Merge pull request #279 from bachlab/Clearance-for-Version-5.1.1

Clearance for Version 5.1.1

doc/PsPM_Developers_Guide.tex

@@ -57,7 +57,7 @@
 \title{Developer's Guide}
 \maketitle
 \begin{center}
-Version 5.1.0
+Version 5.1.1
 \par\end{center}
 
 \medskip{}
@@ -4465,6 +4465,8 @@ \section{List of functions}
 \hline 
 pspm\_bf\_brf & Saurabh Khemka \& Dominik Bach & - & -\tabularnewline
 \hline 
+pspm\_bf\_data & Dominik Bach & x & x\tabularnewline
+\hline 
 pspm\_bf\_FIR & Dominik Bach & - & -\tabularnewline
 \hline 
 pspm\_bf\_Fourier & Dominik Bach & - & -\tabularnewline
@@ -4751,6 +4753,8 @@ \section{List of functions}
 \hline 
 pspm\_trim & Dominik Bach & x & x\tabularnewline
 \hline 
+pspm\_ui & Dadi Zhao & x & x\tabularnewline
+\hline 
 pspm\_version & Tobias Moser & - & -\tabularnewline
 \hline 
 pspm\_write\_channel & Tobias Moser & x & x\tabularnewline

doc/PsPM_Manual.tex

@@ -77,7 +77,7 @@
 \title{PsPM: Psychophysiological Modelling}
 \maketitle
 \begin{center}
-Version 5.1.0
+Version 5.1.1
 \par\end{center}
 
 \medskip{}
@@ -5037,7 +5037,7 @@ \subsection{Split Sessions}
 
 \subsubsection*{Data File}
 
-Choose the data file, in which you want to split sessions.
+Choose one data file, in which you want to split sessions, and only one data file is accepted.
 
 \subsubsection*{Marker Channel}
 
@@ -5058,6 +5058,15 @@ \subsubsection*{Split behaviour}
 \item Marker: Split sessions according to given marker id's.
 \end{itemize}
 
+\subsubsection*{Missing epoch}
+Choose whether you would like to add a missing epochs file, where you would like to split sessions.
+\begin{itemize}
+\item No missing epochs file
+\item Add missing epochs file. \\
+In this option, you can choose one missing epochs file, in which you want to split sessions, and only one missing epochs file is accepted.
+\end{itemize}
+
+
 \subsubsection*{Overwrite Existing File}
 
 Choose ``yes'' if you want to overwrite existing file(s) with the
@@ -7167,6 +7176,39 @@ \subsubsection*{Bugfixes}
 \end{itemize}
 \end{itemize}
 
+\subsection*{PsPM Version 5.1.1}
+\subsubsection*{New Functions}
+\begin{itemize}
+\item \texttt{pspm\_bf\_data}
+\begin{itemize}
+\item New function template to allow users creating their own basis functions (bf) from a data vector.
+\end{itemize}
+\end{itemize}
+\subsubsection*{UI Improvements}
+\begin{itemize}
+\item PsPM now has an improved GUI for the main screen and \texttt{pspm\_display}.
+\item PsPM now uses system specific design for Windows, macOS and Linux.
+\item A bug that affects GUI display has been fixed.
+\end{itemize}
+\subsubsection*{Bugfixes}
+\begin{itemize}
+\item \texttt{pspm\_dcm}
+\begin{itemize}
+\item A bug of channel and data referring that leads to incorrect missing epoch processing has been fixed.
+\item \texttt{pspm\_dcm} now handles empty epochs correctly.
+\end{itemize}
+\item \texttt{pspm\_scr\_pp}
+\begin{itemize}
+\item A bug that throws warning when using GUI has been fixed.
+\end{itemize}
+\item \texttt{pspm\_split\_sessions}
+\begin{itemize}
+\item A bug which leads to GUI crash has been fixed.
+\item \texttt{pspm\_split\_sessions} now accepts correct number of data files and missing epoch files in the GUI.
+\item \texttt{pspm\_split\_sessions} now processes missing epochs correctly.
+\end{itemize}
+\end{itemize}
+
 \clearpage
 \newpage
 \part{Acknowledgements}

doc/release_notes.tex

@@ -69,7 +69,7 @@
 framexleftmargin=1pt,
 frame=l}
 \renewcommand{\lstlistingname}{Listing}
-\title{PsPM 5.1.0 Release notes}
+\title{PsPM Release Notes\\ ~\\ Version 5.1.1}
 
 \begin{document}
 \maketitle
@@ -717,8 +717,7 @@ \subsection*{Bugfixes}
 \begin{itemize}
 \item pspm\_glm
 \begin{itemize}
-\item A bug that leads to the failure of selecting left/right eye has been
-fixed.
+\item A bug that leads to the failure of selecting left/right eye has been fixed.
 \end{itemize}
 \item pspm\_load1 and pspm\_dcm
 \begin{itemize}
@@ -735,6 +734,38 @@ \subsection*{Bugfixes}
 \end{itemize}
 \end{itemize}
 
