[ENH] Bump bids matlab

demos/MoAE/moae_03_create_roi_extract_data.m

@@ -45,12 +45,14 @@
 % rename mask image:
 % add a description and remove a whole bunch of entities
 % from the original name
-newname.entities.desc = 'right auditory cortex';
+newname.entities.hemi = 'R';
+newname.entities.desc = 'auditory cortex';
 newname.entities.task = '';
 newname.entities.label = '';
 newname.entities.p = '';
 newname.entities.k = '';
 newname.entities.MC = '';
+newname.entity_order = {'sub', 'hemi', 'space', 'desc'};
 rightRoiFile = renameFile(roiFile, newname);
 
 %% same but with left hemisphere
@@ -61,7 +63,7 @@
                         'mask2', sphere);
 
 [~, roiFile] = createRoi('expand', specification, conImage, output_dir, saveROI);
-newname.entities.desc = 'left auditory cortex';
+newname.entities.hemi = 'L';
 leftRoiFile = renameFile(roiFile, newname);
 
 %%

src/IO/getData.m

@@ -38,7 +38,7 @@
 
   validationInputFile(bidsDir, 'dataset_description.json');
 
-  BIDS = bids.layout(bidsDir, opt.useBidsSchema);
+  BIDS = bids.layout(bidsDir, 'use_schema', opt.useBidsSchema);
 
   if strcmp(opt.pipeline.type, 'stats')
     BIDS.raw = bids.layout(opt.dir.raw);

src/batches/stats/setBatchResults.m

@@ -29,6 +29,12 @@
   result.outputNameStructure.entities.k = num2str(result.Contrasts.k);
   result.outputNameStructure.entities.MC = result.Contrasts.MC;
 
+  fields = fieldnames(result.outputNameStructure.entities);
+  for i = 1:numel(fields)
+    value = result.outputNameStructure.entities.(fields{i});
+    result.outputNameStructure.entities.(fields{i}) = bids.internal.camel_case(value);
+  end
+
   fieldsToSet = returnDefaultResultsStructure();
   result = setFields(result, fieldsToSet);
   result.Contrasts = replaceEmptyFields(result.Contrasts, fieldsToSet.Contrasts);

src/bids/getROIs.m

@@ -62,8 +62,7 @@
   elseif strcmp(space, 'individual')
 
     % we expect ROI files to have BIDS valid names
-    use_schema = false;
-    BIDS_ROI = bids.layout(opt.dir.roi, use_schema);
+    BIDS_ROI = bids.layout(opt.dir.roi, 'use_schema', false);
 
     if strcmp(subLabel, '')
       msg = sprintf('Provide a subject label amongst those:\n%s\n\n', ...

src/bids/initBids.m

@@ -28,15 +28,10 @@ function initBids(varargin)
 
   if ~exist(descr_file, 'file') || p.Results.force
 
-    isDerivative = true;
+    bids.init(opt.dir.output, 'folders', struct(), 'is_derivative', true);
 
-    bids.init(opt.dir.output, struct(), isDerivative);
-
-    use_schema = false;
-    index_derivatives = false;
-    tolerant = true;
-    verbose = opt.verbosity > 0;
-    BIDS = bids.layout(opt.dir.output, use_schema, index_derivatives, tolerant, verbose);
+    BIDS = bids.layout(opt.dir.output, 'use_schema', false, ...
+                       'index_derivatives', false, 'tolerant', true, 'verbose', opt.verbosity > 0);
 
     pipeline = opt.pipeline.name;
     if ~strcmp(opt.pipeline.type, '')

src/subject_level/padCounfoundMatFile.m

@@ -15,13 +15,13 @@
 
   isSpmSessStruct = @(x) isstruct(x) && isfield(x, 'counfoundMatFile');
 
-  p = inputParser;
-  addRequired(p, 'spmSess', isSpmSessStruct);
-  addRequired(p, 'opt', @isstruct);
-  parse(p, varargin{:});
+  args = inputParser;
+  addRequired(args, 'spmSess', isSpmSessStruct);
+  addRequired(args, 'opt', @isstruct);
+  parse(args, varargin{:});
 
-  spmSess = p.Results.spmSess;
-  opt = p.Results.opt;
+  spmSess = args.Results.spmSess;
+  opt = args.Results.opt;
 
   spmSessOut = spmSess;
 
