Merge remote-tracking branch 'upstream/master'

Conflicts:
	utilities/ft_datatype_sens.m

Author: sarangnemo

contrib/nutmegtrip/private/nmt_ts_intervalpower.m

@@ -1,4 +1,4 @@
-function fun = nmt_ts_intervalpower(fun,meantype);
+function fun = nmt_ts_intervalpower(fun,meantype)
 % when time interval is selected, calculate desired representation of interval power
 switch(meantype)
     case 'msq' % mean power
@@ -10,4 +10,4 @@
     case 'mean'  % simple average
         fun = mean(fun,3);
         fun = mean(fun,2);
-end
+end

contrib/spike/private/cluster_ward.m

@@ -1,4 +1,4 @@
-function [grootte,ordening] = cluster(realdist,optie,absoluut,aantal);
+function [grootte,ordening] = cluster(realdist,optie,absoluut,aantal)
 
 % CLUSTER_WARD Hierarchical cluster algorithm
 %

contrib/spike/private/preproc.m

@@ -270,10 +270,11 @@
 if ~strcmp(cfg.montage, 'no') && ~isempty(cfg.montage)
   % this is an alternative approach for rereferencing, with arbitrary complex linear combinations of channels
   tmp.trial = {dat};
+  tmp.time  = {time};
   tmp.label = label;
-  tmp = ft_apply_montage(tmp, cfg.montage, 'feedback', 'none');
-  dat = tmp.trial{1};
-  label = tmp.label;
+  tmp   = ft_apply_montage(tmp, cfg.montage, 'feedback', 'none');
+  dat   = tmp.trial{1}; % the number of channels can have changed
+  label = tmp.label;    % the channels can be different than the input channel labels
   clear tmp
 end
 

engine/private/ft_platform_supports.m

@@ -55,7 +55,7 @@
 
   case 'onCleanup'
     tf = is_octave() || matlabversion(7.8, Inf);
-
+    
   case 'alim'
     tf = is_matlab();
 
@@ -76,15 +76,15 @@
   case 'stats'
     root_dir=fileparts(which('ft_defaults'));
     external_stats_dir=fullfile(root_dir,'external','stats');
-
+    
     % these files are only used by other functions in the external/stats
     % directory
     exclude_mfiles={'common_size.m',...
-                    'iscomplex.m',...
-                    'lgamma.m'};
-
+      'iscomplex.m',...
+      'lgamma.m'};
+    
     tf = has_all_functions_in_dir(external_stats_dir,exclude_mfiles);
-
+    
   case 'program_invocation_name'
     % Octave supports program_invocation_name, which returns the path
     % of the binary that was run to start Octave
@@ -120,16 +120,16 @@
 
   case 'urlread-timeout'
     tf = is_matlab() && matlabversion('2012b',Inf);
-
+    
   case 'griddata-vector-input'
     tf = is_matlab();
-
+    
   case 'griddata-v4'
     tf = is_matlab() && matlabversion('2009a',Inf);
 
   case 'uimenu'
     tf = is_matlab();
-
+    
   otherwise
     error('unsupported value for first argument: %s', what);
 
@@ -163,19 +163,19 @@
 function tf = has_all_functions_in_dir(in_dir, exclude_mfiles)
 % returns true if all functions in in_dir are already provided by the
 % platform
-  m_files=dir(fullfile(in_dir,'*.m'));
-  n=numel(m_files);
+m_files=dir(fullfile(in_dir,'*.m'));
+n=numel(m_files);
 
-  for k=1:n
-    m_filename=m_files(k).name;
-    if isempty(which(m_filename)) && ...
-                isempty(strmatch(m_filename,exclude_mfiles))
-      tf=false;
-      return;
-    end
+for k=1:n
+  m_filename=m_files(k).name;
+  if isempty(which(m_filename)) && ...
+      isempty(strmatch(m_filename,exclude_mfiles))
+    tf=false;
+    return;
   end
+end
 
-  tf=true;
+tf=true;
 
 end % function
 
@@ -253,46 +253,47 @@
   inInterval = orderedComparison(minMajor, minMinor, maxMajor, maxMinor, major, minor);
 end
 
-  function [year, ab] = parseMatlabRelease(str)
-    if (str == Inf)
-      year = Inf; ab = Inf;
-    elseif (str == -Inf)
-      year = -Inf; ab = -Inf;
-    else
-      year = str2num(str(1:4));
-      ab = str(5);
-    end
-  end
+end % function
 
-  function [major, minor] = parseMatlabVersion(ver)
-    if (ver == Inf)
-      major = Inf; minor = Inf;
-    elseif (ver == -Inf)
-      major = -Inf; minor = -Inf;
-    elseif (isnumeric(ver))
-      major = floor(ver);
-      minor = int8((ver - floor(ver)) * 10);
-    else % ver is string (e.g. '7.10'), parse accordingly
-      [major, rest] = strtok(ver, '.');
-      major = str2num(major);
-      minor = str2num(strtok(rest, '.'));
-    end
-  end
+function [year, ab] = parseMatlabRelease(str)
+if (str == Inf)
+  year = Inf; ab = Inf;
+elseif (str == -Inf)
+  year = -Inf; ab = -Inf;
+else
+  year = str2num(str(1:4));
+  ab = str(5);
+end
+end % function
+
+function [major, minor] = parseMatlabVersion(ver)
+if (ver == Inf)
+  major = Inf; minor = Inf;
+elseif (ver == -Inf)
+  major = -Inf; minor = -Inf;
+elseif (isnumeric(ver))
+  major = floor(ver);
+  minor = int8((ver - floor(ver)) * 10);
+else % ver is string (e.g. '7.10'), parse accordingly
+  [major, rest] = strtok(ver, '.');
+  major = str2num(major);
+  minor = str2num(strtok(rest, '.'));
+end
+end  % function
 
