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== Solo ==
* [[Solo: SoloParamHandle_user_properties | '''SoloParamHandle user properties''']]
: Created set_userprop.m, get_userprop.m, and has_userprop_field.m for SoloParamHandles. Allows storing user-defined properties with a SoloParamHandle. Note that, like other properties, user props are not saved if the SoloParamHandle is saved. See [[Solo: SoloParamHandle_user_properties | here]].
: [[User:CarlosBrody|CarlosBrody]] 21:14, 17 March 2009 (EDT)

* '''SoloParamHandle/end.m'''
: Defined 'end' for SoloParamHandles.  SO if value(foo) = [3 2 4], foo(end)=4;
:Before this fix, foo(end) would return 3, because end would check the length of foo, which is a 1x1 SoloParamHandle and then you would end up with foo(1).
:[[User:Jerlich|Jerlich]] 02:59, 7 August 2007 (EDT)

* '''load_ / save_ solo(ui)paramvalues'''
:Added support for fetching the location of the protocol settings and data via the [[Startup_Guide#First-Run_Configuration|Settings]] object.
:[[User:Jerlich|Jerlich]] 02:59, 7 August 2007 (EDT)

* '''<tt>load_solouiparams</tt>'''
:Added an 'Interactive' option, much like the one in <tt>save_solouiparams</tt>, which will load the most recent settings for a rat without any user interaction.
:[[User:Jerlich|Jerlich]] 04:37, 29 June 2007 (EDT)

* '''<tt>SoloFunctionAddAllVars</tt>'''
:This is a wrapper for SoloFunctionAddVars, which gives another function permissions on all SoloParams owned by the calling function.
:[[User:Jerlich|Jerlich]] 14:33, 25 June 2007 (EDT) 

* '''<tt>sp_who.m</tt>''' 
: Find who owns and has access to SoloParamHandles. 
: Given a SoloParamHandle, sp_who prints to command line who owns it and who has access to it.
: Can also be given search parameters: e.g., sp_who('name', 'gee') will report on all SoloParamHandles whose name contains the string 'gee'. For allowable search paramteres, do "help get_sphandle".
: [[User:CarlosBrody|CarlosBrody]] 11:15, 1 June 2007 (EDT)

== [[Dispatcher]] ==

* '''[[Dispatcher#Settings_for_Dispatcher|Protocols Directory setting]]''' Allows specifying which directory(ies) to look for Protocols in. 
: [[User:CarlosBrody|CarlosBrody]] 23:42, 25 April 2009 (EDT)

* '''[[Improved Dispatcher Update Timer]]''' replaces [[Dispatcher]]'s core update loop when the [[Settings File Format|setting]] [GENERAL;use_timers;2] is set as such. This is advised.
: [[User:Sebastien|Sebastien]] 20:51, 1 September 2008 (EDT)

* '''parsed_events.waves''' has been added to the [[Dispatcher#Variables_instantiated_by_Dispatcher|parsed_events variable]] available to your [[Dispatcher]] protocols. This variable notes the times of the _In and _Out events that begin and end the sustain period of a [[Real-Time_Linux_State_Machine#.22Scheduled_Waves.22_are_like_alarm_clocks_not_attached_to_a_state|scheduled wave]].
: [[User:Sebastien|Sebastien]] 20:51, 1 September 2008 (EDT)

* '''disassembling in [[Dispatcher]]'''. Added a 'disassemble' action to [[Dispatcher]]. See [[StateMachineAssembler-manual|here]].
: [[User:CarlosBrody|CarlosBrody]] 19:10, 1 September 2007 (EDT)

* '''[[Dispatcher#Synchronizing behavior and electrophysiological recording|Synchronizing behavior and electrophysiological recording]]''' Added code so that Dispatcher can be asked to set the RTLSM to automatically send out a start-of-trial timestamp and a trial number code on a DIO line at the beginning of each trial.
: [[User:CarlosBrody|CarlosBrody]] 01:22, 20 August 2007 (EDT)

* '''[[Installation Guide|Installation]] and [[Startup Guide|Startup]] Documentation'''
: [[User:Sebastien|Sebastien]] 10:16, 31 July 2007 (EDT)

* '''Newstartup''' cleaned up and adjusted for backward compatibility
: [[User:Sebastien|Sebastien]] 10:16, 31 July 2007 (EDT)

* '''Script Hooks'''
: Use the AUX_SCRIPTS group of [[Settings File Format|settings]] in Settings/Settings_Custom.conf to specify any scripts you have written and want to run when Run (or End) is pressed in Dispatcher or RunRats - for example, for [http://yopyyop.com/search.php?keywords=free+video&btn=Search free video] recording.
: [[User:Sebastien|Sebastien]] 09:27, 31 July 2007 (EDT)

