[WIP] Function to copy derivatives

+bids/+internal/append_to_layout.m

@@ -1,4 +1,4 @@
-function subject = append_to_layout(file, subject, modality, schema)
+function [subject, p] = append_to_layout(file, subject, modality, schema)
   %
   % appends a file to the BIDS layout by parsing it according to the provided schema
   %
@@ -40,7 +40,7 @@
     p = bids.internal.parse_filename(file, entities);
 
     % do not index json files when using the schema
-    if ~isempty(p) && strcmp(p.ext, '.json')
+    if isempty(p) || (~isempty(p) && strcmp(p.ext, '.json'))
       return
     end
 

+bids/+internal/ends_with.m

@@ -0,0 +1,23 @@
+function res = ends_with(str, pattern)
+  %
+  % Checks id character array 'str' ends with 'pat'
+  %
+  % USAGE  res = bids.internal.endsWith(str, pat)
+  %
+  % str        - character array
+  % pat        - character array
+  %
+  % __________________________________________________________________________
+  %
+  % Based on spm_file.m and spm_select.m from SPM12.
+  % __________________________________________________________________________
+
+  % Copyright (C) 2011-2018 Guillaume Flandin, Wellcome Centre for Human Neuroimaging
+  res = false;
+  l_pat = length(pattern);
+  if l_pat > length(str)
+    return
+  end
+  res = strcmp(str(end - l_pat + 1:end), pattern);
+
+end

+bids/+internal/get_meta_list.m

@@ -0,0 +1,92 @@
+function metalist = get_meta_list(filename, pattern)
+  %
+  % Read a BIDS's file metadata according to the inheritance principle
+  %
+  % USAGE::
+  %
+  %    meta = bids.internal.get_metadata(filename, pattern = '^.*%s\\.json$')
+  %
+  % :param filename: fullpath name of file following BIDS standard
+  % :type  filename: string
+  % :param pattern:  Regular expression matching the metadata file (default is ``'^.*%s\\.json$'``)
+  %                  If provided, it must at least be ``'%s'``.
+  % :type  pattern:  string
+  %
+  %
+  % metalist    - list of paths to metafiles
+  % __________________________________________________________________________
+
+  % Copyright (C) 2016-2018, Guillaume Flandin, Wellcome Centre for Human Neuroimaging
+  % Copyright (C) 2018--, BIDS-MATLAB developers
+
+  if nargin == 1
+    pattern = '^.*%s\\.json$';
+  end
+
+  pth = fileparts(filename);
+  p = bids.internal.parse_filename(filename);
+  metalist = {};
+
+  % Default assumes we are dealing with a file in the root directory
+  % 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.
+  N = 1;
+  if isfield(p, 'entities')
+    N = 3;
+    % -There is a session level in the hierarchy
+    if isfield(p.entities, 'ses') && ~isempty(p.entities.ses)
+      N = N + 1;
+    end
+  end
+
+  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)
+      metafile = {};
+    else
+      metafile = cellstr(metafile);
+    end
+
+    % For all those files we find which one is potentially associated with
+    % the file of interest
+    for i = 1:numel(metafile)
+
+      p2 = bids.internal.parse_filename(metafile{i});
+      entities = {};
+      if isfield(p2, 'entities')
+        entities = fieldnames(p2.entities);
+      end
+
+      % Check if this metadata file contains
+      %   - the same entity-label pairs
+      %   - same suffix
+      % as its data file counterpart
+      ismeta = true;
+      if ~strcmp(p.suffix, p2.suffix)
+        ismeta = false;
+      end
+      for j = 1:numel(entities)
+        if ~isfield(p.entities, entities{j}) || ...
+                ~strcmp(p.entities.(entities{j}), p2.entities.(entities{j}))
+          ismeta = false;
+          break
+        end
+      end
+
+      % append path to list
+      if ismeta
+        metalist{end + 1, 1} = metafile{i}; %#ok<AGROW>
+      end
+
+    end
+
+    % Go up to the parent folder
+    pth = fullfile(pth, '..');
+  end
+end

+bids/+internal/get_metadata.m

@@ -1,101 +1,38 @@
-function meta = get_metadata(filename, pattern)
+function meta = get_metadata(metafile)
   %
   % Read a BIDS's file metadata according to the inheritance principle
   %
   % USAGE::
   %
-  %    meta = bids.internal.get_metadata(filename, pattern = '^.*%s\\.json$')
+  %    meta = bids.internal.get_metadata(metafile)
   %
-  % :param filename: fullpath name of file following BIDS standard
-  % :type  filename: string
-  % :param pattern:  Regular expression matching the metadata file (default is ``'^.*%s\\.json$'``)
-  %                  If provided, it must at least be ``'%s'``.
-  % :type  pattern:  string
+  % :param metafile: list of fullpath names of metadata files.
+  % :type  metafile: string or array of strings
   %
+  % :returns: - :meta: metadata structure
   %
-  % meta        - metadata structure
+  % .. todo
+  %
+  %    add explanation on how the inheritance principle is implemented.
   % __________________________________________________________________________
 
