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Yu-Wei Chang
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Revert "Merge branch 'develop' into alpha2_MultiplexPipelines"
This reverts commit 699938e, reversing changes made to 5c9cca0.
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‎braph2genesis/pipelines/connectivity-functional multiplex group_average/example_CON_FUN_MP_GA_BUD.m‎

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%EXAMPLE_CON_FUN_MP_GA_BUD
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% Script example pipeline CON FUN MP GA BUD
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clear variables %#ok<*NASGU>
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%% Load BrainAtlas
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im_ba = ImporterBrainAtlasXLS( ...
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'FILE', [fileparts(which('SubjectCON_FUN_MP')) filesep 'example data CON-FUN_MP' filesep 'aal90_atlas.xlsx'], ...
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'WAITBAR', true ...
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);
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ba = im_ba.get('BA');
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%% Load Groups of SubjectCON
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im_gr1 = ImporterGroupSubjectCON_XLS( ...
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'DIRECTORY', [fileparts(which('SubjectCON_FUN_MP')) filesep 'example data CON-FUN_MP' filesep 'xls' filesep 'connectivity' filesep 'GroupName1'], ...
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'BA', ba, ...
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'WAITBAR', true ...
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);
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gr1_CON = im_gr1.get('GR');
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im_gr2 = ImporterGroupSubjectCON_XLS( ...
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'DIRECTORY', [fileparts(which('SubjectCON_FUN_MP')) filesep 'example data CON-FUN_MP' filesep 'xls' filesep 'connectivity' filesep 'GroupName2'], ...
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'BA', ba, ...
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'WAITBAR', true ...
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);
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gr2_CON = im_gr2.get('GR');
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%% Load Groups of SubjectFUN
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im_gr1 = ImporterGroupSubjectFUN_XLS( ...
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'DIRECTORY', [fileparts(which('SubjectCON_FUN_MP')) filesep 'example data CON-FUN_MP' filesep 'xls' filesep 'functional' filesep 'GroupName1'], ...
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'BA', ba, ...
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'WAITBAR', true ...
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);
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gr1_FUN = im_gr1.get('GR');
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im_gr2 = ImporterGroupSubjectFUN_XLS( ...
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'DIRECTORY', [fileparts(which('SubjectCON_FUN_MP')) filesep 'example data CON-FUN_MP' filesep 'xls' filesep 'functional' filesep 'GroupName2'], ...
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'BA', ba, ...
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'WAITBAR', true ...
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);
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gr2_FUN = im_gr2.get('GR');
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%% Combine Groups of SubjectCON with Groups of SubjectFUN
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co_gr1 = CombineGroups_CON_FUN( ...
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'GR1', gr1_CON, ...
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'GR2', gr1_FUN, ...
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'WAITBAR', true ...
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);
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gr1 = co_gr1.get('GR');
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co_gr2 = CombineGroups_CON_FUN( ...
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'GR1', gr2_CON, ...
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'GR2', gr2_FUN, ...
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'WAITBAR', true ...
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);
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gr2 = co_gr2.get('GR');
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%% Analysis CON FUN MP GA BUD
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densities = [0 100];
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a_BUD1 = AnalyzeGroup_CON_FUN_MP_GA_BUD( ...
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'GR', gr1, ...
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'DENSITIES', densities ...
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);
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a_BUD2 = AnalyzeGroup_CON_FUN_MP_GA_BUD( ...
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'GR', gr2, ...
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'DENSITIES', densities ...
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);
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% measure calculation
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g_BUD1 = a_BUD1.get('G');
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degree_BUD1 = g_BUD1.getMeasure('Degree').get('M');
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degree_av_BUD1 = g_BUD1.getMeasure('DegreeAv').get('M');
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distance_BUD1 = g_BUD1.getMeasure('Distance').get('M');
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g_BUD2 = a_BUD2.get('G');
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degree_BUD2 = g_BUD2.getMeasure('Degree').get('M');
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degree_av_BUD2 = g_BUD2.getMeasure('DegreeAv').get('M');
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distance_BUD2 = g_BUD2.getMeasure('Distance').get('M');
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% comparison
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c_BUD = CompareGroup( ...
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'P', 10, ...
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'A1', a_BUD1, ...
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'A2', a_BUD2, ...
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'WAITBAR', true, ...
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'VERBOSE', false, ...
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'MEMORIZE', true ...
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);
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degree_BUD_diff = c_BUD.getComparison('Degree').get('DIFF');
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degree_BUD_p1 = c_BUD.getComparison('Degree').get('P1');
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degree_BUD_p2 = c_BUD.getComparison('Degree').get('P2');
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degree_BUD_cil = c_BUD.getComparison('Degree').get('CIL');
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degree_BUD_ciu = c_BUD.getComparison('Degree').get('CIU');
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degree_av_BUD_diff = c_BUD.getComparison('DegreeAv').get('DIFF');
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degree_av_BUD_p1 = c_BUD.getComparison('DegreeAv').get('P1');
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degree_av_BUD_p2 = c_BUD.getComparison('DegreeAv').get('P2');
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degree_av_BUD_cil = c_BUD.getComparison('DegreeAv').get('CIL');
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degree_av_BUD_ciu = c_BUD.getComparison('DegreeAv').get('CIU');
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distance_BUD_diff = c_BUD.getComparison('Distance').get('DIFF');
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distance_BUD_p1 = c_BUD.getComparison('Distance').get('P1');
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distance_BUD_p2 = c_BUD.getComparison('Distance').get('P2');
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distance_BUD_cil = c_BUD.getComparison('Distance').get('CIL');
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distance_BUD_ciu = c_BUD.getComparison('Distance').get('CIU');

