#include <Wire.h>
#include <LiquidCrystal_I2C.h>  // Include the library for the LCD display

// Initialize the LCD (for I2C address 0x27, adjust based on your hardware)
LiquidCrystal_I2C lcd(0x27, 16, 2);  

// Define pins
const int irSensorPin = 2;        // IR sensor pin for cartridge detection
const int buttonPin = 3;          // Push button pin to start the process
const int solenoidValveIN1 = 4;   // IN1 pin for solenoid valve control via L298N
const int solenoidValveIN2 = 5;   // IN2 pin for solenoid valve control via L298N
const int vacuumPumpIN1 = 6;      // IN1 pin for vacuum pump control via L298N
const int vacuumPumpIN2 = 7;      // IN2 pin for vacuum pump control via L298N
const int vacuumPumpEN = 8;       // Enable pin for vacuum pump

// Peristaltic pumps for channels 3, 4, 5
const int pump3IN1 = 9;
const int pump3IN2 = 10;
const int pump4IN1 = 11;
const int pump4IN2 = 12;
const int pump5IN1 = 13;
const int pump5IN2 = 14;

// Global variables for pump control
int pumpPWM3 = 128;     // PWM value for pump on Channel 3
int pumpPWM4 = 150;     // PWM value for pump on Channel 4
int pumpPWM5 = 180;     // PWM value for pump on Channel 5

// Tunable time intervals (in milliseconds)
int forwardTime3 = 3000;  // Forward time for pump on Channel 3
int forwardTime4 = 4000;  // Forward time for pump on Channel 4
int forwardTime5 = 5000;  // Forward time for pump on Channel 5

int backAndForthTime = 2000;  // Time for each forward and backward motion during back-and-forth mixing

void setup() {
  // Initialize serial communication
  Serial.begin(9600);

  // Initialize the LCD
  lcd.begin(16, 2);
  lcd.backlight();  // Turn on the backlight

  // Set up IR sensor, button, and L298N control pins
  pinMode(irSensorPin, INPUT);
  pinMode(buttonPin, INPUT_PULLUP);  // Use internal pull-up resistor for the button

  // L298N Pins Setup
  pinMode(solenoidValveIN1, OUTPUT);
  pinMode(solenoidValveIN2, OUTPUT);
  pinMode(vacuumPumpIN1, OUTPUT);
  pinMode(vacuumPumpIN2, OUTPUT);
  pinMode(vacuumPumpEN, OUTPUT);

  // Peristaltic pump pins setup
  pinMode(pump3IN1, OUTPUT);
  pinMode(pump3IN2, OUTPUT);
  pinMode(pump4IN1, OUTPUT);
  pinMode(pump4IN2, OUTPUT);
  pinMode(pump5IN1, OUTPUT);
  pinMode(pump5IN2, OUTPUT);

  // Initialize L298N outputs
  digitalWrite(solenoidValveIN1, LOW);
  digitalWrite(solenoidValveIN2, LOW);
  digitalWrite(vacuumPumpIN1, LOW);
  digitalWrite(vacuumPumpIN2, LOW);
  analogWrite(vacuumPumpEN, 0); // Ensure the pump is off initially

  // Display welcome message
  lcd.setCursor(0, 0);
  lcd.print("Biofluid System");
  delay(2000);  // Wait for 2 seconds before proceeding
}

void loop() {
  // Check if the cartridge is loaded using the IR sensor
  bool cartridgeDetected = digitalRead(irSensorPin);

  if (cartridgeDetected == HIGH) {  // Assuming HIGH means cartridge is loaded
    lcd.clear();
    lcd.setCursor(0, 0);
    lcd.print("Cartridge Loaded");
    lcd.setCursor(0, 1);
    lcd.print("Load Sample");
    
    Serial.println("Cartridge detected. Waiting for user to press start...");
    
    // Wait for the user to press the push button to start
    waitForButtonPress();
  } else {
    lcd.clear();
    lcd.setCursor(0, 0);
    lcd.print("No Cartridge");
    lcd.setCursor(0, 1);
    lcd.print("Detected");
    
    Serial.println("No cartridge detected. Please load the cartridge.");
    delay(1000);  // Wait and check again after 1 second
  }
}

void waitForButtonPress() {
  lcd.clear();
  lcd.setCursor(0, 0);
  lcd.print("Press Start Button");

  // Loop until the button is pressed
  while (digitalRead(buttonPin) == HIGH) {
    // Button not pressed, do nothing
  }

  lcd.clear();
  lcd.setCursor(0, 0);
  lcd.print("Starting Process");

  Serial.println("Button pressed. Starting the biofluid process...");

  // Open the solenoid valve for the sample
  digitalWrite(solenoidValveIN1, HIGH); // Activate solenoid valve
  digitalWrite(solenoidValveIN2, LOW);
  delay(1000);  // Keep the valve open for 1 second to ensure it's fully open

  // Activate the vacuum pump
  activateVacuumPump();
  
