Merge pull request #624 from robertoostenveld/bug3385-eda

add support for iMotions

compat/matlablt2016b/newline.m

@@ -0,0 +1,10 @@
+function C = newline
+
+% NEWLINE Create newline character 
+%   C = newline creates the character representing a newline.
+%   newline is equivalent to char(10) or sprintf('\n').
+%
+% This is a compatibility function that should only be added to the path on
+% MATLAB versions prior to 2016b.
+
+C = char(10);

fileio/ft_filetype.m

@@ -933,6 +933,11 @@
   type = 'curry_dig';
   manufacturer = 'Curry';
   content = 'digitizer file';
+
+elseif filetype_check_extension(filename, '.txt') && filetype_check_header(filename, '#Study')
+  type = 'imotions_txt';
+  manufacturer = 'iMotions';
+  content = 'various biosignals';
 
 elseif filetype_check_extension(filename, '.txt') && filetype_check_header(filename, '##')
   type = 'smi_txt';

fileio/private/read_eyelink_asc.m

@@ -42,7 +42,7 @@
 fclose(fid);
 
 aline(aline==uint8(sprintf('\r'))) = [];        % remove cariage return
-aline = tokenize(aline, uint8(sprintf('\n')));  % split on newline
+aline = tokenize(aline, uint8(newline));        % split on newline
 
 for i=1:numel(aline)
   tline = aline{i};

fileio/private/read_tobii_tsv.m

@@ -25,7 +25,7 @@
       [key, val] = strtok(line, ':');
       key = fixname(key);
       val = val(2:end); % skip the ':'
-      val = deblank2(val);
+      val = strtrim(val);
       tsv.(key) = val;
     end
 

imotions2fieldtrip.m

@@ -0,0 +1,109 @@
+function [raw, event] = imotions2fieldtrip(filename, varargin)
+
+% IMOTIONS2FIELDTRIP imports an iMotions *.txt file and represents it as a FieldTrip
+% raw data structure.
+%
+% Use as
+%   data = imotions2fieldtrip(filename)
+%
+% See also FT_DATATYPE_RAW, FT_PREPROCESSING
+
+% Copyright (C) 2017, Robert Oostenveld
+%
+% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
+% for the documentation and details.
+%
+%    FieldTrip is free software: you can redistribute it and/or modify
+%    it under the terms of the GNU General Public License as published by
+%    the Free Software Foundation, either version 3 of the License, or
+%    (at your option) any later version.
+%
+%    FieldTrip is distributed in the hope that it will be useful,
+%    but WITHOUT ANY WARRANTY; without even the implied warranty of
+%    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%    GNU General Public License for more details.
+%
+%    You should have received a copy of the GNU General Public License
+%    along with FieldTrip. If not, see <http://www.gnu.org/licenses/>.
+%
+% $Id$
+
+% read the whole ASCII file into memory
+% this will include a MATLAB table with the actual data
+dat = read_imotions_txt(filename);
+
+time    = dat.TimestampInSec;
+numeric = zeros(0,numel(time));
+label   = dat.data.Properties.VariableNames;
+sellab  = false(size(label));
+
+% check for each field/column whether it is numeric
+for i=1:numel(label)
+  % try converting the first element
+  str = dat.data.(label{i})(1);
+  val = str2double(str);
+  if ~isempty(str) && isnan(val)
+    ft_info('column %s is not numeric', label{i});
+    continue
+  end
+
+  % try converting the first 20 elements
+  if numel(time)>10
+    str = dat.data.(label{i})(1:20);
+    val = str2double(str);
+    if ~isempty(str) && any(isnan(val))
+      ft_info('column %s is not numeric', label{i});
+      continue
+    end
+  end
+
+  % try converting the whole column
+  str = dat.data.(label{i});
+  val = str2double(str);
+  if ~isempty(str) && any(isnan(val))
+    ft_info('column %s is not numeric', label{i});
+    continue
+  end
+
+  % if it gets here, it means that the whole column is numeric
+  sellab(i) = true;
+  ft_info('%s is numeric and will be represented as channel', label{i});
+  numeric = cat(1, numeric, val');
+end
+
+% the same timestamp can be on multiple lines in the file
+dt = diff(sort(time));
+
+if any(dt==0)
+  ft_notice('removing overlapping samples...\n');
+  t = 1;
+  while t<numel(time)
+    sel = find(time==time(t));
+    numeric(:,t) = nanmean(numeric(:,sel),2);
+    time(sel(2:end)) = nan;
+    t = t+numel(sel);
+  end
+
+  ft_notice('keeping %.0f of the original samples\n', mean(~isnan(time)));
+  time    = time   (  ~isnan(time));
+  numeric = numeric(:,~isnan(time));
+end
+
+% construct a raw data structure
+raw.time = {time};
+raw.trial = {numeric};
+raw.label = label(sellab);
+
+% interpolate the data
+dt = diff(time);
+dt = median(dt);
+begtime = min(time);
+endtime = max(time);
+
+if any(diff(time)~=dt)
+  ft_notice('resampling onto regularly spaced time axis\n');
+  tmpcfg = [];
+  tmpcfg.time = {begtime:dt:endtime};
+  raw = ft_resampledata(tmpcfg, raw);
+  [~, raw] = rollback_provenance([], raw);
+end

