Merge branch 'develop' into 507-dependencies-do-not-work-on-batch-in-…

…60-works-fine-in-511

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_sf.m

@@ -195,7 +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".']};
 

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_glm.m

@@ -1,4 +1,4 @@
-function varargout = pspm_glm(model, options)
+function glm = pspm_glm(model, options)
 % ● Description
 %   pspm_glm specifies a within subject general linear convolution model of
 %   predicted signals and calculates amplitude estimates for these responses.
@@ -229,6 +229,7 @@
 end
 % 2.9 check options --
 options = pspm_options(options, 'glm');
+options.overwrite = pspm_overwrite(model.modelfile, options.overwrite);
 if options.invalid
   return
 end
@@ -247,43 +248,20 @@
 fprintf('Getting data ...');
 nFile = numel(model.datafile);
 for iFile = 1:nFile
-  [sts, ~, data] = pspm_load_data(model.datafile{iFile}, model.channel);
-  if sts < 1
-    return
-  end
+  % 3.3 get and filter data
+  [sts_load_data, ~, data] = pspm_load_data(model.datafile{iFile}, model.channel);
+  if sts_load_data == -1, return; end
   y{iFile} = data{end}.data(:);
   sr(iFile) = data{end}.header.sr;
   fprintf('.');
   if any(strcmp(model.timeunits, {'marker', 'markers','markervalues'}))
-    [sts, ~, data] = pspm_load_data(model.datafile{iFile}, options.marker_chan_num);
-    if sts < 1
+    [sts_load_data, ~, data] = pspm_load_data(model.datafile{iFile}, options.marker_chan_num);
+    if sts_load_data == -1
       warning('ID:invalid_input', 'Could not load the specified markerchannel');
       return
     end
-    if length(data) > 1
-      data = data{end};
-    end
-    switch class(options.marker_chan_num_event)
-      case 'double'
-        if options.marker_chan_num_event>length(data)
-          warning('ID:invalid_input', ...
-            'options.marker_chan_num_event exceeds the length of data');
-          return
-        else
-          events{iFile} = data{options.marker_chan_num_event}.data(:) * ...
-            data{options.marker_chan_num_event}.header.sr;
-        end
-      case 'char'
-        if strcmp(options.marker_chan_num_event, 'first')
-          events{iFile} = data{1}.data(:) * data{1}.header.sr;
-        elseif strcmp(options.marker_chan_num_event, 'last')
-          events{iFile} = data{end}.data(:) * data{end}.header.sr;
-        else
-          warning('ID:invalid_input', ...
-            'options.marker_chan_num_event can only specify first or last channel as a char.');
-          return
-        end
-    end
+    % first marker_channel is used
+    events{iFile} = data{1}.data(:) * data{1}.header.sr;
     if strcmp(model.timeunits,'markervalues')
       model.timing{iFile}.markerinfo = data{end}.markerinfo;
     end
@@ -304,7 +282,7 @@
     isnumeric(model.filter.down) && isnan(model.filter.down)
   model.filter.down = min(sr);
 else
-% 4.2 check value of model.filter.down --
+  % 4.2 check value of model.filter.down --
   if ~isfield(model.filter, 'down') || ~isnumeric(model.filter.down)
     % tested because the field is used before the call of
     % pspm_prepdata (everything else is tested there)
@@ -344,7 +322,8 @@
       'functions are not allowed.']); return;
   end
 catch
-  warning('ID:invalid_fhandle', 'Specified basis function %s doesn''t exist or is faulty', func2str(model.bf.fhandle)); return;
+  warning('ID:invalid_fhandle', 'Specified basis function %s doesn''t exist or is faulty', func2str(model.bf.fhandle));
+  return;
 end
 % 5.1 set shiftbf
 if bf_x(1) < 0
@@ -697,7 +676,7 @@
       tmp.col = {};
     end
   end
-% 14.3 mean centering --
+  % 14.3 mean centering --
   if model.centering
     for iXCol=1:size(tmp.XC{iCond},2)
       tmp.XC{iCond}(:,iXCol) = tmp.XC{iCond}(:,iXCol) - mean(tmp.XC{iCond}(:,iXCol));
@@ -865,12 +844,4 @@
 
