fix and refactor

cpp-lln-lab · Jul 29, 2024 · 3918ad5 · 3918ad5
1 parent e3e33bc
commit 3918ad5
Show file tree

Hide file tree

Showing 11 changed files with 316 additions and 257 deletions.
diff --git a/src/batches/stats/setBatchFactorialDesign.m b/src/batches/stats/setBatchFactorialDesign.m
@@ -84,7 +84,7 @@
         assert(~checkSpmMat(rfxDir, opt));
 
         if strcmp(glmType, 'two_sample_t_test')
-          factorialDesign = returnTwoSampleTTestBatch(opt, nodeName);
+          factorialDesign = returnTwoSampleTTestBatch(rfxDir);
         else
           factorialDesign = returnOneWayAnovaBatch(rfxDir);
         end
@@ -267,7 +267,9 @@
 
   assert(iscellstr(icell.scans));
 
-  matlabbatch = returnFactorialDesignBatch(matlabbatch, rfxDir, icell, thisGroup);
+  factorialDesign = returnFactorialDesignBatch(rfxDir, icell, thisGroup);
+
+  matlabbatch{end + 1}.spm.stats.factorial_design = factorialDesign;
 
   mask = getInclusiveMask(opt, nodeName);
   matlabbatch{end}.spm.stats.factorial_design.masking.em = {mask};
@@ -278,8 +280,7 @@
                                                                     'before estimation')));
 end
 
-function matlabbatch = returnFactorialDesignBatch(matlabbatch, directory, icell, thisGroup)
-
+function factorialDesign = returnFactorialDesignBatch(directory, icell, thisGroup)
   if isempty(thisGroup)
     thisGroup = 'GROUP';
   end
@@ -294,13 +295,9 @@
   % If 2 groups, then number of levels = 2
   factorialDesign.des.fd.fact.name = thisGroup;
   factorialDesign.des.fd.fact.levels = numel(icell);
-
-  matlabbatch{end + 1}.spm.stats.factorial_design = factorialDesign;
-
 end
 
 function factorialDesign = returnTwoSampleTTestBatch(directory)
-
   factorialDesign = commonFaxtorialDesignBatch(directory);
 
   factorialDesign.cov = struct('c', {}, 'cname', {}, 'iCFI', {}, 'iCC', {});
@@ -310,11 +307,9 @@
 
   factorialDesign.des.t2.scans1 = {};
   factorialDesign.des.t2.scans2 = {};
-
 end
 
 function factorialDesign = returnOneWayAnovaBatch(directory)
-
   factorialDesign = commonFaxtorialDesignBatch(directory);
 
   factorialDesign.cov = struct('c', {}, 'cname', {}, 'iCFI', {}, 'iCC', {});
@@ -323,7 +318,6 @@
   factorialDesign.des.anova = varianceStruct();
 
   factorialDesign.des.anova.icell(1).scans = {};
-
 end
 
 function factorialDesign = commonFaxtorialDesignBatch(directory)
@@ -360,7 +354,7 @@
   [glmType, groupBy] = bm.groupLevelGlmType(nodeName, participants);
 
   % only certain type of model supported for now
-  if ismember(glmType, {'unknown', 'two_sample_t_test'})
+  if ismember(glmType, {'unknown'})
     % TODO update message to with better info for 2 sample T-Test
     msg = sprintf(['Models other than group average / comparisons ', ...
                    'not implemented yet %s'], commonMsg);
@@ -384,11 +378,13 @@
     msg = sprintf('For one-sample t-test only DummyContrasts are implemented %s', commonMsg);
     notImplemented(mfilename(), msg, opt);
     status = false;
+    return
   end
 
-  if ismember(glmType, {'one_way_anova'}) && ...
+  if ismember(glmType, {'one_way_anova', 'two_sample_t_test'}) && ...
           (isempty(datasetLvlContrasts) || not(isempty(datasetLvlDummyContrasts)))
-    msg = sprintf('For one-way ANOVA only contrasts are yet implemented %s', commonMsg);
+    msg = sprintf(['For one-way ANOVA or 2 samples t-test ', ...
+                   'only contrasts are implemented %s'], commonMsg);
     notImplemented(mfilename(), msg, opt);
     status = false;
   end

diff --git a/src/batches/stats/setBatchGroupLevelContrasts.m b/src/batches/stats/setBatchGroupLevelContrasts.m
@@ -72,7 +72,7 @@
 
