/*
  Firmata is a generic protocol for communicating with microcontrollers
  from software on a host computer. It is intended to work with
  any host computer software package.

  To download a host software package, please click on the following link
  to open the list of Firmata client libraries in your default browser.

  https://github.com/firmata/arduino#firmata-client-libraries

  Copyright (C) 2006-2008 Hans-Christoph Steiner.  All rights reserved.
  Copyright (C) 2010-2011 Paul Stoffregen.  All rights reserved.
  Copyright (C) 2009 Shigeru Kobayashi.  All rights reserved.
  Copyright (C) 2009-2016 Jeff Hoefs.  All rights reserved.

  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.

  See file LICENSE.txt for further informations on licensing terms.

  Last updated August 17th, 2017
*/

#include <Servo.h>
#include <Wire.h>
#include <Firmata.h>
#include <AutoPID.h>

//Comment the line below, "#define PID", if you are not using PID else uncomment it and follow further instructions.
#define PID

//------------PID values----------------
// Pin 6  - setPoint  (input value)
// Pin 5  - feedback (input value)
// Pin 15 - control (output value)

//If you use real analog pin for input for PID just uncomment next line with #define REAL_INPUT, if use virtual sources comment this line
//If you use both real will be prefered
//#define REAL_INPUT
// This line define analog pin for read values from real sources
#define AREAD_PIN A1


#define PID_OUTPUT_MIN -512.0
#define PID_OUTPUT_MAX 512.0
#define PID_KP 15
#define PID_KI 10
#define PID_KD 10
#define PID_BANG_BANG 40
#define PID_INTERVAL  100




#define I2C_WRITE                   B00000000
#define I2C_READ                    B00001000
#define I2C_READ_CONTINUOUSLY       B00010000
#define I2C_STOP_READING            B00011000
#define I2C_READ_WRITE_MODE_MASK    B00011000
#define I2C_10BIT_ADDRESS_MODE_MASK B00100000
#define I2C_END_TX_MASK             B01000000
#define I2C_STOP_TX                 1
#define I2C_RESTART_TX              0
#define I2C_MAX_QUERIES             8
#define I2C_REGISTER_NOT_SPECIFIED  -1

// the minimum interval for sampling analog input
#define MINIMUM_SAMPLING_INTERVAL   1


/*==============================================================================
 * GLOBAL VARIABLES
 *============================================================================*/

#ifdef FIRMATA_SERIAL_FEATURE
SerialFirmata serialFeature;
#endif

/* analog inputs */
int analogInputsToReport = 0; // bitwise array to store pin reporting

/* digital input ports */
byte reportPINs[TOTAL_PORTS];       // 1 = report this port, 0 = silence
byte previousPINs[TOTAL_PORTS];     // previous 8 bits sent

/* pins configuration */
byte portConfigInputs[TOTAL_PORTS]; // each bit: 1 = pin in INPUT, 0 = anything else

/* timer variables */
unsigned long currentMillis;        // store the current value from millis()
unsigned long previousMillis;       // for comparison with currentMillis
unsigned int samplingInterval = 19; // how often to run the main loop (in ms)

/* i2c data */
struct i2c_device_info {
  byte addr;
  int reg;
  byte bytes;
  byte stopTX;
};


double currentPoint=0.0, setPoint=0.0, control_value=0.0;

#ifdef PID
  AutoPID myPID(&currentPoint, &setPoint, &control_value, PID_OUTPUT_MIN, PID_OUTPUT_MAX, PID_KP, PID_KI, PID_KD);
#endif


/* for i2c read continuous more */
i2c_device_info query[I2C_MAX_QUERIES];

byte i2cRxData[64];
boolean isI2CEnabled = false;
signed char queryIndex = -1;
// default delay time between i2c read request and Wire.requestFrom()
unsigned int i2cReadDelayTime = 0;

Servo servos[MAX_SERVOS];
byte servoPinMap[TOTAL_PINS];
byte detachedServos[MAX_SERVOS];
byte detachedServoCount = 0;
byte servoCount = 0;

boolean isResetting = false;

// Forward declare a few functions to avoid compiler errors with older versions
// of the Arduino IDE.
void setPinModeCallback(byte, int);
void reportAnalogCallback(byte analogPin, int value);
void sysexCallback(byte, byte, byte*);

