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

cll008 · Nov 15, 2021 · a999767 · a999767
2 parents 62e9cda + 64fd4cc
commit a999767
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Showing 4 changed files with 53 additions and 44 deletions.
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1 @@
+*~
diff --git a/bids_export.m b/bids_export.m
@@ -263,9 +263,10 @@ function bids_export(files, varargin)
     'anattype'  ''        {}    'T1w';
     'chanlocs'  ''        {}    '';
     'chanlookup' 'string' {}    '';
+    'interactive' 'string'  {'on' 'off'}    'off';
     'defaced'   'string'  {'on' 'off'}    'on';
     'createids' 'string'  {'on' 'off'}    'on';
-    'singleEventsJson' 'string'  {'on' 'off'}    'on';
+    'individualEventsJson' 'string'  {'on' 'off'}    'off';
     'exportext' 'string'  { 'edf' 'eeglab' } 'eeglab';
     'README'    'string'  {}    '';
     'CHANGES'   'string'  {}    '' ;
@@ -277,21 +278,22 @@ function bids_export(files, varargin)
 
 % deleting folder
 fprintf('Exporting data to %s...\n', opt.targetdir);
-if exist(opt.targetdir,'dir')
-    uilist = { ...
-        { 'Style', 'text', 'string', 'Output directory exists and all current files will be deleted if continue', 'fontweight', 'bold'  }, ...
-        { 'Style', 'text', 'string', 'Would you want to proceed?'}, ...
-        };
-    geometry = { [1] [1]};
-    geomvert =   [1  1 ];
-    [results,userdata,isOk,restag] = inputgui( 'geometry', geometry, 'geomvert', geomvert, 'uilist', uilist, 'title', 'Warning');
-    if isempty(isOk) 
-        disp('BIDS export cancelled...')
-        return 
-    else
-        disp('Deleting folder...')
-        rmdir(opt.targetdir, 's');
+if exist(opt.targetdir,'dir') 
+    if strcmpi(opt.interactive, 'on')
+        uilist = { ...
+            { 'Style', 'text', 'string', 'Output directory exists and all current files will be deleted if continue', 'fontweight', 'bold'  }, ...
+            { 'Style', 'text', 'string', 'Would you want to proceed?'}, ...
+            };
+        geometry = { [1] [1]};
+        geomvert =   [1  1 ];
+        [results,userdata,isOk,restag] = inputgui( 'geometry', geometry, 'geomvert', geomvert, 'uilist', uilist, 'title', 'Warning');
+        if isempty(isOk)
+            disp('BIDS export cancelled...')
+            return
+        end
     end
+    disp('Folder exist. Deleting folder...')
+    rmdir(opt.targetdir, 's');
 end
 
 disp('Creating sub-directories...')
@@ -473,7 +475,7 @@ function bids_export(files, varargin)
     if ~isfield(opt.eInfoDesc, fields{iField}), opt.eInfoDesc(1).(fields{iField}) = struct([]); end
     opt.eInfoDesc.(fields{iField}) = checkfields(opt.eInfoDesc.(fields{iField}), eInfoDescFields, 'eInfoDesc');
 end
-if strcmpi(opt.singleEventsJson, 'on')
+if strcmpi(opt.individualEventsJson, 'off')
     jsonwrite(fullfile(opt.targetdir, ['task-' opt.taskName '_events.json' ]), opt.eInfoDesc,struct('indent','  '));
 end
 
@@ -764,7 +766,7 @@ function copy_data_bids(fileIn, fileOut, notes, opt, chanlocs, copydata, exportE
 [folderOut,fileOut,~] = fileparts(fileOut);
 fileOut = fullfile(folderOut,fileOut);
 if ~isempty(EEG.event)
-    if strcmpi(opt.singleEventsJson,'off')
+    if strcmpi(opt.individualEventsJson,'on')
         jsonwrite([ fileOut(1:end-3) 'events.json' ], opt.eInfoDesc,struct('indent','  '));
     end
     % --- _events.tsv

diff --git a/pop_exportbids.m b/pop_exportbids.m
@@ -59,7 +59,7 @@
         { 'Style', 'pushbutton', 'string', 'Edit participants' 'tag' 'participants' 'callback' cb_participants }, ...
         { 'Style', 'pushbutton', 'string', 'Edit event info' 'tag' 'events' 'callback' cb_events }, ...
         { 'Style', 'checkbox', 'string', 'Do not use participants ID and create anonymized participant ID instead' 'tag' 'newids' }, ...
-        { 'Style', 'checkbox', 'string', 'Use single top-level events.json' 'tag' 'eventsJson' }, ...
+        { 'Style', 'checkbox', 'string', 'Export individual events.json' 'tag' 'eventsJson' }, ...
         };
     relSize = 0.7;
     geometry = { [1] [1] [1-relSize relSize*0.8 relSize*0.2] [1-relSize relSize] [1] [1] [1 1 1] [1] [1]};
@@ -81,7 +81,7 @@
 %     end
 