       end
 
-    case 'one_way_anova'
+    case {'two_sample_t_test', 'one_way_anova' }
 
       % T test for ANOVA
       %
@@ -123,31 +123,6 @@
 
       end
 
-    case 'two_sample_t_test'
-
-      edge = bm.get_edge('Destination', nodeName);
-      contrastsList = edge.Filter.contrast;
-
-      for j = 1:numel(contrastsList)
-
-        thisContrast = bm.get_contrasts('Name', nodeName);
-
-        spmMatFile = fullfile(getRFXdir(opt, nodeName, contrastsList{j}), 'SPM.mat');
-
-        if ~opt.dryRun
-          assert(exist(spmMatFile, 'file') == 2);
-        end
-
-        for iCon = 1:numel(thisContrast)
-          consess{iCon}.tcon.name = thisContrast{iCon}.Name;
-          consess{iCon}.tcon.convec = thisContrast{iCon}.Weights;
-          consess{iCon}.tcon.sessrep = 'none';
-        end
-
-        matlabbatch = setBatchContrasts(matlabbatch, opt, spmMatFile, consess);
-
-      end
-
     otherwise
       msg = sprintf('Node %s has has model type I cannot handle.\n', nodeName);
       notImplemented(mfilename(), msg, opt);

diff --git a/src/bids_model/getContrastsListForFactorialDesign.m b/src/bids_model/getContrastsListForFactorialDesign.m
@@ -40,7 +40,9 @@
 
       % if no specific dummy contrasts mentioned also include all contrasts from previous levels
       % or if contrasts are mentioned we grab them
-      if ~isfield(node.DummyContrasts, 'Contrasts') || isfield(node, 'Contrasts')
+      if ~isfield(node, 'DummyContrasts') || ...
+              ~isfield(node.DummyContrasts, 'Contrasts') || ...
+              isfield(node, 'Contrasts')
         tmp = getContrastsList(bm, nodeName, participants);
         for i = 1:numel(tmp)
           contrastsList{end + 1} = tmp{i}.Name;

diff --git a/src/bids_model/getDummyContrastsList.m b/src/bids_model/getDummyContrastsList.m
@@ -31,7 +31,7 @@
     end
   end
 
-  if isfield(node.DummyContrasts, 'Contrasts')
+  if isfield(node, 'DummyContrasts') && isfield(node.DummyContrasts, 'Contrasts1')
 
     dummyContrastsList = node.DummyContrasts.Contrasts;
 

diff --git a/src/workflows/stats/bidsRFX.m b/src/workflows/stats/bidsRFX.m
@@ -92,13 +92,13 @@
 
       participants = bids.util.tsvread(fullfile(opt.dir.raw, 'participants.tsv'));
 
+      matlabbatch = {};
+
       for i = 1:numel(datasetNodes)
 
         msg = sprintf('\n PROCESSING NODE: %s\n', nodeName);
         logger('INFO', msg, 'options', opt, 'filename', mfilename());
 
-        matlabbatch = {};
-
         nodeName = datasetNodes{i}.Name;
 
         switch  bm.groupLevelGlmType(nodeName, participants)

diff --git a/tests/tests_slow/tests_workflows/stats/test_bidsRFX.m b/tests/tests_slow/tests_workflows/stats/test_bidsRFX.m
@@ -45,104 +45,6 @@ function test_bidsRFX_rfx()
 
