Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[ENH] use inheritance in get_meta_list #609

Merged
merged 2 commits into from
Aug 5, 2023
Merged

[ENH] use inheritance in get_meta_list #609

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
0c745a3
use inheritance in get_meta_list
Remi-Gau Aug 5, 2023
092cc9e
refactor
Remi-Gau Aug 5, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
42 changes: 26 additions & 16 deletions +bids/+internal/get_meta_list.m
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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 = {};
Expand All @@ -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)
Expand All @@ -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)
Expand All @@ -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)

Expand Down
22 changes: 16 additions & 6 deletions +bids/+internal/get_metadata.m
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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::
%
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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})
Expand Down