Fix pspm_extract_segments

src/pspm_extract_segments.m

@@ -133,6 +133,7 @@
 switch method
     case 'data'
         data_raw = data;
+        if isnumeric(data), data_raw = {data}; end
     case 'file'
         for i_sn = 1:numel(datafile)
             [lsts, alldata{i_sn}] = pspm_load_channel(datafile{i_sn}, channel);
@@ -152,6 +153,9 @@
 case 'model'
     if strcmpi(data.modeltype, 'glm')
         data_raw = data.input.data;
+        timing = data.input.timing;
+        options.timeunits = data.input.timeunits;
+        events = data.input.events;
     elseif strcmpi(data.modeltype, 'dcm')
         data_raw = data.input.scr;
     else
@@ -181,11 +185,6 @@
     session_duration(i_sn, 1) = numel(data_raw{i_sn});
 end
 
-if strcmpi(method, 'model') && strcmpi(data.modeltype, 'glm')
-    timing = data.input.timing;
-end
-
-
 if strcmpi(method, 'model') && strcmpi(data.modeltype, 'dcm')
     % DCM has no condition information
     onsets{1} = cellfun(@(x, y) pspm_time2index(x, sr , y), ...
@@ -194,6 +193,7 @@
     'UniformOutput', false);
     names{1} = 'all';
     n_cond = 1;
+    options.timeunits = 'seconds';
 else
     [lsts, multi] = pspm_get_timing('onsets', timing, options.timeunits);
      [msts, onsets] = pspm_multi2index(options.timeunits, multi, sr, session_duration, events);
@@ -204,6 +204,8 @@
      end
 end
 
+% onsets has the structure: onsets{i_cond}{i_sn}
+
 %% prepare missing
 if isfield(options, 'missing')
     missing = options.missing;

src/pspm_glm.m

@@ -241,7 +241,10 @@
             warning('ID:invalid_input', 'Could not load the specified markerchannel');
             return
         end
-        events{iFile} = data.data(:) * data.header.sr;
+        % here, data.header.sr correponds to the time resolution of the
+        % time stamps which should always be 1, but this will convert any
+        % potentially deviating time stamp resolution to seconds
+        events{iFile} = data.data(:) / data.header.sr;
         if strcmp(model.timeunits,'markervalues')
             model.timing{iFile}.markerinfo = data.markerinfo;
         end
@@ -491,6 +494,7 @@
 %% 12 collect data & regressors for output model
 glm.input.data    = y;
 glm.input.sr      = sr;
+glm.input.events  = events;
 glm.Y             = Y;
 glm.M             = M; % set to 1 if data is missing, otherwise set to 0
 glm.infos.sr      = newsr;
@@ -758,6 +762,7 @@
 
 %% 17 save data
 % 17.1 overwrite is determined in load1 --
+glm.datetime = datetime;
 savedata = struct('glm', glm);
 [sts, data_load1, mdltype_load1] = pspm_load1(model.modelfile, 'save', savedata, options);
 

src/pspm_multi2index.m

@@ -8,7 +8,7 @@
 %   [onsets, durations] = pspm_multi2index('markers', multi, sr, session_duration, events)
 % ● Arguments
 %   *    multi : multi structure from pspm_get_timing
-%           sr : sampling rate, or vector of sampling rates with the same  number of
+%           sr : sampling rate, or vector of sampling rates with the same number of
 %                elements as multi
 %   * sr_ratio : If data was downsampled wrt onset definition, ratio of new_sr/old_sr; or
 %                vector of sampling rate ratios. Otherwise, should be 1.
@@ -23,7 +23,7 @@
     sr = repmat(sr, numel(multi), 1);
 end
 if numel(sr) ~= numel(multi) || numel(session_duration) ~= numel(multi)
-    warning('ID:invalid_input', 'No event definition provided.'); return;
+    warning('ID:invalid_input', 'Number of sessions do not match.'); return;
 end
 if ~isempty(multi)
     for iSn = 1:numel(multi)
@@ -40,8 +40,8 @@
                         events = varargin{1};
                     end
                     % markers are timestamps in seconds
-                    onsets{n}{iSn}    = pspm_time2index(multi(iSn).onsets{n}, sr(iSn), session_duration, 0, events{iSn});
-                    durations{n}{iSn}  = pspm_time2index(multi(iSn).durations{n}, sr(iSn), session_duration, 1);
+                    onsets{n}{iSn}    = pspm_time2index(multi(iSn).onsets{n}, sr(iSn), session_duration(iSn), 0, events{iSn});
+                    durations{n}{iSn}  = pspm_time2index(multi(iSn).durations{n}, sr(iSn), session_duration(iSn), 1);
             end
         end
     end

test/pspm_extract_segments_test.m

@@ -185,9 +185,8 @@ function test_manual_length(this,nr_trial,nan_ratio)
  function test_auto_mode_glm_with_markers(this)
       import matlab.unittest.constraints.IsEqualTo
       import matlab.unittest.constraints.RelativeTolerance
-      rehash
-      load(['ImportTestData' filesep 'fitted_models' filesep 'glm_scr_cond_marker.mat'], 'glm');
-      load(['ImportTestData' filesep 'fitted_models' filesep 'glm_orig_data.mat'], 'data');
+      load(fullfile('ImportTestData',  'fitted_models', 'glm_scr_cond_marker.mat'), 'glm');
+      load(fullfile('ImportTestData',  'fitted_models', 'glm_orig_data.mat'), 'data');
       if ~isfield(glm.input, 'channel') && isfield(glm.input, 'chan')
         glm.input.channel = glm.input.chan;
         glm.input = rmfield(glm.input,'chan'); % rename the field channel to chan
@@ -221,13 +220,13 @@ function test_auto_mode_glm_with_markers(this)
       this.verifyThat(nanmean(seg{3}.data, 1), IsEqualTo(seg{3}.mean, 'Within', RelativeTolerance(1e-10)));
       this.verifyThat(nanstd(seg{3}.data, 0, 1), IsEqualTo(seg{3}.std, 'Within', RelativeTolerance(1e-10)));
       % compute statistics from scratch
-      for i = 1:numel(glm.timing.multi.durations)
+      for i = 1:numel(glm.timing.multi.onsets)
         all_vecs = [];
         seg_len = this.options.length * sr;
-        onset_i = glm.timing.multi.onsets{i};
-        for j = 1:numel(onset_i)
-          onset = round(onset_i(j) * sr) + 1;
-          all_vecs = [all_vecs, input_data(onset : onset + seg_len - 1)];
+        onsets_i = pspm_time2index(marker(glm.timing.multi.onsets{i}), sr);
+        for j = 1:numel(onsets_i)
+            onset = onsets_i(j);
+            all_vecs = [all_vecs, input_data(onset : onset + seg_len - 1)];
         end
         all_vecs = all_vecs';
         expected_mean = nanmean(all_vecs, 1);