 end
 
-function test_bidsRFX_no_overwrite_smoke_test()
-
-  markTestAs('slow');
-
-  opt = setOptions('vislocalizer',  '', 'pipelineType', 'stats');
-  opt.model.file = spm_file(opt.model.file, ...
-                            'basename', ...
-                            'model-vismotionNoOverWrite_smdl');
-  opt.model.bm = BidsModel('file', opt.model.file);
-
-  matlabbatch = bidsRFX('RFX', opt);
-
-  expectedNbBatch = 7;
-  if bids.internal.is_octave()
-    expectedNbBatch = 5;
-  end
-  assertEqual(numel(matlabbatch), expectedNbBatch);
-
-end
-
-function test_bidsRFX_within_group_ttest()
-
-  markTestAs('slow');
-
-  opt = setOptions('vislocalizer',  '', 'pipelineType', 'stats');
-  opt.model.file = spm_file(opt.model.file, ...
-                            'basename', ...
-                            'model-vislocalizerWithinGroup_smdl');
-  opt.model.bm = BidsModel('file', opt.model.file);
-
-  matlabbatch = bidsRFX('RFX', opt);
-
-  if bids.internal.is_octave()
-    assertEqual(numel(matlabbatch), 10);
-  else
-    assertEqual(numel(matlabbatch), 14);
-  end
-
-  % creates 1 batch for
-  %   - specify
-  %   - figure
-  %   - estimate
-  %   - MACS: model space
-  %   - MACS: information criteria
-  %   - review
-  %   - figure
-  % for each group
-
-  batchOrder = {'stats', 'factorial_design'; ...
-                'util',  'print'; ...
-                'stats', 'factorial_design'; ...
-                'util',  'print'};
-  batchOrder = extendBatchOrder(batchOrder);
-  batchOrder = extendBatchOrder(batchOrder);
-  summary = batchSummary(matlabbatch);
-  assertEqual(summary, batchOrder);
-
-  assertEqual(matlabbatch{1}.spm.stats.factorial_design.dir{1}, ...
-              fileparts(matlabbatch{5}.spm.stats.fmri_est.spmmat{1}));
-  if bids.internal.is_octave()
-    assertEqual(matlabbatch{3}.spm.stats.factorial_design.dir{1}, ...
-                fileparts(matlabbatch{8}.spm.stats.fmri_est.spmmat{1}));
-  else
-    assertEqual(matlabbatch{3}.spm.stats.factorial_design.dir{1}, ...
-                fileparts(matlabbatch{10}.spm.stats.fmri_est.spmmat{1}));
-  end
-
-end
-
-function test_bidsRFX_two_sample_ttest()
-
-  markTestAs('slow');
-
-  opt = setOptions('vislocalizer',  '', 'pipelineType', 'stats');
-  opt.model.file = spm_file(opt.model.file, ...
-                            'basename', ...
-                            'model-vislocalizer2sampleTTest_smdl');
-  opt.model.bm = BidsModel('file', opt.model.file);
-
-  matlabbatch = bidsRFX('RFX', opt);
-
-  summary = batchSummary(matlabbatch);
-
-  % creates 1 batch for (specify, figure, estimate, review, figure)
-  batchOrder = {'stats', 'factorial_design'; ...
-                'util', 'print'};
-  batchOrder = extendBatchOrder(batchOrder);
-  assertEqual(summary, batchOrder);
-
-  assertEqual(matlabbatch{1}.spm.stats.factorial_design.dir{1}, ...
-              fileparts(matlabbatch{3}.spm.stats.fmri_est.spmmat{1}));
-
-  % 2 blind and 1 ctrl
-  assertEqual(numel(matlabbatch{1}.spm.stats.factorial_design.des.t2.scans1), 2);
-  assertEqual(numel(matlabbatch{1}.spm.stats.factorial_design.des.t2.scans2), 1);
-
-end
-
 function test_bidsRFX_select_datasets_level_to_run()
 
   markTestAs('slow');
@@ -168,36 +70,6 @@ function test_bidsRFX_select_datasets_level_to_run()
 
 end
 
-function test_bidsRFX_several_datasets_level()
-
-  markTestAs('slow');
-
-  opt = setOptions('vislocalizer',  '', 'pipelineType', 'stats');
-  opt.model.file = spm_file(opt.model.file, ...
-                            'basename', ...
-                            'model-vislocalizerSeveralDatasetLevels_smdl');
-  opt.model.bm = BidsModel('file', opt.model.file);
-
-  matlabbatch = bidsRFX('RFX', opt);
-
-  summary = batchSummary(matlabbatch);
-
-  % only the batches from the last node is returned
-  % creates 1 batch for (specify, figure, estimate, review, figure)
-  batchOrder = {'stats', 'factorial_design'; ...
-                'util', 'print'};
-  batchOrder = extendBatchOrder(batchOrder);
-  assertEqual(summary, batchOrder);
-
-  nbGroupLevelModelsReturned = 1;
-  nbBatchPerModel = 7;
-  if bids.internal.is_octave()
-    nbBatchPerModel = 5;
-  end
-  assertEqual(numel(matlabbatch), nbGroupLevelModelsReturned * nbBatchPerModel);
-
-end
-
 function test_bidsRFX_rfx_on_empty_dir()
 
   markTestAs('slow');