/* utility functions */
void wireWrite(byte data)
{
#if ARDUINO >= 100
  Wire.write((byte)data);
#else
  Wire.send(data);
#endif
}

byte wireRead(void)
{
#if ARDUINO >= 100
  return Wire.read();
#else
  return Wire.receive();
#endif
}

 /*==============================================================================
 * PID
 *==============================================================================*/

void update_setPoint(int value)
{
  
   #ifdef REAL_INPUT
     setPoint=(double)analogRead(AREAD_PIN);
   #else
     setPoint=(double)(value-512);
    #endif
 }

void update_currentPoint(int value)
{
  currentPoint=(double)(value-512); 
}
  
/*==============================================================================
 * FUNCTIONS
 *============================================================================*/

void attachServo(byte pin, int minPulse, int maxPulse)
{
  if (servoCount < MAX_SERVOS) {
    // reuse indexes of detached servos until all have been reallocated
    if (detachedServoCount > 0) {
      servoPinMap[pin] = detachedServos[detachedServoCount - 1];
      if (detachedServoCount > 0) detachedServoCount--;
    } else {
      servoPinMap[pin] = servoCount;
      servoCount++;
    }
    if (minPulse > 0 && maxPulse > 0) {
      servos[servoPinMap[pin]].attach(PIN_TO_DIGITAL(pin), minPulse, maxPulse);
    } else {
      servos[servoPinMap[pin]].attach(PIN_TO_DIGITAL(pin));
    }
  } else {
    Firmata.sendString("Max servos attached");
  }
}

void detachServo(byte pin)
{
  servos[servoPinMap[pin]].detach();
  // if we're detaching the last servo, decrement the count
  // otherwise store the index of the detached servo
  if (servoPinMap[pin] == servoCount && servoCount > 0) {
    servoCount--;
  } else if (servoCount > 0) {
    // keep track of detached servos because we want to reuse their indexes
    // before incrementing the count of attached servos
    detachedServoCount++;
    detachedServos[detachedServoCount - 1] = servoPinMap[pin];
  }

  servoPinMap[pin] = 255;
}

void enableI2CPins()
{
  byte i;
  // is there a faster way to do this? would probaby require importing
  // Arduino.h to get SCL and SDA pins
  for (i = 0; i < TOTAL_PINS; i++) {
    if (IS_PIN_I2C(i)) {
      // mark pins as i2c so they are ignore in non i2c data requests
      setPinModeCallback(i, PIN_MODE_I2C);
    }
  }

  isI2CEnabled = true;

  Wire.begin();
}

/* disable the i2c pins so they can be used for other functions */
void disableI2CPins() {
  isI2CEnabled = false;
  // disable read continuous mode for all devices
  queryIndex = -1;
}

void readAndReportData(byte address, int theRegister, byte numBytes, byte stopTX) {
  // allow I2C requests that don't require a register read
  // for example, some devices using an interrupt pin to signify new data available
  // do not always require the register read so upon interrupt you call Wire.requestFrom()
  if (theRegister != I2C_REGISTER_NOT_SPECIFIED) {
    Wire.beginTransmission(address);
    wireWrite((byte)theRegister);
    Wire.endTransmission(stopTX); // default = true
    // do not set a value of 0
    if (i2cReadDelayTime > 0) {
      // delay is necessary for some devices such as WiiNunchuck
      delayMicroseconds(i2cReadDelayTime);
    }
  } else {
    theRegister = 0;  // fill the register with a dummy value
  }

  Wire.requestFrom(address, numBytes);  // all bytes are returned in requestFrom

  // check to be sure correct number of bytes were returned by slave
  if (numBytes < Wire.available()) {
    Firmata.sendString("I2C: Too many bytes received");
  } else if (numBytes > Wire.available()) {
    Firmata.sendString("I2C: Too few bytes received");
  }

  i2cRxData[0] = address;
  i2cRxData[1] = theRegister;

  for (int i = 0; i < numBytes && Wire.available(); i++) {
    i2cRxData[2 + i] = wireRead();
  }

