Release 6.1.2 update

doc/PsPM_Developers_Guide.lyx

@@ -14,7 +14,8 @@
 % Added by lyx2lyx
 \renewcommand{\textendash}{--}
 \renewcommand{\textemdash}{---}
-
+\renewcommand*\l@subsection{\@dottedtocline{2}{3.8em}{3.2 em}}
+\renewcommand*\l@subsubsection{\@dottedtocline{3}{7.0em}{4.1em}}
 \usepackage{bera}
 \usepackage{enumitem} \setlist[itemize]{noitemsep}
 \end_preamble
@@ -102,7 +103,7 @@ Developer's Guide
 
 \begin_layout Standard
 \align center
-Version 6.1.1
+Version 6.1.2
 \end_layout
 
 \begin_layout Standard

doc/PsPM_Manual.lyx

@@ -18,6 +18,7 @@
 \renewcommand{\textendash}{--}
 \renewcommand{\textemdash}{---}
 \usepackage{bera}
+\renewcommand*\l@subsection{\@dottedtocline{2}{1.8em}{3.2 em}}
 \end_preamble
 \use_default_options true
 \begin_modules
@@ -104,7 +105,7 @@ PsPM: Psychophysiological Modelling
 
 \begin_layout Standard
 \align center
-Version 6.1.1
+Version 6.1.2
 \end_layout
 
 \begin_layout Standard
@@ -21529,6 +21530,67 @@ UI improvements
 PsPM's UI in Linux environment has been improved.
 \end_layout
 
+\begin_layout Subsection*
+Version 6.1.2
+\end_layout
+
+\begin_layout Subsubsection*
+Bug fixes
+\end_layout
+
+\begin_layout Itemize
+GUI
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+A bug that made channel actions in EMG pre-processing unrecognised has been
+ fixed.
+\end_layout
+
+\begin_layout Itemize
+A bug, which sometimes made DCM not run from the GUI, has been fixed.
+\end_layout
+
+\end_deeper
+\begin_layout Itemize
+
+\family typewriter
+pspm_convert_hb2hp
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+A bug, which incorrectly selected heart rate channels, has been fixed.
+\end_layout
+
+\end_deeper
+\begin_layout Itemize
+
+\family typewriter
+pspm_dcm
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+A bug, which could lead to a wrong sample rate being used if more than one
+ SCR channel existed in the file, has been fixed.
+\end_layout
+
+\end_deeper
+\begin_layout Itemize
+
+\family typewriter
+pspm_glm
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+A bug, which leads to markers being taken from the first marker channel
+ but markervalues from the last, has been fixed.
+\end_layout
+
+\end_deeper
 \begin_layout Part
 Acknowledgements
 \end_layout

doc/PsPM_References.lyx

@@ -11,12 +11,12 @@
 \definecolor{colComments}{rgb}{0.53, 0.66, 0.42}
 \definecolor{colString}{rgb}{0.87, 0.36, 0.51}
 \definecolor{barColor}{rgb}{0.43, 0.5, 0.5}
-% Added by lyx2lyx
 \renewcommand{\textendash}{--}
 \renewcommand{\textemdash}{---}
-
 \usepackage{bera}
-\usepackage{enumitem} \setlist[itemize]{noitemsep}
+\renewcommand*\l@subsection{\@dottedtocline{2}{1.8em}{3.2 em}}
+\usepackage{enumitem}
+\setlist[itemize]{noitemsep}
 \end_preamble
 \use_default_options true
 \maintain_unincluded_children false
@@ -98,7 +98,7 @@ PsPM: Option References
 
 \begin_layout Standard
 \align center
-Version 6.1.1
+Version 6.1.2
 \end_layout
 
 \begin_layout Standard

doc/release_notes.tex

@@ -68,7 +68,7 @@
 framexleftmargin=1pt,
 frame=l}
 \renewcommand{\lstlistingname}{Listing}
-\title{PsPM Release Notes\\ ~\\ Version 6.1.1}
+\title{PsPM Release Notes\\ ~\\ Version 6.1.2}
 
 \begin{document}
 \maketitle
@@ -1213,6 +1213,31 @@ \subsection*{UI improvements}
 \item PsPM's UI in Linux environment has been improved.
 \end{itemize}
 
+
+\section{PsPM Version 6.1.2 }
+\subsection*{Bug fixes}
+\begin{itemize}
+\item GUI
+\begin{itemize}
+\item A bug that made channel actions in EMG pre-processing unrecognised has been fixed.
+\item A bug, which sometimes made DCM not run from the GUI, has been fixed.
+\end{itemize}
+\item \texttt{pspm\_convert\_hb2hp}
+\begin{itemize}
+\item A bug, which incorrectly selected heart rate channels, has been
+fixed.
+\end{itemize}
+\item \texttt{pspm\_dcm}
+\begin{itemize}
+\item A bug, which could lead to a wrong sample rate being used if more than one SCR channel existed in the file, has been fixed.
+\end{itemize}
+\item \texttt{pspm\_glm}
+\begin{itemize}
+\item A bug, which leads to markers being taken from the first marker
+channel but markervalues from the last, has been fixed.
+\end{itemize}
+\end{itemize}
+
 \bibliographystyle{pnas2009}
 \bibliography{PsPM}
 

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};