Merge pull request #438 from Remi-Gau/remi-fix_demos

[FIX] Fix facerep demo
cpp-lln-lab · Dec 11, 2021 · 559aa2d · 559aa2d
2 parents 26fbcb0 + 8c96f4b
commit 559aa2d
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Showing 8 changed files with 51 additions and 14 deletions.
diff --git a/demos/MoAE/moae_01_preproc.m b/demos/MoAE/moae_01_preproc.m
@@ -6,7 +6,7 @@
 clear;
 clc;
 
-download_data = false;
+download_data = true;
 clean = false;
 
 try
@@ -16,7 +16,7 @@
 
 opt = moae_get_option();
 
-% download_moae_ds(download_data, clean);
+download_moae_ds(download_data, clean);
 
 % reportBIDS(opt);
 
@@ -44,7 +44,7 @@
 % one may not need it if they are running bidsFFX
 % since it creates a mask.nii by default
 % NEEDS DEBUGGING
-opt.skullstrip.mean = 1;
-mask = bidsWholeBrainFuncMask(opt);
+% opt.skullstrip.mean = 0;
+% mask = bidsWholeBrainFuncMask(opt);
 
 bidsSmoothing(opt);
diff --git a/demos/face_repetition/face_rep_01_preproc_func.m b/demos/face_repetition/face_rep_01_preproc_func.m
@@ -8,7 +8,7 @@
 clear;
 clc;
 
-downloadData = false;
+downloadData = true;
 
 try
   run ../../initCppSpm.m;

diff --git a/demos/face_repetition/face_rep_02_stats.m b/demos/face_repetition/face_rep_02_stats.m
@@ -27,4 +27,4 @@
 bidsFFX('contrasts', opt);
 
 % TODO
-% bidsResults(opt);
+bidsResults(opt);
diff --git a/demos/face_repetition/models/model-faceRepetition_smdl.json b/demos/face_repetition/models/model-faceRepetition_smdl.json
@@ -6,7 +6,7 @@
    },
    "Steps": [
       {
-         "Level": "subject",
+         "Level": "run",
          "Transformations": [
             {
                "Name": "Factor",
@@ -69,6 +69,27 @@
                "type": "t"
             }
          ]
-      }
+      },
+    {
+      "Level": "subject",
+      "Contrasts": [
+            {
+               "Name": "faces_gt_baseline",
+               "ConditionList": [
+                  "trial_type.F1",
+                  "trial_type.F2",
+                  "trial_type.N1",
+                  "trial_type.N2"
+               ],
+               "weights": [
+                  1,
+                  1,
+                  1,
+                  1
+               ],
+               "type": "t"
+            }
+      ]
+    }
    ]
 }
diff --git a/initCppSpm.m b/initCppSpm.m
@@ -41,10 +41,10 @@ function initCppSpm()
                'slice_display', ...
                'panel-2.14', ...
                'utils'};
-           
+
     pathSep = ':';
     if ~isunix
-        pathSep = ';';
+      pathSep = ';';
     end
     for i = 1:numel(libList)
       CPP_SPM_PATHS = cat(2, CPP_SPM_PATHS, pathSep, ...

diff --git a/src/bids_model/returnModelStep.m b/src/bids_model/returnModelStep.m
@@ -5,11 +5,21 @@
   iStep = nan;
   step = {};
 
+  nbSteps = numel(model.Steps);
+
+  if nbSteps == 1
+    model.Steps = {model.Steps};
+  end
+
   levels = cellfun(@(x) x.Level, model.Steps, 'UniformOutput', false);
+
   idx = ismember(levels, nodeType);
   if any(idx)
     step = model.Steps{idx};
     iStep = find(idx);
+  else
+    msg = sprintf('could not find a model step of type %s', nodeType);
+    errorHandling(mfilename(), 'missingModelStep', msg, false, true);
   end
 
 end
diff --git a/src/utils/checkDependencies.m b/src/utils/checkDependencies.m
@@ -43,8 +43,8 @@ function checkDependencies(opt)
   a = which('load_untouch_nii');
   if isempty(a)
     msg = sprintf(['Failed to find the Nifti tools: ' ...
-                  'Are you sure they in the matlab path?\n', ...
-                  'You can download them here: %s'], nifti_tools_url);
+                   'Are you sure they in the matlab path?\n', ...
+                   'You can download them here: %s'], nifti_tools_url);
     tolerant = false;
     errorHandling(mfilename(), 'missingDependency', msg, tolerant, opt.verbosity);
   else

diff --git a/tests/tests_bids_model/test_bidsModel.m b/tests/tests_bids_model/test_bidsModel.m
@@ -9,14 +9,20 @@
 end
 
 function test_returnModelStep()
+
   content = createEmptyStatsModel();
   content.Steps{4} = createEmptyNode('dataset');
+
   [~, iStep] = returnModelStep(content, 'run');
   assertEqual(iStep, 1);
-  [~, iStep] = returnModelStep(content, 'foo');
-  assertEqual(iStep, nan);
+
   [~, iStep] = returnModelStep(content, 'dataset');
   assertEqual(iStep, [3; 4]);
+
+  assertExceptionThrown( ...
+                        @()returnModelStep(content, 'foo'), ...
+                        'returnModelStep:missingModelStep');
+
 end
 
 function test_getHighPassFilter()