Skip to content

Commit

Permalink
Merge pull request bids-standard#95 from Remi-Gau/remi-apply_linter
Browse files Browse the repository at this point in the history 
apply MISS_HIT linter across the board
  • Loading branch information
@Remi-Gau
Remi-Gau committed Nov 21, 2020
2 parents edac655 + 4dfa649 commit 5dc177e
Show file tree
Hide file tree
Showing 17 changed files with 1,835 additions and 1,744 deletions.
385 changes: 194 additions & 191 deletions +bids/+internal/file_utils.m
View file

Large diffs are not rendered by default.

146 changes: 75 additions & 71 deletions +bids/+internal/get_metadata.m
View file
Original file line number Diff line number Diff line change
@@ -1,86 +1,90 @@
function meta = get_metadata(filename, pattern)
% Read a BIDS's file metadata according to the inheritance principle
% FORMAT meta = bids.internal.get_metadata(filename, pattern)
% filename - name of file following BIDS standard
% pattern - regular expression matching metadata file
% meta - metadata structure
%__________________________________________________________________________
% Read a BIDS's file metadata according to the inheritance principle
% FORMAT meta = bids.internal.get_metadata(filename, pattern)
% filename - name of file following BIDS standard
% pattern - regular expression matching metadata file
% meta - metadata structure
% __________________________________________________________________________

% Copyright (C) 2016-2018, Guillaume Flandin, Wellcome Centre for Human Neuroimaging
% Copyright (C) 2018--, BIDS-MATLAB developers
% Copyright (C) 2016-2018, Guillaume Flandin, Wellcome Centre for Human Neuroimaging
% Copyright (C) 2018--, BIDS-MATLAB developers

if nargin == 1
pattern = '^.*%s\\.json$';
end

if nargin == 1, pattern = '^.*%s\\.json$'; end
pth = fileparts(filename);
p = bids.internal.parse_filename(filename);

pth = fileparts(filename);
p = bids.internal.parse_filename(filename);
meta = struct();

meta = struct();
N = 3;

N = 3;
% -There is a session level in the hierarchy
if isfield(p, 'ses') && ~isempty(p.ses)
N = N + 1;
end

%-There is a session level in the hierarchy
if isfield(p,'ses') && ~isempty(p.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
% -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.type));

if isempty(metafile), metafile = {}; else metafile = cellstr(metafile); end

%-For all those files we find which one is potentially associated with

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});
fn = setdiff(fieldnames(p2),{'filename','ext','type'});

%-Check if this metadata file contains the same entity-label pairs as its
% data file counterpart
ismeta = true;
for j=1:numel(fn)
if ~isfield(p,fn{j}) || ~strcmp(p.(fn{j}),p2.(fn{j}))
ismeta = false;
break;
end
for i = 1:numel(metafile)

p2 = bids.internal.parse_filename(metafile{i});
fn = setdiff(fieldnames(p2), {'filename', 'ext', 'type'});

% -Check if this metadata file contains the same entity-label pairs as its
% data file counterpart
ismeta = true;
for j = 1:numel(fn)
if ~isfield(p, fn{j}) || ~strcmp(p.(fn{j}), p2.(fn{j}))
ismeta = false;
break
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

% -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

end

%-Go up to the parent folder
pth = fullfile(pth,'..');

end


%==========================================================================
%-Inheritance principle
%==========================================================================
function s1 = update_metadata(s1,s2,file)
if isempty(s2)
return;
elseif ~isstruct(s2)
error('Metadata file contents were neither struct nor empty. File: %s',file);
end
fn = fieldnames(s2);
for i=1:numel(fn)
if ~isfield(s1,fn{i})
s1.(fn{i}) = s2.(fn{i});

% -Go up to the parent folder
pth = fullfile(pth, '..');

end

% ==========================================================================
% -Inheritance principle
% ==========================================================================
function s1 = update_metadata(s1, s2, file)
if isempty(s2)
return
elseif ~isstruct(s2)
error('Metadata file contents were neither struct nor empty. File: %s', file);
end
fn = fieldnames(s2);
for i = 1:numel(fn)
if ~isfield(s1, fn{i})
s1.(fn{i}) = s2.(fn{i});
end
end
end
90 changes: 45 additions & 45 deletions +bids/+internal/parse_filename.m
View file
Original file line number Diff line number Diff line change
@@ -1,56 +1,56 @@
function p = parse_filename(filename,fields)
% Split a filename into its building constituents
% FORMAT p = bids.internal.parse_filename(filename,fields)
%
% Example:
%
% >> filename = '../sub-16/anat/sub-16_ses-mri_run-1_echo-2_FLASH.nii.gz';
% >> bids.internal.parse_filename(filename)
%
% ans =
%
% struct with fields:
%
% filename: 'sub-16_ses-mri_run-1_echo-2_FLASH.nii.gz'
% type: 'FLASH'
% ext: '.nii.gz'
% sub: '16'
% ses: 'mri'
% run: '1'
% echo: '2'
%__________________________________________________________________________
function p = parse_filename(filename, fields)
% Split a filename into its building constituents
% FORMAT p = bids.internal.parse_filename(filename, fields)
%
% Example:
%
% >> filename = '../sub-16/anat/sub-16_ses-mri_run-1_echo-2_FLASH.nii.gz';
% >> bids.internal.parse_filename(filename)
%
% ans =
%
% struct with fields:
%
% filename: 'sub-16_ses-mri_run-1_echo-2_FLASH.nii.gz'
% type: 'FLASH'
% ext: '.nii.gz'
% sub: '16'
% ses: 'mri'
% run: '1'
% echo: '2'
% __________________________________________________________________________