  // send slave address, register and received bytes
  Firmata.sendSysex(SYSEX_I2C_REPLY, numBytes + 2, i2cRxData);
}

void outputPort(byte portNumber, byte portValue, byte forceSend)
{
  // pins not configured as INPUT are cleared to zeros
  portValue = portValue & portConfigInputs[portNumber];
  // only send if the value is different than previously sent
  if (forceSend || previousPINs[portNumber] != portValue) {
    Firmata.sendDigitalPort(portNumber, portValue);
    previousPINs[portNumber] = portValue;
  }
}

/* -----------------------------------------------------------------------------
 * check all the active digital inputs for change of state, then add any events
 * to the Serial output queue using Serial.print() */
void checkDigitalInputs(void)
{
  /* Using non-looping code allows constants to be given to readPort().
   * The compiler will apply substantial optimizations if the inputs
   * to readPort() are compile-time constants. */
  if (TOTAL_PORTS > 0 && reportPINs[0]) outputPort(0, readPort(0, portConfigInputs[0]), false);
  if (TOTAL_PORTS > 1 && reportPINs[1]) outputPort(1, readPort(1, portConfigInputs[1]), false);
  if (TOTAL_PORTS > 2 && reportPINs[2]) outputPort(2, readPort(2, portConfigInputs[2]), false);
  if (TOTAL_PORTS > 3 && reportPINs[3]) outputPort(3, readPort(3, portConfigInputs[3]), false);
  if (TOTAL_PORTS > 4 && reportPINs[4]) outputPort(4, readPort(4, portConfigInputs[4]), false);
  if (TOTAL_PORTS > 5 && reportPINs[5]) outputPort(5, readPort(5, portConfigInputs[5]), false);
  if (TOTAL_PORTS > 6 && reportPINs[6]) outputPort(6, readPort(6, portConfigInputs[6]), false);
  if (TOTAL_PORTS > 7 && reportPINs[7]) outputPort(7, readPort(7, portConfigInputs[7]), false);
  if (TOTAL_PORTS > 8 && reportPINs[8]) outputPort(8, readPort(8, portConfigInputs[8]), false);
  if (TOTAL_PORTS > 9 && reportPINs[9]) outputPort(9, readPort(9, portConfigInputs[9]), false);
  if (TOTAL_PORTS > 10 && reportPINs[10]) outputPort(10, readPort(10, portConfigInputs[10]), false);
  if (TOTAL_PORTS > 11 && reportPINs[11]) outputPort(11, readPort(11, portConfigInputs[11]), false);
  if (TOTAL_PORTS > 12 && reportPINs[12]) outputPort(12, readPort(12, portConfigInputs[12]), false);
  if (TOTAL_PORTS > 13 && reportPINs[13]) outputPort(13, readPort(13, portConfigInputs[13]), false);
  if (TOTAL_PORTS > 14 && reportPINs[14]) outputPort(14, readPort(14, portConfigInputs[14]), false);
  if (TOTAL_PORTS > 15 && reportPINs[15]) outputPort(15, readPort(15, portConfigInputs[15]), false);
}

// -----------------------------------------------------------------------------
/* sets the pin mode to the correct state and sets the relevant bits in the
 * two bit-arrays that track Digital I/O and PWM status
 */
void setPinModeCallback(byte pin, int mode)
{
  if (Firmata.getPinMode(pin) == PIN_MODE_IGNORE)
    return;

