initial commit

.gitignore

+**/.DS_Store
+**/*.m~

mcode/annotation_example.m

+clear
+close all
+addpath functions 
+
+data_folder = '../data_folder';
+annotate_gui(data_folder)
+%annotate_gui(data_folder,'annotations',YXZ)
+

mcode/functions/annotate_gui.m

+function annotate_gui(data_folder,varargin)
+%ANNOTATE_TRACKING_GUI   GUI for annotating foci in a set of B-scans.
+%   TODO descrube suggested workflow.
+%   ANNOTATE_GUI(DATA)
+%   ANNOTATE_GUI(DATA,Name,Value) sets one or more properties using
+%           name-value pair arguments. Keyboard shortcuts: arrows for
+%           changing B-scan, home and end for first and last, s for save.
+%       DATA_FOLDER, a folder containing tif images.
+%       Name-Value pairs:
+%           'annotations', annotations previously saved from the GUI.
+
+%   Author: vand@dtu.dk, 2020
+
+
+% PARSING INPUTS
+if any(strcmpi(varargin,'ANNOTATIONS'))
+    YXZ = varargin{find(strcmpi(varargin,'ANNOTATIONS'))+1};
+else
+    YXZ = [];
+end
+
+% SETTING UP
+image_list = dir([data_folder,'/*.tif']);
+Y_max = length(image_list);
+readimage = @(y) imread([data_folder,'/',image_list(y).name]);
+Y = 1; % starting with the first image
+current_image = readimage(Y);
+Z_max = size(current_image,1);
+X_max = size(current_image,2);
+
+% for drawing circles
+N = 12; % number of points in the circle
+t = 0:2*pi/N:2*pi*(1-1/N); % radial parameter
+unit_circle = [sin(t); cos(t)]';
+
+% SETTING UP THE FIGURES
+fig_main = figure('Units', 'Normalized', 'Position', [0.0 0.5 1 0.5],...
+    'KeyPressFcn', @key_press, 'WindowButtonUpFcn', @button_up_add_point,...
+    'Name', 'Annotation window');
+fig_3D = figure('Units', 'Normalized', 'Position', [0.3 0.0 0.4 0.3],...
+    'Name','3D visulization window');
+
+R = 5; % initial radius
+circle = R*unit_circle;
+
+update_drawing, hold on, axis image ij, colormap gray
+update_drawing % twice for case when YXZ given
+
+update_surf
+figure(fig_3D), hold on, axis vis3d, figure(fig_main)
+
+
+%%%%%%%%%% CALLBACK FUNCTIONS %%%%%%%%%%
+    function key_press(~,object)
+        % keyboard commands
+        key = object.Key;
+        switch key
+            case 'rightarrow'
+                Y = min(Y+1,Y_max);
+                update_drawing
+            case 'leftarrow'
+                Y = max(Y-1,1);
+                update_drawing
+            case 'home'
+                Y = 1;
+                update_drawing
+            case 'end'
+                Y = Y_max;
+                update_drawing
+%             case 'd'
+%                 if strcmp(object.Modifier,'shift') % only capital letters
+%                     delete_point % TODO
+%                     update_surf
+%                     update_drawing
+%                 end
+            case 's'
+                xlabel('Saving.')
+                drawnow
+                fid = fopen('annotations.txt','w');
+                fprintf(fid,'%d %d %d \n',round(YXZ)');
+                fclose(fid);
+                save('ANNOTIONS_YXZ.mat','YXZ')
+                disp('Ok, saved!')
+                xlabel('Saved.')
+                drawnow
+        end
+    end
+
+
+%%%%%%%%%% HELPING FUNCTIONS %%%%%%%%%%
+    function update_drawing
+        figure(fig_main)
+        current_image = readimage(Y);
+        cla
+        imagesc(current_image)
+        if ~isempty(YXZ)
+            this_image = YXZ(:,1) == Y;
+            if ~isempty(this_image)
+                plot(YXZ(this_image,2)'+circle([1:end,1],1), ...
+                    YXZ(this_image,3)'+circle([1:end,1],2),'r','LineWidth',2)
+            end
+        end
+        title(['Image ', num2str(Y)])
+        xlabel('')
+        drawnow
+    end
+
+    function update_surf
+        figure(fig_3D), cla
+        plot3(...
+            [0,1; 0,1; 0,1; 0,1; 0,0; 1,1; 0,0; 1,1; 0,0; 1,1; 0,0; 1,1]'*(X_max-1)+1,...
+            [0,0; 1,1; 0,0; 1,1; 0,1; 0,1; 0,1; 0,1; 0,0; 0,0; 1,1; 1,1]'*(Y_max-1)+1,...
+            [0,0; 0,0; 1,1; 1,1; 0,0; 0,0; 1,1; 1,1; 0,1; 0,1; 0,1; 0,1]'*(Z_max-1)+1,'k-');
+        if ~isempty(YXZ)
+            plot3(YXZ(:,2),YXZ(:,1),1+Z_max-YXZ(:,3),'ro')
+        end
+        drawnow
+        figure(fig_main)
+    end
+
+    function button_up_add_point(~,~)
+        cp = get(gca,'CurrentPoint');
+        YXZ(end+1,:) = [Y, cp(1,1:2)];
+        update_drawing
+        update_surf
+    end
+
+end
+