Merge branch 'develop' into 509-eyes-observed-incorrectly-inherit-eye…

…-marker

src/ext/matlabbatch/cfg_ui.m

@@ -20,7 +20,7 @@
 %
 % See also: GUIDE, GUIDATA, GUIHANDLES
 %
-% This code is part of a batch job configuration system for MATLAB. See 
+% This code is part of a batch job configuration system for MATLAB. See
 %      help matlabbatch
 % for a general overview.
 %_______________________________________________________________________
@@ -309,7 +309,7 @@ function local_showjob(obj,cjob)
     set(findobj(handles.cfg_ui,'-regexp', 'Tag','.*File(Run)|(RunSerial)$'),'Enable','on');
 else
     set(findobj(handles.cfg_ui,'-regexp', 'Tag','.*File(Run)|(RunSerial)$'),'Enable','off');
-end    
+end
 local_showmod(obj);
 
 % --------------------------------------------------------------------
@@ -378,7 +378,7 @@ function local_showvaledit(obj)
     ciid = {udmodlist.cjob udmodlist.id{cmod} udmodule.id{citem}};
 end;
 contents = cellfun(@(c)subsref(c, substruct('{}',{citem})), udmodule.contents, 'UniformOutput', false);
-sout = cat(2, udmodlist.sout(1:cmod-1));
+sout = cat(2, udmodlist.sout{1:cmod-1});
 cfg_ui_util('showvaledit', fig, ciid, contents, sout, dflag, [], @()local_valedit_update(obj));
 drawnow;
 
@@ -564,7 +564,7 @@ function cfg_ui_CloseRequestFcn(hObject, eventdata, handles)
 end;
 
 % --- Outputs from this function are returned to the command line.
-function varargout = cfg_ui_OutputFcn(hObject, eventdata, handles) 
+function varargout = cfg_ui_OutputFcn(hObject, eventdata, handles)
 % varargout  cell array for returning output args (see VARARGOUT);
 % hObject    handle to figure
 % eventdata  reserved - to be defined in a future version of MATLAB
@@ -612,7 +612,7 @@ function MenuFileLoad_Callback(hObject, eventdata, handles)
         catch
             l = lasterror;
             errordlg(l.message,'Error loading job', 'modal');
-        end    
+        end
         set(handles.modlist, 'userdata', udmodlist);
         set(handles.module, 'userdata', []);
         local_showjob(hObject);
@@ -815,7 +815,7 @@ function MenuViewUpdateView_Callback(hObject, eventdata, handles)
 
 % This function seems to be called on startup without guidata - do nothing
 % there
-if ~isempty(handles) 
+if ~isempty(handles)
     local_setmenu(handles.cfg_ui, [], @local_AddMod, true);
     udmodlist = get(handles.modlist,'Userdata');
     if isstruct(udmodlist)
@@ -872,7 +872,7 @@ function MenuViewShowCode_Callback(hObject, eventdata, handles)
     ctxt = uicontrol('Parent',fg, 'Style','listbox', 'Units','normalized', 'Position',[0 0 1 1], 'FontName','FixedWidth','Tag',[mfilename 'ShowCodeList']);
 else
     figure(fg);
-    ctxt = findobj(fg,'Tag',[mfilename 'ShowCodeList']); 
+    ctxt = findobj(fg,'Tag',[mfilename 'ShowCodeList']);
 end
 um = uicontextmenu;
 um1 = uimenu('Label','Copy', 'Callback',@(ob,ev)local_ShowCode_Copy(ob,ev,ctxt), 'Parent',um);
@@ -1044,7 +1044,7 @@ function MenuFileMultiBatch_Callback(hObject, eventdata, handles)
 
 udmodlist = get(handles.modlist,'userdata');
 cjob = udmodlist.cjob;
-if cfg_util('isjob_id', cjob) 
+if cfg_util('isjob_id', cjob)
     njob = cfg_util('clonejob', cjob);
     cfg_ui_multibatch(njob);
 end

