schemaless layout indexes json files

+bids/+internal/append_to_layout.m

@@ -39,6 +39,11 @@
     entities = bids.schema.return_modality_entities(schema.datatypes.(modality)(idx), schema);
     p = bids.internal.parse_filename(file, entities);
 
+    % do not index json files when using the schema
+    if ~isempty(p) && strcmp(p.ext, '.json')
+      return
+    end
+
   end
 
   % Check any new entity field that needs to be added into the layout or the output

+bids/layout.m

@@ -175,7 +175,7 @@
 
     subject = bids.internal.add_missing_field(subject, modality);
 
-    file_list = return_file_list(modality, subject);
+    file_list = return_file_list(modality, subject, schema);
 
     for i = 1:numel(file_list)
 
@@ -220,7 +220,7 @@
 
     subject = bids.internal.add_missing_field(subject, modality);
 
-    file_list = return_file_list(modality, subject);
+    file_list = return_file_list(modality, subject, schema);
 
     for i = 1:numel(file_list)
 
@@ -256,7 +256,7 @@
 
     subject = bids.internal.add_missing_field(subject, modality);
 
-    file_list = return_file_list(modality, subject);
+    file_list = return_file_list(modality, subject, schema);
 
     for i = 1:numel(file_list)
 
@@ -316,7 +316,7 @@
 
     subject = bids.internal.add_missing_field(subject, modality);
 
-    file_list = return_file_list(modality, subject);
+    file_list = return_file_list(modality, subject, schema);
 
     for i = 1:numel(file_list)
 
@@ -420,7 +420,7 @@ function tolerant_message(use_schema, msg)
   end
 end
 
-function file_list = return_file_list(modality, subject)
+function file_list = return_file_list(modality, subject, schema)
 
   % We list anything but json files
 
@@ -433,6 +433,9 @@ function tolerant_message(use_schema, msg)
 
   % jn to omit json but not .pos file for headshape.pos
   pattern = '_([a-zA-Z0-9]+){1}\\..*[^jn]';
+  if isempty(schema)
+    pattern = '_([a-zA-Z0-9]+){1}\\..*';
+  end
 
   pth = fullfile(subject.path, modality);
 

+bids/query.m

@@ -181,6 +181,11 @@
 
     for j = 1:numel(modalities)
 
+      % Only continue if this modality is one of those filtered
+      if ~ismember(modalities{j}, fieldnames(BIDS.subjects(i)))
+        continue
+      end
+
       d = BIDS.subjects(i).(modalities{j});
 
       for k = 1:numel(d)

tests/test_bids_query.m

@@ -23,7 +23,7 @@
 
 end
 
-function test_bids_query_data()
+function test_query_data()
 
   pth_bids_example = get_test_data_dir();
 
@@ -46,7 +46,7 @@ function test_bids_query_data()
 
 end
 
-function test_bids_query_metadata()
+function test_query_metadata()
 
   pth_bids_example = get_test_data_dir();
 
@@ -63,7 +63,7 @@ function test_bids_query_metadata()
 
 end
 
-function test_bids_query_modalities()
+function test_query_modalities()
 
   pth_bids_example = get_test_data_dir();
 
@@ -98,7 +98,7 @@ function test_bids_query_modalities()
 
 end
 
-function test_bids_query_basic()
+function test_query_basic()
 
   pth_bids_example = get_test_data_dir();
 
@@ -118,7 +118,7 @@ function test_bids_query_basic()
 
 end
 
-function test_bids_query_subjects()
+function test_query_subjects()
 
   pth_bids_example = get_test_data_dir();
 
@@ -129,7 +129,7 @@ function test_bids_query_subjects()
 
 end
 
-function test_bids_query_sessions()
+function test_query_sessions()
 
   pth_bids_example = get_test_data_dir();
 
@@ -144,7 +144,7 @@ function test_bids_query_sessions()
 
 end
 
-function test_bids_query_suffixes()
+function test_query_suffixes()
 
   pth_bids_example = get_test_data_dir();
 

tests/test_bids_query_eeg.m

@@ -14,34 +14,34 @@ function test_bids_query_eeg_basic()
   pth_bids_example = get_test_data_dir();
 
