Unify function output

src/pspm_cfg/pspm_cfg_find_sounds.m

@@ -58,26 +58,6 @@
 roi.help            = {['Region of interest for discovering sounds. ', ...
     'Only sounds between the 2 timestamps will be considered.']};
 
-%% Channel action
-chan_action         = cfg_menu;
-chan_action.name    = 'Channel action';
-chan_action.tag     = 'channel_action';
-chan_action.val     = {'replace'};
-chan_action.values  = {'add', 'replace'};
-chan_action.labels  = {'add', 'replace'};
-chan_action.help    = {['Add will append the new marker channel as ', ...
-    'additional channel to the specified PsPM file. Replace will ', ...
-    'overwrite the last marker channel of the PsPM file ', ...
-    '(be careful with reference markers).']};
-
-%% Create Channel
-new_chan        = cfg_branch;
-new_chan.name   = 'Create Channel';
-new_chan.tag    = 'create_chan';
-new_chan.val    = {chan_action};
-new_chan.help   = {['The new data channel contains by default all ', ...
-    'marker onsets found in the specified data file. If you want ', ...
-    'specific sounds defined by a marker, use the diagnostics option.']};
 
 %% Text only
 text_only       = cfg_const;
@@ -112,19 +92,19 @@
 no.help            = {''};
 
 %% yes
-yes                = cfg_branch;
+yes                = cfg_const;
 yes.name           = 'Yes';
 yes.tag            = 'yes';
-yes.val            = {chan_action};
+yes.val            = {1};
 yes.help           = {''};
 
 %% New corrected channel
 new_corrected_chan         = cfg_choice;
-new_corrected_chan.name    = 'Create channel with specific sounds';
+new_corrected_chan.name    = 'Output specific sounds only';
 new_corrected_chan.tag     = 'create_corrected_chan';
 new_corrected_chan.val     = {no};
 new_corrected_chan.values  = {no, yes};
-new_corrected_chan.help    = {['Create new data channel which contains ', ...
+new_corrected_chan.help    = {['By default, all sounds are outputted. Choose ''yes'' here to create new data channel which contains ', ...
     'only marker onsets which could have been assigned to a ', ...
     'marker in the specified marker channel.']};
 
@@ -162,28 +142,40 @@
     'If too few sounds are found, threshold is lowered until specified ', ...
     'count is reached.']};
 
+%% Diagnostics: which ones?
+diag_yes = cfg_branch;
+diag_yes.name = 'Yes';
+diag_yes.tag    = 'diagnostics';
+diag_yes.val = {diag_output, new_corrected_chan, marker_chan, max_delay, ...
+    min_delay, n_sounds};
+diag_yes.help = {};
+
 %% Diagnostics
-diagnostic        = cfg_branch;
+diagnostic        = cfg_choice;
 diagnostic.name   = 'Diagnostic';
 diagnostic.tag    = 'diagnostic';
-diagnostic.val = {diag_output, new_corrected_chan, marker_chan, max_delay, ...
-    min_delay, n_sounds};
+diagnostic.val    = {no};
+diagnostic.values = {diag_yes, no};
 diagnostic.help   = {['Analyze delays between existing marker channel ', ...
     'and detected sound onsets.']};
 
-%% Output
-output          = cfg_choice;
-output.name     = 'Output';
-output.tag      = 'output';
-output.val      = {new_chan};
-output.values   = {new_chan, diagnostic};
-output.help     = {''};
+%% Channel action
+chan_action         = cfg_menu;
+chan_action.name    = 'Channel action';
+chan_action.tag     = 'channel_action';
+chan_action.val     = {'add'};
+chan_action.values  = {'add', 'replace'};
+chan_action.labels  = {'add', 'replace'};
+chan_action.help    = {['Add will append the new marker channel as ', ...
+    'additional channel to the specified PsPM file. Replace will ', ...
+    'overwrite the last marker channel of the PsPM file ', ...
+    '(be careful with reference markers).']};
 