  if (Firmata.getPinMode(pin) == PIN_MODE_I2C && isI2CEnabled && mode != PIN_MODE_I2C) {
    // disable i2c so pins can be used for other functions
    // the following if statements should reconfigure the pins properly
    disableI2CPins();
  }
  if (IS_PIN_DIGITAL(pin) && mode != PIN_MODE_SERVO) {
    if (servoPinMap[pin] < MAX_SERVOS && servos[servoPinMap[pin]].attached()) {
      detachServo(pin);
    }
  }
  if (IS_PIN_ANALOG(pin)) {
    reportAnalogCallback(PIN_TO_ANALOG(pin), mode == PIN_MODE_ANALOG ? 1 : 0); // turn on/off reporting
  }
  if (IS_PIN_DIGITAL(pin)) {
    if (mode == INPUT || mode == PIN_MODE_PULLUP) {
      portConfigInputs[pin / 8] |= (1 << (pin & 7));
    } else {
      portConfigInputs[pin / 8] &= ~(1 << (pin & 7));
    }
  }
  Firmata.setPinState(pin, 0);
  switch (mode) {
    case PIN_MODE_ANALOG:
      if (IS_PIN_ANALOG(pin)) {
        if (IS_PIN_DIGITAL(pin)) {
          pinMode(PIN_TO_DIGITAL(pin), INPUT);    // disable output driver
#if ARDUINO <= 100
          // deprecated since Arduino 1.0.1 - TODO: drop support in Firmata 2.6
          digitalWrite(PIN_TO_DIGITAL(pin), LOW); // disable internal pull-ups
#endif
        }
        Firmata.setPinMode(pin, PIN_MODE_ANALOG);
      }
      break;
    case INPUT:
      if (IS_PIN_DIGITAL(pin)) {
        pinMode(PIN_TO_DIGITAL(pin), INPUT);    // disable output driver
#if ARDUINO <= 100
        // deprecated since Arduino 1.0.1 - TODO: drop support in Firmata 2.6
        digitalWrite(PIN_TO_DIGITAL(pin), LOW); // disable internal pull-ups
#endif
        Firmata.setPinMode(pin, INPUT);
      }
      break;
    case PIN_MODE_PULLUP:
      if (IS_PIN_DIGITAL(pin)) {
        pinMode(PIN_TO_DIGITAL(pin), INPUT_PULLUP);
        Firmata.setPinMode(pin, PIN_MODE_PULLUP);
        Firmata.setPinState(pin, 1);
      }
      break;
    case OUTPUT:
      if (IS_PIN_DIGITAL(pin)) {
        if (Firmata.getPinMode(pin) == PIN_MODE_PWM) {
          // Disable PWM if pin mode was previously set to PWM.
          digitalWrite(PIN_TO_DIGITAL(pin), LOW);
        }
        pinMode(PIN_TO_DIGITAL(pin), OUTPUT);
        Firmata.setPinMode(pin, OUTPUT);
      }
      break;
    case PIN_MODE_PWM:
      if (IS_PIN_PWM(pin)) {
        pinMode(PIN_TO_PWM(pin), OUTPUT);
        analogWrite(PIN_TO_PWM(pin), 0);
        Firmata.setPinMode(pin, PIN_MODE_PWM);
      }
      break;
    case PIN_MODE_SERVO:
      if (IS_PIN_DIGITAL(pin)) {
        Firmata.setPinMode(pin, PIN_MODE_SERVO);
        if (servoPinMap[pin] == 255 || !servos[servoPinMap[pin]].attached()) {
          // pass -1 for min and max pulse values to use default values set
          // by Servo library
          attachServo(pin, -1, -1);
        }
      }
      break;
    case PIN_MODE_I2C:
      if (IS_PIN_I2C(pin)) {
        // mark the pin as i2c
        // the user must call I2C_CONFIG to enable I2C for a device
        Firmata.setPinMode(pin, PIN_MODE_I2C);
      }
      break;
    case PIN_MODE_SERIAL:
#ifdef FIRMATA_SERIAL_FEATURE
      serialFeature.handlePinMode(pin, PIN_MODE_SERIAL);
#endif
      break;
    default:
      Firmata.sendString("Unknown pin mode"); // TODO: put error msgs in EEPROM
  }
  // TODO: save status to EEPROM here, if changed
}

/*
 * Sets the value of an individual pin. Useful if you want to set a pin value but
 * are not tracking the digital port state.
 * Can only be used on pins configured as OUTPUT.
 * Cannot be used to enable pull-ups on Digital INPUT pins.
 */
void setPinValueCallback(byte pin, int value)
{
  if (pin < TOTAL_PINS && IS_PIN_DIGITAL(pin)) {
    if (Firmata.getPinMode(pin) == OUTPUT) {
      Firmata.setPinState(pin, value);
      digitalWrite(PIN_TO_DIGITAL(pin), value);
    }
  }
}

void analogWriteCallback(byte pin, int value)
{
  if (pin < TOTAL_PINS) {
    switch (Firmata.getPinMode(pin)) {
      case PIN_MODE_SERVO:
        if (IS_PIN_DIGITAL(pin))
          servos[servoPinMap[pin]].write(value);
        Firmata.setPinState(pin, value);
        break;
      case PIN_MODE_PWM:
        if (IS_PIN_PWM(pin))
          //analogWrite(PIN_TO_PWM(pin), value);
          switch(pin)
          {
            case 5:
            update_currentPoint(value);
            break;
            case 6:
            update_setPoint(value);
            }
          
