// MultiStepper.pde Copyright (C) 2009 Mike McCauley
#include <AccelStepper.h>

// Define some steppers and the pins the will use
AccelStepper plateDriver(1,22,23); // "1" specifys mode of, step, direction
int MS1 = 24;
int MS2 = 25;
int SLEEP = 26;
AccelStepper pump(4, 6, 7, 8, 9); // "4" specifys bipolar w the 4 pins following
int ledPin = 53;                // choose the pin for the LED

// front opto interruptor
int optoInterruptorFront = 49;               // choose the input pin
int optoInterruptorFrontVal = 0;             // variable for reading the pin status
// rear opto interruptor
int optoInterruptorRear = 48;               // choose the input pin
int optoInterruptorRearVal = 0;             // variable for reading the pin status

boolean initalZeroFront = false;
boolean zeroedRear = false;

void setup(){
  Serial.begin(9600);
  pinMode(ledPin, OUTPUT);      // declare LED as output
  pinMode(optoInterruptorFront, INPUT);     // declare optoInterruptorFront as input
    // setup of plateDriver
  plateDriver.setMaxSpeed(800.0);
  plateDriver.setAcceleration(600.0);
  pinMode(MS1, OUTPUT);   // set pin 24 to output
  pinMode(MS2, OUTPUT);   // set pin 25 to output
  pinMode(SLEEP, OUTPUT); // set pin 26 to output
  digitalWrite(MS1, LOW);
  digitalWrite(MS2, LOW);
  digitalWrite(SLEEP, HIGH);
    //setup of stepper2
  pump.setMaxSpeed(300.0);
  pump.setAcceleration(100.0);
  //pump.moveTo(10000);
}

void loop(){
  optoInterruptorFrontVal = digitalRead(optoInterruptorFront);  // read input value
  optoInterruptorRearVal = digitalRead(optoInterruptorRear);  // read input value
  digitalWrite(ledPin, LOW);              // turn LED OFF

  while(initalZeroFront == false){
    Serial.println(optoInterruptorFrontVal);
      // Initial zeroing
    while(optoInterruptorFrontVal == HIGH){      // if front opto is HIGH... move plate towards front
    //xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
      plateDriver.move(-1);
      plateDriver.runToPosition();            //rotate plate driver foward
      optoInterruptorFrontVal = digitalRead(optoInterruptorFront);
      Serial.println("zeroing forward");
    }
    initalZeroFront = true;
    digitalWrite(ledPin, HIGH);  // turn LED ON
    digitalWrite(ledPin, LOW);  // turn LED OFF
    Serial.println("ZEROED forward");
    
    // this is when plate would be placed on the stage
    delay(1000);
    

    
  }
  // plate resides at front most position
  // zeroedFront == true at this point
  
  
  frontZeroedTowardsDispenseZero();
  // plate resides directly under dispensing pipettes


  dispenseLoop();
  // microplate filled
  
  
  returnPlateFront();
    
    
}  

void frontZeroedTowardsDispenseZero() {
  Serial.println("massive move backwards");
  plateDriver.move(45000);
  plateDriver.runToPosition();

    // rear zeroing process
  while(optoInterruptorRearVal == HIGH){
    plateDriver.move(1);
    plateDriver.runToPosition();            //rotate plate driver foward
    optoInterruptorRearVal = digitalRead(optoInterruptorRear);
    Serial.println("zeroing back");
  }
  Serial.println("ZEROED under pipettes");
  delay(5000);

}

void dispenseLoop(){
  for(int i = 0; i < 13; i++){
        // rewrite these as non-blocking
    Serial.println(i);

    Serial.println("dispensing " + i);
      // dispense X volume of liquid
    pump.move(100);
    pump.runToPosition();

    Serial.println("advancing");
      // move plate to next well
    plateDriver.move(-1000);
    plateDriver.runToPosition();

    delay(500);
    
    
    
  }
  Serial.println("done dispensing");
}

void returnPlateFront(){
  Serial.println("massive move forwards");
  plateDriver.move(-30000);
  plateDriver.runToPosition();
  
   // front zeroing process
  while(optoInterruptorFrontVal == HIGH){
    plateDriver.move(-1);
    plateDriver.runToPosition();            //rotate plate driver foward
    optoInterruptorFrontVal = digitalRead(optoInterruptorFront);
    Serial.println("zeroing front loop");
  }
  
  Serial.println("ZEROED at front");
  
  for (int i = 0; i < 100; i++){
    Serial.println("done");
    delay(500);
  }
  
}