Merge pull request #715 from Remi-Gau/warning_masks

[FIX] improve warning selecting too many masks

Author: Remi-Gau

src/bids_model/getInclusiveMask.m

@@ -39,8 +39,11 @@
           file = file{1};
 
         elseif numel(file) > 1
-          msg = sprintf('More than 1 mask image found for %s.\n Taking the first one.', ...
-                        createUnorderedList(mask));
+          msg = sprintf(['More than 1 mask image found for %s.\n\n' ...
+                         'Taking the first one:\n\t%s\n\nfrom:%s\n\n'], ...
+                        createUnorderedList(mask), ...
+                        file{1}, ...
+                        createUnorderedList(file));
           id = 'tooManyMasks';
           errorHandling(mfilename(), id, msg, true, opt.verbosity);
           file = file{1};

src/utils/checkMaskOrUnderlay.m

@@ -1,5 +1,14 @@
 function image = checkMaskOrUnderlay(image, opt, type)
   %
+  % USAGE::
+  %
+  %     image = checkMaskOrUnderlay(image, opt, type)
+  %
+  % :param image:
+  % :type  image: path
+  %
+  % :param type: any of ``{'underlay', 'background', 'mask'}``
+  % :type  type: char
   %
   %
   % (C) Copyright 2022 CPP_SPM developers

tests/createDummyDataSet.sh

@@ -240,6 +240,8 @@ for subject in ${subject_list}; do
 				done
 				touch ${this_dir}/${basename}_run-${run}_space-individual_desc-stc${suffix}.nii
 
+				touch ${this_dir}/${basename}_run-${run}_space-IXI549Space_label-brain_mask.nii
+
 			done
 
 			if [ ${ses} = '01' ]; then
@@ -264,6 +266,7 @@ for subject in ${subject_list}; do
 		for desc in ${desc_label_list}; do
 			touch ${this_dir}/sub-${subject}_ses-${ses}_task-${task_name}_space-individual_desc-${desc}${suffix}.nii
 			touch ${this_dir}/sub-${subject}_ses-${ses}_task-${task_name}_space-IXI549Space_desc-${desc}${suffix}.nii
+			touch ${this_dir}/sub-${subject}_ses-${ses}_task-${task_name}_space-IXI549Space_label-brain_mask.nii
 		done
 
 		if [ ${ses} = '01' ]; then

tests/dummyData/models/model-vismotion_smdl.json

@@ -37,7 +37,15 @@
           "Model": "spm"
         },
         "Options": {
-          "HighPassFilterCutoffHz": 0.008
+          "HighPassFilterCutoffHz": 0.008,
+          "Mask": {
+            "suffix": [
+              "mask"
+            ],
+            "desc": [
+              "brain"
+            ]
+          }
         },
         "Software": {
           "SPM": {

tests/tests_batches/stats/test_setBatchSubjectLevelGLMSpec.m

@@ -46,7 +46,7 @@ function test_setBatchSubjectLevelGLMSpec_brain_mask()
 
   opt = setOptions('vislocalizer', subLabel, 'pipelineType', 'stats');
 
-  opt.model.bm.Nodes{1}.Model.Options.Mask = struct('label', 'brain', 'suffix', 'mask');
+  opt.model.bm.Nodes{1}.Model.Options.Mask = struct('desc', 'brain', 'suffix', 'mask');
 
   BIDS = getLayout(opt);
 
@@ -56,7 +56,7 @@ function test_setBatchSubjectLevelGLMSpec_brain_mask()
 
   %% THEN
   assertEqual(spm_file(matlabbatch{1}.spm.stats.fmri_spec.mask, 'filename'), ...
-              {'sub-01_ses-02_task-rest_space-IXI549Space_label-brain_mask.nii'});
+              {'sub-01_ses-01_space-IXI549Space_desc-brain_mask.nii'});
 
   cleanUp(fullfile(pwd, 'derivatives'));
 

tests/tests_unit/test_getInclusiveMask.m

@@ -0,0 +1,73 @@
+function test_suite = test_getInclusiveMask %#ok<*STOUT>
+  % (C) Copyright 2020 CPP_SPM developers
+  try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+    test_functions = localfunctions(); %#ok<*NASGU>
+  catch % no problem; early Matlab versions can use initTestSuite fine
+  end
+  initTestSuite;
+end
+
+function test_getInclusiveMask_too_many()
+
+  subLabel = '01';
+  nodeName = 'run_level';
+
+  opt = setOptions('vismotion', '01');
+
+  opt.verbosity = 2;
+
+  opt.model.bm = BidsModel('file', opt.model.file);
+
+  opt.model.bm.Nodes{1}.Model.Options.Mask.label{1} = 'brain';
+  opt.model.bm.Nodes{1}.Model.Options.Mask.desc{1} = '';
+
+  opt.space = opt.model.bm.Input.space;
+
+  BIDS = getLayout(opt);
+
+  assertWarning(@()getInclusiveMask(opt, nodeName, BIDS, subLabel), ...
+                'getInclusiveMask:tooManyMasks');
+
+end
+
+function test_getInclusiveMask_basic()
+
+  subLabel = '01';
+  nodeName = 'run_level';
+
+  opt = setOptions('vismotion', '01');
+
+  opt.model.bm = BidsModel('file', opt.model.file);
+
+  opt.space = opt.model.bm.Input.space;
+
+  BIDS = getLayout(opt);
+
+  mask = getInclusiveMask(opt, nodeName, BIDS, subLabel);
+
+  assertEqual(size(mask, 1), 1);
+  assertEqual(spm_file(mask, 'filename'), 'sub-01_ses-01_space-IXI549Space_desc-brain_mask.nii');
+
+end
+
+function test_getInclusiveMask_no_image()
+
+  subLabel = '01';
+  nodeName = 'run_level';
+
+  opt = setOptions('vismotion', '01');
+
+  opt.verbosity = 2;
+
+  opt.model.bm = BidsModel('file', opt.model.file);
+
+  opt.model.bm.Nodes{1}.Model.Options.Mask.desc{1} = 'foo';
+
+  opt.space = opt.model.bm.Input.space;
+
+  BIDS = getLayout(opt);
+
+  assertWarning(@()getInclusiveMask(opt, nodeName, BIDS, subLabel), ...
+                'checkMaskOrUnderlay:missingMaskOrUnderlay');
+
+end