        Firmata.setPinState(pin, value);
        break;
    }
  }
}

void digitalWriteCallback(byte port, int value)
{
  byte pin, lastPin, pinValue, mask = 1, pinWriteMask = 0;

  if (port < TOTAL_PORTS) {
    // create a mask of the pins on this port that are writable.
    lastPin = port * 8 + 8;
    if (lastPin > TOTAL_PINS) lastPin = TOTAL_PINS;
    for (pin = port * 8; pin < lastPin; pin++) {
      // do not disturb non-digital pins (eg, Rx & Tx)
      if (IS_PIN_DIGITAL(pin)) {
        // do not touch pins in PWM, ANALOG, SERVO or other modes
        if (Firmata.getPinMode(pin) == OUTPUT || Firmata.getPinMode(pin) == INPUT) {
          pinValue = ((byte)value & mask) ? 1 : 0;
          if (Firmata.getPinMode(pin) == OUTPUT) {
            pinWriteMask |= mask;
          } else if (Firmata.getPinMode(pin) == INPUT && pinValue == 1 && Firmata.getPinState(pin) != 1) {
            // only handle INPUT here for backwards compatibility
#if ARDUINO > 100
            pinMode(pin, INPUT_PULLUP);
#else
            // only write to the INPUT pin to enable pullups if Arduino v1.0.0 or earlier
            pinWriteMask |= mask;
#endif
          }
          Firmata.setPinState(pin, pinValue);
        }
      }
      mask = mask << 1;
    }
    writePort(port, (byte)value, pinWriteMask);
  }
}


// -----------------------------------------------------------------------------
/* sets bits in a bit array (int) to toggle the reporting of the analogIns
 */
//void FirmataClass::setAnalogPinReporting(byte pin, byte state) {
//}
void reportAnalogCallback(byte analogPin, int value)
{
  if (analogPin < TOTAL_ANALOG_PINS) {
    if (value == 0) {
      analogInputsToReport = analogInputsToReport & ~ (1 << analogPin);
    } else {
      analogInputsToReport = analogInputsToReport | (1 << analogPin);
      // prevent during system reset or all analog pin values will be reported
      // which may report noise for unconnected analog pins
      if (!isResetting) {
        // Send pin value immediately. This is helpful when connected via
        // ethernet, wi-fi or bluetooth so pin states can be known upon
        // reconnecting.
        Firmata.sendAnalog(analogPin, analogRead(analogPin));
      }
    }
  }
  // TODO: save status to EEPROM here, if changed
}

void reportDigitalCallback(byte port, int value)
{
  if (port < TOTAL_PORTS) {
    reportPINs[port] = (byte)value;
    // Send port value immediately. This is helpful when connected via
    // ethernet, wi-fi or bluetooth so pin states can be known upon
    // reconnecting.
    if (value) outputPort(port, readPort(port, portConfigInputs[port]), true);
  }
  // do not disable analog reporting on these 8 pins, to allow some
  // pins used for digital, others analog.  Instead, allow both types
  // of reporting to be enabled, but check if the pin is configured
  // as analog when sampling the analog inputs.  Likewise, while
  // scanning digital pins, portConfigInputs will mask off values from any
  // pins configured as analog
}

/*==============================================================================
 * SYSEX-BASED commands
 *============================================================================*/

void sysexCallback(byte command, byte argc, byte *argv)
{
  byte mode;
  byte stopTX;
  byte slaveAddress;
  byte data;
  int slaveRegister;
  unsigned int delayTime;

  switch (command) {
    case I2C_REQUEST:
      mode = argv[1] & I2C_READ_WRITE_MODE_MASK;
      if (argv[1] & I2C_10BIT_ADDRESS_MODE_MASK) {
        Firmata.sendString("10-bit addressing not supported");
        return;
      }
      else {
        slaveAddress = argv[0];
      }

