int Home = 2; //Cylinder Home Sensor
int RodOut = 3;// Rod Out Sensor
int LedGrn1 = 4; //Test 1 ok
int LedGrn2 = 5; //Test 2 ok
int LedGrn3 = 6; //Test 3 ok
int LedRed = 7; //Alarm LED
int DUT = 8;   //Device Under Test
int Start = 9; //Start Button on PCB
int LedYelRodOut = 10; //Timer ON LED

unsigned long previous = 0;
const long interval1 = 1000; // time cylinder rod stays out
const long interval2 = 1000; //interval2 gives 1/2 second to ensure switch is fully depressed before alarm changed to 1 sec

bool Test1 = false;
bool Test2 = false;
bool Test3 = false;
bool Alarm = false;
bool Run = false;
bool AlarmOn = false;

void setup()
{
  pinMode(Home, INPUT);
  pinMode(RodOut, INPUT);
  pinMode(LedGrn1, OUTPUT);
  pinMode(LedGrn2, OUTPUT);
  pinMode(LedGrn3, OUTPUT);
  pinMode(LedRed, OUTPUT);
  pinMode(DUT, INPUT);
  pinMode(Start, INPUT);
  pinMode(LedYelRodOut, OUTPUT);
}

void loop()

// TEST 1 ROUTINE

{
  if ( digitalRead (Start) == HIGH)
  {
    Run = true;
  }

  unsigned long current = millis(); //current register will increment in milliseconds.

  if ((Run == true) && (digitalRead(Home) == HIGH) && (digitalRead (DUT) == LOW) && (Test1 == false) && (Alarm == false)) //Test1 is ok.
  {
    Test1 = true;
    digitalWrite (LedGrn1, Test1);
    previous = current;
  }
  //since Test 1 is ok,we're kicking off the timer process to prepare for the timed cylinder activation.
  // Note: we had to put Test1==false, in the if statement, else the timer would reset again at the rod return cycle.
  // If Test 1 is ok we will ignore lines 62 to 68 and go directly to line 72.

  // If Test1 fails:
  //Here too, we need to have a timer to give some time for the alarm to sound otherwise, the alarm will reset
  //immediately in the reset all sequence. On the other hand, if we don't put AlarmOn bool, the alarm will
  //be enabled again immediately after the timer has timed-out.

  if ((Run == true) && (Test1 == false) && (AlarmOn == false)) //Alarm if Test1 fails.
  {
    Alarm = true;
    digitalWrite (LedRed, Alarm);
    AlarmOn = true;
    previous = current;
  }

  // TIMER >> ACTIVATE CYLINDER ROUTINE

  if ((Run == true) && current - previous < interval1 && (Test1 == true))
  {
    digitalWrite (LedYelRodOut, HIGH);
  }

  else
  {
    digitalWrite (LedYelRodOut, LOW);
  }

  //TEST 2 ROUTINE

  if ((Test1 == true) && (digitalRead (RodOut) == true) && (digitalRead (DUT) == HIGH))
  {
    Test2 = true;
    digitalWrite (LedGrn2, Test2);
  }

  if ((Run == true) && (current - previous > interval2) && (Test2 == false) )
    //interval gives time for sw. to activate before alarm
  {
    Alarm = true;
    digitalWrite (LedRed, Alarm);
  }

  //TEST 3 ROUTINE

  if ((digitalRead(RodOut) == LOW) && (digitalRead (DUT) == LOW) && (Test1 == true) && (Test2 == true) && (Alarm == false))
  {
    Test3 = true;
    digitalWrite (LedGrn3, Test3);
  }

  if ((Test2 == true) && (Test3 == false) && (digitalRead(Home) == HIGH))
  {
    Alarm = true;
    digitalWrite (LedRed, Alarm);
  }

  if ((current - previous > 2500) && ((Alarm == true) || (Test3 == true)))
    // this is a general reset and will avoid the program getting stuck at any point
  {
    Test1 = false;
    Test2 = false;
    Test3 = false;
    Alarm = false;
    Run = false;
    AlarmOn = false;
    digitalWrite (LedGrn1, Test1);
    digitalWrite (LedGrn2, Test2);
    digitalWrite (LedGrn3, Test3);
    digitalWrite (LedRed, Alarm);
  }
}