[NET-314] Scaling and color choice on chord plots

+nla/+edge/+result/Base.m

@@ -44,7 +44,7 @@ function output(obj, net_atlas, flags, prob_label)
 
             fig = nla.gfx.createFigure();
             matrix_plot = nla.gfx.plots.MatrixPlot(fig, coeff_label, obj.coeff, net_atlas.nets, nla.gfx.FigSize.LARGE, 'lower_limit', obj.coeff_range(1),...
-                'upper_limit', obj.coeff_range(2));
+                'upper_limit', obj.coeff_range(2), 'app_plot', false);
             matrix_plot.displayImage();
             w = matrix_plot.image_dimensions("image_width");
             h = matrix_plot.image_dimensions("image_height");

+nla/+gfx/+plots/MatrixPlot.m

@@ -35,6 +35,7 @@
         current_settings % the settings for the plot (upper, lower, scale)
         display_legend
         p_value_max
+        app_plot % Used when called for FC Avg
     end
 
     properties (Dependent)
@@ -112,12 +113,13 @@
             addParameter(matrix_input_parser, 'y_position', 0, validNumberInput);
             addParameter(matrix_input_parser, 'discrete_colorbar', false, @islogical);
             addParameter(matrix_input_parser, 'plot_scale', nla.gfx.ProbPlotMethod.DEFAULT);
-            addParameter(matrix_input_parser, 'p_value_max', 0.05)
+            addParameter(matrix_input_parser, 'p_value_max', 0.05);
+            addParameter(matrix_input_parser, 'app_plot', true, @islogical)
 
             parse(matrix_input_parser, figure, name, matrix, networks, figure_size, varargin{:});
             properties = {'figure', 'name', 'matrix', 'networks', 'figure_size', 'network_clicked_callback',...
                 'marked_networks', 'figure_margins', 'draw_legend', 'draw_colorbar', 'color_map', 'lower_limit',...
-                'upper_limit', 'x_position', 'y_position', 'discrete_colorbar', 'plot_scale', 'p_value_max'};
+                'upper_limit', 'x_position', 'y_position', 'discrete_colorbar', 'plot_scale', 'p_value_max', 'app_plot'};
             for property = properties
                 obj.(property{1}) = matrix_input_parser.Results.(property{1});
                 if property{1} == "marked_networks"
@@ -182,6 +184,18 @@ function displayImage(obj)
                     'HorizontalAlignment', 'center');
             end
 
+            if isequal(obj.app_plot, false)
+                settings_menu = uimenu(obj.figure, 'Text', 'Settings');
+                change_scale_option = uimenu(settings_menu,'Text','Change Scale');
+                change_scale_option.MenuSelectedFcn = {...
+                    @obj.adjustScale, [obj.lower_limit, obj.upper_limit], obj.figure,...
+                    struct('lower_bound', obj.lower_limit, 'upper_bound', obj.upper_limit, 'p_value_plot_max', obj.p_value_max),...
+                    false...
+                };
+                change_color_map = uimenu(settings_menu, 'Text', 'Change Color Map');
+                change_color_map.MenuSelectedFcn = {@obj.adjustColor, obj.figure, struct('color_map', obj.color_map, 'color_map_name', ""), false};
+            end
+
             obj.fixRendering();
             hold(obj.axes, 'off') % This may have been turned on. Does nothing if it wasn't.
 
@@ -196,7 +210,7 @@ function applyScale(obj, ~, ~, upper_limit_box, lower_limit_box, old_scale, new_
             obj.color_bar.Ticks = [];
 
             color_map = color_map_select;
-            if ~isstring(color_map_select) && ~ischar(color_map_select)
+            if ~isstring(color_map_select) && ~ischar(color_map_select) && ~isequal(color_map, false)
                 color_map = get(color_map_select, "Value");
                 color_map = obj.colormap_choices{color_map};
             end
@@ -207,13 +221,20 @@ function applyScale(obj, ~, ~, upper_limit_box, lower_limit_box, old_scale, new_
             if isnumeric(upper_limit_box)
                 obj.upper_limit = upper_limit_box;
             else
-                obj.upper_limit = get(upper_limit_box, "String");
+                obj.upper_limit = get(upper_limit_box, 'String');
             end
 
             if isnumeric(lower_limit_box)
                 obj.lower_limit = lower_limit_box;
             else
-                obj.lower_limit = get(lower_limit_box, "String");
+                obj.lower_limit = get(lower_limit_box, 'String');
+            end
+
+            if isstring(obj.upper_limit) || ischar(obj.upper_limit)
+                obj.upper_limit = str2double(obj.upper_limit);
+            end
+            if isstring(obj.lower_limit) || ischar(obj.lower_limit)
+                obj.lower_limit = str2double(obj.lower_limit);
             end
 