@@ -58,8 +58,7 @@
     bf = bids.File(fileToLoad);
     bf.entities.desc = 'confoundsPadded';
     bf.suffix = 'regressors';
-    bf = bf.create_filename;
-    outputFilename = fullfile(bf.pth, bf.filename);
+    outputFilename = fullfile(fileparts(fileToLoad), bf.filename);
 
     save(outputFilename, 'names', 'R');
     spmSessOut(idxFilesToPad(i)).counfoundMatFile = outputFilename;

src/workflows/bidsCopyInputFolder.m

@@ -55,9 +55,9 @@ function bidsCopyInputFolder(opt, unzip)
     end
 
     bids.copy_to_derivative(BIDS, ...
-                            [opt.pipeline.name '-' opt.pipeline.type], ...
-                            fullfile(opt.dir.output, '..'), ...
-                            filter, ...
+                            'pipeline_name', [opt.pipeline.name '-' opt.pipeline.type], ...
+                            'out_path', fullfile(opt.dir.output, '..'), ...
+                            'filter', filter, ...
                             'unzip', unzip, ...
                             'force', overwrite, ...
                             'skip_dep', skip_dependencies, ...

tests/tests_unit/bids/test_getInfo.m

@@ -138,7 +138,7 @@ function test_getInfo_query_with_session_restriction()
 end
 
 function fileName = returnFullpathExpectedFilename(p)
-  bidsFile = bids.File(p, true);
+  bidsFile = bids.File(p, 'use_schema', true);
   fileName = fullfile(getDummyDataDir(), 'derivatives', 'cpp_spm-preproc', ...
-                      bidsFile.relative_pth, bidsFile.filename);
+                      bidsFile.bids_path, bidsFile.filename);
 end

tests/tests_workflows/stats/test_bidsFFX.m

@@ -68,15 +68,19 @@ function test_bidsFFX_fmriprep_no_smoothing()
   opt.query.space = opt.space; % for bidsCopy only
   opt.fwhm.func = 0;
 
-  opt.dir.stats = fullfile(opt.dir.derivatives, 'cpp_spm-stats');
-  opt.dir.output = opt.dir.stats;
+  opt.dir.preproc = fullfile(opt.dir.derivatives, 'cpp_spm-preproc');
 
   opt = checkOptions(opt);
 
   bidsCopyInputFolder(opt, false());
 
   % No proper valid bids file in derivatives of bids-example
 
+  opt.dir.stats = fullfile(opt.dir.derivatives, 'cpp_spm-stats');
+  opt.dir.output = opt.dir.stats;
+
+  opt = checkOptions(opt);
+
   % bidsFFX('specifyAndEstimate', opt);
   % bidsFFX('contrasts', opt);
   % bidsResults(opt);

tests/tests_workflows/stats/test_bidsResults.m

@@ -10,6 +10,8 @@
 
 function test_bidsResults_basic()
 
+  createDummyData();
+
   %% GIVEN
   opt = setOptions('vislocalizer', '', 'pipelineType', 'stats');
 
@@ -76,6 +78,8 @@ function test_bidsResults_basic()
 
 function test_bidsResults_no_background_for_montage()
 
+  createDummyData();
+
   %% GIVEN
   opt = setOptions('vislocalizer', '', 'pipelineType', 'stats');
 

tests/tests_workflows/test_bidsCopyInputFolder.m

@@ -46,7 +46,7 @@ function test_bidsCopyInputFolder_fmriprep()
 
   bidsCopyInputFolder(opt, false());
 
-  layoutDerivatives = bids.layout(fullfile(opt.dir.preproc), false());
+  layoutDerivatives = bids.layout(fullfile(opt.dir.preproc), 'use_schema', false);
   data = bids.query(layoutDerivatives, 'data', 'extension', '.nii.gz');
   assertEqual(size(data, 1), 16);
 

tests/tests_workflows/test_bidsCreateROI.m

@@ -28,8 +28,7 @@ function test_bidsCreateROI_neuromorphometrics()
 
   bidsCreateROI(opt);
 
-  use_schema = false;
-  BIDS = bids.layout(opt.dir.roi, use_schema);
+  BIDS = bids.layout(opt.dir.roi, 'use_schema', false);
   roiImages = bids.query(BIDS, 'data', 'sub', '^01', 'suffix', 'mask');
 
   assertEqual(size(roiImages, 1), 2);
@@ -58,8 +57,7 @@ function test_bidsCreateROI_wang()
 
   bidsCreateROI(opt);
 
-  use_schema = false;
-  BIDS = bids.layout(opt.dir.roi, use_schema);
+  BIDS = bids.layout(opt.dir.roi, 'use_schema', false);
   roiImages = bids.query(BIDS, 'data', 'sub', '^01', 'suffix', 'mask');
 
   assertEqual(size(roiImages, 1), 4);