Merge pull request #562 from bachlab/559-pspm_convert_ppg2hb-supports…

…-both-optionsreplace-and-optionschannel_action

doc/PsPM_Manual.lyx

@@ -14233,7 +14233,7 @@ status open
 \begin_layout Plain Layout
 \begin_inset Graphics
 	filename Figures/YY1_import.png
-	scale 40
+	scale 50
 
 \end_inset
 
@@ -14283,7 +14283,7 @@ status open
 \begin_layout Plain Layout
 \begin_inset Graphics
 	filename Figures/YY2_trim.png
-	scale 40
+	scale 50
 
 \end_inset
 

src/pspm_cfg/pspm_cfg_run_artefact_rm.m

@@ -1,41 +1,39 @@
 function out = pspm_cfg_run_artefact_rm(job)
-% Executes pspm_pp
-
-% $Id$
-% $Rev$
-
-options = struct;
-options.overwrite = job.overwrite;
-
+% Reviewed and updated on 18-Dec-2023 by Teddy
+options = struct();
+options = pspm_update_struct(options, job, {'overwrite'});
 filtertype = fieldnames(job.filtertype);
 filtertype = filtertype{1};
 datafile = job.datafile;
 datafile = datafile{1};
 channelnumber = job.chan_nr;
-
 switch filtertype
-    case 'median'
-        n = job.filtertype.(filtertype).nr_time_pt;
-        out = pspm_pp(filtertype, datafile, n, channelnumber, options);
-    case 'butter'
-        freq = job.filtertype.(filtertype).freq;
-        out = pspm_pp(filtertype, datafile, freq, channelnumber, options);
-    case 'scr_pp'
-        scr_job = job.filtertype.(filtertype);
-        % Option structure sent to pspm_simple_qa
-        scr = struct();
-        if isfield(scr_job, 'min'), scr.min = scr_job.min; end % Check if min is defined
-        if isfield(scr_job, 'max'), scr.max = scr_job.max; end % Check if max is defined
-        if isfield(scr_job, 'slope'), scr.slope = scr_job.slope; end % Check if slope is defined
-        if isfield(scr_job.missing_epochs, 'write_to_file') % Check if missing_epochs is defined
-            if isfield(scr_job.missing_epochs.write_to_file,'filename') && isfield(scr_job.missing_epochs.write_to_file,'outdir')
-                scr.missing_epochs_filename = fullfile(scr_job.missing_epochs.write_to_file.outdir{1}, scr_job.missing_epochs.write_to_file.filename);
-            end
-        end
-        if isfield(scr_job, 'deflection_threshold'), scr.deflection_threshold = scr_job.deflection_threshold; end % Check if deflection_threshold is defined
-        if isfield(scr_job, 'data_island_threshold'), scr.data_island_threshold = scr_job.data_island_threshold; end % Check if data_island_threshold is defined
-        if isfield(scr_job, 'expand_epochs'), scr.expand_epochs = scr_job.expand_epochs; end % Check if expand_epochs is defined
-        if isfield(scr_job, 'change_data'), scr_job.change_data = scr_job.change_data; else, scr_job.change_data = "replace"; end % Check if data will be changed
-
-        [~, out] = pspm_scr_pp(datafile, scr);
+  case 'median'
+    n = job.filtertype.(filtertype).nr_time_pt;
+    out = pspm_pp(filtertype, datafile, n, channelnumber, options);
+  case 'butter'
+    freq = job.filtertype.(filtertype).freq;
+    out = pspm_pp(filtertype, datafile, freq, channelnumber, options);
+  case 'scr_pp'
+    scr_job = job.filtertype.(filtertype);
+    options = pspm_update_struct(options, scr_job, {'min',...
+                                                    'max',...
+                                                    'slope',...
+                                                    'deflection_threshold',...
+                                                    'data_island_threshold',...
+                                                    'expand_epochs'})
+    if isfield(scr_job.missing_epochs, 'write_to_file')
+      if isfield(scr_job.missing_epochs.write_to_file,'filename') && ...
+          isfield(scr_job.missing_epochs.write_to_file,'outdir')
+        options.missing_epochs_filename = fullfile(...
+          scr_job.missing_epochs.write_to_file.outdir{1}, ...
+          scr_job.missing_epochs.write_to_file.filename);
+      end
+    end
+    if isfield(scr_job, 'change_data')
+      options.channel_action = 'add';
+    else
+      options.channel_action = 'replace';
+    end
+    [~, out] = pspm_scr_pp(datafile, options);
 end

src/pspm_cfg/pspm_cfg_run_combine_markerchannels.m

@@ -1,7 +1,11 @@
 function pspm_cfg_run_combine_markerchannels(job)
+% Updated on 19-12-2023 by Teddy
+%% Variables
+% fn
 fn = job.datafile{1};
-channel_action = job.channel_action;
-marker_channel_number = job.marker_chan_num;
-options = struct('channel_action', channel_action, ...
-                 'marker_chan_num', marker_channel_number);
+% options
+options = struct();
+options = pspm_update_struct(options, job, {'channel_action',...
+                                            'marker_chan_num'})
+%% Run
 pspm_combine_markerchannels(fn, options);