+\section{PsPM Version 5.1.1}
+\subsection*{New Functions}
+\begin{itemize}
+\item \texttt{pspm\_bf\_data}
+\begin{itemize}
+\item New function template to allow users creating their own basis functions (bf) from a data vector.
+\end{itemize}
+\end{itemize}
+\subsection*{UI Improvements}
+\begin{itemize}
+\item PsPM now has an improved GUI for the main screen and \texttt{pspm\_display}.
+\item PsPM now uses system specific design for Windows, macOS and Linux.
+\item A bug that affects GUI display has been fixed.
+\end{itemize}
+\subsection*{Bugfixes}
+\begin{itemize}
+\item \texttt{pspm\_dcm}
+\begin{itemize}
+\item A bug of channel and data referring that leads to incorrect missing epoch processing has been fixed.
+\item \texttt{pspm\_dcm} now handles empty epochs correctly.
+\end{itemize}
+\item \texttt{pspm\_scr\_pp}
+\begin{itemize}
+\item A bug that throws warning when using GUI has been fixed.
+\end{itemize}
+\item \texttt{pspm\_split\_sessions}
+\begin{itemize}
+\item A bug which leads to GUI crash has been fixed.
+\item \texttt{pspm\_split\_sessions} now accepts correct number of data files and missing epoch files in the GUI.
+\item \texttt{pspm\_split\_sessions} now processes missing epochs correctly.
+\end{itemize}
+\end{itemize}
 
 \bibliographystyle{pnas2009}
 \bibliography{PsPM}

src/pspm.m

@@ -1,37 +1,10 @@
 function varargout = pspm(varargin)
-    % tag_PsPM is the main GUI for tag_PsPM
-    %__________________________________________________________________________
-    % tag_PsPM 5.1
-    % (C) 2008-2021 Dominik R Bach (Wellcome Trust Centre for Neuroimaging)
-
-    % $Id: tag_pspm.m 636 2019-03-15 07:56:42Z lciernik $
-    % $Rev: 636 $
-
-    % this code was mainly produced by GUIDE
-    % PsPM_GUI M-file for PsPM_GUI.fig
-    %      PsPM_GUI, by itself, creates a new tag_PsPM or raises the existing
-    %      singleton*.
-    %
-    %      H = tag_pspm returns the handle to a new tag_PsPM or the handle to
-    %      the existing singleton*.
-    %
-    %      tag_PsPM('CALLBACK',hObject,eventData,handles,...) calls the local
-    %      function named CALLBACK in tag_PsPM.M with the given input arguments.
-    %
-    %      tag_PsPM('Property','Value',...) creates a new tag_PsPM or raises the
-    %      existing singleton*.  Starting from the left, property value pairs are
-    %      applied to the GUI before PsPM_OpeningFunction gets called.  An
-    %      unrecognized property name or invalid value makes property application
-    %      stop.  All inputs are passed to PsPM_OpeningFcn via varargin.
-    %
-    %      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
-    %      instance to run (singleton)".
-    %
-    % See also: GUIDE, GUIDATA, GUIHANDLES
-
-    % Edit the above text to modify the response to help tag_PsPM
-
-    % Last Modified by GUIDE v2.5 07-Jul-2021 16:18:18
+
+    % pspm.m handles the main GUI for PsPM
+    % PsPM Version 5.1.1
+    % (C) 2008-2021 Dominik R Bach (Wellcome Centre for Human Neuroimaging)    
+    % Updated 22-07-2021 Teddy (WCHN, UCL)
+
     % initialise
     % -------------------------------------------------------------------------
     global settings;
@@ -289,22 +262,22 @@ function tag_first_level_models_list_Callback(hObject, ~, ~)
     selected = get(hObject,'Value');
 
