reorganize tests and make list of target files to parse for meeg more…

… general

+bids/layout.m

@@ -744,7 +744,7 @@ function tolerant_message(tolerant, msg)
       pattern = '_task-.*\\.nii(\\.gz)|events\\.tsv|physio\\.tsv\\.gz|stim\\.tsv\\.gz?';
 
     case {'eeg', 'meg', 'ieeg'}
-      pattern = ['_task-.*_' modality '\\..*[^json]'];
+      pattern = '_([a-zA-Z0-9]+){1}\\..*[^json]';
 
     case 'beh'
       pattern = '_task-.*_(events\\.tsv|beh\\.json|physio\\.tsv\\.gz|stim\\.tsv\\.gz)';

+bids/query.m

@@ -2,12 +2,17 @@
   % QUERY Query a directory structure formatted according to the BIDS standard
   % FORMAT result = bids.query(BIDS,query,...)
   % BIDS   - BIDS directory name or BIDS structure (from bids.layout)
-  % query  - type of query: {'data', 'metadata', 'sessions', 'subjects',
-  %          'runs', 'tasks', 'runs', 'types', 'modalities'}
+  % query  - type of query:
+  %                          - 'data',
+  %                          - 'metadata',
+  %                          - 'sessions',
+  %                          - 'subjects',
+  %                          - 'runs',
+  %                          - 'tasks',
+  %                          - 'types',
+  %                          - 'modalities'
   % result - outcome of query
   %
-  % See also:
-  % bids
 
   % __________________________________________________________________________
   %

tests/test_bids_query.m

@@ -7,7 +7,7 @@
 end
 
 function test_bids_query_basic()
-  % Test BIDS queries on ds007
+  % Test BIDS queries
   % This dataset comes from https://github.com/bids-standard/bids-examples
   % and is downloaded automatically by the continuous integration framework
   % and is required for the tests to be run.
@@ -30,8 +30,6 @@ function test_bids_query_basic()
   subjs = arrayfun(@(x) sprintf('%02d', x), 1:20, 'UniformOutput', false);
   assert(isequal(bids.query(BIDS, 'subjects'), subjs));
 
-  assert(isempty(bids.query(BIDS, 'sessions')));
-
   assert(isequal(bids.query(BIDS, 'runs'), {'01', '02'}));
 
   tasks = { ...
@@ -46,10 +44,6 @@ function test_bids_query_basic()
   data = bids.query(BIDS, 'data', 'sub', '01', 'task', 'stopsignalwithpseudowordnaming');
   assertEqual(size(data, 1), 4);
 
-  mods = {'anat', 'func'};
-  assert(isequal(bids.query(BIDS, 'modalities'), mods));
-  assert(isequal(bids.query(BIDS, 'modalities', 'sub', '01'), mods));
-
   assert(isempty(bids.query(BIDS, 'runs', 'type', 'T1w')));
 
   runs = {'01', '02'};
@@ -79,31 +73,32 @@ function test_bids_query_basic()
 end
 
 function test_bids_query_sessions()
-  %
-  %   parse a folder with sessions
-  %
 
   pth_bids_example = get_test_data_dir();
 
   BIDS = bids.layout(fullfile(pth_bids_example, 'synthetic'));
-
-  %   test
   sessions = {'01', '02'};
   assert(isequal(bids.query(BIDS, 'sessions'), sessions));
   assert(isequal(bids.query(BIDS, 'sessions', 'sub', '02'), sessions));
 
+  BIDS = bids.layout(fullfile(pth_bids_example, 'ds007'));
+
+  assert(isempty(bids.query(BIDS, 'sessions')));
+
 end
 
 function test_bids_query_modalities()
-  %
-  %   parse a folder with different modalities per session
-  %
 
   pth_bids_example = get_test_data_dir();
 
+  BIDS = bids.layout(fullfile(pth_bids_example, 'ds007'));
+
+  mods = {'anat', 'func'};
+  assert(isequal(bids.query(BIDS, 'modalities'), mods));
+  assert(isequal(bids.query(BIDS, 'modalities', 'sub', '01'), mods));
+
   BIDS = bids.layout(fullfile(pth_bids_example, '7t_trt'));
 
