CROIEditor.m

classdef CROIEditor < handle
    %% CROIEditor
    %
    % A Class with a convenient user interface to define multiple region of 
    % interest (ROI) on a given image.
    % All the imroi tools (freehand, circle, rectangle, polygon) can be used
    % to define these region(s). 
    %
    % Loading and storing of previously defined ROI masks to and from files
    % is easily done via the UI toolbar.
    %
    % Multiple regions are labeled using the connected component labeling
    % method (using the MATLAB built-in bwlabel function).
    %
    % Generated Information: - Binary Mask (obj.roi)
    %                        - Label Mask  (obj.labels)
    %                        - number of independent regions (obj.number)
    % 
    % You can listen to the object's "MaskDefined" event to retrieve the
    % ROI information generated (obj.getROIData) or get them directly from
    % the objects public properties.    
    %
    % Example usage:
    %    myimage = imread('eight.tif');
    %    roiwindow = CROIEditor(myimage);
    %    ...
    %    addlistener(roiwindow,'MaskDefined',@your_roi_defined_callback)
    %    ...
    %    function your_roi_defined_callback(h,e)
    %         [mask, labels, n] = roiwindow.getROIData;
    %         delete(roiwindow); 
    %    end
    %
    % Notes: 
    % - if you assign an new image to the class, the window gets
    %   resized according to the image dimensions to have a smooth looking
    %   UI. Initial height can be defined (set figh).
    % - if you don't like that the window is centered, remove it in
    %   resizeWindow function
    % - you can enable/disable the ROI preview by handing over a 'nopreview'
    %   to the applyclick function
    % - Image Processing Toolbox is needed
    % - please report bugs and suggestions for improvement
    % 
    % autor. Jonas Reber
    % date. Mai 6th 2011
    % email. jonas.reber at gmail dot com
    % web.  desperate-engineers.com
    %
    %%

% Copyright (c) 2011, Jonas Reber
% All rights reserved.
% 
% Redistribution and use in source and binary forms, with or without
% modification, are permitted provided that the following conditions are
% met:
% 
%     * Redistributions of source code must retain the above copyright
%       notice, this list of conditions and the following disclaimer.
%     * Redistributions in binary form must reproduce the above copyright
%       notice, this list of conditions and the following disclaimer in
%       the documentation and/or other materials provided with the distribution
% 
% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
% IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
% ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
% LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
% CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
% SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
% INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
% CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
% ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
% POSSIBILITY OF SUCH DAMAGE.

    events 
        MaskDefined % thrown when "apply" button is hit, listen to this event
                    % to get the ROI information (obj.getROIData)
    end
    
    properties
        image    % image to work on, obj.image = theImageToWorkOn
        roi      % the generated ROI mask (logical)
        labels   % Connected component labens (multi ROI)
        number   % how many ROIs there are
        
        figh = 300; % initial figure height - your image is scaled to fit.
                    % On change of this the window gets resized
    end
    
    properties(Access=private)
        % UI stuff
        guifig    % mainwindow
          imax    % holds working area
          roiax   % holds roid preview image
          imag    % image to work on
          roifig  % roi image 
          tl      % userinfo bar
        
        figw      % initial window height, this is calculated on load
        hwar = 2.1;  % aspect ratio
        
        % Class stuff
        loadmask  % mask loaded from file
        mask      % mask defined by shapes
        current      %  which shape is selected
        shapes = {}; % holds all the shapes to define the mask
        
        % load/save information
        filename
        pathname
    end
    
    %% Public Methods
    methods 
        
        function this = CROIEditor(theImage)    
        % constructor
            % make sure the window appears "nice" (was hard to find this
            % aspect ratio to show a well aligned UI ;)
            this.figw = this.figh*this.hwar;
            
            % invoke the UI window
            this.createWindow;
            
            % load the image
            if nargin > 0
                this.image = theImage;
            else
                this.image = ones(100,100);
            end        

