/* 
  Sketch for 3rd stage GoNoGo, LEFT active nosepoke hole.

  
*/

#include<TimeLib.h>
 
int gatePin = 12; //controls feeder transistor
int houseLight = 8;
int scope = 9;
int buzz = 10; //nose-poke buzzer

int GrLED1 = 6; //green LEDs above ports
int GrLED2 = 7;

int pokes1 = 0; //nosepoke counters (any nose poke)
int pokes2 = 0;
int PREpokes = 0; //premature nose poke counter

int rewards = 0; // reward counter
int GOtrials = 0; //GO trial counter
int PREtrial = 0; //premature trial counter
int omissions = 0;

int tstart = 0; //time tracking
int tstamp = 0;

#define SENSORPIN_A 4
#define SENSORPIN_B 5

// variables will change:
int sensorState_A = 0, lastState_A = 0;
int sensorState_B = 0, lastState_B = 0;
int PREperiodValue = 0; //will be used to store randomly generated PREperiod duration (see below)
bool scopeTrigger = true;

//timer variables

unsigned long OFFtimerStart; //timer for cue light OFF
unsigned long ONtimerStart; //timer for cue light ON
unsigned long PREtimerStart; //timer for premature response period
unsigned long HouseSuccStart; //timer for house light after successful poke
unsigned long BUZZtimerStart;
unsigned long currentMillis;
const unsigned long OFFperiod = 10000;
const unsigned long ONperiod = 3000;
int PREperiod[3] = {3000, 6000, 9000}; //duration of pre-trial period is an array that will be called with a "random" function
const unsigned long HousePeriod = 3000; //duration of house light on after successful poke
const unsigned long BUZZperiod = 250;

void setup()
{
  // initialize the gate pin as an output:
  pinMode(gatePin, OUTPUT);
  
  // initialize the sensor pins as an input and enable internal pullup:
  pinMode(SENSORPIN_A, INPUT_PULLUP);
  pinMode(SENSORPIN_B, INPUT_PULLUP);
  
  //green LEDs above nosepoke holes:
  pinMode(GrLED1, OUTPUT);
  pinMode(GrLED2, OUTPUT);
  
  pinMode(houseLight, OUTPUT);
  pinMode(scope, OUTPUT);
  pinMode(buzz, OUTPUT);
  
  randomSeed(analogRead(0));
  Serial.begin(9600);
  tstart = now();
}

void loop()
{ 
  // timer for session of X milliseconds, stops arduino for Y milliseconds
  if (millis() >= 1800000) //X 
  { Serial.println ("-------------------------------");
    Serial.println ("session end");
    Serial.println ("-------------------------------");
    digitalWrite (GrLED1, LOW);
    digitalWrite (houseLight, LOW);
    digitalWrite (scope, LOW);
    Serial.print("GO trials");
    Serial.print(",");
    Serial.println (GOtrials);
    Serial.print ("rewards");
    Serial.print (",");
    Serial.println (rewards);
    Serial.print ("active");
    Serial.print (",");
    Serial.println (pokes1);
    Serial.print ("inactive"); //port ID
    Serial.print (",");
    Serial.println (pokes2);
    Serial.print("pre-trials");
    Serial.print(",");
    Serial.println(PREtrial);
    Serial.print ("premature");
    Serial.print (",");
    Serial.println (PREpokes);
    Serial.print("omissions");
    Serial.print(",");
    Serial.print(omissions);
    delay (1200000); //Y
  }

  if (scopeTrigger == true)
 { digitalWrite(scope, HIGH);
   Serial.println("scope on");
   scopeTrigger = false;
 }
  
  digitalWrite(GrLED1, LOW);
  digitalWrite(GrLED2, LOW);
  PREperiodValue = PREperiod[random(0,3)]; //randomly select PREperiod duration from selected values
  
  digitalWrite(houseLight, HIGH);//turn house light on
  PREtrial = PREtrial + 1;
  Serial.print("pre-trials");
  Serial.print(",");
  Serial.println(PREtrial);

  PREtimerStart = millis();

  while(digitalRead(houseLight) == HIGH && digitalRead(GrLED1) == LOW) //detect premature nose-poke
  {
  currentMillis = millis();

  if (currentMillis - BUZZtimerStart >= BUZZperiod) digitalWrite(buzz, LOW);//turn off buzzer
  if (currentMillis - PREtimerStart >= PREperiodValue) break; //note upper bound of "random" is exclusive

