Software Descriptions¶

behaviourbox.ino¶

This program delivers sensory stimulation and opens water valve when the animal touches the licking sensor within a certain time window.

The basic flow of the program is shown below

Files¶

The header files in the behaviourbox folder contain the functions required to run the behaviourbox code. There are currently 7 header files:

global_variables.h

Lists the variables that are used with global scope. These variables, unless explicitly stated to be internal, can be updated via the serial communications function.
prototypes.h

This file just lists the function names that will be defined in other files. It is organised such that the prototypes are grouped by the file that they come from, under the appropriate heading
timing.h

Contains the function used to keep all events on time. The Arduino code continuously asks the microcontroller how long it has been running and uses a simple logic of if the current time is > the time an event was supposed to happen : do event
sensors.h

Contains the thresholding function for converting the analog lick sensor values to binary lick events. This function detects rising edges, applies a simple digital smooth, and will play a short feed back tone if the audio flag is set to True.
states.h

This file contains the functions that define the states of the Arduino. All of the nodes in the flow diagram are defined here.
SerialComms.h
This contains a nasty series of if statements and string compares. The UpdateGlobals function is the backbone of this implementations interactivity. I have hard coded all of the variable names and their string representations into a long series of conditional statements. The basic logic is:
Given: "VariableName:Value" Update: VariableName = Value
single_port_setup.h

global_variables.h¶

Contains definitions of all variables that are used by multiple functions and expected to have persistent values between the functions. These include the initialisation time, the various timing parameters, as well as any additional options that are available.

variable	description
t_init	not settable. This is the variable that the other times a measured relative to
t_noLickPer	A time measured in milliseconds. After this amount of time the program will break out of a trial if a lick is detected before the stimulus. If the value is 0 then licks before the stimulus are ignored altogether.
trial_delay	Amount of time in milliseconds to delay the start of a trial
t_rewardDEL	Amount of time in milliseconds to delay checking for licks after a stimulus
t_rewardDUR	Amount of time in milliseconds to check for licks
t_trialDUR	Total time in milliseconds that the trial should last

t_stimONSET	The time in milliseconds, relative to the trial start time, that the stimulus turns on
t_stimDUR	Amount of time in milliseconds to keep the stimulus on

timeout	Boolean value. If True enable the recursive timeout punishment

debounce	Number of milliseconds to delay between reading the lick sensor value.
lickThres	The threshold on the licksensor required to call a lick. This is a number between 0 - 1024 (multiply by 5 V/1024 to get voltage)

minlickCount	The number of licks required to count as a response, ie to open the water valve, or to deliver a punishment
lickTrigReward	Boolean, set true to enable the reward to be delivered immediatly after the min licks are reached. If false the reward is deliverd at the end of the response duration
reward_nogo	Boolean, set true if you want a correct rejection to be rewarded at the end on the reward period

mode	{‘-‘, ‘O’, ‘H’} a character to represent the type of mode to run in. If the mode is ‘H’ the system will delver a stimulus and a reward in response to the animal’s lick. If the mode is ‘O’ the system delivers a stimulus and listens for a response

waterVol	Amount of time in milliseconds to hold the water valve open for
trialType	character code {‘G’ or ‘N’} to determine if this is a go or no go trial. This is used to determine if the water valve will open in response to animal’s lick

verbose	Boolean, if True will enable full debug printing...(might be deprecated?)
punish_tone	deprecated
audio	Boolean, enables auditory cues for the response period

SerialController.py¶

This python script is a wrapper for communicating with the Arduino program. It is a simple loop that reads data transmitted through a serial connection. Note, this is not a necessary component, however it makes running trials a lot easier.

The program starts
The program opens communications with available serial port The program waits until it gets the arduino is active, and prints all output until the ready signal is transmitted.
The program starts a block
The program transmits the dict params, which holds all parameters for a single trial. The condition values get updated; based on the frequencies being sent, all contents of params are transmitted to the behaviour controller.
The program prints the frequencies and the condition to the screen and a random timeout is started.
The program initiates a trial by sending a literal "START" message to the behaviour box.
- The behaviour box runs one trial, with the parameters set previously
The program records the output from behaviorCOMs into a dict, which later will be converted to a data frame for analysis.
The program repeats sending mode flags until all stimuli combinations have been run through.

call signature

usage: SerialControl.py [-h] [-af] [--trials [TRIALS [TRIALS ...]]]
                        [-lt LICKTHRES] [--verbose] [-restore]
                        [--repeats REPEATS] [--port PORT] [--ITI ITI ITI]
                        [-rdur T_RDUR] [-ltr] [--t_stimONSET T_STIMONSET]
                        [--datapath DATAPATH] [-i ID] [-m MODE] [-to TIMEOUT]
                        [-nlp NOLICK] [-w WEIGHT] [-td TRIALDUR]
                        [-rdel T_RDELAY] [-p] [-noise] [-rng] [-lc LCOUNT]

Optional Arguments:¶

These are the arguments which can be supplied to SerialControl.py to modify it’s parameters. Each paramater has default values which can be set by modifying the appropriate value in utilities/args.py, see Adjusting Default Arguments.

help¶

-h, --help

show this help message and exit

audio¶

-af, --audio

provides audio feedback during the trials this is not to be confused with the noise played to simulate / mask the scanners

trials¶

--trials [TRIALS [TRIALS ...]]

stimulus durations to run on each trial. That is, the duration of the stimulus pulse.

lickthres¶

-lt LICKTHRES, --lickThres LICKTHRES

set lickThres in arduino

verbose¶

--verbose

for debug this will print everything if enabled

restore¶

-restore

Use to look up previous settings in the comms.ini file

repeats¶

--repeats REPEATS

the number of times this block should repeat, by default this is 1

port¶

--port PORT

port that the Arduino is connected to

ITI¶

--ITI ITI ITI

an interval for randomising between trials

t_rDUR¶

-rdur T_RDUR, --t_rDUR T_RDUR

set end time of reward epoch

lickTrigReward¶

-ltr, --lickTrigReward

flag to allow licks to trigger the reward immediatly

t_stimONSET¶

--t_stimONSET T_STIMONSET

sets the time after trigger to run the first stimulus

datapath¶

--datapath DATAPATH

path to save data to, by default is the current working directory

ID¶

-i ID, --ID ID

identifier for this animal/run

mode¶

-m MODE, --mode MODE

the mode h abituaton or o perant, by default will look in the config table

timeout¶

-to TIMEOUT, --timeout TIMEOUT

set the timeout duration for incorrect licks

noLick¶

-nlp NOLICK, --noLick NOLICK

set t_noLickPer in arduino

weight¶

-w WEIGHT, --weight WEIGHT

weight of the animal in grams

trialDur¶

-td TRIALDUR, --trialDur TRIALDUR

set minimum trial duration

r_rDELAY¶

-rdel T_RDELAY, --t_rDELAY T_RDELAY

set start time of reward epoch

noise¶

-noise

plays a noise during trials

reward_nogo¶

-rng, --reward_nogo

flag to allow a water delivery following no lick of a no go stim

lcount¶

-lc LCOUNT, --lcount LCOUNT

set minlickCount in arduino