     switch selected
-    case 1
+    case 1 % SCR
         cfg_add_module('pspm.first_level.scr.glm_scr');
     case 2
         cfg_add_module('pspm.first_level.hp.glm_hp_e');
     case 3
         cfg_add_module('pspm.first_level.hp.glm_hp_fc');
     case 4
-        cfg_add_module('pspm.first_level.ps.glm_ps_fc');
-    case 5
         cfg_add_module('pspm.first_level.resp.glm_ra_e');
-    case 6
+    case 5
         cfg_add_module('pspm.first_level.resp.glm_ra_fc');
+    case 6
+        cfg_add_module('pspm.first_level.resp.glm_rfr_e');
     case 7
         cfg_add_module('pspm.first_level.resp.glm_rp_e');
     case 8
-        cfg_add_module('pspm.first_level.resp.glm_rfr_e');
+        cfg_add_module('pspm.first_level.ps.glm_ps_fc');
     case 9
         cfg_add_module('pspm.first_level.sebr.glm_sebr');
     case 10
@@ -325,30 +298,30 @@ function tag_data_preprocessing_list_Callback(hObject, ~, ~)
     selected = get(hObject,'Value');
     switch selected
     case 1
-        cfg_add_module('pspm.data_preprocessing.pp_heart_period.pp_heart_data');
+        cfg_add_module('pspm.data_preprocessing.pp_scr');%pp_scr
     case 2
+        cfg_add_module('pspm.data_preprocessing.pp_heart_period.pp_heart_data');
+    case 3
         %cfg_add_module('tag_pspm.data_preprocessing.pp_heart_period.ecg_editor');
         pspm_ecg_editor();
-    case 3
-        cfg_add_module('pspm.data_preprocessing.resp_pp');
     case 4
-        cfg_add_module('pspm.data_preprocessing.pp_pupil.process_illuminance');
+        cfg_add_module('pspm.data_preprocessing.resp_pp');
     case 5
-        cfg_add_module('pspm.data_preprocessing.pp_pupil.find_valid_fixations');
+        cfg_add_module('pspm.data_preprocessing.pp_pupil.process_illuminance');
     case 6
-        cfg_add_module('pspm.data_preprocessing.pp_pupil.pupil_correct');
+        cfg_add_module('pspm.data_preprocessing.pp_pupil.find_valid_fixations');
     case 7
-        cfg_add_module('pspm.data_preprocessing.pp_pupil.pupil_preprocess');
+        cfg_add_module('pspm.data_preprocessing.pp_pupil.pupil_correct');
     case 8
-        cfg_add_module('pspm.data_preprocessing.pupil_size_convert');
+        cfg_add_module('pspm.data_preprocessing.pp_pupil.pupil_preprocess');
     case 9
-        cfg_add_module('pspm.data_preprocessing.gaze_convert');
+        cfg_add_module('pspm.data_preprocessing.pupil_size_convert');
     case 10
-        cfg_add_module('pspm.data_preprocessing.pp_emg.find_sounds');
+        cfg_add_module('pspm.data_preprocessing.gaze_convert');
     case 11
-        cfg_add_module('pspm.data_preprocessing.pp_emg.pp_emg_data');
+        cfg_add_module('pspm.data_preprocessing.pp_emg.find_sounds');
     case 12
-        cfg_add_module('pspm.data_preprocessing.pp_scr');%pp_scr
+        cfg_add_module('pspm.data_preprocessing.pp_emg.pp_emg_data');
     end
 end
 

src/pspm_cfg/pspm_cfg_data_preprocessing.m

@@ -13,12 +13,10 @@
 cfg        = cfg_repeat;
 cfg.name   = 'Data Preprocessing';
 cfg.tag    = 'data_preprocessing';
-cfg.values = {pspm_cfg_pp_heart_period, ...
+cfg.values = {pspm_cfg_pp_scr,...
+    pspm_cfg_pp_heart_period, ...
     pspm_cfg_resp_pp, ...
     pspm_cfg_pp_pupil, ...
-    pspm_cfg_pupil_size_convert, ...
-    pspm_cfg_gaze_convert, ...
-    pspm_cfg_pp_emg, ...
-    pspm_cfg_pp_scr};
+    pspm_cfg_pp_emg};
 cfg.forcestruct = true;
-cfg.help   = {'Help: Data preprocessing'};
+cfg.help   = {'Help: Data preprocessing'};

src/pspm_cfg/pspm_cfg_gaze_convert.m

@@ -11,7 +11,7 @@
 
 % Initialise
 global settings
-if isempty(settings), pspm_init; end
+%if isempty(settings), pspm_init; end
 
 %% Datafile
 datafile         = cfg_files;
@@ -131,7 +131,7 @@
 chan_action.val     = {'add'};
 chan_action.values  = {'replace', 'add'};
 chan_action.labels  = {'Replace channel', 'Add channel'};
-chan_action.help    = {['Choose whether to ''replace'' the given channel ', ... 
+chan_action.help    = {['Choose whether to ''replace'' the given channel ', ...
     'or ''add'' the converted data as a new channel.']};
 
 %% Executable branch
@@ -141,4 +141,4 @@
 pp_gaze_convert.val    = {datafile, conversion, chan_action};
 pp_gaze_convert.prog   = @pspm_cfg_run_gaze_convert;
 pp_gaze_convert.help   = {['Provides conversion functions for the specified ', ...
-    'data (e.g. gaze data).']};
+    'data (e.g. gaze data).']};