private/read_imotions_txt.m

@@ -0,0 +1,75 @@
+function dat = read_imotions_txt(filename)
+
+% READ_IMOTIONS_TXT reads *.txt files that are exported from the iMotions software.
+%
+% Use as
+%   dat = read_imotions_txt(filename
+%
+% See also TEXTSCAN
+
+% Copyright (C) 2017, Robert Oostenveld
+%
+% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
+% for the documentation and details.
+%
+%    FieldTrip is free software: you can redistribute it and/or modify
+%    it under the terms of the GNU General Public License as published by
+%    the Free Software Foundation, either version 3 of the License, or
+%    (at your option) any later version.
+%
+%    FieldTrip is distributed in the hope that it will be useful,
+%    but WITHOUT ANY WARRANTY; without even the implied warranty of
+%    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%    GNU General Public License for more details.
+%
+%    You should have received a copy of the GNU General Public License
+%    along with FieldTrip. If not, see <http://www.gnu.org/licenses/>.
+%
+% $Id$
+
+fprintf('reading header from %s\n', filename);
+% read the whole file at once
+fid = fopen(filename, 'rt');
+aline = fread(fid, inf, 'char=>char');          % returns a single long string
+fclose(fid);
+
+aline(aline==uint8(sprintf('\r'))) = [];        % remove cariage return
+aline = tokenize(aline, uint8(newline));        % split on newline
+
+dat = [];
+
+% the first section contains multiple lines with general header information
+headerline = 1;
+while startsWith(aline{headerline}, '#')
+  % for example "#Version : 6.3.6059.1"
+  tok = tokenize(aline{headerline}(2:end), ':');
+  key = matlab.lang.makeValidName(strtrim(tok{1}));
+  val = strtrim(tok{2});
+  dat.(key) = val;
+  headerline = headerline + 1;
+end
+
+% there is one line with column headings
+headerline = 1;
+while ~startsWith(aline{headerline}, 'StudyName')
+  headerline = headerline+1;
+end
+dat.Labels = tokenize(aline{headerline});
+dat.Labels = matlab.lang.makeValidName(dat.Labels);
+
+fprintf('parsing tabular data\n');
+% now that the header information is known, the actual content can be scanned
+fid = fopen(filename, 'rt');
+c = textscan(fid, repmat('%s', [1 numel(dat.Labels)]), 'Delimiter', '\t', 'Headerlines', headerline);
+fclose(fid);
+
+% add each column as a variable to the data structure
+for i=1:numel(dat.Labels)
+  dat.data.(dat.Labels{i}) = c{i};
+end
+% convert to a table object (requires MATLAB R2013b and up)
+dat.data = struct2table(dat.data);
+
+fprintf('converting timestamps to seconds\n');
+% convert timestamp to seconds
+dat.TimestampInSec = datenum(dat.data.Timestamp, 'yyyymmdd_hhMMssfff');

private/rollback_provenance.m

@@ -46,7 +46,12 @@
     continue
   end
 
-  fn0 = fieldnames(cfg);
+  if isempty(cfg)
+    % allow for [] as the input cfg
+    fn0 = {};
+  else
+    fn0 = fieldnames(cfg);
+  end
 
   if ~isfield(varargin{i}, 'cfg')
     % input does not contain cfg, so no rollback to be performed