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Merge pull request #279 from bachlab/Clearance-for-Version-5.1.1
Clearance for Version 5.1.1
2 parents ebe5a01 + 118ed56 commit d8c91b0

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‎doc/PsPM_Developers_Guide.pdf

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‎doc/PsPM_Developers_Guide.tex

Lines changed: 5 additions & 1 deletion
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@@ -57,7 +57,7 @@
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\title{Developer's Guide}
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\maketitle
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\begin{center}
60-
Version 5.1.0
60+
Version 5.1.1
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\par\end{center}
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6363
\medskip{}
@@ -4465,6 +4465,8 @@ \section{List of functions}
44654465
\hline
44664466
pspm\_bf\_brf & Saurabh Khemka \& Dominik Bach & - & -\tabularnewline
44674467
\hline
4468+
pspm\_bf\_data & Dominik Bach & x & x\tabularnewline
4469+
\hline
44684470
pspm\_bf\_FIR & Dominik Bach & - & -\tabularnewline
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\hline
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pspm\_bf\_Fourier & Dominik Bach & - & -\tabularnewline
@@ -4751,6 +4753,8 @@ \section{List of functions}
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\hline
47524754
pspm\_trim & Dominik Bach & x & x\tabularnewline
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\hline
4756+
pspm\_ui & Dadi Zhao & x & x\tabularnewline
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\hline
47544758
pspm\_version & Tobias Moser & - & -\tabularnewline
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\hline
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pspm\_write\_channel & Tobias Moser & x & x\tabularnewline

‎doc/PsPM_Manual.pdf

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‎doc/PsPM_Manual.tex

Lines changed: 44 additions & 2 deletions
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@@ -77,7 +77,7 @@
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\title{PsPM: Psychophysiological Modelling}
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\maketitle
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\begin{center}
80-
Version 5.1.0
80+
Version 5.1.1
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\par\end{center}
8282

8383
\medskip{}
@@ -5037,7 +5037,7 @@ \subsection{Split Sessions}
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50385038
\subsubsection*{Data File}
50395039

5040-
Choose the data file, in which you want to split sessions.
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Choose one data file, in which you want to split sessions, and only one data file is accepted.
50415041

50425042
\subsubsection*{Marker Channel}
50435043

@@ -5058,6 +5058,15 @@ \subsubsection*{Split behaviour}
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\item Marker: Split sessions according to given marker id's.
50595059
\end{itemize}
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5061+
\subsubsection*{Missing epoch}
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Choose whether you would like to add a missing epochs file, where you would like to split sessions.
5063+
\begin{itemize}
5064+
\item No missing epochs file
5065+
\item Add missing epochs file. \\
5066+
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.
5067+
\end{itemize}
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\subsubsection*{Overwrite Existing File}
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50635072
Choose ``yes'' if you want to overwrite existing file(s) with the
@@ -7167,6 +7176,39 @@ \subsubsection*{Bugfixes}
71677176
\end{itemize}
71687177
\end{itemize}
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7179+
\subsection*{PsPM Version 5.1.1}
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\subsubsection*{New Functions}
7181+
\begin{itemize}
7182+
\item \texttt{pspm\_bf\_data}
7183+
\begin{itemize}
7184+
\item New function template to allow users creating their own basis functions (bf) from a data vector.
7185+
\end{itemize}
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\end{itemize}
7187+
\subsubsection*{UI Improvements}
7188+
\begin{itemize}
7189+
\item PsPM now has an improved GUI for the main screen and \texttt{pspm\_display}.
7190+
\item PsPM now uses system specific design for Windows, macOS and Linux.
7191+
\item A bug that affects GUI display has been fixed.
7192+
\end{itemize}
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\subsubsection*{Bugfixes}
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\begin{itemize}
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\item \texttt{pspm\_dcm}
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\begin{itemize}
7197+
\item A bug of channel and data referring that leads to incorrect missing epoch processing has been fixed.
7198+
\item \texttt{pspm\_dcm} now handles empty epochs correctly.
7199+
\end{itemize}
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\item \texttt{pspm\_scr\_pp}
7201+
\begin{itemize}
7202+
\item A bug that throws warning when using GUI has been fixed.
7203+
\end{itemize}
7204+
\item \texttt{pspm\_split\_sessions}
7205+
\begin{itemize}
7206+
\item A bug which leads to GUI crash has been fixed.
7207+
\item \texttt{pspm\_split\_sessions} now accepts correct number of data files and missing epoch files in the GUI.
7208+
\item \texttt{pspm\_split\_sessions} now processes missing epochs correctly.
7209+
\end{itemize}
7210+
\end{itemize}
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71707212
\clearpage
71717213
\newpage
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\part{Acknowledgements}