src/ext/matlabbatch/cfg_ui_util.m

@@ -4,7 +4,7 @@
 % module or data summary. It also handles all value display and editing for
 % a particular item.
 %
-% This code is part of a batch job configuration system for MATLAB. See 
+% This code is part of a batch job configuration system for MATLAB. See
 %      help matlabbatch
 % for a general overview.
 %_______________________________________________________________________
@@ -102,21 +102,12 @@
     case {'showitem'}
         % [contents, namestr, datastr] = cfg_ui_util('showitem', ciid, dflag)
         [ciid, dflag] = deal(varargin{1:2});
-        if isstruct(ciid)
-          [id, stop, contents] = ...
-            cfg_util('listmod', ciid(:),...
-            cfg_findspec({{'hidden',false}}), ...
-            cfg_tropts({{'hidden', true}},1,1,1,1,dflag), ...
-            {'name','val','labels','values','class','level', ...
-            'all_set','all_set_item','num','preview'});
-        else
-          [id, stop, contents] = ...
+        [id, stop, contents] = ...
             cfg_util('listmod', ciid{:},...
             cfg_findspec({{'hidden',false}}), ...
             cfg_tropts({{'hidden', true}},1,1,1,1,dflag), ...
             {'name','val','labels','values','class','level', ...
             'all_set','all_set_item','num','preview'});
-        end
         contents = cellfun(@(c)subsref(c, substruct('{}',{1})), contents, 'UniformOutput', false);
         [namestr, datastr] = cfg_ui_util('showitemstr', contents, dflag);
         varargout{1} = contents;
@@ -125,39 +116,21 @@
     case {'showmod'}
         % [id, namestr, datastr, contents] = cfg_ui_util('showmod', cmid, dflag)
         [cmid, dflag] = deal(varargin{1:2});
-        if isstruct(cmid)
-          [id, stop, contents] = ...
-            cfg_util('listmod', cmid(:), [],...
-            cfg_findspec({{'hidden',false}}), ...
-            cfg_tropts({{'hidden', true}},1,Inf,1,Inf,dflag), ...
-            {'name','val','labels','values','class','level', ...
-            'all_set','all_set_item','num','preview'});
-        else
-          [id, stop, contents] = ...
+        [id, stop, contents] = ...
             cfg_util('listmod', cmid{:}, [],...
             cfg_findspec({{'hidden',false}}), ...
             cfg_tropts({{'hidden', true}},1,Inf,1,Inf,dflag), ...
             {'name','val','labels','values','class','level', ...
             'all_set','all_set_item','num','preview'});
-        end
         if isempty(id) || ~cfg_util('isitem_mod_id', id{1})
             % Module not found without hidden flag
             % Try to list top level entry of module anyway, but not module items.
-            if isstruct(cmid)
-              [id, stop, contents] = ...
-                cfg_util('listmod', cmid(:), [],...
-                cfg_findspec({}), ...
-                cfg_tropts({{'hidden', true}},1,1,1,1,dflag), ...
-                {'name','val','labels','values','class','level', ...
-                'all_set','all_set_item','preview'});
-            else
-              [id, stop, contents] = ...
+            [id, stop, contents] = ...
                 cfg_util('listmod', cmid{:}, [],...
                 cfg_findspec({}), ...
                 cfg_tropts({{'hidden', true}},1,1,1,1,dflag), ...
                 {'name','val','labels','values','class','level', ...
                 'all_set','all_set_item','preview'});
-            end
         end;
         namestr = cell(1,numel(id));
         datastr = cell(1,numel(id));

src/pspm_cfg/pspm_cfg_glm.m

@@ -309,9 +309,9 @@
 mrk_chan.strtype = 'i';
 mrk_chan.val     = {0};
 mrk_chan.num     = [1 1];
-mrk_chan.help    = {['Indicate the marker channel. By default the last marker channel is ' ...
+mrk_chan.help    = {['Indicate the marker channel. By default (value 0) the first marker channel is ' ...
     'assumed to contain the relevant markers.'], ['Markers are only used if you have ' ...
-    'specified the time units as �markers�.']};
+    'specified the time units as "markers".']};
 
 % Timeunits
 seconds         = cfg_const;

src/pspm_cfg/pspm_cfg_run_sf.m

@@ -78,7 +78,9 @@
     options.fresp = job.fresp;
 end
 if ~isempty(job.missing)
-  options.missing = job.missing;
+  if ischar(job.missing.missingdata)
+    options.missing = job.missing;
+  end
 end
 options.dispwin = job.dispwin;
 options.dispsmallwin = job.dispsmallwin;

src/pspm_cfg/pspm_cfg_sf.m

@@ -165,6 +165,8 @@
 filter.values = {filter_def, filter_edit};
 filter.help   = {'Specify how you want filter the SCR data.'};
 
+
+
 %% Epochs
 epochfile         = cfg_files;
 epochfile.name    = 'Epoch File';
@@ -193,7 +195,7 @@
 mrk_chan.strtype = 'i';
 mrk_chan.val     = {0};
 mrk_chan.num     = [1 1];
-mrk_chan.help    = {['Indicate the marker channel. By default the first marker channel is ' ...
+mrk_chan.help    = {['Indicate the marker channel. By default (value 0) the first marker channel is ' ...
     'assumed to contain the relevant markers.'], ['Markers are only used if you have ' ...
     'specified the time units as "markers".']};
 
@@ -292,14 +294,29 @@
 fresp.help    = {'Frequency of responses to model.'};
 fresp.hidden  = true;
 
