Output Format¶

The following table shows the output generated from running SerialComms.py with these parameters:

>> SerialComms.py -i G3 -af -lt 1 -lc 2 -noise -nlp 1000
..  -rdur 800 -rdel 50 --trials 0 25 50 100 150 200 -td 5
..  -to 2 --ITI 2 8

	ID	Water	audio	lickThres	minlickCount	mode	post_count	pre_count	response	rew_count	t_noLickPer	t_rewardDEL	t_rewardDUR	t_stimDUR	t_stimONSET	t_trialDUR	time	timeout	trialType	trial_noise	trial_num
0	G3	0	1	204	2	o	0	0		0	1000	50	800	25	2000	5000	18:29:43	2	G	TRUE	0
1	G3	0	1	204	2	o	0	0	R	0	1000	50	800	0	2000	5000	18:30:08	2	N	TRUE	1
2	G3	1	1	204	2	o	6	2	H	11	1000	50	800	50	2000	5000	18:30:19	2	G	TRUE	2
3	G3	0	1	204	2	o			e		1000	50	800		2000	5000	18:30:28	2	G	TRUE	3
4	G3	1	1	204	2	o	11	0	H	10	1000	50	800	200	2000	5000	18:30:38	2	G	TRUE	4
5	G3	0	1	204	2	o			e		1000	50	800		2000	5000	18:30:48	2	G	TRUE	5

The .csv file that gets generated contains a table of variables, that may be relevant to analysis.

Variable	value
ID	The identity string for this animal
Water	Either 0 for no water delivered, or 1 to indicate water was given
audio	Either 0 to indicate audio cues not used on this trial, or 1 to indicate the use of audio cues
block	An integer value that keeps track of which group of trials this trial is part of (increments by 1 after all of the iterable values are exhausted and the session gets repeated)
comment	Space for trial relevant comments
lickThres	The internal value the Arduino uses as the lick threshold. Multiply by 5 / 1024 to get the threshold in volts
lickTrigReward	Either 0 indicating if the reward is delivered at the end of the response period, or 1 to indicate that the animal is rewarded immediately after licking.
minlickCount	The number of licks required on this trial in order to count as a response to the Arduino.
mode	Either ‘o’ for an operant trial or ‘h’ for a habituation trial
post_count	The number of licks counted after the stimulus
pre_count	The number of licks counted in the period before the stimulus
punish_tone	0 or 1 indicating if a tone is used to punish a false alarm
response	The character code of the animals response. One of {‘H’: hit, ‘f’: false alarm, ‘R’: correct rejection, ‘e’: early lick (trial broken), ‘-’: miss}.
rew_count	Number of licks detected in the response period
t_noLickPer	This is the number of milliseconds before the stimulus in which licks would cause the trial to be cut short.
t_rewardDEL	The amount of time delayed between the end of the stimulus and the onset of the response period.
t_rewardDUR	The width of the response period in milliseconds.
t_stimDUR	The duration in milliseconds that the stimulus was on for on this trial
t_stimONSET	The time the stimulus came on, relative to the beginning of the trial, in milliseconds.
t_trialDUR	The duration of this trial in milliseconds.
time	Time on the PC that this trial began (in 24 hour format)
timeout	The number of seconds specified for the timeout period
trialType	The type of trial. Either ‘G’ for a go trial, or ‘N’ for a no-go trial
trial_noise	A Boolean value indicating if the masking noise was played on this trial.

In this example the parameters specified yield the following trial conditions:

-i G3 (or --ID G3):

specifies an identifier for this animal, this identifier is then used in the filename of the generated output. ie: G3_YYMMDD.csv
-af (or --audio):

specify that audio cues are to be used in this trial. Lick events produce a brief click when detected and the reward period, reward event, and punishment are all signalled by different tones.
-lt 1:

Sets the threshold of the lick detection to be 1 V. Rising edges exceeding the lick threshold value will be counted as lick events.
-lc 2:

Specifies the number of licks that are required in order for the Arduino to count a response. At least this number of licks are required in the response period in order to trigger a reward or a punishment. In addition, this is the number of licks necessary to break a trial before the stimulus is delivered.
-noise:

Specifies that a masking noise should be played from the PC speakers. This noise plays during the trial in order to simulate the sounds of the laser scanning mirrors on non-imaging trials.
-nlp 1000:

Specifies the no lick period in milliseconds. This is the number of milliseconds before the stimulus in which licks will cause the trial to be cut short.
-rdur 800:

Specifies the time in milliseconds to listen for licks after the stimulus. That is, the width of the response period in milliseconds.
-rdel 50:

Specifies the time to wait after the end of the stimulus before the response period becomes active. Also in milliseconds.
--trials 0 25 50 100 150 200:

Specifies 6 durations for the stimulus. The program will shuffle through this list for a set number of repeats (by default 500, see Adjusting Default Arguments)
-td 5 :

Specifies that the trial has a duration of 5 seconds. The recording trigger will remain in the HIGH voltage state for this duration, unless a trial is interrupted by early licking.
-to 2:

Specifies a timeout of 2 seconds. In the event that the animal responds to the no-go trial this is the amount of time they must withhold additional licks for the next inter-trial interval to begin. Additional licks within this period will reset the time out.
--ITI 2 8:

Specifies an inter-trial interval of between 2 and 8 seconds. The exact time to wait between any particular two trials is random, between theses two bounds.