% Copyright (C) 2016-2018, Guillaume Flandin, Wellcome Centre for Human Neuroimaging
% Copyright (C) 2018--, BIDS-MATLAB developers
% Copyright (C) 2016-2018, Guillaume Flandin, Wellcome Centre for Human Neuroimaging
% Copyright (C) 2018--, BIDS-MATLAB developers

filename = bids.internal.file_utils(filename,'filename');
filename = bids.internal.file_utils(filename, 'filename');

%-Identify all the BIDS entity-label pairs present in the filename (delimited by "_")
% https://bids-specification.readthedocs.io/en/stable/99-appendices/04-entity-table.html
[parts, dummy] = regexp(filename,'(?:_)+','split','match'); %#ok<ASGLU>
p.filename = filename;
% -Identify all the BIDS entity-label pairs present in the filename (delimited by "_")
% https://bids-specification.readthedocs.io/en/stable/99-appendices/04-entity-table.html
[parts, dummy] = regexp(filename, '(?:_)+', 'split', 'match'); %#ok<ASGLU>
p.filename = filename;

%-Identify the suffix and extension of this file
% https://bids-specification.readthedocs.io/en/stable/02-common-principles.html#file-name-structure
[p.type, p.ext] = strtok(parts{end},'.');
% -Identify the suffix and extension of this file
% https://bids-specification.readthedocs.io/en/stable/02-common-principles.html#file-name-structure
[p.type, p.ext] = strtok(parts{end}, '.');

%-Separate the entity from the label for each pair identified above
for i=1:numel(parts)-1
[d, dummy] = regexp(parts{i},'(?:\-)+','split','match'); %#ok<ASGLU>
% -Separate the entity from the label for each pair identified above
for i = 1:numel(parts) - 1
[d, dummy] = regexp(parts{i}, '(?:\-)+', 'split', 'match'); %#ok<ASGLU>
p.(d{1}) = d{2};
end
end

%-Extra fields can be added to the structure and ordered specifically.
if nargin == 2
for i=1:numel(fields)
if ~isfield(p,fields{i})
p.(fields{i}) = '';
end
% -Extra fields can be added to the structure and ordered specifically.
if nargin == 2
for i = 1:numel(fields)
if ~isfield(p, fields{i})
p.(fields{i}) = '';
end
end
try
p = orderfields(p,['filename','ext','type',fields]);
p = orderfields(p, ['filename', 'ext', 'type', fields]);
catch
warning('Ignoring file ''%s'' not matching template.',filename);
p = struct([]);
warning('Ignoring file ''%s'' not matching template.', filename);
p = struct([]);
end
end
end
45 changes: 23 additions & 22 deletions +bids/+util/jsondecode.m
View file
Original file line number Diff line number Diff line change
@@ -1,30 +1,31 @@
function value = jsondecode(file, varargin)
% Decode JSON-formatted file
% FORMAT value = bids.util.jsondecode(file, opts)
% file - name of a JSON file or JSON string
% opts - structure of optional parameters (only with JSONio):
% replacementStyle: string to control how non-alphanumeric
% characters are replaced {'underscore','hex','delete','nop'}
% [Default: 'underscore']
%
% json - JSON structure
% Decode JSON-formatted file
% FORMAT value = bids.util.jsondecode(file, opts)
% file - name of a JSON file or JSON string
% opts - structure of optional parameters (only with JSONio):
% replacementStyle: string to control how non-alphanumeric
% characters are replaced {'underscore','hex','delete','nop'}
% [Default: 'underscore']
%
% json - JSON structure

% Copyright (C) 2018, Guillaume Flandin, Wellcome Centre for Human Neuroimaging
% Copyright (C) 2018--, BIDS-MATLAB developers
% Copyright (C) 2018, Guillaume Flandin, Wellcome Centre for Human Neuroimaging
% Copyright (C) 2018--, BIDS-MATLAB developers

persistent has_jsondecode
if isempty(has_jsondecode)
persistent has_jsondecode
if isempty(has_jsondecode)
has_jsondecode = ...
exist('jsondecode','builtin') == 5 || ... % MATLAB >= R2016b
ismember(exist('jsondecode','file'), [2 3]); % jsonstuff or other Matlab-compatible implementation
end
exist('jsondecode', 'builtin') == 5 || ... % MATLAB >= R2016b
ismember(exist('jsondecode', 'file'), [2 3]); % jsonstuff / Matlab-compatible implementation
end

if has_jsondecode
if has_jsondecode
value = jsondecode(fileread(file));
elseif exist('spm_jsonread','file') == 3 % SPM12
elseif exist('spm_jsonread', 'file') == 3 % SPM12
value = spm_jsonread(file, varargin{:});
elseif exist('jsonread','file') == 3 % JSONio
elseif exist('jsonread', 'file') == 3 % JSONio
value = jsonread(file, varargin{:});
else
error('JSON library required: install JSONio from https://github.com/gllmflndn/JSONio');
end
else
url = 'https://github.com/gllmflndn/JSONio';
error('JSON library required: install JSONio from: %s', url);
end
Loading

0 comments on commit 5dc177e

Please sign in to comment.