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

Author: arnodelorme

.gitattributes

@@ -1,5 +1,2 @@
-*.fdt filter=lfs diff=lfs merge=lfs -text
-*.set filter=lfs diff=lfs merge=lfs -text
-*.tsv filter=lfs diff=lfs merge=lfs -text
 testing/data/*.set filter=lfs diff=lfs merge=lfs -text
 testing/data/*.fdt filter=lfs diff=lfs merge=lfs -text

bids_export.m

@@ -915,10 +915,13 @@ function copy_data_bids_eeg(sIn, subjectStr, sess, fileStr, opt)
 bids_writeelectrodefile(EEG, fileOutRed, 'export', opt.elecexport);
 if strcmpi(opt.modality, 'eeg')
     bids_writetinfofile(EEG, tInfo, notes, fileOutRed);
+    EEG.etc.datatype = 'eeg';
 elseif strcmpi(opt.modality, 'ieeg')
     bids_writeieegtinfofile(EEG, tInfo, notes, fileOutRed);
+    EEG.etc.datatype = 'ieeg';
 elseif strcmpi(opt.modality, 'meg')
     bids_writemegtinfofile(EEG, tInfo, notes, fileOutRed);
+    EEG.etc.datatype = 'meg';
 end
 
 % write channel information
@@ -1108,7 +1111,7 @@ function writetsv(fileName, matlabArray)
 if fid == -1, error('Cannot write file - make sure you have writing permission'); end
 for iRow=1:size(matlabArray,1)
     for iCol=1:size(matlabArray,2)
-        if isempty(matlabArray{iRow,iCol})
+        if isempty(matlabArray{iRow,iCol}) || isnan(matlabArray{iRow,iCol})
             %disp('Empty value detected, replacing by n/a');
             fprintf(fid, 'n/a');
         elseif ischar(matlabArray{iRow,iCol})

bids_writechanfile.m

@@ -25,7 +25,7 @@ function eeg_writechanfile(EEG, fileOut)
     if contains(fileOut, 'ieeg')
         fprintf(fid, 'name\ttype\tunits\tlow_cutoff\thigh_cutoff\n');
         for iChan = 1:EEG.nbchan
-            fprintf(fid, 'E%d\tEEG\tmicroV\tn/a\tn/a\n', iChan); 
+            fprintf(fid, 'E%d\tiEEG\tmicroV\tn/a\tn/a\n', iChan); 
         end
     else
         fprintf(fid, 'name\ttype\tunits\n');

bids_writeelectrodefile.m

@@ -20,16 +20,10 @@ function bids_writeelectrodefile(EEG, fileOut, varargin)
 else
     flagExport = 'auto';
 end
-isTemplate = false;
-% case { 32 33 }, fileloc = 'GSN-HydroCel-32.sfp';
-% case { 64 65 }, fileloc = 'GSN65v2_0.sfp';
-% case { 128 129 }, fileloc = 'GSN129.sfp';
-% case { 256 257 }, fileloc = 'GSN-HydroCel-257.sfp';
-% 
+
 if isfield(EEG.chaninfo, 'filename') && isequal(flagExport, 'auto')
-    if ~isempty(strfind(EEG.chaninfo.filename, 'standard-10-5-cap385.elp')) || ...
-            ~isempty(strfind(EEG.chaninfo.filename, 'standard_1005.elc'))||...
-            ~isempty(strfind(EEG.chaninfo.filename, 'standard_1005.ced'))
+    templates = {'GSN-HydroCel-32.sfp', 'GSN65v2_0.sfp', 'GSN129.sfp', 'GSN-HydroCel-257.sfp', 'standard-10-5-cap385.elp', 'standard_1005.elc', 'standard_1005.ced'};
+    if any(contains(EEG.chaninfo.filename, templates))
         flagExport = 'off';
         disp('Template channel location detected, not exporting electrodes.tsv file');
     end
@@ -40,7 +34,7 @@ function bids_writeelectrodefile(EEG, fileOut, varargin)
     fprintf(fid, 'name\tx\ty\tz\n');
 
     for iChan = 1:EEG.nbchan
-        if isempty(EEG.chanlocs(iChan).X) || isnan(EEG.chanlocs(iChan).X)
+        if isempty(EEG.chanlocs(iChan).X) || isnan(EEG.chanlocs(iChan).X) || contains(fileOut, 'ieeg')
             fprintf(fid, '%s\tn/a\tn/a\tn/a\n', EEG.chanlocs(iChan).labels );
         else
             fprintf(fid, '%s\t%2.6f\t%2.6f\t%2.6f\n', EEG.chanlocs(iChan).labels, EEG.chanlocs(iChan).X, EEG.chanlocs(iChan).Y, EEG.chanlocs(iChan).Z );

bids_writetinfofile.m

@@ -40,11 +40,12 @@
 end
 if EEG.trials == 1
     tInfo.RecordingType = 'continuous';
+    tInfo.RecordingDuration = EEG.pnts/EEG.srate;
 else
     tInfo.RecordingType = 'epoched';
     tInfo.EpochLength = EEG.pnts/EEG.srate;
+    tInfo.RecordingDuration = (EEG.pnts/EEG.srate)*EEG.trials;
 end
-tInfo.RecordingDuration = EEG.pnts/EEG.srate;
 tInfo.SamplingFrequency = EEG.srate;
 if ~isempty(notes)
     tInfo.SubjectArtefactDescription = notes;