‎braph2genesis/pipelines/connectivity-functional multiplex group_average/example_CON_FUN_MP_GA_WU.m‎

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%EXAMPLE_CON_FUN_MP_GA_WU
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% Script example pipeline CON FUN MP GA WU
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clear variables %#ok<*NASGU>
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%% Load BrainAtlas
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im_ba = ImporterBrainAtlasXLS( ...
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'FILE', [fileparts(which('SubjectCON_FUN_MP')) filesep 'example data CON-FUN_MP' filesep 'aal90_atlas.xlsx'], ...
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'WAITBAR', true ...
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);
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ba = im_ba.get('BA');
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%% Load Groups of SubjectCON
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im_gr1 = ImporterGroupSubjectCON_XLS( ...
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'DIRECTORY', [fileparts(which('SubjectCON_FUN_MP')) filesep 'example data CON-FUN_MP' filesep 'xls' filesep 'connectivity' filesep 'GroupName1'], ...
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'BA', ba, ...
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'WAITBAR', true ...
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);
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gr1_CON = im_gr1.get('GR');
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im_gr2 = ImporterGroupSubjectCON_XLS( ...
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'DIRECTORY', [fileparts(which('SubjectCON_FUN_MP')) filesep 'example data CON-FUN_MP' filesep 'xls' filesep 'connectivity' filesep 'GroupName2'], ...
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'BA', ba, ...
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'WAITBAR', true ...
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);
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gr2_CON = im_gr2.get('GR');
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%% Load Groups of SubjectFUN
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im_gr1 = ImporterGroupSubjectFUN_XLS( ...
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'DIRECTORY', [fileparts(which('SubjectCON_FUN_MP')) filesep 'example data CON-FUN_MP' filesep 'xls' filesep 'functional' filesep 'GroupName1'], ...
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'BA', ba, ...
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'WAITBAR', true ...
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);
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gr1_FUN = im_gr1.get('GR');
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im_gr2 = ImporterGroupSubjectFUN_XLS( ...
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'DIRECTORY', [fileparts(which('SubjectCON_FUN_MP')) filesep 'example data CON-FUN_MP' filesep 'xls' filesep 'functional' filesep 'GroupName2'], ...
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'BA', ba, ...
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'WAITBAR', true ...
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);
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gr2_FUN = im_gr2.get('GR');
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%% Combine Groups of SubjectCON with Groups of SubjectFUN
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co_gr1 = CombineGroups_CON_FUN( ...
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'GR1', gr1_CON, ...
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'GR2', gr1_FUN, ...
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'WAITBAR', true ...
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);
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gr1 = co_gr1.get('GR');
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co_gr2 = CombineGroups_CON_FUN( ...
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'GR1', gr2_CON, ...
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'GR2', gr2_FUN, ...
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'WAITBAR', true ...
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);
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gr2 = co_gr2.get('GR');
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%% Analysis CON FUN MP GA WU
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a_WU1 = AnalyzeGroup_CON_FUN_MP_GA_WU( ...
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'GR', gr1 ...
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);
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a_WU2 = AnalyzeGroup_CON_FUN_MP_GA_WU( ...
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'GR', gr2 ...
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);
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% measure calculation
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g_WU1 = a_WU1.get('G');
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degree_WU1 = g_WU1.getMeasure('Degree').get('M');
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degree_av_WU1 = g_WU1.getMeasure('DegreeAv').get('M');
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distance_WU1 = g_WU1.getMeasure('Distance').get('M');
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g_WU2 = a_WU2.get('G');
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degree_WU2 = g_WU2.getMeasure('Degree').get('M');
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degree_av_WU2 = g_WU2.getMeasure('DegreeAv').get('M');
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distance_WU2 = g_WU2.getMeasure('Distance').get('M');
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% comparison
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c_WU = CompareGroup( ...
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'P', 10, ...
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'A1', a_WU1, ...
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'A2', a_WU2, ...
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'WAITBAR', true, ...
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'VERBOSE', false, ...
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'MEMORIZE', true ...
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);
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degree_WU_diff = c_WU.getComparison('Degree').get('DIFF');
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degree_WU_p1 = c_WU.getComparison('Degree').get('P1');
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degree_WU_p2 = c_WU.getComparison('Degree').get('P2');
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degree_WU_cil = c_WU.getComparison('Degree').get('CIL');
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degree_WU_ciu = c_WU.getComparison('Degree').get('CIU');
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degree_av_WU_diff = c_WU.getComparison('DegreeAv').get('DIFF');
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degree_av_WU_p1 = c_WU.getComparison('DegreeAv').get('P1');
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degree_av_WU_p2 = c_WU.getComparison('DegreeAv').get('P2');
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degree_av_WU_cil = c_WU.getComparison('DegreeAv').get('CIL');
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degree_av_WU_ciu = c_WU.getComparison('DegreeAv').get('CIU');
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distance_WU_diff = c_WU.getComparison('Distance').get('DIFF');
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distance_WU_p1 = c_WU.getComparison('Distance').get('P1');
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distance_WU_p2 = c_WU.getComparison('Distance').get('P2');
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distance_WU_cil = c_WU.getComparison('Distance').get('CIL');
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distance_WU_ciu = c_WU.getComparison('Distance').get('CIU');