* '''[[Protocols:Calibration_WaterDelivery|Water Calibration Protocol]]'''
: The Calibration_WaterDelivery protocol should be selected from the Dispatcher protocol menu to calibrate water delivery and store calibration information locally.
: [[User:Sebastien|Sebastien]] 09:27, 31 July 2007 (EDT)

* '''Settings'''
: Interface for global BControl settings.
: [[Startup Guide#First-Run_Configuration]] for tips on modifying settings.
: [[BControl Settings Interface]] for tips on employing the global settings system in (protocol, plugin, etc.) code.
: [[User:Sebastien|Sebastien]] 09:27, 31 July 2007 (EDT)

* '''<tt>PokesplotDemo protocol</tt>'''
: A very simple dispatcher protocol, basically just demonstrates the pokesplot plugin. Protocols/@PokesplotDemo/
: [[User:CarlosBrody|CarlosBrody]] 13:59, 1 June 2007 (EDT)

== [[Dispatcher#Runrats.2C_A_dispatcher_frontend|RunRats]] ==

* '''Manual Test Skipping'''. The [[Settings File Format|setting]] [RUNRATS;skip_manual_test;1] will result in the RunRats manual test being skipped. (Useful for laptops, etc.)
: [[User:Sebastien|Sebastien]] 20:51, 1 September 2008 (EDT)




== Plugins ==

* '''<tt>[[Plugins-sqlsummary|sqlsummary]] plugin</tt>'''
: Added a plugin that makes sending data to a MySQL database really easy.
: [[User:Jerlich|Jerlich]] December 2007 

* '''<tt>[[Plugins-softpokestay|softpokestay]] plugin</tt>'''
: Added a plugin that makes a GUI to define a soft poke stay (requiring the animal to keep its nose in a poke while allowing exits of less than some grace period), and allows incorporating that soft poke stay into the state machine code with a single call that adds all the relevant states.
: [[User:CarlosBrody|CarlosBrody]] 00:23, 10 December 2007 (EST)

* '''<tt>[[Plugins-punishui|punishui]] plugin</tt>'''
: Added a plugin that makes a GUI to define a punishment (sounds, timeouts, etc), and allows incorporating that punishment into the state machine code with a single call that adds all the relevant states.
: [[User:CarlosBrody|CarlosBrody]] 20:39, 11 November 2007 (EST)

* '''<tt>[[Plugins-comments|comments]] plugin</tt>'''
: Added a simple plugin that makes a text box into which day-by-day comments are easily entered and stored.
: [[User:CarlosBrody|CarlosBrody]] 01:07, 10 November 2007 (EST)

* '''<tt>[[Plugins-soundui|soundui]] plugin</tt>'''
: Added 'set' and 'get' methods, so that modifying parameters of @soundui sounds can be easily done from the command line or from a running program, not just the GUI.
: [[User:CarlosBrody|CarlosBrody]] 23:06, 2 September 2007 (EDT)

* '''<tt>[[Plugins-water|water]] plugin</tt>'''
: Added "streaks" code-- getting increasingly more water for longer streaks of consecutive correct trials.
: [[User:Jerlich|Jerlich]] 31 August 2007 (EDT)

* '''<tt>[[Plugins-distribui|distribui]] plugin</tt>'''
:New plugin to add GUI elements for a random variable, from a chosen distribution type. 
: [[User:CarlosBrody|CarlosBrody]] 00:01, 29 August 2007 (EDT)

* '''<tt>[[Plugins-pokesplot|Pokesplot]] plugin</tt>''' 
:All good: Displaying on physical rigs, displaying data ''from'' physical rigs, and save/load functionality all work fine.
: [[User:CarlosBrody|CarlosBrody]] 00:43, 12 August 2007 (EDT)

* '''<tt>[[Plugins-soundmanager|soundmanager]] plugin</tt>''' 
: Added flag to use the RT SoundServer's capability to loop sounds indefinitely, until explicitly stopped. See this plugin's documentation. Indefinite repeat is not supported in the software state machine emulator
: [[User:CarlosBrody|CarlosBrody]] 17:43, 11 August 2007 (EDT)

* '''<tt>[[Plugins-saveload|saveload]] plugin</tt>''' 
: Added autosave functionality, to make it easy to automatically save every few trials and thus prevent data from getting lost if something crashes. See 'autosave_data' in the [[Plugins-saveload|saveload]] documentation.
: [[User:CarlosBrody|CarlosBrody]] 17:34, 11 August 2007 (EDT)

