only deal with known BIDS suffixes for raw sources

Author: Remi-Gau

run_tests.m

@@ -4,12 +4,16 @@
 
 if isdir(fullfile(thisDir, 'lib', 'bids-matlab'))
     addpath(fullfile(thisDir, 'lib', 'bids-matlab'));
+end
+if isdir(fullfile(thisDir, 'lib', 'JSONio'))
     addpath(fullfile(thisDir, 'lib', 'JSONio'));
 end
 
 folderToCover = fullfile(thisDir, 'src');
 testFolder = fullfile(thisDir, 'tests');
 
+addpath(fullfile(testFolder, 'utils'));
+
 success = moxunit_runtests(testFolder, ...
                            '-verbose', '-recursive', '-with_coverage', ...
                            '-cover', folderToCover, ...

src/defaults/check_cfg.m

@@ -77,6 +77,7 @@
     % just to keep track of all the BIDS entities in the cfg
     bidsFile = bids.File('sub-01_T1.nii', 'use_schema', false);
     bidsFile = bidsFile.reorder_entities;
+    fields_to_set.schema = bids.Schema;
     fields_to_set.all_entity_order = bidsFile.entity_order;
 
     fields_to_set.entity_order = {'hemi'; ...

src/utils/identify_rawsources.m

@@ -43,12 +43,18 @@
         derivatives = strrep(derivatives, '_uw.mat', '.nii');
     end
 
+    % - only deal with files with official BIDS suffixes
     % - remove prefix
     % - remove eventual derivatives entities
     % - change surface extension to a volume one
     % - use only .nii.gz
     bf = bids.File(derivatives, 'verbose', verbose, 'use_schema', false);
 
+    if ~ismember(bf.suffix, fieldnames(map.cfg.schema.content.objects.suffixes))
+       rawsource{1} = 'TODO';
+       return
+    end
+    
     bf.prefix = '';
 
     entities = fieldnames(bf.entities);

tests/test_identify_rawsources.m

@@ -8,6 +8,26 @@
     initTestSuite;
 end
 
+function test_identify_rawsources_skip_unknown_suffix()
+
+    input_output = {'wsub-01_label-brain_mask.nii', ''};
+
+    verbose = false;
+    
+    map = default_mapping();
+
+    for i = 1:size(input_output, 1)
+
+        rawsource = identify_rawsources(input_output{i, 1}, map, verbose);
+
+        assertEqual(rawsource, {'TODO'});
+
+    end
+
+end
+
+
+
 function test_identify_rawsources_surface()
 
     input_output = {'c1sub-01_T1w.surf.gii', 'sub-01_T1w.nii.gz'};