[ENH] add support for BIDS MRS (#718)

* prepare mrs

* update schema

* fix tests

Makefile

@@ -10,3 +10,5 @@ manual:
 
 update_schema:
 	wget https://bids-specification.readthedocs.io/en/latest/schema.json -O schema.json
+# get schema from a PR on the spec
+# wget https://bids-specification--1377.org.readthedocs.build/en/1377/schema.json -O schema.json

tests/test_bids_file.m

@@ -485,6 +485,8 @@ function test_reorder_schemaless()
                                   'task'
                                   'tracksys'
                                   'acq'
+                                  'nuc'
+                                  'voi'
                                   'ce'
                                   'trc'
                                   'stain'

tests/test_bids_schema.m

@@ -20,6 +20,7 @@ function test_get_datatypes()
                                                  'ieeg', ...
                                                  'meg', ...
                                                  'micr', ...
+                                                 'mrs', ...
                                                  'motion', ...
                                                  'nirs', ...
                                                  'perf', ...
@@ -226,7 +227,15 @@ function test_return_suffix_groups_for_datatype()
   assertEqual(datatypes, {'func'});
 
   datatypes = schema.return_datatypes_for_suffix('events');
-  expected_output = {'beh', 'eeg', 'func', 'ieeg', 'meg', 'motion', 'nirs', 'pet'};
+  expected_output = {'beh', ...
+                     'eeg', ...
+                     'func', ...
+                     'ieeg', ...
+                     'meg', ...
+                     'motion', ...
+                     'mrs', ...
+                     'nirs', ...
+                     'pet'};
   assertEqual(sort(datatypes), sort(expected_output));
 
   datatypes = schema.return_datatypes_for_suffix('m0scan');
@@ -326,6 +335,8 @@ function test_schemaless()
               'task'; ...
               'tracksys'; ...
               'acquisition'; ...
+              'nucleus'; ...
+              'volume'; ...
               'ceagent'; ...
               'tracer'; ...
               'stain'; ...

tests/tests_query/test_bids_query_mrs.m

@@ -0,0 +1,60 @@
+function test_suite = test_bids_query_mrs %#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_asl_basic_2dmrsi()
+
+  BIDS = bids.layout(fullfile(get_test_data_dir(), 'mrs_2dmrsi'));
+
+  modalities = {'anat', 'mrs'};
+  assertEqual(bids.query(BIDS, 'modalities'), modalities);
+
+  suffixes = {'T1w', 'mrsi'};
+  assertEqual(bids.query(BIDS, 'suffixes'), suffixes);
+
+  assertEqual(numel(bids.query(BIDS, 'data')), 32);
+
+  filename = bids.query(BIDS, 'data', 'sub', '01', 'suffix', 'mrsi');
+  basename = bids.internal.file_utils(filename, 'basename');
+  assertEqual(basename, {    'sub-01_run-1_mrsi.nii'
+                         'sub-01_run-2_mrsi.nii'
+                         'sub-01_run-3_mrsi.nii'});
+
+end
+
+function test_bids_query_asl_basic_biggaba()
+
+  BIDS = bids.layout(fullfile(get_test_data_dir(), 'mrs_biggaba'));
+
+  modalities = {'anat', 'mrs'};
+  assertEqual(bids.query(BIDS, 'modalities'), modalities);
+
+  suffixes = {'T1w',    'mrsref',    'svs'};
+  assertEqual(bids.query(BIDS, 'suffixes'), suffixes);
+
+  assertEqual(numel(bids.query(BIDS, 'data')), 84);
+
+end
+
+function test_bids_query_asl_basic_fmrs()
+
+  BIDS = bids.layout(fullfile(get_test_data_dir(), 'mrs_fmrs'));
+
+  modalities = {'anat', 'mrs'};
+  assertEqual(bids.query(BIDS, 'modalities'), modalities);
+
+  suffixes = {    'T1w',  'events',   'mrsref',   'svs'};
+  assertEqual(bids.query(BIDS, 'suffixes'), suffixes);
+
+  assertEqual(numel(bids.query(BIDS, 'data')), 90);
+
+  metadata = bids.query(BIDS, 'metadata', 'sub', '01', 'suffix', 'svs');
+
+  metadata{1}.ReferenceSignal;
+  bids.internal.resolve_bids_uri(metadata{1}.ReferenceSignal, BIDS);
+
+end