Merge pull request #684 from softmatterlab/683-eg-CON_Workflow

CON WORKFLOW + GUI

Author: giovannivolpe

braph2/analysis/GUIAnalysis.m

@@ -307,7 +307,7 @@ function init_calc()
 
         for j = 1:1:length(available_settings)
             as = available_settings{j};
-            y_correction = 0.2;
+            y_correction = 0.05;
             inner_panel_y = 1 - j * inner_panel_height + y_correction;
 
             texts(j, 1) = uicontrol('Parent', ui_calc_settings_panel, 'Style', 'text', ...

braph2/analysis/GUIAnalysisSettings.m

@@ -277,7 +277,7 @@ function init_graph_settings()
 
         for j = 1:1:length(available_settings)
             as = available_settings{j};
-            y_correction = 0.2;
+            y_correction = 0.05;
             inner_panel_y = 1 - j * inner_panel_height + y_correction; 
 
             texts(j, 1) = uicontrol('Parent', ui_graph_setttings_inner_panel, 'Style', 'text', ...
@@ -294,11 +294,13 @@ function init_graph_settings()
                 set(fields(j, 1), 'Callback', {@cb_analysis_settings_popup})
             elseif isequal(as{1, 2}, 2) % numerical
                 set(fields(j, 1), 'Style', 'edit');
+                set(fields(j, 1), 'Position', [0.58 inner_panel_y+0.03 0.40 0.04]);
                 set(fields(j, 1), 'String', as{1, 3})  % put default
                 set(fields(j, 1), 'Callback', {@cb_analysis_settings_popup})
             else % logical                
                 set(fields(j, 1), 'Style', 'popup');
                 set(fields(j, 1), 'String', {'true', 'false'}) 
+                set(fields(j, 1), 'FontWeight', 'bold')
                 set(fields(j, 1), 'Callback', {@cb_analysis_settings_popup})
             end
         end
@@ -339,7 +341,11 @@ function cb_analysis_settings_popup(~, ~)
             if rem(j, 2) == 0
                 correlation_rules_array{k} = ['Analysis' dc{1} '.' childs(j).String];
             else
-                correlation_rules_array{k} = childs(j).String{childs(j).Value};
+                if childs(j).Value >= 1
+                    correlation_rules_array{k} = childs(j).String{childs(j).Value};
+                else
+                    correlation_rules_array{k} = childs(j).String;
+                end
             end            
         end
         analysis = ga.getClass();
@@ -608,7 +614,11 @@ function update_matrix()
             if rem(j, 2) == 0
                 correlation_rules_array{k} = ['Analysis' dc{1} '.' childs(j).String];
             else
-                correlation_rules_array{k} = childs(j).String{childs(j).Value};
+                if childs(j).Value >= 1
+                    correlation_rules_array{k} = childs(j).String{childs(j).Value};
+                else
+                    correlation_rules_array{k} = childs(j).String;
+                end
             end            
         end
 

braph2/analysis/GUIMeasurement.m

@@ -1,4 +1,3 @@
-
 function GUIMeasurement(measurement_class, analysis, measure_rules)
 % GUIMEASUREMENT creates a UI figure to specify Measurement settings
 %
@@ -328,7 +327,14 @@ function calculate(analysis, mlist, g)
                             m = analysis.getMeasurement(mlist{mi}, gr, rule, value_step, measure_rules{:}); %#ok<NASGU>
                         end
                     else
-                        m = analysis.getMeasurement(mlist{mi}, gr, rule, value, measure_rules{:}); %#ok<NASGU>
+                        if length(value) > 1
+                            for vals = 1:1:length(value)
+                                value_step = value(vals);
+                                m = analysis.getMeasurement(mlist{mi}, group, rule, value_step, measure_rules{:}); %#ok<NASGU>
+                            end
+                        else
+                            m = analysis.getMeasurement(mlist{mi}, group, rule, value, measure_rules{:}); %#ok<NASGU>
+                        end
                     end
                     msg = ['time = ' int2str(toc(start)) '.'  int2str(mod(toc(start)*10, 10)) 's - group = ' gr.tostring() ' - ' mlist{mi}];
 

braph2/analysis/test_GUIAnalysis.m

@@ -1,6 +1,6 @@
 % test GUIAnalysis
 
-%% Init
+%% Init ST
 
 analysis_file = [fileparts(which('example_workflow_ST_WU.m')) filesep() 'example data ST (MRI)' filesep() 'analysis_example_ST_BUT.analysis'];
 temp = load(analysis_file, '-mat', 'ga', 'BUILD');
@@ -9,4 +9,26 @@
 GUIAnalysis(ga)
 
