fixes

cpp-lln-lab · Jul 30, 2024 · b3722d5 · b3722d5
1 parent 4f103ed
commit b3722d5
Show file tree

Hide file tree

Showing 7 changed files with 55 additions and 79 deletions.
diff --git a/src/batches/stats/setBatchFactorialDesign.m b/src/batches/stats/setBatchFactorialDesign.m
@@ -76,7 +76,7 @@
 
         contrastName = contrastsList{iCon};
 
-        rfxDir = getRFXdir(opt, nodeName, contrastName, '1WayANOVA');
+        rfxDir = getRFXdir(opt, nodeName, contrastName, label);
         overwriteDir(rfxDir, opt);
 
         assert(~checkSpmMat(rfxDir, opt));
@@ -283,7 +283,7 @@
     thisGroup = 'GROUP';
   end
 
-  factorialDesign = commonFaxtorialDesignBatch(directory);
+  factorialDesign = commonFactorialDesignBatch(directory);
 
   factorialDesign.des.fd.icell = icell;
 
@@ -296,7 +296,7 @@
 end
 
 function factorialDesign = returnTwoSampleTTestBatch(directory)
-  factorialDesign = commonFaxtorialDesignBatch(directory);
+  factorialDesign = commonFactorialDesignBatch(directory);
 
   factorialDesign.cov = struct('c', {}, 'cname', {}, 'iCFI', {}, 'iCC', {});
   factorialDesign.multi_cov = struct('files', {}, 'iCFI', {}, 'iCC', {});
@@ -308,7 +308,7 @@
 end
 
 function factorialDesign = returnOneWayAnovaBatch(directory)
-  factorialDesign = commonFaxtorialDesignBatch(directory);
+  factorialDesign = commonFactorialDesignBatch(directory);
 
   factorialDesign.cov = struct('c', {}, 'cname', {}, 'iCFI', {}, 'iCC', {});
   factorialDesign.multi_cov = struct('files', {}, 'iCFI', {}, 'iCC', {});
@@ -318,7 +318,7 @@
   factorialDesign.des.anova.icell(1).scans = {};
 end
 
-function factorialDesign = commonFaxtorialDesignBatch(directory)
+function factorialDesign = commonFactorialDesignBatch(directory)
   factorialDesign.dir = {directory};
   factorialDesign = setBatchFactorialDesignImplicitMasking(factorialDesign);
   factorialDesign = setBatchFactorialDesignGlobalCalcAndNorm(factorialDesign);

diff --git a/src/stats/group_level/getRFXdir.m b/src/stats/group_level/getRFXdir.m
@@ -66,12 +66,8 @@
   end
 
   sub = 'ALL';
-  if ~isempty(contrastName)
-    participants = bids.util.tsvread(fullfile(opt.dir.raw, 'participants.tsv'));
-    groupColumnHdr = opt.model.bm.getGroupColumnHdrFromGroupBy(nodeName, participants);
-    if ~isempty(groupColumnHdr) && ~isempty(thisGroup)
-      sub = thisGroup;
-    end
+  if ~isempty(contrastName) && ~isempty(thisGroup)
+    sub = thisGroup;
   end
 
   glmDirName = ['sub-', sub, '_', glmDirName];

diff --git a/tests/data/models/model-vismotionNoOverWrite_smdl.json b/tests/data/models/model-vismotionNoOverWrite_smdl.json
@@ -191,7 +191,7 @@
     {
       "Level": "Dataset",
       "Name": "between_groups",
-      "Description": "2 sample t-test of the all_olf condition",
+      "Description": "2 sample t-test",
       "GroupBy": [
         "contrast"
       ],
@@ -247,7 +247,15 @@
     },
     {
       "Source": "subject_level",
-      "Destination": "between_groups"
+      "Destination": "between_groups",
+      "Filter": {
+        "contrast": [
+          "VisMot",
+          "VisStat",
+          "VisMot_gt_VisStat",
+          "VisStat_gt_VisMot"
+        ]
+      }
     }
   ]
 }
diff --git a/tests/tests_slow/tests_batches/stats/test_setBatchFactorialDesign.m b/tests/tests_slow/tests_batches/stats/test_setBatchFactorialDesign.m
@@ -8,37 +8,6 @@
   initTestSuite;
 end
 
-function test_setBatchFactorialDesign_complex_alone()
-
-  markTestAs('slow');
-
-  opt = setOptions('vismotion', {'^01'}, 'pipelineType', 'stats');
-
-  [~, opt] = getData(opt, opt.dir.preproc);
-
-  opt.model.file = spm_file(opt.model.file, ...
-                            'basename', ...
-                            'model-vismotionSeveralDatasetLevel_smdl');
-
-  opt.model.bm = BidsModel('file', opt.model.file);
-
-  datasetNode = opt.model.bm.get_nodes('Name', 'complex contrast');
-
-  matlabbatch = {};
-  matlabbatch = setBatchFactorialDesign(matlabbatch, opt, datasetNode.Name);
-
-  % (1 contrasts) specified at the dataset level * 2
-  % batches (design specification + figure design matrix)
-  assertEqual(numel(matlabbatch), 2);
-
-  % check that directory name contains:
-  % desc-Node(dataset).name_contrast_contrastName
-  [~, dir] = fileparts(matlabbatch{1}.spm.stats.factorial_design.dir{1});
-  assertEqual(dir, ...
-              [basedirName 'node-complexContrast_contrast-VisMotGtVisStat']);
-
-end
-
 function test_setBatchFactorialDesign_within_group()
 
   markTestAs('slow');

diff --git a/tests/tests_slow/tests_workflows/stats/test_bidsRFX_2_groups.m b/tests/tests_slow/tests_workflows/stats/test_bidsRFX_2_groups.m
@@ -45,6 +45,12 @@ function test_bidsRFX_within_group_ttest()
   summary = batchSummary(matlabbatch);
   assertEqual(summary, batchOrder);
 
