Code(Arduino\C++)

//Define light
#define Light_1   52
#define Light_2   50
#define Light_3   48
#define Light_4   46

#define buzzer    9

//Define PIR
#define PIR_1     10
#define PIR_2     11
#define PIR_3     12
#define PIR_4     13

#define Test_L1   31
#define Test_L2   33
#define Test_L3   35
#define Test_L4   37
#define Test_L5   39

bool Armed = false;
const int flashSpeed = 500;

bool PIR_A1 = false;
bool PIR_A2 = false;
bool PIR_A3 = false;
bool PIR_A4 = false;

int S1 = 0;
int S2 = 0;
int S3 = 0;
int S4 = 0;

int BuzzState = 0;
int inbyte = 0;

bool PIR1_State = false;
bool PIR2_State = false;
bool PIR3_State = false;
bool PIR4_State = false;

boolean roomL1_state = false;
boolean roomL2_state = false;
boolean roomL3_state = false;
boolean roomL4_state = false;

unsigned long tmp_count1 = 0;
unsigned long tmp_count2 = 0;
unsigned long tmp_count3 = 0;
unsigned long tmp_count4 = 0;

int PIRS_1 = 0;
int PIRS_2 = 0;
int PIRS_3 = 0;
int PIRS_4 = 0;

char strPIR[5] = "zxcv";
char strTrueStatePIR[5] = "uiop";

void setup() {
  // put your setup code here, to run once:
  Serial.begin(9600);

  //Light mode declaration
  pinMode(Light_1, OUTPUT);
  pinMode(Light_2, OUTPUT);
  pinMode(Light_3, OUTPUT);
  pinMode(Light_4, OUTPUT);
  // PIR warm up reading
  digitalRead(PIR_1);
  digitalRead(PIR_2);
  digitalRead(PIR_3);
  digitalRead(PIR_4);

  pinMode(Test_L1, OUTPUT);
  pinMode(Test_L2, OUTPUT);
  pinMode(Test_L3, OUTPUT);
  pinMode(Test_L4, OUTPUT);
  pinMode(Test_L5, OUTPUT);

  
  digitalWrite(Test_L1, 1);
  digitalWrite(Test_L2, 1);
  digitalWrite(Test_L3, 1);
  digitalWrite(Test_L4, 1);
  digitalWrite(Test_L5, 1);
  delay(6000);
  digitalWrite(Test_L1, 0);
  digitalWrite(Test_L2, 0);
  digitalWrite(Test_L3, 0);
  digitalWrite(Test_L4, 0);
  digitalWrite(Test_L5, 0);

}

void loop() {
  if (Serial.available() > 0)
  {
    inbyte = Serial.read();
  }
  //Send state of PIR
  Serial.print(strTrueStatePIR);

  if (inbyte == 'A') //system is armed
  {
    Armed = true;
  }

  if (Armed == true)
  {
    PIR_A1 = true;
    PIR_A2 = true;
    PIR_A3 = true;
    PIR_A4 = true;
    ///////////////////////////////////////////////
    //true PIR states
    //pir1 true state
    if ((digitalRead(PIR_1) == 1))
    {
      strTrueStatePIR[0] = 'U';
      digitalWrite(Test_L1, 1);
    }
    if ((digitalRead(PIR_1) == 0))
    {
      strTrueStatePIR[0] = 'u';
      digitalWrite(Test_L1,0);
    }

    //pir2 true state
    if ((digitalRead(PIR_2) == 1))
    {
      strTrueStatePIR[1] = 'I';
      digitalWrite(Test_L2, 1);
    }
    if ((digitalRead(PIR_2) == 0))
    {
      strTrueStatePIR[1] = 'i';
      digitalWrite(Test_L2, 0);
    }

    //pir3 true state
    if ((digitalRead(PIR_3) == 1))
    {
      strTrueStatePIR[2] = 'O';
      digitalWrite(Test_L3, 1);
    }
    if ((digitalRead(PIR_3) == 0))
    {
      strTrueStatePIR[2] = 'o';
      digitalWrite(Test_L3, 0);
    }