src/pspm_cfg/pspm_cfg_run_contrast1.m

@@ -1,28 +1,21 @@
 function out = pspm_cfg_run_contrast1(job)
-% Executes pspm_con1
-
-% $Id$
-% $Rev$
-
+% Updated on 18-12-2023 by Teddy
+%% Variables
 % modelfile
 modelfile = job.modelfile;
-
-% contrast names & vectors
+% connames, convec
 nrCon = size(job.con,2);
-for iCon=1:nrCon
+for iCon = 1:nrCon
     connames{1,iCon} = job.con(iCon).conname;
     convec{1,iCon} = job.con(iCon).convec;
 end
-
-% delete existing contrast
-deletecon = job.deletecon;
-
-% zscore data
-options.zscored = job.zscored;
-
 % datatype
 datatype = job.datatype;
-
+% deletecon
+deletecon = job.deletecon;
+% options
+options = struct();
+options = pspm_update_struct(options, job, 'zscored')
+%% Run
 pspm_con1(modelfile, connames, convec, datatype, deletecon, options);
-
 out = modelfile;

src/pspm_cfg/pspm_cfg_run_contrast2.m

@@ -1,27 +1,22 @@
 function out = pspm_cfg_run_contrast2(job)
-% Executes pspm_con1
-
-% $Id$
-% $Rev$
-
+% Updated on 19-12-2023 by Teddy
+%% Variables
 % modelfile
 if isfield(job.testtype, 'one_sample')
-    modelfile = job.testtype.one_sample.modelfile';
+  modelfile = job.testtype.one_sample.modelfile';
 else
-    modelfile{1,1} = job.testtype.two_sample.modelfile1';
-    modelfile{1,2} = job.testtype.two_sample.modelfile2';
+  modelfile{1,1} = job.testtype.two_sample.modelfile1';
+  modelfile{1,2} = job.testtype.two_sample.modelfile2';
 end
-
 % outfile
 outfile = [job.outdir{1} filesep  job.filename '.mat'];
-
-% connames & con
+% con and connames
 connames = fieldnames(job.def_con_name);
 connames = connames{1};
 if isfield(job.def_con_name.(connames),'con_all')
-    con = 'all';
+  con = 'all';
 else
-   con = job.def_con_name.(connames).convec;
+  con = job.def_con_name.(connames).convec;
 end
 % nrCon = size(job.def_con_name.(connames).con, 2);
 % if strcmp(connames, 'name')
@@ -35,13 +30,11 @@
 %         con(1,iCon) = job.def_con_name.(connames).con(iCon).conval;
 %     end
 % end
-
 % datatype
-%datatype = job.datatype;
-
+% datatype = job.datatype;
 % options
-options.overwrite = job.overwrite;
-
+options = struct();
+options = pspm_update_struct(options, job, 'overwrite');
+%% Run
 pspm_con2(modelfile, outfile, con, connames, options);
-
 out = {outfile};

src/pspm_cfg/pspm_cfg_run_data_convert.m

@@ -1,30 +1,23 @@
 function [out] = pspm_cfg_run_data_convert(job)
-
-% $Id$
-% $Rev$
-
-channel_action = job.channel_action;
+% Updated on 19-12-2023 by Teddy
 fn = job.datafile{1};
-
-for i=1:numel(job.conversion)
-    options = struct();
-    options.channel_action = channel_action;
-    channel = job.conversion(i).channel;
-    if isfield(job.conversion(i).mode, 'area2diameter')
-        pspm_convert_area2diameter(fn, chan, options);
-    end
-    if isfield(job.conversion(i).mode, 'pixel2unit')
-        width = job.conversion(i).mode.pixel2unit.width;
-        height = job.conversion(i).mode.pixel2unit.height;
-        distance = job.conversion(i).mode.pixel2unit.distance;
-        unit = job.conversion(i).mode.pixel2unit.unit;
-        pspm_convert_pixel2unit(fn, chan, unit, width, height,distance, options);
-    end
-    if isfield(job.conversion(i).mode, 'visangle2sps')
-        options.channels = channel;
-        options.eyes = job.conversion(i).mode.visangle2sps.eyes;
-        pspm_convert_visangle2sps(fn,options);
-    end
+for i = 1:numel(job.conversion)
+  options = struct();
+  options = pspm_update_struct(options, job, 'channel_action');
+  if isfield(job.conversion(i).mode, 'area2diameter')
+    pspm_convert_area2diameter(fn, chan, options);
+  end
+  if isfield(job.conversion(i).mode, 'pixel2unit')
+    width = job.conversion(i).mode.pixel2unit.width;
+    height = job.conversion(i).mode.pixel2unit.height;
+    distance = job.conversion(i).mode.pixel2unit.distance;
+    unit = job.conversion(i).mode.pixel2unit.unit;
+    pspm_convert_pixel2unit(fn, chan, unit, width, height,distance, options);
+  end
+  if isfield(job.conversion(i).mode, 'visangle2sps')
+    options = pspm_update_struct(options, job.conversion(i), 'channel');
+    options = pspm_update_struct(options, job.conversion(i).mode.visangle2sps, 'eyes');
+    pspm_convert_visangle2sps(fn, options);
+  end
 end
-
 out = 1;

src/pspm_cfg/pspm_cfg_run_data_editor.m

@@ -2,7 +2,7 @@ function pspm_cfg_run_data_editor(job)
 fn = job.datafile{1};
 options = struct();
 if isfield(job.outputfile, 'enabled')
-    options.output_file = [job.outputfile.enabled.file_path{1} filesep ...
-        job.outputfile.enabled.file_name];
+  options.output_file = [job.outputfile.enabled.file_path{1} filesep ...
+    job.outputfile.enabled.file_name];
 end
-pspm_data_editor(fn, options);
+pspm_data_editor(fn, options);