 %% 18 User output
 fprintf(' done. \n');
-sts = 1;
-switch nargout
-  case 1
-    varargout{1} = glm;
-  case 2
-    varargout{1} = sts;
-    varargout{2} = glm;
-end
 return

src/pspm_merge.m

@@ -17,7 +17,7 @@
 %   │                   Define whether to overwrite existing output files or not.
 %   │                   Default value: determined by pspm_overwrite.
 %   └.marker_chan_num:  2 marker channel numbers - if undefined
-%                       or 0, first marker channel is used
+%                       or 0, first marker channel of each file is used
 % ● History
 %   Introduced In PsPM 3.0
 %   Written in 2008-2015 by Dominik R Bach (UZH, WTCN)

src/pspm_options.m

@@ -34,6 +34,15 @@
 text_optional_channel_invalid_char = ...
   'options.channel is not a valid channel type.';
 %% 2 Main Processing
+
+% deal with global settings
+if (isfield(options, 'marker_chan_num') && ...
+        numel(options.marker_chan_num) == 1 && ...
+        options.marker_chan_num == 0)
+    options.marker_chan_num = 'marker';
+end
+
+% deal with function-specific settings
 switch FunName
   case 'blink_saccade_filt'
     % 2.1 pspm_blink_saccade_filt --
@@ -271,7 +280,6 @@
     options = autofill(options, 'norm',                   0,          1                 );
     options = autofill(options, 'overwrite',              0,          1                 );
     options = autofill(options, 'marker_chan_num',        'marker',   '*Num*Char'       );
-    options = autofill(options, 'marker_chan_num_event',  'first',    '*Num*Char'       );
     if ~isfield(options, 'exclude_missing')
       options.exclude_missing = struct('segment_length',-1,'cutoff',0);
     else
@@ -303,10 +311,12 @@
     options = autofill(options, 'zscored',                0,          1                 );
   case 'merge'
     %% 2.32 pspm_merge
-    options = autofill(options, 'marker_chan_num',        [1,2],      '*Num'            );
-    if ~all(size(options.marker_chan_num(:))==[2,1])
-      options.invalid = 1;
-      return
+    options = autofill(options, 'marker_chan_num',        [0, 0],      '*Num*Char'      ); % NOTE: the default values will be converted to 'marker' by a subsequent call to pspm_trim
+    if isnumeric(options.marker_chan_num)
+        if ~all(size(options.marker_chan_num(:))==[2,1])
+            options.invalid = 1;
+            return
+        end
     end
     options = autofill(options, 'overwrite',              0,          1                 );
   case 'pfm'
@@ -410,8 +420,7 @@
     options = autofill(options,'dispsmallwin',            0,          1                 );
     options = autofill(options,'dispwin',                 1,          0                 );
     options = autofill(options,'fresp',                   0.5,        '>=', 0           );
-    options = autofill(options,'marker_chan_num',         1,          '*Int*Char'       );
-    options = autofill(options,'missingthresh',           2,          '>', 0            );
+    options = autofill(options,'marker_chan_num',         'marker',   '*Int*Char'       );
     options = autofill(options,'overwrite',               1,          0                 );
     options = autofill(options,'threshold',               0.1,        '>', 0            );
     options = autofill(options,'missingthresh',           2,          '>', 0            );
@@ -463,7 +472,7 @@
   case 'trim'
     % 2.46 pspm_trim --
     options = autofill(options, 'drop_offset_markers',    0,          '*Int'            );
-    options = autofill(options, 'marker_chan_num',        1,          '*Int*Char'       );
+    options = autofill(options, 'marker_chan_num',        'marker',   '*Int*Char'       );
     options = autofill(options, 'overwrite',              0,          1                 );
   case 'write_channel'
     % 2.47 pspm_write_channel --
@@ -863,7 +872,7 @@
 if options.manual_chosen == 1 || ...
     (options.manual_chosen == 0 && strcmpi(options.model_strc.modeltype,'glm'))
   if ~isfield(options, 'marker_chan')
-    options.marker_chan = repmat({1}, numel(options.data_fn),1);
+    options.marker_chan = repmat({'marker'}, numel(options.data_fn),1);
   elseif ~iscell(options.marker_chan)
     options.marker_chan = repmat({options.marker_chan}, size(options.data_fn));
   end
@@ -974,8 +983,6 @@
       return
     end
   end
-else
-  options.marker_chan_num = 'marker';
 end
 if isfield(options,'exclude_missing')
   if ~(isfield(options.exclude_missing, 'segment_length') && ...