             if ~isstring(obj.plot_scale)
@@ -239,7 +260,11 @@ function applyScale(obj, ~, ~, upper_limit_box, lower_limit_box, old_scale, new_
             discrete_colors = NetworkResultPlotParameter().default_discrete_colors;
 
             if new_scale == "nla.gfx.ProbPlotMethod.DEFAULT"
-                new_color_map = NetworkResultPlotParameter.getColormap(discrete_colors, obj.upper_limit, color_map);
+                if ~isequal(color_map, false)
+                    new_color_map = NetworkResultPlotParameter.getColormap(discrete_colors, obj.upper_limit, color_map);
+                else
+                    new_color_map = obj.color_map;
+                end
                 obj.plot_scale = new_scale;
             elseif new_scale == "nla.gfx.ProbPlotMethod.LOG"
                 new_color_map = NetworkResultPlotParameter.getLogColormap(discrete_colors, obj.matrix, obj.upper_limit, color_map);
@@ -337,7 +362,7 @@ function removeLegend(obj)
                 image_height = image_height + 20;
             end
 
-            % colorbar margins
+            % colorbar marginsobj
             if obj.draw_colorbar
                 image_width = image_width + obj.colorbar_width + obj.colorbar_offset + obj.colorbar_text_w;
             end
@@ -435,10 +460,10 @@ function addCallback(obj, x)
                 initial_render = false;
                 upper_value = varargin{2};
                 lower_value = varargin{1};
-                if isstring(upper_value)
+                if isstring(upper_value) || ischar(upper_value) % why are strings not chars???
                     upper_value = str2double(upper_value);
                 end
-                if isstring(lower_value)
+                if isstring(lower_value) || ischar(lower_value)
                     lower_value = str2double(lower_value);
                 end
             end
@@ -677,5 +702,22 @@ function applyColorToData(obj, position_x, position_y, chunk_height, chunk_width
             obj.image_display.CData(position_y:position_y + chunk_height - 1, position_x + chunk_width, :) =...
                 repelem(chunk_color(1:size(chunk_color, 1), size(chunk_color, 2), :), obj.elementSize(), 1);
         end
+
+        function adjustScale(obj, src, ~, bounds, plot_figure, parameters, ~)
+            nla.gfx.scaleSelector(src, bounds, plot_figure, parameters, false, @obj.applyScaleWrapper);
+        end
+
+        function adjustColor(obj, src, ~, plot_figure, parameters, ~)
+            nla.gfx.colorSelector(src, plot_figure, parameters, false, @obj.applyScaleWrapper, obj.colormap_choices);
+        end
+
+        function applyScaleWrapper(obj, ~, ~, upper_limit_box, lower_limit_box, color_map, ~, ~, ~)
+            % This is used for the edge trimatrix, fc avg which is why we keep the ProbPlotMethod to DEFAULT
+            if isequal(upper_limit_box, false)
+                upper_limit_box = obj.upper_limit;
+                lower_limit_box = obj.lower_limit;
+            end
+            obj.applyScale(false, false, upper_limit_box, lower_limit_box, "nla.gfx.ProbPlotMethod.DEFAULT", "nla.gfx.ProbPlotMethod.DEFAULT", color_map)
+        end
     end
 end

