adapt example

cpp-lln-lab · Jul 25, 2024 · e79deeb · e79deeb
1 parent 7f0d048
commit e79deeb
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diff --git a/.flake8 b/.flake8
@@ -9,6 +9,7 @@ exclude =
     tests/*
     _version.py
     demos/*
+    WIP/*
 count = True
 show-source = True
 statistics = True
diff --git a/WIP/find_data_set_with_3_groups.py b/WIP/find_data_set_with_3_groups.py
@@ -0,0 +1,43 @@
+from pathlib import Path
+
+import pandas as pd
+from pandas.errors import ParserError
+
+openneuro = Path("/home/remi/datalad/datasets.datalad.org/openneuro")
+
+for ds in openneuro.iterdir():
+    file = ds / "participants.tsv"
+
+    if file.exists():
+
+        try:
+            df = pd.read_csv(file, sep="\t")
+        except ParserError:
+            ...
+
+        if len(df) < 10:
+            continue
+        if "group" in df.columns:
+            col = "group"
+        elif "Group" in df.columns:
+            col = "Group"
+        else:
+            continue
+        if len(df[col].value_counts()) < 3:
+            continue
+        if "age" in df.columns and df["age"].mean() < 18:
+            continue
+        bold_files = list(ds.glob("**/*bold*"))
+
+        has_func = len(bold_files) > 0
+        if not has_func:
+            continue
+
+        tasks = {x.name.split("task-")[1].split("_")[0] for x in bold_files}
+        if len(tasks) == 1 and "rest" in tasks:
+            continue
+
+        print()
+        print(file)
+        print(df[col].value_counts())
+        print(tasks)
diff --git a/demos/openneuro/ds003397_run.m b/demos/openneuro/ds003397_run.m
@@ -35,7 +35,23 @@
                       'models', ...
                       'model-ds003397_smdl.json');
 
-bidspm(bids_dir, output_dir, 'subject', ...
+opt.results(1) = defaultResultsStructure();
+opt.results(1).nodeName = 'subject_level';
+opt.results(1).name = 'flashing checkerboard';
+
+% bidspm(bids_dir, output_dir, 'subject', ...
+%        'participant_label', participant_label, ...
+%        'action', 'results', ...
+%        'preproc_dir', preproc_dir, ...
+%        'model_file', model_file, ...
+%        'roi_atlas', 'hcpex', ...
+%        'space', space, ...
+%        'fwhm', 0, ...
+%        'skip_validation', true, ...
+%        'verbosity', 3, ...
+%        'opt', opt);
+
+bidspm(bids_dir, output_dir, 'dataset', ...
        'participant_label', participant_label, ...
        'action', 'stats', ...
        'preproc_dir', preproc_dir, ...
@@ -44,4 +60,5 @@
        'space', space, ...
        'fwhm', 0, ...
        'skip_validation', true, ...
-       'verbosity', 3);
+       'verbosity', 3, ...
+       'opt', opt);
diff --git a/demos/openneuro/models/model-ds003397_smdl.json b/demos/openneuro/models/model-ds003397_smdl.json
@@ -61,23 +61,6 @@
         "Test": "t"
       }
     },
-    {
-      "Level": "Dataset",
-      "Name": "dataset_level",
-      "GroupBy": [
-        "contrast",
-        "group"
-      ],
-      "Model": {
-        "Type": "glm",
-        "X": [
-          1
-        ]
-      },
-      "DummyContrasts": {
-        "Test": "t"
-      }
-    },
     {
       "Level": "Dataset",
       "Name": "between_groups",
@@ -94,7 +77,7 @@
       },
       "Contrasts": [
         {
-          "Name": "VisMot_gt_VisStat",
+          "Name": "flashing checkerboard",
           "ConditionList": [
             "group.B",
             "group.I",
@@ -115,10 +98,6 @@
       "Source": "run_level",
       "Destination": "subject_level"
     },
-    {
-      "Source": "subject_level",
-      "Destination": "dataset_level"
-    },
     {
       "Source": "subject_level",
       "Destination": "between_groups",

diff --git a/lib/bids-matlab b/lib/bids-matlab
diff --git a/src/batches/stats/setBatchFactorialDesign.m b/src/batches/stats/setBatchFactorialDesign.m
@@ -75,6 +75,8 @@
 
       availableGroups = unique(BIDS.raw.participants.content.(groupColumnHdr));
 
