comment fix

.doxyfile

@@ -38,13 +38,13 @@ PROJECT_NAME           = "Opticka"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER = 1.22
+PROJECT_NUMBER = 2.04
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
 # quick idea about the purpose of the project. Keep the description short.
 
-PROJECT_BRIEF          = "Opticka is a vision research system for behavioral electrophysiology."
+PROJECT_BRIEF          = "Opticka is a sensory experiment system for behavioral research."
 
 # With the PROJECT_LOGO tag one can specify a logo or an icon that is included
 # in the documentation. The maximum height of the logo should not exceed 55
@@ -1386,7 +1386,7 @@ DISABLE_INDEX          = NO
 # The default value is: NO.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-GENERATE_TREEVIEW      = NO
+GENERATE_TREEVIEW      = YES
 
 # The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
 # doxygen will group on one line in the generated HTML documentation.

LICENCE.md

@@ -0,0 +1,157 @@
+### GNU LESSER GENERAL PUBLIC LICENSE
+
+Version 3, 29 June 2007
+
+Copyright (C) 2007 Free Software Foundation, Inc.
+<https://fsf.org/>
+
+Everyone is permitted to copy and distribute verbatim copies of this
+license document, but changing it is not allowed.
+
+This version of the GNU Lesser General Public License incorporates the
+terms and conditions of version 3 of the GNU General Public License,
+supplemented by the additional permissions listed below.
+
+#### 0. Additional Definitions.
+
+As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the
+GNU General Public License.
+
+"The Library" refers to a covered work governed by this License, other
+than an Application or a Combined Work as defined below.
+
+An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+A "Combined Work" is a work produced by combining or linking an
+Application with the Library. The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+#### 1. Exception to Section 3 of the GNU GPL.
+
+You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+#### 2. Conveying Modified Versions.
+
+If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+-   a) under this License, provided that you make a good faith effort
+    to ensure that, in the event an Application does not supply the
+    function or data, the facility still operates, and performs
+    whatever part of its purpose remains meaningful, or
+-   b) under the GNU GPL, with none of the additional permissions of
+    this License applicable to that copy.
+
+#### 3. Object Code Incorporating Material from Library Header Files.
+
+The object code form of an Application may incorporate material from a
+header file that is part of the Library. You may convey such object
+code under terms of your choice, provided that, if the incorporated
+material is not limited to numerical parameters, data structure
+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+-   a) Give prominent notice with each copy of the object code that
+    the Library is used in it and that the Library and its use are
+    covered by this License.
+-   b) Accompany the object code with a copy of the GNU GPL and this
+    license document.
+
+#### 4. Combined Works.
+
+You may convey a Combined Work under terms of your choice that, taken
+together, effectively do not restrict modification of the portions of
+the Library contained in the Combined Work and reverse engineering for
+debugging such modifications, if you also do each of the following:
+
+-   a) Give prominent notice with each copy of the Combined Work that
+    the Library is used in it and that the Library and its use are
+    covered by this License.
+-   b) Accompany the Combined Work with a copy of the GNU GPL and this
+    license document.
+-   c) For a Combined Work that displays copyright notices during
+    execution, include the copyright notice for the Library among
+    these notices, as well as a reference directing the user to the
+    copies of the GNU GPL and this license document.
+-   d) Do one of the following:
+    -   0) Convey the Minimal Corresponding Source under the terms of
+        this License, and the Corresponding Application Code in a form
+        suitable for, and under terms that permit, the user to
+        recombine or relink the Application with a modified version of
+        the Linked Version to produce a modified Combined Work, in the
+        manner specified by section 6 of the GNU GPL for conveying
+        Corresponding Source.
+    -   1) Use a suitable shared library mechanism for linking with
+        the Library. A suitable mechanism is one that (a) uses at run
+        time a copy of the Library already present on the user's
+        computer system, and (b) will operate properly with a modified
+        version of the Library that is interface-compatible with the
+        Linked Version.
+-   e) Provide Installation Information, but only if you would
+    otherwise be required to provide such information under section 6
+    of the GNU GPL, and only to the extent that such information is
+    necessary to install and execute a modified version of the
+    Combined Work produced by recombining or relinking the Application
+    with a modified version of the Linked Version. (If you use option
+    4d0, the Installation Information must accompany the Minimal
+    Corresponding Source and Corresponding Application Code. If you
+    use option 4d1, you must provide the Installation Information in
+    the manner specified by section 6 of the GNU GPL for conveying
+    Corresponding Source.)
+
+#### 5. Combined Libraries.
+
+You may place library facilities that are a work based on the Library
+side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+-   a) Accompany the combined library with a copy of the same work
+    based on the Library, uncombined with any other library
+    facilities, conveyed under the terms of this License.
+-   b) Give prominent notice with the combined library that part of it
+    is a work based on the Library, and explaining where to find the
+    accompanying uncombined form of the same work.
+
+#### 6. Revised Versions of the GNU Lesser General Public License.
+
+The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+Each version is given a distinguishing version number. If the Library
+as you received it specifies that a certain numbered version of the
+GNU Lesser General Public License "or any later version" applies to
+it, you have the option of following the terms and conditions either
+of that published version or of any later version published by the
+Free Software Foundation. If the Library as you received it does not
+specify a version number of the GNU Lesser General Public License, you
+may choose any version of the GNU Lesser General Public License ever
+published by the Free Software Foundation.
+
+If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.