‎braph2genesis/pipelines/connectivity-functional multiplex group_average/pipeline_connectivity_functional_multiplex_group_comparison_wu.braph2‎

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%% Pipeline Connectivity-Functional Multiplex Group-Average Comparison WU
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% This is the pipeline script to compare two groups of subjects using connectivity-functional multiplex data averaged by group and weighted undirected graphs.
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% 1. It loads a brain atlas from an XLS file (e.g., desikan_atlas.xlsx).
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% 2.1 It loads the connectivity data of two groups of subjects from two directories (e.g., GroupName1 and GroupName2) containing XLS files of each subject.
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% 2.2 It loads the functional data of two groups of subjects from two directories (e.g., GroupName1 and GroupName2) containing XLS files of each subject.
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% 3. It analyzes the first group using connectivity-functional multiplex analyses (CON_FUN_MP) based on weighted undirected graphs (WU) averaged by group (GA).
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% 4. It analyzes the second group using the same parameters selected for the first group.
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% 5. It compares the results of the two analyses.
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%% Brain Atlas
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ba = ImporterBrainAtlasXLS('WAITBAR', true).get('BA'); % Load a Brain Atlas XLS % Brain Atlas
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%% Groups
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gr1 = ImporterGroupSubjectCON_FUN_MP_XLS('BA', ba, 'WAITBAR', true).get('GR'); % Load Group CON_FUN_MP 1 from XLS % Group CON_FUN_MP 1
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gr2 = ImporterGroupSubjectCON_FUN_MP_XLS('BA', ba, 'WAITBAR', true).get('GR'); % Load Group CON_FUN_MP 2 from XLS % Group CON_FUN_MP 2
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%% Analysis 1
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a_WU1 = AnalyzeGroup_CON_FUN_MP_GA_WU('GR', gr1); % Analyze Group 1 % Group 1 Analysis
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%% Analysis 2
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a_WU2 = AnalyzeGroup_CON_FUN_MP_GA_WU('GR', gr2, 'TEMPLATE', a_WU1); % Analyze Group 2 % Group 2 Analysis
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%% Comparison
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c_WU = CompareGroup('P', 10, 'A1', a_WU1, 'A2', a_WU2, 'MEMORIZE', true); % Compare Groups % Group Comparison
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‎braph2genesis/pipelines/connectivity-functional multiplex/_CombineGroups_CON_FUN.gen.m‎