 %% Executable branch
 find_sounds      = cfg_exbranch;
 find_sounds.name = 'Find startle sound onsets';
 find_sounds.tag  = 'find_sounds';
-find_sounds.val  = {datafile, chan, threshold, roi, output};
+find_sounds.val  = {datafile, chan, threshold, roi, diagnostic, chan_action};
 find_sounds.prog = @pspm_cfg_run_find_sounds;
 find_sounds.vout = @pspm_cfg_vout_find_sounds;
 find_sounds.help = {['Translate continuous sound data into an event marker ', ...

src/pspm_cfg/pspm_cfg_merge.m

@@ -16,22 +16,21 @@
 
 %% First file
 first_file          = cfg_files;
-first_file.name     = 'First file(s)';
+first_file.name     = 'First file';
 first_file.tag      = 'first_file';
-first_file.num      = [1 Inf];
+first_file.num      = [1 1];
 first_file.help     = {['Specify the first of the two files to be ', ...
-    'merged. This can be one file or a set of files. The output file ', ...
+    'merged. The output file ', ...
     'will have the name of the first file prepended with an ''m''.'],...
     ' ',settings.datafilehelp};
 
 %% Second file
 second_file         = cfg_files;
-second_file.name    = 'Second file(s)';
+second_file.name    = 'Second file';
 second_file.tag     = 'second_file';
-second_file.num     = [1 Inf];
-second_file.help    = {['Specify the second of the two files to be merged. ', ...
-    'This can be one file or a set of files. This set must have the same ', ...
-    'length as the set defined as first file(s).'],' ',settings.datafilehelp};
+second_file.num     = [1 1];
+second_file.help    = {['Specify the second of the two files to be merged. '], ...
+    '  ', settings.datafilehelp};
 
 %% Data files
 datafiles           = cfg_branch;
@@ -66,8 +65,8 @@
 marker_chan.val     = {[0 0]};
 marker_chan.num     = [1 2];
 marker_chan.strtype = 'i';
-marker_chan.help    = {['Specify for each file (first and second) a ', ...
-    'channel which should be used as marker reference. A 1x2 vector is ', ...
+marker_chan.help    = {['Specify for both files a numerical ', ...
+    'channel index, which should be used as marker reference. A 1x2 vector is ', ...
     'expected. If equal to 0, the first marker channel is used. ', ...
     'Default: [0 0]']};
 
@@ -86,14 +85,10 @@
 merge.prog = @pspm_cfg_run_merge;
 merge.vout = @pspm_cfg_vout_merge;
 merge.help = {['Allows to merge (i.e. stack) two files that were acquired ', ...
-    'simultaneously but contain different channels. Multiple files are ', ...
-    'allowed and are processed in a sequential manner. This means the ', ...
-    'first element of second set of files is merged into the first ', ...
-    'element of first set of files and so on. Therefore first set and ', ...
-    'second set must have the same number of elements. The files are ', ...
+    'simultaneously but contain different channels. The files are ', ...
     'aligned according to the first event of a given marker channel or ', ...
-    'to the start of the file. The output file consists of an ''m'' at ', ...
-    'the beginning and the name of the first file appended. ']};
+    'to the start of the file. The output file name consists of an ''m'' ', ...
+    'prepended to the name of the first file. ']};
 
 function vout = pspm_cfg_vout_merge(job)
 vout = cfg_dep;

src/pspm_cfg/pspm_cfg_pp_scr.m

@@ -214,10 +214,9 @@
         scr_pp_options.channel_action = job.chan_action;
         [sts, output] = pspm_scr_pp(scr_pp_datafile, scr_pp_options);
         if sts == 1
-            % out = {output.channel};
-            out = output{1};
+            out = output;
         else
-            out = {-1};
+            out = -1;
         end
     end
 

src/pspm_cfg/pspm_cfg_rename.m

@@ -8,14 +8,14 @@
 filename.name    = 'File Name';
 filename.tag     = 'filename';
 filename.num     = [1 1];
-%filename.filter  = '\.mat$';
+filename.filter  = '\.mat$';
 filename.help    = {'Choose name of original file.'};
 
 newfilename         = cfg_entry;
 newfilename.name    = 'New File Name';
 newfilename.tag     = 'newfilename';
 newfilename.strtype = 's';
-%newfilename.num     = [1 1];
+newfilename.num     = [1 inf];
 newfilename.help    = {''};
 
 file         = cfg_branch;
@@ -24,17 +24,11 @@
 file.val     = {filename,newfilename};
 file.help    = {''};
 
