Merge pull request #100 from bachlab/hotfix/4.3.0

Release v4.3.0

README.md

@@ -1,4 +1,10 @@
 ## PsPM
+[![GitHub release (latest by date)](https://img.shields.io/github/v/release/bachlab/PsPM)](https://github.com/bachlab/PsPM/releases)
+[![GitHub Release Date](https://img.shields.io/github/release-date/bachlab/PsPM)](https://github.com/bachlab/PsPM/releases)
+[![Build Status](https://sphinx.bli.uzh.ch/jenkins/buildStatus/icon?job=PsPM)](https://github.com/bachlab/PsPM)
+[![Website](https://img.shields.io/website?down_color=lightgrey&down_message=offline&up_color=green&up_message=online&url=https%3A%2F%2Fbachlab.github.io%2FPsPM)](https://bachlab.github.io/PsPM)
+[![License](https://img.shields.io/github/license/bachlab/PsPM)](https://www.gnu.org/licenses/gpl-3.0)
+
 **PsPM** stands for PsychoPhysiological Modelling. It is a powerful matlab toolbox for model-based analysis of psychophysiological signals, for example SCR, ECG, respiration, pupil size, or startle eye-blink EMG. Currently, **PsPM** implements models for all of these modalities, and we are working towards further models, for example, for skin potential and ocular scan path length.
 
 A **PsPM** allows inferring a psychological variable from observable physiological data. For example, associative memory can be inferred from observed skin conductance responses (SCR). This allows for quantitative description of hidden processes, increases the temporal resolution of analysis, and suppresses noise.

doc/PsPM_Developers_Guide.lyx

@@ -98,7 +98,7 @@ Developer's Guide
 
 \begin_layout Standard
 \align center
-Version 4.2.1
+Version 4.3.0
 \end_layout
 
 \begin_layout Standard
@@ -7996,7 +7996,7 @@ Tests:
 
 
 \begin_inset Tabular
-<lyxtabular version="3" rows="9" columns="2">
+<lyxtabular version="3" rows="10" columns="2">
 <features tabularvalignment="middle">
 <column alignment="center" valignment="top" width="6cm">
 <column alignment="center" valignment="top">
@@ -8074,7 +8074,27 @@ pspm_extract_segments('manual',fn,0)
 \begin_inset Text
 
 \begin_layout Plain Layout
-ID:invalid_inpu
+ID:invalid_input
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+pspm_extract_segments('manual',struct('a',10),0,timing)
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+ID:invalid_input
 \end_layout
 
 \end_inset
@@ -8085,7 +8105,7 @@ ID:invalid_inpu
 \begin_inset Text
 
 \begin_layout Plain Layout
-pspm_extract_segments('manual',[0.1,2],0,timing)
+pspm_extract_segments('manual',[1,3],logical(32),timing)
 \end_layout
 
 \end_inset

doc/PsPM_Manual.lyx

@@ -103,7 +103,7 @@ PsPM: Psychophysiological Modelling
 
 \begin_layout Standard
 \align center
-Version 4.2.1
+Version 4.3.0
 \end_layout
 
 \begin_layout Standard
@@ -9765,6 +9765,17 @@ ts designs it needs to be set to false.
 
 \end_layout
 
+\begin_layout Subsubsection*
+Centering
+\end_layout
+
+\begin_layout Standard
+Specify if you want to mean centering the convoluted X data.
+ By default this centering is applied to every model but for some specific
+ cases such as some scanpath length analysis it has to be set to 0 (i.e.
+ False).
+\end_layout
+
 \begin_layout Subsubsection*
 Filter Settings
 \end_layout
@@ -12357,13 +12368,13 @@ Data navigation
 \begin_layout Standard
 Data navigation can be done by zooming (
 \begin_inset Graphics
-	filename icons/button_zoom.PNG
+	filename Figures/icons/button_zoom.PNG
 
 \end_inset
 
 ) and panning (
 \begin_inset Graphics
-	filename icons/button_pan.PNG
+	filename Figures/icons/button_pan.PNG
 
 \end_inset
 
@@ -12390,7 +12401,7 @@ Add epochs
 \begin_layout Standard
 New epochs can be added by clicking the 'add epoch' button (
 \begin_inset Graphics
-	filename icons/button_add_epoch.PNG
+	filename Figures/icons/button_add_epoch.PNG
 
 \end_inset
 
@@ -12409,7 +12420,7 @@ Remove epochs
 \begin_layout Standard
 Existing epochs can be removed by clicking the 'remove epoch' button (
 \begin_inset Graphics
-	filename icons/button_remove_epoch.PNG
+	filename Figures/icons/button_remove_epoch.PNG
 
 \end_inset
 
@@ -12428,7 +12439,7 @@ Epoch navigation
 In order to navigate between epochs it is either possible to use the epoch
  list on the right side or the two epoch navigation buttons (
 \begin_inset Graphics
-	filename icons/button_navigate_epochs.PNG
+	filename Figures/icons/button_navigate_epochs.PNG
 
 \end_inset
 
@@ -13139,6 +13150,75 @@ Onsets: Specify a vector of onsets.
 Duration: Specify the length of the condition.
 \end_layout
 