analysis/analysisCore.m

@@ -2,6 +2,8 @@
 %> @brief analysisCore base class inherited by other analysis classes.
 %> analysisCore is itself derived from optickaCore. Provides a set of shared methods
 %> and some core properties and stats GUI for various analysis classes.
+%>
+%> Copyright ©2014-2021 Ian Max Andolina — released: LGPL3, see LICENCE.md
 % ========================================================================
 classdef analysisCore < optickaCore
 

analysis/eyelinkAnalysis.m

@@ -4,6 +4,8 @@
 %> ends a trial by default) so can parse eye data and plot it for trial groups. You
 %> can also manually find microsaccades, and perform ROI/TOI filtering on the eye
 %> movements.
+%>
+%> Copyright ©2014-2021 Ian Max Andolina — released: LGPL3, see LICENCE.md
 % ========================================================================
 classdef eyelinkAnalysis < analysisCore
 	% eyelinkAnalysis offers a set of methods to load, parse & plot raw EDF files.

analysis/tobiiAnalysis.m

@@ -4,6 +4,8 @@
 %> ends a trial by default) so can parse eye data and plot it for trial groups. You
 %> can also manually find microsaccades, and perform ROI/TOI filtering on the eye
 %> movements.
+%>
+%> Copyright ©2014-2021 Ian Max Andolina — released: LGPL3, see LICENCE.md
 % ========================================================================
 classdef tobiiAnalysis < analysisCore
 	% eyelinkAnalysis offers a set of methods to load, parse & plot raw EDF files.

calibration/calibrateLuminance.m

@@ -23,6 +23,8 @@
 %> lighting conditions etc). You can then save mycal to disk for later use by
 %> your programs. 
 %>
+%>
+%> Copyright ©2014-2021 Ian Max Andolina — released: LGPL3, see LICENCE.md
 % ========================================================================
 classdef calibrateLuminance < handle
 

calibration/colourManager.m

@@ -1,5 +1,7 @@
 % ========================================================================
 %> @brief colourManager manages colours wrapping the CRS Color Toolbox
+%>
+%> Copyright ©2014-2021 Ian Max Andolina — released: LGPL3, see LICENCE.md
 % ========================================================================
 classdef colourManager < optickaCore
 

communication/dPixxManager.m

@@ -6,6 +6,8 @@
 %> It also enables better contrast range modes, critical for threshold type experiments.
 %> Opticka is an object oriented stimulus generator based on Psychophysics toolbox
 %> See http://iandol.github.com/opticka/ for more details
+%>
+%> Copyright ©2014-2021 Ian Max Andolina — released: LGPL3, see LICENCE.md
 % ======================================================================
 classdef dPixxManager < optickaCore
 

communication/dataConnection.m

@@ -24,6 +24,8 @@
 %> There is also an autoServer mode, where the object opens a TCP server
 %> and responds to commands, allowing you to send data and EVAL commands on a
 %> remote machine...
+%>
+%> Copyright ©2014-2021 Ian Max Andolina — released: LGPL3, see LICENCE.md
 % ========================================================================
 classdef dataConnection < handle
 	%dataConnection Allows send/recieve over Ethernet

communication/eyelinkManager.m

@@ -1,28 +1,37 @@
 % ========================================================================
-%> @brief eyelinkManager wraps around the eyelink toolbox functions
-%> offering a simpler interface, with methods for fixation window control
+%> @brief eyelinkManager wraps around the eyelink toolbox functions offering
+%> a simpler interface, with methods for fixation window control
 %>
 %> The core methods enable the user to test for common behavioural eye
 %> tracking tasks with single commands. For example, to initiate a task we
 %> normally place a fixation cross on the screen and ask the subject to
-%> saccade to the cross and maintain fixation for a particular duration. This
-%> is achieved using testSearchHoldFixation('yes','no'), using the properties:
-%> fixation.initTime to time how long the subject has to saccade into the
-%> window, fixation.time for how long they must maintain fixation,
-%> fixation.radius for the radius around fixation.X and fixation.Y
-%> position. The method returns the 'yes' string if the rules are matched, 
-%> and 'no' if they are not, thus enabling experiment code to simply define what 
-%> happened. Other methods include isFixated(), testFixationTime(),
-%> testHoldFixation(). 
+%> saccade to the cross and maintain fixation for a particular duration.
+%> This is achieved using testSearchHoldFixation('yes','no'), using the
+%> properties: fixation.initTime to time how long the subject has to
+%> saccade into the window, fixation.time for how long they must maintain
+%> fixation, fixation.radius for the radius around fixation.X and
+%> fixation.Y position. The method returns the 'yes' string if the rules
+%> are matched, and 'no' if they are not, thus enabling experiment code to
+%> simply call this method until it returns 'yes''. Other methods include
+%> isFixated(), testFixationTime(), testHoldFixation().
 %>
-%> Multiple fixation windows can be assigned, and in addition exclusion
-%> windows can ensure a subject doesn't saccade to particular parts of the
-%> screen. fixInit allows you to define a minimum time with which the subject
-%> must initiate a saccade away from a position (which stops a subject cheating).
+%> Try using the demo mode to see it in action (read the runDemo() code to
+%> understand how to use the class):
+%>   > em = eyelinkManager('verbose', true);
+%>   > em.runDemo();
 %>
-%> For the eyelink we also enable use of remote calibration and can call
-%> reward systems during calibration / validation to improve subject
-%> performance.
+%> Multiple fixation windows can be assigned (either circular or
+%> rectangular), and in addition exclusion windows (exclusionZone) can
+%> ensure a subject doesn't saccade to particular parts of the screen.
+%> fixInit allows you to define a minimum time with which the subject can
+%> initiate a saccade away from a position (which stops a subject cheating
+%> by moving the eyes too soon).
+%>
+%> For the eyelink we also allow the use of remote calibration and can call
+%> a reward systems during calibration / validation to improve subject
+%> performance compared to the eyelink toolbox alone.
+%>
+%> Copyright ©2014-2021 Ian Max Andolina — released: LGPL3, see LICENCE.md
 % ========================================================================
 classdef eyelinkManager < optickaCore
 