-missing         = cfg_files;
-missing.name    = 'Missing epoch file';
-missing.tag     = 'missingfile';
-missing.num     = [1 1];
-missing.filter  = '.*\.(mat|MAT)$';
-missing.help    = {['Missing (e.g. artefact) epochs in the data file, where ',...
+
+
+missingepoch_none        = cfg_const;
+missingepoch_none.name   = 'Not added';
+missingepoch_none.tag    = 'missingdata';
+missingepoch_none.val    = {0};
+missingepoch_none.help   = {'Do not add missing epochs.'};
+
+missingepoch_file         = cfg_files;
+missingepoch_file.name    = 'Missing epoch file';
+missingepoch_file.tag     = 'missingdata';
+missingepoch_file.num     = [1 1];
+missingepoch_file.filter  = '.*\.(mat|MAT)$';
+missingepoch_file.help    = {['Missing (e.g. artefact) epochs in the data file, where ',...
                   'data must always be specified in seconds.']};
 
+missing        = cfg_choice;
+missing.name   = 'Missing Epoch Settings';
+missing.tag    = 'missing';
+missing.val    = {missingepoch_none};
+missing.values = {missingepoch_none, missingepoch_file};
+missing.help   = {'Specify whether you would like to include missing epochs.'};
+
 % Show figures
 dispwin         = cfg_menu;
 dispwin.name    = 'Display Progress Window';

src/pspm_dcm.m

@@ -356,12 +356,16 @@
   else
     missing{iSn} = [];
   end
-  model.filter.sr = data{iSn}{1}.header.sr;
+  y{iSn} = data{iSn}{end}.data; 
+  % to use the last channel in data channels
+  % this is consistent to sf and glm
+  sr{iSn} = data{iSn}{end}.header.sr;
+  model.filter.sr = sr{iSn}; 
 
   % try to find missing epochs according to subsession threshold
-  n_data = size(data{iSn}{1}.data,1);
+  n_data = size(y{iSn},1);
   if isempty(missing{iSn})
-    nan_epochs = isnan(data{iSn}{1}.data);
+    nan_epochs = isnan(y{iSn});
 
     d_nan_ep = transpose(diff(nan_epochs));
     nan_ep_start = find(d_nan_ep == 1);
@@ -388,19 +392,19 @@
 
     % classify if epoch should be considered
     % true for duration > substhresh and for missing epochs
-    ignore_epochs = diff(miss_epochs, 1, 2)/data{iSn}{1}.header.sr > ...
+    ignore_epochs = diff(miss_epochs, 1, 2)/sr{iSn} > ...
       model.substhresh;
 
   else
     % use missing epochs as specified by file
-    miss_epochs = pspm_time2index(missing{iSn},data{iSn}{1}.header.sr);
+    miss_epochs = pspm_time2index(missing{iSn}, sr{iSn});
     ignore_epochs = diff(missing{iSn}, 1, 2) > model.substhresh;
 
     % and set data to NaN to enable later detection of `short` missing
     % epochs
     for k = 1:size(miss_epochs, 1)
       flanks = round(miss_epochs(k,:));
-      data{iSn}{1}.data(flanks(1):flanks(2)) = NaN;
+      y{iSn}(flanks(1):flanks(2)) = NaN;
     end
   end
 
@@ -436,17 +440,17 @@
     n_sbs = numel(se_start);
     % enabled subsessions
     subsessions(end+(1:n_sbs), 1:4) = [ones(n_sbs,1)*iSn, ...
-      [se_start, se_stop]/data{iSn}{1}.header.sr, ...
+      [se_start, se_stop]/sr{iSn}, ...
       zeros(n_sbs,1)];
 
     % missing epochs
     n_miss = sum(ignore_epochs);
     subsessions(end+(1:n_miss), 1:4) = [ones(n_miss,1)*iSn, ...
-      miss_epochs(i_e,:)/data{iSn}{1}.header.sr, ...
+      miss_epochs(i_e,:)/sr{iSn}, ...
       ones(n_miss,1)];
   else
     subsessions(end+1,1:4) = [iSn, ...
-      [1, numel(data{iSn}{1}.data)]/data{iSn}{1}.header.sr, 0];
+      [1, numel(y{iSn})]/sr{iSn}, 0];
 
 
   end

src/pspm_dcm_inv.m

@@ -553,9 +553,10 @@
       priors.SigmaX0 = zeros(7);
       priors.muX0 = zeros(7, 1);
       if trl == 1
-        priors.muX0(1) = mean(y(1:3));%) - min(y);
-        priors.muX0(2) = mean(diff(y(1:3)));
-        priors.muX0(3) = diff(diff(y(1:3)));
+        y_non_nan = y(~isnan(y));
+        priors.muX0(1) = mean(y_non_nan(1:3));%) - min(y);
+        priors.muX0(2) = mean(diff(y_non_nan(1:3)));
+        priors.muX0(3) = diff(diff(y_non_nan(1:3)));
         priors.muX0(7) = 0;%min(y);
         for n = [1:3 7]
           priors.SigmaX0(n, n) = 1e-2;