‎doc/release_notes.pdf

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‎doc/release_notes.tex

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@@ -69,7 +69,7 @@
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framexleftmargin=1pt,
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frame=l}
7171
\renewcommand{\lstlistingname}{Listing}
72-
\title{PsPM 5.1.0 Release notes}
72+
\title{PsPM Release Notes\\ ~\\ Version 5.1.1}
7373

7474
\begin{document}
7575
\maketitle
@@ -717,8 +717,7 @@ \subsection*{Bugfixes}
717717
\begin{itemize}
718718
\item pspm\_glm
719719
\begin{itemize}
720-
\item A bug that leads to the failure of selecting left/right eye has been
721-
fixed.
720+
\item A bug that leads to the failure of selecting left/right eye has been fixed.
722721
\end{itemize}
723722
\item pspm\_load1 and pspm\_dcm
724723
\begin{itemize}
@@ -735,6 +734,38 @@ \subsection*{Bugfixes}
735734
\end{itemize}
736735
\end{itemize}
737736

737+
\section{PsPM Version 5.1.1}
738+
\subsection*{New Functions}
739+
\begin{itemize}
740+
\item \texttt{pspm\_bf\_data}
741+
\begin{itemize}
742+
\item New function template to allow users creating their own basis functions (bf) from a data vector.
743+
\end{itemize}
744+
\end{itemize}
745+
\subsection*{UI Improvements}
746+
\begin{itemize}
747+
\item PsPM now has an improved GUI for the main screen and \texttt{pspm\_display}.
748+
\item PsPM now uses system specific design for Windows, macOS and Linux.
749+
\item A bug that affects GUI display has been fixed.
750+
\end{itemize}
751+
\subsection*{Bugfixes}
752+
\begin{itemize}
753+
\item \texttt{pspm\_dcm}
754+
\begin{itemize}
755+
\item A bug of channel and data referring that leads to incorrect missing epoch processing has been fixed.
756+
\item \texttt{pspm\_dcm} now handles empty epochs correctly.
757+
\end{itemize}
758+
\item \texttt{pspm\_scr\_pp}
759+
\begin{itemize}
760+
\item A bug that throws warning when using GUI has been fixed.
761+
\end{itemize}
762+
\item \texttt{pspm\_split\_sessions}
763+
\begin{itemize}
764+
\item A bug which leads to GUI crash has been fixed.
765+
\item \texttt{pspm\_split\_sessions} now accepts correct number of data files and missing epoch files in the GUI.
766+
\item \texttt{pspm\_split\_sessions} now processes missing epochs correctly.
767+
\end{itemize}
768+
\end{itemize}
738769