+nla/+gfx/colorSelector.m

@@ -0,0 +1,46 @@
+function colorSelector(src, plot_figure, plot_parameters, chord_type, callback_function, color_choices)
+    original_figure = src.Parent.Parent;
+    modal = figure('WindowStyle', 'normal', 'Units', 'pixels', 'Position',...
+        [original_figure.Position(1), original_figure.Position(2), original_figure.Position(3) / 2, original_figure.Position(4) / 3]);
+
+    % Color Map selector
+    % Adapted from colormap-dropdown: https://www.mathworks.com/matlabcentral/fileexchange/43659-colormap-dropdown-menu 
+
+    color_map_select = uicontrol('Style', 'popupmenu',...
+        'Position', [90, 130, 275, 30], "Units", "pixels",...
+        'FontName', 'Courier');
+    uicontrol("Style", "text", "string", "Colormaps", "Units", "pixels",...
+        "Position", [color_map_select.Position(1) - 80, color_map_select.Position(2) - 2, 80, color_map_select.Position(4)]);
+    initial_colors = 16;
+    colormap_html = {};
+    for colors = 1:numel(color_choices)
+        colormap_function = str2func(strcat(strcat("@(x) ",lower(color_choices{colors})), "(x)"));
+        CData = colormap_function(initial_colors);
+        new_html_start = '<HTML> ';
+        new_html = '';
+        for color_iterator = initial_colors:-1:1
+            hex_code = nla.gfx.rgb2hex([CData(color_iterator, 1), CData(color_iterator, 2),...
+                CData(color_iterator, 3)]);
+            new_html = [new_html '<FONT bgcolor="' hex_code ' "color="' hex_code '">__</FONT>'];
+        end
+        new_html_end = [new_html ' </HTML>'];
+        new_html = [new_html_start new_html_end];
+        colormap_html = [colormap_html; new_html];
+    end
+
+    if ~isfield(parameters, "color_map_name")
+        parameters.color_map_name = 1;
+    end
+    set(color_map_select, "Value", parameters.color_map_name, "String", colormap_html);
+
+    apply_button_position = [10, 10, 100, 30];
+    apply_button = uicontrol('String', 'Apply',...
+        "Callback", {callback_function, false, false, color_map_select, plot_figure, parameters, chord_type},...
+        "Units", "pixels",...
+        'Position', apply_button_position);
+
+    close_button_position = [apply_button.Position(1) + apply_button.Position(3) + 10,...
+        apply_button.Position(2), apply_button.Position(3), apply_button.Position(4)];
+    uicontrol('String', 'Close', 'Callback', @(~, ~)close(modal), "Units", "pixels", 'Position',...
+        close_button_position);
+end

+nla/+gfx/scaleSelector.m

@@ -0,0 +1,28 @@
+function scaleSelector(src, bounds, plot_figure, parameters, chord_type, callback_function)
+    original_figure = src.Parent.Parent;
+    modal = figure('WindowStyle', 'normal', 'Units', 'pixels', 'Position',...
+        [original_figure.Position(1), original_figure.Position(2), original_figure.Position(3) / 3, original_figure.Position(4) / 3]);
+
+    upper_limit_box = uicontrol('Style', 'edit', "Units", "pixels", 'Position', [90, 130, 100, 30], "String",...
+        bounds(2));
+    upper_limit_box.Position(4) = upper_limit_box.FontSize * 2;
+    lower_limit_box = uicontrol('Style', 'edit', "Units", "pixels", 'Position', [90, 100, 100, 30], "String",...
+        bounds(1)); 
+    lower_limit_box.Position(4) = lower_limit_box.FontSize * 2;
+
+    uicontrol('Style', 'text', 'String', 'Upper Limit', "Units", "pixels", 'Position',...
+        [upper_limit_box.Position(1) - 80, upper_limit_box.Position(2) - 2, 80, upper_limit_box.Position(4)]);
+    uicontrol('Style', 'text', 'String', 'Lower Limit', "Units", "pixels", 'Position',...
+        [lower_limit_box.Position(1) - 80, lower_limit_box.Position(2) - 2, 80, lower_limit_box.Position(4)]);
+
+    apply_button_position = [10, 10, 100, 30];
+    apply_button = uicontrol('String', 'Apply',...
+        "Callback", {callback_function, upper_limit_box, lower_limit_box, false, plot_figure, parameters, chord_type},...
+        "Units", "pixels",...
+        'Position', apply_button_position);
+
+    close_button_position = [apply_button.Position(1) + apply_button.Position(3) + 10,...
+        apply_button.Position(2), apply_button.Position(3), apply_button.Position(4)];
+    uicontrol('String', 'Close', 'Callback', @(~, ~)close(modal), "Units", "pixels", 'Position',...
+        close_button_position);
+end

+nla/+inputField/NetworkAtlasFuncConn.m

@@ -322,8 +322,9 @@ function buttonViewFCAvgClickedCallback(obj)
             fc_avg = copy(obj.func_conn);
             fc_avg.v = mean(fc_avg.v, 2);
             fig_l = nla.gfx.createFigure();
+
             matrix_plot = nla.gfx.plots.MatrixPlot(fig_l, 'FC Average (Fisher Z(R))', fc_avg, obj.net_atlas.nets,...
-                nla.gfx.FigSize.LARGE);
+                nla.gfx.FigSize.LARGE, "app_plot", false);
             fig_l.Position(3) = matrix_plot.image_dimensions("image_width");
             fig_l.Position(4) = matrix_plot.image_dimensions("image_height");
             matrix_plot.displayImage();