-  %   test
   mods = {'anat', 'fmap', 'func'};
 
   assert(isequal(bids.query(BIDS, 'modalities'), mods));

tests/test_bids_query_asl.m

@@ -8,7 +8,7 @@
 
 function test_bids_query_asl_basic()
   %
-  %   asl specific queries
+  %   asl queries
   %
 
   pth_bids_example = get_test_data_dir();

tests/test_bids_query_eeg.m

@@ -0,0 +1,64 @@
+function test_suite = test_bids_query_eeg %#ok<*STOUT>
+  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_bids_query_eeg_basic()
+  %
+  %   eeg queries
+  %
+
+  pth_bids_example = get_test_data_dir();
+
+  %%
+  BIDS = bids.layout(fullfile(pth_bids_example, 'eeg_cbm'));
+
+  modalities = {'eeg'};
+  assertEqual(bids.query(BIDS, 'modalities'), modalities);
+
+  types = {'channels', 'eeg', 'events'};
+  assertEqual(bids.query(BIDS, 'types'), types);
+
+  %%
+  BIDS = bids.layout(fullfile(pth_bids_example, 'eeg_ds000117'));
+
+  modalities = {'anat', 'eeg'};
+  assertEqual(bids.query(BIDS, 'modalities'), modalities);
+
+  types = {'T1w', 'eeg', 'electrodes', 'events'};
+  % Missing: 'coordsystem', 'channels'
+  assertEqual(bids.query(BIDS, 'types'), types);
+
+  %%
+  BIDS = bids.layout(fullfile(pth_bids_example, 'eeg_face13'));
+
+  modalities = {'eeg'};
+  assertEqual(bids.query(BIDS, 'modalities'), modalities);
+
+  types = {'channels', 'eeg', 'events'};
+  % Missing: 'electrodes'
+  % skipped as it contains a task entity and thus does not match the schema
+  assertEqual(bids.query(BIDS, 'types'), types);
+
+  %%
+  BIDS = bids.layout(fullfile(pth_bids_example, 'eeg_matchingpennies'));
+
+  modalities = {'eeg'};
+  assertEqual(bids.query(BIDS, 'modalities'), modalities);
+
+  types = {'channels', 'eeg', 'events'};
+  assertEqual(bids.query(BIDS, 'types'), types);
+
+  %%
+  BIDS = bids.layout(fullfile(pth_bids_example, 'eeg_rishikesh'));
+
+  modalities = {'eeg'};
+  assertEqual(bids.query(BIDS, 'modalities'), modalities);
+
+  types = {'channels', 'eeg', 'events'};
+  assertEqual(bids.query(BIDS, 'types'), types);
+
+end

tests/test_bids_query_ieeg.m

@@ -0,0 +1,36 @@
+function test_suite = test_bids_query_ieeg %#ok<*STOUT>
+  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_bids_query_ieeg_basic()
+  %
+  %   eeg queries
+  %
+
+  pth_bids_example = get_test_data_dir();
+
+  %%
+  BIDS = bids.layout(fullfile(pth_bids_example, 'ieeg_epilepsy'));
+
+  modalities = {'anat', 'ieeg'};
+  assertEqual(bids.query(BIDS, 'modalities'), modalities);
+
+  types = {'T1w', 'channels', 'electrodes', 'events', 'ieeg'};
+  % Missing: 'coordsystem'
+  assertEqual(bids.query(BIDS, 'types'), types);
+
+  %%
+  BIDS = bids.layout(fullfile(pth_bids_example, 'ieeg_epilepsy_ecog'));
+
+  modalities = {'anat', 'ieeg'};
+  assertEqual(bids.query(BIDS, 'modalities'), modalities);
+
+  types = {'T1w', 'channels', 'electrodes', 'events', 'ieeg', 'photo'};
+  % Missing: 'coordsystem'
+  assertEqual(bids.query(BIDS, 'types'), types);
+
+end

tests/test_bids_query_meg.m

@@ -0,0 +1,28 @@
+function test_suite = test_bids_query_meg %#ok<*STOUT>
+  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_bids_query_meg_basic()
+  %
+  %   meg queries
+  %
+
+  pth_bids_example = get_test_data_dir();
+
+  BIDS = bids.layout(fullfile(pth_bids_example, 'ds000246'));
+
+  modalities = {'anat', 'meg'};
+  assertEqual(bids.query(BIDS, 'modalities'), modalities);
+
+  types = {'T1w', 'channels', 'photo'};
+  % missing:  'meg' 'coordsystem', 'headshape'
+  assertEqual(bids.query(BIDS, 'types'), types);
+
+  BIDS = bids.layout(fullfile(pth_bids_example, 'ds000247'));
+  BIDS = bids.layout(fullfile(pth_bids_example, 'ds000248'));
+
+end

tests/test_layout.m

@@ -9,7 +9,9 @@
 function test_layout_smoke_test()
 
   pth_bids_example = get_test_data_dir();
-  BIDS = bids.layout(fullfile(pth_bids_example, '7t_trt'));
-  BIDS = bids.layout(fullfile(pth_bids_example, 'asl001'));
+
+  BIDS = bids.layout(fullfile(pth_bids_example, 'genetics_ukbb'));
+
+  BIDS = bids.layout(fullfile(pth_bids_example, 'ds210'));
 
 end