    //pir4 true state
    if ((digitalRead(PIR_4) == 1))
    {
      strTrueStatePIR[3] = 'P';
      digitalWrite(Test_L4, 1);
    }
    if ((digitalRead(PIR_4) == 0))
    {
      strTrueStatePIR[3] = 'p';
      digitalWrite(Test_L4, 0);
    }

  }


//  // Send PIR state if armed and triggered
//  if ((PIR_A1 == true) && (digitalRead(PIR_1) == 1))
//  {
//    digitalWrite(Test_L2, 1);
//    //set PIR1 Tx data
//    strPIR[0] = 'Z';
//    // if PIR1 cam test fails
//    if (inbyte == 'H')
//    {
//      //set PIR state back to off or small letter
//      strPIR[0] = 'z';
//    }
//
//  }
//
//  if ((PIR_A2 == true) && (digitalRead(PIR_2) == 1))
//  {
//    strPIR[1] = 'X';
//    if (inbyte == 'J')
//    {
//      strPIR[1] = 'x';
//    }
//
//  }
//
//  if ((PIR_A3 == true) && (digitalRead(PIR_3) == 1))
//  {
//    strPIR[2] = 'C';
//    if (inbyte == 'K')
//    {
//      strPIR[2] = 'c';
//    }
//  }
//
//  if ((PIR_A4 == true) && (digitalRead(PIR_4) == 1))
//  {
//    strPIR[3] = 'V';
//    if (inbyte == 'L')
//    {
//      strPIR[3] = 'v';
//    }
//  }
//
//  if (Armed == true)
//  {
//    //print 'zxcv'
//    Serial.write(strPIR);
//    
//  }


  //alarms triggered sent from matlab
  if (inbyte == 'Q')
  {
    S1 = 1;
  }

  if (inbyte == 'W')
  {
    S2 = 1;
  }

  if (inbyte == 'E')
  {
    S3 = 1;
  }

  if (inbyte == 'R')
  {
    S4 = 1;
  }

  //LIGHT FUNCTION
  if (((millis() - tmp_count1) >= flashSpeed) && (S1 == 1))
  {
    digitalWrite(Light_1, !roomL1_state);
    roomL1_state = !roomL1_state;
    tmp_count1 = millis();
  }

  if (((millis() - tmp_count2) >= flashSpeed) && (S2 == 1))
  {
    digitalWrite(Light_2, !roomL2_state);
    roomL2_state = !roomL2_state;
    tmp_count2 = millis();
  }

  if (((millis() - tmp_count3) >= flashSpeed) && (S3 == 1))
  {
    digitalWrite(Light_3, !roomL3_state);
    roomL3_state = !roomL3_state;
    tmp_count3 = millis();
  }

  if (((millis() - tmp_count4) >= flashSpeed) && (S4 == 1))
  {
    digitalWrite(Light_4, !roomL4_state);
    roomL4_state = !roomL4_state;
    tmp_count4 = millis();
  }

  if (((S1 == 1) || (S2 == 1) || (S3 == 1) || (S4 == 1)) && (BuzzState == 0))
  {
    tone(buzzer, 1000);
    BuzzState = 1;
  }


  if (inbyte == 'a')
  {
    // reset or diable armed state
    Armed  = false;
    PIR_A1 = false;
    PIR_A2 = false;
    PIR_A3 = false;
    PIR_A4 = false;

    //turn buzzer off
    noTone(buzzer);
    BuzzState = 0;

    //switch all lights off
    digitalWrite(Light_1, LOW);
    digitalWrite(Light_2, LOW);
    digitalWrite(Light_3, LOW);
    digitalWrite(Light_4, LOW);

    //reset alarm trigger off
    S1 = 0 ;
    S2 = 0 ;
    S3 = 0 ;
    S4 = 0 ;

    //Reset for light flashing variables
    roomL1_state = false;
    roomL2_state = false;
    roomL3_state = false;
    roomL4_state = false;

    tmp_count1 = 0;
    tmp_count2 = 0;
    tmp_count3 = 0;
    tmp_count4 = 0;
  }

}