-rename_file         = cfg_repeat;
-rename_file.name    = 'Rename';
-rename_file.tag     = 'rename_file';
-rename_file.values  = {file};
-rename_file.help    = {'Choose how many files to rename.'};
-
 %% Executable branch
 rename      = cfg_exbranch;
 rename.name = 'Rename File';
 rename.tag  = 'rename';
-rename.val  = {rename_file};
+rename.val  = {filename, newfilename};
 rename.prog = @pspm_cfg_run_rename;
 rename.vout = @pspm_cfg_vout_rename;
 rename.help = {'Rename PsPM data file. This renames the file and updates the file information.'};

src/pspm_cfg/pspm_cfg_run_dcm.m

@@ -107,14 +107,5 @@
 if eventnameflag
   options.eventnames = eventnames;
 end
-[varargout] = pspm_dcm(model, options);
-if numel(varargout) < 2
-  out = varargout;
-  dcm = [];
-else
-  out = varargout{1};
-  dcm = varargout{2};
-end
-if ~iscell(out)
-  out = {out};
-end
+[out, dcm] = pspm_dcm(model, options);
+

src/pspm_cfg/pspm_cfg_run_find_sounds.m

@@ -8,26 +8,13 @@
   options.roi = job.roi.region;
 end
 options = pspm_update_struct(options, job, 'threshold');
-options.channel_action = 'none';
-f = fieldnames(job.output);
-switch f{1}
-  case 'create_chan'
-    options.diagnostics = false;
-    options = pspm_update_struct(options, job.output.create_chan, 'channel_action');
-    [sts, infos] = pspm_find_sounds(file, options);
-    if sts == 1
-        out = infos.channel;
-    else
-        out = 0;
-    end
-  case 'diagnostic'
-    d = job.output.diagnostic;
+if isfield(job.diagnostic, 'diagnostics')
+    d = job.diagnostic.diagnostics;
     if isfield(d.create_corrected_chan, 'yes')
-      options = pspm_update_struct(options, d.create_corrected_chan.yes, 'channel_action');
-      options.channel_output = 'corrected';
+        options.channel_output = 'corrected';
     end
     options.marker_chan_num = pspm_cfg_channel_selector('run', d.chan);
-    if job.output.diagnostic.n_sounds > 0
+    if d.n_sounds > 0
       options.expectedSoundCount = job.output.diagnostic.n_sounds;
     end
     options.maxdelay = d.max_delay;
@@ -38,8 +25,5 @@
       case 'text_only'
         options.plot = false;
     end
-    [~, infos] = pspm_find_sounds(file, options);
-    if isfield(infos, 'channel')
-      out = infos.channel;
-    end
+    [~, out, infos] = pspm_find_sounds(file, options);
 end

src/pspm_cfg/pspm_cfg_run_import.m

@@ -85,4 +85,4 @@
 end
 options = struct();
 options = pspm_update_struct(options, job, 'overwrite');
-out = pspm_import(datafiles, datatype, import, options);
+[sts, out] = pspm_import(datafiles, datatype, import, options);

src/pspm_cfg/pspm_cfg_run_merge.m

@@ -1,8 +1,8 @@
 function [out] = pspm_cfg_run_merge(job)
 % Updated on 08-01-2024 by Teddy
 % load input files
-infile1 = job.datafiles.first_file;
-infile2 = job.datafiles.second_file;
+infile1 = job.datafiles.first_file{1};
+infile2 = job.datafiles.second_file{1};
 % set reference
 ref = job.reference;
 options = struct();
@@ -12,8 +12,4 @@
   options.marker_chan_num = job.options.marker_chan;
 end
 % run merge
-[out] = pspm_merge(infile1, infile2, ref, options);
-% ensure output is always a cell
-if ~iscell(out)
-  out = {out};
-end
+[sts, out] = pspm_merge(infile1, infile2, ref, options);