   %%
-  BIDS = bids.layout(fullfile(pth_bids_example, 'eeg_cbm'));
+  BIDS = bids.layout(fullfile(pth_bids_example, 'eeg_face13'));
 
   modalities = {'eeg'};
   assertEqual(bids.query(BIDS, 'modalities'), modalities);
 
   suffixes = {'channels', 'eeg', 'events'};
+  % Missing: 'electrodes'
+  % skipped as it contains a task entity and thus does not match the schema
   assertEqual(bids.query(BIDS, 'suffixes'), suffixes);
 
   %%
-  BIDS = bids.layout(fullfile(pth_bids_example, 'eeg_ds000117'));
+  BIDS = bids.layout(fullfile(pth_bids_example, 'eeg_cbm'));
 
-  modalities = {'anat', 'eeg'};
+  modalities = {'eeg'};
   assertEqual(bids.query(BIDS, 'modalities'), modalities);
 
-  suffixes = {'T1w', 'eeg', 'electrodes', 'events'};
-  % Missing: 'coordsystem',
-  % Missing: 'channels' in root folder
+  suffixes = {'channels', 'eeg', 'events'};
   assertEqual(bids.query(BIDS, 'suffixes'), suffixes);
 
   %%
-  BIDS = bids.layout(fullfile(pth_bids_example, 'eeg_face13'));
+  BIDS = bids.layout(fullfile(pth_bids_example, 'eeg_ds000117'));
 
-  modalities = {'eeg'};
+  modalities = {'anat', 'eeg'};
   assertEqual(bids.query(BIDS, 'modalities'), modalities);
 
-  suffixes = {'channels', 'eeg', 'events'};
-  % Missing: 'electrodes'
-  % skipped as it contains a task entity and thus does not match the schema
+  suffixes = {'T1w', 'eeg', 'electrodes', 'events'};
+  % Missing: 'coordsystem',
+  % Missing: 'channels' in root folder
   assertEqual(bids.query(BIDS, 'suffixes'), suffixes);
 
   %%

tests/test_layout_derivatives.m

@@ -6,6 +6,31 @@
   initTestSuite;
 end
 
+function test_layout_parse_json()
+
+  pth_bids_example = get_test_data_dir();
+
+  BIDS = bids.layout(fullfile(pth_bids_example, 'ds000248'));
+
+  data = bids.query(BIDS, 'data', ...
+                    'sub', '01', ...
+                    'modality', 'anat');
+
+  assertEqual(size(data, 1), 2);
+
+  %%
+  use_schema = false();
+
+  BIDS = bids.layout(fullfile(pth_bids_example, 'ds000248'), use_schema);
+
+  data = bids.query(BIDS, 'data', ...
+                    'sub', '01', ...
+                    'modality', 'anat');
+
+  assertEqual(size(data, 1), 4);
+
+end
+
 function test_layout_schemaless()
 
   pth_bids_example = get_test_data_dir();
@@ -18,7 +43,6 @@ function test_layout_schemaless()
   modalities = {'anat', 'figures', 'func'};
   assertEqual(bids.query(BIDS, 'modalities'), modalities);
 
-  % Those fail for now
   data = bids.query(BIDS, 'data', ...
                     'sub', '10', ...
                     'modality', 'func', ...
@@ -27,10 +51,10 @@ function test_layout_schemaless()
                     'res', '2');
 
   basename = bids.internal.file_utils(data, 'basename');
-  assertEqual(basename, {
-                         ['sub-10_task-balloonanalogrisktask_run-1', ...
-                          '_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.nii']
-                        });
+  assertEqual(basename(2), {
+                            ['sub-10_task-balloonanalogrisktask_run-1', ...
+                             '_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.nii']
+                           });
 
   data = bids.query(BIDS, 'data', ...
                     'sub', '10', ...