Merge branch 'dev' of github.com:bids-standard/bids-matlab into nb_js…

…onfile

+bids/+internal/get_meta_list.m

@@ -1,29 +1,40 @@
-function metalist = get_meta_list(filename, pattern)
+function metalist = get_meta_list(varargin)
   %
   % Read a BIDS's file metadata according to the inheritance principle
   %
   % USAGE::
   %
-  %    meta = bids.internal.get_metadata(filename, pattern = '^.*%s\\.json$')
+  %    metalist = bids.internal.get_metadata(filename, ...
+  %                                          pattern, ...
+  %                                          use_inheritance)
   %
   % :param filename: fullpath name of file following BIDS standard
   % :type  filename: char
-  % :param pattern:  Regular expression matching the metadata file (default is ``'^.*%s\\.json$'``)
+  %
+  % :param pattern:  Regular expression matching the metadata file
+  %                  default = ``'^.*%s\\.json$'``
   %                  If provided, it must at least be ``'%s'``.
   % :type  pattern:  char
   %
-  % metalist    - list of paths to metafiles
+  % :return: metalist - list of paths to metafiles
   %
   %
 
   % (C) Copyright 2011-2018 Guillaume Flandin, Wellcome Centre for Human Neuroimaging
-  %
-
   % (C) Copyright 2018 BIDS-MATLAB developers
 
-  if nargin == 1
-    pattern = '^.*%s\\.json$';
-  end
+  args = inputParser;
+
+  addRequired(args, 'filename', @ischar);
+  % Default is to assume it is a JSON file
+  addOptional(args, 'pattern', '^.*%s\\.json$', @ischar);
+  addParameter(args, 'use_inheritance', true, @islogical);
+
+  parse(args, varargin{:});
+
+  filename = args.Results.filename;
+  pattern = args.Results.pattern;
+  use_inheritance = args.Results.use_inheritance;
 
   pth = fileparts(filename);
   metalist = {};
@@ -33,12 +44,12 @@
   end
 
   % Default assumes we are dealing with a file in the root directory
-  % like "participants.tsv"
+  % like "participants.tsv".
   % If the file has underscore separated entities ("sub-01_T1w.nii")
-  % then we look through the hierarchy for potential metadata file associated
-  % with queried file.
+  % then we look through the hierarchy for potential metadata file
+  % associated with queried file.
   N = 1;
-  if isfield(p, 'entities')
+  if use_inheritance && isfield(p, 'entities')
     N = 3;
     % -There is a session level in the hierarchy
     if isfield(p.entities, 'ses') && ~isempty(p.entities.ses)
@@ -49,7 +60,6 @@
   for n = 1:N
 
     % List the potential metadata files associated with this file suffix type
-    % Default is to assume it is a JSON file
     metafile = bids.internal.file_utils('FPList', pth, sprintf(pattern, p.suffix));
 
     if isempty(metafile)
@@ -58,8 +68,8 @@
       metafile = cellstr(metafile);
     end
 
-    % For all those files we find which one is potentially associated with
-    % the file of interest
+    % For all those files we find which one is potentially associated
+    % with the file of interest
     % TODO: not more than one file per level is allowed
     for i = 1:numel(metafile)
 

+bids/+internal/get_metadata.m

@@ -1,6 +1,6 @@
 function meta = get_metadata(metafile)
   %
-  % Read a BIDS's file metadata according to the inheritance principle
+  % Read a BIDS's file metadata according to the inheritance principle.
   %
   % USAGE::
   %
@@ -11,21 +11,20 @@
   %
   % :returns: - :meta: metadata structure
   %
+
   % .. todo
   %
   %    add explanation on how the inheritance principle is implemented.
   %
-  %
 
   % (C) Copyright 2011-2018 Guillaume Flandin, Wellcome Centre for Human Neuroimaging
-  %
-
   % (C) Copyright 2018 BIDS-MATLAB developers
 
   meta = struct();
   metafile = cellstr(metafile);
 
   for i = 1:numel(metafile)
+    % assumes files are read from root level files to deeper files
     if bids.internal.ends_with(metafile{i}, '.json')
       meta = update_metadata(meta, bids.util.jsondecode(metafile{i}), metafile{i});
     else
@@ -35,7 +34,12 @@
   end
 
   if isempty(meta)
-    warning('No metadata for %s', metafile);
+    bids.internal.error_handling( ...
+                                 mfilename(), ...
+                                 'NoMetadata', ...
+                                 sprintf('No metadata for:%s', ...
+                                         bids.internal.create_unordered_list(metafile)), ...
+                                 true, true);
   end
 
 end
@@ -47,8 +51,14 @@
   if isempty(struct_two)
     return
   elseif ~isstruct(struct_two)
-    error('Metadata file contents were neither struct nor empty. File: %s', file);
+    bids.internal.error_handling( ...
+                                 mfilename(), ...
+                                 'WrongInputType', ...
+                                 sprintf('Input was neither struct nor empty for file:\n%s', ...
+                                         file), ...
+                                 false);
   end
+
   fn = fieldnames(struct_two);
   for i = 1:numel(fn)
     if ~isfield(struct_one, fn{i})