    // read the state of the sensors:
  sensorState_A = digitalRead(SENSORPIN_A);
  sensorState_B = digitalRead(SENSORPIN_B);

  if (sensorState_A && !lastState_A)
  {
    digitalWrite(gatePin, LOW); //unnecessary?
  }
  if (!sensorState_A && lastState_A)
  {
    pokes1 = pokes1 + 1;
    PREpokes = PREpokes + 1;
    Serial.print ("active");
    Serial.print (",");
    Serial.println (pokes1);
    Serial.print ("premature");
    Serial.print (",");
    Serial.println (PREpokes);
    
    digitalWrite(houseLight, LOW); //switch house light off after premature nosepoke

  }
  lastState_A = sensorState_A;


  if (sensorState_B && !lastState_B)
  {
    digitalWrite(gatePin, LOW);
  }
  if (!sensorState_B && lastState_B)
  {
    pokes2 = pokes2 + 1;
    Serial.print ("inactive"); //port ID
    Serial.print (",");
    Serial.println(pokes2); //poke counter
  }
  lastState_B = sensorState_B;
  delay(10); // so we don't flood the serial port
  
  }

  
  if (digitalRead(houseLight) == HIGH) //if there was no premature nose poke to turn off the houselight, procede with a GO trial
  {
  digitalWrite(GrLED1, HIGH); //turn on LED1 over left nosepoke
  GOtrials = GOtrials + 1;
  Serial.print("GO trials");
  Serial.print(",");
  Serial.println(GOtrials);
  }

  
  ONtimerStart = millis();

  while(digitalRead(GrLED1) == HIGH) // "GO" trial is initiated by green LED1
  {

  currentMillis = millis(); //record time at each iteration of loop in currentMillis var

  if (currentMillis - BUZZtimerStart >= BUZZperiod) digitalWrite(buzz, LOW);//turn off buzzer
  if (currentMillis - ONtimerStart >= ONperiod) 
  {
    omissions = omissions + 1;
    Serial.print("omissions");
    Serial.print(",");
    Serial.println(omissions);
    
    digitalWrite(houseLight, LOW);
    digitalWrite(GrLED1, LOW);//if the ON period has passed break out of "while ON" loop and the house light goes off
  }
  
  
  // read the state of the sensors:
  sensorState_A = digitalRead(SENSORPIN_A);
  sensorState_B = digitalRead(SENSORPIN_B);

  if (sensorState_A && !lastState_A)
  {
    digitalWrite(gatePin, LOW);
  }
  if (!sensorState_A && lastState_A)
  {
    pokes1 = pokes1 + 1;
    rewards = rewards + 1;
    Serial.print ("active");
    Serial.print (",");
    Serial.println (pokes1); 
    Serial.print ("rewards");
    Serial.print (",");
    Serial.println (rewards);

    BUZZtimerStart = millis();
    digitalWrite(buzz, HIGH);
    
    digitalWrite(gatePin, HIGH);
    delay(75);                  
    digitalWrite(gatePin, LOW);

    digitalWrite(GrLED1, LOW); //switch LED1 off after nosepoke

  }
  lastState_A = sensorState_A;


  if (sensorState_B && !lastState_B)
  {
    digitalWrite(gatePin, LOW);
  }
  if (!sensorState_B && lastState_B)
  {
    pokes2 = pokes2 + 1;
    Serial.print ("inactive"); //port ID
    Serial.print (",");
    Serial.println (pokes2); //poke counter

  }
  lastState_B = sensorState_B;
  delay(10); // so we don't flood the serial port
  }

  lastState_A = sensorState_A; //reset sensor states
  lastState_B = sensorState_B;


  OFFtimerStart = millis(); //record time when "while OFF" loop started in OFFtimerStart var
  HouseSuccStart = millis();

  while(digitalRead(GrLED1) == LOW) // this part of code controls the 10s inter-trial interval when the cue lights are off.
  {

  currentMillis = millis(); //record time at each iteration of loop in currentMillis var

  if (currentMillis - BUZZtimerStart >= BUZZperiod) digitalWrite(buzz, LOW);//turn off buzzer
  if (currentMillis - HouseSuccStart >= HousePeriod) digitalWrite(houseLight, LOW); // controls house light after correct poke: it remains on for 3 sec.
  if (currentMillis - OFFtimerStart >= OFFperiod) break; //if the OFF period has passed break out of "while OFF" loop

  // read the state of the sensors:
  sensorState_A = digitalRead(SENSORPIN_A);
  sensorState_B = digitalRead(SENSORPIN_B);

  if (sensorState_A && !lastState_A)
  {
    digitalWrite(gatePin, LOW);
  }
  if (!sensorState_A && lastState_A)
  {
    pokes1 = pokes1 + 1; //only pokes counted, no rewards since no pellet dispensed
    Serial.print ("active");
    Serial.print (",");
    Serial.println (pokes1); 
    Serial.print ("rewards");
    Serial.print (",");
    Serial.println (rewards);

    // no gatePIN trigger since non-rewarded poke

  }
  lastState_A = sensorState_A;



  if (sensorState_B && !lastState_B)
  {
    digitalWrite(gatePin, LOW);
  }
  if (!sensorState_B && lastState_B)
  {
    pokes2 = pokes2 + 1;
    Serial.print ("inactive"); //port ID
    Serial.print (",");
    Serial.println (pokes2); //poke counter
  }
  lastState_B = sensorState_B;
  delay(10); // so we don't flood the serial port
  }
}