  // After the process, close the solenoid valve
  digitalWrite(solenoidValveIN1, LOW);  // Deactivate solenoid valve
  digitalWrite(solenoidValveIN2, LOW);  // Ensure both pins are LOW

  Serial.println("Process completed.");
  
  // Proceed with the next steps of your process
  startMixingProcess();
}

void activateVacuumPump() {
  digitalWrite(vacuumPumpIN1, HIGH);  // Set direction
  digitalWrite(vacuumPumpIN2, LOW);   // Ensure correct direction
  analogWrite(vacuumPumpEN, pumpPWM3); // Set the PWM value
  delay(3000);  // Run for 3 seconds
  analogWrite(vacuumPumpEN, 0);  // Turn off the pump
  digitalWrite(vacuumPumpIN1, LOW);  // Set direction
  digitalWrite(vacuumPumpIN2, LOW);   // Ensure correct direction
}

// Function to control the forward movement of pumps one by one
void startMixingProcess() {
  Serial.println("Starting forward movement for all channels...");

  // Move each pump forward one by one with tunable time intervals
  movePumpForward(3, pump3IN1, pump3IN2, pumpPWM3, forwardTime3);
  movePumpForward(4, pump4IN1, pump4IN2, pumpPWM4, forwardTime4);
  movePumpForward(5, pump5IN1, pump5IN2, pumpPWM5, forwardTime5);

  lcd.clear();
  lcd.setCursor(0, 0);
  lcd.print("Mixing Fluid");
  
  Serial.println("Mixing fluid forward process completed.");
  
  delay(1000);  // Short delay before starting back-and-forth mixing
  
  // Now perform the back-and-forth movement
  startBackAndForthMixing();
}

void movePumpForward(int channel, int pumpIN1, int pumpIN2, int pumpPWM, int forwardTime) {
  // Forward movement
  lcd.clear();
  lcd.setCursor(0, 0);
  lcd.print("Channel ");
  lcd.print(channel);
  lcd.setCursor(0, 1);
  lcd.print("Forward Motion");
  
  Serial.print("Channel ");
  Serial.print(channel);
  Serial.println(" Forward");

  
  // Open solenoid valve SV1 (open to air)
  digitalWrite(solenoidValveIN1, HIGH); // Activate solenoid valve to keep it open to air
  digitalWrite(solenoidValveIN2, LOW);  // Set correct direction


  analogWrite(pumpIN1, pumpPWM);  // Apply PWM for forward movement
  digitalWrite(pumpIN2, LOW);     // Ensure backward pin is LOW
  delay(forwardTime);  // Run pump forward for the specified time interval

  // Stop the pump
  digitalWrite(pumpIN1, LOW);
  digitalWrite(pumpIN2, LOW);
  delay(500);  // Pause for a moment
}

// Function for back-and-forth movement for a tunable time period
void startBackAndForthMixing() {
  Serial.println("Starting back-and-forth mixing process...");

  // Open solenoid valve SV1 (open to air)
  digitalWrite(solenoidValveIN1, HIGH); // Activate solenoid valve to keep it open to air
  digitalWrite(solenoidValveIN2, LOW);  // Set correct direction
  
  // Back-and-forth movement for each channel
  performBackAndForth(3, pump3IN1, pump3IN2, pumpPWM3, backAndForthTime);
  performBackAndForth(4, pump4IN1, pump4IN2, pumpPWM4, backAndForthTime);
  performBackAndForth(5, pump5IN1, pump5IN2, pumpPWM5, backAndForthTime);

  // Close solenoid valve SV1 after mixing for channel 5 is done
  digitalWrite(solenoidValveIN1, LOW);  // Deactivate solenoid valve (closed)
  digitalWrite(solenoidValveIN2, LOW);  // Ensure both pins are LOW

  Serial.println("Back-and-forth mixing process completed and SV1 closed.");
}


void performBackAndForth(int channel, int pumpIN1, int pumpIN2, int pumpPWM, int mixingTime) {
  // Forward movement
  lcd.clear();
  lcd.setCursor(0, 0);
  lcd.print("Channel ");
  lcd.print(channel);
  lcd.setCursor(0, 1);
  lcd.print("Pump Forward");
  
  Serial.print("Channel ");
  Serial.print(channel);
  Serial.println(" Forward");
  
  digitalWrite(pumpIN1, HIGH);  // Move forward
  digitalWrite(pumpIN2, LOW);
  delay(mixingTime);  // Tunable forward mixing time

  // Reverse movement
  lcd.clear();
  lcd.setCursor(0, 0);
  lcd.print("Channel ");
  lcd.print(channel);
  lcd.setCursor(0, 1);
  lcd.print("Pump Reverse");
  
  Serial.print("Channel ");
  Serial.print(channel);
  Serial.println(" Reverse");

  digitalWrite(pumpIN1, LOW);  // Move backward
  digitalWrite(pumpIN2, HIGH);
  delay(mixingTime);  // Tunable backward mixing time

  // Stop pump after back-and-forth motion
  digitalWrite(pumpIN1, LOW);
  digitalWrite(pumpIN2, LOW);
}