CellCounter.m

classdef CellCounter < handle
    
    properties
        widget_MouseFigure
        widget_ManualCellCounter
        widget_PiaSelector
        widget_ImageBrowser
        widget_FolderBrowser
        
        fig
        currentFileName
        distances
        
    end
    
    methods
        
        function obj = CellCounter()
            addpath(genpath('./submodules/'));

            obj.fig = figure('Position', [0,0, 400, 800]);

            cellCounterPanel = uipanel('Parent', obj.fig,...
                          'Position',[0 .1 1 .1]);

            piaPanel = uipanel('Parent', obj.fig,...
                          'Position',[0 .2 1 .1]);

            imagePanel = uipanel('Parent', obj.fig,...
                          'Position',[0 .3 1 .45]);

            folderPanel = uipanel('Parent', obj.fig,...
                          'Position',[0 .75 1 .25]);
            
            obj.widget_MouseFigure = MouseFigure();
            
            imageAxes = obj.widget_MouseFigure.handle_axes;
            
            set(imageAxes, 'nextPlot', 'add');
            
            obj.widget_ImageBrowser = WidgetImageBrowser('Parent', imagePanel, 'Axes', imageAxes);
            obj.widget_PiaSelector = WidgetPiaSelector('Parent', piaPanel, 'Axes', imageAxes);
            
            obj.widget_ManualCellCounter = WidgetManualCellCounter('Parent', cellCounterPanel, 'Axes', imageAxes);
            obj.widget_FolderBrowser = WidgetFolderBrowser('parent', folderPanel);

            addlistener(obj.widget_FolderBrowser, 'event_newFile', @obj.on_newFile);
            addlistener(obj.widget_MouseFigure, 'event_clickUp', @obj.on_event_clickUp);
            addlistener(obj.widget_MouseFigure, 'event_pressDel', @obj.on_pressDel);
            
            uicontrol('Style', 'pushbutton',...
                'Parent', obj.fig,...
                'String', 'Export',...
                'Units', 'normalized',...
                'Position', [0,0,1,.1],...
                'Callback', @obj.on_export);
        
        end
        
        function obj = on_newFile(obj, ~, event)
            obj.currentFileName = event.userdata;
            obj.widget_ImageBrowser.read(event.userdata);
            obj.widget_ManualCellCounter.reset();
        end
        
        function obj = on_event_clickUp(obj, ~, event) %Event forwarding
            if ~obj.widget_PiaSelector.isCurrentlySelecting
                obj.widget_ManualCellCounter.on_event_clickUp(obj, event);
            end
        end
        
        function obj = on_pressDel(obj, ~, event) %Event forwarding
            obj.widget_ManualCellCounter.on_pressDel(obj, event);
        end
        
        function obj = on_export(obj, ~, ~)
            obj.calculateDistances();
            exportMat = [obj.widget_ManualCellCounter.countIndices, obj.widget_ManualCellCounter.locations, obj.distances];
            
            [pathstr, name, ~] = fileparts(obj.currentFileName);
            exportFileName = [pathstr, filesep, name, '_counts.csv'];
            fid = fopen(exportFileName,'w');
            fprintf(fid, 'counter, x, y, distance from pia [px]\n');
            fclose(fid);
            
            dlmwrite (exportFileName, exportMat, '-append');
            msgbox(['Wrote: ', exportFileName]);
        end
        
        function obj = calculateDistances(obj)
            
            locations = obj.widget_ManualCellCounter.locations;
            piaPos = obj.widget_PiaSelector.piaPos';
           
            obj.distances = nan(size(locations,1),1);
            for i = 1:size(locations,1)
                minDist = Inf;
                for j = 1:size(piaPos,1) 
                    dist = pdist([locations(i,:) ; piaPos(j,:)]);
                    if dist < minDist
                        minDist = dist;
                    end
                end
                obj.distances(i) = minDist;
            end
        end
        
        function delete(~)
            
            if exist('obj', 'var')
                if exist(obj.fig, 'figure')
                    close(obj.fig);
                end
                delete(obj.widget_MouseFigure);
                delete(obj.widget_ManualCellCounter);
                delete(obj.widget_PiaSelector);
                delete(obj.widget_ImageBrowser);
                delete(obj.widget_FolderBrowser);
            end
        end
    
    end
    
end