+\end_deeper
+\end_deeper
+\end_deeper
+\begin_layout Itemize
+
+\series bold
+Raw:
+\series default
+ Specify all the settings manually (i.e.
+ choose manual mode) and provide raw data
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+
+\shape italic
+Data
+\shape default
+: Numeric raw data or a cell array of numeric raw data.
+\end_layout
+
+\begin_layout Itemize
+
+\shape italic
+Sampling rate
+\shape default
+: One sampling rate or an array of sampling rates of the corresponding 
+\shape italic
+Data
+\shape default
+.
+\end_layout
+
+\begin_layout Itemize
+
+\shape italic
+Conditions
+\shape default
+:
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+Condition files: Should be in the format of the conditions defined in a
+ GLM model.
+ Required fields are names, onsets, duration.
+\end_layout
+
+\begin_layout Itemize
+Enter conditions manually: Specify the conditions that you want to include
+ in your design matrix.
+\end_layout
+
+\begin_deeper
+\begin_layout Itemize
+Name: Specify the name of the condition.
+\end_layout
+
+\begin_layout Itemize
+Onsets: Specify a vector of onsets.
+ The length of the vector corresponds to the number of events included in
+ this condition.
+ Onsets have to be indicated in the specified time unit (‘seconds’, ‘samples’).
+\end_layout
+
+\begin_layout Itemize
+Duration: Specify the length of the condition.
+\end_layout
+
 \end_deeper
 \end_deeper
 \end_deeper
@@ -13586,8 +13666,8 @@ Here, we analyze SCR data using a general linear model (GLM).
  downloaded from 
 \begin_inset CommandInset href
 LatexCommand href
-name "https://sourceforge.net/projects/pspm/files/Tutorial_dataset_GLM.zip/download"
-target "https://sourceforge.net/projects/pspm/files/Tutorial_dataset_GLM.zip/download"
+name "https://bachlab.github.io/PsPM/software/"
+target "https://bachlab.github.io/PsPM/software/"
 literal "false"
 
 \end_inset
@@ -13606,6 +13686,8 @@ literal "true"
  that included two short breaks.
  SCR data were recorded using a 0.5 V coupler, optical (wave to pulse) transducer
 , and CED Spike, with a minimum sampling rate of 100 Hz.
+ Be aware that this example uses functions from the MATLAB Signal Processing
+ Toolbox, make sure to have it installed before starting the tutorial.
 \end_layout
 
 \begin_layout Subsection
@@ -14662,8 +14744,8 @@ The example data set comprises SCR data from 20 participants, with 40 trials
  each, which can be downloaded from 
 \begin_inset CommandInset href
 LatexCommand href
-name "pspm.sourceforge.net"
-target "http://pspm.sourceforge.net"
+name "https://bachlab.github.io/PsPM/software/"
+target "https://bachlab.github.io/PsPM/software/"
 literal "false"
 
 \end_inset
@@ -18881,6 +18963,134 @@ pspm_filtfilt
  which crashed when the filter parameters were of dimension one
 \end_layout
 
+\begin_layout Section
+PsPM Version 4.3.0
+\end_layout
+
+\begin_layout Subsection*
+New Features
+\end_layout
+
+\begin_layout Itemize
+In 
+\family typewriter
+pspm_get_events
+\family default
+, 
+\family typewriter
+import.flank
+\family default
+ can be now set to 
+\family typewriter
+'all'
+\family default
+ what would import all markers and data related to them.
+\end_layout
+
+\begin_layout Itemize
+
+\family typewriter
+pspm_display 
+\family default
+allows now to display pupil size units and the gaze x & y coordinate units
+ on the y-axis.
+\end_layout
+
+\begin_layout Itemize
+
+\family typewriter
+pspm_extract_segments 
+\family default
+can be used now with raw data and thus be called easily within another function.
+\end_layout
+
+\begin_layout Subsection*
+Changes
+\end_layout
+
+\begin_layout Itemize
+
+\family typewriter
+pspm_version
+\family default
+ has a new url and thus do not send any warning about version checks anymore.
+\end_layout
+
+\begin_layout Itemize
+
+\family typewriter
+import_eyelink
+\family default
+ do not import markers which are outside the session end time (
+\family typewriter
+END
+\family default
+ marker).
+\end_layout
+
+\begin_layout Itemize
+
+\family typewriter
+import_eyelink
+\family default
+ sends a warning whenever two markers have the same timestamp.
+\end_layout
+
+\begin_layout Itemize
+In 
+\family typewriter
+pspm_get_eyelink
+\family default
+, 
+\family typewriter
+import.flank
+\family default
+ set to 
+\family typewriter
+'all'
+\family default
+.
+\end_layout
+
+\begin_layout Itemize
+The test of 
+\family typewriter
+pspm_extract_segments
+\family default
+ was adapted to the new feature.
+\end_layout
+
+\begin_layout Itemize
+External functions and libraries were regrouped in one folder called 
+\family typewriter
+ext.
+\end_layout
+
+\begin_layout Subsection*
+Bugfixes
+\end_layout
+
+\begin_layout Itemize
+Fix a bux in 
+\family typewriter
+pspm_bf_lcrf_gm
+\family default
+ and 
+\family typewriter
+pspm_bf_ldrf_gm
+\family default
+ where the offset was wrongly implemented.
+\end_layout
+
+\begin_layout Itemize
+Fix a bug in 
+\family typewriter
+pspm_compute_visual_angle
+\family default
+ where there was an error in the conversion factor of pixels wrt.
+ to mm.
+\end_layout
+
 \begin_layout Part
 Acknowledgements
 \end_layout