src/pspm_cfg/pspm_cfg_run_pp_emg_data.m

@@ -7,9 +7,9 @@
 options.mains_freq = job.options(1).mains_freq;
 options.channel_action = job.options(1).chan_action;
 options.channel = pspm_cfg_channel_selector('run', job.options(1).chan);
-[sts, output] = pspm_emg_pp(job.datafile{1}, options);
+[sts, outchannel] = pspm_emg_pp(job.datafile{1}, options);
 if sts == 1
-  out = {output.channel};
+  out = {outchannel};
 else
   out = {-1};
 end

src/pspm_cfg/pspm_cfg_run_pp_heart_data.m

@@ -23,20 +23,20 @@
                                      {'semi', 'twthresh'});
         options = pspm_update_struct(options, job, 'channel_action');
         % call function
-        [sts, winfo] = pspm_convert_ecg2hb(fn, options);
+        [sts, outchannel] = pspm_convert_ecg2hb(fn, options);
       case 'ecg2hb_amri'
         options = pp_field.opt;
         options.channel = chan;
         options = pspm_update_struct(options, job, 'channel_action');
         winfo = struct();
-        [sts, winfo.channel] = pspm_convert_ecg2hb_amri(fn, options);
+        [sts, outchannel] = pspm_convert_ecg2hb_amri(fn, options);
       case 'hb2hp'
         sr = job.pp_type{i}.hb2hp.sr;
         options = struct();
         options.channel = chan;
         options.limit = job.pp_type{i}.hb2hp.limit;
         options = pspm_update_struct(options, job, 'channel_action');
-        [sts, winfo] = pspm_convert_hb2hp(fn, sr, options);
+        [sts, outchannel] = pspm_convert_hb2hp(fn, sr, options);
       case 'ecg2hp'
         sr = job.pp_type{i}.ecg2hp.sr;
         % copy options
@@ -51,16 +51,16 @@
         options = pspm_update_struct(options, job, {'channel_action'});
         options.channel = chan;
         % call ecg2hb
-        [sts, winfo] = pspm_convert_ecg2hb(fn, options);
+        [sts, outchannel] = pspm_convert_ecg2hb(fn, options);
         if sts ~= -1
           % replace channel
           options.channel_action = 'replace';
           options = pspm_update_struct(options, ...
               job.pp_type{i}.ecg2hp, ...
               'limit');
-          options.channel = winfo.channel;
+          options.channel = outchannel;
           % call ecg2hp
-          [sts, winfo] = pspm_convert_hb2hp(fn, sr, options);
+          [sts, outchannel] = pspm_convert_hb2hp(fn, sr, options);
         end
       case 'ppg2hb'
         options = struct();
@@ -73,10 +73,10 @@
         end
         options.channel = chan;
         options = pspm_update_struct(options, job, {'channel_action'});
-        [sts, winfo] = pspm_convert_ppg2hb(fn, options);
+        [sts, outchannel] = pspm_convert_ppg2hb(fn, options);
     end
     if sts ~= -1
-      outputs{i} = winfo.channel;
+      outputs{i} = outchannel;
     else
       outputs{i} = [];
       warning('Error occured during conversion. Could not finish correctly.');

src/pspm_cfg/pspm_cfg_run_rename.m

@@ -1,13 +1,8 @@
 function out = pspm_cfg_run_rename(job)
 % Updated on 08-01-2024 by Teddy
-n = size(job.file,2);
-filename = cell(n,1);
-newfilename = cell(1,n);
-for i = 1:n
-  filename{i} = job.file(i).filename{1};
-  newfilename{i} = job.file(i).newfilename;
-end
-out = pspm_ren(filename, newfilename);
+filename = job.filename{1};
+newfilename = job.newfilename;
+[sts, out] = pspm_rename(filename, newfilename);
 if ~iscell(out)
   out = {out};
 end

src/pspm_cfg/pspm_cfg_run_trim.m

@@ -29,7 +29,5 @@
 if ~isfield(options,'marker_chan_num')
   options.marker_chan_num = 0; % Default value
 end
-out = pspm_trim(job.datafile, from, to, ref, options);
-if ~iscell(out)
-  out = {out};
-end
+[sts, out] = pspm_trim(job.datafile{1}, from, to, ref, options);
+