739770
\bibliographystyle{pnas2009}
740771
\bibliography{PsPM}

‎src/pspm.fig

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‎src/pspm.m

Lines changed: 23 additions & 50 deletions
Original file line numberDiff line numberDiff line change
@@ -1,37 +1,10 @@
11
function varargout = pspm(varargin)
2-
% tag_PsPM is the main GUI for tag_PsPM
3-
%__________________________________________________________________________
4-
% tag_PsPM 5.1
5-
% (C) 2008-2021 Dominik R Bach (Wellcome Trust Centre for Neuroimaging)
6-
7-
% $Id: tag_pspm.m 636 2019-03-15 07:56:42Z lciernik $
8-
% $Rev: 636 $
9-
10-
% this code was mainly produced by GUIDE
11-
% PsPM_GUI M-file for PsPM_GUI.fig
12-
% PsPM_GUI, by itself, creates a new tag_PsPM or raises the existing
13-
% singleton*.
14-
%
15-
% H = tag_pspm returns the handle to a new tag_PsPM or the handle to
16-
% the existing singleton*.
17-
%
18-
% tag_PsPM('CALLBACK',hObject,eventData,handles,...) calls the local
19-
% function named CALLBACK in tag_PsPM.M with the given input arguments.
20-
%
21-
% tag_PsPM('Property','Value',...) creates a new tag_PsPM or raises the
22-
% existing singleton*. Starting from the left, property value pairs are
23-
% applied to the GUI before PsPM_OpeningFunction gets called. An
24-
% unrecognized property name or invalid value makes property application
25-
% stop. All inputs are passed to PsPM_OpeningFcn via varargin.
26-
%
27-
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
28-
% instance to run (singleton)".
29-
%
30-
% See also: GUIDE, GUIDATA, GUIHANDLES
31-
32-
% Edit the above text to modify the response to help tag_PsPM
33-
34-
% Last Modified by GUIDE v2.5 07-Jul-2021 16:18:18
2+
3+
% pspm.m handles the main GUI for PsPM
4+
% PsPM Version 5.1.1
5+
% (C) 2008-2021 Dominik R Bach (Wellcome Centre for Human Neuroimaging)
6+
% Updated 22-07-2021 Teddy (WCHN, UCL)
7+
358
% initialise
369
% -------------------------------------------------------------------------
3710
global settings;
@@ -289,22 +262,22 @@ function tag_first_level_models_list_Callback(hObject, ~, ~)
289262
selected = get(hObject,'Value');
290263

291264
switch selected
292-
case 1
265+
case 1 % SCR
293266
cfg_add_module('pspm.first_level.scr.glm_scr');
294267
case 2
295268
cfg_add_module('pspm.first_level.hp.glm_hp_e');
296269
case 3
297270
cfg_add_module('pspm.first_level.hp.glm_hp_fc');
298271
case 4
299-
cfg_add_module('pspm.first_level.ps.glm_ps_fc');
300-
case 5
301272
cfg_add_module('pspm.first_level.resp.glm_ra_e');
302-
case 6
273+
case 5
303274
cfg_add_module('pspm.first_level.resp.glm_ra_fc');
275+
case 6
276+
cfg_add_module('pspm.first_level.resp.glm_rfr_e');
304277
case 7
305278
cfg_add_module('pspm.first_level.resp.glm_rp_e');
306279
case 8
307-
cfg_add_module('pspm.first_level.resp.glm_rfr_e');
280+
cfg_add_module('pspm.first_level.ps.glm_ps_fc');
308281
case 9
309282
cfg_add_module('pspm.first_level.sebr.glm_sebr');
310283
case 10
@@ -325,30 +298,30 @@ function tag_data_preprocessing_list_Callback(hObject, ~, ~)
325298
selected = get(hObject,'Value');
326299
switch selected
327300
case 1
328-
cfg_add_module('pspm.data_preprocessing.pp_heart_period.pp_heart_data');
301+
cfg_add_module('pspm.data_preprocessing.pp_scr');%pp_scr
329302
case 2
303+
cfg_add_module('pspm.data_preprocessing.pp_heart_period.pp_heart_data');
304+
case 3
330305
%cfg_add_module('tag_pspm.data_preprocessing.pp_heart_period.ecg_editor');
331306
pspm_ecg_editor();
332-
case 3
333-
cfg_add_module('pspm.data_preprocessing.resp_pp');
334307
case 4
335-
cfg_add_module('pspm.data_preprocessing.pp_pupil.process_illuminance');
308+
cfg_add_module('pspm.data_preprocessing.resp_pp');
336309
case 5
337-
cfg_add_module('pspm.data_preprocessing.pp_pupil.find_valid_fixations');
310+
cfg_add_module('pspm.data_preprocessing.pp_pupil.process_illuminance');
338311
case 6
339-
cfg_add_module('pspm.data_preprocessing.pp_pupil.pupil_correct');
312+
cfg_add_module('pspm.data_preprocessing.pp_pupil.find_valid_fixations');
340313
case 7
341-
cfg_add_module('pspm.data_preprocessing.pp_pupil.pupil_preprocess');
314+
cfg_add_module('pspm.data_preprocessing.pp_pupil.pupil_correct');
342315
case 8
343-
cfg_add_module('pspm.data_preprocessing.pupil_size_convert');
316+
cfg_add_module('pspm.data_preprocessing.pp_pupil.pupil_preprocess');
344317
case 9
345-
cfg_add_module('pspm.data_preprocessing.gaze_convert');
318+
cfg_add_module('pspm.data_preprocessing.pupil_size_convert');
346319
case 10
347-
cfg_add_module('pspm.data_preprocessing.pp_emg.find_sounds');
320+
cfg_add_module('pspm.data_preprocessing.gaze_convert');
348321
case 11
349-
cfg_add_module('pspm.data_preprocessing.pp_emg.pp_emg_data');
322+
cfg_add_module('pspm.data_preprocessing.pp_emg.find_sounds');
350323
case 12
351-
cfg_add_module('pspm.data_preprocessing.pp_scr');%pp_scr
324+
cfg_add_module('pspm.data_preprocessing.pp_emg.pp_emg_data');
352325
end
353326
end
354327