            % predefine class variables
            this.current = 1; 
            this.shapes = {}; % no shapes at start
            this.filename = 'mymask'; % default filename
            this.pathname = pwd;      % current directory
        end
        
        function delete(this)
        % destructor
            delete(this.guifig);
        end 
        
        function set.image(this,theImage)
        % set method for image. uses grayscale images for region selection
            if size(theImage,3) == 3
                this.image = im2double(rgb2gray(theImage));
            elseif size(theImage,3) == 1
                this.image = im2double(theImage);
            else
                error('Unknown Image size?');
            end
            this.resetImages;
            this.resizeWindow;
        end
        
        function set.figh(this,height)
            this.figh = height;
            this.figw = this.figh*this.hwar;
            this.resizeWindow;
        end

        function [roi, labels, number] = getROIData(this,varargin)
        % retrieve ROI Data
            roi = this.roi;
            labels = this.labels;
            number = this.number;
        end        
    end
    
    %% private used methods 
    methods(Access=private)
        % general functions -----------------------------------------------
        function resetImages(this)
            this.newROI;
            
            % load images
            this.imag = imshow(this.image,'parent',this.imax); 
            this.roifig = imshow(this.image,'parent',this.roiax);  
            
            % set masks to blank
            this.loadmask = zeros(size(this.image));
        end
        
        function updateROI(this, a)  
            set(this.tl,'String','ROI not saved/applied','Visible','on','BackgroundColor',[255 182 193]./256);
            this.mask = this.loadmask | zeros(size(this.image)) ;
            for i=1:numel(this.shapes)
               BWadd = this.shapes{i}.createMask(this.imag);
               this.mask = this.mask | BWadd;
            end
            set(this.roifig,'CData',this.image.*this.mask);
        end

        function newShapeCreated(this)
            set(this.shapes{end},'Tag',sprintf('imsel_%.f',numel(this.shapes)));
            this.shapes{end}.addNewPositionCallback(@this.updateROI);
            this.updateROI;
        end

       % CALLBACK FUNCTIONS
       % window/figure
        function winpressed(this,h,e,type)
            SelObj = get(gco,'Parent');
            Tag = get(SelObj,'Tag');
            if and(~isempty(SelObj),strfind(Tag,'imsel_'))
                this.current = str2double(regexp(Tag,'\d','match'));
                for i=1:numel(this.shapes)
                   if i==this.current
                       setColor(this.shapes{i},'red');
                   else
                       setColor(this.shapes{i},'blue');
                   end
                end
            end 
        end
        
        function closefig(this,h,e)
            delete(this);
        end;

        % button callbacks ------------------------------------------------
        function polyclick(this, h,e)
            this.shapes{end+1} = impoly(this.imax);
            this.newShapeCreated; % add tag, and callback to new shape
        end

        function elliclick(this, h,e)
            this.shapes{end+1} = imellipse(this.imax);
            this.newShapeCreated; % add tag, and callback to new shape
        end

        function freeclick(this,h,e)
            this.shapes{end+1} = imfreehand(this.imax);
            this.newShapeCreated; % add tag, and callback to new shape
        end

        function rectclick(this,h,e)
            this.shapes{end+1} = imrect(this.imax);
            this.newShapeCreated; % add tag, and callback to new shape
        end

        function deleteclick(this,h,e)
        % delete currently selected shape
            if ~isempty(this.current) && this.current > 0
                n = findobj(this.imax, 'Tag',['imsel_', num2str(this.current)]);
                delete(n);
                % renumbering of this.shapes: (e.g. if 3 deleted: 4=>3, 5=>4,...
                for i=this.current+1:numel(this.shapes)
                    set(this.shapes{i},'Tag',['imsel_', num2str(i-1)]);
                end
                this.shapes(this.current)=[];
                this.current = numel(this.shapes); 
                this.updateROI;
            else
                disp('first select a shape to remove');
            end
        end
        
        function applyclick(this, h, e, varargin)
            set(this.tl,'String','ROI applied','Visible','on','BackgroundColor','g');
            this.roi = this.mask;
            [this.labels, this.number] = bwlabel(this.mask); 
            
            if~(nargin > 3 && strcmp(varargin{1},'nopreview'))
                % preview window
                preview = figure('MenuBar','none','Resize','off',...
                                 'Toolbar','none','Name','Created ROI', ...
                                 'NumberTitle','off','Color','white',...
                                 'position',[0 0 300 300]);
                movegui(preview,'center');

