implement different phases of the task in micropython

[amchagas]

this system is being built for a specific task used in Sarah King's lab. Therefore we need to code the different stages of this task in a way that:

• each stage is a different class
• they can be independently started
• we can use code to make them start in sequence, in a way that the ending condition of one, starts the next one.
• They should be able to play nicely with the code developed in Write python and micropython code to transfer data #6
• Certain variables, defining critical aspects of the task, should be accessible/settable from "outside"
• implementation in a way that users can start/modify things using a jupyter notebook

Phases of the task are:

• Magazine training (train animals to feed at the magazine)
• nose poke training (train animals to put their noses on one of the illuminated holes and getting food for it)

[amchagas]

Here is a more defined outline of the different phases (based on this paper https://www.nature.com/articles/srep42519):

Magazine training (train the mice to get food from the pellet dispenser):

• 50 trials in total (which in this case correspond to the animal getting food 50 times)
• Inter trial interval (a random choice between 4,8,16 and 32 seconds)
• Once ITI finishes, magazine LED turns on, and a food pellet is dispensed
• System keeps waiting indefinetely for input from the IR beam at the food well. When the beam is disrupted, we know the animal found the reward.
• Once animal has broken the beam, the ITI starts again

T1 phase starts immediatly after previous phase is concluded

• all 5 nosepokes illuminate and system waits for a nose poke
• Once a nose poke is registered in any of the doors, NP lights turn off and the light in the food dispenser turns on
• System waits for reward to be collected
• No information on whether or not an ITI was used in this case but I suspect it was similar to magazine training
• this phase ends also with 50 rewards

T2 phase also starts immediatly after previous phase

• trial starts by turning on the food dispenser light and waits for the animal to interact with it (break the IR beam), which turns the light off.
• 5 seconds ITI
• One of the nose poke ports LED turns on. Response in the illuminated port turns the NP LED off and turns the food dispenser LED on, while also dispensing a food pellet. (responses to the non-illuminated NP leads to no rewards, nor time outs).
• Once the food is collected, the food dispenser led turns off
• consumption interval - 20 seconds of "nothing"
• start from the top.
• repeat everything 100 times (100 rewards)

5- choice serial reaction time task PHASE 1

• trial starts similarly to T2.
• 5 second ITI
• one of the NP port LED turns on for a specific amount of time (as defined by stimulus duration variable).
• A response in the illuminated port, during stimulus duration, or up to 4 seconds after it turns the NP LED off.
• Food dispenser LED turns on, food is dispensed.
• Once food is collected, 20 sec of consumption interval
• after consumption interval, start the next trial
• In this phase, incorrect responses (either the wrong NP interaction, or a NP during ITI) or omissions lead to a 5 sec timeout period. After the timeout, the food dispenser LED turns on, so the animal starts the next trial
• In this phase stimulus duration started at 16 seconds, being gradually decreased in steps (8, 4, 2, 1.5, 1 sec) everytime a criteria was met: at least 50 started trials, 60% accuracy and [ommissions<30% OR number of correct responses >=200]. accuracy and ommission percentages were calculated using running averages with window size 20.