doc update

makeDocs

@@ -6,17 +6,17 @@ rm -rf html/
 rm -rf docs/
 
 #Auto-run Matlab, publishing HTML output from optickatest.m
-MATLAB='/Applications/MATLAB_R2016b.app/bin/matlab'
+MATLAB='/Applications/MATLAB_R2017a.app/bin/matlab'
 if [ -f $MATLAB ]; then
-	$MATLAB -nodesktop -nosplash -r "publish('optickatest.m');pause(2);exit"
+	$MATLAB -nodesktop -nosplash -r "Screen('Preference', 'SkipSyncTests', 2);publish('optickatest.m');pause(2);exit"
 fi
 
 # We scrape the version number from the main opticka file
 VER=$(grep -o -E -e "optickaVersion@char\ +=\ +'[0-9\.]+'" opticka.m | grep -o -E -e "[0-9\.]+")
 echo; echo "---> Opticka version = $VER"; echo
 sleep 1
 # and then auto-edit the Doxygen file
-sed -i -e "s/^\(PROJECT_NUMBER\)[ ]*=.*/\1 = $VER/g" .doxyfile
+sed -i -E "s/^\(PROJECT_NUMBER\)[ ]*=.*/\1 = $VER/g" .doxyfile
 if [ $? -eq 0 ]; then
 	echo; echo "---> Edited .doxyfile"; echo
 else

optickatest.m

@@ -160,7 +160,7 @@
 rExp = runExperiment('stimuli', myStim,... %stimulus objects
 	'task', myTask,... %task design object
 	'screen', myScreen,... %screen manager object
-	'debug', false,... %setup screen to complain about sync errors etc.
+	'debug', true,... %setup screen to complain about sync errors etc.
 	'verbose', false); %minimal verbosity
 
 %%

readme.md

@@ -1,6 +1,6 @@
 # Opticka Stimulus Generator #
 
-[![DOI](https://zenodo.org/badge/4521/iandol/opticka.png)](http://dx.doi.org/10.5281/zenodo.12293)  
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.12293.svg)](https://doi.org/10.5281/zenodo.592253)  
 
 Opticka Stimulus Generator is an object oriented framework with optional GUI for the [Psychophysics toolbox (PTB)](http://psychtoolbox.org/wikka.php?wakka=HomePage), allowing randomised interleaved presentation of complex visual stimuli. It is designed to work on OS X, Windows or Linux, and interfaces via strobed words (using either a DataPixx [15+1bit] or a LabJack [11bit]) and ethernet with a Plexon Omniplex for recording neurophysiological and behavioural data. The communication class can send TTLs and strobed words out to other equipment types. Behavioural control uses the Eyelink eye tracker and a full behavioural repertoire is available by using [State-Machine](http://iandol.github.io/OptickaDocs/classstate_machine.html#details) logic. Opticka uses the TCP interface to the Eyelink affording much better control, reliability and data recording over using analog voltages alone. The various base classes can be used without the need to run the GUI (see [optickatest.m](http://iandol.github.io/OptickaDocs/optickatest.html) for an example), and plug-n-play stimuli provide a unified interface (setup, animate, draw, update, reset) to integrate into existing/other PTB routines. The various object methods take care of all the background geometry and normalization, meaning stimuli are much easier to use than “raw” PTB. Full analysis routines are also present for taking the raw Plexon files (.PLX or .PL2), Eyelink files (.EDF) and behavioural responses and parsing them into a consistent structure, interfacing directly with [Fieldtrip](http://fieldtrip.fcdonders.nl/start) for further spike, LFP, and spike-LFP analysis. The data structures also allow the use of Jonathan Victor's [STA toolkit](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2818590/), and [nStat toolbox](http://www.neurostat.mit.edu/nstat/) (a pp-GLM modelling approach to analysing neural data). Opticka, because it is object oriented, is far more modular than MonkeyLogic (as well as having much better graphics).