Merge branch 'master' of github.com:sccn/bids-matlab-tools

JSONio/LICENCE → JSONio/LICENSE

@@ -1,5 +1,5 @@
-JSONio: a MATLAB JSON library
-Copyright (c) 2015-2019 Guillaume Flandin <[email protected]>
+JSONio: a MATLAB/Octave JSON library
+Copyright (c) 2015-2021 Guillaume Flandin <[email protected]>
 
 The MIT License (MIT)
 

JSONio/README.md

@@ -1,42 +1,34 @@
- JSONio: a MATLAB/Octave JSON library
- ====================================
+# JSONio: a MATLAB/Octave JSON library
 
- https://www.artefact.tk/software/matlab/jsonio/
-
- JSONio is a MATLAB/Octave library to read/write data in the JSON (JavaScript Object Notation) data-interchange format. 
+JSONio is a MATLAB/Octave library to read/write data in the JSON (JavaScript Object Notation) data-interchange format. 
 
- * JSON: https://www.json.org/
+* JSON: https://www.json.org/
 
- It relies on the JSON parser jsmn written by Serge Zaitsev:
+It relies on the JSON parser jsmn written by [Serge Zaitsev](https://zserge.com/):
 
- * jsmn: https://zserge.com/jsmn.html
+* jsmn: https://zserge.com/jsmn/
 
- This library is also part of SPM:
+This library is also part of SPM:
 
- * SPM: https://www.fil.ion.ucl.ac.uk/spm/
+* SPM: https://www.fil.ion.ucl.ac.uk/spm/
 
- INSTALLATION
- ------------
+## INSTALLATION
 
- Simply add the JSONio directory to the MATLAB path:
+Simply add the JSONio directory to the MATLAB path:
 
 ```matlab
 addpath /home/login/Documents/MATLAB/JSONio
 ```
 
- A compiled MEX file is provided for 64-bit MATLAB platforms. It needs to be compiled for Octave with:
+A compiled MEX file is provided for 64-bit MATLAB platforms. It needs to be compiled for Octave with:
  ```
 mkoctfile --mex jsonread.c jsmn.c -DJSMN_PARENT_LINKS
  ```
 
- EXAMPLE
- -------
+## EXAMPLE
 
 ```matlab
 json = jsonread(filename)
 
 jsonwrite(filename, json)
 ```
-
- -------------------------------------------------------------------------------
- Copyright (C) 2015-2020 Guillaume Flandin <[email protected]>

JSONio/jsonwrite.m

@@ -10,7 +10,7 @@
 %
 % FORMAT [...] = jsonwrite(...,opts)
 % opts     - structure or list of name/value pairs of optional parameters:
-%              indent: string to use for indentation [Default: '']
+%              prettyPrint: indent output [Default: false]
 %              replacementStyle: string to control how non-alphanumeric
 %                characters are replaced {'underscore','hex','delete','nop'}
 %                [Default: 'underscore']
@@ -22,13 +22,14 @@
 %   jsonencode: https://www.mathworks.com/help/matlab/ref/jsonencode.html
 
 % Guillaume Flandin
-% $Id: jsonwrite.m 7526 2019-02-06 14:33:18Z guillaume $
+% $Id: spm_jsonwrite.m 8031 2020-12-10 13:37:00Z guillaume $
 
 
 %-Input parameters
 %--------------------------------------------------------------------------
 opts = struct(...
     'indent','',...
+    'prettyprint',false,...
     'replacementstyle','underscore',...
     'convertinfandnan',true);
 opt  = {struct([])};
@@ -61,6 +62,9 @@
     if ~isfield(opts,lower(fn{i})), warning('Unknown option "%s".',fn{i}); end
     opts.(lower(fn{i})) = opt.(fn{i});
 end
+if opts.prettyprint
+    opts.indent = '  ';
+end
 optregistry(opts);
 
 %-JSON serialization

pop_importbids.m

@@ -21,6 +21,8 @@
 %  'eventtype'   - [string] BIDS event column to use for EEGLAB event types.
 %                  common choices are usually 'trial_type' or 'value'.
 %                  Default is 'value'.
+%  'bidstask'    - [string] value of a key task- allowing to analyze some
+%                  tasks only
 %
 % Outputs:
 %   STUDY   - EEGLAB STUDY structure
@@ -114,6 +116,10 @@
     }, 'pop_importbids');
 if isstr(opt), error(opt); end
 
+if ~exist('jsondecode.m','file')
+   addpath([fileparts(which('pop_importbids.m')) filesep 'JSONio']) 
+end
+
 % Options:
 % - copy folder
 % - use channel location and event
@@ -136,7 +142,11 @@
 dataset_descriptionFile = fullfile(bidsFolder, 'dataset_description.json');
 bids.dataset_description = '';
 if exist(dataset_descriptionFile,'File')
-    bids.dataset_description = jsondecode(importalltxt( dataset_descriptionFile ));
+    if exist('jsondecode.m','file')
+        bids.dataset_description = jsondecode(importalltxt( dataset_descriptionFile ));
+    else
+        bids.dataset_description = jsonread(dataset_descriptionFile);
+    end
 end
 
 % load participant file
@@ -155,7 +165,11 @@
 participantsJSONFile = fullfile(bidsFolder, 'participants.json');
 bids.participantsJSON = '';
 if exist(participantsJSONFile,'File')
-    bids.participantsJSON = jsondecode(importalltxt( participantsJSONFile ));
+    if exist('jsondecode.m','file')
+        bids.participantsJSON = jsondecode(importalltxt( participantsJSONFile ));
+    else
+        bids.participantsJSON = jsonread(participantsJSONFile);
+    end
 end
 
 % scan participants
@@ -236,7 +250,7 @@
                             ind = strmatch( '.fif', cellfun(@(x)x(end-3:end), allFiles, 'uniformoutput', false) ); % FIF
                             if isempty(ind)
                                 ind = strmatch( '.gz', cellfun(@(x)x(end-2:end), allFiles, 'uniformoutput', false) ); % FIF
-                                if isempty(ind)
+                                if isempty(ind) && ~isempty(allFiles)
                                     fprintf(2, 'No EEG file found for subject %s\n', bids.participants{iSubject,1});
                                 end
                             end
@@ -558,7 +572,7 @@
     parent = fileparts(parent);
 end
 if isempty(outFile)
-    outFile = filterHiddenFile(folder, dir(fullfile(parent, fileName)));
+    outFile = filterHiddenFile(parent, dir(fullfile(parent, fileName)));
 end
 
 function fileList = filterHiddenFile(folder, fileList)
@@ -601,13 +615,21 @@
     if strcmpi(ext, '.tsv')
         data = importtsv( fullfile(localFile(1).folder, localFile(1).name));
     else
-        data = jsondecode( importalltxt( fullfile(localFile(1).folder, localFile(1).name) ));
+        if exist('jsondecode.m','file')
+            data = jsondecode( importalltxt( fullfile(localFile(1).folder, localFile(1).name) ));
+        else
+            data = jsonread(fullfile(localFile(1).folder, localFile(1).name));
+        end
     end        
 elseif ~isempty(globalFile)
     if strcmpi(ext, '.tsv')
         data = importtsv( fullfile(globalFile(1).folder, globalFile(1).name));
     else
-        data = jsondecode( importalltxt( fullfile(globalFile(1).folder, globalFile(1).name) ));
+        if exist('jsondecode.m','file')
+            data = jsondecode( importalltxt( fullfile(globalFile(1).folder, globalFile(1).name) ));
+        else
+            data = jsonread(fullfile(globalFile(1).folder, globalFile(1).name));
+        end
     end
 end