initial commit

CellCounter.m

@@ -0,0 +1,124 @@
+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