 set(gcf, 'CloseRequestFcn', 'closereq')
-close(gcf)
+close(gcf)
+
+%% Init FNC
+
+analysis_file = [fileparts(which('example_workflow_FNC_WU.m')) filesep() 'example data FNC (fMRI)' filesep() 'analysis_example_FNC_BUT.analysis'];
+temp = load(analysis_file, '-mat', 'ga', 'BUILD');
+ga = temp.ga;
+
+GUIAnalysis(ga)
+
+set(gcf, 'CloseRequestFcn', 'closereq')
+close(gcf)
+
+%% INIT CON
+
+analysis_file = [fileparts(which('example_workflow_CON_WU.m')) filesep() 'example data CON (DTI)' filesep() 'analysis_example_CON_BUT.analysis'];
+temp = load(analysis_file, '-mat', 'ga', 'BUILD');
+ga = temp.ga;
+
+GUIAnalysis(ga)
+
+set(gcf, 'CloseRequestFcn', 'closereq')
+close(gcf)

braph2/analysis/test_GUIAnalysisSettings.m

@@ -6,12 +6,32 @@
 set(gcf, 'CloseRequestFcn', 'closereq')
 close(gcf)
 
-%% Pass a cohort
+%% Pass a ST cohort
 cohort_file = [fileparts(which('example_workflow_ST_WU.m')) filesep() 'example data ST (MRI)' filesep() 'cohort_example.cohort'];
 temp = load(cohort_file, '-mat', 'cohort', 'selected_group', 'selected_subjects', 'BUILD');
 cohort = temp.cohort;
 
 GUIAnalysisSettings(cohort, 'AnalysisST_BUD')
 
 set(gcf, 'CloseRequestFcn', 'closereq')
-close(gcf)
+close(gcf)
+
+%% Pass a FNC cohort
+cohort_file = [fileparts(which('example_workflow_FNC_WU.m')) filesep() 'example data FNC (fMRI)' filesep() 'cohort_example.cohort'];
+temp = load(cohort_file, '-mat', 'cohort', 'selected_group', 'selected_subjects', 'BUILD');
+cohort = temp.cohort;
+
+GUIAnalysisSettings(cohort, 'AnalysisFNC_BUD')
+
+set(gcf, 'CloseRequestFcn', 'closereq')
+close(gcf)
+
+%% Pass a CON cohort
+cohort_file = [fileparts(which('example_workflow_CON_WU.m')) filesep() 'example data CON (DTI)' filesep() 'cohort_example.cohort'];
+temp = load(cohort_file, '-mat', 'cohort', 'selected_group', 'selected_subjects', 'BUILD');
+cohort = temp.cohort;
+
+GUIAnalysisSettings(cohort, 'AnalysisCON_BUT')
+
+set(gcf, 'CloseRequestFcn', 'closereq')
+close(gcf)

braph2/atlas/test_PlotBrainGraph.m

@@ -16,8 +16,8 @@
 close(gcf)
 close(gcf)
 
-% %% Edges arrows
-% 
+%% Edges arrows
+
 % bg = PlotBrainGraph(atlas);
 % figure
 % bg.hold_on()

braph2/cohort/GUICohort.m

@@ -1318,11 +1318,14 @@ function init_menu()
         set(ui_menu_subjects_move2bottom, 'Callback', {@cb_groups_move2bottom_sub})
 
         analysis_list = Analysis.getList();
+        analysis_list = reshape(analysis_list', [1 numel(analysis_list)]);
         for i = 1:1:length(analysis_list)
             analysis = analysis_list{i};
-            cohort_analysis_menu = uimenu(ui_menu_analysis);
-            set(cohort_analysis_menu, 'Label', [Analysis.getName(analysis) ' ...'])
-            set(cohort_analysis_menu, 'Callback', {@cb_menu_analysis})            
+            if isequal(cohort.getSubjectClass(), Analysis.getSubjectClass(analysis))
+                cohort_analysis_menu = uimenu(ui_menu_analysis);
+                set(cohort_analysis_menu, 'Label', [Analysis.getName(analysis) ' ...'])
+                set(cohort_analysis_menu, 'Callback', {@cb_menu_analysis})
+            end
         end
 
         function cb_menu_analysis(src, ~)