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%% ¡header!
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CombineGroups_CON_FUN < Element (co, combines the CON subject group with the FUN subject group) combines a group of subjects with connectivity data with a group of subjects with functional data.
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%%% ¡description!
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CombineGroups_CON_FUN combines a group of subjects with connectivity data with a group of subjects with functional data.
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Combines the data uploaded through the connectivity and functional workflows. The ID and covariates of subjects are
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copied from the first group, in this case connectivity.
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%%% ¡seealso!
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Element
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%% ¡props!
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%%% ¡prop!
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ID (data, string) is a few-letter code for the group combiner.
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%%% ¡prop!
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LABEL (metadata, string) is an extended label of the group combiner.
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%%% ¡prop!
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NOTES (metadata, string) are some specific notes about the group combiner.
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%%% ¡prop!
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WAITBAR (metadata, logical) detemines whether to show the waitbar.
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%%% ¡prop!
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GR1 (data, item) is a group of subjects with connectivity data.
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%%%% ¡default!
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Group('SUB_CLASS', 'SubjectCON')
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%%% ¡prop!
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GR2 (data, item) is a group of subjects with functional data.
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%%%% ¡default!
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Group('SUB_CLASS', 'SubjectFUN')
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%%% ¡prop!
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GR (result, item) is a group of subjects with connectivity and functional data.
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%%%% ¡settings!
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'Group'
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%%%% ¡check_value!
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check = any(strcmp(value.get(Group.SUB_CLASS_TAG), subclasses('SubjectCON_FUN_MP', [], [], true)));
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%%%% ¡default!
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Group('SUB_CLASS', 'SubjectCON_FUN_MP', 'SUB_DICT', IndexedDictionary('IT_CLASS', 'SubjectCON_FUN_MP'))
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%%%% ¡calculate!
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wb = braph2waitbar(co.get('WAITBAR'), 0, 'Combining subject groups ...');
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% creates empty Group
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gr = Group( ...
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'SUB_CLASS', 'SubjectCON_FUN_MP', ...
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'SUB_DICT', IndexedDictionary('IT_CLASS', 'SubjectCON_FUN_MP') ...
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);
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% get connectivity and functional groups
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group1 = co.get('GR1');
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group2 = co.get('GR2');
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% assert that the 2 groups have the same number of subjects
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assert(isequal(group1.get('SUB_DICT').length(), group2.get('SUB_DICT').length()), ...
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[BRAPH2.STR ':CombineGroups_CON_FUN:' BRAPH2.BUG_ERR], ...
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['The 2 groups to be combined need to have the same number of subjects while ', ...
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'group 1 has ' tostring(group1.get('SUB_DICT').length()) ' subjects and group 2 has ' tostring(group2.get('SUB_DICT').length()) ' subjects.'])
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% sets group props
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gr.set( ...
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'ID', group1.get('ID'), ...
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'LABEL', group1.get('LABEL'), ...
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'NOTES', 'Combined group with CON and FUN data'...
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);
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subdict = gr.get('SUB_DICT');
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subdict_gr1 = group1.get('SUB_DICT');
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subdict_gr2 = group2.get('SUB_DICT');
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for i = 1:1:group1.get('SUB_DICT').length()
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braph2waitbar(wb, .30 + .70 * i / group1.get('SUB_DICT').length(), ['Combining subject ' num2str(i) ' of ' num2str(group1.get('SUB_DICT').length()) ' ...'])
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sub1 = subdict_gr1.getItem(i);
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sub2 = subdict_gr2.getItem(i);
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CON_FUN_MP = cell(2, 1);
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CON_FUN_MP(1) = {sub1.get('CON')};
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CON_FUN_MP(2) = {sub2.get('FUN')};
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% add CON_FUN_MP subject
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sub = SubjectCON_FUN_MP( ...
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'ID', sub1.get('ID'), ...
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'BA', sub1.get('BA'), ...
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'CON_FUN_MP', CON_FUN_MP, ...
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'age', sub1.get('age'), ...
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'sex', sub1.get('sex') ...
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);
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subdict.add(sub);
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end
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gr.set('sub_dict', subdict);
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value = gr;
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braph2waitbar(wb, 'close')

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