                imshow(label2rgb(this.labels),'InitialMagnification','fit');
                title({'This is your labeled ROI', ...
                       ['you have ', num2str(this.number), ' independent region(s)']});
                uicontrol('style','pushbutton',...
                       'string','OK!','Callback','close(gcf)');
            end
            notify(this, 'MaskDefined');
        end
    
        function saveROI(this, h,e)
        % save Mask to File
            try 
                [this.filename, this.pathname] = uiputfile('*.mask','Save Mask as',this.filename);
                logicmask = this.mask;
                save([this.pathname, this.filename],'logicmask','-mat');
                set(this.tl,'String',['ROI saved: ' this.filename],'Visible','on','BackgroundColor','g');
            catch
                % aborted
            end
        end

        function openROI(this, h,e)
        % load Mask from File
          this.newROI; % delete stuff
          [this.filename,this.pathname,~] = uigetfile('*.mask');
          try
              b = load([this.pathname,this.filename],'-mat');
              if size(b.logicmask)~=size(this.image)
                  set(this.tl,'String',['Size not matching! ' this.filename],'Visible','on','BackgroundColor','r');
              else
                  this.loadmask = b.logicmask;
                  this.updateROI;
                  set(this.tl,'String',['Current: ' this.filename],'Visible','on','BackgroundColor','g');
              end
          catch
              % aborted
          end
        end

        function newROI(this, h,e)
            this.mask = zeros(size(this.image));
            this.loadmask = zeros(size(this.image));
            % remove all the this.shapes
            for i=1:numel(this.shapes)
                delete(this.shapes{i});
            end
            this.current = 1; % defines the currently selected shape - start with 1
            this.shapes = {}; % reset shape holder
            this.updateROI;
        end
    

        % UI FUNCTIONS ----------------------------------------------------
        function createWindow(this, w, h)
            
            this.guifig=figure('MenuBar','none','Resize','on','Toolbar','none','Name','Analyzer - ROI Editor', ...
                'NumberTitle','off','Color','white', 'units','pixels','position',[0 0 this.figw this.figh],...
                'CloseRequestFcn',@this.closefig, 'visible','off');
            
            % buttons
            buttons = [];
            buttons(end+1) = uicontrol('Parent',this.guifig,'String','Polygon',...
                                       'units','normalized',...
                                       'Position',[0.01 0.8 0.15 0.15], ...
                                       'Callback',@(h,e)this.polyclick(h,e));
            buttons(end+1) = uicontrol('Parent',this.guifig,'String','Ellipse',...
                                       'units','normalized',...
                                       'Position',[0.01 0.65 0.15 0.15],...
                                       'Callback',@(h,e)this.elliclick(h,e));
            buttons(end+1) = uicontrol('Parent',this.guifig,'String','Freehand',...
                                       'units','normalized',...
                                       'Position',[0.01 0.5 0.15 0.15],...
                                       'Callback',@(h,e)this.freeclick(h,e));
            buttons(end+1) = uicontrol('Parent',this.guifig,'String','Rectangle',...
                                       'units','normalized',...
                                       'Position',[0.01 0.35 0.15 0.15],...
                                       'Callback',@(h,e)this.rectclick(h,e));
            buttons(end+1) = uicontrol('Parent',this.guifig,'String','Delete',...
                                       'units','normalized',...
                                       'Position',[0.01 0.2 0.15 0.15],...
                                       'Callback',@(h,e)this.deleteclick(h,e));          
            buttons(end+1) = uicontrol('Parent',this.guifig,'String','Apply',...
                                       'units','normalized',...
                                       'Position',[0.01 0.05 0.15 0.15],...
                                       'Callback',@(h,e)this.applyclick(h,e));

            % axes    
            this.imax = axes('parent',this.guifig,'units','normalized','position',[0.18 0.07 0.4 0.87]);
            this.roiax = axes('parent',this.guifig,'units','normalized','position',[0.59 0.07 0.4 0.87]);
            linkaxes([this.imax this.roiax]);

