Net267 remove cohens d effect from user view (#106)

* [NET-267] Hide and disable cohens D, make cohens D calculations zero. Change edge color map to jet(1000)

* Exported mlapp files

---------

Co-authored-by: Andy <me@something.com>
Co-authored-by: Github Action <action@github.com>

Author: 3 people

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

@@ -21,7 +21,7 @@
         figure_size % Size to display. Either nla.gfx.FigSize.SMALL or nla.gfx.FigSize.LARGE
         draw_legend % Legend on/off
         draw_colorbar % Colorbar on/off
-        color_map % Colormap to use (enter 'turbo(256)' for default)
+        color_map % Colormap to use (enter 'jet(1000)' for default)
         marked_networks % networks to mark with a symbol
         discrete_colorbar % colorbar as discrete. TRUE == discrete, FALSE == continuous
         network_clicked_callback % Button function to add to each network. Used for clickable networks
@@ -55,7 +55,7 @@
     end
 
     properties (Constant)
-        colormap_choices = {"Parula", "Turbo", "HSV", "Hot", "Cool", "Spring", "Summer", "Autumn", "Winter", "Gray",...
+        colormap_choices = {"Jet", "Parula", "Turbo", "HSV", "Hot", "Cool", "Spring", "Summer", "Autumn", "Winter", "Gray",...
             "Bone", "Copper", "Pink"}; % Colorbar choices
     end
 
@@ -82,7 +82,7 @@
             % figure_margins = nla.gfx.FigMargins.WHITESPACE
             % draw_legend = true
             % draw_colorbar = true
-            % color_map = turbo(256)
+            % color_map = jet(1000)
             % lower_limit = -0.3
             % upper_limit = 0.3
             % x_position = 0
@@ -104,7 +104,7 @@
             addParameter(matrix_input_parser, 'figure_margins', nla.gfx.FigMargins.WHITESPACE, @isenum);
             addParameter(matrix_input_parser, 'draw_legend', true, @islogical);
             addParameter(matrix_input_parser, 'draw_colorbar', true, @islogical);
-            addParameter(matrix_input_parser, 'color_map', turbo(256));
+            addParameter(matrix_input_parser, 'color_map', jet(1000)); %reverted to jet(1000) by request
             addParameter(matrix_input_parser, 'lower_limit', -0.3, validNumberInput);
             addParameter(matrix_input_parser, 'upper_limit', 0.3, validNumberInput);
             addParameter(matrix_input_parser, 'x_position', 0, validNumberInput);

+nla/+net/+result/+plot/NetworkTestPlotApp.mlapp

@@ -175,28 +175,41 @@ function getPlotTitle(app)
     methods (Access = private)
 
         function cohens_d_filter = createSignificanceFilter(app)
-            cohens_d_filter = nla.TriMatrix(app.edge_test_options.net_atlas.numNets, "logical", nla.TriMatrixDiag.KEEP_DIAGONAL);
-            if isequal(app.CohensDThresholdCheckBox.Enable, true) && isequal(app.CohensDThresholdCheckBox.Value, true)
-                if isequal(app.test_method, "no_permutations") && ~isequal(app.network_test_result.no_permutations, false)
-                    
-                end
-                if isequal(app.test_method, "full_connectome") && ~isequal(app.network_test_result.full_connectome, false)
-                    cohens_d_filter.v = (app.network_test_result.full_connectome.d.v >= app.network_test_options.d_max);
-                end
-                if ~isequal(app.network_test_result.within_network_pair, false) && isfield(app.network_test_result.within_network_pair, "d")...
-                    && ~isequal(app.test_method, "full_connectome")
-                    cohens_d_filter.v = (app.network_test_result.within_network_pair.d.v >= app.network_test_options.d_max);
-                end
-            else
-                cohens_d_filter.v = true(numel(cohens_d_filter.v), 1);   
-            end
+            %REMOVE COHENS D FILTERING UNTIL WE DETERMINE CORRECT CALCULATION FOR IT - ADE 2025MAR24
+            num_nets = app.edge_test_options.net_atlas.numNets;
+            cohens_d_filter = nla.TriMatrix(num_nets, "logical", nla.TriMatrixDiag.KEEP_DIAGONAL);
+            cohens_d_filter.v = true(numel(cohens_d_filter.v), 1);
+            return;
+            
+%             cohens_d_filter = nla.TriMatrix(app.edge_test_options.net_atlas.numNets, "logical", nla.TriMatrixDiag.KEEP_DIAGONAL);
+%             if isequal(app.CohensDThresholdCheckBox.Enable, true) && isequal(app.CohensDThresholdCheckBox.Value, true)
+%                 if isequal(app.test_method, "no_permutations") && ~isequal(app.network_test_result.no_permutations, false)
+%                     
+%                 end
+%                 if isequal(app.test_method, "full_connectome") && ~isequal(app.network_test_result.full_connectome, false)
+%                     cohens_d_filter.v = (app.network_test_result.full_connectome.d.v >= app.network_test_options.d_max);
+%                 end
+%                 if ~isequal(app.network_test_result.within_network_pair, false) && isfield(app.network_test_result.within_network_pair, "d")...
+%                     && ~isequal(app.test_method, "full_connectome")
+%                     cohens_d_filter.v = (app.network_test_result.within_network_pair.d.v >= app.network_test_options.d_max);
+%                 end
+%             else
+%                 cohens_d_filter.v = true(numel(cohens_d_filter.v), 1);   
+%             end
         end
 