communication/ioManager.m

@@ -2,6 +2,8 @@
 %> @brief Input Output manager, currently just a dummy class
 %>
 %> 
+%>
+%> Copyright ©2014-2021 Ian Max Andolina — released: LGPL3, see LICENCE.md
 % ======================================================================
 classdef ioManager < optickaCore
 

communication/labJack.m

@@ -15,6 +15,8 @@
 %> >> lj = labJack('verbose',true) %open labJack verbosely
 %> >> lj.toggleFIO(1) %toggle FIO1 between low and high
 %> >> lj.timedTTL(3,200) % send a 200ms timed TTL pulse on FIO3
+%>
+%> Copyright ©2014-2021 Ian Max Andolina — released: LGPL3, see LICENCE.md
 % ========================================================================
 classdef labJack < handle
 

communication/labJackT.m

@@ -2,6 +2,8 @@
 %> @brief LABJACKT Connects and manages a LabJack T4 / T7
 %> This class handles digital I/O and analog I/O and analog streaming.
 %> Connection can be USB or network.
+%>
+%> Copyright ©2014-2021 Ian Max Andolina — released: LGPL3, see LICENCE.md
 % ========================================================================
 classdef labJackT < handle
 

communication/magstimManager.m

@@ -6,6 +6,8 @@
 %> >> mM = magstimManager() %create magstim manager object
 %> >> mM.open %connect via a LabJack
 %> >> mM.stimulate % run a stimulation protocol
+%>
+%> Copyright ©2014-2021 Ian Max Andolina — released: LGPL3, see LICENCE.md
 % ========================================================================
 classdef magstimManager < optickaCore
 	properties

communication/plusplusManager.m

@@ -2,6 +2,8 @@
 %> @brief Display++ Communication Class
 %>
 %> 
+%>
+%> Copyright ©2014-2021 Ian Max Andolina — released: LGPL3, see LICENCE.md
 % ======================================================================
 classdef plusplusManager < optickaCore
 

communication/tittaCalMovieStimulus.m

@@ -2,6 +2,8 @@
 %> @brief plays an animated movie for a calibration stimulus
 %>
 %>
+%>
+%> Copyright ©2014-2021 Ian Max Andolina — released: LGPL3, see LICENCE.md
 % ========================================================================	
 classdef tittaCalMovieStimulus < handle
 	properties (Access=private, Constant)

communication/tobiiManager.m

@@ -21,6 +21,8 @@
 %> screen. fixInit allows you to define a minimum time with which the subject
 %> must initiate a saccade away from a position (which stops a subject cheating).
 %>
+%>
+%> Copyright ©2014-2021 Ian Max Andolina — released: LGPL3, see LICENCE.md
 % ========================================================================
 classdef tobiiManager < optickaCore
 

omniplex/opxOnline.m

@@ -3,6 +3,8 @@
 %>	for online data display
 %> 
 %>
+%>
+%> Copyright ©2014-2021 Ian Max Andolina — released: LGPL3, see LICENCE.md
 % ========================================================================
 classdef opxOnline < handle
 	properties

opticka.m

@@ -1,8 +1,11 @@
 % ======================================================================
 %> @brief Opticka stimulus generator GUI
 %>
-%> Opticka is an object oriented stimulus generator based on Psychophysics toolbox
-%> See http://iandol.github.com/opticka/ for more details. This class builds the %> main GUI.
+%> Opticka is an object oriented stimulus generator based on Psychophysics
+%> toolbox See http://iandol.github.com/opticka/ for more details. This
+%> class builds and controls the GUI.
+%>
+%> Copyright ©2014-2021 Ian Max Andolina — released: LGPL3, see LICENCE.md
 % ======================================================================
 classdef opticka < optickaCore