     % options
-    options = { 'targetdir' restag.outputfolder 'License' restag.license 'CHANGES' restag.changes 'createids' fastif(restag.newids, 'on', 'off') 'singleEventsJson' fastif(restag.eventsJson, 'on', 'off')};
+    options = { 'targetdir' restag.outputfolder 'License' restag.license 'CHANGES' restag.changes 'createids' fastif(restag.newids, 'on', 'off') 'individualEventsJson' fastif(restag.eventsJson, 'on', 'off')};
 
     if ~isfield(EEG(1), 'BIDS') % none of the edit button was clicked
         EEG = pop_eventinfo(EEG, STUDY, 'default');
@@ -180,7 +180,11 @@
 if ~isempty(pInfo)
     options = [options 'pInfo' {pInfo}];
 end
-bids_export(subjects, options{:});
+if nargin < 3
+    bids_export(subjects, 'interactive', 'on', options{:});
+else
+    bids_export(subjects, options{:});
+end
 disp('Done');
 
 % history

diff --git a/rename_brainvision_files.m b/rename_brainvision_files.m
@@ -73,31 +73,33 @@ function rename_brainvision_files(varargin)
 fclose(fid1);
 fclose(fid2);
 
-oldmarkerfile = fullfile(pathIn , oldmarkerfile);
-newmarkerfile = fullfile(pathOut, newmarkerfile);
-assert(exist(newmarkerfile, 'file')==0, 'the file %s already exists', newmarkerfile);
-fid1 = fopen(oldmarkerfile, 'r');
-fid2 = fopen(newmarkerfile, 'w');
+if exist('oldmarkerfile', 'var')
+    oldmarkerfile = fullfile(pathIn , oldmarkerfile);
+    newmarkerfile = fullfile(pathOut, newmarkerfile);
+    assert(exist(newmarkerfile, 'file')==0, 'the file %s already exists', newmarkerfile);
+    fid1 = fopen(oldmarkerfile, 'r');
+    fid2 = fopen(newmarkerfile, 'w');
 
-while ~feof(fid1)
-  line = fgetl(fid1);
-  if ~isempty(regexp(line, '^HeaderFile', 'once'))
-    [~, rem] = strtok(line, '=');
-    oldheaderfile = rem(2:end);
-    [~, ~, x] = fileparts(oldheaderfile);
-    newheaderfile = [baseNameOut switchcase(x)];
-    line = sprintf('HeaderFile=%s', newheaderfile);
-  elseif ~isempty(regexp(line, '^DataFile', 'once'))
-    [~, rem] = strtok(line, '=');
-    olddatafile = rem(2:end);
-    [~, ~, x] = fileparts(olddatafile);
-    newdatafile = [baseNameOut switchcase('.eeg')];
-    line = sprintf('DataFile=%s', newdatafile);
-  end
-  fprintf(fid2, '%s\r\n', line);
+    while ~feof(fid1)
+        line = fgetl(fid1);
+        if ~isempty(regexp(line, '^HeaderFile', 'once'))
+            [~, rem] = strtok(line, '=');
+            oldheaderfile = rem(2:end);
+            [~, ~, x] = fileparts(oldheaderfile);
+            newheaderfile = [baseNameOut switchcase(x)];
+            line = sprintf('HeaderFile=%s', newheaderfile);
+        elseif ~isempty(regexp(line, '^DataFile', 'once'))
+            [~, rem] = strtok(line, '=');
+            olddatafile = rem(2:end);
+            [~, ~, x] = fileparts(olddatafile);
+            newdatafile = [baseNameOut switchcase('.eeg')];
+            line = sprintf('DataFile=%s', newdatafile);
+        end
+        fprintf(fid2, '%s\r\n', line);
+    end
+    fclose(fid1);
+    fclose(fid2);
 end
-fclose(fid1);
-fclose(fid2);
 
 olddatafile = fullfile(pathIn , olddatafile);
 newdatafile = fullfile(pathOut, newdatafile);
@@ -114,4 +116,4 @@ function rename_brainvision_files(varargin)
     try delete(oldheaderfile); end
     try delete(oldmarkerfile); end
     try delete(olddatafile); end
-end
+end