      // need to invert the logic here since 0 will be default for client
      // libraries that have not updated to add support for restart tx
      if (argv[1] & I2C_END_TX_MASK) {
        stopTX = I2C_RESTART_TX;
      }
      else {
        stopTX = I2C_STOP_TX; // default
      }

      switch (mode) {
        case I2C_WRITE:
          Wire.beginTransmission(slaveAddress);
          for (byte i = 2; i < argc; i += 2) {
            data = argv[i] + (argv[i + 1] << 7);
            wireWrite(data);
          }
          Wire.endTransmission();
          delayMicroseconds(70);
          break;
        case I2C_READ:
          if (argc == 6) {
            // a slave register is specified
            slaveRegister = argv[2] + (argv[3] << 7);
            data = argv[4] + (argv[5] << 7);  // bytes to read
          }
          else {
            // a slave register is NOT specified
            slaveRegister = I2C_REGISTER_NOT_SPECIFIED;
            data = argv[2] + (argv[3] << 7);  // bytes to read
          }
          readAndReportData(slaveAddress, (int)slaveRegister, data, stopTX);
          break;
        case I2C_READ_CONTINUOUSLY:
          if ((queryIndex + 1) >= I2C_MAX_QUERIES) {
            // too many queries, just ignore
            Firmata.sendString("too many queries");
            break;
          }
          if (argc == 6) {
            // a slave register is specified
            slaveRegister = argv[2] + (argv[3] << 7);
            data = argv[4] + (argv[5] << 7);  // bytes to read
          }
          else {
            // a slave register is NOT specified
            slaveRegister = (int)I2C_REGISTER_NOT_SPECIFIED;
            data = argv[2] + (argv[3] << 7);  // bytes to read
          }
          queryIndex++;
          query[queryIndex].addr = slaveAddress;
          query[queryIndex].reg = slaveRegister;
          query[queryIndex].bytes = data;
          query[queryIndex].stopTX = stopTX;
          break;
        case I2C_STOP_READING:
          byte queryIndexToSkip;
          // if read continuous mode is enabled for only 1 i2c device, disable
          // read continuous reporting for that device
          if (queryIndex <= 0) {
            queryIndex = -1;
          } else {
            queryIndexToSkip = 0;
            // if read continuous mode is enabled for multiple devices,
            // determine which device to stop reading and remove it's data from
            // the array, shifiting other array data to fill the space
            for (byte i = 0; i < queryIndex + 1; i++) {
              if (query[i].addr == slaveAddress) {
                queryIndexToSkip = i;
                break;
              }
            }

            for (byte i = queryIndexToSkip; i < queryIndex + 1; i++) {
              if (i < I2C_MAX_QUERIES) {
                query[i].addr = query[i + 1].addr;
                query[i].reg = query[i + 1].reg;
                query[i].bytes = query[i + 1].bytes;
                query[i].stopTX = query[i + 1].stopTX;
              }
            }
            queryIndex--;
          }
          break;
        default:
          break;
      }
      break;
    case I2C_CONFIG:
      delayTime = (argv[0] + (argv[1] << 7));

      if (argc > 1 && delayTime > 0) {
        i2cReadDelayTime = delayTime;
      }

      if (!isI2CEnabled) {
        enableI2CPins();
      }

      break;
    case SERVO_CONFIG:
      if (argc > 4) {
        // these vars are here for clarity, they'll optimized away by the compiler
        byte pin = argv[0];
        int minPulse = argv[1] + (argv[2] << 7);
        int maxPulse = argv[3] + (argv[4] << 7);