 % checks if testA is in interval (lowerA,upperA); if at edges, checks if testB is in interval (lowerB,upperB).
-  function inInterval = orderedComparison(lowerA, lowerB, upperA, upperB, testA, testB)
-    if (testA < lowerA || testA > upperA)
-      inInterval = false;
-    else
-      inInterval = true;
-      if (testA == lowerA)
-        inInterval = inInterval && (testB >= lowerB);
-      end
-      
-      if (testA == upperA)
-        inInterval = inInterval && (testB <= upperB);
-      end
-    end
+function inInterval = orderedComparison(lowerA, lowerB, upperA, upperB, testA, testB)
+if (testA < lowerA || testA > upperA)
+  inInterval = false;
+else
+  inInterval = true;
+  if (testA == lowerA)
+    inInterval = inInterval && (testB >= lowerB);
+  end
+  
+  if (testA == upperA)
+    inInterval = inInterval && (testB <= upperB);
   end
+end
+end  % function
 
-end % function

external/dipoli/loadama.m

@@ -1,4 +1,4 @@
-function [ama] = loadama(filename);
+function [ama] = loadama(filename)
 
 % LOADAMA read an inverted A-matrix and associated geometry information
 % from an ama file that was written by Tom Oostendorp's DIPOLI

external/neurone/EEGLAB Plug-In Instructions 1.0.3.4.pdf

@@ -0,0 +1,37 @@
+NeurOne to EEGLAB data import plugin
+Mega Electronics
+
+Version 1.0.3.4 (2016-06-17)
+- Bug fix in readneuroneevents.m: wrong file ID "fileIdEvents" fixed.
+- New feature: Support for events.bin revisions up to 6.
+
+Version 1.0.3.3 (2015-05-28)
+- New feature: Support for events.bin revisions up to 4.
+
+Version 1.0.3.2 (2013-04-04)
+- New feature: A warning is displayed instead of an error when an unknown filetype revision is found.
+
+Version 1.0.3.1 (2012-06-18)
+- New feature: The reader is now able to read measurements with events.bin revision up to 2.
+
+Version 1.0.3.0 (2012-01-13)
+- First release
+
+Version 1.0.2.0 (2011-12-22)
+- Modifications in 'readneuronedata.m'. When all channels are to be read, the function
+  will read the binary data without a loop to shorten the processing time.
+- The numerical data is stored as double-precision floating point (double) by default.
+
+Version 1.0.1.2 (2011-12-21)
+- Fixed an error which occurred when the numerical data was divided into 
+  multiple binary files.
+- Added a progress indicator in the readneuronedata function.
+
+Version 1.0.1.1 (2011-12-11)
+- Improved event readability. See help readneuroneevents for the new event structure.
+- readneuronedata.m re-created so that one channel will be read at a time.
+- Updated all m-file headers.
+- Fixed some other minor errors.
+
+Version 1.0.1.0 (2011-11-28)
+- First version of the plugin.

external/neurone/Version History.txt

@@ -0,0 +1,54 @@
+% eegplugin_neurone() - EEGLAB plugin to import data from a NeurOne device.
+% 
+% Usage:
+%   >> eegplugin_neurone(fig,try_strings,catch_strings)
+%
+% Inputs:
+%   fig            - [integer]  handle to EEGLAB figure
+%   try_strings    - [struct] "try" strings for menu callbacks.
+%   catch_strings  - [struct] "catch" strings for menu callbacks.
+%
+% NeurOne data import plugin consists of the following files:
+%   pop_readneurone.m
+%   guireadneurone.m
+%   guireadneurone.fig
+%   readneurone.m
+%   readneuronedata.m
+%   readneuroneevents.m
+%   neurone_logo.png
+%   mega_gradient_edit.png
+%
+% This plugin was created according to the instructions provided by the
+% creators of EEGLAB. These instructions can be found e.g. from the website:
+% http://sccn.ucsd.edu/wiki/A07:_Contributing_to_EEGLAB
+% 
+% Current version: 1.0.3.4 (2016-06-17)
+% Author: Mega Electronics
+
+function vers = eegplugin_neurone(fig,try_strings,catch_strings)
+
+vers='NeurOne data import 1.0.3.4';
+
+% Check the number of input arguments
+if nargin < 3
+    error('Not enough input arguments.');
+end
+
+% Add plugin folder to path
+if  ~exist('pop_readneurone.m')               
+    path=which('eegplugin_neurone.m');
+    [path filename]=fileparts(path);
+    path=[path filesep];
+    addpath([path version] );
+end
+
+% Find the 'Import data' -menu
+importmenu=findobj(fig,'tag','import data');
+
+% Construct command
+cmd = [try_strings.no_check '[EEG LASTCOM]=pop_readneurone;' catch_strings.new_and_hist];
+
+% Create the menu for NeurOne import
+uimenu(importmenu,'label','From a NeurOne file (.ses)',...
+    'Callback',cmd,'separator','on');
+