Merge branch 'main' into guiomar-patch-1

+bids/+internal/add_missing_field.m

@@ -4,6 +4,7 @@
   %
   %   structure = add_missing_field(structure, field)
   %
+
   % (C) Copyright 2021 BIDS-MATLAB developers
 
   if ~isfield(structure, field)

+bids/+internal/append_to_layout.m

@@ -7,15 +7,19 @@
   %   subject = append_to_layout(file, subject, modality, schema == [])
   %
   % :param file:
-  % :type  file: string
+  % :type  file: char
+  %
   % :param subject: subject sub-structure from the BIDS layout
   % :type  subject: structure
+  %
   % :param modality:
-  % :type  modality: string
+  % :type  modality: char
+  %
   % :param schema:
   % :type  schema: structure
   %
   %
+
   % (C) Copyright 2021 BIDS-MATLAB developers
 
   pth = [subject.path, filesep, modality];
@@ -156,7 +160,7 @@
 
 function [msg, msg_id] = error_message(msg_id, file, extra)
 
-  msg = sprintf('Skipping file: %s.\n', file);
+  msg = sprintf('Skipping file: %s.\n', bids.internal.format_path(file));
 
   switch msg_id
 

+bids/+internal/camel_case.m

@@ -8,13 +8,14 @@
   %   str = camel_case(str)
   %
   % :param str:
-  % :type str: string
+  % :type str: char
   %
   % :returns:
-  %           :str: (string) returns the input with an upper case for first letter
+  %           :str: (char) returns the input with an upper case for first letter
   %                  for all words but the first one (``camelCase``) and
   %                  removes invalid characters (like spaces).
   %
+
   % (C) Copyright 2018 BIDS-MATLAB developers
 
   % camel case: upper case for first letter for all words but the first one

+bids/+internal/create_unordered_list.m

@@ -0,0 +1,61 @@
+function list = create_unordered_list(list)
+  %
+  % turns a cell string or a structure into a string
+  % that is an unordered list to print to the screen
+  %
+  % USAGE::
+  %
+  %  list = bids.internal.create_unordered_list(list)
+  %
+  % :param list: obligatory argument.
+  % :type list: cell string or structure
+  %
+  %
+
+  % (C) Copyright 2022 Remi Gau
+
+  if bids.internal.is_octave
+    warning('off', 'Octave:mixed-string-concat');
+  end
+
+  prefix = '\n\t- ';
+
+  if ischar(list)
+    list = cellstr(list);
+  end
+
+  if iscell(list)
+
+    for i = 1:numel(list)
+      if isnumeric(list{i})
+        list{i} = num2str(list{i});
+      end
+    end
+
+    list = sprintf([prefix, strjoin(list, prefix), '\n']);
+
+  elseif isstruct(list)
+
+    output = '';
+    fields = fieldnames(list);
+
+    for i = 1:numel(fields)
+      content = list.(fields{i});
+      if ~iscell(content)
+        content = {content};
+      end
+
+      for j = 1:numel(content)
+        if isnumeric(content{j})
+          content{j} = num2str(content{j});
+        end
+      end
+
+      output = [output prefix fields{i} ': {' strjoin(content, ', ') '}'];
+    end
+
+    list = sprintf(output);
+
+  end
+
+end

+bids/+internal/download.m

@@ -4,10 +4,12 @@
   %
   %   filename = download(URL, output_dir, verbose)
   %
+
   % (C) Copyright 2021 BIDS-MATLAB developers
   if nargin < 2
     output_dir = pwd;
   end
+  bids.util.mkdir(output_dir);
 
   msg = sprintf('Downloading dataset from:\n %s\n\n', URL);
   print_to_screen(msg, verbose);
@@ -16,26 +18,32 @@
   protocol = tokens{1};
 
   filename = tokens{end};
+  if strcmp(filename, '?zip=')
+    [~, filename] = fileparts(tempname);
+    filename = [filename '.zip'];
+  end
 
   if exist(filename, 'file')
     delete(filename);
   end
 
-  if strcmp(protocol, 'http:')
+  if ismember(protocol, {'http:', 'https:'})
 
-    if isunix()
-      if verbose
-        system(sprintf('wget %s', URL));
-      else
-        system(sprintf('wget -q %s', URL));
+    try
+      urlwrite(URL, filename); %#ok<*URLWR>
+    catch
+      options = '';
+      if ~verbose
+        options = '-q';
       end
-    else
-      urlwrite(URL, filename);
+      system(sprintf('wget %s %s', options, URL));
     end
 
     % move file in case it was not downloaded in the root dir
     if ~exist(fullfile(output_dir, filename), 'file')
-      print_to_screen([filename ' --> ' output_dir], verbose);
+      print_to_screen([bids.internal.format_path(filename), ...
+                       ' --> ', ...
+                       bids.internal.format_path(output_dir)], verbose);
       movefile(filename, fullfile(output_dir, filename));
     end
     filename = fullfile(output_dir, filename);

+bids/+internal/ends_with.m

@@ -11,11 +11,12 @@
   % :param pattern:
   % :type pattern: character array
   %
-  %
   % Based on the equivalent function from SPM12
   %
+
   % (C) Copyright 2011-2018 Guillaume Flandin, Wellcome Centre for Human Neuroimaging
   %
+
   % (C) Copyright 2018 BIDS-MATLAB developers
 
   res = false;

