Merge pull request fieldtrip#2413 from schoffelen/gdf

gdf event reading

fileio/ft_read_event.m

@@ -492,15 +492,35 @@
       hdr = ft_read_header(filename);
     end
     % the following applies to Biosemi data that is stored in the gdf format
-    statusindx = find(strcmp(hdr.label, 'STATUS'));
-    if length(statusindx)==1
-      % represent the rising flanks in the STATUS channel as events
-      event = read_trigger(filename, 'header', hdr, 'dataformat', dataformat, 'begsample', flt_minsample, 'endsample', flt_maxsample, 'chanindx', statusindx, 'detectflank', 'up', 'trigshift', trigshift, 'trigpadding', trigpadding, 'fixbiosemi', true);
-    else
-      ft_warning('BIOSIG does not have a consistent event representation, skipping events')
-      event = [];
+    if ~isempty(chanindx)
+      chanindx = find(strcmp(hdr.label, 'STATUS'));
     end
-
+    event = [];
+    if length(chanindx)==1
+      % represent the rising flanks in the STATUS (or user specified) channel as events
+      event = read_trigger(filename, 'header', hdr, 'dataformat', dataformat, 'begsample', flt_minsample, 'endsample', flt_maxsample, 'chanindx', chanindx, 'detectflank', detectflank, 'trigshift', trigshift, 'trigpadding', trigpadding, 'fixbiosemi', true);
+    else
+      ft_warning('data does not have a STATUS channel');
+    end
+
+    % make an attempt to get the events from the BIOSIG hdr
+    if isfield(hdr.orig, 'EVENT')
+      % this is code that has been inspired by eeglab's biosig2eeglabevent
+      event_hdr = biosig2fieldtripevent(hdr.orig.EVENT);
+    else 
+      event_hdr = [];
+    end
+
+    if ~isempty(event) && ~isempty(event_hdr)
+      % merge the two structs
+      event = appendstruct(event(:), event_hdr(:));
+      smp   = [event.sample];
+      [srt, indx] = sort(smp);
+      event = event(indx);
+    elseif isempty(event) && ~isempty(event_hdr)
+      event = event_hdr(:);
+    end
+
   case 'AnyWave'
     event = read_ah5_markers(hdr, filename);
 

fileio/private/biosig2fieldtripevent.m

@@ -0,0 +1,79 @@
+function eventout = biosig2fieldtripevent(eventin)
+
+% BIOSIG2FIELDTRIPEVENT converts event information from a biosig hdr into
+% fieldtrip events
+
+ft_hastoolbox('BIOSIG', 1);
+f = which('sopen.m');
+[p,f,e] = fileparts(f);
+
+if contains(p, 'external')
+  % assume the biosig to be shipped with the fieldtrip distro, in which
+  % case we need to look into fullfile(p,'doc')
+else
+  % assume the biosig to be from the official distro, in which case we need
+  % to look into ../doc, relative to p
+  tok = tokenize(p, filesep);
+  p   = fullfile(tok{1:end-1});
+end
+
+try
+  EVT = sopen(fullfile(p, 'doc', 'eventcodes.txt'));sclose(EVT);
+catch
+  warning('failed to load eventcodes');
+  eventout = [];
+  return;
+end
+
+eventout = struct([]);
+if isfield(eventin, 'TYP')
+  for index = 1:length( eventin.TYP )
+    eType = eventin.TYP(index);
+
+    % use file in
+    % https://sccn.ucsd.edu/bugzilla/show_bug.cgi?id=1387 to test
+    % for boundary events
+    if eType < 256 && isfield(eventin,'CodeDesc') && eType < length(eventin.CodeDesc)
+      eventout(index).type  = eventin.CodeDesc{eType};
+      eventout(index).value = eType;
+    elseif isfield(EVT, 'EVENT') && isfield(EVT.EVENT,'CodeIndex') && isfield(EVT.EVENT,'CodeDesc')
+      if any(EVT.EVENT.CodeIndex==eType)
+        eventout(index).type = EVT.EVENT.CodeDesc{EVT.EVENT.CodeIndex==eType};
+      else
+        eventout(index).type = 'event';
+      end
+      eventout(index).value = eType;
+
+      % FIXME I leave the below in for reference, I don't know what it
+      % means, but we might need it in the future
+%       if eType == 32766 || eType == 32767
+%         eventout(index).edfplustype = eventout(index).type;
+%         eventout(index).type = eeg_boundarytype(event);
+%       end
+    else
+      eventout(index).type  = 'event';
+      eventout(index).value = eType;
+    end
+  end
+end
+if isfield(eventin, 'POS')
+  for index = 1:length( eventin.POS )
+    eventout(index).sample = eventin.POS(index);
+  end
+end
+if isfield(eventin, 'DUR')
+  if any( [ eventin.DUR ] )
+    for index = 1:length( eventin.DUR )
+      eventout(index).duration = eventin.DUR(index);
+    end
+  end
+end
+if isfield(eventin, 'CHN')
+  if any( [ eventin.CHN ] )
+    for index = 1:length( eventin.CHN )
+      eventout(index).chanindex = eventin.CHN(index);
+    end
+  end
+end
+
+eventout = eventout(:);

test/test_pull2413.m

@@ -0,0 +1,16 @@
+function test_pull2413
+
+% MEM 1gb
+% WALLTIME 00:10:00
+% DEPENDENCY ft_read_event
+% DATA private
+
+%%
+
+datadir = dccnpath('/home/common/matlab/fieldtrip/data/test/original/eeg/gdf/');
+
+d = dir(fullfile(datadir, '*.gdf'));
+for k = 1:numel(d)
+  event = ft_read_event(fullfile(d(k).folder, d(k).name));
+end
+