+bids/+internal/return_file_index.m

@@ -20,7 +20,7 @@
                    '\n\t- modality: %s', ...
                    '\n\t- file: %s', ...
                    '\nThis may happen if your dataset is not valid.'], ...
-                  BIDS.pth, ...
+                  bids.internal.format_path(BIDS.pth), ...
                   BIDS.subjects(sub_idx).name, ...
                   modality, ...
                   filename);

+bids/+util/create_sessions_tsv.m

@@ -54,7 +54,7 @@
   sessions_list = bids.query(layout, 'sessions');
   if isempty(sessions_list) && use_schema
     msg = sprintf(['There are no session in this dataset:\n', ...
-                   '\t%s'], layout.pth);
+                   '\t%s'], bids.internal.format_path(layout.pth));
     bids.internal.error_handling(mfilename(), 'noSessionInDataset', msg, tolerant, verbose);
     return
   end
@@ -74,7 +74,9 @@
     if exist(sessions_file, 'file')
       msg = sprintf(['"sessions.tsv" %s already exist for the following dataset.', ...
                      'Will not overwrite.\n', ...
-                     '\t%s'], sessions_file, layout.pth);
+                     '\t%s'], ...
+                    bids.internal.format_path(sessions_file), ...
+                    bids.internal.format_path(layout.pth));
       bids.internal.error_handling(mfilename(), 'sessionsFileExist', msg, true, verbose);
       continue
     end
@@ -105,6 +107,8 @@
   end
 
   if verbose && ~isempty(output_filenames)
+    output_filenames = bids.internal.format_path(output_filenames);
+
     fprintf(1, ['\nCreated the following "sessions.tsv" in the dataset.', ...
                 '\n\t%s\n', ...
                 'Please add any extra information manually.\n', ...

+bids/+util/jsondecode.m

@@ -34,7 +34,8 @@
   end
 
   if ~exist(file, 'file')
-    msg = sprintf('Unable to read file ''%s'': file not found', file);
+    msg = sprintf('Unable to read file ''%s'': file not found', ...
+                  bids.internal.format_path(file));
     bids.internal.error_handling(mfilename(), 'FileNotFound', ...
                                  msg, false);
   end
@@ -74,7 +75,8 @@
 end
 
 function warning_cannot_read_json(file)
-  msg = sprintf('Could not read file:\n%s', file);
+  msg = sprintf('Could not read file:\n%s', ...
+                bids.internal.format_path(file));
   bids.internal.error_handling(mfilename(), 'CannotReadJson', ...
                                msg, true, true);
 end

+bids/+util/tsvwrite.m

@@ -14,11 +14,8 @@ function tsvwrite(filename, var)
   %
   % Based on spm_save.m from SPM12.
   %
-  %
 
   % (C) Copyright 2018 Guillaume Flandin, Wellcome Centre for Human Neuroimaging
-  %
-
   % (C) Copyright 2018 BIDS-MATLAB developers
 
   delim = sprintf('\t');
@@ -57,6 +54,7 @@ function tsvwrite(filename, var)
         var = num2cell(var);
       end
 
+      var = convert_datetimes(var);
       var = cellfun(@(x) num2str(x, 16), var, 'UniformOutput', false);
       var = strtrim(var);
       var(cellfun(@(x) strcmp(x, 'NaN'), var)) = {'n/a'};
@@ -66,9 +64,10 @@ function tsvwrite(filename, var)
     write_to_file(filename, var, delim);
 
   elseif isa(var, 'table')
-    writetable(var, filename, ...
-               'FileType', 'text', ...
-               'Delimiter', delim);
+    header = var.Properties.VariableNames;
+    var = table2cell(var);
+    var = cat(1, header, var);
+    bids.util.tsvwrite(filename, var);
 
   else
     error('Unknown data type.');
@@ -77,6 +76,17 @@ function tsvwrite(filename, var)
 
 end
 
+function var = convert_datetimes(var)
+  if bids.internal.is_octave
+    return
+  end
+  is_datetime = find(cellfun(@(x) isdatetime(x), var(:)));
+  for i = 1:numel(is_datetime)
+    idx = is_datetime(i);
+    var{idx} = char(var{idx}, 'yyyy-MM-dd''T''HH:mm:ss.SSS'); % bids-compliant datetime
+  end
+end
+
 function write_to_file(filename, var, delim)
 
   fid = fopen(filename, 'Wt');