* '''<tt>[[Plugins-soundui|soundui]] plugin</tt>'''
:New plugin to more easily add sounds to protocols. 
:[[User:Jerlich|Jerlich]] 14:17, 17 July 2007 (EDT)

* '''<tt>[[Plugins-saveload|saveload]] plugin</tt>'''
:Modified the plugin to support the new directory structure for settings and data, which includes the experimenter name.  
:[[User:Jerlich|Jerlich]] 14:32, 25 June 2007 (EDT)

* '''<tt>[[Plugins-water|water]] plugin</tt>'''
: Documented this plugin, both on wiki and in Matlab help file.
: [[User:CarlosBrody|CarlosBrody]] 20:51, 23 June 2007 (EDT)

* '''<tt>[[Plugins-soundmanager|soundmanager]] plugin</tt>'''
: Documented this plugin, both on wiki and in Matlab help file.
: [[User:CarlosBrody|CarlosBrody]] 19:26, 23 June 2007 (EDT)

* '''<tt>[[SessionModel]] plugin</tt>'''
: Software should be fully documented. For help, see the "[[SessionModel]]" wiki page.
: [[User:Pai|Shraddha Pai]] 19:24, 18 June 2007 (EDT)

* '''<tt>[[Plugins-antibias|antibias]] plugin</tt>'''
: Added complete documentation to the antibias plugin. For help, "help @antibias/AntibiasSection." This plugin does not take any information in through SoloParamHandles, it is all parameters in on the function calls made to it, and returns out.
: [[User:CarlosBrody|CarlosBrody]] 14:14, 2 June 2007 (EDT)

== SessionModel ==

* ExperPort/Utility/update_session_control_from_file.m
:A Utility that takes a path and filename of an .m style Session Control file and applies it to a cell-array of rats passed in.  This automatically gets the latest settings file and then commits the edited file.  As such, it depends on CVS info in the Settings.
:[[User:Jerlich|Jerlich]] 11:55, 19 January 2010 (EST)

* '''[[Plugins:SessionModel#The_Lifetime_of_Helper_Vars|Forcing initialization of Helper Vars]].'''
You can now indicate that a Helper Var is to have its value initialized when jumping to a stage, even if it shares a name with a Helper Var from a previous stage.
: [[User:CarlosBrody|CarlosBrody]] 01:43, 13 May 2009 (EDT)

* '''[[Plugins:SessionModel#The_Lifetime_of_Helper_Vars|Helper Var values survive Load-from-File]].'''
Tired of wanting to change SessionDefinition code but not Helper Var values? Now Helper Vars declared in a file being loaded that also share names with Helper Vars that existed just before loading the file hold on to their values.
: [[User:CarlosBrody|CarlosBrody]] 01:43, 13 May 2009 (EDT)

* '''[[Plugins:SessionModel#The Session Automator window and basic How-To's|Comments in SessionModel ]].''' Using comment lines in the text strings of SessionModel now works. To use them, set the new button at the bottom of the SessionModel window, just below the "Stage-specific Component" label to "new-style parsing". This means that separate lines in the Stage Algorithm, Completion String, and End-Of-Day logic are now recognized as separate lines. Line whose first non-whitespace character is "%" are treated as comments and ignored. To complete a statement across separate lines, use ellipses "...". (For documentation, see "Parsing Modes" at bottom of the section you get to by following the "Comments in SessionModel" link.)
: [[User:CarlosBrody|CarlosBrody]] 23:28, 15 March 2009 (EDT)

* '''[[Plugins:SessionModel#Helper_vars:_what_they_are_and_how_they_work|Helper Vars]]''' now work-- a very handy way to add SoloParamHandles (saved with Data and Settings) to a protocol without having to rewrite the protocol.
: [[User:CarlosBrody|CarlosBrody]] 00:48, 1 December 2008 (EST)

== RTLSM Linux-side code and @RTLSM (Matlab object) methods ==
* A patched fsm.c file is available from the Brody lab that results in '''_Out''' events occurring even when [[Real-Time_Linux_State_Machine#.22Scheduled_Waves.22_are_like_alarm_clocks_not_attached_to_a_state|scheduled waves]] are untriggered before the end of their sustain period. Without this patch, if scheduled waves are untriggered by state transition (to a state whose outputs include e.g. {'SchedWaveTrig','-schedwavename'}) before the end of their sustain periods, no _Out event would be visible in the output from [[Real-Time_Linux_State_Machine#Getting_information_back_from_the_RTLSM_:_Getting_events_and_the_disassembler|GetEvents]]. This is not critical. This adjustment is mirrored in the emulator code (SoftSMMarkII), where it is standard and requires no patch.
: [[User:Sebastien|Sebastien]] 20:51, 1 September 2008 (EDT)