         function applyScaleChange(app)
             progress_bar = uiprogressdlg(app.UIFigure, "Title", "Please Wait", "Message", "Applying Changes...", "Indeterminate", true);
             progress_bar.Message = "Chaning scale of existing TriMatrix...";
             app.matrix_plot.applyScale(false, false, app.UpperLimitEditField.Value, app.LowerLimitEditField.Value, app.PlotScaleDropDown.Value, app.ColormapDropDown.Value)
         end
+        
+        function hideCohensDControls(app)
+            app.CohensDThresholdEditField.Visible = false;
+            app.CohensDThresholdCheckBox.Visible = false;     
+            app.CohensDThresholdEditFieldLabel.Visible = false;
+        
+        end
     end
 
 
@@ -213,6 +226,8 @@ function startupFcn(app, network_test_result, edge_test_result, flags, edge_test
                 test_method = "within_network_pair";
             end
 
+            app.hideCohensDControls(); %keep cohens d controls in code, but hide from user until we get right calcluations - ADE2025MAR24
+            
             app.network_test_result = network_test_result;
             app.edge_test_result = edge_test_result;
             app.test_method = test_method;
@@ -232,7 +247,7 @@ function startupFcn(app, network_test_result, edge_test_result, flags, edge_test
             app.ColormapDropDown.Items = app.colormap_choices;
             app.ColormapDropDown.Value = app.colormap_choices{1};
 
-            app.drawTriMatrixPlot()
+            app.drawTriMatrixPlot();
         end
 
         % Callback function
@@ -451,13 +466,14 @@ function createComponents(app)
             % Create CohensDThresholdEditFieldLabel
             app.CohensDThresholdEditFieldLabel = uilabel(app.Panel);
             app.CohensDThresholdEditFieldLabel.HorizontalAlignment = 'right';
+            app.CohensDThresholdEditFieldLabel.Enable = 'off';
             app.CohensDThresholdEditFieldLabel.Position = [195 237 118 22];
             app.CohensDThresholdEditFieldLabel.Text = 'Cohen''s D Threshold';
 
             % Create CohensDThresholdEditField
             app.CohensDThresholdEditField = uieditfield(app.Panel, 'numeric');
+            app.CohensDThresholdEditField.Enable = 'off';
             app.CohensDThresholdEditField.Position = [339 237 52 22];
-            app.CohensDThresholdEditField.Value = 0.5;
 
             % Create ColormapDropDownLabel
             app.ColormapDropDownLabel = uilabel(app.Panel);
@@ -501,9 +517,9 @@ function createComponents(app)
 
             % Create CohensDThresholdCheckBox
             app.CohensDThresholdCheckBox = uicheckbox(app.Panel);
+            app.CohensDThresholdCheckBox.Enable = 'off';
             app.CohensDThresholdCheckBox.Text = 'Cohen''s D Threshold';
             app.CohensDThresholdCheckBox.Position = [257 207 134 22];
-            app.CohensDThresholdCheckBox.Value = true;
 
             % Create ROIcentroidsonbrainplotsCheckBox
             app.ROIcentroidsonbrainplotsCheckBox = uicheckbox(app.Panel);