‎src/pspm_cfg/pspm_cfg_data_preprocessing.m

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@@ -13,12 +13,10 @@
1313
cfg = cfg_repeat;
1414
cfg.name = 'Data Preprocessing';
1515
cfg.tag = 'data_preprocessing';
16-
cfg.values = {pspm_cfg_pp_heart_period, ...
16+
cfg.values = {pspm_cfg_pp_scr,...
17+
pspm_cfg_pp_heart_period, ...
1718
pspm_cfg_resp_pp, ...
1819
pspm_cfg_pp_pupil, ...
19-
pspm_cfg_pupil_size_convert, ...
20-
pspm_cfg_gaze_convert, ...
21-
pspm_cfg_pp_emg, ...
22-
pspm_cfg_pp_scr};
20+
pspm_cfg_pp_emg};
2321
cfg.forcestruct = true;
24-
cfg.help = {'Help: Data preprocessing'};
22+
cfg.help = {'Help: Data preprocessing'};

‎src/pspm_cfg/pspm_cfg_gaze_convert.m

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@
1111

1212
% Initialise
1313
global settings
14-
if isempty(settings), pspm_init; end
14+
%if isempty(settings), pspm_init; end
1515

1616
%% Datafile
1717
datafile = cfg_files;
@@ -131,7 +131,7 @@
131131
chan_action.val = {'add'};
132132
chan_action.values = {'replace', 'add'};
133133
chan_action.labels = {'Replace channel', 'Add channel'};
134-
chan_action.help = {['Choose whether to ''replace'' the given channel ', ...
134+
chan_action.help = {['Choose whether to ''replace'' the given channel ', ...
135135
'or ''add'' the converted data as a new channel.']};
136136

137137
%% Executable branch
@@ -141,4 +141,4 @@
141141
pp_gaze_convert.val = {datafile, conversion, chan_action};
142142
pp_gaze_convert.prog = @pspm_cfg_run_gaze_convert;
143143
pp_gaze_convert.help = {['Provides conversion functions for the specified ', ...
144-
'data (e.g. gaze data).']};
144+
'data (e.g. gaze data).']};

‎src/pspm_display.fig

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