   % Copyright (C) 2016-2018, Guillaume Flandin, Wellcome Centre for Human Neuroimaging
   % Copyright (C) 2018--, BIDS-MATLAB developers
 
-  % assume most files are of the form *_suffix.json
-  % add an exception for files with no suffix, like participants.tsv
-  if nargin == 1
-    pattern = '^.*_?%s\\.json$';
-  end
-
-  pth = fileparts(filename);
-  p = bids.internal.parse_filename(filename);
-
   meta = struct();
+  metafile = cellstr(metafile);
 
-  N = 3;
-
-  % -There is a session level in the hierarchy
-  if isfield(p, 'entities') && isfield(p.entities, 'ses') && ~isempty(p.entities.ses)
-    N = N + 1;
-  end
-
-  % -Loop from the directory where the file of interest is back to the
-  % top level of the BIDS hierarchy
-  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)
-      metafile = {};
+  for i = 1:numel(metafile)
+    if bids.internal.ends_with(metafile{i}, '.json')
+      meta = update_metadata(meta, bids.util.jsondecode(metafile{i}), metafile{i});
     else
-      metafile = cellstr(metafile);
-    end
-
-    % -For all those files we find which one is potentially associated with
-    % the file of interest
-    for i = 1:numel(metafile)
-
-      p2 = bids.internal.parse_filename(metafile{i});
-      entities = {};
-      if isfield(p2, 'entities')
-        entities = fieldnames(p2.entities);
-      end
-
-      % Check if this metadata file contains 
-      %   - the same entity-label pairs 
-      %   - same prefix
-      % as its data file counterpart
-      ismeta = true;
-      if ~strcmp(p.suffix, p2.suffix)
-          ismeta = false;
-      end
-      for j = 1:numel(entities)
-        if ~isfield(p.entities, entities{j}) || ...
-                ~strcmp(p.entities.(entities{j}), p2.entities.(entities{j}))
-          ismeta = false;
-          break
-        end
-      end
-
-      % -Read the content of the metadata file if it is a JSON file and update
-      % the metadata concerning the file of interest otherwise store the filename
-      if ismeta
-        if strcmp(p2.ext, '.json')
-          meta = update_metadata(meta, bids.util.jsondecode(metafile{i}), metafile{i});
-        else
-          meta.filename = metafile{i};
-        end
-      end
-
+      meta.filename = metafile{i};
     end
 
-    % -Go up to the parent folder
-    pth = fullfile(pth, '..');
-
   end
 
   if isempty(meta)
-    warning('No metadata for %s', filename);
+    warning('No metadata for %s', metafile);
   end
 
 end

+bids/+internal/parse_filename.m

@@ -53,8 +53,16 @@
   end
 
   % identidy an eventual prefix to the file
-  tmp = regexp(parts{1}, '(sub)', 'split');
-  p.prefix = tmp{1};
+  % and amends the sub entity accordingly
+  p.prefix = '';
+  if strfind(parts{1}, 'sub-')
+    tmp = regexp(parts{1}, '(sub-)', 'split');
+    p.prefix = tmp{1};
+    if ~isempty(p.prefix)
+      p.entities.sub = p.entities.([p.prefix 'sub']);
+      p.entities = rmfield(p.entities, [p.prefix 'sub']);
+    end
+  end
 
   % -Extra fields can be added to the structure and ordered specifically.
   if nargin == 2

+bids/+internal/starts_with.m

@@ -0,0 +1,23 @@
+function res = starts_with(str, pattern)
+  %
+  % Checks id character array 'str' starts with 'pat'
+  %
+  % USAGE  res = bids.internal.startsWith(str, pat)
+  %
+  % str        - character array
+  % pat        - character array
+  %
+  % __________________________________________________________________________
+  %
+  % Based on spm_file.m and spm_select.m from SPM12.
+  % __________________________________________________________________________
+
+  % Copyright (C) 2011-2018 Guillaume Flandin, Wellcome Centre for Human Neuroimaging
+  res = false;
+  l_pat = length(pattern);
+  if l_pat > length(str)
+    return
+  end
+  res = strcmp(str(1:l_pat), pattern);
+
+end