+nla/+net/+result/+plot/NetworkTestPlotApp_exported.m

@@ -15,31 +15,40 @@
         end
 
         function result_object = run(obj, edge_test_results, network_atlas, result_object)
-            import nla.TriMatrix nla.TriMatrixDiag
-
-            number_of_networks = network_atlas.numNets();
-
-            for row = 1:number_of_networks
-                for column = 1:row
-
-                    network_rho = edge_test_results.coeff.get(network_atlas.nets(row).indexes,...
-                        network_atlas.nets(column).indexes);
-                    
-                    single_sample_d = abs(mean(network_rho)) / std(network_rho);
-                    d = abs((mean(network_rho) - mean(edge_test_results.coeff.v)) / sqrt(((std(network_rho).^2)) +...
-                        (std(edge_test_results.coeff.v).^2)));
-                    
-                    if isprop(result_object, "no_permutations") && ~isequal(result_object.no_permutations, false)
-                        result_object.no_permutations.d.set(row, column, single_sample_d);
-                    end
-                    if isprop(result_object, "full_connectome") && ~isequal(result_object.full_connectome, false)
-                        result_object.full_connectome.d.set(row, column, d);
-                    end
-                    if isprop(result_object, "within_network_pair") && ~isequal(result_object.within_network_pair, false)
-                        result_object.within_network_pair.d.set(row, column, single_sample_d);
-                    end
-                end
-            end
+            
+            
+            %DETERMINED THAT CURRENT COHEN'S D CALC IS INVALID
+            %RETURN WITHOUT MODIFYING EXISTING D PLACEHOLDER VALUE FROM 0            
+            %RECOMMEND THAT, WHEN REENABLED, THIS FN BE CHANGED TO ACCEPT
+            %VECTOR OF INPUT AND RETURN VECTOR OF OUTPUT RATHER THAN
+            %RESULTS CLASS
+            %ADE 2025MAR24
+            return;
+            
+            
+            
+            
+            %LEAVING COMMENTED CODE BELOW THAT WOULD MODIFY FIELDS AS DONE
+            %PREVIOUSLY FOR REFERENCE.
+%             number_of_networks = network_atlas.numNets();
+% 
+%             for row = 1:number_of_networks
+%                 for column = 1:row
+%                     
+%                     if isprop(result_object, "no_permutations") && ~isequal(result_object.no_permutations, false)
+%                         %this_netpair_nonperm_d = COMPUTE NONPERMUTED D HERE;
+%                         result_object.no_permutations.d.set(row, column, this_netpair_nonperm_d);
+%                     end
+%                     if isprop(result_object, "full_connectome") && ~isequal(result_object.full_connectome, false)
+%                         %this_netpair_fullconn_d = COMPUTE FULLCONN D HERE;
+%                         result_object.full_connectome.d.set(row, column, this_netpair_fullconn_d);
+%                     end
+%                     if isprop(result_object, "within_network_pair") && ~isequal(result_object.within_network_pair, false)
+%                         %this_netpair_withinNP_d = COMPUTE WITHIN NET PAIR D HERE
+%                         result_object.within_network_pair.d.set(row, column, this_netpair_withinNP_d);
+%                     end
+%                 end
+%             end
         end
     end
 end

+nla/+net/CohenDTest.m

@@ -64,8 +64,7 @@
         function ranked_results = collateNetworkPermutationResults(obj, nonpermuted_edge_test_results, network_atlas, nonpermuted_network_test_results,...
             permuted_network_test_results, network_test_options)
 
-            % Run Cohen's D
-            cohen_d_test = nla.net.CohenDTest();
+            
 
             % Warning: Hacky code. Because of the way non-permuted network tests and permuted are called from the front, they are stored
             % in different objects. (Notice the input argument for non-permuted network results). Eventually, it should probably be done
@@ -78,10 +77,15 @@
                     end
                 end
             end
-            for test_index = 1:numNetTests(obj)
-                permuted_network_test_results{test_index} = cohen_d_test.run(nonpermuted_edge_test_results, network_atlas,...
-                    permuted_network_test_results{test_index});
-            end
+            
+            % REMOVE CALL TO COHENS D UNTIL WE DETERMINE CORRECT CALC FOR IT ADE 2025MAR24
+            % Run Cohen's D
+%             cohen_d_test = nla.net.CohenDTest();
+%             for test_index = 1:numNetTests(obj)
+%                 
+%                 permuted_network_test_results{test_index} = cohen_d_test.run(nonpermuted_edge_test_results, network_atlas,...
+%                     permuted_network_test_results{test_index});
+%             end
 
             ranked_results = obj.rankResults(network_test_options, permuted_network_test_results, network_atlas.numNetPairs());
         end
@@ -274,11 +278,11 @@
         end
 
         function ranked_results = rankResults(obj, input_options, permuted_network_results, number_of_network_pairs)
-            import nla.net.ResultRank
+            
 
             ranked_results = permuted_network_results;
             for test = 1:numNetTests(obj)
-                ranker = ResultRank(permuted_network_results{test}, number_of_network_pairs);
+                ranker = nla.net.ResultRank(permuted_network_results{test}, number_of_network_pairs);
                 ranked_results_object = ranker.rank();
                 ranked_results{test} = ranked_results_object;
                 if any(strcmp(ranked_results{test}.test_name, obj.correlation_input_tests))

+nla/TestPool.m

@@ -293,9 +293,7 @@ function initFromResult(app, result, file_name, ~, old_data)
                 app.results = false;
             end
 
-            if ~islogical(result.network_test_results)
-                app.genadjustableNetParams();
-            end
+            
         end
 
         function enableNetButtons(app, val)
@@ -416,7 +414,6 @@ function RunButtonPushed(app, event)
             drawnow();
 
             app.setNesting();
-            app.genadjustableNetParams();
 
             close(prog);
         end