tmp

src/batches/stats/setBatchFactorialDesign.m

@@ -36,7 +36,7 @@
     return
   end
 
-  [BIDS, opt] = getData(opt, opt.dir.preproc);
+  [~, opt] = getData(opt, opt.dir.preproc);
 
   printBatchName(sprintf('specify group level fmri model for node "%s"', nodeName), opt);
 
@@ -71,13 +71,11 @@
       groupColumnHdr = setxor(designMatrix, {'1'});
       groupColumnHdr = groupColumnHdr{1};
 
-      checkColumnParticipantsTsv(BIDS, groupColumnHdr);
-
       % Sorting is important so that we know in which order
       % the groups are entered in the design matrix.
       % Otherwise it will be harder to properly design
       % the contrast vectors later.
-      availableGroups = sort(unique(BIDS.raw.participants.content.(groupColumnHdr)));
+      availableGroups = getAvailableGroups(opt, groupColumnHdr);
 
       label = '1WayANOVA';
 
@@ -103,7 +101,8 @@
         % Note that this will lead to different results
         % depending on the requested subejcts
         %
-        tsv = BIDS.raw.participants.content;
+        tsvFile = fullfile(opt.dir.raw, 'participants.tsv');
+        tsv = bids.util.tsvread(tsvFile);
         subjectsInGroup = strcmp(tsv.(groupColumnHdr), thisGroup);
         subjectsLabel = regexprep(tsv.participant_id(subjectsInGroup), '^sub-', '');
         subjectsLabel = intersect(subjectsLabel, opt.subjects);
@@ -180,7 +179,7 @@
   contrastsList = {};
   groups = {};
 
-  [BIDS, opt] = getData(opt, opt.dir.preproc);
+  [~, opt] = getData(opt, opt.dir.preproc);
 
   contrasts = getContrastsListForFactorialDesign(opt, nodeName);
 
@@ -191,9 +190,7 @@
   groupColumnHdr = setxor(groupBy, {'contrast'});
   groupColumnHdr = groupColumnHdr{1};
 
-  checkColumnParticipantsTsv(BIDS, groupColumnHdr);
-
-  availableGroups = unique(BIDS.raw.participants.content.(groupColumnHdr));
+  availableGroups = getAvailableGroups(opt, groupColumnHdr);
 
   for iGroup = 1:numel(availableGroups)
 
@@ -205,7 +202,8 @@
     % Note that this will lead to different results depending on the requested
     % subejcts
     %
-    tsv = BIDS.raw.participants.content;
+    tsvFile = fullfile(opt.dir.raw, 'participants.tsv');
+    tsv = bids.util.tsvread(tsvFile);
     subjectsInGroup = strcmp(tsv.(groupColumnHdr), thisGroup);
     subjectsLabel = regexprep(tsv.participant_id(subjectsInGroup), '^sub-', '');
     subjectsLabel = intersect(subjectsLabel, opt.subjects);
@@ -352,14 +350,13 @@
 
 function [status, groupBy, glmType] = checks(opt, nodeName)
 
-  thisNode = opt.model.bm.get_nodes('Name', nodeName);
-
   commonMsg = sprintf('for the dataset level node: "%s"', nodeName);
 
   % TODO refactor
   participants = bids.util.tsvread(fullfile(opt.dir.raw, 'participants.tsv'));
   columns = fieldnames(participants);
-  status = checkGroupBy(thisNode, columns);
+
+  status = opt.model.bm.validateGroupBy(nodeName, columns);
 
   [glmType, ~, groupBy] = groupLevelGlmType(opt, nodeName, participants);
 

src/batches/stats/setBatchTwoSampleTTest.m

@@ -44,7 +44,7 @@
   %%
   printBatchName('specify group level paired T-test fmri model', opt);
 
-  [BIDS, opt] = getData(opt, opt.dir.preproc);
+  [~, opt] = getData(opt, opt.dir.preproc);
 
   node = opt.model.bm.get_nodes('Name', nodeName);
 
@@ -67,7 +67,8 @@
   group2 = group2{2};
 