        if (IS_PIN_DIGITAL(pin)) {
          if (servoPinMap[pin] < MAX_SERVOS && servos[servoPinMap[pin]].attached()) {
            detachServo(pin);
          }
          attachServo(pin, minPulse, maxPulse);
          setPinModeCallback(pin, PIN_MODE_SERVO);
        }
      }
      break;
    case SAMPLING_INTERVAL:
      if (argc > 1) {
        samplingInterval = argv[0] + (argv[1] << 7);
        if (samplingInterval < MINIMUM_SAMPLING_INTERVAL) {
          samplingInterval = MINIMUM_SAMPLING_INTERVAL;
        }
      } else {
        //Firmata.sendString("Not enough data");
      }
      break;
    case EXTENDED_ANALOG:
      if (argc > 1) {
        int val = argv[1];
        if (argc > 2) val |= (argv[2] << 7);
        if (argc > 3) val |= (argv[3] << 14);
        analogWriteCallback(argv[0], val);
      }
      break;
    case CAPABILITY_QUERY:
      Firmata.write(START_SYSEX);
      Firmata.write(CAPABILITY_RESPONSE);
      for (byte pin = 0; pin < TOTAL_PINS; pin++) {
        if (IS_PIN_DIGITAL(pin)) {
          Firmata.write((byte)INPUT);
          Firmata.write(1);
          Firmata.write((byte)PIN_MODE_PULLUP);
          Firmata.write(1);
          Firmata.write((byte)OUTPUT);
          Firmata.write(1);
        }
        if (IS_PIN_ANALOG(pin)) {
          Firmata.write(PIN_MODE_ANALOG);
          Firmata.write(10); // 10 = 10-bit resolution
        }
        if (IS_PIN_PWM(pin)) {
          Firmata.write(PIN_MODE_PWM);
          Firmata.write(DEFAULT_PWM_RESOLUTION);
        }
        if (IS_PIN_DIGITAL(pin)) {
          Firmata.write(PIN_MODE_SERVO);
          Firmata.write(14);
        }
        if (IS_PIN_I2C(pin)) {
          Firmata.write(PIN_MODE_I2C);
          Firmata.write(1);  // TODO: could assign a number to map to SCL or SDA
        }
#ifdef FIRMATA_SERIAL_FEATURE
        serialFeature.handleCapability(pin);
#endif
        Firmata.write(127);
      }
      Firmata.write(END_SYSEX);
      break;
    case PIN_STATE_QUERY:
      if (argc > 0) {
        byte pin = argv[0];
        Firmata.write(START_SYSEX);
        Firmata.write(PIN_STATE_RESPONSE);
        Firmata.write(pin);
        if (pin < TOTAL_PINS) {
          Firmata.write(Firmata.getPinMode(pin));
          Firmata.write((byte)Firmata.getPinState(pin) & 0x7F);
          if (Firmata.getPinState(pin) & 0xFF80) Firmata.write((byte)(Firmata.getPinState(pin) >> 7) & 0x7F);
          if (Firmata.getPinState(pin) & 0xC000) Firmata.write((byte)(Firmata.getPinState(pin) >> 14) & 0x7F);
        }
        Firmata.write(END_SYSEX);
      }
      break;
    case ANALOG_MAPPING_QUERY:
      Firmata.write(START_SYSEX);
      Firmata.write(ANALOG_MAPPING_RESPONSE);
      for (byte pin = 0; pin < TOTAL_PINS; pin++) {
        Firmata.write(IS_PIN_ANALOG(pin) ? PIN_TO_ANALOG(pin) : 127);
      }
      Firmata.write(END_SYSEX);
      break;

    case SERIAL_MESSAGE:
#ifdef FIRMATA_SERIAL_FEATURE
      serialFeature.handleSysex(command, argc, argv);
#endif
      break;
  }
}

/*==============================================================================
 * SETUP()
 *============================================================================*/

void systemResetCallback()
{
  isResetting = true;

  // initialize a defalt state
  // TODO: option to load config from EEPROM instead of default

#ifdef FIRMATA_SERIAL_FEATURE
  serialFeature.reset();
#endif

  if (isI2CEnabled) {
    disableI2CPins();
  }

  for (byte i = 0; i < TOTAL_PORTS; i++) {
    reportPINs[i] = false;    // by default, reporting off
    portConfigInputs[i] = 0;  // until activated
    previousPINs[i] = 0;
  }

  for (byte i = 0; i < TOTAL_PINS; i++) {
    // pins with analog capability default to analog input
    // otherwise, pins default to digital output
    if (IS_PIN_ANALOG(i)) {
      // turns off pullup, configures everything
      setPinModeCallback(i, PIN_MODE_ANALOG);
    } else if (IS_PIN_DIGITAL(i)) {
      // sets the output to 0, configures portConfigInputs
      setPinModeCallback(i, OUTPUT);
    }

    servoPinMap[i] = 255;
  }
  // by default, do not report any analog inputs
  analogInputsToReport = 0;

  detachedServoCount = 0;
  servoCount = 0;