+  [~, folder] = fileparts(matlabbatch{1}.spm.stats.factorial_design.dir{1});
+  assert(bids.internal.starts_with(folder, 'sub-blind'));
+
+  [~, folder] = fileparts(matlabbatch{3}.spm.stats.factorial_design.dir{1});
+  assert(bids.internal.starts_with(folder, 'sub-ctrl'));
+
   assertEqual(matlabbatch{1}.spm.stats.factorial_design.dir{1}, ...
               fileparts(matlabbatch{5}.spm.stats.fmri_est.spmmat{1}));
   if bids.internal.is_octave()
@@ -77,6 +83,9 @@ function test_bidsRFX_two_sample_ttest()
   batchOrder = extendBatchOrder(batchOrder);
   assertEqual(summary, batchOrder);
 
+  [~, folder] = fileparts(matlabbatch{1}.spm.stats.factorial_design.dir{1});
+  assert(bids.internal.starts_with(folder, 'sub-2samplesTTest'));
+
   assertEqual(matlabbatch{1}.spm.stats.factorial_design.dir{1}, ...
               fileparts(matlabbatch{3}.spm.stats.fmri_est.spmmat{1}));
 

diff --git a/tests/tests_slow/tests_workflows/stats/test_bidsRFX_3_groups.m b/tests/tests_slow/tests_workflows/stats/test_bidsRFX_3_groups.m
@@ -23,8 +23,13 @@ function test_bidsRFX_one_way_anova()
 
   nodeName = 'between_groups';
   contrastName = 'VisMot_gt_VisStat';
+
+  [~, folder] = fileparts(matlabbatch{1}.spm.stats.factorial_design.dir{1});
+  assert(bids.internal.starts_with(folder, 'sub-1WayANOVA'));
+
   rfxDir = getRFXdir(opt, nodeName, contrastName, '1WayANOVA');
   assertEqual(matlabbatch{1}.spm.stats.factorial_design.dir{1}, rfxDir);
+
   assertEqual(numel(matlabbatch{1}.spm.stats.factorial_design.des.anova.icell), 3);
   assertEqual(numel(matlabbatch{1}.spm.stats.factorial_design.des.anova.icell(1).scans), 2);
   assertEqual(fileparts(matlabbatch{5}.spm.stats.fmri_est.spmmat{1}), rfxDir);

diff --git a/tests/tests_slow/tests_workflows/stats/test_bidsRFX_chain_several_nodes.m b/tests/tests_slow/tests_workflows/stats/test_bidsRFX_chain_several_nodes.m
@@ -18,13 +18,29 @@ function test_bidsRFX_no_overwrite()
                             'model-vismotionNoOverWrite_smdl');
   opt.model.bm = BidsModel('file', opt.model.file);
 
+  opt.ignore = {'qa'};
+
   matlabbatch = bidsRFX('RFX', opt);
 
-  expectedNbBatch = 79;
-  if bids.internal.is_octave()
-    expectedNbBatch = 5;
-  end
-  assertEqual(numel(matlabbatch), expectedNbBatch);
+  % 2 simple dummy contrasts
+  % 1 complex
+  % 8 within group: 4 contrast from run level * 2 groups
+  % 4 between group: 4 contrast from run level * 1 group comparison
+  expected_nb_dsigns = 2 + 1 + 8 + 4;
+  summary = batchSummary(matlabbatch);
+  nb_designs = sum(sum(cellfun(@(x) strcmp(x, 'factorial_design'), summary)));
+  assertEqual(nb_designs, expected_nb_dsigns);
+
+  %   folders = {};
+  %   for i = 1:numel(matlabbatch)
+  %       if isfield(matlabbatch{i}.spm, 'stats') && ...
+  %             isfield(matlabbatch{i}.spm.stats, 'factorial_design')
+  %           [~, tmp] = fileparts(matlabbatch{i}.spm.stats.factorial_design.dir{1});
+  %           folders{end+1, 1} = tmp;
+  %
+  %       end
+  %   end
+  %   folders
 
 end
 
@@ -41,36 +57,9 @@ function test_bidsRFX_several_datasets_level()
   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 batchOrder = extendBatchOrder(batchOrder)
-  if nargin < 1
-    batchOrder = {};
-  end
-  extension = {'stats', 'fmri_est'; ...
-               'tools', 'MACS'; ...
-               'tools', 'MACS'; ...
-               'stats', 'review'; ...
-               'util', 'print'};
-  if bids.internal.is_octave()
-    extension(2:3, :) = [];
-  end
-  batchOrder = cat(1, batchOrder, extension);
+  nb_designs = sum(sum(cellfun(@(x) strcmp(x, 'factorial_design'), summary)));
+  % 2 simple dummy contrasts and one complex
+  assertEqual(nb_designs, 3);
 end
 
 function value = batchSummary(matlabbatch)