   % TODO refactor
-  availableGroups = unique(BIDS.raw.participants.content.(groupField));
+  availableGroups = getAvailableGroups(opt, groupField);
+  participants = bids.util.tsvread(fullfile(opt.dir.raw, 'participants.tsv'));
 
   if any(~ismember({group1, group2}, availableGroups))
     error(['Some requested group is not present: %s.', ...
@@ -103,8 +104,8 @@
 
       subLabel = opt.subjects{iSub};
 
-      idx = strcmp(BIDS.raw.participants.content.participant_id, ['sub-' subLabel]);
-      participantGroup = BIDS.raw.participants.content.(groupField){idx};
+      idx = strcmp(participants.participant_id, ['sub-' subLabel]);
+      participantGroup = participants.(groupField){idx};
 
       if numel(contrastsList) == 1
         file = conImages{iSub};

src/bids/getAvailableGroups.m

@@ -0,0 +1,20 @@
+function availableGroups = getAvailableGroups(opt, groupColumnHdr)
+
+  % (C) Copyright 2024 bidspm developers
+  tsvFile = fullfile(opt.dir.raw, 'participants.tsv');
+
+  assert(exist(tsvFile, 'file') == 2);
+
+  participants = bids.util.tsvread(tsvFile);
+
+  columns = fieldnames(participants);
+  if ~ismember(groupColumnHdr, columns)
+    msg = sprintf(['Could not find column "%s" in participants.tsv.\n', ...
+                   'Available columns are: %s'], ...
+                  columnHdr, ...
+                  bids.internal.create_unordered_list(columns));
+    logger('ERROR', msg, 'filename', mfilename, 'id', 'missingColumn');
+  end
+
+  availableGroups = sort(unique(participants.(groupColumnHdr)));
+end

src/stats/group_level/groupLevelGlmType.m

@@ -10,18 +10,15 @@
   % TODO refactor
   columns = fieldnames(participants);
 
-  srcDesignMatrix = opt.model.bm.getBidsDesignMatrix('Name', nodeName);
-  designMatrix = srcDesignMatrix;
-
   node = opt.model.bm.get_nodes('Name', nodeName);
-
   groupBy = node.GroupBy;
+  srcDesignMatrix = node.Model.X;
 
   type = 'unknown';
-  if isnumeric(designMatrix) && designMatrix == 1
+  if isnumeric(srcDesignMatrix) && srcDesignMatrix == 1
     type = 'one_sample_t_test';
 
-  elseif iscell(designMatrix) && numel(designMatrix) == 2
+  elseif iscell(srcDesignMatrix) && numel(srcDesignMatrix) == 2
 
     designMatrix = cellfun(@(x) num2str(x), srcDesignMatrix, 'uniformoutput', false);
 

src/workflows/stats/bidsFFX.m

@@ -163,23 +163,10 @@ function checkRootNode(opt)
   % This only concerns 'specify' and 'specifyAndEstimate'
   %
 
-  thisNode = opt.model.bm.get_root_node;
-
-  if ismember(lower(thisNode.Level), {'session', 'subject'})
-
-    notImplemented(mfilename(), ...
-                   '"session" and "subject" level Node not implemented yet');
+  opt.model.bm.validateRootNode();
 
-  elseif ismember(lower(thisNode.Level), {'dataset'})
-
-    msg = sprintf(['Your model seems to be having dataset Node at its root\n.', ...
-                   'Validate it: https://bids-standard.github.io/stats-models/validator.html\n']);
-    id = 'wrongLevel';
-    logger('ERROR', msg, 'id', id, 'filename', mfilename());
-
-  end
-
-  checkGroupBy(thisNode);
+  thisNode = opt.model.bm.get_root_node;
+  opt.model.bm.validateGroupBy(thisNode);
 
   % should not be necessary
   % mostly in case users did not validate the model inputs

tests/tests_slow/tests_batches/stats/test_setBatchFactorialDesign_3_groups.m

@@ -11,12 +11,11 @@
 function test_setBatchFactorialDesign_between_3_groups()
 
   opt = setOptions('3_groups', '', 'pipelineType', 'stats');
-  opt.verbosity = 3;
+  opt.verbosity = 0;
 
   matlabbatch = {};
   [matlabbatch, ~, ~] = setBatchFactorialDesign(matlabbatch, ...
                                                 opt, ...
                                                 'between_groups');
-  matlabbatch;
 
 end