  /* send digital inputs to set the initial state on the host computer,
   * since once in the loop(), this firmware will only send on change */
  /*
  TODO: this can never execute, since no pins default to digital input
        but it will be needed when/if we support EEPROM stored config
  for (byte i=0; i < TOTAL_PORTS; i++) {
    outputPort(i, readPort(i, portConfigInputs[i]), true);
  }
  */
  isResetting = false;
}

void setup()
{
  Firmata.setFirmwareVersion(FIRMATA_FIRMWARE_MAJOR_VERSION, FIRMATA_FIRMWARE_MINOR_VERSION);

  Firmata.attach(ANALOG_MESSAGE, analogWriteCallback);
  Firmata.attach(DIGITAL_MESSAGE, digitalWriteCallback);
  Firmata.attach(REPORT_ANALOG, reportAnalogCallback);
  Firmata.attach(REPORT_DIGITAL, reportDigitalCallback);
  Firmata.attach(SET_PIN_MODE, setPinModeCallback);
  Firmata.attach(SET_DIGITAL_PIN_VALUE, setPinValueCallback);
  Firmata.attach(START_SYSEX, sysexCallback);
  Firmata.attach(SYSTEM_RESET, systemResetCallback);

  // to use a port other than Serial, such as Serial1 on an Arduino Leonardo or Mega,
  // Call begin(baud) on the alternate serial port and pass it to Firmata to begin like this:
  // Serial1.begin(57600);
  // Firmata.begin(Serial1);
  // However do not do this if you are using SERIAL_MESSAGE

  Firmata.begin(57600);
  while (!Serial) {
    ; // wait for serial port to connect. Needed for ATmega32u4-based boards and Arduino 101
  }

  systemResetCallback();  // reset to default config
   
  #ifdef PID
   //if temperature is more than 4  below or above setpoint, OUTPUT will be set to min or max respectively
    myPID.setBangBang(PID_BANG_BANG);
    //set PID update interval to 
    myPID.setTimeStep(PID_INTERVAL);
  #endif
}

/*==============================================================================
 * LOOP()
 *============================================================================*/
void loop()
{
  byte pin, analogPin;

  /* DIGITALREAD - as fast as possible, check for changes and output them to the
   * FTDI buffer using Serial.print()  */
  checkDigitalInputs();

  /* STREAMREAD - processing incoming messagse as soon as possible, while still
   * checking digital inputs.  */
  while (Firmata.available())
    Firmata.processInput();

    #ifdef PID
       #ifdef REAL_INPUT
         update_setPoint(1);
       #endif    
       myPID.run(); //call every loop, updates automatically at certain time interval
    #endif
  
  // TODO - ensure that Stream buffer doesn't go over 60 bytes

  currentMillis = millis();
  if (currentMillis - previousMillis > samplingInterval) {
    previousMillis += samplingInterval;
    /* ANALOGREAD - do all analogReads() at the configured sampling interval */
    for (pin = 0; pin < TOTAL_PINS; pin++) {
      if (IS_PIN_ANALOG(pin) && Firmata.getPinMode(pin) == PIN_MODE_ANALOG) {
        analogPin = PIN_TO_ANALOG(pin);
        if (analogInputsToReport & (1 << analogPin)) {
          #ifdef PID
            Firmata.sendAnalog(analogPin, (int)(control_value+512.0));
          #else
            Firmata.sendAnalog(analogPin, analogRead(analogPin));
          #endif
        }
      }
    }
    // report i2c data for all device with read continuous mode enabled
    if (queryIndex > -1) {
      for (byte i = 0; i < queryIndex + 1; i++) {
        readAndReportData(query[i].addr, query[i].reg, query[i].bytes, query[i].stopTX);
      }
    }
  }

#ifdef FIRMATA_SERIAL_FEATURE
  serialFeature.update();
#endif
}