Usage

A set of trials are run through the SerialController.py script. At the windows command prompt cd to the root directory of the behaviour_box repository.

When the program runs the first thing it does is make a new folder to save the logs in. The base of the new directory can be specified by --datapath and the new folder is always the current date is in the format YYMMDD.

In addition it also creates two files, a raw log file which stores all time stamped communications sent and received by the program, and a csv file which contains the same data in tabulated form. The name pattern for the csv is {ID}_{date}_000.csv where ID is given with the -ID argument and date is in the format YYMMDD.

It is important to note that the data files will be appended to each time the program is run over the course of the day, unless a new ID is specified.

Next the program checks the serial port specified by the --port argument. On Windows the serial ports are specified by COMx where x is some integer. In my case my Arduino always occupies COM5, so I have set that as the default port to check. More about adjusting defaults in a bit. If no communications are found the program will exit.

When the connection has been established the program first transmits a number of configuration variables to the arduino, such as the lick threshold, and timing information. These can be updated online later, but it saves time to avoid sending them on each trial if they are unchanged.

The program then begins to loop through the trials variable, which is an iterable list of the stimulus durations. On each loop the program tells the Arduino what duration to play, and weather or not to reward a lick.

At this point the program sends the START message to the Arduino and the trial begins. As the trial runs the program monitors the Arduino status messages as they come in.

At the end of the trial the program collects all the status messages and formats them into a Pandas DataFrame, which is then saved into {ID}_{date}_000.csv