src/pspm_sf.m

@@ -197,9 +197,9 @@
   return
 end
 %% 3 Get data
-missing = cell(size(model.missing));
-for iFile = 1:numel(model.datafile)
-  % 3.1 User output --
+nFile = numel(model.datafile);
+for iFile = 1:nFile
+  % 3.1 User output
   fprintf('SF analysis: %s ...', model.datafile{iFile});
   % 3.2 Check whether model file exists --
   if ~pspm_overwrite(model.modelfile, options)
@@ -208,19 +208,21 @@
   % 3.3 get and filter data --
   [sts_load_data, ~, data] = pspm_load_data(model.datafile{iFile}, model.channel);
   if sts_load_data < 0, return; end
-  Y{1} = data{1}.data; sr(1) = data{1}.header.sr;
+  y{1} = data{end}.data;
+  sr(1) = data{end}.header.sr;
   model.filter.sr = sr(1);
-  [sts_prepdata, Y{2}, sr(2)] = pspm_prepdata(data{1}.data, model.filter);
+  [sts_prepdata, y{2}, sr(2)] = pspm_prepdata(data{end}.data, model.filter);
+  % always use last data channels
   if sts_prepdata == -1
     warning('ID:invalid_input', 'Call of pspm_prepdata failed.');
     return;
   end
-  % 3.4 Check data units --
-  if ~strcmpi(data{1}.header.units, 'uS') && any(strcmpi('dcm', method))
+  % 3.4 Check data units
+  if ~strcmpi(data{end}.header.units, 'uS') && any(strcmpi('dcm', method))
     fprintf(['\nYour data units are stored as %s, ',...
       'and the method will apply an amplitude threshold in uS. ',...
       'Please check your results.\n'], ...
-      data{1}.header.units);
+      data{end}.header.units);
   end
   % 3.5 Get missing epochs --
   % 3.5.1 Load missing epochs --
@@ -243,15 +245,26 @@
   end
   % 3.6 Get marker data --
   if any(strcmp(model.timeunits, {'marker', 'markers'}))
-    if options.marker_chan_num
-      [nsts, ~, ndata] = pspm_load_data(model.datafile{iFile}, options.marker_chan_num);
-      if nsts == -1; warning('ID:invalid_input', 'Could not load data'); return; end
-    else
-      [nsts, ~, ndata] = pspm_load_data(model.datafile{iFile}, 'marker');
-      if nsts == -1; warning('ID:invalid_input', 'Could not load data'); return; end
+    [sts, ~, ndata] = pspm_load_data(model.datafile{iFile}, options.marker_chan_num);
+    if sts < 1
+      warning('ID:invalid_input', 'Could not load data');
+      return;
+    elseif ~strcmp(ndata{1}.header.chantype, 'marker')
+      warning('ID:invalid_option', ...
+        ['Channel %i is no marker channel. ',...
+        'The first marker channel in the file is used instead'],...
+        options.marker_chan_num);
+      [sts_load_data, ~, ~] = pspm_load_data(model.datafile{iFile}, 'marker');
+      if sts_load_data == -1
+        warning('ID:invalid_input', 'Could not load data');
+        return;
+      end
     end
-    events = ndata{1}.data;
   end
+  % use first marker channel
+  events{iFile} = data{1}.data(:);
+
+
   for iEpoch = 1:size(epochs{iFile}, 1)
     if iEpoch > 1, fprintf('\n\t\t\t'); end
     fprintf('epoch %01.0f ...', iEpoch);
@@ -265,14 +278,14 @@
         case 'markers'
           win = round(events(epochs{iFile}(iEpoch, :)) * sr(datatype(k)));
         case 'whole'
-          win = [1 numel(Y{datatype(k)})];
+          win = [1 numel(y{datatype(k)})];
       end
-      if any(win > numel(Y{datatype(k)}) + 1) || any(win < 0)
+      if any(win > numel(y{datatype(k)}) + 1) || any(win < 0)
         warning('\nEpoch %2.0f outside of file %s ...', iEpoch, model.modelfile{iFile});
       else
         % correct issues with using 'round'
         win(1) = max(win(1), 1);
-        win(2) = min(win(2), numel(Y{datatype(k)}));
+        win(2) = min(win(2), numel(y{datatype(k)}));
       end
       % 3.6.1 collect information --
       sf.model{k}(iEpoch).modeltype = method{k};
@@ -281,7 +294,7 @@
       sf.model{k}(iEpoch).samples    = win;
       sf.model{k}(iEpoch).sr         = sr(datatype(k));
       %
-      escr = Y{datatype(k)}(win(1):win(end));
+      escr = y{datatype(k)}(win(1):win(end));
       sf.model{k}(iEpoch).data = escr;
       if any(missing{iFile})
         model.missing_data = zeros(size(escr));
@@ -309,7 +322,7 @@
   sf.infos.date = date;
   sf.infos.file = model.modelfile{iFile};
   sf.modelfile = model.modelfile{iFile};
-  sf.data = Y;
+  sf.data = y;
   if exist('events','var'), sf.events = events; end
   sf.input = model;
   sf.options = options;