.ui.control.Button
        UIAxes             matlab.ui.control.UIAxes
    end

    % Callbacks that handle component events
    methods (Access = private)

        % Button pushed function: SELECTIMAGEButton
        function SELECTIMAGEButtonPushed(app, ~)
            % Button button pushed function
            [file,path] = uigetfile({'*.tif';'*.jpg';'*.bmp';'*.gif';'*.tiff'}, 'Select file');
            if isequal(file,0)
               disp('User selected Cancel');
            else
            T1 = fullfile(path,file);
            FT1 = dir(T1);
            selected_file = fullfile(FT1.folder, FT1.name);
            input_image = imread(selected_file);                                                           
            input_image_uint16 = uint16(input_image); 
            %Loading image
            f = waitbar(0,'Please wait...');
            pause(.5)     
            waitbar(.33,f,'Loading your image');
            pause(1)
            % Automatic segmentation
            warning('off');
            ld = load('unet_VALL');
            netld = ld.net;
            % Processing image
            waitbar(.67,f,'Processing your image');
            pause(1)
            segmented_image = semanticseg(input_image_uint16, netld);
            segmented_image_double = mat2gray(uint8(segmented_image));                     
            % Print outline of segmented image
            segmented_image_uint16 = uint16(255 * segmented_image_double);
            outlined_image_new = PrintOutlineOfMask(input_image_uint16, segmented_image_uint16);
            end
            % Display image
            waitbar(1,f,'Finishing');
            pause(1)    
            close(f)  
            imshow(outlined_image_new, 'parent', app.UIAxes);
        end
    end

    % Component initialization
    methods (Access = private)

        % Create UIFigure and components
        function createComponents(app)

            % Create AUTOMATICSEGMENTATIONOFMINITEMIMAGESUIFigure and hide until all components are created
            app.AUTOMATICSEGMENTATIONOFMINITEMIMAGESUIFigure = uifigure('Visible', 'off');
            app.AUTOMATICSEGMENTATIONOFMINITEMIMAGESUIFigure.Color = [0.502 0.502 0.502];
            app.AUTOMATICSEGMENTATIONOFMINITEMIMAGESUIFigure.Position = [100 100 1342 903];
            app.AUTOMATICSEGMENTATIONOFMINITEMIMAGESUIFigure.Name = 'AUTOMATIC SEGMENTATION OF MINITEM IMAGES';
            app.AUTOMATICSEGMENTATIONOFMINITEMIMAGESUIFigure.Icon = 'icon.jpg';
            app.AUTOMATICSEGMENTATIONOFMINITEMIMAGESUIFigure.WindowState = 'maximized';

            % Create UIAxes
            app.UIAxes = uiaxes(app.AUTOMATICSEGMENTATIONOFMINITEMIMAGESUIFigure);
            title(app.UIAxes, {''; ''; ''; ''; ''; '-'})
            app.UIAxes.AmbientLightColor = 'none';
            app.UIAxes.XTick = [];
            app.UIAxes.YTick = [];
            app.UIAxes.BoxStyle = 'full';
            app.UIAxes.LineWidth = 1.5;
            app.UIAxes.Color = [0.302 0.7451 0.9333];
            app.UIAxes.FontSize = 8;
            app.UIAxes.TitleFontWeight = 'normal';
            app.UIAxes.Clipping = 'off';
            app.UIAxes.Box = 'on';
            app.UIAxes.Position = [352 41 860 847];

            % Create SELECTIMAGEButton
            app.SELECTIMAGEButton = uibutton(app.AUTOMATICSEGMENTATIONOFMINITEMIMAGESUIFigure, 'push');
            app.SELECTIMAGEButton.ButtonPushedFcn = createCallbackFcn(app, @SELECTIMAGEButtonPushed, true);
            app.SELECTIMAGEButton.IconAlignment = 'center';
            app.SELECTIMAGEButton.BackgroundColor = [0.149 0.149 0.149];
            app.SELECTIMAGEButton.FontSize = 20;
            app.SELECTIMAGEButton.FontWeight = 'bold';
            app.SELECTIMAGEButton.FontColor = [0.902 0.902 0.902];
            app.SELECTIMAGEButton.Position = [151 184 202 75];
            app.SELECTIMAGEButton.Text = 'SELECT IMAGE';

            % Show the figure after all components are created
            app.AUTOMATICSEGMENTATIONOFMINITEMIMAGESUIFigure.Visible = 'on';
        end
    end

    % App creation and deletion
    methods (Access = public)

        % Construct app
        function app = AutomaticSegmentation

            % Create UIFigure and components
            createComponents(app)

            % Register the app with App Designer
            registerApp(app, app.AUTOMATICSEGMENTATIONOFMINITEMIMAGESUIFigure)

            if nargout == 0
                clear app
            end
        end

        % Code that executes before app deletion
        function delete(app)

            % Delete UIFigure when app is deleted
            delete(app.AUTOMATICSEGMENTATIONOFMINITEMIMAGESUIFigure)
        end
    end
end