Code Reference

Arduino Code

SerialComms

getSerialInput()

This function reads the data from the serial connection and returns it as a string.

This is used later to update the values

getSepIndex(String input, char separator)

Returns the index of the separator character in a string.

UpdateGlobals(String input)

This is a big ugly function which compares the input string to the names of variables that I have stored in memory; This is very much not the C way to do things...

I think this could be a hash table. I haven’t learned enough about hash table implementation yet and I know this works, so for the moment: If it ain’t broke...

sensors

senseLick()
  1. check to see if the lick sensor has moved:
    if the sensor was in a low state, allow the calling of a rising edge.
  2. check if the sensor is above threshold
  3. report if the state of lickOn has change

single_port_setup

runTrial()

returns 0 if the stimulus was applied returns 1 if a timeout is required until next trial

local variables and initialisation of the trial t_init is initialised such that t_since returns 0 at the start of the trial, and increases from there.

trial_phase0 while the trial has not started

  1. update the time
  2. check for licks
  3. trigger the recording by putting recTrig = HIGH
Habituation()
  1. Determine the appropriate stimulus
  2. set active port
  3. counts number of sequential licks
    • Uses the C ternary operator, which has the form: A = boolean ? assignment if true : assignment if false; the active port count gets incremented to a maximum of ten, while the non-active port count gets decremented to a minimum of zero. This is an important caveat as the counts are made with unsigned variables, meaning that one less than zero is actually 255!

States

ActiveDelay(unsigned long wait, bool break_on_lick)

needs to be documented

deliver_reward(bool water)

Open the water port on port for a duration defined by waterVol

punish(int del)

plays the punishment tone / buzzer

Timeout(unsigned long wait, int depth)

runs a time out

preTrial()
while the trial has not started
  1. update the time
  2. check for licks
  3. trigger the recording by putting recTrig -> HIGH
count_responses(int duration, bool lickTrig) {

Counts the number of hits on the lick sensor over duration of milliseconds.

TrialStimulus()

runs the trial stimulus

conditional_tone(int frequency, int duration)

wrapper function so I don’t need to put a billion if statements

Python Code

Reads the characters in the buffer and modifies the program parameters accordingly

see Interactive Options

Audio

band_limited_noise(min_freq, max_freq, samples=1024, samplerate=1)

Generates noise within a particular band of frequencies

fftnoise(f)

filter used in band_limited_noise

config_loader

write_out_config(params, ID)

writes a subset of parameters to an ini file which can then be used to recover variable values.

ConfigSectionMap(section, Config)

Helper function for reading configuration objects to a dictionary

restore_old_config(ID)

reads the old ini file. checks to see if the current ID is in the ini sections restores the varible values in the global namespace (Hacky solution)

data_directories

timenow()

provides the current time string in the form HH:MM:SS

Returns:the current time in the form HH:MM:SS
Return type:str
today()

provides today’s date as a string in the form YYMMDD

Returns:the date as a string in the form YYMMDD
Return type:str
create_datapath(DATADIR = "", date = today())

make a path to save the data based on today’s date

create_logfile(DATADIR = "", date = today(), port = None, ID = None)

make a logfile to save communications, based on today’s date

serial_wrapper

timenow()

provides the current time string in the form HH:MM:SS

init_serialport(port, logfile = None, ID = None)

Open communications with the arduino; quits the program if no communications are found on port.

If there are communications the script waits 500 ms then reads all incoming lines from the Serial port. These two lines include the arduino code version and a string that says the arduino is online

Serial_monitor(ser, logfile, show = True, ID = None, verbose = None)

Reads from the serial port one line at time.

Continuous_monitor_arduino(ser, end_trial_msg = "- Status Ready", sep = ':', debug_flags = (("#", "t#", "- ")), ID = None, verbose = None, logfile = None)

continously loops through messages from the serial monitor until the end_trial_msg is recieved. messages that are not preceded by debug_flags are stored in a dictionary which is returned by this function.

update_bbox(ser, params, logfile, trial_df = {}, ID = None, verbose = None)

Communicates the contents of the dict params through the serial communications port.

data is sent in the form: parmas[key] = value –> key:value

trail_df dictionary is updated to include the parameters received from the arduino

numerical

Previously held functions to help with numerical handling, these have mostly been replaced, now contains a function for general conversion of strings to numbers

num(s)

First attempts to convert string s to an integer. If that gives a ValueError then it attempts to return s as a float. Finally if s cannot be converted to a float or an int, the string is returned unchanged.