            % create toolbar
            this.createToolbar(this.guifig);
           
            % add listeners
            set(this.guifig,'WindowButtonDownFcn',@(h,e)this.winpressed(h,e,'down'));
            set(this.guifig,'WindowButtonUpFcn',@(h,e)this.winpressed(h,e,'up')) ;
            
            % axis titles
            uicontrol('tag','txtimax','style','text','string','Working Area','units','normalized',...
                        'position',[0.18 0.95 0.4 0.05], ...
                        'BackgroundColor','w');
            uicontrol('tag','txtroiax','style','text','string','ROI Preview','units','normalized',...
                        'position',[0.59 0.95 0.4 0.05], ...
                        'BackgroundColor','w');

            % file load info
            this.tl = uicontrol('tag','txtfileinfo','style','text','string','','units','normalized',...
                        'position',[0.18 0.01 0.81 0.05], ...
                        'BackgroundColor','g','visible','off');
        end
        
        function resizeWindow(this)
            [h,w]=size(this.image);
            f = w/h;
            this.figw = this.figh*this.hwar*f;
            
            set(this.guifig,'position',[0 0 this.figw this.figh]);
            movegui(this.guifig,'center');
            set(this.guifig,'visible','on');
            
        end
        
        function tb=createToolbar(this, fig)
            tb = uitoolbar('parent',fig);

            hpt=[];
            hpt(end+1) = uipushtool(tb,'CData',localLoadIconCData('file_new.png'),...
                         'TooltipString','New ROI',...
                         'ClickedCallback',...
                         @this.newROI);
            hpt(end+1) = uipushtool(tb,'CData',localLoadIconCData('file_open.png'),...
                         'TooltipString','Open ROI',...
                         'ClickedCallback',...
                         @this.openROI);   
            hpt(end+1) = uipushtool(tb,'CData',localLoadIconCData('file_save.png'),...
                         'TooltipString','Save ROI',...
                         'ClickedCallback',...
                         @this.saveROI);      

            %---
            hpt(end+1) = uitoggletool(tb,'CData',localLoadIconCData('tool_zoom_in.png'),...
                         'TooltipString','Zoom In',...
                         'ClickedCallback',...
                         'putdowntext(''zoomin'',gcbo)',...
                        'Separator','on');                
            hpt(end+1) = uitoggletool(tb,'CData',localLoadIconCData('tool_zoom_out.png'),...
                         'TooltipString','Zoom Out',...
                         'ClickedCallback',...
                         'putdowntext(''zoomout'',gcbo)');     
            hpt(end+1) = uitoggletool(tb,'CData',localLoadIconCData('tool_hand.png'),...
                         'TooltipString','Pan',...
                         'ClickedCallback',...
                         'putdowntext(''pan'',gcbo)');    
        end      
    end  % end private methods
end


% this is copied from matlabs uitoolfactory.m, to load the icons for the toolbar
function cdata = localLoadIconCData(filename)
% Loads CData from the icon files (PNG, GIF or MAT) in toolbox/matlab/icons.
% filename = info.icon;

    % Load cdata from *.gif file
    persistent ICONROOT
    if isempty(ICONROOT)
        ICONROOT = fullfile(matlabroot,'toolbox','matlab','icons',filesep);
    end

    if length(filename)>3 && strncmp(filename(end-3:end),'.gif',4)
        [cdata,map] = imread([ICONROOT,filename]);
        % Set all white (1,1,1) colors to be transparent (nan)
        ind = map(:,1)+map(:,2)+map(:,3)==3;
        map(ind) = NaN;
        cdata = ind2rgb(cdata,map);

        % Load cdata from *.png file
    elseif length(filename)>3 && strncmp(filename(end-3:end),'.png',4)
        [cdata map alpha] = imread([ICONROOT,filename],'Background','none');
        % Converting 16-bit integer colors to MATLAB colorspec
        cdata = double(cdata) / 65535.0;
        % Set all transparent pixels to be transparent (nan)
        cdata(alpha==0) = NaN;

        % Load cdata from *.mat file
    else
        temp = load([ICONROOT,filename],'cdata');
        cdata = temp.cdata;
    end
end