+bids/+internal/error_handling.m

@@ -6,15 +6,27 @@ function error_handling(varargin)
   %
   % :param function_name: default = ``bidsMatlab``
   % :type function_name:
+  %
   % :param id: default = ``unspecified``
-  % :type id: string
+  % :type id: char
+  %
   % :param msg: default = ``unspecified``
-  % :type msg: string
+  % :type msg: char
+  %
   % :param tolerant:
-  % :type tolerant: boolean
+  % :type tolerant: logical
+  %
   % :param verbose:
-  % :type verbose:  boolean
+  % :type verbose:  logical
   %
+  % Example
+  % -------
+  %
+  % .. code-block:: matlab
+  %
+  %   bids.internal.error_handling(mfilename(), 'thisError', 'this is an error', tolerant, verbose)
+  %
+
   % (C) Copyright 2018 BIDS-MATLAB developers
 
   default_function_name = 'bidsMatlab';
@@ -23,28 +35,28 @@ function error_handling(varargin)
   default_tolerant = true;
   default_verbose = false;
 
-  p = inputParser;
+  args = inputParser;
 
-  addOptional(p, 'function_name', default_function_name, @ischar);
-  addOptional(p, 'id', default_id, @ischar);
-  addOptional(p, 'msg', default_msg, @ischar);
-  addOptional(p, 'tolerant', default_tolerant, @islogical);
-  addOptional(p, 'verbose', default_verbose, @islogical);
+  addOptional(args, 'function_name', default_function_name, @ischar);
+  addOptional(args, 'id', default_id, @ischar);
+  addOptional(args, 'msg', default_msg, @ischar);
+  addOptional(args, 'tolerant', default_tolerant, @islogical);
+  addOptional(args, 'verbose', default_verbose, @islogical);
 
-  parse(p, varargin{:});
+  parse(args, varargin{:});
 
-  function_name = bids.internal.file_utils(p.Results.function_name, 'basename');
+  function_name = bids.internal.file_utils(args.Results.function_name, 'basename');
 
-  id = [function_name, ':' p.Results.id];
-  msg = p.Results.msg;
+  id = [function_name, ':' args.Results.id];
+  msg = sprintf(['\n' args.Results.msg '\n']);
 
-  if ~p.Results.tolerant
+  if ~args.Results.tolerant
     errorStruct.identifier = id;
     errorStruct.message = msg;
     error(errorStruct);
   end
 
-  if p.Results.verbose
+  if args.Results.verbose
     warning(id, msg);
   end
 

+bids/+internal/file_utils.m

@@ -1,6 +1,6 @@
 function varargout = file_utils(str, varargin)
   %
-  % Character array (or cell array of strings) handling facility
+  % Character array (or cell array of char) handling facility
   %
   % USAGE:
   %
@@ -11,33 +11,32 @@
   %   [dirs]        = bids.internal.file_utils('List',   directory, 'dir', regexp)
   %   [dirs]        = bids.internal.file_utils('FPList', directory, 'dir', regexp)
   %
-  %
   % To get a certain piece of information from a file::
   %
   %   str = bids.internal.file_utils(str, option)
   %
-  % str        - character array, or cell array of strings
+  % str        - character array, or cell array of char
   %
-  % option     - string of requested item - one among:
+  % option     - char of requested item - one among:
   %              {'path', 'basename', 'ext', 'filename', 'cpath', 'fpath'}
   %
-  %
   % To set a certain piece of information from a file::
   %
   %   str = bids.internal.file_utils(str, opt_key, opt_val, ...)
   %
-  % str        - character array, or cell array of strings
+  % str        - character array, or cell array of char
   %
-  % opt_key    - string of targeted item - one among:
+  % opt_key    - char of targeted item - one among:
   %              {'path', 'basename', 'ext', 'filename', 'prefix', 'suffix'}
   %
-  % opt_val    - string of new value for feature
-  %
+  % opt_val    - char of new value for feature
   %
   % Based on spm_file.m and spm_select.m from SPM12.
   %
+
   % (C) Copyright 2011-2018 Guillaume Flandin, Wellcome Centre for Human Neuroimaging
   %
+
   % (C) Copyright 2018 BIDS-MATLAB developers
 
   %#ok<*AGROW>

+bids/+internal/format_path.m

@@ -0,0 +1,31 @@
+function pth = format_path(pth)
+  %
+  % USAGE::
+  %
+  %   pth = bids.internal.format_path(pth)
+  %
+  % Replaces single '\' by '/' in Windows paths
+  % to prevent escaping warning when printing a path to screen
+  %
+  % :param pth: If pth is a cellstr of paths, pathToPrint will work
+  %             recursively on it.
+  % :type pth: char or cellstr$
+  %
+  %
+
+  % (C) Copyright 2022 BIDS-MATLAB developers
+
+  if isunix()
+    return
+  end
+
+  if ischar(pth)
+    pth = strrep(pth, '\', '\\');
+
+  elseif iscell(pth)
+    for i = 1:numel(pth)
+      pth{i} = strrep(pth{i}, '\', '\\');
+    end
+  end
+
+end