+      label = '1WayANOVA';
+
       rfxDir = getRFXdir(opt, nodeName, contrasts{1}, '1WayANOVA');
       overwriteDir(rfxDir, opt);
 
@@ -126,6 +128,9 @@
 
       end
 
+      groups = {label};
+      contrastsList = {contrastsList{1}};
+
   end
 end
 

diff --git a/src/stats/subject_level/specifyDummyContrasts.m b/src/stats/subject_level/specifyDummyContrasts.m
@@ -26,13 +26,13 @@
     return
   end
 
-  if ismember(node.Level, {'session'}) && ~checkGroupBy(node)
+  if ismember(node.Level, {'Session'}) && ~checkGroupBy(node)
     return
   end
-  if strcmp(node.Level, 'subject') && ~checkGroupBy(node)
+  if strcmp(node.Level, 'Subject') && ~checkGroupBy(node)
     return
   end
-  if ismember(node.Level, {'dataset'})
+  if ismember(node.Level, {'Dataset'})
     % see setBatchGroupLevelContrasts
     return
   end

diff --git a/src/workflows/stats/bidsRFX.m b/src/workflows/stats/bidsRFX.m
@@ -59,7 +59,6 @@
 
   % TODO refactor
   % - extract function for anat and mask computation
-  % - merge rfx and ffx into a single "stats" workflow
 
   if ismember(lower(action), {'meananatandmask', 'rfx', 'contrasts'})
     opt.dir.output = fullfile(opt.dir.stats, 'derivatives', 'bidspm-groupStats');
@@ -102,7 +101,7 @@
 
         switch  groupLevelGlmType(opt, nodeName, participants)
 
-          case 'one_sample_t_test'
+          case {'one_sample_t_test', 'one_way_anova'}
             [matlabbatch, contrastsList, groups] = setBatchFactorialDesign(matlabbatch, ...
                                                                            opt, ...
                                                                            datasetNodes{i}.Name);

diff --git a/tests/tests_slow/tests_batches/stats/test_setBatchFactorialDesign_3_groups.m b/tests/tests_slow/tests_batches/stats/test_setBatchFactorialDesign_3_groups.m
@@ -14,9 +14,9 @@ function test_setBatchFactorialDesign_between_3_groups()
   opt.verbosity = 3;
 
   matlabbatch = {};
-  [matlabbatch, contrastsList, groups] = setBatchFactorialDesign(matlabbatch, ...
-                                                                 opt, ...
-                                                                 'between_groups');
+  [matlabbatch, ~, ~] = setBatchFactorialDesign(matlabbatch, ...
+                                                opt, ...
+                                                'between_groups');
   matlabbatch;
 
 end
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
@@ -12,29 +12,19 @@ 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 = setOptions('3_groups', '', 'pipelineType', 'stats');
+
   opt.model.bm = BidsModel('file', opt.model.file);
   opt.verbosity = 3;
 
-  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);
+  matlabbatch = bidsRFX('RFX', opt, 'nodeName', 'between_groups');
 
   assertEqual(matlabbatch{1}.spm.stats.factorial_design.dir{1}, ...
-              fileparts(matlabbatch{3}.spm.stats.fmri_est.spmmat{1}));
+              fileparts(matlabbatch{2}.spm.stats.fmri_est.spmmat{1}));
+  assertEqual(matlabbatch{1}.spm.stats.factorial_design.dir{1}, ...
+              matlabbatch{3}.spm.tools.MACS.MA_model_space.dir{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);
+  summary = batchSummary(matlabbatch);
 
 end