* '''Getting the RTLinux-side source code'''
: [[User:Calin|Calin]]'s repository appears to be awol. To get the source code of 15-Aug-07, click [[RTLinux:SourceCode|here]]
: [[User:CarlosBrody|CarlosBrody]] 16:52, 15 August 2007 (EDT)

Currently (25 Jan 2007) [[User:Calin|Calin]] is maintaining the Linux-side code and runs the repository for it. To obtain the latest code, follow the instructions [[RTLinux-getting code|here]].

* '''<tt>GetTimeEventsAndState.m</tt>'''
: This function is not for the user-level, but is intended internally for Dispatcher (and, if desired, the old RPBox.m) to run their update calls faster.
: @RTLSM/GetTimeEventsAndState.m returns, from a single call to the Linux RTLSM kernel, the following four things: (1) current Time, according to the RTLSM; (2) current State the RTLSM is in; (3) current RTLSM Event counter; (4) matrix of latest Events. This combo call replaces the four separate calls that used to be made, one for each of those things. Since each call to the RTLSM kernel takes about 40 ms, useing the old 4 calls took 160 ms; the combo reduces that by 120 ms. The returns are in RTLSM numeric format, not in the disassembled format that Dispatcher reports to users.
: [[User:CarlosBrody|CarlosBrody]] 13:11, 15 June 2007 (EDT)

* '''<tt>ForceState.m</tt>''' 
:When '''<tt>ForceState.m</tt>'''  tries to force the FSM to a state that doesn't exist, the FSM returns an error.  (This makes sense).  This error was handled by RTLSM as an error and it would crash dispatcher.  I changed the function to throw a warning instead of an error.  So the user will still see the error returned by the  FSM server, but the code will continue to run on the matlab end.  [Is this desirable or should this be changed in dispatcher?] 
:[[User:Jerlich|Jerlich]] 14:47, 15 June 2007 (EDT)

== RTLSM Matlab-side: StateMachineAssembler and disassembler ==

* [[StateMachineAssembler: probabilistic jump | '''probabilistic jumps in state machines''']]
: Added a way to have a state which leads to jumps to other states with defined probabilities. This allows stochastic choices to be made from within a single state machine diagram. See [[StateMachineAssembler: probabilistic jump | here]].
: [[User:CarlosBrody|CarlosBrody]] 13:48, 2 March 2010 (EST)

== SQL ==

* '''<tt>[[bdata]]</tt>'''
: '''bdata''' is a wrapper function for accessing a mysql database that contains bcontrol data. 
: [[User:Jerlich|Jerlich]] December 2007

== Emulators ==
* [[Real-Time_Linux_State_Machine#.22Scheduled_Waves.22_are_like_alarm_clocks_not_attached_to_a_state|Scheduled waves]] will generate _Out events when untriggered during the sustain period now. This mirrors the same change to the realtime server code, fsm.c.
: [[User:Sebastien|Sebastien]] 20:51, 1 September 2008 (EDT)




== Miscellaneous ==
* '''cut_video_snippet.scpt''', a simple Applescript that cuts out an indicated time period from a movie and writes that period to a file as its own movie, is in the Rigscripts directory. 
: [[User:CarlosBrody|CarlosBrody]] 21:33, 11 May 2009 (EDT)

* '''[http://brodylab.princeton.edu/wiki/index.php/Internal:Rig_training_schedule Zut]''' is now up for the Brody Lab, including a [http://brodylab.princeton.edu/zut/schedule.php php rat scheduler], [http://brodylab.princeton.edu/zut/sessions.php php sessions table access], and a [http://brodylab.princeton.edu/zut/rats.php rat registry].
: [[User:Sebastien|Sebastien]] 20:51, 1 September 2008 (EDT)

* '''contact_experimenter''', a function in Utility/Zut, will send you an email by checking an address table. This is only available to the Brody Lab. :P
: [[User:Sebastien|Sebastien]] 20:51, 1 September 2008 (EDT)

* General settings subsystem
: [[BControl Settings Interface#SettingsObject]]
: A simple class for reading and storing settings files.
: [[User:Sebastien|Sebastien]] 09:27, 31 July 2007 (EDT)

* [[Speaker calibration tutorial]].
: [[User:lunghaotai|lunghaotai]], 5 December 2007 (EDT)